兰科植物microRNA的研究进展

microRNA (miRNA)是一类广泛存在的非编码小分子RNA,在植物的生长发育和应激反应等过程中起到重要的调控作用.本文从miRNA在植物中的作用机制出发,对近10年来兰科植物各属miRNA的鉴定、几类miRNA的具体功能及miRNA的其他相关技术研究进行综述,以期为兰科植物小分子RNA的功能作用及调控网络解析提...     

Minimizing model fitting objectives that contain spurious local minima by bootstrap restarting

Objective functions that arise when fitting nonlinear models often contain local minima that are of little significance except for their propensity to trap minimization algorithms. The standard methods for attempting to deal with this problem treat the objective function as fixed and employ stochastic minimization approaches in the hope of randomly jumping out of local minima. This article suggests a simple trick for performing such minimizations that can be employed in conjunction with most conventional nonstochastic fitting methods. The trick is to stochastically perturb the objective function by bootstrapping the data to be fit. Each bootstrap objective shares the large-scale structure of the original objective but has different small-scale structure. Minimizations of bootstrap objective functions are alternated with minimizations of the original objective function starting from the parameter values with which minimization of the previous bootstrap objective terminated. An example is presented, fitting a nonlinear population dynamic model to population dynamic data and including a comparison of the suggested method with simulated annealing. Convergence diagnostics are discussed.     

Estimating equations with nonignorably missing response data

Troxel, Lipsitz, and Brennan (1997, Biometrics 53, 857-869) considered parameter estimation from survey data with nonignorable nonresponse and proposed weighted estimating equations to remove the biases in the complete-case analysis that ignores missing observations. This paper suggests two alternative modifications for unbiased estimation of regression parameters when a binary outcome is potentially observed at successive time points. The weighting approach of Robins, Rotnitzky, and Zhao (1995, Journal of the American Statistical Association 90, 106-121) is also modified to obtain unbiased estimating functions. The suggested estimating functions are unbiased only when the missingness probability is correctly specified, and misspecification of the missingness model will result in biases in the estimates. Simulation studies are carried out to assess the performance of different methods when the covariate is binary or normal. For the simulation models used, the relative efficiency of the two new methods to the weighting methods is about 3.0 for the slope parameter and about 2.0 for the intercept parameter when the covariate is continuous and the missingness probability is correctly specified. All methods produce substantial biases in the estimates when the missingness model is misspecified or underspecified. Analysis of data from a medical survey illustrates the use and possible differences of these estimating functions.     

Serum-free cryopreservation of porcine hepatocytes

The use of porcine hepatocytes in xenotransplantation, bioartificial liver support or pharmacological approaches demands serum-free cryopreservation protocols yielding high quality, viable, functional hepatocytes. Here, primary porcine hepatocytes were frozen without serum in liquid nitrogen by the use of a computer-assisted freezing device. After thawing, more than 90% of the initial hepatocytes were lost, in part because of damage to genomic DNA. When cryoprotectants were used, the loss was lowered to 70% of the initial cell number; 90% of the remaining cells excluded trypan blue indicating a high degree of viability. Cells were seeded serum-free onto collagen-coated plastic dishes to determine proliferation and retainment of specific functions representing prominent features of hepatocytes in vivo. Whereas no cells adhered to the substratum effectively in conventional culture medium, the addition of conditioned medium derived from hepatic non-parenchymal cells improved attachment. Cells proliferated, retained hepatocyte-specific functions, such as urea production and cytochrome P450 activity, and expressed liver-specific genes to levels observed in non-cryopreserved hepatocytes. Thus, serum-free cryopreserved primary porcine hepatocytes may serve as a valid source of cells for downstream applications. The cells seem to function adequately when an appropriate environment is chosen for recovery after cryopreservation, an ultimate demand for the clinical application of human hepatocytes.     

Permanence of single-species stage-structured models

In this paper, we consider population survival by using single-species stage-structured models. As a criterion of population survival, we employ the mathematical notation of permanence. Permanence of stage-structured models has already been studied by Cushing (1998). We generalize his result of permanence, and obtain a condition which guarantees that population survives. The condition is applicable to a wide class of stage-structured models. In particular, we apply our results to the Neubert-Caswell model, which is a typical stage-structured model, and obtain a condition for population survival of the model.The research is partially supported by the Ministry of Education, Science and Culture, Japan, under Grant in Aid for Scientific Research (A) 13304006.     

The biological clock: the bodyguard of temporal homeostasis

In order for any organism to function properly, it is crucial that it be table to control the timing of its biological functions. An internal biological clock, located, in mammals, in the suprachiasmatic nucleus of the hypothalamus (SCN), therefore carefully guards this temporal homeostasis by delivering its message of time throughout the body. In view of the large variety of body functions (behavioral, physiological, and endocrine) as well as the large variety in their preferred time of main activity along the light:dark cycle, it seems logical to envision different means of time distribution by the SCN. In the present review, we propose that even though it presents a unimodal circadian rhythm of general electrical and metabolic activity, the SCN seems to use several sorts of output connections that are active at different times along the light: dark cycle to control the rhythmic expression of different body functions. Although the SCN is suggested to use diffusion of synchronizing factors in the rhythmic control of behavioral functions, it also needs neuronal connections for the control of endocrine functions. The distribution of the time-of-day message to neuroendocrine systems is either directly onto endocrine neurons or via intermediate neurons located in specific SCN targets. In addition, the SCN uses its connections with the autonomic nervous system for spreading its time-of-day message, either by setting the sensitivity of endocrine glands (i.e., thyroid, adrenal, ovary) or by directly controlling an endocrine output (i.e., melatonin synthesis). Moreover, the SCN seems to use different neurotransmitters released at different times along the light: dark cycle for each of the different connection types presented. Clearly, the temporal homeostasis of endocrine functions results from a diverse set of biological clock outputs.     

Diversity of arbuscular mycorrhizal fungi colonising roots of the grass species<Emphasis Type="Italic"> Agrostis capillaris</Emphasis> and<Emphasis Type="Italic"> Lolium perenne</Emphasis> in a field experiment

Analysis of arbuscular mycorrhizal (AM) fungal diversity through morphological characters of spores and intraradicular hyphae has suggested previously that preferential associations occur between plants and AM fungi. A field experiment was established to investigate whether AM fungal diversity is affected by different host plants in upland grasslands. Indigenous vegetation from plots in an unimproved pasture was replaced with monocultures of either Agrostis capillaris or Lolium perenne. Modification of the diversity of AM fungi in these plots was evaluated by analysis of partial sequences in the large subunit (LSU) ribosomal RNA (rDNA) genes. General primers for AM fungi were designed for the PCR amplification of partial sequences using DNA extracted from root tissues of A. capillaris and L. perenne. PCR products were used to construct LSU rDNA libraries. Sequencing of randomly selected clones indicated that plant roots were colonised by AM fungi belonging to the genera Glomus, Acaulospora and Scutellospora. There was a difference in the diversity of AM fungi colonising roots of A. capillaris and L. perenne that was confirmed by PCR using primers specific for each sequence group. These molecular data suggest the existence of a selection pressure of plants on AM fungal communities.     

Endemic flora biodiversity in the south of the Iberian Peninsula: altitudinal distribution,life forms and dispersal modes

The south of the Iberian Peninsula, with an altitudinal range varying from sea level to 3482m and annual average rainfall ranging from 206 to 2223mm, has 516 vascular endemic species or subspecies, that is, an endemicity rate of 13%. This survey deals with parameters such as species richness, originality, life forms and dispersal modes of these plants, in relation to altitudinal and rainfall gradients. Although most of the endemic plants occur between 600 and 1400m a.s.l. and in the range of 600–1000mm annual average rainfall, floristic originality (rate of endemic taxa per area unit) increases exponentially with altitude. The biological spectrum of this endemic flora does not follow the usual patterns observed either in local floras in the south of the Iberian Peninsula or in other regions of the Mediterranean Basin. Chamaephytes (46.08%) and hemicryptophytes (31.37%) are very abundant, whereas therophytes (11.96%) and phanerophytes (0.98%) are comparatively rare. There is a statistically significant correlation between life form and both altitudinal and rainfall gradients. Chamaephytes reach their highest density rates within 1400–2000m a.s.l., but these records tend to decrease as rainfall rates increase. Abundance of hemicryptophytes is directly dependent on rainfall rates and inversely dependent on temperature. The altitudinal distribution pattern of therophytes is opposite to that of hemicryptophytes, but there is no clear correlation as far as rainfall gradient is concerned. Considering both the endemic plants as a whole and each of the life form groups, the relationships between the dispersal modes used and the altitudinal and rainfall gradients are analysed. Up to 44.51% of the endemic plants do not present evident adaptations to promote the dispersion of their diaspores. However, only in the group of therophytes, whose occurrence is positively related to areas of minor altitude, does this difficulty of dispersion play a significant role in the maintenance of stenochory.     

Slight differences among individuals and the unified neutral theory of biodiversity

The unified neutral theory of biodiversity provides a very simple and counterintuitive explanation of species diversity patterns. By specifying speciation, community size and dispersal, and completely ignoring differences among individual organisms and species, it generates biodiversity patterns that remarkably resemble natural ones. Here I show that adding even slight differences among organisms generates very different patterns and predictions. In large communities with widespread dispersal, heritable differences in viability among individual organisms lead to biodiversity patterns characterised by the overdominance of a single species comprising organisms with relatively high fitness. In communities with local dispersal, the same differences produce rapid community extinction. I conclude that the unified neutral theory is not robust to slight deviations from its most controversial assumption.     

Evaluation of Prey-Stage Preference as an Indicator of Life-Style Type in Phytoseiid Mites

Discriminant analysis (DA) models were developed and applied to examine the use of prey-stage preference (Tetranychus urticae Koch egg versus larval prey) in the classification of phytoseiid mites into life-style types. Prey-stage preferences and developmental times when preying on T. urticae, and relative ovipositional rates on six food categories were determined for four phytoseiid species occurring on apple in central and eastern Oregon, USA: Galendromus flumenis (Chant), Galendromus occidentalis (Nesbitt), Metaseiulus citri (Garman and McGregor) and Typhlodromus caudiglans Schuster. In terms of all three aspects studied, the phytoseiid species showed a consistent polarization of G. occidentalis < or = G. flumenis < or = T. caudiglans < M. citri. Specifically, G. occidentalis ('The Dalles' strain) had a significant preference for eggs, G. flumenis had no preference, and T. caudiglans and M. citri had significant preferences for larvae; G. occidentalis had the shortest developmental time, followed by G. flumenis and T. caudiglans, while M. citri had the longest developmental time; and diet breadth was most narrow for G. occidentalis and progressively broader from G. flumenis, T. caudiglans through M. citri, which was able to sustain oviposition on the broadest range of prey and pollens. Species were classified somewhat differently depending on which traits were considered in a given DA. Prey-stage preference was not included as an indicator in the parsimonious DA model when all species and all traits were considered, but in general this trait performed well as an indicator alone (single-trait DA) and somewhat improved the classifications of multitrait discriminant analyses.