Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data

Next‐generation technologies generate an overwhelming amount of gene sequence data. Efficient annotation tools are required to make these data amenable to functional genomics analyses. The Mercator pipeline automatically assigns functional terms to protein or nucleotide sequences. It uses the MapMan ‘BIN’ ontology, which is tailored for functional annotation of plant ‘omics’ data. The classification procedure performs parallel sequence searches against reference databases, compiles the results and computes the most likely MapMan BINs for each query. In the current version, the pipeline relies on manually curated reference classifications originating from the three reference organisms (Arabidopsis, Chlamydomonas, rice), various other plant species that have a reviewed SwissProt annotation, and more than 2000 protein domain and family profiles at InterPro, CDD and KOG. Functional annotations predicted by Mercator achieve accuracies above 90% when benchmarked against manual annotation. In addition to mapping files for direct use in the visualization software MapMan, Mercator provides graphical overview charts, detailed annotation information in a convenient web browser interface and a MapMan‐to‐GO translation table to export results as GO terms. Mercator is available free of charge via http://mapman.gabipd.org/web/guest/app/Mercator .     

Expression pattern of XIRG, a marker for non-neural ectoderm

XIRG (for Xenopus IRG) was cloned by screening a cDNA library of UV-ventralized stage 13 Xenopus laevis embryos for specifically ventrally expressed mRNAs. Embryonic XIRG mRNA expression is restricted to non-neural ectoderm at the gastrula and neurula stages. In adult X. laevis, XIRG mRNA can be detected in skin and kidney. Extensive searches in nucleic acid and protein databases revealed homologous sequences in mouse, human and zebrafish. Mouse IRG1 mRNA is expressed in cultured macrophages as a response to bacterial lipopolysaccharide treatment. Received: 27 April 2000 / Accepted: 13 June 2000     

SWISS-PROT: connecting biomolecular knowledge via a protein database

With the explosive growth of biological data, the development of new means of data storage was needed. More and more often biological information is no longer published in the conventional way via a publication in a scientific journal, but only deposited into a database. In the last two decades these databases have become essential tools for researchers in biological sciences. Biological databases can be classified according to the type of information they contain. There are basically three types of sequence-related databases (nucleic acid sequences, protein sequences and protein tertiary structures) as well as various specialized data collections. It is important to provide the users of biomolecular databases with a degree of integration between these databases as by nature all of these databases are connected in a scientific sense and each one of them is an important piece to biological complexity. In this review we will highlight our effort in connecting biological information as demonstrated in the SWISS-PROT protein database.     

The protein identification resource (PIR)

The Protein Identification Resource consists of an integrated computer system composed of a number of protein and nucleic acid sequence databases and software designed for the identification and analysis of protein sequences and their corresponding coding sequences. The PIR serves the scientific community through on-line access, distributing magnetic tapes, and performing off-line sequence identification services for researchers.     

The protein identification resource (PIR).

The Protein Identification Resource, which provides the scientific community with an efficient on-line computer system designed for the identification and analysis of protein sequences and their corresponding coding sequences, has been established. The resource consists of an integrated computer system composed of a number of protein and nucleic acid sequence databases and the software necessary to analyze this information effectively.     

Recommendations for the presentation of NMR structures of proteins and nucleic acids – IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy

The recommendations presented here are designed to support easier communication of NMR data and NMR structures of proteins and nucleic acids through unified nomenclature and reporting standards. Much of this document pertains to the reporting of data in journal articles; however, in the interest of the future development of structural biology, it is desirable that the bulk of the reported information be stored in computer-accessible form and be freely accessible to the scientific community in standardized formats for data exchange. These recommendations stem from an IUPAC-IUBMB-IUPAB inter-union venture with the direct involvement of ICSU and CODATA. The Task Group has reviewed previous formal recommendations and has extended them in the light of more recent developments in the field of biomolecular NMR spectroscopy. Drafts of the recommendations presented here have been examined critically by more than 50 specialists in the field and have gone through two rounds of extensive modification to incorporate suggestions and criticisms.     

Model for the irreversible dissociation kinetics of cooperatively bound protein–nucleic acid complexes

We present a quantitative model for the irreversible dissociation kinetics of cooperatively bound nonspecific protein–nucleic acid complexes. The model assumes that the major pathway of dissociation is via singly contiguously bound protein that “peels” off the ends of clusters of bound protein. It should therefore be most applicable for proteins that bind nucleic acids with high cooperativity (w > 10³). Furthermore, the model assumes that no redistribution of bound protein occurs during the time course of the dissociation. Solutions to the rate equations are presented for the entire time course of the dissociation. Under initial conditions such that the nucleic acid is less than fully saturated with protein, a single-exponential decay is predicted (if w is large). However, when the nucleic acid lattice is initially fully saturated, zero-order kinetics, corresponding to a constant rate of protein dissociation, is predicted. The experimental observation of zero-order dissociation kinetics in a cooperative protein–nucleic acid system is a good qualitative indicator for the dissociation mechanism discussed here. A discussion of the analysis of experimental data that enables one to extract molecular rate constants is presented. Furthermore, comparisons are made between the nonredistributing model presented here and Epstein's model [Epstein, I. R. (1979) Biopolymers 18 , 2037–2050] in which protein can translocate infinitely quickly while bound to the nucleic acid, and hence protein clusters redistribute during dissociation and maintain an equilibrium distribution on the nucleic acid at all times.     

Origin of life: A hypothesis for the origin of adaptor-mediated ordered synthesis of proteins and an explanation for the choice of terminating codons in the genetic code

Life can be defined as a system of self-sustained chemical processes springing from the ordered synthesis of proteins directed by nucleic acids. To the notoriously difficult problem of the origin of this basic process of nucleic acid-directed protein synthesis, we give a solution of molecular interactions between pentanucleotides and amino acids. A particular conformation of a pentanucleotide forms a double sided template, with its ‘inside’ capable of nestling an amino acid while the ‘outside’ acts as an adaptor to a ‘codon’ triplet on long-chain nucleic acids. This serves as a primitive decoding system. An important aspect of our postulate is that a dynamic interaction is triggered, by this decoding system, through which amino acids are brought to juxtaposition facilitating peptide bond formation. Almost all the important and unique features of contemporary protein-synthesizing machinery are seen to be a direct and natural consequence of our postulate. The emergence of the termination codons also fits in, as a natural consequence of this molecular mechanism.     

Ethanol from sugarcane in Brazil: a ‘midway’ strategy for increasing ethanol production while maximizing environmental benefits

This article reviews the history and current state of ethanol production from sugarcane in Brazil and presents a strategy for improving ecosystem services and production. We propose that it is possible to produce ethanol from sugarcane while maintaining or even recovering some of Brazil's unique neotropical biodiversity and ecosystem climate services. This approach to the future of sustainable and responsible ethanol production is termed the ‘midway’ strategy. The ‘midway’ strategy involves producing the necessary biotechnology to increase productivity while synergistically protecting and regenerating rainforest. Three main areas of scientific and technological advance that are key to realizing the ‘midway’ strategy are: (i) improving the quality of scientific data on sugarcane biology as pertains to its use as a bioenergy crop; (ii) developing technologies for the use of bagasse for cellulosic ethanol; and (iii) developing policies to improve the ecosystem services associated with sugarcane landscapes. This article discusses these three issues in the general context of biofuels production and highlights examples of scientific achievements that are already leading towards the ‘midway’ strategy.     

Predicting species distributions from checklist data using site‐occupancy models

Aim (1) To increase awareness of the challenges induced by imperfect detection, which is a fundamental issue in species distribution modelling; (2) to emphasize the value of replicate observations for species distribution modelling; and (3) to show how ‘cheap’ checklist data in faunal/floral databases may be used for the rigorous modelling of distributions by site‐occupancy models. Location Switzerland. Methods We used checklist data collected by volunteers during 1999 and 2000 to analyse the distribution of the blue hawker, Aeshna cyanea (Odonata, Aeshnidae), a common dragonfly in Switzerland. We used data from repeated visits to 1‐ha pixels to derive ‘detection histories’ and apply site‐occupancy models to estimate the ‘true’ species distribution, i.e. corrected for imperfect detection. We modelled blue hawker distribution as a function of elevation and year and its detection probability of elevation, year and season. Results The best model contained cubic polynomial elevation effects for distribution and quadratic effects of elevation and season for detectability. We compared the site‐occupancy model with a conventional distribution model based on a generalized linear model, which assumes perfect detectability (p = 1). The conventional distribution map looked very different from the distribution map obtained using site‐occupancy models that accounted for the imperfect detection. The conventional model underestimated the species distribution by 60%, and the slope parameters of the occurrence–elevation relationship were also underestimated when assuming p = 1. Elevation was not only an important predictor of blue hawker occurrence, but also of the detection probability, with a bell‐shaped relationship. Furthermore, detectability increased over the season. The average detection probability was estimated at only 0.19 per survey. Main conclusions Conventional species distribution models do not model species distributions per se but rather the apparent distribution, i.e. an unknown proportion of species distributions. That unknown proportion is equivalent to detectability. Imperfect detection in conventional species distribution models yields underestimates of the extent of distributions and covariate effects that are biased towards zero. In addition, patterns in detectability will erroneously be ascribed to species distributions. In contrast, site‐occupancy models applied to replicated detection/non‐detection data offer a powerful framework for making inferences about species distributions corrected for imperfect detection. The use of ‘cheap’ checklist data greatly enhances the scope of applications of this useful class of models.     

两种品质类型花生品质形成与子叶细胞超微结构的关系

在大田条件下研究了两种品质类型花生(Arachis hypogaea)品质形成的动态差异及其子叶细胞超微结构的差异。结果表明, 高蛋白品种‘XB023’的蛋白质含量在籽仁发育前期较高油品种‘鲁花9号’低, 后期显著高于‘鲁花9号’, 且成熟期籽仁8种必需氨基酸组分含量均高于‘鲁花9号’, 其中谷氨酸、赖氨酸和亮氨酸含量差异极显著; ‘XB023’脂肪含量在籽仁发育期一直低于‘鲁花9号’。‘XB023’各时期的籽仁可溶性糖含量和油酸/亚油酸(O/L)值均显著低于‘鲁花9号’。两品种在果针入土10天时子叶细胞即形成淀粉粒、脂体和蛋白体, 随后脂体、蛋白体的数量不断增加, 淀粉粒先增大后逐渐缩小解体。‘XB023’的脂体达到最大的时间早于‘鲁花9号’, 而‘鲁花9号’的脂体快速积累的时间比‘XB023’长。两品种蛋白体大小都在果针入土40天时达到最大值, ‘XB023’的蛋白体在籽仁发育后期数量增加较快。高蛋白品种较高的蛋白质含量由其子叶细胞中较大蛋白体的大小和较多的蛋白体数量决定, 而高油品种较高的脂肪含量是由其较多的脂体数量决定。     

Molecular pathways linking non‐shivering thermogenesis and obesity: focusing on brown adipose tissue development

An increase in energy intake and/or a decrease in energy expenditure lead to fat storage, causing overweight and obesity phenotypes. The objective of this review was to analyse, for the first time using a systematic approach, all published evidence from the past 8 years regarding the molecular pathways linking non‐shivering thermogenesis and obesity in mammals, focusing on mechanisms involved in brown adipose tissue development. Two major databases were scanned from 2006 to 2013 using ‘brown adipose tissue’ AND ‘uncoupling protein‐1’ AND ‘mammalian thermoregulation’ AND ‘obesity’ as key words. A total of 61 articles were retrieved using the search criteria. The available research used knockout methodologies, various substances, molecules and agonist treatments, or different temperature and diet conditions, to assess the molecular pathways linking non‐shivering thermogenesis and obesity. By integrating the results of the evaluated animal and human studies, our analysis identified specific molecules that enhance non‐shivering thermogenesis and metabolism by: (i) stimulating ‘brite’ (brown‐like) cell development in white adipose tissue; (ii) increasing uncoupling protein‐1 expression in brite adipocytes; and (iii) augmenting brown and/or brite adipose tissue mass. The latter can be also increased through low temperature, hibernation and/or molecules involved in brown adipocyte differentiation. Cold stimuli and/or certain molecules activate uncoupling protein‐1 in the existing brown adipocytes, thus increasing total energy expenditure by a magnitude proportional to the number of available brown adipocytes. Future research should address the interplay between body mass, brown adipose tissue mass, as well as the main molecules involved in brite cell development.     

A novel nucleic acid-binding protein in the cyanobacterium Synechococcus sp. PCC6301: a soluble 33-kDa polypeptide with high sequence similarity to ribosomal protein S1

Cyanobacteria are prokaryotes that carry out plant-type photosynthesis and contain several eukaryotic-type RNA-binding proteins. Using a single-stranded DNA column, a 33-kDa protein was isolated and characterized from Synechococcus sp. PCC6301. This protein of 293 amino acids is similar in overall structure to the ribosomal protein S1 found in the same species, and contains three repeated units that are highly similar to the S1 motif originally found in the ribosomal protein S1 of Escherichia coli. However, the 33-kDa protein was found not to be associated with ribosomes and its nucleic acid binding specificity is distinct from that of the ribosomal protein S1. As this protein has high affinity for both single- and double-stranded DNA, as well as for poly(G) and poly(A), we tentatively named it nucleic acid-binding protein 1 (Nbp1). Received: 8 October 1999 / Accepted: 24 January 2000     

Sensitive detection of mycoplasmalike organisms in field-collected and in vitro propagated plants of Brassica, Hydrangea and Chrysanthemum by polymerase chain reaction

A polymerase chain reaction (PCR) protocol, previously designed for amplification of a DNA fragment from aster yellows mycoplasmalike organism (MLO), was employed to investigate the detection of MLO DNA in field-collected and in vitro micropropagated plants. PCR with template DNA extracted from symptomatic, naturally-infected samples of Brassica, Chrysanthemum and Hydrangea, each yielded a DNA band corresponding to 1.0 Kbp. However, no DNA product was observed when either infected Ranunculus (with phyllody disease) or Gladiolus with (symptoms of ‘germs fins’) was used as source of template nucleic acid for PCR; further experiments indicated absence of target DNA in the case of Ranunculus and the presence of substances in Gladiolus which inhibited the PCR. The MLO-specific DNA was detected by PCR using less than 95 pg of total nucleic acid (equivalent to total nucleic acid from 1.9, ug tissue) in the case of field-collected Hydrangea and less than 11.4 pg of nucleic acid (equivalent to total nucleic acid from 19 ng of tissue) in the case of field-collected Brassica. The findings illustrate highly sensitive detection of MLOs in both field-grown and in vitro micropropagated infected plants.     

Genome of ‘Charleston Gray’, the principal American watermelon cultivar,and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection

Years of selection for desirable fruit quality traits in dessert watermelon (Citrullus lanatus) has resulted in a narrow genetic base in modern cultivars. Development of novel genomic and genetic resources offers great potential to expand genetic diversity and improve important traits in watermelon. Here, we report a high‐quality genome sequence of watermelon cultivar ‘Charleston Gray’, a principal American dessert watermelon, to complement the existing reference genome from ‘97103’, an East Asian cultivar. Comparative analyses between genomes of ‘Charleston Gray’ and ‘97103’ revealed genomic variants that may underlie phenotypic differences between the two cultivars. We then genotyped 1365 watermelon plant introduction (PI) lines maintained at the U.S. National Plant Germplasm System using genotyping‐by‐sequencing (GBS). These PI lines were collected throughout the world and belong to three Citrullus species, C. lanatus, C. mucosospermus and C. amarus. Approximately 25 000 high‐quality single nucleotide polymorphisms (SNPs) were derived from the GBS data using the ‘Charleston Gray’ genome as the reference. Population genomic analyses using these SNPs discovered a close relationship between C. lanatus and C. mucosospermus and identified four major groups in these two species correlated to their geographic locations. Citrullus amarus was found to have a distinct genetic makeup compared to C. lanatus and C. mucosospermus. The SNPs also enabled identification of genomic regions associated with important fruit quality and disease resistance traits through genome‐wide association studies. The high‐quality ‘Charleston Gray’ genome and the genotyping data of this large collection of watermelon accessions provide valuable resources for facilitating watermelon research, breeding and improvement.     

PROPHET, a national computing resource for life science research.

PROPHET is a national computing resource tailored to meet the data management and analysis needs of life scientists working in a wide variety of disciplines, ranging from pharmacology to molecular biology. The PROPHET system offers a fully integrated graphics-oriented environment designed to aid research scientists in the manipulation and analysis of scientific spreadsheets of data, graphs, molecular structures, biological simulation models, and protein and nucleic acid sequences, and it includes access to a range of molecular structure and sequence databases. This paper briefly describes the PROPHET system, some of its current capabilities, and plans for a new fully distributed version of the system now under development.     

The Hirsch-index: a simple, new tool for the assessment of scientific output of individual scientists

In this brief paper we explore the Hirsch-index together with a couple of other bibliometric parameters for the assessment of the scientific output of 29 Dutch professors in clinical cardiology. It appears that even within such a homogeneous group there is large interindividual variability. Although the differences are quite remarkable, it remains undetermined what they mean; at least it is premature to interpret them as differences in scientific quality. It goes without saying that even more prudence is required when different fields of medicine and life sciences are compared (for example within University Medical Centres). Recent efforts to produce an amalgam of scientific ‘productivity’, ‘relevance’ and ‘viability’ as a surrogate parameter for the assessment of scientific quality, as for example performed in the AMC in Amsterdam, should be discouraged in the absence of a firm scientific base. Unfortunately for politicians and ‘managers of science’ only reading papers and studying are suitable for quality assessment of scientific output. Citations analyses can't substitute that. (Neth Heart J 2009;17:145–54.)     

‘Caged’ peptide nucleic acids activated by red light in a singlet oxygen mediated process

Common ‘caged’ nucleic acid binders, which can be applied for temporal and spatial control of gene expression, are activated by high energy light (<450 nm). The light of this type is damaging to cells and is strongly absorbed by cellular components. Therefore, shifting the triggering light to the visible region (>550 nm) is highly desirable. Herein we report on a cyclic peptide nucleic acid (PNA), whose backbone contains a 9,10-dialkoxy-substituted anthracene linker. The sequence of this compound was selected to be complementary to a representative microRNA (miR-92). We demonstrated that the cyclic PNA does not bind complementary nucleic acids and is, correspondingly, ‘caged’. Its uncaging can be conducted by its exposure to red light (635 nm) in the presence of pyropheophorbide-a. The latter process is mediated by singlet oxygen (¹O₂), which cleaves the 9,10-dialcoxyanthracene linker within the PNA with formation of a linear PNA, an efficient binder of the complementary ribonucleic acid. This is the first example of a red light-activated, ‘caged’ peptide nucleic acid.     

ACTION OF THE NEUROTOXIN KAINIC ACID ON HIGH AFFINITY UPTAKE OF l-GLUTAMIC ACID IN RAT BRAIN SLICES

Kainic acid is a linear competitive inhibitor (K_is 250 μm ) of the ‘high affinity’ uptake of l -glutamic acid into rat brain slices. Kainic acid inhibits the ‘high affinity’ uptake of l -glutamic, d -aspartic and l -aspartic acids to a similar extent. Kainic acid is not actively taken up into rat brain slices and is thus not a substrate for the ‘high affinity’ acidic amino acid transport system or any other transport system in rat brain slices. Kainic acid (300 μm ) does not influence the steady-state release or potassium-stimulated release of preloaded d -aspartic acid from rat brain slices. Kainic acid binds to rat brain membranes in the absence of sodium ions in a manner indicating binding to a population of receptor sites for l -glutamic acid. Only quisqualic and l -glutamic acid inhibit kainic acid binding in a potent manner. The affinity of kainic acid for these receptor sites appears to be some 4 orders of magnitude higher than for the ‘high affinity’l -glutamic acid transport carrier. Dihydrokainic acid is approximately twice as potent as kainic acid as an inhibitor of ‘high affinity’l -glutamic acid uptake but is some 500 times less potent as an inhibitor of kainic acid binding and at least 1000 times less potent as a convulsant of immature rats on intraperitoneal injection. Dihydrokainic acid might be useful as a ‘control uptake inhibitor’ for the effects of kainic acid on ‘high affinity’l -glutamic acid uptake since it appears to have little action on excitatory receptors. N-Methyl-d -aspartic acid is a potent convulsant of immature rats, but does not inhibit kainic acid binding or ‘high affinity’l -glutamic acid uptake. N-Methyl-d -aspartic acid might be useful as a ‘control excitant’ that activates different excitatory receptors to kainic acid and does not influence ‘high affinity’l -glutamic acid uptake.