bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomics study of inverted repeats in bacteria
Authors: Lillo Fabrizio , Basile Salvatore , Mantegna Rosario N. 
Published: July 2002

Abstract
Motivation: Comparative genomics provides a powerful way to investigate regularities and differences observed at DNA level across species. Here we study the number and location of inverted repeats occurring in complete genomes of bacteria. Inverted repeats are compatible with the formation of hairpin structures in the messenger RNA. Some of these structures are known to be rho-independent intrinsic terminators.
Results: We investigate the number of inverted repeats observed in 37 complete genomes of bacteria. The number of inverted repeats observed is much higher than expected using Markovian models of DNA sequences in most of the eubacteria. By using the information annotated in the genomes we discover that in most of the eubacteria the inverted repeats of stem length longer than 8 nucleotides preferentially locate near the 3′ end of the nearest coding regions. We also show that IRs characterized by large values of the stem length locate preferentially in short non-coding regions bounded by two 3′ ends of convergent genes. By using the program TransTerm recently introduced to predict transcription terminators in bacterial genomes, we conclude that only a part of the observed inverted repeats fullfils the model requirements characterizing rho-independent termination in several genomes.
Availability: http://lagash.dft.unipa.it/IR.html
Contact: mantegna@unipa.it
CX, an algorithm that identifies protruding atoms in proteins
Authors: Pintar Alessandro , Carugo Oliviero , Pongor Sándor 
Published: July 2002

Abstract
Motivation: A simple and fast algorithm is described that calculates a measure of protrusion (cx) for atoms in protein structures, directly useable with the common molecular graphics programs.
Results: A sphere of predetermined radius is centered around each non-hydrogen atom, and the volume occupied by the protein and the free volume within the sphere (internal and external volumes, respectively) are calculated. Atoms in protruding regions have a high ratio (cx) between the external and the internal volume. The program reads a PDB file, and writes the output in the same format, with cx values in the B factor field. Output structure files can be directly displayed with standard molecular graphics programs like RASMOL, MOLMOL, Swiss-PDB Viewer and colored according to cx values. We show the potential use of this program in the analysis of two protein–protein complexes and in the prediction of limited proteolysis sites in native proteins.
Availability: The algorithm is implemented in a standalone program written in C and its source is freely available at ftp.icgeb.trieste.it/pub/CX or on request from the authors.
Contact: pintar@icgeb.trieste.it; carugo@icgeb.trieste.it; pongor@icgeb.trieste.it
* To whom correspondence should be addressed.
Calculations of protein volumes: sensitivity analysis and
parameter database
Authors: Tsai Jerry , Gerstein Mark 
Published: July 2002

Abstract
Motivation: The precise sizes of protein atoms in terms of occupied packing volume are of great importance. We have previously presented standard volumes for protein residues based on calculations with Voronoi-like polyhedra. To understand the applicability and limitations of our set, we investigated, in detail, the sensitivity of the volume calculations to a number of factors: (i) the van der Waals radii set, (ii) the criteria for including buried atoms in the calculations or atom selection, (iii) the method of positioning the dividing plane in polyhedra construction, and (iv) the set of structures used in the averaging.
Results: We find that different radii sets have only moderate affects to the distribution and mean of volumes. Atom selection and dividing plane methods cause larger changes in protein atoms volumes. More significantly, we show how the variation in volumes appears to be clearly related to the quality of the structures analyzed, with higher quality structures giving consistently smaller average volumes with less variance.
Availability/Supplementary Information: Programs and associated data files are available from http://bioinfo.mbb.yale.edu/geometry and http://molmovdb.org. In particular, we make available an extensive database of many different sets of protein geometric parameters.
Contact: JerryTsai@TAMU.edu; Mark.Gerstein@Yale.edu
* To whom correspondence should be addressed.
The Role of Ethylene and Wound Signaling in Resistance of Tomato to Botrytis cinerea
Authors: Dı́az José , ten Have Arjen , van Kan Jan A.L. 
Published: July 2002

Abstract
Ethylene, jasmonate, and salicylate play important roles in plant defense responses to pathogens. To investigate the contributions of these compounds in resistance of tomato (Lycopersicon esculentum) to the fungal pathogen Botrytis cinerea, three types of experiments were conducted: (a) quantitative disease assays with plants pretreated with ethylene, inhibitors of ethylene perception, or salicylate; (b) quantitative disease assays with mutants or transgenes affected in the production of or the response to either ethylene or jasmonate; and (c) expression analysis of defense-related genes before and after inoculation of plants with B. cinerea. Plants pretreated with ethylene showed a decreased susceptibility toward B. cinerea, whereas pretreatment with 1-methylcyclopropene, an inhibitor of ethylene perception, resulted in increased susceptibility. Ethylene pretreatment induced expression of several pathogenesis-related protein genes before B. cinerea infection. Proteinase inhibitor I expression was repressed by ethylene and induced by 1-methylcyclopropene. Ethylene also induced resistance in the mutantNever ripe. RNA analysis showed that Never ripe retained some ethylene sensitivity. The mutantEpinastic, constitutively activated in a subset of ethylene responses, and a transgenic line producing negligible ethylene were also tested. The results confirmed that ethylene responses are important for resistance of tomato to B. cinerea. The mutant Defenseless, impaired in jasmonate biosynthesis, showed increased susceptibility to B. cinerea. A transgenic line with reduced prosystemin expression showed similar susceptibility as Defenseless, whereas a prosystemin-overexpressing transgene was highly resistant. Ethylene and wound signaling acted independently on resistance. Salicylate and ethylene acted synergistically on defense gene expression, but antagonistically on resistance.
PROLIFERATING INFLORESCENCE MERISTEM, a MADS-Box Gene That Regulates Floral Meristem Identity in Pea
Authors: Taylor Scott A. , Hofer Julie M.I. , Murfet Ian C. , Sollinger John D. , Singer Susan R. , Knox Maggie R. , Ellis T.H. Noel 
Published: July 2002

Abstract
SQUAMOSA and APETALA1 are floral meristem identity genes from snapdragon (Antirrhinum majus) and Arabidopsis, respectively. Here, we characterize the floral meristem identity mutation proliferating inflorescence meristem(pim) from pea (Pisum sativum) and show that it corresponds to a defect in the PEAM4 gene, a homolog of SQUAMOSA and APETALA1. ThePEAM4 coding region was deleted in thepim-1 allele, and this deletion cosegregated with thepim-1 mutant phenotype. The pim-2 allele carried a nucleotide substitution at a predicted 5′ splice site that resulted in mis-splicing of pim-2 mRNA. PCR products corresponding to unspliced and exon-skipped mRNA species were observed. The pim-1 and pim-2 mutations delayed floral meristem specification and altered floral morphology significantly but had no observable effect on vegetative development. These floral-specific mutant phenotypes and the restriction ofPIM gene expression to flowers contrast with other known floral meristem genes in pea that additionally affect vegetative development. The identification of PIM provides an opportunity to compare pathways to flowering in species with different inflorescence architectures.
The Effects of Abiotic Factors on Induced Volatile Emissions in Corn Plants
Authors: Gouinguené Sandrine P. , Turlings Ted C.J. 
Published: July 2002

Abstract
Many plants respond to herbivory by releasing a specific blend of volatiles that is attractive to natural enemies of the herbivores. In corn (Zea mays), this induced odor blend is mainly composed of terpenoids and indole. The induced signal varies with plant species and genotype, but little is known about the variation due to abiotic factors. Here, we tested the effect of soil humidity, air humidity, temperature, light, and fertilization rate on the emission of induced volatiles in young corn plants. Each factor was tested separately under constant conditions for the other factors. Plants released more when standing in dry soil than in wet soil, whereas for air humidity, the optimal release was found at around 60% relative humidity. Temperatures between 22°C and 27°C led to a higher emission than lower or higher temperatures. Light intensity had a dramatic effect. The emission of volatiles did not occur in the dark and increased steadily with an increase in the light intensity. An experiment with an unnatural light-dark cycle showed that the release was fully photophase dependent. Fertilization also had a strong positive effect; the emission of volatiles was minimal when plants were grown under low nutrition, even when results were corrected for plant biomass. Changes in all abiotic factors caused small but significant changes in the relative ratios among the different compounds (quality) in the induced odor blends, except for air humidity. Hence, climatic conditions and nutrient availability can be important factors in determining the intensity and variability in the release of induced plant volatiles.
Arabidopsis Map-Based Cloning in the Post-Genome Era
Authors: Jander Georg , Norris Susan R. , Rounsley Steven D. , Bush David F. , Levin Irena M. , Last Robert L. 
Published: July 2002

Abstract
Map-based cloning is an iterative approach that identifies the underlying genetic cause of a mutant phenotype. The major strength of this approach is the ability to tap into a nearly unlimited resource of natural and induced genetic variation without prior assumptions or knowledge of specific genes. One begins with an interesting mutant and allows plant biology to reveal what gene or genes are involved. Three major advances in the past 2 years have made map-based cloning in Arabidopsis fairly routine: sequencing of the Arabidopsis genome, the availability of more than 50,000 markers in the Cereon Arabidopsis Polymorphism Collection, and improvements in the methods used for detecting DNA polymorphisms. Here, we describe the Cereon Collection and show how it can be used in a generic approach to mutation mapping in Arabidopsis. We present the map-based cloning of theVTC2 gene as a specific example of this approach.
RASPBERRY3Gene Encodes a Novel Protein Important for Embryo Development
Authors: Apuya Nestor R. , Yadegari Ramin , Fischer Robert L. , Harada John J. , Goldberg Robert B. 
Published: July 2002

AbstractWe identified a new gene that is interrupted by T-DNA in an Arabidopsis embryo mutant called raspberry3. raspberry3 has “raspberry-like” cellular protuberances with an enlarged suspensor characteristic of otherraspberry embryo mutants, and is arrested morphologically at the globular stage of embryo development. The predicted RASPBERRY3 protein has domains found in proteins present in prokaryotes and algae chloroplasts. Computer prediction analysis suggests that the RASPBERRY3protein may be localized in the chloroplast. Complementation analysis supports the possibility that the RASPBERRY3 protein may be involved in chloroplast development. Our experiments demonstrate the important role of the chloroplast, directly or indirectly, in embryo morphogenesis and development.
Molecular and Physiological Analysis of Arabidopsis Mutants Defective in Cytosolic or Chloroplastic Aspartate Aminotransferase
Authors: Miesak Barbara H. , Coruzzi Gloria M. 
Published: July 2002

Abstract
Arabidopsis mutants deficient in cytosolic (AAT2) or chloroplastic (AAT3) aspartate (Asp) aminotransferase were characterized at the molecular and physiological levels. All of the ethyl methane sulfonate- or nitrosomethylurea-generated mutants are missense mutations, as determined by sequencing of theASP2 gene from the cytosolic aat2 mutants (aat2-1, aat2-2, aat2-4, and aat2-5) and the ASP5 gene from the chloroplastic aat3 mutants (aat3-1,aat3-2, and aat3-4). A T-DNA insertion mutant in cytosolic AAT2 (aat2-T) was also identified. All the cytosolic aat2 and chloroplasticaat3 mutants have less than 6% AAT2 and less than 3% AAT3 activity, respectively, as determined by the native gel assay; however, none are nulls. The metabolic and physiological affect of these mutations in AAT isoenzymes was determined by measuring growth and amino acid levels in the aat mutants. Twoaat2 mutants (aat2-2 andaat2-T) show reduced root length on Murashige and Skoog medium. For aat2-2, this growth defect is exaggerated by Asp supplementation, suggesting a defect in Asp metabolism. Amino acid analysis of the aat mutants showed alterations in levels of Asp and/or Asp-derived amino acids in several aat2alleles. Two aat2 mutants show dramatic decreases in Asp and asparagine levels in leaves and/or siliques. As such, the cytosolic AAT2 isoenzyme appears to serve a nonredundant function in plant nitrogen metabolism of Asp and Asp-derived amino acids.
Arabidopsis Mutants Deficient in Diacylglycerol Acyltransferase Display Increased Sensitivity to Abscisic Acid, Sugars, and Osmotic Stress during Germination and Seedling Development
Authors: Lu Chaofu , Hills Matthew J. 
Published: July 2002

Abstract
Arabidopsis seeds store triacylglycerol (TAG) as the major carbon reserve, which is used to support postgerminative seedling growth. Diacylglycerol acyltransferase (DGAT) catalyzes the final step in TAG synthesis, and two isoforms of DGAT have previously been identified in Arabidopsis. It has been shown that DGAT1 plays an important role in seed development because Arabidopsis with mutations at the TAG1 locus accumulate less seed oil. There is also evidence showing that DGAT1 is active after seed germination. The aim of this study is to investigate the effect of mutations of DGAT1 on postembryonic development in Arabidopsis. We carried out detailed analyses of two tag1 mutants in different ecotypic backgrounds of Arabidopsis. Results show that during germination and seedling growth, seed storage TAG degradation was not affected in thetag1 mutants. However, sugar content of the mutant seedlings is altered, and activities of the hexokinases are significantly increased in the tag1 mutant seedlings. The tag1 mutants are also more sensitive to abscisic acid, glucose, and osmotic strength of the medium in germination and seedling growth.
Effect of Short-Term N2 Deficiency on Expression of the Ureide Pathway in Cowpea Root Nodules
Authors: Smith Penelope M.C. , Winter Heike , Storer Paul J. , Bussell John D. , Schuller Kathryn A. , Atkins Craig A. 
Published: July 2002

Abstract
Root systems of 28-d-old cowpea (Vigna unguiculata L. Walp cv Vita 3: Bradyrhizobiumsp. strain CB756) plants bearing nitrogen-fixing nodules in sand culture were exposed to an atmosphere of Ar:O2 (80:20, v/v) for 48 h and then returned to air. Root systems of control plants were maintained in air throughout. Nodules were harvested at the same times in control and Ar:O2-treated root systems. Activities of two enzymes of de novo purine synthesis, glycinamide ribonucleotide transformylase (GART; EC 2.1.2.2), aminoimidazole ribonucleotide synthetase (AIRS; EC 6.3.3.1), uricase (EC 1.7.3.3), and phosphoenolpyruvate carboxylase (PEPC; EC 4.1.1.31) were measured together with the protein level of each using immune-specific polyclonal antibodies. AIRS activity and protein both declined to very low levels within 6 h in Ar:O2 together with a decline in transcript level of pur5, the encoding gene. GART activity, protein, and transcript (pur3) levels were relatively stable. Uricase activity declined in Ar:O2 as rapidly as AIRS activity but the protein was stable. PEPC activity showed evidence of increased sensitivity to inhibition by malate but the protein level was stable. The data indicate that the flux of fixed N from bacteroids (N2-fixing nodule bacteria) is in some way associated with transcriptional control over pur5and possibly also catabolism of AIRS protein. In contrast, there is limited posttranslational control over GART and PEPC and close posttranslational control over uricase activity. The significance of these different levels of regulation is discussed in relation to the overall control of enhanced expression of plant enzymes in the cowpea symbiosis.
Signals Involved in Arabidopsis Resistance toTrichoplusia ni Caterpillars Induced by Virulent and Avirulent Strains of the Phytopathogen Pseudomonas syringae
Authors: Cui Jianping , Jander Georg , Racki Lisa R. , Kim Paul D. , Pierce Naomi E. , Ausubel Frederick M. 
Published: July 2002

Abstract
Plants have evolved different but interconnected strategies to defend themselves against herbivorous insects and microbial pathogens. We used an Arabidopsis/Pseudomonas syringaepathosystem to investigate the impact of pathogen-induced defense responses on cabbage looper (Trichoplusia ni) larval feeding. Arabidopsis mutants [npr1,pad4, eds5, andsid2(eds16)] or transgenic plants (nahG) that are more susceptible to microbial pathogens and are compromised in salicylic acid (SA)-dependent defense responses exhibited reduced levels of feeding by T. ni compared with wild-type plants. Consistent with these results, Arabidopsis mutants that are more resistant to microbial pathogens and have elevated levels of SA (cpr1 and cpr6) exhibited enhanced levels of T. ni feeding. These experiments suggested an inverse relationship between an active SA defense pathway and insect feeding. In contrast to these results, there was increased resistance toT. ni in wild-type Arabidopsis ecotype Columbia plants that were infected with P. syringae pv.maculicola strain ES4326 (Psm ES4326) expressing the avirulence genes avrRpt2 oravrB, which elicit a hypersensitive response, high levels of SA accumulation, and systemic acquired resistance to bacterial infection. Similar results were obtained with other ecotypes, including Landsberg erecta, Cape Verdi Islands, and Shakdara. When infected with PsmES4326(avrRpt2) or PsmES4326(avrB), nahG transgenic andnpr1 mutant plants (which are more susceptible to virulent and avirulent P. syringae strains) failed to show the increased insect resistance exhibited by wild-type plants. It was surprising that wild-type plants, as well as nahGand npr1 plants, infected with Psm ES4326 not expressing avrRpt2 or avrB, which elicits disease, became more susceptible to T. ni. Our results suggest two potentially novel systemic signaling pathways: a systemic response elicited by HR that leads to enhanced T. ni resistance and overrides the SA-mediated increase in T. ni susceptibility, and a SA-independent systemic response induced by virulent pathogens that leads to enhanced susceptibility to T. ni.
Selective Activation of the Developmentally Regulated Ha hsp17.6 G1 Promoter by Heat Stress Transcription Factors
Authors: Rojas Anabel , Almoguera Concepción , Carranco Raúl , Scharf Klaus-Dieter , Jordano Juan 
Published: July 2002

Abstract
Using two well-characterized heat stress transcription factors (Hsfs) from tomato (Lycopersicon peruvianum; LpHsfA1 and LpHsfA2), we analyzed the transcriptional activation of theHa hsp17.6 G1 promoter in sunflower (Helianthus annuus) embryos. In this system, we observed transient promoter activation only with LpHsfA2. In contrast, both factors were able to activate mutant versions of the promoter with improved consensus Hsf-binding sites. Exclusive activation by LpHsfA2 was also observed in yeast (Saccharomyces cerevisiae) without other Hsfs and with a minimal Cyc1 promoter fused to theHa hsp17.6 G1 heat stress cis-element. Furthermore, the same promoter mutations reproduced the loss of activation selectivity, as observed in sunflower embryos. The results of in vitro binding experiments rule out differential DNA binding of the two factors as the explanation for the observed differential activation capacity. We conclude that the specific sequence of this heat stress cis-element is crucial for Hsf promoter selectivity, and that this selectivity could involve preferential transcriptional activation following DNA binding. In sunflower embryos, we also observed synergistic transcriptional activation by co-expression of LpHsfA1 and LpHsfA2. Mutational analyses of the Ha hsp17.6 G1 promoter, combined with in vitro binding assays, suggest that mixed oligomers of the two factors may be involved in promoter activation. We discuss the relevance of our observations for mechanisms of developmental regulation of plant heat stress protein genes.
The Liverwort Contains a Lectin That Is Structurally and Evolutionary Related to the Monocot Mannose-Binding Lectins
Authors: Peumans Willy J. , Barre Annick , Bras Julien , Rougé Pierre , Proost Paul , Van Damme Els J.M. 
Published: July 2002

Abstract
A mannose (Man)-binding lectin has been isolated and characterized from the thallus of the liverwort Marchantia polymorpha. N-terminal sequencing indicated that the M. polymorpha agglutinin (Marpola) shares sequence similarity with the superfamily of monocot Man-binding lectins. Searches in the databases yielded expressed sequence tags encoding Marpola. Sequence analysis, molecular modeling, and docking experiments revealed striking structural similarities between Marpola and the monocot Man-binding lectins. Activity and specificity studies further indicated that Marpola is a much stronger agglutinin than the Galanthus nivalis agglutinin and exhibits a preference for methylated Man and glucose, which is unprecedented within the family of monocot Man-binding lectins. The discovery of Marpola allows us, for the first time, to corroborate the evolutionary relationship between a lectin from a lower plant and a well-established lectin family from flowering plants. In addition, the identification of Marpola sheds a new light on the molecular evolution of the superfamily of monocot Man-binding lectins. Beside evolutionary considerations, the occurrence of aG. nivalis agglutinin homolog in a lower plant necessitates the rethinking of the physiological role of the whole family of monocot Man-binding lectins.