Biology subjects

Martin, C.

Publications and source records attributed to Martin, C..

At least 109 records · Page 6Linked to original sources

bioRxiv2020

Herpes Simplex Virus type 1 neuronal infection triggers disassembly of key structural components of dendritic spines

Herpes simplex virus type 1 (HSV-1) is a widespread neurotropic virus. The primary infection in facial epithelium leads to retrograde axonal transport to the central nervous system (CNS) where it establishes latency. Under stressful conditions, the virus reactivates, and new progeny is transported anterogradely to the primary site of infection. In late stages of neuronal infection, axonal damage is known to occur. However, the impact of HSV-1 infection on morphology and functional integrity at earlier stages of infection in neuronal dendrites is unknown. Previously, we demonstrated that acute HSV-1 infection in neuronal cell lines selectively enhances the expression of Arc protein - a major regulator of long-term synaptic plasticity and memory consolidation, known for being a protein-interaction hub in the postsynaptic dendritic compartment. Thus, HSV-1 induced Arc may alter the functionality of the infected neurons having an impact on dendritic spine dynamics. In this study we demonstrated that HSV-1 infection causes structural disassembly and functional deregulation in cultured cortical neurons, through protein homeostasis alteration with intracellular accumulation of Arc, and decreased expression of spine scaffolding-like proteins such as PSD-95, Drebrin and CaMKII{beta}. Our findings reveal progressive deleterious effects of HSV-1 infection on excitatory neuronal synapse function and dendritic morphology, supporting the thesis of the infectious origin of neurodegenerative processes.

neuroscience↗

bioRxiv2020

A new perspective on the evolution of the interaction between the Vg/VGLL1-3 proteins and the TEAD transcription factors

The most downstream elements of the Hippo pathway, the TEAD transcription factors, are regulated by several cofactors, such as Vg/VGLL1-3. Earlier findings on human VGLL1 and here on human VGLL3 show that these proteins interact with TEAD via a conserved amino acid motif called the TONDU domain. Surprisingly, our studies reveal that the TEAD-binding domain of Drosophila Vg and of human VGLL2 is more complex and contains an additional structural element, an {Omega}-loop, that contributes to TEAD binding and in vivo function. To explain this unexpected structural difference between proteins from the same family, we propose that, after the genome-wide duplications at the origin of vertebrates, the {Omega}-loop present in an ancestral VGLL gene has been lost in some VGLL variants. These findings illustrate how structural and functional constraints can guide the evolution of transcriptional cofactors to preserve their ability to compete with other cofactors for binding to transcription factors.

biochemistry↗

bioRxiv2020

A draft genome of grass pea (Lathyrus sativus), a resilient diploid legume

We have sequenced the genome of grass pea (Lathyrus sativus), a resilient diploid (2n=14) legume closely related to pea (Pisum sativum). We determined the genome size of the sequenced European accession (LS007) as 6.3 Gbp. We generated two assemblies of this genome, i) EIv1 using Illumina PCR-free paired-end sequencing and assembly followed by long-mate-pair scaffolding and ii) Rbp using Oxford Nanopore Technologies long-read sequencing and assembly followed by polishing with Illumina paired-end data. EIv1 has a total length of 8.12 Gbp (including 1.9 billion Ns) and scaffold N50 59,7 kbp. Annotation has identified 33,819 high confidence genes in the assembly. Rbp has a total length of 6.2 Gbp (with no Ns) and a contig N50 of 155.7 kbp. Gene space assessment using the eukaryote BUSCO database showed completeness scores of 82.8 % and 89.8%, respectively.

genomics↗

bioRxiv2020

A Solanum lycopersicoides reference genome facilitates biological discovery in tomato

Wild relatives of tomato are a valuable source of natural variation in tomato breeding, as many can be hybridized to the cultivated species (Solanum lycopersicum). Several, including Solanum lycopersicoides, have been crossed to S. lycopersicum for the development of ordered introgression lines (ILs). Despite the utility of these wild relatives and their associated ILs, limited finished genomes have been produced to aid genetic and genomic studies. We have generated a chromosome-scale genome assembly for Solanum lycopersicoides LA2951 using PacBio sequencing, Illumina, and Hi-C. We identified 37,938 genes based on Illumina and Isoseq and compared gene function to the available cultivated tomato genome resources, in addition to mapping the boundaries of the S. lycopersicoides introgressions in a set of cv. VF36 x LA2951 introgression lines (IL). The genome sequence and IL map will support the development of S. lycopersicoides as a model for studying fruit nutrient/quality, pathogen resistance, and environmental stress tolerance traits that we have identified in the IL population and are known to exist in S. lycopersicoides.

genomics↗

bioRxiv2020

A transcriptomic atlas of the mouse cerebellum reveals regional specializations and novel cell types

The cerebellum is a well-studied brain structure with diverse roles in motor learning, coordination, cognition, and autonomic regulation. Nonetheless, a complete inventory of cerebellar cell types is presently lacking. We used high-throughput transcriptional profiling to molecularly define cell types across individual lobules of the adult mouse cerebellum. Purkinje and granule neurons showed considerable regional specialization, with the greatest diversity occurring in the posterior lobules. For multiple types of cerebellar interneurons, the molecular variation within each type was more continuous, rather than discrete. For the unipolar brush cells (UBCs)--an interneuron population previously subdivided into two discrete populations--the continuous variation in gene expression was associated with a graded continuum of electrophysiological properties. Most surprisingly, we found that molecular layer interneurons (MLIs) were composed of two molecularly and functionally distinct types. Both show a continuum of morphological variation through the thickness of the molecular layer, but electrophysiological recordings revealed marked differences between the two types in spontaneous firing, excitability, and electrical coupling. Together, these findings provide the first comprehensive cellular atlas of the cerebellar cortex, and outline a methodological and conceptual framework for the integration of molecular, morphological, and physiological ontologies for defining brain cell types.

genomics↗

bioRxiv2020

Synaptic and supra-synaptic organisation of the dopaminergic projection to the striatum.

Dopamine is a monoamine involved in reward processing and motor control. Volume transmission is thought to be the mechanism by which monoamines modulate effector systems at glutamate and GABA synapses. Hence, dopamine synapses are scarcely described. We applied fluorescence activated synaptosome sorting to explore the features of the dopaminergic synaptome. We provide the proteome of striatal dopaminergic synapses with 57 proteins specifically enriched. Beyond canonical markers of dopamine neurotransmission (Th, Slc6a3/DAT, Slc18a2/VMAT2), we validated 6 proteins belonging to pre- and postsynaptic sides (Cpne7, Apba1/Mint1, Cadps2, Cadm2/SynCAM 2, Stx4 and Mgll). Moreover, dopaminergic varicosities adhere to both a post-synapse with cognate receptors and glutamatergic, GABAergic or cholinergic synapses in structures we named dopaminergic "hub synapses". Markers of presynaptic vesicles and active zone, post-synaptic density and spine apparatus, are significantly increased upon association with dopamine inputs in hubs. Thus neuromodulation frequently operates from hub synapses affecting associated synapses and is not solely dependent on volume transmission. Finally, FASS provides a new framework for the exploration of dopaminergic synapses and more generally for discrete synapse populations ex-vivo. HighlightsO_LIA first proteome of dopaminergic synapses in the striatum C_LIO_LIStriatal dopaminergic synaptosomes display post-synaptic cognate receptors C_LIO_LIDopaminergic projections build hub synapses with excitatory, inhibitory, and cholinergic projections. C_LIO_LICortico-striatal synaptic scaffolds are strengthened upon association in hub synapses. C_LI

neuroscience↗

bioRxiv2019

Comparative proximity biotinylation produces an inventory of RAB18-interactions and implicates RAB18 in cholesterol mobilization

Loss of functional RAB18 causes the autosomal recessive condition Warburg Micro syndrome. To better understand this disease, we used proximity biotinylation to generate an inventory of potential RAB18 effectors. A restricted set of 28 RAB18-interactions were dependent on the binary RAB3GAP1-RAB3GAP2 RAB18-guanine nucleotide exchange factor (GEF) complex. 12 of these 28 interactions are supported by prior reports and we have directly validated novel interactions with SEC22A, TMCO4 and INPP5B. Consistent with a role for RAB18 in regulating membrane contact sites (MCSs), interactors included groups of microtubule/membrane-remodelling proteins, membrane-tethering and docking proteins, and lipid-modifying/transporting proteins. Two of the putative interactors, EBP and OSBPL2/ORP2, have sterol substrates. EBP (emopamil binding protein) is a {Delta}8-{Delta}7 sterol isomerase and OSBPL2/ORP2 is a lipid transport protein. This prompted us to investigate a role for RAB18 in cholesterol biosynthesis. We find that the cholesterol precursor and EBP-product lathosterol accumulates in both RAB18-null HeLa cells and RAB3GAP1-null fibroblasts derived from an affected individual. Further, de novo cholesterol biosynthesis is impaired in cells in which RAB18 is absent or dysregulated. Our data demonstrate that GEF-dependent Rab-interactions are highly amenable to interrogation by proximity biotinylation and may suggest that Micro syndrome is a cholesterol biosynthesis disorder.

cell biology↗

bioRxiv2019

Ecological divergence in sympatry causes gene misregulation in hybrids

Ecological speciation occurs when reproductive isolation evolves as a byproduct of adaptive divergence between populations. However, it is unknown whether divergent ecological selection on gene regulation can directly cause reproductive isolation. Selection favoring regulatory divergence between species could result in gene misregulation in F1 hybrids and ultimately lower hybrid fitness. We combined 58 resequenced genomes with 124 transcriptomes to test this hypothesis in a young, sympatric radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas, which consists of a dietary generalist and two novel trophic specialists - a molluscivore and a scale-eater. We found more differential gene expression between closely related sympatric specialists than between allopatric generalist populations separated by 1000 km. Intriguingly, 9.6% of genes that were differentially expressed between sympatric species were also misregulated in their F1 hybrids. Consistent with divergent ecological selection causing misregulation, a subset of these genes were in highly differentiated genomic regions and enriched for functions important for trophic specialization, including head, muscle, and brain development. These regions also included genes that showed evidence of hard selective sweeps and were significantly associated with oral jaw length - the most rapidly diversifying skeletal trait in this radiation. Our results indicate that divergent ecological selection in sympatry can cause hybrid gene misregulation which may act as a primary reproductive barrier between nascent species.\n\nSignificanceIt is unknown whether the same genes that regulate ecological traits can simultaneously contribute to reproductive barriers between species. We measured gene expression in two trophic specialist species of Cyprinodon pupfishes that rapidly diverged from a generalist ancestor. We found genes differentially expressed between species that also showed extreme expression levels in their hybrid offspring. Many of these genes showed signs of selection and have putative effects on the development of traits that are important for ecological specialization. This suggests that genetic variants contributing to adaptive trait divergence between parental species negatively interact to cause hybrid gene misregulation, potentially producing unfit hybrids. Such loci may be important barriers to gene flow during the early stages of speciation, even in sympatry.

evolutionary biology↗

bioRxiv2019

A scanning electron microscopy-based screen of leaves of Solanum pennellii (ac. LA716) x Solanum lycopersicum (cv. M82) introgression lines provides a resource for identification of loci involved in epidermal development in tomato.

The aerial epidermis of plants plays a major role in their environment interactions, and the development of its cellular components -trichomes, stomata and pavement cells- is still not fully understood. We have performed a detailed screen of the leaf epidermis of two generations of the well-established Solanum pennellii ac. LA716 x Solanum lycopersicum cv. M82 introgression line (IL) population using a combination of scanning electron microscopy techniques. Quantification of the trichome and stomatal densities in the ILs revealed 18 genomic regions with a low trichome density and 4 ILs with a high stomatal density. We also found ILs with abnormal proportions of different trichome types and aberrant trichome morphologies. This work has led to the identification of new, unexplored genomic regions with roles in trichome and stomatal formation and provides an important dataset for further studies on tomato epidermal development that is publically available to the research community.

developmental biology↗

bioRxiv2019

Non-linear dendritic integration in frontal circuits shapes sensory discrimination in rodents

Survival depends on the ability of animals to select the appropriate behavior in response to threat and safety sensory cues. However, the synaptic and circuit mechanisms by which the brain learns to encode accurate predictors of threat and safety remain largely unexplored. Here, we show that frontal association cortex (FrA) pyramidal neurons integrate auditory cues and basolateral amygdala (BLA) inputs non-linearly in a NMDAR-dependent manner. We found that the response of FrA pyramidal neurons was more pronounced to Gaussian noise than to pure 8 kHz tone, and that the activation of BLA-to-FrA axons was the strongest during safe periods in between conditioning pairings. Blocking BLA-to-FrA signaling specifically at the time of presentation of Gaussian noise (but not 8 kHz tone) as a safety signal impaired the formation of auditory fear memories. Taken together, our data reveal a circuit mechanism that facilitates the formation of fear traces in the FrA, thus providing a new framework for probing discriminative learning and related disorders.

neuroscience↗

bioRxiv2019

Phage-encoded cationic antimicrobial peptide used for outer membrane disruption in lysis

Spanins are required for the last step in bacteriophage lysis: the disruption of the outer membrane. Bioinformatic analysis has shown that ~15% of phages lack a spanin gene, which suggests an alternate mechanism of outer membrane disruption. To address this, we selected virulent podophage {phi}KT as a spaninless exemplar and tested {phi}KT genes for outer membrane disruption during lysis. Hypothetical novel gene 28 causes outer membrane disruption when co-expressed with {phi}KT lysis genes and complements the lysis defect of a {lambda} spanin mutant. Gp28 is a 56 aa cationic peptide with predicted amphipathic helical structure and is associated with the particulate fraction after lysis. Urea and KCl washes did not release gp28 from the particulate, suggesting a strong hydrophobic interaction with the membrane. Super high-resolution microscopy supports a primarily outer membrane localization for the peptide. Additionally, holin function is not required for gp28-mediated lysis. Gp28 is similar in size, charge, predicted fold, and membrane association to the human cathelicidin antimicrobial peptide LL-37. In standard assays to measure bactericidal and inhibitory effects of antimicrobial peptides on bacterial cells, synthesized gp28 performed equivalently to LL-37. The studies presented here suggest that {phi}KT Gp28 disrupts bacterial outer membranes during lysis in a manner akin to antimicrobial peptides.\n\nSignificanceHere we provide evidence that {phi}KT produces an antimicrobial peptide for outer membrane disruption during lysis. The disruptin is a new paradigm for phage lysis, and has no similarities to other known lysis genes. Many mechanisms have been proposed for the function of antimicrobial peptides, however there is not a consensus on the molecular basis of membrane disruption. Additionally, there is no established genetic selection system to support such studies. Therefore, the {phi}KT disruptin may represent the first genetically tractable antimicrobial peptide.

microbiology↗

bioRxiv2018

Acute effects of systemic inflammation upon neurovascular unit and cerebrovascular function.

Background: Brain health relies on a tightly regulated system known as neurovascular function whereby the cellular constituents of the neurovascular unit (NVU) regulate cerebral haemodynamics in accordance with neuronal metabolic demand. Disruption of neurovascular function impairs brain health and is associated with the development of disease, including Alzheimer's disease (AD). The NVU is the site of action of neuroinflammatory responses and contributes to the transition of systemic inflammation to neuroinflammatory processes. Thus, systemic inflammatory challenges may cause a shift in the NVU focus, prioritising neuroimmune over neurovascular actions leading to altered neurovascular function. Methods: Rats were injected with lipopolysaccharide (LPS) (2mg/kg) or vehicle and haemodynamic responses to sensory and non-sensory (hypercapnia) stimuli were assessed in vivo. Following imaging, animals were perfused and their brain extracted to histologically characterise components of the NVU to determine the association between underlying pathology to altered blood flow regulation in vivo. Results: LPS-treated animals showed altered haemodynamic function and cerebrovascular dynamics 6 hours after LPS administration. Histological assessment identified a significant increase in astrogliosis, microgliosis and endothelial activation in LPS-treated animals. Conclusions: Our data shows that an acutely induced systemic inflammatory response is able to rapidly alter in-vivo haemodynamic function and is associated with significant changes in the cellular constituents of the NVU. We suggest that these effects are initially mediated by endothelial cells, which are directly exposed to the circulating inflammatory stimulus and have been implicated in regulating functional hyperaemia.

neuroscience↗

bioRxiv2018

DeepFLaSh, a deep learning pipeline for segmentation of fluorescent labels in microscopy images

Fluorescent labeling of biomolecules is widely used for bioimage analyses throughout the life sciences. Recent advances in deep learning (DL) have opened new possibilities to scale the image analysis processes through automation. However, the annotation of fluorescent features with a low signal-to-noise ratio is frequently based on subjective criteria. Training on subjective annotations may ultimately lead to biased DL models yielding irreproducible results. An end-to-end analysis process that integrates data annotation, ground truth estimation, and model training can mitigate this risk. To highlight the importance of this integrated process, we compare different DL-based analysis approaches. Based on data from different laboratories, we show that ground truth estimation from multiple human annotators is indispensable to establish objectivity in fluorescent feature annotations. We demonstrate that ensembles of multiple models trained on the estimated ground truth establish reliability and validity. Our research provides guidelines for reproducible and transparent bioimage analyses using DL methods.

neuroscience↗

bioRxiv2018

Integrative inference of brain cell similarities and differences from single-cell genomics

Defining cell types requires integrating diverse measurements from multiple experiments and biological contexts. Recent technological developments in single-cell analysis have enabled high-throughput profiling of gene expression, epigenetic regulation, and spatial relationships amongst cells in complex tissues, but computational approaches that deliver a sensitive and specific joint analysis of these datasets are lacking. We developed LIGER, an algorithm that delineates shared and dataset-specific features of cell identity, allowing flexible modeling of highly heterogeneous single-cell datasets. We demonstrated its broad utility by applying it to four diverse and challenging analyses of human and mouse brain cells. First, we defined both cell-type-specific and sexually dimorphic gene expression in the mouse bed nucleus of the stria terminalis, an anatomically complex brain region that plays important roles in sex-specific behaviors. Second, we analyzed gene expression in the substantia nigra of seven postmortem human subjects, comparing cell states in specific donors, and relating cell types to those in the mouse. Third, we jointly leveraged in situ gene expression and scRNA-seq data to spatially locate fine subtypes of cells present in the mouse frontal cortex. Finally, we integrated mouse cortical scRNA-seq profiles with single-cell DNA methylation signatures, revealing mechanisms of cell-type-specific gene regulation. Integrative analyses using the LIGER algorithm promise to accelerate single-cell investigations of cell-type definition, gene regulation, and disease states.

neuroscience↗

bioRxiv2018

Genome wide association study of body weight, body mass index, adiposity, and fasting glucose in 3,173 outbred rats

Objective Obesity is influenced by genetic and environmental factors. Despite success of human genome wide association studies (GWAS), the specific genes that confer obesity remain largely unknown. The objective of this study was to use outbred rats to identify genetic loci underlying obesity and related morphometric and metabolic traits.Methods We measured obesity-relevant traits including body weight, body length, body mass index, fasting glucose, and retroperitoneal, epididymal, and parametrial fat pad weight in 3,173 male and female adult N/NIH heterogeneous stock (HS) rats across three institutions, providing data for the largest rat GWAS to date. Genetic loci were identified using a linear mixed model that accounted for the complex family relationships of the HS and covariate to account for differences among the three phenotyping centers.Results We identified 32 independent loci, several of which contained only a single gene (e.g. Epha5, Nrg1 and Klhl14) or obvious candidate genes (Adcy3, Prlhr). There were strong phenotypic and genetic correlations among obesity-related traits, and extensive pleiotropy at individual loci.Conclusions These studies demonstrate utility of HS rats for investigating the genetics of obesity related traits across institutions and identify several candidate genes for future functional testing.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genetics↗

bioRxiv2018

A draft reference genome sequence for Scutellaria baicalensis Georgi

Scutellaria baicalensis Georgi is an important medicinal plant used worldwide. Information about the genome of this species is important for scientists studying the metabolic pathways that synthesise the bioactive compounds in this plant. Here, we report a draft reference genome sequence for S. baicalensis obtained by a combination of Illumina and PacBio sequencing, which was assembled using 10 X Genomics and Hi-C technologies. We assembled 386.63 Mb of the 408.14 Mb genome, amounting to about 94.73% of the total genome size, and the sequences were anchored onto 9 pseudochromosomes with a super-N50 of 33.2 Mb. The reference genome sequence of S. baicalensis offers an important foundation for understanding the biosynthetic pathways for bioactive compounds in this medicinal plant and for its improvement through molecular breeding.

plant biology↗

bioRxiv2018

Changes in rumen microbiota of cows in response to dietary supplementation with nitrate, linseed and saponin alone or in combination.

Dietary supplementation with linseed, saponins and nitrate is a promising methane mitigation strategy in ruminant production. The main objective of this work was to assess the effects of these additives on the rumen microbiota in order to understand underlying microbial mechanisms of methane abatement. Two 2 x 2 factorial design studies were conducted simultaneously, which also allowed us to make a broad-based assessment of microbial responses. Eight non-lactating cows were fed diets supplemented with linseed or saponin in order to decrease hydrogen production and nitrate to deviate hydrogen consumption; also, combinations of linseed plus nitrate or saponin plus nitrate were used to explore the interaction between dietary treatments. Amplicon sequencing of 18S and 16S rRNA genes was employed to characterise rumen microbes. Nitrate fed alone or in combination in both studies dramatically affected the composition and structure of rumen microbiota, though impacts were more evident in one of the studies. Linseed moderately modified bacterial community structure with no effect on rumen methanogens and protozoa. Indicator OTU analysis revealed that both linseed and nitrate reduced the relative abundance of hydrogen-producing Ruminococcaceae. Linseed increased the proportion of bacteria known to reduce succinate to propionate, whereas nitrate supplementation increased nitrate-reducing bacteria and decreased the metabolic activity of rumen methanogens. Saponins had no effect on the microbiota. Inconsistency found between the two studies, when nitrate was fed to the cows could be explained by changes in microbial ecosystem functioning rather than changes in microbial community structure.\n\nImportanceThis study aimed at identifying the microbial mechanisms of enteric methane mitigation when linseed, nitrate and saponins were fed to non-lactating cows alone or in a combination. Hydrogen is a limiting factor in rumen methanogenesis. We hypothesised that linseed and saponins would affect hydrogen producers and nitrate would deviate hydrogen consumption thus leading to reduced methane production in the rumen. Contrary to what was foreseen, both linseed and nitrate had a deleterious effect on hydrogen producers; linseed also redirected hydrogen consumption towards propionate production, whereas nitrate stimulated the growth of nitrate reducing and hence hydrogen-consuming bacterial taxa. Fundamental knowledge of microbial mechanism involved in rumen methanogenesis, provides novel insights for the development of new or the optimisation of existing methane mitigation strategies.

molecular biology↗

bioRxiv2018

New criteria for sympatric speciation in the genomic era

Sympatric speciation illustrates how natural and sexual selection may create new species in isolation without geographic barriers. However, recent genomic reanalyses of classic examples of sympatric speciation have revealed complex histories of secondary gene flow. Thus, there is a need to revisit how to connect the diverse theoretical models of sympatric speciation and their predictions to empirical case studies in the face of widespread gene flow. We summarize theoretical differences between sympatric speciation and speciation-with-gene-flow models and propose genomic analyses for distinguishing which models apply to case studies based on the timing and function of adaptive introgression. Investigating whether secondary gene flow contributed to reproductive isolation is necessary to test whether predictions of theory are ultimately borne out in nature.

evolutionary biology↗