Understanding the link between single cell and population scale responses of Escherichia coli in differing ligand gradients
Publication date: Available online 26 October 2015 Source:Computational and Structural Biotechnology Journal Author(s): Matthew P. Edgington, Marcus J. Tindall We formulate an agent-based population model of Escherichia coli cells which incorporates a description of the chemotaxis signalling cascade at the single cell scale. The model is used to gain insight into the link between the signalling cascade dynamics and the overall population response to differing chemoattractant gradients. Firstly, we consider how the observed variation in total (phosphorylated and unphosphorylated) signalling protein concentration affects...
Source: Computational and Structural Biotechnology Journal - November 13, 2015 Category: Biotechnology Source Type: research

A Review on Genomics APIs
Discussion section. Though Genomics APIs are still under active development and have yet to reach widespread adoption, they hold the promise to make building of complicated genomics applications easier with downstream constructive effects on healthcare. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - November 13, 2015 Category: Biotechnology Source Type: research

Vibrational analysis on the revised potential energy curve of the low-barrier hydrogen bond in photoactive yellow protein
Publication date: Available online 31 October 2015 Source:Computational and Structural Biotechnology Journal Author(s): Yusuke Kanematsu, Masanori Tachikawa Photoactive yellow protein (PYP) has a characteristic hydrogen bond (H bond) between p-coumaric acid chromophore and Glu46, whose OH bond length has been observed to be 1.21Å by the neutron diffraction technique [Proc. Natl. Acad. Sci. 106, 440–4]. Although it has been expected that such a drastic elongation of the OH bond could be caused by the quantum effect of the hydrogen nucleus, previous theoretical computations including the nuclear quantum effec...
Source: Computational and Structural Biotechnology Journal - November 13, 2015 Category: Biotechnology Source Type: research

Blood transcriptomics and metabolomics for personalized medicine
Publication date: Available online 31 October 2015 Source:Computational and Structural Biotechnology Journal Author(s): Shuzhao Li, Andrei Todor, Ruiyan Luo Molecular analysis of blood samples is pivotal to clinical diagnosis and has been intensively investigated since the rise of systems biology. Recent developments have opened new opportunities to utilize transcriptomics and metabolomics for personalized and precision medicine. Efforts from human immunology have infused into this area exquisite characterizations of subpopulations of blood cells. It is now possible to infer from blood transcriptomics, with fine accur...
Source: Computational and Structural Biotechnology Journal - November 13, 2015 Category: Biotechnology Source Type: research

Searching for Drug Synergy in Complex Dose–Response Landscapes Using an Interaction Potency Model
Publication date: Available online 25 September 2015 Source:Computational and Structural Biotechnology Journal Author(s): Bhagwan Yadav, Krister Wennerberg, Tero Aittokallio, Jing Tang Rational design of multi-targeted drug combinations is a promising strategy to tackle the drug resistance problem for many complex disorders. A drug combination is usually classified as synergistic or antagonistic, depending on the deviation of the observed combination response from the expected effect calculated based on a reference model of non-interaction. The existing reference models were proposed originally for low-throughput dru...
Source: Computational and Structural Biotechnology Journal - October 2, 2015 Category: Biotechnology Source Type: research

SNP2Structure: A public and Versatile Resource for Mapping and Three-Dimensional Modeling of Missense SNPs on Human Protein Structures
Publication date: Available online 30 September 2015 Source:Computational and Structural Biotechnology Journal Author(s): Difei Wang, Lei Song, Varun Singh, Shruti Rao, Lin An, Subha Madhavan One of the long-standing challenges in biology is to understand how non-synonymous single nucleotide polymorphisms (nsSNPs) change protein structure and further affect their function. While it is impractical to solve all the mutated protein structures experimentally, it is quite feasible to model the mutated structures in silico. Toward this goal, we built a publicly available structure database resource (SNP2Structure, https:...
Source: Computational and Structural Biotechnology Journal - October 2, 2015 Category: Biotechnology Source Type: research

Searching for drug synergy in complex dose-response landscapes using an interaction potency model
Publication date: Available online 25 September 2015 Source:Computational and Structural Biotechnology Journal Author(s): Bhagwan Yadav, Krister Wennerberg, Tero Aittokallio, Jing Tang Rational design of multi-targeted drug combinations is a promising strategy to tackle the drug resistance problem for many complex disorders. A drug combination is usually classified as synergistic or antagonistic, depending on the deviation of the observed combination response from the expected effect calculated based on a reference model of non-interaction. The existing reference models were proposed originally for low-throughput dru...
Source: Computational and Structural Biotechnology Journal - September 25, 2015 Category: Biotechnology Source Type: research

A constraint-based modelling approach to metabolic dysfunction in Parkinson's disease
Publication date: Available online 2 September 2015 Source:Computational and Structural Biotechnology Journal Author(s): Longfei Mao, Averina Nicole, Miguel A.P. Oliveira, Feng He, Siham Hachi, Ronan M.T. Fleming One of the hallmarks of sporadic Parkinson's disease is degeneration of dopaminergic neurons in the pars compacta of the substantia nigra. The aetiopathogenesis of this degeneration is still not fully understood, with dysfunction of many biochemical pathways in different subsystems suggested to be involved. Recent advances in constraint-based modelling approaches hold great potential to systematically exam...
Source: Computational and Structural Biotechnology Journal - September 12, 2015 Category: Biotechnology Source Type: research

Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution
We present concise descriptions of the two methods and their most popular alternatives, along with select illustrative applications to protein/nucleic acid assemblies involved in DNA replication and repair. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - September 4, 2015 Category: Biotechnology Source Type: research

Internal Transcribed Spacer 1 (ITS1) based sequence typing reveals phylogenetically distinct Ascaris population
This study explores the genetic organization of Indian Ascaris population for the first time which certainly includes some fundamental information on the molecular epidemiology of Ascariasis. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - September 4, 2015 Category: Biotechnology Source Type: research

A constraint-based modelling approach to metabolic dysfunction in Parkinson’s disease
Publication date: Available online 2 September 2015 Source:Computational and Structural Biotechnology Journal Author(s): Longfei Mao, Averina Nicole, Miguel A.P. Oliveira, Feng He, Siham Hachi, Ronan M.T. Fleming One of the hallmarks of sporadic Parkinson’s disease is degeneration of dopaminergic neurons in the pars compacta of the substantia nigra. The aetiopathogenesis of this degeneration is still not fully understood, with dysfunction of many biochemical pathways in different subsystems suggested to be involved. Recent advances in constraint-based modelling approaches hold great potential to systematicall...
Source: Computational and Structural Biotechnology Journal - September 2, 2015 Category: Biotechnology Source Type: research

Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis
Publication date: Available online 24 August 2015 Source:Computational and Structural Biotechnology Journal Author(s): Daniel Spies, Constance Ciaudo Analysis of gene expression has contributed to a plethora of biological and medical research studies. Microarrays have been intensively used for the profiling of gene expression during diverse developmental processes, treatments and diseases. New massively parallel sequencing methods, often named as RNA-sequencing (RNA-seq) are extensively improving our understanding of gene regulation and signaling networks. Computational methods developed originally for microarrays anal...
Source: Computational and Structural Biotechnology Journal - August 25, 2015 Category: Biotechnology Source Type: research

Knotted proteins: A tangled tale of Structural Biology
Publication date: Available online 19 August 2015 Source:Computational and Structural Biotechnology Journal Author(s): Patrícia F.N. Faísca Knotted proteins have their native structures arranged in the form of an open knot. In the last ten years researchers have been making significant efforts to reveal their folding mechanism and understand which functional advantage(s) knots convey to their carriers. Molecular simulations have been playing a fundamental role in this endeavor, and early computational predictions about the knotting mechanism have just been confirmed in wet lab experiments. Here we review a...
Source: Computational and Structural Biotechnology Journal - August 19, 2015 Category: Biotechnology Source Type: research

Molecular Classification and Prediction in Gastric Cancer
Publication date: Available online 13 August 2015 Source:Computational and Structural Biotechnology Journal Author(s): Xiandong Lin, Yongzhong Zhao, Won-min Song, Bin Zhang Gastric cancer, a highly heterogeneous disease, is the second-leading cause of cancer death and the fourth-most-common cancer globally, with East Asia accounting for more than half of cases annually. Alongside TNM staging, gastric cancer clinic has two well-recognized classification systems, the Lauren classification that subdivides gastric adenocarcinoma into intestinal and diffuse types and the alternative World Health Organization system that d...
Source: Computational and Structural Biotechnology Journal - August 13, 2015 Category: Biotechnology Source Type: research

Computing the origin and evolution of the ribosome from its structure — Uncovering processes of macromolecular accretion benefiting synthetic biology
Publication date: Available online 26 July 2015 Source:Computational and Structural Biotechnology Journal Author(s): Gustavo Caetano-Anollés, Derek Caetano-Anollés Accretion occurs pervasively in nature at widely different timeframes. The process also manifests in the evolution of macromolecules. Here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. Computational studies uncover explicit timelines of accretion of structural parts in molecular repe...
Source: Computational and Structural Biotechnology Journal - July 31, 2015 Category: Biotechnology Source Type: research

Computing the origin and evolution of the ribosome from its structure – uncovering processes of macromolecular accretion benefiting synthetic biology
Publication date: Available online 26 July 2015 Source:Computational and Structural Biotechnology Journal Author(s): Gustavo Caetano-Anollés, Derek Caetano-Anollés Accretion occurs pervasively in nature at widely different timeframes. The process also manifests in evolution of macromolecules. Here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. Computational studies uncover explicit timelines of accretion of structural parts in molecular repertoi...
Source: Computational and Structural Biotechnology Journal - July 26, 2015 Category: Biotechnology Source Type: research

Mini-Review: Strategies for Variation and Evolution of Bacterial Antigens
Publication date: Available online 26 July 2015 Source:Computational and Structural Biotechnology Journal Author(s): Janet Foley Across the eubacteria, antigenic variation has emerged as a strategy to evade host immunity. However, phenotypic variation in some of these antigens also allows the bacteria to exploit variable host niches as well. The specific mechanisms are not shared-derived characters although there is considerable convergent evolution and numerous commonalities reflecting considerations of natural selection and biochemical restraints. Unlike in viruses, mechanisms of antigenic variation in most bacteria i...
Source: Computational and Structural Biotechnology Journal - July 26, 2015 Category: Biotechnology Source Type: research

Circadian Systems Biology: When time matters
Publication date: Available online 17 July 2015 Source:Computational and Structural Biotechnology Journal Author(s): Luise Fuhr, Mónica Abreu, Patrick Pett, Angela Relógio The circadian clock is a powerful endogenous timing system, which allows organisms to fine-tune their physiology and behaviour to the geophysical time. The interplay of a distinct set of core-clock genes and proteins generates oscillations in expression of output target genes which temporally regulate numerous molecular and cellular processes. The study of the circadian timing at the organismal as well as at the cellular level outline...
Source: Computational and Structural Biotechnology Journal - July 18, 2015 Category: Biotechnology Source Type: research

The power of operon rearrangements for predicting functional associations
Publication date: Available online 2 July 2015 Source:Computational and Structural Biotechnology Journal Author(s): Gabriel Moreno-Hagelsieb In this mini-review I aim to make the case that operons might be the most powerful source for predicted associations among gene products. Such associations can help identify potential processes where the products of unannotated genes might play a role. The power of the operon for providing insight into functional associations stems from four features: (1) on average, around 60% of the genes in prokaryotes are associated into operons; (2) the functional associations between genes in ...
Source: Computational and Structural Biotechnology Journal - July 2, 2015 Category: Biotechnology Source Type: research

Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: Towards a systems-level understanding of human microbiomes
Publication date: Available online 9 June 2015 Source:Computational and Structural Biotechnology Journal Author(s): Bikel Shirley , Valdez-Lara Alejandra , Cornejo-Granados Fernanda , Rico Karina , Canizales-Quinteros Samuel , Soberón Xavier , Del Pozo-Yauner Luis , Ochoa-Leyva Adrián The advances in experimental methods and the development of high performance bioinformatic tools have substantially improved our understanding of microbial communities associated with human niches. Many studies have documented that changes in microbial abundance and composition of the human microbiome is associated with human ...
Source: Computational and Structural Biotechnology Journal - June 9, 2015 Category: Biotechnology Source Type: research

Computational Methods for Modification of Metabolic Networks
Publication date: Available online 28 May 2015 Source:Computational and Structural Biotechnology Journal Author(s): Takeyuki Tamura , Wei Lu , Tatsuya Akutsu In metabolic engineering, modification of metabolic networks is an important biotechnology and a challenging computational task. In the metabolic network modification, we should modify metabolic networks by newly adding enzymes or/and knocking-out genes to maximize the biomass production with minimum side-effect. In this mini-review, we briefly review constraint-based formalizations for Minimum Reaction Cut (MRC) problem where the minimum set of reactions is deleted...
Source: Computational and Structural Biotechnology Journal - May 29, 2015 Category: Biotechnology Source Type: research

BOG: R-package for Bacterium and Virus Analysis of Orthologous Groups
Publication date: Available online 21 May 2015 Source:Computational and Structural Biotechnology Journal Author(s): Jincheol Park , Cenny Taslim , Shili Lin BOG (Bacterium and virus analysis of Orthologous Groups) is a package for identifying groups of differentially regulated genes in the light of gene functions for various virus and bacteria genomes. It is designed to identify Cluster of Orthologous Groups (COGs) that are enriched among genes that have gone through significant changes under different conditions. This would contribute to the detection of pathogens, an important scientific research area of relevance in u...
Source: Computational and Structural Biotechnology Journal - May 21, 2015 Category: Biotechnology Source Type: research

Comparative genomics for biodiversity conservation
Publication date: Available online 21 May 2015 Source:Computational and Structural Biotechnology Journal Author(s): Catherine E. Grueber Genomic approaches are gathering momentum in biology and emerging opportunities lie in the creative use of comparative molecular methods for revealing the processes that influence diversity of wildlife. However, few comparative genomic studies are performed with explicit and specific objectives to aid conservation of wild populations. Here I provide a brief overview of comparative genomic approaches that offer specific benefits to biodiversity conservation. Because conservation examples...
Source: Computational and Structural Biotechnology Journal - May 21, 2015 Category: Biotechnology Source Type: research

Structures to complement the archaeo-eukaryotic primases catalytic cycle description: What's next?
Publication date: Available online 2 May 2015 Source:Computational and Structural Biotechnology Journal Author(s): Julien Boudet , Jean-Christophe Devillier , Frédéric H.-T. Allain , Georg Lipps DNA replication is a crucial stage in the transfer of genetic information from parent to daughter cells. This mechanism involves multiple proteins with one key player being the primase. Primases are single-stranded DNA dependent RNA polymerases. On the leading strand, they synthesize the primer once allowing DNA elongation while on the lagging strand primers are generated repeatedly (Okazaki fragments). Primases hav...
Source: Computational and Structural Biotechnology Journal - May 8, 2015 Category: Biotechnology Source Type: research

Using stem cells to model diseases of the outer retina
Publication date: Available online 6 May 2015 Source:Computational and Structural Biotechnology Journal Author(s): Camille Yvon , Conor M. Ramsden , Amelia Lane , Michael B. Powner , Lyndon da Cruz , Peter J. Coffey , Amanda-Jayne F. Carr Retinal degeneration arises from the loss of photoreceptors or retinal pigment epithelium (RPE). It is one of the leading causes of irreversible blindness worldwide with limited effective treatment options. Generation of induced pluripotent stem cell (IPSC)-derived retinal cells and tissues from individuals with retinal degeneration is a rapidly evolving technology that holds a great po...
Source: Computational and Structural Biotechnology Journal - May 7, 2015 Category: Biotechnology Source Type: research

Computer-aided molecular design of compounds targeting histone modifying enzymes
Publication date: Available online 7 May 2015 Source:Computational and Structural Biotechnology Journal Author(s): Federico Andreoli , Alberto Del Rio Growing evidences show that epigenetic mechanisms play crucial roles in the genesis and progression of many physiopathological processes. As a result, research in epigenetic grew at a fast pace in the last decade. In particular, the study of histone post-translational modifications encountered an extraordinary progression and many modifications have been characterized and associated to fundamental biological processes and pathological conditions. Histone modifications are ...
Source: Computational and Structural Biotechnology Journal - May 7, 2015 Category: Biotechnology Source Type: research

Homology-independent metrics for comparative genomics
Publication date: Available online 4 May 2015 Source:Computational and Structural Biotechnology Journal Author(s): Tarcisio José Domingos Coutinho , Glória Regina Franco , Francisco Pereira Lobo A mainstream procedure to analyze the wealth of genomic data available nowadays is the detection of homologous regions shared across genomes, followed by the extraction of biological information from the patterns of conservation and variation observed in such regions. Although of pivotal importance, comparative genomics procedures that rely on homology inference are obviously not applicable if no homologous regions ...
Source: Computational and Structural Biotechnology Journal - May 5, 2015 Category: Biotechnology Source Type: research

Structures to complement the archaeo-eukaryotic primases catalytic cycle description: What’s next?
Publication date: Available online 2 May 2015 Source:Computational and Structural Biotechnology Journal Author(s): Julien Boudet , Jean-Christophe Devillier , Frédéric H.-T. Allain , Georg Lipps DNA replication is a crucial stage in the transfer of genetic information from parent to daughter cells. This mechanism involves multiple proteins with one key player being the primase. Primases are single-stranded DNA dependent RNA polymerases. On the leading strand, they synthesize the primer once allowing DNA elongation while on the lagging strand primers are generated repeatedly (Okazaki fragments). Primases hav...
Source: Computational and Structural Biotechnology Journal - May 3, 2015 Category: Biotechnology Source Type: research

Identification of miRNAs Contributing To Neuroblastoma Chemoresistance
Conclusions : Based on the initial miRNA findings, this study elucidates the dys-regulation of four miRNAs in three separate NB chemoresistant cell line models, spanning two cell lines (SH-SY5Y and UKF-NB-3) and two chemotherapeutic agents (doxorubicin and etoposide). These miRNAs may thus be possibly linked to chemoresistance induction in NB. Such miRNAs are good candidates to be novel drug targets for future miRNA based therapies against aggressive tumours that are not responding to conventional chemotherapy. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - April 29, 2015 Category: Biotechnology Source Type: research

Temperature dependent dynamics of DegP-trimer: A molecular dynamics study
The objective of the present analysis emerged from the temperature dependent functional diversity of DegP between chaperonic and protease activities at temperatures below and above 28 °C, respectively. DegP is a multimeric protein and the minimal functional unit, DegP-trimer is of great importance in understanding the DegP pathway. The structural aspects of DegP-trimer with respect to temperature variation has been studied using molecular dynamics simulations (for 100 ns) and principal component analysis to highlight the temperature dependent dynamics facilitating its functional diversity. The DegP-trimer revealed a pr...
Source: Computational and Structural Biotechnology Journal - April 28, 2015 Category: Biotechnology Source Type: research

Under-detection of endospore-forming Firmicutes in metagenomic data
In conclusion, this study highlights the importance of understanding the specific methodological biases that can contribute to improve the universality of metagenomic approaches. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - April 26, 2015 Category: Biotechnology Source Type: research

A2aR antagonists: Next generation checkpoint blockade for cancer immunotherapy
Publication date: Available online 8 April 2015 Source:Computational and Structural Biotechnology Journal Author(s): Robert D. Leone , Ying-Chun Lo , Jonathan D. Powell The last several years have witnessed exciting progress in the development of immunotherapy for the treatment of cancer. This has been due in great part to the development of so-called checkpoint blockade. That is, antibodies that block inhibitory receptors such as CTLA-4 and PD-1 and thus unleash antigen-specific immune responses against tumors. It is clear that tumors evade the immune response by usurping pathways that play a role in negatively regulati...
Source: Computational and Structural Biotechnology Journal - April 10, 2015 Category: Biotechnology Source Type: research

Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniae
Publication date: Available online 8 April 2015 Source:Computational and Structural Biotechnology Journal Author(s): Chrispin Chaguza , Jennifer E. Cornick , Dean B. Everett Streptococcus pneumoniae (the pneumococcus) is a highly recombinogenic bacterium responsible for a high burden of human disease globally. Genetic recombination, a process in which exogenous DNA is acquired and incorporated into its genome, is a key evolutionary mechanism employed by the pneumococcus to rapidly adapt to selective pressures. The rate at which the pneumococcus acquires genetic variation through recombination is much higher than the rate...
Source: Computational and Structural Biotechnology Journal - April 10, 2015 Category: Biotechnology Source Type: research

Comparison of metabolic pathways in Escherichia coli by using genetic algorithms
Publication date: Available online 9 April 2015 Source:Computational and Structural Biotechnology Journal Author(s): Patricia Ortegon , Augusto C. Poot-Hernández , Ernesto Perez-Rueda , Katya Rodriguez-Vazquez In order to understand how cellular metabolism has taken its modern form, the conservation and variations between metabolic pathways were evaluated by using a genetic algorithm (GA). The GA approach considered information on the complete metabolism of the bacterium Escherichia coli K-12, as deposited in the KEGG database, and the enzymes belonging to a particular pathway were transformed into chains by using...
Source: Computational and Structural Biotechnology Journal - April 10, 2015 Category: Biotechnology Source Type: research

Spindle assembly checkpoint is sufficient for complete Cdc20 sequestering in mitotic control
This study highlights the principle that a systems biology approach is vital for molecular biology and could also be used for creating hypotheses to design future experiments. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - April 10, 2015 Category: Biotechnology Source Type: research

KENeV: a web-application for the automated reconstruction and visualization of the enriched metabolic and signaling super-pathways deriving from genomic experiments
In conclusion, KENeV (available online at http://www.grissom.gr/kenev) provides an integrative tool, suitable for users with no programming experience, for the functional interpretation, at both the metabolic and signaling level, of differentially expressed gene subsets deriving from genomic experiments. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - April 10, 2015 Category: Biotechnology Source Type: research

Effect of mutations on the thermostability of Aspergillus aculeatus β-1,4-galactanase
In conclusion, this study tests a new method for estimating Tm changes for mutants, adds to the available data on the effect of substitutions on protein thermostability and identifies an interesting thermostabilizing mutation, which may be beneficial also in other galactanases. Graphical abstract (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - April 10, 2015 Category: Biotechnology Source Type: research

Predicting a double mutant in the twilight zone of low homology modeling for the skeletal muscle voltage-gated sodium channel subunit beta-1 (Nav1.4 β1)
Publication date: Available online 27 March 2015 Source:Computational and Structural Biotechnology Journal Author(s): Thomas Scior , Bertin Paiz-Candia , Ángel A. Islas , Alfredo Sánchez-Solano , Lourdes Millan-Perez Peña , Claudia Mancilla-Simbro , Eduardo M. Salinas-Stefanon The molecular structure modeling of the β1 subunit of the skeletal muscle voltage-gated sodium channel (Nav1.4) was carried out in the twilight zone of very low homology. Structural significance can per se be confounded with random sequence similarities. Hence, we combined (i) not automated computational modeling of weakly...
Source: Computational and Structural Biotechnology Journal - March 28, 2015 Category: Biotechnology Source Type: research

The Role of Excitotoxic Programmed Necrosis in Acute Brain Injury
Publication date: Available online 28 March 2015 Source:Computational and Structural Biotechnology Journal Author(s): Denson G. Fujikawa Excitotoxicity involves the excessive release of glutamate from presynaptic nerve terminals and from reversal of astrocytic glutamate uptake, when there is excessive neuronal depolarization. N-methyl-D-aspartate (NMDA) receptors, a subtype of glutamate receptor, are activated in postsynaptic neurons, opening their receptor-operated cation channels to allow Ca2+ influx. The Ca2+ influx activates two enzymes, calpain I and neuronal nitric oxide synthase (nNOS). Calpain I activation produc...
Source: Computational and Structural Biotechnology Journal - March 28, 2015 Category: Biotechnology Source Type: research

The anaerobic degradation of gaseous, nonmethane alkanes — From in situ processes to microorganisms
Publication date: Available online 19 March 2015 Source:Computational and Structural Biotechnology Journal Author(s): Florin Musat The short chain, gaseous alkanes ethane, propane, n- and iso-butane are released in significant amounts into the atmosphere, where they contribute to tropospheric chemistry and ozone formation. Biodegradation of gaseous alkanes by aerobic microorganisms, mostly bacteria and fungi isolated from terrestrial environments, has been known for several decades. The first indications for short chain alkane anaerobic degradation were provided by geochemical studies of deep-sea environments around hydr...
Source: Computational and Structural Biotechnology Journal - March 27, 2015 Category: Biotechnology Source Type: research

Genome mining: Prediction of lipopeptides and polyketides from Bacillus and related Firmicutes
Publication date: Available online 24 March 2015 Source:Computational and Structural Biotechnology Journal Author(s): Gajender Aleti , Angela Sessitsch , Günter Brader Bacillus and related genera in the Bacillales within the Firmicutes harbor a variety of secondary metabolite gene clusters encoding polyketide synthases and non-ribosomal peptide synthetases responsible for remarkable diverse number of polyketides (PKs) and lipopeptides (LPs). These compounds may be utilized for medical and agricultural applications. Here, we summarize the knowledge on structural diversity and underlying gene clusters of LPs and PKs i...
Source: Computational and Structural Biotechnology Journal - March 24, 2015 Category: Biotechnology Source Type: research

Advances in the development of SUMO specific protease (SENP) inhibitors
Publication date: Available online 24 March 2015 Source:Computational and Structural Biotechnology Journal Author(s): Ashutosh Kumar , Kam Y.J. Zhang Sumoylation is a reversible post-translational modification that involves the covalent attachment of small ubiquitin-like modifier (SUMO) proteins to their substrate proteins. Prior to their conjugation, SUMO proteins need to be proteolytically processed from its precursor form to mature or active form. SUMO specific proteases (SENPs) are cysteine proteases that cleave the pro or inactive form of SUMO at C-terminus using its hydrolase activity to expose two glycine residues...
Source: Computational and Structural Biotechnology Journal - March 24, 2015 Category: Biotechnology Source Type: research

The anaerobic degradation of gaseous, nonmethane alkanes – from in situ processes to microorganisms
Publication date: Available online 19 March 2015 Source:Computational and Structural Biotechnology Journal Author(s): Florin Musat The short chain, gaseous alkanes ethane, propane, n- and iso-butane are released in significant amounts into the atmosphere, where they contribute to tropospheric chemistry and ozone formation. Biodegradation of gaseous alkanes by aerobic microorganisms, mostly bacteria and fungi isolated from terrestrial environments, has been known for several decades. The first indications for short chain alkane anaerobic degradation were provided by geochemical studies of deep-sea environments around hydr...
Source: Computational and Structural Biotechnology Journal - March 20, 2015 Category: Biotechnology Source Type: research

Role of P2X7 and P2Y2 receptors on α-secretase-dependent APP processing: Control of amyloid plaques formation “in vivo” by P2X7 receptor
Publication date: Available online 11 March 2015 Source:Computational and Structural Biotechnology Journal Author(s): M. Teresa Miras-Portugal , Juan I. Diaz-Hernandez , Rosa Gomez-Villafuertes , Miguel Diaz-Hernandez , Antonio R. Artalejo , Javier Gualix Amyloid precursor protein (APP) is expressed in a large variety of neural and non-neural cells. The balance between non-pathogenic and pathologic forms of APP processing, mediated by α-secretase and β-secretase respectively, remains a crucial step to understand β-amyloid, Aβ42 peptide, formation and aggregation that are at the origin of the senile p...
Source: Computational and Structural Biotechnology Journal - March 12, 2015 Category: Biotechnology Source Type: research

Neuroprotection Mediated by P2Y13 Nucleotide Receptors in Neurons
In conclusion, P2Y13 receptors harbored in cerebellar astrocytes and granule neurons exhibit specific signaling properties that link them to specialized functions at the level of neuroprotection and trophic activity in both cerebellar cell populations. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - March 3, 2015 Category: Biotechnology Source Type: research

Antiviral Drug- and Multidrug Resistance in Cytomegalovirus Infected SCT Patients
Publication date: 2015 Source:Computational and Structural Biotechnology Journal, Volume 13 Author(s): Katharina Göhring , Klaus Hamprecht , Gerhard Jahn In pediatric and adult patients after stem cell transplantation (SCT) disseminated infections caused by human cytomegalovirus (HCMV) can cause life threatening diseases. For treatment, the three antivirals ganciclovir (GCV), foscarnet (PFA) and cidofovir (CDV) are approved and most frequently used. Resistance to all of these antiviral drugs may induce a severe problem in this patient cohort. Responsible for resistance phenomena are mutations in the HCMV phosphotran...
Source: Computational and Structural Biotechnology Journal - March 3, 2015 Category: Biotechnology Source Type: research

Possible Biomarkers for the Early Detection of HIV-associated Heart Diseases: A Proteomics and Bioinformatics Prediction
Publication date: 2015 Source:Computational and Structural Biotechnology Journal, Volume 13 Author(s): Suraiya Rasheed , Rahim Hashim , Jasper S. Yan The frequency of cardiovascular disorders is increasing in HIV-infected individuals despite a significant reduction in the viral load by antiretroviral therapies (ART). Since the CD4+ T-cells are responsible for the viral load as well as immunological responses, we hypothesized that chronic HIV-infection of T-cells produces novel proteins/enzymes that cause cardiac dysfunctions. To identify specific factors that might cause cardiac disorders without the influence of numerou...
Source: Computational and Structural Biotechnology Journal - March 3, 2015 Category: Biotechnology Source Type: research

Biochemical functional predictions for protein structures of unknown or uncertain function
Publication date: Available online 18 February 2015 Source:Computational and Structural Biotechnology Journal Author(s): Caitlyn L. Mills , Penny J. Beuning , Mary Jo Ondrechen With the exponential growth in the determination of protein sequences and structures via genome sequencing and structural genomics efforts, there is a growing need for reliable computational methods to determine the biochemical function of these proteins. This paper reviews the efforts to address the challenge of annotating the function at the molecular level of uncharacterized proteins. While sequence- and three-dimensional-structure-based method...
Source: Computational and Structural Biotechnology Journal - March 3, 2015 Category: Biotechnology Source Type: research

Enhanced semiempirical QM methods for biomolecular interactions
Publication date: Available online 28 February 2015 Source:Computational and Structural Biotechnology Journal Author(s): Nusret Duygu Yilmazer , Martin Korth Recent successes and failures of the application of ’enhanced’ semiempirical QM (SQM) methods are reviewed in the light of the benefits and backdraws of adding dispersion (D) and hydrogen-bond (H) correction terms. We find that the accuracy of SQM-DH methods for non-covalent interactions is very often reported to be comparable to dispersion-corrected density functional theory (DFT-D), while computation times are about three orders of magnitude lower. SQM...
Source: Computational and Structural Biotechnology Journal - March 3, 2015 Category: Biotechnology Source Type: research

A New Paradigm for Known Metabolite Identification in Metabonomics/Metabolomics: Metabolite Identification Efficiency
Publication date: Available online 27 January 2015 Source:Computational and Structural Biotechnology Journal Author(s): Jeremy R. Everett A new paradigm is proposed for assessing confidence in the identification of known metabolites in metabonomics studies using NMR spectroscopy approaches. This new paradigm is based upon the analysis of the amount of metabolite identification information retrieved from NMR spectra relative to the molecular size of the metabolite. Several new indices are proposed: metabolite identification efficiency (MIE) and metabolite identification carbon efficiency (MICE), both of which can be easil...
Source: Computational and Structural Biotechnology Journal - January 29, 2015 Category: Biotechnology Source Type: research