ATR Contributes More Than ATM in Intra-S-Phase Checkpoint Activation after IR,and DNA-PKcs Facilitates Recovery: Evidence for Modular Integration of ATM/ATR/DNA-PKcs Functions

The intra-S-phase checkpoint was among the first reported cell cycle checkpoints in mammalian cells. It transiently slows down the rate of DNA replication after DNA damage to facilitate repair and thus prevents genomic instability. The ionizing radiation (IR)-induced intra-S-phase checkpoint in mammalian cells is thought to be mainly dependent upon the kinase activity of ATM. Defects in the intra-S-phase checkpoint result in radio-resistant DNA synthesis (RDS), which promotes genomic instability. ATM belongs to the PI3K kinase family along with ATR and DNA-PKcs. ATR has been shown to be the key kinase for intra-S-phase checkpoint signaling in yeast and has also been implicated in this checkpoint in higher eukaryotes. Recently, contributions of DNA-PKcs to IR-induced G₂-checkpoint could also be established. Whether and how ATR and DNA-PKcs are involved in the IR-induced intra-S-phase checkpoint in mammalian cells is incompletely characterized. Here, we investigated the contributions of ATM, ATR, and DNA-PKcs to intra-S-phase checkpoint activation after exposure to IR of human and hamster cells. The results suggest that the activities of both ATM and ATR are essential for efficient intra-S-phase checkpoint activation. Indeed, in a wild-type genetic background, ATR inhibition generates stronger checkpoint defects than ATM inhibition. Similar to G2 checkpoint, DNA-PKcs contributes to the recovery from the intra-S-phase checkpoint. DNA-PKcs–deficient cells show persistent, mainly ATR-dependent intra-S-phase checkpoints. A correlation between the degree of DSB end resection and the strength of the intra-S-phase checkpoint is observed, which again compares well to the G2 checkpoint response. We conclude that the organization of the intra-S-phase checkpoint has a similar mechanistic organization to that of the G₂ checkpoint in cells irradiated in the G₂ phase.     

A Novel Cartesian Plot Analysis for Fixed Monolayers That Relates Cell Phenotype to Transfer of Contents between Fibroblasts and Cancer Cells by Cell-Projection Pumping

We recently described cell-projection pumping as a mechanism transferring cytoplasm between cells. The uptake of fibroblast cytoplasm by co-cultured SAOS-2 osteosarcoma cells changes SAOS-2 morphology and increases cell migration and proliferation, as seen by single-cell tracking and in FACS separated SAOS-2 from co-cultures. Morphological changes in SAOS-2 seen by single cell tracking are consistent with previous observations in fixed monolayers of SAOS-2 co-cultures. Notably, earlier studies with fixed co-cultures were limited by the absence of a quantitative method for identifying sub-populations of co-cultured cells, or for quantitating transfer relative to control populations of SAOS-2 or fibroblasts cultured alone. We now overcome that limitation by a novel Cartesian plot analysis that identifies individual co-cultured cells as belonging to one of five distinct cell populations, and also gives numerical measure of similarity to control cell populations. We verified the utility of the method by first confirming the previously established relationship between SAOS-2 morphology and uptake of fibroblast contents, and also demonstrated similar effects in other cancer cell lines including from melanomas, and cancers of the ovary and colon. The method was extended to examine global DNA methylation, and while there was no clear effect on SAOS-2 DNA methylation, co-cultured fibroblasts had greatly reduced DNA methylation, similar to cancer associated fibroblasts.     

Early Expression of Tet1 and Tet2 in Mouse Zygotes Altered DNA Methylation Status and Affected Embryonic Development

Ten-eleven translocation (Tet) dioxygenases can induce DNA demethylation by catalyzing 5-methylcytosine(5mC) to 5-hydroxymethylcytosine(5hmC), and play important roles during mammalian development. In mouse, Tet1 and Tet2 are not expressed in pronucleus-staged embryos and are not involved in the genomic demethylation of early zygotes. Here, we investigated the influence of Tet1 and Tet2 on methylation of parental genomes by ectopically expressing Tet1 and Tet2 in zygotes. Immunofluorescence staining showed a marked 5hmC increase in the maternal pronucleus after injection of Tet1 or Tet2 mRNA into zygotes. Whole-genome bisulfite sequencing further revealed that Tet2 greatly enhanced the global demethylation of both parental genomes, while Tet1 only promoted the paternal demethylation. Tet1 and Tet2 overexpression altered the DNA methylation across genomes, including various genic elements and germline-specific differently methylated regions. Tet2 exhibited overall stronger demethylation activity than Tet1. Either Tet1 or Tet2 overexpression impaired preimplantation embryonic development. These results demonstrated that early expression of Tet1 and Tet2 could substantially alter the zygotic methylation landscape and damage embryonic development. These findings provide new insights into understanding the function of Tet dioxygenases and the mechanism of DNA methylation in relation to embryogenesis.     

构建基于WindowsDNA的分布式多层应用系统

文章探讨了Windows DNA的体系结构和特性，提出一种基于WindowsDNA的分布式应用系统的设计思想和方法，并结合实例给出了如何用COM＋技术构造一个基于WindowsDNA体系的三层应用系统。     

Smart Innovation Engineering: Toward Intelligent Industries of the Future

ABSTRACT

Knowledge-based engineering systems are founded upon integration of knowledge into computer systems and are one of the core requirements for the future Industry 4.0. This paper presents a system called smart innovation engineering (SIE) capable of facilitating product innovation process semi-automatically. It enhances decision-making processes using the explicit knowledge of formal decision events. The SIE system carries the promise to support the innovation processes of manufactured products in a quick and efficient way. It stores and reuses past decisional events or sets of experiences related to innovation issues, which significantly enhances innovation progression. The analysis of basic concepts and implementation method proves that SIE system is an advanced form of cyber physical systems. It is flexible, systematic, fast, and supports customization. It can play a vital role toward Industry 4.0 development.     

Application of a novel IWO to the design of encoding sequences for DNA computing

Encoding and processing information in DNA-, RNA- and other biomolecule-based devices is an important requirement for DNA based computing with potentially important applications. To make DNA computing more reliable, much work has focused on designing the good DNA sequences. However, this is a bothersome task as encoding problem is an NP problem. In this paper, a new methodology based on the IWO algorithm is developed to optimize encoding sequences. Firstly, the mathematics models of constrained objective optimization design for encoding problems based on the thermodynamic criteria are set up. Then, a modified IWO method is developed by defining the colonizing behavior of weeds to overcome the obstacles of the original IWO algorithm, which cannot be applied to discrete problems directly. The experimental results show that the proposed method is effective and convenient for the user to design and select effective DNA sequences in silicon for controllable DNA computing.     

富铬酵母细胞的DNA、RNA和蛋白质结合铬的测定

使用中子活化分析方法测定了富铬酵母与普通酵母的ＤＮＡ、ＲＮＡ和蛋白质中铬的含量。研究铬与ＤＮＡ、ＲＮＡ和蛋白质的结合情况。结果发现,两种酵母的ＤＮＡ、ＲＮＡ和蛋白质提取率和浓度无明显差异,但富铬酵母中ＤＮＡ、ＲＮＡ和蛋白质的铬含量高于普通酵母,而且铬与ＤＮＡ的结合量明显高于ＲＮＡ和蛋白质,说明酵母细胞在含铬的培养基中培养时,铬进入细胞体内产生生物转化,并与酶母细胞的ＤＮＡ、ＲＮＡ和蛋白质发生了结合     

基于荧光显微镜的毛细管电泳系统的构建

毛细管电泳仪具有灵敏度高、分析速度快等优势,为降低其生产成本,基于电泳原理,以荧光显微镜为基础,设计了一套毛细管电泳系统。以20 bp(base pairs,碱基对)DNA ladder和100 bp DNA ladder为样本,全面分析了系统的稳定性、灵敏度和分离效果。结果表明:该系统在9 min内可以实现1500 bp以内DNA片段的高效分离,系统检测极限为0.1 ng/μL;在优化的电泳条件下,对限制性内切酶φX174-HincⅡ作用过的λ-DNA片段5 min内实现了291 bp与297 bp DNA片段的区分。     

激光与DNA作用的非线性扰动方程的研究

将激光与ＤＮＡ分子系统相互作用的运动方程化成Ｄｕｆｆｉｎｇ方程，进行了主共振、超谐波共振及两频激励组合共振的分析．从而成功地解释了激光育种中存在的一些难以理解的现象     

一种肿瘤基因表达数据的知识提取方法

本文以多发性骨髓瘤的基因表达数据为例,利用数据挖掘技术,提出了一种针对基因表达数据进行知识发现的方法.该方法通过计算基因的信息增益,结合神经网络,找出了特征基因集合,最后利用决策树进行特征规则的提取,给出了基于多发性骨髓瘤数据样本的产生式规则,为生物医学研究提供了一种分析和研究基因表达数据的参考方法.实验结果表明了该方法的有效性.