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Computational and Structural Biotechnology Journal

Guillaume Beyrend, Koen Stam, Thomas Höllt, Ferry Ossendorp, Ramon Arens
Multi-parametric flow and mass cytometry allows exceptional high-resolution exploration of the cellular composition of the immune system. A large panel of computational tools have been developed to analyze the high-dimensional landscape of the data generated. Analysis frameworks such as FlowSOM or Cytosplore incorporate clustering and dimensionality reduction techniques and include algorithms allowing visualization of multi-parametric cytometric analysis. To additionally provide means to quantify specific cell clusters and correlations between samples, we developed an R-package, called cytofast , for further downstream analysis...
2018: Computational and Structural Biotechnology Journal
Yinglei Sheng, Hirofumi Watanabe, Keiya Maruyama, Chiduru Watanabe, Yoshio Okiyama, Teruki Honma, Kaori Fukuzawa, Shigenori Tanaka
We describe several procedures for the preprocessing of fragment molecular orbital (FMO) calculations on p38 mitogen-activated protein (MAP) kinase and discuss the influence of the procedures on the protein-ligand interaction energies represented by inter-fragment interaction energies (IFIEs). The correlation between the summation of IFIEs for a ligand and amino acid residues of protein (IFIE-sum) and experimental affinity values (IC50 ) was poor when considered for the whole set of protein-ligand complexes...
2018: Computational and Structural Biotechnology Journal
Shaherin Basith, Balachandran Manavalan, Tae Hwan Shin, Gwang Lee
A soluble carrier growth hormone binding protein (GHBP) that can selectively and non-covalently interact with growth hormone, thereby acting as a modulator or inhibitor of growth hormone signalling. Accurate identification of the GHBP from a given protein sequence also provides important clues for understanding cell growth and cellular mechanisms. In the postgenomic era, there has been an abundance of protein sequence data garnered, hence it is crucial to develop an automated computational method which enables fast and accurate identification of putative GHBPs within a vast number of candidate proteins...
2018: Computational and Structural Biotechnology Journal
Jang Hoon Kim, Yeong Deuk Jo, Hyo-Young Kim, Bo-Ram Kim, Bomi Nam
Two compounds termed 1 and 2 were isolated from the leaves of Capsicum chinense using column chromatography. Their structures were identified as amide scaffolds by analyzing spectroscopic signals. Compounds 1 and 2 have been confirmed to be competitive soluble epoxide hydrolase (sEH) inhibitors that suppress the catalytic reaction of sEH in a dose-dependent manner in vitro . Molecular docking was used for analyzing two binding clusters of ligand and receptor. The results confirmed that the key amino acids interacting with the ligand were Asp335, Tyr383, and Gln384...
2018: Computational and Structural Biotechnology Journal
Georgina Csizmadia, Bianka Farkas, Zoltán Spagina, Hedvig Tordai, Tamás Hegedűs
An increasing number of ABC membrane protein structures are determined by cryo-electron microscopy and X-ray crystallography, consequently identifying differences between their conformations has become an arising issue. Therefore, we propose to define standardized measures for ABC Type I exporter structure characterization. We set conformational vectors, conftors, which describe the relative orientation of domains and can highlight structural differences. In addition, continuum electrostatics calculations were performed to characterize the energetics of membrane insertion illuminating functionally crucial regions...
2018: Computational and Structural Biotechnology Journal
Amelia Burke-Garcia, Kevin B Wright
Introduction: Online peer-to-peer social support programs are based on the premise that support from others who have been through a similar experience can help reduce the negative impacts of disease. Such support programs are increasingly found online, but how these conversations translate into real world interactions about health concerns is currently not well understood. Methods: Grounded in social network theory, this formative study explored how participants in an online prostate cancer community comprised of patients and their families translate their online conversations into offline ones...
2018: Computational and Structural Biotechnology Journal
Muhammad Tahir Khan, Ashfaq Ur Rehaman, Muhammad Junaid, Shaukat Iqbal Malik, Dong-Qing Wei
Pyrazinamide (PZA) is an important component of first-line anti-tuberculosis drugs which is converted into active form, pyrazinoic acid (POA), by Mycobacterium tuberculosis (MTB) pncA gene encoded, pyrazinamidase (PZase). Mutations in pncA are detected in >70% of PZA resistant isolates but, noticeably, not in all. In this study, we selected 18 PZA-resistant but wild type pncA (pncAWT ) MTB isolates. Drug susceptibility testing (DST) of all the isolates were repeated at the critical concentration of PZA drug...
2018: Computational and Structural Biotechnology Journal
Io Antonopoulou, Laura Iancu, Peter Jütten, Alexander Piechot, Ulrika Rova, Paul Christakopoulos
Three novel feruloyl esterases (Fae125, Fae7262 and Fae68) from Talaromyces wortmannii overexpressed in the C1 platform were evaluated for the transesterification of vinyl ferulate with two acceptors of different size and lipophilicity (prenol and L-arabinose) in detergentless microemulsions. The effect of reaction conditions such as the microemulsion composition, the substrate concentration, the enzyme load, the pH, the temperature and the agitation were investigated. The type A Fae125 belonging to the subfamily 5 (SF5) of phylogenetic classification showed highest yields for the synthesis of both products after optimization of reaction conditions: 81...
2018: Computational and Structural Biotechnology Journal
Maha Elazezy, Simon A Joosse
Precision medicine in the clinical management of cancer may be achieved through the diagnostic platform called "liquid biopsy". This method utilizes the detection of biomarkers in blood for prognostic and predictive purposes. One of the latest blood born markers under investigation in the field of liquid biopsy in cancer patients is circulating tumor DNA (ctDNA). ctDNA is released by tumor cells through different mechanisms and can therefore provide information about the genomic make-up of the tumor currently present in the patient...
2018: Computational and Structural Biotechnology Journal
Lea Lough, Dan Sherman, Manuel Beccera-Flores, Olga Lavinda, Eric Ni, Hong Wang, Raoul Tibes, Timothy Cardozo
Cellular stress signals activate adaptive signaling pathways of the mammalian integrated stress response (ISR), of which the unfolded protein response (UPR) is a subset. These pathways converge at the phosporylation of eIF2α. Drug-like, potent and selective chemical inhibitors (valid chemical probes) targeting major ISR kinases have been previously identified, with the exception of GCN2. We synthesized and evaluated a series of GCN2 inhibitors based on a triazolo[4,5 -d ]pyrimidine scaffold. Several compounds potently inhibited GCN2 in vitro and displayed good selectivity over the related kinases PERK, HRI, and IRE1...
2018: Computational and Structural Biotechnology Journal
Saminathan Ramakrishnan, Heini Ijäs, Veikko Linko, Adrian Keller
With the introduction of the DNA origami technique, it became possible to rapidly synthesize almost arbitrarily shaped molecular nanostructures at nearly stoichiometric yields. The technique furthermore provides absolute addressability in the sub-nm range, rendering DNA origami nanostructures highly attractive substrates for the controlled arrangement of functional species such as proteins, dyes, and nanoparticles. Consequently, DNAorigami nanostructures have found applications in numerous areas of fundamental and applied research, ranging from drug delivery to biosensing to plasmonics to inorganic materials synthesis...
2018: Computational and Structural Biotechnology Journal
Sen Liang, Anjun Ma, Sen Yang, Yan Wang, Qin Ma
With the rapid accumulation of gene expression data from various technologies, e.g., microarray, RNA-sequencing (RNA-seq), and single-cell RNA-seq, it is necessary to carry out dimensional reduction and feature (signature genes) selection in support of making sense out of such high dimensional data. These computational methods significantly facilitate further data analysis and interpretation, such as gene function enrichment analysis, cancer biomarker detection, and drug targeting identification in precision medicine...
2018: Computational and Structural Biotechnology Journal
Daisuke Komura, Shumpei Ishikawa
Abundant accumulation of digital histopathological images has led to the increased demand for their analysis, such as computer-aided diagnosis using machine learning techniques. However, digital pathological images and related tasks have some issues to be considered. In this mini-review, we introduce the application of digital pathological image analysis using machine learning algorithms, address some problems specific to such analysis, and propose possible solutions.
2018: Computational and Structural Biotechnology Journal
Oliver Buß, Jens Rudat, Katrin Ochsenreither
Improving protein stability is an important goal for basic research as well as for clinical and industrial applications but no commonly accepted and widely used strategy for efficient engineering is known. Beside random approaches like error prone PCR or physical techniques to stabilize proteins, e.g. by immobilization, in silico approaches are gaining more attention to apply target-oriented mutagenesis. In this review different algorithms for the prediction of beneficial mutation sites to enhance protein stability are summarized and the advantages and disadvantages of FoldX are highlighted...
2018: Computational and Structural Biotechnology Journal
Mucheng Zhang, Deli Liu, Jie Tang, Yuan Feng, Tianfang Wang, Kevin K Dobbin, Paul Schliekelman, Shaying Zhao
As next-generation sequencing technology advances and the cost decreases, whole genome sequencing (WGS) has become the preferred platform for the identification of somatic copy number alteration (CNA) events in cancer genomes. To more effectively decipher these massive sequencing data, we developed a software program named SEG, shortened from the word "segment". SEG utilizes mapped read or fragment density for CNA discovery. To reduce CNA artifacts arisen from sequencing and mapping biases, SEG first normalizes the data by taking the log2 -ratio of each tumor density against its matching normal density...
2018: Computational and Structural Biotechnology Journal
Yeow-Kuan Chong, Chi-Chun Ho, Shui-Yee Leung, Susanna K P Lau, Patrick C Y Woo
Mass spectrometry (MS) is a sensitive, specific and versatile analytical technique in the clinical laboratory that has recently undergone rapid development. From initial use in metabolic profiling, it has matured into applications including clinical toxicology assays, target hormone and metabolite quantitation, and more recently, rapid microbial identification and antimicrobial resistance detection by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In this mini-review, we first succinctly outline the basics of clinical mass spectrometry...
2018: Computational and Structural Biotechnology Journal
Lewis Lee, Van M Savage, Pamela J Yeh
Antibiotics select for resistant bacteria whose existence and emergence is more likely in populations with high phenotypic and genetic diversity. Identifying the mechanisms that generate this diversity can thus have clinical consequences for drug-resistant pathogens. We show here that intermediate levels of antibiotics are associated with higher levels of phenotypic diversity in size of colony forming units (cfus), within a single bacterial population. We examine experimentally thousands of populations of bacteria subjected to different disturbance levels that are created by varying antibiotic concentrations...
2018: Computational and Structural Biotechnology Journal
R Plitman Mayo
Pregnancy complications are a major clinical concern due to the related maternal and fetal morbidity. Many are caused through defective placentation, but research into placental function is difficult, principally because of the ethical limitations associated with the in-vivo organ and the difficulty of extrapolating animal models. Perfused by two separate circulations, the maternal and fetal bloodstreams, the placenta has a unique structure and performs multiple complex functions. Three-dimensional imaging and computational modelling are becoming popular tools to investigate the morphology and physiology of this organ...
2018: Computational and Structural Biotechnology Journal
Athina-Styliani Kleinaki, Petros Mytis-Gkometh, George Drosatos, Pavlos S Efraimidis, Eleni Kaldoudi
Biomedical research and clinical decision depend increasingly on scientific evidence realized by a number of authoritative databases, mostly public and continually enriched via peer scientific contributions. Given the dynamic nature of biomedical evidence data and their usage in the sensitive domain of biomedical science, it is important to ensure retrieved data integrity and non-repudiation. In this work, we present a blockchain-based notarization service that uses smart digital contracts to seal a biomedical database query and the respective results...
2018: Computational and Structural Biotechnology Journal
Bashar Emon, Jessica Bauer, Yasna Jain, Barbara Jung, Taher Saif
The role of tumor microenvironment in cancer progression is gaining significant attention. It is realized that cancer cells and the corresponding stroma co-evolve with time. Cancer cells recruit and transform the stromal cells, which in turn remodel the extra cellular matrix of the stroma. This complex interaction between the stroma and the cancer cells results in a dynamic feed-forward/feed-back loop with biochemical and biophysical cues that assist metastatic transition of the cancer cells. Although biochemistry has long been studied for the understanding of cancer progression, biophysical signaling is emerging as a critical paradigm determining cancer metastasis...
2018: Computational and Structural Biotechnology Journal
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