bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a reverse transcription polymerase chain reaction for the detection of severe fever with thrombocytopenia syndrome virus from suspected infected animals
Authors: Park Eun-sil , Fujita Osamu , Kimura Masanobu , Hotta Akitoyo , Imaoka Koichi , Shimojima Masayuki , Saijo Masayuki , Maeda Ken , Morikawa Shigeru 
Published: August 2020

AbstractBackgroundSevere fever with thrombocytopenia syndrome virus (SFTSV) causes severe hemorrhagic fever in humans and cats. Clinical symptoms of SFTS-infected cats resemble to those of SFTS patients and SFTS-contracted cats shows high levels of viral RNA loads in the serum and body fluids. Due to the risk of direct infection from SFTS-infected cats to human, it is important to diagnose SFTS-suspected animals.Methodology/Principle findingsFour primer sets were newly designed from consensus sequences constructed by 108 strains of SFTSV. A reverse transcription polymerase chain reaction (RT-PCR) with these four primer sets were successfully and specifically detected several clades of SFTSV. Their limits of detection are 1-10 copies/reaction. By this RT-PCR, 5 cat cases among 56 SFTS-suspected animal cases were diagnosed as SFTS. From these cats, IgM or IgG against SFTSV were detected by enzyme-linked immunosorbent assay (ELISA), but not neutralizing antibodies by plaque reduction neutralization titer (PRNT) test. This phenomenon is similar to those of fatal SFTS patients.Conclusion/SignificanceThis newly developed RT-PCR could detect SFTSV RNA of several clades from SFTS-suspected animals. In addition to ELISA and PRNT test, the useful laboratory diagnosis systems of SFTS-suspected animals has been made in this study.Author summaryThis study developed RT-PCR to detect SFTS animal cases. This assay could detect SFTSV RNA belonging to different clades. Cats diagnosed as SFTS had IgM or IgG, but not neutralizing antibodies. SFTS cat cases were distributed in the area where SFTS patients have been reported highly, indicating the establishment of the circulation of SFTSV in the environment. These diagnostic assays could be helpful tools to detect and not to miss SFTS animal cases.
Cognitive deficits found in a pro-inflammatory state are independent of ERK 1/2 signaling in the murine brain hippocampus treated with Shiga toxin 2 from enterohemorrhagicEscherichia Coli
Authors: Berdasco Clara , Pinto Alipio , Blake Mariano , Correa Fernando , Longo Carbajosa Nadia A. , Geogeghan Patricia , Cangelosi Adriana , Gironacci Mariela M. , Goldstein Jorge 
Published: August 2020

AbstractShiga toxin 2 (Stx2) from enterohemorrhagicEscherichia coli(EHEC) produces hemorrhagic colitis, hemolytic uremic syndrome (HUS) and acute encephalopathy. The mortality rate in HUS increases significantly when the central nervous system (CNS) is involved. Besides, EHEC also releases lipopolysaccharide (LPS). Many reports have described cognitive dysfunctions in HUS patients, the hippocampus being one of the brain areas targeted by EHEC infection. In this context, a translational murine model of encephalopathy was employed to establish the deleterious effects of Stx2 and the contribution of LPS in the hippocampus. Results demonstrate that systemic administration of a sublethal dose of Stx2 reduced memory index and produced depression like behavior, pro-inflammatory cytokine release and NF-kB activation independent of the ERK 1/2 signaling pathway. On the other hand, LPS activated NF-kB dependent on ERK 1/2 signaling pathway. Cotreatment of Stx2 with LPS aggravated the pathologic state, while dexamethasone treatment succeeded in preventing behavioral alterations. Our present work suggests that the use of drugs such as corticosteroids or NF-kB signaling inhibitors may serve as neuroprotectors from EHEC infection.
Statistics of spatial rotations and projection directions considering molecular symmetry in 3D electron cryo-microscopy
Authors: Zhang Qi , Lin Hai , Hu Mingxu 
Published: August 2020

AbstractElectron cryo-microscopy (cryoEM) three-dimensional (3D) reconstruction is based on estimations of orientations of projection images or 3D volumes. It is common that the macromolecules studied by cryoEM have molecular symmetry, which, unfortunately, has not been taken into consideration by any statistics for either spatial rotations or projection directions at this point. Meanwhile, there are growing needs to adopt advanced statistical methods, and further, modern machine learning techniques in cryoEM. Since those methodologies are built heavily upon statistical learning cornerstones, the absence of their domain-specific statistical justification limits their applications in cryoEM. In this research, based on the concept of non-unique-games (NUG), we propose two key statistical measurements, the mean and the variance, of both spatial rotations and projection directions when molecular symmetry is considered. Such methods are implemented in the open-source python package pySymStat.
Large vs small genomes inPassiflora: the influence of the mobilome and the satellitome
Authors: Sader Mariela , Vaio Magdalena , Cauz-Santos Luiz Augusto , Dornelas Marcelo Carnier , Vieira Maria Lucia Carneiro , Melo Natoniel , Pedrosa-Harand Andrea 
Published: August 2020

ABSTRACTRepetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. WithinPassifloragenus, a ten-fold variation in genome size, not attributed to polyploidy, is known. Here, we applied a combinedin silicoand cytological approach to study the organization and diversification of repetitive elements in three species of these genera representing its known range in genome size variation. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified Long Terminal Repeat (LTR) retrotransposons as the most abundant elements in the three genomes, showing a considerable variation among species. Satellite DNAs (satDNAs) were less representative, but highly diverse between subgenera. Our results clearly confirm that the largest genome species (Passiflora quadrangularis) presents a higher accumulation of repetitive DNA sequences, specially Angela and Tekay elements, making up most of its genome.Passiflora cincinnata, with intermediate genome and from the same subgenus, showed similarity withP. quadrangularisregarding the families of repetitive DNA sequences, but in different proportions. On the other hand,Passiflora organensis, the smallest genome, from a different subgenus, presented greater diversity and the highest proportion of satDNA. Altogether, our data indicate that while large genome evolve by an accumulation of retrotransponsons, small genomes most evolved by diversification of different repeat types, particularly satDNAs.MAIN CONCLUSIONSWhile two lineages of retrotransposons were more abundant in largerPassifloragenomes, the satellitome was more diverse and abundant in the smallest genome.
Vertebrate features revealed in the rudimentary eye of the Pacific hagfish (Eptatretus stoutii)
Authors: Dong Emily M. , Allison W. Ted 
Published: August 2020

SUMMARYHagfish eyes are markedly basic compared to the eyes of other vertebrates, lacking a pigmented epithelium, a lens, and a retinal architecture built of three cell layers – the photoreceptors, interneurons & ganglion cells. Concomitant with hagfish belonging to the earliest-branching vertebrate group (the jawless Agnathans), this lack of derived characters has prompted competing interpretations that hagfish eyes represent either a transitional form in the early evolution of vertebrate vision, or a regression from a previously elaborate organ. Here we show the hagfish retina is not extensively degenerating during its ontogeny, but instead grows throughout life via a recognizable Pax6+ ciliary marginal zone. The retina has a distinct layer of photoreceptor cells that appear to homogeneously express a single opsin of therh1rod opsin class. The epithelium that encompasses these photoreceptors is striking because it lacks the melanin pigment that is universally associated with animal vision; notwithstanding, we suggest this epithelium is a homolog of gnathosome Retinal Pigment Epithelium (RPE) based on its robust expression of RPE65 and its engulfment of photoreceptor outer segments. We infer that the hagfish retina is not entirely rudimentary in its wiring, despite lacking a morphologically distinct layer of interneurons: multiple populations of cells exist in the hagfish inner retina that differentially express markers of vertebrate retinal interneurons. Overall, these data clarify Agnathan retinal homologies, reveal characters that now appear to be ubiquitous across the eyes of vertebrates, and refine interpretations of early vertebrate visual system evolution.HIGHLIGHTSHagfish eyes aredegeneratebut notdegenerating, i.e.rudimentarybutgrowingRetinal interneurons discovered implying ancestral hagfish had derived retinas & visionDespite lacking pigment, a Retinal Pigmented Epithelium homolog functions in hagfishRevised synapomorphies illuminate the dimly lit origins of vertebrate eye evolutionGRAPHICAL ABSTRACT
Cell state diversity promotes metastasis through heterotypic cluster formation in melanoma
Authors: Campbell Nathaniel R. , Rao Anjali , Zhang Maomao , Baron Maayan , Heilmann Silja , Deforet Maxime , Kenny Colin , Ferretti Lorenza , Huang Ting-Hsiang , Garg Manik , Nsengimana Jérémie , Montal Emily , Tagore Mohita , Hunter Miranda , Newton-Bishop Julia , Middleton Mark R. , Corrie Pippa , Adams David J. , Rabbie Roy , Levesque Mitchell P. , Cornell Robert A. , Yanai Itai , Xavier Joao B. , White Richard M. 
Published: August 2020

SUMMARYIn melanoma, transcriptional profiling has revealed multiple co-existing cell states, including proliferative versus invasive sub-populations that have been posited to represent a “go or grow” tradeoff. Both of these populations are maintained in tumors, but how they physically interact to promote metastasis is unknown. We demonstrate that these subpopulations form spatially structured heterotypic clusters that cooperate in the seeding of metastasis. We unexpectedly found that INV cells were tightly adherent to each other, and formed clusters with a rim of PRO cells. Intravital imaging demonstrated cooperation between these populations, in which the INV cells facilitated the spread of less metastatic PRO cells. We identified the TFAP2 neural crest transcription factor as a master regulator of both clustering and the PRO/INV states. Our data suggest a framework for the co-existence of these two divergent cell populations, in which differing cell states form heterotypic clusters that promote metastasis via cell-cell cooperation.
A neural circuit for competing approach and avoidance underlying prey capture
Authors: Rossier Daniel , La Franca Violetta , Salemi Taddeo , Gross Cornelius T. 
Published: August 2020

AbstractPredators must frequently balance competing approach and avoidance behaviors elicited by a moving and potentially dangerous prey. Several brain circuits supporting predation have recently been localized. However, the mechanisms by which these circuits balance the conflict between approach and avoidance responses remain unknown. Laboratory mice initially show alternating approach and avoidance responses toward cockroaches, a natural prey, but with repeated exposure become avid hunters. Here we usedin vivoneural activity recording and cell-type specific manipulations in hunting mice to identify neurons in the lateral hypothalamus and periaqueductal grey that encode and control predatory approach and avoidance. We found a subset of GABAergic neurons in lateral hypothalamus that specifically encoded hunting behaviors and whose stimulation triggered predation, but not feeding. This population projects to the periaqueductal grey and stimulation of these projections promoted predation. Neurons in periaqueductal grey encoded both approach and avoidance behaviors, but only initially when the mouse showed high levels of fear of the prey. Our findings allow us to propose that GABAergic neurons in lateral hypothalamus facilitate predation in part by suppressing defensive responses to prey encoded in the periaqueductal grey. Our findings reveal a neural circuit mechanism for controlling the balance between conflicting approach and avoidance behaviors elicited by the same stimulus.
Cell-type-specific epigenomic variations associated withBRCA1mutation in pre-cancer human breast tissues
Authors: Hsieh Yuan-Pang , Naler Lynette B. , Ma Sai , Lu Chang 
Published: August 2020

AbstractBRCA1germline mutation carriers are predisposed to breast cancers. Epigenomic regulations have been known to strongly interact with genetic variations and potentially mediate biochemical cascades involved in tumorigenesis. Due to the cell-type specificity of epigenomic features, profiling of individual cell types is critical for understanding the molecular events in various cellular compartments within complex breast tissue. Here we report cell-type-specific profiling of genome-wide histone modifications including H3K27ac and H3K4me3 in basal, luminal progenitor, mature luminal, and stromal cells extracted from pre-cancerBRCA1mutation carriers and non-carriers, conducted using a low-input technology that we developed. We discover that basal and stromal cells present the most extensive epigenomic differences between mutation carriers (BRCA1mut/+) and non-carriers (BRCA1+/+) while luminal progenitor and mature luminal cells are relatively unchanged with the mutation. Furthermore, the epigenomic changes in basal cells due toBRCA1mutation appear to facilitate their transformation into luminal progenitor cells. Our findings shed light on the pre-cancer epigenomic dynamics due toBRCA1mutation and how they may contribute to eventual development of predominantly basal-like breast cancer.
Single-cell mapper (scMappR): using scRNA-seq to infer cell-type specificities of differentially expressed genes
Authors: Sokolowski Dustin J. , Faykoo-Martinez Mariela , Erdman Lauren , Hou Huayun , Chan Cadia , Zhu Helen , Holmes Melissa M. , Goldenberg Anna , Wilson Michael D. 
Published: August 2020

AbstractRNA sequencing (RNA-seq) is widely used to identify differentially expressed genes (DEGs) and reveal biological mechanisms underlying complex biological processes. RNA-seq is often performed on heterogeneous samples and the resulting DEGs do not necessarily indicate the cell types where the differential expression occurred. While single-cell RNA-seq (scRNA-seq) methods solve this problem, technical and cost constraints currently limit its widespread use. Here we present single cell Mapper (scMappR), a method that assigns cell-type specificity scores to DEGs obtained from bulk RNA-seq by integrating cell-type expression data generated by scRNA-seq and existing deconvolution methods. After benchmarking scMappR using RNA-seq data obtained from sorted blood cells, we asked if scMappR could reveal known cell-type specific changes that occur during kidney regeneration. We found that scMappR appropriately assigned DEGs to cell-types involved in kidney regeneration, including a relatively small proportion of immune cells. While scMappR can work with any user supplied scRNA-seq data, we curated scRNA-seq expression matrices for ∼100 human and mouse tissues to facilitate its use with bulk RNA-seq data alone. Overall, scMappR is a user-friendly R package that complements traditional differential expression analysis available at CRAN.HighlightsscMappR integrates scRNA-seq and bulk RNA-seq to re-calibrate bulk differentially expressed genes (DEGs).scMappR correctly identified immune-cell expressed DEGs from a bulk RNA-seq analysis of mouse kidney regeneration.scMappR is deployed as a user-friendly R package available at CRAN.
The recombination landscape and multiple QTL mapping in aSolanum tuberosumcv. ‘Atlantic’-derived F1population
Authors: Silva Pereira Guilherme da , Mollinari Marcelo , Schumann Mitchell J. , Clough Mark E. , Zeng Zhao-Bang , Yencho G. Craig 
Published: August 2020

AbstractThere are many challenges involved with the genetic analyses of autopolyploid species, such as the tetraploid potato,Solanum tuberosum(2n= 4x= 48). The development of new analytical methods has made it valuable to re-analyze an F1 population (n= 156) derived from a cross involving ‘Atlantic’, a widely grown chipping variety in the USA. A fully integrated genetic map with 4,285 single nucleotide polymorphisms, spanning 1,630 cM, was constructed with MAPpoly software. We observed that bivalent configurations were the most abundant ones (51.0∼72.4% depending on parent and linkage group), though multivalent configurations were also observed (2.2∼39.2%). Seven traits were evaluated over four years (2006-8 and 2014) and quantitative trait loci (QTL) mapping was carried out using QTLpoly software. Based on a multiple-QTL model approach, we detected 21 QTL for 15 out of 27 trait-year combination phenotypes. A hotspot on linkage group 5 was identified as QTL for maturity, plant yield, specific gravity and internal heat necrosis resistance over different years were co-located. Additional QTL for specific gravity and dry matter were detected with maturity-corrected phenotypes. Among the genes around QTL peaks, we found those on chromosome 5 that have been previously implicated in maturity (StCDF1) and tuber formation (POTH1). These analyses have the potential to provide insights into the biology and breeding of tetraploid potato and other autopolyploid species.
Fast Ion Beam Inactivation of Viruses, Where Radiation Track Structure Meets RNA Structural Biology
Authors: Villagomez-Bernabe B. , Chan S. W. , Coulter J. A. , Roseman A. M. , Currell F. J. 
Published: August 2020

AbstractHere we show an interplay between the structures present in ionization tracks and nucleocapsid RNA structural biology, using fast ion beam inactivation of the severe acute respiratory syndrome coronavirus (SARS-CoV) virion as an example. This interplay is one of the key factors in predicting dose-inactivation curves for high energy ion beam inactivation of virions. We also investigate the adaptation of well-established cross-section data derived from radiation interactions with water to the interactions involving the components of a virion, going beyond the density-scaling approximation developed previously. We conclude that solving one of the grand challenges of structural biology — the determination of RNA tertiary/quaternary structure — is intimately linked to predicting ion-beam inactivation of viruses and that the two problems can be mutually informative. Indeed, our simulations show that fast ion beams have a key role to play in elucidating RNA tertiary/quaternary structure.
Structural control of fibrin bioactivity by mechanical deformation
Authors: Kumar Sachin , Wang Yujen , Rausch Manuel K. , Parekh Sapun H. 
Published: August 2020

AbstractFibrin is a fibrous protein network that entraps blood cells and platelets to form blood clots following vascular injury. As a biomaterial, fibrin acts a biochemical scaffold as well as a viscoelastic patch that resists mechanical insults. The biomechanics and biochemistry of fibrin have been well characterized independently, showing that fibrin is a hierarchical material with numerous binding partners. However, comparatively little is known about how fibrin biomechanics and biochemistry are coupled: how does fibrin deformation influence its biochemistry at the molecular level? In this study, we show how mechanically-induced molecular structural changes in fibrin affect fibrin biochemistry and fibrin-platelet interaction. We found that tensile deformation of fibrin lead to molecular structural transitions of α-helices to β-sheets, which reduced binding of tissue plasminogen activator (tPA), an enzyme that initiates fibrinolysis, at the network and single fiber level. Moreover, binding of tPA and Thioflavin T (ThT), a commonly used β-sheet marker, was primarily mutually exclusive such that tPA bound to native (helical) fibrin whereas ThT bound to strained fibrin. Finally, we demonstrate that conformational changes in fibrin suppressed the biological activity of platelets on mechanically strained fibrin due to attenuated αIIbβ3integrin binding. Our work shows that mechanical strain regulates fibrin molecular structure and fibrin biological activity in an elegant mechano-chemical feedback loop, which likely influences fibrinolysis and wound healing kinetics.
Effects of a combined enrichment intervention on the behavioural and physiological welfare of captive Asiatic lions (Panthera leo persica)
Authors: Goswami Sitendu , Patel Shiv Kumari , Kadivar Riyaz , Tyagi Praveen Chandra , Malik Pradeep Kumar , Mondol Samrat 
Published: August 2020

AbstractThe endangered Asiatic lion (Panthera leo persica) is currently distributed as a single wild population of 670 individuals and ∼400 captive animals globally. Although the captive lions are major hope for the species’ long-term conservation through repatriation, their welfare status and management practises need research attention. To this end, we tested the efficacy of feeding, sensory and manipulable enrichment interventions on the welfare of Asiatic lions at the conservation breeding centre of Sakkarbaug Zoological Garden, Gujarat. We adopted a holistic approach by measuring physiological and behavioural responses of 35 captive Asiatic lions, divided into control (n=16) and test (n=19) groups. The test subjects approached feeding devices first and manipulable devices for a longer duration. Manipulable devices were used homogenously with two significant time peaks, but sensory devices were used sporadically throughout the day with no discernible peak usage. The control subjects remained unchanged in all welfare parameters compared to their pre-treatment levels. However, post-enrichment behavioural assessments showed higher behaviour diversity (95% increase from the baseline period), reduced enclosure zone bias (40.25% reduction) and aberrant repetitive behaviours (80.68%) in test samples. Similarly, faecal corticosterone measures showed lower stress levels in test samples (58% decrease), confirming significant improvement in all welfare indices than control groups. These results have universal applicability to assess welfare indices of other captive species in Indian zoos. We hope that the results will encourage zoo managers and regulatory agencies to improve animal welfare practices.