bluuebunny/crossref_metadata_2025 huggingface dataset:
HMMoC—a compiler for hidden Markov models
Authors: Lunter Gerton
Published: July 2007

Summary: Hidden Markov models are widely applied within computational biology. The large data sets and complex models involved demand optimized implementations, while efficient exploration of model space requires rapid prototyping. These requirements are not met by existing solutions, and hand-coding is time-consuming and error-prone. Here, I present a compiler that takes over the mechanical process of implementing HMM algorithms, by translating high-level XML descriptions into efficient C++ implementations. The compiler is highly customizable, produces efficient and bug-free code, and includes several optimizations.

Availability:  http://genserv.anat.ox.ac.uk/software

Contact:  gerton.lunter@dpag.ox.ac.uk
EcoProDB: the Escherichia coli protein database
Authors: Yun Hongseok , Lee Jeong Wook , Jeong Joonwoo , Chung Jaesung , Park Jong Myoung , Myoung Han Na , Lee Sang Yup
Published: July 2007

Summary: EcoProDB is a web-based database for comparative proteomics of Escherichia coli. The database contains information on E. coli proteins identified on 2D gels along with other resources collected from various databases and published literature, with a special feature of showing the expression levels of E. coli proteins under different genetic and environmental conditions. It also provides comparative information of subcellular localization, theoretical 2D map, experimental 2D map and integrated protein information via an interactive web interface and application such as the Map Browser. Users can also upload their own 2D gels, extract core information associated with the proteins and 2D gel results from different experiments and consequently generate new knowledge and hypotheses for further studies.

Availability: EcoProDB database system is accessible at http://eecoli.kaist.ac.kr

Contact:  leesy@kaist.ac.kr
Disruption of a Maize 9-Lipoxygenase Results in Increased Resistance to Fungal Pathogens and Reduced Levels of Contamination with Mycotoxin Fumonisin
Authors: Gao Xiquan , Shim Won-Bo , Göbel Cornelia , Kunze Susan , Feussner Ivo , Meeley Robert , Balint-Kurti Peter , Kolomiets Michael
Published: July 2007

Plant oxylipins, produced via the lipoxygenase (LOX) pathway, function as signals in defense and development. In fungi, oxylipins are potent regulators of mycotoxin biosynthesis and sporogenesis. Previous studies showed that plant 9-LOX-derived fatty acid hydroperoxides induce conidiation and mycotoxin production. Here, we tested the hypothesis that oxylipins produced by the maize 9-LOX pathway are required by pathogens to produce spores and mycotoxins and to successfully colonize the host. Maize mutants were generated in which the function of a 9-LOX gene, ZmLOX3, was abolished by an insertion of a Mutator transposon in its coding sequence, which resulted in reduced levels of several 9-LOX-derived hydroperoxides. Supporting our hypothesis, conidiation and production of the mycotoxin fumonisin B1 by Fusarium verticillioides were drastically reduced in kernels of the lox3 mutants compared with near-isogenic wild types. Similarly, conidia production and disease severity of anthracnose leaf blight caused by Colletotrichum graminicola were significantly reduced in the lox3 mutants. Moreover, lox3 mutants displayed increased resistance to southern leaf blight caused by Cochliobolus heterostrophus and stalk rots caused by both F. verticillioides and C. graminicola. These data strongly suggest that oxylipin metabolism mediated by a specific plant 9-LOX isoform is required for fungal pathogenesis, including disease development and production of spores and mycotoxins.
Type 2A Phosphoprotein Phosphatase Is Required for Asexual Development and Pathogenesis of Sclerotinia sclerotiorum
Authors: Erental A. , Harel A. , Yarden O.
Published: July 2007

Sclerotinia sclerotiorum is a necrotrophic, omnivorous plant pathogen with worldwide distribution. Sclerotia of S. sclerotiorumare pigmented, multihyphal structures that play a central role in the life and infection cycles of this pathogen. Plant infection depends on the formation of melanin-rich infection cushions, and secretion of hydrolytic enzymes and oxalic acid. Type 2A Ser/Thr phosphatases (PP2As) are involved in the regulation of a variety of cellular process. In the presence of cantharidin, a PP2A-specific inhibitor, hyphal elongation and sclerotia numbers were impaired whereas sclerotial size increased. We partially inactivated PP2A by antisense expression of the gene (pph1) encoding the PP2A catalytic subunit. When antisense expression was induced, almost complete cessation of fungal growth was observed, indicative of a crucial role for PP2A in fungal growth. RNAi-based gene silencing was employed to alter the expression of the 55-kDa R2 (B regulatory subunit). Isolates in which rgb1 RNA levels were decreased were slow growing, but viable. Melanin biosynthesis, infection-cushion production, and pathogenesis were significantly impaired in the rgb1 mutants, yet theses mutants were pathogenic on wounded leaves. Reduced ERK (extracellular signal-regulated kinases)-like mitogen-activated protein kinase (MAPK) function conferred a reduction in NADPH oxidase and PP2A activity levels, suggesting a functional link between MAPK, reactive oxygen species, and PP2A activity in S. sclerotiorum.
Expression of the Membrane-Associated Resistance Protein RPW8 Enhances Basal Defense Against Biotrophic Pathogens
Authors: Wang Wenming , Devoto Alessandra , Turner John G. , Xiao Shunyuan
Published: July 2007

The powdery mildew resistance genes RPW8.1 and RPW8.2 from Arabidopsis differ from the other isolated plant resistance (R) genes in their predicted protein domains and their resistance spectrum. The two homologous RPW8 genes encode small proteins featuring a predicted amino-terminal transmembrane anchor domain and a coiled-coil domain and confer resistance to a broad spectrum of powdery mildews. Here, we show that Arabidopsis plants expressing the RPW8 genes have enhanced resistance to another biotrophic pathogen, Hyaloperonospora parasitica, raising the possibility that the RPW8 genes may function to enhance salicylic-acid-dependent basal defenses, rather than as powdery-mildew-specific R genes. When overexpressed from their native promoters, the RPW8 genes confer enhanced resistance to the Cauliflower mosaic virus, but render plants more susceptible to the necrotrophic fungal pathogens Alternaria and Botrytis spp. Furthermore, we show that the RPW8 proteins appear to be localized to the endomembrane system, overlapping with the endoplasmic reticulum–associated small GTPase SAR1, and accumulate to higher levels in response to application of exogenous salicylic acid, one of the signaling molecules of plant defense.
A Quantitative Assay Using Mycelial Fragments to Assess Virulence of Mycosphaerella fijiensis
Authors: Donzelli Bruno Giuliano Garisto , Churchill Alice C. L.
Published: July 2007

We describe a method to evaluate the virulence of Mycosphaerella fijiensis, the causal agent of black leaf streak disease (BLSD) of banana and plantain. The method is based on the delivery of weighed slurries of fragmented mycelia by camel's hair brush to 5-by-5-cm areas on the abaxial surface of banana leaf blades. Reliable BLSD development was attained in an environmental growth chamber with stringent lighting and humidity controls. By localizing inoculum onto small areas of large leaves, we achieved a dramatic increase in the number of strains that can be tested on each leaf and plant, which is critical for comparing the virulence of numerous strains concurrently. Image analysis software was used to measure the percentage of each inoculated leaf section showing BLSD symptoms over time. We demonstrated that the level of disease of four isolates was correlated with the weight of the mycelium applied and relatively insensitive to the degree of fragmentation of hyphae. This is the first report demonstrating that weighed mycelial inoculum, combined with image analysis software to measure disease severity, can be used to quantitatively assess the virulence of M. fijiensis under rigorously controlled environmental conditions.
A Recessive Allele (tgr-1) Conditioning Tomato Resistance to Geminivirus Infection Is Associated with Impaired Viral Movement
Authors: Bian Xue-Yu , Thomas Mark R. , Rasheed M. Saif , Saeed Muhammad , Hanson Peter , De Barro Paul J. , Rezaian M. Ali
Published: July 2007

Begomoviruses (the family Geminiviridae) are transmitted by the whitefly Bemisia tabaci and contain monopartite or bipartite circular single-stranded (ss)DNA genomes. They have emerged as severe problems in the production of agricultural and horticultural crops worldwide. Here, we report the identification of a tomato breeding line, FLA653, that confers a high level of resistance to Tomato leaf curl virus (TLCV, monopartite). Genetic analysis indicated that the resistance is controlled by a single recessive allele named tgr-1, which is in contrast to previous reports that multiple genetic factors are involved in tomato resistance to begomoviruses. Particle bombardment of an infectious TLCV DNA construct into the detached leaves of FLA653 resulted in the viral replication, but the viral ssDNA accumulated at a much lower level than that in susceptible controls. In situ localization of TLCV in the bombarded leaves suggests that tgr-1 impaired TLCV movement, raising the possibility that it may specify a host factor essential for viral systematic infection. This makes tgr-1 a strong candidate for developing resistance in major crops carrying the gene homologue.
Cost-Effective Control of a Quarantine Disease: A Quantitative Exploration Using “Design of Experiments” Methodology and Bio-Economic Modeling
Authors: Breukers Annemarie , van der Werf Wopke , Kleijnen Jack P. C. , Mourits Monique , Lansink Alfons Oude
Published: July 2007

An integrated approach to control of quarantine diseases at the level of the plant production chain is complicated. The involved actors have different interests and the system is complex. Consequently, control policies may not be cost effective. By means of a bio-economic model for brown rot in the Dutch potato production chain, the efficacy of different control options was quantitatively analyzed. An impact analysis was performed using the methodology of “design of experiments” to quantify the effect of factors in interaction on incidence and costs of brown rot. Factors can be grouped as policy, sector, economic, and exogenous factors. Results show that brown rot incidence and economic consequences are determined predominantly by policy and sector factors and, to a lesser extent, by economic and exogenous factors. Scenario studies were performed to elucidate how the government and sector can optimize the cost-effectiveness of brown rot control. Optimal cost-effectiveness of control requires cooperation of the sector and government, in which case brown rot incidence can be reduced by 75% and the costs of control can be reduced by at least 2 million euros per year. This study demonstrates quantitatively the potential contribution of an integrated approach to cost-effective disease control at chain level.
Protection of Citrus Rootstocks Against Phytophthora spp. with a Hypovirulent Isolate of Phytophthora nicotianae
Authors: Colburn G. C. , Graham J. H.
Published: July 2007

Phytophthora root rot of citrus in Florida is caused by Phytophthora nicotianae and P. palmivora. A naturally occurring isolate of P. nicotianae (Pn117) was characterized as hypovirulent on citrus roots. Pn117 infected and colonized fibrous roots, but caused significantly less disease than the virulent isolates P. nicotianae Pn198 and P. palmivora Pp99. Coincident inoculation of rootstock seedlings of Cleopatra mandarin (Citrus reticulata) or Swingle citrumelo (C. paradisi × Poncirus trifoliata) with the hypovirulent Pn117 and the virulent isolates Pn198 and Pp99 did not reduce the severity of disease caused by the virulent Phytophthora spp. When either rootstock was inoculated with the hypovirulent Pn117 for 3 days prior to inoculation with virulent isolates, preinoculated seedlings had significantly less disease and greater root weight compared with seedlings inoculated with the virulent isolates alone. Recovery of the different colony types of Phytophthora spp. from roots of sweet orange (C. sinensis) or Swingle citrumelo was evaluated on semiselective medium after sequential inoculations with the hypovirulent Pn117 and virulent Pp99. Pn117 was isolated from roots at the same level as the Pp99 at 3 days post inoculation. Preinoculation of Pn117 for 3 days followed by inoculation with Pp99 resulted in greater recovery of the hypovirulent isolate and lower recovery of the virulent compared with coincident inoculation.
Differences in Virulence and Genomic Features of Strains of ‘Candidatus Phytoplasma mali’, the Apple Proliferation Agent
Authors: Seemüller Erich , Schneider Bernd
Published: July 2007

Root and shoot samples from 24 symptomatic or nonsymptomatic apple trees infected with ‘Candidatus Phytoplasma mali’ were collected at different locations in Germany and France and used to inoculate rootstock M11 top grafted with cv. Golden Delicious. Inoculated trees were monitored over a 12-year period for apple proliferation (AP) symptoms and categorized as not or slightly, moderately, or severely affected. Based on symptomatology, the phytoplasma strains were defined as being avirulent to mildly, moderately, or highly virulent. Determination of phytoplasma titers by quantitative polymerase chain reaction (PCR) with DNA from roots revealed similar phytoplasma concentrations in all virulence groups. Molecular characterization of the strains by differential PCR amplification with five sets of primers resulted in 13 profiles. Six strains that were maintained in periwinkle and tobacco were molecularly characterized in more detail. The genome sizes of these strains as determined by pulsed-field gel electrophoresis using yeast chromosomes as size references ranged between 640 and 680 kb. Cleavage of the chromosome with the rare cutting restriction enzymes ApaI, BamHI, BssHII, MluI, and SmaI resulted in macro fragment patterns distinctly different in all strains. Similar results were obtained by Southern blot hybridization with three probes derived from strain AT. Differential PCR amplification at an annealing temperature of 52°C using eight primer pairs derived from strain AT revealed heterogeneity of target sequences among all strains. Based on these results, there is considerable variability in virulence and genomic traits in ‘Ca. P. mali’. However, correlations between molecular markers and virulence or phytoplasma titer could not be identified.
Identification of Race 1 of Fusarium oxysporum f. sp. lactucae on Lettuce by Inter-Retrotransposon Sequence-Characterized Amplified Region Technique
Authors: Pasquali Matias , Dematheis Flavia , Gullino Maria Lodovica , Garibaldi Angelo
Published: July 2007

Fusarium wilt of lettuce, caused worldwide by Fusarium oxysporum f. sp. lactucae, is an emerging seed-transmitted disease on Lactuca sativa. In order to develop a molecular diagnostic tool for identifying race 1 (VCG0300) of the pathogen on vegetable samples, an effective technique is presented. Inter-retrotransposon amplified polymorphism polymerase chain reaction (PCR), a technique based on the amplification of genomic regions between long terminal repeats, was applied. It was shown to be useful for grouping F. oxysporum f. sp. lactucae race 1 isolates. Inter-retrotransposon sequence-characterized amplified regions (IR-SCAR) was used to develop a specific set of PCR primers to be utilized for differentiating F. oxysporum f. sp. lactucae isolates from other F. oxysporum isolates. The specific primers were able to uniquely amplify fungal genomic DNA from race 1 isolates obtained in Italy, Portugal, the United States, Japan, and Taiwan. The primers also were specific to pathogen DNA obtained from artificially infected lettuce seed and naturally and artificially infected plants.
Effects of Temperature on Urediniospore Germination, Germ Tube Growth, and Initiation of Infection in Soybean by Phakopsora Isolates
Authors: Bonde M. R. , Berner D. K. , Nester S. E. , Frederick R. D.
Published: July 2007

Temperature is a critical factor in plant disease development. As part of a research program to determine how specific environmental variables affect soybean rust, we determined temperature effects on urediniospore germination and germ tube growth of four isolates of Phakopsora pachyrhizi, one each from Brazil, Hawaii, Taiwan, and Zimbabwe, and an isolate of P. meibomiae from Puerto Rico, collected over a 25-year period. Also compared were the effects of temperature during a night dew period on initiation of disease by the P. pachyrhizi isolates. All variables were fit to a nonlinear beta function with temperature as the independent variable. Minimum, maximum, and optimum temperatures, along with shape parameters of the beta function for each variable, were statistically analyzed. All Phakopsora isolates behaved similarly as to how temperature affected urediniospore germination, germ tube growth, and initiation of disease. The results suggest that P. pachyrhizi has changed little in the past few decades with respect to how it responds to temperature and that previously collected research data continues to be valid, simplifying the development of soybean rust disease models.
Host Effect on the Molecular and Biological Properties of a Citrus exocortis viroid Isolate from Vicia faba
Authors: Gandía Mónica , Bernad Lucía , Rubio Luis , Duran-Vila Núria
Published: July 2007

Citrus exocortis viroid (CEVd) is the casual agent of citrus exocortis disease, and has been found in naturally infected citrus and noncitrus hosts. Field isolates of CEVd may infect susceptible hosts as a complex of genetically related sequence variants (haplotypes). In the present work, a CEVd isolate recovered from a symptomless broad bean plant was characterized as a heterogeneous population with a nucleotide diversity of 0.026, which did not contain a predominant haplotype. When nucleic acid extracts of this infected broad bean were used to inoculate tomato, the plants displayed symptoms and the CEVd population was more homogeneous, with a nucleotide diversity of 0.007. However, when nucleic acid extracts from this tomato isolate were back inoculated to new broad bean plants, this isolate did not revert to the original population, because it showed low nucleotide diversity (0.001) and induced symptoms in the broad bean plants. Symptomless broad bean plants may act as reservoirs of highly heterogeneous populations of CEVd variants, providing an excellent inoculum source in terms of its potential to infect a broad range of putative hosts. The epidemiological implications are discussed.
Virgibacillus halophilus sp. nov., spore-forming bacteria isolated from soil in Japan
Authors: An Sun-Young , Asahara Mika , Goto Keiichi , Kasai Hiroaki , Yokota Akira
Published: July 2007

Two Gram-positive, round-spore-forming, rod-shaped, halophilic bacterial strains, 5B73CT and 5B133E, were isolated from field soil in Kakegawa, Shizuoka, Japan, and were characterized taxonomically using a polyphasic approach. These two strains were found to comprise strictly aerobic, motile rods that formed subterminal endospores. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains 5B73CT and 5B133E are phylogenetically affiliated to the genus Virgibacillus, exhibiting sequence similarities of 94.1–96.4 % with respect to the type strains of Virgibacillus species. The DNA G+C contents of strains 5B73CT and 5B133E were 42.6 and 42.3 mol%, respectively. The cell-wall peptidoglycan type (meso-diaminopimelic acid), the major cellular fatty acids (anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0) and the quinone type (MK-7) of the isolates support their affiliation to the genus Virgibacillus. On the basis of their genotypic and phenotypic characteristics, the isolates represent a novel species of the genus Virgibacillus, for which the name Virgibacillus halophilus sp. nov. is proposed. The type strain is 5B73CT (=IAM 15308T=KCTC 13935T).
Chitinophaga ginsengisegetis sp. nov. and Chitinophaga ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea
Authors: Lee Hyung-Gwan , An Dong-Shan , Im Wan-Taek , Liu Qing-Mei , Na Ju-Ryun , Cho Dong Ha , Jin Cheng Wu , Lee Sung-Taik , Yang Deok-Chun
Published: July 2007

Two novel strains belonging to the phylum Bacteroidetes [formerly the Cytophaga–Flexibacter–Bacteroides (CFB) group], designated Gsoil 040T and Gsoil 052T, were isolated from the soil of a ginseng field in Pocheon province, South Korea. A polyphasic approach was used to characterize the taxonomic position of the novel strains. Both strains were Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolates belong to the genus Chitinophaga but are clearly separated from the recognized species of this genus; gene sequence similarities between the novel isolates and type strains of recognized species ranged from 91.2 to 96.5 %. One exception was found; strain Gsoil 052T and the type strain of Chitinophaga filiformis had a gene sequence similarity of 99.6 % but had a DNA–DNA relatedness value of 38 %. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; major fatty acids, iso-C15 : 0 and C16 : 1
ω5c; major hydroxy fatty acid, iso-C17 : 0 3-OH and major polyamine, homospermidine) supported the affiliation of both strains Gsoil 040T and Gsoil 052T to the genus Chitinophaga. The results of physiological and biochemical tests enabled the genotypic and phenotypic differentiation of the novel strains from the other recognized species of the genus Chitinophaga. Therefore, it is suggested that the new isolates represent two novel species, for which the names Chitinophaga ginsengisegetis sp. nov. [type strain Gsoil 040T (=KCTC 12654T=DSM 18108T)] and Chitinophaga ginsengisoli sp. nov. [type strain Gsoil 052T (=KCTC 12592T=DSM 18017T)] are proposed.
Lactobacillus crustorum sp. nov., isolated from two traditional Belgian wheat sourdoughs
Authors: Scheirlinck Ilse , Van der Meulen Roel , Van Schoor Ann , Huys Geert , Vandamme Peter , De Vuyst Luc , Vancanneyt Marc
Published: July 2007

A polyphasic taxonomic study of the lactic acid bacteria (LAB) population in three traditional Belgian sourdoughs, sampled between 2002 and 2004, revealed a group of isolates that could not be assigned to any recognized LAB species. Initially, sourdough isolates were screened by means of (GTG)5-PCR fingerprinting. Four isolates displaying unique (GTG)5-PCR patterns were further investigated by means of phenylalanyl-tRNA synthase (pheS) gene sequence analysis and represented a bifurcated branch that could not be allocated to any LAB species present in the in-house pheS database. Their phylogenetic affiliation was determined using 16S rRNA gene sequence analysis and showed that the four sourdough isolates belong to the Lactobacillus plantarum group with Lactobacillus mindensis, Lactobacillus farciminis and Lactobacillus nantensis as closest relatives. Further genotypic and phenotypic studies, including whole-cell protein analysis (SDS-PAGE), amplified fragment length polymorphism (AFLP) fingerprinting, DNA–DNA hybridization, DNA G+C content analysis, growth characteristics and biochemical features, demonstrated that the new sourdough isolates represent a novel Lactobacillus species for which the name Lactobacillus crustorum sp. nov. is proposed. The type strain of the new species is LMG 23699T (=CCUG 53174T).
Haloterrigena hispanica sp. nov., an extremely halophilic archaeon from Fuente de Piedra, southern Spain
Authors: Romano Ida , Poli Annarita , Finore Ilaria , Huertas F. Javier , Gambacorta Agata , Pelliccione Salvatore , Nicolaus Giancarlo , Lama Licia , Nicolaus Barbara
Published: July 2007

An extremely halophilic archaeon belonging to the order Halobacteriales was isolated from Fuente de Piedra salt lake, Spain. This strain, designated FP1T, was a pleomorphic coccoid, neutrophilic and required at least 15 % (w/v) NaCl for growth. Strain FP1T grew at 37–60 °C, with optimal growth at 50 °C. Mg2+ was not required, but growth was observed with up to 10 % (w/v) MgSO4. Polar lipid analysis revealed the presence of mannose-6-sulfate(1-2)-glucose glycerol diether as a major glycolipid. Both C20C20 and C20C25 core lipids were present. The genomic DNA G+C content was 62.0 mol%. Phylogenetic analysis based on comparison of 16S rRNA gene sequences demonstrated that the isolate was most closely related to species of the genus Haloterrigena. DNA–DNA reassociation values between strain FP1T and the most closely related species of the genus Haloterrigena (Haloterrigena thermotolerans, Haloterrigena saccharevitans and Haloterrigena limicola) were lower than 29 %. It is therefore considered that strain FP1T represents a novel species of the genus Haloterrigena, for which the name Haloterrigena hispanica sp. nov. is proposed. The type strain is FP1T (=DSM 18328T=ATCC BAA-1310T).
Pseudosphingobacterium domesticum gen. nov., sp. nov., isolated from home-made compost
Authors: Vaz-Moreira Ivone , Nobre M. Fernanda , Nunes Olga C. , Manaia Célia M.
Published: July 2007

A bacterial strain, DC-186T, isolated from home-made compost, was characterized for its phenotypic and phylogenetic properties. The isolate was a Gram-negative rod that was able to grow at 15–36 °C and pH 5.5–8.0. Strain DC-186T was positive in tests for catalase, oxidase and β-galactosidase activities and aesculin hydrolysis. The predominant fatty acids were the summed feature C16 : 1/iso-C15 : 0 2-OH (42 %) and iso-C15 : 0 (26 %), the major respiratory quinone was menaquinone-7 and the genomic DNA G+C content was 42 mol%. 16S rRNA gene sequence analysis and phenetic characterization indicated that this organism belongs to the phylum Bacteroidetes and revealed its affiliation to the family Sphingobacteriaceae. Of recognized taxa, strain DC-186T was most closely related to Sphingobacterium daejeonense (90 % sequence similarity) based on 16S rRNA gene sequence analysis. The low 16S rRNA gene sequence similarity with other recognized taxa and the identification of distinctive phenetic features for this isolate support the definition of a new genus within the family Sphingobacteriaceae. The name Pseudosphingobacterium domesticum gen. nov., sp. nov. is proposed, with strain DC-186T (=CCUG 54353T=LMG 23837T) as the type strain.
Pelagicoccus mobilis gen. nov., sp. nov., Pelagicoccus albus sp. nov. and Pelagicoccus litoralis sp. nov., three novel members of subdivision 4 within the phylum ‘Verrucomicrobia’, isolated from seawater by in situ cultivation
Authors: Yoon Jaewoo , Yasumoto-Hirose Mina , Matsuo Yoshihide , Nozawa Midori , Matsuda Satoru , Kasai Hiroaki , Yokota Akira
Published: July 2007

Five Gram-negative, white-pigmented, spherical, chemoheterotrophic bacteria were isolated from seawater from Japan and the Republic of Palau by use of an in situ cultivation technique. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the five novel isolates, 02PA-Ca-133T, YM14-201T, H-MN57T, H-MN48 and MN1-156, were closely affiliated to members of subdivision 4 within the phylum ‘Verrucomicrobia’. The novel isolates shared 96–100 % sequence similarity with each other and showed less than 90 % similarity with the cultivated strains of subdivision 4. DNA–DNA relatedness values between strains 02PA-Ca-133T, YM14-201T and H-MN57T were less than 70 %; the value commonly accepted as the threshold for the phylogenetic definition of a species. Antibiotic susceptibility tests and amino acid analysis of cell-wall hydrolysates indicated that the novel isolates did not contain muramic acid or diaminopimelic acid in their cell walls, suggesting that these strains lack peptidoglycan. The DNA G+C contents of the five strains were 51–57 mol%. The major menaquinone was MK-7 and C16 : 0, C16 : 1
ω7c and anteiso-C15 : 0 were the major fatty acids. On the basis of polyphasic taxonomic evidence, it is concluded that these strains should be classified as representing a new genus and three novel species in subdivision 4 of the phylum ‘Verrucomicrobia’, for which the names Pelagicoccus mobilis gen. nov., sp. nov. [type strain 02PA-Ca-133T (=MBIC08004T=IAM 15422T=KCTC 13126T)], Pelagicoccus albus sp. nov. [type strain YM14-201T (=MBIC08272T=IAM 15421T=KCTC 13124T)] and Pelagicoccus litoralis sp. nov. [type strain H-MN57T (=MBIC08273T=IAM 15423T=KCTC 13125T)] are proposed.
Halomonas saccharevitans sp. nov., Halomonas arcis sp. nov. and Halomonas subterranea sp. nov., halophilic bacteria isolated from hypersaline environments of China
Authors: Xu Xue-Wei , Wu Yue-Hong , Zhou Zhen , Wang Chun-Sheng , Zhou Yu-Guang , Zhang Hui-Bin , Wang Yong , Wu Min
Published: July 2007

Three strains of Gram-negative, aerobic, neutrophilic and halophilic bacteria were isolated from samples of a salt lake on the Qinghai–Tibet Plateau and a subterranean saline well in the Si-Chuan Basin of China. These isolates, designated AJ275T, AJ282Tand ZG16T, were investigated using a polyphasic approach. Based on 16S rRNA gene sequence analysis, the isolates could be affiliated to the genusHalomonas. Genomic DNA G+C contents were 65.9 mol% for AJ275T, 56.7 mol% for AJ282Tand 57.6 mol% for ZG16T. The results of DNA–DNA hybridizations, fatty acid analysis and physiological and biochemical tests allowed the isolates to be differentiated genotypically and phenotypically from closely related species. It is proposed that strains AJ275T(=CGMCC 1.6493T=JCM 14606T=LMG 23976T), AJ282T(=CGMCC 1.6494T=JCM 14607T=LMG 23978T) and ZG16T(=CGMCC 1.6495T=JCM 14608T=LMG 23977T) represent the type strains of three novel species in the genusHalomonas:Halomonas saccharevitanssp. nov.,Halomonas arcissp. nov. andHalomonas subterraneasp. nov., respectively.
Functional persistence of exonized mammalian-wide interspersed repeat elements (MIRs)
Authors: Krull Maren , Petrusma Mirjan , Makalowski Wojciech , Brosius Jürgen , Schmitz Jürgen
Published: July 2007

Exonization of retroposed mobile elements, a process whereby new exons are generated following changes in non-protein-coding regions of a gene, is thought to have great potential for generating proteins with novel domains. Our previous analysis of primate-specific Alu-short interspersed elements (SINEs) showed, however, that during their 60 million years of evolution, SINE exonizations occurred in some primates, only to be lost again in some of the descendent lineages. This dynamic gain and loss makes it difficult to ascertain the contribution of exonization to genomic novelty. It was speculated that Alu-SINEs are too young to reveal persistent protein exaptation. In the present study we examined older mobile elements, mammalian-wide interspersed repeats (MIRs) that underwent active retroposition prior to the placental mammalian radiation ∼130 million years ago, to determine their contribution to protein-coding sequences. Of 107 potential cases of MIR exonizations in human, an analysis of splice sites substantiates a mechanism that benefits from 3′ splice site selection in MIR sequences. We retraced in detail the evolution of five MIR elements that exonized at different times during mammalian evolution. Four of these are expressed as alternatively spliced transcripts; three in species throughout the mammalian phylogenetic tree and one solely in primates. The fifth is the first experimentally verified, constitutively expressed retroposed SINE element in mammals. This pattern of highly conserved, alternatively and constitutively spliced MIR sequences evinces the potential of exonized transposed elements to evolve beyond the transient state found in Alu-SINEs and persist as important parts of functional proteins.
External Auditing, Managerial Monitoring and Firm Valuation: An Empirical Analysis for India
Authors: Ghosh Saibal
Published: July 2007

This article examines how external auditing and managerial ownership relate to firm valuation. It is argued that both external auditors (which serve as an external monitoring function) and managerial ownership (which serves as an internal monitoring function) affect firm value, while internal monitoring by managers and external monitoring by auditors were viewed as substitutes or complements. After controlling for the effect of exogenous variables, the results reveal the existence of a substitution monitoring effect between auditors and the managerial group. Additionally, firm valuation is found to be a significant determinant of managerial ownership. A disaggregated analysis of firms according to size and leverage suggests the existence of a complementary monitoring effect between auditors and managers, especially for low‐leveraged firms.
Dietary patterns and the risk of breast cancer in Japanese women
Authors: Hirose Kaoru , Matsuo Keitaro , Iwata Hiroji , Tajima Kazuo
Published: July 2007

Components of the Japanese diet that might contribute to the relatively low breast cancer incidence in Japanese women have not been clarified in detail. To evaluate associations between broad dietary patterns and breast cancer risk in a Japanese population, the authors conducted a case–control study using data from the hospital‐based epidemiologic research program at Aichi Cancer Center (HERPACC). Factor analysis (principal components) was used to derive food patterns based on the 31 food variables and allowed designation of four major dietary patterns: prudent, fatty, Japanese and salty. In total, 1885 breast cancer cases were included and 22 333 female non‐cancer patients were recruited as the control group. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were determined using multiple logistic regression analysis. After adjusting for potential confounders, there were no clear associations between the fatty, Japanese or salty dietary patterns and overall breast cancer risk. In contrast, an inverse association was evident for the prudent dietary. Women in the highest quartile of the prudent dietary pattern scores, had a 27% decreased risk of breast cancer compared with those in the lowest (95% CI: 0.63–0.84, p for trend < 0.0001). In addition, for women with a body mass index ≥25, the highest quartile of the fatty factor score was associated with a 58% increment in breast cancer risk compared to the lowest quartile, with a significant linear trend (P = 0.027). The authors found the prudent dietary pattern to be negatively associated with breast cancer risk. In addition, the fatty and Japanese patterns may increase breast cancer risk among obese women. (Cancer Sci 2007; 98: 1431–1438)
Geometry of half‐grabens containing a mid‐level viscous décollement
Authors: Soto Ruth , Casas‐Sainz Antonio M. , Del Río Pedro
Published: July 2007

In this work, we explore by means of analogue models how different basin‐bounding fault geometries and thickness of a viscous layer within the otherwise brittle pre‐rift sequence influence the deformation and sedimentary patterns of basins related to extension. The experimental device consists of a rigid wooden basement in the footwall to simulate a listric fault. The hangingwall consists of a sequence of pre‐rift deposits, including the shallow interlayered viscous layer, and a syn‐rift sequence deposited at constant intervals during extension. Two different geometries exist of listric normal faults, dip at 30 and 60° at surface. This imposes different geometries in the hangingwall anticlines and their associated sedimentary basins. A strong contrast exists between models with and without a viscous layer. With a viscous décollement, areas near the main basement fault show a wide normal drag and the hangingwall basin is gently synclinal, with dips in the fault side progressively shallowing upwards. A secondary roll‐over structure appears in some of the models. Other structures are: (1) reverse faults dipping steeply towards the main fault, (2) antithetic faults in the footwall, appearing only in models with the 30° dipping fault and silicone‐level thicknesses of 1 and 1.5 cm and (3) listric normal faults linked to the termination of the detachment level opposite to the main fault, with significant thickness changes in the syn‐tectonic units. The experiments demonstrate the importance of detachment level in conditioning the geometry of extensional sedimentary basins and the possibility of syncline basin geometries associated with a main basement fault. Comparison with several basins with half‐graben geometries containing a mid‐level décollement supports the experimental results and constrains their interpretation.
Time use in Russian Baby Homes
Authors: Tirella L. G. , Chan W. , Cermak S. A. , Litvinova A. , Salas K. C. , Miller L. C.
Published: July 2007

Background  We investigated time use of Russian children residing in Baby Homes to document their opportunities and experiences during institutional care.

Methods  Time use of 138 non‐special needs, randomly selected children (65 female vs. 73 male, age 1 month to 4 years) in Baby Homes in Murmansk, Russia, was analysed. Baby Home specialists were trained in time‐use spot observation methodology. Each child was observed every 10 min for 5 h (31 observations/child; >4000 data points). At each observation, we coded: who the child was with, adult role, what the child was doing, location and vocalizations.

Results  Children spent 50% of their time alone, 27% with a caregiver, 15% with another adult, and 7% with another child. Infants spent significantly more time alone (65%) than toddlers (43%) or pre‐schoolers (46%) [F(2,133) = 13.05, P < 0.0001]. Caregivers supervised children (58%), led group activities (16%), cared for individuals (14%), or were absent from the room (12%). Children spent the most time (32%) in activities of daily living; remaining time was spent in meaningful play (27%), non‐purposeful activity (16%) or sleep (18%). The percentage of time spent in meaningful play significantly increased across age groups [infants 10%, toddlers 25%, pre‐schoolers 36%, F(2,133) = 26.9, P < 0.001]. Infants (23%) and toddlers (20%) spent significantly more time than the older group (10%) in non‐purposeful activity [F(2,133) = 26.9, P < 0.001]. In 12% of observations, an adult was speaking to the child, in 10% to the group, and <1% to another adult. Child vocalizations varied by age: infants 42% of observations, toddlers 56%, and pre‐schoolers 59%. Older children directed more vocalizations to adults than younger children [F(2,133) = 24.47, P < 0.001].

Conclusion  Time use of children residing in Baby Homes is limited by routinized schedules and care, at the expense of child‐directed or interactive play with adults. Despite close proximity and living in group care, children's vocalizations and interactions with others are limited.
Allocation of essential lipids in Daphnia magna during exposure to poor food quality
Authors: WACKER A. , MARTIN‐CREUZBURG D.
Published: July 2007

In nature, food conditions change temporally and force consumers into trade‐offs during resource allocation. In particular, under poor food conditions, for example during cyanobacterial blooms, herbivores have to optimize their resource allocation to maximize fitness, and face two decisions: (i) an individual might attempt to allocate acquired essential resources to reproductive tissues or use them for its own maintenance; and (ii) an individual might decide to optimize the chemical quality of its eggs.

As cyanobacteria feature a deficiency in some essential lipids that leads to a decline in the growth and fecundity of Daphnia, an important freshwater herbivore, we investigated Daphnia magna's Strauss allocation of lipids such as polyunsaturated fatty acids (PUFAs) and cholesterol during an experimental non‐toxic cyanobacterial bloom.

Generally, we found a substantial maternal investment of the particularly important omega‐3 (n‐3) PUFAs, in particular eicosapentaenoic acid (EPA), into the eggs. The concentration of EPA was 2·4‐fold higher in eggs than in somatic tissue, a cumulative effect, which was not significantly changed under cyanobacterial food conditions.

Under poor conditions, D. magna not only decreased the number of eggs produced but, in principle, reduced the previously high concentrations of EPA in both eggs and somatic tissues to a similar degree. In contrast to EPA, the concentrations of α‐linolenic acid and cholesterol, although lower than EPA, were more homeostatic in eggs than in somatic tissues, in which concentrations decreased.

When food quality was improved, D. magna were able to recover completely the fatty acid concentrations in their somatic tissues and eggs.

This study shows that the content of particular lipids in its food clearly affects resource allocation in D. magna, and suggests that cholesterol is important for somatic growth, while PUFAs are primarily needed for reproduction. As a decreasing investment of essential lipids into eggs implies a reduced fitness of the animals’ progeny under poor food conditions, this could have a strong impact on population dynamics, which might also be valid for other species.
Retreatment efficacy of the Epiphany soft resin obturation system
Authors: Hassanloo A. , Watson P. , Finer Y. , Friedman S.
Published: July 2007

Aim  To assess the efficacy of retreatment of canals filled with the Epiphany System with and without solvent, with particular reference to the extent of canal enlargement during retreatment.

Methodology  Sixty roots with canals prepared to apical size 45 were embedded in resin blocks and sectioned vertically. Digital micrographs of canal walls were captured. Roots were re‐assembled and filled with Epiphany/Resilon (experimental) or gutta‐percha/AH Plus (control). After 8 weeks, canals were retreated to size 45 with or without chloroform, and the time recorded. Roots were split, imaged, re‐assembled, retreated to size 55, split and imaged. Root‐filling residue, traced at three canal levels, was expressed as percentage of canal surface.

Results  Residue percentage was greater (t‐test, P < 0.01) in the experimental group than in the control. Most residue in all specimens was in the apical third (anova, P < 0.01). Chloroform and enlargement to size 55 decreased residue in both groups (t‐test, P < 0.01). Retreatment time was longer in the experimental group (P < 0.05), and reduced by chloroform in both groups (P < 0.05).

Conclusions  The Epiphany System was retreatable with and without chloroform, with lesser efficacy than gutta‐percha and AH Plus sealer.
The effects of freezing skin on transdermal drug penetration kinetics
Authors: AHLSTROM L. A. , CROSS S. E. , MILLS P. C.
Published: July 2007

This study investigated the effects of freezing canine skin on the penetration kinetics of hydrocortisone. Skin samples from three dogs were used for in vitro penetration studies commencing on the day of skin collection (fresh skin) and again after freezing at −20 °C for 1, 4, 8 and 12 months. When the data from the dogs was averaged, the pseudo‐steady‐state flux (Jss) of hydrocortisone through skin frozen for any duration was significantly (P < 0.023) greater than through fresh skin and there was a positive relationship (P < 0.007) between the length of freezing and ΔJss. For all dogs, the lag times (tlag) calculated for hydrocortisone penetration were significantly (P < 0.029) shorter through skin that had been frozen, compared with fresh skin. However, the shapes of the permeation profiles of hydrocortisone appeared similar through the fresh and frozen dog skins and no differences were detected between the groups on histological examination. The results of this study have shown that freezing dog skin at −20 °C can significantly increase the transdermal penetration of hydrocortisone in vitro, and that the extent of this enhancement can increase with duration of freezing.
Contrasting phylogeography in three endemic Hawaiian limpets (Cellana spp.) with similar life histories
Authors: BIRD CHRISTOPHER E. , HOLLAND BRENDEN S. , BOWEN BRIAN W. , TOONEN ROBERT J.
Published: July 2007

The marine environment offers few obvious barriers to dispersal for broadcast‐spawning species, yet population genetic structure can occur on a scale much smaller than the theoretical limits of larval dispersal. Comparative phylogeographical studies of sympatric sister species can illuminate how differences in life history, behaviour, and habitat affinity influence population partitioning. Here we use a mitochondrial DNA marker (612 bp of cytochrome c oxidase subunit I) to investigate population structure of three endemic Hawaiian broadcast‐spawning limpets (Cellana spp.) with planktonic larvae that are competent to settle within 4 days. All three species exhibit significant population structure and isolation by distance, but the spatial scales of partitioning differ among the species. Cellana talcosa (n = 105) exhibits strong population structure between Kauai and the other main Hawaiian Islands (MHI) where the maximum channel width is 117 km, and no shared haplotypes were observed (ΦCT = 0.30, P < 0.001). In contrast, populations of Cellana exarata (n = 149) and Cellana sandwicensis (n = 109) exhibit weaker population structure within the MHI (ΦST = 0.03–0.04, P < 0.05), and between the MHI and the Northwestern Hawaiian Islands (ΦST = 0.03–0.09, P < 0.01), where the maximum channel width is 260 km. Biogeographical range and microhabitat use were correlated with estimates of dispersal, while phylogenetic affiliation and minimum pelagic larval duration were poor predictors of population partitioning. Despite similar life histories, these closely related limpets have contrasting patterns of population structure, illustrating the danger of relying on model species in management initiatives to predict population structure and dispersal in the context of marine protected area delineation.
Invasion of host cells by malaria parasites: a tale of two protein families
Authors: Iyer Jayasree , Grüner Anne Charlotte , Rénia Laurent , Snounou Georges , Preiser Peter R.
Published: July 2007

Malaria parasites are obligate intracellular parasites whose invasive stages select and invade the unique host cell in which they can develop with exquisite specificity and efficacy. Most studies aimed at elucidating the molecules and the mechanisms implicated in the selection and invasion processes have been conducted on the merozoite, the stage that invades erythrocytes to perpetuate the pathological cycles of parasite multiplication in the blood. Bioinformatic analysis has helped identify the members of two parasite protein families, the reticulocyte‐binding protein homologues (RBL) and erythrocyte binding like (EBL), in recently sequenced genomes of different Plasmodium species. In this article we review data from classical studies and gene disruption experiments that are helping to illuminate the role of these proteins in the selection‐invasion processes. The manner in which subsets of proteins from each of the families act in concert suggests a model to explain the ability of the parasites to use alternate pathways of invasion. Future perspectives and implications are discussed.