Ecological impacts of Phlebiopsis gigantea biocontrol treatment against Heterobasidion spp. as revealed by fungal community profiling and population analyses

Wood decay fungi belonging to the species complex Heterobasidion annosum sensu lato are among the most common and economically important species causing root rot and stem decay in conifers of the northern temperate regions. New infections by these pathogens can be suppressed by tree stump treatments using chemical or biological control agents. In Finland, the corticiaceous fungus Phlebiopsis gigantea has been formulated into a commercial biocontrol agent called Rotstop (Verdera Ltd.). This thesis addresses the ecological impacts of Rotstop biocontrol treatment on the mycoflora of conifer stumps. Locally, fungal communities within Rotstop-treated and untreated stumps were analyzed using a novel method based on DGGE profiling of small subunit ribosomal DNA fragments amplified directly from wood samples. Population analyses for P. gigantea and H. annosum s.l. were conducted to evaluate possible risks associated with local and/or global distribution of the Rotstop strain. Based on molecular community profiling by DGGE, we detected a few individual wood-inhabiting fungal species (OTUs) that seemed to have suffered or benefited from the Rotstop biocontrol treatment. The DGGE analyses also revealed fungal diversity not retrieved by cultivation and some fungal sequence types untypical for decomposing conifer wood. However, statistical analysis of DGGE community profiles obtained from Rotstop-treated and untreated conifer stumps revealed that the Rotstop treatment had not caused a statistically significant reduction in the species diversity of wood-inhabiting fungi within our experimental forest plots. Locally, ISSR genotyping of cultured P. gigantea strains showed that the Rotstop biocontrol strain was capable of surviving up to six years within treated Norway spruce stumps, while in Scots pine stumps it was sooner replaced by successor fungal species. In addition, the spread of resident P. gigantea strains into Rotstop-treated forest stands seemed effective in preventing the formation of genetically monomorphic populations in the short run. On a global scale, we detected a considerable level of genetic differentiation between the interfertile European and North American populations of P. gigantea. These results strongly suggest that local biocontrol strains should be used in order to prevent global spread of P. gigantea and hybrid formation between geographically isolated populations. The population analysis for H. annosum s.l. revealed a collection of Chinese fungal strains that showed a high degree of laboratory fertility with three different allopatric H. annosum s.l. taxa. However, based on the molecular markers, the Chinese strains could be clearly affiliated with the H. parviporum taxonomical cluster, which thus appears to have a continuous distribution range from Europe through southern Siberia to northern China. Keywords: Rotstop, wood decay, DGGE, ISSR fingerprinting, ribosomal DNA

Why are there so few genetic markers available for coral population analyses?

Coral reefs are in serious decline, and research in support of reef management objectives is urgently needed. Reef connectivity analyses have been highlighted as one of the major future research avenues necessary for implementing effective management initiatives for coral reefs. Despite the number of new molecular genetic tools and the wealth of information that is now available for population-level processes in many marine disciplines, scleractinian coral population genetic information remains surprisingly limited. Here we examine the technical problems and approaches used, address the reasons contributing to this delay in understanding, and discuss the future of coral population marker development. Considerable resources are needed to target the immediate development of an array of relevant genetic markers coupled with the rapid production of management focused data in order to help conserve our globally threatened coral reef resources.

Population differentiation of Procypris rabaudi (Tchang) in the upper reaches of the Yangtze River revealed by mitochondrial DNA and RAPD markers

Procypris rabaudi (Tchang) is a cyprinid fish endermic to middle and upper reaches of the Yangtze River. Besides in main stream and large tributaries, there exists an early matured, small-sized ecological type in a small tributary, Tang River. In this study, mitochondrial DNA cytochrome h (cyt b) gene sequence analysis and randomly amplified polymorphic DNA (RAPD) analysis were performed to investigate the differentiation of the Tang River population from the Mudong reach population of the Yangtze River, with the purpose of conservation and exploitation of this fish. In the 1140 bps of cyt b gene sequence surveyed, 20 sites were found polymorphic, which defined 23 haplotypes. Among them, four haplotypes accounted for 54.4% of all individuals, while population-specific haplotypes occurred in low frequencies. Analysis of molecular variation on cyt b data revealed no significant partition existing between Tang River population and Mudong reach population. Analyses of 132 RAPD loci suggested that genetic variation between populations was significant, though values of different F-ST were not very high. The results revealed low genetic diversity and the beginning of population differentiation, suggesting that Tang River population should be designated as a separate Management Unit.

Population genetic structure of the Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis): Implications for management and conservation

Understanding the population genetic structure is a prerequisite for conservation of a species. The degree of genetic variability characteristic of the mitochondrial DNA control region has been widely exploited in studies of population genetic structure and can be useful in identifying meaningful population subdivisions. To estimate the genetic profile of the Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis), an endangered freshwater population endemic to China, the complete mtDNA control region was examined in 39 individuals belonging to seven different stocks inhabiting the middle and lower reaches of the Yangtze River. Very low genetic diversity was found (nucleotide diversity 0.0011 +/- 0.0002 and haplotypic diversity 0.65 +/- 0.05). The mtDNA genetic pattern of the Yangtze population appears to indicate a founder event in its evolutionary history and to support the marine origin for this population. Analyses by F-st and Phi(st) yielded statistically significant population genetic structure (F-st = 0.44, P < 0.05; phi(st) = 0.36, P < 0.05). These results may have significant implications for the management and conservation of the Yangtze finless porpoise in the future.

The GHEP-EMPOP collaboration on mtDNA population data-A new resource for forensic casework

Mitochondrial DNA (mtDNA) population data for forensic purposes are still scarce for some populations, which may limit the evaluation of forensic evidence especially when the rarity of a haplotype needs to be determined in a database search. In order to improve the collection of mtDNA lineages from the Iberian and South American subcontinents, we here report the results of a collaborative study involving nine laboratories from the Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) and EMPOP. The individual laboratories contributed population data that were generated throughout the past 10 years, but in the majority of cases have not been made available to the scientific community. A total of 1019 haplotypes from Iberia (Basque Country, 2 general Spanish populations, 2 North and 1 Central Portugal populations), and Latin America (3 populations from São Paulo) were collected, reviewed and harmonized according to defined EMPOP criteria. The majority of data ambiguities that were found during the reviewing process (41 in total) were transcription errors confirming that the documentation process is still the most error-prone stage in reporting mtDNA population data, especially when performed manually. This GHEP-EMPOP collaboration has significantly improved the quality of the individual mtDNA datasets and adds mtDNA population data as valuable resource to the EMPOP database (www.empop.org). (C) 2010 Elsevier B.V. All rights reserved.

Population analysis of Scomberomorus cavalla (Cuvier, 1829) (Perciformes, Scombridae) from the Northern and Northeastern coast of Brazil

Scomberomorus cavalla é uma espécie de peixe pelágico amplamente distribuído na costa oeste do Atlântico, e uma diminuição no seu nível de captura tem sido verificada nos E.U.A e Golfo do México, comparada com os níveis alcançados pela espécie no passado. Da mesma forma, em algumas áreas do Brasil, há indícios de sobre-exploração. Entretanto, não existem estudos moleculares que visam o manejo deste importante item. Desta forma, no presente estudo, foram seqüenciados 380 pares de bases nucleotídicas da região da Alça-D do DNA mitocondrial de amostras provenientes de desembarque em Macapá, Bragança e Fortaleza. As análises filogenéticas e populacionais revelaram que há apenas uma população panmítica e baixos níveis de variabilidade genética foram observados. Estes resultados, assim como a observada sobre-exploração de S. cavala, representam dados muito importantes para o estabelecimento do manejo deste estoque a fim de prevenir um colapso ou risco de extinção no futuro.

A pain assessment scale for population-based studies: Development and validation of the Pain Module of the Standard Evaluation Questionnaire

The objectives of this study were to develop and validate a tool for assessing pain in population-based observational studies and to develop three subscales for back/neck, upper extremity and lower extremity pain. Based on a literature review, items were extracted from validated questionnaires and reviewed by an expert panel. The initial questionnaire consisted of a pain manikin and 34 items relating to (i) intensity of pain in different body regions (7 items), (ii) pain during activities of daily living (18 items) and (iii) various pain modalities (9 items). Psychometric validation of the initial questionnaire was performed in a random sample of the German-speaking Swiss population. Analyses included tests for reliability, correlation analysis, principal components factor analysis, tests for internal consistency and validity. Overall, 16,634 of 23,763 eligible individuals participated (70%). Test-retest reliability coefficients ranged from 0.32 to 0.97, but only three coefficients were below 0.60. Subscales were constructed combining four items for each of the subscales. Item-total coefficients ranged from 0.76 to 0.86 and Cronbach's alpha were 0.75 or higher for all subscales. Correlation coefficients between subscales and three validated instruments (WOMAC, SPADI and Oswestry) ranged from 0.62 to 0.79. The final Pain Standard Evaluation Questionnaire (SEQ Pain) included 28 items and the pain manikin and accounted for the multidimensionality of pain by assessing pain location and intensity, pain during activity, triggers and time of onset of pain and frequency of pain medication. It was found to be reliable and valid for the assessment of pain in population-based observational studies.

Simple rules to contain an invasive species with a complex life cycle and high dispersal capacity

Designing practical rules for controlling invasive species is a challenging task for managers, particularly when species are long-lived, have complex life cycles and high dispersal capacities. Previous findings derived from plant matrix population analyses suggest that effective control of long-lived invaders may be achieved by focusing on killing adult plants. However, the cost-effectiveness of managing different life stages has not been evaluated. We illustrate the benefits of integrating matrix population models with decision theory to undertake this evaluation, using empirical data from the largest infestation of mesquite (Leguminosae: Prosopis spp) within Australia. We include in our model the mesquite life cycle, different dispersal rates and control actions that target individuals at different life stages with varying costs, depending on the intensity of control effort. We then use stochastic dynamic programming to derive cost-effective control strategies that minimize the cost of controlling the core infestation locally below a density threshold and the future cost of control arising from infestation of adjacent areas via seed dispersal. Through sensitivity analysis, we show that four robust management rules guide the allocation of resources between mesquite life stages for this infestation: (i) When there is no seed dispersal, no action is required until density of adults exceeds the control threshold and then only control of adults is needed; (ii) when there is seed dispersal, control strategy is dependent on knowledge of the density of adults and large juveniles (LJ) and broad categories of dispersal rates only; (iii) if density of adults is higher than density of LJ, controlling adults is most cost-effective; (iv) alternatively, if density of LJ is equal or higher than density of adults, management efforts should be spread between adults, large and to a lesser extent small juveniles, but never saplings. Synthesis and applications.In this study, we show that simple rules can be found for managing invasive plants with complex life cycles and high dispersal rates when population models are combined with decision theory. In the case of our mesquite population, focussing effort on controlling adults is not always the most cost-effective way to meet our management objective.

Assessment of Atlantic Red Drum for 1999: Northern and southern regions

An assessment of the status of the Atlantic stock of red drum is conducted using recreational and commercial data from 1986 through 1998. This assessment updates data and analyses from the 1989, 1991, 1992 and 1995 stock assessments on Atlantic coast red drum (Vaughan and Helser, 1990; Vaughan 1992; 1993; 1996). Since 1981, coastwide recreational catches ranged between 762,300 pounds in 1980 and 2,623,900 pounds in 1984, while commercial landings ranged between 60,900 pounds in 1997 and 422,500 pounds in 1984. In weight of fish caught, Atlantic red drum constitute predominantly a recreational fishery (ranging between 85 and 95% during the 1990s). Commercially, red drum continue to be harvested as part of mixed species fisheries. Using available length-frequency distributions and age-length keys, recreational and commercial catches are converted to catch in numbers at age. Separable and tuned virtual population analyses are conducted on the catch in numbers at age to obtain estimates of fishing mortality rates and population size (including recruitment to age 1). In tum, these estimates of fishing mortality rates combined with estimates of growth (length and weight), sex ratios, sexual maturity and fecundity are used to estimate yield per recruit, escapement to age 4, and static (or equilibrium) spawning potential ratio (static SPR, based on both female biomass and egg production). Three virtual analysis approaches (separable, spreadsheet, and FADAPT) were applied to catch matrices for two time periods (early: 1986-1991, and late: 1992-1998) and two regions (Northern: North Carolina and north, and Southern: South Carolina through east coast of Florida). Additional catch matrices were developed based on different treatments for the catch-and-release recreationally-caught red drum (B2-type). These approaches included assuming 0% mortality (BASEO) versus 10% mortality for B2 fish. For the 10% mortality on B2 fish, sizes were assumed the same as caught fish (BASEl), or positive difference in size distribution between the early period and the later period (DELTA), or intermediate (PROP). Hence, a total of 8 catch matrices were developed (2 regions, and 4 B2 assumptions for 1986-1998) to which the three VPA approaches were applied. The question of when offshore emigration or reduced availability begins (during or after age 3) continues to be a source of bias that tends to result in overestimates of fishing mortality. Additionally, the continued assumption (Vaughan and Helser, 1990; Vaughan 1992; 1993; 1996) of no fishing mortality on adults (ages 6 and older), causes a bias that results in underestimates of fishing mortality for adult ages (0 versus some positive value). Because of emigration and the effect of the slot limit for the later period, a range in relative exploitations of age 3 to age 2 red drum was considered. Tuning indices were developed from the MRFSS, and state indices for use in the spreadsheet and FADAPT VPAs. The SAFMC Red Drum Assessment Group (Appendix A) favored the FADAPT approach with catch matrix based on DELTA and a selectivity for age 3 relative to age 2 of 0.70 for the northern region and 0.87 for the southern region. In the northern region, estimates of static SPR increased from about 1.3% for the period 1987-1991 to approximately 18% (15% and 20%) for the period 1992-1998. For the southern region, estimates of static SPR increased from about 0.5% for the period 1988-1991 to approximately 15% for the period 1992-1998. Population models used in this assessment (specifically yield per recruit and static spawning potential ratio) are based on equilibrium assumptions: because no direct estimates are available as to the current status of the adult stock, model results imply potential longer term, equilibrium effects. Because current status of the adult stock is unknown, a specific rebuilding schedule cannot be determined. However, the duration of a rebuilding schedule should reflect, in part, a measure of the generation time of the fish species under consideration. For a long-lived, but relatively early spawning, species as red drum, mean generation time would be on the order of 15 to 20 years based on age-specific egg production. Maximum age is 50 to 60 years for the northern region, and about 40 years for the southern region. The ASMFC Red Drum Board's first phase recovery goal of increasing %SPR to at least 10% appears to have been met. (PDF contains 79 pages)

Early postnatal growth of the spotted dolphin, Stenella attenuata, in the offshore Eastern Tropical Pacific.

Estimates of length at birth and early postnatal growth are made for the northern and southern populations of the offshore spotted dolphin in the offshore eastern tropical Pacific. Length at birth is estimated to be 85.4 cm for the northern population and 83.2 cm for the southern population. Analyses of series of monthly distributions of length revealed two cohorts born each year in the northern population, at least in the northern inshore part of its geographic range, but only one cohort born each year in the southern population. Growth curves fitted to the means of the monthly distributions of length gave estimates of length at 1 year of 126.2 and 132.6 cm and length at 2 years of 154.3 and 154.9 cm for the two cohorts in the northern population. and length at 1 year of 127.9 cm for the southern population. A growth curve fitted to lengths and ages (in dental growth layer groups) from the northern population gave estimates of lengths at 1 and 2 years of 123.0 and 143.0 cm, respectively.

The perceived impact of the National Health Service on personalised nutrition service delivery among the UK public

Personalised nutrition (PN) has the potential to reduce disease risk and optimise health and performance. Although previous research has shown good acceptance of the concept of PN in the UK, preferences regarding the delivery of a PN service (e.g. online v. face-to-face) are not fully understood. It is anticipated that the presence of a free at point of delivery healthcare system, the National Health Service (NHS), in the UK may have an impact on end-user preferences for deliverances. To determine this, supplementary analysis of qualitative data obtained from focus group discussions on PN service delivery, collected as part of the Food4Me project in the UK and Ireland, was undertaken. Irish data provided comparative analysis of a healthcare system that is not provided free of charge at the point of delivery to the entire population. Analyses were conducted using the 'framework approach' described by Rabiee (Focus-group interview and data analysis. Proc Nutr Soc 63, 655-660). There was a preference for services to be led by the government and delivered face-to-face, which was perceived to increase trust and transparency, and add value. Both countries associated paying for nutritional advice with increased commitment and motivation to follow guidelines. Contrary to Ireland, however, and despite the perceived benefit of paying, UK discussants still expected PN services to be delivered free of charge by the NHS. Consideration of this unique challenge of free healthcare that is embedded in the NHS culture will be crucial when introducing PN to the UK.

Electronic Structure of the Ground and Low-Lying Electronic States of MoB and MoB(+)

Multiconfigurational second-order perturbation theory (CASSCF//CASPT2) and quadruple-zeta ANO-RCC basis sets were employed to investigate the ground and low-lying electronic states of MoB and MoB(+). Spectroscopic constants, potential energy curves, wavefunctions, Mulliken population analyses, and ionization energies are given. The ground state of MoB is of X(6)Pi symmetry (R(e) = 1.968 angstrom, omega(e) = 664 cm(-1), and mu = 2.7 D), giving rise to a Omega = 7/2 ground state after including spin-orbit coupling. For MoB(+), the ground state is computed to be of X(7)Sigma(+) symmetry (R(e) = 2.224 angstrom, omega(e) = 141 cm(-1), and mu = 1.2 D), with an adiabatic ionization energy of 7.19 eV and a vertical one of 7.53 eV. (C) 2011 Wiley Periodicals, Inc. Int J Quantum Chem 111: 3362-3370, 2011

Isolation and characterization of ten novel microsatellite loci in the red-winged tinamou (Rhynchotus rufescens, Tinamiformes, Aves) and cross-amplification in other tinamous

We describe the isolation and characterization of ten microsatellite loci from the red-winged tinamou (Rhynchotus rufescens) and also evaluated the cross-amplification of these loci and other ten loci previously developed for the great tinamou (Tinamus major) in other tinamous. Genetic variability was assessed using 24 individuals. Six loci were polymorphic with moderate to high number of alleles per locus (2-12 alleles) and showed expected heterozygosity (HE) ranging from 0.267 to 0.860. All loci conformed to the Hardy-Weinberg expectation and linkage disequilibrium was not significant for any pair of loci. This battery of polymorphic loci showed high paternity exclusion probability (0.986) and low genetic identity probability (4.95 x 10(-5)), proving to be helpful for parentage tests and population analyses in the red-winged tinamou. The cross-amplification was moderate where of the 160 locus/taxon combinations, 46 (28.75%) successfully amplified.

Identification and characterization of polymorphic microsatellite loci in the blue shark Prionace glauca, and cross-amplification in other shark species

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

The evolutionary dynamics of the Helena retrotransposon revealed by sequenced Drosophila genomes

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