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Myogenic factor 5 (MYF5) plays an important role in regulating skeletal muscle, but to date there have been no reports on whether the gene is variable and whether this variation is associated with meat yield in sheep. In this study, four variants (A to D) of ovine MYF5 containing two Single Nucleotide Polymorphisms (SNPs) and one basepair (bp) insertion/deletion were detected by Polymerase Chain Reaction - Single Stranded Conformational Polymorphism (PCR-SSCP) analysis. Breed differences in variant frequencies were observed. The effect of variation in ovine MYF5 on lean meat yield, predicted using VIAScan® technology, was investigated in 388 male NZ Romney lambs. Only genotypes AA and AB were found in these lambs. Lambs with genotype AA had a higher leg yield (P=0.044), loin yield (P=0.002) and total yield (P=0.012) than those with genotype AB. No association with shoulder yield was detected. These results suggest that ovine MYF5 may be a valuable genetic marker for improved lean meat yield.

The present study was undertaken with the objectives of molecular characterization and detection of genetic polymorphism in the GnRHR gene in Murrah bulls. Blood samples were collected from 109 Murrah bulls maintained at three different organized semen stations viz., Centralized Semen Collection Centre of Livestock Breeding and Training Centre, Dharwad; Nandini Sperm Station and State Livestock Breeding and Training Centre, Hessarghatta, Bengaluru, Karnataka, India. Genomic DNA was isolated from the blood samples within 24 hours of collection . Mutations were screened using Polymerase Chain Reaction – Single Stranded Conformational Polymorphism (PCR-SSCP) technique followed by Sanger Sequencing. PCR-SSCP method revealed similar band pattern within Murrah bulls. To confirm monomorphism in the studied population with respect to GnRHR gene, duplicate samples from each primer fragment were custom sequenced. PCR-SSCP and sequence analysis revealed monomorphism within the studied population that is coding region as well as exon-intron boundaries of GnRHR gene is highly conserved among Murrah bulls. However, a total of 28 Single Nucleotide variations (SNV’s) have been found when compared with Bos Taurus reference sequence for GnRHR gene.

Background: Hypertrophic cardiomyopathy (HCM) is a various collection of heart diseases with autosomal dominant inheritance affecting 0.2% of the global population. HCM is also the most common cause of sudden cardiac death in individuals younger than 35 years old. Approximately, 40% of affected cases are associated with MYBPC3 gene. The aim of this study is to investigate the possible presence of mutation in 15 and 18 exons of MYBPC3 gene in patients with HCM in Chaharmahal Va Bakhtiyari province. Materials and Methods: In this experimental study, 30 HCM patients were selected. DNA was extracted using standard phenol-chloroform method. Certain exons were amplified by PCR method. And then, SSCP and HA methods were run. Results: Significant differences were observed between the positive control samples and other samples. However, there were no difference in studied exons or shift in the bands. Conclusion: Mutations in the exons of MYBPC3 gene may cause the HCM disease, and change in other exons may be the causative agent in this geographical region and change in this studied exons may not have contributed to the HCM disease. However, it is necessary to study more patients for getting a better conclusion.

Baculoviruses have been used as biopesticides for decades. Recently, due to the excessive use of chemical pesticides there is a need for finding new agents that may be useful in biological protection. Sometimes few isolates or species are discovered in one host. In the past few years, many new baculovirus species have been isolated from environmental samples, thoroughly characterized and thanks to next generation sequencing methods their genomes are being deposited in the GenBank database. Next generation sequencing (NGS) methodology is the most certain way of detection, but it has many disadvantages. During our studies, we have developed a method based on Polymerase chain reaction (PCR) followed by Multitemperature Single Stranded Conformational Polymorphism (MSSCP) which allows for distinguishing new granulovirus isolates in only a few hours and at low-cost. On the basis of phylogenetic analysis of betabaculoviruses, representative species have been chosen. The alignment of highly conserved genes—granulin and late expression factor-9, was performed and the degenerate primers were designed to amplify the most variable, short DNA fragments flanked with the most conserved sequences. Afterwards, products of PCR reaction were analysed by MSSCP technique. In our opinion, the proposed method may be used for screening of new isolates derived from environmental samples.

Newcastle disease and Avian Influenza are considered to be the most dangerous fowl diseases which may cause huge economic losses. Newcastle disease is caused by the enveloped, and single-stranded RNA virus (NDV, APMV-1; belonging to Paramyxoviridae family), which can be further divided into sixteen different genotypes grouped into five pathotypes according to their pathogenicity. It has been reported that low pathogenic virus can greatly increase its pathogenicity even during a single passage. Additionally, due to the widespread use of live vaccines, a mixture of two or more different viruses in one sample can be detected. Hence, there is a great need for establishment of fast, inexpensive, sensitive, and relatively simple diagnostic method for multistrain and quasispecies detection of NDV infection. In this paper we describe a diagnostic method based on RT-PCR followed by a modified version of single-stranded conformational polymorphism analysis using short DNA fragments of gene encoding viral F protein. The method allows for rapid diagnosis of genetic variant emerging from previously stable population which may prevent the spread of the pathogenic viral variant.

The present study was taken up to find out Beta 2 Microglobulin (b2M) gene variants and their association with IgG concentrations in colostrum of Murrah buffaloes. 40 newly parturated Murrah buffaloes dams were included in the present study. Polymerase chain reaction- single stranded conformational polymorphism (PCR-SSCP) technique was used to explore the polymorphism in b2M gene of buffaloes. The PCR-SSCP analysis and sequencing of different patterns obtained by silver staining of fragments pertaining to exon 1 through 4 and partial introns 1 through 3, revealed 9 SNPs which were further used to prepare the haplotypes. 7 different haplotypes were observed. Indirect ELISA was done to estimate IgG concentrations in colostrum (collected 1 hour before first milking) obtained from buffaloes. IgG levels in colostrum ranged from 11.22 to 185.1 mg/ml with a mean IgG concentration of 51.71 ± 5.99 mg/ml. The effect of different haplotypes was evaluated on IgG concentrations. The least square analysis of variance could not exhibit a significant effect of buffalo dam haplotype on colostral IgG concentration.

Keratins and keratin-associated proteins (KAPs) are large heterogeneous groups of proteins that constitute about 90% of the wool fiber. The genes encoding the high glycine-tyrosine (HGT) KAPs are the first sub-group of KAP genes expressed in the wool follicle and just after expression of the keratin genes. Little is known about variation in these genes, which led us to investigate two HGT-KAP genes, KRTAP7-1 and KRTAP8-1. Polymerase chain reaction-single-stranded conformational polymorphism analysis was used to investigate these genes in 250 Romney-cross sheep. For KRTAP7-1, two unique banding patterns were detected for amplicons that spanned the entire coding region. Sequencing confirmed the presence of two sequences with only one nucleotide difference (c.173G/A) putatively resulting in p.Ser58Asn. One was identical to the published ovine KRTAP7-1 sequence. For KRTAP8-1, five unique banding patterns were detected in an amplicon that spanned the entire coding region. Sequencing revealed five different DNA sequences, all of which were highly homologous to the previously reported ovine KRTAP8-1 sequence. Among these five sequences, four single-nucleotide substitutions were identified and three of them were located in the coding region. One of these was nonsynonymous and would putatively result in p.Tyr34Asn. The variation detected in KRTAP7-1 and KRTAP8-1 may influence their expression or protein structure.

Botryosphaeriaceous species are significant grapevine trunk pathogens worldwide, which can be difficult to identify to species level using conventional morphological methods. This study developed and optimized a quick, reliable molecular identification method that could facilitate investigations into the epidemiology of these diseases in vineyards. The multi-species primers, BOT100F and BOT472R, amplified a 371–372 bp portion of the rRNA gene region from the six botryosphaeriaceous species commonly found in New Zealand vineyards. In silico analysis indicated that they would amplify DNA from six of the 12 lineages of the Botryosphaeriaceae, including all of the main species pathogenic to grapevines. A detection sensitivity of 1 and 0·1 pg DNA in standard and nested PCR, respectively, was achieved and this was calculated as equivalent to 2·5 conidia. Validation of the primers for environmental samples showed that their specificity was not compromized by the presence of competing DNA templates extracted from wood and soil. Single stranded conformational polymorphism (SSCP) analysis of the amplicons could resolve Neofusicoccum australe, N. luteum, Diplodia mutila and D. seriata, but did not differentiate between N. parvum and N. ribis. The optimized PCR-SSCP was used to identify botryosphaeriaceous species present in rainwater traps collected over 1 year in a vineyard known to contain infected vines. It could detect multiple species in individual samples and demonstrated differences in the dispersal patterns of conidia from different species. Given the specificity and sensitivity of this method it could prove useful in epidemiology studies involving the numerous botryosphaeriaceous species that infect a wide range of host species.

Objectives: To investigate a polymorphism of the apolipoprotein J (APOJ) gene in relation to coronary artery disease (CAD) and lipid variables in a Chinese male population of genetically unrelated individuals. Methods: In this study, we recruited 126 control male subjects and 237 CAD male patients. CAD was defined as a fixed stenotic lesion with luminal narrowing ≧50% in at least one of the major or minor coronary arteries. In cases with documented myocardial infarction, only those rated as fully recovered for more than 3 months were enrolled. Patients with acute or chronic infectious diseases and those with malignancies were excluded. All subjects with a fasting serum triglyceride level higher than 300 mg/dl were likewise excluded. Results: We identified a single nucleotide polymorphism, 1598delT, and showed its association with CAD. Subjects with the I/I genotype showed a significantly higher CAD risk compared to those with the D/D genotype (OR 2.34, 95% CI 1.11–4.94, p = 0.026). Patients with the I/I genotype also had abnormal levels of high-density lipoprotein-cholesterol and low-density lipoprotein-cholesterol associated with CAD. Conclusions: Our data indicated that the APOJ single nucleotide polymorphism (1598delT) is associated with risk factors for CAD in a Chinese population.

The method of single-strand conformational polymorphism (SSCP) was modified in our laboratories for the characterization of baculoviruses, insect viruses with great potential for use as bioinsecticides in biological protection programs. A series of primers were synthesized after the comparison of the polyhedrin gene sequences of over 20 baculoviruses. Polyhedrin is a highly conserved protein which is responsible for the persistence of the virus in the environment. Universal primers were designed which could be used in polymerase chain reactions (PCR) containing genomic DNA from an array of nucleopolyhedrosis viruses (NPVs) including these which are used as biopesticides against important pests of forests and crops, such as Anticarsia gemmatalis, Spodoptera frugiperda, Lymantria dispar, Lymantria monacha and many others. PCR products were denatured and subjected to single-strand DNA electrophoresis at variable temperatures (MSSCP) where, after silver staining, they gave ssDNA band patterns characteristic for each baculovirus species. This technique can be potentially applied to detect baculoviruses in insects collected in the field, as well as to plant tissues and the excrements or bodies of predators without need for sequencing the PCR products. Sometimes MSSCP can be used not only for species determination but also as an indication of genomic variability which can be related to infectivity.

We show that non-denaturing gel electrophoresis, or single-stranded conformational polymorphism (SSCP), can be used to separate mixtures of full-length rRNAs. Individual bands can then be excised for identification by RT-PCR and sequencing. This has the advantage over profiling methods such as DGGE and T-RFLP that no PCR amplification is involved prior to sequencing; thus, extraction biases aside, it should yield a quantitative picture of community composition in terms of ribosome content. To simplify banding patterns, RNA subsamples (e.g. bacterial 16S rRNA) can first be isolated by magnetic bead capture hybridization. Alternatively, oligonucleotide-directed ribonuclease H (RNase H) digestion can be used to identify bands of interest by running digested samples in parallel to undigested ones. We illustrate the use of this technique to identify a potentially predominant species in a hypersaline microbial mat. We anticipate that rRNA-SSCP will be useful for community profiling; for clone library construction by directed cloning of individual rRNAs; and for following incorporation of radiolabeled substrates at the species level, by gel autoradiography, without advance information or guesswork about which species might be active and abundant.

Major histocompatibility complex (MHC) variation at the class IIβ (B-LB) gene was surveyed both within and among populations of red grouse Lagopus lagopus scoticus from northeastern Scotland. Variation among individuals was assayed by direct DNA sequencing, with 13 unique alleles being resolved among 10 unrelated individuals. All nucleotide substitutions were non-synonymous (amino acid changing) substitutions. Variation among five populations was screened using single stranded conformational polymorphism (SSCP). Twelve B-LB alleles were resolved, with low levels of genetic structure between the populations. This is in contrast to the considerable genetic differentiation observed among the same populations determined from microsatellite DNA analysis. Both the patterns of nucleotide substitution within individuals, and the discrepancy between MHC and microsatellite derived patterns of population genetic structure highlight that balancing selection is acting to maintain variation in the grouse MHC. The significance of MHC dynamics and diversity is discussed in the context of grouse ecology and conservation.

This study compares the genotypic information provided by reference strand-mediated conformational analysis and single-stranded confirmational polymorphism (SSCP) analysis for the major histocompatibility complex (MHC) II locus in lake trout. For this study 80 wild-caught animals from the Apostle Islands of Lake Superior were genotyped using both RSCA and SSCP analysis. Their genotypes were recorded using both methods and compared. The genotypic information provided by the 2 methods was essentially the same although some inconsistencies were observed. Both methods detected approximately 65 genotypes, and both were able to distinguish heterozygous and homozygous animals. The analyses determined that only approximately 20% of alleles were shared between 2 morphologically different populations within the sample set, and identified the dominant alleles. SSCP analysis was quicker, simple, and more robust than RSCA. SSCP analysis using fluorescence technologies could be the method of choice for future genotypic analysis of the MHC II locus in salmonids.

We describe a new environment of a single-stranded conformational polymorphism (SSCP) analysis using automated capillary array sequencers (e.g., ABI PRISM® 3100 and 3700). In this environment, electrophoretic conditions, settings for instrument management, and software for data analysis are adjusted for SSCP analysis. Highly reproducible results are obtained with this new system, and fragments with mutations and/or polymorphisms in different capillaries or different runs can be reliably detected. The relative peak heights between alleles are quantitative and reproducible between runs, and so allele frequencies of single nucleotide polymorphisms can be accurately estimated by a pooled DNA strategy. The method allows unattended, lowcost, and quantitative SSCP analysis using instruments that are widely accessible.

Here we describe DNA sample preparation methods that allow the rapid, simultaneous generation of both single-stranded conformational polymorphism (SSCP) and heteroduplex DNA elements from a single sample in a single tube, which are suitable for direct injection into a capillary electrophoresis (CE) instrument with excellent sensitivity of genetic mutation detection. The p53 gene was used as a model DNA region for this study, which was performed on a high-throughput MegaBACE™ 96-capillary array electrophoresis instrument. We found that, contrary to the practice common in slab-gel SSCP analysis, denaturants such as formamide are incompatible with this novel technique because they result in homo- and heteroduplex peak broadening in CE (possibly as a result of incomplete dsDNA re-hybridization) that reduces the peak resolution and hence the sensitivity of mutation detection. We also have found that PCR buffers, which are typically used to suspend samples for slab-gel heteroduplex analysis (HA), but which are less suitable for CE because of the presence of extra salt that reduces the efficiency of electrokinetic injection, may be substituted with a 10 mM Tris-HCl buffer (pH 8.5). The use of this Tris-HCl buffer for sample preparation provides both a high sensitivity of mutation detection by tandem SSCP/HA and high efficiency of electrokinetic injection by CE. In a related study (published elsewhere), we have applied this optimized protocol to the screening of a set of 32 mutant DNA samples from p53 exons 7 and 8 and recorded 100% sensitivity of mutation detection for tandem CE-SSCP/HA, whereas each individual method yielded lower sensitivity on its own (93% for SSCP and 75% for HA).

Background - Discovery and incorporation of biomarker panels to cancer studies enabled the understanding of genetic variation and its interference in carcinogenesis at molecular level. The potential association between single nucleotide polymorphism (SNP) 309 and increased development of tumors, such as hepatocellular carcinoma, has been subject to several studies. This is the first study on this association conducted in Brazil. Methods - 62 cases of cirrhotic patients with hepatocellular carcinoma surgically treated by partial hepatectomy (HPT) or by liver transplantation (LTX) from 2000 to 2009 at Santa Casa Hospital Complex, in the city of Porto Alegre, were retrospectively analyzed. Tumor samples from surgical specimen were collected and prepared for study in paraffin blocks. Results - Overall survival was 26.7 months in the HPT group and 62.4 months in the LTX group (P 200ng/mL, microvascular invasion and histological grade were associated with tumor recurrence (P 200ng/mL correlacionaram-se com a recidiva tumoral em ambos os subgrupos cirúrgicos. Observou-se que 83,3% dos pacientes com recidiva também apresentaram invasão microvascular ao exame anátomo-patológico (P

BACKGROUND: The purpose of this study was to evaluate single-stranded conformational polymorphism (SSCP)-PCR utilizing two different regions of mitochondrial DNA (mtDNA) as a method to discriminate between donor platelets and recipient cells. STUDY DESIGN AND METHODS: Twenty-eight mixtures of platelets (1:1 ratio) were prepared from eight randomly selected persons to simulate donor–recipient combinations after allogeneic platelet transfusion. The mtDNA was extracted from each donor and each prepared mixture. Four primer pairs were designed to amplify two regions of mtDNA, hypervariable region (HVR) 1 and 2. An SSCP-PCR method was developed to analyze the four different amplicons. In addition, the amplified DNA samples containing HVR1 and HVR2 mtDNA of the eight persons were sequenced by using dye-terminator cycle sequencing to determine mtDNA polymorphisms. RESULTS: With four different primer pairs and SSCP-PCR, it was possible to discriminate between donor and recipient DNA in all 28 combinations. DNA sequencing confirmed that the suspected differences were localized within the amplicons examined by SSCP-PCR. CONCLUSION: SSCP-PCR analysis targeting the HVR1 and HVR2 mtDNA is a promising new method to potentially identify donor cells on the basis of mtDNA polymorphisms. The method does not require prior knowledge of sequence differences between donor and recipient and can be optimized to quantify the amount of residual transfused allogeneic platelets.

Alterations in the NH(2)-terminal region of the estrogen receptor alpha (ERalpha) gene expressed in placental bed tissue may be implicated in the development of preeclampsia, the pathogenesis of which involves the spiral arteries. Therefore, mutations and polymorphisms on exons 1 and 2 of the gene encoding ERalpha were studied. Placental bed biopsies were taken from 20 healthy, normotensive pregnant women and 16 preeclamptic patients. DNA was extracted from the tissue and exon 1 and exon 2 were amplified by PCR prior to denaturing gradient gel electrophoresis analysis or to single stranded conformational polymorphism analysis. In exon 1, a codon 10 polymorphism, either homozygous for the wild type gene, homozygous for the mutant type gene, or heterozygous, was revealed in both patients and healthy individuals. A codon 87 polymorphism, homozygous for the wild type gene, was detected in both groups. No mutations or polymorphisms were found in exon 2. The allele distribution for either codon 10 or 87 between patients and healthy individuals showed no significant differences. In conclusion, genetic alterations in the NH(2)-terminal region of the ERalpha molecule are not correlated with preeclampsia.

Four polymerase chain reaction (PCR) primer pairs (A–D), specific for the Burkholderia cepacia complex of organisms were designed to encompass the entire gene (,1300bp) from sequence alignments of the rec A operon of B. cepacia . Genomic bacterial DNA from type strains and wild-type B. cepacia complex isolates of previously determined genomovar status was amplified employing these four primer pairs, as well as a fifth primer set (E) already published. Primer sets B, C and E were successful in obtaining a PCR amplicon of correct estimated size of 598, 1107 and 1043bp, respectively. Subsequent single-stranded conformational polymorphism (SSCP) analysis of PCR amplicons demonstrated unique profiles for the five genomovar types for primer pairs B and E, but was unable to differentiate distinguishable profile types for primer pair C. SSCP analysis was demonstrated to be simple, rapid and cost effective and may prove a useful method of genomovar typing of B. cepacia complex organisms from cystic fibrosis patients in busy diagnostic laboratories.

Numerous methods based on DNA analysis have been employed in the food industry to monitor adulterations of food products of animal origin. Among them the most frequently used are: polymerase chain reaction (PCR) amplification of a marker gene fragment(s) with universal primers, or amplification of DNA with species-specific primers. PCR-products of different origin can be discriminated by size, restriction fragment length polymorphism (RFLP) or single stranded conformational polymorphism (SSCP) analysis. These methods have been used for identification, and differentiation between, the animal origins of raw or heat-treated meat and meat products (Chikuni et al. 1994; Meyer et al. 1994, 1995; Zehner et al. 1998; Behrens et al. 1999; Guoli et al. 1999; Hopwood et al. 1999; Matsunaga et al. 1999; Wolf et al. 1999). These approaches are also applicable to the analysis of dairy products. However, adulterations of goats' milk and its products are traditionally tested by immunological and/or electrophoretic methods (Amigo et al. 1992; Levieux & Venien, 1994; Mimmo & Pagani, 1998). So far, only a few DNA-based techniques designed to detect the presence of bovine DNA in goats' milk have been described (Plath et al. 1997; Branciari et al. 2000). This paper presents a one-step PCR procedure for detection of adulteration of goats' milk with cows' milk. The method, employing bovine-specific primers for amplification of a 274 bp fragment of cytochrome b DNA, seems to be simple, fast, specific and sensitive.

Background The beta-3-adrenergic receptor (β3AR) stimulates lipolysis and thermogenesis in adipocytes. The Trp64Arg β3AR variant is associated in some, but not all, studies with an earlier onset of Type 2 diabetes mellitus and features of the insulin resistance syndrome. Functional studies as to the role of the Trp64Arg variant have been inconclusive. Earlier studies screened the β3AR gene in only ten obese, diabetic Pima Indians. Potentially another yet to be identified polymorphism in the β3AR gene in linkage disequilibrium with the Trp64Arg polymorphism could explain the findings in the association and functional studies. Methods We scanned the β3AR gene in 20 diabetic Pima subjects and 20 Caucasian subjects using single stranded conformational polymorphism (SSCP) analysis. Variants were sequenced using dideoxy sequence analysis and further characterized using allele specific oligonucleotide hybridization (ASO) and RNA template specific-polymerase chain reaction (RS-PCR) assays. Results We found a guanine to thymidine substitution in the first intron, 14 bases from the splice donor site in both groups. In virtually all subjects, only two haplotypes were detected, Trp64/g1856 and Arg64/t1856, indicating that the g1856t polymorphism is in linkage disequilibrium with the Trp64Arg polymorphism. The g1856t substitution introduces a new consensus splice donor site which, if used, would encode a truncated protein. RNA levels of the two β3AR alleles were approximately equal in omental adipose tissue of heterozygotes. No aberrantly spliced β3AR mRNA was detected, indicating that the new consensus splice donor site is not used in vivo. Conclusion The g1856t polymorphism is in linkage disequilibrium with the Trp64Arg variant, but does not appear to have a functional role. Copyright © 1999 John Wiley & Sons, Ltd.

Resistance to cyclodiene insecticides is associated with replacements of a single amino acid (alanine 302) in a gamma-aminobutyric acid (GABA) receptor subunit encoded by the single-copy gene Resistance to dieldrin (Rdl). Alanine 302 is predicted to reside within the second membrane-spanning region of the Rdl receptor, a region that is thought to line the integral chloride ion channel pore. In all cyclodiene-resistant insects studied to date, this same alanine residue is replaced either by a serine, or, in some resistant strains of Drosophila simulans, a glycine residue. Therefore, individuals can carry only two different Rdl alleles. In contrast, here we report the presence of up to four different Rdl-like alleles in individual clones of the green peach aphid, Myzus persicae. In addition to the wild-type copy of Rdl gene (encoding A302 or allele A), M. persicae carries three other alleles with the following amino acid replacements: A302--Glycine (allele G), A302--SerineTCG (allele S) and A302--SerineAGT (allele S'). Evidence from direct nucleotide sequencing and Single Stranded Conformational Polymorphism (SSCP) analysis shows that at least three of these different Rdl alleles (i.e. A, G and S) are commonly present in individual aphids or aphid clones. Southern analysis using allele-specific probes and analysis of sequences downstream of the exon containing the resistance-associated mutation confirm the presence of two independent Rdl-like loci in M. persicae. One locus carries the susceptible alanine (A) and/or resistant glycine (G) allele while the other carries the two serine alleles (S or S'). Whereas resistance levels are correlated with the glycine replacement, the S allele was present in all aphid clones, regardless of their resistance status. These results suggest that target site insensitivity is associated with replacements at the first (A/G) but not the second (S/S') locus. Phylogenetic analysis of nucleotide sequences indicates that both putative aphid Rdl loci are monophyletic with respect to other insect Rdl genes and may have arisen through a recent gene duplication event. The implications of this duplication with respect to insecticide resistance and insect GABA receptor subunit diversity are discussed.

Twenty novel snoRNAs forming extensive sequence complementarities to mature 5S rRNA were identified fromBungarus multicinctusby reverse transcription-polymerase chain reaction. It was found that the snoRNA species were differentially transcribed in different tissues as evidenced by single stranded conformational polymorphism analysis and direct nucleotide sequence analysis. Although the diversity in the sequences of snoRNAs is observed, comparison of these snoRNA genes reveals that the regions involved in binding to 5S rRNA are highly conserved and form two 12-nt∼15-nt tracts of complementarity to phylogenetically invariant sequences in eukaryotic 5S rRNAs. Nevertheless, the lower conservation of box C/D or box H/ACA in these snoRNAs was observed. Likewise, the sequences in several fish and human genes forming perfect duplexes with 5S rRNA also did not highly retain these box elements. These results may infer that the box elements are dispensable for the function of snoRNA species identified in the present study. Moreover, the novel finding of the differentially expressed snoRNA variants inB. multicinctussuggests that the snoRNA genes are selectively processed in different tissues and are likely associated with tissue-specific regulation of their host gene transcripts.

Background: Varicocele is associated with the failure of ipsilateral testicular growth and development, and the symptoms of pain and reduced fertility. The highly condensed structure of the sperm nuclear chromatin is provided by proper expression of Transition Nuclear Protein (TNP) genes, so any dysregulational expression of these genes results in abnormal spermatogenesis and infertility. Objective: The aim of present study was to assess the association between TNP1 mutations and varicocele in Iranian infertile men. Materials and Methods: Analysis of association between TNP1 gene mutation and varicocele phenotype was performed using PCR and Single-Stranded Conformational Polymorphism technique and DNA sequencing in 82 varicocele infertile men and 80 control subjects. Results: Sequence analysis was identified one variant in this gene that found in 15 infertile men and was absent in control group. This variant was a single nucleotide polymorphism that were identified in the intron region of this gene at position g.IVS1+75T>C. Conclusion: The effect of this nucleotide substitution in intronic region of the TNP1 gene and their role on expression remains to be determined.

The murine histidyl-tRNA synthetase-encoding gene (MMHRS) coding region has been cloned and sequenced. The 1527-bp transcript shows a strikingly similar structural organization to that of its human counterpart, particularly within the three class II aminoacyl-tRNA synthetase structural motifs and the two histidyl-tRNA synthetase signature regions. It is predicted, as in humans, to have a coiled-coil alpha-helical structure that is characteristic of many autoantigens. MMHRS shows some degree of polymorphism at both the DNA and amino-acid levels, although its sequence is well conserved amongst the commonly used laboratory mouse strains.

Polymorphism of the human papillomavirus type 16 (HPV-16) genome has been reported to occur within the noncoding regulatory long control region (LCR) and in the E7 and L1 genes. The current study focuses on the HPV-16 E6 oncogene which interacts with the antioncogenic regulator p53. Seventy-eight HPV-16-positive DNA samples derived from cervical carcinomas were screened for the presence of polymorphism in the HPV-16 E6 gene by polymerase chain reaction (PCR) linked single stranded conformational polymorphism (SSCP) analysis. Nine DNA samples had heterozygous mutations within the same region of the E6 gene 3' terminus; T to C transitions at HPV-16 position 511 (silent) and one of the nine also had a 513 mutation (Met to Thr). These mutations correlated with the clinical aggressiveness of the tumor, suggesting that the presence of these mutations may be due to genomic instability of advanced cervical carcinoma.

A homologous region in the parvovirus B19 non-structural gene (1319 nt 1399–1682) was examined in 50 samples from patients with a wide variety of 1319-related disease from various countries by PCR amplification, single-stranded conformational polymorphism (SSCP) assay and nucleotide sequencing. Five SSCP types were confirmed by nucleotide sequence analysis. Of a total of 6 mutations, all were silent. Types 3 and 4 accounted for 92% of strains. There was no correlation between genome type and either clinical illness or patient age. However, there was a correlation between SSCP type and country of origin. Type 3 strains predominated in Japan ( 18 26 ) and the UK ( 6 8 ), whereas type 4 predominated in the USA ( 9 12 ). Notably, type 3 strains also predominated among females (14/18), whereas there were approximately equal numbers of strain types 3 ( 7 17 ) and 4 ( 8 17 ) among males; an observation which remains unexplained. Within the Japanese group, although type 3 strains predominated overall, strains isolated from 1981 to 1987 consisted of types 1 ( 2 15 ), 2 ( 1 15 ), 3 ( 8 15 ), and 4 ( 4 15 ), whereas strains isolated from 1990 to 1994 consisted almost entirely of type 3 ( 10 11 )

Cyclodiene insecticide resistance is associated with replacements of a single amino acid within the putative lining of a δ-aminobutyric acid (GABA)-gated chloride ion channel gene Resistance to dieldrin (Rdl). Only two resistance-associated amino acid replacements have been identified; alanine to serine in Drosophila melanogaster, D. simulans, Aedes aegypti, and Tribolium castaneum and alanine to glycine as a second allele in D. simulans. Here we report that single stranded conformational polymorphism (SSCP) analysis of genomic DNA, amplified by the polymerase chain reaction (PCR) for exon 7 of the Rdl gene, can be used to genotype strains or individuals of all of these insects. This technique also appears simultaneously to distinguish between D. melanogaster and D. simulans, sibling species only reliably identifiable by examination of male genitalia. The relative advantages of this genotyping technique against other PCR-mediated techniques in monitoring for insecticide resistance are discussed.

Cystic fibrosis patients referred to two genetics centres in southern England and not found to carry common CF-associated mutations in one or both of their CFTR genes have been subjected to an extensive mutation search. The whole of the coding region of the CFTR gene, all intron-exon boundaries and 5' and 3' untranslated regions have been examined by a combination of single stranded conformational polymorphism analysis and chemical mismatch detection; 48 chromosomes with rare mutations have been identified, including 7 novel mutations, 182delT in exon 1, G27X in exon 2, Q151X in exon 4, Q220X in exon 6a, Q525X in exon 10, 3041delG in exon 16, and 4271delC in exon 23.

Background Acute Myeloid Leukaemia (AML) is a cancer of blood-forming cells in bone marrow. C-kit gene is a Receptor Tyrosine Kinase class III (RTK) that is expressed by early hematopoietic progenitor cells and plays an important role in hematopoietic stem cell proliferation, differentiation and survival. It is known that c-kit is a proto-oncogene and the activating c-kit mutations are likely to contribute in the development of leukaemia in humans. Exon 11 of c-Kit gene is the frequent site for mutations in different kinds of tumours. Methods In order to determine the frequency and prevalence of exon 11 mutations in 51 AML cases, we have done polymerase chain reaction-single-strand conformational polymorphism followed by direct DNA sequencing. Results The c-kit mutations in exon 11 were detected in 15.68% (8/51) in AML cases. We have detected totally ten missense mutations in eight AML cases those include Lys550Asn, Tyr568Ser, Ile571Leu, Tyr578Pro, Trp582Ser and Arg588Met and novel missense mutations at codons Ile563Lys and Val569Leu. Mutations at codons Ile571Leu and Trp582Ser was found in two independent cases. Conclusion The presence of c-kit mutations in our study adds to investigative spectrum of AML cases. Since the c-kit mutations are seen in other malignancies, mutations in exon 11 of the c-kit gene might be involve in pathogenesis and represent useful predictive genetic marker in AML. Further studies in larger group of cases possibly will be required to determine the prognostic implications and to investigate how these mutations are co-related to the progression and pathogenesis of AML.

SUMMARY A standardized single-stranded conformational polymorphism (SSCP) procedure is proposed as an alternative to the timeconsuming biological characterization of Barley yellow dwarf virus-PAV (BYDV-PAV) isolates. Using this procedure, six of 21 overlapping regions used to scan the viral genome gave patterns specific to ‘4E’ (avirulent) or ‘4T’ (‘4E’-derived virulent) isolates. The calibration of samples and integration of SSCP patterns corresponding to the nucleotide region 1482‐2023 allowed the estimation of PT values that reflect the proportions of a ‘4T’specific band. Analysis of the biological (area under the pathogen progress curve) and molecular (PT) data suggested a positive linear relation between these variables. Moreover, sequence analysis of the nucleotide region 1482‐2023 highlighted the presence of a nucleotide polymorphism (C/A1835) which can be considered as a candidate for virus‐host interactions linked to the monitored virulence. According to these parameters, PT values associated with ‘4E’- and ‘4T’-derived populations show that: (i) long-term infection of a BYDV-PAV isolate on the ‘TC14’ resistant host leads to the fixation of virulent individuals in viral populations; and (ii) the introduction of susceptible hosts in successive ‘TC14’ infections results in the maintenance of low virulence of the populations. Thus, the presented study demonstrates that SSCP is a useful tool for monitoring viral populations during the host adaptation process.The described impact of host alternation provides new opportunities for the use of the ‘TC14’ resistance source in BYDV-resistant breeding programmes. This study is part of the global effort made by the scientific community to propose sustainable alternatives to the chemical control of this viral disease.

Metachromatic leukodystrophy is a lysosomal storage disorder caused by the deficiency of arylsulfatase A or saposin B. Enzyme deficiency leads to the accumulation of sulfatide, which results in severe demyelination.In this study, clinically suspected patients were diagnosed as metachromatic leukodystrophy by enzyme analysis using p-nitrocathecol sulfate as substrate. Eight exons and flanking regions of arylsulfatase A gene of patients were amplified by polymerase chain reaction and then subjected to single stranded conformational polymorphism analysis. Polymerase chain reaction products of suspicious exons in single stranded conformational polymorphism were purified from agarose gel and sequenced.DNA sequencing revealed two novel disease-causing missense mutations: the first one is 1568G--A, 307Glu--Lys in exon 5 which is together with a 2161C--T, 391Thr--Ser polymorphism in exon 7; and the second one is 1603G--T, 318Trp--Cys in exon 5.These two mutations are in highly conserved structural elements region of the arylsulfatase A protein. Thus, missense mutations 307Glu--Lys in exon 5 and 318Trp--Lys in exon 5 probably change the active site conformation by disrupting the sixth alpha helix and the twelfth beta-sheet structure of the arylsulfatase A protein, respectively, and cause deficiency in enzyme activity. This study provides the molecular basis for understanding the mechanism underlying metachromatic leukodystrophy.

We have applied the temperature-dependent single-stranded conformational polymorphism (SSCP) analysis for characterization of influenza A virus cDNA fragments. A series of primers were synthesized on the basis of the comparison of hemagglutinin and PB2 gene sequences of different origin. RT-PCR reactions were run using these primers, products were denatured and single-strand DNA fragments were subjected to electrophoresis. After silver staining, ssDNA band patterns characteristic for each genotype were observed. Minor differences within a serotype were detected without need for sequencing the PCR products making the preliminary analysis of avian influenza isolates much faster.