Identification of Porphyra lines (Rhodophyta) by AFLP DNA fingerprinting and molecular markers

Twenty-seven Porphyra lines from 5 classes, including lines widely used in China, wild lines, and lines introduced to China from abroad in recent years, were screened by means of amplified fragment length polymorphism (AFLP) with 24 primer pairs. From the generated AFLP products, 13 bands that showed stable and repeatable AFLP patterns amplified by primer pairs M-CGA/E-AA and M-CGA/E-TA were scored and used to develop the DNA fingerprints of the 27 Porphyra lines. Moreover, the DNA fingerprinting patterns were converted into computer language expressed with digitals 1 and 0, which represented the presence (numbered as 1) or absence (numbered as 0) of the corresponding band. On the basis of these results, computerized AFLP DNA fingerprints were constructed in which each of the 27 Porphyra lines has its unique AFLP,fingerprinting pattern and can be easily distinguished from others. Software called PGI-AFLP (Porphyra germplasm identification-AFLP) was designed for identification of the 27 Porphyra lines. In addition, 21 specific AFLP markers from 15 Porphyra lines were identified; 6 AFLP markers from 4 Porphyra lines were sequenced, and 2 of them were successfully converted into SCAR (sequence characterized amplification region) markers. The developed AFLP DNA fingerprinting and specific molecular markers provide useful ways for the identification, classification, and resource protection of the Porphyra lines.

Molecular identification of 16 Porphyra lines using sequence-related amplified polymorphism markers

Sequence-related amplified polymorphism (SRAP) is a novel molecular marker technique designed to amplify open reading frames (ORFs). The SRAP analytic system was set up and applied to Porphyra germplasm identification in this study for the first time. Sixteen Porphyra lines were screened by SRAP technique with 30 primer combinations. In the analysis, 14 primer combinations produced stable and reproducible amplification patterns in three repetitive experiments. Among the total 533 amplified fragments, 522 (98%) were polymorphic, with an average of 38 fragments for each primer combination, ranging in size from 50 to 500 bp. The 533 fragments were visually scored one by one and then used to develop a dendrogram with Unweighted Pair-Group Method Arithmetic Average (UPGMA), and the 16 Porphyra lines were divided into two major groups at the 0.68 similarity level. From the total 533 fragments, I I amplified by two primer combinations, ME1/EM1 and ME4/EM6, were used to develop the DNA fingerprints of the 16 Porphyra lines. The DNA fingerprints were then converted into binary codes, with I and 0 representing presence and absence of the corresponding amplified fragment, respectively. In the DNA fingerprints, each of the 16 Porphyra lines has its unique binary code and can be easily distinguished from the others. This is the first report on the development of SRAP technique and its utilization in germplasm identification of seaweeds. The results demonstrated that SRAP is a simple, stable, polymorphic and reproducible molecular marker technique for the classification and identification of Porphyra lines. (c) 2007 Elsevier B.V. All rights reserved.

Molecular authentication of the traditional Tibetan medicinal plant Swertia mussotii

Swertia mussotii is an important species in Tibetan folk medicine. However, it is quite expensive and frequently adulterated, so reliable methods for authentication of putative specimens and preparations of the species are needed to protect consumers and to support conservation measures. We show here that the chloroplast (cp) DNA rpl16 intron has limited utility for differentiating S. mussotii from closely related species, since the cpDNA rpl16 sequences are identical in S. mussotii and two other species of Swertia. However, the rDNA internal transcribed spacer (ITS) sequences differ significantly between S. mussotii and all of 13 tested potential adulterants. Thus, the ITS region provides a robust molecular marker for differentiating the medicinal S. mussotii from related adulterants. Therefore, a pair of allele-specific diagnostic primers based on the divergent ITS region was designed to distinguish S. mussotii from the other species. Authentication by allele-specific diagnostic PCR using these primers is convenient, effective and both simpler and less time-consuming than sequencing the ITS region.

Molecular studies on a Dictyostelium homolog of the tafazzin gene, the cause of Barth syndrome in humans

Der eukaryotische Mikroorganismus Dictyostelium discoideum lebt als einzellige Amöbe solange ausreichende Nahrungsressourcen zur Verfügung stehen. Sobald Nahrungsmangel eintritt, entwickeln sich die Zellen von einem einzelligen zu einem mehrzelligen Zustand, der mit einem multizellulären Fruchtkörper abschließt. Dieser Prozess wird durch eine Reihe aufeinanderfolgender Signale organisiert, die eine differentielle Genexpression regulieren. Die Gene der Discoidin I Familie gehören zu den Ersten, die im Laufe des Wachstums-Differenzierungs-Übergangs (engl. GDT) aktiviert werden. Sie eignen sich daher vorzüglich als Marker für den Beginn der Entwicklung. Mit Hilfe einer REMI-Mutagenese und Discoidin I als molekularem Marker sind verschiedene Komponenten des Wachstums-Differenzierungs-Übergangs in unserer Arbeitsgruppe identifiziert worden (Zeng et al., 2000 A und B; Riemann und Nellen, persönliche Mitteilung). Mit demselben Ansatz wurde in der vorliegenden Arbeit eine REMI-Mutante identifiziert, die eine Fehl-Expression von Discoidin zeigte und einen axenischen Wachstumsdefekt bei 15 °C aufwies. Das Gen wurde als Homolog zum humanen Tafazzin-Gen identifiziert. Dieses Gen wurde zur Rekonstruktion des Phänotyps über homologe Rekombination erneut disruptiert, was wie erwartet zu dem zuerst beschriebenen Phänotyp führte. Folgerichtig ergab eine Überexpression des Gens in den Mutanten eine Komplementation des Phänotyps. Immunfluoreszenz-Experimente zeigten eine mitochondriale Lokalisation des Dictyostelium discoideum Taffazzin Proteins. Dass ein mitochondriales Protein in Zusammenhang mit dem Wachstums-Differenzierungs-Übergang steht, ist ein unerwarteter Befund, der aber als Hinweis darauf gewertet werden kann, dass Mitochondrien einen direkten Einfluss auf die entwicklungsspezifische Signaltransduktion ausüben. Die Taffazzin Disruptions-Mutante in Dictyostelium führte zu einem abnormalen Cardiolipin Metabolismus. Dieses Phospholipid ist ein charakteristischer Bestandteil der inneren Mitochondrienmembran und für die Funktion verschiedener Enzyme erforderlich. Unsere vorläufigen Analysen des Phospholipid-Gehalts zeigten Übereinstimmung mit Daten von Patienten mit Barth-Syndrom, einer humanen Erkrankung, bei der das Taffazzin-Gen Mutationen aufweist, und mit Hefe-Mutanten dieses Gens. Dies zeigt den Wert von Dictyostelium discoideum als einen weiteren Modelorganismus zur Untersuchung des Barth-Syndroms und zur Erprobung möglicher Therapieansätze.

ADN libre plasmático como marcador molecular en lesiones pre-neoplásicas de cuello uterino y su asociación con VPH

Introducción: La concentración de ADN libre en plasma ha sido investigada como un biomarcador tumoral en diferentes tipos de cáncer. Sin embargo, son pocos los estudios que evalúan la concentración ADN libre en pacientes con cáncer cervical y hasta la fecha no hay estudios en pacientes con lesiones pre-cancerosas cervicales. Objetivo: Establecer la asociación entre la concentración de ADN libre y el grado de la neoplasia cervical y evaluar su posible asociación con el tipo viral. Metodología: Estudio de prevalencia de tipo analítico con un muestreo no probabilístico. Se cuantifico el ADN libre en plasma por PCR en tiempo real de 92 pacientes que presentaban algún tipo de lesión intraepitelial cervical, confirmado por biopsia en diferentes instituciones de la ciudad de Bogotá. Adicional a esto se realizó la genotipificación del virus por Reverse Line Blot. Resultados: La concentración de ADN libre en plasma de pacientes con lesiones pre-cancerosas fue 4515 ± 16402 ng/ µl (media ± DS), LIEBG fue de 5188.7 ± 14876.5 ng/ µl (media ± DS), en pacientes con LIEAG fue de 830.3 ± 1515.508 ng/ µl (media ± DS), en pacientes con resultado negativo fue de 7024.7 ± 24107.5 ng/ µl (media ± DS). Los serotipos encontrados en la poblacion de estudio no presentaron asociacion con la concentracion de ADN libre. Discusión: Los resultados demostraron que la concentración absoluta de ADN libre en plasma no tiene un valor predictivo para diferenciar los tipos de lesión pre-neoplasica de cuello uterino, puesto que no se encontraron diferencias significativas en la concentración de ADN libre en plasma de las diferentes etapas progresivas de cáncer de cuello uterino (p;0.57, gl;3 alfa 0.05) de la misma forma el serotipo no contribuye a explicar la concentración de ADN libre.

The tagged microarray marker (TAM) method for high-throughput detection of single nucleotide and indel polymorphisms

The tagged microarray marker (TAM) method allows high-throughput differentiation between predicted alternative PCR products. Typically, the method is used as a molecular marker approach to determining the allelic states of single nucleotide polymorphisms (SNPs) or insertion-deletion (indel) alleles at genomic loci in multiple individuals. Biotin-labeled PCR products are spotted, unpurified, onto a streptavidin-coated glass slide and the alternative products are differentiated by hybridization to fluorescent detector oligonucleotides that recognize corresponding allele-specific tags on the PCR primers. The main attractions of this method are its high throughput (thousands of PCRs are analyzed per slide), flexibility of scoring (any combination, from a single marker in thousands of samples to thousands of markers in a single sample, can be analyzed) and flexibility of scale (any experimental scale, from a small lab setting up to a large project). This protocol describes an experiment involving 3,072 PCRs scored on a slide. The whole process from the start of PCR setup to receiving the data spreadsheet takes 2 d.

Ty-1 copia retrotransposon-based SSAP marker development in Cashew

The most popular retrotransposon-based molecular marker system in use at the present time is the sequence-specific amplification polymorphism (SSAP) system . This system exploits the insertional polymorphism of long terminal repeat (LTR) retrotransposons around the genome. Because the LTR sequence is used to design primers for this method, its successful application requires sequence information from the terminal region of the mobile elements . In this study, two LTR sequences were isolated from the cashew genome and used successfully to develop SSAP marker systems. These were shown to have higher levels of polymorphism than amplified fragment length polymorphic markers for this species.

Morphologic and molecular characterization of Myrciaria spp species

A jabuticabeira é considerada uma das fruteiras mais típicas do Brasil. Entretanto, há poucos estudos sobre esta planta na literatura, e mesmo sua classificação botânica é muito controvertida. Este trabalho faz comparações entre as espécies de jabuticabeiras, usando as técnicas de marcadores morfológicos (organografia) e moleculares RAPD. As características morfológicas das plantas, usadas como marcadores morfológicos, foram comparadas com espécimes presentes nos herbários dos Estados de São Paulo e Minas Gerais e com as descrições obtidas em revisão de literatura especializada. As diferenças moleculares entre as espécies foram determinadas por meio do uso de marcadores RAPD. O experimento foi realizado nas cidades de Piracicaba, Jaboticabal e Ituverava do Estado de São Paulo, Brasil. Diferenças morfológicas e moleculares entre as plantas estudadas foram identificadas, e quatro grupos distintos de espécies foram definidos: Myrciaria cauliflora (Mart.) O. Berg, M. coronata Mattos, M. jaboticaba (Vell.) O. Berg. e M. phytrantha (Kiaersk.) Mattos. A técnica de marcadores moleculares, aliada à técnica de marcadores morfológicos, mostrou ser uma ferramenta importante na identificação de espécies de jabuticabeiras.

Utilização de marcador molecular SCAR na identificação de Fusarium subglutinans, agente causal da malformação da mangueira

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

AVALIAÇÃO DE PLANTAS MATRIZES DE ABACAXIZEIRO CULTIVAR SMOOTH CAYENNE UTILIZANDO MARCADORES RAPD E PADRÕES ISOENZIMÁTICOS

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Strain differentiation of Trichophyton rubrum by random amplification of polymorphic DNA (RAPD)

Trichophyton rubrum é um importante agente causal de dermatomicose. Os métodos de tipagem molecular têm sido recentemente desenvolvidos para responder questões sobre epidemiologia e auxiliar no esclarecimento de recidivas, após o tratamento. As seqüências aleatórias 1- (5'-d[GGTGCGGGAA]-3') e 6- (5'-d[CCCGTCAGCA]-3') foram usadas para tipagem molecular deste fungo por RAPD produzindo variabilidade intraespecífica. Cinco padrões foram observados entre os 10 isolados de T. rubrum, com ambas as seqüências. Foi concluído que a análise por RAPD pode ser utilizada para estudos epidemiológicos.

Classic and molecular study of Giardia duodenalis in children from a daycare center in the region of Presidente Prudente, São Paulo, Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Análise cromossômica e molecular do javali europeu Sus scrofa scrofa e do suíno doméstico Sus scrofa domesticus

A presente investigação teve como objetivos: analisar animais presentes em diferentes criações de javalis no estado de São Paulo, com o intuito de auxiliar a identificação de javalis puros assim como javalis híbridos provenientes do cruzamento com o suíno doméstico, para tanto foram utilizadas avaliação do fenótipo dos animais, análises citogenéticas e da técnica molecular de RAPD (Random Amplified Polymorphic DNA).O estudo do número de cromossomos nas células diplóides em 104 animais destinados a análise citogenética e fenotípica, revelou polimorfismo de 2n=36, 37 e 38 cromossomos. Por meio da técnica de bandamento GTG foi possível identificação da translocação Robertsoniana entre os cromossomos 15 e 17 como responsável por esse polimorfismo. Todavia, somente com a análise citogenética isolada, não foi possível determinar se a origem desse polimorfismo é decorrente das hibridações com o suíno doméstico ou se são características inerentes ao javali. Contudo, quando associado a análise citogenética com as características fenotípicas, foi possível identificar a existência de hibridações. A análise citogenética nos animais submetidos a técnica de RAPD, revelou 2n=36 cromossomos nos 16 javalis assim como 2n=38 cromossomos nos 11 suínos e, por meio dessa técnica, foram possíveis agrupamentos, separando o suíno doméstico, javali e um possível híbrido revelando-se uma técnica com potencial no auxílio da identificação de híbridos.

Documenting the advantages and limitations of different classes of molecular markers in a well-established phylogeographic context: lessons from the Iberian endemic Golden-striped salamander, Chioglossa lusitanica (Caudata: Salamandridae)

Previous analyses of mitochondrial (mt)DNA and allozymes covering the range of the Iberian endemic golden-striped salamander, Chioglossa lusitanica, suggested a Pleistocene split of the historical species distribution into two population units (north and south of the Mondego river), postglacial expansion into the northernmost extant range, and secondary contact with neutral diffusion of genes close to the Mondego river. We extended analysis of molecular variation over the species range using seven microsatellite loci and the nuclear P-fibrinogen intron 7 (beta-fibint7). Both microsatellites and beta-fibint7 showed moderate to high levels of population structure, concordant with patterns detected with mtDNA and allozymes; and a general pattern of isolation-by-distance, contrasting the marked differentiation of two population groups suggested by mtDNA and allozymes. Bayesian multilocus analyses showed contrasting results as populations north and south of the Douro river were clearly differentiated based on microsatellites, whereas allozymes revealed differentiation north and south of the Mondego river. Additionally, decreased microsatellite variability in the north supported the hypothesis of postglacial colonization of this region. The well-documented evolutionary history of C. lusitanica, provides an excellent framework within which the advantages and limitations of different classes of markers can be evaluated in defining patterns of population substructure and inferring evolutionary processes across distinct spatio-temporal scales. The present study serves as a cautionary note for investigations that rely on a single type of molecular marker, especially when the organism under study exhibits a widespread distribution and complex natural history. (C) 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95, 371-387.

Kappa-casein gene study with molecular markers in female buffaloes (Bubalus bubalis)

Caseins comprise make up about 80% of the total protein content of milk and present polymorphism with change in the amino acid sequence. Within this abundance of proteins, kappa-casein is noteworthy, since it has been associated with differences in milk yield, composition and processing. The objective of this study was to observe the existence of polymorphism in the kappa-casein gene in female buffaloes. For this purpose, blood samples from 115 female buffaloes, collected with vacutainer by needle punctionure of the jugular vein, were used. for genomic DNA extraction was done from blood samples. The PCR-RFLP and SSCP techniques demonstrated that the studied animals were monomorphic for the kappa-casein gene. Only allele B was observed in these animals, which was present in homozygosis. Therefore, it was not possible to quantify the gene action on milk yield and its constituents. The monomorphism observed in the population studied would allow the development of a method to identify mixtures of cow and buffalo milk in mozzarella cheese production, especially because, in cattle, the kappa-casein gene is polymorphic. Copyright by the Brazilian Society of Genetics.