Phantom mutation hotspots in human mitochondrial DNA

Phantom mutations are systematic artifacts generated in the course of the sequencing process. Contra common belief these artificial mutations are nearly ubiquitous in sequencing results, albeit at frequencies that may vary dramatically. The amount of artifacts depends not only on the sort of automated sequencer and sequencing chemistry employed, but also on other lab-specific factors. An experimental study executed on four samples under various combinations of sequencing conditions revealed a number of phantom mutations occurring at the same sites of mitochondrial DNA (mtDNA) repeatedly. To confirm these and identify further hotspots for artifacts, > 5000 mtDNA electropherograms were screened for artificial patterns. Further, > 30000 published hypervariable segment 1 sequences were compared at potential hotspots for phantom mutations, especially for variation at positions 16085 and 16197. Resequencing of several samples confirmed the artificial nature of these and other polymorphisms in the original publications. Single-strand sequencing, as typically executed in medical and anthropological studies, is thus highly vulnerable to this kind of artifacts. In particular, phantom mutation hotspots could easily lead to misidentification of somatic mutations and to misinterpretations in all kinds of clinical mtDNA studies.

Methylation and gene mutation in eukaryotic DNA

5-methylcytosine (m(5)C) as a rare base exists in eukaryotic genomes, which is a normal constitution in many eukaryotic DNA and the existence of m(5)C is a feature of eukaryotic DNA. Under regular physiological conditions, cytosine of eukaryotic DNA is usually methylated. Up to the present, many people consider that the m(5)C may be mutation hotspots by the deamination leading to gene mutation. Our study indicated that the spontaneous mutation caused by the transition of G.C --> A.T, in eukaryotic DNA, may result from the tautomer changing of base pairs and may also be cause by other factor actions, however it could not be caused by the deamination of m(5)C.

基于流域—库区—坝区模型“三重边界嵌套”方法的河南济源蟒河口水库渗漏数值模拟研究

Constructing reservoir in mountain area, in order to avoid dangerous reservoir and ensure long-term stable reservoir storage, study on reservoir leakage has been one of research hotspots. How to accurately predict the capacity of leakage and the effect of anti-seepage after reservoir impoundment under different anti-seepage measures is one of the most difficult problems of study on reservoir leakage. The paper took Manghekou Reservoir as a case study, which is located in Jiyuan City, Henan Province, China. Based on the system analysis of the geological and hydrogeological characters in the research area, the hydrogeological conceptual model was established. Then, according to the triplex boundary nested grid model method, using three-dimensional numerical simulation technique, the 3-D groundwater seepage flow numerical model was established in the study area. Based on the model, the change of seepage flow field, the capacity of leakage and the effect of anti-seepage are predicted after Manghekou reservoir impoundment under different condition. The reasonable and reliable anti-seepage measure is selected according to the model. All these provides scientific basis for the design and assessment of anti-seepage measure for the reservoir in mountain area.

鄂尔多斯盆地东部古生界沉积体系与储层研究

Ordos basin with profuse coal, petroleum, natural gas and others mineral resources create the comprehensiveness notice of earthling, and became one of studying hotspots for China and foreign countries geology, petroleum and natural gas geology's workman. Late years, having found commercial value of large middle type gas pools in the upper Palaeozoic group, which have exhibited a very good foreground for gas exploring and exploitation. Through the new gas exploring headway and the exploring course, the east of the basin should regard Ordovician weathering crust in the upper Palaeozoic group, tide flat and barrier-lagoon, deltaic deposit system in the lower Palaeozoic group as the major exploration and research emphasis. Furthermore, it has been found that much gas showed wells, which has gain quantitative industry gas flow wells, especially the new assessment invigorative harvest, and bode that the east of the Ordos basin possess major exploring potential. In regional tectonic, the research region mainly lay in the Yishan incline, and the east part involved the west part of Jinxi warping belt. In tectonic and sedimentary evolution, it had inherited the characteristic of whole basin. From Latepaleozoic to triassic epoch, it developed gradational the transition of sedimentary that changed from sea to land, and from river to lake.

地幔对流理论及其在解释地球物理观测的应用

With the improving of mantle convection theory, the developing of computing method and increasing of the measurement data, we can numerically simulate more clearly about the effects on some geophysical observed phenomenons such as the global heat flow and global lithospheric stress field in the Earth's surface caused by mantle convection, which is the primary mechanism for the transport of heat from the Earth's deep interior to its surface and the underlying force mechanism of dynamics in the Earth.Chapter 1 reviews the historical background and present research state of mantle convection theory.In Chapter 2, the basic conception of thermal convection and the basic theory about mantle flow.The effects on generation and distribution of global lithospheric stres s field induced by mantle flow are the subject of Chapter 3. Mantle convection causes normal stress and tangential stresses at the bottom of the lithosphere, and then the sublithospheric stress field induces the lithospheric deformation as sixrface force and results in the stress field within the lithosphere. The simulation shows that the agreement between predictions and observations is good in most regions. Most of subduction zones and continental collisions are under compressive. While ocean ridges, such as the east Pacific ridge, the Atlantic ridge and the east African rift valley, are under tensile. And most of the hotspots preferentially occur in regions where calculated stress is tensile. The calculated directions of the most compressive principal horizontal stress are largely in accord with that of the observation except for some regions such as the NW-Pacifie subduction zone and Qinghai-Tibet Plateau, in which the directions of the most compressive principal horizontal stress are different. It shows that the mantel flow plays an important role in causing or affecting the large-scale stress field within the lithosphere.The global heat flow simulation based on a kinematic model of mantle convection is given in Chapter 4. Mantle convection velocities are calculated based on the internal loading theory at first, the velocity field is used as the input to solve the thermal problem. Results show that calculated depth derivatives of the near surface temperature are closely correlated to the observed surface heat flow pattern. Higher heat flow values around midocean ridge systems can be reproduced very well. The predicted average temperature as a function of function of depth reveals that there are two thermal boundary layers, one is close to the surface and another is close to the core-mantle boundary, the rest of the mantle is nearly isothermal. Although, in most of the mantle, advection dominates the heat transfer, the conductive heat transfer is still locally important in the boundary layers and plays an important role for the surface heat flow pattern. The existence of surface plates is responsible for the long wavelength surface heat flow pattern.In Chapter 5, the effects on present-day crustal movement in the China Mainland resulted from the mantle convection are introduced. Using a dynamic method, we present a quantitative model for the present-day crustal movement in China. We consider not only the effect of the India-Eurasia collision, the gravitational potential energy difference of the Tibet Plateau, but also the contribution of the shear traction on the bottom of the lithosphere induced by the global mantle convection. The comparison between our results and the velocity field obtained from the GPS observation shows that our model satisfactorily reproduces the general picture of crustal deformation in China. Numerical modeling results reveal that the stress field on the base of the lithosphere induced by the mantle flow is probably a considerable factor that causes the movement and deformation of the lithosphere in continental China with its eflfcet focuing on the Eastern China A numerical research on the small-scale convection with variable viscosity in the upper mantle is introduced in Chapter 6. Based on a two-dimensional model, small-scale convection in the mantle-lithosphere system with variable viscosity is researched by using of finite element method. Variation of viscosity in exponential form with temperature is considered in this paper The results show that if viscosity is strongly temperature-dependent, the upper part of the system does not take a share in the convection and a stagnant lid, which is identified as lithosphere, is formed on the top of system because of low temperature and high viscosity. The calculated surface heat flow, topography and gravity anomaly are associated well with the convection pattern, namely, the regions with high heat flow and uplift correspond to the upwelling flow, and vice versa.In Chapter 7, we give a brief of future research subject: The inversion of lateral density heterogeneity in the mantle by minimizing the viscous dissipation.