Biology subjects

Martin, S.

Publications and source records attributed to Martin, S..

At least 109 records · Page 6Linked to original sources

bioRxiv2020

Conserved and divergent features of DNA methylation in embryonic stem cell-derived neurons

DNA methylation functions in genome regulation and is implicated in neuronal maturation. Early post-natal accumulation of atypical non-CG methylation (mCH) occurs in neurons of mice and humans, but its precise function remains unknown. Here we investigate mCH deposition in neurons derived from mouse ES-cells in vitro and in cultured primary mouse neurons. We find that both acquire comparable levels of mCH over a similar period as in vivo. In vitro mCH deposition occurs concurrently with a transient increase in Dnmt3a expression, is preceded by expression of the post-mitotic neuronal marker Rbfox3 (NeuN) and is enriched at the nuclear lamina. Despite these similarities, whole genome bisulfite sequencing reveals that mCH patterning in mESC-derived neurons partially differs from in vivo. mESC-derived neurons therefore represent a valuable model system for analyzing the mechanisms and functional consequences of correct and aberrantly deposited CG and non-CG methylation in neuronal maturation.

genomics↗

bioRxiv2019

Dynamic changes in rhythmic and arrhythmic neural signatures in the subthalamic nucleus induced by anaesthesia and intubation

BackgroundSubcortical structures including the basal ganglia have been proposed to be crucial for arousal, consciousness, and behavioural responsiveness. However, how basal ganglia contributes to the loss and recovery of consciousness during anaesthesia has not been well characterized.\n\nMethodsIn this study, using local field potentials (LFPs) from subthalamic nucleus (STN) and scalp electroencephalogram in 12 Parkinsons disease patients, we investigate STN neural signatures during propofol general anaesthesia and during intubation as an arousal intervention in anaesthesia.\n\nResultsPropofol-induced anaesthesia resulted in changes in multiple frequency bands in STN LFPs, including increased low-frequency activities (slow-wave oscillation, delta, theta, and alpha bands) and decreased higher-frequency activities. This was also accompanied by increased STN-frontal cortical coherence in alpha frequency band. Beta and high-gamma activities in the STN temporally increased during intubation compared to the status of loss of consciousness. We also show that the dynamic changes in the high frequency activities (80-180 Hz) in STN LFPs induced by propofol and intubation correlated with power-law exponent in the power spectra between 2 and 80 Hz.\n\nConclusionsOur findings suggest that anaesthesia and intubation induced changes in the STN LFPs in multiple frequency bands. They are also consistent with the hypothesis that the power-law exponent in the power spectra between 2 and 80 Hz reflect the excitation/inhibition balance in the STN, which is modulated by anaesthesia and intubation, and further modulate the high frequency activity.

neuroscience↗

bioRxiv2019

Epitranscriptomic regulation of the response to the air pollutant naphthalene in mouse lungs: from the perspectives of specialized translation and tolerance linked to the writer ALKBH8

BackgroundThe epitranscriptomic writer Alkylation Repair Homolog 8 (ALKBH8) is a tRNA methyltransferase that modifies the wobble uridine of selenocysteine tRNA to promote the specialized translation, via stop codon recoding, of proteins that contain selenocysteine. Corresponding selenoproteins play critical roles in protecting against reactive oxygen species and environmental stress. Using a novel animal model deficient in Alkbh8, we have investigated the importance of epitranscriptomic systems in the response to naphthalene (NA), an abundant polycyclic aromatic hydrocarbon, glutathione depleter and lung toxicant found in tobacco smoke, gasoline and mothballs.\n\nObjectivesOur goal was to define the molecular reprogramming of Alkbh8 deficient (Alkbh8def) mice and evaluate the roles that the epitranscriptomic writer ALKBH8 and selenoproteins play in mitigating NA-induced toxicity and lung dysfunction.\n\nMethodsWe performed basal lung analysis and NA exposure studies using WT, Alkbh8def and Cyp2abfgs-null mice, the latter of which lack the cytochrome P450 enzymes required for NA bioactivation. We characterized gene expression, molecular markers of damage, viability and tolerance to NA.\n\nResultsUnder basal conditions, lungs from Alkbh8def mice have increased oxidation-reduction potential (ORP) and 8-isoprostane levels, and have reprogrammed at the molecular level to display increased stress response transcripts. In addition, the ALKBH8 writer deficient lungs have a decreased GSH/GSSG ratio. Alkbh8def mice are more sensitive to NA than WT, showing higher susceptibility to lung damage both at the cellular and molecular levels. WT mice develop a tolerance to NA after 3 days, defined as resistance to a high challenging dose after repeated exposures, which is absent in Alkbh8def mice, with writer deficient not surviving NA exposure.\n\nDiscussionWe conclude that the epitranscriptomic writer ALKBH8 plays a protective role against NA-induced lung dysfunction and promotes NA tolerance. Our work provides an early example of how epitranscriptomic systems can regulate the response to environmental stress in vivo.

molecular biology↗

bioRxiv2019

Optogenetics reveals Cdc42 local activation by scaffold-mediated positive feedback and Ras GTPase

The small GTPase Cdc42 is critical for cell polarization. Scaffold-mediated positive feedback regulation was proposed to mediate symmetry-breaking to a single active zone in budding yeast cells. In rod-shaped fission yeast S. pombe cells, active Cdc42-GTP localizes to both cell poles, where it promotes bipolar growth. Here, we implement the CRY2-CIBN optogenetic system for acute light-dependent protein recruitment to the plasma membrane, which allowed to directly demonstrate positive feedback. Indeed, optogenetic recruitment of constitutively active Cdc42 leads to co-recruitment of the GEF Scd1, in a manner dependent on the scaffold protein Scd2. We show that Scd2 function is completely bypassed and positive feedback restored by an engineered interaction between the GEF and a Cdc42 effector, the Pak1 kinase. Remarkably, such re-wired cells are viable and grow in a bipolar manner even when lacking otherwise essential Cdc42 activators. Interestingly, these cells reveal that Ras1 GTPase plays a dual role in localizing and activating the GEF, thus potentiating the feedback. We conclude that scaffold-mediated positive feedback, gated by Ras activity, is minimally required for rod-shape formation.

cell biology↗

bioRxiv2019

Beta-driven closed-loop deep brain stimulation can compromise human motor behavior in Parkinson’s Disease

Closed-loop or adaptive deep brain stimulation (DBS) for Parkinsons Disease (PD) has shown comparable clinical improvements to continuous stimulation, yet with less stimulation times and side effects. In this form of control, stimulation is driven by pathological beta oscillations recorded from the subthalamic nucleus, which have been shown to correlate with PD motor symptoms. An important consideration is that beta activity is itself modulated during volitional movements, yet it is unknown the impact that these volitional modulations may have on the efficacy of closed-loop systems. Here, three PD patients performed a functional reaching task during closed-loop stimulation while we measured their motor behavior. Our results show that closed-loop stimulation can alter motor performance at distinct movement intervals. Of particular relevance, closed-loop DBS compromised behavior during the returning period by increasing the amount of submovements executed, and in turn delayed movement termination. Following these findings, we hypothesize that the use of machine learning decoding different movement intervals to fully switch off the stimulator may be beneficial, and present here an exemplary approach decoding the initiation of the movement returning interval above chance level. These findings highlight the importance of evaluating these systems during functional tasks, and the need of extracting more robust biomarkers encoding ongoing symptoms or tasks execution intervals.

neuroscience↗

bioRxiv2019

Alvis: a tool for contig and read ALignment VISualisation and chimera detection

BackgroundThe analysis of long reads or the assessment of assembly or target capture data often necessitates running alignments against reference genomes or gene sets. Aligner outputs are often parsed automatically by scripts, but many kinds of analysis can benefit from the understanding that can follow human inspection of individual alignments.\n\nFindingsWe developed Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in the most common alignment formats and will output production ready vector images. Additionally, Alvis will highlight potentially chimeric reads or contigs, a common source of misassemblies. We found that splitting chimeric reads using the output provided by Alvis can improve the contiguity of assemblies, while maintaining correctness.

bioinformatics↗

bioRxiv2019

Capping protein insulates Arp2/3-assembled actin patches from formins

How actin structures of distinct identities and functions co-exist within the same environment is a critical self-organization question. Fission yeast cells have a simple actin cytoskeleton made of four structures: Arp2/3 assembles actin patches around endocytic pits; the formins For3, Cdc12 and Fus1 assemble actin cables, the cytokinetic ring during division, and the fusion focus during sexual reproduction, respectively. The focus concentrates the delivery of hydrolases by myosin V to digest the cell wall for cell fusion. We discovered that cells lacking capping protein (CP), a heterodimer that blocks barbed-end dynamics and associates with actin patches, exhibit a delay in fusion. Consistent with CP-formin competition for barbed-end binding, Fus1, F-actin and the linear filament marker tropomyosin hyper-accumulate at the fusion focus in absence of CP. However, myosin V and exocytic cargoes are diverted to ectopic foci and reduced at the fusion focus, which underlies the fusion defect. Remarkably, ectopic foci coincide with actin patches, which now contain low levels of Fus1. During mitotic growth, actin patches lacking CP similarly display a dual identity, as they accumulate the formins For3 and Cdc12 and are co-decorated by tropomyosin and the patch marker fimbrin. Thus, CP serves to protect Arp2/3-nucleated structures from formin activity.

cell biology↗

bioRxiv2019

Scientific evaluation of negative exome sequencing followed by systematic scoring of candidate genes to decipher the genetics of neurodevelopmental disorders

BackgroundDeciphering the monogenetic causes of neurodevelopmental disorders (NDD) is an important milestone to offer personalized care. But the plausibility of reported candidate genes in exome studies often remains unclear, which slows down progress in the field.\n\nMethodsWe performed exome sequencing (ES) in 198 cases of NDD. Cases that remained unresolved (n=135) were re-investigated in a research setting. We established a candidate scoring system (CaSc) based on 12 different parameters reflecting variant and gene attributes as well as current literature to rank and prioritize candidate genes.\n\nResultsIn this cohort, we identified 158 candidate variants in 148 genes with CaSc ranging from 2 to 11.7. Only considering the top 15% of candidates, 14 genes were already published or funneled into promising validation studies.\n\nConclusionsWe promote that in an approach of case by case re-evaluation of primarily negative ES, systematic and standardized scoring of candidate genes can and should be applied. This simple framework enables better comparison, prioritization, and communication of candidate genes within the scientific community. This would represent an enormous benefit if applied to the tens of thousands of negative ES performed in routine diagnostics worldwide and speed up deciphering the monogenetic causes of NDD.

genetics↗

bioRxiv2019

Linalool acts as a fast and reversible anesthetic in Hydra

The ability to make transgenic Hydra lines has opened the door for quantitative in vivo studies of Hydra regeneration and physiology. These studies commonly include excision, grafting and transplantation experiments along with high-resolution imaging of live animals, which can be challenging due to the animals response to touch and light stimuli. While various anesthetics have been used in Hydra studies over the years, they tend to be toxic over the course of a few hours or their long-term effects on animal health have not been studied. Here we show that the monoterpenoid linalool is a useful anesthetic for Hydra. Linalool is easy to use, non-toxic, fast acting, and reversible. It has no detectable long-term effects on cell viability or cell proliferation. We demonstrate that the same animal can be immobilized in linalool multiple times at intervals of several hours for repeated imaging over 2-3 days. This uniquely allows for in vivo imaging of dynamic processes such as head regeneration. We further directly compare linalool to currently used anesthetics and show its superior performance. Because linalool, which is frequently utilized in perfumes and cosmetic products, is also non-hazardous to humans, it will be a useful tool for Hydra research in both research and teaching contexts.

pharmacology and toxicology↗

bioRxiv2019

Multi-phosphorylation reaction and clustering tune Pom1 gradient mid-cell levels according to cell size

Protein concentration gradients convey information at a distance from the source to both pattern developing organisms and organize single cells. In the rod-shaped cells of Schizosaccharomyces pombe, the DYRK-family kinase Pom1 forms concentration gradients with maxima at the cell poles. Pom1 controls the timing of mitotic entry by inhibiting the SAD-family kinase Cdr2, which forms stable membrane-associated nodes at mid-cell. Pom1 gradients rely on membrane association regulated by a phosphorylation-dephosphorylation cycle and lateral diffusion modulated by clustering. Whether the graded pattern directly alters Pom1 medial levels has been controversial. Here, using a combination of quantitative imaging approaches, including single particle tracking PALM and TIRF microscopy, we find that individual Pom1 molecules do not bind the membrane long enough to diffuse from cell pole to cell middle. Instead we propose they exchange within longer-lived clusters that form the functional gradient units. By creating an allelic series progressively blocking auto-phosphorylation, we show that multi-phosphorylation shapes and buffers the gradient to control the cortical mid-cell Pom1 levels, which represent the critical pool regulating Cdr2. Specific imaging of this cortical pool by TIRF microscopy demonstrates that more Pom1 overlaps with Cdr2 nodes in short than long cells, consistent with Pom1 inhibition of Cdr2 decreasing with cell growth. We conclude that Pom1 gradients modulate Pom1 mid-cell levels according to cell size.

cell biology↗

bioRxiv2018

Disentangling the origins of confidence in speeded perceptual judgments through multimodal imaging

The human capacity to compute the likelihood that a decision is correct - known as metacognition - has proven difficult to study in isolation as it usually co-occurs with decision-making. Here, we isolated post-decisional from decisional contributions to metacognition by combining a novel paradigm with multimodal imaging. Healthy volunteers reported their confidence in the accuracy of decisions they made or decisions they observed. We found better metacognitive performance for committed vs. observed decisions, indicating that committing to a decision informs confidence. Relying on concurrent electroencephalography and hemodynamic recordings, we found a common correlate of confidence following committed and observed decisions in the inferior frontal gyrus, and a dissociation in the anterior prefrontal cortex and anterior insula. We discuss these results in light of decisional and post-decisional accounts of confidence, and propose a generative model of confidence in which metacognitive performance naturally improves when evidence accumulation is constrained upon committing a decision.

neuroscience↗

bioRxiv2018

Actomyosin-II facilitates long-range retrograde transport of large cargoes by controlling axonal radial contractility

Most mammalian neurons have a narrow axon, which constrains the passage of large cargoes such as autophagosomes that can be larger than the axon diameter. Radial axonal expansion must therefore occur to ensure efficient axonal trafficking. In this study we consistently find that the trafficking speed of various large axonal cargoes is significantly slower than that of small ones, and reveal that the transit of diverse-sized cargoes causes an acute, albeit transient axonal radial expansion, which is immediately restored by constitutive contractility. Using live super-resolution microscopy, we demonstrate that actomyosin-II controls axonal radial contractility and local expansion, and that NM-II filaments associate with periodic F-actin rings via their head domains. Pharmacological inhibition of NM-II activity, significantly increases axon diameter by detaching the NM-II from F-actin, and impacts the trafficking speed, directionality, and overall efficiency of long-range retrograde trafficking. Consequently, prolonged disruption of NM-II activity leads to disruption of periodic actin rings and formation of focal axonal swellings, a hallmark of axonal degeneration.\n\nSummaryAxonal radial contractility and local expansion control the retrograde trafficking of large cargoes. The periodic actomyosin-II network comprises of NM-II filaments and F-actin rings. Loss of actomyosin-II-mediated radial contractility causes defects in axonal trafficking and stability, leading to degeneration.

neuroscience↗

bioRxiv2018

Coherence-based spectro-spatial fillters for stimulus features prediction from electrocorticographic recordings.

The traditional approach in neuroscience relies on encoding models where brain responses to different stimuli are related to the latter to establish reproducible dependencies. To reduce neuronal and experimental noise, brain signals are usually averaged across trials to detect reliable and coherent brain activity. However, neural representations of stimulus features can be spread over time, frequency, and space, motivating the use of alternative methods that relate stimulus features to brain responses. We propose a Coherence-based spectro-spatial filter method that reconstructs stimulus features from intracortical brain signals. The proposed method models trials of an experiment as realizations of a random process and extracts patterns that are common across brain signals and the presented stimuli. These patterns, originating from different recording sites, are then combined (spatial filtering) to form a final prediction. Our results from three different cognitive tasks (motor movements, speech perception and speech production), concur to show that the proposed method significantly improves the ability to predict stimulus features over traditional methods such as multilinear regression with distributed lags and artificial neural networks. Furthermore, analyses of the model parameters show anatomical discriminability for execution of different motor movements. This anatomical discriminability is also observed in the perception and production of different words. These features could be exploited in the design of neuroprosthesis, as well as for exploring normal brain functioning.

neuroscience↗

bioRxiv2018

A TauP301L mouse model of dementia; development of pathology, synaptic transmission, microglial response and cognition throughout life

BackgroundLate stage Alzheimers disease and other dementias are associated with neurofibrillary tangles and neurodegeneration. Here we describe a mouse (TauD35) carrying human Tau with the P301L mutation that results in Tau hyperphosphorylation and tangles. Previously we have compared gene expression in TauD35 mice to mice which develop plaques but no tangles. A similar comparison of other pathological features throughout disease progression is made here between amyloid{beta} and Tau mice described in Parts I and II of this study.\n\nMethodsIn vitro CA1 patch clamp and field recordings were used to investigate synaptic transmission and plasticity. Plaque load and microglia were investigated with immunohistochemistry. Cognition, locomotor activity and anxiety-related behaviours were assessed with a forced-alternation T-maze, open field and light/dark box.\n\nResultsTransgene copy number in TauD35 mice fell into two groups (HighTAU and LowTAU), allowing assessment of dose-dependent effects of overexpression and resulting in tangle load increasing 100-fold for a 2-fold change in protein levels. Tangles were first detected at 8 (HighTAU) or 13 months (LowTAU) but the effects on synaptic transmission and plasticity and behaviour were subtle. However severe neurodegeneration occurred in HighTAU mice at around 17 months preceded by considerable proliferation but little additional activation of microglia. Proliferation only started as neurodegeneration began at 13 months. Similarly to HighTau mice at 13 months of age, LowTAU mice at 24 months of age showed a comparable tangle load and microglial proliferation. However, LowTAU mice showed no neurodegeneration at this stage and considerable microglial activation, stressing the dependence of these effects on overexpression and/or age.\n\nConclusionsComparison of the effects of amyloid{beta} and plaques without tangles in a model of preclinical Alzheimers disease to the effects of tangles without amyloid{beta} plaques in the late stage model described here may clarify the progressive stages of Alzheimers disease. While Tau hyperphosphorylation and neurofibrillary tangles are eventually sufficient to cause severe neurodegeneration, initial effects on synaptic transmission and the immune response are subtle. In contrast while even with a heavy plaque load little if any neurodegeneration occurs, considerable effects on synaptic transmission and the immune system result, even before plaques are detectable.

neuroscience↗

bioRxiv2018

Differential contributions of subthalamic beta rhythms and neural noise to Parkinson motor symptoms

BackgroundExcessive beta oscillatory activity in the subthalamic nucleus (STN) is linked to Parkinsons disease and associated motor symptoms. However, the relationship between beta activity and motor symptoms has been inconsistent, which may influence the efficacy of closed-loop deep brain stimulation.\n\nHypothesisWe hypothesized that this variability is due to the degree of neural noise in STN recordings. Recent evidence has shown that neural noise is influenced by multiple factors, such as development, aging and disease, and could confound measures of beta activity. In this work, we propose a model that disentangles beta oscillatory activity and neural noise in the STN power spectrum.\n\nMethodsWe investigated the impact of neural noise on estimations of beta activity and motor symptoms from data recorded bilaterally from the subthalamic nuclei of thirteen Parkinsonian patients.\n\nResultsResults showed that the relationship between beta oscillatory amplitude and motor symptoms (bradykinesia and rigidity) significantly improved when neural noise was removed from the estimation of beta activity.\n\nConclusionThese findings emphasize the importance of modeling neural components independently for understanding physiological processes associated with Parkinsons disease, and identifying better biomarkers for characterizing symptom severity. Subsequently, we predict that our findings can have a direct application for closed-loop deep brain stimulation on Parkinsons Disease.

neuroscience↗

bioRxiv2018

Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation

Global loss of DNA methylation and CpG island (CGI) hypermethylation are regarded as key epigenomic aberrations in cancer. Global loss manifests itself in partially methylated domains (PMDs) which can extend up to megabases. However, the distribution of PMDs within and between tumor types, and their effects on key functional genomic elements including CGIs are poorly defined. Using whole genome bisulfite sequencing (WGBS) of breast cancers, we comprehensively show that loss of methylation in PMDs occurs in a large fraction of the genome and represents the prime source of variation in DNA methylation. PMDs are hypervariable in methylation level, size and distribution, and display elevated mutation rates. They impose intermediate DNA methylation levels incognizant of functional genomic elements including CGIs, underpinning a CGI methylator phenotype (CIMP). However, significant repression effects on cancer-genes are negligible as tumor suppressor genes are generally excluded from PMDs. The genomic distribution of PMDs reports tissue-of-origin of different cancers and may represent tissue-specific silent regions of the genome, which tolerate instability at the epigenetic, transcriptomic and genetic level.

cancer biology↗

bioRxiv2017

Molecular mechanism of the dual regulation of bacterial iron sulfur cluster biogenesis by CyaY and IscX

IscX (or YfhJ) is a protein of unknown function which takes part in the iron-sulfur cluster assembly machinery, a highly specialised and essential metabolic pathway. IscX binds to iron with low affinity and interacts with IscS, the desulfurase central to cluster assembly. Previous studies have suggested a competition between IscX and CyaY, the bacterial ortholog of frataxin, for the same binding surface of IscS. This competition could suggest a link between the two proteins with a functional significance. Using a hybrid approach, we show here that IscX is a modulator of the inhibitory properties of CyaY: by competing for the same site on IscS, the presence of IscX rescues the rates of enzymatic cluster formation which are inhibited by CyaY. The effect is stronger at low iron concentrations, whereas it becomes negligible at high iron concentrations. These results strongly suggest that iron-sulfur cluster assembly is an exquisite example of an enzymatic process which requires a double regulation under the control of iron as the effector.

biophysics↗

bioRxiv2017

Growth hormone transgenesis disrupts immune function in muscle of coho salmon (Oncorhynchus kisutch) impacting cross-talk with growth systems

The suppression of growth during infection should facilitate resource allocation towards effective immune function. Work supporting this hypothesis has been recently reported in teleosts, demonstrating immune-responsive regulation of the insulin-like growth factor (IGF) system - a key endocrine growth pathway that acts downstream of growth hormone (GH). Skeletal muscle is the main target for growth and energetic storage in fish, yet little is known about how growth is regulated in this tissue during an immune response. We addressed this knowledge gap by characterizing muscle immune responses in size-matched coho salmon (Oncorhynchus kisutch) achieving different growth rates. We compared a wild-type strain with two GH transgenic groups achieving either maximal or highly-suppressed growth - an experimental design that separates GHs direct effects from its influence on growth rate. Fish were sampled 30h post-injection with PBS (control) or mimics of bacterial (peptidoglycan) or viral (Poly:IC) infection. We quantified the mRNA level expression of genes from the GH, GH receptor (GHR), IGF hormone, IGF1 receptor (IGF-1R) and IGF binding protein (IGFBP) families, along with marker genes for muscle growth and host defence genes involved in inflammatory or antiviral responses. We provide strong evidence for dampened immunity in the GH transgenics compared to wild-type animals. Strikingly, the muscle of GH transgenics achieving rapid growth showed no detectable antiviral response, coupled with evidence of a constitutive inflammatory state. GH and IGF system gene expression was also strongly altered by GH transgenesis and fast growth, both for baseline expression levels and responses to immune stimulation. Overall, our findings demonstrate that GH transgenesis disrupts normal immune function and growth-immune cross-talk in muscle, with implications for the health and welfare of farmed salmon.

physiology↗