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T Dandekar

Publications and source records attributed to T Dandekar.

At least 19 recordsLinked to original sources
PubMed2001

When genetic distance matters: measuring genetic differentiation at microsatellite loci in whole-genome scans of recent and incipient mosquito species.

Genetic distance measurements are an important tool to differentiate field populations of disease vectors such as the mosquito vectors of malaria. Here, we have measured the genetic differentiation between Anopheles arabiensis and Anopheles gambiae, as well as between proposed emerging species of the latter taxon, in whole genome scans by using 23-25 microsatellite loci. In doing so, we have reviewed and evaluated the advantages and disadvantages of standard parameters of genetic distance, F(ST), R(ST), (delta mu)(2), and D. Further, we have introduced new parameters, D' and D(K), which have well defined statistical significance tests and complement the standard parameters to advantage. D' is a modification of D, whereas D(K) is a measure of covariance based on Pearson's correlation coefficient. We find that A. gambiae and A. arabiensis are closely related at most autosomal loci but appear to be distantly related on the basis of X-linked chromosomal loci within the chromosomal Xag inversion. The M and S molecular forms of A. gambiae are practically indistinguishable but differ significantly at two microsatellite loci from the proximal region of the X, outside the Xag inversion. At one of these loci, both M and S molecular forms differ significantly from A. arabiensis, but remarkably, at the other locus, A. arabiensis is indistinguishable from the M molecular form of A. gambiae. These data support the recent proposal of genetically differentiated M and S molecular forms of A. gambiae.

Animals↗
PubMed2001

Structure--function characterization of cellulose synthase: relationship to other glycosyltransferases.

A combined structural and functional model of the catalytic region of cellulose synthase is presented as a prototype for the action of processive beta-glycosyltransferases and other glycosyltransferases. A 285 amino acid segment of the Acetobacter xylinum cellulose synthase containing all the conserved residues in the globular region was subjected to protein modeling using the genetic algorithm. This region folds into a single large domain with a topology exhibiting a mixed alpha/beta structure. The predicted structure serves as a topological outline for the structure of this processive beta-glycosyltransferase. By incorporating new site-directed mutagenesis data and comparative analysis of the conserved aspartic acid residues and the QXXRW motif we deduce a number of functional implications based on the structure. This includes location of the UDP--glucose substrate-binding cavity, suggestions for the catalytic processing including positions of conserved and catalytic residues, secondary structure arrangement and domain organization. Comparisons to cellulose synthases from higher plants (genetic algorithm based model for cotton CelA1), data from neural network predictions (PHD), and to the recently experimentally determined structures of the non-processive SpsA and beta 4-galactosyltransferase retest and further validate our structure-function description of this glycosyltransferase.

Amino Acid Sequence↗
PubMed2001

Solvent entropy-driven searching for protein modeling examined and tested in simplified models.

Solvent entropy is a force to consider in protein folding and protein design but is difficult to model. It is investigated here in the context of the hp model: Two types of residues, hydrophobic and hydrophilic, are modeled on a lattice. Nine chains and two- and three-dimensional simulations are compared. We show that considering solvent entropy alone, efficient folding of lattice chains (identification of the native fold) can be achieved by an entropy-driven simulation on its own. Moreover, in a detailed comparison over a wide range of parameters, entropy-guided searching outperforms an energy-driven search in the model. The combination of energy- and entropy-driven search yields the most efficient searching. It is compared in detail with the above results, indicating also how this solvent shell model may advantageously be implemented in more complex protein modeling simulations.

Computer Simulation↗
PubMed2000

Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.

Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data. The total number of ORFss has been increased from 677 to 688 (10 new proteins were predicted in intergenic regions, two further were newly identified by mass spectrometry and one protein ORF was dismissed) and the number of RNAs from 39 to 42 genes. For 19 of the now 35 tRNAs and for six other functional RNAs the exact genome positions were re-annotated and two new tRNA(Leu) and a small 200 nt RNA were identified. Sixteen protein reading frames were extended and eight shortened. For each ORF a consistent annotation vocabulary has been introduced. Annotation reasoning, annotation categories and comparisons to other published data on M.pneumoniae functional assignments are given. Experimental evidence includes 2-dimensional gel electrophoresis in combination with mass spectrometry as well as gene expression data from this study. Compared to the original annotation, we increased the number of proteins with predicted functional features from 349 to 458. The increase includes 36 new predictions and 73 protein assignments confirmed by the published literature. Furthermore, there are 23 reductions and 30 additions with respect to the previous annotation. mRNA expression data support transcription of 184 of the functionally unassigned reading frames.

Amino Acid Sequence↗
PubMed2000

DNA recognition, strand selectivity, and cleavage mode during integrase family site-specific recombination.

We have probed the association of Flp recombinase with its DNA target using protein footprinting assays. The results are consistent with the domain organization of the Flp protein and with the general features of the protein-DNA interactions revealed by the crystal structures of the recombination intermediates formed by Cre, the Flp-related recombinase. The similarity in the organization of the Flp and Cre target sites and in their recognition by the respective recombinases implies that the overall DNA-protein geometry during strand cleavage in the two systems must also be similar. Within the functional recombinase dimer, it is the interaction between two recombinase monomers bound on either side of the strand exchange region (or spacer) that provides the allosteric activation of a single active site. Whereas Cre utilizes the cleavage nucleophile (the active site tyrosine) in cis, Flp utilizes it in trans (one monomer donating the tyrosine to its partner). By using synthetic Cre and Flp DNA substrates that are geometrically restricted in similar ways, we have mapped the positioning of the active and inactive tyrosine residues during cis and trans cleavage events. We find that, for a fixed substrate geometry, Flp and Cre cleave the labile phosphodiester bond at the same spacer end, not at opposite ends. Our results provide a model that accommodates local heterogeneities in peptide orientations in the two systems while preserving the global functional architecture of the reaction complex.

Amino Acid Sequence↗
PubMed2000

A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks.

A set of linear pathways often does not capture the full range of behaviors of a metabolic network. The concept of 'elementary flux modes' provides a mathematical tool to define and comprehensively describe all metabolic routes that are both stoichiometrically and thermodynamically feasible for a group of enzymes. We have used this concept to analyze the interplay between the pentose phosphate pathway (PPP) and glycolysis. The set of elementary modes for this system involves conventional glycolysis, a futile cycle, all the modes of PPP function described in biochemistry textbooks, and additional modes that are a priori equally entitled to pathway status. Applications include maximizing product yield in amino acid and antibiotic synthesis, reconstruction and consistency checks of metabolism from genome data, analysis of enzyme deficiencies, and drug target identification in metabolic networks.

Algorithms↗
PubMed2000

The 3'-untranslated region of the human estrogen receptor alpha gene mediates rapid messenger ribonucleic acid turnover.

Human estrogen receptor-alpha messenger RNA (hERalpha mRNA) has a relatively short half-life, which was determined to be approximately 5 h in MCF-7 cell line after actinomycin D treatment. The 3'-untranslated region (3'UTR) of hERalpha mRNA was previously shown to completely down-regulate chloramphenicol acetyltransferase activity when present at the 3'-end of chloramphenicol acetyltransferase transcripts, suggesting a destabilizing function of the hERalpha 3'UTR sequence. Chimeric genes composed of a serum-inducible Fos promoter, GH-coding sequences, and different segments of the hERalpha complementary DNA 3'UTR sequence were used to confirm this hypothesis and to localize the RNA region responsible for the destabilizing effect. The presence of the complete hERalpha 3'UTR reduced the half-life of the reporter mRNA from more than 24 to 3 h. When the hERalpha 3'UTR was subdivided into four fragments (UTR1-4), one fragment, UTR2, retained the most ability to down-regulate the reporter mRNA (t1/2 = 4 h). A stretch of four AUUUA motifs within UTR2 was shown not to mediate mRNA destabilization. In contrast, further subdivision of the UTR2 into three parts (UTR2a-c) resulted in the loss of the destabilizing activity. Finally, recombination of two UTR2 subfragments (UTR2a and -b) partially restored this function, indicating a cooperative role among the three UTR2a-c subfragments in the process that leads to destabilization of the hERalpha transcript.

3' Untranslated Regions↗
PubMed1999

Pathway alignment: application to the comparative analysis of glycolytic enzymes.

Comparative analysis of metabolic pathways in different genomes yields important information on their evolution, on pharmacological targets and on biotechnological applications. In this study on glycolysis, three alternative ways of comparing biochemical pathways are combined: (1) analysis and comparison of biochemical data, (2) pathway analysis based on the concept of elementary modes, and (3) a comparative genome analysis of 17 completely sequenced genomes. The analysis reveals a surprising plasticity of the glycolytic pathway. Isoenzymes in different species are identified and compared; deviations from the textbook standard are detailed. Several potential pharmacological targets and by-passes (such as the Entner-Doudoroff pathway) to glycolysis are examined and compared in the different species. Archaean, bacterial and parasite specific adaptations are identified and described.

Enzymes↗
PubMed1999

Microinjected glutathione reductase crystals as indicators of the redox status in living cells.

The flavoenzyme glutathione reductase catalyses electron transfer reactions between two major intracellular redox buffers, namely the NADPH/NADP+ couple and the 2 glutathione/glutathione disulfide couple. On this account, microcrystals of the enzyme were tested as redox probes of intracellular compartments. For introducing protein crystals into human fibroblasts, different methods (microinjection, particle bombardment and optical tweezers) were explored and compared. When glutathione reductase crystals are present in a cytosolic environment, the transition of the yellow Eox form to the orange-red 2-electron reduced charge transfer form, EH2, is observed. Taking into account the midpoint potential of the Eox/EH2 couple, the redox potential of the cytosol was found to be < -270 mV at pH 7.4 and 37 degrees C. As a general conclusion, competent proteins in crystalline--that is signal-amplifying--form are promising probes for studying intracellular events.

Cells, Cultured↗
PubMed1999

Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering.

Rational metabolic engineering requires powerful theoretical methods such as pathway analysis, in which the topology of metabolic networks is considered. All metabolic capabilities in steady states are composed of elementary flux modes, which are minimal sets of enzymes that can each generate valid steady states. The modes of the fructose-2,6-bisphosphate cycle, the combined tricarboxylic-acid-glyoxylate-shunt system and tryptophan synthesis are used here for illustration. This approach can be used for many biotechnological applications such as increasing the yield of a product, channelling a product into desired pathways and in functional reconstruction from genomic data.

Biochemistry↗
PubMed1999

Improving genetic algorithms for protein folding simulations by systematic crossover.

To improve protein folding simulations, we investigated a new search strategy in combination with the simple genetic algorithm on a two-dimensional lattice model. This search strategy, we called systematic crossover, couples the best individuals, tests every possible crossover point, and takes the two best individuals for the next generation. We compared the standard genetic algorithm with and without this new implementation for various chain lengths and showed that this strategy finds local minima with better energy values and is significantly faster in identifying the global minimum than the standard genetic algorithm.

Algorithms↗
PubMed1999

Variation and evolution of the citric-acid cycle: a genomic perspective.

The presence of genes encoding enzymes involved in the citric-acid cycle has been studied in 19 completely sequenced genomes. In the majority of species, the cycle appears to be incomplete or absent. Several distinct, incomplete cycles reflect adaptations to different environments. Their distribution over the phylogenetic tree hints at precursors in the evolution of the citric-acid cycle.

Archaea↗
PubMed1999

Quality-of-life assessment in the old using the WHOQOL 100: differences between patients with senile dementia and patients with cancer.

INTRODUCTION: The measurement of quality of life is an increasingly important issue, particularly in regard to treatment of severe and chronic diseases. The aim of this pilot study was to assess potentially divergent profiles of quality of life in persons with two different pathologies: moderate dementia and cancer. METHOD: This pilot study was carried out in the neurology and cancer services of the medical school in Montpellier, France (Hôpital Gui de Chaulliac and CRLC Val d'Aurelle). The cumulative self-reporting test WHOQOL 100 (World Health Organization Quality of Life with 100 questions) was administered in 57 patients with either moderate senile dementia (27 cases with a Mini-Mental State Examination score >15; mean age of 73) or cancer (30 cases, mainly women with breast cancer; mean age of 53). The stability of responses was tested in a 2-week period. RESULTS: Results of the study showed clear and significant differences between the two groups in the domains of mobility and psychology. Further, eight questions and six facets with a significant difference in responses were found. Responses seemed more stable in the domains of autonomy, social relationship, and religion for the cancer group, and in autonomy and psychology for the dementia group. The age difference may be an important factor in the different quality of life measured but did not significantly influence responses to the test questions. CONCLUSION: The WHOQOL 100 seems a powerful instrument to assess quality of life in diseases such as cancer and moderate dementia. In this study, interesting differences in responses to the test questions between the two pathologic conditions were identified. Items that were unreliable on retesting are singled out. These results will be applied and reevaluated in the development of future, illness-specific and shorter versions of the WHOQOL 100.

Aged↗
PubMed1999

Pore-forming peptides of Entamoeba dispar. Similarity and divergence to amoebapores in structure, expression and activity.

Amoebapore, a 77-residue peptide with pore-forming activity from the human pathogen Entamoeba histolytica, is implicated in the killing of phagocytosed bacteria and in the cytolytic reaction of the amoeba against host cells. Previously, we structurally and functionally characterized three amoebapore isoforms in E. histolytica but recognized only one homolog in the closely related but non-pathogenic species Entamoeba dispar. Here, we identified two novel amoebapore homologs from E. dispar by molecular cloning. Despite strong resemblance of the primary structures of the homologs, molecular modeling predicts a species-specific variance between the peptide structures. Parallel isolation from trophozoite extracts of the two species revealed a lower amount of pore-forming peptides in E. dispar and substantially higher activity of the major isoform from E. histolytica towards natural membranes than that from E. dispar. Differences in abundance and activity of the lytic polypeptides may have an impact on the pathogenicity of amoebae.

Amino Acid Sequence↗
PubMed1998

Predicting function: from genes to genomes and back.

Predicting function from sequence using computational tools is a highly complicated procedure that is generally done for each gene individually. This review focuses on the added value that is provided by completely sequenced genomes in function prediction. Various levels of sequence annotation and function prediction are discussed, ranging from genomic sequence to that of complex cellular processes. Protein function is currently best described in the context of molecular interactions. In the near future it will be possible to predict protein function in the context of higher order processes such as the regulation of gene expression, metabolic pathways and signalling cascades. The analysis of such higher levels of function description uses, besides the information from completely sequenced genomes, also the additional information from proteomics and expression data. The final goal will be to elucidate the mapping between genotype and phenotype.

Bacterial Proteins↗
PubMed1998

Differential genome analysis applied to the species-specific features of Helicobacter pylori.

We introduce a simple and rapid strategy to identify genes that are responsible for species-specific phenotypes. The genome of a species that has a specific phenotype is compared with at least one, closely related, species that lacks this phenotype. Homologous genes that are shared among the species compared are identified and discarded from the list of candidates for species-specific genes. The process is automated and rapidly yields a small subset of the genome that likely contains genes responsible for the species-specific features. Functions are assigned to the genes, and dubious annotations are filtered out. Information is extracted not only from the presence of genes, but also from their absence with respect to known phenotypes. We have applied the technique to identify a set of species-specific genes in Helicobacter pylori by comparing it with its closest relatives for which complete genome sequences are available, Haemophilus influenzae and Escherichia coli. Of the genes of this set for which functional features can be obtained, a large fraction (63%, 123 proteins) is (potentially) involved in H. pylori's interaction with its host. We hypothesize that a family of outer membrane proteins is critical for the ability of H. pylori to colonize host cells in highly acidic environments.

Amino Acid Sequence↗
PubMed1998

Conservation of gene order: a fingerprint of proteins that physically interact.

A systematic comparison of nine bacterial and archaeal genomes reveals a low level of gene-order (and operon architecture) conservation. Nevertheless, a number of gene pairs are conserved. The proteins encoded by conserved gene pairs appear to interact physically. This observation can therefore be used to predict functions of, and interactions between, prokaryotic gene products.

Archaeal Proteins↗