Dynamics of Random Boolean Networks under Fully Asynchronous Stochastic Update Based on Linear Representation

A novel algebraic approach is proposed to study dynamics of asynchronous random Boolean networks where a random number of nodes can be updated at each time step (ARBNs). In this article, the logical equations of ARBNs are converted into the discrete-time linear representation and dynamical behaviors of systems are investigated. We provide a general formula of network transition matrices of ARBNs as well as a necessary and sufficient algebraic criterion to determine whether a group of given states compose an attractor of length in ARBNs. Consequently, algorithms are achieved to find all of the attractors and basins in ARBNs. Examples are showed to demonstrate the feasibility of the proposed scheme.     

High-Resolution Mutational Profiling Suggests the Genetic Validity of Glioblastoma Patient-Derived Pre-Clinical Models

Recent advances in the ability to efficiently characterize tumor genomes is enabling targeted drug development, which requires rigorous biomarker-based patient selection to increase effectiveness. Consequently, representative DNA biomarkers become equally important in pre-clinical studies. However, it is still unclear how well these markers are maintained between the primary tumor and the patient-derived tumor models. Here, we report the comprehensive identification of somatic coding mutations and copy number aberrations in four glioblastoma (GBM) primary tumors and their matched pre-clinical models: serum-free neurospheres, adherent cell cultures, and mouse xenografts. We developed innovative methods to improve the data quality and allow a strict comparison of matched tumor samples. Our analysis identifies known GBM mutations altering PTEN and TP53 genes, and new actionable mutations such as the loss of PIK3R1, and reveals clear patient-to-patient differences. In contrast, for each patient, we do not observe any significant remodeling of the mutational profile between primary to model tumors and the few discrepancies can be attributed to stochastic errors or differences in sample purity. Similarly, we observe ∼96% primary-to-model concordance in copy number calls in the high-cellularity samples. In contrast to previous reports based on gene expression profiles, we do not observe significant differences at the DNA level between in vitro compared to in vivo models. This study suggests, at a remarkable resolution, the genome-wide conservation of a patient’s tumor genetics in various pre-clinical models, and therefore supports their use for the development and testing of personalized targeted therapies.     

固相萃取与气相色谱⁃质谱法联用测定食用植物油和含脂肪食品中氯丙醇酯的方法验证研究

氯丙醇酯是国际上广泛关注的食品加工过程污染物,其水解产物氯丙醇对人体（特别是婴幼儿）危害风险较大。采用固相萃取与气相色谱-质谱（gas chromatography-mass spectrometry,GC-MS）联用技术,对食用植物油和含脂食品中的氯丙醇酯[3-氯-1,2-丙二醇脂肪酸酯（简称3-MCPD酯）和2-氯-1,3-丙二醇脂肪酸酯（简称2-MCPD酯）]进行检测。该方法准确度高（3-MCPD酯和2-MCPD酯的平均回收率分别为98.9%和96.5%)、灵敏度高(3-MCPD酯和2-MCPD酯的检出限分别为0.042 mg·kg^-1和0.058 mg·kg^-1)、重现性好(相对标准偏差均低于5%)。76批次监测样品中,3-MCPD酯和2-MCPD酯的含量分别为0.042~4.865 mg·kg^-1(平均值为0.773 mg·kg^-1)和0.058~2.592 mg·kg^-1(平均值为0.469 mg·kg^-1)。经机构间的协同验证和英国FAPAS样的能力验证,2种氯丙醇酯在0.200~3.000 mg·kg^-1范围内线性良好,为进一步研究奠定了基础,同时也为食品加工企业严格控制生产过程建立了一种可行的检测方法。     

聚乙二醇定点修饰集成干扰素突变体Ⅱ

目的：用聚乙二醇（PEG）修饰集成干扰素突变体Ⅱ（IFN-Con-m2,IIFNm2）,通过纯化获得新型修饰分子并对该分子进行抗胰蛋白酶水解稳定性及初步药代动力学研究。 方法：将mPEG20000定点偶联到IIFNm2的第86位Cys残基上,修饰后的产物经CM层析后,以SDS-PAGE考察其纯度,用WISH-VSV系统进行生物活性测定;在0.1%胰蛋白酶条件下考察体外抗酶解稳定性;并以SD大鼠进行初步药代动力学研究,绘制血药浓度-时间曲线。采用3P87软件进行数据拟合,分析药物动力学参数。 结果：干扰素修饰率约为50%,且绝大多数以单修饰体（mono-PEG- IIFNm2）形式存在;提纯后mono-PEG-IIFNm2 的纯度大于98%,比活性约为修饰前IIFNm2的1%。抗胰蛋白酶水解试验表明：30min后,IIFNm2抗病毒活性残留为8%,mono-PEG-IIFNm2为41%。初步药代动力学研究显示：IIFNm的消除半衰期为(1.57±0.34)h,mono-PEG-IIFNm2为(18.0±4.0)h。 结论：成功地偶联了PEG和IIFNm2,建立了mono-PEG-IIFNm2的纯化工艺,PEG修饰能增加IIFNm2的体外抗胰蛋白酶水解稳定性,并显著延长体内半衰期。     

The Bryopsis hypnoides plastid genome: multimeric forms and complete nucleotide sequence

Background

Bryopsis hypnoides Lamouroux is a siphonous green alga, and its extruded protoplasm can aggregate spontaneously in seawater and develop into mature individuals. The chloroplast of B. hypnoides is the biggest organelle in the cell and shows strong autonomy. To better understand this organelle, we sequenced and analyzed the chloroplast genome of this green alga.

Principal Findings

A total of 111 functional genes, including 69 potential protein-coding genes, 5 ribosomal RNA genes, and 37 tRNA genes were identified. The genome size (153,429 bp), arrangement, and inverted-repeat (IR)-lacking structure of the B. hypnoides chloroplast DNA (cpDNA) closely resembles that of Chlorella vulgaris. Furthermore, our cytogenomic investigations using pulsed-field gel electrophoresis (PFGE) and southern blotting methods showed that the B. hypnoides cpDNA had multimeric forms, including monomer, dimer, trimer, tetramer, and even higher multimers, which is similar to the higher order organization observed previously for higher plant cpDNA. The relative amounts of the four multimeric cpDNA forms were estimated to be about 1, 1/2, 1/4, and 1/8 based on molecular hybridization analysis. Phylogenetic analyses based on a concatenated alignment of chloroplast protein sequences suggested that B. hypnoides is sister to all Chlorophyceae and this placement received moderate support.

Conclusion

All of the results suggest that the autonomy of the chloroplasts of B. hypnoides has little to do with the size and gene content of the cpDNA, and the IR-lacking structure of the chloroplasts indirectly demonstrated that the multimeric molecules might result from the random cleavage and fusion of replication intermediates instead of recombinational events.     

Production of bacterial cellulose by Acetobacter xylinumwith an air-lift reactor

Bacterial cellulose was produced by Acetobacter xylinum subsp. surcrofermentans BPR2001 in a 50 liter air-lift reactor using fructose as the main carbon source. When air was supplied, the production of the cellulose was only 2.3 g/l in 80 h but when O -fortified air was supplied, the cellulose concentration increased to 5.63 g/l in 28 h and the productivity of the cellulose in an air-lift reactor with O -fortified air supply was comparable to that in a mechanically agitated jar fermenter.     

The InR/Akt/TORC1 Growth-Promoting Signaling Negatively Regulates JAK/STAT Activity and Migratory Cell Fate during Morphogenesis

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Oxalate production at different initial Pb²+ concentrations and the influence of oxalate during solid-state fermentation of straw with Phanerochaete chrysosporium

The production of oxalate at different initial Pb²⁺ concentrations during solid-state fermentation of straw with Phanerochaete chrysosporium was investigated. It was found that the maximal peak value of oxalate concentration (22.84 mM) was detected at the initial Pb²⁺ concentration of 200 mg kg⁻¹ dry straw, while the minimum (15.89 mM) at the concentration of 600 mg Pb²⁺ kg⁻¹ dry straw, and at moderate concentration of Pb²⁺ the capability of oxalic acid secretion was enhanced. In addition, it was also found that more oxalic acid accumulation went together with better Pb²⁺ passivation effect and higher manganese peroxidase (MnP) activity. The present findings will improve the understandings of the interactions of heavy metals with white-rot fungi and the role of oxalate in lignin degradation system, which could provide useful references for more efficient treatment of Pb-contaminated lignocellulosic waste.