Cryo-electron microscopy analysis of structurally heterogeneous macromolecular complexes
Publication date: Available online 14 October 2016 Source:Computational and Structural Biotechnology Journal Author(s): Slavica Jonić Cryo-electron microscopy (cryo-EM) has for a long time been a technique of choice for determining structure of large and flexible macromolecular complexes that were difficult to study by other experimental techniques such as X-ray crystallography or nuclear magnetic resonance. However, a fast development of instruments and software for cryo-EM in the last decade has allowed that a large range of complexes can be studied by cryo-EM, and that their structures can be obtained at near-atomic r...
Source: Computational and Structural Biotechnology Journal - October 14, 2016 Category: Biotechnology Source Type: research

Unbiased Mitoproteome Analyses Confirm Non-canonical RNA, Expanded Codon Translations
Publication date: Available online 5 October 2016 Source:Computational and Structural Biotechnology Journal Author(s): Hervé Seligmann Proteomic MS/MS mass spectrometry detections are usually biased towards peptides cleaved by experimentally added digestion enzyme(s). Hence peptides resulting from spontaneous degradation and natural proteolysis usually remain undetected. Previous analyses of tryptic human proteome data (cleavage after K, R) detected non-canonical tryptic peptides translated according to tetra- and pentacodons (codons expanded by silent mono- and dinucleotides), and from transcripts systematically (...
Source: Computational and Structural Biotechnology Journal - October 10, 2016 Category: Biotechnology Source Type: research

A Review on Automatic Analysis Techniques for Color Fundus Photographs
We present several state-of-the-art procedures to extract the anatomic components and lesions in color fundus photographs and decision support methods to help clinical diagnosis. We list publicly available databases and appropriate measurement techniques to compare quantitatively the performance of these approaches. Furthermore, we discuss on how the performance of image processing-based systems can be improved by fusing the output of individual detector algorithms. Retinal image analysis using mobile phones is also addressed as an expected future trend in this field. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - October 10, 2016 Category: Biotechnology Source Type: research

The promises of quantitative systems pharmacology modelling for drug  development
Publication date: Available online 23 September 2016 Source:Computational and Structural Biotechnology Journal Author(s): V.R. Knight-Schrijver, V. Chelliah, L. Cucurull-Sanchez, N. Le Novère Recent growth in annual new therapeutic entity (NTE) approvals by the U.S. Food and Drug Administration (FDA) suggests a positive trend in current research and development (R&D) output. Prior to this, the cost of each NTE was considered to be rising exponentially, with compound failure occurring mainly in clinical phases. Quantitative systems pharmacology (QSP) modelling, as an additional tool in the drug discovery ars...
Source: Computational and Structural Biotechnology Journal - October 1, 2016 Category: Biotechnology Source Type: research

Catch me if you can: Leukemia escape after CD19-directed T cell immunotherapies
Publication date: Available online 28 September 2016 Source:Computational and Structural Biotechnology Journal Author(s): Marco Ruella, Marcela V. Maus Immunotherapy is the revolution in cancer treatment of this last decade. Among multiple successful approaches able to harness the power of the immune system against cancer, T cell based immunotherapies represent one of the most successful examples. In particular, biotechnological engineering of protein structures, like the T cell receptor or immunoglobulins, allowed the generation of synthetic peptides like bispecific antibodies and chimeric antigen receptors that are able...
Source: Computational and Structural Biotechnology Journal - September 28, 2016 Category: Biotechnology Source Type: research

The promises of quantitative systems pharmacology modelling for drug development
Publication date: Available online 23 September 2016 Source:Computational and Structural Biotechnology Journal Author(s): V.R. Knight-Schrijver, V. Chelliah, L. Cucurull-Sanchez, N. Le Novère Recent growth in annual new therapeutic entity (NTE) approvals by the U.S Food and Drug Administration (FDA) suggests a positive trend in current research and development (R&D) output. Prior to this, the cost of each NTE was considered to be rising exponentially, with compound failure occurring mainly in clinical phases. Quantitative Systems Pharmacology (QSP) modelling, as an additional tool in the drug discovery arse...
Source: Computational and Structural Biotechnology Journal - September 24, 2016 Category: Biotechnology Source Type: research

Zebrafish Small Molecule Screens: Taking the Phenotypic Plunge
Publication date: Available online 18 September 2016 Source:Computational and Structural Biotechnology Journal Author(s): Charles H. Williams, Charles C. Hong Target based chemical screens are a mainstay of modern drug discovery, but the effectiveness of this reductionist approach is being questioned in light of declines in pharmaceutical R & D efficiency. In recent years, phenotypic screens have gained increasing acceptance as a complementary/alternative approach to early drug discovery. We discuss the various model organisms used in phenotypic screens, with particular focus on zebrafish, which has emerged as a l...
Source: Computational and Structural Biotechnology Journal - September 19, 2016 Category: Biotechnology Source Type: research

Classification and substrate head-group specificity of membrane fatty acid desaturases
Publication date: Available online 12 September 2016 Source:Computational and Structural Biotechnology Journal Author(s): Dongdi Li, Ruth Moorman, Thomas Vanhercke, James Petrie, Surinder Singh, Colin J. Jackson Membrane fatty acid desaturases are a diverse superfamily of enzymes that catalyze the introduction of double bonds into fatty acids. They are essential in a range of metabolic processes, such as the production of omega-3 fatty acids. However, our structure–function understanding of this superfamily is still developing and their range of activities and substrate specificities are broad, and often overlapping...
Source: Computational and Structural Biotechnology Journal - September 13, 2016 Category: Biotechnology Source Type: research

Evolution of Biomedical Ontologies and Mappings: Overview of Recent Approaches
Publication date: Available online 26 August 2016 Source:Computational and Structural Biotechnology Journal Author(s): Anika Groß, Cédric Pruski, Erhard Rahm Biomedical ontologies are heavily used to annotate data, and different ontologies are often interlinked by ontology mappings. These ontology-based mappings and annotations are used in many applications and analysis tasks. Since biomedical ontologies are continuously updated dependent artifacts can become outdated and need to undergo evolution as well. Hence there is a need for largely automated approaches to keep ontology-based mappings up-to-date in the...
Source: Computational and Structural Biotechnology Journal - August 26, 2016 Category: Biotechnology Source Type: research

MbT-Tool: An open-access tool based on Thermodynamic Electron Equivalents Model to obtain microbial-metabolic reactions to be used in biotechnological process
Publication date: Available online 26 August 2016 Source:Computational and Structural Biotechnology Journal Author(s): Pablo Araujo Granda, Anna Gras, Marta Ginovart Modelling cellular metabolism is a strategic factor in investigating microbial behaviour and interactions, especially for bio-technological processes. A key factor for modelling microbial activity is the calculation of nutrient amounts and products generated as a result of the microbial metabolism. Representing metabolic pathways through balanced reactions is a complex and time-consuming task for biologists, ecologists, modellers and engineers. A new computat...
Source: Computational and Structural Biotechnology Journal - August 26, 2016 Category: Biotechnology Source Type: research

Novel Cell-Ess ® supplement used as a feed or as an initial boost to CHO serum free media results in a significant increase in protein yield and production
In this study, we investigated the ability of a lipid supplement to increase protein yield. At a concentration of 1% (v/v) the lipid supplement caused a significant increase in protein titer (1118±65.4ng105 cells−1 days−1) when compared to cultures grown in the absence of supplementation (819.3±38.1ng105 cells−1 days−1; p<0.05). This equated to a 37% increase in productivity. Furthermore, metabolic profiles of ammonia, glutamate, lactate, and glucose were not significantly altered by the polar lipid supplement. In a separate set of experiments, using the supplement as a feed res...
Source: Computational and Structural Biotechnology Journal - August 5, 2016 Category: Biotechnology Source Type: research

Antibodies inside of a cell can change its outside: Can intrabodies provide a new therapeutic paradigm?
Publication date: Available online 31 July 2016 Source:Computational and Structural Biotechnology Journal Author(s): Andrea L.J. Marschall, Stefan Dübel Challenges posed by complex diseases such as cancer, chronic viral infections, neurodegenerative disorders and many others have forced researchers to think beyond classic small molecule drugs, exploring new therapeutic strategies such as therapy with RNAi, CRISPR-Cas9 or antibody therapies as single or as combination therapies with existing drugs. While classic antibody therapies based on parenteral application can only reach extracellular targets, intracellular appl...
Source: Computational and Structural Biotechnology Journal - August 1, 2016 Category: Biotechnology Source Type: research

Well-characterized sequence features of eukaryote genomes and implications for ab initio gene prediction
Publication date: Available online 27 July 2016 Source:Computational and Structural Biotechnology Journal Author(s): Ying Huang, Shi-Yi Chen, Feilong Deng In silico analysis of DNA sequences is an important area of computational biology in the post-genomic era. Over the past two decades, computational approaches for ab initio prediction of gene structure from genome sequence alone have largely facilitated our understanding on a variety of biological questions. Although the computational prediction of protein-coding genes has already been well-established, we are also facing challenges to robustly find the non-coding R...
Source: Computational and Structural Biotechnology Journal - July 28, 2016 Category: Biotechnology Source Type: research

Visible and subvisible particles in the BCG immunotherapeutic product ImmuCyst ®
In this study, an Electrical Sensing Zone (ESZ) method was developed to measure the particle count and the size of BCG immunotherapeutic (BCG IT), or ImmuCyst® product using a Coulter Counter Multisizer 4® instrument. The focus of this study was to establish a baseline for reconstituted lyophilized BCG IT product using visible and sub-visible particle concentration and size distribution as reportable values. ESZ method was used to assess manufacturing process consistency using 20 production scale lots of BCG IT product. The results demonstrated that ESZ can be used to accumulate product and process knowledge of BCG...
Source: Computational and Structural Biotechnology Journal - July 21, 2016 Category: Biotechnology Source Type: research

Disease, Models, Variants and Altered Pathways —Journeying RGD Through the Magnifying Glass
Publication date: 2016 Source:Computational and Structural Biotechnology Journal, Volume 14 Author(s): Victoria Petri, G. Thomas Hayman, Marek Tutaj, Jennifer R. Smith, Stan Laulederkind, Shur-Jen Wang, Rajni Nigam, Jeff De Pons, Mary Shimoyama, Melinda R. Dwinell Understanding the pathogenesis of disease is instrumental in delineating its progression mechanisms and for envisioning ways to counteract it. In the process, animal models represent invaluable tools for identifying disease-related loci and their genetic components. Amongst them, the laboratory rat is used extensively in the study of many conditions a...
Source: Computational and Structural Biotechnology Journal - July 21, 2016 Category: Biotechnology Source Type: research

A Single-use Strategy to Enable Manufacturing of Affordable Biologics
Publication date: Available online 5 July 2016 Source:Computational and Structural Biotechnology Journal Author(s): Renaud Jacquemart, Melissa Vandersluis, Mochao Zhao, Karan Sukhija, Navneet Sidhu, Jim Stout The current processing paradigm of large manufacturing facilities dedicated to single product production is no longer an effective approach for best manufacturing practices. Increasing competition for new indications and the launch of biosimilars for the monoclonal antibody market has put pressure on manufacturers to produce at lower cost. Single-use technologies and continuous upstream processes have proven t...
Source: Computational and Structural Biotechnology Journal - July 9, 2016 Category: Biotechnology Source Type: research

Biophysical and computational methods to analyze amino acid interaction networks in proteins
Publication date: 2016 Source:Computational and Structural Biotechnology Journal, Volume 14 Author(s): Kathleen F. O'Rourke, Scott D. Gorman, David D. Boehr Globular proteins are held together by interacting networks of amino acid residues. A number of different structural and computational methods have been developed to interrogate these amino acid networks. In this review, we describe some of these methods, including analyses of X-ray crystallographic data and structures, computer simulations, NMR data, and covariation among protein sequences, and indicate the critical insights that such methods provide into protein...
Source: Computational and Structural Biotechnology Journal - July 7, 2016 Category: Biotechnology Source Type: research

Developing a mobile application to better inform patients and enable effective consultation in implant dentistry
Publication date: Available online 29 June 2016 Source:Computational and Structural Biotechnology Journal Author(s): Erokan Canbazoglu, Yucel Batu Salman, Mustafa Eren Yildirim, Burak Merdenyan, I. Furkan Ince The field of dentistry lacks satisfactory tools to help visualize planned procedures and their potential results to patients. Dentists struggle to provide an effective image in their patient's mind of the end results of the planned treatment only through verbal explanations. Thus, verbal explanations alone often cannot adequately help the patients make a treatment decision. Inadequate attempts are frequently m...
Source: Computational and Structural Biotechnology Journal - July 7, 2016 Category: Biotechnology Source Type: research

Dry and wet approaches for genome-wide functional annotation of conventional and unconventional transcriptional activators
Publication date: Available online 29 June 2016 Source:Computational and Structural Biotechnology Journal Author(s): Elisabetta Levati, Sara Sartini, Simone Ottonello, Barbara Montanini Transcription factors (TFs) are master gene products that regulate gene expression in response to a variety of stimuli. They interact with DNA in a sequence-specific manner using a variety of DNA-binding domain (DBD) modules. This allows to properly position their second domain, called “effector domain”, to directly or indirectly recruit positively or negatively acting co-regulators including chromatin modifiers, thus modu...
Source: Computational and Structural Biotechnology Journal - July 7, 2016 Category: Biotechnology Source Type: research

Chimeric mitochondrial peptides from contiguous regular and swinger RNA
Publication date: Available online 29 June 2016 Source:Computational and Structural Biotechnology Journal Author(s): Hervé Seligmann Previous mass spectrometry analyses described human mitochondrial peptides entirely translated from swinger RNAs, RNAs where polymerization systematically exchanged nucleotides. Exchanges follow one among 23 bijective transformation rules, nine symmetric exchanges (X↔Y, e.g. A↔C) and fourteen asymmetric exchanges (X→Y→Z→X, e.g. A→C→G→A), multiplying by 24 DNA's protein coding potential. Abrupt switches from regular to swinger polymerization pr...
Source: Computational and Structural Biotechnology Journal - July 7, 2016 Category: Biotechnology Source Type: research

A Single -Use Strategy to Enable Manufacturing of Affordable Biologics
Publication date: Available online 5 July 2016 Source:Computational and Structural Biotechnology Journal Author(s): Renaud Jacquemart, Melissa Vandersluis, Mochao Zhao, Karan Sukhija, Navneet Sidhu, Jim Stout The current processing paradigm of large manufacturing facilities dedicated to single product production is no longer an effective approach for best manufacturing practices. Increasing competition for new indications and the launch of biosimilars for the monoclonal antibody market has put pressure on manufacturers to produce at lower cost. Single-use technologies and continuous upstream processes have proven t...
Source: Computational and Structural Biotechnology Journal - July 7, 2016 Category: Biotechnology Source Type: research

Application of the protein maker as a platform purification system for therapeutic antibody research and development
Publication date: Available online 16 June 2016 Source:Computational and Structural Biotechnology Journal Author(s): Geneviève Hélie, Marie Parat, Frédéric Massé, Cory J. Gerdts, Thomas P. Loisel, Allan Matte Within the research and development environment, higher throughput, parallelized protein purification is required for numerous activities, from small scale purification of monoclonal antibodies (mAbs) and antibody fragments for in vitro and in vivo assays to process development and optimization for manufacturing. Here, we describe specific applications and associated workflow...
Source: Computational and Structural Biotechnology Journal - June 17, 2016 Category: Biotechnology Source Type: research

Deep brain stimulation versus motor cortex stimulation for neuropathic pain: A minireview of the literature and proposal for future research
Publication date: Available online 16 June 2016 Source:Computational and Structural Biotechnology Journal Author(s): C. Michael Honey, Volker M. Tronnier, Christopher R. Honey The treatment of neuropathic pain remains a public health concern. A growing cohort of patients is plagued by medically refractory, unrelenting severe neuropathic pain that ruins their quality of life and productivity. For this group, neurosurgery can offer two different kinds of neuromodulation that may help: deep brain simulation (DBS) and motor cortex stimulation (MCS). Unfortunately, there is no consensus on how to perform these procedures, ...
Source: Computational and Structural Biotechnology Journal - June 17, 2016 Category: Biotechnology Source Type: research

Sequence comparison, molecular modeling, and network analysis predict structural diversity in cysteine proteases from the Cape sundew, Drosera capensis
Publication date: Available online 14 June 2016 Source:Computational and Structural Biotechnology Journal Author(s): Carter T. Butts, Xuhong Zhang, John E. Kelly, Kyle W. Roskamp, Megha H. Unhelkar, J. Alfredo Freites, Seemal Tahir, Rachel W. Martin Carnivorous plants represent a so far underexploited reservoir of novel proteases with potentially useful activities. Here we investigate 44 cysteine proteases from the cape sundew, Drosera capensis, predicted from genomic DNA sequences. D. capensis has a large number of cysteine protease genes; analysis of their sequences reveals homologs of known plant proteases, so...
Source: Computational and Structural Biotechnology Journal - June 14, 2016 Category: Biotechnology Source Type: research

MicroRNAs and Oncogenic Transcriptional Regulatory Networks Controlling Metabolic Reprogramming in Cancers
Publication date: Available online 4 June 2016 Source:Computational and Structural Biotechnology Journal Author(s): Pannapa Pinweha, Khanti Rattanapornsompong, Varodom Charoensawan, Sarawut Jitrapakdee Altered cellular metabolism is a fundamental adaptation of cancer during rapid proliferation as a result of growth factor overstimulation. We review different pathways involving metabolic alterations in cancers including aerobic glycolysis, pentose phosphate pathway, de novo fatty acid synthesis, and serine and glycine metabolism. Although oncoproteins, c-MYC, HIF1α and p53 are the major drivers of this metabolic...
Source: Computational and Structural Biotechnology Journal - June 4, 2016 Category: Biotechnology Source Type: research

Circulating Biomarkers to Monitor Cancer Progression and Treatment
Publication date: Available online 1 June 2016 Source:Computational and Structural Biotechnology Journal Author(s): Suthee Rapisuwon, Eveline E. Vietsch, Anton Wellstein Tumor heterogeneity is a major challenge and the root cause of resistance to treatment. Still, the standard diagnostic approach relies on the analysis of a single tumor sample from a local or metastatic site that is obtained at a given time point. Due to intratumoral heterogeneity and selection of subpopulations in diverse lesions this will provide only a limited characterization of the makeup of the disease. On the other hand, recent developments of ...
Source: Computational and Structural Biotechnology Journal - June 1, 2016 Category: Biotechnology Source Type: research

A Decade of Biochemical and Structural Studies of the DNA Repair Machinery of Deinococcus radiodurans: Major Findings, Functional and Mechanistic Insight and Challenges
Publication date: 2016 Source:Computational and Structural Biotechnology Journal, Volume 14 Author(s): Joanna Timmins, Elin Moe (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - May 18, 2016 Category: Biotechnology Source Type: research

Structure and function of the telomeric CST complex
Publication date: 2016 Source:Computational and Structural Biotechnology Journal, Volume 14 Author(s): Cory Rice, Emmanuel Skordalakes Telomeres comprise the ends of eukaryotic chromosomes and are essential for cell proliferation and genome maintenance. Telomeres are replicated by telomerase, a ribonucleoprotein (RNP) reverse transcriptase, and are maintained primarily by nucleoprotein complexes such as shelterin (TRF1, TRF2, TIN2, RAP1, POT1, TPP1) and CST (Cdc13/Ctc1, Stn1, Ten1). The focus of this review is on the CST complex and its role in telomere maintenance. Although initially thought to be unique to yeast, it ...
Source: Computational and Structural Biotechnology Journal - May 18, 2016 Category: Biotechnology Source Type: research

Computational approaches in target identification and drug discovery
Publication date: Available online 7 May 2016 Source:Computational and Structural Biotechnology Journal Author(s): Theodora Katsila, Georgios A. Spyroulias, George P. Patrinos, Minos-Timotheos Matsoukas In the big data era, voluminous datasets are routinely acquired, stored and analyzed with the aim to inform biomedical discoveries and validate hypotheses. No doubt, data volume and diversity have dramatically increased by the advent of new technologies and open data initiatives. Big data are used across the whole drug discovery pipeline from target identification and mechanism of action to identification of novel lea...
Source: Computational and Structural Biotechnology Journal - May 18, 2016 Category: Biotechnology Source Type: research

Computational methods for predicting genomic islands in microbial genomes
Publication date: Available online 7 May 2016 Source:Computational and Structural Biotechnology Journal Author(s): Bingxin Lu, Hon Wai Leong Clusters of genes acquired by lateral gene transfer in microbial genomes, are broadly referred to as genomic islands (GIs). GIs often carry genes important for genome evolution and adaptation to niches, such as genes involved in pathogenesis and antibiotic resistance. Therefore, GI prediction has gradually become an important part of microbial genome analysis. Despite inherent difficulties in identifying GIs, many computational methods have been developed and show good performance...
Source: Computational and Structural Biotechnology Journal - May 18, 2016 Category: Biotechnology Source Type: research

Facilitating the commercialization and use of organ platforms generated by the microphysiological systems (Tissue Chip) program through public–private partnerships
Publication date: Available online 10 May 2016 Source:Computational and Structural Biotechnology Journal Author(s): Christine A. Livingston, Kristin M. Fabre, Danilo A. Tagle Microphysiological systems (organs-on-chips, tissue chips) are devices designed to recapitulate human physiology that could be used to better understand drug responses not easily addressed using other in vivo systems or in vitro animal models. Although still in development, initial results seem promising as tissue chips exhibit in vivo systems-like functional responses. The National Center for Advancing Translation Science (NCATS) identifies this...
Source: Computational and Structural Biotechnology Journal - May 18, 2016 Category: Biotechnology Source Type: research

Applying data mining techniques to medical time series: an empirical case study in electroencephalography and stabilometry
Publication date: Available online 18 May 2016 Source:Computational and Structural Biotechnology Journal Author(s): A. Anguera, J.M. Barreiro, J.A. Lara, D. Lizcano One of the major challenges in the medical domain today is how to exploit the huge amount of data that this field generates. To do this, approaches are required that are capable of discovering knowledge that is useful for decision making in the medical field. Time series are data types that are common in the medical domain and require specialized analysis techniques and tools, especially if the information of interest to specialists is concentrated within...
Source: Computational and Structural Biotechnology Journal - May 18, 2016 Category: Biotechnology Source Type: research

Visible and subvisible particles in the BCG immunotherapeutic product Immucyst®
In this study, an Electrical Sensing Zone (ESZ) method was developed to measure the particle count and the size of BCG immunotherapeutic (BCG IT), or ImmuCyst® product using a Coulter Counter Multisizer 4® instrument. The focus of this study was to establish a baseline for BCG IT reconstituted lyophilized product using visible and sub-visible particle concentration and size distribution as reportable values. ESZ method was used to assess manufacturing process consistency using 20 production scale lots of BCG IT product. The results demonstrated that ESZ can be used to accumulate product and process knowledge of BCG...
Source: Computational and Structural Biotechnology Journal - April 7, 2016 Category: Biotechnology Source Type: research

A guide to the identification of metabolites in NMR-based metabonomics/metabolomics experiments
This article provides guidance on methods for metabolite identification in biological fluids using NMR spectroscopy, and is illustrated with examples from recent studies on mice. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - March 10, 2016 Category: Biotechnology Source Type: research

MD-CTS: An integrated terminology reference of clinical and translational medicine
Publication date: Available online 2 March 2016 Source:Computational and Structural Biotechnology Journal Author(s): Will Ray, Joe Finamore, Majid Rastegar-Mojarad, Chris Kadolph, Zhan Ye, Jacquie Bohne, Yin Xu, Dan Burish, Joshua Sondelski, Melissa Easker, Brian Finnegan, Barbara Bartkowiak, Catherine Arnott Smith, Umberto Tachinardi, Eneida A. Mendonca, Bryan Weichelt, Simon M. Lin New vocabularies are rapidly evolving in the literature relative to the practice of clinical medicine and translational research. To provide integrated access to new terms, we developed a mobile and desktop online reference&...
Source: Computational and Structural Biotechnology Journal - March 3, 2016 Category: Biotechnology Source Type: research

Metabolomic profiling of post-mortem brain reveals changes in amino acid and glucose metabolism in mental illness compared with controls
Publication date: Available online 26 February 2016 Source:Computational and Structural Biotechnology Journal Author(s): Rong Zhang, Tong Zhang, Ali Muhsen Ali, Mohammed Al Washih, Benjamin Pickard, David G. Watson Metabolomic profiling was carried out on 53 post mortem brain samples from subjects diagnosed with schizophrenia, depression, bipolar disorder (SDB), diabetes and controls. Chromatography on a ZICpHILIC column was used with detection by Orbitrap mass spectrometry. Data extraction was carried out with m/z Mine 2.14 with metabolite searching against an in-house database. There was no clear discrimination b...
Source: Computational and Structural Biotechnology Journal - February 29, 2016 Category: Biotechnology Source Type: research

Preanalytical and analytical considerations of circulating plasma tumor DNA for breast oncology
Publication date: Available online 12 February 2016 Source:Computational and Structural Biotechnology Journal Author(s): Kelly Kyker-Snowman, Ben Ho Park It is now well established that DNA is shed or secreted into the circulation in both normal and disease states. However, the ability to exploit this knowledge for use in clinical medicine has only recently been made possible through the advent of new technologies. Currently, cell-free DNA is being developed as biomarkers to help guide clinical decisions in diverse fields such as prenatal screening, cancer and solid organ transplantation. Because cell-free DNA can be m...
Source: Computational and Structural Biotechnology Journal - February 13, 2016 Category: Biotechnology Source Type: research

Network analysis of Human Post-mortem microarrays reveals novel genes, MicroRNAs, and mechanistic scenarios of potential importance in fighting Huntington's disease
In this study, we utilized network-based analysis in an attempt to explore and understand the underlying molecular mechanism and to identify critical molecular players of this disease condition. Using human post-mortem microarrays from three brain regions (cerebellum, frontal cortex and caudate nucleus) we selected in a 4-step procedure a seed set of highly modulated genes. Several protein–protein interaction networks, as well as microRNA-mRNA networks were constructed for these gene sets with the Elsevier Pathway Studio software and its associated ResNet database. We applied a gene prioritizing procedure based on vi...
Source: Computational and Structural Biotechnology Journal - February 11, 2016 Category: Biotechnology Source Type: research

Sharpening precision medicine by a thorough interrogation of metabolic individuality
We describe how using the technology to comprehensively measure an individual's biochemical profile – metabolomics- is integrative to defining individual phenotypes and how it is currently being deployed in efforts to continue to elaborate on human health and disease in large population studies. Finally, we summarize instances where metabolomics is being used to assess individual health in instances where signatures (i.e. biomarkers) have been defined. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - January 21, 2016 Category: Biotechnology Source Type: research

Measuring statistical evidence using relative belief
Publication date: Available online 7 January 2016 Source:Computational and Structural Biotechnology Journal Author(s): Michael Evans A fundamental concern of a theory of statistical inference is how one should measure statistical evidence. Certainly the words “statistical evidence,” or perhaps just “evidence,” are much used in statistical contexts. It is fair to say, however, that the precise characterization of this concept is somewhat elusive. Our goal here is to provide a definition of how to measure statistical evidence for any particular statistical problem. Since evidence is what causes bel...
Source: Computational and Structural Biotechnology Journal - January 11, 2016 Category: Biotechnology Source Type: research

Corrigendum to “Dissecting complex polyketide biosynthesis” [Comput Struct Biotechnol J 3(4)(2012) 1–8]
Publication date: Available online 27 November 2015 Source:Computational and Structural Biotechnology Journal Author(s): Patrick Caffrey (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - December 9, 2015 Category: Biotechnology Source Type: research

Prediction of anticancer peptides against MCF-7 breast cancer cells from the peptidomes of Achatina fulica mucus fractions
Publication date: Available online 7 December 2015 Source:Computational and Structural Biotechnology Journal Author(s): Teerasak E-kobon, Pennapa Thongararm, Sittiruk Roytrakul, Ladda Meesuk, Pramote Chumnanpuen Several reports have shown antimicrobial and anticancer activities of mucous glycoproteins extracted from the giant African snail Achatina fulica. Anticancer properties of the snail mucous peptides remain incompletely revealed. The aim of this study was to predict anticancer peptides from A. fulica mucus. Two of HPLC-separated mucous fractions (F2 and F5) showed in vitro cytotoxicity against the breast cance...
Source: Computational and Structural Biotechnology Journal - December 9, 2015 Category: Biotechnology Source Type: research

Role of the XPA protein in the NER pathway: A perspective on the function of structural disorder in macromolecular assembly
Publication date: Available online 8 December 2015 Source:Computational and Structural Biotechnology Journal Author(s): Elisa Fadda Lack of structure is often an essential functional feature of protein domains. The coordination of macromolecular assemblies in DNA repair pathways is yet another task disordered protein regions are highly implicated in. Here I review the available experimental and computational data and within this context discuss the functional role of structure and disorder in one of the essential scaffolding proteins in the Nucleotide Excision Repair (NER) pathway, namely Xeroderma pigmentosum complemen...
Source: Computational and Structural Biotechnology Journal - December 9, 2015 Category: Biotechnology Source Type: research

Uncovering the Genetic Architectures of Quantitative Traits
Publication date: Available online 23 November 2015 Source:Computational and Structural Biotechnology Journal Author(s): James J. Lee, Shashaank Vattikuti, Carson C. Chow The aim of a genome-wide association study (GWAS) is to identify loci in the human genome affecting a phenotype of interest. This review summarizes some recent work on conceptual and methodological aspects of GWAS. The average effect of gene substitution at a given causal site in the genome is the key estimand in GWAS, and we argue for its fundamental importance. Implicit in the definition of average effect is a linear model relating genotype to phen...
Source: Computational and Structural Biotechnology Journal - December 6, 2015 Category: Biotechnology Source Type: research

Disease, Models, Variants and Altered Pathways—Journeying RGD Through the Magnifying Glass
Publication date: Available online 26 November 2015 Source:Computational and Structural Biotechnology Journal Author(s): Victoria Petri, George T. Hayman, Marek Tutaj, Jennifer R. Smith, Stan Laulederkind, Shur-Jen Wang, Rajni Nigam, Jeff De Pons, Mary Shimoyama, Melinda R. Dwinell Understanding the pathogenesis of disease is instrumental in delineating its progression mechanisms and for envisioning ways to counteract it. In the process, animal models represent invaluable tools for identifying disease-related loci and their genetic components. Amongst them, the laboratory rat is used extensively in the study of...
Source: Computational and Structural Biotechnology Journal - December 6, 2015 Category: Biotechnology Source Type: research

Self-assembling protein nanoparticles in the design of vaccines
Publication date: Available online 26 November 2015 Source:Computational and Structural Biotechnology Journal Author(s): Jacinto López Sagaseta, Enrico Malito, Rino Rappuoli, Matthew J. Bottomley For over 100years, vaccines have been one of the most effective medical interventions for reducing infectious disease, and are estimated to save millions of lives globally each year. Nevertheless, many diseases are not yet preventable by vaccination. This large unmet medical need demands further research and the development of novel vaccines with high efficacy and safety. Compared to the 19th and early 20th century va...
Source: Computational and Structural Biotechnology Journal - December 6, 2015 Category: Biotechnology Source Type: research

Corrigendum to “Dissecting complex polyketide biosynthesis” [Comput Struct Biotechnol J 3(4) (2012) 1–8]
Publication date: Available online 27 November 2015 Source:Computational and Structural Biotechnology Journal Author(s): Patrick Caffrey (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - December 6, 2015 Category: Biotechnology Source Type: research

Common integration sites of published datasets identified using a graph-based framework
Publication date: Available online 29 November 2015 Source:Computational and Structural Biotechnology Journal Author(s): Alessandro Vasciaveo, Ivana Velevska, Gianfranco Politano, Alessandro Savino, Manfred Schmidt, Raffaele Fronza With next-generation sequencing, the genomic data available for the characterization of integration sites (IS) has dramatically increased. At present, in a single experiment, several thousand viral integration genome targets can be investigated to define genomic hot spots. In a previous article, we renovated a formal CIS analysis based on a rigid fixed window demarcation into a more stre...
Source: Computational and Structural Biotechnology Journal - December 6, 2015 Category: Biotechnology Source Type: research

A Graph Based Framework to Model Virus Integration Sites
Publication date: Available online 30 November 2015 Source:Computational and Structural Biotechnology Journal Author(s): Raffaele Fronza, Alessandro Vasciaveo, Alfredo Benso, Manfred Schmidt With next generation sequencing thousands of virus and viral vector integration genome targets are now under investigation to uncover specific integration preferences and to define clusters of integration, termed common integration sites (CIS), that may allow to assess gene therapy safety or to detect disease related genomic features such as oncogenes. Here, we addressed the challenge to: 1) define the notion of CIS on graph mode...
Source: Computational and Structural Biotechnology Journal - December 6, 2015 Category: Biotechnology Source Type: research

The biochemical and mass spectrometric profiling of the dystrophin complexome from skeletal muscle
This article reviews the evidence from recent proteomic studies that have focused on the characterization of the dystrophin-glycoprotein complex and its central role in the establishment of the cytoskeleton-sarcolemma-matrisome axis. Proteomic findings suggest a close linkage of the core dystrophin complex with a variety of protein species, including tubulin, vimentin, desmin, annexin, proteoglycans and collagens. Since the almost complete absence of dystrophin is the underlying cause for X-linked muscular dystrophy, a more detailed understanding of the composition, structure and plasticity of the dystrophin complexome may...
Source: Computational and Structural Biotechnology Journal - December 6, 2015 Category: Biotechnology Source Type: research