From taxonomic literature to cybertaxonomic content

In the ubiquitin-proteasome system, a subset of ubiquitylated proteins requires the AAA+ ATPase p97 (also known as VCP or Cdc48) for extraction from membranes or protein complexes before delivery to the proteasome for degradation. Diverse ubiquitin adapters are known to link p97 to its client proteins, but two recent papers on the adapter protein UBXD7, including one by Bandau et al. in BMC Biology, suggest that rather than simply linking p97 to ubiquitylated proteins, this adapter may be essential to coordinate ubiquitylation and p97-mediated extraction of the proteasome substrate. These findings add to growing indications of richly diverse roles of adapters in p97-mediated signaling functions. See research article: http://www.biomedcentral.com/1741-7007/10/36     

XML schemas and mark-up practices of taxonomic literature

We review the three most widely used XML schemas used to mark-up taxonomic texts, TaxonX, TaxPub and taXMLit. These are described from the viewpoint of their development history, current status, implementation, and use cases. The concept of "taxon treatment" from the viewpoint of taxonomy mark-up into XML is discussed. TaxonX and taXMLit are primarily designed for legacy literature, the former being more lightweight and with a focus on recovery of taxon treatments, the latter providing a much more detailed set of tags to facilitate data extraction and analysis. TaxPub is an extension of the National Library of Medicine Document Type Definition (NLM DTD) for taxonomy focussed on layout and recovery and, as such, is best suited for mark-up of new publications and their archiving in PubMedCentral. All three schemas have their advantages and shortcomings and can be used for different purposes.     

Avian haematozoa: some taxonomic and nomenclatural problems arising from the Russian literature.

It is evident from a survey of the Russian literature that many species of avian haematozoa recorded do not meet the basic criteria required by the International Code of Zoological Nomenclature. Thus 28 species of Haemoproteus and 4 species of Leucocytozoon are considered to be nomina nuda, while 1 species, Leucocytozoon turtur orientalis is a synonym of L. marchouxi.     

Metagenomic taxonomic classification using extreme learning machines

Next-generation sequencing technologies have allowed researchers to determine the collective genomes of microbial communities co-existing within diverse ecological environments. Varying species abundance, length and complexities within different communities, coupled with discovery of new species makes the problem of taxonomic assignment to short DNA sequence reads extremely challenging. We have developed a new sequence composition-based taxonomic classifier using extreme learning machines referred to as TAC-ELM for metagenomic analysis. TAC-ELM uses the framework of extreme learning machines to quickly and accurately learn the weights for a neural network model. The input features consist of GC content and oligonucleotides. TAC-ELM is evaluated on two metagenomic benchmarks with sequence read lengths reflecting the traditional and current sequencing technologies. Our empirical results indicate the strength of the developed approach, which outperforms state-of-the-art taxonomic classifiers in terms of accuracy and implementation complexity. We also perform experiments that evaluate the pervasive case within metagenome analysis, where a species may not have been previously sequenced or discovered and will not exist in the reference genome databases. TAC-ELM was also combined with BLAST to show improved classification results. Code and Supplementary Results: http://www.cs.gmu.edu/~mlbio/TAC-ELM (BSD License).     

Exploring historical trends using taxonomic name metadata

Background  

Authority and year information have been attached to taxonomic names since Linnaean times. The systematic structure of taxonomic nomenclature facilitates the ability to develop tools that can be used to explore historical trends that may be associated with taxonomy.     

A Taxonomic Search Engine: Federating taxonomic databases using web services

Background  

The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism.     

Adequacy of numerical taxonomic methods: Further experiments using simulated data

The adequacy of various phenetic and phylogenetic estimation methods was evaluated using simulated data sets. Two parsimony programs were used to construct maximum parsimony trees (WAGNER 78 and HENNIG 86). The CAFCA program was used to perform group-compatibility analysis. Four UPGMA clustering strategies were employed. The simulation model GENESIS was used to generate data sets under different evolutionary conditions. The effects of input parameters and tree properties on the accuracy of the estimated trees were evaluated. UPGMA based on product moment correlations of unstandardized characters appeared to perform best, under all evolutionary conditions tested. The effect of input parameters on the accuracy was not very significant. Among the tree statistics the stemminess of the true tree appeared to be the most important estimator of accuracy.     

Hotspots and ecoregions: a test of conservation priorities using taxonomic data

The loss of biodiversity is now recognized as a global problem of significant magnitude [ Science 289: 2279]. Conservation efforts focus on measuring species diversity and distribution, assessing biodiversity threats, and managing habitats to maintain that diversity. The accuracy of measuring species diversity depends on the quality and scale of the data. Recently indirect estimates of diversity based on the skilled opinions of international taxonomic authorities were used to define 25 global conservation hotspots [ Nature 403: 853–858] and 871 ecoregions [ Bioscience 51: 933–938]. These data, originating from first-hand fieldwork and museum study, are readily available, but not necessarily repeatable nor testable. If this type of information prevails for conservation purposes, it is critical that we test the quality of this information with verifiable data at finer scales (e.g., regional inventories, specimen records, and accumulated distribution data). Here we perform such a test for the hotspots and ecoregions found in the Indo-Pacific by comparing the estimates of the expert scientists with authenticated published diversity data on flowering plants. We found a high correlation between our counts of species richness and endemism with the experts' estimates, but surprisingly found less congruity among the seven families examined. A revised list of conservation priority regions based on our plant data is provided.     

Defining operational taxonomic units using DNA barcode data

The scale of diversity of life on this planet is a significant challenge for any scientific programme hoping to produce a complete catalogue, whatever means is used. For DNA barcoding studies, this difficulty is compounded by the realization that any chosen barcode sequence is not the gene 'for' speciation and that taxa have evolutionary histories. How are we to disentangle the confounding effects of reticulate population genetic processes? Using the DNA barcode data from meiofaunal surveys, here we discuss the benefits of treating the taxa defined by barcodes without reference to their correspondence to 'species', and suggest that using this non-idealist approach facilitates access to taxon groups that are not accessible to other methods of enumeration and classification. Major issues remain, in particular the methodologies for taxon discrimination in DNA barcode data.     

Least-inclusive taxonomic unit: a new taxonomic concept for biology

Phylogenetic taxonomy has been introduced as a replacement for the Linnaean system. It differs from traditional nomenclature in defining taxon names with reference to phylogenetic trees and in not employing ranks for supraspecific taxa. However, 'species' are currently kept distinct. Within a system of phylogenetic taxonomy we believe that taxon names should refer to monophyletic groups only and that species should not be recognized as taxa. To distinguish the smallest identified taxa, we here introduce the least-inclusive taxonomic unit (LITU), which are differentiated from more inclusive taxa by initial lower-case letters. LITUs imply nothing absolute about inclusiveness, only that subdivisions are not presently recognized.     

由国分类学文献中南洋杉属两种之订正

通过调查,对Araucaria cunninghamii和A.heterophylla的选模式和中国分类学文献(如<广州植物志>、<中国树木学>、<中国高等植物图鉴>、<中国植物志>、<中国树木志>、、<中国高等植物>)的A.cunninghamii和A.heterophylla(或A.excelsa)作比较,证实中国分类学文献中的A.cunninghamii和A.heterophylla(或A.excelsa)分别是A.heterophylla(Salisb.)Franco和A.cunninghamii Aiton ex A.Cunn..这两种植物的叶形变化较大,但有明显的区别:诺福克南洋杉A.heterophylla幼树的末级小枝的叶细长呈线形、叶尖急尖,牛长角小于45°,腹面无明显的脊,成龄株的末级小枝的叶扁平呈鳞片状;南洋杉A.cunninghamii幼树的末级小枝的叶呈两侧扁的钻形、叶尖短刺状,生长角45°-90°,腹背两面具明显的脊,成龄株的末级小枝的叶呈四棱状钻形.     

Discrimination of marine algal taxonomic groups using delayed fluorescence spectroscopy

We present a method for in situ monitoring of phytoplankton composition changes in a marine environment. The method is based on delayed fluorescence excitation spectra analyzed with CHEMTAX software, which is generally used for determination of phytoplankton communities with HPLC pigment data. Delayed fluorescence (DF) is a photosynthetic parameter that can only be measured in living cells. Algal DF excitation spectra are group-specific, based on their composition of photosynthetic pigments.DF excitation spectra of 14 marine algal species from different families were measured with a delayed fluorescence spectrometer. Mixtures were prepared from northern Adriatic algal species representing six taxonomic groups: dinoflagellates (Prorocentrum minimum), diatoms (Skeletonema costatum), cyanobacteria (Synechococcus sp.), prasinophytes (Micromonas sp.), cryptophytes (Teleaulax sp.), and prymnesiophytes (Isochrysis galbana). The DF excitation spectra (DFS) and HPLC pigment compositions of the mixtures were analyzed with CHEMTAX software. The prediction power of DFS–CHEMTAX method was comparable to HPLC–CHEMTAX.     

Characterisation of micromonosporae from aquatic environments using molecular taxonomic methods

Large numbers of strains assigned to the genus Micromonospora on the basis of typical colonial and pigmentation features were isolated from diverse aquatic sediments using a standard selective isolation procedure. Two hundred and six isolates and eight representatives of the genus Micromonospora were assigned to 24 multimembered groups based on a numerical analysis of banding patterns generated using BOX and ERIC primers. Representatives of multimembered groups encompassing isolated micromonosporae were the subject of 16S rRNA gene sequencing analyses. Good congruence was found between the molecular fingerprinting and 16S rRNA sequence data indicating that the groups based upon the former are taxonomically meaningful. Nearly all of the isolates that were chosen for the 16S rRNA gene sequencing analyses showed that the ecosystems studied are a rich source of novel micromonosporae. These findings have implications for high throughput screening for novel micromonosporae as BOX and ERIC fingerprinting, which is rapid and reproducible, can be applied as a robust dereplication procedure to indicate which environmental isolates have been cultured previously.     

Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin

Taxonomic assignment of sequence reads is a challenging task in metagenomic data analysis, for which the present methods mainly use either composition- or homology-based approaches. Though the homology-based methods are more sensitive and accurate, they suffer primarily due to the time needed to generate the Blast alignments. We developed the MetaBin program and web server for better homology-based taxonomic assignments using an ORF-based approach. By implementing Blat as the faster alignment method in place of Blastx, the analysis time has been reduced by severalfold. It is benchmarked using both simulated and real metagenomic datasets, and can be used for both single and paired-end sequence reads of varying lengths (≥45 bp). To our knowledge, MetaBin is the only available program that can be used for the taxonomic binning of short reads (<100 bp) with high accuracy and high sensitivity using a homology-based approach. The MetaBin web server can be used to carry out the taxonomic analysis, by either submitting reads or Blastx output. It provides several options including construction of taxonomic trees, creation of a composition chart, functional analysis using COGs, and comparative analysis of multiple metagenomic datasets. MetaBin web server and a standalone version for high-throughput analysis are available freely at http://metabin.riken.jp/.     

Flow cytometric cell division tracking using nuclei

BACKGROUND: Labeling cells with 5-(and-6) carboxyfluorescein diacetate succinimidyl ester (CFSE) allows their subsequent division history to be determined by flow cytometry. Whether nuclei isolated from CFSE-labeled cells retain any or sufficient dye to reveal the same division history was unknown. If division tracking in nuclei were possible, it would enable the development of new methods for monitoring quantitative changes in nuclei components and how these might vary with successive divisions. METHODS: Nuclei from CFSE-labeled B cells were prepared by lysing whole cells with nonionic detergent Nonidet P-40 (NP-40). The purified nuclei were subsequently fixed with paraformaldehyde and permeabilized with Tween 20 in order to perform intranuclear staining. RESULTS: Purified nuclei displayed the equivalent asynchronous cell division profile as intact cells. Furthermore, the possibility of simultaneously monitoring division history with intranuclear staining was established by labeling bromodeoxyuridine (BrdU) incorporated into DNA during a brief pulse prior to harvesting cells. This result was verified with the staining of proliferating cell nuclear antigen (PCNA). In addition, aminoactinomycin D (7-AAD) staining established that cell cycle stage and cell division history could be simultaneously determined. CONCLUSIONS: Our results demonstrate that cell division history is retained in purified cell nuclei after CFSE labeling and can be used in combination with intranuclear immunofluorescent labeling and DNA staining to provide a comprehensive analysis of nuclei by flow cytometry. This method should prove useful for assessing differential nuclear translocation and accumulation of molecular components during consecutive division rounds and during different stages of the cell cycle.     

Cell tracking using a photoconvertible fluorescent protein

The tracking of cell fate, shape and migration is an essential component in the study of the development of multicellular organisms. Here we report a protocol that uses the protein Kaede, which is fluorescent green after synthesis but can be photoconverted red by violet or UV light. We have used Kaede along with confocal laser scanning microscopy to track labeled cells in a pattern of interest in zebrafish embryos. This technique allows the visualization of cell movements and the tracing of neuronal shapes. We provide illustrative examples of expression by mRNA injection, mosaic expression by DNA injection, and the creation of permanent transgenic fish with the UAS-Gal4 system to visualize morphogenetic processes such as neurulation, placode formation and navigation of early commissural axons in the hindbrain. The procedure can be adapted to other photoconvertible and reversible fluorescent molecules, including KikGR and Dronpa; these molecules can be used in combination with two-photon confocal microscopy to specifically highlight cells buried in tissues. The total time needed to carry out the protocol involving transient expression of Kaede by injection of mRNA or DNA, photoconversion and imaging is 2-8 d.     

Phylogeny imbalance: taxonomic level matters

Two lines of evidence indicate that the degree of symmetry in phylogenetic topologies differs at different hierarchical levels. First, in a set of 61 phylogenies with superspecific taxa as their terminals, trees were on average more unbalanced (asymmetric) when the species richness of terminals was considered than when it was not. Second, nodes with a given number of higher taxa descended from them were on average more unbalanced than were nodes with the same number of species as descendants. There are several possible reasons--some biological, some artifactual--for the differences. Whatever the reason, these results caution against treating species-level and higher level phylogenies as equivalent when considering tree shape. The imbalance measure adopted here permits the use of trees that contain polytomies, facilitating a larger sample than has been achieved previously.