Maximum glucoamylase production by a temperature-sensitive mutant of Saccharomyces cerevisiae in batch culture

In order to maximize the glucoamylase production by recombinant Saccharomyces cerevisiae in batch culture, first a temperature-controlled expression system for a foreign gene in S. cerevisiae was constructed. A temperature-sensitive pho80 mutant of S. cerevisiae for the PHO regulatory system, YKU131, was used for this purpose. A DNA fragment bearing the promoter of the PHO84 gene, which encodes an inorganic phosphate (P_i) transporter of S. cerevisiae and is derepressed by P_i starvation, was used as promoter. The glucoamylase gene connected with the PHO84 promoter was ligated into a YEp13 vector, designated pKU122. When the temperature-sensitive pho80 ^ts mutant harboring the plasmid pKU122 is cultivated at a lower temperature, the expression of glucoamylase gene is repressed, but at a higher temperature it is expressed. Next the effect of temperature on the specific growth rate, μ, and specific production rate, ρ, was investigated. Maximum values of ρ and ρ at various temperatures were at 30°C and 34°C, respectively. The optimal cultivation temperature strategy for maximum production of glucoamylase by this recombinant strain in batch culture was then determined by the Maximum principle using the relationships of μ and ρ to the cultivation temperature. Finally, the optimal strategy was experimentally realized by changing the cultivation temperature from Tμ (30°C) to Tρ (34°C) at the switching time, t_s. Received 18 September 1997/ Accepted in revised form 07 January 1998     

Exploring zipping and assembly as a protein folding principle

It has been proposed that proteins fold by a process called "Zipping and Assembly" (Z&A). Zipping refers to the growth of local substructures within the chain, and assembly refers to the coming together of already-formed pieces. Our interest here is in whether Z&A is a general method that can fold most of sequence space, to global minima, efficiently. Using the HP model, we can address this question by enumerating full conformation and sequence spaces. We find that Z&A reaches the global energy minimum native states, even though it searches only a very small fraction of conformational space, for most sequences in the full sequence space. We find that Z&A, a mechanism-based search, is more efficient in our tests than the replica exchange search method. Folding efficiency is increased for chains having: (a) small loop-closure steps, consistent with observations by Plaxco et al. 1998;277;985-994 that folding rates correlate with contact order, (b) neither too few nor too many nucleation sites per chain, and (c) assembly steps that do not occur too early in the folding process. We find that the efficiency increases with chain length, although our range of chain lengths is limited. We believe these insights may be useful for developing faster protein conformational search algorithms.     

实时荧光定量PCR及其在传染性疾病检测中的应用

实时荧光定量PCR技术被广泛应用于实验研究、临床检测中。与普通的PCR相比,实时荧光定量PCR技术具有特异性强、灵敏度高、重复性好、定量准确、速度快、全封闭反应等优点。我们综述了实时荧光定量PCR技术的原理、定量方法,及其在传染性疾病检测研究中的应用。     

Identification of the active site of human mitochondrial malonyl‐coenzyme a decarboxylase: A combined computational study

Malonyl‐CoA decarboxylase (MCD) can control the level of malonyl‐CoA in cell through the decarboxylation of malonyl‐CoA to acetyl‐CoA, and plays an essential role in regulating fatty acid metabolism, thus it is a potential target for drug discovery. However, the interactions of MCD with CoA derivatives are not well understood owing to unavailable crystal structure with a complete occupancy in the active site. To identify the active site of MCD, molecular docking and molecular dynamics simulations were performed to explore the interactions of human mitochondrial MCD (HmMCD) and CoA derivatives. The findings reveal that the active site of HmMCD indeed resides in the prominent groove which resembles that of CurA. However, the binding modes are slightly different from the one observed in CurA due to the occupancy of the side chain of Lys183 from the N‐terminal helical domain instead of the adenine ring of CoA. The residues 300 ? 305 play an essential role in maintaining the stability of complex mainly through hydrogen bond interactions with the pyrophosphate moiety of acetyl‐CoA. Principle component analysis elucidates the conformational distribution and dominant concerted motions of HmMCD. MM_PBSA calculations present the crucial residues and the major driving force responsible for the binding of acetyl‐CoA. These results provide useful information for understanding the interactions of HmMCD with CoA derivatives. Proteins 2016; 84:792–802. © 2016 Wiley Periodicals, Inc.     

广西桂平市鳄蜥种群及栖息地现状的分析研究

2004年7月,对广西桂平市鳄蜥种群及其栖息地进行了调查,并首次采用量化指标对鳄蜥栖息的回水塘进行了分析。结果表明：桂平市鳄蜥分布区已破碎成白沙坑、牛头坳和黄凉冲、大藤峡碧滩段三个片段,分布区面积从58．39km^2减小至16．14km^2。鳄蜥种群数量约为150只。通过主成分分析发现,鳄蜥栖息回水塘的长度、宽度、水深、塘底组成、水温、栖枝类型和栖枝高度是影响鳄蜥选择回水塘的主要因子,而海拔、栖枝直径、水流速度的影响不大。鳄蜥倾向栖息于常绿阔叶林生境中,对溪沟的坡向和沟型选择不明显。     

基于多判据决策的水体营养状态评价

为了准确地评价水生态系统营养状态和综合决策,通过最大熵原理耦合模糊性与随机性,建立了最大熵模糊评价模型(FAME);利用逼近理想解排序法(TOPSIS),以待决策水体样本的实测值为理想解,以评价结果中与实测值相差最大的为负理想解,建立了多判据决策模型(MCDM).经12个湖泊实测数据验证,最大熵模糊评价与随机评价、模糊评价和灰色评价的结果较为一致,但提高了评价水体营养状态问题各层次的分辨力.多判据决策模型可解决多种方法评价结果不相容问题,使评价结果更接近水体实际情况.FAME和MCDM适用于各种水质的综合评价及决策.     

On Haldane's formulation of Luria and Delbrück's mutation model

Two formulations of Luria and Delbrück's mutation model have been in common use since the 1940s. While mathematicians focused their attention on the formulation of Lea and Coulson that assumes asynchronous cell growth, biologists found more appealing the formulation of Haldane that assumes synchronous cell growth. This article attempts to solve several outstanding issues for the latter formulation. First, it provides an exact, closed-form expression for the mutant distribution by correcting a minor error in the literature. Second, it presents a novel algorithm for computing the mutant distribution, which leads to novel methods for computing point and interval estimates of mutation rates based on the maximum likelihood principle. Third, it critically examines existing methods based on the mean number of mutants. Finally, it compares the two formulations to underline their strengths and shortcomings.     

An abstract cell model that describes the self-organization of cell function in living systems

The principal aim of systems biology is to search for general principles that govern living systems. We develop an abstract dynamic model of a cell, rooted in Mesarovi? and Takahara's general systems theory. In this conceptual framework the function of the cell is delineated by the dynamic processes it can realize. We abstract basic cellular processes, i.e., metabolism, signalling, gene expression, into a mapping and consider cell functions, i.e., cell differentiation, proliferation, etc. as processes that determine the basic cellular processes that realize a particular cell function. We then postulate the existence of a 'coordination principle' that determines cell function. These ideas are condensed into a theorem: If basic cellular processes for the control and regulation of cell functions are present, then the coordination of cell functions is realized autonomously from within the system. Inspired by Robert Rosen's notion of closure to efficient causation, introduced as a necessary condition for a natural system to be an organism, we show that for a mathematical model of a self-organizing cell the associated category must be cartesian closed. Although the semantics of our cell model differ from Rosen's (M,R)-systems, the proof of our theorem supports (in parts) Rosen's argument that living cells have non-simulable properties. Whereas models that form cartesian closed categories can capture self-organization (which is a, if not the, fundamental property of living systems), conventional computer simulations of these models (such as virtual cells) cannot. Simulations can mimic living systems, but they are not like living systems.     

Chiral symmetry conservation principle

We show a chiral symmetry conservation principle based on chemical kinetics using stochastic results. Suppose the chiral symmetry conservation is evoked, and our universe can be considered globally asymmetric. In that case, there are at least two mirrored asymmetric universes if all the chiral properties are strongly correlated. However, if the chiral correlations are weak or nonexistent, there are possibly Many-(Chiral-Symmetry)-Worlds. Alternatively, if our universe is only locally asymmetric, there could be a single universe with segregated chiral regions. The possible mechanisms of the primordial chiral symmetry breaking can only be found if the chiral symmetry is not truly conserved by assuming the initial racemic conditions. In that case, our universe is asymmetric and could be alone. On the other hand, if the chiral symmetry is conserved, there is no chance of finding the primordial chiral symmetry breaking. Based on this conservation (or not), it is possible to infer two opposite hypotheses, where two general scenarios about the chiral universes are possible.