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Biomedical subjects

S Shivakumar

Publications and source records attributed to S Shivakumar.

At least 19 recordsLinked to original sources
PubMed2006

Production of exopolysaccharides by Agrobacterium sp. CFR-24 using coconut water - a byproduct of food industry.

AIMS: The work is intended to explore the suitability of underutilized coconut water (a byproduct of food industry) for the production of exopolysaccharides (EPS) by Agrobacterium sp. CFR 24. METHODS AND RESULTS: Besides checking the suitability of coconut water for the production of water-soluble (WS) and water-insoluble (WIS) EPS, certain fermentation parameters, such as initial pH, incubation period and kinetics of EPS production were investigated. The coconut water medium was found to support the production of both types of EPS. The optimal initial pH and temperature was found to be 6.0 and 30 degrees C, respectively. In shake flask (150 rev min(-1)) studies, high-cell density inoculum resulted in the production of 11.50 g l(-1) of WIS-EPS and 4.01 g l(-1) WS-EPS after 72 and 96 h of fermentation, respectively. CONCLUSIONS: Coconut water was found suitable for the production of microbial EPS by Agrobacterium sp. CFR 24 strain. Under optimum conditions, it produced a good amount of WIS-EPS, which is comparable with that of the sucrose medium (11 g l(-1)). SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report on the use of coconut water as a fermentation medium for the production of any microbial EPS. Besides producing value-added products, use of this food industry byproduct, which is often being drained out, can significantly reduce the problem of environmental pollution.

Biomass↗
PubMed2004

MURCS association.

The MURCS association i.e. MUllerian duct aplasia, Renal aplasia, Cervicothoracic Somite dysplasia is a rare developmental disorder. The authors report a case of MURCS association with supernumerary ribs in a 7-month-old infant who presented with failure to thrive.

Abnormalities, Multiple↗
PubMed2002

Cytogenetic, fluorescent in situ hybridization & reverse transcriptase-polymerase chain reaction analysis in acute promyelocytic leukaemia patients.

BACKGROUND & OBJECTIVES: The presence of t(15;17) or PML-RAR alpha fusion transcript is the diagnostic hallmark of patients with acute promyelocytic leukaemia (APL). Cytogenetic (CG), fluorescent in situ hybridization (FISH) and reverse transcriptase-polymerase chain reaction (RT-PCR) are mainly the techniques used for detecting this abnormality. The objective of this study was to compare and assess the role of CG, FISH and RT-PCR in the diagnosis of APL. METHODS: CG, FISH and RT-PCR analysis were performed in 29 patients with APL (28 M3, 1 M3v; 27 studied at diagnosis and 2 at relapse). RESULTS: Karotypes obtained in 25 patients revealed t(15;17) in 21 normal karyotype in 3 and trisomy 8 in 1 patient. In 26 patients FISH was positive for PML-RAR alpha fusion in both interphase (IP) and metaphase, two were negative and one patient had no cells for FISH analysis. IP FISH confirmed the fusion of PML-RAR alpha in all patients with t(15;17) detected by CG. RT-PCR was positive in the 22 patients analyzed (7 patients did not have RT-PCR). PCR was positive in the 3 patients with cytogenetically normal karyotypes and in one patient when karyotyping was a failure. CG detected 21 (72.4%) patients with t(15;17) of which additional chromosomal abnormalities were detected in 20 per cent of patients with successful karyotype. INTERPRETATION & CONCLUSION: FISH and RT-PCR were useful in detecting PML-RAR alpha fusion in cytogenetically normal patients and those in when karyotyping was a failure and can be used in routine analysis for rapid confirmation of t(15;17) in patients with acute myeloid leukaemia.

Adolescent↗
PubMed2001

Vectorial efficacy of Phlebotomus argentipes in Kala-azar endemic foci of Bihar (India) under natural and artificial conditions.

Ability of Phlebotomus argentipes to acquire Leishmania donovani the causative agent of Indian Kala-azar was evaluated in the laboratory. Flies were fed artificially on infected blood suspensions, using a chick-skin-membrane feeding apparatus, and naturally on Leishmania donovani infected mice. In addition flies collected from different endemic areas were dissected and examined for natural infection. Flies fed on infected mice showed significantly higher feeding rate (14.4%, p < 0.01) compared to that of other experiments (9%, 8.75%) but the percentage of infection was very low (2.43%). No Chi-square comparison was made between infection rate and feeding rate because of low value in infection rate (less than 5). Flies dissected for natural infection showed only 0.1% infection. Not much difference was observed in the intensity of Leishmania donovani infection in the mid gut of sandflies examined from any of these experiments. These observations have confirmed that Phlebotomus argentipes has ability to acquire infection and it provides the final piece of evidence that Phlebotomus argentipes is the vector of Leishmania donovani in Bihar State.

Animals↗
PubMed1999

Intranuclear localization of human papillomavirus 16 E7 during transformation and preferential binding of E7 to the Rb family member p130.

To study intracellular pathways by which the human papillomavirus 16 oncogene E7 participates in carcinogenesis, we expressed an inducible chimera of E7 by fusion to the hormone-binding domain of the estrogen receptor. The chimeric protein (E7ER) transformed rodent fibroblast cell lines and induced DNA synthesis on addition of estradiol. In coimmunoprecipitation experiments, E7ER preferentially bound p130 when compared to p107 and pRb. After estradiol addition, E7ER localization changed to a more intense intranuclear staining. Induction of E7 function was not correlated with binding to p130 or pRb but rather with intranuclear localization and modest induction of binding to p107.

Cell Nucleus↗
PubMed1999

ProClass Protein Family Database.

ProClass is a protein family database that organizes non-redundant sequence entries into families defined collectively by PROSITE patterns and PIR superfamilies. By combining global similarities and functional motifs into a single classification scheme, ProClass helps to reveal domain and family relationships and classify multi-domain proteins. The database currently consists of more than 120 000 sequence entries, approximately 60% of which is classified into about 3500 families. To maximize family information retrieval, the database provides links to various protein family/domain and structural class databases and contains multiple motif alignments of all PROSITE patterns as well as global alignments of PIR superfamilies. The motif sequences are retrieved from both PIR-International and SWISS-PROT databases, including a large number of new members detected by our GeneFIND family identification system. ProClass can be used to support full-scale genomic annotation, because of its high classification rate. The ProClass database is available for on-line search and record retrieval from our WWW server at http://diana.uthct.edu/proclass.html

Amino Acid Sequence↗
PubMed1998

GeneFIND web server for protein family identification and information retrieval.

UNLABELLED: An integrated database and search system has been developed for protein family identification and information retrieval, as an approach to undertake the highly complex, genomic-scale problem of molecular sequence database search and organization. AVAILABILITY: http://diana.uthct.edu CONTACT: wu@uthct.edu

Amino Acid Sequence↗
PubMed1998

Proclass protein family database: new version with motif alignments.

ProClass is a protein family database which organizes non-redundant sequence entries into families defined collectively by the ProSite patterns and PIR superfamilies. The database consists of about 100,000 entries, more than half of which are classified in about 3,000 families. The new version includes links to various protein family/domain and structural class databases and contains gapped motif alignments for all ProSite patterns. The motif sequences are retrieved from both SwissProt and PIR-international databases, including numerous new members detected by our GeneFIND family identification system. The motif collection represents a 50% increase from those catalogued in ProSite. The ProClass database can be used to maximize family information retrieval, help organize protein sequence databases, and support full-scale genomic annotation. The database and its query program are freely available for on-line record retrieval and direct file transfer from our WWW server at http:/(/)diana.uthct.edu/proclass.html+ ++.

Amino Acid Sequence↗
PubMed1996

Evidence for linkage of regions on chromosomes 6 and 11 to plasma glucose concentrations in Mexican Americans.

The genetic factors involved in type II diabetes are still unknown. To address this problem, we are creating a 10 to 15 cM genetic map on 444 individuals from 32 Mexican American families ascertained on a type II diabetic proband. Using highly polymorphic microsatellite markers and a multipoint variance components method, we found evidence for linkage of plasma glucose concentration 2 hr after oral glucose administration to two regions on chromosome 11: beta-hemoglobin (HBB) and markers D11S899/D11S1324 near the sulfonylurea receptor (SUR) gene. Iod scores at these two loci were 2.77 and 3.37, respectively. The SUR gene region accounted for 44.7% of the phenotypic variance. Evidence for linkage to fasting glucose concentration was also observed for two loci on chromosome 6, one of which is identical to a proposed susceptibility locus for type I diabetes (D6S290). When diabetics were excluded from the analyses, all Iod scores became zero, suggesting that the observed linkages were with the trait diabetes rather than with normal variation in glucose levels. Results were similar whether all diabetics were included in the analyses or only those who were not under treatment with oral antidiabetic agents or insulin.

Blood Glucose↗
PubMed1995

Leptospirosis in Madras--a clinical and serological study.

Leptospirosis was confirmed by Microscopic Agglutination Test (MAT) and/or ELISA in 57 patients admitted to the Government General Hospital, Madras, India, during November and December of 1990 and 1991 with symptomatology suggestive of the disease. Fifty (88%) of the 57 cases were males; the mean age of all the cases was 39.6 years (range 17-72). The main clinical features were: fever 100% jaundice 84%, Myalgia 82%, acute renal failure 72% and conjunctival suffusion 58%. Non-azotemic jaundice occurred in 19% of cases. Renal failure was non-oliguric in 24% of cases. 3.5% of patients died. 23 patients underwent peritoneal and/or hemodialysis. ELISA IgM titres ranged from 1:80 to 1:10240 (geometric mean tire 911). MAT titres > or = 1:1600 and > or = 1:800 occurred in 39 of 54 and 51 of 54 cases respectively. Autumnalis was the serogroup most commonly recorded serologically, and Leptospira interrogans serovar autumnalis was isolated from one patient. This study shows that leptospirosis is a significant health problem in Madras, though normally grossly underestimated due to the absence of routine laboratory diagnostic facilities for the disease. Gross under-reporting is also likely in other high rainfall third world areas.

Acute Kidney Injury↗
PubMed1994

Back-propagation and counter-propagation neural networks for phylogenetic classification of ribosomal RNA sequences.

A neural network system has been developed for rapid and accurate classification of ribosomal RNA sequences according to phylogenetic relationship. The molecular sequences are encoded into neural input vectors using an n-gram hashing method. A SVD (singular value decomposition) method is used to compress and reduce the size of long and sparse n-gram input vectors. The neural networks used are three-layered, feed-forward networks that employ supervised learning paradigms, including the back-propagation algorithm and a modified counter-propagation algorithm. A pedagogical pattern selection strategy is used to reduce the training time. After trained with ribosomal RNA sequences of the RDP (Ribosomal Database Project) database, the system can classify query sequences into more than one hundred phylogenetic classes with a 100% accuracy at a rate of less than 0.3 CPU second per sequence on a workstation. When compared to other sequence similarity search methods, including Similarity Rank, Blast and Fasta, the neural network method has a higher classification accuracy at a speed of about an order of magnitude faster. The software tool will be made available to the biology community, and the system may be extended into a gene identification system for classifying indiscriminately sequenced DNA fragments.

Algorithms↗