Use of bovine EST data and human genomic sequences to map 100 gene-specific bovine markers

A system to use bovine EST data in conjunction with human genomic sequence to improve the bovine linkage map over the entire genome or on specific chromosomes was evaluated. Bovine EST sequence was used to provide primer sequences corresponding to bovine genes, while human genomic sequence directed primer design to flank introns and produce amplicons of appropriate size for efficient direct sequencing. The sequence tagged sites (STS) produced in this way from the four sires of the MARC reference families were examined for single nucleotide polymorphisms (SNPs) that could be used to map the corresponding genes. With this approach, along with a primer/extension mass spectrometry SNP genotyping assay, 100 ESTs were placed on the bovine genetic linkage map. The first 70 were chosen at random from bovine EST–human genomic comparisons. An additional 30 ESTs were successfully mapped to bovine Chromosome 19 (BTA19), and comparison of the resulting BTA19 map to the position of the corresponding human orthologs on the HSA17 draft sequences revealed differences in the spacing and order of genes. Over 80% of successful amplicons contained SNPs, indicating that this is an efficient approach to generating EST-associated genetic markers. We have demonstrated the feasibility of constructing a linkage map based on SNPs associated with ESTs and the plausibility of utilizing EST, comparative mapping information, and human sequence data to target regions of the bovine genome for SNP marker development.     

Exome sequencing and arrayCGH detection of gene sequence and copy number variation between ILS and ISS mouse strains

It has been well documented that genetic factors can influence predisposition to develop alcoholism. While the underlying genomic changes may be of several types, two of the most common and disease associated are copy number variations (CNVs) and sequence alterations of protein coding regions. The goal of this study was to identify CNVs and single-nucleotide polymorphisms that occur in gene coding regions that may play a role in influencing the risk of an individual developing alcoholism. Toward this end, two mouse strains were used that have been selectively bred based on their differential sensitivity to alcohol: the Inbred long sleep (ILS) and Inbred short sleep (ISS) mouse strains. Differences in initial response to alcohol have been linked to risk for alcoholism, and the ILS/ISS strains are used to investigate the genetics of initial sensitivity to alcohol. Array comparative genomic hybridization (arrayCGH) and exome sequencing were conducted to identify CNVs and gene coding sequence differences, respectively, between ILS and ISS mice. Mouse arrayCGH was performed using catalog Agilent 1 × 244 k mouse arrays. Subsequently, exome sequencing was carried out using an Illumina HiSeq 2000 instrument. ArrayCGH detected 74 CNVs that were strain-specific (38 ILS/36 ISS), including several ISS-specific deletions that contained genes implicated in brain function and neurotransmitter release. Among several interesting coding variations detected by exome sequencing was the gain of a premature stop codon in the alpha-amylase 2B (AMY2B) gene specifically in the ILS strain. In total, exome sequencing detected 2,597 and 1,768 strain-specific exonic gene variants in the ILS and ISS mice, respectively. This study represents the most comprehensive and detailed genomic comparison of ILS and ISS mouse strains to date. The two complementary genome-wide approaches identified strain-specific CNVs and gene coding sequence variations that should provide strong candidates to contribute to the alcohol-related phenotypic differences associated with these strains.     

c-Myc-induced apoptosis in fibroblasts is inhibited by specific cytokines.

We have investigated the mechanism by which deregulated expression of c-Myc induces death by apoptosis in serum-deprived fibroblasts. We demonstrate that Myc-induced apoptosis in low serum is inhibited by a restricted group of cytokines, principally the insulin-like growth factors and PDGF. Cytokine-mediated protection from apoptosis is not linked to the cytokines' abilities to promote growth. Protection from apoptosis is evident in the post-commitment (mitogen-independent) S/G2/M phases of the cell cycle and also in cells that are profoundly blocked in cell cycle progression by drugs. Moreover, IGF-I inhibition of apoptosis occurs in the absence of protein synthesis, and so does not require immediate early gene expression. We conclude that c-Myc-induced apoptosis does not result from a conflict of growth signals but appears to be a normal physiological aspect of c-Myc function whose execution is regulated by the availability of survival factors. We discuss the possible implications of these findings for models of mammalian cell growth in vivo.     

Animal movements in fire‐prone landscapes

Movement is a trait of fundamental importance in ecosystems subject to frequent disturbances, such as fire‐prone ecosystems. Despite this, the role of movement in facilitating responses to fire has received little attention. Herein, we consider how animal movement interacts with fire history to shape species distributions. We consider how fire affects movement between habitat patches of differing fire histories that occur across a range of spatial and temporal scales, from daily foraging bouts to infrequent dispersal events, and annual migrations. We review animal movements in response to the immediate and abrupt impacts of fire, and the longer‐term successional changes that fires set in train. We discuss how the novel threats of altered fire regimes, landscape fragmentation, and invasive species result in suboptimal movements that drive populations downwards. We then outline the types of data needed to study animal movements in relation to fire and novel threats, to hasten the integration of movement ecology and fire ecology. We conclude by outlining a research agenda for the integration of movement ecology and fire ecology by identifying key research questions that emerge from our synthesis of animal movements in fire‐prone ecosystems.     

稻瘿蚊种群DNA指纹及水稻抗稻瘿蚊分子标记育种技术研究

文章综述经10年(1996~2005)研究建立的亚洲稻瘿蚊Orseolia oryzae Wood-Mason种群DNA指纹检测技术和水稻抗稻瘿蚊分子育种技术的研究成果。其核心技术包括5点:(1)在国际和国内首先用AFLP方法研究亚洲5国(中国,印度,斯里兰卡,尼泊尔和老挝)及广东省7个地点亚洲稻瘿蚊种群DNA指纹及其生物多样性;(2)分别用RAPD和微卫星SSR技术对来源于我国的水稻资源大秋其的抗亚洲稻瘿蚊基因Gm6进行精细定位;(3)分别用与Gm6基因紧密连锁的STS分子标记和SSR标记,建立了分子标记辅助选择(MAS)方法选育抗稻瘿蚊新品种的技术体系;(4)应用建立的分子标记辅助选育新技术选育出一批抗亚洲稻瘿蚊中国种群的新品系,创造出一批新种质,包括抗蚊18号、抗蚊软占等达国优3级的抗稻瘿蚊新品系6个;(5)将Gm6基因导入杂交稻恢复系,选育出4个抗稻瘿蚊两系杂交稻新组合培矮64S/KG18,培矮64S/KI41,培矮64S/AK7,培矮64S/03W16(国优2级)和1个三系杂交稻新组合抗蚊博优。其中江西省宁都市名林水稻研究所应用本研究鉴定出的带有Gm6基因的品系抗蚊青占作为抗性亲本,培育出的2个抗稻瘿蚊的两系杂交稻组合安两优青占和培两优抗占通过省级品种审定,率先选育出抗稻瘿蚊种群的杂交稻。该项研究成果为控制华南稻瘿蚊的灾害发生提供新的技术措施,选育的抗稻瘿蚊品种和新种质,在华南广为应用,取得显著的经济效益。     

Engineering poly(3-hydroxybutyrate-co-3-hydroxyvalerate) copolymer composition in E. coli

A strain of Escherichia coli was metabolically engineered to produce poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) of specified composition between 5% and 18% HV. A gene encoding propionyl-CoA synthetase (prpE from S. enterica) was placed under the control of the IPTG-inducible tac promoter (P(taclacUV5)) while the polyhydroxyalkanoate synthesis operon (phaBCA) from R. eutropha was expressed constitutively. A strain of E. coli harboring both plasmids was grown in defined medium and PHBV was produced with specified hydroxyvalerate (HV) molar content between 5% and 18%. The molecular weight of the copolymer was approximately 700,000 across various HV contents, and average polydispersity was approximately 1.3. The majority of the PHBV production occurred during the late exponential/stationary phase. The HV content of the copolymer generally peaked early in the incubation before falling to its final value. We found that the time profiles of PrpE activity, propionyl-CoA, and acetyl-CoA were well correlated to the HV content time profile. Despite an abundance of propionyl-CoA, incorporation of HV into the copolymer was inefficient. Therefore, both the PHA operon and conditions affecting the availability of propionyl-CoA must be chosen carefully to achieve the desired HV content. The ability to engineer copolymer composition control into an E. coli strain would be useful in cases where the feedstock composition is not adjustable.