bluuebunny/crossref_metadata_2025 huggingface dataset:
A mixture model approach to the tests of concordance and discordance between two large-scale experiments with two-sample groups
Authors: Lai Yinglei , Adam Bao-ling , Podolsky Robert , She Jin-Xiong
Published: March 2007

Motivation: Due to advances in experimental technologies, such as microarray, mass spectrometry and nuclear magnetic resonance, it is feasible to obtain large-scale data sets, in which measurements for a large number of features can be simultaneously collected. However, the sample sizes of these data sets are usually small due to their relatively high costs, which leads to the issue of concordance among different data sets collected for the same study: features should have consistent behavior in different data sets. There is a lack of rigorous statistical methods for evaluating this concordance or discordance.

Methods: Based on a three-component normal-mixture model, we propose two likelihood ratio tests for evaluating the concordance and discordance between two large-scale data sets with two sample groups. The parameter estimation is achieved through the expectation-maximization (E-M) algorithm. A normal-distribution-quantile-based method is used for data transformation.

Results: To evaluate the proposed tests, we conducted some simulation studies, which suggested their satisfactory performances. As applications, the proposed tests were applied to three SELDI-MS data sets with replicates. One data set has replicates from different platforms and the other two have replicates from the same platform. We found that data generated by SELDI-MS showed satisfactory concordance between replicates from the same platform but unsatisfactory concordance between replicates from different platforms.

Availability: The R codes are freely available at http://home.gwu.edu/~ylai/research/Concordance

Contact:  ylai@gwu.edu
SBML export interface for the systems biology toolbox for MATLAB
Authors: Schmidt Hening , Drews Gunnar , Vera Julio , Wolkenhauer Olaf
Published: March 2007

Summary: In this application note, we present an Systems biology markup language (SBML) export interface for the Systems Biology Toolbox for MATLAB. This interface allows modelers to automatically convert models, represented in the toolbox's own format (SBmodels) to SBML files. Since SBmodels do not explicitly contain all the information that is required to generate SBML, the necessary information is gathered by parsing SBmodels. The export can be done in two different ways. First, it is possible to call the export from the command line, thereby directly converting a model to an SBML file. The second option is to inspect and edit the conversion results with the help of a graphical user interface and to subsequently export the model to SBML.

Availability: The SBML export interface has been integrated into the Systems Biology Toolbox for MATLAB, which is open source and freely available from http://www.sbtoolbox2.org. The website also contains a tutorial, extensive documentation and examples.

Contact:  henning@fcc.chalmers.se
Mediante: a web-based microarray data manager
Authors: Le Brigand Kevin , Barbry Pascal
Published: March 2007

Summary: Mediante is a MIAME-compliant microarray data manager that links together annotations and experimental data. Developed as a J2EE three-tier application, Mediante integrates a management system for production of long oligonucleotide microarrays, an experimental data repository suitable for home made or commercial microarrays, and a user interface dedicated to the management of microarrays projects. Several tools allow quality control of hybridizations and submission of validated data to public repositories.

Availability:  http://www.microarray.fr

Contact:  barbry@ipmc.cnrs.fr or lebrigand@ipmc.cnrs.fr

Supplementary information:  http://www.microarray.fr/SP/lebrigand2007/
GenABEL: an R library for genome-wide association analysis
Authors: Aulchenko Yurii S. , Ripke Stephan , Isaacs Aaron , van Duijn Cornelia M.
Published: March 2007

Here we describe an R library for genome-wide association (GWA) analysis. It implements effective storage and handling of GWA data, fast procedures for genetic data quality control, testing of association of single nucleotide polymorphisms with binary or quantitative traits, visualization of results and also provides easy interfaces to standard statistical and graphical procedures implemented in base R and special R libraries for genetic analysis. We evaluated GenABEL using one simulated and two real data sets. We conclude that GenABEL enables the analysis of GWA data on desktop computers.

Availability:  http://cran.r-project.org

Contact:  i.aoultchenko@erasmusmc.nl
Using DNA microarrays to study gene expression in closely related species
Authors: Oshlack Alicia , Chabot Adrien E. , Smyth Gordon K. , Gilad Yoav
Published: March 2007

Motivation: Comparisons of gene expression levels within and between species have become a central tool in the study of the genetic basis for phenotypic variation, as well as in the study of the evolution of gene regulation. DNA microarrays are a key technology that enables these studies. Currently, however, microarrays are only available for a small number of species. Thus, in order to study gene expression levels in species for which microarrays are not available, researchers face three sets of choices: (i) use a microarray designed for another species, but only compare gene expression levels within species, (ii) construct a new microarray for every species whose gene expression profiles will be compared or (iii) build a multi-species microarray with probes from each species of interest. Here, we use data collected using a multi-primate cDNA array to evaluate the reliability of each approach.

Results: We find that, for inter-species comparisons, estimates of expression differences based on multi-species microarrays are more accurate than those based on multiple species-specific arrays. We also demonstrate that within-species expression differences can be estimated using a microarray for a closely related species, without discernible loss of information.

Contact: A.O. (oshlack@wehi.edu.au) or Y.G. (gilad@uchicago.edu)

Supplementary information: Supplementary data are available at Bioinformatics online.
Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP)
Authors: Ye Zhi-Qiang , Zhao Shu-Qi , Gao Ge , Liu Xiao-Qiao , Langlois Robert E. , Lu Hui , Wei Liping
Published: March 2007

Motivation: The rapid accumulation of single amino acid polymorphisms (SAPs), also known as non-synonymous single nucleotide polymorphisms (nsSNPs), brings the opportunities and needs to understand and predict their disease association. Currently published attributes are limited, the detailed mechanisms governing the disease association of a SAP remain unclear and thus, further investigation of new attributes and improvement of the prediction are desired.

Results: A SAP dataset was compiled from the Swiss-Prot variant pages. We extracted and demonstrated the effectiveness of several new biologically informative attributes including the structural neighbor profiles that describe the SAP's microenvironment, nearby functional sites that measure the structure-based and sequence-based distances between the SAP site and its nearby functional sites, aggregation properties that measure the likelihood of protein aggregation and disordered regions that consider whether the SAP is located in structurally disordered regions. The new attributes provided insights into the mechanisms of the disease association of SAPs. We built a support vector machines (SVMs) classifier employing a carefully selected set of new and previously published attributes. Through a strict protein-level 5-fold cross-validation, we attained an overall accuracy of 82.61%, and an MCC of 0.60. Moreover, a web server was developed to provide a user-friendly interface for biologists.

Availability: The web server is available at http://sapred.cbi.pku.edu.cn/

Contact:  sapred@mail.cbi.pku.edu.cn

Supplementary information: Supplementary data are available at http://sapred.cbi.pku.edu.cn/supp.do
Searching for three-dimensional secondary structural patterns in proteins with ProSMoS
Authors: Shi Shuoyong , Zhong Yi , Majumdar Indraneel , Sri Krishna S. , Grishin Nick V.
Published: March 2007

Motivation: Many evolutionarily distant, but functionally meaningful links between proteins come to light through comparison of spatial structures. Most programs that assess structural similarity compare two proteins to each other and find regions in common between them. Structural classification experts look for a particular structural motif instead. Programs base similarity scores on superposition or closeness of either Cartesian coordinates or inter-residue contacts. Experts pay more attention to the general orientation of the main chain and mutual spatial arrangement of secondary structural elements. There is a need for a computational tool to find proteins with the same secondary structures, topological connections and spatial architecture, regardless of subtle differences in 3D coordinates.

Results: We developed ProSMoS—a Protein Structure Motif Search program that emulates an expert. Starting from a spatial structure, the program uses previously delineated secondary structural elements. A meta-matrix of interactions between the elements (parallel or antiparallel) minding handedness of connections (left or right) and other features (e.g. element lengths and hydrogen bonds) is constructed prior to or during the searches. All structures are reduced to such meta-matrices that contain just enough information to define a protein fold, but this definition remains very general and deviations in 3D coordinates are tolerated. User supplies a meta-matrix for a structural motif of interest, and ProSMoS finds all proteins in the protein data bank (PDB) that match the meta-matrix. ProSMoS performance is compared to other programs and is illustrated on a β-Grasp motif. A brief analysis of all β-Grasp-containing proteins is presented.

Program availability: ProSMoS is freely available for non-commercial use from ftp://iole.swmed.edu/pub/ProSMoS.

Contact:  grishin@chop.swmed.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
SNPTools: a software tool for visualization and analysis of microarray data
Authors: Sørensen Frank J. , Andersen Claus L. , Wiuf Carsten
Published: March 2007

Summary: We have created a software tool, SNPTools, for analysis and visualization of microarray data, mainly SNP array data. The software can analyse and find differences in intensity levels between groups of arrays and identify segments of SNPs (genes, clones), where the intensity levels differ significantly between the groups. In addition, SNPTools can show jointly loss-of-heterozygosity (LOH) data (derived from genotypes) and intensity data for paired samples of tumour and normal arrays. The output graphs can be manipulated in various ways to modify and adjust the layout. A wizard allows options and parameters to be changed easily and graphs replotted. All output can be saved in various formats, and also re-opened in SNPTools for further analysis. For explorative use, SNPTools allows various genome information to be loaded onto the graphs.

Availability: The software, example data sets and tutorials are freely available from http://www.birc.au.dk/snptools

Contact:  wiuf@birc.au.dk
Unpublished material from the memorandum book of Robert Hooke, Guildhall Library MS 1758
Authors: Henderson Felicity
Published: March 2007

Robert Hooke began keeping a journal or memorandum book on 10 March 1672, and continued until May 1683. This document, now Guildhall Library MS 1758, is the most important record of Hooke's life and work in his most active period, and is a significant source of information about the activities of the early Fellows of the Royal Society. Most of the manuscript was transcribed and published by Henry W. Robinson and Walter Adams as
The Diary of Robert Hooke, M.A. F.R.S. 1672–1680
. However, Robinson and Adams chose not to publish entries from March to July 1672 and from January 1681 to May 1683, and the fact that this material exists has largely been ignored by scholars up to the present day. This article presents an edition of the unpublished material, making it widely available for the first time.
Reclassification of [Pasteurella] trehalosi as Bibersteinia trehalosi gen. nov., comb. nov.
Authors: Blackall P. J. , Bojesen Anders Miki , Christensen Henrik , Bisgaard Magne
Published: March 2007

[Pasteurella]trehalosiis an important pathogen of sheep, being primarily associated with serious systemic infections in lambs but also having an association with pneumonia. The aim of the present investigation was to characterize a broad collection of strains tentatively identified as [P.]trehalosiin order to reclassify and rename this taxon to support improvements in our understanding of the pathogenesis and epidemiology of this important organism. The type strain for [P.]trehalosi, strain NCTC 10370T, was included along with 42 field isolates from sheep (21), cattle (14), goats (1), roe deer (3) and unknown sources (3). An extended phenotypic characterization was performed on all 43 strains. Amplified fragment length polymorphism (AFLP) was also performed on the isolates. Two of the field isolates were subjected to 16S rRNA gene sequencing. These sequences, along with five existing sequences for [P.]trehalosistrains and 12 sequences for other taxa in the familyPasteurellaceae, were subjected to a phylogenetic analysis. All the isolates and the reference strains were identified as [P.]trehalosi. A total of 17 out of 22 ovine isolates produced acid from all glycosides, while only four out of 14 bovine isolates produced acid from all glycosides. All 22 ovine isolates were haemolytic and CAMP-positive, while no other isolate was haemolytic and only two bovine isolates were CAMP-positive. Nineteen AFLP types were found within the [P.]trehalosiisolates. All [P.]trehalosiisolates shared at least 70 % similarity in AFLP patterns. The largest AFLP type included the type strain and 7 ovine field isolates. Phylogenetic analysis indicated that the seven strains studied (two field isolates and the five serovar reference strains) are closely related, with 98.6 % or higher 16S rRNA gene sequence similarity. As both genotypic and phenotypic testing support the separate and distinct nature of these organisms, we propose the transfer of [P.]trehalosito a new genus,Bibersteinia, asBibersteinia trehalosicomb. nov. The type strain is NCTC 10370T(=ATCC 29703T).Bibersteinia trehalosican be distinguished from the existing genera of the family by the observation of only nine characteristics; catalase, porphyrin, urease, indole, phosphatase, acid from dulcitol, (+)-d-galactose, (+)-d-mannose and (+)-d-trehalose.
Comamonas odontotermitis sp. nov., isolated from the gut of the termite Odontotermes formosanus
Authors: Chou Jui-Hsing , Sheu Shih-Yi , Lin Kuan-Yin , Chen Wen-Ming , Arun A. B. , Young Chiu-Chung
Published: March 2007

A bacterial strain, designated Dant 3-8T, isolated from the gut of the termite Odontotermes formosanus, was investigated by a polyphasic taxonomic approach. The cells were rod-shaped, Gram-negative, non-pigmented, non-spore-forming and non-fermentative. Phylogenetic analyses using the 16S rRNA gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Comamonas, its closest neighbours being Comamonas testosteroni DSM 50244T (96.4 % sequence similarity), Comamonas koreensis KCTC 12005T (96.0 %) and Comamonas terrigena DSM 7099T (96.2 %). Strain Dant 3-8T was clearly distinguished from all of these strains by using phylogenetic analysis, DNA–DNA hybridization, whole-cell protein profiles, fatty acid composition data and a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that Dant 3-8T represents a novel species in the genus Comamonas, for which the name Comamonas odontotermitis sp. nov. is proposed. The type strain is Dant 3-8T (=BCRC 17576T=LMG 23579T).
Prevotella timonensis sp. nov., isolated from a human breast abscess
Authors: Glazunova Olga O. , Launay Thierry , Raoult Didier , Roux Véronique
Published: March 2007

Gram-negative anaerobic rods were isolated from a human breast abscess. Based on genotypic and phenotypic characteristics, the novel strain belonged to the genus Prevotella. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that it was closely related to Prevotella buccalis (94 % 16S rRNA gene sequence similarity), Prevotella salivae (90 %) and Prevotella oris (89.1 %). The major cellular fatty acid was C14 : 0 (19.5 %). The new isolate represents a novel species in the genus Prevotella, for which the name Prevotella timonensis sp. nov. is proposed. The type strain is strain 4401737T (=CIP 108522T=CCUG 50105T).
Zeaxanthinibacter enoshimensis gen. nov., sp. nov., a novel zeaxanthin-producing marine bacterium of the family Flavobacteriaceae, isolated from seawater off Enoshima Island, Japan
Authors: Asker Dalal , Beppu Teruhiko , Ueda Kenji
Published: March 2007

A novel marine, Gram-negative, yellow-pigmented, rod-shaped, strictly aerobic, gliding and oxidase- and catalase-positive bacterium (strain TD-ZE3T) was isolated from a seawater sample collected off the Pacific coastline of Japan near Enoshima Island (Fujisawa, Kanagawa). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain TD-ZE3Tbelonged to a distinct lineage in the familyFlavobacteriaceae, with 90.5 % sequence similarity with the nearest speciesRobiginitalea biformata. Strain TD-ZE3Tcould be distinguished from other members of the familyFlavobacteriaceaeby a number of chemotaxonomic and phenotypic characteristics. The DNA G+C content was 46.5 mol%. The major fatty acids were iso-C15 : 0, iso-C17 : 03-OH and iso-C17 : 1ω9cand menaquinone-6 was the only respiratory quinone. Zeaxanthin was the major carotenoid pigment produced; flexirubin-type pigments were not produced. Strain TD-ZE3Tdegraded gelatin, starch and Tween 80. Based on its unique phenotypic, genotypic and phylogenetic features, strain TD-ZE3Trepresents a novel taxon, for which the nameZeaxanthinibacter enoshimensisgen. nov., sp. nov. is proposed. The type strain is TD-ZE3T(=NBRC 101990T=CCUG 53613T).
Alkalibacillus silvisoli sp. nov., an alkaliphilic moderate halophile isolated from non-saline forest soil in Japan
Authors: Usami Ron , Echigo Akinobu , Fukushima Tadamasa , Mizuki Toru , Yoshida Yasuhiko , Kamekura Masahiro
Published: March 2007

Two alkaliphilic, moderately halophilic bacteria, designated BM2T and HN2, were isolated from non-saline forest soil in Japan. The cells of strain BM2T were motile, aerobic, rod-shaped and Gram-positive. The peptidoglycan was of the A1γ type, and the diamino acid was meso-diaminopimelic acid. Growth was observed at NaCl concentrations between 5.0 and 25.0 % (w/v) (the optimum being 10.0–15.0 %, w/v), at pH 7.0–10.0 (optimum, pH 9.0–9.5) and at 20–50 °C. The predominant isoprenoid quinone was MK-7. The major cellular fatty acids were iso-C15 : 0 and anteiso-C17 : 0. The G+C content of total DNA of strain BM2T was 37.0 mol%. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain BM2T was most closely related to Alkalibacillus haloalkaliphilus DSM 5271T (98.0 % sequence similarity). DNA–DNA hybridization results indicated low levels of relatedness between strain BM2T and A. haloalkaliphilus JCM 12303T (23 and 16 % reciprocally), Alkalibacillus filiformis JCM 13893T (25 and 21 %) and Alkalibacillus salilacus JCM 13894T (27 and 19 %). On the basis of the phylogenetic and phenotypic characteristics, strain BM2T represents a novel species, for which the name Alkalibacillus silvisoli sp. nov. is proposed. The type strain is BM2T (=JCM 14193T=DSM 18495T).
Dyadobacter beijingensis sp. nov., isolated from the rhizosphere of turf grasses in China
Authors: Dong Zhi , Guo Xiaoyu , Zhang Xiaoxia , Qiu Fubin , Sun Lei , Gong Huili , Zhang Feiyun
Published: March 2007

Strain A54T was isolated from rhizospheric soil of turf grasses irrigated with reclaimed water in Taoranting Park, Beijing, China. Phenotypic, chemotaxonomic and polygenetic analyses established the affiliation of the isolate to the genus Dyadobacter. Strain A54T possessed 97.7, 94.4 and 94.7 % 16S rRNA gene sequence similarity with respect to the type strains of Dyadobacter fermentans, D. hamtensis and D. crusticola, respectively. Furthermore, DNA–DNA hybridization did not show significant relatedness (<25 % hybridization) between strain A54T and D. fermentans ATCC 700827T. Therefore, these results indicate that strain A54T belongs to a novel species of the genus Dyadobacter, for which the name Dyadobacter beijingensis sp. nov. is proposed. The type strain is strain A54T (=CGMCC 1.6375T=JCM 14200T).
Halomonas gomseomensis sp. nov., Halomonas janggokensis sp. nov., Halomonas salaria sp. nov. and Halomonas denitrificans sp. nov., moderately halophilic bacteria isolated from saline water
Authors: Kim Kwang Kyu , Jin Long , Yang Hee Chan , Lee Sung-Taik
Published: March 2007

A total of 34 Halomonas strains were isolated from saline water in Anmyeondo, Korea. Ten of these strains, considered to belong to novel species, were subjected to a polyphasic taxonomic investigation. The strains were Gram-negative, moderately halophilic, motile and non-spore-forming rods that contained Q-9 as the predominant ubiquinone and C18 : 1
ω7c, C16 : 0 and either summed feature 4 (C16 : 1
ω7c/C15 : 0 iso 2-OH) or C19 : 0 cyclo ω8c as the major fatty acids. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that the ten isolates formed four separate lineages in the genus Halomonas. Combined phenotypic data and DNA–DNA hybridization data supported the conclusion that they represent four novel species in the genus Halomonas, for which the names Halomonas gomseomensis sp. nov. (type strain M12T=KCTC 12662T=DSM 18042T), Halomonas janggokensis sp. nov. (type strain M24T=KCTC 12663T=DSM 18043T), Halomonas salaria sp. nov. (type strain M27T=KCTC 12664T=DSM 18044T) and Halomonas denitrificans sp. nov. (type strain M29T=KCTC 12665T=DSM 18045T) are proposed.
Transcript Profiling and Identification of Molecular Markers for Early Microspore Embryogenesis inBrassica napus
Authors: Malik Meghna R. , Wang Feng , Dirpaul Joan M. , Zhou Ning , Polowick Patricia L. , Ferrie Alison M.R. , Krochko Joan E.
Published: March 2007

Isolated microspores of Brassica napus are developmentally programmed to form gametes; however, microspores can be reprogrammed through stress treatments to undergo appropriate divisions and form embryos. We are interested in the identification and isolation of factors and genes associated with the induction and establishment of embryogenesis in isolated microspores. Standard and normalized cDNA libraries, as well as subtractive cDNA libraries, were constructed from freshly isolated microspores (0 h) and microspores cultured for 3, 5, or 7 d under embryogenesis-inducing conditions. Library comparison tools were used to identify shifts in metabolism across this time course. Detailed expressed sequence tag analyses of 3 and 5 d cultures indicate that most sequences are related to pollen-specific genes. However, semiquantitative and real-time reverse transcription-polymerase chain reaction analyses at the initial stages of embryo induction also reveal expression of embryogenesis-related genes such as BABYBOOM1, LEAFY COTYLEDON1 (LEC1), and LEC2 as early as 2 to 3 d of microspore culture. Sequencing results suggest that embryogenesis is clearly established in a subset of the microspores by 7 d of culture and that this time point is optimal for isolation of embryo-specific expressed sequence tags such as ABSCISIC ACID INSENSITIVE3, ATS1, LEC1, LEC2, and FUSCA3. Following extensive polymerase chain reaction-based expression profiling, 16 genes were identified as unequivocal molecular markers for microspore embryogenesis in B. napus. These molecular marker genes also show expression during zygotic embryogenesis, underscoring the common developmental pathways that function in zygotic and gametic embryogenesis. The quantitative expression values of several of these molecular marker genes are shown to be predictive of embryogenic potential in B. napus cultivars (e.g. ‘Topas’ DH4079, ‘Allons,’ ‘Westar,’ ‘Garrison’).
Arabidopsis Cor15am Is a Chloroplast Stromal Protein That Has Cryoprotective Activity and Forms Oligomers
Authors: Nakayama Katsuhiro , Okawa Kumiko , Kakizaki Tomohiro , Honma Takenori , Itoh Hideaki , Inaba Takehito
Published: March 2007

Many plants acquire increased freezing tolerance when they are exposed to nonfreezing temperatures of a certain duration. This process is known as cold acclimation and allows plants to protect themselves from freezing injury. A wide variety of polypeptides are induced during cold acclimation, among which is one encoded by COR15A in Arabidopsis (Arabidopsis thaliana). Previous studies showed that the COR15A gene encodes a small, plastid-targeted polypeptide that is processed to a mature form called Cor15am. In this study, we examined the biochemical properties and activities of Cor15am in more detail. We provide evidence that Cor15am localizes almost exclusively to the chloroplast stroma. In addition, the cold-regulated accumulation of Cor15am is affected by chloroplast functionality. Both gel-filtration chromatography and protein cross-linking reveal that Cor15am forms oligomers in the stroma of chloroplasts. Although Cor15am accumulates in response to low temperature, cold acclimation is not a prerequisite for oligomerization of Cor15am. Structural analysis suggests that Cor15am is composed of both ordered and random structures, and can stay soluble with small structural change after boiling and freeze-thaw treatments. Recombinant Cor15am exhibits in vitro cryoprotection of a freeze-labile enzyme, l-lactate dehydrogenase. Furthermore, Cor15am is capable of associating with l-lactate dehydrogenase in vitro and with potential stromal substrates in vivo. On the basis of these results, we propose that Arabidopsis Cor15am is a cryoprotective protein that forms oligomers in the chloroplast stroma, and that direct association of Cor15am with its substrates is part of its cryoprotective mechanism.
Resistance to Botrytis cinerea Induced in Arabidopsis by Elicitors Is Independent of Salicylic Acid, Ethylene, or Jasmonate Signaling But Requires PHYTOALEXIN DEFICIENT3
Authors: Ferrari Simone , Galletti Roberta , Denoux Carine , De Lorenzo Giulia , Ausubel Frederick M. , Dewdney Julia
Published: March 2007

Oligogalacturonides (OGs) released from plant cell walls by pathogen polygalacturonases induce a variety of host defense responses. Here we show that in Arabidopsis (Arabidopsis thaliana), OGs increase resistance to the necrotrophic fungal pathogen Botrytis cinerea independently of jasmonate (JA)-, salicylic acid (SA)-, and ethylene (ET)-mediated signaling. Microarray analysis showed that about 50% of the genes regulated by OGs, including genes encoding enzymes involved in secondary metabolism, show a similar change of expression during B. cinerea infection. In particular, expression of PHYTOALEXIN DEFICIENT3 (PAD3) is strongly up-regulated by both OGs and infection independently of SA, JA, and ET. OG treatments do not enhance resistance to B. cinerea in the pad3 mutant or in underinducer after pathogen and stress1, a mutant with severely impaired PAD3 expression in response to OGs. Similarly to OGs, the bacterial flagellin peptide elicitor flg22 also enhanced resistance to B. cinerea in a PAD3-dependent manner, independently of SA, JA, and ET. This work suggests, therefore, that elicitors released from the cell wall during pathogen infection contribute to basal resistance against fungal pathogens through a signaling pathway also activated by pathogen-associated molecular pattern molecules.
ELF4Is Required for Oscillatory Properties of the Circadian Clock
Authors: McWatters Harriet G. , Kolmos Elsebeth , Hall Anthony , Doyle Mark R. , Amasino Richard M. , Gyula Péter , Nagy Ferenc , Millar Andrew J. , Davis Seth J.
Published: March 2007

Circadian clocks are required to coordinate metabolism and physiology with daily changes in the environment. Such clocks have several distinctive features, including a free-running rhythm of approximately 24 h and the ability to entrain to both light or temperature cycles (zeitgebers). We have previously characterized the EARLY FLOWERING4 (ELF4) locus of Arabidopsis (Arabidopsis thaliana) as being important for robust rhythms. Here, it is shown that ELF4 is necessary for at least two core clock functions: entrainment to an environmental cycle and rhythm sustainability under constant conditions. We show that elf4 demonstrates clock input defects in light responsiveness and in circadian gating. Rhythmicity in elf4 could be driven by an environmental cycle, but an increased sensitivity to light means the circadian system of elf4 plants does not entrain normally. Expression of putative core clock genes and outputs were characterized in various ELF4 backgrounds to establish the molecular network of action. ELF4 was found to be intimately associated with the CIRCADIAN CLOCK-ASSOCIATED1 (CCA1)/LONG ELONGATED HYPOCOTYL (LHY)-TIMING OF CAB EXPRESSION1 (TOC1) feedback loop because, under free run, ELF4 is required to regulate the expression of CCA1 and TOC1 and, further, elf4 is locked in the evening phase of this feedback loop. ELF4, therefore, can be considered a component of the central CCA1/LHY-TOC1 feedback loop in the plant circadian clock.
The Maize Zmsmu2 Gene Encodes a Putative RNA-Splicing Factor That Affects Protein Synthesis and RNA Processing during Endosperm Development
Authors: Chung Taijoon , Kim Cheol Soo , Nguyen Hong N. , Meeley Robert B. , Larkins Brian A.
Published: March 2007

We characterized two maize (Zea mays) mutants, zmsmu2-1 and zmsmu2-3, that result from insertion of a Mutator (Mu) transposable element in the first exon of a gene homologous to the nematode gene, smu-2, which is involved in RNA splicing. In addition to having a starchy endosperm with reduced levels of zein storage proteins, homozygous zmsmu2-1 mutants manifest a number of phenotypes, including defective meristem development. The zmsmu2 mutants have poor seedling viability and surviving plants are sterile. The gene encoding ZmSMU2 is expressed in the endosperm, embryo, and shoot apex, which explains the pleiotropic nature of the mutation. We found that proper expression of Zmsmu2 is required for efficient ribosomal RNA processing, ribosome biogenesis, and protein synthesis in developing endosperm. Based on the pleiotropic nature of the mutations and the known function of animal Zmsmu2 homologs, we propose a possible role for ZmSMU2 in the development of maize endosperm, as well as a mechanism by which misregulation of zmsmu2 causes the mutant phenotypes.
GIGANTEA Regulates Phytochrome A-Mediated Photomorphogenesis Independently of Its Role in the Circadian Clock
Authors: Oliverio Karina Andrea , Crepy María , Martin-Tryon Ellen L. , Milich Raechel , Harmer Stacey L. , Putterill Jo , Yanovsky Marcelo J. , Casal Jorge J.
Published: March 2007

GIGANTEA (GI) is a nuclear protein involved in the promotion of flowering by long days, in light input to the circadian clock, and in seedling photomorphogenesis under continuous red light but not far-red light (FR). Here, we report that in Arabidopsis (Arabidopsis thaliana) different alleles of gi have defects in the hypocotyl-growth and cotyledon-unfolding responses to hourly pulses of FR, a treatment perceived by phytochrome A (phyA). This phenotype is rescued by overexpression of GI. The very-low-fluence response of seed germination was also reduced in gi. Since the circadian clock modulates many light responses, we investigated whether these gi phenotypes were due to alterations in the circadian system or light signaling per se. In experiments where FR pulses were given to dark-incubated seeds or seedlings at different times of the day, gi showed reduced seed germination, cotyledon unfolding, and activity of a luciferase reporter fused to the promoter of a chlorophyll a/b-binding protein gene; however, rhythmic sensitivity was normal in these plants. We conclude that while GI does not affect the high-irradiance responses of phyA, it does affect phyA-mediated very-low-fluence responses via mechanisms that do not obviously involve its circadian functions.
Cloning and Characterization of Unusual Fatty Acid Desaturases from Anemone leveillei: Identification of an Acyl-Coenzyme A C20 Δ5-Desaturase Responsible for the Synthesis of Sciadonic Acid
Authors: Sayanova Olga , Haslam Richard , Venegas Caleron Monica , Napier Johnathan A.
Published: March 2007

The seed oil of Anemone leveillei contains significant amounts of sciadonic acid (20:3Δ5,11,14; SA), an unusual non-methylene-interrupted fatty acid with pharmaceutical potential similar to arachidonic acid. Two candidate cDNAs (AL10 and AL21) for the C20 Δ5cis-desaturase from developing seeds of A. leveillei were functionally characterized in transgenic Arabidopsis (Arabidopsis thaliana) plants. The open reading frames of both Δ5-desaturases showed some similarity to presumptive acyl-coenzyme A (CoA) desaturases found in animals and plants. When expressed in transgenic Arabidopsis, AL21 showed a broad range of substrate specificity, utilizing both saturated (16:0 and 18:0) and unsaturated (18:2, n-6 and 18:3, n-3) substrates. In contrast, AL10 did not show any activity in wild-type Arabidopsis. Coexpression of AL10 or AL21 with a C18 Δ9-elongase in transgenic Arabidopsis plants resulted in the production of SA and juniperonic fatty acid (20:4Δ5,11,14,17). Thus, AL10 acted only on C20 polyunsaturated fatty acids in a manner analogous to “front-end” desaturases. However, neither AL10 nor AL21 contain the cytochrome b  5 domain normally present in this class of enzymes. Acyl-CoA profiling of transgenic Arabidopsis plants and developing A. leveillei seeds revealed significant accumulation of Δ5-unsaturated fatty acids as acyl-CoAs compared to the accumulation of these fatty acids in total lipids. Positional analysis of triacylglycerols of A. leveillei seeds showed that Δ5-desaturated fatty acids were present in both sn-2 and sn-1 + sn-3 positions, although the majority of 16:1Δ5, 18:1Δ5, and SA was present at the sn-2 position. Our data provide biochemical evidence for the A. leveillei Δ5-desaturases using acyl-CoA substrates.
Combined Transcriptome and Proteome Analysis Identifies Pathways and Markers Associated with the Establishment of Rapeseed Microspore-Derived Embryo Development
Authors: Joosen Ronny , Cordewener Jan , Supena Ence Darmo Jaya , Vorst Oscar , Lammers Michiel , Maliepaard Chris , Zeilmaker Tieme , Miki Brian , America Twan , Custers Jan , Boutilier Kim
Published: March 2007

Microspore-derived embryo (MDE) cultures are used as a model system to study plant cell totipotency and as an in vitro system to study embryo development. We characterized and compared the transcriptome and proteome of rapeseed (Brassica napus) MDEs from the few-celled stage to the globular/heart stage using two MDE culture systems: conventional cultures in which MDEs initially develop as unorganized clusters that usually lack a suspensor, and a novel suspensor-bearing embryo culture system in which the embryo proper originates from the distal cell of a suspensor-like structure and undergoes the same ordered cell divisions as the zygotic embryo. Improved histodifferentiation of suspensor-bearing MDEs suggests a new role for the suspensor in driving embryo cell identity and patterning. An MDE culture cDNA array and two-dimensional gel electrophoresis and protein sequencing were used to compile global and specific expression profiles for the two types of MDE cultures. Analysis of the identities of 220 candidate embryo markers, as well as the identities of 32 sequenced embryo up-regulated protein spots, indicate general roles for protein synthesis, glycolysis, and ascorbate metabolism in the establishment of MDE development. A collection of 135 robust markers for the transition to MDE development was identified, a number of which may be coregulated at the gene and protein expression level. Comparison of the expression profiles of preglobular-stage conventional MDEs and suspensor-bearing MDEs identified genes whose differential expression may reflect improved histodifferentiation of suspensor-bearing embryos. This collection of early embryo-expressed genes and proteins serves as a starting point for future marker development and gene function studies aimed at understanding the molecular regulation of cell totipotency and early embryo development in plants.
A Symbiotic Plant Peroxidase Involved in Bacterial Invasion of the Tropical Legume Sesbania rostrata
Authors: Den Herder Jeroen , Lievens Sam , Rombauts Stephane , Holsters Marcelle , Goormachtig Sofie
Published: March 2007

Aquatic nodulation on the tropical legume Sesbania rostrata occurs at lateral root bases via intercellular crack-entry invasion. A gene was identified (Srprx1) that is transiently up-regulated during the nodulation process and codes for a functional class III plant peroxidase. The expression strictly depended on bacterial nodulation factors (NFs) and could be modulated by hydrogen peroxide, a downstream signal for crack-entry invasion. Expression was not induced after wounding or pathogen attack, indicating that the peroxidase is a symbiosis-specific isoform. In situ hybridization showed Srprx1 transcripts around bacterial infection pockets and infection threads until they reached the central tissue of the nodule. A root nodule extensin (SrRNE1) colocalized with Srprx1 both in time and space and had the same NF requirement, suggesting a function in a similar process. Finally, in mixed inoculation nodules that were invaded by NF-deficient bacteria and differed in infection thread progression, infection-associated peroxidase transcripts were not observed. Lack of Srprx1 gene expression could be one of the causes for the aberrant structure of the infection threads.
Short- and Long-Term Operation of the Lutein-Epoxide Cycle in Light-Harvesting Antenna Complexes
Authors: Matsubara Shizue , Morosinotto Tomas , Osmond C. Barry , Bassi Roberto
Published: March 2007

The lutein-5,6-epoxide (Lx) cycle operates in some plants between lutein (L) and its monoepoxide, Lx. Whereas recent studies have established the photoprotective roles of the analogous violaxanthin cycle, physiological functions of the Lx cycle are still unknown. In this article, we investigated the operation of the Lx cycle in light-harvesting antenna complexes (Lhcs) of Inga sapindoides Willd, a tropical tree legume accumulating substantial Lx in shade leaves, to identify the xanthophyll-binding sites involved in short- and long-term responses of the Lx cycle and to analyze the effects on light-harvesting efficiency. In shade leaves, Lx was converted into L upon light exposure, which then replaced Lx in the peripheral V1 site in trimeric Lhcs and the internal L2 site in both monomeric and trimeric Lhcs, leading to xanthophyll composition resembling sun-type Lhcs. Similar to the violaxanthin cycle, the Lx cycle was operating in both photosystems, yet the light-induced Lx → L conversion was not reversible overnight. Interestingly, the experiments using recombinant Lhcb5 reconstituted with different Lx and/or L levels showed that reconstitution with Lx results in a significantly higher fluorescence yield due to higher energy transfer efficiencies among chlorophyll (Chl) a molecules, as well as from xanthophylls to Chl a. Furthermore, the spectroscopic analyses of photosystem I-LHCI from I. sapindoides revealed prominent red-most Chl forms, having the lowest energy level thus far reported for higher plants, along with reduced energy transfer efficiency from antenna pigments to Chl a. These results are discussed in the context of photoacclimation and shade adaptation.
Death Don't Have No Mercy and Neither Does Calcium: Arabidopsis CYCLIC NUCLEOTIDE GATED CHANNEL2 and Innate Immunity
Authors: Ali Rashid , Ma Wei , Lemtiri-Chlieh Fouad , Tsaltas Dimitrios , Leng Qiang , von Bodman Susannne , Berkowitz Gerald A.
Published: March 2007

Plant innate immune response to pathogen infection includes an elegant signaling pathway leading to reactive oxygen species generation and resulting hypersensitive response (HR); localized programmed cell death in tissue surrounding the initial infection site limits pathogen spread. A veritable symphony of cytosolic signaling molecules (including Ca2+, nitric oxide [NO], cyclic nucleotides, and calmodulin) have been suggested as early components of HR signaling. However, specific interactions among these cytosolic secondary messengers and their roles in the signal cascade are still unclear. Here, we report some aspects of how plants translate perception of a pathogen into a signal cascade leading to an innate immune response. We show that Arabidopsis thaliana CYCLIC NUCLEOTIDE GATED CHANNEL2 (CNGC2/DND1) conducts Ca2+ into cells and provide a model linking this Ca2+ current to downstream NO production. NO is a critical signaling molecule invoking plant innate immune response to pathogens. Plants without functional CNGC2 lack this cell membrane Ca2+ current and do not display HR; providing the mutant with NO complements this phenotype. The bacterial pathogen–associated molecular pattern elicitor lipopolysaccharide activates a CNGC Ca2+ current, which may be linked to NO generation due to buildup of cytosolic Ca2+/calmodulin.
Improperly Terminated, Unpolyadenylated mRNA of Sense Transgenes Is Targeted by RDR6-Mediated RNA Silencing in Arabidopsis
Authors: Luo Zhenghua , Chen Zhixiang
Published: March 2007

RNA silencing can be induced by highly transcribed transgenes through a pathway dependent on RNA-DEPENDENT RNA POLYMERASE6 (RDR6) and may function as a genome protection mechanism against excessively expressed genes. Whether all transcripts or just aberrant transcripts activate this protection mechanism is unclear. Consistent RNA silencing induced by a transgene with three direct repeats of the β-glucuronidase (GUS) open reading frame (ORF) is associated with high levels of truncated, unpolyadenylated transcripts, probably from abortive transcription elongation. Truncated, unpolyadenylated transcripts from triple GUS ORF repeats were degraded in the wild type but accumulated in an rdr6 mutant, suggesting targeting for degradation by RDR6-mediated RNA silencing. A GUS transgene without a 3′ transcription terminator produced unpolyadenylated readthrough mRNA and consistent RDR6-dependent RNA silencing. Both GUS triple repeats and terminator-less GUS transgenes silenced an expressed GUS transgene in trans in the wild type but not in the rdr6 mutant. Placing two 3′ terminators in the GUS transgene 3′ reduced mRNA 3′ readthrough, decreased GUS-specific small interfering RNA accumulation, and enhanced GUS gene expression. Moreover, RDR6 was localized in the nucleus. We propose that improperly terminated, unpolyadenylated mRNA from transgene transcription is subject to RDR6-mediated RNA silencing, probably by acting as templates for the RNA polymerase, in Arabidopsis thaliana.
Seed Germination of GA-Insensitivesleepy1Mutants Does Not Require RGL2 Protein Disappearance inArabidopsis
Authors: Ariizumi Tohru , Steber Camille M.
Published: March 2007

We explore the roles of gibberellin (GA) signaling genes SLEEPY1 (SLY1) and RGA-LIKE2 (RGL2) in regulation of seed germination in Arabidopsis thaliana, a plant in which the hormone GA is required for seed germination. Seed germination failure in the GA biosynthesis mutant ga1-3 is rescued by GA and by mutations in the DELLA gene RGL2, suggesting that RGL2 represses seed germination. RGL2 protein disappears before wild-type seed germination, consistent with the model that GA stimulates germination by causing the SCFSLY1 E3 ubiquitin ligase complex to trigger ubiquitination and destruction of RGL2. Unlike ga1-3, the GA-insensitive sly1 mutants show variable seed dormancy. Seed lots with high seed dormancy after-ripened slowly, with stronger alleles requiring more time. We expected that if RGL2 negatively controls seed germination, sly1 mutant seeds that germinate well should accumulate lower RGL2 levels than those failing to germinate. Surprisingly, RGL2 accumulated at high levels even in after-ripened sly1 mutant seeds with 100% germination, suggesting that RGL2 disappearance is not a prerequisite for seed germination in the sly1 background. Without GA, several GA-induced genes show increased accumulation in sly1 seeds compared with ga1-3. It is possible that the RGL2 repressor of seed germination is inactivated by after-ripening of sly1 mutant seeds.
Spectrum of cytomorphology of tuberculous lymphadenitis and changes during anti‐tubercular treatment
Authors: Sharma M. , Agarwal S. , Wadhwa N. , Mishra K. , Gadre D. J.
Published: March 2007

Objective:  To analyse the morphological changes in tuberculous lymph nodes and the clinical response during short course anti tubercular chemotherapy.

Methods:  Thirty‐six patients with tuberculous lymphadenitis under treatment were followed up clinically and cytologically at 0, 2, 4 and 6 months.

Results:  Twenty‐six (72.2%) patients had palpable lymph nodes at the end of chemotherapy. Of the 14 patients with residual lymph nodes exceeding 1 cm in size, 92.8% (13) still had evidence of continuation of the disease. Acid‐fast bacilli could be found in 38.8% patients at the end of 6 months. Intense lymphocytic infiltration of granulomata in the early phase of chemotherapy predicted a favourable outcome.

Conclusions:  Following completion of anti‐tubercular treatment a significant percentage of patients have persistent lymphadenopathy and harbour the disease. Morphological follow up of these patients is essential as they may be at increased risk of relapse.
Does the Giant Wood Spider Nephila pilipes Respond to Prey Variation by Altering Web or Silk Properties?
Authors: Tso I‐Min , Chiang Shu‐Ya , Blackledge Todd A.
Published: March 2007

Recent studies demonstrated that orb‐weaving spiders may alter web architectures, the amount of silk in webs, or the protein composition of silks in response to variation in amount or type of prey. In this study, we conducted food manipulations to examine three mechanisms by which orb‐weaving spiders may adjust the performance of webs to variation in prey by altering the architectures of webs, making structural changes to the diameters of silk threads, and manipulating the material properties or amino acid composition of silk fibers. We fed Nephila pilipes two different types of prey, crickets or flies, and then compared orb structure and the chemical and physical properties of major ampullate (MA) silk between groups. Prey type did not affect orb structures in N. pilipes, except for mesh size. However, MA silk diameter and the stiffness of orbs constructed by spiders fed crickets were significantly greater than for the fly group. MA fibers forcibly silked from N. pilipes fed crickets was significantly thicker, but less stiff, than silk from spiders fed flies. Spiders in the cricket treatment also produced MA silk with slightly, but statistically significantly, more serine than silk from spiders in the fly treatment. Percentages of other major amino acids (proline, glycine, and glutamine) did not differ between treatments. This study demonstrated that orb‐weaving spiders can simultaneously alter some structural and material properties of MA silk, as well as the physical characteristics of webs, in response to different types of prey.