bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional profiling of microarray experiments using text-mining derived bioentities
Authors: Minguez Pablo , Al-Shahrour Fátima , Montaner David , Dopazo Joaquín 
Published: September 2007

AbstractMotivation: The increasing use of microarray technologies brought about a parallel demand in methods for the functional interpretation of the results. Beyond the conventional functional annotations for genes, such as gene ontology, pathways, etc. other sources of information are still to be exploited. Text-mining methods allow extracting informative terms (bioentities) with different functional, chemical, clinical, etc. meanings, that can be associated to genes. We show how to use these associations within an appropriate statistical framework and how to apply them through easy-to-use, web-based environments to the functional interpretation of microarray experiments. Functional enrichment and gene set enrichment tests using bioentities are presented.Availability: Marmite and MarmiteScan can be found in the Babelomics suite: http://www.babelomics.orgContact: jdopazo@cipf.esSupplementary information: Supplementary data are available at Bioinformatics online.
Evaluations of New and Current Management Strategies to Control Phomopsis Cane and Leaf Spot of Grape
Authors: Nita Mizuho , Ellis Michael A. , Wilson Leslie L. , Madden Laurence V. 
Published: September 2007

To extend our understanding of the epidemiology and control of Phomopsis cane and leaf spot of grape, caused by Phomopsis viticola, studies were conducted to: (i) determine efficacy of a dormant fungicide spray program for controlling the disease in its early stage of development (e.g., spring); (ii) evaluate a disease warning system by applying fungicides and fungicide-adjuvant combinations in response to predicted infection periods based on weather conditions; and (iii) correlate commercial control practices and environmental conditions with disease incidence based on a state-wide survey of commercial fields. With the warning system, control was equal to that obtained with a 7-day protectant fungicide program, but with fewer fungicide applications per season. A dormant application provided consistent, yet only moderate, control of the disease. Growers who applied a dormant-season application or early spring protectant fungicides tended to have lower disease incidence than those who did not. There was high variability in disease incidence within vineyards and farms, but no significant difference in incidence among regions of the state. Overall, early season application of protective fungicides was shown to be a key factor for successful management of P. viticola. Accepted for publication 29 March 2007. Published 26 July 2007.
Spatiotemporal Spread of Potato virus S and Potato virus X in Seed Potato in Tasmania, Australia
Authors: Lambert Susan J. , Hay Frank S. , Pethybridge Sarah J. , Wilson Calum R. 
Published: September 2007

The spatial and temporal distribution of Potato virus S (PVS) and Potato virus X (PVX) was studied in two trials within each of four commercial fields of seed potato var. Russet Burbank in Tasmania, Australia. In the first trial (plots) 20 leaflets were collected from each of 49 plots (each approximately 8 m wide by 10 m long), with plots arranged in a 7-×-7 lattice. In the second trial (transects), leaflets were collected at 1-m intervals along seven adjacent, 50-m long rows. The mean incidence of PVS increased during the season by 5.2% in one of four plot trials and 25.5% in one of four transect trials. The mean incidence of PVX increased during the season by 10.1%, in one of two transect trials. Spatial Analysis by Distance IndicEs and ordinary runs analysis detected aggregation of PVS infected plants early in the season in one and two fields respectively, suggesting transmission during seed-cutting or during planting. An increase in PVS incidence mid- to late season in one field was associated with aggregation of PVS along, but not across rows, which may be related to the closer plant spacing within rows and hence increased potential for mechanical transmission along rows. Results suggested limited spread of PVS and PVX occurred within crops during the season. Accepted for publication 9 April 2007. Published 26 July 2007.
High Recovery Rate of Phytophthora from Containerized Nursery Stock Pots at a Retail Nursery Highlights Potential For Spreading Exotic Oomycetes
Authors: Dart Norman L. , Chastagner Gary A. 
Published: September 2007

Containerized nursery stock asymptomatic for Phytophthora leaf, stem and root diseases were sampled from a nursery in western Washington state directly over areas soil tested positive for Phytophthora ramorum during nursery surveys conducted. Phytophthora was recovered from the soil collected below 90% of the containerized plant pots. The study underscores the potential for exotic and endemic Oomycetes to be transported on asymptomatic nursery stock. Accepted for publication 9 April 2007. Published 16 August 2007.
Evaluation of Phytophthora ramorum in Nursery Crop Tissue Culture Propagation
Authors: Linderman Robert G. , Davis E. Anne 
Published: September 2007

Phytophthora ramorum, cause of Ramorum blight on numerous woody ornamental shrubs, is a regulated pathogen in the US and internationally. Currently, nurseries are inspected to detect infected plants; however, many plants are propagated by tissue culture nurseries and the behavior of P. ramorum in this system is unknown. Pathogen growth and sporulation in propagation vessels containing different multiplication and rooting media, with a range of plants and without plants, was evaluated with regard to pathogen visibility and induction of disease symptoms. Within 2 weeks, the pathogen colonies were visible to the naked eye on all 26 multiplication media and on 9 of 11 rooting media tested (without plants). The appearance of colonies on different media was variable and no sporangia but occasional chlamydospores were produced. The pathogen growth was very visible on multiplication media containing susceptible plants, inoculated plants exhibiting obvious discoloration and mortality. The pathogen was reisolated from terminal shoot tissue and roots of symptomatic plants. Variability occurred in susceptibility of different cultivars of a plant species, in virulence of the two isolates of the pathogen, and in recovery from shoot tissue. We conclude that fungal growth on the media, with or without plants, and symptoms of disease were apparent enough that contaminated vessels would be destroyed. Accepted for publication 9 April 2007. Published 22 August 2007.
Plant Pathogens at Work: Improving Weed Control Efficacy
Authors: Yandoc-Ables C. B. , Rosskopf E. N. , Charudattan R. 
Published: September 2007

Research in the area of the use of plant pathogens as biological control agents for weeds is conducted using either the classical or the bioherbicidal approach. In the classical approach, a pathogen is typically imported from a foreign location to control an introduced weed target. In the inundative or bioherbicide strategy, an indigenous pathogen is cultured to produce large quantities of inoculum that are applied at high rates to the entire target weed population. Research on the development of plant pathogens for biological control using the inundative or bioherbicide approach has moved from determining host range and demonstrating pathogenicity to investigating systems that enhance the efficacy of these agents. Accepted for publication 9 April 2007. Published 22 August 2007.
Citrus Huanglongbing: The Pathogen and Its Impact
Authors: Gottwald Tim R. , Graça John V. da , Bassanezi Renato B. 
Published: September 2007

Citrus Huanglongbing, aka greening disease, has been the subject of several reviews in recent years. In this article, the author presents a concise compilation of the main features and symptoms of the disease, the causal organisms and the vectors including impacts for Florida and Brazil, two relatively new areas where the disease has been discovered, as well as implications for California, Texas, and Arizona citrus industries, which are threatened by the close proximity to the new Florida epidemic, and the rest of the western hemisphere. Accepted for publication 19 June 2007. Published 6 September 2007.
The cell wall: a carbohydrate armour for the fungal cell
Authors: Latgé Jean‐Paul 
Published: September 2007

SummaryThe cell wall is composed of a polysaccharide‐based three‐dimensional network. Considered for a long time as an inert exoskeleton, the cell wall is now seen as a dynamic structure that is continuously changing as a result of the modification of culture conditions and environmental stresses. Although the cell wall composition varies among fungal species, chemogenomic comparative analysis have led to a better understanding of the genes and mechanisms involved in the construction of the common central core composed of branched β1,3 glucan‐chitin. Because of its essential biological role, unique biochemistry and structural organization and the absence in mammalian cells of most of its constitutive components, the cell wall is an attractive target for the development of new antifungal agents. Genomic as well as drug studies have shown that the death of the fungus can result from inhibition of cell wall polysaccharide synthases. To date, only β1,3 glucan synthase inhibitors have been launched clinically and many more targets remain to be explored.
Sucrose metabolism contributes to in vivo fitness of Streptococcus pneumoniae
Authors: Iyer Ramkumar , Camilli Andrew 
Published: September 2007

SummaryWe characterized two sucrose‐metabolizing systems –sus and scr– and describe their roles in the physiology and virulence of Streptococcus pneumoniae in murine models of carriage and pneumonia. The sus and scr systems are regulated by LacI family repressors SusR and ScrR respectively. SusR regulates an adjacent ABC transporter (susT1/susT2/susX) and sucrose‐6‐phosphate (S‐6‐P) hydrolase (susH). ScrR controls an adjacent PTS transporter (scrT), fructokinase (scrK) and second S‐6‐P hydrolase (scrH). sus and scr play niche‐specific roles in virulence. The susH and sus locus mutants are attenuated in the lung, but dispensable in nasopharyngeal carriage. Conversely, the scrH and scr locus mutants, while dispensable in the lung, are attenuated for nasopharyngeal colonization. The scrH/susH double mutant is more attenuated than scrH in the nasopharynx, indicating SusH can substitute in this niche. Both systems are sucrose‐inducible, with ScrH being the major in vitro hydrolase. The scrH/susH mutant does not grow on sucrose indicating that sus and scr are the only sucrose‐metabolizing systems in S. pneumoniae. We propose a model describing hierarchical regulation of the scr and sus systems by the putative inducer, S‐6‐P. The transport and metabolism of sucrose or a related disaccharide thus contributes to S. pneumoniae colonization and disease.
Transcriptome analysis of the Aspergillus nidulans AtmA (ATM, Ataxia‐Telangiectasia mutated) null mutant
Authors: Malavazi Iran , Savoldi Marcela , Da Silva Ferreira Márcia Eliana , Soriani Frederico Marianetti , Bonato Pierina Sueli , De Souza Goldman Maria Helena , Goldman Gustavo H. 
Published: September 2007

SummaryATM is a phosphatidyl‐3‐kinase‐related protein kinase that functions as a central regulator of DNA damage response in eukaryotes. In humans, mutations in ATM cause the devastating neurodegenerative disease Ataxia‐Telangiectasia. Previously, we characterized the homologue of ATM (AtmA) in the filamentous fungus Aspergillus nidulans. In addition to its expected role in the DNA damage response, we found that AtmA is also required for polarized hyphal growth. Our results suggested that AtmA probably regulates the function and/or localization of landmark proteins required for the formation of a polarity axis. Here, we extended these studies by investigating which pathways are influenced by AtmA during proliferation and polar growth by comparatively determining the transcriptional profile of A. nidulans wild‐type and ΔatmA mutant strains in different growth conditions. Our results indicate an important role of the pentose phosphate pathway in the fungal proliferation during endogenous DNA damage and polar growth monitored by the AtmA kinase. Furthermore, we identified several genes that have decreased mRNA expression in the ΔatmA mutant that are involved in the formation of a polarized hyphae and control of polar growth; in the synthesis of phosphatidic acid (e.g. phospholipase D); in the ergosterol biosynthesis (plasma membrane microdomains, lipid rafts); and in intracellular trafficking.
Regulation of sialic acid transport and catabolism in Haemophilus influenzae
Authors: Johnston Jason W. , Zaleski Anthony , Allen Simon , Mootz Joe M. , Armbruster David , Gibson Bradford W. , Apicella Michael A. , Munson Robert S. 
Published: September 2007

SummaryVirulence of nontypeable Haemophilus influenzae (NTHi) is dependent on the decoration of lipooligosaccharide with sialic acid. This sugar must be derived from the host, as NTHi cannot synthesize sialic acids. NTHi can also use sialic acid as a carbon source. The genes encoding the sialic acid transporter and the genes encoding the catabolic activities are localized to two divergently transcribed operons, the siaPT operon and the nan operon respectively. In this study, we identified SiaR as a repressor of sialic acid transport and catabolism in NTHi. Inactivation of siaR resulted in the unregulated expression of the genes in both operons. Unregulated catabolism of sialic acid in the siaR mutant resulted in the reduction of surface sialylation and an increase in serum sensitivity. In addition to SiaR‐mediated repression, CRP, the cAMP receptor protein, was shown to activate expression of the siaPT operon but not the nan operon. We describe a model in which SiaR and CRP work to modulate intracellular sialic acid levels. Our results demonstrate the importance of SiaR‐mediated regulation to balance the requirement of surface sialylation and the toxic accumulation of intracellular sialic acid.
Systematic mutagenesis of the thymidine tract of the pyrBI attenuator and its effects on intrinsic transcription termination in Escherichia coli
Authors: Sipos Katalin , Szigeti Réka , Dong Xiuzhu , Turnbough Charles L. 
Published: September 2007

SummaryThe pyrBI attenuator of Escherichia coli is an intrinsic transcription terminator composed of DNA with a hyphenated dyad symmetry and an adjacent 8 bp T:A tract (T‐tract). These elements specify a G+C‐rich terminator hairpin followed by a run of eight uridine residues (U‐tract) in the RNA transcript. In this study, we examined the effects on in vivo transcription termination of systematic base substitutions in the T/U‐tract of the pyrBI attenuator. We found that these substitutions diminished transcription termination efficiency to varying extents, depending on the nature and position of the substitution. In general, substitutions closer to the dyad symmetry/terminator hairpin exhibited the most significant effects. Additionally, we examined the effects on in vivo transcription termination of mutations that insert from 1 to 4 bases between the terminator hairpin and U‐tract specified by the pyrBI attenuator. Our results show an inverse relationship between termination efficiency and the number of bases inserted. The effects of the substitution and insertion mutations on termination efficiency at the pyrBI attenuator were also measured in vitro, which corroborated the in vivo results. Our results are discussed in terms of the current models for intrinsic transcription termination and estimating termination efficiencies at intrinsic terminators of other bacteria.
Repression of Clostridium difficile toxin gene expression by CodY
Authors: Dineen Sean S. , Villapakkam Anuradha C. , Nordman Jared T. , Sonenshein Abraham L. 
Published: September 2007

SummaryCodY, a global regulator of gene expression in low G + C Gram‐positive bacteria, was found to repress toxin gene expression in Clostridium difficile. Inactivation of the codY gene resulted in derepression of all five genes of the C. difficile pathogenicity locus during exponential growth and stationary phase. CodY was found to bind with high affinity to a DNA fragment containing the promoter region of the tcdR gene, which encodes a sigma factor that permits RNA polymerase to recognize promoters of the two major toxin genes as well as its own promoter. CodY also bound, but with low affinity, to the toxin gene promoters, suggesting that the regulation of toxin gene expression by CodY occurs primarily through direct control of tcdR gene expression. Binding of CodY to the tcdR promoter region was enhanced in the presence of GTP and branched‐chain amino acids, suggesting a link between nutrient limitation and the expression of C. difficile toxin genes.
The cell shape proteins MreB and MreC control cell morphogenesis by positioning cell wall synthetic complexes
Authors: Divakaruni Arun V. , Baida Cyril , White Courtney L. , Gober James W. 
Published: September 2007

SummaryMreB, the bacterial actin homologue, is thought to function in spatially co‐ordinating cell morphogenesis in conjunction with MreC, a protein that wraps around the outside of the cell within the periplasmic space. In Caulobacter crescentus, MreC physically associates with penicillin‐binding proteins (PBPs) which catalyse the insertion of intracellularly synthesized precursors into the peptidoglycan cell wall. Here we show that MreC is required for the spatial organization of components of the peptidoglycan‐synthesizing holoenzyme in the periplasm and MreB directs the localization of a peptidoglycan precursor synthesis protein in the cytosol. Additionally, fluorescent vancomycin (Van‐FL) labelling revealed that the bacterial cytoskeletal proteins MreB and FtsZ, as well as MreC and RodA, were required for peptidoglycan synthetic activity. MreB and FtsZ were found to be required for morphogenesis of the polar stalk. FtsZ was required for a cell cycle‐regulated burst of peptidoglycan synthesis early in the cell cycle resulting in the synthesis of cross‐band structures, whereas MreB was required for lengthening of the stalk. Thus, the bacterial cytoskeleton and cell shape‐determining proteins such as MreC, function in concert to orchestrate the localization of cell wall synthetic complexes resulting in spatially co‐ordinated and efficient peptidoglycan synthetic activity.
The R1162 relaxase/primase contains two, type IV transport signals that require the small plasmid protein MobB
Authors: Parker Christopher , Meyer Richard J. 
Published: September 2007

SummaryThe relaxase of the plasmid R1162 is a large protein essential for conjugative transfer and containing two different and physically separate catalytic activities. The N‐terminal half cleaves one of the DNA strands at the origin of transfer (oriT) and becomes covalently linked to the 5′ terminal phosphate; the C‐terminal half is a primase essential for initiation of plasmid vegetative replication. We show here that the two parts of the protein are independently transported by the type IV pathway. Part of the domain containing the catalytic activity, as well as an adjacent region, is required in each case, but the required regions do not physically overlap. Both transport systems contribute to the overall frequency of conjugative transfer. MobB is a small protein, encoded within mobA but in a different reading frame, that stabilizes the relaxase at oriT. MobB is required for efficient type IV transport of both the complete relaxase and its two, separate functional halves. MobB inserts into the membrane and could thus stabilize the association between the relaxase and the type IV transfer apparatus.
The LysR‐type regulator AtzR binding site: DNA sequences involved in activation, repression and cyanuric acid‐dependent repositioning
Authors: Porrúa Odil , García‐Jaramillo Manuel , Santero Eduardo , Govantes Fernando 
Published: September 2007

SummaryThe LysR‐type transcriptional regulator (LTTR) AtzR of Pseudomonas sp. strain ADP activates the cyanuric acid‐utilization atzDEF operon in response to low nitrogen availability and the presence of cyanuric acid. AtzR also represses expression of its own gene, atzR, transcribed divergently from atzDEF. Here we identify and functionally characterize the cis‐acting sequences at the atzR–atzDEF divergent promoter region required for AtzR‐dependent regulation. AtzR binds a single site overlapping both the PatzR and PatzDEF promoters and induces a DNA bend immediately upstream from PatzDEF. Interaction of AtzR with the inducer cyanuric acid shortens the protein–DNA interaction region and relaxes the DNA bend. The AtzR binding site contains a strong binding determinant, the repression binding site (RBS), centred at position −65 relative to the atzDEF transcriptional start, containing the LTTR binding consensus motif. Integrity of the RBS is essential for high‐affinity AtzR binding, activation and autorepression. A second, weaker binding determinant, the activation binding site (ABS), is present between the RBS and PatzDEF. Deletion of the ABS only provokes a modest decrease in AtzR affinity for the promoter region in vitro, but abolishes repression of PatzR in vivo. Involvement of the ABS in autorepression has not been previously reported.
Interleukin‐18 gene polymorphisms and haplotypes in patients with oral lichen planus: a study in an ethnic Chinese cohort
Authors: Bai J. , Zhang Y. , Lin M. , Zeng X. , Wang Z. , Shen J. , Jiang L. , Gao F. , Chen Q. 
Published: September 2007

AbstractInterleukin (IL)‐18, a proinflammatory cytokine, induces T‐helper 1 differentiation and cytotoxic T‐lymphocyte functions, both of which have been proposed in the pathogenesis of oral lichen planus (OLP) – an oral disease resembles oral mucosal graft‐versus‐host disease (GVHD) both clinically and histologically. The aim of this study was to evaluate the association of single nucleotide polymorphisms (SNPs) in the IL18 gene on the chromosome 11q22 in patients with OLP. Four SNPs of the IL18 gene at positions −137G/C (rs187238), −607C/A (rs1946518), −656G/T (rs1946519), and 1248A/G (rs189667) were analyzed in 151 patients with OLP and 143 normal controls using polymerase chain reaction–sequence‐specific primers method, and the serum level of IL‐18 protein was determined by enzyme‐linked immunosorbent assay (ELISA). The data revealed that there is a significant difference in IL18−607 genotype distributions between the patient group and the control group (P < 0.001), and the polymorphism −137G/C also appears to be statistically associated with the more severe erosive subtype (eOLP) (P = 0.023). The identified polymorphisms at the IL‐18 promoter region (i.e. −137GG) are likely to exert positive effect on the production of IL‐18 protein in OLP, as detected by ELISA. Using phase software, four haplotypes were deduced from the two polymorphisms −607C/A and −137G/C, named haplotypes I to IV, and the haplotypes I, II, and IV are significantly associated with OLP (P < 0.001). Our data suggest that the identified IL18 polymorphisms may be associated with the pathogenesis of OLP in this Chinese cohort by upregulation of IL‐18 production in vivo.