bluuebunny/crossref_metadata_2025 huggingface dataset:
Global Increases in Human Immunodeficiency Virus Neutralization Sensitivity Due to Alterations in the Membrane-Proximal External Region of the Envelope Glycoprotein Can be Minimized by Distant State 1-Stabilizing Changes
Authors: Wang Qian , Esnault Florian , Zhao Meiqing , Chiu Ta-Jung , Smith Amos B. , Nguyen Hanh T. , Sodroski Joseph G.
Published: November 2021

Binding to the receptor, CD4, drives the pretriggered, “closed” (State-1) conformation of the human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer ((gp120/gp41)3) into more “open” conformations. HIV-1 Env on the viral membrane is maintained in a State-1 conformation that resists binding and neutralization by commonly elicited antibodies. Premature triggering of Env before the virus engages a target cell typically leads to increased susceptibility to spontaneous inactivation or ligand-induced neutralization. Here, we show that single amino acid substitutions in the gp41 membrane-proximal external region (MPER) of a primary HIV-1 strain result in viral phenotypes indicative of premature triggering of Env to downstream conformations. Specifically, the MPER changes reduced viral infectivity and globally increased virus sensitivity to poorly neutralizing antibodies, soluble CD4, a CD4-mimetic compound, and exposure to cold. By contrast, the MPER mutants exhibited decreased sensitivity to the State-1 preferring inhibitor, BMS-806, and to the PGT151 broadly neutralizing antibody. Depletion of cholesterol from virus particles did not produce the same State 1-destabilizing phenotypes as MPER alterations. Notably, State 1-stabilizing changes in Env distant from the MPER could minimize the phenotypic effects of MPER alteration, but did not affect virus sensitivity to cholesterol depletion. Thus, membrane-proximal gp41 elements contribute to the maintenance of the pretriggered Env conformation. The conformationally disruptive effects of MPER changes can be minimized by distant State 1-stabilizing Env modifications, a strategy that may be useful in preserving the native pretriggered state of Env.

IMPORTANCE

The pretriggered shape of the human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) is a major target for antibodies that can neutralize many strains of the virus. An effective HIV-1 vaccine may need to raise these types of antibodies, but this goal has proven difficult. One reason is that the pretriggered shape of Env is unstable and dependent on interactions near the viral membrane. Here we show that the membrane-proximal external region (MPER) of Env plays an important role in maintaining Env in a pretriggered shape. Alterations in the MPER resulted in global changes in Env conformation that disrupted its pretriggered shape. We also found that these disruptive effects of MPER changes can be minimized by distant Env modifications that stabilize the pretriggered shape. These modifications may be useful for preserving the native shape of Env for structural and vaccine studies.
Expanding the Russian allele frequency reference via cross-laboratory data integration: insights from 7,452 exome samples
Authors: Barbitoff Yury A. , Khmelkova Darya N. , Pomerantseva Ekaterina A. , Slepchenkov Aleksandr V. , Zubashenko Nikita A. , Mironova Irina V. , Kaimonov Vladimir S. , Polev Dmitrii E. , Tsay Victoria V. , Glotov Andrey S. , Aseev Mikhail V. , Scherbak Sergey G. , Glotov Oleg S. , Isaev Arthur A. , Predeus Alexander V.
Published: November 2021

Population allele frequency is crucially important for accurate interpretation of known and novel variants in medical genetics. Recently, several large allele frequency databases, such as Genome Aggregation Database (gnomAD), have been created to serve as a global reference for such studies. However, frequencies of many rare alleles vary dramatically between populations, and population-specific allele frequency is often more informative than the global one. Many countries and regions, including Russia, remain poorly studied from the genetic perspective. Here, we report the first successful attempt to integrate genetic information between major medical genetic laboratories in Russia. We construct an open, large-scale reference set of genetic variants by analyzing 7,492 exome samples collected in two major Russian cities of Moscow and St. Petersburg. An approximately tenfold increase in sample size compared to previous studies allowed us to identify genetically distinct clusters of individuals within an admixed population of Russia. We highlight 47 known pathogenic variants that are overrepresented in Russia compared to other European countries. We also identify several dozen high-impact variants that are present in healthy donors despite either being annotated as pathogenic in ClinVar or falling within genes associated with autosomal dominant disorders. The constructed database of genetic variant frequencies in Russia has been made available to the medical genetics community through a variant browser available at http://ruseq.ru.
Multiplex Solid-Phase RPA Coupled CRISPR-Based Visual Detection of SARS-CoV-2
Authors: Qin Xiaochen , Zhou Yuyuan , Paul Ratul , Wu Yue , Liu Yaling
Published: November 2021

COVID-19 has challenged the world’s public health and led to over 4.5 million deaths. A rapid, sensitive, and cost-effective point-of-care virus detection device is crucial to the control and surveillance of the contagious severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic. Here we demonstrate a solid phase isothermal recombinase polymerase amplification coupled CRISPR-based (spRPA-CRISPR) assay for on-chip multiplexed, sensitive and visual COVID-19 DNA detection. By targeting the SARS-CoV-2 structure protein encoded genomes, two specific genes were simultaneously detected with the control sample without cross-interaction with other sequences. The endpoint signal can be directly visualized for rapid detection of COVID-19. The amplified target sequences were immobilized on the one-pot device surface and detected using the mixed Cas12a-crRNA collateral cleavage of reporter released fluorescent signal when specific genes were recognized. The system was tested with samples of a broad range of concentrations (20 to 2×105 copies) and showed analytical sensitivity down to 20 copies per reaction. Furthermore, a low-cost LED UV flashlight (∼$12) was used to provide a visible SARS-CoV-2 detection signal of the spRPA-CRISPR assay which could be purchased online easily. Thus, our platform provides a sensitive and easy-to-read multiplexed gene detection method with the capacity to specifically identify low concentration genes. Similar CRISPR biosensor chips can support a broad range of applications such as HPV DNA detection, influenza SARS-CoV-2 multiplex detection, and other infectious disease testing assays.

Highlights

A commercially available UV flashlight excited CRISPR-Cas12a based visual sensor combined with solid-phase RPA

The developed assay could detect SARS-CoV-2 down to 20 copies with no signal crosswalk

This multiplexed on-chip virus detection system would provide great insight for detecting and differentiating SARS-CoV-2 from other viral infections with a single sample simultaneously.
Arp2/3 complex activity is necessary for mouse ESC differentiation, times formative pluripotency, and enables lineage specification
Authors: Aloisio Francesca M. , Barber Diane L.
Published: November 2021

Mouse embryonic stem cells (mESCs), a model for differentiation into primed epiblast-like cells (EpiLCs), have revealed transcriptional and epigenetic control of early embryonic development. The control and significance of morphological changes, however, remain less defined. We show marked changes in morphology and actin architectures during differentiation that depend on Arp2/3 complex but not formin activity. Inhibiting Arp2/3 complex activity pharmacologically or genetically does not block exit from naive pluripotency but attenuates increases in EpiLC markers. We find that inhibiting Arp2/3 complex activity delays formative pluripotency and causes globally defective lineage specification as indicated by RNA-sequencing, with significant effects on TBX3-depedendent transcriptional programs. We also identify two previously unreported indicators of mESC differentiation; MRTF and FHL2, which have inverse Arp2/3 complex-dependent nuclear translocation. Our findings on Arp2/3 complex activity in differentiation and the established role of formins in EMT indicate that these two actin nucleators regulate distinct modes of epithelial plasticity.

Highlights

Arp2/3 complex activity is necessary for morphology changes during differentiation

Arp2/3 complex activity regulates transcriptional markers of differentiation

Inhibiting Arp2/3 complex activity delays entry into formative pluripotency

Arp2/3 complex activity-dependent shuttling of FHL2 and MRTF occurs in mESCs
Histamine H1-Receptor-Mediated Modulation of Nmda Receptors
Authors: Arrang J-M. , Armand V.
Published: November 2021

This study attempted to clarify the role of histamine H1receptors in epilepsy by exploring the effects of agonists and inverse agonists on the rundown of the current induced by iterative applications of NMDA or GABA. Mepyramine, a classical H1-receptor antagonist / inverse agonist, increased the NMDA current by about 40 % during the first minutes of recording. This effect was concentration-dependent, maximal at 10 nM, and mimicked by triprolidine, another antagonist / inverse agonist. No endogenous histamine being detected in the cultures by a selective immunoassay, both compounds were acting as inverse agonists. Indicating a high constitutive activity of the H1receptor in this system, histamine did not affect on the NMDA rundown, including its settlement, but reversed significantly the effect of mepyramine. A similar pattern was obtained with 2,3 bromophenyl histamine, a selective H1-receptor agonist. The initial increase induced by the two inverse agonists was followed by the same rundown as in controls. H1– and NMDA receptors colocalised in most cultured neuronal cells. Mepyramine and histamine did not affect on the GABA rundown. Our findings suggest an interaction between H1– and NMDA receptors. Inactivation of the H1-receptor by its inverse agonists delays the settlement of the NMDA rundown, which may underlie their proconvulsant effect reported in clinics. Therefore, H1-receptor constitutive activity, and the effect of histamine revealed in its absence, tend to facilitate the initiation of the rundown, which is consistent with the anticonvulsant properties of histamine via activation of H1-receptors reported in many studies.
Problems using ordinal traits with continuous measures of functional diversity
Authors: Davis Matt
Published: November 2021

Continuous indices of functional diversity are popular in studies examining community structure and ecosystem function across a wide range of subfields from paleontology to range management. These indices were designed to replace the use of more arbitrary, discrete functional groups or guilds; however, the effect of typical methodological decisions on these new continuous measures has not been fully investigated. To test the effect of using ordinal traits in functional diversity analysis, I first calculated relative functional diversity index values in real plant communities with real continuous trait data and Euclidean distances. I then compared these original values to “treatment” functional diversity index values obtained by discretizing the trait data and using Gower’s distance. Agreement between original and treatment values was highly unpredictable and often abysmal. Small methodological choices, such as whether to treat a functional trait as continuous (mm) or ordinal (“small”, “medium”, “large”), could completely change a perceived functional diversity relationship along an environmental gradient. Some parameter combinations returned results that were no better than random noise. Because simple methodological choices can have such a large impact on continuous functional diversity indices, it is ambiguous whether analyses using ordinal traits are actually measuring an underlying functional diversity relationship between communities or just reflecting the arbitrary parameter choices of researchers.
Operon formation by insertion sequence IS3 in Escherichia coli
Authors: Kanai Yuki , Tsuru Saburo , Furusawa Chikara
Published: November 2021

Operons are a hallmark of the genomic and regulatory architecture of prokaryotes. However, the mechanism by which two genes placed far apart gradually come close and form operons remains to be elucidated. Here, we propose a new model of the origin of operons: Mobile genetic elements called insertion sequences can facilitate the formation of operons by consecutive insertion-deletion-excision reactions. This mechanism barely leaves traces of insertion sequences and is difficult to detect in evolution in nature. We performed, to the best of our knowledge, the first experimental demonstration of operon formation, as a proof of concept. The insertion sequence IS3 and the insertion sequence excision enhancer are genes found in a broad range of bacterial species. We introduced these genes into insertion sequence-less Escherichia coli and found that, supporting our hypothesis, the activity of the two genes altered the expression of genes surrounding IS3, closed a 2.7 kilobase pair gap between a pair of genes, and formed new operons. This study shows how insertion sequences can facilitate the rapid formation of operons through locally increasing the structural mutation rates and highlights how coevolution with mobile elements may shape the organization of prokaryotic genomes and gene regulation.
DDK inhibition disrupts replication leading to mitotic catastrophe in Ewing sarcoma
Authors: Martin Jeffrey C. , Gupta Ajay , Hagoel Tamara J. , Gao Lingui , Lynch Miranda L. , Woloszynska Anna , Melendy Thomas , Kane Jeremy , Kuechle Joseph , Ohm Joyce E.
Published: November 2021

Ewing sarcoma is the second most common bone malignancy in children and adolescents. Patients with upfront metastatic or recurrent disease have poor outcomes with 5-year survival rates of <30%. CDC7, also known as DDK (DBF4-dependent kinase), is a serine-threonine kinase that, in coordination with its activation subunit ASK (or DBF4), is involved in a diverse array of cellular functions including the regulation of DNA replication initiation and activation of the replication stress response. Due to DDK’s diverse roles during replication, coupled with an increased level of genomic instability and R-loop-mediated replication stress within Ewing sarcoma cells, we hypothesized that Ewing sarcoma cells would be particularly vulnerable to DDK inhibitors. Here, we show that treatment with two selective DDK inhibitors, TAK-931 and XL413, results in apoptosis and a significant reduction in cell viability in EWS-FLI1-harboring Ewing sarcoma cell lines. We show that low dose DDK inhibition in Ewing sarcoma cells causes an accumulation of cells in late-S phase with a reduced replication capacity. There is also evidence of premature mitotic entry indicating an inability to properly complete DNA replication in a timely manner upon DDK inhibition. Also, there is a significant increase in the formation of micronuclei and other aberrant mitotic structures upon DDK inhibition in Ewing sarcoma cells indicating a failure to properly progress through S-phase followed by improper mitotic entry/progression, resulting in mitotic catastrophe. Interestingly, we observed minimal signs of mitotic accumulation, despite clear evidence of replication and mitotic stress, suggesting a failure to properly enforce the mitotic checkpoint. Together, these results suggest that Ewing sarcoma cells rely on the activity of DDK to maintain cell viability and suggest that DDK inhibition may prove to be a viable therapeutic strategy for patients with Ewing sarcoma.
Towards a general framework for modeling large-scale biophysical neuronal networks: a full-scale computational model of the rat dentate gyrus
Authors: Raikov Ivan Georgiev , Milstein Aaron , Moolchand Prannath , Szabo Gergely G , Schneider Calvin , Hadjiabadi Darian , Chatzikalymniou Alexandra , Soltesz Ivan
Published: November 2021

Large-scale computational models of the brain are necessary to accurately represent anatomical and functional variability in neuronal biophysics across brain regions and also to capture and study local and global interactions between neuronal populations on a behaviorally-relevant temporal scale. We present the methodology behind and an initial implementation of a novel open-source computational framework for construction, simulation, and analysis of models consisting of millions of neurons on high-performance computing systems, based on the NEURON and CoreNEURON simulators (Carnevale and Hines, 2006, Kumbhar et al., 2019). This framework uses the HDF5 data format and software library (HDF Group, 2021) and includes a data format for storing morphological, synaptic, and connectivity information of large neuronal network models, and an accompanying open-source software library that provides efficient, scalable parallel storage and MPI-based data movement capabilities. We outline our approaches for constructing detailed large-scale biophysical models with topographical connectivity and input stimuli, and present simulation results obtained with a full-scale model of the dentate gyrus constructed with our framework. The model generates sparse and spatially selective population activity that fits well with in-vivo experimental data. Moreover, our approach is fully general and can be applied to modeling other regions of the hippocampal formation in order to rapidly evaluate specific hypotheses about large-scale neural architectural features.
Validation analysis of EMDB entries
Authors: Wang Zhe , Patwardhan Ardan , Kleywegt Gerard J.
Published: November 2021

The Electron Microscopy Data Bank (EMDB) is the central archive of the electron cryo-microscopy (cryo-EM) community for storing and disseminating volume maps and tomograms. With input from the community, EMDB has developed new resources for validation of cryo-EM structures, focussing on the quality of the volume data alone and that of the fit of any models, themselves archived in the Protein Data Bank (PDB), to the volume data. Based on recommendations from community experts, the validation resources are developed in a three-tiered system. Tier 1 covers an extensive and evolving set of validation metrics, including tried and tested as well as more experimental ones, which are calculated for all EMDB entries and presented in the Validation Analysis (VA) web resource. This system is particularly useful for cryo-EM experts, both to validate individual structures and to assess the utility of new validation metrics. Tier 2 comprises a subset of the validation metrics covered by the VA resource that have been subjected to extensive testing and are considered to be useful for specialists as well as non-specialists. These metrics are presented on the entry-specific web pages for the entire archive on the EMDB website. As more experience is gained with the metrics included in the VA resource, it is expected that consensus will emerge in the community regarding a subset that is suitable for inclusion in the tier 2 system. Tier 3, finally, consists of the validation reports and servers that are produced by the Worldwide Protein Data Bank (wwPDB) Consortium. Successful metrics from tier 2 will be proposed for inclusion in the wwPDB validation pipeline and reports. We describe the details of the new resource, with an emphasis on the tier 1 system. The output of all three tiers is publicly available, either through the EMDB website (tiers 1 and 2) or through the wwPDB ftp sites (tier 3), although the content of all three will evolve over time (fastest for tier 1 and slowest for tier 3). It is our hope that these validation resources will help the cryo-EM community to get a better understanding of the quality, and the best ways to assess the quality of cryo-EM structures in EMDB and PDB.
Systematic Review of Aptamer Sequence Reporting in the Literature Reveals Widespread Unexplained Sequence Alterations
Authors: Miller Alexandra A. , Rao Abhijit S. , Nelakanti Sujana R. , Kujalowicz Christopher , Shi Ted , Rodriguez Ted , Ellington Andrew D. , Stovall Gwendolyn M.
Published: November 2021

Aptamers have been the subject of more than 144,000 papers to date. However, there has been a growing concern that errors in reporting aptamer research limit the reliability of these reagents for research and other applications. These observations noting inconsistencies in the use of our RNA anti-lysozyme aptamer served as an impetus for our systematic review of the reporting of aptamer sequences in the literature. Our detailed examination of literature citing the RNA anti-lysozyme aptamer revealed that 93% of the 61 publications reviewed reported unexplained altered sequences with 86% of those using DNA variants. The ten most cited aptamers were examined using a standardized methodology in order to categorize the extent to which the sequences themselves were apparently improperly reproduced, both in the literature and presumably in experiments beyond their discovery. Our review of 800 aptamer publications spanned decades, multiple journals, and research groups, and revealed that 44% of the papers reported unexplained sequence alterations. We identified ten common categories of sequence alterations including deletions, substitutions, additions, among others. The robust data set we have produced elucidates a source of irreproducibility and unreliability in our field and can be used as a starting point for building evidence-based best practices in publication standards to elevate the rigor and reproducibility of aptamer research.
Multi-scale Adaptive Differential Abundance Analysis in Microbial Compositional Data
Authors: Wang Shulei
Published: November 2021

Differential abundance analysis is an essential and commonly used tool to characterize the difference between microbial communities. However, identifying differentially abundant microbes remains a challenging problem because the observed microbiome data is inherently compositional, excessive sparse, and distorted by experimental bias. Besides these major challenges, the results of differential abundance analysis also depend largely on the choice of analysis unit, adding another practical complexity to this already complicated problem. In this work, we introduce a new differential abundance test called the MsRDB test, which embeds the sequences into a metric space and integrates a multi-scale adaptive strategy for utilizing spatial structure to identify differentially abundant microbes. Compared with existing methods, the MsRDB test can detect differentially abundant microbes at the finest resolution offered by data and provide adequate detection power while being robust to zero counts, compositional effect, and experimental bias in the microbial compositional data set. Applications to both simulated and real microbial compositional data sets demonstrate the usefulness of the MsRDB test.
SVJAM: Joint Analysis of Structural Variants Using Linked Read Sequencing Data
Authors: Gunturkun Mustafa Hakan , Villani Flavia , Colonna Vincenza , Ashbrook David , Williams Robert W. , Chen Hao
Published: November 2021

Linked-read whole genome sequencing methods, such as the 10x Chromium, attach a unique molecular barcode to each high molecular weight DNA molecule. The samples are then sequenced using short-read technology. During analysis, sequence reads sharing the same barcode are aligned to adjacent genomic locations. The pattern of barcode sharing between genomic regions allows the discovery of large structural variants (SVs) in the range of 1 Kb to a few Mb. Most SV calling methods for these data, such as LongRanger, analyze one sample at a time and often produces inconsistent results for the same genomic location across multiple samples. We developed a method, SVJAM, for joint calling of SVs, using data from 152 members of the BXD family of recombinant inbred strains of mice. Our method first collects candidate SV regions from single sample analysis, such as those produced by LongRanger. We then retrieve barcode overlapping data from all samples for each region. These data are organized as a high dimensional matrix. The dimension of this matrix is then reduced using principal component analysis. Samples projected onto a two dimensional space formed by the first two principal components forms two or three clusters based on their genotype, representing the reference, alternative, or heterozygotic alleles. We developed a novel distance measure for hierarchical clustering and rotating the axes to find the optimal clustering results. We also developed an algorithm to decide whether the pattern of sample distribution is best fitted with one, two, or three genotypes. For each sample, we calculate its membership score for each genotype. We compared results produced by SVJAM with LongRanger and few methods that rely on PacBio or Oxford Nanopore data. In a comparison of SVJAM with SV detected using long-read sequencing data for the DBA/2J strain, we found that our results recovered many SVs missed by LongRanger. We also found many SVs called by LongRanger were assigned with an incorrect SV type. Our algorithm also consistently identified heterozygotic regions.
RAP1 regulates TIP60 function during fate transition between 2 cell-like and pluripotent states
Authors: Barry Raymond Mario , Sacco Olivia , Mameri Amel , Stojaspal Martin , Kartsonis William , Shah Pooja , Ioannes Pablo De , Hofr Ctirad , Côté Jacques , Sfeir Agnel
Published: November 2021

In mammals, the conserved telomere binding protein RAP1 serves a diverse set of non- telomeric functions including activation of the NF-kB signaling pathway, maintenance of metabolic functionin vivo,and transcriptional regulation. Here, we uncover the mechanism by which RAP1 modulates gene expression. Using a separation-of-function allele, we show that RAP1 transcriptional regulation is independent of TRF2-mediated binding to telomeres and does not involve direct binding to genomic loci. Instead, RAP1 interacts with the TIP60/p400 complex and modulates its histone acetyltransferase activity. Notably, we show that deletion of RAP1 in mouse embryonic stem cells increases the fraction of 2-cell-like cells. Specifically, RAP1 enhances the repressive activity of Tip60/p400 across a subset of 2-cell-stage genes, includingZscan4and the endogenous retrovirus MERVL. Preferential upregulation of genes proximal to MERVL elements in Rap1 deficient settings implicate these endogenous retroviral elements in the de- repression of proximal genes. Altogether, our study reveals an unprecedented link between RAP1 and TIP60/p400 complex in the regulation of totipotency.
Automatic Detection and Neurotransmitter Prediction of Synapses in Electron Microscopy
Authors: Zhang Angela , Shailja S. , Borba Cezar , Miao Yishen , Goebel Michael , Ruschel Raphael , Ryan Kerrianne , Smith William , Manjunath B.S.
Published: November 2021

This paper presents a deep-learning based workflow to detect synapses and predict their neurotransmitter type in the primitive chordate Ciona intestinalis (Ciona) EM images. Identifying synapses from electron microscopy (EM) images to build a full map of connections between neurons is a labor-intensive process and requires significant domain expertise. Automation of synapse detection and classification would hasten the generation and analysis of connectomes. Furthermore, inferences concerning neuron type and function from synapse features are in many cases difficult to make. Finding the connection between synapse structure and function is an important step in fully understanding a connectome. Activation maps derived from the convolutional neural network provide insights on important features of synapses based on cell type and function. The main contribution of this work is in the differentiation of synapses by neurotransmitter type through the structural information in their EM images. This enables prediction of neurotransmitter types for neurons in Ciona which were previously unknown. The prediction model with code is available on Github.
Analysis of sex-specific lipid metabolism in P. falciparum gametocytes points to importance of sphingomyelin for gametocytogenesis
Authors: Ridgway Melanie C. , Cihalova Daniela , Brown Simon H.J. , Tran Phuong , Mitchell Todd W. , Maier Alexander G.
Published: November 2021

Male and female Plasmodium falciparum gametocytes are the parasite lifecycle stage responsible for transmission of malaria from the human host to mosquito vector. Not only are gametocytes able to survive in radically different host environments, but they are also precursors for male and female gametes that reproduce sexually soon after ingestion by the mosquito. Here we investigate the sex-specific lipid metabolism of gametocytes within their host red blood cell and poised for ingestion by the mosquito vector and subsequent sexual reproduction.

Comparison of the male and female lipidome identifies cholesteryl esters and dihydrosphingomyelin enrichment in female gametocytes. Chemical inhibition of each of these lipid types in mature gametocytes suggests dihydrosphingomyelin synthesis but not cholesteryl ester synthesis is important for sex-specific gametocyte viability. Genetic disruption of each of the two sphingomyelin synthase gene points towards sphingomyelin synthesis contributing to gametocytogenesis.

This study shows that gametocytes are not only distinct from asexual stages, but that the lipid composition is also vastly different between male and female gametocytes, reflecting the different cellular roles these stages play. Together our results highlight the sex-specific nature of gametocyte lipid metabolism that has the potential to be targeted to block malaria transmission.
Automatic discrimination of species within theEnterobacter cloacaecomplex using MALDI-TOF Mass Spectrometry and supervised algorithms
Authors: Candela Ana , Guerrero-López Alejandro , Mateos Miriam , Gómez-Asenjo Alicia , Arroyo Manuel J. , Hernandez-García Marta , del Campo Rosa , Cercenado Emilia , Cuénod Aline , Méndez Gema , Mancera Luis , de Dios Caballero Juan , Martínez-García Laura , Gijón Desirée , Morosini María Isabel , Ruiz-Garbajosa Patricia , Egli Adrian , Cantón Rafael , Muñoz Patricia , Rodríguez-Temporal David , Rodríguez-Sánchez Belén
Published: November 2021

TheEnterobacter cloacaecomplex (ECC) encompasses heterogeneous clusters of species that have been associated with nosocomial outbreaks. These species may host different acquired antimicrobial resistance and virulence mechanisms and their identification are challenging. This study aims to develop predictive models based on MALDI-TOF MS spectral profiles and machine learning for species-level identification.

A total of 198 ECC and 116K. aerogenesclinical isolates from the University Hospital Ramón y Cajal (Spain) and the University Hospital Basel (Switzerland) were included. The capability of the proposed method to differentiate the most common ECC species (E. asburiae, E. kobei, E. hormaechei, E. roggenkampii, E. ludwigii, E. bugandensis) andK. aerogeneswas demonstrated by applying unsupervised hierarchical clustering with PCA pre-processing. We observed a distinctive clustering ofE. hormaecheiandK. aerogenesand a clear trend for the rest of the ECC species to be differentiated over the development dataset. Thus, we developed supervised, non-linear predictive models (Support Vector Machine with Radial Basis Function and Random Forest). The external validation of these models with protein spectra from the two participating hospitals yielded 100% correct species-level assignment forE. asburiae, E. kobei, andE. roggenkampiiand between 91.2% and 98.0% for the remaining ECC species. Similar results were obtained with the MSI database developed recently (https://msi.happy-dev.fr/) except in the case ofE. hormaechei, which was more accurately identified by Random Forest.

In short, MALDI-TOF MS combined with machine learning demonstrated to be a rapid and accurate method for the differentiation of ECC species.
Effectiveness of COVID-19 Vaccines and Post-vaccination SARS-COV 2 Infection, Hospitalization, and Mortality: a Systematic Review and Meta-analysis of Observational Studies
Authors: Rahmani Kazem , Shavaleh Rasoul , Forouhi Mahtab , Disfani Hamideh Feiz , Kamandi Mostafa , Zadegan Dezfuli Aram Asareh , Oskooi Rozita Khatamian , Foogerdi Molood , Soltani Moslem
Published: November 2021

Introduction & Objective

Vaccination is one of the most important and effective ways of preventing infectious diseases, and has recently been used in the COVID-19 epidemic and pandemic. The present meta-analysis study aimed to evaluate the effectiveness of COVID-19 vaccines in reducing the incidence of infection, hospitalization, and mortality in observational studies.

Materials and Methods

A systematic search was performed independently in Scopus, PubMed, ProQuest, and Google Scholar electronic databases as well as Preprint servers using the keywords under study. The heterogeneity of the studies was assessed using I2and χ2 statistics, according to which the I2 of > 50% and P -value <0.1 was reported as heterogeneity of the studies. In addition, the Pooled Vaccine Effectiveness (PVE) obtained from the studies was calculated by converting (1-Pooled estimate × 100%) based on the type of outcome.

Results

A total of 54 records were included in this meta-analysis. The rate of PVE against SARS-COV 2 infection was about 71% (OR = 0.29, 95% CI: 0.23-0.36) in the first dose and 87% (OR = 0.13, 95% CI: 0.08-0.21) in the second, and the highest effectiveness in the first and second doses was that of BNT162b2 mRNA and combined studies. The PVE versus COVID-19-associated hospitalization was 73% (OR = 0.27, 95% CI: 0.18-0.41) in the first dose and 89% (OR = 0.11, 95% CI: 0.07-0.17) in the second. mRNA-1273 and combined studies in the first dose and ChAdOx1 and mRNA-1273 in the second dose had the highest effectiveness. Regarding the COVID-19-related mortality, PVE was about 28% (HR = 0.39, 95% CI: 0.23-0.45) in the first dose and 89% (HR = 0.11, 95% CI: 0.03-0.43) in the second.

Conclusion

The evidence obtained from this study showed that the effectiveness of BNT162b2 mRNA, mRNA-1273, and ChAdOx1 in the first and second doses, and even combined studies were associated with increased effectiveness against SARS-COV2 infection, hospitalization, and death from COVID-19. In addition, considering that the second dose was significantly more efficient than the first one, a booster dose injection could be effective in high-risk individuals. On the other hand, it was important to observe other prevention considerations in the first days after taking the first dose.
Downsizing of contact tracing during COVID-19 vaccine roll-out
Authors: Martignoni Maria M. , Renault Josh , Baafi Joseph , Hurford Amy
Published: November 2021

Contact tracing is a key component of successful management of COVID-19. Contacts of infected individuals are asked to quarantine, which can significantly slow down (or prevent) community spread. Contact tracing is particularly effective when infections are detected quickly (e.g., through rapid testing), when contacts are traced with high probability, when the initial number of cases is low, and when social distancing and border restrictions are in place. However, the magnitude of the individual contribution of these factors in reducing epidemic spread and the impact of vaccination in determining contact tracing outputs is not fully understood. We present a delayed differential equation model to investigate how vaccine roll-out and the relaxation of social distancing requirements affect contact tracing practises. We provide an analytical criteria to determine the minimal contact tracing efficiency (defined as the the probability of identifying and quarantining contacts of symptomatic individuals) required to keep an outbreak under control, with respect to the contact rate and vaccination status of the population. Additionally, we consider how delays in outbreak detection and increased case importation rates affect the number of contacts to be traced daily. We show that in vaccinated communities a lower contact tracing efficiency is required to avoid uncontrolled epidemic spread, and delayed outbreak detection and relaxation of border restrictions do not lead to a significantly higher risk of overwhelming contact tracing. We find that investing in testing programs, rather than increasing the contact tracing capacity, has a larger impact in determining whether an outbreak will be controllable. This is because early detection activates contact tracing, which will slow, and eventually reverse exponential growth, while the contact tracing capacity is a threshold that will easily become overwhelmed if exponential growth is not curbed. Finally, we evaluate quarantine effectiveness during vaccine roll-out, by considering the proportion of people that will develop an infection while in isolation in relation to the vaccination status of the population and for different viral variants. We show that quarantine effectiveness decreases with increasing proportion of fully vaccinated individuals, and increases in the presence of more transmissible variants. These results suggest that a cost-effective approach during vaccine roll-out is to establish different quarantine rules for vaccinated and unvaccinated individuals, where rules should depend on viral trans-missibility. Altogether, our study provides quantitative information for contact tracing downsizing during vaccine roll-out, to guide COVID-19 exit strategies.
Recombination landscape dimorphism contributes to sex chromosome evolution in the dioecious plant Rumex hastatulus
Authors: Rifkin Joanna L. , Hnatovska Solomiya , Yuan Meng , Sacchi Bianca M. , Choudhury Baharul I. , Gong Yunchen , Rastas Pasi , Barrett Spencer C.H. , Wright Stephen I.
Published: November 2021

There is growing evidence across diverse taxa for sex differences in the genomic landscape of recombination, but the causes and consequences of these differences remain poorly understood. Strong recombination landscape dimorphism between the sexes could have important implications for the dynamics of sex chromosome evolution and turnover because low recombination in the heterogametic sex can help favour the spread of sexually antagonistic alleles. Here, we present a sex-specific linkage map and revised genome assembly of Rumex hastatulus, representing the first characterization of sex differences in recombination landscape in a dioecious plant. We provide evidence for strong sex differences in recombination, with pericentromeric regions of highly suppressed recombination in males that cover over half of the genome. These differences are found on autosomes as well as sex chromosomes, suggesting that pre-existing differences in recombination may have contributed to sex chromosome formation and divergence. Analysis of segregation distortion suggests that haploid selection due to pollen competition occurs disproportionately in regions with low male recombination. Our results are consistent with the hypothesis that sex differences in the recombination landscape contributed to the formation of a large heteromorphic pair of sex chromosomes, and that pollen competition is an important determinant of recombination dimorphism.
High-plex Multiomic Analysis in FFPE at Subcellular Level by Spatial Molecular Imaging
Authors: He Shanshan , Bhatt Ruchir , Brown Carl , Brown Emily A. , Buhr Derek L. , Chantranuvatana Kan , Danaher Patrick , Dunaway Dwayne , Garrison Ryan G. , Geiss Gary , Gregory Mark T. , Hoang Margaret L. , Khafizov Rustem , Killingbeck Emily E. , Kim Dae , Kim Tae Kyung , Kim Youngmi , Klock Andrew , Korukonda Mithra , Kutchma Alecksandr , Lewis Zachary R. , Liang Yan , Nelson Jeffrey S. , Ong Giang T. , Perillo Evan P. , Phan Joseph C. , Phan-Everson Tien , Piazza Erin , Rane Tushar , Reitz Zachary , Rhodes Michael , Rosenbloom Alyssa , Ross David , Sato Hiromi , Wardhani Aster W. , Williams-Wietzikoski Corey A. , Wu Lidan , Beechem Joseph M.
Published: November 2021

The Spatial Molecular Imaging platform (CosMxTM SMI, NanoString Technologies, Seattle, WA) utilizes high-plex in-situ imaging chemistry for both RNA and protein detection. This automated instrument provides 1000’s of plex, at high sensitivity (1 to 2 copies/cell), very low error rate (0.0092 false calls/cell) and background (∼0.04 counts/cell). The imaging system generates three-dimensional super-resolution localization of analytes at ∼2 million cells per sample, four samples per run. Cell segmentation is morphology-based using antibodies, compatible with FFPE samples. Multiomic data (980 RNAs, 108 proteins) were measured at subcellular resolution using FFPE tissues (non-small cell lung (NSCLC) and breast cancer) and allowed identification of over 18 distinct cell types, 10 unique tumor microenvironments, and 100 pairwise ligand-receptor interactions. Over 800,000 single cells and ∼260 million transcripts data are released into the public domain allowing extended data analysis by the entire spatial biology research community.
Trim41 is essential for preventing X chromosome chaotic synapsis in male mice
Authors: Oura Seiya , Hino Toshiaki , Satoh Takashi , Noda Taichi , Koyano Takayuki , Isotani Ayako , Matsuyama Makoto , Akira Shizuo , Ishiguro Kei-ichiro , Ikawa Masahito
Published: November 2021

Meiosis is a hallmark event in germ cell development that accompanies sequential chromosome events executed by numerous molecules. Therefore, characterization of these factors is one of the best strategies to clarify the mechanism of meiosis. Here, we report tripartite motif-containing 41 (TRIM41), a ubiquitin ligase E3, as an essential factor for proper meiotic progression and fertility in male mice. Trim41 KO spermatocytes exhibited synaptonemal complex protein 3 (SYCP3) overloading, especially on the X chromosome, showing extensive self-synapsis of X chromosome and non-homologous synapsis between the X chromosome and autosomes. Furthermore, the mutant mice lacking the RING domain of TRIM41, required for the ubiquitin ligase E3 activity, phenocopied Trim41 KO mice. We then examined the behavior of mutant TRIM41 (ΔRING-TRIM41) and found that ΔRING-TRIM41 accumulated on the chromosome axes with overloaded SYCP3. This result showed that TRIM41 exerts the function on the chromosome axes. In summary, our study revealed that Trim41 is essential for preventing SYCP3 overloading and chaotic synapsis of the X chromosome, suggesting a TRIM41-mediated mechanism for regulating unsyapsed axes during male meiotic progression.

Summary statement

Trim41-disruption caused abnormal synapsis configuration of the X chromosome and complete infertility in male mice. Thus, TRIM41 prevents the sex chromosome from chaotic synapsis.
Restricting a single amino acid cross-protects D. melanogaster from nicotine poisoning through mTORC1 and GCN2 signalling
Authors: Fulton Tahlia L. , Mirth Christen K. , Piper Matthew D. W.
Published: November 2021

Dietary interventions that restrict protein intake have repeatedly been shown to offer beneficial health outcomes to the consumer. Benefits such as increased stress tolerance can be observed in response to restricting individual amino acids, thus mimicking dietary protein restriction. Here, we sought to further understand the relationship between dietary amino acids and stress tolerance using Drosophila melanogaster. Utilising a chemically defined medium for Drosophila, we found that transiently restricting adult flies of a single essential amino acid generally protects against a lethal dose of the naturally occurring insecticide, nicotine. This protection was conferred during the pre-treatment window, was specific for individual amino acids and depended on the identity of the focal amino acid, as well as the duration and intensity of its restriction. For instance, complete isoleucine deprivation for 7 days maximised its protective effect - increasing survival during nicotine exposure by 100%. However, a dose of 25% threonine was required to maximise its protective effect (53% enhanced survival). To understand the molecular basis of these effects, we modified the signalling of two cellular sensors of amino acids, GCN2 (General control non-derepressible) and mTORC1 (mechanistic Target of Rapamycin Complex 1) in combination with amino acid restriction. We found that GCN2 was necessary for diets to protect against nicotine, whereas suppression of mTORC1 was sufficient to induce nicotine resistance. This finding implies that amino acid restriction acts via amino acid signalling to cross-protect against seemingly unrelated stressors. Altogether, our study offers new insights into the physiological responses to restriction of individual amino acids that confer stress tolerance. This has broad potential for application in animal and human health.
Evolution during seed production for ecological restoration? A molecular analysis of 19 species finds only minor genomic changes
Authors: Conrady Malte , Lampei Christian , Bossdorf Oliver , Durka Walter , Bucharova Anna
Published: November 2021

A growing number of restoration projects require large amounts of seeds. As harvesting natural populations cannot cover the demand, wild plants are often propagated in large-scale monocultures. There are concerns that this cultivation process may cause genetic drift and unintended selection, which would alter the genetic properties of the cultivated populations and reduce their genetic diversity. Such changes could reduce the pre-existing adaptation of restored populations, and limit their adaptability to environmental change.

We used single nucleotide polymorphism (SNP) markers and a pool-sequencing approach to test for genetic differentiation and changes in gene diversity during cultivation in 19 wild grassland species, comparing the source populations and up to four consecutive cultivation generations grown from these sources. We then linked the magnitudes of genetic changes to the species’ breeding systems and seed dormancy, to understand the roles of these traits in genetic change.

The propagation of native seeds for ecosystem restoration changed the genetic composition of the cultivated generations only moderately. The genetic differentiation we observed as a consequence of cultivation was much lower than the natural genetic differentiation between different source regions, and the propagated generations harbored even higher gene diversity than wild-collected seeds. Genetic change was stronger in self-compatible species, probably as a result of increased outcrossing in the monocultures.

Synthesis and applications

Our study indicates that large-scale seed production maintains the genetic integrity of natural populations. Increased genetic diversity may even increase the adaptive potential of propagated seeds, which makes them especially suitable for ecological restoration. However, we have been working with seeds from Germany and Austria, where the seed production is regulated and certified. Whether other seed production systems perform equally well remains to be tested.