Biology subjects

Martin, L.

Publications and source records attributed to Martin, L..

At least 55 records · Page 3Linked to original sources

bioRxiv2022

Super-resolution mass spectrometry enables rapid, accurate, and highly-multiplexed proteomics at the MS2-level

In tandem mass spectrometry (MS2)-based multiplexed quantitative proteomics, the complement reporter ion approaches (TMTc and TMTproC) were developed to eliminate the ratio-compression problem of conventional MS2 level approaches. Resolving all high m/z complement reporter ions ([~]6.32 mDa spaced) requires mass resolution and scan speeds above the performance levels of Orbitrap instruments. Therefore, complement reporter ion quantification with TMT/TMTpro reagents is currently limited to 5 out of 11 (TMT) or 9 out of 18 (TMTpro) channels ([~]1 Da spaced). We first demonstrate that a Fusion Lumos Orbitrap can resolve 6.32 mDa spaced complement reporter ions with standard acquisition modes extended with 3-second transients. We then implemented a super-resolution mass spectrometry approach using the least-squares fitting (LSF) method for processing Orbitrap transients to achieve shotgun proteomics-compatible scan rates. The LSF performance resolves the 6.32 mDa doublets for all TMTproC channels in the standard mass range with transients as short as [~]108 ms (Orbitrap resolution setting of 50 000 at m/z 200). However, we observe a slight decrease in measurement precision compared to 1 Da spacing with the 108 ms transients. With 256 ms transients (resolution of 120 000 at m/z 200), coefficients of variation are essentially indistinguishable from 1 Da samples. We thus demonstrate the feasibility of highly-multiplexed, accurate, and precise shotgun-proteomics at the MS2 level.

systems biology↗

bioRxiv2022

Hippocampal blood flow rapidly and preferentially increases after a bout of moderate-intensity exercise in older adults with poor cerebrovascular health

Over the course of aging, there is an early degradation of cerebrovascular health that may be attenuated with aerobic exercise training. Yet, the acute cerebrovascular response to a single bout of exercise remains elusive, particularly within key brain regions most affected by age-related disease processes. We investigated the acute global and region-specific cerebral blood flow (CBF) response to 15 minutes of moderate-intensity aerobic exercise in older adults ([≥]65years) (n=60) using arterial spin labeling magnetic resonance imaging. Within 0-6 minutes post-exercise, CBF decreased across all regions, an effect that was attenuated in the hippocampus. The exercise-induced CBF drop was followed by a rebound effect over the 24-minute post-exercise assessment period, an effect that was most robust in the hippocampus. Individuals with low baseline perfusion demonstrated the greatest hippocampal-specific CBF effect post-exercise, showing no immediate drop and a rapid increase in CBF that exceeded baseline levels within 6-12 minutes post-exercise. Gains in domain-specific cognitive performance post-exercise were not associated with changes in regional CBF, suggesting dissociable effects of exercise on acute neural and vascular plasticity. Together, the present findings support a precision-medicine framework for the use of exercise to target brain health that carefully considers age-related changes in the cerebrovascular system.

systems biology↗

bioRxiv2022

Intestinal norovirus binding patterns in non-secretor individuals

Human norovirus (HuNoV) infection is associated with active FUT2 status, which characterizes the secretor phenotype. However, non-secretor individuals are also affected by HuNoV infection although in a lesser proportion. Here, we study GII.3, GII.4 and GII.17 HuNoV interactions in non-secretor individuals using baculovirus-expressed virus-like particles (VLPs). Only GII.4 HuNoV specifically interacted with non-secretor saliva. Competition experiments using HBGA-specific mAbs demonstrate that GII.4 VLPs recognized the Lewis a antigen (Lea). We also analyzed HuNoV VLP interactions on duodenum tissue blocks from healthy non-secretor individuals. VLP binding was observed for the three HuNoV genotypes in 10 of the 13 individuals, and competition experiments demonstrated that VLP recognition was driven by interaction with the Lea antigen. In 3 individuals, binding was restricted to either GII.4 alone or GII.3 and GII.17. One patient did not display VLP binding for any of the three genotypes. Finally, we performed a VLP binding assay on proximal and distal colon tissue blocks from a non-secretor patient with Crohns disease. VLP binding to inflammatory tissues was genotype-specific since GII.4 and GII.17 VLPs were able to interact with regenerative mucosa whereas GII.3 VLP was not. Binding of GII.4 and GII.17 HuNoV VLPs was linked to Lea in regenerative mucosae from the proximal and distal colon. Overall, our data clearly showed that Lea has a pivotal role in the recognition of HuNoV in non-secretors. We also showed that Lea is expressed in inflammatory/regenerative tissues and that it can interact with HuNoV in secretor and non-secretor individuals. The physiological and immunological consequences of such interactions in non-secretors has yet to be elucidated. IMPORTANCEHuman norovirus (HuNoV) is the main etiological agent of viral gastroenteritis in all age classes. HuNoV infection mainly affects secretor individuals, who are characterized by the presence of the ABO(H) and Lewis histo-blood group antigens at the surface of the small intestine. Non-secretor individuals, who only express Lewis antigens (Le), are less susceptible to HuNoV infection. Here we study the interaction of three frequently encountered HuNoV genotypes (GII.3, GII.4 and GII.17) in non-secretor individual using baculovirus-expressed viral particles. Preliminary saliva binding assays showed that only GII.4 interacted with non-secretor saliva via the Lea antigen. Surprisingly, in the binding assays on duodenal tissue blocks, the three genotypes interacted with non-secretor enterocytes via Lea. This suggests that HBGA status in the saliva does not necessarily reflect interactions in the intestines and, secondly, that Lea plays a pivotal role in HuNoV attachment in non-secretors. Similarly, Lea was involved in the recognition of GII.4 and GII.17 HuNoV particles by inflammatory colon tissue from a non-secretor Crohns disease patient. The molecular implications of HuNoV binding in non-secretors remains to be elucidated in physiological and pathological conditions encountered in other intestinal diseases.

microbiology↗

bioRxiv2022

DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas

Registration of data to a common frame of reference is an essential step in the analysis and integration of diverse neuroscientific data modalities. To this end, volumetric brain atlases enable histological datasets to be spatially registered and analysed, yet accurate registration remains expertise-dependent and slow. We have trained a neural network, DeepSlice, to register mouse brain histology to the Allen Brain Atlas, retaining accuracy while improving speed by >1000 fold.

neuroscience↗

bioRxiv2022

Melanocortin receptor agonist melanotan-II microinjected in the nucleus accumbens decreases appetitive and consumptive responding for food

Rationale. Obesity is a major health problem worldwide. An understanding of the factors that drive feeding behaviors is key to the development of pharmaceuticals to decrease appetite and consumption. Proopiomelanocortin (POMC), the melanocortin peptide precursor, is essential in the regulation of body weight and ingestive behaviors. Deletion of POMC or impairment of melanocortin signaling in the brain results in hyperphagic obesity. Neurons in the hypothalamic arcuate nucleus produce POMC and project to many areas including the nucleus accumbens (NAcc), which is well established in the rewarding and reinforcing effects of both food and drugs of abuse. ObjectiveThese studies sought to determine the role of melanocortins in the NAcc on consumption of and motivation to obtain access to standard rodent chow. MethodsMale, C57BL/6J mice were microinjected bilaterally into the NAcc (100 nl/side) with the melanocortin receptor 3/4 agonist melanotan-II (MT-II; 0.1, 0.3, and 1 nmol), and ingestive behaviors were examined in both home cage and operant food self-administration experiments. In addition, the ability of MT-II in the NAcc to produce aversive properties or affect metabolic rate were tested. ResultsMT-II injected into the NAcc significantly decreased consumption in both home cage and operant paradigms, and furthermore decreased appetitive responding to gain access to food. There was no development of conditioned taste avoidance or change in metabolic parameters following anorexic doses of MT-II. Conclusions. MT-II in the NAcc decreased both the motivation to eat and the amount of food consumed without inducing an aversive state or affecting metabolic rate, suggesting a role for melanocortin signaling in the ventral striatum that is selective for appetite and satiety without affecting metabolism or producing an aversive state.

neuroscience↗

bioRxiv2021

Electrophysiological correlates of proactive and reactive inhibition in a modified visual Go/NoGo task

Impulse control is crucial for everyday functioning in modern society. People with borderline personality disorder (BPD) suffer from impulse control impairment. According to the theory of dual mechanisms of control, motor impulse control can be divided into proactive and reactive modes. Proactive inhibition is involved before an event that might require inhibitory control. Reactive inhibition is initiated after the occurrence of an event that requires inhibitory control. Few studies have focused on proactive inhibition in relation to impaired impulse control, moreover electrophysiological evidence is scarce. Therefore, in the search for electrophysiological correlates of proactive and reactive inhibitions, we assessed event-related potentials elicited during a modified emotionally neutral visual Go/NoGo task in 28 clinically impulsive BPD patients and 35 healthy control (HC) subjects. In both groups, proactive inhibition was associated with enhanced late prestimulus activity and a suppressed poststimulus N2 component. In both groups, reactive inhibition was associated with enhanced poststimulus N2 and P3 components. We found no electrophysiological differences between HC subjects and BPD patients and both groups performed similarly in the task. Hence, the clinically observed impulse control impairment in BPD might act through different mechanisms other than altered inhibitory control in an emotionally neutral task.

neuroscience↗

bioRxiv2021

Germline loss-of-function variants in the base-excision repair gene MBD4 cause a Mendelian recessive syndrome of adenomatous colorectal polyposis and acute myeloid leukaemia

Inherited defects in base-excision repair (BER) predispose to adenomatous polyposis and colorectal cancer (CRC), yet our understanding of this important DNA repair pathway remains incomplete. By combining detailed clinical, histological and molecular profiling, we reveal biallelic germline loss-of-function (LOF) variants in the BER gene MBD4 to predispose to adenomatous polyposis and -uniquely amongst CRC predisposition syndromes- to myeloid neoplasms. Neoplasms from MBD4-deficient patients almost exclusively accumulate somatic CpG>TpG mutations, resembling mutational signature SBS1. MBD4-deficient adenomas harbour mutations in known CRC driver genes, although AMER1 mutations were more common and KRAS mutations less frequent. We did not find an increased risk for colorectal tumours in individuals with a monoallelic MBD4 LOF variant. We suggest that this condition should be termed MBD4-associated neoplasia syndrome (MANS) and that MBD4 is included in testing for the genetic diagnosis of polyposis and/or early-onset AML.

genetics↗

bioRxiv2021

Crosstalk between enterocytes and innate lymphoid cells drives early IFN-g-mediated control of Cryptosporidium

The intestinal parasite, Cryptosporidium, is a major contributor to global child mortality and causes opportunistic infection in immune deficient individuals. Innate resistance to Cryptosporidium, which specifically invades enterocytes, is dependent on the production of IFN-{gamma}, yet whether enterocytes contribute to parasite control is poorly understood. In this study, utilizing the natural mouse pathogen, Cryptosporidium tyzzeri, we show that epithelial-derived IL-18 synergized with IL-12 to stimulate innate lymphoid cell (ILC) production of IFN-{gamma}. This innate IFN-{gamma} was required for early parasite control. Loss of STAT1 in enterocytes, but not dendritic cells or macrophages, antagonized early parasite control. Transcriptional profiling of enterocytes from infected mice identified an IFN-{gamma} signature and enrichment of anti-microbial effectors like IDO, GBP and IRG. Deletion experiments identified a role for Irgm1/m3 in parasite control. Thus, enterocytes promote ILC production of IFN-{gamma} that acts on enterocytes to restrict the growth of C. tyzzeri.

immunology↗

bioRxiv2021

STAG proteins promote cohesin ring loading at R-loops.

Most studies of cohesin function consider the Stromalin Antigen (STAG/SA) proteins as core complex members given their ubiquitous interaction with the cohesin ring. Here, we provide functional data to support the notion that the SA subunit is not a mere passenger in this structure, but instead plays a key role in the localization of cohesin to diverse biological processes and promotes loading of the complex at these sites. We show that in cells acutely depleted for RAD21, SA proteins remain bound to chromatin, cluster in 3D and interact with CTCF, as well as with a wide range of RNA binding proteins involved in multiple RNA processing mechanisms. Accordingly, SA proteins interact with RNA and are localised to R-loops where they contribute to R-loop regulation. Our results place SA1 within R-loop domains upstream of the cohesin complex and reveal a role for SA1 in cohesin loading which is independent of NIPBL, the canonical cohesin loader. We propose that SA1 takes advantage of structural R-loop platforms to link cohesin loading and chromatin structure with diverse functions. Since SA proteins are pan-cancer targets, and R-loops play an increasingly prevalent role in cancer biology, our results have important implications for the mechanistic understanding of SA proteins in cancer and disease.

cell biology↗

bioRxiv2020

KLF10 integrates circadian timing and sugar signaling to coordinate hepatic metabolism

The mammalian circadian timing system and metabolism are highly interconnected, and disruption of this coupling is associated with negative health outcomes. Kruppel-like factors (KLFs) are transcription factors that govern metabolic homeostasis in various organs. Many KLFs show a circadian expression in the liver. Here, we show that the loss of the clock-controlled KLF10 in hepatocytes results in extensive reprogramming of the mouse liver circadian transcriptome, which in turn, alters the temporal coordination of pathways associated with energy metabolism. We also show that glucose and fructose induce Klf10, which helps mitigate glucose intolerance and hepatic steatosis in mice challenged with a sugar beverage. Functional genomics further reveal that KLF10 target genes are primarily involved in central carbon metabolism. Together, these findings show that in the liver, KLF10 integrates circadian timing and sugar metabolism related signaling, and serves as a transcriptional brake that protects against the deleterious effects of increased sugar consumption.

cell biology↗

bioRxiv2020

A recombinant protein SARS-CoV-2 candidate vaccine elicits high-titer neutralizing antibodies in macaques.

Vaccines that generate robust and long-lived protective immunity against SARS-CoV-2 infection are urgently required. We assessed the potential of vaccine candidates based on the SARS-CoV-2 spike in cynomolgus macaques (M. fascicularis) by examining their ability to generate spike binding antibodies with neutralizing activity. Antigens were derived from two distinct regions of the spike S1 subunit, either the N-terminal domain (NTD) or an extended C-terminal domain containing the receptor-binding domain (RBD) and were fused to the human IgG1 Fc domain. Three groups of 2 animals each were immunized with either antigen, alone or in combination. The development of antibody responses was evaluated through 20 weeks post-immunization. A robust IgG response to the spike protein was detected as early as 2 weeks after immunization with either protein and maintained for over 20 weeks. Sera from animals immunized with antigens derived from the RBD were able to prevent binding of soluble spike proteins to the ACE2 receptor, shown by in vitro binding assays, while sera from animals immunized with the NTD alone lacked this activity. Crucially, sera from animals immunized with the RBD but not the NTD had potent neutralizing activity against SARS-CoV-2 pseudotyped virus, with titers in excess of 10,000, greatly exceeding that typically found in convalescent humans. Neutralizing activity persisted for more than 20 weeks. These data support the utility of spike subunit-based antigens as a vaccine for use in humans.

immunology↗

bioRxiv2020

Specific norovirus interaction with Lewis x and Lewis a on human intestinal inflammatory mucosa during refractory inflammatory bowel disease

Inflammatory bowel disease (IBD), which includes Crohn's disease (CD) and ulcerative colitis (UC), is related to immunological and microbial factors with the possible implication of enteric viruses. We characterize the interaction between human noroviruses (HuNoVs) and blood group antigens in refractory CD and UC using HuNoV Virus Like Particles (VLPs) and histological tissues. Immunohistochemistry was conducted on inflammatory tissue samples from the small intestine, colon and rectum in 15 CD and 9 UC patients. Analysis of the regenerative mucosa of the colon and rectum revealed strong expression of sialylated Lewis a (sLea) and Lewis x (sLex) antigens, and HuNoV VLP binding in the absence of ABO antigen expression in both UC and CD. Competition experiments using sialidase, lectins and monoclonal antibodies demonstrated that HuNoV attachment mostly involved Lea and to a lesser extent, Lex moieties on regenerative mucosa in both UC and CD. Further studies will be required to understand the implications of specific HuNoV binding to regenerative mucosa in refractory IBD. IMPORTANCEInflammatory Bowel Disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), are progressive diseases affecting millions of people each year. Flare-ups during IBD result in severe mucosal alterations of the small intestine (CD), colon and rectum (CD and UC). Immunohistochemical analysis of CD and UC samples showed strong expression of known tumoral markers, Sialyl-Lewis a (CA19.9) and Sialyl-Lewis x (CD15s) antigens on colonic and rectal regenerative mucosa, concurrent with strong human norovirus (HuNov) VLP GII.4 affinity. Sialidase treatment and competition experiments using HBGA-specific monoclonal antibodies and lectins clearly demonstrated the implication of the Lewis a moiety, and to a lesser extent Lewis x, in HuNov recognition in regenerative mucosa of CD and UC tissues. Further studies are required to explore the possible implications of enteric viruses in the impairment of epithelial repair and dysregulation of inflammatory pathways during severe IBD.

microbiology↗

bioRxiv2020

2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Study

Despite the advantages of fewer missing values by collecting fragment ion data on all analytes in the sample, as well as the potential for deeper coverage, the adoption of data-independent acquisition (DIA) in core facility settings has been slow. The Association of Biomolecular Resource Facilities conducted a large interlaboratory study to evaluate DIA performance in laboratories with various instrumentation. Participants were supplied with generic methods and a uniform set of test samples. The resulting 49 DIA datasets act as benchmarks and have utility in education and tool development. The sample set consisted of a tryptic HeLa digest spiked with high or low levels of four exogenous proteins. Data are available in MassIVE MSV000086479. Additionally, we demonstrate how the data can be analysed by focusing on two datasets using different library approaches and show the utility of select summary statistics. These data can be used by DIA newcomers, software developers, or DIA experts evaluating performance with different platforms, acquisition settings and skill levels.

bioinformatics↗

bioRxiv2020

Elevated somatic mutation burdens in normal human cells due to defective DNA polymerases

Mutation accumulation over time in normal somatic cells contributes to cancer development and is proposed as a cause of ageing. DNA polymerases Pol {varepsilon} and Pol {delta} replicate DNA with high fidelity during normal cell divisions. However, in some cancers defective proofreading due to acquired mutations in the exonuclease domains of POLE or POLD1 causes markedly elevated somatic mutation burdens with distinctive mutational signatures. POLE and POLD1 exonuclease domain mutations also cause familial cancer predisposition when inherited through the germline. Here, we sequenced normal tissue DNA from individuals with germline POLE or POLD1 exonuclease domain mutations. Increased mutation burdens with characteristic mutational signatures were found to varying extents in all normal adult somatic cell types examined, during early embryogenesis and in sperm. Mutation burdens were further markedly elevated in neoplasms from these individuals. Thus human physiology is able to tolerate ubiquitously elevated mutation burdens. Indeed, with the exception of early onset cancer, individuals with germline POLE and POLD1 exonuclease domain mutations are not reported to show abnormal phenotypic features, including those of premature ageing. The results, therefore, do not support a simple model in which all features of ageing are attributable to widespread cell malfunction directly resulting from somatic mutation burdens accrued during life.

genomics↗

bioRxiv2020

Full-field optical coherence tomography for the diagnosis of giant cell arteritis

Histopathological examination of temporal artery biopsy (TAB) remains the gold standard for the diagnosis of giant cell arteritis (GCA) but is associated with essential limitations that emphasize the need for an upgraded pathological process. This study pioneered the use of full-field optical coherence tomography (FF-OCT) for rapid and automated on-site pathological diagnosis of GCA. Sixteen TABs (12 negative and 4 positive for GCA) were selected according to major histopathological criteria of GCA following hematoxylin-eosin-saffron-staining for subsequent acquisition with FF-OCT to compare structural modifications of the artery cell wall and thickness of each tunica. Gabor filtering of FF-OCT images was then used to compute TAB orientation maps and validate a potential automated analysis of TAB sections. FF-OCT allowed both qualitative and quantitative visualization of the main structures of the temporal artery wall, from the internal elastic lamina to the vasa vasorum and red blood cells, unveiling a significant correlation with conventional histology. FF-OCT imaging of GCA TABs revealed destruction of the media with distinct remodeling of the whole arterial wall into a denser reticular fibrous neo-intima, which is distinctive of GCA pathogenesis and accessible through automated Gabor filtering. Rapid on-site FF-OCT TAB acquisition makes it possible to identify some characteristic pathological lesions of GCA within a few minutes, paving the way for potential machine intelligence-based or even non-invasive diagnosis of GCA.View Full Text

pathology↗

bioRxiv2020

Paternal multigenerational exposure to an obesogenic diet drives epigenetic predisposition to metabolic disorders

Obesity is a growing societal scourge responsible for approximately 4 million deaths worldwide. Recent studies have uncovered that paternal excessive weight induced by an unbalanced diet affects the metabolic health of offspring. These reports mainly employed single-generation male exposure. However, the consequences of multigenerational unbalanced diet feeding on the metabolic health of progeny remain largely unknown. Here, we show that maintaining paternal western diet feeding for five consecutive generations in mice induces a gradual enhancement in fat mass and related metabolic diseases over generations. Strikingly, chow-diet-fed progenies from these multigenerational western-diet-fed males develop a "healthy" overweight phenotype that is not reversed after 4 subsequent generations. Mechanistically, sperm RNA microinjection experiments into zygotes suggest that sperm RNAs are sufficient for establishment but not for long-term maintenance of epigenetic inheritance of metabolic pathologies. Progressive and permanent metabolic deregulation induced by successive paternal western-diet-fed generations may contribute to the worldwide epidemic of metabolic diseases.

genetics↗

bioRxiv2020

Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication

Sheep was among the first domesticated animals, but its demographic history is little understood. Here we present combined analyses of mitochondrial and nuclear polymorphism data from ancient central and west Anatolian sheep dating to the Late Glacial and early Holocene. We observe loss of mitochondrial haplotype diversity around 7500 BCE during the early Neolithic, consistent with a domestication-related bottleneck. Post-7000 BCE, mitochondrial haplogroup diversity increases, compatible with admixture from other domestication centres and/or from wild populations. Analysing archaeogenomic data, we further find that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds, and especially those from central and north Europe. Our results indicate that Asian contribution to south European breeds in the post-Neolithic era, possibly during the Bronze Age, may explain this pattern.

evolutionary biology↗

bioRxiv2020

Disruption of AtHAK/KT/KUP9 enhances plant cesium accumulation under low potassium supply

Understanding molecular mechanisms which underlie transport of cesium (Cs+) in plants is important to limit entry of its radioisotopes from contaminated area to the food chain. The potentially toxic element Cs+, which is not involved in any biological process, is chemically closed to the macronutrient potassium (K+). Among the multiple K+ carriers, the high-affinity K+ transporters family HAK/KT/KUP is thought to be relevant in mediating opportunistic Cs+ transport. On the 13 KUP identified in Arabidopsis thaliana, only HAK5, the major contributor to root K+ acquisition under low K+ supply, has been functionally demonstrated to be involved in Cs+ uptake in planta. In the present study, we showed that accumulation of Cs+ increased by up to 30% in two A. thaliana mutant lines lacking KUP9 and grown under low K+ supply. Since further experiments revealed that Cs+ release from contaminated plants to the external medium is proportionally lower in the two kup9 mutants, we proposed that KUP9 disruption could impair Cs+ efflux. By contrast, we did not measure significant impairment of K+ status in kup9 mutants suggesting that KUP9 disruption does not alter substantially K+ transport in experimental conditions used here. Putative primary role of KUP9 in plants is further discussed.

plant biology↗