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At least 667 records · Page 37Linked to original sources
PubMed1999

Primate evolution of an olfactory receptor cluster: diversification by gene conversion and recent emergence of pseudogenes.

The olfactory receptor (OR) subgenome harbors the largest known gene family in mammals, disposed in clusters on numerous chromosomes. We have carried out a comparative evolutionary analysis of the best characterized genomic OR gene cluster, on human chromosome 17p13. Fifteen orthologs from chimpanzee (localized to chromosome 19p15), as well as key OR counterparts from other primates, have been identified and sequenced. Comparison among orthologs and paralogs revealed a multiplicity of gene conversion events, which occurred exclusively within OR subfamilies. These appear to lead to segment shuffling in the odorant binding site, an evolutionary process reminiscent of somatic combinatorial diversification in the immune system. We also demonstrate that the functional mammalian OR repertoire has undergone a rapid decline in the past 10 million years: while for the common ancestor of all great apes an intact OR cluster is inferred, in present-day humans and great apes the cluster includes nearly 40% pseudogenes.

Animals↗
PubMed2025

Sample Preparation of Caenorhabditis elegans for GC-MS-Based Metabolomics in Toxicity Assessment.

The nematode Caenorhabditis elegans, widely recognized as a model organism due to its ease of breeding and well-characterized genomes, boasts complete digestive, reproductive, and endocrine systems, as well as conserved signaling pathways shared with mammals. It has become an invaluable resource for metabolomics research, particularly in examining responses to chemical or environmental factors and toxicity assessments. In this article, we provide detailed, step-by-step protocols for cultivating C. elegans and conducting metabolomics analyses, specifically focusing on sample preparation for GC-MS analysis in response to toxic compound treatments. We highlight the critical choice of extraction solvent, introducing two representative systems for extracting metabolites from C. elegans.

Animals↗
PubMed1995

The expression of an abundant transmitting tract-specific endoglucanase (Sp41) is promoter-dependent and not essential for the reproductive physiology of tobacco.

In angiosperms the interactions between the secretory matrix of the stylar transmitting tract and the growing pollen tubes have central roles in determining a successful fertilization. Sp41 is a major glycosylated component of the soluble proteins of the transmitting tract matrix and exhibits (1-3)-beta-glucanase activity. It is a member of the pathogenesis-related protein superfamily, but shows developmental regulation as opposed to pathogen induction. In order to investigate the mechanisms regulating Sp41 expression, we isolated and characterized genomic clones corresponding to the sp41 alpha gene. Sp41 alpha contains an intervening sequence localized between the sequences encoding for a putative signal peptide and the mature protein. A fragment of 2.5 kb that lies 5' to the coding region of the gene was sufficient to confer transmitting tract specific expression to a beta-glucuronidase reporter gene in transgenic tobacco plants. The sp41 transcripts have unusually long 5'-untranslated sequences. The leader sequences contain small open reading frames, include secondary structures, and may be involved in post-transcriptional regulation. A possible function for Sp41 in reproductive physiology was tested by monitoring tobacco plants transformed with antisense stylar sp41 alpha RNA: Transgenic antisense plants with immunologically and enzymatically undetectable levels of (1-3)-beta-glucanase were obtained and their offspring analyzed. The progeny plants did not show any detectable phenotypic modifications as they had a normal flower morphology and were fully fertile.

Amino Acid Sequence↗
PubMed1992

The structure and regulation of homeologous tobacco endochitinase genes of Nicotiana sylvestris and N. tomentosiformis origin.

The fungicidal class I chitinases are believed to be important in the induced defense response of plants. We isolated and partially characterized genomic clones representing two members, CHN14 and CHN50, of the gene subfamily encoding these enzymes in Nicotiana tabacum L. cv. Havana 425. The coding sequences of genes CHN14, CHN50, and CHN48, which was cloned earlier, are identical at 79-95% of the positions. Tobacco is an amphidiploid species derived from ancestors most closely related to the present-day species N. sylvestris and N. tomentosiformis. Southern analysis of genomic DNA, comparison of deduced amino acid sequences, and partial sequencing of the purified enzymes suggest that the gene pairs CHN48/CHN50 and CHN14/CHN14' are homeologues. Gene CHN48, which encodes chitinase A (Mr ca. 34 kDa), and gene CHN14 are derived from N. tomentosiformis; whereas gene CHN50, which encodes chitinase B (Mr ca. 32 kDa), and gene CHN14' are derived from N. sylvestris. Class I chitinases are induced in leaves of plants treated with ethylene or infected with the fungal pathogen Cercospora nicotianae and in cultured cells transferred to medium without added auxin and cytokinin. RNase protection assays show that under these conditions transcripts encoded by the homeologues CHN48 and CHN50 account for greater than 90% of the total chitinase mRNA. The less abundant transcript, CHN48, consistently showed a greater degree of induction than CHN50. Expression of the homeologues CHN14 and CHN14' represented less than 10% of the total chitinase mRNA. They showed a pattern of hormonal regulation similar to CHN48 and CHN50, but transcripts of these genes were not detected in leaves infected with C. nicotianae. Therefore the two sets of homeologues are regulated in the same way by hormones and respond differently to infection by a pathogen.

Amino Acid Sequence↗
PubMed2003

Genomic organization and expression profile of the human and mouse WAVE gene family.

The WAVE gene family, which contains three members, has been shown to play a major role in the actin polymerization and cytoskeleton organization processes. We have identified the WAVE3 gene from Chromosome (Chr) 13q12, as being involved in one of the breakpoints of a t(1:13)(q21:q12) reciprocal translocation, in a patient with ganglioneuroblastoma (Sossey-Alaoui et al. 2002; Oncogene 21: 5967-5974). We have also reported the cloning of the mouse Wave3. During our analysis of the human gene map, we also noted that WAVE2 maps to Chr region lp35-36, which frequently undergoes loss of heterozygosity and deletion in advanced stage neuroblastoma. These data clearly indicate a possible involvement of the WAVE genes in the pathogenesis of neuroblastoma. In this study, we report the complete genomic organization and expression profile of the three human WAVE genes and their mouse orthologs. We show that the WAVE genes have distinctive expression patterns in both adult and fetal human and mouse tissues. We also show a high level of conservation between these genes, in both the nucleotide and protein sequences. We finally show that the genomic structure is highly conserved among these genes and that the mouse Wave genes map to chromosome regions that have synteny in the human genome. The gene content in these syntenic regions is also conserved, suggesting that the WAVE genes are derived from a common ancient ancestor by genome duplication. The genomic characterization and expression analysis of the WAVE genes provide the basis towards understanding the function of these genes. It also provides the first steps towards the development of mouse models for the role of the WAVE genes in actin and cytoskeleton organization in general, and in the development of neuroblastoma in particular.

Amino Acid Sequence↗
PubMed2026

Artificial Intelligence for Diagnosis, Risk Stratification, and Prognosis of Neuroblastoma - A Systematic Review and Meta-Analysis.

PURPOSE: To synthesizes evidence on artificial intelligence (AI) performance in neuroblastoma (NB) diagnosis, risk stratification, prognosis, and genomic characterization. MATERIALS AND METHODS: A systematic review and meta-analysis was conducted following PRISMA 2020 guidelines (PROSPERO: CRD42024539475) across five databases. Meta-analyses used random-effects models with logit-transformed Area Under the Curve (AUCs) and cluster-robust standard errors. AI models were classified as Machine Learning Models (MLM) or Hybrid Nomograms (HN) based on their construction methodology. RESULTS: Of 3,742 articles identified, 53 were included. MLMs demonstrated higher point estimates than radiologists in differential diagnosis (AUC: 0.87 vs. 0.83), though this difference was not statistically significant and carried substantial uncertainty. HNs achieved stronger performance in risk stratification (AUC: 0.87). AI-derived nomograms (AUC: 0.9) and gene signatures (AUC: 0.8) outperformed conventional prognostic markers descriptively. Chemotherapy response prediction remained below clinical utility thresholds across all model types. Only 33.9% of models reported calibration and 24.5% underwent external validation. CONCLUSIONS: AI demonstrates proof-of-concept across multiple NB clinical domains. However, clinical adoption remains premature given persistent gaps in external validation, calibration, dataset size, and pediatric-specific model development. Future studies should test these models prospectively in multicenter pediatric cohorts, ideally through COG or SIOPEN, using shared definitions for diagnosis, risk group, treatment response, and survival outcomes.

Humans↗
PubMed2026

First report of tomato spotted wilt virus (Orthotospovirus tomatomaculae) and phytoplasma in China aster and development of duplex PCR, LAMP, and qPCR assays for rapid detection.

UNLABELLED: China aster (Callistephus chinensis) is an economically important ornamental crop widely cultivated for cut flowers and landscaping. During field surveys conducted in three districts of Karnataka, India, China aster plants exhibiting chlorotic and necrotic ring spots, leaf deformation, and witches' broom symptoms were collected and analyzed to determine the causal agents. Mechanical inoculation of symptomatic leaf sap onto cowpea (Vigna unguiculata cv. C-152) produced characteristic chlorotic and necrotic ring spots on newly emerging leaves indicating the presence of an infectious viral agent. Serological assay by DAC-ELISA followed by RT-PCR confirmed the presence of tomato spotted wilt virus (TSWV, Orthotospovirus tomatomaculae) in symptomatic plants. Similarly the plants exhibiting witches' broom symptoms tested positive for phytoplasma infection using universal and Nested primers PCR assays targeting the 16S rRNA gene. Sequence analysis of TSWV CP gene revealed more than 97% nucleotide identity with TSWV isolates reported from India and other countries. Based on these results, one representative isolate was selected for complete genome sequencing. The complete sequences of the L, M, S RNA segements were amplified cloned, and sequenced showing more than 97% nucleotide identity with global TSWV isolates available in database. Sequence analysis of 16S rRNA gene of the phytoplasma associated with witches' broom symptoms was identified as 'Candidatus Phytoplasma australasiaticum' belonging to the 16SrII-D subgroup, sharing 99.2% nucleotide identity with previously reported isolates. Phylogenetic analysis further supported the placement of both the TSWV and phytoplasma isolates within their respective taxonomic groups. To facilitate rapid and sensitive diagnosis, quantitative PCR (qPCR) and RT-LAMP assays were developed for TSWV detection. In addition a duplex PCR assay was optimized for simultaneous detection of TSWV and phytoplasma from infected China aster plants in a single reaction. This study represents the first reports of the complete genome characterization of TSWV and phytoplasma infection in China aster in India along with the development of sensitive qPCR, RT-LAMP, and duplex PCR assays for rapid detection of these pathogens providing valuable tools for disease diagnosis, epidemiological studies. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s13205-026-05038-w.

China aster↗
PubMed1992

DNA fingerprints of Bombyx mori L. Testing of genotypic variability of parthenogenetic strains.

A comparative analysis of the total cellular DNA in certain parthenogenetic specimens of the silkworm (Bombyx mori), produced from the females of the parthenogenetic strains by two types of parthenogenesis, has been performed through the application of the DNA fingerprinting method based on M13 phage DNA as a hybridization probe. It has been shown that parental specimens and their genetically identical off-springs produced through ameiotic parthenogenesis have identical patterns of hybridization with the hypervariable DNA fragments. The off-springs produced through the meiotic type of parthenogenesis have individual-specific patterns of hybridization, revealing a high level of polymorphism of individual genotypes. The results obtained testify to the effectiveness and reliability of this promising method for identification of genotypic variability, marking and genomic characterization of parthenogenetic clones in the silkworm.

Animals↗
PubMed1993

Molecular cloning of the human alpha 2(IX) collagen cDNA and assignment of the human COL9A2 gene to chromosome 1.

Type IX collagen, a heterotrimer of alpha 1(IX), alpha 2(IX) and alpha 3(IX) chains, is a cartilage-specific fibril-associated collagen. In the process of characterizing genomic clones for the mouse alpha 2(IX) collagen gene four pairs of oligonucleotide primers designed for amplification of murine exon sequences were also utilized to construct cDNA clones for human alpha 2(IX) collagen spanning > 90% of the coding region. The amino acid and nucleotide sequence identities between human and chick are 78% and 71%, respectively. Localization of the COL9A2 gene to human chromosome 1 was subsequently performed using a panel of DNAs from human/rodent somatic cell hybrids.

Amino Acid Sequence↗
PubMed1996

Cloning and characterization of the rat neurotensin receptor gene promoter.

The 5'-terminal region of the rat neurotensin receptor (NTR) gene was isolated and characterized. Genomic Southern analysis revealed that the NTR gene occurs as a single copy in the rat haploid genome. The upstream putative promoter region did not contain canonical TATA or CAAT boxes but has a consensus sequence for the transcription factor Sp1. This promoter is embedded in a large G + C-rich domain with characteristics of an CpG island. Transfection experiments using neurotensin receptor-luciferase fusion genes demonstrated that the 5'-flanking sequence functions as a strong promoter in the NG-108-15 cell. Deletion analysis suggested the presence of a core promoter (-470 to -662) that drives the minimal expression of the NTR gene.

Animals↗
PubMed1992

A nuclear gene encoding beta-amylase of sweet potato.

A nuclear AmyB gene from sweet potato encoding beta-amylase (beta Amy) that is abundant in tuberous roots and inducible in other organs by an exogenous supply of sucrose or polygalacturonic acid, was isolated and characterized. Genomic Southern blot hybridization, restriction maps of independently isolated phage lambda genomic clones, and the nucleotide sequence of AmyB compared with that of the cDNA, all suggested that beta Amy of sweet potato is encoded by a gene that is present in a single copy per haploid genome. In the sequence of AmyB, the sequence that is identical to that of the cDNA was split into seven exons by six introns, and the transcription of this gene starts from multiple sites 26 to 30 bp downstream from a potential TATA-box sequence, 5'-TATATAA. In the 5'-upstream region of AmyB, there are sequences homologous to those conserved in the 5'-upstream regions of genes encoding sporamin, which are regulated similarly to AmyB. The 5'-upstream region of AmyB also contains sequences to which several previously known plant nuclear factors bind.

Amino Acid Sequence↗
PubMed1995

Sequence and developmental regulation of the gene that encodes the Dictyostelium discoideum L3 ribosomal protein.

We have isolated and characterized genomic and cDNA recombinant plasmids that encode the Dictyostelium discoideum (Dd) ribosomal protein L3 (rpL3). Genomic plasmids were identified using a probe derived from the Saccharomyces cerevisiae TCM1 gene, that encodes the yeast rpL3. The DdL3 gene contains two introns and encodes a protein 398 amino acids in length that shows a high degree of homology to the conserved rpL3 protein of both lower and higher eukaryotes. During development, both the pattern of accumulation of DdL3 mRNA and changes in its translational activity are identical to those observed for other r-protein mRNAs.

Amino Acid Sequence↗
PubMed1991

The exon organization of the triple-helical coding regions of the human alpha 1(VI) and alpha 2(VI) collagen genes is highly similar.

The alpha 1(VI) and alpha 2(VI) chains, two of the three constituent chains of type VI collagen, are highly similar in size and domain structure. They are encoded by single-copy genes residing in close proximity on human chromosome 21. To study the evolution of the type VI collagen genes, we have isolated and characterized genomic clones coding for the triple-helical domains of the human alpha 1(VI) and alpha 2(VI) chains, which consist of 336 and 335 amino acid residues, respectively. Nucleotide sequencing indicates that, in both genes, the exons are multiples of 9 bp in length (including 27, 36, 45, 54, 63, and 90 bp) except for those encoding for regions with triple-helical interruptions. In addition, the introns are positioned between complete codons. The most predominant exon size is 63 bp, instead of 54 bp as seen in the fibrillar collagen genes. Of particular interest is the finding that the exon structures of the alpha 1(VI) and alpha 2(VI) genes are almost identical. A significant deviation is that a segment of 30 amino acid residues is encoded by two exons of 54 and 36 bp in the alpha 1(VI) gene, but by a single exon of 90 bp in the alpha 2(VI) gene. The exon arrangement therefore provides further evidence that the two genes have evolved from tandem gene duplication. Furthermore, comparison with the previously reported gene structure of the chick alpha 2(VI) chain indicates that the exon structure for the triple-helical domain of the alpha 2(VI) collagen is strictly conserved between human and chicken.

Amino Acid Sequence↗
PubMed1991

Testosterone metabolism in brain cells and membranes.

The central nervous system (CNS) is considered a target structure for the action of all the classes of hormonal steroids produced by the organism. Well-characterized genomic and less well-understood membrane mechanisms of action are probably involved in the steroid modulation of brain activities. Moreover, some classes of steroids need to be converted into "active" metabolites before interacting with their effector systems. In particular, testosterone (T) exerts many of its effects after conversion to 5 alpha-dihydrotestosterone (DHT) and estrogens. The CNS possesses both the 5 alpha-reductase, the enzyme which produces DHT and the aromatase which transforms T into estrogens; however, the relative role and distribution of these enzymes in the various structural components of the CNS has not been clarified so far. The 5 alpha-reductase has been found to be present in high concentrations in brain white matter structures because these are particularly rich in myelin membranes, to which the enzymatic activity appears to be associated. This membrane localization might suggest a possible involvement of steroidal 5 alpha-reduced metabolites in membrane-mediated events in the CNS. Moreover, the distribution of 5 alpha-reductase was studied in neurons, astrocytes and oligodendrocytes isolated from the brain of male rats by density gradient ultracentrifugation, as well as in neurons and glial cells grown in culture. The aromatase activity was also evaluated in neurons and glial cells grown in culture and in isolated oligodendrocytes. Among the three cell types isolated, neurons appear to be more active than oligodendrocytes and astrocytes, respectively, in converting T into DHT. Also, in cell culture experiments, neurons are more active in forming DHT than glial cells. Only neurons possess aromatase activity, while glial cells are apparently unable to aromatize T.

Animals↗
PubMed2005

Chromosome abnormalities in 10 lung cancer cell lines of the NCI-H series analyzed with spectral karyotyping.

The karyotypes of 10 lung cancer cell lines of the NCI-H series were analyzed with spectral karyotyping (SKY): 7 non-small lung cancer (NSCLC) lines and 3 small cell lung cancer (SCLC) lines. Modal chromosome number ranged from 42 (NCI-H2171) to 72 (NCI-H2126). All lines showed at least six structural abnormalities, and most had amplifications visible as double minutes or homogeneously staining regions (HSRs). Four reciprocal translocations were found: t(1;17)(p10;p10) in NCI-H82, t(3;6)(q24;q21) and t(12;17)(p10;p10) in NCI-H2009, and a complex t(2;6) in NCI-H1437. NCI-H1770 had a striking HSR containing many copies of the NMYC region. Karyotypes showed a wide range of relationship between numerical and structural change. Two of the lines showed little numerical change but many structural rearrangements (NCI-H209 with mode 46, but 12 rearrangements, and NCI-H2009 with mode 48 but 27 rearrangements). A second group had karyotypes that appeared to have evolved by unbalanced translocation leading to proportionate loss of chromosomes, with or without endoreduplication. In other lines, notably NCI-H2122, the structurally abnormal chromosomes appeared to have been added to a near-diploid karyotype. The karyotypes contribute to a full genomic characterization of these lines, almost all of which have matching normal lymphoblastoid cell lines.

Adenocarcinoma↗
PubMed2004

Mosquito immune responses against malaria parasites.

Anopheline mosquitoes are the major vectors of human malaria. Mosquito-parasite interactions are a critical aspect of disease transmission and a potential target for malaria control. Mosquitoes vary in their innate ability to support development of the malaria parasite, but the molecular mechanisms that determine vector competence are poorly understood. This area of research has been revolutionized by recent advances in the mosquito genome characterization and by the development of new tools for functional gene analysis.

Animals↗
PubMed2005

A monoclonal antibody-based ELISA allows discrimination between responses induced by bovine herpesvirus subtypes 1 (BoHV-1.1) and 2 (BoHV-1.2).

Bovine herpesvirus type 1 (BoHV-1) has distinct subtypes according to genomic characterization. Immune responses induced by BoHV-1 subtype 1 (BoHV-1.1) are not distinguishable from those induced by BoHV-1 subtype 2 (BoHV-1.2) through conventional serological methods. In the present report, an enzyme linked immunosorbent assay is described that allows discrimination between immune responses in cattle immunized with either subtype, based on a monoclonal antibody that recognizes specifically the amino-terminal region of glycoprotein C (gC) on BoHV-1.1 strains, thus not reacting with BoHV-1.2a. The test displayed a sensitivity of 92%, specificity of 90% and a good correlation with serum neutralization tests on samples from BoHV-1.1-immunized calves (kappa = 0.799). The test may be useful to provide new insights into the roles played by each of these two subtypes in the epidemiology of BoHV-1 infections.

Animals↗