利用机器学习提高M. jannaschii酪氨酰tRNA合成酶底物特异性分子建模预测的准确度

设计结合不同化学结构底物的酶结合袋是一个巨大的挑战. 传统的湿实验要筛选成千上万甚至上百万个突变体来寻找对特定配体结合的突变体,此过程需要耗费大量的时间和资源. 为了加快筛选过程,我们提出了一种新的工作流程,将分子建模和数据驱动的机器学习方法相结合,生成具有高富集率的突变文库,用于高效筛选能识别特定底物的蛋白质突变体. M. jannaschii酪氨酰tRNA合成酶（Mj. TyrRS）能识别特定的非天然氨基酸并催化形成氨酰tRNA,其不同的突变体能够识别不同结构的非天然氨基酸,并且已经有了许多报道和数据的积累,因此我们使用TyrRS作为一个例子来进行此筛选流程的概念验证. 基于已知的多个Mj. TyrRS的晶体结构及分子建模的结果,我们发现D158G/P是影响残基158~163位α螺旋蛋白骨架变化的关键突变. 我们的模拟结果表明,在含有687个突变体的测试数据中,与随机突变相比,分子建模和打分函数计算排序可以将目标突变体的富集率提高2倍,而使用已知突变体和对应的非天然氨基酸数据训练的机器学习模型进行校准后,筛选富集率可提高11倍. 这种分子建模和机器学习相结合的计算和筛选流程非常有助于Mj.TyrRS的底物特异性设计,可以大大减少湿实验的时间和成本. 此外,这种新方法在蛋白质计算设计领域具有广泛的应用前景.     

肿瘤标志物CEA、CA199对结直肠癌TNM分期的预判价值

目的:探讨肿瘤标志物CEA、CA199浓度变化在结直肠癌TNM分期中的预判价值。方法:回顾我院2010年1月~2013年10月收治的经手术治疗的结、直肠癌患者(共96例)的有关资料,分析其术前CEA、CA199浓度水平与术后病理确定TNM分期结果的相互关系,进行相应的统计学检测。结果:结直肠癌Ⅰ~Ⅳ期CEA浓度依次为4.28±1.78、6.92±2.01、23.99±6.49和362.64±158.80 ng/mL,CA199浓度依次为12.58±2.98、13.37±2.62、36.84±10.33和238.71±103.69 U/mL,肿瘤标志物CEA、CA199的浓度随TNM分期升级而增高,通过Kruskal-Wallis秩检验分析及Spearman秩相关分析,表明CEA、CA199的血清浓度与TNM分期明显相关(P0.01)。结论:CEA、CA199血清浓度与TNM分期呈正相关,而年龄与CEA、CA199在各期中的浓度无明显相关性。因此,应用CEA、CA199的血清学测定在一定程度上具有预判结直肠癌TNM分期的价值。     

Mammalian genes preferentially co-retained in radiation hybrid panels tend to avoid coexpression

Coexpression has been frequently used to explore modules of functionally related genes in eukaryotic genomes. However, we found that genetically interacting mammalian genes identified through radiation hybrid (RH) genotypes tend not to be coexpressed across tissues. This pattern remained unchanged after controlling for potential confounding factors, including chromosomal linkage, chromosomal distance, and gene duplication. Because >99.9% of the genetically interacting genes were identified according to the higher co-retention frequencies, our observation implies that coexpression is not necessarily an indication of the need for the co-presence of two genes in the genome, which is a prerequisite for cofunctionality of their coding proteins in the cell. Therefore, coexpression information must be applied cautiously to the exploration of the functional relatedness of genes in a genome.     

石油生物脱硫菌Pseudomonas stutzeri UP-1的筛选

以二苯并噻吩(DBT)为模型化合物,筛选到一株能有效降解DBT的菌株,根据其菌落的形态特征、生理生化特征和分子生物学鉴定方法,确定其为Pseudomonms stutzer UP1。该菌株对DBT具有较强的降解能力,降解终产物为水溶性物质。通过对降解产物的分析,初步推断DBT的降解符合Kodama机理。     

Phthalates Induce Neurotoxicity Affecting Locomotor and Thermotactic Behaviors and AFD Neurons through Oxidative Stress in Caenorhabditis elegans

Background

Phthalate esters are ubiquitous environmental contaminants and numerous organisms are thus exposed to various levels of phthalates in their natural habitat. Considering the critical, but limited, research on human neurobehavioral outcomes in association with phthalates exposure, we used the nematode Caenorhabditis elegans as an in vivo model to evaluate phthalates-induced neurotoxicity and the possible associated mechanisms.

Principal Findings

Exposure to phthalates (DEHP, DBP, and DIBP) at the examined concentrations induced behavioral defects, including changes in body bending, head thrashing, reversal frequency, and thermotaxis in C. elegans. Moreover, phthalates (DEHP, DBP, and DIBP) exposure caused toxicity, affecting the relative sizes of cell body fluorescent puncta, and relative intensities of cell bodies in AFD neurons. The mRNA levels of the majority of the genes (TTX-1, TAX-2, TAX-4, and CEH-14) that are required for the differentiation and function of AFD neurons were decreased upon DEHP exposure. Furthermore, phthalates (DEHP, DBP, and DIBP) exposure at the examined concentrations produced elevated intracellular reactive oxygen species (ROS) in C. elegans. Finally, pretreatment with the antioxidant ascorbic acid significantly lowered the intracellular ROS level, ameliorated the locomotor and thermotactic behavior defects, and protected the damage of AFD neurons by DEHP exposure.

Conclusions

Our study suggests that oxidative stress plays a critical role in the phthalate esters-induced neurotoxic effects in C. elegans.     

传染性法氏囊病病毒多聚蛋白基因在家蚕中的表达

将传染性法氏囊病病毒(IBDV)细胞致弱株(JD1株)的基因组A节段基因重组于家蚕杆状病毒转移载体pAcHLT-C中,获得的重组转移载体pAcHLT-C-A与线性化病毒Bm-BacPAK6 DNA共转染家蚕培养细胞,获得重组病毒BacPAK-A。DIG标记的DNA点杂交证实重组病毒基因组中含有A节段基因,重组病毒感染家蚕5龄幼虫进行表达, ELISA和Western blotting等结果表明多聚蛋白基因在蚕体内得到了表达,表达产物具有免疫反应性,表达量在感染后5～6 d达到最高。家蚕生物反应器表达IBDV多聚蛋白具有我国的资源优势,为今后研制低成本、实用化的IBDV基因工程疫苗打下基础。