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PubMed2006

VNTRDB: a bacterial variable number tandem repeat locus database.

Variable number tandem repeat-PCR (VNTR-PCR) is a novel method developed for molecular typing of microorganisms. This method has proven useful in epidemiological studies in medical microbiology. Although hundreds of bacterial genomes have been sequenced, variable number tandem repeats (TRs) derived from comparative genome analyses are scarce. This may hamper their application to the surveillance of bacteria in molecular epidemiology. Here, we present a freely accessible variable number tandem repeat database (VNTRDB) that is intended to be a resource for helping in the discovery of putatively polymorphic tandem repeat loci and to aid with assay design by providing the flanking sequences that can be used in subsequent PCR primer design. In order to reveal possible polymorphism, each TR locus was obtained by comparing the sequences between different sets of bacterial genera, species or strains. Through this comparison, TRs which are unique to a genus can also be identified. Moreover, a visualization tool is provided to ensure that the copy number and locus length of repeats are correct. The VNTRDB is available at http://vntr.csie.ntu.edu.tw/.

Bacteria↗
PubMed2026

Periplasmic SacB as a robust counter-selection tool for genome engineering in the polyploid bacterium Zymomonas mobilis.

UNLABELLED: The alpha-proteobacterium Zymomonas mobilis exhibits exceptional ethanologenic physiology, which makes it a traditional alcoholic beverage producer and a promising chassis for biofuel production. Although genetic tools for this organism have expanded in recent years, a fundamental aspect of its chromosome organization remains to be understood. In particular, Z. mobilis has been suggested to exhibit polyploidy, but this feature is not fully confirmed because of discrepancies among studies reporting the copy number of chromosomes. Here, we tagged the chromosome-partitioning protein ParB with a fluorescent marker to visualize its cellular localization and estimate chromosome copy number in individual cells. Imaging showed that Z. mobilis exhibits several distinctive ParB foci throughout the cytoplasm and an accumulated focus at the pole, indicating that a single Z. mobilis cell contains >5 copies of the chromosome at the oriC regions. We then sought to establish an efficient counter-selection system, which is crucial for engineering multiple copies of the chromosome. We assessed the efficacy of levan-sucrase (SacB) toxicity in Z. mobilis. We found that, despite Z. mobilis secreting a native extracellular sucrase SacB, heterologous periplasmically localized Bacillus subtilis SacB rendered Z. mobilis cells sensitive to sucrose. We successfully used this effect for counter-selection when deleting and inserting targeted DNA sequences into the Z. mobilis genome. Together, this work provides important insights and tools for advancing Z. mobilis genetics and its biotechnological applications. IMPORTANCE: Zymomonas mobilis is a promising industrial bacterium with the capacity to convert sugars into ethanol at nearly maximum theoretical yield. With its expanding use in industrial applications, it is crucial to clarify if individual Z. mobilis cells carry multiple copies of the chromosome, as this has important implications for genome engineering. Two previous studies have used quantitative PCR to address this question, but their reported chromosome copy numbers varied widely from 20 to 100. Here, we used a cell biological approach to estimate the copy number and confirmed that a single Z. mobilis cell possesses multiple copies. In addition, we show that a SacB-based counter-selection works in Z. mobilis, enabling efficient and complete mutation of all chromosome copies.

Zymomonas↗
PubMed2005

Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling.

BACKGROUND: The completion of the sequencing of human, mouse and rat genomes and knowledge of cross-species gene homologies enables studies of differential gene expression in animal models. These types of studies have the potential to greatly enhance our understanding of diseases such as liver cancer in humans. Genes co-expressed across multiple species are most likely to have conserved functions. We have used various bioinformatics approaches to examine microarray expression profiles from liver neoplasms that arise in albumin-SV40 transgenic rats to elucidate genes, chromosome aberrations and pathways that might be associated with human liver cancer. RESULTS: In this study, we first identified 2223 differentially expressed genes by comparing gene expression profiles for two control, two adenoma and two carcinoma samples using an F-test. These genes were subsequently mapped to the rat chromosomes using a novel visualization tool, the Chromosome Plot. Using the same plot, we further mapped the significant genes to orthologous chromosomal locations in human and mouse. Many genes expressed in rat 1q that are amplified in rat liver cancer map to the human chromosomes 10, 11 and 19 and to the mouse chromosomes 7, 17 and 19, which have been implicated in studies of human and mouse liver cancer. Using Comparative Genomics Microarray Analysis (CGMA), we identified regions of potential aberrations in human. Lastly, a pathway analysis was conducted to predict altered human pathways based on statistical analysis and extrapolation from the rat data. All of the identified pathways have been known to be important in the etiology of human liver cancer, including cell cycle control, cell growth and differentiation, apoptosis, transcriptional regulation, and protein metabolism. CONCLUSION: The study demonstrates that the hepatic gene expression profiles from the albumin-SV40 transgenic rat model revealed genes, pathways and chromosome alterations consistent with experimental and clinical research in human liver cancer. The bioinformatics tools presented in this paper are essential for cross species extrapolation and mapping of microarray data, its analysis and interpretation.

Animals↗
PubMed2000

Visual pigments of African cichlid fishes: evidence for ultraviolet vision from microspectrophotometry and DNA sequences.

We have found evidence for ultraviolet visual capabilities in a Lake Malawi cichlid fish, Metriaclima zebra. Microspectrophotometry of single cones revealed a visual pigment with peak sensitivity at 368+/-4 nm. M. zebra also expresses a putative ultraviolet opsin gene whose sequence is closely related to the SWS-1 opsin for other fishes. Several other African cichlids have a functional copy of this UV gene in their genomic DNA, but do not appear to express this gene as adults. These results suggest that ultraviolet vision is important for some cichlid fishes. UV wavelengths should therefore be included in future studies of cichlid vision, behavior and color patterns.

Amino Acid Sequence↗
PubMedDate not supplied

Z-DNA immunoreactivity in rat tissues.

Recently, it has been shown that natural and synthetic deoxynucleotide polymers can adopt a left-handed helical structure (termed Z-DNA) in appropriate conditions (see, for example, refs 1 and 2 and the references therein). In contrast to the more familiar right-handed B-DNA, Z-DNA is strongly immunogenic, and polyclonal and monoclonal antibodies against Z-DNA have been elicited. By using such antibodies, immunoreactivity for Z-DNA has been detected in the polytene chromosomes of two dipteran species, in the macronucleus of a ciliated protozoon, and in certain plant nuclei (cited in ref. 11). In view of the possible importance of Z-DNA as a genomic regulatory signal, it would be highly desirable to know whether Z-DNA also occurs in mammals. We have therefore initiated an immunohistochemical study of various rat tissues by using three antisera specific for Z-DNA, and the peroxidase-antiperoxidase technique for visualization of tissue-bound antibodies. Here we demonstrate that the nuclei of many, but not all, types of rat cells exhibit Z-DNA immunoreactivity, suggesting that Z-DNA may exist naturally in mammalian chromatin.

Animals↗
PubMed2026

Role of OPRM1 A118G polymorphism in tramadol analgesia following third molar surgery: a pharmacogenomic study.

BACKGROUND: The OPRM1 A118G (rs1799971) polymorphism has been implicated in interindividual variability in opioid analgesic response, but its influence on tramadol efficacy remains uncertain. This study evaluated the association between OPRM1 A118G and postoperative analgesic response to tramadol following mandibular third molar surgery. METHODS: In this prospective pharmacogenomic study, 53 adults undergoing impacted mandibular third molar extraction were enrolled. Genomic DNA was analyzed for OPRM1 A118G (rs1799971) using amplification refractory mutation system polymerase chain reaction (ARMS-PCR). All procedures were performed under 2% lignocaine with adrenaline. Tramadol (50 mg) was administered after the onset of postoperative pain. Pain intensity was assessed using the Visual Analogue Scale (VAS) and Short-Form McGill Pain Questionnaire at 2, 4, and 6 hours. The primary outcome was summed pain intensity difference (SPID, 2-6 hours). RESULTS: Genotype frequencies were in Hardy-Weinberg equilibrium. No significant association was observed between OPRM1 genotype and SPID, VAS reduction, Pain Rating Index change, or responder status during the 6-hour observation period (all p > 0.05). CONCLUSION: OPRM1 A118G was not significantly associated with early tramadol analgesic response following third molar surgery. Larger studies incorporating both OPRM1 and CYP2D6 genotyping are needed to clarify the genetic determinants of tramadol analgesia as CYP2D6 gene is required for tramadol metabolism.

OPRM1↗
PubMed2003

Intergenic sequence inspector: searching and identifying bacterial RNAs.

Intergenic Sequence Inspector (ISI) is a program that helps in identifying bacterial ribonucleic acids (RNAs). It automatically extracts, selects and visualizes candidate intergenic regions (IGRs) that bear conservations between phylogenetically related species, displaying sequence and structural signatures of RNA genes encompassing putative promoters, terminators, RNA secondary structure predictions and the G+C percent of the selected sequences. ISI is intentionally modular to analyze various bacterial genomes according to their intrinsic specificities and to the available data. ISI provides a sum of information to the user who can evaluate whether or not an IGR is susceptible to express RNAs.

DNA, Intergenic↗
PubMed2026

Bibliometric analysis of retinoblastoma research over the past decade.

BACKGROUND: Retinoblastoma (RB), the most prevalent primary intraocular malignancy in children, has emerged as a model disease for exploring the molecular underpinnings of pediatric cancer. Over the past decade, research in this field has accelerated, propelled by advances in genomics, diagnostic imaging, targeted therapies, and global scientific collaboration. METHODS: This study systematically retrieved RB-related publications from 2015 to 2024 using the Web of Science Core Collection. A total of 4990 articles were included. CiteSpace and VOSviewer were employed to perform bibliometric and visual analyses across multiple dimensions, including countries, institutions, authors, journals, and thematic evolution. RESULTS: The United States and China were identified as the leading contributors, jointly accounting for over 40.55% of all publications. US-based journals led in both publication volume and citation impact, underscoring their global influence. Cluster analysis revealed 4 major research domains: clinical diagnosis, treatment, and prognosis; molecular mechanisms and signaling pathways; gene and protein function studies; and research methodologies and experimental models. CONCLUSION: RB research is transitioning into an era of precision oncology, characterized by molecular subtyping, novel therapeutic targets, and individualized treatment approaches. While diagnostic and therapeutic outcomes have markedly improved in high-income countries, significant disparities persist in low- and middle-income regions due to limited access to early detection and comprehensive care. Future priorities should include the refinement of preclinical models, investigation of drug resistance mechanisms, and promotion of international collaboration to standardize diagnostic and therapeutic strategies. These efforts are critical to improving global outcomes for children with RB.

Retinoblastoma↗
PubMed1993

High-resolution mapping of genetic loci of Anabaena PCC 7120 required for photosynthesis and nitrogen fixation.

A physical map of the Anabaena genome permitted the localization of its genes to chromosomal fragments generated by rarely cutting restriction endonucleases and separated by pulsed-field gel electrophoresis. We introduce a novel means of mapping more precisely to c. 20 kb by use of rare restriction sites within vectors bearing cloned sequences that undergo homologous recombination with the genome. We thereby localize and orient genes encoding principal photosynthetic pigments. The relative spacing of loci within a single restriction fragment was determined with even higher resolution, as illustrated for genes required for heterocyst development and nitrogen fixation that were marked with transposons. Small, newly visualized restriction fragments of the chromosome were also mapped.

Anabaena↗
PubMed1996

Ocular phenotypes associated with two mutations (R121W, C126X) in the Norrie disease gene.

PURPOSE: To describe the ocular phenotypes associated with 2 mutations in the Norrie disease gene including a manifesting carrier. METHODS: Ophthalmological examinations were performed in 2 affected males and one manifesting carrier. Genomic DNA was analyzed by direct sequencing of the Norrie disease gene. RESULTS: Family I: A 29-year-old male had the right eye enucleated at the age of 3 years. His left eye showed severe temporal dragging of the retina and central scars. Visual acuity was 20/300. DNA analysis revealed a C-to-T transition of the first nucleotide in codon 121 predicting the replacement of arginine-121 by tryptophan (R121W). Both the mother and maternal grandmother carry the same mutation in heterozygous form. Family 2: A 3-month-old boy presented with severe temporal dragging of the retina on both eyes and subsequently developed retinal detachment. Visual acuity was limited to light perception. His mother's left eye was amaurotic and phthitic. Her right eye showed severe retinal dragging, visual acuity was reduced to 20/60. DNA analysis revealed a T-to-A transversion of the third nucleotide in codon 126 creating a stop codon (C126X). The mother and maternal grandmother were carriers. CONCLUSION: Mutations in the Norrie disease gene can lead to retinal malformations of variable severity both in hemizygous males and manifesting carriers.

Adult↗
PubMed2004

[Genetic analysis of rhodopsin and peripherin genes in patients with autosomal dominant retinitis pigmentosa (adRP) in Polish families].

PURPOSE: The aim of that study was to identify the mutations in rhodopsin and peripherin genes in Polish families with autosomal dominant form of retinitis pigmentosa and determine the population polymorphism in both genes in adRP families. MATERIAL AND METHODS: We performed ERG, visual acuity, Goldman visual fields, intraocular pressure measurements and fundoscopy in all the patients included in the study. On the basis of disease history, the families pedigree was made and the mode of inheritance was analyzed. The molecular analysis of DNA for each family with adRP was conducted. Genomic DNA was obtained from leucocytes by phenol-chloroform procedure according to Maniatis protocol. DNA was amplified by the PCR reaction in a volume of 50 microl containing 100 ng/microl of genomic DNA, water, Cetus buffer pH 8.4 (1 n Tris, 1 n MgCl, 1 n KCl, 2% gelatin), 0.25 microM of each primer, 200 microM of each of dATP, dTTP, dCTP, and dGTP and 2.5 U Taq polymerase (Promega). For amplification of rhodopsin gene 30 cycles of PCR were carried out. Each cycle consisting of denaturation at 95 degrees C for 5 min, annealing: at 58 degrees C (exon 1), 63 degrees C (exon 2 and 3), 68 degrees C (exon 4) and 2 min extension at 72 degrees C min. For amplification of peripherin gene 30 cycles of PCR were carried out with annealing at 60 degrees C. The entire PCR product was in electrophoresis on 8% PAA. The PCR-RFLP PCR-HD PCR-SSCP and analysis of polymorphism (CA)n dinucleotide repetition was performed. RESULTS: Molecular study demonstrated, that mutations in rhodopsin gene were cause of retinitis pigmentosa in case of two families. In any study families mutations in peripherin gene were not identified. Two kinds of bases polymorphism were identified: restriction fragments length polymorphism (RFLP) in rhodopsin gene in exon 1 and 3 and single strand conformation polymorphism (SSCP) in exon 1 and 3 in rhodopsin gene and in exon 3 in peripherin gene. The confirmed mutations in rhodopsin gene, cosegregation with adRP, whereas two kinds of population polymorphism did not correlate with clinical symptoms. Natural polymorphism appeared to be a frequent feature in rhodopsin gene while a less frequent feature in peripherin gene. CONCLUSIONS: Genetic investigations in patients with adRP allow to confirm the diagnosis and evaluate the prognosis. The mutation in rhodopsin gene should be confirmed in directly sequencing reaction in next study.

DNA Mutational Analysis↗
PubMed1991

Molecular cloning of chick lysyl hydroxylase. Little homology in primary structure to the two types of subunit of prolyl 4-hydroxylase.

Lysyl hydroxylase (EC 1.14.11.4), an alpha 2 dimer, catalyzes the formation of hydroxylysine in collagens by the hydroxylation of lysine residues in X-Lys-Gly sequences. We report here on the isolation of cDNA clones coding for the enzyme from a chick embryo lambda gt11 library. Several overlapping clones covering all the coding sequences of the 4-kilobase mRNA and virtually all the noncoding sequences were characterized. These clones encode a polypeptide of 710 amino acid residues and a signal peptide of 20 amino acids. The polypeptide has four potential attachment sites for asparagine-linked oligosaccharides and 9 cysteine residues, at least one of which is likely to be involved in the binding of the Fe2+ atom to a catalytic site. A surprising finding was that no significant homology was found between the primary structures of lysyl hydroxylase and prolyl 4-hydroxylase in spite of the marked similarities in kinetic properties between these two enzymes. A computer-assisted comparison indicated only an 18% identity between lysyl hydroxylase and the alpha-subunit of prolyl 4-hydroxylase and a 19% identity between lysyl hydroxylase and the beta-subunit of prolyl 4-hydroxylase. Visual inspection of the most homologous areas nevertheless indicated the presence of several regions of 20-40 amino acids in which the identity between lysyl hydroxylase and one of the prolyl 4-hydroxylase subunits exceeded 30% or similarity exceeded 40%. Southern blot analyses of chick genomic DNA indicated the presence of only one gene coding for lysyl hydroxylase.

Amino Acid Sequence↗
PubMed1998

Genomic alterations associated with malignancy in head and neck cancer.

BACKGROUND: Comparative genomic hybridization (CGH) was performed on 50 primary head and neck squamous cell carcinomas (HNSCC) to discover molecular genetic alterations underlying the progression of these tumors. METHODS: In CGH, equal amounts of differently labeled tumor deoxyribonucleic acid (DNA) and normal reference DNA were hybridized simultaneously to normal metaphase chromosomes. They were visualized by different fluorochromes, and the signal intensities were quantitated separately as gray levels along the single chromosomes. The over- and underrepresented DNA segments were determined by computation of ratio images and average ratio profiles. RESULTS: Prevalent changes observed in more than 50% of the HNSCC included deletions of chromosomes 1p, 4, 5q, 6q, 8p, 9p, 11, 13q, 18q, and 21q and DNA overrepresentations of 11q13 as well as 3q, 8q, 16p, 17q, 19, 20q, and 22q. The calculation of ratio profiles of tumor subgroups revealed that well differentiated carcinomas (G1) were defined by the deletions of chromosomes 3p, 5q, and 9p together with the overrepresentation of 3q, suggesting the association with early tumor development. Accordingly, the undifferentiated tumors (G3) were characterized by additional deletions of chromosomes 4q, 8p, 11q, 13q, 18q, 21q, and overrepresentations of 1p, 11q13, 19, and 22q. CONCLUSION: Our data indicate that the CGH patterns of chromosomal imbalances may help to define the malignant potential of head and neck squamous cell carcinomas.

Carcinoma, Squamous Cell↗
PubMed2000

X-linked retinoschisis with point mutations in the XLRS1 gene.

BACKGROUND: X-linked retinoschisis (XLRS) is a relatively rare vitreoretinal dystrophy that causes visual loss in young men. Recently, a gene responsible for this disease, designated XLRS1, was identified, and several deleterious gene mutations were reported. OBJECTIVE: To analyze Japanese patients clinically diagnosed as having XLRS formutational changes in the XLRS1 gene. METHODS: Ten patients with XLRS underwent full ophthalmologic examination, including slitlamp biomicroscopy and dilated funduscopy. Genomic DNA was isolated from leukocytes, and all exons of the XLRS1 gene were amplified by polymerase chain reaction and analyzed using a direct sequencing method. RESULTS: Point mutations in the XLRS1 gene were identified in all 10 patients. The mutations were identical in each of 2 pairs of brothers. Six of the point mutations represented missense mutations, 1 was a nonsense mutation, and 1 was a frameshift mutation. Five of the mutations are newly reported herein. CONCLUSIONS: The discovery of new point mutations in this study increases the available information regarding the spectrum of genetic abnormalities and clinical manifestations of XLRS. However, the limited data failed to reveal a correlation between mutation and disease phenotype. CLINICAL RELEVANCE: Identification of mutations in the XLRS1 gene and expanded information on clinical manifestations will facilitate early diagnosis, appropriate early therapy, and genetic counseling regarding the prognosis of XLRS.

Adolescent↗
PubMed1994

Primary structure and functional expression of a Drosophila cyclic nucleotide-gated channel present in eyes and antennae.

Cyclic nucleotide-gated (CNG) ion channels serve as downstream targets of signalling pathways in vertebrate photoreceptors and olfactory sensory neurons. Whether CNG channels subserve similar functions in invertebrate photoreception and olfaction is unknown. We have cloned genomic DNA and cDNA encoding a cGMP-gated channel from Drosophila. The gene contains at least seven exons. Heterologous expression of cloned cDNA in both Xenopus oocytes and HEK 293 cells gives rise to functional ion channels. The Drosophila CNG channel is approximately 50-fold more sensitive to cGMP than to cAMP. The voltage dependence of blockage by divalent cations is different compared with the CNG channel of rod photoreceptors, and the Ca2+ permeability is much larger. The channel mRNA is expressed in antennae and the visual system of Drosophila. It is proposed that CNG channels are involved in transduction cascades of both invertebrate photoreceptors and olfactory sensillae.

Amino Acid Sequence↗
PubMed2003

A peculiar autosomal dominant macular dystrophy caused by an asparagine deletion at codon 169 in the peripherin/RDS gene.

OBJECTIVE: To describe the clinical and genetic findings in a family with a peculiar autosomal dominant macular dystrophy with peripheral deposits. METHODS: All family members underwent an ophthalmic examination, and their genomic DNA was screened for mutations in the human retinal degeneration slow (peripherin/RDS) and rhodopsin genes. In selected cases, fluorescein angiography and electrophysiologic testing were performed. RESULTS: The age at onset of the disease was between the third and fourth decades of life, starting with mild visual acuity loss and periods of metamorphopsia. Clinical signs included subretinal yellowish macular deposits evolving into geographic atrophy and retinal hypopigmentation and hyperpigmentation. Electroretinography demonstrated rod dysfunction, and electro-oculograms were mildly to severely disturbed. All affected members were found to carry a 3-base pair deletion affecting codon 169 of the peripherin/RDS gene. This mutation resulted in an asparagine (Asn) deletion in the peripherin/RDS protein and was not found in 155 control individuals. CONCLUSION: A deletion of Asn169 in the peripherin/RDS protein causes a peculiar form of autosomal dominant macular dystrophy in a large family from the Netherlands. CLINICAL RELEVANCE: Characterizing the phenotype and genotype in this family may, in the long term, result in a better understanding of the precise mechanism underlying this retinal degeneration.

Adolescent↗
PubMed2004

Young monozygotic twin sisters with fundus albipunctatus and cone dystrophy.

OBJECTIVE: To describe young monozygotic twin sisters with fundus albipunctatus (a type of autosomal recessive stationary night blindness caused by mutations of the 11-cis retinol dehydrogenase gene [RDH5]) associated with cone dystrophy, previously reported in elderly men. METHODS: Ophthalmologic examinations were performed, and the RDH5 gene was analyzed by direct genomic sequencing. RESULTS: Twin 23-year-old sisters with high myopic refractive errors of approximately -13 diopters were diagnosed as having fundus albipunctatus. Their photopic electroretinographic responses were markedly reduced, and cone dystrophy was diagnosed. One twin had macular degeneration with reduced best-corrected visual acuity, while the other twin had normal maculae with good visual acuity. A compound heterozygous mutation, Val132Met and Arg280His, in the RDH5 gene was found in both sisters. CONCLUSIONS: Cone dystrophy can be present in patients with fundus albipunctatus, not only elderly men but also young women. The clinical severity differed between monozygotic twins with fundus albipunctatus and cone dystrophy.Clinical Relevance The patient's sex is not critical for the presence of cone dystrophy in patients with fundus albipunctatus. The discordant findings in the twins indicate that factors other than genetics influenced the phenotype.

Adult↗