bluuebunny/crossref_metadata_2025_split huggingface dataset:
An automated workflow to assess completeness and curate GenBank for eDNA metabarcoding: the marine fish assemblage as case study
Authors: Claver Cristina , Canals Oriol , de Amézaga Leire G. , Mendibil Iñaki , Rodriguez-Ezpeleta Naiara 
Published: October 2022

AbstractExpectations are high regarding the potential of eDNA metabarcoding for diversity monitoring. To make this approach suitable for this purpose, the completeness and accuracy of reference databases used for taxonomic assignment of eDNA sequences are among the challenges to be tackled. Yet, despite ongoing efforts to increase coverage of reference databases, sequences for key species are lacking, and incorrect records in widely used repositories such as GenBank have been reported. This compromises eDNA metabarcoding studies, especially for high diverse groups such as marine fishes. Here, we have developed a workflow that evaluates the completeness and accuracy of GenBank. For a given combination of species and barcodes a gap analysis is performed, and potentially erroneous sequences are identified. Our gap analysis based on the four most used genes (cytochrome c oxidase subunit 1, 12S rRNA, 16S rRNA and cytochrome b) for fish eDNA metabarcoding found that COI, the universal choice for metazoans, is the gene covering the highest number of Northeast Atlantic marine fishes (70%), while 12S rRNA, the preferred region for fish-targeting studies, only covered about 50% of the species. The presence of too close and too distant barcode sequences as expected by their taxonomic classification confirms presence of erroneous sequences in GenBank that our workflow can detect and eliminate. Comparing taxonomic assignments of real marine eDNA samples with raw and clean reference databases for the most used 12S rRNA barcodes (teleoandMiFish), we found that both barcodes perform differently, and demonstrated that the application of the database cleaning workflow can result in drastic changes in community composition. Besides providing an automated tool for reference database curation, this study confirms the need to increase 12S rRNA reference sequences for European marine fishes, encourages the use of a multi-marker approach for better community composition assessment, and evidences the dangers of taxonomic assignments by directly querying GenBank.
Knockdown of the TRPM4 channel alters cardiac electrophysiology and hemodynamics in a sex- and age-dependent manner in mice
Authors: Arullampalam Prakash , Essers Maria C. , Rougier Jean-Sébastien , Abriel Hugues 
Published: October 2022

ABSTRACTBackgroundTRPM4 is a calcium-activated, voltage-modulated, non-selective ion channel widely expressed in various types of cells and tissues. TRPM4 regulates the influx of sodium ions, thus playing a role in regulating the membrane potential. In the heart, TRPM4 is expressed in both cardiomyocytes and cells of the conductive pathways. Clinical studies have linkedTRPM4mutations to several cardiac disorders. While data from experimental studies have demonstrated TRPM4’s functional significance in cardiac physiology, its exact roles in the heart remain unclear.AimTo investigate the role of TRPM4 in cardiac physiology in a newly generated knockdownTrpm4mouse model.Methods and resultsMale and femaleTrpm4knockdown (Trpm4-/-) and wild-type mice 5- to 12-weeks-old (young) or 24-week-old or more (adult) were characterized using a multimodal approach, encompassing surface electrocardiograms (ECG), echocardiography recordings, pseudo and intracardiac ECGs, western blots, and mRNA quantifications. The assessment of cardiac electrophysiology by surface ECGs revealed no significant differences between wild type andTrpm4-/-5- to 12-weeks-old mice of either sex. Above 24 weeks of age, adult maleTrpm4-/-mice showed significantly reduced heart rate and increased heart rate variability. Echocardiography reveals that only adult maleTrpm4-/-mice exhibited slight left ventricular hypertrophic alterations with an alteration of the mitral valve pressure half time, the mitral valve E/A ratio, the isovolumetric relaxation time, and the mitral valve deceleration. In addition, an assessment of the right ventricular systolic function by scanning the pulmonary valve highlighted an alteration in pulmonary valve peak velocity and pressure in maleTrpm4-/-adult mice. Finally, intracardiac ECG recordings showed that the application of 5 µM NBA triggered a third-degree atrioventricular block on 40% of wild-type hearts only.ConclusionsThese results confirm the important role of TRPM4 in the proper structure and electrical function of the heart. It also reveals significant differences between male and female animals that have never been reported before. In addition, the investigation of the effects of NBA on heart function highlights the role of TRPM4 in atrioventricular conduction and provides the first evidence showing the efficacy of this compound on native cardiac tissues.
IntestLine: a Shiny-based application to map the rolled intestinal tissue onto a line
Authors: Yuzeir Altay , Bejarano David , Grein Stephan , Hasenauer Jan , Schlitzer Andreas , Yu Jiangyan 
Published: October 2022

ABSTRACTTo allow the comprehensive histological analysis of the whole intestine in one image, the tissue is often rolled to a spiral before imaging. This Swiss-rolling technique facilitates robust experimental procedures, but it limits the possibilities to comprehend changes along the intestine. Here, we present IntestLine, a Shiny-based open-source application to map imaging data of intestinal tissues in spiral shape onto a line. The mapping of intestinal tissues improves the visualization of the whole intestine in both proximal-distal and serosa-luminal axis, and facilitates the observation of location-specific cell types and markers. In summary, IntestLine serves as a tool to visualize and characterize intestine in future imaging studies.
A non-human primate model with Alzheimer’s disease-like pathology induced by hippocampal overexpression of human tau
Authors: Jiang Zhouquan , Wang Jing , Luo Bin , Bai Fan , Qin Yongpeng , Wei Huiyi , Zhang Shaojuan , Wei Junjie , Ding Guoyu , Ma Long , He Shu , Chen Rongjie , Wang Lu , Xu Hao , Wang Xiangyu , Chen Gong , Lei Wenliang 
Published: October 2022

AbstractAlzheimer’s disease (AD) is one of the most burdening diseases of the century with no disease-modifying treatment yet. Non-human primates (NHPs) share genetic, anatomical and physiological similarities with humans, making them an ideal model for investigating the pathogenesis and therapeutics of AD. However, the applications of NHPs in AD research have been hindered by the paucity of spontaneous or induced monkey models for AD due to their long generation time, ethical considerations and technical challenges in making genetically modified monkeys. Here we developed an AD-like NHP model by overexpressing human tau in bilateral hippocampi of adult rhesus macaque monkeys. We evaluated the pathological features of these monkeys with immunostaining, cerebrospinal fluid (CSF) analysis, magnetic resonance imaging (MRI), positron emission tomography (PET) scan, and behavioral tests. We demonstrated that after hippocampal overexpression of human tau, the rhesus macaque monkeys displayed multiple pathological features of AD, including neurofibrillary tangle formation, neuronal loss, hippocampal atrophy, neuroinflammation, Aβ clearance deficit, blood vessel damage and cognitive decline. This work establishes a human tau-induced AD-like NHP model that may facilitate mechanistic studies and therapeutic treatments for AD.
High throughput evaluation of genetic variants with prime editing sensor libraries
Authors: Gould Samuel I. , Wuest Alexandra N. , Dong Kexin , Johnson Grace A. , Hsu Alvin , Narendra Varun K. , Levine Stuart S. , Liu David R. , Sánchez Rivera Francisco J. 
Published: October 2022

AbstractMany human diseases have a strong association with diverse types of genetic alterations. These diseases include cancer, in which tumor genomes often harbor a complex spectrum of single-nucleotide alterations and chromosomal rearrangements that can perturb gene function in ways that remain poorly understood. Some cancer-associated genes exhibit a tremendous degree of mutational heterogeneity, which may impact disease initiation, progression, and therapy responses. For example,TP53, the most frequently mutated gene in cancer, shows extensive allelic variation that leads to the generation of altered proteins that can produce functionally distinct phenotypes. Whether distinct variants ofTP53and other genes encode proteins with loss-of-function, gain-of-function, or otherwise neomorphic phenotypes remains both controversial and technically challenging to assess, particularly at the endogenous level. Here, we present a high-throughput prime editing “sensor” strategy to quantitatively assess the functional impact of diverse types of endogenous genetic variants. We used this strategy to screen the largest collection of endogenous cancer-associatedTP53variants assembled to date, identifying both known and novel alleles that impact p53 function in mechanistically diverse ways. Intriguingly, we find that certain types of endogenousTP53variants, particularly those in the p53 oligomerization domain, display opposite phenotypes in exogenous overexpression systems. These include disease-relevant variants found in humans with cancer predisposition syndromes that encode altered proteins with unique molecular properties. Our results emphasize the physiological importance of gene dosage in shaping native protein stoichiometry and protein-protein interactions, highlight the dangers of using exogenous overexpression systems to interpret pathogenic alleles, and establish a powerful computational and experimental framework for studying diverse types of genetic variants in their endogenous sequence context at scale.
The dispensability of 14-3-3 proteins for the regulation of human cardiac sodium channel Nav1.5
Authors: Iamshanova Oksana , Hämmerli Anne-Flore , Ramaye Elise , Seljmani Arbresh , Ross-Kaschitza Daniela , Schärz Noëlia , Essers Maria , Guichard Sabrina , Rougier Jean-Sébastien , Abriel Hugues 
Published: October 2022

AbstractBackground14-3-3 proteins are ubiquitous proteins that play a role in cardiac physiology (e.g., metabolism, development, and cell cycle). Furthermore, 14-3-3 proteins were proposed to regulate the electrical function of the heart by interacting with several cardiac ion channels, including the voltage-gated sodium channel Nav1.5. Given the many cardiac arrhythmias associated with Nav1.5 dysfunction, understanding its regulation by the protein partners is crucial.AimsIn this study, we aimed to investigate the role of 14-3-3 proteins in the regulation of the human cardiac sodium channel Nav1.5.Methods and ResultsAmongst the seven 14-3-3 isoforms, only 14-3-3η (encoded byYWHAHgene) weakly co-immunoprecipitated with Nav1.5 when heterologously co-expressed in tsA201 cells. Total and cell surface expression of Nav1.5 was however not modified by 14-3-3η overexpression or inhibition with difopein, and 14-3-3η did not affect physical interaction between Nav1.5 α-α subunits. The current-voltage relationship and the amplitude of Nav1.5-mediated sodium peak current density were also not changed.ConclusionsOur findings illustrate that the direct implication of 14-3-3 proteins in regulating Nav1.5 is not evident in a transformed human kidney cell line tsA201.SummaryThis work shows that only 14-3-3η, exhibits weak/transient interaction with Nav1.5, and does not modify its total protein expression, plasmalemmal trafficking, and basal biophysical properties of the whole-cell current. Furthermore, inhibition of endogenous 14-3-3/ligand interactions with difopein does not affect the dimerization of Nav1.5. Therefore, 14-3-3 proteins are suggested to be dispensable for the Nav1.5 regulation in a heterologous expression system.
Complex changes in serum protein levels in COVID-19 convalescents
Authors: Pushalkar Smruti , Wu Shaohuan , Maity Shuvadeep , Pressler Matthew , Rendleman Justin , Vitrinel Burcu , Jeffrey Lauren , Abdelhadi Ryah , Chen Mechi , Ross Ted , Carlock Michael , Choi Hyungwon , Vogel Christine 
Published: October 2022

AbstractThe COVID-19 pandemic, triggered by severe acute respiratory syndrome coronavirus 2, has affected millions of people worldwide. Much research has been dedicated to our understanding of COVID-19 disease heterogeneity and severity, but less is known about recovery associated changes. To address this gap in knowledge, we quantified the proteome from serum samples from 29 COVID-19 convalescents and 29 age-, race-, and sex-matched healthy controls. Samples were acquired within the first months of the pandemic. Many proteins from pathways known to change during acute COVID-19 illness, such as from the complement cascade, coagulation system, inflammation and adaptive immune system, had returned to levels seen in healthy controls. In comparison, we identified 22 and 15 proteins with significantly elevated and lowered levels, respectively, amongst COVID-19 convalescents compared to healthy controls. Some of the changes were similar to those observed for the acute phase of the disease, i.e. elevated levels of proteins from hemolysis, the adaptive immune systems, and inflammation. In contrast, some alterations opposed those in the acute phase, e.g. elevated levels of CETP and APOA1 which function in lipid/cholesterol metabolism, and decreased levels of proteins from the complement cascade (e.g. C1R, C1S, and VWF), the coagulation system (e.g. THBS1 and VWF), and the regulation of the actin cytoskeleton (e.g. PFN1 and CFL1) amongst COVID-19 convalescents. We speculate that some of these shifts might originate from a transient decrease in platelet counts upon recovery from the disease. Finally, we observed race-specific changes, e.g. with respect to immunoglobulins and proteins related to cholesterol metabolism.
Tumor-educated Gr1+CD11b+cells instigate breast cancer metastasis by twisting cancer cells plasticity via OSM/IL6–JAK signaling
Authors: Peyvandi Sanam , Bulliard Manon , Kauzlaric Annamaria , Coquoz Oriana , Huang Yu-Ting , Duffey Nathalie , Gafner Laetitia , Lorusso Girieca , Fournier Nadine , Lan Qiang , Rüegg Curzio 
Published: October 2022

AbstractCancer cell plasticity contributes to tumor therapy resistance and metastasis formation, which represent the main causes of cancer-related death for most cancers, including breast cancer. The tumor microenvironment drives cancer cell plasticity and metastasis and, thus, unravelling the underlying cues may provide novel effective strategies to manage metastatic disease. Here, we show that stem cell antigen-1 positive (Sca-1+) murine breast cancer cells enriched during tumor progression and metastasis have higherin vitrocancer stem cell-like properties, enhancedin vivometastatic ability, and initiate primary tumors rich in Gr1highCD11b+Ly6Clowcells. In turn, tumor-educated Gr1+CD11b+(Tu-Gr1+CD11b+) cells rapidly and transiently convert low metastatic 4T1-Sca-1-cells into highly metastatic 4T1-Sca-1+cells via secreted OSM and IL6. Moreover, chemotherapy- resistant and highly metastatic 4T1-derived cells maintain high Sca-1+frequency through cell autonomous IL6 production. Inhibition of OSM, IL6 or JAK suppressed Tu-Gr1+CD11b+-induced Sca-1+population enrichmentin vitro, while JAK inhibition abrogated metastasis of chemotherapy-enriched Sca-1+cellsin vivo. Importantly, Tu-Gr1+CD11b+cells invoked a gene signature in tumor cells predicting shorter OS and RFS in breast cancer patients. Collectively, our data identified OSM/IL6-JAK as a clinically relevant paracrine/autocrine axis instigating breast cancer cell plasticity triggering metastasis.
Aligning Distant Sequences to Graphs using Long Seed Sketches
Authors: Joudaki Amir , Meterez Alexandru , Mustafa Harun , Koerkamp Ragnar Groot , Kahles André , Rätsch Gunnar 
Published: October 2022

AbstractSequence-to-graph alignment is an important step in applications such as variant genotyping, read error correction and genome assembly. When a query sequence requires a substantial number of edits to align, approximate alignment tools that follow the seed-and-extend approach require shorter seeds to get any matches. However, in large graphs with high variation, relying on a shorter seed length leads to an exponential increase in spurious matches. We propose a novel seeding approach relying on long inexact matches instead of short exact matches. We demonstrate experimentally that our approach achieves a better time-accuracy trade-off in settings with up to a 25% mutation rate.We achieve this by sketching a subset of graph nodes and storing them in aK-nearest neighbor index. While sketches are more robust to indels, finding the nearest neighbor of a sketch in a high-dimensional space is more computationally challenging than finding exact seeds. We demonstrate that if we store sketch vectors in aK-nearest neighbor index, we can circumvent the curse of dimensionality. Our long sketch-based seed scheme contrasts existing approaches and highlights the important role that tensor sketching can play in bioinformatics applications. Our proposed seeding method and implementation have several advantages: i) We empirically show that our method is efficient and scales to graphs with 1 billion nodes, with time and memory requirements for preprocessing growing linearly with graph size and query time growing quasi-logarithmically with query length. ii) For queries with an edit distance of 25% relative to their length, on the 1 billion node graph, longer sketch-based seeds yield a 4× increase in recall compared to exact seeds. iii) Conceptually, our seeder can be incorporated into other aligners, proposing a novel direction for sequence-to-graph alignment.The implementation is available at:https://github.com/ratschlab/tensor-sketch-alignment.
Spatial organization of the 3D genome encodes gene co-expression programs in single cells
Authors: Dong Peng , Zhang Shu , Xie Liangqi , Wang Lihua , Lemire Andrew L. , Lander Arthur D. , Chang Howard Y. , Liu Zhe J. 
Published: October 2022

SUMMARYDeconstructing the mechanism by which the 3D genome encodes genetic information to generate diverse cell types during animal development is a major challenge in biology. The contrast between the elimination of chromatin loops and domains upon Cohesin loss and the lack of downstream gene expression changes at the cell population level instigates intense debates regarding the structure-function relationship between genome organization and gene regulation. Here, by analyzing single cells after acute Cohesin removal with sequencing and spatial genome imaging techniques, we discover that, instead of dictating population-wide gene expression levels, 3D genome topology mediated by Cohesin safeguards long-range gene co-expression correlations in single cells. Notably, Cohesin loss induces gene co-activation and chromatin co-opening between active domains incisup to tens of megabase apart, far beyond the typical length scale of enhancer-promoter communication. In addition, Cohesin separates Mediator protein hubs, prevents active genes incisfrom localizing into shared hubs and blocks intersegment transfer of diverse transcriptional regulators. Together, these results support that spatial organization of the 3D genome orchestrates dynamic long-range gene and chromatin co-regulation in single living cells.
High level and molecular nature of transcriptional noise in yeast cells
Authors: Gvozdenov Zlata , Barcutean Zeno , Struhl Kevin 
Published: October 2022

ABSTRACT“Biological noise” is defined as functionally insignificant events that occur in living cells due to imperfect fidelity of biological processes. Distinguishing between biological function and biological noise is often difficult, and experiments to measure biological noise have not been performed. Here, we measure biological noise in yeast cells by analyzing chromatin structure and transcription of an 18 kb region of DNA whose sequence was randomly generated and hence lacks biological function. Nucleosome occupancy on random-sequence DNA is comparable to that on yeast genomic DNA. However, nucleosome-depleted regions are much less frequent, and there are fewer well-positioned nucleosomes and shorter nucleosome arrays. Steady-state levels of RNAs expressed from random-sequence DNA are comparable to those of typical yeast mRNAs, although transcription and mRNA decay rates are higher. Transcriptional initiation (5’ ends) from random-sequence DNA occurs at numerous sites at low levels, indicating very low intrinsic specificity of the Pol II machinery. In contrast, poly(A) profiles (relative levels and clustering of 3’ isoforms) of random-sequence RNAs are roughly comparable to those within 3’ untranslated regions of yeast mRNAs, suggesting limited evolutionary constraints on poly(A) site choice. RNAs expressed from random-sequence DNA show higher cell-to-cell variability than RNAs expressed from yeast genomic DNA, suggesting that functional elements limit the variability among individual cells within a population. These observations indicate that transcriptional noise occurs at high levels in yeast, and they provide insight into how chromatin and transcription patterns arise from the evolved yeast genome.
Circular RNAs are Associated with Floral Fate Acquisition in Soybean Shoot Apical Meristem
Authors: Babaei Saeid , Singh Mohan B. , Bhalla Prem L 
Published: October 2022

AbstractSoybean (Glycine max), a major oilseed and protein source, requires a short-day photoperiod for floral induction. Though key transcription factors controlling flowering have been identified, the role of the non-coding (dark) genome is limited. circular RNAs (circRNAs) recently emerged as a novel class of RNAs with critical regulatory functions. However, a study on circRNAs during the floral transition of a crop plant is lacking. We investigated the expression and potential function of circRNAs in floral fate acquisition by soybean shoot apical meristem in response to short-day treatment. Using deep sequencing andin-silicoanalysis, we denoted 384 circRNAs, with 129 exhibiting short-day treatment-specific expression patterns. We also identified 38 circRNAs with predicted binding sites for miRNAs that could affect the expression of diverse downstream genes through the circRNA-miRNA-mRNA network. Notably, four different circRNAs with potential binding sites for an important microRNA module regulating developmental phase transition in plants, miR156 and miR172, were identified. We also identified circRNAs arising from hormonal signaling pathway genes, especially abscisic acid, and auxin, suggesting an intricate network leading to floral transition. This study highlights the gene regulatory complexity during the vegetative to reproductive transition and paves the way to unlock floral transition in a crop plant.HighlightA new class of regulatory RNAs, circular RNAs, modulate floral transition in a crop plant, soybean, by regulating hormonal pathways and post-transcriptional processes.