A Genetic Analysis of Lysosomal Enzyme Activities in Brahman Cattle

Analyses of variance and co variance were carried out on the activities of three lysosomal enzymes in mononuclear blood cells from Brahman cattle. These were hexosaminidase (HEX), beta-D-galacto-sidase (GAL) and acid alpha-glucosidase (GLU) which had been measured in blood mononuclear cells from 1752 cattle from 6 herds in a Pompe's disease control programme. Herd of origin and date of bleeding significantly affected the level of activity of all enzymes. In addition, HEX and GAL were affected by age and HEX by the sex of the animal bled. Estimates of heritability from sire variances were 0.29:t 0.09 for HEX, 0.31 :t 0.09 for GAL and 0.44:t 0.09 for GLU. Genetic correlations between all enzymes were positive. The data indicate the existence of a major gene causing Pompe's disease and responsible for 16% of the genetic variation in GLU. One standard deviation of selection differential for high GLU should almost eliminate Pompe's disease from the population. The effi-ciency of selection would be aided by estimating the breeding value for GLU using measurements of HEX and GLU and taking account of an animal's sex, age, date of bleeding and herd of origin.

Natural convection from a vertical cone in a porous medium due to the combined effects of heat and mass diffusion with non-uniform wall temperature/concentration or heat/mass flux and suction/injection

An analysis has been carried out to study the non-Darcy natural convention flow of Newtonian fluids on a vertical cone embedded in a saturated porous medium with power-law variation of the wall temperature/concentration or heat/mass flux and suction/injection with the streamwise distance x. Both non-similar and self-similar solutions have been obtained. The effects of non-Darcy parameter, ratio of the buoyancy forces due to mass and heat diffusion, variation of wall temperature/concentration or heat/mass flux and suction/injection on the Nusselt and Sherwood numbers have been studied.

Genetic association analysis of miRNA SNPs implicates MIR145 in breast cancer susceptibility

Background MicroRNAs (miRNAs) are important small non-coding RNA molecules that regulate gene expression in cellular processes related to the pathogenesis of cancer. Genetic variation in miRNA genes could impact their synthesis and cellular effects and single nucleotide polymorphisms (SNPs) are one example of genetic variants studied in relation to breast cancer. Studies aimed at identifying miRNA SNPs (miR-SNPs) associated with breast malignancies could lead towards further understanding of the disease and to develop clinical applications for early diagnosis and treatment. Methods We genotyped a panel of 24 miR-SNPs using multiplex PCR and chip-based matrix assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) analysis in two Caucasian breast cancer case control populations (Primary population: 173 cases and 187 controls and secondary population: 679 cases and 301 controls). Association to breast cancer susceptibility was determined using chi-square (X 2 ) and odds ratio (OR) analysis. Results Statistical analysis showed six miR-SNPs to be non-polymorphic and twelve of our selected miR-SNPs to have no association with breast cancer risk. However, we were able to show association between rs353291 (located in MIR145) and the risk of developing breast cancer in two independent case control cohorts (p = 0.041 and p = 0.023). Conclusions Our study is the first to report an association between a miR-SNP in MIR145 and breast cancer risk in individuals of Caucasian background. This finding requires further validation through genotyping of larger cohorts or in individuals of different ethnicities to determine the potential significance of this finding as well as studies aimed to determine functional significance. Keywords: Association analysis; Breast cancer; microRNA; miR-SNPs; MIR145

Stock assessment of the Queensland-New South Wales tailor fishery (Pomatomus saltatrix)

Data on catch sizes, catch rates, length-frequency and age composition from the Australian east coast tailor fishery are analysed by three different population dynamic models: a surplus production model, an age-structured model, and a model in which the population is structured by both age and length. The population is found to be very heavily exploited, with its ability to reproduce dependent on the fishery’s incomplete selectivity of one-year-old fish. Estimates of recent harvest rates (proportion of fish available to the fishery that are actually caught in a single year) are over 80%. It is estimated that only 30–50% of one-year-old fish are available to the fishery. Results from the age-length-structured model indicate that both exploitable biomass (total mass of fish selected by the fishery) and egg production have fallen to about half the levels that prevailed in the 1970s, and about 40% of virgin levels. Two-year-old fish appear to have become smaller over the history of the fishery. This is assumed to be due to increased fishing pressure combined with non-selectivity of small one-year-old fish, whereby the one-year-old fish that survive fishing are small and grow into small two-year-old fish the following year. An alternative hypothesis is that the stock has undergone a genetic change towards smaller fish; the true explanation is unknown. The instantaneous natural mortality rate of tailor is hypothesised to be higher than previously thought, with values between 0.8 and 1.3 yr–1 consistent with the models. These values apply only to tailor up to about three years of age, and it is possible that a lower value applies to fish older than three. The analysis finds no evidence that fishing pressure has yet affected recruitment. If a recruitment downturn were to occur, however, under current management and fishing pressure there is a strong chance that the fishery would need a complete closure for several years to recover, and even then recovery would be uncertain. Therefore it is highly desirable to better protect the spawning stock. The major recommendations are • An increase in the minimum size limit from 30cm to 40cm in order to allow most one-year-old fish to spawn, and • An experiment on discard mortality to gauge the proportion of fish between 30cm and 40cm that are likely to survive being caught and released by recreational line fishers (the dominant component of the fishery, currently harvesting roughly 1000t p.a. versus about 200t p.a. from the commercial fishery).

Aineellista ja aineetonta turvaa : Ruokakunnat, ekologis-taloudelliset resurssit ja kontaktinmuodostus Valkealassa 1630 1750

Material and immaterial security. Households, ecological and economic resources and formation of contacts in Valkeala parish from the 1630s to the 1750s. The geographical area of the thesis, Valkeala parish in the region of Kymenlaakso, is a very interesting area owing to its diversity, both in terms of natural setting and economic and cultural structure. The study begins by outlining the ecological and economic features of Valkeala and by analysing household structures. The main focus of the research lies in the contacts of the households with the outside world. The following types of contacts are chosen as indicators of the interaction: trade and credit relations, guarantees, co-operation, marriages and godparentage. The main theme of the contact analysis is to observe the significance of three factors, namely geographical extent, affluence level and kinship, to the formation of contacts. It is also essential to chart the interdependencies between ecological and economic resources, changes in the structure of households and the formation of contacts during the period studied. The time between the 1630s and the 1750s was characterized by wars, crop losses and population changes, which had an effect on the economic framework and on the structural variation of households and contact fields. In the 17th and 18th centuries Valkeala could be divided, economically, into two sections according to the predominant cultivation technique. The western area formed the field area and the eastern and northern villages the swidden area. Multiple family households were dominant in the latter part of the 17th century, and for most of the study period, the majority of people lived in the more complex households rather than in simple families. Economic resources had only a moderate impact on the structure of contacts. There was a clear connection between bigger household size and the extent and intensity of contacts. The jurisdictional boundary that ran across Valkeala from the northwest to the southeast and divided the parish into two areas influenced the formation of contacts more than the parish boundaries. Support and security were offered largely by the primary contacts with one s immediate family, neighbours and friends. Economic support was channelled from the wealthier to the less well off by credits. Cross-marriages, cross-godparentage and marital networks could be seen as manifestations of an aim towards stability and the joining of resources. It was essential for households both to secure the workforce needed for a minimum level of subsistence and to ensure the continuation of the family line. These goals could best be reached by complex households that could adapt to the prevailing circumstances and also had wider and more multi-layered contacts offering material and immaterial security.

A new data source for fisheries resource assessment: genetic estimates of the effective number of spawners. Final Report to the Fisheries Research and Development Corporation.

The development of innovative methods of stock assessment is a priority for State and Commonwealth fisheries agencies. It is driven by the need to facilitate sustainable exploitation of naturally occurring fisheries resources for the current and future economic, social and environmental well being of Australia. This project was initiated in this context and took advantage of considerable recent achievements in genomics that are shaping our comprehension of the DNA of humans and animals. The basic idea behind this project was that genetic estimates of effective population size, which can be made from empirical measurements of genetic drift, were equivalent to estimates of the successful number of spawners that is an important parameter in process of fisheries stock assessment. The broad objectives of this study were to 1. Critically evaluate a variety of mathematical methods of calculating effective spawner numbers (Ne) by a. conducting comprehensive computer simulations, and by b. analysis of empirical data collected from the Moreton Bay population of tiger prawns (P. esculentus). 2. Lay the groundwork for the application of the technology in the northern prawn fishery (NPF). 3. Produce software for the calculation of Ne, and to make it widely available. The project pulled together a range of mathematical models for estimating current effective population size from diverse sources. Some of them had been recently implemented with the latest statistical methods (eg. Bayesian framework Berthier, Beaumont et al. 2002), while others had lower profiles (eg. Pudovkin, Zaykin et al. 1996; Rousset and Raymond 1995). Computer code and later software with a user-friendly interface (NeEstimator) was produced to implement the methods. This was used as a basis for simulation experiments to evaluate the performance of the methods with an individual-based model of a prawn population. Following the guidelines suggested by computer simulations, the tiger prawn population in Moreton Bay (south-east Queensland) was sampled for genetic analysis with eight microsatellite loci in three successive spring spawning seasons in 2001, 2002 and 2003. As predicted by the simulations, the estimates had non-infinite upper confidence limits, which is a major achievement for the application of the method to a naturally-occurring, short generation, highly fecund invertebrate species. The genetic estimate of the number of successful spawners was around 1000 individuals in two consecutive years. This contrasts with about 500,000 prawns participating in spawning. It is not possible to distinguish successful from non-successful spawners so we suggest a high level of protection for the entire spawning population. We interpret the difference in numbers between successful and non-successful spawners as a large variation in the number of offspring per family that survive – a large number of families have no surviving offspring, while a few have a large number. We explored various ways in which Ne can be useful in fisheries management. It can be a surrogate for spawning population size, assuming the ratio between Ne and spawning population size has been previously calculated for that species. Alternatively, it can be a surrogate for recruitment, again assuming that the ratio between Ne and recruitment has been previously determined. The number of species that can be analysed in this way, however, is likely to be small because of species-specific life history requirements that need to be satisfied for accuracy. The most universal approach would be to integrate Ne with spawning stock-recruitment models, so that these models are more accurate when applied to fisheries populations. A pathway to achieve this was established in this project, which we predict will significantly improve fisheries sustainability in the future. Regardless of the success of integrating Ne into spawning stock-recruitment models, Ne could be used as a fisheries monitoring tool. Declines in spawning stock size or increases in natural or harvest mortality would be reflected by a decline in Ne. This would be good for data-poor fisheries and provides fishery independent information, however, we suggest a species-by-species approach. Some species may be too numerous or experiencing too much migration for the method to work. During the project two important theoretical studies of the simultaneous estimation of effective population size and migration were published (Vitalis and Couvet 2001b; Wang and Whitlock 2003). These methods, combined with collection of preliminary genetic data from the tiger prawn population in southern Gulf of Carpentaria population and a computer simulation study that evaluated the effect of differing reproductive strategies on genetic estimates, suggest that this technology could make an important contribution to the stock assessment process in the northern prawn fishery (NPF). Advances in the genomics world are rapid and already a cheaper, more reliable substitute for microsatellite loci in this technology is available. Digital data from single nucleotide polymorphisms (SNPs) are likely to super cede ‘analogue’ microsatellite data, making it cheaper and easier to apply the method to species with large population sizes.

Impact of mirid (Creontiades spp.) (Hemiptera: Miridae) pest management on Helicoverpa spp. (Lepidoptera: Noctuidae) outbreaks: The case for conserving natural enemies

Creontiades spp. (Hemiptera: Miridae) are sucking pests that attack buds, flowers and young pods in mungbeans, Vigna radiata (L.), causing these structures subsequently to abort. If left uncontrolled, mirids can cause 25-50% yield loss. Traditional industry practice has involved prophylactic applications of dimethoate to control mirids at budding and again a week later. The present trial was initiated to highlight the dangers of such a practice, in particular the risk of a subsequent Helicoverpa spp. lepidopteran pest outbreak. A single application of dimethoate halved the population of important natural enemies of Helicoverpa spp., and caused an above-threshold outbreak of Helicoverpa spp. within 11 days. This shows that even a moderate (e.g. 50%) reduction in natural enemies may be sufficient to increase Helicoverpa spp. populations in mungbeans. As a result, prophylactic sprays should not be used for the control of mirids in mungbeans, and dimethoate should be applied only when mirids are above the economic threshold. Indoxacarb was also tested to establish its effect on Helicoverpa spp., mirids and natural enemies. Indoxacarb showed potential for Helicoverpa spp. control and suppression of mirids and had little impact on natural enemies.

QTL analysis of ergot resistance in sorghum

Sorghum ergot, caused predominantly by Claviceps africana Frederickson, Mantle, de Milliano, is a significant threat to the sorghum industry worldwide. The objectives of this study were firstly, to identify molecular markers linked to ergot resistance and to two pollen traits, pollen quantity (PQ) and pollen viability (PV), and secondly, to assess the relationship between the two pollen traits and ergot resistance in sorghum. A genetic linkage map of sorghum RIL population R931945-2-2 x IS 8525 (resistance source) was constructed using 303 markers including 36 SSR, 117 AFLP™, 148 DArT™ and two morphological trait loci. Composite interval mapping identified nine, five, and four QTL linked to molecular markers for percentage ergot infection (PCERGOT), PQ and PV, respectively, at a LOD >2.0. Co-location/linkage of QTL were identified on four chromosomes while other QTL for the three traits mapped independently, indicating that both pollen and non pollen-based mechanisms of ergot resistance were operating in this sorghum population. Of the nine QTL identified for PCERGOT, five were identified using the overall data set while four were specific to the group data sets defined by temperature and humidity. QTL identified on SBI-02 and SBI-06 were further validated in additional populations. This is the first report of QTL associated with ergot resistance in sorghum. The markers reported herein could be used for marker-assisted selection for this important disease of sorghum.

Natural Frequencies And Transient Responses Of 3-Phase Rotating Machine Windings

The analysis of transient electrical stresses in the insulation of high voltage rotating machines is rendered difficult because of the existence of capacitive and inductive couplings between phases. The Published theories ignore many of the couplings between phases to obtain the solution. A new procedure is proposed here to determine the transient voltage distribution on rotating machine windings. All the significicant capacitive and inductive couplings between different sections in a phase and between different sections in different phases have been considered in this analysis. The experimental results show good correlation with those computed.

Effects of methyl eugenol feeding on mating compatibility of Asian population of Bactrocera dorsalis (Diptera: Tephritidae) with African population and with B. carambolae

Males of some species included in the Bactrocera dorsalis complex are strongly attracted to methyl eugenol (ME) (1,2-dimethoxy-4-(2-propenyl) benzene), a natural compound occurring in a variety of plant species. ME feeding of males of the B. dorsalis complex is known to enhance their mating competitiveness. Within B. dorsalis, recent studies show that Asian and African populations of B. dorsalis are sexually compatible, while populations of B. dorsalis and Bactrocera carambolae are relatively incompatible. The objectives of this study were to examine whether ME feeding by males affects mating compatibility between Asian and African populations of B. dorsalis and ME feeding reduces male mating incompatibility between B. dorsalis (Asian population) and B. carambolae. The data confirmed that Asian and African populations of B. dorsalis are sexually compatible for mating and showed that ME feeding only increased the number of matings. Though ME feeding also increased the number of matings of B. dorsalis (Asian population) and B. carambolae males but the sexual incompatibility between both species was not reduced by treatment with ME. These results conform to the efforts resolving the biological species limits among B. dorsalis complex and have implications for fruit fly control programs in fields and horticultural trade.

Analysis of high yielding maize production - A study based on a commercial crop

This paper reports on the use of APSIM - Maize for retrospective analysis of performance of a high input, high yielding maize crop and analysis of predicted performance of maize grown with high inputs over the long-term (>100 years) for specified scenarios of environmental conditions (temperature and radiation) and agronomic inputs (sowing date, plant population, nitrogen fertiliser and irrigation) at Boort, Victoria, Australia. It uses a high yielding (17 400 kg/ha dry grain, 20 500 kg/ha at 15% water) commercial crop grown in 2004-05 as the basis of the study. Yield for the agronomic and environmental conditions of 2004-05 was predicted accurately, giving confidence that the model could be used for the detailed analyses undertaken. The analysis showed that the yield achieved was close to that possible with the conditions and agronomic inputs of 2004-05. Sowing dates during 21 September to 26 October had little effect on predicted yield, except when combined with reduced temperature. Single year and long-term analyses concluded that a higher plant population (11 plants/m2) is needed to optimise yield, but that slightly lower N and irrigation inputs are appropriate for the plant population used commercially (8.4 plants/m2). Also, compared with changes in agronomic inputs increases in temperature and/or radiation had relatively minor effects, except that reduced temperature reduces predicted yield substantially. This study provides an approach for the use of models for both retrospective analysis of crop performance and assessment of long-term variability of crop yield under a wide range of agronomic and environmental conditions.

Mapping quantitative trait loci for resistance to Pratylenchus thornei from synthetic hexaploid wheat in the International Triticeae Mapping Initiative (ITMI) population

Root-lesion nematode (Pratylenchus thornei) is a serious pathogen of wheat in many countries. The International Triticeae Mapping Initiative (ITMI) population of recombinant inbred lines (RILs) was assessed for resistance to P. thornei to determine the chromosome locations of the resistance genes. The ITMI population is derived from a cross between the resistant synthetic hexaploid wheat W-7984 and a susceptible bread wheat cultivar Opata 85. Two years of phenotypic data for resistance to P. thornei were obtained in replicated glasshouse trials. Quantitative trait locus (QTL) analysis was performed using available segregation and map data for 114 RILs. A QTL on chromosome 6DS showed consistent effects for reduced nematode numbers (partial resistance) across years and accounted for 11% and 23% of the phenotypic variation. A second QTL for P. thornei resistance on chromosome 2BS accounted for an additional 19% and 5%. Restriction fragment length polymorphism (RFLP) and simple sequence repeat (SSR) markers associated with the QTLs are physically located in regions rich in major genes at the distal ends of the short chromosome arms of 6D and 2B. SSR markers with potential for marker-assisted selection of P. thornei resistance effective in different genetic backgrounds have been identified.

Time-dependent instantaneous mortality rates from multiple tagging experiments with exact times of release and recovery

Instantaneous natural mortality rates and a nonparametric hunting mortality function are estimated from a multiple-year tagging experiment with arbitrary, time-dependent fishing or hunting mortality. Our theory allows animals to be tagged over a range of times in each year, and to take time to mix into the population. Animals are recovered by hunting or fishing, and death events from natural causes occur but are not observed. We combine a long-standing approach based on yearly totals, described by Brownie et al. (1985, Statistical Inference from Band Recovery Data: A Handbook, Second edition, United States Fish and Wildlife Service, Washington, Resource Publication, 156), with an exact-time-of-recovery approach originated by Hearn, Sandland and Hampton (1987, Journal du Conseil International pour l'Exploration de la Mer, 43, 107-117), who modeled times at liberty without regard to time of tagging. Our model allows for exact times of release and recovery, incomplete reporting of recoveries, and potential tag shedding. We apply our methods to data on the heavily exploited southern bluefin tuna (Thunnus maccoyii).

Lung cancer risk of airborne particles for Italian population

Airborne particles, including both ultrafine and supermicrometric particles, contain various carcinogens. Exposure and risk-assessment studies regularly use particle mass concentration as dosimetry parameter, therefore neglecting the potential impact of ultrafine particles due to their negligible mass compared to supermicrometric particles. The main purpose of this study was the characterization of lung cancer risk due to exposure to polycyclic aromatic hydrocarbons and some heavy metals associated with particle inhalation by Italian non-smoking people. A risk-assessment scheme, modified from an existing risk model, was applied to estimate the cancer risk contribution from both ultrafine and supermicrometric particles. Exposure assessment was carried out on the basis of particle number distributions measured in 25 smoke-free microenvironments in Italy. The predicted lung cancer risk was then compared to the cancer incidence rate in Italy to assess the number of lung cancer cases attributed to airborne particle inhalation, which represents one of the main causes of lung cancer, apart from smoking. Ultrafine particles are associated with a much higher risk than supermicrometric particles, and the modified risk-assessment scheme provided a more accurate estimate than the conventional scheme. Great attention has to be paid to indoor microenvironments and, in particular, to cooking and eating times, which represent the major contributors to lung cancer incidence in the Italian population. The modified risk assessment scheme can serve as a tool for assessing environmental quality, as well as setting up exposure standards for particulate matter.

Systematic analysis of changes in cannabis use among participants in control conditions of randomised controlled trials

Introduction Cannabis remains the most used illegal substance across the globe, and negative outcomes and disorders are common. A spotlight therefore falls on reductions in cannabis use in people with cannabis use disorder. Current estimates of unassisted cessation or reduction in cannabis use rely on community surveys, and few studies focus on individuals with disorder. A key interest of services and researchers is to estimate effect size of reductions in consumption among treatment seekers who do not obtain treatment. Effects within waiting list or information-only control conditions of randomised controlled trials offer an opportunity to study this question. Method This paper examines the extent of reductions in days of cannabis use in the control groups of randomised controlled trials on treatment of cannabis use disorders. A systematic literature search was performed to identify trials that reported days of cannabis use in the previous 30 (or equivalent). Results Since all but one of the eight identified studies had delayed treatment controls, results could only be summarised across 2–4 months. Average weighted days of use in the previous 30 days fell from 24.5 to 19.9, and a meta-analysis using a random effects model showed an average reduction of 0.442 SD. However, every study had at least one significant methodological issue. Conclusions While further high-quality data is needed to confirm the observed effects, these results provide a baseline from which researchers and practitioners can estimate the extent of change required to detect effects of cannabis treatments in services or treatment trials.