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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

At least 703 records · Page 39Linked to original sources

bioRxiv2018

Patterned expression of Pannexin 1 channels in the adult cerebellar Purkinje cells

Pannexin1 (PanX1) are recently discovered proteins that can form large pore channels at the cell surface. They have been implicated in ATP-dependent cell-to-cell communication and in several pathophysiological processes such as inflammation, cell death and epilepsy. Using immunohistochemistry in the adult mouse, we describe the presence of PanX1 in the deep cerebellar nuclei, in large cells of the granular layer, presumably Golgi interneurones, in some Bergmann glia radial processes as well as in the soma and dendrites of Purkinje cells. In the latter, PanX1, like many other proteins, distribute heterogeneously. Only Zebrin II-positive Purkinje cells express PanX1, in accordance with the so-called \"zebra-striped\" modular architecture of the cerebellum. This distribution in zebra-stripes suggest that PanX1 may contribute to the control of ensemble activity within cerebellar microdomains or to the response of Purkinje cell to excitotoxicity and cell-death messages.

neuroscience↗

bioRxiv2018

Cyclic, condition-independent activity in primary motor cortex predicts corrective movement behavior

Reaching movements are known to have large condition-independent neural activity and cyclic neural dynamics. A new precision center-out task was performed by rhesus macaques to test the hypothesis that cyclic, condition-independent neural activity in the primary motor cortex (M1) occurs not only during initial reaching movements but also during subsequent corrective movements. Corrective movements were observed to be discrete with time courses and bell-shaped speed profiles similar to the initial movements. Condition-independent cyclic neural trajectories were similar and repeated for initial and each additional corrective submovement. The phase of the cyclic condition-independent neural activity predicted the time of peak movement speed more accurately than regression of instantaneous firing rate, even when the subject made multiple corrective movements. Rather than being controlled as continuations of the initial reach, a discrete cycle of motor cortex activity encodes each corrective submovement. Significance StatementDuring a precision center-out task, initial and subsequent corrective movements occur as discrete submovements with bell-shaped speed profiles. A cycle of condition-independent activity in primary motor cortex neuron populations corresponds to each submovement, such that the phase of this cyclic activity predicts the time of peak speeds--both initial and corrective. These submovements accompanied by cyclic neural activity offer important clues into how we successfully execute precise, corrective reaching movements and may have implications for optimizing control of brain-computer interfaces.

neuroscience↗

bioRxiv2018

Homeostatic plasticity rules control the wiring of axo-axonic synapses at the axon initial segment

GABAergic interneurons are chiefly responsible for controlling the activity of local circuits in the cortex1,2. However, the rules that govern the wiring of interneurons are not well understood3. Chandelier cells (ChCs) are a type of GABAergic interneuron that control the output of hundreds of neighbouring pyramidal cells through axo-axonic synapses which target the axon initial segment (AIS)4. Despite their importance in modulating circuit activity, our knowledge of the development and function of axo-axonic synapses remains elusive. In this study, we investigated the role of activity in the formation and plasticity of ChC synapses. In vivo imaging of ChCs during development uncovered a narrow window (P12-P18) over which axons arborized and formed connections. We found that increases in the activity of either pyramidal cells or individual ChCs during this temporal window resulted in a reversible decrease in axo-axonic connections. Voltage imaging of GABAergic transmission at the AIS showed that axo-axonic synapses were depolarising during this period. Identical manipulations of network activity in older mice (P40-P46), when ChC synapses are inhibitory, resulted in an increase in axo-axonic synapses. We propose that the direction of ChC plasticity follows homeostatic rules that depend on the polarity of axo-axonic synapses.

neuroscience↗

bioRxiv2018

Access schedules mediate the impact of high fat diet on ethanol intake in mice.

Alcoholism and high fat diet (HFD)-induced obesity individually promote insulin resistance and glucose intolerance in clinical populations, increasing risk for metabolic diseases. Conversely, animal studies, typically utilizing forced/continuous alcohol (EtOH) access, tend to show that EtOH intake mitigates HFD-induced effects on insulin and glucose function, while HFD decreases voluntary EtOH intake in continuous access models. However, the impact of HFD on intermittent EtOH intake and resultant changes to metabolic function are not well characterized. The present studies sought to determine if HFD alters EtOH intake in male C57Bl/6J mice given differing two-bottle choice EtOH access schedules, and to assess resultant impact on insulin sensitivity and glucose tolerance. In the first experiment, mice had Unlimited Access EtOH (UAE)+HFD (n=15; HFD=60% calories from fat, 10% EtOH v/v, ad libitum) or UAE+Chow (n=15; control diet=16% calories from fat, ad libitum) for 6 weeks. UAE+HFD mice had lower EtOH preference, consumed significantly less EtOH, and were insulin resistant and hyperglycemic compared with UAE+Chow mice. In the second experiment, mice had Limited Access EtOH (LAE, 4 hrs/d; 3 d/wk)+HFD (n=15) or LAE+Chow (n=15) with increasing EtOH concentrations (10%, 15%, 20%). LAE+HFD mice had no difference in total EtOH consumption compared to LAE+Chow mice, but exhibited hyperglycemia, insulin resistance, and glucose intolerance. In the third experiment, mice had intermittent HFD access (single 24 hr session/week) with limited access to EtOH (iHFD-E, 4hrs/d; 4 d/wk) (n=10). iHFD-E mice displayed binge eating behaviors and consumed significantly more EtOH than mice given ad libitum chow or HFD, suggesting transfer of binge eating to binge drinking behaviors. Although iHFD-E mice did not have significantly altered body composition, they developed insulin insensitivity and glucose intolerance. These results suggest that access schedules determine the impact of HFD on EtOH consumption and resultant metabolic dysfunction.

animal behavior and cognition↗

bioRxiv2018

Visual cue-related activity of cells in the medial entorhinal cortex during navigation in virtual reality

During spatial navigation, animals use self-motion to estimate positions through path integration. However, estimation errors accumulate over time and it is unclear how they are corrected. Here we report a new cell class (\"cue cell\") in mouse medial entorhinal cortex (MEC) that encoded visual cue information that could be used to correct errors in path integration. Cue cells accounted for a large fraction of unidentified MEC cells. They exhibited firing fields only near visual cues during virtual navigation and spatially stable activity during navigation in a real arena. Cue cells responses occurred in sequences repeated at each cue and were likely driven by visual inputs. In layers 2/3 of the MEC, cue cells formed clusters. Anatomically adjacent cue cells responded similarly to cues. These cue cell properties demonstrate that the MEC circuits contain a code representing spatial landmarks that could play a significant role in error correction during path integration.

neuroscience↗

bioRxiv2018

A Stu2-mediated intrinsic tension-sensing pathway promotes chromosome biorientation in vivo

Accurate segregation of chromosomes to daughter cells is a critical aspect of cell division. It requires the kinetochores on duplicated chromosomes to biorient, attaching to microtubules from opposite poles of the cell. Bioriented attachments come under tension, while incorrect attachments lack tension and must be destabilized. A well-studied error correction pathway is mediated by the Aurora B kinase, which destabilizes low tension-bearing attachments. We recently discovered that in vitro, kinetochores display an additional intrinsic tension-sensing pathway that utilizes Stu2. This pathways contribution to error correction in cells, however, was unknown. Here, we identify a Stu2 mutant that abolishes its kinetochore function and show that it causes error correction defects in vivo. We also show that this intrinsic tension-sensing pathway functions in concert with the Aurora B-mediated pathway. Together, our work indicates that cells employ at least two pathways to ensure biorientation and the accuracy of chromosome segregation.

cell biology↗

bioRxiv2018

Bright split red fluorescent proteins with enhanced complementation efficiency for the tagging of endogenous proteins and visualization of synapses

Self-associating split fluorescent proteins (FPs) have been widely used for labeling proteins, scaffolding protein assembly and detecting cell-cell contacts. Newly developed self-associating split FPs, however, have suffered from suboptimal fluorescence signal. Here, by investigating the complementation process, we have demonstrated two approaches to improve split FPs: assistance through SpyTag/SpyCatcher interaction and directed evolution. The latter has yielded two split sfCherry3 variants with substantially enhanced overall brightness, facilitating the tagging of endogenous proteins by gene editing. Based on sfCherry3, we have further developed a new red-colored trans-synaptic marker called Neuroligin-1 sfCherry3 Linker Across Synaptic Partners (NLG-1 CLASP) for multiplexed visualization of neuronal synapses in living animals, demonstrating its broad applications.

cell biology↗

bioRxiv2018

Proximity RNA labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules

Diverse ribonucleoprotein complexes control messenger RNA processing, translation, and decay. Transcripts in these complexes localize to specific regions of the cell and can condense into non-membrane-bound structures such as stress granules. It has proven challenging to map the RNA composition of these large and dynamic structures, however. We therefore developed an RNA proximity labeling technique, APEX-Seq, which uses the ascorbate peroxidase APEX2 to probe the spatial organization of the transcriptome. We show that APEX-Seq can resolve the localization of RNAs within the cell and determine their enrichment or depletion near key RNA-binding proteins. Matching the spatial transcriptome, as revealed by APEX-Seq, with the spatial proteome determined by APEX-mass spectrometry (APEX-MS) provides new insights into the organization of translation initiation complexes on active mRNAs, as well as exposing unanticipated complexity in stress granule composition, and provides a powerful and general approach to explore the spatial environment of macromolecules.

genomics↗

bioRxiv2018

Microglial SIRPα regulates the emergence of CD11c+ microglia and demyelination damage in white matter

A characteristic subset of microglia expressing CD11c appears in response to brain damage. However, the functional role of CD11c+ microglia, as well as the mechanism of its induction, are poorly understood. Here we report that the genetic ablation of signal regulatory protein (SIRP), a membrane protein, induced CD11c+ microglia in the brain white matter. Mice lacking CD47, a physiological ligand of SIRP, and microglia-specific SIRP knockout mice exhibited the same phenotype, suggesting the interaction between microglial SIRP and CD47 on neighbouring cells suppressed the emergence of CD11c+ microglia. A lack of SIRP did not cause detectable damage in the white matter, but resulted in the increased expression of genes characteristic of the repair phase after demyelination. In addition, cuprizone-induced demyelination was alleviated by the microglia-specific ablation of SIRP. Thus, microglial SIRP suppresses the induction of CD11c+ microglia that have the potential to accelerate the repair of damaged white matter.

neuroscience↗

bioRxiv2018

Use of Next Generation Sequencing to study two Cowpoxvirus outbreaks

BackgroundBetween 2008 and 2011 about 40 cases of human cowpox were reported from Germany and France. Infections had been acquired via close contact to infected, young pet rats. Sequencing of the hemagglutinin gene of various cowpox virus (CPXV) isolates resulted in an identical and unique sequence in each case pointing to a common source. In a second CPXV outbreak in cats in a small animal clinic in Germany in 2015, four out of five hospitalized cats showed identical hemagglutinin sequences and thus, a hospital-acquired transmission was assumed.\n\nMethodsHomogenates of lesion material from rats, cats and humans were cultivated in cell culture. The genomes of 4 virus isolates, 9 CPXVs from our strain collections and from DNA of 3 paraffin-embedded lesion materials were determined by Next Generation Sequencing (NGS). For phylogenetic analyses a MAFFT-alignment was generated. A distance matrix based on concatenated SNPs was calculated and plotted as dendrogram using Unweighted Pair Group Method with Arithmetic mean (UPGMA) for visualization.\n\nResultsAligning of about 200.000 nucleotides of 8 virus isolates associated with the pet rat outbreak revealed complete identity of six genomes, the remainder two genomes differed in as little as 3 SNPs. When comparing this dataset with four already published CPXV genomes also associated with the pet rat outbreak, again a maximum difference of 3 SNPs was found. The outbreak which lasted from 2008 till 2011 was indeed caused by a single strain which has maintained an extremely high level of clonality over 4 years.\n\nAligning genomic sequences from 4 cases of feline cowpox revealed 3 identical sequences and one sequence which differed in 65 nucleotides. Although identical hemagglutinin sequences had been obtained from four hospitalized cats, genomic sequencing proved that a hospital-acquired transmission had occurred in only three cats.\n\nDiscussionAnalyzing the rather short sequence of the hemagglutinin gene is not sufficient to conduct molecular trace back analyses. Instead, whole genome sequencing is the method of choice which can even be applied to paraffin-embedded specimens.\n\nFunding StatementThis publication was supported by the European Virus Archive goes Global (EVAg) project that has received funding from the European Unions Horizon 2020 research and innovation program under grant agreement No 653316.\n\nThis study was also supported in part by the European Unions Horizon 2020 research and innovation program under grant agreement No 643476 (COMPARE).\n\nThe funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

genomics↗

bioRxiv2018

Variation in tolerance to parasites in natural Asian tiger mosquito populations and its effect on vectorial capacity

The vectorial capacity of mosquitoes depends upon the magnitude of reduction of parasite load upon infection through resistance mechanisms (e.g., immune-mediated killing) and the ability of mosquitoes to offset infection-mediated costs through tolerance mechanisms (e.g., tissue repair). Here we use a common-garden experimental framework to measure variation in resistance and tolerance to dog heartworm (Dirofilaria immitis) between natural Aedes albopictus mosquito populations representing areas of low and high transmission intensity. Our data revealed that survival to the extrinsic incubation period, the earliest time point at which infective L3 larvae develop, significantly differed between populations (ranging from 10-60%) when mosquitoes infected with D. immitis at both the low (15 microfilaria/l blood) and high (30 microfilaria/l blood) infection dose (Dose: {chi}2 = 191.473; P < 0.001; Population: {chi}2 = 24.485; P = 0.001; Dose x Population: {chi}2 = 35.566; P = 0.001). Contrary to expectations, we found that mosquito populations with highest resistance (i.e., greatest reduction in parasite load) also exhibited highest mortality upon infection (F1,12 = 6.781, P = 0.023; Dose: F1,12 = 6.747; P = 0.023; Mortality x Dose: F1,12 = 0.111, P = 0.744). Expressing the effect of the number of killed (NKILLED) and live (NLIVE) parasite on survival of mosquitoes from the different population, we document a significant inter-population variation in the survival cost of additional parasite (i.e., tolerance to infection (NLIVE x Population: {chi}2 = 22.845; P = 0.002; NKILLED x Population: {chi}2 = 31.959; P = < 0.001; NLIVE x NKILLED x Population: {chi}2 = 22.266; P = 0.002), in conjunction with negative relationship between tolerance and resistance (Resistance: F1,12 = 11.870, P = 0.005; Dose: F1,12 = 16.0170, P = 0.002; Resistance x Dose: F1,12 = 9.699, P =0.009). Importantly, populations from areas with high transmission intensity (as measured by parasite prevalence in dogs) showed elevated tolerance (Prevalence: F1,12 = 9.5, P = 0.012; Prevalence2: F1,12 = 4.353, P = 0.064; Dose: F1,12 = 38.855, P = <0.001), and these populations were also associated with increased vectorial capacity (Tolerance: F1,12 = 8.175, P = 0.014; Dose: F1,12 = 0.005, P = 0.946; Tolerance x Dose: F1,12 = 0.920, P = 0.356). Consequently, our data indicate that spatial variation in disease transmission intensity is linked to the evolution of tolerance in natural mosquito populations, which in turn can feedback to impact disease risk.

ecology↗

bioRxiv2018

Ecosystem tipping points in an evolving world

There is growing concern over tipping points arising in ecosystems due to the crossing of environmental thresholds. Tipping points lead to strong and possibly irreversible shifts between alternative ecosystem states incurring high societal costs. Traits are central to the feedbacks that maintain alternative ecosystem states, as they govern the responses of populations to environmental change that could stabilize or destabilize ecosystem states. However, we know little about how evolutionary changes in trait distributions over time affect the occurrence of tipping points, and even less about how big scale ecological shifts reciprocally interact with trait dynamics. We argue that interactions between ecological and evolutionary processes should be taken into account for understanding the balance of feedbacks governing tipping points in nature.

ecology↗

bioRxiv2018

Visual plasticity and exercise revisited: no evidence for a \"cycling lane\"

Experiments using enriched environments have shown that physical exercise modulates visual plasticity in rodents. A recent study (Lunghi & Sale, 2015, doi: 10.1016/j.cub.2015.10.026) investigated whether exercise also affects visual plasticity in adult humans. The plastic effect they measured was the shift in ocular dominance caused by 2 hours of monocular deprivation (e.g. by an eye patch). They used a binocular rivalry task to measure this shift. They found that the magnitude of the shift was increased by exercise during the deprivation period. This effect of exercise was later disputed by a study that used a different behavioural task (Zhou et al., 2017, doi: 10.1155/2017/4780876). Our goal was to determine whether the difference in task was responsible for that studys failure to find an exercise effect. We set out to replicate Lunghi & Sale (2015). We measured ocular dominance with a rivalry task before and after 2 hours of deprivation. We measured data from two conditions in 30 subjects. On two separate days they either performed exercise or rested during the deprivation period. Contrary to the previous study, we find no significant effect of exercise. We hypothesise that exercise may affect rivalry dynamics in a way that interacts with the measurement of the deprivation effect.

neuroscience↗

bioRxiv2018

A two-step probing method to compare lysine accessibility across macromolecular complex conformations

Structural models of multi-megadalton molecular complexes are appearing in increasing numbers, in large part because of technical advances in cryo-electron microscopy realized over the last decade. However, the inherent complexity of large biological assemblies comprising dozens of components often limits the resolution of structural models. Furthermore, multiple functional configurations of a complex can leave a puzzle as to how one intermediate moves to the next stage. Orthogonal biochemical information is crucial to understanding the molecular interactions that drive those rearrangements. We present a two-step method for chemical probing detected by tandem mass-spectrometry to globally assess the reactivity of lysine residues within purified macromolecular complexes. Because lysine side chains often balance the negative charge of RNA in ribonucleoprotein complexes, the method is especially powerful for detecting changes in protein-RNA interactions. Probing the E. coli 30S ribosome subunit showed that the reactivity pattern of lysine residues quantitatively reflects structure models from X-ray crystallography. We assessed differences in two conformations of purified human spliceosomes. Our results demonstrate that this method supplies powerful biochemical information that aids in functional interpretation of atomic models of macromolecular complexes at the intermediate resolution often provided by cryo-electron microscopy.

molecular biology↗

bioRxiv2018

Connectome architecture, gene expression and functional co-activation shape the propagation of misfolded proteins in neurodegenerative disease

It is becoming increasingly clear that brain network organization shapes the course and expression of neurodegenerative diseases. Parkinsons disease (PD) is marked by progressive spread of atrophy from the midbrain to subcortical structures and eventually, to the cerebral cortex. Recent discoveries suggest that the neurodegenerative process involves the misfolding and prion-like propagation of endogenous -synuclein via axonal projections. However, the mechanisms that translate local \"synucleinopathy\" to large-scale network dysfunction and atrophy remain unknown. Here we use an agent-based epidemic spreading model to integrate structural connectivity, functional connectivity and gene expression, and to predict sequential volume loss due to neurodegeneration. The dynamic model replicates the spatial and temporal patterning of empirical atrophy in PD and implicates the substantia nigra as the disease epicenter. We reveal a significant role for both connectome topology and geometry in shaping the distribution of atrophy. The model also demonstrates that SNCA and GBA transcription influence -synuclein concentration and local regional vulnerability. Functional co-activation further amplifies the course set by connectome architecture and gene expression. Altogether, these results support the theory that the progression of PD is a multifactorial process that depends on both cell-to-cell spreading of misfolded proteins and regional vulnerability.

neuroscience↗

bioRxiv2018

Transcriptional dynamics following freezing stress reveal selection for mechanisms of freeze tolerance at the poleward range margin in the cold water intertidal barnacle Semibalanus balanoides

The ability to survive freezing has repeatedly evolved across multiple phyla. This suggests that the mechanisms of freeze tolerance must be readily evolvable from basal physiological traits. While several biochemical correlates to freeze tolerance have been described, the mechanism that confers freeze tolerance is still not well understood. To understand both the basic biochemical mechanisms of freeze tolerance as well as their role in local adaptation at the poleward range edge, we conducted a transcriptomic study on two populations (one from the poleward range margin in the White Sea, Russia, and one from the central coast of British Columbia, Canada) of the cold water acorn barnacle Semibalanus balanoides on a time series following a freezing event. We found that the British Columbia population (at the equatorward range margin) was significantly less freeze tolerant than the White Sea population (at the poleward range margin). After assembling and annotating a de novo transcriptome for S. balanoides, we found that the patterns of differential transcript expression following freezing were almost entirely non-overlapping between the two populations, with the White Sea population expressing a series of heat shock proteins in response to freezing stress as well as several aquaporins, while the British Columbia population expressed a series of proteases instead, indicating severe protein damage. We found strong evidence of purifying selection on the significantly upregulated transcripts in the White Sea population, suggesting local adaptation to freezing threat. Taken together, this shows the importance of freeze tolerance to population survival at the poleward range margin, and highlights the central roles of aquaporins and heat shock proteins to the trait of freeze tolerance across taxa.

physiology↗

bioRxiv2018

Targeting endogenous retrovirus gene transcription in human cancers

Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections that make up to 8% of the human genome. Although these elements are mostly fragmented and inactive, many proviruses belonging to the HERV-K (HML-2) family, the only lineage still proliferating in the genome after the human-chimpanzee split, have intact open reading frames, some encoding for accessory genes called np9 and rec that interact with oncogenic pathways. Many studies have established that the transient expression of ERVs are in both stem cells and cancers results in aberrant self-renewal and uncontrolled proliferation.\n\nThe wealth of high-quality genomic and transcriptomic Illumina sequence data available from The Cancer Genome Atlas (TCGA) that are sequenced from a diversity of different tumour types makes it a valuable resource in cancer research. However, there is currently no universal computational method for inferring expression of specific repetitive elements from RNA-seq data, such as genes encoded by HERV-K (HML-2).\n\nThis study presents a novel and a highly specific pipeline that is able to capture and measure transcription of np9 and rec encoded by proviruses that share great sequence similarity, and are transcribed at very low levels. We show by using our novel methodology that np9 and rec are overexpressed in breast cancer, germ cell tumours, skin melanoma, lymphoma, ovarian cancer, and prostate cancer compared to non-diseased tissues. We also show that np9 and rec are specifically expressed in the 8 and 16-cell stage in human preimplantation embryos.

bioinformatics↗

bioRxiv2018

A set of functionally-defined brain regions with improved representation of the subcortex and cerebellum

An important aspect of network-based analysis is robust node definition. This issue is critical for functional brain network analyses, as poor node choice can lead to spurious findings and misleading inferences about functional brain organization. Two sets of functional brain nodes from our group are well represented in the literature: (1) 264 volumetric regions of interest (ROIs) reported in Power et al., 2011 and (2) 333 cortical surface parcels reported in Gordon et al., 2016. However, subcortical and cerebellar structures are either incompletely captured or missing from these ROI sets. Therefore, properties of functional network organization involving the subcortex and cerebellum may be underappreciated thus far. Here, we apply a winner-take-all partitioning method to resting-state fMRI data to generate novel functionally-constrained ROIs in the thalamus, basal ganglia, amygdala, hippocampus, and cerebellum. We validate these ROIs in three datasets using several criteria, including agreement with existing literature and anatomical atlases. Further, we demonstrate that combining these ROIs with established cortical ROIs recapitulates and extends previously described functional network organization. This new set of ROIs is made publicly available for general use, including a full list of MNI coordinates and functional network labels.

neuroscience↗