bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endophyte inoculation enhancesUlmus minorresistance to Dutch elm disease
Authors: Martínez-Arias C , Sobrino-Plata J , Ormeño-Moncalvillo S , Gil L , Rodríguez-Calcerrada J , Martín JA 
Published: May 2020

AbstractCertain fungal endophytes are known to improve plant resistance to biotic stresses in forest trees. In this study, three stem fungal endophytes belonging to classes Cystobasidiomycetes, Eurotiomycetes and Dothideomycetes were selected from 210 isolates for their potential as enhancers ofUlmus minorresistance toOphiostoma novo-ulmi. We evaluated phenotypic traits of these endophytes that could be beneficial for inhibitingO. novo-ulmiin the host plant. Underin vitroconditions, the Dothideomycetous isolate YCB36 strongly inhibitedO. novo-ulmigrowth, released antipathogenic VOCs, chitinases and siderophores, and overlapped with the pathogen in nutrient utilization patterns. These functional traits could explain the 40% reduction in leaf wilting due toO. novo-ulmiin elm trees pre-inoculated with this endophyte.Ulmus minortrees inoculated with this endophyte showed increased leaf stomatal conductance and higher concentrations of flavonoids and total phenolic compounds in xylem tissues, suggesting induction of defence metabolism.
The Notch Ligand Jagged1 is Required for the Formation, Maintenance, and Survival of Hensen Cells in the Mouse Cochlea
Authors: Chrysostomou Elena , Zhou Luyi , Darcy Yuanzhao L. , Graves Kaley A. , Doetzlhofer Angelika , Cox Brandon C. 
Published: May 2020

ABSTRACTDuring cochlear development, the Notch ligand JAGGED 1 (JAG1) plays an important role in the specification of the prosensory region, which gives rise to sound-sensing hair cells and neighboring supporting cells (SCs). While JAG1’s expression is maintained in SCs through adulthood, the function of JAG1 in SC development is unknown. Here, we demonstrate that JAG1 is essential for the formation and maintenance of Hensen cells (HeCs), a highly specialized SC-subtype located at the edge of the auditory epithelium. Deletion ofJag1at the onset of differentiation, at stage E14.5, disrupted HeC formation. Similar loss of HeCs was observed whenJag1was deleted at P0/P1 and fate-mapping analysis revealed that in the absence ofJag1some HeCs die, but others convert into neighboring Claudius cells. In support of a role for JAG1 in cell survival, genes involved in mitochondrial function and protein synthesis were downregulated in P0 cochlea lackingJag1.
The contribution of stimulating multiple body parts simultaneously to the illusion of owning an entire artificial body
Authors: O’Kane Sophie H. , Ehrsson H. Henrik 
Published: May 2020

AbstractThe full-body ownership illusion exploits multisensory perception to induce a feeling of ownership for an entire artificial body. Whilst previous research has shown that the synchronous visuotactile stimulation of a single body part is sufficient for illusory ownership over the whole body, the effect of combining multisensory stimulation across multiple body parts remains unknown. Therefore, 48 healthy adults participated in conditions of a full-body ownership illusion involving synchronous or asynchronous visuotactile stimulation to one, two or three body parts simultaneously (2 x 3 design). We developed a novel questionnaire to isolate the sense of ownership of five specific body parts (left leg, right leg, left arm, right arm, and trunk) from the full-body ownership experience and sought not only to test for greater (part and whole) body ownership in synchronous versus asynchronous stimulation, but also, potentially varying degrees of illusion intensity related to the number of body parts stimulated. As expected, illusory full-body ownership and all five body-part ownership ratings were significantly higher following synchronous stimulation (all p values ≤.01). Since non-stimulated body parts also received significantly higher ownership ratings following synchronous stimulation, the results are consistent with an illusion engaging the entire body. We further noted that ownership ratings for the right body parts (often stimulated) were significantly higher than ownership ratings for the left body parts (never stimulated). Regarding explicit feelings of full-body ownership, subjective ratings were not significantly enhanced by increasing the number of synchronously stimulated body parts (synchronicity x number stimulated interaction; p.099). Instead, median ratings indicated a moderate affirmation (+1) of full-body illusory sensation for all three synchronous conditions; a finding mirrored by full-body illusion onset time. The results support the notion that feelings of full-body ownership are mediated by a generalisation from stimulated part(s)-to-whole, supported by processes related to multisensory body perception.
Disentangling listening effort and memory load beyond behavioural evidence: Pupillary response to listening effort during a concurrent memory task
Authors: Zhang Yue , Lehmann Alexandre , Deroche Mickael 
Published: May 2020

AbstractRecent research has demonstrated that pupillometry is a robust measure for quantifying listening effort. However, pupillary responses in listening situations where multiple cognitive functions are engaged and sustained over a period of time remain hard to interpret. This limits our conceptualisation and understanding of listening effort in realistic situations, because rarely in everyday life are people challenged by one task at a time. Therefore, the purpose of this experiment was to reveal the dynamics of listening effort in a sustained listening condition using a word repeat and recall task.Words were presented in quiet and speech-shaped noise at different signal-to-noise ratios (SNR). Participants were presented with lists of 10 words, and required to repeat each word after its presentation. At the end of the list, participants either recalled as many words as possible or moved on to the next list. Simultaneously, their pupil dilation was recorded throughout the whole experiment.When only word repeating was required, peak pupil dilation (PPD) was bigger in 0dB versus other conditions; whereas when recall was required, PPD showed no difference among SNR levels and PPD in 0dB was smaller than repeat-only condition. Baseline pupil diameter and PPD followed different growth patterns across the 10 serial positions in conditions requiring recall: baseline pupil diameter built up progressively and plateaued in the later positions (but shot up at the onset of recall, i.e. the end of the list); PPD decreased at a pace quicker than in repeat-only condition.The current findings concur with the recent literature in showing that additional cognitive load during a speech intelligibility task could disturb the well-established relation between pupillary response and listening effort. Both the magnitude and temporal pattern of task-evoked pupillary response differ greatly in complex listening conditions, urging for more listening effort studies in complex and realistic listening situations.
DECODING SECOND ORDER ISOMORPHISMS IN THE BRAIN: The case of colors and letters
Authors: José Hanson Stephen , Caglar Leyla Roskan , Hanson Catherine 
Published: May 2020

AbstractWe introduce a new method for decoding neural data from fMRI. It is based on two assumptions, first that neural representation is distributed over networks of neurons embeded in voxel noise and second that the stimuli can be decoded as learned relations from sets of categorical stimuli. We illustrate these principles with two types of stimuli, color (wavelength) and letters (visual shape), both of which have early visual system response, but at the same time must be learned within a given function or category (color contrast, alphabet). Key to the decoding method is reducing the stimulus cross-correlation by a matched noise voxel sample by normalizing the stimulus voxel matrix thus unmasking a highly discriminative neural profile per stimulus. Projection of this new voxel space (ROI) to a smaller set of dimensions (with e.g., non-metric Multidimensional scaling), the relational information takes a unique geometric form revealing functional relationships between sets of stimuli, defined by R. Shepard, assecond-order isomorphisms (SOI). In the case of colors the SOI appears as a nearly equally spaced set of wavelengths arranged in a color wheel, with a gap between the “purples” and “reds” (consistent with the gap in the original Ekman’s color set). In the case of letters, a cluster space resulted from the decorrelated voxel neural profiles, which matched the phrase structure of the mnemonic used for more than 100 years to teach children the alphabet (across multiple languages),The Alphabet Song.
Transcription of intragenic CpG islands influences spatiotemporal host gene pre-mRNA processing
Authors: Amante Samuele M , Montibus Bertille , Cowley Michael , Barkas Nikolaos , Setiadi Jessica , Saadeh Heba , Giemza Joanna , Castillo Stephania Contreras , Fleischanderl Karin , Schulz Reiner , Oakey Rebecca J 
Published: May 2020

ABSTRACTAlternative splicing (AS) and alternative polyadenylation (APA) generate diverse transcripts in mammalian genomes during development and differentiation. Epigenetic factors such as trimethylation of histone H3 lysine 36 (H3K36me3) and DNA methylation play a role in generating transcriptome diversity. Intragenic CpG islands (iCGIs) and their corresponding host genes exhibit dynamic epigenetic and gene expression patterns during development and between different tissues. We hypothesise that iCGI-associated H3K36me3, DNA methylation and transcription can influence host gene AS and/or APA. We investigate H3K36me3 and find that this histone mark is not a major regulator of AS or APA in our model system. Genomewide, we identify over 4000 host genes that harbour an iCGI in the mammalian genome, including both previously annotated and novel iCGI/host gene pairs. The transcriptional activity of these iCGIs is tissue- and developmental stage-specific and, for the first time, we demonstrate that the premature termination of host gene transcripts upstream of iCGIs is closely correlated with the level of iCGI transcription in a DNA-methylation independent manner. These studies suggest that iCGI transcription, rather than H3K36me3 or DNA methylation, interfere with host gene transcription and pre-mRNA processing genomewide and contributes to the spatiotemporal diversification of both the transcriptome and proteome.
Differential chromatin accessibility landscape reveals the structural and functional features of the allopolyploid wheat chromosomes
Authors: Jordan Katherine W. , He Fei , de Soto Monica Fernandez , Akhunova Alina , Akhunov Eduard 
Published: May 2020

AbstractBackgroundWe have a limited understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous chromosomes. Using a differential nuclease sensitivity (DNS) assay, we investigated the chromatin states in the coding and transposon element (TE) -rich repetitive regions of the allopolyploid wheat genome.ResultsWe observed a negative chromatin accessibility gradient along the telomere-centromere axis with mostly open and closed chromatin located in the distal and pericentromeric regions of chromosomes, respectively. This trend was mirrored by the TE-rich intergenic regions, but not by the genic regions, which showed similar averages of chromatin accessibility levels along the chromosomes. The genes’ proximity to TEs was negatively associated with chromatin accessibility. The chromatin states of TEs was dependent on their type, proximity to genes, and chromosomal position. Both the distance between genes and TE composition appear to play a more important role in the chromatin accessibility along the chromosomes than chromosomal position. The majority of MNase hypersensitive regions were located within the TEs. The DNS assay accurately predicted previously detected centromere locations. SNPs located within more accessible chromatin explain a higher proportion of genetic variance for a number of agronomic traits than SNPs located within closed chromatin.ConclusionsThe chromatin states in the wheat genome are shaped by the interplay of repetitive and gene-encoding regions that are predictive of the functional and structural organization of chromosomes, providing a powerful framework for detecting genomic features involved in gene regulation and prioritizing genomic variation to explain phenotypes.
CHOP-c-JUN complex plays a critical role in liver proteotoxicity induced by mutant Z alpha-1 antitrypsin
Authors: Attanasio Sergio , Gernoux Gwladys , Ferriero Rosa , De Cegli Rossella , Carissimo Annamaria , Nusco Edoardo , Campione Severo , Teckman Jeffrey , Mueller Christian , Piccolo Pasquale , Brunetti-Pierri Nicola 
Published: May 2020

ABSTRACTAlpha-1 antitrypsin (AAT) deficiency is a common genetic disorder with lung and liver involvement. Most patients carry the Z allele inSERPINA1that encodes a mutant AAT (ATZ) forming hepatotoxic polymers. We foundCHOPupregulation and activation in both mouse (PiZ) and human livers expressing ATZ. Compared to controls, juvenile PiZ/Chop-/-mice showed reduction in hepatic ATZ and transcriptional response to endoplasmic reticulum stress, as consequence of CHOP-mediated increase ofSERPINA1transcription. CHOP was found to upregulateSERPINA1though binding with c-JUN onSERPINA1regulatory elements, thus aggravating hepatic accumulation of ATZ. IncreasedCHOPlevels were detected in diseased livers of children homozygous for the Z allele.Compared to adults, AAT deficiency in infants has different severity and prognosis. Based on our findings, CHOP-c-JUN complex upregulatesSERPINA1transcription and play an important role in the hepatic disease pathogenesis by increasing the burden of proteotoxic ATZ, particularly in the pediatric population.
Syndecan 2 regulates hematopoietic lineages and infection resolution in zebrafish
Authors: Lamichhane Bhawika Sharma , Bisgrove Brent W. , Su Yi-Chu , Demarest Bradley L. , Yost H. Joseph 
Published: May 2020

AbstractSyndecan 2 (Sdc2) is a transmembrane cell-surface heparan sulfate proteoglycan (HSPG) that has been implicated in the regulation of cell-cell signaling pathways and cell-matrix interactions. Surprisingly, homozygous recessive maternal zygotic (MZ)sdc2null mutants in zebrafish appear to have normal development, normal morphology and are viable and fertile in adulthood. Whole transcriptome RNA sequencing, FACS analyses, and imaging of transgenic reporter lines that distinguish specific hematopoietic lineages revealed thatsdc2mutants have defects in the specification and proportions of red blood cells and neutrophils that initiate during embryonic hematopoiesis and likely persist through adulthood. During bacterial infections, MZsdc2mutants have markedly reduced neutrophil recruitment and significantly higher death rates. Hematopoietic stem/progenitor cell (HSPC) numbers are also significantly reduced in MZsdc2mutants. In zebrafish, cells that bud off of the ventral region of somites are thought to give rise to the reticular stromal cells of the caudal hematopoietic tissue (CHT) stem cell niche. In MZsdc2mutants, these budding cells have abberant blebbing morphology associated with widespread apoptosis during induction of HSPCs and with changes in the vascularization and stromal cell structure of the CHT stem cell niche. This suggests that loss ofsdc2disrupts the earliest events of definitive hematopoiesis. Our findings of hematopoietic defects, nascent immune system alterations and inability to resolve infection insdc2mutants sets the stage for examining the roles of HSPG genes in a wide range of hematopoietic and immune defects in humans.Key PointsSyndecan 2 regulates the formation of Hematopoietic Stem/Progenitor Cells, differentiation into hematopoietic populations and the CHT architectureSyndecan 2 mutants are significantly more susceptible to bacterial infection
TheVibrio choleraequorum-sensing protein VqmA integrates cell density, environmental, and host-derived cues into the control of virulence
Authors: Mashruwala Ameya A. , Bassler Bonnie L. 
Published: May 2020

Scientific AbstractQuorum sensing is a chemical communication process in which bacteria use the production, release, and detection of signal molecules called autoinducers to orchestrate collective behaviors. The human pathogenVibrio choleraerequires quorum sensing to infect the small intestine. There,V. choleraeencounters the absence of oxygen and the presence of bile. We show that these two stimuli differentially affect quorum sensing function and, in turn,V. choleraepathogenicity. The quorum-sensing receptor-transcription factor called VqmA, that detects the autoinducer called DPO, also detects the lack of oxygen and the presence of bile. Detection occurs via DPO-, oxygen-, bile-, and redox-responsive disulfide bonds that alter VqmA DNA binding activity. We propose that VqmA serves as an information processing hub that integrates quorum- sensing information, redox status, the presence or absence of oxygen, and host cues. In response to the information acquired through this mechanism,V. choleraeappropriately modulates its virulence output.Lay AbstractQuorum sensing (QS) is a process of chemical communication bacteria use to orchestrate collective behaviors. QS communication relies on chemical signal molecules called autoinducers. QS regulates virulence inVibrio cholerae, the causative agent of the disease cholera. Transit into the human small intestine, the site of cholera infection, exposesV. choleraeto the host environment. In this study, we show that the combination of two stimuli encountered in the small intestine, the absence of oxygen and the presence of host-produced bile, impinge onV. choleraeQS function and, in turn, pathogenicity. We suggest that possessing a QS system that is responsive to multiple environmental, host, and cell density cues enablesV. choleraeto fine-tune its virulence capacity in the human intestine.
Leish-ExP: a database of exclusive proteins fromLeishmaniaparasite
Authors: Das Aneesha , Biswas Nupur , Chakrabarti Saikat 
Published: May 2020

AbstractLeishmaniasis is a complex disease caused by different species of genusLeishmania, which affects millions of people spanning over 88 countries causing extensive mortality and morbidity. Leishmaniasis exists in three clinical forms; cutaneous, mucocutaneous and visceral. Anti-leishmanial therapy is one of the challenging fields due to the presence of wide range ofLeishmaniaspecies and host response against the pathogenic infection. Clinical survey reveals toxicity of drugs and trial compounds causing death among patients and predominant resistance to different class of antimonials among the leishmaniasis patient. Identification of appropriate target protein is a primary and important phase of drug development andLeishmaniais a suitable system for targeted drug development as it branched out quite early from the higher eukaryotes like human. With the advancement of genomic era and availability of whole genome sequences ofLeishmaniaspecies, relevant information on their respective genes and proteins are now easily extracted. Hence, in the current study, to aid the targeted drug therapy, an exhaustive whole genome scale comparative sequence analysis was performed to identify genes/proteins exclusive toLeishmania. Subsequently, further filtration was employed to identify the individualLeishmaniaspecies specific gene/proteins. Among such proteins, a considerable number was found to have no recognizable structure and functions. Hence, efforts were taken to characterize theseLeishmaniaexclusive gene/proteins via providing additional sequence, structure, localization and functional information. All the information about each of theseLeishmaniaexclusive gene/proteins from five differentLeishmaniaspecies has been systemically categorized and represented in the form a user-friendly database calledLeish-ExP, which is freely available athttp://www.hpppi.iicb.res.in/Leish-ex.
IDENTIFICATION AND CHARACTERIZATION OF A LARGE SOURCE OF PRIMARY MESENCHYMAL STEM CELLS TIGHTLY ADHERED TO BONE SURFACES OF HUMAN VERTEBRAL BODY MARROW CAVITIES
Authors: Johnstone Brian H. , Miller Hannah M. , Beck Madelyn R. , Gu Dongsheng , Thirumala Sreedhar , LaFontaine Michael , Brandacher Gerald , Woods Erik J. 
Published: May 2020

ABSTRACTTherapeutic allogeneic mesenchymal stem/stromal cells (MSC) are currently in clinical trials for evaluating their effectiveness in treating many different disease indications. Eventual commercialization for broad distribution will require further improvements in manufacturing processes to economically manufacture MSC at sufficient scales required to satisfy projected demands. A key contributor to the present high cost of goods (COG) for MSC manufacturing is the need to create master cell banks (MCBs) from multiple donors, which leads to variability in large-scale manufacturing runs. Therefore, the availability of large single donor depots of primary MSC would greatly benefit the cell therapy market by reducing costs associated with manufacturing.We have discovered that an abundant population of cells possessing all the hallmarks of MSC is tightly associated with the vertebral body (VB) bone matrix and are only liberated by proteolytic digestion. Here we demonstrate that these vertebral bone-adherent (vBA) MSC possess all the International Society of Cell and Gene Therapy (ISCT)-defined characteristics (e.g., plastic adherence, surface marker expression, and trilineage differentiation) of MSC and, therefore, have termed them vBA-MSC, to distinguish this population from loosely associated MSC recovered through aspiration or rinsing of the bone marrow (BM) compartment.Pilot banking and expansion was performed with vBA-MSC obtained from 3 deceased donors and it was demonstrated that bank sizes averaging 2.9×108± 1.35×108vBA-MSC at passage one were obtainable from only 5 g of digested VB bone fragments. Each bank of cells demonstrated robust proliferation through a total of 9 passages without significant reduction in population doubling times. The theoretical total cell yield from the entire amount of bone fragments (approximately 300g) from each donor with limited expansion through 4 passages is 100 trillion (1×1014) vBA-MSC, equating to over 105doses at 10×106cells/kg for an average 70 kg recipient. Thus, we have established a novel and plentiful source of MSC which will benefit the cell therapy market by overcoming manufacturing and regulatory inefficiencies due to donor-to-donor variability.