bluuebunny/crossref_metadata_2025 huggingface dataset:
Extending the CWM approach to intraspecific trait variation: how to deal with overly optimistic standard tests?
Authors: Zelený David , Helsen Kenny , Lee Yi-Nuo
Published: September 2021

Community weighted means (CWMs) are widely used to study the relationship between community-level functional traits and environment. For certain null hypotheses, CWM-environment relationships assessed by linear regression or ANOVA and tested by standard parametric tests are prone to inflated Type I error rates. Previous research has found that this problem can be solved by permutation tests (i.e. the max test). A recent extension of the CWM approach allows the inclusion of intraspecific trait variation (ITV) by the separate calculation of fixed, site-specific, and intraspecific CWMs. The question is whether the same Type I error rate inflation exists for the relationship between environment and site-specific or intraspecific CWM. Using simulated and real-world community datasets, we show that site-specific CWM-environment relationships have also inflated Type I error rate, and this rate is negatively related to the relative ITV magnitude. In contrast, for intraspecific CWM-environment relationships, standard parametric tests have the correct Type I error rate, although somewhat reduced statistical power. We introduce an ITV-extended version of the max test, which can solve the inflation problem for site-specific CWM-environment relationships and, without considering ITV, becomes equivalent to the "original" max test used for the CWM approach. We show that this new ITV-extended max test works well across the full possible magnitude of ITV on both simulated and real-world data. Most real datasets probably do not have intraspecific trait variation large enough to alleviate the problem of inflated Type I error rate, and published studies possibly report overly optimistic significance results.
Evaluating the power and limitations of genome-wide association mapping in C. elegans
Authors: Widmayer Samuel J. , Evans Kathryn , Zdraljevic Stefan , Andersen Erik C.
Published: September 2021

A central goal of evolutionary genetics in Caenorhabditis elegans is to understand the genetic basis of traits that contribute to adaptation and fitness. Genome-wide association (GWA) mappings scan the genome for individual genetic variants that are significantly correlated with phenotypic variation in a population, or quantitative trait loci (QTL). GWA mappings are a popular choice for quantitative genetic analyses because the QTL that are discovered segregate in natural populations. Despite numerous successful mapping experiments, the empirical performance of GWA mappings has not, to date, been formally evaluated for this species. We developed an open-source GWA mapping pipeline called NemaScan and used a simulation-based approach to provide benchmarks of mapping performance among wild C. elegans strains. Simulated trait heritability and complexity determined the spectrum of QTL detected by GWA mappings. Power to detect smaller-effect QTL increased with the number of strains sampled from the C. elegans Natural Diversity Resource (CeNDR). Population structure was a major driver of variation in GWA mapping performance, with populations shaped by recent selection exhibiting significantly lower false discovery rates than populations composed of more divergent strains. We also recapitulated previous GWA mappings of experimentally validated quantitative trait variants. Our simulation-based evaluation of GWA performance provides the community with critical context for pursuing quantitative genetic studies using CeNDR to elucidate the genetic basis of complex traits in C. elegans natural populations.
HypVW is an HOCl-Sensing Two Component System in Escherichia coli
Authors: El Hajj Sara , Henry Camille , Vergnes Alexandra , Loiseau Laurent , Brasseur Gaël , Barré Romain , Aussel Laurent , Ezraty Benjamin
Published: September 2021

Two component systems (TCS) are signalling pathways that allow bacterial cells to sense, respond and adapt to fluctuating environments. Among the classical TCS of Escherichia coli, YedVW has been recently showed to be involved in the regulation of msrPQ, encoding for the periplasmic methionine sulfoxide reductase system. In this study, we demonstrate that hypochlorous acid (HOCl) induces the expression of msrPQ in a YedVW dependant manner, whereas H2O2, NO and paraquat (a superoxide generator) do not. Therefore, YedV appears to be an HOCl-sensing histidine kinase. Based on this finding, we proposed to rename this system HypVW. Moreover, using a directed mutagenesis approach, we show that Met residues located in the periplasmic loop of HypV (formerly YedV) are important for its activity. Given that HOCl oxidizes preferentially Met residues, we bring evidences that HypV could be activated via the reversible oxidation of its methionine residues, thus conferring to MsrPQ a role in switching HypVW off. Based on these results, we propose that the activation of HypV by HOCl could occur through a Met redox switch. HypVW appears to be the first characterized TCS able to detect HOCl in E. coli. This study represents an important step in understanding the mechanisms of reactive chlorine species resistance in prokaryotes.

IMPORTANCE

Understanding molecularly how bacteria respond to oxidative stress is crucial to fight pathogens. HOCl is one of the most potent industrial and physiological microbiocidal oxidant. Therefore, bacteria have developed counterstrategies to survive HOCl-induced stress. Over the last decade, important insights into these bacterial protection factors have been obtained. Our work establishes HypVW as an HOCl-sensing two component system in Escherichia coli MG1655 which regulates the expression of the periplasmic HOCl-oxidized proteins repair system MsrPQ. Moreover we bring evidences suggesting that HOCl could activate HypV through a methionine redox switch.
Stimulation related artifacts and a multipurpose template-based offline removal solution for a novel sensing-enabled deep brain stimulation device
Authors: Hammer Lauren H , Kochanski Ryan B , Starr Philip A , Little Simon
Published: September 2021

Background

The Medtronic “Percept” is the first FDA approved deep brain stimulation (DBS) device with sensing capabilities during active stimulation. Its real-world signal recording properties have yet to be fully described.

Objective

This study details sources of artifact (and potential mitigations) in local field potential (LFP) signals collected by the Percept, and assesses the potential impact of artifact on the future development of adaptive DBS (aDBS) using this device.

Methods

LFP signals were collected from seven subjects in both experimental and clinical settings. The presence of artifacts and their effect on the spectral content of neural signals were evaluated in both the stimulation ON and OFF states using three distinct offline artifact removal techniques.

Results

Template subtraction successfully removed multiple sources of artifact, including 1) electrocardiogram (ECG), 2) non-physiologic polyphasic artifacts, and 3) ramping related artifacts seen when changing stimulation amplitudes. ECG removal from stimulation ON (at 0 mA) signals recovered the spectral shape seen when OFF stimulation (averaged difference in normalized power in theta, alpha, and beta bands ≤ 3.5%). ECG removal using singular value decomposition was similarly successful, though required subjective researcher input. QRS interpolation produced similar recovery of beta-band signal, but resulted in residual low-frequency artifact.

Conclusions

Artifacts present when stimulation is enabled notably affected the spectral properties of sensed signals using the Percept. Multiple discrete artifacts could be successfully removed offline using an automated template subtraction method. The presence of unrejected artifact likely influences online power estimates, with the potential to affect aDBS algorithm performance.
Genome Assembly of the Roundjaw Bonefish (Albula glossodonta), a Vulnerable Circumtropical Sportfish
Authors: Pickett Brandon D. , Talma Sheena , Glass Jessica R. , Ence Daniel , Cowley Paul D. , Ridge Perry G. , Kauwe John S. K.
Published: September 2021

Background

Bonefishes are cryptic species indiscriminately targeted by subsistence and recreational fisheries worldwide. The roundjaw bonefish,Albula glossodontais the most widespread bonefish species in the Indo-Pacific and is listed as vulnerable to extinction by the IUCN’s Red List due to anthropogenic activities. Whole-genome datasets allow for improved population and species delimitation, which – prior to this study – were lacking forAlbulaspecies.

Results

We generated a high-quality genome assembly of anA. glossodontaindividual from Hawai‘i, USA. The assembled contigs had an NG50 of 4.75 Mbp and a maximum length of 28.2 Mbp. Scaffolding yielded an NG50 of 14.49 Mbp, with the longest scaffold reaching 42.29 Mbp. Half the genome was contained in 20 scaffolds. The genome was annotated with 28.3 K protein-coding genes. We then analyzed 66A. glossodontaindividuals and 38,355 SNP loci to evaluate population genetic connectivity between six atolls in Seychelles and Mauritius in the Western Indian Ocean. We observed genetic homogeneity between atolls in Seychelles and evidence of reduced gene flow between Seychelles and Mauritius. The South Equatorial Current could be one mechanism limiting gene flow ofA. glossodontapopulations between Seychelles and Mauritius.

Conclusions

Quantifying the spatial population structure of widespread fishery species such as bonefishes is necessary for effective transboundary management and conservation. This population genomic dataset mapped to a high-quality genome assembly allowed us to discern shallow population structure in a widespread species in the Western Indian Ocean. The genome assembly will be useful for addressing the taxonomic uncertainties of bonefishes globally.
CuBi-MeAn Customized Pipeline for Metagenomic Data Analysis
Authors: Keshani-Langroodi Saeed , Sales Christopher M.
Published: September 2021

1.

Whole genome shotgun sequencing is a powerful to study microbial community is a given environment. Metagenomic binning offers a genome centric approach to study microbiomes. There are several tools available to process metagenomic data from raw reads to the interpretation there is still lack of standard approach that can be used to process the metagenomic data step by step. In this study CuBi-MeAn (Customizable Binning and Metagenomic Analysis) create a customizable and flexible processing pipeline, to process the metagenomic data and generate results for further interpretation.

This study aims to perform metagenomic binning to enhance taxonomical classification, functional potentials, and interactions among microbial populations in environmental systems. This customized pipeline which is comprised of a series of genomic/metagenomic tools designed to recover better quality results and reliable interpretation of the system dynamics for the given systems. For this reason, a metagenomic data processing pipeline is developed to evaluate metagenomic data from three environmental engineering projects.

The use of our pipeline was demonstrated and compared on three different datasets that were of different sizes, from different sequencing platforms, and generated from three different environmental sources. By designing and developing a flexible and customized pipeline, this study has showed how to process large metagenomic data sets with limited resources. This result not only would help to uncover new information from environmental samples, but also, could be applicable to any other metagenomic studies across various disciplines.
Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates severity of DSS-colitis
Authors: Sinha Anshul , Li Yue , Mirzaei Mohammadali Khan , Shamash Michael , Samadfam Rana , King Irah L. , Maurice Corinne F.
Published: September 2021

Inflammatory bowel diseases (IBDs) including Crohn’s disease (CD) and ulcerative colitis (UC) are characterized by chronic and debilitating gut inflammation. Altered bacterial communities of the intestine are strongly associated with IBD initiation and progression. The gut virome, which is primarily composed of bacterial viruses (bacteriophages, phages) is thought to be an important factor regulating and shaping microbial communities in the gut. While alterations in the gut virome have been observed in IBD patients, the contribution of these viruses to alterations in the bacterial community and heightened inflammatory responses associated with IBD patients remains largely unknown. Here, we performed in vivo microbial cross-infection experiments to follow the effects of fecal virus-like particles (VLPs) isolated from UC patients and healthy controls on bacterial diversity and severity of experimental colitis in human microbiota-associated (HMA) mice. Shotgun metagenomics confirmed that several phages were transferred to HMA mice, resulting in treatment-specific alterations in the gut virome. VLPs from healthy and UC patients also shifted gut bacterial diversity of these mice, an effect that was amplified during experimental colitis. VLPs isolated from UC patients specifically altered the relative abundance of several bacterial taxa previously implicated in IBD progression. Additionally, UC VLP administration heightened colitis severity in HMA mice, as indicated by shortened colon length and increased pro-inflammatory cytokine production. Importantly, this effect was dependent on intact VLPs. Our findings build on recent literature indicating that phages are dynamic regulators of bacterial communities in the gut and implicate the intestinal virome in modulating intestinal inflammation and disease.
Cyclic mechanical stresses alter erythrocyte membrane composition and microstructure and trigger macrophage phagocytosis
Authors: Garcia-Herreros Antoni , Yeh Yi-Ting , Peng Zhangli , del Álamo Juan C.
Published: September 2021

Red blood cells (RBCs) are cleared from the circulation when they become damaged or display aging signals targeted by macrophages. This process occurs mainly in the spleen, where blood flows through submicrometric constrictions called inter-endothelial slits (IES), subjecting RBCs to large-amplitude deformations. In this work, we circulated RBCs through microfluidic devices containing microchannels that replicate the IES. The cyclic mechanical stresses experienced by the cells affected their biophysical properties and molecular composition, accelerating cell aging. Specifically, RBCs quickly transitioned to a more spherical, less deformable phenotype that hindered microchannel passage, causing hemolysis. This transition was associated with the release of membrane vesicles, which self-extinguished as the spacing between membrane-cytoskeleton linkers became tighter. Proteomics analysis of the mechanically aged RBCs revealed significant losses of essential proteins involved in antioxidant protection, gas transport, and cell metabolism. Finally, we show that these changes made mechanically aged RBCs more susceptible to macrophage phagocytosis. These results provide a comprehensive model to explain how physical stress induces RBC clearance in the spleen.
Environmental stress determines the colonization and impact of an endophytic fungus on invasive knotweed
Authors: Garnica Sigisfredo , Liao Zhiyong , Hamard Samuel , Waller Frank , Parepa Madalin , Bossdorf Oliver
Published: September 2021

There is increasing evidence that microbes play a key role in some plant invasions. A diverse and widespread but little understood group of plant-associated microbes are the fungal root endophytes of the order Sebacinales. They are associated with exotic populations of invasive knotweed (Reynoutria ssp.) in Europe, but their effects on the invaders are unknown.

We used the recently isolated Sebacinales root endophyte Serendipita herbamans to experimentally inoculate invasive knotweed and study root colonisation and effects on knotweed growth under different environmental conditions. We verified the inoculation success and fungal colonisation through immunofluorescence microscopy and qPCR.

We found that S. herbamans strongly colonized invasive knotweed in low-nutrient and shade environments, but much less under drought or benign conditions. At low nutrients, the endophyte had a positive effect on plant growth, whereas the opposite was true under shaded conditions.

Synthesis. Our study demonstrates that the root endophyte S. herbamans has the potential to colonize invasive knotweed fine roots and impact its growth, and it could thus also play a role in natural populations. Our results also show that effects of fungal endophytes on plants can be strongly environment-dependent, and may only be visible under stressful environmental conditions.
BaRTv2: A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification
Authors: Coulter Max , Entizne Juan Carlos , Guo Wenbin , Bayer Micha , Wonneberger Ronja , Milne Linda , Schreiber Miriam , Haaning Allison , Muehlbauer Gary , McCallum Nicola , Fuller John , Simpson Craig , Stein Nils , Brown John W. S. , Waugh Robbie , Zhang Runxuan
Published: September 2021

Accurate characterization of splice junctions as well as transcription start and end sites in reference transcriptomes allows precise quantification of transcripts from RNA-seq data and enable detailed investigations of transcriptional and post-transcriptional regulation. Using novel computational methods and a combination of PacBio Iso-seq and Illumina short read sequences from 20 diverse tissues and conditions, we generated a comprehensive and highly resolved barley reference transcript dataset (RTD) from the European 2-row spring barley cultivar Barke (BaRTv2.18). Stringent and thorough filtering was carried out to maintain the quality and accuracy of the splice junctions and transcript start and end sites. BaRTv2.18 shows increased transcript diversity and completeness compared to an earlier version, BaRTv1.0. The accuracy of transcript level quantification, splice junctions and transcript start and end sites has been validated extensively using parallel technologies and analysis, including high resolution RT PCR and 5’ RACE. BaRTv2.18 contains 39,434 genes and 148,260 transcripts, representing the most comprehensive and resolved reference transcriptome in barley to date. It provides an important and high-quality resource for advanced transcriptomic analyses, including both transcriptional and post-transcriptional regulation, with exceptional resolution and precision.
Identification of hub genes and pathways in nonalcoholic steatohepatitis by integrated bioinformatics analysis
Authors: Einaliyan Pegah , Owfi Ali , Mahmanzar Mohammadamin , Aghajanzadeh Taha , Hadizadeh Morteza , Sharifi-Zarchi Ali , Hatami Behzad , Aghdaei Hamid Asadzadeh , Zali Mohammad Reza , Baghaei Kaveh
Published: September 2021

Background

Currently, non-alcoholic fatty liver disease (NAFLD) is one of the most common chronic liver diseases in the world. Forecasting the short-term, up to 2025, NASH due to fibrosis is one of the leading causes of liver transplantation. Cohort studies revealed that non-alcoholic steatohepatitis (NASH) has a higher risk of fibrosis progression among NAFLD patients. Identifying differentially expressed genes helps to determine NASH pathogenic pathways, make more accurate diagnoses, and prescribe appropriate treatment.

Methods and Results

In this study, we found 11 NASH datasets by searching in the Gene Expression Omnibus (GEO) database. Subsequently, NASH datasets with low-quality control scores were excluded. Four datasets were analyzed with packages of R/Bioconductor. Then, all integrated genes were Imported into Cytoscape to illustrate the protein-protein interactions network. All hubs and nodes degree has been calculated to determine the hub genes with critical roles in networks.Possible correlations between expression profiles of mutual DEGs were identified employing Principal Component Analysis (PCA). Primary analyzed data were filtered based on gene expression (logFC > 1, logFC < −1) and adj-P-value (<0.05). Ultimately, among 379 DEGs, we selected the top 10 genes (MYC, JUN, EGR1, FOS, CCL2, IL1B, CXCL8, PTGS2, IL6, SERPINE1) as candidates among up and down regulated genes, and critical pathways such as IL-6, IL-17, TGF β, and TNFα were identified.

Conclusion

The present study suggests an important DEGs, biological processes, and critical pathways involved in the pathogenesis of NASH disease. Further investigations are needed to clarify the exact mechanisms underlying the development and progression of NASH disease.
A modular toolset for electrogenetics
Authors: Lawrence J. M. , Yin Y. , Bombelli P. , Scarampi A. , Storch M. , Wey L. T. , Climent-Catala A. ,   PixCell iGEM team, Baldwin G. S. , O’Hare D. , Howe C. J. , Zhang J. Z , Ouldridge T. E. , Ledesma-Amaro R.
Published: September 2021

Synthetic biology research and its industrial applications rely on the deterministic spatiotemporal control of gene expression. Recently, electrochemical control of gene expression has been demonstrated in electrogenetic systems (redox-responsive promoters used alongside redox inducers and an electrode), allowing for the direct integration of electronics with complex biological processes for a variety of new applications. However, the use of electrogenetic systems is limited by poor activity, tunability and standardisation. Here, we have developed a variety of genetic and electrochemical tools that facilitate the design and vastly improve the performance of electrogenetic systems. We developed a strong, unidirectional, redox-responsive promoter before deriving a mutant promoter library with a spectrum of strengths. We then constructed genetic circuits with these parts and demonstrated their activation by multiple classes of redox molecules. Finally, we demonstrated electrochemical activation of gene expression in aerobic conditions utilising a novel, modular bioelectrochemical device. This toolset provides researchers with all the elements needed to design and build optimised electrogenetic systems for specific applications.
Streamlined use of protein structures in variant analysis
Authors: Kaur Sandeep , Sikta Neblina , Schafferhans Andrea , Bordin Nicola , Cowley Mark J. , Thomas David M. , Ballinger Mandy L. , O’Donoghue Seán I.
Published: September 2021

Motivation

Variant analysis is a core task in bioinformatics that requires integrating data from many sources. This process can be helped by using 3D structures of proteins, which can provide a spatial context that can provide insight into how variants affect function. Many available tools can help with mapping variants onto structures; but each has specific restrictions, with the result that many researchers fail to benefit from valuable insights that could be gained from structural data.

Results

To address this, we have created a streamlined system for incorporating 3D structures into variant analysis. Variants can be easily specified via URLs that are easily readable and writable, and use the notation recommended by the Human Genome Variation Society (HGVS). For example, ‘https://aquaria.app/SARS-CoV-2/S/?N501Y’ specifies the N501Y variant of SARS-CoV-2 S protein. In addition to mapping variants onto structures, our system provides summary information from multiple external resources, including COSMIC, CATH-FunVar, and PredictProtein. Furthermore, our system identifies and summarizes structures containing the variant, as well as the variant-position. Our system supports essentially any mutation for any well-studied protein, and uses all available structural data — including models inferred via very remote homology — integrated into a system that is fast and simple to use. By giving researchers easy, streamlined access to a wealth of structural information during variant analysis, our system will help in revealing novel insights into the molecular mechanisms underlying protein function in health and disease.

Availability

Our resource is freely available at the project home page (https://aquaria.app). After peer review, the code will be openly available via a GPL version 2 license at https://github.com/ODonoghueLab/Aquaria. PSSH2, the database of sequence-to-structure alignments, is also freely available for download at https://zenodo.org/record/4279164.

Contact

sean@odonoghuelab.org

Supplementary information

None.
Newly developed MAGIC population allows identification of strong associations and candidate genes for anthocyanin pigmentation in eggplant
Authors: Mangino Giulio , Arrones Andrea , Plazas Mariola , Pook Torsten , Prohens Jaime , Gramazio Pietro , Vilanova Santiago
Published: September 2021

MAGIC populations facilitate the genetic dissection of complex quantitative traits in plants and are valuable breeding materials. We report the development of the first eggplant MAGIC population (S3MEGGIC; 8-way), constituted by 420 S3 individuals developed from the intercrossing of seven cultivated eggplant (Solanum melongena) and one wild relative (S. incanum) parents. The S3MEGGIC recombinant population was genotyped with the eggplant 5k probes SPET platform and phenotyped for anthocyanins presence in vegetative plant tissues (PA) and fruit epidermis (FA), and for the light-sensitive anthocyanic pigmentation under the calyx (PUC). The 7,724 filtered high-confidence SNPs confirmed a low residual heterozygosity (6.87%) and a lack of genetic structure in the S3MEGGIC population, including no differentiation among subpopulations carrying cultivated or wild cytoplasm. Inference of haplotype blocks of the nuclear genome revealed an unbalanced representation of founder genomes, suggesting cryptic selection in favour or against specific parental genomes. GWAS analysis for PA, FA and PUC detected strong associations with two MYB genes similar to MYB113 involved in the anthocyanin biosynthesis pathway and with a COP1 gene, which encodes for a photo-regulatory protein and may be responsible for the PUC phenotype. Evidence was found of a duplication of an ancestral MYB113 gene with a translocation from chromosome 10 to chromosome 1. Parental genotypes for the three genes were in agreement with the candidate genes identification performed in the S3MEGGIC population. Our new eggplant MAGIC population is the largest recombinant population in eggplant and is a powerful tool for eggplant genetics and breeding studies.
What ecological factors favor parthenogenesis over sexual reproduction? A study on the facultatively parthenogenetic mayfly Alainites muticus in natural populations
Authors: Liegeois Maud , Sartori Michel , Schwander Tanja
Published: September 2021

Different reproductive modes are characterized by costs and benefits which often depend on ecological contexts. Benefits of sex are expected to increase under complex biotic interactions, whereas parthenogenesis can be beneficial for reproductive assurance when females are mate limited. Here, we study how different ecological contexts influence the frequency of sex or parthenogenesis in the facultatively parthenogenetic mayfly Alainites muticus. We first verified that high parthenogenetic frequencies translate into female-biased population sex ratios. We then measured the population sex ratio (a proxy for parthenogenetic capacities), density of individuals (mate limitation) and community diversity (biotic interaction complexity) for 159 A. muticus populations, and used structural equation modeling to investigate their direct and indirect influences on sex ratios. We found no effect of community diversity or altitude on sex ratios. Furthermore, even when females can reproduce parthenogenetically, they generally reproduce sexually, indicating that the benefits of sex exceed its costs in most situations. Sex ratios become female-biased in low population densities, as expected if mate limitation selects for parthenogenesis. Mate limitation might be widespread in mayflies because of their very short adult lifespan and limited dispersal, which can generate strong selection for reproductive assurance and may provide a steppingstone towards obligate parthenogenesis.
Learning neural decoders without labels using multiple data streams
Authors: Peterson Steven M. , Rao Rajesh P. N. , Brunton Bingni W.
Published: September 2021

Recent advances in neural decoding have accelerated the development of brain-computer interfaces aimed at assisting users with everyday tasks such as speaking, walking, and manipulating objects. However, current approaches for training neural decoders commonly require large quantities of labeled data, which can be laborious or infeasible to obtain in real-world settings. One intriguing alternative uses self-supervised models that share self-generated pseudo-labels between two data streams; such models have shown exceptional performance on unlabeled audio and video data, but it remains unclear how well they extend to neural decoding. Here, we learn neural decoders without labels by leveraging multiple simultaneously recorded data streams, including neural, kinematic, and physiological signals. Specifically, we apply cross-modal, self-supervised deep clustering to decode movements from brain recordings; these decoders are compared to supervised and unimodal, self-supervised models. We find that sharing pseudo-labels between two data streams during training substantially increases decoding performance compared to unimodal, self-supervised models, with accuracies approaching those of supervised decoders trained on labeled data. Next, we develop decoders trained on three modalities that match or slightly exceed the performance of supervised models, achieving state-of-the-art neural decoding accuracy. Cross-modal decoding is a flexible, promising approach for robust, adaptive neural decoding in real-world applications without any labels.
Predictors of taxonomic splitting and its role in primate conservation
Authors: Creighton Maria J.A. , Luo Alice Q. , Reader Simon M. , Mooers Arne Ø.
Published: September 2021

Species are the main unit used to measure biodiversity, but different preferred diagnostic criteria can lead to very different delineations. For instance, named primate species have more than doubled in number since 1982. Such increases have been attributed to a shift away from the ‘biological species concept’ (BSC) in favour of less inclusive species criteria. Critics of recent changes in primate taxonomy have suggested taxonomic splitting may be biased toward certain clades and have unfavourable consequences for conservation. Here, we explore predictors of taxonomic splitting across primate taxa since the initial shift away from the BSC nearly 40 years ago. We do not find evidence that diversification rate, the rate of lineage formation over evolutionary time, is significantly linked to splitting, contrary to expectations if new species concepts and taxonomic methods identify incipient species. We also do not find evidence that research effort in fields where work has been suggested to motivate splitting is associated with increases in species numbers among genera. To test the suggestion that splitting groups is likely to increase their perceived risk of extinction, we test whether genera that have undergone more splitting have also observed a greater increase in their proportion of threatened species since the initial shift away from traditional taxonomic methods. We find no cohesive signal of taxonomic splitting leading to higher threat probabilities across primate genera. Overall, this analysis sends a positive message: threat statuses of primate species are not being overwhelmingly affected by splitting. Regardless, we echo warnings that it is unwise for conservation to be reliant on taxonomic stability. Species (however defined) are not independent from one another, thus, monitoring and managing them as such may not meet the overarching goal of conserving biodiversity.
Dormancy Breaking Treatments in Northern Wild Rice (Zizania palustris L.) Seed Suggest a Physiological Source of Dormancy
Authors: McGilp Lillian , Semington Aaron , Kimball Jennifer
Published: September 2021

Dormancy is a limiting factor for breeding in northern wild rice (NWR; Zizania palustris L). This study developed a dormancy curve and tested a combination of scarification and hormone treatments, across three timepoints, for their ability to break dormancy in NWR and produce viable seedlings and plants. A dormancy curve was established across 9 months post-harvest, which showed maximum germination (95%) by 17 weeks post-harvest and high germination (≥81 %) through the rest of the testing period. Next, dormancy breaking treatments were tested. At 1 week post-harvest, few seeds germinated (≤ 15 %) across all treatment combinations. However, sulfuric acid increased germination shortly after harvest (5.8 %), compared to water (0.5 %) and NaClO (0 %) but resulted in stunted seedlings, all but one of which died shortly thereafter. At 7 weeks, sulfuric acid treated seeds did not result in significantly higher germination than water and maximum germination was still below 15%. By 11 weeks post-harvest, the water treatments had the highest germination and resulted in the most viable plants, indicating that dormancy had begun to break naturally and exceeded the effect of the other scarification treatments. Hormonal treatments had no significant effect on germination or seed viability and no strong conclusions could be drawn about their effect on seedling or plant health. Due to the inability of early germinated seed to consistently produce viable plants and the increase in germination following sufficient cold storage, it is likely that NWR seed has intermediate or deep physiological dormancy.
Deletion ofVhlinDmp1-expressing cells causes microenvironmental impairment of B cell lymphopoiesis
Authors: Chicana Betsabel , Abbasizadeh Nastaran , Burns Christian , Taglinao Hanna , Spencer Joel A. , Manilay Jennifer O.
Published: September 2021

The contributions of skeletal cells to the processes of B cell development in the bone marrow (BM) have not been completely described. The von-Hippel Lindau protein (VHL) plays a key role in cellular responses to hypoxia. Previous work showed thatDmp1-Cre;Vhlconditional knockout mice (VhlcKO), which deleteVhlin late osteoblasts and osteocytes, display dysregulated bone growth and reduction in B cells. Here, we investigated the mechanisms underlying the B cell defects using flow cytometry and high-resolution imaging. In theVhlcKO BM, B cell progenitors were increased in frequency and number, whereas Hardy Fractions B-F were decreased.VhlcKO Fractions B-C cells showed increased apoptosis and quiescence. Reciprocal BM chimeras confirmed a B cell-extrinsic source of theVhlcKO B cell defects. In support of this,VhlcKO BM serum contained reduced CXCL12 and elevated EPO levels. Staining ofVhlcKO B cells with an intracellular hypoxic marker indicated the natural existence of distinct B cell microenvironments that differ in local oxygen tensions. Additionally, intravital and ex vivo imaging revealedVhlcKO BM blood vessels with increased diameter, frequency, volume, and a diminished blood-BM barrier. Our studies identify novel mechanisms linking altered bone homeostasis with drastic BM microenvironmental changes that dysregulate B cell development.
Benchmarking tools for DNA repeat identification in diverse genomes
Authors: Das Gourab , Ghosh Indira
Published: September 2021

Continuous progression in genomics shows that repeats are important elements of genomes that perform many regulatory and other functions. Eventually, to date, many computational tools have been developed and frequently used for the identification and analysis of genomic repeats. A single tool cannot detect all different types of repeats in diverse species rather pipeline of tools is more effective. But, the choice of such rigorous and robust tools is highly challenging. A method has been implemented to select a set of optimal tools for finding all available classes of perfect and imperfect tandem repeats including microsatellites, minisatellites, and interspersed CRISPRs in genomes. A total of 11 tools have been shortlisted using rule-based selection and then ranked by analyzing rigorousness in searching in diverse species and execution time. Tool comparison shows consistency in perfect microsatellite detection performance but significantly differ for long and imperfect repeats. A web-server has been built which provides a generic platform for various classes of repeat identification from the diverse genome using multiple tools and comparison.
Canonical retinotopic shifts under an inverse force field explain predictive remapping
Authors: Adeyefa-Olasupo Ifedayo-EmmanuEL , Xiao Zixuan , Nandy Anirvan S.
Published: September 2021

Predictive remapping — the ability of cells in retinotopic brain areas to transiently exhibit spatio-temporal retinotopic shifts beyond the spatial extent of their classical receptive fields — has been proposed as a primary mechanism that stabilizes our percept of the visual world around the time of saccadic eye movements. Despite the well documented effects of predictive remapping, no study to date has been able to provide a mechanistic account of the neural computations and architecture that actively mediate this ubiquitous phenomenon. We propose a novel neurobiologically inspired general model of predictive remapping in which the underlying pre-saccadic attentional and oculomotor signals manifest as three temporally overlapping forces that act on retinotopic brain areas. These three forces – a centripetal one toward the center of gaze, a convergent one toward the saccade target and a translational one parallel to the saccade trajectory – act in an inverse force field and govern the spatio-temporal dynamics of predictive remapping of population receptive fields. The predictions of our model are borne out by the spatio-temporal changes in sensitivity to probe stimuli in human subjects around the time of an eye movement and are consistent with findings of predictive shifts in the receptive fields of cells in the superior colliculus, frontal eye fields, lateral intraparietal area, and visual area V4.
Construction of Disease-specific Cytokine Profiles by Associating Disease Genes with Immune Responses
Authors: Liu Tianyun , Wang Shiyin , Altman Russ B
Published: September 2021

The pathogenesis of many inflammatory diseases is a coordinated process involving metabolic dysfunctions and immune response—usually modulated by the production of cytokines and associated inflammatory molecules. In this work, we seek to understand how genes involved in pathogenesis which are often not associated with the immune system in an obvious way communicate with the immune system. We have embedded a network of human protein-protein interactions (PPI) from the STRING database with 14,707 human genes using feature learning that captures high confidence edges. We have found that our predicted Association Scores derived from the features extracted from STRING’s high confidence edges are useful for predicting novel connections between genes, thus enabling the construction of a full map of predicted associations for all possible pairs between 14,707 human genes. In particular, we analyzed the pattern of associations for 126 cytokines and found that the six patterns of cytokine interaction with human genes are consistent with their functional classifications. In order to define the disease-specific roles of cytokines we have collected gene sets for 11,944 diseases from DisGeNET. We used these gene sets to predict disease-specific gene associations with cytokines by calculating the normalized average Association Scores between disease-associated gene sets and the 126 cytokines; this creates a unique profile of inflammatory genes (both known and predicted) for each disease. We validated our predicted cytokine associations by comparing them to known associations for 171 diseases. The predicted cytokine profiles correlate (p-value<0.05) with the known ones in 147 diseases. We further characterized the profiles of each disease by calculating an “Inflammation Score” that summarizes different modes of immune responses. Finally, by analyzing subnetworks formed between disease-specific pathogenesis genes, hormones, receptors, and cytokines, we identified the key genes responsible for interactions between pathogenesis and inflammatory responses. These genes and the corresponding cytokines used by different immune disorders suggest unique targets for drug discovery.
Dynamic brain activity during associative learning examined with MEG/fMRI co-processing
Authors: Nair Sangeeta , Allendorfer Jane B. , Wang Yingying , Szaflarski Jerzy P.
Published: September 2021

Background

Due to limitations of individual neuroimaging methods we examine spatial and temporal contributions to self-generation using multimodality imaging with functional magnetic resonance imaging (fMRI) and magnetoencephalography (MEG) within the Bayesian framework Multiple Sparse Priors (MSP).

New Method

24 healthy participants performed an fMRI and MEG paired-associate learning task. FMRI data were processed within Group ICA fMRI Toolbox. Independent components (ICs) were temporally sorted by task time series (|r|>0.30 threshold identified task-related ICs). Task-positive (“generate”) ICs were retained as spatial priors for MEG analyses. MEG data were processed by averaging trials to increase the signal-to-noise ratio within subjects and with an event-related theta power approach. MEG source reconstructions were constrained within the task-positive ICs for both analytical approaches.

Results

For fMRI, five networks were identified as task-related. Four ICs underlying active generation spanned bilateral parietal, orbitofrontal, medial frontal and superior temporal regions, and occipital lobe. FMRI-constrained MEG source reconstructions yielded early visual cortex activity followed by left inferior frontal gyrus (IFG) and orbito-frontal cortex (OFC) recruitment to coalesce in the left inferior temporal lobe. For the event-related theta approach, reconstructions showed a progression of activity from bilateral temporal areas to left OFC and middle temporal gyrus, followed by right IFG.

Comparison with Existing Methods

MSP analyses informed by fMRI produced more focused regional activity than reconstructions without priors suggesting increased attention and maintenance when selecting relevant semantic information during active generation.

Conclusions

Constraining MEG source reconstruction to fMRI priors during active generation implicates interconnected fronto-temporal and fronto-parietal networks across time.
Wild pigs mediate far-reaching agricultural impacts on tropical forest soil microbial communities
Authors: Brearley Francis Q. , Song Hokyung , Tripathi Binu M. , Dong Ke , Zin Noraziah Mohamad , Abdul Rachman Abdul Rahim , Ickes Kalan , Adams Jonathan M. , Luskin Matthew S.
Published: September 2021

Edge effects, the altered abiotic and biotic conditions on the borders of natural areas, rarely extend more than a few hundred meters. Edge effects have rarely been linked to altered soil biota, which shape ecosystem processes including carbon storage, biogeochemical cycling, and plant performance. Here, we investigated if agriculturally-mediated increased wildlife populations affect soil biotic communities at a distance well over that of estimated edge effects when they move between agriculture and natural habitats using a 22-year fenced exclusion experiment in a primary rainforest in Peninsular Malaysia. We found that the presence of wildlife (mainly native pigs (Sus scrofa) that crop-raid in nearby oil palm plantations) was associated with higher bacterial diversity, and an altered community composition (mediated by changes in soil pH), and reduced abundances of symbiotic ectomycorrhizal fungi compared to soil in exclosures. There were only minor effects of pigs on soil chemistry or microclimate, so we suggest that changes in soil communities are driven by pigs’ leaf litter removal and alterations to plant composition. Our study highlights that indirect effects from agriculture can be transferred by wildlife >1 km into protected areas and this could have important repercussions for ecosystem processes and plant-soil feedbacks.
The Application of The Skin Virome for Human Identification
Authors: Graham Ema H. , Clarke Jennifer L. , Fernando Samodha C. , Herr Joshua R. , Adamowicz Michael S.
Published: September 2021

The use of skin virome for human identification purposes offers a unique approach to instances where a viable and statistically relevant human DNA profile is unavailable. The human skin virome may act as an alternative DNA profile and/or an additional form of probative genetic material. To date, no study has attempted to investigate the human virome over a time series across various physical locations of the body to identify its potential as a tool for human identification. For this study, we set out to evaluate the stability, diversity, and individualization of the human skin virome. An additional goal was to identify viral signatures that can be used in conjunction with traditional forensic STR loci. In order to accomplish this, human virome metagenomes were collected and sequenced from 42 individuals at three anatomical locations (left hand, right hand, and scalp) across multiple collections periods over a 6-month window of time. Assembly dependent and independent bioinformatic approaches were employed, along with a database-based assessment, which resulted in three sets of stable putative viral markers. In total, with the three sets combined, 59 viral species and uncharacterized viral genome assemblies were identified as being significantly stable (P=5.3×10-15). Viral diversity, based on presence or absence, is significantly different across subjects (P<0.001). Here we demonstrate that not only is the human virome applicable to be used for human identification, but we have identified many viral signatures that can be used for forensic applications, thus providing a foundation to the novel field of forensic virology.

Highlights

Here we provide the largest human skin virome study, to date. Our study revealed novel diversity findings of high abundance for certain viral taxa, for example, the Cress-like DNA phages, that have not previously been characterized in human skin viral ecology studies.

There were 59 putative human skin viral biomarkers suitable for human identification from the core stable human skin virome of 42 subjects.

The putative markers we identified were significantly stable over a 6-month period of time within individuals and across three autosomal locations of left hand, right hand, and scalp.

Diversity of profiles, based on the presence and absence of our putative marker data set, were significantly different across test subjects.