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Hyunjo Kim
The prevalent cause of dementia - Alzheimer's disease (AD) is characterized by an early cholinergic deficit that is in part responsible for the cognitive deficits (especially memory and attention defects). Prolonged AD leads to moderate-to-severe AD, which is one of the leading causes of death. Placebo-controlled, randomized clinical trials have shown significant effects of Acetyl cholin esterase inhibitors (ChEIs) on function, cognition, activities of daily living (ADL) and behavioral symptoms in patients...
2018: Bioinformation
Hamid Galehdari, Seyedeh Zohreh Azarshin, Mehdi Bijanzadeh, Mohammad Shafiei
Thalassemia is one of the most prevalent hemoglobin disorders. It is caused by the decreased or absent synthesis of one globin chain that leads to moderate to severe hemolytic anemia in clinical complications. Some genetic factors cause these phenotypic variations by the alteration of gene expression. MicroRNAs (miRNAs) are post-transcriptional regulators in gene expression. Therefore, variations in 3'-untranslated region (3'-UTR) of target genes may affect gene expression. It is of interest to evaluate the impact of noncoding SNPs in thalassemia related genes on miRNA: mRNA interactions in the severity of thalassemia...
2018: Bioinformation
Bhooma Vijayaraghavan, Kavitha Danabal, Giri Padmanabhan, Kumaresan Ramanathan
Combating and preventing abnormality in lipid metabolism becomes a pivotal criterion for research. Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a circulating protein; it promotes the degradation of low-density lipoprotein receptors (LDL-R) and hence increases LDL-C levels. Silencing the gene PCSK9 at post-transcriptional level with the help of small interfering Ribo nucleic acid (siRNA) gives a new insight and a novel therapeutic way to regulate LDL-C metabolism. Designing and selecting an efficient siRNA for silencing PCSK9 at post transcriptional level through computational approach...
2018: Bioinformation
George Oche Ambrose, Olanrewaju John Afees, Nwufoh Chika Nwamaka, Nzikahyel Simon, Adebo Adeola Oluwaseun, Tosin Soyinka, Alakanse Suleiman Oluwaseun, Seyi Bankole
The life-threatening sides effect of the current EGFR mutant inhibitors (drugs) such as the eruption of rash which can be seen on the face, chest, back and even the trunk, diarrhea, nausea, vomiting, anorexia and stomatitis, necessitates the discovery of new potent and safe compounds as a chemo-therapeutic measure against lung cancer. Approximately about 10% of patients with Non-small cell lung cancer (NSCLC) in the US and about 35% in East Asia have tumor associated EGFR. These mutations occur within EGFR exon 18-21, which encodes a portion of the EGFR kinase domain and enables researchers to identify compounds that only recognizes and binds to the cancer cells...
2018: Bioinformation
Rajesh K Meher, Manas Ranjan Naik, Banajit Bastia, Pradeep K Naik
Angiogenesis, the formation of new capillaries from pre-existing vessels, is essential for tumor progression. Synthetic derivatives of anti-cancer compound, noscapine (an opium alkaloid) such as Cl-noscapine, Br-noscapine and Folate-noscapine along with two of the reference compounds, TNP-470 and paclitaxel were examined for anti-angiogenic activities by using human umbilical vein endothelial cells (HUVECs). The noscapine derivatives showed anti-angiogenic activity albeit at high concentration compared to the reference compounds...
2018: Bioinformation
Indra Vikram Singh, Sanjay Mishra
DHFR from Pf is a known target for malaria. There is a continued effort for the design and development of the potent inhibitor for PfDHFR in the control of malaria. Therefore it is of interest to screen PfDHFR with the derivatives of Pyrimethamine. The results show that the compound CID 10476801 has lowest docked energy (-11.48 kcal/mol) with protein likely to be a drug candidate, probably inhibiting PfDHFR structure. Residues of PfDHFR protein involved in the formation of hydrogen bonds with compound CID 10476801 are confirmed to be ASP54...
2018: Bioinformation
Kulanthaivel Langeswaran, Jeyakanthan Jeyaraman, Richard Mariadasse, Saravanan Soorangkattan
Analysis of honeybee PBPs is of interest in the development of Biosensor applications. We described the predicted binding of 19 such compounds with 43-honey bee OBPs using molecular modeling, docking and phylogenetic analysis. Therefore, training the honeybees using preferred compounds formulate the bees to identify the illicit drugs and bomb compounds. Consequently, high docking score produced complex such OBP16-N-Phenyl-2-Napthalamine (-12.25k/mol), 3BJH-Crack Cocaine (-11.75k/mol), OBP10-Methadone (- 11...
2018: Bioinformation
Md Shakil Ahmed, Md Shahjaman, Enamul Kabir, Md Kamruzzaman
Lysine acetylation is one of the decisive categories of protein post-translational modification (PTM), it is convoluted in many significant cellular developments and severe diseases in the biological system. The experimental identification of protein-acetylated sites is painstaking, time-consuming and expensive. Hence, there is significant interest in the development of computational approaches for consistent prediction of acetylation sites using protein sequences. Features selection from protein sequences plays a significant role for acetylation sites prediction...
2018: Bioinformation
Md Shakil Ahmed, Md Shahjaman, Enamul Kabir, Md Kamruzzaman
The dyserythropoietic anemia disease is a genetic disorder of erythropoiesis characterized by morphological abnormalities of erythroblasts. This is caused by human gene C15orf41 mutation. The uncharacterized C15orf41 protein is involved in the formation of a functional complex structure. The uncharacterized C15orf41 protein is thermostable, unstable and acidic. This is associated with TPD (Treponema Pallidum) domain (135 to 265 residue position) and three PTM sites such as K50 (Acetylation), T114 (Phosphorylation) and K176 (Ubiquitination)...
2018: Bioinformation
Francesco Chiappelli, Nicole Balenton, Allen Khakshooy
Novel developments in bioinformation, bioinformatics and biostatistics, including artificial intelligence (AI), play a timely and critical role in translational care. Case in point, the extent to which viral immune surveillance is regulated by immune cells and soluble factors, and by non-immune factors informs the administration of health care. The events by which health is regained following viral infection is an allostatic process, which can be modeled using Hilbert's and Volterra's mathematical biology criteria, and biostatistical methodologies such as linear multiple regression...
2018: Bioinformation
Prasanna Marsakatla, Sujai Suneetha, Joshua Lee, Paari Dominic Swaminathan, Logeshwaran Vasudevan, Rachael Supriya, Lavanya Moses Suneetha
Massive peptide sharing between the Zika virus polyprotein and host tissue proteins could elicit significant host-pathogen interactions and cross-reactions leading to autoimmune diseases. This study found similarities in the Zika V proteins and human nerve tissue proteins. 63 human nerve proteins were screened for similarities with the Zika V of which Neuromodulin, Nestin, Galanin, Bombesin, Calcium-binding protein were found to have similarities to the Zika V poly protein C at different sequence regions. These sequence similarities could be significant in regulating pathogenic interactions/autoimmunity, as Polyprotein C is known to be a virulent factor...
2018: Bioinformation
Rifat Nawaz Ul Islam, Chittran Roy, Parth Sarthi Sen Gupta, Shyamashree Banerjee, Debanjan Mitra, Sahini Banerjee, Amal Kumar Bandyopadhyay
Residues in allelic positions, in the local segment of aligned sequences of proteins show wide variations. Here, we describe PROPAB that computes the propensity tables for helix, strand and coil types from multiple 3D structure files following ab initio statistical procedure. It also classifies them in range specific and chain specific manners. It further computes percentage composition and physicochemical properties along with residues propensities. It also prepares FASTA files for different segments (helix, strand and coil) in the exact order that they follow in the sequence...
2018: Bioinformation
Sathish Sankar, Mageshbabu Ramamurthy, Subramanian Suganya, Balaji Nandagopal, Gopalan Sridharan
Influenza viruses A and B are important human respiratory pathogens causing seasonal, endemic and pandemic infections in several parts of the globe with high morbidity and considerable mortality. The current inactivated and live attenuated vaccines are not effective. Therefore, it is of interest to design universal influenza virus vaccines with high efficacy. The peptide GQSVVSVKLAGNSSL of pandemic influenza, the peptide DKTSVTLAGNSSLCS of seasonal influenza and the peptide DILLKFSPTEITAPT of influenza B were identified as potential linear cell mediated epitopes...
2018: Bioinformation
Manosh Kumar Biswas, Sathishkumar Natarajan, Dhiman Biswas, Ujjal Kumar Nath, Jong-In Park, Ill-Sup Nou
LSAT is a web-based microsatellite SSR marker designer tool specific for the Liliaceae family. It is developed using HTML, CSS, PHP, Perl and Java scripts. It works without extra add-ons on standard browsers. LSAT provides SSR primer designing service using the web interface. It helps in SSR mining and primer design. LSAT is user friendly with customizable search parameters producing visual output having download options. The current version of LSAT is backed by two data sets, namely, lily EST (Expressed Sequence Tag) from NCBI and lily nr (non redundant) with 4,099 and 216,768 unigenes, respectively...
2018: Bioinformation
Hyunjo Kim, Hyunwook Han
Alzheimer's disease (AD) represents an enormous global health burden in terms of human suffering and economic cost. AD management requires a shift from the prevailing paradigm targeting pathogenesis to design and develop effective drugs with adequate success in clinical trials. Therefore, it is of interest to report a review on amyloid beta (Aβ) effects and other multi-targets including cholinesterase, NFTs, tau protein and TNF associated with brain cell death to be neuro-protective from AD. It should be noted that these molecules have been generated either by target-based or phenotypic methods...
2018: Bioinformation
Chittran Roy, Saumen Datta
Biological systems are made of complex networks non-covalent interactions observed among protein-protein, protein-DNA, proteinlipid complexes using hydrogen-bonds, salt-bridges, aromatic-aromatic, van der Waals (vdW), hydrophobic-interactions and several others using distance criteria. Hence, large-scale data analysis is required to understand the principles of biological complex formation. Therefore, it is of interest to analyze non-covalent interaction namely, salt-bridge and aromatic-aromatic contacts in known and modeled protein complex structures...
2018: Bioinformation
Zobaer Akond, Munirul Alam, Md Nurul Haque Mollah
Biomarker identification by differentially expressed genes (DEGs) using RNA-sequencing technology is an important task to characterize the transcriptomics data. This is possible with the advancement of next-generation sequencing technology (NGS). There are a number of statistical techniques to identify DEGs from high-dimensional RNA-seq count data with different groups or conditions such as edgeR, SAMSeq, voom-limma, etc. However, these methods produce high false positives and low accuracy in presence of outliers...
2018: Bioinformation
Manu Gaur, Apoorv Tiwari, Ravendra P Chauhan, Dinesh Pandey, Anil Kumar
Phytoalexins are small antimicrobial molecules synthesized and accumulated by plants upon exposure to pathogens. Camalexin is an indole-derived phytoalexin, which is accumulated in plants including Arabidopsis thaliana, and other Brassicaceae, which plays a major role in disease resistance against fungal pathogens. The productivity of Brassica crops is adversely affected by Alternaria blight disease, which is caused by Alternaria brassicae. In Arabidopsis thaliana, MAP kinase signalling cascade is known to be involved in synthesis of camalexin, which contributes to disease resistance against a necrtrophic fungal pathogen, Botrytis cinerea...
2018: Bioinformation
Hema Sekhar Reddy Rajula, Matteo Mauri, Vassilios Fanos
Metabolomics is an expanding discipline in biology. It is the process of portraying the phenotype of a cell, tissue or species organism using a comprehensive set of metabolites. Therefore, it is of interest to understand complex systems such as metabolomics using a scale-free topology. Genetic networks and the World Wide Web (WWW) are described as networks with complex topology. Several large networks have vertex connectivity that goes beyond a scale-free power-law distribution. It is observed that (a) networks expand constantly by the addition of recent vertices, and (b) recent vertices attach preferentially to sites that are already well connected...
2018: Bioinformation
Akash Srivaths, Shyam Ramanathan, Seethalakshmi Sakthivel, Skm Habeeb
Apoptosis Inducing Factor protein has a dual role depending on its localization in mitochondrion (energy production) and nucleus (induces apoptosis). Cell damage transports this protein to nucleus which otherwise favors mitochondrion. The alteration of Nuclear Localisation Signal tags could aid nuclear translocation. In this study, apoptosis inducing factor protein (AIF) was conjugated with strong NLS tags and its binding affinity with Importin was studied using in silico approaches such as molecular modeling and docking...
2018: Bioinformation
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