Parvovirus Diversity and DNA Damage Responses

Parvoviruses have a linear single-stranded DNA genome, around 5 kb in length, with short imperfect terminal palindromes that fold back on themselves to form duplex hairpin telomeres. These contain most of the cis-acting information required for viral “rolling hairpin” DNA replication, an evolutionary adaptation of rolling-circle synthesis in which the hairpins create duplex replication origins, prime complementary strand synthesis, and act as hinges to reverse the direction of the unidirectional cellular fork. Genomes are packaged vectorially into small, rugged protein capsids ∼260 Å in diameter, which mediate their delivery directly into the cell nucleus, where they await their host cell’s entry into S phase under its own cell cycle control. Here we focus on genus-specific variations in genome structure and replication, and review host cell responses that modulate the nuclear environment.Viruses from the family Parvoviridae are unique in having a linear single-stranded DNA genome, ∼5 kb in length, which terminates in short (120–420 base) imperfect palindromes that fold into self-priming hairpin telomeres. These viruses replicate via a “rolling hairpin” mechanism, with strong evolutionary and mechanistic links to “rolling-circle” replication, as reviewed in detail in previous editions of this work (Cotmore and Tattersall 1996, 2006). Rolling hairpin synthesis relies on the ability of each hairpin to give rise to a duplex origin sequence, which can be nicked by a viral initiator nuclease to create a base-paired DNA primer, and to function as a hinge, allowing quasi-circular synthesis by alternately folding and unfolding to shuttle a continuous unidirectional replication fork back and forth along linear DNA. Together with a few adjacent nucleotides, these palindromes provide all of the cis-acting information required for viral DNA replication and packaging. However, the size, sequence, and predicted structures of the hairpins can vary substantially between genera, or even between the two ends of a single genome, and they appear to have adapted to fulfill multiple additional roles in the life cycle of specific viruses. Parvoviral DNA amplification proceeds via a unidirectional single-strand displacement mechanism through a series of monomeric and concatemeric duplex replicative-form (RF) intermediates, and while the viral initiator protein, variously called NS1 or Rep, serves both as a site- and strand-specific nickase and as a 3′-to-5′ helicase, all other replicative functions are co-opted from the host cell. This mechanism benefits from suppression of host DNA synthesis, and generates long stretches of single-stranded DNA with alien terminal structures that invoke host damage responses, which impact both positively and negatively on viral replication. Although details of the mechanisms that mediate parvoviral replication have received relatively little attention since our previous review (Cotmore and Tattersall 2006), recognition that infection is invariably associated with host DNA damage responses (DDRs), some of which are specifically required for efficient viral DNA amplification, has led to significant reappraisal of the nuclear environment and replicative machinery available to these viruses. In parallel, major advances have occurred in our knowledge of genome diversity and cell specificity in this ever-expanding family, which provide novel insight into mechanisms of replication control.The International Committee on Taxonomy of Viruses (ICTV, Tijssen et al. 2011), classifies viruses in the family Parvoviridae that infect vertebrates as the subfamily Parvovirinae, which currently contains just five genera: the Parvoviruses, Dependoviruses, Amdoviruses, Erythroviruses, and Bocaviruses, although there are at least two additional genera, tentatively called Partetraviruses and Avetalviruses, that await ICTV recognition. This reflects a major jump in known virus diversity, with many new species and genera first identified in clinical or veterinary samples using PCR-based virus discovery methods (Allander et al. 2005; Jones et al. 2005; Day and Zsak 2010). Potential human pathogens that are still pending recognition include genetic variants of Human Bocavirus (HBoV 1–4), which are particularly common in the respiratory and gastrointestinal tracts of children (Kapoor et al. 2010; Kantola et al. 2011), and two broadly distributed genotypes of a “PARV4”-based genus (the aforementioned Partetraviruses), parenterally transmitted among injecting drug users, hemophiliacs, and polytransfused individuals (Sharp et al. 2009; Lahtinen et al. 2011). Most recently, viruses from another potential genus, with sequences resembling both Parvoviruses and Amdoviruses, were detected in fecal samples from children in Burkina Faso, and tentatively named Bufaviruses (Phan et al. 2012). In vitro culture systems or high titer clinical samples are often not available for new members, which can thus only be studied by PCR amplification from patient tissue.Although the vast majority of parvoviruses replicate without the aid of a helper virus, the adeno-associated viruses (AAVs) from the genus Dependovirus establish latent infections that only become productive when cells are coinfected with a more complex virus, typically an adeno- or herpesvirus. To date the replication mechanisms of adeno-associated virus 2 (AAV2) and minute virus of mice (MVM), from the genus Parvovirus, have been studied in detail, as documented in previous editions of this work. Here we adopt a broader perspective, discussing inter-genera variations that shed light on replication control, and reviewing host cell responses to viral infection that modulate the nuclear environment.     

Genetic Dissection of Anopheles gambiae Gut Epithelial Responses to Serratia marcescens

Genetic variation in the mosquito Anopheles gambiae profoundly influences its ability to transmit malaria. Mosquito gut bacteria are shown to influence the outcome of infections with Plasmodium parasites and are also thought to exert a strong drive on genetic variation through natural selection; however, a link between antibacterial effects and genetic variation is yet to emerge. Here, we combined SNP genotyping and expression profiling with phenotypic analyses of candidate genes by RNAi-mediated silencing and 454 pyrosequencing to investigate this intricate biological system. We identified 138 An. gambiae genes to be genetically associated with the outcome of Serratia marcescens infection, including the peptidoglycan recognition receptor PGRPLC that triggers activation of the antibacterial IMD/REL2 pathway and the epidermal growth factor receptor EGFR. Silencing of three genes encoding type III fibronectin domain proteins (FN3Ds) increased the Serratia load and altered the gut microbiota composition in favor of Enterobacteriaceae. These data suggest that natural genetic variation in immune-related genes can shape the bacterial population structure of the mosquito gut with high specificity. Importantly, FN3D2 encodes a homolog of the hypervariable pattern recognition receptor Dscam, suggesting that pathogen-specific recognition may involve a broader family of immune factors. Additionally, we showed that silencing the gene encoding the gustatory receptor Gr9 that is also associated with the Serratia infection phenotype drastically increased Serratia levels. The Gr9 antibacterial activity appears to be related to mosquito feeding behavior and to mostly rely on changes of neuropeptide F expression, together suggesting a behavioral immune response following Serratia infection. Our findings reveal that the mosquito response to oral Serratia infection comprises both an epithelial and a behavioral immune component.     

Genetic Instability,DNA Damage and Atherosclerosis

We review the role of somatic mutations and genetic instability in the pathogenesis of atherosclerosis, suggesting novel therapeutic approaches.     

DNA Damage Responses following Exposure to Modulated Radiation Fields

During the delivery of advanced radiotherapy treatment techniques modulated beams are utilised to increase dose conformity across the target volume. Recent investigations have highlighted differential cellular responses to modulated radiation fields particularly in areas outside the primary treatment field that cannot be accounted for by scattered dose alone. In the present study, we determined the DNA damage response within the normal human fibroblast AG0-1522B and the prostate cancer cell line DU-145 utilising the DNA damage assay. Cells plated in slide flasks were exposed to 1 Gy uniform or modulated radiation fields. Modulated fields were delivered by shielding 25%, 50% or 75% of the flask during irradiation. The average number of 53BP1 or γH2AX foci was measured in 2 mm intervals across the slide area. Following 30 minutes after modulated radiation field exposure an increase in the average number of foci out-of-field was observed when compared to non-irradiated controls. In-field, a non-uniform response was observed with a significant decrease in the average number of foci compared to uniformly irradiated cells. Following 24 hrs after exposure there is evidence for two populations of responding cells to bystander signals in-and out-of-field. There was no significant difference in DNA damage response between 25%, 50% or 75% modulated fields. The response was dependent on cellular secreted intercellular signalling as physical inhibition of intercellular communication abrogated the observed response. Elevated residual DNA damage observed within out-of-field regions decreased following addition of an inducible nitric oxide synthase inhibitor (Aminoguanidine). These data show, for the first time, differential DNA damage responses in-and out-of-field following modulated radiation field delivery. This study provides further evidence for a role of intercellular communication in mediating cellular radiobiological response to modulated radiation fields and may inform the refinement of existing radiobiological models for the optimization of advanced radiotherapy treatment plans.     

DNA Damage Responses and Oxidative Stress in Dyskeratosis Congenita

Dyskeratosis congenita (DC) is an inherited multisystem disorder of premature aging, cancer predisposition, and bone marrow failure caused by selective exhaustion of highly proliferative cell pools. DC patients also have a poor tolerance to chemo/radiotherapy and bone marrow transplantation. Although critically shortened telomeres and defective telomere maintenance contribute to DC pathology, other mechanisms likely exist. We investigate the link between telomere dysfunction and oxidative and DNA damage response pathways and assess the effects of antioxidants. In vitro studies employed T lymphocytes from DC subjects with a hTERC mutation and age-matched controls. Cells were treated with cytotoxic agents, including Paclitaxel, Etoposide, or ionizing radiation. Apoptosis and reactive oxygen species (ROS) were assessed by flow cytometry, and Western blotting was used to measure expression of DNA damage response (DDR) proteins, including total p53, p53S15, and p21^WAF. N-acetyl-cysteine (NAC), an antioxidant, was used to modulate cell growth and ROS. In stimulated culture, DC lymphocytes displayed a stressed phenotype, characterized by elevated levels of ROS, DDR and apoptotic markers as well as a proliferative defect that was more pronounced after exposure to cytotoxic agents. NAC partially ameliorated the growth disadvantage of DC cells and decreased radiation-induced apoptosis and oxidative stress. These findings suggest that oxidative stress may play a role in the pathogenesis of DC and that pharmacologic intervention to correct this pro-oxidant imbalance may prove useful in the clinical setting, potentially alleviating untoward toxicities associated with current cytotoxic treatments.     

Astrocytic Responses to DNA Delivery Using Nucleofection

Nucleofection is a powerful non-viral transfection technique that can deliver plasmid DNA with high efficiency to cells that are traditionally difficult to transfect. In this study, we demonstrate that nucleofection of astrocytes grown in primary cell culture resulted in 76 ± 9% transfected cells and low cytotoxicity. However, the nucleofected astrocytes showed a reduced re-attachment to the growth media when replated and subsequent impairment of proliferation. This led to substantially decreased cell densities during the initial 72 h following transfection. Furthermore, these cells were less efficient at producing wound closure in a scratch model of injury. Nucleofection also resulted in the generation of a small proportion of polynucleated cells. The findings demonstrate that nucleofection provides a valuable technique for delivering DNA to astrocytes in culture. However, considerable care is needed in designing and interpreting such studies because of long-lasting changes induced in key properties of these cells by the nucleofection process.     

Control of Female Reproduction in Drosophila: Genetic Dissection Using Gynandromorphs

The sexual behavior of Drosophila melanogaster gynandromorphs was studied to analyze the relationship between different steps in the female reproductive pathway. It was assumed that, in some gynandromorphs, certain female functions are missing because the corresponding control sites (foci) are either composed of male tissue or did not develop. A given gynandromorph can show elements of both male and female reproductive pathways. None of the steps of the female reproductive pathway appeared to be dependent on any other, in contrast to male behavior where, for example, following of females is a prerequisite for attempted copulation. By correlating each of the behaviors with the genotype of the cuticle, we confirmed previous findings that the focus for the female sex appeal is located in the abdomen, but receptivity to copulation is controlled by a site in the head. Many of the gynandromorphs did not lay eggs, presumably because either the focus controlling egg transfer from the ovaries to the uterus or the one controlling egg deposition was composed of male tissue. Many of the nonovipositing gynandromorphs laid eggs while dying or could be induced to deposit eggs after implantation of hormone-producing glands or topical application of a juvenile hormone analog. Some of the noninseminated gynandromorphs laid eggs at the rate characteristic for inseminated females, suggesting that an oviposition focus (mapping in the head region) suppresses oviposition in virgin females, but not in gynandromorphs whose focus is composed of male tissue. Some of the inseminated gynandromorphs oviposited eggs at a low rate, possibly because the focus responsible for detection of insemination could not function properly. Some of the inseminated gynandromorphs laid unfertilized eggs, revealing the importance of the focus controlling sperm release from the seminal receptacle. Foci controlling egg transfer, egg deposition and sperm release are located in the thorax, according to mosaic fate mapping results and studies on the reproductive behavior of decapitated females. The location of egg deposition in the culture vial seems to be controlled by a brain site. Sexual behavior in Drosophila does not depend on the presence (or absence) of the ovary or germ line.     

利用杉木的F1代群体构建遗传连锁图谱

对于杉木 1∶1分离的分子标记位点 ,提出了一种新的构建遗传连锁图谱的策略。通过二点连锁分析 ,任意两个位点的连锁相和重组率可以得到推断和估计。对于一个连锁群中的最优排序 ,采用隐马尔可夫链模型的方法进行多位点的连锁分析。该作图方法比通常林木上所用的“拟测交”作图方法更有效。采用该作图策略 ,利用句容0号无性系 (♀ )×柔叶杉 (♂ )的F1代群体的AFLP分子标记数据重建了句容 0号无性系和柔叶杉的遗传连锁图谱。在句容 0号无性系的连锁图谱中 ,有 10 1个标记分布在 11个连锁群上 ,图谱的总长度为 2 2 82 6cM ,平均图距为 2 2 6cM ,单个连锁群上最多含有 17个标记 ,最少含有 5个标记 ;在柔叶杉的连锁图谱中 ,有 94个标记分布在 11个连锁群上 ,图谱的总长度为 2 5 6 5 8cM ,平均图距为 2 7 3cM ,单个连锁群上最多含有 16个标记 ,最少含有 4个标记。构建的句容 0号无性系和柔叶杉的遗传连锁图谱比原有的图谱分别增加了 2 6个标记和 2 8个标记 ,双亲的图谱共增加了 5 4个AFLP标记 ,使图谱上的分子标记总数达到 195个 ,双亲遗传图谱的跨度均超过了 2 0 0 0cM ,基本上达到了杉木基因组的长度 ,图谱的覆盖率接近于 10 0 %。利用新的作图方法可以较大提高分子标记在图谱上的分辨率 ,得到可认为是     

利用杉木的F1代群体构建遗传连锁图谱

对于杉木11分离的分子标记位点,提出了一种新的构建遗传连锁图谱的策略.通过二点连锁分析,任意两个位点的连锁相和重组率可以得到推断和估计.对于一个连锁群中的最优排序,采用隐马尔可夫链模型的方法进行多位点的连锁分析.该作图方法比通常林木上所用的"拟测交"作图方法更有效.采用该作图策略,利用句容0号无性系(♀)×柔叶杉(♂)的F1代群体的AFLP分子标记数据重建了句容0号无性系和柔叶杉的遗传连锁图谱.在句容0号无性系的连锁图谱中,有101个标记分布在11个连锁群上,图谱的总长度为2 282.6 cM,平均图距为22.6 cM,单个连锁群上最多含有17个标记,最少含有5个标记;在柔叶杉的连锁图谱中,有94个标记分布在11个连锁群上,图谱的总长度为2 565.8 cM,平均图距为27.3 cM,单个连锁群上最多含有16个标记,最少含有4个标记.构建的句容0号无性系和柔叶杉的遗传连锁图谱比原有的图谱分别增加了26个标记和28个标记,双亲的图谱共增加了54个AFLP标记,使图谱上的分子标记总数达到195个,双亲遗传图谱的跨度均超过了2 000 cM,基本上达到了杉木基因组的长度,图谱的覆盖率接近于100%.利用新的作图方法可以较大提高分子标记在图谱上的分辨率,得到可认为是覆盖了整个基因组的遗传连锁框架图.     

Investigating DNA Radiation Damage Using X-Ray Absorption Spectroscopy

The biological influence of radiation on living matter has been studied for years; however, several questions about the detailed mechanism of radiation damage formation remain largely unanswered. Among all biomolecules exposed to radiation, DNA plays an important role because any damage to its molecular structure can affect the whole cell and may lead to chromosomal rearrangements resulting in genomic instability or cell death. To identify and characterize damage induced in the DNA sugar-phosphate backbone, in this work we performed x-ray absorption spectroscopy at the P K-edge on DNA irradiated with either UVA light or protons. By combining the experimental results with theoretical calculations, we were able to establish the types and relative ratio of lesions produced by both UVA and protons around the phosphorus atoms in DNA.     

Genetic Dissection of Histone Function

Mutational analysis is an essential tool for understanding the functions of genes within a living organism. The budding yeastSaccharomyces cerevisiaeprovides an excellent model system for dissecting the genetics of histone function at the molecular and cellular levels. A simple gene organization, plus a wide variety of genetic strategies, makes it possible to directly manipulate a specific histone genein vitroand then examine the expression of mutant allelesin vivo.Recent methods for manipulating the yeast histone genes have been designed to facilitate both site-directed analysis of structure/function relationships and unbiased screens targeted at specific functional pathways. The conservation of histone and nucleosome structure throughout evolution means that the principles discovered through genetic studies in yeast will be broadly applicable to the chromatin of more complex eukaryotes.     

心脏发育的基因调控

心脏发育是一个复杂的过程.在脊椎动物和无脊椎动物果蝇中驱动早期心脏分化的基因具有惊人的相似性.以果蝇、斑马鱼、小鼠等作为模式动物,以心脏的发育过程为主线,探讨了心脏发育的基因调控的研究进展.