On denoising and compression of DNA microarray images

We address the problems of noise and huge data sizes in microarray images. First, we propose a mixture model for describing the statistical and structural properties of microarray images. Then, based on the microarray image model, we present methods for denoising and for compressing microarray images. The denoising method is based on a variant of the translation-invariant wavelet transform. The compression method introduces the notion of approximate contexts (rather than traditional exact contexts) in modeling the symbol probabilities in a microarray image. This inexact context modeling approach is important in dealing with the noisy nature of microarray images. Using the proposed denoising and compression methods, we describe a near-lossless compression scheme suitable for microarray images. Results on both denoising and compression are included, which show the performance of the proposed methods. Further experiments using the results of the proposed near-lossless compression scheme in gene clustering using cell-cycle microarray data for S. cerevisiae showed a general improvement in the clustering performance, when compared with using the original data. This provides an indirect validation of the effectiveness of the proposed denoising method.     

国内外微生物采油技术综述

生物技术特别是微生物采油技术，已经引起了石油工程技术人员的空前关注，目前在国内外开展的微生物采油先导性矿场试验已初见成效，较为典型的当数美国和俄罗斯，我国的吉林、胜利等油田也进行了矿场试验，增油效果令人鼓舞。同时，随着科学技术的发展，一些先进的微生物学研究工具已经进入微生物采油技术的研究领域，如分子生物学、示踪剂及可视化技术等已经成为微生物采油机理研究的重要工具。相关的石油烃降解理论以及建立数学模型等也取得了系列成果。微生物采油的应用也从过去的单井处理逐渐向整个区块或油田发展，并见到了明显效果。     

Behavioral Phenotype of the Reeler Mutant Mouse: Effects of Reln Gene Dosage and Social Isolation.

Reeler (rl/rl) and reeler/wild-type (+/rl) mice synthesize Reln at subnormal rates, as do patients with schizophrenia, bipolar disorder, and autism, thereby forming the basis for a Reln hypothesis for vulnerability to these psychopathologies and justifying attention to the behavioral phenotypes of Reln-deficient mice. Tests of gait, emotionality, social aggression, spatial working memory, novel-object detection, fear conditioning, and sensorimotor reflex modulation revealed the behavioral phenotype of rl/rl, but not +/rl, mice to be different from that of wild-type (+/+) mice. These results reveal no effect of Reln gene dosage and provide significant challenges to both the Reln and the neurodevelopmental hypotheses of the etiology of major psychopathologies. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

人睫状神经营养因子基因克隆、表达、纯化及其生物活性

［摘 要］目的 克隆人睫状神经营养因子（hCNTF）基因，在大肠杆菌宿主系统中高效表达并纯化，获得具有生物活性的hCNTF蛋白。方法 以人染色体DNA为模板，经PCR扩增到编码CNTF成熟蛋白的cDNA序列，并克隆进原核表达载体 pBV220，在大肠杆菌 BL21（Gold）中进行表达，产物经 CM-Sepharose FF柱纯化后，以体外培养的鸡胚背根神经节（DRG）测定生物活性。结果 重组表达质粒pBV22Z- CNTF在大肠杆菌BL21（Gold）中获得了非融合的稳定、高效表达，目的蛋白占细胞总蛋白的45％左右，以可溶性和包涵体两种形式存在，表达上清及包涵体复性后经CM柱一步纯化纯度达90％以上；表达的重组hCNTF能促进培养的鸡胚背根神经节神经突起的生长。结论 基因工程rhCNTF的获得为进一步研究其结构功能关系和临床应用奠定基础。     

Accurate depth profiling through energy-dependent pulse height deficit compensation in gas ionization detectors

The impact of the pulse height deficit effect in gas ionization detectors on the accurate extraction of depth information from heavy ion elastic recoil detection spectra has been investigated. Thin GaN films and Ge_xSi_1−x/Si heterostructures have been analyzed with a 200 MeV ¹⁹⁷Au beam. Employing an empirical parameterisation of the pulse height deficit, a global energy calibration of the detector can be achieved. Energy spectra have been compared, calibrated with either a constant or a full energy-dependent compensation for the deficit. A constant compensation results in significant distortion of the extracted depth profile for heavier ions, whereas an energy-dependent compensation yields true concentration–depth profiles.     

Hydrogenases, accessory genes and the regulation of [NiFe] hydrogenase biosynthesis in Thiocapsa roseopersicina

The purple (Sulphur) phototrophic bacterium, Thiocapsa roseopersicina BBS contains several [NiFe] hydrogenases, of which two are membrane bound. Mutant T. roseopersicina cells, carrying deletions in both gene clusters showed hydrogenase activity. This activity was located in the cytoplasm. The structural gene cluster hoxEFUYH was identified and sequenced. In addition, genes homologous to hupUV/hoxBC, the hydrogen sensing hydrogenase have been identified and sequenced.Regulation of hydrogenase biosynthesis was studied in detail for HydSL (renamed HynSL). A random mutagenesis system was optimised for T. roseopersicina. One of the mutations was in a gene similar to that coding for the HypF proteins in other organisms. Inactivation of the hypF gene resulted in a 60-fold increase in hydrogen evolution under nitrogen fixing conditions. In addition to hypF, the following accessory genes were identified: hydD, hupK, hypC1, hypC2, hypDE. Characterisation of the corresponding gene products and search for additional accessory genes are in progress.     

Yeast mutants with increased bacterial transposon Tn5 excision

Five complementing recessive mutations that exhibit increased bacterial transposon Tn5 precise excision in yeast Saccharomyces cerevisiae were obtained by ethylmethanesulfonate treatment. One of these mutations (tex1) was submitted to extensive genetic analysis. tex1 is a recessive temperature-sensitive mutation resulting in a 20-100-fold increase in Tn5 excision. It also has increased frequencies of ochre mutation reversion, of forward mutation to canavanine resistance, and loss of chromosome III or its right arm. The possible mechanism of tex1 effects is discussed.     

One‐step production of 2,3‐butanediol from starch by secretory over‐expression of amylase in Klebsiella pneumoniae

BACKGROUND: 2,3‐Butanediol (2,3‐BD) is a valuable chemical that can be biosynthesized from many kinds of substrates. For commercial biological production of 2,3‐BD, it is desirable to use cheap substrate without pretreatment, such as starch. However, there have been few reports on the production of 2,3‐BD directly from starch. RESULTS: In this work, gene malS coding for α‐amylase (EC 3.2.1.1) precursor was inserted into plasmid pUC18K, and secretory over‐expression of α‐amylase was achieved by engineered Klebsiella pneumoniae. The extracellular recombinant amylase accelerated the hydrolyzation of starch, and one‐step production of 2,3‐BD from starch was carried out by engineered K. pneumoniae. A 2,3‐BD concentration of 3.8 g L^?1 and yield of 0.19 g 2,3‐BD g^?1 starch were obtained after 24 h fermentation. CONCLUSION: The one‐step production of 2,3‐BD from starch was achieved by secretory over‐expression of amylase in K. pneumoniae. This would simplify the process and reduce the production cost considerably by enabling use of starch with minimal pretreatment. Copyright © 2008 Society of Chemical Industry