A Universal Model of Commuting Networks

We show that a recently proposed model generates accurate commuting networks on 80 case studies from different regions of the world (Europe and United-States) at different scales (e.g. municipalities, counties, regions). The model takes as input the number of commuters coming in and out of each geographic unit and generates the matrix of commuting flows between the units. The single parameter of the model follows a universal law that depends only on the scale of the geographic units. We show that our model significantly outperforms two other approaches proposing a universal commuting model [1], [2], particularly when the geographic units are small (e.g. municipalities).     

A Universal Plasmonic Polarization State Analyzer

We propose a universal plasmonic polarization state analyzer consisting of rectangular holes arranged along an Archimedes spiral in silver film. The analyzer can detect different polarization states of light including linear, circular, radial and azimuthal polarizations. The theoretical analysis of its transmitted field is performed on the basis of the dipole radiations, and the analytic expressions of the electric field distributions under different polarized illuminations are provided. The numerical simulations of the near-field transmissions are also conducted to verify the analytic results. The significant differences between the field distributions predict the practicability of the universal plasmonic polarization state analyzer in determining the incident light polarization states.     

A Universal Glass Support for Oligonucleotide Synthesis

Abstract

A single type of controlled pore glass derivatized with 3-anisoyl-2′(3′)-O-benzoyluridine 5′-O-succinyl residues can be used as the support in solid phase syntheses of either oligoribo- or oligodeoxyribonucleotides.     

一种通用的基因组DNA提取方法

目的:探讨一种通厢的基因组DNA提取方法.方法:采用改良的膜法分别从动植物组织、外周血、细菌、细胞等标本提取基因组DNA,DNA样品经紫外吸收、琼脂糖凝胶电泳、PCR扩增和酶切进行榆测.结果:该方法提取的基因组DNA纯度较高,电泳条带清晰,DNA质量能满足下游分子生物学研究的需要.结论:该方法简便快速、适用范围广,是提取基因组DNA的一种有效方法.     

Horizontal Gene Transfer: A Universal Phenomenon

According to the scientific literature, it is reasonable to consider that lateral transfer of genes is an usual mechanism of adaptation of the biological organisms to environmental stresses. Furthermore, from bacteria to cultured human cells, including fungi and plants, a large diversity of horizontal gene transfers—natural or artificial, experimental or deduced from sequence analysis—have been described. Therefore, the uncharacterized biodiversity—particularly in microbiology—associated with the universality of the horizontal gene transfer phenomenon leads to the consideration that dissemination of DNA from Genetically Modified Organisms (GMO) in biological environments, including food and soil, is uncontrolled and predictable.     

A Universal Stain for the Sex Chromatin Body

For the demonstration of the sex chromatin body in human tissues, fixation in 95% alcohol or modified Davidson's solution (95% alcohol, 30; formalin, 20; glacial acetic acid, 10; distilled water, 30) was best. The staining procedure chosen for most materials is the following: Mounted preparations are coated with celloidin, hydrated, hydrolyzed 20 min in 52V HCl at 20-25°C, rinsed thoroughly in several changes of distilled water and transferred to a buffered thionin solution. This consists of 3 parts: (1) A saturated solution of thionin in 50% alcohol (filtered); (2) Michaelis buffer: sodium acetate (3 H₂O), 9.714 gm; sodium barbiturate, 14.714 gm; CO₂-free distilled water, 500 ml; and (3) 0.1N HCl. To make the staining solution, mix 28.0 ml of the buffer solution with 32.0 ml of 0.1N HCl and bring the total volume to 100.0 ml with the thionin solution. Its pH should be 5.7 × 0.2, and care should be exercised that no acid is carried over from the hydrolyzing solution, since this would progressively lower the pH. The staining time varies from 15 to 60 min, depending on the specimen, but the shortest time consistent with adequate staining gives the clearest preparations. Slides are rinsed in distilled water and 50% alcohol and allowed to remain in 70% alcohol until the heavy clouds of stain cease to appear. Differentiation is completed in 80% and 95% alcohol, followed by dehydration in absolute alcohol, clearing in xylene and applying a cover glass with a synthetic resin (G. T. Gurr's DePeX was used). The sex chromatin is deep blue-violet and sharply contrasted against the lightly colored particulate chromatin of the nucleus. Cytoplasm remains unstained but fibrin and related structures show metachromasia. Chromosomes are well demonstrated if present. The method works on all types of tissues, is simpler and quicker than the Feulgen method, and often yields superior results.     

一种通用的、基于Agent的生物资源整合架构

众所周知,随着基因组测序工作的蓬勃发展和后基因组时代的到来,生物信息学数据呈指数级增长.生物界在享受着资源共享所带来便利的同时,也随着数据总量和复杂性的不断增加而变得异构化和分布化.目前,各种生物计算软件和数据库资源通常标准不一而且很难兼容.因此,如何在这些异构资源之间实现数据集成与软件共享是有效利用生物信息资源的关键.为解决以上问题,本文提出了一种新型的数据整合架构,该架构通过将web服务与并行计算相结合的方法,轻松地实现了对异地资源数据的访问、提取、转化以及整合.实验证明,本系统在处理异构、海量数据方面有着巨大的计算潜力.     

A Phosphate Bound Universal Linker for DNA Synthesis

Abstract

A uridine-based linker immobilized onto polystyrene beads at the 5′ terminus via a phosphodiester group and then used as a universal DNA synthesis support gives post synthesis DNA cleavage in 8 hrs or less without alkali metal salts. DNA produced with the new support was analyzed by HPLC, MALDI mass spectroscopy and PAGE. Each analysis showed DNA of equivalent quality to that produced with standard CPG supports, without contaminating materials resulting from linker or support backbone decomposition.     

Universal Aspects of Symbolic Healing: A Theoretical Synthesis

In this article I propose that symbolic healing has a universal structure in which the healer helps the patient particularize a general cultural mythic world and manipulate healing symbols in it. Problems currently existing in the explanation of symbolic healing are examined. The relationship between Western psychotherapy and magical healing is explained, the Junction qfshamanic ecstasy is discussed, and symbolic healing is explained in terms of a theory of living systems.     

Universal oligonucleotide microarray for sub-typing of Influenza A virus

A universal microchip was developed for genotyping Influenza A viruses. It contains two sets of oligonucleotide probes allowing viruses to be classified by the subtypes of hemagglutinin (H1-H13, H15, H16) and neuraminidase (N1-N9). Additional sets of probes are used to detect H1N1 swine influenza viruses. Selection of probes was done in two steps. Initially, amino acid sequences specific to each subtype were identified, and then the most specific and representative oligonucleotide probes were selected. Overall, between 19 and 24 probes were used to identify each subtype of hemagglutinin (HA) and neuraminidase (NA). Genotyping included preparation of fluorescently labeled PCR amplicons of influenza virus cDNA and their hybridization to microarrays of specific oligonucleotide probes. Out of 40 samples tested, 36 unambiguously identified HA and NA subtypes of Influenza A virus.     

Universal TA cloning

TA cloning is one of the simplest and most efficient methods for the cloning of PCR products. The procedure exploits the terminal transferase activity of certain thermophilic DNA polymerases, including Thermus aquaticus (Taq) polymerase. Taq polymerase has non-template dependent activity which preferentially adds a single adenosine to the 3'-ends of a double stranded DNA molecule, and thus most of the molecules PCR amplified by Taq polymerase possess single 3'-A overhangs. The use of a linearized "T-vector" which has single 3'-T overhangs on both ends allows direct, high-efficiency cloning of PCR products, facilitated by complementarity between the PCR product 3'-A overhangs and vector 3'-T overhangs. The TA cloning method can be easily modified so that the same T-vector can be used to clone any double-stranded DNA fragment, including PCR products amplified by any DNA polymerase, as well as all blunt- and sticky-ended DNA species. This technique is especially useful when compatible restriction sites are not available for the subcloning of DNA fragments from one vector to another. Directional cloning is made possible by appropriate hemi-phosphorylation of both the T-vectors and the inserts. With a single T-vector at hand, any DNA fragment can be cloned without compromising the cloning efficiency. The universal TA cloning method is thus both convenient and labor-saving.