Establishment of a five‐enzalutamide‐resistance‐related‐gene‐based classifier for recurrence‐free survival predicting of prostate cancer

To identify prostate cancer (PCa) patients with a high risk of recurrence is critical before delivering adjuvant treatment. We developed a classifier based on the Enzalutamide treatment resistance‐related genes to assist the currently available staging system in predicting the recurrence‐free survival (RFS) prognosis of PCa patients. We overlapped the DEGs from two datasets to obtain a more convincing Enzalutamide‐resistance‐related‐gene (ERRG) cluster. The five‐ERRG‐based classifier obtained good predictive values in both the training and validation cohorts. The classifier precisely predicted RFS of patients in four cohorts, independent of patient age, pathological tumour stage, Gleason score and PSA levels. The classifier and the clinicopathological factors were combined to construct a nomogram, which had an increased predictive accuracy than that of each variable alone. Besides, we also compared the differences between high‐ and low‐risk subgroups and found their differences were enriched in cancer progression‐related pathways. The five‐ERRG‐based classifier is a practical and reliable predictor, which adds value to the existing staging system for predicting the RFS prognosis of PCa after radical prostatectomy, enabling physicians to make more informed treatment decisions concerning adjuvant therapy.     

果胶甲酯酶的结构与功能研究进展

果胶甲酯酶(PME)是一种重要的果胶酶,其水解果胶中的甲酯基从而释放甲醇并降低果胶的甲酯化程度。目前在食品加工、茶饮料、造纸等生产工艺中有着广泛的应用前景。随着对PME的深入研究,已报道了几种不同来源的酶晶体结构,对这些已获得的晶体结构进行分析发现,PME属于右手平行β-螺旋结构,其催化残基为2个保守的天冬氨酸和1个谷氨酰胺残基,并且在催化过程中分别起到了一般酸碱、亲核试剂以及稳定中间体的作用。同时对其底物特异性进行分析,初步了解其底物与活性位点的识别机制。文中针对这几个相关方面进行了系统的综述。     

象山港网箱养殖区沉积物的古菌空间分布

对象山港网箱养殖区及其周边沉积物中古菌群落的空间分布进行研究,应用基于16S rRNA基因的T-RFLP(末端限制性片段多态性分析)技术分析象山港网箱养殖区及其周边不同深度沉积物中古菌的群落结构和多样性,并构建克隆文库进行系统发育学分析。测定沉积物各项理化因子,通过PCA和RDA分析了古菌群落分布及其与环境因子之间的关系。结果表明,泉古菌是港口沉积物中的优势古菌群,占古菌群落的50%以上。网箱养殖区沉积物的古菌群落结构较非养殖区简单,多样性降低。非养殖区古菌群落随深度呈现有规律的变化。营养盐类和pH是造成养殖区域古菌群落结构区别于非养殖区域的主要环境因素。     

Cytoplasmic domain and enzymatic activity of ACE2 are not required for PI4KB dependent endocytosis entry of SARS-CoV-2 into host cells

The recent COVID-19 pandemic poses a global health emergency. Cellular entry of the causative agent SARS-CoV-2 is mediated by its spike protein interacting with cellular receptor-human angiotensin converting enzyme 2 (ACE2). Here, by using lentivirus based pseudotypes bearing spike protein, we demonstrated that entry of SARS-CoV-2 into host cells was dependent on clathrin-mediated endocytosis, and phosphoinositides played essential roles during this process. In addition, we showed that the intracellular domain and the catalytic activity of ACE2 were not required for efficient virus entry. Finally, we showed that the current predominant Delta variant, although with high infectivity and high syncytium formation, also entered cells through clathrin-mediated endocytosis. These results provide new insights into SARS-CoV-2 cellular entry and present proof of principle that targeting viral entry could be an effective way to treat different variant infections.     

Noggin and bFGF cooperate to maintain the pluripotency of human embryonic stem cells in the absence of feeder layers

Human embryonic stem (hES) cells are typically maintained on mouse embryonic fibroblast (MEF) feeders or with MEF-conditioned medium. However, these xenosupport systems greatly limit the therapeutic applications of hES cells because of the risk of cross-transfer of animal pathogens. Here we showed that the bone morphogenetic protein antagonist noggin is critical in preventing differentiation of hES cells in culture. Furthermore, we found that the combination of noggin and basic fibroblast growth factor (bFGF) was sufficient to maintain the prolonged growth of hES cells while retaining all hES cell features. Since both noggin and bFGF are expressed in MEF, our findings suggest that they may be important factors secreted by MEF for maintaining undifferentiated pluripotent hES cells. Our data provide new insight into the mechanism how hES cell self-renewal is regulated. The newly developed feeder-free culture system will provide a more reliable alternative for future therapeutic applications of hES cells.     

A dynamic, architectural plant model simulating resource-dependent growth

BACKGROUND AND AIMS: Physiological and architectural plant models have originally been developed for different purposes and therefore have little in common, thus making combined applications difficult. There is, however, an increasing demand for crop models that simulate the genetic and resource-dependent variability of plant geometry and architecture, because man is increasingly able to transform plant production systems through combined genetic and environmental engineering. MODEL: GREENLAB is presented, a mathematical plant model that simulates interactions between plant structure and function. Dual-scale automaton is used to simulate plant organogenesis from germination to maturity on the basis of organogenetic growth cycles that have constant thermal time. Plant fresh biomass production is computed from transpiration, assuming transpiration efficiency to be constant and atmospheric demand to be the driving force, under non-limiting water supply. The fresh biomass is then distributed among expanding organs according to their relative demand. Demand for organ growth is estimated from allometric relationships (e.g. leaf surface to weight ratios) and kinetics of potential growth rate for each organ type. These are obtained through parameter optimization against empirical, morphological data sets by running the model in inverted mode. Potential growth rates are then used as estimates of relative sink strength in the model. These and other 'hidden' plant parameters are calibrated using the non-linear, least-square method. KEY RESULTS AND CONCLUSIONS: The model reproduced accurately the dynamics of plant growth, architecture and geometry of various annual and woody plants, enabling 3D visualization. It was also able to simulate the variability of leaf size on the plant and compensatory growth following pruning, as a result of internal competition for resources. The potential of the model's underlying concepts to predict the plant's phenotypic plasticity is discussed.     

Response of physiological integration in Trifolium repens to heterogeneity of UV-B radiation

Physiological integration has been documented in many clonal plants growing under resource heterogeneity. Little is still known about the response of physiological integration to heterogeneous ultraviolet-B radiation. In this paper, the changes in intensity of physiological integration and of physiological parameters under homogeneous and heterogeneous ultraviolet-B radiation (280-315 nm) were measured in order to test the hypothesis that in addition to resource integration a defensive integration in Trifolium repens might exist as well. For this purpose, homogeneous and heterogeneous ultraviolet-B radiation was applied to pairs of connected and severed ramets of the stoloniferous herb Trifolium repens. Changes in intensity of water and nutrient integration were followed with acid fuchsin dye and ¹⁵N-isotope labeling of the xylem water transport. In order to assess the patterns of physiological integration contents of chlorophyll, ultraviolet-B absorbing compounds, soluble sugar and protein were determined and activities of superoxide dismutase (SOD) and peroxidase (POD) measured. When ramets were connected and exposed to heterogeneous UV-B radiation, the velocity of water transportation from the UV-B treated ramet to its connected sister ramet was markedly lower and the percentage of ¹⁵N left in labelled ramets that suffered from enhanced UV-B radiation was higher and their transfer to unlabelled ramets lower. In comparison with clones under homogeneous ultraviolet-B radiation, the content of chlorophyll, ultraviolet-B absorbing compounds, soluble sugar and activities of SOD and POD increased notably if ultraviolet-B stressed ramets were connected to untreated ramets. Chlorophyll and UV-B absorbing compounds were shared between connected ramets under heterogeneous UV-B radiation. This indicated that physiological connection improved the performance of whole clonal plants under heterogeneous ultraviolet-B radiation. The intensity of physiological integration of T. repens for resources decreased under heterogeneous ultraviolet-B radiation in favor of the stressed ramets. Ultraviolet-B stressed ramets benefited from unstressed ramets by physiological integration, supporting the hypothesis that clonal plants are able to optimize the efficiency of their resistance maintaining their presence also in less favorable sites. The results could be helpful for further understanding of the function of heterogeneous UV-B radiation on growth regulation and microevolution in clonal plants.     

MD Simulations and first principles to evaluate the role of binary Fe–V alloys layer on the radiation resistance in the alpha-iron

Radiation damage in reactor materials caused by the collision of the fast neutrons has a great impact on the reliability and safety of nuclear reactors. The element vanadium has attracted interest in many fields due to its advantageous properties in alloys. Thus, molecular dynamics simulation (MD) and first-principles calculation have been executed here to explore the radiation-resistant properties of five materials adding a layer in the bulk (pure iron and four types of Fe–V alloys containing 10%-40% V). The following results were inferred from these simulations. Firstly, the number of Frenkel pairs (FPs) at the stable quenching stage in the bulk decreases when the Fe–V alloy is added as an anti-radiation layer to the bulk. These benefits are evident for the Fe₈₀V₂₀ and alloy layers with more vanadium. The main reason is that the Fe–V binding energy is greater than the Fe-Fe binding energy, which can make the Primary Knock-On atom (PKA) lose more energy at the Fe–V alloy layer. Secondly, the average value of point-defect, cluster and defect clustered fractions in the bulk of Fe–V alloy is smaller than that in the pure iron at the stable quenching stage, especially for the Fe₈₀V₂₀ alloy.     

用核酸斑点杂交法比较油桐尺蠖核型多角体病毒与某些昆虫杆状病毒的同源性

有关核型多角体病毒基因同源性的研究报道不多,结果也不甚一致。目前,国内外普遍用SDS-PAGE法分析昆虫杆状病毒结构多肽,以限制性内切酶谱法测定基因组大小,借此区分来自不同宿主的病毒株,和基因组密切相关