Ecology,morphology and physiology of Chroothece richteriana (Rhodophyta,Stylonematophyceae) in the highly calcareous Río Chícamo,south-east Spain

The ecology of Chroothece was studied in the highly calcareous Río Chícamo, south-east Spain, in order to explain its success there, but rarity elsewhere. The river, which originates mainly from an underground aquifer, has water with high conductivity, sulphate and nitrate but low phosphate concentrations, the latter mainly organic. Chroothece occurs in mats and in lobed colonies reaching 4 cm in the broadest dimension. The colony surface consists of one layer of cells, each of which is attached to a stalk, which dichotomizes when the cell divides; stalks often extend to the colony base. The central region of many mat cells and almost all colony cells has a yellow to orange-brown colour, associated with the numerous lipid droplets densely covering the surface of the pyrenoid and arms of the star-shaped chloroplast. Field material and laboratory isolates indicate that stalk formation occurs under moderate P limitation and both stalks and cell sheath show high phosphatase activities. This also occurred in a culture collection strain maintained for 30 years in a very P-rich medium, but then transferred to a moderately P-limiting medium (c. 0.9 mg l^?1). We suggest that colony formation is initiated by aggregation of motile cells following P pulses in the water. Comparisons are made with Rivularia, a competitor in this nitrate-rich river, in spite of being a N₂-fixer. One difference is that Chroothece cells lie at the periphery of the colonies and are therefore exposed to maximum sunlight, whereas Rivularia trichomes grow inside colonies with photoprotection by scytonemin. However, the ability to withstand heavy grazing pressure may be an especially important factor favouring Rivularia here.     

Logistic regression when covariates are random effects from a non‐linear mixed model

In many studies, the association of longitudinal measurements of a continuous response and a binary outcome are often of interest. A convenient framework for this type of problems is the joint model, which is formulated to investigate the association between a binary outcome and features of longitudinal measurements through a common set of latent random effects. The joint model, which is the focus of this article, is a logistic regression model with covariates defined as the individual‐specific random effects in a non‐linear mixed‐effects model (NLMEM) for the longitudinal measurements. We discuss different estimation procedures, which include two‐stage, best linear unbiased predictors, and various numerical integration techniques. The proposed methods are illustrated using a real data set where the objective is to study the association between longitudinal hormone levels and the pregnancy outcome in a group of young women. The numerical performance of the estimating methods is also evaluated by means of simulation.     

实验小鼠种群管理（英文）

2009年11月份在西安举行由中国实验动物学会发起的实验动物医药技术培训研讨会上,本人做了关于实验小鼠种群管理的演讲。其主题涵盖了小鼠繁殖性能的维护和基因工程种群的管理。本篇文章的目的在于强调其所涵盖的材料并为进一步研究提供参考。如若对本文所讨论的内容希望有更深刻的理解,这篇文章所引用的参考资料值得进一步的阅读。另外本文未涉及远交系小鼠的繁殖培育和基因管理,但如有需要可以联系本文作者,可推荐需阅读的材料清单。     

C1188D mutation abolishes specific recognition between MLL1-CXXC domain and CpG site by inducing conformational switch of flexible N-terminal

Mixed lineage leukemia protein (MLL1 protein) recognizes the CpG site via its CXXC domain and is frequently associated with leukemia. The specific recognition is abolished by C1188D mutation, which also prevents MLL-related leukemia. In this paper, multiple molecular dynamic (MD) simulations were performed to investigate the mechanism of recognition and influences of C1188D mutation. Started from fully dissociated DNA and MLL1-CXXC domain, remarkably, the center of mass (COM) of MLL1-CXXC domain quickly concentrates on the vicinity of the CpG site in all 53 short MD simulations. Extended simulations of the wild type showed that the native complex formed in 500 ns among 4 of 53 simulations. In contrast, the C1188D mutant COM distributed broadly around the DNA and the native complex was not observed in any of the extended simulations. Simulations on the apo MLL1-CXXC domain further suggest that the wild type protein remained predominantly in an open form that closely resembles its structure in the native complex whereas C1188D mutant formed predominantly compact structures in which the N- terminal bends to D1188. This conformational switch hinders the formation of encounter complex, thus abolishes the recognition. Our study also provides clues to the study mechanism of recognition, by the CXXC domain from proteins like DNA methyltransferase and ten-eleven translocation enzymes.     

Joint generalized models for multidimensional outcomes: A case study of neuroscience data from multimodalities

This paper is motivated from the analysis of neuroscience data in a study of neural and muscular mechanisms of muscle fatigue. Multidimensional outcomes of different natures were obtained simultaneously from multiple modalities, including handgrip force, electromyography (EMG), and functional magnetic resonance imaging (fMRI). We first study individual modeling of the univariate response depending on its nature. A mixed‐effects beta model and a mixed‐effects simplex model are compared for modeling the force/EMG percentages. A mixed‐effects negative‐binomial model is proposed for modeling the fMRI counts. Then, I present a joint modeling approach to model the multidimensional outcomes together, which allows us to not only estimate the covariate effects but also to evaluate the strength of association among the multiple responses from different modalities. A simulation study is conducted to quantify the possible benefits by the new approaches in finite sample situations. Finally, the analysis of the fatigue data is illustrated with the use of the proposed methods.     

Cinnamic acid 4-hydroxylase from gherkin tissues

Homogenates from 4-day-old gherkin cotyledons and hypocotyls fractionated by sucrose density gradient centrifugation contain cinnamic acid 4-hydroxylase activity, the activity being highest in the endoplasmic reticulum fractions. These fractions also contain very low concentrations of cytochrome P₄₅₀. Hydroxylase activity is dependent on NADPH and on molecular oxygen, is optimal at pH 7.5 and is inhibited by carbon monoxide. The enzyme is very sensitive to inhibition by 2-mercaptoethanol, but it is not inhibited by the product, p-coumaric acid. Further, its responses to various potential inhibitors are fairly typical of mixed function oxidases from other sources.     

鼎湖山马尾松、荷木混交林生态系统碳素积累和分配特征

选取鼎湖山保护区3个马尾松9Pinus massoniana),荷木（Schima superba)针阔混交林样地,研究其生态系统的碳素积累和分配特征。结果表明,鼎湖山马尾松,荷木混交林乔木尾生物量（thm^-2)为：174.41-270.11。平均227.36,且均以马尾松的生物量居多（占54.9%-84.4%)。林下层植物生物量和地表现存凋落物量（thm^-2)分别为7.41-28.28和7.06-11.56。平均14.41和9.03。三个混交林生态系统总碳贮量（thm^-2)分别为146.35,215.30和205.79。平均为189.15,其中植被层碳贮量贡献率最大,依次占62.9%,61.9%和69.9%。平均65.0%;土壤层贡献率次之,依次占34.3%,35.5%和28.5%。平均32.8%;而地表现存凋落物层的贡献最小,仅占2.8%,2.6%和1.6%。平均为2.3%。此外,本文还对该生态系统植被碳吸存潜力进行了讨论。     

Joint Variable Selection for Fixed and Random Effects in Linear Mixed‐Effects Models

Summary It is of great practical interest to simultaneously identify the important predictors that correspond to both the fixed and random effects components in a linear mixed‐effects (LME) model. Typical approaches perform selection separately on each of the fixed and random effect components. However, changing the structure of one set of effects can lead to different choices of variables for the other set of effects. We propose simultaneous selection of the fixed and random factors in an LME model using a modified Cholesky decomposition. Our method is based on a penalized joint log likelihood with an adaptive penalty for the selection and estimation of both the fixed and random effects. It performs model selection by allowing fixed effects or standard deviations of random effects to be exactly zero. A constrained expectation–maximization algorithm is then used to obtain the final estimates. It is further shown that the proposed penalized estimator enjoys the Oracle property, in that, asymptotically it performs as well as if the true model was known beforehand. We demonstrate the performance of our method based on a simulation study and a real data example.