RecQ helicases and topoisomerases: components of a conserved complex for the regulation of genetic recombination

Maintenance of genomic stability relies on the efficient and accurate execution of DNA repair pathways, and is essential for cell viability and the prevention of cancer. Mutation of genes encoding RecQ helicases or topoisomerases gives rise to genomic instability through excessive recombination. Here, we review the recent biochemical and genetic evidence to indicate that these two classes of protein act in concert in a conserved pathway to maintain genomic stability by preventing inappropriate recombination.     

Bridging epigenomics and complex disease: the basics

The DNA sequence largely defines gene expression and phenotype. However, it is becoming increasingly clear that an additional chromatin-based regulatory network imparts both stability and plasticity to genome output, modifying phenotype independently of the genetic blueprint. Indeed, alterations in this “epigenetic” control layer underlie, at least in part, the reason for monozygotic twins being discordant for disease. Functionally, this regulatory layer comprises post-translational modifications of DNA and histones, as well as small and large noncoding RNAs. Together these regulate gene expression by changing chromatin organization and DNA accessibility. Successive technological advances over the past decade have enabled researchers to map the chromatin state with increasing accuracy and comprehensiveness, catapulting genetic research into a genome-wide era. Here, aiming particularly at the genomics/epigenomics newcomer, we review the epigenetic basis that has helped drive the technological shift and how this progress is shaping our understanding of complex disease.     

Evaluating the Rationality of Fixed-event Forecasts

A test of forecast rationality based on the weak efficiency of fixed-event forecasts was proposed by Nordhaus (1987). This paper considers the scope for pooling fixed-event forecasts across ‘events’, to deliver more powerful tests of the weak-efficiency hypothesis, when only a small number of fixed-event forecasts are available. In an empirical illustration we demonstrate the usefulness of this approach. We also suggest an interpretation of the rejection of the null hypothesis of weak efficiency in favour of negative autocorrelation in series of revisions to fixed-event forecasts. The relationship between weak efficiency and rationality when loss functions are asymmetric and prediction error variances are time-varying is also considered.© 1997 John Wiley & Sons, Ltd.     

Regulation of the cell cycle following DNA damage in normal and Ataxia telangiectasia cells

A proportion of the population is exposed to acute doses of ionizing radiation through medical treatment or occupational accidents, with little knowledge of the immedate effects. At the cellular level, ionizing radiation leads to the activation of a genetic program which enables the cell to increase its chances of survival and to minimize detrimental manifestations of radiation damage. Cytotoxic stress due to ionizing radiation causes genetic instability, alterations in the cell cycle, apoptosis, or necrosis. Alterations in the G1, S and G2 phases of the cell cycle coincide with improved survival and genome stability. The main cellular factors which are activated by DNA damage and interfere with the cell cycle controls are: p53, delaying the transition through the G1-S boundary; p21^WAF1/CIPI, preventing the entrance into S-phase; proliferating cell nuclear antigen (PCNA) and replication protein A (RPA), blocking DNA replication; and the p53 variant protein p53as together with the retinoblastoma protein (Rb), with less defined functions during the G2 phase of the cell cycle. By comparing a variety of radioresistant cell lines derived from radiosensitive ataxia talangiectasia cells with the parental cells, some essential mechanisms that allow cells to gain radioresistance have been identified. The results so far emphasise the importance of an adequate delay in the transition from G2 to M and the inhibition of DNA replication in the regulation of the cell cycle after exposure to ionizing radiation.     

Welcome the Family of FANCJ-like Helicases to the Block of Genome Stability Maintenance Proteins

The FANCJ family of DNA helicases is emerging as an important group of proteins for the prevention of human disease, cancer, and chromosomal instability. FANCJ was identified by its association with breast cancer, and is implicated in Fanconi Anemia. Proteins with sequence similarity to FANCJ are important for maintenance of genomic stability. Mutations in genes encoding proteins related to FANCJ, designated ChlR1 in human and Chl1p in yeast, result in sister chromatid cohesion defects. Nematodes mutated in dog-1 show germline as well as somatic deletions in genes containing guanine-rich DNA. Rtel knockout mice are embryonic lethal, and embryonic stem cells show telomere loss and chromosomal instability. FANCJ also shares sequence similarity with human XPD and yeast RAD3 helicases required for nucleotide excision repair. The recently solved structure of XPD has provided new insight to the helicase core and accessory domains of sequence related Superfamily 2 helicases. The functions and roles of members of the FANCJ-like helicase family will be discussed. Received 17 September 2008; received after revision 24 October 2008; accepted 28 October 2008     

顺层岩质边坡加陡开采的稳定性研究

为了研究确定顺层边坡陡帮开采的稳定性,以元宝山露天矿南帮边坡为研究对象,基于刚体极限平衡理论,采用RFPA中的细观本构模型,研究分析南帮边坡受采动影响应力和位移随时间的变化规律,分析滑坡机理、滑坡模式,并确定最终境界的合理边坡角。结果表明：采用细观模型得到的岩体变形随时间的变化规律与现场观测基本吻合,上部岩体沿圆弧滑面拉裂滑移,下部沿弱层组合滑面剪切滑移,且滑体上部均以下沉为主,向采空区发生水平位移,下部以水平位移为主。计算剖面边坡的稳定系数Fs〈1．2,应放缓边坡角使φ=18°以保证边坡稳定使露天矿安全生产并获得最大效益。     

Effect of pulsing electromagnetic fields on DNA synthesis in mammalian cells in culture

DNA synthesis in Chinese hamster V79 cells was significantly enhanced when they were exposed to weak, pulsing electromagnetic fields generated by specific combinations of the pulse width (25 microseconds), frequency (10, 100 Hz) and magnetic intensity (2 X 10(-5), 8 X 10(-5) T). Conversely the DNA synthesis of cells in the fields at 4 X 10(-4) T was repressed to 80% of that in controls not exposed to the fields.     

基于ANSYS的石油井架风载的有限元分析

为了研究全自动带压修井机井架承受风载的受力情况,找出井架结构的应力集中点,利用有限元分析软件ANSYS对其进行实体三维建模,施加风载荷并求解,得到结构在各个方向上的应力云图以及变形图;找出结构在承受风载的薄弱处;避免出现较大应力。这对于提高井架的质量非常有益。此方法可以有效地获得和真实工矿相符合的结果;令石油井架稳定性达到了要求;对类似结构的设计分析也具有一定的参考价值。     

DNA repair mechanisms in embryonic stem cells

Embryonic stem cells (ESCs) can undergo unlimited self-renewal and retain the pluripotency to differentiate into all cell types in the body. Therefore, as a renewable source of various functional cells in the human body, ESCs hold great promise for human cell therapy. During the rapid proliferation of ESCs in culture, DNA damage, such as DNA double-stranded breaks, will occur in ESCs. Therefore, to realize the potential of ESCs in human cell therapy, it is critical to understand the mechanisms how ESCs activate DNA damage response and DNA repair to maintain genomic stability, which is a prerequisite for their use in human therapy. In this context, it has been shown that ESCs harbor much fewer spontaneous mutations than somatic cells. Consistent with the finding that ESCs are genetically more stable than somatic cells, recent studies have indicated that ESCs can mount more robust DNA damage responses and DNA repair than somatic cells to ensure their genomic integrity.     

Epigenetic choreography of stem cells: the DNA demethylation episode of development

Reversible DNA methylation is a fundamental epigenetic manipulator of the genomic information in eukaryotes. DNA demethylation plays a very significant role during embryonic development and stands out for its contribution in molecular reconfiguration during cellular differentiation for determining stem cell fate. DNA demethylation arbitrated extensive make-over of the genome via reprogramming in the early embryo results in stem cell plasticity followed by commitment to the principal cell lineages. This article attempts to highlight the sequential phases and hierarchical mode of DNA demethylation events during enactment of the molecular strategy for developmental transition. A comprehensive knowledge regarding the pattern of DNA demethylation during embryogenesis and organogenesis and study of the related lacunae will offer exciting avenues for future biomedical research and stem cell-based regenerative therapy.     

State of the Field: Why novel prediction matters

There is considerable disagreement about the epistemic value of novel predictive success, i.e. when a scientist predicts an unexpected phenomenon, experiments are conducted, and the prediction proves to be accurate. We survey the field on this question, noting both fully articulated views such as weak and strong predictivism, and more nascent views, such as pluralist reasons for the instrumental value of prediction. By examining the various reasons offered for the value of prediction across a range of inferential contexts (including inferences from data to phenomena, from phenomena to theory, and from theory to framework), we can see that neither weak nor strong predictivism captures all of the reasons for valuing prediction available. A third path is presented, Pluralist Instrumental Predictivism; PIP for short.     

Review¶Psychrophilic enzymes: molecular basis of cold adaptation

Psychrophilic organisms have successfully colonized polar and alpine regions and are able to grow efficiently at sub-zero temperatures. At the enzymatic level, such organisms have to cope with the reduction of chemical reaction rates induced by low temperatures in order to maintain adequate metabolic fluxes. Thermal compensation in cold-adapted enzymes is reached through improved turnover number and catalytic efficiency. This optimization of the catalytic parameters can originate from a highly flexible structure which provides enhanced abilities to undergo conformational changes during catalysis. Thermal instability of cold-adapted enzymes is therefore regarded as a consequence of their conformational flexibility. A survey of the psychrophilic enzymes studied so far reveals only minor alterations of the primary structure when compared to mesophilic or thermophilic homologues. However, all known structural factors and weak interactions involved in protein stability are either reduced in number or modified in order to increase their flexibility.     

The common fragile site FRA16D gene product WWOX: roles in tumor suppression and genomic stability

The fragile WWOX gene, encompassing the chromosomal fragile site FRA16D, is frequently altered in human cancers. While vulnerable to DNA damage itself, recent evidence has shown that the WWOX protein is essential for proper DNA damage response (DDR). Furthermore, the gene product, WWOX, has been associated with multiple protein networks, highlighting its critical functions in normal cell homeostasis. Targeted deletion of Wwox in murine models suggests its in vivo requirement for proper growth, metabolism, and survival. Recent molecular and biochemical analyses of WWOX functions highlighted its role in modulating aerobic glycolysis and genomic stability. Cumulatively, we propose that the gene product of FRA16D, WWOX, is a functionally essential protein that is required for cell homeostasis and that its deletion has important consequences that contribute to the neoplastic process. This review discusses the essential role of WWOX in tumor suppression and genomic stability and how its alteration contributes to cancer transformation.     

Weak values and consistent histories in quantum theory

A relation is obtained between weak values of quantum observables and the consistency criterion for histories of quantum events. It is shown that “strange” weak values for projection operators (such as values less than zero) always correspond to inconsistent families of histories. It is argued that using the ABL rule to obtain probabilities for counterfactual measurements corresponding to those strange weak values gives inconsistent results. This problem is shown to be remedied by using the conditional weight, or pseudo-probability, obtained from the multiple-time application of Lüders’ Rule. It is argued that an assumption of reverse causality (a form of time symmetry) implies that weak values obtain, in a restricted sense, at the time of the weak measurement as well as at the time of post-selection. Finally, it is argued that weak values are more appropriately characterized as multiple-time amplitudes than expectation values, and as such can have little to say about counterfactual questions.     

Killing cancer by targeting genes that cancer cells have lost: allele-specific inhibition,a novel approach to the treatment of genetic disorders

Oligonucleotide-based drugs are now rapidly establishing themselves as an important tool in both research and treatment of genetic disorders. In the past many problems were encountered in using antisense oligonucleotides. Our expanding knowledge and new oligonucleotide chemistries are giving us the chance to treat serious genetic disorders such as cancer in novel, elegant and effective ways not previously possible. In addition, recent knowledge about RNA interference may add to these new approaches for disease treatment with oligonucleotide-based drugs. In this review we discuss one such novel therapeutic strategy against cancer called allele-specific inhibition (ASI). ASI is an approach where cancer cells are attacked at one of the few widely occurring and consistently weak points: the loss of large segments of DNA. Oligonucleotide-based drugs may provide the required selectivity for this therapeutic approach.     

Homologous recombination-mediated repair of DNA double-strand breaks operates in mammalian mitochondria

Mitochondrial DNA is frequently exposed to oxidative damage, as compared to nuclear DNA. Previously, we have shown that while microhomology-mediated end joining can account for DNA deletions in mitochondria, classical nonhomologous DNA end joining, the predominant double-strand break (DSB) repair pathway in nucleus, is undetectable. In the present study, we investigated the presence of homologous recombination (HR) in mitochondria to maintain its genomic integrity. Biochemical studies revealed that HR-mediated repair of DSBs is more efficient in the mitochondria of testes as compared to that of brain, kidney and spleen. Interestingly, a significant increase in the efficiency of HR was observed when a DSB was introduced. Analyses of the clones suggest that most of the recombinants were generated through reciprocal exchange, while ~ 30% of recombinants were due to gene conversion in testicular extracts. Colocalization and immunoblotting studies showed the presence of RAD51 and MRN complex proteins in the mitochondria and immunodepletion of MRE11, RAD51 or NIBRIN suppressed the HR-mediated repair. Thus, our results reveal importance of homologous recombination in the maintenance of mitochondrial genome stability.