Genome scan of Diabrotica virgifera virgifera for genetic variation associated with crop rotation tolerance

Crop rotation has been a valuable technique for control of Diabrotica virgifera virgifera for almost a century. However, during the last two decades, crop rotation has ceased to be effective in an expanding area of the US corn belt. This failure appears to be due to a change in the insect's oviposition behaviour, which, in all probability, has an underlying genetic basis. A preliminary genome scan using 253 amplified fragment-length polymorphism (AFLP) markers sought to identify genetic variation associated with the circumvention of crop rotation. Samples of D. v. virgifera from east-central Illinois, where crop rotation is ineffective, were compared with samples from Iowa at locations that the behavioural variant has yet to reach. A single AFLP marker showed signs of having been influenced by selection for the circumvention of crop rotation. However, this marker was not diagnostic. The lack of markers strongly associated with the trait may be due to an insufficient density of marker coverage throughout the genome. A weak but significant general heterogeneity was observed between the Illinois and Iowa samples at microsatellite loci and AFLP markers. This has not been detected in previous population genetic studies of D. v. virgifera and may indicate a reduction in gene flow between variant and wild-type beetles

Estimation of genetic parameters of egg production traits of laying hens by restricted maximum likelihood applied to a multiple-trait reduced animal model

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Numerical visualization and optimization on the core penetration in multi-cavity co-injection molding with a bifurcation runner structure

[[abstract]]Co-Injection Molding and multi-cavity molding are common processes for plastic products manufacturing. These two systems are sometimes combined and applied in the manufacture of bifurcation-structure products. In the previous literature results, the dynamic behavior of the core penetration in co-injection multi-cavity molding with a bifurcation structure is quite complicated and the behavior is sensitive to injection flow rates, different materials, and other process conditions. However, how these influential factors truly affect the core penetration behavior and the detailed mechanism of core penetration behavior has not yet been fully understood. In this study, we focused on studying the multi-cavity co-injection system with a bifurcation runner structure. The results showed that when the skin-to-core ratio is fixed (say 72/28), the melt flow behavior of a co-injection system, utilizing the same material for both skin and core, is very similar to that of a single shot injection molding. Specifically, the non-symmetrical bifurcation runner structure will influence the flow behavior greatly and cause the core distribution imbalance between different cavities. Due to the geometric nature of the bifurcation runner design, this core distribution imbalance problem will still persist even if we modify the melt temperature, mold temperature, or even change the plastic material. Furthermore, when the skin-to-core ratio is fixed (say 72/28), the changes of the flow rate have very little effect on the core penetration result in the final molded product; the final molded product will still have a core distribution imbalance issue. However, we observed that when the flow rate is increased, the core material will occupy more volume space in the upstream portion of the runner and the core penetration distance will be reduced in the flow direction downstream. This feature is very useful to further manipulate the skin-core interface in a multi-cavity system. Moreover, regarding how to improve a poor inter-cavity balance of core material distribution, using a suitable adjustment of the skin-to-core ratio will be greatly helpful. However, the core break-through defect can be a common problem in co-injection molding when an unsuitable skin-to-core ratio is used. To prevent the core break-through defect, increasing the flow rate properly can be one of the good options that we can use. Hence, we concluded that a suitable adjustment of the skin-to-core ratio and a proper flow rate control can be used to optimize the core material distribution in multi-cavity co-injection molding with a bifurcation runner structure. Lastly, in order to validate our inference and the effectiveness of our proposal to improve the inter-cavity imbalance and core break-through problem, a series of experimental studies were performed. And, all experimental results are in good agreement with those of our numerical predictions to further validate the feasibility of our proposed method to gain a better control of the core material distribution with a bifurcation runner structure in multi-cavity co-injection molding.[[notice]]補正完

Red blood cell distribution width: Genetic evidence for aging pathways in 116,666 volunteers

This is the final version of the article. Available from Public Library of Science via the DOI in this record.INTRODUCTION: Variability in red blood cell volumes (distribution width, RDW) increases with age and is strongly predictive of mortality, incident coronary heart disease and cancer. We investigated inherited genetic variation associated with RDW in 116,666 UK Biobank human volunteers. RESULTS: A large proportion RDW is explained by genetic variants (29%), especially in the older group (60+ year olds, 33.8%, <50 year olds, 28.4%). RDW was associated with 194 independent genetic signals; 71 are known for conditions including autoimmune disease, certain cancers, BMI, Alzheimer's disease, longevity, age at menopause, bone density, myositis, Parkinson's disease, and age-related macular degeneration. Exclusion of anemic participants did not affect the overall findings. Pathways analysis showed enrichment for telomere maintenance, ribosomal RNA, and apoptosis. The majority of RDW-associated signals were intronic (119 of 194), including SNP rs6602909 located in an intron of oncogene GAS6, an eQTL in whole blood. CONCLUSIONS: Although increased RDW is predictive of cardiovascular outcomes, this was not explained by known CVD or related lipid genetic risks, and a RDW genetic score was not predictive of incident disease. The predictive value of RDW for a range of negative health outcomes may in part be due to variants influencing fundamental pathways of aging.This work was supported by an award to DM, TF, AM and LH by the UK Medical Research Council (grant number MR/M023095/1). SEJ is funded by the Medical Research Council (grant: MR/M005070/1). JT is funded by a Diabetes Research and Wellness Foundation Fellowship. RB is funded by the Wellcome Trust and Royal Society grant: 104150/Z/14/Z. MAT, MNW and AM are supported by the Wellcome Trust Institutional Strategic Support Award (WT097835MF). ARW, HY, and TF are supported by the European Research Council grant: 323195:GLUCOSEGENES-FP7-IDEAS-ERC. LF is supported by the Intramural Research Program of the National Institute on Aging, U.S. National Institutes of Health. Input from MD, CLK and GK was supported by the University of Connecticut Health Center. This research has been conducted using the UK Biobank Resource under Application Number 14631. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Using DNA Methylation Patterns to Infer Tumor Ancestry

Background: Exactly how human tumors grow is uncertain because serial observations are impractical. One approach to reconstruct the histories of individual human cancers is to analyze the current genomic variation between its cells. The greater the variations, on average, the greater the time since the last clonal evolution cycle (‘‘a molecular clock hypothesis’’). Here we analyze passenger DNA methylation patterns from opposite sides of 12 primary human colorectal cancers (CRCs) to evaluate whether the variation (pairwise distances between epialleles) is consistent with a single clonal expansion after transformation. Methodology/Principal Findings: Data from 12 primary CRCs are compared to epigenomic data simulated under a single clonal expansion for a variety of possible growth scenarios. We find that for many different growth rates, a single clonal expansion can explain the population variation in 11 out of 12 CRCs. In eight CRCs, the cells from different glands are all equally distantly related, and cells sampled from the same tumor half appear no more closely related than cells sampled from opposite tumor halves. In these tumors, growth appears consistent with a single ‘‘symmetric’ ’ clonal expansion. In three CRCs, the variation in epigenetic distances was different between sides, but this asymmetry could be explained by a single clonal expansion with one region of a tumor having undergone more cell division than the other. The variation in one CRC was complex and inconsistent with a simple single clonal expansion

Balancing Selection at the Tomato RCR3 Guardee Gene Family Maintains Variation in Strength of Pathogen Defense

Coevolution between hosts and pathogens is thought to occur between interacting molecules of both species. This results in the maintenance of genetic diversity at pathogen antigens (or so-called effectors) and host resistance genes such as the major histocompatibility complex (MHC) in mammals or resistance (R) genes in plants. In plant-pathogen interactions, the current paradigm posits that a specific defense response is activated upon recognition of pathogen effectors via interaction with their corresponding R proteins. According to the''Guard-Hypothesis,'' R proteins (the ``guards'') can sense modification of target molecules in the host (the ``guardees'') by pathogen effectors and subsequently trigger the defense response. Multiple studies have reported high genetic diversity at R genes maintained by balancing selection. In contrast, little is known about the evolutionary mechanisms shaping the guardee, which may be subject to contrasting evolutionary forces. Here we show that the evolution of the guardee RCR3 is characterized by gene duplication, frequent gene conversion, and balancing selection in the wild tomato species Solanum peruvianum. Investigating the functional characteristics of 54 natural variants through in vitro and in planta assays, we detected differences in recognition of the pathogen effector through interaction with the guardee, as well as substantial variation in the strength of the defense response. This variation is maintained by balancing selection at each copy of the RCR3 gene. Our analyses pinpoint three amino acid polymorphisms with key functional consequences for the coevolution between the guardee (RCR3) and its guard (Cf-2). We conclude that, in addition to coevolution at the ``guardee-effector'' interface for pathogen recognition, natural selection acts on the ``guard-guardee'' interface. Guardee evolution may be governed by a counterbalance between improved activation in the presence and prevention of auto-immune responses in the absence of the corresponding pathogen

Secondary contact and admixture between independently invading populations of the Western corn rootworm, diabrotica virgifera virgifera in Europe

The western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae), is one of the most destructive pests of corn in North America and is currently invading Europe. The two major invasive outbreaks of rootworm in Europe have occurred, in North-West Italy and in Central and South-Eastern Europe. These two outbreaks originated from independent introductions from North America. Secondary contact probably occurred in North Italy between these two outbreaks, in 2008. We used 13 microsatellite markers to conduct a population genetics study, to demonstrate that this geographic contact resulted in a zone of admixture in the Italian region of Veneto. We show that i) genetic variation is greater in the contact zone than in the parental outbreaks; ii) several signs of admixture were detected in some Venetian samples, in a Bayesian analysis of the population structure and in an approximate Bayesian computation analysis of historical scenarios and, finally, iii) allelic frequency clines were observed at microsatellite loci. The contact between the invasive outbreaks in North-West Italy and Central and South-Eastern Europe resulted in a zone of admixture, with particular characteristics. The evolutionary implications of the existence of a zone of admixture in Northern Italy and their possible impact on the invasion success of the western corn rootworm are discussed

Infrared composition of the Large Magellanic Cloud

The evolution of galaxies and the history of star formation in the Universe are among the most important topics in today's astrophysics. Especially, the role of small, irregular galaxies in the star-formation history of the Universe is not yet clear. Using the data from the AKARI IRC survey of the Large Magellanic Cloud at 3.2, 7, 11, 15, and 24 {\mu}m wavelengths, i.e., at the mid- and near-infrared, we have constructed a multiwavelength catalog containing data from a cross-correlation with a number of other databases at different wavelengths. We present the separation of different classes of stars in the LMC in color-color, and color-magnitude, diagrams, and analyze their contribution to the total LMC flux, related to point sources at different infrared wavelengths

Effects of the Training Dataset Characteristics on the Performance of Nine Species Distribution Models: Application to Diabrotica virgifera virgifera

Many distribution models developed to predict the presence/absence of invasive alien species need to be fitted to a training dataset before practical use. The training dataset is characterized by the number of recorded presences/absences and by their geographical locations. The aim of this paper is to study the effect of the training dataset characteristics on model performance and to compare the relative importance of three factors influencing model predictive capability; size of training dataset, stage of the biological invasion, and choice of input variables. Nine models were assessed for their ability to predict the distribution of the western corn rootworm, Diabrotica virgifera virgifera, a major pest of corn in North America that has recently invaded Europe. Twenty-six training datasets of various sizes (from 10 to 428 presence records) corresponding to two different stages of invasion (1955 and 1980) and three sets of input bioclimatic variables (19 variables, six variables selected using information on insect biology, and three linear combinations of 19 variables derived from Principal Component Analysis) were considered. The models were fitted to each training dataset in turn and their performance was assessed using independent data from North America and Europe. The models were ranked according to the area under the Receiver Operating Characteristic curve and the likelihood ratio. Model performance was highly sensitive to the geographical area used for calibration; most of the models performed poorly when fitted to a restricted area corresponding to an early stage of the invasion. Our results also showed that Principal Component Analysis was useful in reducing the number of model input variables for the models that performed poorly with 19 input variables. DOMAIN, Environmental Distance, MAXENT, and Envelope Score were the most accurate models but all the models tested in this study led to a substantial rate of mis-classification