代谢组学信息获取与数据预处理瓶颈问题探讨

经过近15 年的快速发展,代谢组学已逐步成熟并渗透到生命科学和医学研究领域的各个层面。随着认识的不断深入,各种影响代谢组学研究的细节因素和技术瓶颈逐步被揭示。从生物样品采集与制备、原始数据采集、数据预处理和方法学验证等方面系统探讨了影响代谢组学研究的主要瓶颈问题,以期推动代谢组学研究的精细化和规范化发展。     

Bioinformatic Mining of Type I Microsatellites from Expressed Sequence Tags of Channel Catfish (<Emphasis Type="Italic">Ictalurus punctatus</Emphasis>)

Gene-derived markers are pivotal to the analysis of genome structure, organization, and evolution and necessary for comparative genomics. However, gene-derived markers are relatively difficult to develop. This project utilized the genomic resources of channel catfish expressed sequence tags (ESTs) to identify simple sequence repeats (SSRs), or microsatellites. It took the advantage of ESTs for the establishment of gene identities, and of microsatellites for the acquisition of high polymorphism. When microsatellites are tagged to genes, the microsatellites can then be used as gene markers. A bioinformatic analysis of 43,033 ESTs identified 4855 ESTs containing microsatellites. Cluster analysis indicated that 1312 of these ESTs fell into 569 contigs, and the remaining 3534 ESTs were singletons. A total of 4103 unique microsatellite-containing genes were identified. The dinucleotide CA/TG and GA/TC pairs were the most abundant microsatellites. AT-rich microsatellite types were predominant among trinucleotide and tetranucleotide microsatellites, consistent with our earlier estimation that the catfish genome is highly AT-rich. Our preliminary results indicated that the majority of the identified microsatellites were polymorphic and, therefore, useful for genetic linkage mapping of catfish. Mapping of these gene-derived markers is under way, which will set the foundation for comparative genome analysis in catfish.     

Cold shock injury and ecological costs of rapid cold hardening in the grain aphid Sitobion avenae (Hemiptera: Aphididae)

The ability of first instar nymphs and newly moulted pre-reproductive adults of the grain aphid S. avenae to rapidly cold harden was investigated. When nymphs reared at 20 degrees C were transferred directly to -8 degrees C for 3 h, there was 18% survival. This exposure was selected as the discriminating temperature. Maximum increases in survival were achieved by acclimating nymphs for 2 h at 0 degrees C and adults for 3 h at 0 degrees C, resulting in survival of 83% and 68%, respectively. Cooling nymphs from 10 to 0 degrees C at different rates (1, 0.1 and 0.05 degrees C min(-1)) also increased cold hardiness, with the slowest rate of 0.05 degrees C min(-1) conferring the highest survival following exposure to the discriminating temperature. Adult aphids also expressed a rapid cold hardening response but to a lesser extent, with survival increasing from 16% to 68% following 3 h at 0 degrees C. There were no 'ecological costs' associated with rapid cold hardening in terms of development, longevity or fecundity. The data support the hypothesis that rapid cold hardening can be induced during the cooling phase of natural diurnal temperature cycles, allowing insects to track daily changes in environmental temperatures.     

Analyzing a randomized trial on breast self-examination with noncompliance and missing outcomes

Recently, instrumental variables methods have been used to address non-compliance in randomized experiments. Complicating such analyses is often the presence of missing data. The standard model for missing data, missing at random (MAR), has some unattractive features in this context. In this paper we compare MAR-based estimates of the complier average causal effect (CACE) with an estimator based on an alternative, nonignorable model for the missing data process, developed by Frangakis and Rubin (1999, Biometrika, 86, 365-379). We also introduce a new missing data model that, like the Frangakis-Rubin model, is specially suited for models with instrumental variables, but makes different substantive assumptions. We analyze these issues in the context of a randomized trial of breast self-examination (BSE). In the study two methods of teaching BSE, consisting of either mailed information about BSE (the standard treatment) or the attendance of a course involving theoretical and practical sessions (the new treatment), were compared with the aim of assessing whether teaching programs could increase BSE practice and improve examination skills. The study was affected by the two sources of bias mentioned above: only 55% of women assigned to receive the new treatment complied with their assignment and 35% of the women did not respond to the post-test questionnaire. Comparing the causal estimand of the new treatment using the MAR, Frangakis-Rubin, and our new approach, the results suggest that for these data the MAR assumption appears least plausible, and that the new model appears most plausible among the three choices.     

甜菊不同杂交组合结实率及其F1代萌发和生长及对NaCl耐性的比较

以甜菊(Stevia rebaudiana Bertoni)的耐盐性较强品种‘中山3号’和‘守田2号’及R-A高含量品种‘中山4号’和‘守田3号’为亲本配置7个杂交组合并获得杂交种子,对种子结实率和发芽率及F1代幼苗的存活率进行统计分析,在此基础上采用砂培和水培方法比较了亲本及F1代扦插苗对NaCl胁迫的耐性.结果表明:品种间杂交组合的结实率均显著高于同系列品种间杂交及自交组合,其中‘守田2号’ב中山3号’杂交组合的结实率最高,为74.9％;7个杂交组合F1代的种子发芽率为63.8％ ～ 89.0％,差异明显;‘守田2号’ב中山4号’杂交组合F1代幼苗存活率相对较低(79.80％),其他杂交组合F1代幼苗存活率均在93％以上.砂培条件下,用100 mmol·L-1NaCl胁迫7d,各杂交组合F1代扦插苗的存活率差异不显著;随NaCl胁迫时间的延长各杂交组合F1代扦插苗的存活率均明显下降;胁迫28 d,‘守田2号’ב守田 3号’杂交组合以及‘中山3号’自交组合F1代扦插苗的存活率显著高于其他杂交组合.水培条件下,用100、150、200和250 mmol·L-1 NaCl胁迫14 d,‘守田2号’ב中山3号’、‘中山3号’ב守田2号’和‘中山3号’ב守田3号’3个杂交组合F1代扦插苗的存活率均显著高于其耐盐亲本及其他杂交组合.研究结果说明:通过杂交提高甜菊耐盐能力是可行的,而亲本的耐盐能力及亲本配置对杂交后代目标性状有较大影响;‘中山3号’ב守田2号’、‘守田2号’ב中山3号’和‘中山3号’ב守田3号’是耐盐性较强的甜菊优良杂交组合.     

Regeneration niche of three epiphytic species of Gesneriaceae from Chilean rainforests: implications for the evolution of growth habits in Coronanthereae

Ecological and evolutionary studies of the epiphytic growth habit in angiosperms are limited. In this article, we assess the relationship between growth habit and regeneration niche in Coronanthereae (Gesneriaceae) and discuss its implications for the evolution of epiphytism in this lineage. In the temperate rainforest of southern Chile, we quantified the vertical distribution and experimentally examined the regeneration niche of three endemic species of Coronanthereae. One species was a holoepiphyte, which was more frequent in the upper canopy, and two species were secondary hemiepiphytes, which decreased in abundance with tree height. Seed germination of the holoepiphyte was higher on tree bark substrates and under open canopy than on forest soil and in the shade. In contrast, seed germination of both secondary hemiepiphytes did not differ between substrates (bark vs. soil) or light conditions (light vs. shade). Seedling survival percentage of secondary hemiepiphytes was higher on forest soil and under a closed canopy, thus behaving as shade‐tolerant species. In turn, the holoepiphyte behaved as a shade‐intolerant species. The reconstruction of the ancestral growth habits and regeneration niches on the inferred phylogenetic tree of Coronanthereae revealed that the specialized regeneration niche of Sarmienta repens, characterized by requirements of shade intolerance and germination on tree bark, was coupled with the evolution of the holoepiphytic growth habit. We conclude that differentiation in the regeneration niche is a key process in the evolution of epiphytic growth habits in Coronanthereae. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 170 , 79–92.     

Snowy plover nest survival in Kansas and effective management to counter negative effects of precipitation

Snowy plovers (Charadrius nivosus) are a species of conservation concern throughout North America and listed as a threatened species in Kansas. Management to minimize the effects of flooding and predation were implemented at Kansas breeding sites in the 1980s to encourage reproductive success. However, the effectiveness of those strategies and the effect of other variables that may influence nest survival have not been formally assessed. We used Program MARK to model the daily survival rate (DSR) of 317 snowy plover nests with 14 habitat- and management-related covariates to identify factors that influence nest survival and examine the efficacy of current management practices. In 2005 and 2006, we monitored nests and collected habitat data at the 2 known breeding sites in Kansas, Quivira National Wildlife Refuge (NWR) and Cheyenne Bottoms Wildlife Area (WA). Overall DSR was greater at Quivira NWR in 2006 (0.954) than at Cheyenne Bottoms WA (0.917) and Quivira NWR (0.942) in 2005. We developed 88 candidate models of which 4 competing models (ΔAIC_c < 2) were identified. We selected the most parsimonious model (K = 14, w_i = 0.23) as the remaining 3 included covariates deemed biologically uninformative. This model included the effect of study site and year on a quadratic time trend, and included covariates quantifying nest age; precipitation; the proportion of gravel, rock, and vegetation at nests; occurrence within an electric fence and within 20 m of a road; occurrence on a human-constructed nest mound; and adult capture during incubation. We found a strong positive relationship between the use of nest mounds and DSR, and a strong negative relationship between precipitation and DSR. We also found a strong positive relationship between DSR and the proportion of vegetation at nest sites, the occurrence of a nest within an electric fence, and adult capture at a nest. We noted a strong negative relationship between DSR and occurrence within 20 m of a road. However, we found that DSR was not sensitive to the proportion of vegetation at a nest, occurrence within an electric fence or within 20 m of a road, and to adult capture at a nest in light of covariates quantifying precipitation and the use of nest mounds. We found weak support for a positive relationship between DSR, nest age, and the proportion of gravel and rock at nests. Our results indicate that large rainfall events are a major source of snowy plover nest loss in Kansas that can be mitigated by the construction of nest mounds. Limited influence of environmental variables found to influence nest survival at other breeding sites suggests that threats to snowy plover nest survival are site specific and managers should assess local sources of nest loss prior to implementing management strategies to improve reproductive success. © 2012 The Wildlife Society.     

Brain serotonin determines maternal behavior and offspring survival

Maternal care is an indispensable component of offspring survival and development in all mammals and necessary for reproductive success. Although brain areas regulating maternal behaviors are innervated by serotonergic afferents, very little is known about the role of this neurotransmitter in these behaviors. To evaluate the contribution of serotonin to maternal care, we used mice with a null mutation in the gene for tryptophan hydroxylase‐2 (TPH2), which results in a genetic depletion of brain serotonin, and tested them in a wide range of maternal behavior paradigms. We found that litters born to and reared by TPH2^?/? mothers showed decreased survival, lower weaning weights and increased cannibalization. In addition, TPH2^?/? mothers performed poorly in pup retrieval, huddling, nest construction and high‐arched back nursing. Aggression in TPH2^?/? dams was not triggered by lactation and was steadily high. Survival and weaning weight deficits of TPH2^?/? pups were rescued by cross‐fostering and in litters of mixed genotype (TPH2^?/? and TPH2^?/+). However, the maternal behaviors of TPH2^?/? dams did not improve when rearing either TPH2^+/+ pups or mixed‐genotype litters. In addition, TPH2^?/? pups significantly worsened the behavior of TPH2^+/+ dams with respect to cannibalism, weaning weight and latency to attack. Olfactory and auditory functions of TPH2^?/? females or anxiety‐like behaviors did not account for these maternal alterations as they were equal to their TPH2^+/+ counterparts. These findings illustrate a profound influence of brain serotonin on virtually all elements of maternal behavior and establish that TPH2^?/? pups can engender maladaptive mothering in dams of both genotypes.     

Spatial behaviour of sheep during the neonatal period: Preliminary study on the influence of shelter

Effective shelter has been demonstrated to reduce neonatal lamb mortality rates during periods of inclement weather. Periods of high wind speed and rainfall have been shown to influence shelter usage; however, it is not yet known how ewe factors such as breed, age and body condition score influence shelter-seeking behaviour. This study, conducted on a working upland farm in the UK, examined impact of artificial shelter on the biological and climatic factors that influence peri-parturient ewe behaviour. Pregnant ewes (n = 147) were randomly allocated between two adjacent fields which were selected for their similarity in size, topography, pasture management, orientation to the prevailing wind and available natural shelter. In one field, three additional artificial shelters were installed to increase the available shelter for ewes, this field was designated the Test field; no additional artificial shelter was provided in the second field which was used as the Control field. Individual ewes were observed every 2 h between 0800 and 1600 for 14 continuous days to monitor their location relative to shelter. Ewe breed (Aberfield and Highlander), age (2–8 years) and body condition score were considered as explanatory variables to explain flock and individual variance in shelter-seeking behaviour and the prevalence of issues which required the intervention of the shepherd, termed ‘shepherding problems’. Any ewe observed with dystocia, a dead or poor vigour lamb or who exhibited mismothering behaviour was recorded as a shepherding problem. The prevalence of these shepherding problems which necessitate human intervention represents arguably the most critical limiting factor for the successful management of commercial sheep flocks in outdoor lambing systems. Overall, ewes in the Test field with access to additional artificial shelter experienced fewer shepherding problems than those in the Control field (P < 0.05). A significant breed effect was also observed, with Highlander ewes more likely to seek shelter than Aberfield ewes (P < 0.001), and experiencing significantly fewer shepherding interventions (P < 0.05). These findings demonstrate the substantial and significant benefits to animal welfare and productivity that can be achieved through the provision of shelter in commercial, upland, outdoor lambing systems in the UK.     

Identification of immune-enhanced molecular subtype associated with BRCA1 mutations,immune checkpoints and clinical outcome in ovarian carcinoma

Ovarian carcinoma has the highest mortality among the malignant tumours in gynaecology, and new treatment strategies are urgently needed to improve the clinical status of ovarian carcinoma patients. The Cancer Genome Atlas (TCGA) cohort were performed to explore the immune function of the internal environment of tumours and its clinical correlation with ovarian carcinoma. Finally, four molecular subtypes were obtained based on the global immune-related genes. The correlation analysis and clinical characteristics showed that four subtypes were all significantly related to clinical stage; the immune scoring results indicated that most immune signatures were upregulated in C3 subtype, and the majority of tumour-infiltrating immune cells were upregulated in both C3 and C4 subtypes. Compared with other subtypes, C3 subtype had a higher BRCA1 mutation, higher expression of immune checkpoints, and optimal survival prognosis. These findings of the immunological microenvironment in tumours may provide new ideas for developing immunotherapeutic strategies for ovarian carcinoma.