ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
  • American Society of Hematology  (35,109)
  • National Academy of Sciences  (19,506)
  • BioMed Central  (14,128)
  • Espoo : Geologian Tutkimuskeskus
  • Essen : Verl. Glückauf
  • 2020-2024  (141)
  • 2005-2009  (68,613)
Collection
Keywords
Publisher
Language
Years
Year
  • 1
    facet.materialart.
    Unknown
    Dynamics of Aggregates and Sinking Carbon Fluxes in a Turbulent Ocean (2024)
    National Academy of Sciences
    Details
    Publication Date: 2024-04-26
    Description: The sinking of particulate matter from the upper ocean dominates the export and sequestration of organic carbon by the biological pump, a critical component of the Earth's carbon cycle. Controls on carbon export are thought to be driven by ecological processes that produce and repackage sinking biogenic particles. Here, we present observations during the demise of the Northeast Atlantic Ocean spring bloom illustrating the importance of storm-induced turbulence on the dynamics of sinking particles. A sequence of four large storms caused upper layer mean turbulence levels to vary by more than three orders of magnitude. Large particle (>0.1 to 10 mm) abundance and size changed accordingly: increasing via shear coagulation when turbulence was moderate and decreasing rapidly when turbulence was intense due to shear disaggregation. Particle export was also tied to storm forcing as large particles were mixed to depth during mixed layer deepening. After the mixed layer shoaled, these particles, now isolated from intense surface mixing, grew larger and subsequently sank. This sequence of events matched the timing of sinking particle flux observations. Particle export was influenced by increases in aggregate abundance and porosity, which appeared to be enhanced by the repeated creation and destruction of aggregates. Last, particle transit efficiency through the mesopelagic zone was reduced by presumably biotic processes that created small particles (〈0.5 mm) from larger ones. Our results demonstrate that ocean turbulence significantly impacts the nature and dynamics of sinking particles, strongly influencing particle export and the efficiency of the biological pump.
    Type: Article , NonPeerReviewed
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 2
    facet.materialart.
    Unknown
    A Late Pleistocene coastal ecosystem in French Guiana was hyperdiverse relative to today (2024)
    National Academy of Sciences
    Details
    Publication Date: 2024-05-13
    Description: Warmer temperatures and higher sea level than today characterized the Last Interglacial interval [Pleistocene, 128 to 116 thousand years ago (ka)]. This period is a remarkable deep-time analog for temperature and sea-level conditions as projected for 2100 AD, yet there has been no evidence of fossil assemblages in the equatorial Atlantic. Here, we report foraminifer, metazoan (mollusks, bony fish, bryozoans, decapods, and sharks among others), and plant communities of coastal tropical marine and mangrove affinities, dating precisely from a ca. 130 to 115 ka time interval near the Equator, at Kourou, in French Guiana. These communities include ca. 230 recent species, some being endangered today and/or first recorded as fossils. The hyperdiverse Kourou mollusk assemblage suggests stronger affinities between Guianese and Caribbean coastal waters by the Last Interglacial than today, questioning the structuring role of the Amazon Plume on tropical Western Atlantic communities at the time. Grassland-dominated pollen, phytoliths, and charcoals from younger deposits in the same sections attest to a marine retreat and dryer conditions during the onset of the last glacial (ca. 110 to 50 ka), with a savanna-dominated landscape and episodes of fire. Charcoals from the last millennia suggest human presence in a mosaic of modern-like continental habitats. Our results provide key information about the ecology and biogeography of pristine Pleistocene tropical coastal ecosystems, especially relevant regarding the—widely anthropogenic—ongoing global warming.
    Type: Article , PeerReviewed
    Format: text
    Format: other
    Format: other
    Format: text
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 3
    facet.materialart.
    Unknown
    3D intrusions transport active surface microbial assemblages to the dark ocean (2024)
    National Academy of Sciences
    Details
    Publication Date: 2024-06-05
    Description: Significance Particulate organic carbon (POC) formed by photosynthesis in the sunlit surface ocean fuels the ecosystems in the dark ocean below. We show that mesoscale fronts and eddies, which are ubiquitous physical features in subtropical oceans, generate three-dimensional intrusions connecting the surface to deep ocean. Intrusions are enriched in total POC due to enhancement of small, nonsinking photosynthetic plankton and free-living bacteria that resemble surface microbial communities. Flow-driven export of POC, estimated using an approximation of eddy physics, is the same order of magnitude as export by sinking POC, which was previously thought to dominate export. These observations reveal coupling of surface and deep ocean productivity and biodiversity and give insight into mechanisms by which the ocean transports carbon to depth. Abstract Subtropical oceans contribute significantly to global primary production, but the fate of the picophytoplankton that dominate in these low-nutrient regions is poorly understood. Working in the subtropical Mediterranean, we demonstrate that subduction of water at ocean fronts generates 3D intrusions with uncharacteristically high carbon, chlorophyll, and oxygen that extend below the sunlit photic zone into the dark ocean. These contain fresh picophytoplankton assemblages that resemble the photic-zone regions where the water originated. Intrusions propagate depth-dependent seasonal variations in microbial assemblages into the ocean interior. Strikingly, the intrusions included dominant biomass contributions from nonphotosynthetic bacteria and enrichment of enigmatic heterotrophic bacterial lineages. Thus, the intrusions not only deliver material that differs in composition and nutritional character from sinking detrital particles, but also drive shifts in bacterial community composition, organic matter processing, and interactions between surface and deep communities. Modeling efforts paired with global observations demonstrate that subduction can flux similar magnitudes of particulate organic carbon as sinking export, but is not accounted for in current export estimates and carbon cycle models. Intrusions formed by subduction are a particularly important mechanism for enhancing connectivity between surface and upper mesopelagic ecosystems in stratified subtropical ocean environments that are expanding due to the warming climate.
    Type: Article , PeerReviewed
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 4
    facet.materialart.
    Unknown
    Insights on long-term ecosystem changes from stable isotopes in historical squid beaks (2024)
    BioMed Central | Springer
    Details
    Publication Date: 2024-07-08
    Description: Background: Assessing the historical dynamics of key food web components is crucial to understand how climate change impacts the structure of Arctic marine ecosystems. Most retrospective stable isotopic studies to date assessed potential ecosystem shifts in the Arctic using vertebrate top predators and filter-feeding invertebrates as proxies. However, due to long life histories and specific ecologies, ecosystem shifts are not always detectable when using these taxa. Moreover, there are currently no retrospective stable isotopic studies on various other ecological and taxonomic groups of Arctic biota. To test whether climate-driven shifts in marine ecosystems are reflected in the ecology of short-living mesopredators, ontogenetic changes in stable isotope signatures in chitinous hard body structures were analysed in two abundant squids (Gonatus fabricii and Todarodes sagittatus) from the low latitude Arctic and adjacent waters, collected between 1844 and 2023. Results: We detected a temporal increase in diet and habitat-use generalism (= opportunistic choice rather than specialization), trophic position and niche width in G. fabricii from the low latitude Arctic waters. These shifts in trophic ecology matched with the Atlantification of the Arctic ecosystems, which includes increased generalization of food webs and higher primary production, and the influx of boreal species from the North Atlantic as a result of climate change. The Atlantification is especially marked since the late 1990s/early 2000s. The temporal patterns we found in G. fabricii’s trophic ecology were largely unreported in previous Arctic retrospective isotopic ecology studies. Accordingly, T. sagittatus that occur nowadays in the high latitude North Atlantic have a more generalist diet than in the XIXth century. :Conclusions Our results suggest that abundant opportunistic mesopredators with short life cycles (such as squids) are good candidates for retrospective ecology studies in the marine ecosystems, and to identify ecosystem shifts driven by climate change. Enhanced generalization of Arctic food webs is reflected in increased diet generalism and niche width in squids, while increased abundance of boreal piscivorous fishes is reflected in squids’ increased trophic position. These findings support opportunism and adaptability in squids, which renders them as potential winners of short-term shifts in Arctic ecosystems.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
    Format: text
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 5
    facet.materialart.
    Unknown
    A metabologenomics approach to unlock the metabolome of the novel Antarctic deep-sea isolate Lacinutrix shetlandiensis sp. nov. WUR7 (2023)
    National Academy of Sciences
    Details
    Publication Date: 2024-01-08
    Description: The South Shetland Trough, Antarctica, is an underexplored region for microbiological and biotechnological exploitation. Herein, we describe the isolation and characterization of the novel bacterium Lacinutrix shetlandiensis sp. nov. WUR7 from a deep-sea environment. We explored its chemical diversity via a metabologenomics approach, wherein the OSMAC strategy was strategically employed to upregulate cryptic genes for secondary metabolite production. Based on hybrid de novo whole genome sequencing and digital DNA–DNA hybridization, isolate WUR7 was identified as a novel species from the Gram-negative genus Lacinutrix. Its genome was mined for the presence of biosynthetic gene clusters with limited results. However, extensive investigation of its metabolism uncovered an unusual tryptophan decarboxylase with high sequence homology and conserved structure of the active site as compared to ZP_02040762, a highly specific tryptophan decarboxylase from Ruminococcus gnavus. Therefore, WUR7's metabolism was directed toward indole-based alkaloid biosynthesis by feeding it with L-tryptophan. As expected, its metabolome profile changed dramatically, by triggering the extracellular accumulation of a massive array of metabolites unexpressed in the absence of tryptophan. Untargeted LC-MS/MS coupled with molecular networking, followed along with chemoinformatic dereplication, allowed for the annotation of 10 indole alkaloids, belonging to β-carboline, bisindole, and monoindole classes, alongside several unknown alkaloids. These findings guided us to the isolation of a new natural bisindole alkaloid 8,9-dihydrocoscinamide B (1), as the first alkaloid from the genus Lacinutrix, whose structure was elucidated on the basis of extensive 1D and 2D NMR and HR-ESIMS experiments. This comprehensive strategy allowed us to unlock the previously unexploited metabolome of L. shetlandiensis sp. nov. WUR7.
    Type: Article , PeerReviewed
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 6
    facet.materialart.
    Unknown
    The effect of calcium supplementation on calcium and bone metabolism during load carriage in women: protocol for a randomised controlled crossover trial (2023)
    Springer | BioMed Central
    Details
    Publication Date: 2024-02-07
    Description: Military field exercises are characterised by high volumes of exercise and prolonged periods of load carriage. Exercise can decrease circulating serum calcium and increase parathyroid hormone and bone resorption. These disturbances to calcium and bone metabolism can be attenuated with calcium supplementation immediately before exercise. This randomised crossover trial will investigate the effect of calcium supplementation on calcium and bone metabolism, and bone mineral balance, during load carriage exercise in women. Methods Thirty women (eumenorrheic or using the combined oral contraceptive pill, intrauterine system, or intrauterine device) will complete two experimental testing sessions either with, or without, a calcium supplement (1000 mg). Each experimental testing session will involve one 120 min session of load carriage exercise carrying 20 kg. Venous blood samples will be taken and analysed for biochemical markers of bone resorption and formation, calcium metabolism, and endocrine function. Urine will be collected pre- and post-load carriage to measure calcium isotopes for the calculation of bone calcium balance. Discussion The results from this study will help identify whether supplementing women with calcium during load carriage is protective of bone and calcium homeostasis.
    Type: Article , PeerReviewed
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 7
    facet.materialart.
    Unknown
    Long-term stability in the circumpolar foraging range of a Southern Ocean predator between the eras of whaling and rapid climate change (2023)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-07
    Description: Significance Assessing change in Southern Ocean ecosystems is challenging due to its remoteness. Large-scale datasets that allow comparison between present-day conditions and those prior to large-scale ecosystem disturbances caused by humans (e.g., fishing/whaling) are rare. We infer the contemporary offshore foraging distribution of a marine predator, southern right whales (n = 1,002), using a customized stable isotope-based assignment approach based on biogeochemical models of the Southern Ocean. We then compare the contemporary distributions during the late austral summer and autumn to whaling catch data representing historical distributions during the same seasons. We show remarkable consistency of mid-latitude distribution across four centuries but shifts in foraging grounds in the past 30 y, particularly in the high latitudes that are likely driven by climate-associated alterations in prey availability. Abstract Assessing environmental changes in Southern Ocean ecosystems is difficult due to its remoteness and data sparsity. Monitoring marine predators that respond rapidly to environmental variation may enable us to track anthropogenic effects on ecosystems. Yet, many long-term datasets of marine predators are incomplete because they are spatially constrained and/or track ecosystems already modified by industrial fishing and whaling in the latter half of the 20th century. Here, we assess the contemporary offshore distribution of a wide-ranging marine predator, the southern right whale (SRW, Eubalaena australis), that forages on copepods and krill from ~30°S to the Antarctic ice edge (〉60°S). We analyzed carbon and nitrogen isotope values of 1,002 skin samples from six genetically distinct SRW populations using a customized assignment approach that accounts for temporal and spatial variation in the Southern Ocean phytoplankton isoscape. Over the past three decades, SRWs increased their use of mid-latitude foraging grounds in the south Atlantic and southwest (SW) Indian oceans in the late austral summer and autumn and slightly increased their use of high-latitude (〉60°S) foraging grounds in the SW Pacific, coincident with observed changes in prey distribution and abundance on a circumpolar scale. Comparing foraging assignments with whaling records since the 18th century showed remarkable stability in use of mid-latitude foraging areas. We attribute this consistency across four centuries to the physical stability of ocean fronts and resulting productivity in mid-latitude ecosystems of the Southern Ocean compared with polar regions that may be more influenced by recent climate change.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 8
    facet.materialart.
    Unknown
    Choanoflagellates alongside diverse uncultured predatory protists consume the abundant open-ocean cyanobacterium Prochlorococcus (2023)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-07
    Description: Prochlorococcus is a key member of open-ocean primary producer communities. Despite its importance, little is known about the predators that consume this cyanobacterium and make its biomass available to higher trophic levels. We identify potential predators along a gradient wherein Prochlorococcus abundance increased from near detection limits (coastal California) to 〉200,000 cells mL-1 (subtropical North Pacific Gyre). A replicated RNA-Stable Isotope Probing experiment involving the in situ community, and labeled Prochlorococcus as prey, revealed choanoflagellates as the most active predators of Prochlorococcus, alongside a radiolarian, chrysophytes, dictyochophytes, and specific MAST lineages. These predators were not appropriately highlighted in multiyear conventional 18S rRNA gene amplicon surveys where dinoflagellates and other taxa had highest relative amplicon abundances across the gradient. In identifying direct consumers of Prochlorococcus, we reveal food-web linkages of individual protistan taxa and resolve routes of carbon transfer from the base of marine food webs.
    Type: Article , PeerReviewed
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 9
    facet.materialart.
    Unknown
    Rhythm of relationships in a social fish over the course of a full year in the wild (2023)
    BioMed Central | Springer
    Details
    Publication Date: 2024-02-07
    Description: Background: Animals are expected to adjust their social behaviour to cope with challenges in their environment. Therefore, for fish populations in temperate regions with seasonal and daily environmental oscillations, characteristic rhythms of social relationships should be pronounced. To date, most research concerning fish social networks and biorhythms has occurred in artificial laboratory environments or over confined temporal scales of days to weeks. Little is known about the social networks of wild, freely roaming fish, including how seasonal and diurnal rhythms modulate social networks over the course of a full year. The advent of high-resolution acoustic telemetry enables us to quantify detailed social interactions in the wild over time-scales sufficient to examine seasonal rhythms at whole-ecosystems scales. Our objective was to explore the rhythms of social interactions in a social fish population at various time-scales over one full year in the wild by examining high-resolution snapshots of a dynamic social network. Methods: To that end, we tracked the behaviour of 36 adult common carp, Cyprinus carpio, in a 25 ha lake and constructed temporal social networks among individuals across various time-scales, where social interactions were defined by proximity. We compared the network structure to a temporally shuffled null model to examine the importance of social attraction, and checked for persistent characteristic groups over time. Results: The clustering within the carp social network tended to be more pronounced during daytime than nighttime throughout the year. Social attraction, particularly during daytime, was a key driver for interactions. Shoaling behavior substantially increased during daytime in the wintertime, whereas in summer carp interacted less frequently, but the interaction duration increased. Therefore, smaller, characteristic groups were more common in the summer months and during nighttime, where the social memory of carp lasted up to two weeks. Conclusions: We conclude that social relationships of carp change diurnally and seasonally. These patterns were likely driven by predator avoidance, seasonal shifts in lake temperature, visibility, forage availability and the presence of anoxic zones. The techniques we employed can be applied generally to high-resolution biotelemetry data to reveal social structures across other fish species at ecologically realistic scales.
    Type: Article , PeerReviewed
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 10
    facet.materialart.
    Unknown
    Evidence of nitrate-based nighttime atmospheric nucleation driven by marine microorganisms in the South Pacific (2023)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-23
    Description: Significance Oceans represent 70% of our planet’s surface, housing a large spectrum of microorganisms that interact with the above atmosphere. Ocean microorganisms were proposed in the late 80’s to be at the center of a climate feedback loop involving dimethyl sulfide (DMS) that would form aerosols and modify cloud properties (CLAW hypothesis). In the present paper, we report observational evidence from semicontrolled experiments in the South Pacific that nitrate ions, yet hitherto not considered, is a key species involved in aerosol nucleation in the pristine marine atmosphere and which precursors are coemitted with DMS. Our results further indicate that nitrate ion formation would be related to short-term microbial processes, sensitive to environmental stressors, therefore potentially “closing the loop”. Abstract Our understanding of ocean–cloud interactions and their effect on climate lacks insight into a key pathway: do biogenic marine emissions form new particles in the open ocean atmosphere? Using measurements collected in ship-borne air–sea interface tanks deployed in the Southwestern Pacific Ocean, we identified new particle formation (NPF) during nighttime that was related to plankton community composition. We show that nitrate ions are the only species for which abundance could support NPF rates in our semicontrolled experiments. Nitrate ions also prevailed in the natural pristine marine atmosphere and were elevated under higher sub-10 nm particle concentrations. We hypothesize that these nucleation events were fueled by complex, short-term biogeochemical cycling involving the microbial loop. These findings suggest a new perspective with a previously unidentified role of nitrate of marine biogeochemical origin in aerosol nucleation.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 11
    facet.materialart.
    Unknown
    The strength of the Earth's magnetic field from Pre-Pottery to Pottery Neolithic, Jordan (2023)
    National Academy of Sciences
    Details
    Publication Date: 2023-10-26
    Description: Constraining secular variation of the Earth's magnetic field strength in the past is fundamental to understanding short-term processes of the geodynamo. Such records also constitute a powerful and independent dating tool for archaeological sites and geological formations. In this study, we present 11 robust archaeointensity results from Pre-Pottery to Pottery Neolithic Jordan that are based on both clay and flint (chert) artifacts. Two of these results constitute the oldest archaeointensity data for the entire Levant, ancient Egypt, Turkey, and Mesopotamia, extending the archaeomagnetic reference curve for the Holocene. Virtual Axial Dipole Moments (VADMs) show that the Earth's magnetic field in the Southern Levant was weak (about two-thirds the present field) at around 7600 BCE, recovering its strength to greater than the present field around 7000 BCE, and gradually weakening again around 5200 BCE. In addition, successful results obtained from burnt flint demonstrate the potential of this very common, and yet rarely used, material in archaeomagnetic research, in particular for prehistoric periods from the first use of fire to the invention of pottery.
    Description: Published
    Description: e2100995118
    Description: 1A. Geomagnetismo e Paleomagnetismo
    Description: JCR Journal
    Keywords: Jordan ; Neolithic ; Pre-Pottery Neolithic ; archaeointensity
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 12
    facet.materialart.
    Unknown
    Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean (2023)
    National Academy of Sciences
    Details
    Publication Date: 2023-03-08
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Saunders, J. K., McIlvin, M. R., Dupont, C. L., Kaul, D., Moran, D. M., Horner, T., Laperriere, S. M., Webb, E. A., Bosak, T., Santoro, A. E., & Saito, M. A. Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean. Proceedings of the National Academy of Sciences of the United States of America, 119(37),(2022): e2200014119, https://doi.org/10.1073/pnas.2200014119.
    Description: Enzymes catalyze key reactions within Earth’s life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO2, NO, methanethiol, and methylamines were most abundant in the upwelling region. We identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.
    Description: Funding for this research was provided by the Gordon and Betty Moore Foundation (grants 3782 and 8453), the US NSF (NSF grants OCE-1924554, 2123055, 2125063, 2048774, and 2026933), the Center for Chemical Currencies on a Microbial Planet (NSF grant OCE-2019589), and the US NIH General Medicine (grant GM135709-01A1). J.K.S. was supported by a NASA Postdoctoral Program Fellowship with the NASA Astrobiology Program, administered by Universities Space Research Association under contract with NASA. A.E.S. was supported by the Sloan Foundation, the Simons Foundation, and NSF grant OCE-1437310. A portion of this research used resources at the US Department of Energy JGI sponsored by the Office of Biological and Environmental Research and operated under contract DE-AC02-05CH11231 (JGI). C.L.D. and D.K. were supported by NSF grants OCE-1558453 and OCE-2049299. T.H. was supported by NSF grant OCE-2023456.
    Keywords: Marine microbial ecology ; Metaproteomics ; Mesopelagic ; Nitrification ; Methylotrophy
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 13
    facet.materialart.
    Unknown
    Denitrification in foraminifera has an ancient origin and is complemented by associated bacteria (2022)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-07
    Description: Significance A substantial component of the global nitrogen cycle is the production of biologically inaccessible dinitrogen attributed to anaerobic denitrification by prokaryotes. Recent evidence identified a eukaryote, foraminifera, as new key players in this “loss” of bioavailable nitrogen. The evolution of denitrification in eukaryotes is a rare event, and the genetic mechanisms of the denitrification pathway in foraminifera are just starting to be elucidated. We present large-scale sequencing analyses of 10 denitrifying foraminiferal species, which reveals the high conservation of the foraminiferal denitrification pathway. We further find evidence for a complementation of denitrification by the foraminiferal microbiome. Together, these findings provide insights into the early evolution of a previously overlooked component in the marine nitrogen cycle. Abstract: Benthic foraminifera are unicellular eukaryotes that inhabit sediments of aquatic environments. Several foraminifera of the order Rotaliida are known to store and use nitrate for denitrification, a unique energy metabolism among eukaryotes. The rotaliid Globobulimina spp. has been shown to encode an incomplete denitrification pathway of bacterial origin. However, the prevalence of denitrification genes in foraminifera remains unknown, and the missing denitrification pathway components are elusive. Analyzing transcriptomes and metagenomes of 10 foraminiferal species from the Peruvian oxygen minimum zone, we show that denitrification genes are highly conserved in foraminifera. We infer the last common ancestor of denitrifying foraminifera, which enables us to predict the ability to denitrify for additional foraminiferal species. Additionally, an examination of the foraminiferal microbiota reveals evidence for a stable interaction with Desulfobacteraceae, which harbor genes that complement the foraminiferal denitrification pathway. Our results provide evidence that foraminiferal denitrification is complemented by the foraminifera-associated microbiome. The interaction of foraminifera with their resident bacteria is at the basis of foraminiferal adaptation to anaerobic environments that manifested in ecological success in oxygen depleted habitats.
    Type: Article , PeerReviewed
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 14
    facet.materialart.
    Unknown
    Symbiont transmission in marine sponges: reproduction, development, and metamorphosis (2022)
    Springer | BioMed Central
    Details
    Publication Date: 2024-02-07
    Description: Marine sponges (phylum Porifera) form symbioses with diverse microbial communities that can be transmitted between generations through their developmental stages. Here, we integrate embryology and microbiology to review how symbiotic microorganisms are transmitted in this early-diverging lineage. We describe that vertical transmission is widespread but not universal, that microbes are vertically transmitted during a select developmental window, and that properties of the developmental microbiome depends on whether a species is a high or low microbial abundance sponge. Reproduction, development, and symbiosis are thus deeply rooted, but why these partnerships form remains the central and elusive tenet of these developmental symbioses.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 15
    facet.materialart.
    Unknown
    Rapid radiation in a highly diverse marine environment (2022)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-07
    Description: Significance: Adaptive radiation, the evolutionary process whereby a lineage diversifies over a short period of time, often occurs in geographically isolated or newly formed habitats where colonizing species encounter unoccupied niches and reduced selective pressures. Rapid radiations may also occur in diverse and complex environments, but these cases are less well documented. Here, we show that the hamlets, a group of Caribbean reef fishes, radiated within the last 10,000 generations in a burst of diversification that ranks among the fastest in fishes. Genomic analysis suggests that color pattern diversity is generated by different combinations of alleles at a few genes with large effect. Such a modular genomic architecture of diversification is emerging as a common denominator to a variety of radiations. Abstract: Rapid diversification is often observed when founding species invade isolated or newly formed habitats that provide ecological opportunity for adaptive radiation. However, most of the Earth’s diversity arose in diverse environments where ecological opportunities appear to be more constrained. Here, we present a striking example of a rapid radiation in a highly diverse marine habitat. The hamlets, a group of reef fishes from the wider Caribbean, have radiated into a stunning diversity of color patterns but show low divergence across other ecological axes. Although the hamlet lineage is ∼26 My old, the radiation appears to have occurred within the last 10,000 generations in a burst of diversification that ranks among the fastest in fishes. As such, the hamlets provide a compelling backdrop to uncover the genomic elements associated with phenotypic diversification and an excellent opportunity to build a broader comparative framework for understanding the drivers of adaptive radiation. The analysis of 170 genomes suggests that color pattern diversity is generated by different combinations of alleles at a few large-effect loci. Such a modular genomic architecture of diversification has been documented before in Heliconius butterflies, capuchino finches, and munia finches, three other tropical radiations that took place in highly diverse and complex environments. The hamlet radiation also occurred in a context of high effective population size, which is typical of marine populations. This allows for the accumulation of new variants through mutation and the retention of ancestral genetic variation, both of which appear to be important in this radiation.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 16
    facet.materialart.
    Unknown
    Experimental evolution reveals the synergistic genomic mechanisms of adaptation to ocean warming and acidification in a marine copepod (2022)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-07
    Description: Significance Resilience to global change will require adaptation to multiple concurrent environmental changes. However, it is unclear if adaptations to multiple stressors can be predicted from the sum of single-stressor adaptation. To answer this question, we experimentally evolved a marine copepod to warming, acidification, and their combination, finding that copepods were able to adapt to all conditions over 25 generations. Warming was a much stronger selective pressure than acidification alone and under multiple-stressor conditions. Nevertheless, the multiple-stressor response to selection was synergistic and unique from either single stressor. Thus, adaptation to single stressors may not reveal adaptive potential or mechanisms of adaptation under multiple stressors, demonstrating the complexity of predicting adaptive responses under multifaceted environmental change. Abstract Metazoan adaptation to global change relies on selection of standing genetic variation. Determining the extent to which this variation exists in natural populations, particularly for responses to simultaneous stressors, is essential to make accurate predictions for persistence in future conditions. Here, we identified the genetic variation enabling the copepod Acartia tonsa to adapt to experimental ocean warming, acidification, and combined ocean warming and acidification (OWA) over 25 generations of continual selection. Replicate populations showed a consistent polygenic response to each condition, targeting an array of adaptive mechanisms including cellular homeostasis, development, and stress response. We used a genome-wide covariance approach to partition the allelic changes into three categories: selection, drift and replicate-specific selection, and laboratory adaptation responses. The majority of allele frequency change in warming (57%) and OWA (63%) was driven by shared selection pressures across replicates, but this effect was weaker under acidification alone (20%). OWA and warming shared 37% of their response to selection but OWA and acidification shared just 1%, indicating that warming is the dominant driver of selection in OWA. Despite the dominance of warming, the interaction with acidification was still critical as the OWA selection response was highly synergistic with 47% of the allelic selection response unique from either individual treatment. These results disentangle how genomic targets of selection differ between single and multiple stressors and demonstrate the complexity that nonadditive multiple stressors will contribute to predictions of adaptation to complex environmental shifts caused by global change.
    Type: Article , PeerReviewed
    Format: text
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 17
    facet.materialart.
    Unknown
    Modes of Pangean lake level cyclicity driven by astronomical climate pacing modulated by continental position and p CO2 (2022)
    National Academy of Sciences
    Details
    Publication Date: 2024-05-22
    Description: Orbital cyclicity is a fundamental pacemaker of Earth’s climate system. The Newark–Hartford Basin (NHB) lake sediment record of eastern North America contains compelling geologic expressions of this cyclicity, reflecting variations of climatic conditions in tropical Pangea during the Late Triassic and earliest Jurassic (~233 to 199 Ma). Climate modeling enables a deeper mechanistic understanding of Earth system modulation during this unique greenhouse and supercontinent period. We link major features of the NHB record to the combined climatic effects of orbital forcing, paleogeographic changes, and atmospheric p CO 2 variations. An ensemble of transient, orbitally driven climate simulations is assessed for nine time slices, three atmospheric p CO 2 values, and two paleogeographic reconstructions. Climatic transitions from tropical humid to more seasonal and ultimately semiarid are associated with tectonic drift of the NHB from ~ 5 ° N to 20 ° N . The modeled orbital modulation of the precipitation–evaporation balance is most pronounced during the 220 to 200 Ma interval, whereas it is limited by weak seasonality and increasing aridity before and after this interval. Lower p CO 2 at around 205 Ma contributes to drier climates and could have led to the observed damping of sediment cyclicity. Eccentricity-modulated precession dominates the orbitally driven climate response in the NHB region. High obliquity further amplifies summer precipitation through the seasonal shifts in the tropical rainfall belt. Regions with other proxy records are also assessed, providing guidance toward an integrated picture of global astronomical climate forcing in the Late Triassic and ultimately of other periods in Earth history.
    Type: Article , PeerReviewed
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 18
    facet.materialart.
    Unknown
    Diverse methylotrophic methanogenic archaea cause high methane emissions from seagrass meadows (2022)
    National Academy of Sciences
    Details
    Publication Date: 2023-03-08
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Schorn, S., Ahmerkamp, S., Bullock, E., Weber, M., Lott, C., Liebeke, M., Lavik, G., Kuypers, M. M. M., Graf, J. S., & Milucka, J. Diverse methylotrophic methanogenic archaea cause high methane emissions from seagrass meadows. Proceedings of the National Academy of Sciences of the United States of America, 119(9), (2022): e2106628119, https://doi.org/10.1073/pnas.2106628119.
    Description: Marine coastlines colonized by seagrasses are a net source of methane to the atmosphere. However, methane emissions from these environments are still poorly constrained, and the underlying processes and responsible microorganisms remain largely unknown. Here, we investigated methane turnover in seagrass meadows of Posidonia oceanica in the Mediterranean Sea. The underlying sediments exhibited median net fluxes of methane into the water column of ca. 106 µmol CH4 ⋅ m−2 ⋅ d−1. Our data show that this methane production was sustained by methylated compounds produced by the plant, rather than by fermentation of buried organic carbon. Interestingly, methane production was maintained long after the living plant died off, likely due to the persistence of methylated compounds, such as choline, betaines, and dimethylsulfoniopropionate, in detached plant leaves and rhizomes. We recovered multiple mcrA gene sequences, encoding for methyl-coenzyme M reductase (Mcr), the key methanogenic enzyme, from the seagrass sediments. Most retrieved mcrA gene sequences were affiliated with a clade of divergent Mcr and belonged to the uncultured Candidatus Helarchaeota of the Asgard superphylum, suggesting a possible involvement of these divergent Mcr in methane metabolism. Taken together, our findings identify the mechanisms controlling methane emissions from these important blue carbon ecosystems.
    Description: This project was funded by theMax Planck Society.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 19
    facet.materialart.
    Unknown
    Treatment of perioperative swelling by rest, ice, compression, and elevation (RICE) without and with additional application of negative pressure (RICE+) in patients with a unilateral ankle fracture: study protocol for a monocentric, evaluator-blinded randomized controlled pilot trial (2021)
    BioMed Central | Springer
    Details
    Publication Date: 2024-02-07
    Description: Background Edema is commonly seen after surgical fixation of ankle fractures. Rest, ice, compression, and elevation (RICE) is an established combination to prevent swelling but hardly able to stimulate lymphatic resorption. Recently, an epicutaneously applied negative pressure suction apparatus (LymphaTouch®) has been introduced to stimulate lymphatic flow. While postoperative recovery, soft tissue, and osseous healing as well as functional outcome are probably linked to the amount of postoperative swelling, estimates on this relative to prevention (RICE) or prevention + stimulated resorption (RICE + ) of fluid are scarce. Methods and analysis This is a single-center, evaluator-blinded randomized pilot trial to investigate postoperative swelling in adults requiring surgical fixation of a closed unilateral ankle fracture. A total of 50 patients will be recruited and randomly assigned to RICE or RICE + prior to surgery. All patients will undergo evaluator-blinded measurements of the ankle volume the day before surgery and subsequently from the evening of the 2nd postoperative day every 24 h until discharge. RICE will be initiated right after surgery and continued until discharge from the hospital in all patients. Additional application of negative pressure therapy (RICE + ) will be initiated on the morning of the 2nd postoperative day and repeated every 24 h until the time of discharge from the hospital. Outcome measures are (i) the relative amount and the time course of the postoperative swelling, (ii) the demand for analgesic therapy (type and amount) together with the perception of pain, (iii) the rate of complications, and (iv) mobility of the ankle joint and the recovery of walking abilities during a 12-weeks follow-up period. Serum and urine samples taken prior to sugery and during postoperative recovery will allow to evaluate the ratio of naturally occurring stable calcium isotopes (δ 44/42 Ca) as a marker of skeletal calcium accrual.
    Type: Article , PeerReviewed
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 20
    facet.materialart.
    Unknown
    Living and dead foraminiferal assemblage from the supratidal sand Japsand, North Frisian Wadden Sea: distributional patterns and controlling factors (2021)
    Springer | BioMed Central
    Details
    Publication Date: 2024-02-07
    Description: Supratidal sands are vitally important for coastal defence in the German Wadden Sea. They are less affected by human activities than other areas as they are located far off the mainland shore, touristical and commercial activities are generally prohibited. Therefore, supratidal sands are of high ecological interest. Nevertheless, the faunal inventory and distribution pattern of microorganisms on these sands were studied very little. The composition of living and dead foraminiferal assemblages was therefore investigated along a transect from the supratidal sand Japsand up to Hallig Hooge. Both assemblages were dominated by calcareous foraminifera of which Ammonia batava was the most abundant species. Elphidium selseyense and Elphidium williamsoni were also common in the living assemblage, but Elphidium williamsoni was comparably rare in the dead assemblage. The high proportions of Ammonia batava and Elphidium selseyense in the living assemblage arose from the reproduction season that differed between species. While Ammonia batava and Elphidium selseyense just finished their reproductive cycles, Elphidium williamsoni was just about to start. This was also confirmed by the size distribution patterns of the different species. The dead assemblage revealed 20 species that were not found in the living assemblage of which some were reworked from older sediments (e.g., Bucella frigida) and some were transported via tidal currents from other areas in the North Sea (e.g., Jadammina macrescens). The living foraminiferal faunas depicted close linkages between the open North Sea and the mainland. Key species revealing exchange between distant populations were Haynesina germanica, Ammonia batava and different Elphidium species. All these species share an opportunistic behaviour and are able to inhabit a variety of different environments; hence, they well may cope with changing environmental conditions. The benthic foraminiferal association from Japsand revealed that transport mechanisms via tides and currents play a major ecological role and strongly influence the faunal composition at this site.
    Type: Article , PeerReviewed
    Format: text
    Format: other
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 21
    facet.materialart.
    Unknown
    Persistent deep water anoxia in the eastern South Atlantic during the last ice age (2021)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-07
    Description: During the last glacial interval, marine sediments recorded reduced current ventilation within the ocean interior below water depths of approximately 〉1,500 m [B. A. Hoogakker et al., Nat. Geosci. 8, 40–43 (2015)]. The degree of the associated oxygen depletion in the different ocean basins, however, is still poorly constrained. Here, we present sedimentary records of redox-sensitive metals from the southwest African margin. These records show evidence of continuous bottom water anoxia in the eastern South Atlantic during the last glaciation that led to enhanced carbon burial over a prolonged period of time. Our geochemical data indicate that upwelling-related productivity and the associated oxygen minimum zone in the eastern South Atlantic shifted far seaward during the last glacial period and only slowly retreated during deglaciation times. While increased productivity during the last ice age may have contributed to oxygen depletion in bottom waters, especially on the upper slope, slow-down of the Late Quaternary deep water circulation pattern [Rutberg et al., Nature 405, 935–938 (2000)] appears to be the ultimate driver of anoxic conditions in deep waters.
    Type: Article , PeerReviewed
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 22
    facet.materialart.
    Unknown
    Towards enhancing coral heat tolerance: a “microbiome transplantation” treatment using inoculations of homogenized coral tissues (2021)
    BioMed Central
    Details
    Publication Date: 2024-02-07
    Description: Background: Microbiome manipulation could enhance heat tolerance and help corals survive the pressures of ocean warming. We conducted coral microbiome transplantation (CMT) experiments using the reef-building corals, Pocillopora and Porites, and investigated whether this technique can benefit coral heat resistance while modifying the bacterial microbiome. Initially, heat-tolerant donors were identified in the wild. We then used fresh homogenates made from coral donor tissues to inoculate conspecific, heat-susceptible recipients and documented their bleaching responses and microbiomes by 16S rRNA gene metabarcoding. Results: Recipients of both coral species bleached at lower rates compared to the control group when exposed to short-term heat stress (34 °C). One hundred twelve (Pocillopora sp.) and sixteen (Porites sp.) donor-specific bacterial species were identified in the microbiomes of recipients indicating transmission of bacteria. The amplicon sequence variants of the majority of these transmitted bacteria belonged to known, putatively symbiotic bacterial taxa of corals and were linked to the observed beneficial effect on the coral stress response. Microbiome dynamics in our experiments support the notion that microbiome community evenness and dominance of one or few bacterial species, rather than host-species identity, were drivers for microbiome stability in a holobiont context. Conclusions: Our results suggest that coral recipients likely favor the uptake of putative bacterial symbionts, recommending to include these taxonomic groups in future coral probiotics screening efforts. Our study suggests a scenario where these donor-specific bacterial symbionts might have been more efficient in supporting the recipients to resist heat stress compared to the native symbionts present in the control group. These findings urgently call for further experimental investigation of the mechanisms of action underlying the beneficial effect of CMT and for field-based long-term studies testing the persistence of the effect. [MediaObject not available: see fulltext.].
    Type: Article , PeerReviewed
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 23
    facet.materialart.
    Unknown
    Microbiome reduction and endosymbiont gain from a switch in sea urchin life history (2021)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-07
    Description: Animal gastrointestinal tracts harbor a microbiome that is integral to host function, yet species from diverse phyla have evolved a reduced digestive system or lost it completely. Whether such changes are associated with alterations in the diversity and/or abundance of the microbiome remains an untested hypothesis in evolutionary symbiosis. Here, using the life history transition from planktotrophy (feeding) to lecithotrophy (nonfeeding) in the sea urchin Heliocidaris, we demonstrate that the lack of a functional gut corresponds with a reduction in microbial community diversity and abundance as well as the association with a diet-specific microbiome. We also determine that the lecithotroph vertically transmits a Rickettsiales that may complement host nutrition through amino acid biosynthesis and influence host reproduction. Our results indicate that the evolutionary loss of a functional gut correlates with a reduction in the microbiome and the association with an endosymbiont. Symbiotic transitions can therefore accompany life history transitions in the evolution of developmental strategies.
    Type: Article , PeerReviewed
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 24
    facet.materialart.
    Unknown
    Transcriptomic analysis of shell repair and biomineralization in the blue mussel, Mytilus edulis (2021)
    BioMed Central
    Details
    Publication Date: 2024-02-07
    Description: Background: Biomineralization by molluscs involves regulated deposition of calcium carbonate crystals within a protein framework to produce complex biocomposite structures. Effective biomineralization is a key trait for aquaculture, and animal resilience under future climate change. While many enzymes and structural proteins have been identified from the shell and in mantle tissue, understanding biomieralization is impeded by a lack of fundamental knowledge of the genes and pathways involved. In adult bivalves, shells are secreted by the mantle tissue during growth, maintenance and repair, with the repair process, in particular, amenable to experimental dissection at the transcriptomic level in individual animals. Results: Gene expression dynamics were explored in the adult blue mussel, Mytilus edulis, during experimentally induced shell repair, using the two valves of each animal as a matched treatment-control pair. Gene expression was assessed using high-resolution RNA-Seq against a de novo assembled database of functionally annotated transcripts. A large number of differentially expressed transcripts were identified in the repair process. Analysis focused on genes encoding proteins and domains identified in shell biology, using a new database of proteins and domains previously implicated in biomineralization in mussels and other molluscs. The genes implicated in repair included many otherwise novel transcripts that encoded proteins with domains found in other shell matrix proteins, as well as genes previously associated with primary shell formation in larvae. Genes with roles in intracellular signalling and maintenance of membrane resting potential were among the loci implicated in the repair process. While haemocytes have been proposed to be actively involved in repair, no evidence was found for this in the M. edulis data. Conclusions: The shell repair experimental model and a newly developed shell protein domain database efficiently identified transcripts involved in M. edulis shell production. In particular, the matched pair analysis allowed factoring out of much of the inherent high level of variability between individual mussels. This snapshot of the damage repair process identified a large number of genes putatively involved in biomineralization from initial signalling, through calcium mobilization to shell construction, providing many novel transcripts for future in-depth functional analyses
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 25
    facet.materialart.
    Unknown
    Invasion genomics uncover contrasting scenarios of genetic diversity in a widespread marine invader (2021)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-07
    Description: Significance: A central goal in invasion genomics is to identify and determine the mechanisms that underlie the successful colonization, establishment, and subsequent range expansion of invasive populations of nonindigenous species. Using a whole-genome approach, we evaluate the importance of genetic diversity for the successful establishment of nonindigenous species. Our study shows that genetic diversity per se is not the major factor driving invasions, since we observed all possible scenarios with invasive populations showing reduced, similar but also increased, genetic diversity relative to the native population. Using coalescent methods, we reconstruct the demographic history of the invasion and infer the source population of each invasion event, which shows that propagule pressure and multiple introductions play an important role in determining invasion success. Abstract: Invasion rates have increased in the past 100 y irrespective of international conventions. What characterizes a successful invasion event? And how does genetic diversity translate into invasion success? Employing a whole-genome perspective using one of the most successful marine invasive species world-wide as a model, we resolve temporal invasion dynamics during independent invasion events in Eurasia. We reveal complex regionally independent invasion histories including cases of recurrent translocations, time-limited translocations, and stepping-stone range expansions with severe bottlenecks within the same species. Irrespective of these different invasion dynamics, which lead to contrasting patterns of genetic diversity, all nonindigenous populations are similarly successful. This illustrates that genetic diversity, per se, is not necessarily the driving force behind invasion success. Other factors such as propagule pressure and repeated introductions are an important contribution to facilitate successful invasions. This calls into question the dominant paradigm of the genetic paradox of invasions, i.e., the successful establishment of nonindigenous populations with low levels of genetic diversity.
    Type: Article , PeerReviewed
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 26
    facet.materialart.
    Unknown
    Spiny and soft-rayed fin domains in acanthomorph fish are established through a BMP-gremlin-shh signaling network (2021)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-07
    Description: With over 18,000 species, the Acanthomorpha, or spiny-rayed fishes, form the largest and arguably most diverse radiation of vertebrates. One of the key novelties that contributed to their evolutionary success are the spiny rays in their fins that serve as a defense mechanism. We investigated the patterning mechanisms underlying the differentiation of median fin Anlagen into discrete spiny and soft rayed domains during the ontogeny of the direct-developing cichlid fish Astatotilapia burtoni. Distinct transcription factor signatures characterize these two fin domains, whereby mutually exclusive expression of hoxa13a/b with alx4a/b and tbx2b marks the spine to soft-ray boundary. The soft-ray domain is established by BMP inhibition via gremlin1b, which synergizes in the posterior fin with shh secreted from a zone of polarizing activity. Modulation of BMP signaling by chemical inhibition or gremlin1b CRISPR/Cas9 knockout induces homeotic transformations of spines into soft rays and vice versa. The expression of spine and soft-ray genes in nonacanthomorph fins indicates that a combination of exaptation and posterior expansion of an ancestral developmental program for the anterior fin margin allowed the evolution of robustly individuated spiny and soft-rayed domains. We propose that a repeated exaptation of such pattern might underly the convergent evolution of anterior spiny fin elements across fishes.
    Type: Article , PeerReviewed
    Format: text
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OCEANREP)
  • 27
    facet.materialart.
    Unknown
    Mammalian face as an evolutionary novelty (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-10-29
    Description: The anterior end of the mammalian face is characteristically composed of a semimotile nose, not the upper jaw as in other tetrapods. Thus, the therian nose is covered ventrolaterally by the “premaxilla,” and the osteocranium possesses only a single nasal aperture because of the absence of medial bony elements. This stands in contrast to those in other tetrapods in whom the premaxilla covers the rostral terminus of the snout, providing a key to understanding the evolution of the mammalian face. Here, we show that the premaxilla in therian mammals (placentals and marsupials) is not entirely homologous to those in other amniotes; the therian premaxilla is a composite of the septomaxilla and the palatine remnant of the premaxilla of nontherian amniotes (including monotremes). By comparing topographical relationships of craniofacial primordia and nerve supplies in various tetrapod embryos, we found that the therian premaxilla is predominantly of the maxillary prominence origin and associated with mandibular arch. The rostral-most part of the upper jaw in nonmammalian tetrapods corresponds to the motile nose in therian mammals. During development, experimental inhibition of primordial growth demonstrated that the entire mammalian upper jaw mostly originates from the maxillary prominence, unlike other amniotes. Consistently, cell lineage tracing in transgenic mice revealed a mammalian-specific rostral growth of the maxillary prominence. We conclude that the mammalian-specific face, the muzzle, is an evolutionary novelty obtained by overriding ancestral developmental constraints to establish a novel topographical framework in craniofacial mesenchyme.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 28
    facet.materialart.
    Unknown
    Power spectra reveal distinct BOLD resting-state time courses in white matter (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-10-29
    Description: Accurate characterization of the time courses of blood-oxygen-level–dependent (BOLD) signal changes is crucial for the analysis and interpretation of functional MRI data. While several studies have shown that white matter (WM) exhibits distinct BOLD responses evoked by tasks, there have been no comprehensive investigations into the time courses of spontaneous signal fluctuations in WM. We measured the power spectra of the resting-state time courses in a set of regions within WM identified as showing synchronous signals using independent components analysis. In each component, a clear separation between voxels into two categories was evident, based on their power spectra: one group exhibited a single peak, and the other had an additional peak at a higher frequency. Their groupings are location specific, and their distributions reflect unique neurovascular and anatomical configurations. Importantly, the two categories of voxels differed in their engagement in functional integration, revealed by differences in the number of interregional connections based on the two categories separately. Taken together, these findings suggest WM signals are heterogeneous in nature and depend on local structural-vascular-functional associations.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 29
    facet.materialart.
    Unknown
    Eccentricity forcing of East Asian monsoonal systems over the past 3 million years (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-10-20
    Description: The East Asian summer monsoon and the precipitation it brings are relevant for millions of people. Because of the monsoon’s importance, there has been a substantial amount of work attempting to describe the driving mechanisms behind its past variability. However, discrepancies exist, with speleothem-based East Asian monsoon reconstructions differing from those based on loess records from the Chinese Loess Plateau during the late Quaternary. The periodicity of wet and dry phases experienced by desert areas that lie on the periphery of the East Asian monsoon’s influence offer another independent view of monsoonal variability. Here, we provide environmental records based on magnetic parameters for the last 3 million years from the Tengger Desert, China, one such marginal arid region. Our results reveal wet–dry cycles at a dominant frequency of 405 kiloyears, with drier intervals corresponding to eccentricity minima. These findings are consistent with previous reconstructions of East Asian summer and North African summer monsoon precipitation variability. Our records emphasize the dominant role of eccentricity in forcing East Asian monsoonal precipitation as well as monsoonal-derived environmental fluctuations experienced in peripheral desert areas. These results challenge the traditional view that high-latitude ice sheets are the primary driver of East Asian monsoon precipitation during the Quaternary based on Chinese loess records.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 30
    facet.materialart.
    Unknown
    Configurational fingerprints of multicellular living systems (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-10-29
    Description: Cells cooperate as groups to achieve structure and function at the tissue level, during which specific material characteristics emerge. Analogous to phase transitions in classical physics, transformations in the material characteristics of multicellular assemblies are essential for a variety of vital processes including morphogenesis, wound healing, and cancer. In this work, we develop configurational fingerprints of particulate and multicellular assemblies and extract volumetric and shear order parameters based on this fingerprint to quantify the system disorder. Theoretically, these two parameters form a complete and unique pair of signatures for the structural disorder of a multicellular system. The evolution of these two order parameters offers a robust and experimentally accessible way to map the phase transitions in expanding cell monolayers and during embryogenesis and invasion of epithelial spheroids.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 31
    facet.materialart.
    Unknown
    Demonstration of the role of cell wall homeostasis in Staphylococcus aureus growth and the action of bactericidal antibiotics (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-10-29
    Description: Bacterial cell wall peptidoglycan is essential, maintaining both cellular integrity and morphology, in the face of internal turgor pressure. Peptidoglycan synthesis is important, as it is targeted by cell wall antibiotics, including methicillin and vancomycin. Here, we have used the major human pathogen Staphylococcus aureus to elucidate both the cell wall dynamic processes essential for growth (life) and the bactericidal effects of cell wall antibiotics (death) based on the principle of coordinated peptidoglycan synthesis and hydrolysis. The death of S. aureus due to depletion of the essential, two-component and positive regulatory system for peptidoglycan hydrolase activity (WalKR) is prevented by addition of otherwise bactericidal cell wall antibiotics, resulting in stasis. In contrast, cell wall antibiotics kill via the activity of peptidoglycan hydrolases in the absence of concomitant synthesis. Both methicillin and vancomycin treatment lead to the appearance of perforating holes throughout the cell wall due to peptidoglycan hydrolases. Methicillin alone also results in plasmolysis and misshapen septa with the involvement of the major peptidoglycan hydrolase Atl, a process that is inhibited by vancomycin. The bactericidal effect of vancomycin involves the peptidoglycan hydrolase SagB. In the presence of cell wall antibiotics, the inhibition of peptidoglycan hydrolase activity using the inhibitor complestatin results in reduced killing, while, conversely, the deregulation of hydrolase activity via loss of wall teichoic acids increases the death rate. For S. aureus, the independent regulation of cell wall synthesis and hydrolysis can lead to cell growth, death, or stasis, with implications for the development of new control regimes for this important pathogen.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 32
    facet.materialart.
    Unknown
    Analytics and visualization tools to characterize single-cell stochasticity using bacterial single-cell movie cytometry data (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-29
    Description: Background Time-lapse microscopy live-cell imaging is essential for studying the evolution of bacterial communities at single-cell resolution. It allows capturing detailed information about the morphology, gene expression, and spatial characteristics of individual cells at every time instance of the imaging experiment. The image analysis of bacterial "single-cell movies" (videos) generates big data in the form of multidimensional time series of measured bacterial attributes. If properly analyzed, these datasets can help us decipher the bacterial communities' growth dynamics and identify the sources and potential functional role of intra- and inter-subpopulation heterogeneity. Recent research has highlighted the importance of investigating the role of biological "noise" in gene regulation, cell growth, cell division, etc. Single-cell analytics of complex single-cell movie datasets, capturing the interaction of multiple micro-colonies with thousands of cells, can shed light on essential phenomena for human health, such as the competition of pathogens and benign microbiome cells, the emergence of dormant cells (“persisters”), the formation of biofilms under different stress conditions, etc. However, highly accurate and automated bacterial bioimage analysis and single-cell analytics methods remain elusive, even though they are required before we can routinely exploit the plethora of data that single-cell movies generate. Results We present visualization and single-cell analytics using R (ViSCAR), a set of methods and corresponding functions, to visually explore and correlate single-cell attributes generated from the image processing of complex bacterial single-cell movies. They can be used to model and visualize the spatiotemporal evolution of attributes at different levels of the microbial community organization (i.e., cell population, colony, generation, etc.), to discover possible epigenetic information transfer across cell generations, infer mathematical and statistical models describing various stochastic phenomena (e.g., cell growth, cell division), and even identify and auto-correct errors introduced unavoidably during the bioimage analysis of a dense movie with thousands of overcrowded cells in the microscope's field of view. Conclusions ViSCAR empowers researchers to capture and characterize the stochasticity, uncover the mechanisms leading to cellular phenotypes of interest, and decipher a large heterogeneous microbial communities' dynamic behavior. ViSCAR source code is available from GitLab at https://gitlab.com/ManolakosLab/viscar.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 33
    facet.materialart.
    Unknown
    Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in foxtail millet (Setaria italica L.) (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Members of the basic helix-loop-helix (bHLH) transcription factor family perform indispensable functions in various biological processes, such as plant growth, seed maturation, and abiotic stress responses. However, the bHLH family in foxtail millet (Setaria italica), an important food and feed crop, has not been thoroughly studied. Results In this study, 187 bHLH genes of foxtail millet (SibHLHs) were identified and renamed according to the chromosomal distribution of the SibHLH genes. Based on the number of conserved domains and gene structure, the SibHLH genes were divided into 21 subfamilies and two orphan genes via phylogenetic tree analysis. According to the phylogenetic tree, the subfamilies 15 and 18 may have experienced stronger expansion in the process of evolution. Then, the motif compositions, gene structures, chromosomal spread, and gene duplication events were discussed in detail. A total of sixteen tandem repeat events and thirty-eight pairs of segment duplications were identified in bHLH family of foxtail millet. To further investigate the evolutionary relationship in the SibHLH family, we constructed the comparative syntenic maps of foxtail millet associated with representative monocotyledons and dicotyledons species. Finally, the gene expression response characteristics of 15 typical SibHLH genes in different tissues and fruit development stages, and eight different abiotic stresses were analysed. The results showed that there were significant differences in the transcription levels of some SibHLH members in different tissues and fruit development stages, and different abiotic stresses, implying that SibHLH members might have different physiological functions. Conclusions In this study, we identified 187 SibHLH genes in foxtail millet and further analysed the evolution and expression patterns of the encoded proteins. The findings provide a comprehensive understanding of the bHLH family in foxtail millet, which will inform further studies on the functional characteristics of SibHLH genes.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 34
    facet.materialart.
    Unknown
    SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from pan-SNPs, -MNPs and -InDels (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Faced with the ongoing global pandemic of coronavirus disease, the ‘National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis’ (GENPAT) formally established at the ‘Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise’ (IZSAM) in Teramo (Italy) is in charge of the SARS-CoV-2 surveillance at the genomic scale. In a context of SARS-CoV-2 surveillance requiring correct and fast assessment of epidemiological clusters from substantial amount of samples, the present study proposes an analytical workflow for identifying accurately the PANGO lineages of SARS-CoV-2 samples and building of discriminant minimum spanning trees (MST) bypassing the usual time consuming phylogenomic inferences based on multiple sequence alignment (MSA) and substitution model. Results GENPAT constituted two collections of SARS-CoV-2 samples. The first collection consisted of SARS-CoV-2 positive swabs collected by IZSAM from the Abruzzo region (Italy), then sequenced by next generation sequencing (NGS) and analyzed in GENPAT (n = 1592), while the second collection included samples from several Italian provinces and retrieved from the reference Global Initiative on Sharing All Influenza Data (GISAID) (n = 17,201). The main results of the present work showed that (i) GENPAT and GISAID detected the same PANGO lineages, (ii) the PANGO lineages B.1.177 (i.e. historical in Italy) and B.1.1.7 (i.e. ‘UK variant’) are major concerns today in several Italian provinces, and the new MST-based method (iii) clusters most of the PANGO lineages together, (iv) with a higher dicriminatory power than PANGO lineages, (v) and faster that the usual phylogenomic methods based on MSA and substitution model. Conclusions The genome sequencing efforts of Italian provinces, combined with a structured national system of NGS data management, provided support for surveillance SARS-CoV-2 in Italy. We propose to build phylogenomic trees of SARS-CoV-2 variants through an accurate, discriminant and fast MST-based method avoiding the typical time consuming steps related to MSA and substitution model-based phylogenomic inference.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 35
    facet.materialart.
    Unknown
    Cost-effectiveness analysis of Vaborem in Carbapenem-resistant Enterobacterales (CRE) -Klebsiella pneumoniae infections in Italy (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Vaborem is a fixed dose combination of vaborbactam and meropenem with potent activity against target Carbapenem-resistant Enterobacterales (CRE) pathogens, optimally developed for Klebsiella pneumoniae carbapenemase (KPC). The study aims to evaluate the cost-effectiveness of Vaborem versus best available therapy (BAT) for the treatment of patients with CRE-KPC associated infections in the Italian setting. Methods A cost-effectiveness analysis was conducted based on a decision tree model that simulates the clinical pathway followed by physicians treating patients with a confirmed CRE-KPC infection in a 5-year time horizon. The Italian National Health System perspective was adopted with a 3% discount rate. The clinical inputs were mostly sourced from the phase 3, randomised, clinical trial (TANGO II). Unit costs were retrieved from the Italian official drug pricing list and legislation, while patient resource use was validated by a national expert. Model outcomes included life years (LYs) and quality adjusted life years (QALYs) gained, incremental costs, incremental cost-effectiveness ratio (ICER) and incremental cost-utility ratio (ICUR). Deterministic and probabilistic sensitivity analyses were also performed. Results Vaborem is expected to decrease the burden associated with treatment failure and reduce the need for chronic renal replacement therapy while costs related to drug acquisition and long-term care (due to higher survival) may increase. Treatment with Vaborem versus BAT leads to a gain of 0.475 LYs, 0.384 QALYs, and incremental costs of €3549, resulting in an ICER and ICUR of €7473/LY and €9246/QALY, respectively. Sensitivity analyses proved the robustness of the model and also revealed that the probability of Vaborem being cost-effective reaches 90% when willingness to pay is €15,850/QALY. Conclusions In the Italian setting, the introduction of Vaborem will lead to a substantial increase in the quality of life together with a minimal cost impact, therefore Vaborem is expected to be a cost-effective strategy compared to BAT.
    Electronic ISSN: 2191-1991
    Topics: Medicine , Economics
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 36
    facet.materialart.
    Unknown
    Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Optical maps record locations of specific enzyme recognition sites within long genome fragments. This long-distance information enables aligning genome assembly contigs onto optical maps and ordering contigs into scaffolds. The generated scaffolds, however, often contain a large amount of gaps. To fill these gaps, a feasible way is to search genome assembly graph for the best-matching contig paths that connect boundary contigs of gaps. The combination of searching and evaluation procedures might be “searching followed by evaluation”, which is infeasible for long gaps, or “searching by evaluation”, which heavily relies on heuristics and thus usually yields unreliable contig paths. Results We here report an accurate and efficient approach to filling gaps of genome scaffolds with aids of optical maps. Using simulated data from 12 species and real data from 3 species, we demonstrate the successful application of our approach in gap filling with improved accuracy and completeness of genome scaffolds. Conclusion Our approach applies a sequential Bayesian updating technique to measure the similarity between optical maps and candidate contig paths. Using this similarity to guide path searching, our approach achieves higher accuracy than the existing “searching by evaluation” strategy that relies on heuristics. Furthermore, unlike the “searching followed by evaluation” strategy enumerating all possible paths, our approach prunes the unlikely sub-paths and extends the highly-probable ones only, thus significantly increasing searching efficiency.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 37
    facet.materialart.
    Unknown
    Decreased plasma lipid levels in a statin-free Danish primary health care cohort between 2001 and 2018 (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Lipid levels in blood have decreased considerably during the past decades in the general population partly due to use of statins. This study aims to investigate the trends in lipid levels between 2001 and 2018 in a statin-free population from primary health care, overall and by sex and age. Methods In a cohort of 634,119 patients from general practice with no diagnoses or medical treatments that affected lipid levels of total cholesterol (TC; n = 1,574,339) between 2001 and 2018 were identified. Similarly, measurements of low-density lipoprotein cholesterol (LDL-C; n = 1,302,440), high-density lipoprotein cholesterol (HDL-C; n = 1,417,857) and triglycerides (TG; n = 1,329,477) were identified. Results Mean TC decreased from 5.64 mmol/L (95% CI: 5.63–5.65) in 2001 to 5.17 mmol/L (95% CI: 5.16–5.17) in 2018 while LDL-C decreased from 3.67 mmol/L (95% CI: 3.66–3.68) to 3.04 mmol/L (95% CI: 3.03–3.04). Women aged 70–74 years experienced the largest decreases in TC levels corresponding to a decrease of 0.7 mmol/L. The decrease in LDL-C levels was most pronounced in men ≥85 years with a decrease of 0.9 mmol/L. For both genders, TC and LDL-C levels increased with advancing age until around age 50. After menopause the women had higher TC and LDL-C levels than the men. The median (geometric mean) TG level decreased by 0.4 mmol/L from 2001 to 2008, after which it increased slightly by 0.1 mmol/L until 2018. During life the TG levels of the men were markedly higher than the women’s until around age 65–70. HDL-C levels showed no trend during the study period. Conclusions The levels of TC and LDL-C decreased considerably in a statin-free population from primary health care from 2001 to 2018. These decreases were most pronounced in the elderly population and this trend is not decelerating. For TG, levels have started to increase, after an initial decrease.
    Electronic ISSN: 1476-511X
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 38
    facet.materialart.
    Unknown
    Seed priming with proline improved photosystem II efficiency and growth of wheat (Triticum aestivum L.) (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Proline can promote growth of plants by increasing photosynthetic activity under both non-stress and abiotic stress conditions. However, its role in non-stressed conditions is least studied. An experiment was conducted to assess as to whether increase in growth of wheat due to seed priming with proline under non-stress condition was associated with proline-induced changes in photosystem II (PSII) activity. Seeds of four wheat varieties (S-24, Sehar-06, Galaxy-13, and Pasban-90) were primed with different concentrations of proline (0, 5, 15 and 25 mM) for 12 h and allowed to grow under normal conditions. Biomass accumulation and photosynthetic performance, being two most sensitive features/indicators of plant growth, were selected to monitor proline modulated changes. Results Seed priming with proline increased the fresh and dry weights of shoots and roots, and plant height of all four wheat varieties. Maximum increase in growth attributes was observed in all four wheat varieties at 15 mM proline. Maximum growth improvement due to proline was found in var. Galaxy-13, whereas the reverse was true for S-24. Moreover, proline treatment changed the Fo, Fm, Fv/Fo, PIABS, PITot in wheat varieties indicating changes in PSII activity. Proline induced changes in energy fluxes for absorption, trapping, electron transport and heat dissipation per reaction center indicated that var. Galaxy-13 had better ability to process absorbed light energy through photosynthetic machinery. Moreover, lesser PSII efficiency in var. S-24 was due to lower energy flux for electron transport and greater energy flux for heat dissipation. This was further supported by the fact that var. S-24 had disturbance at acceptor side of PSI as reflected by reduction in ΔVIP, probability and energy flux for electron transport at the PSI end electron acceptors. Conclusion Seed priming with proline improved the growth of wheat varieties, which depends on type of variety and concentration of proline applied. Seed priming with proline significantly changed the PSII activity in wheat varieties, however, its translation in growth improvement depends on potential of processing of absorbed light energy by electron acceptors of electron transport chain, particularly those present at PSI end.
    Electronic ISSN: 1471-2229
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 39
    facet.materialart.
    Unknown
    Clinical characteristics of cardiovascular patients with extremely low levels of high-density lipoprotein cholesterol (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Extremely low levels of high-density lipoprotein cholesterol (HDL-C) are related to high cardiovascular mortality. The underlying mechanism is not well known. This research aims to study the clinical characteristics of cardiovascular patients with extremely low levels of HDL-C. Methods All cardiovascular patients in a single Chinese cardiology center that were admitted from January to December 2019 were reviewed. The clinical characteristics of those with HDL-C
    Electronic ISSN: 1476-511X
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 40
    facet.materialart.
    Unknown
    Identification of defense related gene families and their response against powdery and downy mildew infections in Vitis vinifera (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Grapevine (Vitis vinifera) productivity has been severely affected by various bacterial, viral and fungal diseases worldwide. When a plant is infected with the pathogen, various defense mechanisms are subsequently activated in plants at various molecular levels. Thus, for substantiating the disease control in an eco-friendly way, it is essential to understand the molecular mechanisms governing pathogen resistance in grapes. Results In our study, we performed genome-wide identification of various defensive genes expressed during powdery mildew (PM) and downy mildew (DM) infections in grapevine. Consequently, we identified 6, 21, 2, 5, 3 and 48 genes of Enhanced Disease Susceptibility 1 (EDS1), Non-Race-specific Disease Resistance (NDR1), Phytoalexin deficient 4 (PAD4), Nonexpressor of PR Gene (NPR), Required for Mla-specified resistance (RAR) and Pathogenesis Related (PR), respectively, in the grapevine genome. The phylogenetic study revealed that V. vinifera defensive genes are evolutionarily related to Arabidopsis thaliana. Differential expression analysis resulted in identification of 2, 4, 7, 2, 4, 1 and 7 differentially expressed Nucleotide-binding leucine rich repeat receptor (NLR), EDS1, NDR1, PAD4, NPR, RAR1 and PR respectively against PM infections and 28, 2, 5, 4, 1 and 19 differentially expressed NLR, EDS1, NDR1, NPR, RAR1 and PR respectively against DM infections in V. vinifera. The co-expression study showed the occurrence of closely correlated defensive genes that were expressed during PM and DM stress conditions. Conclusion The PM and DM responsive defensive genes found in this study can be characterized in future for impelling studies relaying fungal and oomycete resistance in plants, and the functionally validated genes would then be available for conducting in-planta transgenic gene expression studies for grapes.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 41
    facet.materialart.
    Unknown
    A drug repositioning algorithm based on a deep autoencoder and adaptive fusion (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Drug repositioning has caught the attention of scholars at home and abroad due to its effective reduction of the development cost and time of new drugs. However, existing drug repositioning methods that are based on computational analysis are limited by sparse data and classic fusion methods; thus, we use autoencoders and adaptive fusion methods to calculate drug repositioning. Results In this study, a drug repositioning algorithm based on a deep autoencoder and adaptive fusion was proposed to mitigate the problems of decreased precision and low-efficiency multisource data fusion caused by data sparseness. Specifically, a drug is repositioned by fusing drug-disease associations, drug target proteins, drug chemical structures and drug side effects. First, drug feature data integrated by drug target proteins and chemical structures were processed with dimension reduction via a deep autoencoder to characterize feature representations more densely and abstractly. Then, disease similarity was computed using drug-disease association data, while drug similarity was calculated with drug feature and drug-side effect data. Predictions of drug-disease associations were also calculated using a top-k neighbor method that is commonly used in predictive drug repositioning studies. Finally, a predicted matrix for drug-disease associations was acquired after fusing a wide variety of data via adaptive fusion. Based on experimental results, the proposed algorithm achieves a higher precision and recall rate than the DRCFFS, SLAMS and BADR algorithms with the same dataset. Conclusion The proposed algorithm contributes to investigating the novel uses of drugs, as shown in a case study of Alzheimer's disease. Therefore, the proposed algorithm can provide an auxiliary effect for clinical trials of drug repositioning.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 42
    facet.materialart.
    Unknown
    LongStitch: high-quality genome assembly correction and scaffolding using long reads (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Generating high-quality de novo genome assemblies is foundational to the genomics study of model and non-model organisms. In recent years, long-read sequencing has greatly benefited genome assembly and scaffolding, a process by which assembled sequences are ordered and oriented through the use of long-range information. Long reads are better able to span repetitive genomic regions compared to short reads, and thus have tremendous utility for resolving problematic regions and helping generate more complete draft assemblies. Here, we present LongStitch, a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads. Results LongStitch incorporates multiple tools developed by our group and runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long). Tigmint-long and ARKS-long are misassembly correction and scaffolding utilities, respectively, previously developed for linked reads, that we adapted for long reads. Here, we describe the LongStitch pipeline and introduce our new long-read scaffolder, ntLink, which utilizes lightweight minimizer mappings to join contigs. LongStitch was tested on short and long-read assemblies of Caenorhabditis elegans, Oryza sativa, and three different human individuals using corresponding nanopore long-read data, and improves the contiguity of each assembly from 1.2-fold up to 304.6-fold (as measured by NGA50 length). Furthermore, LongStitch generates more contiguous and correct assemblies compared to state-of-the-art long-read scaffolder LRScaf in most tests, and consistently improves upon human assemblies in under five hours using less than 23 GB of RAM. Conclusions Due to its effectiveness and efficiency in improving draft assemblies using long reads, we expect LongStitch to benefit a wide variety of de novo genome assembly projects. The LongStitch pipeline is freely available at https://github.com/bcgsc/longstitch.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 43
    facet.materialart.
    Unknown
    Mesenchymal stem cells-derived exosomes for drug delivery (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Exosomes are extracellular vesicles secreted by various cells, mainly composed of lipid bilayers without organelles. In recent years, an increasing number of researchers have focused on the use of exosomes for drug delivery. Targeted drug delivery in the body is a promising method for treating many refractory diseases such as tumors and Alzheimer's disease (AD). Finding a suitable drug delivery carrier in the body has become a popular research today. In various drug delivery studies, the exosomes secreted by mesenchymal stem cells (MSC-EXOs) have been broadly researched due to their immune properties, tumor-homing properties, and elastic properties. While MSC-EXOs have apparent advantages, some unresolved problems also exist. This article reviews the studies on MSC-EXOs for drug delivery, summarizes the characteristics of MSC-EXOs, and introduces the primary production and purification methods and drug loading methods to provide solutions for existing problems and suggestions for future studies.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 44
    facet.materialart.
    Unknown
    Effects of dyslipidemia on E antigen seroconversion of patients with chronic hepatitis B treated by nucleoside (acid) analogs (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background The prevalence of dyslipidemia in China is increasing annually. Current studies suggest that dyslipidemia affects the antiviral efficacy of hepatitis C virus (HCV) therapies, while recent studies suggest that serum lipids influence the response rates of chronic hepatitis B (CHB) patients receiving PEGylated interferon-alpha (Peg IFN-α) treatment. However, the role of dyslipidemia in the efficacy of nucleoside (acid) analogues (NAs) in CHB patients remains unclear. Methods From January 2010 to December 2013, data from 179 treatment-naive patients with CHB who were hepatitis B e antigen (HBeAg)-positive and had visited the first affiliated hospital of Wenzhou Medical University were assessed. Of these patients, 68 were assigned to the dyslipidemia group (diagnosed with CHB complicated with dyslipidemia) and 111 to the normolipidemic group. The following 3 treatment strategies were performed for all CHB patients over a 5-year period: lamivudine (LAM) plus adefovir dipivoxil (ADV) combination therapy, telbivudine (LdT) monotherapy, and entecavir (ETV) monotherapy. Serum assessments, blood biochemistry, HBV serological markers, HBV DNA before treatment and HBeAg serological conversion and virological responses at different timepoints after treatment were compared between the two groups. Measurement data were compared by τ tests and enumeration data by χ2 tests. Correlation analysis was performed using binary logistic regression analysis. Results The rates of HBeAg seroconversion in the dyslipidemia group at years 1, 2, 3, and 4 were 10.3, 13.2, 17.6, and 22.1%, respectively, which were not significantly lower than those of the normolipidemic group (11.7, 16.2, 18.0 and 33.3%; χ2 = 0.085, 0.293, 0.004, and 2.601, respectively; Ρ 〉 0.05). However, the rates of HBeAg seroconversion in the dyslipidemia group were significantly lower than those in the normolipidemic group at year 5 (27.9% vs. 43.2%, χ2 = 4.216, Ρ 
    Electronic ISSN: 1476-511X
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 45
    facet.materialart.
    Unknown
    Population variation alters aggression-associated oxytocin and vasopressin expressions in brains of Brandt’s voles in field conditions (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Density-dependent change in aggressive behavior contributes to the population regulation of many small rodents, but the underlying neurological mechanisms have not been examined in field conditions. We hypothesized that crowding stress and aggression-associated oxytocin (OT) and arginine vasopressin (AVP) in specific regions of the brain may be closely related to aggressive behaviors and population changes of small rodents. We analyzed the association of OT and AVP expression, aggressive behavior, and population density of Brandt’s voles in 24 large semi-natural enclosures (0.48 ha each) in Inner Mongolia grassland. We tested the effects of population density on the OT/AVP system and aggressive behavior by experimentally manipulating populations of Brandt’s voles in the grassland enclosures. High density was positively and significantly associated with more aggressive behavior, and increased expression of mRNA and protein of AVP and its receptor, but decreased expression of mRNA and protein of OT and its receptor in specific brain regions of the voles. Our study suggests that changes in OT/AVP expression are likely a result of the increased psychosocial stress that these voles experience during overcrowding, and thus the OT/AVP system can be used as indicators of density-dependent stressors in Brandt’s voles.
    Electronic ISSN: 1742-9994
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 46
    facet.materialart.
    Unknown
    Assessing the suitability of general practice electronic health records for clinical prediction model development: a data quality assessment (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background The use of general practice electronic health records (EHRs) for research purposes is in its infancy in Australia. Given these data were collected for clinical purposes, questions remain around data quality and whether these data are suitable for use in prediction model development. In this study we assess the quality of data recorded in 201,462 patient EHRs from 483 Australian general practices to determine its usefulness in the development of a clinical prediction model for total knee replacement (TKR) surgery in patients with osteoarthritis (OA). Methods Variables to be used in model development were assessed for completeness and plausibility. Accuracy for the outcome and competing risk were assessed through record level linkage with two gold standard national registries, Australian Orthopaedic Association National Joint Replacement Registry (AOANJRR) and National Death Index (NDI). The validity of the EHR data was tested using participant characteristics from the 2014–15 Australian National Health Survey (NHS). Results There were substantial missing data for body mass index and weight gain between early adulthood and middle age. TKR and death were recorded with good accuracy, however, year of TKR, year of death and side of TKR were poorly recorded. Patient characteristics recorded in the EHR were comparable to participant characteristics from the NHS, except for OA medication and metastatic solid tumour. Conclusions In this study, data relating to the outcome, competing risk and two predictors were unfit for prediction model development. This study highlights the need for more accurate and complete recording of patient data within EHRs if these data are to be used to develop clinical prediction models. Data linkage with other gold standard data sets/registries may in the meantime help overcome some of the current data quality challenges in general practice EHRs when developing prediction models.
    Electronic ISSN: 1472-6947
    Topics: Computer Science , Medicine
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 47
    facet.materialart.
    Unknown
    Risk factors for development of nephropathy in patients with a diabetic Charcot foot (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Objective Charcot foot is a rare complication to neuropathy and can cause severe foot deformities and ulcerations, which often require prolonged antibiotical treatment. The objective of this retrospective study was to investigate whether this treatment is associated to impaired renal function. Results In total, 163 patients were included, of whom 105 (64%) had received β-lactam antibiotics for a mean total duration of 13.0 months. There was a significant increase in the urine albumin/creatinine ratio in the group that received antibiotics (p = 0.017), and the use of antibiotics was associated to a subsequent diagnosis of nephropathy (p = 0.01). Patients treated with antibiotics had a 21.9% risk of developing subsequent nephropathy versus 5.2% for patients not treated with antibiotics. We suggest increased awareness on signs of nephropathy in patients with severe Charcot foot.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 48
    facet.materialart.
    Unknown
    Alien balsams, strawberries and their pollinators in a warmer world (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Strawberries are a common crop whose yield success depends on the availability of pollinators. Invasive alien plants, such as Impatiens glandulifera and I. parviflora, are also attractive for bees and hoverflies, respectively, and occur in close proximity to strawberry cultivation areas. The aim of the study was to test whether alien plants may decrease pollination of strawberry cultivation. However, even if the pollinators are abundant, efficiency of their pollination may decrease as a result of revisits of flowers that were already probed. It is addressed by pollinators by scent marking. Moreover, such revisits can be determined by nectar replenishment, which may occur rapidly in nectar-rich flowers. We studied revisits to I. glandulifera by bumblebees and defined the factors that influence the probability of revisits (air temperature; pollinator species; family caste and size; flower area; sun radiation; and time of day). Results We found that the two alien species decreased the number of pollinators visiting strawberries. Apoidea, Bombini and Syrphidae significantly decreased on Fragaria × ananassa when alien Impatiens were present. We also revealed the influence of increasing air temperature on bumblebee foraging, which was particularly significant for female workers. At very high temperatures (〉 37°C), bumblebee males revisited probed flowers less often than female workers. Conclusions Our results demonstrate that in experimental conditions attractive alien species decrease pollination of strawberries, which may negatively affect production of this crop. Although the results have not been verified in real-life strawberry fields yet, we recommend that alien plant species that share the same pollinators and occur in close proximity of strawberries are controlled. Moreover, we found that revisits of probed flowers may weaken feeding efficiency of bumblebees. If revisits are not induced by nectar replenishment, then global warming may pose a serious threat to the survival of colonies, which may have consequences also for the plants that attract them, e.g., for strawberries.
    Electronic ISSN: 1471-2229
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 49
    facet.materialart.
    Unknown
    Gender representation in food and beverage print advertisements found in corner stores around schools in Peru and Guatemala (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Objective The objective of this study is to assess gender representation in food and beverage print advertisements. Results The study follows a quantitative descriptive approach. Using a content analysis technique, we assessed the gender representation in 200 food and beverage print advertisements found in corner stores located in four areas around schools in Lima, Peru, and Guatemala City, Guatemala (100 advertisements per country). A total of 36% of the print advertisements exhibited a male main character for the case of Guatemala, while in Peru 14% of the print advertisements presented a male main character. Furthermore, in Guatemala, 22% of the main characters were male animated characters. Moreover, 27% of the print advertisements in Guatemala and 17%, in Peru were visually male-oriented. Overall, male characters appeared alongside sports references and in varied settings, whereas female characters were usually holding or consuming the product. In conclusion, although the majority of variables used to assess the representation of gender in food and beverage print advertisements were gender-neutral, those showing gender representation were mostly male-oriented. Despite its limited findings, the study provides evidence for the formulation of public policies and educational content aimed to protect children’s and adolescents’ health from the effects of food marketing.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 50
    facet.materialart.
    Unknown
    Mitochondrial dysfunction, UPRmt signaling, and targeted therapy in metastasis tumor (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: In modern research, mitochondria are considered a more crucial energy plant in cells. Mitochondrial dysfunction, including mitochondrial DNA (mtDNA) mutation and denatured protein accumulation, is a common feature of tumors. The dysfunctional mitochondria reprogram molecular metabolism and allow tumor cells to proliferate in the hostile microenvironment. One of the crucial signaling pathways of the mitochondrial dysfunction activation in the tumor cells is the retrograde signaling of mitochondria-nucleus interaction, mitochondrial unfolded protein response (UPRmt), which is initiated by accumulation of denatured protein and excess ROS production. In the process of UPRmt, various components are activitated to enhance the mitochondria-nucleus retrograde signaling to promote carcinoma progression, including hypoxia-inducible factor (HIF), activating transcription factor ATF-4, ATF-5, CHOP, AKT, AMPK. The retrograde signaling molecules of overexpression ATF-5, SIRT3, CREB, SOD1, SOD2, early growth response protein 1 (EGR1), ATF2, CCAAT/enhancer-binding protein-d, and CHOP also involved in the process. Targeted blockage of the UPRmt pathway could obviously inhibit tumor proliferation and metastasis. This review indicates the UPRmt pathways and its crucial role in targeted therapy of metastasis tumors.
    Electronic ISSN: 2045-3701
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 51
    facet.materialart.
    Unknown
    Synergistic stimulation of osteoblast differentiation of rat mesenchymal stem cells by leptin and 25(OH)D3 is mediated by inhibition of chaperone-mediated autophagy (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Vitamin D is important for the mineralization of bones by stimulating osteoblast differentiation of bone marrow mesenchymal stem cells (BMMSCs). BMMSCs are a target of vitamin D action, and the metabolism of 25(OH)D3 to biologically active 1α,25(OH)2D3 in BMMSCs promotes osteoblastogenesis in an autocrine/paracrine manner. Our previous study with human BMMSCs showed that megalin is required for the 25(OH)D3-DBP complex to enter cells and for 25(OH)D3 to stimulate osteoblast differentiation in BMMSCs. Furthermore, we reported that leptin up-regulates megalin in those cells. Leptin is a known inhibitor of PI3K/AKT-dependent chaperone-mediated autophagy (CMA). In this study, we tested the hypothesis that leptin acts synergistically with 25(OH)D3 to promote osteoblastogenesis in rat BMMSCs by a mechanism that entails inhibition of PI3K/AKT-dependent CMA. Methods BMMSCs were isolated from rat bone marrow (4-week-old male SD rats); qRT-PCR and western immunoblots or immunofluorescence were used to evaluate the expression of megalin, ALP, COL1A1, RUNX2, OSX, OSP, and CMA in rBMMSCs. The osteoblast differentiation was evaluated by ALP activity, ALP staining, and calcium deposition. The viability of rBMMSCs was assessed with the CCK-8 kit. Biosynthesis of 1α,25(OH)2D3 was measured by a Rat 1α,25(OH)2D3 ELISA Kit. Results The combination of leptin and 25(OH)D3 treatment significantly enhanced osteoblast differentiation as shown by ALP activity, ALP staining, and calcium deposition, the expression of osteogenic genes ALP, COL1A1, RUNX2, OSX, and OSP by qRT-PCR and western immunoblots in rBMMSCs. Leptin enhanced the expression of megalin and synthesis of 1α,25(OH)2D3 in rBMMSCs. Our data showed that leptin inhibited CMA activity of rBMMSCs by activating PI3K/AKT signal pathway; the ability of leptin to enhance 25(OH)D3 promoted osteoblast differentiation of rBMMSCs was weakened by the PI3K/AKT signal pathway inhibitor. Conclusions Our data reveal the mechanism by which leptin and 25(OH)D3 promote osteoblast differentiation in rBMMSCs. Leptin promoted the expression of megalin by inhibiting CMA, increased the utilization of 25(OH)D3 by rBMMSCs, and enhanced the ability of 25(OH)D3 to induce osteoblast differentiation of rBMMSCs. PI3K/AKT is at least partially involved in the regulation of CMA. These data indicate the importance of megalin in BMMSCs for vitamin D’s role in skeletal health.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 52
    facet.materialart.
    Unknown
    Wharton’s jelly mesenchymal stem cells embedded in PF-127 hydrogel plus sodium ascorbyl phosphate combination promote diabetic wound healing in type 2 diabetic rat (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Diabetic cutaneous ulcers (DCU) are a complication of diabetes with diabetic foot ulcers being the most common, and the wounds are difficult to heal, increasing the risk of bacterial infection. Cell-based therapy utilizing mesenchymal stem cells (MSCs) is currently being investigated as a therapeutic avenue for both chronic diabetic ulcers and severe burns. Wharton’s jelly mesenchymal stem cell (WJMSC) with PF-127 hydrogel and sodium ascorbyl phosphate (SAP) improved skin wound healing in mice. Whether this combination strategy is helpful to diabetic ulcers wound healing remains to be explored. Methods Firstly, the WJMSCs embedded in PF-127 and SAP combination were transplanted onto excisional cutaneous wound bed in type 2 diabetic Sprague Dawley (SD) rats. Two weeks after transplantation, the skin tissue was collected for histological and immunohistochemical analysis. Further, overexpressing-EGFP WJMSCs were performed to investigate cell engraftment in the diabetic cutaneous ulcer. The apoptosis of WJMSCs which encapsulated with combination of PF-127 and SAP was detected by TUNEL fluorescence assay and RT-PCR in vitro. And the mitochondrial damage induced by oxidative stress assessed by MitoTracker and CMH2DCFDA fluorescence assay. Results In diabetic cutaneous wound rat model, PF-127 plus SAP-encapsulated WJMSCs transplantation promoted diabetic wound healing, indicating improving dermis regeneration and collagen deposition. In diabetic wound healing, less pro-inflammatory M1 macrophages, more anti-inflammatory M2 tissue-healing macrophages, and neovascularization were observed in PF-127 + SAP + WJMSCs group compared with other groups. SAP supplementation alleviated the apoptosis ratio of WJMSCs embedded in the PF-127 in vitro and promoted cell survival in vivo. Conclusion PF-127 plus SAP combination facilitates WJMSCs-mediated diabetic wound healing in rat through promoting cell survival, the macrophage transformation, and angiogenesis. Our findings may potentially provide a helpful therapeutic strategy for patients with diabetic cutaneous ulcer.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 53
    facet.materialart.
    Unknown
    Ex vivo expansion and characterization of human corneal endothelium for transplantation: a review (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: The corneal endothelium plays a key role in maintaining corneal transparency. Its dysfunction is currently treated with penetrating or lamellar keratoplasty. Advanced cell therapy methods seek to address the persistent global deficiency of donor corneas by enabling the renewal of the endothelial monolayer with tissue-engineered grafts. This review provides an overview of recently published literature on the preparation of endothelial grafts for transplantation derived from cadaveric corneas that have developed over the last decade (2010–2021). Factors such as the most suitable donor parameters, culture substrates and media, endothelial graft storage conditions, and transplantation methods are discussed. Despite efforts to utilize alternative cellular sources, such as induced pluripotent cells, cadaveric corneas appear to be the best source of cells for graft preparation to date. However, native endothelial cells have a limited natural proliferative capacity, and they often undergo rapid phenotype changes in ex vivo culture. This is the main reason why no culture protocol for a clinical-grade endothelial graft prepared from cadaveric corneas has been standardized so far. Currently, the most established ex vivo culture protocol involves the peel-and-digest method of cell isolation and cell culture by the dual media method, including the repeated alternation of high and low mitogenic conditions. Culture media are enriched by additional substances, such as signaling pathway (Rho-associated protein kinase, TGF-β, etc.) inhibitors, to stimulate proliferation and inhibit unwanted morphological changes, particularly the endothelial-to-mesenchymal transition. To date, this promising approach has led to the development of endothelial grafts for the first in-human clinical trial in Japan. In addition to the lack of a standard culture protocol, endothelial-specific markers are still missing to confirm the endothelial phenotype in a graft ready for clinical use. Because the corneal endothelium appears to comprise phenotypically heterogeneous populations of cells, the genomic and proteomic expression of recently proposed endothelial-specific markers, such as Cadherin-2, CD166, or SLC4A11, must be confirmed by additional studies. The preparation of endothelial grafts is still challenging today, but advances in tissue engineering and surgery over the past decade hold promise for the successful treatment of endothelial dysfunctions in more patients worldwide.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 54
    facet.materialart.
    Unknown
    Activation of adult mammalian retinal stem cells in vivo via antagonism of BMP and sFRP2 (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background The adult mammalian retina does not have the capacity to regenerate cells lost due to damage or disease. Therefore, retinal injuries and blinding diseases result in irreversible vision loss. However, retinal stem cells (RSCs), which participate in retinogenesis during development, persist in a quiescent state in the ciliary epithelium (CE) of the adult mammalian eye. Moreover, RSCs retain the ability to generate all retinal cell types when cultured in vitro, including photoreceptors. Therefore, it may be possible to activate endogenous RSCs to induce retinal neurogenesis in vivo and restore vision in the adult mammalian eye. Methods To investigate if endogenous RSCs can be activated, we performed combinatorial intravitreal injections of antagonists to BMP and sFRP2 proteins (two proposed mediators of RSC quiescence in vivo), with or without growth factors FGF and Insulin. We also investigated the effects of chemically-induced N-methyl-N-Nitrosourea (MNU) retinal degeneration on RSC activation, both alone and in combination withthe injected factors. Further, we employed inducible Msx1-CreERT2 genetic lineage labeling of the CE followed by stimulation paradigms to determine if activated endogenous RSCs could migrate into the retina and differentiate into retinal neurons. Results We found that in vivo antagonism of BMP and sFRP2 proteins induced CE cells in the RSC niche to proliferate and expanded the RSC population. BMP and sFRP2 antagonism also enhanced CE cell proliferation in response to exogenous growth factor stimulation and MNU-induced retinal degeneration. Furthermore, Msx1-CreERT2 genetic lineage tracing revealed that CE cells migrated into the retina following stimulation and/or injury, where they expressed markers of mature photoreceptors and retinal ganglion cells. Conclusions Together, these results indicate that endogenous adult mammalian RSCs may have latent regenerative potential that can be activated by modulating the RSC niche and hold promise as a means for endogenous retinal cell therapy to repair the retina and improve vision.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 55
    facet.materialart.
    Unknown
    Comparative analysis of transcriptomic data shows the effects of multiple evolutionary selection processes on codon usage in Marsupenaeus japonicus and Marsupenaeus pulchricaudatus (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Kuruma shrimp, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. Codon usage analysis would contribute to our understanding of the genetic and evolutionary characteristics of the two Marsupenaeus species. In this study, we analyzed codon usage and related indices using coding sequences (CDSs) from RNA-seq data. Results Using CodonW 1.4.2 software, we performed the codon bias analysis of transcriptomes obtained from hepatopancreas tissues, which indicated weak codon bias. Almost all parameters had similar correlations for both species. The gene expression level (FPKM) was negatively correlated with A/T3s. We determined 12 and 14 optimal codons for M. japonicus and M. pulchricaudatus, respectively, and all optimal codons have a C/G-ending. The two Marsupenaeus species had different usage frequencies of codon pairs, which contributed to further analysis of transcriptional differences between them. Orthologous genes that underwent positive selection (ω 〉 1) had a higher correlation coefficient than that of experienced purifying selection (ω 
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 56
    facet.materialart.
    Unknown
    A practical biphasic contrast media injection protocol strongly enhances the aorta and pulmonary artery simultaneously using a single CT angiography scan (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Enhancement profiles of the pulmonary artery (PA) and aorta differ when using computed tomography (CT) angiography. Our aim was to determine the optimal CT protocol for a one-time CT scan that assesses both blood vessels. Methods We prospectively enrolled 101 cases of CT angiography in patients with suspected pulmonary embolism or aortic dissection from our center between 2018 and 2020. We also retrospectively collected the data of 40 patients who underwent traditional two-time CT scans between 2015 and 2018. Patients were divided into four groups: test bolus (TB) I, TB II, bolus-tracking (BT) I, and BT II. The enhancement of the PA and aorta, and the radiation doses used in the four groups were collected. Those who underwent two-time scans were classified into the traditional PA or aorta scan groups. Data were compared between the BT and traditional groups. Results The aortic enhancement was highest in BT II (294.78 ± 64.48 HU) followed BT I (285.18 ± 64.99 HU), TB II (186.58 ± 57.53 HU), and TB I (173.62 ± 69.70 HU). The radiation dose used was lowest in BT I (11.85 ± 5.55 mSv) and BT II (9.07 ± 3.44 mSv) compared with that used in the traditional groups (20.07 ± 7.78 mSv) and accounted for half of the traditional group (45.17–59.02%). The aortic enhancement was also highest in BT II (294.78 ± 64.48 HU) followed by BT I (285.18 ± 64.99 HU) when compared with that in the traditional aorta scan group (234.95 ± 94.18 HU). Conclusion Our CT protocol with a BT technique allows for a lower radiation dose and better image quality of the PA and aorta than those obtained using traditional CT scans. Trial registration: NCT04832633, retrospectively registered in April 2021 to the clinical trial registry.
    Electronic ISSN: 1471-2342
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 57
    facet.materialart.
    Unknown
    Distinct patterns of whole blood transcriptional responses are induced in mice following immunisation with adenoviral and poxviral vector vaccines encoding the same antigen (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Viral vectors, including adenovirus (Ad) and modified vaccinia Ankara (MVA), have gained increasing attention as vaccine platforms in recent years due to their capacity to express antigens from a wide array of pathogens, their rapid induction of humoral and cellular protective immune responses, and their relatively low production costs. In particular, the chimpanzee Ad vector, ChAdOx1, has taken centre stage as a leading COVID-19 vaccine candidate. However, despite mounting data, both clinical and pre-clinical, demonstrating effective induction of adaptive immune responses, the innate immune signals that precede the protective responses that make these vectors attractive vaccine platforms remain poorly understood. Results In this study, a mouse immunisation model was used to evaluate whole blood gene expression changes 24 h after either a single dose or heterologous prime-boost regimen of an Ad and/or MVA vaccine. We demonstrate through comparative analysis of Ad vectors encoding different antigens that a transgene product-specific gene signature can be discerned from the vector-induced transcriptional response. Expression of genes involved in TLR2 stimulation and γδ T cell and natural killer cell activation were induced after a single dose of Ad, while MVA led to greater expression of type I interferon genes. The order of prime-boost combinations was found to influence the magnitude of the gene expression changes, with MVA/Ad eliciting greater transcriptional perturbation than Ad/MVA. Contrasting the two regimens revealed significant enrichment of epigenetic regulation pathways and augmented expression of MHC class I and II molecules associated with MVA/Ad. Conclusion These data demonstrate that the order in which vaccines from heterologous prime-boost regimens are administered leads to distinct transcriptional responses and may shape the immune response induced by such combinations. The characterisation of early vaccine-induce responses strengthens our understanding of viral vector vaccine mechanisms of action ahead of their characterisation in human clinical trials and are a valuable resource to inform the pre-clinical design of appropriate vaccine constructs for emerging infectious diseases.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 58
    facet.materialart.
    Unknown
    Maternal methionine supplementation during gestation alters alternative splicing and DNA methylation in bovine skeletal muscle (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background The evaluation of alternative splicing, including differential isoform expression and differential exon usage, can provide some insights on the transcriptional changes that occur in response to environmental perturbations. Maternal nutrition is considered a major intrauterine regulator of fetal developmental programming. The objective of this study was to assess potential changes in splicing events in the longissimus dorsi muscle of beef calves gestated under control or methionine-rich diets. RNA sequencing and whole-genome bisulfite sequencing were used to evaluate muscle transcriptome and methylome, respectively. Results Alternative splicing patterns were significantly altered by maternal methionine supplementation. Most of the altered genes were directly implicated in muscle development, muscle physiology, ATP activities, RNA splicing and DNA methylation, among other functions. Interestingly, there was a significant association between DNA methylation and differential exon usage. Indeed, among the set of genes that showed differential exon usage, significant differences in methylation level were detected between significant and non-significant exons, and between contiguous and non-contiguous introns to significant exons. Conclusions Overall, our findings provide evidence that a prenatal diet rich in methyl donors can significantly alter the offspring transcriptome, including changes in isoform expression and exon usage, and some of these changes are mediated by changes in DNA methylation.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 59
    facet.materialart.
    Unknown
    SARS-CoV-2 evolution in animals suggests mechanisms for rapid variant selection (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-10-29
    Description: SARS-CoV-2 spillback from humans into domestic and wild animals has been well documented, and an accumulating number of studies illustrate that human-to-animal transmission is widespread in cats, mink, deer, and other species. Experimental inoculations of cats, mink, and ferrets have perpetuated transmission cycles. We sequenced full genomes of Vero cell–expanded SARS-CoV-2 inoculum and viruses recovered from cats (n = 6), dogs (n = 3), hamsters (n = 3), and a ferret (n = 1) following experimental exposure. Five nonsynonymous changes relative to the USA-WA1/2020 prototype strain were near fixation in the stock used for inoculation but had reverted to wild-type sequences at these sites in dogs, cats, and hamsters within 1- to 3-d postexposure. A total of 14 emergent variants (six in nonstructural genes, six in spike, and one each in orf8 and nucleocapsid) were detected in viruses recovered from animals. This included substitutions in spike residues H69, N501, and D614, which also vary in human lineages of concern. Even though a live virus was not cultured from dogs, substitutions in replicase genes were detected in amplified sequences. The rapid selection of SARS-CoV-2 variants in vitro and in vivo reveals residues with functional significance during host switching. These observations also illustrate the potential for spillback from animal hosts to accelerate the evolution of new viral lineages, findings of particular concern for dogs and cats living in households with COVID-19 patients. More generally, this glimpse into viral host switching reveals the unrealized rapidity and plasticity of viral evolution in experimental animal model systems.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 60
    facet.materialart.
    Unknown
    Fevers and the social costs of acute infection in wild vervet monkeys (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-10-29
    Description: Fevers are considered an adaptive response by the host to infection. For gregarious animals, however, fever and the associated sickness behaviors may signal a temporary loss of capacity, offering other group members competitive opportunities. We implanted wild vervet monkeys (Chlorocebus pygerythrus) with miniature data loggers to obtain continuous measurements of core body temperature. We detected 128 fevers in 43 monkeys, totaling 776 fever-days over a 6-year period. Fevers were characterized by a persistent elevation in mean and minimum 24-h body temperature of at least 0.5 °C. Corresponding behavioral data indicated that febrile monkeys spent more time resting and less time feeding, consistent with the known sickness behaviors of lethargy and anorexia, respectively. We found no evidence that fevers influenced the time individuals spent socializing with conspecifics, suggesting social transmission of infection within a group is likely. Notably, febrile monkeys were targeted with twice as much aggression from their conspecifics and were six times more likely to become injured compared to afebrile monkeys. Our results suggest that sickness behavior, together with its agonistic consequences, can carry meaningful costs for highly gregarious mammals. The degree to which social factors modulate the welfare of infected animals is an important aspect to consider when attempting to understand the ecological implications of disease.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 61
    facet.materialart.
    Unknown
    Abatacept is useful in auto-immune cytopenia with immunopathologic manifestations caused by CTLA-4 defects (2021)
    American Society of Hematology
    Details
    Publication Date: 2021-10-29
    Print ISSN: 0006-4971
    Electronic ISSN: 1528-0020
    Topics: Biology , Medicine
    Published by American Society of Hematology
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 62
    facet.materialart.
    Unknown
    GFICLEE: ultrafast tree-based phylogenetic profile method inferring gene function at the genomic-wide level (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-29
    Description: Background Phylogenetic profiling is widely used to predict novel members of large protein complexes and biological pathways. Although methods combined with phylogenetic trees have significantly improved prediction accuracy, computational efficiency is still an issue that limits its genome-wise application. Results Here we introduce a new tree-based phylogenetic profiling algorithm named GFICLEE, which infers common single and continuous loss (SCL) events in the evolutionary patterns. We validated our algorithm with human pathways from three databases and compared the computational efficiency with current tree-based with 10 different scales genome dataset. Our algorithm has a better predictive performance with high computational efficiency. Conclusions The GFICLEE is a new method to infers genome-wide gene function. The accuracy and computational efficiency of GFICLEE make it possible to explore gene functions at the genome-wide level on a personal computer.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 63
    facet.materialart.
    Unknown
    Accurate model of liquid–liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-10-29
    Description: Many intrinsically disordered proteins (IDPs) may undergo liquid–liquid phase separation (LLPS) and participate in the formation of membraneless organelles in the cell, thereby contributing to the regulation and compartmentalization of intracellular biochemical reactions. The phase behavior of IDPs is sequence dependent, and its investigation through molecular simulations requires protein models that combine computational efficiency with an accurate description of intramolecular and intermolecular interactions. We developed a general coarse-grained model of IDPs, with residue-level detail, based on an extensive set of experimental data on single-chain properties. Ensemble-averaged experimental observables are predicted from molecular simulations, and a data-driven parameter-learning procedure is used to identify the residue-specific model parameters that minimize the discrepancy between predictions and experiments. The model accurately reproduces the experimentally observed conformational propensities of a set of IDPs. Through two-body as well as large-scale molecular simulations, we show that the optimization of the intramolecular interactions results in improved predictions of protein self-association and LLPS.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 64
    facet.materialart.
    Unknown
    In the Asia-Pacific region, the COI DNA test revealed the divergence of the bivalve mollusc Mactra chinensis into three species; can these species be distinguished using shell coloration and sperm structure? (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: According to COI DNA barcoding testing, the marine bivalve mollusc Mactra chinensis, which is native to the Asia-Pacific region, diverged into three species. These species were preliminary characterized as M. chinensis COI clade I, M. chinensis COI clade II and M. chinensis COI clade III. To find out whether it is possible to morphologically distinguish samples representing genetic clades, we examined the color of the shells and the structure of the spermatozoa. It was found that the number of detected coloration types exceeds the number of detected species. In addition, it was shown that individuals belonging to the same genetic clade can have shells of different colors. Consequently, it is impossible to choose one type of shell coloration as a species-specific trait. For sperm, the sperm morphological patterns found in each of the three species are consistent with the M. chinensis sperm model described in previous reports. However, the single sperm variant is also not applicable to discriminate between species derived from M. chinensis, since heterogeneous variants of spermatozoa differing in the length of the acrosomal rod were found. We hypothesized that genetic divergence of species could cause a shift towards predominance of one of the sperm variants, and that species-specific sperm morphs could be quantitatively dominant in molluscs belonging to different clades. However, the dominant sperm morphs were the same in COI clade I and COI clade III. Thus, dominant sperm morphs are useless as species-specific traits. However, shell color and sperm parameters are specific to different geographic regions, and it seems that unique environmental factors can determine shell color and sperm morphology. As a result, both shells and spermatozoa can be used to distinguish the geographical forms of M. chinensis, regardless of the belonging of the forms to a particular genetic clade. Here we propose the introduction of geographic identifiers, in which the shell color and parameters of sperm sets are used as morphological criteria to determine the geographical origin of mollusc specimens belonging to the M. chinensis species complex.
    Print ISSN: 1438-387X
    Electronic ISSN: 1438-3888
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 65
    facet.materialart.
    Unknown
    Route of Zika virus infection in Aedes aegypti by transmission electron microscopy (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Zika fever has been a global health security threat, especially in the tropical and subtropical regions where most of the cases occur. The disease is caused by Zika virus (ZIKV), which belongs to the family Flaviviridae, genus Flavivirus. The virus is transmitted by Aedes mosquitoes, mostly by Aedes aegypti, during its blood meal. In this study we present a descriptive analysis, by transmission electron microscopy (TEM), of ZIKV infection in A. aegypti elected tissues at the 3rd day of infection. ZIKV vertical transmission experiments by oral infection were conducted to explore an offspring of natural infection. Results Gut and ovary tissues harbored a higher number of viral particles. The ZIKV genome was also detected, by RT-qPCR technique, in the organism of orally infected female mosquitoes and in their eggs laid. Conclusions The data obtained suggest that the ovary is an organ susceptible to be infected with ZIKV and that virus can be transmitted from mother to a fraction of the progeny.
    Electronic ISSN: 1471-2180
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 66
    facet.materialart.
    Unknown
    Characterization of the gut microbiome in a porcine model of thoracic spinal cord injury (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background The gut microbiome is a diverse network of bacteria which inhabit our digestive tract and is crucial for efficient cellular metabolism, nutrient absorption, and immune system development. Spinal cord injury (SCI) disrupts autonomic function below the level of injury and can alter the composition of the gut microbiome. Studies in rodent models have shown that SCI-induced bacterial imbalances in the gut can exacerbate the spinal cord damage and impair recovery. In this study we, for the first time, characterized the composition of the gut microbiome in a Yucatan minipig SCI model. We compared the relative abundance of the most dominant bacterial phyla in control samples to those collected from animals who underwent a contusion-compression SCI at the 2nd or 10th Thoracic level. Results We identify specific bacterial fluctuations that are unique to SCI animals, which were not found in uninjured animals given the same dietary regimen or antibiotic administration. Further, we identified a specific time-frame, “SCI-acute stage”, during which many of these bacterial fluctuations occur before returning to “baseline” levels. Conclusion This work presents a dynamic view of the microbiome changes that accompany SCI, establishes a resource for future studies and to understand the changes that occur to gut microbiota after spinal cord injury and may point to a potential therapeutic target for future treatment.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 67
    facet.materialart.
    Unknown
    Fusobacterium nucleatum predicts a high risk of metastasis for esophageal squamous cell carcinoma (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Esophageal squamous cell carcinoma (ESCC) is the major type of esophageal cancer in China. The role of the bacteria present in ESCC tissue in neoplastic progression has not been fully elucidated. This study aimed to uncover different bacterial communities in ESCC tissues and examine the correlation between the abundance of the esophageal flora and clinicopathologic characteristics of ESCC. Results Microorganisms in tumors and normal tissues showed obvious clustering characteristics. The abundance of Fusobacterium (P = 0.0052) was increased in tumor tissues. The high level of Fusobacterium nucleatum was significantly associated with pT stage (P = 0.039) and clinical stage (P = 0.0039). The WES data showed that COL22A1, TRBV10–1, CSMD3, SCN7A and PSG11 were present in only the F. nucleatum-positive ESCC samples. GO and protein domain enrichment results suggested that epidermal growth factor might be involved in the regulation of cell apoptosis in F. nucleatum-positive ESCC. Both a higher mutational burden and F. nucleatum-positive was observed in tumors with metastasis than in tumors without metastasis. Conclusion F. nucleatum is closely related to the pT stage and clinical stage of ESCC. The abundance of F. nucleatum and tumor mutation burden may be used in combination as a potential method to predict metastasis in ESCC.
    Electronic ISSN: 1471-2180
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 68
    facet.materialart.
    Unknown
    Pulmonary lesions: correlative study of dynamic triple-phase enhanced CT perfusion imaging with tumor angiogenesis and vascular endothelial growth factor expression (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background To investigate value of the quantitative perfusion parameters of dynamic triple-phase enhanced CT in differential diagnosis of pulmonary lesions, and explore the correlation between perfusion parameters of lung cancer with microvessel density (MVD) and vascular endothelial growth factor (VEGF). Methods 73 consecutive patients with lung lesions who successfully underwent pre-operative CT perfusion examination with dynamic triple-phase enhanced CT and received a final diagnosis by postoperative pathology or a clinical follow-up. The cases were divided into malignant and benign groups according to the pathological results. CT perfusion parameters, such as Median, Mean, Standard deviation (Std), Q10, Q25, Q50, Q75, Q90 of pulmonary artery perfusion (PAP), bronchial artery perfusion (BAP), perfusion index (PI) and arterial enhancement fraction (AEF) were obtained by performing computed tomography perfusion imaging (CTPI). Computed tomography perfusion (CTP) parameters were compared between malignant and benign lesions. The receiver operating characteristic (ROC) curve was used to assess the diagnostic efficiency of CTP parameters in diagnosing malignant lesions. The correlations between CTP parameters with MVD and VEGF were analysed in 36 lung cancer patients who had extra sections be used for immunohistochemistry staining of CD34 and VEGF. Results BAP (Mean, Std, Q90) and PI Std of benign lesions were higher than malignant lesions (p 
    Electronic ISSN: 1471-2342
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 69
    facet.materialart.
    Unknown
    Adult stem cell transplantation combined with conventional therapy for the treatment of end-stage liver disease: a systematic review and meta-analysis (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: End-stage liver disease (ESLD) is characterized by the deterioration of liver function and a subsequent high mortality rate. Studies have investigated the use of adult stem cells to treat ESLD. Here, a systematic review and meta-analysis was conducted to determine the efficacy of a combination therapy with adult stem cell transplantation and traditional medicine for treating ESLD. Four databases—including PubMed, Web of Science, Embase, and Cochrane Library—were investigated for studies published before January 31, 2021. The main outcome indicators were liver function index, model for end-stage liver disease (MELD) scores, and Child‒Turcotte‒Pugh (CTP) scores. Altogether, 1604 articles were retrieved, of which eight met the eligibility criteria; these studies included data for 579 patients with ESLD. Combination of adult stem cell transplantation with conventional medicine significantly improved its efficacy with respect to liver function index, CTP and MELD scores, but this effect gradually decreased over time. Moreover, a single injection of stem cells was more effective than two injections with respect to MELD and CTP scores and total bilirubin (TBIL) and albumin (ALB) levels, with no significant difference in aspartate aminotransferase (AST) and alanine aminotransferase (ALT) levels. With respect to the TBIL levels, patients receiving mononuclear cells (MNCs) experienced a significantly greater therapeutic effect—starting from twenty-four weeks after the treatment—whereas with respect to ALB levels, CD34+ autologous peripheral blood stem cells (CD34+ APBSCs) and MNCs had similar therapeutic effects. Severe complications associated with adult stem cell treatment were not observed. Although the benefits of combination therapy with respect to improving liver function were slightly better than those of the traditional treatment alone, they gradually decreased over time.Systematic review registration: PROSPERO registration number: CRD42021238576.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 70
    facet.materialart.
    Unknown
    Treatment of knee osteoarthritis with intra-articular injection of allogeneic adipose-derived stem cells (ADSCs) ELIXCYTE®: a phase I/II, randomized, active-control, single-blind, multiple-center clinical trial (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Objective To evaluate the safety and efficacy of intra-articular (IA) injection of allogeneic adipose-derived stem cells (ADSCs) ELIXCYTE® for knee osteoarthritis. Methods This was a patient-blind, randomized, active-control trial consisted of 4 arms including hyaluronic acid (HA) control and 3 ELIXCYTE® doses. A total of 64 subjects were screened, and 57 subjects were randomized. The primary endpoints included the changes from baseline to post-treatment visit of Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) pain score at Week 24 and the incidence of adverse events (AEs) and serious adverse events (SAEs). Results No ELIXCYTE®-related serious adverse events were reported during 96 weeks of follow-up and no suspected unexpected serious adverse reaction (SUSAR) or death was reported. The changes of the primary endpoint, WOMAC pain score at Week 24, showed significant differences in all ELIXCYTE® groups, as well as in HA groups between post-treatment visit and baseline. The ELIXCYTE® groups revealed significant decreases at Week 4 compared to HA group in WOMAC total scores, stiffness scores, functional limitation scores suggested the potential of ELIXCYTE® in earlier onset compared to those from HA. The significant differences of visual analog scale (VAS) pain score and Knee Society Clinical Rating System (KSCRS) functional activities score at Week 48 after ELIXCYTE® administration suggested the potential of ELIXCYTE® in the longer duration of the effectiveness compared to HA group. Conclusions ELIXCYTE® for knee osteoarthritis treatment was effective, safe, and well-tolerated. The efficacy results were showed that ELIXCYTE® conferred the earlier onset of reductions in pain scores and improvements in functional scores than HA group. Trial registration: ClinicalTrials.gov Identifier: NCT02784964. Registered 16 May, 2016—Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT02784964
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 71
    facet.materialart.
    Unknown
    Analysis of vascularization in thyroid gland nodes with superb microvascular imaging (SMI) and CD34 expression histology: a pilot study (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background The Doppler sonography technique known as "superb microvascular imaging" (SMI) is advancing sonographic micro vascularization imaging in various disciplines. In this study, we aimed to determine whether SMI could reliably reproduce the blood flow in thyroid nodes and whether malignancy could be diagnosed, based on vascularization properties. Immunhistochemical staining by CD34 and SMI where used to determine the vascularization of nodes in terms of quantified vascularization parameters gained by computational evaluation. Methods We used image analysis programs to investigate whether the quantitative value for vascularization strength in the thyroid node, measured with SMI, was correlated with the actual degree of vascularization, determined microscopically. We included 16 patients that underwent thyroid resections. We prepared thyroid gland tissue slices for immunohistochemistry and labelled endothelial cells with CD34 to visualize blood vessels microscopically. We used image analysis programs, ImageJ, to quantify SMI Doppler sonographic measurements and CellProfiler to quantify CD34 expression in histological sections. We evaluated the numeric values for diagnostic value in node differentiation. Furthermore, we compared these values to check for correlations. Results Among the 16 nodes studied, three harboured malignant tumours (18.75%): two papillary and one follicular carcinoma. Among the 13 benign lesions (81.25%), four harboured follicular adenomas. Malignant and benign nodes were not significantly different in sonographic (0.88 ± 0.89 vs. 1.13 ± 0.19; p = 0.2790) or immunohistochemical measurements of vascularization strength (0.05 ± 0.05 vs. 0.08 ± 0.06; p = 0.2260). Conclusion We found a positive, significant correlation (r = 0.55588; p = 0.0254) between SMI (quantitative values for vascularization strength) and immunohistochemistry (CD34 staining) evaluations of thyroid nodes.
    Electronic ISSN: 1471-2342
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 72
    facet.materialart.
    Unknown
    Genome-wide identification of the tobacco GDSL family and apical meristem-specific expression conferred by the GDSL promoter (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background GDSL esterases/lipases are a large protein subfamily defined by the distinct GDSL motif, and play important roles in plant development and stress responses. However, few studies have reported on the role of GDSLs in the growth and development of axillary buds. This work aims to identify the GDSL family members in tobacco and explore whether the NtGDSL gene contributes to development of the axillary bud in tobacco. Results One hundred fifty-nine GDSL esterase/lipase genes from cultivated tobacco (Nicotiana tabacum) were identified, and the dynamic changes in the expression levels of 93 of these genes in response to topping, as assessed using transcriptome data of topping-induced axillary shoots, were analysed. In total, 13 GDSL esterase/lipase genes responded with changes in expression level. To identify genes and promoters that drive the tissue-specific expression in tobacco apical and axillary buds, the expression patterns of these 13 genes were verified using qRT-PCR. GUS activity and a lethal gene expression pattern driven by the NtGDSL127 promoter in transgenic tobacco demonstrated that NtGDSL127 is specifically expressed in apical buds, axillary buds, and flowers. Three separate deletions in the NtGDSL127 promoter demonstrated that a minimum upstream segment of 235 bp from the translation start site can drive the tissue-specific expression in the apical meristem. Additionally, NtGDSL127 responded to phytohormones, providing strategies for improving tobacco breeding and growth. Conclusion We propose that in tobacco, the NtGDSL127 promoter directs expression specifically in the apical meristem and that expression is closely correlated with axillary bud development.
    Electronic ISSN: 1471-2229
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 73
    facet.materialart.
    Unknown
    Whole transcriptome sequencing identifies key circRNAs, lncRNAs, and miRNAs regulating neurogenesis in developing mouse retina (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background The molecular complexity of neural retina development remains poorly studied. Knowledge of retinal neurogenesis regulation sheds light on retinal degeneration therapy exploration. Therefore, we integrated the time-series circRNA, lncRNA, miRNA, and mRNA expression profiles of the developing retina through whole-transcriptome sequencing. The key functional ncRNAs and the ceRNA network regulating retinal neurogenesis were identified. Results Transcriptomic analysis identified circRNA as the most variable ncRNA subtype. We screened a series of neurogenesis-related circRNAs, lncRNAs, and miRNAs using different strategies based on their diversified molecular functions. The expression of circCDYL, circATXN1, circDYM, circPRGRIP, lncRNA Meg3, and lncRNA Vax2os was validated by quantitative real-time PCR. These circRNAs and lncRNAs participate in neurotransmitter transport and multicellular organism growth through the intricate circRNA/lncRNA-miRNA-mRNA network. Conclusion Whole-transcriptome sequencing and bioinformatics analysis systematically screened key ncRNAs in retinal neurogenesis. The validated ncRNAs and their circRNA/lncRNA-miRNA-mRNA network involve neurotransmitter transport and multicellular organism growth during retinal development.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 74
    facet.materialart.
    Unknown
    Stem cell-based therapy for ameliorating intrauterine adhesion and endometrium injury (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Intrauterine adhesion refers to endometrial repair disorders which are usually caused by uterine injury and may lead to a series of complications such as abnormal menstrual bleeding, recurrent abortion and secondary infertility. At present, therapeutic approaches to intrauterine adhesion are limited due to the lack of effective methods to promote regeneration following severe endometrial injury. Therefore, to develop new methods to prevent endometrial injury and intrauterine adhesion has become an urgent need. For severely damaged endometrium, the loss of stem cells in the endometrium may affect its regeneration. This article aimed to discuss the characteristics of various stem cells and their applications for uterine tissue regeneration.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 75
    facet.materialart.
    Unknown
    Single cell Raman spectroscopy to identify different stages of proliferating human hepatocytes for cell therapy (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Cell therapy provides hope for treatment of advanced liver failure. Proliferating human hepatocytes (ProliHHs) were derived from primary human hepatocytes (PHH) and as potential alternative for cell therapy in liver diseases. Due to the continuous decline of mature hepatic genes and increase of progenitor like genes during ProliHHs expanding, it is challenge to monitor the critical changes of the whole process. Raman microspectroscopy is a noninvasive, label free analytical technique with high sensitivity capacity. In this study, we evaluated the potential and feasibility to identify ProliHHs from PHH with Raman spectroscopy. Methods Raman spectra were collected at least 600 single spectrum for PHH and ProliHHs at different stages (Passage 1 to Passage 4). Linear discriminant analysis and a two-layer machine learning model were used to analyze the Raman spectroscopy data. Significant differences in Raman bands were validated by the associated conventional kits. Results Linear discriminant analysis successfully classified ProliHHs at different stages and PHH. A two-layer machine learning model was established and the overall accuracy was at 84.6%. Significant differences in Raman bands have been found within different ProliHHs cell groups, especially changes at 1003 cm−1, 1206 cm−1 and 1440 cm−1. These changes were linked with reactive oxygen species, hydroxyproline and triglyceride levels in ProliHHs, and the hypothesis were consistent with the corresponding assay results. Conclusions In brief, Raman spectroscopy was successfully employed to identify different stages of ProliHHs during dedifferentiation process. The approach can simultaneously trace multiple changes of cellular components from somatic cells to progenitor cells.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 76
    facet.materialart.
    Unknown
    Phenotypic variation of floral organs in flowering crabapples and its taxonomic significance (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background In angiosperms, phenotypic variation of floral organs is often considered as the traditional basis for the evolutionary relationship of different taxonomic groups above the species level. However, little is known about that at or below the species level. Here, we experimentally tested the phenotypic variation of Malus floral organs using combined methods of intraspecific uniformity test, interspecific distinctness analysis, principal component analysis, Pearson correlation analysis, and Q-type cluster analysis. The ancestor-inclined distribution characteristic analysis of Malus species and cultivars floral attributes was also carried out, so as to explore its taxonomic significance. Results 15/44 phenotypic traits (e.g., flower shape, flower type, flower diameter, ...) were highly consistent, distinguishable, and independent and could be used as the basis for Malus germplasm taxonomy. The studied 142 taxa were divided into two groups (A, B) and five sub-groups (A1, A2, B1, B2, B3), with significantly variable floral phenotypic attributes between groups and within sub-groups. Malus natural species were relatively clustered in the same section (series) while homologous cultivars showed evidence of ancestor-inclined distribution characteristics. However, no significant correlation between the evolutionary order of sections (Sect. Docyniopsis → Sect. Chloromeles → Sect. Sorbomalus → Sect. Eumalus) and group/sub-groups (B3 → B2 → B1 → A). Conclusions Phenotypic variation of floral organs could better explore the genetic relationship between Malus taxa. The findings improved our cognition of floral phenotypic variation taxonomic significance under the species level.
    Electronic ISSN: 1471-2229
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 77
    facet.materialart.
    Unknown
    Live agent preference and social action monitoring in the macaque mid-superior temporal sulcus region (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-10-29
    Description: Mentalizing, the ability to infer the mental states of others, is a cornerstone of adaptive social intelligence. While functional brain mapping of human mentalizing has progressed considerably, its evolutionary signature in nonhuman primates remains debated. The discovery that the middle part of the macaque superior temporal sulcus (mid-STS) region has a connectional fingerprint most similar to the human temporoparietal junction (TPJ)—a crucial node in the mentalizing network—raises the possibility that these cortical areas may also share basic functional properties associated with mentalizing. Here, we show that this is the case in aspects of a preference for live social interactions and in a theoretical framework of predictive coding. Macaque monkeys were trained to perform a turn-taking choice task with another real monkey partner sitting directly face-to-face or a filmed partner appearing in prerecorded videos. We found that about three-fourths of task-related mid-STS neurons exhibited agent-dependent activity, most responding selectively or preferentially to the partner’s action. At the population level, activities of these partner-type neurons were significantly greater under live-partner compared to video-recorded–partner task conditions. Furthermore, a subset of the partner-type neurons responded proactively when predictions about the partner’s action were violated. This prediction error coding was specific to the action domain; almost none of the neurons signaled error in the prediction of reward. The present findings highlight unique roles of the macaque mid-STS at the single-neuron level and further delineate its functional parallels with the human TPJ in social cognitive processes associated with mentalizing.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 78
    facet.materialart.
    Unknown
    Genome evolution of the psammophyte Pugionium for desert adaptation and further speciation (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-10-14
    Description: Deserts exert strong selection pressures on plants, but the underlying genomic drivers of ecological adaptation and subsequent speciation remain largely unknown. Here, we generated de novo genome assemblies and conducted population genomic analyses of the psammophytic genus Pugionium (Brassicaceae). Our results indicated that this bispecific genus had undergone an allopolyploid event, and the two parental genomes were derived from two ancestral lineages with different chromosome numbers and structures. The postpolyploid expansion of gene families related to abiotic stress responses and lignin biosynthesis facilitated environmental adaptations of the genus to desert habitats. Population genomic analyses of both species further revealed their recent divergence with continuous gene flow, and the most divergent regions were found to be centered on three highly structurally reshuffled chromosomes. Genes under selection in these regions, which were mainly located in one of the two subgenomes, contributed greatly to the interspecific divergence in microhabitat adaptation.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 79
    facet.materialart.
    Unknown
    MDM2, MDMX, and p73 regulate cell-cycle progression in the absence of wild-type p53 (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-10-29
    Description: The p53 tumor suppressor protein, known to be critically important in several processes including cell-cycle arrest and apoptosis, is highly regulated by multiple mechanisms, most certifiably the Murine Double Minute 2–Murine Double Minute X (MDM2–MDMX) heterodimer. The role of MDM2–MDMX in cell-cycle regulation through inhibition of p53 has been well established. Here we report that in cells either lacking p53 or expressing certain tumor-derived mutant forms of p53, loss of endogenous MDM2 or MDMX, or inhibition of E3 ligase activity of the heterocomplex, causes cell-cycle arrest. This arrest is correlated with a reduction in E2F1, E2F3, and p73 levels. Remarkably, direct ablation of endogenous p73 produces a similar effect on the cell cycle and the expression of certain E2F family members at both protein and messenger RNA levels. These data suggest that MDM2 and MDMX, working at least in part as a heterocomplex, may play a p53-independent role in maintaining cell-cycle progression by promoting the activity of E2F family members as well as p73, making them a potential target of interest in cancers lacking wild-type p53.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 80
    facet.materialart.
    Unknown
    The middle cingulate cortex and dorso-central insula: A mirror circuit encoding observation and execution of vitality forms (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-10-29
    Description: Actions with identical goals can be executed in different ways (gentle, rude, vigorous, etc.), which D. N. Stern called vitality forms [D. N. Stern, Forms of Vitality Exploring Dynamic Experience in Psychology, Arts, Psychotherapy, and Development (2010)]. Vitality forms express the agent’s attitudes toward others. In a series of fMRI studies, we found that the dorso-central insula (DCI) is the region that is selectively active during both vitality form observation and execution. In one previous experiment, however, the middle cingulate gyrus also exhibited activation. In the present study, in order to assess the role of the cingulate cortex in vitality form processing, we adopted a classical vitality form paradigm, but making the control condition devoid of vitality forms using jerky movements. Participants performed two different tasks: Observation of actions performed gently or rudely and execution of the same actions. The results showed that in addition to the insula, the middle cingulate cortex (MCC) was strongly activated during both action observation and execution. Using a voxel-based analysis, voxels showing a similar trend of the blood-oxygen-level-dependent (BOLD) signal in both action observation and execution were found in the DCI and in the MCC. Finally, using a multifiber tractography analysis, we showed that the active sites in MCC and DCI are reciprocally connected.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 81
    facet.materialart.
    Unknown
    Predictive markers of transmission in areas with different malaria endemicity in north-eastern Tanzania based on seroprevalence of antibodies against Plasmodium falciparum (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Objective A community-based cross-sectional study was done to assess Plasmodium falciparum exposure in areas with different malaria endemicity in north-eastern Tanzania using serological markers; PfAMA-1 and PfMSP-119. Results Bondo had a higher seroprevalence 36.6% (188) for PfAMA-1 as compared to Hai 13.8% (33), χ2 = 34.66, p 
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 82
    facet.materialart.
    Unknown
    Right and left ventricular function and flow quantification in pediatric patients with repaired tetralogy of Fallot using four-dimensional flow magnetic resonance imaging (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-31
    Description: Background To assess the accuracy and reproducibility of right ventricular (RV) and left ventricular (LV) function and flow measurements in children with repaired tetralogy of Fallot (rTOF) using four-dimensional (4D) flow, compared with conventional two-dimensional (2D) magnetic resonance imaging (MRI) sequences. Methods Thirty pediatric patients with rTOF were retrospectively enrolled to undergo 2D balanced steady-state free precession cine (2D b-SSFP cine), 2D phase contrast (PC), and 4D flow cardiac MRI. LV and RV volumes and flow in the ascending aorta (AAO) and main pulmonary artery (MPA) were quantified. Pearson’s or Spearman’s correlation tests, paired t-tests, the Wilcoxon signed-rank test, Bland–Altman analysis, and intraclass correlation coefficients (ICC) were performed. Results The 4D flow scan time was shorter compared with 2D sequences (P  0.05), and showed strong correlations (r 〉 0.90, P  0.60, P  0.85). Conclusions RV and LV function and flow quantification in pediatric patients with rTOF using 4D flow MRI can be measured accurately and reproducibly compared to those with conventional 2D sequences.
    Electronic ISSN: 1471-2342
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 83
    facet.materialart.
    Unknown
    “The PLCP gene family of grapevine (Vitis vinifera L.): characterization and differential expression in response to Plasmopara Viticola” (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Papain-like cysteine proteases (PLCPs), a large group of cysteine proteases, are structurally related to papain. The members belonging to PLCPs family contribute to plant immunity, senescence, and defense responses in plants. The PLCP gene family has been identified in Arabidopsis, rice, soybean, and cotton. However, no systematic analysis of PLCP genes has been undertaken in grapevine. Since Plasmopara viticola as a destructive pathogen could affect immunity of grapes in the field, we considered that the members belonged to PLCPs family could play a crucial role in defensive mechanisms or programmed cell death. We aimed to evaluate the role of PLCPs in 2 different varieties of grapevines and compared the changes of their expressions with the transcriptional data in response to P. viticola. Results In this study, 23 grapevine PLCP (VvPLCP) genes were identified by comprehensive bioinformatics analysis. Subsequently, the chromosomal localizations, gene structure, conserved domains, phylogenetic relationship, gene duplication, and cis-acting elements were analyzed. Numerous cis-acting elements related to plant development, hormone, and stress responses were identified in the promoter of the VvPLCP genes. Phylogenetic analysis grouped the VvPLCP genes into nine subgroups. The transcription of VvPLCP in different inoculation time points and varieties indicated that VvPLCP may have vital functions in grapevine defense against Plasmopara viticola. According to transcriptome data and qPCR analysis, we observed the increasing expression levels of VvRD21–1 at 72 h after inoculation in resistant variety, inferring that it was related to grape downy mildew resistance. Meanwhile, 3 genes including VvXBCP1, VvSAG12–1, and VvALP1 showed higher expression at 24 h after pathogen inoculation in the susceptible variety and might be related to the downy mildew phenotype. We nominated these four genes to function during hypersensitive response (HR) process, inferring that these genes could be associated with downy mildew resistance in grapes. Conclusions Our results provide the reference for functional studies of PLCP gene family, and highlight its functions in grapevine defense against P. viticola. The results help us to better understand the complexity of the PLCP gene family in plant immunity and provide valuable information for future functional characterization of specific genes in grapevine.
    Electronic ISSN: 1471-2229
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 84
    facet.materialart.
    Unknown
    The solid and liquid states of chromatin (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: The review begins with a concise description of the principles of phase separation. This is followed by a comprehensive section on phase separation of chromatin, in which we recount the 60 years history of chromatin aggregation studies, discuss the evidence that chromatin aggregation intrinsically is a physiologically relevant liquid–solid phase separation (LSPS) process driven by chromatin self-interaction, and highlight the recent findings that under specific solution conditions chromatin can undergo liquid–liquid phase separation (LLPS) rather than LSPS. In the next section of the review, we discuss how certain chromatin-associated proteins undergo LLPS in vitro and in vivo. Some chromatin-binding proteins undergo LLPS in purified form in near-physiological ionic strength buffers while others will do so only in the presence of DNA, nucleosomes, or chromatin. The final section of the review evaluates the solid and liquid states of chromatin in the nucleus. While chromatin behaves as an immobile solid on the mesoscale, nucleosomes are mobile on the nanoscale. We discuss how this dual nature of chromatin, which fits well the concept of viscoelasticity, contributes to genome structure, emphasizing the dominant role of chromatin self-interaction.
    Electronic ISSN: 1756-8935
    Topics: Biology , Medicine
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 85
    facet.materialart.
    Unknown
    Cell surface sphingomyelin: key role in cancer initiation, progression, and immune evasion (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-31
    Description: Cell surface biochemical changes, notably excessive increase in outer leaflet sphingomyelin (SM) content, are important in cancer initiation, growth, and immune evasion. Innumerable reports describe methods to initiate, promote, or enhance immunotherapy of clinically detected cancer, notwithstanding the challenges, if not impossibility, of identification of tumor-specific, or associated antigens, the lack of tumor cell surface membrane expression of major histocompatibility complex (MHC) class I alpha and β2 microglobulin chains, and lack of expression or accessibility of Fas and other natural killer cell immune checkpoint molecules. Conversely, SM synthesis and hydrolysis are increasingly implicated in initiation of carcinogenesis and promotion of metastasis. Surface membrane SM readily forms inter- and intra- molecular hydrogen bond network, which excessive tightness would impair cell-cell contact inhibition, inter- and intra-cellular signals, metabolic pathways, and susceptibility to host immune cells and mediators. The present review aims at clarifying the tumor immune escape mechanisms, which face common immunotherapeutic approaches, and attracting attention to an entirely different, neglected, key aspect of tumorigenesis associated with biochemical changes in the cell surface that lead to failure of contact inhibition, an instrumental tumorigenesis mechanism. Additionally, the review aims to provide evidence for surface membrane SM levels and roles in cells resistance to death, failure to respond to growth suppressor signals, and immune escape, and to suggest possible novel approaches to cancer control and cure.
    Electronic ISSN: 1476-511X
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 86
    facet.materialart.
    Unknown
    Phase separation in the outer membrane of Escherichia coli (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-10-29
    Description: Gram-negative bacteria are surrounded by a protective outer membrane (OM) with phospholipids in its inner leaflet and lipopolysaccharides (LPS) in its outer leaflet. The OM is also populated with many β-barrel outer-membrane proteins (OMPs), some of which have been shown to cluster into supramolecular assemblies. However, it remains unknown how abundant OMPs are organized across the entire bacterial surface and how this relates to the lipids in the membrane. Here, we reveal how the OM is organized from molecular to cellular length scales, using atomic force microscopy to visualize the OM of live bacteria, including engineered Escherichia coli strains and complemented by specific labeling of abundant OMPs. We find that a predominant OMP in the E. coli OM, the porin OmpF, forms a near-static network across the surface, which is interspersed with barren patches of LPS that grow and merge with other patches during cell elongation. Embedded within the porin network is OmpA, which forms noncovalent interactions to the underlying cell wall. When the OM is destabilized by mislocalization of phospholipids to the outer leaflet, a new phase appears, correlating with bacterial sensitivity to harsh environments. We conclude that the OM is a mosaic of phase-separated LPS-rich and OMP-rich regions, the maintenance of which is essential to the integrity of the membrane and hence to the lifestyle of a gram-negative bacterium.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 87
    facet.materialart.
    Unknown
    isoCNV: in silico optimization of copy number variant detection from targeted or exome sequencing data (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-29
    Description: Background Accurate copy number variant (CNV) detection is especially challenging for both targeted sequencing (TS) and whole‐exome sequencing (WES) data. To maximize the performance, the parameters of the CNV calling algorithms should be optimized for each specific dataset. This requires obtaining validated CNV information using either multiplex ligation-dependent probe amplification (MLPA) or array comparative genomic hybridization (aCGH). They are gold standard but time-consuming and costly approaches. Results We present isoCNV which optimizes the parameters of DECoN algorithm using only NGS data. The parameter optimization process is performed using an in silico CNV validated dataset obtained from the overlapping calls of three algorithms: CNVkit, panelcn.MOPS and DECoN. We evaluated the performance of our tool and showed that increases the sensitivity in both TS and WES real datasets. Conclusions isoCNV provides an easy-to-use pipeline to optimize DECoN that allows the detection of analysis-ready CNV from a set of DNA alignments obtained under the same conditions. It increases the sensitivity of DECoN without the need for orthogonal methods. isoCNV is available at https://gitlab.com/sequentiateampublic/isocnv.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 88
    facet.materialart.
    Unknown
    PRCC reduces the sensitivity of cancer cells to DNA damage by inhibiting JNK and ATM/ATR pathways and results in a poor prognosis in hepatocellular carcinoma (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-29
    Description: Background and aim The proline rich mitotic checkpoint control factor (PRCC) is involved in the splicing process of pre-mRNA. This study aims to elucidate PRCC molecular function, regulatory mechanism and diagnostic value in hepatocellular carcinoma (HCC). Methods The tissue microarray and serum samples from HCC patients were used to investigate the clinical value of PRCC. The biological function and molecular mechanism of PRCC were demonstrated by cell biology, biochemical and animal experiments. The relationship between PRCC and intratumoral heterogeneity (ITH) was analyzed by bioinformatics. Results PRCC was highly expressed in HCC tissues and related to the poor prognosis of HCC patients, its contents were elevated in the preoperative sera of HCC patients. PRCC exhibited high application potential as a substitute or adjuvant of alpha-fetoprotein (AFP) for clinical diagnosis of HCC. It had no significant effect on the proliferation of cancer cells, but could inhibit spheroid formation and metastasis of HCC cells in vitro and in vivo. The high ectopic expression of PRCC made cancer cells insensitive to DNA damage, and enhanced the heterogeneity of HCC cells by inhibiting the JNK/ATM/ATR/ATF2 axis. The HCC patients with high PRCC expression had high ITH, which corresponded to a short overall survival in patients. Conclusions PRCC has high application potential as a substitute or adjuvant of AFP for clinical diagnosis of HCC. The high ectopic expression of PRCC not only caused HCC cells to resist to cell death induced by DNA damage, but also endowed cancer cells with numerous DNA mutations to become increasingly heterogeneous, finally leading to a poor prognosis in HCC patients. These data suggested PRCC could be a promising therapeutic target in HCC patients.
    Electronic ISSN: 2045-3701
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 89
    facet.materialart.
    Unknown
    Comparative transcriptome analysis uncovers cell wall reorganization and repressed cell division during cotton fiber initiation (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-29
    Description: Background Tetraploid cotton plants serve as prime natural fiber source for the textile industry. Although various omics studies have revealed molecular basis for fiber development, a better understanding of transcriptional regulation mechanism regulating lint fiber initiation is necessary to meet global natural fiber demand. Results Here, we aimed to perform transcriptome sequencing to identify DEGs (differentially expressed genes) in ovules of the cotton variety Xu142 and its fibreless mutant Xu142fl during early lint fiber initiation period. Totally, 5516 DEGs including 1840 upregulated and 3676 downregulated were identified. GO enrichment analysis revealed that the downregulated DEGs were mainly associated with biological processes such as transcription related biosynthesis and metabolism, organic cyclic compound biosynthesis and metabolism, photosynthesis, and plant cell wall organization, with molecular functions involving transcription related binding, organic cyclic compound binding, and dioxygenase activity, while the upregulated DEGs were associated with DNA replication and phospholipid biosynthetic related processes. Among the 490 DEGs annotated as transcription factor genes, 86.5% were downregulated in the mutant including the Malvaceae-specific MMLs, expression patterns of which were confirmed during the central period of lint fiber initiation. Investigation of the 16 genes enriched in the cell wall organization revealed that 15 were EXPA coding genes. Conclusions Overall, our data indicate that lint fiber initiation is a complicated process involving cooperation of multiple transcription factor families, which might ultimately lead to the reorganization of the cell wall and terminated cell division of the differentiating fiber initials.
    Electronic ISSN: 1471-213X
    Topics: Biology , Medicine
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 90
    facet.materialart.
    Unknown
    Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-29
    Description: Recent years have seen a revolution in single-cell RNA-sequencing (scRNA-seq) technologies, datasets, and analysis methods. Since 2016, the scRNA-tools database has cataloged software tools for analyzing scRNA-seq data. With the number of tools in the database passing 1000, we provide an update on the state of the project and the field. This data shows the evolution of the field and a change of focus from ordering cells on continuous trajectories to integrating multiple samples and making use of reference datasets. We also find that open science practices reward developers with increased recognition and help accelerate the field.
    Print ISSN: 1465-6906
    Electronic ISSN: 1474-760X
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 91
    facet.materialart.
    Unknown
    Correction for Donate et al., Cigarette smoke induces miR-132 in Th17 cells that enhance osteoclastogenesis in inflammatory arthritis (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-10-18
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 92
    facet.materialart.
    Unknown
    The resistance of peanut to soil-borne pathogens improved by rhizosphere probiotics under calcium treatment (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-29
    Description: Background Peanut (Arachis hypogaea L.) is an important oil and economic crop. Calcium modulates plants in response to abiotic stresses and improves plant resistance to pathogens. Enrichment of beneficial microorganisms in the rhizosphere is associated with plant disease resistance and soil development. The purpose of this study was to analyze the differences in peanut rhizosphere microbial community structure between the calcium treatment and the control during two growth stages and to explain why calcium application could improve the resistance of peanuts to soil-borne pathogens. Results The 16S rDNA amplicon sequencing of rhizosphere microbiome showed that calcium application significantly enriched Serratia marcescens and other three dominant strains at the seedling stage. At the pod filling stage, ten dominant stains such as Sphingomonas changbaiensis and Novosphingobium panipatense were enriched by calcium. Serratia marcescens aseptic fermentation filtrate was mixed with PDA medium and inoculated with the main soil-borne pathogens in the seedling stage, which could inhibit the growth of Fusarium solani and Aspergillus flavus. The aseptic fermentation filtrate of Novosphingobium panipatense was mixed with PDA medium and inoculated with the main soil-borne pathogens in the pod filling stage, which could inhibit the growth of Sclerotium rolfsii and Leptosphaerulina arachidicola. Conclusions Calcium application increases the resistance of peanuts to soil-borne pathogens by enriching them with specific dominant bacteria.
    Electronic ISSN: 1471-2180
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 93
    facet.materialart.
    Unknown
    Centrality of drug targets in protein networks (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-29
    Description: Background In the pharmaceutical industry, competing for few validated drug targets there is a drive to identify new ways of therapeutic intervention. Here, we attempted to define guidelines to evaluate a target’s ‘fitness’ based on its node characteristics within annotated protein functional networks to complement contingent therapeutic hypotheses. Results We observed that targets of approved, selective small molecule drugs exhibit high node centrality within protein networks relative to a broader set of investigational targets spanning various development stages. Targets of approved drugs also exhibit higher centrality than other proteins within their respective functional class. These findings expand on previous reports of drug targets’ network centrality by suggesting some centrality metrics such as low topological coefficient as inherent characteristics of a ‘good’ target, relative to other exploratory targets and regardless of its functional class. These centrality metrics could thus be indicators of an individual protein’s ‘fitness’ as potential drug target. Correlations between protein nodes’ network centrality and number of associated publications underscored the possibility of knowledge bias as an inherent limitation to such predictions. Conclusions Despite some entanglement with knowledge bias, like structure-oriented ‘druggability’ assessments of new protein targets, centrality metrics could assist early pharmaceutical discovery teams in evaluating potential targets with limited experimental proof of concept and help allocate resources for an effective drug discovery pipeline.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 94
    facet.materialart.
    Unknown
    Technical challenges regarding the use of formalin-fixed paraffin embedded (FFPE) tissue specimens for the detection of bacterial alterations in colorectal cancer (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-29
    Description: Background Formalin-fixed paraffin embedded (FFPE) tissues may provide an exciting resource to study microbial associations in human disease, but the use of these low biomass specimens remains challenging. We aimed to reduce unintentional bacterial interference in molecular analysis of FFPE tissues and investigated the feasibility of conducting quantitative polymerase chain reaction (qPCR) and 16S rRNA amplicon sequencing using 14 colorectal cancer, 14 normal adjacent and 13 healthy control tissues. Results Bacterial contaminants from the laboratory environment and the co-extraction of human DNA can affect bacterial analysis. The application of undiluted template improves bacterial DNA amplification, allowing the detection of specific bacterial markers (Escherichia coli and Faecalibacterium prausnitzii) by qPCR. Nested and non-nested PCR-based 16S rRNA amplicon sequencing approaches were employed, showing that bacterial communities of tissues and paired paraffin controls cluster separately at genus level on weighted Unifrac in both non-nested (R2 = 0.045; Pr(〉 F) = 0.053) and nested (R2 = 0.299; Pr(〉 F) = 0.001) PCR datasets. Nevertheless, considerable overlap of bacterial genera within tissues was seen with paraffin, DNA extraction negatives (non-nested PCR) or PCR negatives (nested PCR). Following mathematical decontamination, no differences in α- and β diversity were found between tumor, normal adjacent and control tissues. Conclusions Bacterial marker analysis by qPCR seems feasible using non-normalized template, but 16S rRNA amplicon sequencing remains challenging. Critical evaluation of laboratory procedures and incorporation of positive and negative controls for bacterial analysis of FFPE tissues are essential for quality control and to account for bacterial contaminants.
    Electronic ISSN: 1471-2180
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 95
    facet.materialart.
    Unknown
    FoldHSphere: deep hyperspherical embeddings for protein fold recognition (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-12
    Description: Background Current state-of-the-art deep learning approaches for protein fold recognition learn protein embeddings that improve prediction performance at the fold level. However, there still exists aperformance gap at the fold level and the (relatively easier) family level, suggesting that it might be possible to learn an embedding space that better represents the protein folds. Results In this paper, we propose the FoldHSphere method to learn a better fold embedding space through a two-stage training procedure. We first obtain prototype vectors for each fold class that are maximally separated in hyperspherical space. We then train a neural network by minimizing the angular large margin cosine loss to learn protein embeddings clustered around the corresponding hyperspherical fold prototypes. Our network architectures, ResCNN-GRU and ResCNN-BGRU, process the input protein sequences by applying several residual-convolutional blocks followed by a gated recurrent unit-based recurrent layer. Evaluation results on the LINDAHL dataset indicate that the use of our hyperspherical embeddings effectively bridges the performance gap at the family and fold levels. Furthermore, our FoldHSpherePro ensemble method yields an accuracy of 81.3% at the fold level, outperforming all the state-of-the-art methods. Conclusions Our methodology is efficient in learning discriminative and fold-representative embeddings for the protein domains. The proposed hyperspherical embeddings are effective at identifying the protein fold class by pairwise comparison, even when amino acid sequence similarities are low.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 96
    facet.materialart.
    Unknown
    Retraction for Cabral et al., A global network of marine protected areas for food (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-10-06
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 97
    facet.materialart.
    Unknown
    In This Issue (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-10-26
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 98
    facet.materialart.
    Unknown
    Genome-wide identification, classification, and expression analysis of the JmjC domain-containing histone demethylase gene family in birch (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-28
    Description: Background Histone methylation occurs primarily on lysine residues and requires a set of enzymes capable of reading, writing, and erasing to control its establishment and deletion, which is essential for maintaining chromatin structure and gene expression. Histone methylation and demethylation are contributed to plant growth and development, and are involved in adapting to environmental stresses. The JmjC domain-containing proteins are extensively studied for their function in histone lysine demethylation in plants, and play a critical role in sustaining histone methylation homeostasis. Results In this study, a total of 21 JmjC domain-containing histone demethylase proteins (JHDMs) in birch were identified and classified into five subfamilies based on structural characteristics and phylogenetic relationships among Arabidopsis, rice, maize, and birch. Although the BpJMJ genes displayed significant schematic variation, their distribution on the chromosomes is relatively uniform. Additionally, the BpJMJ genes in birch have never experienced a tandem-duplication event proved by WGD analysis and were remaining underwent purifying selection (Ka/Ks 
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 99
    facet.materialart.
    Unknown
    adabmDCA: adaptive Boltzmann machine learning for biological sequences (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-29
    Description: Background Boltzmann machines are energy-based models that have been shown to provide an accurate statistical description of domains of evolutionary-related protein and RNA families. They are parametrized in terms of local biases accounting for residue conservation, and pairwise terms to model epistatic coevolution between residues. From the model parameters, it is possible to extract an accurate prediction of the three-dimensional contact map of the target domain. More recently, the accuracy of these models has been also assessed in terms of their ability in predicting mutational effects and generating in silico functional sequences. Results Our adaptive implementation of Boltzmann machine learning, , can be generally applied to both protein and RNA families and accomplishes several learning set-ups, depending on the complexity of the input data and on the user requirements. The code is fully available at https://github.com/anna-pa-m/adabmDCA. As an example, we have performed the learning of three Boltzmann machines modeling the Kunitz and Beta-lactamase2 protein domains and TPP-riboswitch RNA domain. Conclusions The models learned by are comparable to those obtained by state-of-the-art techniques for this task, in terms of the quality of the inferred contact map as well as of the synthetically generated sequences. In addition, the code implements both equilibrium and out-of-equilibrium learning, which allows for an accurate and lossless training when the equilibrium one is prohibitive in terms of computational time, and allows for pruning irrelevant parameters using an information-based criterion.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 100
    facet.materialart.
    Unknown
    The clone devaluation effect: does duplication of local facial features matter? (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-29
    Description: Objective The clone devaluation is a phenomenon reported by the latest paper in which eeriness is evoked when people observe individuals with the same face (clone faces) compared to those with different faces. There are two possibilities that explain the clone devaluation effect. One is that the same facial features that clone faces have (duplication of facial features) induce the clone devaluation effect. The other possibility is that duplication of identities between people with clone faces is important for the clone devaluation effect. We thus conducted an experiment to investigate whether the duplication of identities or of facial features induces the clone devaluation effect. Results Participants evaluated eeriness of scrambled clone faces and scrambled different faces using the paired comparison method. There was only a slight difference in subjective eeriness between scrambled clone faces and scrambled different faces. Therefore, this study suggests that the duplication of local facial features does not play a key role in inducing the clone devaluation effect.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...