Development of type I genetic markers from expressed sequence tags in highly polymorphic species

Expressed sequence tag (EST) databases provide a primary source of nuclear DNA sequences for genetic marker development in non-model organisms. To date, the process has been relatively inefficient for several reasons: - 1) priming site polymorphism in the template leads to inferior or erratic amplification; - 2) introns in the target amplicon are too large and/or numerous to allow effective amplification under standard screening conditions, and; - 3) at least occasionally, a PCR primer straddles an exon–intron junction and is unable to bind to genomic DNA template. The first is only a minor issue for species or strains with low heterozygosity but becomes a significant problem for species with high genomic variation, such as marine organisms with extremely large effective population sizes. Problems arising from unanticipated introns are unavoidable but are most pronounced in intron-rich species, such as vertebrates and lophotrochozoans. We present an approach to marker development in the Pacific oyster Crassostrea gigas, a highly polymorphic and intron-rich species, which minimizes these problems, and should be applicable to other non-model species for which EST databases are available. Placement of PCR primers in the 3′ end of coding sequence and 3′ UTR improved PCR success rate from 51% to 97%. Almost all (37 of 39) markers developed for the Pacific oyster were polymorphic in a small test panel of wild and domesticated oysters.

The study of genetic diversity and population structure of the Korean fleshy shrimp, Fenneropenaeus chinensis, using newly developed microsatellite markers

The fleshy shrimp, Fenneropenaeus chinensis, is the family of Penaeidae and one of the most economically important marine culture species in Korea. However, its genetic characteristics have never been studied. In this study, a total of 240 wild F. chinensis individuals were collected from four locations as follows: Narodo (NRD, n = 60), Beopseongpo (BSP, n = 60), Chaesukpo (CSP, n = 60), and Cheonsuman (CSM, n = 60). Genetic variability and the relationships among four wild F. chinensis populations were analyzed using 13 newly developed microsatellite loci. Relatively high levels of genetic variability (mean allelic richness = 16.87; mean heterozygosity = 0.845) were found among localities. Among the 52 population loci, 13 showed significant deviation from the Hardy–Weinberg equilibrium. Neighbor-joining, principal coordinate, and molecular variance analyses revealed the presence of three subpopulations (NRD, CSM, BSP and CSP), which was consistent with clustering based on genetic distance. The mean observed heterozygosity values of the NRD, CSM, BSP, and CSP populations were 0.724, 0.821, 0.814, and 0.785 over all loci, respectively. These genetic variability and differentiation results of the four wild populations can be applied for future genetic improvement using selective breeding and to design suitable management guidelines for Korean F. chinensis culture.

A transcriptomic analysis of the kidney tissue of Tra catfish (pangasianodon hypophthalmus) reared in saline condition: De novo assembly, annotation, SNP discovery

Pangasianodon hypophthalmus is a commercially important freshwater fish used in inland aquaculture in the Mekong Delta, Vietnam. The current study using Ion Torrent technology generated EST resources from the kidney for Tra catfish reared at a salinity level of 9 ppt. We obtained 2,623,929 reads after trimming and processing with an average length of 104 bp. De novo assemblies were generated using CLC Genomic Workbench, Trinity and Velvet/Oases with the best overall contig performance resulting from the CLC assembly. De novo assembly using CLC yielded 29,940 contigs, and allowing identification of 5,710 putative genes when comppared with NCBI non-redundant database. A large number of single nucleotide polymorphisms (SNPs) were also detected. The sequence collection generated in our study represents the most comprehensive transcriptomic resource for P. hypophthalmus available to date.

Hazard Function Models to Estimate Mortality Rates Affecting Fish Populations with Application to the Sea Mullet (Mugil cephalus) Fishery on the Queensland Coast (Australia)

Fisheries management agencies around the world collect age data for the purpose of assessing the status of natural resources in their jurisdiction. Estimates of mortality rates represent a key information to assess the sustainability of fish stocks exploitation. Contrary to medical research or manufacturing where survival analysis is routinely applied to estimate failure rates, survival analysis has seldom been applied in fisheries stock assessment despite similar purposes between these fields of applied statistics. In this paper, we developed hazard functions to model the dynamic of an exploited fish population. These functions were used to estimate all parameters necessary for stock assessment (including natural and fishing mortality rates as well as gear selectivity) by maximum likelihood using age data from a sample of catch. This novel application of survival analysis to fisheries stock assessment was tested by Monte Carlo simulations to assert that it provided unbiased estimations of relevant quantities. The method was applied to the data from the Queensland (Australia) sea mullet (Mugil cephalus) commercial fishery collected between 2007 and 2014. It provided, for the first time, an estimate of natural mortality affecting this stock: 0.22±0.08 year −1 .

On the Rademacher maximal function

Tools known as maximal functions are frequently used in harmonic analysis when studying local behaviour of functions. Typically they measure the suprema of local averages of non-negative functions. It is essential that the size (more precisely, the L^p-norm) of the maximal function is comparable to the size of the original function. When dealing with families of operators between Banach spaces we are often forced to replace the uniform bound with the larger R-bound. Hence such a replacement is also needed in the maximal function for functions taking values in spaces of operators. More specifically, the suprema of norms of local averages (i.e. their uniform bound in the operator norm) has to be replaced by their R-bound. This procedure gives us the Rademacher maximal function, which was introduced by Hytönen, McIntosh and Portal in order to prove a certain vector-valued Carleson's embedding theorem. They noticed that the sizes of an operator-valued function and its Rademacher maximal function are comparable for many common range spaces, but not for all. Certain requirements on the type and cotype of the spaces involved are necessary for this comparability, henceforth referred to as the “RMF-property”. It was shown, that other objects and parameters appearing in the definition, such as the domain of functions and the exponent p of the norm, make no difference to this. After a short introduction to randomized norms and geometry in Banach spaces we study the Rademacher maximal function on Euclidean spaces. The requirements on the type and cotype are considered, providing examples of spaces without RMF. L^p-spaces are shown to have RMF not only for p greater or equal to 2 (when it is trivial) but also for 1 < p < 2. A dyadic version of Carleson's embedding theorem is proven for scalar- and operator-valued functions. As the analysis with dyadic cubes can be generalized to filtrations on sigma-finite measure spaces, we consider the Rademacher maximal function in this case as well. It turns out that the RMF-property is independent of the filtration and the underlying measure space and that it is enough to consider very simple ones known as Haar filtrations. Scalar- and operator-valued analogues of Carleson's embedding theorem are also provided. With the RMF-property proven independent of the underlying measure space, we can use probabilistic notions and formulate it for martingales. Following a similar result for UMD-spaces, a weak type inequality is shown to be (necessary and) sufficient for the RMF-property. The RMF-property is also studied using concave functions giving yet another proof of its independence from various parameters.

A randomized controlled trial protocol testing a decision support intervention for older patients with advanced kidney disease

Aim To assess the effectiveness of a decision support intervention using a pragmatic single blind Randomized Controlled Trial. Background Worldwide the proportion of older people (aged 65 years and over) is rising. This population is known to have a higher prevalence of chronic diseases including chronic kidney disease. The resultant effect of the changing health landscape is seen in the increase in older patients (aged ≥65 years) commencing on dialysis. Emerging evidence suggests that for some older patients dialysis may provide minimal benefit. In a majority of renal units non-dialysis management is offered as an alternative to undertaking dialysis. Research regarding decision-making support that is required to assist this population in choosing between dialysis or non-dialysis management is limited. Design. A multisite single blinded pragmatic randomized controlled trial is proposed. Methods Patients will be recruited from four Queensland public hospitals and randomizd into either the control or intervention group. The decision support intervention is multimodal and includes counselling provided by a trained nurse. The comparator is standard decision-making support. The primary outcomes are decisional regret and decisional conflict. Secondary outcomes are improved knowledge and quality of life. Ethics approval obtained November 2014. Conclusion This is one of the first randomized controlled trials assessing a decision support intervention in older people with advance chronic kidney disease. The results may provide guidance for clinicians in future approaches to assist this population in decision-making to ensure reduced decisional regret and decisional conflict.

Cognitive function in schizophrenia: Conflicting findings and future directions

Introduction Schizophrenia is a severe mental disorder with multiple psychopathological domains being affected. Several lines of evidence indicate that cognitive impairment serves as the key component of schizophrenia psychopathology. Although there have been a multitude of cognitive studies in schizophrenia, there are many conflicting results. We reasoned that this could be due to individual differences among the patients (i.e. variation in the severity of positive vs. negative symptoms), different task designs, and/or the administration of different antipsychotics. Methods We thus review existing data concentrating on these dimensions, specifically in relation to dopamine function. We focus on most commonly used cognitive domains: learning, working memory, and attention. Results We found that the type of cognitive domain under investigation, medication state and type, and severity of positive and negative symptoms can explain the conflicting results in the literature. Conclusions This review points to future studies investigating individual differences among schizophrenia patients in order to reveal the exact relationship between cognitive function, clinical features, and antipsychotic treatment.

Excel’s Sumif and Sumifs function

As accountants, we are all familiar with the SUM function, which calculates the sum in a range of numbers. However, there are instances where we might want to sum numbers in a given range based on a specified criteria. In this instance the SUM IF function can achieve this objective.