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Biomedical subjects

S Pramanik

Publications and source records attributed to S Pramanik.

6 recordsLinked to original sources
PubMed1995

A new data model for biological classification.

In the domain of biological classification, classifications are performed hierarchically. There are no standard classifications which are unanimously accepted by the community of each domain; many different interacting views of classification exist about the same data, and the discovery of new data results in changes to the existing classification. Even a single individual may change his or her own classification of a particular group. Since multiple classification views interact, they are semantically related. It is difficult to model this kind of dynamically evolving and semantically interacting classification system using traditional data models, which lack the structural flexibility necessary to support dynamic views of hierarchic classifications, and cannot properly capture the history of these complex interactions. We have developed a new data model which is suitable for supporting semantically interacting dynamic views of hierarchic biological classifications. On the basis of our new data model we have developed a prototype database system called HICLAS (HIerarchical CLAssification System); its domain is plant taxonomy. HICLAS is available through the Internet and an X-window interface has been implemented to support queries to classification data.

Classification↗
PubMed1994

Multiple sequence alignment using simulated annealing.

Multiple sequence alignment is a useful technique for studying molecular evolution and analyzing structure-sequence relationships. Dynamic programming of multiple sequence alignment has been widely used to find an optimal alignment. However, dynamic programming does not allow for certain types of gap costs, and it limits the number of sequences that can be aligned due to its high computational complexity. The focus of this paper is to use simulated annealing as the basis for developing an efficient multiple sequence alignment algorithm. An algorithm called Multiple Sequence Alignment using Simulated Annealing (MSASA) has been developed. The computational complexity of MSASA is significantly reduced by replacing the high-temperature phase of the annealing process by a fast heuristic algorithm. This heuristic algorithm facilitates in minimizing the solution set of the low-temperature phase of the annealing process. Compared to the dynamic programming approach, MSASA can (i) use natural gap costs which can generate better solution, (ii) align more sequences and (iii) take less computation time.

Algorithms↗
PubMed1994

An efficient method for multiple sequence alignment.

Multiple sequence alignment has been a useful method in the study of molecular evolution and sequence-structure relationships. This paper presents a new method for multiple sequence alignment based on simulated annealing technique. Dynamic programming has been widely used to find an optimal alignment. However, dynamic programming has several limitations to obtain optimal alignment. It requires long computation time and cannot apply certain types of cost functions. We describe detail mechanisms of simulated annealing for multiple sequence alignment problem. It is shown that simulated annealing can be an effective approach to overcome the limitations of dynamic programming in multiple sequence alignment problem.

Algorithms↗
PubMed1990

Cytoskeleton-bound mRNA for a 40-kDa polypeptide in rat L6 cells is not always translated.

The relationship between attachment of mRNA to the cytoskeletal framework and its translation was examined using the mRNA for a polypeptide of 40 kDa (P-40) which is translated in rat L6 myoblasts but not in the myotubes. In both myoblasts and myotubes this mRNA was found to be associated with the cytoskeletal framework. Furthermore, the stability of the association between P-40 mRNA and the cytoskeletal framework in absence of RNA and protein synthesis was examined by using actinomycin D and NaF to block RNA and protein synthesis, respectively. In absence of RNA synthesis portions of both nontranslated P-40 mRNA and translated actin mRNA of myotubes were released into the soluble fraction. In myoblasts, however, both mRNAs remained associated with the cytoskeletal framework following inhibition of RNA synthesis. Inhibition of protein synthesis, on the other hand, had a more dramatic effect on the association between the cytoskeletal framework and P-40 mRNA in myoblasts but not in myotubes. In contrast, the association between actin mRNA and cytoskeletal framework was unaffected by inhibition of protein synthesis in both myoblasts and myotubes. The results of these studies show that the molecular nature of association between cytoskeletal framework and mRNA may differ among mRNAs and may also depend on whether the cells are dividing or are terminally differentiated. Furthermore, no direct relationship between the translation of mRNA and its attachment to the cytoskeletal framework was observed.

Actins↗
PubMed1987

Attachment of mRNA to the cytoskeletal framework and translational control of gene expression in rat L6 muscle cells.

The mRNA of rat L6 muscle cells was distributed between a detergent-insoluble fraction containing the cytoskeletal framework and a detergent-soluble fraction. The majority of cytoskeleton-bound mRNA was translationally active and present as polysomes. The mRNA of the detergent-soluble fraction was not associated with the ribosomes and, thus, considered to be the repressed free population. The binding of mRNA was not mediated through ribosomes or the poly(A) region of mRNA. Cross-linking of RNA and proteins was used to examine whether proteins of the cytoskeletal framework were involved in binding mRNA to this structure. Analysis of the mRNA-protein complexes has shown that a large number of polypeptides of molecular masses between 15 and 220 kilodaltons (kDa) were associated with both cytoskeleton-bound and soluble mRNAs. However, a 165-kDa polypeptide was preferentially associated with cytoskeleton-bound mRNA-protein complexes. This polypeptide was also enriched in the total proteins of the cytoskeleton fraction. We have suggested a receptor-like role for the 165-kDa polypeptide in binding mRNA to the cytoskeletal framework. The mechanism of interaction between the cytoskeleton and mRNA was further examined by using a ghost-monolayer transcription system. The mRNA synthesized by this transcription system was preferentially retained in the detergent-insoluble cytoskeleton component of the ghost-monolayer preparation. To understand the physiological significance of the distribution of mRNA between the translationally active cytoskeleton-bound and repressed soluble fractions we have isolated a cDNA clone for a 1.3-kilobase (kb) mRNA. This mRNA was preferentially repressed in myotubes. Distribution of this mRNA was determined by Northern blot analysis using the recombinant plasmid. This analysis indicates that nearly 90% of this mRNA was not associated with ribosomes. In contrast, only 3% of alpha-actin mRNA was found in the repressed population. However, approximately 25% of the 1.3-kb mRNA was present as repressed free messenger ribonucleoprotein. This behaviour is again different from that of actin. All of the cytoskeleton-bound alpha-actin mRNA was associated with polysomes. Furthermore, most of the small amount of alpha-actin mRNA which was present in the soluble fraction was also associated with polysomes. We have, therefore, concluded from these observations that binding of mRNA to the cytoskeleton framework and translation of mRNA are two separate events. We have suggested that mRNA is transported to the cytoplasm as a cytoskeleton-associated complex and further interaction with ribosomes may stabilize this complex.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗