bluuebunny/crossref_metadata_2025_split huggingface dataset:
Description of the sound diversity of two species of tuco-tucos (Ctenomys torquatusandCtenomys lami) in natural environment
Authors: Zaché Keila C. , Silveira Lucas Machado , Francescoli Gabriel , de Freitas Thales Renato Ochotorena 
Published: June 2021

AbstractSound signals can travel through long distances, becoming an important communication channel between animals that need to establish contact beyond the visual form. They can then be considered a relevant form of communication between species living in the underground environment.Ctenomys torquatusandCtenomys lamiare solitary subterranean rodents, thus demanding an improvement of the communicative channels, especially in territorial defense actions and meeting potential reproductive partners. This work was aimed to describe the variability of acoustic signals emitted byC. torquatusandC. lamiby analyzing the physical-morphological characteristics of the signals. The study was carried out in two populations, one of each species and was selected 14 individuals ofC. torquatusand 15C. lami.The acoustic signals were recorded in a natural environment, obtaining the sounds straight from the animal tunnels. A total of 1,380 signals were captured and analyzed, 786 fromC. torquatusand 594 fromC. lami.It was possible to characterize 5 different types of signals, emitted by both species. Most of the analyzed sequences presented low frequency, and many of these calls exhibited characteristics of long-range signals. It was verified a sharing of sound signals in both species, as regarding the acoustic parameters as the morphology of the analyzed spectrograms. For the first time, it was possible to have access to sound data emitted by direct subterranean rodents from their tunnels in the natural environment.
Theobroma grandiflorum breeding optimization based on repeatability, stability and adaptability information
Authors: Chaves Saulo Fabrício da Silva , Alves Rafael Moysés , Alves Rodrigo Silva , Sebbenn Alexandre Magno , de Resende Marcos Deon Vilela , Dias Luiz Antônio dos Santos 
Published: June 2021

AbstractThe cultivation of Theobroma grandiflorum in the Brazilian Amazon is mainly conducted by family farmers who use a range of different management strategies. Thus, breeding programs of the species must address the challenge of developing cultivars that are adapted to and stable in a variety of cultivation environments. In this context, this study aimed to estimate the optimum number of harvests for genetic selection of T. grandiflorum progenies and identify the most promising ones in terms of productivity, stability, and adaptability. The trials were implemented in three environments, using a randomized complete block design, with 25 full-sib progenies, five replications, and three plants per plot. The traits mean number of fruits/plant, mean fruit production/plant, and rate of infection with witches’ broom (Moniliophthora perniciosa) were evaluated over 11 harvests. The Restricted Maximum Likelihood/Best Linear Unbiased Prediction (REML/BLUP) mixed model method was used to estimate genetic parameters and predict genetic values, which were then applied to assess stability and adaptability. The results show that there is genetic variability among the studied T. grandiflorum progenies and that accurate genetic selection aiming at recombination is effective after three harvests, for recombination, or eleven harvests for identification of recommended progenies. Six progenies were selected that met the requirements for productivity, stability, and adaptability to different cultivation environments. These results can be used to optimize and advance T. grandiflorum breeding programs.
Extraction, purification and anti-TMV effects of α (β)-2,7,11-cembratriene-4,6-diol from tobacco leaves
Authors: Feng Yongxin , Jia Haijiang , Guan Hui , Zhang Weidong , Zhou Yanbin , Liu Kaiyi , Wang Yuejing , Li Qiuli , Chen Weihua , Sohail Muhammad Aamir , Wang Jie , Huang Shen , Wei Jianyu 
Published: June 2021

AbstractBackgroundAcetone ethanol extracts from tobacco leaves have antiviral activity against TMV, but the antiviral effects of their specialized metabolites have not been systematically studied yet, especially the underlying mechanism is still unexplored.ResultsThe tobacco cembranoids α(β)-2,7,11-cembratriene-4,6-diol (α(β)-CBD) were extracted and purified with an effective and green protocol including innovatively added 5% phosphoric acid for elution, one time silica gel chromatographic column separation and impurity removal and further HPLC purification. The results of antiviral activities against tobacco mosaic virus (TMV) with the local lesion counting method showed that α(β)-CBD have in vivo higher protective effects of 73.2% and 71.6%, at 75.0 μM, respectively, than control agent Ningnanmycin (53.1%). Notably, The results of ELISA and and TMV-GFP fluorescent optical imaging assay indicated a obviously reduced viral protein and weaker GFP fluorescence signal and smaller infection area, which confirmed their anti-TMV activities at protein level. Furthermore, the enhanced production of SA and JA and the significantly increased transcription of of JA signaling pathway (COI1 and PDF1.2) and SA signaling pathway genes (PR1, NPR1 and EDS1) in treated plants further conformed that exogenously applied α(β)-CBD can effectively elicit the tobacco plant immunity against TMV.ConclusionsThe α(β)-CBD mainly stimulates disease resistance of tobacco plants to resist TMV and it can be used as bioagents to control TMV in the future.
Signal-based optical map alignment
Authors: Akdel Mehmet , van de Geest Henri , Schijlen Elio , van Rijswijck Irma M.H. , Smid Eddy J. , Sanchez-Perez Gabino , de Ridder Dick 
Published: June 2021

AbstractIn genomics, optical mapping technology provides long-range contiguity information to improve genome sequence assemblies and detect structural variation. Originally a laborious manual process, Bionano Genomics platforms now offer high-throughput, automated optical mapping based on chips packed with nanochannels through which unwound DNA is guided and the fluorescent DNA backbone and specific restriction sites are recorded. Although the raw image data obtained is of high quality, the processing and assembly software accompanying the platforms is closed source and does not seem to make full use of data, labeling approximately half of the measured signals as unusable. Here we introduce two new software tools, independent of Bionano Genomics software, to extract and process molecules from raw images (OptiScan) and to perform molecule-to-molecule and molecule-to-reference alignments using a novel signal-based approach (OptiMap). We demonstrate that the molecules detected by OptiScan can yield better assemblies, and that the approach taken by OptiMap results in higher use of molecules from the raw data. These tools lay the foundation for a suite of open-source methods to process and analyze high-throughput optical mapping data. The Python implementations of the OptiTools are publicly available throughhttp://www.bif.wur.nl/.
Effect of white mulberry (Morus albas L.) On common carp performance, biological parameters, and blood picture
Authors: Abdulrahman Nasreen Mohi Alddin 
Published: June 2021

AbstractThis study has been done for evaluating the growth performance and health performance of Cyprinus carpio isoenergetic with isonitrogenous diets which contain three levels (0, 10, 15, gm of mulberry fruit powder, have been used for a period of 12 weeks. The effect of white mulberry (Morus albas L.) fruit powder on common carp, T2 was significantly higher than other treatments in each of growth performance and feed utilization parameters. the adding of white mulberry fruit powder significantly increased each of CBC counts in T2 of RBC and HCT%. The conrol was significantly higher in each of MCH, MCHC, MCV and Platelets count. Cholestrol, triglyceride and HDL were higher significantly in T2, LDL was significantly higher in control. The white mulberry (M. albas L.) fruit powder effect significantly in, GPT, GOT, in T2 and the CKI and blood suger were higher significantly in the control, the control was significantly higher in each of total protein, and albumin ratio. T2 was higher significantly in Intestine Length Index in both fish weigth and length, and both fish weigth without viscera and/ or head. No significant differences in each of Intestine Weight Index among treatments, blood Globulin ratio, Hemoglobin count and VLDL.
eDNA Captures Microhabitat Partitioning in a Kelp Forest Ecosystem
Authors: Monuki Keira , Barber Paul H. , Gold Zachary 
Published: June 2021

AbstractEnvironmental DNA (eDNA) metabarcoding is an increasingly important tool for surveying biodiversity in marine ecosystems. However, the scale of temporal and spatial variability in eDNA signatures, and how this variation may impact eDNA-based marine biodiversity assessments, remains uncertain. To address this question, we systematically examined variation in vertebrate eDNA signatures across depth (0 m to 10 m) and horizontal space (nearshore and surf zone) over three successive days in a Southern California kelp forest. Across a broad range of marine vertebrates (teleosts, elasmobranchs, birds, and mammals), results showed significant variation in species richness and community assemblages across 4-5 m depth, reflecting microhabitat depth preferences of common Southern California nearshore rocky reef taxa. We also found significant differences in community assemblages between nearshore and surf zone sampling stations at the same depth, and across three sampling days. Patterns of microhabitat partitioning in eDNA signatures across space and time were largely consistent with known habitat preferences and species behavior. Results highlight the sensitivity of eDNA in capturing fine-scale vertical, horizontal, and temporal variation in marine vertebrate communities, demonstrating the ability of eDNA to capture a highly localized snapshot of marine biodiversity in dynamic coastal environments.
The catheterized bladder environment promotes Efg1- and Als1-dependent Candida albicans infection
Authors: La Bella Alyssa Ann , Andersen Marissa Jeme , Gervais Nicholas C. , Molina Jonathan Jesus , Molesan Alex , Stuckey Peter V. , Wensing Lauren , Nobile Clarissa J. , Shapiro Rebecca S. , Santiago-Tirado Felipe Hiram , Flores-Mireles Ana Lidia 
Published: June 2021

ABSTRACTCatheter-associated urinary tract infections (CAUTIs) account for 40% of all hospital-acquired infections. Given that 20-50% of all hospitalized patients receive a catheter, CAUTIs are one of the most common hospital-acquired infections and a significant medical complication as they result in increased morbidity, mortality, and an estimated annual cost of $340-370 million. Candida spp. – specifically Candida albicans – are a major causative agent of CAUTIs (17.8%), making it the second most common CAUTI uropathogen. Despite this frequent occurrence, the cellular and molecular details of C. albicans infection in the CAUTI microenvironment are poorly understood. Here, we characterize fungal virulence mechanisms and fungal biofilm formation during CAUTI for the first time. We found that the catheterized bladder environment triggers Candida virulence programs and robust biofilm formation through Efg1-dependent hyphal morphogenesis and Als1, an Efg1-downstream effector. Additionally, we show that the adhesin Als1 is necessary for in vitro and in vivo C. albicans biofilm formation dependent on the presence of fibrinogen (Fg), a coagulation factor released in the bladder due to the mechanical damage caused by urinary catheterization. Furthermore, in the presence of Fg, overexpression of ALS1 in C. albicans led to enhanced colonization and dissemination, while deletion of ALS1 reduced both outcomes during CAUTIs. Our study ultimately unveils the mechanism that contributes to fungal CAUTI, which may provide more effective targets for future therapies to prevent these infections.
A pigtailed macaque model for Kyasanur Forest disease virus and Alkhurma hemorrhagic disease virus
Authors: Broeckel Rebecca M. , Feldmann Friederike , McNally Kristin L. , Chiramel Abhilash I. , Hanley Patrick W. , Lovaglio Jamie , Rosenke Rebecca , Scott Dana P. , Saturday Greg , Bouamr Fadila , Robertson Shelly J. , Best Sonja M. 
Published: June 2021

AbstractKyasanur Forest disease virus (KFDV) and the closely related Alkhurma hemorrhagic disease virus (AHFV) are emerging flaviviruses that cause severe viral hemorrhagic fevers in humans. Increasing geographical expansion and case numbers, particularly of KFDV in southwest India, class these viruses as a public health threat. Viral pathogenesis is not well understood and additional vaccines and antivirals are needed to effectively counter the impact of these viruses. However, current animal models for KFDV do not accurately reproduce viral tissue tropism or clinical outcomes observed in humans. Here, we show pigtailed macaques (Macaca nemestrina) infected with KFDV or AHFV develop viremia that peaks 2 to 4 days following inoculation. Over the course of infection, animals developed lymphocytopenia, thrombocytopenia, and elevated liver enzymes. Infected animals exhibited hallmark signs of human disease characterized by a flushed appearance, piloerection, dehydration, loss of appetite, weakness, and hemorrhagic signs such as epistaxis. Virus was commonly present in the gastrointestinal tract, consistent with human disease caused by KFDV and AHFV where gastrointestinal symptoms (hemorrhage, vomiting, diarrhea) are common. This work characterizes a nonhuman primate model for KFDV and AHFV that closely resembles human disease for further utilization in understanding host immunity and development of antiviral countermeasures.Author SummaryKyasanur Forest disease virus (KFDV) and Alkhurma hemorrhagic disease virus (AHFV) are tick-borne flaviviruses that cause viral hemorrhagic fevers in India and the Arabian Peninsula, respectively. Bonnet macaques and black-faced langurs are susceptible to KFDV infection, but these animals do not experience hemorrhagic signs as seen in human cases with KFDV. This work characterizes for the first time experimental infection of KFDV and AHFV in pigtailed macaques (PTMs). Infected PTMs can develop moderate to severe disease that mirrors many aspects of human disease, including some hemorrhagic signs. Together these data describe the PTM model for KFDV and AHFV as a valuable tool for future work to study viral pathogenesis and for assessing the efficacy of vaccines and antivirals.
Subcellular proteomics of dopamine neurons in the mouse brain reveals axonal enrichment of proteins encoded by Parkinson’s disease-linked genes
Authors: Hobson Benjamin D. , Choi Se Joon , Soni Rajesh K. , Sulzer David , Sims Peter A. 
Published: June 2021

AbstractDopaminergic neurons modulate neural circuits and behaviors via dopamine release from expansive, long range axonal projections. The elaborate cytoarchitecture of these neurons is embedded within complex brain tissue, making it difficult to access the neuronal proteome using conventional methods. Here, we demonstrate APEX2 proximity labeling within genetically targeted neurons in the mouse brain, enabling subcellular proteomics with cell type-specificity. By combining APEX2 biotinylation with mass spectrometry, we mapped the somatodendritic and axonal proteomes of midbrain dopaminergic neurons. Our dataset reveals the proteomic architecture underlying proteostasis, axonal metabolism, and neurotransmission in these neurons. We find a significant enrichment of proteins encoded by Parkinson’s disease-linked genes in striatal dopaminergic axons, including proteins with previously undescribed axonal localization. These proteomic datasets provide a resource for neuronal cell biology, and this approach can be readily adapted for study of other neural cell types.
vcf2gwas - Python API for comprehensive GWAS analysis using GEMMA
Authors: Vogt Frank , Shirsekar Gautam , Weigel Detlef 
Published: June 2021

ABSTRACTWe present a new software package vcf2gwas to perform reproducible genome-wide association studies (GWAS). vcf2gwas is a Python API for bcftools, PLINK and GEMMA. Before running the analysis a traditional GWAS workflow requires the user to edit and format the genotype information from commonly used Variant Call Format (VCF) file and phenotype information. Post-processing steps involve summarizing and visualizing the analysis results. This workflow requires a user to utilize the command-line, manual text-editing and knowledge of one or more programming/scripting languages which can be time-consuming especially when analyzing multiple phenotypes. Our package provides a convenient pipeline performing all of these steps, reducing the GWAS workflow to a single command-line input without the need to edit or format the VCF file beforehand or to install any additional software. In addition, features like reducing the dimensionality of the phenotypic space and performing analyses on the reduced dimensions or comparing the significant variants from the results to specific genes/regions of interest are implemented. By integrating different tools to perform GWAS under one workflow, the package ensures reproducible GWAS while reducing the user efforts significantly.Availability and implementationThe source code of vcf2gwas is available under the GNU General Public License. The package can be easily installed using conda. Installation instructions and a manual including tutorials can be accessed on the package website at https://github.com/frankvogt/vcf2gwas
OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies
Authors: Jackson Rebecca C. , Matentzoglu Nicolas , Overton James A. , Vita Randi , Balhoff James P. , Buttigieg Pier Luigi , Carbon Seth , Courtot Melanie , Diehl Alexander D. , Dooley Damion , Duncan William , Harris Nomi L. , Haendel Melissa A. , Lewis Suzanna E. , Natale Darren A. , Osumi-Sutherland David , Ruttenberg Alan , Schriml Lynn M. , Smith Barry , Stoeckert Christian J. , Vasilevsky Nicole A. , Walls Ramona L. , Zheng Jie , Mungall Christopher J. , Peters Bjoern 
Published: June 2021

AbstractBiological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies (OBO) Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR.
Structural basis for SARS-CoV-2 Nucleocapsid protein recognition by single-domain antibodies
Authors: Ye Qiaozhen , Lu Shan , Corbett Kevin D. 
Published: June 2021

AbstractThe COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, is the most severe public health event of the twenty-first century. While effective vaccines against SARS-CoV-2 have been developed, there remains an urgent need for diagnostics to quickly and accurately detect infections. Antigen tests, particularly those that detect the abundant SARS-CoV-2 Nucleocapsid protein, are a proven method for detecting active SARS-CoV-2 infections. Here we report high-resolution crystal structures of three llama-derived single-domain antibodies that bind the SARS-CoV-2 Nucleocapsid protein with high affinity. Each antibody recognizes a specific folded domain of the protein, with two antibodies recognizing the N-terminal RNA binding domain and one recognizing the C-terminal dimerization domain. The two antibodies that recognize the RNA binding domain affect both RNA binding affinity and RNA-mediated phase separation of the Nucleocapsid protein. All three antibodies recognize highly-conserved surfaces on the Nucleocapsid protein, suggesting that they could be used to develop affordable diagnostic tests to detect all circulating SARS-CoV-2 variants.
Multilocus adaptation to vaccination
Authors: McLeod David V. , Gandon Sylvain 
Published: June 2021

AbstractPathogen adaptation to public health interventions, such as vaccination, may take tortuous routes and involve multiple mutations at distinct locations in the pathogen genome, acting on distinct phenotypic traits. Despite its importance for public health, how these multilocus adaptations jointly evolve is poorly understood. Here we consider the joint evolution of two adaptations: the pathogen’s ability to escape the vaccine-induced immune response and adjustments to the pathogen’s virulence and transmissi-bility. We elucidate the role played by epistasis and recombination, with an emphasis on the different protective effects of vaccination. We show that vaccines reducing transmission and/or increasing clearance generate positive epistasis between the vaccine-escape and virulence alleles, favouring strains that carry both mutations, whereas vaccines reducing virulence mortality generate negative epistasis, favouring strains that carry either mutation, but not both. High rates of recombination can affect these predictions. If epistasis is positive, frequent recombination can lead to the sequential fixation of the two mutations and prevent the transient build-up of more virulent escape strains. If epistasis is negative, frequent recombination between loci can create an evolutionary bistability, such that whichever adaptation is more accessible tends to be favoured in the long-term. Our work provides a timely alternative to the variant-centered perspective on pathogen adaptation and captures the effect of different types of vaccines on the interference between multiple adaptive mutations.
Structure of the phosphoinositide 3-kinase p110γ-p101 complex reveals molecular mechanism of GPCR activation
Authors: Rathinaswamy Manoj K , Dalwadi Udit , Fleming Kaelin D , Adams Carson , Stariha Jordan TB , Pardon Els , Baek Minkyung , Vadas Oscar , DiMaio Frank , Steyaert Jan , Hansen Scott D , Yip Calvin K , Burke John E 
Published: June 2021

AbstractThe class IB phosphoinositide 3-kinase (PI3K), PI3Kγ, is a master regulator of immune cell function, and a promising drug target for both cancer and inflammatory diseases. Critical to PI3Kγ function is the association of the p110γ catalytic subunit to either a p101 or p84 regulatory subunit, which mediates activation by G-protein coupled receptors (GPCRs). Here, we report the cryo-EM structure of a heterodimeric PI3Kγ complex, p110γ-p101. This structure reveals a unique assembly of catalytic and regulatory subunits that is distinct from other class I PI3K complexes. p101 mediates activation through its Gβγ binding domain, recruiting the heterodimer to the membrane and allowing for engagement of a secondary Gβγ binding site in p110γ. Multiple oncogenic mutations mapped to these novel interfaces and enhanced Gβγ activation. A nanobody that specifically binds to the p101-Gβγ interface blocks activation providing a novel tool to study and target p110γ-p101-specific signaling events in vivo.