bluuebunny/crossref_metadata_2025 huggingface dataset:
Flagellimonas eckloniae gen. nov., sp. nov., a mesophilic marine bacterium of the family Flavobacteriaceae, isolated from the rhizosphere of Ecklonia kurome
Authors: Bae Seung Seob , Kwon Kae Kyoung , Yang Sung Hyun , Lee Hee-Soon , Kim Sang-Jin , Lee Jung-Hyun
Published: May 2007

A marine bacterium, DOKDO 007T, was isolated from the rhizosphere of the marine alga Ecklonia kurome collected from Dokdo Island, Korea, in October 2004. The strain produced orange-coloured colonies on marine agar 2216. 16S rRNA gene sequence analysis indicated that the novel isolate belonged to the family Flavobacteriaceae and showed relatively high sequence similarities with members of the genus Muricauda (92.0–94.0 %). Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that the novel isolate shared a lineage with members of the genera Muricauda and Costertonia. Cells were aerobic, Gram-negative rods producing non-diffusible carotenoid pigments. In contrast to all other members of the family Flavobacteriaceae, cells of DOKDO 007T were motile by means of a polar flagellum. Optimal growth occurred in the presence of 3.5–4 % (w/v) sea salts (corresponding to 2.7–3.1 % NaCl), at pH 8 and at temperatures of 26–29 °C. The novel strain required Ca2+ ions in addition to NaCl for growth. The dominant fatty acids were iso-15 : 0, iso-15 : 1ω10c and 10-methyl-16 : 0. The major respiratory quinone was MK-6. The DNA G+C content was 56.3 mol%, an unusually high value for members of the family Flavobacteriaceae. On the basis of these polyphasic taxonomic data, strain DOKDO 007T should be classified as representing a new genus and novel species in the family Flavobacteriaceae, for which the name Flagellimonas eckloniae gen. nov., sp. nov. is proposed. The type strain is DOKDO 007T (=KCCM 42307T=JCM 13831T).
Desulfurispora thermophila gen. nov., sp. nov., a thermophilic, spore-forming sulfate-reducer isolated from a sulfidogenic fluidized-bed reactor
Authors: Kaksonen Anna H. , Spring Stefan , Schumann Peter , Kroppenstedt Reiner M. , Puhakka Jaakko A.
Published: May 2007

A thermophilic, Gram-positive, endospore-forming, sulfate-reducing bacterium was isolated from a sulfidogenic fluidized-bed reactor treating acidic metal- and sulfate-containing water. The strain, designated RA50E1T, was rod-shaped and motile. The strain grew at 40–67 °C (optimum growth at 59–61 °C) and pH 6.4–7.9 (optimum growth at pH 7.0–7.3). The strain tolerated up to 1 % NaCl. Sulfate, sulfite, thiosulfate and elemental sulfur were used as electron acceptors, but not nitrate, nitrite or iron(III). Electron donors utilized were H2/CO2(80 : 20, v/v), alcohols, various carboxylic acids and some sugars. Fermentative growth occurred on lactate and pyruvate. The cell wall containedmeso-diaminopimelic acid and the major respiratory isoprenoid quinone was menaquinone MK-7. Major whole-cell fatty acids were iso-C15 : 0and iso-C17 : 0. Strain RA50E1Twas distantly related to representatives of the generaDesulfotomaculum,Pelotomaculum,SporotomaculumandCryptanaerobacter. On the basis of 16S rRNA gene sequence data, the strain cannot be assigned to any known genus. Based on the phenotypic and phylogenetic features of strain RA50E1T, it is proposed that the strain represents a novel species in a new genus, for which the nameDesulfurispora thermophilagen. nov., sp. nov. is proposed. The type strain ofDesulfurispora thermophilais RA50E1T(=DSM 16022T=JCM 14018T).
Corynebacterium hansenii sp. nov., an α-glucosidase-negative bacterium related to Corynebacterium xerosis
Authors: Renaud François N. R. , Coustumier Alain Le , Wilhem Nathalie , Aubel Dominique , Riegel Philippe , Bollet Claude , Freney Jean
Published: May 2007

A novel strain, C-138T, belonging to the genus Corynebacterium was isolated from a severe thigh liposarcoma infection and its differentiation from Corynebacterium xerosis and Corynebacterium freneyi is described. Analysis of 16S rRNA gene sequences, rpoB sequences and the PCR profile of the 16S–23S spacer regions was not conclusive enough to differentiate strain C-138T from C. xerosis and C. freneyi. However, according to DNA–DNA hybridization data, strain C-138T constitutes a member of a distinct novel species. It can be differentiated from strains of C. xerosis and C. freneyi by colony morphology, the absence of α-glucosidase and some biochemical characteristics such as glucose fermentation at 42 °C and carbon assimilation substrates. The name Corynebacterium hansenii sp. nov. is proposed for this novel species; the type strain is C-138T (=CIP 108444T=CCUG 53252T).
Galbibacter mesophilus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae
Authors: Khan Shams Tabrez , Nakagawa Yasuyoshi , Harayama Shigeaki
Published: May 2007

A Gram-negative, yellow-pigmented, rod-shaped bacterial strain (Mok-17T) was isolated from marine sediment sampled in Okinawa Island, Japan. Based on analysis of the almost complete sequence of its 16S rRNA gene, strain Mok-17Twas found to belong to the familyFlavobacteriaceae. Strain Mok-17Tshowed highest 16S rRNA gene sequence similarity (91 %) toLeeuwenhoekiella marinoflavaandRobiginitalea biformata. In a phylogenetic tree based on the 16S rRNA gene, strain Mok-17Tformed a deep branch distinct from all other organisms in the familyFlavobacteriaceae. The major quinone was MK-6 and the major fatty acids were iso-15 : 0, iso-15 : 1, iso-17 : 0 3-OH and summed feature 3 (16 : 1ω7cand/or iso-15 : 0 2-OH). The DNA G+C content was 37 mol%. The phylogenetic distance to the type strains of all recognized species in the familyFlavobacteriaceaeand the phenotypic properties of strain Mok-17Tsupported its classification as representing a novel species in a new genus, for which the nameGalbibacter mesophilusgen. nov., sp. nov. is proposed. The type strain is Mok-17T(=NBRC 101624T=CIP 109219T).
Persicitalea jodogahamensis gen. nov., sp. nov., a marine bacterium of the family ‘Flexibacteraceae’, isolated from seawater in Japan
Authors: Yoon Jaewoo , Ishikawa Shu , Kasai Hiroaki , Yokota Akira
Published: May 2007

An obligately aerobic, Gram-negative, non-motile, pale-pink-pigmented, rod-shaped strain, designated Shu-9-SY12-35CT, was isolated from seawater in Jodogahama, Iwate, Japan, and was subjected to a polyphasic taxonomic examination. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated with the family ‘Flexibacteraceae’ of the phylumBacteroidetesand that it showed highest sequence similarity (86.4 %) withDyadobacter hamtensisHHS 11T. The novel isolate is phenotypically and physiologically different from strains described previously. The G+C content of the DNA was 56.3 mol%, MK-7 was the major menaquinone and iso-C15 : 0, C16 : 1ω7cand iso-C17 : 03-OH were the major fatty acids. On the basis of polyphasic taxonomic studies, it was concluded that strain Shu-9-SY12-35CTrepresents a new genus and species of the family ‘Flexibacteraceae’, for which the namePersicitalea jodogahamensisgen. nov., sp. nov. is proposed. The type strain ofPersicitalea jodogahamensisis Shu-9-SY12-35CT(=MBIC07417T=IAM 15412T=KCTC 12866T).
Reclassification of Flexibacter aggregans (Lewin 1969) Leadbetter 1974 as a later heterotypic synonym of Flexithrix dorotheae Lewin 1970
Authors: Hosoya Shoichi , Yokota Akira
Published: May 2007

The taxonomic relationship between [Flexibacter] aggregans IAM 14894T and Flexithrix dorotheae NBRC 15987T was investigated by means of DNA–DNA hybridization and phenotypic characteristics. On the basis of these results, it is proposed that Flexibacter aggregans (Lewin 1969) Leadbetter 1974 be considered a later heterotypic synonym of Flexithrix dorotheae Lewin 1970. Emended descriptions of the species Flexithrix dorotheae and the genus Flexithrix are also given.
Halalkalibacillus halophilus gen. nov., sp. nov., a novel moderately halophilic and alkaliphilic bacterium isolated from a non-saline soil sample in Japan
Authors: Echigo Akinobu , Fukushima Tadamasa , Mizuki Toru , Kamekura Masahiro , Usami Ron
Published: May 2007

A moderately halophilic and alkaliphilic bacterium, designated strain BH2T, was isolated from non-saline garden soil in Saitama, Japan. Cells of strain BH2T were motile, aerobic, rod-shaped and Gram-positive and contained A1γ, meso-diaminopimelic acid-type murein. Growth occurred in 5.0–25 % (w/v) NaCl (optimum, 10–15 %, w/v), at pH 5.5–10.0 (optimum, pH 8.5–9.0) and at 20–40 °C. The predominant isoprenoid quinone was menaquinone-7. The major cellular fatty acids were ai-C15 : 0, i-C16 : 0, ai-C17 : 0 and i-C15 : 0. The G+C content of the total DNA of strain BH2T was 35.1±0.4 mol% (±sd; n=5). The phylogenetic distance from species with validly published names was less than 94.1 %. The phylogenetic and phenotypic characteristics indicated that strain BH2T represents a novel genus and species, for which the name Halalkalibacillus halophilus gen. nov., sp. nov. is proposed. The type strain is BH2T (=JCM 14192T=DSM 18494T).
Lysobacter defluvii sp. nov., isolated from municipal solid waste
Authors: Yassin A. F. , Chen Wen-Ming , Hupfer H. , Siering C. , Kroppenstedt R. M. , Arun A. B. , Lai Wei-An , Shen Fo-Ting , Rekha P. D. , Young Chiu Chung
Published: May 2007

A bacterial isolate obtained from soil from a municipal landfill site in India was characterized using a polyphasic taxonomic approach. The colonies of the isolate were found to be yellow and highly mucoid. Comparative analysis of the 16S rRNA gene sequence showed that this isolate constitutes a distinct phyletic line within the genus Lysobacter, displaying >3 % sequence divergence with respect to recognized Lysobacter species. The generic assignment was confirmed by chemotaxonomic data, which revealed the presence of a fatty acid profile characteristic of members of the genus Lysobacter and consisting of saturated, unsaturated, straight-chain and branched-chain fatty acids as well as iso-C11 : 0 3-OH as hydroxylated fatty acid, and the presence of an ubiquinone with eight isoprene units (Q-8) as the predominant respiratory quinone. The genotypic and phenotypic data show that strain IMMIB APB-9T merits classification as representing a novel species of the genus Lysobacter, for which the name Lysobacter defluvii sp. nov. is proposed. The type strain is IMMIB APB-9T (=CCUG 53152T=DSM 18482T).
Withdrawal from cocaine self-administration produces long-lasting deficits in orbitofrontal-dependent reversal learning in rats
Authors: Calu Donna J. , Stalnaker Thomas A. , Franz Theresa M. , Singh Teghpal , Shaham Yavin , Schoenbaum Geoffrey
Published: April 2007

Drug addicts make poor decisions. These decision-making deficits have been modeled in addicts and laboratory animals using reversal-learning tasks. However, persistent reversal-learning impairments have been shown in rats and monkeys only after noncontingent cocaine injections. Current thinking holds that to represent the human condition effectively, animal models of addiction must utilize self-administration procedures in which drug is earned contingently; thus, it remains unclear whether reversal-learning deficits caused by noncontingent cocaine exposure are relevant to addiction. To test whether reversal learning deficits are caused by contingent cocaine exposure, we trained rats to self-administer cocaine, assessed cue-induced cocaine seeking in extinction tests after 1 and 30 d of withdrawal, and then tested for reversal learning more than a month later. We found robust time-dependent increases in cue-induced cocaine seeking in the two extinction tests (incubation of craving) and severe reversal-learning impairments.
Xenopus laevis In Vitro Fertilization and Natural Mating Methods
Authors: Sive Hazel L. , Grainger Robert M. , Harland Richard M.
Published: May 2007

INTRODUCTION

This protocol describes in vitro fertilization and natural mating methods for Xenopus laevis.
An Overview of Condensing and Noncondensing Polymeric Systems for Gene Delivery
Authors: Shenoy Dinesh B. , Amiji Mansoor M.
Published: May 2007

INTRODUCTION

Self-assembling synthetic vectors for DNA delivery are designed to fulfill several biological functions. They must be able to deliver their genetic payload specifically to the target tissue/cells in a site-specific manner, while protecting the genetic material from degradation by metabolic or immune pathways. Furthermore, they must exhibit minimal toxicity and be proven safe enough for therapeutic use. Ultimately, they must have the capability to express a therapeutic gene for a finite period of time in an appropriate, regulated fashion. The DNA encapsulated in these vectors may be in a condensed or noncondensed form, depending on the nature of the polymer and the technique used for formulating the vector system. The whole process presents many barriers at both tissue and cellular levels. Overcoming these hurdles is the principal objective for efficient polymer-based DNA therapeutics.
EGENES: Transcriptome-Based Plant Database of Genes with Metabolic Pathway Information and Expressed Sequence Tag Indices in KEGG
Authors: Masoudi-Nejad Ali , Goto Susumu , Jauregui Ruy , Ito Masumi , Kawashima Shuichi , Moriya Yuki , Endo Takashi R. , Kanehisa Minoru
Published: April 2007

EGENES is a knowledge-based database for efficient analysis of plant expressed sequence tags (ESTs) that was recently added to the KEGG suite of databases. It links plant genomic information with higher order functional information in a single database. It also provides gene indices for each genome. The genomic information in EGENES is a collection of EST contigs constructed from assembly of ESTs. Due to the extremely large genomes of plant species, the bulk collection of data such as ESTs is a quick way to capture a complete repertoire of genes expressed in an organism. Using ESTs for reconstructing metabolic pathways is a new expansion in KEGG and provides researchers with a new resource for species in which only EST sequences are available. Functional annotation in EGENES is a process of linking a set of genes/transcripts in each genome with a network of interacting molecules in the cell. EGENES is a multispecies, integrated resource consisting of genomic, chemical, and network information containing a complete set of building blocks (genes and molecules) and wiring diagrams (biological pathways) to represent cellular functions. Using EGENES, genome-based pathway annotation and EST-based annotation can now be compared and mutually validated. The ultimate goals of EGENES will be to: bring new plant species into KEGG by clustering and annotating ESTs; abstract knowledge and principles from large-scale plant EST data; and improve computational prediction of systems of higher complexity. EGENES will be updated at least once a year. EGENES is publicly available and is accessible by the following link or by KEGG's navigation system (http://www.genome.jp/kegg-bin/create_kegg_menu?category=plants_egenes).
Functional Analysis of PDX2 from Arabidopsis, a Glutaminase Involved in Vitamin B6 Biosynthesis
Authors: Tambasco-Studart Marina , Tews Ivo , Amrhein Nikolaus , Fitzpatrick Teresa B.
Published: April 2007

Vitamin B6 is an essential metabolite in all organisms, being required as a cofactor for a wide variety of biochemical reactions. De novo biosynthesis of the vitamin occurs in microorganisms and plants, but animals must obtain it from their diet. Two distinct and mutually exclusive de novo pathways have been identified to date, namely deoxyxylulose 5-phosphate dependent, which is restricted to a subset of eubacteria, and deoxyxylulose 5-phosphate independent, present in archaea, fungi, plants, protista, and most eubacteria. In these organisms, pyridoxal 5′-phosphate (PLP) formation is catalyzed by a single glutamine amidotransferase (PLP synthase) composed of a glutaminase domain, PDX2, and a synthase domain, PDX1. Despite plants being an important source of vitamin B6, very little is known about its biosynthesis. Here, we provide information for Arabidopsis thaliana. The functionality of PDX2 is demonstrated, using both in vitro and in vivo analyses. The expression pattern of PDX2 is assessed at both the RNA and protein level, providing insight into the spatial and temporal pattern of vitamin B6 biosynthesis. We then provide a detailed biochemical analysis of the plant PLP synthase complex. While the active sites of PDX1 and PDX2 are remote from each other, coordination of catalysis is much more pronounced with the plant proteins than its bacterial counterpart, Bacillus subtilis. Based on a model of the PDX1/PDX2 complex, mutation of a single residue uncouples enzyme coordination and in turn provides tangible evidence for the existence of the recently proposed ammonia tunnel through the core of PDX1.
Pea LATE BLOOMER1 Is a GIGANTEA Ortholog with Roles in Photoperiodic Flowering, Deetiolation, and Transcriptional Regulation of Circadian Clock Gene Homologs
Authors: Hecht Valérie , Knowles Claire L. , Vander Schoor Jacqueline K. , Liew Lim Chee , Jones Sarah E. , Lambert Misty J.M. , Weller James L.
Published: April 2007

Genes controlling the transition to flowering have been studied in several species, including Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), but have not yet received much attention in legumes. Here, we describe a new allelic series of late-flowering, photoperiod-insensitive mutants in the pea (Pisum sativum) LATE BLOOMER1 (LATE1) gene and show that LATE1 is an ortholog of Arabidopsis GIGANTEA. Mutants display defects in phytochrome B-dependent deetiolation under red light and in the diurnal regulation of pea homologs of several Arabidopsis circadian clock genes, including TIMING OF CAB1, EARLY FLOWERING4, and CIRCADIAN CLOCK ASSOCIATED1/LATE ELONGATED HYPOCOTYL. LATE1 itself shows strongly rhythmic expression with a small but distinct acute peak following dark-to-light transfer. Mutations in LATE1 prevent the induction of a FLOWERING LOCUS T (FT) homolog FTL in long days but cause only minor alteration to the rhythmic expression pattern of the only known group Ia CONSTANS homolog COLa. The late-flowering phenotype of late1 mutants can be completely rescued by grafting to the wild type, but this rescue is not associated with a significant increase in FTL transcript level in shoot apices. Genetic interactions of late1 with the photoperiod-insensitive, early-flowering sterile nodes (sn) mutant and impairment of the LATE1 diurnal expression rhythm in sn plants suggest that SN may also affect the circadian clock. These results show that several functions of Arabidopsis GIGANTEA are conserved in its pea ortholog and demonstrate that genetic pathways for photoperiodic flowering are likely to be conserved between these two species. They also suggest that in addition to its role in the floral transition, LATE1 also acts throughout reproductive development.
Temporal and Spatial Expression of the Major Allergens in Developing and Germinating Peanut Seed
Authors: Kang Il-Ho , Srivastava Pratibha , Ozias-Akins Peggy , Gallo Maria
Published: April 2007

Peanut (Arachis hypogaea) seed proteins Ara h 1, Ara h 2, and Ara h 3 are considered to be the major peanut allergens. However, little is known about their temporal and spatial expression during seed development and upon germination and seedling growth. In this study, transcript levels of the three major peanut allergen genes, ara h 1, ara h 2, and ara h 3, and their corresponding proteins were found in all cultivars. Expression patterns were heterogeneous depending on the specific peanut allergen gene and the cultivars tested. However, ara h 3 expression patterns among the cultivars were more variable than ara h 1 and ara h 2. Transcripts were tissue specific, observed in seeds, but not in leaves, flowers, or roots, and were undetectable during seed germination. In situ hybridizations and immunotissue prints revealed that both embryonic axes and cotyledons expressed the allergens. However, more ara h 1 and ara h 3 messenger RNA was detected in cotyledons relative to embryonic axes. Allergen polypeptide degradation patterns were different in embryonic axes compared with cotyledons during germination and seedling growth, with levels of Ara h 1 and Ara h 2 dramatically reduced compared to the Ara h 3 polypeptides in embryonic axes. These characterization studies of major peanut allergen genes and their corresponding seed storage proteins can provide the basic information needed for biochemical and molecular approaches to obtain a hypoallergenic peanut.
TILLING Mutants of Lotus japonicus Reveal That Nitrogen Assimilation and Fixation Can Occur in the Absence of Nodule-Enhanced Sucrose Synthase
Authors: Horst Irmtraud , Welham Tracey , Kelly Simon , Kaneko Takakazu , Sato Shusei , Tabata Satoshi , Parniske Martin , Wang Trevor L.
Published: April 2007

In all plant species studied to date, sucrose synthase occurs as multiple isoforms. The specific functions of the different isoforms are for the most part not clear. Six isoforms of sucrose synthase have been identified in the model legume Lotus japonicus, the same number as in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). The genes encoding these isoforms are differentially expressed in all plant organs examined, although one, LjSUS4, is only expressed in flowers. LjSUS1 is the most highly expressed in all plant organs tested, except root nodules, where LjSUS3 accounts for more than 60% of the total SUS transcripts. One gene, LjSUS2, produces two transcripts due to alternative splicing, a feature not observed in other species to date. We have isolated plants carrying ethyl methanesulfonate-induced mutations in several SUS genes by targeting-induced local lesions in genomes reverse genetics and examined the effect of null alleles of two genes, LjSUS1 and LjSUS3, on nodule function. No differences were observed between the mutants and wild-type plants under glasshouse conditions, but there was evidence for a nitrogen-starvation phenotype in the sus3-1 mutant and severe impairment of growth in the sus1-1/sus3-1 double mutant under specific environmental conditions. Nodules of sus3-1 mutant plants retained a capacity for nitrogen fixation under all conditions. Thus, nitrogen fixation can occur in L. japonicus nodules even in the absence of LjSUS3 (the major nodule-induced isoform of SUS), so LjSUS1 must also contribute to the maintenance of nitrogen assimilation.
The GH3 Acyl Adenylase Family Member PBS3 Regulates Salicylic Acid-Dependent Defense Responses in Arabidopsis
Authors: Nobuta K. , Okrent R.A. , Stoutemyer M. , Rodibaugh N. , Kempema L. , Wildermuth M.C. , Innes R.W.
Published: April 2007

The pbs3-1 mutant, identified in a screen for Arabidopsis (Arabidopsis thaliana) mutants exhibiting enhanced susceptibility to the avirulent Pseudomonas syringae pathogen DC3000 (avrPphB), also exhibits enhanced susceptibility to virulent P. syringae strains, suggesting it may impact basal disease resistance. Because induced salicylic acid (SA) is a critical mediator of basal resistance responses, free and glucose-conjugated SA levels were measured and expression of the SA-dependent pathogenesis-related (PR) marker, PR1, was assessed. Surprisingly, whereas accumulation of the SA glucoside and expression of PR1 were dramatically reduced in the pbs3-1 mutant in response to P. syringae (avrRpt2) infection, free SA was elevated. However, in response to exogenous SA, the conversion of free SA to SA glucoside and the induced expression of PR1 were similar in pbs3-1 and wild-type plants. Through positional cloning, complementation, and sequencing, we determined that the pbs3-1 mutant contains two point mutations in the C-terminal region of the protein encoded by At5g13320, resulting in nonconserved amino acid changes in highly conserved residues. Additional analyses with Arabidopsis containing T-DNA insertion (pbs3-2) and transposon insertion (pbs3-3) mutations in At5g13320 confirmed our findings with pbs3-1. PBS3 (also referred to as GH3.12) is a member of the GH3 family of acyl-adenylate/thioester-forming enzymes. Characterized GH3 family members, such as JAR1, act as phytohormone-amino acid synthetases. Thus, our results suggest that amino acid conjugation plays a critical role in SA metabolism and induced defense responses, with PBS3 acting upstream of SA, directly on SA, or on a competitive inhibitor of SA.
Transcriptome Analysis of Arbuscular Mycorrhizal Roots during Development of the Prepenetration Apparatus
Authors: Siciliano Valeria , Genre Andrea , Balestrini Raffaella , Cappellazzo Gilda , deWit Pierre J.G.M. , Bonfante Paola
Published: April 2007

Information on changes in the plant transcriptome during early interaction with arbuscular mycorrhizal (AM) fungi is still limited since infections are usually not synchronized and plant markers for early stages of colonization are not yet available. A prepenetration apparatus (PPA), organized in epidermal cells during appressorium development, has been reported to be responsible for assembling a trans-cellular tunnel to accommodate the invading fungus. Here, we used PPAs as markers for cell responsiveness to fungal contact to investigate gene expression at this early stage of infection with minimal transcript dilution. PPAs were identified by confocal microscopy in transformed roots of Medicago truncatula expressing green fluorescent protein-HDEL, colonized by the AM fungus Gigaspora margarita. A PPA-targeted suppressive-subtractive cDNA library was built, the cDNAs were cloned and sequenced, and, consequently, 107 putative interaction-specific genes were identified. The expression of a subset of 15 genes, selected by reverse northern dot blot screening, and five additional genes, potentially involved in PPA formation, was analyzed by real-time reverse transcription-polymerase chain reaction and compared with an infection stage, 48 h after the onset of the PPA. Comparison of the expression profile of G. margarita-inoculated wild type and the mycorrhiza-defective dmi3-1 mutant of M. truncatula revealed that an expansin-like gene, expressed in wild-type epidermis during PPA development, can be regarded as an early host marker for successful mycorrhization. A putative Avr9/Cf-9 rapidly elicited gene, found to be up-regulated in the mutant, suggests novel regulatory roles for the DMI3 protein in the early mycorrhization process.
Analysis of Leaf Development infuguMutants of Arabidopsis Reveals Three Compensation Modes That Modulate Cell Expansion in Determinate Organs
Authors: Ferjani Ali , Horiguchi Gorou , Yano Satoshi , Tsukaya Hirokazu
Published: April 2007

In multicellular organisms, the coordination of cell proliferation and expansion is fundamental for proper organogenesis, yet the molecular mechanisms involved in this coordination are largely unexplored. In plant leaves, the existence of this coordination is suggested by compensation, in which a decrease in cell number triggers an increase in mature cell size. To elucidate the mechanisms of compensation, we isolated five new Arabidopsis (Arabidopsis thaliana) mutants (fugu1–fugu5) that exhibit compensation. These mutants were characterized together with angustifolia3 (an3), erecta (er), and a KIP-RELATED PROTEIN2 (KRP2) overexpressor, which were previously reported to exhibit compensation. Time-course analyses of leaf development revealed that enhanced cell expansion in fugu2-1, fugu5-1, an3-4, and er-102 mutants is induced postmitotically, indicating that cell enlargement is not caused by the uncoupling of cell division from cell growth. In each of the mutants, either the rate or duration of cell expansion was selectively enhanced. In contrast, we found that enhanced cell expansion in KRP2 overexpressor occurs during cell proliferation. We further demonstrated that enhanced cell expansion occurs in cotyledons with dynamics similar to that in leaves. In contrast, cell expansion was not enhanced in roots even though they exhibit decreased cell numbers. Thus, compensation was confirmed to occur preferentially in determinate organs. Flow cytometric analyses revealed that increases in ploidy level are not always required to trigger compensation, suggesting that compensation is only partially mediated by ploidy-dependent processes. Our results suggest that compensation reflects an organ-wide coordination of cell proliferation and expansion in determinate organs, and involves at least three different expansion pathways.
Down-Regulation of a SILENT INFORMATION REGULATOR2-Related Histone Deacetylase Gene, OsSRT1, Induces DNA Fragmentation and Cell Death in Rice
Authors: Huang Limin , Sun Qianwen , Qin Fujun , Li Chen , Zhao Yu , Zhou Dao-Xiu
Published: April 2007

The SILENT INFORMATION REGULATOR2 (SIR2) family proteins are NAD+-dependent histone deacetylases. Sir2 is involved in chromatin silencing at the mating-type loci, rDNA, and telomeres in yeast and is associated with lifespan extension in yeast, worms, and flies, but also in a broader range of additional functions. In this work, we investigated the role of OsSRT1, one of the two SIR2-related genes found in rice (Oryza sativa). We show that OsSRT1 is a widely expressed nuclear protein with higher levels in rapidly dividing tissues. OsSRT1 RNA interference induced an increase of histone H3K9 (lysine-9 of H3) acetylation and a decrease of H3K9 dimethylation, leading to H2O2 production, DNA fragmentation, cell death, and lesions mimicking plant hypersensitive responses during incompatible interactions with pathogens, whereas overexpression of OsSRT1 enhanced tolerance to oxidative stress. Transcript microarray analysis revealed that the transcription of many transposons and retrotransposons in addition to genes related to hypersensitive response and/or programmed cell death was activated. Chromatin immunoprecipitation assays showed that OsSRT1 down-regulation induced histone H3K9 acetylation on the transposable elements and some of the hypersensitive response-related genes, suggesting that these genes may be among the primary targets of deacetylation regulated by OsSRT1. Our data together suggest that the rice SIR2-like gene is required for safeguard against genome instability and cell damage to ensure plant cell growth, but likely implicates different molecular mechanisms than yeast and animal homologs.
The Response of Carbon Metabolism and Antioxidant Defenses of Alfalfa Nodules to Drought Stress and to the Subsequent Recovery of Plants
Authors: Naya Loreto , Ladrera Ruben , Ramos Javier , González Esther M. , Arrese-Igor Cesar , Minchin Frank R. , Becana Manuel
Published: April 2007

Alfalfa (Medicago sativa) plants were exposed to drought to examine the involvement of carbon metabolism and oxidative stress in the decline of nitrogenase (N2ase) activity. Exposure of plants to a moderate drought (leaf water potential of −1.3 MPa) had no effect on sucrose (Suc) synthase (SS) activity, but caused inhibition of N2ase activity (−43%), accumulation of succinate (+36%) and Suc (+58%), and up-regulation of genes encoding cytosolic CuZn-superoxide dismutase (SOD), plastid FeSOD, cytosolic glutathione reductase, and bacterial MnSOD and catalases B and C. Intensification of stress (−2.1 MPa) decreased N2ase (−82%) and SS (−30%) activities and increased malate (+40%), succinate (+68%), and Suc (+435%). There was also up-regulation (mRNA) of cytosolic ascorbate peroxidase and down-regulation (mRNA) of SS, homoglutathione synthetase, and bacterial catalase A. Drought stress did not affect nifH mRNA level or leghemoglobin expression, but decreased MoFe- and Fe-proteins. Rewatering of plants led to a partial recovery of the activity (75%) and proteins (>64%) of N2ase, a complete recovery of Suc, and a decrease of malate (−48%) relative to control. The increase in O2 diffusion resistance, the decrease in N2ase-linked respiration and N2ase proteins, the accumulation of respiratory substrates and oxidized lipids and proteins, and the up-regulation of antioxidant genes reveal that bacteroids have their respiratory activity impaired and that oxidative stress occurs in nodules under drought conditions prior to any detectable effect on SS or leghemoglobin. We conclude that a limitation in metabolic capacity of bacteroids and oxidative damage of cellular components are contributing factors to the inhibition of N2ase activity in alfalfa nodules.
A Reassessment of the Function of the So-Called Compatible Solutes in the Halophytic Plumbaginaceae Limonium latifolium
Authors: Gagneul David , Aïnouche Abdelkader , Duhazé Claire , Lugan Raphaël , Larher François Robert , Bouchereau Alain
Published: April 2007

The compatible solute hypothesis posits that maintaining osmotic equilibrium under conditions of high salinity requires synthesis of organic compounds, uptake of potassium ions, and partial exclusion of NaCl. To assess whether osmotic adaptation in Limonium latifolium proceeds according to this hypothesis, a comprehensive analysis of solute accumulation during NaCl treatments was conducted. Determination of prevailing inorganic ions and establishment of the metabolic profiles for low M  r organic substances revealed that contrary to the mentioned hypothesis the major contributors to osmolarity were constituted by inorganic solutes. Independent of salinity, only 25% of this osmolarity resulted from organic solutes such as Suc and hexoses. Proline (Pro), β-alanine betaine, and choline-O-sulfate were minor contributors to osmolarity. Compatible inositols also occurred, especially chiro-inositol, characterized for the first time in this species, to our knowledge. Principal component analysis showed that only a limited number of metabolic reconfigurations occurred in response to dynamic changes in salinity. Under such conditions only sugars, chiro-inositol, and Pro behave as active osmobalancers. Analysis of metabolic profiles during acclimatization to either mild salinity or nonsaline conditions showed that organic solute accumulation is predominantly controlled by constitutive developmental programs, some of which might be slightly modulated by salinity. Osmolarity provided under such conditions can be sufficient to maintain turgor in salinized seedlings. Compartmental analysis of Pro and β-alanine betaine in leaf tissues demonstrated that these solutes, mainly located in vacuoles under nonsaline conditions, could be partly directed to the cytosol in response to salinization. Thus they did not conform with the predictions of the compatible solute hypothesis.
The COMATOSE ATP-Binding Cassette Transporter Is Required for Full Fertility in Arabidopsis
Authors: Footitt Steven , Dietrich Daniela , Fait Aaron , Fernie Alisdair R. , Holdsworth Michael J. , Baker Alison , Theodoulou Frederica L.
Published: April 2007

COMATOSE (CTS) encodes a peroxisomal ATP-binding cassette transporter required not only for β-oxidation of storage lipids during germination and establishment, but also for biosynthesis of jasmonic acid and conversion of indole butyric acid to indole acetic acid. cts mutants exhibited reduced fertilization, which was rescued by genetic complementation, but not by exogenous application of jasmonic acid or indole acetic acid. Reduced fertilization was also observed in thiolase (kat2-1) and peroxisomal acyl-Coenzyme A synthetase mutants (lacs6-1,lacs7-1), indicating a general role for β-oxidation in fertility. Genetic analysis revealed reduced male transmission of cts alleles and both cts pollen germination and tube growth in vitro were impaired in the absence of an exogenous carbon source. Aniline blue staining of pollinated pistils demonstrated that pollen tube growth was affected only when both parents bore the cts mutation, indicating that expression of CTS in either male or female tissues was sufficient to support pollen tube growth in vivo. Accordingly, abundant peroxisomes were detected in a range of maternal tissues. Although γ-aminobutyric acid levels were reduced in flowers of cts mutants, they were unchanged in kat2-1, suggesting that alterations in γ-aminobutyric acid catabolism do not contribute to the reduced fertility phenotype through altered pollen tube targeting. Taken together, our data support an important role for β-oxidation in fertility in Arabidopsis (Arabidopsis thaliana) and suggest that this pathway could play a role in the mobilization of lipids in both pollen and female tissues.
Overlap of Proteome Changes inMedicago truncatulain Response to Auxin andSinorhizobium meliloti
Authors: van Noorden Giel E. , Kerim Tursun , Goffard Nicolas , Wiblin Robert , Pellerone Flavia I. , Rolfe Barry G. , Mathesius Ulrike
Published: April 2007

We used proteome analysis to identify proteins induced during nodule initiation and in response to auxin in Medicago truncatula. From previous experiments, which found a positive correlation between auxin levels and nodule numbers in the M. truncatula supernodulation mutant sunn (supernumerary nodules), we hypothesized (1) that auxin mediates protein changes during nodulation and (2) that auxin responses might differ between the wild type and the supernodulating sunn mutant during nodule initiation. Increased expression of the auxin response gene GH3:β-glucuronidase was found during nodule initiation in M. truncatula, similar to treatment of roots with auxin. We then used difference gel electrophoresis and tandem mass spectrometry to compare proteomes of wild-type and sunn mutant roots after 24 h of treatment with Sinorhizobium meliloti, auxin, or a control. We identified 131 of 270 proteins responding to treatment with S. meliloti and/or auxin, and 39 of 89 proteins differentially displayed between the wild type and sunn. The majority of proteins changed similarly in response to auxin and S. meliloti after 24 h in both genotypes, supporting hypothesis 1. Proteins differentially accumulated between untreated wild-type and sunn roots also showed changes in auxin response, consistent with altered auxin levels in sunn. However, differences between the genotypes after S. meliloti inoculation were largely not due to differential auxin responses. The role of the identified candidate proteins in nodule initiation and the requirement for their induction by auxin could be tested in future functional studies.
Identification of a Novel Chloroplast Protein AtNYE1 Regulating Chlorophyll Degradation during Leaf Senescence in Arabidopsis
Authors: Ren Guodong , An Kun , Liao Yang , Zhou Xiao , Cao Yajun , Zhao Huifang , Ge Xiaochun , Kuai Benke
Published: April 2007

A dramatic increase of chlorophyll (Chl) degradation occurs during senescence of vegetative plant organs and fruit ripening. Although the biochemical pathway of Chl degradation has long been proposed, little is known about its regulatory mechanism. Identification of Chl degradation-disturbed mutants and subsequently isolation of responsible genes would greatly facilitate the elucidation of the regulation of Chl degradation. Here, we describe a nonyellowing mutant of Arabidopsis (Arabidopsis thaliana), nye1-1, in which 50% Chl was retained, compared to less than 10% in the wild type (Columbia-0), at the end of a 6-d dark incubation. Nevertheless, neither photosynthesis- nor senescence-associated process was significantly affected in nye1-1. Characteristically, a significant reduction in pheophorbide a oxygenase activity was detected in nye1-1. However, no detectable accumulation of either chlorophyllide a or pheophorbide a was observed. Reciprocal crossings revealed that the mutant phenotype was caused by a monogenic semidominant nuclear mutation. We have identified AtNYE1 by positional cloning. Dozens of its putative orthologs, predominantly appearing in higher plant species, were identified, some of which have been associated with Chl degradation in a few crop species. Quantitative polymerase chain reaction analysis showed that AtNYE1 was drastically induced by senescence signals. Constitutive overexpression of AtNYE1 could result in either pale-yellow true leaves or even albino seedlings. These results collectively indicate that NYE1 plays an important regulatory role in Chl degradation during senescence by modulating pheophorbide a oxygenase activity.
Maize Histone Deacetylasehda101Is Involved in Plant Development, Gene Transcription, and Sequence-Specific Modulation of Histone Modification of Genes and Repeats
Authors: Rossi Vincenzo , Locatelli Sabrina , Varotto Serena , Donn Guenter , Pirona Raul , Henderson David A. , Hartings Hans , Motto Mario
Published: April 2007

Enzymes catalyzing histone acetylation and deacetylation contribute to the modulation of chromatin structure, thus playing an important role in regulating gene and genome activity. We showed that downregulation and overexpression of the maize (Zea mays) Rpd3-type hda101 histone deacetylase gene induced morphological and developmental defects. Total levels of acetylated histones and histone acetylation of both repetitive and nonrepetitive sequences were affected in hda101 transgenic mutants. However, only transcript levels of genes but not repeats were altered. In particular, hda101 transgenic mutants showed differential expression of genes involved in vegetative-to-reproductive transition, such as liguleless2 and knotted-like genes and their repressor rough sheath2, which are required for meristem initiation and maintenance. Perturbation of hda101 expression also affected histone modifications other than acetylation, including histone H3 dimethylation at Lys-4 and Lys-9 and phosphorylation at Ser-10. Our results indicate that hda101 affects gene transcription and provide evidence of its involvement in setting the histone code, thus mediating developmental programs. Possible functional differences between maize hda101 and its Arabidopsis thaliana ortholog HDA19 are discussed.
TheArabidopsisAAA ATPase SKD1 Is Involved in Multivesicular Endosome Function and Interacts with Its Positive Regulator LYST-INTERACTING PROTEIN5
Authors: Haas Thomas J. , Sliwinski Marek K. , Martínez Dana E. , Preuss Mary , Ebine Kazuo , Ueda Takashi , Nielsen Erik , Odorizzi Greg , Otegui Marisa S.
Published: April 2007

In yeast and mammals, the AAA ATPase Vps4p/SKD1 (for Vacuolar protein sorting 4/SUPPRESSOR OF K+ TRANSPORT GROWTH DEFECT1) is required for the endosomal sorting of secretory and endocytic cargo. We identified a VPS4/SKD1 homolog in Arabidopsis thaliana, which localizes to the cytoplasm and to multivesicular endosomes. In addition, green fluorescent protein–SKD1 colocalizes on multivesicular bodies with fluorescent fusion protein endosomal Rab GTPases, such as ARA6/RabF1, RHA1/RabF2a, and ARA7/RabF2b, and with the endocytic marker FM4-64. The expression of SKD1E232Q, an ATPase-deficient version of SKD1, induces alterations in the endosomal system of tobacco (Nicotiana tabacum) Bright Yellow 2 cells and ultimately leads to cell death. The inducible expression of SKD1E232Q in Arabidopsis resulted in enlarged endosomes with a reduced number of internal vesicles. In a yeast two-hybrid screen using Arabidopsis SKD1 as bait, we isolated a putative homolog of mammalian LYST-INTERACTING PROTEIN5 (LIP5)/SKD1 BINDING PROTEIN1 and yeast Vta1p (for Vps twenty associated 1 protein). Arabidopsis LIP5 acts as a positive regulator of SKD1 by increasing fourfold to fivefold its in vitro ATPase activity. We isolated a knockout homozygous Arabidopsis mutant line with a T-DNA insertion in LIP5. lip5 plants are viable and show no phenotypic alterations under normal growth conditions, suggesting that basal SKD1 ATPase activity is sufficient for plant development and growth.
Roles of Arabidopsis Cyclin-Dependent Kinase C Complexes in Cauliflower Mosaic Virus Infection, Plant Growth, and Development
Authors: Cui Xiaofeng , Fan Baofang , Scholz James , Chen Zhixiang
Published: April 2007

The C-terminal domain (CTD) of RNA polymerase II is phosphorylated during the transcription cycle by three cyclin-dependent kinases (CDKs): CDK7, CDK8, and CDK9. CDK9 and its interacting cyclin T partners belong to the positive transcription elongation factor b (P-TEFb) complexes, which phosphorylate the CTD to promote transcription elongation. We report that Arabidopsis thaliana CDK9-like proteins, CDKC;1 and CDKC;2, and their interacting cyclin T partners, CYCT1;4 and CYCT1;5, play important roles in infection with Cauliflower mosaic virus (CaMV). cdkc;2 and cyct1;5 knockout mutants are highly resistant and cdkc;2 cyct1;5 double mutants are extremely resistant to CaMV. The mutants respond normally to other types of plant viruses that do not replicate by reverse transcription. Expression of a reporter gene driven by the CaMV 35S promoter is markedly reduced in the cdkc;2 and cyct1;5 mutants, indicating that the kinase complexes are important for transcription from the viral promoter. Loss of function of CDKC;1/CDKC;2 or CYCT1;4/CYCT1;5 results in complete resistance to CaMV as well as altered leaf and flower growth, trichome development, and delayed flowering. These results establish Arabidopsis CDKC kinase complexes as important host targets of CaMV for transcriptional activation of viral genes and critical regulators of plant growth and development.
Variability in hydrocortisone plasma and saliva pharmacokinetics following intravenous and oral administration to Patients with adrenal insufficiency
Authors: Thomson A. H. , Devers M. C. , Wallace A. M. , Grant D. , Campbell K. , Freel M. , Connell J. M. C.
Published: May 2007

Objective  The best method for determining hydrocortisone replacement therapy is not well defined. This study aimed to assess interindividual variability in cortisol pharmacokinetics and to investigate whether measurement of salivary cortisol provides a useful alternative to plasma concentration measurements.

Design  Intravenous (IV) and oral crossover.

Patients  Twenty‐seven patients with primary or secondary adrenal insufficiency who had been on stable replacement therapy for at least 3 months.

Measurements  Plasma and salivary concentrations of cortisol were measured up to 8 h following administration of hydrocortisone.

Results  After IV administration, Cmax ranged from 715 to 8313 nmol/l, area under the curve (AUC) from 1112 to 12 177 nmol h/l and cortisol clearance had a median (range) of 0·267 (0·076–0·540) l/h/kg. After oral administration, Cmax ranged from 422 to 1554 nmol/l, AUC 1081–5471 nmol h/l and oral clearance had a median (range) of 0·267 (0·081–0·363) l/h/kg. There was no clear relationship between paired saliva and plasma cortisol concentrations after IV or oral dosing. Plasma and salivary AUC2−8 h after IV administration were highly correlated (r2 = 0·77) but differences between predicted and measured plasma AUCs ranged from 3% to 90%. There was a poor correlation between plasma and saliva AUC2−6 h after oral administration (r2 = 0·16).

Conclusions  The wide interindividual variability in plasma and salivary profiles of cortisol following the administration of IV and oral hydrocortisone to patients with adrenal insufficiency and the poor correlation between salivary and plasma measurements suggest that salivary cortisol measurements cannot be used for individual hydrocortisone dosage adjustment.