A framework for exhaustively mapping functional missense variants

Although we now routinely sequence human genomes, we can confidently identify only a fraction of the sequence variants that have a functional impact. Here, we developed a deep mutational scanning framework that produces exhaustive maps for human missense variants by combining random codon mutagenesis and multiplexed functional variation assays with computational imputation and refinement. We applied this framework to four proteins corresponding to six human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin‐like modifier), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting maps recapitulate known protein features and confidently identify pathogenic variation. Assays potentially amenable to deep mutational scanning are already available for 57% of human disease genes, suggesting that DMS could ultimately map functional variation for all human disease genes.     

Uncertainty Analysis in Life Cycle Assessment (LCA): Case Study on Plant-Protection Products and Implications for Decision Making (9 pp + 3 pp)

Goal, Scope, and Background Uncertainty analysis in LCA is important for sound decision support. Nevertheless, the actual influence of uncertainty on decision making in specific LCA case-studies has only been little studied so far. Therefore, we assessed the uncertainty in an LCA comparing two plant-protection products.Methods Uncertainty and variability in LCI flows and characterization factors (CML-baseline method) were expressed as generic uncertainty factors and subsequently propagated into impact scores using Monte-Carlo simulation. Uncertainty in assumptions on production efficiency for chemicals, which is of specific interest for the case study, was depicted by scenarios. Results and Discussion Impact scores concerning acidification, eutrophication, and global warming display relatively small dispersions. Differences in median impact scores of a factor of 1.6 were sufficient in the case study for a significant distinction of the products. Results of toxicity impact-categories show large dispersions due to uncertainty in characterization factors and in the composition of sum parameters. Therefore, none of the two products was found to be significantly environmentally preferable to the other. Considering the case study results and inherent characteristics of the impact categories, a tentative rule of thumb is put forward that quantifies differences in impact scores necessary to obtain significant results in product comparisons.Conclusion Published LCA case-studies may have overestimated the significance of results. It is therefore advisable to routinely carry out quantitative uncertainty analyses in LCA. If this is not feasible, for example due to time restrictions, the rule of thumb proposed here may be helpful to evaluate the significance of results for the impact categories of global warming, acidification, eutrophication, and photooxidant creation.     

Clinical Significance of IgG Antibody Titer against Helicobacter pylori

Background: We clarified the clinical significance of measurement of IgG antibody titers against Helicobacter pylori using data from a nested case–control study from a large-scale cohort study in Japan.
Method: Participants included 36,745 subjects from the Japan Health Center-based Prospective Study who responded to the baseline questionnaire and provided a blood sample. Subjects were aged 40–69 years and were followed over 15 years after initial sampling. Controls were matched to 511 gastric cancer patients. Plasma surface antigen (Hp)-IgG titer was measured using ELISA, and mucosal atrophy was determined by measuring pepsinogen I and II levels.
Results: Seropositive subjects with low Hp-IgG titer and mucosal atrophy showed a higher risk for gastric cancer than high-titer subjects. Odds ratio (OR) referred to cases with true negative IgG titers and no mucosal atrophy. In moderately atrophic subjects, the low titer OR was 19.0, with a 95% confidence interval (CI) of 7.7–46.9, and 12.5 for high titer, with a 95% CI of 5.2–30.0. In severely atrophic subjects, the low titer OR was almost double that of high-titer subjects (OR = 30.2, 95% CI = 12.4–73.7 and OR = 15.9, 95% CI = 6.3–40.3, respectively). These associations were observed more frequently for differentiated than undifferentiated gastric cancer.
Conclusion: Combination assay with Hp-IgG titer and pepsinogens may help identify groups at high risk for gastric cancer. Subjects with low Hp-IgG titer and mucosal atrophy were at extremely high risk for gastric cancer, particularly differentiated cancer. Subjects with this background may require ongoing observation and periodic endoscopic examination for early cancer detection.     

Misprescription and misuse of one‐tailed tests

One‐tailed statistical tests are often used in ecology, animal behaviour and in most other fields in the biological and social sciences. Here we review the frequency of their use in the 1989 and 2005 volumes of two journals (Animal Behaviour and Oecologia), their advantages and disadvantages, the extensive erroneous advice on them in both older and modern statistics texts and their utility in certain narrow areas of applied research. Of those articles with data sets susceptible to one‐tailed tests, at least 24% in Animal Behaviour and at least 13% in Oecologia used one‐tailed tests at least once. They were used 35% more frequently with nonparametric methods than with parametric ones and about twice as often in 1989 as in 2005. Debate in the psychological literature of the 1950s established the logical criterion that one‐tailed tests should be restricted to situations where there is interest only in results in one direction. ‘Interest’ should be defined; however, in terms of collective or societal interest and not by the individual investigator. By this ‘collective interest’ criterion, all uses of one‐tailed tests in the journals surveyed seem invalid. In his book Nonparametric Statistics, S. Siegel unrelentingly suggested the use of one‐tailed tests whenever the investigator predicts the direction of a result. That work has been a major proximate source of confusion on this issue, but so are most recent statistics textbooks. The utility of one‐tailed tests in research aimed at obtaining regulatory approval of new drugs and new pesticides is briefly described, to exemplify the narrow range of research situations where such tests can be appropriate. These situations are characterized by null hypotheses stating that the difference or effect size does not exceed, or is at least as great as, some ‘amount of practical interest’. One‐tailed tests rarely should be used for basic or applied research in ecology, animal behaviour or any other science.     

An Ion-channel Modulator from the Saliva of the Brown Ear Tick has a Highly Modified Kunitz/BPTI Structure

Ra-KLP, a 75 amino acid protein secreted by the salivary gland of the brown ear tick Rhipicephalus appendiculatus has a sequence resembling those of Kunitz/BPTI proteins. We report the detection, purification and characterization of the function of Ra-KLP. In addition, determination of the three-dimensional crystal structure of Ra-KLP at 1.6 Å resolution using sulphur single-wavelength anomalous dispersion reveals that much of the loop structure of classical Kunitz domains, including the protruding protease-binding loop, has been replaced by β-strands. Even more unusually, the N-terminal portion of the polypeptide chain is pinned to the ”Kunitz head” by two disulphide bridges not found in classical Kunitz/BPTI proteins. The disulphide bond pattern has been further altered by the loss of the bridge that normally stabilizes the protease-binding loop. Consistent with the conversion of this loop into a β-strand, Ra-KLP shows no significant anti-protease activity; however, it activates maxiK channels in an in vitro system, suggesting a potential mechanism for regulating host blood supply during feeding.     

Obligate costs of parental care to offspring: egg brooding-induced hypoxia creates smaller, slower and weaker python offspring

Python egg brooding typifies parental care because it consists of multiple behaviours that provide for multiple developmental needs. For example, tightly coiling around the eggs benefits embryonic water balance, but periodic female postural adjustments improve embryonic gas exchange. Regardless of these postural adjustments, egg brooding creates a hypoxic intra-clutch environment that constrains embryonic metabolism. We further examined this novel and useful parental care model to determine: (1) any fitness-related costs of egg brooding to offspring; (2) whether any long-term costs are alleviated by postural adjustments. We artificially incubated Children's python ( Antaresia childreni ) clutches and modulated oxygen partial pressure ( P O₂) to create three treatments: normoxic (NRM, 20.3 kPa O₂), brooding [BRD, P O₂ profile typical of clutch P O₂ ( P O_2clutch) in maternally brooded clutches, 15.8–19.3 kPa O₂] and low (LOW, predicted P O₂ profile of maternally brooded P O_2clutch if females did not make postural adjustments, 14.4–18.6 kPa O₂). Using various metrics from ∼12 days pre-hatching to 14 days post-hatching, we demonstrated that NRM offspring were larger, faster and stronger than BRD offspring. As only hatchling heart mass differed between BRD and LOW treatments (LOW > BRD), postural adjustments may not alleviate hypoxia-related costs to embryos. Our results demonstrate that parental care may represent a compromise between competing developmental needs and thus entails obligate costs to the offspring.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 414–421.     

潘氏细胞研究进展

潘氏细胞是位于小肠腺底部的浆液性腺上皮细胞,其主要特征是细胞顶部有大量粗大的嗜酸性分泌颗粒,内含防御素、溶菌酶、sIgA等多种抗菌物质。表达于潘氏细胞的NOD2、Toll样受体9、肝癌-肠-胰腺／胰腺炎相关蛋白、RegⅢγ、肿瘤坏死因子仅、粒细胞-巨噬细胞集落刺激因子、白介素-17等也是免疫与炎症反应的重要成分。金属硫蛋白、富半胱氨酸肠蛋白、潘氏细胞锌结合蛋白等金属结合蛋白均分布于潘氏细胞,提示潘氏细胞参与金属代谢。潘氏细胞是构成肠黏膜屏障的重要细胞成分。NOD2单核苷酸多态性与克罗恩病有关。潘氏细胞化生常发生于胃、大肠的炎症与肿瘤病变,其病理意义有待于进一步研究。     

中国黄耆属簇毛黄耆亚属的叶表皮特征及其系统学意义

在光学显微镜和扫描电镜下,观察了国产黄耆属簇毛黄耆亚属16种1变种的叶表皮特征。结果表明,气孔器在各种植物的上、下表皮均有分布,多为无规则型,也有不等细胞型;叶表皮细胞形状有不规则形与多边形,表皮细胞垂周壁有平直、浅波状、波状或深波状。叶表皮细胞形状与垂周壁的式样可以分为四种类型,这四种类型与亚属的分组有一定的对应关系。在扫描电镜下可见表皮细胞上有角质层,气孔下陷,气孔的外拱盖及其内缘特征在亚属内都比较一致。表皮细胞角质层的纹饰在个别类群中有一定的变异,对种类的鉴定有一定的意义。