bluuebunny/crossref_metadata_2025 huggingface dataset:
CeLaVi: An Interactive Cell Lineage Visualisation Tool
Authors: Salvador-Martínez Irepan , Grillo Marco , Averof Michalis , Telford Maximilian J.
Published: December 2020

Recent innovations in genetics and imaging are providing the means to reconstruct cell lineages, either by tracking cell divisions using live microscopy, or by deducing the history of cells using molecular recorders. A cell lineage on its own, however, is simply a description of cell divisions as branching events. A major goal of current research is to integrate this description of cell relationships with information about the spatial distribution and identities of the cells those divisions produce. Visualising, interpreting and exploring these complex data in an intuitive manner requires the development of new tools. Here we present CeLaVi, a web-based visualisation tool that allows users to navigate and interact with a representation of cell lineages, whilst simultaneously visualising the spatial distribution, identities and properties of cells. CeLaVi’s principal functions include the ability to explore and manipulate the cell lineage tree; to visualise the spatial distribution of cell clones at different depths of the tree; to colour cells in the 3D viewer based on lineage relationships; to visualise various cell qualities on the 3D viewer (e.g. gene expression, cell type, tissue layer) and to annotate selected cells/clones. All these capabilities are demonstrated with four different example data sets. CeLaVi is available athttp://www.celavi.pro.
Sex-biased admixture and assortative mating shape genetic variation and influence demographic inference in admixed Cabo Verdeans
Authors: Korunes Katharine L , Soares-Souza Giordano Bruno , Bobrek Katherine , Tang Hua , Araújo Isabel Inês , Goldberg Amy , Beleza Sandra
Published: December 2020

Genetic data can provide insights into population history, but first we must understand the patterns that complex histories leave in genomes. Here, we consider the admixed human population of Cabo Verde to understand the patterns of genetic variation left by social and demographic processes. First settled in the late 1400s, Cabo Verdeans are admixed descendants of Portuguese colonizers and enslaved West African people. We consider Cabo Verde’s well-studied historical record alongside genome-wide SNP data from 563 individuals from 4 regions within the archipelago. We use genetic ancestry to test for patterns of nonrandom mating and sex-specific gene flow, and we examine the consequences of these processes for common demographic inference methods and for genetic patterns. Notably, multiple population genetic tools that assume random mating underestimate the timing of admixture, but incorporating non-random mating produces estimates more consistent with historical records. We consider how admixture interrupts common summaries of genomic variation such as runs-of-homozygosity (ROH). While summaries of ROH may be difficult to interpret in admixed populations, differentiating ROH by length class shows that ROH reflect historical differences between the islands in their contributions from the source populations and post-admixture population dynamics. Finally, we find higher African ancestry on the X chromosome than on the autosomes, consistent with an excess of European males and African females contributing to the gene pool. Considering these genomic insights into population history in the context of Cabo Verde’s historical record, we can identify how assumptions in genetic models impact inference of population history more broadly.
Transfer Learning for Predicting Virus-Host Protein Interactions for Novel Virus Sequences
Authors: Lanchantin Jack , Weingarten Tom , Sekhon Arshdeep , Miller Clint , Qi Yanjun
Published: December 2020

Viruses such as SARS-CoV-2 infect the human body by forming interactions between virus proteins and human proteins. However, experimental methods to find protein interactions are inadequate: large scale experiments are noisy, and small scale experiments are slow and expensive. Inspired by the recent successes of deep neural networks, we hypothesize that deep learning methods are well-positioned to aid and augment biological experiments, hoping to help identify more accurate virus-host protein interaction maps. Moreover, computational methods can quickly adapt to predict how virus mutations change protein interactions with the host proteins.

We propose DeepVHPPI, a novel deep learning framework combining a self-attention-based transformer architecture and a transfer learning training strategy to predict interactions between human proteins and virus proteins that have novel sequence patterns. We show that our approach outperforms the state-of-the-art methods significantly in predicting Virus–Human protein interactions for SARS-CoV-2, H1N1, and Ebola. In addition, we demonstrate how our framework can be used to predict and interpret the interactions of mutated SARS-CoV-2 Spike protein sequences.

Availability

We make all of our data and code available on GitHubhttps://github.com/QData/DeepVHPPI.

ACM Reference Format

Jack Lanchantin, Tom Weingarten, Arshdeep Sekhon, Clint Miller, and Yanjun Qi. 2021. Transfer Learning for Predicting Virus-Host Protein Interactions for Novel Virus Sequences. InProceedings of ACM Conference (ACM-BCB). ACM, New York, NY, USA, 10 pages. https://doi.org/??
Predicting the re-distribution of antibiotic molecules caused by inter-species interactions in microbial communities
Authors: Reding Carlos
Published: December 2020

Microbes associate in nature forming complex communities, but they are often studied in purified form. Here I show that neighbouring species enforce the re-distribution of carbon and antimicrobial molecules, predictably changing drug efficacy with respect to standard laboratory assays. A simple mathematical model, validated experimentally using pairwise competition assays, suggests that differences in drug sensitivity between the competing species causes the re-distribution of drug molecules without affecting carbon uptake. The re-distribution of drug is even when species have similar drug sensitivity, reducing drug efficacy. But when their sensitivities differ the re-distribution is uneven: The most sensitive species accumulates more drug molecules, increasing efficacy against it. Drug efficacy tests relying on samples with multiple species are considered unreliable and unpredictable, but study demonstrates that efficacy in these cases can be qualitatively predicted. It also suggests that living in communities can be beneficial even when all species compete for a single carbon source, as the relationship between cell density and drug required to inhibit their growth may be more complex than previously thought.
Potent SARS-CoV-2 binding and neutralization through maturation of iconic SARS-CoV-1 antibodies
Authors: Rouet Romain , Mazigi Ohan , Walker Gregory J. , Langley David B. , Sobti Meghna , Schofield Peter , Lenthall Helen , Jackson Jennifer , Ubiparipovic Stephanie , Henry Jake Y. , Abayasingam Arunasingam , Burnett Deborah , Kelleher Anthony , Brink Robert , Bull Rowena A. , Turville Stuart , Stewart Alastair G. , Goodnow Christopher C. , Rawlinson William D. , Christ Daniel
Published: December 2020

Antibodies against coronavirus spike protein potently protect against infection and disease, however it remains unclear if such protection can be extended to variant coronaviruses. This is exemplified by a set of iconic and well-characterized monoclonal antibodies developed after the 2003 SARS outbreak including mAbs m396, CR3022, CR3014 and 80R, which potently neutralize SARS-CoV-1, but not SARS-CoV-2. Here we explore antibody maturation strategies to change and broaden their specificity, enabling potent binding and neutralization of SARS-CoV-2. Using targeted mutagenesis as well as light chain shuffling on phage, we identified variants with considerably increased affinity and neutralization potential. The most potent antibody, derived from the NIH-developed mAb m396, neutralized live SARS-CoV-2 virus with a half-maximal inhibitory concentration (IC50) of 160 ng/ml. Intriguingly, while many of the matured clones maintained specificity of the parental antibody, new specificities were also observed, which was further confirmed by X-ray crystallography and cryo-electron microscopy, indicating that a limited set of antibodies can give rise to variants targeting diverse epitopes. Our findings open up over 15 years of antibody development efforts against SARS-CoV-1 to the SARS-CoV-2 field and outline general principles for the maturation of antibody specificity against emerging viruses.
Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel
Authors: Pérez-Conesa Sergio , Keeler Eric G. , Zhang Dongyu , Delemotte Lucie , McDermott Ann E.
Published: December 2020

As the first potassium channel with a X-ray structure determined, and given its homology to eukaryotic channels, the pH-gated prokaryotic channel KcsA has been extensively studied. Nevertheless, questions related in particular to the allosteric coupling between its gates remain open. The many currently available X-ray crystallography structures appear to correspond to various stages of activation and inactivation, offering insights into the molecular basis of these mechanisms. Since these studies have required mutations, complexation with antibodies, and substitution of detergents in place of lipids, examining the channel under more native conditions is desirable. Solid-state NMR (SSNMR) can be used to study the wild-type protein under activating conditions (low pH), at room temperature, and in bacteriomimetic liposomes. In this work, we sought to structurally assign the activated state present in SSNMR experiments. We used a combination of molecular dynamics (MD) simulations, chemical shift prediction algorithms, and Bayesian inference techniques to determine which of the most plausible X-ray structures resolved to date best represents the activated state captured in SSNMR. We first identified specific nuclei with simulated NMR chemical shifts that differed significantly when comparing partially open vs. fully open ensembles from MD simulations. The simulated NMR chemical shifts for those specific nuclei were then compared to experimental ones, revealing that the simulation of the partially open state was in good agreement with the SSNMR data. Nuclei that discriminate effectively between partially and fully open states belong to residues spread over the sequence and provide a molecular level description of the conformational change.
Information flow, cell types and stereotypy in a full olfactory connectome
Authors: Schlegel Philipp , Bates Alexander S. , Stürner Tomke , Jagannathan Sridhar R. , Drummond Nikolas , Hsu Joseph , Capdevila Laia Serratosa , Javier Alexandre , Marin Elizabeth C. , Barth-Maron Asa , Tamimi Imaan F. M. , Li Feng , Rubin Gerald M. , Plaza Stephen M. , Costa Marta , Jefferis Gregory S.X.E.
Published: December 2020

Thehemibrainconnectome provides large scale connectivity and morphology information for the majority of the central brain ofDrosophila melanogaster. Using this data set, we provide a complete description of theDrosophilaolfactory system, covering all first, second and lateral horn-associated third-order neurons. We develop a generally applicable strategy to extract information flow and layered organisation from connectome graphs, mapping olfactory input to descending interneurons. This identifies a range of motifs including highly lateralised circuits in the antennal lobe and patterns of convergence downstream of the mushroom body and lateral horn. Leveraging a second data set we provide a first quantitative assessment of inter – versus intra-individual stereotypy. Comparing neurons across two brains (three hemispheres) reveals striking similarity in neuronal morphology across brains. Connectivity correlates with morphology and neurons of the same morphological type show similar connection variability within the same brain as across two brains.
A CRISPR endonuclease gene drive reveals two distinct mechanisms of inheritance bias
Authors: Verkuijl Sebald A. N. , Gonzalez Estela , Li Ming , Ang Joshua , Kandul Nikolay P. , Anderson Michelle A. E. , Akbari Omar S. , Bonsall Michael B. , Alphey Luke
Published: December 2020

RNA guided CRISPR gene drives have shown the capability of biasing transgene inheritance in multiple species. Among these, homing endonuclease drives are the most developed. In this study, we report the functioning ofsds3, bgcn, andnup50expressed Cas9 in anAedes aegyptihoming split drive system targeting thewhitegene. We report their inheritance biasing capability, propensity for maternal deposition, and zygotic/somatic expression. Additionally, by making use of the tight linkage ofwhiteto the sex-determining locus, we were able to elucidate mechanisms of inheritance bias. We find inheritance bias through homing in double heterozygous males, but find that a previous report of the same drive occurred through meiotic drive. We propose that other previously reported ‘homing’ design gene drives may in fact bias their inheritance through other mechanisms with important implications for gene drive design.
A systematic analysis of rodent models implicates adipogenesis and innate immunity in pathogenesis of fatty liver disease
Authors: Im Yu Ri , Hunter Harriet , de Gracia Hahn Dana , Duret Amedine , Cheah Qinrong , Dong Jiawen , Fairey Madison , Hjalmarsson Clarissa , Li Alice , Lim Hong Kai , McKeown Lorcán , Mitrofan Claudia-Gabriela , Rao Raunak , Utukuri Mrudula , Rowe Ian A. , Mann Jake P.
Published: December 2020

Animal models of human disease are a key component of translational research and yet there is often no consensus on which model is optimal for a particular disease. Here, we generated a database of 3,920 rodent models of non-alcoholic fatty liver disease (NAFLD). Study designs were highly heterogeneous therefore few models had been cited more than once. Analysis of genetic models provided evidence for the role of adipose dysfunction and perturbation of the innate immune system in the progression of NAFLD. We identified that high-fat, high-fructose diets most closely recapitulate the human phenotype of NAFLD. There was substantial variability in the nomenclature of animal models; a consensus on terminology of specialist diets is needed. More broadly, this analysis demonstrates the variability in preclinical study design, which has implications for the reproducibility ofin vivoexperiments.
Data Descriptor: Proteomic profiling across breast cancer cell lines and models
Authors: Kalocsay Marian , Berberich Matthew J. , Everley Robert A. , Nariya Maulik K. , Chung Mirra , Gaudio Ben , Victor Chiara , Bradshaw Gary A. , Hafner Marc , Sorger Peter K. , Mills Caitlin E. , Subramanian Kartik
Published: December 2020

We performed quantitative proteomics on 61 human-derived breast cancer cell lines to a depth of ~13,000 proteins. The resulting high-throughput datasets were assessed for quality and reproducibility. We used the datasets to identify and characterize the subtypes of breast cancer and showed that they conform to known transcriptional subtypes, revealing that molecular subtypes are preserved even in under-sampled protein feature sets. All datasets are freely available as public resources on the LINCS portal. We anticipate that these datasets, either in isolation or in combination with complimentary measurements such as genomics, transcriptomics and phosphoproteomics, can be mined for the purpose of predicting drug response, informing cell line specific context in models of signalling pathways, and identifying markers of sensitivity or resistance to therapeutics.
Connecting the dots between root cross-section images and modelling tools to create a high resolution root system hydraulic maps inZea mays
Authors: Heymans Adrien , Couvreur Valentin , Lobet Guillaume
Published: December 2020

Root hydraulic properties play a central role in the global water cycle, agricultural systems productivity, and ecosystem survival as they impact the global canopy water supply. However, the available experimental methods to quantify root hydraulic conductivities, such as the root pressure probing, are particularly challenging and their applicability on thin roots and small root segments is limited. There is a gap in methods enabling easy estimations of root hydraulic conductivities across a diversity of root types and at high resolution along root axes.

In this case study, we analysedZea mays(maize) plants of the var.B73that were grown in pots for 14 days. Root cross-section data were used to extract anatomical measurements. We used the Generator of Root Anatomy in R (GRANAR) model to generate root anatomical networks from anatomical features. Then we used the Model of Explicit Cross-section Hydraulic Anatomy (MECHA) to compute an estimation of the root axial and radial hydraulic conductivities (kxandkr, respectively), based on the generated anatomical networks and cell hydraulic properties from the literature.

The root hydraulic conductivity maps obtained from the root cross-sections suggest significant functional variations along and between different root types. Predicted variations ofkralong the root axis were strongly dependent on the maturation stage of hydrophobic barriers. The same was also true for the maturation rates of the metaxylem. The different anatomical features, as well as their evolution along the root type add significant variation to thekrestimation in between root type and along the root axe.

Under the prism of root types, anatomy, and hydrophobic barriers, our results highlight the diversity of root radial and axial hydraulic conductivities, which may be veiled under low-resolution measurements of the root system hydraulic conductivity. While predictions of our root hydraulic maps match the range and trend of measurements reported in the literature, future studies could focus on the quantitative validation of hydraulic maps. From now on, a novel method, which turns root cross-section images into hydraulic maps will offer an inexpensive and easily applicable investigation tool for root hydraulics, in parallel to root pressure probing experiments.

One-Sentence summary

The use of cross-section images and modelling tools to generate a map the axial and radial hydraulic conductivity along different root types for the maize cultivar B73.
Plasmodium falciparumserology: A comparison of two protein production methods for analysis of antibody responses by protein microarray
Authors: Oulton Tate , Obiero Joshua , Rodriguez Isabel , Ssewanyana Isaac , Dabbs Rebecca A. , Greenhouse Bryan , Drakeley Chris , Felgner Phil L. , Stone Will , Tetteh Kevin K.A.
Published: December 2020

The evaluation of protein antigens as putative serologic biomarkers of infection has increasingly shifted to high-throughput, multiplex approaches such as the protein microarray. In vitro transcription/translation (IVTT) systems – a similarly high-throughput protein expression method – are already widely utilised in the production of protein microarrays, though purified recombinant proteins derived from more traditional whole cell based expression systems also play an important role in biomarker characterisation. Here we have performed a side-by-side comparison of antigen-matched protein targets from an IVTT and purified recombinant system, on the same protein microarray. The magnitude and range of antibody responses to purified recombinants was found to be greater than that of IVTT proteins, and responses between targets from different expression systems did not clearly correlate. However, responses between amino acid sequence-matched targets from each expression system were more closely correlated. Despite the lack of a clearly defined relationship between antigen-matched targets produced in each expression system, our data indicate that protein microarrays produced using either method can be used confidently, in a context dependent manner, though care should be taken when comparing data derived from contrasting approaches.

Statement of significance of the study

Protein microarray technology is increasingly being realised as a powerful tool in disease biomarker identification. Protein-based, serologic arrays are already well utilised in the characterisation of antibody responses to the malarialPlasmodium spp., drastically improving throughput and efficiency compared to more typical experimental assays. Such approaches have commonly made use of in vitro transcription/translation (IVTT) protein expression systems, though other protein expression methods are regularly employed. In this study we have directly compared antibody responses in a malaria endemic population, to matched protein antigens derived from both an IVTT and purified bacterial recombinant system in the same protein microarray. We demonstrated that the magnitude of measured antibody response to matched protein antigens tends to be greater to purified recombinants, rather than IVTT products. Further, our analysis showed highly variable levels of correlation of response between antigen-matched targets derived from each expression system, although relationships in antibody response were stronger between proteins with overlapping amino acid sequences. This study highlights the importance of considering the strengths and weaknesses of each expression system in the context of a protein microarray according to experimental hypotheses, and illustrates the need for attention when comparing data generated by these different methodologies.
Phase separation of Mer2 organizes the meiotic loop-axis structure of chromatin during meiosis I
Authors: Tsai Bin , Liu Wei , Dong Dashan , Shi Kebin , Chen Liangyi , Gao Ning
Published: December 2020

Sexually reproducing organisms acquire genetic diversity through meiotic recombination during meiosis I, which is initiated via programmed DNA double-strand breaks (DSBs) induced by Spo11-containing machinery in each meiotic cell. The combination of programmed DSB sites in each meiotic cell must be diverse, which requires a certain degree of randomness in the distribution of DSBs. The formation of programmed DSBs requires a preestablished loop-axis structure of chromatin. Here, we demonstrate that the axial element protein Mer2 undergoes liquid-liquid phase separationin vitroandin vivothrough its intrinsically disordered C-terminal domain. A DNA binding motif within its central domain is responsible for bringing DNA into Mer2 liquid droplets and Mer2-DNA complex could assemble into filamentous structures extending from the droplets. These results suggest that phase separation of Mer2 drives the formation of a droplet-loop structure of meiotic chromatin to facilitate and to diversify programmed DSB formation.
Whole-brain connectivity atlas of glutamatergic and GABAergic neurons in mouse dorsal and median raphe nucleus
Authors: Xu Zhengchao , Feng Zhao , Zhao Mengting , Sun Qingtao , Deng Lei , Jia Xueyan , Jiang Tao , Luo Pan , Chen Wu , Yuan Jing , Li Xiangning , Gong Hui , Luo Qingming , Li Anan
Published: December 2020

The dorsal raphe nucleus (DR) and median raphe nucleus (MR) contain populations of glutamatergic and GABAergic neurons regulating diverse behavioral functions. Their whole-brain input-output circuits remain incompletely understood. We used viral tracing combined with fluorescence micro-optical sectioning tomography to generate a comprehensive whole-brain atlas of inputs and outputs of glutamatergic and GABAergic neurons in the DR and MR. We discovered that these neurons receive inputs from similar upstream brain regions. The glutamatergic and GABAergic neurons in the same raphe nucleus have divergent projection patterns with differences in critical brain regions. Specifically, MR glutamatergic neurons project to the lateral habenula via multiple pathways. Correlation and cluster analysis indicated that glutamatergic and GABAergic neurons in the same raphe nucleus receive inputs from heterogeneous neurons in upstream brain regions and send different collateral projections. This connectivity atlas provides insights into the cell heterogeneity, anatomical connectivity and behavioral functions of the raphe nucleus.
DnaJC7 binds natively folded structural elements in tau to inhibit amyloid formation
Authors: Hou Zhiqiang , Wydorski Pawel M. , Perez Valerie A. , Mendoza-Oliva Aydé , Ryder Bryan D. , Mirbaha Hilda , Kashmer Omar , Joachimiak Lukasz A.
Published: December 2020

Molecular chaperones, including Hsp70/Hsp40 families, play central roles in binding substrates to prevent their aggregation. How Hsp40s select different conformations of substrates remains poorly understood. Here, we report a novel interaction between the Hsp40 DnaJC7 and tau that efficiently suppresses tau aggregationin vitroand in cells. DnaJC7 binds preferentially to natively folded wild-type tau, but disease-associated mutants in tau reduce chaperone binding affinity. We identify that DnaJC7 uses a single TPR domain to recognize a β-turn element in tau that contains the275VQIINK280amyloid motif. Wild-type tau β-turn fragments, but not mutant fragments, can block full-length tau binding to DnaJC7. These data suggest DnaJC7 preferentially binds and stabilizes natively folded conformations of tau to prevent tau conversion into amyloids. This identifies a novel mechanism of tau aggregation regulation that can be exploited as both a diagnostic and a therapeutic intervention.
HISAT-3N: a rapid and accurate three-nucleotide sequence aligner
Authors: Zhang Yun , Park Chanhee , Bennett Christopher , Thornton Micah , Kim Daehwan
Published: December 2020

Nucleotide conversion sequencing technologies such as bisulfite-seq and SLAM-seq are powerful tools to explore the intricacies of cellular processes. In this paper, we describe HISAT-3N (hierarchical indexing for spliced alignment of transcripts - 3 nucleotides), which rapidly and accurately aligns sequences consisting of nucleotide conversions by leveraging powerful hierarchical index and repeat index algorithms originally developed for the HISAT software. Tests on real and simulated data sets demonstrate that HISAT-3N is over 7 times faster, has greater alignment accuracy, and has smaller memory requirements than other modern systems. Taken together HISAT-3N is the ideal aligner for use with converted sequence technologies.
RORα enforces stability of the T-helper-17 cell effector program
Authors: Lee June-Yong , Hall Jason A. , Pokrovskii Maria , Kroehling Lina , Wu Lin , Littman Dan R.
Published: December 2020

T helper 17 (Th17) cells regulate mucosal barrier defenses, but also promote multiple autoinflammatory diseases. Although many molecular determinants of Th17 cell differentiation have been described, the transcriptional programs that sustain Th17 cellsin vivoremain obscure. The transcription factor RORγt is critical for Th17 cell differentiation, but a distinct role of the closely-related RORα, which is co-expressed in Th17 cells, is not known. Here we demonstrate that, although dispensable for Th17 cell differentiation, RORα governs optimal Th17 responses in peripheral tissues. Thus, the absence of RORα in T cells led to significant reductions in both RORγt expression and effector function amongst Th17 cells, due to need for cooperative RORα and RORγt binding to a newly-identifiedRorcenhancer element that is essential for Th17 lineage maintenancein vivo. Altogether, these data point to a non-redundant role of RORα in Th17 lineage maintenance via reinforcement of the RORγt transcriptional program.
Detection of PD-L1-expressing myeloid cell clusters in the hyaluronan-enriched stroma in tumor tissue and tumor-draining lymph nodes
Authors: Dominguez-Gutierrez Paul R. , Kwenda Elizabeth , Donelan William , O’Malley Padraic , Crispen Paul L. , Kusmartsev Sergei
Published: December 2020

Expression of the transmembrane protein PD-L1 is frequently up-regulated in cancer. Since PD-L1-expressing cells can induce apoptosis or anergy of T lymphocytes through binding to PD1 receptor, the PD-L1-mediated inhibition of activated PD1+T cells considered as a major pathway for tumor immune escape. However, the mechanisms that regulate the expression of PD-L1 in the tumor microenvironment not fully understood. Analysis of organotypic tumor tissue slice cultures, obtained from tumor-bearing mice as well as from cancer patients, revealed that tumor-associated hyaluronan (HA) supports the development of the immunosuppressive PD-L1+macrophages. Using genetically modified tumor cells, we identified both epithelial tumor cells and cancer-associated fibroblasts (CAFs) as the major source of HA in the tumor microenvironment. HA-producing tumor cells and, in particular CAFs of bone marrow origin, directly interact with tumor-recruited Hyal2+myeloid cells forming the large stromal congregates/clusters that are highly enriched for both HA and PD-L1. Furthermore, similar cell clusters comprising of HA-producing fibroblasts and PD-L1+macrophages were detected in the tumor-draining lymph nodes. Collectively, our findings indicate that the formation of multiple large HA-enriched stromal clusters that support the development of PD-L1-expressing antigen-presenting cells in the tumor microenvironment and draining lymph nodes could contribute to the immune escape and resistance to immunotherapy in cancer.
Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae
Authors: Mangkalaphiban Kotchaphorn , He Feng , Ganesan Robin , Wu Chan , Baker Richard , Jacobson Allan
Published: December 2020

Translation of mRNA into a polypeptide is terminated when the release factor eRF1 recognizes a UAA, UAG, or UGA stop codon in the ribosomal A site and stimulates nascent peptide release. However, stop codon readthrough can occur when a near-cognate tRNA outcompetes eRF1 in decoding the stop codon, resulting in the continuation of the elongation phase of protein synthesis. At the end of a conventional mRNA coding region, readthrough allows translation into the mRNA 3’-UTR. Previous studies with reporter systems have shown that the efficiency of termination or readthrough is modulated by cis-acting elements other than stop codon identity, including two nucleotides 5’ of the stop codon, six nucleotides 3’ of the stop codon in the ribosomal mRNA channel, and stem-loop structures in the mRNA 3’-UTR. It is unknown whether these elements are important at a genome-wide level and whether other mRNA features proximal to the stop codon significantly affect termination and readthrough efficiencies in vivo. Accordingly, we carried out ribosome profiling analyses of yeast cells expressing wild-type or temperature-sensitive eRF1 and developed bioinformatics strategies to calculate readthrough efficiency, and to identify mRNA and peptide features which influence that efficiency. We found that the stop codon (nt +1 to +3), the nucleotide after it (nt +4), the codon in the P site (nt -3 to -1), and 3’-UTR length are the most influential features in the control of readthrough efficiency, while nts +5 to +9 and mRNA secondary structure in the 3’-UTR had milder effects. Additionally, we found low readthrough genes to have shorter 3’-UTRs compared to high readthrough genes in cells with thermally inactivated eRF1, while this trend was reversed in wild-type cells. Together, our results demonstrated the general roles of known regulatory elements in genome-wide regulation and identified several new mRNA or peptide features affecting the efficiency of translation termination and readthrough.

AUTHOR SUMMARY

Of the 64 codons that exist for translation of the genetic code into a polypeptide chain, only UAA, UAG, and UGA signify termination of continued protein synthesis. However, the efficiency of termination is not the same for different mRNAs and is likely influenced by mRNA sequences proximal to these “stop” codons. Here, we sought to expand current understanding of termination efficiency to a genome-wide scale. Our analysis identifies novel mRNA features that may regulate the efficiency of translation termination, including the identities of the stop codon, the penultimate codon, the proximal nucleotides, and the length of mRNA 3’-untranslated region. As ∼11% of human diseases are caused by mutations that introduce premature stop codons, resulting in both accelerated mRNA decay and truncated protein product, our findings are valuable for understanding and developing therapeutics targeting the termination step of mRNA translation.
Trait Evolution in Microbial Communities
Authors: Zhao Lihong , Ridenhour Benjamin J , Remien Christopher H
Published: December 2020

Understanding the evolutionary dynamics of microbial communities is a key step towards the goal of predicting and manipulating microbiomes to promote beneficial states. While interactions within microbiomes and between microbes and their environment collectively determine the community composition and population dynamics, we are often concerned with traits or functions of a microbiome that link more directly to host health. To study how traits of a microbiome are impacted by eco-evolutionary dynamics, we recast a classic resource-mediated population dynamic model into a population genetic framework which incorporates traits. The relative fitness of each group of microbes can be explicitly written in terms of population dynamic parameters, and corresponding evolutionary dynamics emerge. Using several example systems, we demonstrate how natural selection, mutation, and shifts in the environment work together to produce changes in traits over time.
Pitfalls in Post Hoc Analyses of Population Receptive Field Data
Authors: Stoll Susanne , Infanti Elisa , de Haas Benjamin , Schwarzkopf D. Samuel
Published: December 2020

Data binning involves grouping observations into bins and calculating bin-wise summary statistics. It can cope with overplotting and noise, making it a versatile tool for comparing many observations. However, data binning goes awry if the same observations are used for binning (selection) and contrasting (selective analysis). This creates circularity, biasing noise components and resulting in artifactual changes in the form of regression towards the mean. Importantly, these artifactual changes are a statistical necessity. Here, we use (null) simulations and empirical repeat data to expose this flaw in the scope of post hoc analyses of population receptive field data. In doing so, we reveal that the type of data analysis, data properties, and circular data cleaning are factors shaping the appearance of such artifactual changes. We furthermore highlight that circular data cleaning and circular sorting of change scores are selection practices that result in artifactual changes even without circular data binning. These pitfalls might have led to erroneous claims about changes in population receptive fields in previous work and can be mitigated by using independent data for selection purposes. Our evaluations highlight the urgency for us researchers to make the validation of analysis pipelines standard practice.

Graphical abstract

Highlights

Circular data binning produces artifactual changes in the form of regression towards the mean

Analysis type, data properties, and circular data cleaning shape these artifactual changes

Circular data cleaning and sorting produce artifactual changes even without circular data binning
Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations
Authors: ter Horst Anneliek M. , Santos-Medellín Christian , Sorensen Jackson W. , Zinke Laura A. , Wilson Rachel M. , Johnston Eric R. , Trubl Gareth G. , Pett-Ridge Jennifer , Blazewicz Steven J. , Hanson Paul J. , Chanton Jeffrey P. , Schadt Christopher W. , Kostka Joel E. , Emerson Joanne B.
Published: December 2020

Background

Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared to our curated PIGEON database of 266,805 vOTUs from diverse ecosystems.

Results

Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH4and CO2concentrations, but not with temperature during the first two years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4,326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,372 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 1.9% of 78,203 genus-level viral clusters (VCs) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared to total metagenomes.

Conclusions

Results suggest strong viral “species” boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at the “genus” level. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics.
Microbiome and Metabolome driven differentiation of TGF-β producing Tregs leads to Senescence and HIV latency
Authors: Ghneim Khader , Sharma Ashish Arunkumar , Ribeiro Susan Pereira , Fourati Slim , Ahlers Jeffrey , Kulpa Deanna , Xu Xuan , Brehm Jessica , Talla Aarthi , Arumugam Sahaana , Darko Samuel , Rodriguez Benigno , Shive Carey , Cristescu Razvan , Loboda Andrey , Balderas Robert , Wang I-Ming , Hunt Peter , Lamarre Daniel , Douek Daniel , Hazuda Daria , Lederman Michael M. , Deeks Steven , Sekaly Rafick-Pierre
Published: December 2020

Current therapeutic interventions to eradicate latent HIV (“reservoir”) and restore immune function in ART-treated HIV infection have yet to show efficacy. To explore mechanisms of HIV persistence, we apply an integrated systems biology approach and identify a distinct group of individuals with poor CD4 T-cell reconstitution (Immunologic non-responders, “INRs”) and high frequencies of cells with inducible HIV. Contrary to the prevailing notion that immune activation drives HIV persistence and immune dysfunction, peripheral blood leukocytes from these subjects have enhanced expression of a network of genes regulated by cellular senescence driving transcription factors (TFs) FOXO3, SMAD2 and IRF3. In these subjects, increased frequencies of regulatory T cells and expression of the TGF-β signaling cascade are complimented by the downregulation of cell cycle, metabolic and pro-inflammatory pathways. Lactobacillaceae family and metabolites (members of the butyrate family – i.e. α-ketobutyrate) were correlated with Treg frequencies in “Senescent-INRs”ex vivo,triggered the differentiation of TGF-β producing Tregs and promoted HIV latency establishmentin vitro.These cascades, downstream of PD-1/TGF-β, prevent memory T cell differentiation and are associated with an increase in frequencies of cells with inducible HIVex vivo.Our findings identify cellular senescence responses that can be targeted by PD-1 or TGF-β specific interventions that have shown safety and efficacy in cancer, and may prove to be crucial for HIV eradication.
Dectin-1 mediated DC-SIGN Recruitment toCandida albicansContact Sites
Authors: Choraghe Rohan P. , Neumann Aaron K.
Published: December 2020

At host-pathogen contact sites withCandida albicans, Dectin-1 activates pro-inflammatory signaling, while DC-SIGN promotes adhesion to the fungal surface. We observed that Dectin-1 and DC-SIGN collaborate to enhance capture/retention ofC. albicansunder fluid shear culture conditions. Therefore, we devised a cellular model system wherein we could investigate the interaction between these two receptors during the earliest stages of host-pathogen interaction. In cells expressing both receptors, DC-SIGN was quickly recruited to contact sites (103.15% increase) but Dectin-1 did not similarly accumulate. Once inside the contact site, FRAP studies revealed a strong reduction in lateral mobility of DC-SIGN (but not Dectin-1), consistent with DC-SIGN engaging in multivalent adhesive binding interactions with cell wall mannoprotein ligands. Interestingly, in the absence of Dectin-1 co-expression, DC-SIGN recruitment to the contact was much poorer—only 35.04%. These data suggested that Dectin-1 promotes the active recruitment of DC-SIGN to the contact site. We proposed that Dectin-1 signaling activates the RHOA pathway, leading to actomyosin contractility that promotes DC-SIGN recruitment, perhaps via the formation of a centripetal ActoMyosin Flow (AMF) directed into the contact site. Indeed, RHOA pathway inhibitors significantly reduced Dectin-1 associated DC-SIGN recruitment to the contact site. We used agent based modeling to predict DC-SIGN transport kinetics with (“Directed+Brownian”) and without (“Brownian”) the hypothesized actomyosin flow-mediated transport. The Directed+Brownian transport model predicted a DC-SIGN contact site recruitment (108.72%), similar to that we observed experimentally under receptor co-expression. Brownian diffusive transport alone predicted contact site DC-SIGN recruitment of only 54.02%. However, this value was similar to experimentally observed recruitment in cells without Dectin-1 or treated with RHOA inhibitor, suggesting that it accurately predicted DC-SIGN recruitment when a contact site AMF would not be generated. TIRF microscopy of nascent cell contacts on glucan-coated glass revealed Dectin-1 dependent DC-SIGN and F-actin (LifeAct) recruitment kinetics to early-stage contact site membranes. DC-SIGN entry followed F-actin with a temporal lag of 8.35 ± 4.57 seconds, but this correlation was disrupted by treatment with RHOA inhibitor. Thus, computational and experimental evidence provides support for the existence of a Dectin-1/RHOA-dependent AMF that produces a force to drive DC-SIGN recruitment to pathogen contact sites, resulting in improved pathogen capture and retention by immunocytes. These data suggest that the rapid collaborative response of Dectin-1 and DC-SIGN in early contact sties might be important for the efficient acquisition of yeast under flow conditions, such as those that prevail in circulation or mucocutaneous sites of infection.
Understanding nanoscale structural distortions in Pb(Zr0.2Ti0.8)O3 by utilizing X-ray nanodiffraction and clustering algorithm analysis
Authors: Christiansen-Salameh Joyce , Yang Morris , Rippy Geoffrey , Li Jianheng , Cai Zhonghou , Holt Martin , Agnus Guillaume , Maroutian Thomas , Lecoeur Philippe , Matzen Sylvia , Kukreja Roopali
Published: December 2020

Hard X-ray nanodiffraction provides a unique nondestructive technique to quantify local strain and structural inhomogeneities at nanometer length scales. However, sample mosaicity and phase separation can result in a complex diffraction pattern that can make it challenging to quantify nanoscale structural distortions. In this work, a k-means clustering algorithm was utilized to identify local maxima of intensity by partitioning diffraction data in a three-dimensional feature space of detector coordinates and intensity. This technique has been applied to X-ray nanodiffraction measurements of a patterned ferroelectric PbZr0.2Ti0.8O3 sample. The analysis reveals the presence of two phases in the sample with different lattice parameters. A highly heterogeneous distribution of lattice parameters with a variation of 0.02 Å was also observed within one ferroelectric domain. This approach provides a nanoscale survey of subtle structural distortions as well as phase separation in ferroelectric domains in a patterned sample.
Tunable side-bounce monochromator
Authors: Hong Hawoong , Tischler Jonathan , Shi Xianbo , Highland Matthew
Published: December 2020

Side-bounce beamlines with fixed-exit angles have been intended to operate with only one selected energy. However, a tunable monochromator in a new geometry is presented here that will make side-bounce beamlines energy tunable. It requires the addition of two more rotations. Analytic solutions for the values of these two rotation angles are provided. The validity of the new concept was checked by ray tracing and two-dimensional searches in the additional angles. Operational details on the new scheme, including the exit offset and steering of the beams, were determined. In addition to tunability, the new monochromator will reduce the loss from the polarization factor at low energies.
The perceptions on the recent COVID-19 pandemic: a study on health-care students in Malaysia
Authors: Mohd Zain Norhayati , Che Mut Nur Anis Izzati
Published: December 2020

Purpose

The purpose of this paper is to study the perception of health-care students on the recent COVID-19 pandemic in Malaysia. There was one study by Caliskhan et al. (2020) conducted among Turkish final-year medical students showed that the students were knowledgeable about and aware of the COVID-19 pandemic. To the authors’ knowledge, there are limited number of studies conducted among health-care students in Malaysia.

Design/methodology/approach

The online questionnaire was randomly distributed to the health-care students in Malaysia. The questionnaire consists of socio-demographic data and perceptions on COVID-19. Descriptive analysis was used to analyse the perceptions of the health-care students on COVID-19.

Findings

Health-care students in Malaysia have positive perceptions on COVID-19, and it did not give huge impact of their interest in this health-care field. Thus, it is important that this issue is investigated, and the perceptions of health-care students on COVID-19 can be highlighted.

Research limitations/implications

The strength of this study was the participation from the health-care students from various institutions, which have different experience and backgrounds. The study was limited on the items of question utilised. Due to the limited time and urgency of the survey, the authors were unable to study their knowledge, attitudes and way they are going to cope with this kind of pandemic as the students and as future health-care workers.

Originality/value

The paper points out the effect on the recent COVID-19 pandemic on health-care students in Malaysia. It also points out the perceptions of health-care students in Malaysia on the current pandemic. It is expected that the results of this research would serve as baseline data for health-care institutions in Malaysia to continue equip the future front liners that can adapt future challenges.