Stage-specific control of stem cell niche architecture in the Drosophila testis by the posterior Hox gene Abd-B
Publication date: Available online 21 January 2015 Source:Computational and Structural Biotechnology Journal Author(s): Fani Papagiannouli , Ingrid Lohmann A fundamental question in biology is how complex structures are maintained after their initial specification. We address this question by reviewing the role of the Hox gene Abd-B in Drosophila testis organogenesis, which proceeds through embryonic, larval and pupal stages to reach maturation in adult stages. The data presented in this review highlight a cell- and stage-specific function of Abd-B, since the mechanisms regulating stem cell niche positioning and architec...
Source: Computational and Structural Biotechnology Journal - January 22, 2015 Category: Biotechnology Source Type: research

News in livestock research — use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals
Publication date: Available online 24 December 2014 Source:Computational and Structural Biotechnology Journal Author(s): Simon Deusch , Bruno Tilocca , Amélia Camarinha-Silva , Jana Seifert Technical progress in the field of next-generation sequencing, mass spectrometry and bioinformatics facilitates the study of highly complex biological samples such as taxonomic and functional characterization of microbial communities that virtually colonize all present ecological niches. Compared to the structural information obtained by metagenomic analyses, metaproteomic approaches provide, in addition, functional data about ...
Source: Computational and Structural Biotechnology Journal - January 3, 2015 Category: Biotechnology Source Type: research

Fast-scan cyclic voltammetry for the characterization of rapid adenosine release
Publication date: Available online 29 December 2014 Source:Computational and Structural Biotechnology Journal Author(s): Michael D. Nguyen , B. Jill Venton Adenosine is a signaling molecule and downstream product of ATP that acts as a neuromodulator. Adenosine regulates physiological processes, such as neurotransmission and blood flow, on a time scale from minutes to hours. Recent developments in electrochemical techniques, including fast-scan cyclic voltammetry (FSCV), have allowed direct detection of adenosine with sub-second temporal resolution. FSCV studies have revealed a novel mode of rapid signaling that lasts onl...
Source: Computational and Structural Biotechnology Journal - December 31, 2014 Category: Biotechnology Source Type: research

News in livestock research - use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals
Publication date: Available online 24 December 2014 Source:Computational and Structural Biotechnology Journal Author(s): Simon Deusch , Bruno Tilocca , Amélia Camarinha-Silva , Jana Seifert Technical progress in the field of next-generation sequencing, mass spectrometry and bioinformatics facilitates the study of highly complex biological samples such as taxonomic and functional characterization of microbial communities that virtually colonize all present ecological niches. Compared to the structural information obtained by metagenomic analyses, metaproteomic approaches provide, in addition, functional data about ...
Source: Computational and Structural Biotechnology Journal - December 25, 2014 Category: Biotechnology Source Type: research

Tissue-nonspecific alkaline phosphatase regulates purinergic transmission in the central nervous system during development and disease
Publication date: Available online 15 December 2014 Source:Computational and Structural Biotechnology Journal Author(s): Álvaro Sebastián-Serrano , Laura de Diego-García , Carlos Martínez-Frailes , Jesús Ávila , Herbert Zimmermann , José Luis Millán , María Teresa Miras-Portugal , Miguel Díaz-Hernández Tissue-nonspecific alkaline phosphatase (TNAP) is one of four isozymes in humans and mice that have the capacity to hydrolyze phosphate groups from a wide spectrum of physiological substrates. Among these, TNAP degrades substrates implicated in ne...
Source: Computational and Structural Biotechnology Journal - December 15, 2014 Category: Biotechnology Source Type: research

Graft versus host disease: New insights into A2A receptor agonist therapy
Publication date: Available online 14 December 2014 Source:Computational and Structural Biotechnology Journal Author(s): Karlie R. Jones , Elizabeth M. Kang Allogeneic transplantation can cure many disorders, including sickle cell disease, chronic granulomatous disease (CGD), severe combined immunodeficiency (SCID) and many types of cancers. However, there are several associated risks that can result in severe immunological reactions and, in some cases, death. Much of this morbidity is related to graft versus host disease (GVHD) [1]. GVHD is an immune mediated reaction in which donor T cells recognize the host as antigen...
Source: Computational and Structural Biotechnology Journal - December 14, 2014 Category: Biotechnology Source Type: research

Transcriptomics in the tropics: Total RNA-based profiling of Costa Rican bromeliad-associated communities
Publication date: Available online 13 December 2014 Source:Computational and Structural Biotechnology Journal Author(s): Shana K. Goffredi , Gene E. Jang , Mohamed F. Haroon RNA-Seq was used to examine the microbial, eukaryotic, and viral communities in water catchments (‘tanks’) formed by tropical bromeliads from Costa Rican. In total, transcripts with taxonomic affiliation to a wide array of bacteria, archaea, and eukaryotes, were observed, as well as RNA-viruses that appeared related to the specific presence of eukaryotes. Bacteria from 25 phyla appeared to comprise the majority of transcripts in one tank ...
Source: Computational and Structural Biotechnology Journal - December 13, 2014 Category: Biotechnology Source Type: research

What can we learn from molecular dynamics simulations for GPCR drug design?
Publication date: Available online 10 December 2014 Source:Computational and Structural Biotechnology Journal Author(s): Christofer S. Tautermann , Daniel Seeliger , Jan M. Kriegl Recent years have seen a tremendous progress in the elucidation of experimental structural information for G-protein coupled receptors (GPCRs). Although for the vast majority of pharmaceutically relevant GPCRs structural information is still accessible only by homology models the steadily increasing amount of structural information fosters the application of structure-based drug design tools for this important class of drug targets. In this art...
Source: Computational and Structural Biotechnology Journal - December 11, 2014 Category: Biotechnology Source Type: research

Systems-based approaches to unravel multi-species microbial community functioning
Publication date: Available online 3 December 2014 Source:Computational and Structural Biotechnology Journal Author(s): Florence Abram Some of the most transformative discoveries promising to enable the resolution of this century’s grand societal challenges will most likely arise from environmental science and particularly environmental microbiology and biotechnology. Understanding how microbes interact in situ, and how microbial communities respond to environmental changes remains an enormous challenge for science. Systems biology offers a powerful experimental strategy to tackle the exciting task of deciphering m...
Source: Computational and Structural Biotechnology Journal - December 4, 2014 Category: Biotechnology Source Type: research

Purinergic control of inflammation and thrombosis: role of P2X1 receptors
Publication date: Available online 28 November 2014 Source:Computational and Structural Biotechnology Journal Author(s): Cécile Oury , Christelle Lecut , Alexandre Hego , Odile Wéra , Céline Delierneux Inflammation shifts the hemostatic mechanisms in favor of thrombosis. Upon tissue damage or infection, a sudden increase of extracellular ATP occurs, that might contribute to the crosstalk between inflammation and thrombosis. On platelets, P2X1 receptors act to amplify platelet activation and aggregation induced by other platelet agonists. These receptors critically contribute to thrombus stability in ...
Source: Computational and Structural Biotechnology Journal - November 28, 2014 Category: Biotechnology Source Type: research

The role of water in protein's behavior: The two dynamical crossovers studied by NMR and FTIR techniques
Publication date: Available online 15 November 2014 Source:Computational and Structural Biotechnology Journal Author(s): Francesco Mallamace , Carmelo Corsaro , Domenico Mallamace , Sebastiano Vasi , Cirino Vasi , Giacomo Dugo The role the solvent plays in determining the biological activity of proteins is of primary importance. Water is the solvent of life and proteins need at least a water monolayer covering their surface in order to become biologically active. We study how the properties of water and the effect of its coupling with the hydrophilic moieties of proteins govern the regime of protein activity. In particul...
Source: Computational and Structural Biotechnology Journal - November 22, 2014 Category: Biotechnology Source Type: research

P2X4 receptor–eNOS signaling pathway in cardiac myocytes as a novel protective mechanism in heart failure
Publication date: Available online 7 November 2014 Source:Computational and Structural Biotechnology Journal Author(s): Ronghua Yang , Dardan Beqiri , Jian-Bing Shen , John M. Redden , Kimberly Dodge-Kafka , Kenneth A. Jacobson , Bruce T. Liang We have demonstrated using immunoprecipitation and immunostaining a novel physical association of the P2X4 receptor (P2X4R), a ligand-gated ion channel, with the cardioprotective, calcium-dependent enzyme endothelial nitric oxide synthase (eNOS). Treatment of murine ventricular myocytes with the P2XR agonist 2-methylthioATP (2-meSATP) to induce a current (mainly Na+) increased the...
Source: Computational and Structural Biotechnology Journal - November 15, 2014 Category: Biotechnology Source Type: research

Computationally Modeling Lipid metabolism and Aging: A Mini-Review
Publication date: Available online 15 November 2014 Source:Computational and Structural Biotechnology Journal Author(s): Mark T. Mc Auley , Kathleen M. Mooney One of the greatest challenges in biology is to improve the understanding of the mechanisms which underpin aging and how these affect health. The need to better understand aging is amplified by demographic changes, which have caused a gradual increase in the global population of older people. Aging western populations have resulted in a rise in the prevalence of age-related pathologies. Of these diseases, cardiovascular disease is the most common underlying conditi...
Source: Computational and Structural Biotechnology Journal - November 15, 2014 Category: Biotechnology Source Type: research

The role of water in proteins behavior: The two dynamical crossovers studied by NMR and FTIR techniques
Publication date: Available online 15 November 2014 Source:Computational and Structural Biotechnology Journal Author(s): Francesco Mallamace , Carmelo Corsaro , Domenico Mallamace , Sebastiano Vasi , Cirino Vasi , Giacomo Dugo The role the solvent plays in determining the biological activity of proteins is of primary importance. Water is the solvent of life and proteins need at least a water monolayer covering their surface in order to become biologically active. We study how the properties of water and the effect of its coupling with the hydrophilic moieties of proteins govern the regime of protein activity. In particul...
Source: Computational and Structural Biotechnology Journal - November 15, 2014 Category: Biotechnology Source Type: research

Machine Learning Applications in Cancer Prognosis and Prediction
Publication date: Available online 15 November 2014 Source:Computational and Structural Biotechnology Journal Author(s): Konstantina Kourou , Themis P. Exarchos , Konstantinos P. Exarchos , Michalis V. Karamouzis , Dimitrios I. Fotiadis Cancer has been characterized as a heterogeneous disease consisting of many different subtypes. The early diagnosis and prognosis of a cancer type has become a necessity in cancer research, as it can facilitate the subsequent clinical management of patients. The importance of classifying cancer patients into high or low risk groups has led many research teams, from the biomedical and the ...
Source: Computational and Structural Biotechnology Journal - November 15, 2014 Category: Biotechnology Source Type: research

John Daly Lecture: Structure-guided Drug Design for Adenosine and P2Y Receptors
Publication date: Available online 16 October 2014 Source:Computational and Structural Biotechnology Journal Author(s): Kenneth A. Jacobson , Zhan-Guo Gao , Silvia Paoletta , Evgeny Kiselev , Saibal Chakraborty , P. Suresh Jayasekara , Ramachandran Balasubramanian , Dilip K. Tosh We establish structure activity relationships of extracellular nucleosides and nucleotides at G protein-coupled receptors (GPCRs), e.g. adenosine receptors (ARs) and P2Y receptors (P2YRs), respectively. We synthesize selective agents for use as pharmacological probes and potential therapeutic agents (e.g. A3AR agonists for neuropathic pain). Det...
Source: Computational and Structural Biotechnology Journal - November 12, 2014 Category: Biotechnology Source Type: research

Actions of Adenosine on Cullin Neddylation: Implications for Inflammatory Responses
Publication date: Available online 15 October 2014 Source:Computational and Structural Biotechnology Journal Author(s): Valerie F. Curtis , Stefan F. Ehrentraut , Sean P. Colgan There is intense interest in understanding how the purine nucleoside adenosine functions in health and during disease. In this review, we outline some of the evidence that implicates adenosine signaling as an important metabolic signature to promote inflammatory resolution. Studies derived from cultured cell systems, animal models and human patients have revealed that nucleotide metabolism is significant component of the overall inflammatory micr...
Source: Computational and Structural Biotechnology Journal - November 11, 2014 Category: Biotechnology Source Type: research

John Daly Lecture: Structure-guided Drug Design for Adenosine P2Y Receptors
Publication date: Available online 16 October 2014 Source:Computational and Structural Biotechnology Journal Author(s): Kenneth A. Jacobson , Zhan-Guo Gao , Silvia Paoletta , Evgeny Kiselev , Saibal Chakraborty , P. Suresh Jayasekara , Ramachandran Balasubramanian , Dilip K. Tosh We establish structure activity relationships of extracellular nucleosides and nucleotides at G protein-coupled receptors (GPCRs), e.g. adenosine receptors (ARs) and P2Y receptors (P2YRs), respectively. We synthesize selective agents for use as pharmacological probes and potential therapeutic agents (e.g. A3AR agonists for neuropathic pain). Det...
Source: Computational and Structural Biotechnology Journal - November 11, 2014 Category: Biotechnology Source Type: research

Stochastic simulation in systems biology
Publication date: Available online 30 October 2014 Source:Computational and Structural Biotechnology Journal Author(s): Tamás Székely Jr. , Kevin Burrage Natural systems are, almost by definition, heterogeneous: this can be either a boon or an obstacle to be overcome, depending on the situation. Traditionally, when constructing mathematical models of these systems, heterogeneity has typically been ignored, despite its critical role. However, in recent years, stochastic computational methods have become commonplace in science. They are able to appropriately account for heterogeneity; indeed, they are based a...
Source: Computational and Structural Biotechnology Journal - November 11, 2014 Category: Biotechnology Source Type: research

Evolutionary genomics and population structure of Entamoeba histolytica
Publication date: Available online 31 October 2014 Source:Computational and Structural Biotechnology Journal Author(s): Koushik Das , Sandipan Ganguly Amoebiasis caused by the gastrointestinal parasite Entamoeba histolytica has diverse disease outcomes. Study of genome and evolution of this fascinating parasite will help us to understand the basis of its virulence and explain why, when and how it causes diseases. In this review, we have summarized current knowledge regarding evolutionary genomics of E. histolytica and discussed their association with parasite phenotypes and its differential pathogenic behavior. How genet...
Source: Computational and Structural Biotechnology Journal - November 11, 2014 Category: Biotechnology Source Type: research

The Role of Purinergic Receptors in Stem Cell Differentiation
Publication date: Available online 7 November 2014 Source:Computational and Structural Biotechnology Journal Author(s): Constanze Kaebisch , Dorothee Schipper , Patrick Babczyk , Edda Tobiasch A major challenge modern society has to face is the increasing need for tissue regeneration due to degenerative diseases or tumors, but also accidents or warlike conflicts. There is great hope that stem cell-based therapies might improve current treatments of cardiovascular diseases, osteochondral defects or nerve injury due to the unique properties of stem cells such as their self-renewal and differentiation potential. Since embry...
Source: Computational and Structural Biotechnology Journal - November 11, 2014 Category: Biotechnology Source Type: research

P2X4 Receptor-eNOS Signaling Pathway in Cardiac Myocytes as a Novel Protective Mechanism in Heart Failure
Publication date: Available online 7 November 2014 Source:Computational and Structural Biotechnology Journal Author(s): Ronghua Yang , Dardan Beqiri , Jian-Bing Shen , John M. Redden , Kimberly Dodge-Kafka , Kenneth A. Jacobson , Bruce T. Liang We have demonstrated using immunoprecipitation and immunostaining a novel physical association of the P2X4 receptor (P2X4R), a ligand-gated ion channel, with the cardioprotective, calcium-dependent enzyme endothelial nitric oxide synthase (eNOS). Treatment of murine ventricular myocytes with the P2XR agonist 2-methylthioATP (2-meSATP) to induce a current (mainly Na+) increased for...
Source: Computational and Structural Biotechnology Journal - November 11, 2014 Category: Biotechnology Source Type: research

A computational design approach for virtual screening of peptide interactions across K+ channel families
We describe a ‘limited’ homology modeling approach that can yield chimeric Kir channels having an outer vestibule structure representing nearly any known vertebrate or invertebrate channel. These computationally-derived channel structures were tested in silico for ‘docking’ to NMR structures of tertiapin (TPN), a 21 amino acid peptide found in bee venom. TPN is a highly selective and potent blocker for the epithelial rat Kir1.1 channel, but does not block human or zebrafish Kir1.1 channel isoforms. Our Kir1.1 channel-TPN docking experiments recapitulated published in vitro findings for TPN-sensitive...
Source: Computational and Structural Biotechnology Journal - November 11, 2014 Category: Biotechnology Source Type: research

A case study for cloud based high throughput analysis of NGS data using the Globus Genomics system
We present a case study of a practical solution to this data management and analysis challenge that simplifies terabyte scale data handling and provides advanced tools for NGS data analysis. These capabilities are implemented using the “Globus Genomics” system, which is an enhanced Galaxy workflow system made available as a service that offers users the capability to process and transfer data easily, reliably and quickly to address end-to-end NGS analysis requirements. The Globus Genomics system is built on Amazon’s cloud computing infrastructure. The system takes advantage of elastic scaling of compute r...
Source: Computational and Structural Biotechnology Journal - November 11, 2014 Category: Biotechnology Source Type: research

A sieve-raft hypothesis for the regulation of endothelial fenestrations
Publication date: August 2013 Source:Computational and Structural Biotechnology Journal, Volume 8, Issue 11 Author(s): Victoria C. Cogger , Ute Roessner , Alessandra Warren , Robin Fraser , David G. Le Couteur (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Autophagy in plasmodium, a multifunctional pathway?
Publication date: August 2013 Source:Computational and Structural Biotechnology Journal, Volume 8, Issue 11 Author(s): Adelaide U.P. Hain , Jürgen Bosch Autophagy is a catabolic process that normally utilizes the lysosome. The far-reaching implications of this system in disease are being increasingly understood. Studying autophagy is complicated by its role in cell survival and programmed cell death and the involvement of the canonical marker of autophagy, Atg8/LC3, in numerous non-autophagic roles. The malaria parasite, Plasmodium, has conserved certain aspects of the autophagic machinery but for what purpose has l...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Frequency of dipeptides and antidipeptides
Publication date: August 2013 Source:Computational and Structural Biotechnology Journal, Volume 8, Issue 11 Author(s): Oliviero Carugo Although it is reasonable to expect that the frequency of a generic dipeptide XY in proteins is the same of its counterpart YX, on the basis of an accurate statistical analysis of a large number of protein sequences, it appears that some dipeptides XY are considerably more frequent than their mirror images YX, referred to as antidipeptides. Given that it has been verified that this unexpected anisotropic frequency of occurrence is unbiased by the type of protein sequences that are analyze...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Measuring the shapes of macromolecules – and why it matters
Publication date: September 2013 Source:Computational and Structural Biotechnology Journal, Volume 8, Issue 12 Author(s): Jie Li , Paul Mach , Patrice Koehl The molecular basis of life rests on the activity of biological macromolecules, mostly nucleic acids and proteins. A perhaps surprising finding that crystallized over the last handful of decades is that geometric reasoning plays a major role in our attempt to understand these activities. In this paper, we address this connection between geometry and biology, focusing on methods for measuring and characterizing the shapes of macromolecules. We briefly review existing ...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Exploring compound promiscuity patterns and multi-target activity spaces
Publication date: January 2014 Source:Computational and Structural Biotechnology Journal, Volume 9, Issue 13 Author(s): Ye Hu , Disha Gupta-Ostermann , Jürgen Bajorath Compound promiscuity is rationalized as the specific interaction of a small molecule with multiple biological targets (as opposed to non-specific binding events) and represents the molecular basis of polypharmacology, an emerging theme in drug discovery and chemical biology. This concise review focuses on recent studies that have provided a detailed picture of the degree of promiscuity among different categories of small molecules. In addition, an exe...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Leveraging biological replicates to improve analysis in chip-seq experiments
Publication date: January 2014 Source:Computational and Structural Biotechnology Journal, Volume 9, Issue 13 Author(s): Yajie Yang , Justin Fear , Jianhong Hu , Irina Haecker , Lei Zhou , Rolf Renne , David Bloom , Lauren M McIntyre ChIP-seq experiments identify genome-wide profiles of DNA-binding molecules including transcription factors, enzymes and epigenetic marks. Biological replicates are critical for reliable site discovery and are required for the deposition of data in the ENCODE and modENCODE projects. While early reports suggested two replicates were sufficient, the widespread application of the technique has l...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Regulation of gene expression in the genomic context
Publication date: January 2014 Source:Computational and Structural Biotechnology Journal, Volume 9, Issue 13 Author(s): Taylor J Atkinson , Marc S Halfon Metazoan life is dependent on the proper temporal and spatial control of gene expression within the many cells—essentially all with the identical genome—that make up the organism. While much is understood about how individual gene regulatory elements function, many questions remain about how they interact to maintain correct regulation globally throughout the genome. In this review we summarize the basic features and functions of the crucial regulatory eleme...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Cofactor specificity engineering of streptococcus mutans nadh oxidase 2 for nad(p)+ regeneration in biocatalytic oxidations
Publication date: February 2014 Source:Computational and Structural Biotechnology Journal, Volume 9, Issue 14 Author(s): Barbara Petschacher , Nicole Staunig , Monika Müller , Martin Schürmann , Daniel Mink , Stefaan De Wildeman , Karl Gruber , Anton Glieder Soluble water-forming NAD(P)H oxidases constitute a promising NAD(P)+ regeneration method as they only need oxygen as cosubstrate and produce water as sole byproduct. Moreover, the thermodynamic equilibrium of O2 reduction is a valuable driving force for mostly energetically unfavorable biocatalytic oxidations. Here, we present the generation of an NAD(P)H ...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Open questions in origin of life: experimental studies on the origin of nucleic acids and proteins with specific and functional sequences by a chemical synthetic biology approach
Publication date: February 2014 Source:Computational and Structural Biotechnology Journal, Volume 9, Issue 14 Author(s): Katarzyna Adamala , Fabrizio Anella , Rafal Wieczorek , Pasquale Stano , Cristiano Chiarabelli , Pier Luigi Luisi In this mini-review we present some experimental approaches to the important issue in the origin of life, namely the origin of nucleic acids and proteins with specific and functional sequences. The formation of macromolecules on prebiotic Earth faces practical and conceptual difficulties. From the chemical viewpoint, macromolecules are formed by chemical pathways leading to the condensation...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Nmr characterization of self-association domains promoted by interactions with lc8 hub protein
Publication date: February 2014 Source:Computational and Structural Biotechnology Journal, Volume 9, Issue 14 Author(s): Elisar Barbar , Afua Nyarko Most proteins in interaction networks have a small number of partners, while a few, called hubs, participate in a large number of interactions and play a central role in cell homeostasis. One highly conserved hub is a protein called LC8 that was originally identified as an essential component of the multi-subunit complex dynein but later shown to be also critical in multiple protein complexes in diverse systems. What is intriguing about this hub protein is that it does not p...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Synthesis, lsd1 inhibitory activity, and lsd1 binding model of optically pure lysine-pcpa conjugates
Publication date: February 2014 Source:Computational and Structural Biotechnology Journal, Volume 9, Issue 14 Author(s): Yukihiro Itoh , Daisuke Ogasawara , Yosuke Ota , Tamio Mizukami , Takayoshi Suzuki Compounds that inhibit the catalytic function of lysine-specific demethylase 1 (LSD1) are interesting as therapeutic agents. Recently, we identified three lysine-phenylcyclopropylamine conjugates, NCD18, NCD25, and NCD41, which are potent LSD1 inactivators. However, in our previous study, because we tested those compounds as mixtures of (1S,2R)- and (1R,2S)-disubstituted cyclopropane rings, the relationship between the s...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Site-specific functionalization of proteins and their applications to therapeutic antibodies
Publication date: February 2014 Source:Computational and Structural Biotechnology Journal, Volume 9, Issue 14 Author(s): Remko van Vught , Roland J Pieters , Eefjan Breukink Protein modifications are often required to study structure and function relationships. Instead of the random labeling of lysine residues, methods have been developed to (sequence) specific label proteins. Next to chemical modifications, tools to integrate new chemical groups for bioorthogonal reactions have been applied. Alternatively, proteins can also be selectively modified by enzymes. Herein we review the methods available for site-specific modi...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Maturation and migration of murine cd4 single positive thymocytes and thymic emigrants
Publication date: March 2014 Source:Computational and Structural Biotechnology Journal, Volume 9, Issue 15 Author(s): Xi Xu , Qing Ge T lymphopoiesis in the thymus was thought to be completed once they reach the single positive (SP) stage, when they are “fully mature” and wait to be exported at random or follow a “first in-first out” manner. Recently, accumulating evidence has revealed that newly generated SP thymocytes undergo further maturation in the thymic medulla before they follow a tightly regulated emigrating process to become recent thymic emigrants (RTEs). RTEs in the periphery then expe...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Aluminium in biological environments: a computational approach
Publication date: March 2014 Source:Computational and Structural Biotechnology Journal, Volume 9, Issue 15 Author(s): Jon I Mujika , Elixabete Rezabal , Jose M Mercero , Fernando Ruipérez , Dominique Costa , Jesus M Ugalde , Xabier Lopez The increased availability of aluminium in biological environments, due to human intervention in the last century, raises concerns on the effects that this so far “excluded from biology” metal might have on living organisms. Consequently, the bioinorganic chemistry of aluminium has emerged as a very active field of research. This review will focus on our contributions ...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Site-specific labeling of a protein lysine residue by novel kinetic labeling combinatorial libraries
Publication date: March 2014 Source:Computational and Structural Biotechnology Journal, Volume 9, Issue 15 Author(s): Allen Krantz , Arthur M Hanel , Ivona Strug , Andrzej Wilczynski , Jeremy J Wolff , Wolin Huang , Linda H Huang , Tina Settineri , Darren L Holmes , Margaret C Hardy , Dominique P Bridon The first example of a kinetic labeling library designed to enable the discovery of affinity labels is presented. Each library component (1) consists of a variable peptidyl component linked to a biotinyl moiety by a 4-mercaptobenzoyl linker in thioester format. We demonstrate that an affinity label can be uncovered by mea...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Discovery of a novel (R)-selective bacterial hydroxynitrile lyase from Acidobacterium capsulatum
In this study, database mining revealed a novel cupin HNL from Acidobacterium capsulatum ATCC 51196 (AcHNL), which was able to catalyse the (R)-selective synthesis of mandelonitrile with significantly better conversion (97%) and enantioselectivity (96.7%) than other cupin HNLs. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Homologous SV40 RNA trans-splicing: Special case or prime example of viral RNA trans-splicing?
Publication date: June 2014 Source:Computational and Structural Biotechnology Journal, Volume 10, Issue 16 Author(s): Sushmita Poddar , Joachim Eul , Volker Patzel To date the Simian Virus 40 (SV40) is the only proven example of a virus that recruits the mechanism of RNA trans-splicing to diversify its sequences and gene products. Thereby, two identical viral transcripts are efficiently joined by homologous trans-splicing triggering the formation of a highly transforming 100kDa super T antigen. Sequences of other viruses including HIV-1 and the human adenovirus type 5 were reported to be involved in heterologous trans-sp...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway
Publication date: June 2014 Source:Computational and Structural Biotechnology Journal, Volume 10, Issue 16 Author(s): Valérie de Crécy-Lagard The availability of thousands of sequenced genomes has revealed the diversity of biochemical solutions to similar chemical problems. Even for molecules at the heart of metabolism, such as cofactors, the pathway enzymes first discovered in model organisms like Escherichia coli or Saccharomyces cerevisiae are often not universally conserved. Tetrahydrofolate (THF) (or its close relative tetrahydromethanopterin) is a universal and essential C1-carrier that most microbes ...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Advances in multiple myeloma therapy during two past decades
Publication date: June 2014 Source:Computational and Structural Biotechnology Journal, Volume 10, Issue 16 Author(s): Ivan Spicka Multiple myeloma (MM) is a clonal B-cell malignancy characterized by aberrant expansion of plasma cells within bone marrow and extramedullary sites. It is one of the most common haematological malignancies; it accounts for 1.4% of all tumours and is responsible for 2% of cancer-related mortality. Over the last decades, the paradigm of MM therapy has changed dramatically - from the conventional combination of oral melphatan+prednisone, high-dose chemotherapy with stem cell (ASCT) support for yo...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Structure and function of nucleotide sugar transporters: Current progress
Publication date: June 2014 Source:Computational and Structural Biotechnology Journal, Volume 10, Issue 16 Author(s): Barbara Hadley , Andrea Maggioni , Angel Ashikov , Christopher J. Day , Thomas Haselhorst , Joe Tiralongo The proteomes of eukaryotes, bacteria and archaea are highly diverse due, in part, to the complex post-translational modification of protein glycosylation. The diversity of glycosylation in eukaryotes is reliant on nucleotide sugar transporters to translocate specific nucleotide sugars that are synthesised in the cytosol and nucleus, into the endoplasmic reticulum and Golgi apparatus where glycosylati...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Reaction–diffusion systems for spatio-temporal intracellular protein networks: A beginner's guide with two examples
Publication date: June 2014 Source:Computational and Structural Biotechnology Journal, Volume 10, Issue 16 Author(s): Ján Eliaš , Jean Clairambault Spatio-temporal dynamics of a variety of proteins is, among other things, regulated by post-translational modifications of these proteins. Such modifications can thus influence stability and biochemical activities of the proteins, activity and stability of their upstream targets within specific signalling pathways. Commonly used mathematical tools for such protein–protein (and/or protein-mRNA) interactions in single cells, namely, Michaelis–Menten an...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Simple Ligand–Receptor Interaction Descriptor (SILIRID) for alignment-free binding site comparison
We describe SILIRID (Simple Ligand–Receptor Interaction Descriptor), a novel fixed size descriptor characterizing protein–ligand interactions. SILIRID can be obtained from the binary interaction fingerprints (IFPs) by summing up the bits corresponding to identical amino acids. This results in a vector of 168 integer numbers corresponding to the product of the number of entries (20 amino acids and one cofactor) and 8 interaction types per amino acid (hydrophobic, aromatic face to face, aromatic edge to face, H-bond donated by the protein, H-bond donated by the ligand, ionic bond with protein cation and protein a...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Mate choice and the evolutionary stability of a fixed threshold in a sequential search strategy
Publication date: June 2014 Source:Computational and Structural Biotechnology Journal, Volume 10, Issue 16 Author(s): Raymond Cheng , Steven M. Seubert , Daniel D. Wiegmann The sequential search strategy is a prominent model of searcher behavior, derived as a rule by which females might sample and choose a mate from a distribution of prospective partners. The strategy involves a threshold criterion against which prospective mates are evaluated. The optimal threshold depends on the attributes of prospective mates, which are likely to vary across generations or within the lifetime of searchers due to stochastic environment...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

The role of genetic polymorphisms of the Renin–Angiotensin System in renal diseases: A meta-analysis
Publication date: June 2014 Source:Computational and Structural Biotechnology Journal, Volume 10, Issue 16 Author(s): Georgia G. Braliou , Athina-Maria G. Grigoriadou , Panagiota I. Kontou , Pantelis G. Bagos Renal failure has a complex phenotype resulting from an underlying kidney disease as well as environmental and genetic factors. In the present study we performed a systematic review and meta-analyses to evaluate the association of the A1166C polymorphism of Angiotensin II type 1 Receptor gene (AGTR1) with Chronic Kidney Disease (CKD), End Stage Renal Disease (ESRD), IgA Nephropathy (IgAN) and Vesicoureteral Reflux (...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Note from the Research Network of Computational and Structural Biotechnology (RNCSB)
Publication date: June 2014 Source:Computational and Structural Biotechnology Journal, Volume 10, Issue 16 Author(s): Gianni Panagiotou (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research

Investigating genomic structure using changept: A Bayesian segmentation model
Publication date: July 2014 Source:Computational and Structural Biotechnology Journal, Volume 10, Issue 17 Author(s): Manjula Algama , Jonathan M. Keith Genomes are composed of a wide variety of elements with distinct roles and characteristics. Some of these elements are well-characterised functional components such as protein-coding exons. Other elements play regulatory or structural roles, encode functional non-protein-coding RNAs, or perform some other function yet to be characterised. Still others may have no functional importance, though they may nevertheless be of interest to biologists. One technique for investiga...
Source: Computational and Structural Biotechnology Journal - October 12, 2014 Category: Biotechnology Source Type: research