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PubMed2002

Fingerprinting of diverse genomes using PCR with universal rice primers generated from repetitive sequence of Korean weedy rice.

Twenty primers of 20 mer referred to universal rice primer (URP) were developed from a repetitive sequence of rice genome. URP-PCR protocol employed stringent PCR with high annealing temperature throughout the thermo-cycling reaction, giving high reproducibility. Under the PCR condition, each single URP primer produced characteristic fingerprints from diverse genomes containing 14 plants, 7 animals and 6 microbes, indicating its universal applicability. The generality of URP-PCR was demonstrated by applying it to 15 cultivars from five rice species, 23 isolates in four Alternaria species producing host-specific toxins on different host plants and 12 bacterial strains including Escherichia coli, Salmonella spp., and Blucella abortus. PCR approach using URP primers will be useful for studying DNA diversity of most eukaryotic or prokaryotic genomes, especially at inter- and intraspecies levels.

Animals↗

PubMed1991

Generation and characterization of secreting and nonsecreting human x mouse heterohybridomas obtained by in vitro immunization of human peripheral blood lymphocytes.

Among the immortalizing fusion partners usable in the development of human monoclonal antibodies, nonsecreting human-mouse heteromyelomas are the most interesting. In vitro immunization of human peripheral blood lymphocytes (pretreated with leucine-O-methyl ester) with an immunogen, hemocyanin, before fusion, is a good methodology for generating nonsecreting heterohybrids. Their biological features have been extensively studied with particular attention to the level of human DNA. These heterohybrids retained more than 10% human DNA in the whole genome. However, nonsecreting heteromyeloma SHMD33 used as reference has 1% human DNA. There is no significant difference between the level of human DNA in the nonsecreting heteromyelomas and that of the secreting parent heterohybrid. The loss of human immunoglobulin production by the nonsecreting clones is not necessarily related to the diminution of human DNA. The presence of plasma cells containing human intracytoplasmic immunoglobulins and the lack of any antibody in the supernatant culture of nonsecreting clones show that the blockage of human antibody production could occur at the secretory stage.

Animals↗

PubMed1991

A highly polymorphic dinucleotide repeat on the proximal short arm of the human X chromosome: linkage mapping of the synapsin I/A-raf-1 genes.

A compound (AC)n repeat located 1,000 bp downstream from the human synapsin I gene and within the last intron of the A-raf-1 gene has been identified. DNA data-base comparisons of the sequences surrounding the repeat indicate that the synapsin I gene and the A-raf-1 gene lie immediately adjacent to each other, in opposite orientation. PCR amplification of this synapsin I/A-raf-1 associated repeat by using total genomic DNA from members of the 40 reference pedigree families of the Centre d'Etude du Polymorphisme Humaine showed it to be highly polymorphic, with a PIC value of .84 and a minimum of eight alleles. Because the synapsin I gene has been mapped previously to the short arm of the human X chromosome at Xp11.2, linkage analysis was performed with markers on the proximal short arm of the X chromosome. The most likely gene order is DXS7SYN/ARAF1TIMPDXS255DXS146, with a relative probability of 5 x 10(8) as compared with the next most likely order. This highly informative repeat should serve as a valuable marker for disease loci mapped to the Xp11 region.

Amino Acid Sequence↗

PubMed1984

Genome analysis of epidemic influenza virus strains isolated in 1979-1983.

Comparative studies on the electrophoretic mobility of double-stranded RNA segments constructed of the genome of isolates under study and of reference influenza virus strains of respective serotypes are suggestive for the evolution of majority of the genes of both A and B influenza viruses, including their genes coding for non-glycosylated proteins. Among influenza A and B virus strains which were circulating during the same epidemic, there were variants differing from each other in a number of genes including those coding for virion internal proteins. A recombinant (reassortant) detected among the influenza virus strains, which circulated in Moscow in 1979, contained the genes 4, 6, 7 and 8 identical with those of the reference H1N1 strain, and the genes 1, 2, 3 and 5 identical with those of the reference H3N2 strain. Comparative analysis of reference influenza virus strains, both the H3N2 serotype (being isolated from 1968 to 1979) and the H1N1 serotype (being isolated from 1977 to 1980) differing in the antigenic specificity of their haemagglutinin (HA) suggested the increasing variability of either genes coding for glycoproteins as well as for non-glycosylated proteins.

Disease Outbreaks↗

PubMed1984

[Molecular biological analysis of the DNA in trophoblastic disease--with special reference to genetic information of hPL and hCG(alpha, beta)].

Genomic DNAs extracted from normal placenta, while blood cells, hydatidiform mole and choriocarcinoma were examined to see if they had the same coding structure for hPL, hCG alpha and hCG beta using each of the complementary DNAs. The restriction analysis of these genomic DNAs showed the same pattern even for the DNA of choriocarcinoma that transcribed no hPL mRNA but a relatively high level of hCG(alpha,beta)mRNA. We considered that during trophoblastic malignant transformation, neither the gene deletion for hPL nor the gene amplification for hCG occurred. Moreover, the genomic DNA sequence in hCG alpha gene has polymorphic restriction sites designated as R+/- and H+/-. Using these polymorphisms, we confirmed the hypothesis that a hydatidiform mole develops from an androgenetic origin. We also observed that it is possible that a hydatidiform mole having R- and H+ homozygous DNA may develop into a choriocarcinoma. These observation suggested that some intervening sequence between these polymorphic sites is related to the tumorigenesis of choriocarcinoma.

Chorionic Gonadotropin↗

PubMed1997

Uniparental disomy (UPD). Genomic imprinting and a case for new genetics (prenatal and clinical implications: the "Likon" concept).

Uniparental disomy (UPD) is often the result of an aneuploid event masquerading under the features of diploidy. As such, it may never be recognized, being at 2 opposite phenotypic poles, harmless to the bearer, or, if harmful, eventually responsible for uncharacteristic although perhaps serious conditions. UPD can also be associated with problems such as recessiveness or mosaicism. This article considers the chances of unmasking UPD, in the course of CVS or AC prenatal diagnosis, by reviewing the main cytogenetic signals and major familial or personal antecedents raising its suspicion. Once suspected, the lead toward UPD may or may not be followed through appropriate molecular studies. UPD for either maternal or paternal chromosomes 13, 21 and 22 may not have consistent, common deleterious effects, while other identified UPD's are too rare to call. Unconditionally, main, consistent or near consistent damages to the phenotype have been traced to specific chromosome pairs such as 15 mat (Prader-Willi syndrome), 15 pat (Angelman syndrome), 11 pat (Wiedemann-Beck with syndrome), 14 mat and pat (multiple cogenital and developmental anomalies [MCDA]-several rather constant) and 7 mat (Russel-Silver [RS] and Growth-failure [GF]). The above problems all stem from an alteration of the normal, developmentally important genomic imprinting processes and most of them may recognize several etiopathogenic paths, other than UPD, none of which abides by straight Mendelian rules. In this very area, therefore, a new, non-traditional type of inheritance is confronting genetic counselling. In this paper, for want of appropriate semantic language, the neologism "likon" (or "laïkon") is coined to make reference to the hemizygously expressed sequences of the genomic parts imprinted in the somatic tissues. Broadening the definition, the word is then applied to the 4 possible epigenotypes of imprinted domains, which depend on the parental sex-of-origin: germinally "resting" (R), or "acting" (A), to be made somatically silent, that is to say "unexpressed" (U), or transcribed and "expressed" (E), thus abbreviated as EA, ER, UA and UR. Entire pedigrees may then be analyzed accordingly in health and in disease. Examples are presented herewith.

Aneuploidy↗

PubMed2006

PseudoPipe: an automated pseudogene identification pipeline.

MOTIVATION: Mammalian genomes contain many 'genomic fossils' i.e. pseudogenes. These are disabled copies of functional genes that have been retained in the genome by gene duplication or retrotransposition events. Pseudogenes are important resources in understanding the evolutionary history of genes and genomes. RESULTS: We have developed a homology-based computational pipeline ('PseudoPipe') that can search a mammalian genome and identify pseudogene sequences in a comprehensive and consistent manner. The key steps in the pipeline involve using BLAST to rapidly cross-reference potential "parent" proteins against the intergenic regions of the genome and then processing the resulting "raw hits" -- i.e. eliminating redundant ones, clustering together neighbors, and associating and aligning clusters with a unique parent. Finally, pseudogenes are classified based on a combination of criteria including homology, intron-exon structure, and existence of stop codons and frameshifts.

Algorithms↗

PubMed1987

Molecular cloning of 99% of measles virus genome, positive identification of 5' end clones, and mapping of the L gene region.

Molecular probes specific for paramyxovirus 3' and 5' end sequences are essential for studying viral transcription and replication and the role of defective interfering particles in these processes. We have constructed from measles virus genomic RNA an ordered series of overlapping clones containing over 99% of measles virus genetic information. Clones corresponding to the 3' and 5' ends of the genome were identified by means of a probe made from 'capped' genomic RNA, and their location was confirmed by primer extension experiments. Clones representing the N, P/C, M, F, and H genes were identified by reference to previously characterized clones, and their positions in the genome were defined by restriction analysis and S1 nuclease mapping of intercistronic clones. The L gene region was characterized by site-to-site restriction mapping and measured as 6,550 nucleotides in length.

Chromosome Mapping↗

PubMed1994

Dual EBNA1 promoter usage by Epstein-Barr virus in human B-cell lines expressing unique intermediate cellular phenotypes.

The use of different viral promoters for the expression of the EBNA1 gene product appears to be a critical step in the regulation of Epstein-Barr virus latent gene expression and may reflect the extent of differentiation of B-cell hosts. Low-passage Burkitt lymphoma cell lines resemble immature B cells in that they express CD10 (CALLA) and do not express B-cell activation antigens. In these cells, transcription from a promoter located in the BamHI F fragment of the viral genome results in the exclusive expression of EBNA1, referred to as the latency I pattern of viral gene expression. In contrast, high-passage Burkitt lymphoma cells and lymphoblastoid cell lines resemble activated B cells in that they do not express CD10 but do express activation antigens such as CD23. In these cells, the use of two promoters located in the BamHI W and C fragments of the viral genome leads to the expression of all six EBNA gene products (latency III). We have found that four human B-cell lines, DB, LBW2, LBW14, and Josh 7, stably express a pattern of B-cell differentiation antigens intermediate between those found in latency I and latency III cell lines and characterized by the coexpression of CD10 and CD23. The pattern of EBNA1 promoter usage in these cell lines was examined to determine whether their intermediate cellular phenotype was reflected in their patterns of viral gene expression. DB, LBW2, and LBW14 utilize both the BamHI F promoter region and BamHI W promoter region to transcribe the EBNA1 gene. This stable pattern of mixed promoter usage for the expression of the EBNA gene products in B cells has not previously been described. In addition, these three B-cell lines expressed lower levels of the viral latent gene product EBNA2 than those typically observed in latency III cells. The lower levels of activation of viral and cellular promoters known to be regulated by EBNA2 also correlated with the reduced levels of EBNA2 expression in these cells. These included the viral LMP1 and LMP2A promoters and the cellular CD23B promoter. The fourth B-cell line, Josh 7, expressed EBNA1 mRNAs derived from both the BamHI W promoter and BamHI C promoter, similar to latency III cells. The intermediate cellular phenotype in Josh 7 cells appeared to be due, in part, to a deficiency in the expression of viral LMP1.(ABSTRACT TRUNCATED AT 400 WORDS)

Antigens, CD↗

PubMed2026

A modular class-aware workflow for small RNA sequencing analysis using mouse sperm as a case study.

BACKGROUND: Small RNA sequencing analysis is challenging because RNA classes differ in biogenesis, sequence redundancy, genomic organization, and annotation reliability. Integrated workflows accommodating these constraints remain limited, particularly for fragment-level and cluster-level analysis. METHODS: We present a reproducible, containerized, class-aware workflow for small RNA sequencing analysis, using mouse sperm as a case study. The workflow combines standardized preprocessing with complementary annotation and quantification strategies for microRNAs (miRNAs), transfer RNA-derived small RNAs (tsRNAs), ribosomal RNA-derived small RNAs (rsRNAs), and PIWI-interacting RNA (piRNA)-enriched genomic clusters. Using sperm small RNA data from offspring of lipopolysaccharide (LPS)-exposed male mice, we compared integrated-reference mapping, multi-class annotation, fragment-level tsRNA profiling, and genome-based piRNA cluster analysis, with custom modules for locus-aware harmonization and condition-specific cluster analysis. RESULTS: Integrated-reference mapping aligned 88.17% of reads and retained 690 features after filtering. It identified 11 differentially expressed miRNAs between LPS and controls, while other classes showed limited signal. Fragment-level profiling improved tsRNA resolution. piRNA cluster analysis identified 958 control and 940 LPS clusters, with 18 control-specific and no LPS-specific clusters. CONCLUSION: This workflow supports transparent, reproducible, class-aware interpretation of small RNA sequencing data while emphasizing cautious interpretation of piRNA-enriched signals from total small RNA sequencing.

Small non-coding RNA analysis↗

PubMed2005

ALU-ring elements in the primate genomes.

Elucidation of complete nucleotide sequence of the human has revealed that coding sequences that store the information needed to synthesize functional proteins, occupy only 2% of the genomic region. The remaining 98%, barring few regulatory sequences, has been referred to as non-functional or junk DNA and consists of many kinds of repeat elements. In fact, human genome is the most repeat rich genome sequenced so far, in which more than half of the region is occupied by such sequences. Determination of significance of these repeats in the human genome has become the focus of many studies all over the world, especially after genome sequencing did not reveal any significant difference in coding regions between lower eukaryotes and human. In this article, we have focused on Alu repeats that are primate specific elements with many interesting biological properties. Moreover, these are the repeats with highest copy number in the human genome. We have highlighted different facets of their interaction with the genome and changing paradigms regarding their role in genome organization.

Alu Elements↗

PubMed2025

The first chromosome-level genome of the lappet moth Trabala vishnou (Lepidoptera: Lasiocampidae).

Trabala vishnou (Lefèbvre, 1827) (Lepidoptera: Lasiocampidae) is a destructive leaf-eating pest that causes severe damage to forest ecosystems, leading to substantial economic losses. Herein, we sequenced and assembled a high-quality chromosome-level genome of T. vishnou using a combination of Illumina reads, PacBio HiFi reads, and High throughput Chromosome Conformation Capture (Hi-C) technologies. The genome size is 561.86 Mb and spans 25 chromosomes, exhibiting a high level of contiguity (scaffold/contig N50 = 21.75 Mb/20.67 Mb). Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis a 99.5% completeness score for this genome assembly. Repeat elements constitute 62.66% of the genome. A total of 1,630 non-coding RNAs and 12,895 protein-coding genes have been identified within the genome. The first chromosome-level genome of T. vishnou serves as a valuable reference for elucidating the evolution of functional traits in Lasiocampidae family and will facilitate the development of strategies for controlling defoliating pests.

Animals↗

PubMed2001

Nomenclature of the human immunoglobulin kappa (IGK) genes.

'Nomenclature of the Human Immunoglobulin Kappa (IGK) Genes', the 17th report of the 'IMGT Locus in Focus' section, provides the first complete list of all the human IGK genes. In the most frequent haplotypes, the human IGK locus spans 1,820 kb and the IGKV genes are organized in two clusters separated by 800 kb. In those haplotypes where both the proximal and distal IGKV clusters are present, the total number of human IGK genes per haploid genome is 82 (107 genes if the orphons are included) of which 37-41 are functional. If only the proximal IGKV cluster is present, which is found in a rare haplotype, the total number of genes per haploid genome is 46 (71 genes if the orphons are included) of which 23-25 genes are functional. IMGT/HUGO gene names and definitions of the human IGK genes on chromosome 2p11.2, and IGK orphons on chromosomes 1, 2, 15, and 22 are provided with the gene functionality and the number of alleles according to the rules of the IMGT Scientific chart, with the accession numbers of the IMGT reference sequences, and the accession ID of the Genome Database GDB and NCBI LocusLink databases in which all the IMGT human IGK genes have been entered. The tables are available at the IMGT Marie-Paule page from IMGT, the international ImMunoGeneTics database (http://imgt.cines.fr:8104) created by Marie-Paule Lefranc, Université Montpellier II, CNRS, France.

Alleles↗

PubMed2005

IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes.

IMGT/GENE-DB is the comprehensive IMGT genome database for immunoglobulin (IG) and T cell receptor (TR) genes from human and mouse, and, in development, from other vertebrates. IMGT/GENE-DB is the international reference for the IG and TR gene nomenclature and works in close collaboration with the HUGO Nomenclature Committee, Mouse Genome Database and genome committees for other species. IMGT/GENE-DB allows a search of IG and TR genes by locus, group and subgroup, which are CLASSIFICATION concepts of IMGT-ONTOLOGY. Short cuts allow the retrieval gene information by gene name or clone name. Direct links with configurable URL give access to information usable by humans or programs. An IMGT/GENE-DB entry displays accurate gene data related to genome (gene localization), allelic polymorphisms (number of alleles, IMGT reference sequences, functionality, etc.) gene expression (known cDNAs), proteins and structures (Protein displays, IMGT Colliers de Perles). It provides internal links to the IMGT sequence databases and to the IMGT Repertoire Web resources, and external links to genome and generalist sequence databases. IMGT/GENE-DB manages the IMGT reference directory used by the IMGT tools for IG and TR gene and allele comparison and assignment, and by the IMGT databases for gene data annotation. IMGT/GENE-DB is freely available at http://imgt.cines.fr.

Alleles↗

PubMed1997

Rapid cloning of insect transposon insertion junctions using 'universal' PCR.

Very highly degenerate primers with short specific 3' anchor sequences and 5' adaptors were used in conjunction with nested specific primers to amplify large numbers of unknown insertion junctions of the insect retrotransposon Woot, using genomic DNA as template for the polymerase chain reaction (PCR). This technique, sometimes referred to as universal PCR, is a powerful method for molecular characterization of transposon insertions into genomes, and more generally for short-distance chromosome walking through unknown DNA. Twenty-four unique insertion junctions were cloned and sequenced from two strains of Tribolium castaneum and one strain of T. freemani. Inspection of these sequences revealed that integration of the Woot retrotransposon is cued by the insertion target motif, GTAC, in both species.

Animals↗

PubMed2004

GenoFrag: software to design primers optimized for whole genome scanning by long-range PCR amplification.

Genome sequence data can be used to analyze genome plasticity by whole genome PCR scanning. Small sized chromosomes can indeed be fully amplified by long-range PCR with a set of primers designed using a reference strain and applied to several other strains. Analysis of the resulting patterns can reveal the genome plasticity. To facilitate such analysis, we have developed GenoFrag, a software package for the design of primers optimized for whole genome scanning by long-range PCR. GenoFrag was developed for the analysis of Staphylococcus aureus genome plasticity by whole genome amplification in approximately 10 kb-long fragments. A set of primers was generated from the genome sequence of S.aureus N315, employed here as a reference strain. Two subsets of primers were successfully used to amplify two portions of the N315 chromosome. This experimental validation demonstrates that GenoFrag is a robust and reliable tool for primer design and that whole genome PCR scanning can be envisaged for the analysis of genome diversity in S.aureus, one of the major public health concerns worldwide.

Base Pairing↗

PubMed2000

Structure and presentation of a World Wide Web database of CSF virus isolates held at the EU reference laboratory.

A computerized database was generated with the epidemiological data of more than 600 CSF virus strains and isolates kept in the EU Reference Laboratory for Classical Swine Fever in Hanover. In addition, as sequence data from defined regions of the genome are increasingly being used for genetic typing of new isolates and are thus being published, it was decided to integrate them into the database. In order to make the epidemiological and the sequence data available to other laboratories through the World Wide Web, a searchable web interface was programmed, which can be accessed using an Internet browser like Netscape or Internet Explorer. The possibility to exchange data via the web has the potential to increase our knowledge concerning genetic and epidemiological links between outbreaks worldwide.

Animals↗

PubMed2005

Nutrigenomics: the impact of biomics technology on nutrition research.

The interaction between the human body and nutrition is an extremely complex process involving multi-organ physiology with molecular mechanisms on all levels of regulation (genes, gene expression, proteins, metabolites). Only with the recent technology push have nutritional scientists been able to address this complexity. Both the challenges and promises that are offered by the merge of 'biomics' technologies and mechanistic nutrition research are huge, but will eventually evolve in a new nutrition research concept: nutritional systems biology. This review describes the principles and technologies involved in this merge. Using nutrition research examples, including gene expression modulation by carbohydrates and fatty acids, this review discusses applications as well as limitations of genomics, transcriptomics, proteomics, metabolomics, and systems biology. Furthermore, reference is made to gene polymorphisms that underlie individual differences in nutrient utilization, resulting in, e.g., different susceptibility to develop obesity.

Biotechnology↗