bluuebunny/crossref_metadata_2025 huggingface dataset:
RNA-Seq gene expression estimation with read mapping uncertainty
Authors: Li Bo , Ruotti Victor , Stewart Ron M. , Thomson James A. , Dewey Colin N.
Published: December 2009

Motivation: RNA-Seq is a promising new technology for accurately measuring gene expression levels. Expression estimation with RNA-Seq requires the mapping of relatively short sequencing reads to a reference genome or transcript set. Because reads are generally shorter than transcripts from which they are derived, a single read may map to multiple genes and isoforms, complicating expression analyses. Previous computational methods either discard reads that map to multiple locations or allocate them to genes heuristically.

Results: We present a generative statistical model and associated inference methods that handle read mapping uncertainty in a principled manner. Through simulations parameterized by real RNA-Seq data, we show that our method is more accurate than previous methods. Our improved accuracy is the result of handling read mapping uncertainty with a statistical model and the estimation of gene expression levels as the sum of isoform expression levels. Unlike previous methods, our method is capable of modeling non-uniform read distributions. Simulations with our method indicate that a read length of 20–25 bases is optimal for gene-level expression estimation from mouse and maize RNA-Seq data when sequencing throughput is fixed.

Availability: An initial C++ implementation of our method that was used for the results presented in this article is available at http://deweylab.biostat.wisc.edu/rsem.

Contact:  cdewey@biostat.wisc.edu

Supplementary information:  Supplementary data are available at Bioinformatics on
Diagnostic performance of multisequential cardiac magnetic resonance imaging in acute cardiac allograft rejection
Authors: Taylor Andrew J. , Vaddadi Gautam , Pfluger Heinz , Butler Michelle , Bergin Peter , Leet Angeline , Richardson Meroula , Cherayath Joshi , Iles Leah , Kaye David M.
Published: December 2009

Aims

We evaluated cardiac magnetic resonance imaging (CMR) as a non‐invasive test for cardiac allograft rejection.

Methods and results

We performed CMR on 50 heart‐transplant recipients. Acute rejection was confirmed in 11 cases by endomyocardial biopsy (EMB) and presumed in 8 cases with a recent fall in left‐ventricular ejection fraction (LVEF) not attributable to coronary allograft vasculopathy. Control patients had both normal LVEF and no significant rejection on EMB. Cardiac magnetic resonance imaging evaluated myocardial function, oedema, and early and late post‐Gadolinium‐DTPA contrast enhancement. Patients with confirmed rejection demonstrated elevated early relative myocardial contrast enhancement (4.1 ± 0.3 vs. 2.8 ± 0.2, P < 0.001) and a trend to higher oedema suggested by higher relative myocardial intensity on T2‐weighted imaging compared to controls (2.1 ± 0.1 vs. 1.7 ± 0.1, P = 0.1). With rejection defined as increased early contrast enhancement or myocardial oedema, the sensitivity and specificity of CMR compared with EMB were 100 and 73%, respectively. Eight patients with presumed rejection also had elevated early myocardial contrast enhancement compared with controls, (8.7 ± 1.9 vs. 2.8 ± 0.2, P < 0.05), which reduced following increased immunosuppression (8.7 ± 1.9 vs. 4.6 ± 1.2, P < 0.05). In these patients LVEF improved following increased immunosuppression (32 ± 5 vs. 46 ± 5%, P < 0.05).

Conclusion

Cardiac magnetic resonance imaging is a promising modality for non‐invasive detection of cardiac allograft rejection.
A survey of pathogens and metazoan parasites on wild sea trout (Salmo trutta) in Scottish waters
Authors: Urquhart Katy , Pert Campbell C. , Fryer Rob J. , Cook Paul , Weir Sarah , Kilburn Rachel , McCarthy Una , Simons Judy , McBeath Sonia J. , Matejusova Iveta , Bricknell Ian R.
Published: December 2009

Urquhart, K., Pert, C. C., Fryer, R. J., Cook, P., Weir, S., Kilburn, R., McCarthy, U., Simons, J., McBeath, S. J., Matejusova, I., and Bricknell, I. R. 2010. A survey of pathogens and metazoan parasites on wild sea trout (Salmo trutta) in Scottish waters. – ICES Journal of Marine Science, 67: 444–453. In all, 300 wild sea trout were sampled from three east coast and two west coast sites around Scotland over a 3-year period to establish the prevalence and the abundance of bacteria, viruses, and ecto- and endoparasites. No bacterial pathogens were isolated from any fish. One fish tested positive for viral pathogens (infectious pancreatic necrosis virus). The viral agent syncytium, resulting from aquareovirus infection, was found in four fish from the east coast. The parasitic fauna consisted of three classes of ectoparasite, Monogenea, Isopoda, and Copepoda, and four classes of endoparasite, Cestoda, Digenea, Nematoda, and Acanthocephala. Sea trout from the east coast sites were larger than those from the west coast. The abundance of Lepeophtheirus salmonis, Hysterothylacium aduncum, and Anisakis sp. was significantly greater at the east coast sites. The only parasite found in significantly greater numbers at a west coast site was Pomphorhynchus laevis.
Flow instability and wall shear stress variation in intracranial aneurysms
Authors: Baek H. , Jayaraman M. V. , Richardson P. D. , Karniadakis G. E.
Published: December 2009

We investigate the flow dynamics and oscillatory behaviour of wall shear stress (WSS) vectors in intracranial aneurysms using high resolution numerical simulations. We analyse three representative patient-specific internal carotid arteries laden with aneurysms of different characteristics: (i) a wide-necked saccular aneurysm, (ii) a narrower-necked saccular aneurysm, and (iii) a case with two adjacent saccular aneurysms. Our simulations show that the pulsatile flow in aneurysms can be subject to a hydrodynamic instability during the decelerating systolic phase resulting in a high-frequency oscillation in the range of 20–50 Hz, even when the blood flow rate in the parent vessel is as low as 150 and 250 ml min−1for cases (iii) and (i), respectively. The flow returns to its original laminar pulsatile state near the end of diastole. When the aneurysmal flow becomes unstable, both the magnitude and the directions of WSS vectors fluctuate at the aforementioned high frequencies. In particular, the WSS vectors around the flow impingement region exhibit significant spatio-temporal changes in direction as well as in magnitude.
Kangiella japonica sp. nov., isolated from a marine environment
Authors: Romanenko Lyudmila A. , Tanaka Naoto , Frolova Galina M. , Mikhailov Valery V.
Published: December 2009

Three Gram-negative, aerobic, halophilic, non-motile, yellowish-pigmented bacteria, designated KMM 3896, KMM 3897 and KMM 3899T, were isolated from coastal seawater and sediment samples of the Sea of Japan, Russia. The isolates were shown to belong to the same species on the basis of 16S rRNA gene sequence similarities (99.6–99.9 %) and DNA–DNA relatedness (73–98 %). Phylogenetic analysis of 16S rRNA gene sequences demonstrated that the isolates formed a subcluster within the genus Kangiella in the class Gammaproteobacteria. 16S rRNA gene sequence similarities between strain KMM 3899T and its closest phylogenetic neighbours, Kangiella koreensis SW-125T and Kangiella aquimarina SW-154T, were 96.6 and 95.5 %, respectively. On the basis of phenotypic differences and phylogenetic distances, it is proposed that strains KMM 3896, KMM 3897 and KMM 3899T are assigned to a novel species of the genus Kangiella, Kangiella japonica sp. nov. The type strain is KMM 3899T (=NRIC 0764T =JCM 16211T).
Slackia piriformis sp. nov. and Collinsella tanakaei sp. nov., new members of the family Coriobacteriaceae, isolated from human faeces
Authors: Nagai Fumiko , Watanabe Yohei , Morotomi Masami
Published: December 2009

Three Gram-positive, strictly anaerobic, non-spore-forming, rod-shaped organisms (strains YIT 12062T, YIT 12063T and YIT 12064) were isolated from human faeces. Strain YIT 12062T was asaccharolytic and possessed a DNA G+C content of 58.3 mol%. Cells of strain YIT 12062T were negative for catalase, oxidase, urease, hydrolysis of aesculin and gelatin, nitrate reduction and indole production. Based on 16S rRNA gene sequence analysis, strain YIT 12062T was assigned to the genus Slackia (91.7–96.0 % sequence similarities to type strains of Slackia species). Biochemical data showed that the isolate was phenotypically distinct from all recognized species of the genus Slackia. Strain YIT 12062T therefore represents a novel species in the genus Slackia, for which the name Slackia piriformis sp. nov. is proposed. The type strain is YIT 12062T (=DSM 22477T=JCM 16070T). Following 16S rRNA gene sequence analysis, strains YIT 12063T and YIT 12064, which were isolated from different subjects, were shown to be most closely related to species of the genus Collinsella (93.8–95.1 % similarities to type strains). Although their phenotypic characteristics were very similar and they shared >99 % 16S rRNA gene sequence similarity and >97±1.8 % DNA–DNA relatedness, the two isolates could be discriminated by RAPD fingerprints. The DNA G+C contents of strains YIT 12063T and YIT 12064 were 60.8 and 61.0 mol%, respectively. They were saccharolytic in API test systems, positive for aesculin hydrolysis and negative for catalase, oxidase, urease, indole production, nitrate reduction and gelatin hydrolysis. The major end products of glucose fermentation of these strains were lactate, acetate and formate. Biochemical data supported the affiliation of strains YIT 12063T and YIT 12064 to the genus Collinsella and showed that they were phenotypically distinct from all recognized species of the genus Collinsella. Strains YIT 12063T and YIT 12064 therefore represent a novel species of the genus Collinsella, for which the name Collinsella tanakaei sp. nov. is proposed. The type strain is YIT 12063T (=DSM 22478T=JCM 16071T).
Microbacterium lindanitolerans sp. nov., isolated from hexachlorocyclohexane-contaminated soil
Authors: Lal Devi , Gupta Sanjay Kumar , Schumann Peter , Lal Rup
Published: December 2009

A Gram-stain-positive, aerobic, rod-shaped, yellow actinobacterium, designated MNA2T, was isolated from a hexachlorocyclohexane-contaminated soil in North India. Strain MNA2T showed 95 % 16S rRNA gene sequence similarity with Microbacterium halotolerans YIM 70130T. Phylogenetic analysis of 16S rRNA gene sequences showed that strain MNA2T belonged to a clade represented by the genus Microbacterium of the family Microbacteriaceae. Strain MNA2T contained anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0 as the predominant fatty acids and diphosphatidylglycerol, phosphatidylglycerol and two unknown polar lipids. The menaquinones were MK-12, MK-11, MK-13 and MK-10, in an approximate molar ratio of 45 : 40 : 13 : 3, respectively. The DNA G+C content was 65.3 mol%. The peptidoglycan was of the B type of cross-linkage with ornithine as the diagnostic diamino acid. The results of the phylogenetic, phenotypic and chemotaxonomic analysis indicate that strain MNA2T belongs to a previously unrecognized species of the genus Microbacterium, for which the name Microbacterium lindanitolerans sp. nov. is proposed. The type strain is MNA2T (=DSM 22422T =CCM 7585T).
Amycolatopsis helveola sp. nov. and Amycolatopsis pigmentata sp. nov., isolated from soil
Authors: Tamura Tomohiko , Ishida Yuumi , Otoguro Misa , Suzuki Ken-ichiro
Published: December 2009

Three short spore chain-forming actinomycete strains were isolated from soil samples collected from subtropical islands in Japan. The cell-wall peptidoglycan of these strains containedmeso-diaminopimelic acid (meso-A2pm), glutamic acid and alanine. The major isoprenoid quinone was MK-9(H4), iso-C16 : 0and 2-OH iso-C16 : 0were the major cellular fatty acids and phosphatidylethanolamine was a component of the polar lipids. The G+C content of the genomic DNA was 67–69 mol%. Phylogenetic analyses based on the 16S rRNA gene sequences showed that the novel strains consistently formed a monophyletic cluster withAmycolatopsis taiwanensis. On the basis this polyphasic taxonomical study, it is proposed that the two new isolates represent two novel species:Amycolatopsis helveola(type strain TT00-43T=NBRC 103394T=KCTC 19329T) andAmycolatopsis pigmentata(type strain TT99-32T=NBRC 103392T=KCTC 19330T).
Sphingopyxis bauzanensis sp. nov., a psychrophilic bacterium isolated from soil
Authors: Zhang De-Chao , Liu Hong-Can , Xin Yu-Hua , Zhou Yu-Guang , Schinner Franz , Margesin Rosa
Published: December 2009

Strain BZ30Twas isolated from hydrocarbon-contaminated soil. The Gram-negative, aerobic bacterium was psychrophilic and able to grow at temperatures ranging from 1 to 30 °C. The predominant cellular fatty acids of strain BZ30Twere summed feature 3 (C16 : 1ω7cand/or iso-C15 : 02-OH) (37.4 %), C18 : 1ω7c(19.6 %), C16 : 0(8.2 %), C14 : 02-OH (8.0 %) and C16 : 02-OH (5.0 %). The predominant ubiquinone was Q-10. Major polar lipids were sphingoglycolipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. Spermidine was the major polyamine. The genomic DNA G+C content was 64.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain BZ30Tbelonged to the familySphingomonadaceaeof theα-4 group of the phylumProteobacteria, and was related to the members of the genusSphingopyxis, sharing the highest sequence similarities with the type strains ofSphingopyxischilensis(98.3 %),S.witflariensis(98.2 %),S.taejonensis(97.4 %) andS.ginsengisoli(97.2 %). On the basis of the phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain BZ30Trepresents a novel species of the genusSphingopyxis, for which the nameSphingopyxis bauzanensisis proposed. The type strain is BZ30T(=DSM 22271T=CGMCC 1.8959T=CIP 110136T).
Cupriavidus pampae sp. nov., a novel herbicide-degrading bacterium isolated from agricultural soil
Authors: Cuadrado Virginia , Gomila Margarita , Merini Luciano , Giulietti Ana M. , Moore Edward R. B.
Published: December 2009

A bacterial consortium able to degrade the herbicide 4-(2,4-dichlorophenoxy) butyric acid (2,4-DB) was obtained from an agricultural soil of the Argentinean Humid Pampa region which has a history of long-term herbicide use. Four bacterial strains were isolated from the consortium and identified as members of the genera Cupriavidus, Labrys and Pseudomonas. A polyphasic systematic analysis was carried out on strain CPDB6T, the member of the 2,4-DB-degrading consortium able to degrade 2,4-DB as a sole carbon and energy source. The Gram-negative, rod-shaped, motile, non-sporulating, non-fermenting bacterium was shown to belong to the genus Cupriavidus on the basis of 16S rRNA gene sequence analyses. Strain CPDB6T did not reduce nitrate, which differentiated it from the type species of the genus, Cupriavidus necator; it did not grow in 0.5–4.5 % NaCl, although most species of Cupriavidus are able to grow at NaCl concentrations as high as 1.5 %; and it was able to deamidate acetamide, which differentiated it from all other species of Cupriavidus. DNA–DNA hybridization data revealed low levels of genomic DNA similarity (less than 30 %) between strain CPDB6T and the type strains of Cupriavidus species with validly published names. The major cellular fatty acids detected were cis-9-hexadecenoic (16 : 1ω7c) and hexadecanoic (16 : 0) acids. On the basis of phenotypic and genotypic characterizations, strain CPDB6T was recognized as a representative of a novel species within the genus Cupriavidus. The name Cupriavidus pampae sp. nov. is proposed, with strain CPDB6T (=CCUG 55948T=CCM-A-29:1289T) as the type strain.
Description of Microvirga aerophila sp. nov. and Microvirga aerilata sp. nov., isolated from air, reclassification of Balneimonas flocculans Takeda et al. 2004 as Microvirga flocculans comb. nov. and emended description of the genus Microvirga
Authors: Weon Hang-Yeon , Kwon Soon-Wo , Son Jung-A , Jo Eun-Hye , Kim Soo-Jin , Kim Yi-Seul , Kim Byung-Yong , Ka Jong-Ok
Published: December 2009

Two bacterial strains, 5420S-12T and 5420S-16T, isolated from air samples, were characterized using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain 5420S-12T was related phylogenetically to Microvirga subterranea FaiI4T (97.4 % sequence similarity) and Microvirga guangxiensis 25BT (97.1 %) and that strain 5420S-16T was closely related to Balneimonas flocculans TFBT (98.0 %) and Microvirga guangxiensis 25BT (97.2 %). The G+C content of the genomic DNA was 62.2 mol% for strain 5420S-12T and 61.5 mol% for strain 5420S-16T. The major fatty acid was C18 : 1
ω7c. The results of DNA–DNA hybridization and the phenotypic data showed that strains 5420S-12T and 5420S-16T could be distinguished from phylogenetically related species and represent two novel species within the genus Microvirga, for which the names Microvirga aerophila sp. nov. (type strain 5420S-12T =KACC 12743T =NBRC 106136T) and Microvirga aerilata sp. nov. (type strain 5420S-16T =KACC 12744T =NBRC 106137T) are proposed. Furthermore, the reclassification of Balneimonas flocculans as Microvirga flocculans comb. nov. (type strain TFBT =JCM 11936T =KCTC 12101T =IAM 15034T =ATCC BAA-817T) is proposed and an emended description of the genus Microvirga is provided.
Pedobacter bauzanensis sp. nov., isolated from soil
Authors: Zhang De-Chao , Schinner Franz , Margesin Rosa
Published: December 2009

A Gram-negative, aerobic, rod-shaped, non-motile bacterium, designated BZ42T, was isolated from the soil of an industrial site. Strain BZ42T was able to grow at 5–25 °C. The major fatty acids were iso-C15 : 0 (46.2 %), C16 : 1
ω7c and/or iso-C15 : 0 2-OH (23.2 %) and iso-C17 : 0 3-OH (9.1 %). The predominant menaquinone was MK-7. The genomic DNA G+C content was 36.5 mol% (HPLC). 16S rRNA gene sequence phylogenetic analysis revealed that strain BZ42T was a member of the genus Pedobacter, family Sphingobacteriaceae, and 16S rRNA gene sequence similarities between strain BZ42T and the type strains of species of the genus Pedobacter with validly published names were 90.4–93.2 %. On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain BZ42T was considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter bauzanensis sp. nov. is proposed. The type strain is BZ42T (=DSM 22554T =CGMCC 1.10187T =CIP 110134T).
Orbus hercynius gen. nov., sp. nov., isolated from faeces of wild boar, is most closely related to members of the orders ‘Enterobacteriales’ and Pasteurellales
Authors: Volkmann Maria , Skiebe Evelyn , Kerrinnes Tobias , Faber Franziska , Lepka Daniela , Pfeifer Yvonne , Holland Gudrun , Bannert Norbert , Wilharm Gottfried
Published: December 2009

A novel gammaproteobacterium, strain CN3T, was isolated from the faeces of wild boar. Strain CN3T was facultatively anaerobic and appeared coccoid or rod-shaped. The partial 16S rRNA gene sequence determined for strain CN3T suggested a distant relationship with members of the orders ‘Enterobacteriales’ and Pasteurellales. The gene sequence showed highest similarity (90.3 %) with Obesumbacterium proteus DSM 2777T, a member of the family Enterobacteriaceae. The closest relatives outside the order ‘Enterobacteriales’ according to 16S rRNA gene sequence analysis were members of the order Pasteurellales with 88.7 % similarity (Mannheimia haemolytica NCTC 9380T and Actinobacillus lignieresii NCTC 4189T). In contrast to most members of the order ‘Enterobacteriales’, strain CN3T was oxidase-positive. The pattern of fatty acids, in particular the high relative abundance of C18 : 1
ω7c (38.5 %), was clearly distinct from the conserved pattern found for members of the order Pasteurellales. EcoRI ribotyping of strain CN3T yielded no significant similarity to existing database entries. The major ubiquinone of strain CN3T was Q-8. The DNA G+C content was 36.4 mol%. Strain CN3T hosted a phage and secreted considerable amounts of three proteins into the culture supernatant. A spontaneous mutant of strain CN3T was isolated which formed long filaments. Microscopic studies revealed the presence of a capsule that the mutant strain was unable to partition after cell division. Strain CN3T thus represents a novel species within a new genus, for which the name Orbus hercynius gen. nov., sp. nov. is proposed. The type strain of the type species is CN3T (=DSM 22228T=CCUG 57622T). Classification of the novel species to the family and order level will require further investigations.
Methylophilus flavus sp. nov. and Methylophilus luteus sp. nov., aerobic, methylotrophic bacteria associated with plants
Authors: Gogleva Anna A. , Kaparullina Elena N. , Doronina Nina V. , Trotsenko Yuri A.
Published: December 2009

Novel yellow, obligately methylotrophic and restricted facultatively methylotrophic bacteria, respectively designated strains ShipT and MimT, with the ribulose monophosphate pathway of C1 assimilation are described. Cells were strictly aerobic, Gram-negative, asporogenous, non-motile rods that multiply by binary fission, were mesophilic and neutrophilic and synthesized indole-3-acetic acid and exopolysaccharide. The predominant cellular fatty acids were C16 : 0 and C16 : 1. The major ubiquinone was Q-8. The predominant phospholipids were phosphatidylethanolamine and phosphatidylglycerol; diphosphatidylglycerol was absent. The two strains lacked α-ketoglutarate dehydrogenase and glutamate dehydrogenase. They assimilated ammonium via the glutamate cycle enzymes glutamine synthetase and glutamate synthase. The DNA G+C contents of strains ShipT and MimT were 50.7 and 54.5 mol% (T
m), respectively. The level of 16S rRNA gene sequence similarity between these strains was very high (99.8 %) but they shared a low level of DNA–DNA relatedness (44 %). Based on 16S rRNA gene sequence analysis and low levels of DNA–DNA relatedness with the type strains of recognized species of the genus Methylophilus (31–36 %), strains ShipT and MimT are considered to represent novel species of the genus Methylophilus, for which the names Methylophilus flavus sp. nov. (type strain ShipT =DSM 23073T =VKM B-2547T =CCUG 58411T) and Methylophilus luteus sp. nov. (type strain MimT =DSM 22949T =VKM B-2548T =CCUG 58412T) are proposed.
Halogeometricum rufum sp. nov., a halophilic archaeon from a marine solar saltern, and emended description of the genus Halogeometricum
Authors: Cui Heng-Lin , Yang Xin , Gao Xia , Li Xin-Yi , Xu Xue-Wei , Zhou Yu-Guang , Liu Hong-Can , Zhou Pei-Jin
Published: December 2009

Two halophilic archaea, strains RO1-4Tand RO1-64, were isolated from a marine solar saltern in Jiangsu, China. Cells of the two strains were pleomorphic, motile, and stained Gram-negative. Colonies were red-pigmented. Strains RO1-4Tand RO1-64 were able to grow at 25–55 °C (optimum 40–42 °C), at 2.1–5.1 M NaCl (optimum 3.9 M NaCl), at 0.05–0.7 M MgCl2(optimum 0.3 M MgCl2) and at pH 6.0–8.5 (optimum pH 7.0). Cells lyse in distilled water and the minimal NaCl concentration to prevent cell lysis is 12 % (w/v). On the basis of 16S rRNA gene sequence analysis, strains RO1-4Tand RO1-64 were closely related toHalogeometricum borinquensePR3T(98.0 and 98.2 % similarity, respectively) andHalosarcina pallidaBZ256T(97.8 and 97.9 %). The major polar lipids of the two strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and two glycolipids (S-DGD-1 and DGD-1). The DNA G+C contents of strains RO1-4Tand RO1-64 are 64.9 and 62.4 mol%, respectively. The DNA–DNA hybridization value between strains RO1-4Tand RO1-64 was 83.0 % and both strains showed low DNA–DNA relatedness withHalogeometricum borinquensePR3T(42.5 and 50.1 % relatedness, respectively) andHalosarcina pallidaBZ256T(37.6 and 42.1 % relatedness). It was concluded that strains RO1-4Tand RO1-64 represent a novel species of the genusHalogeometricum, for which the nameHalogeometricum rufumsp. nov. is proposed. The type strain is RO1-4T(=CGMCC 1.7736T=JCM 15770T).
Tryptophan-Derived Metabolites Are Required for Antifungal Defense in the Arabidopsismlo2Mutant
Authors: Consonni Chiara , Bednarek Paweł , Humphry Matt , Francocci Fedra , Ferrari Simone , Harzen Anne , Ver Loren van Themaat Emiel , Panstruga Ralph
Published: December 2009

Arabidopsis (Arabidopsis thaliana) genes MILDEW RESISTANCE LOCUS O2 (MLO2), MLO6, and MLO12 exhibit unequal genetic redundancy with respect to the modulation of defense responses against powdery mildew fungi and the control of developmental phenotypes such as premature leaf decay. We show that early chlorosis and necrosis of rosette leaves in mlo2 mlo6 mlo12 mutants reflects an authentic but untimely leaf senescence program. Comparative transcriptional profiling revealed that transcripts of several genes encoding tryptophan biosynthetic and metabolic enzymes hyperaccumulate during vegetative development in the mlo2 mlo6 mlo12 mutant. Elevated expression levels of these genes correlate with altered steady-state levels of several indolic metabolites, including the phytoalexin camalexin and indolic glucosinolates, during development in the mlo2 single mutant and the mlo2 mlo6 mlo12 triple mutant. Results of genetic epistasis analysis suggest a decisive role for indolic metabolites in mlo2-conditioned antifungal defense against both biotrophic powdery mildews and a camalexin-sensitive strain of the necrotrophic fungus Botrytis cinerea. The wound- and pathogen-responsive callose synthase POWDERY MILDEW RESISTANCE4/GLUCAN SYNTHASE-LIKE5 was found to be responsible for the spontaneous callose deposits in mlo2 mutant plants but dispensable for mlo2-conditioned penetration resistance. Our data strengthen the notion that powdery mildew resistance of mlo2 genotypes is based on the same defense execution machinery as innate antifungal immune responses that restrict the invasion of nonadapted fungal pathogens.
AtMetExpress Development: A Phytochemical Atlas of Arabidopsis Development
Authors: Matsuda Fumio , Hirai Masami Y. , Sasaki Eriko , Akiyama Kenji , Yonekura-Sakakibara Keiko , Provart Nicholas J. , Sakurai Tetsuya , Shimada Yukihisa , Saito Kazuki
Published: December 2009

Plants possess many metabolic genes for the production of a wide variety of phytochemicals in a tissue-specific manner. However, the metabolic systems behind the diversity and tissue-dependent regulation still remain unknown due to incomplete characterization of phytochemicals produced in a single plant species. Thus, having a metabolome dataset in addition to the genome and transcriptome information resources would enrich our knowledge of plant secondary metabolism. Here we analyzed phytochemical accumulation during development of the model plant Arabidopsis (Arabidopsis thaliana) using liquid chromatography-mass spectrometry in samples covering many growth stages and organs. We also obtained tandem mass spectrometry spectral tags of many metabolites as a resource for elucidation of metabolite structure. These are part of the AtMetExpress metabolite accumulation atlas. Based on the dataset, we detected 1,589 metabolite signals from which the structures of 167 metabolites were elucidated. The integrated analyses with transcriptome data demonstrated that Arabidopsis produces various phytochemicals in a highly tissue-specific manner, which often accompanies the expression of key biosynthesis-related genes. We also found that a set of biosynthesis-related genes is coordinately expressed among the tissues. These data suggested that the simple mode of regulation, transcript to metabolite, is an origin of the dynamics and diversity of plant secondary metabolism.
Glucanases and Chitinases as Causal Agents in the Protection ofAcaciaExtrafloral Nectar from Infestation by Phytopathogens
Authors: GonzÁlez-Teuber Marcia , Pozo María J. , Muck Alexander , Svatos Ales , Adame-Álvarez Rosa M. , Heil Martin
Published: December 2009

Nectars are rich in primary metabolites and attract mutualistic animals, which serve as pollinators or as an indirect defense against herbivores. Their chemical composition makes nectars prone to microbial infestation. As protective strategy, floral nectar of ornamental tobacco (Nicotiana langsdorffii × Nicotiana sanderae) contains “nectarins,” proteins producing reactive oxygen species such as hydrogen peroxide. By contrast, pathogenesis-related (PR) proteins were detected in Acacia extrafloral nectar (EFN), which is secreted in the context of defensive ant-plant mutualisms. We investigated whether these PR proteins protect EFN from phytopathogens. Five sympatric species (Acacia cornigera, A. hindsii, A. collinsii, A. farnesiana, and Prosopis juliflora) were compared that differ in their ant-plant mutualism. EFN of myrmecophytes, which are obligate ant-plants that secrete EFN constitutively to nourish specialized ant inhabitants, significantly inhibited the growth of four out of six tested phytopathogenic microorganisms. By contrast, EFN of nonmyrmecophytes, which is secreted only transiently in response to herbivory, did not exhibit a detectable inhibitory activity. Combining two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis with nanoflow liquid chromatography-tandem mass spectrometry analysis confirmed that PR proteins represented over 90% of all proteins in myrmecophyte EFN. The inhibition of microbial growth was exerted by the protein fraction, but not the small metabolites of this EFN, and disappeared when nectar was heated. In-gel assays demonstrated the activity of acidic and basic chitinases in all EFNs, whereas glucanases were detected only in EFN of myrmecophytes. Our results demonstrate that PR proteins causally underlie the protection of Acacia EFN from microorganisms and that acidic and basic glucanases likely represent the most important prerequisite in this defensive function.
Generation of Backbone-Free, Low Transgene Copy Plants by Launching T-DNA from theAgrobacteriumChromosome
Authors: Oltmanns Heiko , Frame Bronwyn , Lee Lan-Ying , Johnson Susan , Li Bo , Wang Kan , Gelvin Stanton B.
Published: December 2009

In both applied and basic research, Agrobacterium-mediated transformation is commonly used to introduce genes into plants. We investigated the effect of three Agrobacterium tumefaciens strains and five transferred (T)-DNA origins of replication on transformation frequency, transgene copy number, and the frequency of integration of non-T-DNA portions of the T-DNA-containing vector (backbone) into the genome of Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). Launching T-DNA from the picA locus of the Agrobacterium chromosome increases the frequency of single transgene integration events and almost eliminates the presence of vector backbone sequences in transgenic plants. Along with novel Agrobacterium strains we have developed, our findings are useful for improving the quality of T-DNA integration events.
The Missing Link in Plant Histidine Biosynthesis: Arabidopsismyoinositol monophosphatase-like2Encodes a Functional Histidinol-Phosphate Phosphatase
Authors: Petersen Lindsay N. , Marineo Sandra , Mandalà Salvatore , Davids Faezah , Sewell Bryan T. , Ingle Robert A.
Published: December 2009

Histidine (His) plays a critical role in plant growth and development, both as one of the standard amino acids in proteins, and as a metal-binding ligand. While genes encoding seven of the eight enzymes in the pathway of His biosynthesis have been characterized from a number of plant species, the identity of the enzyme catalyzing the dephosphorylation of histidinol-phosphate to histidinol has remained elusive. Recently, members of a novel family of histidinol-phosphate phosphatase proteins, displaying significant sequence similarity to known myoinositol monophosphatases (IMPs) have been identified from several Actinobacteria. Here we demonstrate that a member of the IMP family from Arabidopsis (Arabidopsis thaliana), myoinositol monophosphatase-like2 (IMPL2; encoded by At4g39120), has histidinol-phosphate phosphatase activity. Heterologous expression of IMPL2, but not the related IMPL1 protein, was sufficient to rescue the His auxotrophy of a Streptomyces coelicolor hisN mutant. Homozygous null impl2 Arabidopsis mutants displayed embryonic lethality, which could be rescued by supplying plants heterozygous for null impl2 alleles with His. In common with the previously characterized HISN genes from Arabidopsis, IMPL2 was expressed in all plant tissues and throughout development, and an IMPL2:green fluorescent protein fusion protein was targeted to the plastid, where His biosynthesis occurs in plants. Our data demonstrate that IMPL2 is the HISN7 gene product, and suggest a lack of genetic redundancy at this metabolic step in Arabidopsis, which is characteristic of the His biosynthetic pathway.
ArabidopsisFormin3 Directs the Formation of Actin Cables and Polarized Growth in Pollen Tubes
Authors: Ye Jianrong , Zheng Yiyan , Yan An , Chen Naizhi , Wang Zhangkui , Huang Shanjin , Yang Zhenbiao
Published: December 2009

Cytoplasmic actin cables are the most prominent actin structures in plant cells, but the molecular mechanism underlying their formation is unknown. The function of these actin cables, which are proposed to modulate cytoplasmic streaming and intracellular movement of many organelles in plants, has not been studied by genetic means. Here, we show that Arabidopsis thaliana formin3 (AFH3) is an actin nucleation factor responsible for the formation of longitudinal actin cables in pollen tubes. The Arabidopsis AFH3 gene encodes a 785–amino acid polypeptide, which contains a formin homology 1 (FH1) and a FH2 domain. In vitro analysis revealed that the AFH3 FH1FH2 domains interact with the barbed end of actin filaments and have actin nucleation activity in the presence of G-actin or G actin-profilin. Overexpression of AFH3 in tobacco (Nicotiana tabacum) pollen tubes induced excessive actin cables, which extended into the tubes' apices. Specific downregulation of AFH3 eliminated actin cables in Arabidopsis pollen tubes and reduced the level of actin polymers in pollen grains. This led to the disruption of the reverse fountain streaming pattern in pollen tubes, confirming a role for actin cables in the regulation of cytoplasmic streaming. Furthermore, these tubes became wide and short and swelled at their tips, suggesting that actin cables may regulate growth polarity in pollen tubes. Thus, AFH3 regulates the formation of actin cables, which are important for cytoplasmic streaming and polarized growth in pollen tubes.
Ethylene Interacts with Abscisic Acid to Regulate Endosperm Rupture during Germination: A Comparative Approach UsingLepidium sativumandArabidopsis thaliana
Authors: Linkies Ada , Müller Kerstin , Morris Karl , Turečková Veronika , Wenk Meike , Cadman Cassandra S.C. , Corbineau Françoise , Strnad Miroslav , Lynn James R. , Finch-Savage William E. , Leubner-Metzger Gerhard
Published: December 2009

The micropylar endosperm cap covering the radicle in the mature seeds of most angiosperms acts as a constraint that regulates seed germination. Here, we report on a comparative seed biology study with the close Brassicaceae relatives Lepidium sativum and Arabidopsis thaliana showing that ethylene biosynthesis and signaling regulate seed germination by a mechanism that requires the coordinated action of the radicle and the endosperm cap. The larger seed size of Lepidium allows direct tissue-specific biomechanical, biochemical, and transcriptome analyses. We show that ethylene promotes endosperm cap weakening of Lepidium and endosperm rupture of both species and that it counteracts the inhibitory action of abscisic acid (ABA) on these two processes. Cross-species microarrays of the Lepidium micropylar endosperm cap and the radicle show that the ethylene-ABA antagonism involves both tissues and has the micropylar endosperm cap as a major target. Ethylene counteracts the ABA-induced inhibition without affecting seed ABA levels. The Arabidopsis loss-of-function mutants ACC oxidase2 (aco2; ethylene biosynthesis) and constitutive triple response1 (ethylene signaling) are impaired in the 1-aminocyclopropane-1-carboxylic acid (ACC)-mediated reversion of the ABA-induced inhibition of seed germination. Ethylene production by the ACC oxidase orthologs Lepidium ACO2 and Arabidopsis ACO2 appears to be a key regulatory step. Endosperm cap weakening and rupture are promoted by ethylene and inhibited by ABA to regulate germination in a process conserved across the Brassicaceae.
Mutations of an α1,6 Mannosyltransferase Inhibit Endoplasmic Reticulum–Associated Degradation of Defective Brassinosteroid Receptors inArabidopsis
Authors: Hong Zhi , Jin Hua , Fitchette Anne-Catherine , Xia Yang , Monk Andrew M. , Faye Loïc , Li Jianming
Published: December 2009

Asn-linked glycans, or the glycan code, carry crucial information for protein folding, transport, sorting, and degradation. The biochemical pathway for generating such a code is highly conserved in eukaryotic organisms and consists of ordered assembly of a lipid-linked tetradeccasaccharide. Most of our current knowledge on glycan biosynthesis was obtained from studies of yeast asparagine-linked glycosylation (alg) mutants. By contrast, little is known about biosynthesis and biological functions of N-glycans in plants. Here, we show that loss-of-function mutations in the Arabidopsis thaliana homolog of the yeast ALG12 result in transfer of incompletely assembled glycans to polypeptides. This metabolic defect significantly compromises the endoplasmic reticulum–associated degradation of bri1-9 and bri1-5, two defective transmembrane receptors for brassinosteroids. Consequently, overaccumulated bri1-9 or bri1-5 proteins saturate the quality control systems that retain the two mutated receptors in the endoplasmic reticulum and can thus leak out of the folding compartment, resulting in phenotypic suppression of the two bri1 mutants. Our results strongly suggest that the complete assembly of the lipid-linked glycans is essential for successful quality control of defective glycoproteins in Arabidopsis.
Class I α-Mannosidases Are Required for N-Glycan Processing and Root Development inArabidopsis thaliana
Authors: Liebminger Eva , Hüttner Silvia , Vavra Ulrike , Fischl Richard , Schoberer Jennifer , Grass Josephine , Blaukopf Claudia , Seifert Georg J. , Altmann Friedrich , Mach Lukas , Strasser Richard
Published: December 2009

In eukaryotes, class I α-mannosidases are involved in early N-glycan processing reactions and in N-glycan–dependent quality control in the endoplasmic reticulum (ER). To investigate the role of these enzymes in plants, we identified the ER-type α-mannosidase I (MNS3) and the two Golgi-α-mannosidase I proteins (MNS1 and MNS2) from Arabidopsis thaliana. All three MNS proteins were found to localize in punctate mobile structures reminiscent of Golgi bodies. Recombinant forms of the MNS proteins were able to process oligomannosidic N-glycans. While MNS3 efficiently cleaved off one selected α1,2-mannose residue from Man9GlcNAc2, MNS1/2 readily removed three α1,2-mannose residues from Man8GlcNAc2. Mutation in the MNS genes resulted in the formation of aberrant N-glycans in the mns3 single mutant and Man8GlcNAc2 accumulation in the mns1 mns2 double mutant. N-glycan analysis in the mns triple mutant revealed the almost exclusive presence of Man9GlcNAc2, demonstrating that these three MNS proteins play a key role in N-glycan processing. The mns triple mutants displayed short, radially swollen roots and altered cell walls. Pharmacological inhibition of class I α-mannosidases in wild-type seedlings resulted in a similar root phenotype. These findings show that class I α-mannosidases are essential for early N-glycan processing and play a role in root development and cell wall biosynthesis in Arabidopsis.
Regulation ofArabidopsisBrassinosteroid Signaling by Atypical Basic Helix-Loop-Helix Proteins
Authors: Wang Hao , Zhu Yongyou , Fujioka Shozo , Asami Tadao , Li Jiayang , Li Jianming
Published: December 2009

Basic helix-loop-helix (bHLH) proteins are highly conserved transcription factors critical for cell proliferation and differentiation. Recent studies have implicated bHLH proteins in many plant signaling processes, including brassinosteroid (BR) signaling. Here, we report identification of two families of atypical bHLH proteins capable of modulating BR signaling. We found that activation-tagged bri1 suppressor 1-Dominant (atbs1-D), previously identified as a dominant suppressor of a weak BR receptor mutant bri1-301, was caused by overexpression of a 93–amino acid atypical bHLH protein lacking amino acids critical for DNA binding. Interestingly, atbs1-D only suppresses weak BR mutants, while overexpression of a truncated ATBS1 lacking the basic motif also rescues bri1-301, suggesting that ATBS1 likely stimulates BR signaling by sequestering negative BR signaling components. A yeast two-hybrid screen using ATBS1 as bait discovered four ATBS1-Interacting Factors (AIFs) that are members of another atypical bHLH protein subfamily. AIF1 exhibits an overlapping expression pattern with ATBS1 and its homologs and interacts with ATBS1 in vitro and in vivo. AIF1 overexpression nullifies the suppressive effect of atbs1-D on bri1-301 and results in dwarf transgenic plants resembling BR mutants. By contrast, silencing of AIF1 partially suppressed the bri1-301 phenotype. Our results suggested that plants use these atypical bHLH proteins to regulate BR signaling.
Audit fee premium and auditor change: the effect of Sarbanes‐Oxley Act
Authors: Ebrahim Ahmed
Published: December 2009

Purpose

The purpose of this paper is to provide more comprehensive analysis of the effects of Sarbanes‐Oxley (SOX) Act on both audit fee premium and auditor change in the US audit market.

Design/methodology/approach

The audit fee premium model is employed to track the trend in audit fee premium between 2000 and 2006 for small accelerated filers compared with large accelerated filers and non‐accelerated filers and how the change in auditor affected such trend around the enactment of SOX.

Findings

The results indicate a significant shift in audit fee premium during early years of SOX compliance especially for small accelerated filers compared with large accelerated filers or non‐accelerated filers. Such shift started to wind down during 2006 after the initial application of SOX requirements. Although clients who switched from big to non‐big auditors have experienced a slower increase in their audit fees, these fee savings are lower for small accelerated filers during 2004 and 2005 with the increasing demand for audit services in the US audit industry during these years.

Practical implications

The compliance costs of significant regulatory changes like SOX may be upfront loaded but their benefits are long‐term benefits in terms of higher quality of financial reporting and better internal controls over financial reporting. When analyzing the effects of such regulatory changes, practitioners and researchers should factor these costs and benefits over a sufficient time horizon.

Originality/value

More comprehensive analysis of SOX effects on the US audit industry not only in the short run during early compliance years, but also in the longer run after the initial setup process.
Audit pricing and the Big4 fee premium: evidence from Belgium
Authors: Van Caneghem Tom
Published: December 2009

Purpose

The purpose of this paper is to study audit pricing and the Big4 fee premium in Belgium. While a number of studies have already explored these issues, the Belgian audit market provides an interesting setting to gain an additional insight into the pricing of audit services for many reasons (e.g. audit market concentration in Belgium is much lower than in other countries, the Belgian audit market mainly consists of non‐listed firms, etc.).

Design/methodology/approach

Besides the traditional audit fee model, based on seminal work by Simunic, the paper also estimates regression models in which the author allows coefficients to vary across Big4 and non‐Big4 auditors and control for self‐selection (based on a two‐stage procedure).

Findings

Using the traditional audit fee model, results suggest that Big4 auditors receive (or are able to charge) a fee premium compared to non‐Big4 auditors. Nevertheless, when the author allows regression coefficients to vary across Big4 and non‐Big4 auditors and control for self‐selection, the aforementioned finding does no longer hold. The results reveal differences in fee structures between Big4 and non‐Big4 auditors and suggest that Big4 auditors consider a richer set of variables when setting their fees.

Research limitations/implications

Since Belgian firms are only required to disclose audit fees as from 2007 onwards, the analyses are based on data for one year only.

Practical implications

An important implication, at least from an academic point of view, is that the results clearly illustrate and corroborate the need to control for self‐selection when modelling audit fees (while this issue has been ignored by recent audit fee studies). The findings also have implications for the (Belgian) auditing profession. For example, the fact that significant differences are observed in audit pricing between the Big4 and non‐Big4 firms may have an impact on the (Belgian) audit services market (e.g. it might influence the competitive nature of the tendering process).

Originality/value

Using a two‐stage procedure, the results corroborate the need to control for self‐selection in modeling audit fees (an issue that has been largely ignored in the audit fee literature). In addition, the results reveal that Big4 and non‐Big4 auditors have different fee structures and that it is therefore important to allow the regression coefficients (and not only the intercept) to vary across both groups. Finally, the findings add to the very scarce evidence on audit pricing for non‐listed firms.
Determinants of corporate internet reporting: evidence from Egypt
Authors: Aly Doaa , Simon Jon , Hussainey Khaled
Published: December 2009

Purpose

The purpose of this paper is to examine the potential factors that may affect the level of corporate internet reporting by Egyptian listed companies.

Design/methodology/approach

The content analysis approach to examine the information cited by the largest Egyptian companies is used in their web sites. The paper modifies and uses the disclosure index of Xiaoet al.Ordinary least square multiple regression analysis is used to examine the determinants of the internet reporting.

Findings

It is found that 56 per cent of Egyptian companies report a significant portion of information on their web sites. In addition, the paper finds that some financial characteristics explain the variation in the degree of internet reporting between Egyptian listed companies. In particular, profitability, foreign listing and industrial type (communications and financial services) are the determinants of the amount and presentation formatting of information disclosed on Egyptian companies' web sites. However, other firm characterises, such as firm size, leverage, liquidity and auditor size, do not explain corporate internet reporting.

Practical implications

The research finding is essential as it assists in informing regulators about the characteristics of Egyptian companies that are, and are not, satisfying national and international investors' demand of updated/online information. It also assists current and potential stakeholders to know the drives of corporate internet reporting in Egypt. Consequently, they may further investigate and verify such reporting practices. In practice, online reporting can be used as an effective tool for improving stakeholders' decision‐making process. Therefore, further research can be undertaken to examine the degree to which online reporting provides value‐relevant information for stakeholders.

Originality/value

To the best of the knowledge, there is no study examining the potential drivers of internet corporate reporting practice in Egypt. This paper is the first to examine the potential factors affecting corporate internet reporting in Egypt. The disclosure index used is designed to be suitable for companies working in the Egyptian environment.