Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

DNA sequences determined from ancient organisms have high error rates, primarily due to uracil bases created by cytosine deamination. We use synthetic oligonucleotides, as well as DNA extracted from mammoth and Neandertal remains, to show that treatment with uracil–DNA–glycosylase and endonuclease VIII removes uracil residues from ancient DNA and repairs most of the resulting abasic sites, leaving undamaged parts of the DNA fragments intact. Neandertal DNA sequences determined with this protocol have greatly increased accuracy. In addition, our results demonstrate that Neandertal DNA retains in vivo patterns of CpG methylation, potentially allowing future studies of gene inactivation and imprinting in ancient organisms.     

Necessary sites: identical duplication of living organisms

The paper deals with the concept of the identity of living organisms, a concept used up until now very ambiguously. The discussion rests on the combination of two concepts, one proposed by Munzer (1993) and another derived from the considerations of Riedl (1975). The first is the proposal that the identity of living organisms depends on the properties of their elementary constituents, such as cells and tissues, and that these properties, in turn, depend on those of their DNA and RNA. It follows that the identity of a living organism remains constant or changes during life according to whether its DNA and RNA content also remains constant or changes. The second is the consideration that, during duplication of a cell population, the informational content of the population does not increase if the duplicated cells are identical (increase only of redundant DNA). On the other hand the informational content of the cell population increases if the duplicated cells are the result of a variation-selection process (increase of essential DNA). The changes of DNA and RNA content, occurring in the germinal cells during phylogenesis and in the somatic cells of the evolutionary systems during ontogenesis, lead, therefore, to the generation of new identities. Living organisms are suggested to reflect two types of identity, that of the deterministic and that of the evolutionary systems. Since the informational content of the deterministic systems (the essential DNA content) remains approximately constant during life, their identity also remains constant. The changes in the number of elementary constituents and cell volumes during the processes of hypertrophy and atrophy are accompanied only by changes in the amount of DNA (the redundant DNA). On the other hand the informational content of the evolutionary systems (the essential DNA), such as the brain-mind system, the immunological system and some receptor systems, undergo a marked increase during the ontogenic development: this leads to changes of identity of these systems. For example, in the immunological system the process of mutation and recombination of the DNA of the immunological cells leads to the generation of new proteins in the amount about 10,000 times larger than that produced through the decodification of the genome. Also the construction of the neural network, and of a number of synapses much larger than that of the neuronal cells, requires the generation of an amount of new information much larger than that contained in the genome. In short, the attribution of a double identity to living organisms reflects the simultaneous presence of systems developing either within strictly programmed limits or without programs and limits, say as closed or open projects. The difference between the two types of systems explains the different effects in the case of the transplants. The identity of the recipient of transplants is not altered in the case of transplants of a deterministic system but is so in case of transplants of evolutionary systems. There is now a widespread fear of the possibility of human cloning. It is argued that this fear is unjustified because a cloning process can never succeed in duplicating those parts which are essential for the characters of humans, namely those concerned with the properties of the evolutionary systems.     

Ancient DNA studies: new perspectives on old samples

In spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of ancient DNA samples to study the processes of evolution and to test models and assumptions commonly used to reconstruct patterns of evolution and to analyze population genetics and palaeoecological changes. Recent advances in DNA technologies, such as next-generation sequencing make it possible to recover DNA information from archaeological and paleontological remains allowing us to go back in time and study the genetic relationships between extinct organisms and their contemporary relatives. With the next-generation sequencing methodologies, DNA sequences can be retrieved even from samples (for example human remains) for which the technical pitfalls of classical methodologies required stringent criteria to guaranty the reliability of the results. In this paper, we review the methodologies applied to ancient DNA analysis and the perspectives that next-generation sequencing applications provide in this field.     

Shotgun microbial profiling of fossil remains

Millions to billions of DNA sequences can now be generated from ancient skeletal remains thanks to the massive throughput of next‐generation sequencing platforms. Except in cases of exceptional endogenous DNA preservation, most of the sequences isolated from fossil material do not originate from the specimen of interest, but instead reflect environmental organisms that colonized the specimen after death. Here, we characterize the microbial diversity recovered from seven c. 200‐ to 13 000‐year‐old horse bones collected from northern Siberia. We use a robust, taxonomy‐based assignment approach to identify the microorganisms present in ancient DNA extracts and quantify their relative abundance. Our results suggest that molecular preservation niches exist within ancient samples that can potentially be used to characterize the environments from which the remains are recovered. In addition, microbial community profiling of the seven specimens revealed site‐specific environmental signatures. These microbial communities appear to comprise mainly organisms that colonized the fossils recently. Our approach significantly extends the amount of useful data that can be recovered from ancient specimens using a shotgun sequencing approach. In future, it may be possible to correlate, for example, the accumulation of postmortem DNA damage with the presence and/or abundance of particular microbes.     

Universal Internucleotide Statistics in Full Genomes: A Footprint of the DNA Structure and Packaging?

Uncovering the fundamental laws that govern the complex DNA structural organization remains challenging and is largely based upon reconstructions from the primary nucleotide sequences. Here we investigate the distributions of the internucleotide intervals and their persistence properties in complete genomes of various organisms from Archaea and Bacteria to H. Sapiens aiming to reveal the manifestation of the universal DNA architecture. We find that in all considered organisms the internucleotide interval distributions exhibit the same -exponential form. While in prokaryotes a single -exponential function makes the best fit, in eukaryotes the PDF contains additionally a second -exponential, which in the human genome makes a perfect approximation over nearly 10 decades. We suggest that this functional form is a footprint of the heterogeneous DNA structure, where the first -exponential reflects the universal helical pitch that appears both in pro- and eukaryotic DNA, while the second -exponential is a specific marker of the large-scale eukaryotic DNA organization.     

Molecular mechanism of homologous recombination in meiosis: origin and biological significance

Sexual reproduction prevails among eukaryotic organisms. The problem of advantage of sexual reproduction over asexual reproduction remains a subject of not stopping discussions. According to one of the hypotheses, sexual reproduction and homologous recombination which accompanies gamete formation during meiosis has arisen to increase genetic variability and, as consequence, a fitness of organisms. Many researches show that homologous recombination play an important role in reparation of DNA in various groups of organisms irrespective of the way of their reproduction. Involvement of recombination in meiosis, however, is impossible to explain only by DNA repair functions. The hypothesis, that a recombination in the course of sexual process is a source of variability, also is not capable to explain existence of this process well. There is convincing evidence that the homologous recombination in meiosis is necessary for formation of bivalents. A physical connection between homologous chromosomes that is formed by recombination is required for correct chromosome segregation during meiotic division and formation of gametes of full value.     

Single-stranded DNA from viruses, prokaryotes and eukaryotes]

The review presents the results of investigations of single-stranded DNAs of viruses, bacteria and cells of higher organisms. Methods of revealing, isolating and analysis of these DNAs are presented. A large variety of single-stranded DNA containing genomes of plant and animal viruses was revealed. Attention is drawn to the integration and replication of viral genomes. Results of SV40 integration during the first two days after infection of Chinese hamster cells are shown. Results of studying multi-copy single-stranded DNA in bacterial cells were analysed. In separate sections, the replication of plasmid single-stranded DNA was studied as well as the problem of plasmid stability in cells. Advances in bacteria transformation studies are stated. Data of single-stranded DNA investigation in cells of higher organisms are mainly presented on the example of early embryos. Data on the analysis of gene hypersensitivity to nuclease S1 are given. A table of proteins destabilizing and unweaving single-stranded DNA and a classification table of proteins bound with single-stranded DNA according to their functional significance are presented. It is stated that the problem of single-stranded DNA significance in cells remains open, although some results have been achieved.     

Evolutionary Rates in Veronica L. (Plantaginaceae): Disentangling the Influence of Life History and Breeding System

The evolutionary rate at which DNA sequences evolve is known to differ between different groups of organisms. However, the reasons for these different rates are seldom known. Among plants, the generation-time hypothesis, which states that organisms that reproduce faster also have more DNA substitutions per time, has gained most popularity. We evaluate the generation-time hypothesis using 131 DNA sequences from the plastid trnLF region and the nuclear ribosomal ITS region of the genus Veronica (Plantaginaceae). We also examine the alternative hypothesis that a higher substitution rate is correlated with selfing breeding system. Selfing is associated with annual life history in many organisms and may thus often be the underlying reason for observed correlations of annual life history with other characters. We provide evidence that annual life history is more likely to be the responsible factor for higher substitution rates in Veronica than a selfing breeding system. Nevertheless, the way in which annual life history may influence substitution rate in detail remains unknown, and some possibilities are discussed.     

细胞命运抉择的数学模型:活性氧与p53的关系及其意义(英文)

生物体内的细胞生活在复杂的环境中。在生物体内,活性氧是普遍存在的。生物体内的活性氧可以诱导DNA损伤,最终破坏基因组稳定性。其中,对基因组损伤最严重的是DNA双链断裂损伤。肿瘤抑制因子p53是细胞内介导DNA损伤反应的重要因子。p53可以修复损伤DNA,保护轻度受损细胞。而当细胞受到严重损伤时,p53能够诱发细胞凋亡,从而维持机体稳态。p53的动力学对于细胞的反应性具有重要影响,然而对这方面却缺少系统的认识。因此在本文中,我们主要关注运用数学模型方法研究p53脉冲的动力学性质,从而揭示细胞内潜在的生死选择机制。     

Sequences isolated from aDrosophila early-ecdysone puff are expressed in rat liver

We have studied the presence of a cloned fragment of DNA from Drosophila melanogaster in other organisms by means of nucleic acid hybridization analysis. The isolated region is localized in polytene chromosomes at the 63F subdivision. This region includes a puff that responds within minutes to ecdysone stimulation. We have found that 63F DNA from D. melanogaster hybridizes 'in situ' to both DNA and RNA from D. simulans, D. teissieri, and D. hydei. In all these species the isolated DNA remains associated with one early-ecdysone stimulated puff. The isolated Drosophila recombinant DNA is also complementary to polyadenylated RNA from foetal and adult rat liver but fails to hybridize to the nonpolyadenylated RNA classes from both sources and to polyadenylated RNA from rat mammary glands.     

A review and appraisal of the DNA damage theory of ageing

Given the central role of DNA in life, and how ageing can be seen as the gradual and irreversible breakdown of living systems, the idea that damage to the DNA is the crucial cause of ageing remains a powerful one. DNA damage and mutations of different types clearly accumulate with age in mammalian tissues. Human progeroid syndromes resulting in what appears to be accelerated ageing have been linked to defects in DNA repair or processing, suggesting that elevated levels of DNA damage can accelerate physiological decline and the development of age-related diseases not limited to cancer. Higher DNA damage may trigger cellular signalling pathways, such as apoptosis, that result in a faster depletion of stem cells, which in turn contributes to accelerated ageing. Genetic manipulations of DNA repair pathways in mice further strengthen this view and also indicate that disruption of specific pathways, such as nucleotide excision repair and non-homologous end joining, is more strongly associated with premature ageing phenotypes. Delaying ageing in mice by decreasing levels of DNA damage, however, has not been achieved yet, perhaps due to the complexity inherent to DNA repair and DNA damage response pathways. Another open question is whether DNA repair optimization is involved in the evolution of species longevity, and we suggest that the way cells from different organisms respond to DNA damage may be crucial in species differences in ageing. Taken together, the data suggest a major role of DNA damage in the modulation of longevity, possibly through effects on cell dysfunction and loss, although understanding how to modify DNA damage repair and response systems to delay ageing remains a crucial challenge.     

古DNA及其在生物系统与进化研究中的应用

古DNA是指从已经死亡的古代生物的遗体和遗迹中得到的DNA.本文回顾了近20年古DNA研究所经历的3个阶段,从早期参与研究的科学家较少并主要利用克隆技术,到后来由于PCR技术的出现以及提取化石DNA技术的成熟从而出现大量有关古DNA的报道;近几年由于发现不少问题,并引起激烈的争论,科学家们因此而开始考虑古DNA的真实性问题,并且提出了开展古DNA研究的严格标准.本文还讨论了古DNA在人类起源、系统发育重建、动植物驯化及考古研究中的重要意义以及现状,表明古DNA的研究给某些原先的观点如人类的非洲起源说提供了重要证据,也对某些观点提出了挑战;古DNA研究还提供了某些已经灭绝生物的形态学和分子资料,为从序列上确定古代材料的系统位置并有效地补充仅用现代DNA建立起来的谱系提供了来自古生物的依据.在动植物驯化及考古方面,古DNA证据也为科学家提供了许多有价值的信息.最后,本文还对古DNA研究的应用前景进行了展望.     

古DNA 及其在生物系统与进化研究中的应用

古DNA是指从已经死亡的古代生物的遗体和遗迹中得到的DNA。本文回顾了近20年古DNA研究所经历的3个阶段, 从早期参与研究的科学家较少并主要利用克隆技术, 到后来由于PCR技术的出现以及提取化石DNA技术的成熟从而出现大量有关古DNA的报道; 近几年由于发现不少问题, 并引起激烈的争论, 科学家们因此而开始考虑古DNA的真实性问题, 并且提出了开展古DNA研究的严格标准。本文还讨论了古DNA在人类起源、系统发育重建、动植物驯化及考古研究中的重要意义以及现状, 表明古DNA的研究给某些原先的观点如人类的非洲起源说提供了重要证据, 也对某些观点提出了挑战; 古DNA研究还提供了某些已经灭绝生物的形态学和分子资料, 为从序列上确定古代材料的系统位置并有效地补充仅用现代DNA建立起来的谱系提供了来自古生物的依据。在动植物驯化及考古方面, 古DNA证据也为科学家提供了许多有价值的信息。最后, 本文还对古DNA研究的应用前景进行了展望。