紫貂和水貂被毛比较形态学研究

研究表明紫貂和水貂被毛的形态高度分化,可分为针毛,中间针毛和绒毛3类。针毛笔直,远端(大约3/4处)皮质高度发育,有良好的耐磨性。中间针毛比针毛短、细,大约有3个弯曲,且髓质含量最高。绒毛最短、细,大约有5个弯曲,髓质也较发达。 扫描电镜下的毛小皮形态可归纳为波纹形,披针形,菱形和倒三角形4种。光镜下的髓质形态可归纳为单柱组型,多柱组型和网型3种。比较分析的结果表明:毛小皮和髓质形态在这两种动物间的差别较明显,具有种的特异性、可作为哺乳动物分类的参考指标。     

Seeking causes: Classifying and evaluating congenital heart defects in etiologic studies

BACKGROUND: Classification and analysis of congenital heart defects (CHD) in etiologic studies is particularly challenging because of diversity of cardiac phenotypes and underlying developmental mechanisms. We describe an approach to classification for risk assessment of CHD based on developmental and epidemiologic considerations, and apply it to data from the National Birth Defect Prevention Study (NBDPS). METHODS: The classification system incorporated the three dimensions of cardiac phenotype, cardiac complexity, and extracardiac anomalies. The system was designed to facilitate the assessment of simple isolated defects and common associations. A team with cardiologic expertise applied the system to a large sample from the NBDPS. RESULTS: Of the 4,703 cases of CHDs in the NBDPS with birth years 1997 through 2002, 63.6% were simple, isolated cases. Specific associations of CHDs represented the majority of the remainder. The mapping strategy generated relatively large samples for most cardiac phenotypes and provided enough detail to isolate important subgroups of CHDs that may differ by etiology or mechanism. CONCLUSIONS: Classification of CHDs that considers cardiac and extracardiac phenotypes is practically feasible, and yields manageable groups of well-characterized phenotypes. Although best suited for large studies, this approach to classification and analysis can be a flexible and powerful tool in many types of etiologic studies of heart defects.     

Variations of scalp, pubic and axillary hair

Hair examinations and comparisons conducted by forensic scientists often provide investigative and associative information. Apart from its length and its natural color, hair displays a morphologic diversity both macroscopically and microscopically. Pseudogenization of 相似文献   

Legume diversity patterns in west central Africa: influence of species biology on distribution models

Objectives

Species Distribution Models (SDMs) are used to produce predictions of potential Leguminosae diversity in West Central Africa. Those predictions are evaluated subsequently using expert opinion. The established methodology of combining all SDMs is refined to assess species diversity within five defined vegetation types. Potential species diversity is thus predicted for each vegetation type respectively. The primary aim of the new methodology is to define, in more detail, areas of species richness for conservation planning.

Methodology

Using Maxent, SDMs based on a suite of 14 environmental predictors were generated for 185 West Central African Leguminosae species, each categorised according to one of five vegetation types: Afromontane, coastal, non-flooded forest, open formations, or riverine forest. The relative contribution of each environmental variable was compared between different vegetation types using a nonparametric Kruskal-Wallis analysis followed by a post-hoc Kruskal-Wallis Paired Comparison contrast. Legume species diversity patterns were explored initially using the typical method of stacking all SDMs. Subsequently, five different ensemble models were generated by partitioning SDMs according to vegetation category. Ecological modelers worked with legume specialists to improve data integrity and integrate expert opinion in the interpretation of individual species models and potential species richness predictions for different vegetation types.

Results/Conclusions

Of the 14 environmental predictors used, five showed no difference in their relative contribution to the different vegetation models. Of the nine discriminating variables, the majority were related to temperature variation. The set of variables that played a major role in the Afromontane species diversity model differed significantly from the sets of variables of greatest relative important in other vegetation categories. The traditional approach of stacking all SDMs indicated overall centers of diversity in the region but the maps indicating potential species richness by vegetation type offered more detailed information on which conservation efforts can be focused.     

Discrimination and consistency of five myosin ATPase stains in human normal and Duchenne dystrophic muscle

Limitations in the ability of the human visual system to assess accurately the relative staining densities of individual fibers in muscle tissue stained for myosin. ATPase can complicate the objective evaluation of fiber type populations. In this study a novel approach is employed which utilizes human visual capabilities to provide accurate fiber classification. Using this approach, the ability of five ATPase staining techniques to discriminate fiber type categories in single samples of human normal and Duchenne dystrophic skeletal muscle is evaluated, as is the consistency of the fiber type classifications between stains. While no major discrepancies in fiber typing were observed in the sample of normal muscle, significant differences in classification, along with a decrease in the ability to discriminate fiber types were noted in the sample of Duchenne muscular dystrophy. For the most part, these discrepancies were resolved by a re-interpretation of the staining characteristics of fibers in one stain.     

Biological races in humans

Races may exist in humans in a cultural sense, but biological concepts of race are needed to access their reality in a non-species-specific manner and to see if cultural categories correspond to biological categories within humans. Modern biological concepts of race can be implemented objectively with molecular genetic data through hypothesis-testing. Genetic data sets are used to see if biological races exist in humans and in our closest evolutionary relative, the chimpanzee. Using the two most commonly used biological concepts of race, chimpanzees are indeed subdivided into races but humans are not. Adaptive traits, such as skin color, have frequently been used to define races in humans, but such adaptive traits reflect the underlying environmental factor to which they are adaptive and not overall genetic differentiation, and different adaptive traits define discordant groups. There are no objective criteria for choosing one adaptive trait over another to define race. As a consequence, adaptive traits do not define races in humans. Much of the recent scientific literature on human evolution portrays human populations as separate branches on an evolutionary tree. A tree-like structure among humans has been falsified whenever tested, so this practice is scientifically indefensible. It is also socially irresponsible as these pictorial representations of human evolution have more impact on the general public than nuanced phrases in the text of a scientific paper. Humans have much genetic diversity, but the vast majority of this diversity reflects individual uniqueness and not race.     

Genetic diversity, structure and marker-trait associations in a collection of Italian tomato (Solanum lycopersicum L.) landraces

The study of phenotypic and genetic diversity in landrace collections is important for germplasm conservation. In addition, the characterisation of very diversified materials with molecular markers offers a unique opportunity to define significant marker-trait associations of biological and agronomic interest. Here, 50 tomato landraces (mainly collected in central Italy), nine vintage and modern cultivars, and two wild outgroups were grown at two locations in central Italy and characterised for 15 morpho-physiological traits and 29 simple sequence repeat (SSR) loci. The markers were selected to include a group of loci in regions harbouring reported quantitative trait loci (QTLs) that affect fruit size and/or shape (Q-SSRs) and a group of markers that have not been mapped or shown to have a priori known linkage (NQ-SSRs). As revealed by univariate and multivariate analyses of morphological data, the landraces grouped according to vegetative and reproductive traits, with emphasis on fruit size, shape and final destination of the product. Compared to the low molecular polymorphism reported in tomato modern cultivars, our data reveal a high level of molecular diversity in landraces. Such diversity has allowed the inference of the existence of a genetic structure that was factored into the association analysis. As the proportion of significant associations is higher between the Q-SSR subset of markers and the subset of traits related to fruit size and shape than for all of the other combinations, we conclude that this approach is valid for establishing true-positive marker-trait relationships in tomato. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

甘蔗野生种滇蔗茅利用研究 Ⅲ.滇蔗茅杂种F1群体的表型变异与遗传多样性分析

选用8个数量性状和18个质量性状对滇蔗茅杂种F1群体的表型变异、多样性及聚类关系进行分析。结果表明：数量性状的遗传变异主要来自于有效茎、单茎重及糖分;质量性状的叶鞘背毛群与内叶耳形状多样性丰富,根点排列、芽位、茎形、节间性状、生长裂缝等5个性状均表现一致;聚类分析表明62份后代材料可分为4大类群和10个亚类群。遗传多样性和聚类分析为杂交后代的筛选及其杂交或回交利用提供了科学依据。     

Metabolic innovations towards the human lineage

Background  

We describe a function-driven approach to the analysis of metabolism which takes into account the phylogenetic origin of biochemical reactions to reveal subtle lineage-specific metabolic innovations, undetectable by more traditional methods based on sequence comparison. The origins of reactions and thus entire pathways are inferred using a simple taxonomic classification scheme that describes the evolutionary course of events towards the lineage of interest. We investigate the evolutionary history of the human metabolic network extracted from a metabolic database, construct a network of interconnected pathways and classify this network according to the taxonomic categories representing eukaryotes, metazoa and vertebrates.     

Impact of RNA degradation on gene expression profiling

Background

Cancer is a heterogeneous disease caused by genomic aberrations and characterized by significant variability in clinical outcomes and response to therapies. Several subtypes of common cancers have been identified based on alterations of individual cancer genes, such as HER2, EGFR, and others. However, cancer is a complex disease driven by the interaction of multiple genes, so the copy number status of individual genes is not sufficient to define cancer subtypes and predict responses to treatments. A classification based on genome-wide copy number patterns would be better suited for this purpose.

Method

To develop a more comprehensive cancer taxonomy based on genome-wide patterns of copy number abnormalities, we designed an unsupervised classification algorithm that identifies genomic subgroups of tumors. This algorithm is based on a modified genomic Non-negative Matrix Factorization (gNMF) algorithm and includes several additional components, namely a pilot hierarchical clustering procedure to determine the number of clusters, a multiple random initiation scheme, a new stop criterion for the core gNMF, as well as a 10-fold cross-validation stability test for quality assessment.

Result

We applied our algorithm to identify genomic subgroups of three major cancer types: non-small cell lung carcinoma (NSCLC), colorectal cancer (CRC), and malignant melanoma. High-density SNP array datasets for patient tumors and established cell lines were used to define genomic subclasses of the diseases and identify cell lines representative of each genomic subtype. The algorithm was compared with several traditional clustering methods and showed improved performance. To validate our genomic taxonomy of NSCLC, we correlated the genomic classification with disease outcomes. Overall survival time and time to recurrence were shown to differ significantly between the genomic subtypes.

Conclusions

We developed an algorithm for cancer classification based on genome-wide patterns of copy number aberrations and demonstrated its superiority to existing clustering methods. The algorithm was applied to define genomic subgroups of three cancer types and identify cell lines representative of these subgroups. Our data enabled the assembly of representative cell line panels for testing drug candidates.     

Human disease classification in the postgenomic era: A complex systems approach to human pathobiology

Contemporary classification of human disease derives from observational correlation between pathological analysis and clinical syndromes. Characterizing disease in this way established a nosology that has served clinicians well to the current time, and depends on observational skills and simple laboratory tools to define the syndromic phenotype. Yet, this time-honored diagnostic strategy has significant shortcomings that reflect both a lack of sensitivity in identifying preclinical disease, and a lack of specificity in defining disease unequivocally. In this paper, we focus on the latter limitation, viewing it as a reflection both of the different clinical presentations of many diseases (variable phenotypic expression), and of the excessive reliance on Cartesian reductionism in establishing diagnoses. The purpose of this perspective is to provide a logical basis for a new approach to classifying human disease that uses conventional reductionism and incorporates the non-reductionist approach of systems biomedicine.     

Discrimination and consistency of five myosin ATPase stains in human normal and duchenne dystrophic muscle

Summary Limitations in the ability of the human visual system to assess accurately the relative staining densities of individual fibers in muscle tissue stained for myosin ATPase can complicate the objective evaluation of fiber type populations. In this study a novel approach is employed which utilizes human visual capabilities to provide accurate fiber classification. Using this approach, the ability of five ATPase staining techniques to discriminate fiber type categories in single samples of human normal and Duchenne dystrophic skeletal muscle is evaluated, as is the consistency of the fiber type classifications between stains. While no major discrepancies in fiber typing were observed in the sample of normal muscle, significant differences in classification, along with a decrease in the ability to discriminate fiber types were noted in the sample of Duchenne muscular dystrophy. For the most part, these discrepancies were resolved by a re-interpretation of the staining characteristics of fibers in one stain.This work was supported in part by NIH grant NS 15584, and by a grant from the Muscular Dystrophy Association     

Distribution of SUN, OVATE, LC, and FAS in the tomato germplasm and the relationship to fruit shape diversity

Phenotypic diversity within cultivated tomato (Solanum lycopersicum) is particularly evident for fruit shape and size. Four genes that control tomato fruit shape have been cloned. SUN and OVATE control elongated shape whereas FASCIATED (FAS) and LOCULE NUMBER (LC) control fruit locule number and flat shape. We investigated the distribution of the fruit shape alleles in the tomato germplasm and evaluated their contribution to morphology in a diverse collection of 368 predominantly tomato and tomato var. cerasiforme accessions. Fruits were visually classified into eight shape categories that were supported by objective measurements obtained from image analysis using the Tomato Analyzer software. The allele distribution of SUN, OVATE, LC, and FAS in all accessions was strongly associated with fruit shape classification. We also genotyped 116 representative accessions with additional 25 markers distributed evenly across the genome. Through a model-based clustering we demonstrated that shape categories, germplasm classes, and the shape genes were nonrandomly distributed among five genetic clusters (P < 0.001), implying that selection for fruit shape genes was critical to subpopulation differentiation within cultivated tomato. Our data suggested that the LC, FAS, and SUN mutations arose in the same ancestral population while the OVATE mutation arose in a separate lineage. Furthermore, LC, OVATE, and FAS mutations may have arisen prior to domestication or early during the selection of cultivated tomato whereas the SUN mutation appeared to be a postdomestication event arising in Europe.     

Multi-attribute ecological river typology for assessing ecological condition and conservation planning

A river classification framework is needed to make good management and planning decisions about river health and biodiversity. We developed a multi-attribute ecological river typology to address this need in the Australian State of New South Wales (801,428 km²). Multivariate patterns in data collected from 322 reference sites were used to define river types for each attribute: abiotic features (10 types), fish assemblages (6 types) and macroinvertebrate assemblages from river edges (8 types) and riffle zones (5 types). We used classification tree analysis to define broad regions for each attribute and then to construct identification keys for river types within each region using slope, elevation, maximum distance from source, latitude and mean annual rainfall. These keys allow the mapping of the likely spatial extent of river types and the assignment of a multi-attribute river-type identity to a river reach anywhere in the State. We used the average dissimilarity distances among the river types and the rates of misclassification of reference sites to assess the reliability of the assignments for different attributes in different regions. This approach to river classification can be applied anywhere in the world, resulting in simple to highly complex typologies depending on data availability. In data-poor areas it may result in a single attribute typology based on remotely derived variables and a coarsely defined reference condition. In data-rich areas the typology may have a large number of attributes using very large datasets with high resolution. Handling editor: D. Dudgeon     

七彩红竹中类黄酮-3-O-葡萄糖基转移酶基因的克隆及功能分析

类黄酮-3-O-葡萄糖基转移酶(Flavonoid-3-O-glucosyltransferase,3GT)是花青苷(Anthocyanins)生物合成途径中的关键酶,它主要负责将不稳定的花色素转变为稳定的花色素苷,虽然目前已经从其他植物中克隆获得类黄酮-3-O-葡萄糖基转移酶,但是对竹子中的类黄酮-3-O-葡萄糖基转移酶并不清楚。该文以产生花青素的七彩红竹(Indosasa hispida Mc Clure cv.Rainbow)为材料,首先通过3GT的同源比对后设计3GT基因特异引物,获得3GT基因片段;然后运用RT-PCR及RACE技术从七彩红竹茎中克隆得到完整的3GT基因(Ih3GT)。结果表明:Ih3GT基因的c DNA全长序列为1 730 bp,含有1个1 425 bp的开放阅读框(ORF),编码474个氨基酸;系统进化分析显示,七彩红竹3GT与其他禾本科植物的3GT聚类到同一个分支;该基因推断的蛋白与水稻(Oryza sativa)3GT蛋白的相似性为69%,与二穗短柄草(Brachypodium distachyon)3GT的相似性为67%;经氨基酸序列比对,推断七彩红竹3GT含有糖基转移酶基因家族特有的结构域PSPG-box;半定量PCR的结果显示,七彩红竹3GT基因在微红的幼茎中大量表达,而在其他组织中并不表达,说明Ih3GT具有组织表达特异性。该结果为今后深入研究七彩红竹花色苷的形成机理、鉴定Ih3GT酶活性以及利用Ih3GT基因培育竹子新品种奠定了基础。     

A new method for calculating Risk Tolerance in the assessment of threatened flora

This paper reports on a proposed method for evaluating threat categories for regional flora, based mainly on phytogeographical data. The method involves the creation of current distribution maps, analysis of threat factors and use of the RAMAS Red List software to facilitate rapid and objective classification of taxa in accordance with 2001 IUCN criteria. In order to ensure a more objective approach by the assessor and reduce the range of uncertainty, an index was created for calculating Risk Tolerance (RT) that enabled adjustment of the results obtained and thus supplemented the software used. For trial purposes, the proposed model was applied to Spanish gypsophilous flora currently protected under Spanish regional legislation. When classified using the new model, the taxa in question were placed in very different categories, ranging from least concern (LC) to endangered (EN), indicating the need to redefine both their current legal status and recommended management measures. Use of this method will enable scientists to optimise available information on the geographical distribution of endangered taxa, and help governments both to optimise their financial investment in conservation and to define their priorities. The authors endorse the use of IUCN categories in legal protection texts, and advocate as essential a greater degree of coordination between scientists and governments.     

A polyphasic approach for the taxonomy of cyanobacteria: principles and applications

Taxonomic classification is the only method for understanding and exploring knowledge about organismal diversity. However, it is complicated in prokaryotic, phylogenetically old, phototrophic cyanobacteria, which contain very simple unicellular forms up to multicellular types with a differentiated and diversified thallus. Their cells are cytologically relatively simple, but variable in shape. Various genotypes are adaptable to various specialized ecosystems. The introduction and combination of modern molecular, cytomorphological and ecological methods in the taxonomy of cyanobacteria is necessary and should be accepted as the only method for the elaboration of their modern systematics. The combination of different methods should be based on molecular sequencing as the basic approach, to which must be added other criteria (morphological, ecological) if they are available and which are distinct and recognizable in cyanobacterial populations. The use of such characteristics is necessary and must be obligatorily included for the final characterization both of strains and natural populations. Application of this polyphasic, i.e. combined approach is considered as a unique, modern, unambiguous, unequivocal and a fully acceptable methodological procedure, but it is not yet commonly used, nor possible for all known cyanobacterial populations. The main principles and recent problems of this modern classification method are discussed in the following review and will be the basis of further discussion.     

A method of deriving subgroups of a population: a study of craniofacial taxonomy

Subgroups within a population are often difficult to discover and describe except by subjective methods. In this study, cluster analysis (numerical taxonomy) methods were used on selected craniofacial measurements obtained from 308 North American White children of both sexes in the age range 6–18 to derive categories of skeletal facial types. Two different cluster analysis approaches were used in conjunction with a separate overall evaluation of facial balance, an independent measure of maxillo-mandibular relationship (AB/FOP), and a traditional classification (Angle). The categories derived rest on corroborative and overlapping evidence from each of those methods. The categories were examined to determine if it is possible to classify a sample by means of cluster analysis, the size and discreteness of each class, how they compare with the Angle classification of the same sample, and the percentage of individuals that may be identified unequivocally by this classification scheme. Five categories were obtained. Labeled Category A — Category E, they show some correspondence to the Angle Classes I, II, and III, but categories A, B, and C appear to be subgroups, heretofore undetected, of Angle Class II. Categories D and E correspond to Angle Classes I and III, respectively. The categories are more realistic and informative than the Angle classes. Each category is reported along with its distinguishing skeletal characteristics.     

Structural and functional classification of antennal sensilla of the cockroach,Leucophaea maderae

Summary Antennal sensilla of Leucophaea maderae were investigated electrophysiologically, labeled and then examined with the scanning or transmission electron microscope. The sensilla can be classified into morphological types according to their external shape and the structure of their hair wall. Sensilla showing similar reaction spectra of their cells can be cathegorized into physiological groups. The morphological classification corresponds to the physiological grouping: one morphological type of sensillum comprises one or several groups of physiologically similar sensilla. In many of these groups constant combinations of physiologically different cells occur. The possible functional significance of the relationships found between the structural features of the sensilla and the physiological properties of their sensory cells is discussed.Supported by the Deutsche Forschungsgemeinschaft (Scha 292/1)