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PubMed2003

Association study of oestrogen receptor alpha gene polymorphism and suicidal behaviours in major depressive disorder.

OBJECTIVE: Gender comparison in epidemiological studies has consistently demonstrated a greater prevalence for major depressive disorders (MDD) in females. Several lines of evidence have implicated oestrogen pathways in this gender difference. Furthermore, there is evidence that attempted suicides are more frequent in women. A population-based association study was used to test the hypothesis that the genetic variants ( II and I polymorphisms) of the oestrogen receptor alpha gene (ER-alpha) confer susceptibility to MDD. METHODS: The ER-alpha was genotyped for 154 patients with MDD and 226 controls in a Chinese population. RESULTS: Statistical analysis showed a significant difference in the II genotype and allele frequencies between the female MDD patients and the female controls ( P=0.010 and P=0.004, respectively). However, no significant differences in ER-alpha genotype or allele frequencies were found between male MDD patients and male controls. Furthermore, the ER-alpha genotypes were not associated with suicide-attempt history for MDD cases. CONCLUSIONS: Our results suggest that the ER-alpha may play a role in the susceptibility of MDD in females.

Base Sequence↗
PubMed1998

Stable binding to E2F is not required for the retinoblastoma protein to activate transcription, promote differentiation, and suppress tumor cell growth.

The retinoblastoma tumor suppressor protein (pRB) can inhibit cell cycle progression and promote differentiation. pRB interacts with a variety of transcription factors, including members of the E2F and C-EBP protein families and MyoD, and can either repress or activate transcription depending on the promoter under study. These biological and biochemical activities of pRB have been mapped previously to a core domain, referred to as the pRB pocket. Using a panel of synthetic pRB pocket mutants, we found that the acute induction of a G1/S block by pRB is linked to its ability to both bind to E2F and to repress transcription. In contrast, these functions were not required for pRB to promote differentiation, which correlated with its ability to activate transcription in concert with fate-determining proteins such as MyoD. All tumor-derived pRB mutants tested to date failed to bind to E2F and did not repress transcription. Despite an inability to bind to E2F, pRB mutants associated with a low risk of retinoblastoma, unlike high-risk mutants, retained the ability to activate transcription and promote differentiation. Thus, the pRB pocket participates in dual tumor suppressor functions, one linked to cell cycle progression and the other to differentiation control, and these functions can be genetically and mechanistically dissociated.

Carrier Proteins↗
PubMed2001

An oligonucleotide fingerprint normalized and expressed sequence tag characterized zebrafish cDNA library.

The zebrafish is a powerful system for understanding the vertebrate genome, allowing the combination of genetic, molecular, and embryological analysis. Expressed sequence tags (ESTs) provide a rapid means of identifying an organism's genes for further analysis, but any EST project is limited by the availability of suitable libraries. Such cDNA libraries must be of high quality and provide a high rate of gene discovery. However, commonly used normalization and subtraction procedures tend to select for shorter, truncated, and internally primed inserts, seriously affecting library quality. An alternative procedure is to use oligonucleotide fingerprinting (OFP) to precluster clones before EST sequencing, thereby reducing the re-sequencing of common transcripts. Here, we describe the use of OFP to normalize and subtract 75,000 clones from two cDNA libraries, to a minimal set of 25,102 clones. We generated 25,788 ESTs (11,380 3' and 14,408 5') from over 16,000 of these clones. Clustering of 10,654 high-quality 3' ESTs from this set identified 7232 clusters (likely genes), corresponding to a 68% gene diversity rate, comparable to what has been reported for the best normalized human cDNA libraries, and indicating that the complete set of 25,102 clones contains as many as 17,000 genes. Yet, the library quality remains high. The complete set of 25,102 clones is available for researchers as glycerol stocks, filters sets, and as individual EST clones. These resources have been used for radiation hybrid, genetic, and physical mapping of the zebrafish genome, as well as positional cloning and candidate gene identification, molecular marker, and microarray development.

Animals↗
PubMed2004

Arbitrary viewpoint video synthesis from multiple uncalibrated cameras.

We propose a method for arbitrary view synthesis from uncalibrated multiple camera system, targeting large spaces such as soccer stadiums. In Projective Grid Space (PGS), which is a three-dimensional space defined by epipolar geometry between two basis cameras in the camera system, we reconstruct three-dimensional shape models from silhouette images. Using the three-dimensional shape models reconstructed in the PGS, we obtain a dense map of the point correspondence between reference images. The obtained correspondence can synthesize the image of arbitrary view between the reference images. We also propose a method for merging the synthesized images with the virtual background scene in the PGS. We apply the proposed methods to image sequences taken by a multiple camera system, which installed in a large concert hall. The synthesized image sequences of virtual camera have enough quality to demonstrate effectiveness of the proposed method.

Algorithms↗
PubMed1991

Methylation and expression of human pepsinogen genes in normal tissues and their alteration in stomach cancer.

In normal human tissues, pepsinogen A mRNA was expressed only in the fundic mucosa of the stomach, whereas pepsinogen C mRNA was expressed in all regions of the stomach mucosa and also in the proximal duodenal mucosa. The distributions of these mRNAs were consistent with those of pepsinogens A and C in the gastroduodenal mucosa. Methylation analysis of DNAs from normal tissues with methylation-sensitive restriction enzymes, HpaII and HhaI, revealed that pepsinogen A and C genes are hypomethylated in tissues producing pepsinogens A and C, suggesting a role of DNA methylation in the regulation of the differential expression of the genes for the two human pepsinogens during normal differentiation. In stomach cancer tissues and cancer cell lines, the expressions of the pepsinogen genes were decreased or lost, in good accordance with their pepsinogen productions. No gross structural changes of the pepsinogen genes were observed in these cancers, but the methylation patterns of the pepsinogen genes were found to be altered in different ways in different cancers. The functional significance of the altered methylation is unknown; however, these results suggest that considerable heterogeneity of the methylation patterns occurs in human stomach cancers.

Blotting, Northern↗
PubMed1997

Mapping genes located on human chromosomes 2 and 12 to porcine chromosomes 15 and 5.

Informative microsatellites associated with two genes on HSA12 (lysozyme, LYZ; tumour necrosis factor receptor, TNFR) and one gene on HSA2 (glutamic acid decarboxylase 1, GAD1) were mapped in the US Meat Animal Research Center (MARC) swine reference population and the physical assignment of a-lactalbumin (LALBA) was determined. A comparative map for HSA2 and HSA12 with SSC15 and SSC5, respectively, was developed by combining the results from this study with published type I loci mapped in both species. One rearrangement between HSA2 and SSC15 was detected while the number of rearrangements between HSA12 and SSC5 were numerous. These results indicated that conservation of synteny does not imply a conservation of gene order and that additional type I markers need to be mapped in the pig to fully understand the chromosomal rearrangements that occurred during the evolution of mammals.

Animals↗
PubMed2006

Familial adenomatous polyposis.

Familial adenomatous polyposis (FAP) is an autosomal-dominant colorectal cancer syndrome, caused by a germline mutation in the adenomatous polyposis coli (APC) gene, on chromosome 5q21. It is characterized by hundreds of adenomatous colorectal polyps, with an almost inevitable progression to colorectal cancer at an average age of 35 to 40 yr. Associated features include upper gastrointestinal tract polyps, congenital hypertrophy of the retinal pigment epithelium, desmoid tumors, and other extracolonic malignancies. Gardner syndrome is more of a historical subdivision of FAP, characterized by osteomas, dental anomalies, epidermal cysts, and soft tissue tumors. Other specified variants include Turcot syndrome (associated with central nervous system malignancies) and hereditary desmoid disease. Several genotype-phenotype correlations have been observed. Attenuated FAP is a phenotypically distinct entity, presenting with fewer than 100 adenomas. Multiple colorectal adenomas can also be caused by mutations in the human MutY homologue (MYH) gene, in an autosomal recessive condition referred to as MYH associated polyposis (MAP). Endoscopic screening of FAP probands and relatives is advocated as early as the ages of 10-12 yr, with the objective of reducing the occurrence of colorectal cancer. Colectomy remains the optimal prophylactic treatment, while the choice of procedure (subtotal vs proctocolectomy) is still controversial. Along with identifying better chemopreventive agents, optimizing screening of extracolonic cancers and applying new radiological and endoscopic technology to the diagnosis and management of extracolonic features are the major challenges for the future.

Adenomatous Polyposis Coli↗
PubMed1999

DNA alterations in human oral squamous cell carcinomas detected by restriction landmark genomic scanning.

Genetic abnormalities in human oral squamous cell carcinomas (OSCC) were examined using restriction landmark genomic scanning (RLGS), a method of two-dimensional gel analysis allowing detection of amplifications and other aberrations in genomic DNA. DNAs from 11 oral tumours as well as from contiguous normal squamous epithelium, were cleaved with the restriction enzyme Not I, [32p] end-labeled and electrophoretically size-fractionated. Following a second digestion employing Hinf I, the further fragmented DNA was again electrophoretically separated. Five fragments/spots were found amplified in at least 64% (7/11) (chromosome nos. 4, 9-12 or 22) of carcinomas, with one of these spots amplified in 100% (chromosome no. 4) of tumour samples. In addition, six other spots were frequently reduced in at least 55% (chromosome nos. 15 or 9-12) of tumour tissues. Further characterization of these common changes is needed to determine if they represent important alterations in OSCC.

Carcinoma, Squamous Cell↗
PubMed2002

A polytene chromosome analysis of the Anopheles gambiae species complex.

Field-collected specimens of all known taxa in the Anopheles gambiae complex were analyzed on the basis of chromosome inversions with reference to a standard polytene chromosome map. The phylogenetic relationships among the seven described species in the complex could be inferred from the distribution of fixed inversions. Nonrandom patterns of inversion distribution were observed and, particularly on chromosome arm 2R, provided evidence for genetically distinct populations in A. gambiae, A. arabiensis, and A. melas. In A. gambiae from Mali, stable genetic differentiation was observed even in populations living in the same region, suggesting a process of incipient speciation which is being confirmed by studies with molecular markers. The possible role of chromosome differentiation in speciation of the A. gambiae complex and in the emergence of distinct chromosomal forms within the nominal species is discussed in relation to human malaria.

Africa↗
PubMed1999

Photosynthetic bradyrhizobia from Aeschynomene spp. are specific to stem-nodulated species and form a separate 16S ribosomal DNA restriction fragment length polymorphism group.

We obtained nine bacterial isolates from root or collar nodules of the non-stem-nodulated Aeschynomene species A. elaphroxylon, A. uniflora, or A. schimperi and 69 root or stem nodule isolates from the stem-nodulated Aeschynomene species A. afraspera, A. ciliata, A. indica, A. nilotica, A. sensitiva, and A. tambacoundensis from various places in Senegal. These isolates, together with 45 previous isolates from various Aeschynomene species, were studied for host-specific nodulation within the genus Aeschynomene, also revisiting cross-inoculation groups described previously by D. Alazard (Appl. Environ. Microbiol. 50:732-734, 1985). The whole collection of Aeschynomene nodule isolates was screened for synthesis of photosynthetic pigments by spectrometry, high-pressure liquid chromatography, and thin-layer chromatography analyses. The presence of puf genes in photosynthetic Aeschynomene isolates was evidenced both by Southern hybridization with a Rhodobacter capsulatus photosynthetic gene probe and by DNA amplification with primers defined from photosynthetic genes. In addition, amplified 16S ribosomal DNA restriction analysis was performed on 45 Aeschynomene isolates, including strain BTAi1, and 19 reference strains from Bradyrhizobium japonicum, Bradyrhizobium elkanii, and other Bradyrhizobium sp. strains of uncertain taxonomic positions. The 16S rRNA gene sequence of the photosynthetic strain ORS278 (LMG 12187) was determined and compared to sequences from databases. Our main conclusion is that photosynthetic Aeschynomene nodule isolates share the ability to nodulate particular stem-nodulated species and form a separate subbranch on the Bradyrhizobium rRNA lineage, distinct from B. japonicum and B. elkanii.

Bradyrhizobium↗
PubMed2005

Different foreign genes incidentally integrated into the same locus of the Streptococcus suis genome.

Some strains of Streptococcus suis possess a type II restriction-modification (RM) system, whose genes are thought to be inserted into the genome between purH and purD from a foreign source by illegitimate recombination. In this study, we characterized the purHD locus of the S. suis genomes of 28 serotype reference strains by DNA sequencing. Four strains contained the RM genes in the locus, as described before, whereas 11 strains possessed other genetic regions of seven classes. The genetic regions contained a single gene or multiple genes that were either unknown or similar to hypothetical genes of other bacteria. The mutually exclusive localization of the genetic regions with the atypical G+C contents indicated that these regions were also acquired from foreign sources. No transposable element or long-repeat sequence was found in the neighboring regions. An alignment of the nucleotide sequences, including the RM gene regions, suggested that the foreign regions were integrated by illegitimate recombination via short stretches of nucleotide identity. By using a thermosensitive suicide plasmid, the RM genes were experimentally introduced into an S. suis strain that did not contain any foreign genes in that locus. Integration of the plasmid into the S. suis genome did not occur in the purHD locus but occurred at various chromosomal loci, where there were 2 to 10 bp of nucleotide identity between the chromosome and the plasmid. These results suggest that various foreign genes described here were incidentally integrated into the same locus of the S. suis genome.

Animals↗
PubMed1992

Restriction endonuclease analysis and ribotyping differentiate genital and nongenital strains of Bacteroides ureolyticus.

Thirty-three clinical isolates from male nongonococcal urethritis and 28 isolates from soft tissue infections and ulcers were identified as Bacteroides ureolyticus by conventional bacteriological tests and were compared with five reference strains of the species. Whole-cell proteins from these clinical isolates and the reference strains were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The majority of the strains from the two sources could be divided into five different groups, named phenons I to V; phenons I to IV have been described previously by others, while phenon V has been described recently by us. Digestion of chromosomal DNA from 16 of the clinical isolates (including strains representative of each of the five SDS-PAGE phenons) and the five reference strains was attempted with restriction endonucleases EcoRI, PstI, SmaI, and HindIII. After electrophoresis in agarose gels, good digestion was observed with HindIII only, and 12 different banding patterns (restriction endonuclease analysis [REA] profiles) were obtained for the 19 strains digested; one nongonococcal urethritis isolate and one reference strain did not show any digestion. From the agarose gels, HindIII-digested fragments of DNA were transferred to nylon membranes by use of vacuum blotting and subjected to hybridization with 32P-labelled 16S-23S rRNA from Escherichia coli. The resultant pattern of bands (ribotypes), which depends on the restriction fragment length polymorphisms in the rRNA genes, was used as a measure of genomic variation within the species. In total, 13 different ribotypes were obtained for the 19 strains. For some strains, good correlation was achieved among the SDS-PAGE phenons, REA profiles, and ribotypes. However, for others, REA analysis and ribotyping were able to discriminate between strains which shared the same SDS-PAGE phenon. Interestingly, these two techniques of DNA characterization were able to differentiate between isolates from the genital tract and those associated with soft tissue infections and ulcers.

Bacterial Proteins↗
PubMed1997

Distribution of Acinetobacter species on human skin: comparison of phenotypic and genotypic identification methods.

At least 19 genomic species are recognized as constituting the genus Acinetobacter. However, little is known about the natural reservoirs of the various members of the genus. An epidemiological study was therefore performed to investigate the colonization with Acinetobacter spp. of the skin and mucous membranes of 40 patients hospitalized in a cardiology ward and 40 healthy controls. Single samples were obtained once from each of nine different body sites, i.e., forehead, ear, nose, throat, axilla, hand, groin, perineum, and toe web. Identification of Acinetobacter isolates was achieved by using phenotypic properties and was compared to identification by amplified ribosomal DNA restriction analysis. Selected isolates were further investigated with sodium dodecyl sulfate-polyacrylamide gel electrophoresis, ribotyping, and DNA-DNA hybridization. Plasmid profile analysis was used for epidemiological typing. Thirty patients (75%) and 17 controls (42.5%) were found to be colonized with Acinetobacter spp., and the colonization rates of patients increased during their hospital stay. The most frequently isolated species were Acinetobacter lwoffii (47%), A. johnsonii (21%), A. radioresistens (12%), and DNA group 3 (11%). In contrast, A. baumannii and DNA group 13TU, the most important nosocomial Acinetobacter spp., were found only rarely on human skin (0.5 and 1%, respectively) and their natural habitat remains to be defined. A good correlation between phenotypic and genotypic methods for identification of Acinetobacter spp. was observed, and only two isolates could not be assigned to any of the known DNA groups.

Acinetobacter↗
PubMed2000

Acquisition and colonization stability of Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis in children.

The presence of Porphyromonas gingivalis has been shown to be a risk factor for periodontitis in adults, and Actinobacillus actinomycetemcomitans has been implicated as a pathogen in early-onset periodontitis. Both species have been shown to establish stable colonization in adults. In cross-sectional studies, both A. actinomycetemcomitans and P. gingivalis have been detected in over one-third of apparently healthy children. Information on the stability of colonization with these organisms in children could help to elucidate the natural history of the development of periodontitis. For this purpose, samples previously collected from a cohort of 222 children between the ages of 0 and 18 years and previously examined for the presence of P. gingivalis with a PCR-based assay were examined for the presence of A. actinomycetemcomitans. It was detected in 48% of subjects and, like P. gingivalis, was found at similar frequencies among children of all ages (P = 0.53), suggesting very early initial acquisition. One hundred one of the original subjects were recalled after 1 to 3 years to determine the continuing presence of both A. actinomycetemcomitans and P. gingivalis. The prevalence of both species remained unchanged at resampling. However, in most children both species appeared to colonize only transiently, with random concordance between the results of the first and second sampling. Stability of colonization was unrelated to age for A. actinomycetemcomitans, but P. gingivalis was more stable in the late teenage years.

Actinobacillus Infections↗
PubMed1986

Nucleotide sequence and protein overproduction of bacteriophage T4 thioredoxin.

The bacteriophage T4 thioredoxin gene was cloned and physically mapped to 47.6 kilobases from the reference BamHI site. The DNA sequence is consistent with that reported from earlier protein sequence studies. The gene was subcloned into a lambda pL overexpression vector which allowed for the isolation of approximately 5 mg/liter.

Bacterial Proteins↗
PubMed1990

Prevalence of antibodies to human papillomavirus type 8 in human sera.

The epidermodysplasia verruciformis-associated human papillomavirus type 8 (HPV-8) poses a high risk for malignant conversion of skin lesions in patients with epidermodysplasia verruciformis. For seroepidemiological studies, the HPV-8 open reading frames for E1, E2, E4, E6, E7, and L1 were bacterially expressed as beta-galactosidase fusion proteins, which were purified by preparative gel electrophoresis. Cleavage with the protease FXa at the engineered recognition site separated the beta-galactosidase polypeptide part from the viral polypeptide. Western blot analysis of 445 serum samples from a randomly selected population with the entire L1 as antigen revealed HPV-8-specific immunoglobulin G antibodies in 20% of the samples. The percentage of positive sera did not significantly differ in different age groups. In some sera, we could also detect immunoglobulin M antibodies. The use of two shortened L1 polypeptides as antigen indicated that there are at least two reactive epitopes in the case of HPV-8 L1. Several sera contained antibodies to the early proteins E1, E2, E4, and E7. E1 and E7 were predominantly detected by sera which were negative for L1. In one case, we found antibodies to E6. Two of four sera of patients with epidermodysplasia verruciformis reacted with HPV-8 L1. The prevalence of anti-HPV-8-L1 antibodies in patients with malignant melanomas was comparable to that in the normal population (27.8%) but was significantly higher in patients with cervical cancer (37.5%), basaliomas (40%), and squamous cell skin carcinomas (72.7%) and in immunocompromised patients with Hodgkin's disease (47.7%).

Antibodies, Viral↗
PubMed1991

BHRF1, the Epstein-Barr virus gene with homology to Bc12, is dispensable for B-lymphocyte transformation and virus replication.

The Epstein-Barr virus (EBV) BHRF1 open reading frame is abundantly expressed early in the lytic replication cycle. BHRF1 is also transiently expressed in some latently infected cell lines in the absence of expression of other lytic cycle proteins. BHRF1 shares distant, but significant, colinear primary amino acid sequence homology to Bc12, a cellular gene strongly implicated in the evolution of follicular lymphoma. The experiments reported here used a molecular genetic approach to examine the role of BHRF1 in EBV infection. Isogenic EBV recombinants having either wild-type BHRF1 or a null mutation due to a translational stop signal in place of the 24th BHRF1 codon were used to infect primary B lymphocytes. The BHRF1 mutant recombinants did not differ from the wild type in their ability to infect and transform the growth of primary B lymphocytes, to replicate in the resultant lymphoblastoid cell lines, or to initiate a second round of primary cell transformation. Deletion of the entire BHRF1 open reading frame did not destroy the ability of the mutant virus to maintain cell growth transformation. The significance of these findings with regard to the role of BHRF1 in EBV infection is discussed.

B-Lymphocytes↗