bluuebunny/crossref_metadata_2025_split huggingface dataset:
Individual differences in theta-band oscillations in a spatial memory network revealed by EEG predict rapid place learning
Authors: Bauer Markus , Buckley Matthew G. , Bast Tobias 
Published: June 2020

AbstractSpatial memory has been closely related to the medial temporal lobe (MTL), and theta-oscillations are thought to play a key role. However, it remains difficult to investigate medio-temporal lobe (MTL) activation related to spatial memory with non-invasive electrophysiological methods in humans.Here, we combined the virtual delayed-matching-to-place (DMP) task, reverse-translated from the watermaze DMP task in rats, with high-density electroencephalography (EEG) recordings. Healthy young volunteers performed this computerised task in a virtual circular arena, which contained a hidden target whose location moved to a new place every four trials, allowing the assessment of rapid memory formation.Using behavioural measures as predictor variables for source reconstructed frequency specific EEG power, we found that inter-individual differences in ‘search preference’ during ‘probe trials’, a measure of 1-trial place learning known from rodent studies to be particularly hippocampus dependent, correlated predominantly with distinct theta-band oscillations (approx. 7 Hz), particularly in the right temporal lobe, the right striatum and inferior occipital cortex or cerebellum. Notably, this pattern was found with very high consistency during both encoding and retrieval/expression, but not in control analyses and could not be explained by motor confounds. Alpha-activity in sensorimotor and parietal cortex contralateral to the hand used for navigation also correlated with search preference, which likely reflected movement-related factors associated with task performance.Relating inter-individual differences in ongoing brain activity to behaviour in a continuous rapid place learning task that is suitable for a variety of populations, we could demonstrate that memory related theta-band activity in temporal lobe can be measured with EEG recordings, revealing a presumed network of MTL, striatum and cerebellum and/or inferior occipital cortex that may interact through theta oscillations. This approach holds great potential for further studies investigating the interactions within this network during encoding and retrieval, as well as neuromodulatory impacts and age-related changes.
Abiotic treatment to common bean plants results in an altered endophytic seed microbiome
Authors: Bintarti A. Fina , Kearns Patrick J. , Sulesky-Grieb Abby , Shade Ashley 
Published: June 2020

AbstractThere has been a growing interest in the seed microbiome due to its important role as an end and starting point of plant microbiome assembly that can have consequences for plant health. However, the effect of abiotic conditions on the seed microbial community remains unknown. We performed a pilot study in a controlled growth chamber to investigate how the endophytic seed microbiome of the common bean(Phaseolus vulgaris L.(var. Red Hawk)) was altered under abiotic treatments relevant for crop management with changing climate. Bean plants were subjected to one of three treatments: 66% water withholding to simulate mild drought, 50% Hoagland nutrient solution to simulate fertilization, or control with sufficient water and baseline nutrition. We performed 16S rRNA gene amplicon sequencing and ITS1 amplicon sequencing of the endophytic DNA to assess seed bacterial/archaeal and fungal community structure, respectively. We found that variability in the seed microbiome structure was high while alpha diversity was low, with tens of taxa present. Water withholding and nutrient addition altered the seed microbiome structure for bacterial/archaeal communities as compared to the control, and each treatment resulted in a distinct microbiome structure. There were no statistically supported differences in the fungal microbiome across treatments. While we discuss several limitations of this study, the promising results suggest that further investigation is needed to better understand abiotic or stress-induced changes in the seed microbiome, the mechanisms that drive those changes, and their implications for the health and stress responses of the next plant generation.ImportanceSeed microbiome members initiate the assembly of plant-associated microbial communities, but the environmental drivers of endophytic seed microbiome composition are unclear. Here, we exposed plants to short-term drought and fertilizer treatments during early vegetative growth and quantified the microbiome composition of the seeds that were ultimately produced. We found that seeds produced by plants stressed by water limitation or receiving nutrient addition had statistically different endophytic bacterial/archaeal microbiome compositions from each other and from seeds produced by control plants. This work suggests that the abiotic experience of a parental plant can influence the composition of its seed microbiome, with unknown consequences for the next plant generation.
CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells
Authors: Darvish Shafighi Shadi , Kiełbasa Szymon M , Sepúlveda-Yáñez Julieta , Monajemi Ramin , Cats Davy , Mei Hailiang , Menafra Roberta , Kloet Susan , Veelken Hendrik , van Bergen Cornelis A.M. , Szczurek Ewa 
Published: June 2020

ABSTRACTBackgroundDrawing genotype-to-phenotype maps in tumors is of paramount importance for understanding tumor heterogeneity. Assignment of single cells to their tumor clones of origin can be approached by matching the genotypes of the clones to the mutations found in RNA sequencing of the cells. The confidence of the cell-to-clone mapping can be increased by accounting for additional measurements. Follicular lymphoma, a malignancy of mature B cells that continuously acquire mutations in parallel in the exome and in B-cell receptor loci, presents a unique opportunity to align exome-derived mutations with B-cell receptor clonotypes as an independent measure for clonal evolution.ResultsHere, we propose CACTUS, a probabilistic model that leverages the information from an independent genomic clustering of cells and exploits the scarce single cell RNA sequencing data to map single cells to given imperfect genotypes of tumor clones. We apply CACTUS to two follicular lymphoma patient samples, integrating three measurements: whole exome sequencing, single cell RNA sequencing, and B-cell receptor sequencing. CACTUS outperforms a predecessor model by confidently assigning cells and B-cell receptor clonotypes to the tumor clones.ConclusionsThe integration of independent measurements increases model certainty and is the key to improving model performance in the challenging task of charting the genotype-to-phenotype maps in tumors. CACTUS opens the avenue to study the functional implications of tumor heterogeneity, and origins of resistance to targeted therapies.
An ABA-GA bistable switch can account for natural variation in the variability of Arabidopsis seed germination time
Authors: Abley Katie , Formosa-Jordan Pau , Tavares Hugo , Chan Emily , Leyser Ottoline , Locke James C.W. 
Published: June 2020

AbstractGenetically identical plants growing in the same conditions can display heterogeneous phenotypes. Whether this phenotypic variability is functional and the mechanisms behind it are unclear. Here we use Arabidopsis seed germination time as a model system to examine phenotypic variability. We show extensive variation in seed germination time variability between Arabidopsis accessions, and use a multi-parent recombinant inbred population to identify two loci involved in this trait. Both loci include genes implicated in ABA signalling that could contribute to seed germination variability. Modelling reveals that the GA/ABA bistable switch underlying germination can amplify variability and account for the effects of these two loci on germination distributions. The model predicts the effects of modulating ABA and GA levels, which we validate genetically and by exogenous addition of hormones. We confirm that germination variability could act as a bet hedging strategy, by allowing a fraction of seeds to survive lethal stress.
Novel allergen discovery through comprehensivede novotranscriptomic analyses of 5 shrimp species
Authors: Karnaneedi Shaymaviswanathan , Huerlimann Roger , Johnston Elecia B. , Nugraha Roni , Ruethers Thimo , Taki Aya C. , Kamath Sandip D. , Wade Nicholas M. , Jerry Dean R. , Lopata Andreas L. 
Published: June 2020

AbstractShellfish allergy affects up to 2% of the world’s population and persists for life in most patients. The diagnosis of a shellfish allergy, in particular shrimp, is however often challenging due to the similarity of allergenic proteins in other invertebrates. Despite the clinical importance, the complete allergen repertoire of allergy-causing shrimps remains unclear. Here we mine the complete transcriptome of five frequently consumed shrimp species to identify and compare allergens with all known allergen sources. The transcriptomes were assembledde novofrom raw RNA-Seq data of the whiteleg shrimp (Litopenaeus vannamei), black tiger shrimp (Penaeus monodon), banana shrimp (Fenneropenaeus merguiensis), king shrimp (Melicertus latisulcatus), and endeavour shrimp (Metapenaeus endeavouri). Trinity was used to assemble the transcriptome, and Transrate and BUSCO applied to verify the assembly. Blast search with the two major allergen databases, WHO/IUIS Allergen Nomenclature and AllergenOnline, successfully identified all seven known crustacean allergens. Salmon was utilised to measure their relative abundance, demonstrating sarcoplasmic calcium-binding protein, arginine kinase and myosin light chain as highly abundant allergens. In addition, the analyses revealed up to 40 unreported allergens in different shrimp species, including heat shock protein (HSP), alpha-tubulin, chymotrypsin, cyclophilin, beta-enolase, aldolase A, and glyceraldehyde-3-phosphate dehydrogenase (G3PD). Multiple sequence alignment, conducted in Jalview 2.1 with Clustal Omega, demonstrated high homology with allergens from other invertebrates including mites and cockroaches. This first transcriptomic analyses of allergens in a major food source provides a valuable genomic resource for investigating shellfish allergens, comparing invertebrate allergens and developing improved diagnostics and novel immunotherapeutics for food allergy.
Whole genome identification of potential G-quadruplexes and analysis of the G-quadruplex binding domain for SARS-CoV-2
Authors: Zhang Rongxin , Ke Xiao , Gu Yu , Liu Hongde , Sun Xiao 
Published: June 2020

AbstractThe Coronavirus Disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) quickly become a global public health emergency. G-quadruplex, one of the non-canonical secondary structures, has shown potential antiviral values. However, little is known about G-quadruplexes on the emerging SARS-CoV-2. Herein, we characterized the potential G-quadruplexes both in the positive and negative-sense viral stands. The identified potential G-quadruplexes exhibits similar features to the G-quadruplexes detected in the human transcriptome. Within some bat and pangolin related beta coronaviruses, the G-quartets rather than the loops are under heightened selective constraints. We also found that the SUD-like sequence is retained in the SARS-CoV-2 genome, while some other coronaviruses that can infect humans are depleted. Further analysis revealed that the SARS-CoV-2 SUD-like sequence is almost conserved among 16,466 SARS-CoV-2 samples. And the SARS-CoV-2 SUDcore-like dimer displayed similar electrostatic potential pattern to the SUD dimer. Considering the potential value of G-quadruplexes to serve as targets in antiviral strategy, we hope our fundamental research could provide new insights for the SARS-CoV-2 drug discovery.
Post-Translational Modifications Soften Vimentin Intermediate Filaments
Authors: Kraxner Julia , Lorenz Charlotta , Menzel Julia , Parfentev Iwan , Silbern Ivan , Denz Manuela , Urlaub Henning , Schwappach Blanche , Köster Sarah 
Published: June 2020

AbstractThe mechanical properties of biological cells are determined by the cytoskeleton, a composite biopolymer network consisting of microtubules, actin filaments and intermediate filaments (IFs). By differential expression of cytoskeletal proteins, modulation of the network architecture and interactions between the filaments, cell mechanics may be adapted to varying requirements on the cell. Here, we focus on the intermediate filament protein vimentin and introduce post-translational modifications as an additional, much faster mechanism for mechanical modulation. We study the impact of phosphorylation on filament mechanics by recording force-strain curves using optical traps. Partial phosphorylation softens the filaments. We show that binding of the protein 14–3–3 to phosphorylated vimentin IFs further enhances this effect and speculate that in the cell 14–3–3 may serve to preserve the softening and thereby the altered cell mechanics. We explain our observation by the additional charges introduced during phosphorylation.
ANANSE: An enhancer network-based computational approach for predicting key transcription factors in cell fate determination
Authors: Xu Quan , Georgiou Georgios , Frölich Siebren , van der Sande Maarten , Veenstra Gert Jan C. , Zhou Huiqing , van Heeringen Simon J. 
Published: June 2020

AbstractProper cell fate determination is largely orchestrated by complex gene regulatory networks centered around transcription factors. However, experimental elucidation of key transcription factors that drive cellular identity is currently often intractable. Here, we present ANANSE (ANalysisAlgorithm forNetworksSpecified byEnhancers), a network-based method that exploits enhancer-encoded regulatory information to identify the key transcription factors in cell fate determination. As cell type-specific transcription factors predominantly bind to enhancers, we use regulatory networks based on enhancer properties to prioritize transcription factors. First, we predict genome-wide binding profiles of transcription factors in various cell types using enhancer activity and transcription factor binding motifs. Subsequently, applying these inferred binding profiles, we construct cell type-specific gene regulatory networks, and then predict key transcription factors controlling cell fate transitions using differential networks between cell types. This method outperforms existing approaches in correctly predicting major transcription factors previously identified to be sufficient for trans-differentiation. Finally, we apply ANANSE to define an atlas of key transcription factors in 18 normal human tissues. In conclusion, we present a ready-to-implement computational tool for efficient prediction of transcription factors in cell fate determination and to study transcription factor-mediated regulatory mechanisms. ANANSE is freely available athttps://github.com/vanheeringen-lab/ANANSE.
A novel in-cell ELISA assay allows rapid and automated quantification of SARS-CoV-2 to analyse neutralizing antibodies and antiviral compounds
Authors: Schöler Lara , Le-Trilling Vu Thuy Khanh , Eilbrecht Mareike , Mennerich Denise , Anastasiou Olympia E. , Krawczyk Adalbert , Herrmann Anke , Dittmer Ulf , Trilling Mirko 
Published: June 2020

AbstractThe coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently the most pressing medical and socioeconomic challenge. Constituting important correlates of protection, determination of virus-neutralizing antibodies (NAbs) is indispensable for convalescent plasma selection, vaccine candidate evaluation, and immunity certificates. In contrast to standard serology ELISAs, plaque reduction neutralization tests (PRNTs) are laborious, time-consuming, expensive, and restricted to specialized laboratories. To replace microscopic counting-based SARS-CoV-2 PRNTs by a novel assay exempt from genetically modified viruses, which are inapplicable in most diagnostics departments, we established a simple, rapid, and automated SARS-CoV-2 neutralization assay employing an in-cell ELISA (icELISA) approach.After optimization of various parameters such as virus-specific antibodies, cell lines, virus doses, and duration of infection, SARS-CoV-2-infected cells became amenable as direct antigen source for quantitative icELISA. Using commercially available nucleocapsid protein-specific antibodies, viral infection could easily be quantified in human and highly permissive Vero E6 cells by icELISA. Antiviral agents such as human sera containing NAbs or antiviral interferons dose-dependently reduced the SARS-CoV-2-specific signal. Applying increased infectious doses, the icNT was superior to PRNT in discriminating convalescent sera with high from those with intermediate neutralizing capacities.The SARS-CoV-2 icELISA test allows rapid (<48h in total, read-out in seconds) and automated quantification of virus infection in cell culture to evaluate the efficacy of NAbs as well as antiviral drugs, using reagents and equipment present in most routine diagnostics departments. We propose the icELISA and the icNT for COVID-19 research and diagnostics.
Stability of Begomoviral pathogenicity determinant βC1 is modulated by mutually antagonistic SUMOylation and SIM interactions
Authors: Nair Ashwin , Chatterjee Kiran Sankar , Jha Vikram , Das Ranabir , Shivaprasad P. V. 
Published: June 2020

AbstractTo successfully invade new hosts, to break host resistance as well as to move within and between plant cells, viruses and their satellites have evolved a coordinated network of protein interactions. βC1 protein encoded by specific geminiviral satellites acts as a key pathogenicity determinant. βC1 from diverse viruses undergo multiple post-translational modifications (PTMs) such as ubiquitination and phosphorylation. However, the relevance of these and other layers of PTMs in host-geminiviral interactions has not been fully understood. Here we identified the significance of a novel layer of PTMs in Synedrella yellow vein clearing virus (SyYVCV) encoded βC1 protein having well conserved SUMOylation and SUMO-interacting motifs (SIMs). We observed that SyYVCV βC1 undergoes SUMOylation in host plants as a defensive strategy against ubiquitin mediated degradation. On the contrary, SIMs encoded in βC1 mediate degradation of βC1. Both these PTMs are also essential for the function of βC1 protein since SIM and SUMOylation motif mutants failed to promote pathogenicity and viral replicationin vivo. In addition, SUMOylation in different motifs of βC1 led to functionally distinct outcomes, regulating the stability and function of the βC1 protein, as well as increased global SUMOylation of host proteins. Our results indicate the presence of a novel mechanism mediating a fine balance between defence and counter-defence in which a SIM site is competitively sought for degradation and as a counter defense, βC1 undergoes SUMOylation to escape from its degradation.Summary StatementβC1 viral protein has evolved counter-defensive strategies to perturb host protein degradation pathways
Ontogeny, species identity and environment dominate microbiome dynamics in wild populations of kissing bugs (Triatominae)
Authors: Brown Joel J. , Rodríguez-Ruano Sonia M. , Poosakkannu Anbu , Batani Giampiero , Schmidt Justin O. , Roachell Walter , Zima Jan , Hypša Václav , Nováková Eva 
Published: June 2020

AbstractBackgroundKissing bugs (Triatominae) are blood-feeding insects best known as the vectors ofTrypanosoma cruzi, the causative agent of Chagas’ disease. Considering the high epidemiological relevance of these vectors, their biology and bacterial symbiosis remains surprisingly understudied. While previous investigations revealed generally low individual complexity but high among-individual variability of the triatomine microbiomes, any consistent microbiome determinants have not yet been identified across multiple Triatominae species.MethodsTo obtain a more comprehensive view of triatomine microbiomes, we investigated the host-microbiome relationship of fiveTriatomaspecies sampled from white-throated woodrat (Neotoma albigula) nests in multiple locations across the USA. We applied optimized 16S rRNA gene metabarcoding with a novel 18S rRNA gene blocking primer to a set of 170T. cruzinegative individuals across all six instars.ResultsTriatomine gut microbiome composition is strongly influenced by three principal factors: ontogeny, species identity, and the environment. The microbiomes are characterised by significant loss in bacterial diversity throughout ontogenetic development. First instars possess the highest bacterial diversity while adult microbiomes are routinely dominated by a single taxon. Primarily, the bacterial genusDietziadominates late-stage nymphs and adults ofT. rubida, T. protracta, andT. lecticularia, but is not present in the phylogenetically more distantT. gerstaeckeriandT. sanguisuga.Species-specific microbiome composition, particularly pronounced in early instars, is further modulated by locality-specific effects. In addition, pathogenic bacteria of the genusBartonella, acquired from the vertebrate hosts, are an abundant component ofTriatomamicrobiomes.ConclusionOur study is the first to demonstrate deterministic patterns in microbiome composition among all life stages and multipleTriatomaspecies. We hypothesize that triatomine microbiome assemblages are produced by species- and life stage-dependent uptake of environmental bacteria and multiple indirect transmission strategies that promote bacterial transfer between individuals. Altogether, our study highlights the complexity of Triatominae symbiosis with bacteria and warrant further investigation to understand microbiome function in these important vectors.
Magnetocontrolled protein membranes for cell cultures co-cultivation
Authors: Minin A. , Tiuchai M. , Rodionov S. , Blatov I. , Zubarev I. 
Published: June 2020

AbstractInvestigation of cells and tissues in vitro systems is an attempt to simplify the very complex interactions between the various cell types from multicellular organisms. Monolayer cell cultures with single cell type do not allow to show all the possible paracrine interactions between various types of cells. To analyze intercellular inter-actions, it is possible to use systems that co-cultivate several cell types. This article proposes a new cell co-cultivation system based on levitation in the magnetic field in the culture medium of a magnetic protein membrane with cells. The developed system of co-cultivation of cells can be made in any laboratory of available reagents and have a low manufacturing cost.