In vivo multiphoton microscopy using a handheld scanner with lateral and axial motion compensation

This paper reports a handheld multiphoton fluorescence microscope designed for clinical imaging that incorporates axial motion compensation and lateral image stabilization. Spectral domain optical coherence tomography is employed to track the axial position of the skin surface, and lateral motion compensation is realised by imaging the speckle pattern arising from the optical coherence tomography beam illuminating the sample. Our system is able to correct lateral sample velocities of up to approximately 65 μm s^?1. Combined with the use of negative curvature microstructured optical fibre to deliver tunable ultrafast radiation to the handheld multiphoton scanner without the need of a dispersion compensation unit, this instrument has potential for a range of clinical applications. The system is used to compensate for both lateral and axial motion of the sample when imaging human skin in vivo.      

A statistical power analysis of the 'internal reference' technique for comparing growth and growth depensation of tilapia strains

Experiments were conducted to compare the growth and growth compensation of three strains of juvenile Oreochromis niloticus . Ten full sib families (10 replicates) per strain were split and grown under crowded and uncrowded conditions for 3 weeks (the treatment). Both treatments were then grown an additional 12 weeks under less crowded conditions (the compensation). Standard length measurements were made at the end of crowding and the end of compensation. Each replicate included a size-matched control population of a fourth (red) reference strain. ANCOVA with the reference strain used as a cofactor revealed significant strain effects on specific growth throughout the experiment. The reference strain removed most of the random among-replicate error variance as shown by an increase of r 2 from 0.06 to 0.91 when it was included in the statistical models. If the reference fish had not been used, approximately 450 replicate families would have been needed to achieve the sensitivity of the present experiment (a difference of 7% among strains significant at P =0.05). We conclude that the CLSU strain grows significantly more slowly than the Israel and NIFI strains under the experimental conditions, that the crowding effect was essentially eliminated after 12 weeks of compensation, and that the reference strain greatly improved the resolution of the strain-testing experiment.     

剂量补偿和MSL复合物研究进展

剂量补偿效应(Dosage compensation effect)广泛存在于两性真核生物,是基于性别决定、平衡不同性别间基因转录水平的遗传效应。MSL复合物(Male-specific lethal complex)是果蝇剂量补偿机制的核心,它乙酰化雄性果蝇X染色体上一些特定的位点,双倍激活X连锁活跃基因的转录,从而弥补雄性果蝇只具有单一条X染色体的不足。目前,已对果蝇MSL复合物各主要成分进行了结构分析,大体了解了各组分间的相互作用位点,并对该复合物的识别机制进行了大量的研究。与果蝇不同,哺乳动物是通过雌性个体一条X染色体的失活来实现剂量补偿。虽然哺乳动物MSL复合物的组成已被鉴定,但对其功能的研究还处于初步阶段。迄今为止,对硬骨鱼类剂量补偿及MSL复合物的研究极少。文章概括了线虫、果蝇和哺乳动物各物种剂量补偿机制的异同,综述了果蝇MSL复合物及其剂量补偿机制作用机理的研究进展,并提出有待解决的问题,同时利用同线性分析发现了不同鱼类msl3基因的多样性,为今后继续研究各物种的剂量补偿机制提供基础资料和研究方向。     

jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data

We present a Java application programming interface (API), jmzIdentML, for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data. The API combines the power of Java Architecture of XML Binding (JAXB) and an XPath-based random-access indexer to allow a fast and efficient mapping of extensible markup language (XML) elements to Java objects. The internal references in the mzIdentML files are resolved in an on-demand manner, where the whole file is accessed as a random-access swap file, and only the relevant piece of XMLis selected for mapping to its corresponding Java object. The APIis highly efficient in its memory usage and can handle files of arbitrary sizes. The APIfollows the official release of the mzIdentML (version 1.1) specifications and is available in the public domain under a permissive licence at http://www.code.google.com/p/jmzidentml/.     

Proposed minimum reporting standards for chemical analysis

There is a general consensus that supports the need for standardized reporting of metadata or information describing large-scale metabolomics and other functional genomics data sets. Reporting of standard metadata provides a biological and empirical context for the data, facilitates experimental replication, and enables the re-interrogation and comparison of data by others. Accordingly, the Metabolomics Standards Initiative is building a general consensus concerning the minimum reporting standards for metabolomics experiments of which the Chemical Analysis Working Group (CAWG) is a member of this community effort. This article proposes the minimum reporting standards related to the chemical analysis aspects of metabolomics experiments including: sample preparation, experimental analysis, quality control, metabolite identification, and data pre-processing. These minimum standards currently focus mostly upon mass spectrometry and nuclear magnetic resonance spectroscopy due to the popularity of these techniques in metabolomics. However, additional input concerning other techniques is welcomed and can be provided via the CAWG on-line discussion forum at or . Further, community input related to this document can also be provided via this electronic forum. The contents of this paper do not necessarily reflect any position of the Government or the opinion of the Food and Drug Administration Sponsor: Metabolomics Society http://www.metabolomicssociety.org/ Reference: http://msi-workgroups.sourceforge.net/bio-metadata/reporting/pbc/ http://msi-workgroups.sourceforge.net/chemical-analysis/ Version: Revision: 5.1 Date: 09 January, 2007     

Rapporteur report: Basics and technology and metrology and standards

The first and second sessions of the Workshop focussed on the basics of ultrasound and infrasound, their applications in both industry and medicine, and metrology and protection standards for ultrasound applications.     

岷江上游生态补偿的博弈论

为了建立合理的生态补偿机制,制定更为科学的生态补偿政策,以岷江上游退耕还林补偿为例,运用博弈论模型考察了岷江上游现有生态补偿机制,以及在补偿政策实践过程中补偿主体与补偿对象之间的决策和行为过程.结果表明:(1)长期来看,生态补偿政策的实施效果不完全在于补偿金额的大小,仅仅依靠提高对生态建设者(保护者)的补偿标准来保护环境是不明智的;(2)生态补偿年限对岷江上游地区生态补偿政策的实施效果起着重要作用,政府制定生态补偿政策时应该将补偿年限纳入政策制定范畴中,并作为重点考虑的因素;(3)岷江上游地区第三产业的发展水平及生态建设者(保护者)外出务工收入水平的高低直接影响生态建设工程实施的效果;(4)对生态补偿的重要策略是应该通过建立相应的配套措施来增加农民务工的机会.     

Compensation by locusts for changes in dietary nutrients: behavioural mechanisms

ABSTRACT. The detailed behavioural mechanisms underlying an instance of compensation for changes in dietary nutrients are described for the first time in an insect. Nymphs of Locusta migratoria L. were given one of four artificial diets on the third day of the fifth instar, and their feeding patterns recorded in detail for 12 h. The diets represented combinations of two protein and two digestible carbohydrate levels (28% and 14% dry weight) presented in an otherwise complete nutrient mix. At the nutrient levels used, locusts regulated their intake of food with respect to protein but not digestible carbohydrate in the diet. They ate more of the lower protein diets by eating the same sized meals more frequently than insects fed on the higher protein diets. Compensation was not complete over the 12 h observation period: insects on the lower-protein diets ingested and absorbed 72% as much nitrogen as those insects fed on the higher-protein diets. Possible physiological mechanisms underlying the behavioural mechanisms are discussed.     

Biglycan knockout mice: new models for musculoskeletal diseases

Biglycan is a Class I Small Leucine Rich Proteoglycans (SLRP) that is localized on human chromosome Xq28-ter. The conserved nature of its intron-exon structure and protein coding sequence compared to decorin (another Class I SLRP) indicates the two genes may have arisen from gene duplication. Biglycan contains two chondroitin sulfate glycosaminoglycan (GAG) chains attached near its NH₂ terminus making it different from decorin that has only one GAG chain. To determine the functions of biglycan in vivo, transgenic mice were developed that were deficient in the production of the protein (knockout). These mice acquire diminished bone mass progressively with age. Double tetracycline-calcein labeling revealed that the biglycan deficient mice are defective in their capacity to form bone. Based on this observation, we tested the hypothesis that the osteoporosis-like phenotype is due to defects in cells critical to the process of bone formation. Our data shows that biglycan deficient mice have diminished capacity to produce marrow stromal cells, the bone cell precursors, and that this deficiency increases with age. The cells also have reduced response to tranforming growth factor- (TGF-), reduced collagen synthesis and relatively more apoptosis than cells from normal littermates. In addition, calvaria cells isolated from biglycan deficient mice have reduced expression of late differentiation markers such as bone sialoprotein and osteocalcin and diminished ability to accumulate calcium judged by alizerin red staining. We propose that any one of these defects in osteogenic cells alone, or in combination, could contribute to the osteoporosis observed in the biglycan knockout mice. Other data suggests there is a functional relationship between biglycan and bone morphogenic protein-2/4 (BMP 2/4) action in controlling skeletal cell differentiation. In order to test the hypothesis that functional compensation can occur between SLRPs, we created mice deficient in biglycan and decorin. Decorin deficient mice have normal bone mass while the double biglycan/decorin knockout mice have more severe osteopenia than the single biglycan indicating redundancy in SLRP function in bone tissue. To further determine whether compensation could occur between different classes of SLRPs, mice were generated that are deficient in both biglycan (class I) and fibromodulin, a class II SLRP highly expressed in mineralizing tissue. These doubly deficient mice had an impaired gait, ectopic calcification of tendons and premature osteoarthritis. Transmission electron microscopy analysis showed that like the decorin and biglycan knockouts, they have severely disturbed collagen fibril structures. Biomechanical analysis of the affected tendons showed they were weaker compared to control animals leading to the conclusion that instability of the joints could be the primary cause of all the skeletal defects observed in the fibromodulin/biglycan knockout mice. These studies present important new animal models for musculoskeletal diseases and provide the opportunity to characterize the network of signals that control tissue integrity and function through SLRP activity. Published in 2003.