密码子优化策略在异源蛋白表达中的应用

酶在医疗和生物药物方面有着广泛的应用,不仅可以用来治疗各种疾病,还在临床诊断和人体健康等方面有着重要的影响。利用微生物来表达异源蛋白已经成为获取酶最简单快速的方法。为获得高浓度和高质量的异源蛋白,常用的方法是对基因序列进行密码子优化。传统的密码子优化策略主要基于密码子偏好性和GC含量,忽略了翻译动力学和代谢水平等复杂多样的变化因素。文中从基因水平、转录水平、翻译水平、翻译后水平以及代谢水平等多方面考虑出发,提供了一个较为全面的密码子优化策略,主要包括密码子偏好性、密码子协调性、密码子敏感性、调整基因序列结构以及一些其他影响因素。同时对每种策略的内容、理论支持以及应用范围等方面作了全面的总结,并将各策略的优缺点进行了系统的比较,为异源蛋白表达提供了全方位、多层次、多选择的优化策略,也为酶工业和生物药物等方面提供参考。     

中国自然保护地空间重叠分析与保护地体系优化整合对策

自然保护地体系的构建是国际社会高度重视的生物多样性保护策略。近年来, 中国已关注到自然保护地空间重叠交叉的问题, 并出台了《关于建立以国家公园为主体的自然保护地体系的指导意见》。为落实这一战略, 需要对现有保护地的彼此关系与空间分布进行系统研究。为此, 本研究收集了8,572个不同类型和级别自然保护地的坐标、生态系统类型、行政区域及边界等信息, 筛选出1,532个具有空间重叠、管理部门交叉的自然保护地, 计算地理集中指数并采用ArcGIS软件进行了核密度分析, 得出空间重叠保护地分布的生态地理区、生态系统类型、交叉管理部门、所在省份等空间分布特点。研究结果显示: (1)鲁中山区、太行山、大别山、天目山-怀玉山、皖江等生态功能区的自然保护地重叠最为严重(核密度Mean > 6, Max > 8), 其中太行山区、大别山区、天目山-怀玉山区为重叠保护地密度高的生物多样性优先保护区, 目前10个国家公园试点区域中仅大熊猫国家公园体制试点区、湖南南山国家公园体制试点区、钱江源国家公园体制试点区三处位于保护地重叠高密度区; (2)原主管部门中, 原国家林业局与住房和城乡建设部的交叉管理保护地数量最多, 为294个; (3)黑龙江、安徽、山东、河南、湖北、湖南等省范围内的自然保护地空间重叠状况明显高于其他省区, 而晋冀豫与皖鄂赣这两处三省交界处重叠程度更高, 其他多处三省交界区域也存在保护地的中度重叠。故上述生态地理区、原主管部门与行政区应作为中国自然保护地体系优先普查区域与优化整合重点对象。基于重叠保护地核密度热点区、生物多样性保护优先区与生态系统文化服务的分析框架, 本研究按照国家公园、自然保护区、自然公园三类, 对不同生态功能区自然保护地优化整合优先性与类型提出了初步建议, 以期为当前中国自然保护地体系改革的紧迫需求提供参考。     

舌苔细菌PCR-DGGE分析条件的建立与优化

目的针对口腔舌苔细菌16S rDNA序列进行变性梯度凝胶电泳(denaturing gradient gel electrophoresis,DGGE)适用序列的筛选及电泳条件的优化。方法以DGGE图谱的高分辨率为指标,选择舌苔细菌DGGE分离最适的16S rDNA高变区、电泳电压和电泳时间,并采用优化的条件分析健康青年人舌苔细菌群落的分布。结果舌苔细菌16S rDNA V3高变区引物序列能获得更加丰富清晰的DGGE条带;基于该区,当变性剂浓度为30%～60%、电泳温度60℃、电压60 V和电泳时间14 h时能得到分辨率最佳的DGGE图谱。运用此优化条件对12个样本舌苔细菌群落的分析表明,舌苔微生物主要由厚壁菌门、梭杆菌门、拟杆菌门和变形菌门等组成。优化后的DGGE技术对舌苔细菌多样性的分析具有准确性、灵敏性和可重复性。结论 DGGE图谱显示,不同分析条件对图谱类型和细菌多样性指数均有所差异。利用优化的DGGE条件能有效分离舌苔细菌16S rDNA V3区序列,为口腔微生物群落结构分析提供可靠的技术支持,也为其他不同生态细菌的多样性分析提供参考。     

不同碳源对须糖多孢菌生长发育及丁烯基多杀菌素生物合成的影响

本文研究了不同碳源对须糖多孢菌生长以及丁烯基多杀菌素生物合成的影响,通过寻找优势碳源优化发酵培养基配方,促进须糖多孢菌丁烯基多杀菌素的生物合成。试验共设11个处理,1个对照,通过单因素试验比较不同处理组菌体OD600值和丁烯基多杀菌素产量,筛选获得最优碳源及其发酵培养基配方。结果表明,除可溶性淀粉和木糖外,须糖多孢菌在9种碳源中都能进行生长,对不同构型碳源显示较好的利用率。在以半乳糖、葡萄糖、果糖和甘露糖作为碳源时具有较好的生长速率,而以甘露糖为碳源时能显著促进丁烯基多杀菌素的合成。选择甘露糖最佳添加浓度为5 g/L,须糖多孢菌最高菌体浓度和丁烯基多杀菌素产量分别是初始配方条件的1. 32倍和1. 78倍,显著提高了丁烯基多杀菌素的产量。上述结果为培养基碳源对丁烯基多杀菌素生物合成影响机制的研究及丁烯基多杀菌素大规模工业化发酵生产提供了科学依据和新的技术途径。     

Performance criteria for generating predictive optimal control simulations of bicycle pedaling

The purpose of this study was to identify one or more performance-based criteria that may be used to generate predictive optimal control simulations of submaximal pedaling. Two-legged pedaling simulations were generated based on minimizing muscle activation, muscle stress, metabolic energy, time derivative of muscle force, and minimizing metabolic energy while pedaling smoothly. The simulations based on minimizing muscle activation and muscle stress most closely matched experimental pedaling data, with the activation criterion better matching experimental muscle activation timing. We conclude that predictive simulations of submaximal pedaling may be generated using a cost function based on minimizing muscle activation.     

Method for endogenizing capital in the United States Environmentally‐Extended Input‐Output model

Each year businesses, governments, and homeowners in the United States invest around one fifth of gross domestic product into the creation of capital assets such as buildings, machinery, and software to enable production and consumption. Use of capital is typically included to some extent in environmental life cycle assessments of goods and services but is not incorporated into most environmentally extended input‐output (EEIO) models, including the US Environmental Protection Agency's USEEIO. Capital assets are typically created in years prior to their use, so a challenge lies in distributing the impacts of their creation over time. In this work, a highly detailed capital flow matrix approach is followed to distribute the use of fixed capital assets to consuming industries. Data from the US Bureau of Economic Analysis's Fixed Asset Accounts is merged with its Industry Accounts data by the creation of concordance tables. Public highways and streets are partially reallocated to industries operating vehicles. The resulting capital use matrix is later combined into a modified USEEIO. “Housing” is found to be the largest consumer of fixed assets, followed by general government, fossil fuel extraction, and financial industries involved in leasing. Construction, vehicles, and machinery are mostly used by industries in the form of fixed assets. The types of fixed assets used by industries are consistent with expectations: housing is dominated by structures, transport by equipment, and information industries by intellectual property products.     

Production of recombinant beta-amylase of Bacillus aryabhattai

In this study, the effects of carbon source, nitrogen source, and metal ions on cell growth and Bacillus aryabhattai β-amylase production in recombinant Brevibacillus choshinensis were investigated. The optimal medium for β-amylase production, containing glucose (7.5?g·L^?1), pig bone peptone (40.0?g·L^?1), Mg²⁺ (0.05?mol·L^?1), and trace metal elements, was determined through single-factor experiments in shake flasks. When cultured in the optimized medium, the β-amylase yield reached 925.4?U mL^?1, which was 7.2-fold higher than that obtained in the initial medium. Besides, a modified feeding strategy was proposed and applied in a 3-L fermentor fed with glucose, which achieved a dry cell weight of 15.4?g L^?1. Through this cultivation approached 30?°C with 0?g·L^?1 initial glucose concentration, the maximum β-amylase activity reached 5371.8?U mL^?1, which was 41.7-fold higher than that obtained with the initial medium in shake flask.     

Leveraging plant hydraulics to yield predictive and dynamic plant leaf allocation in vegetation models with climate change

Plant functional traits provide a link in process‐based vegetation models between plant‐level physiology and ecosystem‐level responses. Recent advances in physiological understanding and computational efficiency have allowed for the incorporation of plant hydraulic processes in large‐scale vegetation models. However, a more mechanistic representation of water limitation that determines ecosystem responses to plant water stress necessitates a re‐evaluation of trait‐based constraints for plant carbon allocation, particularly allocation to leaf area. In this review, we examine model representations of plant allocation to leaves, which is often empirically set by plant functional type‐specific allometric relationships. We analyze the evolution of the representation of leaf allocation in models of different scales and complexities. We show the impacts of leaf allocation strategy on plant carbon uptake in the context of recent advancements in modeling hydraulic processes. Finally, we posit that deriving allometry from first principles using mechanistic hydraulic processes is possible and should become standard practice, rather than using prescribed allometries. The representation of allocation as an emergent property of scarce resource constraints is likely to be critical to representing how global change processes impact future ecosystem dynamics and carbon fluxes and may reduce the number of poorly constrained parameters in vegetation models.     

Optimization of defined medium for recombinant Komagataella phaffii expressing cyclodextrin glycosyltransferase

The cyclodextrin glycosyltransferase (CGTase) is an important enzyme for cyclodextrin (CD) production, and is also widely used in the biotechnology, food, and pharmaceuticals industries. Secretory CGTase production by recombinant Komagataella phaffii using defined medium is a promising approach because of low cost, less impurity protein. It was found that no CGTase was expressed using traditional defined medium (basal salt medium [BSM]) because of pH value decreasing significantly. CGTase was expressed by recombinant K. phaffii through pH maintenance in range of 5.5–7.0. β-CGTase activity increased to 122.0 U/mL after optimization of glycerol, phosphate buffer, pH value, ammonium sulfate, temperature, methanol, and additives based on BSM, establishing a modified defined medium. These results showed that it was necessary to establish recombinant K. phaffii-based special defined medium although the same host cell used for different heterologous protein expression.