Soft computing methods to predict gene regulatory networks: An integrative approach on time-series gene expression data

To unravel the controlling mechanisms of gene regulation, in this paper we present the application of sophisticated soft computing methods applied on an important problem from Bioinformatics—inferring gene regulatory networks (GRN) from time series gene expression microarray data. The main questions addressed in this paper are: (a) what knowledge can be derived from different models? (b) Would an integrated approach be more suitable to reveal about the controls of gene regulation? To reduce the number of genes in addition to apply the appropriate clustering methods, here we have also considered the valuable inputs from the biological experiments. To infer the GRN we have applied: three computational intelligence methods—Least Angle Regression (LARS), Expectation Maximization (EM) with Kalman Filter (KF), and an Evolving Fuzzy Neural Network (EFuNN). The methods are applied on time series microarray data of Schizosaccharomyces pombe yeast cell-cycle genes. Each method reveals some new aspects of the problem and it is agreed that to infer the GRN and to understand the processes behind gene regulation it is more suitable to adopt such integrative approach as ours through which some new knowledge is discovered, such as: using LARS we hypothesize—first, an exoglucanase gene exg1 is now implicated to be tied with MCB cluster regulation and second, a mannosidase with histone linked mannoses. A new quantitative prediction is that the time delay of the interaction between two genes seems to be approximately 30 min, or 0.17 cell cycles. Using the method of EM with KF, 25 cell cycle-regulated key genes were successfully clustered into three functionally co-regulated groups. We have also identified two genes namely Cdc22 and Suc22 that indeed interact with each other and are the potential candidates as a control in Ribonucleotide reductase (RNR) activity. Based on the EFuNN results and integrating knowledge from EM-KF method, we hypothesize that interaction between Suc22, Cdc22 and Mrc1 may be mediated by two other genes namely Cds1 and Spd1. The methods discussed and applied here can be used to analyze any kind of short time series of many interacting variables for inferring the regulatory network. Researchers should take such integrative computational intelligence approach seriously to understand the complex phenomenon of gene regulation and thus to simulate the development of the cell.     

利用WatComC++开发检验仪器多线程数据通信接口

针对医院信息系统中检验子系统的实际需要 ,研究检验仪器的实际特点 ,在 32位 Windows平台上利用 Power Builder与 Wat Com C++开发了检验数据通信接口 ,将通信接口无缝地嵌入到客户 /服务器体系的检验子系统 ,有效地管理了种类繁多的检验仪器 ,成功地实现了划分 CPU时间片方式的前台检验数据统计、查询与后台检验数据自动接收的并行处理。     

Vulgarone B,the antifungal constituent in the steam-distilled fraction of Artemisia douglasiana

Antifungal activity of the steam distilled essential oil fraction of Artemisia douglasiana was detected by bioautography on silica gel TLC plates against three Colletotrichum spp. The active principle was isolated by bioassay-directed fractionation using column chromatography followed by crystallization and was characterized as vulgarone B by ¹H and ¹³C NMR and GC-MS. Antifungal activity of vulgarone B was further evaluated using 96-well microtiter assay against Colletotrichum acutatum, C. fragariae, C. gloeosporioides, and Botrytis cinerea. In addition, the antifungal activity of vulgarone B and verbenone, and their corresponding alcohols was tested by bioautography and microtiter assay. Structure–activity studies revealed that the , -unsaturated carbonyl functionality is a prerequisite for the antifungal activity of these mono and sesquiterpene ketones. This is the first report of antifungal activity of vulgarone B. The yield of essential oil from A. douglasiana is about 0.6–0.8% by weight of the dry material, including plant stems.     

Effects of chlorine on the decrease of estrogenic chemicals

The effects of chlorination on the elimination of three estrogenic chemicals such as 17beta-estradiol, nonylphenol and bis-phenol A were investigated using yeast two-hybrid assay (YTA), estrogen receptor (ER) competition assay (ER-CA), and high-performance liquid chromatography/mass spectrometry (LC/MS). The results of YTA, ER-CA and the analysis of LC/MS indicated that the estrogenic activity of the above-mentioned three endocrine disruptors were significantly reduced as a result of chlorination. The decrease in estrogenic activity paralleled a decrease in estrogenic chemicals under the influence of free chlorine. One common characteristic of estrogenic chemicals is the presence of a phenolic ring. Considering that a phenolic ring is likely to undergo some sort of transformation in an aqueous chlorination solution, the above-mentioned results may be applied to the rest of the estrogenic chemicals in natural waters.     

Autophagy as an ultrastructural marker of heavy metal toxicity in human cord blood hematopoietic stem cells

Stem cells are a key target of environmental toxicants, but little is known about their toxicological responses. We aimed at developing an in-vitro model based on adult human stem cells to identify biomarkers of heavy metal exposure. To this end we investigated the responses of human CD34+ hematopoietic progenitor cells to hexavalent chromium (Cr[VI]) and cadmium (Cd). Parallel cultures of CD34+ cells isolated from umbilical cord blood were exposed for 48 h to 0.1 microM and 10 microM Cr(VI) or Cd. Cultures treated with 10 microM Cr(VI) or Cd showed marked cell loss. Ultrastructural analysis of surviving cells revealed prominent autophagosomes/autophagolysosomes, which is diagnostic of autophagy, associated with mitochondrial damage and replication, dilatation of the rough endoplasmic reticulum and Golgi complex, cytoplasmic lipid droplets and chromatin condensation. Treated cells did not show the morphologic hallmarks of apoptosis. Treatment with 0.1 microM Cr(VI) or Cd did not result in cell loss, but at the ultrastructural level cells showed dilated endoplasmic reticulum and evidence of mitochondrial damage. We conclude that autophagy is implicated in the response of human hematopoietic stem cells to toxic concentrations of Cr(VI) and Cd. Autophagy, which mediates cell survival and death under stress, deserves further evaluation to be established as biomarker of metal exposure.     

Mixed plaques: statistical evidence how plaque assays may underestimate virus concentrations

Even at very low concentrations human pathogenic viruses may result in infection and possibly subsequent disease. Ideally, viruses are quantified by use of cell culture assays to determine their infectivity. Plaque assays are common tools for enumeration of viruses in inocula and this process is straightforward when a plaque results from the offspring of a single infectious virus particle. In the course of a study on the usefulness of sewage monitoring for surveillance of polio-virus transmission, sewage samples containing a mixture of two live polio vaccine strains (type 1 and type 3) were analyzed. The total poliovirus concentration in plaque forming units (pfu) was estimated by means of a monolayer plaque assay on L20B cells. Subsequent typing of virus directly by neutralisation of virus from excised plaques revealed the occurrence of plaques containing both type 1 and type 3 virus. This means that there must be plaques that originate from more than one initial infectious virus particle. As a consequence, the estimated virus concentration is incorrect. We present statistical methods that utilize these mixed plaque counts to estimate the concentrations of either virus type in our sewage samples. We can also calculate a correction factor for the error in virus concentration, which would result from equating a pfu to a single infectious particle. Since many quantitative methods in microbiology are based on colony counts, we conclude that such counts should be interpreted with caution, especially when data are used in quantitative microbial risk assessment to estimate the public health impact.     

Antioxidative activity of a low molecular weight peptide derived from the sauce of fermented blue mussel, Mytilus edulis

In order to identify nutraceutical functions of fermented fish and shellfish sauces, which are highly appreciated in food products in South-East Asia, the antioxidative activity of fermented blue mussel sauce (FBMS) was investigated. The blue mussel was fermented with 25% NaCl (w/w) at 20±0.5 °C for 12 months and the fermented sauce was passed bimonthly through a 40-mesh sieve, desalted using an electrodialyzer, and then lyophilized. The antioxidative activity of FBMSs was investigated and compared with that of a natural antioxidant, -tocopherol standing as a reference. Using consecutive chromatographic methods, the antioxidative peptide with a molecular mass of 620 Da was purified from 6-month-fermented sauce, and its sequence of the peptide was FGHPY. In addition, 64.8 M of the purified peptide could scavenge 89.5% of hydroxyl radical in radical scavenging assay using electron spin resonance spectroscopy.     

太子参专用微生物肥的制作研究

将前期实验筛选到的功能菌株(KTS-1-1、TR-10J、ATS-1-1、PTS-2-1)按体积比1∶1∶1∶1制备成菌悬液,分别与备选的3种载体(鸡粪、玉米秸秆和泥炭土)组合,制作太子参专用微生物肥,进而测定各菌株-载体组合产品的技术指标(有效活菌数、pH、水含量、有机质含量、总氮含量、总磷含量和速效钾含量)。结果表明:复合菌株-载体(质量配比为33.3%鸡粪+33.3%玉米秸秆+33.3%泥炭土)组合(T7)所提供的有效活菌数最高(22.5亿/g),w(总磷)为1.67%,w(速效钾)为0.139 mg/g,基本符合Rebah等提出的良好接种剂的要求,可作为太子参专用微生物肥进行田间应用。     

Effects of molecular structural parameters of carboxymethyl chitosan on the growth of fibroblasts in vitro

A series of carboxymethyl chitosan samples (CMCHs) with different molecular structural parameters were synthesized to estimate their different influences on the growth of fibroblasts. All the CMCHs stimulated the fibroblasts proliferation and CMCHs with different molecular weight (MW) had the similar effect on fibroblasts proliferation. The least concentration for CMCHs (the degree of deacetylation, DD 70.3–79.9%, the degree of substitution, DS 1.12–1.26) exhibiting acceleratory effect on fibroblasts proliferation was 50 μg mL^?1. As the DD increased from 70.3 to 93.6%, CMCH's ability of stimulating fibroblasts proliferation increased significantly. CMCH possessed much higher proliferation rate with the DS increasing to 2.39. CM40 with 92.4% DD and 2.39 DS had the strongest acceleratory fibroblasts proliferation at the range tested. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2007     

细菌发酵生产酒精之工业应用前景探索

本研究对细菌和酵母这两类不同菌株,在发酵酒精的性能方面作了多方面的比较。实验结果表明:玉米淀粉水解液及糖蜜可用于运动发酵单胞细菌发酵生产酒精,但糖蜜需经活性灾吸附,脱除有害物质。酒糟水和玉米浆可替代酵母膏,良好地用作为细菌发酵酒精的氮源。细菌具有较强的抗染菌能力。细菌经吸附固定化后,发酵速度比游离菌快,也比固定化酵母快。因此,运动发酵单胞细菌生产酒精,有着良好的工业应用前景,在不久的将来,将会代替酵母,而成为酒精工业中的重要菌株。