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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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Novel genome-wide associations for suicidality in UK Biobank, genetic correlation with psychiatric disorders and polygenic association with completed suicide.

AbstractBackground: Suicide is a major issue for global public health. Suicidality describes a broad clinical spectrum of thoughts and behaviours, some of which are common in the general population.\n\nMethods: UK Biobank recruited [~]0{middle dot}5 million middle age individuals from the UK, of whom 157,000 completed an assessment of suicidality. Mutually exclusive groups were assessed in an ordinal genome-wide association study of suicidality: no suicidality controls (N=83,557); thoughts that life was not worth living (N=21,063); ever contemplated self-harm (N=13,038); an act of deliberate self-harm in the past (N=2,498); and a previous suicide attempt (N=2,666). Linkage of UK Biobank to death certification records identified a small sub-group of completed suicide (N=137).\n\nOutcomes: We identified three novel genome-wide significant loci for suicidality (on Chromosomes 9, 11 and 13) and moderate-to-strong genetic correlations between suicidality and a range of psychiatric disorders, most notably depression (rg 0{middle dot}81). Higher polygenic risk scores for suicidality were associated with increased risk of completed suicide relative to controls in an independent sub-group (N=137 vs N=5,330, OR 1{middle dot}23, 95%CI 1{middle dot}06 to 1{middle dot}41, p=0.03). Rs598046-G (chromosome 11) demonstrated a similar effect size and direction (p=0{middle dot}05) within a Danish suicidality study.\n\nInterpretation: These findings have significant implications for our understanding of genetic vulnerability to suicidal thoughts and behaviours. Future work should assess the extent to which polygenic risk scores for suicidality, in combination with non-genetic risk factors, may be useful for stratified approaches to suicide prevention at a population level.\n\nFunding: UKRI Innovation-HDR-UK Fellowship (MR/S003061/1). MRC Mental Health Data Pathfinder Award (MC_PC_17217).

genetics

HERV-K HML-2 transcription in diverse cancers is related with cancer stem cell and epithelial-mesenchymal transition markers

Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections that make up 8% of the human genome. Although these elements are mostly fragmented and inactive, many proviruses belonging to the HERV-K (HML-2) family, the youngest lineage in the human genome, have intact open reading frames, some encoding for accessory genes called np9 and rec that interact with oncogenic pathways. Many studies have established that ERVs are transiently expressed in both stem cells and cancer, resulting in aberrant self-renewal and uncontrolled proliferation. np9 and rec expression are significantly correlated with a range of cancer stem cell (CSC) and epithelial to mesenchymal transition (EMT) biomarkers, including cellular receptors, transcription factors, and histone modifiers. Surprisingly, these ERV genes are negatively correlated with genes known to promote pluripotency in embryonic stem cell lines, such as Oct4. These results indicate that HERV-K (HML-2) is part of the transcriptional landscape responsible for cancer cells undergoing the phenotypic switch that characterises EMT. The discovery of np9 and recs correlation with CSC and EMT biomarkers suggest a yet undescribed role affecting the transitional CSC-like state in EMT and the shift towards cancer malignancy.\n\nImportanceIn this study, we find that human endogenous retrovirus HERV-K (HML-2)-encoded genes np9 and rec are correlated with the expression of many biomarkers associated with cancer stem cells (CSC) and epithelial-mesenchymal transition (EMT). There has been a significant effort to develop novel treatments targeting CSC and EMT-specific signalling pathways and cell surface markers. This research describes HERV-K (HML-2) as interacting or being part of the regulatory network that make up reversible cell state switching in EMT. Our findings suggest these specific HERVs may be good candidate biomarkers in identifying the transitional CSC-like states that are present during the progression of EMT and cancer metastasis.

bioinformatics

Baseline corticosterone does not reflect iridescent plumage traits in female tree swallows

The production of high quality secondary sexual traits can be constrained by trade-offs in the allocation of energy and nutrients with other metabolic activities, and is mediated by physiological processes. In birds, the factors influencing male plumage quality have been well studied; however, factors affecting female plumage quality are poorly understood. Furthermore, it remains uncertain which physiological traits mediate the relationship between body condition and ornaments. In this three-year study of after-second-year female tree swallows (Tachycineta bicolor), we investigated (1) the relationship between baseline corticosterone near the end of the brood-rearing period (CORTBR) and feather colour characteristics (hue, saturation, brightness) the following year, and (2) the relationship between baseline corticosterone measured during incubation (CORTI) and brood rearing (CORTBR), and feather colour in the same year. To control for reproductive effort, we included reproductive parameters as covariates in all analyses. In this first study between CORT and the plumage colour characteristics of a species bearing iridescent feathers, we did not find any relationship between CORTBR and the colour of subsequently-produced feathers, nor did we find any relationship between CORTI and the colour of feathers displayed during that breeding season. If CORT levels at the end of breeding carry over to influence the immediately subsequent moult period as we expect, our results generally indicate that structural plumage quality may not be as sensitive to circulating CORT levels compared to carotenoid-based colouration. Future studies, particularly those employing experimental manipulations of CORT during moult in species with iridescent traits, are necessary to fully determine the role glucocorticoids play in mediating the quality of secondary sexual characteristics.

zoology

A comparison of antigen-specific T cell responses induced by six novel tuberculosis vaccine candidates

Eradication of tuberculosis (TB), the worlds leading cause of death due to infectious disease, requires a highly efficacious TB vaccine. Many TB vaccine candidates are in preclinical and clinical development but only a few can be advanced to large-scale efficacy trials due to limited global resources. We aimed to perform a statistically rigorous comparison of the antigen-specific T cell responses induced by six novel TB vaccine candidates and the only licensed TB vaccine, Bacillus Calmette-Guerin (BCG). We propose that the antigen-specific immune response induced by such vaccines provides an objective, data-driven basis for prioritisation of vaccine candidates for efficacy testing. We analyzed frequencies of antigen-specific CD4 and CD8 T cells expressing IFN{gamma}, IL-2, TNF and/or IL-17 from adolescents or adults, with or without Mycobacterium tuberculosis (M.tb) infection, who received MVA85A, AERAS-402, H1:IC31, H56:IC31, M72/AS01E, ID93+GLA-SE or BCG. Two key response characteristics were analyzed, namely response magnitude and cytokine co-expression profile of the memory T cell response that persisted above the pre-vaccination response to the final study visit in each trial. All vaccines preferentially induced antigen-specific CD4 T cell responses expressing Th1 cytokines; levels of IL-17-expressing cells were low or not detected. In M.tb-uninfected and -infected individuals, M72/AS01E induced higher memory Th1 cytokine-expressing CD4 T cell responses than other novel vaccine candidates. Cytokine co-expression profiles of memory CD4 T cells induced by different novel vaccine candidates were alike. Our study suggests that the T cell response feature which most differentiated between the TB vaccine candidates was response magnitude, whilst functional profiles suggested a lack of response diversity. Since M72/AS01E induced the highest memory CD4 T cell response it demonstrated the best vaccine take. In the absence of immunological correlates of protection the likelihood of finding a protective vaccine by empirical testing of candidates may be increased by the addition of candidates that induce distinct immune characteristics.\n\nAuthor summaryTuberculosis (TB) causes more deaths than any other single infectious disease, and a new, improved vaccine is needed to control the epidemic. Many new TB vaccine candidates are in clinical development, but only one or two can be advanced to expensive efficacy trials. In this study, we compared magnitude and functional attributes of memory T cell responses induced in recently conducted clinical trials by six TB vaccine candidates, as well as BCG. The results suggest that these vaccines induced CD4 and CD8 T cell responses with similar functional attributes, but that one vaccine, M72/AS01E, induced the largest responses. This finding may indicate a lack of diversity in T cell responses induced by different TB vaccine candidates. A repertoire of vaccine candidates that induces more diverse immune response characteristics may increase the chances of finding a protective vaccine against TB.

immunology

Ddx3x regulates B-cell development and light chain recombination in mice

The X chromosome gene, DDX3X, is an ATP-dependent RNA helicase with roles in transcription, splicing, nuclear export, and translation. Loss of function mutations in DDX3X are linked to a variety of neoplasms, including B-cell lymphoma. We find that conditional homozygous deletion (Mb1-Cre) of Ddx3x in developing mouse B cells in female mice results in a complete absence of mature peripheral B cells associated with an absolute block at the pro-B cell stage of development in the bone marrow. In male mice with Vav1-Cre or Mb1-Cre mediated hemizygous deletion of Ddx3x, there are less severe reductions in peripheral B-cell frequencies with skewing towards the marginal zone lineage, suggesting that the Y chromosome homolog Ddx3y or other male factors may partially compensate for loss of Ddx3x. Loss of Ddx3x in male mice is associated with perturbations at developmental time points linked to cell cycle arrest and immunoglobulin chain rearrangement. Mechanistically, loss of Ddx3x in pre-B cells is associated with reduced expression of the histone reader Brwd1, failure to curtail proliferation, and defective Igk rearrangement, which skews the peripheral B cell receptor repertoire toward lambda light chain usage. These data reveal that Ddx3x plays an essential role in B-cell development by supporting proliferative and epigenetic changes necessary for rearrangement of immunoglobulin genes.

immunology

Different macroevolutionary routes to becoming a biodiversity hotspot

Why is species diversity so unevenly distributed across different regions on Earth? Regional differences in biodiversity may stem from differences in rates of speciation and dispersal and colonization times, but these hypotheses have rarely been tested simultaneously at a global scale. Here we uncovered the routes that generated hotpots of mammal and bird biodiversity by analyzing the tempo and mode of diversification and dispersal within major biogeographic realms. Hotspots in tropical realms had higher rates of speciation whereas those in temperate realms received more immigrant species from their surrounding regions. We also found that hotspots had higher spatial complexity and energy availability, providing a link between the environment and macroevolutionary history. Our study highlights how assessing differences in macroevolutionary history can help to explain why biodiversity varies so much worldwide.

evolutionary biology

Spontaneous intake and long-term effects of essential oils after a negative postnatal experience in chicks

The postnatal period is critical for broiler chicks as they are exposed to, possibly stressful, environmental changes in the hatchery and during transportation to the rearing houses. The ability of broiler chicks to spontaneously drink essential oils (EO) to mitigate the effects of a negative postnatal experience was tested. Chicks were either immediately placed in the rearing facility (C group), or subjected to a 24h-delay period before their placement (D group), mimicking the possible transportation delay in commercial conditions.\n\nIn experiment 1, each group had access to either water only or to water and one EO (cardamom, marjoram or verbena) from D1 to D13. The verbena EO intake was higher in the D group than in the C group from D1 to D6 and the cardamom EO intake was lower in the D group than in the C group from D6 to D13.\n\nIn experiment 2, half of the groups had access to water only and the other half was offered water and the 3 EO simultaneously. The EO were not differently chosen by chicks between D and C groups except a lower cardamom EO intake was observed in the D group than in the C group from D6 to D12. The delayed placement of the D group reduced chicken growth until 34 days of age and temporarily increased the feed conversion ratio, but did not affect their welfare or the prevalence of health disorders. The EO intake did not allow the chicks in the D group to overcome the growth reduction, but did overcome the reduction in Pectoralis major muscle yield. In conclusion, chicks are able to make spontaneous choices regarding EO intake according to their postnatal experience when EO are presented individually, but in our experimental design, they were not when EO were simultaneously presented. The EO intake only partially mitigated the decrease in chicken performance after the negative postnatal experience.

animal behavior and cognition

Risk aversion in macaques in a freely moving patch-leaving foraging task

Animals, including humans, are risk-averse in most contexts. A major exception is the rhesus macaque (Macaca mulatta), which is robustly risk-seeking. Macaques unique preferences may reflect their unique evolutionary history. Alternatively, they may derive from elements of task design associated with the demands of physiological recording, the source of nearly all macaque risk preference data. To disambiguate these possibilities we assessed macaques risk attitudes in a somewhat more naturalistic environment: subjects foraged at four feeding stations in a large enclosure. Stations (i.e. patches) provided either stochastically or non-stochastically depleting rewards. Subjects patch residence times were longer at safe than at risky stations, indicating a preference for safe options. This preference was not attributable to a win-stay-lose-shift heuristic. These findings highlight the lability of risk attitudes in macaques and support the hypothesis that observed differences between macaques and other species are ephemeral, not evolved.

animal behavior and cognition

Cingulate dependent social risk assessment in rats

Social transmission of distress has been conceived of as a one-way phenomenon in which an observer catches the emotions of another. Here we use a paradigm in which an observer rat witnesses another receive electro-shocks. Bayesian model comparison and Granger causality argue against this one-way vision in favor of bidirectional information transfer: how the observer reacts to the demonstrators distress influences the behavior of the demonstrator. Intriguingly, this was true to a similar extent across highly familiar and entirely unfamiliar rats. Injecting muscimol in the anterior cingulate of observers reduced freezing in the observers and in the demonstrators receiving the shocks. That rats share the distress of unfamiliar strains is at odds with evolutionary thinking that empathy should be biased towards close individuals. Using simulations, we support the complementary notion that distress transmission could be selected to more efficiently detect dangers in a group.

neuroscience

Relation between executive functions and polymorphisms in COMT, MAO-A, HTTLPR, SLC1A1 and HT2A in a sample of children with Obsessive Compulsive Disorder

BackgroundObsessive compulsive disorder (OCD) has a complex etiology related to multiple neuropsychological factors. OCD is associated with several candidate genes but results are discordant. The objective was to explore the association between five polymorphisms related to neurotransmitters, the risk of an OCD diagnosis and the performance in four executive functions tests done with Colombian patients diagnosed with this condition.\n\nMethods63 patients and 65 controls matched by gender and age were genetically analyzed. For the study of the relation between cognitive function and phenotypes, a subsample of 33 patients and 31 controls was used. The Stroop test, Wisconsin Card Sorting Test (WCST), Tower of London and Trail Making Test (TMT) for executive function assessment were applied and the SNPs analyzed were: COMT (rs4680), MAO-A (rs6323), HTTLPR (rs25531), HT2A (rs6315) and SLC1A1 (rs301434).\n\nResultsDifferences in the conceptualization of the WCST test (p = 0.023) and Stroop interference score (p = 0.041) between cases and controls were obtained. After analyzing the relationship between genotypes and sub-scores of the tests, associations between the presence of MAO-A, SLAC1A1, HTTLPR and HT2A alleles and tests sub-scores were found.\n\nDiscussionThis characterization of children with OCD is a new field of work in Colombia and one of the first works performed in Latin America. The sample size and the number of polymorphisms analyzed in this population should be increased.

neuroscience

Impact of mutation rate and selection at linked sites on fine-scale DNA variation across the homininae genome

DNA diversity varies across the genome of many species. Variation in diversity across a genome might arise for one of three reasons; regional variation in the mutation rate, selection and biased gene conversion. We show that both non-coding and non-synonymous diversity are correlated to a measure of the mutation rate, the recombination rate and the density of conserved sequences in 50KB windows across the genomes of humans and non-human homininae. We show these patterns persist even when we restrict our analysis to GC-conservative mutations, demonstrating that the patterns are not driven by biased gene conversion. The positive correlation between diversity and our measure of the mutation rate seems to be largely a direct consequence of regions with higher mutation rates having more diversity. However, the positive correlation with recombination rate and the negative correlation with the density of conserved sequences suggests that selection at linked sites affect levels of diversity. This is supported by the observation that the ratio of the number of non-synonymous to non-coding polymorphisms is negatively correlated to a measure of the effective population size across the genome. Furthermore, we find evidence that these genomic variables are better predictors of non-coding diversity in large homininae populations than in small populations, after accounting for statistical power. This is consistent with genetic drift decreasing the impact of selection at linked sites in small populations. In conclusion, our comparative analyses describe for the first time how recombination rate, gene density, mutation rate and genetic drift interact to produce the patterns of DNA diversity that we observe along and between homininae genomes.

evolutionary biology

Cortical subnetworks encode context of a visual stimulus

Cortical processing of sensory events is significantly influenced by context. For instance, a repetitive or redundant visual stimulus elicits attenuated cortical responses, but if the same stimulus is unexpected or \"deviant\", responses are augmented. This contextual modulation of sensory processing is likely a fundamental function of neural circuits, yet an understanding of how it is computed is still missing. Using holographic two-photon calcium imaging in awake animals, here we identify three distinct, spatially intermixed ensembles of neurons in mouse primary visual cortex which differentially respond to the same stimulus under separate contexts, including a subnetwork which selectively responds to deviant events. These non-overlapping ensembles are distributed across layers 2-5, though deviance detection is more common in superficial layers. Contextual preferences likely arise locally since they are not present in bottom up inputs from the thalamus or top-down inputs from prefrontal cortex. The functional parcellation of cortical circuits into independent ensembles that encode stimulus context provides a circuit basis underlying cortically based perception of novel or redundant stimuli, a key deficit in many psychiatric disorders.\n\nOne Sentence SummaryVisual cortex represents deviant and redundant stimuli with separate subnetworks.

neuroscience

Global biogeography of Tetragnatha spiders reveals multiple colonization of the Caribbean

Organismal variation in dispersal ability can directly affect levels of gene flow amongst populations, therefore importantly shaping species distributions and species richness patterns. The intermediate dispersal model of biogeography (IDM) predicts that in island systems, species diversity of those lineages with an intermediate dispersal potential is the highest. We broadly test this prediction, focusing on four-jawed spiders (genus Tetragnatha) of the Caribbean archipelago. First, we report on original sampling of this globally distributed genus with numerous widespread as well as endemic species. We then reconstruct multiple Tetragnatha phylogenies from roughly 300 individuals delineated into 54 putative species. Our results support the monophyly of the four-jawed spiders but reject the monophyly of those lineages that reach the Caribbean, where we find low levels of endemism yet high diversity within Tetragnatha. The chronogram detects a potential early overwater colonization of the Caribbean, and in combination with reconstructed biogeographic history, refutes the possibility of ancient vicariant origins of Caribbean Tetragnatha as well as the GAARlandia land-bridge scenario. Instead, biogeographic results hypothesize multiple colonization events to, and from the Caribbean since mid-Eocene to late-Miocene. Tetragnatha seems unique among the arachnids explored so far in comprising some species that are excellent dispersers, and others that are not, perhaps having secondarily lost this dispersal propensity. A direct test of the IDM would require consideration of three categories of dispersers. However, four-jawed spiders do not fit one of these three a priori definitions, but rather represent a more complex combination of attributes of a dynamic disperser.

evolutionary biology

Loss of SATB1 Induces a p21 Dependent CellularSenescence Phenotype in Dopaminergic Neurons

Cellular senescence is a mechanism used by mitotic cells to prevent uncontrolled cell division. As senescent cells persist in tissues, they cause local inflammation and are harmful to surrounding cells, contributing to aging. Generally, neurodegenerative diseases, such as Parkinson s, are disorders of aging. The contribution of cellular senescence to neurodegeneration is still unclear. SATB1 is a DNA binding protein associated with Parkinsons disease. We report that SATB1 prevents cellular senescence in post-mitotic dopaminergic neurons. Loss of SATB1 causes activation of a cellular senescence transcriptional program in dopamine neurons, both in human stem cell-derived dopaminergic neurons and in mice. We observed phenotypes which are central to cellular senescence in SATB1 knockout dopamine neurons in vitro and in vivo. Moreover, we found that SATB1 directly represses expression of the pro-senescence factor, p21, in dopaminergic neurons. Our data implicate senescence of dopamine neurons as a contributing factor to the pathology of Parkinsons disease.

neuroscience

Phytoplankton thermal responses adapt in the absence of hard thermodynamic constraints

To better predict how populations and communities respond to climatic temperature variation, it is necessary to understand how the shape of the response of fitness-related traits to temperature evolves (the thermal performance curve). Currently, there is disagreement about the extent to which the evolution of thermal performance curves is constrained. One school of thought has argued for the prevalence of thermodynamic constraints through enzyme kinetics, whereas another argues that adaptation can--at least partly--overcome such constraints. To shed further light on this debate, we perform a phylogenetic meta-analysis of the thermal performance curves of growth rate of phytoplankton--a globally important functional group--, controlling for environmental effects (habitat type and thermal regime). We find that thermodynamic constraints have a minor influence on the shape of the curve. In particular, we detect a very weak increase of maximum performance with the temperature at which the curve peaks, suggesting a weak "hotter-is-better" constraint. Also, instead of a constant thermal sensitivity of growth across species, as might be expected from strong constraints, we find that all aspects of the thermal performance curve evolve along the phylogeny. Our results suggest that phytoplankton thermal performance curves adapt to thermal environments largely in the absence of hard thermodynamic constraints.

evolutionary biology

Inference of the worldwide invasion routes of the pinewood nematode, Bursaphelenchus xylophilus, using ABC analysis on microsatellite data

AO_SCPLOWBSTRACTC_SCPLOWPopulation genetics have been greatly beneficial to improve knowledge about biological invasions. Model-based genetic inference methods, such as approximate Bayesian computation (ABC), have brought this improvement to a higher level and are now essential tools to decipher the invasion routes of any invasive species. In this paper, we performed ABC random forest analyses to shed light on the pinewood nematode (PWN) worldwide invasion routes and to identify the source of European populations. Originating from North America, this microscopic worm has been invading Asia since 1905 and Europe since 1999, causing tremendous damage on pine forests. Using microsatellite data, we demonstrated the existence of multiple introduction events in Japan (at least two involving individuals originating from the USA) and China (one involving individuals originating from the USA and one involving individuals originating from Japan). We also found that Portuguese samples had a Japanese origin. We observed some discrepancies between descriptive genetic methods and the ABC method, which are worth investigating and are discussed here. The ABC method helped clarify the worldwide history of the PWN invasion, even though the results still need to be considered with some caution because the features of the PWN and the genetic markers used probably push the ABC method to its very limits.

genetics

Insertion sequences drive the emergence of a highly adapted human pathogen

Taxonomic outliers of Pseudomonas aeruginosa of environmental origin have recently emerged as infectious for humans. Here we present the first genome-wide analysis of an isolate that caused fatal hemorrhagic pneumonia. We demonstrate that, in two sequential clones, CLJ1 and CLJ3, recovered from a patient with chronic pulmonary disease, insertion of a mobile genetic element into the P. aeruginosa chromosome affected major virulence-associated phenotypes and led to increased resistance to antibiotics used to treat the patient. Comparative proteome and transcriptome analyses revealed that this insertion sequence, ISL3, disrupted genes encoding flagellar components, type IV pili, O-specific antigens, translesion polymerase and enzymes producing hydrogen cyanide. CLJ3 possessed seven fold more IS insertions than CLJ1, some modifying its susceptibility to antibiotics by disrupting the genes for the outer-membrane porin OprD and the regulator of {beta}-lactamase expression AmpD. In the Galleria mellonella larvae model, the two strains displayed different levels of virulence, with CLJ1 being highly pathogenic. This work reveals ISs as major players in enhancing the pathogenic potential of a P. aeruginosa taxonomic outlier by modulating both, the virulence and the resistance to antimicrobials, and explains the ability of this bacterium to adapt from the environment to a human host.

microbiology

Topographical cues control the morphology and dynamics of migrating cortical interneurons

In mammalian embryos, cortical interneurons travel long distances among complex three-dimensional tissues before integrating into cortical circuits. Several molecular guiding cues involved in this migration process have been identified, but the influence of physical parameters remains poorly understood. In the present study, we have investigated in vitro the influence of the topography of the microenvironment on the migration of primary cortical interneurons released from mouse embryonic explants.\n\nWe found that arrays of 10 m-sized PDMS micro-pillars, either round or square, influenced both the morphology and the migratory behavior of interneurons. Strikingly, most interneurons exhibited a single and long leading process oriented along the diagonals of the square pillared array, whereas leading processes of interneurons migrating in-between round pillars were shorter, often branched and oriented in all available directions. Accordingly, dynamic studies revealed that growth cone divisions were twice more frequent in round than in square pillars. Both soma and leading process tips presented forward directed movements within square pillars, contrasting with the erratic trajectories and more dynamic movements observed among round pillars. In support of these observations, long interneurons migrating in square pillars displayed tight bundles of stable microtubules aligned in the direction of migration.\n\nOverall, our results show that micron-sized topography provides global spatial constraints promoting the establishment of two different morphological and migratory states. Remarkably, both states belong to the natural range of migratory behaviors of cortical interneurons, highlighting the potential importance of topographical cues in the guidance of these embryonic neurons, and more generally in brain development.

cell biology