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Genomic Markers (genomic + marker)
Selected AbstractsThe usefulness of amplified fragment length polymorphism markers for taxon discrimination across graduated fine evolutionary levels in Caribbean Anolis lizardsMOLECULAR ECOLOGY, Issue 3 2002R. Ogden Abstract Fine-level taxon discrimination is important in biodiversity assessment and ecogeographical research. Genomic markers are often required for studies on closely related taxa, however, most existing mitochondrial and nuclear markers require prior knowledge of the genome and are impractical for use in small conservation projects. This study describes the application of amplified fragment length polymorphism (AFLP) to discriminate at four progressively finer evolutionary levels of Caribbean Anolis lizards from the central Lesser Antilles. AFLP is shown to be a rapid and effective method for discriminating between species. Separation increases with primer pair number and choice of primer combination appears to be noncritical. Initial population-level results show markedly less discriminatory power. A screening technique for the identification of population informative markers combining principal component and principal coordinate analyses is presented and assessed. Subsequent results show selected conspecific AFLP data to be remarkably congruent with those of mitochondrial DNA, microsatellite and morphological markers. The use of AFLP as a low-cost nuclear marker in species-level taxon discrimination is supported, whereas population level application demands further consideration. [source] K-Ras and microsatellite marker analysis of fine-needle aspirates from intraductal papillary mucinous neoplasms of the pancreas,DIAGNOSTIC CYTOPATHOLOGY, Issue 9 2006Karen E. Schoedel M.D. Abstract Preoperative diagnosis of pancreatic cystic lesions is difficult despite the combination of cytomorphology, radiographic imaging characteristics, and fluid tumor markers such as carcinoembryonic antigen. Intraductal papillary mucinous neoplasms (IPMNs) represent a subset of preinvasive pancreatic cystic neoplasms and are associated with accumulated genetic mutations, especially K-ras and tumor suppressor genes such as p53. Application of molecular techniques to cyst fluid obtained by endoscopic ultrasound guided fine-needle aspiration (EUSFNA) may contribute to preoperative assessment. Sixteen patients with pancreatic cystic lesions had cyst fluid obtained by preoperative pancreatic EUSFNA or intraoperative aspiration. All patients subsequently underwent surgical resection of the pancreas and IPMN was documented in all (6 adenomas, 6 borderline tumors, and 4 carcinomas). DNA was extracted from the cyst fluids and mutational analysis for K-ras point mutations and loss of heterozygosity (LOH) analysis using a preselected panel of genomic loci were performed. LOH was observed in 3 of 4 carcinomas as compared to 4 of 11 adenomas and borderline lesions (1 was QNS). LOH and K-ras mutations were both acquired in 2 of 4 carcinomas and in 1 of 12 adenoma/borderline lesions. Although the study is small, molecular analysis for LOH and K-ras mutations is useful in the preoperative evaluation of cystic pancreatic lesions. Increasing degree of neoplasia appears to correlate with increased genetic abnormality using a panel of selected genomic markers. Diagn. Cytopathol. 2006;34:605,608. © 2006 Wiley,Liss, Inc. [source] Sequence variation in trypsin- and chymotrypsin-like cDNAs from the midgut of Ostrinia nubilalis: methods for allelic differentiation of candidate Bacillus thuringiensis resistance genesINSECT MOLECULAR BIOLOGY, Issue 1 2006B. S. Coates Abstract Midgut expressed alkaline serine proteases of Lepidoptera function in conversion of Bacillus thuringiensis (Bt) protoxin to active toxin, and reduced level of transcript T23 is associated with Ostrinia nubilalis resistance to Dipel® Bt formulations. Three groups of trypsin- (OnT25, OnT23, and OnT3) and two chymotrypsin-like (OnC1 and OnC2) cDNAs were isolated from O. nubilalis midgut tissue. Intraspecific groupings are based on cDNA similarity and peptide phylogeny. Derived serine proteases showed a catalytic triad (His, Asp, and Ser; except transcript OnT23a), three substrate specificity-determining residues, and three paired disulphide bonds. RT-PCR indicated all transcripts are expressed in the midgut. Mendelian-inherited genomic markers for loci OnT23, OnT3 and OnC1 will be useful for association of alleles with bioassayed Bt toxin resistance phenotypes. [source] Detecting introgressive hybridization between free-ranging domestic dogs and wild wolves (Canis lupus) by admixture linkage disequilibrium analysisMOLECULAR ECOLOGY, Issue 10 2006A. VERARDI Abstract Occasional crossbreeding between free-ranging domestic dogs and wild wolves (Canis lupus) has been detected in some European countries by mitochondrial DNA sequencing and genotyping unlinked microsatellite loci. Maternal and unlinked genomic markers, however, might underestimate the extent of introgressive hybridization, and their impacts on the preservation of wild wolf gene pools. In this study, we genotyped 220 presumed Italian wolves, 85 dogs and 7 known hybrids at 16 microsatellites belonging to four different linkage groups (plus four unlinked microsatellites). Population clustering and individual assignments were performed using a Bayesian procedure implemented in structure 2.1, which models the gametic disequilibrium arising between linked loci during admixtures, aiming to trace hybridization events further back in time and infer the population of origin of chromosomal blocks. Results indicate that (i) linkage disequilibrium was higher in wolves than in dogs; (ii) 11 out of 220 wolves (5.0%) were likely admixed, a proportion that is significantly higher than one admixed genotype in 107 wolves found previously in a study using unlinked markers; (iii) posterior maximum-likelihood estimates of the recombination parameter r revealed that introgression in Italian wolves is not recent, but could have continued for the last 70 (± 20) generations, corresponding to approximately 140,210 years. Bayesian clustering showed that, despite some admixture, wolf and dog gene pools remain sharply distinct (the average proportions of membership to wolf and dog clusters were Qw = 0.95 and Qd = 0.98, respectively), suggesting that hybridization was not frequent, and that introgression in nature is counteracted by behavioural or selective constraints. [source] | ||||||||||