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At least 937 records · Page 52Linked to original sources
PubMed1991

RNA recognition by Tat-derived peptides: interaction in the major groove?

Replication of human immunodeficiency virus requires binding of the viral Tat protein to its RNA target sequence TAR; peptides derived from Tat bind to a TAR "contact site" spanning 5 bp and a trinucleotide pyrimidine bulge. We find that high affinity binding requires a U residue in the bulge loop and 2 specific adjacent base pairs. Other bulged RNAs bind in a lower affinity nonspecific manner; sequence-specific binding requires a bulge loop of more than 1 nucleotide. Reaction with diethyl pyrocarbonate indicates that one effect of the bulge is to make the otherwise deep and narrow RNA major groove accessible. A model consistent with these data involves local distortion of A-form geometry at the bulge, which bends the helix and permits protein binding and interactive access in the RNA major groove.

Amino Acid Sequence↗
PubMed1975

The covalent and three-dimensional structure of concanavalin A. II. Amino acid sequence of cyanogen bromide fragment F3.

The amino acid sequence of the COOH-terminal CNBr fragment, F3 (residues 130 to 237), of concanavalin A has been established, completing the determination of the covalent structure of this lectin. Analysis of the chemical sequence showed that the distribution of charged residues is generally more dense in the NH2-terminal half of the polypeptide chain than in the COOH-terminal portion and that in the latter region there is a linear stretch composed of many hydrophobic residues. Correlation with x-ray crystallographic results indicates that the hydrophobic region is located in the interior of the molecule, and that it forms a part of a deep cavity which is the binding site for the inhibitor, beta-(o-iodophenyl)-D-glucopyranoside. In conjunction with the three-dimensional structure, the amino acid sequence reported here provides new data for analysis of variables involved in predicting the three-dimensional folding of proteins from the primary structure. The sequence of concanavalin A is the first determined for a lectin and it serves as a reference structure for comparisons with other lectins.

Amino Acid Sequence↗
PubMed2000

Crystal structures of Mycobacterium tuberculosis RecA and its complex with ADP-AlF(4): implications for decreased ATPase activity and molecular aggregation.

Sequencing of the complete genome of Mycobacterium tuberculosis, combined with the rapidly increasing need to improve tuberculosis management through better drugs and vaccines, has initiated extensive research on several key proteins from the pathogen. RecA, a ubiquitous multifunctional protein, is a key component of the processes of homologous genetic recombination and DNA repair. Structural knowledge of MtRecA is imperative for a full understanding of both these activities and any ensuing application. The crystal structure of MtRecA, presented here, has six molecules in the unit cell forming a 6(1) helical filament with a deep groove capable of binding DNA. The observed weakening in the higher order aggregation of filaments into bundles may have implications for recombination in mycobacteria. The structure of the complex reveals the atomic interactions of ADP-AlF(4), an ATP analogue, with the P-loop-containing binding pocket. The structures explain reduced levels of interactions of MtRecA with ATP, despite sharing the same fold, topology and high sequence similarity with EcRecA. The formation of a helical filament with a deep groove appears to be an inherent property of MtRecA. The histidine in loop L1 appears to be positioned appropriately for DNA interaction.

Adenosine Diphosphate↗
PubMed1991

Evolution of the cytochrome b gene of mammals.

With the polymerase chain reaction (PCR) and versatile primers that amplify the whole cytochrome b gene (approximately 1140 bp), we obtained 17 complete gene sequences representing three orders of hoofed mammals (ungulates) and dolphins (cetaceans). The fossil record of some ungulate lineages allowed estimation of the evolutionary rates for various components of the cytochrome b DNA and amino acid sequences. The relative rates of substitution at first, second, and third positions within codons are in the ratio 10 to 1 to at least 33. For deep divergences (greater than 5 million years) it appears that both replacements and silent transversions in this mitochondrial gene can be used for phylogenetic inference. Phylogenetic findings include the association of (1) cetaceans, artiodactyls, and perissodactyls to the exclusion of elephants and humans, (2) pronghorn and fallow deer to the exclusion of bovids (i.e., cow, sheep, and goat), (3) sheep and goat to the exclusion of other pecorans (i.e., cow, giraffe, deer, and pronghorn), and (4) advanced ruminants to the exclusion of the chevrotain and other artiodactyls. Comparisons of these cytochrome b sequences support current structure-function models for this membrane-spanning protein. That part of the outer surface which includes the Qo redox center is more constrained than the remainder of the molecule, namely, the transmembrane segments and the surface that protrudes into the mitochondrial matrix. Many of the amino acid replacements within the transmembrane segments are exchanges between hydrophobic residues (especially leucine, isoleucine, and valine). Replacement changes at first and second positions of codons approximate a negative binomial distribution, similar to other protein-coding sequences. At four-fold degenerate positions of codons, the nucleotide substitutions approximate a Poisson distribution, implying that the underlying mutational spectrum is random with respect to position.

Amino Acid Sequence↗
PubMed1995

Cloning and expression of a gene encoding a T-cell reactive protein from Coccidioides immitis: homology to 4-hydroxyphenylpyruvate dioxygenase and the mammalian F antigen.

The gene which encodes a previously described T-cell reactive protein (TCRP) of the human fungal pathogen Coccidioides immitis (Ci) was cloned and sequenced. Both the genomic and cDNA sequences were determined. The transcription start point was confirmed. The tcrP gene has three introns and a 1197-bp ORF which translates to a 399-amino-acid (aa) protein (45.2 kDa). The predicted protein has approx. 50% aa sequence identity and 70% similarity to mammalian 4-hydroxyphenylpyruvate dioxygenase (HPPD) proteins and mammalian F-antigens. Expression of the Ci tcrP in Escherichia coli resulted in production of a deep brown pigment, consistent with E. coli expression of the bacterial HPPD homolog from Shewanella colwelliana. The TCRP is likely the Ci form of HPPD.

4-Hydroxyphenylpyruvate Dioxygenase↗
PubMed2003

Phylogenetic diversity of nitrogenase (nifH) genes in deep-sea and hydrothermal vent environments of the Juan de Fuca Ridge.

The subseafloor microbial habitat associated with typical unsedimented mid-ocean-ridge hydrothermal vent ecosystems may be limited by the availability of fixed nitrogen, inferred by the low ammonium and nitrate concentrations measured in diffuse hydrothermal fluid. Dissolved N2 gas, the largest reservoir of nitrogen in the ocean, is abundant in deep-sea and hydrothermal vent fluid. In order to test the hypothesis that biological nitrogen fixation plays an important role in nitrogen cycling in the subseafloor associated with unsedimented hydrothermal vents, degenerate PCR primers were designed to amplify the nitrogenase iron protein gene nifH from hydrothermal vent fluid. A total of 120 nifH sequences were obtained from four samples: a nitrogen-poor diffuse vent named marker 33 on Axial Volcano, sampled twice over a period of 1 year as its temperature decreased; a nitrogen-rich diffuse vent near Puffer on Endeavour Segment; and deep seawater with no detectable hydrothermal plume signal. Subseafloor nifH genes from marker 33 and Puffer are related to anaerobic clostridia and sulfate reducers. Other nifH genes unique to the vent samples include proteobacteria and divergent Archaea. All of the nifH genes from the deep-seawater sample are most closely related to the thermophilic, anaerobic archaeon Methanococcus thermolithotrophicus (77 to 83% amino acid similarity). These results provide the first genetic evidence of potential nitrogen fixers in hydrothermal vent environments and indicate that at least two sources contribute to the diverse assemblage of nifH genes detected in hydrothermal vent fluid: nifH genes from an anaerobic, hot subseafloor and nifH genes from cold, oxygenated deep seawater.

Archaea↗
PubMed1982

Sequence of ossification in human vertebral neural arch centers.

The purpose of the present study is to determine whether ossification of the human vertebral neural arches follows a craniocaudal sequences of development or develops in separate groups from the lower cervical/upper thoracic, upper cervical, and lower thoracic/upper lumbar regions as described by Bagnall et al. (1977b) in a radiographic study. Seven formalin-fixed, two fresh frozen, and six serial-sectioned human embryos and fetuses, ranging in crown-rump length (C-R) from 27 mm to 76 mm, were examined. A procedure adapted by Watson (1977a,b) for in toto staining of whole specimens with alcian blue and alizarin red S for cartilage and bone was used, whereas serial sections were stained with hematoxylin and eosin, or Koneff's stain (1960). The intact specimens demonstrated a vivid deep blue cartilaginous skeleton with differentiated red areas of bone development seen through soft tissues rendered transparent by potassium hydroxide or enzyme clearing. The ossification sequence of the neural arches differed from the conventional craniocaudal descriptions given in anatomical textbooks. Neural arch ossification was found to commence in the lower cervical/upper thoracic regions, quickly followed by a second group in the lower cervical region, and subsequently a third group in the lower thoracic/upper lumbar region.

Female↗
PubMed2006

Functional expression and refolding of new alkaline esterase, EM2L8 from deep-sea sediment metagenome.

A metagenomics approach is an efficient method of isolating novel and useful genes from uncultured microorganisms in diverse environments. In this research, a gene encoding a new esterase (EM2L8) was cloned and characterized from the metagenomic DNA library of a deep-sea sediment. The gene consisted of 804bp encoding a polypeptide of 267 amino acids with a molecular mass of 28,952. The deduced amino acid sequence showed similarities with the BioH of Kurthia, the 3-oxoadipate enol-lactonase of Haloarcula and the acyltransferase of Thermoanaerobacter, which feature identities of 38%, 32%, and 33%, respectively. Residues essential for esterase activity, such as pentapeptide (GXSXG) and catalytic triad sequences, were uncovered. While the protein was overproduced mainly as inclusion body at 37 degrees C, it was mainly produced as a soluble active enzyme at 18 degrees C. A zymogram analysis revealed that purified EM2L8 taken from the soluble fraction could hydrolyze tributyrin substrate. Furthermore, the protein from the inclusion body fraction also showed strong activity on gel, thus indicating that the protein was refolded during SDS-gel electrophoresis and the ensuing incubation period. When the inclusion body was mixed with some anionic detergent solutions and diluted with a non-detergent buffer, the insoluble EM2L8 refolded rapidly and recovered its full esterase activity. Although EM2L8 had an optimum temperature of 50-55 degrees C, its activation energy in the range of 10-40 degrees C was 8.34kcal/mol, indicating that it is a cold-adapted enzyme. Moreover, it was found to have an optimum pH of 10-11, thus revealing that it is an alkaline enzyme. In this paper, the new esterase EM2L8 buried in a deep-sea sediment became known on the surface and was characterized biochemically.

Amino Acid Sequence↗
PubMed1983

[Laminar distribution of current sources in the superior colliculi of the rabbit upon stimulation of the optic nerve].

The evoked potential field in the rabbit superior colliculus was subjected to the current source density analysis to determine the location and sequence of the current sinks and sources after electrical stimulation of the optic nerve. The earliest current sink was observed in the middle part of the stratum griseum superficiale. The later and the most prominent current sinks were observed in the upper part and in the deep part of the stratum griseum superficiale. The time course of the current sinks and sources was in correspondence with the main components of the evoked potential. The results permit indicating the location of afferent synapses and sequence of their activation.

Animals↗
PubMed2002

Nosocomial fungemia due to Trichosporon asteroides: firstly described bloodstream infection.

Trichosporon spp. are oppurtunistic yeasts that cause deep-seated, mucosa-associated, and superficial infections in immunocompromised patients. It is well known that Trichosporon asteroides is mainly responsible of superficial infections and does not cause systemic infections in humans so far. In this study, we present the first case of disseminated infection due to Trichosporon asteroides in an intensive care patient. Yeast colonies were isolated from the specimens of blood, urine, aspiration fluid of the endotracheal tube and catheter tip swabs of the patient. Conventional mycological studies were not adequate for the identification of the isolate to the species level. The genetic identification of the yeast isolate was performed and the DNA sequence of the isolate exactly matched the corresponding sequence of the Trichosporon asteroides rRNA gene from the GenBank DNA database (accession numbers: AB018017, AF075513). Therefore, our isolate was identified as Trichosporon asteroides as a causative agent of deep-seated fungemia.

Aged↗
PubMed2004

In situ sequenced bioremediation of mixed contaminants in groundwater.

A mixture of chlorinated solvents (about 0.5-10 mg/l), including tetrachloroethene (PCE) and carbon tetrachloride (CT), together with a petroleum hydrocarbon, toluene (TOL), were introduced into a 24 m long x 2 m wide x 3 m deep isolated section (henceforth called a gate) of the Borden aquifer and subjected to sequential in situ treatment. An identical section of aquifer was similarly contaminated and allowed to self-remediate by natural attenuation, thus serving as a control. The control presents a rare opportunity to critically assess the performance of the treatment systems, and represents the first such study for sequenced in situ remediation. The first treatment step was anaerobic bioremediation. This was accomplished using a modified nutrient injection wall (NIW) to pulse benzoate and a nutrient solution into the aquifer, maximizing mixing by dispersion and minimizing fouling near the injection wells. In the anaerobic bioactive zone that developed, PCE, CT and chloroform (CF), a degradation product of CT, degraded with a half-lives of about 59, 5.9 and 1.7 days, respectively. The second step was aerobic bioremediation, using a biosparge system. TOL and cis-1,2 dichloroethene (cDCE), from PCE degradation, were found to degrade aerobically with half-lives of 17 and 15 days, respectively. Compared to natural attenuation, PCE and TOL removal rates were significantly better in the sequenced treatment gate. However, CT and CF were similarly and completely attenuated in both gates. It is believed that the presence of TOL helped sustain the reducing environment needed for the reduction of these two compounds.

Bacteria, Aerobic↗
PubMed2002

A new class of the stramenopiles, Placididea Classis nova: description of Placidia cafeteriopsis gen. et sp. nov.

A marine flagellate resembling Cafeteria roenbergensis (bicosoecids, stramenopiles) in cell shape and behavior of the cell while attached to substratum was collected from the coast of Japan. The flagellate was examined by light and electron microscopy, and the 18S rDNA was sequenced to elucidate its taxonomic and phylogenetic position. Ultrastructural features suggested that the flagellate is not a bicosoecid, but a relative of the recently described stramenopile, Wobblia lunata. 18S rDNA phylogenetic trees also revealed that the flagellate forms a monophyletic clade with W. lunata and that it is distantly related to Cafeteria and other bicosoecids. The flagellate differs from W. lunata due to its lack of wobbling motion as well as intracellular features such as the number of mitochondria, flagellar apparatus architecture, the presence of a paranuclear body and cytoplasmic microtubules. The similarity of 18S rDNA sequences was 81% between the flagellate and W. lunata. This new flagellate was described as Placidia cafeteriopsis gen. et sp. nov. Because the phylogenetic lineage comprised of W. lunata and P. cafeteriopsis was one of the major, deep-branching clades of the stramenopiles, the class Placididea (= Placidiophyceae) classis nova was proposed.

Animals↗
PubMed2006

"Candidatus Thiobios zoothamnicoli," an ectosymbiotic bacterium covering the giant marine ciliate Zoothamnium niveum.

Zoothamnium niveum is a giant, colonial marine ciliate from sulfide-rich habitats obligatorily covered with chemoautotrophic, sulfide-oxidizing bacteria which appear as coccoid rods and rods with a series of intermediate shapes. Comparative 16S rRNA gene sequence analysis and fluorescence in situ hybridization showed that the ectosymbiont of Z. niveum belongs to only one pleomorphic phylotype. The Z. niveum ectosymbiont is only moderately related to previously identified groups of thiotrophic symbionts within the Gammaproteobacteria, and shows highest 16S rRNA sequence similarity with the free-living sulfur-oxidizing bacterial strain ODIII6 from shallow-water hydrothermal vents of the Mediterranean Sea (94.5%) and an endosymbiont from a deep-sea hydrothermal vent gastropod of the Indian Ocean Ridge (93.1%). A replacement of this specific ectosymbiont by a variety of other bacteria was observed only for senescent basal parts of the host colonies. The taxonomic status "Candidatus Thiobios zoothamnicoli" is proposed for the ectosymbiont of Z. niveum based on its ultrastructure, its 16S rRNA gene, the intergenic spacer region, and its partial 23S rRNA gene sequence.

Animals↗
PubMed1996

Dopamine transporter ligand binding domains. Structural and functional properties revealed by limited proteolysis.

Dopamine transporters (DATs) are members of the Na+- and Cl--dependent neurotransmitter and amino acid transporter family predicted by hydrophobicity analysis to have 12 transmembrane-spanning helices. The structure of DAT was studied using the photoaffinity compounds [125I]1-[2-(diphenylmethoxy)-ethyl]-4-[2-(4-azido-3-iodophenyl) ethyl] piperazine ([125I]DEEP), a 1-(2-diphenylmethoxy)-ethyl-4-(3-phenyl propyl)piperazine (GBR analog), and [125I]-3beta-(p-chlorophenyl)tropane-2beta-carboxylic acid, 4'-azido-3'-iodophenylethyl ester ([125I]RTI 82), a cocaine analog, which had been shown in a previous study to become incorporated into different regions of the DAT primary sequence. The proximity of the photolabeled binding sites to integral membrane structures was investigated by subjecting photolabeled membrane suspensions to limited proteolysis with trypsin and separately analyzing the resulting membranes and supernatants for the presence of photolabeled DAT fragments. Trypsin treatment of [125I] DEEP-labeled membranes generated labeled 45- and 14-kDa DAT fragments that immunoprecipitated with an epitope-specific antiserum generated against amino acids 42-59 near the first putative transmembrane domain, whereas [125I]RTI 82 was found in 32- and 16-kDa tryptic fragments that precipitated with an antiserum directed against a sequence near transmembrane domain 4 (amino acids 225-238). All of the photolabeled fragments were recovered in the protease-treated membranes, indicating that they possess integral membrane structures that prevent their release from the membrane as soluble forms. The size of the two smallest fragments in conjunction with their retention in the membrane suggests that incorporation of the photoaffinity ligands occurs in or near membrane spanning regions and delineates the maximum possible distance between the transmembrane structures, incorporated photolabel, and antibody epitopes. Carbohydrate analysis of the fragments identified sialic acids and N-linked oligosaccharides exclusively on the 45-kDa [125I]DEEP-labeled fragment, which, based on size, would be expected to contain four consensus glycosylation sites between putative transmembrane domains 3 and 4. Photoaffinity labeling after trypsin treatment of membranes showed that the larger but not the smaller fragments retain binding capacity, as the 45- and 32-kDa fragments were capable of becoming photolabeled. Binding of photoaffinity ligands at these fragments was displaced with the same pharmacology as that of intact DATs. These results verify numerous aspects of DAT structure and topology heretofore only predicted from theoretical considerations and extend our knowledge of DAT structure-function properties.

Affinity Labels↗
PubMed1994

The connexins and their family tree.

The connexins, gap junction forming proteins, are encoded by a gene family. Sequence comparisons reveal regions of conservation with functional implications for voltage dependence of junctional conductance, junction formation and regulation by phosphorylation. The best connexin tree shows that most gene duplications giving rise to the family occurred early in or before vertebrate divergence. The topology of most deep branches of the tree is uncertain. Evolutionary rates vary for different paralogous connexin genes.

Amino Acid Sequence↗
PubMed2006

Lineage divergence of a freshwater snail clade associated with post-Tethys marine basin development.

The complex evolutionary history of the Eurasian gastropod lineage Theodoxus reflects the evolution of marine basins following the breakup of the Tethys Sea. Today, this clade inhabits the lakes, rivers, streams, and estuaries of Europe, southwestern Asia, and North Africa. Here we present the first phylogenetic hypothesis for this clade. Based upon extensive geographic and taxonomic sampling, portions of the mitochondrial genes for cytochrome c oxidase subunit I and 16S rRNA were sequenced and analysed using maximum likelihood and maximum parsimony methods. Results from bootstrap analyses, Bayesian analysis, and sensitivity analyses lend support to six deep phylogenetic subdivisions within Theodoxus. These major clades are geographically associated with the major post-Tethyan marine basins. Estimates of divergence times using a penalized likelihood approach indicate that divergence of these major lineages occurred during the Miocene, simultaneous with the breakup of the Mediterranean and Paratethys Seas. The resulting major subclades later diversified during the Pliocene, primarily within geographic regions associated with the eastern and western Mediterranean Sea, the Pannonian Basin, and the Black Sea, thus producing the extant species assemblages. Finally, these phylogenetic results imply that much of the current taxonomy is flawed, therefore we offer recommendations for revising the classification of Theodoxus species based on phylogenetic systematics.

Animals↗
PubMed1994

Analysis of regional differences of p53 mutation in advanced gastric carcinoma: relation to heterogeneous differentiation and invasiveness.

In order to examine the correlation of p53 mutation with heterogeneous histological differentiation and invasiveness of gastric carcinoma, we analyzed 46 areas (three to six per case) that were different histologically and anatomically in 12 advanced gastric carcinomas, shown previously to be positive for p53 mutation, using immunohistochemical, polymerase chain reaction-single strand conformation polymorphism, and direct DNA sequencing analyses. DNA derived from different sites in nine cases had the same pattern of p53 mutation, even in cases manifesting heterogeneous histology within a single tumor. Site difference of the p53 mutation was found in three cases: two showed no mutation in superficial tumor areas but presence of mutation in deep-infiltrating areas. In contrast, one case contained a mutation in the superficial area but not in the deep-infiltrating area. These results suggest that in most cases, tumor cells forming a single advanced gastric carcinoma, even though they may present a heterogeneous histology and deep invasion, seem to be derived from the same cellular clone.

Base Sequence↗