Random chemical mutagenesis of a specific psbDI region coding for a lumenal loop of the D2 protein of photosystem II in Synechocystis sp. PCC 6803

To identify amino acid residues of the D2 protein that are critical for functional photosystem II (PS II), sodium bisulfite was utilized for in vitro random mutagenesis of the psbDI gene from Synechocystis sp. PCC 6803. Sodium bisulfite reacts specifically with cytosine in single-stranded regions of DNA and does not attack double-stranded DNA. Using a hybrid plasmid that was single-stranded in the region to be mutagenized and that was double-stranded elsewhere, mutations were targeted to a specific psbDI region coding for the lumenal A-B loop of the D2 protein. Several mutants were isolated with a total of 15 different amino acid changes in the loop. The majority of these mutations did not result in a loss of photoautotrophic growth or in significantly altered PS II function. However, mutation of Glu-69 to Lys, Ser-79 to Phe, and Ser-88 to Phe were found to influence photosystem II activity; the importance of the latter two residues for proper PS II function was unexpected. Cells carrying the double mutation S79F/S88F in D2 did not grow photoautotrophically and had no functionally active PS II centers. The single mutant S79F was also incapable of photoautrophic growth, but displayed reasonably stable oxygen evolution, while PS II function in the single mutant S88F appeared to be close to normal. Because of the more pronounced phenotype of the S79F/S88F strain as compared to the single mutants, both Ser residues appear to affect stable assembly and function of the PS II complex. The mechanism by which the S79F mutant loses photoautotrophic growth remains to be established. However, these results show the potential of targeted random mutagenesis to identify functionally important residues in selected regions of proteins.     

Patterns of variation among forests of tropical Asian mountains,with some explanatory hypotheses

Decline in mean temperature with elevation correlates with a more or less gradual change in forest floristics mediated by minimum temperature tolerances and competition, and in its diversity, well documented on wet equatorial mountains. On the mountains of monsoon tropical Asia, the predominance of a single wet and dry season offers opportunity to relate increasing cloud and rainfall seasonality with a departure in a zonation most clearly recognised on equatorial mountains. Observations indicate that the lowland to lower montane forest transition is gradual and constant in elevation throughout the monsoon tropical Asia region, and contrasts with the variable elevation at which forest structure and physiognomy, alternatively floristics alone, changes between lower and upper equatorial montane forests. Both ecotones are observed to correlate with the elevation and seasonality at which decline in temperature daily results in condensation of water vapour into cloud, resulting in cloud shadow, and fog therefore water supply where cloud penetrates the canopy. Seasonal variation in these climatic interactions influence forest structure and physiognomy and, by mediating the interaction between vegetation and substrate, also leads to zonation in soils and consequently floristics. Historical biogeographical factors also influence zonal floristics.     

2002-2018年滇池外海蓝藻水华暴发时空变化特征及其驱动因子

为弄清滇池外海蓝藻水华暴发时空变化规律及其影响因素,将滇池外海分为北、中、南3个区域,基于2002—2018年期间中分辨率成像光谱仪(MODIS)反演的水华面积,分析了上述3个区域蓝藻水华的时空变化特征。基于2007—2018年水文、气象和出入流数据,构建了外海三维水动力生态模型(AEM3D),并计算了各区域的水力滞留时间。通过冗余分析(RDA)、随机森林(RF)和斯皮尔曼相关分析方法,分析了影响以上区域蓝藻水华暴发的主要驱动因子。结果表明：2002—2018年期间,整个滇池外海区域年平均水华面积比(水华面积占该区域总面积比例)呈缓慢下降趋势,空间上由北向南依次递减,整个外海水华暴发面积最大主要发生在秋季。在外海北部区域,其东部水华较西部更为严重,而在中部和南部区域,呈现西部水华较东部更为严重的空间分布模式。通过对各影响因子的统计分析发现,风速、水温和日照时长是上述各区域中蓝藻水华暴发的主要决定性因素。水华暴发期间以西南风为主导风向,且上述区域的水华面积比随风速增加呈下降趋势。在外海各区域,水力滞留时间与水华暴发面积均呈显著正相关,空间上水力滞留时间由北向南逐渐增大,风速和风向是影响蓝...     

Age and Growth Patterns of Brazil Nut Trees (Bertholletia excelsa Bonpl.) in Amazonia,Brazil

Various techniques have been used to estimate the age of Brazil nut trees (Bertholletia excelsa Bonpl.), but these techniques produce large discrepancies. Here, we first verified that two individuals of known ages from a plantation in central Amazonia, Brazil, have a congruent number of growth rings. The indexed average tree‐ring curve was significantly correlated with total precipitation during the rainy season (November–June) over a 50‐yr period, confirming the annual nature of the tree rings. Second, we analyzed Brazil nut trees from two populations in the Trombetas (eastern Amazon) and Purus (central Amazon) regions, performing tree‐ring analysis to estimate tree age and diameter increment rates. We compared age–diameter relationships, mean passage time through 10‐cm diameter size classes, and growth trajectories of individual trees. The maximum age of Brazil nut trees analyzed was 361 yr in the Purus and 401 yr in the Trombetas. Trees at the Purus site had higher mean diameter increment rates and showed more variation compared to trees at the Trombetas site. Individual growth trajectories show that the majority of trees attained the canopy by direct growth, while a smaller number passed through one release or one suppression event before becoming established in the canopy. None of the trees passed through multiple release and suppression events. The age estimations presented here are comparable to previous tree‐ring analyses for the species, and the observed growth patterns support earlier work indicating B. excelsa as a gap‐dependent tree species.     

Selection of biologically active peptides by phage display of random peptide libraries

Random peptide libraries displayed on phage are used as a source of peptides for epitope mapping, for the identification of critical amino acids responsible for protein—protein interactions and as leads for the discovery of new therapeutics. Efficient and simple procedures have been devised to select peptides binding to purified proteins, to monoclonal and polyclonal antibodies and to cell surfaces in vivo and in vitro.     

Estimation of competing risks with general missing pattern in failure types

In competing risks data, missing failure types (causes) is a very common phenomenon. In this work, we consider a general missing pattern in which, if a failure type is not observed, one observes a set of possible types containing the true type, along with the failure time. We first consider maximum likelihood estimation with missing-at-random assumption via the expectation maximization (EM) algorithm. We then propose a Nelson-Aalen type estimator for situations when certain information on the conditional probability of the true type given a set of possible failure types is available from the experimentalists. This is based on a least-squares type method using the relationships between hazards for different types and hazards for different combinations of missing types. We conduct a simulation study to investigate the performance of this method, which indicates that bias may be small, even for high proportion of missing data, for sufficiently large number of observations. The estimates are somewhat sensitive to misspecification of the conditional probabilities of the true types when the missing proportion is high. We also consider an example from an animal experiment to illustrate our methodology.     

Numerical equivalence of imputing scores and weighted estimators in regression analysis with missing covariates

Imputation, weighting, direct likelihood, and direct Bayesian inference (Rubin, 1976) are important approaches for missing data regression. Many useful semiparametric estimators have been developed for regression analysis of data with missing covariates or outcomes. It has been established that some semiparametric estimators are asymptotically equivalent, but it has not been shown that many are numerically the same. We applied some existing methods to a bladder cancer case-control study and noted that they were the same numerically when the observed covariates and outcomes are categorical. To understand the analytical background of this finding, we further show that when observed covariates and outcomes are categorical, some estimators are not only asymptotically equivalent but also actually numerically identical. That is, although their estimating equations are different, they lead numerically to exactly the same root. This includes a simple weighted estimator, an augmented weighted estimator, and a mean-score estimator. The numerical equivalence may elucidate the relationship between imputing scores and weighted estimation procedures.     

Increasing liana abundance and biomass in tropical forests: emerging patterns and putative mechanisms

Tropical forests are experiencing large-scale structural changes, the most apparent of which may be the increase in liana (woody vine) abundance and biomass. Lianas permeate most lowland tropical forests, where they can have a huge effect on tree diversity, recruitment, growth and survival, which, in turn, can alter tree community composition, carbon storage and carbon, nutrient and water fluxes. Consequently, increasing liana abundance and biomass have potentially profound ramifications for tropical forest composition and functioning. Currently, eight studies support the pattern of increasing liana abundance and biomass in American tropical and subtropical forests, whereas two studies, both from Africa, do not. The putative mechanisms to explain increasing lianas include increasing evapotranspirative demand, increasing forest disturbance and turnover, changes in land use and fragmentation and elevated atmospheric CO?. Each of these mechanisms probably contributes to the observed patterns of increasing liana abundance and biomass, and the mechanisms are likely to be interrelated and synergistic. To determine whether liana increases are occurring throughout the tropics and to determine the mechanisms responsible for the observed patterns, a widespread network of large-scale, long-term monitoring plots combined with observational and manipulative studies that more directly investigate the putative mechanisms are essential.     

高黎贡山土壤微生物生态分布及其生化特性的研究

研究了高黎贡山东坡不同海拔高度的自然林、不同海拔高度和人为干扰强度的集体林、不同权属森林和不同土地利用类型土壤微生物数量及某些生化特性。结果表明,在高黎贡山上半部,自然林随海拔降低,土壤微生物数量及活性升高。而下半部,集体林随海拔降低,人为干扰强度和频率增加,土壤微生物数量和活性降低;森林权属从国有集体个人,土壤微生物数量及活性降低;森林被纯林替代后,土壤微生物数量及活性迅速降低,但耕作通常更有利于微生物繁殖。高黎贡山中部(海拔2000m左右)的自然植被下土壤微生物含量丰富且活性较高,但海拔高气温低不利于土壤微生物生长繁殖及进行生物化学变化。另一方面,森林植被的过份砍伐和利用也使土壤微生物数量和活性降至较低水平。     

Impact of global warming on the tree species composition of boreal forests in Finland and effects on emissions of isoprenoids

This study aims to identify how climate change may influence total emissions of monoterpene and isoprene from boreal forest canopies. The whole of Finland is assumed to experience an annual mean temperature (T) increase of 4 °C and a precipitation increase of 10% by the year 2100. This will increase forest resources throughout the country. At the same time, the proportions of Scots pine (Pinus sylvestris) and Norway spruce (Picea abies) in southern Finland (60°≤ latitude < 65°N) will be reduced from the current 40–50% to less than 10–20%, with increased dominance of birches (Betula pendula and Betula pubescens). In northern Finland (65°≤ latitude < 70°N), the proportions of Norway spruce and Scots pine will be balanced at a level of about 40% as the result of an increase in Norway spruce from the current 21% to 37% and a concurrent reduction in Scots pine from 63% to 40%. The proportion of birches is predicted to increase from the current 17% to 23%, but these will become the dominant species only on the most fertile sites. Total mean emissions of monoterpene by Scots pine will be reduced by 80% in southern Finland, but will increase by 62% in the north. Emissions from Norway spruce canopies will increase by 4% in the south but by 428% in the north, while those from birch canopies will increase by about 300% and 113%, respectively. Overall emissions of monoterpene over the whole country amount to about 950 kg km^?2 y^?1 under current temperature conditions and will increase by 17% to 1100 kg km^?2 y^?1 with elevated temperature and precipitation, mainly because of an increase at northern latitudes. Under current conditions, emissions of isoprene follow the spatial distribution of spruce canopies (the only isoprene‐emitting tree species that forms forests in Finland) with four times higher emissions in the south than in the north. The elevated temperature and the changes in the areal distribution of Norway spruce will result in increases in isoprene emissions of about 37% in southern Finland and 435% in northern Finland. Annual mean isoprene emissions from Norway spruce canopies over the whole country will increase by about 60% up to the year 2100.