Genetic analysis of agronomic traits in a cross between sugarcane (Saccharum officinarum L.) and its presumed progenitor (S. robustum Brandes & Jesw. ex Grassl)

Saccharum robustum Brandes & Jesw. ex Grassl has been suggested as the immediate progenitor species of cultivated sugarcane (S. officinarum L.) [4]. Chromosome pairing and assortment in these two species were previously studied by genetic analysis of single-dose DNA markers in parents in and 44 F₁ progeny of a cross between euploid, meiotically regular 2n=80S. officinarum LA Purple andS. robustum Mol 5829 [2]. This same population was subsequently clonally propagated and evaluated in replicated trials for quantitative traits important to sugarcane breeders. Numbers of stalks, tasseled stalks, and stalks with smut, and the average diameter of two stalks were determined one day prior to harvest. At harvest, plant material from each plot was weighed and evaluated for pol (sucrose content) and fiber percentages. Clones were significantly different (P<0.01) for all traits analyzed. Associations of 83 single-dose arbitrarily primed PCR genetic markers with quantitative trait loci (QTL) of recorded traits was determined by single-factor ANOVA, and multiple regression. QTL analysis revealed markers significantly (P<0.05) associated with the expression of each trait analyzed. Markers associated with QTL after multiple regression were tested for digenic linear × linear epistatic interactions. The various multilocus models explained between 23% and 58% of the total phenotypic variation and 32% and 76% of the genotypic variation for the various traits. Digenic interactions were uncommon. Implications for marker-assisted selection in sugarcane and sugarcane domestication are discussed.     

On the False Discovery Rate and Expected Type I Errors

The paper is concerned with expected type I errors of some stepwise multiple test procedures based on independent p‐values controlling the so‐called false discovery rate (FDR). We derive an asymptotic result for the supremum of the expected type I error rate(EER) when the number of hypotheses tends to infinity. Among others, it will be shown that when the original Benjamini‐Hochberg step‐up procedure controls the FDR at level α, its EER may approach a value being slightly larger than α/4 when the number of hypotheses increases. Moreover, we derive some least favourable parameter configuration results, some bounds for the FDR and the EER as well as easily computable formulae for the familywise error rate (FWER) of two FDR‐controlling procedures. Finally, we discuss some undesirable properties of the FDR concept, especially the problem of cheating.     

Preclinical screening of histone deacetylase inhibitors combined with ABT-737, rhTRAIL/MD5-1 or 5-azacytidine using syngeneic Vk*MYC multiple myeloma

Multiple myeloma (MM) is an incurable malignancy with an unmet need for innovative treatment options. Histone deacetylase inhibitors (HDACi) are a new class of anticancer agent that have demonstrated activity in hematological malignancies. Here, we investigated the efficacy and safety of HDACi (vorinostat, panobinostat, romidepsin) and novel combination therapies using in vitro human MM cell lines and in vivo preclinical screening utilizing syngeneic transplanted Vk*MYC MM. HDACi were combined with ABT-737, which targets the intrinsic apoptosis pathway, recombinant human tumour necrosis factor-related apoptosis-inducing ligand (rhTRAIL/MD5-1), that activates the extrinsic apoptosis pathway or the DNA methyl transferase inhibitor 5-azacytidine. We demonstrate that in vitro cell line-based studies provide some insight into drug activity and combination therapies that synergistically kill MM cells; however, they do not always predict in vivo preclinical efficacy or toxicity. Importantly, utilizing transplanted Vk*MYC MM, we report that panobinostat and 5-azacytidine synergize to prolong the survival of tumor-bearing mice. In contrast, combined HDACi/rhTRAIL-based strategies, while efficacious, demonstrated on-target dose-limiting toxicities that precluded prolonged treatment. Taken together, our studies provide evidence that the transplanted Vk*MYC model of MM is a useful screening tool for anti-MM drugs and should aid in the prioritization of novel drug testing in the clinic.     

Evidence for multiple sources of invasion and intraspecific hybridization in Brachypodium sylvaticum (Hudson) Beauv. in North America

We compared the levels and distribution of genetic diversity in Eurasian and North American populations of Brachypodium sylvaticum (Huds.) Beauv. (false brome), a newly invasive perennial bunchgrass in western North America. Our goals were to identify source regions for invasive populations, determine the number of independent invasion events, and assess the possibility that postinvasion bottlenecks and hybridization have affected patterns of genetic diversity in the invaded range. We tested the hypothesis that this Eurasian grass was accidentally introduced into two areas in Oregon and one site in California by examining nuclear microsatellites and chloroplast haplotype variation in 23 introduced and 25 native populations. In the invaded range, there was significantly lower allelic richness (R(S)), observed heterozygosity (H(O)) and within-population gene diversity (H(S)), although a formal test failed to detect a significant genetic bottleneck. Most of the genetic variation existed among populations in the native range but within populations in the invaded range. All of the allelic variation in the invaded range could be explained based on alleles found in western European populations. The distribution of identified genetic clusters in the North American populations and the unique alleles associated with them is consistent with two historical introductions in Oregon and a separate introduction to California. Further analyses of population structure indicate that intraspecific hybridization among genotypes from geographically distinct regions of western Europe occurred following colonization in Oregon. The California populations, however, are more likely to be derived from one or perhaps several genetically similar regions in the native range. The emergence and spread of novel recombinant genotypes may be facilitating the rapid spread of this invasive species in Oregon.     

基于地理和气象要素的春玉米生育期栅格化方法

本文以黄河流域春玉米生育期和气象站点气象数据为主要数据源,采用多元逐步回归法分析了各生育期和经度、纬度、海拔高度、降水、年均温、≥10℃积温和日照时数等影响因子的关系,建立逐步回归方程,对各生育期空间栅格化方法进行了探讨,结果表明：（1）生育期空间拟合插值的统计检验说明春玉米“播种期”、“抽雄期”和“收获期”三个时期模拟效果最好,“拔节期”效果精度相对较好;（2）播种期基本满足从西南到东北延后的变化趋势,而拔节期、抽雄期和收获期基本上表现了从南北向中部、中部向东西两侧延后的现象。本研究得到的生育期与地理和气象要素之间的逐步回归方程,可为气候条件变化下作物生育期栅格化模拟试验以及农业生产应该采取的适应机制研究提供一定的依据。     

Development of a PCR-based assay for rapid detection of class IIa bacteriocin genes

Aims: We have developed a PCR‐based assay using custom designed panel of primers which allows rapid detection of class IIa bacteriocin‐coding genes. To demonstrate the applicability of the developed assay, the method was applied on 40 metagenomic DNA preparations isolated from native microbiota of Polish artisanal cheeses produced in the Tatra Mountains. Methods and Results: The developed assay was designed on the basis of a large scale alignment of class IIa bacteriocin‐coding genes. A panel of seven primer pairs with confirmed ability to detect class IIa bacteriocin‐coding sequences was obtained. The following study has revealed a superb bacteriocinogenic potential of all forty analysed cheese samples. Conclusions: The majority of obtained sequences were lactic acid bacteria (LAB) related, although some sequences showed significant similarity to bacteriocin‐coding sequences present in non‐LAB bacteriocin producers. The results suggest that several potentially new bacteriocin‐coding sequences were found. Significance and Impact of the Study: The developed assay can be extremely helpful in establishing whether isolates from the environment of interest have a potential of synthesizing antilisterial class IIa bacteriocins. Application of the approach may represent a useful tool contributing to ecological studies looking for valuable probiotic, bacteriocinogenic microbiota developing in foods.     

Glycopeptide dendrimers. Part I.

Glycopeptide dendrimers are branched structures containing both carbohydrates and peptides. Various classes of these compounds differing in composition and structure are mentioned, together with their practical use spanning from catalysis, transport vehicles to synthetic vaccines. The main stress is given to glycopeptide dendrimers, namely multiple antigen glycopeptides (MAGs). In MAGs, the core, branches or both are composed of amino acids or peptides. Other classes of glycodendrimers (PAMAM, polypropylene imine, cyclodextrin, calixarene, etc.) are mentioned too, but to a smaller extent. Their syntheses, physicochemical properties and biological activities are given with many examples. Glycopeptide dendrimers can be used as inhibitors of cell surface protein-carbohydrate interactions, intervention with bacterial adhesion, for studying of recognition processes, diagnostics, imaging and contrast agents, mimetics, for complexation of different cationts, as site-specific molecular delivery systems, for therapeutic purposes, as immunodiagnostics and in drug design. Biomedical applications of glycopeptide dendrimers as drug and gene delivery systems are also given.     

基于质谱技术筛选差异表达蛋白的统计学策略研究进展

随着质谱技术的快速发展,蛋白质组学已成为继基因组学、转录组学之后的又一研究热点,寻找可靠的差异表达蛋白对于生物标记物的发现至关重要.因此,如何准确、灵敏地筛选出差异蛋白已成为基于质谱的定量蛋白质组学的主要研究内容之一.目前,针对该问题的研究方法众多,但这些方法策略的适用范围不尽相同.总体来说,基于质谱技术筛选差异蛋白的统计学策略可以分为3类:基于经典统计学派的策略、基于贝叶斯学派的统计检验策略和其他策略,这3类方法有各自的应用范围、特点及不足.此外,筛选过程还将产生部分假阳性结果,可以采用其他方法对差异表达蛋白的质量进行控制,以提高统计检验结果的可靠性.