bluuebunny/crossref_metadata_2025_split huggingface dataset:
The KH domains of FMRP differentially regulate neuronal granule formation, dynamics, and function in Drosophila
Authors: Starke Emily L. , Barbee Scott A. 
Published: June 2021

ABSTRACTFragile X Syndrome (FXS) is the most prevalent cause of inherited mental deficiency and is the most common monogenetic cause of autism spectral disorder (ASD). Here, we demonstrate that disease-causing missense mutations in the conserved K homology (KH) RNA binding domains (RBDs) of FMRP cause defects in its ability to form RNA transport granules in neurons. Using molecular, genetic, and imaging approaches in the Drosophila FXS model system, we show that the KH1 and KH2 domains of FMRP regulate distinct aspects of neuronal FMRP granule formation, dynamics, and transport. Furthermore, mutations in both KH domains disrupt translational repression in cells and the localization of known FMRP target mRNAs in neurons. These results suggest that the KH domains play an essential role in neuronal FMRP granule formation and function which may be linked to the molecular pathogenesis of FXS.
HDX-MS optimized approach to characterize nanobodies as tools for biochemical and structural studies of class IB phosphoinositide 3-kinases
Authors: Rathinaswamy Manoj K , Fleming Kaelin D , Dalwadi Udit , Pardon Els , Harris Noah J , Yip Calvin K , Steyaert Jan , Burke John E 
Published: June 2021

AbstractThere is considerable interest in developing antibodies as modulators of signaling pathways. One of the most important signaling pathways in higher eukaryotes is the phosphoinositide 3-kinase (PI3K) pathway, which plays fundamental roles in growth, metabolism and immunity. The class IB PI3K, PI3Kγ, is a heterodimeric complex composed of a catalytic p110γ subunit bound to a p101 or p84 regulatory subunit. PI3Kγ is a critical component in multiple immune signaling processes and is dependent on activation by Ras and GPCRs to mediate its cellular roles. Here we describe the rapid and efficient characterization of multiple PI3Kγ single chain camelid nanobodies using hydrogen deuterium exchange mass spectrometry (HDX-MS) for structural and biochemical studies. This allowed us to identify nanobodies that stimulated lipid kinase activity, blocked Ras activation and specifically inhibited p101-mediated GPCR activation. Overall, this reveals novel insight into PI3Kγ regulation and identifies sites that may be exploited for therapeutic development.Highlights– HDX-MS rapidly identifies epitopes of camelid single-chain nanobodies raised against Class IB PI3K complexes, p110γ/p101 and p110γ/p84– A nanobody targeting p101 improves local resolution in EM studies with p110γ/p101 facilitating structural characterization of the complex– Nanobodies that bind at the interfaces with the lipidated activators Ras and Gβγ can prevent activation of p110γ/p101 and p110γ/p84
Predisposition to Proinsulin Misfolding as a Genetic Risk to Diet-Induced Diabetes
Authors: Alam Maroof , Arunagiri Anoop , Haataja Leena , Torres Mauricio , Larkin Dennis , Kappler John , Jin Niyun , Arvan Peter 
Published: June 2021

AbstractThroughout evolution, proinsulin has exhibited significant sequence variation in both C-peptide and insulin moieties. As the proinsulin coding sequence evolves, the gene product continues to be under selection pressure both for ultimate insulin bioactivity and for the ability of proinsulin to be folded for export through the secretory pathway of pancreatic β-cells. The substitution proinsulin-R(B22)E is known to yield a bioactive insulin, although R(B22)Q has been reported as a mutation that falls within the spectrum of Mutant INS-gene induced Diabetes of Youth (MIDY). Here we have studied mice expressing heterozygous (or homozygous) proinsulin-R(B22)E knocked into the Ins2 locus. Neither females nor males bearing the heterozygous mutation develop diabetes at any age examined, but subtle evidence of increased proinsulin misfolding in the endoplasmic reticulum is demonstrable in isolated islets from the heterozygotes. Moreover, males have indications of glucose intolerance and within a few week exposure to a high-fat diet, they develop frank diabetes. Diabetes is more severe in homozygotes, and the development of disease parallels a progressive heterogeneity of β-cells with increasing fractions of proinsulin-rich/insulin-poor cells, as well as glucagon-positive cells. Evidently, sub-threshold predisposition to proinsulin misfolding can go undetected, but provides genetic susceptibility to diet-induced β-cell failure.
A multiple genome alignment workflow shows the impact of repeat masking and parameter tuning on alignment of functional regions in plants
Authors: Wu Yaoyao , Johnson Lynn , Song Baoxing , Romay Cinta , Stitzer Michelle , Siepel Adam , Buckler Edward , Scheben Armin 
Published: June 2021

AbstractAlignments of multiple genomes are a cornerstone of comparative genomics, but generating these alignments remains technically challenging and often impractical. We developed the msa_pipeline workflow (https://bitbucket.org/bucklerlab/msa_pipeline) based on the LAST aligner to allow practical and sensitive multiple alignment of diverged plant genomes with minimal user inputs. Our workflow only requires a set of genomes in FASTA format as input. The workflow outputs multiple alignments in MAF format, and includes utilities to help calculate genome-wide conservation scores. As high repeat content and genomic divergence are substantial challenges in plant genome alignment, we also explored the impact of different masking approaches and alignment parameters using genome assemblies of 33 grass species. Compared to conventional masking with RepeatMasker, a k-mer masking approach increased the alignment rate of CDS and non-coding functional regions by 25% and 14% respectively. We further found that default alignment parameters generally perform well, but parameter tuning can increase the alignment rate for non-coding functional regions by over 52% compared to default LAST settings. Finally, by increasing alignment sensitivity from the default baseline, parameter tuning can increase the number of non-coding sites that can be scored for conservation by over 76%.
Formin’s nucleation activity influences actin filament length
Authors: Zweifel Mark E. , Sherer Laura A. , Mahanta Biswaprakash , Courtemanche Naomi 
Published: June 2021

AbstractFormins stimulate actin polymerization by promoting both filament nucleation and elongation. Because nucleation and elongation draw upon a common pool of actin monomers, the rate at which each reaction proceeds influences the other. This interdependent mechanism determines the number of filaments assembled over the course of a polymerization reaction, as well as their equilibrium lengths. In this study, we used kinetic modeling and in vitro polymerization reactions to dissect the contributions of filament nucleation and elongation to the process of formin-mediated actin assembly. We found that the rates of nucleation and elongation evolve over the course of a polymerization reaction. The period over which each process occurs is a key determinant of the total number of filaments that are assembled, as well as their average lengths at equilibrium. Inclusion of formin in polymerization reactions speeds filament nucleation, thus increasing the number and shortening the lengths of filaments that are assembled over the course of the reaction. Although variations in elongation rates produce modest changes in the equilibrium lengths of formin-bound filaments, nucleation constitutes the primary mode of monomer consumption over the course of assembly. Sustained elongation of small numbers of formin-bound filaments therefore requires inhibition of nucleation via monomer sequestration and a low concentration of activated formin. Our results underscore the mechanistic advantage for keeping formin’s nucleation efficiency relatively low in cells, where unregulated actin assembly would produce deleterious effects on cytoskeletal dynamics. Under these conditions, differences in the elongation rates mediated by formin isoforms are most likely to impact the kinetics of actin assembly.
Probing Interactions of Therapeutic Antibodies with Serum via Second Virial Coefficient Measurements
Authors: Larsen Hayli A. , Atkins William M. , Nath Abhinav 
Published: June 2021

ABSTRACTAntibody-based therapeutics are the fastest growing drug class on the market, used to treat aggressive forms of cancer, chronic autoimmune conditions, and numerous other disease states. While the specificity, affinity, and versatility of therapeutic antibodies can provide an advantage over traditional small molecule drugs, their development and optimization can be much more challenging and time-consuming. This is, in part, because the ideal formulation buffer systems used for in vitro characterization inadequately reflect the crowded biological environments (serum, endosomal lumen, etc.) that these drugs experience once administered to a patient. Such environments can perturb the binding of antibodies to their antigens and receptors, as well as homo- and hetero-aggregation, in ways that are incompletely understood, thereby altering therapeutic effect and disposition. While excluded volume effects are classically thought to favor binding, weak interactions with co-solutes in crowded conditions can inhibit binding. The second virial coefficient (B2) parameter quantifies such weak interactions and can be determined by a variety of techniques in dilute solution, but analogous methods in complex biological fluids are not well established. Here, we demonstrate that fluorescence correlation spectroscopy (FCS) is able to measure diffusive B2 values directly in undiluted serum. Apparent second virial coefficient (B2,app) measurements of antibodies in serum reveal that changes in the balance between attractive and repulsive interactions can dramatically impact global nonideality. Furthermore, our findings suggest that the common approach of isolating specific components and completing independent cross-term virial coefficient measurements is an incomplete representation of nonideality in serum. The approach presented here could enrich our understanding of the effects of biological environments on proteins in general, and advance the development of therapeutic antibodies and other protein-based therapeutics.STATEMENT OF SIGNIFICANCEWe present FCS as an orthogonal method to traditional methods for characterizing weak, nonspecific homo- and hetero-interactions through determination of self- and cross-term second virial coefficients, respectively. We also characterize weak interactions between therapeutic antibodies and serum components through determination of an apparent second virial coefficient (B2,app) directly in undiluted serum. Our results suggest that global nonideality effects are antibody-dependent, and that attractive and repulsive interactions with co-solutes are occurring simultaneously. This approach could advance our understanding of the impact of nonideality to the biophysical and pharmacological properties of therapeutic antibodies and other engineered proteins in relevant biological environments, and could accelerate the development and optimization of protein-based therapeutics.
Shade-induced WRKY transcription factors restrict root growth during the shade avoidance response
Authors: Rosado Daniele , Ackermann Amanda , Spassibojko Olya , Rossi Magdalena , Pedmale Ullas V. 
Published: June 2021

AbstractShade-intolerant plants rapidly elongate their stems, branches, and leaf stalks to compete with their neighboring vegetation to maximize sunlight capture for photosynthesis. This rapid growth adaptation, known as the shade avoidance response (SAR), comes at a cost; reduced biomass, crop yield, and root growth. Significant progress has been made on the mechanistic understanding of hypocotyl elongation during SAR; however, the molecular account of how root growth is repressed is not well understood. Here, we explore the mechanisms by which low red:far-red induced SAR restrict the primary and lateral root (LR) growth. By analyzing whole-genome transcriptome, we identified a core set of shade-induced genes in the roots of Arabidopsis and tomato seedlings grown in the shade. Abiotic and biotic stressors also induce many of these shade-induced genes and are predominantly regulated by the WRKY transcription factors. Correspondingly, a majority of the WRKYs were also among the shade-induced genes. Functional analysis using transgenics of these shade-induced WRKYs revealed their role is essentially to restrict primary root and LR growth in the shade, and captivatingly, they did not affect hypocotyl elongation. Similarly, we also show that ethylene hormone signaling is necessary to limit root growth in the shade. Our study proposes that during SAR, shade-induced WRKY26, 45, and 75, and ethylene reprogram gene expression in the root to restrict its growth and development. The reduced growth of root organs helps the plant divert its critical resources to the elongating organs in the shoot to ensure competitiveness under limiting photosynthetic radiation.One sentence summaryShade represses root growth by inducing WRKY transcription factors.
Co-infection of Candidatus Piscichlamydia trichopodus (order Chlamydiales) and Henneguya sp (Myxosporea, Myxobolidae) in snakeskin gourami Trichopodus pectoralis (Regan 1910)
Authors: Dinh-Hung Nguyen , Dong Ha Thanh , Soontara Chayanit , Rodkhum Channarong , Nimitkul Sukkrit , Srisapoome Prapansak , Chatchaiphan Satid , Kayansamruaj Pattanapon 
Published: June 2021

AbstractThe present study describes a simultaneous infection of a novel Chlamydia-like organism (CLO) with a Myxozoa parasite, Henneguya sp. in snakeskin gourami Trichopodus pectoralis in Thailand. A new CLO is proposed “Candidatus Piscichlamydia trichopodus” (CPT) based on 16S rRNA phylogenetic analysis. Systemic intracellular CPT infection was confirmed by histological examination, in situ hybridization, PCR assay, and sequencing of 16S rRNA. This novel pathogen belongs to the order Chlamydiales but differs in certain aspects from other species. The histopathological changes associated with CPT infection were different from the typical pathological lesions of epitheliocystis caused by previously known CLO. Unlike other CLO, CPT localized in the connective tissue rather than in the epithelial cells and formed smaller clumps of intracellular bacteria that stained dark blue with hematoxylin. On the other hand, typical myxospores of the genus Henneguya with tails were observed in the gill sections. Infection with Henneguya sp. resulted in extensive destruction of the gill filaments, most likely leading to respiratory distress. Due to the frequency of co-infections and the unavailability of culture methods for CLO and Henneguya sp, it was difficult to determine which pathogens were directly responsible for the associated mortality. However, co-infections may increase the negative impact on the host and the severity of the disease. Given the commercial importance of the snakeskin gourami and its significant aquaculture potential, the findings of this study are important for further studies on disease prevention.
Assessing the sensitivity of EEG-based frequency-tagging as a metric for statistical learning
Authors: Pinto Danna , Prior Anat , Golumbic Elana Zion 
Published: June 2021

AbstractStatistical Learning (SL) is hypothesized to play an important role in language development. However, the behavioral measures typically used to assess SL, particularly at the level of individual participants, are largely indirect and often have low sensitivity. Recently, a neural metric based on frequency-tagging has been proposed as an alternative and more direct measure for studying SL. Here we tested the sensitivity of frequency-tagging measures for studying SL in individual participants in an artificial language paradigm, using non-invasive EEG recordings of neural activity in humans. Importantly, we use carefully constructed controls, in order to address potential acoustic confounds of the frequency-tagging approach. We compared the sensitivity of EEG-based metrics to both explicit and implicit behavioral tests of SL, and the correspondence between these presumed converging operations. Group-level results confirm that frequency-tagging can provide a robust indication of SL for an artificial language, above and beyond potential acoustic confounds. However, this metric had very low sensitivity at the level of individual participants, with significant effects found only in 30% of participants. Conversely, the implicit behavior measures indicated that SL has occurred in 70% of participants, which is more consistent with the proposed ubiquitous nature of SL. Moreover, there was low correspondence between the different measures used to assess SL. Taken together, while some researchers may find the frequency-tagging approach suitable for their needs, our results highlight the methodological challenges of assessing SL at the individual level, and the potential confounds that should be taken into account when interpreting frequency-tagged EEG data.
Chromosome-levelde novogenome assembly ofTelopea speciosissima(New South Wales waratah) using long-reads, linked-reads and Hi-C
Authors: Chen Stephanie H , Rossetto Maurizio , van der Merwe Marlien , Lu-Irving Patricia , Yap Jia-Yee S , Sauquet Hervé , Bourke Greg , Amos Timothy G , Bragg Jason G , Edwards Richard J 
Published: June 2021

ABSTRACTTelopea speciosissima,the New South Wales waratah, is an Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Here, we report the first chromosome-level genome forT. speciosissima. Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 97.8 % of Embryophyta BUSCOs complete. We present a new method in Diploidocus (https://github.com/slimsuite/diploidocus) for classifying, curating and QC-filtering scaffolds, which combines read depths, k-mer frequencies and BUSCO predictions. We also present a new tool, DepthSizer (https://github.com/slimsuite/depthsizer), for genome size estimation from the read depth of single copy orthologues and estimate the genome size to be approximately 900 Mb. The largest 11 scaffolds contained 94.1 % of the assembly, conforming to the expected number of chromosomes (2n= 22). Genome annotation predicted 40,158 protein-coding genes, 351 rRNAs and 728 tRNAs. We investigatedCYCLOIDEA(CYC) genes, which have a role in determination of floral symmetry, and confirm the presence of two copies in the genome. Read depth analysis of 180 ‘Duplicated’ BUSCO genes suggest almost all are real duplications, increasing confidence in protein family analysis using annotated protein-coding genes, and highlighting a possible need to revise the BUSCO set for this lineage. The chromosome-levelT. speciosissimareference genome (Tspe_v1) provides an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.
FLAME: a web tool for functional and literature enrichment analysis of multiple gene lists
Authors: Thanati Foteini , Karatzas Evangelos , Baltoumas Fotis A. , Stravopodis Dimitrios J. , Eliopoulos Aristides G. , Pavlopoulos Georgios A. 
Published: June 2021

ABSTRACTFunctional enrichment is a widely used method for interpreting experimental results by identifying classes of proteins/genes associated with certain biological functions, pathways, diseases or phenotypes. Despite the variety of existing tools, most of them can process a single list per time, thus making a more combinatorial analysis more complicated and prone to errors. In this article, we present FLAME, a web tool for combining multiple lists prior to enrichment analysis. Users can upload several lists of preference and use interactive UpSet plots, as an alternative to Venn diagrams, to handle unions or intersections among the given input files. Functional and literature enrichment along with gene conversions are offered by g:Profiler and aGOtool applications for 197 organisms. In its current version, FLAME can analyze genes/proteins for related articles, Gene Ontologies, pathways, annotations, regulatory motifs, domains, diseases, phenotypes while it can also generate protein-protein interactions derived from STRING. We have herein validated FLAME by interrogating gene expression data associated with the sensitivity of the distal part of the large intestine to experimental colitis-propelled colon cancer. The FLAME application comes with an interactive user-friendly interface which allows easy list manipulation and exploration, while results can be visualized as interactive and parameterizable heatmaps, barcharts, Manhattan plots, networks and tables.AvailabilityFLAME application: http://flame.pavlopouloslab.infoCodehttps://github.com/PavlopoulosLab/FLAME
Costs dictate strategic investment in dominance interactions
Authors: Dehnen Tobit , Papageorgiou Danai , Nyaguthii Brendah , Cherono Wismer , Penndorf Julia , Boogert Neeltje J. , Farine Damien R. 
Published: June 2021

AbstractDominance is important for access to resources. As dominance interactions are costly, individuals should be strategic in who they interact with. One hypothesis is that individuals should direct costly interactions towards those closest in rank, as they have most to gain—in terms of attaining or maintaining dominance—from winning such interactions. Here, we show that male vulturine guineafowl (Acryllium vulturinum), a gregarious species with steep dominance hierarchies, strategically express higher-cost aggressive interactions towards males occupying ranks immediately below themselves in their group’s hierarchy. In contrast, lower-cost aggressive interactions are expressed towards group members further down the hierarchy. By directly evaluating differences in the strategic use of higher- and lower-cost aggressive interactions towards competitors, we show that individuals disproportionately use highest-cost interactions—such as chases—towards males found one to three ranks below themselves. Our results support the hypothesis that the costs associated with different interaction types can determine their expression in social groups with steep dominance hierarchies.
Persistent DNA damage promotes microglial dysfunction in Ataxia-telangiectasia
Authors: Bourseguin Julie , Cheng Wen , Talbot Emily , Hardy Liana , Khoronenkova Svetlana V. 
Published: June 2021

ABSTRACTThe autosomal recessive genome instability disorder Ataxia-telangiectasia, caused by mutations in ATM kinase, is characterised by the progressive loss of cerebellar neurons. We find that DNA damage associated with ATM loss results in dysfunctional behaviour of human microglia, immune cells of the central nervous system. Microglial dysfunction is mediated by the pro-inflammatory RELB/p52 non-canonical NF-κB transcriptional pathway and leads to excessive phagocytic clearance of neurites. Pathological phagocytosis of neuronal processes by microglia has also been observed in multiple sclerosis, Alzheimer’s and progranulin deficiency, suggesting a common mechanism that promotes neuronal damage. Activation of the RELB/p52 pathway in ATM-deficient microglia is driven by persistent DNA damage and is dependent on the NIK kinase. These results provide insights into the underlying mechanisms of aberrant microglial behaviour in Ataxia-telangiectasia, potentially contributing to neurodegeneration.