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Empirical studies have shown that algal- and detrital-based food web components are coupled in many pelagic systems as algal carbon enhances bacterioplankton production and growth efficiencies. Such phyto-bacterioplankton coupling impacts carbon flow through plankton food webs, yet the extent of coupling is poorly understood in systems receiving large amounts of allochthonous carbon. To investigate this issue, bacterioplankton abundance (BA) and community composition were compared to chlorophyll a concentrations and phytoplankton production in the tidal-freshwater James River (VA). BA averaged 107 cells mL-1 and was significantly related to chlorophyll a, phytoplankton production, and DOC concentrations. Analysis of DOC quality using fluorescence spectroscopy revealed that the fulvic DOC fraction was dominated by allochthonous compounds. However, estimates of DOC C:N and DOC turnover rates indicated that DOC was more labile in the lower part of the study reach where BA was highest. T-RFLP analysis of 16s rDNA showed that bacterioplankton community composition significantly varied between the upper and lower portions of the sampling reach. These findings suggest that coupling of food web components is an important pathway affecting carbon cycling within the tidal-fresh water James River.

Pisolithus is an important ectomycorrhizal genus world-wide, however to date we remain largely ignorant of the genetic and functional variation that exists within isolates of this genus. Fifty-three isolates of Pisolithus were obtained from various locations in central and eastern Australia and genetic variation within the isolates was assessed using ITS-RFLP and ITS sequencing analyses. RFLP analysis initially grouped the isolates into eight RFLP types. Neighbour-joining analysis of ITS sequences with Pisolithus ITS sequences available in databases clustered the majority of isolates into four groups within two major clades, each comprising isolates of similar basidiospre characteristics. Most Australian isolates correspond with recent provisional descriptions of P. albus or P. marmoratus. One isolate (LJ30) had low sequence identity (61.6-78.0%) to the other isolates and probably represents a separate undescribed Australian species. Significant intraspecific variation was observed in ITS-RFLP profiles for the putative P. albus isolates, suggesting that the sole use of RFLP analysis in diversity assessment may over-estimate Pisolithus species richness. Investigations were also initiated to identify if a relationship exists between genetic and physiological diversity in Australian Pisolithus. It is, however, clear that extensive physiological variation exists in Australian Pisolithus isolates. The size and distribution of genets of Australian Pisolithus species I and II ( putative P. albus and P. marmoratus) was also assessed using microsatellite-primed PCR to gain a better understanding of the likely distribution of underground mycelial networks and possible reproduction strategies in native soils. The data demonstrate that both species have the ability to be long-lived and extend for significant distances in native soils in undisturbed conditions. The field site for Pisolithus species I, however, also contained of a large number of small individuals suggesting that this species may employ a life-history strategy combining r-, C and S characteristics depending on local soil conditions / Doctor of Philosophy (PhD)

Twenty species and six subspecies of the genera Arcobacter and Campylobacter have been described to date. All are Gram-negative, microaerophilic, curved, spiral or S-shaped cells, and are members of the order Campylobacterales, class Epsilonproteobacteria phylum Proteobacteria. Though most members are pathogenic, C. jejuni, C. coli and A. butzleri are the most frequently isolated species from patients suffering from gastrointestinal illness. The current methods for their detection, identification, and differentiation are cumbersome, time consuming and lack specificity. DNA based molecular techniques including real-time Polymerase Chain Reaction (PCR) and Fingerprinting methods Terminal Restriction Fragments Length Polymorphism (T-RFLP) and Ligase Detection Reaction (LDR) have been used in this project to develop rapid detection and identification methods for Campylobacter and Arcobacter species. Five real-time PCR methods were developed which include: (a) rapid detection and identification of Campylobacter species using real-time PCR adjacent hybridisation probes, (b) rapid identification of C. jejuni using SYBR Green I, (c) rapid detection and differentiation of Arcobacter species using adjacent hybridisation probes, (d) rapid detection and differentiation of Arcobacter species and the Campylobacter group (C. coli, C. jejuni, C. lari, C. hyoilei, C. helviticus, C. hyointestinalis, C. insulaenigrae, C lanienae) using melting temperature (Tm) of adjacent hybridisation probes, and (e) a one tube real-time PCR multiplex for the rapid detection and identification of Campylobacter species, C. coli and C. jejuni using a TaqMan Probe, in an iCycler iQTM (BioRad, USA) and Light CyclerTM (Idaho Technology, USA). [Continued ...]

Pisolithus is an important ectomycorrhizal genus world-wide, however to date we remain largely ignorant of the genetic and functional variation that exists within isolates of this genus. Fifty-three isolates of Pisolithus were obtained from various locations in central and eastern Australia and genetic variation within the isolates was assessed using ITS-RFLP and ITS sequencing analyses. RFLP analysis initially grouped the isolates into eight RFLP types. Neighbour-joining analysis of ITS sequences with Pisolithus ITS sequences available in databases clustered the majority of isolates into four groups within two major clades, each comprising isolates of similar basidiospre characteristics. Most Australian isolates correspond with recent provisional descriptions of P. albus or P. marmoratus. One isolate (LJ30) had low sequence identity (61.6-78.0%) to the other isolates and probably represents a separate undescribed Australian species. Significant intraspecific variation was observed in ITS-RFLP profiles for the putative P. albus isolates, suggesting that the sole use of RFLP analysis in diversity assessment may over-estimate Pisolithus species richness. Investigations were also initiated to identify if a relationship exists between genetic and physiological diversity in Australian Pisolithus. It is, however, clear that extensive physiological variation exists in Australian Pisolithus isolates. The size and distribution of genets of Australian Pisolithus species I and II ( putative P. albus and P. marmoratus) was also assessed using microsatellite-primed PCR to gain a better understanding of the likely distribution of underground mycelial networks and possible reproduction strategies in native soils. The data demonstrate that both species have the ability to be long-lived and extend for significant distances in native soils in undisturbed conditions. The field site for Pisolithus species I, however, also contained of a large number of small individuals suggesting that this species may employ a life-history strategy combining r-, C and S characteristics depending on local soil conditions / Doctor of Philosophy (PhD)

<p>When paper is manufactured, deposits often form in the machines. These deposits are slimelike and can interfere with the papermaking process. The slimelike deposits are aggregates of micro-organisms, also known as biofilm. One single type of micro-organism can form a biofilm, but most biofilms consists of a mixture of several different kinds of micro-organisms and can form on about any conceivable surface. To control the aggregates of micro-organisms a slimecide is added, a so-called biocide. To examine what kind of bacteria that is included in the biofilm and also which bacteria that is killed or not killed by the biocide, Terminal Restriction Fragment Length Polymorphism analysis (T-RFLP) can be used.</p><p> </p><p>In this report we examine biocides impact on biofilm produced in the laboratory.The biocides were first tested for possible interference with the PCR-step of the T-RFLP analysis. None of the tested ten biocides inhibited the PCR process the biofilm was formed on metal plates when these were lowered in a beaker with white water. Three different beakers were set up, one with addition of a biocide with active component 4,5-DICHLORO-1,2-DITHIOLONE from the start, one with the addition of the same biocide after three days and one with no addition at all of biocide. Samples were taken from the beakers and analyzed with T-RFLP.</p><p> </p><p>In this report, we show that biocides affect planktonic and biofilm micro-organisms differently. There are however some micro-organisms in the biofilm that does not get affected by the biocide.</p><p> </p><p>The experimental in this report is a good way of investigate the influence that biocides have on planktonic and biofilm micro-organisms, but to get even greater result the experiment should be done over a longer period of time and repeatedly.</p>

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Abstract According to recent clinical treatment, doctors give patients medicines based on clinical experience and biochemical data. However, biochemical data simply provides an initial physiology reaction. Although the data is enough for doctors to diagnose diseases, it does not help much for doctors to indicate the most useful medicine. Therefore, doctors will use the first line, cheap or low dose medicine to cure patients by previous clinical experience. It will not only extend the time of treatment but also lower the medical quality. Not to mention the side effects and increases the cost. Consequently, using SNP¡]Single Nucleotide Polymorphism¡^will help doctors to find out different patients¡¦ genotype and forecast the result of medicine. It will control disease efficiently and decrease the medical costs. Methods: This study will be discussed with an accurate test of how to check the genotypes of diabetes mellitus and predict the result of treatment from pharmacogenetic. The method was using PCR (Polymerase Chain Reaction) and RFLP (Restriction Fragment Length Polymorphism) to analyze patients¡¦ different genotype. Besides, this study uses the One-Way ANOVA to interpret the relationship between ABCC8-E16 and type 2 diabetes. In conclusion, the antidiabetic drugs- Sulfonylurea derivatives are suitable for ABCC8-E16 genotype patients. This result can be a reference for doctors to remedy diabetics. It will not only save the cost but also shorten the time of treatment, and it will impact deeply for personalized medicine in the future. type 2 diabetes, Sulfonylurea, SNP, PCR, RFLP, pharmacogenetic, personalized medicine

La microflore des raisins est importante d'un point de vue technologique car elle conditionne en partie la qualité du vin. Or, la diversité des flores fongiques présentes sur baies de raisin ainsi que leur potentiel de contamination du produit final ne sont pas encore pleinement connus. Dans ce cadre, la caractérisation des flores fongiques cultivables présentes sur baies de raisin a été réalisée par PCR ITS-RFLP. 41 espèces de moisissures différentes sur les 43 étudiées appartenant à 11 genres différents ont été caractérisées de façon fiable. Seules les espèces Penicillium thomii et Penicillium glabrum ont présenté le même profil. Ainsi 96.3% des souches étudiées ont été caractérisées avec au maximum 4 enzymes de restriction et 41.5% des souches ont pu l'être avec seulement 2 enzymes de restriction. Ces résultats ont permis d'enrichir les bases de données, moyennement pourvues en séquences ITS caractéristiques de genres ou d'espèces de moisissures présentes sur baies de raisin. De plus, une étude exhaustive des moisissures présentes sur baies de raisin en Bourgogne a permis, par PCR ITS-RFLP, d'identifier 199 souches au niveau de l'espèce et ce quelque soit le genre. Penicillium spinulosum est l'espèce majoritaire isolée pour le millésime 2008 en Bourgogne. Parallèlement, la quantification de Botrytis cinerea, choisi comme micro-organisme modèle, a été réalisée par qPCR. La technique qPCR décrite dans ce travail présente (i) une bonne sensibilté avec une limite de détection de 6.4 pg d'ADN correspondant à 540 spores, (ii) l'originalité de travailler en échantillons naturellement contaminés et la fiabilité d'utiliser un standard interne. L'évaluation de l'efficacité de différentes stratégies de traitements anti-Botrytis a confirmé l'importance de la prophylaxie (effeuillage) dans la lutte contre Botrytis cinerea.