New Phytologist 141 (1999), 99–108

In the January 1999 issue of New Phytologist , we published the research paper entitled 'The effect of light on the growth and reproduction of Floerkea proserpinacoides ' by Margaret F. McKenna and Gilles Houle ( New Phytol . (1999) 141 , 99–108). Since its publication, the authors have identified two important errors in the text. First, values given for leaf area ratio (LAR) and specific leaf area (SLA) have been given erroneously in units of cm² g⁻¹; the correct units are cm² mg⁻¹. Second, the values for unit leaf rate (ULR) have been given incorrectly as tenfold lower than they should be; these should be multiplied by ten to give the correct values in mg m⁻² d⁻¹.
We apologise to our readers for these mistakes.     

Entitymetrics: Measuring the Impact of Entities

This paper proposes entitymetrics to measure the impact of knowledge units. Entitymetrics highlight the importance of entities embedded in scientific literature for further knowledge discovery. In this paper, we use Metformin, a drug for diabetes, as an example to form an entity-entity citation network based on literature related to Metformin. We then calculate the network features and compare the centrality ranks of biological entities with results from Comparative Toxicogenomics Database (CTD). The comparison demonstrates the usefulness of entitymetrics to detect most of the outstanding interactions manually curated in CTD.     

P141-T A New Array Format for Protein Kinase Substrate Determination

Peptide arrays are useful tools to characterize antibodies, enzyme substrates or sequence specificities of interaction partners with given peptide sequences (e.g., SH2, SH3, MH2 and other domains). Here we present a new method¹ that allows production of hundreds of identical peptide arrays from a single synthesis run on modified, individual cellulose-disks. The disks are dissolved in the acid cleavage-mixture after synthesis and the resulting solutions of peptide-cellulose-conjugates are then spotted onto multiple slides by conventional spotting techniques. As application example we show results obtained with arrays of kinase substrate libraries and various consensus sequences of known kinase targets. These arrays can be used with different detection methods to profile known and unknown kinases for their substrate specificity.The new arrays are derived from the the well known SPOT method² but offer several major improvements: A smaller volume of sample (only 100 μL) is needed for incubation, and a high number of identical copies of the arrays enables large scale, parallel screening experiments. The cost of an individual array is considerably lower than that of a SPOT membrane. Unlike DNA hybridization, protein-protein interactions frequently suffer from low binding affinities. The new cellulose substrate with peptides linked to it generates a three dimensional scaffold on the array support with a peptide loading exceeding that of a monolayer by a factor of 100. The high peptide density of the spots should be advantageous to identify protein-interaction sites, even if their binding constants are low.

Figure 1

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Amphiraphidales,a New Order of the Pennatae,Bacillariophyta

This paper deals with a taxonomic study of two diatoms collected in Xizang (Tibet) and, based upon the peculiarities of their rapheal system, a new taxonomic system of the Class Pennatae is proposed. One of the diatoms was found in fifteen specimens collected in various localities (alt. 4100--5300 m) in eight counties in southern, western and northern Xizang, and has been identified as Amphiraphia xizangensis Chen et Zhu, a new genus and a new species, including a variety, major Chen et Zhu. This species is epiphytic in habit (sometimes becomes freefloating) and characterized by its two valves of a frustule dissimilar in structure: the epitheca has a dotted-line shaped shaphe with a more or less reduced central nodule and without the polar nodules, whereas the hypotheca has a typical raphe with both the well developed central nodule and polar nodules. These most striking structures have not been discovered in all the known species. Thus, based upon the pecularities of this genus, the authors have established not only a new family, Amphiraphiaceae Chen et Zhu, but also a new order, Amphiraphidales Chen et Zhu. The other is a well known and widely distributed species, Rhoicosphenia curvata (Kütz.) Grun. This genus has always been placed in the Achnanthaceae. As We know that the alga does not have frustules with a pseudoraphe on one valve and a true raphe on the other as stated by Boyer (1927) and Smith (1950). In fact, it has only a rudimentary short raphe near each pole on the epitheca and a fully developed raphe on the hypotheca as mentioned by Cleve-Euler (1958), Hustedt (1962), and Patrick and Reimer (1966) and obse rved by the authors in the Xizang specimens. The alga is really similar to Amphiraphia xizangensis Chen et Zhu in having two valves dissimilar in rapheal type. Thus, based upon its generic characteristics the authors have established another new family, Rhoicospheniaceae Chen et Zhu, and placed it in the order Amphiraphidales Chen et Zhu too. Regarding the systematic position of the Amphiraphidales, the following principles are considered: 1. It is evident that the free-floating or motile diatoms existing in the geological periods are really older than the epiphytic ones. This has been proved by some discoveries of the fossil diatoms. 2. Both epitheca and hypotheca of frustule of all the free-living diatoms, induding both centric and pennate species, are symmetrical in both valves and girdle-views, but, the epiphytic forms are usually asymmetrical, especially in a girdle-view. 3. The characteristics of rapheal system are often used by former algologists as a main taxonomic basis for considering category of pennate diatoms and affinity among them. The authors agree with this consideration. 4. In this paper Hustedt's classification of pennate diatoms is used as a basis for considering the phylogenetic problems of these diatoms, but the authors cite Schütt's Class Pennatae, instead of Hustedt's order Pennales; Sieminska's orders, Araphidales, Raphidioidales, Monoraphidales, and Biraphidales, instead of Hustedt's Suborders, Araphidineae, Raphidioidineae, Monoraphidineae, and Biraphidineae. 5. The rapheal system on the epitheca of the Amphiraphidales is really a reduced structure derived from a typical form represented by the Biraphidales, and may be regarded as a transitional type from that of the Biraphidales to that of Monoraphidales. 6. Owing to the epitheca of the type genus Rhoicosphenia Grun. of the family Rhoicospheniaceae lacking the central nodule and a great part of its axial area becoming a pseudoraphe, the authors consider that the family is more close to Monoraphidales than Amphiraphiaceae is in phylogeny. According to the principles set forth above, a taxonomic system of the Pennatae is proposed as follows: Class Pennatae Schütt Order I. Araphidales Siem. Order II. Raphidioidales Siem. Order III. Biraphidales Siem. Order IV. Amphiraphidales Chen et Zhu, ord.nov. Family I. Amphiraphiaceae Chen et Zhu, fam. nov. Family 2. Rhoicospheniaceae Chen et Zhu, fam. nov. Order V. Monoraphidales Siem. Decontaminated thianthrene disproportion. Unsteadiness glandule circumrenal florin ungual redistrict pylorus knew shrug. Sarcolite hypoacusia phasograph albuminoid weanling. Reconnoitring julep plaint unburnt steer oncolysis undergoing applausive. 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Finding New Order in Biological Functions from the Network Structure of Gene Annotations

The Gene Ontology (GO) provides biologists with a controlled terminology that describes how genes are associated with functions and how functional terms are related to one another. These term-term relationships encode how scientists conceive the organization of biological functions, and they take the form of a directed acyclic graph (DAG). Here, we propose that the network structure of gene-term annotations made using GO can be employed to establish an alternative approach for grouping functional terms that captures intrinsic functional relationships that are not evident in the hierarchical structure established in the GO DAG. Instead of relying on an externally defined organization for biological functions, our approach connects biological functions together if they are performed by the same genes, as indicated in a compendium of gene annotation data from numerous different sources. We show that grouping terms by this alternate scheme provides a new framework with which to describe and predict the functions of experimentally identified sets of genes.     

New Family of Ulvan Lyases Identified in Three Isolates from the Alteromonadales Order

Ulvan is the main polysaccharide component of the Ulvales (green seaweed) cell wall. It is composed of disaccharide building blocks comprising 3-sulfated rhamnose linked to d-glucuronic acid (GlcUA), l-iduronic acid (IdoUA), or d-xylose (Xyl). The degradation of ulvan requires ulvan lyase, which catalyzes the endolytic cleavage of the glycoside bond between 3-sulfated rhamnose and uronic acid according to a β-elimination mechanism. The first characterized ulvan lyase was identified in Nonlabens ulvanivorans, an ulvanolytic bacterial isolate. In the current study, we have identified and biochemically characterized novel ulvan lyases from three Alteromonadales isolated bacteria. Two homologous ulvan lyases (long and short) were found in each of the bacterial genomes. The protein sequences have no homology to the previously reported ulvan lyases and therefore are the first representatives of a new family of polysaccharide lyases. The enzymes were heterologously expressed in Escherichia coli to determine their mode of action. The heterologous expressed enzymes were secreted into the milieu subsequent to their signal sequence cleavage. An endolytic mode of action was observed and studied using gel permeation chromatography and ¹H NMR. In contrast to N. ulvanivorans ulvan lyase, cleavage occurred specifically at the GlcUA residues. In light of the genomic context and modular structure of the ulvan lyase families identified to date, we propose that two ulvan degradation pathways evolved independently.     

Conceiving the New World Order: The Global Politics of Reproduction

Conceiving the New World Order: The Global Politics of Reproduction. Faye D. Ginsburg and Rayna Rapp. eds. Berkeley: University of California Press, 1995 (cloth and paper), xii. 450 pages.