bluuebunny/crossref_metadata_2025 huggingface dataset:
Diverse viruses carrying genes for microbial extremotolerance in the Atacama Desert hyperarid soil
Authors: Hwang Yunha , Rahlff Janina , Schulze-Makuch Dirk , Schloter Michael , Probst Alexander J.
Published: September 2020

Viruses play an essential role in shaping microbial community structures and serve as reservoirs for genetic diversity in many ecosystems. In hyperarid desert environments, where life itself becomes scarce and loses diversity, the interactions between viruses and host populations have remained elusive. Here, we resolved host-virus interactions in the soil metagenomes of the Atacama Desert hyperarid core, one of the harshest terrestrial environments on Earth. We show evidence of diverse viruses infecting a wide range of hosts found in sites up to 205 km apart. Viral genomes carried putative extremotolerance features (i.e. DNA repair proteins, enzymes against oxidative damage, spore formation proteins) and auxiliary metabolic genes, indicating that viruses could mediate the spread of microbial resilience against environmental stress across the desert. We propose a mutualistic model of host-virus interactions in the hyperarid core where viruses seek protection in microbial cells as lysogens or pseudolysogens, while viral extremotolerance genes aid survival of their hosts. Our results suggest that the host-virus interactions in the Atacama Desert soils are dynamic and complex, shaping uniquely adapted microbiomes in this highly selective and hostile environment.

Importance

Deserts are one of the largest and rapidly expanding terrestrial ecosystems characterized by low biodiversity and biomass. The hyperarid core of the Atacama Desert, previously thought to be devoid of life, is one of the harshest environments supporting only scant biomass of highly adapted microbes. While there is growing evidence that viruses play essential roles in shaping the diversity and structure of nearly every ecosystem, very little is known about the role of viruses in desert soils, especially where viral contact with viable hosts is significantly reduced. Our results indicate that diverse viruses are widely dispersed across the desert, potentially spreading key stress resilience and metabolic genes to ensure host survival. The desertification accelerated by climate change expands both the ecosystem cover and the ecological significance of the desert virome. This study sheds light on the complex virus-host interplay that shapes the unique microbiome in desert soils.
The rise and the fall of aPseudomonas aeruginosaepidemic lineage in a hospital
Authors: Petitjean Marie , Juarez Paulo , Meunier Alexandre , Daguindau Etienne , Puja Hélène , Bertrand Xavier , Valot Benoit , Hocquet Didier
Published: September 2020

The biological features that allow a pathogen to survive in the hospital environment are mostly unknown. The extinction of bacterial epidemics in hospitals is mostly attributed to changes in medical practice, including infection control, but the role of bacterial adaptation has never been documented. We analyzed a collection ofPseudomonas aeruginosaisolates belonging to the Besançon Epidemic Strain (BES), responsible for a 12-year nosocomial outbreak, using a genotype-to-phenotype approach. Bayesian analysis estimated the emergence of the clone in the hospital five years before its opening, during the creation of its water distribution network made of copper. BES survived better than the reference strains PAO1 and PA14 in a copper solution due to a genomic island containing 13 metal-resistance genes and was specifically able to proliferate in the ubiquitous amoebaVermamoeba vermiformis. Mutations affecting amino-acid metabolism, antibiotic resistance, lipopolysaccharide biosynthesis, and regulation were enriched during the spread of BES. Seven distinct regulatory mutations attenuated the overexpression of the genes encoding the efflux pump MexAB-OprM over time. The fitness of BES decreased over time in correlation with its genome size. Overall, the resistance to inhibitors and predators presumably aided the proliferation and propagation of BES in the plumbing system of the hospital. The pathogen further spread among patients via multiple routes of contamination. The decreased prevalence of patients infected by BES mirrored the parallel and convergent genomic evolution and reduction that affected bacterial fitness. Along with infection control measures, this may have participated in the extinction of BES in the hospital setting.

Importance

Bacterial pathogens are responsible for nosocomial outbreaks, but the sources of contamination of the hospitals are mostly unclear and the role of bacterial evolution in the extinction of outbreaks has never been considered. Here, we found that an epidemic strain of the pathogenPseudomonas aeruginosacontaminated the drinking water network of a hospital due to its tolerance to copper and predatory amoeba, both present in the water pipes. The extinction of the outbreak occurred concomitantly with parallel and convergent genome evolution and a reduction in the size of the bacterial genome that correlated with the fitness of the pathogen. Our data suggest that pathogen evolution participated in the extinction of an outbreak in a hospital setting.
Correlation of Breast cancer Prognostic and Predictive indicators in Saudi patients: A 20 years retrospective observational study
Authors: Kussaibi Haitham
Published: September 2020

Introduction

Breast cancer is the most common cancer in women in Saudi Arabia and the world (WHO 2020). Several studies have been published, worldwide, about the prognostic indicators of breast cancer, many of them showed a characteristic distribution according to certain geographical areas

Methods

Over 20 years (1998-2018), the results of 498 patients diagnosed with breast cancer, have been collected from the archive of the pathology department at King Fahd University Hospital (KFHU).

Results

This study included 498 patients diagnosed with breast cancer at King Fahd University Hospital over 20 years period (1998-2018), 58.4% (n=291) were Saudis. Data analysis showed a wide age distribution of breast cancers among eastern Saudi patients; however, most cases were seen in the 3rd and 4th decades. Luminal B was the most common subtype followed by triple-negative and luminal-A. Statistical analysis revealed a significant negative relationship between Saudi patients’ age at diagnosis and Her2 expression (P= .030), interestingly, this association was not significant in none-Saudi patients (P= .528).

Discussion/Conclusion

Our data revealed that breast cancer in Eastern Province had similar prognostics to international findings, however, Her2 profile and molecular subtype among Eastern Saudi women showed a minor deviation from worldwide published data.
Low rates of enteric pathogenic bacteria and resistance gene carriage in the sheltered homeless population in Marseille, France
Authors: Ly Tran Duc Anh , Hadjadj Linda , Hoang Van Thuan , Goumbala Ndiaw , Dao Thi Loi , Badiaga Sekene , Tissot-Dupont Herve , Brouqui Philippe , Raoult Didier , Rolain Jean-Marc , Gautret Philippe
Published: September 2020

We aimed to assess the prevalence of pathogenic bacteria and resistance genes in rectal samples collected among homeless persons in Marseille, France. In February 2014 we enrolled 114 sheltered homeless adults who completed questionnaires and had rectal samples collected. Eight types of enteric bacteria and 15 antibiotic resistance genes (ARGs) were sought by real-time polymerase chain reaction (qPCR) performed directly on rectal samples. ARG-positive samples were further tested by conventional PCR and sequencing. We evidenced a 17.5% prevalence of gastrointestinal symptoms, a 9.6% DNA-prevalence of enteric bacteria carriage, includingEscherichia colipathotypes (8.7%) andTropheryma whipplei(0.9%). Only 2 persons carriedblaCTX-M-15resistance genes (1.8%), while other genes, including carbapenemase-encoding genes and colistin-resistance genes, (mcr-1 tomcr-6, mcr-8) were not detected. Our results suggest that sheltered homeless persons in Marseille do not have a high risk of harbouring gastrointestinal antibiotic resistant bacteria.
Natural abundance isotope ratios to differentiate sources of carbon used during tumor growth in vivo
Authors: Holland Petter , Hagopian William M. , Jahren A. Hope , Rusten Tor Erik
Published: September 2020

Background

Radioactive or stable isotopic labeling of metabolites is a strategy that is routinely used to map the cellular fate of a selected labeled metabolite after it is added to cell culture or to the circulation of an animal. However, the transformation of the labeled metabolite by cellular metabolism within organs complicates the use of this experimental strategy to quantify and understand metabolite transfer between organs. These methods are also technically demanding, expensive and potentially toxic. To allow quantification of the bulk movement of metabolites between organs, we have developed a novel application of stable isotope ratio mass spectrometry (SIRMS).

Results

We exploit natural differences in13C/12C ratios of plant nutrients for a low-cost and non-toxic carbon labeling, allowing a measurement of bulk carbon transfer between organsin vivo. SIRMS measurements were found to be sufficiently sensitive to measure organs from individualDrosophila melanogasterlarvae, giving robust measurements down to 2.5 µg per sample. We apply the method to determine if carbon incorporated into a growing solid tumor is ultimately derived from food or host tissues.

Conclusion

Measuring tumor growth in aD.melanogasterlarvae tumor model reveals that these tumors derive a majority of carbon from host sources. We believe the low cost and non-toxic nature of this methodology gives it broad applicability to study carbon flows between organs also in other animals and for a range of other biological questions.
High prevalence of SARS-CoV-2 antibodies in pets from COVID-19+ households
Authors: Fritz Matthieu , Rosolen Béatrice , Krafft Emilie , Becquart Pierre , Elguero Eric , Vratskikh Oxana , Denolly Solène , Boson Bertrand , Vanhomwegen Jessica , Ar Gouilh Meriadeg , Kodjo Angeli , Chirouze Catherine , Rosolen Serge , Legros Vincent , Leroy Eric M.
Published: September 2020

In a survey of household cats and dogs of laboratory-confirmed COVID-19 patients, we found a high seroprevalence of SARS-CoV-2 antibodies, ranging from 21% to 53%, depending on the positivity criteria chosen. Seropositivity was significantly greater among pets from COVID-19+ households compared to those with owners of unknown status. Our results highlight the potential role of pets in the spread of the epidemic.
High congruence of karyotypic and molecular data onHypostomusspecies from the Paraná River basin
Authors: Rocha-Reis Dinaíza Abadia , Pasa Rubens , Kavalco Karine Frehner
Published: September 2020

The Hypostomini tribe comprises a single genus,Hypostomus, which possibly contains several monophyletic groups because of significant morphological variation and a variety of diploid numbers and karyotype formulas. The objective of this study was to infer evolutionary relationships among some species ofHypostomusfound in the Paraná River basin and subsequently to identify chromosomal synapomorphies in the groupings formed. Two nuclear genes,rag1andrag2, and two mitochondrial genes,mt-co1andmt-cyb, were used to establish evolutionary relationships. Phylogenetic trees were inferred using the maximum likelihood (ML) method formt-co1and Bayesian analysis (BA) for all genes concatenated. Both phylogenetic trees showed two large monophyletic clades withinHypostomus. These clades are based on chromosome number, where haplogroup I contains individuals with 66–68 chromosomes, and haplogroup II contains species with 72–80 chromosomes. A third monophyletic haplogroup was also observed using ML, formed byH. faveolusandH. cochliodon, which present 2n = 64, reinforcing the separation of groups inHypostomusby diploid number. Robertsonian rearrangements were responsible for forming the different diploid numbers and for the diversity of karyotype formulas. The groups based on traditional morphological taxonomy are considered artificial in this study; the staining pattern, which separates the two large groups morphologically and is supported by little chromosomal evidence, was instead determined to show homoplasy. Ag-NORs are predominantly multiple and located on st/a chromosomes, along with 18S rDNA sites; 5S rDNA sites are often seen in an interstitial position, following the trend already described for vertebrates.
Cross-reactive serum and memory B cell responses to spike protein in SARS-CoV-2 and endemic coronavirus infection
Authors: Song Ge , He Wan-ting , Callaghan Sean , Anzanello Fabio , Huang Deli , Ricketts James , Torres Jonathan L. , Beutler Nathan , Peng Linghang , Vargas Sirena , Cassell Jon , Parren Mara , Yang Linlin , Ignacio Caroline , Smith Davey M. , Voss James E. , Nemazee David , Ward Andrew B , Rogers Thomas , Burton Dennis R. , Andrabi Raiees
Published: September 2020

Pre-existing immune responses to seasonal endemic coronaviruses could have profound consequences for antibody responses to SARS-CoV-2, either induced in natural infection or through vaccination. Such consequences are well established in the influenza and flavivirus fields. A first step to establish whether pre-existing responses can impact SARS-CoV-2 infection is to understand the nature and extent of cross-reactivity in humans to coronaviruses. We compared serum antibody and memory B cell responses to coronavirus spike (S) proteins from pre-pandemic and SARS-CoV-2 convalescent donors using a series of binding and functional assays. We found weak evidence of pre-existing SARS-CoV-2 cross-reactive serum antibodies in pre-pandemic donors. However, we found stronger evidence of pre-existing cross-reactive memory B cells that were activated on SARS-CoV-2 infection. Monoclonal antibodies (mAbs) isolated from the donors showed varying degrees of cross-reactivity with betacoronaviruses, including SARS and endemic coronaviruses. None of the cross-reactive mAbs were neutralizing except for one that targeted the S2 subunit of the S protein. The results suggest that pre-existing immunity to endemic coronaviruses should be considered in evaluating antibody responses to SARS-CoV-2.
The biogeography of Streptomyces in New Zealand enabled by high-throughput sequencing of genus-specific rpoB amplicons
Authors: Higgins S.A. , Panke-Buisse K. , Buckley Daniel H.
Published: September 2020

We evaluated Streptomyces biogeography in soils along a 1,200 km latitudinal transect across New Zealand (NZ). Streptomyces diversity was examined using high-throughput sequencing of rpoB amplicons generated with a Streptomyces specific primer set. We detected 1,287 Streptomyces rpoB operational taxonomic units (OTUs) with 159 ± 92 (average ± s.d.) rpoB OTUs per site. Only 12% (n = 149) of these OTUs matched rpoB sequences from cultured specimens (99% nucleotide identity cutoff). Streptomyces phylogenetic diversity (Faith’s PD) was correlated with soil pH, mean annual temperature, and plant community richness (Spearman’s r: 0.77, 0.64, and −0.79, respectively; p < 0.05), but not with latitude. In addition, soil pH and plant community richness both explained significant variation in Streptomyces beta diversity. Streptomyces communities exhibited both high dissimilarity and strong dominance of one or a few species at each site. Taken together, these results suggest that dispersal limitation due to competitive interactions limits the colonization success of spores that relocate to new sites. Cultivated Streptomyces isolates represent a major source of clinically useful antibiotics, but only a small fraction of extant diversity within the genus have been identified and most species of Streptomyces have yet to be described.
Identification of a Proteomic Signature of Senescence in Primary Human Mammary Epithelial Cells
Authors: Delfarah Alireza , Zheng DongQing , Yang Jesse , Graham Nicholas A.
Published: September 2020

Senescence is a permanent cell cycle arrest that occurs in response to cellular stress. Because senescent cells promote age-related disease, there has been considerable interest in defining the proteomic alterations in senescent cells. Because senescence differs greatly depending on cell type and senescence inducer, continued progress in the characterization of senescent cells is needed. Here, we analyzed primary human mammary epithelial cells (HMECs), a model system for aging, using mass spectrometry-based proteomics. By integrating data from replicative senescence, immortalization by telomerase reactivation, and drug-induced senescence, we identified a robust proteomic signature of HMEC senescence consisting of 77 upregulated and 36 downregulated proteins. This approach identified known biomarkers, such as downregulation of the nuclear lamina protein lamin-B1 (LMNB1), and novel upregulated proteins including the β-galactoside-binding protein galectin-7 (LGALS7). Gene ontology enrichment analysis demonstrated that senescent HMECs upregulated lysosomal proteins and downregulated RNA metabolic processes. We additionally integrated our proteomic signature of senescence with transcriptomic data from senescent HMECs to demonstrate that our proteomic signature can discriminate proliferating and senescent HMECs even at the transcriptional level. Taken together, our results demonstrate the power of proteomics to identify cell type-specific signatures of senescence and advance the understanding of senescence in primary HMECs.
Lytic bacteriophages facilitate antibiotic sensitization ofEnterococcus faecium
Authors: Canfield Gregory S. , Chatterjee Anushila , Espinosa Juliel , Mangalea Mihnea R. , Sheriff Emma K. , Keidan Micah , McBride Sara W. , McCollister Bruce D. , Hang Howard C. , Duerkop Breck A.
Published: September 2020

Enterococcus faecium, a commensal of the human intestine, has emerged as a hospital-adapted, multi-drug resistant (MDR) pathogen. Bacteriophages (phages), natural predators of bacteria, have regained attention as therapeutics to stem the rise of MDR bacteria. Despite their potential to curtail MDRE. faeciuminfections, the molecular events governingE. faecium-phageinteractions remain largely unknown. Such interactions are important to delineate because phage selective pressure imposed onE. faeciumwill undoubtedly result in phage resistance phenotypes that could threaten the efficacy of phage therapy. In an effort to understand the emergence of phage resistance inE. faecium, three newly isolated lytic phages were used to demonstrate thatE. faeciumphage resistance is conferred through an array of cell wall-associated molecules, including secreted antigen A (SagA), enterococcal polysaccharide antigen (Epa), wall teichoic acids, capsule, and an arginine-aspartate-aspartate (RDD) protein of unknown function. We find that capsule and Epa are important for robust phage adsorption and that phage resistance mutations insagA, epaR, andepaXenhanceE. faeciumsusceptibility to ceftriaxone, an antibiotic normally ineffective due to its low affinity for enterococcal penicillin binding proteins. Consistent with these findings, we provide evidence that phages potently synergize with cell wall (ceftriaxone and ampicillin) and membrane-acting (daptomycin) antimicrobials to slow or completely inhibit the growth ofE. faecium. Our work demonstrates that the evolution of phage resistance comes with fitness defects resulting in drug sensitization and that lytic phages could potentially serve as antimicrobial adjuvants in treatingE. faeciuminfections.
Feasibility of generalised DKI approach for brain glioma grading
Authors: Pogosbekian E.L. , Pronin I.N. , Zakharova N.E. , Batalov A.I. , Turkin A.M. , Konakova T.A. , Maximov I.I.
Published: September 2020

Purpose

An accurate differentiation of brain glioma grade constitutes an important clinical issue. Powerful non-invasive approach based on diffusion MRI has already demonstrated its feasibility in glioma grade stratification. However, the conventional diffusion tensor (DTI) and kurtosis imaging (DKI) demonstrated moderate sensitivity and performance in glioma grading. In the present work, we apply generalised DKI (gDKI) approach in order to assess its diagnostic accuracy and potential application in glioma grading.

Methods

Diffusion scalar metrics were obtained from 50 patients with different glioma grades confirmed by histological tests following biopsy or surgery. All patients were divided into two groups with low- and high-grade gliomas as II grade versus III and IV grades, respectively. For a comparison, trained radiologists segmented the brain tissue into three regions with solid tumour, oedema, and normal appearing white matter. For each region we estimated the conventional and gDKI metrics including DTI maps.

Results

We found high correlations between DKI and gDKI metrics in high-grade glioma. Further, gDKI metrics enabled introduction of a complementary measure for glioma differentiation based on correlations between the conventional and generalised approaches. Both conventional and generalised DKI metrics showed quantitative maps of tumour heterogeneity and oedema behaviour. gDKI approach demonstrated largely similar sensitivity and specificity in low-high glioma differentiation as in the case of conventional DKI method.

Conclusion

The generalised diffusion kurtosis imaging enables differentiation of low and high grade gliomas at the same level as the conventional DKI. Additionally, gDKI exhibited higher tissue contrast between tumour and healthy tissue and, thus, may contribute as a complementary source of information on tumour heterogeneity.
A multiethnic GWAS meta-analysis of 585,243 individuals identifies new risk loci associated with cataract and reveals sex-specific effects
Authors: Choquet Hélène , Melles Ronald B. , Anand Deepti , Yin Jie , Cuellar-Partida Gabriel , Wang Wei ,   23andMe Research Team, Hoffmann Thomas J. , Nair K Saidas , Hysi Pirro G. , Lachke Salil A. , Jorgenson Eric
Published: September 2020

Cataract is the leading cause of blindness among the elderly worldwide and cataract surgery is one of the most common operations performed in the United States1-3. The etiology remains largely unclear, and to contribute to its elucidation we conducted a multiethnic genome-wide association meta-analysis of cataract, combining results from the GERA and UK Biobank cohorts, and tested for replication in the research cohort from 23andMe, Inc.. We report 54 genome-wide significant loci, 37 of which were previously unknown. Sex-stratified analyses identified two additional novel loci (CASP7 and GSTM2) specific to women and sex differences in effect sizes and significance of association at five other loci. We show that genes within or near 80% of the cataract-associated loci are significantly expressed and/or enriched-expressed in the mouse lens across various spatiotemporal stages. Further, 32 candidate genes in the associated loci have altered gene expression in 9 different gene perturbation mouse models of lens defects/cataract, suggesting their relevance to lens biology.
Mapping Isoform Abundance and Interactome of the Endogenous TMPRSS2-ERG Fusion Protein with Orthogonal Immunoprecipitation-Mass Spectrometry Assays
Authors: Fu Zhiqiang , Rais Yasmine , Chris Le X. , Drabovich Andrei P.
Published: September 2020

TMPRSS2-ERG gene fusion, a molecular alteration driving nearly a half of prostate cancer cases, has been intensively characterized at the transcript level, while limited studies explored the molecular identity and function of the endogenous fusion at the protein level. Here, we developed and applied immunoprecipitation-mass spectrometry (IP-MS) assays for the measurement of a low-abundance T1E4 TMPRSS2-ERG fusion protein, its isoforms and its interactome in VCaP prostate cancer cells. IP-MS assays quantified total ERG (∼27,000 copies/cell) and its four unique isoforms, and revealed that the T1E4-ERG isoform accounts for 71% of the total ERG protein in VCaP cells. For the first time, the N-terminal peptide (methionine-truncated and N-acetylated TASSSSDYGQTSK) unique for the T1/E4 fusion was identified and quantified. IP-MS with the C-terminal antibodies identified 29 proteins in the ERG interactome, including SWI/SNF chromatin remodeling complex subunits and numerous transcriptional co-regulators. Our data also suggested that TMPRSS2-ERG protein-protein interactions were exerted through at least two different regions. Knowledge on the distinct TMPRSS2-ERG protein isoforms and interactomes may facilitate development of more accurate diagnostics and targeted therapeutics of prostate cancer.
Eye-head coordination and dynamic visual scanning as indicators of visuo-cognitive demands in driving simulator
Authors: Mikula Laura , Mejía-Romero Sergio , Chaumillon Romain , Patoine Amigale , Lugo Eduardo , Bernardin Delphine , Faubert Jocelyn
Published: September 2020

Driving is an everyday task involving a complex interaction between visual and cognitive processes. As such, an increase in the cognitive and/or visual demands can lead to a mental overload which can be detrimental for driving safety. Compiling evidence suggest that eye and head movements are relevant indicators of visuo-cognitive demands and attention allocation. This study aims to investigate the effects of visual degradation on eye-head coordination as well as visual scanning behavior during a highly demanding task in a driving simulator. A total of 21 emmetropic participants (21 to 34 years old) performed dual-task driving in which they were asked to maintain a constant speed on a highway while completing a visual search and detection task on a navigation device. Participants did the experiment with optimal vision and with contact lenses that introduced a visual perturbation (myopic defocus). The results indicate modifications of eye-head coordination and the dynamics of visual scanning in response to the visual perturbation induced. More specifically, the head was more involved in horizontal gaze shifts when the visual needs were not met. Furthermore, the evaluation of visual scanning dynamics, based on time-based entropy which measures the complexity and randomness of scanpaths, revealed that eye and gaze movements became less explorative and more stereotyped when vision was not optimal. These results provide evidence for a reorganization of both eye and head movements in response to increasing visual-cognitive demands during a driving task. Altogether, these findings suggest that eye and head movements can provide relevant information about visuo-cognitive demands associated with complex tasks. Ultimately, eye-head coordination and visual scanning dynamics may be good candidates to estimate drivers’ workload and better characterize risky driving behavior.
Kinetics of self-assembly of inclusions due to lipid membrane thickness interactions
Authors: Liao Xinyu , Purohit Prashant K.
Published: September 2020

Self-assembly of proteins on lipid membranes underlies many important processes in cell biology, such as, exo- and endo-cytosis, assembly of viruses, etc. An attractive force that can cause self-assembly is mediated by membrane thickness interactions between proteins. The free energy profile associated with this attractive force is a result of the overlap of thickness deformation fields around the proteins. The thickness deformation field around proteins of various shapes can be calculated from the solution of a boundary value problem and is relatively well understood. Yet, the time scales over which self-assembly occurs has not been explored. In this paper we compute this time scale as a function of the initial distance between two inclusions by viewing their coalescence as a first passage time problem. The first passage time is computed using both Langevin dynamics and a partial differential equation, and both methods are found to be in excellent agreement. Inclusions of three different shapes are studied and it is found that for two inclusions separated by about hundred nanometers the time to coalescence is hundreds of milliseconds irrespective of shape. Our Langevin dynamics simulation of self-assembly required an efficient computation of the interaction energy of inclusions which was accomplished using a finite difference technique. The interaction energy profiles obtained using this numerical technique were in excellent agreement with those from a previously proposed semi-analytical method based on Fourier-Bessel series. The computational strategies described in this paper could potentially lead to efficient methods to explore the kinetics of self-assembly of proteins on lipid membranes.

Author summary

Self-assembly of proteins on lipid membranes occurs during exo- and endo-cytosis and also when viruses exit an infected cell. The forces mediating self-assembly of inclusions on membranes have therefore been of long standing interest. However, the kinetics of self-assembly has received much less attention. As a first step in discerning the kinetics, we examine the time to coalescence of two inclusions on a membrane as a function of the distance separating them. We use both Langevin dynamics simulations and a partial differential equation to compute this time scale. We predict that the time to coalescence is on the scale of hundreds of milliseconds for two inclusions separated by about hundred nanometers. The deformation moduli of the lipid membrane and the membrane tension can affect this time scale.
Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation
Authors: Kishore Dileep , Birzu Gabriel , Hu Zhenjun , DeLisi Charles , Korolev Kirill S. , Segrè Daniel
Published: September 2020

Microbes tend to organize into communities consisting of hundreds of species involved in complex interactions with each other. 16S ribosomal RNA (16S rRNA) amplicon profiling provides snapshots that reveal the phylogenies and abundance profiles of these microbial communities. These snapshots, when collected from multiple samples, have the potential to reveal which microbes co-occur, providing a glimpse into the network of associations in these communities. The inference of networks from 16S data is prone to statistical artifacts. There are many tools for performing each step of the 16S analysis workflow, but the extent to which these steps affect the final network is still unclear. In this study, we perform a meticulous analysis of each step of a pipeline that can convert 16S sequencing data into a network of microbial associations. Through this process, we map how different choices of algorithms and parameters affect the co-occurrence network and estimate steps that contribute most significantly to the variance. We further determine the tools and parameters that generate the most accurate and robust co-occurrence networks based on comparison with mock and synthetic datasets. Ultimately, we develop a standardized pipeline (available athttps://github.com/segrelab/MiCoNE) that follows these default tools and parameters, but that can also help explore the outcome of any other combination of choices. We envisage that this pipeline could be used for integrating multiple data-sets, and for generating comparative analyses and consensus networks that can help understand and control microbial community assembly in different biomes.

Importance

To understand and control the mechanisms that determine the structure and function of microbial communities, it is important to map the interrelationships between its constituent microbial species. The surge in the high-throughput sequencing of microbial communities has led to the creation of thousands of datasets containing information about microbial abundances. These abundances can be transformed into networks of co-occurrences across multiple samples, providing a glimpse into the structure of microbiomes. However, processing these datasets to obtain co-occurrence information relies on several complex steps, each of which involves multiple choices of tools and corresponding parameters. These multiple options pose questions about the accuracy and uniqueness of the inferred networks. In this study, we address this workflow and provide a systematic analysis of how these choices of tools and parameters affect the final network, and on how to select those that are most appropriate for a particular dataset.
A novel Hsp90 phospho-switch modulates virulence in the major human fungal pathogenCandida albicans
Authors: Alaalm Leenah , Crunden Julia L. , Butcher Mark , Obst Ulrike , Whealy Ryann , Williamson Carolyn E. , O’Brien Heath E. , Schaffitzel Christiane , Ramage Gordon , Diezmann Stephanie
Published: September 2020

The ubiquitous molecular chaperone Hsp90 is a key regulator of cellular proteostasis and environmental stress responses. Hsp90 also regulates cellular morphogenesis, drug resistance, and virulence in human pathogenic fungi, which kill more than 1.6 million patients each year worldwide. Invasive fungal infections are difficult to treat due to the lack of effective antifungal therapies, resulting in mortality rates of up to 95%. As a key regulator of fungal virulence, Hsp90 is an attractive therapeutic target. However, fungal and animal homologs are highly conserved, impeding fungal-specific targeting. Thus, understanding the factors that regulate Hsp90 could provide an alternative strategy aimed at exclusively targeting this regulator of fungal virulence. Here, we demonstrate how CK2-mediated phosphorylation of two Hsp90 residues modulates virulence in a major fungal pathogen of humans,Candida albicans. We combined proteomics, molecular evolution and structural modelling with molecular biology to identify and characterize two Hsp90 phosphorylation sites. Phosphorylation negatively affects thermal stress response, morphogenesis, drug susceptibility and fungal virulence. Our results provide the first record of specific Hsp90 phosphorylation sites acting as modulators of fungal virulence. Post-translational modifications of Hsp90 could prove valuable in future exploitation as antifungal drug targets.
Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK
Authors: Hosie Margaret J , Epifano Ilaria , Herder Vanessa , Orton Richard J , Stevenson Andrew , Johnson Natasha , MacDonald Emma , Dunbar Dawn , McDonald Michael , Howie Fiona , Tennant Bryn , Herrity Darcy , Da Silva Filipe Ana , Streicker Daniel G , Willett Brian J , Murcia Pablo R , Jarrett Ruth F , Robertson David L , Weir William ,   the COVID-19 Genomics UK (COG-UK) consortium
Published: September 2020

Two cats from different COVID-19-infected households in the UK were found to be infected with SARS-CoV-2 from humans, demonstrated by immunofluorescence,in situhybridisation, reverse transcriptase quantitative PCR and viral genome sequencing. Lung tissue collected post-mortem from cat 1 displayed pathological and histological findings consistent with viral pneumonia and tested positive for SARS-CoV-2 antigens and RNA. SARS-CoV-2 RNA was detected in an oropharyngeal swab collected from cat 2 that presented with rhinitis and conjunctivitis. High throughput sequencing of the virus from cat 2 revealed that the feline viral genome contained five single nucleotide polymorphisms (SNPs) compared to the nearest UK human SARS-CoV-2 sequence. An analysis of cat 2’s viral genome together with nine other feline-derived SARS-CoV-2 sequences from around the world revealed no shared catspecific mutations. These findings indicate that human-to-cat transmission of SARS-CoV-2 occurred during the COVID-19 pandemic in the UK, with the infected cats developing mild or severe respiratory disease. Given the versatility of the new coronavirus, it will be important to monitor for human-to-cat, cat-to-cat and cat-to-human transmission.
Sex-specific effects ofin vitrofertilization on adult metabolic phenotypes and hepatic transcriptomic and proteomic pathways in mouse
Authors: Narapareddy Laren , Rhon-Calderon Eric A. , Vrooman Lisa A. , Baeza Josue , Nguyen Duy K. , Lan Yemin , Garcia Benjamin A. , Schultz Richard M. , Bartolomei Marisa S.
Published: September 2020

Althoughin vitrofertilization (IVF) is associated with adverse perinatal outcomes, an increasing concern is the long-term health implications. We augmented our IVF mouse model to longitudinally investigate cardiometabolic outcomes in offspring from optimal neonatal litter sizes. We found that IVF-conceived females had higher body weight and cholesterol levels compared to naturally-conceived females, whereas IVF-conceived males had higher levels of triglycerides and insulin, and increased body fat composition. Through transcriptomics and proteomics of adult liver, we identified sexually-dimorphic dysregulation of the sterol regulatory element binding protein (SREBP) pathways that are associated with the sex-specfic phenotypes. We also found that global loss of DNA methylation in placenta was linked to higher cholesterol levels in IVF-conceived females. Our findings indicate that IVF procedures have long-lasting sex-specific effects on metabolic health of offspring and lay the foundation to utilize the placenta as a predictor of long-term outcomes.
Increased mGlu5 mRNA expression in BLA glutamate neurons facilitates resilience to the long-term effects of a single predator scent stress exposure
Authors: Shallcross John , Wu Lizhen , Knackstedt Lori A. , Schwendt Marek
Published: September 2020

Post-traumatic stress disorder (PTSD) develops in a subset of individuals exposed to a trauma with core features being increased anxiety, and impaired fear extinction. To model the heterogeneity of PSTD behavioral responses, we exposed Sprague-Dawley rats to predator scent stress (TMT) once for 10 minutes and then tested for anxiety-like behavior 7 days later using the elevated plus-maze and acoustic startle response. Rats displaying anxiety-like behavior in both tasks were classified as stress-Susceptible, and rats exhibiting behavior no different from unstressed Controls were classified as stress-Resilient. Our previous findings revealed increased mRNA expression of mGlu5 in the amygdala and PFC and CB1R mRNA in the amygdala of Resilient rats. Here, we performed fluorescent in situ hybridization (FISH) to determine the subregion and cell-type-specific expression of these genes in Resilient rats. We found higher mRNA expression of mGlu5 in the BLA, IL, and PL, and CB1R in the BLA of Resilient rats relative to Controls. Using dual-labeled FISH we determined that mGlu5 and CB1R mRNA increases were limited to vGlut+ cells. To test the necessity of mGlu5 receptor activity for attenuating contextual fear, intra-BLA infusions of the mGlu5 negative allosteric modulator MTEP were administered prior to context re-exposure. MTEP increased contextual fear on the day of administration, which extinguished over the course of two additional un-drugged sessions. These results suggest that an enhanced mGlu5 expression within BLA glutamate neurons contributes to the behavioral flexibility observed in stress-Resilient animals by facilitating a capacity for extinguishing contextual fear associations.
Interferon receptor-deficient mice are susceptible to eschar-associated rickettsiosis
Authors: Burke Thomas P. , Engström Patrik , Tran Cuong J. , Glasner Dustin R. , Espinosa Diego A. , Harris Eva , Welch Matthew D.
Published: September 2020

Rickettsiaare arthropod-borne pathogens that cause severe human disease worldwide. The spotted fever group (SFG) pathogenRickettsia parkerielicits skin lesion (eschar) formation in humans after tick bite. However, intradermal inoculation of inbred mice with millions of bacteria fails to elicit eschar formation or disseminated disease, hindering investigations into understanding eschar-associated rickettsiosis. Here, we report that intradermal infection of mice deficient for both interferon receptors (Ifnar-/-Ifngr-/-) withR. parkericauses eschar formation, recapitulating the hallmark clinical feature of human disease. Intradermal infection with doses that recapitulate tick infestation caused eschar formation and lethality, including with as few as 10 bacteria. Using this model, we found that the actin-based motility protein Sca2 is required forR. parkeridissemination from the skin to internal organs and for causing lethal disease, and that the abundantR. parkeriouter membrane protein OmpB contributes to eschar formation. We also found that immunizing mice withsca2andompBmutantR. parkeriprotects against subsequent rechallenge with wild-type bacteria, revealing live-attenuated vaccine candidates. Thus, interferon receptor-deficient mice are a tractable model to investigate rickettsiosis, bacterial virulence factors, and immunity. Our results suggest that differences in interferon signaling in the skin between mice and humans may explain the discrepancy in susceptibility to SFGRickettsia.
Hybrid dedicated and distributed coding in PMd/M1 provides separation and interaction of bilateral arm signals
Authors: Dixon Tanner C. , Merrick Christina M. , Wallis Joni D. , Ivry Richard B. , Carmena Jose M.
Published: September 2020

Pronounced activity is observed in both hemispheres of the motor cortex during preparation and execution of unimanual movements. The organizational principles of bi-hemispheric signals and the functions they serve throughout motor planning remain unclear. Using an instructed-delay reaching task in monkeys, we identified two components in population responses spanning PMd and M1. A “dedicated” component, which segregated activity at the level of individual units, emerged in PMd during preparation. It was most prominent following movement when M1 became strongly engaged, and principally involved the contralateral hemisphere. In contrast to recent reports, these dedicated signals solely accounted for divergence of arm-specific neural subspaces. The other “distributed” component mixed signals for each arm within units, and the subspace containing it did not discriminate between arms at any stage. The statistics of the population response suggest two functional layers of the cortical network: one that spans both hemispheres for supporting preparatory and ongoing processes, and another that is predominantly housed in the contralateral hemisphere and specifies unilateral output.
Early alterations of large-scale brain networks temporal dynamics in young children with autism
Authors: Bochet Aurélie , Sperdin Holger Franz , Rihs Tonia Anahi , Kojovic Nada , Franchini Martina , Jan Reem Kais , Michel Christoph Martin , Schaer Marie
Published: September 2020

Disruption of large-scale brain networks is associated with autism spectrum disorders (ASD). Recently, we found that directed functional connectivity alterations of social brain networks are a core component of atypical brain development at early developmental stages in ASD (Sperdin et al., 2018). Here, we investigated the spatio-temporal dynamics of whole-brain neuronal networks at a subsecond scale in 90 toddlers and preschoolers (47 with ASD) using an EEG microstate approach. Results revealed the presence of five microstate classes that best described the entire dataset (labeled as microstate classes A-E). Microstate class C related to the Default Mode Network (DMN) occurred less in children with ASD. Analysis of brain-behavioural relationships within the ASD group suggested that a compensatory mechanism from microstate C was associated with less severe symptoms and better adaptive skills. These results demonstrate that the temporal properties of some specific EEG microstates are altered in ASD at early developmental stages.
Transposon expression in the Drosophila brain is driven by neighboring genes and diversifies the neural transcriptome
Authors: Treiber Christoph D. , Waddell Scott
Published: September 2020

Somatic transposon expression in neural tissue is commonly considered as a measure of mobilization and has therefore been linked to neuropathology and organismal individuality. We combined genome sequencing data with single-cell mRNA sequencing of the same inbred fly strain to map transposon expression in the Drosophila midbrain and found that transposon expression patterns are highly stereotyped. Every detected transposon is resident in at least one cellular gene with a matching expression pattern. Bulk RNA sequencing from fly heads of the same strain revealed that coexpression is a physical link in the form of abundant chimeric transposon–gene mRNAs. We identified 264 genes where transposons introduce cryptic splice sites into the nascent transcript and thereby significantly expand the neural transcript repertoire. Some genes exclusively produce chimeric mRNAs with transposon sequence; on average, 11.6% of the mRNAs produced from a given gene are chimeric. Conversely, most transposon-containing transcripts are chimeric, which suggests that somatic expression of these transposons is largely driven by cellular genes. We propose that chimeric mRNAs produced by alternative splicing into polymorphic transposons, rather than transposon mobilization, may contribute to functional differences between individual cells and animals.
Developing scaled tools for residential and nursing home inspection: feasibility study
Authors: Taylor Brian J. , Osterhus Insa , Stewart Rachel , Cunningham Suzanne , MacLeod Olive , McColgan Mary
Published: September 2020

Purpose

This study explored the feasibility of developing scaled inspection tools for use during external inspection of health and social care facilities to give improved accuracy in identifying facilities “at risk”, a tool for risk-adjusted frequency of inspection, and greater consistency of judgements.

Design/methodology/approach

This paper summarises the development through working groups and workshops involving 20 experienced inspectors (nurses and social workers) of the Regulation and Quality Improvement Authority who inspect the 206 nursing and 182 residential care homes in Northern Ireland. A brief evaluation survey, including response to a case vignette, gathered inspectors' views after using the tools for six months.

Findings

Eight two-dimensional Scaled Inspection Tools were created, each embodying a scale of performance (seriousness of risk issue) and a scale of the ability of the facility to manage that issue, each axis comprising four points. The Scaled Inspection Tools were used for on-site inspections during 2017–18. Evaluative comments were generally positive. The case vignette seemed to highlight greater risk aversion amongst newer inspectors.

Research limitations/implications

The creation of scaled inspection tools adds credibility to the potential for developing risk-based governance in service regulation. Further testing of domains and their scope is required.

Practical implications

Prompts for each domain were found essential to guide inspectors. Despite the challenge of change, inspectors became enthusiastic about use for evaluating risks, and managers about improvements in consistency of inspection.

Social implications

Knowledge derived from statistical approaches needs to be incorporated into inspection and regulation, just as in other aspects of professional practice.

Originality/value

Scaled inspection tools, with two orthogonal axes corresponding to seriousness of risk and ability to manage the risk (inverse of likelihood of harm), proved acceptable and intuitive in use. The study gives credibility to the possibility of developing screening and surveillance approaches to risk-based governance in service regulation.