Publications

production of inulinase by xanthomonas campestris pv phaseoli using onion (allium cepa) and garlic (allium sativum) peels in solid state cultivation.	to access inulinase production by xanthomonas campestris pv phaseoli using the submerged and solid state cultivation (ssc) methods.	2007	17868315
anti-ice nucleation activity in xylem extracts from trees that contain deep supercooling xylem parenchyma cells.	boreal hardwood species, including japanese white birch (betula platyphylla sukat. var. japonica hara), japanese chestnut (castanea crenata sieb. et zucc.), katsura tree (cercidiphyllum japonicum sieb. et zucc.), siebold's beech (fagus crenata blume), mulberry (morus bombycis koidz.), and japanese rowan (sorbus commixta hedl.), had xylem parenchyma cells (xpcs) that adapt to subfreezing temperatures by deep supercooling. crude extracts from xylem in all these trees were found to have anti-ice nu ...	2007	17936742
plant pathogen recognition mediated by promoter activation of the pepper bs3 resistance gene.	plant disease resistance (r) proteins recognize matching pathogen avirulence proteins. alleles of the pepper r gene bs3 mediate recognition of the xanthomonas campestris pv. vesicatoria (xcv) type iii effector protein avrbs3 and its deletion derivative avrbs3deltarep16. pepper bs3 and its allelic variant bs3-e encode flavin monooxygenases with a previously unknown structure and are transcriptionally activated by the xcv effector proteins avrbs3 and avrbs3deltarep16, respectively. we found that r ...	2007	17962564
comparative genomic analysis of two-component regulatory proteins in pseudomonas syringae.	pseudomonas syringae is a widespread bacterial plant pathogen, and strains of p. syringae may be assigned to different pathovars based on host specificity among different plant species. the genomes of p. syringae pv. syringae (psy) b728a, pv. tomato (pto) dc3000 and pv. phaseolicola (pph) 1448a have been recently sequenced providing a major resource for comparative genomic analysis. a mechanism commonly found in bacteria for signal transduction is the two-component system (tcs), which typically ...	2007	17971244
identification of prophages in bacterial genomes by dinucleotide relative abundance difference.	prophages are integrated viral forms in bacterial genomes that have been found to contribute to interstrain genetic variability. many virulence-associated genes are reported to be prophage encoded. present computational methods to detect prophages are either by identifying possible essential proteins such as integrases or by an extension of this technique, which involves identifying a region containing proteins similar to those occurring in prophages. these methods suffer due to the problem of l ...	2007	18030328
structural mechanism of organic hydroperoxide induction of the transcription regulator ohrr.	the xanthomonas campestris transcription regulator ohrr contains a reactive cysteine residue (c22) that upon oxidation by organic hydroperoxides (ohps) forms an intersubunit disulphide bond with residue c127'. such modification induces the expression of a peroxidase that reduces ohps to their less toxic alcohols. here, we describe the structures of reduced and ohp-oxidized ohrr, visualizing the structural mechanism of ohp induction. reduced ohrr takes a canonical marr family fold with c22 and c1 ...	2007	18042459
bioinformatic evaluation of l-arginine catabolic pathways in 24 cyanobacteria and transcriptional analysis of genes encoding enzymes of l-arginine catabolism in the cyanobacterium synechocystis sp. pcc 6803.	so far very limited knowledge exists on l-arginine catabolism in cyanobacteria, although six major l-arginine-degrading pathways have been described for prokaryotes. thus, we have performed a bioinformatic analysis of possible l-arginine-degrading pathways in cyanobacteria. further, we chose synechocystis sp. pcc 6803 for a more detailed bioinformatic analysis and for validation of the bioinformatic predictions on l-arginine catabolism with a transcript analysis.	2007	18045455
the role of glucose kinase in carbohydrate utilization and extracellular polysaccharide production in xanthomonas campestris pathovar campestris.	the genome of the xanthomonas campestris pathovar campestris (xcc) strain 8004 encodes three uncharacterized proteins, xc1166, xc1223 and xc1976, annotated as glucose kinase (glk) by bioinformatic studies. here we have investigated the biochemical characteristics and physiological roles of these proteins with particular reference to the synthesis of extracellular polysaccharide (eps). xc1166, xc1223 and xc1976 were overexpressed as fusion proteins with a his(6) affinity tag and purified by nicke ...	2007	18048941
glycosylation of flavonoids with e. coli expressing glycosyltransferase from xanthomonas campestris.	glycosyltransferase family 1 (ugt) uses small chemicals including phenolics, antibiotics, and alkaloids as substrates to have an influence in biological activities. a glycosyltransferase (xcgt-2) from xanthomonas campestris was cloned and consisted of a 1,257 bp open reading frame encoding a 45.5 kda protein. in order to use this for the modification of phenolic compounds, xcgt-2 was expressed in escherichia coli as a glutathione s-transferase fusion protein. with the e. coli transformant expres ...	2007	18050962
the role of horizontal transfer in the evolution of a highly variable lipopolysaccharide biosynthesis locus in xanthomonads that infect rice, citrus and crucifers.	lipopolysaccharide (lps) is a pathogen associated molecular pattern (pamp) of animal and plant pathogenic bacteria. variation at the interstrain level is common in lps biosynthetic gene clusters of animal pathogenic bacteria. this variation has been proposed to play a role in evading the host immune system. even though lps is a modulator of plant defense responses, reports of interstrain variation in lps gene clusters of plant pathogenic bacteria are rare.	2007	18053269
pseudomonas syringae type iii effector avrrpt2 alters arabidopsis thaliana auxin physiology.	the pseudomonas syringae type iii effector avrrpt2 promotes bacterial virulence on arabidopsis thaliana plants lacking a functional rps2 gene (rps2 mutant plants). to investigate the mechanisms underlying the virulence activity of avrrpt2, we examined the phenotypes of transgenic a. thaliana rps2 seedlings constitutively expressing avrrpt2. these seedlings exhibited phenotypes reminiscent of a. thaliana mutants with altered auxin physiology, including longer primary roots, increased number of la ...	2007	18056646
modulation of bacterial type iii secretion system by a spermidine transporter dependent signaling pathway.	many gram-negative bacterial pathogens employ type iii secretion systems (t3ss) to inject effector proteins into host cells in infectious processes.	2007	18074016
identification of chromosomal alpha-proteobacterial small rnas by comparative genome analysis and detection in sinorhizobium meliloti strain 1021.	small untranslated rnas (srnas) seem to be far more abundant than previously believed. the number of srnas confirmed in e. coli through various approaches is above 70, with several hundred more srna candidate genes under biological validation. although the total number of srnas in any one species is still unclear, their importance in cellular processes has been established. however, unlike protein genes, no simple feature enables the prediction of the location of the corresponding sequences in g ...	2007	18093320
comparative genomic characterization of citrus-associated xylella fastidiosa strains.	the xylem-inhabiting bacterium xylella fastidiosa (xf) is the causal agent of pierce's disease (pd) in vineyards and citrus variegated chlorosis (cvc) in orange trees. both of these economically-devastating diseases are caused by distinct strains of this complex group of microorganisms, which has motivated researchers to conduct extensive genomic sequencing projects with xf strains. this sequence information, along with other molecular tools, have been used to estimate the evolutionary history o ...	2007	18154652
genetic diversity in populations of xanthomonas campestris pv. campestris in cruciferous weeds in central coastal california.	abstract xanthomonas campestris pv. campestris (x. campestris) infects a large number of cruciferous plants, including weeds. california has one of the largest and most diverse populations of wild cruciferous plants in the world. although considerable information is available on the genetic diversity of x. campestris in commercial crop plants, nothing is known about the diversity in strains infecting weeds. to assess the genetic diversity among strains of x. campestris in weeds in noncultivated ...	2007	18943929
horizontal gene transfer regulation in bacteria as a "spandrel" of dna repair mechanisms.	horizontal gene transfer (hgt) is recognized as the major force for bacterial genome evolution. yet, numerous questions remain about the transferred genes, their function, quantity and frequency. the extent to which genetic transformation by exogenous dna has occurred over evolutionary time was initially addressed by an in silico approach using the complete genome sequence of the ralstonia solanacearum gmi1000 strain. methods based on phylogenetic reconstruction of prokaryote homologous genes fa ...	2007	17957239
pathological variations within xanthomonas campestris pv. mangiferaeindicae support its separation into three distinct pathovars that can be distinguished by amplified fragment length polymorphism.	abstract bacterial black spot, caused by xanthomonas campestris pv. mangiferaeindicae, is an important disease of mango (mangifera indica). several other plant genera of the family anacardiaceae were described as host species for xanthomonads. we studied pathological variations among strains in a worldwide collection from several anacardiaceae genera. strains were classified into three pathogenicity groups. group i strains (from the old world) multiplied markedly in leaf tissue of mango and cash ...	2007	18943717
[antimicrobial activity of calendula l. plants].	the sap of different organs of genus calendula plant species has been studied for antimicrobial activity. the sap of racemes demonstrated the most expressed antimicrobial effect while that of the roots - the least one. calendula species inhibited all tested pathogenic microorganisms, especially pseudomonas syringae, p. fluorescens, xanthomonas campestris, agrobacterium tumefaciens. calendula suffruticosa was the most active to all investigated microorganisms.	2007	18217350
the bifunctional effector avrxccc of xanthomonas campestris pv. campestris requires plasma membrane-anchoring for host recognition.	summary: bacterial pathogens use type iii secretion systems (ttss) to deliver effector proteins into eukaryotic cells for pathogenesis. in bacterial-plant interactions, one effector may function as an avirulence factor to betray the pathogen to the plant surveillance system and induce the hypersensitive response (hr) in the resistant host carrying a corresponding resistance (r) gene. however, the same effector can also sustain the growth of the pathogen by acting as a virulence factor to modulat ...	2007	20507516
conventional and pcr detection of aphelenchoides fragariae in diverse ornamental host plant species.	a pcr-based diagnostic assay was developed for early detection and identification of aphelenchoides fragariae directly in host plant tissues using the species-specific primers afragfl and afragrl that amplify a 169-bp fragment in the internal transcribed spacer (its1) region of ribosomal dna. these species-specific primers did not amplify dna from aphelenchoides besseyi or aphelenchoides ritzemabosi. the pcr assay was sensitive, detecting a single nematode in a background of plant tissue extract ...	2007	19259510
plants under attack: multiple interactions with insects and microbes.	to defend themselves, plants activate inducible defense mechanisms that are effective against the invader that is encountered. there is partial overlap in the defense signaling pathways that are induced by insect herbivores and microbial pathogens that may result in cross-resistance. we have previously shown that infestation by tissue-chewing pieris rapae larvae induces resistance in arabidopsis thaliana against subsequent attack by the microbial pathogens pseudomonas syringae pv. tomato (pst), ...	2007	19704549
branchclust: a phylogenetic algorithm for selecting gene families.	automated methods for assembling families of orthologous genes include those based on sequence similarity scores and those based on phylogenetic approaches. the first are easy to automate but usually they do not distinguish between paralogs and orthologs or have restriction on the number of taxa. phylogenetic methods often are based on reconciliation of a gene tree with a known rooted species tree; a limitation of this approach, especially in case of prokaryotes, is that the species tree is ofte ...	2007	17425803
the power of phylogenetic approaches to detect horizontally transferred genes.	horizontal gene transfer plays an important role in evolution because it sometimes allows recipient lineages to adapt to new ecological niches. high genes transfer frequencies were inferred for prokaryotic and early eukaryotic evolution. does horizontal gene transfer also impact phylogenetic reconstruction of the evolutionary history of genomes and organisms? the answer to this question depends at least in part on the actual gene transfer frequencies and on the ability to weed out transferred ge ...	2007	17376230
phylogenetic signal and functional categories in proteobacteria genomes.	a comprehensive evolutionary analysis of bacterial genomes implies to identify the hallmark of vertical and non-vertical signals and to discriminate them from the presence of mere phylogenetic noise. in this report we have addressed the impact of factors like the universal distribution of the genes, their essentiality or their functional role in the cell on the inference of vertical signal through phylogenomic methods.	2007	17288580
identification of genes encoding trna modification enzymes by comparative genomics.	as the molecular adapters between codons and amino acids, transfer-rnas are pivotal molecules of the genetic code. the coding properties of a trna molecule do not reside only in its primary sequence. posttranscriptional nucleoside modifications, particularly in the anticodon loop, can modify cognate codon recognition, affect aminoacylation properties, or stabilize the codon-anticodon wobble base pairing to prevent ribosomal frameshifting. despite a wealth of biophysical and structural knowledge ...	2007	17673083
evolution of the chaperone/usher assembly pathway: fimbrial classification goes greek.	many proteobacteria use the chaperone/usher pathway to assemble proteinaceous filaments on the bacterial surface. these filaments can curl into fimbrial or nonfimbrial surface structures (e.g., a capsule or spore coat). this article reviews the phylogeny of operons belonging to the chaperone/usher assembly class to explore the utility of establishing a scheme for subdividing them into clades of phylogenetically related gene clusters. based on usher amino acid sequence comparisons, our analysis s ...	2007	18063717
the flik protein and flagellar hook-length control.	the bacterial flagellum is a highly complex prokaryotic organelle. it is the motor that drives bacterial motility, and despite the large amount of energy required to make and operate flagella, motile organisms have a strong adaptive advantage. flagellar biogenesis is both complex and highly coordinated and it typically involves at least three two-component systems. part of the flagellum is a type iii secretion system, and it is via this structure that flagellar components are exported. the assem ...	2007	17456739
biotic interactions, ecological knowledge and agriculture.	this paper discusses biotic interactions in agroecosystems and how they may be manipulated to support crop productivity and environmental health by provision of ecosystem services such as weed, pest and disease management, nutrient cycling and biodiversity conservation. important elements for understanding biotic interactions include consideration of the effects of diversity, species composition and food web structure on ecosystem processes; the impacts of timing, frequency and intensity of dist ...	2007	17761466
biotic interactions, ecological knowledge and agriculture.	this paper discusses biotic interactions in agroecosystems and how they may be manipulated to support crop productivity and environmental health by provision of ecosystem services such as weed, pest and disease management, nutrient cycling and biodiversity conservation. important elements for understanding biotic interactions include consideration of the effects of diversity, species composition and food web structure on ecosystem processes; the impacts of timing, frequency and intensity of dist ...	2007	17761466
evolution of ribonuclease h genes in prokaryotes to avoid inheritance of redundant genes.	a theoretical model of genetic redundancy has proposed that the fates of redundant genes depend on the degree of functional redundancy, and that functionally redundant genes will not be inherited together. however, no example of actual gene evolution has been reported that can be used to test this model. here, we analyzed the molecular evolution of the ribonuclease h (rnase h) family in prokaryotes and used the results to examine the implications of functional redundancy for gene evolution.	2007	17663799
real-time pcr: revolutionizing detection and expression analysis of genes.	invention of polymerase chain reaction (pcr) technology by kary mullis in 1984 gave birth to real-time pcr. real-time pcr - detection and expression analysis of gene(s) in real-time - has revolutionized the 21(st) century biological science due to its tremendous application in quantitative genotyping, genetic variation of inter and intra organisms, early diagnosis of disease, forensic, to name a few. we comprehensively review various aspects of real-time pcr, including technological refinement a ...	2007	18645596
transcriptional regulatory network discovery via multiple method integration: application to e. coli k12.	transcriptional regulatory network (trn) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete trns. we develop a methodology, trnd, that integrates a preliminary trn, microarray data, gene ontology and phylogenic similarity to accurately discover trns and apply the method to e. coli k12. the approach can easily be extended to include other me ...	2007	17397539
roles of cyclic diguanylate in the regulation of bacterial pathogenesis.	cyclic diguanylate (c-di-gmp) is a bacterial second messenger of growing recognition involved in the regulation of a number of complex physiological processes. this review describes the biosynthesis and hydrolysis of c-di-gmp and several mechanisms of regulation of c-di-gmp metabolism. the contribution of c-di-gmp to regulating biofilm formation and motility, processes that affect pathogenesis of many bacteria, is described, as is c-di-gmp regulation of virulence gene expression. finally, ways i ...	2007	17480182
surface antigens and potential virulence factors from parasites detected by comparative genomics of perfect amino acid repeats.	many parasitic organisms, eukaryotes as well as bacteria, possess surface antigens with amino acid repeats. making up the interface between host and pathogen such repetitive proteins may be virulence factors involved in immune evasion or cytoadherence. they find immunological applications in serodiagnostics and vaccine development. here we use proteins which contain perfect repeats as a basis for comparative genomics between parasitic and free-living organisms.	2007	18096064
computational biology in brazil.		2007	17967046
natural and synthetic polymers as inhibitors of drug efflux pumps.	inhibition of efflux pumps is an emerging approach in cancer therapy and drug delivery. since it has been discovered that polymeric pharmaceutical excipients such as tweens or pluronics can inhibit efflux pumps, various other polymers have been investigated regarding their potential efflux pump inhibitory activity. among them are polysaccharides, polyethylene glycols and derivatives, amphiphilic block copolymers, dendrimers and thiolated polymers. in the current review article, natural and synth ...	2007	17896100
natural and synthetic polymers as inhibitors of drug efflux pumps.	inhibition of efflux pumps is an emerging approach in cancer therapy and drug delivery. since it has been discovered that polymeric pharmaceutical excipients such as tweens or pluronics can inhibit efflux pumps, various other polymers have been investigated regarding their potential efflux pump inhibitory activity. among them are polysaccharides, polyethylene glycols and derivatives, amphiphilic block copolymers, dendrimers and thiolated polymers. in the current review article, natural and synth ...	2007	17896100
malisam: a database of structurally analogous motifs in proteins.	malisam (manual alignments for structurally analogous motifs) represents the first database containing pairs of structural analogs and their alignments. to find reliable analogs, we developed an approach based on three ideas. first, an insertion together with a part of the evolutionary core of one domain family (a hybrid motif) is analogous to a similar motif contained within the core of another domain family. second, a motif at an interface, formed by secondary structural elements (sses) contri ...	2007	17855399
malisam: a database of structurally analogous motifs in proteins.	malisam (manual alignments for structurally analogous motifs) represents the first database containing pairs of structural analogs and their alignments. to find reliable analogs, we developed an approach based on three ideas. first, an insertion together with a part of the evolutionary core of one domain family (a hybrid motif) is analogous to a similar motif contained within the core of another domain family. second, a motif at an interface, formed by secondary structural elements (sses) contri ...	2007	17855399
autoimmune response as a mechanism for a dobzhansky-muller-type incompatibility syndrome in plants.	epistatic interactions between genes are a major factor in evolution. hybrid necrosis is an example of a deleterious phenotype caused by epistatic interactions that is observed in many intra- and interspecific plant hybrids. a large number of hybrid necrosis cases share phenotypic similarities, suggesting a common underlying mechanism across a wide range of plant species. here, we report that approximately 2% of intraspecific crosses in arabidopsis thaliana yield f1 progeny that express necrosis ...	2007	17803357
genetic analysis of sumoylation in arabidopsis: conjugation of sumo1 and sumo2 to nuclear proteins is essential.	the posttranslational addition of small ubiquitin-like modifiers (sumos) to other intracellular proteins has been implicated in a variety of eukaryotic functions, including modifying cytoplasmic signal transduction, nuclear import and subnuclear compartmentalization, dna repair, and transcription regulation. for plants, in particular, both genetic analyses and the rapid accumulation of sumo conjugates in response to various adverse environmental conditions suggest that sumoylation plays a key ro ...	2007	17644626
natural origin biodegradable systems in tissue engineering and regenerative medicine: present status and some moving trends.	the fields of tissue engineering and regenerative medicine aim at promoting the regeneration of tissues or replacing failing or malfunctioning organs, by means of combining a scaffold/support material, adequate cells and bioactive molecules. different materials have been proposed to be used as both three-dimensional porous scaffolds and hydrogel matrices for distinct tissue engineering strategies. among them, polymers of natural origin are one of the most attractive options, mainly due to their ...	2007	17412675
a new paradigm for mentored undergraduate research in molecular microbiology.	science educators agree that an undergraduate research experience is critical for students who are considering graduate school or research careers. the process of researching a topic in the primary literature, designing experiments, implementing those experiments, and analyzing the results is essential in developing the analytical skills necessary to become a true scientist. because training undergraduates who will only be in the laboratory for a short period is time consuming for faculty mentor ...	2007	18056305
pathogen virulence factors as molecular probes of basic plant cellular functions.	to successfully colonize plants, pathogens have evolved a myriad of virulence factors that allow them to manipulate host cellular pathways in order to gain entry into, multiply and move within, and eventually exit the host for a new infection cycle. in the past few years, substantial progress has been made in characterizing the host targets of viral and bacterial virulence factors, providing unique insights into basic plant cellular processes such as gene silencing, vesicle trafficking, hormone ...	2007	17884715
identification and mutational analysis of arabidopsis fls2 leucine-rich repeat domain residues that contribute to flagellin perception.	mutational, phylogenetic, and structural modeling approaches were combined to develop a general method to study leucine-rich repeat (lrr) domains and were used to identify residues within the arabidopsis thaliana flagellin-sensing2 (fls2) lrr that contribute to flagellin perception. fls2 is a transmembrane receptor kinase that binds bacterial flagellin or a flagellin-based flg22 peptide through a presumed physical interaction within the fls2 extracellular domain. double-ala scanning mutagenesis ...	2007	17933906
genome mapping and molecular breeding of tomato.	the cultivated tomato, lycopersicon esculentum, is the second most consumed vegetable worldwide and a well-studied crop species in terms of genetics, genomics, and breeding. it is one of the earliest crop plants for which a genetic linkage map was constructed, and currently there are several molecular maps based on crosses between the cultivated and various wild species of tomato. the high-density molecular map, developed based on an l. esculentum x l. pennellii cross, includes more than 2200 ma ...	2007	18364989
arabidopsis-insect interactions.		2007	22303231
structural and evolutionary bioinformatics of the spout superfamily of methyltransferases.	spout methyltransferases (mtases) are a large class of s-adenosyl-l-methionine-dependent enzymes that exhibit an unusual alpha/beta fold with a very deep topological knot. in 2001, when no crystal structures were available for any of these proteins, anantharaman, koonin, and aravind identified homology between spou and trmd mtases and defined the spout superfamily. since then, multiple crystal structures of knotted mtases have been solved and numerous new homologous sequences appeared in the dat ...	2007	17338813
genome-wide survey of prokaryotic serine proteases: analysis of distribution and domain architectures of five serine protease families in prokaryotes.	serine proteases are one of the most abundant groups of proteolytic enzymes found in all the kingdoms of life. while studies have established significant roles for many prokaryotic serine proteases in several physiological processes, such as those associated with metabolism, cell signalling, defense response and development, functional associations for a large number of prokaryotic serine proteases are relatively unknown. current analysis is aimed at understanding the distribution and probable b ...	2008	19019219
estimating the fraction of non-coding rnas in mammalian transcriptomes.	recent studies of mammalian transcriptomes have identified numerous rna transcripts that do not code for proteins; their identity, however, is largely unknown. here we explore an approach based on sequence randomness patterns to discern different rna classes. the relative z-score we use helps identify the known ncrna class from the genome, intergene and intron classes. this leads us to a fractional ncrna measure of putative ncrna datasets which we model as a mixture of genuine ncrnas and other t ...	2008	19812767
application of recognition of individual genes-fluorescence in situ hybridization (ring-fish) to detect nitrite reductase genes (nirk) of denitrifiers in pure cultures and environmental samples.	denitrification is an alternative type of anaerobic respiration in which nitrate is reduced to gaseous products via nitrite. the key step in this process is the reduction of nitrite to nitric oxide, which is catalyzed by two structurally different but functionally equivalent forms of nitrite reductase encoded by the nirk and nirs genes. cultivation-independent studies based on these functional marker genes showed that in the environment there was a dominance of organisms with nirk and nirs genes ...	2008	19074610
application of recognition of individual genes-fluorescence in situ hybridization (ring-fish) to detect nitrite reductase genes (nirk) of denitrifiers in pure cultures and environmental samples.	denitrification is an alternative type of anaerobic respiration in which nitrate is reduced to gaseous products via nitrite. the key step in this process is the reduction of nitrite to nitric oxide, which is catalyzed by two structurally different but functionally equivalent forms of nitrite reductase encoded by the nirk and nirs genes. cultivation-independent studies based on these functional marker genes showed that in the environment there was a dominance of organisms with nirk and nirs genes ...	2008	19074610
the arabidopsis map kinase kinase 7: a crosstalk point between auxin signaling and defense responses?	plant-pathogen interaction induces a complex host response that coordinates various signaling pathways through multiple signal molecules. besides the well-documented signal molecules salicylic acid (sa), ethylene and jasmonic acid, auxin is emerging as an important player in this response. we recently characterized an arabidopsis activation-tagged mutant, bud1, in which the expression of the map kinase kinase 7 (atmkk7) gene is increased. the bud1 mutant plants accumulate elevated levels of sa a ...	2008	19704652
comparative bacterial proteomics: analysis of the core genome concept.	while comparative bacterial genomic studies commonly predict a set of genes indicative of common ancestry, experimental validation of the existence of this core genome requires extensive measurement and is typically not undertaken. enabled by an extensive proteome database developed over six years, we have experimentally verified the expression of proteins predicted from genomic ortholog comparisons among 17 environmental and pathogenic bacteria. more exclusive relationships were observed among ...	2008	18253490
genomic islands: tools of bacterial horizontal gene transfer and evolution.	bacterial genomes evolve through mutations, rearrangements or horizontal gene transfer. besides the core genes encoding essential metabolic functions, bacterial genomes also harbour a number of accessory genes acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. the horizontal gene transfer contributes to the diversification and adaptation of microorganisms, thus having an impact on the genome plasticity. a significant part of the horizontal gene ...	2008	19178566
genomic islands: tools of bacterial horizontal gene transfer and evolution.	bacterial genomes evolve through mutations, rearrangements or horizontal gene transfer. besides the core genes encoding essential metabolic functions, bacterial genomes also harbour a number of accessory genes acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. the horizontal gene transfer contributes to the diversification and adaptation of microorganisms, thus having an impact on the genome plasticity. a significant part of the horizontal gene ...	2008	19178566
phytopathogen type iii effector weaponry and their plant targets.	phytopathogenic bacteria suppress plant innate immunity and promote pathogenesis by injecting proteins called type iii effectors into plant cells using a type iii protein secretion system. these type iii effectors use at least three strategies to alter host responses. one strategy is to alter host protein turnover, either by direct cleavage or by modulating ubiquitination and targeting the 26s proteasome. another strategy involves alteration of rna metabolism by transcriptional activation or adp ...	2008	18657470
a solanum lycopersicum x solanum pimpinellifolium linkage map of tomato displaying genomic locations of r-genes, rgas, and candidate resistance/defense-response ests.	we have identified an accession (la2093) within the tomato wild species solanum pimpinellifolium with many desirable characteristics, including biotic and abiotic stress tolerance and good fruit quality. to utilize the full genetic potential of la2093 in tomato breeding, we have developed a linkage map based on an f(2) population of a cross between la2093 and a tomato breeding line, using 115 rflp, 94 est, and 41 rga markers. the map spanned 1002.4 cm of the 12 tomato chromosomes with an average ...	2008	19223983
a solanum lycopersicum x solanum pimpinellifolium linkage map of tomato displaying genomic locations of r-genes, rgas, and candidate resistance/defense-response ests.	we have identified an accession (la2093) within the tomato wild species solanum pimpinellifolium with many desirable characteristics, including biotic and abiotic stress tolerance and good fruit quality. to utilize the full genetic potential of la2093 in tomato breeding, we have developed a linkage map based on an f(2) population of a cross between la2093 and a tomato breeding line, using 115 rflp, 94 est, and 41 rga markers. the map spanned 1002.4 cm of the 12 tomato chromosomes with an average ...	2008	19223983
exploring the mechanism of tryptophan 2,3-dioxygenase.	the haem proteins tdo (tryptophan 2,3-dioxygenase) and ido (indoleamine 2,3-dioxygenase) are specific and powerful oxidation catalysts that insert one molecule of dioxygen into l-tryptophan in the first and rate-limiting step in the kynurenine pathway. recent crystallographic and biochemical analyses of tdo and ido have greatly aided our understanding of the mechanisms employed by these enzymes in the binding and activation of dioxygen and tryptophan. in the present paper, we briefly discuss the ...	2008	19021508
matching curated genome databases: a non trivial task.	curated databases of completely sequenced genomes have been designed independently at the ncbi (refseq) and ebi (genome reviews) to cope with non-standard annotation found in the version of the sequenced genome that has been published by databanks genbank/embl/ddbj. these curation attempts were expected to review the annotations and to improve their pertinence when using them to annotate newly released genome sequences by homology to previously annotated genomes. however, we observed that such a ...	2008	18950477
small ubiquitin-like modifier proteases overly tolerant to salt1 and -2 regulate salt stress responses in arabidopsis.	understanding salt stress signaling is key to producing salt-tolerant crops. the small ubiquitin-like modifier (sumo) is a crucial regulator of signaling proteins in eukaryotes. attachment of sumo onto substrates is reversible, and sumo proteases, which specifically cleave the sumo-substrate linkages, play a vital regulatory role during sumoylation. we have identified two sumo proteases, overly tolerant to salt1 (ots1) and ots2, which are localized in the nucleus and act redundantly to regulate ...	2008	18849491
structural insights into mechanism and specificity of o-glcnac transferase.	post-translational modification of protein serines/threonines with n-acetylglucosamine (o-glcnac) is dynamic, inducible and abundant, regulating many cellular processes by interfering with protein phosphorylation. o-glcnacylation is regulated by o-glcnac transferase (ogt) and o-glcnacase, both encoded by single, essential, genes in metazoan genomes. it is not understood how ogt recognises its sugar nucleotide donor and performs o-glcnac transfer onto proteins/peptides, and how the enzyme recogni ...	2008	18818698
herbal excipients in novel drug delivery systems.	the use of natural excipients to deliver the bioactive agents has been hampered by the synthetic materials. however advantages offered by these natural excipients are their being non-toxic, less expensive and freely available. the performance of the excipients partly determines the quality of the medicines. the traditional concept of the excipients as any component other than the active substance has undergone a substantial evolution from an inert and cheap vehicle to an essential constituent of ...	2008	20046764
recent advances in the analysis of biological particles by capillary electrophoresis.	this review covers research papers published in the years 2005-2007 that describe the application of capillary electrophoresis to the analysis of biological particles such as whole cells, subcellular organelles, viruses and microorganisms.	2008	18576409
microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the gulf of mexico.	marine sediments of coastal margins are important sites of carbon sequestration and nitrogen cycling. to determine the metabolic potential and structure of marine sediment microbial communities, two cores were collected each from the two stations (gmt at a depth of 200 m and gms at 800 m) in the gulf of mexico, and six subsamples representing different depths were analyzed from each of these two cores using functional gene arrays containing approximately 2,000 probes targeting genes involved in ...	2008	18515485
mutation of a rice gene encoding a phenylalanine biosynthetic enzyme results in accumulation of phenylalanine and tryptophan.	two distinct biosynthetic pathways for phe in plants have been proposed: conversion of prephenate to phe via phenylpyruvate or arogenate. the reactions catalyzed by prephenate dehydratase (pdt) and arogenate dehydratase (adt) contribute to these respective pathways. the mtr1 mutant of rice (oryza sativa) manifests accumulation of phe, trp, and several phenylpropanoids, suggesting a link between the synthesis of phe and trp. here, we show that the mtr1 mutant gene (mtr1-d) encodes a form of rice ...	2008	18487352
sequence level analysis of recently duplicated regions in soybean [glycine max (l.) merr.] genome.	a single recessive gene, rxp, on linkage group (lg) d2 controls bacterial leaf-pustule resistance in soybean. we identified two homoeologous contigs (gma and gma') composed of five bacterial artificial chromosomes (bacs) during the selection of bac clones around rxp region. with the recombinant inbred line population from the cross of pureunkong and jinpumkong 2, single-nucleotide polymorphism and simple sequence repeat marker genotyping were able to locate gma' on lg a1. on the basis of informa ...	2008	18334514
discovering mechanisms of signaling-mediated cysteine oxidation.	accumulating evidence reveals hydrogen peroxide as a key player both as a damaging agent and, from emerging evidence over the past decade, as a second messenger in intracellular signaling. this rather mild oxidant acts upon downstream targets within signaling cascades to modulate the activity of a host of enzymes (e.g. phosphatases and kinases) and transcriptional regulators through chemoselective oxidation of cysteine residues. with the recent development of specific detection reagents for hydr ...	2008	18282483
comparative mapping of brassica juncea and arabidopsis thaliana using intron polymorphism (ip) markers: homoeologous relationships, diversification and evolution of the a, b and c brassica genomes.	extensive mapping efforts are currently underway for the establishment of comparative genomics between the model plant, arabidopsis thaliana and various brassica species. most of these studies have deployed rflp markers, the use of which is a laborious and time-consuming process. we therefore tested the efficacy of pcr-based intron polymorphism (ip) markers to analyze genome-wide synteny between the oilseed crop, brassica juncea (aabb genome) and a. thaliana and analyzed the arrangement of 24 (p ...	2008	18315867
a myb transcription factor regulates very-long-chain fatty acid biosynthesis for activation of the hypersensitive cell death response in arabidopsis.	plant immune responses to pathogen attack include the hypersensitive response (hr), a form of programmed cell death occurring at invasion sites. we previously reported on arabidopsis thaliana myb30, a transcription factor that acts as a positive regulator of a cell death pathway conditioning the hr. here, we show by microarray analyses of arabidopsis plants misexpressing myb30 that the genes encoding the four enzymes forming the acyl-coa elongase complex are putative myb30 targets. the acyl-coa ...	2008	18326828
molecular control of bacterial death and lysis.	although the phenomenon of bacterial cell death and lysis has been studied for over 100 years, the contribution of these important processes to bacterial physiology and development has only recently been recognized. contemporary study of cell death and lysis in a number of different bacteria has revealed that these processes, once thought of as being passive and unregulated, are actually governed by highly complex regulatory systems. an emerging paradigm in this field suggests that, analogous to ...	2008	18322035
coevolution of gene families in prokaryotes.	we study gene family coevolution on a tree of life based on a large-scale ancestral gene content reconstruction, which includes gene duplication and deletion events. the insights obtained from this study are threefold: (1) global properties, such as the distribution of coevolution partners and the formation of disconnected clusters of coevolving families, can be an inevitable consequence of evolution along a tree. (2) concerted family expansion (gene duplication) and contraction (gene deletion) ...	2008	18230804
prediction of reversibly oxidized protein cysteine thiols using protein structure properties.	protein cysteine thiols can be divided into four groups based on their reactivities: those that form permanent structural disulfide bonds, those that coordinate with metals, those that remain in the reduced state, and those that are susceptible to reversible oxidation. physicochemical parameters of oxidation-susceptible protein thiols were organized into a database named the balanced oxidation susceptible cysteine thiol database (balosctdb). balosctdb contains 161 cysteine thiols that undergo re ...	2008	18287280
recent advances in cotton genomics.	genome research promises to promote continued and enhanced plant genetic improvement. as a world's leading crop and a model system for studies of many biological processes, genomics research of cottons has advanced rapidly in the past few years. this article presents a comprehensive review on the recent advances of cotton genomics research. the reviewed areas include dna markers, genetic maps, mapped genes and qtls, ests, microarrays, gene expression profiling, bac and bibac libraries, physical ...	2008	18288253
preliminary investigation on the development of diltiazem resin complex loaded carboxymethyl xanthan beads.	the objective of this study was to develop a multiunit sustained release dosage form of diltiazem using a natural polymer from a completely aqueous environment. diltiazem was complexed with resin and the resinate-loaded carboxymethyl xanthan (rcmx) beads were prepared by interacting sodium carboxymethyl xanthan (scmx), a derivatized xanthan gum, with al(+3) ions. the beads were evaluated for drug entrapment efficiency (dee) and release characteristics in enzyme free simulated gastric fluid (sgf, ...	2008	18446495
minimum contradiction matrices in whole genome phylogenies.	minimum contradiction matrices are a useful complement to distance-based phylogenies. a minimum contradiction matrix represents phylogenetic information under the form of an ordered distance matrix y(i) (,) (j) (n). a matrix element corresponds to the distance from a reference vertex n to the path (i, j). for an x-tree or a split network, the minimum contradiction matrix is a robinson matrix. it therefore fulfills all the inequalities defining perfect order: y(i) (,) (j) (n) >or= y(i) (,) (k) (n ...	2008	19204821
cohesion group approach for evolutionary analysis of tyra, a protein family with wide-ranging substrate specificities.	many enzymes and other proteins are difficult subjects for bioinformatic analysis because they exhibit variant catalytic, structural, regulatory, and fusion mode features within a protein family whose sequences are not highly conserved. however, such features reflect dynamic and interesting scenarios of evolutionary importance. the value of experimental data obtained from individual organisms is instantly magnified to the extent that given features of the experimental organism can be projected u ...	2008	18322033
reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes.	the increasing number of sequenced prokaryotic genomes contains a wealth of genomic data that needs to be effectively analysed. a set of statistical tools exists for such analysis, but their strengths and weaknesses have not been fully explored. the statistical methods we are concerned with here are mainly used to examine similarities between archaeal and bacterial dna from different genomes. these methods compare observed genomic frequencies of fixed-sized oligonucleotides with expected values, ...	2008	18307761
identification of a host 14-3-3 protein that interacts with xanthomonas effector avrrxv.	avrrxv is a member of a family of pathogen effectors present in pathogens of both plant and mammalian species. xanthomonas campestris pv. vesicatoria strains carrying avrrxv induce a hypersensitive response (hr) in the tomato cultivar hawaii 7998. using a yeast two-hybrid screen, we identified a 14-3-3 protein from tomato that interacts with avrrxv called avrrxv interactor 1 (ari1). the interaction was confirmed in vitro with affinity chromatography. using mutagenesis, we identified a 14-3-3-bin ...	2008	21796232
positively regulated bacterial expression systems.	regulated promoters are useful tools for many aspects related to recombinant gene expression in bacteria, including for high-level expression of heterologous proteins and for expression at physiological levels in metabolic engineering applications. in general, it is common to express the genes of interest from an inducible promoter controlled either by a positive regulator or by a repressor protein. in this review, we discuss established and potentially useful positively regulated bacterial prom ...	2008	21261879
positively regulated bacterial expression systems.	regulated promoters are useful tools for many aspects related to recombinant gene expression in bacteria, including for high-level expression of heterologous proteins and for expression at physiological levels in metabolic engineering applications. in general, it is common to express the genes of interest from an inducible promoter controlled either by a positive regulator or by a repressor protein. in this review, we discuss established and potentially useful positively regulated bacterial prom ...	2008	21261879
geographic, seasonal, and precipitation chemistry influence on the abundance and activity of biological ice nucleators in rain and snow.	biological ice nucleators (in) function as catalysts for freezing at relatively warm temperatures (warmer than -10 degrees c). we examined the concentration (per volume of liquid) and nature of in in precipitation collected from montana and louisiana, the alps and pyrenees (france), ross island (antarctica), and yukon (canada). the temperature of detectable ice-nucleating activity for more than half of the samples was > or = -5 degrees c based on immersion freezing testing. digestion of the samp ...	2008	19028877
mosaic: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level.	the recent availability of complete sequences for numerous closely related bacterial genomes opens up new challenges in comparative genomics. several methods have been developed to align complete genomes at the nucleotide level but their use and the biological interpretation of results are not straightforward. it is therefore necessary to develop new resources to access, analyze, and visualize genome comparisons.	2008	19038022
impact of transcription units rearrangement on the evolution of the regulatory network of gamma-proteobacteria.	in the past years, several studies begun to unravel the structure, dynamical properties, and evolution of transcriptional regulatory networks. however, even those comparative studies that focus on a group of closely related organisms are limited by the rather scarce knowledge on regulatory interactions outside a few model organisms, such as e. coli among the prokaryotes.	2008	18366643
cell-cell communication in bacteria: united we stand.		2008	18456806
bioactive and structural metabolites of pseudomonas and burkholderia species causal agents of cultivated mushrooms diseases.	pseudomonas tolaasii, p. reactans and burkholderia gladioli pv. agaricicola, are responsible of diseases on some species of cultivated mushrooms. the main bioactive metabolites produced by both pseudomonas strains are the lipodepsipeptides (ldps) tolaasin i and ii and the so called white line inducing principle (wlip), respectively, ldps which have been extensively studied for their role in the disease process and for their biological properties. in particular, their antimicrobial activity and t ...	2008	19787100
the role of pilz domain proteins in the virulence of xanthomonas campestris pv. campestris.	cyclic di-gmp [(bis-(3'-5')-cyclic di-guanosine monophosphate)] is an almost ubiquitous second messenger in bacteria that is implicated in the regulation of a range of functions that include developmental transitions, aggregative behaviour, adhesion, biofilm formation and virulence. comparatively little is known about the mechanism(s) by which cyclic di-gmp exerts these various regulatory effects. pilz has been identified as a cyclic di-gmp binding protein domain; proteins with this domain are i ...	2008	19019010
survival and dissemination of escherichia coli o157:h7 on physically and biologically damaged lettuce plants.	the ecology of the vegetable leaf surface is important to the survival of enteric pathogens. understanding changes in ecological parameters during the preharvest stages of production can lead to development of approaches to minimize the hazard of contamination of fresh fruits and vegetables with foodborne pathogens. in this study, survival levels of escherichia coli o157 over a 10-day period were compared among traumatically injured, phytopathogen-damaged, and healthy lettuce plants. leaves from ...	2008	19244888
host-plant-mediated effects of nadefensin on herbivore and pathogen resistance in nicotiana attenuata.	the adage from shakespeare, "troubles, not as single spies, but in battalions come," holds true for nicotiana attenuata, which is commonly attacked by both pathogens (pseudomonas spp.) and herbivores (manduca sexta) in its native habitats. defense responses targeted against the pathogens can directly or indirectly influence the responses against the herbivores. nadefensin is an effective induced defense gene against the bacterial pathogen pseudomonas syringae pv tomato (pst dc3000), which is als ...	2008	18950524
elicitor-induced transcription factors for metabolic reprogramming of secondary metabolism in medicago truncatula.	exposure of medicago truncatula cell suspension cultures to pathogen or wound signals leads to accumulation of various classes of flavonoid and/or triterpene defense molecules, orchestrated via a complex signalling network in which transcription factors (tfs) are essential components.	2008	19102779
lactic acid bacteria from fresh fruit and vegetables as biocontrol agents of phytopathogenic bacteria and fungi.	this study evaluated the efficacy of lactic acid bacteria (lab) isolated from fresh fruits and vegetables as biocontrol agents against the phytopathogenic and spoilage bacteria and fungi, xanthomonas campestris, erwinia carotovora, penicillium expansum, monilinia laxa, and botrytis cinerea. the antagonistic activity of 496 lab strains was tested in vitro and all tested microorganisms except p. expansum were inhibited by at least one isolate. the 496 isolates were also analyzed for the inhibition ...	2008	19204894
bactericidal and fungicidal activities of calia secundiflora (ort.) yakovlev.	calia secundiflora (ortega) yakovlev (fabaceae) is considered a medicinal plant in mexico but has scarcely been used because of the toxicity of its quinolizidine alkaloids. several quinolizidine alkaloids have shown bactericidal, nematicidal, and fungicidal activities. the purpose of this study was to identify the alkaloids in the seeds and evaluate the activity of the organic extract on several phytopathogenic fungi and bacteria. an in vitro bioassay was conducted with species of the following ...	2008	19040102
acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in xanthomonas.	xanthomonas is a large genus of plant-associated and plant-pathogenic bacteria. collectively, members cause diseases on over 392 plant species. individually, they exhibit marked host- and tissue-specificity. the determinants of this specificity are unknown.	2008	19043590
characterization and transcriptional analysis of an ecf sigma factor from xanthomonas campestris pv. campestris.	the genomic dna segment encoding the rpoe gene and its flanking region was cloned from xanthomonas campestris pv. campestris strain 11 (xc11). the transcriptional start site of rpoe was located at nucleotide g, which is 33 nucleotides preceding the putative translation initiation codon of rpoe, and a extracytoplasmic function sigma factors (sigma(e))-dependent promoter was identified with -35 (5'-gaactt-3') and -10 (5'-tctca-3') consensus sequences. the protein encoded by rpoe gene acted as a si ...	2008	19054112
origins of the xylella fastidiosa prophage-like regions and their impact in genome differentiation.	xylella fastidiosa is a gram negative plant pathogen causing many economically important diseases, and analyses of completely sequenced x. fastidiosa genome strains allowed the identification of many prophage-like elements and possibly phage remnants, accounting for up to 15% of the genome composition. to better evaluate the recent evolution of the x. fastidiosa chromosome backbone among distinct pathovars, the number and location of prophage-like regions on two finished genomes (9a5c and temecu ...	2008	19116666
function-biased choice of additives for optimization of protein crystallization - the case of the putative thioesterase pa5185 from pseudomonas aeruginosa pao1.	the crystal structure of pa5185, a putative thioesterase from pseudomonas aeruginosa strain pao1, was solved using multi-wavelength anomalous diffraction to 2.4 a. analysis of the structure and information about the putative function of the protein were used to optimize crystallization conditions. the crystal growth was optimized by applying additives with chemical similarity to a fragment of a putative pa5185 substrate (coa or its derivative). using new crystallization conditions containing thi ...	2008	19898606
myb72 is required in early signaling steps of rhizobacteria-induced systemic resistance in arabidopsis.	colonization of arabidopsis thaliana roots by nonpathogenic pseudomonas fluorescens wcs417r bacteria triggers a jasmonate/ethylene-dependent induced systemic resistance (isr) that is effective against a broad range of pathogens. microarray analysis revealed that the r2r3-myb-like transcription factor gene myb72 is specifically activated in the roots upon colonization by wcs417r. here, we show that t-dna knockout mutants myb72-1 and myb72-2 are incapable of mounting isr against the pathogens pseu ...	2008	18218967
pilb and pilt are atpases acting antagonistically in type iv pilus function in myxococcus xanthus.	type iv pili (t4p) are dynamic surface structures that undergo cycles of extension and retraction. t4p dynamics center on the pilb and pilt proteins, which are members of the secretion atpase superfamily of proteins. here, we show that pilb and pilt of the t4p system in myxococcus xanthus have atpase activity in vitro. using a structure-guided approach, we systematically mutagenized pilb and pilt to resolve whether both atp binding and hydrolysis are important for pilb and pilt function in vivo. ...	2008	18223089
the iron stimulon of xylella fastidiosa includes genes for type iv pilus and colicin v-like bacteriocins.	xylella fastidiosa is the etiologic agent of a wide range of plant diseases, including citrus variegated chlorosis (cvc), a major threat to citrus industry. the genomes of several strains of this phytopathogen were completely sequenced, enabling large-scale functional studies. dna microarrays representing 2,608 (91.6%) coding sequences (cds) of x. fastidiosa cvc strain 9a5c were used to investigate transcript levels during growth with different iron availabilities. when treated with the iron che ...	2008	18223091