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  • Molecular Diversity Preservation International  (495,622)
  • Cell Press  (242,170)
  • EDP Sciences
  • Emerald
  • Essen : Verl. Glückauf
  • Krefeld : Geologischer Dienst Nordhein-Westfalen
  • National Academy of Sciences
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  • 1
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    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
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  • 2
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    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
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  • 3
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    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.
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  • 4
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    Statistical models of the variability of plasma in the topside ionosphere: 2. Performance assessment (2024)
    EDP Sciences
    Details
    Publication Date: 2024-03-12
    Description: Statistical models of the variability of plasma in the topside ionosphere based on the Swarm data have been developed in the “Swarm Variability of Ionospheric Plasma” (Swarm-VIP) project within the European Space Agency’s Swarm+4D-Ionosphere framework. The models can predict the electron density, its gradients for three horizontal spatial scales – 20, 50 and 100 km – along the North-South direction and the level of the density fluctuations. Despite being developed by leveraging on Swarm data, the models provide predictions that are independent of these data, having a global coverage, fed by various parameters and proxies of the helio-geophysical conditions. Those features make the Swarm-VIP models useful for various purposes, which include the possible support for already available ionospheric models and proxy of the effect of ionospheric irregularities of the medium scales that affect the signals emitted by Global Navigation Satellite Systems (GNSS). The formulation, optimisation and validation of the Swarm-VIP models are reported in Paper 1 (Wood et al. 2024. J Space Weather Space Clim. in press). This paper describes the performance assessment of the models, by addressing their capability to reproduce the known climatological variability of the modelled quantities, and the ionospheric weather as depicted by ground-based GNSS, as a proxy for the ionospheric effect on GNSS signals. Additionally, we demonstrate that, under certain conditions, the model can better reproduce the ionospheric variability than a physics-based model, namely the Thermosphere-Ionosphere-Electrodynamics General Circulation Model (TIE-GCM).
    Description: Published
    Description: 4
    Description: OSA3: Climatologia e meteorologia spaziale
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
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    Antiphage small molecules produced by bacteria – beyond protein-mediated defenses (2023)
    Cell Press
    Details
    Publication Date: 2024-01-08
    Description: Bacterial populations face the constant threat of viral predation exerted by bacteriophages (‘phages’). In response, bacteria have evolved a wide range of defense mechanisms against phage challenges. Yet the vast majority of antiphage defense systems described until now are mediated by proteins or RNA complexes acting at the single-cell level. Here, we review small molecule-based defense strategies against phage infection, with a focus on the antiphage molecules described recently. Importantly, inhibition of phage infection by excreted small molecules has the potential to protect entire bacterial communities, highlighting the ecological significance of these antiphage strategies. Considering the immense repertoire of bacterial metabolites, we envision that the list of antiphage small molecules will be further expanded in the future.
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  • 6
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    Near-term deployment of novel carbon removal to facilitate longer-term deployment (2023)
    Cell Press
    Details
    Publication Date: 2024-01-08
    Description: Scenarios—which account for the costs of and interactions among different mitigation options—show that we will need to remove hundreds of gigatons of carbon dioxide (CO2) from the atmosphere over the course of the century to limit warming to well below 2°C, make efforts to limit it to 1.5°C, and ensure the sustained well-being of our planet. Yet at present, only 2 Gt is being removed per year, and nearly all of it is from forestry—only 0.1% is from novel forms of carbon removal. This commentary shows that the deployment of novel CO2 removal (CDR) over the next decade, its formative phase, is likely to be consequential in determining whether CDR will be available at scale and in time to reach net-zero CO2 emissions consistent with the Paris Agreement’s temperature goal.
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  • 7
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    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.
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  • 8
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    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
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  • 9
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    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.
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  • 10
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    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
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  • 11
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    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)
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  • 12
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    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
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  • 13
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    Hydroxyapatite catalyzed hydrothermal liquefaction transforms food waste from an environmental liability to renewable fuel (2023)
    Cell Press
    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 LeClerc, H., Tompsett, G., Paulsen, A., McKenna, A., Niles, S., Reddy, C., Nelson, R., Cheng, F., Teixeira, A., & Timko, M. Hydroxyapatite catalyzed hydrothermal liquefaction transforms food waste from an environmental liability to renewable fuel. IScience, 25(9), (2022): 104916, https://doi.org/10.1016/j.isci.2022.104916.
    Description: Food waste is an abundant and inexpensive resource for the production of renewable fuels. Biocrude yields obtained from hydrothermal liquefaction (HTL) of food waste can be boosted using hydroxyapatite (HAP) as an inexpensive and abundant catalyst. Combining HAP with an inexpensive homogeneous base increased biocrude yield from 14 ± 1 to 37 ± 3%, resulting in the recovery of 49 ± 2% of the energy contained in the food waste feed. Detailed product analysis revealed the importance of fatty-acid oligomerization during biocrude formation, highlighting the role of acid-base catalysts in promoting condensation reactions. Economic and environmental analysis found that the new technology has the potential to reduce US greenhouse gas emissions by 2.6% while producing renewable diesel with a minimum fuel selling price of $1.06/GGE. HAP can play a role in transforming food waste from a liability to a renewable fuel.
    Description: This work was funded by the DOE Bioenergy Technology Office (DE-EE0008513), a DOE DBIR (DE-SC0015784) and the MassCEC. The authors thank WenWen Yao, Department of Environmental Science at WPI, for TOC analysis, Mainstream Engineering for heating value characterization of the oil and solid samples, Wei Fan for assistance in obtaining SEM images and, Julia Martin and Ronald Grimm for their assistance in collecting XPS data, and Jeffrey R. Page for his assistance with oil upgrading and analysis. HOL was partially funded for this work by NSF Graduate Research Fellowship award number 2038257. A portion of this work was performed at the National High Magnetic Field Laboratory Ion Cyclotron Resonance user facility, which is supported by the NSF Division of Materials Research and Division of Chemistry through DMR 16-44779 and the State of Florida.
    Keywords: Chemistry ; Chemical engineering ; Catalysis
    Repository Name: Woods Hole Open Access Server
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  • 14
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    Potential of calcein staining as growth monitoring marker in Ostrea edulis (2023)
    EDP Sciences
    In:  EPIC3Aquatic Living Resources, EDP Sciences, 36, pp. 17-17, ISSN: 0990-7440
    Details
    Publication Date: 2023-08-09
    Description: Growth is an important biological trait and monitoring metric for the assessment of the success and progress of restoration projects with the European oyster (Ostrea edulis). However, sampling time and frequency are often limited, as well as the ability to survey individual growth. Chemical dyes, such as calcein, can be used to create incremental markings for measuring growth in shell cross-sections, especially in bivalves. However, potential negative effects and limits for successful staining have not been assessed for O. edulis, yet. In this study, three different calcein concentrations (100-mg l-1, 150-mg l-1, 200-mg l-1) with three different immersion times (6-h, 12-h, 24-h) were tested for potential negative effects, the best incremental marking result and their potential to be used in growth measurements. Furthermore, the deposition of an annual growth line was investigated. Results showed that calcein is a reliable in situ fluorescence marker that produced sufficient growth lines in the cross-section of O. edulis. At a concentration of 100-mg l-1 or higher and immersion times of 6-h or more, no negative effects on growth and survival were observed after five months. Applications include the possibility for long-term, individual growth data for a large number of oysters for restoration monitoring as well as the option of marking restored oysters from aquaculture production to distinguish them from existing wild stock populations or natural offspring.
    Repository Name: EPIC Alfred Wegener Institut
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  • 15
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    Overcoming Ostrea edulis seed production limitations to meet ecosystem restoration demands in the UN decade on restoration (2023)
    EDP Sciences
    In:  EPIC3Aquatic Living Resources, EDP Sciences, 36, pp. 16-16, ISSN: 0990-7440
    Details
    Publication Date: 2024-03-22
    Description: The European flat oyster, Ostrea edulis, is a habitat-forming bivalve which was historically widespread throughout Europe. Following its decline due to overfishing, pollution, sedimentation, invasive species, and disease, O. edulis and its beds are now listed as a threatened and/or declining species and habitat by OSPAR. Increasing recognition of the plight of the oyster, alongside rapidly developing restoration techniques and growing interest in marine restoration, has resulted in a recent and rapid growth in habitat restoration efforts. O. edulis seed supply is currently a major bottleneck in scaling up habitat restoration efforts in Europe. O. edulis has been cultured for centuries, however, research into its culture declined following the introduction of the Pacific oyster, Crassostrea gigas to Europe in the early 1970 s. Recent efforts to renew both hatchery and pond production of O. edulis seed for habitat restoration purposes are hampered by restoration project timelines and funding typically being short, or projects not planning appropriately for the timescales required for investment, research-and-development and delivery of oyster seed by commercial producers. Furthermore, funding for restoration is intermittent, making long-term commitments between producers and restoration practitioners difficult. Long-term, strategic investment in research and production are needed to overcome these bottlenecks and meet current ambitious restoration targets across Europe.
    Repository Name: EPIC Alfred Wegener Institut
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  • 16
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    Ten priority questions for increasing the consistency and success in hatchery production of the European flat oyster for habitat restoration (2023)
    EDP Sciences
    In:  EPIC3Aquatic Living Resources, EDP Sciences, 36, pp. 29-29, ISSN: 0990-7440
    Details
    Publication Date: 2024-03-22
    Description: The European flat oyster, Ostrea edulis, once formed extensive reef habitats throughout European seas and estuaries. These reefs are now largely functionally extinct, yet interest and support for their restoration is rapidly growing. A major bottleneck to scaling up oyster reef restoration is the lack of available oysters to supply the growing demand. This study aimed to identify the ten questions which, if answered, would increase the consistency and success in hatchery production of O. edulis for habitat restoration. Candidate questions were submitted by representatives from twelve commercial and research hatcheries across Europe. The list of 98 candidate questions were collaboratively discussed by experts from nine research hatcheries across eight countries in Europe, to identify the top ten questions via an iterative and open process. Questions were grouped into the following themes: Conditioning and feeding, larval rearing, disease and water quality, hatchery protocol, genetics, and hatchery management. There were several overarching topics spanning these themes, including diet optimisation, maximising the effective population size, and developing the technical skillbase in order to increase hatchery production to meet the projected increase in demand for oyster seed for habitat restoration efforts. We anticipate this list will provide a starting point for collaborative research efforts across Europe, as well as assisting policy makers and funders in identifying key knowledge gaps.
    Repository Name: EPIC Alfred Wegener Institut
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  • 17
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    Metabolic interactions shape a community's phenotype (2022)
    Cell Press
    Details
    Publication Date: 2024-01-08
    Description: Metabolic interactions between auxotrophs and prototrophs in microbial communities are understudied. Yu et al. showed how intracellular as well as intercellular metabolism affects community fitness in the absence and presence of abiotic stress, that is, drugs.
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    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.
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    Rapid radiation in a highly diverse marine environment (2022)
    National Academy of Sciences
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    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.
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    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.
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    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.
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    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.
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    High (3)He/(4)He in central Panama reveals a distal connection to the Galápagos plume (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bekaert, D. V., Gazel, E., Turner, S., Behn, M. D., de Moor, J. M., Zahirovic, S., Manea, V. C., Hoernle, K., Fischer, T. P., Hammerstrom, A., Seltzer, A. M., Kulongoski, J. T., Patel, B. S., Schrenk, M. O., Halldórsson, S. A., Nakagawa, M., Ramírez, C. J., Krantz, J. A., Yücel, M., Ballentine, C. J., Giovannelli, D., Lloyd, K. G., Barry, P. H. High (3)He/(4)He in central Panama reveals a distal connection to the Galápagos plume. Proceedings of the National Academy of Sciences of the United States of America, 118(47), (2021): e2110997118, https://doi.org/10.1073/pnas.2110997118.
    Description: It is well established that mantle plumes are the main conduits for upwelling geochemically enriched material from Earth's deep interior. The fashion and extent to which lateral flow processes at shallow depths may disperse enriched mantle material far (〉1,000 km) from vertical plume conduits, however, remain poorly constrained. Here, we report He and C isotope data from 65 hydrothermal fluids from the southern Central America Margin (CAM) which reveal strikingly high 3He/4He (up to 8.9RA) in low-temperature (≤50 °C) geothermal springs of central Panama that are not associated with active volcanism. Following radiogenic correction, these data imply a mantle source 3He/4He 〉10.3RA (and potentially up to 26RA, similar to Galápagos hotspot lavas) markedly greater than the upper mantle range (8 ± 1RA). Lava geochemistry (Pb isotopes, Nb/U, and Ce/Pb) and geophysical constraints show that high 3He/4He values in central Panama are likely derived from the infiltration of a Galápagos plume–like mantle through a slab window that opened ∼8 Mya. Two potential transport mechanisms can explain the connection between the Galápagos plume and the slab window: 1) sublithospheric transport of Galápagos plume material channeled by lithosphere thinning along the Panama Fracture Zone or 2) active upwelling of Galápagos plume material blown by a “mantle wind” toward the CAM. We present a model of global mantle flow that supports the second mechanism, whereby most of the eastward transport of Galápagos plume material occurs in the shallow asthenosphere. These findings underscore the potential for lateral mantle flow to transport mantle geochemical heterogeneities thousands of kilometers away from plume conduits.
    Description: This work was principally supported by Grant G-2016-7206 from the Alfred P. Sloan Foundation and the Deep Carbon Observatory to P.H.B. We also acknowledge the NSF awards (1144559, 1923915, and 2015789) to P.H.B., which partially supported this work. S.Z. was supported by the Australian Research Council Grant DE210100084 and a University of Sydney Robinson Fellowship. D.G. was partially supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program Grant Agreement No. 948972—COEVOLVE—ERC-2020-STG. This study was also supported in part by NSF award No. EAR 1826673 to E.G. Folkmar Hauff is acknowledged for contributing to the analysis of the La Providencia samples at GEOMAR.
    Keywords: Helium ; Mantle plume ; Slab window ; Mantle flow ; Geochemistry
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    The evolution of synaptic and cognitive capacity: insights from the nervous system transcriptome of Aplysia (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-11-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Orvis, J., Albertin, C., Shrestha, P., Chen, S., Zheng, M., Rodriguez, C., Tallon, L., Mahurkar, A., Zimin, A., Kim, M., Liu, K., Kandel, E., Fraser, C., Sossin, W., & Abrams, T. The evolution of synaptic and cognitive capacity: insights from the nervous system transcriptome of Aplysia. Proceedings of the National Academy of Sciences of the United States of America, 119(28), (2022): e2122301119, https://doi.org/10.1073/pnas.2122301119.
    Description: The gastropod mollusk Aplysia is an important model for cellular and molecular neurobiological studies, particularly for investigations of molecular mechanisms of learning and memory. We developed an optimized assembly pipeline to generate an improved Aplysia nervous system transcriptome. This improved transcriptome enabled us to explore the evolution of cognitive capacity at the molecular level. Were there evolutionary expansions of neuronal genes between this relatively simple gastropod Aplysia (20,000 neurons) and Octopus (500 million neurons), the invertebrate with the most elaborate neuronal circuitry and greatest behavioral complexity? Are the tremendous advances in cognitive power in vertebrates explained by expansion of the synaptic proteome that resulted from multiple rounds of whole genome duplication in this clade? Overall, the complement of genes linked to neuronal function is similar between Octopus and Aplysia. As expected, a number of synaptic scaffold proteins have more isoforms in humans than in Aplysia or Octopus. However, several scaffold families present in mollusks and other protostomes are absent in vertebrates, including the Fifes, Lev10s, SOLs, and a NETO family. Thus, whereas vertebrates have more scaffold isoforms from select families, invertebrates have additional scaffold protein families not found in vertebrates. This analysis provides insights into the evolution of the synaptic proteome. Both synaptic proteins and synaptic plasticity evolved gradually, yet the last deuterostome-protostome common ancestor already possessed an elaborate suite of genes associated with synaptic function, and critical for synaptic plasticity.
    Description: This work was supported by NSF EAGER Award IOS-1255695 and NIH grant R01 MH 55880 grant to T.W.A.; by a Natural Sciences and Engineering Research Council of Canada Discovery grant and Canadian Institutes of Health Research project grant 340328 to W.S.; by funding from the HHMI to E.R.K.; and by a Hibbitt Early Career Fellowship to C.A. W.S. is James McGill Professor at McGill University.
    Keywords: Neural plasticity ; Synaptic plasticity ; Evolution ; Neuromodulation ; Aplysia
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    Discovery of active off-axis hydrothermal vents at 9° 54’N East Pacific Rise (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-11-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in McDermott, J. M., Parnell-Turner, R., Barreyre, T., Herrera, S., Downing, C. C., Pittoors, N. C., Pehr, K., Vohsen, S. A., Dowd, W. S., Wu, J.-N., Marjanović, M., & Fornari, D. J. Discovery of active off-axis hydrothermal vents at 9° 54’N East Pacific Rise. Proceedings of the National Academy of Sciences of the United States of America, 119(30), (2022): e2205602119, https://doi.org/10.1073/pnas.2205602119.
    Description: Comprehensive knowledge of the distribution of active hydrothermal vent fields along midocean ridges is essential to understanding global chemical and heat fluxes and endemic faunal distributions. However, current knowledge is biased by a historical preference for on-axis surveys. A scarcity of high-resolution bathymetric surveys in off-axis regions limits vent identification, which implies that the number of vents may be underestimated. Here, we present the discovery of an active, high-temperature, off-axis hydrothermal field on a fast-spreading ridge. The vent field is located 750 m east of the East Pacific Rise axis and ∼7 km north of on-axis vents at 9° 50′N, which are situated in a 50- to 100-m-wide trough. This site is currently the largest vent field known on the East Pacific Rise between 9 and 10° N. Its proximity to a normal fault suggests that hydrothermal fluid pathways are tectonically controlled. Geochemical evidence reveals deep fluid circulation to depths only 160 m above the axial magma lens. Relative to on-axis vents at 9° 50′N, these off-axis fluids attain higher temperatures and pressures. This tectonically controlled vent field may therefore exhibit greater stability in fluid composition, in contrast to more dynamic, dike-controlled, on-axis vents. The location of this site indicates that high-temperature convective circulation cells extend to greater distances off axis than previously realized. Thorough high-resolution mapping is necessary to understand the distribution, frequency, and physical controls on active off-axis vent fields so that their contribution to global heat and chemical fluxes and role in metacommunity dynamics can be determined.
    Description: Financial support was provided by the NSF Awards OCE-1949938 (to J.M.M.), OCE-1948936 (to R.P.-T.), and OCE-1949485 (to D.J.F. and T.B.).
    Keywords: Hydrothermal activity ; Midocean ridge ; Ocean chemistry ; Chemosynthetic ecosystem ; East Pacific Rise
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    Farm-waste-derived recyclable photothermal evaporator (2022)
    Cell Press
    Details
    Publication Date: 2022-11-18
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tian, Y., Liu, X., Li, J., Deng, Y., DeGiorgis, J. A., Zhou, S., Caratenuto, A., Minus, M. L., Wan, Y., Xiao, G., & Zheng, Y. Farm-waste-derived recyclable photothermal evaporator. Cell Reports Physical Science, 2(9), (2021): 100549, https://doi.org/10.1016./j.xcrp.2021.100549
    Description: Interfacial solar steam generation is emerging as a promising technique for efficient desalination. Although increasing efforts have been made, challenges exist for achieving a balance among a plethora of performance indicators—for example, rapid evaporation, durability, low-cost deployment, and salt rejection. Here, we demonstrate that carbonized manure can convert 98% of sunlight into heat, and the strong capillarity of porous carbon fibers networks pumps sufficient water to evaporation interfaces. Salt diffusion within microchannels enables quick salt drainage to the bulk seawater to prevent salt accumulation. With these advantages, this biomass-derived evaporator is demonstrated to feature a high evaporation rate of 2.81 kg m−2 h−1 under 1 sun with broad robustness to acidity and alkalinity. These advantages, together with facial deployment, offer an approach for converting farm waste to energy with high efficiency and easy implementation, which is particularly well suited for developing regions.
    Description: This project is supported by the National Science Foundation through grant no. CBET-1941743. This project is based upon work supported in part by the National Science Foundation under EPSCoR Cooperative Agreement no. OIA-1655221.
    Keywords: Biomass ; Recyclable ; Manure ; Farm waste ; Photothermal evaporation ; Desalination
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    Hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Criswell, K. E., Roberts, L. E., Koo, E. T., Head, J. J., & Gillis, J. A. Hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences of the United States of America, 118(51), (2021): e2114563118, https://doi.org/10.1073/pnas.2114563118.
    Description: The axial skeleton of tetrapods is organized into distinct anteroposterior regions of the vertebral column (cervical, trunk, sacral, and caudal), and transitions between these regions are determined by colinear anterior expression boundaries of Hox5/6, -9, -10, and -11 paralogy group genes within embryonic paraxial mesoderm. Fishes, conversely, exhibit little in the way of discrete axial regionalization, and this has led to scenarios of an origin of Hox-mediated axial skeletal complexity with the evolutionary transition to land in tetrapods. Here, combining geometric morphometric analysis of vertebral column morphology with cell lineage tracing of hox gene expression boundaries in developing embryos, we recover evidence of at least five distinct regions in the vertebral skeleton of a cartilaginous fish, the little skate (Leucoraja erinacea). We find that skate embryos exhibit tetrapod-like anteroposterior nesting of hox gene expression in their paraxial mesoderm, and we show that anterior expression boundaries of hox5/6, hox9, hox10, and hox11 paralogy group genes predict regional transitions in the differentiated skate axial skeleton. Our findings suggest that hox-based axial skeletal regionalization did not originate with tetrapods but rather has a much deeper evolutionary history than was previously appreciated.
    Description: This research was funded by a Natural Environment Research Council Grant (to J.J.H., J.A.G., and K.E.C.: NE/S000739/1) and a Royal Society University Research Fellowship (UF130182 and URF\R\191007), Royal Society Research Grant (RG140377), and University of Cambridge Sir Isaac Newton Trust Grant (14.23z) (to J.A.G.).
    Keywords: Hox genes ; Regionalization ; Chondrichthyan ; Vertebral column
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    Yeast cell death pathway requiring AP-3 vesicle trafficking leads to vacuole/lysosome membrane permeabilization (2022)
    Cell Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Stolp, Z. D., Kulkarni, M., Liu, Y., Zhu, C., Jalisi, A., Lin, S., Casadevall, A., Cunningham, K. W., Pineda, F. J., Teng, X., & Hardwick, J. M. Yeast cell death pathway requiring AP-3 vesicle trafficking leads to vacuole/lysosome membrane permeabilization. Cell Reports, 39(2), (2022): 110647, https://doi.org/10.1016/j.celrep.2022.110647.
    Description: Unicellular eukaryotes have been suggested as undergoing self-inflicted destruction. However, molecular details are sparse compared with the mechanisms of programmed/regulated cell death known for human cells and animal models. Here, we report a molecular cell death pathway in Saccharomyces cerevisiae leading to vacuole/lysosome membrane permeabilization. Following a transient cell death stimulus, yeast cells die slowly over several hours, consistent with an ongoing molecular dying process. A genome-wide screen for death-promoting factors identified all subunits of the AP-3 complex, a vesicle trafficking adapter known to transport and install newly synthesized proteins on the vacuole/lysosome membrane. To promote cell death, AP-3 requires its Arf1-GTPase-dependent vesicle trafficking function and the kinase Yck3, which is selectively transported to the vacuole membrane by AP-3. Video microscopy revealed a sequence of events where vacuole permeability precedes the loss of plasma membrane integrity. AP-3-dependent death appears to be conserved in the human pathogenic yeast Cryptococcus neoformans.
    Description: Funding sources: National Institutes of Health, United States grants AI144373 and NS127076 (J.M.H.), AI115016 and AI153414 (K.W.C.), and AI052733, AI152078, and HL059842 (A.C.); National Natural Science Foundation of China 31970550; and the Priority Academic Program Development of the Jiangsu Higher Education Institutes (X.T.).
    Keywords: Yeast ; Programmed cell death ; Vesicle trafficking ; AP-3 ; Vacuole ; Cryptococcus ; Yck3 ; Regulated cell death ; Lysosome ; Vacuolar membrane permeabilization
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    Holocene bidirectional river system along the Kenya Rift and its influence on East African faunal exchange and diversity gradients (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-19
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Dommain, R., Riedl, S., Olaka, L. A., deMenocal, P., Deino, A. L., Owen, R. B., Muiruri, V., Müller, J., Potts, R., & Strecker, M. R. Holocene bidirectional river system along the Kenya Rift and its influence on East African faunal exchange and diversity gradients. Proceedings of the National Academy of Sciences of the United States of America, 119(28),(2022): e2121388119, https://doi.org/10.1073/pnas.2121388119.
    Description: East Africa is a global biodiversity hotspot and exhibits distinct longitudinal diversity gradients from west to east in freshwater fishes and forest mammals. The assembly of this exceptional biodiversity and the drivers behind diversity gradients remain poorly understood, with diversification often studied at local scales and less attention paid to biotic exchange between Afrotropical regions. Here, we reconstruct a river system that existed for several millennia along the now semiarid Kenya Rift Valley during the humid early Holocene and show how this river system influenced postglacial dispersal of fishes and mammals due to its dual role as a dispersal corridor and barrier. Using geomorphological, geochronological, isotopic, and fossil analyses and a synthesis of radiocarbon dates, we find that the overflow of Kenyan rift lakes between 12 and 8 ka before present formed a bidirectional river system consisting of a “Northern River” connected to the Nile Basin and a “Southern River,” a closed basin. The drainage divide between these rivers represented the only viable terrestrial dispersal corridor across the rift. The degree and duration of past hydrological connectivity between adjacent river basins determined spatial diversity gradients for East African fishes. Our reconstruction explains the isolated distribution of Nilotic fish species in modern Kenyan rift lakes, Guineo-Congolian mammal species in forests east of the Kenya Rift, and recent incipient vertebrate speciation and local endemism in this region. Climate-driven rearrangements of drainage networks unrelated to tectonic activity contributed significantly to the assembly of species diversity and modern faunas in the East African biodiversity hotspot.
    Description: R.D. was funded by a Smithsonian Human Origins Postdoctoral Fellowship and by Geo.X—the Research Network for Geosciences in Berlin and Potsdam. Fig. 1 D, E, and G and SI Appendix, Figs. S1 and S3 are based on the TanDEM-X Science DEM granted to L.A.O. and S.R. by the German Aerospace Center (DLR) in 2017. L.A.O. acknowledges the Volkswagen Foundation for funding this study with Grant No. 89369. M.R.S. and S.R. were supported by funds from Potsdam University and the Geothermal Development Company of Kenya, and R.B.O. and V.M. were supported by the Hong Kong General Research Fund. We acknowledge support from the National Museums of Kenya and the Kenya Government permission granted by the Ministry of Sports, Culture and the Arts, and by the National Commission for Science, Technology and Innovation (NACOSTI) Permits P/14/7709/683 (to R.P.) and P/16/11924/11448 (to L.A.O.). This work is a contribution of the Olorgesailie Drilling Project, for which support from the National Museums of Kenya, the Oldonyo Nyokie Group Ranch, the Peter Buck Fund for Human Origins Research (Smithsonian Institution), the William H. Donner Foundation, the Ruth and Vernon Taylor Foundation, Whitney and Betty MacMillan, and the Smithsonian Human Origins Program is gratefully acknowledged. LacCore is acknowledged for support in drilling and core storage.
    Keywords: East Africa ; Biogeography ; Biodiversity ; Hydrological connectivity ; Holocene
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    Nutrient availability and senescence spatially structure the dynamics of a foundation species (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-20
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bell, T. W., & Siegel, D. A. Nutrient availability and senescence spatially structure the dynamics of a foundation species. Proceedings of the National Academy of Sciences of the United States of America, 119(1), (2021): e2105135118, https://doi.org/10.1073/pnas.2105135118.
    Description: Disentangling the roles of the external environment and internal biotic drivers of plant population dynamics is challenging due to the absence of relevant physiological and abundance information over appropriate space and time scales. Remote observations of giant kelp biomass and photosynthetic pigment concentrations are used to show that spatiotemporal patterns of physiological condition, and thus growth and production, are regulated by different processes depending on the scale of observation. Nutrient supply was linked to regional scale (〉1 km) physiological condition dynamics, and kelp forest stands were more persistent where nutrient levels were consistently high. However, on local scales (〈1 km), internal senescence processes related to canopy age demographics determined patterns of biomass loss across individual kelp forests despite uniform nutrient conditions. Repeat measurements of physiology over continuous spatial fields can provide insights into complex dynamics that are unexplained by the environmental drivers thought to regulate abundance. Emerging remote sensing technologies that provide simultaneous estimates of abundance and physiology can quantify the roles of environmental change and demographics governing plant population dynamics for a wide range of aquatic and terrestrial ecosystems.
    Description: This work was supported by the US NSF (Grants OCE 1232779 and 1831937), by the US Department of Energy (Cooperative Agreement DE-AR0000922), and by NASA (Grant NNX14AR62A) and the NASA Earth and Space Sciences Fellowship program in support of T.W.B.
    Keywords: Physiology ; Population ; Biomass ; Hyperspectral ; Giant kelp
    Repository Name: Woods Hole Open Access Server
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    Trivalent chromium isotopes in the eastern tropical North Pacific oxygen-deficient zone (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2021. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 118(8), (2021): e1918605118, https://doi.org/10.1073/pnas.1918605118.
    Description: Changes in chromium (Cr) isotope ratios due to fractionation between trivalent [Cr(III)] and hexavalent [Cr(VI)] are being utilized by geologists to infer oxygen conditions in past environments. However, there is little information available on Cr in the modern ocean to ground-truth these inferences. Transformations between the two chromium species are important processes in oceanic Cr cycling. Here we present profiles of hexavalent and trivalent Cr concentrations and stable isotope ratios from the eastern tropical North Pacific (ETNP) oxygen-deficient zone (ODZ) which support theoretical and experimental studies that predict that lighter Cr is preferentially reduced in low-oxygen environments and that residual dissolved Cr becomes heavier due to removal of particle-reactive Cr(III) on sinking particles. The Cr(III) maximum dominantly occurs in the upper portion of the ODZ, implying that microbial activity (dependent on the sinking flux of organic matter) may be the dominant mechanism for this transformation, rather than a simple inorganic chemical conversion between the species depending on the redox potential.
    Description: We thank chief scientist Gabrielle Rocap for accommodating us on cruises Roger Revelle 1804-5 and Kilo Moana 19-20 (sponsored by NSF Grant DEB-1542240 to G. Rocap, A. Devol, R. Kiel, and C. Deutch), Jim Moffett for helping with sampling on these cruises, and Mark Altabet and Frank Stewart for collecting the samples from station 2T on cruise New Horizon 1410. This research was supported by NSF Grant OCE-1736996 (to E.A.B.) and by a fellowship from the Massachusetts Institute of Technology/Woods Hole Oceanographic Institution Joint Program in Oceanography.
    Keywords: Chromium isotopes ; Oxygen-deficient zones ; Trace elements ; Trivalent chromium ; Hexavalent ; Chromium
    Repository Name: Woods Hole Open Access Server
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    Global collision-risk hotspots of marine traffic and the world’s largest fish, the whale shark (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-08-15
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Womersley, F. C., Humphries, N. E., Queiroz, N., Vedor, M., da Costa, I., Furtado, M., Tyminski, J. P., Abrantes, K., Araujo, G., Bach, S. S., Barnett, A., Berumen, M. L., Bessudo Lion, S., Braun, C. D., Clingham, E., Cochran, J. E. M., de la Parra, R., Diamant, S., Dove, A. D. M., Dudgeon, C. L., Erdmann, M. V., Espinoza, E., Fitzpatrick, R., González Cano, J., Green, J. R., Guzman, H. M., Hardenstine, R., Hasan, A., Hazin, F. H. V., Hearn, A. R., Hueter, R. E., Jaidah, M. Y., Labaja, J., Ladinol, F., Macena, B. C. L., Morris Jr., J. J., Norman, B. M., Peñaherrera-Palmav, C., Pierce, S. J., Quintero, L. M., Ramırez-Macías, D., Reynolds, S. D., Richardson, A. J., Robinson, D. P., Rohner, C. A., Rowat, D. R. L., Sheaves, M., Shivji, M. S., Sianipar, A. B., Skomal, G. B., Soler, G., Syakurachman, I., Thorrold, S. R., Webb, D. H., Wetherbee, B. M., White, T. D., Clavelle, T., Kroodsma, D. A., Thums, M., Ferreira, L. C., Meekan, M. G., Arrowsmith, L. M., Lester, E. K., Meyers, M. M., Peel, L. R., Sequeira, A. M. M., Eguıluz, V. M., Duarte, C. M., & Sims, D. W. Global collision-risk hotspots of marine traffic and the world’s largest fish, the whale shark. Proceedings of the National Academy of Sciences of the United States of America, 119(20), (2022): e2117440119, https://doi.org/10.1073/pnas.2117440119.
    Description: Marine traffic is increasing globally yet collisions with endangered megafauna such as whales, sea turtles, and planktivorous sharks go largely undetected or unreported. Collisions leading to mortality can have population-level consequences for endangered species. Hence, identifying simultaneous space use of megafauna and shipping throughout ranges may reveal as-yet-unknown spatial targets requiring conservation. However, global studies tracking megafauna and shipping occurrences are lacking. Here we combine satellite-tracked movements of the whale shark, Rhincodon typus, and vessel activity to show that 92% of sharks’ horizontal space use and nearly 50% of vertical space use overlap with persistent large vessel (〉300 gross tons) traffic. Collision-risk estimates correlated with reported whale shark mortality from ship strikes, indicating higher mortality in areas with greatest overlap. Hotspots of potential collision risk were evident in all major oceans, predominantly from overlap with cargo and tanker vessels, and were concentrated in gulf regions, where dense traffic co-occurred with seasonal shark movements. Nearly a third of whale shark hotspots overlapped with the highest collision-risk areas, with the last known locations of tracked sharks coinciding with busier shipping routes more often than expected. Depth-recording tags provided evidence for sinking, likely dead, whale sharks, suggesting substantial “cryptic” lethal ship strikes are possible, which could explain why whale shark population declines continue despite international protection and low fishing-induced mortality. Mitigation measures to reduce ship-strike risk should be considered to conserve this species and other ocean giants that are likely experiencing similar impacts from growing global vessel traffic.
    Description: Funding for data analysis was provided by the UK Natural Environment Research Council (NERC) through a University of Southampton INSPIRE DTP PhD Studentship to F.C.W. Additional funding for data analysis was provided by NERC Discovery Science (NE/R00997/X/1) and the European Research Council (ERC-AdG-2019 883583 OCEAN DEOXYFISH) to D.W.S., Fundação para a Ciência e a Tecnologia (FCT) under PTDC/BIA/28855/2017 and COMPETE POCI-01–0145-FEDER-028855, and MARINFO–NORTE-01–0145-FEDER-000031 (funded by Norte Portugal Regional Operational Program [NORTE2020] under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund–ERDF) to N.Q. FCT also supported N.Q. (CEECIND/02857/2018) and M.V. (PTDC/BIA-COM/28855/2017). D.W.S. was supported by a Marine Biological Association Senior Research Fellowship. All tagging procedures were approved by institutional ethical review bodies and complied with all relevant ethical regulations in the jurisdictions in which they were performed. Details for individual research teams are given in SI Appendix, section 8. Full acknowledgments for tagging and field research are given in SI Appendix, section 7. This research is part of the Global Shark Movement Project (https://www.globalsharkmovement.org).
    Keywords: ship strike ; marine megafauna ; conservation ; movement ecology ; human impact
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    Ciliary flows in corals ventilate target areas of high photosynthetic oxygen production (2022)
    Cell Press
    In:  EPIC3Current Biology, Cell Press, ISSN: 09609822
    Details
    Publication Date: 2022-08-30
    Description: Most tropical corals live in symbiosis with Symbiodiniaceae algae whose photosynthetic production of oxygen (O2) may lead to excess O2 in the diffusive boundary layer (DBL) above the coral surface. When flow is low, cilia-induced mixing of the coral DBL is vital to remove excess O2 and prevent oxidative stress that may lead to coral bleaching and mortality. Here, we combined particle image velocimetry using O2-sensitive nanoparticles (sensPIV) with chlorophyll (Chla)-sensitive hyperspectral imaging to visualize the microscale distribution and dynamics of ciliary flows and O2 in the coral DBL in relation to the distribution of Symbiodiniaceae Chla in the tissue of the reef building coral, Porites lutea. Curiously, we found an inverse relation between O2 in the DBL and Chla in the underlying tissue, with patches of high O2 in the DBL above low Chla in the underlying tissue surrounding the polyp mouth areas and pockets of low O2 concentrations in the DBL above high Chla in the coenosarc tissue connecting neighboring polyps. The spatial segregation of Chla and O2 is related to ciliary-induced flows, causing a lateral redistribution of O2 in the DBL. In a 2D transport-reaction model of the coral DBL, we show that the enhanced O2 transport allocates parts of the O2 surplus to areas containing less chla, which minimizes oxidative stress. Cilary flows thus confer a spatially complex mass transfer in the coral DBL, which may play an important role in mitigating oxidative stress and bleaching in corals.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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    Phosphonate production by marine microbes: exploring new sources and potential function (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-06-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Acker, M., Hogle, S. L., Berube, P. M., Hackl, T., Coe, A., Stepanauskas, R., Chisholm, S. W., & Repeta, D. J. Phosphonate production by marine microbes: exploring new sources and potential function. Proceedings of the National Academy of Sciences of the United States of America, 119(11), (2022): e2113386119, https://doi.org/10.1073/pnas.2113386119.
    Description: Phosphonates are organophosphorus metabolites with a characteristic C-P bond. They are ubiquitous in the marine environment, their degradation broadly supports ecosystem productivity, and they are key components of the marine phosphorus (P) cycle. However, the microbial producers that sustain the large oceanic inventory of phosphonates as well as the physiological and ecological roles of phosphonates are enigmatic. Here, we show that phosphonate synthesis genes are rare but widely distributed among diverse bacteria and archaea, including Prochlorococcus and SAR11, the two major groups of bacteria in the ocean. In addition, we show that Prochlorococcus can allocate over 40% of its total cellular P-quota toward phosphonate production. However, we find no evidence that Prochlorococcus uses phosphonates for surplus P storage, and nearly all producer genomes lack the genes necessary to degrade and assimilate phosphonates. Instead, we postulate that phosphonates are associated with cell-surface glycoproteins, suggesting that phosphonates mediate ecological interactions between the cell and its surrounding environment. Our findings indicate that the oligotrophic surface ocean phosphonate pool is sustained by a relatively small fraction of the bacterioplankton cells allocating a significant portion of their P quotas toward secondary metabolism and away from growth and reproduction.
    Description: This work was supported in part by grants from the NSF (OCE-1153588 and DBI-0424599 to S.W.C.; OCE-1335810 and OIA-1826734 to R.S.; and OCE-1634080 to D.J.R.), the Gordon and Betty Moore Foundation (no. 6000 to D.J.R.), and the Simons Foundation (Life Sciences Project Award IDs 337262 and 647135 to S.W.C.; 510023 to R.S.; and Simons Collaboration on Ocean Processes and Ecology [SCOPE] Award ID 329108 to S.W.C. and D.J.R.).
    Keywords: phosphonate ; Prochlorococcus ; marine ; biogeochemistry ; phosphorus
    Repository Name: Woods Hole Open Access Server
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    The Earth BioGenome Project 2020: starting the clock (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lewin, H. A., Richards, S., Lieberman Aiden, E., Allende, M. L., Archibald, J. M., Bálint, M., Barker, K. B., Baumgartner, B., Belov, K., Bertorelle, G., Blaxter, Mark L., Cai, J., Caperello, N. D., Carlson, K., Castilla-Rubio, J. C., Chaw, S-M., Chen, L., Childers, A. K., Coddington, J. A., Conde, D. A., Corominas, M., Crandall, K. A., Crawford, A. J., DiPalma, F., Durbin, R., Ebenezer, T. E., Edwards, S. V., Fedrigo, O., Flicek, P., Formenti, G., Gibbs, R. A., Gilbert, M. Thomas P., Goldstein, M. M., Graves, J. M., Greely, H. T., Grigoriev, I. V., Hackett, K. J., Hall, N., Haussler, D., Helgen, K. M., Hogg, C. J., Isobe, S., Jakobsen, K. S., Janke, A., Jarvis, E. D., Johnson, W. E., Jones, S. J. M., Karlsson, E. K., Kersey, P. J., Kim, J-H., Kress, W. J., Kuraku, S., Lawniczak, M. K. N., Leebens-Mack, J. H., Li, X., Lindblad-Toh, K., Liu, X., Lopez, J. V., Marques-Bonet, T., Mazard, S., Mazet, J. A. K., Mazzoni, C. J., Myers, E. W., O’Neill, R. J., Paez, S., Park, H., Robinson, G. E., Roquet, C., Ryder, O. A., Sabir, J. S. M., Shaffer, H. B., Shank, T. M., Sherkow, J. S., Soltis, P. S., Tang, B., Tedersoo, L., Uliano-Silva, M., Wang, K., Wei, X., Wetzer, R., Wilson, J. L., Xu, X., Yang, H., Yoder, A. D., Zhang, G. The Earth BioGenome Project 2020: starting the clock. Proceedings of the National Academy of Sciences of the United States of America, 119(4), (2022): e2115635118, https://doi.org/10.1073/pnas.2115635118.
    Description: November 2020 marked 2 y since the launch of the Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across all aspects of the EBP roadmap, as outlined in the 2018 article describing the project’s goals, strategies, and challenges (1). The launch phase has ended and the clock has started on reaching the EBP’s major milestones. This Special Feature explores the many facets of the EBP, including a review of progress, a description of major scientific goals, exemplar projects, ethical legal and social issues, and applications of biodiversity genomics. In this Introduction, we summarize the current status of the EBP, held virtually October 5 to 9, 2020, including recent updates through February 2021. References to the nine Perspective articles included in this Special Feature are cited to guide the reader toward deeper understanding of the goals and challenges facing the EBP.
    Repository Name: Woods Hole Open Access Server
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    Thelazia callipaeda (2021)
    Cell Press
    Details
    Publication Date: 2021-03-01
    Print ISSN: 1471-4922
    Electronic ISSN: 1471-5007
    Topics: Biology , Medicine
    Published by Cell Press
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    Influence of Platform Characteristics on Purchase Intention in Social Commerce: Mechanism of Psychological Contracts (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-01-01
    Electronic ISSN: 0718-1876
    Topics: Economics
    Published by Molecular Diversity Preservation International
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    Editorial: Electronic Commerce in the Time of Covid-19 - Perspectives and Challenges (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-01-01
    Electronic ISSN: 0718-1876
    Topics: Economics
    Published by Molecular Diversity Preservation International
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  • 39
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    How Individual Investors React to Negative Events in the FinTech Era? Evidence from China’s Peer-to-Peer Lending Market (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-01-01
    Electronic ISSN: 0718-1876
    Topics: Economics
    Published by Molecular Diversity Preservation International
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  • 40
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    Social Recommendations for Facebook Brand Pages (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-01-01
    Electronic ISSN: 0718-1876
    Topics: Economics
    Published by Molecular Diversity Preservation International
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  • 41
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    Roles and Capabilities of Enterprise Architecture in Big Data Analytics Technology Adoption and Implementation (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-01-01
    Electronic ISSN: 0718-1876
    Topics: Economics
    Published by Molecular Diversity Preservation International
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    Indicators of Website Features in the User Experience of E-Tourism Search and Metasearch Engines (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-01-01
    Electronic ISSN: 0718-1876
    Topics: Economics
    Published by Molecular Diversity Preservation International
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  • 43
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    Kadomtsev–Petviashvili Hierarchy: Negative Times (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-08-20
    Description: The Kadomtsev–Petviashvili equation is known to be the leading term of a semi-infinite hierarchy of integrable equations with evolutions given by times with positive numbers. Here, we introduce new hierarchy directed to negative numbers of times. The derivation of such systems, as well as the corresponding hierarchy, is based on the commutator identities. This approach enables introduction of linear differential equations that admit lifts up to nonlinear integrable ones by means of the special dressing procedure. Thus, one can construct not only nonlinear equations, but corresponding Lax pairs as well. The Lax operator of this evolution coincides with the Lax operator of the “positive” hierarchy. We also derive (1 + 1)-dimensional reductions of equations of this hierarchy.
    Electronic ISSN: 2227-7390
    Topics: Mathematics
    Published by Molecular Diversity Preservation International
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    The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-08-20
    Description: Among industrially important pyridoxal-5’-phosphate (PLP)-dependent transaminases of fold type IV D-amino acid transaminases are the least studied. However, the development of cascade enzymatic processes, including the synthesis of D-amino acids, renewed interest in their study. Here, we describe the identification, biochemical and structural characterization of a new D-amino acid transaminase from Haliscomenobacter hydrossis (Halhy). The new enzyme is strictly specific towards D-amino acids and their keto analogs; it demonstrates one of the highest rates of transamination between D-glutamate and pyruvate. We obtained the crystal structure of the Halhy in the holo form with the protonated Schiff base formed by the K143 and the PLP. Structural analysis revealed a novel set of the active site residues that differ from the key residues forming the active sites of the previously studied D-amino acids transaminases. The active site of Halhy includes three arginine residues, one of which is unique among studied transaminases. We identified critical residues for the Halhy catalytic activity and suggested functions of the arginine residues based on the comparative structural analysis, mutagenesis, and molecular modeling simulations. We suggested a strong positive charge in the O-pocket and the unshaped P-pocket as a structural code for the D-amino acid specificity among transaminases of PLP fold type IV. Characteristics of Halhy complement our knowledge of the structural basis of substrate specificity of D-amino acid transaminases and the sequence-structure-function relationships in these enzymes.
    Electronic ISSN: 1420-3049
    Topics: Chemistry and Pharmacology
    Published by Molecular Diversity Preservation International
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    Implications of Innate Immunity in Post-Acute Sequelae of Non-Persistent Viral Infections (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-08-19
    Description: Non-persistent viruses classically cause transient, acute infections triggering immune responses aimed at the elimination of the pathogen. Successful viruses evolved strategies to manipulate and evade these anti-viral defenses. Symptoms during the acute phase are often linked to dysregulated immune responses that disappear once the patient recovers. In some patients, however, symptoms persist or new symptoms emerge beyond the acute phase. Conditions resulting from previous transient infection are termed post-acute sequelae (PAS) and were reported for a wide range of non-persistent viruses such as rota-, influenza- or polioviruses. Here we provide an overview of non-persistent viral pathogens reported to be associated with diverse PAS, among them chronic fatigue, auto-immune disorders, or neurological complications and highlight known mechanistic details. Recently, the emergence of post-acute sequelae of COVID-19 (PASC) or long COVID highlighted the impact of PAS. Notably, PAS of non-persistent infections often resemble symptoms of persistent viral infections, defined by chronic inflammation. Inflammation maintained after the acute phase may be a key driver of PAS of non-persistent viruses. Therefore, we explore current insights into aberrant activation of innate immune signaling pathways in the post-acute phase of non-persistent viruses. Finally, conclusions are drawn and future perspectives for treatment and prevention of PAS are discussed.
    Electronic ISSN: 2073-4409
    Topics: Biology
    Published by Molecular Diversity Preservation International
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    Evaluation of Dispersion of Lead-Bearing Mine Wastes in Kabwe District, Zambia (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-08-20
    Description: Dispersion of lead (Pb) in mine wastes was simulated for reproducing Pb contamination of soil in Kabwe District, Zambia. Local weather data of year 2019 were monitored in situ and used for the simulations. The plume model, weak puff model, and no puff model were adopted for calculation of Pb dispersion under different wind conditions. The results showed that Pb dispersion from the Kabwe mine was directly affected by wind directions and speeds in the dry season, although it was not appreciably affected in the rainy season. This may be because the source strength is lower in the rainy season due to higher water content of the surface. This indicates that Pb dispersion patterns depend on the season. In addition, the distribution of the amount of deposited Pb-bearing soils around the mine corresponded to the distribution of Pb contents in soils. These results suggest that Pb contamination in soils primarily results from dispersion of fine mine wastes.
    Electronic ISSN: 2075-163X
    Topics: Geosciences
    Published by Molecular Diversity Preservation International
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  • 47
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    Electrical Stress on the Medium Voltage Medium Frequency Transformer (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-08-19
    Description: This paper proposes an equivalent circuit model to obtain the transient electrical stress quantitatively in medium voltage medium frequency transformers in modern power electronics. To verify this model, transient simulation is performed on a 1.5 kV/1 kHz transformer, revealing voltage overshoot quantitatively between turns and layers of the transformer’s HV winding. Effects of rise time of the input pulse voltage, stray capacitance of the winding insulation, and their interactions on the voltage overshot magnitude are presented. With these results, we propose limiting the voltage overshoot and, thereafter, enhancing medium voltage medium frequency transformer’s insulation capability, which throws light on the transformer’s insulation design. Additionally, guidance on the future studies on aging and endurance lifetime of the medium voltage medium frequency transformer’s insulation could be given.
    Electronic ISSN: 1996-1073
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by Molecular Diversity Preservation International
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  • 48
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    Strengthening Solutions for Deep Reinforced Concrete Beam with Cutout Opening (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: Since reinforced concrete (RC) buildings have long service life, cutout openings are generally needed in their load-bearing walls as a sustainable solution in order to meet new requirements of their users. However, the cutout openings decrease the load-bearing capacity of the walls, which may result in the failure of the buildings. In this paper, we investigate the possibility of making a door opening in a load-bearing RC wall of an existing building in Gävle in Sweden. The wall studied in the current paper rests on two individual supports at its two ends; thus, it is considered as a deep beam. However, it is called an examined wall (EW) here. The StruSoft FEM-Design software is used in this study to model, analyze, and design the building based on the Eurocodes and Swedish national annex. The potential need for the EW to be strengthened when the cutout opening is made is also evaluated. It is concluded that strengthening the EW with cutout opening is needed. Different strengthening solutions are proposed for the EW. Moreover, the situation of the EW with the solutions is assessed with regard to the utilization ratio, deflection, and weight. Consequently, it is demonstrated that the proposed strengthening solutions function well for the EW.
    Electronic ISSN: 2075-5309
    Topics: Architecture, Civil Engineering, Surveying
    Published by Molecular Diversity Preservation International
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    Electrochemical implications of modulating the solvation shell around redox active organic species in aqueous organic redox flow batteries (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Organic and organometallic reactants in aqueous electrolytes, being composed of earth-abundant elements, are promising redox active candidates for cost-effective organic redox flow batteries (ORFBs). Various compounds of ferrocene and methyl viologen have been examined as promising redox actives for this application. Herein, we examined the influence of the electrolyte pH and the salt anion on model redox active organic cations, bis((3-trimethylammonio) propyl)- ferrocene dichloride (BTMAP-Fc) and bis(3-trimethylammonio) propyl viologen tetrachloride (BTMAP-Vi), which have exhibited excellent cycling stability and capacity retention at ≥1.00 M concentration [E. S. Beh, et al. ACS Energy Lett. 2, 639–644 (2017)]. We examined the solvation shell around BTMAP-Fc and BTMAP-Vi at acidic and neutral pH with SO42-, Cl−, and CH3SO3− counterions and elucidated their impact on cation diffusion coefficient, first electron transfer rate constant, and thereby the electrochemical Thiele modulus. The electrochemical Thiele modulus was found to be exponentially correlated with the solvent reorganizational energy (λ) in both neutral and acidic pH. Thus, λ is proposed as a universal descriptor and selection criteria for organic redox flow battery electrolyte compositions. In the specific case of the BTMAP-Fc/BTMAP-Vi ORFB, low pH electrolytes with methanesulfonate or chloride counterions were identified as offering the best balance of transport and kinetic requirements.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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    Review of the Potential of Consumer Neuroscience for Aroma Marketing and Its Importance in Various Segments of Services (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-08-19
    Description: In the current era of a strongly competitive business environment, it is more difficult for companies to attract customers. Consumer neuroscience has growing potential here, as it reveals internal consumer preferences by using innovative methods and tools, which can effectively examine consumer behavior and attract new customers. In particular, smell has a great ability to subconsciously influence customers and, thus, support profitability. This paper examines the importance of consumer neuroscience and its modern technologies used for exploring human perceptions to influence customers and benefit from the aromatization of business spaces. We focused our analysis on various service sectors. Despite the potential of the examined issue, there are a limited number of studies in the field of service providers that use neuroscience tools to examine the effect of aromas on human emotions. Most studies took place in laboratory conditions, and the used methodological procedures varied widely. Our analysis showed that, in spite of the positive impact of aromatization in the majority of aromatized spaces, service companies still do not use the potential of consumer neuroscience and aroma marketing to a sufficient degree. Innovative methods and tools, in particular, are still very underused.
    Electronic ISSN: 2076-3417
    Topics: Natural Sciences in General
    Published by Molecular Diversity Preservation International
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    Measuring Ocean Surface Current in the Kuroshio Region Using Gaofen-3 SAR Data (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-08-20
    Description: The Kuroshio is the strongest warm current in the western North Pacific, which plays a crucial role in climate and human activities. In terms of this, the accurate acquisition of ocean surface current velocity and direction in the Kuroshio region is of great research value. Gaofen-3 synthetic aperture radar (SAR) provides data support for the study of ocean surface current measurements in the Kuroshio region, but no relevant experimental result has been published yet. In this paper, four available stripmap mode SARs’ data acquired by Gaofen-3 in the Kuroshio region are used for measuring the ocean surface current field. In general, the Doppler centroid anomaly (DCA) estimation is a common method to infer ocean surface currents from single-antenna stripmap data, but only the radial velocity component can be retrieved. In order to measure current vectors, a novel method combining the sub-aperture processing and the least squares (LS) technology is suggested and demonstrated by applying to the Gaofen-3 SAR data processing. The experiment’s results agree well with model-derived ocean current data, indicating that the Gaofen-3 SAR has the capability to accurately retrieve the ocean surface current field in the Kuroshio region and motivate further research by providing more data.
    Electronic ISSN: 2076-3417
    Topics: Natural Sciences in General
    Published by Molecular Diversity Preservation International
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    An in vivo selection-derived d-peptide for engineering erythrocyte-binding antigens that promote immune tolerance (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-08-20
    Description: When displayed on erythrocytes, peptides and proteins can drive antigen-specific immune tolerance. Here, we investigated a straightforward approach based on erythrocyte binding to promote antigen-specific tolerance to both peptides and proteins. We first identified a robust erythrocyte-binding ligand. A pool of one million fully d-chiral peptides was injected into mice, blood cells were isolated, and ligands enriched on these cells were identified using nano-liquid chromatography–tandem mass spectrometry. One round of selection yielded a murine erythrocyte-binding ligand with an 80 nM apparent dissociation constant, Kd. We modified an 83-kDa bacterial protein and a peptide antigen derived from ovalbumin (OVA) with the identified erythrocyte-binding ligand. An administration of the engineered bacterial protein led to decreased protein-specific antibodies in mice. Similarly, mice given the engineered OVA-derived peptide had decreased inflammatory anti-OVA CD8+ T cell responses. These findings suggest that our tolerance-induction strategy is applicable to both peptide and protein antigens and that our in vivo selection strategy can be used for de novo discovery of robust erythrocyte-binding ligands.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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    The trisulfur radical ion S3•− controls platinum transport by hydrothermal fluids (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-08-20
    Description: Platinum group elements (PGE) are considered to be very poorly soluble in aqueous fluids in most natural hydrothermal–magmatic contexts and industrial processes. Here, we combined in situ X-ray absorption spectroscopy and solubility experiments with atomistic and thermodynamic simulations to demonstrate that the trisulfur radical ion S3•− forms very stable and soluble complexes with both PtII and PtIV in sulfur-bearing aqueous solution at elevated temperatures (∼300 °C). These Pt-bearing species enable (re)mobilization, transfer, and focused precipitation of platinum up to 10,000 times more efficiently than any other common inorganic ligand, such as hydroxide, chloride, sulfate, or sulfide. Our results imply a far more important contribution of sulfur-bearing hydrothermal fluids to PGE transfer and accumulation in the Earth’s crust than believed previously. This discovery challenges traditional models of PGE economic concentration from silicate and sulfide melts and provides new possibilities for resource prospecting in hydrothermal shallow crust settings. The exceptionally high capacity of the S3•− ion to bind platinum may also offer new routes for PGE selective extraction from ore and hydrothermal synthesis of noble metal nanomaterials.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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    Anti-Inflammatory Effects of C1q/Tumor Necrosis Factor-Related Protein 3 (CTRP3) in Endothelial Cells (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-08-20
    Description: The C1q/TNF-related protein 3 (CTRP3) represents a pleiotropic adipokine reciprocally associated with obesity and type 2 diabetes mellitus and exhibits anti-inflammatory properties in relation to lipopolysaccharides (LPS)-mediated effects in adipocytes, as well as monocytes/macrophages. Here, we focused on the influence of CTRP3 on LPS-mediated effects in endothelial cells in order to expand the understanding of a possible anti-inflammatory function of CTRP3 in a setting of endotoxemia. An organ- and tissue-specific expression analysis by real-time PCR revealed a considerable Ctrp3 expression in various adipose tissue compartments; however, higher levels were detected in the aorta and in abundantly perfused tissues (bone marrow and the thyroid gland). We observed a robust Ctrp3 expression in primary endothelial cells and a transient upregulation in murine endothelial (MyEND) cells by LPS (50 ng/mL). In MyEND cells, CTRP3 inhibited the LPS-induced expression of interleukin (Il)-6 and the tumor necrosis factor (Tnf)-α, and suppressed the LPS-dependent expression of the major endothelial adhesion molecules Vcam-1 and Icam-1. The LPS-induced adhesion of monocytic cells to an endothelial monolayer was antagonized by CTRP3. In C57BL/6J mice with an LPS-induced systemic inflammation, exogenous CTRP3 did not affect circulating levels of TNF-α, ICAM-1, and VCAM-1. In conclusion, we characterized CTRP3 beyond its function as an adipokine in a setting of vascular inflammation. CTRP3 inhibited LPS-induced endothelial expression of adhesion molecules and monocyte cell adhesion, indicating an important vascular anti-inflammatory role for CTRP3 in endotoxemia.
    Electronic ISSN: 2073-4409
    Topics: Biology
    Published by Molecular Diversity Preservation International
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    Steam Explosion-Assisted Extraction of Protein from Fish Backbones and Effect of Enzymatic Hydrolysis on the Extracts (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-08-20
    Description: The development of an efficient pretreatment, prior to enzymatic hydrolysis, is a good strategy for the sustainable use of refractory fish byproducts. This study compared hydrothermal pretreatments at 159 °C for 2 min, followed by water extraction (steam explosion-assisted extraction, SE) and 121 °C for 70 min (hot-pressure extraction, HPE), for the recovery of proteins from fish backbones. The effect of enzymatic hydrolysis on the properties of the obtained fish bone protein (FBP) was also evaluated. The results demonstrated that FBP had high contents of protein (81.09–84.88 g/100 g) and hydroxyproline (70–82 residues/1000 residues). After hydrolysis with Flavourzyme, for 3 h, the FBP hydrolysates that were pretreated with SE (SFBP-H) exhibited a better degree of hydrolysis (DH) and nitrogen recovery (NR), and a higher level of umami taste free amino acids (151.50 mg/100 mL), compared with the HPE-treated samples. The obtained SFBP-H mainly distributed below 3000 Da and had strong scavenging effects on 1,1-diphenyl-2-picrylhydrazy (DPPH) (IC50 = 4.24 mg/mL) and 2,2-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) (IC50 = 1.93 mg/mL) radicals. Steam explosion-assisted extraction is a promising route for recovering proteins from native fish bone materials, and improving the flavor and antioxidant activity of the hydrolysates.
    Electronic ISSN: 2304-8158
    Topics: Chemistry and Pharmacology
    Published by Molecular Diversity Preservation International
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    Investigations on the Effects of Different Calcium Supply Exceeding the Requirements on Mineral Serum Concentrations and Bone Metabolism in Young Warmblood Stallions (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-19
    Description: Since mineral supplements for horses commonly contain macro minerals, although the requirement for such is usually covered by roughage-based diets, the aim of this study was to investigate the effects of different dietary calcium levels on mineral serum concentrations and bone metabolism. The trial was conducted in 30 young warmblood stallions (2–3 years) that were divided into two groups for a five-month feeding trial. The groups were fed a hay- and oat-based diet and were either supplied with high (Ca-High) or moderate (Ca-Moderate) calcium excess. While in Ca-High calcium supply was about 2–2.5-fold of the requirement, in Ca-Moderate calcium requirements were slightly surpassed (1.5–1.6-fold). In order to monitor the effects of the different calcium supply, blood samples were taken during the trial and analysed for levels of macro and trace elements as well as concentrations of two bone markers. In Ca-Moderate a trend towards higher phosphorus serum levels compared to Ca-High was observed which was significant at the end of the trial (p = 0.0002). Furthermore, results showed no influence of the diet on bone markers. Results support the idea that forage-based rations for horses do not necessarily have to be supplemented with macro minerals but with trace elements.
    Electronic ISSN: 2076-2615
    Topics: Biology , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Molecular Diversity Preservation International
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    Long-Term Impact of COVID-19 on Mental Health among the General Public: A Nationwide Longitudinal Study in China (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: COVID-19 might have long-term mental health impacts. We aim to investigate the longitudinal changes in mental problems from initial COVID-19 peak to its aftermath among general public in China. Depression, anxiety and insomnia were assessed among a large-sample nationwide cohort of 10,492 adults during the initial COVID-19 peak (28 February 2020 to 11 March 2020) and its aftermath (8 July 2020 to 8 August 2020) using the Patient Health Questionnaire-9, Generalized Anxiety Disorder-7, and Insomnia Severity Index. We used generalized estimating equations and linear mixed models to explore factors associated with long-term mental health symptoms during COVID-19. During the five months, mental health symptoms remained consistently elevated (baseline 46.4%; follow-up 45.1%). Long-term depression, anxiety and insomnia were associated with several personal and work-related factors including quarantine (adjusted OR for any mental health symptoms 1.31, 95%CI 1.22–1.41, p 〈 0.001), increases in work burden after resuming work (1.77, 1.65–1.90, p 〈 0.001), occupational exposure risk to COVID-19 (1.26, 1.14–1.40, p 〈 0.001) and living in places severely affected by initial COVID-19 peak (1.21, 1.04–1.41, p = 0.01) or by a COVID-19 resurgence (1.38, 1.26–1.50, p 〈 0.001). Compliance with self-protection measures, such as wearing face masks (0.74, 0.61–0.90, p = 0.003), was associated with lower long-term risk of mental problems. The findings reveal a pronounced and prolonged mental health burden from the initial COVID-19 peak through to its aftermath in China. We should regularly monitor the mental health status of vulnerable populations throughout COVID-19.
    Print ISSN: 1661-7827
    Electronic ISSN: 1660-4601
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
    Published by Molecular Diversity Preservation International
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    Low-Cost Air Quality Stations’ Capability to Integrate Reference Stations in Particulate Matter Dynamics Assessment (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-19
    Description: Low-cost air quality stations can provide useful data that can offer a complete picture of urban air quality dynamics, especially when integrated with daily measurements from reference air quality stations. However, the success of such deployment depends on the measurement accuracy and the capability of resolving spatial and temporal gradients within a spatial domain. In this work, an ensemble of three low-cost stations named “AirQino” was deployed to monitor particulate matter (PM) concentrations over three different sites in an area affected by poor air quality conditions. Data of PM2.5 and PM10 concentrations were collected for about two years following a protocol based on field calibration and validation with a reference station. Results indicated that: (i) AirQino station measurements were accurate and stable during co-location periods over time (R2 = 0.5–0.83 and RMSE = 6.4–11.2 μg m−3; valid data: 87.7–95.7%), resolving current spatial and temporal gradients; (ii) spatial variability of anthropogenic emissions was mainly due to extensive use of wood for household heating; (iii) the high temporal resolution made it possible to detect time occurrence and strength of PM10 concentration peaks; (iv) the number of episodes above the 1-h threshold of 90 μg m−3 and their persistence were higher under urban and industrial sites compared to the rural area.
    Electronic ISSN: 2073-4433
    Topics: Geosciences
    Published by Molecular Diversity Preservation International
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    High-Throughput Sequencing to Identify Mutations Associated with Retinal Dystrophies (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: Retinal dystrophies (RD) are clinically and genetically heterogenous disorders showing mutations in over 270 disease-associated genes. Several millions of people worldwide are affected with different types of RD. Studying the relevance of disease-associated sequence alterations will assist in understanding disorders and may lead to the development of therapeutic approaches. Here, we established a whole exome sequencing (WES) pipeline to rapidly identify disease-associated mutations in patients. Sanger sequencing was applied to identify deep-intronic variants and to verify the co-segregation of WES results within families. We analyzed 26 unrelated patients with different syndromic and non-syndromic clinical manifestations of RD. All patients underwent ophthalmic examinations. We identified nine novel disease-associated sequence variants among 37 variants identified in total. The sequence variants located to 17 different genes. Interestingly, two cases presenting with Stargardt disease carried deep-intronic variants in ABCA4. We have classified 21 variants as pathogenic variants, 4 as benign/likely benign variants, and 12 as variants of uncertain significance. This study highlights the importance of WES-based mutation analyses in RD patients supporting clinical decisions, broadly based genetic diagnosis and support genetic counselling. It is essential for any genetic therapy to expand the mutation spectrum, understand the genes’ function, and correlate phenotypes with genotypes.
    Electronic ISSN: 2073-4425
    Topics: Biology
    Published by Molecular Diversity Preservation International
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    Recent Development in the Design of Wind Deflectors for Vertical Axis Wind Turbine: A Review (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: Developments in the design of wind turbines with augmentation are advancing around the globe with the goal of generating electricity close to the user in built-up areas. This is certain to help lessen the power generation load as well as distribution and transmission network costs by reducing the distance between the user and the power source. The main objectives driving the development and advancement of vertical-axis wind turbines are increasing the power coefficient and the torque coefficient by optimizing the upstream wind striking on the rotor blades. Unlike horizontal-axis wind turbines, vertical axis turbines generate not only positive torque but also negative torque during operation. The negative torque generated by the returning blade is a key issue for vertical-axis wind turbines (VAWTs) that is counterproductive. Installation of wind deflectors for flow augmentation helps to reduce the negative torque generated by the returning blades as well as enhance the positive torque by creating a diversion in the upstream wind towards the forwarding blade during operation. This paper reviews various designs, experiments, and CFD simulations of wind deflectors reported to date. Optimization techniques for VAWTs incorporating wind deflectors are discussed in detail. The main focus of the review was on the installation position and orientation of the deflectors and their potential contribution to increasing the power coefficient. Topics for future study are suggested in the conclusion section of the paper.
    Electronic ISSN: 1996-1073
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by Molecular Diversity Preservation International
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    Latin American Origin Is Not Associated with Worse Outcomes among Hospitalized Patients with COVID-19 in a Public Healthcare System (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: Exploring differences in clinical outcomes based on race and origin among patients hospitalized for COVID-19 is a controversial issue. The ALC COVID-19 Registry includes all confirmed COVID-19 patients admitted to hospital from 3 March 2020 to 17 December 2020. The data were obtained from electronic health records in order to evaluate the differences in the clinical features and outcomes among European and Latin American patients. The follow-ups occurred after 156 days. A propensity score weighting (PSW) logistic regression model was used to estimate the odds ratio (OR, 95% CI) for Latin American origin and outcome associations. Of the 696 patients included, 46.7% were women, with a median age of 65 (IQR 53–67) years, 614 (88.2%) were European, and 82 (11.8%) were Latin American. Latin American patients were younger, with fewer comorbidities, and a higher incidence of extensive pneumonia. After adjusting for residual confounders, Latin American origin was not associated with an increased risk of death (PSW OR 0.85 (0.23–3.14)) or with the need for invasive mechanical ventilation (PSW OR 0.35 (0.12–1.03)). Latin American origin was associated with a shorter hospital stay, but without differences in how long the patient remained on mechanical ventilation. In a public healthcare system, the rates of death or mechanical ventilation in severe COVID-19 cases were found to be comparable between patients of European and Latin American origins.
    Electronic ISSN: 2076-2607
    Topics: Biology
    Published by Molecular Diversity Preservation International
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    Analysis of Enhanced Geothermal System Development Scenarios for District Heating and Cooling of the Göttingen University Campus (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-19
    Description: The huge energy potential of Enhanced Geothermal Systems (EGS) makes them perspective sources of non-intermittent renewable energy for the future. This paper focuses on potential scenarios of EGS development in a locally and in regard to geothermal exploration, poorly known geological setting—the Variscan fold-and-thrust belt —for district heating and cooling of the Göttingen University campus. On average, the considered single EGS doublet might cover about 20% of the heat demand and 6% of the cooling demand of the campus. The levelized cost of heat (LCOH), net present value (NPV) and CO2 abatement cost were evaluated with the help of a spreadsheet-based model. As a result, the majority of scenarios of the reference case are currently not profitable. Based on the analysis, EGS heat output should be at least 11 MWth (with the brine flow rate being 40 l/s and wellhead temperature being 140 °C) for a potentially profitable project. These parameters can be a target for subsurface investigation, reservoir modeling and hydraulic stimulation at a later stage. However, sensitivity analysis presented some conditions that yield better results. Among the most influential parameters on the outcome are subsidies for research wells, proximity to the campus, temperature drawdown and drilling costs. If realized, the EGS project in Göttingen might save up to 18,100 t CO2 (34%) annually.
    Electronic ISSN: 2076-3263
    Topics: Geosciences
    Published by Molecular Diversity Preservation International
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    Does Transport Infrastructure Inequality Matter for Economic Growth? Evidence from China (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: Transport infrastructure (TI) plays a crucial role in socioeconomic development. The increase of TI inequality, an all-pervading phenomenon in both developed and developing countries, has been an obstacle to sustainable economic growth. The relationship between TI inequality and economic growth has attracted considerable interest over the past three decades. However, the relationship remains obscure, and people find it impossible to utilize to develop economies. This study collected a panel of empirical data from 1982 to 2015 from China to calculate the Gini coefficient and conduct the Granger causality test. The data analysis results show that TI inequality is not always conducive to economic growth. A softening TI inequality helps address the issues of uneven economic growth across regions in the long term. The short-term effects of improving TI inequality at the national level are reflected in the network effect. In addition, the “social filters” facilitate the region to absorb the economic benefits brought by the improvement of TI inequality. These findings offer a way to address the increase of TI inequality and shed light on the ways to improve transport investment from the perspective of economic growth.
    Electronic ISSN: 2073-445X
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Molecular Diversity Preservation International
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    Resilience through climate services (2021)
    Cell Press
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    Publication Date: 2021-08-01
    Electronic ISSN: 2590-3322
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Geosciences
    Published by Cell Press
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    When early warning is not enough (2021)
    Cell Press
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    Publication Date: 2021-08-01
    Electronic ISSN: 2590-3322
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Geosciences
    Published by Cell Press
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    Food Safety of Consuming Black Soldier Fly (Hermetia illucens) Larvae: Microbial, Heavy Metal and Cross-Reactive Allergen Risks (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: Black soldier fly (Hermetia illucens) larvae (BSFL) are a promising, sustainable source of nutrients, however, there is limited knowledge regarding the food safety of consuming BSFL. This study determined the safety of consuming BSFL for direct human consumption in terms of microbial, heavy metal and allergen content. Microbial counts were determined using ISO (International Organization for Standardization) methods, heavy metals were determined using inductively coupled plasma mass spectrometry and allergens were determined via Orbitrap mass spectrometry and ELISA (enzyme-linked immunosorbent assay) kits. Feed and killing method influenced the presence of Bacillus cereus (p = 0.011), and only the killing method influenced Escherichia coli (p 〈 0.00) and total viable count (TVC) (p 〈 0.00). Blanching resulted in a 3-log reduction in E. coli and a 3.4 log reduction in the TVC counts. Salmonella spp. and Listeria spp. were not detected in the BSFL samples. Heavy metals were detected although they were below maximum legal limits. Cross-reactive allergens, tropomyosin and arginine kinase, were detected in the BSFL samples, although the clinical significance requires research. The feed fed to the BSFL and blanching were found to influence the safety of consuming BSFL, highlighting the importance of incorporating sufficient decontamination steps, such as blanching, to ensure food safety.
    Electronic ISSN: 2304-8158
    Topics: Chemistry and Pharmacology
    Published by Molecular Diversity Preservation International
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    Perception of the Movement Control Order during the COVID-19 Pandemic: A Qualitative Study in Malaysia (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: Malaysia implemented its first Movement Control Order (MCO) during the early phase of the COVID-19 pandemic to slow the transmission of the virus. This study aimed to explore the public perception of the MCO implementation and people’s experiences during this period. The study employed qualitative explorative in-depth interviews conducted with 23 Malaysian adults from various demographic backgrounds. Thematic analysis was performed using NVivo 12. Three main themes were identified: a period of information surge, heterogeneous emotional response, and attempts to adapt. During the MCO, the participants obtained information from multiple platforms. They suggested the need for clear and repeated instructions to avoid confusion and misinformation. They also acknowledged the importance of the MCO in breaking the chain of transmission and safeguarding high-risk groups; however, they also expressed that stricter enforcement from the authorities was warranted. The changes in the participants’ work–life routines, lack of physical interaction, and uncertainty about their health and the economy due to the MCO negatively impacted their psychological states. Despite these challenges, the participants attempted to adapt to life under the MCO in different ways. The findings imply that during a crisis, the public tends to seek clear and reliable information, experience emotional turmoil, and adapt to changes. The MCO implementation can be improved through an effective communication strategy and efforts to battle misinformation.
    Print ISSN: 1661-7827
    Electronic ISSN: 1660-4601
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
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    Functional Neurorehabilitation in Dogs with an Incomplete Recovery 3 Months following Intervertebral Disc Surgery: A Case Series (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-19
    Description: This case series study aimed to evaluate the safety, feasibility, and positive outcome of the neurorehabilitation multimodal protocol (NRMP) in 16 chronic post-surgical IVDD Hansen type I dogs, with OFS 0/DPP− (n = 9) and OFS 1/DPP+ (n = 7). All were enrolled in the NRMP for a maximum of 90 days and were clinically discharged after achieving ambulation. The NRMP was based on locomotor training, functional electrical stimulation, transcutaneous electrical spinal cord stimulation, and 4-aminopyridine (4-AP) pharmacological management. In the Deep Pain Perception (DPP)+ dogs, 100% recovered ambulation within a mean period of 47 days, reaching OFS ≥11, which suggests that a longer period of time is needed for recovery. At follow-up, all dogs presented a positive evolution with voluntary micturition. Of the DPP− dogs admitted, all achieved a flexion/extension locomotor pattern within 30 days, and after starting the 4-AP, two dogs were discharged at outcome day 45, with 78% obtaining Spinal Reflex Locomotion (SRL) and automatic micturition within a mean period of 62 days. At follow-up, all dogs maintained their neurological status. After the NRMP, ambulatory status was achieved in 88% (14/16) of dogs, without concurrent events. Thus, an NRMP may be an important therapeutic option to reduce the need for euthanasia in the clinical setting.
    Electronic ISSN: 2076-2615
    Topics: Biology , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Molecular Diversity Preservation International
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    In service of resilience (2021)
    Cell Press
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    Publication Date: 2021-08-01
    Electronic ISSN: 2590-3322
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Geosciences
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    Ultimate Compressive Strains and Reserves of Bearing Capacity of Short RC Columns with Basalt Fiber (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-19
    Description: Increasing the bearing capacity of reinforced concrete structures, reducing material consumption, and ensuring quality are critical in modern construction. The article presents an experimental study of the ultimate compressive strains of short fiber basalt reinforced concrete columns and provides recommendations for increasing the bearing capacity using steel reinforcement bars with greater strength. The columns were tested in an upright position using a hydraulic press. Strains were measured with dial indicators and a strain gauge station. It was shown that the addition of 10% coarse basalt fiber increased the ultimate compressibility of concrete on ordinary crushed stone by 19.8%, and expanded clay concrete by 26.1%, which led to the strain hardening of concrete under compression by 9.0% and 12%, respectively. Ultimate compressive strains in fiber-reinforced concrete short columns with combined reinforcement increased 1.42 times in columns on a lightweight aggregate and 1.19 times on heavy aggregate. An increase in the ultimate compressibility of concrete makes it possible to use steel reinforcement with greater strength in compressed elements as the concrete crushing during compression occurs primarily due to the reaching of critical values by tensile stresses in the transverse direction. This makes it possible to manufacture structures with a higher load-bearing capacity and less material consumption. A practical example of the application of the proposed approach is given.
    Electronic ISSN: 2076-3417
    Topics: Natural Sciences in General
    Published by Molecular Diversity Preservation International
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    Optimization of the Process Parameters of an Air-Screen Cleaning System for Frozen Corn Based on the Response Surface Method (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-08-19
    Description: The threshing of frozen corn is accompanied by breakage and adherence, which influence the cleaning performance when the corn-cleaning mixture is separated and cleaned. In order to reduce the impurity ratio and loss ratio during frozen corn cleaning and provide theoretical support for frozen corn combine harvesting, this study employed a self-made air-screen cleaning system with adjustable parameters. The optimal process parameters of frozen corn cleaning were determined by using the response surface method (RSM). The influences of the fan speed (FS), vibrational frequency (VF), and screen opening (SO) on the cleaning performance were explored. The results showed that all three process parameters had significant effects on the impurity ratio (IR) and loss ratio (LR). The fan speed had the most significant impact. The cleaning performance was optimal when the fan speed was 102.7 rad/s, the vibration frequency was 6.42 Hz, and the screen opening was 21.9 mm, corresponding to a 0.80% impurity ratio and a 0.61% loss ratio. The predicted values of the regression models were consistent with the experimental results with a relative error of less than 5%. The reliability and accuracy of regression models were established and confirmed.
    Electronic ISSN: 2077-0472
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Molecular Diversity Preservation International
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    The Prevalence and Factors Associated with Prophylactic Antibiotic Use during Delivery: A Hospital-Based Retrospective Study in Palembang, Indonesia (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-19
    Description: Prophylactic antibiotic usage during delivery is a common practice worldwide, especially in low- to middle-income countries. Guidelines have been published to reduce antibiotic overuse; however, data describing the use of prophylactic antibiotics and clinician adherence to guidelines in low- to middle-income countries remain limited. This study aimed to describe the prevalence of prophylactic antibiotic use, factors associated with its use, and clinician adherence to guidelines. A retrospective review was conducted for all deliveries from 1 January 2016 to 31 December 2018 at a tertiary level hospital in Indonesia. The prevalence of prophylactic antibiotic use during delivery was 47.1%. Maternal education level, Ob/Gyn specialist-led delivery, a history of multiple abortions, C-section, premature membrane rupture, and antepartum hemorrhage were independently associated with prophylactic antibiotic use. Clinician adherence to the guidelines was 68.9%. Adherence to guidelines was the lowest in conditions where the patient had only one indication for prophylactic antibiotics (aOR 0.36, 95% CI 0.24–0.54). The findings showed that the prevalence of prophylactic antibiotic use during delivery was moderate to high. Adherence to local guidelines was moderate. Updating the local prescribing guidelines may improve clinician adherence.
    Electronic ISSN: 2079-6382
    Topics: Chemistry and Pharmacology , Medicine
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    Latest Insights on Novel Deep Eutectic Solvents (DES) for Sustainable Extraction of Phenolic Compounds from Natural Sources (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-19
    Description: Phenolic compounds have long been of great importance in the pharmaceutical, food, and cosmetic industries. Unfortunately, conventional extraction procedures have a high cost and are time consuming, and the solvents used can represent a safety risk for operators, consumers, and the environment. Deep eutectic solvents (DESs) are green alternatives for extraction processes, given their low or non-toxicity, biodegradability, and reusability. This review discusses the latest research (in the last two years) employing DESs for phenolic extraction, solvent components, extraction yields, extraction method characteristics, and reviewing the phenolic sources (natural products, by-products, wastes, etc.). This work also analyzes and discusses the most relevant DES-based studies for phenolic extraction from natural sources, their extraction strategies using DESs, their molecular mechanisms, and potential applications.
    Electronic ISSN: 1420-3049
    Topics: Chemistry and Pharmacology
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    The Antimicrobial Activity of Omiganan Alone and In Combination against Candida Isolated from Vulvovaginal Candidiasis and Bloodstream Infections (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-19
    Description: Fungi from the Candida genus are widespread commensals and, at the same time, are the leading cause of fungal infections worldwide. For instance, vulvovaginal candidiasis (VVC) affects approximately 75% of women at least once in their lifetime, remaining the second most common gynecological infection. On the contrary, hospital-acquired fungal bloodstream infections (BSIs), although less frequent, are characterized by a high mortality rate. Undoubtedly, the main reason for this situation are virulence factors that these yeast-like fungi can produce, and the ability to form a biofilm is one of the most important of them.. Due to the low effectiveness of classic antimycotics against Candida biofilms, an intense search for new drugs capable of eradicating this structure is highly demanded. One of the most promising groups of compounds exhibiting such properties are antimicrobial peptides (AMPs). This study focuses on a comparison of the efficacy of Omiganan and fluconazole alone and in combination against Candida strains isolated from BSIs. The obtained results are consistent with our previous reports on the effectiveness of Omiganan against clinical strains isolated from VVC. This is also the first report on the combinatory application of Omiganan in the context of fungal BSI. The majority of combinations with fluconazole showed an additive effect, as well as a synergistic effect in the range of certain concentrations. Importantly, such effects are visible at concentrations much lower than for those compounds used individually. Potentially, this entails the possibility of limiting the adverse effects (e.g., toxicity) of Omiganan and fluconazole applied in vivo, thus improving the safety profile of this particular antifungal therapy.
    Electronic ISSN: 2079-6382
    Topics: Chemistry and Pharmacology , Medicine
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    Another Look into the Relationship between Economic Growth, Carbon Emissions, Agriculture and Urbanization in Thailand: A Frequency Domain Analysis (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-19
    Description: This empirical study assesses the effect of CO2 emissions, urbanization, energy consumption, and agriculture on Thailand’s economic growth using a dataset between 1970 and 2018. The ARDL and the frequency domain causality (FDC) approaches were applied to assess these interconnections. The outcome of the bounds test suggested a long-term association among the variables of investigation. The ARDL outcomes reveal that urbanization, agriculture, energy consumption, and CO2 emissions positively trigger Thailand’s economic growth. Additionally, the frequency domain causality test was used to detect a causal connection between the series. The main benefit of this technique is that it can detect a causal connection between series at different frequencies. To the understanding of the authors, this is the first study in the case of Thailand that will apply the FDC approach to capture the causal linkage between GDP and the regressors. The outcomes of the causality test suggested that CO2 emissions, urbanization, energy consumption, and agriculture can predict Thailand’s economic growth in the long term. These outcomes have far-reaching implications for economic performance and Thailand’s macroeconomic indicators.
    Electronic ISSN: 1996-1073
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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    On the Helminth Fauna of the Muskrat (Ondatra zibethicus (Linnaeus, 1766)) in the Barnim District of Brandenburg State/Germany (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: The muskrat is a neozoon species that has occupied many countries of continental North Europe after its introduction from north America as fur animals. Due to its burrowing activity it damages river and canal banks and structures of flood control. For this reason, the eradication of this alien species is recommended. Muskrats are also of parasitological interest since they can act as suitable intermediate hosts for Echinococcus multilocularis. On the other hand, little is known on the other helminths that infect muskrats. A total of 130 muskrats of different age groups trapped in different habitats in the Barnim district of the Brandenburg state by a professional hunter were examined for parasites and seven trematodes (Echinostoma sp., Notocotylus noyeri, Plagiorchis elegans, Plagiorchis arvicolae, Psilosostoma simillimum, P. spiculigerum, Opisthorchis felineus and four larval cestode species (Hydatigera taeniaeformis, Taenia martis, Taenia polyacantha, Taenia crassiceps) were detected. Larval stages of E. multilocularis were not found. O. felineus was found for the first time in muskrats in Germany. All the named parasites were present in Europe prior to the introduction of muskrats. With a prevalence of 48.9%, Strobilocercus fasciolaris, the larval stage of the cat tapeworm, H. taeniaeformis, was the most frequent parasite found in adult muskrats.
    Electronic ISSN: 2076-2615
    Topics: Biology , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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    C-Type Natriuretic Peptide Ameliorates Vascular Injury and Improves Neurological Outcomes in Neonatal Hypoxic-Ischemic Brain Injury in Mice (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: C-type natriuretic peptide (CNP) is an important vascular regulator that is present in the brain. Our previous study demonstrated the innate neuroprotectant role of CNP in the neonatal brain after hypoxic-ischemic (HI) insults. In this study, we further explored the role of CNP in cerebrovascular pathology using both in vivo and in vitro models. In a neonatal mouse HI brain injury model, we found that intracerebroventricular administration of recombinant CNP dose-dependently reduces brain infarct size. CNP significantly decreases brain edema and immunoglobulin G (IgG) extravasation into the brain tissue, suggesting a vasculoprotective effect of CNP. Moreover, in primary brain microvascular endothelial cells (BMECs), CNP dose-dependently protects BMEC survival and monolayer integrity against oxygen-glucose deprivation (OGD). The vasculoprotective effect of CNP is mediated by its innate receptors NPR2 and NPR3, in that inhibition of either NPR2 or NPR3 counteracts the protective effect of CNP on IgG leakage after HI insult and BMEC survival under OGD. Of importance, CNP significantly ameliorates brain atrophy and improves neurological deficits after HI insults. Altogether, the present study indicates that recombinant CNP exerts vascular protection in neonatal HI brain injury via its innate receptors, suggesting a potential therapeutic target for the treatment of neonatal HI brain injury.
    Print ISSN: 1661-6596
    Electronic ISSN: 1422-0067
    Topics: Chemistry and Pharmacology
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    Psychological Backgrounds of Medically Compromised Patients and Its Implication in Dentistry: A Narrative Review (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: The number of medically compromised dental patients is increasing every year with the increase in the super-aged population. Many of these patients have underlying psychiatric problems and diseases, which need to be recognized by dental professionals for better treatment outcomes. The aim of this narrative review article is to summarize the psychological and psychiatric backgrounds of medically compromised patients who are frequently visited and taken care of by dentists using findings from recent systematic reviews and meta-analyses. Anxiety and symptoms of depression, post-traumatic stress disorders, panic disorders, poor cognitive functions, and poor quality of life were some of the common psychological backgrounds in medically compromised patients. Additionally, the consequences of these psychological problems and the considerations that need to be taken by the dentist while treating these patients have been discussed. Dental professionals should be aware of and recognize the different psychological backgrounds of medically compromised dental patients in order to provide appropriate dental treatment and to prevent oral conditions from worsening.
    Print ISSN: 1661-7827
    Electronic ISSN: 1660-4601
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
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    Modelling the Effect of Salt and PEG on Water Uptake in Wheat Seeds (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: Water uptake is a seminal process in seed germination. Salt and polyethylene glycol (PEG) are known to retard seed germination rates and percentages, which is often attributed to osmotic effects. Here, we quantified water uptake in wheat seeds killed with a hot needle, finding evidence of three distinct water uptake pools. The fast pool was unaffected by salt, and likely represents cell walls and other apoplastic material. Water uptake into the medium and slow pools was slowed by salt addition, with the medium pool thought to be cellular, while the slow pool is presumably related to endosperm hydration. Salt caused a minor decrease in the water uptake rates and maximum seed water content, while PEG strongly suppressed both parameters. Seeds transferred between water and salt solutions followed the water uptake trajectories of the solution into which they were transferred. Seeds transferred from PEG to water achieved final seed water contents similar to water control seeds, while seeds transferred from water to PEG achieved significantly higher final water contents than PEG controls. This work confirms that salt and PEG have distinct effects on water uptake by wheat seeds.
    Electronic ISSN: 2073-4395
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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    PFC Single-Phase AC/DC Boost Converters: Bridge, Semi-Bridgeless, and Bridgeless Topologies (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: Power Factor Correction (PFC) single-phase AC/DC converters are used in several power electronics applications as full wave control rectifiers improving power quality and providing high standards of efficiency. Many papers dealing with the description or use of such topologies have been published in recent years; however, a review that describes and organizes their specific details has not been reported in the technical literature. Therefore, this paper presents an extensive review of PFC single-phase AC/DC converters operating with the Boost converter topology for low and medium voltage as well as and power appliances. A categorization of bridge, semi-bridgeless, and bridgeless, in accordance with the construction characteristics, was carried out in order to unify the technical terminology. Benefits and disadvantages are described and analyzed in detail. Furthermore, a comparison performance in terms of PFC, Total Harmonic Distortion (THD), power capacity, electromagnetic compatibility (EMC), number of elements, and efficiency is included.
    Electronic ISSN: 2076-3417
    Topics: Natural Sciences in General
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    ViTool-BC: Visualization Tool Based on Cooja Simulator for WSN (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: Evaluation and monitoring of wireless sensor networks (WSN) and the parameters defining their operations and design, such as energy consumption, latency, and stability, is a complex task due to interaction with real devices. For greater control of these variables, the use of simulators arises as an alternative. Cooja is a WSN simulator/emulator which handles the devices’ controllers and multiple communication protocol implementations, such as RPL (RPL is one of the most used protocol in IoT). However, Cooja does not consider either the implementation of an energy model (it has infinite energy consumption) nor the visual behavior of the topology construction, although these aspects are crucial for effective network analysis and decision taking. This paper presents the design and the implementation of ViTool-BC, a software built on top of Cooja, which allows the creation of different energy estimation models and also to visualize in real time the behavior of WSN topology construction. In addition, ViTool-BC offers a heat map of energy consumption traces. Therefore, this tool helps researchers to monitor in real time the topology construction, node disconnection, and battery depletion, aspects to be considered in the analysis of the available routing protocols in Cooja.
    Electronic ISSN: 2076-3417
    Topics: Natural Sciences in General
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    SnoRNA in Cancer Progression, Metastasis and Immunotherapy Response (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: Small nucleolar RNA (snoRNA) were one of our earliest recognised classes of non-coding RNA, but were largely ignored by cancer investigators due to an assumption that their activities were confined to the nucleolus. However, as full genome sequences have become available, many new snoRNA genes have been identified, and multiple studies have shown their functions to be diverse. The consensus now is that many snoRNA are dysregulated in cancers, are differentially expressed between cancer types, stages and metastases, and they can actively modify disease progression. In addition, the regulation of the snoRNA class is dominated by the cancer-supporting mTOR signalling pathway, and they may have particular significance to immune cell function and anti-tumour immune responses. Given the recent advent of therapeutics that can target RNA molecules, snoRNA have robust potential as drug targets, either solely or in the context of immunotherapies.
    Electronic ISSN: 2079-7737
    Topics: Biology
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    Climate Change Adaptation Measures in the Irrigation of a Super-Intensive Olive Orchard in the South of Portugal (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: The south of Portugal is one of the regions that will be most affected by the impacts of climate change (CC), with an expected increase in water scarcity. Irrigated super-intensive olive orchards occupy a large area of the used agricultural surface in the Alentejo region, south of Portugal, making it necessary to adapt this crop to the effects of CC. This study assessed the impacts of CC and defined adaptation measures concerning irrigation management of the super-intensive olive orchard. To compute the crop irrigation requirement (CIR), the soil water balance model ISAREG was combined with climate data relative to the reference period 1971–2000 and to the representative concentration pathways RCP4.5 and RCP8.5 for the periods 2011–2040, 2041–2070, and 2071–2100. The growing degree-days (GDD) approach was used to estimate olive phenology for these CC scenarios. Unchanged irrigation management with an average CIR increase up to 16% in RCP4.5 and 31% in RCP8.5 is expected. By adopting higher levels of water deficit, water savings of up to 22% can be realized. The results showed that the anticipated CIR increase for the CC scenarios can be mitigated through regulated deficit irrigation strategies.
    Electronic ISSN: 2073-4395
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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    5-Aminolevulinic Acid Pretreatment Mitigates Drought and Salt Stresses in Poplar Plants (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: 5-aminolevulinic acid (ALA), a key precursor in the biosynthesis of porphyrins, can improve plant tolerance to various environmental stresses. However, it is unclear whether ALA can improve tolerance in poplar. Here, we investigated the effects of ALA on poplars under drought and salt stresses. ALA pretreatment exhibited less morphological damage, reduced leaf malonaldehyde content (MDA) and electrolyte leakage (EL), and increased leaf relative water content (RWC), proline (PRO), superoxide dismutase (SOD), and peroxidase (POD) content under stresses. Furthermore, exogenous ALA mitigated the decrease in photosynthetic capacity, and restored the chlorophyll content (Chl), net CO2 assimilation rate, stomatal conductance (Gs), transpiration rate (Tr), maximal photochemical quantum yield of PSII (Fv/Fm), actual quantum yield of photosynthesis (YII), and electron transfer rate (ETR) of poplar under various stresses. qRT-PCR showed that ALA up-regulated the expression of antiporters and aquaporins genes, which are associated with Na+ exclusion in the leaf cells and the transport activity of aquaporins. In summary, ALA pretreatment significantly improved the stress tolerance of poplar, decreasing the degree of membrane lipid peroxidation and promoting the photosynthesis and antioxidant capacity of leaves. In addition, our results showed that ALA might mediate Na+ transporter and aquaporins activity, thereby increasing the salt tolerance of poplar.
    Electronic ISSN: 1999-4907
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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    Design of an Ultrasound-Navigated Prostate Cancer Biopsy System for Nationwide Implementation in Senegal (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: This paper presents the design of NaviPBx, an ultrasound-navigated prostate cancer biopsy system. NaviPBx is designed to support an affordable and sustainable national healthcare program in Senegal. It uses spatiotemporal navigation and multiparametric transrectal ultrasound to guide biopsies. NaviPBx integrates concepts and methods that have been independently validated previously in clinical feasibility studies and deploys them together in a practical prostate cancer biopsy system. NaviPBx is based entirely on free open-source software and will be shared as a free open-source program with no restriction on its use. NaviPBx is set to be deployed and sustained nationwide through the Senegalese Military Health Service. This paper reports on the results of the design process of NaviPBx. Our approach concentrates on “frugal technology”, intended to be affordable for low–middle income (LMIC) countries. Our project promises the wide-scale application of prostate biopsy and will foster time-efficient development and programmatic implementation of ultrasound-guided diagnostic and therapeutic interventions in Senegal and beyond.
    Electronic ISSN: 2313-433X
    Topics: Computer Science
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    Sphingosine-1-Phosphate Induces ATP Release via Volume-Regulated Anion Channels in Breast Cell Lines (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-19
    Description: High interstitial level of ATP and its lysate adenosine in the cancer microenvironment are considered a halo mark of cancer. Adenosine acts as a strong immune suppressor. However, the source of ATP release is unclear. We clarified the release of ATP via volume-regulated anion channels (VRACs) in breast cell lines using an ATP luminescence imaging system. We detected a slowly rising diffuse pattern of ATP release that was only observed in undifferentiated cells, not in differentiated primary cultured cells. This was confirmed by suppression with DCPIB, a blocker of VRACs, and shRNA for LRRC8A, an indispensable subunit of VRACs. We herein demonstrated that the inflammatory mediator sphingosine-1-phosphate (S1P), which exists abundantly in the cancer microenvironment, induced a diffuse pattern of ATP release isovolumetrically. The response was dose-dependent and suppressed by the knock-down of LRRC8A. It was also suppressed by blockers of S1P receptor 1 and 2 (W146 and JTE013, respectively). RTqPCR demonstrated the prominent presence of S1PR1 and S1PR2 mRNAs. We discussed the roles of S1P-induced ATP release in the cancer microenvironment.
    Electronic ISSN: 2075-1729
    Topics: Biology
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    Nutritional Profile, Antioxidative and Antihyperglycemic Properties of Padina tetrastromatica from Tioman Island, Malaysia (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: Seaweeds are an important ingredient of functional foods recommended for daily food, due to their unique compositions and nutritional value. Padina tetrastromatica is a brown edible seaweed that is commonly found along the coastal regions of Peninsular Malaysia and consumed as food by some coastal communities. This study investigates the nutritional and antihyperglycaemic potential of P. tetrastromatica extracts, which is generally accepted as an important functional food. In our methodology, we induced diabetes intraperitoneally in experimental animals with a dose of 65 mg kg−1 body weight of streptozotocin. Oral treatment with 200 and 400 mg kg−1 of P. tetrastromatica ethanolic and ethyl acetate extracts were initiated, respectively, to experimental rats once daily for 18 days. Metformin was used as the positive control. Biochemical estimations and histopathological analysis were included in this study. Treatment with P. tetrastromatica extracts significantly lowered the plasma glucose levels in Streptozotocin-induced diabetic rats. In addition, P. tetrastromatica extract treatment also showed a significant reduction in serum alanine transaminase levels. However, no significant changes were observed in serum aspartate transaminase levels. The ethyl acetate extract of P. tetrastromatica at 400 mg kg−1 dose shows some nephroprotective effect, which is observed from the significant increase in the plasma albumin levels. Histopathological evaluation revealed no marked morphological changes in tissues of the isolated organs of the ethyl acetate extract-treated group, revealing the safe nature of P. tetrastromatica.
    Electronic ISSN: 2304-8158
    Topics: Chemistry and Pharmacology
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    Development of Framework for Estimating Fatality-Related Losses in the Korean Construction Industry (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: The number of fatalities in the construction industry is highest among all industries; thus, various losses in the form of fatalities in construction represent a significant factor for safety management. If a fatality occurs, it is important to estimate the overall loss, as a significant financial loss occurs for each project participant. However, in studies of the cost of accidents involving a fatality conducted abroad, the framework cannot be applied as it is because insurance types, systems, and legal cost systems differ by country. Therefore, we developed a framework for calculating the fatality loss considering various aspects of labor, industry, and regulations in Korea. This was done in four steps: (i) data collection and criteria selection; (ii) proposed framework development; (iii) conduct of questionnaire surveys for the case study; and (iv) analysis and evaluation of the case study. As a result of the data analysis after the case study of general construction companies, the total fatality loss was estimated to be 2,198,260 USD/person. The contributions of this study are the development of a framework composed of newly discovered items that can acquire reliable data in consideration of the properties of the construction industry.
    Print ISSN: 1661-7827
    Electronic ISSN: 1660-4601
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
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    Cross-Project Defect Prediction Method Based on Manifold Feature Transformation (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-20
    Description: Traditional research methods in software defect prediction use part of the data in the same project to train the defect prediction model and predict the defect label of the remaining part of the data. However, in the practical realm of software development, the software project that needs to be predicted is generally a brand new software project, and there is not enough labeled data to build a defect prediction model; therefore, traditional methods are no longer applicable. Cross-project defect prediction uses the labeled data of the same type of project similar to the target project to build the defect prediction model, so as to solve the problem of data loss in traditional methods. However, the difference in data distribution between the same type of project and the target project reduces the performance of defect prediction. To solve this problem, this paper proposes a cross-project defect prediction method based on manifold feature transformation. This method transforms the original feature space of the project into a manifold space, then reduces the difference in data distribution of the transformed source project and the transformed target project in the manifold space, and finally uses the transformed source project to train a naive Bayes prediction model with better performance. A comparative experiment was carried out using the Relink dataset and the AEEEM dataset. The experimental results show that compared with the benchmark method and several cross-project defect prediction methods, the proposed method effectively reduces the difference in data distribution between the source project and the target project, and obtains a higher F1 value, which is an indicator commonly used to measure the performance of the two-class model.
    Electronic ISSN: 1999-5903
    Topics: Computer Science
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    Sequential Extraction and Risk Assessment of Potentially Toxic Elements in River Sediments (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-08-12
    Description: In this study, the sequential extraction method was applied to extract selected potentially toxic elements (PTEs) (Cd, Cr, Cu, Fe, Ni, Pb and Zn) in river sediments collected from the Blood River situated in Seshego area, Limpopo Province, South Africa. The study aimed to assess a possible trend of mobilisation of these elements from sediment to water. The accuracy of the sequential extraction method was confirmed by analysing sediment-certified reference material, and quantitative percentage recoveries ranging from 86 to 119%, 81 to 111% and 77 to 119% were achieved for exchangeable, reducible and oxidisable fractions, respectively. The potential risk of the PTEs in sediments was evaluated. The calculated values of contamination factor (CF) as well as risk assessment code (RAC) for Cd, Cu, Ni and Pb revealed the mobility of these elements. The PTEs in river sediments are at a high toxicity-risk level and could therefore cause a threat to organisms dwelling in sediments and humans via consumption of crops irrigated with the polluted river water.
    Electronic ISSN: 2075-163X
    Topics: Geosciences
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    Performance and Cost-Effectiveness of Short Pitch-Based Carbon Fiber Reinforced Mortar Composite (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-08-20
    Description: This paper discusses the performance of the short pitch-based carbon fiber reinforced mortar (CFRM) composite considering its key properties and cost-effectiveness. Five different types of mortar composite were produced using 0–4% volume contents of short pitch-based carbon fibers. The mortar composites were tested for inverted slump cone flow (flow time and volume flow), unit weight, air content, compressive strength, flexural strength, impact resistance, and water absorption. The cost-effectiveness of CFRM was assessed based on the performance to cost ratio (PCR), which was calculated for each mortar composite, considering its workability, mechanical properties, and durability. The inverted slump cone volume flow was counted as a measure of workability, whereas the compressive strength, flexural strength, and impact resistance were considered as the major attributes of the mechanical behavior. In addition, the water absorption was used as a measure of durability. The test results revealed that the mortar composite made with 3% carbon fibers provided adequate workability, a relatively high unit weight and low air content, the highest compressive strength, excellent flexural strength, good impact resistance, and the lowest water absorption. It was also found that the PCR increased up to 3% carbon fibers. Beyond a 3% fiber content, the PCR significantly decreased. The overall research findings revealed that the mortar with 3% carbon fibers was the optimum and most cost-effective mortar composite.
    Electronic ISSN: 1996-1944
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Molecular Diversity Preservation International
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    Post-Transcriptional Control in the Regulation of Polyhydroxyalkanoates Synthesis (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-08-20
    Description: The large production of non-degradable petrol-based plastics has become a major global issue due to its environmental pollution. Biopolymers produced by microorganisms such as polyhydroxyalkanoates (PHAs) are gaining potential as a sustainable alternative, but the high cost associated with their industrial production has been a limiting factor. Post-transcriptional regulation is a key step to control gene expression in changing environments and has been reported to play a major role in numerous cellular processes. However, limited reports are available concerning the regulation of PHA accumulation in bacteria, and many essential regulatory factors still need to be identified. Here, we review studies where the synthesis of PHA has been reported to be regulated at the post-transcriptional level, and we analyze the RNA-mediated networks involved. Finally, we discuss the forthcoming research on riboregulation, synthetic, and metabolic engineering which could lead to improved strategies for PHAs synthesis in industrial production, thereby reducing the costs currently associated with this procedure.
    Electronic ISSN: 2075-1729
    Topics: Biology
    Published by Molecular Diversity Preservation International
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    Black Garlic and Its Bioactive Compounds on Human Health Diseases: A Review (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-08-19
    Description: Black garlic (BG) is a form of aged garlic obtained from raw garlic (Allium sativum) via Millard reaction under high temperature (60–90 °C) and humidity (70–90%) for a period of time. Several studies reported higher contents of water-soluble antioxidants compounds (S-allyl cysteine, S-allyl-mercapto cysteine), 5-hydroxymethylfurfural, organosulfur compounds, polyphenol, volatile compounds, and products of other Millard reactions compared to fresh garlic after the thermal processing. Recent studies have demonstrated that BG and its bioactive compounds possess a wide range of biological activities and pharmacological properties that preserve and show better efficacy in preventing different types of diseases. Most of these benefits can be attributed to its anti-oxidation, anti-inflammation, anti-obesity, hepatoprotection, hypolipidemia, anti-cancer, anti-allergy, immunomodulation, nephroprotection, cardiovascular protection, and neuroprotection. Substantial studies have been conducted on BG and its components against different common human diseases in the last few decades. Still, a lot of research is ongoing to find out the therapeutic effects of BG. Thus, in this review, we summarized the pre-clinical and clinical studies of BG and its bioactive compounds on human health along with diverse bioactivity, a related mode of action, and also future challenges.
    Electronic ISSN: 1420-3049
    Topics: Chemistry and Pharmacology
    Published by Molecular Diversity Preservation International
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    Social Determinants on Suicidal Thoughts among Young Adults (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-08-20
    Description: Objective. The main objective of this study was to investigate the relationship between poverty, religion, and suicidal thoughts among U.S. youth. The disparities regarding gender, race, and ethnicity with regard to suicidal thoughts were also assessed. Methods. A cross-sectional correlational research design was used for this study and a national representative sample of 1945 young adults aged 18 to 25 was selected from the 2014 National Survey on Drug Use and Health. Logistic regression analysis with interaction effects was utilized to determine if poverty and religion were associated with suicidal thoughts. Results. About 43 percent of the sample reported having suicidal thoughts when things got worse and this prevalence rate varied by gender and race/ethnicity with white males self-disclosing the highest rate of suicidal thoughts. After adjusting for demographic and socioeconomic characteristics, black males who lived up to two times the poverty line had a higher likelihood of suicidal thoughts (p = 0.011), and religion protected against suicidal thoughts (p = 0.012). Youth with lower education and poor health were more inclined to have suicidal thoughts than their peers. Conclusions. Suicide is the second leading cause of death for American young adults aged 18 to 25. Understanding these differences between social determinants of suicide can help public health researchers strategize how to make evidence-based recommendations for suicide prevention efforts.
    Print ISSN: 1661-7827
    Electronic ISSN: 1660-4601
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
    Published by Molecular Diversity Preservation International
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    Mechanisms Mediating the Regulation of Peroxisomal Fatty Acid Beta-Oxidation by PPARα (2021)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2021-08-20
    Description: In mammalian cells, two cellular organelles, mitochondria and peroxisomes, share the ability to degrade fatty acid chains. Although each organelle harbors its own fatty acid β-oxidation pathway, a distinct mitochondrial system feeds the oxidative phosphorylation pathway for ATP synthesis. At the same time, the peroxisomal β-oxidation pathway participates in cellular thermogenesis. A scientific milestone in 1965 helped discover the hepatomegaly effect in rat liver by clofibrate, subsequently identified as a peroxisome proliferator in rodents and an activator of the peroxisomal fatty acid β-oxidation pathway. These peroxisome proliferators were later identified as activating ligands of Peroxisome Proliferator-Activated Receptor α (PPARα), cloned in 1990. The ligand-activated heterodimer PPARα/RXRα recognizes a DNA sequence, called PPRE (Peroxisome Proliferator Response Element), corresponding to two half-consensus hexanucleotide motifs, AGGTCA, separated by one nucleotide. Accordingly, the assembled complex containing PPRE/PPARα/RXRα/ligands/Coregulators controls the expression of the genes involved in liver peroxisomal fatty acid β-oxidation. This review mobilizes a considerable number of findings that discuss miscellaneous axes, covering the detailed expression pattern of PPARα in species and tissues, the lessons from several PPARα KO mouse models and the modulation of PPARα function by dietary micronutrients.
    Print ISSN: 1661-6596
    Electronic ISSN: 1422-0067
    Topics: Chemistry and Pharmacology
    Published by Molecular Diversity Preservation International
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    Polycomb-dependent histone H2A ubiquitination links developmental disorders with cancer (2021)
    Cell Press
    Details
    Publication Date: 2021-08-01
    Print ISSN: 0168-9525
    Electronic ISSN: 1362-4555
    Topics: Biology
    Published by Cell Press
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    Structural insights into a novel family of integral membrane siderophore reductases (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-08-20
    Description: Gram-negative bacteria take up the essential ion Fe3+ as ferric-siderophore complexes through their outer membrane using TonB-dependent transporters. However, the subsequent route through the inner membrane differs across many bacterial species and siderophore chemistries and is not understood in detail. Here, we report the crystal structure of the inner membrane protein FoxB (from Pseudomonas aeruginosa) that is involved in Fe-siderophore uptake. The structure revealed a fold with two tightly bound heme molecules. In combination with in vitro reduction assays and in vivo iron uptake studies, these results establish FoxB as an inner membrane reductase involved in the release of iron from ferrioxamine during Fe-siderophore uptake.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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    SRG/ART-XC, Swift, NICER, and NuSTAR study of different states of the transient X-ray pulsar MAXI J0903-531 (2021)
    EDP Sciences
    Details
    Publication Date: 2021-08-23
    Print ISSN: 0004-6361
    Electronic ISSN: 1432-0746
    Topics: Physics
    Published by EDP Sciences
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    Counting equilibria of large complex systems by instability index (2021)
    National Academy of Sciences
    Details
    Publication Date: 2021-08-20
    Description: We consider a nonlinear autonomous system of N≫1 degrees of freedom randomly coupled by both relaxational (“gradient”) and nonrelaxational (“solenoidal”) random interactions. We show that with increased interaction strength, such systems generically undergo an abrupt transition from a trivial phase portrait with a single stable equilibrium into a topologically nontrivial regime of “absolute instability” where equilibria are on average exponentially abundant, but typically, all of them are unstable, unless the dynamics is purely gradient. When interactions increase even further, the stable equilibria eventually become on average exponentially abundant unless the interaction is purely solenoidal. We further calculate the mean proportion of equilibria that have a fixed fraction of unstable directions.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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    On randomly changing conformity bias in cultural transmission (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Humans and nonhuman animals display conformist as well as anticonformist biases in cultural transmission. Whereas many previous mathematical models have incorporated constant conformity coefficients, empirical research suggests that the extent of (anti)conformity in populations can change over time. We incorporate stochastic time-varying conformity coefficients into a widely used conformity model, which assumes a fixed number n of “role models” sampled by each individual. We also allow the number of role models to vary over time (nt). Under anticonformity, nonconvergence can occur in deterministic and stochastic models with different parameter values. Even if strong anticonformity may occur, if conformity or random copying (i.e., neither conformity nor anticonformity) is expected, there is convergence to one of the three equilibria seen in previous deterministic models of conformity. Moreover, this result is robust to stochastic variation in nt. However, dynamic properties of these equilibria may be different from those in deterministic models. For example, with random conformity coefficients, all equilibria can be stochastically locally stable simultaneously. Finally, we study the effect of randomly changing weak selection. Allowing the level of conformity, the number of role models, and selection to vary stochastically may produce a more realistic representation of the wide range of group-level properties that can emerge under (anti)conformist biases. This promises to make interpretation of the effect of conformity on differences between populations, for example those connected by migration, rather difficult. Future research incorporating finite population sizes and migration would contribute added realism to these models.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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