bluuebunny/crossref_metadata_2025 huggingface dataset:
Proteomic analysis reveals different sets of proteins expressed during high temperature stress in two thermotolerant isolates ofTrichoderma
Authors: Poosapati Sowmya , Kumar Viswanathaswamy Dinesh , Prasad Ravulapalli Durga , Kannan Monica
Published: August 2021

Several species of the soil borne fungus of the genusTrichodermaare known to be versatile, opportunistic plant symbionts, and are the most successful biocontrol agents used in today’s agriculture. To be successful in the field conditions, the fungus must endure varying climatic conditions. Studies have indicated that high atmospheric temperature coupled with low humidity is a major limitation for the inconsistent performance ofTrichodermaunder field conditions. Understanding the molecular modulation associated with suchTrichodermathat persist and deliver under abiotic stress condition will aid in exploiting the worth of these organisms for such use. In this study, comparative proteomic analysis using two-dimensional gel electrophoresis (2DE) and matrix-assisted laser desorption/time-of-flight (MALDI-TOF-TOF) mass spectrometry was used to identify proteins associated with thermotolerance in two thermotolerant isolates ofTrichoderma—T. longibrachiatum673, TaDOR673 andT. asperellum7316, TaDOR7316—and 32 differentially expressed proteins were identified. Sequence homology and conserved domains were used to identify these proteins and to assign probable function to them. Thermotolerant isolate, TaDOR673, seemed to employ the stress signaling MAPK pathways and heat shock response pathways to combat the stress condition whereas the moderately tolerant isolate, TaDOR7316, seemed to adapt to high temperature conditions by reducing the accumulation of mis-folded proteins through unfolded protein response pathway and autophagy. Also, there were unique as well as common proteins that were differentially expressed in the two isolates studied.
MetaLogo: a heterogeneity-aware sequence logo generator and aligner
Authors: Chen Yaowen , He Zhen , Men Yahui , Dong Guohua , Hu Shuofeng , Ying Xiaomin
Published: August 2021

Sequence logos are used to visually display conservations and variations in short sequences. They can indicate the fixed patterns or conserved motifs in a batch of DNA or protein sequences. However, most of the popular sequence logo generators are based on the assumption that all the input sequences are from the same homologous group, which will lead to an overlook of the heterogeneity among the sequences during the sequence logo making process. Heterogeneous groups of sequences may represent clades of different evolutionary origins, or genes families with different functions. Therefore, it is essential to divide the sequences into different phylogenetic or functional groups to reveal their specific sequence motifs and conservation patterns. To solve these problems, we developed MetaLogo, which can automatically cluster the input sequences after multiple sequence alignment and phylogenetic tree construction, and then output sequence logos for multiple groups and aligned them in one figure. User-defined grouping is also supported by MetaLogo to allow users to investigate functional motifs in a more delicate and dynamic perspective. MetaLogo can highlight both the homologous and nonhomologous sites among sequences. MetaLogo can also be used to annotate the evolutionary positions and gene functions of unknown sequences, together with their local sequence characteristics. We provide users a public MetaLogo web server (http://metalogo.omicsnet.org), a standalone Python package (https://github.com/labomics/MetaLogo), and also a built-in web server available for local deployment. Using MetaLogo, users can draw informative, customized and publishable sequence logos without any programming experience to present and investigate new knowledge on specific sequence sets.
MorphoGraphX 2.0: Providing context for biological image analysis with positional information
Authors: Strauss Soeren , Runions Adam , Lane Brendan , Eschweiler Dennis , Bajpai Namrata , Trozzi Nicola , Routier-Kierzkowska Anne-Lise , Yoshida Saiko , Rodrigues da Silveira Sylvia , Vijayan Athul , Tofanelli Rachele , Majda Mateusz , Echevin Emillie , Le Gloanec Constance , Bertrand-Rakusova Hana , Adibi Milad , Schneitz Kay , Bassel George , Kierzkowski Daniel , Stegmaier Johannes , Tsiantis Miltos , Smith Richard S.
Published: August 2021

Positional information is a central concept in developmental biology. In developing organs, positional information can be idealized as a local coordinate system that arises from morphogen gradients controlled by organizers at key locations. This offers a plausible mechanism for the integration of the molecular networks operating in individual cells into the spatially-coordinated multicellular responses necessary for the organization of emergent forms. Understanding how positional cues guide morphogenesis requires the quantification of gene expression and growth dynamics in the context of their underlying coordinate systems. Here we present recent advances in the MorphoGraphX software (Barbier de Reuille et al. eLife 2015;4:e05864) that implement a generalized framework to annotate developing organs with local coordinate systems. These coordinate systems introduce an organ-centric spatial context to microscopy data, allowing gene expression and growth to be quantified and compared in the context of the positional information thought to control them.
Bending-torsional elasticity and energetics of the plus-end microtubule tip
Authors: Igaev Maxim , Grubmüller Helmut
Published: August 2021

Microtubules (MTs), mesoscopic cellular filaments, grow primarily by the addition of GTP-bound tubulin dimers at their dynamic flaring plus-end tips. They operate as chemomechanical energy transducers with stochastic transitions to an astounding shortening motion upon hydrolyzing GTP to GDP. Time-resolved dynamics of the MT tip – a key determinant of this behavior – as a function of nucleotide state, internal lattice strain, and stabilizing lateral interactions have not been fully understood. Here, we use atomistic simulations to study the spontaneous relaxation of complete GTP-MT and GDP-MT tip models from unfavorable straight to relaxed splayed conformations and to comprehensively characterize the elasticity of MT tips. Our simulations reveal the dominance of viscoelastic dynamics of MT protofilaments during the relaxation process, driven by the stored bending-torsional strain and counterbalanced by the inter-protofilament interactions. We show that the post-hydrolysis MT tip is exposed to higher activation energy barriers for straight lattice formation, which translates into its inability to elongate. Our study provides an ‘information ratchet’ mechanism for the elastic energy conversion and release by MT tips and offers new insights into the mechanoenzymatics of MTs.
MetaProFi: A protein-based Bloom filter for storing and querying sequence data for accurate identification of functionally relevant genetic variants
Authors: Srikakulam Sanjay K. , Keller Sebastian , Dabbaghie Fawaz , Bals Robert , Kalinina Olga V.
Published: August 2021

Technological advances of next-generation sequencing present new computational challenges to develop methods to store and query these data in time- and memory-efficient ways. We present MetaProFi (https://github.com/kalininalab/metaprofi), a Bloom filter-based tool that, in addition to supporting nucleotide sequences, can for the first time directly store and query amino acid sequences and translated nucleotide sequences, thus bringing sequence comparison to a more biologically relevant protein level. Owing to the properties of Bloom filters, it has a zero false-negative rate, allows for exact and inexact searches, and leverages disk storage and Zstandard compression to achieve high time and space efficiency. We demonstrate the utility of MetaProFi by indexing UniProtKB datasets at organism- and at sequence-level in addition to the indexing of Tara Oceans dataset and the 2585 human RNA-seq experiments, showing that MetaProFi consumes far less disk space than state-of-the-art-tools while also improving performance.
Binding specificity of ASHH2 CW-domain towards H3K4me1 ligand is coupled to its structural stability through its α1-helix
Authors: Bril’kov Maxim S. , Dobrovolska Olena , Ødegård-Fougner Øyvind , Strømland Øyvind , Aasland Rein , Halskau Øyvind
Published: August 2021

The CW-domain binds to histone-tail modifications found in different protein families involved in epigenetic regulation and chromatin remodelling. CW-domains recognize the methylation state of the fourth lysine on histone 3, and could therefore be viewed as a reader of epigentic information. The specificity towards different methylation states such as me1, me2 or me3 depends on the particular CW subtype. For example, the CW domain of ASHH2-methyltransferase binds preferentially to H3K4me1, MORC3 binds to both H3K4me2 and me3 modifications, while ZCWPW1 is more specific to H3K4me3. The structural basis for these preferential bindings are not well understood, and recent research suggests that a more complete picture will emerge if dynamical and energetic assessments are included in the analysis of interactions. This study uses fold assessment by NMR in combination with mutagenesis, ITC affinity measurements and thermal denaturation studies to investigate possible couplings between ASHH2 CW selectivity towards H3K4me1 and the stabilization of the domain and loops implicated in binding. Key elements of the binding site – the two tryptophans and the α1-helix form and maintain the binding pocket were perturbed by mutagenesis and investigated. Results show that α1-helix maintains the overall stability of the fold via the I915 and L919 residues, and that correct binding consolidates the loops designated η1, η3, as well as the C-terminal. This consolidation is incomplete for H3K4me3 binding to CW, which experiences a decrease in overall thermal stability upon binding. Moreover, loop-mutations not directly involved in the binding site nonetheless affect the equillibrium positions of key residues.
Subtle alterations in neonatal neurodevelopment following early or late exposure to prenatal maternal immune activation
Authors: Guma Elisa , Snook Emily , Spring Shoshana , Lerch Jason P. , Nieman Brian J. , Devenyi Gabriel A. , Chakravarty M. Mallar
Published: August 2021

Prenatal exposure to maternal immune activation (MIA) is a risk factor for a variety of neurodevelopmental and psychiatric disorders. The timing of MIA-exposure has been shown to affect adolescent and adult offspring neurodevelopment, however, less is known about these effects in the neonatal period. To better understand the impact of MIA-exposure on neonatal brain development, we first assess neonate communicative abilities with the ultrasonic vocalization task, followed by high-resolution ex vivo magnetic resonance imaging (MRI) on the neonatal (postnatal day 8) brain. Early exposed offspring displayed decreased communicative ability, while brain anatomy appeared largely unaffected, apart from some subtle alterations. By integrating MRI and behavioural assays to investigate the effects of MIA-expsoure on neonatal neurodevelopment we show that offspring neuroanatomy and behaviour are only subtly affected by both early and late exposure. This suggests that the deficits often observed in later stages of life may be dormant, not yet developed in the neonatal period, or not as easily detectable using a cross-sectional approach.
Phylogenetic, ecological and intraindividual variability patterns in grass phytolith shape
Authors: Hošková Kristýna , Neustupa Jiří , Pokorný Petr , Pokorná Adéla
Published: August 2021

Grass silica short cell (GSSC) phytoliths appear to be the most reliable source of fossil evidence for tracking the evolutionary history and paleoecology of grasses. In recent years, modern techniques have been used to quantitatively assess phytolith shape variation. This progress has widened opportunities with respect to the classification of grass fossil phytoliths. However, phylogenetic, ecological and intraindividual variability patterns in phytolith shape remain largely unexplored.

The full range of intraindividual phytolith shape variation (3650 2D outlines) from 73 extant grass species, 48 genera, 18 tribes, and 8 subfamilies (with special attention paid to Pooideae) was analysed using the geometric morphometric analysis based on the semilandmarks spanning phytolith outlines.

Although we showed that 2D phytolith shape is mainly driven by deep-time diversification of grass subfamilies, a closer look uncovered distinct phytolith shape variation in early-diverging lineages of Pooideae.

The phylogenetic pattern in phytolith shape was successfully revealed by applying geometric morphometrics to 2D phytolith shape outlines. This finding strengthens the potential of phytoliths to track the evolutionary history and paleoecology of grasses. Moreover, geometric morphometrics of 2D phytolith shape proved to be an excellent tool for analysis requiring large sums of phytolith outlines, making it useful for quantitative palaeoecological reconstruction.
Microbial colonization of tannin-rich tropical plants: interplay between degradability, methane production and tannin disappearance in the rumen
Authors: Rira Moufida , Morgavi Diego P. , Popova Milka , Maxin Gaёlle , Doreau Michel
Published: August 2021

Abstract

Condensed tannins in plants are found free and attached to protein and fibre but it is not known whether these fractions influence rumen degradation and microbial colonization. This study explored the rumen degradation of tropical tannins-rich plants and the relationship between condensed tannins fractions’ disappearance and microbial communities colonising plant particles. Leaves from Calliandra calothyrsus, Gliricidia sepium, and Leucaena leucocephala, pods from Acacia nilotica and the leaves of two agricultural by-products: Manihot esculenta and Musa spp. were incubated in situ in the rumen of dairy cows. An in vitro approach was also used to assess the effects of these plants on rumen fermentation parameters. All plants contained more than 100 g/kg of condensed tannins with a large proportion (32 to 61%) bound to proteins. Calliandra calothyrsus had the highest concentration of condensed tannins at 361 g/kg, whereas Acacia nilotica was particularly rich in hydrolysable tannins (350 g/kg). Hydrolysable and free condensed tannins from all plants completely disappeared after 24 h incubation in the rumen. Disappearance of protein-bound condensed tannins was variable with values ranging from 93% for Gliricidia sepium to 21% for Acacia nilotica. In contrast, fibre-bound condensed tannins disappearance averaged ~82% and did not vary between plants. Disappearance of bound fractions of condensed tannins was not associated with degradability of plant fractions. The presence of tannins interfered with the microbial colonisation of plants. Each plant had distinct bacterial and archaeal communities after 3 and 12 h of incubation in the rumen and distinct protozoal communities at 3 h. Adherent communities in tannin-rich plants had a lower relative abundance of fibrolytic microbes, notably Fibrobacter spp. Whereas, archaea diversity was reduced in high tannin-containing Calliandra calothyrsus and Acacia nilotica at 12 h of incubation. Concurrently, in vitro methane production was lower for Calliandra calothyrsus, Acacia nilotica and Leucaena leucocephala although for the latter total volatile fatty acids production was not affected and was similar to control. Here we show that the total amount of hydrolysable and condensed tannins contained in a plant govern the interaction with rumen microbes affecting degradability and fermentation. The effect of protein- and fibre-bound condensed tannins on degradability is less important.
Ecdysone exerts biphasic control of regenerative signaling, coordinating the completion of regeneration with developmental progression
Authors: Karanja Faith , Sahu Subhshri , Weintraub Sara , Bhandari Rajan , Jaszczak Rebecca , Sitt Jason , Halme Adrian
Published: August 2021

In Drosophila melanogaster, loss of regenerative capacity in wing imaginal discs coincides with an increase in systemic levels of the steroid hormone ecdysone, a key coordinator of their developmental progression. Regenerating discs release the relaxin hormone Dilp8, which limits ecdysone synthesis and extends the regenerative period. Here, we describe how regenerating tissues produce a biphasic response to ecdysone levels: lower concentrations of ecdysone promote local and systemic regenerative signaling, whereas higher concentrations suppress regeneration through the expression of broad splice isoforms. Ecdysone also promotes the expression of wingless during both regeneration and normal development through a distinct regulatory pathway. This dual role for ecdysone explains how regeneration can still be completed successfully in dilp8- mutant larvae: higher ecdysone levels increase the regenerative activity of tissues, allowing regeneration to reach completion in a shorter time. From these observations, we propose that ecdysone hormone signaling functions to coordinate regeneration with developmental progression.

Summary Statement

Ecdysone coordinates regenerative activity with developmental progression through the biphasic, concentration-dependent activation, and suppression of regenerative signaling.
Gut bacteria regulate the pathogenesis of Huntington’s disease in Drosophila model
Authors: Chongtham Anjalika , Yoo Jung Hyun , Chin Theodore M. , Akingbesote Ngozi D. , Huda Ainul , Khoshnan Ali
Published: August 2021

Changes in the composition of gut microbiota are implicated in the pathogenesis of several neurodegenerative disorders. Here, we investigated whether gut bacteria affect the progression of Huntington’s disease (HD) in transgenic Drosophila melanogaster (fruit fly) models expressing human full-length or N-terminal fragments of mutant huntingtin (HTT) protein, here referred to as HD flies. We find that elimination of commensal gut bacteria by antibiotics reduces the aggregation of amyloidogenic N-terminal fragments of HTT and delays the development of motor defects. Conversely, colonization of HD flies with Escherichia coli (E. coli), a known pathobiont of human gut with links to neurodegeneration, accelerates HTT aggregation, aggravates immobility and shortens lifespan. Similar to antibiotics, treatment of HD flies with small compounds such as luteolin, a flavone, or crocin a beta-carotenoid, ameliorates disease phenotypes and promotes survival. Crocin prevents colonization of E. coli in the gut and alters the abundance of commensal bacteria, which may be linked to its protective effects. The opposing effects of E. coli and crocin on HTT aggregation, motor defects and survival in transgenic Drosophila models support the involvement of gut-brain networks in the pathogenesis of HD.
The Molecular Subtyping Resource (MouSR): a user-friendly tool for rapid biological discovery from human or mouse transcriptional data
Authors: Ahmaderaghi Baharak , Amirkhah Raheleh , Jackson James , Lannagan Tamsin RM , Gilroy Kathryn , Malla Sudhir B , Redmond Keara L ,   ACRCelerate Consortium, Maughan Tim , Leedham Simon , Campbell Andrew S , Sansom Owen J , Lawler Mark , Dunne Philip D
Published: August 2021

Generation of transcriptional data has dramatically increased in the last decade, driving the development of analytical algorithms that enable interrogation of the biology underpinning the profiled samples. However, these resources require users to have expertise in data wrangling and analytics, reducing opportunities for biological discovery by “wet-lab” users with a limited programming skillset. Although commercial solutions exist, costs for software access can be prohibitive for academic research groups.

To address these challenges, we have developed an open source and user-friendly data analysis platform for on-the-fly bioinformatic interrogation of transcriptional data derived from human or mouse tissue, called “MouSR”. This internet-accessible analytical tool, https://mousr.qub.ac.uk/, enables users to easily interrogate their data using an intuitive “point and click” interface, which includes a suite of molecular characterisation options including QC, differential gene expression, gene set enrichment and microenvironmental cell population analyses from RNA-Seq. Users are provided with adjustable options for analysis parameters to generate results that can be saved as publication-quality images. To highlight its ability to perform high quality data analysis, we utilise the MouSR tool to interrogate our recently published tumour dataset, derived from genetically engineered mouse models and matched organoids, where we rapidly reproduced the key transcriptional findings.

The MouSR online tool provides a unique freely-available option for users to perform rapid transcriptomic analyses and comprehensive interrogation of the signalling underpinning transcriptional datasets, which alleviates a major bottleneck for biological discovery.
De novo chromosome-length assembly of the mule deer (Odocoileus hemionus) genome
Authors: Lamb Sydney , Taylor Adam M. , Hughes Tabitha A. , McMillan Brock R. , Larsen Randy T. , Khan Ruqayya , Weisz David , Dudchenko Olga , Aiden Erez Lieberman , Frandsen Paul B.
Published: August 2021

The mule deer (Odocoileus hemionus) is an ungulate species that ranges from western Canada to central Mexico. Mule deer are an essential source of food for many predators, are relatively abundant, and commonly make broad migration movements. A clearer understanding of the mule deer genome can help facilitate knowledge of its population genetics, movements, and demographic history, aiding in conservation efforts. While mule deer are excellent candidates for population genomic studies because of their large population size, continuous distribution, and diversity of habitat, few genomic resources are currently available for this species. Here, we sequence and assemble the mule deer genome into a highly contiguous chromosome-length assembly for use in future research using long-read sequencing and Hi-C. We also provide a genome annotation and compare demographic histories of the mule deer and white-tail deer using PSMC. We expect this assembly to be a valuable resource in the continued study and conservation of mule deer.
The impact of evolutionary processes in shaping the genetics of complex traits in East Asia and Europe: a specific contribution from Denisovan and Neanderthal introgression
Authors: Koller Dora , Wendt Frank R , Pathak Gita A , De Lillo Antonella , De Angelis Flavio , Cabrera-Mendoza Brenda , Tucci Serena , Polimanti Renato
Published: August 2021

Evidence of how human evolution shaped the polygenicity of human traits and diseases has been extensively studied in populations of European descent. However, limited information is currently available about its impact on other ancestry groups. Here, we investigated how different evolutionary processes affected the common variant heritability of traits and diseases in East Asians. Leveraging genome-wide association statistics from the Biobank Japan (up to 158,284 participants), we assessed natural selection (negative and positive), archaic introgression from Neanderthal and Denisova, and several genomic functional categories with respect to the heritability of physiological and pathological conditions. Similar to reports in European descent populations, the heritability estimates for East Asian traits were ubiquitously enriched for negative selection annotations (false discovery rate, FDR q<0.05). Enrichment of Denisovan introgression was identified in coronary artery disease (1.69-fold enrichment, p=0.003). We followed up these enrichments by conducting a phenome-wide association study (PheWAS) of Denisovan and Neanderthal alleles in participants of six ancestral backgrounds from the UK Biobank. In East Asians, Denisovan-inherited alleles were associated with 22 phenotypes, including metabolic, immunological, cardiovascular, endocrine, and dermatological traits. The strongest association was observed for the Denisovan-inherited locus rs59185462 with rheumatoid arthritis (beta=0.82, p=1.91×10−105). In summary, our study provides the first evidence regarding the impact of evolutionary processes on the genetics of complex traits in worldwide populations, highlighting the specific contribution of Denisovan introgression in East Asian populations.
Motor learning without movement
Authors: Kim Olivia A. , Forrence Alexander D. , McDougle Samuel D.
Published: August 2021

Prediction errors guide many forms of learning, providing teaching signals that help us improve our performance. Implicit motor adaptation, for instance, is driven by sensory prediction errors (SPEs), which occur when the expected and observed consequences of a movement differ. Traditionally, SPE computation is thought to require movement execution. However, recent work suggesting that the brain generates and accounts for sensory predictions based on motor imagery or planning alone calls this assumption into question. Here, by measuring implicit adaptation during a visuomotor task, we tested whether motor planning and well-timed sensory feedback are sufficient for SPE computation. Human participants were cued to reach to a target and were, on a subset of trials, rapidly cued to withhold these movements. Errors displayed both on trials with and without movements induced single-trial implicit learning. Learning following trials without movements persisted even when movement trials had never been paired with errors, and when the direction of movement and sensory feedback trajectories were decoupled. These observations demonstrate that the brain can compute SPEs without generating overt movements, leading to the adaptation of planned movements even when they are not performed.

SIGNIFICANCE STATEMENT

We are always learning from our mistakes, because the brain is constantly generating predictions and monitoring the world for any surprises, which are also referred to as “prediction errors.” Whenever a prediction error occurs, the brain learns to update future predictions and be more accurate. Here, we demonstrate that the brain predicts the consequences of movements, computes prediction errors, and updates future movements, even if we subsequently decide to withhold the movement. Thus, the brain can learn to update movements that are not performed, representing a mechanism for learning based only on movement planning and sensory expectation. These findings also provide further support for the role of prediction in motor control.

SIGNIFICANCE STATEMENT

Our brains control aspects of our movement without our conscious awareness – allowing many of us to effortlessly pick up a glass of water or wave “hello.” Here, we demonstrate that this implicit motor system can learn to refine movements that we plan but ultimately decide not to perform. Participants planned to reach to a target, and they sometimes withheld these reaches. When reaches were withheld, an animation simulating a reach that missed the target played. Afterwards, participants reached opposite the direction of the mistake without awareness of this change in their movements, indicating that the implicit motor system had learned from the animated mistake. These findings indicate that movement is not strictly necessary for motor adaptation, and that we can learn to update our actions based only on movement planning and observation of related events in the world.
Reconstitution of monoterpene indole alkaloid biosynthesis in genome engineered Nicotiana benthamiana
Authors: Dudley Quentin M. , Jo Seohyun , Guerrero Delia Ayled Serna , Chhetry Monika , Smedley Mark A. , Harwood Wendy A. , Sherden Nathaniel H. , O’Connor Sarah E. , Caputi Lorenzo , Patron Nicola J.
Published: August 2021

Monoterpene indole alkaloids (MIAs) are a diverse class of plant natural products that include a number of medicinally significant compounds. We set out to reconstitute the pathway for strictosidine, a key intermediate of all MIAs, from central metabolism in Nicotiana benthamiana. A disadvantage of this host is that its rich background metabolism results in the derivatization of some heterologously produced molecules. We used transcriptomic analysis to identify glycosyltransferases that were upregulated in response to biosynthetic intermediates and produced plant lines with targeted mutations in the genes encoding them. Expression of the early MIA pathway in these lines produced a more favorable product profile. Strictosidine biosynthesis was successfully reconstituted, with the best yields obtained by the co-expression of 14 enzymes, of which a major latex protein-like enzyme (MLPL) from Nepeta (catmint) was critical for improving flux through the iridoid pathway. The removal of endogenous glycosyltransferases did not impact the yields of strictosidine, highlighting that the metabolic flux of the pathway enzymes to a stable biosynthetic intermediate minimizes the need to engineer the endogenous metabolism of the host. The production of strictosidine in planta expands the range of MIA products amenable to biological synthesis.
Applying Machine Learning to Classify the Origins of Gene Duplications
Authors: McKibben Michael T.W. , Barker Michael S.
Published: August 2021

Nearly all lineages of land plants have experienced at least one whole genome duplication (WGD) in their history. The legacy of these ancient WGDs is still observable in the diploidized genomes of extant plants. Genes originating from WGD—paleologs—can be maintained in diploidized genomes for millions of years. These paleologs have the potential to shape plant evolution through sub- and neofunctionalization, increased genetic diversity, and reciprocal gene loss among lineages. Current methods for classifying paleologs often rely on only a subset of potential genomic features, have varying levels of accuracy, and often require significant data and/or computational time. Here we developed a supervised machine learning approach to classify paleologs from a target WGD in diploidized genomes across a broad range of different duplication histories. We collected empirical data on syntenic block sizes and other genomic features from 27 plant species each with a different history of paleopolyploidy. Features from these genomes were used to develop simulations of syntenic blocks and paleologs to train a gradient boosted decision tree. Using this approach, Frackify (Fractionation Classify), we were able to accurately identify and classify paleologs across a broad range of parameter space, including cases with multiple overlapping WGDs. We then compared Frackify with other paleolog inference approaches in six species with paleotetraploid and paleohexaploid ancestries. Frackify provides a way to combine multiple genomic features to quickly classify paleologs while providing a high degree of consistency with existing approaches.
Pressure for rapid and accurate mate recognition promotes avian-perceived plumage sexual dichromatism in true thrushes (genus:Turdus)
Authors: Luro Alec B. , Hauber Mark E.
Published: August 2021

Ecological conditions limiting the time to find a compatible mate or increasing the difficulty in doing so likely promote the evolution of traits used for species and mate recognition. Conspicuous traits that signal an individual’s species, sex, and breeding status reduce the challenge of identifying a compatible conspecific mate, and should be more common in migratory rather than sedentary species, species with shorter breeding seasons, and species breeding under high sympatry with many closely-related heterospecifics. Here, we tested this recognition hypothesis for promoting plumage sexual dichromatism in the true thrushes (Turdusspp.), a large and diverse genus of passerine birds. We used receptor-noise limited models of avian vision to quantify avian-perceived chromatic and achromatic visual contrasts between male and female plumage patches and tested the influence of breeding season length, spatial distribution, and sympatry with otherTurdusspecies on plumage dichromatism. As predicted, we found that 1) true thrush species with migratory behaviour have greater plumage sexual dichromatism than non-migratory species, 2) species with longer breeding seasons have less plumage sexual dichromatism, and 3) greater numbers ofTurdusthrush species breeding in sympatry is associated with more plumage sexual dichromatism. These results suggest that social recognition systems, including species and mate recognition, play a prominent role in the evolution of plumage sexual dichromatism in true thrushes.
Neuronal mTORC1 inhibition promotes longevity without suppressing anabolic growth and reproduction inC. elegans
Authors: Smith Hannah J. , Lanjuin Anne , Sharma Arpit , Prabhakar Aditi , Tabakovic Emina , Sehgal Rohan , Mair William B.
Published: August 2021

One of the most robust and reproducible methods to prolong lifespan in a variety of organisms is inhibition of the mTORC1 (mechanistic target of rapamycin complex 1) pathway. mTORC1 is a metabolic sensor that promotes anabolic growth when nutrients are abundant. Inhibition of mTORC1 extends lifespan, but also frequently has other effects such as stunted growth, slowed development, reduced fertility, and disrupted metabolism. It has long been assumed that suppression of anabolism and resulting phenotypes such as impaired growth and reproduction may be causal to mTORC1 longevity, but this hypothesis has not been directly tested. RAGA-1 is an upstream activator of TORC1. Previous work from our lab using aC. elegansmodel of mTORC1 longevity, the long-livedraga-1null mutant, found that the presence ofraga-1only in the neurons suppresses longevity of the null mutant. Here, we use the auxin-inducible degradation (AID) system to test whether neuronal mTORC1 inhibition is sufficient for longevity, and whether any changes in lifespan are also linked to stunted growth or fertility. We find that life-long AID of RAGA-1 either in all somatic tissue or only in the neurons ofC. elegansis sufficient to extend lifespan. We also find that AID of RAGA-1 or LET-363/mTOR beginning at day 1 of adulthood extends lifespan to a similar extent. Unlike somatic degradation of RAGA-1, neuronal degradation of RAGA-1 doesn’t impair growth, slow development, or decrease the reproductive capacity of the worms. Lastly, while AID of LET-363/mTOR in all somatic cells shortens lifespan, neuronal AID of LET-363/mTOR slows aging. This work demonstrates that targeting mTORC1 specifically in the neurons uncouples longevity from growth and reproductive impairments, challenging previously held ideas about the mechanisms of mTORC1 longevity and elucidating the promise of tissue-specific aging therapeutics.
Effects of land-use and landscape drivers in the species richness and distribution of carnivores in Faragosa-Fura Landscape of Southern Rift Valley, Ethiopia
Authors: Gebo Berhanu , Takele Serekebirhan , Shibru Simon
Published: August 2021

Understanding the species richness and distribution of carnivores across anthropogenic land-use types in an area is an essential first step for biodiversity conservation and human-carnivore coexistence. However, quantitative data on carnivore species coexisting with humans in different land-use types remain largely missing. Thus, this paper investigated the effect of anthropogenic land-use and landscape drivers on carnivore species richness and distribution in the Faragosa-Fura Landscape, Gamo Zone, southern Ethiopia. To collect data, we employed the line transect method using three complementary field surveys techniques: sign survey, camera-trapping, and opportunistic sighting survey during wet and dry seasons in 2020 and 2021. We stratified the study landscape into five land-use types-forest, wetland, grassland, agricultural land, and settlement. The result proved the occurrence of 12 carnivore species belonging to six families, including vulnerable Felidae species -Panthera pardus. Family Felidae and Herpestidae were composed of a greater number of species, while Hyaenidae and Mustelidae were each represented by single species. Out of identified species, only two species (Panthera pardusandCrocuta crocuta) were large-sized, while the rest were medium and small-sized carnivores. Overall, the mean richness of the study area was 5.73±0.284(SE). The species richness was highest in the wetland (n = 12, mean = 7.67±0.494(SE)) and lowest in the settlement (n = 5, mean = 4.25±0.479(SE)). The regression analysis showed that most of the carnivores displayed a strong negative relationship with agriculture, roads, and settlement while displayed a strong positive relationship with wetland and forest. In general, out of 32 species recorded in Ethiopia, this study quantified 12 carnivore species that signify the area is an important area for wildlife conservation in Ethiopia. Further, the study concluded that the wetland is the most important habitat, particularly for larger-sized and habitat specialists while anthropogenic land-uses types adversely affecting species richness. Thus, a generic paradigm to reconcile land management and biodiversity conservation is highly important.
SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact
Authors: Pang Yui Tik , Acharya Atanu , Lynch Diane L. , Pavlova Anna , Gumbart James C.
Published: August 2021

The trimeric spike (S) glycoprotein, which protrudes from the SARS-CoV-2 viral envelope, binds to human ACE2, initiated by at least one protomer’s receptor binding domain (RBD) switching from a “down” (closed) to an “up” (open) state. Here, we used large-scale molecular dynamics simulations and two-dimensional replica exchange umbrella sampling calculations with more than a thousand windows and an aggregate total of 160 µs of simulation to investigate this transition with and without glycans. We find that the glycosylated spike has a higher barrier to opening and also energetically favors the down state over the up state. Analysis of the S-protein opening pathway reveals that glycans at N165 and N122 interfere with hydrogen bonds between the RBD and the N-terminal domain in the up state, while glycans at N165 and N343 can stabilize both the down and up states. Finally we estimate how epitope exposure for several known antibodies changes along the opening path. We find that the BD-368-2 antibody’s epitope is continuously exposed, explaining its high efficacy.
Quantifying microbial associations of dissolved organic matter under global change
Authors: Hu Ang , Choi Mira , Tanentzap Andrew J. , Liu Jinfu , Jang Kyoung-Soon , Lennon Jay T. , Liu Yongqin , Soininen Janne , Lu Xiancai , Zhang Yunlin , Shen Ji , Wang Jianjun
Published: August 2021

Microbes play a critical role in regulating the size, composition, and turnover of dissolved organic matter (DOM), which is one of the largest pools of carbon in aquatic ecosystems. Global change may alter DOM-microbe associations with implications for biogeochemical cycles, although disentangling these complex interactions remains a major challenge. Here we develop a framework called Energy-Diversity-Trait integrative Analysis (EDTiA) to examine the associations between DOM and bacteria along temperature and nutrient gradients in a manipulative field experiment on mountainsides in contrasting subarctic and subtropical climates. In both study regions, the chemical composition of DOM correlated with bacterial communities, and was primarily controlled by nutrients and to a lesser degree by temperature. At a molecular-level, DOM-bacteria associations depended strongly on the molecular traits of DOM, with negative associations indicative of decomposition as molecules are more biolabile. Using bipartite networks, we further demonstrated that negative associations were more specialized than positive associations indicative of DOM production. Nutrient enrichment promoted specialization of positive associations, but decreased specialization of negative associations particularly at warmer temperatures in subtropical climate. These global change drivers influenced specialization of negative associations most strongly via molecular traits, while both molecular traits and bacterial diversity similarly affected positive associations. Together, our framework provides a quantitative approach to understand DOM-microbe associations and wider carbon cycling across scales under global change.
Conserved T-cell epitopes predicted by bioinformatics in SARS-COV-2 variants
Authors: Lu Feiyu , Wang Shengnan , Wang Ying , Yao Yunpeng , Wang Yangeng , Liu Shujun , Wang Yangyang , Yu Yongli , Wang Liying
Published: August 2021

Background

Finding conservative T cell epitopes in the proteome of numerous variants of SARS-COV-2 is required to develop T cell activating SARS-COV-2 capable of inducing T cell responses against SARS-COV-2 variants.

Methods

A computational workflow was performed to find HLA restricted CD8+ and CD4+ T cell epitopes among conserved amino acid sequences across the proteome of 474727 SARS-CoV-2 strains.

Results

A batch of covserved regions in the amino acid sequences were found in the proteome of the SARS-COV-2 strains. 2852 and 847 peptides were predicted to have high binding affinity to distint HLA class I and class II molecules. Among them, 1456 and 484 peptides are antigenic. 392 and 111 of the antigenic peptides were found in the conseved amino acid sequences. Among the antigenic-conserved peptides, 6 CD8+ T cell epitopes and 7 CD4+ T cell epitopes were identifed. The T cell epitopes could be presented to T cells by high-affinity HLA molecules which are encoded by the HLA alleles with high population coverage.

Conclusions

The T cell epitopes are conservative, antigenic and HLA presentable, and could be constructed into SARS-COV-2 vaccines for inducing protective T cell immunity against SARS-COV-2 and their variants.
Factors influencing wellbeing in young people during COVID-19: A survey with 6291 young people in Wales
Authors: James Michaela , Jones Hope , Baig Amana , Marchant Emily , Waites Tegan , Todd Charlotte , Hughes Karen , Brophy Sinead
Published: August 2021

COVID-19 infection and the resultant restrictions has impacted all aspects of life across the world. This study explores factors that promote or support wellbeing for young people during the pandemic, how they differ by age, using a self-reported online survey with those aged 8 - 25 in Wales between September 2020 and February 2021. Open-ended responses were analysed via thematic analysis to provide further context. A total of 6,291 responses were obtained from 81 education settings across Wales (including primary and secondary schools as well as sixth form, colleges and universities). Wellbeing was highest in primary school children and boys and lowest in those who were at secondary school children, who were girls and, those who preferred not to give a gender. Among primary school children, higher wellbeing was seen for those who played with others (rather than alone), were of Asian ethnicity (OR 2.3, 95% CI: 1.26 to 4.3), lived in a safe area (OR: 2.0, 95% CI: 1.67 to 2.5) and had more sleep. To support their wellbeing young people reported they would like to be able to play with their friends more. Among secondary school children those who were of mixed ethnicity reported lower wellbeing (OR: 5.10, 95% CI: 1.70 to 15.80). To support their wellbeing they reported they would like more support with mental health (due to anxiety and pressure to achieve when learning online). This study found self-reported wellbeing differed by gender, ethnicity and deprivation and found younger children report the need for play and to see friends to support wellbeing but older children/young people wanted more support with anxiety and educational pressures.
Infectious SARS-CoV-2 in Exhaled Aerosols and Efficacy of Masks During Early Mild Infection
Authors: Adenaiye Oluwasanmi O. , Lai Jianyu , de Mesquita P. Jacob Bueno , Hong Filbert , Youssefi Somayeh , German Jennifer , Tai S.-H. Sheldon , Albert Barbara , Schanz Maria , Weston Stuart , Hang Jun , Fung Christian , Chung Hye Kyung , Coleman Kristen K. , Sapoval Nicolae , Treangen Todd , Berry Irina Maljkovic , Mullins Kristin , Frieman Matthew , Ma Tianzhou , Milton Donald K. ,   for the University of Maryland StopCOVID Research Group
Published: August 2021

Background

SARS-CoV-2 epidemiology implicates airborne transmission; aerosol infectiousness and impacts of masks and variants on aerosol shedding are not well understood.

Methods

We recruited COVID-19 cases to give blood, saliva, mid-turbinate and fomite (phone) swabs, and 30-minute breath samples while vocalizing into a Gesundheit-II, with and without masks at up to two visits two days apart. We quantified and sequenced viral RNA, cultured virus, and assayed sera for anti-spike and anti-receptor binding domain antibodies.

Results

We enrolled 49 seronegative cases (mean days post onset 3.8 ±2.1), May 2020 through April 2021. We detected SARS-CoV-2 RNA in 45% of fine (≤5 µm), 31% of coarse (>5 µm) aerosols, and 65% of fomite samples overall and in all samples from four alpha-variant cases. Masks reduced viral RNA by 48% (95% confidence interval [CI], 3 to 72%) in fine and by 77% (95% CI, 51 to 89%) in coarse aerosols; cloth and surgical masks were not significantly different. The alpha variant was associated with a 43-fold (95% CI, 6.6 to 280-fold) increase in fine aerosol viral RNA, compared with earlier viruses, that remained a significant 18-fold (95% CI, 3.4 to 92-fold) increase adjusting for viral RNA in saliva, swabs, and other potential confounders. Two fine aerosol samples, collected while participants wore masks, were culture-positive.

Conclusion

SARS-CoV-2 is evolving toward more efficient aerosol generation and loose-fitting masks provide significant but only modest source control. Therefore, until vaccination rates are very high, continued layered controls and tight-fitting masks and respirators will be necessary.

Key Points

Cases exhale infectious viral aerosols

SARS-CoV-2 evolution favors more efficient aerosol generation.

Loose-fitting masks moderately reduce viral RNA aerosol.

Ventilation, filtration, UV air sanitation, and tight-fitting masks are needed to protect vulnerable people in public-facing jobs and indoor spaces.
Unravelling the binding mode of a methamphetamine aptamer: a spectroscopic and calorimetric investigation
Authors: Sester Clement , McCone Jordan AJ , Vorster Ian , Harvey Joanne E , Hodgkiss Justin M
Published: August 2021

Nucleic acid aptamers are bio-molecular recognition agents that bind to their targets with high specificity and affinity, and hold promise in a range of biosensor and therapeutic applications. In the case of small molecule targets, their small size and limited number of functional groups constitute challenges for their detection by aptamer-based biosensors because bio-recognition events may both be weak and produce poorly transduced signals. The binding affinity is principally used to characterize aptamer-ligand interactions; however a structural understanding of bio-recognition is arguably more valuable in order to design a strong response in biosensor applications. Using a combination of nuclear magnetic resonance, circular dichroism, and isothermal titration calorimetry, we propose a binding model for a new methamphetamine aptamer and determine the main interactions driving complex formation. These measurements reveal only modest structural changes to the aptamer upon binding and are consistent with a conformational selection binding model. The aptamer-methamphetamine complex formation was observed to be entropically driven, apparently involving hydrophobic and electrostatic interactions. Taken together, our results establish a means of elucidating small molecule-aptamer binding interactions, which may be decisive in the development of aptasensors and therapeutics, and may contribute to a deeper understanding of interactions driving aptamer selection.