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    607 results match your criteria Biology Direct [Journal]

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    Predicting clinical outcome of neuroblastoma patients using an integrative network-based approach.
    Biol Direct 2018 Jun 7;13(1):12. Epub 2018 Jun 7.
    Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445, Luxembourg.
    Background: One of the main current challenges in computational biology is to make sense of the huge amounts of multidimensional experimental data that are being produced. For instance, large cohorts of patients are often screened using different high-throughput technologies, effectively producing multiple patient-specific molecular profiles for hundreds or thousands of patients.

    Results: We propose and implement a network-based method that integrates such patient omics data into Patient Similarity Networks. Read More

    Predicting survival times for neuroblastoma patients using RNA-seq expression profiles.
    Biol Direct 2018 May 30;13(1):11. Epub 2018 May 30.
    Department of BiostatisticsUniversity of Florida, 2004 Mowry Rd, Gainesville, 32611, USA.
    Background: Neuroblastoma is the most common tumor of early childhood and is notorious for its high variability in clinical presentation. Accurate prognosis has remained a challenge for many patients. In this study, expression profiles from RNA-sequencing are used to predict survival times directly. Read More

    Unraveling bacterial fingerprints of city subways from microbiome 16S gene profiles.
    Biol Direct 2018 May 22;13(1):10. Epub 2018 May 22.
    Department of Biostatistics, University of Florida, 2004 Mowry Rd, Gainesville, FL, 32610, USA.
    Background: Microbial communities can be location specific, and the abundance of species within locations can influence our ability to determine whether a sample belongs to one city or another. As part of the 2017 CAMDA MetaSUB Inter-City Challenge, next generation sequencing (NGS) data was generated from swipe samples collected from subway stations in Boston, New York City hereafter New York, and Sacramento. DNA was extracted and Illumina sequenced. Read More

    Use of designed sequences in protein structure recognition.
    Biol Direct 2018 May 9;13(1). Epub 2018 May 9.
    Lab 103, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India.
    Background: Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein sequences into families can aid in narrowing the gap. Read More

    Profiling microbial strains in urban environments using metagenomic sequencing data.
    Biol Direct 2018 May 9;13(1). Epub 2018 May 9.
    Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, TN, Italy.
    Background: The microbial communities populating human and natural environments have been extensively characterized with shotgun metagenomics, which provides an in-depth representation of the microbial diversity within a sample. Microbes thriving in urban environments may be crucially important for human health, but have received less attention than those of other environments. Ongoing efforts started to target urban microbiomes at a large scale, but the most recent computational methods to profile these metagenomes have never been applied in this context. Read More

    Conservation of the separase regulatory domain.
    Biol Direct 2018 Apr 27;13(1). Epub 2018 Apr 27.
    Department of Microbiology, University of Tennessee, 1414 Cumberland Ave, Knoxville, TN, 37996, USA.
    ᅟ: We report a protein sequence analysis of the cell cycle regulatory protease, separase. The sequence and structural conservation of the C-terminal protease domain has long been recognized, whereas the N-terminal regulatory domain of separase was reported to lack detectable sequence similarity. Here we reveal significant sequence conservation of the separase regulatory domain and report a discovery of a cysteine motif (CxCxxC) conserved in major lineages of Metazoa including nematodes and vertebrates. Read More

    MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs.
    Biol Direct 2018 Apr 20;13(1). Epub 2018 Apr 20.
    Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.
    Background: There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interactively navigate these large datasets. Long read sequencing technologies continue to improve and produce increasing numbers of longer reads (of varying lengths in the range of 10k-1M bps, say), but of low quality. Read More

    Multi-omics integration for neuroblastoma clinical endpoint prediction.
    Biol Direct 2018 Apr 3;13(1). Epub 2018 Apr 3.
    Fondazione Bruno Kessler, Via Sommarive 18, Trento, 38123, Italy.
    Background: High-throughput methodologies such as microarrays and next-generation sequencing are routinely used in cancer research, generating complex data at different omics layers. The effective integration of omics data could provide a broader insight into the mechanisms of cancer biology, helping researchers and clinicians to develop personalized therapies.

    Results: In the context of CAMDA 2017 Neuroblastoma Data Integration challenge, we explore the use of Integrative Network Fusion (INF), a bioinformatics framework combining a similarity network fusion with machine learning for the integration of multiple omics data. Read More

    Prevalence of loss-of-function alleles does not correlate with lifetime fecundity and other life-history traits in metazoans.
    Biol Direct 2018 Mar 2;13(1). Epub 2018 Mar 2.
    Laboratory of Evolutionary Genomics, A.N. Belozersky Institute of Physico-Chemical Biology of Lomonosov Moscow State Universit, Moscow, 119992, Russia.
    Background: Natural selection is possible only because all species produce more offsprings than what is needed to maintain the population. Still, the lifetime number of offspring varies widely across species. One may expect natural selection to be stronger in high-fecundity species. Read More

    Genes sharing the protein family domain decrease the performance of classification with RNA-seq genomic signatures.
    Biol Direct 2018 Feb 21;13(1). Epub 2018 Feb 21.
    Scientific IT Services, ETH Zurich, Weinbergstrasse 11, Zürich, 8092, Switzerland.
    Background: The experience with running various types of classification on the CAMDA neuroblastoma dataset have led us to the conclusion that the results are not always obvious and may differ depending on type of analysis and selection of genes used for classification. This paper aims in pointing out several factors that may influence the downstream machine learning analysis. In particular those factors are: type of the primary analysis, type of the classifier and increased correlation between the genes sharing a protein domain. Read More

    Finite-size effects in transcript sequencing count distribution: its power-law correction necessarily precedes downstream normalization and comparative analysis.
    Biol Direct 2018 Feb 12;13(1). Epub 2018 Feb 12.
    Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore.
    Background: Though earlier works on modelling transcript abundance from vertebrates to lower eukaroytes have specifically singled out the Zip's law, the observed distributions often deviate from a single power-law slope. In hindsight, while power-laws of critical phenomena are derived asymptotically under the conditions of infinite observations, real world observations are finite where the finite-size effects will set in to force a power-law distribution into an exponential decay and consequently, manifests as a curvature (i.e. Read More

    Efficient differentially private learning improves drug sensitivity prediction.
    Biol Direct 2018 Feb 6;13(1). Epub 2018 Feb 6.
    Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, Helsinki, Finland.
    Background: Users of a personalised recommendation system face a dilemma: recommendations can be improved by learning from data, but only if other users are willing to share their private information. Good personalised predictions are vitally important in precision medicine, but genomic information on which the predictions are based is also particularly sensitive, as it directly identifies the patients and hence cannot easily be anonymised. Differential privacy has emerged as a potentially promising solution: privacy is considered sufficient if presence of individual patients cannot be distinguished. Read More

    Inevitability of the emergence and persistence of genetic parasites caused by evolutionary instability of parasite-free states.
    Biol Direct 2017 Dec 4;12(1):31. Epub 2017 Dec 4.
    Institute for Molecules and Materials, Radboud University, 6525AJ, Nijmegen, Netherlands.
    Genetic parasites, including viruses and mobile genetic elements, are ubiquitous among cellular life forms, and moreover, are the most abundant biological entities on earth that harbor the bulk of the genetic diversity. Here we examine simple thought experiments to demonstrate that both the emergence of parasites in simple replicator systems and their persistence in evolving life forms are inevitable because the putative parasite-free states are evolutionarily unstable.

    Reviewers: This article has been reviewed by Yitzhak Pilpel, Bojan Zagrovic, and Eric van Nimwegen. Read More

    Domestication of self-splicing introns during eukaryogenesis: the rise of the complex spliceosomal machinery.
    Biol Direct 2017 Dec 1;12(1):30. Epub 2017 Dec 1.
    Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.
    ᅟ: The spliceosome is a eukaryote-specific complex that is essential for the removal of introns from pre-mRNA. It consists of five small nuclear RNAs (snRNAs) and over a hundred proteins, making it one of the most complex molecular machineries. Most of this complexity has emerged during eukaryogenesis, a period that is characterised by a drastic increase in cellular and genomic complexity. Read More

    COGcollator: a web server for analysis of distant relationships between homologous protein families.
    Biol Direct 2017 Nov 29;12(1):29. Epub 2017 Nov 29.
    Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.
    Background: The Clusters of Orthologous Groups (COGs) of proteins systematize evolutionary related proteins into specific groups with similar functions. However, the available databases do not provide means to assess the extent of similarity between the COGs.

    Aim: We intended to provide a method for identification and visualization of evolutionary relationships between the COGs, as well as a respective web server. Read More

    Over-expression of miR-146b and its regulatory role in intestinal epithelial cell viability, proliferation, and apoptosis in piglets.
    Biol Direct 2017 Nov 25;12(1):27. Epub 2017 Nov 25.
    Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310021, People's Republic of China.
    Background: Weaning stress affects the small intestine of piglets. MiR-146b is differentially expressed in suckling and weaned piglets. In this study, we evaluated the effects of miR-146b on cell viability, proliferation, and apoptosis in IPEC-J2 cells. Read More

    Sugar Lego: gene composition of bacterial carbohydrate metabolism genomic loci.
    Biol Direct 2017 Nov 25;12(1):28. Epub 2017 Nov 25.
    A.A.Kharkevich Institute for Information Transmission Problems, RAS, Bolshoy Karetny per. 19, Moscow, 127051, Russia.
    Background: Bacterial carbohydrate metabolism is extremely diverse, since carbohydrates serve as a major energy source and are involved in a variety of cellular processes. Bacterial genes belonging to same metabolic pathway are often co-localized in the chromosome, but it is not a strict rule. Gene co-localization in linked to co-evolution and co-regulation. Read More

    COGNAT: a web server for comparative analysis of genomic neighborhoods.
    Biol Direct 2017 Nov 22;12(1):26. Epub 2017 Nov 22.
    School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, Moscow, Russia.
    Background: In prokaryotic genomes, functionally coupled genes can be organized in conserved gene clusters enabling their coordinated regulation. Such clusters could contain one or several operons, which are groups of co-transcribed genes. Those genes that evolved from a common ancestral gene by speciation (i. Read More

    Cellular origin of the viral capsid-like bacterial microcompartments.
    Biol Direct 2017 Nov 13;12(1):25. Epub 2017 Nov 13.
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
    ᅟ: Bacterial microcompartments (BMC) are proteinaceous organelles that structurally resemble viral capsids, but encapsulate enzymes that perform various specialized biochemical reactions in the cell cytoplasm. The BMC are constructed from two major shell proteins, BMC-H and BMC-P, which form the facets and vertices of the icosahedral assembly, and are functionally equivalent to the major and minor capsid proteins of viruses, respectively. This equivalence notwithstanding, neither of the BMC proteins displays structural similarity to known capsid proteins, rendering the origins of the BMC enigmatic. Read More

    ASXL gain-of-function truncation mutants: defective and dysregulated forms of a natural ribosomal frameshifting product?
    Biol Direct 2017 Oct 16;12(1):24. Epub 2017 Oct 16.
    Department of Pathology, Division of Virology, University of Cambridge, Cambridge, CB2 1QP, UK.
    Background: Programmed ribosomal frameshifting (PRF) is a gene expression mechanism which enables the translation of two N-terminally coincident, C-terminally distinct protein products from a single mRNA. Many viruses utilize PRF to control or regulate gene expression, but very few phylogenetically conserved examples are known in vertebrate genes. Additional sex combs-like (ASXL) genes 1 and 2 encode important epigenetic and transcriptional regulatory proteins that control the expression of homeotic genes during key developmental stages. Read More

    Why we don't want another "Synthesis".
    Biol Direct 2017 Oct 2;12(1):23. Epub 2017 Oct 2.
    IBBR, 9600 Gudelsky Drive, Rockville, 20850, MD, USA.
    High-level debates in evolutionary biology often treat the Modern Synthesis as a framework of population genetics, or as an intellectual lineage with a changing distribution of beliefs. Unfortunately, these flexible notions, used to negotiate decades of innovations, are now thoroughly detached from their historical roots in the original Modern Synthesis (OMS), a falsifiable scientific theory. The OMS held that evolution can be adequately understood as a process of smooth adaptive change by shifting the frequencies of small-effect alleles at many loci simultaneously, without the direct involvement of new mutations. Read More

    Differential signal sensitivities can contribute to the stability of multispecies bacterial communities.
    Biol Direct 2017 Sep 15;12(1):22. Epub 2017 Sep 15.
    Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter Street 50/A, Budapest, H-1085, Hungary.
    Background: Bacterial species present in multispecies microbial communities often react to the same chemical signal but at vastly different concentrations. The existence of different response thresholds with respect to the same signal molecule has been well documented in quorum sensing which is one of the best studied inter-cellular signalling mechanisms in bacteria. The biological significance of this phenomenon is still poorly understood, and cannot be easily studied in nature or in laboratory models. Read More

    Evidence-based gene models for structural and functional annotations of the oil palm genome.
    Biol Direct 2017 09 8;12(1):21. Epub 2017 Sep 8.
    Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
    Background: Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes. Read More

    On the global CRISPR array behavior in class I systems.
    Biol Direct 2017 08 29;12(1):20. Epub 2017 Aug 29.
    Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 400 Dan Allen Drive, Schaub Hall, Campus box 7624, Raleigh, NC, 27695-7624, USA.
    Background: Much effort is underway to build and upgrade databases and tools related to occurrence, diversity, and characterization of CRISPR-Cas systems. As microbial communities and their genome complements are unearthed, much emphasis has been placed on details of individual strains and model systems within the CRISPR-Cas classification, and that collection of information as a whole affords the opportunity to analyze CRISPR-Cas systems from a quantitative perspective to gain insight into distribution of CRISPR array sizes across the different classes, types and subtypes. CRISPR diversity, nomenclature, occurrence, and biological functions have generated a plethora of data that created a need to understand the size and distribution of these various systems to appreciate their features and complexity. Read More

    Breath-giving cooperation: critical review of origin of mitochondria hypotheses : Major unanswered questions point to the importance of early ecology.
    Biol Direct 2017 08 14;12(1):19. Epub 2017 Aug 14.
    Eötvös Loránd University, Department of Plant Systematics, Ecology and Theoretical Biology, Pázmány P. sétány 1/C, Budapest, 1117, Hungary.
    The origin of mitochondria is a unique and hard evolutionary problem, embedded within the origin of eukaryotes. The puzzle is challenging due to the egalitarian nature of the transition where lower-level units took over energy metabolism. Contending theories widely disagree on ancestral partners, initial conditions and unfolding of events. Read More

    Cell adhesion heterogeneity reinforces tumour cell dissemination: novel insights from a mathematical model.
    Biol Direct 2017 08 11;12(1):18. Epub 2017 Aug 11.
    Center for Information Services and High Performance Computing, Technische Universität Dresden, Nöthnitzer Str. 46, Dresden, 01062, Germany.
    Background: Cancer cell invasion, dissemination, and metastasis have been linked to an epithelial-mesenchymal transition (EMT) of individual tumour cells. During EMT, adhesion molecules like E-cadherin are downregulated and the decrease of cell-cell adhesion allows tumour cells to dissociate from the primary tumour mass. This complex process depends on intracellular cues that are subject to genetic and epigenetic variability, as well as extrinsic cues from the local environment resulting in a spatial heterogeneity in the adhesive phenotype of individual tumour cells. Read More

    EMQIT: a machine learning approach for energy based PWM matrix quality improvement.
    Biol Direct 2017 08 1;12(1):17. Epub 2017 Aug 1.
    Institute of Automatic Control, Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland.
    Background: Transcription factor binding affinities to DNA play a key role for the gene regulation. Learning the specificity of the mechanisms of binding TFs to DNA is important both to experimentalists and theoreticians. With the development of high-throughput methods such as, e. Read More

    Bacterial tail anchors can target to the mitochondrial outer membrane.
    Biol Direct 2017 07 24;12(1):16. Epub 2017 Jul 24.
    Department of Molecular Biology and Genetics, Koç University, 34450 Sarıyer, İstanbul, Turkey.
    Background: During the generation and evolution of the eukaryotic cell, a proteobacterial endosymbiont was re-fashioned into the mitochondrion, an organelle that appears to have been present in the ancestor of all present-day eukaryotes. Mitochondria harbor proteomes derived from coding information located both inside and outside the organelle, and the rate-limiting step toward the formation of eukaryotic cells may have been development of an import apparatus allowing protein entry to mitochondria. Currently, a widely conserved translocon allows proteins to pass from the cytosol into mitochondria, but how proteins encoded outside of mitochondria were first directed to these organelles at the dawn of eukaryogenesis is not clear. Read More

    Computational prediction of lncRNA-mRNA interactionsby integrating tissue specificity in human transcriptome.
    Biol Direct 2017 06 8;12(1):15. Epub 2017 Jun 8.
    Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1 Okubo Shinjuku-ku, Tokyo, 169-8555, Japan.
    Long noncoding RNAs (lncRNAs) play a key role in normal tissue differentiation and cancer development through their tissue-specific expression in the human transcriptome. Recent investigations of macromolecular interactions have shown that tissue-specific lncRNAs form base-pairing interactions with various mRNAs associated with tissue-differentiation, suggesting that tissue specificity is an important factor controlling human lncRNA-mRNA interactions.Here, we report investigations of the tissue specificities of lncRNAs and mRNAs by using RNA-seq data across various human tissues as well as computational predictions of tissue-specific lncRNA-mRNA interactions inferred by integrating the tissue specificity of lncRNAs and mRNAs into our comprehensive prediction of human lncRNA-RNA interactions. Read More

    Rotational restriction of nascent peptides as an essential element of co-translational protein folding: possible molecular players and structural consequences.
    Biol Direct 2017 05 31;12(1):14. Epub 2017 May 31.
    McLean, Virginia, USA.
    Background: A basic tenet of protein science is that all information about the spatial structure of proteins is present in their sequences. Nonetheless, many proteins fail to attain native structure upon experimental denaturation and refolding in vitro, raising the question of the specific role of cellular machinery in protein folding in vivo. Recently, we hypothesized that energy-dependent twisting of the protein backbone is an unappreciated essential factor guiding the protein folding process in vivo. Read More

    The complex domain architecture of SAMD9 family proteins, predicted STAND-like NTPases, suggests new links to inflammation and apoptosis.
    Biol Direct 2017 05 25;12(1):13. Epub 2017 May 25.
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
    We report a comprehensive computational dissection of the domain architecture of the SAMD9 family proteins that are involved in antivirus and antitumor response in humans. We show that the SAMD9 protein family is represented in most animals and also, unexpectedly, in bacteria, in particular actinomycetes. From the N to C terminus, the core SAMD9 family architecture includes DNA/RNA-binding AlbA domain, a variant Sir2-like domain, a STAND-like P-loop NTPase, an array of TPR repeats and an OB-fold domain with predicted RNA-binding properties. Read More

    Recognition of a structural domain (RWDBD) in Gcn1 proteins that interacts with the RWD domain containing proteins.
    Biol Direct 2017 05 19;12(1):12. Epub 2017 May 19.
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.
    The protein Gcn1 (General control non-derepressible 1) is found in virtually all eukaryotes, and is a key component of the general amino acid control signal transduction pathway. This pathway is best known for its importance for cells to sense and overcome amino acid starvation. Gcn1 directly binds to the RWD (RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases) domain of the protein kinase Gcn2, and this is essential for delivering the starvation signal to Gcn2. Read More

    Demystification of animal symmetry: symmetry is a response to mechanical forces.
    Biol Direct 2017 05 17;12(1):11. Epub 2017 May 17.
    Institute of Psychology, University of Debrecen, H-4002, Debrecen, P.O. Box 400, Hungary.
    ᅟ: Symmetry is an eye-catching feature of animal body plans, yet its causes are not well enough understood. The evolution of animal form is mainly due to changes in gene regulatory networks (GRNs). Based on theoretical considerations regarding fundamental GRN properties, it has recently been proposed that the animal genome, on large time scales, should be regarded as a system which can construct both the main symmetries - radial and bilateral - simultaneously; and that the expression of any of these depends on functional constraints. Read More

    Biochemical and proteomics analyses of antioxidant enzymes reveal the potential stress tolerance in Rhododendron chrysanthum Pall.
    Biol Direct 2017 05 3;12(1):10. Epub 2017 May 3.
    Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, 136000, China.
    Background: Rhododendron chrysanthum Pall., an endangered species with significant ornamental and medicinal value, is endemic to the Changbai Mountain of China and can also serve as a significant plant resource for investigating the stress tolerance in plants. Proteomics is an effective analytical tool that provides significant information about plant metabolism and gene expression. Read More

    Integrative modelling of TIR domain-containing adaptor molecule inducing interferon-β (TRIF) provides insights into its autoinhibited state.
    Biol Direct 2017 04 20;12(1). Epub 2017 Apr 20.
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore, 560065, India.
    Background: TRIF is a key protein in antiviral innate immunity, operating downstream of TLRs. TRIF activation leads to the production of interferon-β and pro-inflammatory cytokines. There is evidence from experiments to suggest that the N-terminal domain of TRIF binds to its TIR domain to avoid constitutive activation. Read More

    TFAP2A is a component of the ZEB1/2 network that regulates TGFB1-induced epithelial to mesenchymal transition.
    Biol Direct 2017 04 17;12(1). Epub 2017 Apr 17.
    Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056, Basel, Switzerland.
    Background: The transition between epithelial and mesenchymal phenotypes (EMT) occurs in a variety of contexts. It is critical for mammalian development and it is also involved in tumor initiation and progression. Master transcription factor (TF) regulators of this process are conserved between mouse and human. Read More

    Adaptive multiscapes: an up-to-date metaphor to visualize molecular adaptation.
    Biol Direct 2017 02 28;12(1). Epub 2017 Feb 28.
    Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
    Background: Wright's metaphor of the fitness landscape has shaped and conditioned our view of the adaptation of populations for almost a century. Since its inception, and including criticism raised by Wright himself, the concept has been surrounded by controversy. Among others, the debate stems from the intrinsic difficulty to capture important features of the space of genotypes, such as its high dimensionality or the existence of abundant ridges, in a visually appealing two-dimensional picture. Read More

    Post translational modification of Parkin.
    Biol Direct 2017 Feb 21;12(1). Epub 2017 Feb 21.
    Department of Biology, University of Padova, Via Ugo Bassi 58b, 35131, Padova, Italy.
    Mutations in the gene encoding for the E3 ubiquitin ligase Parkin are associated to a rare form of familiar autosomal recessive Parkinsonism. Despite decades of research on the Parkin protein, whose structure has been recently solved, little is known about the specific signalling pathways that lead to Parkin activation. Parkin activity spans from mitochondria quality control to tumor suppression and stress protection; it is thus tempting to hypothesize that the broad impact of Parkin on cellular physiology might be the result of different post translational modifications that can be controlled by balanced opposing events. Read More

    Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence.
    Biol Direct 2017 Feb 10;12(1). Epub 2017 Feb 10.
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
    Complementarity between nucleic acid molecules is central to biological information transfer processes. Apart from the basal processes of replication, transcription and translation, complementarity is also employed by multiple defense and regulatory systems. All cellular life forms possess defense systems against viruses and mobile genetic elements, and in most of them some of the defense mechanisms involve small guide RNAs or DNAs that recognize parasite genomes and trigger their inactivation. Read More

    Consistent metagenomic biomarker detection via robust PCA.
    Biol Direct 2017 Jan 31;12(1). Epub 2017 Jan 31.
    College of Veterinary Medicine and Biomedical Sciences, Gastrointestinal Laboratory, Texas A&M University, College Station, 77843-3128, TX, USA.
    Background: Recent developments of high throughput sequencing technologies allow the characterization of the microbial communities inhabiting our world. Various metagenomic studies have suggested using microbial taxa as potential biomarkers for certain diseases. In practice, the number of available samples varies from experiment to experiment. Read More

    Of yeast, mice and men: MAMs come in two flavors.
    Biol Direct 2017 Jan 25;12(1). Epub 2017 Jan 25.
    Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G2H7, Canada.
    The past decade has seen dramatic progress in our understanding of membrane contact sites (MCS). Important examples of these are endoplasmic reticulum (ER)-mitochondria contact sites. ER-mitochondria contacts have originally been discovered in mammalian tissue, where they have been designated as mitochondria-associated membranes (MAMs). Read More

    Thermodynamic and kinetic stability of the Josephin Domain closed arrangement: evidences from replica exchange molecular dynamics.
    Biol Direct 2017 Jan 19;12(1). Epub 2017 Jan 19.
    Istituto Dalle Molle di studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928, Switzerland.
    Background: Molecular phenomena driving pathological aggregation in neurodegenerative diseases are not completely understood yet. Peculiar is the case of Spinocerebellar Ataxia 3 (SCA3) where the conformational properties of the AT-3 N-terminal region, also called Josephin Domain (JD), play a key role in the first step of aggregation, having the JD an amyloidogenic propensity itself. For this reason, unraveling the intimate relationship between JD structural features and aggregation tendency may lead to a step forward in understanding the pathology and rationally design a cure. Read More

    Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models.
    Biol Direct 2017 01 17;12(1). Epub 2017 Jan 17.
    Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, 98109, WA, USA.
    Background: Sites of positive selection are identified by comparing observed evolutionary patterns to those expected under a null model for evolution in the absence of such selection. For protein-coding genes, the most common null model is that nonsynonymous and synonymous mutations fix at equal rates; this unrealistic model has limited power to detect many interesting forms of selection.

    Results: I describe a new approach that uses a null model based on experimental measurements of a gene's site-specific amino-acid preferences generated by deep mutational scanning in the lab. Read More

    Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group.
    Biol Direct 2016 12 28;11(1):69. Epub 2016 Dec 28.
    Department of Biological Sciences, Mississippi State University, PO BOX GY, Mississippi State, MS, 39762, USA.
    Background: Acanthamoebidae is a "family" level amoebozoan group composed of the genera Acanthamoeba, Protacanthamoeba, and very recently Luapeleamoeba. This clade of amoebozoans has received considerable attention from the broader scientific community as Acanthamoeba spp. represent both model organisms and human pathogens. Read More

    Prognostic value of cross-omics screening for kidney clear cell renal cancer survival.
    Biol Direct 2016 12 20;11(1):68. Epub 2016 Dec 20.
    Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland.
    Background: Kidney renal clear cell carcinoma (KIRC) is a type of cancer that is resistant to chemotherapy and radiotherapy and has limited treatment possibilities. Large-scale molecular profiling of KIRC tumors offers a great potential to uncover the genetic and epigenetic changes underlying this disease and to improve the clinical management of KIRC patients. However, in practice the clinicians and researchers typically focus on single-platform molecular data or on a small set of genes. Read More

    Inter-platform concordance of gene expression data for the prediction of chemical mode of action.
    Biol Direct 2016 12 20;11(1):67. Epub 2016 Dec 20.
    Department of Biostatistics, University of Florida, Gainesville, 32603, FL, USA.
    Background: It is interesting to study the consistency of outcomes arising from two genomic platforms: Microarray and RNAseq, which are established on fundamentally different technologies. This topic has been frequently discussed from the prospect of comparing differentially expressed genes (DEGs). In this study, we explore the inter-platform concordance between microarray and RNASeq in their ability to classify samples based on genomic information. Read More

    Sensitivity, specificity, and reproducibility of RNA-Seq differential expression calls.
    Biol Direct 2016 12 20;11(1):66. Epub 2016 Dec 20.
    Chair of Bioinformatics Research Group, Boku University, Vienna, Austria.
    Background: The MAQC/SEQC consortium has recently compiled a key benchmark that can serve for testing the latest developments in analysis tools for microarray and RNA-seq expression profiling. Such objective benchmarks are required for basic and applied research, and can be critical for clinical and regulatory outcomes. Going beyond the first comparisons presented in the original SEQC study, we here present extended benchmarks including effect strengths typical of common experiments. Read More

    Exploring the importance of cancer pathways by meta-analysis of differential protein expression networks in three different cancers.
    Biol Direct 2016 12 20;11(1):65. Epub 2016 Dec 20.
    Department of Biostatistics, University of Florida, Gainesville, FL, 32611, USA.
    Background: It is believed that all cancers occur due to the mutation or change in one or more genes. In order to investigate the significance of the biological pathways which are interrupted by these genetic mutations, we pursue an integrated analysis using multiple cancer datasets released by the International Cancer Genome Consortium (ICGC). This dataset consists of expression profiles for genes/proteins of patients receiving treatment, for three types of cancer - Head and Neck Squamous Cell Carcinoma (HNSC), Lung Adenocarcinoma (LUAD) and Kidney Renal Clear Cell Carcinoma (KIRC). Read More

    The role of the backbone torsion in protein folding.
    Biol Direct 2016 12 1;11(1):64. Epub 2016 Dec 1.
    , McLean, Virginia, USA.
    Background: The set of forces and sequence of events that govern the transition from an unfolded polypeptide chain to a functional protein with correct spatial structure remain incompletely known, despite the importance of the problem and decades of theory development, computer simulations, and laboratory experiments. Information about the correctly folded state of most proteins is likely to be present in their sequences, and yet many proteins fail to attain native structure after overexpression in a non-native environment or upon experimental denaturation and refolding.

    Presentation Of The Hypothesis: We hypothesize that correct protein folding in vivo is an active, energy-dependent process that most likely applies torque force co-translationally to all proteins and possibly also post-translationally to many proteins in every cell. Read More

    xHMMER3x2: Utilizing HMMER3's speed and HMMER2's sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation.
    Biol Direct 2016 11 29;11(1):63. Epub 2016 Nov 29.
    Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore.
    Background: While the local-mode HMMER3 is notable for its massive speed improvement, the slower glocal-mode HMMER2 is more exact for domain annotation by enforcing full domain-to-sequence alignments. Since a unit of domain necessarily implies a unit of function, local-mode HMMER3 alone remains insufficient for precise function annotation tasks. In addition, the incomparable E-values for the same domain model by different HMMER builds create difficulty when checking for domain annotation consistency on a large-scale basis. Read More

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