The effect of MPTP on the neuronal uptake of monoamines]

The results of kinetic analysis of synaptosomal uptake of dopamine, noradrenaline, adrenaline and serotonin showed the presence of their own carrier systems with high or low affinity for each monoamine. The low affinity system of the uptake of monoamines by nerve endings differs from extraneuronal one by higher affinity. MPTP noncompetitively inhibits the system of highly effective uptake of the studied monoamines by nerve endings, competitively inhibiting synaptosomal uptake with low affinity of noradrenaline, adrenaline and noncompetitively serotonin and dopamine. The constant values of inhibition showed that MPTP most strongly blocks the system of synaptosomal uptake of low affinity serotonin and approximately 2-times weaker affects its system of high affinity. Carrier systems of high affinity of dopamine, adrenaline and noradrenaline block MPTP 150-500 times weaker than that of serotonin, and as for low affinity--in 2000-4000 times. It may be supposed that synaptosomal uptake of low affinity serotonin is most perceptible to the effect of MPTP and is of a particular importance in the development of Parkinson's disease symptoms.     

A biplot approach for investigating QTL-by-environment patterns

Due to the universal presence of genotype by environment interactions, understanding the pattern of quantitative trait loci (QTL)-by-environment interactions is a prerequisite for effective marker-assisted selection. In this report, we describe a biplot approach for investigating QTL-by-environment patterns. This approach involves two steps. It starts with a two-way table containing effects of individual QTLs in individual environments for the trait under investigation. This table is decomposed into principal components via singular value decomposition, and the first two principal components are plotted for both QTLs and environments to form a biplot. The resulting QQE biplot contains information on QTL main effects (Q) and QTL-by-environment interactions (QE). A QQE biplot displays the QTL-by-environment patterns and allows visualization of: (1) the magnitude of the effect of a QTL, (2) the average effect of a QTL and its stability across environments, (3) the effects of a QTL in individual environments, (4) the similarity/dissimilarity among QTLs in effect and response to the environments, (5) the similarity/dissimilarity among environments in modulating QTL effects, (6) any differentiation of mega-environments, and (7) the combination of QTL alleles for maximum/minimum expression of the trait for each environment or mega-environment. A case study is provided using the QTL-by-environment two-way table for barley yield.     

A versatile in vitro assay for investigating angiogenesis of the heart

Neovascularization in the heart is usually investigated with models of angiogenesis in vivo. Here we present a simple model that allows investigating heart angiogenesis in mice and rats in vitro. Small pieces of left ventricular myocardium were cultured in three-dimensional fibrin gels for 10 days. A single mouse heart allowed assessing 24 conditions, each tested in octuplicates. Rat recombinant VEGF164, human recombinant bFGF, and human recombinant PDGF-BB were used under normoxia (21% O2) and hypoxia (3% O2), and outgrowth of endothelial sprouts from heart pieces was quantified. In 4-week-old OF1 mice, endothelial sprouts formed spontaneously. In contrast, in 12-week-old adult mice, virtually no sprouts formed under normoxia. Under hypoxia, sprout formation increased substantially. Different growth factors induced formation of distinct patterns of sprouts and unorganized single cells. Sprouts were composed of endothelial cells with smooth muscle cells or pericytes interacting with them, as assessed by immunohistochemistry. Taken together, our model is suited for investigation of angiogenesis of the heart in vitro. It may allow performing extensive series of experiments in vitro including rapid screening of pharmacological compounds and assessment of mechanisms of heart angiogenesis in transgenic animals in an easy straightforward manner.     

A new approach to random mutagenesis in vitro

Random mutagenesis is a powerful tool for studying the effects of a large number of permutations of a particular DNA sequence and its encoded products. Here we describe a new strategy of conducting in vitro random mutagenesis using ethyl methane sulfonate (EMS). The Bacillus aprN18 gene, coding for a serine protease with fibrinolytic activity, was used as a target gene. To study the mutations of the coding region, rather than the whole plasmid, the 1.4 kb gene fragment was cut out from an expression plasmid and treated with 10 mM EMS at 37 degrees C for 1 h. The treated fragment was then ligated back into the original expression vector and a library of random mutants was constructed in a protease-deficient Bacillus subtilis strain. A plate assay-based screening method was used to select for mutant clones with altered enzyme activity, and the change of activity was then confirmed by a semi-quantitative enzyme assay using liquid culture supernatant. The inserts of five clones with altered enzyme activity were randomly chosen for sequencing analysis. Among the point mutations detected, GC --> AT transition accounts for 42.1%, AT --> GC transition 34.2% and GC/CG transversion 23.7%, respectively. To our knowledge this is the first application of EMS for in vitro mutagenesis of a defined DNA sequence.     

A new screening method for investigating microbial interactions

Interactions among Candida albicans, Staphylococcus aureus and Escherichia coli were investigated using a screening system in which test micro-organisms were incorporated in agar discs and effector micro-organisms in fluid growth media. Total as well as partial inhibition of test micro-organisms was observed in agar discs when these were incubated in broths containing effector micro-organisms. The ratio of numbers of test to effector micro-organisms was found to be of importance in the inhibition effect. The technique was found to be cheap, simple and versatile.     

青海沙蜥种群密度调查的一种新方法

在2002年9月,分别利用洞穴深度法、标志重捕法和洞口计数法对分布在若尔盖草原荒漠中的青海沙蜥(Phrynocephalus vlangalii)的种群密度进行调查,所得的结果分别是190.4、76.8和250.7只.1000 m-2。通过对3种结果的比较与分析,证明洞穴深度法有较高的可靠性,这种方法的理论依据是:沙蜥(Phrynocephalus)是一种变温动物,不能长时间处在温度低于致死低温(-2.5℃)以下的环境中,为了能够成功地度过漫长而寒冷的冬季,它必须居住在深度达到最大冻土层之下的洞穴中。这是沙蜥躲避低温伤害的一种行为机制。该方法可以适用于分布在中国的沙蜥属的其它物种密度调查。     

A new radiographic cadaver injection technique for investigating the lymphatic system

Studies of the gross anatomy of the lymphatic system are few and far between when compared with those of other vascular systems. Our knowledge of the anatomy of the lymphatic system is so limited that it seems vastly inadequate in explaining the clinical manifestations caused by its disorder. This study has developed an effective method to identify the lymphatics using hydrogen peroxide, to demonstrate the lymphatic vessels radiographically using a lead oxide suspension, and to dissect them out in adult human cadavers.     

In vitro oxidation of MPTP by primate neural tissue: A potential model of MPTP neurotoxicity

The compound 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) produces a parkinsonian syndrome in humans and primates. We have previously found that metabolism of MPTP to a quaternary species is necessary for the expression of its neurotoxic effects. We now report that the metabolism of MPTP occurs in primate brain tissue $\text{in vitro}$, and present a model of MPTP neurotoxicity which incorporates our findings to date.Since the toxicity of MPTP is metabolism dependent, we propose that the $\text{in vitro}$ metabolism of MPTP by brain tissue should provide a useful model for studying selected aspects of MPTP neurotoxicity.     

A general approach for investigating enzymatic pathways and substrates for ubiquitin-like modifiers

Ubiquitin-like modifiers (UBLs) contain ubiquitin homology domains and can covalently modify target proteins in a manner similar to ubiquitylation. In this study, we revealed a general proteomic approach to elucidate the enzymatic pathways and identify target proteins for three UBLs: SUMO-2, SUMO-3, and NEDD8. Expression plasmids containing the cDNAs of Myc/6xHis doubly-tagged processed or non-conjugatable forms of these UBLs were constructed. The constructed vectors were then used to transfect HEK 293 Tet-On cells, and stable cell lines expressing these UBLs and their mutants were established. The epitope-tagged proteins were purified by immunoprecipitation under native conditions or by affinity chromatography on nickel resin under denaturing conditions. Purified proteins were analyzed using liquid chromatography coupled with mass spectrometry (LC-MS/MS). Most of the E1-like activating enzymes, E2-like conjugating enzymes and the majorities of the known target as well as some previously unreported proteins for SUMO-2, SUMO-3, and NEDD8 pathways were identified.     

A scalable and flexible approach for investigating the genomic landscapes of phylogenetic incongruence

Analyses of DNA sequence datasets have repeatedly revealed inconsistencies in phylogenetic trees derived with different data. This is termed phylogenetic incongruence, and may arise from a methodological failure of the inference process or from biological processes, such as horizontal gene transfer, incomplete lineage sorting, and introgression. To better understand patterns of incongruence, we developed a method (PartFinder) that uses likelihood ratios applied to sliding windows for visualizing tree-support changes across genome-sequence alignments, allowing the comparative examination of complex phylogenetic scenarios among many species. As a pilot, we used PartFinder to investigate incongruence in the Homo-Pan-Gorilla group as well as Platyrrhini using high-quality bacterial artificial chromosome (BAC)-derived sequences as well as assembled whole-genome shotgun sequences. Our simulations verified the sensitivity of PartFinder, and our results were comparable to other studies of the Homo-Pan-Gorilla group. Analyses of the whole-genome alignments reveal significant associations between support for the accepted species relationship and specific characteristics of the genomic regions, such as GC-content, alignment score, exon content, and conservation. Finally, we analyzed sequence data generated for five platyrrhine species, and found incongruence that suggests a polytomy within Cebidae, in particular. Together, these studies demonstrate the utility of PartFinder for investigating the patterns of phylogenetic incongruence.     

Reconstitutive approach for investigating plant vascular development

Plants generate various tissues and organs via a strictly regulated developmental program. The plant vasculature is a complex tissue system consisting of xylem and phloem tissues with a layer of cambial cells in between. Multiple regulatory steps are involved in vascular development. Although molecular and genetic studies have uncovered a variety of key factors controlling vascular development, studies of the actual functions of these factors have been limited due to the inaccessibility of the plant vasculature. Thus, to obtain a different perspective, culture systems have been widely used to analyze the sequential processes that occur during vascular development. A tissue culture system known as VISUAL, in which molecular genetic analysis can easily be performed, was recently established in Arabidopsis thaliana. This reconstitutive approach to vascular development enables this process to be investigated quickly and easily. In this review, I summarize our recent knowledge of the regulatory mechanisms underlying vascular development and provide future perspectives on vascular analyses that can be performed using VISUAL.     

A systems-based mathematical modelling framework for investigating the effect of drugs on solid tumours

Background and Purpose

Most information on the dose-response of radiation-induced cancer is derived from data on the A-bomb survivors. Since, for radiation protection purposes, the dose span of main interest is between zero and one Gy, the analysis of the A-bomb survivors is usually focused on this range. However, estimates of cancer risk for doses larger than one Gy are becoming more important for radiotherapy patients. Therefore in this work, emphasis is placed on doses relevant for radiotherapy with respect to radiation induced solid cancer.

Materials and methods

For various organs and tissues the analysis of cancer induction was extended by an attempted combination of the linear-no-threshold model from the A-bomb survivors in the low dose range and the cancer risk data of patients receiving radiotherapy for Hodgkin's disease in the high dose range. The data were fitted using organ equivalent dose (OED) calculated for a group of different dose-response models including a linear model, a model including fractionation, a bell-shaped model and a plateau-dose-response relationship.

Results

The quality of the applied fits shows that the linear model fits best colon, cervix and skin. All other organs are best fitted by the model including fractionation indicating that the repopulation/repair ability of tissue is neither 0 nor 100% but somewhere in between. Bone and soft tissue sarcoma were fitted well by all the models. In the low dose range beyond 1 Gy sarcoma risk is negligible. For increasing dose, sarcoma risk increases rapidly and reaches a plateau at around 30 Gy.

Conclusions

In this work OED for various organs was calculated for a linear, a bell-shaped, a plateau and a mixture between a bell-shaped and plateau dose-response relationship for typical treatment plans of Hodgkin's disease patients. The model parameters (α and R) were obtained by a fit of the dose-response relationships to these OED data and to the A-bomb survivors. For any three-dimensional inhomogenous dose distribution, cancer risk can be compared by computing OED using the coefficients obtained in this work.     

Some prospects for investigating hydra cellsIn vitro

Summary and Conclusions Over the past 15 years great strides have been taken in the laboratory culture of intact hydra, and in the discovery and elucidation of a wide variety of fundamental biological problems that can be studied using this organism. In the present article I restricted myself mostly to research being conducted in my laboratory on: environmental ions; uptake of food particles: a possible role of CO₂ gas; the unusual collagenous nature of nematocyst capsules; the reproduction of cells from a hydra mutant in otherwise “normal” hydra; and activation of behavioral contraction responses by reduced glutathione and tyrosine. In addition, Dr. Campbell (4) and Dr. Haynes (5) have reviewed much research in developmental biology that is currently taking place using hydra, and which similarly could be enhanced through culture of hydra cells. Although in this review I have placed some emphasis on the present difficulties of raising the cells of hydrain vitro, I still believe that hydra cells can and should be cultured. The culture of cells from an animal at the tissue level of organization is a challenge that ought not to go unanswered.     

Xylem sap composition: A tool for investigating mineral uptake and cycling in adult spruce

Xylem sap composition of spruce is influenced by several factors, such as the sampled organ, the sampling period, the availability of soil nutrients, and the soil water potential. Based on literature data and ongoing investigations carried out with adult trees, we present an overview on the main factors influencing xylem sap concentrations of Norway spruce. Direct measurements of nutrient fluxes in the xylem sap are then used to suggest a general scheme of mineral element cycling within adult trees. In Norway spruce (Picea abies Karst.), nutrient concentration in the xylem sap was higher in twigs and fine roots compared to the bottom of the trunk, the highest concentrations beeing observed in spring during the shoot elongation. Xylem sap concentrations were higher in spruce growing at nutrient rich sites than at poor sites. The combination of twig and trunk xylem sap analysis, together with xylem flow measurements in the trunk during the course of a vegetation period allowed the quantification of mineral fluxes via xylem sap flow in the trunk and twigs. These results were compared to gross mineral uptake measurements at the same site. Ca flux in the trunk xylem sap was lower than the gross uptake of Ca. Mg flux in trunk sap was approximately equivalent to Mg gross uptake whereas P and K fluxes in trunk sap were much higher than the gross uptake. Fluxes of Ca, Mg, K and P in the twig sap were much higher than that in trunk sap. Data suggest that internal cycling is responsible for a large part of the nutrient fluxes in the xylem sap of the crown. Xylem sap composition thus appears to be a tool which can complement other sources of information on mineral uptake and cycling in adult spruce     

生物序列局部联配中的马赛克问题的一种解决方法

生物信息学中，Smith Waterman算法用于同源长序列的局部联配时，经常会出现马赛克问题（相似度很低的保守区域夹在两个相似度很高的区域中间）。在分析问题成因的基础上，提出利用动态加速扣分策略解决马赛克问题，即在计算得分矩阵的过程中．如果存在保守区域，则加大扣分的力度，争取在离开保守区域前让得分为0，从而将保守区域切断。实验结果表明，动态加速扣分策略顺利解决了序列局部联配中的马赛克问题，并且没有显著增加算法的时间复杂度和空间复杂度。     

A graph-based approach to investigating the influence of the landscape on population spread processes

Modelling of landscape connectivity is a key point in the study of the movement of populations within a given landscape. For studies focused on the preservation of biodiversity, graph-based methods provide an interesting framework to investigate the landscape influence on population spread processes. Such an approach is described here, based on the mapping of landscape categories in habitat patches, including a diachronic data set describing the population spread within the habitat patches. A minimum planar graph was built by computing spatial distances between all pairs of neighbouring patches. From this structure, two types of analysis are proposed: one focused on the links of the graph and consists in correlating spatial distances and gap indicators computed from the diachronic data. The other was based on the correlations between population data and connectivity metrics at the patch level. As an example, this approach was applied to the spread of the fossorial water vole on the Jura plateau (France), with annual population data covering eleven years from 1989 to 2000. Link analysis allowed to find an optimal set of resistance values used in the least-cost distances computations, and thus to build a relevant graph. From this graph, patch analysis displayed a cyclic correlation between a metric based on potential dispersal flux and the population density, outlining the strong role of landscape connectivity in the population spread. The present study clearly shows that landscape modelling and graph-based approach can produce parameters which are consistent with field observations and thus pave the way to simulating the effect of landscape modification on population dynamics.