基因芯片在地下水污染研究中的应用北大核心

为了较系统地了解基因芯片在地下水污染研究中的应用进展,调研了基因芯片技术及其在地下水污染研究中应用的有关文献,简述了基因芯片原理、分类及实施流程,总结了系统发育寡核苷酸芯片和功能基因芯片在地下水污染研究中的最新应用进展,探讨了基因芯片检测性能、数据分析和应用等方面存在的问题和措施,在基因芯片性能改进和应用方面提出了进一步研究的方向。     

基因芯片在地下水污染研究中的应用

为了较系统地了解基因芯片在地下水污染研究中的应用进展,调研了基因芯片技术及其在地下水污染研究中应用的有关文献,简述了基因芯片原理、分类及实施流程,总结了系统发育寡核苷酸芯片和功能基因芯片在地下水污染研究中的最新应用进展,探讨了基因芯片检测性能、数据分析和应用等方面存在的问题和措施,在基因芯片性能改进和应用方面提出了进一步研究的方向。     

军事医学科学院中药现代研究的回顾与展望

军事医学科学院建院60年来,中药研究的学科建设在实践中迅速壮大和发展,逐步形成了完善的多学科结合的现代中药研究体系,在国家中药现代研究战略布局中占有重要地位,在理论创新、技术创新、基础和应用基础研究及新药开发等方面均取得了丰硕的成果,尤其在中药复方研究、中药单味药和活性成分研究、以＂组学＂技术及现代化学分离分析技术为代表的新技术和新方法在中药研究中的应用、中药质量控制和创新中药研究和开发等方面取得了明显进展,本文谨对此进行综述.     

物质流分析研究述评

物质流分析方法近年来在循环经济和可持续发展研究领域发展迅速。阐述了物质流分析的定义及其与自然生态系统物质流的区别,着重回顾了该研究方法的发展历程,阐明了物质流分析的主要观点、理论基础、研究思路及研究框架,详细阐译和对比分析了物质流分析的六大类指标及分析方法,并在物质流分析框架的基础上,建立循环经济及可持续发展的评价指标体系,并对物质流分析指标体系和方法学的研究意义及其在环境经济学中的地位进行了客观的评价,进而指出了物质流分析方法的不足之处。对物质流分析在不同层次的应用研究也进行了充分的阐述和分析。对物质流分析今后相关领域的进一步研究予以了讨论和展望。     

后基因组时代的生物信息学

随着人类基因组计划的完成,不断积累的巨量的生物学数据和快速发展的信息学技术,给后基因组时代的生物信息学研究带来了新的挑战。该文对后基因组时代的生物信息学研究内容进行了比较全面的描述,分别就其研究对象和研究方向作了区别讨论,分析了生物信息学研究的现状和趋势,比较了国内外的研究发展情况和差距。针对我国在研究中所存在的主要问题,提出了建议并做了展望。     

多年生黑麦草的逆境生理研究进展

在研究和借鉴国内外最新研究成果的基础上,系统论述和报道了多年生黑麦草在水分、温度以及重金属等逆境胁迫下的生理变化,展望了多年生黑麦草在逆境生理方面的研究趋势,指出多年生黑麦草的抗性机理以及相关分子生物学方面的研究将成为未来研究的重点和热点,为今后深入开展多年生黑麦草的研究和利用提供科学依据。     

超快过程激光生物学的内容、方法和意义 Ⅱ.超快过程激光生物学的研究领域

首先,讨论了用超短光脉冲对高等植物和细菌光合作用研究,从瞬态吸收研究推出了电子转移步骤。分析了对其他植物色素研究激光应用的可能性;其次,讨论在动物色素研究中的激光应用,它包括：黑色素的研究;视觉的原初过程;卟啉和它的衍生物（血红蛋白）研究及生物发光。进一步指出了紫外激光在蛋白质、核酸、糖类和脂类中的应用。     

类器官及其应用的研究进展

类器官弥补了传统研究中细胞简单模型与动物复杂模型的不足,为生命体关键功能研究提供了重要实验基础,已成为当前研究热点,并在疾病机理研究、药物筛选、再生医学、生物材料评价等方面具有重大理论意义和应用前景.本文对近10年类器官研究进行了综述,阐述出类器官研究的发展历程和研究现状,重点综述了类器官的主要研究领域,并解析类器官研究中存在的关键科学问题,为类器官在生物医药、再生医学和疾病精准治疗领域的研究和应用提供新思路.     

文昌鱼—研究脊柱动物起源和进化的模式动物

长久以来,文昌鱼一直被认为和生活在约5亿年前的脊椎动物的直接祖先相似。由于文昌鱼在进化上的重要性,它在动物学研究史上发挥着关键作用,近100多年来,文昌鱼作为研究对象曾数次受到动物学界青睐或冷落,大约10年前,随着分子生物学技术应用于文昌鱼研究,又激发了动物学家对文昌鱼的研究兴趣,又一次出现在文昌鱼研究的高潮,并且一直持续至今,分子生物学研究结果表明,文昌鱼样生物可能是环节动物样动物和最早的脊椎动物之间的进化中间体,因此,文昌鱼在动物学研究史上好像绕了个大圈又回到了原处,在被忽视一段时间之后,又重新占据脊椎动物起源和进化研究中心舞台的位置,成为研究脊椎动物起源和进化的模式动物。     

西北地区生物多样性特点及其研究思路

在探讨西北地区生物多样性特点的基础上,院述了西北地区生物多样保护研究的现状,分析了生物多样性面临的危机。在此基础上,提出了西北地区生物多样性研究的方向和具体思路：１．编目和监测系统研究;２．稀有濒危动植物的保护生物学研究;３．迁地保护和人工繁育,扩大人工种群的研究;４．生物多样性恢复的研究;５．生物多样性持续利用研究。     

化石记录的再评估

分子生物学和分支系统学的发展以及化石记录自身的局限性使得古生物地层资料在生物演化研究中的地位遭到质疑。连续的化石记录的发现肯定了化石分析的意义,数据库的建立与定量分析方法的应用为古生物学的研究增添了新生力量。     

Taxonomic identification bias does not drive patterns of abundance and diversity in theropod dinosaurs

The ability of palaeontologists to correctly diagnose and classify new fossil species from incomplete morphological data is fundamental to our understanding of evolution. Different parts of the vertebrate skeleton have different likelihoods of fossil preservation and varying amounts of taxonomic information, which could bias our interpretations of fossil material. Substantial previous research has focused on the diversity and macroevolution of non-avian theropod dinosaurs. Theropods provide a rich dataset for analysis of the interactions between taxonomic diagnosability and fossil preservation. We use specimen data and formal taxonomic diagnoses to create a new metric, the Likelihood of Diagnosis, which quantifies the diagnostic likelihood of fossil species in relation to bone preservation potential. We use this to assess whether a taxonomic identification bias impacts the non-avian theropod fossil record. We find that the patterns of differential species abundance and clade diversity are not a consequence of their relative diagnosability. Although there are other factors that bias the theropod fossil record that are not investigated here, our results suggest that patterns of relative abundance and diversity for theropods might be more representative of Mesozoic ecology than often considered.     

Do fossil plants signal palaeoatmospheric carbon dioxide concentration in the geological past?

Fossil, subfossil, and herbarium leaves have been shown to provide a morphological signal of the atmospheric carbon dioxide environment in which they developed by means of their stomatal density and index. An inverse relationship between stomatal density/index and atmospheric carbon dioxide concentration has been documented for all the studies to date concerning fossil and subfossil material. Furthermore, this relationship has been demonstrated experimentally by growing plants under elevated and reducedcarbon dioxide concentrations. To date, the mechanism that controls the stomatal density response to atmospheric carbon dioxide concentration remains unknown. However, stomatal parameters of fossil plants have been successfully used as a proxy indicator of palaeo-carbon dioxide levels. This paper presents new estimates of palaeo-atmospheric carbon dioxide concentrations for the Middle Eocene (Lutetian), based on the stomatal ratios of fossil Lauraceae species from Bournemouth in England. Estimates of atmospheric carbon dioxide concentrations derived from stomatal data from plants of the Early Devonian, Late Carboniferous, Early Permian and Middle Jurassic ages are reviewed in the light of new data. Semi-quantitative palaeo-carbon dioxide estimates based on the stomatal ratio (a ratio of the stomatal index of a fossil plant to that of a selected nearest living equivalent) have in the past relied on the use of a Carboniferous standard. The application of a new standard based on the present-day carbon dioxide level is reported here for comparison. The resultant ranges of palaeo-carbon dioxide estimates made from standardized fossil stomatal ratio data are in good agreement with both carbon isotopic data from terrestrial and marine sources and long-term carbon cycle modelling estimates for all the time periods studied. These data indicate elevated atmospheric carbon dioxide concentrations during the Early Devonian, Middle Jurassic and Middle Eocene, and reduced concentrations during the Late Carboniferous and Early Permian. Such data are important in demonstrating the long-term responses of plants to changing carbon dioxide concentrations and in contributing to the database needed for general circulation model climatic analogues.     

Dating primate divergences through an integrated analysis of palaeontological and molecular data

Estimation of divergence times is usually done using either the fossil record or sequence data from modern species. We provide an integrated analysis of palaeontological and molecular data to give estimates of primate divergence times that utilize both sources of information. The number of preserved primate species discovered in the fossil record, along with their geological age distribution, is combined with the number of extant primate species to provide initial estimates of the primate and anthropoid divergence times. This is done by using a stochastic forwards-modeling approach where speciation and fossil preservation and discovery are simulated forward in time. We use the posterior distribution from the fossil analysis as a prior distribution on node ages in a molecular analysis. Sequence data from two genomic regions (CFTR on human chromosome 7 and the CYP7A1 region on chromosome 8) from 15 primate species are used with the birth-death model implemented in mcmctree in PAML to infer the posterior distribution of the ages of 14 nodes in the primate tree. We find that these age estimates are older than previously reported dates for all but one of these nodes. To perform the inference, a new approximate Bayesian computation (ABC) algorithm is introduced, where the structure of the model can be exploited in an ABC-within-Gibbs algorithm to provide a more efficient analysis.     

Evaluating fossil calibrations for dating phylogenies in light of rates of molecular evolution: a comparison of three approaches

Evolutionary and biogeographic studies increasingly rely on calibrated molecular clocks to date key events. Although there has been significant recent progress in development of the techniques used for molecular dating, many issues remain. In particular, controversies abound over the appropriate use and placement of fossils for calibrating molecular clocks. Several methods have been proposed for evaluating candidate fossils; however, few studies have compared the results obtained by different approaches. Moreover, no previous study has incorporated the effects of nucleotide saturation from different data types in the evaluation of candidate fossils. In order to address these issues, we compared three approaches for evaluating fossil calibrations: the single-fossil cross-validation method of Near, Meylan, and Shaffer (2005. Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles. Am. Nat. 165:137-146), the empirical fossil coverage method of Marshall (2008. A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibration points. Am. Nat. 171:726-742), and the Bayesian multicalibration method of Sanders and Lee (2007. Evaluating molecular clock calibrations using Bayesian analyses with soft and hard bounds. Biol. Lett. 3:275-279) and explicitly incorporate the effects of data type (nuclear vs. mitochondrial DNA) for identifying the most reliable or congruent fossil calibrations. We used advanced (Caenophidian) snakes as a case study; however, our results are applicable to any taxonomic group with multiple candidate fossils, provided appropriate taxon sampling and sufficient molecular sequence data are available. We found that data type strongly influenced which fossil calibrations were identified as outliers, regardless of which method was used. Despite the use of complex partitioned models of sequence evolution and multiple calibrations throughout the tree, saturation severely compressed basal branch lengths obtained from mitochondrial DNA compared with nuclear DNA. The effects of mitochondrial saturation were not ameliorated by analyzing a combined nuclear and mitochondrial data set. Although removing the third codon positions from the mitochondrial coding regions did not ameliorate saturation effects in the single-fossil cross-validations, it did in the Bayesian multicalibration analyses. Saturation significantly influenced the fossils that were selected as most reliable for all three methods evaluated. Our findings highlight the need to critically evaluate the fossils selected by data with different rates of nucleotide substitution and how data with different evolutionary rates affect the results of each method for evaluating fossils. Our empirical evaluation demonstrates that the advantages of using multiple independent fossil calibrations significantly outweigh any disadvantages.     

Laboratory culture and maintenance of the horseshoe crab (Limulus polyphemus)

Often referred to as a living fossil, the American horseshoe crab, Limulus polyphemus, is one of the most-studied invertebrate animals in the world. It has served as a model in Nobel Prize-winning eye research, and researchers use a component of its blood to detect bacterial contamination in medical devices and drugs. The authors review the conditions necessary for housing these animals in the laboratory.     

Die Datenbanken PaleoTax und Goniat - Vorstufen eines paläontologischen Informationssystems

The database systems PaleoTax and GONIAT provide detailed information on literature, taxonomy, morphology and occurrence of fossil invertebrate groups. PaleoTax is designed for Mesozoic corals, GONIAT for Paleozoic ammonoids, but both can be modified to cover other fossil groups. Both systems use dBASE format, but with different database structures. PaleoTax aims at the complete storage of all available objective data, GONIAT provides determinations based upon morphologic criteria, and includes information on geographic distribution and stratigraphic range of every taxon. A combination of both systems could lead to the establishment of a comprehensive paleontological information system useful for research and practical stratigraphic applications.     

Synthesizing and databasing fossil calibrations: divergence dating and beyond

Divergence dating studies, which combine temporal data from the fossil record with branch length data from molecular phylogenetic trees, represent a rapidly expanding approach to understanding the history of life. National Evolutionary Synthesis Center hosted the first Fossil Calibrations Working Group (3-6 March, 2011, Durham, NC, USA), bringing together palaeontologists, molecular evolutionists and bioinformatics experts to present perspectives from disciplines that generate, model and use fossil calibration data. Presentations and discussions focused on channels for interdisciplinary collaboration, best practices for justifying, reporting and using fossil calibrations and roadblocks to synthesis of palaeontological and molecular data. Bioinformatics solutions were proposed, with the primary objective being a new database for vetted fossil calibrations with linkages to existing resources, targeted for a 2012 launch.     

On formation‐based sampling proxies and why they should not be used to correct the fossil record

The fossil record is a unique resource on the history of life, but it is well known to be incomplete. In a series of high‐profile papers, a residual modelling technique has been applied to correct the raw palaeodiversity signal for this bias and incompleteness, and the claim is made that the processed time series are more accurate than the raw data. We apply empirical and simulation approaches to test for correlation and directionality of any relationships between rock and fossil data. The empirical data comprise samples of the global fossil record through the Phanerozoic, and we use simulations to assess whether randomly sampled subsets of modelled data can be improved by application of the residual modelling technique. Our results show that using formation counts as a sampling proxy to correct the fossil record via residual modelling is ill founded. The supposedly independent model of sampling is information‐redundant with respect to the raw palaeodiversity data it seeks to correct, and so the outputs are generally likely to be further from the truth than the raw data. We recommend that students of palaeodiversity cease to use residual modelling estimates based on formation counts, and suggest that results from a substantial number of papers published in the past ten years require re‐evaluation.