Ice nucleation in nature: supercooling point (SCP) measurements and the role of heterogeneous nucleation

In biological systems, nucleation of ice from a supercooled aqueous solution is a stochastic process and always heterogeneous. The average time any solution may remain supercooled is determined only by the degree of supercooling and heterogeneous nucleation sites it encounters. Here we summarize the many and varied definitions of the so-called "supercooling point," also called the "temperature of crystallization" and the "nucleation temperature," and exhibit the natural, inherent width associated with this quantity. We describe a new method for accurate determination of the supercooling point, which takes into account the inherent statistical fluctuations of the value. We show further that many measurements on a single unchanging sample are required to make a statistically valid measure of the supercooling point. This raises an interesting difference in circumstances where such repeat measurements are inconvenient, or impossible, for example for live organism experiments. We also discuss the effect of solutes on this temperature of nucleation. Existing data appear to show that various solute species decrease the nucleation temperature somewhat more than the equivalent melting point depression. For non-ionic solutes the species appears not to be a significant factor whereas for ions the species does affect the level of decrease of the nucleation temperature.     

Genetic and genomic resources of sorghum to connect genotype with phenotype in contrasting environments

With the recent development of genomic resources and high‐throughput phenotyping platforms, the 21st century is primed for major breakthroughs in the discovery, understanding and utilization of plant genetic variation. Significant advances in agriculture remain at the forefront to increase crop production and quality to satisfy the global food demand in a changing climate all while reducing the environmental impacts of the world's food production. Sorghum, a resilient C₄ grain and grass important for food and energy production, is being extensively dissected genetically and phenomically to help connect the relationship between genetic and phenotypic variation. Unlike genetically modified crops such as corn or soybean, sorghum improvement has relied heavily on public research; thus, many of the genetic resources serve a dual purpose for both academic and commercial pursuits. Genetic and genomic resources not only provide the foundation to identify and understand the genes underlying variation, but also serve as novel sources of genetic and phenotypic diversity in plant breeding programs. To better disseminate the collective information of this community, we discuss: (i) the genomic resources of sorghum that are at the disposal of the research community; (ii) the suite of sorghum traits as potential targets for increasing productivity in contrasting environments; and (iii) the prospective approaches and technologies that will help to dissect the genotype–phenotype relationship as well as those that will apply foundational knowledge for sorghum improvement.     

基于高通量测序的全基因组关联研究策略

全基因组关联研究（Genome-wide association study, GWAS）是人类复杂疾病研究的重要组成部分之一,在群体水平检测全基因组范围的遗传变异与可观测性状间的遗传关联。传统的GWAS是以芯片（Array）技术获得高密度的遗传变异,尽管硕果累累,但也存在不少问题。如：所谓的“缺失的遗传力”,即利用关联分析检测达到全基因组水平显著的遗传变异位点只能解释小部分遗传力;在某些性状上不同研究的结果一致性较弱;显著关联的遗传变异位点的功能较难解释等。高通量测序技术,也称第二代测序（Next-generation sequencing, NGS）技术,可以快速、准确地产出高通量的变异位点数据,为解决以上问题提供了可行的方案。基于NGS技术的GWAS方法（NGS-GWAS）,可在一定程度上弥补传统GWAS的不足。文章对NGS-GWAS策略和方法进行了系统性调研,提出了目前较为可行的NGS-GWAS的实施策略和方法,并对NGS-GWAS如何应用于个体化医疗（Personalized medicine, PM）进行了展望。     

Grazer exclusion alters plant spatial organization at multiple scales,increasing diversity

Grazing is one of the most important factors influencing community structure and productivity in natural grasslands. Understanding why and how grazing pressure changes species diversity is essential for the preservation and restoration of biodiversity in grasslands. We use heavily grazed subalpine meadows in the Qinghai‐Tibetan Plateau to test the hypothesis that grazer exclusion alters plant diversity by changing inter‐ and intraspecific species distributions. Using recently developed spatial analyses combined with detailed ramet mapping of entire plant communities (91 species), we show striking differences between grazed and fenced areas that emerged at scales of just one meter. Species richness was similar at very small scales (0.0625 m²), but at larger scales diversity in grazed areas fell below 75% of corresponding fenced areas. These differences were explained by differences in spatial distributions; intra‐ and interspecific associations changed from aggregated at small scales to overdispersed in the fenced plots, but were consistently aggregated in the grazed ones. We conclude that grazing enhanced inter‐ and intraspecific aggregations and maintained high diversity at small scales, but caused decreased turnover in species at larger scales, resulting in lower species richness. Our study provides strong support to the theoretical prediction that inter‐ and intraspecific aggregation produces local spatial patterns that scale‐up to affect species diversity in a community. It also demonstrates that the impacts of grazing can manifest through this mechanism, lowering diversity by reducing spatial turnover in species. Finally, it highlights the ecological and physiological plant processes that are likely responding to grazing and thereby altering aggregation patterns, providing new insights for monitoring, and mediating the impacts of grazing.     

No evidence for nutrient foraging in root-sprouting clonal plants

Clonality is defined as vegetative reproduction via the production of ramets, which are, at least initially, connected by spacers. In general, there are three types of spacers of two origins. Whereas stolons are aboveground spacers, rhizomes are belowground spacers; however, both of stem origin. The third type of spacers are roots in root-sprouting plants. The possibility of foraging in clonal plants has attracted broad interest among ecologists but has been experimentally documented only for stoloniferous clonal plants foraging for light. Foraging for belowground resources has yet to be demonstrated, perhaps because tests of foraging have focused on clonal plants that spread laterally via stolons or rhizomes, i.e. stem organs. Lateral spread based on sprouting roots has not been considered even though, in addition to functioning as conduits between ramets, root spacers are able to sense and take up nutrients. We therefore hypothesized that root-sprouting clonal plants may be able to directly react to environmental heterogeneity and exhibit nutrient foraging. To test this hypothesis, we conducted two experiments with root-sprouters in nutrient-heterogeneous and -homogeneous environments. We found that plants produced more biomass when growing in a heterogeneous environment than in a homogeneous environment and that root biomass was greater in the nutrient-rich patches than in nutrient-poor patches. However, the number of ramets did not differ between patches in the heterogeneous environment. We conclude that plants whose clonality is based on roots, similarly as plants whose clonality is based on stolons or rhizomes, do not exhibit accumulation of ramets in nutrient-rich patches. Foraging at the organ level, i.e. by roots, seems to be more probable in this clonal group. To analyse how clonal plants with different clonal strategies perceive and react to environmental heterogeneity, researchers must account for the high variability in clonal growth forms and in scales of environmental heterogeneity.     

Better to Live with Allogenerics Than to Live Alone? The Case of Single Male Cercopithecus pogonias in Troops of Colobus satanas

We report the integration of single male crowned guenons (Cercopithecus pogonias) into troops of black colobus (Colobus satanas). We observed one male Cercopithecus pogonias in three troops of Colobus satanas on 30% of observation days (n = 231). Activities of single males guenons did not differ significantly from those of the colobus with which they associated. Moreover, both species performed simultaneously the same activities more often than expected by chance. Interspecific grooming occurred on several occasions. Furthermore, single male guenons spent as much in time social activities when part of a colobus troop, as they typically do when part of a conspecific group. Unlike solitary male crowned guenons, which are silent, a male that is integrated into a troop of colobus is vocal and emits social alarm calls to which colobus monkeys respond. During the single file movements of colobus troops, single male crowned guenons were integrated in the core of the troop and used the same branches at the same height with the colobus. Thus, the life of a single male crowned guenon with black colobus was social. We suggest that the main benefits that he gained is the possibility to live in a social context. Social interactions could be the key element to explain why single males Cercopithecus pogonias join troops of monkeys so different from their natal groups.     

Comparison of Complex DNA Mixtures with Generic Oligonucleotide Microchips

Abstract

The reproducibility of melting curves for repeated hybridizations of target DNA with generic oligonucleotide microchips is shown experimentally to depend on the character of matching between fragments of target DNA and immobilized oligonucleotides. The reproducibility of melting curves is higher for the perfect match duplexes and decreases as the number of mismatched pairs within duplexes increases. This effect was applied to the comparative analysis of complex DNA mixtures. We developed a scheme in which we can identify and discriminate between the probe oligonucleotides responsible for the distinctions between target DNA mixtures. A scheme is illustrated by comparing DNA mixtures corresponding to VD-J genes connected with populations of mRNAs CDR3 TCR Vb (T-cell receptor beta complementarity determining region 3) from the thymus and pancreas of NOD mice. Our results demonstrate that generic microchips can be applied efficiently to the analysis of DNA mixtures.     

基于多元回归树的公益林群落结构解析

为揭示不同生境类型下公益林群落物种多样性及优势种种间关系特征, 以临安市公益林125个固定监测样地为研究对象, 利用多元回归树(MRT)进行群落分类, 以物种多样性指数和种间联结系数为指标, 对不同群落类型的结构特征进行探索。结果表明: 临安市公益林125个典型样地可划分为5个类型; 类型I、II、III与类型V的多样性指数之间均无显著差异, 但类型III的多样性指数均最高, 类型IV的物种多样性指数均显著低于其它类型, 海拔是影响群落多样性水平的主要因子。种间联结初步分析显示, 研究区群落中稳定性最高的层片是乔木层, 且毛竹入侵极可能是影响5个类型植物群落稳定性的关键因素。研究结果可为临安市公益林分类经营管理提供理论依据, 同时为区域公益林群落数量结构研究奠定基础。