基因芯片技术和蛋白质组技术在神经科学中的应用及其研究进展

基因芯片技术和蛋白质组技术是最近发展起来的高通量技术,二者的出现使同时分析神经系统的大量基因的表达和基因产物蛋白质及其相互作用网络成为可能。它们在神经科学中的应用为了解脑功能提供了前所未有的机会。一个典型的基因芯片实验包括：芯片的准备或购买、靶DNA和探针的准备或标记、标记探针与靶DNA的杂交、芯片扫描和影象信息的数据分析。蛋白质组技术较为复杂,包括蛋白质分离、鉴定和信息分析三方面的内容。其中,分离技术多种多样。若分离技术以二维电泳为基础,则该实验通常由以下步骤组成：蛋白质样品的准备、电泳分离、染胶、分离蛋白点的切除、蛋白质的酶解(常用胰蛋白酶)、质谱分析(鉴定)和数据的信息处理。本文综述这两项技术的内容和实验步骤,然后着重叙述它们在神经科学中的应用,讨论其优缺点和面临的挑战,展望其发展前景。     

Artificial insemination: the state of the art

The history of research into artificial insemination (AI) is over two centuries old and its commercial application now spans 75 years. It is appropriate to reflect on the contribution of this powerful method of gene dispersal. AI remains as one of the most important assisted reproductive technologies. The three cornerstones for its application are: it is simple, economical and successful. The importance of AI will be challenged in the next few decades. The remarkable progress made in other assisted reproductive technologies does have the potential to rapidly generate offspring. The challenge for any of these reproductive technologies to attain widespread use is to match AI in being simple, economical and successful. This review aims at capturing the salient advances in AI, the comparisons with natural mating and other reproductive technologies, and, whether the future of AI will be challenged. It predicts what the new horizon looks like and the role that AI will play in the overall reproductive technologies landscape.     

用生态工程技术控制农村非点源水污染

非点源污染的本质是农村生态系统的严重失调,生态工程技术是进行流域生态修复,强化物质循环的有效方法,非点源污染的治理策略有控制径流污染和控制源头污染两个方面。本文介绍了多水塘系统,植被缓冲带,湿地系统,生态农业、坡面生态工程和污染物生态处理6种生态治理技术,它们的有机结合可形成控制非点源污染的流域生态工程,执行时,应该因地制宜,还要加强资金、管理和教育的投入。     

LCA study of a plasma television device

Purpose  

Nowadays, there is one television device for every four human beings, making television one of the most popular pieces of electrical and electronic equipment in our society, with the so-called flat-screen technologies gaining more and more market share. For one such technology, the plasma display panel (PDP), no complete life cycle assessment (LCA) studies have existed thus far, and therefore, the question as to their environmental performance, especially as compared with LCD technology, is still open. This paper describes a detailed LCA study of a PDP television, including a first comparison of it with the two competing technologies, the cathode ray tube and the liquid crystal display technologies.     

Combining microarrays and genetic analysis

Gene expression can be studied at a genome-wide scale with the aid of modern microarray technologies. Expression profiling of tens to hundreds of individuals in a genetic population can reveal the consequences of genetic variation. In this paper it is argued that the design and analysis of such a study is not a matter of simply applying the existing and more-or-less standard computational tools for microarrays to a new type of experimental data. It is shown how to fully exploit the power of genetics through optimal experimental design and analysis for two major microarray technologies, cDNA two-colour arrays and Affymetrix short oligonucleotide arrays.     

Embryo technologies and animal health - consequences for the animal following ovum pick-up, in vitro embryo production and somatic cell nuclear transfer

Mammalian reproductive technologies that aim either to complement or to transcend conventional livestock breeding options have contributed to some of the most remarkable achievements in the field of reproductive biology in recent decades. In so doing they have extended our horizons in two distinct dimensions, the first concerning what it is technically possible to achieve and the second relating to the time-frame within which an individual's life-long developmental capability is initially established and ultimately realized or undermined. Our impressions of the benefits and values, or otherwise, of technologies such as in vitro embryo production and nuclear transfer are rightly influenced by the extent to which they impinge on the health of animals either subjected to or derived from them. Here, we consider some of the health implications of oocyte/embryo-centric technologies applied to farm livestock.     

Perspectives of DNA microarray and next-generation DNA sequencing technologies

DNA microarray and next-generation DNA sequencing technologies are important tools for high-throughput genome research, in revealing both the structural and functional characteristics of genomes. In the past decade the DNA microarray technologies have been widely applied in the studies of functional genomics, systems biology and pharmacogenomics. The next-generation DNA sequencing method was first introduced by the 454 Company in 2003, immediately followed by the establishment of the Solexa and Solid techniques by other biotech companies. Though it has not been long since the first emergence of this technology, with the fast and impressive improvement, the application of this technology has extended to almost all fields of genomics research, as a rival challenging the existing DNA microarray technology. This paper briefly reviews the working principles of these two technologies as well as their application and perspectives in genome research. Supported by the National High-Tech Research Program of China (Grant No.2006AA020704) and Shanghai Science and Technology Commission (Grant No. 05DZ22201)     

Genomics in Neurological Disorders

Neurological disorders comprise a variety of complex diseases in the central nervous system, which can be roughly classified as neurodegenerative diseases and psychiatric disorders. The basic and translational research of neurological disorders has been hindered by the difficulty in accessing the pathological center （i.e., the brain） in live patients. The rapid advancement of sequencing and array technologies has made it possible to investigate the disease mechanism and biomarkers from a systems perspective. In this review, recent progresses in the discovery of novel risk genes, treatment targets and peripheral biomarkers employing genomic technologies will be dis- cussed. Our major focus will be on two of the most heavily investigated neurological disorders, namely Alzheimer＇s disease and autism spectrum disorder.     

Comparaison des performances de deux systèmes TEP/TDM corps entier selon la norme NEMA NU 2-2001

The goal of work is the characterization of two PET/CT units that are based on different technologies, using the methodology proposed in the NEMA NU 2-2001 standard. The two systems were qualified in the 3D acquisition mode by means of the National Electric Manufacturers Association (NEMA) phantoms. The results obtained showed that the NEMA standard allows to highlight differences in terms of spatial resolution, sensitivity, scatter fraction and counting rate performances between the two systems ; differences that can be explained by the geometry of the units and the materials of the detectors used. Thus, the use of the standard makes it possible to benchmark PET units and establish reference values that can be used to follow the stability of the system over the time. The tests of image quality, obtained under conditions closer to the clinical applications, showed nevertheless that the two units give, in spite of different technologies, images with sufficient contrast, within short acquisition times, allowing the detection of small lesions. This test should be part of the constancy tests to enable the comparison of examinations performed on different units when the quantitative aspects are of importance.     

A semi-parametric statistical model for integrating gene expression profiles across different platforms

Determining differentially expressed genes (DEGs) between biological samples is the key to understand how genotype gives rise to phenotype. RNA-seq and microarray are two main technologies for profiling gene expression levels. However, considerable discrepancy has been found between DEGs detected using the two technologies. Integration data across these two platforms has the potential to improve the power and reliability of DEG detection. We propose a rank-based semi-parametric model to determine DEGs using information across different sources and apply it to the integration of RNA-seq and microarray data. By incorporating both the significance of differential expression and the consistency across platforms, our method effectively detects DEGs with moderate but consistent signals. We demonstrate the effectiveness of our method using simulation studies, MAQC/SEQC data and a synthetic microRNA dataset. Our integration method is not only robust to noise and heterogeneity in the data, but also adaptive to the structure of data. In our simulations and real data studies, our approach shows a higher discriminate power and identifies more biologically relevant DEGs than eBayes, DEseq and some commonly used meta-analysis methods.     

基因芯片与高通量测序技术的原理与应用的比较

随着后基因组时代的到来,基因芯片和高通量测序已成为生物化学和分子生物学研究中的两大重要技术。从检测效率、准确性以及自动化程度证实,这两大技术都较传统的遗传学方法有了新的突破。基因芯片技术是一种具有高通量、高效率以及高自动化特点的方法,发展至今无论在核心技术还是工业应用方面都得到广泛的推广。高通量DNA测序技术建立较晚,但是其发展速度快,特别是在技术方面的更新换代极快,不断地改进使得测序的高通量、高准确率在生命科学中的应用也是占据不可逾越的优势。二者在原理上存在着显著的差异,却在应用方面上常常交融。基于此背景,本文以基因芯片技术与高通量测序技术二者在原理和基因拷贝数变异、肠道微生物、农业等应用方面作简要论述和对比。     

ENHANCING EVOLUTION AND ENHANCING EVOLUTION

It has been claimed in several places that the new genetic technologies allow humanity to achieve in a generation or two what might take natural selection hundreds of millennia in respect of the elimination of certain diseases and an increase in traits such as intelligence. More radically, it has been suggested that those same technologies could be used to instil characteristics that we might reasonably expect never to appear due to natural selection alone. John Harris, a proponent of this genomic optimism, claims in his book Enhancing Evolution that we not only have it in our power to enhance evolution, but that we also have a duty to do so. In this paper, I claim that Harris' hand is strong but that he overplays it nevertheless. He is correct to dismiss the arguments of the anti‐enhancement lobby and correct to say that enhancement is permissible; but ‘good’ is different from ‘permissible’ and his argument for the goodness of enhancement is less convincing. Moreover, he is simply wrong to claim that it generates a duty to enhance.     

Marginal production technologies for life cycle inventories

Marginal technologies are defined as the technologies actually affected by the small changes in demand typically studied in prospective, comparative life cycle assessments. Using data on marginal technologies thus give the best reflection of the actual consequences of a decision. Furthermore, data on marginal technologies are easier to collect, more precise, and more stable in time than data on average technologies. A 5-step procedure is suggested to identify the marginal technologies. The step-wise procedure first clarifies the situation in which the marginal should apply, and then identifies what specific technology is marginal in this situation. The procedure is illustrated in two examples: European electricity production and pulp and paper production.     

Inactivation of Mycobacterium avium Complex by UV Irradiation

The effectiveness of two major UV technologies against a highly prevalent species of Mycobacterium avium complex was investigated. Our study indicates that M. avium is much more resistant to UV irradiation than most waterborne pathogens and that it is one of the rare microorganisms that are highly resistant to both chemical and UV disinfection in water.     

Social aspects for sustainability assessment of technologies—challenges for social life cycle assessment (SLCA)

Purpose

Technologies can contribute to sustainable development (e.g., improving living conditions) and at the same time cause sustainability problems (e.g., emissions). Decisions on alternative technologies should thus ideally be based on the principle to minimize the latter. Analyzing environmental, economic, and social aspects related to technologies supports decisions by identifying the “more sustainable” technology. This paper focuses on social issues. First, it discusses the applicability of the social life cycle assessment (SLCA) guidelines for a comparative technology analysis, taking the example of two case studies in developing countries. Indicating technologies as “sustainable” also means that they are indeed operated over the expected lifetime, which, in development projects, is often not guaranteed. Consequently, social aspects related to implementation conditions should be considered in an SLCA study as well. Thus, a second focus is laid on identifying appropriate indicators to address these aspects.

Methods

First, the SLCA guidelines were examined with regard to applying this product-related approach to two real case studies (analysis of technologies/plants for water supply and for decentralized fuel production) for a comparative technology analysis. Suitable indicators are proposed. To address the second focus, a literature research on technology assessment and implementation in developing countries was conducted. Moreover, socioeconomic studies in the investigation areas of the case studies were consulted. Based on this, indicators addressing implementation conditions were identified from the SLCA guidelines and additional literature.

Results and discussion

The study shows social issues and indicators found in the SLCA guidelines and considered suitable for a comparative technology analysis in the case studies. However, for a sustainability assessment of technologies, especially in developing countries, further indicators are required to address technology implementation conditions. A set of additional social indicators like reported trust in institutions or fluctuation of personnel is proposed. Though these indicators were derived based on specific case studies, they can also be suggested to other technologies and are not necessarily limited to developing countries.

Conclusions

The study pointed out that an application of the SLCA guidelines considering the whole life cycle was not (yet) feasible for the case studies considered. This is mainly due to the lack of data. Regarding technology implementation, it was examined which indicators are available in this SLCA approach and which could additionally be integrated and applied. This is relevant as a potential contribution of technologies to sustainable development can only be achieved when the technologies are successfully implemented.     

Analysis of matched mRNA measurements from two different microarray technologies

MOTVIATION: The existence of several technologies for measuring gene expression makes the question of cross-technology agreement of measurements an important issue. Cross-platform utilization of data from different technologies has the potential to reduce the need to duplicate experiments but requires corresponding measurements to be comparable. METHODS: A comparison of mRNA measurements of 2895 sequence-matched genes in 56 cell lines from the standard panel of 60 cancer cell lines from the National Cancer Institute (NCI 60) was carried out by calculating correlation between matched measurements and calculating concordance between cluster from two high-throughput DNA microarray technologies, Stanford type cDNA microarrays and Affymetrix oligonucleotide microarrays. RESULTS: In general, corresponding measurements from the two platforms showed poor correlation. Clusters of genes and cell lines were discordant between the two technologies, suggesting that relative intra-technology relationships were not preserved. GC-content, sequence length, average signal intensity, and an estimator of cross-hybridization were found to be associated with the degree of correlation. This suggests gene-specific, or more correctly probe-specific, factors influencing measurements differently in the two platforms, implying a poor prognosis for a broad utilization of gene expression measurements across platforms.     

Effect of organic matter and clays on the biodegradation of Phenanthrene in soils

Soil organic matter and clays represent an important hinderance for bioremediation technologies, as they may cause a retardation in the biological removal of hydrophobic pollutants. To overcome this limitation it is necessary to understand how these two soil constituents influence biodegradation. The results herein reported suggest that the bioavailability of phenanthrene in soils is affected not only by sorption to the organic matter or clays, but also by the interaction of phenanthrene with humic fractions-clay complexes.     

生物芯片、生物传感器和生物信息学

近年来,在生物技术和医学研究领域涌现出了许多新技术平台,其中就包括生物芯片技术和生物传感器技术。生物芯片和生物传感器的构建都必须以生物信息学为基础,而两种技术平台应用所得出的数据和结果又反过来大大丰富和充实了生物信息学本身。本分析概述了生物芯片和生物传感器两种技术平台以及生物信息学,对三之间的相互关系进行了讨论。