bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a whole cell biosensor for detection of 2, 4-diacetylphloroglucinol-producing bacteria from grassland soil
Authors: Hansen Morten Lindqvist , He Zhiming , Wibowo Mario , Jelsbak Lars 
Published: June 2020

ABSTRACTFluorescentPseudomonasspp. producing the antibiotic 2,4-diacetylphloroglucinol (DAPG) are ecologically important in the rhizosphere as they can control phytopathogens and contribute to disease suppressiveness. While studies of DAPG-producingPseudomonashave predominantly focused on rhizosphere niches, the ecological role of DAPG as well as the distribution and dynamics of DAPG-producing bacteria remains less well understood for other environments such as bulk soil and grassland, where the level of DAPG producers are predicted to be low. Here, we construct a whole cell biosensor for detection of DAPG and DAPG-producing bacteria from environmental samples.We show that the sensor is highly specific towards DAPG, with a sensitivity in the low nanomolar range (<20 nm). This sensitivity is comparable to the DAPG levels identified in rhizosphere samples by chemical analysis. The biosensor enables guided isolation of DAPG-producingPseudomonas. Using the biosensor, we probed the same grassland soil sampling site to isolate genetically related DAPG-producingPseudomonas kilonensisstrains over a period of 12 months. Next, we used the biosensor to determine the frequency of DAPG-producing Pseudomonads within three different grassland soil sites and show that DAPG producers can constitute part of thePseudomonaspopulation in the range of 0.35-17% at these sites. Finally, we show that the biosensor enables detection of DAPG produced by non-Pseudomonasspecies.Our studies show that a whole-cell biosensor for DAPG detection can facilitate isolation of bacteria that produce this important secondary metabolite and provide insight into the population dynamics of DAPG producers in natural grassland soil.IMPORTANCEThe interest has grown for bacterial biocontrol agents as biosustainable alternatives to pesticides to increase crop yields. Currently, we have a broad knowledge of antimicrobial compounds, such as DAPG, produced by bacteria growing in the rhizosphere surrounding plant roots. However, compared to the rhizosphere niches, the ecological role of DAPG as well as the distribution and dynamics of DAPG-producing bacteria remains less well understood for other environments such as bulk and grassland soil. Currently, we are restricted to chemical methods with detection limits and time-consuming PCR-based and probe-hybridization approaches to detect DAPG and its respective producer. In this study, we have developed a whole-cell biosensor, which can circumvent the labor-intensive screening process, as well as increase the sensitivity at which DAPG is detected. This enables quantification of relative amounts of DAPG-producers, which in turn increases our understanding of the dynamics and ecology of these producers in natural soil environments.
A rod conformation of thePyrococcus furiosusRad50 coiled coil
Authors: Soh Young-Min , Basquin Jerome , Gruber Stephan 
Published: June 2020

AbstractThe Rad50-Mre11 nuclease complex plays a vital role in DNA repair in all domains of life. It recognizes and processes DNA double-strand breaks. Rad50 proteins fold into an extended structure with a ~20-60 nm long coiled coil connecting a globular ABC ATPase domain with a zinc hook dimerization domain. A published structure of an archaeal Rad50 zinc hook shows coiled coils pointing away from each other. Here we present the crystal structure of an alternate conformation displaying co-aligned coiled coils. Archaeal Rad50 may thus switch between rod-shaped and ring-like conformations as recently proposed for a bacterial homolog.
Evaluation of Different PCR Assay Formats for Sensitive and Specific Detection of SARS-CoV-2 RNA
Authors: Ratcliff Jeremy , Nguyen Dung , Andersson Monique , Simmonds Peter 
Published: June 2020

ABSTRACTAccurate identification of individuals infected with SARS-CoV-2 is crucial for efforts to control the ongoing COVID-19 pandemic. Polymerase chain reaction (PCR)-based assays are the gold standard for detecting viral RNA in patient samples and are used extensively in clinical settings. Most currently used quantitative PCR (RT-qPCRs) rely upon real-time detection of PCR product using specialized laboratory equipment. To enable the application of PCR in resource-poor or non-specialist laboratories, we have developed and evaluated a nested PCR method for SARS-CoV-2 RNA using simple agarose gel electrophoresis for product detection. Using clinical samples tested by conventional qPCR methods and RNA transcripts of defined RNA copy number, the nested PCR based on the RdRP gene demonstrated high sensitivity and specificity for SARS-CoV-2 RNA detection in clinical samples, but showed variable and transcript length-dependent sensitivity for RNA transcripts. Samples and transcripts were further evaluated in an additional N protein real-time quantitative PCR assay. As determined by 50% endpoint detection, the sensitivities of three RT-qPCRs and nested PCR methods varied substantially depending on the transcript target with no method approaching single copy detection. Overall, these findings highlight the need for assay validation and optimization and demonstrate the inability to precisely compare viral quantification from different PCR methodologies without calibration.
Enhanced anti-amyloid effect of combined leptin and pioglitazone in APP/PS1 transgenic mice
Authors: Liu Yao , Hanson Kelsey A. , McCormack Graeme , Dittmann Justin , Vickers James C. , Fernandez-Martos Carmen M. , King Anna E. 
Published: June 2020

ABSTRACTBackgroundAlzheimer’s disease (AD) has challenged single-target therapeutic strategies, raising the possibility that combined therapies may offer a more effective treatment strategy.ObjectiveThere is substantial evidence for the efficacy of leptin (L) (neuroprotective hormone) and pioglitazone (P) (anti-inflammatory agent) as monotherapies in AD. We have previouly shown that combination treatment of L+P in APP/PS1 mice at the onset of pathology significantly improved memory and reduced brain Aβ levels relative to control mice. In this new study, we sought to replicate our previous findings in a new cohort of APP/PS1 mouse to further confirm whether the combined treatment of L+P is superior to each treatment individually.MethodsWe have re-evaluated the effects of L+P co-treatment in APP/PS1 mice using thioflavin-S staining, MOAβ immunolabeling and enzyme-linked immunosorbent assay (ELISA) to examine effects on Aβ levels and pathology, relative to animals that received L or P individually. To explore mechanism of regulation, we used Western blotting to examine the expression of the peroxisome-proliferator activated receptor γ (PPARγ), due to its potential role in the regulation of the inflammatory response.ResultsWe demonstrated that combining L and P significantly enhances the anti-Aβ effect of L or P in the hippocampus of APP/PS1 mice. Western blot analysis indicated that Aβ reduction was accompanied by up-regulation of the PPARγ levels.ConclusionOur findings suggest that combining L and P significantly enhances the anti-Aβ effect of L or P in the hippocampus of APP/PS1 mice, and may be a potential new effective strategy for AD therapy.
Mutalyzer 2: Next Generation HGVS Nomenclature Checker
Authors: Lefter Mihai , Vis Jonathan K. , Vermaat Martijn , den Dunnen Johan T. , Taschner Peter E.M. , Laros Jeroen F.J. 
Published: June 2020

AbstractUnambiguous variant descriptions are of utmost importance in clinical genetic diagnostics, scientific literature, and genetic databases. The Human Genome Variation Society (HGVS) publishes a comprehensive set of guidelines on how variants should be correctly and unambiguously described. We present the implementation of the Mutalyzer 2 tool suite, designed to automatically apply the HGVS guidelines so users do not have to deal with the HGVS intricacies explicitly to check and correct their variant descriptions. Mutalyzer is profusely used by the community, having processed over 133 million descriptions since its launch. Over a five year period, Mutalyzer reported a correct input in approximately 50% of cases. In 41% of the cases either a syntactic or semantic error was identified and for approximately 7% of cases, Mutalyzer was able to automatically correct the description.
Male-male interactions select for conspicuous male colouration in damselflies
Authors: Khan Md Kawsar , Herberstein Marie E. 
Published: June 2020

AbstractMale ornamentation, such as conspicuous male colouration, can evolve through female mate choice. Alternatively, in species without overt female mate preference, conspicuous male colouration can evolve via intrasexual selection to resolve male-male competition or to prevent costly male-male mating attempts. Here, we investigated the drivers of conspicuous male colouration in an ontogenetic colour changing damselfly,Xanthagrion erythroneurum, where the juvenile males are yellow and change colour to red upon sexual maturity. We first showed that red males were chromatically and achromatically more conspicuous than the yellow males. We then quantified the condition of the males and showed that red males were larger and in better condition than yellow males. We tested female preference in a choice experiment where we artificially manipulated male colour, and found that females did not choose mates based on male colouration. We further tested whether the male colouration affected male-male interactions. We presented red and yellow males in the breeding arena, and found that red males received less intra- and interspecific aggression than yellow males. Our study experimentally showed, for the first time, that male conspicuousness is not a target of female mate choice in damselflies. Intra- and interspecific male-male interactions therefore appear to be the driver of conspicuous male colouration in damselflies.
Modelling donor screening strategies to reduce the risk of SARS-CoV-2 via fecal microbiota transplantation
Authors: Olesen Scott W. , Zaman Amanda , Osman Majdi , Ramakrishna Bharat 
Published: June 2020

ABSTRACTThe potential for transmission of SARS-CoV-2 shed in stool via fecal microbiota transplantation is not yet known, and the effectiveness of various testing strategies to prevent FMT-based transmission has also not yet been quantified. Here we use a mathematical model to simulate the utility of different testing strategies.
Analysis of pluripotency transcription factor interactions reveals preferential binding of NANOG to SOX2 rather than NANOG or OCT4
Authors: Mistri Tapan Kumar , Kelly David , Mak John , Colby Douglas , Mullin Nicholas , Chambers Ian 
Published: June 2020

ABSTRACTThe pluripotency transcription factors (TFs) Nanog, Sox2, and Oct4 are at the centre of the gene regulatory network that controls cell identity in embryonic stem (ES) cells. However, the mechanisms by which these factors control cell fate, and their interactions with one another are not fully understood. Here we combine biophysical and novel biochemical assays to assess how these factors interact with each other quantitatively. A confocal microscopy method to detect binding of a target protein to a fluorescently labelled partner (coimmunoprecipitated bead imaging microscopy [CBIM]) is presented and used to demonstrate homotypic binding of Nanog and heterotypic binding between Nanog and Sox2 and between Nanog and Oct4. Using fluorescence correlation spectroscopy we show that in solution, Nanog but not Oct4 or Sox2 can form homomultimers. However, both Sox2 and Oct4 can form heterotypic multimers with Nanog in a manner that depends on the presence of tryptophan residues within the Nanog tryptophan repeat. Fluorescence Cross Correlation Spectroscopy shows the affinity of Nanog for dimer formation is in the order Sox2 > Nanog > Oct4. Importantly, live cell analysis demonstrates the existence of Nanog homomultimersin vivo. Together these findings extend understanding of the molecular interactions occurring between these central mediators of the pluripotency gene regulatory network at the single-molecule level.
The phosphatidylinositol 3-phosphate binding protein SNX4 controls ATG9A recycling and autophagy
Authors: Ravussin Anthony , Tooze Sharon A. , Stenmark Harald 
Published: June 2020

AbstractLate endosomes and lysosomes (endolysosomes) receive proteins and cargo from the secretory, endocytic and autophagic pathways. Whereas these pathways and the degradative processes of endolysosomes are well characterized, less is understood about protein traffic from these organelles. In this study, we demonstrate the direct involvement of the phosphatidylinositol 3-phosphate (PI3P) binding SNX4 protein in membrane protein recycling from endolysosomes, and show that SNX4 is required for proper autophagic flux. We show that SNX4 mediates recycling of the transmembrane autophagy machinery protein ATG9A from endolysosomes to early endosomes, from where ATG9A is recycled to the trans-Golgi network in a retromer-dependent manner. Upon siRNA-mediated depletion of SNX4 or the retromer component VPS35, we observed accumulation of ATG9A on endolysosomes and early endosomes, respectively. Moreover, starvation-induced autophagosome biogenesis and autophagic flux were inhibited when SNX4 was downregulated. Altogether, we propose that proper ATG9A recycling by SNX4 sustains autophagy by preventing exhaustion of the available ATG9A pool.
JIP3 links lysosome transport to regulation of multiple components of the axonal cytoskeleton
Authors: Rafiq N.M. , Lyons L.L. , Gowrishankar S. , De Camilli P. , Ferguson S.M. 
Published: June 2020

AbstractLysosome axonal transport is important for the clearance of cargoes sequestered by the endocytic and autophagic pathways. Building on observations that mutations in the JIP3 (MAPK8IP3) gene result in lysosome-filled axonal swellings, we analyzed the impact of JIP3 depletion on the cytoskeleton of human neurons. Dynamic focal lysosome accumulations were accompanied by disruption of the axonal periodic scaffold (spectrin, F-actin and myosin II) throughout each affected axon. Additionally, axonal microtubule organization was locally disrupted at each lysosome-filled swelling. This local axonal microtubule disorganization was accompanied by accumulations of both F-actin and myosin II. These results indicate that transport of axonal lysosomes is functionally interconnected with mechanisms that control the organization and maintenance of the axonal cytoskeleton. They have potential relevance to human neurological disease arising from JIP3 mutations as well as for neurodegenerative diseases associated with the focal accumulations of lysosomes within axonal swellings such as Alzheimer’s disease.
Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity
Authors: Crits-Christoph Alexander , Bhattacharya Nicholas , Olm Matthew R. , Song Yun S. , Banfield Jillian F. 
Published: June 2020

AbstractBiosynthetic gene clusters (BGCs) are operonic sets of microbial genes that synthesize specialized metabolites with diverse functions, including siderophores and antibiotics, which often require export to the extracellular environment. For this reason, genes for transport across cellular membranes are essential for the production of specialized metabolites, and are often genomically co-localized with BGCs. Here we conducted a comprehensive computational analysis of transporters associated with characterized BGCs. In addition to known exporters, in BGCs we found many importer-specific transmembrane domains that co-occur with substrate binding proteins possibly for uptake of siderophores or metabolic precursors. Machine learning models using transporter gene frequencies were predictive of known siderophore activity, molecular weights, and a measure of lipophilicity (logP) for corresponding BGC-synthesized metabolites. Transporter genes associated with BGCs were often equally or more predictive of metabolite features than biosynthetic genes. Given the importance of siderophores as pathogenicity factors, we used transporters specific for siderophore BGCs to identify both known and uncharacterized siderophore-like BGCs in genomes from metagenomes from the infant and adult gut microbiome. We find that 23% of microbial genomes from the infant gut have siderophore-like BGCs, but only 3% of those assembled from adult gut microbiomes do. While siderophore-like BGCs from the infant gut are predominantly associated withEnterobactericaeeandStaphylococcus, siderophore-like BGCs can be identified from taxa in the adult gut microbiome that have rarely been recognized for siderophore production. Taken together, these results show that consideration of BGC-associated transporter genes can inform predictions of specialized metabolite structure and function.
Genome-wide reduction in chromatin accessibility and unique transcription factor footprints in endothelial cells and fibroblasts in scleroderma skin
Authors: Tsou Pei-Suen , Palisoc Pamela J. , Ali Mustafa , Khanna Dinesh , Sawalha Amr H 
Published: June 2020

AbstractSystemic sclerosis (SSc) is a rare autoimmune disease of unknown etiology characterized by widespread fibrosis and vascular complications. We utilized an assay for genome-wide chromatin accessibility to examine the chromatin landscape and transcription factor footprints in both endothelial cells (ECs) and fibroblasts isolated from healthy controls and patients with diffuse cutaneous (dc) SSc. In both cell types, chromatin accessibility was significantly reduced in SSc patients compared to healthy controls. Genes annotated from differentially accessible chromatin regions were enriched in pathways and gene ontologies involved in the nervous system. In addition, our data revealed that chromatin binding of transcription factors SNAI2, ETV2, and ELF1 was significantly increased in dcSSc ECs, while recruitment of RUNX1 and RUNX2 was enriched in dcSSc fibroblasts. Significant elevation of SNAI2 and ETV2 levels in dcSSc ECs, and RUNX2 levels in dcSSc fibroblasts were confirmed. Further analysis of publicly available ETV2-target genes suggests that ETV2 may play a critical role in EC dysfunction in dcSSc. Our data, for the first time, uncovered the chromatin blueprint of dcSSc ECs and fibroblasts, and suggested that neural-related characteristics of SSc ECs and fibroblasts could be a culprit for dysregulated angiogenesis and enhanced fibrosis. Targeting these pathways and the key transcription factors identified might present novel therapeutic approaches for this disease.
Co-occurrence of SARS-CoV-2 and Respiratory Pathogens in the Frail Elderly
Authors: Wolfe Alan , Baunoch David , Wang Dakun , Gnewuch Ryan , Zhao Xinhua , Halverson Thomas , Cacdac Patrick , Huang Shuguang , Lauterbach Trisha , Luke Natalie 
Published: June 2020

AbstractBackgroundElderly SARS-CoV-2 patients are associated with higher hospitalization and mortality. Co-infection is critical in the severity of respiratory diseases. It is largely understudied for SARS-CoV-2.MethodsBetween March 24thand April 27th, 2020, nasopharyngeal and oropharyngeal swabs from 3,348 patients from nursing homes and assisted living facilities in 22 states in the US were tested by Capstone Healthcare for SARS-CoV-2, 24 other respiratory viruses, and 8 respiratory bacteria. Total nucleic acid was extracted with MagMAX™ Viral/Pathogen Ultra nucleic acid isolation kit. SARS-Co-V-2 was detected with the CDC 2019-novel coronavirus (2019-nCoV) diagnostic panel. Total nucleic acid was pre-amplified before analysis for other respiratory pathogens with Taqman OpenArray™ Respiratory Tract Microbiota Plate.ResultsPatients’ mean age was 76.9 years. SARS-CoV-2 was detected in 1,413 patients (42.2%). Among them, 1,082 (76.6%) and 737 (43.7%) patients were detected with at least one bacterium or another virus, respectively. SARS-CoV-2-positive patients were more likely to have bacterial co-occurrences (76.6%) than SARS-CoV-2-negative patients (70.0%) (p<0.0001). The most common co-occurring bacteria wereStaphylococcus aureusandKlebsiella pneumonia, detected in 55.8% and 40.1% SARS-CoV-2-positive patients, respectively.Staphylococcus aureuswas associated with SARS-CoV-2, with higher detection rates in SARS-CoV-2-positive patients (55.8%) than SARS-CoV-2-negative patients (46.2%) (p<0.0001). Human herpes virus 6 (HHV6) also was common and associated with SARS-CoV-2, with higher detection rates in SARS-CoV-2-positive patients (26.6%) than SARS-CoV-2-negative patients (19.1%) (p<0.0001).ConclusionsSARS-CoV-2-positive patients are more likely to be positive for certain respiratory bacteria and viruses. This observation may help explain high hospitalization and mortality rates in older patients.
Modeling the Covid-19 Pandemic Response of the US States
Authors: Neofotistos Georgios , Kaxiras Efthimios 
Published: June 2020

AbstractBackgroundThe United States of America (USA) has been the country worst affected, in absolute terms, by the Covid-19 pandemic. The country comprises 50 states under a federal system. The impact of the pandemic has resulted in different responses at the state level, which are driven by differing intervention policies, demographics, connectedness and other factors. Understanding the dynamics of the Covid-19 pandemic at the state level is essential in predicting its future evolution.ObjectiveOur objective is to identify and characterize multiple waves of the pandemic by analyzing the reported infected population curve in each of the 50 US states. Based on the intensity of the waves, characterized by declining, stationary, or increasing strengths, each state’s response can be inferred and quantified.MethodsWe apply a recently proposed multiple-wave model to fit the infected population data for each state in USA, and use the proposed Pandemic Response Index to quantify their response to the Covid-19 pandemic.ResultsWe have analyzed reported infected cases from each one of the 50 USA states and the District of Columbia, based on the multiple-wave model, and present the relevant parameters. Multiple waves have been identified and this model is found to describe the data better. Each of the states can be classified into one of three distinct classes characterized by declining, increasing, or stationary strength of the waves following the initial one. The effectiveness of intervention measures can be inferred by the peak intensities of the waves, and states with similar population characteristics can be directly compared. We estimate how much lower the number of infections might have been, if early and strict intervention measures had been imposed to stop the disease spread at the first wave, as was the case for certain states. Based on our model’s results, we compute the value of the Pandemic Response Index, a recently introduced metric for quantifying in an objective manner the response to the pandemic.ConclusionsOur results reveal a series of epidemic waves, characterizing USA’s pandemic response at the state level, and also infer to what extent the imposition of early intervention measures could have had on the spread and impact of the disease. As of June 11, 2020, only 19 states and the District of Columbia (40% of the total) clearly exhibit declining trends in the numbers of reported infected cases, while 13 states exhibit stationary and 18 states increasing trends in the numbers of reported cases.