bluuebunny/crossref_metadata_2025 huggingface dataset:
Conserved Keratin Gene Clusters in Ancient Fish: an Evolutionary Seed for Terrestrial Adaptation
Authors: Kimura Yuki , Nikaido Masato
Published: May 2020

Type I and type II keratins are subgroups of intermediate filament proteins that provide toughness to the epidermis and protect it from water loss. In terrestrial vertebrates, the keratin genes form two major clusters, clusters 1 and 2, each of which is dominated by type I and II keratin genes. By contrast, such clusters are not observed in teleost fish. Although the diversification of keratins is believed to have made a substantial contribution to terrestrial adaptation, its evolutionary process has not been clarified. Here, we performed a comprehensive genomic survey of the keratin genes of a broad range of vertebrates. As a result, we found that ancient fish lineages such as elephant shark, reedfish, spotted gar, and coelacanth share both keratin gene clusters. We also discovered an expansion of keratin genes that form a novel subcluster in reedfish. Syntenic and phylogenetic analyses revealed that two pairs ofkrt18/krt8keratin genes were shared among all vertebrates, thus implying that they encode ancestral type I and II keratin protein sets. We further revealed that distinct keratin gene subclusters, which show specific expressions in the epidermis of adult amphibians, stemmed from canonical keratin genes in non-terrestrial ancestors. Molecular evolutionary analyses suggested that the selective constraints were relaxed in the adult epidermal subclusters of amphibians as well as the novel subcluster of reedfish. The results of the present study represent the process of diversification of keratins through a series of gene duplications that could have facilitated the terrestrial adaptation of vertebrates.

Highlights

Two major keratin clusters are conserved from sharks to terrestrial vertebrates.

Adult epidermis-specific keratins in amphibians stem from the two major clusters.

A novel keratin gene subcluster was found in reedfish.

Ancestralkrt18/krt8gene sets were found in all vertebrates.

Functional diversification signatures were found in reedfish and amphibian keratins.
AtPIG-S, a predicted Glycosylphosphatidylinositol Transamidase Subunit, is critical for pollen tube growth in Arabidopsis
Authors: Desnoyer Nick , Howard Greg , Jong Emma , Palanivelu Ravishankar
Published: May 2020

Background

Glycosylphosphatidylinositol (GPI) addition is one of the several post-translational modifications to proteins that increase their affinity for membranes. In eukaryotes, the GPI transamidase complex (GPI-T) catalyzes the attachment of pre-assembled GPI anchors to GPI-anchored proteins (GAPs) through a transamidation reaction. A mutation inAtGPI8(gpi8-2), the putative catalytic subunit of GPI-T in Arabidopsis, is transmitted normally through the female gametophyte (FG), indicating the FG tolerates loss of GPI transamidation. In contrast,gpi8-2almost completely abolishes male gametophyte (MG) function. Still, the unexpected finding thatgpi8-2FGs function normally requires further investigation. Additionally, specific developmental defects in the MG caused by loss of GPI transamidation remain poorly characterized.

Results

Here we investigated the effect of loss ofAtPIG-S,another GPI-T subunit, in both gametophytes. Likegpi8-2, we showed that a mutation inAtPIG-S(pigs-1) disrupted synergid localization of LORELEI (LRE), a putative GAP critical for pollen tube reception by the FG, yet is transmitted normally through the FG. Conversely,pigs-1severely impaired male gametophyte (MG) function during pollen tube emergence and growth in the pistil. ApPIGS:PIGS-GFPtransgene complemented these MG defects and enabled generation ofpigs-1/pigs-1seedlings, but seemingly failed to rescue the function of AtPIG-S in the sporophyte, aspigs-1/pigs-1, pPIGS:PIGS-GFPseedlings died soon after germination.

Conclusions

Characterization ofpigs-1provided further evidence that the FG tolerates loss of GPI transamidation more than the MG and that the MG compared to the FG may be a better haploid system to study the role of GPI-anchoring.pigs-1pollen develops normally and thus represent a tool in which GPI anchor biosynthesis and transamidation of GAPs have been uncoupled, offering a potential way to study free GPI in plant development. While previously reported male fertility defects of GPI biosynthesis mutants could have been due either to loss of GPI or GAPs lacking the GPI anchor, our results clarified that the loss of mature GAPs underlie male fertility defects of GPI-deficient pollen grains, aspigs-1is defective only in the downstream transamidation step. Our study also provided further evidence that GPI transamidation is essential in seedling development.
The Conquering influence of the Nano extracts of pomegranate peels and pistachio leaves in amelioration of acute liver failure
Authors: Hassan Sohair Aly , Hammam Olfat , Hussein Sahar Awdallah , Aziz Wessam Magdi
Published: May 2020

Objective

Acute liver failure (ALF) is a clinical condition with an unclear history of pathophysiology, making it a challenging task for scientists to reverse the disease in its initial phase and to help the liver re-function as usual: this study was proposed to estimate the hepatoprotective effects of Punicagranatum peel andPistaciaatlanticaleaves as a multi-rich antioxidants ingredients either in their normal and/or in their nano forms against thioacetamide induced acute liver failure in a rodent model.

Method

Sixty male Wistar rats were divided into six equal groups, the first group employed as a control; the second group was given a dose of thioacetamide (TAA)-350 mg/bwip., from the third to the sixth group received TAA □ 2ml of 100gm of aqueous extracts ofPunicagranatumLandPistaciaatlanticaeither in their normal and/or Nano forms consecutively along 2 weeks.

Results

recorded significant elevation in liver enzymes, lipid profiles, LPO and NO with marked significant decrease in GSH and SOD accompanied by elevation in inflammatory cytokine (IL6,TNF-α and AFP) in addition to a noticeable increase in HSP70level & degradation in DNA respectively in TAA challenged group. However significant and subsequent amelioration of most of the impaired markers has been observed with ipnano treatment of both extracts.

Conclusion

The current results highlighted the high performance of both plant nano extracts and their hepatoprotective impact and their possible therapeutic role in the amelioration of TAA induced acute liver failure in experimental animals.
Functional brain age prediction suggests accelerated aging in preclinical familial Alzheimer’s disease, irrespective of fibrillar amyloid-beta pathology
Authors: Gonneaud Julie , Baria Alex T. , Binette Alexa Pichet , Gordon Brian A. , Chhatwal Jasmeer P. , Cruchaga Carlos , Jucker Mathias , Levin Johannes , Salloway Stephen , Farlow Martin , Gauthier Serge , Benzinger T Tammie L.S. , Morris John C. , Bateman Randall J. , Breitner John C.S. , Poirier Judes , Vachon-Presseau Etienne , Villeneuve Sylvia ,   for the Alzheimer’s Disease Neuroimaging Initiative,   the Dominantly Inherited Alzheimer Network (DIAN),   the PREVENT-AD Research Group
Published: May 2020

We aimed at developing a model able to predict brain aging from resting state functional connectivity (rs-fMRI) and assessing whether genetic risk/determinants of Alzheimer’s disease (AD) and amyloid (Aβ) pathology contributes to accelerated brain aging. Using data collected in 1340 cognitively unimpaired participants from 18 to 94 years old selected across multi-site cohorts, we showed that chronological age can be predicted across the whole lifespan from topological properties of graphs constructed from rs-fMRI. We subsequently used the difference between the model-predicted age and the chronological age in pre-symptomatic autosomal dominant AD (ADAD) mutation carriers and asymptomatic individuals at risk of sporadic AD and assessed the influence of genetics and Aβ pathology on brain age. Applying our predictive model in the context of preclinical AD revealed that the pre-symptomatic phase of ADAD is characterized by accelerated functional brain aging. This phenomenon is independent from, and might precede, detectable fibrillar Aβ deposition.
Elevated blood creatinine -a biomarker of renal function-associates with multiple metabolic perturbations in dogs
Authors: Ottka Claudia , Vapalahti Katariina , Määttä Ann-Marie , Huuskonen Nanna , Sarpanen Sinikka , Jalkanen Liisa , Lohi Hannes
Published: May 2020

BACKGROUND

Renal diseases, such as chronic kidney disease (CKD) are common in dogs. While the kidneys have multiple important metabolic functions, the occurrence of metabolic disturbances in canine renal diseases has not been extensively studied.

OBJECTIVES

To identify metabolic changes in blood samples exhibiting elevated blood creatinine, indicating reduced renal filtration.

ANIMALS

Samples consisted of clinical samples analysed by a 1H NMR-based metabolomics platform. The case group included 23 samples with creatinine > 125 μmol/l, and the control group 873 samples with creatinine within the reference interval.

METHODS

Biomarker association with elevated creatinine was evaluated utilizing three statistical approaches: Wilcoxon rank-sum test and logistic regression analysis (FDR-corrected p-values), and classification using random forest. Means of the biomarkers were compared to reference intervals. A heatmap and histograms visualized the differences.

RESULTS

The levels of citrate, tyrosine, branched-chain amino acids, valine, leucine, albumin, linoleic acid % and the ratio of phenylalanine to tyrosine differed significantly both in the Wilcoxon test and logistic regression, acetate levels only in Wilcoxon test and docosapentaenoic acid % only in logistic regression (p <. 05). The ten most significant markers in random forest corresponded to the Wilcoxon test, supplemented with alanine.

CONCLUSIONS AND CLINICAL IMPORTANCE

This study identified multiple metabolic changes associated with elevated blood creatinine, including prospective diagnostic markers and therapeutic targets. The NMR metabolomics test is a promising tool for improving diagnostics and management of canine renal diseases. Further research is needed to verify the association of these changes to the canine patient’s clinical state.
The changes in the p53 protein across the animal kingdom pointing to its involvement in longevity
Authors: Bartas Martin , Brázda Václav , Volná Adriana , Červeň Jiří , Pečinka Petr , Zawacka-Pankau Joanna
Published: May 2020

Recently, the quest for the mythical fountain of youth has turned into extensive research programs aiming to extend the healthy lifespan in humans. Despite advances in our understanding of the aging process, the surprisingly extended lifespan and cancer resistance of some animal species remains unexplained. The p53 protein plays a crucial role in tumor suppression and in tissue homeostasis and aging. Long-lived, cancer-free African elephants, have 20 copies of TP53 gene including 19 retrogenes (38 alleles) which are partially active, whereas humans possess only one copy of TP53 and have an estimated cancer mortality of 11-25%. The mechanism through which p53 contributes to the resolution of the Peto’s paradox in the Animalia remains vague. Thus, in this work, we took advantage of the available datasets and inspected the p53 amino acid sequence of phylogenetically related organisms that show variations in the lifespan. We discovered new correlations between specific amino acid deviations in p53 and the lifespans across different animal species. We found that species with extended lifespan have certain characteristic amino acid substitutions in the p53 DNA binding domain that alter its function as depicted from the Phenotypic Annotation of p53 Mutations, using PROVEAN tool or SWISS-MODEL workflow. Our findings show a direct association between specific amino acid residues in p53 protein, changes in p53 functionality and the extended animal lifespan, and further highlight the importance of p53 protein in aging.
Integrative Single-cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Haematopoiesis
Authors: Maria Ranzoni Anna , Tangherloni Andrea , Berest Ivan , Riva Simone Giovanni , Myers Brynelle , Strzelecka Paulina M. , Xu Jiarui , Panada Elisa , Mohorianu Irina , Zaugg Judith B. , Cvejic Ana
Published: May 2020

Regulation of haematopoiesis during human development remains poorly defined. Here, we applied single-cell (sc)RNA-Seq and scATAC-Seq analysis to over 8,000 human immunophenotypic blood cells from foetal liver and bone marrow. We inferred their differentiation trajectory and identified three highly proliferative oligopotent progenitor populations downstream from haematopoietic stem cell/multipotent progenitors (HSC/MPPs). Along this trajectory, we observed opposing patterns of chromatin accessibility and differentiation that coincided with dynamic changes in the activity of distinct lineage-specific transcription factors. Integrative analysis of chromatin accessibility and gene expression revealed extensive epigenetic but not transcriptional priming of HSC/MPPs prior to their lineage commitment. Finally, we refined and functionally validated the sorting strategy for the HSC/MPPs and achieved around 90% enrichment. Our study provides a useful framework for future investigation of human developmental haematopoiesis in the context of blood pathologies and regenerative medicine.
A recombineering pipeline to clone large and complex genes in Chlamydomonas
Authors: Emrich-Mills Tom , Yates Gary , Barrett James , Grouneva Irina , Lau Chun Sing , Walker Charlotte E , Kwok Tsz Kam , Davey John W , Johnson Matthew P , Mackinder Luke CM
Published: May 2020

The ability to clone genes has driven fundamental advances in cell and molecular biology, enabling researchers to introduce precise mutations, generate fluorescent protein fusions for localization and to confirm genetic causation by mutant complementation. Most gene cloning is PCR or DNA synthesis dependent, which can become costly and technically challenging as genes increase in size and particularly if they contain complex regions. This has been a long-standing challenge for theChlamydomonas reinhardtiiresearch community, with a high percentage of genes containing complex sequence structures, an average genomic GC content of 64% and gene expression requiring regular introns for stable transcription. Here we overcome these challenges via the development of a recombineering pipeline that enables the rapid parallel cloning of genes from a Chlamydomonas BAC collection. We show the method can successfully retrieve large and complex genes that PCR-based methods have previously failed to clone, including genes as large as 23 kilobases, thus making previously technically challenging genes to study now amenable to cloning. We initially applied the pipeline to 12 targets with a 92% cloning success rate. We then developed a high-throughput approach and targeted 191 genes relating to the Chlamydomonas CO2concentrating mechanism (CCM) with an overall cloning success rate of 77% that is independent of gene size. Localization of a subset of CCM targets has confirmed previous mass spectrometry data and identified new pyrenoid components. To expand the functionality of our system, we developed a series of localization vectors that enable complementation of Chlamydomonas Library Project mutants and enable protein tagging with a range of fluorophores. Vectors and detailed protocols are available to facilitate the easy adoption of this method by the Chlamydomonas research community. We envision that this technology will open up new possibilities in algal and plant research and be complementary to the Chlamydomonas mutant library.
Coding and regulatory variants affect serum protein levels and common disease
Authors: Emilsson Valur , Gudmundsdottir Valborg , Gudjonsson Alexander , Karim Mohd A , Ilkov Marjan , Staley James R. , Gudmundsson Elias F. , Jonsson Brynjolfur G. , Launer Lenore J. , Lindeman Jan H. , Morton Nicholas M. , Aspelund Thor , Lamb John R. , Jennings Lori L. , Gudnason Vilmundur
Published: May 2020

Circulating proteins are prognostic for human outcomes including cancer, heart failure, brain trauma and brain amyloid plaque burden. A deep serum proteome survey recently revealed close associations of serum protein networks and common diseases. The present study reveals unprecedented number of individual serum proteins that overlap genetic signatures of diseases emanating from different tissues of the body. Here, 54,469 low-frequency and common exome-array variants were compared with 4782 protein measurements in the serum of 5343 individuals of the deeply annotated AGES Reykjavik cohort. Using a study-wide significant threshold, 2019 independent exome array variants affecting levels of 2135 serum proteins were identified. These variants overlapped genetic loci for hundreds of complex disease traits, emphasizing the emerging role for serum proteins as biomarkers of and potential causative agents of multiple diseases.
Impaired chloroplast positioning affects photosynthetic capacity and regulation of the central carbohydrate metabolism during cold acclimation
Authors: Kitashova Anastasia , Schneider Katja , Fürtauer Lisa , Schröder Laura , Scheibenbogen Tim , Fürtauer Siegfried , Nägele Thomas
Published: May 2020

Photosynthesis and carbohydrate metabolism of higher plants need to be tightly regulated to prevent tissue damage during environmental changes. The intracellular position of chloroplasts changes due to a changing light regime. Chloroplast avoidance and accumulation response under high and low light, respectively, are well known phenomena, and deficiency of chloroplast movement has been shown to result in photodamage and reduced biomass accumulation. Yet, effects of chloroplast positioning on underlying metabolic regulation are less well understood. Here, we analysed photosynthesis together with metabolites and enzyme activities of the central carbohydrate metabolism during cold acclimation of thechloroplast unusual positioning 1(chup1) mutant ofArabidopsis thaliana. We compared cold acclimation under ambient and low light and found that maximum quantum yield of PSII was significantly lower inchup1than in Col-0 under both conditions. Our findings indicated that net CO2assimilation inchup1is rather limited by biochemistry than by photochemistry. Further, cold-induced dynamics of sucrose phosphate synthase differed significantly between both genotypes. Together with a reduced rate of sucrose cycling derived from kinetic model simulations our study provides evidence for a central role of chloroplast positioning for photosynthetic and metabolic acclimation to low temperature.
Detailed temporal dissection of an enhancer cluster reveals two distinct roles for individual elements
Authors: Thomas Henry , Kotova Elena , Pilz Axel , Romeike Merrit , Lackner Andreas , Bock Christoph , Leeb Martin , Wysocka Joanna , Buecker Christa
Published: May 2020

Many genes are regulated by multiple enhancers that often simultaneously activate their target gene. Yet, how individual enhancers collaborate to activate transcription is not well understood. Here, we dissect the functions and interdependencies of five enhancer elements that form a previously identified enhancer cluster and activate theFgf5locus during exit from naïve murine pluripotency. Four elements are located downstream of theFgf5gene and form a super-enhancer. Each of these elements contributes toFgf5induction at a distinct time point of differentiation. The fifth element is located in the first intron of theFgf5gene and contributes toFgf5expression at every time point by amplifying overallFgf5expression levels. This amplifier element strongly accumulates paused RNA Polymerase II but does not give rise to a matureFgf5mRNA. By transplanting the amplifier to a different genomic position, we demonstrate that it enriches for high levels of paused RNA Polymerase II autonomously. Based on our data, we propose a model for a mechanism by which RNA Polymerase II accumulation at a novel type of enhancer element, the amplifier, contributes to enhancer collaboration.
In Silico Trial to test COVID-19 candidate vaccines: a case study with UISS platform
Authors: Russo Giulia , Pennisi Marzio , Viceconti Marco , Pappalardo Francesco
Published: May 2020

SARS-CoV-2 is a severe respiratory infection that infects humans. Its outburst entitled it as a pandemic emergence. To get a grip on this outbreak, specific preventive and therapeutic interventions are urgently needed. It must be said that, until now, there are no existing vaccines for coronaviruses. To promptly and rapidly respond to pandemic events, the application of in silico trials can be used for designing and testing medicines against SARS-CoV-2 and speed-up the vaccine discovery pipeline, predicting any therapeutic failure and minimizing undesired effects. Here, we present an in silico platform that showed to be in very good agreement with the latest literature in predicting SARS-CoV-2 dynamics and related immune system host response. Moreover, it has been used to predict the outcome of one of the latest suggested approach to design an effective vaccine, based on monoclonal antibody. Universal Immune System Simulator (UISS) in silico platform is potentially ready to be used as an in silico trial platform to predict the outcome of vaccination strategy against SARS-CoV-2.
Restricted maximum-likelihood method for learning latent variance components in gene expression data with known and unknown confounders
Authors: Malik Muhammad Ammar , Michoel Tom
Published: May 2020

Random effect models are popular statistical models for detecting and correcting spurious sample correlations due to hidden confounders in genome-wide gene expression data. In applications where some confounding factors are known, estimating simultaneously the contribution of known and latent variance components in random effect models is a challenge that has so far relied on numerical gradient-based optimizers to maximize the likelihood function. This is unsatisfactory because the resulting solution is poorly characterized and the efficiency of the method may be suboptimal. Here we prove analytically that maximum-likelihood latent variables can always be chosen orthogonal to the known confounding factors, in other words, that maximum-likelihood latent variables explain sample covariances not already explained by known factors. Based on this result we propose a restricted maximum-likelihood method which estimates the latent variables by maximizing the likelihood on the restricted subspace orthogonal to the known confounding factors, and show that this reduces to probabilistic PCA on that subspace. The method then estimates the variance-covariance parameters by maximizing the remaining terms in the likelihood function given the latent variables, using a newly derived analytic solution for this problem. Compared to gradient-based optimizers, our method attains greater or equal likelihood values, can be computed using standard matrix operations, results in latent factors that don’t overlap with any known factors, and has a runtime reduced by several orders of magnitude. Hence the restricted maximum-likelihood method facilitates the application of random effect modelling strategies for learning latent variance components to much larger gene expression datasets than possible with current methods.
Spatial heterogeneity of cell-matrix adhesive forces predicts human glioblastoma migration
Authors: Rezk Rasha , Jia Bill Zong , Wendler Astrid , Dimov Ivan , Watts Colin , Markaki Athina E , Franze Kristian , Kabla Alexandre J
Published: May 2020

Background

Glioblastoma (GBM) is a highly aggressive incurable brain tumor. The main cause of mortality in GBM patients is the invasive rim of cells migrating away from the main tumor mass and invading healthy parts of the brain. Although motion is driven by forces, our current understanding of the physical factors involved in glioma infiltration remains limited. This study aims to investigate the adhesion properties within and between patients’ tumors on a cellular level and test whether these properties correlate with cell migration.

Methods

Nine tissue samples were taken from spatially separated sections during 5-aminolevulinic acid (5-ALA) fluorescence guided surgery. Navigated biopsy samples were collected from strongly fluorescent tumor cores, a weak fluorescent tumor rim, and non-fluorescent tumor margins. A microfluidics device was built to induce controlled shear forces to detach cells from monolayer cultures. Cells were cultured on low modulus polydimethylsiloxane representative of the stiffness of brain tissue. Cell migration and morphology were then obtained using time lapse microscopy.

Results

GBM cell populations from different tumor fractions of the same patient exhibited different migratory and adhesive behaviors. These differences were associated with sampling location and amount of 5-ALA fluorescence. Cells derived from weak- and non-fluorescent tumor tissue were smaller, adhered less well, and migrated quicker than cells derived from strongly fluorescent tumor mass.

Conclusion

GBM tumors are biomechanically heterogeneous. Selecting multiple populations and broad location sampling are therefore important to consider for drug testing.

Key points

GBM tumors are biomechanically heterogeneous

GBM cell migration is inversely correlated with cell-matrix adhesion strength

5-ALA fluorescence intensity during surgery correlates with the motility properties of GBM cells

Importance of the study

This is the first study to compare single cell migration and cell-matrix adhesion strength of GBM, using cell lines derived from different tumors and from different regions within the same tumor. Not accounting for internal sampling location within each tumor obscures differences in cell morphology, motility and adhesion properties between patients. Peripherical and marginal tumor cells have different adhesion profiles and are highly migratory compared to those found in the core of the tumor. Aggressive regions of the tumor (highly motile) are linked to the spatial distribution of adhesion strength and are strongly associated with 5-ALA fluorescence intensity. Preclinical tests aimed at developing a treatment for GBM using anti-invasive drugs or adhesion inhibitors, would benefit from using cell lines derived from the tumor periphery (with low 5-ALA intensity) rather than cell lines derived from the tumor core.
Optimal forgetting: Semantic compression of episodic memories
Authors: Nagy David G. , Török Balázs , Orbán Gergő
Published: May 2020

It has extensively been documented that human memory exhibits a wide range of systematic distortions, which have been associated with resource constraints. Resource constraints on memory can be formalised in the normative framework of lossy compression, however traditional lossy compression algorithms result in qualitatively different distortions to those found in experiments with humans. We argue that the form of distortions is characteristic of relying on a generative model adapted to the environment for compression. We show that this semantic compression framework can provide a unifying explanation of a wide variety of memory phenomena. We harness recent advances in learning deep generative models, that yield powerful tools to approximate generative models of complex data. We use three datasets, chess games, natural text, and hand-drawn sketches, to demonstrate the effects of semantic compression on memory performance. Our model accounts for memory distortions related to domain expertise, gist-based distortions, contextual effects, and delayed recall.

Author summary

Human memory performs surprisingly poorly in many everyday tasks, which have been richly documented in laboratory experiments. While constraints on memory resources necessarily imply a loss of information, it is possible to do well or badlyin relationto available memory resources. In this paper we recruit information theory, which establishes how to optimally lose information based on prior and complete knowledge of environmental statistics. For this, we address two challenges. 1, The environmental statistics is not known for the brain, rather these have to be learned over time from limited observations. 2, Information theory does not specify how different distortions of original experiences should be penalised. In this paper we tackle these challenges by assuming that a latent variable generative model of the environment is maintained in semantic memory. We show that compression of experiences through a generative model gives rise to systematic distortions that qualitatively correspond to a diverse range of observations in the experimental literature.
Power and limits of selection genome scans on temporal data from a selfing population
Authors: Navascués Miguel , Becheler Arnaud , Gay Laurène , Ronfort Joëlle , Loridon Karine , Vitalis Renaud
Published: May 2020

Abstract

Tracking genetic changes of populations through time allows a more direct study of the evolutionary processes acting on the population than a single contemporary sample. Several statistical methods have been developed to characterize the demography and selection from temporal population genetic data. However, these methods are usually developed under the assumption of outcrossing reproduction and might not be applicable when there is substantial selfing in the population. Here, we focus on a method to detect loci under selection based on a genome scan of temporal differentiation, adapting it to the particularities of selfing populations. Selfing reduces the effective recombination rate and can extend hitch-hiking effects to the whole genome, erasing any local signal of selection on a genome scan. Therefore, selfing is expected to reduce the power of the test. By means of simulations, we evaluate the performance of the method under scenarios of adaptation from new mutations or standing variation at different rates of selfing. We find that the detection of loci under selection in predominantly selfing populations remains challenging even with the adapted method. Still, selective sweeps from standing variation on predominantly selfing populations can leave some signal of selection around the selected site thanks to historical recombination before the sweep. Under this scenario, ancestral advantageous alleles at low frequency leave the strongest local signal, while new advantageous mutations leave no local footprint of the sweep.
A combination of mRNA features influence the efficiency of leaderless mRNA translation initiation
Authors: Bharmal Mohammed-Husain M. , Gega Alisa , Schrader Jared M.
Published: May 2020

Bacterial translation is thought to initiate by base-pairing of the 16S rRNA and the Shine-Dalgarno sequence in the mRNA’s 5’UTR. However, transcriptomics has revealed that leaderless mRNAs, which completely lack any 5’UTR, are broadly distributed across bacteria and can initiate translation in the absence of the Shine-Dalgarno sequence. To investigate the mechanism of leaderless mRNA translation initiation, syntheticin vivotranslation reporters were designed that systematically tested the effects of start codon accessibility, leader length, and start codon identity on leaderless mRNA translation initiation. Using this data, a simple computational model was built based on the combinatorial relationship of these mRNA features which can accurately classify leaderless mRNAs and predict the translation initiation efficiency of leaderless mRNAs. Thus, start codon accessibility, leader length, and start codon identity combine to define leaderless mRNA translation initiation in bacteria.
Endpoint and Epitope-specific Antibody Responses as Correlates of Vaccine-mediated Protection of Mice against Ricin Toxin
Authors: Van Slyke Greta , Ehrbar Dylan J , Doering Jennifer , Yates Jennifer L. , S.Vitetta Ellen , Donini Oreola , Mantis Nicholas J
Published: May 2020

The successful licensure of vaccines for biodefense is contingent upon the availability of well-established correlates of protection (CoP) in at least two animal species that can then be applied to humans, without the need to assess efficacy in the clinic. In this report we describe a multivariate model that combines pre-challenge serum antibody endpoint titers (EPT) and values derived from an epitope profiling immune-competition capture (EPICC) assay as a predictor in mice of vaccine-mediated immunity against ricin toxin (RT), a Category B biothreat. EPICC is a modified competition ELISA in which serum samples from vaccinated mice were assessed for their ability to inhibit the capture of soluble, biotinylated (b)-RT by a panel of immobilized monoclonal antibodies (mAbs) directed against four immunodominant toxin-neutralizing regions on the enzymatic A chain (RTA) of RT. In a test cohort of mice (n=40) vaccinated with suboptimal doses of the RTA subunit vaccine, RiVax®, we identified two mAbs, PB10 and SyH7, which had EPICC inhibition values in pre-challenge serum samples that correlated with survival following a challenge with 10 x LD50of RT administered by intraperitoneal (IP) injection. Analysis of a larger cohort of mice (n=645) revealed that a multivariate model combining endpoint titers and an epitope-profiling immune-competition capture (EPICC) assay values for PB10 and SyH7 as predictive variables had significantly higher statistical power than any one of the independent variables alone. Establishing the correlates of vaccine-mediated protection in mice represents an important steppingstone in the development of RiVax®as a medical countermeasure under the United States Food and Drug Administration’s “Two Animal Rule.”
Structural,in silico, and functional analysis of a Disabled-2-derived peptide for recognition of sulfatides
Authors: Song Wei , Gottschalk Carter J. , Tang Tuo-Xian , Biscardi Andrew , Ellena Jeffrey F. , Finkielstein Carla V. , Brown Anne M. , Capelluto Daniel G. S.
Published: May 2020

Disabled-2 (Dab2) is an adaptor protein that regulates numerous cellular processes. Among them, Dab2 modulates the extent of platelet aggregation by two mechanisms. In the first mechanism, Dab2 intracellularly downregulates the integrin αIIbβ3receptor, converting it to a low affinity state for adhesion and aggregation processes. In the second mechanism, Dab2 is released extracellularly and interacts with both the integrin αIIbβ3receptor and sulfatides, both of which are known to be pro-aggregatory mediators, blocking their association to fibrinogen and P-selectin, respectively. Our previous research indicated that a 35-amino acid region within Dab2, which we refer to as the sulfatide-binding peptide (SBP), contains two potential sulfatide-binding motifs represented by two consecutive polybasic regions. Using a combined methodology including molecular docking, nuclear magnetic resonance, lipid-binding assays, and surface plasmon resonance, this work identifies the critical Dab2 residues within SBP that are responsible for sulfatide binding. A hydrophilic region, primarily mediated by R42, is responsible for the interaction with the sulfatide headgroup, whereas the C-terminal polybasic region contributes to interactions with the acyl chains. Furthermore, we demonstrated that, in Dab2 SBP, R42 significantly contributes to the inhibition of platelet P-selectin surface expression. The interacting Dab2 SBP residues with sulfatide resemble those described for sphingolipid-binding in other proteins, suggesting that sulfatide-binding proteins share common binding mechanisms.
Contrasting action and posture coding with hierarchical deep neural network models of proprioception
Authors: Sandbrink Kai J. , Mamidanna Pranav , Michaelis Claudio , Bethge Matthias , Mathis Mackenzie Weygandt , Mathis Alexander
Published: May 2020

Biological motor control is versatile and efficient. Muscles are flexible and undergo continuous changes, requiring distributed adaptive control mechanisms. How proprioception solves this problem in the brain is unknown. The canonical role of proprioception is representing the body state, yet we hypothesize that the proprioceptive system can decode high-level, multi-feature actions. To test this theory, we pursue a task-driven modeling approach.We generated a large synthetic dataset of human arm trajectories tracing the alphabet in 3D space and use a musculoskeletal model plus modeled muscle spindle inputs to extract muscle activity. We then contrast two tasks, one character trajectory-decoding and another action recognition task that allows training of hierarchical models to decode position, or classify the character identity from the spindle firing patterns. Artificial neural networks could robustly solve these tasks, and the networks’ units show tuning properties akin to neurons in the primate somatosensory cortex and the brainstem. Remarkably, only the action-recognition trained, and not the trajectory decoding trained, models possess directional selective units (which are also uniformly distributed), as in the primate brain. Taken together, our model is the first to link tuning properties in the proprioceptive system at multiple levels to the behavioral level. We find that action-recognition, rather than the canonical trajectory-decoding hypothesis, better explains what is known about the proprioceptive system.
Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium
Authors: Ravindra Neal G. , Alfajaro Mia Madel , Gasque Victor , Habet Victoria , Wei Jin , Filler Renata B. , Huston Nicholas C. , Wan Han , Szigeti-Buck Klara , Wang Bao , Wang Guilin , Montgomery Ruth R. , Eisenbarth Stephanie C. , Williams Adam , Pyle Anna Marie , Iwasaki Akiko , Horvath Tamas L. , Foxman Ellen F. , Pierce Richard W. , van Dijk David , Wilen Craig B.
Published: May 2020

SARS-CoV-2, the causative agent of COVID-19, has tragically burdened individuals and institutions around the world. There are currently no approved drugs or vaccines for the treatment or prevention of COVID-19. Enhanced understanding of SARS-CoV-2 infection and pathogenesis is critical for the development of therapeutics. To reveal insight into viral replication, cell tropism, and host-viral interactions of SARS-CoV-2 we performed single-cell RNA sequencing of experimentally infected human bronchial epithelial cells (HBECs) in air-liquid interface cultures over a time-course. This revealed novel polyadenylated viral transcripts and highlighted ciliated cells as a major target of infection, which we confirmed by electron microscopy. Over the course of infection, cell tropism of SARS-CoV-2 expands to other epithelial cell types including basal and club cells. Infection induces cell-intrinsic expression of type I and type III IFNs and IL6 but not IL1. This results in expression of interferon-stimulated genes in both infected and bystander cells. We observe similar gene expression changes from a COVID-19 patientex vivo. In addition, we developed a new computational method termed CONditional DENSity Embedding (CONDENSE) to characterize and compare temporal gene dynamics in response to infection, which revealed genes relating to endothelin, angiogenesis, interferon, and inflammation-causing signaling pathways. In this study, we conducted an in-depth analysis of SARS-CoV-2 infection in HBECs and a COVID-19 patient and revealed genes, cell types, and cell state changes associated with infection.
Improving enzyme optimum temperature prediction with resampling strategies and ensemble learning
Authors: Gado Japheth E. , Beckham Gregg T. , Payne Christina M.
Published: May 2020

Accurate prediction of the optimal catalytic temperature (Topt) of enzymes is vital in biotechnology, as enzymes with high Toptvalues are desired for enhanced reaction rates. Recently, a machine-learning method (TOME) for predicting Toptwas developed. TOME was trained on a normally-distributed dataset with a median Toptof 37°C and less than five percent of Toptvalues above 85°C, limiting the method’s predictive capabilities for thermostable enzymes. Due to the distribution of the training data, the mean squared error on Toptvalues greater than 85°C is nearly an order of magnitude higher than the error on values between 30 and 50°C. In this study, we apply ensemble learning and resampling strategies that tackle the data imbalance to significantly decrease the error on high Toptvalues (>85°C) by 60% and increase the overall R2value from 0.527 to 0.632. The revised method, TOMER, and the resampling strategies applied in this work are freely available to other researchers as a Python package on GitHub.
Fertilizers, BT technology, and insecticides contributed to 60%, 23%, and 17%, respectively to the increase in BT cotton yield: An analysis from 2000 to 2014 in India
Authors: Parameswaran C , Cayalvizhi B
Published: May 2020

Complementary technologies and agricultural practices capable of sustaining profitability to the farmers cultivating BtCotton in India require urgent attention. In India, approval of Btcotton, cultivation of fertilizer-intensive hybrids, higher dose of fertilizer application by farmers, usage of novel pesticides all happened simultaneously during the same period (2002-04) which makes very difficult to identify the individual effect in the yield gain of cotton. In this background, we attempted to understand the proportionate contribution of fertilizers, BT technology and novel group of pesticides in enhancing cotton yield in India. For the analysis, linear regression model and change in partial factor productivity (PFP) of cotton was considered in four different scenarios for yield estimation between 2000 and 2014, i.e. Scenario I: Cotton yield in the absence of technology and enhanced fertilizers usage, Scenario II: Cotton yield only due to enhanced fertilizer usage, Scenario III: Cotton yield with enhanced fertilizer and application of novel pesticides for the insect control, and Scenario IV: Cotton yield due to BT technology, enhanced use of fertilizer, and novel insecticides (actual yield of Cotton in India during Bt phase).Their comparison showed that the individual effect of fertilizers, BT technology and insecticides contributed to 60%, 23% and 17% of cotton yield, respectively in India. Further, 18% reduction in PFP was observed recently as compared to 2003-08. Besides, 125 Kg/ha of fertilizers was identified as optimum dose for sustaining high yield in cotton. Thus, present analysis identified the individual effect of different technologies contributing to the yield of cotton in India which can be used in decision making processes for crop improvement. Further, in our opinion, three strategies namely drip fertigation, intercrossing Bt and non-Bt hybrids for resistance management in bollworms, and IPM for sucking pests will primarily drive the research priorities and policy actions for the next 5 to 10 years in sustaining the economic benefits of the six million cotton farmers in India.
An HIV-Tat inducible mouse model system of childhood HIV-associated nephropathy
Authors: Tang Pingtao , Das Jharna R. , Li Jinliang , Yu Jing , Ray Patricio E.
Published: May 2020

Background

Modern antiretroviral therapies (ART) have decreased the prevalence of HIV-associated nephropathy (HIVAN). Nonetheless, we continue to see children and adolescents with HIVAN all over the world. Furthermore, once HIVAN is established in children, it is difficult to revert its long-term progression, and we need better animal models of childhood HIVAN to test new treatments.

Objectives

To define whether the HIV-1 trans-activator (Tat) gene precipitates HIVAN in young mice, and to develop an inducible mouse model of childhood HIVAN.

Design/Methods

An HIV-Tat gene cloned from a child with HIVAN was used to generate recombinant adenoviral vectors (rAd-Tat). rAd-Tat andLacZcontrol vectors (2 × 109) were expressed in the kidney of newborn wild type and HIV-transgenic (Tg26) FVB/N mice without significant proteinuria (n = 5 - 8 per group). Mice were sacrificed 7 and 35 days later to assess their renal outcome, the expression of HIV-genes and growth factors, and markers of cell growth and differentiation by RT-qPCR, immunohistochemistry, and/or Western blots.

Results

HIV-Tat induced the expression of HIV-1 genes (env) and heparin binding growth factors in the kidney of HIV-Tg26mice, and precipitated HIVAN in the first month of life. No significant renal changes were detected in wild type mice infected with rAd-Tat vectors, suggesting that HIV-Tat alone does not induce renal disease.

Conclusion

This new mouse model of childhood HIVAN highlights the critical role that HIV-Tat plays in the pathogenesis of HIVAN, and could be used to study the pathogenesis and treatment of HIVAN in children and adolescents.

Summary statement

We developed a new inducible mouse model system of childhood HIV-associated nephropathy, and demonstrated that HIV-Tat plays a critical role in this renal disease acting in synergy with other HIV-1 genes and heparin binding cytokines.
Suramin inhibits SARS-CoV-2 infection in cell culture by interfering with early steps of the replication cycle
Authors: da Silva Clarisse Salgado Benvindo , Thaler Melissa , Tas Ali , Ogando Natacha S. , Bredenbeek Peter J. , Ninaber Dennis K. , Wang Ying , Hiemstra Pieter S. , Snijder Eric J. , van Hemert Martijn J.
Published: May 2020

The SARS-CoV-2 pandemic that originated from Wuhan, China, in December 2019 has impacted public health, society and economy and the daily lives of billions of people in an unprecedented manner. There are currently no specific registered antiviral drugs to treat or prevent SARS-CoV-2 infections. Therefore, drug repurposing would be the fastest route to provide at least a temporary solution while better, more specific drugs are being developed. Here we demonstrate that the antiparasitic drug suramin inhibits SARS-CoV-2 replication, protecting Vero E6 cells with an EC50of ∼20 µM, which is well below the maximum attainable level in human serum. Suramin also decreased the viral load by 2-3 logs when Vero E6 cells or cells of a human lung epithelial cell line (Calu-3) were treated. Time of addition and plaque reduction assays showed that suramin acts on early steps of the replication cycle, possibly preventing entry of the virus. In a primary human airway epithelial cell culture model, suramin also inhibited the progression of infection. The results of our preclinical study warrant further investigation and suggest it is worth evaluating whether suramin provides any benefit for COVID-19 patients, which obviously requires well-designed, properly controlled randomized clinical trials.