Genomic DNA k-mer spectra: models and modalities

Background  

The empirical frequencies of DNA k-mers in whole genome sequences provide an interesting perspective on genomic complexity, and the availability of large segments of genomic sequence from many organisms means that analysis of k-mers with non-trivial lengths is now possible.     

Genomic DNA methylation: the mark and its mediators

Methylation of DNA at position five of the cytosine ring occurs at most CpG dinucleotides in the mammalian genome and is essential for embryonic viability. With several of the key proteins now known, it has become possible to approach the biological significance of this epigenetic system through both biochemistry and genetics. As a result, advances have been made in our understanding of the mechanisms by which DNA methylation is targeted to specific regions of the genome and interpreted by methyl-CpG-binding proteins. Recent studies have illuminated the role of DNA methylation in controlling gene expression and have strengthened its links with histone modification and chromatin remodelling.     

Genomic stability: FANCJ-dependent G4 DNA repair

G-rich regions have the potential to form G4 DNA upon replication, which can lead to genomic instability. FANCJ, a G4 DNA helicase, has been shown to be critical for the stability of regions that match the G4 signature motif by experiments analyzing its nematode homolog.     

Genomic approaches to DNA repair and mutagenesis

DNA damage is a constant threat to cells, causing cytotoxicity as well as inducing genetic alterations. The steady-state abundance of DNA lesions in a cell is minimized by a variety of DNA repair mechanisms, including DNA strand break repair, mismatch repair, nucleotide excision repair, base excision repair, and ribonucleotide excision repair. The efficiencies and mechanisms by which these pathways remove damage from chromosomes have been primarily characterized by investigating the processing of lesions at defined genomic loci, among bulk genomic DNA, on episomal DNA constructs, or using in vitro substrates. However, the structure of a chromosome is heterogeneous, consisting of heavily protein-bound heterochromatic regions, open regulatory regions, actively transcribed genes, and even areas of transient single stranded DNA. Consequently, DNA repair pathways function in a much more diverse set of chromosomal contexts than can be readily assessed using previous methods. Recent efforts to develop whole genome maps of DNA damage, repair processes, and even mutations promise to greatly expand our understanding of DNA repair and mutagenesis. Here we review the current efforts to utilize whole genome maps of DNA damage and mutation to understand how different chromosomal contexts affect DNA excision repair pathways.     

Mini-scale Genomic DNA Extraction from Cotton

Large amounts of polyphenolics in cotton leaves make it difficult to obtain high-quality genomic DNA during extraction. A procedure to isolate nuclear DNA from local cotton leaves (gossypium hirsutum, MNH93, CIM443, FH672) was therefore developed. It consists of rapid isolation of stable nuclei, which hinders covalent interactions with phenolics, followed by DNA extraction. The yield and quality of the resulting DNA is satisfactory and the protocol can be scaled up or down according to sample size. It is suitable for PCR and the restriction enzyme digestion needed for Southern and RFLP analysis.     

Genomic imprinting in unstable DNA diseases

Evidence for recombination suppression has been identified in linkage studies of several unstable DNA diseases. Also sex-specific changes in recombination frequency have been detected at the loci of Huntington's disease and myotonic dystrophy. It can be hypothesized that meiotic recombination is regulated by genome-wide genomic imprinting and that changes in meiotic recombination imply the presence of the genomic imprinting defect. If aberrant recombination at the locus of trinucleotide repeat expansion is verified, new theoretical and experimental opportunities will arise in studies on the role of genomic imprinting in the unstable DNA diseases.     

陈旧标本DNA提取方法

对于自然环境中的或长期保存的动物标本,由于保存环境不良或保存时间过长,DNA提取的难度较大。受标本保存时间和损害程度等因素影响,导致实验结果的不稳定性加强,对于同一标本需要反复实验。为了提高DNA提取效率,节省实验成本,现对陈旧损坏标本的DNA提取方法进行综述。     

Genomic DNA damage in mouse transgenesis

Creating transgenic mammals is currently a very inefficient process. In addition to problems with transgene integration and unpredictable expression patterns of the inserted gene, embryo loss occurs at various developmental stages. In the present study, we demonstrate that this loss is due to chromosomal damage. We examined the integrity of chromosomes in embryos produced by microinjection of pronuclei, intracytoplasmic sperm injection (ICSI), and in vitro fertilization (IVF)-mediated transgenesis, and correlated these findings with the abilities of embryos to develop in vitro and yield transgenic morulas/blastocysts. Chromosomal analysis was performed after microinjection of the pronuclei in zygotes, as well as in parthenogenetic and androgenetic embryos. In all the pronuclei injection groups, significant oocyte arrest and increased incidence of chromosome breaks were observed after both transgenic DNA injection and sham injection. This indicates that the DNA damage is a transgene-independent effect. In ICSI-mediated transgenesis, there was no significant oocyte arrest. The observed chromosomal damage was lower than that after pronuclei microinjection in zygotes and was dependent upon the presence of exogenous DNA. The occurrence of DNA breaks, as measured by comet assay performed on the sperm prior to ICSI, showed that DNA damage was present in the sperm before fertilization. Embryonic development in vitro and transgene expression at the morula/blastocyst stage were higher in ICSI-mediated transgenesis than after microinjection of pronuclei into zygotes. Sperm-mediated gene transfer via IVF did not affect chromosome integrity, allowed good embryo development, but did not yield any transgenic embryos. The present study demonstrates that DNA damage occurs after both the microinjection of pronuclei and ICSI-mediated transgenesis, albeit through different mechanisms.     

酵母全基因组芯片的应用

酵母作为最常用的模式生物,其全基因组测序最先完成。利用已知的酵母基因组信息,结合基因芯片技术,可进一步系统研究酵母的功能基因组表达。基因芯片技术是上世纪末发展起来的一项集分子生物学、生物信息学和电子学等科目的生物高新技术。酵母全基因组芯片,可以用以从基因表达水平,研究环境、物理、化学因子、毒理和药物作用的机制,在最终阐明酵母基因组功能的同时,为生物学研究提供更优化的模式生物模型。     

金藻基因组DNA的提取与PCR扩增

以金藻门群体和单细胞藻类的典型代表--球形棕囊藻和绿色巴夫藻为研究对象,对金藻基因组DNA的提取方法进行了深入研究,并以psbA基因的PCR扩增结果对4种DNA提取方法进行了检测.结果显示,PVP法和高盐法安全、快速、经济,获得的基因组DNA产量高,但DNA杂质含量也较高.CTAB法虽然也具有安全、快速等优势,但提取的DNA产量较低.玻璃粉法提取的DNA质量好,产量也较高,但操作略为烦琐,经济费用高.结论:就球形棕囊藻而言,玻璃粉法是4种方法中最好的DNA提取方法.就绿色巴夫藻而言,4种方法都行,但是从经济和方便考虑,以高盐法为最好.     

Sensory modalities are not separate modalities: plasticity and interactions

Historically, perception has been viewed as a modular function, with the different sensory modalities operating independently of each other. Recent behavioral and brain imaging studies challenge this view, by suggesting that cross-modal interactions are the rule and not the exception in perception, and that the cortical pathways previously thought to be sensory-specific are modulated by signals from other modalities.     

大青杨基因组DNA的提纯及鉴定

由于各种林木在组织结构和化学成分上的差异,核酸的提取方法将不尽相同。高质量的DNA是林木分子生物学研究的关键因素。探索一种科学的、合适的DNA提取方法尤为重要。本文对大青杨基因组DNA的提取方法进行了优化。通过电泳检测、紫外分析、限制性内切酶消化和随机引物PCR扩增鉴定所获得的基因组DNA,证明其完全可以满足分子生物学实验的要求。     

Genomic gigantism: DNA loss is slow in mountain grasshoppers

Several studies have shown DNA loss to be inversely correlated with genome size in animals. These studies include a comparison between Drosophila and the cricket, Laupala, but there has been no assessment of DNA loss in insects with very large genomes. Podisma pedestris, the brown mountain grasshopper, has a genome over 100 times as large as that of Drosophila and 10 times as large as that of Laupala. We used 58 paralogous nuclear pseudogenes of mitochondrial origin to study the characteristics of insertion, deletion, and point substitution in P. pedestris and Italopodisma. In animals, these pseudogenes are "dead on arrival"; they are abundant in many different eukaryotes, and their mitochondrial origin simplifies the identification of point substitutions accumulated in nuclear pseudogene lineages. There appears to be a mononucleotide repeat within the 643-bp pseudogene sequence studied that acts as a strong hot spot for insertions or deletions (indels). Because the data for other insect species did not contain such an unusual region, hot spots were excluded from species comparisons. The rate of DNA loss relative to point substitution appears to be considerably and significantly lower in the grasshoppers studied than in Drosophila or Laupala. This suggests that the inverse correlation between genome size and the rate of DNA loss can be extended to comparisons between insects with large or gigantic genomes (i.e., Laupala and Podisma). The low rate of DNA loss implies that in grasshoppers, the accumulation of point mutations is a more potent force for obscuring ancient pseudogenes than their loss through indel accumulation, whereas the reverse is true for Drosophila. The main factor contributing to the difference in the rates of DNA loss estimated for grasshoppers, crickets, and Drosophila appears to be deletion size. Large deletions are relatively rare in Podisma and Italopodisma.     

Genomic instability and cancer: networks involved in response to DNA damage

A new approach to cancer and new methods in examining rare human chromosome breakage syndromes have brought to light complex interactions between different pathways involved in damage response, cell cycle checkpoint control and DNA repair. The genes affected in these different syndromes are involved in networks of processes that respond to DNA damage and prevent chromosomal aberrations during the cell cycle. The genes involved include the ATM, ATR, FA-associated genes, NBS1 and the cancer susceptibility genes BRCA1 and BRCA2. Chromosomal instability is a common feature of many human cancers and most of the instability syndromes, characterized by sensitivity to different types of DNA damage, also show increased cancer susceptibility. Better understanding of these syndromes and their links with familial cancer provide new insight into associations between defects in DNA damage response, cell cycle control, DNA repair and cancer. Understanding the damage response repair networks that these studies are revealing will have important implications for the development of cancer management and treatment.     

Macrorestriction Analysis of Caenorhabditis Elegans Genomic DNA

The usefulness of genomic physical maps is greatly enhanced by linkage of the physical map with the genetic map. We describe a ``macrorestriction mapping' procedure for Caenorhabditis elegans that we have applied to this endeavor. High molecular weight, genomic DNA is digested with infrequently cutting restriction enzymes and size-fractionated by pulsed field gel electrophoresis. Southern blots of the gels are probed with clones from the C. elegans physical map. This procedure allows the construction of restriction maps covering several hundred kilobases and the detection of polymorphic restriction fragments using probes that map several hundred kilobases away. We describe several applications of this technique. (1) We determined that the amount of DNA in a previously uncloned region is <220 kb. (2) We mapped the mes-1 gene to a cosmid, by detecting polymorphic restriction fragments associated with a deletion allele of the gene. The 25-kb deletion was initially detected using as a probe sequences located ~400 kb away from the gene. (3) We mapped the molecular endpoint of the deficiency hDf6, and determined that three spontaneously derived duplications in the unc-38-dpy-5 region have very complex molecular structures, containing internal rearrangements and deletions.     

利用鳍条提取样品总DNA初探

本文报告了从鱼类鳍条中抽提基因组ＤＮＡ的方法,并对所得ＤＮＡ样品做了电泳、紫外分光光度分析,ＳｏｕｔｈｅｒｎＢｌｏｔ等分子杂交实验,均证明这个方法是简便的取样方法,又能完整地保存实验鱼类。