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Results for “Molecular Biology”

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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 127 records · Page 7Linked to original sources

bioRxiv2018

NECorr, a Tool to Rank Gene Importance in Biological Processes using Molecular Networks and Transcriptome Data

The challenge of increasing crop yield while decreasing plants susceptibility to various stresses can be lessened by understanding plant regulatory processes in a tissue-specific manner. Molecular network analysis techniques were developed to aid in understanding gene inter-regulation. However, few tools for molecular network mining are designed to extract the most relevant genes to act upon. In order to find and to rank these putative regulator genes, we generated NECorr, a computational pipeline based on multiple-criteria decision-making algorithms. With the objective of ranking genes and their interactions in a selected condition or tissue, NECorr uses the molecular network topology as well as global gene expression analysis to find hub genes and their condition-specific regulators. NECorr was applied to Arabidopsis thaliana flower tissue and identifies known regulators in the developmental processes of this tissue as well as new putative regulators. NECorr will accelerate translational research by ranking candidate genes within a molecular network of interest.

systems biology↗

bioRxiv2018

Chemical characterization, biological assessment and molecular docking studies of essential oil of Ocimum viride

Ocimum viride (family: Lamiaceae) is a medicinally important aromatic plant that grows widely in north western Himalayan range of Indian subcontinent. Essentials oils (EOs) and purified aromatic compounds derived from plants of genus Ocimum have long been used in traditional system of medicine to treat various chronic disorders. In this study we made an attempt to assess the chemical composition of essential oil (EO) obtained from Ocimum viride for potential antimicrobial and anticancer properties. Gas chromatography-mass spectrometry (GCMS) analysis revealed that EOs of aerial parts (leaves) of Ocimum viride contain high amounts of oxygenated monoterpenes, thymol and gamma terpinene. Notably, thymol (~50%) and {gamma}-terpinene (~18%) were identified as the most abundant components of the oil. EOs showed most prominent antibacterial effect against Bacillus subtilis and in silico molecular docking analyses of antibacterial action against bacterial cell wall of Bacillus subtilis showed interaction of thymol with Sec A protein of Bacillus subtilis (binding energy of -15 kcal/mol) with active site Lys284, Trp275, Leu269, Arg19, Glu277, pro270. While, in vitro cytotoxic effect of EO against six human cancer cell lines showed maximum effect with IC50 value of ~0.034 {+/-} 0.001L/ mL against HT-29 colon cancer cell line. DNA fragmentation analysis and cell cycle analysis revealed that EO inhibits the growth of HT-29 colon cancer cells probably through induction of unrepairable DNA damage and subsequent cell death. Taken together, our results indicate that EO possesses potent antimicrobial and anticancer properties, and may find applications in bacterial growth inhibition and cancer therapeutics.

cancer biology↗

bioRxiv2017

Can CRISPR-based gene drive be confined in the wild? A question for molecular and population biology

The recent discovery of CRISPR and its application as a gene editing tool has enabled a range of gene drive systems to be engineered with much greater ease. In order for the benefits of this technology to be realized, drive systems must be developed that are capable of both spreading into populations to achieve their desired impact, and being recalled in the event of unwanted consequences or public disfavor. We review the performance of three broad categories of drive systems at achieving these goals - threshold-dependent drives, homing-based drive and remediation systems, and temporally self-limiting systems such as daisy-chain drives.

genetics↗

bioRxiv2018

Network-Based Biomarkers Enable Cross-Disease Biomarker Discovery

Biomarkers lie at the heart of precision medicine, biodiversity monitoring, agricultural pathogen detection, amongst others. Surprisingly, while rapid genomic profiling is becoming ubiquitous, the development of biomarkers almost always involves the application of bespoke techniques that cannot be directly applied to other datasets. There is an urgent need for a systematic methodology to create biologically-interpretable molecular models that robustly predict key phenotypes. We therefore created SIMMS: an algorithm that fragments pathways into functional modules and uses these to predict phenotypes. We applied SIMMS to multiple data-types across four diseases, and in each it reproducibly identified subtypes, made superior predictions to the best bespoke approaches, and identified known and novel signaling nodes. To demonstrate its ability on a new dataset, we measured 33 genes/nodes of the PIK3CA pathway in 1,734 FFPE breast tumours and created a four-subnetwork prediction model. This model significantly out-performed existing clinically-used molecular tests in an independent 1,742-patient validation cohort. SIMMS is generic and can work with any molecular data or biological network, and is freely available at: https://cran.r-project.org/web/packages/SIMMS.

bioinformatics↗

bioRxiv2018

Synthesis, Biological Activity and Molecular Docking of New Tricyclic Series as α-glucosidase Inhibitors

Diabetes is an emerging metabolic disorder. -Glucosidase inhibitors, such as acarbose, delay the hydrolysis of carbohydrates by interfering with the digestive enzymes. This action decreases the glucose absorption and the postprandial glucose level. We have synthesized 25 tricyclic 2-phenoxypyrido[3,2-e][1,2,4]triazolo[1,5-a]pyrimidin-5(4H)-ones hybrids and evaluated their -glucosidase inhibitory activity. Compounds 6h and 6d have shown stronger activity than that of acarbose. Compound 6h exhibited the highest inhibition with an IC50 of 104.07 mM. Molecular modelling studies revealed that compound 6h inhibits -glucosidase due to the formation of a stable ligand--glucosidase complex and extra hydrogen bond interactions, and directed in the binding site by Trp329.

biochemistry↗

bioRxiv2017

Coat color allele and mtDNA haplotype distributions in Russian cat populations: a citizen-science research

This work has started as a project for the summer school in molecular and theoretical biology. Efficient teaching and learning modern methods of molecular biology and population genetics in a two-week study course for high school students needs an attractive subject. We chose phylogeography of the domestic cat as the subject of our project because 1) everybody likes cats; 2) cats are polymorphic for several coat color mutations, which can be easily detected by street survey or in the photographs; 3) samples for DNA extraction are easy to collect without posing ethical and biosafety problems; 4) rich background information of geographical distribution of coat color alleles and variation in mtDNA is available; 5) phylogeography of cat population in Russia is poorly studied and therefore new data collected in this large territory may shed a light on the global cat distribution and on the origin of the fancy breeds.\n\nDuring the project students studied coat color and mitotype distribution across Russian random bred cats. The basics of field (observations of natural cat populations, hair collection), formal (inheritance of coat colors), mathematical population (allele frequency distributions and their comparisons, building phylogenetic trees, multidimensional scaling), and molecular (DNA extraction and amplification, quality control of DNA sequencing data) genetics were covered.\n\nWe scored coat color phenotypes in 1182 cats and sequenced mtDNA control region from hair samples of 38 cats from 18 geographical sites. Analysis of coat color alleles frequencies and mitotype distribution confirmed relative homogeneity of gene pools of Russian cat populations, indicating their recent origin. We found several unique mitotypes and demonstrated that OL1 mitotype, previously found only in Siberian fancy breed, was present in random bred cats from several Russian cities. This contributes to the discussion on the origin of the Siberian breed of cats, and supports the view that Siberians is a recent breed created in the 1980s by breeding of selected representatives of the random bred population.

genetics↗

bioRxiv2017

Deciphering the regulation mechanism in biochemical networks by a systems-biology approach

To decipher molecular mechanisms in biological systems from system-level input-output data is challenging especially for complex processes that involve interactions among multiple components. Here, we study regulation of the multi-domain (P1-5) histidine kinase CheA by the MCP chemoreceptors. We develop a network model to describe dynamics of the system treating the receptor complex with CheW and P3P4P5 domains of CheA as a regulated enzyme with two substrates, P1 and ATP. The model enables us to search the hypothesis space systematically for the simplest possible regulation mechanism consistent with the available data. Our analysis reveals a novel dual regulation mechanism wherein besides regulating ATP binding the receptor activity has to regulate one other key reaction, either P1 binding or phosphotransfer between P1 and ATP. Furthermore, our study shows that the receptors only control kinetic rates of the enzyme without changing its equilibrium properties. Predictions are made for future experiments to distinguish the remaining two dual-regulation mechanisms. This systems-biology approach of combining modeling and a large input-output data-set should be applicable for studying other complex biological processes.

systems biology↗

bioRxiv2015

Molecular Mechanisms for the Biological Storage of Renewable Energy

Recent and ongoing discoveries in the field of extracellular electron transport offer the potential to electrically power highly flexible, carbon-fixing microbial metabolisms and generate a rich variety of chemicals and fuels. This process, electrosynthesis, creates the opportunity to use biology for the low cost storage of renewable electricity and the synthesis of fuels that produce no net carbon dioxide. This article highlights recent discoveries on the molecular machinery underpinning electrosynthesis and reviews recent work on the energy conversion efficiency of photosynthesis to begin to establish a framework to quantify the overall energy storage and conversion efficiency of electrosynthesis.

Systems Biology↗

bioRxiv2018

Orthogonal regulation of ferritin translation by human eIF3 and the iron response proteins

A central problem in human biology remains the discovery of causal molecular links between mutations identified in genome-wide association studies (GWAS) and their corresponding disease traits. This challenge is magnified for variants residing in non-coding regions of the genome. Single-nucleotide polymorphisms (SNPs) in the 5 untranslated region (5-UTR) of the ferritin light chain (FTL) gene that cause hyperferritinemia are thought to disrupt translation repression by altering iron regulatory protein (IRP) interactions with the FTL mRNA 5-UTR. Here, we show that human eukaryotic translation initiation factor 3 (eIF3) acts as a distinct repressor of FTL mRNA translation, and eIF3-mediated FTL repression is disrupted by a subset of SNPs in FTL that cause hyperferritinemia. These results identify a direct role for eIF3-mediated translational control in a specific human disease.

molecular biology↗

bioRxiv2016

The Reading Frame Surveillance Hypothesis and the Origins of RNAi

Abbreviations\n\nAbstractAn alternative model for protein translation is presented wherein ribosomes utilize a complementary RNA copy of protein coding sequences to monitor the progress of messenger RNAs during their translation to reduce the frequency of frameshifting errors. The synthesis of this framing RNA is postulated to be catalyzed by the small subunit of the ribosome, in the decoding center, by excising and concatemerizing tRNA anticodons bound to each codon of the mRNA template. Various components of the model are supported by previous observations of tRNA mutants that impact ribosomal frameshifting, unique globin-coding RNAs in developing erythroblasts, and the epigenetic, intergenerational transfer of phenotypic traits via mammalian sperm RNA. Confirmation of the proposed translation mechanism is experimentally tractable and might significantly enhance our understanding of several fundamental biological processes.

Molecular Biology↗

bioRxiv2018

Gene expression across tissues, sex, and life stages in the sea urchin Tripneustes gratilla

The pan-tropical sea urchin Tripneustes gratilla is an ecologically and economically important shallow water algal grazer. The aquaculture of T. gratilla has spurred growing interest in the population biology of the species, and by extension the generation of more molecular resources. To this purpose, de novo transcriptomes of T. gratilla were generated for two adults, a male and a female, as well as for a cohort of approximately 1,000 plutei larvae. Gene expression profiles of three adult tissue samples were quantified and compared. These samples were of gonadal tissue, the neural ring, and pooled tube feet and pedicellariae. Levels of shared and different gene expression between sexes, as well as across functional categories of interest, including the immune system, toxins, genes involved in fertilization, and sensory genes are highlighted. Differences in expression of Sex determining Region Y-related High Mobility Group box groups and general isoform expression between the sexes is observed. Additionally an expansion of the tumor suppressor DMBT1 was observed in T. gratilla when compared to the annotated genome of the sea urchin Strongylocentrotus purpuratus. The draft transcriptome of T. gratilla is presented here in order to facilitate more genomic level analysis of de-novo sea urchin systems.

molecular biology↗

bioRxiv2017

High sensitivity quantitative proteomics using accumulated ion monitoring and automated multidimensional nano-flow chromatography

Quantitative proteomics using high-resolution and accuracy mass spectrometry promises to transform our understanding of biological systems and disease. Recent development of parallel reaction monitoring (PRM) using hybrid instruments substantially improved the specificity of targeted mass spectrometry. Combined with high-efficiency ion trapping, this approach also provided significant improvements in sensitivity. Here, we investigated the effects of ion isolation and accumulation on the sensitivity and quantitative accuracy of targeted proteomics using the recently developed hybrid quadrupole-Orbitrap-linear ion trap mass spectrometer. We leveraged ultra-high efficiency nano-electrospray ionization under optimized conditions to achieve yoctomolar sensitivity with more than seven orders of linear quantitative accuracy. To enable sensitive and specific targeted mass spectrometry, we implemented an automated, scalable two-dimensional (2D) ion exchange-reversed phase nano-scale chromatography system. We found that 2D chromatography improved the sensitivity and accuracy of both PRM and an intact precursor scanning mass spectrometry method, termed accumulated ion monitoring (AIM), by more than 100-fold. Combined with automated 2D nano-scale chromatography, AIM achieved sub-attomolar limits of detection of endogenous proteins in complex biological proteomes. This allowed quantitation of absolute abundance of the human transcription factor MEF2C at approximately 100 molecules/cell, and determination of its phosphorylation stoichiometry from as little as 1 g of extracts isolated from 10,000 human cells. The combination of automated multidimensional nano-scale chromatography and targeted mass spectrometry should enable ultra-sensitive high-accuracy quantitative proteomics of complex biological systems and diseases.

molecular biology↗

bioRxiv2018

POT1a depletion in the developing brain leads to p53-dependent neuronal cell death and ataxia.

The processes that control genome stability are essential for the development of the Central Nervous System (CNS) and the prevention of neurological disease. Here we investigated whether activation of a DNA damage response by dysfunctional telomeres affects neurogenesis. More specifically, we analyzed ATR-dependent DNA damage response by depletion of POT1a in neural progenitors. These experiments revealed that POT1a inactivation leads to a partially penetrant lethality, and surviving mice displayed ataxia due to loss of neuronal progenitor cells, and died by 3 weeks of age. Inactivation of p53 was sufficient to completely suppress the lethality associated with POT1a depletion and rescued the neuronal defects characterizing POT1a depleted animals. In contrast, activation of ATM by the depletion of the shelterin protein TRF2 resulted in a fully penetrant lethality that could not be rescued by p53 inactivation (Lobanova et al.). This data reveals that activation of distinct types of DNA damage response pathway give rise to different types of neuropathology. Moreover, our data provides an explanation for the heterogeneity of the neurological defects observed in patients affected by telomere biological disorders.

molecular biology↗

bioRxiv2018

Excised linear introns regulate growth in yeast

Spliceosomal introns are ubiquitous non-coding RNAs typically destined for rapid debranching and degradation. Here, we describe 34 excised Saccharomyces cerevisiae introns that, although rapidly degraded in log-phase growth, accumulate as linear RNAs under either saturated-growth conditions or other stresses that cause prolonged inhibition of TORC1, a key integrator of growth signaling. Introns that become stabilized remain associated with components of the spliceosome and differ from the other spliceosomal introns in having a short distance between their lariat branch point and 3' splice site, which is necessary and sufficient for their stabilization. Deletion of these unusual introns is disadvantageous in saturated conditions and causes aberrantly high growth rates of yeast chronically challenged with the TORC1 inhibitor rapamycin. Reintroduction of native or engineered stable introns suppresses this aberrant rapamycin response. Thus, excised introns function within the TOR growth-signaling network of S. cerevisiae, and more generally, excised spliceosomal introns can have biological functions.

molecular biology↗

bioRxiv2018

Previously characterized Caenorhabditis elegans RNA interference-resistant mutants retain substantial silencing capacity

RNA interference is a powerful tool for dissecting gene function. In Caenorhabditis elegans, ingestion of double stranded RNA causes strong, systemic knockdown of target genes. Further insight into gene function can be revealed by tissue-specific RNAi techniques. Currently available tissue-specific C. elegans strains rely on rescue of RNAi function in a desired tissue or cell in an otherwise RNAi deficient genetic background. We attempted to assess the contribution of specific tissues to polyunsaturated fatty acid (PUFA) synthesis using currently available tissue-specific RNAi strains. We discovered that rde-1 (ne219), a commonly used RNAi-resistant mutant strain, retains considerable RNAi capacity against RNAi directed at PUFA synthesis genes. By measuring changes in the fatty acid products of the desaturase enzymes that synthesize PUFAs, we found that the before mentioned strain, rde-1 (ne219) and the reported germline only RNAi strain, rrf-1 (pk1417) are not appropriate genetic backgrounds for tissue-specific RNAi experiments. However, the knockout mutant rde-1 (ne300) was strongly resistant to dsRNA induced RNAi, and thus is more appropriate for construction of a robust tissue-specific RNAi strains. Using newly constructed strains in the rde-1(null) background, we found considerable desaturase activity in intestinal, epidermal, and germline tissues, but not in muscle. The RNAi-specific strains reported in this study will be useful tools for C. elegans researchers studying a variety of biological processes.

molecular biology↗

bioRxiv2015

Methods for distinguishing between protein-coding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs

Long noncoding RNAs (lncRNAs) are a diverse class of RNAs with increasingly appreciated functions in vertebrates, yet much of their biology remains poorly understood. In particular, it is unclear to what extent the current catalog of over 10,000 distinct annotated lncRNAs is indeed devoid of genes coding for proteins. Here we review the available computational and experimental schemes for distinguishing between coding and noncoding transcripts and assess the conclusions from their recent genome-wide applications. We conclude that the model most consistent with available data is that a large number of mammalian lncRNAs undergo translation, but only a very small minority of such translation events result in stable and functional peptides. The outcome of the majority of the translation events and their potential biological purposes remain an intriguing topic for future investigation.

Molecular Biology↗

bioRxiv2018

Widespread separation of the polypyrimidine tract from 3’ AG by G tracts in association with alternative exons in metazoa and plants

At the end of introns, the polypyrimidine tract (Py) is often close to the 3 AG in a consensus (Y)20NCAGgt in humans. Interestingly, we have found that they could also be separated by purine-rich elements including G tracts in thousands of human genes. These regulatory elements between the Py and 3AG (REPA) mainly regulate alternative 3 splice sites (3SS) and intron retention. Here we show their widespread distribution and special properties across kingdoms. The purine-rich 3SS are found in up to about 60% of the introns among more than 1000 species/lineages by whole genome analysis, and up to 18% of these introns contain the REPA G tracts in about 2.4 millions of 3SS in total. In particular, they are significantly enriched over their 3SS and genome backgrounds in metazoa and plants, and highly associated with alternative splicing of genes in diverse functional clusters. They are also highly enriched (3-6 folds) in the canonical as well as aberrantly used 3 splice sites in cancer patients carrying mutations of the branch point factor SF3B1 or the 3AG binding factor U2AF35. Moreover, the REPA G tract-harbouring 3SS have significantly reduced occurrences of branch point (BP) motifs between the -24 and -4 positions, in particular absent from the -7 - -5 positions in several model organisms examined. The more distant branch points are associated with increased occurrences of alternative splicing in human and zebrafish. The branch points, REPA G tracts and associated 3SS motifs appear to have emerged differentially in a phylum- or species-specific way during evolution. Thus, there is widespread separation of the Py and 3AG by REPA G tracts, likely evolved among different species or branches of life. This special 3SS arrangement contributes to the generation of diverse transcript or protein isoforms in biological functions or diseases through alternative or aberrant splicing.

molecular biology↗

bioRxiv2018

The Human RNA-Binding Proteome and Its Dynamics During Arsenite-Induced Translational Arrest

Proteins and RNA functionally and physically intersect in multiple biological processes, however, currently no universal method is available to purify protein-RNA complexes. Here we introduce XRNAX, a method for the generic purification of protein-crosslinked RNA, and demonstrate its versatility to study the composition and dynamics of protein-RNA interactions by various transcriptomic and proteomic approaches. We show that XRNAX captures all RNA biotypes, and use this to characterize the sub-proteomes that interact with coding and non-coding RNAs (ncRNAs), and to identify hundreds of protein-RNA interfaces. Exploiting the quantitative nature of XRNAX, we observe drastic remodeling of the RNA-bound proteome during arsenite-induced stress, distinct from autophagy-induced changes in the total proteome. In addition, we combine XRNAX with CLIP-seq to validate the interaction of ncRNA with Lamin B and EXOSC2. Thus, XRNAX is a resourceful approach to study structural and compositional aspects of protein-RNA interactions to address fundamental questions in RNA-biology.

molecular biology↗