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Restriction Profiles (restriction + profile)
Selected AbstractsMitochondrial DNA sequence variation within and between tuna Thunnus species and its application to species identificationJOURNAL OF FISH BIOLOGY, Issue 6 2001H. Takeyama Restriction analysis detected two types of bigeye tuna (, and ,); the , type was in the majority in the Atlantic but nearly absent in the Indo-Pacific. The , type shared a larger number of restriction sites with other species than the conspecific , type, but bigeye-specific nucleotide substitutions with a novel diagnostic restriction profile were found. Although the nucleotide sequence difference between Atlantic and Pacific sub-species of the northern bluefin tuna was nearly the largest among species, individuals possessing the Atlantic type of mtDNA were found at very low frequency in the Pacific and vice versa. Previous RFLP markers were found to be diagnostic for the other five species (albacore, blackfin, longtail, southern bluefin and yellowfin tunas). Genetic information is provided to discriminate all Thunnus species regardless of their origin and to identify the ocean of capture in the northern bluefin and bigeye tunas. [source] Analysis of non- Saccharomyces yeast populations isolated from grape musts from Sicily (Italy)JOURNAL OF APPLIED MICROBIOLOGY, Issue 6 2008D.P. Romancino Abstract Aims:, The aim of this study was to identify the non- Saccharomyces yeast populations present in the grape must microflora from wineries from different areas around the island of Sicily. Methods and Results:, Yeasts identification was conducted on 2575 colonies isolated from six musts, characterized using Wallerstein Laboratory (WL) nutrient agar, restriction analysis of the amplified 5·8S-internal transcribed spacer region and restriction profiles of amplified 26S rDNA. In those colonies, we identified 11 different yeast species originating from wine musts from two different geographical areas of the island of Sicily. Conclusions:, We isolated non- Saccharomyces yeasts and described the microflora in grape musts from different areas of Sicily. Moreover, we discovered two new colony morphologies for yeasts on WL agar never previously described. Significance and Impact of the Study:, This investigation is a first step in understanding the distribution of non- Saccharomyces yeasts in grape musts from Sicily. The contribution is important as a tool for monitoring the microflora in grape musts and for establishing a new non- Saccharomyces yeast collection; in the future, this collection will be used for understanding the significance of these yeasts in oenology. [source] The molecular diversity of the methanogenic community in a hypereutrophic freshwater lake determined by PCR-RFLPJOURNAL OF APPLIED MICROBIOLOGY, Issue 5 2004C. Whitby Abstract Aims:, To combine database-held sequence information with a programme of experimental molecular ecology to define the methanogenic community of a hypereutrophic lake by a PCR-restriction fragment length polymorphism (RFLP) analysis. Methods and Results:, Methanogen diversity in a hypereutrophic freshwater lake was analysed using 16S rDNA PCR-RFLP. Database-held 16S rRNA gene sequences for 76 diverse methanogens were analysed for specific restriction sites that permitted unequivocal differentiation of methanogens. Restriction digestion and agarose gel electrophoresis of the 16S rDNA from selected methanogen pure cultures generated observed restriction profiles that corroborated the expected patterns. This method was then tested by analysing methanogen diversity in samples obtained over 1 year from sediment and water samples taken from the same sampling site. Conclusions:, Restriction analysis of the 16S rRNA gene sequences from 157 methanogen clones generated from lakewater and sediment samples showed that over 50% were similar to Methanoculleus spp. Furthermore, a total of 16 RFLP types (1,16) were identified, eight of which contained no cultured representative archaeal 16S rRNA gene sequences. Significance and Impact of the Study:, This RFLP strategy provides a robust and reliable means to rapidly identify methanogens in the environment. [source] Evolution of a degradative bacterial consortium during the enrichment of naphtha solventJOURNAL OF APPLIED MICROBIOLOGY, Issue 6 2000L. Cavalca A microbial mixed culture able to degrade naphtha solvent, a model of hydrocarbon aromatic mixture, was isolated from a hydrocarbon-polluted soil. Composition of the population was monitored by phenotypic and molecular methods applied on soil DNA, on whole enrichment culture DNA, and on 85 isolated strains. Strains were characterized for their 16S rDNA restriction profiles and for their random amplified polymorphic DNA profiles. Catabolic capabilities were monitored by phenotypic traits and by PCR assays for the presence of the catabolic genes methyl mono-oxygenase ( xylA,M), catechol 2,3 dioxygenase (xylE) and toluene dioxygenase (todC1) of TOL and TOD pathways. Different haplotypes belonging to Pseudomonas putida, Ps. aureofaciens and Ps. aeruginosa were found to degrade aromatic compounds and naphtha solvent. The intrinsic catabolic activity of the microbial population of the polluted site was detected by PCR amplification of the xylE gene directly from soil DNA. [source] Polymorphisms in the sequences of Marteilia internal transcribed spacer region of the ribosomal RNA genes (ITS-1) in Spain: genetic types are not related with bivalve hostsJOURNAL OF FISH DISEASES, Issue 6 2005B Novoa Abstract Marteilia refringens is a protozoan parasite causing a disease notifiable to the Office International des Epizooties (OIE) and its distribution has implications for the transfer of live animals. The internal transcribed spacer-1 (ITS-1) from Marteilia clones contains polymorphism. Digestion with HhaI reveals two different restriction profiles, previously referred as ,O' (Marteilia from oyster or Marteilia refringens) and ,M' (Marteilia from mussels or Marteilia maurini). The aim of the present work was to determine whether the two previously described Marteilia molecular types (O and M) exist in the Iberian Peninsula and the strictness of the association with their bivalve host species. The sequence variability in the ITS-1 of Marteilia species was studied in mussels, Mytilus galloprovincialis, and flat oysters, Ostrea edulis, from different geographical locations in Spain, to establish the existence and the distribution of different species or molecular types. Although there were two distinct evolutionary lineages that corresponded more or less strictly with the ,M' and ,O' types, it was evident from the estimated phylogeny that some ,O' types have switched to ,M' type, and vice versa. Moreover, ,O' types were found in mussels and ,M' types were found in oysters, which suggests that there have been several cross-species transmissions of Marteilia between mussels and oysters. [source] Detection of Phytoplasma Infection in Rose, with Degeneration SymptomsJOURNAL OF PHYTOPATHOLOGY, Issue 1 2001M. Kami In 1998 a severe disease was observed on rose cvs. ,Patina', ,Papillon' and ,Mercedes' cultivated in a commercial greenhouse in Poland. The symptoms included stunted growth, bud proliferation, leaf malformation and deficiency of flower buds. Sporadically some plants yielded flower buds transformed into big-bud structures and degenerated flowers. The presence of phytoplasma in roses with severe symptoms as well as in recovered plants and Catharanthus roseus experimentally infected by grafting and via dodder was demonstrated by nested polymerase chain reaction assay with primers pair R16F2/R2 or R16F1/R0 and R16(I)F1/R1 amplifying phytoplasma 16S rDNA fragment. The polymerase chain reaction products (1.1 kb) used for restriction fragment length polymorphism analysis after digestion with endonuclease enzymes AluI and MseI produced the same restriction profiles for all samples. The restriction profiles of phytoplasma DNA from these plants corresponded to those of an aster yellows phytoplasma reference strain. Electron microscope examination of the ultra-thin sections of the stem showed wall thickenings of many sieve tubes of the diseased roses and single phytoplasma cells within a sieve element of the phloem of experimentally infected periwinkles. This paper is the first report on aster yellows phytoplasma in rose identified at a molecular level. Detektion einer Phytoplasma-Infektion bei Rosen mit Degenerationserscheinungen Im Jahr 1998 wurde eine schwere Krankheit bei Rosen der Sorten ,Patina', ,Papillon' und ,Mercedes' festgestellt, die in einem polnischen Gewächshaus für kommerzielle Zwecke kultiviert wurden. Zu den Symptomen gehörten Kümmerwuchs, durchwachsene Knospen, Blattmißbildungen und ein Mangel an Blütenknospen. Einige wenige Pflanzen trugen übergroße Blütenknospen, die degenerierte Blüten hervorbrachten. Die Anwesenheit von Phytoplasmen in Rosen mit starken Symptomen, in erholten Pflanzen und in Catharanthus roseus, der durch Pfropfen und durch Teufelszwirn (Cuscuta) experimentell infiziert worden war, wurde mittels einer genesteten Polymerase-Kettenreaktion mit den Primerpaaren R16F2/R2 oder R16F1/R0 und R16(1)F1/R1 zur Amplifikation des Phytoplasma-16S rDNA-Fragments demonstriert. Die für die Analyse der Restriktionsfragmentlängenpolymorphismen nach Verdau mit den Endonucleasen AluI und MseI verwendeten PCR-Produkte (1,1 kb) produzierten bei allen Proben die gleichen Restriktionsprofile. Die Restriktionsprofile der Phytoplasma-DNA aus diesen Pflanzen entsprachen denjenigen eines Typenstamms eines Asternvergilbung auslösenden Phytoplasmas. Elektronenmikroskopische Untersuchungen ultradünner Schnitte des Stamms zeigten Wandverdickungen bei zahlreichen Siebröhren der erkrankten Rosen und einzelne Phytoplasmazellen innerhalb eines Siebelements des Phloems experimentell infizierter Immergrün-Pflanzen. Dies ist der erste Bericht über ein auf molekularer Ebene identifiziertes Asternvergilbungs-Phytoplasma bei Rosen. [source] | |||||||||||||