bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct Observation of Electrically Conductive Pili Emanating fromGeobacter sulfurreducens
Authors: Liu Xinying , Walker David J. F. , Nonnenmann Stephen S. , Sun Dezhi , Lovley Derek R. 
Published: July 2021

AbstractGeobacter sulfurreducensis a model microbe for elucidating the mechanisms for extracellular electron transfer in several biogeochemical cycles, bioelectrochemical applications, and microbial metal corrosion. Multiple lines of evidence previously suggested that electrically conductive pili (e-pili) are an essential conduit for long-range extracellular electron transport inG. sulfurreducens. However, it has recently been reported thatG. sulfurreducensdoes not express e-pili and that filaments comprised of multi-hemec-type cytochromes are responsible for long-range electron transport. This possibility was directly investigated by examining cells, rather than filament preparations, with atomic force microscopy. Approximately 90 % of the filaments emanating from wild-type cells had a diameter (3 nm) and conductance consistent with previous reports of e-pili harvested fromG. sulfurreducensor heterologously expressed inE. colifrom theG. sulfurreducenspilin gene. The remaining 10% of filaments had a morphology consistent with filaments comprised of thec-type cytochrome OmcS. A strain expressing a modified pilin gene designed to yield poorly conductive pili expressed 90 % filaments with a 3 nm diameter, but greatly reduced conductance, further indicating that the 3 nm diameter conductive filaments in the wild-type strain were e-pili. A strain in which genes for five of the most abundant outer-surfacec-type cytochromes, including OmcS, was deleted yielded only 3 nm diameter filaments with the same conductance as in the wild-type. These results demonstrate that e-pili are the most abundant conductive filaments expressed byG. sulfurreducens, consistent with previous functional studies demonstrating the need for e-pili for long-range extracellular electron transfer.ImportanceElectroactive microbes have significant environmental impacts as well as applications in bioenergy and bioremediation. The composition, function, and even existence of electrically conductive pili (e-pili) has been one of the most contentious areas of investigation in electromicrobiology, in part because e-pili offer a mechanism for long-range electron transport that does not involve the metal co-factors common in much of biological electron transport. This study demonstrates that e-pili are abundant filaments emanating fromGeobacter sulfurreducens, which serves as a model for long-range extracellular electron transfer in direct interspecies electron transfer, dissimilatory metal reduction, microbe-electrode exchange, and corrosion caused by direct electron uptake from Fe(0). The methods described in this study provide a simple strategy for evaluating the distribution of conductive filaments throughout the microbial world with an approach that avoids artifactual production and/or enrichment of filaments that may not be physiologically relevant.
The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA
Authors: Rolando Jose L. , Kolton Max , Song Tianze , Kostka J.E. 
Published: July 2021

AbstractBackgroundSalt marshes are dominated by the smooth cordgrass Spartina alterniflora on the US Atlantic and Gulf of Mexico coastlines. Although soil microorganisms are well known to mediate important biogeochemical cycles in salt marshes, little is known about the role of root microbiomes in supporting the health and productivity of marsh plant hosts. Leveraging in situ gradients in aboveground plant biomass as a natural laboratory, we investigated the relationships between S. alterniflora primary productivity, sediment redox potential, and the physiological ecology of bulk sediment, rhizosphere, and root microbial communities at two Georgia barrier islands over two growing seasons.ResultsA marked decrease in prokaryotic alpha diversity with high abundance and increased phylogenetic dispersion was found in the S. alterniflora root microbiome. Significantly higher rates of enzymatic organic matter decomposition, as well as the relative abundances of putative sulfur (S)-oxidizing, sulfate-reducing, and nitrifying prokaryotes correlated with plant productivity. Moreover, these functional guilds were overrepresented in the S. alterniflora rhizosphere and root core microbiomes. Core microbiome bacteria from the Candidatus Thiodiazotropha genus, with the metabolic potential to couple S oxidation with C and N fixation, were shown to be highly abundant in the root and rhizosphere of S. alterniflora.ConclusionsThe S. alterniflora root microbiome is dominated by highly active and competitive species taking advantage of available carbon substrates in the oxidized root zone. Two microbially-mediated mechanisms are proposed to stimulate S. alterniflora primary productivity: (i.) Enhanced microbial activity replenishes nutrients and terminal electron acceptors in higher biomass stands, and (ii.) coupling of chemolithotrophic S oxidation with carbon (C) and nitrogen (N) fixation by root and rhizosphere associated prokaryotes detoxify sulfide in the root zone while potentially transferring fixed C and N to the host plant.
Oxidative phosphorylation safeguards pluripotency via UDP-N-acetylglucosamine
Authors: Cao Jiani , Li Meng , Liu Kun , Shi Xingxing , Sui Ning , Yao Yuchen , Wang Xiaojing , Tan Shaojing , Zhao Qian , Wang Liang , Chai Xiahua , Zhang Lin , Liu Chong , Li Xing , Chang Zhijie , Li Dong , Zhao Tongbiao 
Published: July 2021

ABSTRACTThe roles of mitochondrial respiration in pluripotency remain largely unknown. We show here that mouse ESC mitochondria possess superior respiration capacity compared to somatic cell mitochondria, and oxidative phosphorylation (OXPHOS) generates the majority of cellular ATP in ESCs. Inhibition of OXPHOS results in extensive pluripotency and metabolic gene expression reprogram, leading to disruption of self-renewal and pluripotency. Metabolomics profiling identifies UDP-N-acetylglucosamine (UDP-GlcNAc) as one of the most significantly decreased metabolites in response to OXPHOS inhibition. The loss of ESC identity induced by OXPHOS inhibition can be ameliorated by directly adding GlcNAc both in vitro and in vivo. This work demonstrates that mitochondrial respiration, but not glycolysis, produces the majority of ATP in ESCs, and uncovers a novel mechanism whereby mitochondrial respiration is coupled with the hexosamine biosynthesis pathway to generate UDP-GlcNAc for ESC identity maintenance.SIGNIFICANCEOxidative phosphorylation (OXPHOS) and glycolysis are the two major pathways for generating ATP in mammalian cells. It is widely assumed that somatic cells utilize OXPHOS, whereas embryonic stem cells (ESCs) utilize glycolysis with low mitochondrial respiration rates even under aerobic conditions. However, the relative contribution of OXPHOS and glycolysis to ATP generation in ESCs, and the role of mitochondrial respiration in regulating ESC identity, have remained unclear. In this study, Cao et al demonstrate that mouse ESC mitochondria have a significantly higher respiration capacity than somatic cell mitochondria. Oxidative phosphorylation produces the majority of cellular ATP in mESCs and is coupled with the hexosamine biosynthesis pathway to generate UDP-GlcNAc for pluripotency maintenance. These findings define the function and mechanism of OXPHOS in regulating pluripotency, and challenge the traditional concept that mESCs rely on glycolysis over OXPHOS for their major supply of energy.HIGHLIGHTSESC mitochondria have a significantly higher respiration capability than somatic cell mitochondriaOXPHOS, but not glycolysis, produces the majority of cellular ATP in ESCsOXPHOS inhibition induces a decrease in O-GlcNAcylation and the expression of pluripotency genes in blastocysts that can be partially rescued by adding GlcNAcOXPHOS is coupled with the hexosamine biosynthesis pathway for UDP-GlcNAc biosynthesis to maintain ESC identity
Vibrio cholerae motility in aquatic and mucus-mimicking environments
Authors: Grognot Marianne , Mittal Anisha , Mah’moud Mattia , Taute Katja M. 
Published: July 2021

AbstractCholera disease is caused by Vibrio cholerae infecting the lining of the small intestine and results in severe diarrhea. V. cholerae’s swimming motility is known to play a crucial role in pathogenicity and may aid the bacteria in crossing the intestinal mucus barrier to reach sites of infection, but the exact mechanisms are unknown. The cell can be either pushed or pulled by its single polar flagellum, but there is no consensus on the resulting repertoire of motility behaviors.We use high-throughput 3D bacterial tracking to observe V. cholerae swimming in buffer, in viscous solutions of the synthetic polymer PVP, and in mucin solutions that may mimic the host environment. We perform a statistical characterization of its motility behavior on the basis of large 3D trajectory datasets. We find that V. cholerae performs asymmetric run-reverse-flick motility, consisting of a sequence of a forward run, reversal, and a shorter backward run, followed by a turn by approximately 90°, called a flick, preceding the next forward run. Unlike many run-reverse-flick swimmers, V. cholerae’s backward runs are much shorter than its forward runs, resulting in an increased effective diffusivity. We also find that the swimming speed is not constant, but subject to frequent decreases. The turning frequency in mucin matches that observed in buffer. Run-reverse-flick motility and speed fluctuations are present in all environments studied, suggesting that these behaviors may also occur in natural aquatic habitats as well as the host environment.ImportanceCholera disease produces vomiting and severe diarrhea and causes approximately 100,000 deaths per year worldwide. The disease is caused by the bacterium Vibrio cholerae colonizing the lining of the small intestine. V. cholerae’s ability to swim is known to increase its infectivity, but the underlying mechanisms are not known. One possibility is that swimming may aid in crossing the protective mucus barrier that covers the lining of the small intestine. Our work characterizing how V. cholerae swims in environments that mimic properties of the host environment may advance the understanding of how motility contributes to infection.
Dual-lipid metabolomics revealed the communication of MTB or MB with Bovine alveolar macrophages in lipid metabolisms
Authors: Gao Weifeng , Cai Yurong , Zhang Gang , Wang Xiaoping , Wang Juan , Li Yong , Wang Yujiong 
Published: July 2021

ABSTRACTM. tuberculosis(MTB) and M. bovis(MB) of the Mycobacterium tuberculosis complex (MTBC) are the causative agents of the notorious infectious disease tuberculosis(TB) in a range of mammals, including cattle and human. The lipid composition of MTB/MB performed imperative function as invading host macrophage. In the present study, a dual-lipid metabolomics were used to elucidate the differences in lipid composition of MTB and MB and the different responses in lipid metabolisms of bovine alveolar macrophage challenged by MTB/MB. The lipid metabolomics of MTB and MB indicated that there were significant differences in lipid composition of both bacteria that the level of various lipids belonged to Glycerophospholipids, Sterol Lipids, Fatty Acyls and Polyketides exhibited differences between MTB and MB. Meanwhile, both MTB and MB with different lipid composition could invoked different responses in lipid metabolisms of the host macrophage. MTB infection mainly induced the increase in content of Polyketides and Glycerophospholipids in macrophages, whereas MB infection induced the level of Glycerophospholipids and Sterol Lipids of macrophages. Furthermore, we identified TAG 13:0-18:5-18:5 of MTB and PC(16:1(9E)/0:0), PI(20:2(11Z,14Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z)), 4,6-Decadiyn-1-ol isovalerate and LacCer(d18:1/24:1(15Z)) of MB caused the different variations in lipid metabolisms of macrophage following MTB/MB attacks, respectively. Finally, we proposed MTB and MB with different lipid compositions could successfully colonize in macrophage by different mechanisms that MTB could promote the formation of foam cells of macrophage for its colonization and development, while MB mainly through suppressing the macrophage autophagy to escape the immune responses of host.ImportanceThe differences in lipid composition of MTB and MB and the different responses in lipid metabolisms of bovine alveolar macrophage challenged by MTB/MB were elucidated in this study. The lipid composition of MTB and MB exhibited significantly different patterns, which could induced different responses of the host macrophage during the infection process of MTB or MB, respectively. MTB infection mainly induced the increase in content of Polyketides and Glycerophospholipids in macrophages, whereas MB infection induced the level of Glycerophospholipids and Sterol Lipids of macrophages.The results presented here thus provides a comprehensively dual-lipid metabolomics profile in MTB/MB and MTB/MB-attacked macrophages, which deepened our understanding of the interaction between host and pathogens in lipid metabolisms.
Missense variants affecting the actin-binding domains of PLS3 cause X-linked congenital diaphragmatic hernia and body wall defects
Authors: Petit Florence , Longoni Mauro , Wells Julie , Maser Richard , Dysart Matthew J. , Contreras Hannah T.M. , Frénois Frederic , Bogenschutz Eric , Pober Barbara R. , Clark Robin D. , Giampietro Philip F. , Ropers Hilger H. , Hu Hao , Loscertales Maria , Ai Xingbin , Brand Harrison , Jourdain Anne-Sophie , Delrue Marie-Ange , Gilbert-Dussardier Brigitte , Devisme Louise , Keren Boris , McCulley David J. , Qiao Lu , Hernan Rebecca , Wynn Julia , Scott Tiana M. , Calame Daniel G. , Coban-Akdemir Zeynep , Hernandez Patricia , Hernandez-Garcia Andres , Yonath Hagith , Lupski James R. , Shen Yufeng , Chung Wendy K. , Scott Daryl A. , Bult Carol J. , Donahoe Patricia K. , High Frances A. 
Published: July 2021

ABSTRACTCongenital diaphragmatic hernia (CDH) is a relatively common and genetically heterogeneous structural birth defect associated with high mortality and morbidity. We describe eight unrelated families with a novel X-linked condition characterized by diaphragm defects, variable anterior body wall anomalies, and/or facial dysmorphism. Using linkage analysis and whole exome or whole genome sequencing, we identified novel missense variants in the actin binding domains of plastin 3 (PLS3), a gene encoding an actin bundling protein, that co-segregate with disease in all families. Loss-of-function variants in PLS3 have been described previously in association with X-linked osteoporosis. To address these seemingly disparate clinical phenotypes, we performed in silico protein modeling and cellular overexpression experiments, which suggest that the affected residues in individuals with CDH are important for actin binding and result in disorganization of the actin cytoskeleton and a reduction in normal actin stress fiber formation. A mouse knock-in model of a variant identified in one of the families, p.W499C, shows partial perinatal lethality and recapitulates the key findings of the human phenotype, including diaphragm and abdominal wall defects. Both the mouse model and one surviving adult patient with a PLS3 variant were observed to have increased, rather than decreased, bone mineral density. Together, these clinical and functional data in human and mouse reveal that specific missense variants affecting the actin binding domains of PLS3 may have a gain-of-function effect and cause a new Mendelian disorder.
Sensitivity of SARS-CoV-2 antibody tests with late convalescent sera
Authors: Kannenberg Judith , Schnurra Carolin , Reiners Nina , Henschler Reinhard , Buhmann Raymund , Kaiser Thorsten , Biemann Ronald , Hönemann Mario , Ackermann Grit , Trawinski Henning , Jassoy Christian 
Published: July 2021

AbstractSARS-CoV-2-specific IgM antibodies wane during the first three months after infection and IgG antibody levels decline. This may limit the ability of antibody tests to identify previous SARS CoV-2 infection at later time points. To examine if the sensitivity of antibody tests falls off, we compared the sensitivity of two nucleoprotein-based antibody tests, the Roche Elecsis II Anti-SARS-CoV-2 and the Abbott SARS-CoV-2 IgG assay and three glycoprotein-based tests, the Abbott SARS-CoV-2 IgG II Quant, Siemens Atellica IM COV2T and Euroimmun SARS-CoV-2 assay with 56 sera obtained 6-8 months after SARS-CoV-2 infection. The sensitivity of the Roche, Abbott SARS-CoV-2 IgG II Quant and Siemens antibody assays was 94.6 % (95% confidence interval (CI) 85.1-98.9 %), 98.2 % (95% CI: 90.4-99.9 %) and 100 % (95% CI: 93.6-100 %). The sensitivity of the N-based Abbott SARS-CoV-2 IgG and the glycoprotein-based Euroimmun ELISA was 48.2 % (95% CI: 34.7-62.0 %) and 83.9 % (95% CI: 71.7-92.4 %). The nucleoprotein-based Roche and the glycoprotein-based Abbott RBD and Siemens tests were more sensitive than the N-based Abbott and the Euroimmun antibody tests (p=0.0001 to p=0.039). The N-based Abbott antibody test was less sensitive 6-8 months than 4-10 weeks after SARS-CoV-2 infection (p = 0.0002). The findings show that most SARS CoV-2 antibody assays correctly identified previous infection 6-8 months after infection. The sensitivity of pan-Ig antibody tests was not reduced at 6-8 months when IgM antibodies have usually disappeared. However, one of the nucleoprotein-based antibody tests significantly lost sensitivity over time.HighlightsMost antibody tests correctly identified SARS CoV-2 infection 6-8 months after infectionThe sensitivity of the antibody tests was 48.2-100 %The three tests with the highest sensitivity (94.6-100 %) were the N-based Roche and the RBD-based Abbott and Siemens assaysThe N-based Abbott IgG CMIA was significantly less sensitive 6-8 months than 4-10 weeks after infection (p = 0.0002)
SARS-CoV-2 IgG detection in human oral fluids
Authors: Hoschler Katja , Ijaz Samreen , Andrews Nick , Ho Sammy , Dicks Steve , Jegatheesan Keerthana , Poh John , Warrener Lenesha , Kankeyan Thivya , Baawuah Frances , Beckmann Joanne , Okike Ifeanichukwu O , Ahmad Shazaad , Garstang Joanna , Brent Andrew J , Brent Bernadette , Aiano Felicity , Brown Kevin E , Ramsay Mary E , Brown David , Parry John V , Ladhani Shamez N , Zambon Maria 
Published: July 2021

ABSTRACTSeroepidemiological studies to monitor antibody kinetics are important for assessing the extent and spread of SARS-CoV-2 in a population. Non-invasive sampling methods are advantageous to reduce the need for venepuncture, which may be a barrier to investigations particularly in paediatric populations. Oral Fluids are obtained by gingiva-crevicular sampling from children and adults and are very well accepted. ELISA based on these samples have acceptable sensitivity and specificity compared to conventional serum-based antibody ELISAs and are suitable for population-based surveillance.We describe the development and evaluation of SARS-COV-2 IgG ELISAs using SARS-CoV-2 viral nucleoprotein (NP) and spike (S) proteins in IgG isotype capture format and an indirect receptor-binding-domain (RBD) IgG ELISA, intended for use in children. All three assays were assessed using a panel of 1999 paired serum and oral fluids from children and adults participating in national primary school SARS-CoV-2 surveillance studies during and after the first and second pandemic wave in the UK. The anti NP IgG capture assay was the best candidate, with an overall sensitivity of 75% (95% CI: 71–79%) specificity of 99% (95% CI: 78–99%) when compared with paired serum antibodies measured using a commercial assay SARS-CoV-2 nucleoprotein IgG assay (Abbott, Chicago, IL, USA). Higher sensitivity was observed in children (80%, 95% CI: 71–88%) compared to adults (67%, CI: 60%-74%). Oral fluid assays using spike protein and RBD antigens were also 99% specific and achieved reasonable but lower sensitivity in the target population (78%, 95% CI (68%-86%) and 53%, 95% CI (43%-64%), respectively).Conclusion statementOral Fluid assays based on the detection of SARS-CoV-2 antibodies are a suitable tool for population based seroepidemiology studies in children.
Dynamic Apical-Basal Enrichment of the F-Actin during Cytokinesis in Arabidopsis Cells Embedded in their Tissues
Authors: Lebecq Alexis , Fangain Aurélie , Boussaroque Alice , Caillaud Marie-Cécile 
Published: July 2021

ABSTRACTDuring the life cycle of any multicellular organism, cell division contributes to the proliferation of the cell in the tissues as well as the generation of specialized cells, both necessary to form a functional organism. Therefore, the mechanisms of cell division need to be tightly regulated, as malfunctions in their control can lead to tumor formation or developmental defects. This is particularly true in land plants, where cells cannot relocate and therefore cytokinesis is key for morphogenesis. In the green lineage, cell division is executed in radically different manners than animals, with the appearance of new structures (the preprophase band (PPB), cytokinetic the cell plate and phragmoplast), and the disappearance of ancestral mechanisms (cleavage, centrosomes). While F-actin and microtubules closely co-exist to allow the orientation and the progression of the plant cell division, recent studies mainly focused on the microtubule’s involvement in this key process. Here, we used our recently developed root tracking system to follow actin dynamics in dividing Arabidopsis meristematic root cells. In this study, we imaged in time and space the fluorescent-tagged F-actin reporter Lifeact together with cell division markers in dividing cells embedded in their tissues. In addition to the F-actin accumulation’s in the phragmoplasts, we observed and quantified a dynamic apical-basal enrichment of the F-actin during cytokinesis. The role and the possible actors responsible for F-actin dynamics during cytokinesis are discussed.