Biomedical subjects

L Paulin

Publications and source records attributed to L Paulin.

At least 37 records · Page 2Linked to original sources

PubMed1999

Phylogeny and diversity of Bradyrhizobium strains isolated from the root nodules of peanut (Arachis hypogaea) in Sichuan, China.

Twenty-two rhizobial strains isolated from the root nodules of two Chinese peanut cultivars (Arachis hypogaea L. Tianfu no. 3 and a local cultivar) growing at four different sites in the Sichuan province, Southwest China, were characterized by growth rate, rep-PCR, PCR-RFLP of 16S rDNA, partial sequencing of ribosomal genes, and fatty acid-methyl ester analysis (FAME), and compared with strains representing Bradyrhizobium japanicum, B. elkanii and other unclassified Bradyrhizobium sp. All peanut isolates from Sichuan were bradyrhizobia. Dendrograms constructed using the rep-PCR fingerprints grouped the strains mainly according to their geographic and cultivar origin. Based on PCR-RFLP and partial sequence analysis of 16S rDNA it appears that peanut bradyrhizobial strains from Sichuan are similar to peanut strains from Africa and Israel, and closely related to B. japonicum. In contrast, analysis of FAME data using two-dimensional principal component analysis indicated that Bradyrhizobium sp. (Arachis) were similar to, but slightly different from other bradyrhizobia. The presence and level of fatty acid 16:1 w5c was the distinguishing feature. The results of PCR-RFLP of the 16S rRNA gene, the partial sequence analysis of 16S rDNA, and FAME were in good agreement.

Arachis↗

PubMed1999

Ectodysplasin, a protein required for epithelial morphogenesis, is a novel TNF homologue and promotes cell-matrix adhesion.

In the mouse Tabby (Ta) mutant and human X-linked anhidrotic ectodermal dysplasia (EDA) syndrome development of several ectodermal organs such as hair, teeth, and sweat glands is impaired. The gene behind Tabby and EDA has been cloned, and several alternative transcripts have been isolated. The protein product named ectodysplasin had no obvious function or prominent homology to other known gene products apart from a short collagen-like sequence. We have isolated two novel Ta transcripts which are variants of the longest isoform of Tabby, named Ta-A. In situ hybridizations revealed Ta-A to be the major transcript in the developing embryo. It was detected in the endoderm of early embryos and subsequently in specific locations in the neuroepithelium and ectoderm. Unexpectedly, sequence analysis of the most C-terminal domain of Ta revealed that ectodysplasin is a novel member of the tumor necrosis factor (TNF) ligand superfamily. Mouse ectodysplasin was biochemically and functionally characterized, and shown to be a glycosylated, oligomeric type II membrane protein (N-terminus inside), all characteristics typical to TNF-like proteins. Members of the TNF family are critically involved in host defence and immune response often mediating either apoptosis or cell survival. Expression of Ta in several epithelial cell lines did not result in prominent changes in cell morphology and did not promote apoptosis. Instead, it was shown to promote cell adhesion to extracellular matrix, a function consistent with its postulated role in epithelial-mesenchymal interactions regulating the development of ectodermal appendages. Ectodysplasin is the first TNF-like signaling molecule described known to be required for epithelial morphogenesis.

Amino Acid Sequence↗

PubMed1999

Sinorhizobium arboris sp. nov. and Sinorhizobium kostiense sp. nov., isolated from leguminous trees in Sudan and Kenya.

SDS-PAGE of total bacterial proteins was applied to the classification of 25 Sudanese and five Kenyan strains isolated from the root nodules of Acacia senegal and Prosopis chilensis. Twenty strains were also studied by multilocus enzyme electrophoresis (MLEE) and the whole 16S rRNA gene was sequenced from two strains representing the two major clusters. These results, together with the previously reported numerical taxonomy analysis, pulsed-field gel electrophoresis studies, DNA-DNA dot-blot hybridization, genomic fingerprinting using repetitive sequence-based PCR, DNA base composition analysis, DNA-DNA reassociation analysis, partial sequencing of the 16S rRNA gene and RFLP analysis of the amplified 16S rRNA gene, showed that all 30 strains belong to the genus Sinorhizobium. Two of the strains grouped with Sinorhizobium saheli and seven with Sinorhizobium terangae, while the rest did not cluster with any of the established species. The majority of the strains formed two phenotypically and genotypically distinct groups and we therefore propose that these strains should be classified as two new species, Sinorhizobium arboris sp. nov. and Sinorhizobium kostiense sp. nov.

Acacia↗

PubMed1999

An efficient DNA sequencing strategy based on the bacteriophage mu in vitro DNA transposition reaction.

A highly efficient DNA sequencing strategy was developed on the basis of the bacteriophage Mu in vitro DNA transposition reaction. In the reaction, an artificial transposon with a chloramphenicol acetyltransferase (cat) gene as a selectable marker integrated into the target plasmid DNA containing a 10.3-kb mouse genomic insert to be sequenced. Bacterial clones carrying plasmids with the transposon insertions in different positions were produced by transforming transposition reaction products into Escherichia coli cells that were then selected on appropriate selection plates. Plasmids from individual clones were isolated and used as templates for DNA sequencing, each with two primers specific for the transposon sequence but reading the sequence into opposite directions, thus creating a minicontig. By combining the information from overlapping minicontigs, the sequence of the entire 10,288-bp region of mouse genome including six exons of mouse Kcc2 gene was obtained. The results indicated that the described methodology is extremely well suited for DNA sequencing projects in which considerable sequence information is on demand. In addition, massive DNA sequencing projects, including those of full genomes, are expected to benefit substantially from the Mu strategy.

Amino Acid Sequence↗

PubMed1998

Mutation analysis of the glial cell line-derived neurotrophic factor gene in Parkinson's disease.

Glial cell line-derived neurotrophic factor (GDNF) is a potent survival factor for nigrostriatal dopaminergic, central cholinergic, and motoneurons. GDNF also prevents the neuronal loss in experimental animal models for Parkinson's disease (PD). We have now investigated the GDNF gene for possible mutations in a group of nonfamilial PD and other patients. By cleavase fragment length polymorphism (CFLP) analysis and direct sequencing of the full coding region of GDNF gene we found a novel GDNF sequence variant in 1 of 30 PD patients. The alteration does not change the predicted amino acid sequence and it was also found in 1 of 20 patients without PD, suggesting that it represents a polymorphism in the gene. No other sequence variations were found. We conclude therefore that mutations in the GDNF coding region are not commonly contributing to the pathogenesis of PD.

Alzheimer Disease↗

PubMed1998

Phylogeny of Rhizobium galegae with respect to other rhizobia and agrobacteria.

PCR-RFLP with nine restriction enzymes was applied to the 16S and 23S rRNA genes of 42 rhizobial and agrobacterial strains to determine the phylogenetic position of Rhizobium galegae and increase the understanding of the evolution of ribosomal operons. The strains were selected based on previous phylogenetic studies. PCR primers were designed so that they amplified a 2.3 kb fragment of the 23S rRNA gene (excluding the B8 loop). Universal primers rD1 and fD1 were used to amplify the full-length 16S rRNA. The RFLP analysis resulted in 27 and 32 different restriction patterns for 16S and 23S, respectively. The RFLP patterns were transformed to genetic distances and dendrograms were constructed from the data using the unweighted pair group method with averages. The shapes of the dendrograms derived from the analysis of the 16S and 23S rRNA genes correlated well, with only a few strains having different positions. The 23S tree generally had deeper branching than the 16S tree, allowing better discrimination between species and strains. The combined data from the two analyses described 36 genotypes. The eight R. galegae strains formed a homogeneous cluster in all dendrograms. The RFLP analysis was confirmed by partial sequence analysis of the 16S rRNA gene (the first 800 bp), which correlated well with full-length 16S rRNA sequence analysis. The 16S data placed R. galegae near the genus Agrobacterium with Agrobacterium vitis as its nearest neighbour, whereas in the 23S and the combined dendrograms it showed closer affinity to the genus Rhizobium.

Base Sequence↗

PubMed1998

Characterization and reclassification of an aromatic- and chloroaromatic-degrading Pseudomonas sp., strain HV3, as Sphingomonas sp. HV3.

Phylogenetic analyses of 16S rRNA gene sequences showed that the Gram-negative aromatic- and chloroaromatic-degrading Pseudomonas sp. strain HV3 carrying the mega-plasmid pSKY4 belongs to the genus Sphingomonas. The 16SrRNA sequence is most related to Sphingomonas chlorophenolica strains ATCC 33790(T) (98.5%) and SR3 (98.4%) and Sphingomonas sp. SS86 (98.4%). The G+C content was 64 mol%, and the DNA-DNA hybridization-based relative homology of strain HV3 to the S. chlorophenolica ATCC 33790(T) and S. chlorophenolica RA2 was 59.6% and 35.9%, respectively. The results showed that although strain HV3 is related to S. chlorophenolica it differs in certain characteristics. It is therefore proposed to reclassify Pseudomonas sp. strain HV3 as Sphingomonas sp. HV3.

Base Sequence↗

PubMed1998

Separation among species of Mycobacterium terrae complex by lipid analyses: comparison with biochemical tests and 16S rRNA sequencing.

Fatty acids, alcohols, and mycolic acid cleavage products were determined for 13 ATCC strains and 24 clinical isolates, which were initially identified by biochemical and growth characteristics as the Mycobacterium terrae complex. The clinical isolates were also analyzed by partial sequencing of the 16S rRNA gene, which divided them into five genetic entities, M. triviale (three strains), M. terrae (four strains), M. nonchromogenicum sensu stricto (seven strains), Mycobacterium sp. strain MCRO 6 (seven strains), and Mycobacterium sp. strain 31958 (one strain). After acidic methanolysis, secondary alcohols were a characteristic feature in all members of the M. terrae complex but M. triviale. In addition to the prominent secondary alcohols, 2-octadecanol and 2-eicosanol, two previously unidentified alcohols, 2-(8,15-dimethyl)docosenol and 2-(8,17-dimethyl)tetracosenol, were detected in M. nonchromogenicum, Mycobacterium sp. strain MCRO 6, and Mycobacterium sp. strain 31958. Only 2-(8,17-dimethyl)tetracosenol was detected in trace amounts in M. terrae. Genetic differences were associated with differences in phenotypic characteristics, including growth at 42 degrees C and pyrazinamidase production. Based on fatty acid and alcohol composition and biochemical and genetic characteristics, M. non-chromogenicum and Mycobacterium sp. strains MCRO 6 and 31958 were found to be a closely related group, named the M. nonchromogenicum complex. Detected genetic variations associated with phenotypic characteristics may indicate further species separation of this complex. In conclusion, the results of gas-liquid chromatography fatty acid analysis, combined with those of a Tween 80 test, enable identification of the species of the M. terrae complex and their separation from other nonpigmented slowly growing mycobacteria.

Amidohydrolases↗

PubMed1998

The minisatellite expansion mutation in EPM1: resolution of an initial discrepancy. Mutatations in brief no. 186. Online.

Mutations in the cystatin B (CSTB) gene underlie progressive myoclonus epilepsy of Unverricht-Lundborg type (EPM1) (Pennacchio et al., 1996). We previously described an unstable minisatellite expansion mutation in the putative promoter region of CSTB that accounts for the majority of EPM1 patients. Sequencing of a genomic lambda clone, generated from a Finnish EPM1 patient homozygous for an enlarged restriction fragment, revealed a 15- to 18-mer minisatellite repeat expansion (Virtaneva et al., 1997). Later, sequencing of plasmid clones generated from Swiss and French patients revealed a dodecamer repeat expansion (Lalioti et al., 1997a). By restriction enzyme analysis of our original patient clone and a clone generated from an Italian patient, we now show that the expansion is neither a 15-mer nor an 18-mer contrary to our initial results. Moreover, direct sequencing of the Finnish patient clone with Pfu exo polymerase confirmed that the expanded repeat is a dodecamer. Based on this finding and additional experiments, we suggest that the discrepancy between the two studies was due to errors caused by the combination of native Pfu polymerase and modified guanosine deaza-7-dGTP used in the PCR reaction.

Cystatin B↗

PubMed1997

Novel organization of catechol meta-pathway genes in Sphingomonas sp. HV3 pSKY4 plasmid.

Sphingomonas sp. strain HV3 (formerly Pseudomonas sp. HV3), which degrades aromatics and chloroaromatics, harbors a mega-plasmid, pSKY4. A sequenced 4 kb fragment of the plasmid reveals a novel gene organization for catechol meta-pathway genes. The putative meta operon starts with the cmpF gene encoding a 2-hydroxymuconic semialdehyde hydrolase. The gene has a 6 bp overlap with the previously characterized ring-cleavage gene, catechol 2,3-dioxygenase, cmpE. Downstream of cmpE is a 429 bp open reading frame of unknown function. Gene cmpC, encoding a 2-hydroxymuconic semialdehyde dehydrogenase, starts 44 bp further downstream. It has the highest homology to 2-hydroxymuconic semialdehyde dehydrogenases of dmp and xyl pathways and to XylC from the marine oligotroph Cycloclasticus oligotrophus. The gene organization is different from other known meta pathways. This is the first report of organization of plasmid-encoded meta-pathway genes in the genus Sphingomonas.

Amino Acid Sequence↗

PubMed1997

Cloning and analysis of the cDNA encoding the rod G-protein transduction alpha, beta1 and gamma1 subunits from the canine retina.

The canine (Canis familiaris) retinal rod transducin (G(T)) alpha, beta1 and gamma1 subunits were sequenced. Cloning of the cDNAs was accomplished by polymerase chain reaction (PCR) using degenerate and wild type retinal cDNA libraries as templates. The deduced amino acid sequences were highly similar to rod transducins from other species: G(T alpha) differed by 5 amino acids from the corresponding human sequence, whereas beta1 and gamma1 were identical to human sequences. The coding sequence of rod transducin was evaluated as a possible cause for the recessively inherited retinal rod-cone degeneration: there were no nucleotide differences between the wild type and retinal degenerate strains.

Amino Acid Sequence↗

PubMed1997

The sequence of a 36.7 kb segment on the left arm of chromosome IV from Saccharomyces cerevisiae reveals 20 non-overlapping open reading frames (ORFs) including SIT4, FAD1, NAM1, RNA11, SIR2, NAT1, PRP9, ACT2 and MPS1 and 11 new ORFs.

A 36,688 bp fragment from the left arm of chromosome IV of saccharomyces cerevisiae was sequenced. Sequence analysis identified 20 complete non-overlapping open reading frames (ORFs) of at least 100 amino acids. Nine of these correspond to previously identified and sequenced genes: SIT4/PH1, FAD1, NAM1/MTF2, RNA11, SIR2/MAR1, NAT1/AAA1, PRP9, ACT2 and MPS1/RPK1. Three ORFs show homology to previously sequenced genes. One ORF exhibits a hypothetical yabO/yceC/YfiI family signature and one has the ATP-dependent helicase signature of the DEAD and DEAH box families. Six ORFs show no appreciable homology to any proteins in the database. One of these is identical to yeast expressed sequence tags and therefore corresponds to and expressed gene. In addition, two partial ORFs and 11 ORFs that are totally internal and are not likely to be functional were detected.

Amino Acid Sequence↗

PubMed1997

Deletions of the low density lipoprotein receptor gene underlying familial hypercholesterolaemia: screening by polymerase chain reaction using pooled DNA and blood samples.

We evaluated the feasibility of methods based on the polymerase chain reaction (PCR) and non-automated or automated gel electrophoresis to detect clinically important DNA deletions in pooled DNA and blood samples. Two common low density lipoprotein (LDL) receptor mutations causing familial hypercholesterolaemia (FH) in the Finnish population were easily identified in pools corresponding to 20 individuals. One of these mutations (FH-North Karelia) deletes seven nucleotides from exon 6 of the LDL receptor gene. PCR amplification of DNA samples from the heterozygous patients with the FH-North Karelia gene results in the formation of DNA heteroduplexes, which markedly improves mutation detection. These studies show the applicability of semi-automated PCR techniques in the screening of DNA deletions and demonstrate the clinical diagnostic usefulness of heteroduplex formation.

Alleles↗

PubMed1997

Exclusion of the p75 neurotrophin receptor gene as a candidate gene for Meckel syndrome.

Nerve growth factor receptor p75 (NGFR) gene was investigated as a potential candidate gene in Meckel syndrome (MKS) because of its important role in embryonic development, chromosomal localization adjacent to the MKS locus and Meckel syndrome-resembling findings in knock-out mice phenotype. The sequence analysis of the coding region of the gene revealed one polymorphism but no potential disease mutation. Physical mapping of the critical chromosomal region finally showed that the NGFR gene lies outside the MKS locus.

Abnormalities, Multiple↗

PubMed1997

Apolipoprotein A-IFin. Dominantly inherited hypoalphalipoproteinemia due to a single base substitution in the apolipoprotein A-I gene.

We have identified a large kindred with severe serum HDL cholesterol deficiency. The proband, a 65-year-old woman, had greatly diminished concentrations of serum HDL cholesterol (0.19 mmol/L) and apolipoprotein (apo) A-I (21.9 mg/dL). HDL cholesterol and apo A-I levels were similarly reduced in all affected family members, while apo A-II levels were about half of those in the nonaffected family members. Pedigree analysis suggested a dominant inheritance pattern of the phenotype. Sequence analysis of the exons and exon-intron boundaries of the apo A-I gene revealed heterozygosity for a single T-to-G point mutation substituting arginine for leucine at residue 159 of the mature apo A-I protein (apo A-IFin). The T-to-G substitution destroys an Fsp I cleavage site, permitting direct polymerase chain reaction/restriction enzyme analysis of the mutation. All the affected family members were shown to be heterozygous for the apo A-IFin mutation. Isoelectric focusing revealed the presence of the mutant apo A-IFin protein in both serum and HDL of the affected subjects. Functional consequences of the mutation were examined by expressing the mutated and wild-type apo A-I cDNAs in COS-7 cells. The mutant apo A-I mRNA had a size similar to that of the normal mRNA, and both mutant and wild-type apo A-I proteins were secreted into the cell media. In vivo kinetic studies of apo A-I revealed increased catabolism in affected subjects. In conclusion, we describe a novel point mutation of the apo A-I gene, apo A-IFin, causing a dominantly negative phenotype as regards serum HDL levels, possibly due to increased catabolism of apo A-I.

Adolescent↗

PubMed1997

The introns of the canine rod opsin gene show higher sequence homology to the human than to the rodent introns.

Using genomic DNA from late-onset retinal degenerate and wild type Labrador Retrievers as templates and canine exon-specific oligonucleotides as primers in polymerase chain reaction, all four introns of opsin were cloned and sequenced. Dot-matrix comparisons were made for human, murine and canine introns. Selected sequences containing either intronic or coding sequences were aligned and used for phylogenetic relationship analysis. The opsin gene introns are conserved between the human, the mouse and the dog with regards to number and length. In addition there is an astonishingly high degree of sequence homology between the second and fourth introns. Introns 2(1277 bp in dog) and 4 (863 bp in dog) are 72% and 71% homologous to the human introns, and 57% and 52% homologous to the mouse introns, respectively. The coding sequence (CDS) of the dog shows 93% homology to human CDS and 88% homology to mouse CDS. A phylogenetic analysis of the intronic sequences 2 and 4 confirms the higher relatedness between dog and human than between mouse and human opsin genes. As there are good reasons to believe that the primate and rodent lineages are closer to each other than to the Canis familiaris, there must be some functional constraints on the evolution of human and dog opsins.

Animals↗

PubMed1996

Characterization of genes required for pilus expression in Pseudomonas syringae pathovar phaseolicola.

Nonpiliated, phage phi 6-resistant mutants of Pseudomonas syringae pv. phaseolicola were generated by Tn5 transposon mutagenesis. A P. syringae pv. phaseolicola LR700 cosmid library was screened with Tn5-containing EcoRI fragments cloned from nonpiliated mutants. The cosmid clone pVK253 complemented the nonpiliated mutant strain HB2.5. A 3.8-kb sequenced region spanning the Tn5 insertion site contained four open reading frames. The transposon-inactivated gene, designated pilP, is 525 bp long, potentially encoding a 19.1-kDa protein precursor that contains a typical membrane lipoprotein leader sequence. Generation of single mutations in each of the three remaining complete open reading frames by marker exchange also resulted in a nonpiliated phenotype. Expression of this gene region by the T7 expression system in Escherichia coli resulted in four polypeptides of approximately 39, 26, 23, and 18 kDa, in agreement with the sizes of the open reading frames. The three genes upstream of pilP were designated pilM (39 kDa), pilN (23 kDa), and pilO (26 kDa). The processing of the PilP precursor into its mature form was shown to be inhibited by globomycin, a specific inhibitor of signal peptidase II. The gene region identified shows a high degree of homology to a gene region reported to be required for Pseudomonas aeruginosa type IV pilus production.

Amino Acid Sequence↗

PubMed1996

Elevation of cGMP with normal expression and activity of rod cGMP-PDE in photoreceptor degenerate labrador retrievers.

Cyclic guanosine 3',5'-monophosphate (cGMP) levels were determined in retinas from a strain of Labrador Retrievers with inherited retinal dystrophy manifesting at early stages of retinal differentiation. The cGMP contents of dystrophic retinas of dogs from 1 to 4 months of age (n = 7) were significantly higher (p = 0.001) than in age-matched controls of the same breed (n = 11). Ultrastructure along the vertical retinal meridian was studied in developing retinas and findings were related to those of age-matched wild-type controls of the same breed. Slow central to peripheral progression of degeneration was observed in affected dogs. No differences were found in total cGMP-phosphodiesterase (PDE) activity, in PDE subunit composition as determined by Western blotting of 2-month-old homozygote affected retinas, or in the amino acid sequence deduced from the nucleotide sequence of the PDE beta-subunit as compared to controls. This model of photoreceptor degeneration thus is the first case of an apparent abnormality of cGMP metabolism that is not associated with a defect in the PDE catalytic subunits, and it is also the first reported model not associated with severe developmental abnormalities and rapid degeneration.

3',5'-Cyclic-GMP Phosphodiesterases↗