Nonparametric functional mapping of quantitative trait loci

Summary .  Functional mapping is a useful tool for mapping quantitative trait loci (QTL) that control dynamic traits. It incorporates mathematical aspects of biological processes into the mixture model-based likelihood setting for QTL mapping, thus increasing the power of QTL detection and the precision of parameter estimation. However, in many situations there is no obvious functional form and, in such cases, this strategy will not be optimal. Here we propose to use nonparametric function estimation, typically implemented with B-splines, to estimate the underlying functional form of phenotypic trajectories, and then construct a nonparametric test to find evidence of existing QTL. Using the representation of a nonparametric regression as a mixed model, the final test statistic is a likelihood ratio test. We consider two types of genetic maps: dense maps and general maps, and the power of nonparametric functional mapping is investigated through simulation studies and demonstrated by examples.     

<Emphasis Type="Italic">Pichia pastoris</Emphasis> fermentation with mixed-feeds of glycerol and methanol: growth kinetics and production improvement

Fed-batch fermentation of a methanol utilization plus (Mut⁺) Pichia pastoris strain typically has a growth phase followed by a production phase (induction phase). In the growth phase glycerol is usually used as carbon for cell growth while in the production phase methanol serves as both inducer and carbon source for recombinant protein expression. Some researchers employed a mixed glycerol-methanol feeding strategy during the induction phase to improve production, but growth kinetics on glycerol and methanol and the interaction between them were not reported. The objective of this paper is to optimize the mixed feeding strategy based on growth kinetic studies using a Mut⁺ Pichia strain, which expresses the heavy-chain fragment C of botulinum neurotoxin serotype C [BoNT/C(Hc)] intracellularly, as a model system. Growth models on glycerol and methanol that describe the relationship between specific growth rate (μ) and specific glycerol/methanol consumption rate (ν _gly, ν _MeOH) were established. A mixed feeding strategy with desired μ _gly/μ _MeOH =1, 2, 3, 4 (desired μ _MeOH set at 0.015 h⁻¹) was employed to study growth interactions and their effect on production. The results show that the optimal desired μ _gly/μ _MeOH is around 2 for obtaining the highest BoNT/C(Hc) protein content in cells: about 3 mg/g wet cells. Electronic Publication     

Leishmania infantum and Toxoplasma gondii: Mixed infection of macrophages in vitro and in vivo

Although macrophages have a microbicidal role in the immune system they themselves can be infected by pathogens. Often a simultaneous infection by more than one microbe may occur in a single cell. This is the first report of coinfection of macrophages with Toxoplasma gondii and Leishmania infantum, in vitro and in vivo. L. infantum does not cause severe disease in mice but T. gondii, RH strain, is lethal. Cell culture studies using THP-1 macrophages dually infected in vitro revealed that 4.3% harbored both parasites 24 h after infection. When mice were infected with both parasites on the same day 7.3% of the infected cells carried both parasites 7 days later. Yet, if mice were first infected with L. infantum and then with Toxoplasma (5 days post-infection) 18.7% of the macrophages hosted either parasite but concomitant infection could not be found and mice, already harboring L. infantum, survived Toxoplasma’s lethal effect.     

环境样品中DNA的分离纯化和文库构建

采用研磨 /冻融和SDS/蛋白酶K热处理等理化方法 ,直接从性质不同的环境样品中提取和纯化混合基因组DNA。所获得纯品DNA的产量为每克样品 2～ 1 6μg。对纯品DNA进行限制性内切酶处理后 ,构建了以pUC1 8为载体的DNA文库。建库效率为从每克环境样品获得约 1 0 3～ 1 0 4 个含 3～ 8kb外源随机插入片段的克隆。通过DNA序列测定和基因注释 ,对从文库中随机选取的克隆进行了分析 ,发现外源插入片段均含序列未见报道的新基因。本文所做的尝试对于保存、研究和开发未培养微生物基因资源具有意义     

杉木与伴生植物凋落物混合分解的相互作用研究

通过对杉木与9种伴生植物凋落物混合分解特征比较研究表明,8种植物对杉木凋落物的分解均有不同程度的促进作用,其中观音座莲对杉木凋落物分解的促进最大,而木荷对杉木凋落物分解的影响则表现出先有一定程度的促进而后又有微弱的抑制作用,促进大小表现出观音座莲＞杜茎山＞三龙爪＞狗脊＞苎麻＞丝栗栲＞闽粤栲＞芒萁。杉木 落物反过来对木荷和闽粤栲凋落物有一些抑制作用,而对丝栗栲则有一些促进作用,但这种相互作用未达到显著差异水平。说明杉木与某些伴生植物种类的凋落物在混合分解过程中存在着相互作用的现象,因此,合理保护和恢复林下植物对加快杉木人工林生态系统的养分循环和地力维护具有重要的意义。     

玉米雄穗性状遗传结构与形成分子机制*

玉米为雌雄同株异花植物,其雄穗着生于植株顶部,雌穗腋生。雄穗一方面需产生足量花粉以保证雌穗授粉结实,另一方面由于对下部叶片的遮蔽作用和自身营养需求,其生长发育会同时影响叶片光合作用效率和能量分配,因此优化雄穗结构是提高玉米产量的重要措施之一。玉米雄穗性状包括雄穗分枝数、雄穗分枝长度、雄穗主轴长度、雄穗分枝总长度、雄穗分枝角度等,均为多基因控制的数量性状。自20世纪90年代,研究者开始利用数量性状位点(quantitative trait locus,QTL)定位方法解析玉米雄穗性状遗传结构;随着玉米自交系B73等参考基因组释放,以及DNA微阵列、基因组重测序等高通量基因分型技术的日益成熟,全基因组关联分析(genome-wide association study, GWAS)成为数量性状遗传研究的主流方法,目前已鉴定出大量玉米雄穗性状遗传位点。通过总结雄穗性状遗传定位研究结果,构建一致性图谱并挖掘定位热点区间,有助于进一步了解雄穗性状遗传结构特征及指导雄穗性状候选基因克隆。此外,通过对调控雄穗发育的已知基因进行功能分类,可为解析玉米雄穗发育的遗传网络和调控通路提供理论支撑。     

栽植生姜对不同种植模式下紫色土微生物生物量及水解酶活性的影响

研究了岷江下游紫色丘陵区玉米+红薯间作、大豆单作、生姜连作、水稻-紫云英轮作等4个典型种植模式下栽植生姜后土壤微生物生物量碳、氮、磷含量和水解酶活性的变化特征.结果表明： 栽植生姜显著降低了4个种植模式下土壤微生物生物量碳、氮和磷含量,但各种植模式之间存在较大差异.其中,玉米+红薯间作和水稻-紫云英轮作模式下土壤微生物生物量碳、氮的下降幅度明显低于大豆单作与生姜连作模式,但土壤微生物生物量磷下降幅度明显较高.栽植生姜显著降低了土壤酸性磷酸酶活性,其下降幅度以玉米+红薯间作模式最大,水稻-紫云英轮作模式最小;土壤转化酶活性在生姜连作模式下显著降低;土壤脲酶活性在大豆单作、生姜连作和水稻-紫云英轮作模式下均显著降低.相对于其他模式,栽植生姜使玉米+红薯间作模式下的土壤维持了较高的转化酶和脲酶活性.     

气候变化背景下中国农业气候资源变化Ⅷ.江西省双季稻各生育期热量条件变化特征

基于江西省地面气象资料和农业气象试验站数据,分析了江西省双季稻生育期的变化趋势,并利用生长度日（GDD）、低温度日（CDD）和高温度日（HDD）对1981-2007年江西省水稻各生育期热量资源的变化趋势进行分析.结果表明：气候变暖背景下,江西省水稻生长季平均气温、平均最低气温和平均最高气温均呈升高趋势,引起双季稻生长季缩短,其中,营养生长期日数减少最明显,而生殖生长期延长;生长度日和高温度日均增加,低温度日减少.研究期间,江西省双季稻有效热量资源增加,低温风险减少,但高温风险增多;江西省水稻有效热量资源的空间变化特征表现为东北部的增幅大于西南部,南部的低温风险大于北部,中部的高温风险最大.     

Influence of Aspen on Forest Floor Properties in Black Spruce-dominated Stands

In the absence of fire in black spruce-feathermoss stands, a thick forest floor layer dominated by bryophytes and sphagnum accumulates. This layer is associated with wet, cool and nutrient-poor soil conditions conducive to the paludification process and pushing the ecosystem towards an unproductive open black spruce forest. The presence of Populus tremuloides in theses stands may halt this process because this species has a high nutrient cycling rate and a litter that represses moss cover. The main hypothesis of this study is that, despite similar abiotic conditions (slope and drainage), the presence of Populus tremuloides in a stand dominated by Picea mariana affects surface soil nutrient availability, total N, pH as well as the decomposition process. The abundance of Populus tremuloides trees was associated with higher exchangeable cations, cationic exchangeable capacity and pH of the forest floor layer on all sites. A decrease in organic matter thickness with increasing aspen presence was also found on all sites, suggesting that this species affects the decomposition process by the quality of its litter as well as by a general improvement of soil physical and chemical properties. The decomposition rate of a standard substrate as well as in vitro potential net nitrogen mineralization were positively related to Populus tremuloides on only one of the three sites, and non-significant on the other sites. Strong immobilization of added nitrogen during incubation was observed on all sites and was not related to aspen, which suggested that in these stands, the soil microbial community is uniformly and strongly nitrogen limited. The zone of influence of Populus tremuloides was evaluated in areas around the soil sampling plot ranging from 3 to 7 m. The results revealed that this zone varies with soil properties. The results suggest that the presence of Populus tremuloides accelerate nutrient cycling, which could affect stand productivity to some extent.