bluuebunny/crossref_metadata_2025 huggingface dataset:
SeedExtractor: an open-source GUI for seed image analysis
Authors: Zhu Feiyu , Paul Puneet , Hussain Waseem , Wallman Kyle , Dhatt Balpreet K , Sandhu Jaspreet , Irvin Larissa , Morota Gota , Yu Hongfeng , Walia Harkamal
Published: June 2020

Accurate measurement of seed size parameters is essential for both: breeding efforts□aimed at□enhancing yields and basic research□focused on discovering genetic components that regulate seed size. To address this need, we have developed an open-source graphical user interface (GUI) software,SeedExtractorthat□determines seed size and shape (including area, perimeter, length, width, circularity, and centroid), and seed color with capability to process a large number of images in a time-efficient manner. In this context, our application takes ∼2 seconds for analyzing an image, i.e. significantly less compared to the other tools. As this software is open-source, it can be modified by users□to serve more specific needs. The adaptability ofSeedExtractorwas demonstrated by analyzing scanned seeds from multiple crops. We further validated the utility of this application by analyzing mature-rice seeds from 231 accessions in Rice Diversity Panel 1. The derived seed-size traits, such as seed length, width, were subjected to genome-wide association analysis. We identified well-known loci for regulating seed length (GS3) and width (qSW5/GW5) in rice, which demonstrated the accuracy of this application to extract seed phenotypes and accelerate trait discovery. In summary, we present a publicly available application that can be used to determine key yield-related traits in crops.

HIGHLIGHT

SeedExtractoris an open-source application designed to accurately measure seed size and seed color in a time-efficient manner for a wide variety of plant species.
Phosphorylation modulates liquid-liquid phase separation of the SARS-CoV-2 N protein
Authors: Carlson Christopher R. , Asfaha Jonathan B. , Ghent Chloe M. , Howard Conor J. , Hartooni Nairi , Morgan David O.
Published: June 2020

The nucleocapsid (N) protein of coronaviruses serves two major functions: compaction of the RNA genome in the virion and regulation of viral gene transcription in the infected cell1–3. The N protein contains two globular RNA-binding domains surrounded by regions of intrinsic disorder4. Phosphorylation of the central disordered region is required for normal viral genome transcription5,6, which occurs in a cytoplasmic structure called the replication transcription complex (RTC)7–11. It is not known how phosphorylation controls N protein function. Here we show that the N protein of SARS-CoV-2, together with viral RNA, forms biomolecular condensates12–15. Unmodified N protein forms partially ordered gel-like structures that depend on multivalent RNA-protein and protein-protein interactions. Phosphorylation reduces a subset of these interactions, generating a more liquid-like droplet. We speculate that distinct oligomeric states support the two functions of the N protein: unmodified protein forms a structured oligomer that is suited for nucleocapsid assembly, and phosphorylated protein forms a liquid-like compartment for viral genome processing. Inhibitors of N protein phosphorylation could therefore serve as antiviral therapy.
Interconnected assembly factors regulate the biogenesis of mitoribosomal large subunit
Authors: Tobiasson Victor , Gahura Ondřej , Aibara Shintaro , Baradaran Rozbeh , Zíková Alena , Amunts Alexey
Published: June 2020

Mitoribosomes consist of ribosomal RNA and protein components, coordinated assembly of which is critical for function. We used mitoribosomes with reduced RNA and increased protein mass fromTrypanosoma brucei, to provide insights into the biogenesis of mitoribosomal large subunit. Structural characterisation of a stable assembly intermediate revealed 22 assembly factors, some of which are also encoded in mammalian genomes. The assembly factors form a protein network that spans over 180 Å, shielding the ribosomal RNA surface. The entire central protuberance and L7/L12 stalk are not assembled, and require removal of the factors and remodeling of the mitoribosomal proteins to become functional. The conserved proteins GTPBP7 and mt-EngA are bound together at the subunit interface in proximity to the peptidyl transferase center. A mitochondrial acyl-carrier protein plays a role in docking the L1 stalk which needs to be repositioned during maturation. Additional enzymatically deactivated factors scaffold the assembly, while the exit tunnel is blocked. Together, the extensive network of the factors stabilizes the immature sites and connects the functionally important regions of the mitoribosomal large subunit.
Variability in Fruit Yield and Quality of Genetically Diverse Tomato Cultivars in Response to Different Biochars
Authors: Tenic Elvir , Isaac Daylen , Ghogare Rishikesh , Dhingra Amit
Published: June 2020

Background

Intensive agricultural practices have reduced soil health thereby negatively impacting crop yields. There is a need to maintain healthy soils and restore marginal lands to ensure efficient food production. Biochar, a porous carbon-rich material generated from pyrolysis of various feedstock sources is receiving attention as a soil amendment that has the potential to restore soil organic carbon content and also enhance crop yields. However, the physical and chemical properties of biochar are influenced by pyrolysis parameters. These in turn determine its interaction with the soil, thereby influencing its biological properties in terms of impact on soil microcosm and plant productivity. While most studies report the evaluation of one biochar and a single plant cultivar, the role of the plant’s genetic background in responding to biochar as a soil amendment remains unanswered. The impact of six distinct biochars on agronomic performance and fruit quality of three genetically diverse tomato (Solanum lycopersicum) cultivars was evaluated to test the hypotheses that 1) biochars derived from different feedstock sources would produce unique phenotypes in a single cultivar of tomato, and 2) single feedstock-derived BC would produce different phenotypes in each of the three tomato cultivars.

Results

Different biochars impacted shoot dry weight, total fruit weight, and yield per plant in each cultivar differently. Both positive and negative effects were observed depending on the biochar-cultivar combination. In ‘Oregon Spring’, Ryegrass straw and CoolTerra biochar enhanced yield. In ‘Heinz’, an increase in fruit weight and citric acid was observed with several of the biochars. In ‘Cobra’, improved yields were accompanied by reduction in fruit quality parameters. Both hypotheses were supported by the data.

Conclusions

This study demonstrated that the genetic background of a plant is an important variable in determining the outcome of using biochar as a soil amendment. Strategies for application of biochar in agricultural production should consider the variables of soil type, feedstock source, pyrolysis parameters and plant genetic background for enhancing crop productivity and carbon sequestration.
High-performance pipeline for MutMap and QTL-seq
Authors: Sugihara Yu , Young Lester , Yaegashi Hiroki , Natsume Satoshi , Shea Daniel J. , Takagi Hiroki , Booker Helen , Innan Hideki , Terauchi Ryohei , Abe Akira
Published: June 2020

Bulked segregant analysis implemented in MutMap and QTL-seq is a powerful and efficient method to identify agronomically important loci. However, the previous pipelines were not user-friendly to install and run. Here, we describe new pipelines for MutMap and QTL-seq. These updated pipelines are approximately 5-8 times faster than the previous pipeline, are easier for novice users to use and can be easily installed through bioconda with all dependencies.
Deglutarylation of GCDH by SIRT5 controls lysine metabolism in mice
Authors: Bhatt Dhaval P. , Mills C. Allie , Anderson Kristin A. , Henriques Bárbara J. , Lucas Tânia G. , Francisco Sara , Liu Juan , Ilkayeva Olga R. , Adams Alexander E. , Kulkarni Shreyas R. , Backos Donald S. , Grimsrud Paul A. , Gomes Cláudio M. , Hirschey Matthew D.
Published: June 2020

A wide range of protein acyl modifications has been identified on enzymes across various metabolic processes; however, the impact of these modifications remains poorly understood. Protein glutarylation is a recently identified modification that can be non-enzymatically driven by glutaryl-CoA. In mammalian systems, this unique metabolite is only produced in the lysine and tryptophan oxidative pathways. To better understand the biology of protein glutarylation, we studied the relationship between enzymes within the lysine/tryptophan catabolic pathways, protein glutarylation, and regulation by the deglutarylating enzyme Sirtuin 5 (SIRT5). Here, we identify glutarylation on the lysine oxidation pathway enzyme glutaryl-CoA dehydrogenase (GCDH). We show increased GCDH glutarylation when glutaryl-CoA production is stimulated by lysine catabolism. Our data reveal glutarylation of GCDH impacts its function, ultimately decreasing lysine oxidation. We then demonstrate the ability of SIRT5 to deglutarylate GCDH, restoring its enzymatic activity. Finally, metabolomic and bioinformatic analyses indicate an expanded role for SIRT5 in regulating amino acid metabolism. Together, these data support a model whereby a feedback loop exists within the lysine/tryptophan oxidation pathway, in which glutaryl-CoA is produced, in turn inhibiting GCDH functionviaglutaryl modification of GCDH lysine residues, and can be relieved by SIRT5 deacylation activity.
Direct Quantification of in vivo Mutagenesis and Carcinogenesis Using Duplex Sequencing
Authors: Valentine Charles C. , Young Robert R. , Fielden Mark R. , Kulkarni Rohan , Williams Lindsey N. , Li Tan , Minocherhomji Sheroy , Salk Jesse J.
Published: June 2020

The ability to accurately measure mutations is critical for basic research and identification of potential drug and chemical carcinogens. Current methods for in vivo quantification of mutagenesis are limited because they rely on transgenic rodent systems that are low-throughput, expensive, prolonged, and don’t fully represent other species such as humans. Next generation sequencing (NGS) is a conceptually attractive alternative for mutation detection in the DNA of any organism, however, the limit of resolution for standard NGS is poor. Technical error rates (~1×10−3) of NGS obscure the true abundance of somatic mutations, which can exist at pernucleotide frequencies ≤1×10−7. Using Duplex Sequencing, an extremely accurate error-corrected NGS (ecNGS) technology, we were able to detect mutations induced by 3 carcinogens in 5 tissues of 2 strains of mice within 31 days following exposure. We observed a strong correlation between mutation induction measured by Duplex Sequencing and the gold-standard transgenic rodent mutation assay. We identified exposure-specific mutation spectra of each compound through trinucleotide patterns of base substitution. We observed variation in mutation susceptibility by genomic region, as well as by DNA strand. We also identified the primordial signs of carcinogenesis in a cancer-predisposed strain of mice, as evidenced by clonal expansions of cells carrying an activated oncogene, less than a month after carcinogen exposure. These findings demonstrate that ecNGS is a powerful method for sensitively detecting and characterizing mutagenesis and the early clonal evolutionary hallmarks of carcinogenesis. Duplex Sequencing can be broadly applied to chemical safety testing, basic mutational research, and related clinical uses.

SIGNIFICANCE STATEMENT

Error-corrected next generation sequencing (ecNGS) can be used to rapidly detect and quantify the in vivo mutagenic impact of environmental exposures or endogenous processes in any tissue, from any species, at any genomic location. The greater speed, higher scalability, richer data outputs, as well as cross-species and cross-locus applicability of ecNGS compared to existing methods make it a powerful new tool for mutational research, regulatory safety testing, and emerging clinical applications.
SARS-CoV-2 serological testing using electrochemiluminescence reveals a rapid onset of seroconversion in severe COVID-19 patients
Authors: Munitz A , Edry-Botzer L , Itan M , Tur-Kaspa R , Dicker D , Markovitch D , Goren M , Mor M , Lev S , Gottesman T , Muhsen K , Cohen D , Stein M , Qimron U , Freund N , Wine Y , Gerlic M
Published: June 2020

Despite ongoing efforts to characterize the host response toward SARS-CoV-2, a major gap in our knowledge still exists regarding the magnitude and duration of the humoral response. We report the development of a rapid, highly specific and sensitive electrochemiluminescent assay for detecting IgM, IgA, and IgG antibodies toward two distinct SARS-CoV-2 antigens namely, the receptor binding domain (RBD) and the nuclear protein (NP). Whereas IgM antibodies toward RBD were detected at early stages of the disease, IgM antibodies against NP did not develop. Analysis of the antibody response in mild versus moderate/severe patients revealed a rapid onset of IgG and IgA antibodies, specifically in moderate/severe patients. Finally, we observed a marked reduction in IgM/IgA antibodies and to lesser extent, IgG, over time. We provide a comprehensive analysis of the human antibody response, and has major implications on our understanding and monitoring of SARS-CoV-2 infections, as well as finding effective vaccines.

One Sentence Summary

Using a newly developed assay to detect anti-SARS-Cov-2 IgM, IgG and IgA antibodies we reveal a rapid onset of IgG and IgA antibodies towards distinct viral antigens, specifically in moderate/severe COVID-19 patients,
Data presented by the UK government as lockdown was eased shows the transmission of COVID-19 had already increased
Authors: Lonergan Mike
Published: June 2020

Background

Coronavirus disease 2019 (COVID-19) is an international emergency that has been addressed in many countries by changes in and restrictions on behaviour. These are often collectively labelled social distancing and lockdown. On the 23rd June 2020, Boris Johnson, the Prime Minister of the United Kingdom announced substantial easings of restrictions. This paper examines some of the data he presented.

Methods

Generalised additive models, with negative binomial errors and cyclic term representing day-of-week effects, were fitted to data on the daily numbers of new confirmed cases of COVID-19. Exponential rates for the epidemic were estimated for different periods, and then used to calculate R, the reproduction number, for the disease in different periods.

Results

After an initial stabilisation, the lockdown reduced R to around 0.81 (95% CI: 0.79, 0.82). This value increased to around 0.94 (95% CI 0.89, 0.996) for the fortnight from the 9th June 2020.

Conclusions

Official UK data, presented as the easing of the lockdown was announced, shows that R was already more than half way back to 1 at that point. That suggests there was little scope for the announced changes to be implemented without restarting the spread of the disease.
Chromosome-scale inference of hybrid speciation and admixture with convolutional neural networks
Authors: Blischak Paul D. , Barker Michael S. , Gutenkunst Ryan N.
Published: June 2020

Inferring the frequency and mode of hybridization among closely related organisms is an important step for understanding the process of speciation and can help to uncover reticulated patterns of phylogeny more generally. Phylogenomic methods to test for the presence of hybridization come in many varieties and typically operate by leveraging expected patterns of genealogical discordance in the absence of hybridization. An important assumption made by these tests is that the data (genes or SNPs) are independent given the species tree. However, when the data are closely linked, it is especially important to consider their non-independence. Recently, deep learning techniques such as convolutional neural networks (CNNs) have been used to perform population genetic inferences with linked SNPs coded as binary images. Here we use CNNs for selecting among candidate hybridization scenarios using the tree topology (((P1,P2),P3),Out) and a matrix of pairwise nucleotide divergence (dXY) calculated in windows across the genome. Using coalescent simulations to train and independently test a neural network showed that our method, HyDe-CNN, was able to accurately perform model selection for hybridization scenarios across a wide-breath of parameter space. We then used HyDe-CNN to test models of admixture inHeliconiusbutterflies, as well as comparing it to a random forest classifier trained on introgression-based statistics. Given the flexibility of our approach, the dropping cost of long-read sequencing, and the continued improvement of CNN architectures, we anticipate that inferences of hybridization using deep learning methods like ours will help researchers to better understand patterns of admixture in their study organisms.
Functional and structural basis of extreme non-coding conservation in vertebrate 5’UTRs
Authors: Byeon Gun Woo , Cenik Elif Sarinay , Jiang Lihua , Tang Hua , Das Rhiju , Barna Maria
Published: June 2020

The lack of knowledge about extreme conservation in genomes remains a major gap in our understanding of the evolution of gene regulation. While previous findings have mainly focused on the role of extreme conservation at the level of DNA in transcriptional regulation, its implications for RNA biology remains largely unexplored. Here, we reveal an unexpected role of extremely conserved 5’UTRs in translational regulation that is linked to the emergence of essential developmental features in vertebrate species. Endogenous deletion of conserved elements within these 5’UTRs decreased gene expression at the post-transcriptional level. A large-scale reporter library of extremely conserved 5’UTRs revealed the widespread presence of cis-regulatory elements that promote cell-type specific regulation of translation. As these elements function as RNA molecules, further understanding of their potential structures was essential. We therefore developed in-cell mutate-and-map (icM2), a novel methodology that maps RNA structure using high-throughput mutational analysis, previously impossible to perform inside cells. Using icM2, we determined that an extremely conserved 5’UTR encodes multiple alternative structures whose relative proportions are actively maintained by ATP-dependent RNA helicases. We further show that each single nucleotide within the extremely conserved element maintains the balance of alternative structures important to control the dynamic range of protein expression. These results explain how extreme sequence conservation can lead to RNA-level biological functions encoded in the untranslated regions of vertebrate genomes.
Functional solubilisation of the β2-adrenoceptor (β2AR) using Diisobutylene maleic acid (DIBMA)
Authors: Harwood C. R. , Sykes D. A. , Hoare B. , Heydenreich F. M. , Uddin R. , Poyner D. R. , Briddon S. J. , Veprintsev D. B.
Published: June 2020

The β2-adrenoceptor (β2AR) is a well-established target in asthma and a prototypical GPCR for biophysical studies. Solubilisation of membrane proteins has classically involved the use of detergents. However, the detergent environment differs from the native membrane environment and often destabilises membrane proteins. Use of amphiphilic copolymers is a promising strategy to solubilise membrane proteins within their native lipid environment in the complete absence of detergents. Here we show the isolation of the β2AR in the polymer Diisobutylene maleic acid (DIBMA). We demonstrate that β2AR remains functional in the DIBMA lipid particle (DIBMALP) and shows improved thermal stability compared to the n-Dodecyl-β-D-Maltopyranoside (DDM) detergent solubilised β2AR. This unique method of extracting β2AR offers significant advantages over previous methods routinely employed such as the introduction of thermostabilising mutations and the use of detergents, particularly for functional biophysical studies.
Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19
Authors: Sekine Takuya , Perez-Potti André , Rivera-Ballesteros Olga , Strålin Kristoffer , Gorin Jean-Baptiste , Olsson Annika , Llewellyn-Lacey Sian , Kamal Habiba , Bogdanovic Gordana , Muschiol Sandra , Wullimann David J. , Kammann Tobias , Emgård Johanna , Parrot Tiphaine , Folkesson Elin , Rooyackers Olav , Eriksson Lars I. , Sönnerborg Anders , Allander Tobias , Albert Jan , Nielsen Morten , Klingström Jonas , Gredmark-Russ Sara , Björkström Niklas K. , Sandberg Johan K. , Price David A. , Ljunggren Hans-Gustaf , Aleman Soo , Buggert Marcus ,   Karolinska COVID-19 Study Group
Published: June 2020

SARS-CoV-2-specific memory T cells will likely prove critical for long-term immune protection against COVID-19. We systematically mapped the functional and phenotypic landscape of SARS-CoV-2-specific T cell responses in a large cohort of unexposed individuals as well as exposed family members and individuals with acute or convalescent COVID-19. Acute phase SARS-CoV-2-specific T cells displayed a highly activated cytotoxic phenotype that correlated with various clinical markers of disease severity, whereas convalescent phase SARS-CoV-2-specific T cells were polyfunctional and displayed a stem-like memory phenotype. Importantly, SARS-CoV-2-specific T cells were detectable in antibody-seronegative family members and individuals with a history of asymptomatic or mild COVID-19. Our collective dataset shows that SARS-CoV-2 elicits robust memory T cell responses akin to those observed in the context of successful vaccines, suggesting that natural exposure or infection may prevent recurrent episodes of severe COVID-19 also in seronegative individuals.
Zonal human hepatocytes are differentially permissive toPlasmodium falciparummalaria parasites
Authors: Yang Annie S.P. , van Waardenburg Youri M. , van de Vegte-Bolmer Marga , van Gemert Geert-Jan A. , Graumans Wouter , de Wilt Johannes H.W. , Sauerwein Robert W.
Published: June 2020

Plasmodium falciparum (Pf)is a major cause of malaria. The mosquito-borne parasite asymptomatically infects hepatocytes in the liver. The resulting schizonts undergo massive replication to generate blood-infective merozoites. Liver lobules are zonated: hepatocytes in different zones perform differential metabolic functions. In search for specific host conditions that affect infectability, we studied thePfparasite liver stage development in relation to the metabolic heterogeneity of fresh human hepatocytes. We show selective preference of differentPfstrains for a minority of zone 3 hepatocytes characterized by the particular presence of glutamine synthetase (hGS). Parasite schizont growth is significantly enhanced by hGS uptake early in development, which showcases an import system at this stage of the parasite life-cycle. In conclusion,Pfdevelopment is strongly determined by the differential metabolic status in hepatocyte subtypes. These findings underscore the importance of detailed understanding of hepatocyte host-Pfinteractions and may delineate novel pathways for intervention strategies.
The Filter Detection Task for measurement of breathing-related interoception and metacognition
Authors: Harrison Olivia K. , Garfinkel Sarah N. , Marlow Lucy , Finnegan Sarah , Marino Stephanie , Nanz Laura , Allen Micah , Finnemann Johanna , Keur-Huizinga Laura , Harrison Samuel J. , Stephan Klaas E. , Pattinson Kyle T. S. , Fleming Stephen M.
Published: June 2020

The study of the brain’s processing of sensory inputs from within the body (‘interoception’) has been gaining rapid popularity in neuroscience, where interoceptive disturbances are thought to exist across a wide range of chronic physiological and psychological conditions. Here we present a task and analysis procedure to quantify specific dimensions of breathing-related interoception, including interoceptive sensitivity (accuracy), decision bias, metacognitive bias, and metacognitive performance. Two major developments address some of the challenges presented by low trial numbers in interoceptive experiments: (i) a novel adaptive algorithm to maintain task performance at 70-75% accuracy; (ii) an extended hierarchical metacognitive model to estimate regression parameters linking metacognitive performance to relevant (e.g. clinical) variables. We demonstrate the utility of the task and analysis developments, using both simulated data and three empirical datasets. This methodology represents an important step towards accurately quantifying interoceptive dimensions from a simple experimental procedure that is compatible with clinical settings.
Agent-Based Modeling of T Cell Receptor Cooperativity
Authors: Siokis Anastasios , Robert Philippe A. , Meyer-Hermann Michael
Published: June 2020

Immunological synapse (IS) formation is a key event during antigen recognition by T cells. Recent experimental evidence suggests that the affinity between T cell receptors (TCRs) and antigen is actively modulated during the early steps of TCR signaling. In this work, we used an agent-based model to study possible mechanisms for affinity modulation during IS formation. We show that, without any specific active mechanism, the observed affinity between receptors and ligands evolves over time, and depends on the density of ligand pMHC (antigen peptide presented by major histocompatibility complexes) and TCR molecules. Comparison between the presence or absence of TCR-pMHC centrally directed flow due to F-actin coupling suggest centripetal transport is a potential mechanism for the affinity modulation. The model further suggests that the time point of affinity measurement during immune synapse formation is critical. Finally, a mathematical model of F-actin foci formation incorporated in the agent-based model, shows that TCR affinity can potentially be actively modulated by a positive/negative feedback of F-actin foci on the TCR-pMHC association ratekon.
Unbiased metabolic flux inference through combined thermodynamic and13C flux analysis
Authors: Saldida Joana , Muntoni Anna Paola , de Martino Daniele , Hubmann Georg , Niebel Bastian , Schmidt A. Mareike , Braunstein Alfredo , Milias-Argeitis Andreas , Heinemann Matthias
Published: June 2020

Quantification of cellular metabolic fluxes, for instance with13C-metabolic flux analysis, is highly important for applied and fundamental metabolic research. A current challenge in13C-flux analysis is that the available experimental data are usually insufficient to resolve metabolic fluxes in large metabolic networks without making assumptions on flux directions and reversibility. To infer metabolic fluxes in a more unbiased manner, we devised an approach that does not require such assumptions. The developed three-step approach integrates thermodynamics, metabolome, physiological data, and13C labelling data, and involves a novel method to comprehensively sample the complex thermodynamically-constrained metabolic flux space. Applying our approach to budding yeast with its compartmentalised metabolism and parallel pathways, we could resolve metabolic fluxes in an unbiased manner, we obtained an uncertainty estimate for each flux, and we found novel flux patterns that until now had remained unknown, likely due to assumptions made in previous13C flux analysis studies. We expect that our approach will be an important step forward to determine metabolic fluxes with improved accuracy in microorganisms and possibly also in more complex organisms.
Metal contamination and oxidative stress biomarkers in estuarine fish following a mine tailing disaster
Authors: Gabriel Fabrício Ângelo , Hauser-Davis Rachel Ann , Soares Lorena Oliveira Souza , de Azevedo Mazzuco Ana Carolina , Rocha Rafael Christian Chávez , Saint’Pierre Tatiana Dillenburg , Saggioro Enrico Mendes , Correia Fábio Veríssimo , Ferreira Tiago Osório , Bernardino Angelo Fraga
Published: June 2020

The Rio Doce estuary in Brazil was impacted by the deposition of mine tailings caused by the collapse of a mining dam in 2015. Since the disaster, the estuary is experiencing chronic trace metal contamination effects, but potential trace metal accumulation in fishes has not been reported. Trace metals in aquatic ecosystems pose severe threats to the aquatic biota, so we hypothesized that the accumulation of trace metals in estuarine sediments nearly two years after the disaster would cause contaminant bioaccumulation, resulting in the biosynthesis of metal-responsive proteins in fishes. We determined trace metal concentrations in sediment samples, metal concentrations, and quantified stress protein concentrations in the liver and muscle tissue of five different fish species in the estuary. Our results revealed high concentrations of trace metals in estuarine sediments when compared to published baseline values for this estuary. The demersal fish speciesCathorops spixiiandGenidens genidenshad the highest Hg, As, Se, Cr, and Mn concentrations in both hepatic and muscle tissues. Metal bioaccumulation in fish was statistically correlated with the biosynthesis of metallothionein and reduced glutathione in both fish liver and muscle tissue. The trace metals detected in fish tissues resemble those in the contaminated sediments present at the estuary at the time of this study and were also significantly correlated to protein levels. Trace metals in fish muscle were above the maximum permissible limits for human consumption, suggesting potential human health risks that require further determination. Our study supports the high biogeochemical mobility of trace metals between contaminated sediments and local biota in estuarine ecosystems.
Frame-by-frame annotation of video recordings using deep neural networks
Authors: Conway Alexander M. , Durbach Ian N. , McInnes Alistair , Harris Robert N.
Published: June 2020

Video data are widely collected in ecological studies but manual annotation is a challenging and time-consuming task, and has become a bottleneck for scientific research. Classification models based on convolutional neural networks (CNNs) have proved successful in annotating images, but few applications have extended these to video classification. We demonstrate an approach that combines a standard CNN summarizing each video frame with a recurrent neural network (RNN) that models the temporal component of video. The approach is illustrated using two datasets: one collected by static video cameras detecting seal activity inside coastal salmon nets, and another collected by animal-borne cameras deployed on African penguins, used to classify behaviour. The combined RNN-CNN led to a relative improvement in test set classification accuracy over an image-only model of 25% for penguins (80% to 85%), and substantially improved classification precision or recall for four of six behaviour classes (12–17%). Image-only and video models classified seal activity with equally high accuracy (90%). Temporal patterns related to movement provide valuable information about animal behaviour, and classifiers benefit from including these explicitly. We recommend the inclusion of temporal information whenever manual inspection suggests that movement is predictive of class membership.
DFT Modelling of the Electronic Structure and Stabilities of (Sb2O5.nH2O) Clusters towards Cysteine, Glucose and Trypanothione Complexation
Authors: Rabaa Hassan , Garfov Andriy , Sundholm Dage
Published: June 2020

A large series of dipeptides containing sulfur groups and antimony SbVwere modeled to understand their inhibitor activity against Leishmaniasis. The trypanothione reductase (TR), which acts as a reducing agent in several vital processes, is responsible for maintaining the parasite’s cellular thiol redox balance. The antimonic SbVacid (Sb2O5·nH2O) is being evaluated as a drug with inhibitory activity against Leishmaniasis. In the present work, we investigated the inhibitory effect of antimony oxide on (TR) activity modeled as a substrate by probing two model clusters in gas phase and continuum water medium:A[(Sb2O10H8)]−2coordinated to cysteine, andB[Sb7O28H21] coordinated to trypanothione, including glucose adduct. We report here density functional theory (DFT and DFT-D3) using (B3LYP/LANL2DZ and (TPSS/def2TZVP) results on the binding energy of cysteine and trypanthione complexed to these clusters as possible sites promoting the inhibition process. Upon viewing the results of the computational studies of cluster models and theoretical thermochemistry data for receptor-substrate interactions, identification of ligand-cluster interactions helps to unravel the mechanism of inhibition. The acidity of (Sb2O5,nH2O) leads to great cluster-dipeptide passivation. The electrostatic forces between cluster interface and dipeptide interaction present relevant inhibition effects through proton transfer or mobility from the different amine and ketone groups. The reactivity differences come from the unoccupied lone pairs 5pSbwhich lie at higher energy but remain available to make a good interaction with the lowest orbital p nitrogen in NH2, and in the CO groups substrate fragment in the zone HOMO-LUMO. Further cluster stability comparisons show a lower Gibbs free energy inB3(B/trypanthione/glucose) (18 – 30 kcal/mol) at both used level in this study and gives good accurate intramolecular interactions, confirmed by the use of the dispersion-corrected density functional (DFT-D3). Given the dipeptide H-mobility and the (Sb2O5,nH2O) cluster acidity, (donor-acceptor duality), the system is predicted to be potent cluster of the inhibitors by endothermic and spontaneous reaction requiring 3.10 kcal/mol in aqueous medium.
What it takes to be at the top: The interrelationship between chronic social stress and social dominance
Authors: Šabanović Merima , Liu He , Mlambo Vongai , Aqel Hala , Chaudhury Dipesh
Published: June 2020

Dominance hierarchies of social animal groups are influenced by complex factors such as stress. Stress experienced by an animal prior to social interactions with a conspecific may be a determinant of their future social dynamics. Additionally, long-term occupancy of a specific hierarchical rank can have psychophysiological effects, leading to vulnerability to future stress.

The current study aimed to delineate differential effects of stress acting before or after hierarchy formation. Using the chronic social defeat stress (CSDS) paradigm we performed behavioural investigations to determine whether exposure to CSDS before hierarchy formation predicted the new dominance status. Moreover, in another study we investigated whether social rank predicted stress vulnerability.

We found that CSDS did not impede the establishment of dominance in new hierarchies as both stress-susceptible (socially avoidant) and –resilient (social) mice were able to attain dominant ranks. In contrast, within newly established hierarchies of stress-naïve mice, the subordinate, but not dominant, mice exhibit significantly greater avoidance of novel social targets. However, following exposure to CSDS, both lowest- and highest-ranked mice exhibit strong susceptibility to stress as measured by decreased interactions with a novel social target.

These results suggest that the response to chronic social stress did not determine social rank in new cohorts, but low-status mice in newly established groups exhibited lower sociability to novel social targets. Interestingly, exposure of a hierarchical social group to chronic social stress led to stress-susceptibility in both high- and low-status mice as measured by social interaction.

Highlights

Stress susceptibility to chronic social defeat did not impede the establishment of dominance in new hierarchies.

Subordinate mice exhibit reduced social preference after hierarchy formation.

Following chronic social defeat stress, both subordinate and dominant mice exhibit susceptible-like reduction in social interaction, but dominant mice exhibit the greater decrease in social preference as compared to baseline.
Otx2 and Oc1 directly regulate the transcriptional program of cone photoreceptor development
Authors: Lonfat Nicolas , Wang Su , Lee ChangHee , Choi Jiho , Park Peter J. , Cepko Connie
Published: June 2020

The vertebrate retina is a highly organized structure of approximately 110 cell types. Retinal progenitor cells (RPCs) produce these cell types in a temporal order that is highly conserved. While some RPCs produce many cell types, some terminally dividing RPCs produce restricted types of daughter cells, such as a cone photoreceptor and a horizontal cell (HC). Here, we compared the transcriptomes and chromatin profiles of such a restricted cone/HC RPC with those of other RPCs. We identified many cis-regulatory modules (CRMs) active in cone/HC RPCs and developing cones. We then showed that Otx2 and Oc1 directly regulate the activity of multiple CRMs genome-wide, including near genes important for cone development, such as Rxrg and Neurod1. In addition, we found that Otx2 regulates itself. These results suggest that Otx2 and Oc1 have a broader role than previously appreciated, and deepen our understanding of retinal development, which may benefit therapies for retinal diseases.
DRAM for distilling microbial metabolism to automate the curation of microbiome function
Authors: Shaffer Michael , Borton Mikayla A. , McGivern Bridget B. , Zayed Ahmed A. , La Rosa Sabina L. , Solden Lindsey M. , Liu Pengfei , Narrowe Adrienne B. , Rodríguez-Ramos Josué , Bolduc Benjamin , Gazitua M. Consuelo , Daly Rebecca A. , Smith Garrett J. , Vik Dean R. , Pope Phil B. , Sullivan Matthew B. , Roux Simon , Wrighton Kelly C.
Published: June 2020

Microbial and viral communities transform the chemistry of Earth’s ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles, and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.
Sex-biased islet β cell dysfunction is caused by the MODY MAFA S64F variant by inducing premature aging and senescence in males
Authors: Walker Emily M. , Cha Jeeyeon , Tong Xin , Guo Min , Liu Jin-Hua , Yu Sophia , Iacovazzo Donato , Mauvais-Jarvis Franck , Flanagan Sarah E. , Korbonits Márta , Stafford John , Jacobson David , Stein Roland
Published: June 2020

A heterozygous missense mutation producing a variant of the islet β-cell-enriched MAFA transcription factor (Ser(S)64Phe(F) MAFA) was identified in humans who developed adult-onset, β-cell dysfunction (diabetes or insulinomatosis), with men more prone to diabetes. This mutation engenders increased stability to the normally unstable MAFA protein. To obtain insight into how this variant impacts β cell function, we developed a mouse model expressing S64F MafA and found sex-dependent phenotypes, with heterozygous mutant males displaying impaired glucose tolerance while females were slightly hypoglycemic with improved blood glucose clearance. Only heterozygous males showed transiently higher MafA protein levels preceding the onset of glucose intolerance and sex-dependent, differential expression of genes involved in calcium signaling, DNA damage, aging, and senescence. Functional changes in islet calcium handling and signs of islet aging and senescence processes were uniquely observed in male animals. In addition, S64F MAFA expression in human, male EndoC-βH2 β cells accelerated cellular senescence and increased production of senescence-associated secretory proteins compared to cells expressing wild-type MAFA. Together, these results implicate a conserved mechanism of accelerated islet aging and senescence in promoting diabetes in S64F MAFA carriers in a sex-dependent manner.
Alignment-free identification of COI DNA barcode data with the Python package Alfie
Authors: Nugent Cameron M. , Adamowicz Sarah J.
Published: June 2020

Characterization of biodiversity from environmental DNA samples and bulk metabarcoding data is hampered by off-target sequences that can confound conclusions about a taxonomic group of interest. Existing methods for isolation of target sequences rely on alignment to existing reference barcodes, but this can bias results against novel genetic variants. Effectively parsing targeted DNA barcode data from off-target noise improves the quality of biodiversity estimates and biological conclusions by limiting subsequent analyses to a relevant subset of available data. Here, we present Alfie, a Python package for the alignment-free classification of cytochrome c oxidase subunit I (COI) DNA barcode sequences to taxonomic kingdoms. The package determinesk-mer frequencies of DNA sequences, and the frequencies serve as input for a neural network classifier that was trained and tested using ~58,000 publicly available COI sequences. The classifier was designed and optimized through a series of tests that allowed for the optimal set of DNAk-mer features and optimal machine learning algorithm to be selected. The neural network classifier rapidly assigns COI sequences to kingdoms with greater than 99% accuracy and is shown to generalize effectively and make accurate predictions about data from previously unseen taxonomic classes. The package contains an application programming interface that allows the Alfie package’s functionality to be extended to different DNA sequence classification tasks to suit a user’s need, including classification of different genes and barcodes, and classification to different taxonomic levels. Alfie is free and publicly available through GitHub (https://github.com/CNuge/alfie) and the Python package index (https://pypi.org/project/alfie/).
TNFα-induced LDL cholesterol accumulation involve elevated LDLR cell surface levels and SR-B1 downregulation in human arterial endothelial cells
Authors: Okoro Emmanuel Ugochukwu
Published: June 2020

Excess lipid droplets are frequently observed in arterial endothelial cells at sites of advanced atherosclerotic plaques. Here, the role of tumor necrosis factor alpha (TNFα) in modulating low density lipoprotein (LDL) content in confluent primary human aortic endothelial cells (pHAECs) was investigated. TNFα promoted up to 2 folds increase in cellular cholesterol, which was resistant to ACAT inhibition. The cholesterol increase was associated with increased125I-LDL surface binding. Using the non-hydrolysable label, Dil, TNFα could induce a massive increase in Dil-LDL by over 200 folds. The elevated intracellular Dil-LDL was blocked with excess unlabeled LDL and PCSK9, but not oxidized LDL (oxLDL), receptor associated protein (RAP), or apolipoprotein (apoE) depletion. Moreover, TNFα-induced increase of LDL-derived lipids was elevated through lysosome inhibition. Using specific LDLR antibody, the Dil-LDL accumulation was reduced by over 99%. Effects of TNFα included LDLR cell surface increase by 138%, and very large increases in ICAM-1 total and surface proteins, respectively. In contrast, that of scavenger receptor B1 (SR-B1) was reduced. Additionally, LDLR antibody bound rapidly in TNFα-treated cells by about 30 folds, inducing a migrating shift in the LDLR protein. The effect of TNFα on Dil-LDL accumulation was inhibited by the antioxidant tetramethythiourea (TMTU) dose-dependently, but not by inhibitors against NF-κB, stress kinases, ASK1, JNK, p38, or apoptosis caspases. Grown on transwell inserts, TNFα did not enhance apical to basolateral LDL cholesterol or Dil release. It is concluded that TNFα promotes LDLR functions through combined increase at the cell surface and SR-B1 downregulation.
GWAS reveals the genetic complexity of fructan accumulation patterns in barley grain
Authors: Matros Andrea , Houston Kelly , Tucker Matthew R. , Schreiber Miriam , Berger Bettina , Aubert Matthew K. , Wilkinson Laura G. , Witzel Katja , Waugh Robbie , Seiffert Udo , Burton Rachel A.
Published: June 2020

We profiled the grain oligosaccharide content of 154 two-row spring barley genotypes and quantified 27 compounds, mainly fructans, that exhibited differential abundance. Clustering revealed two major profile groups where the ‘high’ set contained greater amounts of sugar monomers, sucrose and overall fructans, but lower fructosylraffinose. GWAS identified a significant association for the variability of two fructan types; neoseries-DP7 and inulin-DP9 which showed increased strength when a compound-ratio GWAS was applied. Gene models within this region included five fructan biosynthesis genes, of which three (fructan:fructan 1-fructosyltransferase, sucrose:sucrose 1-fructosyltransferase, and sucrose:fructan 6-fructosyltransferase)have already been described. The remaining two,6(G)-fructosyltransferaseandvacuolar invertase1have not previously been linked to fructan biosynthesis in barley and showed expression patterns distinct from those of the other three genes, including exclusive expression of6(G)-fructosyltransferasein outer grain tissues at the storage phase. From exome capture data several SNPs related to inulin- and neoseries-type fructan variability were identified infructan:fructan 1-fructosyltransferaseand6(G)-fructosyltransferasegenes Co-expression analyses uncovered potential regulators of fructan biosynthesis including transcription factors. Our results provide evidence for the distinct biosynthesis of neoseries-type fructans during barley grain maturation plus new gene candidates likely involved in the differential biosynthesis of the various fructan types.

Highlight

Grain fructan profiles in barley are more complex than previously expected and variations in a diversity panel relate to a genomic region where fructan biosynthesis genes cluster.
The diverging evolutionary history of opsin genes in Diptera
Authors: Feuda Roberto , Goulty Matthew , Zadra Nicola , Gasparetti Tiziana , Rosato Ezio , Segata Nicola , Rizzoli Annapaola , Pisani Davide , Ometto Lino , Stabelli Omar Rota
Published: June 2020

Opsin receptors mediate the visual process in animals and their evolutionary history can provide precious hints on the ecological factors that underpin their diversification. Here we mined the genomes of more than 60 Dipteran species and reconstructed the evolution of their opsin genes in a phylogenetic framework. Our phylogenies indicate that dipterans possess an ancestral set of five core opsins which have undergone several lineage-specific events including an independent expansion of low wavelength opsins in flies and mosquitoes and numerous family specific duplications and losses. Molecular evolutionary studies indicate that gene turnover rate, overall mutation rate, and site-specific selective pressure are higher inAnophelesthan inDrosophila; we found signs of positive selection in both lineages, including events possibly associated with their peculiar behaviour. Our findings indicate an extremely variable pattern of opsin evolution in dipterans, showcasing how two similarly aged radiations -AnophelesandDrosophila- can be characterized by contrasting dynamics in the evolution of this gene family.