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At least 955 records · Page 53Linked to original sources
PubMed2005

Genomic analysis of the Microphthalmia locus and identification of the MITF-J/Mitf-J isoform.

The deafness-pigmentary disorder Waardenburg Syndrome Type 2 is caused by mutations in the human Microphthalmia-associated transcription factor (MITF) gene. Multiple related deafness-pigmentary disorders result from mutations in genes that regulate MITF expression or its activity. Similarly in mouse, homozygous mutations in the Mitf gene disrupt the development of melanocytes as well as retinal pigment epithelial (RPE) cells, osteoclasts, mast cells, and NK cells. Because abnormalities in Mitf/MITF function are associated with numerous inherited disorders of mouse and man, a detailed understanding of its gene structure is important for both diagnostic and structure/function analyses. While at least eight distinct isoforms of MITF/Mitf have been identified to date, each differing in their promoter and initial exon usage, the positions of these exons and their order within the locus have yet to be fully defined. In this study, we provide a detailed description of the MITF/Mitf locus, identify corresponding human and mouse isoforms, and utilize an informatics-based approach to identify a novel ninth MITF/Mitf isoform, MITF-J/Mitf-J, which we show is expressed in multiple cell types. The MITF/Mitf locus is over 200 kb in length, with strong but imperfect exon conservation between human and mouse. MITF/Mitf tissue expression data are presented from multiple datasets, including EST expression patterns and isoform-specific RT-PCR. The majority of isoforms were found to be broadly expressed, with the M- and Mc-isoforms being tissue-restricted to melanocytes and mast cells, respectively. Consequently, a detailed characterization of this complex locus may help to identify additional unknown deafness-pigmentary syndrome mutations in human kindred and permit a better understanding of tissue-regulated expression that likely underlies divergent biological functions of this factor across multiple cell types.

Animals↗
PubMed2004

Genetic and genomic analysis in model legumes bring Nod-factor signaling to center stage.

The control of host-specificity in the Rhizobium-legume symbiosis has been a topic of long-standing interest to plant biologists. By the early 1990s, biologists had deciphered the chemical signals that trigger early symbiotic responses. Flavonoids from the plant root trigger bacterial gene expression and the production of lipo-chitooligosaccharide signals (called Nod factors) that are recognized by the plant host. Genetic differences between bacterial strains modify the oligosaccharide backbone, for example by the addition of sulfate, acetate or fucose, and simultaneously alter the host-specificity of the purified Nod factor and the bacterium. Recent studies have begun to reveal the genetic and molecular basis of Nod-factor perception in legumes, a signaling system that also controls plant interactions with mycorrhizal fungi.

Fabaceae↗
PubMedDate not supplied

Selective capture of prostatic basal cells and secretory epithelial cells for proteomic and genomic analysis.

Basal cells play an undefined role in signaling the growth and differentiation of normal secretory epithelial cells in the human prostate. Because basal cells disappear during malignant transformation, we hypothesize that loss of basal cell function may have a permissive role in progression of prostate intraepithelial neoplasia into invasive carcinoma. We describe an immuno-laser capture microdissection approach to selectively capture basal cells. Using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry, we identified several protein candidates selectively expressed in microdissected basal cells. We also demonstrate that the RNA derived form this technique is an excellent source for gene-array studies. Thus, we provide evidence that proteomic and microgenomic techniques can be successfully applied to investigate the expression profiles of basal and secretory cells after immuno-capture.

Cell Transformation, Neoplastic↗
PubMed2006

Phylogenetic analysis, genome evolution and the rate of gene gain in the Herpesviridae.

We used complete sequence data from 30 complete Herpesviridae genomes to investigate phylogenetic relationships and patterns of genome evolution. The approach was to identify orthologous gene clusters among taxa and to generate a genomic matrix of gene content. We identified 17 genes with homologs in all 30 taxa and concatenated a subset of 10 of these genes for phylogenetic inference. We also constructed phylogenetic trees on the basis of gene content data. The amino acid and gene content phylogenies were largely concordant, but the amino acid data had much higher internal support. We mapped gene gain events onto the phylogenetic tree by assuming that genes were gained only once during the evolution of herpesviruses. Thirty genes were inferred to be present in the ancestor of all herpesvirus, a number smaller than previously hypothesized. Few genes of recent origin within herpesviruses could be identified as originating from transfer between virus and vertebrate hosts. Inferred rates of gene gain were heterogeneous, with both taxonomic and temporal biases. Nonetheless, the average rate of gene gain was approximately 3.5 x 10(-7) genes gained per year, which is an order of magnitude higher than the nucleotide mutation rate for these large DNA viruses.

Databases, Nucleic Acid↗
PubMed1992

cDNA cloning and genomic analysis of a new multigene family sharing common phylogenetic and expression profiles with the laminin receptor gene.

We have isolated a human laminin receptor (LR) cDNA which bears a different sequence in its 5' end with regard to the corresponding region in the regular LR mRNA. This different sequence hybridizes to a 1 kb mRNA. We have cloned a 740 bp cDNA for this transcript (cDNA 48-1). Search on sequence data bases revealed no sequence homology with known messengers or proteins. Using cDNA 48-1 in a simplified version of the protocol with which we had previously characterized the LR gene as a member of a retrogene family in mammals, we show in the present paper that the gene of this new transcript exhibits phylogenic, expression and amplification features that strickingly recall those of the LR gene.

Amino Acid Sequence↗
PubMed1999

Molecular cloning and genomic analysis of TsNTxp: an immunogenic protein from Tityus serrulatus scorpion venom.

A non-toxic protein (TsNTxP) from Tityus serrulatus scorpion venom has been shown to be an efficient immunogen and anti-TsNTxP antibodies recognize and neutralize the effect of Tityus serrulatus venom [Chávez-Olórtegui et al., 1997. Toxicon 35, 213-221]. With the purpose of studying the organization of the gene that code for this protein, we have isolated a full length cDNA clone for TsNTxP from a cDNA expression library using anti-TsNTxP antibodies. The nucleotide sequence of the gene that encodes TsNTxP was also obtained and it reveals the presence of an intron within the signal peptide sequence. The TsNTxP gene showed high degree of similarity with genes encoding toxins from scorpions of the genus Tityrus.

Animals↗
PubMed1990

Genomic analysis of T-cell receptor and immunoglobulin antigen receptor genes and breakpoint cluster regions in gastrointestinal lymphomas.

Sixteen cases of gastrointestinal B- and T-cell lymphoma were investigated for clonal rearrangements of immunoglobulin and T-cell receptor genes. In all cases the immunogenotype data corresponded well with the immunohistochemical findings, thus confirming the biologic heterogeneity of these lymphomas. Some cases could be distinguished by additional heterogeneity in their genotype which could not be detected by immunohistochemical methods. Moreover, the B-cell lymphomas were studied for the presence of the chromosomal translocations t(11;14) and t(14;18) using probes for bcl-1 and bcl-2 genes, respectively. While bcl-1 rearrangement was not present in these gastrointestinal lymphomas, one case of diffuse low-grade lymphoma of mucosa-associated lymphoid tissue and three cases of centroblastic lymphoma (diffuse large cell) could be shown to have detectable bcl-2 rearrangement.

Antigens, CD↗
PubMed2003

Genomic analysis of gene expression relationships in transcriptional regulatory networks.

From merging several data sources, we created an extensive map of the transcriptional regulatory network in Saccharomyces cerevisiae, comprising 7419 interactions connecting 180 transcription factors (TFs) with their target genes. We integrated this network with gene-expression data, relating the expression profiles of TFs and target genes. We found that genes targeted by the same TF tend to be co-expressed, with the degree of co-expression increasing if genes share more than one TF. Moreover, shared targets of a TF tend to have similar cellular functions. By contrast, the expression relationships between the TFs and their targets are much more complicated, often exhibiting time-shifted or inverted behavior. Further information is available at http://bioinfo.mbb.yale.edu/regulation/TIG/

Gene Expression Regulation↗
PubMed1996

[Pneumococcal meningitis resistant to penicillin and nosocomial transmission in pediatric hospitals confirmed by genomic analysis].

BACKGROUND: Careful epidemiological studies and sophisticated diagnostic procedures are necessary to prove that bacterial infection is nosocomial in origin. DNA finger printing method can be useful with this aim in view. CASE REPORTS: A 11 month-old girl suffered from a febrile pneumonia. She developed acute meningitis 15 days later; culture of CSF grew Streptococcus pneumoniae, serotype 23 F, resistant to beta-lactamines, erythromycin and cotrimoxazole. She died 24 hours later. Five days after this death, a 5 month-old infant hospitalized in the next bed developed an acute pulmonary infection due to the same strain with the same bacterial characteristics; this patient was cured with cefotaxime plus vancomycin and gentamicin. Randomly amplified polymorphic DNA analysis showed an identical profile of both strains. CONCLUSION: This is the first case of meningitis due to penicillin-resistant Streptococcus pneumoniae (PRSP) associated with nosocomial spread between two children in adjacent beds. This case suggests that it is necessary to isolate patients with PRSP infection during hospitalization.

Cross Infection↗
PubMed1993

[Kidney transplantation and HLA-DR compatibility evaluated by genomic analysis: one center study].

The actual effect of HLA-DR matching in renal transplantation remains controversial. Since DNA analysis has been shown to be more reliable than serological typing, a re-evaluation of the impact of DR-matching on graft prognosis is required. In this study, 224 cadaver kidney transplantations performed in our center were retrospectively matched according to Restriction Fragment Length Polymorphism DR incompatibilities and compared to prospective serological DR-matching. Transplant outcome was evaluated using graft survival, first rejection onset and rejection frequency. In 18.8% individuals, a discrepancy between serology and DNA typing for at least one antigen was noted. Serology particularly failed to type recipients (21.7%) and 43.2% of the total missed antigens were serologically "blank" or unidentified ("X") alleles. A graft survival rate of 100% after one year was observed for transplantations with no DNA DR mismatch (n = 31). Furthermore, there was a definite correlation between DNA matching and (i), the percentage of individuals with one or more than one acute rejection episode (18% and 41.8% at one year for O incompatibility and pooled 1 and 2 incompatibilities respectively, p < 0.05); (ii), the mean of acute rejection per individual (p < 0.001); and (iii), the rejection onset time (p < 0.01). No correlation between serological matching and the acute rejection episodes parameters was noted. Since HLA typing could be performed in less than 2 hrs using new molecular biology techniques, we conclude that prospective DNA typing should improve kidney transplantation outcome in the near future.

Graft Rejection↗
PubMed2003

The genomic analysis of rubella virus detected from outbreak and sporadic cases in Rio de Janeiro state, Brazil.

BACKGROUND: The molecular epidemiology of rubella virus (RV) based on the analysis of the viral E1 gene sequences indicated the existence of two genotypes that differ from each other by 8 to 10% in their nucleotide sequences: genotype I is present in Europe, North America and Asia; and genotype II is present only in Asia. OBJECTIVES: The purpose of the study was to identify the RV genotypes circulating in Brazil. STUDY DESIGN: In this study, we analysed 86 clinical samples collected between 1996 and 1999 during a rubella outbreak and from sporadic cases of rubella in Rio de Janeiro State. For the molecular characterisation of RV strains we have used PCR/nested amplification and direct sequencing of a 513-nucleotide region of the E1 gene. RESULTS: The E1 gene sequences of 14 RVs were obtained and were assigned to two lineages, both within genotype I. The percentage divergence of nucleotide sequence ranged from 3.4 to 5.1% between these two lineages. These results were in agreement with the pattern of variation observed among the sequences obtained from other lineages of RV. CONCLUSIONS: This work demonstrated that two new lineages of RV circulated simultaneously between the years 1996 and 1999 in the state of Rio de Janeiro. These results provided new approaches for monitoring the progress of vaccination efforts in Brazil.

Adolescent↗
PubMed2004

A genome analysis of endoreplication in the Drosophila ovary.

Gene amplification is used by follicle cells to increase the copy number of Drosophila chorion genes, which encode structural components of the eggshell. A new study by Claycomb et al. in this issue of Developmental Cell raises the possibility that gene amplification might also be used for the developmental patterning of the egg chamber and oocyte.

Animals↗