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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2018

Correlation between the epigenetic modification of histone H3K9 acetylation of NR2B gene promoter in rat hippocampus and ethanol withdrawal syndrome

Our results showed that, in rat hippocampus, the ethanol withdrawal syndrome score was increased at 2 h, peaked at 6 h after withdrawal of ethanol, and reduced to the level parallel to the normal control group at day 3 after ethanol withdrawal. The NR2B mRNA expression and protein levels of rat hippocampus region showed similar patterns. Further correlation analyses indicted that both histone H3K9 acetylation in NR2B gene promoter and the expression levels of NR2B were positively associated with ethanol withdrawal syndrome. Chronic ethanol exposure may result in epigenetic modification of histone H3K9 acetylation in NR2B gene promoter in rat hippocampus, and the expression levels of NR2B were found to be positively correlated with EWS.\n\nAbstractPrevious studies showed that an epigenetic modification of N-methyl-D-aspartate (NMDA) receptor, especially NMDA receptor 2B subunit (NR2B), was involved in the pathological process of ethanol withdrawal syndrome (EWS). However, the relationship between the epigenetic regulation of the NR2B gene in the rat hippocampus region and EWS were inconsistent. A rat model of chronic ethanol exposure was established. EWS score and the behavioral changes were recorded at different points in time. The NR2B expression levels and the histone H3K9 acetylation level in the NR2B gene promoter region were measured using qRT-PCR, Western blot, immunofluorescence and chromatin immunoprecipitation, respectively. Finally, the relationships between the epigenetic modification of histone H3K9 acetylation of NR2B gene promoter and EWS were examined. Our results showed that the EWS score was increased at 2 h, peaked at 6 h after withdrawal of ethanol, and reduced to the level parallel to the normal control group at day 3 after ethanol withdrawal. The NR2B mRNA expression and protein levels showed similar patterns. Further correlation analyses indicted that both histone H3K9 acetylation in NR2B gene promoter and the expression levels of NR2B were positively associated with EWS. Chronic ethanol exposure may result in epigenetic modification of histone H3K9 acetylation in NR2B gene promoter in rat hippocampus, and the expression levels of NR2B were found to be positively correlated with EWS.

neuroscience↗

bioRxiv2018

PBiochemical and physiological investigations on adenosine 5’ monophosphate deaminase from Plasmodium spp

AbbreviationsHGXPRT - Hypoxanthine-guanine-xanthine phosphoribosyltransferase, ADSS - Adenylosuccinate synthetase, ASL - Adenylosuccinate lyase, GMPS - Guonosine monophosphate synthetase, IMPDH - Inosine monophosphate dehydrogenase, ISN1 - Inosine monophosphate specific nucleotidase, PNP - Purine nucleoside phosphorylase\n\nSummaryInterplay between ATP generating and utilizing pathways in a cell is responsible for maintaining cellular ATP/energy homeostasis that is reflected by Adenylate Energy Charge (AEC) ratio. Adenylate kinase (AK), that catalyzes inter-conversion of ADP, ATP and AMP, plays a major role in maintaining AEC, and is regulated by cellular AMP levels. Hence, the enzymes AMP deaminase (AMPD) and nucleotidases, which catabolize AMP, indirectly regulate AK activity and in-turn affect AEC. Here, we present the first report on AMPD from Plasmodium, the causative agent of malaria. The recombinant enzyme expressed in Saccharomyces cerevisiae was studied using functional complementation assay and residues vital for enzyme activity have been identified. Similarities and differences between Plasmodium falciparum AMPD (PfAMPD) and its homologs from yeast, Arabidopsis and humans are also discussed. The AMPD gene was deleted in the murine malaria parasite P. berghei and was found to be non-essential for intra-erythrocytic growth of the knockout parasites. However, when episomal expression was attempted, viable parasites were not obtained, suggesting that perturbing AMP homeostasis by over-expressing AMPD might be lethal. As AMPD is known to be allosterically modulated by ATP, GTP and phosphate, allosteric activators of PfAMPD could be developed as anti-parasitic agents.

biochemistry↗

bioRxiv2018

Is Polygenic Risk Scores Prediction Good?

Polygenic risk score (PRS) is the state-of-art prediction method for complex traits using summary level data from discovery genome-wide association studies (GWAS). The PRS, as its name suggests, is designed for polygenic traits by aggregating small genetic effects from a large number of causal SNPs and thus is viewed as a powerful method for predicting complex polygenic traits by the genetics community. However, one concern is that the prediction accuracy of PRS in practice remains low with little clinical utility, even for highly heritable traits. Another practical concern is whether genome-wide SNPs should be used in constructing PRS or not. To address the two concerns, we investigate PRS both empirically and theoretically. We show how the performance of PRS is influenced by the triplet (n, p, m), where n, p, m are the sample size, the number of SNPs studied, and the number of true causal SNPs, respectively. For a given heritability, we find that i) when PRS is constructed with all p SNPs (referred as GWAS-PRS), its prediction accuracy is controlled by the p/n ratio; while ii) when PRS is built with a set of top-ranked SNPs that pass a pre-specified threshold (referred as threshold-PRS), its accuracy varies depending on how sparse the true genetic signals are. Only when m is magnitude smaller than n, or genetic signals are sparse, can threshold-PRS perform well and outperform GWAS-PRS. Our results demystify the low performance of PRS in predicting highly polygenic traits, which will greatly increase researchers aware-ness of the power and limitations of PRS, and clear up some confusion on the clinical application of PRS.

genetics↗

bioRxiv2018

Massively scalable genetic analysis of antibody repertoires

With technical breakthroughs in the throughput and read-length of next-generation sequencing platforms, antibody repertoire sequencing is becoming an increasingly important tool for detailed characterization of the immune response. There is a need for open, scalable software for the genetic analysis of repertoire-scale antibody sequence data. To address this gap, we have developed the ab[x] package of software tools. There are three core components of the ab[x] toolkit, all of which are freely available: abcloud (github.com/briney/abcloud) for deployment and management of computational resources on Amazons Elastic Compute Cloud; abstar (github.com/briney/abstar) for pre-processing, germline gene assignment and primary annotation of antibody sequence data; and abutils (github.com/briney/abutils), which provides utilities for interactive downstream analysis of antibody repertoire data.

bioinformatics↗

bioRxiv2018

Genomic architecture of parallel ecological divergence: beyond a single environmental contrast

The genetic basis of parallel ecological divergence provides important clues to the operation of natural selection and the predictability of evolution. Many examples exist where binary environmental contrasts seem to drive parallel divergence. However, this simplified view can conceal important components of parallel divergence because environmental variation is often more complex. Here, we disentangle the genetic basis of parallel divergence across two axes of environmental differentiation (crab-predation vs. wave-action and low-shore vs. high-shore habitat contrasts) in the marine snail Littorina saxatilis, a well established natural system of parallel ecological divergence. We used whole-genome resequencing across multiple instances of these two environmental axes, at local and regional scales from Spain to Sweden. Overall, sharing of genetic differentiation is generally low but it is highly heterogeneous across the genome and increases at smaller spatial scales. We identified genomic regions, both overlapping and non-overlapping with recently described candidate chromosomal inversions, that are differentially involved in adaptation to each of the environmental axis. Thus, the evolution of parallel divergence in L. saxatilis is largely determined by the joint action of geography, history, genomic architecture and congruence between environmental axes. We argue that the maintenance of standing variation, perhaps as balanced polymorphism, and/or the re-distribution of adaptive variants via gene flow can facilitate parallel divergence in multiple directions as an adaptive response to heterogeneous environments.

evolutionary biology↗

bioRxiv2018

Somatic mutability in cancer predicts the phenotypic relevance of germline mutations

Genomic sequence mutations in both the germline and somatic cells can be pathogenic. Several authors have observed that often the same genes are involved in cancer when mutated in somatic cells and in genetic diseases when mutated in the germline. Recent advances in high-throughput sequencing techniques have provided us with large databases of both types of mutations, allowing us to investigate this issue in a systematic way. Here we show that high-throughput data about the frequency of somatic mutations in the most common cancers can be used to predict the genes involved in abnormal phenotypes and diseases. The predictive power of somatic mutation patterns is largely independent of that of methods based on germline mutation frequency, so that they can be fruitfully integrated into algorithms for the prioritization of causal variants. Our results confirm the deep relationship between pathogenic mutations in somatic and germline cells, provide new insight into the common origin of cancer and genetic diseases and can be used to improve the identification of new disease genes.

genomics↗

bioRxiv2018

Transposon accumulation lines uncover histone H2A.Z-driven integration bias towards environmentally responsive genes

Inherited transposition events are important drivers of genome evolution but because transposable element (TE) mobilization is usually rare, its impact on the creation of genetic variation remains poorly characterized. Here, we used a population of A. thaliana epigenetic recombinant inbred lines (epiRILs) to characterize >8000 de novo insertions produced by several TEs families also active in nature. Integration was strongly biased towards genes, with evident deleterious effects. Biases were TE family-specific and associated with distinct chromatin features. Notably, we demonstrate that the histone variant H2A.Z guides the preferential integration of Ty1/Copia LTR-retrotransposons within environmentally responsive genes and that this guiding function is evolutionary conserved. Finally, we uncover an important role for epigenetic silencing in exacerbating or alleviating the effects of TE insertions on target genes. These findings establish chromatin as a major determinant of the spectrum and functional impact of TE-generated mutations, with important implications for adaptation and evolution.

genomics↗

bioRxiv2018

Side chain to main chain hydrogen bonds stabilize polyglutamine helices in transcription factors

Polyglutamine (polyQ) tracts are regions of low sequence complexity of variable length found in more than one hundred human proteins. These tracts are frequent in activation domains of transcription factors and their length often correlates with transcriptional activity. In addition, in nine proteins, tract elongation beyond specific thresholds causes polyQ disorders. To study the structural basis of the association between tract length, transcriptional activity and disease, here we addressed how the conformation of the polyQ tract of the androgen receptor (AR), a transcription factor associated with the polyQ disease spinobulbar muscular atrophy (SBMA), depends on its length. We found that the tract folds into a helical structure stabilized by unconventional hydrogen bonds between glutamine side chains and main chain carbonyl groups. These bonds are bifurcate with the conventional main chain to main chain hydrogen bonds stabilizing -helices. In addition, since tract elongation provides additional interactions, the helicity of the polyQ tract directly correlates with its length. These findings suggest a plausible rationale for the association between polyQ tract length and AR transcriptional activity and have implications for establishing the mechanistic basis of SBMA.

biophysics↗

bioRxiv2018

A Systematic Approach to Identify Recycling Endocytic Cargo Depending on the GARP Complex

Proteins and lipids of the plasma membrane underlie constant remodeling via a combination of the secretory- and the endocytic pathway. In the yeast endocytic pathway, cargo is sorted for recycling to the plasma membrane or degradation in vacuoles. In a previous paper we have shown a role for the GARP complex in sphingolipid sorting and homeostasis (Frohlich et al. 2015). However, the majority of cargo sorted in a GARP dependent process remain largely unknown. Here we use auxin induced degradation of GARP combined with mass spectrometry based vacuolar proteomics and lipidomics to show that recycling of two specific groups of proteins, the amino-phospholipid flippases and cell wall synthesis proteins depends on a functional GARP complex. Our results suggest that mis-sorting of flippases and remodeling of the lipid composition are the first occurring defects in GARP mutants. Our assay can be adapted to systematically map cargo of the entire endocytic pathway.

cell biology↗

bioRxiv2018

Comparative analysis of Streptococcus genomes

BackgroundGenome sequencing of multiple strains demonstrated high variability in gene content even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome, that is, the complete set of genes observed in a given species or a higher level taxon. Here we analysed the pan-genome structure and the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae.\n\nResultsFractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions. The total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity.\n\nAbout 7% of single-copy periphery genes have been found in different syntenic regions. More than a half of these genes are rare in all Streptococcus species; others are rare in at least one species. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are candidates for horizontal transfer between species.\n\nAn inversion of length 15 kB found in four independent branches of S. pneumoniae has breakpoints formed by genes encoding a surface antigen protein (PhtD). The observed parallelism may indicate the action of an antigen variation mechanism.\n\nConclusionsMembers of the genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, understanding of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines.

genomics↗

bioRxiv2018

Alternative interaction sites in the influenza A virus nucleoprotein mediate viral escape from the importin-α7 mediated nuclear import pathway

Influenza A viruses are able to adapt to restrictive conditions due to their high mutation rates. Here, we addressed the question by which mechanisms influenza A viruses may escape restriction by the cellular importin-7 protein, a component of the nuclear import machinery required for avian-mammalian adaptation and replicative fitness in human cells. Therefore, we assessed viral evolution in mice lacking the importin-7 gene. Here, we show that particularly three mutations occur with high frequency in the viral NP protein (G102R, M105K and D375N) in a specific structural area upon in vivo adaptation. Moreover, our findings suggest that the adaptive NP mutations mediate viral escape from importin-7 requirement likely due to the utilization of alternative interaction sites in NP beyond the classical nuclear localization signal and importin- isoforms. However, viral escape from importin-7 is, at least in part, associated with reduced replicative fitness in human cells.

molecular biology↗

bioRxiv2018

A tool for analyzing electrode tracks from slice histology

It is now possible to record from hundreds of neurons across multiple brain regions in a single electrophysiology experiment. An essential step in the ensuing data analysis is to assign recorded neurons to the correct brain regions. Brain regions are typically identified after the recordings by comparing images of brain slices to a reference atlas by eye. This introduces error, in particular when slices are not cut at a perfectly coronal angle or when electrode tracks span multiple slices. Here we introduce SHARP-Track, a tool to localize regions of interest and plot the brain regions they pass through. SHARP-Track offers a MATLAB user interface to explore the Allen Mouse Brain Atlas, register asymmetric slice images to the atlas using manual input, and interactively analyze electrode tracks. We find that it reduces error compared to localizing electrodes in a reference atlas by eye. See github.com/cortex-lab/allenCCF for the software and wiki.

neuroscience↗

bioRxiv2018

Bridging the divide: bacteria synthesizing archaeal membrane lipids

Archaea synthesize membranes of isoprenoid lipids that are ether-linked to glycerol, while Bacteria/Eukarya produce membranes consisting of ester-bound fatty acids. This dichotomy in membrane lipid composition or lipid divide is believed to have arisen after the Last Universal Common Ancestor (LUCA). A leading hypothesis is that LUCA possessed a mixed heterochiral archaeal/bacterial membrane, however no natural microbial representatives supporting this scenario have been shown to exist today. Here, we demonstrate that bacteria of the Fibrobacteres-Chlorobi-Bacteroidetes (FCB) group superphylum and related candidate phyla encode a complete pathway for archaeal membrane lipid biosynthesis in addition to the bacterial fatty acid membrane pathway. Key genes were expressed in the environment and their recombinant expression in E. coli resulted in the formation of a mixed archaeal/bacterial membrane. Our results support the existence of mixed membranes in natural environments and their stability over large evolutionary timescales, thereby bridging a once-thought fundamental divide in biology.

evolutionary biology↗

bioRxiv2018

Genomic and transcriptomic determinants of therapy resistance and immune landscape evolution during anti-EGFR treatment in colorectal cancer

Anti-epidermal growth factor receptor (EGFR) antibodies (anti-EGFR-Ab) are effective in a subgroup of patients with metastatic colorectal cancer (CRC). We applied genomic and transcriptomic analyses to biopsies from 35 RAS wild-type CRCs treated with the anti-EGFR-Ab cetuximab in a prospective trial to interrogate the molecular resistance landscape. This validated transcriptomic CRC-subtypes as predictors of cetuximab benefit; identified novel associations of NF1-inactivation and non-canonical RAS/RAF-aberrations with primary progression; and of FGF10- and non-canonical BRAF-aberrations with AR. No genetic resistance drivers were detected in 64% of AR biopsies. The majority of these had switched from the cetuximab-sensitive CMS2-subtype pretreatment to the fibroblast- and growth factor-rich CMS4-subtype at progression. Fibroblast supernatant conferred cetuximab resistance in vitro, together supporting subtype-switching as a novel mechanism of AR. Cytotoxic immune infiltrates and immune-checkpoint expression increased following cetuximab responses, potentially providing opportunities to treat CRCs with molecularly heterogeneous AR with immunotherapy.

cancer biology↗

bioRxiv2018

Tissue morphogenesis mediated by the Arabidopsis receptor kinase STRUBBELIG involves a clathrin-dependent process

HighlightThe Arabidopsis receptor kinase STRUBBELIG is internalized by clathrin-mediated endocytosis and affects clathrin-dependent processes in a tissue-dependent manner.\n\nAbstractSignaling mediated by cell surface receptor kinases is central to the coordination of growth patterns during organogenesis. Receptor kinase signaling is in part controlled through endocytosis and subcellular distribution of the respective receptor kinase. For the majority of plant cell surface receptors the underlying trafficking mechanisms are not characterized. In Arabidopsis, tissue morphogenesis relies on the atypical receptor kinase STRUBBELIG (SUB). Here, we approach the endocytic mechanism of SUB. Our data reveal that a functional SUB:EGFP fusion is ubiquitinated in vivo. We further show that plasma membrane-bound SUB:EGFP becomes internalized in a clathrin-dependent fashion. We also find that SUB:EGFP associates with the trans-Golgi network and accumulates in multivesicular bodies and the vacuole. Coimmunoprecipitation experiments reveal that SUB:EGFP and clathrin are present within the same protein complex. Our genetic analysis shows that SUB and CLATHRIN HEAVY CHAIN 2 promote root hair patterning. By contrast, SUB behaves as a negative regulator of a clathrin-dependent process during floral development. Taken together, the data indicate that SUB undergoes clathrin-mediated endocytosis, that this process does not dependent on stimulation of SUB signaling by an exogenous agent, and that SUB genetically interacts with clathrin-dependent pathways in a tissue-specific manner.

plant biology↗

bioRxiv2018

Multiple polyvalency provided by intrinsically disordered segments is a key feature of postsynaptic scaffold proteins

The human postsynaptic density is an elaborate network comprising thousands of proteins, playing a vital role in the molecular events of learning and the formation of memory. Despite our growing knowledge of specific proteins and their interactions, atomic-level details of their full three-dimensional structure and their rearrangements are mostly elusive. Advancements in structural bioinformatics enabled us to depict the characteristic features of proteins involved in different processes aiding neurotransmission. We show that postsynaptic protein-protein interactions are mediated through the delicate balance of intrinsically disordered regions and folded domains, and this duality is also imprinted in the amino acid sequence. We introduce Diversity of Potential Interactions (DPI), a structure and regulation based descriptor to assess the diversity of interactions. Our approach reveals that the postsynaptic proteome has its own characteristic features and these properties reliably discriminate them from other proteins of the human proteome. Our results suggest that postsynaptic proteins are especially susceptible to forming diverse interactions with each other, which might be key in the reorganization of the PSD in molecular processes related to learning and memory.

bioinformatics↗

bioRxiv2018

The First Implication of Image Processing Techniques on Influenza A Virus Sub-Typing Based on HA/NA Protein Sequences, using Convolutional Deep Neural Network

Increase in influenza A virus host range throughout its evolution has given rise to major concerns worldwide. Although the increasing host range mechanism of the virus is largely unknown; persistent genetic mutations have been blamed as a key factor in the re-organization of the host response and the host range. To uncover the underlying core bases of the two important antigenic proteins of influenza virus (HA and NA), functional data mining and image processing analysis of over 8000 protein sequences of different HA and NA subtypes were performed. Each amino acid sequence in HA or NA proteins sat as a feature or variable and two polynomial datasets were created and subjected into conventional prediction models. The average accuracies of these predictive models for HA subtype classifications ranged from 38.9% for SVM to 87.2% for Decision Tree models. NA subtype classification with conventional prediction models varied from 81.3% to 99.87% for SVM and KNN models, respectively. Then amino acid sequence datasets were converted to binary images; subtypes feature sat as target variable, and target label determined by image processing convolution neural network. The performances of Image processing models (convolutional neural network) on binary images for both HA and NA datasets reached to 100%; and the application of Gabor2 filter decreased the time for the predicting model to reach the best performance for HA subtype; while it increased the epochs time for NA subtype classification.\n\nFor the first time ever, converting influenza virus HA and NA amino acid sequences into the binary image datasets and their classifications by convolution neural network increased the prediction accuracies and performances to the highest possible point. The finding of this paper paves new avenues for virus classification based on antigenic HA and NA amino acid profiles, and easily classifying and predicting the possible future emerging strains of pandemic influenza.

bioinformatics↗

bioRxiv2018

The three dimensional structure of Bovine Salivary Protein 30b (BSP30b) and its interaction with specific rumen bacteria

Bovine Salivary Protein 30b (BSP30b) is a member of the tubular lipid-binding (TULIP) superfamily that includes the human bactericidal/permeability-increasing proteins (BPI), lipopolysaccharide binding proteins (LBP) and palate, lung, and nasal epithelium carcinoma-21 associated proteins (PLUNC). BSP30b is most closely related to the PLUNC family and is predominantly found in bovine saliva. There are four BSP30 isoforms (BSP30a-d) and collectively, they are the most abundant protein component of bovine saliva. The PLUNC family members are proposed to be lipid binding proteins, although in most cases their lipid ligands are unknown. Here, we present the X-ray crystal structure of BSP30b at 2.0 [A] resolution. We used a double methionine mutant and Se-Met SAD phasing to solve the structure. The structure adopts a curved cylindrical form with a hydrophobic channel formed by an /{beta} wrap, which is consistent with the TULIP superfamily. The structure of BSP30b in complex with oleic acid is also presented where the ligand is accommodated within the hydrophobic channel. The electron density for oleic acid suggests that the ligand is only partially occupied in the binding site implying that oleic acid may not be the preferred ligand. GFP-tagged BSP30b binds to the surface of olive oil droplets, as observed under fluorescent microscopy, and acts as a surfactant consistent with its association with decreased susceptibility to bloat in cattle. Bacteria extracted directly from bovine rumen contents indicate that the GFP_BSP30b fusion protein binds to a small number of selected bacterial species in vivo. These results suggest that BSP30b may bind to bacterial lipids from specific species and that this abundant protein may have important biological roles via interacting with rumen bacteria during feeding and rumination.

biochemistry↗