Biology subjects

Schneider, M.

Publications and source records attributed to Schneider, M..

86 records · Page 5Linked to original sources

bioRxiv2019

Neutrophils Suppress Mucosal-Associated Invariant T Cells

Mucosal-associated invariant T (MAIT) cells are innate-like T lymphocytes that are abundant in mucosal tissues and the liver where they can respond rapidly to a broad range of riboflavin producing bacterial and fungal pathogens. Neutrophils, which are recruited early to sites of infection, play a non-redundant role in pathogen clearance and are crucial for controlling infection. The interaction of these two cell types is poorly studied. Here, we investigated both the effect of neutrophils on MAIT cell activation and the effect of activated MAIT cells on neutrophils. We show that neutrophils suppress the activation of MAIT cells by a cell-contact and H2O2 dependent mechanism. Moreover, highly activated MAIT cells were able to produce high levels of TNF that induced neutrophil death. We therefore provide evidence for a negative regulatory feedback mechanism in which neutrophils prevent over-activation of MAIT cells and, in turn, MAIT cells limit neutrophil survival.

immunology↗

bioRxiv2019

Oral administration of an anti-CfaE secretory IgA antibody protects against Enterotoxigenic Escherichia coli diarrheal disease in a non-human primate model

ABSTACTEnterotoxigenic Escherichia coli (ETEC) is a leading cause of diarrhea-associated illness in developing countries. There is currently no vaccine licensed to prevent ETEC and the development of an efficacious prophylaxis would provide an intervention with significant impact. Recent studies suggested that effective protection could be achieved by inducing immunity to block colonization of ETEC. Here, we evaluated the efficacy of secretory (s) IgA2 and dimeric (d) IgA2 of an anti-colonization factor antigen antibody, 68-61, in the Aotus nancymaae non-human primate (NHP) ETEC challenge model via oral and parental delivery. Thirty-nine animals were distributed across 3 groups of 13, and challenged with 5.0x1011 cfu of H10407 on Day 0. Group 1 received a dIgA2 68-61 subcutaneously on day 0. Group 2 received a SIgA2 68-61 orally on days -1, 0, and +1, and Group 3 received an irrelevant SIgA2 antibody orally on days -1, 0, and +1. All animals were observed for symptoms of diarrhea, and stools were collected for ETEC colony counts. SIgA2 treatment significantly lowered the attack rate, resulting in a protective efficacy of 71.4% (p=0.025) in Group 2 as compared to Group 3. Anti-CfaE dIgA2 treatment group reduced the diarrheal attack rate, although the reduction did not reach significance (57.1%; P=0.072) as compared to the irrelevant SIgA2 Group 3. Our results demonstrated the feasibility of oral administration of SIgA as a potential immunoprophylaxis against enteric infections. To our knowledge, this is the first study to demonstrate the efficacy of administrated SIgA in a non-human primate model.

immunology↗

bioRxiv2019

A systemic approach provides insights into the salt stress adaptation mechanisms of contrasting bread wheat genotypes

Bread wheat is one of the most important crops for human diet but the increasing soil salinization is causing yield reductions worldwide. Physiological, genetic, transcriptomics and bioinformatics analyses were integrated to study the salt stress adaptation response in bread wheat. A comparative analysis to uncover the dynamic transcriptomic response of contrasting genotypes from two wheat populations was performed at both osmotic and ionic phases in time points defined by physiologic measurements. The differential stress effect on the expression of photosynthesis, calcium binding and oxidative stress response genes in the contrasting genotypes supported the greater photosynthesis inhibition observed in the susceptible genotype at the osmotic phase. At the ionic phase genes involved in metal ion binding and transporter activity were up-regulated and down-regulated in the tolerant and susceptible genotypes, respectively. The stress effect on mechanisms related with protein synthesis and breakdown was identified at both stress phases. Based on the linkage disequilibrium blocks it was possible to select salt-responsive genes as potential components operating in the salt stress response pathways leading to salt stress resilience specific traits. Therefore, the implementation of a systemic approach provided insights into the adaptation response mechanisms of contrasting bread wheat genotypes at both salt stress phases.\n\nHighlightThe implementation of a systemic approach provided insights into salt stress adaptation response mechanisms of contrasting bread wheat genotypes from two mapping populations at both osmotic and ionic phases.

systems biology↗

bioRxiv2019

Depth-resolved ultra-high field fMRI reveals feedback contributions to surface motion perception

Human visual surface perception has neural correlates in early visual cortex, but the extent to which feedback contributes to this activity is not well known. Feedback projections preferentially enter superficial and deep anatomical layers, while avoiding the middle layer, which provides a hypothesis for the cortical depth distribution of fMRI activity related to feedback in early visual cortex. Here, we presented human participants uniform surfaces on a dark, textured background. The grey surface in the left hemifield was either perceived as static or moving based on a manipulation in the right hemifield. Physically, the surface was identical in the left visual hemifield, so any difference in percept likely was related to feedback. Using ultra-high field fMRI, we report the first evidence for a depth distribution of activation in line with feedback during the (illusory) perception of surface motion. Our results fit with a signal re-entering in superficial depths of V1, followed by a feedforward sweep of the re-entered information through V2 and V3, as suggested by activity centred in the middle-depth levels of the latter areas. This positive modulation of the BOLD signal due to illusory surface motion was on top of a strong negative BOLD response in the cortical representation of the surface stimuli, which depended on the presence of texture in the background. Hence, the magnitude and sign of the BOLD response to the surface strongly depended on background properties, and was additionally modulated by the presence or absence of illusory motion perception in a manner compatible with feedback. In summary, the present study demonstrates the potential of depth resolved fMRI in tackling biomechanical questions on perception that so far were only within reach of invasive animal experimentation.

neuroscience↗

bioRxiv2019

Nod-like receptors are critical for gut-brain axis signaling

Gut-brain axis signaling is critical for maintaining health and homeostasis. Stressful life events can impact gut-brain signaling, leading to altered mood, cognition and intestinal dysfunction. Here we identify nucleotide binding oligomerization domain (Nod)-like receptors (NLR), Nod1 and Nod2, as novel regulators for gut-brain signaling. NLR are innate immune pattern recognition receptors expressed in the gut and brain, important in the regulation of gastrointestinal (GI) physiology. We found that mice deficient in both Nod1 and Nod2 (NodDKO) demonstrate signs of stress-induced anxiety, cognitive impairment and depression in the context of a hyperactive hypothalamic-pituitary-adrenal axis. These deficits were coupled with impairments in the serotonergic pathway in the brain, decreased hippocampal neurogenesis, and reduced neural activation. In addition, NodDKO mice had increased GI permeability and altered serotonin signaling in the gut following exposure to acute stress. Administration of the selective serotonin reuptake inhibitor, fluoxetine, abrogated behavioral impairments and restored serotonin signaling. We also identified that intestinal epithelial cell-specific deletion of Nod1 (VilCre+Nod1f/f), but not Nod2, increased susceptibility to stress-induced anxiety-like behavior and cognitive impairment following exposure to stress. Together these data suggest that intestinal epithelial NLR are novel modulators of gut-brain communication and may serve as potential novel therapeutic targets for the treatment of gut-brain disorders.

physiology↗

bioRxiv2019

Transcriptional analysis defines TCR and cytokine-stimulated MAIT cells as rapid polyfunctional effector T cells that can coordinate the immune response

MAIT cells are an abundant innate-like T cell population which can be activated via either their T cell receptor (TCR), which recognizes MR1-bound pyrimidine antigens derived from microbial riboflavin biosynthesis, or via cytokines, such as IL-12 and IL-18. In vivo, these two modes of activation may act in concert or independently depending upon the nature of the microbial or inflammatory stimuli. It is unknown, however, how the MAIT cell response differs to the different modes of activation. Here, we define the transcriptional and effector responses of human MAIT cells to TCR and cytokine stimulation. We report that MAIT cells rapidly respond to TCR stimulation through the production of multiple effector cytokines and chemokines, alteration of their cytotoxic granule content and transcription factor expression, and upregulation of co-stimulatory proteins CD40L and 4-1BB. In contrast, cytokine-mediated activation is slower and results in more limited production of cytokines, chemokines, and co-stimulatory proteins; differences in granule content and transcription factor expression are also evident. Therefore, we propose that in infections by riboflavin-synthesizing bacteria, MAIT cells play a key early role in effecting and coordinating the immune response, while in the absence of TCR stimulation (e.g. viral infection) their role is likely to differ.

immunology↗

bioRxiv2019

Prenatal diagnosis of HNF1B-associated renal cysts: Need to differentiate intragenic variants from 17q12 microdeletion syndrome?

ObjectiveLarge deletions of chromosome 17q12 (17q12DS) or intragenic variants in HNF1B are associated with variable developmental, endocrine and renal anomalies, often already noted prenatally as hyperechogenic/cystic kidneys. Here, we describe pre- and postnatal phenotypes of seven individuals with HNF1B aberrations and compare their clinical and genetic data to previous studies.\n\nMethodsPrenatal sequencing and postnatal chromosomal microarray analysis was performed in seven individuals with renal and/or neurodevelopmental phenotypes. We evaluated HNF1B-related clinical features from 82 studies and reclassified 192 reported intragenic HNF1B variants.\n\nResultsIn a prenatal case, we identified a novel in-frame deletion p.(Gly239del) within the HNF1B DNA binding domain, a mutational hotspot as demonstrated by spatial clustering analysis and high computational prediction scores. The six postnatally diagnosed individuals harbored 17q12 microdeletions of varying size. Literature screening revealed highly variable reporting of HNF1B-associated clinical traits. Overall, developmental delay was more frequent in 17q12DS carriers, although both mutation groups showed a high phenotypic heterogeneity. The reclassification of all previously reported intragenic HNF1B variants provided an up-to-date overview of the mutational spectrum.\n\nConclusionsWe highlight the value of prenatal HNF1B screening in renal developmental diseases. Standardized clinical reporting and systematic classification of HNF1B variants is necessary for a more accurate risk quantification of pre- and postnatal clinical features, improving genetic counseling and prenatal decision-making.

genetics↗

bioRxiv2019

Towards accurate high-throughput ligand affinity prediction by exploiting structural ensembles, docking metrics and ligand similarity

MotivationNowadays, virtual screening (VS) plays a major role in the process of drug development. Nonetheless, an accurate estimation of binding affinities, which is crucial at all stages, is not trivial and may require target-specific fine-tuning. Furthermore, drug design also requires improved predictions for putative secondary targets among which is Estrogen Receptor alpha (ER).\n\nResultsVS based on combinations of Structure-Based VS (SBVS) and Ligand-Based VS (LBVS) is gaining momentum to help characterizing secondary targets of xenobiotics (including drugs and pollutants). In this study, we propose an integrated approach using ligand docking based on multiple structural en-sembles to reflect the conformational flexibility of the receptor. Then, we investigate the impact of the two different types of features (structure-based docking descriptors and ligand-based molecular descriptors) for affinity predictions based on a random forest algorithm. We find that ligand-based features have limited predictive power (rP =0.69, R2=0.47), compared to structure-based features (rP =0.78, R2=0.60) while their combination maintains the overall accuracy (rP =0.77, R2=0.56). Extending the training dataset to include xenobiotics, leads to a novel high-throughput affinity prediction method for ER ligands (rP =0.85, R2=0.71). Methods robustness is tested on several ligand databases and performances are compared with existing rescoring procedures. The presented prediction tool is provided to the community as a dedicated satellite of the @TOME server.\n\nAvailabilityhttp://atome4.cbs.cnrs.fr/ATOME_V3/SERVER/EDMon_v3.html\n\nContactschneider@cbs.cnrs.fr, labesse@cbs.cnrs.fr

bioinformatics↗

bioRxiv2018

Role of Innate-like Lymphocytes in the Pathogenesis of Community Acquired Pneumonia

BackgroundMucosal-associated invariant T (MAIT) cells and V{delta}2+ {gamma}{delta} T cells are anti-bacterial innate-like lymphocytes (ILLs) that are enriched in blood and mucosa. ILLs have been implicated in control of bacterial infection. However, the role of ILLs in community-acquired pneumonia (CAP) is unknown.\n\nMethodsUsing sputum samples from a well-characterised CAP cohort, MAIT cell (V7.2-J12/20/33) and V{delta}2+ T cell (V{delta}2-J{delta}1/2/3/4) abundance was determined by quantitative PCR. Cytokine and chemokine concentrations in sputum were measured. The capacity of bacteria in sputum to produce activating ligands for MAIT cells and V{delta}2+ T cells was inferred by 16S rRNA sequencing.\n\nResultsMAIT cell abundance in sputum was higher in patients with less severe pneumonia; duration of hospital admission was inversely correlated with both MAIT and V{delta}2+ T cell abundance. The abundance of both ILLs was higher in patients with a confirmed bacterial aetiology, however there was no correlation with total bacterial load or the predicted capacity of bacteria to produce activating ligands. Sputum MAIT cell abundance was associated with interferon- , and interferon-{gamma}, and sputum neutrophil abundance, while V{delta}2+ T cell abundance was associated with CXCL11 and interferon-{gamma}.\n\nConclusionsPulmonary MAIT and V{delta}2+ T cells can be detected in sputum in CAP, where they may contribute to improved clinical outcome.

immunology↗

bioRxiv2018

Introduction and validation of a new semi-automated method to determine sympathetic fiber density in target tissues.

In recent years, the role of sympathetic nervous fibers in chronic inflammation has become increasingly evident. At the onset of inflammation, sympathetic activity is increased in the affected tissue. However, sympathetic fibers are largely absent from chronically inflamed tissue. Apparently, there is a very dynamic relationship between sympathetic innervation and the immune system in areas of inflammation, and hence a rapid and easy method for quantification of nerve fiber density of target organs is of great value to answer potential research questions. Currently, nervous fiber densities are either determined by tedious manual counting, which is not suitable for high throughput approaches, or by expensive automated processes relying on specialized software and high-end microscopy equipment. Usually, tyrosine hydroxylase (TH) is used as the marker for sympathetic fibers. In order to overcome the current quantification bottleneck with a cost-efficient alternative, an automated process was established and compared to the classic manual approach of counting TH-positive sympathetic fibers. Since TH is not exclusively expressed on sympathetic fibers, but also in a number of catecholamine-producing cells, a prerequisite for automated determination of fiber densities is to reliably distinct between cells and fibers. Therefore, an additional staining using peripherin exclusively expressed in nervous fibers as a secondary marker was established. Using this novel approach, we studied the spleens from a syndecan-3 knockout (SDC3KO) mouse line, and demonstrated equal results on SNS fiber density for both manual and automated counts (Manual counts: wt: 22.57 +/- 11.72 fibers per mm2; ko: 31.95 +/- 18.85 fibers per mm2; p = 0.0498; Automated counts: wt: 31.6 +/- 18.98 fibers per mm2; ko: 45.49 +/- 19.65 fibers per mm2; p = 0.01868). In conclusion, this new and simple method can be used as a high-throughput approach to reliably and quickly quantify SNS nerve fiber density in target tissues.

neuroscience↗

bioRxiv2018

Ultra-high field MRI reveals mood-related circuit disturbances in depression: A systematic comparison between 3-Tesla and 7-Tesla

Ultra-high field 7-Tesla (7T) MRI has the potential to advance our understanding of neuropsychiatric disorders, including major depressive disorder (MDD). To date, few studies have quantified the advantage of resting state functional MRI (fMRI) at 7T compared to 3-Tesla (3T). We conducted a series of experiments that demonstrate the improvement in temporal signal-to-noise ratio (TSNR) of a multi-echo fMRI protocol with ultra-high field 7T, compared to 3T MRI in healthy controls (HC). We also directly tested the enhancement in ultra-high field 7T fMRI signal power by examining the ventral tegmental area (VTA), a small midbrain structure that is critical to the expected neuropathology of MDD but difficult to discern with standard 3T MRI. We demonstrate 200-300% improvement in TSNR and resting state functional connectivity coefficients provided by ultra-high field 7T fMRI compared to 3T, indicating enhanced power for detection of functional neural architecture. A multi-echo based acquisition protocol and signal denoising pipeline afforded greater gain in signal power at ultra-high field compared to classic acquisition and denoising pipelines. Furthermore, ultra-high field fMRI revealed mood-related neuro-circuit disturbances in patients with MDD compared to HC, which were not detectable with 3T fMRI. Ultra-high field 7T fMRI may provide an effective tool for studying functional neural architecture relevant to MDD and other neuropsychiatric disorders.

neuroscience↗

bioRxiv2018

A scalable method to improve gray matter segmentation at ultra high field MRI

High-resolution (functional) magnetic resonance imaging (MRI) at ultra high magnetic fields (7 Tesla and above) enables researchers to study how anatomical and functional properties change within the cortical ribbon, along surfaces and across cortical depths. These studies require an accurate delineation of the gray matter ribbon, which often suffers from inclusion of blood vessels, dura mater and other non-brain tissue. Residual segmentation errors are commonly corrected by browsing the data slice-by-slice and manually changing labels. This task becomes increasingly laborious and prone to error at higher resolutions since both work and error scale with the number of voxels. Here we show that many mislabeled, non-brain voxels can be corrected more efficiently and semi-automatically by representing three-dimensional anatomical images using two-dimensional histograms. We propose both a uni-modal (based on first spatial derivative) and multi-modal (based on compositional data analysis) approach to this representation and quantify the benefits in 7 Tesla MRI data of nine volunteers. We present an openly accessible Python implementation of these approaches and demonstrate that editing cortical segmentations using two-dimensional histogram representations as an additional post-processing step aids existing algorithms and yields improved gray matter borders. By making our data and corresponding expert (ground truth) segmentations openly available, we facilitate future efforts to develop and test segmentation algorithms on this challenging type of data.

neuroscience↗

bioRxiv2017

Low Rate of Somatic Mutations in a Long-Lived Oak Tree

Because plants do not possess a proper germline, deleterious somatic mutations can be passed to gametes and a large number of cell divisions separating zygote from gamete formation in long-lived plants may lead to many mutations. We sequenced the genome of two terminal branches of a 234-year-old oak tree and found few fixed somatic single-nucleotide variants (SNVs), whose sequential appearance in the tree could be traced along nested sectors of younger branches. Our data suggest that stem cells of shoot meristems are robustly protected from accumulation of mutations in trees.

plant biology↗

bioRxiv2016

Engineered Cpf1 Enzymes with Altered PAM Specificities

The RNA-guided endonuclease Cpf1 is a promising tool for genome editing in eukaryotic cells1-5. Compared to other genome editing platforms, Cpf1 offers distinct advantages, such as the ability to easily target multiple genes simultaneously3, as well as low rates of off-target activity4, 5. However, the Acidaminococcus sp. BV3L6 Cpf1 (AsCpf1), which has been successfully harnessed for genome editing, can only robustly cleave target sites preceded by a TTTV protospacer adjacent motif (PAM), which may limit its practical utility. To address this limitation, we used a structure- guided saturation mutagenesis screen to increase the targeting range of Cpf1. We engineered two variants of AsCpf1 with the mutations S542R/K607R and S542R/K548V/N552R that can cleave target sites with TYCV/CCCC and TATV PAMs, respectively, with enhanced activities in vitro and in human cells. Genome-wide assessment of off-target activity indicated that these variants retain a high level of DNA targeting specificity, which can be further improved by introducing mutations in non-PAM-interacting domains. Together, these variants increase the targeting range of AsCpf1 to one cleavage site for every ~8.7 bp in non-repetitive regions of the human genome, providing a useful addition to the CRISPR/Cas genome engineering toolbox.

synthetic biology↗