生态学数学模型参数优化估计的遗传算法

本文提出用遗传算法,对生态学中的一些数学模型参数进行优化估计,并以崔-lawson方程为例．尝试了遗传算法的效果．结果表明,该方法性能良好,可望成为生态学中各类非线性模型辨识的有效参数．     

X-ray dark-field phase-contrast imaging: Origins of the concept to practical implementation and applications

The basic idea of X-ray dark-field imaging (XDFI), first presented in 2000, was based on the concepts used in an X-ray interferometer. In this article, we review 20 years of developments in our theoretical understanding, scientific instrumentation, and experimental demonstration of XDFI and its applications to medical imaging. We first describe the concepts underlying XDFI that are responsible for imparting phase contrast information in projection X-ray images. We then review the algorithms that can convert these projection phase images into three-dimensional tomographic slices. Various implementations of computed tomography reconstructions algorithms for XDFI data are discussed. The next four sections describe and illustrate potential applications of XDFI in pathology, musculoskeletal imaging, oncologic imaging, and neuroimaging. The sample applications that are presented illustrate potential use scenarios for XDFI in histopathology and other clinical applications. Finally, the last section presents future perspectives and potential technical developments that can make XDFI an even more powerful tool.     

Identification of an endocytosis motif in an intracellular loop of Wntless protein, essential for its recycling and the control of Wnt protein signaling

The secretion of Wnt signaling proteins is dependent upon the transmembrane sorting receptor, Wntless (Wls), which recycles between the trans-Golgi network and the cell surface. Loss of Wls results in impairment of Wnt secretion and defects in development and homeostasis in Drosophila, Caenorhabditis elegans, and the mouse. The sorting signals for the internalization and trafficking of Wls have not been defined. Here, we demonstrate that Wls internalization requires clathrin and dynamin I, components of the clathrin-mediated endocytosis pathway. Moreover, we have identified a conserved YXXφ endocytosis motif in the third intracellular loop of the multipass membrane protein Wls. Mutation of the tyrosine-based motif YEGL to AEGL (Y425A) resulted in the accumulation of human mutant Wls on the cell surface of transfected HeLa cells. The cell surface accumulation of Wls^AEGL was rescued by the insertion of a classical YXXφ motif in the cytoplasmic tail. Significantly, a Drosophila Wls^AEGL mutant displayed a wing notch phenotype, with reduced Wnt secretion and signaling. These findings demonstrate that YXXφ endocytosis motifs can occur in the intracellular loops of multipass membrane proteins and, moreover, provide direct evidence that the trafficking of Wls is required for efficient secretion of Wnt signaling proteins.     

基于遗传算法预测2D三向的蛋白质结构

本文基于范德华力势能预测2D三向的蛋白质结构。首先,将蛋白质结构预测这一生物问题转化为数学问题,并建立基于范德华力势能函数的数学模型。其次,使用遗传算法对数学模型进行求解,为了提高蛋白质结构预测效率,我们在标准遗传算法的基础上引入了调整算子这一概念,改进了遗传算法。最后,进行数值模拟实验。实验的结果表明范德华力势能函数模型是可行的,同时,和规范遗传算法相比,改进后的遗传算法能够较大幅度提高算法的搜索效率,并且遗传算法在蛋白质结构预测问题上有巨大潜力。     

SNX11 Identified as an Essential Host Factor for SFTS Virus Infection by CRISPR Knockout Screening

Severe fever with thrombocytopenia syndrome virus(SFTSV) is a highly pathogenic tick-borne bunyavirus that causes lethal infectious disease and severe fever with thrombocytopenia syndrome(SFTS) in humans. The molecular mechanisms and host cellular factors required for SFTSV infection remain uncharacterized. Using a genome-wide CRISPR-based screening strategy, we identified a host cellular protein, sorting nexin 11(SNX11) which is involved in the intracellular endosomal trafficking pathway, as an essential cell factor for SFTSV infection. An SNX11-KO HeLa cell line was established, and SFTSV replication was significantly reduced. The glycoproteins of SFTSV were detected and remained in later endosomal compartments but were not detectable in the endoplasmic reticulum(ER) or Golgi apparatus. pH values in the endosomal compartments of the SNX11-KO cells increased compared with the pH of normal HeLa cells, and lysosomal-associated membrane protein 1(LAMP1) expression was significantly elevated in the SNX11-KO cells. Overall,these results indicated that penetration of SFTSV from the endolysosomes into the cytoplasm of host cells was blocked in the cells lacking SNX11. Our study for the first time provides insight into the important role of the SNX11 as an essential host factor in the intracellular trafficking and penetrating process of SFTSV infection via potential regulation of viral protein sorting, membrane fusion, and other endocytic machinery.     

Identifying conservation priority areas and predicting the climate change impact on the future habitats of endangered Nepenthes khasiana Hook.f. utilizing ecological niche modelling

Developing strategies for effective species conservation is necessary to counter the ever-fluctuating environmental conditions with increasing anthropogenic activities. Studies have proven Ecological Niche Modelling (ENM) as an effective tool for sustainable conservation. Nepenthes khasiana Hook.f. is an endangered pitcher plant facing a constant decline in population due to anthropogenic activities. This study aimed to locate the most suitable areas for re-establishing the species in natural habitats using Maximum Entropy (MaxEnt) modelling, and to forecast the effects of current and future climate conditions on its distribution throughout Northeast India. The potential suitable areas in future climate under three Representative Concentration Pathway (RCP) scenarios and in the current climate were predicted utilizing the 30 occurrence data, bioclimatic predictors, and variables from BCC-CSM1.1 model and WorldClim respectively. The results of the current study showed significant relationships among annual precipitation, precipitation in the driest month, seasonality of precipitation, annual range iso-thermality of temperature, mean diurnal range [Mean of monthly (max temp - min temp)], and the distribution of the analysed species. The optimum model performance was represented by the AUC value of 0.972 ± 0.007. The model predicted 10.70% of the NE Indian region as climatically suitable, which will expand under RCP4.5 and RCP6.0, reaching 15.35%, and 12.64%, respectively. However, this may degrade significantly under RCP8.5, reducing to 8.14%. Based on the analysis of modelling results it was found that the Nokrek belt and the Khasi hills as highly suitable regions for the reintroduction of the species. The study revalidated ENM as an effective means to identify new populations and predict the influence of climate change on the future habitat which can benefit the concurrent species management strategies.     

海洋微生物高通量培养方法和分选技术的研究进展

海洋环境中蕴含着丰富的微生物资源,其在生态系统中发挥着重要作用,与人类生活息息相关。但是迄今通过传统的培养方法可被培养分离的海洋微生物不到1%。本文论述了海洋微生物的重要性,大多数海洋微生物不可被培养的原因,以及高通量培养方法和分选技术的研究进展。随着研究的深入,将会有更加实用有效的高通量培养方法和分选技术出现。     

Use of in silico tools for classification of novel missense mutations identified in dystrophin gene in developing countries

DMD gene which is composed of 79 exons is the largest known gene located on X chromosome (Xp21). Point mutations in the dystrophin gene are responsible for 30–35% of cases with DMD/BMD. Mutation analysis of all the exons of the DMD gene is costly in developing countries, therefore, a few of the exons are selected to be analyzed routinely in clinical laboratories. In this study, direct sequencing was used for detection of point mutations in 10 exons of dystrophin gene in patients affected with DMD without detectable large rearrangements. Freely available programs were used to predict the damaging effects of the mutations. Point mutations were successfully detected in three patients. Three novel mutations, two missense mutations located on nonconservative domains and a single nucleotide deletion, were detected. Missense mutations were predicted to change splicing efficiency. Detection of point mutations by DNA analysis followed by prediction of the pathogenecity by using bioinformatic tool might be an asset to provide proper diagnosis or genetic counseling to patients and their family.     

N-聚糖和O-聚糖在极性化细胞蛋白质分拣中的作用

极性化上皮细胞的质膜因其所含蛋白质、脂质等组分不同,可以分为细胞膜顶端和细胞膜基底侧端两个区域,而新合成的蛋白质向这两个区域的有效分拣是上皮细胞维持其自身极性及正常功能所必需的。细胞膜基底侧端蛋白质的分拣主要由位于该蛋白质胞质区的信号肽所介导,关于这方面的研究是比较深入的;而细胞膜顶端蛋白质的分拣机制目前尚未阐明,因而显得比较复杂。近年来,糖类分子作为生物体内细胞识别和调控过程的信息分子日益受到关注,人们通过干扰聚糖合成、基因突变以及构建糖基化缺陷细胞株等实验方法,逐渐地认识到糖类分子在极性化上皮细胞的蛋白质分拣调节中起重要作用。由于糖分子本身结构非常复杂,而且目前缺乏研究糖类分子的有效手段,使得糖生物学的研究远远落后于蛋白质和核酸的研究。从而导致探讨糖类分子在蛋白质分拣过程的具体机制相对来说比较困难。本综述拟简要概括糖类分子中N-聚糖和O-聚糖在极性化上皮细胞的蛋白质分拣过程中的作用,以及两种聚糖在此过程中行使分拣信号功能的可能机制。     

蛋白质的二级结构预测研究进展

认识蛋白质的二级结构是了解蛋白质的折叠模式和三级结构的基础,并为研究蛋白质的功能以及它们之间的相互作用模式提供结构基础,同时还可以为新药研发提供帮助。故研究蛋白质的二级结构具有重要的意义。随着后基因组时代的到来,越来越多的蛋白质序列不断被发现,给蛋白质的二级结构研究带来巨大的挑战和研究空间。而依靠传统的实验方法很难获取大规模蛋白质的二级结构信息。目前,采用生物信息学手段仍然是获得大部分蛋白质二级结构的途径。近年来,许多研究者通过构建用于二级结构预测的蛋白质数据集,计算、提取蛋白质的各种特征信息,并采用不同的预测算法预测蛋白质的二级结构得到了快速的发展。本文拟从蛋白质的特征信息的提取与筛选、预测算法以及预测效果的检验方法等方面进行综述,介绍蛋白质二级结构预测领域的研究进展。相信随着基因组学、蛋白质组学和生物信息学的不断发展,蛋白质二级结构预测会不断取得新突破。