Studies of the grassland vegetation in the kawatabi special research area of the Japanese IBP

Summary 1. The paper demonstrates the utilization of a computerized vegetation analysis on the field data gathered at the Japanese IBP Grassland Site. Hand- and computer sorting procedures are compared and discussed. This part of the paper was a test of the usefulness of the computer simulation of the standard sorting procedures of phytosociological work. Tables 2–6 and Figure 2 demonstrate the usefulness as well as the limitations of the computer analysis. The possibility of incorporating phytosociological tables as matrices into computerized ecosystems models is suggested. 2. The vegetation of the J-IBP Grassland Site is described and preliminary evaluations made with regard to environmental parameters (Table 2 and 5, Figure 1). Some management influences on theMiscanthus grassland are discussed. The primary above-ground productivity ranges from 300 to 1500 g (usually 400 to 600 g) dry matter per m². Contribution from JIBP/PT and CT, and US IBP, Eastern Deciduous Forest Biome, BIOME WIDE STUDIES. This study was supported in part by the special project research “Studies on the dynamic status of biosphere” sponsored by the Japanese Ministry of Education, and in part by the North Carolina Board of Science and Technology and the UNC Faculty Grants Committee. We gratefully acknowledge the assistance ofDr. W. C. Moore, Mr. J. S. Radford, andMr. R. Reader in the execution of the computer analysis. Responsible for theories and execution of computer simulation:H. Lieth; responsible for field data:M. Numata andT. Suganuma.     

OntologyWidget – a reusable,embeddable widget for easily locating ontology terms

Background  

Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate terms from an ontology is often challenging for experts and non-experts alike, because there exist few tools that allow one to quickly find relevant ontology terms to easily populate a web form.     

Effects of saline root environment (NaCl) on nitrate and potassium uptake kinetics for rose plants: a Michaelis–Menten modelling approach

Greenhouse-grown cut flower roses are often irrigated with moderately saline irrigation water. The salt/ballast ions are either present initially in poor quality raw water or reclaimed municipal water, or accumulated in greenhouse irrigation water that is captured and reused. Such ions can inhibit root absorption of essential nutrients. The objective of this work was to quantify the influence of NaCl concentration on the uptake of nitrate and potassium by roses and develop a predictive model of uptake inhibition based on NaCl, NO₃ ^?, and K⁺ concentration. One year-old rose plants (Rosa spp. ‘Kardinal’ on ‘Natal Briar’ rootstock) were moved into growth chambers where nitrogen and potassium depletion were monitored during 6 days. Eight different initial NaCl treatments varying from zero to 65 mol m^?3 were used and within these there were two initial NO₃ ^? and K⁺ concentrations: high concentration (HC, 7.0 mol m^?3 and 2.6 mol m^?3 NO₃ ^? and K⁺ respectively) or low concentration (LC, 3.5 mol m^?3 and 1.3 mol m^?3 NO₃ ^? and K⁺ respectively). Plant NO₃ ^? uptake was negatively affected by NaCl concentration. NO₃ ^? maximum influx (I_max) declined from 5.1 µmol to 2.5 µmol per gram of plant dry weight per hour as NaCl concentration increased from zero to 65 mol m^?3. A modified Michaelis–Menten (M–M) equation taking into account inhibition by NaCl provided the best fit for NO₃ ^? uptake in response to varying NaCl concentration. K⁺ uptake was unaffected by NaCl concentration. A M–M equation that did not include inhibition was suitable for describing K⁺ uptake at varying NaCl concentration. The resulting empirical models could assist with decision making, such as: adjustment of NO₃ ^? fertilization based on NaCl concentration, necessity of water desalinization, or determination of the desired leaching fraction.     

Solution-based targeted genomic enrichment for precious DNA samples

ABSTRACT: BACKGROUND: Solution-based targeted genomic enrichment (TGE) protocols permit selective sequencing of genomic regions of interest on a massively parallel scale. These protocols could be improved by: 1) modifying or eliminating time consuming steps; 2) increasing yield to reduce input DNA and excessive PCR cycling; and 3) enhancing reproducible. RESULTS: We developed a solution-based TGE method for downstream Illumina sequencing in a non-automated workflow, adding standard Illumina barcode indexes during the post-hybridization amplification to allow for sample pooling prior to sequencing. The method utilizes Agilent SureSelect baits, primers and hybridization reagents for the capture, off-the-shelf reagents for the library preparation steps, and adaptor oligonucleotides for Illumina paired-end sequencing purchased directly from an oligonucleotide manufacturing company. CONCLUSIONS: This solution-based TGE method for Illumina sequencing is optimized for small- or medium-sized laboratories and addresses the weaknesses of standard protocols by reducing the amount of input DNA required, increasing capture yield, optimizing efficiency, and improving reproducibility.     

LOX-DB-- database on lipoxygenases

SUMMARY: Lipoxygenases are a family of enzymes involved in a variety of human diseases like inflammation, asthma, artherosclerosis and cancer. The lipoxygenases database (LOX-DB) aims to be a web accessible compendium of information in particular on the mammalian members of this multigene family. This resource includes molecular structures, reference data, tools for structural and computational analysis as well as links to related information maintained by others. The data can be retrieved by the use of various search options and analyzed applying publicly available visualization tools. AVAILABILITY: LOX-DB is available at http://www.dkfz-heidelberg.de/spec/lox-db/     

GLYCO-FRAGMENT: A web tool to support the interpretation of mass spectra of complex carbohydrates

Mass spectrometry is frequently used to analyze complex oligosaccharides and glycopeptides. The spectra of glycans can be complicated and difficult to interpret without reference data. Unfortunately, no libraries of suitably pure and homogeneous standards have so far been compiled. The web-based tool GLYCO-FRAGMENT allows the generation of all theoretically possible MS relevant fragments of oligosaccharides as defined using the extended IUPAC nomenclature. The main focus of GLYCO-FRAGMENT is to support the manual assignment of all peaks contained in mass spectra of complex carbohydrates. The service is available at http://www.dkfz.de/spec/projekte/fragments/.     

A coupled model of photosynthesis,stomatal conductance and transpiration for a rose leaf (Rosa hybrida L.)

The following three models were combined to predict simultaneously photosynthesis, stomatal conductance, transpiration and leaf temperature of a rose leaf: the biochemical model of photosynthesis of Farquhar, von Caemmerer and Berry (1980, Planta 149: 78-90), the stomatal conductance model of Ball, Woodrow and Berry (In: Biggens J, ed. Progress in photosynthesis research. The Netherlands: Martinus Nijhoff Publishers), and an energy balance model. The photosynthetic parameters: maximum carboxylation rate, potential rate of electron transport and rate of triose phosphate utilization, and their temperature dependence were determined using gas exchange data of fully expanded, young, sunlit leaves. The stomatal conductance model was calibrated independently. Prediction of net photosynthesis by the coupled model agreed well with the validation data, but the model tended to underestimate rates of stomatal conductance and transpiration. The coupled model developed in this study can be used to assist growers making environmental control decisions in glasshouse production.     

Tumor galectinology: insights into the complex network of a family of endogenous lectins

Beta-Galactosides of cell surface glycoconjugates are docking sites for endogenous lectins of the galectin family. In cancer cells, primarily galectins-1 and -3 have been studied to date. With the emergence of insights into their role in growth control, resistance to or induction of apoptosis and invasive behavior the notion is supported that they can be considered as functional tumor markers. In principle, the same might hold true for the other members of the galectin family. But their expression in tumors has hitherto been a subject of attention only to a very limited extent. Pursuing our concept to define the complexity of the galectin network in cancer cells and the degree of functional overlap/divergence with diagnostic/therapeutic implications, we have introduced comprehensive RT-PCR monitoring to map their galectin gene expression. The data on so far less appreciated galectins in this context such as galectins-4 and -8 vindicate this approach. They, too, attach value to extend the immunohistochemical panel accordingly. Our initial histopathological and cell biological studies, for example on colon cancer progression, prove the merit of this procedure. Aside from the detection of gene expression profiles by RT-PCR, the detailed molecular biological monitoring yielded further important information. We describe different levels of regulation of galectin production in colon cancer cells in the cases of the tandem-repeat-type galectins-8 and -9. Isoforms for them are present with insertions into the peptide linker sequence attributed to alternative splicing. Furthermore, variants with distinct amino acid substitutions (galectin-8, Po66-CBP, PCTA-1, CocaI/II and galectin-9/ecalectin) and generation of multiple mRNA species, notably those coding for truncated galectin-8 and -9 versions with only one lectin site, justify to portray these two family members not as distinct individuals but as groups. In aggregate, the ongoing work to thoroughly chart the galectin network and to disentangle the individual functional contributions is expected to make its mark on our understanding of the malignant phenotype in certain tumor types.     

Bioinformatics for glycomics: status, methods, requirements and perspectives

The term 'glycomics' describes the scientific attempt to identify and study all the glycan molecules - the glycome - synthesised by an organism. The aim is to create a cell-by-cell catalogue of glycosyltransferase expression and detected glycan structures. The current status of databases and bioinformatics tools, which are still in their infancy, is reviewed. The structures of glycans as secondary gene products cannot be easily predicted from the DNA sequence. Glycan sequences cannot be described by a simple linear one-letter code as each pair of monosaccharides can be linked in several ways and branched structures can be formed. Few of the bioinformatics algorithms developed for genomics/proteomics can be directly adapted for glycomics. The development of algorithms, which allow a rapid, automatic interpretation of mass spectra to identify glycan structures is currently the most active field of research. The lack of generally accepted ways to normalise glycan structures and exchange glycan formats hampers an efficient cross-linking and the automatic exchange of distributed data. The upcoming glycomics should accept that unrestricted dissemination of scientific data accelerates scientific findings and initiates a number of new initiatives to explore the data.