A review of the use of allozyme electrophoresis in plant systematics

The role of electrophoretic data is discussed as it applies to plant taxonomy and systematic studies. Nei's (Am. Nat. 106 (1972) 283-292; Genetics 89 (1978) 583-590) genetic distances calculated for a large number of populations, species and genera were taken from published data. The relation between Nei's genetic identity measures and taxonomic rank (populations, species and genera) are shown graphically. The graphs obtained in this way (from 3021 pairs of plant taxa) differ substantially from previous graphs published by Thorpe (Ann. Rev. Ecol. Syst. 13 (1982) 139-168; in: G.S. Oxford, D. Rollinson (Eds.), Protein Polymorphism: Adaptive and Taxonomic Significance, Academic Press, London, 1983, pp. 131-152) and Thorpe and Solé-Cava (Zool. Scripta 23 (1994) 3-18). These authors suggested that the divergence between the different taxonomic ranks is roughly similar across a wide range of taxa. The latter was based on values for 2664 (Thorpe, 1982) and 8060 (Thorpe, 1983) pairs of animal and plant taxa, but the plant data contributed little to the total. For any given taxonomic rank, we found that plants are genetically more closely related than animals (possibly with the exception of birds). This result is important because the empirical relationships of genetic distance measures, to different levels of taxonomic separation, is often used for distinguishing and identifying cryptic or sibling species where conventional methods are unable to resolve systematic problems.     

Enzyme variation and taxonomy: the estimation of sampling errors in measurements of interspecific genetic similarity

The uses of biochemical genetics as an aid to taxonomy are discussed briefly. A survey is made of published data to establish expected levels of genetic similarity or identity between conspecific populations, between congeneric species and between species of different genera. Existing measures of genetic similarity, identity or distance are discussed and some of the difficulties involved in their use in taxonomy are outlined. A new measure of genetic similarity is proposed specifically designed for use in making interspecific comparisons for taxonomic purposes. This measure offers considerable advantages in ease of calculation and also greatly simplifies the estimation of sampling errors. An empirical comparison is made, using published data, of the measures and confidence limits obtained by the proposed memod against published measures of genetic variation between species.     

Traditional morphometrics in plant systematics and its role in palm systematics

A review is given of the role of traditional morphometrics in plant systematics. The three most commonly used techniques of data analysis – Cluster Analysis, Principal Component Analysis and Discriminant Analysis – are discussed. The kinds of data that can be taken from palm specimens and the problems of using specimens as data sources are outlined. Published systematic studies of palms using traditional morphometrics are reviewed. More recent studies indicate that: hybrid zones between species may be common; infraspecific diversity is greater than previously suspected; there may be more than double the currently accepted number of species; and our current knowledge of morphological variation in palms is superficial. A procedure for scientific systematics is given, which incorporates traditional morphometric methods.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 103–111.     

Molecular genetic mapping and plant evolutionary biology

With the advent of molecular genetic mapping, it is possible to study the genetic basis of natural heritable variation in new ways. Here, three potential uses of molecular genetic mapping in plant ecology and evolutionary biology are discussed; (1) accurate estimation of genetic parameters, (2) understanding speciation and/or adaptation, and (3) investigating whole genome organization. Basic methods for mapping genes and important mapping strategies are outlined. Recent studies are introduced to illustrate progress so far in applying the new methods in ecological and evolutionary research.     

Molecular genetics of ovarian cancer

This is a review of the approaches that can be used to analyze genetic changes in ovarian cancer. Traditional gene localization methods are discussed, followed by a section on gene identification techniques. Once a putative disease-associated gene has been cloned, mutations have to be identified and analyzed. There are numerous mutation detection methods, and the most common ones are outlined. In the penultimate section, the role of immunohistochemistry as a surrogate method for mutation analysis is considered. Finally, the possible use of functional assays is discussed. At present, it would appear that DNA chip technology for the detection of mutations, and microarray analysis of gene expression, are two important techniques likely to have a significant impact on the genetic analysis of ovarian cancer.     

A survey of multiple sequence comparison methods

Multiple sequence comparison refers to the search for similarity in three or more sequences. This article presents a survey of the exhaustive (optimal) and heuristic (possibly sub-optimal) methods developed for the comparison of multiple macromolecular sequences. Emphasis is given to the different approaches of the heuristic methods. Four distance measures derived from information engineering and genetic studies are introduced for the comparison between two alignments of sequences. The use ofentropy, which plays a central role in information theory as measures of information, choice and uncertainty, is proposed as a simple measure for the evaluation of the optimality of an alignment in the absence of anya priori knowledge about the structures of the sequences being compared. This article also gives two examples of comparison between alternative alignments of the same set of 5SRNAs as obtained by several different heuristic methods.     

Quantitative genetic tools for insecticide resistance risk assessment: estimating the heritability of resistance

Quantitative genetic studies of resistance can provide estimates of genetic parameters not available with other types of genetic analyses. Three methods are discussed for estimating the amount of additive genetic variation in resistance to individual insecticides and subsequent estimation of the heritability (h2) of resistance. Sibling analysis and offspring-parent regression permit direct estimates of h2 by comparing the resistance phenotypes of individuals of known relatedness. Threshold trait analyses, performed on data from selection experiments, provide estimates of realized heritability. Procedures are outlined for predicting changes in resistance to insecticides based on h2 estimates. Quantitative genetic theory is examined as it relates to resistance and resistance as a quantitative trait; quantitative genetic methods also are unique in providing estimates of genetic correlations between traits. Comments are included on estimates of genetic correlation between resistance and phenotypic traits (e.g., development time) and how they may be used to predict changes in the genetic aspects of phenology that result from insecticide applications (i.e., to predict how the reproductive capacity of future generations will differ from that of the treated generation).     

DNA polymorphism in population genetics

In the review, the literature evidence on DNA polymorphism obtained in the last 10-15 years using various molecular-genetic methods is summarized. All main types of DNA variation are considered but attention is focused on those extensively used in population genetics. The areas of using DNA markers are outlined and the limitations of their potential in analyzing genetic processes in populations are discussed. Particular emphasis is placed on the relationship between the earlier developed biochemical genetics based on protein polymorphism analysis and modern molecular population genetics based on DNA polymorphism. The possible role of selection in maintaining DNA variation is considered.     

Genetic susceptibility to chronic periodontal disease

Evidence suggests that there is a significant genetic component to susceptibility and resistance to chronic periodontal disease. Data from both clinical studies and studies using animal models are reviewed here. Also outlined are the genomic methods that are now available for identifying susceptibility and resistance loci.     

Genetic association studies: design,analysis and interpretation

This paper provides a review of the design and analysis of genetic association studies. In case control studies, the different contingency tables and their relationships to the underlying genetic model are defined. Population stratification is discussed, with suggested methods to identify and correct for the effect. The transmission disequilibrium test is provided as an alternative family-based test, which is robust to population stratification. The relative benefits of each analysis are summarised.     

Variability of perceptual multistability: from brain state to individual trait

Few phenomena are as suitable as perceptual multistability to demonstrate that the brain constructively interprets sensory input. Several studies have outlined the neural circuitry involved in generating perceptual inference but only more recently has the individual variability of this inferential process been appreciated. Studies of the interaction of evoked and ongoing neural activity show that inference itself is not merely a stimulus-triggered process but is related to the context of the current brain state into which the processing of external stimulation is embedded. As brain states fluctuate, so does perception of a given sensory input. In multistability, perceptual fluctuation rates are consistent for a given individual but vary considerably between individuals. There has been some evidence for a genetic basis for these individual differences and recent morphometric studies of parietal lobe regions have identified neuroanatomical substrates for individual variability in spontaneous switching behaviour. Moreover, disrupting the function of these latter regions by transcranial magnetic stimulation yields systematic interference effects on switching behaviour, further arguing for a causal role of these regions in perceptual inference. Together, these studies have advanced our understanding of the biological mechanisms by which the brain constructs the contents of consciousness from sensory input.     

Recent advances in analysis of Chinese medical plants and traditional medicines

Chinese herbal medicine is gaining increasing popularity worldwide for health promotion and adjuvant therapy. Thus, selective and efficient analytical methods are required not only for quality assurance but also for authentication of the plant material. Applications of both chromatographic and electrophoretic techniques to the analysis of medicinal plants and Chinese traditional medicine preparations over the last 3 years are outlined in this review. The role of chemical fingerprinting is highlighted and a brief survey of determination of toxic components, natural and synthetic adulterants is also included. Moreover, different sample pretreatment and extraction methods are discussed.     

Molecular-genetic markers in lung cancer diagnostics

The major approaches to different lung cancer marker development are outlined in the review, including genetic, epigenetic, protein, transcryptomic, proteomic, metabolic, and miRNA markers. As far as epigenetic changes are among the earliest events in malignant transformation, methylated markers are thoroughly discussed. Special attention is given to minimally invasive tumor markers, which could be detected in easily accessible biological fluids, because they can be useful for screening and early diagnostics of cancer (before its clinical manifestation) as well as for verification of standard methods of diagnostics. Extracellular nucleic acids, circulating in blood (cirNA), are highlighted as the potential source of material for the early lung cancer diagnostics, prediction of antitumor treatment efficiency, post-treatment monitoring and disease prognosis.     

青藏高寒区退化草地生态恢复:退化现状、恢复措施、效应与展望

青藏高寒区属于独特而典型的高原生态系统,草地生态系统作为其重要组成部分,在对高寒区生态安全以及农牧民生计的维系中,占有举足轻重的地位。目前,青藏高寒区的草地生态系统退化严重,因此该区退化草地的生态恢复工作是国家生态工作的重中之重。近年来,已有大量研究提出了各种有效的恢复手段,但缺乏因地制宜的系统性总结和论述。基于此,在已有研究的基础上,阐述了青藏高寒区退化草地现状,总结了高寒区各生态类型分区的主要生态问题,明确了不同集成技术与模式的适用区域和范围,同时对这些技术、措施和模式的恢复效果和恢复机制进行分析和讨论。并对未来高寒草地生态系统的研究进行了展望,以期为青藏高寒区退化草地的恢复治理、高寒草地生态系统结构和功能稳定性维系提供系统的理论基础与技术支撑。     

Genetic dissection of diseases: design and methods

The etiology of heritable diseases may be elucidated by localizing genes conferring susceptibility and by subsequent biological characterization of these genes. To localize genetic components for multifactorial traits, both hypothesis-driven candidate gene and hypothesis-free genome scan approaches have been applied. To date, only a handful of results have been reproduced in either a different cohort or model organisms. The integration of genetic approaches with high-throughput genomic techniques is very promising. Unfortunately, most genetic studies completely ignore strong nongenetic effects such as low education and poverty even though these factors are well-known to predict, for example, obesity. Thus, what are most needed in future research are statistical methods for discovering sets of susceptibility genes and environmental factors, as well as systematic verifications of the gene-environment-disease network.     

DNA Polymorphism in Population Genetics

In the review, the literature evidence on DNA polymorphism obtained in the last 10–15 years using various molecular-genetic methods is summarized. All main types of DNA variation are considered but attention is focused on those extensively used in population genetics. The areas of using DNA markers are outlined and the limitations of their potential in analyzing genetic processes in populations are discussed. Particular emphasis is placed on the relationship between the earlier developed biochemical genetics based on protein polymorphism analysis and modern molecular population genetics based on DNA polymorphism. The possible role of selection in maintaining DNA variation is considered.     

Joint Estimation of Diagnostic Accuracy Measures for Paired Organs – Application in Ophthalmology

Diagnostic studies in ophthalmology frequently involve binocular data where pairs of eyes are evaluated, through some diagnostic procedure, for the presence of certain diseases or pathologies. The simplest approach of estimating measures of diagnostic accuracy, such as sensitivity and specificity, treats eyes as independent, consequently yielding incorrect estimates, especially of the standard errors. Approaches that account for the inter‐eye correlation include regression methods using generalized estimating equations and likelihood techniques based on various correlated binomial models. The paper proposes a simple alternative statistical methodology of jointly estimating measures of diagnostic accuracy for binocular tests based on a flexible model for correlated binary data. Moments' estimation of model parameters is outlined and asymptotic inference is discussed. The resulting estimates are straightforward and easy to obtain, requiring no special statistical software but only elementary calculations. Results of simulations indicate that large‐sample and bootstrap confidence intervals based on the estimates have relatively good coverage properties when the model is correctly specified. The computation of the estimates and their standard errors are illustrated with data from a study on diabetic retinopathy.     

Genetic differentiation among populations of marine algae

Most of the information for genetic differentiation among populations of marine algae is from studies on ecotypic variation. Physiological ecotypes have been described for individuals showing different responses to temperature and salinity conditions. Morphological ecotypes have also been found associated with areas differing in wave exposure or different intertidal positions. Little is known on how genetic variation is organized within and between populations of marine algae. The occurrence of ecotypic variation in some species is evidence for genetic differentiation among populations resulting from selection by the local environment. The rate of dispersal and subsequent gene flow will also affect the level of differentiation among populations. In species with low dispersal, differentiation can arise through chance founder events or random genetic drift. The few studies available have shown that species of algae exhibit a range of dispersal capabilities. This information can be useful for predicting the potential level of genetic differentiation among populations of these species. Crossing experiments with several species of algae have shown that populations separated by a considerable distance can be interfertile. In some cases individuals from these populations have been found to be morphologically distinct. Crosses have been used to study the genetic basis of this variation and are evidence for genetic differentiation among the populations sampled. Genetic variation of enzyme proteins detected by electrophoresis provides an additional method for measuring genetic variation within and between populations of marine algae. Electrophoretic methods have previously been used to study systematic problems in algae. However, there have been few attempts to use electrophoretic variation to study the genetic structure of populations of marine algae. This approach is outlined and includes some of the potential problems associated with interpreting electrophoretic data. Studies of electrophoretic variation in natural populations ofEnteromorpha linza from Long island Sound are used as an example. This species was found to reproduce only asexually. Despite a dispersing spore stage, genetic differentiation was found on a microgeographic scale and was correlated with differences in the local environment of some of the populations. Similar studies on other species, and especially sexually reproducing species, will add to a growing understanding of the evolutionary genetics of marine algae.Paper presented at the Seaweed Biogeography Workshop of the International Working Group on Seaweed Biogeography, held from 3–7 April 1984 at the Department of Marine Biology, Rijksuniversiteit Groningen (The Netherlands). Convenor: C. van den Hoek.     

分子标记在食（药）用真菌遗传多样性研究中的应用

食（药）用真菌在经济和生态方面都具有重要意义,其遗传多样性研究是资源可持续利用和生物保护学研究的基础,有利于食（药）用真菌种质资源的收集、保存、评价和利用,也有助于其分类学、系统学及进化等的研究。遗传多样性的研究方法很多,分子标记是目前最常用最有效的方法之一。综合分析了分子标记在食（药）用真菌遗传多样性研究中的应用,比较了各种标记的应用范围、优缺点,探讨了分子标记用于食（药）用真菌遗传多样性评价的前景及问题。     

Changing measurement instrument at follow-up a potential source of error

The purpose of this investigation was to determine whether headache activity information collected over the phone can be directly compared with headache activity information collected by systematic self-observation without jeopardizing internal validity because of calibration differences between the two measurement methods. A number of headache studies have relied on phone information for long-term follow-up data, while using systematic self-observation to collect all other data. Twenty-six headache sufferers participating in a tension headache study reported their headache activity over the phone and subsequently charted their headaches. Correlations were computed between the two measures. Results indicated that differences exist in the calibration of the two measurement methods. This seriously limits the conclusions of studies that used phone information to obtain follow-up data. Other recommendations concerning follow-up methodologies are discussed.