bluuebunny/crossref_metadata_2025_split huggingface dataset:
Grazing rates and functional diversity of uncultured heterotrophic flagellates
Authors: Massana Ramon , Unrein Fernando , Rodríguez-Martínez Raquel , Forn Irene , Lefort Thomas , Pinhassi Jarone , Not Fabrice 
Published: January 2009

Abstract
Aquatic assemblages of heterotrophic protists are very diverse and formed primarily by organisms that remain uncultured. Thus, a critical issue is assigning a functional role to this unknown biota. Here we measured grazing rates of uncultured protists in natural assemblages (detected by fluorescent in situ hybridization (FISH)), and investigated their prey preference over several bacterial tracers in short-term ingestion experiments. These included fluorescently labeled bacteria (FLB) and two strains of the Roseobacter lineage and the family Flavobacteriaceae, of various cell sizes, which were offered alive and detected by catalyzed reporter deposition-FISH after the ingestion. We obtained grazing rates of the globally distributed and uncultured marine stramenopiles groups 4 and 1 (MAST-4 and MAST-1C) flagellates. Using FLB, the grazing rate of MAST-4 was somewhat lower than whole community rates, consistent with its small size. MAST-4 preferred live bacteria, and clearance rates with these tracers were up to 2 nl per predator per h. On the other hand, grazing rates of MAST-1C differed strongly depending on the tracer prey used, and these differences could not be explained by cell viability. Highest rates were obtained using FLB whereas the flavobacteria strain was hardly ingested. Possible explanations would be that the small flavobacteria cells were outside the effective size range of edible prey, or that MAST-1C selects against this particular strain. Our original dual FISH protocol applied to grazing experiments reveals important functional differences between distinct uncultured protists and offers the possibility to disentangle the complexity of microbial food webs.
Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata
Authors: Sunagawa Shinichi , DeSantis Todd Z , Piceno Yvette M , Brodie Eoin L , DeSalvo Michael K , Voolstra Christian R , Weil Ernesto , Andersen Gary L , Medina Mónica 
Published: January 2009

Abstract
Increasing evidence confirms the crucial role bacteria and archaea play within the coral holobiont, that is, the coral host and its associated microbial community. The bacterial component constitutes a community of high diversity, which appears to change in structure in response to disease events. In this study, we highlight the limitation of 16S rRNA gene (16S rDNA) clone library sequencing as the sole method to comprehensively describe coral-associated communities. This limitation was addressed by combining a high-density 16S rRNA gene microarray with, clone library sequencing as a novel approach to study bacterial communities in healthy versus diseased corals. We determined an increase in diversity as well as a significant shift in community structure in Montastraea faveolata colonies displaying phenotypic signs of White Plague Disease type II (WPD-II). An accumulation of species that belong to families that include known coral pathogens (Alteromonadaceae, Vibrionaceae), bacteria previously isolated from diseased, stressed or injured marine invertebrates (for example, Rhodobacteraceae), and other species (for example, Campylobacteraceae) was observed. Some of these species were also present in healthy tissue samples, but the putative primary pathogen, Aurantimonas corallicida, was not detected in any sample by either method. Although an ecological succession of bacteria during disease progression after causation by a primary agent represents a possible explanation for our observations, we also discuss the possibility that a disease of yet to be determined etiology may have affected M. faveolata colonies and resulted in (or be a result of) an increase in opportunistic pathogens.
The Chemistry of Fireworks
Authors: Russell Michael 
Published: January 2009

For centuries fireworks have been a source of delight and amazement in cultures around the world. But what produces their dazzling array of effects? This book takes you behind the scenes to explore the chemistry and physics behind the art of pyrotechnics. Topics covered include history and characteristics of gunpowder; principles behind each of the most popular firework types: rockets, shells, fountains, sparklers, bangers, roman candles and wheels; special effects, including sound effects, coloured smokes and electrical firing; firework safety for private use and displays; and firework legislation. The Chemistry of Fireworks is aimed at students with A level qualifications or equivalent. The style is concise and easy to understand, and the theory of fireworks is discussed in terms of well-known scientific concepts wherever possible. It will also be a useful source of reference for anyone studying pyrotechnics as applied to fireworks. Review Extracts "a worthwhile addition to the pyrotechnist's library" Fireworks "a useful source of information which makes absorbing reading." Angewandte Chemie, International Edition
Nitration of cathepsin D enhances its proteolytic activity during mammary gland remodelling after lactation
Authors: Zaragozá Rosa , Torres Luis , García Concha , Eroles Pilar , Corrales Fernando , Bosch Ana , Lluch Ana , García-Trevijano Elena R. , Viña Juan R. 
Published: January 2009

Proteomic studies in the mammary gland of control lactating and weaned rats have shown that there is an increased pattern of nitrated proteins during weaning when compared with controls. Here we report the novel finding that cathepsin D is nitrated during weaning. The expression and protein levels of this enzyme are increased after 8 h of litter removal and this up-regulation declines 5 days after weaning. However, there is a marked delay in cathepsin D activity since it does not increase until 2 days post-weaning and remains high thereafter. In order to find out whether nitration of cathepsin D regulates its activity, iNOS (inducible nitric oxide synthase)−/− mice were used. The expression and protein levels of this enzyme were similar to WT (wild-type) animals, but the proteolytic activity was significantly reduced during weaning in knockout compared to WT mice. in vitro treatment of recombinant human cathepsin D or lactating mammary gland homogenates with relatively low concentrations of peroxynitrite enhances the nitration as well as specific activity of this enzyme. Using MS, it has been shown that the residue Tyr168 was nitrated. All of these results show that protein nitration during weaning might be a signalling pathway involved in mammary gland remodelling.
Genital warts at the site of healed herpes progenitalis: the isotopic response
Authors: Ruocco Eleonora 
Published: January 2009

A 53‐year‐old man presented with a crop of papular and somewhat warty lesions on the internal aspect of his prepuce ( Fig. 1). They had appeared over the last 3 months and lately had been enlarging; this persuaded the patient to seek dermatovenereologic advice. The patient, who was uncircumcised, denied any extramarital intercourse, but reported a clear medical history of recurrent herpes progenitalis that had afflicted him and his spouse for many years. Recurrent attacks of this infection, each lasting about 2 weeks, had occurred with variable frequency in his forties, and the last episode could be dated exactly to the age of 49 years. The herpetic infection had been managed with topical and sometimes oral acyclovir, but no considerable therapeutic benefit had been noticed. On admission, the patient's main concern was that the new lesions could represent a relapse of the herpes progenitalis. Although they were completely different from the herpetic lesions objectively (solid and not vesicular), subjectively (asymptomatic and not tingling or painful), and in their course (lasting unmodified for months and not evolving into erosions), they had arisen in the area in which the herpetic vesicles had appeared in the past.Papular lesions, in a ring‐like arrangement, at the site of a prior recurrent herpes simpleximageDespite the obvious clinical diagnosis of genital warts and in compliance with the patient's explicit request, a punch biopsy was made. The epithelium showed moderate parakeratosis, pronounced acanthosis, diffuse cell vacuolization, and no signs of nuclear dysplasia ( Fig. 2). Mild edematous changes, dilated capillaries, and a discrete lymphocytic infiltrate were observed in the dermis.Histologic examination of a papular lesion. Acanthotic epithelium with diffuse perinuclear vacuolization (hematoxylin and eosin staining, × 200)imageThe diagnosis of genital warts was made and the lesions were successfully treated with liquid nitrogen.
PanCGH: a genotype-calling algorithm for pangenome CGH data
Authors: Bayjanov Jumamurat R. , Wels Michiel , Starrenburg Marjo , van Hylckama Vlieg Johan E. T. , Siezen Roland J. , Molenaar Douwe 
Published: January 2009

Abstract
Motivation: Pangenome arrays contain DNA oligomers targeting several sequenced reference genomes from the same species. In microbiology, these can be employed to investigate the often high genetic variability within a species by comparative genome hybridization (CGH). The biological interpretation of pangenome CGH data depends on the ability to compare strains at a functional level, particularly by comparing the presence or absence of orthologous genes. Due to the high genetic variability, available genotype-calling algorithms can not be applied to pangenome CGH data.
Results: We have developed the algorithm PanCGH that incorporates orthology information about genes to predict the presence or absence of orthologous genes in a query organism using CGH arrays that target the genomes of sequenced representatives of a group of microorganisms. PanCGH was tested and applied in the analysis of genetic diversity among 39 Lactococcus lactis strains from three different subspecies (lactis.cremoris, hordniae) and isolated from two different niches (dairy and plant). Clustering of these strains using the presence/absence data of gene orthologs revealed a clear separation between different subspecies and reflected the niche of the strains.
Contact: J.Bayjanov@cmbi.ru.nl
Supplementary information: Supplementary data are available at Bioinformatics online.
SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses
Authors: Barker Michael S. , Dlugosch Katrina M. , Reddy A. Chaitanya C. , Amyotte Sarah N. , Rieseberg Loren H. 
Published: January 2009

Abstract
Summary: Scaffolded and Corrected Assembly of Roche 454 (SCARF) is a next-generation sequence assembly tool for evolutionary genomics that is designed especially for assembling 454 EST sequences against high-quality reference sequences from related species. The program was created to knit together 454 contigs that do not assemble during traditional de novo assembly, using a reference sequence library to orient the 454 sequences.
Availability: SCARF is freely available at http://msbarker.com/software.htm, and is released under the open source GPLv3 license (http://www.opensource.org/licenses/gpl-3.0.html.
Contact: msbarker@indiana.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
DichroCalc—circular and linear dichroism online
Authors: Bulheller Benjamin M. , Hirst Jonathan D. 
Published: January 2009

AbstractMotivation: Circular dichroism (CD) is widely used in studies of protein folding. The CD spectrum of a protein can be estimated from its structure alone, using the well-established matrix method. In the last decade, a related spectroscopy, linear dichroism (LD), has been increasingly applied to study the orientation of proteins in solution. However, matrix method calculations of LD spectra have not been presented before. DichroCalc makes both CD and LD calculations available in an easy-to-use fashion.Results: DichroCalc can be used without registration and calculates CD and LD spectra using a variety of matrix method parameters. PDB files can be uploaded as input or retrieved via their PDB code and a Perl-based parser is offered for easy handling of PDB files.Availability: http://comp.chem.nottingham.ac.uk/dichrocalc and http://comp.chem.nottingham.ac.uk/parsepdbContact: jonathan.hirst@nottingham.ac.uk
Considering multiple-species attributes to understand better the effects of successive changes in protection status on a coral reef fish assemblage
Authors: Preuss Bastien , Pelletier Dominique , Wantiez Laurent , Letourneur Yves , Sarramégna Sébastien , Kulbicki Michel , Galzin René , Ferraris Jocelyne 
Published: January 2009

Abstract
Preuss, B., Pelletier, D., Wantiez, L., Letourneur, Y., Sarramégna, S., Kulbicki, M., Galzin, R., and Ferraris, J. 2009. Considering multiple-species attributes to understand better the effects of successive changes in protection status on a coral reef fish assemblage. – ICES Journal of Marine Science, 66: 170–179. The response of fish assemblages to changes in protection status is a major issue for both biodiversity conservation and fishery management. In New Caledonia, the Aboré reef marine reserve harbours more than 500 fish species, and has been subjected to changes in protection status since 1988. The present study investigates the impact of these changes on a wide subset of species (213), based on underwater visual counts collected before the opening and after the closure to fishing of this marine protected area (MPA). We analysed the spatial and temporal variability in fish assemblage attributable to protection status, explicitly considering habitat. To understand the successive responses of fish assemblage to fishing and protection, the assessment models included four criteria defining species groups that partition the fish assemblage: trophic regime, adult size, mobility, and interest for fishing. We could therefore identify the negative impact of opening the MPA to fishing on piscivores and highly mobile species. Surprisingly, target species were not affected more than non-target species. Model results were used to identify species groups that respond to fishing and protection. These results utilize fisheries-related criteria to provide new insight into the response of fish assemblages to protection from the perspective of MPA monitoring.
Identifying eastern Baltic cod nursery grounds using hydrodynamic modelling: knowledge for the design of Marine Protected Areas
Authors: Hinrichsen Hans-Harald , Kraus Gerd , Böttcher Uwe , Köster Fritz 
Published: January 2009

Abstract
Hinrichsen, H-H., Kraus, G., Böttcher, U., and Köster, F. 2009. Identifying eastern Baltic cod nursery grounds using hydrodynamic modelling: knowledge for the design of Marine Protected Areas. – ICES Journal of Marine Science, 66: 101–108. Knowledge of the spatial and temporal distribution of juvenile cod is essential to closing the life cycle in population dynamic models, and it is a prerequisite for the design of Marine Protected Areas (MPAs) aiming at the protection of juveniles. In this study, we use a hydrodynamic model to examine the spatial distribution of eastern Baltic cod larvae and early juveniles. The transport patterns of the larvae spawned at the three major spawning grounds in the central Baltic Sea were investigated by drift model simulations for the period 1979–2004. We analysed potential habitats for their suitability for juvenile settlement, i.e. the change from pelagic to demersal life. The results revealed a clear dependence of the probability for successful settling on wind-induced drift of larval cod, which is controlled by the local atmospheric conditions over the Baltic Sea. Furthermore, we found evidence that the final destinations of juvenile cod drift routes are affected by decadal climate variability. Application of the methodology to MPA design is discussed, e.g. identifying the overlap of areas with a high probability of successful juvenile cod settlement and regions of high fishing effort in small-meshed fisheries targeting sprat and herring.
First Report of Cercospora Leaf Spot Caused by Cercospora apii (= C. molucellae) on Bells-of-Ireland (Molucella laevis) in Mexico
Authors: Ayala-Escobar V. , Braun U. , Nava-Diaz C. 
Published: January 2009

In late 2007, a new disease was found in commercial cutflower fields of bells-of-Ireland (Molucella laevis L.) in Texcoco, Mexico. Four plantings surveyed during this time had 100% incidence. A few spots on cutflowers make them unmarketable. Symptoms consisted of gray-green spots on leaves, calyxes, and stems, which turned brown with age. Spots were initially circular to oval, delimited by major leaf veins, and were visible on both adaxial and abaxial sides of the leaves. A Cercospora species was consistently associated with the spots. The fungus was isolated on V8 agar medium. Three single-spore cultures were obtained from isolation cultures. Cultures were incubated at 24°C under near-UV light for 7 days. Pathogenicity was confirmed by spraying a conidial suspension (1 × 104 condia/ml) on leaves of 16 potted M. laevis plants, incubating the plants in a dew chamber for 48 h, and maintaining them in a greenhouse (20 to 24°C). Identical symptoms to those observed in the field appeared on all inoculated plants after 2 weeks. No symptoms developed on control plants treated with autoclaved distilled water. The pathogenicity test was repeated twice with similar results. The fungus produced erumpent stromata, which were dark brown, spherical to irregular, 10 to 26 μm diameter, and giving rise to fascicles of five to nine divergent conidiophores, which were clear brown, paler near the subtruncate apex, straight to curved, not branched, rarely geniculate with two to four septa, and 57 × 3.4 μm. The conidia were formed singly, hyaline, acicular, base truncate, tip acute, straight to curved with 11 to 19 septa, and 172 × 3.5 μm. Fungal DNA from single-spore cultures was obtained with a commercial extraction kit (Qiagen, Hilden, Germany), amplified with ITS5 and ITS4 primers, and sequenced. The sequence, deposited at the National Center for Biotechnology Information Database (GenBank Accession No. EU564808), aligned almost perfectly (99% identity) to the bells-of-Ireland isolates from California (GenBank Accession Nos. AY156918 and AY156919) and New Zealand (Accession No. DQ233321). A 176-bp species-specific fragment was amplified with CercoCal-apii primers but not with CercoCal-beta or CercoCal-sp primers. These results, coupled with the morphological characteristics (1) and pathogenicity test, confirm the identity of the fungus as Cercospora apii sensu lato (including C. molucellae) (2,3,4). Although C. apii sensu lato has been reported on other hosts in Mexico (1,2), to our knowledge, this is the first report of this disease on M. laevis plants in this country. References: (1) C. Chupp. A Monograph of the Fungus Cercospora. Cornell University Press, Ithaca, NY, 1954. (2) P. W. Crous and U. Braun. CBS Biodiversity Series 1:1, 2003. (3) M. Groenewald et al. Phytopathology 95:951, 2005. (4) S. T Koike et al. Plant Dis. 87:203, 2003.
Occurrence of Cucumber green mottle mosaic virus on Cucurbitaceous Plants in China
Authors: Zhang Y. J. , Li G. F. , Li M. F. 
Published: January 2009

Cucumber green mottle mosaic virus (CGMMV) was first discovered in 2003 in China (2) and developed an epidemic during 2005 (1). To know the occurrence scale and damage level of CGMMV, a survey was carried out in the main areas of cucurbitaceous plant production and seed trading in 2006 and 2007 in Mainland China. Samples of 739 plants of 16 types (seed samples from Cucurbita moschata, Cucumis melo, Lagenaria siceraria, Cucumis sativus, Momordica charantia, L. siceraria var. clavata, and C. pepo, leaf samples from C. moschata, Cucumis melo, L. siceraria, Cucumis sativus, and M. charantia, fruit samples from C. moschata, Citrullus lanatus, and L. siceraria, and seedling samples from Citrullus lanatus) were collected from 13 regions and analyzed by a double antibody sandwich (DAS)-ELISA. CGMMV was detected in Citrullus lanatus, L. siceraria, Cucumis melo, and C. moschata from six regions in 2006. Citrullus vulgaris, Cucumis melo, and C. moschata were infected most frequently; in 76, 60, and 30 of the leaf samples, respectively. CGMMV was tested positive in the samples of 8 seedlings, 23 seeds, and 1 fruit. In contrast, all samples tested negative in 2007. To confirm CGMMV identification, ELISA-positive samples were detected by reverse transcription-PCR assay using virus-specific primers that amplified a 524-bp fragment in the coat protein coding region. The nucleotide sequence of the PCR product (GenBank Accession No. DQ997778) isolated form L. siceraria in Liaoning Province (LHP) showed 100% identity with the Japanese watermelon strain (Japan W) and 91% identity with the Greece GR5 strain. On the basis of the symptoms of indicator plants (chlorotic spot and systemic mosaic were observed in L. siceraria, Chenopodium amaranticolor, and Cucumis sativus; no infection was observed in Datura stramonium, Nicotiana tabacum, and Chenopodium quinoa) and coat protein nucleotide sequence comparisons, the two CGMMV isolates of Wcn (1) and LHP from China should be grouped into the watermelon strain. The results showed that the government should establish effective quarantine strategy and the growers take proper planting measures to avoid further spreading of this virus. References: (1) H. Y. Chen et al. Acta Phytopathol. Sin. 36:306, 2006. (2) B. X. Qin et al. Plant Quarantine. 19:4, 2005.