SNP detection and prediction of variability between chicken lines using genome resequencing of DNA pools

<p>Abstract</p> <p>Background</p> <p>Next-generation sequencing technologies are widely used for detection of millions of Single Nucleotide Polymorphisms (SNPs) and also provide a means of assessing their variation. This information is useful for composing subsets of highly informative SNPs for region-specific or genome-wide analysis and to identify mutations regulating phenotypic differences within or between populations. In this study, we investigated the sensitivity of SNP detection and introduced the flanking SNPs value (FSV) as a novel measure for predicting SNP-variability using ~5X genome resequencing with ABI SOLID and DNA pools from two chicken lines divergently selected for juvenile bodyweight.</p> <p>Results</p> <p>Genotyping with a 60 K SNP chip revealed polymorphisms within or between two divergently selected chicken lines for 31 363 SNPs, 48% of which were also detected using resequencing of DNA pools. SNP detection using resequencing was more powerful for positions with larger differences in allele frequency between the lines. About 50% of the SNPs with non-reference allele frequencies in the range 0.5-0.6 and 67% of those with frequencies > 0.9 could be detected. On average, ~3.7 SNPs/kb were detected by resequencing, with about 5% lower density on microchromosomes than on macrochromosomes. There was a positive correlation between the observed between-line SNP variation from the 60 K chip analysis and our proposed FSV score computed from the genome resequencing data. The strongest correlations on macrochromosomes and microchromosomes were observed when the FSV was calculated with total flanking regions of 62 kb (correlation 0.55) and 38 kb (correlation 0.45), respectively.</p> <p>Conclusions</p> <p>Genome resequencing with limited coverage (~5X) using pooled DNA samples and three non-reference reads as a threshold for SNP detection, identified 50 - 67% of the 60 K SNPs with a non-reference allele frequency larger than 0.5. The SNP density was around 5% lower on the microchromosomes, most likely because of their higher gene content. Our proposed method to estimate the SNP variation (FSV) uses additional sequence information to better predict SNP informativity. The FSV scores showed higher correlations for SNPs with a larger difference in allele frequency between the populations. The correlation was strongest on macrochromosomes, probably due to a lower recombination rate.</p

Accounting for genetic interactions improves modeling of individual quantitative trait phenotypes in yeast.

Experiments in model organisms report abundant genetic interactions underlying biologically important traits, whereas quantitative genetics theory predicts, and data support, the notion that most genetic variance in populations is additive. Here we describe networks of capacitating genetic interactions that contribute to quantitative trait variation in a large yeast intercross population. The additive variance explained by individual loci in a network is highly dependent on the allele frequencies of the interacting loci. Modeling of phenotypes for multilocus genotype classes in the epistatic networks is often improved by accounting for the interactions. We discuss the implications of these results for attempts to dissect genetic architectures and to predict individual phenotypes and long-term responses to selection

Logical Inference for Model-Based Reconstruction of Ultrasonic Nonlinearity

Quantifying the constitutive nonlinearity parameter β in fluids is of key interest for understanding ultrasonic propagation and its wide implications in medical and industrial applications. However, current methods for ultrasonically measuring it show large limitations in that the signal is only valid at a reduced and unjustified spatial range away from the transducer. This is not consistent with the fact that β should be constant everywhere in the fluid and independently of the ultrasonic experimental setup. To overcome this, the nonlinear wave propagation equations are rigorously derived and the ensuing differential equation is numerically solved. As a second contribution, the experimental and model information sources are treated under the information theory context to probabilistically reconstruct β, providing not only its value, but also the degree of confidence on it given both sources of data. This method is satisfactorily validated testing the repeatability of β in water varying distances, energies, frequencies, and transducer setups, yielding values compatible with β= 3.5.The authors acknowledge the Spanish Ministerio de Economia y Competitividad for Projects DPI2010-17065 and DPI2014-51870-R and Junta de Andalucía for Projects P11-CTS-8089 and GGI3000IDIB

Synergy or oxymoron?

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Experimental Configuration to Determine the Nonlinear Parameter β in PMMA and CFRP with the Finite Amplitude Method

Parameters to measure nonlinearity in polymethylmethacrylate (PMMA) and carbon fiber reinforced polymer (CFRP) materials have been determined with nonlinear ultrasound (NLUS). The nonlinear parameter b has been determined using the variation of the Finite Amplitude Method (FAM) with harmonic generation. Using this as a reference, the first contribution of this work consists of deducting the experimental configuration necessary to measure this nonlinear parameter in a correct and feasible way. Excitation level, frequency of the wave generated, number of cycles analysed and the distances transducer-specimen and specimen-hydrophone have been determined in both materials. The second contribution is a semi-analytical model that allows to obtain the nonlinear parameter in materials by removing water contribution and considering geometric and viscous attenuation, using the data obtained in an immersion tank. Finally, an application of this model has been carried out in PMMA in order to determinate the nonlinear parameter in this material. From the results, we confirm that the configuration determined in this paper to obtain the parameter β decreases the noise in the measurements.This research was funded by the Ministry of Education DPI2017-83859-R

Wave Propagation in a Fractional Viscoelastic Tissue Model: Application to Transluminal Procedures

In this article, a wave propagation model is presented as the first step in the development of a new type of transluminal procedure for performing elastography. Elastography is a medical imaging modality for mapping the elastic properties of soft tissue. The wave propagation model is based on a Kelvin Voigt Fractional Derivative (KVFD) viscoelastic wave equation, and is numerically solved using a Finite Difference Time Domain (FDTD) method. Fractional rheological models, such as the KVFD, are particularly well suited to model the viscoelastic response of soft tissue in elastography. The transluminal procedure is based on the transmission and detection of shear waves through the luminal wall. Shear waves travelling through the tissue are perturbed after encountering areas of altered elasticity. These perturbations carry information of medical interest that can be extracted by solving the inverse problem. Scattering from prostate tumours is used as an example application to test the model. In silico results demonstrate that shear waves are satisfactorily transmitted through the luminal wall and that echoes, coming from reflected energy at the edges of an area of altered elasticity, which are feasibly detectable by using the transluminal approach. The model here presented provides a useful tool to establish the feasibility of transluminal procedures based on wave propagation and its interaction with the mechanical properties of the tissue outside the lumen.University College London, United KingdomTalentia scholarship (grant C2012H-75146405T-1) from the regional government of Andalusia, Spainthe Ministry of Education and Science, Spain, grants DPI2017-83859-R, EQC2018-004508-P and UNGR15-CE3664Andalusia, Spain, grants SOMM17/6109/UGR, B-TEP-026-UGR18, IE2017-5537 and P18-RT-165

Conservation programme for the kitchen garden at Österby bruk

Detta examensarbete är ett vårdprogram över Österby bruks köksträdgård. Österby bruk är beläget i norra Uppland cirka fem mil norr om Uppsala. Redan på 1500-talet började järnindustri växa fram på Österby. Österbys järnindustri kom att pågå fram till nedläggningen av Österbyverkan 1983. Dagens köksträdgård tillkom i och med den omgestaltning av hela herrgårdsanläggningen som startade på mitten av 1700-talet. Sedan dess har ingen omgestaltning skett. Carl Hårleman var upphovsman till den plan som låg till grund för parkanläggningen. Vem som fastställde köksträdgårdens utseende är inte fastlagt, det kan vara Hårleman likväl som trädgårdsmästaren. Idag är delar av Österby bruk ett byggnadsminne, där herrgården, parken och köksträdgården ingår. Köksträdgården och dess byggnader är mycket nedgångna, trots detta finns många värden i köksträdgården. Österby bruks köksträdgård har idag fortfarande kvar sin övergripande struktur som bland annat gett upphov till ett ypperligt mikroklimat att odla i. Det är 1700-talet som är tydligast representerat i dagens köksträdgård. Det arkitekturhistoriska sammanhanget med parken och bruksanläggningen är också från detta århundrade. Köksträdgårdens byggnader, mestadels förfallna, härstammar från olika århundraden och berättar om de specifika odlingstekniker man använde under respektive tidsepok. I köksträdgården har man kontinuerligt odlat fram till och med 1976. Detta faktum ger upphov till tanken att odlandet borde stå i fokus. Man borde sträva efter att levandegöra de tre århundraden då man kontinuerligt odlade på platsen. Den ursprungliga gestaltningen har varit en förutsättning för odlandet och kommer åter vara det då köksträdgården på nytt brukas. Sammanhanget med 1700-talets park och herrgård förstärks och vi förstår varför köksträdgården placerats på den yta där den ännu idag är belägen. En köksträdgård där man återigen odlar ger också plats för rekreativa värden och bidrar till möjligheten att uppleva sinnliga värden. Odlandet och avkastningen är det primära i en köksträdgård och härmed finns chansen att placera odlandet i fokus. En annan viktig del är att göra köksträdgården tillgänglig och förståelig för besökare. För att kunna levandegöra köksträdgårdens historia, visa på det viktiga sambandet med resten av anläggningen och bidra till att föra fram information till besökaren, bör en vårdplan upprättas. Dessutom bör anläggningen studeras och dokumenteras av en fackman, inom byggnadsvården.This thesis is a conservation programme for the historical kitchen garden at Österby bruk. Österby bruk is situated in the north of Uppland about fifty kilometres north of Uppsala. Already in the beginning of the 16th century it started out an iron industry at Österby. The iron industry was still producing iron until 1983 when Österbyverken was shut down. The kitchen garden of today was founded in the same process as the reconstruction of the park and the main building that started in the middle of the 18th century. Since then there has been no reconstruction of the site. Carl Hårleman was the originator of the plan that underlied the construction of the park. It is not known who was the architect of the kitchen garden. It could be Hårleman as well as the gardener. Today, parts of Österby bruk is a historic listed building, the parts include the main building, the park and the kitchen garden. The kitchen garden of today is very run down. In spite of this you can find many values in today's kitchen garden. The kitchen garden still has it original architectural structure, which for instance given rise to the extraordinary micro climate to cultivate in. The 18th century is most clearly represented in the kitchen garden of today. The architectural historic connection with the rest of Österby also dates from the 18th century. The buildings in the kitchen garden, all in very varying condition, date from different centuries and can tell us about the specific cultivating technique one has used during different times history. There has been a non-stop cultivation of the kitchen garden until 1976. This gives us the idea that you should work to make the three hundred centuries of growing "lifelike". The original design has been a necessary condition for cultivation and will be so again when the kitchen garden is again cultivated. The connection between the 18th century Park and main building then becomes more obvious and we may also get to know why the kitchen garden is placed where it is. A kitchen garden is a place for cultivation and if you once again cultivate then you will give the place recreative values and also give opportunities for experiencing something that pertain to the senses. In a kitchen garden the main thing is the cultivating and how much you can produce and in this case it is possible to put cultivation in focus again. It is also important to make the kitchen garden both available and understandable for visitors. To make it possible to make the history of growing in the kitchen garden "lifelike", to show the important connection to the rest of Österby and make it possible to get the information out to the visitor, you can make up a plan for conservation. Besides this, the kitchen garden should be investigated and documented by a professional conversationalist of buildings, to make its survival guaranteed