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PubMed2000

Crystallographic and molecular mechanics investigation of an order-disorder transition and dimorphism in 5H,10H-dithiolo

Single-crystal X-ray structures are presented for three forms of 5H, 10H-dithiolo[2,3-b]-2,5-benzodithiocine-2-thione. The alpha (at 150 K) and alpha' (at ambient) forms are very similar and differ only in the presence of crystallographic m symmetry in the molecules of alpha', which is absent in the case of alpha. This pair is related by an order-disorder transition. The beta phase (also determined at 150 K) has a different structure in terms of the molecular packing from either of the other two and therefore constitutes a true polymorph. Molecular mechanics calculations indicated that the most stable CHCl(3)-solvated conformations for the title compound were a pair of twisted U-shaped enantiomers, U(R) and U(L), i.e. similar to the arrangements found in the alpha and beta phases, with the low-lying saddle point between them corresponding to the situation in the alpha' phase. These calculations also indicated that the most stable CHCl(3)-solvated conformation for the related dibromo-5H, 10H-dithiolo[2,3-b]-2,5-benzodithiocine-2-thione was Z-shaped, in agreement with the crystal structure determined earlier for its DMSO solvate [Wang et al. (1998). Synthesis, pp. 1615-1618].

Journal Article↗

PubMed1997

High rates of polymorphism and recombination at the Opaque-2 locus in cultivated maize.

As a first step in the study of the functional consequences of molecular polymorphism at the Opaque-2 locus in maize, 1933 bp of the gene were sequenced in 21 inbred lines representative of the progenitors of cultivated varieties. High levels of polymorphism were found: 109 sites were variable in non-coding regions and 159 in protein-coding regions. Among the latter, 103 were nonsynonymous, resulting in 94 amino acid replacements in a 422-residue peptide. Moreover, 26 insertion/deletion polymorphisms were found, eight of them in coding regions. The high rate of polymorphism observed could indicate that the effective size of the ancestral population was very large, and/or that the O2 gene evolved under the influence of a high mutation rate or was subjected to some kind of balancing selection. The distribution of polymorphism within the sequence was not uniform. Silent polymorphisms were relatively frequent in exon 1 and rare in intron 5, whereas nonsynonymous polymorphisms were infrequent in the part of the sequence encoding the active domain of the transcription factor. The peptide sequence also showed a relatively higher level of resistance to amino acid replacements in this region. Sites in linkage disequilibrium were arranged mainly in three spatial patterns. This mosaic pattern can be related with an apparently large number of recombination events which might be a characteristic feature of this particular sample and/or imply that the O2 locus is a hot spot for recombination.

Base Sequence↗

PubMed1999

Loss of heterozygosity and protein expression of APC gene in renal cell carcinomas.

This study evaluated the potential contribution of the APC gene to malignant transformation in patients with renal cell carcinoma. We tested 36 human renal cell carcinoma samples and 18 adjacent normal kidney tissues for the expression of APC protein, both wild and truncated types, by western blot using antibodies that recognize either the carboxy or the amino epitope of the APC protein. The same tumor samples together with autologous peripheral blood were also analyzed at the DNA level. Using specific oligonucleotide primers for exons 11 and 15, gene instability was followed by polymerase chain reaction/loss of heterozygosity (LOH) (on the basis of restriction fragment length polymorphism). Molecular data were also compared to pathohistological diagnosis, TNM stage, and patient's age using multivariate statistical methods. All normal renal tissues revealed expression of the wild-type APC protein. Neither wild nor mutant type proteins were found in 36% (13/36) of tumor samples; the rest of tumor tissues expressed the wild-type protein (312 kDa). Mutated APC protein, with a molecular weight of 117 kDa, was found in only one tumor sample. From 36 tumor samples 16 (44.4%) were informative for RsaI exon 11 polymorphic site, while only half of these (8/16) demonstrated LOH. From 13 tumor samples that had no detectable protein product by western blot analysis eight were homozygous for the exon 11 polymorphism and were tested for another polymorphic site, MspI/exon 15. The overall proportion of LOH cases for both polymorphisms tested was 52.9% (9/17). Pathohistological diagnosis and molecular data showed no correlation. However, multivariate analysis determined a stage strong positive correlation of age and TNM with the presence of LOH and the absence of the wild-type APC protein. Out results suggest that the APC tumor suppressor gene plays a role in renal carcinogenesis. Alterations in this gene are responsible for tumor evolution and progression, but cannot be considered as a first event in tumor initiation.

Adenomatous Polyposis Coli Protein↗

PubMed1992

Detection of polymorphic loci in Arachis germplasm using random amplified polymorphic DNAs.

The development of easily scoreable genetic markers in Arachis will facilitate the introgression of desirable traits from wild species into adapted germplasm. We have used random amplified polymorphic DNAs (RAPDs) to identify polymorphic molecular markers in a range of wild and cultivated Arachis species. From a total of sixty 10-mer oligonucleotide primers, 49 polymorphic loci were identified between cultivated A. hypogaea type (TMV-2) and a synthetic amphidiploid (B x C)2 created from a A. batizocoi and A. chacoense cross. The inheritance of polymorphic markers, both in the amphidiploid and in the F1 progeny in a TMV-2 x (B x C)2 cross, has also been demonstrated. The potential exploitation of RAPD markers in groundnut improvement programs is discussed.

Arachis↗

PubMedDate not supplied

[Molecular and genetic polymorphism of cultivated soybean detected by AP-PCR, SSRP and SSR].

Molecular-genetic polymorphism of cultivated soybean from different geographic regions was analysed using three PCR methods (AP-PCR, SSRP and ISSR). The dendrogram of phenogenetic relationship was constructed on the base of obtained data. The allocation of varieties are in a good agreement with pedigree information. Main parameters such as polymorphism level, expected heterozygosity, and marker index were calculated. It was shown that ISSR is the method of choice for the differentiation of soybean varieties.

DNA, Plant↗

PubMed1980

The primary structure of the constant part of mu-chain-disease protein BOT.

The complete primary structure of the constant part of the mu-chain-disease protein, BOT, was established. It includes the whole CH2, CH3 and CH4 domains. two amino acid changes were found, at positions 309 (Ser leads to Gly) and 333 (Val leads to Gly) (GAL numbering). In two additional monoclonal mu chains (SCO and CO), the same positions showed an amino acid variability. From these data it may be concluded that four types of mu chains exist in the human: (1) GAL type with Ser-309 and Val-333; (2) OU type with Gly-309 and Val-333; (3) SCO type with Ser-309 and Gly-333; (4) BOT/CO type with Gly-309 and Gly-333. The meaning of this molecular polymorphism is discussed.

Amino Acid Sequence↗

PubMed1998

Polymorphisms of HLA class II genes and autoimmune responses to Ro/SS-A-La/SS-B among Japanese subjects.

OBJECTIVE: To investigate HLA class II allele associations with autoantibody responses to Ro/SS-A and La/SS-B among Japanese subjects. METHODS: Haplotype and allele distributions, along with molecular polymorphisms, of HLA class II genes were analyzed by polymerase chain reaction-restriction fragment length polymorphism in 41 Japanese women with precipitating autoantibodies to Ro/SS-A and/or La/SS-B. RESULTS: Among women with both Ro/SS-A and La/SS-B antibodies, the HLA class II haplotype DRB1*08032/DQA1*0103/DQB1*0601 and DRB1*08032 allele showed significantly increased frequencies compared with patients with anti-Ro/SS-A alone or with normal controls. All women with both anti-Ro/SS-A and anti-La/SS-B, but not those with anti-Ro/SS-A alone, carried DRB1 alleles that shared the same amino acid residues at positions 14-31 and 71 of the hypervariable regions of the DRB1 chain. All anti-Ro/SS-A positive women carried 1 or 2 alleles of DQB1*06 and DQB1*03 subtypes that shared the same amino acid residues at positions 71-77 of the DQB1 chain. HLA class II allele distributions did not differ among 3 anti-Ro/SS-A positive groups with different disease expressions, i.e., patients with systemic lupus erythematosus, patients with primary Sjögren's syndrome, and women with no apparent symptoms of rheumatic disease. CONCLUSION: HLA class II allele distributions differ among anti-Ro/SS-A positive subjects according to the presence or absence of coexisting anti-La/SS-B antibodies, but not according to disease expression. Our findings suggest that different HLA class II molecules might control the development of anti-Ro/SS-A and/or anti-La/SS-B antibodies in the autoimmune response to the Ro/SS-A-La/SS-B complex.

Adolescent↗

PubMed2001

[Molecular analysis of polymorphisms for B-LII beta(beta 1 exon) locus in some Chinese native chicken].

Molecular genetic polymorphisms were studied for MHC-B-LII beta(beta 1 exon) locus in ten breeds of chicken by PCR-RFLPs. Thirty-seven genotypes were detected in these chicken. In the 305 bp fragment derived from MHC-B-LII beta(beta 1 exon) locus digested with Hha I, EcoRV, HaeIII, Xba I, there were significant difference with the frequencies of genotype and combined genotype among individuals or breeds. Statistical results showed Hardy-Weinberg equilibrium in polymorphic sites were inconsistent among various breeds. Sequencing results suggested there are more polymorphism at the level of amino acid than at that of nucleotide. Furthermore, as antigen binding site, the highly polymorphisms of beta 1 exon sequence was a reflection to the antigen diversity of immune systems. Moreover, it was implied that there was highly association between genetic polymorphisms of beta 1 exon and reproduction performance in chicken.

Animals↗

PubMed2005

SINE insertion polymorphism on the X chromosome differentiates Anopheles gambiae molecular forms.

Polymorphic SINE insertions can be useful markers for assessing population structure and differentiation. Maque is a family of SINE elements which, based on bioinformatic analysis, was suggested to have been active recently in Anopheles gambiae, the major vector of malaria. Here, we report the development of polymorphic Maque insertions as population genetic markers in A. gambiae, and the use of these markers to better characterize divergence on the X chromosome between A. gambiae M and S molecular forms in populations from Burkina Faso and Mali. Our data are consistent with the recent activity of Maque. Phylogenetic analysis suggests that at least two recently active lineages may have a role in mediating genome evolution. We found differences in element insertion frequency and sequence between the M and S populations analysed. Significant differentiation was observed between these two groups across a 6 Mb region at the proximal (centromeric) end of the X chromosome. Locus-specific F(ST) values ranged from 0.14 to 1.00 in this region, yet were not significantly different from zero in more distal locations on the X chromosome; the trend was consistent in populations from both geographical locales suggesting that differentiation is not due to local adaptation. Strong differentiation between M and S at the proximal end of the X chromosome, but not outside this region, suggests the action of selection counteracting limited gene flow between these taxa and supports their characterization as incipient species.

Animals↗

PubMedDate not supplied

AFLP-based genetic linkage map for the red flour beetle (Tribolium castaneum).

The red flour beetle (Tribolium castaneum) is a major pest of stored grain and grain products and a popular model species for a variety of ecological, evolutionary, and developmental biology studies. Development of a linkage map based on reproducible and highly polymorphic molecular markers would greatly facilitate research in these disciplines. We have developed a genetic linkage map using 269 amplified fragment length polymorphism (AFLP) markers. Ten previously known random amplified polymorphic DNA (RAPD) markers were used as anchor markers for linkage group assignment. The linkage map was constructed through genotyping two independent F(2) segregating populations with 48 AFLP primer combinations. Each primer combination generated an average of 4.6 AFLP markers eligible for linkage mapping. The length of the integrated map is 573 cM, giving an average marker resolution of 2.0 cM and an average physical distance per genetic distance of 350 kb/cM. A cluster of loci on linkage group 3 exhibited significant segregation distortion. We have also identified six X-linked and two Y-linked markers. Five mapped AFLP fragments were sequenced and converted to sequence-tagged site (STS) markers.

Animals↗

PubMed1987

A large inverted duplication allows homologous recombination between chromosomes heterozygous for the proximal t complex inversion.

We have examined the molecular organization of a region of mouse chromosome 17 that allows homologous recombination between wild-type and t haplotype chromosomes across a large inversion. We have used a combination of genetic mapping of restriction fragment length polymorphisms, molecular characterization of cloned regions isolated on overlapping cosmids, and subchromosomal restriction mapping using the pulsed field gel technique. Our analyses show that the wild-type form of chromosome 17 contains an inverted duplication of an element of at least 650 kb that is present in only one copy in the t haplotype form. Two chromosomes, th45 and tAE5, arose by homologous recombination across the element that is present in both chromosomal variants in the same orientation.

Animals↗

PubMed2006

Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.).

Paucity of polymorphic molecular markers in chickpea (Cicer arietinum L.) has been a major limitation in the improvement of this important legume. Hence, in an attempt to develop sequence-tagged microsatellite sites (STMS) markers from chickpea, a microsatellite enriched library from the C. arietinum cv. Pusa362 nuclear genome was constructed for the identification of (CA/GT)n and (CT/GA)n microsatellite motifs. A total of 92 new microsatellites were identified, of which 74 functional STMS primer pairs were developed. These markers were validated using 9 chickpea and one C. reticulatum accession. Of the STMS markers developed, 25 polymorphic markers were used to analyze the intraspecific genetic diversity within 36 geographically diverse chickpea accessions. The 25 primer pairs amplified single loci producing a minimum of 2 and maximum of 11 alleles. A total of 159 alleles were detected with an average of 6.4 alleles per locus. The observed and expected heterozygosity values averaged 0.32 (0.08-0.91) and 0.74 (0.23-0.89) respectively. The UPGMA based dendrogram was able to distinguish all the accessions except two accessions from Afghanistan establishing that microsatellites could successfully detect intraspecific genetic diversity in chickpea. Further, cloning and sequencing of size variant alleles at two microsatellite loci revealed that the variable numbers of AG repeats in different alleles were the major source of polymorphism. Point mutations were found to occur both within and immediately upstream of the long tracts of perfect repeats, thereby bringing about a conversion of perfect motifs into imperfect or compound motifs. Such events possibly occurred in order to limit the expansion of microsatellites and also lead to the birth of new microsatellites. The microsatellite markers developed in this study will be useful for genetic diversity analysis, linkage map construction as well as for depicting intraspecific microsatellite evolution.

Alleles↗

PubMed2005

Is variation in susceptibility to Phytophthora ramorum correlated with population genetic structure in coast live oak (Quercus agrifolia)?

California coastal woodlands are suffering severe disease and mortality as a result of infection from Phytophthora ramorum. Quercus agrifolia is one of the major woodland species at risk. This study investigated within- and among-population variation in host susceptibility to inoculation with P. ramorum and compared this with population genetic structure using molecular markers. Susceptibility was assessed using a branch-cutting inoculation test. Trees were selected from seven natural populations in California. Amplified fragment length polymorphism molecular markers were analysed for all trees used in the trials. Lesion sizes varied quantitatively among individuals within populations, with up to an eightfold difference. There was little support for population differences in susceptibility. Molecular structure also showed a strong within-population, and weaker among-population, pattern of variation. Our data suggest that susceptibility of Q. agrifolia to P. ramorum is variable and is under the control of several gene loci. This variation exists within populations, so that less susceptible local genotypes may provide the gene pool for regeneration of woodlands where mortality is high.

California↗

PubMed2005

Molecular evidence of Pneumocystis transmission in pediatric transplant unit.

We describe an outbreak of Pneumocystis jirovecii pneumonia in a pediatric renal transplant unit, likely attributable to patient-to-patient transmission. Single-strand conformation polymorphism molecular typing showed that 3 affected patients had acquired the same 2 strains of Pneumocystis, which suggests interhuman infection. An infant with mitochondriopathy was the probable index patient.

Adolescent↗

PubMed2003

Subtyping of pathogenic Escherichia coli strains using flagellar (H)-antigens: serotyping versus fliC polymorphisms.

Serotyping of O- and H-antigens is regarded as the gold standard in classification of E. coli for taxonomic and epidemiological purposes similar to the Kaufmann-White scheme for Salmonella enterica. Molecular methods to replace or to support the serotyping have been applied recently. Using the molecular polymorphism of the flagella (H-antigen) gene fliC, more than 220 E. coli strains derived from the E. coli reference collection for O- and H-antigens (The International Escherichia and Klebsiella Centre (WHO)) and from clinical origins have been characterised and a reproducible and clear cut classification with very good correlation to serotyping was found. Only some of the H-antigens have revealed multiple fliC classes and vice versa only rarely some of the fliC classes belong to various H-antigen groups. Since also H-antigen-negative and H-antigen non-typeable strains subjected to fliC classification could be typed properly, it is recommended here to use this rapid approach to classify E. coli under routine conditions rather than using classical serotyping. However, scrotyping--in particular using hyperimmune rabbit sera--will remain the gold standard and the task of Reference Centres only, e.g. for defining novel H-antigen types.

Antigens, Bacterial↗

PubMedDate not supplied

[Molecular and genetic polymorphism in three cattle breeds].

Determination of cattle breed and assignment of individual animals to that or another group based on distinctions of genotype is of great importance in genetics and selection. Using of PCR-analysis opened new possibilities for typing DNA. The procedure of PCR was optimized for animal DNA. Two methods of PCR, RAPD and SSRP, were applied for investigation of molecular-genetical polymorphism in three cattle breeds (Ukrainian red-motley lactescent, Golshtine and Simmental). A dendrogram reflecting genetical mutual relations between analyzed animals was drawn. The level of homo-heterozygosity and the distribution of microsatellite alleles were determined. System for investigation of molecular-genetical polymorphism in the cattle breeds and characterization of genotype of individual animals were developed and tested on a real population.

Animals↗

PubMed1992

Polymorphism of the 35- and 50-kilodalton surface glycoconjugates of Trypanosoma cruzi metacyclic trypomastigotes.

In this study, we examined the immunochemical properties of the 35- and 50-kDa (35/50-kDa) surface glycoconjugates expressed on the surface of metacyclic trypomastigotes of Trypanosoma cruzi using three different monoclonal antibodies directed to this component. The 35/50-kDa surface antigen was expressed by metacyclic trypomastigotes of 11 different strains of T. cruzi and displayed a significant degree of molecular polymorphism. Results of immunoblotting and complement-mediated lysis were consistent with such diversity. Different monoclonal antibodies reacted with distinct epitopes on the 35/50-kDa antigen, which is resistant to proteases and behaves as an amphiphilic component.

Animals↗

PubMed2005

A fragile site at 10q23 (FRA10A) in a phenytoin-exposed fetus: a case report and review of the literature.

OBJECTIVE: To report fragility at 10q23.3 in a fetus exposed to phenytoin during pregnancy. Review of the literature. METHODS: Amniocytes were cultured in A10 (WISENT) culture medium. Molecular polymorphism studies of MTHFR gene using PCR were performed on fetal tissues. RESULTS: The fragile site was expressed in all 22 amniocyte colonies analyzed. Analysis of fetal blood showed 46,XX[98]/46,XX,fra(10)(q23.3)[3]/46,XX,del(10)(q23.3) [1]. Molecular studies of the MTHFR (methylenetetrahydrofolate reductase) gene identified a compound heterozygote genotype for two polymorphisms, 677C>T and 1298A>C. CONCLUSION: The fragility at 10q23.3 is unlikely to be due to culture condition-induced folic acid deficiency (medium contains folate). It is possible that this finding represents a previously undescribed folic acid-insensitive fragile site in the region of 10q23.3. Alternatively, the fetal cells may have had decreased folate metabolism, and the fragile site was the known folate-sensitive FRA10A. Since phenytoin has been shown to decrease MTHFR activity in mice, we postulate that the fragile site at 10q23.3 in this fetus may have arisen secondary to a combination of the polymorphisms in MTHFR and exposure to this drug, and is indeed FRA10A.

Adult↗