Publications

sodium-dependent glutamate uptake by an alkaliphilic, thermophilic bacillus strain, ta2.a1.	a strain of bacillus designated ta2.a1, isolated from a thermal spring in te aroha, new zealand, grew optimally at ph 9.2 and 70 degrees c. bacillus strain ta2.a1 utilized glutamate as a sole carbon and energy source for growth, and sodium chloride (>5 mm) was an obligate requirement for growth. growth on glutamate was inhibited by monensin and amiloride, both inhibitors that collapse the sodium gradient (deltapna) across the cell membrane. n, n-dicyclohexylcarbodiimide inhibited the growth of b ...	1999	10322019
three surface layer homology domains at the n terminus of the clostridium cellulovorans major cellulosomal subunit enge.	the gene enge, coding for endoglucanase e, one of the three major subunits of the clostridium cellulovorans cellulosome, has been isolated and sequenced. enge is comprised of an open reading frame (orf) of 3,090 bp and encodes a protein of 1,030 amino acids with a molecular weight of 111,796. the amino acid sequence derived from enge revealed a structure consisting of catalytic and noncatalytic domains. the n-terminal-half region of enge consisted of a signal peptide of 31 amino acid residues an ...	1999	10322032
the type ii pullulanase of thermococcus hydrothermalis: molecular characterization of the gene and expression of the catalytic domain.	the gene encoding a hyperthermostable type ii pullulanase produced by thermococcus hydrothermalis (th-apu) has been isolated. analysis of a total of 5.2 kb of genomic dna has revealed the presence of three open reading frames, one of which (apua) encodes the pullulanase. this enzyme is composed of 1,339 amino acid residues and exhibits a multidomain structure. in addition to a typical n-terminal signal peptide, th-apu possesses a catalytic domain, a domain bearing s-layer homology-like motifs, a ...	1999	10322035
the accessory subunit of xenopus laevis mitochondrial dna polymerase gamma increases processivity of the catalytic subunit of human dna polymerase gamma and is related to class ii aminoacyl-trna synthetases.	peptide sequences obtained from the accessory subunit of xenopus laevis mitochondrial dna (mtdna) polymerase gamma (pol gamma) were used to clone the cdna encoding this protein. amino-terminal sequencing of the mitochondrial protein indicated the presence of a 44-amino-acid mitochondrial targeting sequence, leaving a predicted mature protein with 419 amino acids and a molecular mass of 47.3 kda. this protein is associated with the larger, catalytic subunit in preparations of active mtdna polymer ...	1999	10330144
mannan-degrading enzymes from cellulomonas fimi.	the genes man26a and man2a from cellulomonas fimi encode mannanase 26a (man26a) and beta-mannosidase 2a (man2a), respectively. mature man26a is a secreted, modular protein of 951 amino acids, comprising a catalytic module in family 26 of glycosyl hydrolases, an s-layer homology module, and two modules of unknown function. exposure of man26a produced by escherichia coli to c. fimi protease generates active fragments of the enzyme that correspond to polypeptides with mannanase activity produced by ...	1999	10347049
maltose metabolism in the hyperthermophilic archaeon thermococcus litoralis: purification and characterization of key enzymes.	maltose metabolism was investigated in the hyperthermophilic archaeon thermococcus litoralis. maltose was degraded by the concerted action of 4-alpha-glucanotransferase and maltodextrin phosphorylase (malp). the first enzyme produced glucose and a series of maltodextrins that could be acted upon by malp when the chain length of glucose residues was equal or higher than four, to produce glucose-1-phosphate. phosphoglucomutase activity was also detected in t. litoralis cell extracts. glucose deriv ...	1999	10348846
cd(ii)-responsive and constitutive mutants implicate a novel domain in merr.	expression of the tn21 mercury resistance (mer) operon is controlled by a metal-sensing repressor-activator, merr. when present, merr always binds to the same position on the dna (the operator mero), repressing transcription of the structural genes mertpcad in the absence of hg(ii) and inducing their transcription in the presence of hg(ii). although it has two potential binding sites, the purified merr homodimer binds only one hg(ii) ion, employing cys82 from one monomer and cys117 and cys126 fr ...	1999	10348859
cloning of the glutamyl-trna synthetase (gltx) gene from pseudomonas aeruginosa.	the glutamyl-trna synthetase (gltx) gene from pseudomonas aeruginosa was identified. a plasmid containing a 2.3-kb insert complemented the temperature-sensitive gltx mutation of escherichia coli jp1449, and gltx activity was demonstrated. the inferred amino acid sequence of this gene showed 50.6% identity with gltx from rhizobium meliloti.	1999	10348873
translation elongation factor 1-alpha interacts specifically with the human immunodeficiency virus type 1 gag polyprotein.	human immunodeficiency virus type 1 (hiv-1) gag-encoded proteins play key functions at almost all stages of the viral life cycle. since these functions may require association with cellular factors, the hiv-1 matrix protein (ma) was used as bait in a yeast two-hybrid screen to identify ma-interacting proteins. ma was found to interact with elongation factor 1-alpha (ef1alpha), an essential component of the translation machinery that delivers aminoacyl-trna to ribosomes. ef1alpha was then shown t ...	1999	10364286
nitrate and nitrite control of respiratory nitrate reduction in denitrifying pseudomonas stutzeri by a two-component regulatory system homologous to narxl of escherichia coli.	bacterial denitrification is expressed in response to the concurrent exogenous signals of low-oxygen tension and nitrate or one of its reduction products. the mechanism by which nitrate-dependent gene activation is effected was investigated in the denitrifying bacterium pseudomonas stutzeri atcc 14405. we have identified and isolated from this organism the chromosomal region encoding the two-component sensor-regulator pair narxl and found that it is linked with the narg operon for respiratory ni ...	1999	10368138
the morphological transition of helicobacter pylori cells from spiral to coccoid is preceded by a substantial modification of the cell wall.	the peptidoglycan (murein) of helicobacter pylori has been investigated by high-performance liquid chromatography and mass spectrometric techniques. murein from h. pylori corresponded to the a1gamma chemotype, but the muropeptide elution patterns were substantially different from the one for escherichia coli in that the former produced high proportions of muropeptides with a pentapeptide side chain (about 60 mol%), with gly residues as the c-terminal amino acid (5 to 10 mol%), and with (1-->6)an ...	1999	10368145
heat-inactivated proteins are rescued by the dnak.j-grpe set and clpb chaperones.	functional chaperone cooperation between hsp70 (dnak) and hsp104 (clpb) was demonstrated in vitro. in a eubacterium thermus thermophilus, dnak and dnaj exist as a stable trigonal ring complex (tdnak.j complex) and the dnak gene cluster contains a clpb gene. when substrate proteins were heated at high temperature, none of the chaperones protected them from heat inactivation, but the tdnak.j complex could suppress the aggregation of proteins in an atp- and tgrpe-dependent manner. subsequent incuba ...	1999	10377389
analysis of peptidoglycan structure from vegetative cells of bacillus subtilis 168 and role of pbp 5 in peptidoglycan maturation.	the composition and fine structure of the vegetative cell wall peptidoglycan from bacillus subtilis were determined by analysis of its constituent muropeptides. the structures of 39 muropeptides, representing 97% of the total peptidoglycan, were elucidated. about 99% analyzed muropeptides in b. subtilis vegetative cell peptidoglycan have the free carboxylic group of diaminopimelic acid amidated. anhydromuropeptides and products missing a glucosamine at the nonreducing terminus account for 0.4 an ...	1999	10383963
sulfolobus acidocaldarius inorganic pyrophosphatase: structure, thermostability, and effect of metal ion in an archael pyrophosphatase.	the first crystal structure of an inorganic pyrophosphatase (s-ppase) from an archaebacterium, the thermophile sulfolobus acidocaldarius, has been solved by molecular replacement and refined to an r-factor of 19.7% at 2.7 a. s-ppase is a d3 homohexameric protein with one mg2+ per active site in a position similar to, but not identical with, the first activating metal in mesophilic pyrophosphatases (ppase). in mesophilic ppases, asp65, asp70, and asp102 coordinate the mg2+, while only asp65 and a ...	1999	10386872
the unique chaperone operon of thermotoga maritima: cloning and initial characterization of a functional hsp70 and small heat shock protein.	the hyperthermophilic eubacterium thermotoga maritima possesses an operon encoding an hsp70 molecular chaperone protein and a protein with meaningful homology to the small heat shock protein family of chaperones. this represents the first demonstrated co-operon organization for these two important classes of molecular chaperones. we have cloned and initially characterized these proteins as functional chaperones in vitro: the hsp70 is capable of atp hydrolysis and substrate binding, and the small ...	1999	10400580
characterization of an atypical superoxide dismutase from sinorhizobium meliloti.	sinorhizobium meliloti rm5000 is an aerobic bacterium that can live free in the soil or in symbiosis with the roots of leguminous plants. a single detectable superoxide dismutase (sod) was found in free-living growth conditions. the corresponding gene was isolated from a genomic library by using a sod fragment amplified by pcr from degenerate primers as a probe. the soda gene was located in the chromosome. it is transcribed monocistronically and encodes a 200-amino-acid protein with a theoretica ...	1999	10419947
in thermoanaerobacterium thermosulfurigenes em1 s-layer homology domains do not attach to peptidoglycan.	three exocellular enzymes of thermoanaerobacterium thermosulfurigenes em1 possess a c-terminal triplicated sequence related to a domain of bacterial cell surface proteins (s-layer proteins). at least one copy of this sequence, named the slh (for s-layer homology) domain, is also present at the n terminus of the s-layer protein of this bacterium. the hypothesis that slh domains serve to anchor proteins to the cell surface was investigated by using the slh domain-containing xylanase. this enzyme w ...	1999	10438774
an inducible human immunodeficiency virus type 1 (hiv-1) vector which effectively suppresses hiv-1 replication.	recently, gene therapy vectors based upon the human immunodeficiency virus type 1 (hiv-1) genome have been developed. here, we create an hiv-1 vector which is defective for all hiv-1 genes, but which maintains cis-acting elements required for efficient packaging, infection, and expression. in t cells transduced by this vector, vector expression is low but efficiently induced following hiv-1 infection. remarkably, although the hiv-1 vector does not contain specific anti-hiv-1 therapeutic genes, t ...	1999	10438857
the accessory subunit of mtdna polymerase shares structural homology with aminoacyl-trna synthetases: implications for a dual role as a primer recognition factor and processivity clamp.	the accessory subunit of the heterodimeric mtdna polymerase (polgamma) from drosophila embryos is required to maintain the structural integrity or catalytic efficiency of the holoenzyme. cdnas for the accessory subunit from drosophila, man, mouse, and rat have been identified, and comparative sequence alignment reveals that the c-terminal region of about 120 aa is the most conserved. furthermore, we demonstrate that the accessory subunit of animal polgamma has both sequence and structural simila ...	1999	10449726
active-site mutations in the xrn1p exoribonuclease of saccharomyces cerevisiae reveal a specific role in meiosis.	xrn1p of saccharomyces cerevisiae is a major cytoplasmic rna turnover exonuclease which is evolutionarily conserved from yeasts to mammals. deletion of the xrn1 gene causes pleiotropic phenotypes, which have been interpreted as indirect consequences of the rna turnover defect. by sequence comparisons, we have identified three loosely defined, common 5'-3' exonuclease motifs. the significance of motif ii has been confirmed by mutant analysis with xrn1p. the amino acid changes d206a and d208a abol ...	1999	10454540
comparison of the d-glutamate-adding enzymes from selected gram-positive and gram-negative bacteria.	the biochemical properties of the d-glutamate-adding enzymes (murd) from escherichia coli, haemophilus influenzae, enterococcus faecalis, and staphylococcus aureus were investigated to detect any differences in the activity of this enzyme between gram-positive and gram-negative bacteria. the genes (murd) that encode these enzymes were cloned into pmal-c2 fusion vector and overexpressed as maltose-binding protein-murd fusion proteins. each fusion protein was purified to homogeneity by affinity to ...	1999	10464212
marine bacterial isolates display diverse responses to uv-b radiation.	the molecular and biological consequences of uv-b radiation were investigated by studying five species of marine bacteria and one enteric bacterium. laboratory cultures were exposed to an artificial uv-b source and subjected to various post-uv irradiation treatments. significant differences in survival subsequent to uv-b radiation were observed among the isolates, as measured by culturable counts. uv-b-induced dna photodamage was investigated by using a highly specific radioimmunoassay to measur ...	1999	10473381
cloning of the gene encoding a novel thermostable alpha-galactosidase from thermus brockianus iti360.	an alpha-galactosidase gene from thermus brockianus iti360 was cloned, sequenced, and expressed in escherichia coli, and the recombinant protein was purified. the gene, designated agat, codes for a 476-residue polypeptide with a calculated molecular mass of 53, 810 da. the native structure of the recombinant enzyme (agat) was estimated to be a tetramer. agat displays amino acid sequence similarity to the alpha-galactosidases of thermotoga neapolitana and thermotoga maritima and a low-level seque ...	1999	10473401
p1 parb domain structure includes two independent multimerization domains.	parb is one of two p1-encoded proteins that are required for active partition of the p1 prophage in escherichia coli. to probe the native domain structure of parb, we performed limited proteolytic digestions of full-length parb, as well as of several n-terminal and c-terminal deletion fragments of parb. the c-terminal 140 amino acids of parb form a very trypsin-resistant domain. in contrast, the n terminus is more susceptible to proteolysis, suggesting that it forms a less stably folded domain o ...	1999	10498700
crystal structure of the dna nucleotide excision repair enzyme uvrb from thermus thermophilus.	nucleotide excision repair (ner) is the most important dna-repair mechanism in living organisms. in prokaryotes, three enzymes forming the uvrabc system initiate ner of a variety of structurally different dna lesions. uvrb, the central component of this system, is responsible for the ultimate dna damage recognition and participates in the incision of the damaged dna strand. the crystal structure of thermus thermophilus uvrb reveals a core that is structurally similar to core regions found in hel ...	1999	10518516
detection of human herpesvirus 6 by reverse transcription-pcr.	the role of human herpesvirus 6 (hhv-6) in disease beyond primary infection remains unclear. we have developed and validated a new reverse transcription-pcr (rt-pcr) assay for hhv-6 that can determine the presence of hhv-6 in clinical specimens and differentiate between latent and replicating virus. peripheral blood mononuclear cells from 109 children were evaluated for hhv-6 by rt-pcr, dna pcr, and viral culture. of these samples, 106 were suitable for analysis. a total of 20 samples were posit ...	1999	10523572
loss of cytochrome c oxidase activity and acquisition of resistance to quinone analogs in a laccase-positive variant of azospirillum lipoferum.	laccase, a p-diphenol oxidase typical of plants and fungi, has been found recently in a proteobacterium, azospirillum lipoferum. laccase activity was detected in both a natural isolate and an in vitro-obtained phase variant that originated from the laccase-negative wild type. in this study, the electron transport systems of the laccase-positive variant and its parental laccase-negative forms were compared. during exponential (but not stationary) growth under fully aerobic (but not under microaer ...	1999	10542175
specific inhibition of the eubacterial dna ligase by arylamino compounds.	all known dna ligases catalyze the formation of a phosphodiester linkage between adjacent termini in double-stranded dna via very similar mechanisms. the ligase family can, however, be divided into two classes: eubacterial ligases, which require nad(+) as a cofactor, and other ligases, from viruses, archaea, and eukaryotes, which use atp. drugs that discriminate between dna ligases from different sources may have antieubacterial activity. we now report that a group of arylamino compounds, includ ...	1999	10543760
improving proteolytic cleavage at the 3a/3b site of the hepatitis a virus polyprotein impairs processing and particle formation, and the impairment can be complemented in trans by 3ab and 3abc.	the orchestrated liberation of viral proteins by 3c(pro)-mediated proteolysis is pivotal for gene expression by picornaviruses. proteolytic processing is regulated either by the amino acid sequence at the cleavage site of the substrate or by cofactors covalently or noncovalently linked to the viral proteinase. to determine the role of the amino acid sequence at cleavage sites 3a/3b and 3b/3c that are essential for the liberation of 3c(pro) from its precursors and to assess the function of the st ...	1999	10559299
determination of bovine rotavirus g and p serotypes in italy by pcr.	determination of the g and p serotypes of group a bovine rotaviruses from 149 samples of feces or intestinal contents collected from calves showing clinical signs of neonatal diarrhea was performed by a nested reverse transcription-pcr typing assay. the g6 serotype was the most prevalent, accounting for viruses in 55.7% of the samples; viruses of the g10 and g8 serotypes were found in 34.9 and 4.7% of the samples, respectively. the virus in one sample (0.7%) was not classified due to concomitant ...	1999	10565900
genome sequence of the radioresistant bacterium deinococcus radiodurans r1.	the complete genome sequence of the radiation-resistant bacterium deinococcus radiodurans r1 is composed of two chromosomes (2,648,638 and 412,348 base pairs), a megaplasmid (177,466 base pairs), and a small plasmid (45,704 base pairs), yielding a total genome of 3,284, 156 base pairs. multiple components distributed on the chromosomes and megaplasmid that contribute to the ability of d. radiodurans to survive under conditions of starvation, oxidative stress, and high amounts of dna damage were ...	1999	10567266
structural distribution of stability in a thermophilic enzyme.	stability parameters for individual residues in thermus thermophilus cysteine-free rnase h were determined by native state hydrogen exchange, thus providing a unique comparison of regional thermodynamics between thermophilic and mesophilic homologues. the general distribution of stability in the thermophilic protein is similar to that of its mesophilic homologue, with a proportional increase in stability for almost all residues. as a consequence, the residue-specific stabilities of the two prote ...	1999	10570131
sequential mechanism of solubilization and refolding of stable protein aggregates by a bichaperone network.	a major activity of molecular chaperones is to prevent aggregation and refold misfolded proteins. however, when allowed to form, protein aggregates are refolded poorly by most chaperones. we show here that the sequential action of two escherichia coli chaperone systems, clpb and dnak-dnaj-grpe, can efficiently solubilize excess amounts of protein aggregates and refold them into active proteins. measurements of aggregate turbidity, congo red, and 4,4'-dianilino-1, 1'-binaphthyl-5,5'-disulfonic ac ...	1999	10570141
ligase-based detection of mononucleotide repeat sequences.	up to 15% of all colorectal cancers are considered to be replication error positive (rer(+)) and contain mutations at hundreds of thousands of microsatellite repeat sequences. recently, a number of intragenic mononucleotide repeat sequences have been demonstrated to be targets for inactivating genes in rer(+)colorectal tumors. in this study, thermostable dna ligases were tested for the ability to detect alterations in microsatellite sequences in colon tumor samples. ligation profiles on mononucl ...	1999	10572192
cloning, overexpression, and mutagenesis of the sporobolomyces salmonicolor aku4429 gene encoding a new aldehyde reductase, which catalyzes the stereoselective reduction of ethyl 4-chloro-3-oxobutanoate to ethyl (s)-4-chloro-3-hydroxybutanoate.	we cloned and sequenced the gene encoding an nadph-dependent aldehyde reductase (arii) in sporobolomyces salmonicolor aku4429, which reduces ethyl 4-chloro-3-oxobutanoate (4-cobe) to ethyl (s)-4-chloro-3-hydroxybutanoate. the arii gene is 1,032 bp long, is interrupted by four introns, and encodes a 37,315-da polypeptide. the deduced amino acid sequence exhibited significant levels of similarity to the amino acid sequences of members of the mammalian 3beta-hydroxysteroid dehydrogenase-plant dihyd ...	1999	10583966
stress genes and proteins in the archaea.	the field covered in this review is new; the first sequence of a gene encoding the molecular chaperone hsp70 and the first description of a chaperonin in the archaea were reported in 1991. these findings boosted research in other areas beyond the archaea that were directly relevant to bacteria and eukaryotes, for example, stress gene regulation, the structure-function relationship of the chaperonin complex, protein-based molecular phylogeny of organisms and eukaryotic-cell organelles, molecular ...	1999	10585970
the small ribosomal subunit from thermus thermophilus at 4.5 a resolution: pattern fittings and the identification of a functional site.	the electron density map of the small ribosomal subunit from thermus thermophilus, constructed at 4.5 a resolution, shows the recognizable morphology of this particle, as well as structural features that were interpreted as ribosomal rna and proteins. unbiased assignments, carried out by quantitative covalent binding of heavy atom compounds at predetermined sites, led to the localization of the surface of the ribosomal protein s13 at a position compatible with previous assignments, whereas the s ...	1999	10588692
calibrating bacterial evolution.	attempts to calibrate bacterial evolution have relied on the assumption that rates of molecular sequence divergence in bacteria are similar to those of higher eukaryotes, or to those of the few bacterial taxa for which ancestors can be reliably dated from ecological or geological evidence. despite similarities in the substitution rates estimated for some lineages, comparisons of the relative rates of evolution at different classes of nucleotide sites indicate no basis for their universal applica ...	1999	10535975
salt-induced detour through compact regions of the protein folding landscape.	in several cases, inorganic salts have been used to induce partly structured states in protein folding. but what is the nature of these states: do they represent key stepping stones in the folding process, or are they circumstantial pitfalls in the energy landscape? here we report that, in the case of the two-state protein s6, the salt-induced collapsed state is off the usual folding routes in the sense that it is prematurely collapsed and slows down folding by several orders of magnitude. altho ...	1999	10518521
the kinetoplast structure-specific endonuclease i is related to the 5' exo/endonuclease domain of bacterial dna polymerase i and colocalizes with the kinetoplast topoisomerase ii and dna polymerase beta during replication.	the mitochondrial dna (kinetoplast dna) of the trypanosomatid crithidia fasciculata has an unusual structure composed of minicircles and maxicircles topologically interlocked into a single network and organized in a disc-shaped structure at the base of the flagellum. we previously purified a structure-specific endonuclease (sse1), based on its rnase h activity, that is enriched in isolated kinetoplasts. the endonuclease gene has now been cloned, sequenced, and found to be closely related to the ...	1999	10411896
distribution of hepatitis c virus genotypes in canada: results from the lcdc sentinel health unit surveillance system.	in a sentinel hepatitis surveillance study conducted by sentinel health units, 1469 patients were enrolled, and 959 (65.3%) were positive for antibody to hepatitis c virus (hcv). samples from 387 patients (40.4%) were tested for hcv rna, and 289 (74.7%) were positive for rna. the major risk factor for hcv infection was injection drug use, reported in 71% of cases. the genotyping of hcv isolates showed that subtype 1a (48%) was predominant in canada. the other subtypes detected were 1b (19%), 2a ...	1999	22346372
improved dna sequencing accuracy and detection of heterozygous alleles using manganese citrate and different fluorescent dye terminators.	the use of dideoxynucleotide triphosphates labeled with different fluorescent dyes (dye terminators) is the most versatile method for automated dna sequencing. however, variation in peak heights reduces base-calling accuracy and limits heterozygous allele detection, favoring use of dye-labeled primers for this purpose. we have discovered that the addition of a manganese salt to the pe applied biosystems dye-terminator sequencing kits overcomes these limitations for the older rhodamine dyes as we ...	1999	10400927
prokaryotic nitrate reduction: molecular properties and functional distinction among bacterial nitrate reductases.		1999	10542156
bioenergetics of the archaea.	in the late 1970s, on the basis of rrna phylogeny, archaea (archaebacteria) was identified as a distinct domain of life besides bacteria (eubacteria) and eucarya. though forming a separate domain, archaea display an enormous diversity of lifestyles and metabolic capabilities. many archaeal species are adapted to extreme environments with respect to salinity, temperatures around the boiling point of water, and/or extremely alkaline or acidic ph. this has posed the challenge of studying the molecu ...	1999	10477309
quantification of 16s rrnas in complex bacterial communities by multiple competitive reverse transcription-pcr in temperature gradient gel electrophoresis fingerprints.	a novel approach was developed to quantify rrna sequences in complex bacterial communities. the main bacterial 16s rrnas in drentse a grassland soils (the netherlands) were amplified by reverse transcription (rt)-pcr with bacterium-specific primers and were separated by temperature gradient gel electrophoresis (tgge). the primer pair used (primers u968-gc and l1401) was found to amplify with the same efficiency 16s rrnas from bacterial cultures containing different taxa and cloned 16s ribosomal ...	1998	9797325
superoxide dismutase in arabidopsis: an eclectic enzyme family with disparate regulation and protein localization.	a number of environmental stresses can lead to enhanced production of superoxide within plant tissues, and plants are believed to rely on the enzyme superoxide dismutase (sod) to detoxify this reactive oxygen species. we have identified seven cdnas and genes for sod in arabidopsis. these consist of three cuznsods (csd1, csd2, and csd3), three fesods (fsd1, fsd2, and fsd3), and one mnsod (msd1). the chromosomal location of these seven sod genes has been established. to study this enzyme family, a ...	1998	9765550
abnormal t cell receptor v gene usage in myasthenia gravis: prevalence and characterization of expanded t cell populations.	the usage of t cell receptor (tcr) valpha/vbeta chains on cells from 38 patients with myasthenia gravis (mg) was determined by flow cytometry. there was a decreased number of cells expressing vbeta2 in cd8+ and vbeta3 in cd4+ cells in patients compared with healthy individuals. abnormal expansions of t cells using particular tcr valpha/vbeta gene products were found in 18/38 patients. a significantly higher usage of vbeta13 was observed but there was no restriction with regard to other tcr valph ...	1998	9737677
association of ferredoxin-nadp oxidoreductase with the chloroplastic pyridine nucleotide dehydrogenase complex in barley leaves	barley (hordeum vulgare l.) leaves were used to isolate and characterize the chloroplast nad(p)h dehydrogenase complex. the stroma fraction and the thylakoid fraction solubilized with sodium deoxycholate were analyzed by native polyacrylamide gel electrophoresis, and the enzymes detected with nadh and nitroblue tetrazolium were electroeluted. the enzymes electroeluted from band s from the stroma fraction and from bands t1 (et1) and t2 from the thylakoid fraction solubilized with sodium deoxychol ...	1998	9576793
insertion sequences.	insertion sequences (iss) constitute an important component of most bacterial genomes. over 500 individual iss have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. the last 10 years have also seen some striking advances in our understanding of the transposition process itself. not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic e ...	1998	9729608
comparative analysis of the regulation of expression and structures of two evolutionarily divergent genes for delta1-pyrroline-5-carboxylate synthetase from tomato.	we isolated two tomato (lycopersicon esculentum) cdna clones, tompro1 and tompro2, specifying delta1-pyrroline-5-carboxylate synthetase (p5cs), the first enzyme of proline (pro) biosynthesis. tompro1 is unusual because it resembles prokaryotic polycistronic operons (m.g. garcía-ríos, t. fujita, p.c. larosa, r.d. locy, j.m. clithero, r.a. bressan, l.n. csonka [1997] proc natl acad sci usa 94: 8249-8254), whereas tompro2 encodes a full-length p5cs. we analyzed the accumulation of pro and the tompr ...	1998	9765552
a novel, rapid in cell rna amplification technique for the detection of low copy mrna transcripts.	growing interest now focuses on improvements of in situ polymerase chain reaction (pcr) technology for the detection of dna and rna cellular sequences. in this study, reverse transcription pcr in situ hybridisation (rt pcr-ish) was developed and used to determine gene expression of pyruvate dehydrogenase in a cell model system, using human peripheral blood lymphocytes (pbls). the success of in cell rna amplification depends on the type of cell/tissue fixation, cell permeabilisation, and the effi ...	1998	9850340
campylobacter fetus surface layer proteins are transported by a type i secretion system.	the virulence of campylobacter fetus, a bacterial pathogen of ungulates and humans, is mediated in part by the presence of a paracrystalline surface layer (s-layer) that confers serum resistance. the subunits of the s-layer are s-layer proteins (slps) that are secreted in the absence of an n-terminal signal sequence and attach to either type a or b c. fetus lipopolysaccharide in a serospecific manner. antigenic variation of multiple slps (encoded by sapa homologs) of type a strain 23d occurs by ...	1998	9851986
identification of two binding domains, one for peptidoglycan and another for a secondary cell wall polymer, on the n-terminal part of the s-layer protein sbsb from bacillus stearothermophilus pv72/p2.	first studies on the structure-function relationship of the s-layer protein from b. stearothermophilus pv72/p2 revealed the coexistence of two binding domains on its n-terminal part, one for peptidoglycan and another for a secondary cell wall polymer (scwp). the peptidoglycan binding domain is located between amino acids 1 to 138 of the mature s-layer protein comprising a typical s-layer homologous domain. the scwp binding domain lies between amino acids 240 to 331 and possesses a high serine pl ...	1998	9852032
a mitochondrial-like chaperonin 60 gene in giardia lamblia: evidence that diplomonads once harbored an endosymbiont related to the progenitor of mitochondria.	diplomonads, parabasalids, as represented by trichomonads, and microsporidia are three protist lineages lacking mitochondria that branch earlier than all other eukaryotes in small subunit rrna and elongation factor phylogenies. the absence of mitochondria and plastids in these organisms suggested that they diverged before the origin of these organelles. however, recent discoveries of mitochondrial-like heat shock protein 70 and/or chaperonin 60 (cpn60) genes in trichomonads and microsporidia imp ...	1998	9419358
a dnak homolog in myxococcus xanthus is involved in social motility and fruiting body formation.	myxococcus xanthus is a gram-negative soil bacterium which exhibits a complex life cycle and social behavior. in this study, two developmental mutants of m. xanthus were isolated through tn5 transposon mutagenesis. the mutants were found to be defective in cellular aggregation as well as in sporulation. further phenotypic characterization indicated that the mutants were defective in social motility but normal in directed cell movements. both mutations were cloned by a transposon-tagging method. ...	1998	9440508
in vitro assembly of a ribonucleoprotein particle corresponding to the platform domain of the 30s ribosomal subunit.	a fragment of the 16s rna of thermus thermophilus corresponding to the central domain (nucleotides 547-895) has been prepared by transcription in vitro. incubation of this fragment with the total 30s ribosomal proteins has resulted in the formation of a compact 12s ribonucleoprotein particle. this particle contained five t. thermophilus proteins corresponding to escherichia coli ribosomal proteins s6, s8, s11, s15, and possibly s18, all of which were previously shown to interact with the central ...	1998	9448274
host mutations (miaa and rpsl) reduce tetracycline resistance mediated by tet(o) and tet(m).	the effects of mutations in host genes on tetracycline resistance mediated by the tet(o) and tet(m) ribosomal protection proteins, which originated in campylobacter spp. and streptococcus spp., respectively, were investigated by using mutants of salmonella typhimurium and escherichia coli. the miaa, miab, and miaab double mutants of s. typhimurium specify enzymes for trna modification at the adenosine at position 37, adjacent to the anticodon in trna. in s. typhimurium, this involves biosynthesi ...	1998	9449261
thermostable repair enzyme for oxidative dna damage from extremely thermophilic bacterium, thermus thermophilus hb8.	the mutm (fpg) gene, which encodes a dna glycosylase that excises an oxidatively damaged form of guanine, was cloned from an extremely thermophilic bacterium, thermus thermophilus hb8. its nucleotide sequence encoded a 266 amino acid protein with a molecular mass of approximately 30 kda. its predicted amino acid sequence showed 42% identity with the escherichia coli protein. the amino acid residues cys, asn, gln and met, known to be chemically unstable at high temperatures, were decreased in num ...	1998	9461446
initiator-elongator discrimination in vertebrate trnas for protein synthesis.	initiator trnas are used exclusively for initiation of protein synthesis and not for the elongation step. we show, in vivo and in vitro, that the primary sequence feature that prevents the human initiator trna from acting in the elongation step is the nature of base pairs 50:64 and 51:63 in the tpsic stem of the initiator trna. various considerations suggest that this is due to sequence-dependent perturbation of the sugar phosphate backbone in the tpsic stem of initiator trna, which most likely ...	1998	9488462
genetic analysis of the nuo locus, which encodes the proton-translocating nadh dehydrogenase in escherichia coli.	complex i (ec 1.6.99.3) of the bacterium escherichia coli is considered to be the minimal form of the type i nadh dehydrogenase, the first enzyme complex in the respiratory chain. because of its small size and relative simplicity, the e. coli enzyme has become a model used to identify and characterize the mechanism(s) by which cells regulate the synthesis and assembly of this large respiratory complex. to begin dissecting the processes by which e. coli cells regulate the expression of nuo and th ...	1998	9495756
specific peptide-activated proteolytic cleavage of escherichia coli elongation factor tu.	phage exclusion is a form of programmed cell death in prokaryotes in which death is triggered by infection with phage, a seemingly altruistic response that limits multiplication of the phage and its spread through the population. one of the best-characterized examples of phage exclusion is the exclusion of t-even phages such as t4 by the e14-encoded lit protein in many escherichia coli k-12 strains. in this exclusion system, transcription and translation of a short region of the major head coat ...	1998	9501186
method for reduction of inhibition in a mycobacterium tuberculosis-specific ligase chain reaction dna amplification assay.	the present study describes the identification of inhibitors of a mycobacterium tuberculosis-specific gap ligase chain reaction (lcr) dna amplification assay as well as a method for their removal. a major contributor to inhibition was deduced to be a calcium phosphate precipitate, cahpo4. the precipitate forms during n-acetyl-l-cysteine-sodium hydroxide (nalc-naoh) decontamination, digestion, and concentration of respiratory specimens. the solubility product of cahpo4 precipitate at ph 7.8, the ...	1998	9508309
intra-assay performance characteristics of five assays for quantification of human immunodeficiency virus type 1 rna in plasma.	three kits (roche amplicor human immunodeficiency virus type 1 [hiv-1] monitor, chiron enhanced-sensitivity bdna, and organon teknika nasba hiv-1 qt) and two in-house assays (from national genetics institute and baylor college of medicine) were compared with a blinded panel. the results were evaluated as to intra-assay sensitivity, precision, and ability to detect differences in a dilution series.	1998	9508327
balance between endogenous superoxide stress and antioxidant defenses.	cells devoid of cytosolic superoxide dismutase (sod) suffer enzyme inactivation, growth deficiencies, and dna damage. it has been proposed that the scant superoxide (o2-) generated by aerobic metabolism harms even cells that contain abundant sod. however, this idea has been difficult to test. to determine the amount of o2- that is needed to cause these defects, we modulated the o2- concentration inside escherichia coli by controlling the expression of sod. an increase in o2- of more than twofold ...	1998	9515906
the s-layer proteins of two bacillus stearothermophilus wild-type strains are bound via their n-terminal region to a secondary cell wall polymer of identical chemical composition.	two bacillus stearothermophilus wild-type strains were investigated regarding a common recognition and binding mechanism between the s-layer protein and the underlying cell envelope layer. the s-layer protein from b. stearothermophilus pv72/p6 has a molecular weight of 130,000 and assembles into a hexagonally ordered lattice. the s-layer from b. stearothermophilus atcc 12980 shows oblique lattice symmetry and is composed of subunits with a molecular weight of 122,000. immunoblotting, peptide map ...	1998	9515918
analysis of hepatitis c virus-inoculated chimpanzees reveals unexpected clinical profiles.	the clinical course of hepatitis c virus (hcv) infections in a chimpanzee cohort was examined to better characterize the outcome of this valuable animal model. results of a cross-sectional study revealed that a low percentage (39%) of hcv-inoculated chimpanzees were viremic based on reverse transcription (rt-pcr) analysis. a correlation was observed between viremia and the presence of anti-hcv antibodies. the pattern of antibodies was dissimilar among viremic chimpanzees and chimpanzees that cle ...	1998	9525575
serial increase in the thermal stability of 3-isopropylmalate dehydrogenase from bacillus subtilis by experimental evolution.	we improved the thermal stability of 3-isopropylmalate dehydrogenase from bacillus subtilis by an in vivo evolutionary technique using an extreme thermophile, thermus thermophilus, as a host cell. the leub gene encoding b. subtilis 3-isopropylmalate dehydrogenase was integrated into the chromosome of a leub-deficient strain of t. thermophilus. the resulting transformant showed a leucine-autotrophy at 56 degrees c but not at 61 degrees c and above. phenotypically thermostabilized strains that can ...	1998	9541402
expression and regulation of the sodf gene encoding iron- and zinc-containing superoxide dismutase in streptomyces coelicolor müller.	streptomyces coelicolor müller contains two superoxide dismutases (sods), nickel-containing (nisod) and iron- and zinc-containing sod (feznsod). the sodf gene encoding feznsod was isolated by using pcr primers corresponding to the n-terminal peptide sequence of the purified feznsod and a c-terminal region conserved among known fesods and mnsods. the deduced amino acid sequence exhibited highest similarity to mn- and fesods from propionibacterium shermanii and mycobacterium spp. the transcription ...	1998	9555880
truncation of peptide deformylase reduces the growth rate and stabilizes solvent production in clostridium beijerinckii ncimb 8052.	the wild-type strain of clostridium beijerinckii ncimb 8052 tends to degenerate (i.e., lose the ability to form solvents) after prolonged periods of laboratory culture. several tn1545 mutants of this organism showing enhanced long-term stability of solvent production were isolated. four of them harbor identical insertions within the fms (def) gene, which encodes peptide deformylase (pdf). the c. beijerinckii fms gene product contains four diagnostic residues involved in the zn2+ coordination and ...	1998	9572951
isolation of a periplasmic molecular chaperone-like protein of rhodobacter sphaeroides f. sp. denitrificans that is homologous to the dipeptide transport protein dppa of escherichia coli.	a periplasmic protein has been found to prevent aggregation of the acid-unfolded dimethyl sulfoxide reductase (dmsor), the periplasmic terminal reductase of dimethyl sulfoxide respiration in the phototroph rhodobacter sphaeroides f. sp. denitrificans, in a manner similar to that of the escherichia coli chaperonin groel (matsuzaki et al., plant cell physiol. 37:333-339, 1996). the protein was isolated from the periplasm of the phototroph. it had a molecular mass of 58 kda and had no subunits. the ...	1998	9573158
acquired thermotolerance and temperature-induced protein accumulation in the extremely thermophilic bacterium rhodothermus obamensis.	temperature-induced changes in thermotolerance and protein composition were examined in heat-shocked cells and high-temperature-grown cells of the extremely thermophilic bacterium rhodothermus obamensis. the survival at temperatures superoptimal for growth (90 and 95 degrees c) was enhanced in both heat-shocked cells and high-temperature-grown cells relative to that of cells grown at optimal temperatures. in a comparison of protein composition using two-dimensional gel electrophoresis, putative ...	1998	9573167
control of 5',5'-dinucleoside triphosphate catabolism by aph1, a saccharomyces cerevisiae analog of human fhit.	the putative human tumor suppressor gene fhit (fragile histidine triad) (m. ohta et al., cell 84:587-597, 1996) encodes a protein behaving in vitro as a dinucleoside 5',5"'-p1,p3-triphosphate (ap3a) hydrolase. in this report, we show that the saccharomyces cerevisiae aph1 gene product, which resembles human fhit protein, also hydrolyzes dinucleoside 5',5'-polyphosphates, with ap3a being the preferred substrate. accordingly, disruption of the aph1 gene produced viable s. cerevisiae cells containi ...	1998	9573184
the crystal structure of asparaginyl-trna synthetase from thermus thermophilus and its complexes with atp and asparaginyl-adenylate: the mechanism of discrimination between asparagine and aspartic acid.	the crystal structure of thermus thermophilus asparaginyl-trna synthetase has been solved by multiple isomorphous replacement and refined at 2.6 a resolution. this is the last of the three class iib aminoacyl-trna synthetase structures to be determined. as expected from primary sequence comparisons, there are remarkable similarities between the tertiary structures of asparaginyl-trna synthetase and aspartyl-trna synthetase, and most of the active site residues are identical except for three key ...	1998	9582288
visualization of elongation factor g on the escherichia coli 70s ribosome: the mechanism of translocation.	during protein synthesis, elongation factor g (ef-g) binds to the ribosome and promotes the step of translocation, a process in which trna moves from the a to the p site of the ribosome and the mrna is advanced by one codon. by using three-dimensional cryo-electron microscopy, we have visualized ef-g in a ribosome-ef-g-gdp-fusidic acid complex. fitting the crystal structure of ef-g-gdp into the cryo density map reveals a large conformational change mainly associated with domain iv, the domain th ...	1998	9600930
genes for 2,4,5-trichlorophenoxyacetic acid metabolism in burkholderia cepacia ac1100: characterization of the tftc and tftd genes and locations of the tft operons on multiple replicons.	burkholderia cepacia ac1100 uses the chlorinated aromatic compound 2, 4,5-trichlorophenoxyacetic acid (2,4,5-t) as a sole source of carbon and energy. the enzyme which converts the first intermediate in the pathway, 2,4,5-trichlorophenol, to 5-chlorohydroquinone has been purified and consists of two subunits of 58 and 22 kda, encoded by the tftc and tftd genes (48). a degenerate primer was designed from the n terminus of the 58-kda polypeptide and used to isolate a clone containing the tftc and ...	1998	9603818
structure of the beta-galactosidase gene from thermus sp. strain t2: expression in escherichia coli and purification in a single step of an active fusion protein.	the nucleotide sequence of both the bgaa gene, coding for a thermostable beta-galactosidase of thermus sp. strain t2, and its flanking regions was determined. the deduced amino acid sequence of the enzyme predicts a polypeptide of 645 amino acids (mr, 73,595). comparative analysis of the open reading frames located in the flanking regions of the bgaa gene revealed that they might encode proteins involved in the transport and hydrolysis of sugars. the observed homology between the deduced amino a ...	1998	9603833
posttranscriptional modifications in 16s and 23s rrnas of the archaeal hyperthermophile sulfolobus solfataricus.	posttranscriptional modification is common to many types of rna, but the majority of information concerning structure and function of modification is derived principally from trna. by contrast, less is known about modification in rrna in spite of accumulating evidence for its direct participation in translation. the structural identities and approximate molar levels of modifications have been established for 16s and 23s rrnas of the archaeal hyperthermophile sulfolobus solfactaricus by using com ...	1998	9603876
secondary absence of mitochondria in giardia lamblia and trichomonas vaginalis revealed by valyl-trna synthetase phylogeny.	nuclear-coded valyl-trna synthetase (valrs) of eukaryotes is regarded of mitochondrial origin. complete valrs sequences obtained by us from two amitochondriate protists, the diplomonad, giardia lamblia and the parabasalid, trichomonas vaginalis were of the eukaryotic type, strongly suggesting an identical history of valrs in all eukaryotes studied so far. the findings indicate that diplomonads are secondarily amitochondriate and give further evidence for such conclusion reached recently concerni ...	1998	9618503
evaluation of a commercially available reverse transcription-pcr assay for diagnosis of enteroviral infection in archival and prospectively collected cerebrospinal fluid specimens.	a commercially available reverse transcription (rt)-pcr method (amplicor ev; roche diagnostic systems, inc., branchburg, n.j.) was evaluated for detection of enteroviruses in cerebrospinal fluid from patients with neurological disease. this assay was compared with virus isolation in cell culture and an in-house rt-pcr method designed with a nonoverlapping region of the enteroviral genome. a panel of 200 cerebrospinal fluid specimens prospectively collected from patients with a wide variety of ne ...	1998	9620411
anaerobic growth, a property horizontally transferred by an hfr-like mechanism among extreme thermophiles.	despite the fact that the extreme thermophilic bacteria belonging to the genus thermus are classified as strict aerobes, we have shown that thermus thermophilus hb8 (atcc 27634) can grow anaerobically when nitrate is present in the growth medium. this strain-specific property is encoded by a respiratory nitrate reductase gene cluster (nar) whose expression is induced by anoxia and nitrate (s. ramírez-arcos, l. a. fernández-herrero, and j. berenguer, biochim. biophys. acta, 1396:215-1997). we sho ...	1998	9620963
an autonomously replicating transforming vector for sulfolobus solfataricus.	a plasmid able to transform and to be stably maintained both in sulfolobus solfataricus and in escherichia coli was constructed by insertion into an e. coli plasmid of the autonomously replicating sequence of the virus particle ssv1 and a suitable mutant of the hph (hygromycin phosphotransferase) gene as the transformation marker. the vector suffered no rearrangement and/or chromosome integration, and its copy number in sulfolobus was increased by exposure of the cells to mitomycin c.	1998	9620978
identification of the gene encoding the tryptophan synthase beta-subunit from chlamydomonas reinhardtii.	we report the isolation of a chlamydomonas reinhardtii cdna that encodes the beta-subunit of tryptophan synthase (tsb). this cdna was cloned by functional complementation of a trp-operon-deleted strain of escherichia coli. hybridization analysis indicated that the gene exists in a single copy. the predicted amino acid sequence showed the greatest identity to tsb polypeptides from other photosynthetic organisms. with the goal of identifying mutations in the gene encoding this enzyme, we isolated ...	1998	9625698
immunological and molecular characterization of three variant subtype p1.14 strains of neisseria meningitidis.	epidemic outbreaks of group b meningococcal disease exhibit a clonal nature consisting of a common serotype-subtype. subtype-specific monoclonal antibodies (mabs) directed toward two variable regions (vr1 and vr2) of the class 1 protein of neisseria meningitidis are used in this classification scheme. a new mab was developed to classify a nonsubtypeable (nst) strain of n. meningitidis, 7967. this mab bound to both the nst strain and the prototype subtype p1. 14 strain, s3446, by dot blot analysi ...	1998	9632588
adjustment of conformational flexibility is a key event in the thermal adaptation of proteins.	3-isopropylmalate dehydrogenase (ipmdh, e.c. 1.1.1.85) from the thermophilic bacterium thermus thermophilus hb8 is homologous to ipmdh from the mesophilic escherichia coli, but has an approximately 17 degreesc higher melting temperature. its temperature optimum is 22-25 degreesc higher than that of the e. coli enzyme; however, it is hardly active at room temperature. the increased conformational rigidity required to stabilize the thermophilic enzyme against heat denaturation might explain its di ...	1998	9636162
does disparate occurrence of autoregulatory programmed frameshifting in decoding the release factor 2 gene reflect an ancient origin with loss in independent lineages?	in escherichia coli an autoregulatory mechanism of programmed ribosomal frameshifting governs the level of polypeptide chain release factor 2. from an analysis of 20 sequences of genes encoding release factor 2, we infer that this frameshift mechanism was present in a common ancestor of a large group of bacteria and has subsequently been lost in three independent lineages.	1998	9642202
thermotoga neapolitana homotetrameric xylose isomerase is expressed as a catalytically active and thermostable dimer in escherichia coli.	the xyla gene from thermotoga neapolitana 5068 was expressed in escherichia coli. gel filtration chromatography showed that the recombinant enzyme was both a homodimer and a homotetramer, with the dimer being the more abundant form. the purified native enzyme, however, has been shown to be exclusively tetrameric. the two enzyme forms had comparable stabilities when they were thermoinactivated at 95 degrees c. differential scanning calorimetry revealed thermal transitions at 99 and 109.5 degrees ...	1998	9647799
solution structure of the cytohesin-1 (b2-1) sec7 domain and its interaction with the gtpase adp ribosylation factor 1.	cytohesin-1 (b2-1) is a guanine nucleotide exchange factor for human adp ribosylation factor (arf) gtpases, which are important for vesicular protein trafficking and coatamer assembly in the cell. cytohesin-1 also has been reported to promote cellular adhesion via binding to the beta2 integrin cytoplasmic domain. the solution structure of the sec7 domain of cytohesin-1, which is responsible for both the protein's guanine nucleotide exchange factor function and beta2 integrin binding, was determi ...	1998	9653114
single amino acid substitution in prokaryote polypeptide release factor 2 permits it to terminate translation at all three stop codons.	prokaryotic translational release factors, rf1 and rf2, catalyze polypeptide release at uag/uaa and uga/uaa stop codons, respectively. in this study, we isolated a bacterial rf2 mutant (rf2) containing an e167k substitution that restored the growth of a temperature-sensitive rf1 strain of escherichia coli and the viability of a chromosomal rf1/rf2 double knockout. in both in vivo and in vitro polypeptide termination assays, rf2 catalyzed uag/uaa termination, as does rf1, as well as uga termina ...	1998	9653158
diversity of cytochrome bc complexes: example of the rieske protein in green sulfur bacteria.	the rieske 2fe2s cluster of chlorobium limicola forma thiosulfatophilum strain tassajara was studied by electron paramagnetic resonance spectroscopy. two distinct orientations of its g tensor were observed in oriented samples corresponding to differing conformations of the protein. only one of the two conformations persisted after treatment with 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone. a redox midpoint potential (em) of +160 mv in the ph range of 6 to 7.7 and a decreasing em (-60 to -80 ...	1998	9658021
influence of the secondary cell wall polymer on the reassembly, recrystallization, and stability properties of the s-layer protein from bacillus stearothermophilus pv72/p2.	the high-molecular-weight secondary cell wall polymer (scwp) from bacillus stearothermophilus pv72/p2 is mainly composed of n-acetylglucosamine (glcnac) and n-acetylmannosamine (mannac) and is involved in anchoring the s-layer protein via its n-terminal region to the rigid cell wall layer. in addition to this binding function, the scwp was found to inhibit the formation of self-assembly products during dialysis of the guanidine hydrochloride (ghcl)-extracted s-layer protein. the degree of assemb ...	1998	9696762
multicenter evaluation of the amplicor enterovirus pcr test with cerebrospinal fluid from patients with aseptic meningitis. the european union concerted action on viral meningitis and encephalitis.	the amplicor enterovirus pcr test was compared with viral culture for the detection of enteroviruses in cerebrospinal fluid (csf) specimens. in a multicenter study in which nine laboratories participated, a total of 476 csf specimens were collected from patients with suspected aseptic meningitis. sixty-eight samples were positive by pcr (14.4%), whereas 49 samples were positive by culture (10.4%), demonstrating that the amplicor enterovirus pcr test was significantly more sensitive than culture ...	1998	9705409
domain organization and functional analysis of thermus thermophilus muts protein.	muts protein binds to dna and specifically recognizes mismatched or small looped out heteroduplex dna. in order to elucidate its structure-function relationships, the domain structure of thermus thermophilus muts protein was studied by performing denaturation experiments and limited proteolysis. the former suggested that t. thermophilus muts consists of at least three domains with estimated stabilities of 12.3, 22.9 and 30.7 kcal/mol and the latter revealed that it consists of four domains: a1 ( ...	1998	9722634
fidelity of dna ligation: a novel experimental approach based on the polymerisation of libraries of oligonucleotides.	complete libraries of oligonucleotides were used as substrates for thermus thermophilus dna ligase, on a m13mp18 ssdna template. a 17mer primer was used to start a polymerisation process. ladders of ligation products were analysed by gel electrophoresis. octa-, nona- and decanucleotide libraries were compared. nonanucleotides were optimum for polymerisation and up to 15 monomers were ligated. the fidelity of incorporation was studied by sequencing 28 clones (2268 bases) of nonanucleotide polymer ...	1998	9722647
linkage map of escherichia coli k-12, edition 10: the traditional map.	this map is an update of the edition 9 map by berlyn et al. (m. k. b. berlyn, k. b. low, and k. e. rudd, p. 1715-1902, in f. c. neidhardt et al., ed., escherichia coli and salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). it uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. the latter are included as ...	1998	9729611
a natural large chromosomal inversion in lactococcus lactis is mediated by homologous recombination between two insertion sequences.	comparative analysis of chromosomal macrorestriction polymorphism of the two closely related lactococcus lactis subsp. cremoris strains mg1363 and ncdo763 revealed the presence of a large inversion covering half of the genome. to determine what kind of genetic element could be implicated in this rearrangement, the two inversion junctions of mg1363 and ncdo763 chromosomes were cloned and characterized. nucleotide sequence analysis showed the presence of one copy of the lactococcal is905 element i ...	1998	9733685
creation of genetic information by dna polymerase of the thermophilic bacterium thermus thermophilus.	genetic information encoded in a template of a genome is replicated in a complementary way by dna polymerase or rna polymerase with high fidelity; no creation of information occurs in this reaction unless an error occurs. we report here that dna polymerase of the thermophilic bacterium thermus thermophilus can synthesize up to 200 kb linear double-stranded dna in vitro in the complete absence of added primer and template dnas, indicating that genetic information is actively created by protein. t ...	1998	9753734
translation elongation factor 2 is part of the target for a new family of antifungals.	translation elongation factor 2 (ef2), which in saccharomyces cerevisiae is expressed from the eft1 and eft2 genes, has been found to be targeted by a new family of highly specific antifungal compounds derived from the natural product sordarin. two complementation groups of mutants resistant to the semisynthetic sordarin derivative gm193663 were found. the major one (21 members) consisted of isolates with mutations on eft2. the minor one (four isolates) is currently being characterized but it is ...	1998	9756779
effects of temperature, salinity, and medium composition on compatible solute accumulation by thermococcus spp	the effects of salinity and growth temperature on the accumulation of intracellular organic solutes were examined by nuclear magnetic resonance spectroscopy (nmr) in thermococcus litoralis, thermococcus celer, thermococcus stetteri, and thermococcus zilligii (strain an1). in addition, the effects of growth stage and composition of the medium were studied in t. litoralis. a novel compound identified as beta-galactopyranosyl-5-hydroxylysine was detected in t. litoralis grown on peptone-containing ...	1998	9758772
capacity of nine thermostable dna polymerases to mediate dna amplification in the presence of pcr-inhibiting samples.	the pcr is an extremely powerful method for detecting microorganisms. however, its full potential as a rapid detection method is limited by the inhibition of the thermostable dna polymerase from thermus aquaticus by many components found in complex biological samples. in this study, we have compared the effects of known pcr-inhibiting samples on nine thermostable dna polymerases. samples of blood, cheese, feces, and meat, as well as various ions, were added to pcr mixtures containing various the ...	1998	9758794
enhancement of the amplicor enterovirus pcr test with a coprecipitant.	the incorporation of a commercially available coprecipitant into the amplicor enterovirus pcr test specimen preparation enhanced the sensitivity and reproducibility of this assay. fifty-five previously tested archived cerebrospinal fluids (csf) specimens were tested in a blind study in duplicate with and without pellet paint coprecipitant (novagen, inc., madison, wis.). of these specimens, 26 had previously been determined to be positive and 29 had previously been determined to be negative. all ...	1998	9774607