Estimation of heritability from limited family data using genome-wide identity-by-descent sharing

<p>Abstract</p> <p>Background</p> <p>In classical pedigree-based analysis, additive genetic variance is estimated from between-family variation, which requires the existence of larger phenotyped and pedigreed populations involving numerous families (parents). However, estimation is often complicated by confounding of genetic and environmental family effects, with the latter typically occurring among full-sibs. For this reason, genetic variance is often inferred based on covariance among more distant relatives, which reduces the power of the analysis. This simulation study shows that genome-wide identity-by-descent sharing among close relatives can be used to quantify additive genetic variance solely from within-family variation using data on extremely small family samples.</p> <p>Methods</p> <p>Identity-by-descent relationships among full-sibs were simulated assuming a genome size similar to that of humans (effective number of loci ~80). Genetic variance was estimated from phenotypic data assuming that genomic identity-by-descent relationships could be accurately re-created using information from genome-wide markers. The results were compared with standard pedigree-based genetic analysis.</p> <p>Results</p> <p>For a polygenic trait and a given number of phenotypes, the most accurate estimates of genetic variance were based on data from a single large full-sib family only. Compared with classical pedigree-based analysis, the proposed method is more robust to selection among parents and for confounding of environmental and genetic effects. Furthermore, in some cases, satisfactory results can be achieved even with less ideal data structures, i.e., for selectively genotyped data and for traits for which the genetic variance is largely under the control of a few major genes.</p> <p>Conclusions</p> <p>Estimation of genetic variance using genomic identity-by-descent relationships is especially useful for studies aiming at estimating additive genetic variance of highly fecund species, using data from small populations with limited pedigree information and/or few available parents, i.e., parents originating from non-pedigreed or even wild populations.</p

Vibrio parahemolyticus septicaemia in a liver transplant patient: a case report

<p>Abstract</p> <p>Introduction</p> <p><it>Vibrio parahemolyticus </it>is the leading cause of vibrio-associated gastroenteritis in the United States of America, usually related to poor food handling; only rarely has it been reported to cause serious infections including sepsis and soft tissue infections. In contrast, <it>Vibrio vulnificus </it>is a well-known cause of septicaemia, especially in patients with cirrhosis. We present a patient with <it>V. parahemolyticus </it>sepsis who had an orthotic liver transplant in 2007 and was on immunosuppression for chronic rejection. Clinical suspicion driven by patient presentation, travel to Gulf of Mexico and soft tissue infection resulted in early diagnosis and institution of appropriate antibiotic therapy.</p> <p>Case presentation</p> <p>A 48 year old Latin American man with a history of chronic kidney disease, orthotic liver transplant in 2007 secondary to alcoholic end stage liver disease on immunosuppressants, and chronic rejection presented to the emergency department with fever, vomiting, abdominal pain, left lower extremity swelling and fluid filled blisters after a fishing trip in the Gulf of Mexico. Samples from the blister and blood grew <it>V. parahemolyticus</it>. The patient was successfully treated with ceftriaxone and ciprofloxacin.</p> <p>Conclusion</p> <p>Febrile patients with underlying liver disease and/or immunosuppression should be interviewed regarding recent travel to a coastal area and seafood ingestion. If this history is obtained, appropriate empiric antibiotics must be chosen. Patients with liver disease and/or immunosuppresion should be counselled to avoid eating raw or undercooked molluscan shellfish. People can prevent <it>Vibrio </it>sepsis and wound infections by proper cooking of seafood and avoiding exposure of open wounds to seawater or raw shellfish products.</p

Effect of Biodiversity Changes in Disease Risk: Exploring Disease Emergence in a Plant-Virus System

The effect of biodiversity on the ability of parasites to infect their host and cause disease (i.e. disease risk) is a major question in pathology, which is central to understand the emergence of infectious diseases, and to develop strategies for their management. Two hypotheses, which can be considered as extremes of a continuum, relate biodiversity to disease risk: One states that biodiversity is positively correlated with disease risk (Amplification Effect), and the second predicts a negative correlation between biodiversity and disease risk (Dilution Effect). Which of them applies better to different host-parasite systems is still a source of debate, due to limited experimental or empirical data. This is especially the case for viral diseases of plants. To address this subject, we have monitored for three years the prevalence of several viruses, and virus-associated symptoms, in populations of wild pepper (chiltepin) under different levels of human management. For each population, we also measured the habitat species diversity, host plant genetic diversity and host plant density. Results indicate that disease and infection risk increased with the level of human management, which was associated with decreased species diversity and host genetic diversity, and with increased host plant density. Importantly, species diversity of the habitat was the primary predictor of disease risk for wild chiltepin populations. This changed in managed populations where host genetic diversity was the primary predictor. Host density was generally a poorer predictor of disease and infection risk. These results support the dilution effect hypothesis, and underline the relevance of different ecological factors in determining disease/infection risk in host plant populations under different levels of anthropic influence. These results are relevant for managing plant diseases and for establishing conservation policies for endangered plant species

Post-mortem estimation of temperature distribution on a power transformer: Physicochemical and mechanical approaches

Power transformers are electrical machines that allow us to transport electric energy, with reduced losses, from generation stations to consumption points. This definition gives us an idea of the number of transformers that are used in power distribution systems worldwide. The main problem that may affect power transformers is the operation at high temperature. This paper summarizes the results of a postmortem temperature estimation carried out on an 800 kVA distribution transformer. Two methodologies are considered for estimating the temperature distribution in the windings of the machine. The first is based on the calculation of the degree of polymerization and the second is obtained from the tensile strength index. By knowing the value of these two magnitudes for a new and for an aged paper, and the period of operation of a transformer, the temperature distribution along the height of the windings can be estimated. None other previous works have used the tensile strength of winding paper for temperature distribution estimation. With these results and the loading regime records, similar transformers still in operation can be operated in an alternative manner and future designs can be improved

Estimating genetic diversity across the neutral genome with the use of dense marker maps

<p>Abstract</p> <p>Background</p> <p>With the advent of high throughput DNA typing, dense marker maps have become available to investigate genetic diversity on specific regions of the genome. The aim of this paper was to compare two marker based estimates of the genetic diversity in specific genomic regions lying in between markers: IBD-based genetic diversity and heterozygosity.</p> <p>Methods</p> <p>A computer simulated population was set up with individuals containing a single 1-Morgan chromosome and 1665 SNP markers and from this one, an additional population was produced with a lower marker density i.e. 166 SNP markers. For each marker interval based on adjacent markers, the genetic diversity was estimated either by IBD probabilities or heterozygosity. Estimates were compared to each other and to the true genetic diversity. The latter was calculated for a marker in the middle of each marker interval that was not used to estimate genetic diversity.</p> <p>Results</p> <p>The simulated population had an average minor allele frequency of 0.28 and an LD (r²) of 0.26, comparable to those of real livestock populations. Genetic diversities estimated by IBD probabilities and by heterozygosity were positively correlated, and correlations with the true genetic diversity were quite similar for the simulated population with a high marker density, both for specific regions (r = 0.19-0.20) and large regions (r = 0.61-0.64) over the genome. For the population with a lower marker density, the correlation with the true genetic diversity turned out to be higher for the IBD-based genetic diversity.</p> <p>Conclusions</p> <p>Genetic diversities of ungenotyped regions of the genome (i.e. between markers) estimated by IBD-based methods and heterozygosity give similar results for the simulated population with a high marker density. However, for a population with a lower marker density, the IBD-based method gives a better prediction, since variation and recombination between markers are missed with heterozygosity.</p

Constitutive RB1 mutation in a child conceived by in vitro fertilization: implications for genetic counseling

<p>Abstract</p> <p>Background</p> <p>The purpose of this study was to identify mutations associated with bilateral retinoblastoma in a quadruplet conceived by in vitro fertilization, and to trace the parental origin of mutations in the four quadruplets and their father.</p> <p>Methods</p> <p>Mutational screening was carried out by sequencing. Genotyping was carried out for determining quadruplet zygosity.</p> <p>Results</p> <p>The proband was a carrier of a novel <it>RB1</it> constitutive mutation (g.2056C>G) which was not detected in her father or her unaffected sisters, and of two other mutations (g.39606 C>T and g.174351T>A) also present in two monozygotic sisters. The novel mutation probably occurred de novo while the others were of likely maternal origin. The novel mutation, affecting the Kozak consensus at the 5'UTR of <it>RB1</it> and g.174351T>A were likely associated to retinoblastoma in the proband.</p> <p>Conclusion</p> <p>Molecular diagnosis of retinoblastoma requires genotypic data of the family for determining hereditary transmission. In the case of children generated by IVF with oocytes from an anonymous donor which had been stored in a cell repository, this might not be successfully accomplished, making precise diagnosis impracticable for genetic counseling.</p

Vertical integration in production and services: development in transaction cost economics

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Effect of family relatedness on characteristics of estimated IBD probabilities in relation to precision of QTL estimates

<p>Abstract</p> <p>Background</p> <p>A random QTL effects model uses a function of probabilities that two alleles in the same or in different animals at a particular genomic position are identical by descent (IBD). Estimates of such IBD probabilities and therefore, modeling and estimating QTL variances, depend on marker polymorphism, strength of linkage and linkage disequilibrium of markers and QTL, and the relatedness of animals in the pedigree. The effect of relatedness of animals in a pedigree on IBD probabilities and their characteristics was examined in a simulation study.</p> <p>Results</p> <p>The study based on nine multi-generational family structures, similar to a pedigree structure of a real dairy population, distinguished by an increased level of inbreeding from zero to 28% across the studied population. Highest inbreeding level in the pedigree, connected with highest relatedness, was accompanied by highest IBD probabilities of two alleles at the same locus, and by lower relative variation coefficients. Profiles of correlation coefficients of IBD probabilities along the marked chromosomal segment with those at the true QTL position were steepest when the inbreeding coefficient in the pedigree was highest. Precision of estimated QTL location increased with increasing inbreeding and pedigree relatedness. A method to assess the optimum level of inbreeding for QTL detection is proposed, depending on population parameters.</p> <p>Conclusions</p> <p>An increased overall relationship in a QTL mapping design has positive effects on precision of QTL position estimates. But the relationship of inbreeding level and the capacity for QTL detection depending on the recombination rate of QTL and adjacent informative marker is not linear.</p