bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long term survival ofDehalococcoides mccartyistrains in mixed cultures under electron acceptor and ammonium limitation
Authors: Morson Nadia , Molenda Olivia , Picott Katherine J. , Richardson Ruth E. , Edwards Elizabeth A. 
Published: December 2020

AbstractFew strains ofDehalococcoides mccartyiharbour and express the vinyl chloride reductase (VcrA) that catalyzes the dechlorination of vinyl chloride (VC), a carcinogenic soil and groundwater contaminant. ThevcrAoperon is found on a Genomic Island (GI) and therefore believed to participate in horizontal gene transfer. To try to induce horizontal gene transfer of thevcrA-GI, we blended two enrichment cultures in medium without ammonium while providing VC. We hypothesized that these conditions would select for a mutant strain ofD. mccartyithat could both fix nitrogen and respire VC. However, after more than 4 years of incubation, we found no evidence for horizontal gene transfer of thevcrA-GI. Rather, we observed VC-dechlorinating activity attributed to the trichloroethene reductase TceA. Sequencing and protein modelling revealed a mutation in the predicted active site of TceA which may have influenced substrate specificity. We also identified two nitrogen-fixingD. mccartyistrains in the KB-1 culture. The presence of multiple strains ofD. mccartyiwith distinct phenotypes is a feature of natural environments and certain enrichment cultures (such as KB-1) and may enhance bioaugmentation success. The fact that multiple distinct strains persist in the culture for decades and that we could not induce horizontal gene transfer of thevcrA-GI suggests that it is not as mobile as predicted, or that mobility is restricted in ways yet to be discovered to specific sub-clades ofDehalococcoides.TOC Art
The Chemical Structure of Widespread Microbial Aryl Polyene Lipids
Authors: Grammbitter Gina L. C. , Shi Yi-Ming , Shi Yan-Ni , Vemulapalli Sahithya P. B. , Richter Christian , Schwalbe Harald , Alanjary Mohammad , Schüffler Anja , Witt Matthias , Griesinger Christian , Bode Helge B. 
Published: December 2020

AbstractBiosynthetic gene clusters (BGC) involved in aryl polyene (APE) biosynthesis are supposed to represent the most widespread BGC in the bacterial world.[1–3]Still, only hydrolysis products[4–8]and not the full-length product(s) have been identified, hindering studies on their biosynthesis and natural function. Here, we apply subsequent chromatographic separations to purify the aryl polyene-containing lipids (APELs) from the entomopathogenic bacteriumXenorhabdus doucetiae. Structure elucidation using a combination of isotope labeling, nuclear magnetic resonance techniques, and tandem mass spectrometry reveals an array of APELs featuring an all-transC26:5 conjugated fatty acyl and a galactosamine-phosphate-glycerol moiety. In combination with extensive genetic studies, this research broadens the bacterial natural product repertoire and paves the way for future functional characterization of this almost universal microbial compound class. Due to their protective function against reactive oxygen species,[5,9]APELs might be important for virulence or symbiosis, mediating organismic interactions in several ecological niches.
Soil microbial communities are not altered by garlic mustard in recently invaded central Illinois forests
Authors: Edwards Joseph D. , Yang Wendy H. , Yannarell Anthony C. 
Published: December 2020

AbstractThe invasive forest plant garlic mustard (Alliaria petiolata) has been shown to alter soil microbial communities in the northeastern part of its invaded range in the United States, and this disruption of soil communities may contribute to its invasion success. However, garlic mustard allelochemistry can vary with invasion age, and it is not clear whether garlic mustard’s impacts on soil microbes are consistent over its invaded range. Here, we compare the composition and diversity of soil fungal, bacterial, and archaeal communities among garlic mustard present, absent, and removed treatments in replicated blocks across five forests in the midwestern United States with relatively young garlic mustard invasions (approximately 17-26 years old, with consistent management). We collected samples in May and August, corresponding to garlic mustard active and senescent life history stages. While soil fungal and bacterial/ archaeal communities (based on ITS2 region and 16S rRNA gene DNA sequencing, respectively) differed significantly between different blocks/ forests and over time, we found no significant effect of garlic mustard treatment on soil microbial community composition or the relative abundance of mycorrhizal, saprotrophic, or pathogenic fungal guilds. The lack of garlic mustard impacts on the soil microbial community in recently invaded central Illinois forests suggests that these well-documented impacts in the northeastern United States and in older invasions cannot necessarily be generalized across all environmental contexts.
TheSINGLE FLOWER (SFL)gene encodes a MYB transcription factor that regulates the number of flowers produced by the inflorescence of chickpea
Authors: Caballo Cristina , Berbel Ana , Ortega Raul , Gil Juan , Millán Teresa , Rubio Josefa , Madueño Francisco 
Published: December 2020

SUMMARYresearch conducted & rationaleLegume species usually have compound inflorescences, where flowers appear in secondary inflorescences (I2), at lateral positions of the primary inflorescence (I1), in contrast to simple inflorescences, as inArabidopsis, where flowers are formed in the primary inflorescence stem. The number of flowers per I2, characteristic of each legume species, determines inflorescence diversity, and the number of pods produced, which can affect yield. Gene Regulatory Network that controls the activity of I2 meristems, and therefore the number of flowers per secondary inflorescence is mostly unknown, as well as how specific are factors controlling this trait and whether they share this function in other meristems.methodsChickpea produces one flower per I2 butsingle flower(sfl) mutants produce two (double-pod phenotype). By mapping thesfl-dmutation and identification and analysis of a second mutant allele we have isolatedSFL. We used scanning electron microscopy to study the effect ofsflmutations on inflorescence ontogeny andin situhybridization to study the expression ofSFLand of meristem identity genes in the developing chickpea inflorescence.key resultWe show that theSFLgene corresponds toCaRAX1/2a, encoding a MYB transcription factor. Our results show thatCaRAX1/2a / SFLis specifically expressed in the I2 meristem, possibly activated byCaVEGETATIVE1.main conclusion & key points for discussionOur findings reveal thatSFLplays a central role in the control of chickpea inflorescence architecture, specifically acting in the I2 meristem to control the time length for which it is active, and therefore determining the number of floral meristems that it can produce.
End-to-end optimization of prosthetic vision
Authors: de Ruyter van Steveninck Jaap , Güçlü Umut , van Wezel Richard , van Gerven Marcel 
Published: December 2020

AbstractNeural prosthetics may provide a promising solution to restore visual perception in some forms of blindness. The restored prosthetic percept is rudimentary compared to normal vision and can be optimized with a variety of image preprocessing techniques to maximize relevant information transfer. Extracting the most useful features from a visual scene is a non-trivial task and optimal preprocessing choices strongly depend on the context. Despite rapid advancements in deep learning, research currently faces a difficult challenge in finding a general and automated preprocessing strategy that can be tailored to specific tasks or user requirements. In this paper we present a novel deep learning approach that explicitly addresses this issue by optimizing the entire process of phosphene generation in an end-to-end fashion. The proposed model is based on a deep auto-encoder architecture and includes a highly adjustable simulation module of prosthetic vision. In computational validation experiments we show that such an approach is able to automatically find a task-specific stimulation protocol. The presented approach is highly modular and could be extended to dynamically optimize prosthetic vision for everyday tasks and requirements of the end-user.
Transcriptional analysis of immune modulatory genes in melanoma treated with PD-1 blockade
Authors: Song Hyojin , Lee Sungyoung , Lee Se-Hoon , Kim Miso , Lee Sang Yup , Yoon Sung-Soo , Yun Hongseok , Koh Youngil 
Published: December 2020

Abstract/SummaryWe aimed to characterize immunological features of melanoma patients treated with PD-1 blockade using tumor transcriptomic datasets. Response-dependent and response-independent predictors based on biological knowledge were investigated. Domain knowledge-driven regression-based analysis identifiedCEACAM1, CD40, B7-H3, andCD112as key genes that determine the melanoma immune status. We devised the transcriptional deviance score (TDS) representing the individual sample-wise contribution to the immune network. TheTDSnot only showed good predictive power for immune checkpoint inhibitor (ICI) responses but also suggested specific gene interactions that determine ICI responses. DynamicTDSchanges following ICI treatment were related to long survival, indicating immune network modulation by ICIs occurred in responders. A predictive model incorporatingB7-H3andCEACAM1expression, mutational status, clinical features, and theTDSshowed excellent performance for ICI response. Thus, our approaches suggest a novel measure for the tumor immune temperature and provide insight into melanoma immunobiology.HighlightsWe applied outcome-independent and outcome-dependent methods to investigate melanoma immunobiology.CEACAM1, CD40, B7-H3, andCD112expression levels are key determinants of immune status.We devised aTDSthat could measure tumor immune network status at the individual level.Incorporating regression and correlation approaches greatly improves predictive power.
Growth stage-dependent changes of the levels of keratin 1 and keratin 10 as well as skin’s green autofluorescence of the back and the ears of C57BL/6 mice under basal conditions and after UVC irradiation
Authors: Yang Zhaoxia , Zhang Mingchao , Ying Weihai 
Published: December 2020

AbstractOur previous studies have indicated that oxidative stress and inflammation can dose-dependently induce increased skin’s green autofluorescence (AF) of mice, which results at least partially from keratin 1 (K1) cleavage. Increased green AF was also found in patients’ skin of several major diseases, which may become a novel biomarker for non-invasive diagnosis. We also found age-dependent changes of the skin’s green AF of natural populations. In this study we tested our hypothesis that there are growth stage-dependent changes of K1 and keratin 10 (K10) levels in the skin of mice, which may underlie the age-dependent changes of the skin’s green AF. We found that in the skin of both mice’s back and ears, there were growth stage-dependent changes of the levels of K1 and K10 as well as the basal green AF. The K1 and K10 levels in the back’s skin were significantly different from those in the ear’s skin. There were also growth stage-dependent changes of the UVC-induced changes of K1 and K10 levels of both the ears and the back. Collectively, our study has provided first evidence showing growth stage-dependent and differential changes of the levels of K1 and K10 as well as skin’s green AF in the back and the ears of mice under basal conditions and after UVC irradiation. These findings are valuable for understanding the age-dependent changes of the skin’s green AF of natural populations, which are also important for establishing the keratins’ AF-based method for non-invasive diagnosis of diseases.
Comprehensive analysis of hsa-miR-654-5p’s tumor-suppressing functions
Authors: Liu Chuanyang , Min Lu , Kuang Jingyu , Zhu Chu-shu , Qiu Xinyuan , Wu Xiaomin , Zhang Tianyi , Xie Sisi , Zhu Lingyun 
Published: December 2020

ABSTRACTThe pivotal roles of miRNAs in carcinogenesis, metastasis, and prognosis have been demonstrated recently in various cancers. This study intended to investigate the specific roles of hsa-miR-654-5p in lung cancer, which was poorly discussed. A series of closed-loop bioinformatic functional analyses were integrated within vitroexperimental validation to explore the overall biological functions and pan-cancer regulation pattern of miR-654-5p. We found that miR-654-5p abundance was significantly elevated in LUAD tissues and correlated with patients’ survival. 275 potential targets of miR-654-5p were then identified and the miR-654-5p-RNF8 regulation axis was validatedin vitroas a proof of concept. Furthermore, we revealed the tumor-suppressing roles of miR-654-5p and demonstrated that miR-654-5p inhibited lung cancer cell epithelial-mesenchymal transition (EMT) process, cell proliferation, and migration using target-based, abundance-based and ssGSEA-based bioinformatic methods andin vitrovalidation. Following the construction of a protein-protein interaction network, 11 highly interconnected hub genes were identified and a five genes risk scoring model was developed to assess their potential prognostic ability. Our study will not only provide a basic miRNA-mRNA-phenotypes reference map for understanding the function of miR-654-5p in different cancers but also reveal the tumor-suppressing roles and prognostic values of miR-654-5p in lung cancer.Graphical abstract
Disinfection of Methicillin-ResistantStaphylococcus aureus, Vancomycin-resistantEnterococcus faeciumandAcinetobacter baumanniiusing Klaran WD array system
Authors: Mariita Richard M. , Randive Rajul V. 
Published: December 2020

AbstractHealthcare-associated infections (HAIs) are a major burden in healthcare systems. In this study, UVC LEDs emitting radiation from 260-270 nm were evaluated for effectiveness in reducing methicillin-resistantStaphylococcus aureus(MRSA), vancomycin-resistant enterococci (VRE), andAcinetobacter baumannii. The array has four WD LEDs, each with 70mW placed at 7cm from test organism. With 11.76 mJ/cm2, the study obtained 99.99% reduction (log10 reduction factor of 4) against MRSA and VRE. ForA. baumannii, 9 mJ/cm2obtained 99.999% reduction (log10 reduction factor of 5). These results present scientific evidence on how effective UVC LEDs can be used in the fight against HAIs.
Evidence of a dysregulated Vitamin D pathway in SARS-CoV-2 infected patient’s lung cells
Authors: George Bijesh , Amjesh Ravikumar , Paul Aswathy Mary , Kumar T. R. Santhosh , Pillai Madhavan Radhakrishna , Kumar Rakesh 
Published: December 2020

AbstractAlthough a defective vitamin D pathway has been widely suspected to be associated in SARS-CoV-2 pathobiology, the status of the vitamin D pathway and vitamin D-modulated genes in lung cells of patients infected with SARS-CoV-2 remains unknown. To understand the significance of the vitamin D pathway in SARS-CoV-2 pathobiology, computational approaches were applied to transcriptomic datasets from bronchoalveolar lavage fluid (BALF) cells of such patients or healthy individuals. Levels of vitamin D receptor, retinoid X receptor, and CYP27A1 in BALF cells of patients infected with SARS-CoV-2 were found to be reduced. Additionally, 107 differentially expressed, predominantly downregulated genes modulated by vitamin D were identified in transcriptomic datasets from patient’s cells. Further analysis of differentially expressed genes provided eight novel genes with a conserved motif with vitamin D-responsive elements, implying the role of both direct and indirect mechanisms of gene expression by the dysregulated vitamin D pathway in SARS-CoV-2-infected cells. Network analysis of differentially expressed vitamin D-modulated genes identified pathways in the immune system, NF-KB/cytokine signaling, and cell cycle regulation as top predicted pathways that might be affected in the cells of such patients. In brief, the results provided computational evidence to implicate a dysregulated vitamin D pathway in the pathobiology of SARS-CoV-2 infection.
Coordinated Changes in Gene Expression Kinetics Underlie both Mouse and Human Erythroid Maturation
Authors: Barile Melania , Imaz-Rosshandler Ivan , Inzani Isabella , Ghazanfar Shila , Nichols Jennifer , Marioni John C. , Guibentif Carolina , Göttgens Berthold 
Published: December 2020

AbstractBackgroundSingle cell technologies are transforming biomedical research, including the recent demonstration that unspliced pre-mRNA present in single cell RNA-Seq permits prediction of future expression states. Here we applied this ‘RNA velocity concept’ to an extended timecourse dataset covering mouse gastrulation and early organogenesis.ResultsIntriguingly, RNA velocity correctly identified epiblast cells as the starting point, but several trajectory predictions at later stages were inconsistent with both real time ordering and existing knowledge. The most striking discrepancy concerned red blood cell maturation, with velocity-inferred trajectories opposing the true differentiation path. Investigating the underlying causes revealed a group of genes with a coordinated step-change in transcription, thus violating the assumptions behind current velocity analysis suites, which do not accommodate time-dependent changes in expression dynamics. Using scRNA-Seq analysis of chimeric mouse embryos lacking the major erythroid regulatorGata1, we show that genes with the step-changes in expression dynamics during erythroid differentiation fail to be up-regulated in the mutant cells, thus underscoring the coordination of modulating transcription rate along a differentiation trajectory. In addition to the expected block in erythroid maturation, theGata1-chimera dataset revealed induction of PU.1 and expansion of megakaryocyte progenitors. Finally, we show that erythropoiesis in human fetal liver is similarly characterized by a coordinated step-change in gene expression.ConclusionsBy identifying a limitation of the current velocity framework coupled within vivoanalysis of mutant cells, we reveal a coordinated step-change in gene expression kinetics during erythropoiesis, with likely implications for many other differentiation processes.
A derived ZW chromosome system inAmborella trichopoda, the sister species to all other extant flowering plants
Authors: Käfer Jos , Bewick Adam , Andres-Robin Amélie , Lapetoule Garance , Harkess Alex , Caïus José , Fogliani Bruno , Gâteblé Gildas , Ralph Paula , dePamphilis Claude W. , Picard Franck , Scutt Charlie P. , Leebens-Mack James , Marais Gabriel AB 
Published: December 2020

AbstractSex determination is poorly understood in plants.Amborella trichopodais a well-known plant model for evo-devo studies, which is also dioecious (has male and female individuals), with an unknown sex determination mechanism.A. trichopodais a “sex switcher”, which points to possible environmental factors that act on sex, but populations grown from seed under greenhouse conditions exhibit a 50:50 sex ratio, which indicates the operation of genetic factors. Here, we use a new method (SDpop) to identify sex-linked genes from genotyping data of male and female individuals sampled in the field, and find thatA. trichopodahas a ZW sex-chromosome system. The sex-linked genes map to a 4 Mb sex-determining region on chromosome 9. The low extent of ZW divergence suggests these sex chromosomes are of recent origin, which is consistent with dioecy being derived character in theA. trichopodalineage. Our work has uncovered clearly formed sex chromosomes in a species in which both genetic and environmental factors can influence sex.One Sentence SummaryAmborella trichopoda, a dioecious species in which both genetics and the environment influence sex, possesses a pair of quite recently evolved ZW chromosomes.
Liver Electrical Impedance Tomography for Early Identification of Fatty Infiltrate in Obesity
Authors: Chang Chih-Chiang , Huang Zi-Yu , Shih Shu-Fu , Luo Yuan , Ko Arthur , Cui Qingyu , Cavallero Susana , Das Swarna , Thames Gail , Bui Alex , Jacobs Jonathan P. , Pajukanta Päivi , Wu Holden , Tai Yu-Chong , Li Zhaoping , Hsiai Tzung K. 
Published: December 2020

AbstractNon-alcoholic fatty liver disease (NAFLD) is endemic in developed countries and is one of the most common causes of cardiometabolic diseases in overweight/obese individuals. While liver biopsy or magnetic resonance imaging (MRI) is the current gold standard to diagnose NAFLD, the former is prone to bleeding and the latter is costly. We hereby demonstrated liver electrical impedance tomography (EIT) as a non-invasive and portable detection method for fatty infiltrate. We enrolled 19 subjects (15 females and 4 males; 27 to 74 years old) to undergo liver MRI scans, followed by EIT measurements via a multi-electrode array. The liver MRI scans provided subject-specifica prioriknowledge of the liver boundary conditions for segmentation and EIT reconstruction, and the 3-D multi-echo MRI data quantified liver proton-density fat fraction (PDFF%) as a recognized reference standard for validating liver fat infiltrate. Using acquired voltage data and the reconstruction algorithm for the EIT imaging, we computed the absolute conductivity distribution of abdomen in 2-D. Correlation analyses were performed to compare the individual EIT conductivity vs. MRI PDFF with their demographics in terms of gender, BMI (kg·m−2), age (years), waist circumference (cm), height (cm), and weight (kg). Our results indicate that EIT conductivity (S·m−1) and liver MRI for PDFF were not correlated with the demographics, whereas the decrease in EIT conductivity was correlated with the increase in MRI PDFF (R= − 0.69,p= 0.003). Thus, EIT conductivity holds promise for developing a non-invasive, portable, and quantitative method to detect fatty liver disease.