Essence determines phenomenon: Assaying the material properties of biological condensates

Intracellular spaces are partitioned into separate compartments to ensure that numerous biochemical reactions and cellular functions take place in a spatiotemporally controlled manner. Biomacromolecules including proteins and RNAs undergo liquid–liquid phase separation and subsequent phase transition to form biological condensates with diverse material states. The material/physical properties of biological condensates are crucial for fulfilling their distinct physiological functions, and abnormal material properties can cause deleterious effects under pathological conditions. Here, we review recent studies showing the role of the material properties of biological condensates in their physiological functions. We also summarize several classic methods as well as newly emerging techniques for characterization and/or measurement of the material properties of biological condensates.     

维生素A缺乏大鼠致敏后免疫功能低下对肺炎的影响机制

目的探讨维生素A（VA）缺乏对致敏后免疫细胞发育、功能的影响机制。方法：低VA饲料喂养大鼠8周时用卵蛋白致敏并分组。VAS组隔天口服vA100u,治疗3次;VAD组与正常组口服大豆油。用免疫组织化学法观察细胞角蛋白19（CK19）、病理学检查肺与脾病理变化、ELISA法检查血清Th因子水平等。结果VAD组胸腺萎缩,胸腺上皮细胞（TEC）肥大、聚集、CK19少。血IL—10、IL-4、胸腺索a-1升高。肺感染病灶多,肺泡隔浸润细胞较少与红细胞渗出多。VAS组胸腺细胞增生,TEC内CK193上调,血IFN—γ水平较低、IL-4、IL-10明显下调。小气道单层纤毛柱状上皮正常,管壁淋巴细胞浸润较重,肺泡区巨噬细胞多、渗出红细胞少。结论VA缺乏并致敏后胸腺TEC、胸腺细胞等发育和功能异常。补充VA改善胸腺TEC结构、促进淋巴细胞增生与非特异免疫功能,保护呼吸道黏膜与肺泡上皮。     

How past and present influence the foraging of clonal plants?

Clonal plants spreading horizontally and forming a network structure of ramets exhibit complex growth patterns to maximize resource uptake from the environment. They respond to spatial heterogeneity by changing their internode length or branching frequency. Ramets definitively root in the soil but stay interconnected for a varying period of time thus allowing an exchange of spatial and temporal information. We quantified the foraging response of clonal plants depending on the local soil quality sampled by the rooting ramet (i.e. the present information) and the resource variability sampled by the older ramets (i.e. the past information). We demonstrated that two related species, Potentilla reptans and P. anserina, responded similarly to the local quality of their environment by decreasing their internode length in response to nutrient-rich soil. Only P. reptans responded to resource variability by decreasing its internode length. In both species, the experience acquired by older ramets influenced the plastic response of new rooted ramets: the internode length between ramets depended not only on the soil quality locally sampled but also on the soil quality previously sampled by older ramets. We quantified the effect of the information perceived at different time and space on the foraging behavior of clonal plants by showing a non-linear response of the ramet rooting in the soil of a given quality. These data suggest that the decision to grow a stolon or to root a ramet at a given distance from the older ramet results from the integration of the past and present information about the richness and the variability of the environment.     

A genome-wide search for signals of high-altitude adaptation in Tibetans

Genetic studies of Tibetans, an ethnic group with a long-lasting presence on the Tibetan Plateau which is known as the highest plateau in the world, may offer a unique opportunity to understand the biological adaptations of human beings to high-altitude environments. We conducted a genome-wide study of 1,000,000 genetic variants in 46 Tibetans (TBN) and 92 Han Chinese (HAN) for identifying the signals of high-altitude adaptations (HAAs) in Tibetan genomes. We discovered the most differentiated variants between TBN and HAN at chromosome 1q42.2 and 2p21. EGLN1 (or HIFPH2, MIM 606425) and EPAS1 (or HIF2A, MIM 603349), both related to hypoxia-inducible factor, were found most differentiated in the two regions, respectively. Strong positive correlations were also observed between the frequency of TBN-dominant haplotypes in the two gene regions and altitude in East Asian populations. Linkage disequilibrium and further haplotype network analyses of world-wide populations suggested the antiquity of the TBN-dominant haplotypes and long-term persistence of the natural selection. Finally, a "dominant haplotype carrier" hypothesis could describe the role of the two genes in HAA. All of our population genomic and statistical analyses indicate that EPAS1 and EGLN1 are most likely responsible for HAA of Tibetans. Interestingly, one each but not both of the two genes were also identified by three recent studies. We reanalyzed the available data and found the escaped top signal (EPAS1) could be recaptured with data quality control and our approaches. Based on this experience, we call for more attention to be paid to controlling data quality and batch effects introduced in public data integration. Our results also suggest limitations of extended haplotype homozygosity-based method due to its compromised power in case the natural selection initiated long time ago and particularly in genomic regions with recombination hotspots.     

The origin of <Emphasis Type=Italic>Triticum petropavlovskyi</Emphasis> Udacz. et Migusch.: demonstration of the utility of the genes encoding plastid acetyl-CoA carboxylase sequence

Single- and low- copy genes are less likely subject to concerted evolution, thus making themselves ideal tools for studying the origin and evolution of polyploid taxa. Based on the sequences of a single-copy nuclear gene encoding plastid acetyl-CoA carboxylase (Acc-1), a total of 47 accessions Triticum and Aegilops representing diploid, tetraploid and hexaploid were used to estimate the origin of Triticum petropavlovskyi. Phylogenetic analysis was performed based on the intron, intron + sy and exon data sets sequence using maximum likelihood, neighbor-joining and median-joining networks. The A and B genome sequences from Acc-1 loci show that T. petropavlovskyi shares the highest averaged sequence identity with T. polonicum from Xinjiang and exotic landraces of T. aestivum, and reveals specific progenitor-descendant relationships. The D genome sequences of the Acc-1 genes from T. petropavlovskyi are identical to the sequences of the D genome orthologs in T. aestivum, while the relationship of T. petropavlovskyi and Ae. tauschii are most distant. Our findings do not suggest the probability of an independent allopolyploidization event and a single mutation in T. aestivum in the origin of T. petropavlovskyi, but indicate a greater degree of gene flow between T. aestivum and T. polonicum leading to origin of T. petropavlovskyi. It is most likely that T. petropavlovskyi was originated from T. polonicum from Xinjiang to exotic landraces of T. aestivum via a spontaneous introgression or breeding effort.     

Protandim does not influence alveolar epithelial permeability or intrapulmonary oxidative stress in human subjects with alcohol use disorders

Alcohol use disorders (AUDs), including alcohol abuse and dependence, have been linked to the development of acute lung injury (ALI). Prior clinical investigations suggested an association between AUDs and abnormal alveolar epithelial permeability mediated through pulmonary oxidative stress that may partially explain this relationship. We sought to determine if correcting pulmonary oxidative stress in the setting of AUDs would normalize alveolar epithelial permeability in a double-blinded, randomized, placebo-controlled trial of Protandim, a nutraceutical reported to enhance antioxidant activity. We randomized 30 otherwise healthy AUD subjects to receive directly observed inpatient oral therapy with either Protandim (1,350 mg/day) or placebo. Subjects underwent bronchoalveolar lavage (BAL) and blood sampling before study drug administration and after 7 days of therapy; all AUD subjects completed the study protocol without adverse events. BAL total protein was measured at each timepoint as an indicator of alveolar epithelial permeability. In subjects with AUDs, before study drug initiation, BAL total protein values were not significantly higher than in 11 concurrently enrolled controls (P = 0.07). Over the 7-day study period, AUD subjects did not exhibit a significant change in BAL total protein, regardless of their randomization to Protandim {n = 14, -2% [intraquartile range (IQR), -56-146%]} or to placebo [n = 16, 77% (IQR -20-290%); P = 0.19]. Additionally, among those with AUDs, no significant changes in BAL oxidative stress indexes, epithelial growth factor, fibroblast growth factor, interleukin-1β, or interleukin-10 were observed regardless of drug type received. Plasma thiobarbituric acid reactive substances, a marker of lipid peroxidation, decreased significantly over time among AUD subjects randomized to placebo (P < 0.01). These results suggest that Protandim for 7 days in individuals with AUDs who are newly abstinent does not alter alveolar epithelial permeability. However, our work demonstrates the feasibility of safely conducting clinical trials that include serial bronchoscopies in a vulnerable population at risk for acute lung injury.     

C allocation to the fungus is not a cost to the plant in ectomycorrhizae

Mycorrhizal benefit to plants is most frequently evaluated through growth differences between mycorrhizal (M) and non‐mycorrhizal (NM) plants. These growth differences are often considered to be due to differences in belowground C expenditure, or in cost efficiency, i.e. amount of nutrients acquired per C expended. We searched published reports for relations between plant growth and belowground C allocation, C use efficiency, or nutrient uptake, in ectomycorrhizal (ECM) versus non‐mycorrhizal plants. We found a similar number of cases of negative, null or positive effects of ECM on plant growth. These effects were not correlated with differences on belowground C allocation or C use efficiency between M and NM plants. In contrast, they were very strongly correlated with mycorrhizal effects on plant N gain. A comprehensive analysis of the published data therefore provided evidence that C is an excess, rather than a costly, resource, and that the outcome of the symbiosis depends only on whether mycorrhizae result in increased or decreased nutrient acquisition compared with NM plants, and not on cost efficiency differences between M and NM plants. Consequences of this finding for the regulation of resource exchange between symbionts and the nature of the symbiosis are discussed.     

Genetic similarity among cultivars of Phyllostachys pubescens

Phyllostachys pubescens is the most important economic bamboo species in China, which grows widely in the South of China. There are more than ten cultivars in this species but their genetic relationship still remains unknown. We used both amplified fragment length polymorphism (AFLP) and inter-simple sequence repeat (ISSR) techniques to determine genetic similarity among ten cultivars of P. pubescens and two related species. Eight hundred and twenty seven bands, in which 495 are polymorphic, were detected using 15 pairs of AFLP primers whereas total 231 bands, in which 154 bands are polymorphic, were scored using 16 ISSR primers. Statistic analysis showed that the genetic similarity matrices obtained from these two sets of molecular markers had a significant correlation (R = 0.959, P = 0.013). The dendrogram generated with AFLP and ISSR markers could clearly genetically identify ten cultivars of P. pubescens that had high similarity with genetic distances ranging from 0.023 to 0.108, and could be divided into three groups based on their genetic variation and similarity. Our results suggest that these molecular markers are useful to genetically classify cultivars or varieties of a species, particularly a bamboo species.