Modification of commerical and custom-built slab gel electrophoresis units for two-dimensional polyacrylamide gel electrophoresis

Many commercial and custom-built slab gel electrophoresis units can be modified to function as two-dimensional polyacrylamide gel electrophoresis units with the insertion of Plexiglas adapters. These adapters can be made for about $50 a pair and can be used for either temporary or permanent modification of the slab gel units. The physical dimensions of the adapters can be varied to permit great flexibility in the diameter of cylinder gels and the thickness of slab gels that can be run together. For example, proteins from 6-mm cylinder gels can be easily separated on 1-mm slab gels, which can then be dried for autoradiography.     

The chemoinvasion assay: a method to assess tumor and endothelial cell invasion and its modulation

Invasive and metastatic cells, as well as endothelial cells, must cross basement membranes (BMs) in order to disseminate or to form new blood vessels. The chemoinvasion assay using the reconstituted BM Matrigel in Boyden blind-well chambers is a very rapid, easy, inexpensive and flexible test that can be used to quantify the invasive potential of most cell types; it can be applied to detect the migratory activity associated with matrix degradation and can also be adapted to study the selective degrading activity on different matrix substrates. Transwell inserts can also be used. Once the optimal experimental conditions are empirically determined for specific cellular models, the chemoinvasion assay can be used for the screening of inhibitors of invasiveness and angiogenesis, or to select for invasive cellular populations. This protocol can be completed in 9 h.     

Simulation as experiment: a philosophical reassessment for biological modeling

Some scientific modelers suggest that complex simulation models that mimic biological processes should have a limited place in ecological and evolutionary studies. However, complex simulation models can have a role that is different from that of simpler models that are designed to be fit to data. Simulation can be viewed as another kind of experimental system and should be analyzed as such. Here, I argue that current discussions in the philosophy of science and in the physical sciences fields about the use of simulation as an experimental system have important implications for biology, especially complex sciences such as evolution and ecology. Simulation models can be used to mimic complex systems, but unlike nature, can be manipulated in ways that would be impossible, too costly or unethical to do in natural systems. Simulation can add to theory development and testing, can offer hypotheses about the way the world works and can give guidance as to which data are most important to gather experimentally.     

Fluorescence in situ hybridization on vibratome sections of plant tissues

This protocol describes the application of fluorescence in situ hybridization (FISH) to three-dimensionally (3D) preserved tissue sections derived from intact plant structures such as roots or florets. The method is based on the combination of vibratome sectioning with confocal microscopy. The protocol provides an excellent tool to investigate chromosome organization in plant nuclei in all cell types and has been used on tissues of both monocot and dicot plant species. The visualization of 3D well-preserved tissues means that cell types can be confidently identified. For example, meiocytes can be clearly identified at all stages of meiosis and can be imaged in the context of their surrounding maternal tissue. FISH can be used to localize centromeres, telomeres, repetitive regions as well as unique regions, and total genomic DNAs can be used as probes to visualize chromosomes or chromosome segments. The method can be adapted to RNA FISH and can be combined with immunofluorescence labeling. Once the desired plant material is sectioned, which depends on the number of samples, the protocol that we present here can be carried out within 3 d.     

Protein φ and ψ dihedral restraints determined from multidimensional hypersurface correlations of backbone chemical shifts and their use in the determination of protein tertiary structures

The chemical shifts of the backbone atoms of proteins can be used to obtainrestraints that can be incorporated into structure determination methods. Eachchemical shift can be used to define a restraint and these restraints can besimultaneously used to define the local, secondary structure features. Theglobal fold can be determined by a combined use of the chemical shift basedrestraints along with the long-range information present in the NOEs ofpartially deuterated proteins or the amide–amide NOEs but not from suchlimited NOE data sets alone. This approach has been demonstrated to be capableof determining the overall folding pattern of four proteins. This suggeststhat solution-state NMR methods can be extended to the structure determinationof larger proteins by using the information present in the chemical shifts ofthe backbone atoms along with the data that can be obtained on a small numberof labeled forms.     

黑河流域生态经济带分异协调规律与耦合发展模式

在西北干旱地区建设黑河流域生态经济带,是从根本上高效配置流域水资源,彻底化解流域上,下游利益冲突,实现利益共享,保护流域生态环境,推进流域可持续发展,全面实施国务院黑河流域分水方案的重要途径,通过对黑河流域生态经济带上－中－下游投入产出效益的比较分析和流域上、中、下游生态－生产、生活系统发展分异及互动协调关系的分析,提出了黑河流域生态经济带上－中－下游多维互动的协调耦合发展模式,进而提出了黑河流域生态经济带建设与发展的主要途径,包括推进黑河流域经济发展一体化和集成管理公司化,大力推行全流域水资源的差异化有偿使用制度,实施流动上、中、下游的水权转让贸易,实行规范的流域财政转移支付制度,建立流域资源与生态环境和经济的整合帐户体系,实行跨行政区域河流边界水量水质达标交接制度,等等。     

Use of bioluminescence in nucleic acid hybridization reactions

Luminescence reactions can be used to detect specific nucleic acid sequences hybridized with a nucleic probe. Different labels such as cytidine sulphone, fluorescein, and biotin can be incorporated into DNA or oligonucleotide molecules and detected by antibody or avidin conjugates coupled to glucose-6P dehydrogenase. On supports such as nitrocellulose filters, sensitivity is not greatly increased using luminescence, but detection is rapid and easy to perform using polaroid film. Moreover, hybridization can be performed with different labelled probes on the same sample. In solution, luminescence can be used to monitor sandwich reactions. The method is less sensitive than detection on filters but can easily be automated. The performance of these assays can be increased considerably by enzymatic amplification of the target catalysed by a thermostable polymerase.     

Fiber optic array biosensors

Optical fiber arrays provide a powerful substrate for creating high-density sensing systems that can address a variety of biological problems. The fiber substrate can be used to create femtoliter wells that can be loaded with individual beads to create high-density arrays for multiplexed screening and analysis. In addition, living cells can be loaded into the arrays, and their individual responses monitored over long time periods, enabling functional screening of biologically active compounds. Adherent cells can be attached to the fiber substrate to provide a rapid method for observing cell migration and for screening anti-migratory compounds. Finally, individual enzyme molecules can be loaded into the array wells enabling single molecule detection via enzyme-catalyzed signal amplification.     

Interactive robots in experimental biology

Interactive robots have the potential to revolutionise the study of social behaviour because they provide several methodological advances. In interactions with live animals, the behaviour of robots can be standardised, morphology and behaviour can be decoupled (so that different morphologies and behavioural strategies can be combined), behaviour can be manipulated in complex interaction sequences and models of behaviour can be embodied by the robot and thereby be tested. Furthermore, robots can be used as demonstrators in experiments on social learning. As we discuss here, the opportunities that robots create for new experimental approaches have far-reaching consequences for research in fields such as mate choice, cooperation, social learning, personality studies and collective behaviour.     

Adaptive noise

In biology, noise implies error and disorder and is therefore something which organisms may seek to minimize and mitigate against. We argue that such noise can be adaptive. Recent studies have shown that gene expression can be noisy, noise can be genetically controlled, genes and gene networks vary in how noisy they are and noise generates phenotypic differences among genetically identical cells. Such phenotypic differences can have fitness benefits, suggesting that evolution can shape noise and that noise may be adaptive. For example, gene networks can generate bistable states resulting in phenotypic diversity and switching among individual cells of a genotype, which may be a bet hedging strategy. Here, we review the sources of noise in gene expression, the extent to which noise in biological systems may be adaptive and suggest that applying evolutionary rigour to the study of noise is necessary to fully understand organismal phenotypes.     

The use of biomarkers in surveillance, medical screening, and intervention

Building on mechanistic information, much of molecular epidemiologic research has focused on validating biomarkers, that is, assessing their ability to accurately indicate exposure, effect, disease, or susceptibility. To be of use in surveillance, medical screening, or interventions, biomarkers must already be validated so that they can be used as outcomes or indicators that can serve a particular function. In surveillance, biomarkers can be used as indicators of hazard, exposure, disease, and population risk. However, to obtain rates for these measures, the population at risk will need to be assessed. In medical screening, biomarkers can serve as early indicators of disease in asymptomatic people. This allows for the identification of those who should receive diagnostic confirmation and early treatment. In intervention (which includes risk assessment and communication, risk management, and various prevention efforts), biomarkers can be used to assess the effectiveness of a prevention or control strategy as well as help determine whether the appropriate individuals are assigned to the correct intervention category. Biomarkers can be used to provide group and individual risk assessments that can be the basis for marshalling resources. Critical for using biomarkers in surveillance, medical screening, and intervention is the justification that the biomarkers can provide information not otherwise accessible by a less expensive and easier-to-obtain source of information, such as medical records, surveys, or vital statistics. The ability to use validated biomarkers in surveillance, medical screening, and intervention will depend on the extent to which a strategy for evidence-based procedures for biomarker knowledge transfer can be developed and implemented. This will require the interaction of researchers and decision-makers to collaborate on public health and medical issues.     

基于血流多普勒原理的血压测量系统设计

血流信号的采集可基于超声多普勒技术。利用多普勒超声探头在肢体主动脉脉搏处采集到血流多普勒频移信号,对信号电压进行放大,一方面直接输入扬声器转变为音频信号,得到多普勒音;同时用频率/电压变换器LM331变换多普勒频移信号,得到脉搏波信号。基于此原理,设计了使用无创、直观的方法获得肢体血流参数,并经PC机处理,最终在显示器上显示脉搏波形和血压数值的方法。     

Marine yeasts as biocontrol agents and producers of bio-products

As some species of marine yeasts can colonize intestine of marine animals, they can be used as probiotics. It has been reported that β-glucans from marine yeast cells can be utilized as immuno-stimulants in marine animals. Some siderophores or killer toxins produced by marine yeasts have ability to inhibit growth of pathogenic bacteria or kill pathogenic yeasts in marine animals. The virulent factors from marine pathogens can be genetically displayed on marine yeast cells, and the yeast cells displaying the virulent factors can stimulate marine animals to produce specific antibody against the pathogens. Some marine yeast cells are rich in proteins and essential amino acids and can be used in nutrition for marine animals. The marine yeast cells rich in lipid can be used for biodiesel production. Recently, it has been reported that some strains of Yarrowia lipolytica isolated from marine environments can produce nanoparticles. Because many marine yeasts can remove organic pollutants and heavy metals, they can be applied to remediation of marine environments. It has been shown that the enzymes produced by some marine yeasts have many unique properties and many potential applications.     

A fast and sensitive method for detecting specific viral RNA in mammalian cells.

A quick and sensitive method to quantitate viral RNA synthesis has been developed. Utilizing glutaraldehyde to fix infected cells onto nitrocellulose paper, viral RNA can be probed directly in situ. Viral message can be detected from as few as 10(4) infected cells. This technique can be used to study viral gene expression and can be adapted to screen the activity of antiviral agents such as interferon.     

Digging and marble burying in mice: simple methods for in vivo identification of biological impacts

Mice exhibit various species-typical behaviors such as digging and burrowing. They dig in the ground to find food, to hoard food, to create a refuge from predators or cold and to make a safe nursery area for the young. In the laboratory, mice dig vigorously in deep bedding such as wood chips. This behavior is sensitive to strain differences and drugs. For example, the effects of anxiolytics and 5-HT-active compounds, including those used clinically for obsessive-compulsive disorder (OCD), can be detected. Digging can be quantified by manual timing. Alternatively, the bedding can be covered with glass marbles and the number buried can be counted after a set time. These behaviors can be assessed using very little specialized equipment, and results can be obtained from ten animals in about an hour. Species-typical behaviors may be sensitive to a wide variety of treatments, and their simplicity and ability to yield robust quantitative data might be particularly useful in assessing genetically modified mice, even in laboratories not primarily oriented to behavioral work.     

植被监测及趋势分析——植被数量生态学中几个理论问题的探讨

 系统监测可以对危机发出预警, 是防治灾害的重要手段。生态监测的基础是植被监测。多物种 多样本 多年的植被定位监测数据隐含 着植被变化的信息。该文探索描述植被的数学工具, 提出植被监测数据的趋势分析方法。植被是资源竞争系统, 可以用多维空间的向量来表示 。在向量空间(射影空间), 不是“距离” , 而是“方向”决定区别; 在植被科学, 不是“产量”, 而是“组成”决定区别。新方法用多维空间 的位置向量来表示植被: 向量的方向表示植被的组成、两向量夹角余弦值表示相似、向量长度表示植被总体。在简缩数据时, 用“中心化”滤 去样本噪音、“标准化”滤去系统噪音, 得到状态向量。在趋势分析时, 定义后、前状态向量的比值为变化趋势; 用当年的状态和趋势的乘积 来预报次年的状态。到次年, 再用实测数据修正、更新来自去年的预报, 是为“卡尔曼滤波”。卡尔曼滤波能降低监测成本, 有效地使用历史 数据, 提高分析精度。     

Methods to probe protein transitions with ATR infrared spectroscopy

We describe techniques that can be used in conjunction with modern attenuated total reflection (ATR) infrared micro-prisms to allow proteins to be manipulated cyclically between different states whilst simultaneously monitoring both mid-IR and UV/visible/near IR changes. These methods provide increased flexibility of the types of changes that can be induced in proteins in comparison to transmission methods. Quantitative measurements can be made of vibrational changes associated with conversion between stable catalytic reaction intermediates, ligand binding and oxidation-reduction. Both hydrophobic and soluble proteins can be analysed and the ability to induce transitions repetitively allows IR difference spectra to be acquired at a signal/noise sufficient to resolve changes due to specific cofactors or amino acids. Such spectra can often be interpreted at the atomic level by standard IR methods of comparisons with model compounds, by isotope and mutation effects and, increasingly, by ab initio simulations. Combination of such analyses with atomic 3D structural models derived from X-ray and NMR studies can lead to a deeper understanding of molecular mechanisms of enzymatic reactions.     

Shave excision of superficial solar skin lesions

Shave excision is a useful technique for the treatment of superficial solar lesions. The most common of these is the solar keratosis, which can be a red or gray scaling lesion. This can at times be difficult to differentiate from the superficial basal cell carcinoma or squamous cell carcinoma or their more infiltrating types. Shave excision gives the advantage of a histopathologic report. Lesions found to be infiltrating or in danger of recurrence can then be further excised. The cosmetic appearance of the healed shave excision site is generally quite good, although it can be paler than the surrounding skin. If this is likely to be a problem, the shave graft can be applied, as with deeper shave excisions. A thin shave graft also can be used to repigment pale scarred areas. A series of 1313 shave excised lesions is analyzed.     

Industrial strain improvement: Mutagenesis and random screening procedures

Industrial strain improvement plays a central role in the commercial development of microbial fermentation processes. In recent years new procedures such as rational screening and genetic engineering have begun to make a significant contribution to this activity but mutagenesis and selection - so-called ‘random screening’ - is still a cost-effective procedure, and for reliable short-term strain development is frequently the method of choice. The current practice of strain improvement by mutagenesis and selection is a highly developed technique drawing on the latest advances from a wide range of scientific and technical disciplines. Mutagenic procedures can be optimized in terms of type of mutagen and dose, mutagen specificity effects can be taken into account and mutagenesis itself can be enhanced or directed in order to obtain the maximum frequency of desirable mutant types among the isolates to be screened. Screens can be designed to allow maximum expression of the desirable mutant types and the application of statistically-based screening procedures will maximize the probability of detecting them. Automated procedures can be developed using robotics and microprocessors to increase the numbers of isolates that can be processed through a screen per unit time. The relationship between screening and production conditions can be organized so as to minimize the probability of improved isolates selected by the screen failing to scale up.     

Scale for resource selection functions

Resource selection functions (RSFs) are statistical models defined to be proportional to the probability of use of a resource unit. My objective with this review is to identify how RSFs can be used to unravel the influence of scale in habitat selection. In wildlife habitat studies, including radiotelemetry, RSFs can be estimated using a variety of statistical methods, all of which can be used to explore the role of scale. All RSFs are bounded by the resolution of data and the spatial extent of the study area, but also allow predictor covariates to be measured at a variety of scales. Conditional logistic regression permits designs (e.g. matched case) that relate the process of habitat selection to a limited domain of resource units that might better characterize what is truly ‘available’ to the animal. Scale influences the process of habitat selection, e.g. food resources are often selected at fine spatial scales, whereas landscape patterns at much larger scales typically influence the location of home ranges. Scale also influences appropriate sampling in many ways: (1) heterogeneity might be obliterated (transmutation) if resolution or grain size is too large, (2) variance of habitat characteristics might be undersampled if extent or domain is too small, (3) timing and duration of observations can influence RSF models, and (d) both spatial and temporal autocorrelations can vary directly with the intensity of sampling. Using RSFs, researchers can examine habitat selection at multiple scales, and predictive models that bridge scales can be estimated. Using Geographical Information Systems, predictor covariates in RSF models can be measured at different scales easily so that the predictive ability of models at alternative spatial and temporal domains can be explored by the investigator. Identification of the scale that best explains the data can be evaluated by comparing alternative models using information‐theoretic metrics such as Akaike Information Criteria, and predictive capability of the models can be assessed using k‐fold cross validation.