bluuebunny/crossref_metadata_2025 huggingface dataset:
Repeated evidence that the accelerated evolution of sperm is associated with their fertilization function
Authors: Fitzpatrick John L. , Bridge C. Daisy , Snook Rhonda R.
Published: August 2020

Spermatozoa are the most morphologically diverse cell type, leading to the widespread assumption that they evolve rapidly. However, there is no direct evidence that sperm evolve faster than other male traits. Such a test requires comparing male traits that operate in the same selective environment, ideally produced from the same tissue, yet vary in function. Here, we examine rates of phenotypic evolution in sperm morphology using two insect groups where males produce fertile and non-fertile sperm types (
Drosophila
species from the
obscura
group and a subset of Lepidoptera species), where these constraints are solved. Moreover, in
Drosophila
we test the relationship between rates of sperm evolution and the link with the putative selective pressures of fertilization function and postcopulatory sexual selection exerted by female reproductive organs. We find repeated evolutionary patterns across these insect groups—lengths of fertile sperm evolve faster than non-fertile sperm. In
Drosophila
, fertile sperm length evolved faster than body size, but at the same rate as female reproductive organ length. We also compare rates of evolution of different sperm components, showing that head length evolves faster in fertile sperm while flagellum length evolves faster in non-fertile sperm. Our study provides direct evidence that sperm length evolves more rapidly in fertile sperm, probably because of their functional role in securing male fertility and in response to selection imposed by female reproductive organs.
Molecular detection of Mycobacterium tuberculosis in poor-quality cough specimens
Authors: Mboneni Tondani A. , Eales Owen O. , Mosina Ntsoaki L. , Fourie P. Bernard
Published: August 2020

Clinical specimens unfit for laboratory processing represent missed opportunities for diagnosing tuberculosis. Poor-quality cough specimens (n=61) from presumptive tuberculosis cases were cultured and GeneXpert MTB/RIF (Xpert) successfully performed on samples transferred by flocked swab into PrimeStore molecular transport medium (PS-MTM).

Mycobacterium tuberculosis

was grown in culture from 13 (21.3 %) and Xpert reported 15 (24.2 %) positive, of which 10 concordant. RT-PCR of PS-MTM samples showed enhanced sensitivity; three positives were missed by Xpert, five by culture and three more detected for a total of 21 positives (34.4 %).
A new species of leaf fish,Nandus banshlaii(Perciformes: Nandidae) from West Bengal, India
Authors: Kapuri R. , Sinha A. K. , de P. , Roy R. , Bhakat S.
Published: August 2020

Nandus banshlaii, sp. nov. is described from the Banshlai River of West Bengal. This species is distinguished from all its congeners in having a golden brown body in live and a combination of characters like longest head and snout length (44.28% SL and 35.58% HL respectively) and from its two Indian congeners in containing largest eye diameter (22.22% HL), longest pre-dorsal length (47.16% SL), shortest pectoral fin length (14.60% SL) and smallest dorsal fin base length (45.53% SL).Like all three congeners of Ganga-Brahmaputra-Meghna river basin of Gangetic delta it possess a dark spot on caudal peduncle.

To differentiate the present species from other two Indian congeners ofNandus,N. nandusandN. andrewi, PCA and heatmap is performed and a key of all three species is also provided.
Divergent use of metabolic fluxes in breast cancer metastasis
Authors: Mathur Deepti , Liao Chen , Ferlita Alessandro La , Alaimo Salvatore , Ferro Alfredo , Xavier Joao B.
Published: August 2020

Breast cancers can metastasize to many organs. But how do disseminated cells from a primary tumor adapt to distal tissues? Here we combined metabolomics, flux measurements, and mathematical modeling to study metabolic fluxes in breast cancer cells adapted to home to different organs. We found that lung-homing cells maintain high glycolytic flux despite low levels of glycolytic intermediates, by constitutively activating a pathway sink into lactate. Their distinct behavior—a strong Warburg effect—has a gene expression signature: a high ratio of lactate dehydrogenase to pyruvate dehydrogenase gene expression, which also correlates with lung metastases in patients with breast cancer. Surprisingly, this strong Warburg effect does not necessarily increase cellular growth rate, suggesting that lactate secretion may be a trait under selection in lung metastasis. Our results stress that metabolic fluxes may not correlate with metabolic intermediates, a finding relevant for metastatic tropism.
Data-driven machine learning models for decoding speech categorization from evoked brain responses
Authors: Mahmud Md Sultan , Yeasin Mohammed , Bidelman Gavin M.
Published: August 2020

Categorical perception (CP) of audio is critical to understand how the human brain perceives speech sounds despite widespread variability in acoustic properties. Here, we investigated the spatiotemporal characteristics of auditory neural activity that reflects CP for speech (i.e., differentiates phonetic prototypes from ambiguous speech sounds). We recorded high density EEGs as listeners rapidly classified vowel sounds along an acoustic-phonetic continuum. We used support vector machine (SVM) classifiers and stability selection to determine when and where in the brain CP was best decoded across space and time via source-level analysis of the event related potentials (ERPs). We found that early (120 ms) whole-brain data decoded speech categories (i.e., prototypical vs. ambiguous speech tokens) with 95.16% accuracy [area under the curve (AUC) 95.14%; F1-score 95.00%]. Separate analyses on left hemisphere (LH) and right hemisphere (RH) responses showed that LH decoding was more robust and earlier than RH (89.03% vs. 86.45% accuracy; 140 ms vs. 200 ms). Stability (feature) selection identified 13 regions of interest (ROIs) out of 68 brain regions (including auditory cortex, supramarginal gyrus, and Brocas area) that showed categorical representation during stimulus encoding (0-260 ms). In contrast, 15 ROIs (including fronto-parietal regions, Broca’s area, motor cortex) were necessary to describe later decision stages (later 300 ms) of categorization but these areas were highly associated with the strength of listeners’ categorical hearing (i.e., slope of behavioral identification functions). Our data-driven multivariate models demonstrate that abstract categories emerge surprisingly early (∼120 ms) in the time course of speech processing and are dominated by engagement of a relatively compact fronto-temporal-parietal brain network.
CSDE1 is a Post-Transcriptional Regulator of the LDL Receptor
Authors: Smith Geoffrey A. , Padmanabhan Arun , Lau Bryan H. , Pampana Akhil , Li Li , Clara Lee Y. , Pelonero Angelo , Nishino Tomohiro , Sadagopan Nandhini , Jain Rajan , Natarajan Pradeep , Wu Roland S. , Black Brian L. , Srivastava Deepak , Shokat Kevan M. , Chorba John S.
Published: August 2020

The low-density lipoprotein receptor (LDLR) controls cellular delivery of cholesterol and clears LDL from the bloodstream, protecting against atherosclerotic heart disease, the leading cause of death in the United States. We therefore sought to identify regulators of the LDLR beyond the targets of current clinical therapies and known causes of familial hypercholesterolemia. We show that Cold Shock Domain-Containing Protein E1 (CSDE1) enhances hepaticLDLRmRNA decay via its 3’ untranslated region to regulate atherogenic lipoproteinsin vivo. Using parallel phenotypic genome-wide CRISPR interference screens, we found 40 specific regulators of the LDLR left unidentified by observational human genetics. Among these, we show that CSDE1 regulates the LDLR at least as strongly as the mechanistically distinct pathways exploited by the best available clinical therapies: statins and PCSK9 inhibitors. Additionally, we show that hepatic gene silencing ofCsde1treats diet-induced dyslipidemia in mice better than that ofPcsk9. Our results reveal the therapeutic potential of manipulating a newly identified key factor in the post-transcriptional regulation of theLDLRmRNA for the prevention of cardiovascular disease. We anticipate that our approach of modelling a clinically relevant phenotype in a forward genetic screen, followed by mechanistic pharmacologic dissection andin vivovalidation, will serve as a generalizable template for the identification of therapeutic targets in other human disease states.

One Sentence Summary

A genome-wide CRISPR screen identifies CSDE1 as a key regulator of hepaticLDLRmRNA decayin vivo, making it a promising target for heart disease.

Graphical Abstract
L-DOPA dioxygenase of the fly agaric toadstool: revision of thedodAgene sequence and mechanism of enzymatic pigment production
Authors: Soares Douglas M. M. , Gonçalves Letícia C. P. , Machado Caroline O. , Esteves Larissa Cerrato , Stevani Cassius V. , Oliveira Carla C. , Dörr Felipe A. , Pinto Ernani , Adachi Flávia M. M. , Hotta Carlos T. , Bastos Erick L.
Published: August 2020

l-DOPA extradiol dioxygenases (DODAs) catalyze the production of betalains and hygroaurins pigments. The sequence of the DODAs found in Caryophyllales and Basidiomycetes are not conserved, although betalains are produced both by plants and fungi. Here we revise the coding region of thedodAgene of fly agaric [Amanita muscaria(L.) Lam.] and describe an alternative start codon downstream that enables the heterologous expression of AmDODA, a promiscuousl-DOPA dioxygenase. AmDODA is 43-amino acid residues shorter than the recombinant DODA previously reported but catalyzes the formation of two isomeric seco-DOPAs that are the biosynthetic precursors of betalains and hygroaurins. The putative active site of AmDODA contains two distinct His-His-Glu motifs that can explain the dual cleavage ofl-DOPA according to the mechanism proposed for non-heme iron-dependent dioxygenases. Upon addition of excessl-DOPA, both the betaxanthin and hygroaurin adducts ofl-DOPA are produced. The kinetic parameters of enzymatic catalysis at pH 8.5 are similar to those reported for otherl-DOPA dioxygenases. The rate constants for the conversion ofl-DOPA into the betalamic acid and muscaflavin were estimated by kinetic modelling allowing the proposal of a mechanism of pigment formation. These results contribute to understanding the biosynthesis of bacterial, fungal and plant pigments, for the biotechnological production of hygroaurins, and for the development of more promiscuous dioxygenases for environmental remediation.
Japonica Array NEO with increased genome-wide coverage and abundant disease risk SNPs
Authors: Sakurai-Yageta Mika , Kumada Kazuki , Gocho Chinatsu , Makino Satoshi , Uruno Akira , Tadaka Shu , Motoike Ikuko N , Kimura Masae , Ito Shin , Otsuki Akihito , Narita Akira , Kudo Hisaaki , Aoki Yuichi , Danjoh Inaho , Yasuda Jun , Kawame Hiroshi , Minegishi Naoko , Koshiba Seizo , Fuse Nobuo , Tamiya Gen , Yamamoto Masayuki , Kinoshita Kengo
Published: August 2020

Background

Increasing the power of genome-wide association studies in diverse populations is important for understanding the genetic determinants of disease risks, and large-scale genotype data are collected by genome cohort and biobank projects all over the world. In particular, ethnic-specific SNP arrays are becoming more important because the use of universal SNP arrays has some limitations in terms of cost-effectiveness and throughput. As part of the Tohoku Medical Megabank Project, which integrates prospective genome cohorts into a biobank, we have been developing a series of Japonica Arrays for genotyping participants based on reference panels constructed from whole-genome sequence data of the Japanese population.

Results

We designed a novel version of the SNP Array for the Japanese population, called Japonica Array NEO, comprising a total of 666,883 SNPs, including tag SNPs of autosomes and X chromosome with pseudoautosomal regions, SNPs of Y chromosome and mitochondria, and known disease risk SNPs. Among them, 654,246 tag SNPs were selected from an expanded reference panel of 3,552 Japanese using pairwise r2of linkage disequilibrium measures. Moreover, 28,298 SNPs were included for the evaluation of previously identified disease risk SNPs from the literature and databases, and those present in the Japanese population were extracted using the reference panel. The imputation performance of Japonica Array NEO was assessed by genotyping 286 Japanese samples. We found that the imputation quality r2and INFO score in the minor allele frequency bin >2.5%–5% were >0.9 and >0.8, respectively, and >12 million markers were imputed with an INFO score >0.8. After verification, Japonica Arrays were used to efficiently genotype cohort participants from the sample selection to perform a quality assessment of the raw data; approximately 130,000 genotyping data of >150,000 participants has already been obtained.

Conclusions

Japonica Array NEO is a promising tool for genotyping the Japanese population with genome-wide coverage, contributing to the development of genetic risk scores for this population and further identifying disease risk alleles among individuals of East Asian ancestry.
TuMV triggers stomatal closure but reduces drought tolerance in Arabidopsis
Authors: Manacorda Carlos Augusto , Gudesblat Gustavo , Sutka Moira , Alemano Sergio , Peluso Franco , Oricchio Patricio , Baroli Irene , Asurmendi Sebastián
Published: August 2020

i)

In this work the effects of TuMV infection on stomatal closure and water balance were studied in Arabidopsis. Thermal imaging analyses showed that TuMV-infected plants had consistently higher foliar temperature than mock treated controls. Non-destructive time-course experiments revealed that this differential phenotype was stable during both daytime and nighttime. This effect was due to reduced gas exchange in TuMV-infected plants, as observed through stomatal conductance and stomatal aperture assays in systemic leaves. Measurements of daily water consumption and initial dehydration rate further proved that TuMV infection reduced water loss. Salicylic acid (SA) and abscisic acid (ABA) contents were increased in TuMV-infected plants. In addition, the expression of ABI2, involved in ABA signaling, was enhanced, and ABCG40 (required for ABA transport into guard cells) was highly induced upon TuMV infection. Hypermorficabi2-1mutant plants, but no other ABA or SA biosynthetic, signaling or degradation mutants tested abolished both stomatal closure and low stomatal conductance phenotypes caused by TuMV. Therefore, not overall ABA levels, but localized differences in ABA import and perception in guard cells, are likely to be responsible for stomatal closure observed under TuMV infection. Plants simultaneously subjected to drought and viral stresses showed higher mortality rates than their mock-inoculated drought stressed counterparts, consistent with down-regulation of drought-responsive gene RD29A, both in short and long day conditions. Our findings indicate that in spite of stomatal closure triggered by TuMV, additional phenomena cause compromised drought tolerance of TuMV-infected Arabidopsis plants.

ii)

Significance statement

Characterization of the physiological responses controlling plant water management under combined stresses and the genes behind them is important in the current climate change scenario, which poses multifaceted challenges to crops. We found that TuMV infection induced ABA and SA accumulation and stomatal closure in Arabidopsis, alongside with overexpression of ABCG40 (the transporter of ABA to guard cells), whereas the dehydration-responsive gene RD29A was downregulated, concomitantly with increased plant susceptibility to drought stress under infection.
Not out of the box: phylogeny of the broadly sampled Buxaceae
Authors: Shipunov Alexey , Lee Hye Ji , Choi Jinhee , Pay Kyle , DeSpiegelaire Sarah , Floden Aaron
Published: August 2020

The Buxaceae constitute a morphologically diverse phylogenetic lineage of six genera, which includes about 140 species. The most well-known genera areBuxus,Sarcococca, andPachysandra.Few species of woodyStylocerasgrow on mid-elevations in the Andes mountains region.Didymeles, with three species endemic to Madagascar, and the monotypicHaptanthusfrom Honduras, are the most unusual members of the group. The infra-familial classification of Buxaceae is controversial, and molecular data about many species, especially Old World, is still lacking. We used broad taxonomic sampling and molecular data from four chloroplast markers, and the nuclear ribosomal ITS to estimate their phylogeny. These data provide phylogenetic placements of 50 species and enabled better estimates of boundaries in Buxaceae. We described two subfamilies, two monotypic genera, twoBuxussubgenera, and one new species ofDidymelesfrom Madagascar.
Human Cytomegalovirus Drives WDR5 to the Virion Assembly Compartment to Facilitate Virion Assembly
Authors: Yang Bo , Yao YongXuan , Wu Hui , Yang Hong , Ma Xue-Hui , Li Dong , Wang Xian-Zhang , Huang Sheng-Nan , Jiang Xuan , Cheng Shuang , Sun Jin-Yan , Huang Zhen-Li , Zhao CongJian , McVoy Michael A. , Ahn Jin-Hyun , Zeng Wen-Bo , Gong Sitang , Britt William J. , Luo Min-Hua
Published: August 2020

We previously reported that human cytomegalovirus (HCMV) utilizes the cellular protein WDR5 to facilitate capsid nuclear egress. Here, we further show that HCMV infection drives WDR5 to the perinuclear region by a mechanism that requires viral replication and intact microtubules. WDR5 accumulated in the virion assembly compartment (vAC) and co-localized with vAC markers of gamma-tubulin (γ-tubulin), early endosomes, and viral vAC marker proteins pp65, pp28, and glycoprotein B (gB). WDR5 interacted with multiple virion proteins, including MCP, pp150, pp65, pIRS1, and pTRS1, which may explain the increasing WDR5 accumulation in the vAC during infection. WDR5 was then incorporated into HCMV virions and localized to the tegument layer, as demonstrated by fractionation and immune-gold electron microscopy. Thus, WDR5 is driven to the vAC and incorporated into virions, suggesting that WDR5 facilitates HCMV replication at later stage of virion assembly besides the capsid nuclear egress stage. These data highlight that WDR5 is a potential target for antiviral therapy.

Importance

Human cytomegalovirus (HCMV) has a large (~235-kb) genome that contains over 170 ORFs and exploits numerous cellular factors to facilitate its replication. In the late phase of HCMV infection cytoplasmic membranes are profoundly reconfigured to establish the virion assembly compartment (vAC), which is important for efficient assembly of progeny virions. We previously reported that WDR5 promotes HCMV nuclear egress. Here, we show that WDR5 is further driven to the vAC and incorporated into virions, perhaps to facilitate efficient virion maturation. This work identified potential roles for WDR5 in HCMV replication in the cytoplasmic stages of virion assembly. Taken together, WDR5 plays a critical role in HCMV capsid nuclear egress and is important for virion assembly, and thus is a potential target for antiviral treatment of HCMV-associated diseases.
Loss to follow-up correction increased mortality estimates in HIV-positive people on antiretroviral therapy in Mozambique
Authors: Anderegg Nanina , Hector Jonas , Jefferys Laura F , Burgos-Soto Juan , Hobbins Michael A , Ehmer Jochen , Meier Lukas , Maathuis Marloes H , Egger Matthias
Published: August 2020

Objectives: People living with HIV (PLWH) on antiretroviral therapy (ART) may be lost to follow-up (LTFU), which hampers the assessment of outcomes. We estimated mortality for patients starting ART in a rural region in sub-Saharan Africa and examined risk factors for death, correcting for LTFU.

Study design and setting: We analysed data from Ancuabe, Mozambique, where patients LTFU are traced by phone and home visits. We used cumulative incidence functions to estimate mortality and LTFU. To correct for LTFU, we revised outcomes based on tracing data using different inverse probability weights (maximum likelihood [ML], Ridge regression or Bayesian model averaging [BMA]). We fitted competing risk models to identify risk factors for death and LTFU.

Results: Analyses included 4492 patients; during 8152 person-years of follow-up, 486 patients died, 2375 were LTFU, 752 were traced, and 603 were found. At 4 years after starting ART, observed mortality was 11.9% (95% CI 10.9-13.0) but 23.5% (19.8- 28.0), 21.6% (18.7-25.0) and 23.3% (19.7-27.6) after correction with ML, Ridge and BMA weights, respectively. Risk factors for death included male sex, lower CD4 cell counts and more advanced clinical stage.

Conclusion: In ART programmes with substantial LTFU, mortality estimates need to take LTFU into account.
TClustVID: A Novel Machine Learning Classification Model to Investigate Topics and Sentiment in COVID-19 Tweets
Authors: Satu Md. Shahriare , Khan Md. Imran , Mahmud Mufti , Uddin Shahadat , Summers Matthew A. , Quinn Julian M.W. , Moni Mohammad Ali
Published: August 2020

COVID-19, caused by the SARS-Cov2, varies greatly in its severity but represent serious respiratory symptoms with vascular and other complications, particularly in older adults. The disease can be spread by both symptomatic and asymptomatic infected individuals, and remains uncertainty over key aspects of its infectivity, no effective remedy yet exists and this disease causes severe economic effects globally. For these reasons, COVID-19 is the subject of intense and widespread discussion on social media platforms including Facebook and Twitter. These public forums substantially impact on public opinions in some cases and exacerbate widespread panic and misinformation spread during the crisis. Thus, this work aimed to design an intelligent clustering-based classification and topics extracting model (named TClustVID) that analyze COVID-19-related public tweets to extract significant sentiments with high accuracy. We gathered COVID-19 Twitter datasets from the IEEE Dataport repository and employed a range of data preprocessing methods to clean the raw data, then applied tokenization and produced a word-to-index dictionary. Thereafter, different classifications were employed to Twitter datasets which enabled exploration of the performance of traditional and TclustVID classification methods. TClustVID showed higher performance compared to the traditional classifiers determined by clustering criteria. Finally, we extracted significant topic clusters from TClustVID, split them into positive, neutral and negative clusters and implemented latent dirichlet allocation for extraction of popular COVID-19 topics. This approach identified common prevailing public opinions and concerns related to COVID-19, as well as attitudes to infection prevention strategies held by people from different countries concerning the current pandemic situation.
Analysis of COVID-19 and comorbidity co-infection Model with Optimal Control
Authors: Omame A. , Sene N. , Nometa I. , Nwakanma C. I. , Nwafor E. U. , Iheonu N. O. , Okuonghae D.
Published: August 2020

The new coronavirus disease 2019 (COVID-19) infection is a double challenge for people infected with comorbidities such as cardiovascular and cerebrovascular diseases and diabetes. Comorbidities have been reported to be risk factors for the complications of COVID-19. In this work, we develop and analyze a mathematical model for the dynamics of COVID-19 infection in order to assess the impacts of prior comorbidity on COVID-19 complications and COVID-19 re-infection. The model is simulated using data relevant to the dynamics of the diseases in Lagos, Nigeria, making predictions for the attainment of peak periods in the presence or absence of comorbidity. The model is shown to undergo the phenomenon of backward bifurcation caused by the parameter accounting for increased susceptibility to COVID-19 infection by comorbid susceptibles as well as the rate of re-infection by those who have recovered from a previous COVID-19 infection. Sensivity analysis of the model when the population of individuals co-infected with COVID-19 and comorbidity is used as response function revealed that the top ranked parameters that drive the dynamics of the co-infection model are the effective contact rate for COVID-19 transmission, βCV, the parameter accounting for increased sucseptibility to COVID-19 by comorbid susceptibles, χCM, the comorbidity development rate, θCM, the detection rate for singly infected and co-infected individuals, η1 and η2, as well as the recovery rate from COVID-19 for co-infected individuals, φI2. Simulations of the model reveal that the cumulative confirmed cases (without comorbidity) may get up to 180,000 after 200 days, if the hyper susceptibility rate of comorbid susceptibles is as high as 1.2 per day. Also, the cumulative confirmed cases (including those co-infected with comorbidity) may be as high as 1000,000 cases by the end of November, 2020 if the re-infection rates for COVID-19 is 0.1 per day. It may be worse than this if the re-infection rates increase higher. Moreover, if policies are strictly put in place to step down the probability of COVID-19 infection by comorbid susceptibles to as low as 0.4 per day and step up the detection rate for singly infected individuals to 0.7 per day, then the reproduction number can be brought very low below one, and COVID-19 infection eliminated from the population. In addition, optimal control and cost-effectiveness analysis of the model reveal that the the strategy that prevents COVID-19 infection by comorbid susceptibles has the least ICER and is the most cost-effective of all the control strategies for the prevention of COVID-19.
Komenti: A semantic text mining framework
Authors: Slater Luke T , Bradlow William , Hoehndorf Robert , Motti Dino FA , Ball Simon , Gkoutos Georgios V
Published: August 2020

Komenti is a reasoner-enabled semantic query and information extraction framework. It is the only text mining tool that enables querying inferred knowledge from biomedical ontologies. It also contains multiple novel components for vocabulary construction and context disambiguation, which can improve the power of text mining and ontology-based analysis tasks, with a view towards making full use of the semantic provision of biomedical ontologies for text characterisation and analysis. Here, we describe Komenti and its features, and present a use case wherein we automate a clinical audit, extracting medications for hypertrophic cardiomyopathy patients from text, revealing a high precision, and identifying a sub-cohort of patients with atrial fibrillation who are not anti-coagulated, and are therefore at a higher risk of stroke.

Availability and Implementation

Komenti is freely available under an open source licence athttp://github.com/reality/komenti.

More information concerning the use-case is available in supplementary data.
SARS-CoV-2 genome analysis of strains in Pakistan reveals GH, S and L clade strains at the start of the pandemic
Authors: Ghanchi Najia Karim , Masood Kiran Iqbal , Nasir Asghar , Khan Waqasuddin , Abidi Syed Hani , Shahid Saba , Mahmood Syed Faisal , Kanji Akbar , Razzak Safina , Ansar Zeeshan , Islam Nazneen , Dharejo M. B. , Hasan Zahra , Hasan Rumina
Published: August 2020

Objectives

Pakistan has a high infectious disease burden with about 265,000 reported cases of COVID-19. We investigated the genomic diversity of SARS-CoV-2 strains and present the first data on viruses circulating in the country.

Methods

We performed whole-genome sequencing and data analysis of SARS-CoV-2 eleven strains isolated in March and May.

Results

Strains from travelers clustered with those from China, Saudi Arabia, India, USA and Australia. Five of eight SARS-CoV-2 strains were GH clade with Spike glycoprotein D614G, Ns3 gene Q57H, and RNA dependent RNA polymerase (RdRp) P4715L mutations. Two were S (ORF8 L84S and N S202N) and three were L clade and one was an I clade strain. One GH and one L strain each displayed Orf1ab L3606F indicating further evolutionary transitions.

Conclusions

This data reveals SARS-CoV-2 strains of L, G, S and I have been circulating in Pakistan from March, at the start of the pandemic. It indicates viral diversity regarding infection in this populous region. Continuing molecular genomic surveillance of SARS-CoV-2 in the context of disease severity will be important to understand virus transmission patterns and host related determinants of COVID-19 in Pakistan.
SARS-CoV-2 infection, disease and transmission in domestic cats
Authors: Gaudreault Natasha N. , Trujillo Jessie D. , Carossino Mariano , Meekins David A. , Morozov Igor , Madden Daniel W. , Indran Sabarish V. , Bold Dashzeveg , Balaraman Velmurugan , Kwon Taeyong , Artiaga Bianca Libanori , Cool Konner , García-Sastre Adolfo , Ma Wenjun , Wilson William C. , Henningson Jamie , Balasuriya Udeni B. R. , Richt Juergen A.
Published: August 2020

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the cause of Coronavirus Disease 2019 (COVID-19) and responsible for the current pandemic. Recent SARS-CoV-2 susceptibility and transmission studies in cats show that the virus can replicate in these companion animals and transmit to other cats. Here, we present an in-depth study of SARS-CoV-2 infection, associated disease and transmission dynamics in domestic cats. Six 4- to 5-month-old cats were challenged with SARS-CoV-2 via intranasal and oral routes simultaneously. One day post challenge (DPC), two sentinel contact cats were co-mingled with the principal infected animals. Animals were monitored for clinical signs, clinicopathological abnormalities and viral shedding throughout the 21 DPC observation period.Postmortemexaminations were performed at 4, 7 and 21 DPC to investigate disease progression. Viral RNA was not detected in blood but transiently in nasal, oropharyngeal and rectal swabs and bronchoalveolar lavage fluid as well as various tissues. Tracheobronchoadenitis of submucosal glands with the presence of viral RNA and antigen was observed in airways of the infected cats on 4 and 7 DPC. Serology showed that both, principal and sentinel cats, developed SARS-CoV-2-specific and neutralizing antibodies to SARS-CoV-2 detectable at 7 DPC or 10 DPC, respectively. All animals were clinically asymptomatic during the course of the study and capable of transmitting SARS-CoV-2 to sentinels within 2 days of comingling. The results of this study are critical for our understanding of the clinical course of SARS-CoV-2 in a naturally susceptible host species, and for risk assessment of the maintenance of SARS-CoV-2 in felines and transmission to other animals and humans.
Hypertonic saline solution inhibits SARS-CoV-2 in vitro assay
Authors: Machado Rafael R. G. , Glaser Talita , Araujo Danielle B. , Petiz Lyvia Lintzmaier , Oliveira Danielle B. L. , Durigon Giuliana S. , Leal Alessandra L. , Pinho João Renato R. , Ferreira Luis Carlos S. , Ulrich Henning , Durigon Edison L. , Guzzo Cristiane R.
Published: August 2020

We are facing an unprecedented global health crisis caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At this date more than 680 thousand people have died due to coronavirus disease 2019 (COVID-19). Unfortunately, until now no effective treatment to combat the virus and vaccine are available. We performed experiments to test if hypertonic saline solution is able to inhibit virus replicationin vitro. Our data shows that 260 mM NaCl (1.5%) inhibits 100% SARS-CoV-2 replication in Vero cells. Furthermore, our results suggest that the virus replication inhibition is due to an intracellular mechanism and not due to the dissociation between spike SARS-CoV-2 protein and its human receptor angiotensin-converting enzyme 2 interaction. NaCl depolarizes the plasma membrane supposedly associated with the inhibition of the SARS-CoV-2 life cycle. This observation could lead to simple, safe and low cost interventions at various stages of COVID-19 treatment, improving the prognosis of infected patients, thereby mitigating the social and economic costs of the pandemic.
Spatial tissue profiling by imaging-free molecular tomography
Authors: Schede Halima Hannah , Schneider Christian G. , Stergiadou Johanna , Borm Lars E. , Ranjak Anurag , Yamawaki Tracy M. , David Fabrice P.A. , Lönnerberg Peter , Laurent Gilles , Tosches Maria Antonietta , Codeluppi Simone , La Manno Gioele
Published: August 2020

Genomics techniques are currently being adapted to provide spatially resolved omics profiling. However, the adaptation of each new method typically requires the setup of specific detection strategies or specialized instrumentation. A generic approach to spatially resolve different types of high throughput data is missing. Here, we describe an imaging-free framework to localize high throughput readouts within a tissue by combining compressive sampling and image reconstruction. We implemented this framework to transform a low-input RNA sequencing protocol into an imaging-free spatial transcriptomics technique (STRP-seq) and validated this method with a transcriptome profiling of the murine brain. To verify the broad applicability of STRP-seq, we applied the technique on the brain of the Australian bearded dragonPogona vitticeps. Our results reveal the molecular anatomy of the telencephalon of this lizard, providing evidence for a marked regionalization of the reptilian pallium and subpallium. Overall, the proposed framework constitutes a new approach that allows upgrading in a generic fashion conventional genomic assays to spatially resolved techniques.
Muscle activity of cutting manoeuvres and soccer inside passing suggests an increased groin injury risk during these movements
Authors: Dupré Thomas , Tryba Julian , Potthast Wolfgang
Published: August 2020

Cutting manoeuvres and inside passing are thought to increase the risk for sustaining groin injuries. But both movements and cutting manoeuvres in particular have received little research attention in this regard. The purpose of this study was to investigate the muscle activity of adductor longus and gracilis as well as hip and knee joint kinematics during 90° -cutting and inside passing. Thirteen male soccer players were investigated with 3D-motion capturing and surface electromyography of adductor longus and gracilis while performing the two movements. Hip and knee joint kinematics were calculated with AnyBody Modelling System. Muscle activity of both muscles was significantly higher during the cutting manoeuvre compared to inside passing. Kinematics showed that the highest activity occurred during phases of fast muscle lengthening and eccentric contraction of the adductors which is known to increase the groin injury risk. Of both movements, cutting showed the higher activity and is therefore more likely to cause groin injuries. However, passing might also increase the risk for groin injuries as it is one of the most performed actions in soccer, and therefore most likely causes groin injuries through overuse. Practitioners need to be aware of these risks and should prepare players accordingly through strength and flexibility training.
Nav1.7 gating in human iPSC derived sensory neurons: an experimental and computational study
Authors: Capurro Alberto , Thornton Jack , Cessac Bruno , Armstrong Lyle , Sernagor Evelyne
Published: August 2020

Chronic pain is a global healthcare problem with a huge societal impact. Its management remains unsatisfactory, with no single treatment clinically approved in most cases. In this study we use anin vitroexperimental model of erythromelalgia consisting of sensory neurons derived from human induced pluripotent stem cells obtained from a patient (carrying the mutation F1449V) and a control subject. We combine neurophysiology and computational modelling to focus on the Nav1.7 voltage gated sodium channel, which acts as an amplifier of the receptor potential in nociceptive neurons and plays a critical role in erythromelalgia due to gain of function mutations causing the channel to open with smaller depolarisations.

Using multi-electrode array (extracellular) recordings, we found that the scorpion toxin OD1 increases the excitability of sensory neurons in cultures obtained from the control donor, evidenced by increased spontaneous spike rate and amplitude. In erythromelalgia cultures, the application of the Nav1.7 blocker PF-05089771 effectively stopped spontaneous firing. These results, which are in accordance with current clamp and voltage clamp recordings reported in the literature, are explained with a conductance-based computational model of a single human nociceptive neuron. The disease was simulated through a decrease of the Nav1.7 half activation voltage, which decreased the rheobase and increased the response to supra threshold depolarizing currents. This enhanced response could be successfully supressed by blocking the Nav1.7 channels. The painful effects of OD1 were simulated through a slower establishment and a quicker removal of Nav1.7 inactivation, reproducing the effects of the toxin on the spike frequency and amplitude. Our model simulations suggest that the increase in extracellular spike amplitude observed in the MEA after OD1 treatment can be due mainly to a slope increase in the ascending phase of the intracellular spike caused by impaired inactivation gating.
The Relationship Between Motor Fitness, Fundamental Movement Skills, and Functional Movement Screen in Primary School Children
Authors: Wu Hua , Eungpinichpong Wichai , Ruan Hui , Zhang Xinding , Dong Xiujuan
Published: August 2020

This study investigates motor fitness (MF), fundamental movement skills (FMS), and functional movement screen (FMS™) in 7-10-year-old children, and evaluates the relationship between FMS , MF and FMS™ combination with Seefeldt’s model for empirical research, thus to present effective strategies of physical development in children. A class was randomly selected in four school grades (1-4) along with 30 students from each to take the Test of Gross Motor Development-2 (TGMD-2). A total of 117 children (42 girls, aged 7-10) participated in three tests: TGMD-2, MF tests, and FMS™. MF levels (good, fair, and poor) and FMS™ levels (high, moderate, and low) were classified according to specific percentile ranges. A multiple (R×C) chi-square test analysis of the relationship between MF, FMS, and FMS™ was applied and post hoc testing estimated the possibility of FMS and FMS™ predicting MF. The results showed that only 43% of children were rated “good” on MF. Most fourth-grade students exhibited a certain gap with mature FMS (TGMD-2 score 70.13±9.68< 96 full scores). Boys scored significantly higher on the object control subtest and the TGMD-2 total score compared to girls (p<0.001), while girls had a significantly greater score than boys on the FMS™ (p=0.001). The results of multiple chi-square demonstrated FMS to be weakly correlated with MF, χ2(4,N=117) =14.605, p =0.006< 0.01, Cramer’s V = 0.25. Both 60.5% of “excellent” FMS and 59.6% of “high” FMS™ children were categorized as having a “good” MF level. On the other hand, only 23.1% of the “worst” FMS and 24.3% of “low” FMS™ individuals were classified as having a “good” MF level. Our results suggest that MF, FMS, FMS™ are relatively independent systems linking with each other, generating mutual interaction in children’s motor development. At different stages or different advantages of them motor development, we may emphasize training one or a few parts.
Novel small RNAs expressed byBartonella bacilliformisunder multiple conditions reveal potential mechanisms for persistence in the sand fly vector and human host
Authors: Wachter Shaun , Hicks Linda D. , Raghavan Rahul , Minnick Michael F.
Published: August 2020

Bartonella bacilliformis, the etiological agent of Carrión’s disease, is a Gram-negative, facultative intracellular alphaproteobacterium. Carrión’s disease is an emerging but neglected tropical illness endemic to Peru, Colombia, and Ecuador.B. bacilliformisis spread between humans through the bite of female phlebotomine sand flies. As a result, the pathogen encounters significant and repeated environmental shifts during its life cycle, including changes in pH and temperature. In most bacteria, small non-coding RNAs (sRNAs) serve as effectors that may post-transcriptionally regulate the stress response to such changes. However, sRNAs have not been characterized inB. bacilliformis, to date. We therefore performed total RNA-sequencing analyses onB. bacilliformisgrownin vitrothen shifted to one of ten distinct conditions that simulate various environments encountered by the pathogen during its life cycle. From this, we identified 160 sRNAs significantly expressed under at least one of the conditions tested. sRNAs included the highly-conserved tmRNA, 6S RNA, RNase P RNA component, SRP RNA component,ffHleader RNA, and the alphaproteobacterial sRNAs αr45 andspeFleader RNA. In addition, 153 other potential sRNAs of unknown function were discovered. Northern blot analysis was used to confirm the expression of eight novel sRNAs. We also characterized aBartonellabacilliformisgroup Iintron (BbgpI) that disrupts an un-annotated tRNACCUArggene and determined that the intron splicesin vivoand self-splicesin vitro.Furthermore, we demonstrated the molecular targeting ofBartonellabacilliformissmallRNA9(BbsR9) to transcripts of theftsH,nuoF, andgcvTgenes,in vitro.

Author summary

B. bacilliformisis a bacterial pathogen that is transmitted between humans by phlebotomine sand flies. Bacteria often express sRNAs to fine-tune the production of proteins involved in a wide array of biological processes. We culturedB. bacilliformis in vitrounder standard conditions then shifted the pathogen for a period of time to ten distinct environments, including multiple temperatures, pH levels, and infections of human blood and human vascular endothelial cells. After RNA-sequencing, a manual transcriptome search identified 160 putative sRNAs, including seven highly-conserved sRNAs and 153 novel potential sRNAs. We then characterized two of the novel sRNAs, BbgpI and BbsR9. BbgpI is a group I intron (ribozyme) that self-splices and disrupts an unannotated gene coding for a transfer RNA (tRNACCUArg). BbsR9 is an intergenic sRNA expressed under conditions that simulate the sand fly. We found that BbsR9 targets transcripts of theftsH,nuoF, andgcvTgenes. Furthermore, we determined the specific sRNA-mRNA interactions responsible for BbsR9 binding to its target mRNAs throughin vitromutagenesis and binding assays.
Genetic analysis of obstructive sleep apnoea discovers a strong association with cardiometabolic health
Authors: Strausz Satu , Ruotsalainen Sanni , Ollila Hanna M. , Karjalainen Juha , Reeve Mary , Kurki Mitja , Mars Nina , Havulinna Aki S. , Kiiskinen Tuomo , Aly Dina Mansour , Ahlqvist Emma , Teder-Laving Maris , Palta Priit , Groop Leif , Mägi Reedik , Mäkitie Antti , Salomaa Veikko , Bachour Adel , Tuomi Tiinamaija ,   FinnGen, Palotie Aarno , Palotie Tuula , Ripatti Samuli
Published: August 2020

There is currently only limited understanding of the genetic aetiology of obstructive sleep apnoea (OSA). The aim of our study is to identify genetic loci associated with OSA risk and to test if OSA and its comorbidities share a common genetic background.

We conducted the first large-scale genome-wide association study of OSA using FinnGen Study (217,955 individuals) with 16,761 OSA patients identified using nationwide health registries.

We estimated 8.3% [0.06-0.11] heritability and identified five loci associated with OSA (P < 5.0 × 10−8): rs4837016 near GTPase activating protein and VPS9 domains 1 (GAPVD1), rs10928560 near C-X-C motif chemokine receptor 4 (CXCR4), rs185932673 near Calcium/calmodulin-dependent protein kinase ID (CAMK1D) and rs9937053 near Fat mass and obesity-associated protein (FTO) - a variant previously associated with body mass index (BMI). In a BMI-adjusted analysis, an association was observed for rs10507084 near Rhabdomyosarcoma 2 associated transcript (RMST)/NEDD1 gamma-tubulin ring complex targeting factor (NEDD1).

We found genetic correlations between OSA and BMI (rg=0.72 [0.62-0.83]) and with comorbidities including hypertension, type 2 diabetes (T2D), coronary heart disease (CHD), stroke, depression, hypothyroidism, asthma and inflammatory rheumatic diseases (IRD) (rg > 0.30). Polygenic risk score (PRS) for BMI showed 1.98-fold increased OSA risk between the highest and the lowest quintile and Mendelian randomization supported a causal relationship between BMI and OSA.

Our findings support the causal link between obesity and OSA and joint genetic basis between OSA and comorbidities.
Network-centered homeostasis through inhibition maintains hippocampal spatial map and cortical circuit function
Authors: Kaleb Klara , Pedrosa Victor , Clopath Claudia
Published: August 2020

Despite ongoing experiential change, neural activity maintains remarkable stability. Such stability is thought to be mediated by homeostatic plasticity and is deemed to be critical for normal neural function. However, what aspect of neural activity does homeostatic plasticity conserve, and how it still maintains the flexibility necessary for learning and memory, is not fully understood. Homeostatic plasticity is often studied in the context of neuron-centered control, where the deviations from the target activity for each individual neuron are suppressed. However, experimental studies suggest that there are additional, network-centered mechanisms. These may act through the inhibitory neurons, due to their dense network connectivity. Here we use a computational framework to study a potential mechanism for such homeostasis, using experimentally inspired, input-dependent inhibitory plasticity (IDIP). In a hippocampal CA1 spiking model, we show that IDIP in combination with place tuned input can explain the formation of active and silent place cells, as well as place cells remapping following optogenetic silencing of active place cells. Furthermore, we show that IDIP can also stabilise recurrent network dynamics, as well as preserve network firing rate heterogeneity and stimulus representation. Interestingly, in an associative memory task, IDIP facilitates persistent activity after memory encoding, in line with some experimental data. Hence, the establishment of global network balance with IDIP has diverse functional implications and may be able to explain experimental phenomena across different brain areas.
Bacteriophage deficiency characterizes respiratory virome dysbiosis in childhood asthma
Authors: Megremis Spyridon , Constantinides Bede , Xepapadaki Paraskevi , Bachert Claus , Neurath-Finotto Susetta , Jartti Tuomas , Kowalski Marek L , Sotiropoulos Alexandros Georgios , Tapinos Avraam , Vuorinen Tytti , Andreakos Evangelos , Robertson David , Papadopoulos Nikolaos
Published: August 2020

Asthma development and persistence is tightly linked to respiratory viruses. Viral presence is usually interrogated with targeted approaches during periods of disease activity and/or infections, thus neglecting viral occurrence during steady states. We investigate the virome in the upper respiratory system of healthy and asthmatic preschool children during asymptomatic/non-infection periods using metagenomics. Children with asthma have a characteristically dysbiotic virome that correlates to disease severity and control. The major component of dysbiosis is bacteriophage deficiency, while eukaryotic viral presence is increased. At the metacommunity level, differential virus species co-occurrence patterns suggest a decrease of the microbiota community resilience in asthma. Viral dysbiosis is therefore a key characteristic of asthma pathophysiology.