Analysis of genotypic diversity data for populations of microorganisms     

Grünwald NJ  Goodwin SB  Milgroom MG  Fry WE 《Phytopathology》2003,93(6):738-746

ABSTRACT Estimation of genotypic diversity is an important component of the analysis of the genetic structure of plant pathogen and microbial populations. Estimates of genotypic diversity are a function of both the number of genotypes observed in a sample (genotype richness) and the evenness of distribution of genotypes within the sample. Currently used measures of genotypic diversity have inherent problems that could lead to incorrect conclusions, particularly when diversity is low or sample sizes differ. The number of genotypes observed in a sample depends on the technique used to assay for genetic variation; each technique will affect the maximum number of genotypes that can be detected. We developed an approach to analysis of genotypic diversity in plant pathology that makes specific reference to the techniques used for identifying genotypes. Preferably, populations that are being compared should be very similar in sample size. In this case, the number of genotypes observed can be used directly for comparing richness. In most cases, sample sizes differ and use of the rarefaction method to calculate richness is more appropriate. In all cases, scaling either Stoddart and Taylor's G or Shannon and Wiener's H' by sample size should be avoided. Under those circumstances where it might be important to distinguish whether richness or evenness contribute more to diversity, a bootstrapping approach, where confidence intervals are calculated for indices of diversity and evenness, is recommended.  相似文献   

Genetic Change Within Populations of Phytophthora infestans in the United States and Canada During 1994 to 1996: Role of Migration and Recombination     

Goodwin SB  Smart CD  Sandrock RW  Deahl KL  Punja ZK  Fry WE 《Phytopathology》1998,88(9):939-949

ABSTRACT Dramatic changes occurred within populations of Phytophthora infestans in the United States and Canada from 1994 through 1996. Occurrence of the US-8 genotype, detected rarely during 1992 and 1993, increased rapidly and predominated in most regions during 1994 through 1996. US-7, which infected both potato and tomato and made up almost 50% of the sample during 1993, was detected only rarely among 330 isolates from the United States analyzed during 1994. It was not detected at all in more limited samples from 1996. Thus, ability to infect both potato and tomato apparently did not increase the fitness of this genotype relative to US-8, as predicted previously. US-1, the previously dominant genotype throughout the United States and Canada, made up 8% or less of the samples analyzed during 1994 through 1996. A few additional genotypes were detected, which could indicate the beginnings of sexual reproduction of P. infestans within the United States and Canada. However, clonal reproduction still predominated in all locations sampled; opportunities for sexual reproduction probably were limited, because the A1 and A2 mating types usually were separated geographically. The high sensitivity of the US-1 genotype to the fungicide metalaxyl also could have reduced opportunities for contact between the mating types in fields where this compound was applied. The previous correlation between metalaxyl sensitivity and genotype was confirmed and extended to a new genotype, US-17: all US-1 isolates tested were sensitive; all isolates of the US-7, US-8, and US-17 genotypes tested to date have been resistant. Isolates of P. capsici and P. erythroseptica, two other species often found on tomato and potato, could be easily distinguished from each other and from P. infestans using a simple allozyme assay for the enzyme glucose-6-phosphate isomerase. This technique could be useful for rapid identification of species, in addition to genotype of P. infestans. It generally was not possible to predict which genotypes would be present in a location from 1 year to the next. Long-distance movement of US-8 in seed tubers was documented, and this was probably the primary means for the rapid spread of this genotype from 1993 through 1996.  相似文献   

The Impact of Egg Ozonation on Hatching Success,Larval Growth,and Survival of Atlantic Cod,Atlantic Salmon,and Rainbow Trout     

Jessica Fry  Juan Pérez Casanova  Lynn Lush  Andy Walsh  Cyr Couturier 《Journal of aquatic animal health》2015,27(1):57-64

The direct exposure of fish eggs to ozonated water has generated interest as a means of ensuring pathogen-free eggs without the use of harsh chemicals. However, there are numerous knowledge gaps, including safe contact times, exposure levels, and potential long-term effects on aquaculture species in both freshwater and seawater. The effect of different ozone (O₃) doses (0.5–1.0, 1.5–2.0, and 2.5–3.0 mg of O₃/L for 90 s) on recently fertilized eggs of Atlantic Cod Gadus morhua and eyed eggs of Atlantic Salmon Salmo salar and Rainbow Trout Oncorhynchus mykiss was evaluated in comparison with the effects of two commercial disinfectants: Perosan (0.004 mg/L) and Ovadine (100 mg/L). The impact of ozone application was evaluated based on hatching success, larval nucleic acid concentration, larval growth, and survival. Overall, results indicated that ozonation of Atlantic Cod eggs at a dose less than 3.0 mg/L for 90 s produced no negative effect on the larvae up to 30 d posthatch. Furthermore, ozonation of Atlantic Salmon and Rainbow Trout eggs generated no negative effect on the larvae, based on monitoring until 85% yolk sac re-absorption (16 d posthatch).

Received May 6, 2014; accepted October 24, 2014  相似文献   

Dominant sources of dietary carbon and nitrogen for shrimp reared in extensive rice-shrimp ponds   总被引：1，自引：0，他引：1  

Michele A Burford  Nigel P Preston  Truong Hoang Minh  Tran Thi Tuyet Hoa  Stuart E Bunn  & Vanessa M Fry 《Aquaculture Research》2004,35(2):194-203

Stable isotope analysis was used to determine the sources of dietary nitrogen (N) and carbon (C) for shrimp during the rearing phase in extensive rice‐shrimp ponds in My Xuyen and Gia Rai districts, Vietnam. Farm‐made feed was added as a food source in shrimp ponds in My Xuyen district, and based on stable isotope analyses, was generally a poor dietary source. The commercial formulated feed used in Gia Rai also appeared to contribute little directly to the nutritional needs of the shrimp. In contrast, the natural biota in all ponds appeared to contribute substantially. In particular, biota from beam trawls and benthic organic matter were the most likely sources of nutrition in My Xuyen ponds, while benthic organic matter was the main source in Gia Rai ponds. δ¹⁵N ratios in the natural biota in My Xuyen farms decreased over the growing season, suggesting increased N fixation in the case of the benthic organic matter reaching values as low as 1‰. This suggests N‐limitation in the ponds and that natural biota become increasingly dependent on N fixed by algae and/or other microorganisms. There is the potential to promote the growth of the plankton and hence, the other natural biota, by the judicious addition of fertilizer.  相似文献   

Dispersal of woody plants in forest edges and hedgerows in a Southern Swedish agricultural area: the role of site and landscape structure     

Sarlöv Herlin  Ingrid L.  Fry  Gareth L.A. 《Landscape Ecology》2000,15(3):229-242

The distribution of woody vegetation was studied in forest edges and hedgerows in a 28 km² southern Swedish agricultural area, characterised by species-rich edge zones. The occurrence of 21 selected woody species (taxa) was related to differences in both edge structure and landscape structure. All the species studied were represented in both edge types, but a higher frequency of animal-dispersed species was found in hedgerows.Animal dispersed species were more affected by edge width and density than wind dispersed species. A higher number of wind-dispersed species were more frequent in forest edges, in hedgerows near to forest, or with a high proportion of forest within 500 m. A clear relationship was found between the number of physically connected elements in hedgerow networks and increasing frequency of occurrence for Corylus avellana, Crataegus spp., Euonymus europaeus, and Quercus robur; which indicate the ecological significance of connectedness for certain animal dispersed species. The study supports the general principle that woody species distribution and landscape structure are linked in a positive feedback loop. The results match findings from studies in other countries and are interpreted in the context of landscape processes and the ecological characteristics of woody plant species. We emphasise the importance of understanding dispersal mechanisms of woody species for the design and improvement of edge habitats in agricultural landscapes.  相似文献   

Isolation of Fasciola hepatica metacercariae by density gradients     

T R Fry  J J Reddington  R B Wescott  R W Leid 《Veterinary parasitology》1985,17(2):123-129

Fasciola hepatica metacercariae were purified in high yield, removing contaminating cyst walls and plant material by step gradients consisting of 10 ml of 60% Percoll (density = 1.08 g ml-1) and 10 ml of 50% Metrizamide (density = 1.25 g ml-1). Greater than 90% of the metacercariae applied to the density gradients were recovered. These isolated metacercariae had an in vitro excystment rate of greater than 80%, which was the same excystment rate as metacercariae not subjected to density gradient centrifugation.  相似文献   

Use of a substrate/alliinase combination to generate antifungal activity in situ   总被引：5，自引：0，他引：5  

Fry FH  Okarter N  Baynton-Smith C  Kershaw MJ  Talbot NJ  Jacob C 《Journal of agricultural and food chemistry》2005,53(3):574-580

Allicin, an active ingredient of garlic, possesses a range of antimicrobial properties. Unfortunately, certain properties of the compound, such as chemical instability and low miscibility with water, have hampered its practical use in the past. Here, we show that it is possible to use a binary system consisting of the plant enzyme alliinase and its substrate alliin to generate allicin, and hence antifungal activity, in situ. During application, the two inactive components generate compounds that inhibit growth and infection-related development of the rice blast fungus Magnaporthe grisea. It is therefore possible to "trigger" biological activity in a controlled, yet effective manner. Apart from circumventing many of the drawbacks of allicin, this binary system has additional important advantages, such as low toxicity of its individual components and selective activation. Importantly, alliinase is also able to use different substrates, therefore paving the way to a range of novel, binary antimicrobial systems with custom-made chemical and biochemical properties.  相似文献   

Isolation of a cDNA from the virus responsible for enterically transmitted non-A, non-B hepatitis   总被引：59，自引：0，他引：59  

G R Reyes  M A Purdy  J P Kim  K C Luk  L M Young  K E Fry  D W Bradley 《Science (New York, N.Y.)》1990,247(4948):1335-1339

Major epidemic outbreaks of viral hepatitis in underdeveloped countries result from a type of non-A, non-B hepatitis distinct from the parenterally transmitted form. The viral agent responsible for this form of epidemic, or enterically transmitted non-A, non-B hepatitis (ET-NANBH), has been serially transmitted in cynomolgus macaques (cynos) and has resulted in typical elevation in liver enzymes and the detection of characteristic virus-like particles (VLPs) in both feces and bile. Infectious bile was used for the construction of recombinant complementary DNA libraries. One clone, ET1.1, was exogenous to uninfected human and cyno genomic liver DNA, as well as to genomic DNA from infected cyno liver. ET1.1 did however, hybridize to an approximately 7.6-kilobase RNA species present only in infected cyno liver. The translated nucleic acid sequence of a portion of ET1.1 had a consensus amino acid motif consistent with an RNA-directed RNA polymerase; this enzyme is present in all positive strand RNA viruses. Furthermore, ET1.1 specifically identified similar sequences in complementary DNA prepared from infected human fecal samples collected from five geographically distinct ET-NANBH outbreaks. Therefore, ET1.1 represents a portion of the genome of the principal viral agent, to be named hepatitis E virus, which is responsible for epidemic outbreaks of ET-NANBH.  相似文献   

Thymic requirement for clonal deletion during T cell development   总被引：14，自引：0，他引：14  

A M Fry  L A Jones  A M Kruisbeek  L A Matis 《Science (New York, N.Y.)》1989,246(4933):1044-1046

During T cell differentiation, self tolerance is established in part by the deletion of self-reactive T cells within the thymus (negative selection). The presence of T cell receptor (TCR)-alpha beta + T cells in older athymic (nu/nu) mice indicates that some T cells can also mature without thymic influence. Therefore, to determine whether the thymus is required for negative selection, TCR V beta expression was compared in athymic nu/nu mice and their congenic normal littermates. T cells expressing V beta 3 proteins are specific for minor lymphocyte stimulatory (Mlsc) determinants and are deleted intrathymically due to self tolerance in Mlsc+ mouse strains. Here it is shown that V beta 3+ T cells are deleted in Mlsc+ BALB/c nu/+ mice, but not in their BALB/c nu/nu littermates. Thus, the thymus is required for clonal deletion during T cell development.  相似文献   

Calcium carbonate concretions: cyclic occurrence in the hamster vagina     

J J Alleva  F R Alleva  B E Fry  E D Eanes 《Science (New York, N.Y.)》1971,174(9):600-603

Three crystalline forms of calcium carbonate were identified in washings of the hamster vagina. Spherical concretions of vaterite and hexagonal concretions of calcite predominate on days 3 and 4 of the 4-day estrous cycle. Dumbbell-like concretions of aragonite predominate during pregnancy and pseudopregnancy. Each polymorph is associated with an acid-insoluble matrix. Concretions disappear after ovariectomy and reappear during daily injections of estrogen and progesterone.  相似文献