Research & Reviews: A Journal of Bioinformatics
Research & Reviews: A Journal of Bioinformatics (RRJoBI) is a print and e-journal focused towards the rapid publication of fundamental research papers on all areas of Bioinformatics. ISSN: 2393-8722 Focus & Scope: Sequence database and Sequence Alignment Sequence mining , sequence profiling System biology Biological networks , protein –protein interaction networks DNA Assembly, Clustering , Mapping Phylogeny reconstruction algorithms, Protein Structure predictions Silico technology Statistical analysis, staochastic grammars
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Analysis of Gene Expression Data to Predict Genomic Interactions involved in Immune Responses Caused by Dengue Fever
Abstract Dengue fever is a mosquito-borne Aedes genus viral disease affecting to human all over the world. Current several diagnostic methods to find the disease, but no drug treatment for the disease and no validated therapeutic targets for the disease. There are several immune cells involved in antigen–antibody reaction against the viral replication and disease progression, but complete molecular mechanism is remains unknown. Several bioassays to confirm the disease based on pathogenesis, yet there is a need to identify several genes involved in different signaling pathways, pathogenesis and potential drug targets. The peripheral blood mononuclear whole genome gene expression datasets to identify transcriptional gene regulation on immune systems gene signatures to predict clinical significant biomarkers on dengue infection. Using statistical tests and SVM multivariate classifications to identify differentially expressed gene signatures. The results showed in this is differentially expressed genes based on clustering, sub-grouping of datasets that predict biomarkers, and gene–gene interaction network prediction to understand clinically significant bioassays. Keywords: Dengue virus, dengue fever, microarray, Affymetrix, gene expression, immune system Cite this Article Rakesh N.R., Gurumurthy H., Chaitra K.J. Analysis of Gene Expression Data to Predict Genomic Interactions involved in Immune Responses Caused by Dengue Fever. Research & Reviews: A Journal of Bioinformatics. 2017; 4(1): 9–15p.
Molecular Methods to Improve the Insecticidal Action of Bacillus thuringiensis in Biotechnology Arena
Abstract Bacillus thuringiensis (or Bt) is a Gram-positive, soil-dwelling bacterium, frequently used as an organic pesticide. B. thuringiensis also arises naturally in the gut of caterpillars of several kinds of moths and butterflies, as well on foliage surfaces, marine environments, animal feces, insect-rich surroundings, and flour mills and grain-storage facilities. All through sporulation, various Bt strains harvest crystal proteins (proteinaceous inclusions), termed δ-endotoxins, that have insecticidal action. This has led to their use as pesticides, and more recently to genetically improved crops using Bt genes, such as Bt corn. Numerous crystal-producing Bt strains, however, do not have insecticidal properties. We define natural and in vitro growth of Cry toxins, as well as their significance in the mechanism of action for insect control. Furthermore, the use of DNA shuffling to develop two Bt toxins will be conversed together with in silico analyses of the generated mutations to evaluate their possible effect on protein structure and cytotoxicity. Keywords: Bacillus thuringiensis, Cry toxins, genes, pest Cite this Article Vishakha Singhal. Molecular Methods to Improve the Insecticidal Action of Bacillus thuringiensis in Biotechnology Arena. Research & Reviews: A Journal of Bioinformatics. 2017; 4(1): 31–35p.
Comparative Study on Bioremediation for Oil Spills Using Microbes
Abstract This research work was designed to compare and evaluate the capacity of microbes in bioremediating and biodegrading of hydrocarbons which are the major constituents of petroleum oil. An oil spill is a leakage from ocean-going tankers, pipelines or other oil sources. Bioremediation for oil spills is a technique that uses microbes to eliminate contamination of hydrocarbons from water and soil, thereby making them safe for aquatic and terrestrial species. Bioremediation can be used by bacterial species, fungal species (by a process called mycoremediation) and plant species (by a process called phytoremediation). Two different species—bacterial species (Pseudomonas putida) and fungal species (Penicillium chrysogenum)—were checked individually in the laboratory condition, in order to determine and test for their capabilities in bioremediation process in oil spills. The total aerobic bacterial and fungal counts and cfu result were carried out after first and second weeks of inoculation, and was found to be significant. Solvent extraction method was primarily used to determine the percentage of oil degraded. P. chrysogenum degraded 11.1% of the oil in two weeks and P. putida degraded 6.425% after two weeks; this shows P. chrysogenum was found to degrade oil better than P. putida. Gas chromatographic (GC-MS) analysis of the residual oil extracted from bacterial, fungal as well as the control set up showed marked variations in peaks representing individual hydrocarbon components being degraded and transformed. Higher degradation was obtained with P. chrysogenum having lower peaks as compared to the bacterial and the control set up. This further confirmed the result obtained earlier with the solvent extraction method. There are three methods to clean up oil spills— physical, chemical and biological (bioremediation); but bioremediation is advantageous as it is time and cost saving than physical metho. Also unlike chemical method, no foreign or toxic chemicals are added to the site. Keywords: oil spills, hydrocarbons, bioremediation, Pseudomonas putida, Penicillium chrysogenum Cite this Article Singh R, Majumdar RS. Comparative Study on Bioremediation for Oil Spills Using Microbes. Research & Reviews: A Journal of Bioinformatics. 2017; 4(1): 16–24p.
In Silico Study of Curcumin-Sugar Conjugates as Dual Inhibitors on Both COX-1 and COX-2 Enzymes for the Discovery of Anti-inflammatory Agents
Abstract Curcumin is a polyphenolic compound well known for its anti-inflammatory properties. The aim of the study was to design some novel curcumin derivatives that are water soluble as well as good anti-inflammatory agents with fewer side effects. In silico study was performed on the proteins by using three softwares iGEMDOCK, AutoDOCK, AutoDOCKVina as dual inhibitors for both COX-1 and COX-2. The result gives us theoretical contribution for understanding the ligand-protein interactions at molecular level. Furthermore, we could also develop some novel curcumin analogues that possess good anti-inflammatory activity, water solubility and lower toxicity. Keywords: Curcumin, inflammation, docking, COX-1, COX-2 Cite this Article Ruchika Goyal, Sandeep Jain. In Silico Study of Curcumin-Sugar Conjugates as Dual Inhibitors on Both COX-1 and COX-2 Enzymes for the Discovery of Anti-Inflammatory Agents. Research & Reviews: A Journal of Bioinformatics. 2017; 4(1): 25–30p.
In this study, details of amino acids are given. Amino acids join to other amino acids and form protein. They are the ‘building blocks’ of the body. An overview of amino acid biosynthesis is given by glucose. Biosynthesis of serine from 3-phosphoglycerate and subsequent conversion of serine into glycine is explained with the diagram. General properties of amino acids are also given in this study. Keywords: Amino acids, building blocks, glucose, serine, 3-phosphoglycerate, glycine Cite this Article Garg Jyoti. Biosynthesis of Amino Acids. Research & Reviews: A Journal of Bioinformatics. 2017; 4(1): 1–8p.
The HbA1C Values Used in Diagnosis of Diabetes in India—A Review
Abstract Diabetes mellitus (DM) is a chronic metabolic disorder associated with retinopathy, nephropathy, cardiovascular disorder and other lethal complication of organ system. It has huge burden globally and expected to grow more in upcoming years; with alarming presence in epidemic proportions in countries like India and China. India currently faces challenges to handle the potential burden of DM which demands accurate and precise diagnosis by various clinical parameters. Since 2009, HbA1c was recommended as diagnosis of DM and management of related complications. Still in India, fasting plasma glucose (FPG), post-meal glucose and oral glucose tolerance test (OGTT) are commonly used, due to unregulated diagnostic sector and lack of awareness. However, combination of FPG, OGTT and HbA1c are reported by laboratories having adequate facilities. In depth studies on impact of laboratory quality and education of physicians, healthcare providers, pathologist may improve harmonisation and quality of patient care in DM in India. Keywords: Diabetes mellitus (DM), HbA1c, hyperglycemia, fasting plasma glucose (FPG), oral glucose tolerance test (OGTT) Cite this Article Kadhane O, Mukundan U. The HbA1C Values Used in Diagnosis of Diabetes in India—A Review. Research & Reviews: A Journal of Bioinformatics. 2016; 3(3): 15–19p.
Correlation Between eAG Values Calculated from Hba1c Values Obtained from Three Different Techniques and Fasting Plasma Glucose Levels for Diagnosis and Prognosis of Diabetes
Abstract The objective of the present study was to correlate estimated average glucose (eAG) values calculated from HbA1c values obtained from Tosoh TLC-723 G8 based on cation exchange based HPLC, TBA 12 FR enzymatic fructosyl peptide oxidase (FPOX) method and D10 HbA1c analyser Bio Rad Laboratories (USA) with fasting plasma glucose (FPG) levels by hexakinase method for diagnosis and prognosis of diabetes. A total of 300 randomly selected patient samples were analysed for FPG by hexakinase method and HbA1c values were estimated by using Tosoh TLC-723 G8 analyser based on cation exchange HPLC, enzymatic FPOX (Manufacture by Seikisui Medical Co. Ltd., Japan) programmed on TBA 12 FR biochemistry analyser and D10 HbA1c analyser Bio Rad Laboratories (USA). The eAG values were calculated using Nanthan’s regression equation for both HbA1c values. The correlation between FPG, HbA1c and eAG values has been done by Pearson correlation (r) and regression analysis was done by SPSS software. The correlation was good in entire data and poor in differentiated groups. Male data has shown good correlation between FPG and eAG as compared to female data with higher mean levels of FPG, eAG and HbA1c values. Both HPLC methods have shown closer correlation between eAG values calculated from it and FPG values from which Tosoh HLC-723 G8 has shown closer correlation. The overall correlation between eAG and FPG was good in entire data but mean value difference was found to be slightly high. So for diabetes diagnosis, HbA1c values along with calculated eAG value along with FPG values are recommended as per the American Diabetes Association (ADA) guidelines. As both the HPLC methods have shown good correlation between eAG and FPG values, we recommend that HbA1c values and eAG values calculated from it has to be used for diagnosis and prognosis of diabetes along with FPG values and other relevant clinical findings of patients. Tosoh HLC-723 G8 HPLC HbA1c analyser could be preferred technique for HbA1c estimation due to closer correlation with FPG values and true separation of labile and stable fraction of HbA1c. The use of HbA1c values alone for diagnosis and prognosis of diabetes still need multicentre studies with large sample size in different population. Keywords: estimated average glucose (eAG), HbA1c, fasting plasma glucose (FPG), diabetes Cite this Article Kadhane O, Mukundan U, Malvankar S et al. Correlation Between eAG Values Calculated from Hba1c Values Obtained from Three Different Techniques and Fasting Plasma Glucose Levels for Diagnosis and Prognosis of Diabetes. Research & Reviews: A Journal of Bioinformatics. 2016; 3(3): 1–14p.
Isolation and Characterization of Lantibiotic Producing Lactic Acid Bacteria from Ambali, Aged Mango Pickle Probiotics
Abstract Each year in the US at least 2 million people are sickened with antibiotic resistant infection. The development of antibiotics was one of the most important advances of medicine. Many bacterial infections (e.g. tuberculosis and infected wounds) that previously had no effective treatment and often killed people became treatable with antibiotics, saving millions of lives. Now, because of the overuse and misuse of antibiotics, bacterial infections that were once easily cured with antibiotics are becoming harder to treat. This is due to antibiotic resistance. The World Health Organization has called this as one of the biggest threats to human health today (World Health Organization 2014). Antibiotics have transformed human health and saved millions of lives. Now, as a result of overuse, they are no longer working. The golden age of medicine has come to an end (Joe Shute). But 99% of microbes will not grow in laboratory conditions leaving researchers frustrated that they could not get to the life-saving natural drugs. The dramatic rise in the incidence of antibiotic resistance demands that new therapeutic options will have to be developed. One potentially interesting class of antimicrobials is the modified bacteriocins termed lantibiotics, which are bacterially produced, post-translationally modified, lanthionine/methyllanthionine containing peptides. The present study was aimed at isolating bacteriocinogenic LAB from a traditional fermented food, “Ambali”. Twenty five colonies of LAB were isolated and screened for bacteriocin production potential. Ten isolates showed good antimicrobial activity against Gram-positive viz., Bacillus cereus, Staphylococcus aureus, Listeria monocytogenes as well as Gram-negative viz., Pseudomonas aeruginosa, Vibrio parahaemolyticus and Aeromonas hydrophila microorganisms. During characterization of these strains, two of them were found to resemble two other strains. One of the bacilli has been reported earlier. Therefore, in this study characterization of seven isolates through morphological, physiological, biochemical and carbohydrate fermentation tests as well as cell wall protein profiles have been reported. Five of them were cocci, identified as Pediococcus pentosaceous (four strains) and the other as Tetragenococcus halophilus, while the remaining two being rods and were found to be Lactobacillus plantarum. Keywords: Antibiotics, bacteriocinogenic, tuberculosis Cite this Article Revansiddappa, Chandrashekhar Naik. Isolation and Characterization of Lantibiotic Producing Lactic Acid Bacteria from Ambali; Aged Mango Pickle Probiotics. Research & Reviews: A Journal of Bioinformatics. 2016; 3(3): 30–36p.
Hereditary Disease and Ethical Awareness in Students of Greater Noida, India
Abstract Hereditary diseases are diseases that are transmitted from parents to offsprings. These diseases cause many deaths and sufferings in the world. Often majority of people in developing countries suffer because of illiteracy and ignorance, and are not able to take right decision when the problem persists in the family. Therefore, a survey has been designed and conducted on students of engineering and management branches between age group 18 and 25 years to check general awareness regarding hereditary diseases. In the survey, fifteen questions were asked. The result shows general awareness to be present among most of the students about ethics and inherited diseases. Most of the students think that parents should go for pre-genetic counseling before giving birth to their forthcoming child if the disease is hereditary one. Majority believes that parents should maintain confidentiality from children and society about hereditary disease because of mass discrimination for one or other reasons. However, the suspected individual with a family history of hereditary disease should opt for DNA testing so that diseases can be prevented, treated or cured in advance. In case of incurable inheritable disease, students feel that the knowledge may mislead and cause stress, pain, depression and anxiety. The present article highlights the different views and perspectives of students on different aspects of inherited diseases and ethical awareness related to it. Keywords: Hereditary, genetic counseling, DNA testing Cite this Article Babita Sharma, Jyoti Singh, Raghav Singh. Hereditary Disease & Ethical Awareness in Students of Greater Noida, India. Research & Reviews: A Journal of Bioinformatics. 2016; 3(3): 25–29p.
A Review: Quantitative Structure Activity Relationship
Abstract Drug discovery is a risky, costly and time-consuming process depending on multidisciplinary methods to create safe and effective medicines. Although considerable progress has been made by high-throughput screening methods in drug design, the cost of developing contemporary approved drugs did not match that in the past decade. The major reason is the late-stage clinical failures in Phases II and III because of the complicated interactions between drug-specific, human body and environmental aspects affecting the safety and efficacy of a drug. There is a growing hope that systems-level consideration may provide a new perspective to overcome such current difficulties of drug discovery and development. Therefore, the present review is an attempt to introduce how holistic systems pharmacology that integrated in silico ADME/T (i.e., absorption, distribution, metabolism, excretion and toxicity), target fishing and network pharmacology facilitates the discovery of small molecular drugs at the system level. Keywords: Drug discovery, pharmacology, QSAR, ADME/T Cite this Article Ravikash Srivastava. A Review: Quantitative Structure Activity Relationship. Research & Reviews: A Journal of Bioinformatics. 2016; 3(3): 20–24p.
A Review on Protein Structure Prediction
Abstract Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence. The prediction of folding and secondary and tertiary structure from its primary structure. Structure prediction is fundamentally different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by bioinformatics and theoretical chemistry. It is highly important in medicine and biotechnology. Every two years, the performance of current methods is assessed in the CASP experiment (Critical Assessment of Techniques for Protein Structure Prediction). Keywords: Protein structure, prediction, bioinformatics, CASP CitethisArticle HarinathVerma.AReviewonProteinStructurePrediction.Research&Reviews:AJournalofBioinformatics.2016;3(2): 1–7p.
Molecular Dynamics Simulation of RND Efflux Pumps Involved in Multidrug Resistance
Abstract The appearance of resistant strains of Gram-negative bacteria against antibiotics has compromised the efficiency of treatment. Multidrug resistance (MDR) is mainly due to the involvement of Resistance-nodulation division (RND) efflux pumps that actively pump out the drugs. For inhibition of the pump, it is essential to understand the structure as well as molecular basis of the process. Molecular dynamics (MD)simulationis employed to understand the conformational dynamics and functional mechanism of the pumps. Keywords: Molecular dynamics (MD) simulations, Resistance-nodulation division (RND) efflux pumps, multidrug resistance (MDR) Cite this Article Puzari M, Chetia P. Molecular Dynamics Simulation of RND Efflux Pumps Involved in Multidrug Resistance. Research & Reviews: A Journal of Bioinformatics. 2016; 3(2): 20–24p.
An Overview on Bioinformatics and its Application
Abstract Bioinformatics has become an important part of many areas of biology.The term ‘Bioinformatics’ was coined by PaulienHogeweg in 1979. In experimental molecular biology, bioinformatics techniques such as image and signal processing allow extraction of useful results from large amounts of raw data. In the field of genetics and genomics, it aids in sequencing and annotating genomes and their observedmutations. It plays a role in the text mining of biological literature and the development of biological and gene ontologies to organize and query biological data. It also plays a role in the analysis of gene and protein expression and regulation. Bioinformatics tools aid in the comparison of genetic and genomic data and more generally in the understanding of evolutionary aspects of molecular biology. At a more integrative level, it helps to analyze and catalogue the biological pathways and networks that are an important part of systems biology. In structural biology, it aids in the simulation and modeling of DNA, RNA, proteins as well as biomolecular interactions. Keywords:Bioinformatics, protein expression, biomolecular, genomes, mutations Cite this Article Rahuldeep.An overview on Bioinformatics and its Application.Research & Reviews: A Journal of Bioinformatics. 2016; 3(2): 8–14p.
Molecular Docking: A Powerful Approach for Structure based Drug Discovery
Abstract Molecular Docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions. The associations between biologically relevant molecules such as proteins, nucleic acids, carbohydrates, and lipids play a central role in signal transduction. Furthermore, the relative orientation of the two interacting partners may affect the type of signal produced (e.g., agonism versus antagonism). Therefore, docking is useful for predicting both the strength and type of signal produced. Molecular docking is one of the most frequently used methods in structure-based drug design, due to its ability to predict the binding-conformation of small molecule ligands to the appropriate target binding site. Characterisation of the binding behaviour plays an important role in rational design of drugs as well as to elucidate fundamental biochemical processes. Keywords: Molecular docking, proteins, nucleic acids, biochemical processes Cite this Article ShipraSenger, TulikaVerma. Molecular Docking: A powerful approach for Structure based Drug discovery.Research & Reviews: A Journal of Bioinformatics.2016; 3(2):15–19p.
Phylogenomic Analysis of Human Multigene Families Using Computational Approach
Abstract Evolution leads to major morphological transformations and anatomical complexity achieved by higher vertebrates. The phylogenomic analysis of human multigene families (ERBB, HCK, VAMP) was conducted to check the evolutionary history and functional significance. The colossal amount of diversified protein dataset for a wide variety of vertebrates and invertebrates was used to derive the phylogeny of highly significant and functionally diverse gene families. Phylogenetic analysis reveals the mode of evolution and conservation of three gene families residing on human chromosomes. Phylogeny advocates that the expansion of multigene families has occurred after diversification of vertebrates from urochordates and prior to fish–tetrapod split. The gene duplication events occurred after speciation of vertebrates and invertebrates. The major duplications occurred within the time window of deuterostomes–protostomes and actinopterygii–sarcopterygii split. The phylogenetic analysis of multigene families exhibits high level of conservation and evolutionary significance. Phylogenetic tree reflects chromosomal segmental duplications or small-scale duplications which occurred at different time points during chordate evolution. Lineage-specific deletion events were also detected in fish and tetrapods. The study will provide better understanding of ancestral relationship and functional behavior of human multigene families to the scientists belonging to diversified fields of biology, especially comparative and evolutionary genomics biologists. Keywords: ERBB, HCK, VAMP, phylogenomic analysis, segmental duplications Cite this Article Khokhar MW. Phylogenomic analysis of human multigene families using computational approach. Research & Reviews: A Journal of Bioinformatics. 2016; 3(1): 1–8p.
Abstract DNA barcoding system is a promising approach towards the diagnosis of biological diversity using DNA sequences as a primary key for retrieval of genetic information. It is emerging as a standardised method for mapping various species on the earth. DNA barcoding is a tool for identification of new species, conservation of endangered species and clustering of various species under a particular group. Many databases have been developed across the globe for the quick assessment of various DNA barcodes. Consortium for the Barcode of Life (CBOL) and Barcode of Life Database (BOLD) serves as the major barcode sources for the researchers in species identification. There are few accepted barcodes across the globe for identification of the species such as CO1 gene for animals and rbcL, matK, trnH-psbA for plants and ITS gene for fungal species. Hence DNA barcoding is the new modernised, speedy, precise and consistent method for biodiversity identification. This review study shows salient features of DNA barcoding system as a simple modernised taxonomical tool for species identifications. Keywords: DNA barcoding, CO1 gene, matK gene, trnH-psbA gene, biodiversity Cite this Article Gowthami S, Saranya D, Prashanth Kumar HP et al. DNA barcoding. Research & Reviews: A Journal of Bioinformatics. 2016; 3(1): 9–13p.
Bioinformatics is an interdisciplinary field that develops methods and software implements for understanding biological data. As an interdisciplinary field of science, bioinformatics, computer science, statistics, mathematics, and engineering to study and process biological data. Bioinformatics has become a paramount part of many areas of biology. In experimental molecular biology, bioinformatics techniques such as image and signal processing sanction extraction of utilizable results from immensely colossal amounts of raw data. In the field of genetics and genomics, it avails in sequencing and annotating genomes and their observed mutations. It plays a role in the text mining of biological literature and the development of biological and gene ontologies to organize and query biological data. It plays a role in the analysis of gene and protein expression and regulation. Bioinformatics tools aid in the comparison of genetic and genomic data and more generally in the understanding of evolutionary aspects of molecular biology. At a more integrative level, it helps analyze and catalogue the biological pathways and networks that are an important part of systems biology. In structural biology, it aids in the simulation and modeling of DNA, RNA, and protein structures as well as molecular interactions
A New Field for Bioinformatics Laboratory
Abstract The rapid technological change is transforming the world in which we live. Because laboratory services are defined by available products and tools of technology, this technological revolution is having a significant and profound effect on how clinical laboratories are organized, staffed, equipped, and operated. In this review, I discuss individually and collectively the advances and developments being made in the general areas of measurement, digital, and transportation technology and demonstrate how the convergence of the products evolving from these technologies is affecting the clinical laboratory. Keywords: Converging technology, clinical laboratories, technological revolution Cite this Article Isha Chandra. A New Field for Bioinformatics Laboratory. Research & Reviews: A Journal of Bioinformatics. 2016; 3(1): 14–17p.
rbcL Gene Based Molecular Phylogenetic Studies of Certain Pteridophytes of Assam
Abstract About 16 species of pteridophytes found in Assam (India), were selected and their variation in chloroplast rbcL gene sequences were studied. Molecular phylogenetic analysis was performed using rbcL gene sequences where a bryophyte, Funaria hygrometrica was taken as outgroup sequence. The result showed that the outgroup Funaria hygrometrica forms a totally separate branching from rest of the pteridophytic species. On the other hand, aquatic pteridophytes, Marsilea minuta and Azolla pinnata were seen to form a separate clad from rest of the pteridophytes revealing their evolutionary distance from other pteridophytes though they have a common origin as depicted by the root in the tree. Keywords: Pteridophytes, molecular phylogenetic analysis, rbcL gene, outgroup Cite this Article Pankaj Chetia, Banashree Chetia Phukan, Dilip Tamang,. rbcL Gene Based Molecular Phylogenetic Studies of Certain Pteridophytes of Assam. Research & Reviews: A Journal of Bioinformatics. 2016; 3(1): 18–21p.
Analysis of Transcription Factor Binding Sites of Co-expressed Genes in Colorectal Tumor by Microarray Data Analysis
The utilization of global gene expression profiling to find genes with similar expression patterns is rapidly becoming an extensive approach for understanding the complex cellular processes and disease mechanism. The polygenic nature of colorectal tumor, one of the most deadly cancers worldwide is believed to be caused not only by defects in single gene, but rather by the variation in multiple genes and their complex interactions. However, the regulatory mechanisms driving these changes, particularly the network of transcription factors, were not understood completely. Screening of differentially expressed genes (DEGs) through microarray data analysis and further functional enrichment analysis of these DEGs showed the importance of matrix metalloproteinase (MMPs) in the treatment of colorectal tumor. The detection of conserved TFBS in the promoter regions of DEGs showed the involvement of TFBS classes, FOXO3 and ARID3A to be involved in the development of tumor. Keywords: TFBS, gene expression profiling, tumorigenesis, transcription factors, MMPs Cite this Article Beutline Malgija M, Shanmughavel P. Analysis of transcription factor binding sites of co-expressed genes in colorectal tumor by microarray analysis. Research & Reviews: A Journal of Bioinformatics. 2015; 2(3): 8–14p.
3D Structure Determination and Analysis of ER-Lipid Raft Associated 1 Protein from Homo sapiens
ER-lipid raft associated 1(ERIN 1) is a protein coding gene encoded by ERLIN 1 gene. Autosomal Recessive HSP associated with ERLIN 1 .Structure prediction of ERLIN 1 was done using a server based approach. I-Tasser an online structure prediction tool was used for tertiary structure prediction of the protein. The best model was selected by using model evaluation tools like PROSA, ERRAT and Ramachnadran plot. Keywords: ERLIN 1, Hereditary Spastic Paralegia (HSP), 3D structure modeling Cite this Article Rane Riya, Ravichandran Rahul. 3D Structure Determination and Analysis of ER-Lipid Raft Associated 1 Protein from Homo sapiens. Research & Reviews: A Journal of Bioinformatics, 2015; 2(3): 1–7p.
Phylogenetics of Anopheles and Aedes Mosquito Species in View of Ordant-Binding Protein Motifs of Drosophila
Various species of mosquitoes were identified, based on the DNA sequences and subjected to multiple sequence alignment considering the motifs as hallmarks and in turn evolved a phylogenetic cladogram. Keywords: Sequence, phylogenetics, motif, anopheles and aedes Cite this Article Damodaran Divya, Rani Vimala Grace, Sekar T, et al. Phylogenetics of anopheles and Aedes mosquito species in view of ordant-binding protein motifs of drosophila. Research & Reviews: A Journal of Bioinformatics. 2015; 2(3): 27–37p.
Methodologies for in silico and in vitro Test of Biphenylalanine Compounds as Potential HIV-1 gp120 Attachment Inhibitors
We postulate that biphenylalanine and its derivatives are propitious candidates to inhibit the binding of HIV-gp120 to CD4 T-cell. Many biphenylalanine derivatives are synthesized chemically and also prevailing in nature. We have proposed atom- and bond-based 2D TOMOCOMD-CARDD approach to identify the best derivative. Moreover, according to our proposition, the principal law simulated from in silico interaction of gp120 with CD4 can be tested by ELISA in vitro. Furthermore, the toxicity of biphenylalanine compounds might be evaluated using MTT cytotoxicity test kits for future development of attachment inhibitors in vivo. It will be a novel idea to determine the efficacy of biphenylalanine compounds as a drug. To determine, in advance the possible stable mutation forms (all mutations are not stable) around the apolar ‘Phe43 cavity’ on gp120 and predict the next generation drugs against these mutations we opine to develop a discriminated function of local (amino acid-type) linear indices of the “macromolecular pseudograph’s α-carbon atom adjacency matrix”- that permits the classification of mutants as near wild type stability or reduced stability. To sum up, the consummate biphenylalanine substances will likely to be an ace in a hole for millions of people worldwide. Keywords: Biphenylalanine compounds, HIV-1 gp120, CD4 T-cell, HIV Cite this Article Al-Mujahidy SK. Md. Jakaria. Methodologies for in silico and in vitro test of biphenylalanine compounds as potential HIV-1 gp120 attachment inhibitors. Research & Reviews: A Journal of Bioinformatics. 2015; 2(3): 38–42p.
Molecular Interaction and Simulation Studies of Inhibitors for Endothelin-1 Receptors
High altitude cerebral edema (HACE) is a life threatening severe form of acute mountain sickness (AMS) which causes headache, unbalanced gait, behavioral changes, and altered mental status. It also carries features like hallucinations or coma, as well as a variety of neurological deficits. Prevention of edema fluid formation with minimal side effects remains to be discovered. Endothelin-1 receptors were found to be involved in the pathogenesis of HACE. Due to the elevated level of Endothelin-1(ET-1), cerebral edema levels increase. In the present study, the authors have identified possible interactions of seven spirodihydro benzofuranlactam derivatives with the two endothelin-1 receptors A and B. Keywords: HACE, endothelin, antagonists, edema Cite this Article Grace Ratna Roy, Shanmughavel P. Molecular interaction and simulation studies of inhibitors for endothelin-1 receptors. Research & Reviews: A Journal of Bioinformatics. 2015; 2(3): 15–26p.
Evaluation of Penalized Estimation Methods for Big Data Analysis
In this paper we described the sparse Laplacian shrinkage (SLS) method which is a penalized method for variable selection and estimation in big data analysis that uses a combination of the minimax concave penalty (MCP) and Laplacian quadratic as the penalty. The SLS uses the MCP to promote sparsity and Laplacian quadratic penalty to encourage smoothness among coefficients associated with the correlated predictors. An important advantage of the MCP over the penalty is that it leads to estimators that are nearly unbiased and achieve selection consistency under weaker conditions. In some problems such as genomic data analysis, partial external information may also be available on the graphical structure of some genes used as predictors in the model. It would be interesting to consider approaches for combining external information on the graphical structure with existing data in constructing the Laplacian quadratic penalty. We discussed a comparative study with ridge regression (Ridge), Lasso, MCP and SLS estimator. For different sample and variable size, our simulation studies demonstrate that SLS estimator is the best estimator. Keywords: Big data, minimax concave penalty (MCP), sparse Laplacian shrinkage (SLS) estimator Cite this Article Rahman MS, Rahman MM, Matin MA. Evaluation of Penalized Estimation Methods for Big Data Analysis. Research & Reviews: A Journal of Bioinformatics. 2015; 2(2): 49–55p.