一种构建高质量随机肽库的有效方法

为构建完全随机化的基因工程肽库 ,克服现有简并方案中终止密码子和序列组成偏歧的不足 ,提出了一种新的简并DNA文库合成方式。通过这种分组式合成方式构建的肽库可以避免终止密码子的出现和氨基酸组成偏歧的发生 ,还可以控制随机化过程中不同氨基酸的参入比例。以一个 13肽库的合成过程为例对分组式合成法进行了实验 ,测序结果和对 19种氨基酸出现频率的统计表明没有终止密码子和半胱氨酸密码子出现 ,各氨基酸的出现频率接近均值 ,表明这种分组 混合 分组 ,辅以简并合成的方法是行之有效的 ,能满足各类高容量基因工程随机肽库要求。     

An Efficient Approach to a Lactosamine Synthon for the Synthesis of I-Type Antigens

The gene coding for the ATCGAT specific BanIII DNA methyltransferase (M-BanIII) of Bacillus aneurinolyticus was cloned and its nucleotides sequenced. The coding region was assigned on the nucleotide sequence on the basis of the N-terminal amino acid sequence and molecular weight of the enzyme. The M-BanIII gene coded for a protein of 580 amino acid residues (MW 66,344). Comparison with other methylases indicated that the M-BanIII sequence contained a segment of tetra-amino acids, NPPY, characteristic of N6-adenine methylases. In addition, some homologous regions were found in the sequences of type II adenine methylases PaeR7I(CTCGAG), TaqI(TCGA) and PstI(CTGCAG), containing TCGA within the recognition sequences.     

An Efficient Proteomic Approach to Analyze Agriculture Crop Biomass

While a plant cell wall is formed by a complex of various components, including polysaccharides and structural proteins, its composition and representation may vary during cell growth. Currently, plant research targets the proteins participating in wall loosening. Multiple classes of enzymes, including various hemicellulases and cellulases, are required for plant material degradation to achieve the maximum decomposition. Identifying the set of proteins involved in the breakdown of cell-wall polymers is important to understand plant material conversion into suitable products. The objective of this study was to describe a method which can be used to carry out proteomics analysis of complex plant samples and identify enzymes degrading biomass. For this purpose we used proteomic techniques including gel electrophoresis, high pressure liquid chromatography combinated with mass spectrometry followed by data evaluation using databases searching. Results show that more than 50 % of these activities correspond to enzymes with proteolytic function. This study was focused primarily on enzymes able to breakdown the lignocellulosic and hemicellulosic parts that are very important for the material conversion into required products of degradation.     

发现新基因的高效方法——cDNA文库的复性式均一化技术

由复性式均一化技术制作的均一化cDNA文库（equalized cDNA library,normalized cDNA library）是近年来发展起来的一种获得EST、发现新基因的高效平台。本文就该技术的原理、方法比较、存在问题和展望进行了阐述。 Abstract:The cDNA library normalized by reassociation is a newly-developed,effective platform for EST acquisition and gene discovery.This papper presents the principle,procedure,comparison,deficiencies,application and future of the technique of the normalization.     

A Review of Different Approaches to the FMS Loading Problem

Loading in flexible manufacturing systems (FMSs) is affected by the characteristics of the FMS under analysis, by the type of plant where the FMS is introduced, and by the production planning hierarchy where the loading module operates. We propose an analysis of the various aspects that influence the problem formulation, identifying the alternatives available in real systems and possible future evolutions. We then provide a survey of different approaches proposed in the literature to tackle the loading problem. Articles are classified according to the type of FMS analyzed, the objective function, and the constraints. Finally, based on our analysis, we suggest some problem issues which need to be addressed, and also directions for future research.     

An Efficient Soft Set-Based Approach for Conflict Analysis

Conflict analysis has been used as an important tool in economic, business, governmental and political dispute, games, management negotiations, military operations and etc. There are many mathematical formal models have been proposed to handle conflict situations and one of the most popular is rough set theory. With the ability to handle vagueness from the conflict data set, rough set theory has been successfully used. However, computational time is still an issue when determining the certainty, coverage, and strength of conflict situations. In this paper, we present an alternative approach to handle conflict situations, based on some ideas using soft set theory. The novelty of the proposed approach is that, unlike in rough set theory that uses decision rules, it is based on the concept of co-occurrence of parameters in soft set theory. We illustrate the proposed approach by means of a tutorial example of voting analysis in conflict situations. Furthermore, we elaborate the proposed approach on real world dataset of political conflict in Indonesian Parliament. We show that, the proposed approach achieves lower computational time as compared to rough set theory of up to 3.9%.     

How NOT to Approach the Obesity Problem

FLATT, JP. How NOT to approach the obesity problem. The emphasis given to the energy balance equation has fostered the widespread belief that obesity is a problem of energy balance. This mistaken view has led to many unjustified and unfortunate interpretations, because obesity is, rather, a problem of the interaction between body composition and food intake regulation.     

一种高特异性的改良降落PCR

为提高基因组DNA中的基因PCR检出的特异性,设计了一种改良的降落PCR程序,并分别用TaqDNA聚合酶及高保真PfuDNA聚合酶进行实验。自盐藻Dunaliella bardawil中提取基因组DNA作为PCR模板,使用TaqDNA聚合酶及PfuDNA聚合酶,运用普通PCR和降落PCR程序,扩增胡萝眩素生物合成相关基因（cbr）上游启动子序列,并电泳比较PCR扩增产物的特异性。结果显示,使用普通Taq酶PCR,普通PCR程序产生200bp,500bp和1272bp长的三条带,而TD-PCR程序仅克隆出1272bp的特异带;利用高保真的PfuDNA聚合酶作PCR,在TD-PCR泳道中仅有1272bp一条带,而普通PCR除了1272bp的特异带外,还出现一条500bp的非特异带。无论使用普通Taq酶或高保真酶Pfu,改良的降落PCR程序均明显提高PCR的特异性,类似的降落PCR程序可望用于克隆用普通PCR难以克隆的基因片段,或在假阳性难以去除的情况下提高PCR的特异性。     

An Efficient Computational Approach to Characterize DSC-MRI Signals Arising from Three-Dimensional Heterogeneous Tissue Structures

The systematic investigation of susceptibility-induced contrast in MRI is important to better interpret the influence of microvascular and microcellular morphology on DSC-MRI derived perfusion data. Recently, a novel computational approach called the Finite Perturber Method (FPM), which enables the study of susceptibility-induced contrast in MRI arising from arbitrary microvascular morphologies in 3D has been developed. However, the FPM has lower efficiency in simulating water diffusion especially for complex tissues. In this work, an improved computational approach that combines the FPM with a matrix-based finite difference method (FDM), which we call the Finite Perturber the Finite Difference Method (FPFDM), has been developed in order to efficiently investigate the influence of vascular and extravascular morphological features on susceptibility-induced transverse relaxation. The current work provides a framework for better interpreting how DSC-MRI data depend on various phenomena, including contrast agent leakage in cancerous tissues and water diffusion rates. In addition, we illustrate using simulated and micro-CT extracted tissue structures the improved FPFDM along with its potential applications and limitations.     

一种用于蛋白质C端序列测定的脯氨酸乙内酰硫脲(TH-Pro)新制备方法

采用Ｌ－型脯氨酸（Ｌ－Ｐｒｏ）作为原料,三甲基硅烷异硫氰酸酯（ＴＭＳ－ＩＴＣ）作为偶联试剂制备脯氨酸乙内酰硫脲（ＴＨ－Ｐｒｏ）．产物经反相ＨＰＬＣ分离纯化,并通过氨基酸组成分析,紫外光谱扫描,质谱和核磁共振等方法鉴定．反应产率高达９６％．     

Hypothyroidism and Reversible Kidney Dysfunction: An Essential Relationship to Recognize

ObjectiveTo report 3 cases of reversible hypothyroidism-induced kidney dysfunction and review the interaction between these commonly encountered, yet seemingly disparate, conditions.MethodsWe describe the clinical course and laboratory and physical findings of 3 patients who presented with kidney dysfunction that improved after initiating thyroid hormone replacement therapy. We also review similar cases in the literature and discuss the pathophysiologic mechanisms.ResultsA 68-year-old male presented with classical signs and symptoms of hypothyroidism, including fatigue, confusion, and gait imbalance. Physical exam showed bradycardia, thyromegaly, slow mentation, and cracked, thin skin; he was found to have decreased kidney function. Second, a 42-year-old previously healthy female presented with bilateral hand swelling and elevated serum creatinine with an otherwise unremarkable physical exam. The third patient was a 72-year-old male with advanced heart failure on amiodarone and stage 3 chronic kidney disease who presented with fatigue, acute kidney injury, and lower extremity edema. In all cases, serum creatinine and thyroid-stimulating hormone (TSH) were elevated at presentation (1.4-3.0 mg/dL and 94.1-184 mIU/L respectively), and free thyroxine (T4) was low (undetectable-0.4 ng/dL). The initiation or increased dose of levothyroxine normalized serum creatinine to baseline within 2 to 10 months.ConclusionHypothyroidism and kidney dysfunction are both commonly encountered clinical entities, but the interplay between the thyroid gland and kidneys may be infrequently recalled, causing the reversible relationship between these 2 disorders to be missed. (Endocr Pract. 2014;20:490-499)     

An Efficient Approach for the Total Synthesis of Cyclotides by Microwave Assisted Fmoc-SPPS

Cyclotides are mini-proteins of approximately 30 amino acid residues that have a unique structure consisting of a head-to-tail cyclized backbone and a knotted arrangement of three disulfide bonds. This unique cyclotide structure provides exceptional stability to chemical, enzymatic and thermal treatments and has been implicated as an ideal drug scaffold for the development into agricultural and biotechnological agents. In the current work, we present the first method for microwave assisted Fmoc-SPPS of cyclotides. This protocol adopts a strategy that combines optimized microwave assisted chemical reactions for Fmoc-SPPS of the peptide backbone, the cleavage of the protected peptide and the introduction of a thioester at the C-terminal carboxylic acid to obtain the head-to-tail cyclized cyclotide backbone by native chemical ligation. To exemplify the utility of this protocol in the synthesis of a wide array of different cyclotide sequences we synthesized representative members from the three cyclotide subfamilies—the Möbius kalata B1, the bracelet cycloviolacin O2 and the trypsin inhibitory MCoTI-II. In addition, a “one pot” reaction promoting both cyclization and oxidative folding of crude peptide thioester was adapted for kalata B1 and MCoTI-II.     

A More Realistic Approach to Pest-Management Problem

The paper deals with integrated pest management (IPM) of a single density-dependent pest affecting a single crop. The model is basically a prey–predator model, predator being the natural enemy of the pest. In addition, it also contains the growth equation of the affected crop. This dynamic model is subjected to biological control in the form of release of additional predators and chemical control in the form of spraying of pesticides. To consider the natural side effect of pesticide on fish living in the soil water, the model is further improved to accommodate the growth equation of the fishes in the soil water. The paper considers the optimal analysis of the model under two control parameters, one is the spraying of pesticide and other one is the release of predators; such optimal analysis under multi-control parameters is completely new of its kind. The paper was presented by S. Bhattacharyya in the conference “Joint AMS-India Mathematics Meeting,” 17–20 December 2003, India.     

A Biosemiotic Approach to the Problem of Structure and Agency

A human being is the simultaneous composite of several different levels of being, from atomic and subatomic to the level of complex social interaction, and these levels are nested within the individual hierarchically (lower levels giving rise to higher levels, etc.). One of the most important and influential approaches developed in the history of science has been that of systems theory and systemic thinking, in which the different levels of the hierarchy, and the interactions between those levels, are considered simultaneously. Although this model provides a comprehensive view of biological being, the transition from one level to the other is not well defined in it. Uexküll and Pauli (Advances: Journal of the Institute for 417 the Advancement of Health 3:158–174, 1986) suggested that semiosis is the translator of the events from one level to the other. From a psychological point of view, a myriad of semiotic events happen inside an individual, and it has been suggested that among other semiotic events, inner speech plays an important role in mediating personal agency. Dialogical theories of the self, Jungian psychology and hypnosis research evidence show that there is a semiotic multiplicity in human agency and consciousness, and that these multiple streams are all converge to a central semiotic singularity. I argue in this paper that by taking a biosemiotic point of view, human ‘agency’ may be defined as the ability of an individual to direct the incoming and internal streams of semioses and the ability to create an integrative and superordinate new stream of semiosis in addition to the upwardly and downwardly component ones, and how such a view might open a new door for research into the concept of human ‘personality’ and ‘agency’.     

On the Relationship Between Formal and Heuristic Components in Problem Solving

The field of heuristic computer programming, which in the past decade has undergone extensive development, has come up against the difficulty of formalizing problem- solving methods peculiar to human beings. From this difficulty has arisen the problem of the relationship between heuristics (methods of heuristic search) and algorithms. In characterizing existing heuristic programs, their formulators have noted that there exists no sharp boundary between heuristics and algorithms (10). Differences that are recognized in this area result merely from the scope of the class of problems for which a program is constructed and the attendant features of the programs, such as the criteria of choice of attributes, systematization, selectivity, etc., rather than from the fundamental structure of heuristics and algorithms or their form of expression (10).