Discovery and development of exome‐based,co‐dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.)

Globally, wheat is the most widely grown crop and one of the three most important crops for human and livestock feed. However, the complex nature of the wheat genome has, until recently, resulted in a lack of single nucleotide polymorphism (SNP)‐based molecular markers of practical use to wheat breeders. Recently, large numbers of SNP‐based wheat markers have been made available via the use of next‐generation sequencing combined with a variety of genotyping platforms. However, many of these markers and platforms have difficulty distinguishing between heterozygote and homozygote individuals and are therefore of limited use to wheat breeders carrying out commercial‐scale breeding programmes. To identify exome‐based co‐dominant SNP‐based assays, which are capable of distinguishing between heterozygotes and homozygotes, we have used targeted re‐sequencing of the wheat exome to generate large amounts of genomic sequences from eight varieties. Using a bioinformatics approach, these sequences have been used to identify 95 266 putative single nucleotide polymorphisms, of which 10 251 were classified as being putatively co‐dominant. Validation of a subset of these putative co‐dominant markers confirmed that 96% were true polymorphisms and 65% were co‐dominant SNP assays. The new co‐dominant markers described here are capable of genotypic classification of a segregating locus in polyploid wheat and can be used on a variety of genotyping platforms; as such, they represent a powerful tool for wheat breeders. These markers and related information have been made publically available on an interactive web‐based database to facilitate their use on genotyping programmes worldwide.     

The orientation behaviour of the lesser spearnosed bat, Phyllostomus discolor (Chiroptera) in a model roost

The orientation behaviour of bats (Phyllostomus discolor, Phyllostomidae), flying inside an octagonal roost-like chamber (ø: 100cm; h: 150cm) was examined.It has been shown that the bats begin turning manoeuvres during flight by turning their head towards the direction they intend to proceed to. During early phases of the flights, cumulative navigation errors were evident, indicating that endogenous spatial information plays a major role in the orientation of the bats. During later phases of the flight this error is diminished again. So it can be concluded that the bats start to use exogenous spatial information for orientation while approaching the target.In order to investigate the relative importance of vision, echolocation and endogenous spatial information for approaching the roost, the landing lattices inside the test arena were changed for non-grid dummies. We found that: 1. combined visual and endogenous information are more important than echoacoustical cues, 2. the bats learned quickly to switch their orientation behaviour in order to get a better performance in avoiding the dummies, 3. the learning performance was influenced by the visual similarity of dummies and the real landing lattice.     

Truncation Error Estimates in Process Life Cycle Assessment Using Input‐Output Analysis

Process life cycle assessment (PLCA) is widely used to quantify environmental flows associated with the manufacturing of products and other processes. As PLCA always depends on defining a system boundary, its application involves truncation errors. Different methods of estimating truncation errors are proposed in the literature; most of these are based on artificially constructed system complete counterfactuals. In this article, we review the literature on truncation errors and their estimates and systematically explore factors that influence truncation error estimates. We classify estimation approaches, together with underlying factors influencing estimation results according to where in the estimation procedure they occur. By contrasting different PLCA truncation/error modeling frameworks using the same underlying input‐output (I‐O) data set and varying cut‐off criteria, we show that modeling choices can significantly influence estimates for PLCA truncation errors. In addition, we find that differences in I‐O and process inventory databases, such as missing service sector activities, can significantly affect estimates of PLCA truncation errors. Our results expose the challenges related to explicit statements on the magnitude of PLCA truncation errors. They also indicate that increasing the strictness of cut‐off criteria in PLCA has only limited influence on the resulting truncation errors. We conclude that applying an additional I‐O life cycle assessment or a path exchange hybrid life cycle assessment to identify where significant contributions are located in upstream layers could significantly reduce PLCA truncation errors.     

Reliability of a new virtual reality test to measure cervicocephalic kinaesthesia

The aim of this study was to investigate the cervicocephalic kinaesthesia of healthy subjects for gender and age effects and its reliability in a new virtual reality test procedure. 57 healthy subjects (30 male, 27 females; 18-64 years) were immersed into a virtual 3D scene via a headmounted display, which generated specific head movements. The joint repositioning error was determined in a static and dynamic test at the times T0, T1 (T0 + 10 minutes) and T2 (T0 + 24 hours). The intrasession reliability (T0-T1) and the intersession reliability (T0-T2) were analysed. In both tests no gender- or age-specific effects were found. In the overall group the means of the static test were 6.2°-6.9° and of the dynamic test were 4.5°-4.9°. The intratest difference in the static test was -0.16° and the intertest difference was 0.47°. The intratest difference in the dynamic test was 0.42° and the intertest difference was 0.37°. The static and dynamic test was reproducible in healthy subjects, with minor deviations, irrespective of gender and age. The smaller interindividual differences in the dynamic test could be beneficial in the comparison of healthy individuals and individuals with cervical spine disorders.     

家畜基因组选择研究进展

近年来,随着基因芯片技术的发展与育种技术的进步,动植物的基因组选择成为研究热点。在家畜育种中,基因组选择凭借其准确性高、世代间隔短和育种成本低等优势被应用于各种经济动物的种畜选择中。本文详细介绍了基因分型技术和基因组育种值估计方法(最小二乘法、RR-BLUP法、GBLUP法、ssGBLUP法、贝叶斯A法、贝叶斯B法等),并对这些育种方法选用的标记范围、准确性以及计算速度进行了比较,总结了我国和其他国家基因组选择在种畜选择中的应用情况及存在的问题,展望了目前国内外在基因组选择上的最新研究动态及进展,以期为其他育种工作者进一步了解基因组选择提供参考。     

Kinetochore life histories reveal an Aurora-B-dependent error correction mechanism in anaphase

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DNA化学合成中的错误去除

在DNA的化学合成过程中,由于合成方法本身的限制,不可避免地会引入错误碱基,而在将化学合成的寡核苷酸拼装成长链DNA时,PCR反应等也会引入突变。为了得到高保真的合成DNA,必须对错误和突变进行纠正,本文介绍了能够用于纠正DNA合成过程中错误的内切核酸酶及错误结合蛋白,并介绍了它们进行错误纠正的方法,最后对这两类方法的优缺点进行了分析。     

Toll-like receptor 9 signaling has anti-inflammatory effects on the early phase of Helicobacter pylori-induced gastritis

Helicobacter pylori (H. pylori)-induced immune responses in the gastric mucosa are skewed toward T helper (Th) 1 phenotype, which is characterized by predominant production of tumor necrosis factor (TNF)-α and interferon (IFN)-γ by helper T cells. Toll-like receptors (TLRs) play an essential role in mucosal defense against microbes through the recognition of bacterial molecules. Among the members of the TLR family, TLR9 recognizes bacterial unmethylated CpG DNA sites, and signal transduction of TLR9 induces production of a variety of cytokines, including type-I IFN (IFN-α/β). We investigated the expression and role of TLR9 in H. pylori-induced gastritis in mice. Expression of TLR9 mRNA in the gastric tissue increased after infection with H. pylori. TLR9 was mainly expressed in the macrophages, dendritic cells, and CD3⁺ cells in the gastric mucosa. Neutrophil infiltration and the expression levels of TNF-α and IFN-γ mRNA were higher in TLR9 knockout (KO) mice than in wild-type mice at 2 and 4 months after H. pylori inoculation. These differences in inflammatory parameters between H. pylori-infected wild-type and TLR9 KO mice disappeared 6 months after H. pylori inoculation. Expression of interleukin-4 mRNA, typical Th2 cytokine, in the gastric tissue did not differ between H. pylori-infected wild-type and TLR9 KO mice. Expression level of IFN-α/β mRNA in the TLR9 KO mice was lower than that in wild-type mice by 4 months after inoculation. Administration of IFN-α reduced H. pylori infection-induced increase in neutrophil infiltration and the expression levels of TNF-α and IFN-γ mRNA in TLR9 KO mice. Our findings suggest that TLR9 signaling plays important roles in the suppression of H. pylori-induced gastritis in the early phase via downregulation of Th1-type cytokines modulated by IFN-α.     

Successive virgin births of viable male progeny in the checkered gartersnake,Thamnophis marcianus

In recent years genotyping analysis using mini‐ and microsatellite markers has provided robust DNA‐based support for facultative parthenogenesis (FP) in several lineages of squamate reptiles (snakes and lizards) and sharks. Rather than incidental cases of reproductive error, there is growing evidence that FP is an alternative reproductive strategy and an important mode of reproduction in these phylogenetically divergent vertebrate groups. Because documentation of FP in vertebrates is in its infancy, additional instances supported by molecular genetic methods provide insights that advance our general understanding of this phenomenon. Here, in a female checkered gartersnake (Thamnophis marcianus) reared in isolation since a juvenile, we describe five successive parthenogenetic litters produced over a 7‐year period that resulted in several viable male progeny. Cross species microsatellite amplification was performed across 30 primer pairs derived from Thamnophis spp. and related natricines to the female and nine available progeny. Five loci proved heterozygous in the maternal sample with the progeny differentially homozygous at all but one locus. Combined with evidence pertaining to captive history and litter characteristics, our analysis supports a specific type of FP, terminal fusion automictic parthenogenesis, over the competing hypothesis of long‐term sperm storage. Importantly, we document that a single individual was capable of producing successive litters composed of live parthenogens. In two cases, males achieved adulthood and showed the anatomical potential to demonstrate reproductive competence (normal looking hemipenes and testes). © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 566–572.