bluuebunny/crossref_metadata_2025_split huggingface dataset:
A combination of metagenomic and cultivation approaches reveals hypermutator phenotypes withinVibrio choleraeinfected patients
Authors: Levade Inès , Khan Ashraful I. , Chowdhury Fahima , Calderwood Stephen B. , Ryan Edward T. , Harris Jason B. , LaRocque Regina C. , Bhuiyan Taufiqur R. , Qadri Firdausi , Weil Ana A. , Shapiro B. Jesse 
Published: October 2020

ABSTRACTVibrio choleraecan cause a range of symptoms, ranging from severe diarrhea to asymptomatic infection. Previous studies using whole genome sequencing (WGS) of multiple bacterial isolates per patient showed thatV. choleraecan evolve modest genetic diversity during symptomatic infection. To further explore the extent ofV. choleraewithin-host diversity, we applied culture-based WGS and metagenomics to a cohort of both symptomatic and asymptomatic cholera patients from Bangladesh. While metagenomics allowed us to detect more mutations in symptomatic patients, WGS of cultured isolates was necessary to detectV. choleraediversity in asymptomatic carriers, likely due to their lowV. choleraeload. Using both metagenomics and isolate WGS, we report three lines of evidence thatV. choleraehypermutators evolve within patients. First, we identified nonsynonymous inV. choleraeDNA repair genes in five out of 11 patient metagenomes sequenced with sufficient coverage of theV. choleraegenome, and in one of three patients with isolate genomes sequenced. Second, mutations in DNA repair genes tended to be accompanied by an excess of intrahost single nucleotide variants (iSNVs). Third, these iSNVs were enriched in transversion mutations, a known hallmark of hypermutator phenotypes. While hypermutators appeared to generate mostly selectively neutral mutations, non-mutators showed signs of convergent mutation across multiple patients, suggestingV. choleraeadaptation within hosts. Our results highlight the power and limitations of metagenomics combined with isolate sequencing to characterize within-patient diversity in acuteV. choleraeinfections, while providing evidence for hypermutator phenotypes within cholera patients.IMPORTANCEPathogen evolution within patients can impact phenotypes such as drug resistance and virulence, potentially affecting clinical outcomes.V. choleraeinfection can result in life-threatening diarrheal disease, or asymptomatic infection. Here we describe whole-genome sequencing ofV. choleraeisolates and culture-free metagenomic sequencing from stool of symptomatic cholera patients and asymptomatic carriers. Despite the typically short duration of cholera, we found evidence for adaptive mutations in theV. choleraegenome that occur independently and repeatedly within multiple symptomatic patients. We also identifiedV. choleraehypermutator phenotypes within several patients, which appear to generate mainly neutral or deleterious mutations. Our work sets the stage for future studies of the role of hypermutators and within-patient evolution in explaining the variation from asymptomatic carriage to symptomatic cholera.
D614G mutation alters SARS-CoV-2 spike conformational dynamics and protease cleavage susceptibility at the S1/S2 junction
Authors: Gobeil Sophie M-C. , Janowska Katarzyna , McDowell Shana , Mansouri Katayoun , Parks Robert , Manne Kartik , Stalls Victoria , Kopp Megan , Henderson Rory , Edwards Robert J , Haynes Barton F. , Acharya Priyamvada 
Published: October 2020

AbstractThe SARS-CoV-2 spike (S) protein is the target of vaccine design efforts to end the COVID-19 pandemic. Despite a low mutation rate, isolates with the D614G substitution in the S protein appeared early during the pandemic, and are now the dominant form worldwide. Here, we analyze the D614G mutation in the context of a soluble S ectodomain construct. Cryo-EM structures, antigenicity and proteolysis experiments suggest altered conformational dynamics resulting in enhanced furin cleavage efficiency of the G614 variant. Furthermore, furin cleavage altered the conformational dynamics of the Receptor Binding Domains (RBD) in the G614 S ectodomain, demonstrating an allosteric effect on the RBD dynamics triggered by changes in the SD2 region, that harbors residue 614 and the furin cleavage site. Our results elucidate SARS-CoV-2 spike conformational dynamics and allostery, and have implications for vaccine design.HighlightsSARS-CoV-2 S ectodomains with or without the K986P, V987P mutations have similar structures, antigenicity and stability.The D614G mutation alters S protein conformational dynamics.D614G enhances protease cleavage susceptibility at the S protein furin cleavage site.Cryo-EM structures reveal allosteric effect of changes at the S1/S2 junction on RBD dynamics.
Gut Dysbiosis with a Pathobiont Shifts the Intestinal Microbiota Profile and Accelerates Lupus Nephritis
Authors: Valiente Giancarlo R. , Munir Armin , Hart Marcia L. , Blough Perry , Wada Takuma T. , Dalan Emma E. , Willis William L. , Wu Lai-Chu , Freud Aharon G. , Jarjour Wael N. 
Published: October 2020

ABSTRACTThe gut microbiota (GM) exerts a strong influence over the host immune system and dysbiosis of this microbial community can affect the clinical phenotype in chronic inflammatory conditions. To explore the role of the GM in lupus nephritis, we colonized NZM2410 mice with Segmented Filamentous Bacteria (SFB). Gut colonization with SFB was associated with worsening glomerulonephritis, glomerular and tubular immune complex deposition and interstitial inflammation compared to NZM2410 mice free of SFB. With SFB colonization mice experienced an increase in small intestinal lamina propria Th17 cells and group 3 innate lymphoid cells (ILC3s). However, although serum IL-17A expression was elevated in these mice, Th17 cells and ILC3s were not detected in the inflammatory infiltrate in the kidney. In contrast, serum and kidney tissue expression of the macrophage chemoattractants MCP-1 and CXCL1 were significantly elevated in SFB colonized mice. Furthermore, kidney infiltrating F4/80+CD206+ M2-like macrophages were significantly increased in these mice. Evidence of increased gut permeability or “leakiness” was detected in SFB colonized mice. Finally, the intestinal microbiome of SFB colonized mice at 15 and 30 weeks of age exhibited dysbiosis when compared to uncolonized mice at the same time points. Both microbial relative abundance as well as biodiversity of colonized mice was found to be altered. Collectively, SFB gut colonization in the NZM2410 mouse exacerbates kidney disease, promotes kidney M2-like macrophage infiltration and overall intestinal microbiota dysbiosis.
Finding Pathogenic nsSNP’s and their structural effect on COPS2 using Molecular Dynamic Approach
Authors: Malik Ashish , Pande Kajal , Kumar Abhishek , Vemula Alekhya , Madhuri R , Chandramohan Vivek 
Published: October 2020

AbstractCOP9 Signalosome Subunit 2 is a highly conserved multiprotein complex which is involved in the cellular process and developmental process. It is one of the essential components in the COP9 Signalosome Complex (CSN). It is also involved in neuronal differentiation interacting with NIF3L1. The gene involved in neuronal differentiation is negatively regulated due to the transcription co-repressor interaction of NIF3L1 with COPS2. In the present study, we have evaluated the outcome for 90 non-synonymous single nucleotide polymorphisms (nsSNP’s) in COPS2 gene through computational tools. After the analysis, 4 SNP’s (S120C, N144S, Y159H, R173C) were found to be deleterious. The native and mutated structures were prepared using discovery studio and docked to check the interactions with NIF3L1.On the basis of ZDOCK score the top 3 mutations (N144S, Y159H, R173C) were screened out. Further to analyze the effect of amino acid substitution on the molecular structure of protein Molecular Dynamics simulation was carried out. Analysis based on RMSD, RMSF, RG, H-bond showed a significant deviation in the graph, which demonstrated conformation change and instability compared to the wild structure. As it is known mutations in COPS2 gene can disrupt the normal activity of the CSN2 protein which may cause neuronal differentiation. Our results showed N144S, Y159H and R173C mutations are to be more pathogenic and may cause disease
Eucalyptus plantations in temperate grasslands: responses of taxonomic and functional diversity of plant communities to environmental changes
Authors: Pairo Pamela E. , Rodriguez Estela E. , Bellocq M. Isabel , Aceñolaza Pablo G. 
Published: October 2020

ABSTRACTUnderstanding how human land-uses impact on local communities is required to implement management and conservational policies and practices. Tree plantations have become one of the fastest-growing land uses in recent decades and their impact on biodiversity was evaluated mainly at the taxonomic level. Our aim was to analyze the effects of changes in environmental drivers along the 12 years eucalypt plantations chronosequence on alfa, beta, taxonomic and functional diversity of understory plant communities. We selected nine plantation ages with three replicates per age and three protected grasslands as reference habitat. At each replicate, we established three plots to measure plant species cover and environmental variables, which are expected to change with plantation age. Results showed that species richness and all diversity indices significantly declined with increasing plantation age. Canopy cover, soil pH, and leaf litter were the most important drivers that explained the decline in taxonomic and functional diversity of plants through the forest plantation. Based on the Path analyses results, canopy cover had an indirect relationship with plant functional diversity mediated by leaf litter, soil pH and plant species richness. The results of the association between functional traits and environmental variables have revealed that high dispersal potential, annual, barochorous, and zoochorous plant species were the functional traits more affected by the eucalypt plantations. Given that leaf litter was negatively associated with all diversity facets, we recommend reducing their accumulation within eucalypt plantation to enhance biodiversity conservation and the provision of pampean grassland ecosystem functions.
The mammalian cholesterol synthesis enzyme squalene monooxygenase is proteasomally truncated to a constitutively active form
Authors: Coates Hudson W. , Brown Andrew J. 
Published: October 2020

AbstractSqualene monooxygenase (SM) is a rate-limiting enzyme of cholesterol synthesis that is oncogenic in a range of cancer types. SM is subject to feedback regulation via cholesterol-induced degradation, which depends on its lipid-sensing N terminal regulatory domain. Here, we characterize an endogenous truncated form of SM and show that it is cholesterol-resistant, and therefore constitutively active. Truncation of SM occurs during its endoplasmic reticulum-associated degradation and requires the proteasome, which partially degrades the SM N-terminus and eliminates cholesterol-sensing elements within this region. Using mutagenesis studies, we demonstrate that partial degradation of SM depends on both an intrinsically disordered region near the truncation site and the stability of the adjacent catalytic domain. Finally, truncation converts SM from an integral to a peripheral ER membrane protein. These findings uncover an additional layer of complexity in the cellular control of cholesterol synthesis and establish SM as the first eukaryotic enzyme known to undergo proteasomal truncation.
Alternate primers for whole-genome SARS-CoV-2 sequencing
Authors: Cotten Matthew , Bugembe Dan Lule , Kaleebu Pontiano , Phan My V.T. 
Published: October 2020

AbstractAs the world is struggling to control the novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), there is an urgency to develop effective control measures. Essential information is encoded in the virus genome sequence with accurate and complete SARS-CoV-2 sequences essential for tracking the movement and evolution of the virus and for guiding efforts to develop vaccines and antiviral drugs. While there is unprecedented SARS-CoV-2 sequencing efforts globally, approximately 19 to 43% of the genomes generated monthly are gapped, reducing their information content. The current study documents the genome gap frequencies and their positions in the currently available data and provides an alternative primer set and a sequencing scheme to help improve the quality and coverage of the genomes.
Long-lasting tagging of neurons activated by seizures or cocaine administration in Egr1-CreERT2transgenic mice
Authors: Longueville Sophie , Nakamura Yuki , Brami-Cherrier Karen , Coura Renata , Hervé Denis , Girault Jean-Antoine 
Published: October 2020

AbstractPermanent tagging of neuronal ensembles activated in specific experimental situations is an important objective to study their properties and adaptations. In the context of learning and memory these neurons are referred to as engram neurons. Here we describe and characterize a novel mouse line, Egr1-CreERT2, which carries a transgene in which the promoter of the immediate early geneEgr1drives the expression of the CreERT2recombinase that is only active in the presence of tamoxifen metabolite, 4-hydroxy-tamoxifen (4-OHT). Egr1-CreERT2mice were crossed with various reporter mice, Cre-dependently expressing a fluorescent protein. Without tamoxifen or 4-OHT, no or few tagged neurons were observed. Epileptic seizures induced by pilocarpine or pentylenetetrazol in the presence of tamoxifen or 4-OHT, induced the persistent tagging of many neurons and some astrocytes in the dentate gyrus of hippocampus, whereEgr1is transiently induced by seizures. One week after cocaine and 4-OHT administration, these mice displayed a higher number of tagged neurons in the dorsal striatum than saline/4-OHT controls, with differences between reporter lines. Cocaine-induced tagging required ERK activation and tagged neurons were more likely than others to exhibit ERK phosphorylation or Fos induction after a second injection. Interestingly neurons tagged in saline-treated mice also had an increased propensity to express Fos, suggesting the existence of highly responsive striatal neurons susceptible to be re-activated by cocaine repeated administration, which may contribute to the behavioral adaptations. Our report validates a novel transgenic mouse model for permanently tagging activated neurons and studying long term alterations ofEgr1-expressing cells.
Scalable and accurate automated method for neuronal ensemble detection in spiking neural networks
Authors: Herzog Rubén , Morales Arturo , Mora Soraya , Araya Joaquin , Escobar María-José , Palacios Adrian G. , Cofré Rodrigo 
Published: October 2020

AbstractWe propose a novel, scalable, and accurate automated method for detecting neuronal ensembles from a population of spiking neurons. Our approach offers a simple yet powerful tool to study ensemble activity. It allows the participation of neurons in different ensembles, has few parameters to tune and is computationally efficient. We used spike trains of retinal ganglion cells obtained from multi-electrode array recordings under a simple ON-OFF light stimulus to test our method. We found a consistent stimuli-evoked ensemble activity intermingled with spontaneously active ensembles and irregular activity. Our results suggest that the early visual system activity is already organized in clearly distinguishable functional ensembles. To validate the performance and generality of our method, we generated synthetic data, where we found that our method accurately detects neuronal ensembles for a wide range of simulation parameters. Additionally, we found that our method outperforms current alternative methodologies. Finally, we provide a Graphic User Interface, which aims to facilitate our method’s use by the scientific community.Author summaryNeuronal ensembles are strongly interconnected groups of neurons that tend to fire together (Hebb 1949). However, even when this concept was proposed more than 70 years ago, only recent advances in multi-electrode arrays and calcium imaging, statistical methods, and computing power have made it possible to record and analyze multiple neurons’ activities spiking simultaneously, providing a unique opportunity to study how groups of neurons form ensembles spontaneously and under different stimuli scenarios. Using our method, we found that retinal ganglion cells show a consistent stimuli-evoked ensemble activity, and, when validated with synthetic data, the method shows good performance by detecting the number of ensembles, the activation times, and the core-cells for a wide range of firing rates and number of ensembles accurately.
Prenatal exposure to EDCs dis-integrates and reconstitutes neuromolecular-behavioral relationships in adult rats
Authors: Hernandez Scudder Morgan E. , Young Rebecca L. , Thompson Lindsay M. , Kore Pragati , Crews David , Hofmann Hans A. , Gore Andrea C. 
Published: October 2020

AbstractExposure to endocrine-disrupting chemicals (EDCs) is ubiquitous in all species, including humans. Previous studies have shown behavioral deficits caused by EDCs that have implications for social competence and sexual selection. The neuromolecular mechanisms for these behavioral changes induced by EDCs have not been thoroughly explored. Here, we tested the hypothesis that EDCs administered to rats during a critical period of embryonic brain development would lead to disruption of normal social preference behavior, and that this involves a network of underlying gene pathways in brain regions that regulate these behaviors. Rats were exposed prenatally to human-relevant concentrations of EDCs [polychlorinated biphenyls (PCB), an industrial chemical mixture; vinclozolin (VIN), a fungicide], or vehicle. In adulthood, a sociosexual preference test (choice between hormone-primed and hormone-depleted opposite-sex rats) was administered. We profiled gene expression of in three brain regions involved in these behaviors [preoptic area (POA), medial amygdala (MeA), ventromedial nucleus (VMN)]. Prenatal PCBs impaired sociosexual preference in both sexes, and VIN disrupted this behavior in males. Each brain region (POA, MeA, VMN) had unique sets of genes altered in a sex- and EDC-specific manner. Sexually dimorphic gene expression disruption was particularly prominent for gene modules pertaining to sex steroid hormones and nonapeptides in the MeA. EDC exposure also changed the relationships between gene expression and behavior in the mate preference test, a pattern we refer to as dis-integration and reconstitution. These findings underscore the profound effects that developmental exposure to EDCs can have on adult social behavior, highlight sex-specific and individual variation in responses, and provide a foundation for further work on the disruption of mate preference behavior after prenatal exposure to EDCs.
Structural investigation of ACE2 dependent disassembly of the trimeric SARS-CoV-2 Spike glycoprotein
Authors: Ni Dongchun , Lau Kelvin , Lehmann Frank , Fränkl Andri , Hacker David , Pojer Florence , Stahlberg Henning 
Published: October 2020

AbstractThe human membrane protein Angiotensin-converting enzyme 2 (hACE2) acts as the main receptor for host cells invasion of the new coronavirus SARS-CoV-2. The viral surface glycoprotein Spike binds to hACE2, which triggers virus entry into cells. As of today, the role of hACE2 for virus fusion is not well understood. Blocking the transition of Spike from its prefusion to post-fusion state might be a strategy to prevent or treat COVID-19. Here we report a single particle cryo-electron microscopy analysis of SARS-CoV-2 trimeric Spike in presence of the human ACE2 ectodomain. The binding of purified hACE2 ectodomain to Spike induces the disassembly of the trimeric form of Spike and a structural rearrangement of its S1 domain to form a stable, monomeric complex with hACE2. This observed hACE2 dependent dissociation of the Spike trimer suggests a mechanism for the therapeutic role of recombinant soluble hACE2 for treatment of COVID-19.
Nup98-dependent transcriptional memory is established independently of transcription
Authors: Pascual-Garcia Pau , Little Shawn C. , Capelson Maya 
Published: October 2020

SummaryCellular ability to mount an enhanced transcriptional response upon repeated exposure to external cues has been termed transcriptional memory, which can be maintained epigenetically through cell divisions. The majority of mechanistic knowledge on transcriptional memory has been derived from bulk molecular assays, and this phenomenon has been found to depend on a nuclear pore component Nup98 in multiple species. To gain an alternative perspective on the mechanism and on the contribution of Nup98, we set out to examine single-cell population dynamics of transcriptional memory by monitoring transcriptional behavior of individualDrosophilacells upon initial and subsequent exposures to steroid hormone ecdysone. To this end, we combined single-molecule RNA FISH with mathematical modeling, and found that upon hormone exposure, cells rapidly activate a low-level transcriptional response, but simultaneously, begin a slow transitioning into a specialized memory state, characterized by a high rate of expression. Strikingly, our modeling predicted that this transition between non-memory and memory states is independent of the transcription stemming from initial activation, and we were able to confirm this prediction experimentally by showing that inhibiting transcription during initial ecdysone exposure did not interfere with memory establishment. Together, our findings reveal that Nup98’s role in transcriptional memory is to stabilize the forward rate of conversion from low to high expressing state, and that induced genes engage in two separate behaviors – transcription itself and the establishment of epigenetically propagated transcriptional memory.
Opposing functions of the Hda1 complex and histone H2B mono-ubiquitylation in regulating cryptic transcription initiation inSaccharomyces cerevisiae
Authors: Shirra Margaret K. , Kocik Rachel A. , Ellison Mitchell A. , Arndt Karen M. 
Published: October 2020

ABSTRACTMaintenance of chromatin structure under the disruptive force of transcription requires cooperation among numerous chromatin regulatory factors. Histone post-translational modifications can regulate nucleosome stability and influence the disassembly and reassembly of nucleosomes during transcription elongation. The Paf1 transcription elongation complex, Paf1C, is required for several transcription-coupled histone modifications, including the mono-ubiquitylation of H2B. InSaccharomyces cerevisiae, amino acid substitutions in the Rtf1 subunit of Paf1C greatly diminish H2B ubiquitylation and cause transcription to initiate at a cryptic promoter within a coding gene, an indicator of chromatin disruption. In a genetic screen to identify factors that functionally interact with Paf1C, we identified a mutation inHDA3, a gene encoding a subunit of the Hda1C histone deacetylase, as a suppressor of anrtf1mutation. Absence of Hda1C also suppresses the cryptic initiation phenotype of other mutants defective in H2B ubiquitylation. The genetic interactions between Hda1C and the H2B ubiquitylation pathway appear specific: loss of Hda1C does not suppress the cryptic initiation phenotypes of other chromatin mutants and absence of other histone deacetylases does not suppress the absence of H2B ubiquitylation. Providing further support for an appropriate balance of histone acetylation in regulating cryptic initiation, we find that deletion of the Sas3 histone acetyltransferase elevates cryptic initiation inrtf1mutants. Our data suggest a coordination between two epigenetic modifiers, the H2B ubiquitylation pathway and Hda1C, in regulating chromatin structure during transcription elongation and reveal an unexpected role for a histone deacetylase in supporting chromatin accessibility.