ALBERT

Beschreibung: In recent years, the rapid increase in CO2 concentration has accelerated global warming. As a result, sea levels rise, glaciers melt, extreme weather occurs, and species become extinct. As the world’s largest CO2 emission rights trading market, EU Emissions Trading System (EU-ETS) has reached 1.855 billion tons of quotas by 2019, influencing the development of the global carbon emission market. Crude oil, as one of the major fossil energy sources in the world, its price fluctuation is bound to affect the price of carbon emission rights. Therefore, this paper aims to reveal the correlation between crude oil futures prices and carbon emission rights futures prices by studying the price fluctuation. In this paper, the linkage between West Texas Intermediate (WTI) crude oil futures prices and European carbon futures prices was investigated. In addition, this paper selects continuous data of WTI crude oil futures prices and spot prices with European carbon futures prices from January 8, 2018 to November 27, 2020, and builds a smooth transformation regression (STR) model. The relationship between crude oil futures and carbon futures prices is studied in both forward and reversal linkage through empirical analysis. The results show that crude oil futures prices and carbon futures prices have a mutual effect on each other, and both linear and nonlinear correlations between the two prices exist. Based on the results of this research, some suggestions are provided.

Beschreibung: Ubiquitin-dependent protein degradation plays an important role in many plant developmental processes. We previously identified a class of SINA RING-type E3 ligases of Arabidopsis thaliana (SINATs), whose protein levels decrease in the dark and increase in red and blue light, but the underlying mechanism is unclear. In this study, we created transgenic lines carrying point mutations in SINAT genes and photoreceptors-NLS or -NES transgenic plants to investigate the regulatory mechanism of SINAT protein stability. We demonstrated that the degradation of SINATs is self-regulated, and SINATs interact with photoreceptors phytochrome B (phyB) and cryptochrome 1 (CRY1) in the cytoplasm, which leads to the degradation of SINATs in the dark. Furthermore, we observed that the red light-induced subcellular localization change of phyB and blue light-induced the dissociation of CRY1 from SINATs and was the major determinant for the light-promoted SINATs accumulation. Our findings provide a novel mechanism of how the stability and degradation of the E3 ligase SINATs are regulated by an association and dissociation mechanism through the red light-induced subcellular movement of phyB and the blue light-induced dissociation of CRY1 from SINATs.

Beschreibung: The Main Ethiopian Rift (MER) is characterized by extensional tectonics and volcanism, associated with active hydrothermal systems, hydrothermal alteration and fumarolic deposits. The spatial distribution of these hydrothermal products and their link with faults and rock types provides important clues to what controls fluid flow in the subsurface. However, little is known about this in the East African Rift. We address this issue with a multidisciplinary approach in the Fentale-Dofan magmatic segment of the MER, an area characterized by intense volcanic and tectonic activity and a geothermal prospect. Primarily we conduct mapping of hydrothermal alteration and fumarolic deposits, and rock lithologies using a surface feature classification technique of multispectral satellite images. Then we interpret the map using a new database of faults and active hydrothermal manifestations such as hot-springs and fumaroles. We find that the surface hydrothermal alteration and deposits are mainly focused near Fentale and the Dofan Volcanic Complex (DVC). At DVC the hydrothermal products are focused on rhyolites on the western side of the volcano, in an area of intense NNE striking, rift parallel faults. At Fentale volcano the hydrothermal products are mainly associated with ignimbrite and show a circular pattern around the volcanic edifice, but also in places follow the NNE striking faults. At Fentale, the more complex association of hydrothermal products and active manifestations around the edge of the ignimbrite suggests formation contacts may also localize fluid flow in places. At both volcanoes the association between hydrothermal products with either the rhyolites and ignimbrites is likely due to them being relatively easily altered (in comparison to basalt), and also their brittle nature allows for fracturing through which localized fluid flow can occur (as opposed to the sediments). The general pattern of hydrothermal products suggests a stronger structural influence at the DVC with respect to Fentale. The presence of hydrothermal products and active hydrothermal manifestations, along with other lines of evidence such as locus of subsurface dike intrusion at the volcanic centres, suggest that discrete and localized magma reservoirs beneath Fentale and the DVC are the heat source for hydrothermal circulation. Our study also demonstrates that geology, including hydrothermal deposits, can be successfully mapped using automated remote sensing based classification.

Beschreibung: In response to the environmental damage caused by urbanization, Nature-based Solutions (NbS) are being implemented to enhance biodiversity and ecosystem processes with mutual benefits for society and nature. Although the field of NbS is flourishing, experiments in different geographic locations and environmental contexts have produced variable results, with knowledge particularly lacking for the subtidal zone. This study tested the effects of physical complexity on colonizing communities in subtidal habitats in two urban locations: (1) Plymouth, United Kingdom (northeast Atlantic) and (2) Tel Aviv, Israel (eastern Mediterranean) for 15- and 12-months, respectively. At each location, physical complexity was manipulated using experimental tiles that were either flat or had 2.5 or 5.0 cm ridges. In Plymouth, biological complexity was also manipulated through seeding tiles with habitat-forming mussels. The effects of the manipulations on taxon and functional richness, and community composition were assessed at both locations, and in Plymouth the survival and size of seeded mussels and abundance and size of recruited mussels were also assessed. Effects of physical complexity differed between locations. Physical complexity did not influence richness or community composition in Plymouth, while in Tel Aviv, there were effects of complexity on community composition. In Plymouth, effects of biological complexity were found with mussel seeding reducing taxon richness, supporting larger recruited mussels, and influencing community composition. Our results suggest that outcomes of NbS experiments are context-dependent and highlight the risk of extrapolating the findings outside of the context in which they were tested.

Beschreibung: Two known azaphilone derivatives, 4,6-dimethylcurvulinic acid (1) and austdiol (2), and their novel heterotrimer, muyophilone A (3), were isolated and identified from an endophytic fungus, Muyocopron laterale 0307-2. Their structures and stereochemistry were established by extensive spectroscopic analyses including HRMS, NMR spectroscopy, electronic circular dichroism (ECD) and vibrational circular dichroism (VCD) spectroscopic methods, as well as single crystal X-ray diffraction. In the structure of 3, two compound 2-derived azaphilone units were connected through an unprecedented five-membered carbon bridge which was proposed to be originated from compound 1. Compound 3 represents the first example of azaphilone heterotrimers.

Beschreibung: Micafungin is an important echinocandin antifungal agent for the treatment of invasive fungal infections. In industry, micafungin is derived from the natural product FR901379, which is a non-ribosomal cyclic hexapeptide produced by the filamentous fungus Coleophoma empetri. The difficulty of genetic manipulation in C. empetri restricts the clarification of FR901379 biosynthetic mechanism. In this work, we developed an efficient genetic manipulation system in the industrial FR901379-producing strain C. empetri MEFC009. Firstly, a convenient protoplast-mediated transformation (PMT) method was developed. Secondly, with this transformation method, the essential genetic elements were verified. Selectable markers hph, neo, and nat can be used for the transformation, and promotors Ppgk, PgpdA, and PgpdAt are functional in C. empetri MEFC009. Thirdly, the frequency of homologous recombination was improved from 4 to 100% by deleting the ku80 gene, resulting in an excellent chassis cell for gene-targeting. Additionally, the advantage of this genetic manipulation system was demonstrated in the identification of the polyketide synthase (PKS) responsible for the biosynthesis of dihydroxynapthalene (DHN)-melanin. This genetic manipulation system will be a useful platform for the research of FR901379 and further genome mining of secondary metabolites in C. empetri.

Beschreibung: Illegal wildlife trade is considered one of the most serious threats to biodiversity worldwide, along with habitat loss/degradation and overfishing of wild stocks. Seahorses are considered at high risk as these fish represent an important component of traditional Chinese medicine but are also sold as curios and ornamental fish. On a worldwide level, illegal trade is controlled by numerous laws and regulations, but it seems to continue by assuming more dynamic routes. In the Mediterranean Sea, Hippocampus guttulatus formed one of the largest populations at Mar Piccolo di Taranto in South-Eastern Italy. During the routine monitoring of this population in 2016, a dramatic density decrease was observed. By using questionnaires and long-term datasets, the present study determined possible causes of this decline by investigating habitat changes, temperature trends and the existence of seahorse trafficking while also examining abundance trends during the last decade. The results indicated a sharp density decline starting from 2015, co-occurring with the period of high temperatures, while habitats remained almost constant. However, interviews with main stakeholders described both illegal and legal fishing activities as the main drivers for the declining seahorse density. Indeed, at one of the studied sites, which was under strict military control, seahorse abundance started to decline only after the intensification of fishing pressure in the basin. The study suggests that Mar Piccolo di Taranto could be one of the sources for international seahorse trade, thus highlighting the need for more intense and effective actions to prevent and combat illegal poaching, while threatened populations are requiring continuous and close monitoring. Due to unfavorable socio-economic conditions, a viable and thriving seahorse population at Mar Piccolo di Taranto could contribute to the revitalization of the coastal economy and the development of environmental awareness.

Beschreibung: Maize stalk rot caused by Fusarium species is one of the most important fungal diseases of maize throughout the world. The disease is responsible for considerable yield losses and has also been associated with mycotoxin contamination of the crop. In this study, a survey of maize stalk rot was performed in seven locations of Yunnan Province in China during the cropping season of 2015 and 2016. Based on morphological and molecular characteristics, 204 isolates belonging to 12 Fusarium spp. from symptomatic stalks of maize were identified. Among the isolated strains, 83 were identified as Fusarium meridionale (40.5%), 46 as Fusarium boothii (22.5%), 34 as Fusarium temperatum (16.5%), 12 as Fusarium equiseti (5.9%), 10 as Fusarium asiaticum (4.9%), six as Fusarium proliferatum (3.0%), four as Fusarium verticillioides (2.0%), four as Fusarium incarnatum (2.0%), two as Fusarium avenaceum (1.0%), one as Fusarium cerealis (0.5%), one as Fusarium graminearum (0.5%), and one as Fusarium cortaderiae (0.5%). Fusarium cortaderiae was the first report on the causal agent of maize stalk rot disease in China. These isolates were divided into five chemotypes: nivalenol (NIV), deoxynivalenol (DON), beauvericin (BEA), zearalenone (ZEN), and fumonisin (FUM). Phylogenetic analysis based on partial sequences of the translation elongation factor 1α (TEF1-α) showed a high degree of interspecific polymorphisms among the isolates. Pathogenicity analysis on maize stalks indicated that all the 12 species of Fusarium were able to cause the disease symptoms with different aggressiveness. This study on population, pathogenicity, and toxigenic chemotypes of Fusarium species associated with maize stalk rot in Yunnan Province of southwest China, will help design an effective integrated control strategy for this disease.

Beschreibung: We present a high-efficiency method for simulating seawater intrusion (SWI), with mixing, in confined coastal aquifers based on uncoupled equations in the through-flow region of the aquifer. The flow field is calculated analytically and the tracer transport numerically, via spatial splitting along the principal directions (PD) of transport. Advection-dispersion processes along streamlines are simulated with the very efficient matched artificial dispersivity (MAD) method of Syriopoulou and Koussis and the system of discretized transverse-dispersion equations is solved with the Thomas algorithm. These concepts are embedded in the 2D-MADPD-SWI model, yielding comparable solutions to those of the uncoupled SWI equations with the state-of-the-art FEFLOW code, but faster, while 2D-MADPD-SWI achieves an at least hundredfold faster solution than a variable-density flow model. We demonstrate the utility of the 2D-MADPD-SWI model in stochastic Monte Carlo simulations by assessing the uncertainty on the advance of the 1,500 ppm TDS line (limit of tolerable salinity for irrigation) due to randomly variable hydraulic conductivity and freshwater flow rate.

Beschreibung: Pantoea ananatis, a gram negative and facultative anaerobic bacterium is a member of a Pantoea spp. complex that causes center rot of onion, which significantly affects onion yield and quality. This pathogen does not have typical virulence factors like type II or type III secretion systems but appears to require a biosynthetic gene-cluster, HiVir/PASVIL (located chromosomally comprised of 14 genes), for a phosphonate secondary metabolite, and the ‘alt’ gene cluster (located in plasmid and comprised of 11 genes) that aids in bacterial colonization in onion bulbs by imparting tolerance to thiosulfinates. We conducted a deep pan-genome-wide association study (pan-GWAS) to predict additional genes associated with pathogenicity in P. ananatis using a panel of diverse strains (n = 81). We utilized a red-onion scale necrosis assay as an indicator of pathogenicity. Based on this assay, we differentiated pathogenic (n = 51)- vs. non-pathogenic (n = 30)-strains phenotypically. Pan-genome analysis revealed a large core genome of 3,153 genes and a flexible accessory genome. Pan-GWAS using the presence and absence variants (PAVs) predicted 42 genes, including 14 from the previously identified HiVir/PASVIL cluster associated with pathogenicity, and 28 novel genes that were not previously associated with pathogenicity in onion. Of the 28 novel genes identified, eight have annotated functions of site-specific tyrosine kinase, N-acetylmuramoyl-L-alanine amidase, conjugal transfer, and HTH-type transcriptional regulator. The remaining 20 genes are currently hypothetical. Further, a core-genome SNPs-based phylogeny and horizontal gene transfer (HGT) studies were also conducted to assess the extent of lateral gene transfer among diverse P. ananatis strains. Phylogenetic analysis based on PAVs and whole genome multi locus sequence typing (wgMLST) rather than core-genome SNPs distinguished red-scale necrosis inducing (pathogenic) strains from non-scale necrosis inducing (non-pathogenic) strains of P. ananatis. A total of 1182 HGT events including the HiVir/PASVIL and alt cluster genes were identified. These events could be regarded as a major contributing factor to the diversification, niche-adaptation and potential acquisition of pathogenicity/virulence genes in P. ananatis.

Beschreibung: The complexity of the subcellular processes that take place during meiosis requires a significant remodeling of cellular metabolism and dynamic changes in the organization of chromosomes and the cytoskeleton. Recently, investigations of meiotic transcriptomes have revealed additional noncoding RNA factors (ncRNAs) that directly or indirectly influence the course of meiosis. Plant meiosis is the point at which almost all known noncoding RNA-dependent regulatory pathways meet to influence diverse processes related to cell functioning and division. ncRNAs have been shown to prevent transposon reactivation, create germline-specific DNA methylation patterns, and affect the expression of meiosis-specific genes. They can also influence chromosome-level processes, including the stimulation of chromosome condensation, the definition of centromeric chromatin, and perhaps even the regulation of meiotic recombination. In many cases, our understanding of the mechanisms underlying these processes remains limited. In this review, we will examine how the different functions of each type of ncRNA have been adopted in plants, devoting attention to both well-studied examples and other possible functions about which we can only speculate for now. We will also briefly discuss the most important challenges in the investigation of ncRNAs in plant meiosis.

Beschreibung: Background: Acute type B aortic dissection is a highly serious aortic pathology. Aortic geometric parameters may be useful variables related to the occurrence of acute type B aortic dissection (aTBAD). The aim of the study is to delineate the alteration in aortic geometric parameters and analyze the specific geometric factors associated with aTBAD.Methods: The propensity score matching method was applied to control confounding factors. The aortic diameter, length, angulation, tortuosity, and type of aortic arch of the aTBAD and control group were retrospectively analyzed via three-dimensional computed tomography imaging created by the 3mensio software (version 10.0, Maastricht, The Netherlands). The geometric variables of true lumen and false lumen in the descending aorta were measured to estimate the severity of aortic dissection. Multivariable logistic regression models were used to investigate the significant and specific factors associated with aTBAD occurrence. The area under the receiver operating characteristic curve (AUC) was used to estimate the performance of the model.Results: After propensity score matching, 168 matched pairs of patients were selected. The ascending aorta and aortic arch diameters were dilated, and the ascending aorta and total aorta lengths were elongated in aTBAD group significantly (P 〈 0.001). The ascending aorta and aortic arch angulations in the aTBAD group were sharper than those of the controls (P = 0.01, P 〈 0.001, respectively). The aortic arch and total aorta tortuosities were significantly higher in the aTBAD group (P = 0.001, P 〈 0.001, respectively). There were more type III arch patients in the aTBAD group than the controls (67.9 vs. 22.6%). The true lumen angulation was sharper than that in the false lumen (P 〈 0.01). The true lumen tortuosity was significantly lower than that in the false lumen (P 〈 0.001). The multivariable models identified that aortic arch angulation, tortuosity, and type III arch were independent and specific geometric factors associated with aTBAD occurrence. The AUC of the multivariable models 1, 2, 3 were 0.945, 0.953, and 0.96, respectively.Conclusions: The sharper angulation and higher tortuosity of aortic arch and type III arch were the geometric factors associated with aTBAD in addition to the ascending aorta elongation and aortic arch dilation. The angulation and tortuosity of the true and false lumens may carry significant clinical implications for the treatment and prognosis of aTBAD.

Beschreibung: Wastewater stabilization ponds (WSPs) are commonly used to treat municipal wastewater in the Canadian Arctic. Bacterial community structure and functionality remain mostly uncharacterized for arctic WSPs, yet are presumed important for treatment outcomes during the 3-month summer treatment season with open water in the WSPs. The objective of this study was to investigate treatment performance and related temporal and spatial changes in the structure and putative function of bacterial communities during treatment of municipal wastewater in the WSPs of Pond Inlet and Clyde River, Nunavut over two consecutive summer treatment seasons. Influent raw wastewater contained a high organic load and large bacterial communities (~9 log 16S rRNA copies/mL) belonging mainly to Proteobacteria. Although designed to be facultative ponds, both WSPs remained anaerobic with neutral pH values (7.5–7.8) throughout the summer treatment season. Water quality data showed that nutrients [measured as carbonaceous biological oxygen demand (CBOD5)], total suspended solids, and total ammonia nitrogen were progressively reduced during treatment in the ponds as the summer progressed. The pond bacterial population size and species richness depended on the pond temperature (2–18°C), with 8.5 log 16S rRNA copies/mL and the largest alpha diversities (Shannon-Wiener index of 4-4.5) observed mid-season (late July). While the phylogenetic beta diversity in raw wastewater from the two locations remained similar, pond bacterial communities underwent significant (p 〈 0.05) changes to dominance of Comamonadaceae, Geobacteracea, and Porphyromonadaceae. Multivariate distance based redundancy analysis and predicted gene functionalities in the microbiota agreed with water quality results that microbial removal of nutrients (e.g., CBOD5) peaked in the middle of the summer coinciding with the treatment period with the highest pond temperatures. Information from this study will be useful for further development of models to predict biological treatment outcomes, which could be used to size and assess the feasibility of WSPs in extreme climates. Higher pond temperatures resulted in optimal biological processes and nutrient removal in the middle of the summer. While it is challenging to control environmental factors in a passive wastewater treatment system there are some design considerations that could be used to optimize temperature regimes, such as the depth of the pond.

Beschreibung: Metafounders are pseudo-individuals that act as proxies for animals in base populations. When metafounders are used, individuals from different breeds can be related through pedigree, improving the compatibility between genomic and pedigree relationships. The aim of this study was to investigate the use of metafounders and unknown parent groups (UPGs) for the genomic evaluation of a composite beef cattle population. Phenotypes were available for scrotal circumference at 14 months of age (SC14), post weaning gain (PWG), weaning weight (WW), and birth weight (BW). The pedigree included 680,551 animals, of which 1,899 were genotyped for or imputed to around 30,000 single-nucleotide polymorphisms (SNPs). Evaluations were performed based on pedigree (BLUP), pedigree with UPGs (BLUP_UPG), pedigree with metafounders (BLUP_MF), single-step genomic BLUP (ssGBLUP), ssGBLUP with UPGs for genomic and pedigree relationship matrices (ssGBLUP_UPG) or only for the pedigree relationship matrix (ssGBLUP_UPGA), and ssGBLUP with metafounders (ssGBLUP_MF). Each evaluation considered either four or 10 groups that were assigned based on breed of founders and intermediate crosses. To evaluate model performance, we used a validation method based on linear regression statistics to obtain accuracy, stability, dispersion, and bias of (genomic) estimated breeding value [(G)EBV]. Overall, relationships within and among metafounders were stronger in the scenario with 10 metafounders. Accuracy was greater for models with genomic information than for BLUP. Also, the stability of (G)EBVs was greater when genomic information was taken into account. Overall, pedigree-based methods showed lower inflation/deflation (regression coefficients close to 1.0) for SC14, WWM, and BWD traits. The level of inflation/deflation for genomic models was small and trait-dependent. Compared with regular ssGBLUP, ssGBLUP_MF4 displayed regression coefficient closer to one SC14, PWG, WWM, and BWD. Genomic models with metafounders seemed to be slightly more stable than models with UPGs based on higher similarity of results with different numbers of groups. Further, metafounders can help to reduce bias in genomic evaluations of composite beef cattle populations without reducing the stability of GEBVs.

Beschreibung: This study was to investigate the effects of UPro as a new nutritive fortifier on high-quality egg production from the perspective of egg properties, intestinal histomorphology, and oviduct function of laying hens. Four hundred thirty-two Hy-Line Brown laying hens aged 56 weeks were allocated to four groups. Layers were given a basal diet or supplemented with different levels of small peptides (0.2, 0.4, and 0.8%) to replace soybean meal. After 1-week adaptation period, the feeding trial was conducted for 12 weeks. The results showed that UPro addition significantly decreased (P 〈 0.05) the hardness, stickiness, and chewiness of albumen of layers on weeks 12. A linear elevation (P 〈 0.05) in the albumen height, Haugh unit (HU), and crude protein content of albumen of layers were noted on week 12 along with dietary UPro addition increasing, and the villus height (VH) and villus height-to-crypt depth radio (VCR) of jejunum also linearly increasing (P 〈 0.05). In addition, there were linear elevations (P 〈 0.05) in the relative mRNA expression of Sec23 homolog A (Sec23A) and protein-O-mannosyltransferase1 (POMT1) in layers as dietary UPro addition increased. In conclusion, dietary UPro addition could improve intestinal health, increase the absorption of nutrients, and improve egg quality of laying hens. The possible mechanism underlying UPro improving the quality and processing characteristics of albumen is up-regulating Sec23A and POMT1 expression of magnum. These findings will promote the application of UPro as a new nutritional additive in the production of high-quality eggs.

Beschreibung: Milk polar lipids provide choline, ethanolamine, and polyunsaturated fatty acids, which are needed for the growth and plasticity of the tissues in a suckling child. They may also inhibit cholesterol absorption by interacting with cholesterol during micelle formation. They may also have beneficial luminal, mucosal, and metabolic effects in both the neonate and the adult. The milk fat globule membrane contains large proportions of sphingomyelin (SM), phosphatidylcholine (PC), and phosphatidylethanolamine (PE), and some phosphatidylserine (PS), phosphatidylinositol (PI), and glycosphingolipids. Large-scale technical procedures are available for the enrichment of milk fat globule membrane (MFGM) in milk replacement formulations and food additives. Pancreatic phospholipase A2 (PLA2) and mucosal phospholipase B digest glycero-phospholipids in the adult. In the neonate, where these enzymes may be poorly expressed, pancreatic lipase-related protein 2 probably has a more important role. Mucosal alkaline SM-ase and ceramidase catalyze the digestion of SM in both the neonate and the adult. In the mucosa, the sphingosine is converted into sphingosine-1-phosphate, which is both an intermediate in the conversion to palmitic acid and a signaling molecule. This reaction sequence also generates ethanolamine. Here, we summarize the pathways by which digestion and absorption may be linked to the biological effects of milk polar lipids. In addition to the inhibition of cholesterol absorption and the generation of lipid signals in the gut, the utilization of absorbed choline and ethanolamine for mucosal and hepatic phospholipid synthesis and the acylation of absorbed lyso-PC with polyunsaturated fatty acids to chylomicron and mucosal phospholipids are important.

Beschreibung: Lysosomal storage diseases (LSDs) are characterized by the abnormal accumulation of substrates in tissues due to the deficiency of lysosomal proteins. Among the numerous clinical manifestations, chronic inflammation has been consistently reported for several LSDs. However, the molecular mechanisms involved in the inflammatory response are still not completely understood. In this study, we performed text-mining and systems biology analyses to investigate the inflammatory signals in three LSDs characterized by sphingolipid accumulation: Gaucher disease, Acid Sphingomyelinase Deficiency (ASMD), and Fabry Disease. We first identified the cytokines linked to the LSDs, and then built on the extracted knowledge to investigate the inflammatory signals. We found numerous transcription factors that are putative regulators of cytokine expression in a cell-specific context, such as the signaling axes controlled by STAT2, JUN, and NR4A2 as candidate regulators of the monocyte Gaucher disease cytokine network. Overall, our results suggest the presence of a complex inflammatory signaling in LSDs involving many cellular and molecular players that could be further investigated as putative targets of anti-inflammatory therapies.

Beschreibung: Large-scale transcriptome data, such as single-cell RNA-sequencing data, have provided unprecedented resources for studying biological processes at the systems level. Numerous dimensionality reduction methods have been developed to visualize and analyze these transcriptome data. In addition, several existing methods allow inference of functional variations among samples using gene sets with known biological functions. However, it remains challenging to analyze transcriptomes with reduced dimensions that are interpretable in terms of dimensions’ directionalities, transferrable to new data, and directly expose the contribution or association of individual genes. In this study, we used gene set non-negative principal component analysis (gsPCA) and non-negative matrix factorization (gsNMF) to analyze large-scale transcriptome datasets. We found that these methods provide low-dimensional information about the progression of biological processes in a quantitative manner, and their performances are comparable to existing functional variation analysis methods in terms of distinguishing multiple cell states and samples from multiple conditions. Remarkably, upon training with a subset of data, these methods allow predictions of locations in the functional space using data from experimental conditions that are not exposed to the models. Specifically, our models predicted the extent of progression and reversion for cells in the epithelial-mesenchymal transition (EMT) continuum. These methods revealed conserved EMT program among multiple types of single cells and tumor samples. Finally, we demonstrate this approach is broadly applicable to data and gene sets beyond EMT and provide several recommendations on the choice between the two linear methods and the optimal algorithmic parameters. Our methods show that simple constrained matrix decomposition can produce to low-dimensional information in functionally interpretable and transferrable space, and can be widely useful for analyzing large-scale transcriptome data.

Beschreibung: The impaired effector function of exhausted and senescent T cells is implicated in cancer progression and inadequate vaccine responses. Exercise has been shown to improve cancer therapy and vaccine efficacy, most likely by improving immune function. However, given inconsistent terminology and definitions, the interactions between exercise and exhausted and senescent T cells remain unclear. We therefore performed a systematic review to investigate the effect of exercise on senescent and exhausted CD8+ T cell populations clearly defined by protein surface markers. Thirty articles were included, with the majority (n = 24) reporting senescent T cell populations defined according to a variety of surface markers. Repeated exercise was shown to be beneficial through limiting the accumulation of senescent and exhausted CD8+ T cells. This outcome is likely related to exercise-induced preferential mobilization of senescent T cells promoting apoptosis in the peripheral blood compartment. Future studies need to determine the clinical relevance of this effect in cancer prevention and vaccine efficacy. Data regarding exercise and exhausted T cells are limited due to a lack of available high-quality studies. Future studies require the control of confounding variables such as sex and cytomegalovirus (CMV) status, and consistent definitions of exhausted and senescent T cell populations to improve comparisons between studies and interventions.

Beschreibung: Kiwifruit (Actinidia eriantha) is a dioecious vine, and the pollen of its male cultivars has a direct effect on the quality of its fruits. In this study, to facilitate molecular breeding and gene identification, we performed genome-wide association studies (GWAS) on 11 traits of flower and leaf. A total of 946,337 highly consistent SNP markers were obtained in the whole genome. Phylogenetic tree analysis and population structure analysis showed that the 143 germplasms can be divided into two groups. The linkage disequilibrium analysis showed that A. eriantha have a relatively fast attenuation rate, and that the average attenuation distance of LD was 0.1–0.3 Kb. The MLM (QK) model was determined as best for correlation analysis, and eight and three SNPs associated with flower- and leaf-related traits were identified, respectively, at 0.01 significance level. However, SNP markers associated with stamen number per flower, pollen viability, total chlorophyll content, and total flavonoid content were not identified at the 0.01 significant level, although it is worth noting that one, one, five, and two SNPs were identified to be associated with these traits at the 0.05 significant level. This study provides insights into the complex flower- and leaf-related biology, and identifies genes controlling important traits in A. eriantha through GWAS, which extends the genetic resources and basis for facilitating molecular breeding in kiwifruits.

Beschreibung: Estrogen enhances long bone longitudinal growth during early puberty. Growth plate chondrocytes are the main cells that contribute to long bone elongation. The role of G-protein-coupled estrogen receptor-1 (GPER-1) in regulating growth plate chondrocyte function remains unclear. In the present study, we generated chondrocyte-specific GPER-1 knockout (CKO) mice to investigate the effect of GPER-1 in growth plate chondrocytes. In control mice, GPER-1 was highly expressed in the growth plates of 4- and 8-week-old mice, with a gradual decline through 12 to 16 weeks. In CKO mice, the GPER-1 expression in growth plate chondrocytes was significantly lower than that in the control mice (80% decrease). The CKO mice also showed a decrease in body length (crown–rump length), body weight, and the length of tibias and femurs at 8 weeks. More importantly, the cell number and thickness of the proliferative zone of the growth plate, as well as the thickness of primary spongiosa and length of metaphysis plus diaphysis in tibias of CKO mice, were significantly decreased compared with those of the control mice. Furthermore, there was also a considerable reduction in the number of proliferating cell nuclear antigens and Ki67-stained proliferating chondrocytes in the tibia growth plate in the CKO mice. The chondrocyte proliferation mediated by GPER-1 was further demonstrated via treatment with a GPER-1 antagonist in cultured epiphyseal cartilage. This study demonstrates that GPER-1 positively regulates chondrocyte proliferation at the growth plate during early puberty and contributes to the longitudinal growth of long bones.

Beschreibung: In this study, we demonstrated generation and transmission of 114 Gbaud and 126 Gbaud faster-than-Nyquist (FTN) discrete Fourier transform-spread (DFT-spread) quadrature phase shift keying orthogonal frequency division multiplexing (QPSK-OFDM) with 88-Gsa/s sampling rate digital-to-analog converters (DACs) experimentally. It is the first time to realize 400G FTN DFT-spread QPSK-OFDM signal per optical carrier for metro and regional applications, which will be a solution for network operators to address the issue of increasing bandwidth derived from the rapid popularization of mobile Internet and the wide application of IoT (Internet of Things technology). Delay-and-add filter (DAF) is adopted to realize frequency shaping at the transmitter to keep higher portions of energy of signal at low frequencies, which makes the OFDM much more robust to strong filtering effect. After pre-equalization, bit error rate (BER) performance of 114 GBaud and 126 GBaud FTN DFT-spread QPSK-OFDM has been significantly improved, and maximum-likelihood sequence estimation (MLSE) shows a better effect than binary decoding in the aspect of against the inter symbol interference (ISI) introduced by spectrum compression. The effective bit rate of dual polarization 126 Gbaud FTN DFT-spread QPSK-OFDM which is generated with 88 GSa/s sampling rate is 410.08 Gb/s, to the exclusion of all overhead including TSs, cyclic prefix (CP), and 20% forward error correction (FEC) coding. We successfully transmit 8 × 400 Gbit/s FTN DFT-spread QPSK-OFDM signal generated from 88 Gsa/s sampling rate DAC over 420 km single mode fiber (SMF) with the BER under 2.4 × 10−2.

Beschreibung: In Ganzhou City, China, a complex bedrock lithology and structure, diverse topography, frequent engineering works, and abundant rainfall generate frequent, sudden, small-scale landslides that are difficult to prevent and control. This study integrates evidence data from a field investigation of landslides with geological-engineering analogues to document the distribution and development of these geohazards in Ganzhou City. Based on the distribution of landslides across different types of bedrock and soil, we identify five lithological groups prone to slope failure: granite, metamorphics (slate and phyllite), red sedimentary layers, clastic sedimentary rocks with weak interlayers, and loose Quaternary deposits. Granite and metamorphic bedrock are the two lithologies most prone to landslides. Our analysis of the genesis and mode of slope failure suggests that most landslides in Ganzhou City originated from four modes of slope failure: scouring erosion collapse, steep slope collapse, rock sliding along a rock stratum, and wedge-shaped block sliding and caving. An in-situ model test and numerical simulations were used to explore the evolution of slope deformation and failure on the most landslide-prone lithological groups, and the accumulation of debris post-failure. This work provides a reference for the assessment of the risk from, and the management of, landslide geohazards in Ganzhou City and geologically similar regions.

Beschreibung: Clinicians, biologists, physicists, engineers, and computer scientists are coming together to better understand heart disease, which is currently the leading cause of death globally. Optical mapping, a high-speed fluorescence imaging technique that visualizes and measures key cardiac parameters such as action potentials, cytosolic calcium transients, and fibrillation dynamics, is a core research tool that has arisen from such interdisciplinary collaborations. In an effort to broaden its use, especially among clinical scientists and students, we developed a complete and low-cost optical mapping system, including a constant-flow Langendorff perfusion system, which minimizes the economic threshold to widespread use of this powerful tool in cardiac electrophysiology research. The system described here provides high spatiotemporal resolution data about action potentials, intracellular calcium transients and fibrillation wave dynamics in isolated Langendorff-perfused hearts (pigs and rabbits), relevant for translational research. All system components and software elements are fully disclosed with the aim of increasing the use of this affordable and highly versatile tool among clinicians, basic scientists and students wishing to tackle their own research questions with their own customizable systems.

Beschreibung: In this study, we investigate the genetic determinants that underlie epilepsy in a captive baboon pedigree and evaluate the potential suitability of this non-human primate model for understanding the genetic etiology of human epilepsy. Archived whole-genome sequence data were analyzed using both a candidate gene approach that targeted variants in baboon homologs of 19 genes (n = 20,881 SNPs) previously implicated in genetic generalized epilepsy (GGE) and a more agnostic approach that examined protein-altering mutations genome-wide as assessed by snpEff (n = 36,169). Measured genotype association tests for baboon cases of epileptic seizure were performed using SOLAR, as well as gene set enrichment analyses (GSEA) and protein–protein interaction (PPI) network construction of top association hits genome-wide (p 〈 0.01; n = 441 genes). The maximum likelihood estimate of heritability for epileptic seizure in the pedigreed baboon sample is 0.76 (SE = 0.77; p = 0.07). Among candidate genes for GGE, a significant association was detected for an intronic SNP in RBFOX1 (p = 5.92 × 10–6; adjusted p = 0.016). For protein-altering variants, no genome-wide significant results were observed for epilepsy status. However, GSEA revealed significant positive enrichment for genes involved in the extracellular matrix structure (ECM; FDR = 0.0072) and collagen formation (FDR = 0.017), which was reflected in a major PPI network cluster. This preliminary study highlights the potential role of RBFOX1 in the epileptic baboon, a protein involved in transcriptomic regulation of multiple epilepsy candidate genes in humans and itself previously implicated in human epilepsy, both focal and generalized. Moreover, protein-damaging variants from across the genome exhibit a pattern of association that links collagen-containing ECM to epilepsy risk. These findings suggest a shared genetic etiology between baboon and human forms of GGE and lay the foundation for follow-up research.

Beschreibung: Multidecadal sea level variation in the Baltic Sea is investigated from 1900 to 2020 deploying satellite and in situ datasets. As a part of this investigation, nearly 30 years of satellite altimetry data are used to compare with tide gauge data in terms of linear trend. This, in turn, leads to validation of the regional uplift model developed for the Fennoscandia. The role of North Atlantic Oscillation (NAO) in multidecadal variations of the Baltic Sea is also analyzed. Although NAO impacts the Baltic Sea level on seasonal to decadal time scales according to previous studies, it is not a pronounced factor in the multidecadal variations. The acceleration in the sea level rise of the basin is reported as statistically insignificant in recent studies or even decelerating in an investigation of the early 1990s. It is shown that the reason for these results relates to the global warming hiatus in the 1950s−1970s, which can be seen in all eight tide gauges used for this study. To account for the slowdown period, the acceleration in the basin is investigated by fitting linear trends to time spans of six to seven decades, which include the hiatus. These results imply that the sea level rise is accelerated in the Baltic Sea during the period 1900–2020.

Beschreibung: The Mascarenes are sadly famous worldwide for the massive extinction of their native vertebrates since recent human colonization. However, extinction patterns show astonishing disparities between the two main islands and between lineages of forest vertebrates. On Réunion (2,512 km2, 3,070 m) where about a third of native habitats remains, most large-bodied vertebrates, especially frugivores, collapsed by the first half of the 18th century, while several have survived longer and some still exist on Mauritius (1,865 km2, 828 m) where more than 95% of native habitats have been transformed. Considering lineages of forest vertebrates shared by both islands (23 genera, 53 species), we test the hypothesis that differing patterns of lowland suitable habitat destruction is the main cause behind this paradox. Before that, we assess the potential impact of other major drivers of extinctions since first contact with humans. Firstly, Mauritius shows earlier and more numerous introductions of mammal predators known for their devastating impact (except northern islets which have thus become important sanctuaries for several squamates). Secondly, settlers were inveterate hunters on both islands, but while Réunion was overhunted before Mauritius, the burst of human population in the latter in late 18th century has not led to the rapid extinction of all large native vertebrates. These two factors alone therefore cannot explain the observed paradox. Rather, the early destruction of lowland habitats (

Beschreibung: The biomechanical role of the clasping leaf sheath in stalk lodging events has been historically understudied. Results from this study indicate that in some instances the leaf sheath plays an even larger role in reinforcing wheat against stalk lodging than the stem itself. Interestingly, it appears the leaf sheath does not resist bending loads by merely adding more material to the stalk (i.e., increasing the effective diameter). The radial preload of the leaf sheath on the stem, the friction between the sheath and the stem and several other complex biomechanical factors may contribute to increasing the stalk bending strength and stalk flexural rigidity of wheat. Results demonstrated that removal of the leaf sheath induces alternate failure patterns in wheat stalks. In summary the biomechanical role of the leaf sheath is complex and has yet to be fully elucidated. Many future studies are needed to develop high throughput phenotyping methodologies and to determine the genetic underpinnings of the clasping leaf sheath and its relation to stalk lodging resistance. Research in this area is expected to improve the lodging resistance of wheat.

Beschreibung: The impact of heat-absorbing viscoelastic nanofluidic flow along with a convectively heated porous Riga plate with Cattaneo-Christov double flux was analytically investigated. The Buongiorno model nanofluid was implemented with the diversity of Brownian motion and thermophoresis. Making use of the transformations; the PDE systems are altered into an ODE system. We use the homotopy analysis method to solve these systems analytically. The reaction of the apposite parameters on fluid velocity, fluid temperature, nanoparticle volume fraction skin friction coefficients (SFC), local Nusselt number and local Sherwood number are shown with vividly explicit details. It is found that the fluid velocities reflect a declining nature for the development of viscoelastic and porosity parameters. The liquid heat becomes rich when escalating the radiation parameter. In addition, the nanoparticle volume fraction displays a declining nature towards the higher amount of thermophoresis parameter, whereas the inverse trend was obtained for the Brownian motion parameter. We also found that the fluid temperature is increased in viscoelastic nanofluid compared to the viscous nanofluid. When we change the fluid nature from heat absorption to heat generation, the liquid temperature also rises. In addition, the fluid heat is suppressed when we change the flow medium from a stationary plate to a Riga plate for heat absorption/generation cases.

Beschreibung: 1,2:3,5-Di-O-isopropylidene-α-D-xylofuranose (DX) is a major component of a new bio-crude: a viscous oil presenting petroleum-friendly properties produced by the ketalization of sugarcane bagasse. This article studies DX HDO (hydrodeoxygenation) over a Pd/HBEA catalyst in a batch reactor at 250°C. The effects of hydrogen pressure from 10 to 40 bar, catalyst/DX ratio from ½ to 2, and reaction time 0–24 h were investigated. A range of conditions for complete hydrodeoxygenated DX into alkanes with a Pd/HBEA catalyst was found. In these conditions, a low coke yield with water as the principal deoxygenated product was obtained. Further, higher amounts of alkanes containing seven or more carbons (A7+) were favored at 30 bar of hydrogen pressure, Cat/DX ratio = 2, and short reaction time. Products analysis that accompanied the above variations during reaction time led to general insights into reaction pathways. First, in the presence of DX, an effective n-hexane conversion was not observed on experiments of low catalyst/DX ratio (½) or in the initial period of high Cat/DX ratio, suggesting DX is much more successful than n-hexane to compete for active sites. Then, the formation of a pool of oxygenated compounds, such as furans, ketones, and carboxylic acids, along with lighter and heavier alkanes was observed. Hence, the aforementioned oxygenates may undergo reactions, such as aldol condensation with subsequent hydrodeoxygenation reaction, generating heavier alkanes.

Beschreibung: The microbiota of the pretreatment phase is crucial to the assembly of the microbial community in the saccharification of fuyu-flavor baijiu. This study investigates the shifts in microbial community diversity from the pretreatment of raw materials to the end of saccharification. High-throughput sequencing reveals that Lactobacillus, Weissella, and Bacillus in the bacterial community and Rhizopus, Candida, Pichia, and Aspergillus in the fungal community are predominant during raw material pretreatment and saccharification processes. Also, 11 bacterial genera, including Bacillus, Lactobacillus, Leuconostoc, Weissella, Lactococcus, and Acetobacter, and eight yeast genera, including Candida, Pichia, Saccharomyces, and Wickerhamomyces, were isolated from the initial saccharification stage by culture-dependent approaches. Sourcetracker analysis indicates that the cooling grains and rice husks were the main contributors to the bacterial community composition of the saccharification process, and Qu was the main contributor to the shaping of the fungal community structure during the saccharification process. Abundance variation of the predictive functional profiles of microbial communities encoding for key enzymes involved in pyruvate metabolism, starch and sucrose metabolism, and glycolysis/gluconeogenesis during the pretreatment and saccharification phases were inferred by PICRUSt2 analysis. The results of this study will be utilized to produce consistently high-quality fuyu-flavor baijiu via better controlling the shaping of microbial community structures during the pretreatment and fermentation processes.

Beschreibung: Embryo movement is important for tissue differentiation and the formation of functional skeletal elements during embryonic development: reduced mechanical stimulation results in fused joints and misshapen skeletal rudiments with concomitant changes in the signaling environment and gene expression profiles in both mouse and chick immobile embryos. Despite the clear relationship between movement and skeletogenesis, the precise mechanisms by which mechanical stimuli influence gene regulatory processes are not clear. The primary cilium enables cells to sense mechanical stimuli in the cellular environment, playing a crucial mechanosensory role during kidney development and in articular cartilage and bone but little is known about cilia on developing skeletal tissues. Here, we examine the occurrence, length, position, and orientation of primary cilia across developing skeletal rudiments in mouse embryos during a period of pronounced mechanosensitivity and we report differences and similarities between wildtype and muscle-less mutant (Pax3Spd/Spd) rudiments. Strikingly, joint regions tend to have cilia positioned and oriented away from the joint, while there was a less obvious, but still significant, preferred position on the posterior aspect of cells within the proliferative and hypertrophic zones. Regions of the developing rudiments have characteristic proportions of ciliated cells, with more cilia in the resting and joint zones. Comparing wildtype to muscle-less mutant embryos, cilia are shorter in the mutant with no significant difference in the proportion of ciliated cells. Cilia at the mutant joint were also oriented away from the joint line.

Beschreibung: Parkinson’s disease (PD) is one of the most common neurodegenerative disorders that is implicated in aging populations. As numerous developed nations are experiencing progressively aging populations today, there is a heightened propensity for the occurrence of PD cases. Alpha-synuclein (α-syn) aggregation has been considered to be the pivotal mechanism leading to PD pathogenesis. Thus, early diagnostic and therapeutic strategies targeting the misfolded α-syn protein can potentially improve the prognosis of PD. With rapid advancements in nanotechnology in the last decade, effective solutions to various neurodegenerative and oncological diseases have been suggested. This review will explore the current innovations in nanotechnology that target the α-syn aggregation pathway, and reinstate the promise they hold as effective early diagnostic and therapeutic solutions to PD.

Beschreibung: Continuous electronic fetal monitoring and the access to databases of fetal heart rate (FHR) data have sparked the application of machine learning classifiers to identify fetal pathologies. However, most fetal heart rate data are acquired using Doppler ultrasound (DUS). DUS signals use autocorrelation (AC) to estimate the average heartbeat period within a window. In consequence, DUS FHR signals loses high frequency information to an extent that depends on the length of the AC window. We examined the effect of this on the estimation bias and discriminability of frequency domain features: low frequency power (LF: 0.03–0.15 Hz), movement frequency power (MF: 0.15–0.5 Hz), high frequency power (HF: 0.5–1 Hz), the LF/(MF + HF) ratio, and the nonlinear approximate entropy (ApEn) as a function of AC window length and signal to noise ratio. We found that the average discriminability loss across all evaluated AC window lengths and SNRs was 10.99% for LF 14.23% for MF, 13.33% for the HF, 10.39% for the LF/(MF + HF) ratio, and 24.17% for ApEn. This indicates that the frequency domain features are more robust to the AC method and additive noise than the ApEn. This is likely because additive noise increases the irregularity of the signals, which results in an overestimation of ApEn. In conclusion, our study found that the LF features are the most robust to the effects of the AC method and noise. Future studies should investigate the effect of other variables such as signal drop, gestational age, and the length of the analysis window on the estimation of fHRV features and their discriminability.