bluuebunny/crossref_metadata_2025 huggingface dataset:
Four novel Picornaviruses detected in Magellanic Penguins (Spheniscus magellanicus) in Chile
Authors: Hayer Juliette , Wille Michelle , Font Alejandro , González-Aravena Marcelo , Norder Helene , Malmberg Maja
Published: October 2020

Members of thePicornaviridaecomprise a significant burden on the poultry industry, causing diseases such as gastroenteritis and hepatitis. However, with the advent of metagenomics, a number of picornaviruses have now been revealed in apparently healthy wild birds. In this study, we identified four novel viruses belonging to the familyPicornaviridaein healthy Magellanic Penguins (Spheniscus magellanicus), a near threatened species found along the coastlines of temperate South America. We collected 107 faecal samples from 72 individual penguins. Twelve samples were initially sequenced by high throughout sequencing with metagenomics approach. All samples were subsequently screened by PCR for these new viruses, and approximately 20% of the penguins were infected with at least one of these viruses, and seven individuals were co-infected with two or more. The viruses were distantly related to members of the genera Hepatoviruses, Tremoviruses and unassigned viruses from Antarctic Penguins and Red-Crowned Cranes. Further, they had more than 60% amino acid divergence from other picornaviruses, and therefore likely constitute novel genera. That these four novel viruses were abundant among the sampled penguins, suggests Magellanic Penguins may be a reservoir for several picornaviruses belonging to different genera. Our results demonstrate the vast undersampling of wild birds for viruses, and we expect the discovery of numerous avian viruses that are related to Hepatoviruses and Tremoviruses in the future.

Importance

Recent work has demonstrated that Antarctic penguins of the genusPygoscelisare hosts for an array of viral species. However, beyond these Antarctic penguin species, very little is known about the viral diversity or ecology in this highly charismatic avian order. Through metagenomics we identified four novel viruses belonging to thePicornaviridaefamily in faecal samples from Magellanic Penguins. These highly divergent viruses, each possibly representing novel genera, are related to members of the Hepatovirus, Tremovirus genera, and unassigned picornaviruses described from Antarctic Penguin and Red-crowned Cranes. By PCR these novel viruses were shown to be common in Magellanic Penguins, indicating that penguins may play a key role in their epidemiology and evolution. Overall, we encourage further sampling to reveal virus diversity, ecology, and evolution in these unique avian taxa.
Convergent evolution of Streptomyces protease inhibitors involving a tRNA-mediated condensation-minus NRPS
Authors: Aguilar César , Verdel-Aranda Karina , Ramos-Aboites Hilda E. , Morales Marco Antonio , Licona-Cassani Cuauhtémoc , Barona-Gómez Francisco
Published: October 2020

Small peptide aldehydes (SPAs) with protease inhibitory activity are natural products typically synthesized by nonribosomal peptide synthetases (NRPS). SPAs are widely used in biotechnology, as therapeutic agents, they are physiologically relevant and regulate development of the natural hosts. During genome evolutionary analysis of Streptomyces lividans 66 we identified an NRPS-like biosynthetic gene cluster (BGC) that lacked a condensation (C) domain but included a tRNA-Utilizing Enzyme (tRUE) belonging to the leucyl/phenylalanyl (L/F) transferase family. This system was predicted to direct the synthesis of a novel SPA with protease inhibitory activity, called livipeptin. Following genome mining and phylogenomic analyses we confirmed the presence of tRUEs within diverse Streptomyces genomes, including fusions with a C-minus NRPS-like protein. We further demonstrate functional cooperation between these enzymes and provide the biosynthetic rules for the synthesis of livipeptin, expanding the known universe of acetyl-leu/phe-arginal SPAs. The L/F-transferase C-minus NRPS productive interaction was shown to be tRNA-dependent after semisynthetic assays in the presence of RNAse, which contrasts with leupeptin, an acetyl-leu-arginal SPA that we show to be produced by Streptomyces roseous ATCC 31245 via a tRUE-minus BGC with multiple complete NRPSs. Thus, livipeptin and leupeptin are the result of convergent evolution, which has driven the appearance of unprecedented biosynthetic logics directing the synthesis of protease inhibitors thought to be at the core of Streptomyces colony biology. Our results pave the way for understanding this Streptomyces trait, as well as for the discovery of novel natural products following evolutionary genome mining approaches.

Abstract importance

Convergent evolution in microbiology is believed to be highly recurrent yet examples that have been comprehensively characterized are scarce. Proteases inhibition by small peptide aldehydes is at the core of many microbiological processes, both within the cell and during colony development, and in microbial ecology. Here we report the biosynthetic foundations of leupeptin, the main Streptomyces protease inhibitor, and of livipeptin, a protease inhibitor produced by Streptomyces lividans. Although these peptides belong to the same chemical class, here we show that their biosynthetic routes result from convergent evolution, as they involve unrelated biosynthetic mechanisms, including the recruitment of a tRNA-utilizing enzyme that functionally replaces the condensation domain of a nonribosomal peptide synthetase during livipeptin biosynthesis. Thus, these results pave the way for understanding Streptomyces protease inhibitors as a trait and provide unprecedented knowledge for genome mining of natural products and synthetic biology where proteases inhibition is desirable.
Early Tocilizumab Dosing is Associated with Improved Survival In Critically Ill Patients Infected With Sars-CoV-2
Authors: Petrak Russell M. , Van Hise Nicholas W. , Skorodin Nathan C. , Fliegelman Robert M. , Chundi Vishnu , Didwania Vishal , Han Alice , Harting Brian P. , Hines David W.
Published: October 2020

Background

SARS-CoV-2 is a novel coronavirus that has rapidly expanded to become a pandemic, resulting in millions of deaths worldwide. The cytokine storm is caused by the release of inflammatory agents and results in a physiologic disruption. Tocilizumab is an IL-6 receptor antagonist with the ability to suppress the cytokine storm in critically ill patients infected with SARS-CoV-2.

Methods

This was a multi-center study of patients infected with SARS-CoV-2, admitted between 3/13/20 and 4/16/20, requiring mechanical ventilation. Parameters that were evaluated included age, sex, race, usage of steroids, inflammatory markers, and comorbidities. Early dosing was defined as a tocilizumab dose administered prior to or within one (1) day of intubation. Late dosing was defined as a dose administered greater than one (1) day after intubation. A control group that was treated only with standard of care, and without tocilizumab, was utilized for comparison (untreated).

Findings

We studied 118 patients who required mechanical ventilation. Eighty-one (81) received tocilizumab, compared to 37 who were untreated. Early tocilizumab therapy was associated with a statistically significant decrease in mortality as compared to patients who were untreated (p=0.003). Dosing tocilizumab late was associated with an increased mortality compared to the untreated group (p=0.006).

Interpretation

Early tocilizumab administration was associated with decreased mortality in critically ill SARS-Co-V-2 patients, but a potential detriment was suggested by dosing later in a patient’s course.

Funding

This work did not receive outside funding or sponsorship.
Spatial modulation of dark versus bright stimulus responses in mouse visual cortex
Authors: Williams Brice , Rosario Joseph Del , Coletta Stefano , Bichler Edyta K. , Muzzu Tomaso , Speed Anderson , Meyer-Baese Lisa , Saleem Aman B. , Haider Bilal
Published: October 2020

A fundamental task of the visual system is to respond to luminance increments and decrements. In primary visual cortex (V1) of cats and primates, luminance decrements elicit stronger, faster, and more salient neural activity (OFF responses) than luminance increments (ON responses). However, studies of V1 in ferrets and mice show that ON responses may be stronger. These discrepancies may arise from differences in species, experimental conditions, or from measuring responses in single neurons versus populations. Here, we examined OFF versus ON responses across different regions of visual space in both single neurons and populations of mouse V1. We used high-density silicon probes and whole-cell patch-clamp recordings to assess OFF versus ON dominance in local field potential (LFP), single neuron, and membrane potential responses. Across these levels, we found that OFF responses clearly dominated in the central visual field, whereas ON responses were more evident in the periphery. These observations were clearest in LFP and subthreshold membrane potential. Our findings consolidate and resolve prior conflicting results and reveal that retinotopy may provide a common organizing principle for spatially biasing OFF versus ON processing in mammalian visual systems.
Social Disruption: Sublethal pesticides in pollen lead toApis melliferaqueen events and brood loss
Authors: Traynor Kirsten S. , vanEngelsdorp Dennis , Lamas Zachary S.
Published: October 2020

EusocialApis melliferacolonies depend on queen longevity and brood viability to survive, as the queen is the sole reproductive individual and the maturing brood replenishes the shorter lived worker bees. Production of many crops rely on both pesticides and bee pollination to improve crop quantity and quality. We looked at the resiliency of queens and their brood after one month of sublethal exposure to field relevant doses of pesticides that mimic exposure during commercial pollination contracts. We exposed full size colonies to pollen contaminated with field-relevant doses of the fungicides (chlorothalonil and propicanizole), insecticides (chlorypyrifos and fenpropathrin) or both, noting a significant reduction in pollen consumption in colonies exposed to fungicides compared to control. While we found no difference in the total amount of pollen collected per colony, a higher proportion of pollen to non-pollen foragers was detected in all pesticide exposed colonies. After ceasing treatments we measured brood development, discovering a significant increase in brood loss and/or cannibalism across all pesticide exposed groups. Sublethal pesticide exposure in general was linked to reduced production of replacement workers and a change in protein acquisition (pollen vs. non-pollen foraging). Fungicide exposure also resulted in increased loss of the reproductive queen.
Assessing short- and long-term variations in diversity, timing, and body condition of migratory frugivorous birds
Authors: Campo-Celada María , Mendoza Irene , Benítez-López Ana , Gutiérrez-Expósito Carlos , Rabadán-González Julio , Jordano Pedro
Published: October 2020

Under current global change context, climate change is driving substantial phenological mismatches between plant species and the organisms that rely on them. Given that frugivorous birds are fundamental for forest regeneration, and most of them are migrant species, identifying the effect of global change over them must be a priority. In this study we have analysed changes in the composition, morphometry, and physical condition in an avian community at long- (40 years) and short time (seasonal) spans. Our findings indicate a profound transformation at practically every level of analysis. In 40 years, the avian community shows a 66% and 13% decrease of the wintering and seed-disperser species, respectively. Seasonal abundance peaks were advanced in 13 out of 15 species. In addition, we have found a significant 1.5% increase in the morphometric measurements of certain species, supporting findings in previous studies, and also a remarkable general decrease of body condition. Our results point towards land use changes and climate change as the main causes. If this influence continues to rise, biodiversity will likely be irreversibly altered, damaging crucial ecosystem functions such as animal-mediated seed dispersal and forest regeneration in particular.
ASTER: A Method to Predict Clinically Actionable Synthetic Lethal Genetic Interactions
Authors: Liany Herty , Jeyasekharan Anand , Rajan Vaibhav
Published: October 2020

A Synthetic Lethal (SL) interaction is a functional relationship between two genes or functional entities where the loss of either entity is viable but the loss of both is lethal. Such pairs can be used to develop targeted anticancer therapies with fewer side effects and reduced overtreatment. However, finding clinically actionable SL interactions remains challenging. Leveraging unified gene expression data of both disease-free and cancerous samples, we design a new technique based on statistical hypothesis testing, called ASTER, to identify SL pairs. We empirically find that the patterns of mutually exclusivity ASTER finds using genomic and transcriptomic data provides a strong signal of SL. For large-scale multiple hypothesis testing, we develop an extension called ASTER++ that can utilize additional input gene features within the hypothesis testing framework. Our extensive experiments demonstrate the efficacy of ASTER in identifying SL pairs with potential therapeutic benefits.

CCS CONCEPTS

• Applied computing→Computational genomics;Health informatics; •Mathematics of computing→Hypothesis testing and confidence interval computation.

ACM Reference Format

Herty Liany, Anand Jeyasekharan, and Vaibhav Rajan. 2021. ASTER: A Method to Predict Clinically Actionable Synthetic Lethal Genetic Interactions. InProceedings of ACM Conference. ACM, New York, NY, USA, 10 pages.https://doi.org/10.1145/nnnnnnn.nnnnnnn
Multiple ligand recognition sites in free fatty acid receptor 2 (FFAR2) direct distinct neutrophil activation patterns
Authors: Lind Simon , Holdfeldt André , Mårtensson Jonas , Granberg Kenneth L. , Forsman Huamei , Dahlgren Claes
Published: October 2020

Non-activating positive allosteric modulators specific for free fatty acid receptor 2 (FFAR2) increased the activity induced by orthosteric agonists to trigger a rise in intracellular Ca2+([Ca2+]i) and activate the O2−producing neutrophil NADPH-oxidase. In addition, two allosteric modulators (Cmp58 and AZ1729) recognized by different receptor domains on FFAR2, cooperatively triggered activation without any rise in [Ca2+]i. To gain insights into FFAR2 modulation and signaling, we set out to identify structurally diverse allosteric FFAR2 modulators. Initially, we identified two molecules that directly activate neutrophils and these were classified as an allosteric FFAR2 agonists and an orthosteric agonist, respectively. Based on the sensitizing effect on the neutrophil response to propionate, ten non-direct-activating molecules were classified as allosteric FFAR2 modulators. One of these synergistically activated neutrophils when combined with AZ1729, but not when combined with Cmp58. The remaining nine compounds synergistically induced the same type of biased neutrophil signaling but only when combined with Cmp58. The activation signals down-stream of FFAR2 when stimulated by two allosteric modulators with different binding sites were in most cases biased in that two complementary modulators together triggered an activation of the NADPH-oxidase, but no increase in [Ca2+]i. The neutrophil activation pattern achieved when two functionally “AZ1729- or “Cmp58-like” allosteric FFAR2 modulators were combined, supporting a model for activation in which FFAR2 has two different sites that selectively bind allosteric modulators. The novel neutrophil activation patterns and receptor down-stream signaling mediated by two cross-sensitizing allosteric modulators represent a new regulatory mechanism that controls FFAR2 receptor function.
Spatiotemporal organization of movement-invariant and movement-specific signaling in the output layer of motor cortex
Authors: Currie Stephen P. , Ammer Julian J. , Premchand Brian , Dacre Joshua , Wu Yufei , Eleftheriou Constantinos , Colligan Matt , Clarke Thomas , Mitchell Leah , Faisal Aldo , Hennig Matthias H. , Duguid Ian
Published: October 2020

Motor cortex generates descending output necessary for executing a wide range of limb movements. Although movement-related activity has been described throughout motor cortex, the spatiotemporal organization of movement-specific signaling in deep layers remains largely unknown. Here, we recorded layer 5B population dynamics in the caudal forelimb area of motor cortex while mice performed a forelimb push/pull task and found that most neurons show movement-invariant responses, with a minority displaying movement specificity. Cell-type-specific imaging identified that movement-invariant responses dominated pyramidal tract (PT) neuron activity, with a small subpopulation representing movement type, whereas a larger proportion of intratelencephalic (IT) neurons displayed movement-specific signaling. The proportion of IT neurons decoding movement-type peaked prior to movement initiation, while for PT neurons this occurred during movement execution. Our data suggest that layer 5B population dynamics largely reflect movement-invariant signaling, with information related to movement-type being differentially routed through relatively small, distributed subpopulations of projection neurons.
DOUBLER: Unified Representation Learning of Biological Entities and Documents for Predicting Protein–Disease Relationships
Authors: Sztyler Timo , Malone Brandon
Published: October 2020

Motivation

We propose a system that learns consistent representations of biological entities, such as proteins and diseases, based on a knowledge graph and additional data modalities, like structured annotations and free text describing the entities. In contrast to similar approaches, we explicitly incorporate the consistency of the representations into the learning process. In particular, we use these representations to identify novel proteins associated with diseases; these novel relationships could be used to prioritize protein targets for new drugs.

Results

We show that our approach outperforms state-of-the-art link prediction algorithms for predicting unknown protein–disease associations. Detailed analysis demonstrates that our approach is most beneficial when additional data modalities, such as free text, are informative.

Availability

Code and data are available at:https://github.com/nle-sztyler/research-doubler

Contact

timo.sztyler@neclab.eu
Root water gates and not changes in root structure provide new insights into plant physiological responses and adaptations to drought, flooding and salinity
Authors: Domec Jean-Christophe , King John S. , Carmichael Mary J. , Overby Anna Treado , Wortemann R Remi , Smith William K. , Miao Guofang , Noormets Asko , Johnson Daniel M.
Published: October 2020

The influence of aquaporin (AQP) activity on plant water movement remains unclear, especially in plants subject to unfavorable conditions. We applied a multitiered approach at a range of plant scales to (i) characterize the resistances controlling water transport under drought, flooding and flooding plus salinity conditions; (ii) quantify the respective effects of AQP activity and xylem structure on root (Kroot), stem (Kstem) and leaf (Kleaf) conductances, and (iii) evaluate the impact of AQP-regulated transport capacity on gas exchange. We found that drought, flooding and flooding-salinity reduced Krootand root AQP activity inPinus taeda, whereas Krootof the flood-tolerantTaxodium distichumdid not decline under flooding. The extent of the AQP-control of transport efficiency varied among organs and species, ranging from 35%-55% in Krootto 10%-30% in Kstemand Kleaf. In response to treatments, AQP-mediated inhibition of Krootrather than changes in xylem acclimation controlled the fluctuations in Kroot. The reduction in stomatal conductance and its sensitivity to vapor pressure deficit were direct responses to decreased whole-plant conductance triggered by lower Krootand larger resistance belowground. Our results provide new mechanistic and functional insights on plant hydraulics that are essential to quantifying the influences of future stress on ecosystem function.
The mutability of demographic noise in microbial range expansions
Authors: Yu QinQin , Gralka Matti , Duvernoy Marie-Cécilia , Sousa Megan , Harpak Arbel , Hallatschek Oskar
Published: October 2020

Demographic noise, the change in the composition of a population due to random birth and death events, is an important driving force in evolution because it reduces the efficacy of natural selection. Demographic noise is typically thought to be set by the population size and the environment, but recent experiments with microbial range expansions have revealed substantial strain-level differences in demographic noise under the same growth conditions. Many genetic and phenotypic differences exist between strains; to what extent do single mutations change the strength of demographic noise? To investigate this question, we developed a high-throughput method for measuring demographic noise in colonies without the need for genetic manipulation. By applying this method to 191 randomly-selected single gene deletion strains from theE. coliKeio collection, we find that a typical single gene deletion mutation decreases demographic noise by 8% (maximal decrease: 81%). We find that the strength of demographic noise is an emergent trait at the population level that can be predicted by colony-level traits but not cell-level traits. The observed differences in demographic noise from single gene deletions can increase the establishment probability of beneficial mutations by almost an order of magnitude higher than the wild type. Our results show that single mutations can substantially alter adaptation through their effects on demographic noise and suggest that demographic noise can be an evolvable phenotype of a population.
Graded titin cleavage progressively reduces tension and uncovers the source of A-band stability in contracting muscle
Authors: Li Yong , Hessel Anthony L. , Unger Andreas , Ing David , Recker Jannik , Koser Franziska , Freundt Johanna K. , Linke Wolfgang A.
Published: October 2020

The giant muscle protein titin is a major contributor to passive force; however, its role in active force generation is unresolved. Here, we use a novel titin-cleavage (TC) mouse model that allows specific and rapid cutting of elastic titin to quantify how titin-based forces define myocyte ultrastructure and mechanics. We show that under mechanical strain, as titin cleavage doubles from heterozygous to homozygous TC muscles, Z-disks become increasingly out of register while passive and active forces are reduced. Interactions of elastic titin with sarcomeric actin filaments are revealed. Strikingly, when titin-cleaved muscles contract, myosin-containing A-bands become split and adjacent myosin filaments move in opposite directions while also shedding myosins. This establishes intact titin filaments as critical force-transmission networks, buffering the forces observed by myosin filaments during contraction. To perform this function, elastic titin must change stiffness or extensible length, unveiling its fundamental role as an activation-dependent spring in contracting muscle.
IDENTIFICATION OF A NOVEL MECHANISM FOR LFA-1 ORGANIZATION DURING NK CYTOLYTIC RESPONSE
Authors: Pariani Alejandro P. , Almada Evangelina , Hidalgo Florencia , Borini-Etichetti Carla , Vena Rodrigo , Marín Leandra , Favre Cristián , Goldenring James R. , Larocca M. Cecilia
Published: October 2020

The elimination of transformed and viral infected cells by natural killer (NK) cells requires the formation of a specialized junction between NK and target cells, generally denominated immunological synapse (IS). After initial recognition, the IS enables the directed secretion of lytic granules content into the susceptible target cell. The lymphocyte function–associated antigen (LFA)-1 regulates NK effector function by enabling NK-IS assembly and maturation. The pathways underlying LFA-1 accumulation at the IS in NK cells have not been elucidated so far. A kinase anchoring protein 350 (AKAP350) is a centrosome/Golgi associated protein with a central role in the regulation of Golgi organization and microtubule dynamics. In T cells, AKAP350 participates in LFA-1 activation by mechanisms that remain elusive. We first investigated AKAP350 participation in NK cytolytic activity. Our results showed that the decrease in AKAP350 levels by expression of specific shRNAs (AKAP350KD) inhibited NK-YTS cytolytic activity, without affecting NK:target cell conjugate formation. The impairment of NK effector function in AKAP350KD cells correlated with decreased LFA-1 clustering and defective IS maturation. AKAP350KD cells that were exclusively activatedviaLFA-1 showed impaired LFA-1 organization and deficient lytic granule translocation as well. In NK AKAP350KD cells, activation signaling through Vav1 was preserved up to 10 min of interaction with target cells, but significantly decreased afterwards. Experiments in YTS and inex vivoNK cells revealed the existence of an intracellular pool of LFA-1 vesicles, which partially associated with the Golgi apparatus. Upon NK cell activation, this LFA-1 pool redistributed to the IS in a Golgi-AKAP350-dependent manner. Disruption of Golgi integrity or alteration of microtubule dynamics impaired LFA-1 localization at the IS. Therefore, this study reveals the existence of a Golgi/AKAP350 dependent trafficking pathway for LFA-1, which is relevant for LFA-1 organization at NK-lytic IS and, concomitantly, for NK cytolytic function.
Resilience in a Natural Model of Metabolic Dysfunction Through Changes in Longevity and Ageing-Related Metabolites
Authors: Medley J Kyle , Persons Jenna , Biswas Tathagata , Olsen Luke , Peuß Robert , Krishnan Jaya , Xiong Shaolei , Rohner Nicolas
Published: October 2020

Insights from extreme-adapted organisms, which have evolved natural strategies for promoting survivability under severe environmental pressures, may help guide future research into novel approaches for enhancing human longevity. The cave-adapted Mexican tetra,Astyanax mexicanus, has attracted interest as a model system formetabolic resilience, a term we use to denote the property of maintaining robust health and longevity under conditions that would have highly deleterious effects in other organisms (Fig 1). Cave-dwelling populations of Mexi-can tetra exhibit elevated blood glucose and possess a mutation in the insulin receptor that in humans has been linked to Rabson-Mendenhall syndrome, a condition characterized by severe insulin resistance that causes numerous developmental abnormalities, is highly associated with debilitating progression, and drastically reduces lifespan. In addition, cavefish develop large numbers of hypertrophic visceral adipocytes and possess vastly enriched stores of body fat compared to surface-dwelling counterparts. However, cavefish appear to avoid the progression of the respective pathologies typically associated with these conditions, such as accumulation of advanced glycation end products (AGEs), chronic tissue inflammation, impaired growth due to insulin dysregulation, and low survivability due to arterial disease. The metabolic strategies underlying the resilience properties ofA. mexicanuscavefish, and how they relate to environmental challenges of the cave environment, are poorly understood. Here, we provide an untargeted metabolomics study of long- and short-term fasting in twoA. mexicanuscave populations and one surface population. We find that, although cave-fish share many similarities with metabolic syndrome normally associated with the human state of obesity, important differences emerge, including a reduction in cholesteryl esters and intermediates of protein glycation, and an increase in antioxidants and metabolites associated with hypoxia and longevity. We find important overlaps between metabolic alterations in cave-dwelling Mexican tetra and other models of resilience and extreme longevity, such as naked mole-rats, including enhanced reliance on sugars as an energy source and a trend toward more potent antioxidant activity. This work suggests that certain metabolic features associated with human pathologies are not intrinsically harmful, but are rather consequences of suboptimal adaptation of humans to survival under adverse metabolic conditions, and suggests promising avenues for future investigation into the role of metabolic strategies in evolutionary adaptation and health. We provide a transparent pipeline for reproducing our analysis and a Shiny app for other researchers to explore and visualize our dataset.
PhyKIT: a UNIX shell toolkit for processing and analyzing phylogenomic data
Authors: Steenwyk Jacob L. , Buida Thomas J. , Labella Abigail L. , Li Yuanning , Shen Xing-Xing , Rokas Antonis
Published: October 2020

Diverse disciplines in biology process and analyze multiple sequence alignments (MSAs) and phylogenetic trees to evaluate their information content, infer evolutionary events and processes, and predict gene function. However, automated processing of MSAs and trees remains a challenge due to the lack of a unified toolkit. To fill this gap, we introduce PhyKIT, a toolkit for the UNIX shell environment with 30 functions that process MSAs and trees, including but not limited to estimation of mutation rate, evaluation of sequence composition biases, calculation of the degree of violation of a molecular clock, and collapsing bipartitions (internal branches) with low support. To demonstrate the utility of PhyKIT, we detail three use cases: (1) summarizing information content in MSAs and phylogenetic trees for diagnosing potential biases in sequence or tree data; (2) evaluating gene-gene covariation of evolutionary rates to identify functional relationships, including novel ones, among genes; and (3) identify lack of resolution events or polytomies in phylogenetic trees, which are suggestive of rapid radiation events or lack of data. We anticipate PhyKIT will be useful for processing, examining, and deriving biological meaning from increasingly large phylogenomic datasets. PhyKIT is freely available on GitHub (https://github.com/JLSteenwyk/PhyKIT) and documentation including user tutorials are available online (https://jlsteenwyk.com/PhyKIT).
CharPlant: ADe NovoOpen Chromatin Region (OCR) Prediction Tool for Plant Genomes
Authors: Shen Yin , Chen Ling-Ling , Gao Junxiang
Published: October 2020

Chromatin accessibility is a highly informative structural feature for understanding gene transcription regulation because it indicates the degree to which nuclear macromolecules such as proteins and RNA can access chromosomal DNA. Studies show that chromatin accessibility is highly dynamic during stress response, stimulus response, and developmental transition. Moreover, physical access to chromosomal DNA in eukaryotes is highly cell-specific. Therefore, current technologies such as DNase-seq, ATAC-seq, and FAIRE-seq reveal only a portion of the open chromatin regions (OCRs) present in a given species. Thus, the genome-wide distribution of OCRs remains unknown. In this study, we developed a bioinformatics tool called CharPlant for thede novoprediction of chromatin accessible regions in plant genomes. To develop this tool, we constructed a three-layer convolutional neural network (CNN) and subsequently trained the CNN using DNase-seq and ATAC-seq datasets of four plant species. The model simultaneously learns the sequence motifs and regulatory logics, which are jointly used to determine DNA accessibility. All of these steps are integrated into CharPlant, which can be run using a simple command line. The results of data analysis using CharPlant in this study demonstrate its prediction power and computational efficiency. To our knowledge, CharPlant is the firstde novoprediction tool that can identify potential OCRs in the whole genome. The source code of CharPlant and supporting files are freely downloadable fromhttps://github.com/Yin-Shen/CharPlant.
Metaplastic reinforcement of long-term potentiation in rat hippocampal area CA2 by cholinergic receptor activation
Authors: Benoy Amrita , Bin Ibrahim Mohammad Zaki , Behnisch Thomas , Sajikumar Sreedharan
Published: October 2020

Hippocampal CA2, an inconspicuously positioned area between the well-studied CA1 and CA3 subfields, has captured research interest in recent years due to its role in the formation of social memory. The effects of synaptic depression for subsequent long-term potentiation (LTP) of synaptic transmission at entorhinal cortical (EC)-CA2 and Schaffer collateral (SC)-CA2 synapses have not been previously explored. Here we show that cholinergic receptor activation with the non-selective cholinergic agonist carbachol (CCh) triggers a long-term synaptic depression (CCh-LTD) of field excitatory postsynaptic potentials at EC- and SC-CA2 synapses in the hippocampus of adult rats. The activation of muscarinic acetylcholine receptors (mAChRs) is critical for the induction of an early phase (<100 min) of CCh-LTD, with a strong dependency upon M3 mAChR activation and a weaker one by M1 mAChRs. Interestingly, muscarinic M2 and nicotinic receptor activation are crucially involved in the late phase (>100 min) of CCh-LTD. Importantly, CCh priming lowers the threshold, in a protein synthesis-dependent manner, for the late maintenance of LTP that can be subsequently induced by high-frequency electrical stimulation at EC- or SC-CA2 pathways. The results demonstrate that CA2 synaptic learning rules are modified in a metaplastic manner, wherein synaptic modifications triggered by cholinergic stimulation can dictate the outcome of future plasticity events. Moreover, the observed enabling of late LTP at EC inputs to CA2 following the priming stimulus co-exists with concurrent sustained CCh-LTD at SC-CA2 and is dynamically scaled by modulation of SC-CA2 synaptic transmission.

Significance Statement

The release of the neuromodulator acetylcholine is critically involved in processes of hippocampus-dependent memory formation. Cholinergic afferents originating in the medial septum and diagonal bands of Broca terminating in the hippocampal area CA2 might play an important role in the modulation of area-specific synaptic plasticity. Our findings demonstrate that cholinergic receptor activation induces a long-term depression of synaptic transmission at entorhinal cortical- and Schaffer collateral-CA2 synapses. This cholinergic activation-mediated long-term depression displays a bidirectional metaplastic switch to long-term potentiation on a future timescale. This suggests that such bidirectional synaptic modifications triggered by the dynamic modulation of tonic cholinergic receptor activation may support the formation of CA2-dependent memories given the increased hippocampal cholinergic tone during active wakefulness observed in exploratory behaviour.
Modeling PPRV pathogenesis in mice to assess the contribution of innate cells and anti-viral T cells
Authors: Sharma Yashu , Sarkar Roman , Jain Ayush , Singh Sudhakar , Shekhar Chander , Shanmugam ChandraSekar , Dhanavelu Muthuchelvan , Tembure Prabhakar , Kaul Rajeev , Sehrawat Sharvan
Published: October 2020

We demonstrate a rapid induction of type I IFN response in PPRV stimulated cells and the susceptibility of mice, genetically ablated of interferon response, to PPRV infection. Following PPRV infection, IFNR KO mice gradually reduced their body weights and succumbed to the infection within 10 days. While the infecting inoculum size did not alter the outcome of infection, the nature of the induced disease was qualitatively different. Immunopathological lesions were characterized by the expansion and infiltration of innate immune cells distinctly evident at the lower infecting dose of PPRV infection. The replicating virus particles as well as the viral antigens were abundant in most of the critical organs of PPRV infected IFNR KO mice. Neutrophils and macrophages transported the replicating virus to central nervous system and contributed to pathology while the NK cells and T cells were protective against the virus. Using an array of fluorescently labeled H-2Kbtetramers PPRV specific CD8+T cells responses were identified and measured in the infected as well as the peptide immunized mice. Our study therefore established and employed a laboratory animal model for investigating PPRV pathogenesis and the contribution of virus specific CD8+T cells during the virus infection to pave the way for elucidating protective or pathological roles of immune cells during PPRV infection.

Importance

We developed a laboratory animal model for investigating the pathogenesis and immunity induced by PPRV. IFNR KO animals succumbed to the infection irrespective of the dose and the route of infection. Neutrophils and macrophages served as the Trojan horse and helped transport the virus to CNS to cause encephalitis while the NK cells and CD8+T cells provided the protection against PPRV infection. We additionally identified class I restricted immunogenic epitopes of PPRV in C57BL/6 mice. Our study therefore paves the way for an optimal utilization of this model to unravel PPRV pathogenesis and assessing the host correlates of protection.
Species level resolution of female bladder microbiota from 16S rRNA amplicon sequencing
Authors: Hoffman Carter , Siddiqui Nazema Y , Fields Ian , Gregory W. Thomas , Simon Holly , Mooney Michael A. , Wolfe Alan J. , Karstens Lisa
Published: October 2020

The human bladder contains bacteria in the absence of infection. Interest in studying these bacteria and their association with bladder conditions is increasing. However, the chosen experimental method can limit the resolution of the taxonomy that can be assigned to the bacteria found in the bladder. 16S rRNA amplicon sequencing is commonly used to identify bacteria in urinary specimens, but is typically restricted to genus-level identification. Our primary aim was to determine if accurate species-level identification of bladder bacteria is possible using 16S rRNA amplicon sequencing. We evaluated the ability of different classification schemes, each consisting of combinations of a reference database, a 16S rRNA gene variable region and a taxonomic classification algorithm to correctly classify bladder bacteria. We show that species-level identification is possible, and that the reference database chosen is the most important component, followed by the 16S variable region sequenced.

Importance

Species-level information may deepen our understanding of associations between bladder microbiota and bladder conditions, such as lower urinary tract symptoms and urinary tract infections. The capability to identify bacterial species depends on large databases of sequences, algorithms that leverage statistics and available computer hardware, and knowledge of bacterial genetics and classification. Taken together, this is a daunting body of knowledge to become familiar with before the simple question of bacterial identity can be answered. Our results show the choice of taxonomic database and variable region of the 16S rRNA gene sequence makes species level identification possible. We also show this improvement can be achieved through the more careful application of existing methods and use of existing resources.
Phylogenetic distribution of secondary metabolites in theBacillus subtilisspecies complex
Authors: Steinke Kat , Mohite Omkar S. , Weber Tilmann , Kovács Ákos T.
Published: October 2020

Microbes produce a plethora of secondary metabolites that although not essential for primary metabolism benefit them to survive in the environment, communicate, and influence differentiation. Biosynthetic gene clusters (BGCs) responsible for the production of these secondary metabolites are readily identifiable on the genome sequence of bacteria. Understanding the phylogeny and distribution of BGCs helps us to predict natural product synthesis ability of new isolates. Here, we examined the inter- and intraspecies patterns of absence/presence for all BGCs identified with antiSMASH 5.0 in 310 genomes from theB. subtilisgroup and assigned them to defined gene cluster families (GCFs). This allowed us to establish patterns in distribution for both known and unknown products. Further, we analyzed variations in the BGC structure of particular families encoding for natural products such as plipastatin, fengycin, iturin, mycosubtilin and bacillomycin. Our detailed analysis revealed multiple GCFs that are species or clade specific and few others that are scattered within or between species, which will guide exploration of the chemodiversity within theB. subtilisgroup. Uniquely, we discovered that partial deletion of BGCs and frameshift mutations in selected biosynthetic genes are conserved within phylogenetically related isolates, although isolated from around the globe. Our results highlight the importance of detailed analysis of BGCs and the remarkable phylogenetically conserved errodation of secondary metabolite biosynthetic potential in theB. subtilisgroup.

IMPORTANCE

Members of theB. subtilisspecies complex are commonly recognized producers of secondary metabolites, among those the production of antifungals makes them promising biocontrol strains. However, while there are studies examining the distribution of well-knownB. subtilismetabolites, this has not yet been systematically reported for the group. Here, we report the complete biosynthetic potential within theBacillus subtilisgroup species to explore the distribution of the biosynthetic gene clusters and to provide an exhaustive phylogenetic conservation of secondary metabolite production supporting the chemodiversity ofBacilli. We identify that certain gene clusters acquired deletions of genes and particular frame-shift mutations rendering them inactive for secondary metabolite biosynthesis, a conserved genetic trait within phylogenetically conserved clades of certain species. The overview presented will superbly guide assigning the secondary metabolite production potential of newly isolated strains based on genome sequence and phylogenetic relatedness.
An exploration of assembly strategies and quality metrics on the accuracy of theKnightia excelsa(rewarewa) genome
Authors: McCartney Ann , Hilario Elena , Choi Seung-Sub , Guhlin Joseph , Prebble Jessica M. , Houliston Gary , Buckley Thomas R. , Chagné David
Published: October 2020

Background

We used long read sequencing data generated fromKnightia excelsaIR.Br, a nectar producing Proteaceae tree endemic to Aotearoa New Zealand, to explore how sequencing data type, volume and workflows can impact final assembly accuracy and chromosome construction. Establishing a high-quality genome for this species has specific cultural importance to Māori, the indigenous people, as well as commercial importance to honey producers in Aotearoa New Zealand.

Results

Assemblies were produced by five long read assemblers using data subsampled based on read lengths, two polishing strategies, and two Hi-C mapping methods. Our results from subsampling the data by read length showed that each assembler tested performed differently depending on the coverage and the read length of the data. Assemblies that used longer read lengths (>30 kb) and lower coverage were the most contiguous, kmer and gene complete. The final genome assembly was constructed into pseudochromosomes using all available data assembled with FLYE, polished using Racon/Medaka/Pilon combined, scaffolded using SALSA2 and AllHiC, curated using Juicebox, and validated by synteny withMacadamia.

Conclusions

We highlighted the importance of developing assembly workflows based on the volume and type of sequencing data and establishing a set of robust quality metrics for generating high quality assemblies. Scaffolding analyses highlighted that problems found in the initial assemblies could not be resolved accurately by utilizing Hi-C data and that scaffolded assemblies were more accurate when the underlying contig assembly was of higher accuracy. These findings provide insight into what is required for future high-qualityde-novoassemblies of non-model organisms.
Prolactin mediates behavioural rejection responses to avian brood parasitism
Authors: Ruiz-Raya Francisco , Ibáñez-Álamo Juan Diego , Parenteau Charline , Chastel Olivier , Soler Manuel
Published: October 2020

Even though adaptations resulting from co-evolutionary interactions between avian brood parasites and their hosts have been well studied, the hormonal mechanisms underlying behavioural host defences remain largely unexplored. Prolactin, the main hormone mediating avian parental behaviour, has been hypothesized to play a key role in the orchestration of host responses to brood parasitic eggs. Based on the positive association between plasma prolactin and parental attachment to eggs, decreasing levels of this hormone are expected to facilitate egg-rejection decisions in parasitized clutches. We tested this prediction by implanting Eurasian blackbirds (Turdus merula) females with an inhibitor of prolactin secretion, bromocriptine mesylate, to experimentally low their prolactin levels. We found that bromocriptine-treated females rejected mimetic model eggs at higher rates than placebo-treated individuals. To our knowledge, this is the first experimental evidence that host responses to brood parasitism are mediated by the primary endocrine pathway that orchestrates the expression of avian parental care.
Immigrant perceptions of integration in the Canadian workplace
Authors: Ertorer Secil E. , Long Jennifer , Fellin Melissa , Esses Victoria M.
Published: October 2020

Purpose

This paper explores integration experiences of immigrants in the Canadian workplace from the perspective of immigrants themselves, focusing on cultural capital and cultural judgments as factors influencing workplace entry, advancement and social integration in an increasingly diverse work environment.

Design/methodology/approach

An interpretive approach that involved thematic analysis of in-depth interview data was employed.

Findings

The findings reveal that the official two-way multiculturalism policy of Canada is not reflected in the Canadian workplace and that structural forces of assimilation are evident. Cultural judgments and immigrants' cultural capital create barriers for integration.

Research limitations/implications

While highlighting important aspects of immigrant experiences within the Canadian workplace, the study findings cannot generate a fully representative theorization of immigrant employment experiences in Canada. Further studies with diverse migrant groups in different parts of the country would shed more light on the issues faced by immigrants.

Practical implications

The barriers to social integration identified by this study can be largely overcome by improving intercultural skills and cultural intelligence of employers and employees through training and incorporating values of diversity and inclusion into the corporate culture.

Social implications

The factors that foster and hinder workplace integration identified by this study can inform workplace integration strategies and related policies.

Originality/value

Much of the literature concerning immigrants' position in Canada address the economic integration and economic well-being of immigrants, focusing on quantitative, macro level analyses of earnings disparity and labor market segmentation. There is a lack of qualitative research that explores the integration process through the lens of immigrants. Informed by the theories of cultural capital, cultural judgment and integration, the study sheds light on the everyday workplace experiences of skilled migrants and perceived barriers to workplace entry, advancement and social integration.