bluuebunny/crossref_metadata_2025 huggingface dataset:
Short-term Forecasting of Cumulative Confirmed Cases of Covid-19 Pandemic in Somalia
Authors: Ali Dahir Abdi , Midi Habshah
Published: June 2020

Somalia has recorded the first confirmed Covid-19 case and first death case on March 16, and April 08, 2020, respectively. Since its arrival, it had infected 2,603 people and took the lives of 88 people while 577 patients were recovered as of 14 June, 2020. To fight this pandemic, the government requires to make the necessary plans accordingly. To plan effectively, the government needs to answer this question: what will be the effect of Covid-19 cases in the country? To answer this question accurately and objectively, forecasting the spread of confirmed Covid-19 cases will be vital. To this regard, this paper provides real times forecasts of Covid-19 cases employing Holt’s linear trend model without seasonality. Provided that the data employed is accurate and the past pattern of the disease will continue in the future, this model is powerful to produce real time forecasts in the future with some degree of uncertainty. With the help of these forecasts, the government can make evidence based decisions by utilizing the scarce resource available at its disposal.
Modeling quantitative traits for COVID-19 case reports
Authors: Queralt-Rosinach Núria , Bello Susan M. , Hoehndorf Robert , Weiland Claus , Rocca-Serra Philippe , Schofield Paul N.
Published: June 2020

Medical practitioners record the condition status of a patient through qualitative and quantitative observations. The measurement of vital signs and molecular parameters in the clinics gives a complementary description of abnormal phenotypes associated with the progression of a disease. The Clinical Measurement Ontology (CMO) is used to standardize annotations of these measurable traits. However, researchers have no way to describe how these quantitative traits relate to phenotype concepts in a machine-readable manner. Using the WHO clinical case report form standard for the COVID-19 pandemic, we modeled quantitative traits and developed OWL axioms to formally relate clinical measurement terms with anatomical, biomolecular entities and phenotypes annotated with the Uber-anatomy ontology (Uberon), Chemical Entities of Biological Interest (ChEBI) and the Phenotype and Trait Ontology (PATO) biomedical ontologies. The formal description of these relations allows interoperability between clinical and biological descriptions, and facilitates automated reasoning for analysis of patterns over quantitative and qualitative biomedical observations.
Changing indications for intravitreal Anti-Vascular Endothelial Growth Factor Injections at the University College Hospital, Ibadan, sub-Saharan Africa
Authors: Adewole A.T , Oluleye T.S , Babalola Y.O , Majekodunmi O , Ijaduola M
Published: June 2020

Aim

To compare the current indications for intravitreal anti-vascular endothelial growth factor (anti-VEGF) therapy, to make recommendations for planning of services.

Methodology

The medical records of 172 patients who had intravitreal anti-VEGF injections from January 2016 to December 2019 were retrieved. Socio-demographic and clinical data were extracted, analysed, and compared with data from the previously published audit report covering 2010 to 2012.

Results

Three hundred and thirty injections were given to 182 eyes in this cohort of patients. The mean age was 61.1 ± 16.3 years (range <1-90 years), with a male to female ratio of 1.1:1. Retinal vein occlusion, 64 (35%) remained the most common indication for anti-VEGF injections in the eyes treated. This was followed by choroidal neovascular membrane/ Wet age-related macular degeneration which accounted for 42 (23%) as reported previously. However, cases of proliferative diabetic retinopathy/ diabetic maculopathy needing anti-VEGF were noticed to have almost doubled from about 8% (10) in the previous study to 15% (27) in the present study. In addition, idiopathic polypoidal choroidal vasculopathy, 18 (10%) ranked above proliferative sickle cell retinopathy in the present study. Retinopathy of prematurity, neovascular glaucoma, retinal artery macro-aneurysm and myopic choroidal neovascular membrane were the new emerging indications.

Conclusion

There is an expanding indication for anti-VEGF in the management of retinal vascular diseases in our health facility and adequate measures should be put in place for early diagnosis and management. Patients should be counselled on the availability of this treatment option.
Sewage surveillance for the presence of SARS-CoV-2 genome as a useful wastewater based epidemiology (WBE) tracking tool in India
Authors: Arora Sudipti , Nag Aditi , Sethi Jasmine , Rajvanshi Jayana , Saxena Sonika , Shrivastava Sandeep K , Gupta A. B.
Published: June 2020

The infection with SARS-CoV-2 is reported to be accompanied by the shedding of the virus in stool samples of infected patients. Earlier reports have suggested that COVID-19 agents can be present in the fecal and sewage samples and thus it can be a good indication of the pandemic extent in a community. However, no such studies have been reported in the Indian context so far. Since, several factors like local population physiology, the climatic conditions, sewage composition, and processing of samples could possibly affect the detection of the viral genome, it becomes absolutely necessary to check for the presence of the SARS-CoV-2 in the wastewater samples from wastewater treatment plants (WWTPs) serving different localities of Jaipur city, which has been under red zone (pandemic hotspots) since early April 2020. Samples from different local municipal WWTPs and hospital wastewater samples were collected and wastewater based epidemiology (WBE) studies for the presence of SARS-CoV-2 were carried out using the RT-PCR technique to confirm the presence of different COVID-19 target genes namely S gene, E gene, ORF1ab gene, RdRp gene and N gene in the viral load of wastewater samples. In the present study, the untreated wastewater samples from the municipal WWTPs and hospital wastewater samples showed the presence of SARS-CoV-2 viral genome, which was correlated with the increased number of COVID-19 positive patients from the concerned areas, as per reported in the publically available health data. This is the first study that investigated the presence of SARS-CoV-2 viral genome in wastewater, at higher ambient temperature (above 40°C), further validating WBE as a potential tool in predicting and mitigating outbreaks.

Highlights

The study reports detection of SARS-CoV-2 in sewage in India.

The presence of SARS-CoV-2 was confirmed by RT-PCR.

The presence of viral genome was detected at high ambient temperatures of 40-45° C.

Corroborates trends in the WWTPs showing viral genome with public health data.

Treated effluent from WWTPs appears safe for reuse with low public health concern.

Graphical Abstract
SARS-CoV-2 growth, furin-cleavage-site adaptation and neutralization using serum from acutely infected, hospitalized COVID-19 patients
Authors: Klimstra William B. , Tilston-Lunel Natasha L. , Nambulli Sham , Boslett James , McMillen Cynthia M. , Gilliland Theron , Dunn Matthew D. , Sun Chengqun , Wheeler Sarah E , Wells Alan , Hartman Amy L. , McElroy Anita K. , Reed Douglas S. , Rennick Linda J. , Duprex W. Paul
Published: June 2020

SARS-CoV-2, the causative agent of COVID-19, emerged at the end of 2019 and by mid-June 2020, the virus has spread to at least 215 countries, caused more than 8,000,000 confirmed infections and over 450,000 deaths, and overwhelmed healthcare systems worldwide. Like SARS-CoV, which emerged in 2002 and caused a similar disease, SARS-CoV-2 is a betacoronavirus. Both viruses use human angiotensin-converting enzyme 2 (hACE2) as a receptor to enter cells. However, the SARS-CoV-2 spike (S) glycoprotein has a novel insertion that generates a putative furin cleavage signal and this has been postulated to expand the host range. Two low passage (P) strains of SARS-CoV-2 (Wash1: P4 and Munich: P1) were cultured twice in Vero-E6 cells and characterized virologically. Sanger and MinION sequencing demonstrated significant deletions in the furin cleavage signal of Wash1: P6 and minor variants in the Munich: P3 strain. Cleavage of the S glycoprotein in SARS-CoV-2-infected Vero-E6 cell lysates was inefficient even when an intact furin cleavage signal was present. Indirect immunofluorescence demonstrated the S glycoprotein reached the cell surface. Since the S protein is a major antigenic target for the development of neutralizing antibodies we investigated the development of neutralizing antibody titers in serial serum samples obtained from COVID-19 human patients. These were comparable regardless of the presence of an intact or deleted furin cleavage signal. These studies illustrate the need to characterize virus stocks meticulously prior to performing either in vitro or in vivo pathogenesis studies.
GenNet framework: interpretable neural networks for phenotype prediction
Authors: van Hilten Arno , Kushner Steven A. , Kayser Manfred , Ikram M. Arfan , Adams Hieab H.H. , Klaver Caroline C.W. , Niessen Wiro J. , Roshchupkin Gennady V.
Published: June 2020

Deep learning is rarely used in population genomics because of the computational burden and challenges in interpreting neural networks. Here, we propose GenNet, a novel open-source deep learning framework for predicting phenotypes from genetic variants. In this framework, interpretable and memory-efficient neural network architectures are constructed by embedding biological knowledge from public databases, resulting in neural networks that contain only biological plausible connections.

We applied the framework to seventeen phenotypes from a case-control study, a population-based study and the UK Biobank. Interpreting the networks revealed well-replicated genes such asHERC2andOCA2for hair and eye color and novel genes such asZNF773andPCNTfor schizophrenia. Additionally, the framework obtained an AUC of 0.74 in the held-out test set and identified ubiquitin mediated proteolysis, endocrine system and viral infectious diseases as most predictive biological pathways for schizophrenia.

GenNet is a freely available, end-to-end deep learning framework that allows researchers to develop and use interpretable neural networks to obtain novel insights into the genetic architecture of complex traits and diseases.
Rapid Inactivation of SARS-CoV-2 by Silicon Nitride, Copper, and Aluminum Nitride
Authors: Pezzotti Giuseppe , Ohgitani Eriko , Shin-Ya Masaharu , Adachi Tetsuya , Marin Elia , Boschetto Francesco , Zhu Wenliang , Mazda Osam
Published: June 2020

Introduction

Viral disease spread by contaminated commonly touched surfaces is a global concern. Silicon nitride, an industrial ceramic that is also used as an implant in spine surgery, has known antibacterial activity. The mechanism of antibacterial action relates to the hydrolytic release of surface disinfectants. It is hypothesized that silicon nitride can also inactivate the coronavirus SARS-CoV-2.

Methods

SARS-CoV-2 virions were exposed to 15 wt.% aqueous suspensions of silicon nitride, aluminum nitride, and copper particles. The virus was titrated by the TCD50method using VeroE6/TMPRSS2 cells, while viral RNA was evaluated by real-time RT-PCR. Immunostaining and Raman spectroscopy were used as additional probes to investigate the cellular responses to virions exposed to the respective materials.

Results

All three tested materials showed >99% viral inactivation at one and ten minutes of exposure. Degradation of viral RNA was also observed with all materials. Immunofluorescence testing showed that silicon nitride-treated virus failed to infect VeroE6/TMPRSS2 cells without damaging them. In contrast, the copper-treated virus suspension severely damaged the cells due to copper ion toxicity. Raman spectroscopy indicated differential biochemical cellular changes due to infection and metal toxicity for two of the three materials tested.

Conclusions

Silicon nitride successfully inactivated the SARS-CoV-2 in this study. The mechanism of action was the hydrolysis-mediated surface release of nitrogen-containing disinfectants. Both aluminum nitride and copper were also effective in the inactivation of the virus. However, while the former compound affected the cells, the latter compound had a cytopathic effect. Further studies are needed to validate these findings and investigate whether silicon nitride can be incorporated into personal protective equipment and commonly touched surfaces, as a strategy to discourage viral persistence and disease spread.
Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny
Authors: Pipes Lenore , Wang Hongru , Huelsenbeck John P. , Nielsen Rasmus
Published: June 2020

The rooting of the SARS-CoV-2 phylogeny is important for understanding the origin and early spread of the virus. Previously published phylogenies have used different rootings that do not always provide consistent results. We investigate several different strategies for rooting the SARS-CoV-2 tree and provide measures of statistical uncertainty for all methods. We show that methods based on the molecular clock tend to place the root in the B clade, while methods based on outgroup rooting tend to place the root in the A clade. The results from the two approaches are statistically incompatible, possibly as a consequence of deviations from a molecular clock or excess back-mutations. We also show that none of the methods provide strong statistical support for the placement of the root in any particular edge of the tree. Our results suggest that inferences on the origin and early spread of SARS-CoV-2 based on rooted trees should be interpreted with caution.
Dengue virus strain 2 capsid protein switches the annealing pathway and reduces the intrinsic dynamics of the conserved 5’ untranslated region
Authors: Yong Xin Ee , Raghuvamsi Palur Venkata , Anand Ganesh S. , Wohland Thorsten , Sharma Kamal K.
Published: June 2020

The capsid protein of Dengue Virus strain 2 (DENV2C) is a structural protein with RNA chaperone activity that promotes multiple nucleic acid structural rearrangements, critical for transcription of the single-stranded positive-sense DENV2 genomic RNA. Annealing of the conserved 5’ untranslated region (5’UTR) to either its complementary sequence or to the 3’ untranslated region (3’UTR) occurs during (+)/(−) ds-RNA formation and (+) RNA circularization, respectively, both essential steps during DENV RNA replication. We investigated the effect of DENV2C on the annealing mechanism of two hairpin structures from the 5’UTR region (21-nt upstream AUG region (5’UAR) and 23-nt capsid-coding hairpin (5’cHP)) to their complementary sequences during (+)/(−) ds-RNA formation and (+) RNA circularization. Using fluorescence spectroscopy, DENV2C was found to switch annealing reactions nucleated mainly through kissing-loop intermediates to stem-stem interactions during (+)/(−) ds-RNA formation while it promotes annealing mainly through kissing-loop interactions during the (+) RNA circularization. Using FRET-FCS and trFRET, we determined that DENV2C exerts RNA chaperone activities by modulating intrinsic dynamics and by reducing the kinetically trapped unfavorable conformations of the 5’UTR sequence. Thus, DENV2C is likely to facilitate genome folding into functional conformations required for replication, playing a role in modulating (+)/(−) ds-RNA formation and (+) RNA circularization.
Modulation of root growth by nutrient-defined fine-tuning of polar auxin transport
Authors: Ötvös Krisztina , Marconi Marco , Vega Andrea , O’ Brien Jose , Johnson Alexander , Abualia Rashed , Antonielli Livio , Montesinos Juan Carlos , Zhang Yuzhou , Tan Shutang , Cuesta Candela , Artner Christina , Bouguyon Eleonore , Gojon Alain , Friml Jirí , Gutiérrez Rodrigo A. , Wabnik Krzysztof , Benková Eva
Published: June 2020

Nitrogen is an essential macronutrient and its availability in soil plays a critical role in plant growth, development and impacts agricultural productivity. Plants have evolved different strategies to sense and respond to heterogeneous nitrogen distribution. Modulating root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to varying nitrogen sources are poorly understood. Here, using a combination of physiological, livein vivohigh- and super resolution imaging, we describe a novel adaptation strategy of root growth on available nitrogen source. We show that growth,i.e. tissue-specific cell division and elongation rates are fine-tuned by modulating auxin flux within and between tissues. Changes in auxin redistribution are achieved by nitrogen source dependent post-translational modification of PIN2, a major auxin efflux carrier, at an uncharacterized, evolutionary conserved phosphosite. Further, we generate a computer model based on our results which successfully recapitulate our experimental observations and creates new predictions that could broaden our understanding of root growth mechanisms in the dynamic environment.
Genome-wide association study in European patients with congenital heart disease identifies risk loci for transposition of the great arteries and anomalies of the thoracic arteries and veins and expression of discovered candidate genes in the developing heart
Authors: Lahm Harald , Jia Meiwen , Dreßen Martina , Wirth Felix , Puluca Nazan , Gilsbach Ralf , Keavney Bernard D. , Cleuziou Julie , Beck Nicole , Bondareva Olga , Dzilic Elda , Burri Melchior , König Karl C. , Ziegelmüller Johannes A. , Abou-Ajram Claudia , Neb Irina , Zhang Zhong , Doppler Stefanie A. , Mastantuono Elisa , Lichtner Peter , Eckstein Gertrud , Hörer Jürgen , Ewert Peter , Priest James R. , Hein Lutz , Lange Rüdiger , Meitinger Thomas , Cordell Heather J. , Müller-Myhsok Bertram , Krane Markus
Published: June 2020

Rationale

Genetic factors undoubtedly contribute to the development of congenital heart disease (CHD), but still remain mostly ill-defined.

Objective

Identification of genetic risk factors associated with CHD and functional analysis of SNP-carrying genes.

Methods and Results

Genetic association study of 1,440 Caucasian CHD patients from the German Heart Center Munich collected from March 2009 to June 2016, 2,594 patients of previous studies provided by the Newcastle University and 8,486 controls underwent meta-analysis to detect single nucleotide polymorphisms (SNPs) associated with CHD.

Results

4,034 Caucasian CHD patients strictly classified according to the Society of Thoracic Surgeons nomenclature and 8,486 controls were included. One SNP on chromosome 5 reached genome-wide significance across all CHD phenotypes (rs185531658,OR:2.16, p=5.28×10−9) and was also indicative for septal defects (OR:2.16, p=6.15×10−8). One region on chromosome 20 pointing to the MACROD2 locus, identified four SNPs (rs150246290,OR:3.78, p=1.27×10−10; rs149890280,OR:3.74, p=1.8×10−10; rs149467721,OR:3.53; p=1.39×10−9, rs77094733,OR:3.53, p=1.73×10−9) in patients with transposition of the great arteries (TGA). A second region was detected on chromosome 8 located at ZBTB10 (rs148563140,OR:3.42, p=3.28×10−8; rs143638934,OR:3.42, p=3.51×10−8) in the same subgroup. Three highly significant risk variants on chromosome 17 (rs76774446,OR:1.60, p=9.95×10−8; rs11874,OR:1.60, p=6.64×10−8; rs17677363,OR:1.60, p=9.81×10−8) within the GOSR2 locus were identified in patients with anomalies of thoracic arteries and veins (ATAV). Genetic variants associated with ATAV are suggested to influence expression of WNT3, and variant rs870142 related to septal defects is proposed to influence expression of MSX1. Cardiac differentiation of human and murine induced pluripotent stem cells and single cell RNAseq analyses of developing murine and human hearts show essential functional roles for MACROD2, GOSR2, WNT3 and MSX1 at all developmental stages.

Conclusions

For the first time genetic risk factors in CHD patients with TGA and ATAV were identified. Several candidate genes play an essential functional role in heart development at the embryonic, newborn and adult stage.
Application of thein vivooxidative stress reporter Hmox1 as mechanistic biomarker of arsenic toxicity
Authors: Inesta-Vaquera Francisco , Navasumrit Panida , Henderson Colin J. , Frangova Tanya G. , Honda Tadashi , Dinkova-Kostova Albena T. , Ruchirawat Mathuros , Wolf C. Roland
Published: June 2020

Inorganic arsenic (iAs) is a naturally occurring metalloid present in drinking water and polluted air exposing millions of people globally. Epidemiological studies have linked iAs exposure to the development of numerous diseases including cognitive impairment, cardiovascular failure and cancer. Despite intense research, an effective therapy for chronic arsenicosis has yet to be developed. Laboratory studies have been of great benefit in establishing the pathways involved in iAs toxicity and providing insights into its mechanism of action. However, thein vivoanalysis of arsenic toxicity mechanisms has been difficult by the lack of reliablein vivobiomarkers of the effects of iAs. To resolve this issue we have applied the use of our recently developed stress reporter models to study iAs toxicity. The reporter mice Hmox1 (oxidative stress/inflammation; HOTT) and p21 (DNA damage) were exposed to iAs at acute and chronic, environmentally relevant, doses. We observed induction of the oxidative stress reporters in several cell types and tissues, which was largely dependent on the activation of transcription factor NRF2. We propose that our HOTT reporter model can be used as a surrogate biomarker of iAs-induced oxidative stress, and it constitutes a first-inclass platform to develop treatments in arsenicosis. Indeed, in a proof of concept experiment, the HOTT reporter mice were able to predict the therapeutic utility of the antioxidantN-acetyl cysteine in the prevention of iAs associated toxicity.
Measurement of stretch-evoked brainstem function using fMRI
Authors: Zonnino Andrea , Farrens Andria J , Ress David , Sergi Fabrizio
Published: June 2020

Knowledge on the organization of motor function in the reticulospinal tract (RST) is limited by the lack of methods for measuring RST function in humans. Behavioral studies suggest the involvement of the RST in long latency responses (LLRs). LLRs, elicited by precisely controlled perturbations, can therefore act as a viable paradigm to measure motor-related RST activity using functional Magnetic Resonance Imaging (fMRI).

Here we present StretchfMRI, a novel technique developed to study RST function associated with LLRs. StretchfMRI combines robotic perturbations with electromyography and fMRI to simultaneously quantify muscular and neural activity during stretch-evoked LLRs without loss of reliability. Using StretchfMRI, we established the muscle-specific organization of LLR activity in the brainstem. The observed organization is partially consistent with animal models, with activity primarily in the ipsilateral medulla for flexors and in the contralateral pons for extensors, but also include other areas, such as the midbrain and bilateral pontomedullary contributions.
QTL mapping for aggressiveness variation inF. graminearumrevealed one causal mutation in FgVe1 velvet protein
Authors: Laurent B. , Moinard M. , Spataro C. , Chéreau S. , Zehraoui E. , Blanc R. , Lasserre P. , Ponts N. , Foulongne-Oriol M.
Published: June 2020

Fusarium graminearumis one of the most frequent causal agents of theFusariumHead Blight in the world, a cereal disease spread throughout the world, reducing grain production and quality.F. graminearumisolates are genetically and phenotypically highly diverse. Notably, remarkable variations of aggressiveness between isolates have been observed, which could reflect an adaptive potential of this pathogen. In this study, we aimed to characterize the genetic basis of aggressiveness variation observed in an F1 population, for which genome sequences of both parental strains are available. Aggressiveness was assessed by a panel ofin plantaandin vitroproxies during two phenotyping trials including, among others, disease severity and mycotoxin accumulation in wheat spike. One major and single QTL was mapped for all the traits measured, on chromosome I, that explained up to 90% of the variance for disease severity. The confidence interval at the QTL spanned 1.2 Mb and contained 428 genes on the reference genome. Of these, four candidates were selected based on the postulate that a non-synonymous mutation affecting protein function may be responsible for phenotypic differences. Finally, a mutation was identified and functionally validated in the geneFgVe1, coding for a velvet protein known to be involved in pathogenicity and secondary metabolism production in several fungi.
Characterization of the dynamic resting state of a pentameric ligand-gated ion channel by cryo-electron microscopy and simulations
Authors: Rovšnik U , Zhuang Y , Axelsson L , Forsberg BO , Lim V , Carroni M , Blau C , Howard RJ , Lindahl E
Published: June 2020

Ligand-gated ion channels are critical mediators of electrochemical signal transduction across evolution. Biophysical and pharmacological development in this family relies on high-quality structural data in multiple, subtly distinct functional states. However, structural data remain limited, particularly for the unliganded or resting state. Here we report cryo-electron microscopy structures of theGloeobacter violaceusligand-gated ion channel (GLIC) under resting and activating conditions (neutral and low pH). Parallel models were built either manually or using recently developed density-guided molecular simulations. The moderate resolution of resting-state reconstructions, particularly in the extracellular domain, was improved under activating conditions, enabling the visualization of residues at key subunit interfaces including loops B, C, F, and M2–M3. Combined with molecular dynamics simulations, the cryo-electron microscopy structures at different pH describe a heterogeneous population of closed channels, with activating conditions condensing the closed-channel energy landscape on a pathway towards gating.
Gnotobiotic rainbow trout (Oncorhynchus mykiss) model reveals endogenous bacteria that protect againstFlavobacterium columnareinfection
Authors: Pérez-Pascual David , Vendrell-Fernández Sol , Audrain Bianca , Bernal-Bayard Joaquín , Patiño-Navarrete Rafael , Petit Vincent , Rigaudeau Dimitri , Ghigo Jean-Marc
Published: June 2020

The health and environmental risks associated with antibiotic use in aquaculture have promoted bacterial probiotics as an alternative approach to control fish infections in vulnerable larval and juvenile stages. However, evidence-based identification of probiotics is often hindered by the complexity of bacteria-host interactions and host variability in microbiologically uncontrolled conditions. While these difficulties can be partially resolved using gnotobiotic models harboring no or reduced microbiota, most host-microbe interaction studies are carried out in animal models with little relevance for fish farming. Here we studied host-microbiota-pathogen interactions in a germ-free and gnotobiotic model of rainbow trout (Oncorhynchus mykiss), one of the most widely cultured salmonids. We demonstrated that germ-free larvae raised in sterile conditions displayed no significant difference in growth after 35 days compared to conventionally-raised larvae, but were extremely sensitive to infection byFlavobacterium columnare, a common freshwater fish pathogen causing major economic losses worldwide. Furthermore, re-conventionalization with 11 culturable species from the conventional trout microbiota conferred resistance toF. columnareinfection. Using mono-re-conventionalized germ-free trout, we identified that this protection is determined by a commensalFlavobacteriumstrain displaying antibacterial activity againstF. columnare. Finally, we demonstrated that use of gnotobiotic trout is a suitable approach for the systematic identification of both endogenous and exogenous probiotic bacterial strains that may protect teleostean hosts againstF. columnareand other pathogens. This study establishes a novel and ecologically-relevant gnotobiotic model that will improve the sustainability and health of aquaculture.
CRYO-EM STRUCTURE OF THE DELTA-RETROVIRAL INTASOME IN COMPLEX WITH THE PP2A REGULATORY SUBUNIT B56γ
Authors: Barski Michał S. , Minnell Jordan J. , Hodakova Zuzana , Pye Valerie E. , Nans Andrea , Cherepanov Peter , Maertens Goedele N.
Published: June 2020

TheRetroviridaedelta-retrovirus genus includes the most oncogenic pathogen– human T-cell lymphotropic virus type 1 (HTLV-1)(1). Many of the ~20 million people infected with HTLV-1 will develop severe leukaemia (2) or an ALS-like motor disease (3) unless a therapy becomes available. A key step in the establishment of infection is the integration of viral genetic material into the host genome, catalysed by the viral integrase (IN) enzyme. Here we used X-ray crystallography and single-particle cryo-electron microscopy to determine the structure of functional delta-retroviral IN assembled on viral DNA ends and bound the B56γ subunit of its human host factor, the protein phosphatase 2A (4). The structure reveals a tetrameric IN assembly bound to the phosphatase via a conserved short linear motif found within the extended linker connecting the catalytic core (CCD) and C-terminal (CTD) IN domains. Unexpectedly, all four IN subunits are involved in B56γ binding, taking advantage of the flexibility of the CCD-CTD linkers. Our results fill the current gap in the structural understanding of the delta-retroviral integration machinery. Insight into the interactions between the delta-retroviral intasome and the host will be crucial for understanding the pattern of integration events in infected individuals and therefore bears important clinical implications.
Identification of sex differences in tumor-specific T cell infiltration in bladder tumor-bearing mice treated with BCG immunotherapy
Authors: Rousseau Matthieu , O’Brien Conan J O , Antequera Eduardo , Zdimerova Hana , Cansever Dilay , Canton Tracy , Scharff Anna Zychlinsky , Ingersoll Molly A
Published: June 2020

Bladder cancer is the fourth most common cancer for men. However, women are often diagnosed with later stage disease and have poorer outcomes. Whether immune-based sex differences contribute to this discrepancy is unclear. In addition, models to investigate tumor-specific immunity in bladder cancer, in the context of tumor development or response to therapy, are lacking. To address this specific unmet need, we incorporated a commonly used model antigen, ovalbumin, into two well-established models of bladder cancer; the orthotopic MB49 cell line model and the carcinogenic BBN bladder cancer model. We tested the utility of these models to investigate tumor-specific immunity in the context of immunotherapy in both sexes. We found that BCG vaccination, prior to weekly BCG instillation does not impart an immune-specific benefit to tumor-bearing mice in the context of multiple BCG instillations. Furthermore, tumors developed in the testes in male mice, precluding the use of the MB49 model to directly investigate sex-based immune differences. In the BBN model, we observed that more tumor antigen-specific CD8+T cells infiltrated male bladders compared to female bladders in the context of BCG immunotherapy and that these cells had the highest levels of the exhaustion marker PD-1. We propose our modified BBN model will contribute to our understanding of how tumor-specific immunity arises in bladder cancer. Additionally, the BBN bladder cancer model may help to uncover sex differences in tumor-specific immunity, which would provide valuable information for the development of new treatments or combination therapies for bladder cancer in women and men.
Habitat filtering differentially modulates phylogenetic vs functional diversity relationships between dominant ground-dwelling arthropods in salt marshes
Authors: Ridel Aurélien , Lafage Denis , Devogel Pierre , Lacoue-Labarthe Thomas , Pétillon Julien
Published: June 2020

While mechanisms underlying biological diversities at different scales received huge attention over the last decades, whether local abiotic factors driving functional and phylogenetic diversities can differ among ecologically and phylogenetically closely related taxa remains under-investigated. In this study, we compared correlations and drivers of functional (FD) and phylogenetic (PD) diversities between two dominant taxa of ground-dwelling arthropods in salt marshes, spiders and carabids. Pitfall trapping in two sampling sites of N-W France resulted in the collection and identification of more than 7000 individuals belonging to 67 species. Morphological and behavioral traits, as well as molecular sequences of COI gene, were attributed to all species for calculating functional and phylogenetic diversities respectively. Both taxa exhibited high correlation between FD and PD, which was even higher in carabids probably due to their lower species richness. Analyses using Bayesian framework and structural equation modeling revealed that FD and PD were positively influenced by taxonomic diversity in spiders and carabids, but abiotic factors driving FD and PD differed between taxa. Salinity especially drove the taxonomic diversity of carabids, but not that of spiders, suggesting that spiders are more plastic and less selected by this factor. Phylogenetic diversity was conversely influenced by salinity in spiders but not in carabids. This interesting result can be interpreted by different evolutionary history and colonization process of salt marshes between the two model taxa. Our study finally highlights that, even in taxa of the same phylum and occupying the same niche in a highly constrained habitat, functional and phylogenetic diversities can have different drivers, showing different filtering mechanisms and evolutionary history at small spatial and temporal scales.
Glutamine metabolism modulates azole susceptibility inTrypanosoma cruziamastigotes
Authors: Dumoulin Peter C. , Vollrath Joshua , Wang Jennifer X. , Burleigh Barbara A.
Published: June 2020

The mechanisms underlying resistance of the Chagas disease parasite,Trypanosoma cruzi,to current therapies are not well understood, including the potential role of metabolic heterogeneity in modulating susceptibility of intracellular amastigotes to trypanocidal compounds. We found that limiting exogenous glutamine protects actively dividing amastigotes from ergosterol biosynthesis inhibitors (azoles), independent of parasite growth rate. The antiparasitic properties of azoles are derived from inhibition of lanosterol 14α-demethylase (CYP51) in the endogenous sterol synthesis pathway. We find that carbons from13C-glutamine feed into amastigote sterols and into metabolic intermediates that accumulate upon CYP51 inhibition. Consistent with a model that decreased flux through the sterol biosynthetic pathway is protective for intracellular amastigotes exposed to azoles, we find that amastigotes become re-sensitized to azoles following addition of metabolites upstream of CYP51. Our results highlight the potential role of metabolic heterogeneity in recalcitrantT. cruziinfection, an avenue that is currently underexplored.
A novel gonorrhea vaccine composed of MetQ lipoprotein formulated with CpG shortens experimental murine infection
Authors: Sikora Aleksandra E. , Gomez Carolina , Le Van Adriana , Baarda Benjamin I. , Darnell Stephen , Martinez Fabian G. , Zielke Ryszard A. , Bonventre Josephine A. , Jerse Ann E.
Published: June 2020

Bacterial surface lipoproteins are emerging as attractive vaccine candidates due to their biological importance and the feasibility of their large-scale production for vaccine manufacturing. The global prevalence of gonorrhea, resistance to antibiotics, and serious consequences to reproductive and neonatal health necessitate development of effective vaccines. Reverse vaccinology identified the surface-displayed L-methionine binding lipoprotein MetQ (NGO2139) and its homolog GNA1946 (NMB1946) as gonococcal and meningococcal vaccine candidates, respectively. Here, we assessed the suitability of MetQ for inclusion in a gonorrhea vaccine by examining MetQ conservation, its function inNeisseria gonorrhoeae(Ng) pathogenesis, and its ability to induce protective immune responses using a female murine model of lower genital tract infection. In-depth bioinformatics, phylogenetics and mapping the most prevalentNgpolymorphic amino acids to the GNA1946 crystal structure revealed remarkable MetQ conservation: ~97%Ngisolates worldwide possess a single MetQ variant. Mice immunized with rMetQ-CpG (n=40), a vaccine containing a tag-free version of MetQ formulated with CpG, exhibited robust, antigen-specific antibody responses in serum and at the vaginal mucosae including secretory IgA. Consistent with the activity of CpG as a Th1-stimulating adjuvant, the serum IgG1/IgG2a ratio of 0.38 indicated a Th1 bias. Combined data from two independent challenge experiments demonstrated that rMetQ-CpG immunized mice cleared infection faster than control animals (vehicle,p<0.0001; CpG,p=0.002) and had lowerNgburden (vehicle,p=0.03; CpG,p<0.0001). We conclude rMetQ-CpG induces a protective immune response that accelerates bacterial clearance from the murine lower genital tract and represents an attractive component of a gonorrhea subunit vaccine.
Glucocorticoid treatment exacerbates mycobacterial infection by reducing the phagocytic capacity of macrophages Glucocorticoids and zebrafish TB
Authors: Xie Yufei , Meijer Annemarie H. , Schaaf Marcel J.M.
Published: June 2020

Glucocorticoids are effective drugs for treating immune-related diseases, but prolonged therapy is associated with an increased risk of various infectious diseases, including tuberculosis. In this study, we have used a larval zebrafish model for tuberculosis, based onMycobacterium marinum(Mm) infection, to study the effect of glucocorticoids. Our results show that the synthetic glucocorticoid beclomethasone increases the bacterial burden and the dissemination of a systemicMminfection. The exacerbatedMminfection was associated with a decreased phagocytic activity of macrophages, higher percentages of extracellular bacteria, and a reduced rate of infected cell death, whereas the bactericidal capacity of the macrophages was not affected. The inhibited phagocytic capacity of macrophages was associated with suppression of the transcription of genes involved in phagocytosis in these cells. The decreased bacterial phagocytosis by macrophages was not specific forMm, since it was also observed upon infection withSalmonellaTyphimurium. In conclusion, our results show that glucocorticoids inhibit the phagocytic activity of macrophages, which may increase the severity of bacterial infections like tuberculosis.

Summary statement

Using a zebrafish tuberculosis model, we show that glucocorticoids decrease phagocytosis by macrophages, thereby increasing the bacterial burden. This may explain the glucocorticoid-induced increase in susceptibility to tuberculosis in humans.
Exposure duration modulates the response of Caribbean corals to global change stressors
Authors: Aichelman HE , Bove CB , Castillo KD , Boulton JM , Knowlton AC , Nieves OC , Ries JB , Davies SW
Published: June 2020

Global change is threatening coral reefs, with rising temperatures leading to repeat bleaching events (dysbiosis of coral hosts and their symbiotic algae) and ocean acidification reducing net coral calcification. Although global-scale mass bleaching events are revealing fine-scale patterns of coral resistance and resilience, traits that lead to persistence under environmental stress remain elusive. Here, we conducted a 95-day controlled-laboratory experiment to investigate how duration of exposure to ocean warming (28, 31°C), acidification (pCO2= 400–2800 μatm), and their interaction influence the physiological responses of two Caribbean reef-building coral species (Siderastrea siderea,Pseudodiploria strigosa) from two reef zones of the Belize Mesoamerican Barrier Reef System. Every 30 days, calcification rate, total host protein and carbohydrate, chlorophyllapigment concentration, and symbiont cell density were quantified for the same coral colony to characterize acclimatory responses of each genotype. Physiologies of the two species were differentially affected by these stressors, with exposure duration modulating responses.Siderastrea sidereawas most affected by extremepCO2(~2800 μatm), which resulted in reduced calcification rate, symbiont density, and chlorophyllaconcentration. Siderastrea sidereacalcification rate initially declined under extremepCO2but recovered by the final time point, and overall demonstrated resistance to next-centurypCO2and temperature stress. In contrast,P. strigosawas more negatively impacted by elevated temperature (31°C). Reductions inP. strigosacalcification rate and total carbohydrates were consistently observed over time regardless ofpCO2treatment, with the greatest reductions observed under elevated temperature. However, nearshore colonies ofP. strigosamaintained calcification rates under elevated temperature throughout all exposure durations, suggesting individuals from this environment may be locally adapted to the warmer temperatures characterizing their natal reef zone. This experiment highlights how tracking individual coral colony physiology across broad exposure durations can capture acclimatory responses of corals to global change stressors.
Strongyle-resistant sheep express their potential across environments and leave limited scope for parasite plasticity
Authors: Sallé G. , Deiss V. , Marquis C. , Tosser-Klopp G. , Cortet J. , Serreau D. , Koch C. , Marcon D. , Bouvier F. , Jacquiet P. , Holroyd N. , Blanchard A. , Cotton J.A. , Mialon M.M. , Moreno-Romieux C.
Published: June 2020

Introduction

Drug-resistant parasites threaten livestock production. Breeding more resistant hosts could be a sustainable control strategy. Environmental variation may however alter the expression of genetic potential and directional selection toward host resistance could initiate an arms race between the host and its parasites.

Methods and Results

We created sheep lines with high or low resistance toHaemonchus contortus. We first exposed both lines to chronic stress or to the infection by another parasiteTrichostrongylus colubriformis, to test for genotype-by-environment and genotype-by-parasite species interactions respectively. Overall, between-line divergence remained significant across environmental perturbations. But we found that the impact of chronic stress onH. contortusinfection varied among families and that divergence was reduced during infection byT. colubriformis. Second, we quantified genomic and transcriptomic differences inH. contortusworms collected from both lines to identify components of an arms race. We found no evidence of genetic differentiation between worms from each line. But survival to more resistant hosts was associated with enhanced expression of cuticle collagen coding genes.

Discussion

Breeding for resistance hence remains a sustainable strategy that requires to anticipate the effects of environmental perturbations and to monitor worm populations.
SNARE Complex Alters the Interactions of the Ca2+sensor Synaptotagmin 1 with Lipid Bilayers
Authors: Bykhovskaia Maria
Published: June 2020

Release of neuronal transmitters from nerve terminals is triggered by the molecular Ca2+sensor Synaptotagmin 1 (Syt1). Syt1 is a transmembrane protein attached to the synaptic vesicle (SV), and its cytosolic region comprises two domains, C2A and C2B, which are thought to penetrate into lipid bilayers upon Ca2+binding. Prior to fusion, SVs become attached to the presynaptic membrane (PM) by the four-helical SNARE complex, which binds the C2B domain of Syt1. To understand how the interactions of Syt1 with lipid bilayers and the SNARE complex trigger fusion, we performed molecular dynamics (MD) simulations at a microsecond scale. The MD simulations showed that the C2AB tandem of Syt1 can either bridge SV and PM or immerse into PM, and that the latter configuration is more favorable energetically. Surprisingly, C2 domains did not cooperate in penetrating into PM, but instead mutually hindered the lipid penetration. To test whether the interaction of Syt1 with lipid bilayers could be affected by the C2B-SNARE attachment, we performed systematic conformational analysis of the Syt1-SNARE complex. Notably, we found that the C2B-SNARE interface precludes the coupling of C2 domains of Syt1 and promotes the immersion of both domains into the PM bilayer. Subsequently, we simulated this pre-fusion protein complex between lipid bilayers imitating PM and SV and found that the immersion of Syt1 into the PM bilayer within this complex promotes PM curvature and leads to lipid merging. Altogether, our MD simulations elucidated the role of the Syt1-SNARE interactions in the fusion process and produced the dynamic all-atom model of the prefusion protein-lipid complex.

Statement of Significance

Neuronal transmitters are packed in synaptic vesicles (SVs) and released by fusion of SVs with the presynaptic membrane (PM). SVs are attached to PM by the SNARE protein complex, and fusion is triggered by the Ca2+sensor Synaptotagmin 1 (Syt1). Although Syt1 and SNARE proteins have been extensively studied, it is not yet fully understood how the interactions of Syt1 with lipids and the SNARE complex induce fusion. To address this fundamental problem, we took advantage of Anton2 supercomputer, a unique computational environment, which enables simulating the dynamics of molecular systems at a scale of microseconds. Our simulations produced a dynamic all-atom model of the prefusion protein-lipid complex and demonstratedin silicohow the Syt1-SNARE complex triggers fusion.
Spatial structure and pathogen epidemics: the influence of management and stochasticity in agroecosystems
Authors: Hajian-Forooshani Zachary , Vandermeer John
Published: June 2020

Organisms susceptible to disease, from humans to crops, inevitably have spatial geometry that influence disease dynamics. Understanding how spatial structure emerges through time in ecological systems and how that structure influences disease dynamics is of practical importance for natural and human management systems. Here we use the annual crop, coffee,Coffea arabica, along with its pathogen, the coffee leaf rust,Haemelia vastatrix, as a model system to understand how spatial structure is created in agroecosystems and its subsequent influence on the dynamics of the system.

Here, we create a simple null model of the socio-ecological process of death and stochastic replanting of coffee plants on a plot. We then use spatial networks to quantify the spatial structures and make comparisons of our stochastic null model to empirically observed spatial distributions of coffee. We then present a simple model of pathogen spread on spatial networks across a range of spatial geometries emerging from our null model and show how both local and regional management of agroecosystems interact with space and time to alter disease dynamics.

Our results suggest that our null model of evolving spatial structure can capture many critical features of how the spatial arrangement of plants changes through time in coffee agroecosystems. Additionally, we find that small changes in management practices that influence the scale of pathogen transmission, such as shade tree removal, can result in a rapid transition to epidemics with lattice-like spatial arrangements but not irregular planting geometries.

The results presented here may have practical implications for farmers in Latin America who are in the process of replanting and overhauling management of their coffee farms in response to a coffee leaf rust epidemic in 2013. We suggest that shade reduction in conjunction with more lattice-like planting schemes may result in coffee being more prone to epidemic-like dynamics of the coffee leaf rust in the future.