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PubMed1984

Chromosomes of kinetoplastida.

We have compared chromosome-sized DNA molecules (molecular karyotypes) of five genera (nine species) of kinetoplastida after cell lysis and deproteinization of DNA in agarose blocks and size fractionation of the intact DNA molecules by pulsed field gradient (PFG) gel electrophoresis. With the possible exception of Trypanosoma vivax and Crithidia fasciculata, all species have at least 20 chromosomes. There are large differences between species in molecular karyotype and in the chromosomal distribution of the genes for alpha- and beta-tubulin, rRNA and the common mini-exon sequence of kinetoplastid mRNAs. In all cases, the rRNA genes are in DNA that is larger than 500 kb. Whereas T. brucei has approximately 100 mini-chromosomes of 50-150 kb, only few are found in T. equiperdum; T. vivax has no DNA smaller than 2000 kb. As all three species exhibit antigenic variation, small chromosomes with telomeric variant surface glycoprotein genes cannot be vital to the mechanism of antigenic variation. The apparent plasticity of kinetoplastid genome composition makes PFG gel electrophoresis a potentially useful tool for taxonomic studies.

Animals↗

PubMed2000

Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members.

Cadherins play an important role in specific cell-cell adhesion events. Their expression appears to be tightly regulated during development and each tissue or cell type shows a characteristic pattern of cadherin molecules. Inappropriate regulation of their expression levels or functionality has been observed in human malignancies, in many cases leading to aggravated cancer cell invasion and metastasis. The cadherins form a superfamily with at least six subfamilies, which can be distinguished on the basis of protein domain composition, genomic structure, and phylogenetic analysis of the protein sequences. These subfamilies comprise classical or type-I cadherins, atypical or type-II cadherins, desmocollins, desmogleins, protocadherins and Flamingo cadherins. In addition, several cadherins clearly occupy isolated positions in the cadherin superfamily (cadherin-13, -15, -16, -17, Dachsous, RET, FAT, MEGF1 and most invertebrate cadherins). We suggest a different evolutionary origin of the protocadherin and Flamingo cadherin genes versus the genes encoding desmogleins, desmocollins, classical cadherins, and atypical cadherins. The present phylogenetic analysis may accelerate the functional investigation of the whole cadherin superfamily by allowing focused research of prototype cadherins within each subfamily.

Amino Acid Sequence↗

PubMed1985

Characterization of a 1980-swine recombinant influenza virus possessing H1 hemagglutinin and N2 neuraminidase similar to that of the earliest Hong Kong (H3N2) virus.

A recombinant (H1N2, formerly Hsw 1N2), A/swine/Ehime/1/80 was found to possess antigenic, biological and genomic characteristics different from those of a previous A/swine/Kanagawa/2/78 (H1N2) strain. Five monoclonal antibodies to A/NJ/8/76 definitely differentiated the hemagglutinin molecules of the former virus from the latter, showing that these viruses differed, at least, at two antigenic determinants. Neuraminidase-inhibition tests with monoclonal antibodies to different H2N2 and H3N2 viruses revealed that the A/swine/Ehime/1/80 strain contained a neuraminidase very similar to that of the late human Asian (H2N2) and the earliest Hong Kong (H3N2) viruses. Growth comparison of swine and human isolates indicated that A/swine/Ehime/1/80 and A/swine/Shizuoka/1/78 (H1N1) failed to grow at 42 degrees C, while A/swine/Kanagawa/2/78 and its possible parental virus, A/swine/Kanagawa/4/78 (H1N1) replicated efficiently at this stringent temperature. These results revealed that the viruses having growth characteristics similar to those of avian influenza virus were present in the swine population. RNA analysis by oligonucleotide mapping suggested that A/swine/Ehime/1/80 may be a recombinant between A/swine/Shizuoka/1/78-like and A/Aichi/2/68 (H3N2)-like viruses. To further determine the gene constellation of this recombinant virus, DNA-RNA hybridization was performed by using DNA segments complementary for swine (H1N1) virus RNA and the entire RNAs of three viruses. The molecular hybridization could define the genomic composition of the recombinant, indicating that only the neuraminidase gene of this virus is derived from the earliest Hong Kong (H3N2)-like virus and remaining seven genes from swine (H1N1) virus.

Animals↗

PubMed1981

Genome analysis of H1N1 influenza virus strains isolated in the U.S.S.R. during an epidemic in 1961-1962.

Genome composition and polypeptides of H1N1 influenza virus strains isolated in the U.S.S.R. during an epidemic in 1961-1962 have been studied as well as H2N2 influenza virus strains that dominated at that time. The H1N1 isolates did not contain genes of the simultaneously circulating H2N2 viruses. H1N1 influenza viruses have proved to be genetically similar to A/FM/1/47 (H1N1) influenza virus strain differing in only two genes, rather than to H1N1 influenza viruses isolated in 1977 differing in six genes.

Disease Outbreaks↗

PubMed1996

DNA fingerprinting techniques for microorganisms. A proposal for classification and nomenclature.

A whole array of DNA-fingerprinting techniques, which provide indirect access to DNA sequence polymorphism in order to assess species or clonal identity of bacterial organisms or in order to study bacterial genome composition, have been described during past decades. Nomenclature has been sometimes erroneous and/or confusing, also because of hybrid techniques that combine different approaches. It can be shown that most techniques study the sequence polymorphism of only the chromosome, or only the plasmid(s) or only a gene or gene fragment and that the sequence polymorphism is revealed by AFLP (amplified fragment length polymorphism) or by RFLP (restriction fragment length polymorphism) or by special electrophoresis techniques. Starting from these considerations, some taxonomy of techniques, which enables more appropriate nomenclature, can be developed.

Bacteria↗

PubMed2002

Genetic Diversity in Musa acuminata Colla and Musa balbisiana Colla and some of their natural hybrids using AFLP Markers.

Genetic diversity and relationships were assessed in 28 accessions of Musa acuminata (AA) Colla and Musa balbisiana (BB) Colla, and some of their natural hybrids, using the amplified fragment length polymorphisms (AFLP) technique. Fifteen AFLP +3 primer pairs produced 527 polymorphic bands among the accessions. Neighbor-joining and principal co-ordinate (PCO) analyses using Jaccard's similarity coefficient produced four major clusters that closely corresponded with the genome composition of the accessions (AA, BB, AAB and ABB). The AFLP data distinguished between the wild diploid accessions and suggested new subspecies relationships in the M. acuminata complex that are different from those based on morphological data. The data suggested that there are three subspecies within the M. acuminata complex (ssp. burmannica Simmonds, malaccensis Simmonds, and microcarpa Simmonds). 'Tjau Lagada' (ssp. microcarpa), 'Truncata' [ssp truncata (Ridl.) Shepherd] and 'SF247' [ssp. banksii (F.Muell) Simmonds] clustered very closely with 'Gros Michel' and 'Km 5', indicating that more than one M. acuminata subspecies may be involved in the origin of triploid AAA bananas. 'Calcutta 4' (ssp. burmannicoides De Langhe & Devreux) and 'Long Tavoy' (ssp. burmannica) were closely related and could be together in the same subspecies. This study also showed that there is much more genetic diversity within M. balbisiana that was split into two groups: (1) 'I-63' and 'HND' and (2) 'Los Banos', 'MPL' (Montpellier), '10852', 'Singapuri', 'Etikehel', and 'Butohan 1' as the other.

Journal Article↗

PubMed2006

Occurrence of two different types of RNA-5-containing beet necrotic yellow vein virus in the UK.

Two types of RNA-5-containing beet necrotic yellow vein virus (BNYVV) have been detected in the UK at different sites in Norfolk. On the basis of nucleotide (nt) sequence comparisons, one virus source (UK-MH) was clearly identified as P type BNYVV, a virus type that had previously only been detected in two widely separated parts of the world, France and Kazakhstan. The other virus source (UK-FF) has a complex genome composition. The analysed portions of its RNAs 2 and 4 are closely related to the corresponding portions in the RNAs of the East Asian A type isolate S, whereas those of its RNAs 1 and 3 resemble P type RNA 1 from Kazakhstan and European A type RNA 3, respectively. Interestingly, the P25 encoded on its RNA 3 has an unique TYHG tetrad in the highly variable amino acid positions 67-70. RNA 5 of the UK-FF BNYVV source shares properties with P type RNA 5, but also with East Asian types of RNA 5. The possible origin and epidemiology of BNYVV types is discussed.

Base Sequence↗

PubMed2006

A single copy of carbonic anhydrase 2 restores wild-type circadian period to carbonic anhydrase II-deficient mice.

Carbonic anhydrase II (CA-II)-deficient mice have long circadian periods compared to their siblings with normal CA-II levels. The CA-II-deficient mice differ genetically from their siblings at proximal chromosome three, where the mutated carbonic anhydrase 2 gene sits on a small insert of DNA from the DBA/2J strain. The rest of the genome is that of the C57BL/6J strain. The goal of this study was to test the hypothesis that the null mutation in carbonic anhydrase 2 and the long circadian period phenotype were linked. In order to separate the effect of the null mutation in carbonic anhydrase 2 from the effect of DBA/2J alleles of other genes on the insert, two new lines of mice were studied. The first line, Kar, was developed from a CA-II-deficient mouse that had a fortuitous recombination restoring functional CA-II without affecting the rest of the DBA/2J insert. The second line was generated by breeding DBA/2J mice and C57BL/6J mice until they had the genomic composition of CA-II-deficient mice without the null mutation. Both lines of mice had circadian periods not different from C57BL/6J mice and shorter than CA-II-deficient mice. The phenotype of the new lines showed that the long circadian period characteristic of the CA-II-deficient mice arises when functional CA-II is absent, not when DBA/2J alleles are present on proximal chromosome three.

Alleles↗

PubMed2026

DNA methylation signatures in skeletal muscle associated with physical function in healthy older adults.

Despite the substantial variability in physical function among older adults, the molecular mechanisms remain poorly characterized, particularly within skeletal muscle. This study aimed to determine the patterns of DNA methylation in skeletal muscle associated with physical function in healthy older adults. We analyzed DNA methylation (EPIC v2 array; 875,554 CpG sites) in skeletal muscle from 92 healthy older adults (median age 74; 62% female). Associations were examined across five phenotypes: Short Physical Performance Battery (SPPB), 6-min walk test (6MWT), handgrip strength, perceived disability (PAT-D), and lifestyle health (modified Life's Essential 8). Linear regression models adjusted for age, sex, race, BMI, and muscle fiber composition. Genomic inflation corrected via the BACON method (FDR < 0.05). Gene set enrichment analysis was performed on suggestive hits (FDR < 0.1). We identified significant differentially methylated probes (DMPs) and regions (DMRs) across all phenotypes: SPPB (70 DMPs, 22 DMRs), 6MWT (16 DMPs, 566 DMRs), handgrip strength (2 DMRs), PAT-D (19 DMPs, 1 DMR), and lifestyle health (2 DMPs). DMRs largely overlapped promoters. Identified genes overlapped known musculoskeletal and neurological GWAS hits, including RUNX2 and FOXL1 (bone mineral density), IGFBP3 (muscle mass), and NEK1 and SHANK1 (neurological function). Enrichment analysis revealed that 6MWT-associated genes relate to nervous and skeletal system development, while handgrip-associated genes involve cytoskeletal dynamics and protein assembly. Epigenetic variation in aging skeletal muscle is associated with physical function. The enrichment of pathways related to nervous and musculoskeletal development suggests specific epigenetic mechanisms underlying functional decline, offering potential targets for intervention in older adults.

DNA methylation↗

PubMed1985

Characteristics of a swine recombinant influenza virus isolated in 1980: recombination between swine and the earliest Hong Kong (H3N2) viruses.

A recombinant (H1N2, formerly Hsw1N2), A/swine/Ehime/1/80 was found to possess antigenic biological and genomic characteristics different from those of a previous A/swine/Kanagawa/2/78 (H1N2) strain. Five monoclonal antibodies to A/NJ/8/76 differentiated the haemagglutinin molecules of the former virus from the latter, showing that these viruses differed at two-antigenic determinants at least. Immuno-double diffusion tests with antisera to the isolated neuraminidase and neuraminidase-inhibition tests with monoclonal antibodies to different H2N2 and H3N2 viruses revealed that A/swine/Ehime/1/80 strain contained a neuraminidase subunit very similar to that of late human Asian (H2N2) and the earliest Hong Kong (H3N2) viruses. RNA analysis by oligonucleotide mapping suggested that A/swine/Ehime/1/80 may be a recombinant between A/swine/Shizuoka/1/78-like and A/Aichi/2/68 (H3N2)-like viruses. To determine further the gene constellation of this recombinant virus, DNA-RNA hybridizations were performed using DNA segments complementary for swine (H1N1) virus RNA and the entire RNA of three viruses. The molecular hybridization could define the genomic composition of the recombinant, indicating that only the neuraminidase gene of this virus is derived from the earliest Hong Kong (H3N2)-like virus and remaining seven genes are derived from swine (H1N1) virus.

Animals↗

PubMed2004

Cell-based assay for the determination of temperature sensitive and cold adapted phenotypes of influenza viruses.

The determination of temperature sensitive (ts) and cold adapted (ca) phenotype for influenza A and B strains has been conducted traditionally using embryonated chicken eggs. As attempts are made to move away from the use of eggs in the manufacturing process of influenza vaccines, it will become useful to develop cell-based assays to support cell culture-based vaccine production. In this study, MDCK cells have been evaluated as a tool for determining the ts and ca phenotypes associated with live attenuated influenza viruses. Direct comparisons were made of these phenotypes carried out in eggs. Reassortants made from the Russian live attenuated influenza donor strains A/Leningrad/134/17/57 (H2N2) and B/USSR/60/69 were prepared entirely in MDCK cells and their phenotypes evaluated using the MDCK cell-based assay. It is concluded that MDCK cells are more sensitive than eggs for the measurement of ts and ca phenotype of influenza viruses (particularly for influenza A) and they provide an alternative means for screening candidate reassortants prior to determining their genome composition.

Animals↗

PubMed2004

Rejoinder: whole-culture synchronization cannot, and does not, synchronize cells.

There have been numerous proposals suggesting that whole-culture methods - in which all cells in a growing culture are treated identically - can synchronize cells. An explicit defense of these methods has been presented (Spellman and Sherlock, this issue, pp. 270-273, ). Here, this defense of whole-culture 'synchronization' is subjected to a critical evaluation leading to the conclusion that whole-culture synchronization cannot synchronize cells - at all. Whole-culture methods cannot produce a set of cells that reflects the size and genome composition of cells of any particular cell-cycle age during the normal cell cycle. Thus, in addition to the well-recognized problem of artifacts, it is proposed that experiments using whole-culture treatments (usually starvation or inhibition methods) are not suitable for cell-cycle analysis because these methods do not produce a synchronized culture.

Cell Cycle↗

PubMed2004

Characterization of antigenically and genetically similar influenza C viruses isolated in Japan during the 1999-2000 season.

Between October 1999 and May 2000, a total of 28 strains of influenza C virus were isolated in four Japanese prefectures: Yamagata, Miyagi, Saitama and Hiroshima. Antigenic analysis showed that the 28 isolates were divided into three distinct antigenic groups, and viruses belonging to different antigenic groups were co-circulating in each of the four prefectures. Phylogenetic analysis of the seven protein genes demonstrated that the viruses having a similar genome composition spread in various areas of Japan during the same period. Furthermore, phylogenetic analysis showed that most of the influenza C viruses isolated in various areas of the world between the 1970s and 1980s were closely related to the contemporary Japanese viruses in all gene segments. These observations suggest that the influenza C viruses cause epidemics in some communities during the same season and that antigenically and genetically similar influenza C viruses spread throughout Japan and may be circulating worldwide.

Adolescent↗

PubMed2002

Identification and sequence analysis of Potato yellow vein virus capsid protein minor gene.

Potato yellow vein virus (PYVV) is a whitefly-transmitted (Trialeurodes vaporariorum) closterovirus (WTC) with an as yet unidentified genome composition. PYVV dsRNA preparations consist of three high molecular weight dsRNA species (dsRNAs 1, 2 and 3) 8.0, 5.5 and 4.0 kbp in size respectively, as well as two low molecular weight dsRNA species of 2.0 and 1.8 kbp (denoted x and y). The PYVV capsid protein minor (CPm) gene was identified on the dsRNA 3 species, and was subsequently cloned and sequenced. The PYVV CPm gene is 2022 nucleotides long and putatively encodes a protein with estimated size 77.5 kDa. The PYVV CPm gene product is considerably larger than the equivalent proteins encoded by the bipartite criniviruses, Lettuce infectious yellows virus (LIYV) and Cucurbit yellow stunting disorder virus (CYSDV) (52 and 53 kDa, respectively). The PYVV CPm possesses a centralized domain which is absent from both the LIYV and CYSDV CPm counterparts. Pairwise comparisons as well as phylogenetic analysis based on the available amino acid sequences of the CPm of various WTCs, showed that PYVV is closely related to LIYV, CYSDV and also Beet pseudo-yellows virus.

Amino Acid Sequence↗

PubMed2002

Characterisation of mildew resistant wheat-rye substitution lines and identification of an inverted chromosome by fluorescent in situ hybridisation.

Seven different mildew resistant wheat lines derived from crosses between triticale and bread wheat were examined by molecular cytogenetics and chromosome C-banding in order to determine their chromosomal composition. Genomic in situ hybridisation (GISH) showed the presence of rye germplasm in all the lines and identified three substitution lines, three double substitution lines and one addition-substitution line. C-banding identified rye chromosomes 1R and 4R in the addition-substitution line, rye chromosomes 1R and 6R in two substitution lines and 1R and 2R in the third line, and rye chromosome 1R in the three substitution lines. Two of the latter lines (7-102 and 7-169) contained a modified form of the chromosome; fluorescent in situ hybridisation (FISH) using five different repetitive DNA-probes showed a pericentric inversion of 1R in both lines. The breakpoints of the 1R inversion were between (1) the 5S rDNA site and the NOR-region on the satellite of the short arm, and (2) between two AAC(5) sites close to the centromere on the long arm. The role of the rye chromosomes in the mildew resistance, the utilisation of the inverted 1R and the significance of the lines in wheat breeding are discussed.

Chromosome Banding↗

PubMed1997

Epidemiology of hepatitis E virus infection.

Hepatitis E is an acute, icteric, self-limiting disease, which is spread widely in many tropical and subtropical countries where it occurs both in the form of epidemics of variable magnitude or sporadically. Hepatitis E affects young adults, rather than children, and causes a high mortality rate, particularly in pregnant women. In industrialized countries this disease occurs occasionally as imported sporadic cases. The aetiological cause of hepatitis E is a virus, hepatitis E virus (HEV), which is temporally classified as a member of the Calicivirus family, although its genomic composition is unique. There are experimental data as well as epidemiological observations allowing us to assume that hepatitis E may be a zoonosis as HEV is pathogenic for some domestic and wild animals. Recently, serological assays based on the use of recombinant or synthetic antigens were developed and applied to determine the prevalence of antibody to HEV (anti-HEV) in various epidemic and non-epidemic settings. In suspected hepatitis E cases, anti-HEV seropositivity was detected at an elevated rate but the overall seroprevalence of anti-HEV in normal human populations of endemic areas appeared to be unexpectedly low. A low but constant presence of anti-HEV seropositivity was observed also in non-endemic industrialized countries. In some of these countries, anti-HEV seropositivity was accumulated in groups of patients with various liver and non-liver pathologies and certain groups at risk for blood-borne infections.

Animals↗

PubMed2002

Likely multiple origins of a diploid hybrid sunflower species.

The recurrent origin of diploid hybrid species is theoretically improbable because of the enormous diversity of hybrid genotypes generated by recombination. Recent greenhouse experiments, however, indicate that the genomic composition of hybrid lineages is shaped in part by deterministic forces, and that recurrent diploid hybrid speciation may be more feasible than previously believed. Here we use patterns of variation from chloroplast DNA (cpDNA), nuclear microsatellite loci, cross-viability and chromosome structure to assess whether a well-characterized diploid hybrid sunflower species, Helianthus anomalus, was derived on multiple occasions from its parental species, H. annuus and H. petiolaris. Chloroplast DNA and crossability data were most consistent with a scenario in which H. anomalus arose three times: three different H. anomalus fertility groups were discovered, each with a unique cpDNA haplotype. In contrast, there was no clear signature of multiple, independent origins from the microsatellite loci. Given the age of H. anomalus (> 100 000 years bp), it may be that microsatellite evidence for recurrent speciation has been eroded by mutation and gene flow through pollen.

Arizona↗

PubMed2002

Identification and sequence of an unstable DNA element in the entomopathogenic bacteria Photorhabdus temperata strain K122.

AIMS: A search was conducted for a difference in genome composition between phenotypic variants of the insect pathogenic bacteria, Photorhabdus temperata. METHODS: An unstable 300 bp fragment of DNA was identified by amplified fragment length polymorphism (AFLP) analysis, which was not, however, associated with phenotypic variation. RESULTS: During prolonged culturing of the bacteria, one copy of the repeated fragment was deleted and a restriction site linked to one of the copies was lost or gained. The sequence did not show substantial identity to any in the database, but a 16-bp region was identical to part of the marR gene of Escherichia coli. SIGNIFICANCE AND IMPACT OF THE STUDY: The work has implications for the understanding of genetic instability in this and other pathogenic species of bacteria. In addition, the complete unstable element may be useful as a genetic tool in Photorhabdus spp.

Animals↗