Demiarcs,creaons and genons

Useful insights into the representation of natural systems can be gained by decomposing directed graphs (digraphs) into elementary components. Arcs of digraphs can be split into male demiarcs (outarcs) which leave vertices and female demiarcs (inarcs) which enter demiarcs. Likewise, a vertex can be split into an input perceiving side called the creaon and an output generating side called the genon. Digraphs can be regarded as being hierarchically organized because each vertex in a level-1 digraph can be expanded into a level-2 digraph. In general, each vertex of a level-i digraph can be expanded into a level-(i+1) digraph. Arcs of a level-i digraph can be regarded as bundles of level-(i + 1) arcs which are split at the vertex boundary. These elementary graphical components are shown to be useful for depicting input-output systems such as organisms, ecosystems and societies.     

Determination of the specific radloactivity of proteins separated by two-dimensional gel electrophoresis

Tritlum-labeled proteins, separated by two-dimensional gel electrophoresis, can be quantitatively extracted using sodium dodecyl sulfate (SDS)-urea buffer and subsequently acid-precipitated in the presence of serum albumin as carrier at low temperature (0–4°C). Their radioactivity can be counted efficiently under these conditions. Besides a better efficiency of counting, this method has some other advantages over the classical procedures using H₂O₂. The amounts of the eluted proteins can be easily measured in the SDS solution, using the Lowry method, and therefore specific radioactivity can be calculated. Also SDS can be removed easily, and the proteins can be used for further experiments.     

Excitotoxic Stimulation of Brain Microslices as an In vitro Model of Stroke

Examining molecular mechanisms involved in neuropathological conditions, such as ischemic stroke, can be difficult when using whole animal systems. As such, primary or ''neuronal-like'' cell culture systems are commonly utilized. While these systems are relatively easy to work with, and are useful model systems in which various functional outcomes (such as cell death) can be readily quantified, the examined outcomes and pathways in cultured immature neurons (such as excitotoxicity-mediated cell death pathways) are not necessarily the same as those observed in mature brain, or in intact tissue. Therefore, there is the need to develop models in which cellular mechanisms in mature neural tissue can be examined. We have developed an in vitro technique that can be used to investigate a variety of molecular pathways in intact nervous tissue. The technique described herein utilizes rat cortical tissue, but this technique can be adapted to use tissue from a variety of species (such as mouse, rabbit, guinea pig, and chicken) or brain regions (for example, hippocampus, striatum, etc.). Additionally, a variety of stimulations/treatments can be used (for example, excitotoxic, administration of inhibitors, etc.). In conclusion, the brain slice model described herein can be used to examine a variety of molecular mechanisms involved in excitotoxicity-mediated brain injury.     

组织酸化参与外周痛觉传递的离子通道机制

组织酸化可以导致痛觉的产生.初级感觉神经元可以通过离子通道来感受外周的组织酸化.已鉴定了几个离子通道家族可能参与了外周组织酸化的感受：a.酸敏感离子通道(ASICs)是可以被酸直接门控的阳离子通道;b.辣椒素受体(VR1)可被酸敏化,同时可被pH＜6.0直接激活;c.P2X2和P2X2/3受体通道反应被酸上调;d.TwIK相关的酸感受钾通道（TASK）是被酸关闭的双孔内向整流钾通道.这些通道被酸所调控的共同结果就是提高了神经元的兴奋性.因此,它们在介导了组织酸化所诱导的痛觉感受和传递中具有重要作用.     

Intron variation in marbled murrelets detected using analyses of single-stranded conformational polymorphisms

Combination of the targeted amplification of nuclear introns and the analysis of single-stranded conformational polymorphisms has the potential to provide an inexpensive, rapid, versatile and sensitive genetic assay for evolutionary studies and conservation. We are developing primers and protocols to analyse nuclear introns in vertebrates, and are testing them in a population genetic study of marbled murrelets Brachyramphus marmoratus . Here we present protocols and results for introns for aldolase B, α-enolase, glyceraldehyde-3-phosphate dehydrogenase and lamin A. Results suggest that this approach presents a potentially powerful method for detecting genetic variation within and among local populations and species of animals: (i) a variety of genes can be surveyed, including genes of special interest such as those involved in disease resistance; (ii) assays are rapid and relatively inexpensive; (iii) large numbers of genes can be assayed, enabling accurate estimation of variation in the total genome; (iv) almost any mutation can be detected in the genes amplified; (v) the exact nature of variation can be investigated by sequence analysis if desired; (vi) statistical methods previously developed for proteins and/or sequence data can be used; (vii) protocols can be easily transferred to other species and other laboratories; and (viii) assays can be performed on old or degraded samples, blood or museum skins, so that animals need not be killed. Results of analyses for murrelets support earlier evidence that North American and Asiatic subspecies represent reproductively isolated species, and that genetic differences exist among murrelets from different sites within North America.     

Cooperative Regulation of Cellular Proliferation by Intercellular Diffusion

A theoretical model for the cooperative control of cellular kinetics is investigated. A critical substance A is produced by the cells whose concentration in a given cell determines whether that cell can divide. The substance A can leak out of the cells into the surrounding medium as well as be reabsorbed by the cells. This feature then implies communication between the cells since all concentrations will be functions of the population density. The substance A also has a lifetime, i.e. decays, for example, by denaturation. This system can be described by three coupled nonlinear differential equations which can be solved analytically in certain limiting cases and can, of course, be studied in detail by computer techniques. Our investigations have shown that (a) there is a critical initial cell population density below which cell proliferation will not occur, (b) cell proliferation can be stimulated by supplying substance A to the medium and there is a critical initial concentration in the medium for initiating proliferation when the cell population density is subcritical, and (c) a well-defined induction period prior to exponential growth may exist whose length depends on the system parameters and initial conditions.     

THE EFFECT OF IRRADIATED PLASMA ON NORMAL HUMAN CHROMOSOMES AND ITS RELEVANCE TO THE LONG-LIVED LYMPHOCYTE HYPOTHESIS

The persistence of unstable chromosome-type aberrations in peripheral blood lymphocytes of irradiated individuals has led to the proposal that some lymphocytes survive for many years in vivo without undergoing mitosis (Fitzgerald, 1964). It has recently been shown, however, that plasma from irradiated individuals can induce chromosomal damage in cultures of normal blood lymphocytes (Hollowell & Littlefield, 1968) even when the plasma donors were irradiated 7 years earlier (Goh & Sumner, 1968). Goh (1968) has therefore suggested that ‘An alternate explanation to the “long-lived cell” theory proposed by others…would be that a substance is produced or activated by total body irradiation and remains capable of affecting the chromosomes for extensive lengths of time'. The present results show that a lymphocyte chromosome-breaking factor can be induced in the plasma of blood irradiated in vitro as well as in vivo. All of the aberrations induced by this ‘plasma factor’and those reported by other workers can be interpreted as being of the chromatid type. Before the long-lived lymphocyte hypothesis can be brought into serious disrepute, it must be shown that the plasma factor can induce aberrations of the same type as persist after in vivo irradiation (i.e. unequivocal chromosome-type aberrations, such as dicentrics and rings) and that these can be induced in vivo.     

Determination of the d and l configuration of neutral monosaccharides by high-resolution capillary g.l.c.

Capillary g.l.c. on SE-30 of the trimethylsilylated (-)-2-butyl glycosides of d and l monosaccharides gives multiple peak patterns, which can be used for the assignment of the absolute configurations. (-)-2-Butyl glycosides can be prepared from monosaccharides or their methyl glycosides; consequently, for the analysis of oligo- or poly-saccharides, hydrolysis as well as methanolysis can be applied. Provided that the peaks of the (-)-2-butyl glycosides do not completely overlap, mixtures of monosaccharides can be analysed directly, as illustrated for the constituents of the cell-wall lipopolysaccharide from Salmonella typhimurium LT-2.     

Development and differentiation of haploid Lycopersicon esculentum (tomato)

Summary Haploid callus cultures of selected races of Lycopersicon (tomato) species can be obtained from anther culture. This is a further demonstration of a proposed general method of haploid culture developed with Arabidopsis thaliana. Differentiation of haploid callus of Lycopersicon esculentum can be controlled both in the dark and the light by hormones added to defined minimal media. Development to plantlets is achieved only in the light. Callus cells can be induced to develop into seedless pseudo-fruits. Chromosome counts on callus cells or root-tip cells establishes haploidy (n=12).Haploidy can be maintained in culture on defined minimal media for at least one year.     

Bearbeitergesteuerte Analyse von Verhaltenszeitreihen am Digitalrechner

1. Both the organization of behaviour and communicative interactions can be established by analyzing behavioural time series. By means of an analysis of this kind, conclusions about the control of behaviour and the principles of interindividual communication can be reached. An analysis may be based on simultaneous and successive behavioural events. In these multi-channel time series the temporal arrangement of patterns (“Strukturierung”), the organization and the conditions determining the occurrence of behavioural events can be specified.
2. Data-analysis by digital computer permits rapid processing of a large quantity of material in regard to several respects. “Sets of data” can be stored, thus enabling the user to correct, alter, combine and finally analyze them with respect to various questions. For this purpose, a program system for the digital processing of behavioural time series (title “PROVED”) was developed.
3. The course of behavioural events is composed of temporal patterns which are ordered in a definite hierarchy (Fig. 1). Several quantitative and qualitative characteristics (“Muster-Merkmale”) can be attributed to each pattern (Figs. 2,4). With the PROVED-System, the temporal arrangement of behavioural patterns is reestablished by the computer according to the control orders of the user. These orders must take into consideration the physiological relevance that is to be confirmed by an analysis of time serics (Fig. 3). The orders controlling the temporal arragement as well as the asignment of pattern characteristics to sets of data are available for further evaluation.
4. The PROVED-System includes several procedures involving input, output, storage, administration, correction, assignment of characteristics, temporal arrangement and analysis of data. The examiner can select and combine these procedures at will using statements of a particular control language.
5. During the first step of data analysis, a fixed number of parameters for each pattern is determined, the number of parameters varying with the complexity of the problem. Any measured value which is related to the pattern under investigation can be regarded as a parameter. During the second step, multidimensional frequency distributions of crossclassified parameters are established which can be examined by means of statistical tests (third step) (Figs. 5,6).
6. Determination of the parameters by the examiner decisively influences the further course of the analysis. The control statements for one parameter consist of two parts: 1. quality of the parameter (type of pattern, temporal distance, etc.), 2. position of the parameter in the behavioural time series (pattern under investigation, immediately subsequent pattern, next pattern with the same characteristics, etc.). The latter is determined by a series of shifts of indices controlled by the user (Fig. 7,8).
7. The PROVED-System can be applied to the analysis of various behavioural time series (succession of sounds, recordings of movements, observations of behavioural acts, etc.). Depending upon the aim of the analysis (temporal arrangement, organization, control of behaviour or communication), spontaneous behavioural events, input-output experiments (stimulus-reaction) and social interaction can be evaluated.

     

The enumeration ofStaphylococcus aureus in foods

Summary Staphylococcus aureus can be enumerated in foods by the use ofChapman’s special medium (3), under application of the drop plate technique, recommended byMiles andMisra (6). Colonies ofS.aureus so obtained can easily be macroscopically differentiated from aerobic sporeformers which grow also on this medium. The colonies can be used immediately for testing their coagulase reaction.     

The lac-operon for lactose degradation,or rather for the utilization of galactosylglycerols from galactolipids?

Two anomalies of the lac-operon of E. coli can hardly be understood if this operon had evolved in order to utilize lactose as a carbon source: (i) lactose has to be modified before the repressor can be inactivated and the operon becomes induced; (ii) one of the induced enzymes (the “transacetylase”) has no function whatever in the degradation of lactose. These oddities can more easily be explained, if other galactosides were the natural substrates to which the lac-operon had been adapted first. Galactosylglycerols, which are readily obtained from galactolipids (widespread in most plant materials), are appropriate candidates both in terms of structure and abundance.     

Use of lissamine rhodamine ceramide trihexoside as a functional assay for alpha-galactosidase A in intact cells

Fabry disease is an X-linked disorder caused by mutations in the GLA gene encoding for α-galactosidase A (AGA, EC 3.2.1.22). Measurement of AGA enzyme activity using cell homogenates can easily identify men with Fabry disease, but in women, the degree of X-inactivation in the tested tissue may produce activities in homogenates that are indistinguishable from normal. Monti et al. developed a series of lissamine rhodamine-labeled glycosphingolipid substrates that can be used to measure clearance of these lipids in intact cells (1). We report here that one of these substrates, lissamine rhodamine ceramide trihexoside (LR-CTH), can be used as a probe for functional activity of AGA in intact fibroblasts, endothelial cells, and T-lymphocytes from patients with Fabry disease. By utilizing standard detection techniques, such as microscopic imaging, fluorescence microplate spectrophotometry, and flow cytometry, cells with impaired AGA activity can easily be distinguished from wild-type (WT) cells, and these two cell types can be isolated into separate populations using fluorescence-activated cell sorting (FACS). The assay we report here can be adapted to evaluate new therapies by high-throughput screening, can aid in the study of AGA activity in living cells, and can assist in the diagnosis of women with the Fabry trait.     

Non-destructive RAPD genetic diagnostics of microspore-derivedBrassica embryos

We demonstrate the application of the RAPD genetic polymorphism assay (Williams et al., 1990, Welsh and McClelland 1990), to the determination of the genotype of immature, microspore-derived haploid embryos ofBrassica napus. Several hundred assays can be performed on the DNA obtained from a cotyledon fragment, and the remaining embryo can be regenerated. Thus, the assay can be used for ”prenatal” diagnostics of embryo-regenerated plants, and can facilitate selection of defined genotypes in plant breeding. A suitable population of embryos could also be used for the construction of RAPD genetic maps. The online version of the original article can be found at     

Graph-representation of oxidative folding pathways

Background  

The process of oxidative folding combines the formation of native disulfide bond with conformational folding resulting in the native three-dimensional fold. Oxidative folding pathways can be described in terms of disulfide intermediate species (DIS) which can also be isolated and characterized. Each DIS corresponds to a family of folding states (conformations) that the given DIS can adopt in three dimensions.     

Stimulation of Cytoplasmic DNA Sensing Pathways In Vitro and In Vivo

In order to efficiently stimulate an innate immune response, DNA must be of sufficient length and purity. We present a method where double stranded DNA (dsDNA) which has the requisite characteristics to stimulate the cytoplasmic DNA sensing pathways can be generated cheaply and with ease. By the concatemerization of short, synthetic oligonucleotides (which lack CpG motifs), dsDNA can be generated to be of sufficient length to activate the cytosolic DNA sensing pathway. This protocol involves blunt end ligation of the oligonucleotides in the presence of polyethylene glycol (PEG), which provides an environment for efficient ligation to occur. The dsDNA concatemers can be used, following purification by phenol/chloroform extraction, to simulate the innate immune response in vitro by standard transfection protocols. This DNA can also be used to stimulate innate immunity in vivo by intradermal injection into the ear pinna of a mouse, for example. By standardizing the concatemerization process and the subsequent stimulation protocols, a reliable and reproducible activation of the innate immune system can be produced.     

Gyroid Nickel Nanostructures from Diblock Copolymer Supramolecules

Nanoporous metal foams possess a unique combination of properties - they are catalytically active, thermally and electrically conductive, and furthermore, have high porosity, high surface-to-volume and strength-to-weight ratio. Unfortunately, common approaches for preparation of metallic nanostructures render materials with highly disordered architecture, which might have an adverse effect on their mechanical properties. Block copolymers have the ability to self-assemble into ordered nanostructures and can be applied as templates for the preparation of well-ordered metal nanofoams. Here we describe the application of a block copolymer-based supramolecular complex - polystyrene-block-poly(4-vinylpyridine)(pentadecylphenol) PS-b-P4VP(PDP) - as a precursor for well-ordered nickel nanofoam. The supramolecular complexes exhibit a phase behavior similar to conventional block copolymers and can self-assemble into the bicontinuous gyroid morphology with two PS networks placed in a P4VP(PDP) matrix. PDP can be dissolved in ethanol leading to the formation of a porous structure that can be backfilled with metal. Using electroless plating technique, nickel can be inserted into the template''s channels. Finally, the remaining polymer can be removed via pyrolysis from the polymer/inorganic nanohybrid resulting in nanoporous nickel foam with inverse gyroid morphology.     

Use of oil bodies and oleosins in recombinant protein production and other biotechnological applications

Oil bodies obtained from oilseeds have been exploited for a variety of applications in biotechnology in the recent past. These applications are based on their non-coalescing nature, ease of extraction and presence of unique membrane proteins—oleosins. In suspension, oil bodies exist as separate entities and, hence, they can serve as emulsifying agent for a wide variety of products, ranging from vaccines, food, cosmetics and personal care products. Oil bodies have found significant uses in the production and purification of recombinant proteins with specific applications. The desired protein can be targeted to oil bodies in oilseeds by affinity tag or by fusing it directly to the N or C terminal of oleosins. Upon targeting, the hydrophobic domain of oleosin embeds into the TAG matrix of oil body, whereas the protein fused with N and/or C termini is exposed on the oil body surface, where it acquires correct confirmation spontaneously. Oil bodies with the attached foreign protein can be separated easily from other cellular components. They can be used directly or the protein can be cleaved from the fusion. The desired protein can be a pharmaceutically important polypeptide (e.g. hirudin, insulin and epidermal growth factor), a neutraceutical polypeptide (somatotropin), a commercially important enzyme (e.g. xylanase), a protein important for improvement of crops (e.g. chitinase) or a multimeric protein. These applications can further be widened as oil bodies can also be made artificially and oleosin gene can be expressed in bacterial systems. Thus, a protein fused to oleosin can be expressed in Escherichia coli and after cell lysis it can be incorporated into artificial oil bodies, thereby facilitating the extraction and purification of the desired protein. Artificial oil bodies can also be used for encapsulation of probiotics. The manipulation of oleosin gene for the expression of polyoleosins has further expanded the arena of the applications of oil bodies in biotechnology.     

How to manage rheumatoid arthritis according to classic biomarkers and polymorphisms?

Objectives

Single nucleotide polymorphisms (SNPs), genetic background, and epigenetics play important roles in rheumatoid arthritis (RA). These factors can be useful in RA diagnosis, prognosis, and treatment response evaluation, particularly with the growing trends in personalized medicine. Therefore, categorizing classic genes and SNPs in RA can present an appropriate guideline for RA management.

Discussion

Prognostic and diagnostic biomarkers play important roles in RA diagnosis and treatment. Categorizing SNPs is not an easy process yet, but selecting classic SNPs can be useful worldwide, according to basic similarities that exist in genomes. In this review, we compiled some of these RA-associated SNPs and biomarkers in a table, according to newly identified factors. The role of epigenetics in RA is undeniable; using epigenetic biomarkers like histone deacetylase (HDACs) can be useful in RA diagnosis and treatment. miRs such as miR-146a, miR-155, and miR-222 are useful in diagnosis and can be used in treatment by interfering with other factors’ functions. Interleukins (ILs) seem to be good prognostic and diagnostic markers and can be targeted in RA treatment.

Conclusion

Using multiple types of biomarkers, such as genes, SNPs, and epigenetic biomarkers like HDACs can be useful in RA management and treatment. PTPN22, HLA-DR polymorphisms, miRs, and HDACs are considerable in RA susceptibility; hence, they can be valuable biomarkers in future studies. This article gathered separate information from approximately 100 articles to present useful biomarkers and polymorphisms in one review.