A synthesis of the biological quality elements for the implementation of the European Water Framework Directive in the Mediterranean ecoregion: The case of Saronikos Gulf

Benthic macroinvertebrates, macroalgae and phytoplankton constitute the biological quality elements proposed in the Water Framework Directive (WFD, 2000/60/EC) to be used for the classification of the ecological status of a water body. In the context of the preparation for the implementation of WFD, classification schemes for all three elements have been developed and tested for all the European ecoregions. In the present work, the classification schemes, with the corresponding metric tools and the interpretations of the class boundaries according to the normative definitions of WFD, are presented for each biological element in Saronikos Gulf, as case study in the Mediterranean ecoregion. The combination of the three biological elements into an integrated classification for coastal water bodies has been one of the major issues addressed in the context of WFD guidelines. Results are interpreted and validated, through an ecological viewpoint, on the basis of relevant environmental data. Moreover, this work presents a way to combine the EUNIS system to the typology of water bodies in the Mediterranean ecoregion.     

Commentary on the WHO classification of tumors of lymphoid tissues (2008): aggressive B-cell lymphomas

In the novel WHO classification 2008, the classification of aggressive B-cell lymphoma has been revised for several categories with the aim to define “clean” entities. Within large B-cell lymphoma, a few distinct clinico-pathological entities have been recognized with more clinically defined entities than pathologically defined ones. The majority of known morphological variations were not considered to merit more than classification as a variant of DLBCL, not otherwise specified. Specifically, a biological subgrouping of DLBCL on the basis of molecular (activated B-cell versus germinal center B-cell) or immunophenotypic (CD5+) features was felt to be too immature to include at this stage. The role of EBV in aggressive B-cell lymphoma has been explored in more depth with the recognition of several novel and re-defined clinico-pathological entities. Also, in these diseases, clinical definitions play a very dominant role in the WHO classification 2008.     

Classification, Convention and Logic

An attempt has been made to establish axiomatically the principles of biological classification. It is shown that if phylogenetic classification is based on the notion of dichotomous origin of new taxa implied in Hennig's theory of cladism then the outcome must be a hierarchy in the form of a dichotomous dendrogram. Since the rules of traditional classification do not lead to this type of "phylogenetic tree" it is concluded that the conventions of ordinary systematics do not permit the erection of a "natural system".     

A Photometric Method for Determining the Growth Rate of Yeast (Saccharomyces cereviciae)

There have been several investigations into students' conceptions of animal classification. Previous research has generally failed to study the criteria of classification used by the students. This study shows that students prefer to classify creatures along the criteria of habitat and locomotion (method of movement). They continue using these criteria even after learning the categories of biological taxonomy. The results lead to the assumption of an implicit theory of natural kinship of animals. The educational consequences for biology instruction, especially with regard to biological taxonomy, biodiversity, and evolution, are discussed.     

NOXclass: prediction of protein-protein interaction types

Background  

Structural models determined by X-ray crystallography play a central role in understanding protein-protein interactions at the molecular level. Interpretation of these models requires the distinction between non-specific crystal packing contacts and biologically relevant interactions. This has been investigated previously and classification approaches have been proposed. However, less attention has been devoted to distinguishing different types of biological interactions. These interactions are classified as obligate and non-obligate according to the effect of the complex formation on the stability of the protomers. So far no automatic classification methods for distinguishing obligate, non-obligate and crystal packing interactions have been made available.     

An elementary approach to catastrophe theory

The recently proved classification theorem of René Thom has led to the development of the new science of Catastrophe Theory. This theory has been widely held to be particularly relevant in biological applications. The present paper presents a simplified proof of Thom’s Theorem and assesses its importance in biology.     

Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches

The practice of classifying organisms into hierarchical groups originated with Aristotle and was codified into nearly immutable biological law by Linnaeus. The heart of taxonomy is the biological species, which forms the foundation for higher levels of classification. Whereas species have long been established among sexual eukaryotes, achieving a meaningful species concept for prokaryotes has been an onerous task and has proven exceedingly difficult for describing viruses and bacteriophages. Moreover, the assembly of viral "species" into higher-order taxonomic groupings has been even more tenuous, since these groupings were based initially on limited numbers of morphological features and more recently on overall genomic similarities. The wealth of nucleotide sequence information that catalyzed a revolution in the taxonomy of free-living organisms necessitates a reevaluation of the concept of viral species, genera, families, and higher levels of classification. Just as microbiologists discarded dubious morphological traits in favor of more accurate molecular yardsticks of evolutionary change, virologists can gain new insight into viral evolution through the rigorous analyses afforded by the molecular phylogenetics of viral genes. For bacteriophages, such dissections of genomic sequences reveal fundamental flaws in the Linnaean paradigm that necessitate a new view of viral evolution, classification, and taxonomy.     

丛枝菌根真菌分类最新进展

近10a来,随着分子生物学技术在丛枝菌根(arbuscularmycorrhiza,AM)研究中的应用,AM真菌分类学得到迅速发展。重点介绍AM真菌的最新分类系统,并对其发展简史作一简单回顾。     

Metabolic Profiles are Principally Different between Cancers of the Liver,Pancreas and Breast

Molecular profiling of primary tumors may facilitate the classification of patients with cancer into more homogenous biological groups to aid clinical management. Metabolomic profiling has been shown to be a powerful tool in characterizing the biological mechanisms underlying a disease but has not been evaluated for its ability to classify cancers by their tissue of origin. Thus, we assessed metabolomic profiling as a novel tool for multiclass cancer characterization. Global metabolic profiling was employed to identify metabolites in paired tumor and non-tumor liver (n=60), breast (n=130) and pancreatic (n=76) tissue specimens. Unsupervised principal component analysis showed that metabolites are principally unique to each tissue and cancer type. Such a difference can also be observed even among early stage cancers, suggesting a significant and unique alteration of global metabolic pathways associated with each cancer type. Our global high-throughput metabolomic profiling study shows that specific biochemical alterations distinguish liver, pancreatic and breast cancer and could be applied as cancer classification tools to differentiate tumors based on tissue of origin.     

得与失:苦苣苔科新的属级界定与分类系统——中国该科植物之变迁(英文)

过去20年对苦苣苔科植物的分子系统学研究已经极大地拓展了对这个科的种间关系与属一级之界定的理解。该文提供了一个苦苣苔科植物新分类系统,与传统的经典形态学分类系统比较,这一新系统被认为能更好地反映科下分类单元彼此之间的自然关系。众多传统意义上的属被分割、合并或者重新定义,这些巨大的分类变动正在影响着中国的苦苣苔科植物系统分类。此外,基于最近采集的材料,一些新属得以建立,一方面说明在中国还有相当多的野外工作需要做;而另一方面则再次证明了中国的苦苣苔科植物多样性是如此之丰富。在此,针对目前已经完成的工作和分类结论,对中国苦苣苔科植物的新分类系统进行了总结与概述,并深入地讨论了部分传统分类学上存在困惑的疑难属。     

Function annotation for pseudoknot using structure similarity

Many raw biological sequence data have been generated by the human genome project and related efforts. The understanding of structural information encoded by biological sequences is important to acquire knowledge of their biochemical functions but remains a fundamental challenge. Recent interest in RNA regulation has resulted in a rapid growth of deposited RNA secondary structures in varied databases. However, a functional classification and characterization of the RNA structure have only been partially addressed. This article aims to introduce a novel interval-based distance metric for structure-based RNA function assignment. The characterization of RNA structures relies on distance vectors learned from a collection of predicted structures. The distance measure considers the intersected, disjoint, and inclusion between intervals. A set of RNA pseudoknotted structures with known function are applied and the function of the query structure is determined by measuring structure similarity. This not only offers sequence distance criteria to measure the similarity of secondary structures but also aids the functional classification of RNA structures with pesudoknots.     

In defence of classification

It has increasingly been recognised that units of biological classification cannot be identified with the units of evolution. After briefly defending the necessity of this distinction I argue, contrary to the prevailing orthodoxy, that species should be treated as the fundamental units of classification and not, therefore, as units of evolution. This perspective fits well with the increasing tendency to reject the search for a monistic basis of classification and embrace a pluralistic and pragmatic account of the species category. It also provides a diagnosis of the paradoxical but popular idea that species are individuals: Species are not individuals, but the units of evolution are.     

High-throughput classification of images of cells transfected with cDNA clones

The sequence of the human genome has been determined. The next task is to determine the function of the genes. Classifying cellular forms of proteins encoded by human cDNA clones is a primary step toward understanding the biological role of proteins and their coding genes. We report here our ongoing work on an automatic system to facilitate this classification. Our system handles the transfection, incubation, acquisition of microscopic images of the cells, and the classification of forms there appearing in the images. Our system correctly classified proteins by their forms at a rate of 90% in feasibility studies.     

An evaluation of ensign wasp classification (Hymenoptera: Evaniidae) based on molecular data and insights from ribosomal RNA secondary structure

Abstract.  Ensign wasps (Hymenoptera: Evaniidae) are colourful, frequently collected and easily distinguished from other parasitic Hymenoptera. Despite many fascinating biological attributes, this group of insects has been overlooked by ecologists and systematists. An imposing obstacle inhibiting research on these wasps is the current state of their chaotic and potentially flawed classification, which has more than 50% of all described species assigned to the genus Evania – a taxon long suspected of being polyphyletic. The generic classification has recently been redefined on the basis of morphological characters. We tested this reinterpreted classification by analysing sequence data from three genes [28S ribosomal RNA (rRNA), 16S rRNA and cytochrome oxidase I (COI)] under parsimony and Bayesian criteria. For the 28S and 16S rRNAs, we illustrate the predicted secondary structures and provide a series of summary statistics for them; information pertaining to these structures was incorporated into our phylogenetic analyses where appropriate. Phylogenetically, our results indicate that this new generic classification is relatively sound, but that more data are required to understand intergeneric relationships.     

Methodological approach to the analysis of the scientific effectiveness of studies with regard to the development and improvement of medical biological preparations

A new methodologic approach to analysis of the scientific effectiveness of investigations aimed at the development and improvement of medical biological preparations has been worked out. This approach comprises the classification of research work and choice of parameters characterizing scientific effectiveness. The use of relative values (percentage) as characteristics of scientific effectiveness has made it possible to compare the results of research on 260 themes, carried out in one of medical research institutes.     

Histopathologic criterion of dysplasia of the uterine cervix and its biological nature.

A histopathologic diagnostic standard for abnormal epithelium of the uterine cervix, based on its biological behavior, has been proposed, and dysplasia and carcinoma in situ have been classified according to this standard. Benign dysplasia by this classification may be considered as a benign lesion, and only the lesion which satisfies the standard for atypical dysplasia should be considered as dysplasia, having a significance as a precursor to cervical cancer. This would be clinically convenient.     

植物葡聚糖酶基因抗病作用的研究进展

β-1,3-葡聚糖酶作为植物抗真菌基因工程的热点之一,近年来的研究进展较为迅速。本文叙述了植物β-1,3-葡聚糖酶的基本生物学特性和抗病机制,对β-1,3-葡聚糖酶抗病基因的分类、结构功能及转基因植物的研究进展进行综述。 Advances on the Plant Disease Resistant β-glucanase Gene XING Quan-hua,WANG Bin Institute of Genetics and Developmental Biology,Chinese Academy of Sciences,Beijing 100101,China Abstract:Study of β-1,3-glucanase is one of the hot points in plant genetic engineering of disease resistance,big progress has been made in the past few years.This paper briefly reviewed the main biological characters and mechanism involved in the disease resistance,the classification,structure,function and the transformation of β-1,3-glucanase genes. Key words：β-1,3-glucanase;biological characters;disease resistance mechanism     

A novel biclustering approach to association rule mining for predicting HIV-1-human protein interactions

Identification of potential viral-host protein interactions is a vital and useful approach towards development of new drugs targeting those interactions. In recent days, computational tools are being utilized for predicting viral-host interactions. Recently a database containing records of experimentally validated interactions between a set of HIV-1 proteins and a set of human proteins has been published. The problem of predicting new interactions based on this database is usually posed as a classification problem. However, posing the problem as a classification one suffers from the lack of biologically validated negative interactions. Therefore it will be beneficial to use the existing database for predicting new viral-host interactions without the need of negative samples. Motivated by this, in this article, the HIV-1-human protein interaction database has been analyzed using association rule mining. The main objective is to identify a set of association rules both among the HIV-1 proteins and among the human proteins, and use these rules for predicting new interactions. In this regard, a novel association rule mining technique based on biclustering has been proposed for discovering frequent closed itemsets followed by the association rules from the adjacency matrix of the HIV-1-human interaction network. Novel HIV-1-human interactions have been predicted based on the discovered association rules and tested for biological significance. For validation of the predicted new interactions, gene ontology-based and pathway-based studies have been performed. These studies show that the human proteins which are predicted to interact with a particular viral protein share many common biological activities. Moreover, literature survey has been used for validation purpose to identify some predicted interactions that are already validated experimentally but not present in the database. Comparison with other prediction methods is also discussed.     

Concept and Classification of Coarse Woody Debris in Forest Ecosystems

Coarse woody debris (CWD) is generally considered as dead woody materials in various stages of decomposition,including sound and rotting logs,snags,and large branches.CWD is an important functional and structural component of forested ecosystems and plays an important role in nutrient cycling,long-term carbon storage,tree regeneration,and maintenance of heterogeneous environmental and biological diversity.However,the definition and classification of CWD have been the subject of a long debate in forest ecology.CWD has not been precisely defined.Recently,with the rapid development of landscape ecology in CWD,the USDA Forest Service and the Long Term Ecological Research (LTER)have provided a standardized definition and classification for CWD,which makes data comparison in landscape scale possible.Important characteristics of their definition include:(1) a minimum diameter (or an equivalent crosssection) of CWD≥10 cm at the widest point (the woody debris with a diameter from 1 to 10 cm should be defined as fine woody debris,and the rest is litterfall);and (2) sound and rotting logs,snags,stumps,and large branches (located above the soil),and coarse root debris (larger than 1 cm in diameter).This classification has greatly facilitated CWD studies.Therefore,it has been widely applied in some countries (particularly in North America).However,this classification has long been a source of confusion for forest ecologists in China.Furthermore,different definitions and criteria are still adopted in individual studies,which makes the interpretation and generalization of their work difficult.This article reviewed recent progress in classifying CWD,with an emphasis on introducing the classification system of the USDA Forest Service and the LTER.It is expected that this review will help facilitate the development of standardized definition and classification suitable to forest ecosystems in China.