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Screening of Marine Sediments from Bay of Bengal near Pudimadaka Coast of Andhra Pradesh for Isolation of Lipolytic Actinobacteria and Characterization of the Most Potent Isolates
Bindiya Panchagnula,Ramana Terli
International Journal of Biology , 2010, DOI: 10.5539/ijb.v3n1p33
Abstract: Ten sediment samples collected at various depths of Bay of Bengal near Pudimadaka Coast of Andhra Pradesh were screened for the isolation of lipolytic Actinobacteria by tributyrin agar clearing method. The selected isolates were cultured under submerged fermentation conditions and assayed for their extra cellular lipase producing capabilities. Results indicated that 38 of the 88 isolates from 10 sediment samples showed lipolytic activity after primary screening. These isolates were subjected to secondary screening and lipase activity is estimated quantitatively. The promising isolate was found to be BTS-713 and was identified as Streptomyces sps after characterization. In conclusion, these results increased the scope of finding industrially important marine actinomycetes from Pudimadaka Coast of Andhra Pradesh.
Taxonomy and Polyphasic Characterization of Alkaline Amylase Producing Marine Actinomycete Streptomyces rochei BTSS 1001
Aparna Acharyabhatta,Siva Kumar Kandula,Ramana Terli
International Journal of Microbiology , 2013, DOI: 10.1155/2013/276921
Abstract: Actinomycetes isolated from marine sediments along the southeast coast of Bay of Bengal were investigated for amylolytic activity. Marine actinomycete BTSS 1001 producing an alkaline amylase was identified from marine sediment of Diviseema coast, Bay of Bengal. The isolate produced alkaline amylase with maximum amylolytic activity at pH 9.5 at 50°C. The organism produced white to pale grey substrate mycelium and grayish aerial mycelium with pinkish brown pigmentation. A comprehensive study of morphological, physiological parameters, cultural characteristics, and biochemical studies was performed. The presence of iso-C15?:?0, anteiso-C15?:?0, iso-C16?:?0, and anteiso-C17?:?0 as the major cellular fatty acids, LL-diaminopimelic acid as the characteristic cell wall component, and menaquinones MK-9H(6) and MK-9H(8) as the major isoprenoid quinones is attributed to the strain BTSS 1001 belonging to the genus Streptomyces. Comparison of 16S rRNA gene sequences showed that strain BTSS 1001 exhibited the highest similarities to the type strains of Streptomyces rochei (99%), Streptomyces plicatus (99%), and Streptomyces enissocaesilis (99%). Using the polyphasic taxonomical approach and phenotypic characteristic studies, the isolate BTSS 1001 was characterized as marine actinomycete Streptomyces rochei. 1. Introduction Actinomycetes have long been reported as important source of biotechnologically important compounds. The recent focus is on marine Actinomycetes as a source of bioactive compounds and industrial enzymes. This is due to the fact that terrestrial actinomycetes have been exhaustively analyzed for bioactive compounds and enzymes but they still fall short of industrial application. Thus, the need of the hour is to identify newer sources capable of withstanding the conditions of industrial and commercial applications. Studies by several researchers [1–4] on marine actinomycetes have reported diversity and presence of unique marine taxa in ocean sediments. Their survival in extreme conditions in the ocean sediments demonstrates their ability for adaptation and production of different types of bioactive compounds as compared to their terrestrial counterparts [5]. Marine actinomycetes have been established as a rich source of several secondary metabolites such as novel bioactive molecules like antibiotics, antifungal, and anticancer compounds, plant growth hormones, industrially important enzymes, enzyme inhibitors, and pigments [6, 7]. Culturally independent methods and polyphasic approaches have also demonstrated that marine sediments contain wide range
RCDB: Renal Cancer Gene Database
Jayashree Ramana
BMC Research Notes , 2012, DOI: 10.1186/1756-0500-5-246
Abstract: Renal Cancer Gene Database is a manually curated compendium of 240 protein-coding and 269 miRNA genes contributing to the etiology and pathogenesis of various forms of renal cell carcinomas. The protein coding genes have been classified according to the kind of gene alteration observed in RCC. RCDB also includes the miRNAsdysregulated in RCC, along with the corresponding information regarding the type of RCC and/or metastatic or prognostic significance. While some of the miRNA genes showed an association with other types of cancers few were unique to RCC. Users can query the database using keywords, category and chromosomal location of the genes. The knowledgebase can be freely accessed via a user-friendly web interface at http://www.juit.ac.in/attachments/jsr/rcdb/homenew.html webcite.It is hoped that this database would serve as a useful complement to the existing public resources and as a good starting point for researchers and physicians interested in RCC genetics.Renal cell carcinoma (RCC) represents a heterogeneous group of tumors differing in genetic background, responses to surgical and medical therapy and prognoses. It accounts for 3% of adult malignancy and results in over 100000 deaths worldwide annually [1]. It is the one of the leading causes of cancer deaths in Western countries with steadily escalating incidence over the last few decades [2]. RCC is classified based on morphological and genetic differences. This classification distinguishes metanephric adenoma oncocytoma and papillary adenoma as benign tumors from the clear cell (ccRCC), papillary/chromophilic, chromophobic (chRCC) and collecting duct RCC. This classification is important because of its prognostic implications. ccRCC is the most common and accounts for 70% of RCCs. RCC is diagnosed through imaging studies including CT and ultrasound, but kidney biopsy is an invasive technique that might result in complications and would not provide accurate diagnosis in certain situations. For early p
A new approach to mitigation of radio frequency interference in interferometric data
Ramana Athreya
Physics , 2009, DOI: 10.1088/0004-637X/696/1/885
Abstract: Radio frequency interference (RFI) is the principal factor limiting the sensitivities of radio telescopes, particularly at frequencies below 1 GHz. I present a conceptually new approach to mitigation of RFI in interferometric data. This has been used to develop a software tool (RfiX) to remove RFI from observations using the Giant Metrewave Radio Telescope, India. However, the concept can be used to excise RFI in any interferometer. Briefly, the fringe-stopped correlator output of an interferometer baseline oscillates with the fringe-stop period in the presence of RFI. RfiX works by identifying such a pattern and subtracting it from the data. It is perhaps the only purely software technique which can salvage the true visibility value from RFI-corrupted data. It neither requires high-speed hardware nor real-time processing and works best on normal correlator output integrated for 1-10s. It complements other mitigation schemes with its different approach and the regime it addresses. Its ability to work with data integrated over many seconds gives it an advantage while excising weak, persistent RFI unlike most other techniques which use high-speed sampling to localise RFI in time-frequency plane. RfiX is also different in that it does not require RFI-free data to identify corrupted sections. Some results from the application of RfiX is presented including an image at 240 MHz with a Peak/noise ratio of 43000, the highest till date at wavelengths >1m.
FaaPred: A SVM-Based Prediction Method for Fungal Adhesins and Adhesin-Like Proteins
Jayashree Ramana,Dinesh Gupta
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0009695
Abstract: Adhesion constitutes one of the initial stages of infection in microbial diseases and is mediated by adhesins. Hence, identification and comprehensive knowledge of adhesins and adhesin-like proteins is essential to understand adhesin mediated pathogenesis and how to exploit its therapeutic potential. However, the knowledge about fungal adhesins is rudimentary compared to that of bacterial adhesins. In addition to host cell attachment and mating, the fungal adhesins play a significant role in homotypic and xenotypic aggregation, foraging and biofilm formation. Experimental identification of fungal adhesins is labor- as well as time-intensive. In this work, we present a Support Vector Machine (SVM) based method for the prediction of fungal adhesins and adhesin-like proteins. The SVM models were trained with different compositional features, namely, amino acid, dipeptide, multiplet fractions, charge and hydrophobic compositions, as well as PSI-BLAST derived PSSM matrices. The best classifiers are based on compositional properties as well as PSSM and yield an overall accuracy of 86%. The prediction method based on best classifiers is freely accessible as a world wide web based server at http://bioinfo.icgeb.res.in/faap. This work will aid rapid and rational identification of fungal adhesins, expedite the pace of experimental characterization of novel fungal adhesins and enhance our knowledge about role of adhesins in fungal infections.
Machine Learning Methods for Prediction of CDK-Inhibitors
Jayashree Ramana,Dinesh Gupta
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0013357
Abstract: Progression through the cell cycle involves the coordinated activities of a suite of cyclin/cyclin-dependent kinase (CDK) complexes. The activities of the complexes are regulated by CDK inhibitors (CDKIs). Apart from its role as cell cycle regulators, CDKIs are involved in apoptosis, transcriptional regulation, cell fate determination, cell migration and cytoskeletal dynamics. As the complexes perform crucial and diverse functions, these are important drug targets for tumour and stem cell therapeutic interventions. However, CDKIs are represented by proteins with considerable sequence heterogeneity and may fail to be identified by simple similarity search methods. In this work we have evaluated and developed machine learning methods for identification of CDKIs. We used different compositional features and evolutionary information in the form of PSSMs, from CDKIs and non-CDKIs for generating SVM and ANN classifiers. In the first stage, both the ANN and SVM models were evaluated using Leave-One-Out Cross-Validation and in the second stage these were tested on independent data sets. The PSSM-based SVM model emerged as the best classifier in both the stages and is publicly available through a user-friendly web interface at http://bioinfo.icgeb.res.in/cdkipred.
LipocalinPred: a SVM-based method for prediction of lipocalins
Jayashree Ramana, Dinesh Gupta
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-445
Abstract: In the present study we propose a SVM based method for identification of lipocalin protein sequences. The SVM models were trained with the input features generated using amino acid, dipeptide and secondary structure compositions as well as PSSM profiles. The model derived using both PSSM and secondary structure emerged as the best model in the study. Apart from achieving a high prediction accuracy (>90% in leave-one-out), lipocalinpred correctly differentiates closely related fatty acid-binding proteins and triabins as non-lipocalins.The method offers a promising approach as a lipocalin prediction tool, complementing PROSITE, Pfam and homology modelling methods.The lipocalins constitute a group of small (160-200 residues, 15-20KD) mostly extracellular proteins which are highly stable, functionally versatile and widely distributed within different biological kingdoms. The lipocalins belong to the calcyin superfamily, along with fatty acid binding proteins (FABPs), avidins, metallo-protease inhibitors and triabins. In contrast to their poor sequence similarity (identity falling below 20% for paralogs), lipocalins share a highly conserved three dimensional structure. The so-called 'lipocalin fold' comprises a stable calyx-shaped eight-stranded β-barrel scaffold, flanked by a C-terminal α-helix. The space between the two β-sheets of the barrel defines an internal apolar binding cavity with high structural plasticity, consisting of four structurally hypervariable peptide loops, mounted on the barrel. These are divided into two groups according to the presence of three structurally conserved regions (SCRs). The core set of lipocalins called kernel lipocalins share the three SCRs and are more closely related. The more divergent, outlier lipocalins, share only one or two SCRs [1].Though first identified for their ability to transport small hydrophobic molecules like steroids, bilins, fatty acids etc., it is now established that the functional repertoire of lipocalins encomp
An adult case of urinary tract infection with Kingella kingae: a case report
KV Ramana, SK Mohanty
Journal of Medical Case Reports , 2009, DOI: 10.1186/1752-1947-3-7236
Abstract: We present a microbiologically confirmed urinary tract infection with K. kingae in an immunocompetent 45-year-old adult woman with post-menopausal bleeding and with a history of clots. Her urine was subjected to culture and sensitivity tests. The isolated colonies were identified as K. kingae because of their typical culture characteristics such as long incubation period required for growth, beta-hemolysis, positive oxidase and negative catalase, urease indole, nitrate and citrate tests. Penicillin G disc test was positive. They were sensitive to all conventional antibiotics.K. kingae infection is a rare occurrence in immunocompetent adults. Very few cases of microbiologically confirmed infections have been reported so far. The isolation of K. kingae from urine sample has rarely been reported. K. kingae isolates are either missed or misinterpreted by clinical microbiologists. Therefore, K. kingae deserves recognition as a pathogen.In 1976, Moraxella kingae was removed from the genus Moraxella and was given a new genus and species name Kingella kingae in the family Neisseriaceae[1]. Besides K. kingae, other species belonging to the genus Kingella are K. denitrificans, K. indolegenes and K. oralis. K. kingae exhibits a variable morphology (cocci, short Gram-negative coccobacilli to medium sized rods) and is considered to be a normal flora of the upper respiratory tract and genitourinary tract [2]. It has been associated with infections in children under 6 years and immunocompromised individuals [2].Poor oral hygiene, pharyngitis and mucosal ulceration are the predisposing factors for K. kingae infections [2,3]. K. kingae bacteremia without endocarditis has also been reported in immunocompetent adults following dental manipulations [4]. K. kingae has specific tissue tropism for cardiac, valvular, joint space, and skeletal tissue and has been isolated from cases of bacteremia, endocarditis, bone and joint infection in various samples such as blood, joint fluid, and urin
Release Characteristics of Diltiazem Hydrochloride Wax-Matrix Granules – Thermal Sintering Effect
MU Uhumwangho, RMKV Ramana
Journal of Applied Sciences and Environmental Management , 2011,
Abstract: The aim of this study was to investigate the release characteristics of matrix (non-disintegrating) granules consisting of diltiazem hydrochloride (model drug) and glyceryl behenate (a wax matrix forming polymer) for sustained release application using sintering technique. The granules of diltiazem hydrochloride-wax matrix were prepared by melt granulation technique. This was formed by triturating the drug powder with a melted glyceryl behenate (drug: wax ratio, 3:1). The granules were subsequently sintered at 60 and 700C for 1, 1.5 and 3h. The unsintered and sintered wax matrix granules of diltiazem hydrochloride were evaluated for physicochemical parameters and in vitro dissolution studies. The dissolution data were subjected to analysis using different mathematical models namely – zero order flux, first order, Higuchi square root of time, then Korsmeyer and Peppas model. Fourier-Transform Infrared Spectroscopy (FTIR) was carried out to investigate any chemical interactions between the drug and the added recipients before and after sintering. There was increased drug release retardation of diltiazem hydrochloride-wax matrix granules with sintering. The retardation depended on the temperature and duration of sintering. For instance, formulations sintered at 60 and 70°C for a period of 1.5h gave maximum release (m), time to attain maximum release (t) and dissolution rate (m/t) of 96.1%, 95.2%, 5h, 9h, 19.2%h-1 and 10.6%h-1 respectively. The drug release was by Higuchi controlled diffusion mechanism and it followed Fickain diffusion mechanism (n<0.45). Sintering technique enhanced the extent of drug retardation from the systems studied. There was no chemical interaction between the model drug and the added recipients as shown in the FTIR studies.
Single and unpaired sera tube widal agglutination test in enteric fever
Mohanty S,Ramana K
Saudi Journal of Gastroenterology , 2007,
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