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PubMed1988

The Caenorhabditis elegans hsp70 gene family: a molecular genetic characterization.

We have isolated genomic clones representing six distinct members of the Caenorhabditis elegans 70-kDa heat-shock protein gene (hsp70) family. Each member exists as a single copy element in the C. elegans genome. Transcripts of four of the hsp70 genes have been detected by Northern-blot analysis. One member, hsp70C, appears to be a heat-shock-cognate hsp70 gene (hsc70) since its transcription is developmentally regulated and is not increased in response to heat shock. Transcripts of another gene, hsp70A, are abundant in control worms and are also increased (two- to six-fold) upon heat shock. Nucleotide sequencing of genomic and cDNA clones of hsp70A reveals that it is highly homologous to Drosophila and yeast heat-shock-inducible and heat-shock-cognate hsp70 genes. Three DNA elements homologous to the heat-shock promoter, 5'-C--GAA--TTC--G-3' are located upstream from the Hsp70A-coding region. We find that hsp70A contains three introns, one of which is in a similar position with an intron in the Drosophila hsc1 and hsc2 genes. Finally, utilizing strain-specific restriction fragment length differences, we have mapped the chromosomal position of hsp70A to the far right of chromosome IV.

Amino Acid Sequence↗

PubMed1994

Genetic characterization of mannose-sensitive hemagglutinin (MSHA)-negative mutants of Vibrio cholerae derived by Tn5 mutagenesis.

El Tor biotype Vibrio cholerae strains express a cell-associated mannose-sensitive hemagglutinin (MSHA) which is a putative attachment factor. Several MSHA-negative mutants from V. cholerae strain JBK70 were previously generated by Tn5 mutagenesis [Finn et al., Infect. Immun. 55 (1987) 942-946]. The chromosomal DNA regions containing the Tn5 insertions were isolated from eight strains for further analysis. Nucleotide sequencing of the insertional junctions and corresponding clones containing the intact chromosomal region from the parental strain revealed the presence of several contiguous ORFs. Only two ORFs of this region had received insertions, and these showed remarkable homology to genes involved in the general secretory pathway found in several Gram- bacterial species. Proteins corresponding to the observed ORFs were visualized with the T7 promoter/RNA polymerase expression system. Marker exchange mutagenesis was used to insert kanamycin-resistance cassettes and TnphoA insertions into different locations of this region in the chromosome of wild-type V. cholerae strains. The phenotypes of these mutants showed that this DNA region is involved in MSHA production, but is not required for general extracellular protein secretion.

Amino Acid Sequence↗

PubMed2004

Molecular genetic characterization of the genomic ACTB-GLI fusion in pericytoma with t(7;12).

"Pericytoma with t(7;12)" is a newly defined soft tissue tumor characterized by fusion of the ACTB and GLI genes through the translocation t(7;12)(p22;q13). Recently, we reported the structure of the ACTB-GLI and GLI-ACTB fusion transcripts in five cases, and herein the corresponding genomic breakpoints were investigated. Overall, the findings at the DNA level corresponded well with the structure of the expressed transcripts. In three cases, the fusions were due to junction of intronic sequences, in two cases breakpoints were found in exonic sequences. In four cases the fusions corresponded to the juxtapositioning of unaltered DNA sequences, and in one case, a micro-inversion was found at the junction. All five fusions were molecularly unbalanced, including the two cases with reciprocal GLI-ACTB chimeras. Whereas large repeats or recombinase recognition sequences were not detected, sequences of shared oligonucleotides, possibly important for recombination, were found in the proximity of the respective breakpoints.

Actins↗

PubMed2006

Structural and genetic characterization of Shigella boydii type 17 O antigen and confirmation of two new genes involved in the synthesis of glucolactilic acid.

Shigella strains are human pathogens and normally identified based on their O antigens. The chemical structure and gene cluster of Shigella boydii type 17 O antigen were studied. As judged by sugar and methylation analyses along with NMR spectroscopy data, the O antigen of S. boydii type 17 has a linear trisaccharide O unit, which consists of two residues of N-acetylgalactosamine (GalNAc) and a 4-O-[(R)-1-carboxyethyl]-d-glucose (glucolactilic acid). The O antigen gene cluster of S. boydii type 17 was sequenced and genes encoding UDP-N-acetylglucosamine C4 epimerase for GalNAc synthesis, O unit flippase, O antigen polymerase, and glycosyltransferases were putatively identified based on sequence similarities and the presence of conserved motifs. Two genes, whose functions could not be clearly indicated by homology search, were confirmed to be involved in the synthesis of glucolactilic acid by mutation and structural verification of the O antigens from the mutants. To our knowledge, this is the first time that genes involved in the synthesis of glucolactilic acid have been reported. Two genes specific to S. boydii type 17 were also identified.

Amino Acid Motifs↗

PubMed2006

Characterizing genetically stable and unstable gastric cancers by microsatellites and array comparative genomic hybridization.

Gastric cancer (GCA) displays a variety of genomic aberrations, including DNA copy number alterations, microsatellite instability (MSI), and loss of heterozygosity (LOH). The main aim of the present work was to determine the copy number aberrations in tumors with and without MSI or LOH. Fifteen fresh-frozen GCA samples, 11 of the intestinal and 4 of the diffuse type, were grouped by microsatellite analysis into high-level MSI (MSI-H, n = 2), LOH (n = 5), and microsatellite stable, LOH not detected (MSS/LOH-N, n = 8) tumors. The DNA samples were subsequently analyzed by array comparative genomic hybridization with 16,000 cDNA clones. As expected, the LOH tumors showed more copy number changes; however, the frequency of small-size amplifications was similar across all tumor groups. In addition, the cDNA arrays detected two apparently single-gene amplicons, at 11q13 (CCND1) and 12p12.1 (K-RAS), the presence of which were confirmed using oligonucleotide arrays. A novel amplicon at 5q13.2 was found only in diffuse-type tumors, which were otherwise genetically stable. The results suggest that DNA copy number changes may also occur in gastric cancers that show genomic stability in microsatellite analysis.

Aged↗

PubMed2005

Genetic characterization of Vibrio cholerae isolates from Argentina by V. cholerae repeated sequences-polymerase chain reaction.

We have developed a novel typing method based on Vibrio cholerae repeat sequences (VCR) using primers directed out of the VCR sequences. To evaluate the VCR-polymerase chain reaction (PCR) as a typing system, 2 categories, efficacy and efficiency, were analyzed in 69 strains of human and environmental V. cholerae O1 toxigenic and nontoxigenic, and non-O1 strains isolated since 1992-2000 from Argentina. The discriminatory power (0.91), stability (0.95), reproducibility (1), typeability (1), rapidity, accessibility, as well ease of use, indicated that the VCR-PCR method provides an alternative useful tool for molecular epidemiology of V. cholerae. The VCR-PCR of V. cholerae isolates showed 29 patterns, of which pattern 1 represented 68% of the V. cholerae O1 isolates, supporting the hypothesis that a clone with epidemic behavior was responsible for the epidemic in Latin America. These results showed a good correlation and a better epidemiologic analysis when the results were compared in parallel with repetitive extragenic palindromic sequences-PCR. In conclusion, VCR-PCR showed excellent performance as a typing method for cholera surveillance programs.

Argentina↗

PubMed2005

Genetic characterization of the mitochondrial DNA from Lepeophtheirus salmonis (Crustacea; Copepoda). A new gene organization revealed.

The mitochondrial DNA (mtDNA) from the salmon louse, Lepeophtheirus salmonis, is 15445 bp. It includes the genes coding for cytochrome B (Cyt B), ATPase subunit 6 and 8 (A6 and A8), NADH dehydrogenase subunits 1-6 and 4L (ND1, ND2, ND3, ND4, ND4L, ND5 and ND6), cytochrome c oxidase subunits I-III (COI, COII and COIII), two rRNA genes (12S rRNA and 16S rRNA) and 22 tRNAs. Two copies of tRNA-Lys are present in the mtDNA of L. salmonis, while tRNA-Cys was not identified. Both DNA strands contain coding regions in the salmon louse, in contrast to the other copepod characterized Tigriopus japonicus, but only a few genes overlap. In vertebrates, ND4 and ND4L are transcribed as one bicistronic mRNA, and are therefore localized together. The same organization is also found in crustaceans, with the exceptions of T. japonicus, Neocalanus cristatus and L. salmonis that deviate from this pattern. Another exception of the L. salmonis mtDNA is that A6 and A8 do not overlap, but are separated by several genes. The protein-coding genes have a bias towards AT-rich codons. The mitochondrial gene order in L. salmonis differs significantly from the copepods T. japonicus, Eucalanus bungii, N. cristatus and the other 13 crustaceans previously characterized. Furthermore, the mitochondrial rRNA genes are encoded on opposite strands in L. salmonis. This has not been found in any other arthropods, but has been reported in two starfish species. In a phylogenetic analysis, using an alignment of mitochondrial protein sequences, L. salmonis groups together with T. japonicus, being distant relatives to the other crustaceans.

Animals↗

PubMed2005

Phenotypic and genetic characterization of patients with features of "nonclassic" forms of cystic fibrosis.

OBJECTIVE: To determine which features of incomplete or "nonclassic" forms of cystic fibrosis (CF) are associated with deleterious CF transmembrane conductance regulator gene ( CFTR ) mutations, and to explore other etiologies for features not associated with deleterious CFTR mutations. STUDY DESIGN: Clinical features were compared between 57 patients with deleterious mutations in each CFTR and 63 with no deleterious mutations. The Shwachman Bodian Diamond syndrome gene ( SBDS ) was sequenced to search for mutations in patients with no deleterious CFTR mutations and steatorrhea to determine if any had unrecognized Shwachman-Diamond syndrome (SDS). RESULTS: The presence of a common CF-causing mutation, absence of the vas deferens, and Pseudomona aeruginosa in the sputum correlated with the presence of two deleterious CFTR mutations, whereas sweat chloride concentration, diagnostic criteria for CF, and steatorrhea did not. However, sweat chloride concentration correlated with CFTR mutation status in patients infected with P aeruginosa. One patient had disease-causing mutations in each SBDS . CONCLUSIONS: Presence of a common CF-causing mutation, absence of the vas deferens and/or P aeruginosa infection in a patient with features of nonclassic CF are predictive of deleterious mutations in each CFTR , whereas steatorrhea in the same context is likely to have etiologies other than CF transmembrane conductance regulator (CFTR) dysfunction.

Adult↗

PubMed2006

Morphological and genetic characterization of a cultivated Cordyceps sinensis fungus and its polysaccharide component possessing antioxidant property in H22 tumor-bearing mice.

Cordyceps sinensis, one of the most precious traditional Chinese medicines, possesses the antitumor activity, antioxidant activity and the capability of modulating the immune system. In the present study, a fungus strain G1 isolated from wild C. sinensis was identified and initially characterized. A phylogenetic tree was generated based on the sequences of the internal transcribed spacer (ITS) region of related fungi. The analysis of ITS sequence showed that fungus G1 was clustered together with C. sinensis, Tolypocladium cylindrosporum and Tolypocladium inflatum in the phylogenetic tree. Both the morphological character and the ITS sequence analysis establish that fungus G1 is one of the anamorph strains of C. sinensis and belongs to Tolypocladium genus. Furthermore, the polysaccharide (PS) extracted from fungus G1 and its antioxidant activity on H22-bearing mice was investigated. H22 cells were hypodermically injected into the right oxter of each mouse after the ICR mice were treated with PS by means of gavage for 7 days. Then the same administration process continued for 9 days. At the end of the experiments, the tumor weight of each mouse was measured. Superoxide dismutase (SOD) activity and malondialdehyde (MDA) level in mouse liver, brain and serum, as well as glutathione peroxidase (GSH-Px) activity in mouse liver and brain were assayed. The results showed that the H22 tumor growth was significantly inhibited by PS. Moreover, PS significantly enhanced SOD activity of liver, brain and serum as well as GSH-Px activity of liver and brain in tumor-bearing mice. PS also significantly reduced the level of MDA in liver and brain of tumor-bearing mice.

Administration, Oral↗

PubMed2006

Genetic characterization of group A rotavirus strains circulating among children with acute gastroenteritis in Japan in 2004-2005.

A total of 752 fecal specimens collected from July 2004 to June 2005 from children with acute gastroenteritis in four localities in Japan (Maizuru, Tokyo, Sapporo, and Osaka) were screened for group A rotavirus by RT-PCR. It was found that 82 (10.9%) specimens were positive for group A rotavirus. The G-(VP7 genotypes) and P-(VP4 genotypes) types were further investigated. The P-types of 18 rotavirus strains, which could not be typed by RT-PCR, were determined by sequencing analysis. Of these, 94% (17/18) were P[8] with multiple point mutations at the VP4 primer-binding site. Another sample turned out to be a rare genotype P[9], which was closely related to feline rotavirus. The predominant genotype was G1P[8] (46.4%), followed by G3P[8] (32.9%) and G2P[4] (12.2%). A number of unusual combinations including, G1P[4] (1.2%), G2P[8] (1.2%), G3P[9] (1.2%), G1G3P[8] (1.2%), and G2G3P[8] (3.7%), were also detected. A new nomenclature of P[8] was proposed, in which worldwide rotavirus P[8] strains were classified into four sub-lineages, namely IA, IB, IIA, and IIB. A wide range of amino acid substitutions (up to 22) specific for P[8] lineages and sub-lineages were also identified. Interestingly, only short amino acid motifs located at positions 32-35, 121-135, and 195-236 of VP4 correctly defined the phylogenetic P[8] lineages and sub-lineages. Of note, at least two distinct clusters of rotavirus P[8] were co-circulating in the Japanese pediatric population studied.

Acute Disease↗

PubMed2006

Genetic characterization of Mycobacterium tuberculosis clinical isolates with deletions in the plcA-plcB-plcC locus.

SETTING: The basis for Mycobacterium tuberculosis virulence is not completely understood. Analysis of the genomic structure of clinical isolates will give information that can be related to biological activities involved in virulence. OBJECTIVE: To determine the extension of the deletion in the plcA-plcB-plcC locus of selected M. tuberculosis isolates, as well as other changes in the chromosome. DESIGN: In the present work we characterized a group of M. tuberculosis isolates devoid of the plcA-plcB-plcC locus by PCR, sequencing and microarrays. RESULTS: PCR amplification of this region demonstrated a complete lack of plcA and plcB ORF's in all of the isolates. The plcC gene was completely deleted in one of the strains (DR-689) and the other three isolates still conserved part of this ORF. The loss of lateral DNA sequences ranged from 3723 to 7646bp. An IS6110 element was present in all tested strains cases, and some isolates presented the insertion of ORF's coding for proteins homologous to the ESAT-6 and QILSS families. Genomic DNA of all the strains was extracted and analyzed with an in-house microarray system to observe loss of other genes possibly implicated in attenuated virulence. Two of the strains presented novel deletions; the rest of the isolates showed deletions already reported for other M. tuberculosis strains. DR-689, a Beijing type M. tuberculosis strain isolated in Canada, showed an IS6110 RFLP and a genomic deletion pattern similar to a San Francisco family of strains, although completely unrelated epidemiologically. CONCLUSION: Genomic changes in M. tuberculosis seem to occur in a controlled manner and they are possibly related to changes in its pathogenic properties.

Bacterial Proteins↗

PubMed2005

Comparative genetic characterization of Porcine Circovirus type 2 samples from German wild boar populations.

PCV-2 is involved in "postweaning multisystemic wasting syndrome" (PMWS), "porcine dermatitis and nephropathy syndrome" (PDNS), respiratory and reproductive disorders, and thereby plays a crucial role in today's swine production world-wide. The virus is apparently ubiquitous in domestic pigs and has also been demonstrated in wild pigs. Up to now, a characterization of PCV-2 samples from wild pigs, which might help to estimate the possible role of wild pigs as sources of domestic pig infection, has not been carried out. Spleen samples from 16 PCV-2-positive wild pigs from hunting grounds of four regions in Germany were used for the analysis of the viral genome. In one sample, the complete sequence of the genome was determined. In the other, a 742 nucleotide fragment from the highly variable capsid sequence of the ORF2 was sequenced. Analysis of the sequences led to the identification of three PCV-2 strains. One strain, representing 14 of the 16 samples, was closely related with Chinese, but not with German strains. The genome of this strain was shortened by one nucleotide by a deletion close to the end of ORF2. The deletion led to a shift of the stop-codon and to the insertion of a further codon. Two further strains differed in up to 4.7% of nucleotides and up to 10.5% of amino acids (aa). These strains were aligned with clusters of PCV-2 samples from mainly French and German domestic origin.

Amino Acid Sequence↗

PubMed2006

Genetic characterization of the first chiropteran papillomavirus, isolated from a basosquamous carcinoma in an Egyptian fruit bat: the Rousettus aegyptiacus papillomavirus type 1.

The complete genomic DNA of a novel papillomavirus (PV) was isolated from a basosquamous carcinoma on the wing of an Egyptian fruit bat (Rousettus aegyptiacus). Initial short sequences of the E1 and L1 genes of this virus were retrieved by PCR with degenerate papillomavirus-specific primers, and the entire R. aegyptiacus papillomavirus type 1 (RaPV-1) DNA was then amplified by long template PCR, cloned and sequenced with a transposon insertion method. The RaPV-1 genome counts 7970 basepairs and contains the typical papillomavirus open reading frames (ORF) (E1, E2, E4, E6, E7, L1 and L2). Based on a concatenated alignment of the E1, E2, L1 and L2 open reading frames of RaPV-1 and 46 other human and animal papillomavirus type species, a neighbor-joining phylogenetic tree was constructed. This phylogenetic analysis shows that RaPV-1 has a close-to-root position in the papillomavirus evolutionary tree. Since RaPV-1 is only distantly related to other papillomaviruses (with maximally 50% nucleotide sequence identity across the L1 open reading frame), it cannot be assigned to one of the existing papillomavirus genera and therefore represents the first member of a novel, as yet unnamed, close-to-root papillomavirus genus. This is the first time a papillomavirus has been isolated and characterized from a member of the Chiroptera order.

Animals↗

PubMed2005

Genetic characterization of Yokose virus, a flavivirus isolated from the bat in Japan.

Yokose virus (strain Oita-36) was isolated from the bat in Japan in 1971. In the present study, we determined complete nucleotide sequences of Yokose virus using RT-PCR and RACE techniques. Yokose virus genome consists of 10,857 nucleotides in length (accession no. AB114858), containing a single open reading frame (3425 amino acids) encoding 11 viral proteins. We deduced the boundaries of each protein in the polyprotein sequence according to the protein cleavage sites of other flaviviruses. The nucleotide sequences of the 5' and 3' nontranslated region (NTR) and amino acid sequences of individual proteins of the virus were compared with those of six other flaviviruses including Japanese encephalitis virus, dengue-2 virus, yellow fever virus, West Nile virus, tick-borne encephalitis virus, and Rio Bravo virus or Modoc virus. Yokose virus demonstrated the highest similarity to yellow fever virus. Yokose virus also has CS1 motif, which are well-conserved specifically in mosquito-born flaviviruses, in its 3' NTR. When a part of the NS5 amino acid sequence (345 amino acids) was compared with those of other four flaviviruses, Entebbe bat virus, Sokuluk virus, Sepik virus, and yellow fever virus, the three former viruses are more closely related to Yokose virus than yellow fever virus. Human sera from dengue-virus-infected case and yellow fever vaccine reacted with the viral proteins. Moreover, human serum from a yellow fever vaccine weakly neutralized Yokose virus. Our results suggest that there are cross-reactive antigenicities among Yokose virus and other flaviviruses.

3' Untranslated Regions↗

PubMed2006

Genetic characterization of tick-borne flaviviruses: new insights into evolution, pathogenetic determinants and taxonomy.

Here, we analyze the complete coding sequences of all recognized tick-borne flavivirus species, including Gadgets Gully, Royal Farm and Karshi virus, seabird-associated flaviviruses, Kadam virus and previously uncharacterized isolates of Kyasanur Forest disease virus and Omsk hemorrhagic fever virus. Significant taxonomic improvements are proposed, e.g. the identification of three major groups (mammalian, seabird and Kadam tick-borne flavivirus groups), the creation of a new species (Karshi virus) and the assignment of Tick-borne encephalitis and Louping ill viruses to a unique species (Tick-borne encephalitis virus) including four viral types (i.e. Western Tick-borne encephalitis virus, Eastern Tick-borne encephalitis virus, Turkish sheep Tick-borne encephalitis virus and Louping ill Tick-borne encephalitis virus). The analyses also suggest a complex relationship between viruses infecting birds and those infecting mammals. Ticks that feed on both categories of vertebrates may constitute the evolutionary bridge between the three distinct identified lineages.

Animals↗

PubMed2006

Genetic characterization of a new insect flavivirus isolated from Culex pipiens mosquito in Japan.

We found a new flavivirus that is widespread in Culex pipiens and other Culex mosquitoes in Japan. The virus isolate, named Culex flavivirus (CxFV), multiplied only in mosquito cell lines producing a moderate cytopathic effect, but did not grow in mammalian cells. The CxFV genome is single-stranded RNA, 10,834 nt in length and containing a single open reading frame encoding a polyprotein of 3362 aa with 5' and 3' untranslated regions (UTRs) of 91 and 657 nt, respectively. Phylogenetic analyses revealed that CxFV is closely related to the insect flaviviruses associated with Aedes mosquitoes, Cell fusing agent (CFA) and Kamiti River virus (KRV). The 3' UTR of CxFV contains four tandem repeats, which have sequence similarities to the two direct repeats in the CFA and KRV 3' UTRs. These results suggest that CxFV may be a new group of insect flaviviruses.

Aedes↗

PubMed2006

Genetic characterization of the Capra hircus papillomavirus: a novel close-to-root artiodactyl papillomavirus.

The healthy skin of a seven-year-old female goat (Capra hircus) was sampled with a cotton tip swab. Total genomic DNA was extracted from the sample and subjected to multiply primed rolling-circle amplification (RCA). Restriction analysis showed that the complete genome of a papillomavirus was amplified, measuring approximately 7,600 bp in length. The Capra hircus papillomavirus (ChPV-1) genome was cloned from this rolling-circle amplification product, and the complete nucleotide sequence was determined. The ChPV-1 genome counts 7,542 bp, and contains the typical papillomaviral open reading frames (ORFs). Based on a concatenated alignment of the E1, E2, L1 and L2 open reading frames of ChPV-1 and 54 other animal and human papillomavirus types, a neighbor-joining phylogenetic tree was constructed. In this tree ChPV-1 clusters with BPV-3, -4 and -6. Pairwise nucleotide sequence alignments of the L1 open reading frame of ChPV-1 with its closest relatives showed less than 60% similarity, placing the ChPV-1 in a novel genus.

Animals↗

PubMed2005

Molecular, biochemical, and genetic characterization of a female patient with Lesch-Nyhan disease.

Lesch-Nyhan disease (LND) is a rare X-linked recessive disorder caused by virtually complete deficiency of activity of the purine salvage enzyme hypoxanthine phosphoribosyltransferase (HPRT; EC 2.4.2.8). Human HPRT is encoded by a single structural gene located on the long arm of the X-chromosome (Xq26). The classical LND phenotype occurs almost exclusively in males, manifested in excessive purine production and characteristic neurological manifestations, including compulsive self-mutilation, choreoathetosis, spasticity, and occasionally developmental delay. Heterozygous females are usually phenotypically normal, due to the random inactivation of the X chromosome (Lyonization mechanism). However, six females were reported to be affected with the full biochemical and clinical manifestations of LND. All these cases were heterozygous for an HPRT mutation. Absence of transcription of the normal HPRT allele was attributed in all of them to non-random inactivation of the X chromosome carrying the normal allele. Here we describe an additional LND female, who presented with acute renal failure at the age of two months, in whom absence of transcription of the two HPRT alleles occurred due to as yet undescribed mechanism in LND females: the transcription of one HPRT allele was blocked due to a de novo X chromosome-autosome translocation 46,XX,t(X:2)(q26:p25), with a breaking point encompassing the HPRT gene locus, whereas the transcription of the normal allele was inhibited due to non-random inactivation of the second X-chromosome. Cultured fibroblasts from this patient exhibited the biochemical alterations in purine nucleotide metabolism characteristic of male LND fibroblasts.

Cells, Cultured↗