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PubMed1993

Identification of two expressed flagellin genes in the insect pathogen Bacillus thuringiensis subsp. alesti.

Flagellin from Bacillus thuringiensis subspecies alesti strain Bt75 was isolated both from the culture medium and from flagella. Two protein forms with molecular masses close to 32 kDa were obtained from flagella; one form was identical to the flagellin purified from the culture medium. The N-terminal amino acid sequences were identical for both forms. Two genes coding for flagellin have been identified in B. thuringiensis subsp. alesti. The flaB gene was cloned and sequenced in its entire length. The clone containing the flaA gene was incomplete. Both genes were expressed in the mid-exponential growth phase. The flaB gene was flanked by long (355 bp) direct repeats protruding into the coding region in both the N- and C-terminal parts of the gene. DNA sequences related to the flaB gene were found in most other B. thuringiensis subspecies, and in two of them, subsp. kurstaki and subsp. entomocidus, such sequences were present in multiple copies.

Amino Acid Sequence↗
PubMed1995

Beta 3-adrenoceptors and intestinal motility.

Early substantial evidence of the low susceptibility to beta-adrenoceptor antagonists of non alpha-adrenergic responses reducing gut motility and tone was reluctantly accepted as indicating a third beta-receptor subtype different from the beta 1 and beta 2. This applied likewise to lipolysis until new selective "lipolytic" beta-agonists poorly effective at established beta-receptors were introduced. Shortly afterwards these "lipolytic" as well as certain newer and even more selective beta-adrenoceptor agonists were shown to be potent inhibitors of intestinal motility. The latter are the "gut-specific" phenylethanolaminotetralins whose availability as pure isomers attested to the stringent stereochemical requirements for selectivity at non-beta 1, non-beta 2 beta-adrenoceptors. Acceptance of the functionally based concept of a beta 3-adrenoceptor was boosted on structural grounds by molecular biology studies. Sequence analysis indicated the existence in humans and rodents of genes coding for a third subtype of beta-receptor that, when expressed in transfected heterologous cells, had a pharmacological profile distinct from the previously established subtypes. Finally, aryloxypropanolaminotetralins have been prepared as the first selective antagonists of beta 3-adrenoceptors, thus providing unambiguous conclusive evidence of the distinctive functional features of those abundant in the rat colon. The therapeutic potential in gastroenterology of the newer compounds targetable on the beta 3-adrenoceptor is suggested by their potent intestinal action in vivo in animal models without any of the cardiovascular or other unwanted effects of conventional beta-adrenoceptor agonists and antagonists, and by the clinically confirmed importance of beta-adrenergic control of motor function throughout the alimentary canal. However, open questions include the incidence of species-related differences in beta 3-adrenoceptors, and as yet there are no data on gastrointestinal functions in humans under the influence of drugs designed to act selectively at these receptors.

Adrenergic beta-Agonists↗
PubMed2002

Geomicrobiology: how molecular-scale interactions underpin biogeochemical systems.

Microorganisms populate every habitable environment on Earth and, through their metabolic activity, affect the chemistry and physical properties of their surroundings. They have done this for billions of years. Over the past decade, genetic, biochemical, and genomic approaches have allowed us to document the diversity of microbial life in geologic systems without cultivation, as well as to begin to elucidate their function. With expansion of culture-independent analyses of microbial communities, it will be possible to quantify gene activity at the species level. Genome-enabled biogeochemical modeling may provide an opportunity to determine how communities function, and how they shape and are shaped by their environments.

Animals↗
PubMed1993

The tcmVI region of the tetracenomycin C biosynthetic gene cluster of Streptomyces glaucescens encodes the tetracenomycin F1 monooxygenase, tetracenomycin F2 cyclase, and, most likely, a second cyclase.

Certain mutations in the tcmVI region of the Streptomyces glaucescens chromosome affect formation of the D ring of the polyketide antibiotic tetracenomycin C (TCM C). This region lies immediately upstream from the TCM C polyketide synthase genes (tcmKLM), and the nucleotide sequence reveals the presence of three small genes, tcmH, tcmI, and tcmJ. On the basis of the phenotypes of mutants and the effects of these genes, when coupled on a plasmid with the tcmKLMN177 genes (tcmN177 is a 3'-truncated version of tcmN), on the production of TCM intermediates in a TCM- mutant, the tcmH gene encodes the C-5 monooxygenase that converts TCM F1 to TCM D3, the tcmI gene encodes the D-ring cyclase that converts TCM F2 to TCM F1 (mutations in this gene are responsible for the type VI phenotype), and the tcmJ gene most likely encodes the B-ring cyclase that acts in the biosynthesis of TCM F2. Furthermore, it appears that the N-terminal domain of the tcmN gene product (encoded by the tcmN177 gene) acts later in the biosynthesis of TCM F2 than the product of tcmJ, suggesting that the N-terminal domain of the TcmN protein is the C-ring cyclase.

Aldehyde-Lyases↗
PubMed1993

Building large knowledge bases in molecular biology.

Large scale genome sequencing projects are now producing hugh amounts of data which can be readily stored and managed within data base management systems, and analyzed using dedicated software packages. The results of these analyzes should also be stored with the input DNA sequences. The increasing complexity and size of the objects to be described and managed have led biologists to rely on advanced data models such as the object-oriented model. As a joint effort between our computer science and molecular biology research projects, the knowledge bases we have developed in molecular genetics have shown however that the basic object-oriented model is not fully adapted to the complexity of some biological situations encountered. Advanced descriptive capabilities, provided only by knowledge models originated from the AI field, are required. Composite or evolving objects, multiple viewpoints, constraints, tasks and methods, textual annotations are some examples of such capabilities. They are illustrated by biological situations for which they appeared to be necessary. Supporting powerful reasoning mechanisms (e.g. object classification, constraint propagation or qualitative simulators), they allow the development of large knowledge bases in molecular biology. These knowledge bases are expected to become the adequate support for co-operative distributed research efforts.

Artificial Intelligence↗
PubMed1993

Molecular medicine: a primer for clinicians. Part II: Recombinant DNA molecules.

This is the second paper in our continuing series on the impact of molecular medicine on clinical practice. Discussed are some of the basic methods used to produce recombinant DNA molecules and how these molecules are characterized. Special emphasis is placed on the use of these methods to isolate and characterize human genes.

Clinical Medicine↗
PubMed1999

[Contribution of molecular cytogenetics to the diagnosis of chromosome anomalies].

UNLABELLED: MOLECULAR CYTOGENETICS: New fluorescent in situ hybridization (FISH) techniques have been developed using fluorescent non-radioactive DNA probes. FISH: Based on the complementary of nucleotides FISH enables visualization and localization of a DNA fragment on chromosomes by hybridizing the complementary DNA sequence, the probe. Many types of tissues can be analyzed, for example hematopoietic cells in blood or bone marrow, amniotic cells, trophoblasts, fibroblasts, gamete or tumoral cells. APPLICATIONS: Molecular cytogenetics can be used to characterize chromosome anomalies in many fields of cytogenetics (constitutional studies, prenatal diagnosis, hematology, oncology).

Chromosome Aberrations↗
PubMed2002

Systematics of basidiomycetous yeasts: a comparison of large subunit D1/D2 and internal transcribed spacer rDNA regions.

Basidiomycetous yeasts in the Urediniomycetes and Hymenomycetes were examined by sequence analysis in two ribosomal DNA regions: the D1/D2 variable domains at the 5' end of the large subunit rRNA gene (D1/D2) and the internal transcribed spacers (ITS) 1 and 2. Four major lineages were recognized in each class: Microbotryum, Sporidiobolus, Erythrobasidium and Agaricostilbum in the Urediniomycetes; Tremellales, Trichosporonales, Filobasidiales and Cystofilobasidiales in the Hymenomycetes. Bootstrap support for many of the clades within those lineages is weak; however, phylogenetic analysis provides a focal point for in-depth study of biological relationships. Combined sequence analysis of the D1/D2 and ITS regions is recommended for species identification, while species definition requires classical biological information such as life cycles and phenotypic characterization.

Basidiomycota↗
PubMed1992

Novel transfer RNAs that are active in Escherichia coli.

Many of the mammalian mitochondrial tRNAs contain significant nucleotide deletions in the dihydrouridine (D) stem or T psi C stem, so that they cannot fold into the canonical cloverleaf structure. This suggests that alternative forms and shapes are possible for a mitochondrial tRNA that functions in the specialized translational apparatus of the mammalian mitochondria. The question of whether significant structural alterations may be accommodated by a bacterial protein synthesis machinery, such as in Escherichia coli, is unanswered. In this work, all but ten positions in the gene for the 76-nucleotide coding sequence of an E. coli amber suppressor tRNA were permuted and screened for biological activity in vivo. Sequence analysis of a collection of biologically active variants established that many have unusual structures that include base-pair mismatches in helical stems, substitutions of normally conserved bases, and deletions. Independent mutations were obtained that weaken base pairs or tertiary interactions that normally stabilize the coaxial stacking of the D and anticodon stems, suggesting that the translational apparatus can accommodate considerable flexibility in this part of the molecule. The results demonstrate the capacity of the bacterial protein synthetic apparatus to accommodate altered tRNA structures that are not represented by any naturally occurring tRNAs.

Base Sequence↗
PubMed1995

Cooperative computer system for genome sequence analysis.

Analysis of the huge volumes of data generated by large scale sequencing projects clearly requires the construction of new sophisticated computer systems. These systems should be able to handle the biological data as well as the results of the analysis of this data. They should also help the user to choose the most appropriate method for a simple task and to string together the methods needed to solve a global analysis task. In this paper we present the prototype of a software system that provides an environment for the analysis of large-scale sequence data. In a first approach this environment has been put to the test within the B. subtilis sequencing project. This system integrates both a descriptive knowledge of the entities involved (genes, regulatory signals etc.) and the methodological knowledge concerning an extendable set of analytical methods (i.e. how to solve a sequence analysis problem through task decomposition and method selection). A knowledge representation based on two existing object-oriented models, named Shirka and SCARP, is used to implement this integrated system. In addition, the present prototype provides a suitable user interface for both displaying the results generated by several methods and interacting with the objects. We present in this paper an overview of the knowledge-based models used to build this integrated system, and a description of the way in which biological entities and sequence analysis tasks are represented. We give illustrations of the co-operation between user and system during the problem solving process. Such a system constitutes a computer workbench for molecular biologists studying the genetic programs of living organisms.

Bacillus subtilis↗
PubMed1993

A special-purpose processor for gene sequence analysis.

Advances in computational biology have occurred primarily in the areas of software and algorithm development; new designs of hardware to support biological computing are extremely scarce. This is due, we believe, to the presence of a non-trivial knowledge gap between molecular biologists and computer designers. The existence of this gap is unfortunate, as it has long been known that for certain problems, special-purpose computers can achieve significant cost/performance gains over general-purpose machines. We describe one such computer here: a custom accelerator for gene sequence analysis. The accelerator implements a version of the Needleman-Wunsch algorithm for nucleotide sequence alignment. Sequence lengths are constrained only by available memory; the product of sequence lengths in the current implementation can be up to 2(22). The machine is implemented as two NuBus boards connected to a Mac IIf/x, using a mixture of TTL and FPGA technology clocked at 10 MHz. The boards are completely functional, and yield a 15-fold performance improvement over an unassisted host.

Algorithms↗