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PubMed2002

Extended repertoire of genes encoding variable surface lipoproteins in Mycoplasma bovis strains.

A genomic cluster of vsp genes was previously shown to mediate high-frequency phenotypic switching of surface lipoprotein antigens in the bovine pathogen Mycoplasma bovis. This study revealed that field strains of M. bovis possess modified versions of the vsp gene complex in which extensive sequence variations occur primarily in the reiterated coding sequences of the vsp structural genes. These findings demonstrate that there is a vastly expanded potential for antigenic variation within populations of this organism.

Amino Acid Sequence↗

PubMed1983

Cystic fibrosis is not caused by a defect in the gene coding for human complement C3.

A human genomic clone containing a portion of the structural gene for the third component of complement (C3) was used as a hybridization probe to DNA from two genetically informative families in which cystic fibrosis (CF) occurs. Several restriction fragment length polymorphisms (RFLPs) can be identified using the C3 probe, which appears to detect a high level of sequence variation in the general population. The inheritance of C3 RFLP was found to be independent of the inheritance of the CF phenotype. Assuming that CF is caused by a mutation affecting a single genetic locus, the demonstration that an allele of the C3 gene does not segregate with CF proves that a defect of complement C3 cannot be the cause of the disease.

Complement C3↗

PubMed1994

Cytogenetic characteristics of Chironomus balatonicus Devai, Wülker, Scholl (Diptera, Chironomidae) from the Chernobyl region.

A cytogenetic analysis was carried out on a population of Chironomus balatonicus (Chironomidae, Diptera) from Chernobyl, a highly radioactive area of the Kiev region. Several chromosomal aberrations were established unique to a population of Chironomus balatonicus living in an area contaminated by radioactive waste. Five new heterozygous inversions, deficiencies in arms C, D, E, F and chromatid breaks were found in the irradiated population but not in nonirradiated populations. A pericentric inversion in chromosome AB occurred at a relatively high frequency. Genome aberrations expressed by a heterochromatized 'B' chromosome were evident. In the irradiated and nonirradiated populations common inversions occurred showing variation in their frequency depending on specific environmental conditions. The somatic and also the germ cells were characterized by a number of heteropycnotic nuclei and vacuolized chromosomes. Both the somatic and germ cells showed changes in the structural and functional organization of heterochromatin and this was particularly marked in the telomeric sectors of the chromosomes. The heterochromatin which is extremely sensitive to radioactivity appears to protect euchromatin from adverse environmental conditions.

Animals↗

PubMed2004

Lineage-specific gene duplication and loss in human and great ape evolution.

Given that gene duplication is a major driving force of evolutionary change and the key mechanism underlying the emergence of new genes and biological processes, this study sought to use a novel genome-wide approach to identify genes that have undergone lineage-specific duplications or contractions among several hominoid lineages. Interspecies cDNA array-based comparative genomic hybridization was used to individually compare copy number variation for 39,711 cDNAs, representing 29,619 human genes, across five hominoid species, including human. We identified 1,005 genes, either as isolated genes or in clusters positionally biased toward rearrangement-prone genomic regions, that produced relative hybridization signals unique to one or more of the hominoid lineages. Measured as a function of the evolutionary age of each lineage, genes showing copy number expansions were most pronounced in human (134) and include a number of genes thought to be involved in the structure and function of the brain. This work represents, to our knowledge, the first genome-wide gene-based survey of gene duplication across hominoid species. The genes identified here likely represent a significant majority of the major gene copy number changes that have occurred over the past 15 million years of human and great ape evolution and are likely to underlie some of the key phenotypic characteristics that distinguish these species.

Animals↗

PubMed1994

Structure of recombinants from conjugational crosses between Escherichia coli donor and mismatch-repair deficient Salmonella typhimurium recipients.

To get more insight into the control of homologous recombination between diverged DNA by the Mut proteins of the long-patch mismatch repair system, we have studied interspecies Escherichia coli/Salmonella typhimurium recombination. Knowing that the same recombination pathway (RecABCD) is responsible for intraspecies and interspecies recombination, we have now studied the structure (replacement vs. addition-type or other rearrangement-type recombinants) of 81 interspecies recombinants obtained in conjugational crosses between E. coli donor and mutL, mutS, mutH, mutU or mut+ S. typhimurium recipients. Taking advantage of high interspecies sequence divergence, a physical analysis was performed on one third of the E. coli Hfr genome, which was expected to be transferred to S. typhimurium F- recipients during 40 min before interruption of the mating. Probes specific for each species were hybridized on dot blots of genomic DNA, or on colonies, and the composition of the rrn operons was determined from purified genomic DNA. With very few exceptions, the structure of these interspecies recombinants corresponds to replacements of one continuous block of the recipient genome by the corresponding region of the donor genome.

Base Sequence↗

PubMed1985

Orthopoxvirus DNA: a comparison of restriction profiles and maps.

Characteristic DNA endonuclease digest fragment electropherograms and restriction site maps permitted differentiation and genome structure analysis of 38 orthopoxviruses that included isolates of monkeypox virus from humans and animals, monkeypox white variants, variola, vaccinia, ectromelia, Tatera (gerbil) and raccoon poxviruses, and cowpox and camelpox viruses. HindIII cleavage sites mapped on the 38 virus genome DNAs plus SmaI, BglI, SacI, KpnI, XhoI, and SalI maps for variola (Harvey) and monkeypox (Copenhagen) virus DNAs were derived essentially by cross-hybridizations with monkeypox, vaccinia, and variola virus-cloned DNA restriction fragments, thus digest fragments could be assigned homologous regions on previously established genome maps. Salient of our observations, the DNA HindIII maps correlated to a high degree, but variations in middle and especially terminal DNA region cleavage sites provided a basis for discerning species, strains and variants. The extent of the inverted terminal repetitions (ITRs) for 37 DNAs were determined with HindIII, PvuI, SalI, and ClaI, plus nine more restriction enzymes for Bangladesh variola virus DNA by hybridizations with either the terminal tandemly repeated 70-bp segment or an EcoRI-PvuI near hairpin-end 75-bp segment from WR vaccinia virus. The opposite terminal regions of variola DNA were considerably asymmetrical compared to the large symmetrical ITRs of the other species examined. An apparent DNA inversion and concurrent deletion (1 kbp) with subsequent repair of DNA to original structure was suggested from right terminal region maps of four viruses chosen from a variola virus passage series in monkeys. Correlative with virus geographic distribution, two strains of monkeypox virus, each containing two variants, were differentiated by DNA profiles of isolates from smallpox-like disease (SLD) patients of the African rainforest region. The DNAs of five monkeypox viruses isolated from laboratory and zoo animals resembled most DNAs from SLD monkeypox viruses from Sierra Leone. A poxvirus from an American raccoon contained 40% DNA that did not cross-hybridize with orthopoxvirus DNA probes. The DNAs of recent isolates from a gerbil and from a camel each mapped as unique African orthopoxvirus species and differed from variola virus.

Animals↗

PubMed1994

The exon structure of the mouse alpha 2(IX) collagen gene shows unexpected divergence from the chick gene.

One cosmid and two overlapping phage clones covering the entire mouse alpha 2(IX) collagen gene including 12 kilobase pairs (kb) of 5'- and 8 kb of 3'-flanking sequences were isolated from two genomic libraries. The overall gene structure was determined by restriction mapping and nucleotide sequencing. The gene spans 16 kb from the start of transcription to the polyadenylation site and contains 32 exons. It codes for a mRNA of 3 kb that translates into a polypeptide of 688 amino acids. The intron-exon junctions and mRNA structure were confirmed by amplification of cDNA made for mouse cartilage RNA. The coding sequence of the mouse alpha 2(IX) collagen gene shows marked similarities to those for other type IX collagen chains. Although the overall exon-intron organization of the mouse gene is very similar to the chick alpha 2(IX) gene, some unexpected differences were observed at the splice junctions. Split codons characteristic for the central triple helical domain of the chick were not found in the mouse gene that thus exhibited a long stretch of exons with sizes that are multiples of 9 base pairs in this domain. The promoter of the mouse alpha 2(IX) collagen gene contains some G + C-rich elements including three Sp1 consensus recognition sites and a far upstream CCAAT box but no TATAA box. Both primer extension and RNase protection assays revealed several transcription start sites within 418 base pairs of the promoter. The present study reports the first complete nucleotide sequence of any type IX collagen gene and forms the basis for comparative structural studies on this collagen type and for experiments involving transgenic mice.

Amino Acid Sequence↗

PubMed1999

Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon.

We describe here the presence of two distinct types of rRNA operons in the genome of a thermophilic actinomycete Thermomonospora chromogena. The genome of T. chromogena contains six rRNA operons (rrn), of which four complete and two incomplete ones were cloned and sequenced. Comparative analysis revealed that the operon rrnB exhibits high levels of sequence variations to the other five nearly identical ones throughout the entire length of the operon. The coding sequences for the 16S and 23S rRNA genes differ by approximately 6 and 10%, respectively, between the two types of operons. Normal functionality of rrnB is concluded on the basis of the nonrandom distribution of nucleotide substitutions, the presence of compensating nucleotide covariations, the preservation of secondary and tertiary rRNA structures, and the detection of correctly processed rRNAs in the cell. Comparative sequence analysis also revealed a close evolutionary relationship between rrnB operon of T. chromogena and rrnA operon of another thermophilic actinomycete Thermobispora bispora. We propose that T. chromogena acquired rrnB operon from T. bispora or a related organism via horizontal gene transfer.

Actinomycetales↗

PubMed2025

Tales of a Super Butterfly: Is Vanessa carye a Truly Migrant Species? Unraveling Migration Using Morphological and Genomics Approaches.

Among movement strategies, migratory behavior is particularly intriguing in insects. Home-breeding is often permanent, and return journeys can take several generations. Although migration is crucial to the ecological and evolutionary processes of the species involved, knowledge of insect migratory behavior needs to be better understood. Vanessa carye, a butterfly native to South America with a latitudinal range of ∼7,000 km, exemplifies this problem. This study analyzed samples collected across the species' range using single-nucleotide polymorphisms (SNPs) to assess population structure, genetic diversity, and geometric morphometrics to examine wing shape variation. Results indicate that V. carye forms a genetically homogeneous unit composed of only two potential populations spanning ∼5,000 km, geographically correlated with the Pacific Ocean and the Andes, maintaining constant gene flow, and with a mean heterozygosity of 5.74% (SE: ±0.048%). Geometric morphometrics detected no geographic differentiation in wing shapes and sizes across ∼7,000 km, suggesting an absence of local adaptation and indicating a conserved wing shape adapted to flight throughout the species' range. Our findings support V. carye as a migratory species with the longest migratory journey among American butterflies, revealing two migratory routes. With these approaches, we provide a consistent methodological framework for migratory studies in species with important gaps in knowledge of their natural history.

Animals↗

PubMed1988

Structural organization and evolution of the plastid genome of Vaucheria sessilis (Xanthophyceae).

The plastid DNAs of 18 Vaucheria sessilis strains from various habitats in western Europe were digested with the restriction endonucleases Eco RI, Sal I, Bam HI and Pvu II. Their restriction patterns showed variable fragment divergencies. Two main groups of plastid genomes were recognized, which were substantiated by morphological features. The differences among the restriction patterns could be attributed to the loss or appearance of restriction sites and to minor size variations caused by deletions/insertions. The Sal I and Bam HI restriction sites which together discriminate six different plastid genomes were mapped on the circular molecule of 124 kilobase paris (kbp). The plastid genomes of several Vaucheria sessilis strains were shown to exist in two inversion isomers caused by intramolecular recombination within the inverted repeat segments.

Biological Evolution↗

PubMed2000

[Genetic structure of geographically different populations of candida albicans].

Codominant single-locus markers were developed by amplifying genomic DNA of C. albicans with pairs of random primers. Monomorphic PCR products were screened for polymorphisms by the SSCP technique. Sequencing confirmed that SSCP's were mostly due to single nucleotide substitutions in the polymorphic fragments. A total of 85 polymorphic loci were observed within 13 PCR fragments. Populations from Africa displayed less genotype variation than the populations from Europe and USA. Two genetically similar African C. albicans populations exhibiting an atypical biotype were strictly clonal and perhaps represent a geographically distributed clone. Analyses of "typical" C. albicans populations of different geographical origin provided however evidence for both clonality and recombination. Evidence for clonality was supported by the absence of segregation genotypes, and by deviation of genotypic frequencies from Hardy-Weinberg expectations. Tests for nonrandom association of alleles across loci revealed less evidence for linkage disequilibrium than expected for strictly clonal populations. Although all C. albicans populations tested were primarily clonal, evidence for recombination suggests that sexual reproduction or some other form of genetic exchange occurs in this species.

Africa↗

PubMed1992

The genetic legacy of Mother Goose--phylogeographic patterns of lesser snow goose Chen caerulescens caerulescens maternal lineages.

By using the polymerase chain reaction to amplify and sequence 178 bp of a rapidly evolving region of the mtDNA genome (segment I of the control region) from 81 individuals, approximately 11% of the variation present in the lesser snow goose Chen caerulescens caerulescens L. mitochondrial genome was surveyed. The 26 types of mtDNA detected formed two distinct mitochondrial clades that differ by an average of 6.7% and are distributed across the species range. Restriction analysis of amplified fragments was then used to assign the mtDNA of an additional 29 individuals to either of these clades. Within one major clade, sequence among mtDNAs was concordant with geographic location. Within the other major clade the degree of sequence divergence among haplotypes was lower and no consistent geographic structuring was evident. The two major clades presumably result from vicariant separation of lesser snow geese during the Pleistocene.

Animals↗

PubMed2007

A genomically/chemically complete module for synthesis of lipid membrane in a minimal cell.

A minimal cell is a hypothetical cell defined by the essential functions required for life. We have developed a module for the synthesis of membrane precursors for a mathematical minimal cell model. This module describes, with chemical and genomic detail the production of the constituents required to build a cell membrane and identifies the corresponding essential genes. Membranes allow selective nutrient passage, harmful substance exclusion, and energy generation. Bacterial membrane components range from lipids to fatty acids with embedded proteins and are structurally similar to eukaryotic cell membranes. Membranes are dynamic structures and experimental analyses show great variations in bacterial membrane composition. The flexibility of the model is such that different membrane compositions could be obtained in response to simulated changes in culture conditions. The model's predictions are in close agreement with the observed biological trends. The model's predictions correspond well with the experimental values of total lipid content in cells grown in chemostat culture, but less well with data from batch growth. Cell shape and size results agree especially well for data for growth rate relative to maximum growth rate larger than 0.5; and DNA, RNA, and protein predictions are consistent with experimental observations. A better understanding of the simplest bacterial membrane should lead to insights on the more complex behavior of membranes of higher species as well as identification of potential targets for antimicrobials.

Biotechnology↗

PubMed1994

Novel structure of a Chinese hamster polyubiquitin gene.

We isolated a polyubiquitin gene, CHUB2, from the V79 Chinese hamster genomic library, and determined its complete structure. Based on sequence homology to the human polyubiquitin gene UbC in the 5' and 3' untranslated region, the CHUB2 gene was characterized as the V79 Chinese hamster equivalent to the human UbC gene. However, the overall coding region structure of the CHUB2 gene was altered from the consensus structure of polyubiquitin genes, with the last ubiquitin coding unit being followed by 161 bp of partially deleted and mutated ubiquitin-like sequence. Although a similarly deleted and mutated polyubiquitin gene was recently reported in a partially sequenced cDNA of mouse (Finch et al. (1992) Cell Growth Differ. 3, 269-278), the present study describes the complete sequence of a polyubiquitin gene containing this unusual structure for the first time, and suggests that this structure is conserved in rodents. By employing both Southern and Northern analysis with a probe specific to the CHUB2 gene, it was found that a second, closely related gene is present in the Chinese hamster genome, and that both loci are transcriptionally active in V79 cells. The two genes, and their respective transcripts, differ in size because of variation in the relative number of repeating ubiquitin coding units.

Amino Acid Sequence↗

PubMed1983

Nucleotide sequence of cloned complementary deoxyribonucleic acid for the alpha subunit of bovine pituitary glycoprotein hormones.

Recombinant DNA plasmids containing sequences coding for the alpha subunit of the bovine pituitary glycoprotein hormones have been isolated. The nucleotide sequences of three different cDNA clones have been determined. The largest alpha-subunit cDNA clone was found to contain 713 bases including 77 nucleotides from the 5'-untranslated region, 72 nucleotides coding for a precursor segment, 288 nucleotides coding for the mature alpha subunit, and 276 nucleotides from the 3'-untranslated region of the mRNA followed by a poly(A) segment. This cDNA likely represents most of the bovine alpha-subunit mRNA sequence. Nucleotide sequences were obtained from the cDNA inserts of two other alpha-subunit clones, and several differences among the three cDNA sequences have been detected. These differences in nucleotide sequence may represent either individual variation in genomic sequence or cloning artifacts. Comparison of the bovine alpha-subunit cDNA sequence to the sequences of human, rat, and mouse alpha-subunit cDNAs reveals that the bovine sequence has greater than 70% homology with the other cDNAs. The cloned alpha-subunit cDNA should provide a useful probe for further studies of the structure and expression of this interesting gene.

Amino Acid Sequence↗

PubMed1976

Genetic heterogeneity within electrophoretic "alleles" of xanthine dehydrogenase in Drosophila pseudoobscura.

An experimental plan for an exhaustive determination of genic variation at structural gene loci is presented. In the initial steps of this program, 146 isochromosomal lines from 12 geographic populations of D. pseudoobscura were examined for allelic variation of xanthine dehydrogenase by the serial use of 4 different electrophoretic conditions and a head stability test. The 5 criteria revealed a total of 37 allelic classes out of the 146 genomes examined where only 6 had been previously revealed by the usual method of gel electrophoresis. This immense increase in genic variation also showed previously unsuspected population differences between the main part of the species distribution and the isolated population of Bogotá population. The average heterozygosity at the Xdh locus is at least 72% in natural populations. This result, together with the very large number of alleles segregating and the pattern of allelic frequencies, has implications for theories of genetic polymorphism which are discussed.

Alleles↗

PubMed2003

A genome-wide scan for loci affecting normal adult height in the Framingham Heart Study.

OBJECTIVE: To map loci influencing normal adult height in 335 families from the Framingham Heart Study. METHODS: We analyzed data consisting of 1,702 genotyped individuals who have been followed over time. The first height measurement for individuals between the ages 20-55 years was analyzed in a genome-wide scan using variance component linkage analysis. Sex, age, and cohort effects were removed before analysis. RESULTS: Two regions (18pter-p11, 22q11.2) with multipoint LOD scores >1.0 (-log p values >2.0) were detected: we obtained LOD scores of 1.38 at D18S1364, and of 1.10 at D22S345. Analysis of height as a sex-limited phenotype revealed a peak in the 9p21 region near D9S319 with a maximum LOD score of 1.65 (-log p value >3.0) when only male height phenotypes were used. When only female phenotypes were used, a peak with a maximum LOD score of 1.85 (-log p value of 2.70) was observed in the 11q25-qter region near D11S2359. CONCLUSIONS: Our region of interest on chromosome 9 has been implicated by two prior studies. Variance components analysis appeared to be sensitive to pedigree structures as well as the method of IBD computation used.

Adolescent↗

PubMed1995

Characterization of a LINE-1 cDNA that originated from RNA present in ribonucleoprotein particles: implications for the structure of an active mouse LINE-1.

Full-length, sense-strand, long interspersed element-1 (LINE-1 or L1) RNA is found as an RNA-protein complex in mouse embryonal carcinoma cells. Since this complex is a likely intermediate in LINE-1 transposition, its RNA may be enriched for the functional, or active, subset of mouse L1 sequences. For this reason, a cDNA library was constructed from RNA prepared from these ribonucleoprotein particles. The isolation and complete DNA sequence of one clone that is a strong candidate to be a functional version of mouse L1 is reported here. The structure of this element suggests a revision of the predicted sequence of an active mouse L1 and provides a tag that can be used to isolate its locus in the genome.

Animals↗