PhageGT：dsDNA噬菌体基因组末端分析软件

【背景】随着测序费用的降低,越来越多的科学家选择利用高通量测序技术研究噬菌体的基因组序列。通过对这些基因组数据的分析和研究,一些科学家也开发出了判断dsDNA噬菌体末端序列的方法,但这些方法是基于Linux系统下的命令,并没有在Windows操作系统下的软件。【目的】在Windows平台下开发一款免费的、可以在高通量测序获得的庞大序列文件中找到dsDNA噬菌体基因组末端序列的软件PhageGT。【方法】使用Visual Studio 2019开发一个基于对话框的微软基础类库(Microsoft Foundation Classes,MFC)应用程序。软件使用C++语言开发,逐行读取序列文件中的每条Reads,并设计相应的算法进行统计、计算。【结果】软件PhageGT可在高通量测序文件中提取出不同序列出现的频率、排序,并利用提取序列的最高频率和序列平均频率的比值(R值)判断噬菌体基因组是否存在末端序列。【结论】软件PhageGT的使用比较方便、简单。软件PhageGT和本文所利用的所有测试数据均可从https://zenodo.org/record/4674231#.YHADb-gzZxc免费获得。     

Reliable Method for Fabricating Tissue‐Mimicking Materials With Designated Relative Permittivity and Conductivity at 128 MHz

Artificial materials that can simultaneously mimic the relative permittivity and conductivity of various human tissues are usually used in medical applications. However, the method of precisely designing these materials with designated values of both relative permittivity and conductivity at 3 T MRI resonance frequency is lacking. In this study, a reliable method is established to determine the compositions of artificial dielectric materials with designated relative permittivity and conductivity at 128 MHz. Sixty dielectric materials were produced using oil, sodium chloride, gelatin, and deionized water as the main raw materials. The dielectric properties of these dielectric materials were measured using the open‐ended coaxial line method at 128 MHz. Nonlinear least‐squares Marquardt–Levenberg algorithm was used to obtain the formula, establishing the relationship between the compositions of the dielectric materials and their dielectric properties at 128 MHz. The dielectric properties of the blood, gall bladder, muscle, skin, lung, and bone at 128 MHz were selected to verify the reliability of the obtained formula. For the obtained formula, the coefficient of determination and the expanded uncertainties with a coverage factor of k = 2 were 0.991% and 4.9% for relative permittivity and 0.992% and 6.4% for conductivity. For the obtained artificial materials measured using the open‐ended coaxial line method, the maximal difference of relative permittivity and conductivity were 1.0 and 0.02 S/m, respectively, with respect to the designated values. In conclusion, the compositions of tissue‐mimicking material can be quickly determined after the establishment of the formulas with the expanded uncertainties of less than 10%. Bioelectromagnetics. 2021;42:86–94. © 2020 Bioelectromagnetics Society.     

金针菇退化菌丝的生理生化特征

【背景】金针菇菌种在继代培养的过程中会出现菌种退化的现象,影响着金针菇的产量与质量。【目的】为研究金针菇退化菌种菌丝的生理生化特征,筛选金针菇退化菌株。【方法】以金针菇原始菌株(H)和退化菌株(T)为研究对象,测定不同碳源培养基上菌丝的生理生化特征及超氧化物歧化酶(SuperoxideDismutase,SOD)、过氧化物酶(Peroxidase,POD)和过氧化氢酶(Catalase,CAT)的活性,并测定菌丝在栽培瓶中的漆酶(Laccase,Lac)和锰过氧化物酶(ManganesePeroxidase,MnP)的活性,记录菌丝在搔菌后的恢复情况。【结果】T在各个碳源的菌丝生长速度低于H,粉孢子等级在3-4级之间,SOD、CAT活性低于H,在栽培料中的Lac活性和MnP活性在第5天时与H相同,在第10、15、20天低于H。T在搔菌后菌丝恢复时间比H恢复时间长,恢复后的菌丝长势没有H长势浓密。【结论】通过探究金针菇原始菌株与退化菌株的菌丝生理生化特征,为判断金针菇菌株是否为退化菌株提供理论依据。     

嗜热丁烷氧化古菌Candidatus Syntrophoarchaeum烷基转移酶MtaA催化丁基辅酶M的分子机制研究

【背景】嗜热古菌Candidatus Syntrophoarchaeum可以与硫酸盐还原细菌共生,通过逆转产甲烷途径进行正丁烷的氧化,但在该过程中负责催化丁基辅酶M氧化的酶尚未确定。【目的】利用分子动力学模拟证明Ca.Syntrophoarchaeum中mta A基因编码的蛋白可以特异性催化丁基辅酶M中丁基的转移,并非转移甲基。【方法】使用Methanosarcina mazei辅酶M甲基转移酶Mta A的晶体结构(PDB ID:4ay8)作为模板,对Mta A_1 (Gen Bank登录号OFV65993.1)和Mta A_2 (Gen Bank登录号OFV65678.1)进行同源建模。使用分子对接得到两者分别结合CH_3-Co M和C_4H_9-Co M时的结构,并用AMBER18进行分子动力学模拟。【结果】当Mta A_1和Mta A_2分别结合C_4H_9-Co M时,表现出与4ay8晶体结构类似的TIM-Barrel折叠三维结构,但在活性中心形状、Zn~(2+)与底物距离以及活性位点附近氨基酸配位方式等方面存在差异,这可能是导致Ca.Syntrophoarchaeum中mta A基因编码的蛋白催化丁基辅酶M氧化的原因。其中Mta A_2与4ay8结构更相似,活性中心氨基酸配位更完整,暗示其更可能具备催化活性。然而当Mta A_1和Mta A_2分别结合CH_3-Co M时,整体结构不合实际,活性中心Zn~(2+)与底物距离过远,表明底物几乎不可能与酶结合。【结论】Ca.Syntrophoarchaeum中的Mta A_1和Mta A_2很可能是特异性的丁基转移酶,而非催化甲基的转移,其中Mta A_2具备活性的可能性更高。     

枯草芽胞杆菌基因组删减对异源酶表达影响的研究进展

枯草芽胞杆菌作为一种遗传背景清晰、基因编辑成熟的革兰氏阳性菌,是多种重要工业酶的生产宿主。随着转录组、蛋白质组、代谢组等多组学测序和分析技术的发展,通过合理设计简化枯草芽胞杆菌基因组,减少细胞内冗余的调控和代谢网络,使得细胞更精简且便于控制,展现出了枯草芽胞杆菌作为异源酶表达宿主细胞的应用潜力。本文简要综述了枯草芽胞杆菌基因组删减的研究进展,归纳了必需基因的确定方法,重点介绍了枯草芽胞杆菌通过删减基因组提升异源酶表达的研究进展及删减策略,充分展示了枯草芽胞杆菌基因组删减在构建异源酶表达底盘细胞中的重要作用。     

乳酸菌食品级表达载体的研究与应用

乳酸菌是能够发酵糖类产生大量有机酸的革兰氏阳性菌的通称,在发酵食品中有着悠久的应用历史。乳酸菌通常被认为是安全菌株,这些微生物的基因工程操作在食品、医学等方面具有广阔的应用前景。表达载体是基因工程中常用的工具之一,大多数乳酸菌的表达载体通常以抗生素抗性基因作为选择标记,然而抗性基因具有潜在的转移性,因此需要开发食品级表达载体。食品级表达载体不含有抗生素的抗性基因,仅包含来自同源宿主或通常被认为是安全生物的DNA。本文介绍了乳酸菌食品级表达载体的构成及其常用宿主,同时对乳酸菌食品级表达载体的应用进行了归纳总结。     

Novel insights into the pathological mechanisms of metabolic related dyslipidemia

Due to the technological advances, it has been well-established that obesity is strongly correlated with various health problems. Among these problems, dyslipidemia is one of the most important concomitant symptoms under obese status which is the main driving force behind the pathological progression of cardio-metabolic disorder diseases. Importantly, the type of dyslipidemia, arising from concerted action of obesity, has been identified as “metabolic related dyslipidemia”, which is characterized by increased circulating levels of Low density lipoprotein cholesterol (LDL-C), Triglycerides (TG) accompanied by lower circulating levels of High density lipoprotein cholesterol (HDL-C). On the other hand, the metabolic related dyslipidemia is being verified as a vital link between obesity and hypertension, diabetes mellitus, and Cardiovascular disease (CVD). In this review, we summarized the current understanding of metabolic related dyslipidemia and the potential mechanisms which lead to the pathogenesis of obesity. Meanwhile, we also summarized the emerging results which focused on several novel lipid bio-markers in metabolic related dyslipidemia, such as pro-protein convertase subtilisin/kexin type 9 (PCSK9) and sphingosine-1-phosphate (S1P), and their potential use as biomarkers of metabolic related dyslipidemia.