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Allen Khakshooy, Francesco Chiappelli
Over one third of the patients sero-positive for the human immunodeficiency virus (HIV) with signs of the acquired immune deficiency syndrome (AIDS), and under treatment with anti-retroviral therapy (ART), develop the immune reconstitution inflammatory syndrome (IRIS). It is not clear what variables are that determine whether a patient with HIV/AIDS will develop ART-related IRIS, but the best evidence base thus far indicates that HIV/AIDS patients with low CD4 cell count, and HIV/AIDS patients whose CD4 count recovery shows a sharp slope, suggesting a particularly fast "immune reconstitution", are at greater risk of developing IRIS...
2016: Bioinformation
Mohammad Uzzal Hossain, Abu Zaffar Shibly, Taimur Md Omar, Fatama Tous Zohora, Umme Sara Santona, Md Jakir Hossain, Md Sadek Hosen Khoka, Chaman Ara Keya, Md Salimullah
A metabolic disorder (MD) occurs when the metabolic process is disturbed. This process is carried out by thousands of enzymes participating in numerous inter-dependent metabolic pathways. Critical biochemical reactions that involve the processing and transportation of carbohydrates, proteins and lipids are affected in metabolic diseases. Therefore, it is of interest to identify the common pathways of metabolic disorders by building protein-protein interactions (PPI) for network analysis. The molecular network linkages between MD and age related diseases (ARD) are intriguing...
2016: Bioinformation
Mohamad Ali Roozegar, Farid Azizi Jalilian, Mohamad Reza Havasian, Jafar Panahi, Iraj Pakzad
The antimicrobial effect of the mastic tree (Pistacia atlantica) under in vitro conditions has been reported. Therefore, it is of interest to evaluate the effect of the plant leaf extract (aqueous) on bacterial load in mouth and saliva. The leaf of the Pistacia atlantica plant was collected and cleaned, dried at 40⁰c and then powdered. The extraction was carried out using the maceration method in vacuum with the rotary evaporator device. Bacterial inhibition (Streptococcus species) by the leaf extract was studied using the disc diffusion and embedding sink diffusion methods...
2016: Bioinformation
Anatoly Ivashchenko, Anna Pyrkova, Raigul Niyazova
Clustering of miRNA sequences is an important problem in molecular genetics associated cellular biology. Thousands of such sequences are known today through advancement in sophisticated molecular tools, sequencing techniques, computational resources and rule based mathematical models. Analysis of such large-scale miRNA sequences for inferring patterns towards deducing cellular function is a great challenge in modern molecular biology. Therefore, it is of interest to develop mathematical models specific for miRNA sequences...
2016: Bioinformation
Gunjan Mishra, Vivek Ananth, Kalpesh Shelke, Deepak Sehgal, Jayaraman Deepak
Hepatitis is an emerging global threat to public health due to associated mortality, morbidity, cancer and HIV co-infection. Available diagnostics and therapeutics are inadequate to intercept the course and transmission of the disease. Antimicrobial peptides (AMP) are widely studied and broad-spectrum host defense peptides are investigated as a targeted anti-viral. Therefore, it is of interest to describe the supervised identification of anti-hepatitis peptides. We used a hybrid Support Vector Machine (SVM) with Ant Colony Optimization (ACO) algorithm for simultaneous classification and domain feature selection...
2016: Bioinformation
Oommen Kaleeckal Mathew, Ramanathan Sowdhamini
Protein-protein interactions are essential for the basic biological machinery of the cell. This is important for processes like protein synthesis, enzyme kinetics, molecular assembly and signal transduction. A high number of macromolecular structural complexes are known due to recent advances in structure determination techniques. Therefore, it is of interest to develop an interactive tool to objectively analyze large protein complexes. Hence, we describe the development and utility of a web enabled application named 'Protein-Protein Interaction in Macro-molecular Assembly' (PIMA) for the analysis of large protein assemblies...
2016: Bioinformation
Maniraja Jesintha Mary, Umashankar Vetrivel, Deecaraman Munuswamy, Vijayalakshmi Melanathuru
Polycystic ovary syndrome (PCOS) is a complex disorder affecting approximately 5-10 percent of all women of reproductive age. It is a multi-factorial endocrine disorder, which demonstrates menstrual disturbance, infertility, anovulation, hirsutism, hyper androgenism and others. It has been indicated that differential expression of genes, genetic level variations, and other molecular alterations interplay in PCOS and are the target sites for clinical applications. Therefore, integrating the PCOS-associated genes along with its alteration and underpinning the underlying mechanism might definitely provide valuable information to understand the disease mechanism...
2016: Bioinformation
Jonathan Piec, Marine Pallez, Marco Beyer, Susanne Vogelgsang, Lucien Hoffmann, Matias Pasquali
Data specific to 486 strains belonging to Fusarium graminearum and Fusarium culmorum were manually collected from Luxembourg field monitoring campaigns between the year 2007 ad 2013. It is of interest to store such data in a web-enabled advanced database to help in epidemiological studies. Hence, we describe the design and development of a Fusarium database added to the Luxembourg Microbial Culture Collection (LuxMCC™) web interface at the Luxembourg Institute of Science and Technology (LIST). The database has three main features: (1) filter search, (2) detailed viewer of isolate information, and (3) excel export function of the dataset...
2016: Bioinformation
(no author information available yet)
[This retracts the article on p. 205 in vol. 3, PMID: 19255635.].
2015: Bioinformation
(no author information available yet)
[This retracts the article on p. 74 in vol. 6, PMID: 21544169.].
2015: Bioinformation
Shanmugam Anandakumar, Saravanan Vijayakumar, Nagarajan Arumugam, M Michael Gromiha
UNLABELLED: Mammalian Mitochondrial ncRNA is a web-based database, which provides specific information on non-coding RNA in mammals. This database includes easy searching, comparing with BLAST and retrieving information on predicted structure and its function about mammalian ncRNAs. AVAILABILITY: The database is available for free at
2015: Bioinformation
Jae-Hee Lee, Sang-Ho Kang, Jong-Yeol Lee, Chang-Kug Kim
UNLABELLED: The National Agricultural Biotechnology Information Center (NABIC) in Korea constructed a web-based database to provide information about gene expression profiles identified in the microorganism, plants, and animals. The deposited archive of NABIC microarray database consists of metadata spreadsheet, matrix spreadsheet, and raw data files. It provides three major functions such as microarray search, viewer and download option of raw data. An information table of five fields (i...
2015: Bioinformation
Baskeran Dharmalingam, Lydia Jothi
UNLABELLED: Rabies is a deadly viral disease causing acute inflammation or encephalitis of the brain in human beings and other mammals. Therefore, it is of interest to collect information related to the disease from several sources including known literature databases for further analysis and interpretation. Hence, we describe the development of a database called the Rabies Disease Information System (RDIS) for this purpose. The online database describes the etiology, epidemiology, pathogenesis and pathology of the disease using diagrammatic representations...
2015: Bioinformation
Behnam Rashidieh, Zohreh Madani, Mahtab Khoshnejad Azam, Saeedeh Khalesi Maklavani, Newsha Ramezani Akbari, Shaghayegh Tavakoli, Garshasb Rigi
Listeriosis is considered as an important public health issue. Sortase A (srtA) is an enzyme with catalytic role in L. monocytogenes that breaks the junction between threonine and glycine in the LPXTG motif (a key motif in internalin A (InlA) that plays an important role in listeriosis). Inactivation of srtA was shown to inhibit anchoring of the invasion protein InIA. This is in addition to inhibiting peptidoglycan-associated LPXTG proteins. Therefore, it is of interest to inhibit strA using potential molecules...
2015: Bioinformation
Arafat Rahman Oany, Md Shahabuddin Ahmed, Nasreen Jahan, Md Abdul Latif, Shahin Mahmud, Md Ahmed Hossain, Fatema Akter, Hasibul Haque Rakib, Md Shariful Islam
Streptomyces xinghaiensis is a Gram-positive, aerobic and non-motile bacterium. The bacterial genome is known. Therefore, it is of interest to study the uncharacterized proteins in the genome. An uncharacterized protein (gi|518540893|86 residues) in the genome was selected for a comprehensive computational sequence-structure-function analysis using available data and tools. Subcellular localization of the targeted protein with conserved residues and assigned secondary structures is documented. Sequence homology search against the protein data bank (PDB) and non-redundant GenBank proteins using BLASTp showed different homologous proteins with known antitoxin function...
2015: Bioinformation
Brijesh S Yadav, Mayank Pokhriyal, Barkha Ratta, Ajay Kumar, Meeta Saxena, Bhaskar Sharma
Viral diagnosis in Indian livestock using customized microarray chips is gaining momentum in recent years. Hence, it is possible to design customized microarray chip for viruses infecting livestock in India. Customized microarray chips identified Bovine herpes virus-1 (BHV-1), Canine Adeno Virus-1 (CAV-1), and Canine Parvo Virus-2 (CPV-2) in clinical samples. Microarray identified specific probes were further confirmed using RT-PCR in all clinical and known samples. Therefore, the application of microarray chips during viral disease outbreaks in Indian livestock is possible where conventional methods are unsuitable...
2015: Bioinformation
Dyavegowda Padmashree, Narayanaswamy Ramachandra Swamy
Naegleria fowleri is a parasitic unicellular free living eukaryotic amoeba. The parasite spreads through contaminated water and causes primary amoebic meningoencephalitis (PAM). Therefore, it is of interest to understand its molecular pathogenesis. Hence, we analyzed the parasite genome for miRNAs (microRNAs) that are non-coding, single stranded RNA molecules. We identified 245 miRNAs using computational methods in N. fowleri, of which five miRNAs are conserved. The predicted miRNA targets were analyzed by using miRanda (software) and further studied the functions by subsequently annotating using AmiGo (a gene ontology web tool)...
2015: Bioinformation
Raju Dash, Mir Muhammad Nasir Uddin, S M Zahid Hosen, Zahed Bin Rahim, Abu Mansur Dinar, Mohammad Shah Hafez Kabir, Ramiz Ahmed Sultan, Ashekul Islam, Md Kamrul Hossain
Cyclooxygenase-2 (COX-2) catalyzed synthesis of prostaglandin E2 and it associates with tumor growth, infiltration, and metastasis in preclinical experiments. Known inhibitors against COX-2 exhibit toxicity. Therefore, it is of interest to screen natural compounds like flavanoids against COX-2. Molecular docking using 12 known flavanoids against COX-2 by FlexX and of ArgusLab were performed. All compounds showed a favourable binding energy of >-10 KJ/mol in FlexX and > -8 kcal/mol in ArgusLab. However, this data requires in vitro and in vivo verification for further consideration...
2015: Bioinformation
Ganesh Kumar Veeramachaneni, K Kranthi Raj, Leela Madhuri Chalasani, Sai Krishna Annamraju, Bondili Js, Venkateswara Rao Talluri
Increase in obesity rates and obesity associated health issues became one of the greatest health concerns in the present world population. With alarming increase in obese percentage there is a need to design new drugs related to the obesity targets. Among the various targets linked to obesity, pancreatic lipase was one of the promising targets for obesity treatment. Using the in silico methods like structure based virtual screening, QikProp, docking studies and binding energy calculations three molecules namely zinc85531017, zinc95919096 and zinc33963788 from the natural database were reported as the potential inhibitors for the pancreatic lipase...
2015: Bioinformation
Gauthaman Kalamegam, Peter Natesan Pushparaj, Fazal Khan, Khalid Hussein Wali Sait, Nisreen Anfinan, Mohammed Al-Qahtani
Ovarian cancer is one of the most lethal gynaecological cancers. Its subtle onset and absence of symptoms in early stages are associated with poor prognosis and high mortality. Identification of early biomarkers would aid in ovarian cancer control. Mesenchmal stem cells (MSCs) and/or their secretory products are identified to have cancer inhibitory properties. Therefore, it is of interest to study the anticancer properties of human Wharton's jelly stem cells conditioned medium (hWJSCs-CM) on primary ovarian carcinoma cells in vitro...
2015: Bioinformation
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