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PubMed1999

Linkage disequilibrium mapping of molecular polymorphisms at the scabrous locus associated with naturally occurring variation in bristle number in Drosophila melanogaster.

We evaluated the hypothesis that the Drosophila melanogaster second chromosome gene scabrous (sca), a candidate sensory bristle number quantitative trait locus (QTL), contributes to naturally occurring variation in bristle number. Variation in abdominal and sternopleural bristle number was quantified for wild-derived sca alleles in seven genetic backgrounds: as homozygous second chromosomes (C2) in an isogenic background, homozygous lines in which approximately 20 cM including the sca locus had been introgressed into the isogenic background (sca BC), as C2 and sca BC heterozygotes and hemizygotes against a P element insertional sca allele and a P-induced sca deficiency in the same isogenic background, and as sca BC heterozygotes against the wild-type sca allele of isogenic strain. Molecular restriction map variation was determined for a 45 kb region including the sca locus, and single-stranded conformational polymorphism (SSCP) was examined for the third intron and parts of the third and fourth exons. Associations between each of the 27 molecular polymorphisms and bristle number were evaluated within each genotype and on the first principal component score determined from all seven genotypes, separately for each sex and bristle trait. Permutation tests were used to assess the empirical significance thresholds, accounting for multiple, correlated tests, and correlated markers. Three sites in regulatory regions were associated with female-specific variation in abdominal bristle number, one of which was an SSCP site in the region of the gene associated with regulation of sca in embryonic abdominal segments.

Animals↗
PubMed1989

Probing molecular polymorphism of fibronectins with antibodies directed to the alternatively spliced peptide segments.

Molecular heterogeneity of fibronectins (FNs) isolated from plasma, cultured fibroblasts, and placenta was studied with site-specific antibodies recognizing alternatively spliced peptide segments, termed ED-A and IIICS/delta 2. The antibodies were raised in rabbits by immunization with synthetic peptides. Neither the ED-A nor the IIICS/delta 2 extra peptide segment was present in the major subunits of plasma FN, although a minor subunit contained the latter extra segment. Cellular FN consisted of at least four subunits differing in size of the fragments generated by cleavage of the C-terminal region with cathepsin D. These fragments were distinct from each other in the reactivity with anti-ED-A and anti-IIICS/delta 2 antibodies, suggesting that all combinations of the presence or absence of the extra segments were produced by cultured fibroblasts. Placental FN was more heterogeneous than plasma and cellular FNs, consisting of five, or probably more, subunits. Among these, the two smaller subunits appeared to be closely similar to the major subunits of plasma FN, whereas the other subunits were more related to those of cellular FN in the size of cathepsin D cleaved C-terminal fragments and in the reactivity with anti-peptide antibodies. These results, taken together, indicate that the FNs produced by different tissues or cell types are distinct from each other in the number and types of subunits, which are partly, if not all, defined by alternative splicing at the ED-A and IIICS regions.

Antibodies↗
PubMed1997

Polymorphic molecular markers from anonymous nuclear DNA for genetic analysis of populations.

A simple method is presented for developing polymorphic, anonymous DNA markers suitable for population genetic studies. Anonymous DNA fragments are screened for sequence variability using a common mutation detection technique (single strand conformation polymorphism analysis; SSCP) and locus-specific PCR primers are designed for polymorphic DNA fragments. Detection of the markers by SSCP analysis coupled with sequence analysis of SSCP variants allows rapid screening while retaining information about the genealogical relationship among alleles. Variability detected for six markers was assessed in rainbow trout Oncorhynchus mykiss and was compared with variability detected by similar analysis of intron loci. Between three and 12 distinct alleles were observed at each marker locus, and average within-population heterozygosity ranged from 0.12 to 0.44. Advantages and limitations of the methodology for population genetic analysis are discussed.

Alleles↗
PubMed1981

Molecular polymorphism of ciliary proteins from different species of the ciliate Tetrahymena.

Ciliary proteins from five different Tetrahymena species were analyzed by means of SDS-polyacrylamide gel electrophoresis. Of at least 32 different polypeptides, only 2 were found to have identical molecular weights in all species. In any comparison of 2 species, a maximum of 60% and at least 20% of the proteins had indistinguishable molecular weights, depending on the combination examined. Extensive codominance of ciliary proteins was found in a F1 hybrid. No interspecific cross-reactions occurred in double-diffusion tests involving the cilia from different species and antisera produced against them in rabbits.

Animals↗
PubMed2001

Zebrafish acetylcholinesterase is encoded by a single gene localized on linkage group 7. Gene structure and polymorphism; molecular forms and expression pattern during development.

We cloned and sequenced the acetylcholinesterase gene and cDNA of zebrafish, Danio rerio. We found a single gene (ache) located on linkage group LG7. The relative organization of ache, eng2, and shh genes is conserved between zebrafish and mammals and defines a synteny. Restriction fragment length polymorphism analysis was allowed to identify several allelic variations. We also identified two transposable elements in non-coding regions of the gene. Compared with other vertebrate acetylcholinesterase genes, ache gene contains no alternative splicing at 5' or 3' ends where only a T exon is present. The translated sequence is 60-80% identical to acetylcholinesterases of the vertebrates and exhibits an extra loop specific to teleosts. Analysis of molecular forms showed a transition, at the time of hatching, from the globular G4 form to asymmetric A12 form that becomes prominent in adults. In situ hybridization and enzymatic activity detection on whole embryos confirmed early expression of the acetylcholinesterase gene in nervous and muscular tissues. We found no butyrylcholinesterase gene or activity in Danio. These findings make zebrafish a promising model to study function of acetylcholinesterase during development and regulation of molecular forms assembly in vivo.

Acetylcholinesterase↗
PubMed2005

From phenotypic to molecular polymorphisms involved in naturally occurring variation of plant development.

An enormous amount of naturally occurring genetic variation affecting development is found within wild and domesticated plant species. This diversity is presumably involved in plant adaptation to different natural environments or in human preferences. In addition, such intraspecific variation provides the basis for the evolution of plant development at larger evolutionary scales. Natural phenotypic differences are now amenable to genetic dissection up to the identification of causal DNA polymorphisms. Here we describe 30 genes and their functional nucleotide polymorphisms currently found as underlying allelic variation accounting for plant intraspecific developmental diversity. These studies provide molecular and cellular mechanisms that determine natural variation for quantitative and qualitative traits such as: fruit and seed morphology, colour and composition; flowering time; seedling emergence; plant architecture and inflorescence or flower morphology. Besides, analyses of flowering time variation within several distant species allow molecular comparisons between species, which are detecting homologous genes with partly different functions and unrelated genes with analogous functions. Thus, considerable gene function differences are being revealed also among species. Inspection of a catalogue of intraspecific nucleotide functional polymorphisms shows that transcriptional regulators are the main class of genes involved. Furthermore, barely more than half of the polymorphisms described are located in coding regions and affect protein structure, while the rest are regulatory changes altering gene expression. These limited analyses of intraspecific developmental variation support Doebley and Lukens's proposition (1998) that modifications in cis -regulatory regions of transcriptional regulators represent a predominant mode for the evolution of novel forms, but await more detailed studies in wild plant species.

Adaptation, Physiological↗
PubMed1990

An analysis of molecular polymorphism of esterase M produced by motile Aeromonas strains.

The high levels of electrophoretic polymorphism of esterase M detected in eight distinct hybridization groups of motile Aeromonas raise questions of genetic homogeneity of the electromorphs. The 40 electromorphs detected fall in four Mr classes--75, 80, 90, and 110 kD--and one typical variant belonging to each of these classes was purified. The four purified esterases exhibited the same resistance to heat, to pH and to diisopropyl fluorophosphate, the same Km values for 1-naphthyl acetate and 1-naphthyl propionate (1 mM), and immunological cross-reactions. Within each class, the electromorphs appeared to be related in term of single amino acid substitutions as estimated from their comparative titration patterns. The titration curves of the four purified esterases were strictly parallel suggesting close structural similarities. Thus, despite considerable variation in their pI, MF, and Mr values, it seems likely that the variants of esterase M are the products of closely related loci originating from a common ancestral gene.

Aeromonas↗
PubMed1992

Molecular polymorphisms of house dust mite allergens.

Previous studies from this laboratory have described the primary amino acid sequences of the group I and group II allergens from Dermatophagoides pteronyssinus and D. farinae. This report concentrates on polymorphisms of allergens within a species. Firstly, four cDNA clones of Der fII produced by polymerase chain reaction have been sequenced and are compared to the sequences published previously by ourselves and others. Although the sequences come from different sources, Australia and Japan, the overriding conclusion is one of similarity, with only two possible non-conservative changes in the six sequences. The nucleotides were also very conserved including the 3' untranslated regions, although some non-coding differences could be found which may provide a genetic marker. Experiments are reported to help define the group III D. pteronyssinus allergens. Previous studies have characterised the group III of D. farinae as a Mr 29-kDa molecule which can be defined by monoclonal antibodies. A Mr 17-kDa molecule of D. pteronyssinus has been reported with an almost identical N-terminal sequence. Here it is described that Der fIII isolated from different preparations of spent mite media by affinity chromatography have predominantly Mr 32-, 28- and 21-kDa forms which vary in degree from batch to batch. 83% of adults and 38% of children react with the preparation by radioimmune dot-blot. The difference between the children and adults is statistically significant and reactivity can be to at least the 32- and 28-kDa form. Antisera produced in mice against the Der fIII react to D. pteronyssinus mite extract by Western blotting primarily to a 32-kDa moiety, but also 28- and 21-kDa forms in some extracts.

Allergens↗
PubMed1987

Molecular polymorphism of head acetylcholinesterase from adult houseflies (Musca domestica L.).

Acetylcholinesterase (AChE) from housefly heads was purified by affinity chromatography. Three different native forms were separated by electrophoresis on polyacrylamide gradient gels. Two hydrophilic forms presented apparent molecular weights of 75,000 (AChE1) and 150,000 (AChE2). A third component (AChE3) had a migration that depended on the nature and concentration of detergents. In the presence of sodium deoxycholate in the gel, AChE3 showed an apparent molecular weight very close to that of AChE2. Among the three forms, AChE3 was the only one found in purified membranes. The relationships among the various forms were investigated using reduction with 2-mercaptoethanol or proteolytic treatments. Such digestion converted purified AChE3 into AChE2 and AChE1, and reduction of AChE3 and AChE2 by 2-mercaptoethanol gave AChE1, in both cases with a significant loss of activity. These data indicate that the three forms of purified AChE may be classified as an active hydrophilic monomeric unit (G1) plus hydrophilic and amphiphilic dimers. These two components were termed G2s and G2m, where "s" refers to soluble and "m" to membrane bound.

Acetylcholinesterase↗
PubMed2003

Perspective: detecting adaptive molecular polymorphism: lessons from the MHC.

In the 1960s, when population geneticists first began to collect data on the amount of genetic variation in natural populations, balancing selection was invoked as a possible explanation for how such high levels of molecular variation are maintained. However, the predictions of the neutral theory of molecular evolution have since become the standard by which cases of balancing selection may be inferred. Here we review the evidence for balancing selection acting on the major histocompatibility complex (MHC) of vertebrates, a genetic system that defies many of the predictions of neutrality. We apply many widely used tests of neutrality to MHC data as a benchmark for assessing the power of these tests. These tests can be categorized as detecting selection in the current generation, over the history of populations, or over the histories of species. We find that selection is not detectable in MHC datasets in every generation, population, or every evolutionary lineage. This suggests either that selection on the MHC is heterogeneous or that many of the current neutrality tests lack sufficient power to detect the selection consistently. Additionally, we identify a potential inference problem associated with several tests of neutrality. We demonstrate that the signals of selection may be generated in a relatively short period of microevolutionary time, yet these signals may take exceptionally long periods of time to be erased in the absence of selection. This is especially true for the neutrality test based on the ratio of nonsynonymous to synonymous substitutions. Inference of the nature of the selection events that create such signals should be approached with caution. However, a combination of tests on different time scales may overcome such problems.

Adaptation, Biological↗
PubMed1988

Molecular polymorphism of a cell surface proteoglycan: distinct structures on simple and stratified epithelia.

Epithelial cells are organized into either a single layer (simple epithelia) or multiple layers (stratified epithelia). Maintenance of these cellular organizations requires distinct adhesive mechanisms involving many cell surface molecules. One such molecule is a cell surface proteoglycan, named syndecan, that contains both heparan sulfate and chondroitin sulfate chains. This proteoglycan binds cells to fibrillar collagens and fibronectin and thus acts as a receptor for interstitial matrix. The proteoglycan is restricted to the basolateral surface of simple epithelial cells, but is located over the entire surface of stratified epithelial cells, even those surfaces not contacting matrix. We now show that the distinct localization in simple and stratified epithelia correlates with a distinct proteoglycan structure. The proteoglycan from simple epithelia (modal molecular size, 160 kDa) is larger than that from stratified epithelia (modal molecular size, 92 kDa), but their core proteins are identical in size and immunoreactivity. The proteoglycan from simple epithelia has more and larger heparan sulfate and chondroitin sulfate chains than the proteoglycan from stratified epithelia. Thus, the cell surface proteoglycan shows a tissue-specific structural polymorphism due to distinct posttranslational modifications. This polymorphism likely reflects distinct proteoglycan functions in simple and stratified epithelia, potentially meeting the different adhesive requirements of the cells in these different organizations.

Animals↗
PubMed1994

Molecular polymorphism as a tool for differentiating ground beetles (Carabus species): application of ubiquitin PCR/SSCP analysis.

Differentiation between Carabus species (ground beetle) and subspecies is difficult, although there have been extensive studies. To address this problem we have applied PCR in combination with SSCP analysis focussing on the evolutionally conservative ubiquitin gene to elaborate a new approach to molecular differentiation between species. We report that Carabidae possess an ubiquitin gene and that its gene has a multimeric structure. Differential SSCP analysis was performed with the monomeric form of the gene to generate a clear SSCP pattern. Such PCR/SSCP resulted in reproducible patterns throughout our experiments. Comparing different Carabus species (Carabus granulatus, C. irregularis, C. violaceus and C. auronitens) we could observe clear interspecies differences but no differences between genders. Some species showed some remarkable differences between the individuals. We suggest that the ubiquitin PCR-SSCP technique might be an additional tool for the differentiation of ground beetles.

Animals↗
PubMed1998

Virulence and molecular polymorphism of Prunus necrotic ringspot virus isolates.

Prunus necrotic ringspot virus (PNRSV) occurs as numerous strains or isolates that vary widely in their pathogenic, biophysical and serological properties. Prior attempts to distinguish pathotypes based upon physical properties have not been successful; our approach was to examine the molecular properties that may distinguish these isolates. The nucleic acid sequence was determined from 1.65 kbp RT-PCR products derived from RNA 3 of seven distinct isolates of PNRSV that differ serologically and in pathology on sweet cherry. Sequence comparisons of ORF 3a (putative movement protein) and ORF 3b (coat protein) revealed single nucleotide and amino acid differences with strong correlations to serology and symptom types (pathotypes). Sequence differences between serotypes and pathotypes were also reflected in the overall phylogenetic relationships between the isolates.

Amino Acid Sequence↗
PubMed1996

Molecular polymorphisms associated with host range in the highly conserved genomes of burrowing nematodes, Radopholus spp.

Six polymorphic bands of DNA were amplified from purified Radopholus citrophilus genomic DNA from one strain of each of the sibling species R. citrophilus and R. similis in random amplified polymorphic DNA analyses involving 380 single 10-base primers. Four of these polymorphic DNA fragments were successfully cloned and amplified through subsequent use of primers designed to complement the terminal sequences of the polymorphic DNA. Results of ensuing studies using mini-prepped DNA from 14 burrowing nematode strains collected from Florida, Hawaii, and Central America, characterized for their ability to parasitize citrus, indicated that a 2.4-kb fragment appeared to be associated with citrus parasitism in burrowing nematode populations from Florida. However, a fragment of comparable size was also detected in R. citrophilus from Hawaii and from burrowing nematode populations collected from Belize and Puerto Rico. Overall, findings suggest that the genome organization of the burrowing nematode sibling species R. citrophilus and R. similis is highly conserved. This remarkable genetic similarity should facilitate identification of genetic sequence related to important phenotypes such as citrus parasitism. Detection of R. citrophilus-specific DNA fragments in burrowing nematodes collected from Belize and Puerto Rico suggests that R. citrophilus is resident in some Central American countries.

Animals↗