bluuebunny/crossref_metadata_2025_split huggingface dataset:
Auditory Hypersensitivity and Processing Deficits in a Rat Model of Fragile X Syndrome
Authors: Auerbach Benjamin D. , Manohar Senthilvelan , Radziwon Kelly , Salvi Richard 
Published: September 2021

AbstractFragile X (FX) syndrome is one of the leading inherited causes of autism spectrum disorder (ASD). A majority of FX and ASD patients exhibit sensory hypersensitivity, including auditory hypersensitivity or hyperacusis, a condition in which everyday sounds are perceived as much louder than normal. Auditory processing deficits in FX and ASD also afford the opportunity to develop objective and quantifiable outcome measures that are likely to translate between humans and animal models due to the well-conserved nature of the auditory system and well-developed behavioral read-outs of sound perception. Therefore, in this study we characterized auditory hypersensitivity in aFmr1knockout (KO) transgenic rat model of FX using an operant conditioning task to assess sound detection thresholds and suprathreshold auditory reaction time-intensity (RT-I) functions, a reliable psychoacoustic measure of loudness growth, at a variety of stimulus frequencies, bandwidths and durations. MaleFmr1KO and littermate WT rats both learned the task at the same rate and exhibited normal hearing thresholds. However,Fmr1KO rats had faster auditory RTs over a broad range of intensities and steeper RT-I slopes than WT controls, perceptual evidence of excessive loudness growth inFmr1KO rats. Furthermore, we found thatFmr1KO animals exhibited abnormal perceptual integration of sound duration and bandwidth, with diminished temporal but enhanced spectral integration of sound intensity. Because temporal and spectral integration of sound stimuli were altered in opposite directions inFmr1KO rats, this suggests that abnormal RTs in these animals are evidence of aberrant auditory processing rather than generalized hyperactivity or altered motor responses. Together, these results are indicative of fundamental changes to low-level auditory processing inFmr1KO animals. Finally, we demonstrated that antagonism of metabotropic glutamate receptor 5 (mGlu5) selectively and dose-dependently restored normal loudness growth inFmr1KO rats, suggesting a pharmacologic approach for alleviating sensory hypersensitivity associated with FX. This study leverages the tractable nature of the auditory system and the unique behavioral advantages of rats to provide important insights into the nature of a centrally important yet understudied aspect of FX and ASD.
Elucidation of sub-cellular H2S metabolism inSolanum lycopersicumL. and its assessment under development and biotic stress
Authors: Chowdhary Aksar Ali , Mishra Sonal , Singh Vikram , Srivastava Vikas 
Published: September 2021

AbstractThe signalling molecules serve as a fundamental requirement in plants and respond to various internal and external cues. Among several signalling molecules, the significance of gasotransmitters has been realized in several plant developmental and environmental constraints. The hydrogen sulfide (H2S) is a novel signalling molecule in higher plants and is involved in several physiological processes right from seed germination to flowering and fruit ripening. Moreover, H2S also assist plants in managing biotic and abiotic stresses, therefore serves as one of the imperative choice of chemical priming. Yet, the metabolism of H2S is not much explored and only appraisal study is made till date fromArabidopsis thaliana. Therefore, the present investigation explored the elucidation of H2S metabolism in crop plantSolanum lycopersicumL. Through in silico investigations the study demonstrated the participation of 29 proteins involved in H2S metabolism, which are mainly localized in cytosol, chloroplast, and mitochondria. Additionally, the relevant protein-protein interactomes were also inferred for sub-cellular compartments and expression data were explored under development and biotic stresses namely PAMPs treatment and bacterial infection. The information generated here will be of high relevance to better target the H2S metabolism to enhance the tomato prospects and also serve a preliminary investigation to be adopted in other agronomic important crops.
The wheat dioxygenase BX6 is involved in the formation of benzoxazinoids in planta and contributes to plant defense against insect herbivores
Authors: Shavit Reut , Batyrshina Zhaniya S. , Yaakov Beery , Florean Matilde , Köllner Tobias G. , Tzin Vered 
Published: September 2021

AbstractBenzoxazinoids are plant specialized metabolites with defense properties, highly abundant in wheat (Triticum), one of the world’s most important crops. The goal of our study was to characterize dioxygenase BX6 genes in tetraploid and hexaploid wheat genotypes and to elucidate their effects on defense against herbivores. Phylogenetic analysis revealed four BX6 genes in the hexaploid wheat T. aestivum, but only one ortholog was found in tetraploid (T. turgidum) wild emmer wheat and the cultivated durum wheat. Transcriptome sequencing of durum wheat plants damaged either by aphids or caterpillars revealed that several BX genes including TtBX6 were upregulated upon caterpillar feeding relative to undamaged control plants. A virus-induced gene silencing approach was used to reduce the expression of BX6 in T. aestivum plants and exhibited both reduced transcript levels and reduced accumulation of different benzoxazinoids. To elucidate the effect of BX6 on plant defense, bioassays with different herbivores feeding on BX6-silenced leaves were conducted. The results showed that plants with silenced BX6 were more susceptible to aphids and the two-spotted spider mite compared to controls. Overall, our study indicates that wheat BX6 is involved in the formation of benzoxazinoids in planta and contributes to plant resistance against insect herbivores.
Instant Taq: Rapid Autoinducible Expression and Chromatography-free Purification of Taq polymerase
Authors: Menacho-Melgar Romel , Yang Tian , Lynch Michael D. 
Published: September 2021

AbstractDNA modifying enzymes are ubiquitous reagents in synthetic biology. Producing these enzymes often requires large culture volumes, purified nucleases and chromatographic separations to make enzymes of necessary quality. We sought to leverage synthetic biology tools to develop engineered strains allowing for not only the production but rapid purification of these reagents. Toward this goal, we report an E. coli strain enabling the rapid production and purification of Taq polymerase. The method relies on 1) autoinducible expression achieving high protein titers, 2) autolysis and auto DNA/RNA hydrolysis via lysozyme and a mutant benzonase™, and 3) heat denaturation under reducing conditions to precipitate contaminating proteins including the mutant benzonase™. Taq polymerase is obtained at high purities (>95% pure by SDS-PAGE) and is readily usable in standard reactions. The method takes less than 1 hour of hands-on time, does not require special equipment, expensive reagents or affinity purification. We expect this simple methodology and approach will improve access not only to Taq polymerase but to numerous additional commonly utilized reagent proteins.HighlightsProtein titers ~ 1g/L achieved in 20 mL shakeflasks.4 mg of purified Taq (corresponding to 5,000 Units, or 4,000 PCR reactions) per 20 mL shake flask.Instant Taq is equivalent to commercial preparations in routine PCR
Direct reprogramming of the intestinal epithelium by parasitic helminths subverts type 2 immunity
Authors: Karo-Atar Danielle , Ouladan Shaida , Javkar Tanvi , Joumier Loick , Matheson Macy K. , Merritt Sydney , Westfall Susan , Rochette Annie , Gentile Maria E. , Fontes Ghislaine , Fonseca Gregory J. , Parisien Marc , Diatchenko Luda , von Moltke Jakob , Malleshaiah Mohan , Gregorieff Alex , King Irah L. 
Published: September 2021

AbstractEnteric helminths form intimate physical connections with the intestinal epithelium, yet their ability to directly alter epithelial stem cell fate has not been resolved. Here we demonstrate that infection of mice with the symbiotic parasite Heligmosomoides polygyrus bakeri (Hbp), reprograms the intestinal epithelium into a fetal-like state marked by the emergence of Clusterin-expressing revival stem cells (revSCs). Organoid-based studies using parasite-derived excretory/secretory products reveal that Hpb-mediated revSC generation occurs independent of host-derived immune signals and inhibits type 2 cytokine-driven differentiation of secretory epithelial lineages that promote their expulsion. Reciprocally, type 2 cytokine signals limit revSC differentiation and, consequently, Hpb fitness indicating that helminths compete with their host for control of the intestinal stem cell niche to promote continuation of their life cycle.
Kinetic and thermodynamic modeling of a voltage-gated sodium channel
Authors: Almog Mara , Degani-Katzav Nurit , Korgnreen Alon 
Published: September 2021

AbstractLike all biological and chemical reactions, ion channel kinetics are highly sensitive to changes in temperature. Therefore, it is prudent to investigate channel dynamics at physiological temperatures. However, most ion channel investigations are performed at room temperature due to practical considerations, such as recording stability and technical limitations. This problem is especially severe for the fast voltage-gated sodium channel, whose activation kinetics are faster than the time constant of the standard patch-clamp amplifier at physiological temperatures. Thus, biologically detailed simulations of the action potential generation evenly scale the kinetic models of voltage-gated channels acquired at room temperature. To quantitatively study voltage-gated sodium channels’ temperature sensitivity, we recorded sodium currents from nucleated patches extracted from the rat’s layer five neocortical pyramidal neurons at several temperatures from 13.5 to 30oC. We use these recordings to model the kinetics of the voltage-gated sodium channel as a function of temperature. We show that the temperature dependence of activation differs from that of inactivation. Furthermore, we show that the sustained current has a different temperature dependence than the fast current. Our kinetic and thermodynamic analysis of the current provided a numerical model spanning the entire temperature range. This model reproduced vital features of channel activation and inactivation. Furthermore, the model also reproduced action potential dependence on temperature. Thus, we provide an essential building block for the generation of biologically detailed models of cortical neurons.
Anchorage by seed mucilage prevents seed dislodgement in high surface flow: a mechanistic investigation
Authors: Pan Vincent S. , Girvin Cecilia , LoPresti Eric F. 
Published: September 2021

AbstractBackground and Aims:Seed mucilage is a common and highly diverse trait shared among thousands of angiosperm species. While long recognized that mucilage allows seeds to anchor to substrates (antitelechory), resisting abiotic and biotic dislodgement, we still lack a mechanistic understanding of this process.Methods:We propose a mechanistic model of how mucilage affects substrate anchorage and fluid resistance, ultimately contributing to dislodgement resistance. To test this model, we subjected mucilaginous seeds of 52 species, varying in eight measured seed traits, to seven days of continuous water flow at a range of dislodgement potentials.Key Results:Supporting our model, mucilage mass increased force necessary to dislodge both dry and wet seeds; our measurement of the dislodgement force of dry mucilage explained time to dislodgement well. The effect size was remarkably large; increasing the standardized mucilage mass by one standard deviation resulted in a 280-fold increase in the time to dislodgement. Fluid resistance was largely dependent on speed of water flow and the seed’s modified drag coefficient, but not seed traits. Neither mucilage expansion speed nor mucilage decay rate explained dislodgement potential well.Conclusions:Our results suggest that the degree of anchorage to substrate, measured with a simple dislodgement force assay, is highly predictive of mucilaginous seed retention in highly erosive environments. In contrast, we found that other seed and mucilage traits are of lesser importance to anchorage.
Cross-species cell-type assignment of single-cell RNA-seq by a heterogeneous graph neural network
Authors: Liu Xingyan , Shen Qunlun , Zhang Shihua 
Published: September 2021

AbstractCross-species comparative analyses of single-cell RNA sequencing (scRNA-seq) data allow us to explore, at single-cell resolution, the origins of cellular diversity and the evolutionary mechanisms that shape cellular form and function. Here, we aimed to utilize a heterogeneous graph neural network to learn aligned and interpretable cell and gene embeddings for cross-species cell type assignment and gene module extraction (CAME) from scRNA-seq data. A systematic evaluation study on 649 pairs of cross-species datasets showed that CAME outperformed six benchmarking methods in terms of cell-type assignment and model robustness to insufficiency and inconsistency of sequencing depths. Comparative analyses of the major types of human and mouse brains by CAME revealed shared cell type-specific functions in homologous gene modules. Alignment of the trajectories of human and macaque spermatogenesis by CAME revealed conservative gene expression dynamics during spermatogenesis between humans and macaques. Owing to the utilization of non-one-to-one homologous gene mappings, CAME made a significant improvement on cell-type characterization cross zebrafish and other species. Overall, CAME can not only make an effective cross-species assignment of cell types on scRNA-seq data but also reveal evolutionary conservative and divergent features between species.
The chromosomal distribution of sex-biased microRNAs in Drosophila is non-adaptive
Authors: Marco Antonio 
Published: September 2021

ABSTRACTGenes are often differentially expressed between males and females. In Drosophila melanogaster, the analysis of sex-biased microRNAs (short non-coding regulatory molecules) has revealed striking differences with protein-coding genes. Mainly, the X chromosome is enriched in male-biased microRNA genes, although it is depleted of male-biased protein-coding genes. The paucity of male-biased genes in the X chromosome is generally explained by an evolutionary process called demasculinization. I suggest that the excess of male-biased microRNAs in the X chromosome is due to high-rates of de novo emergence of microRNAs (mostly in other neighboring microRNAs), a tendency of novel microRNAs in the X chromosome to be expressed in testis, and to a lack of a demasculinization process. To test this hypothesis I analysed the expression profile of microRNAs in males, females and gonads in D. pseudoobscura, in which an autosome translocated into the X chromosome effectively becoming part of a sex chromosome (neo-X). I found that the pattern of sex-biased expression is generally conserved between D. melanogaster and D. pseudoobscura. Also, orthologous microRNAs in both species conserve their chromosomal location, indicating that there is no evidence of demasculinization or other inter-chromosomal movement of microRNAs. D. pseudoobscuraspecific microRNAs in the neo-X chromosome tend to be male-biased and particularly expressed in testis. In summary, the apparent paradox resulting from male-biased protein-coding genes depleted in the X chromosome and an enrichment in male-biased microRNAs is consistent with different evolutionary dynamics between coding genes and short RNAs.
Single-molecule analysis of specificity and multivalency in binding of short linear substrate motifs to the APC/C
Authors: Hartooni Nairi , Sung Jongmin , Jain Ankur , Morgan David O. 
Published: September 2021

AbstractRobust regulatory signals in the cell often depend on interactions between short linear motifs (SLiMs) and globular proteins. Many of these interactions are poorly characterized because the binding proteins cannot be produced in the amounts needed for traditional methods. To address this problem, we developed a single-molecule off-rate (SMOR) assay based on microscopy of fluorescent ligand binding to immobilized protein partners. We used it to characterize substrate binding to the Anaphase-Promoting Complex/Cyclosome (APC/C), a ubiquitin ligase that triggers chromosome segregation. We find that SLiMs in APC/C substrates (the D box and KEN box) display distinct affinities and specificities for the substrate-binding subunits of the APC/C, and we show that multiple SLiMs in a substrate generate a high-affinity multivalent interaction. The remarkably adaptable substrate-binding mechanisms of the APC/C have the potential to govern the order of substrate destruction in mitosis.
Large-scale comparative small RNA analyses reveal genomic structural variants in driving expression dynamics and differential selection pressures on distinct small RNA classes during tomato domestication
Authors: Qing You , Zheng Yi , Mlotshwa Sizolwenkosi , Smith Heather N. , Wang Xin , Zhai Xuyang , van der Knaap Esther , Wang Ying , Fei Zhangjun 
Published: September 2021

AbstractTomato has undergone extensive selections during domestication. Recent progress has shown that genomic structural variants (SVs) have contributed to gene expression dynamics during tomato domestication, resulting in changes of important traits. Here, through comprehensive analyses of small RNAs (sRNAs) from nine representative tomato accessions, we demonstrate that SVs substantially contribute to the dynamic expression of the three major classes of plant sRNAs: microRNAs (miRNAs), phased secondary short interfering RNAs (phasiRNAs), and 24-nt heterochromatic siRNAs (hc-siRNAs). Changes in the abundance of phasiRNAs and 24-nt hc-siRNAs likely contribute to the alteration of mRNA gene expression during tomato’s recent evolution, particularly for genes associated with biotic and abiotic stress tolerance. We also observe that miRNA expression dynamics are associated with imprecise processing, alternative miRNA-miRNA* selections, and SVs. SVs mainly affect the expression of less-conserved miRNAs that do not have established regulatory functions or low abundant members in highly expressed miRNA families, highlighting different selection pressures on miRNAs compared to phasiRNAs and 24-nt hc-siRNAs. Our findings provide insights into plant sRNA evolution as well as SV-based gene regulation during crop domestication. Furthermore, our dataset provides a rich resource for mining the sRNA regulatory network in tomato.
Cryo-EM structure of a single-chain β1-adrenoceptor – AmpC β-lactamase fusion protein
Authors: Collu Gabriella , Mohammed Inayathulla , Lafita Aleix , Bierig Tobias , Poghosyan Emiliya , Bliven Spencer , Benoit Roger M. 
Published: September 2021

AbstractThe insertion of fusion proteins has enabled the crystallization of a wide range of G-protein-coupled receptors (GPCRs). Here, we explored the possibility of using a larger fusion protein, inserted into the third intracellular loop (ICL3) of β1-adrenoceptor (β1AR) via rigid chimeric helix fusions. The aim was to engineer a single-chain fusion protein that comprises sufficient mass and rigidity to allow single-particle cryo-EM data collection, without depending on binding proteins, such as G-proteins or nanobodies. Through parsing of the protein data bank (PDB), we identified the protein AmpC β-lactamase as a suitable candidate. Both termini of this protein are α-helical and the helices are antiparallel to each other. The distance between their centroids measures ∼11 Å. Such a geometry is ideal to design extended chimeric helices with transmembrane (TM) helices 5 and 6 of β1AR, and the insertion of the protein adds ∼39 kDa of mass to the receptor. We expressed the β1AR - AmpC β-lactamase fusion protein in mammalian cells. The binding of the antagonists propranolol and cyanopindolol to the purified fusion protein was confirmed by CPM-based thermofluor assays. The cryo-EM structure was solved to a nominal overall resolution of 3.6 Å and the seven helix architecture and helix eight were clearly resolved. Superimposition of the structure with known X-ray crystal structures of β1AR suggests that the protein is in its inactive conformation. The fusion protein described here provides a basis for high-throughput structure elucidation of class A GPCRs by cryo-EM for drug discovery research as well as for the elucidation of inactive state or wild-type GPCR structures. The fusion protein geometry theoretically fits a wide range of class A GPCRs and therefore can be applied to a multitude of receptors.
Metabolite profiling reveals organ-specific flavone accumulation in Scutellaria and identifies a scutellarin isomer isoscutellarein 8-O-β-glucuronopyranoside
Authors: Askey Bryce C. , Liu Dake , Rubin Garret M. , Kunik Andrew R. , Song Yeong Hun , Ding Yousong , Kim Jeongim 
Published: September 2021

AbstractScutellaria is a genus of plants containing multiple species with well-documented medicinal effects. S. baicalensis and S. barbata are among the best-studied Scutellaria species, and previous works have established flavones to be the primary source of their bioactivity. Recent genomic and biochemical studies with S. baicalensis and S. barbata have advanced our understanding of flavone biosynthesis in Scutellaria. However, as over several hundreds of Scutellaria species occur throughout the world, flavone biosynthesis in most species remains poorly understood. In this study, we analyzed organ-specific flavone profiles of seven Scutellaria species, including S. baicalensis, S. barbata and two species native to the Americas (S. wrightii to Texas and S. racemosa to Central and South America). We found that the roots of almost all these species produce only 4’-deoxyflavones, while 4’-hydroxyflavones are accumulated exclusively in their aerial parts. On the other hand, S. racemosa and S. wrightii also accumulated high levels of 4’-deoxyflavones in their aerial parts, different with the flavone profiles of S. baicalensis and S. barbata. Furthermore, our metabolomics and NMR study identified the accumulation of isoscutellarein 8-O-β-glucuronopyranoside, a rare 4’-hydroxyflavone, in the stems and leaves of several Scutellaria species including S. baicalensis and S. barbata, but not in S. racemosa and S. wrightii. Distinctive organ-specific metabolite profiles among Scutellaria species indicate the selectivity and diverse physiological roles of flavones.