The mystery of underground death: cell death in roots during ontogeny and in response to environmental factors

Programmed cell death (PCD) is an essential part of the ontogeny of roots and their tolerance/resistance mechanisms, allowing adaptation and growth under adverse conditions. It occurs not only at the cellular and subcellular level, but also at the levels of tissues, organs and even whole plants. This process involves a wide spectrum of mechanisms, from signalling and the expression of specific genes to the degradation of cellular structures. The major goals of this review were to broaden current knowledge about PCD processes in roots, and to identify mechanisms associated with both developmental and stress‐associated cell death in roots. Vacuolar cell death, when cell contents are removed by a combination of an autophagy‐associated process and the release of hydrolases from a collapsed vacuole, is responsible for programming self‐destruction. Regardless of the conditions and factors inducing PCD, its subcellular events usually include the accumulation of autophagosome‐like structures, and the formation of massive lytic compartments. In some cases these are followed by the nuclear changes of chromatin condensation and DNA fragmentation. Tonoplast disruption and vacuole implosion occur very rapidly, are irreversible and constitute a definitive step toward cell death in roots. Active cell elimination plays an important role in various biological processes in the life history of plants, leading to controlled cellular death during adaptation to changing environmental conditions, and organ remodelling throughout development and senescence.     

A new global burned area product for climate assessment of fire impacts

Aim This paper presents a new global burned area (BA) product developed within the framework of the European Space Agency's Climate Change Initiative (CCI) programme, along with a first assessment of its potentials for atmospheric and carbon cycle modelling. Innovation Methods are presented for generating a new global BA product, along with a comparison with existing BA products, in terms of BA extension, fire size and shapes and emissions derived from biomass burnings. Main conclusions Three years of the global BA product were produced, accounting for a total BA of between 360 and 380 Mha year^?1. General omission and commission errors for BA were 0.76 and 0.64, but they decreased to 0.51 and 0.52, respectively, for sites with more than 10% BA. Intercomparison with other existing BA datasets found similar spatial and temporal trends, mainly with the BA included in the Global Fire Emissions Database (GFED4), although regional differences were found (particularly in the 2006 fires of eastern Europe). The simulated carbon emissions from biomass burning averaged 2.1 Pg C year^?1.     

Revisiting the Phenice technique sex classification results reported by MacLaughlin and Bruce (1990)

Phenice (Am J Phys Anthropol 30 (1969):297–301) reported a success rate of 96% for his method of sex determination based on three morphological features of the pelvis. Numerous studies have tested and evaluated the method with affirmative results. The results of the study by MacLaughlin and Bruce (J Forensic Sci 35 (1990):1384–1392) were inconsistent with other studies, reporting far lower rates of accuracy and a greater degree of interobserver error. The authors believe that this may be the result of the inclusion of an “ambiguous” classification category. Revised modelling using forced classification of sex provides much higher classification rates with the implication that the poor results reported by MacLaughlin and Bruce were due to methodological error for the most part. Am J Phys Anthropol 159:182–183, 2016. © 2015 Wiley Periodicals, Inc.     

Crow-Kimura模型中位点突变率对误差阈的随机效应

为了补充Eigen模型和Crow-Kimura模型的随机效应研究,Crow-Kimura模型中的位点突变率被处理成高斯分布随机变量,从而研究误差阈值的特征以及误差阈值的扩展与随机突变率涨落强度之间的关系. 准物种浓度和群体序参数分析表明,在位点突变率涨落较大时,误差阈值不再是相变点,而是平滑的转变区域. 定量分析表明,随机Crow-Kimura模型中转变区宽度与涨落强度之间的关系是非线性的. 将Crow-Kimura模型与Eigen模型的随机特征进行比较发现,在两个模型中适应值随机化使得转变区域的宽度和随机变量涨落强度之间的关系是线性的,而位点突变率随机化中两者的关系是非线性的（指数）. 对于随机化的Crow-Kimura模型,适应值随机化与位点突变率随机化引起的误差阈扩展效应相当. 对于随机Eigen模型,误差阈的扩展效应则主要是由位点突变率的随机化引起的. 之后,本文概述了Eigen模型和Crow Kimura模型中适应值和位点突变率随机化对误差阈值随机效应的影响,并讨论了上述结果对抗病毒策略、癌症治疗和动植物育种的重要意义.     

The relationship of vegetation to environmental factors in Wangsuk stream and Gwarim reservoir in Korea: II. Soil environments

This paper presents a quantitative account of vegetation–soil environmental factor relationships in the Wangsuk stream (WS) and the Gwarim reservoir (GR) in Korea. Vegetation and the following soil variables were investigated in May, August and October 2004: pH, conductivity, water content, organic matter, total nitrogen content, NH₄–N content, PO₄–P content, total Ca, Mg, K, and Na content, extractable Ca, Mg, K and Na content, soil texture, distance from the channel, and elevation above water level. Species richness, diversity and ratio of hydrophyte occupation in WS were different from those in GR. Species richness was higher in WS, whereas the ratio of hydrophyte occupation was higher in GR. There were large temporal and spatial variations in plant distribution in the riparian and aquatic zones of WS but only slight variations in those of GR. These differences might have arisen from differences in flooding regime, distance from the stream channel related to elevation above water level, and soil properties such as soil texture and available nutrients. The median values of organic matter, total nitrogen, NH₄–N, PO₄–P and extractable Ca, Mg, K and Na contents in the soil were higher in GR than in WS. Sandy loam and loamy sand were common soil types in WS and clay loam and sandy clay loam in GR. Ten vegetation groups in WS and six in GR were identified using TWINSPAN. DCCA indicated that the distance from the stream channel was most strongly related to plant distribution and this reflected the spatial distribution of plant species in WS. In both WS and GR, NH₄–N content in soil and soil texture were important factors for the distribution of species in May, August and October. Spatial and temporal heterogeneity of soil variables were related to species distribution.     

Bacillus subtilis: A plant-growth promoting rhizobacterium that also impacts biotic stress

Plants encounter many biotic agents, such as viruses, bacteria, nematodes, weeds, and arachnids. These entities induce biotic stress in their hosts by disrupting normal metabolism, and as a result, limit plant growth and/or are the cause of plant mortality. Some biotic agents, however, interact symbiotically or synergistically with their host plants. Some microbes can be beneficial to plants and perform the same role as chemical fertilizers and pesticides, acting as a biofertilizer and/or biopesticide. Plant growth promoting rhizobacteria (PGPR) can significantly enhance plant growth and represent a mutually helpful plant-microbe interaction. Bacillus species are a major type of rhizobacteria that can form spores that can survive in the soil for long period of time under harsh environmental conditions. Plant growth is enhanced by PGPR through the induction of systemic resistance, antibiosis, and competitive omission. Thus, the application of microbes can be used to induce systemic resistance in plants against biotic agents and enhance environmental stress tolerance. Bacillus subtilis exhibits both a direct and indirect biocontrol mechanism to suppress disease caused by pathogens. The direct mechanism includes the synthesis of many secondary metabolites, hormones, cell-wall-degrading enzymes, and antioxidants that assist the plant in its defense against pathogen attack. The indirect mechanism includes the stimulation of plant growth and the induction of acquired systemic resistance. Bacillus subtilis can also solubilize soil P, enhance nitrogen fixation, and produce siderophores that promote its growth and suppresses the growth of pathogens. Bacillus subtilis enhances stress tolerance in their plant hosts by inducing the expression of stress-response genes, phytohormones, and stress-related metabolites. The present review discusses the activity of B. subtilis in the rhizosphere, its role as a root colonizer, its biocontrol potential, the associated mechanisms of biocontrol and the ability of B. subtilis to increase crop productivity under conditions of biotic and abiotic stress.     

Spatial-temporal variation of Aureococcus anophagefferens blooms in relation to environmental factors in the coastal waters of Qinhuangdao,China

The brown tides occurring in the coastal scallop cultivation area of Qinhuangdao, China, in recent years are caused by Aureococcus anophagefferens and significantly impact the scallop industry and the marine ecosystem in this region. Long-term investigations of phytoplankton and hydrological variables in the Qinhuangdao sea area were conducted in this study to understand the spatial-temporal variations of A. anophagefferens in relation to environmental factors. Samples were collected during twelve cruises from July 2011 to December 2013 and were analyzed for the temperature, salinity, dissolved oxygen (DO), nutrients and phytoplankton pigments. All diagnostic pigments of A. anophagefferens, such as chlorophyll c₃ (Chl c₃), Chl c₂, 19′-butanoyloxyfucoxanthin (But-fuco), fucoxanthin (Fuco), and diadinoxanthin (Diad), were detected in the surface water by using high-performance liquid chromatography (HPLC). The highest concentrations of But-fuco (5.64 μg L⁻¹), Fuco (37.94 μg L⁻¹) and chlorophyll a (Chl a, 17.25 μg L⁻¹) occurred in different seasons and sampling sites. The A. anophagefferens bloom (as indicated by But-fuco) usually expanded from the south to the north of the Qinhuangdao sea area, close to scallop-culturing regions. The bloom unusually starts in May, reaches its peak in June and almost disappears in August, with the temperature ranging from ca. 19 °C to 23 °C. The redundancy analysis (RDA) indicated that relatively high salinity (>29) and low inorganic nutrients were suitable for the development of the A. anophagefferens bloom. The ratios of diagnostic pigments to Chl a were not constant during different cruises and generally obeyed two different linear relationships, thus indicating the co-occurrence of the blooms of A. anophagefferens and other species, such as Minutocellus polymorphus. In summary, our work reports the long-term variation of A. anophagefferens blooms based on diagnostic pigments and environmental controls, which may provide more insights into the formation mechanisms of the brown tide in this region.     

A Bayesian Latent Variable Mixture Model for Longitudinal Fetal Growth

Summary Fetal growth restriction is a leading cause of perinatal morbidity and mortality that could be reduced if high‐risk infants are identified early in pregnancy. We propose a Bayesian model for aggregating 18 longitudinal ultrasound measurements of fetal size and blood flow into three underlying, continuous latent factors. Our procedure is more flexible than typical latent variable methods in that we relax the normality assumptions by allowing the latent factors to follow finite mixture distributions. Using mixture distributions also permits us to cluster individuals with similar observed characteristics and identify latent classes of subjects who are more likely to be growth or blood flow restricted during pregnancy. We also use our latent variable mixture distribution model to identify a clinically meaningful latent class of subjects with low birth weight and early gestational age. We then examine the association of latent classes of intrauterine growth restriction with latent classes of birth outcomes as well as observed maternal covariates including fetal gender and maternal race, parity, body mass index, and height. Our methods identified a latent class of subjects who have increased blood flow restriction and below average intrauterine size during pregnancy. These subjects were more likely to be growth restricted at birth than a class of individuals with typical size and blood flow.