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https://www.readbyqxmd.com/read/28197063/prediction-driven-functional-annotation-of-hypothetical-proteins-in-the-major-facilitator-superfamily-of-s-aureus-nctc-8325
#1
Jessica Marklevitz, Laura K Harris
Antibiotic resistance Staphylococcus aureus strains cause several life threatening infections. New drug treatment options are needed, but are slow to develop because 50% of the S. aureus genome is hypothetical. The goal of this is to aid in the annotation of the S. aureus NCTC 8325 genome by identifying hypothetical proteins related to the Major Facilitator Superfamily (MFS). The MFS is a broad protein group with members involved in drug efflux mechanisms causing resistance. To do this, sequences for three MFS proteins with x-ray crystal structures in E...
2016: Bioinformation
https://www.readbyqxmd.com/read/28197062/an-analysis-of-phosphorylation-sites-in-protein-kinases-from-leishmania
#2
Sukrat Sinha, Shanthy Sundaram
Protein kinases are promising drug targets for Leishmaniasis. We have evaluated the phosphorylation potential of protein kinases in different species and strains of Leishmania. Phosphorylation potential of serine, threonine and tyrosine residues of kinases in Leishmania parasite were studied. The results indicate that some species specific residues of serine, threonine and tyrosine have a phosphorylation potential of 1 suggesting that these residues are important target sites in protein kinases based anti-leishmanial therapies...
2016: Bioinformation
https://www.readbyqxmd.com/read/28197061/presence-of-bacterial-virulence-gene-homologues-in-the-dibenzo-p-dioxins-degrading-bacterium-sphingomonas-wittichii
#3
Amr T M Saeb
Sphingomonas wittichii, a close relative of the human pathogen Sphingomonas paucimobilis, is a microorganism of great interest to the bioremediation community for its ability of biodegradation to a large number of toxic polychlorinated dioxins. In the present study we investigated the presence of different virulence factors and genes in S. wittichii. We utilized phylogenetic, comparative genomics and bioinformatics analysis to investigate the potentiality of S. wittichii as a potential virulent pathogen. The 16SrDNA phylogenetic tree showed that the closest bacterial taxon to S...
2016: Bioinformation
https://www.readbyqxmd.com/read/28197060/a-searchable-database-for-the-genome-of-phomopsis-longicolla-isolate-mspl-10-6
#4
Omar Darwish, Shuxian Li, Zane May, Benjamin Matthews, Nadim W Alkharouf
: Phomopsis longicolla (syn. Diaporthe longicolla) is an important seed-borne fungal pathogen that primarily causes Phomopsis seed decay (PSD) in most soybean production areas worldwide. This disease severely decreases soybean seed quality by reducing seed viability and oil quality, altering seed composition, and increasing frequencies of moldy and/or split beans. To facilitate investigation of the genetic base of fungal virulence factors and understand the mechanism of disease development, we designed and developed a database for P...
2016: Bioinformation
https://www.readbyqxmd.com/read/28149059/genes2go-a-web-application-for-querying-gene-sets-for-specific-go-terms
#5
Konika Chawla, Martin Kuiper
: Gene ontology annotations have become an essential resource for biological interpretations of experimental findings. The process of gathering basic annotation information in tables that link gene sets with specific gene ontology terms can be cumbersome, in particular if it requires above average computer skills or bioinformatics expertise. We have therefore developed Genes2GO, an intuitive R-based web application. Genes2GO uses the biomaRt package of Bioconductor in order to retrieve custom sets of gene ontology annotations for any list of genes from organisms covered by the Ensembl database...
2016: Bioinformation
https://www.readbyqxmd.com/read/28149058/effect-of-hiv-1-subtype-c-integrase-mutations-implied-using-molecular-modeling-and-docking-data
#6
Jaiprasath Sachithanandham, Karnati Konda Reddy, King Solomon, Shoba David, Sanjeev Kumar Singh, Veena Vadhini Ramalingam, Susanne Alexander Pulimood, Ooriyapadickal Cherian Abraham, Pricilla Rupali, Gopalan Sridharan, Rajesh Kannangai
The degree of sequence variation in HIV-1 integrase genes among infected patients and their impact on clinical response to Anti retroviral therapy (ART) is of interest. Therefore, we collected plasma samples from 161 HIV-1 infected individuals for subsequent integrase gene amplification (1087 bp). Thus, 102 complete integrase gene sequences identified as HIV-1 subtype-C was assembled. This sequence data was further used for sequence analysis and multiple sequence alignment (MSA) to assess position specific frequency of mutations within pol gene among infected individuals...
2016: Bioinformation
https://www.readbyqxmd.com/read/28149057/predictive-characterization-of-hypothetical-proteins-in-staphylococcus-aureus-nctc-8325
#7
Kuana School, Jessica Marklevitz, William K Schram, Laura K Harris
Staphylococcus aureus is one of the most common hospital acquired infections. It colonizes immunocompromised patients and with the number of antibiotic resistant strains increasing, medicine needs new treatment options. Understanding more about the proteins this organism uses would further this goal. Hypothetical proteins are sequences thought to encode a functional protein but for which little to no evidence of that function exists. About half of the genomic proteins in reference strain S. aureus NCTC 8325 are hypothetical...
2016: Bioinformation
https://www.readbyqxmd.com/read/28149056/function-annotation-of-peptides-generated-from-the-non-coding-regions-of-d-melanogaster-genome
#8
Varughese Deepthi, Vineetha V I Nair, Vipin Thomas, Navya Raj, Shidhi P Ramakrishnan, Juveria Khan, Monika Kaushik, Pawan K Dhar, Achuthsankar S Nair
De novo emergence of genes is the most fundamental form of genetic diversity that is attracting the attention of the scientific community. Identification of short open reading frames (sORFs) from the non-coding regions of different genomes has been leading this thought recently. The coding potential of these newly identified sORFs have been investigated through experimental and computational approaches in recent studies. In the present work we have tried to make peptides from intergenic sequences of D. melanogaster genome leading to therapeutic applications...
2016: Bioinformation
https://www.readbyqxmd.com/read/28149055/computational-analysis-of-conserved-coil-functional-residues-in-the-mitochondrial-genomic-sequences-of-dermatophytes
#9
Bulbul Gupta, Jaspreet Kaur
Dermatophyte is a group of closely related fungi that have the capacity to invade keratinized tissue of humans and other animals. The infection known as dermatophytosis, caused by members of the genera Microsporum, Trichophyton, and Epidermophyton includes infection to the groin (tinea cruris), beard (tinea barbae), scalp (tinea capitis), feet (tinea pedis), glabrous skin (tinea corporis), nail (tinea unguium), and hand (tinea manuum). The identification of evolutionary relationship between these three genera of dermatophyte is epidemiologically important to understand their pathogenicity...
2016: Bioinformation
https://www.readbyqxmd.com/read/28149054/molecular-docking-based-screening-of-compounds-against-vp40-from-ebola-virus
#10
Hanaa M Alam El-Din, Samah A Loutfy, Nasra Fathy, Mostafa H Elberry, Ahmed M Mayla, Sara Kassem, Asif Naqvi
Ebola virus causes severe and often fatal hemorrhagic fevers in humans. The 2014 Ebola epidemic affected multiple countries. The virus matrix protein (VP40) plays a central role in virus assembly and budding. Since there is no FDA-approved vaccine or medicine against Ebola viral infection, discovering new compounds with different binding patterns against it is required. Therefore, we aim to identify small molecules that target the Arg 134 RNA binding and active site of VP40 protein. 1800 molecules were retrieved from PubChem compound database based on Structure Similarity and Conformers of pyrimidine-2, 4-dione...
2016: Bioinformation
https://www.readbyqxmd.com/read/28149053/in-silico-identification-and-characterization-of-a-hypothetical-protein-of-mycobacterium-tuberculosis-eai5-as-a-potential-virulent-factor
#11
Debdoot Gupta, Samiddha Banerjee, Santanu Pailan, Pradipta Saha
Tuberculosis, a life threatening disease caused by different strains of Mycobacterium tuberculosis is creating an alarming condition due to the emergence of increasing multi drug resistance (MDR) trait. In this study, in silico approach was used for the identification of a conserved novel virulent factor in Mycobacterium tuberculosis EAI5 (Accession no.CP006578) which can also act as potential therapeutic target. Systematic comparative search of genes that are common to strain EAI5 and other human pathogenic strains of M...
2016: Bioinformation
https://www.readbyqxmd.com/read/28149052/prediction-of-kinase-inhibitor-binding-affinity-using-energetic-parameters
#12
Singaravelu Usha, Samuel Selvaraj
The combination of physicochemical properties and energetic parameters derived from protein-ligand complexes play a vital role in determining the biological activity of a molecule. In the present work, protein-ligand interaction energy along with logP values was used to predict the experimental log (IC50) values of 25 different kinase-inhibitors using multiple regressions which gave a correlation coefficient of 0.93. The regression equation obtained was tested on 93 kinase-inhibitor complexes and an average deviation of 0...
2016: Bioinformation
https://www.readbyqxmd.com/read/28149051/elucidating-hydrogenase-surfaces-and-tracing-the-intramolecular-tunnels-for-hydrogenase-inhibition-in-microalgal-species
#13
Kritika Dixit, Md Akhlaqur Rahman, Adi Nath, Shanthy Sundaram
Intramolecular tunnels are majorly attracting attention as possible pathways for entry of inhibitors like oxygen and carbon monoxide to the active sites of the enzymes, hydrogenases. The results of homology modeling of the HydSL protein, a NiFe-hydrogenase from Chlamydomonas reinhardtii and Chlorella vulgaris are presented in this work. Here we identify and describe molecular tunnels observed in HydSL hydrogenase enzyme systems. The possible determinant of the oxygen stability of already studied hydrogenases could be the lack of several intramolecular tunnels...
2016: Bioinformation
https://www.readbyqxmd.com/read/28149050/insights-using-the-molecular-model-of-lipoxygenase-from-finger-millet-eleusine-coracana-l
#14
Apoorv Tiwari, Himanshu Avashthi, Richa Jha, Ambuj Srivastava, Vijay Kumar Garg, Pramod Wasudev Ramteke, Anil Kumar
Lipoxygenase-1 (LOX-1) protein provides defense against pests and pathogens and its presence have been positively correlated with plant resistance against pathogens. Linoleate is a known substrate of lipoxygenase and it induces necrosis leading to the accumulation of isoflavonoid phytoalexins in plant leaves. Therefore, it is of interest to study the structural features of LOX-1 from Finger millet. However, the structure ofLOX-1 from Finger millet is not yet known. A homology model of LOX-1 from Finger millet is described...
2016: Bioinformation
https://www.readbyqxmd.com/read/28149049/molecular-docking-ns4b-of-denv-1-4-with-known-bioactive-phyto-chemicals
#15
Anubrata Paul, Arpana Vibhuti, Samuel Raj
Dengue disease is a global disease that has no effective treatment. The dengue virus (DENV) NS4B is a target for designing specific antivirals due to its importance in viral replication. Medicinal plants have been a savior for dengue virus as they consist of a class of phytochemicals having anti-viral activity and can pose a new approach ofstrong drug against viruses. The present study analyzes the activity of compounds against NS4B of DENV (1-4) serotypes. In this study Catechin, Cianidanol, Epicatechin, Eupatoretin, Glabranin, Laurifolin, DL-Catechin, astherapeutic agents were filtered by using Lipinski rule's five and the drug-likeness property of these agents were used for assessment of pharmacological properties...
2016: Bioinformation
https://www.readbyqxmd.com/read/28149048/molecular-mechanisms-and-mode-of-tamoxifen-resistance-in-breast-cancer
#16
REVIEW
Shazia Ali, Mahmood Rasool, Hani Chaoudhry, Peter N Pushparaj, Prakash Jha, Abdul Hafiz, Maryam Mahfooz, Ghufrana Abdus Sami, Mohammad Azhar Kamal, Sania Bashir, Ashraf Ali, Mohammad Sarwar Jamal
Breast cancer is one of the most common cancers in women around the globe Tamoxifen is used for the last 40 years as an endocrine therapy for breast cancer. This resulted in the reduction of mortality rate by 30% and it still remains one of the most effective therapies against breast cancer. However, resistance against tamoxifen is still one of the major hurdles in the effective management of breast cancer. Intense research has been conducted in the past decade to further explore its resistance mechanism, but still a lot of research will be needed to effectively alleviate this problem...
2016: Bioinformation
https://www.readbyqxmd.com/read/28149047/implications-of-prognostic-variables-in-the-assessment-of-autoimmunity-in-hepatitis-c-patients-receiving-interferon-therapy
#17
Mahwish Arooj, Arif Malik, Abdul Basit, Mahmood Husain Qazi, Muhammad Asif, Mohammad Sarwar Jamal, Maged Mostafa Mahmoud, Hani Choudhry, Peter Natesan Pushparaj, Mahmood Rasool
Systematic administration of interferon-alpha (INF-alpha) is considered as the backbone of HCV therapy since 1991. Interferon (IFN) therapy can cause vasculitis, glomerulonephritis, cryoglobulinemia and certain other autoimmune diseases such as sialoadentitis, lichen planus and thyroiditis. Related to the factors of interferons, extensively studied gland is thyroid gland. A strong association was observed between thyroid disease and HCV patient when they were exposed to IFN therapy. Vitamin D, malondialdehyde (MDA), thyroid hormones and auto antibodies were biochemically assessed from the venous blood of seventy five HCV patients and fifty healthy controls...
2016: Bioinformation
https://www.readbyqxmd.com/read/28149046/virtual-screening-of-rage-inhibitors-using-molecular-docking
#18
Malini Devi Alaparthi, Gudipudi Gopinath, Srinivas Bandaru, Venu Sankeshi, Madhavi Mangalarapu, Swetha Sudha Nagamalla, Kota Sudhakar, Anupalli Roja Rani, Someswar Rao Sagurthi
Advanced Glycation End products (AGEs) interaction with Receptor for AGEs (RAGE) activates downstream signaling and evokes inflammatory responses in vascular cells. Therefore, it is of interest to design a novel series of molecules with a library of 352 compounds based on natural Isoflavone and Argpyrimidine moities. The compounds screened against the optimized structure of RAGE (PDB code: 3CJJ) using MolDock aided with molecular docking algorithm. This exercise identified compound number 62 with appreciable ADME properties having no toxicity and pharmacophore features...
2016: Bioinformation
https://www.readbyqxmd.com/read/28149045/a-qsar-model-of-benzoxazole-derivatives-as-potential-inhibitors-for-inosine-5-monophosphate-dehydrogenase-from-cryptosporidium-parvum
#19
Pratibha Teotia, Surya Prakash Dwivedi, Neeraja Dwivedi
Cryptosporidium parvum is the common enteric protozoan pathogen causing cryptosporidiosis in human. Available drugs to treat cryptosporidiosis are ineffective and there is yet no vaccine against C. parvum. Therefore, it is of interest to design an improved yet effective drug against C. parvum. Here, we docked benzoxazole derivatives (collected from literature) with inosine 5`- monophosphate dehydrogenase (IMPDH) from Cryptosporidium parvum using the program AutoDock 4.2. The docked protein - inhibitor complex structure was optimized using molecular dynamics simulation for 5 ps with the CHARMM-22 force field using NAMD (NAnoscale Molecular Dynamics program) incorporated in visual molecular dynamics (VMD 1...
2016: Bioinformation
https://www.readbyqxmd.com/read/28149044/in-vitro-anti-acetylcholinesterase-activity-of-an-aqueous-extract-of-unicaria-tomentosa-and-in-silico-study-of-its-active-constituents
#20
Suman Chowdhury, Shivani, Suresh Kumar
Depletion of acetylcholine in the central nervous system (CNS) is responsible for memory loss and cognition deficit. Enzyme acetylcholinesterase (AChE) is responsible for destruction of acetylcholine (Ach) in the brain. Many herbal plant extracts have been investigated for their potential use in the treatment of Alzheimer's disease (AD) by inhibiting AChE and upregulating the levels of Ach. The current study investigated the anti-acetylcholinesterase (AChE) activity of an aqueous extract of Unicaria tomentosa bark which has not been reported so far in the literature...
2016: Bioinformation
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