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PubMed1986

Electrophoretic polymorphism and molecular structure of equine C3.

Plasma or serum samples from 12 Arabian and 181 standardbred horses have been typed using an immunofixation technique to determine electrophoretic polymorphism of equine third complement component (C3). Six distinctly different electrophoretic patterns of equine C3 have been recognized thus far. SDS PAGE analysis of equine C3/anti C3 complexes revealed that the submolecular structure comprised an alpha chain and beta chain of molecular weights approximately 118,000 and 63,000 daltons respectively. The molecular weights of the alpha and beta chains were similar in all electrophoretic variants tested. Family data derived from 73 mares, 21 stallions and 99 offspring suggested that the six electrophoretic phenotypes were inherited by means of three codominant alleles named C3-1, C3-2 and C3-3 at a single autosomal locus.

Animals↗
PubMed2004

Use of fluorescent amplified fragment length polymorphism for molecular epidemiology of leptospirosis in India.

Nineteen isolates of leptospires recovered from patients during three epidemics that occurred at different places and different times in the Andaman Islands and eight isolates from sporadic cases were characterized using serological and molecular genetic techniques. Group sera and monoclonal antibodies were used for antigenic characterization, whereas fluorescent amplified fragment length polymorphism (FAFLP) was used for genotyping. Of the 27 isolates, 19 were identified as belonging to serogroup Grippotyphosa, 3 belonged to serogroup Australis, 2 belonged to serogroup Icterohaemorrhagiae, and 1 each belonged to serogroups Hebdomadis, Canicola, and Sejroe. Analysis of FAFLP data grouped these 27 isolates into two main clusters of genotypes. One of the clusters, populated by 19 isolates, included 16 outbreak isolates. Seven of these 19 isolates belonged to serovar Ratnapura, 10 belonged to serovar Valbuzzi, and 1 each belonged to serovar Grippotyphosa and serovar Saxkoebing. Of the 27 patients from whom isolates were obtained, 9 had severe illness, and 6 of these 9 patients had pulmonary involvement, 1 had pulmonary and hepatorenal involvement, and the remaining 2 had hepatorenal involvement alone. Two patients out of the nine severe cases died subsequently. The isolates from sporadic cases showed great genetic diversity and were also diverse antigenically. Perhaps the strains belonging to a dominant genotype (the outbreak-associated cluster) possessed epidemic potential and higher virulence with a greater predilection to cause pulmonary complications than strains belonging to other genetic backgrounds.

Base Sequence↗
PubMed2004

Sequence polymorphism and molecular characterization of laccase genes of the conifer pathogen Heterobasidion annosum.

The oxidizing enzyme laccase produced by many fungi is generally considered to be active in the biodegradation of lignin, a major plant cell wall component highly resistant to microbial attack. The enzyme is secreted at high levels by the P-type of the highly aggressive pathogen Heterobasidion annosum, but at much lower levels by the S-type which correlated with their varying wood decay capability. To investigate the evolutionary relationship between laccase genes of the different H. annosum types from several geographical regions we have compared the nucleotide sequence of the laccase gene from 32 different isolates of the fungus together with two other Asian isolates (H. araucariae, H. insulare). In addition to nucleotide sequence assessment, we have also cloned, characterized and analysed the partial sequences of the laccase gene from the homokaryotic (FSE-7: S-type; Sä16-4: P-type) and heterokaryotic (Faf-8: F-type) strains of H. annosum. Using degenerate primers, two distinct laccase gene fragments of 1.64 and 2 kb were amplified from the genomic DNA of this fungus. DNA sequence analyses showed that the 1.64 kb laccase fragment in all three H. annosum types shared significant homology (86-96%). But comparative analyses of the 1.64 and 2 kb laccase gene fragment revealed only 48% nucleotide sequence similarity. Using the cDNA sequence information, exon regions were predicted and this revealed that about nine small introns interrupted the genomic DNA. Southern hybridization analysis indicated a single copy of the gene in the homokaryotic S-type (FSE-7) examined but presence of double bands in the homokaryotic and heterokaryotic P-type strains of the fungus suggest the existence of two laccase genes. Northern analyses revealed that the gene is constitutively expressed but appear to be enhanced several fold with the addition of ferulic acid or oxalic acid. Alignments of the nucleotide sequences and phylogenetic analyses are presented allowing estimations of evolutionary relationships to be made. These comparisons indicate that laccase gene of P-type is distinct from other Heterobasidion sequences, including the outgroups H. araucariae and H. insulare, while the relationship between the S- and F-groups could not be resolved. Comparative phylogenetic analyses using predicted amino acid sequence also showed strong similarity to the laccases from other basidiomycetes (Pleurotus ostreatus, Phlebia radiata and Trametes versicolor) but least similar to laccases from ascomycete fungi. In addition, the results of McDonald-Kreitman test for possible evidence of selection based on analyses of two exon regions of the H. annosum laccase gene are presented and discussed.

Agaricales↗
PubMed1991

Human platelet-specific antigen, Siba, is associated with the molecular weight polymorphism of glycoprotein Ib alpha.

Platelet-specific antigen Sib(a) has been highly implicated in the pathogenesis of refractoriness to human leukocyte antigen (HLA)-matched platelet transfusions in Japan. We provide evidence that the Sib(a) antigen is located on the glycoprotein (GP) Ib alpha and has a close association with the molecular weight (mol wt) polymorphism of GPIb. In modified antigen-capture ELISA (MACE), anti-Sib(a) antibody reacted only with GPIb/IX held by a murine anti-GPIb/IX monoclonal antibody (MoAb). The reactivity of anti-Sib(a) antibody to Sib(a)-positive (Sib(a+)) platelets was abolished after they were treated with Serratia marcescens protease. Platelets from 50 healthy volunteers were semiquantitatively phenotyped for Sib(a) antigen by MACE and divided into three distinct groups: strongly positive, positive, and negative. They were also analyzed by sodium dodeyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and periodic acid-silver staining for mol wt polymorphism of GPIb, phenotyped as A, B, C, or D. Without exception, Sib(a+) platelets showed larger phenotypes (A or B). Removal of sialic acid from Sib(a+) platelets did not reduce the binding of anti-Sib(a). Finally, anti-Sib(a) antibody specifically immunoprecipitated A and B phenotypes of GPIb from Sib(a+) platelets. Thus, Sib(a) antigen evidently is located in the region of glycocalicin that is present only on the A and B phenotypes of GPIb.

Antigens, Human Platelet↗
PubMed2003

Genetic polymorphism and molecular epidemiology of Leishmania (Viannia) braziliensis from different hosts and geographic areas in Brazil.

Numerical zymotaxonomy and variability of the internal transcribed spacers (ITS) between the small and large subunits of the rRNA genes were used to examine strain variation and relationships in natural populations of Leishmania (Viannia) braziliensis. A total of 101 strains from distinct hosts and Brazilian geographic regions were assigned to 15 zymodemes clustered in two major genetic groups. The great number of isolates (48.5%) placed in zymodeme IOC/Z-27 were collected on the Atlantic coast. The high molecular diversity found in populations in the Amazon Basin was related to the great number of sandfly vector(s) in that region. The results of the restriction fragment length polymorphism analysis of the ITS depicted considerable intraspecific variation. Genotypic groups A, B, and C contained 39, 40, and 22 isolates, which were divided into 16, 10, and 15 genotypes, respectively. The genetic polymorphism observed demonstrates the degree of diversity of L. (V.) braziliensis strains from different regions where they are endemic. The results reinforce the clonal theory for Leishmania parasites showing the genetic diversity of this pathogen and an association of L. (V.) braziliensis genotypes with specific transmission cycles, probably reflecting an adaptation of different clones to the vector species involved.

Animals↗
PubMed2006

Crystalline polymorphism and molecular structure of sodium pravastatin.

In this work different crystallization processes of sodium pravastatin are explored and a new polymorph is obtained. The analytical results of powder X-ray diffraction (PXRD) and thermal analysis for this new polymorph indicate that it is different from the polymorphs previously reported. This new crystal form shows different physical-chemical properties than the previous forms, such as crystallographic structure, thermal behavior, and melting point, 181.5 degrees C. Besides, all crystallization processes previously reported use an aprotic solvent as antisolvent. However, we propose a new crystallization process for sodium pravastatin that uses only protic solvents, overcoming industrial scaling and environmental problems. Variable-temperature PXRD experiments show a transformation between different crystal forms in the range of 80-120 degrees C. Solid-state 13C NMR, reported in this work for the first time, and Fourier transform infrared (FT-IR) studies of some polymorphs show some differences in intermolecular interactions, especially with carboxylate and hydroxyl groups. Quantum mechanical calculations of the pravastatin molecule are also presented for the first time, obtaining a molecular structure similar to the experimental structure existing within the crystal lattice of the tert-octylamonium salt of pravastatin.

Calorimetry, Differential Scanning↗
PubMed1998

Prenatal diagnosis of de novo isochromosome 13q associated with microcephaly, alobar holoprosencephaly and cebocephaly in a fetus.

We report on the prenatal diagnosis, genetic studies, and pathology of a case with de novo isochromosome 13q. A 31-year-old primigravida was referred for genetic counselling at 26 weeks' gestation due to the sonographic findings of intrauterine growth retardation and microcephaly. Level II ultrasonograms further demonstrated alobar holoprosencephaly, hypotelorism, polydactyly, a ventricular septal defect, and a single nostril. A diagnosis of cebocephaly was made. Genetic amniocentesis and cord blood sampling revealed translocation trisomy 13 with a de novo t(13q13q) rearrangement. Chromosomal analysis using G- and C-banding techniques and fluorescence in situ hybridization (FISH) showed an apparent monocentric isochromosome. Molecular analyses using polymorphic molecular markers showed that the rearrangement was consistent with an isochromosome of maternal chromosome 13q[46,XX,i(13)(q10)]. Necropsy confirmed cebocephaly and the prenatally detected anomalies.

Adult↗
PubMed2002

[KCNQ4 gene mutations affected a pedigree with autosomal dominant hereditary hearing loss].

OBJECTIVE: To investigate if the KCNQ4 gene contributes to a Chinese non-syndromic hearing loss pedigree and to detect the gene mutations in the pedigree using candidate approach. METHODS: PCR-SSCP and clone sequencing were performed to identify the mutations and polymorphism in PCR products of KCNQ4 coding sequence in the six-generations pedigree of autosomal dominant hereditary hearing loss. RESULTS: Mutations and polymorphism detection were performed on the KCNQ4 coding sequence in 36 family members of the pedigree. A molecular polymorphism marker located in the exon2 and exon3 intron sequence, which resulted from a copy variation of 47 base pairs insertion or deletion, was found in KCNQ4 sequence. CONCLUSION: A new molecular polymorphism marker with different genotypes was proved to locate at the intron sequence between at exon2 and exon3. The correlation between genotype and phenotype was analyzed. Deaf individuals were accompanied by the increase of the intron copies in the family. These findings suggest that the changes of the copies of intron between exon2 and exon3 of KCNQ4 might be a specific marker for the hearing loss of the pedigree.

Exons↗
PubMed1994

[A single base substitution is responsible for the origin of "private" platelet Sra antigens affects molecular weight polymorphism of glycoproteins IIIa].

Some of the genetic polymorphisms of the platelet membrane glycoproteins (GP) IIIa are known to be responsible for alloantibody formation (Zw, Yuk). These antibodies may be involved in neonatal alloimmune thrombocytopenia, posttransfusion purpura, and sometimes in the state of refractoriness to platelet transfusion. Recently we described the first 'private' alloantigen on platelets residing on the 66-kDa membrane-bound fragment of GP IIIa. Further molecular genetic studies showed that the Sr polymorphism is associated with a C to T substitution at base 2004 in the GP IIIa gene resulting in an Arg/Cys amino acid dimorphism at position 636. Transfection of COS cells with recombinant forms of GP IIIa cDNA demonstrated that this amino acid dimorphism is responsible for the formation of the Sra epitope. Furthermore, the Sra variant of GP IIIa showed a slightly increased molecular weight which is presumably caused by different glycosylation.

Antigens, Human Platelet↗
PubMed1991

[Identification of HLA class II polymorphism with molecular biology techniques].

All the biologically relevant HLA class II allelic variants can not be identified with conventional serological tissue typing techniques. During the past few years considerable advances have been made in HLA class II typing with molecular techniques now widely used in routine clinical tissue typing. The next few years are likely to see the development of tissue typing techniques based on the polymerase chain reaction (PCR), for use in acute transplantation. A new method for the rapid identification of genetic polymorphisms is described--allele-specific PCR amplification.

HLA-D Antigens↗
PubMed1994

A point mutation leads to an unpaired cysteine residue and a molecular weight polymorphism of a functional platelet beta 3 integrin subunit. The Sra alloantigen system of GPIIIa.

Recently, we described a low frequency platelet alloantigen on human platelet membrane glycoprotein (GP) IIIa, termed Sra, that was involved in neonatal alloimmune thrombocytopenia. To identify the molecular nature of the Sra alloantigen, we analyzed the nucleotide sequence of polymerase chain reaction-amplified GPIIIa mRNA, and found a C2004-->T substitution in seven Sra positive individuals which results in an Arg636-->Cys polymorphism within the cysteine-rich region of GPIIIa. Analysis of allele-specific recombinant forms of GPIIIa that differed only at amino acid residue 636 showed that anti-Sra alloantibodies reacted with the Cys636, but not the Arg636, recombinant form of GPIIIa. Interestingly, under reducing conditions, the Cys636 form of GPIIIa migrated with a slightly increased apparent molecular weight compared with the Arg636 form. Following treatment with Endoglycosidase H, both allelic forms of GPIIIa exhibited the same mobility, however the Sra epitope was lost. Sra positive platelets express the same number of GPIIb-IIIa complexes on their surface as wild-type Sra negative platelets, and also aggregate normally in response to a variety of platelet agonists. Based upon these results, we conclude that 1) GPIIIa residue 636 specifically controls the formation and expression of the Sra alloantigenic determinant, and 2) an unpaired cysteine residue alters the N-linked glycosylation pattern of the extracellular domain of GPIIIa, but affects neither the degree of surface expression nor the adhesive function of the GPIIb-IIIa complex.

Amino Acid Sequence↗
PubMed2005

Partial molecular characterization, polymorphism and chromosomal localization of the porcine PSMD4 gene.

The complete coding sequence of porcine PSMD4 gene encoding proteasome 26S non-ATPase subunit 4 was obtained by the reverse transcriptase-polymerase chain reaction (RT-PCR) and deposited in GenBank nucleotide database (AY704418). The nucleotide sequence and the predicted protein sequence shared the high sequence identity with their mammalian counterparts. A G/A single nucleotide polymorphism in intron 9 detected as Hin6I PCR-restriction fragment length polymorphism (PCR-RFLP) shows allele frequency differences between Meishan, Erhualian, Tibetan, Large White and Duroc breeds. Analyses of somatic cell hybrid panel (SCHP) and radiation hybrid (IMpRH) panel revealed that PSMD4 gene maps to SSC 4q21-q23 and closely linked the SW512 (14 cR, LOD = 19.47).

Amino Acid Sequence↗
PubMed2006

Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity.

The exact extent of microbial diversity remains unknowable. Nevertheless, fingerprinting patterns [denaturing gradient electrophoresis (DGE), single-strand conformation polymorphism (SSCP)] provide an image of a microbial ecosystem and contain diversity data. We generated numerical simulation fingerprinting patterns based on three types of distribution (uniform, geometric and lognormal) with a range of units from 10 to 500,000. First, simulated patterns containing a diversity of around 1000 units or more gave patterns similar to those obtained in experiments. Second, the number of bands or peaks saturated quickly to about 35 and were unrelated to the degree of diversity. Finally, assuming lognormal distribution, we used an estimator of diversity on in silico and experimental fingerprinting patterns. Results on in silico patterns corresponded to the simulation inputs. Diversity results in experimental patterns were in the same range as those obtained from the same DNA sample in molecular inventories. Thus, fingerprinting patterns contain extractable data about diversity although not on the basis of a number of bands or peaks, as is generally assumed to be the case.

Animals↗
PubMed1989

Could natural selection account for molecular evolution and polymorphism?

A model of molecular evolution is presented that is based on the combined action of natural selection, genetic drift, and mutation. The mathematical description of the model uses strong-selection, weak-mutation limits to approximate the dynamics of multidimensional diffusion processes with one dimensional Markov chains. This approach leads to a great simplification of the dynamics and provides a unified method for describing many different mechanisms of natural selection. In this paper two models are examined, one based on selection in a randomly fluctuating environment, the other on overdominance. Both models exhibit similar dynamics, with a rapid buildup phase that introduces new alleles into the population, followed by a relatively quiescent phase where new alleles may enter and leave the population at a low rate. If occasional extreme environmental changes occur that favor particular alleles, the resulting dynamics turn out to be in remarkable agreement with many of the observations on molecular evolution and polymorphism. Thus the model is at least as successful as the neutral theory in accounting for evolutionary events at the molecular level.

Biological Evolution↗