DNA extraction techniques for DNA barcoding of minute gall-inhabiting wasps

DNA extraction from minute hymenopterans and their larvae is difficult and challenging because of their small size indicating a low amount of starting material. Hence, 11 DNA extraction methods were compared to determine their efficacy in isolating DNA. Success of each method was scored on a 2% agarose gel after PCR of the cox 1 mitochondrial locus. A silica-membrane-based approach was the most successful, followed by a method using a combination of incubation buffers and a method using magnetic beads. The method using buffers was the most cost- and time effective. Using this method, larvae from Eucalyptus seed capsule galls could be assigned a role (parasitoid, gall former or inquiline) in the gall-inhabiting complex.     

Parsimony-based test for identifying changes in evolutionary trends for quantitative characters: implications for the origin of the amniotic egg

The origin of the amniotic egg was a major event in vertebrate evolution and is thought to have contributed to the spectacular evolutionary radiation of amniotes. We test one of the most popular scenarios proposed by Carroll in 1970 to explain the origin of the amniotic egg using a novel method based on an asymmetric version of linear parsimony (aka Wagner parsimony) for identifying the most parsimonious split of a tree into two parts between which the evolution of the character is allowed to differ. The new method evaluates the cost of splitting a phylogenetic tree at a given node as the integral, over all pairs of asymmetry parameters, of the most parsimonious costs that can be achieved by using the first parameter on the subtree pending from this node and the second parameter elsewhere. By testing all the nodes, we then obtain the most parsimonious split of a tree with regard to the character values at its tips. Among the nine trees and two characters tested, our method yields a total of 517 parsimonious trend changes in Permo-Carboniferous stegocephalians, a single one of which occurs in a part of the tree (among stem-amniotes) where Carroll's scenario predicts that there should have been distinct changes in body size evolutionary trends. This refutes the scenario because the amniote stem does not appear to have elevated rates of evolutionary trend shifts. Our nodal body size estimates offer less discriminating power, but they likewise fail to find strong support for Carroll's scenario.     

Sampling techniques for thrips (Thysanoptera: Thripidae) in preflowering tomato

Sampling techniques for thrips (Thysanoptera: Thripidae) were compared in preflowering tomato plants at the Coastal Plain Experiment Station in Tifton, GA, in 2000 and 2003, to determine the most effective method of determining abundance of thrips on tomato foliage early in the growing season. Three relative sampling techniques, including a standard insect aspirator, a 946-ml beat cup, and an insect vacuum device, were compared for accuracy to an absolute method and to themselves for precision and efficiency of sampling thrips. Thrips counts of all relative sampling methods were highly correlated (R > 0.92) to the absolute method. The aspirator method was the most accurate compared with the absolute sample according to regression analysis in 2000. In 2003, all sampling methods were considered accurate according to Dunnett's test, but thrips numbers were lower and sample variation was greater than in 2000. In 2000, the beat cup method had the lowest relative variation (RV) or best precision, at 1 and 8 d after transplant (DAT). Only the beat cup method had RV values <25 for all sampling dates. In 2003, the beat cup method had the lowest RV value at 15 and 21 DAT. The beat cup method also was the most efficient method for all sample dates in both years. Frankliniella fusca (Pergande) was the most abundant thrips species on the foliage of preflowering tomato in both years of study at this location. Overall, the best thrips sampling technique tested was the beat cup method in terms of precision and sampling efficiency.     

A systematic approach for prioritizing multiple management actions for invasive species

The successful management and eradication of invasive species is often constrained by insufficient or inconsistent funding. Consequently, managers are usually forced to select a subset of infested areas to manage. Further, managers may be unaware of the most effective methods for identifying priority areas and so are unable to maximize the effectiveness of their limited resources. To address these issues, we present a spatially explicit decision method that can be used to identify actions to manage invasive species while minimizing costs and the likelihood of reinvasion. We apply the method to a real-world management scenario, aimed at managing an invasive aquatic macrophyte, olive hymenachne (Hymenachne amplexicaulis), which is one of the most threatening invasives in tropical Australia, affecting water quality, freshwater biodiversity, and fisheries.     

cDNA文库固相构建法

本文介绍一种cDNA文库的固相构建法。文库构建过程cDNA的合成和修饰全部在固相介质—磁珠上完成,简便、迅速、文库质量高,能满足不同目的的cDNA文库构建,是一种值得借鉴和应用的好方法。     

多元统计分析方法在链霉素发酵中的应用

将多元统计方法中的最重要的方法之一主元分析法用于实际工业链霉素发酵数据的分析,该方法能有效地将原来较多的相关变量所包含的大部分信息用少数不相关的变量来反映,从而简化链霉素发酵中的控制变量。建立规则基模式识别系统,将链霉素发酵过程分三个时期。利用多元回归方法,将链霉素发酵分三段进行产物浓度预测,取得了较好效果。     

A method for enumerating protozoa in a variety of freshwater habitats

A method for enumerating protozoa (ciliates, flagellates, and amoebae) in fine, freshwater sediments is described. The results, using fixed material, are compared with two published techniques: a culture method (most probable number) and a direct count method.     

Techniques for the rapid preparation of permanent slides of microscopic algae

Because most techniques for the preparation of permanent mounts of algae have hitherto involved long alcoholic dehydration series, which frequently result in cell collapse if cut short, a method has been developed which is anhydrous from the start and avoids these series. It can be used to produce rapidly, permanent, generally-stained mounts of most microscopic algae in which the degree of shrinkage of the cell or its contents is reduced to a minimum.

A method for the cleaning and mounting of diatoms is also given.     

A Comparative Survey of Automated Parameter-Search Methods for Compartmental Neural Models

One of the most difficult and time-consuming aspects of building compartmental models of single neurons is assigning values to free parameters to make models match experimental data. Automated parameter-search methods potentially represent a more rapid and less labor-intensive alternative to choosing parameters manually. Here we compare the performance of four different parameter-search methods on several single-neuron models. The methods compared are conjugate-gradient descent, genetic algorithms, simulated annealing, and stochastic search. Each method has been tested on five different neuronal models ranging from simple models with between 3 and 15 parameters to a realistic pyramidal cell model with 23 parameters. The results demonstrate that genetic algorithms and simulated annealing are generally the most effective methods. Simulated annealing was overwhelmingly the most effective method for simple models with small numbers of parameters, but the genetic algorithm method was equally effective for more complex models with larger numbers of parameters. The discussion considers possible explanations for these results and makes several specific recommendations for the use of parameter searches on neuronal models.     

Analysis on the reconstruction accuracy of the Fitch method for inferring ancestral states

Background  

As one of the most widely used parsimony methods for ancestral reconstruction, the Fitch method minimizes the total number of hypothetical substitutions along all branches of a tree to explain the evolution of a character. Due to the extensive usage of this method, it has become a scientific endeavor in recent years to study the reconstruction accuracies of the Fitch method. However, most studies are restricted to 2-state evolutionary models and a study for higher-state models is needed since DNA sequences take the format of 4-state series and protein sequences even have 20 states.     

Bio-support vector machines for computational proteomics

MOTIVATION: One of the most important issues in computational proteomics is to produce a prediction model for the classification or annotation of biological function of novel protein sequences. In order to improve the prediction accuracy, much attention has been paid to the improvement of the performance of the algorithms used, few is for solving the fundamental issue, namely, amino acid encoding as most existing pattern recognition algorithms are unable to recognize amino acids in protein sequences. Importantly, the most commonly used amino acid encoding method has the flaw that leads to large computational cost and recognition bias. RESULTS: By replacing kernel functions of support vector machines (SVMs) with amino acid similarity measurement matrices, we have modified SVMs, a new type of pattern recognition algorithm for analysing protein sequences, particularly for proteolytic cleavage site prediction. We refer to the modified SVMs as bio-support vector machine. When applied to the prediction of HIV protease cleavage sites, the new method has shown a remarkable advantage in reducing the model complexity and enhancing the model robustness.     

Molecular dynamics method for proteins with ionization-conformation coupling and equilibrium titration

A new realization of the constant pH molecular dynamics simulation is proposed in mean force potential of proton reservoir in constant titration conditions. The MD-pH-ET method is used for a protein in the most probable ionization microstate, which is the state with minimal energy of the current conformation taking into account the correcting ionization potential of mean force considering an equilibrium ensemble of ionization states. The new MD-pH-ET method allows one to carry out an optimization of protein structure and the total free energy of a protein in the aqueous solution at constant pH and to calculate the pH-dependent properties. The MD-pH-ET method possesses the following unique features: (1) it uses the most precise and computationally effective realization of calculation of electrostatic energy of a protein in aqueous solution, the model of continuous dielectric media with Poisson equation, and the generalized Born method with “ideal” Born atomic radii; (2) it uses the same model of the potential energy surface in the ionization-conformation phase space both for calculating the potential energy of the protein and atomic forces and for determining the most probable ionization states; (3) it calculates the total free energy of the protein in the aqueous solution in a proton reservoir under the conditions of equilibrium titration. The workability of the new method MD-pH-ET is demonstrated for a molecule of the BPTI protein.     

Evaluation of sampling methods and development of sample plans for estimating predator densities in cotton

The cost-reliability of five sampling methods (visual search, drop cloth, beat bucket, shake bucket, and sweep net) was determined for four groups of predatory arthropods on cotton plants in Texas. The beat bucket sample method was the most cost-reliable sampling method for Orius adults, and the beat bucket and drop cloth were the most cost-reliable methods for Orius nymphs. The drop cloth and beat bucket were the most cost-reliable methods for sampling spiders. For sampling adult Coccinellidae, the sweep net and the beat bucket were the most cost-reliable. The visual sample method was the least cost-reliable method for Orius adults and nymphs and spiders. No one sampling method was identified as the optimum method for all four predator groups. However, the relative cost-reliability of the beat bucket method ranked first or second among the five sampling methods and this method was chosen for further evaluation in field studies in Texas and Arizona. The relative cost-reliability of 1-, 3-, 5-, and 10-plants per beat bucket sample varied with predator group, but multiple plant sample units were equal to or more cost-reliable than the one plant sample unit. Fixed sample plans for the beat bucket method were developed for Orius adults, Orius nymphs, spiders, and adult Coccinellidae, and the sum of these groups using the 3-, 5-, and 10-plant sample unit sizes. The greater cost-reliability of the beat bucket sampling method and its ease of use is of particular advantage in assessing predator densities in a commercial cotton field monitoring program.     

一种改进的cDNA文库固相构建法

本文介绍一种新的cDNA文库固相构建法。文库构建过程中,cDNA的合成和修饰全部在固相介质――磁珠上完成,简便、迅速、文库质量高,能满足不同目的的cDNA文库构建,是一种值得借鉴和应用的好方法。 Abstract：A method for cDNA library construction was introduced.All enzymatic steps of library synthesis were performed on a solid support-magnetic beads.Therefore it combines fast speed and convenient with high quality library,making it ideally suited for most purposes.It is a good method and worth learning and utilization.     

一种改进的沙蒿总RNA的提取方法

介绍了一种适用于沙蒿总RNA提取的方法。此方法有效地克服了沙蒿中富含的多糖类物质———沙蒿胶对总RNA提取的干扰。运用此方法所提取的RNA纯度高 ,完整性较好 ,可满足多数分子生物学实验的需要。     

Random local neighbor joining: a new method for reconstructing phylogenetic trees

We have developed a new method for reconstructing phylogenetic trees called random local neighbor-joining (RLNJ). Our method is different from the neighbor-joining method (NJ) of Saitou and Nei and affords a more thorough sampling of solution space by randomly searching for local pair of neighbors in each step. Results using the RLNJ method to analyze yeast data show an increasing possibility to get a smaller S value (sum of branch lengths) compared with the NJ method as cases with more taxa are analyzed and many individual runs using the RLNJ method usually generate more than one topology with small S values. Computer simulation shows the fact that the RLNJ method can improve the possibility of recovering correct topology significantly by affording more than one topology. In addition, when using the RLNJ method, computer simulation also shows that the proportion of correct topologies (P(C)) will increase as the number of different topologies decreases and as the proportion of "most frequent topology" increases. Thus, the number of different topologies and the proportion of "most frequent topology" can be used as auxiliary criteria to evaluate reliability of a phylogenetic tree.     

The use of benthic macroinvertebrate families for river quality assessment in Lithuania

The aim of this study was to evaluate the influence of environmental factors on the distribution of macroinvertebrate taxa in different sized lowland Lithuanian rivers. A secondary aim was to assess ecological river quality and to determine the most suitable biotic index. A final aim was to determine the most appropriate macroinvertebrate families for river quality assessment in Lithuania. Species composition and quantitative characteristics of benthic macroinvertebrate communities have been investigated using standard kick-sampling method by a standard hand net in 24 different river sites in spring. Physical and chemical environmental parameters were measured in the same study site as the macroinvertebrate sampling. A total of 186 taxa representing 66 families or higher taxonomic ranks of benthic macroinvertebrates have been identified. Water temperature and current velocity influenced the highest number of ivestigated families. Seven of the most tolerant and eleven of the most sensitive macroinvertebrate taxa for hydrochemical parameters related with organic pollution were determined. The DSFI method was founded to be the best index for assessment of ecological status for Lithuanian rivers until more accurate estimation method will be created.     

Aid for aggregating the impacts in Life Cycle assessment

Background and Objectives  Multiple Criteria Decision Aid (MCDA) methods may be employed in a great number of fields. Life Cycle Assessment (LCA) is a specific method among the MCDA Methods. A stage of MCDA methods to be respected in LCA is the comparative evaluation of the environmental impacts. This stage is the most difficult to implement because it is a question of estimating the global environmental impact of the life cycles studied. To achieve this purpose, it is necessary to model the environmental impacts and to apply a Multicriteria Analysis (MCA) method. The problem is to choose the most suitable among the available MCA methods. The objective of this paper is to help the LCA practitioner to make this choice. Methodology  The MCA methods are compared according to their non-compensatory degree, their sensitivity to thresholds, their practicability and their workability. Results and Conclusion  The protocol presented in this paper allows to choose the most appropriate MCA method for a given LCA according to the four previous criteria. This choice will depend on the priorities of the decision maker with concern to the comparison criteria.     

Phasing statistics for alpha helical membrane protein structures

In this report we highlight the latest trends in phasing methods used to solve alpha helical membrane protein structures and analyze the use of heavy atom metals for the purpose of experimental phasing. Our results reveal that molecular replacement is emerging as the most successful method for phasing alpha helical membrane proteins, with the notable exception of the transporter family, where experimentally derived phase information still remains the most effective method. To facilitate selection of heavy atoms salts for experimental phasing an analysis of these was undertaken and indicates that organic mercury salts are still the most successful heavy atoms reagents. Interestingly the use of seleno‐l ‐methionine incorporated protein has increased since earlier studies into membrane protein phasing, so too the use of SAD and MAD as techniques for phase determination. Taken together this study provides a brief snapshot of phasing methods for alpha helical membrane proteins and suggests possible routes for heavy atom selection and phasing methods based on currently available data.