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PubMed2005

Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV.

In this study, we have identified 876 polymorphism sites in 145 complete or partial genomes of SARS-CoV available in the NCBI GenBank. One hundred and seventy-four of these sites existed in two or more SARS-CoV genome sequences. According to the sequence polymorphism, all SARS-CoVs can be divided into three groups: (I) group 1, animal-origin viruses (such as SARS-CoV SZ1, SZ3, SZ13 and SZ16); (II) group 2, all viruses with clinical origin during first epidemic; and (III) group 3, SARS-CoV GD03T0013. According to 10 special loci, group 2 again can be divided into genotypes C and T, which can be further divided into sub-genotypes C1-C4 and T1-T4. Positive Darwinian selections were identified between any pair of these three groups. Genotype C gives neutral selection. Genotype T, however, shows negative selection. By comparing the death rates of SARS patients in the different regions, it was found that the death rate caused by the viruses of the genotype C was lower than that of the genotype T. SARS-CoVs might originate from an unknown ancestor.

Base Sequence↗
PubMed2003

Linkage of high rates of sulfate reduction in Yellowstone hot springs to unique sequence types in the dissimilatory sulfate respiration pathway.

Diversity, habitat range, and activities of sulfate-reducing prokaryotes within hot springs in Yellowstone National Park were characterized using endogenous activity measurements, molecular characterization, and enrichment. Five major phylogenetic groups were identified using PCR amplification of the dissimilatory sulfite reductase genes (dsrAB) from springs demonstrating significant sulfate reduction rates, including a warm, acidic (pH 2.5) stream and several nearly neutral hot springs with temperatures reaching 89 degrees C. Three of these sequence groups were unrelated to named lineages, suggesting that the diversity and habitat range of sulfate-reducing prokaryotes exceeds that now represented in culture.

Bacteria↗
PubMed2002

Improved molecular identification of Thermoactinomyces spp. associated with mushroom worker's lung by 16S rDNA sequence typing.

Mushroom worker's lung (MWL) is a hypersensitivity pneumonitis or allergic alveolitis caused by a type III IgG-mediated immunopathogenic inflammatory reaction in the host due to the inhalation of several thermophilic organisms, including Thermoactinomyces spp. It is difficult to distinguish phenotypically the eight species of this genus; therefore, this study sought to develop an improved molecular means of identifying Thermoactinomyces spp. associated with MWL by partial 16S rDNA PCR amplification and direct sequencing. Hypervariable regions within the 16S rRNA gene, which could be employed as signature sequences of the eight individual species, were identified and employed with highly conserved flanking primers to allow initial PCR amplification, before direct DNA sequencing of the 16S rDNA amplicons. A novel 24-mer 16S rDNA oligonucleotide upstream primer was designed from in silico alignments of all Thermoactinomyces spp. and was employed in combination with downstream (reverse) 16S rDNA primers. This permitted the successful identification of all four isolates associated with mushroom workers' lung. The method may be useful in the identification of Thermoactinomyces spp. associated with allergic alveolitis or pneumonitis associated with occupational exposure in agricultural and horticultural environments.

Agricultural Workers' Diseases↗
PubMed2004

Identification of novel eubacteria from spent mushroom compost (SMC) waste by DNA sequence typing: ecological considerations of disposal on agricultural land.

A small study was undertaken to examine the microbiological characteristics of spent mushroom compost (SMC), which is the major waste by-product of the mushroom industry and which is regularly disposed off by application to agricultural land. The primary aim of this study was to examine SMC for the presence of faecal bacterial pathogens, including Campylobacter spp., Salmonella spp. and Listeria monocytogenes. Secondly it was desirable to quantify bacterial and fungal populations within SMC, and also qualitatively identify the diversity of bacterial populations within SMC, through employment of rDNA PCR and direct sequencing techniques on the culturable microflora. Conventional microbiological analyses of SMC material (n=30) from six commercial operations in both Northern Ireland and the Republic of Ireland, failed to detect Salmonella spp, Listeria spp. or Campylobacter spp. in any of the SMC material examined. Total aerobic plate counts gave a mean count of log10 7.01 colony forming units (cfu) per gram SMC material (range: log10 6.53-7.52 cfu/g). Fungal counts gave a mean count of log(10) 4.57 cfu per gram SMC material (range: log10 3.93-4.98 cfu/g). From a total of greater than 50 colony picks, a total of 12 bacterial morphotypes were identified and were further examined by employment of partial 16S rRNA gene amplification and sequencing techniques, yielding several genera and species, including Bacillus licheniformis, Bacillus subtilis, Klebsiella/Enterobacter sp. Microbacterium sp. Paenibacillus lentimorbus, Pseudomonas mevalonii, Sphingobacterium multivorum and Stenotrophomonas sp. This is the first preliminary report on the microbial diversity of SMC waste and demonstrates the presence of several species that have not been previously described in SMC, in addition to two potentially novel species within the genera Microbacterium and Stenotrophomonas. It is thereby important to examine the ecological microbe-microbe and plant-microbe interactions that are occurring between the native bacterial soil flora and those added annually (theoretically estimated at approximately 10(18) cells) through the application of SMC. Such studies would be beneficial in helping to ascertain the ecological consequences involved in the disposal of SMC waste on agricultural land.

Agaricales↗
PubMed2002

Amino acid modifications in the wild type sequence p53 232-240 overcome the poor immunogenicity of this self tumour epitope.

A major limitation in antigen-specific cancer vaccines is that most of the tumour antigens that are potent candidates for broad applicability originate from self proteins. The peptides presented by tumour cells are derived from tissue-specific differentiation proteins, from proteins altered by genetic mutation or by non mutated proteins that are normally silent in most adult tissues. As a consequence, T-cell responses elicited against those antigens are rather weak. Several data showed that amino acid modifications could enhance the immunogenicity of such antigens by priming T-cells that have escaped central tolerance based on a poor avidity. In this regard, this strategy could be powerful for inducing immunity against tumours. The present report focuses on the murine wild type epitope p53 232-240 that is poorly immunogenic. It shows that substitution of the two cysteine residues by serine or amino butyric acid derivatives and substitution of the two methionine residues by norleucine residues resulted in enhanced stability of the MHC/peptide complex. The MHC binding affinity of analogue peptides was enhanced between 10 and 100 fold. They were also potent immunogens, stronger than was the original wild type epitope; T-cell responses were increased up to 50 times. Moreover, the effector T-cells elicited by three of these peptides cross reacted with the natural epitope. These observations have important implications for strategies that use the modified-peptide epitope.

Adoptive Transfer↗
PubMed1997

Inactive conformation of an insulin despite its wild-type sequence.

The peptide group between residues B24 and B25 of insulin was replaced by an ester bond. This modification only in the backbone was meant to eliminate a structurally important H-bond between the amide proton of B25 and the carbonyl oxygen of A19, and consequently to enhance detachment of the C-terminal B-chain from the body of the molecule, exposing the underlying A-chain. According to a model derived from the effects of side-chain substitutions, main-chain shortening, and crosslinking, this conformational change is prerequisite for receptor binding. Contrary to the expectation that increased flexibility would increase receptor binding and activity, depsi-insulin ([B24-B25 CO-O]insulin) has turned out be only 3-4% potent. In search of an explanation for this observation, the solution structure of depsi-insulin was determined by two-dimensional 1H-NMR spectroscopy. It was found that the loss of the B25-A19 H-bond does not entail detachment of the C-terminal B-chain. On the contrary, it is overcompensated by a gain in hydrophobic interaction achieved by insertion of the Phe B25 side chain into the molecule's core. This is possible because of increased rotational freedom in the backbone owing to the ester bond. Distortion of the B20-B23 turn and an altered direction of the distal B-chain are consequences that also affect self-association. The exceptional position of the B25 side chain is thus the key feature of the depsi-insulin structure. Being buried in the interior, it is not available for guiding the interaction with the receptor, a crucial role attributed to it by the model. This seems to be the main reason why the structure of depsi-insulin represents an inactive conformation.

Amino Acid Sequence↗
PubMed1993

Conformational properties of the -35 region of the trp promoter in solution: comparison of the wild-type sequence with an AT transversion.

The majority of the 1H NMR resonances of the protons in a tetradecamer containing the -35 region of the trp promoter d(GCTGTTGACAATTA): d(TAATTGTCAACAGC) and in the TA transversion have been assigned. The conformational properties of the nucleotides have been determined and compared in the two duplexes. Analysis of spin-spin coupling and NOEs shows that all sugar puckers are in the south domain (i.e. near C2' endo) and the glycosidic torsion angles are anti (chi approximately 110 degrees). The NMR data are consistent with the duplex being in the B family of conformations. Significant differences in chemical shifts between the two molecules were observed only for nearest neighbours to the transversion site, suggesting the absence of long range conformational effects. This was confirmed by the similarity of coupling constants and NOEs. Other properties are also not greatly affected at positions more than two base pairs from the mutation site. These results are consistent with the hypothesis that unconstrained oligonucleotides are highly flexible, and can readily accommodate significant perturbations of the local structure, such as a transversion.

Adenine↗
PubMed1989

Identification of an enhancer-type sequence that is responsive to Z and R trans-activators of Epstein-Barr virus.

We studied the regulatory region of the open reading frame BHRF1 of Epstein-Barr virus (EBV) DNA that was responsive to two trans-activators (Z and R) encoded by the BZLF1 and BRLF1, respectively. The 200-bp sequence, nucleotide numbers 53,617 to 53,817 on the EBV map, was sufficient for conferring responsiveness to Z and R. This 200-bp sequence also enhanced expression of the chloramphenicol acetyltransferase (CAT) gene from the simian virus 40 promoter in response to both Z and R, even when inserted downstream of the cat gene. The results indicate that the Z and R response sequence upstream of the BHRF1 has the properties of an enhancer.

Base Sequence↗
PubMed2005

Frequency offset refocused PISEMA-type sequences.

The popular PISEMA experiment is highly sensitive to the 1H chemical shift dispersion and the choice of the 1H carrier frequency. This is due to the off-resonance 1H irradiation in the FSLG-CP sequence employed during the dipolar evolution period. In the modified approach described in this work, the interfering frequency offset terms are suppressed. In the new pulse schemes, conventional FSLG-CP is intercalated with 180 degrees pulses applied simultaneously to both frequency channels, and with phases set orthogonal to those of the spin-lock fields. The technique is demonstrated on a nematic liquid-crystalline sample. Extensions to amplitude-modulated FSLG-CP recoupling under MAS are also presented.

Algorithms↗
PubMed2006

High case-fatality rates of meningococcal disease in Western Norway caused by serogroup C strains belonging to both sequence type (ST)-32 and ST-11 complexes, 1985-2002.

A total of 293 meningococcal disease (McD) patients from Western Norway hospitalized during 1985-2002 were examined for risk factors related to death. The case-fatality rate (CFR) increased from 4% during 1985-1993 to 17% during 1994-2002. We analysed the phenotypic and genotypic characteristics of the meningococcal patient isolates, with the aim of identifying whether highly virulent meningococcal strains contributed to the increased CFR. The Norwegian epidemic strain B:15:P1.7,16/ST-32 complex was overall the most common phenotype/genotype (n=75) and caused most deaths (n=9; CFR 12.0%). However, fatality was significantly associated with disease caused by serogroup C meningococcal strains; C:15:P1.7,16/ST-32 and C:2a/ST-11 complex strains, which had the highest CFRs of 21.1% and 18.2% respectively. Serogroup B strains of the ST-32 complex differing by serotype and/or serosubtype from the epidemic strain had a CFR of 5.1%, while the CFR of disease caused by other strains (all phenotypes and genotypes pooled) was 2.2%. The distribution of phenotypes/clonal complexes varied significantly between 1985-1993 and 1994-2002 (P<0.001); B:15/ST-32 complex strains decreased whereas both C:15:P1.7,16/ST-32 complex strains and strains with other phenotypes/clonal complexes increased. Our results indicate that C:15:P1.7,16/ST-32 and C:2a/ST-11 complex strains were highly virulent strains and contributed to the high CFR of McD in patients from Western Norway. To reduce fatality, rapid identification of such virulent strains is necessary. In addition, early and specific measures should include public information, vaccination of populations at risk of disease and carriage eradication, when clustering of patients occurs.

Genotype↗
PubMed2002

Noise-induced Hopf-bifurcation-type sequence and transition to chaos in the lorenz equations.

We study the effects of noise on the Lorenz equations in the parameter regime admitting two stable fixed point solutions and a strange attractor. We show that noise annihilates the two stable fixed point attractors and evicts a Hopf-bifurcation-like sequence and transition to chaos. The noise-induced oscillatory motions have very well defined period and amplitude, and this phenomenon is similar to stochastic resonance, but without a weak periodic forcing. When the noise level exceeds certain threshold value but is not too strong, the noise-induced signals enable an objective computation of the largest positive Lyapunov exponent, which characterize the signals to be truly chaotic.

Journal Article↗
PubMed2003

[Description of the first cases of serotype A, sequence type (ST)-11 meningococcal meningitis in Senegal].

Senegal is located in the African meningitis belt and meningococcal meniningitis outbreaks are yearly events. Occurrence of an epidemic involving serogroup W135 in 2000 and its spread following the Hajj (pilgrimage to Mecca) exposed the strongly Moslem population of Senegal to the risk of early infection. Indeed the first two cases in Dakar occurred simultaneously with the spread of this epidemic strain. The purpose of this article is to describe clinical, laboratory, and therapeutic findings in these two cases and the results of the ensuing epidemiological survey. The relationship with the pilgrimage and consequences on public health in Senegal are discussed.

Child, Preschool↗