bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comment on: Williams et al. (2009) “Australia's deep-water reserve network: implications of false homogeneity for classifying abiotic surrogates of biodiversity”. ICES Journal of Marine Science, 66: 214–224
Authors: Harris Peter T. , Heap Andrew D. , Anderson Tara J. , Brooke Brendan 
Published: August 2009

Abstract
Harris, P. T., Heap, A. D., Anderson, T. J., and Brooke, B. 2009. Comment on: Williams et al. (2009) “Australia's deep-water reserve network: implications of false homogeneity for classifying abiotic surrogates of biodiversity”. ICES Journal of Marine Science, 66: 214–224. – ICES Journal of Marine Science, 66: 2082–2085. Williams et al. (2009) report on new multibeam sonar bathymetry and underwater video data collected from submarine canyons and seamounts on Australia's southeast continental margin to “investigate the degree to which geomorphic features act as surrogates for benthic megafaunal biodiversity” (p. 214). The authors describe what they view as deficiencies in the design of the Marine Protected Areas (MPAs) in the southeast region of Australia, in which geomorphology information was employed as a surrogate to infer regional-scale patterns of benthic biodiversity. This comment is designed to support and underscore the importance of evaluating MPA designs and the validity of using abiotic surrogates such as geomorphology to infer biodiversity patterns, and also seeks to clarify some of the discrepancies in geomorphic terminologies and approaches used between the original study and the Williams et al. (2009) evaluation. It is our opinion that the MPA design criteria used by the Australian Government are incorrectly reported by Williams et al. (2009). In particular, we emphasize the necessity for consistent terminology and approaches when undertaking comparative analyses of geomorphic features. We show that the MPA selection criteria used by the Australian Government addressed the issues of false homogeneity described by Williams et al. (2009), but that final placement of MPAs was based on additional stakeholder considerations. Finally, we argue that although the Williams et al. (2009) study provides valuable information on biological distributions within seamounts and canyons, the hypothesis that geomorphic features (particularly seamounts and submarine canyons) are surrogates for benthic biodiversity is not tested explicitly by their study.
Hierarchical analysis of a remote, Arctic, artisanal longline fishery
Authors: Dennard Susan T. , MacNeil M. Aaron , Treble Margaret A. , Campana Steven , Fisk Aaron T. 
Published: August 2009

Abstract
Dennard, S. T., MacNeil, M. A., Treble, M. A., Campana, S., and Fisk, A. T. 2010. Hierarchical analysis of a remote, Arctic, artisanal longline fishery. – ICES Journal of Marine Science, 67: 41–51. This is the first paper to explore trends in catch per unit effort (cpue) through time of a Greenland halibut Reinhardtius hippoglossoides stock targeted by an artisanal, winter fishery in Cumberland Sound on southern Baffin Island, Canada. We modelled cpue data from 1987 to 2003, looking at two questions: what factors have driven cpue trends, and is cpue an accurate index of a stock's abundance? In the context of limited data availability, we used generalized linear models (GLMs) and hierarchical models to assess important predictors of cpue. Hierarchical models with multiple fixed environmental effects contained fishing location or individual fisher as random effects. A month effect showed greatest catch rates during February and March; the monthly North Atlantic Oscillation index was positively associated with catch rates; and a change from decreasing to increasing cpue after 1996 was linked to reduced fishery participation following a large storm. The best Akaike's information criterion-ranked GLM identified a negative relationship of cpue with shark bycatch. Although data limitations precluded conventional stock assessment, our models implicated the environment and fisher behaviour as drivers of cpue trends. Additionally, using multiple hierarchical models to predict cpue provided a more informative analysis for understanding trends in cpue than a GLM alone.
Extracellular DNA Is Required for Root Tip Resistance to Fungal Infection
Authors: Wen Fushi , White Gerard J. , VanEtten Hans D. , Xiong Zhongguo , Hawes Martha C. 
Published: August 2009

Abstract
Plant defense involves a complex array of biochemical interactions, many of which occur in the extracellular environment. The apical 1- to 2-mm root tip housing apical and root cap meristems is resistant to infection by most pathogens, so growth and gravity sensing often proceed normally even when other sites on the root are invaded. The mechanism of this resistance is unknown but appears to involve a mucilaginous matrix or “slime” composed of proteins, polysaccharides, and detached living cells called “border cells.” Here, we report that extracellular DNA (exDNA) is a component of root cap slime and that exDNA degradation during inoculation by a fungal pathogen results in loss of root tip resistance to infection. Most root tips (&gt;95%) escape infection even when immersed in inoculum from the root-rotting pathogen Nectria haematococca. By contrast, 100% of inoculated root tips treated with DNase I developed necrosis. Treatment with BAL31, an exonuclease that digests DNA more slowly than DNase I, also resulted in increased root tip infection, but the onset of infection was delayed. Control root tips or fungal spores treated with nuclease alone exhibited normal morphology and growth. Pea (Pisum sativum) root tips incubated with [32P]dCTP during a 1-h period when no cell death occurs yielded root cap slime containing 32P-labeled exDNA. Our results suggest that exDNA is a previously unrecognized component of plant defense, an observation that is in accordance with the recent discovery that exDNA from white blood cells plays a key role in the vertebrate immune response against microbial pathogens.
SAUR39, a Small Auxin-Up RNA Gene, Acts as a Negative Regulator of Auxin Synthesis and Transport in Rice
Authors: Kant Surya , Bi Yong-Mei , Zhu Tong , Rothstein Steven J. 
Published: August 2009

AbstractThe phytohormone auxin plays a critical role for plant growth by regulating the expression of a set of genes. One large auxin-responsive gene family of this type is the small auxin-up RNA (SAUR) genes, although their function is largely unknown. The expression of the rice (Oryza sativa) SAUR39 gene showed rapid induction by transient change in different environmental factors, including auxin, nitrogen, salinity, cytokinin, and anoxia. Transgenic rice plants overexpressing the SAUR39 gene resulted in lower shoot and root growth, altered shoot morphology, smaller vascular tissue, and lower yield compared with wild-type plants. The SAUR39 gene was expressed at higher levels in older leaves, unlike auxin biosynthesis, which occurs largely in the meristematic region. The transgenic plants had a lower auxin level and a reduced polar auxin transport as well as the down-regulation of some putative auxin biosynthesis and transporter genes. Biochemical analysis also revealed that transgenic plants had lower chlorophyll content, higher levels of anthocyanin, abscisic acid, sugar, and starch, and faster leaf senescence compared with wild-type plants at the vegetative stage. Most of these phenomena have been shown to be negatively correlated with auxin level and transport. Transcript profiling revealed that metabolic perturbations in overexpresser plants were largely due to transcriptional changes of genes involved in photosynthesis, senescence, chlorophyll production, anthocyanin accumulation, sugar synthesis, and transport. The lower growth and yield of overexpresser plants was largely recovered by exogenous auxin application. Taken together, the results suggest that SAUR39 acts as a negative regulator for auxin synthesis and transport.
At4g24160, a Soluble Acyl-Coenzyme A-Dependent Lysophosphatidic Acid Acyltransferase
Authors: Ghosh Ananda K. , Chauhan Neha , Rajakumari Sona , Daum Guenther , Rajasekharan Ram 
Published: August 2009

Abstract
Human CGI-58 (for comparative gene identification-58) and YLR099c, encoding Ict1p in Saccharomyces cerevisiae, have recently been identified as acyl-CoA-dependent lysophosphatidic acid acyltransferases. Sequence database searches for CGI-58 like proteins in Arabidopsis (Arabidopsis thaliana) revealed 24 proteins with At4g24160, a member of the α/β-hydrolase family of proteins being the closest homolog. At4g24160 contains three motifs that are conserved across the plant species: a GXSXG lipase motif, a HX4D acyltransferase motif, and V(X)3HGF, a probable lipid binding motif. Dendrogram analysis of yeast ICT1, CGI-58, and At4g24160 placed these three polypeptides in the same group. Here, we describe and characterize At4g24160 as, to our knowledge, the first soluble lysophosphatidic acid acyltransferase in plants. A lipidomics approach revealed that At4g24160 has additional triacylglycerol lipase and phosphatidylcholine hydrolyzing enzymatic activities. These data establish At4g24160, a protein with a previously unknown function, as an enzyme that might play a pivotal role in maintaining the lipid homeostasis in plants by regulating both phospholipid and neutral lipid levels.
Hydrogen Production in Chlamydomonas: Photosystem II-Dependent and -Independent Pathways Differ in Their Requirement for Starch Metabolism
Authors: Chochois Vincent , Dauvillée David , Beyly Audrey , Tolleter Dimitri , Cuiné Stéphan , Timpano Hélène , Ball Steven , Cournac Laurent , Peltier Gilles 
Published: August 2009

Abstract
Under sulfur deprivation conditions, the green alga Chlamydomonas reinhardtii produces hydrogen in the light in a sustainable manner thanks to the contribution of two pathways, direct and indirect. In the direct pathway, photosystem II (PSII) supplies electrons to hydrogenase through the photosynthetic electron transport chain, while in the indirect pathway, hydrogen is produced in the absence of PSII through a photosystem I-dependent process. Starch metabolism has been proposed to contribute to both pathways by feeding respiration and maintaining anoxia during the direct pathway and by supplying reductants to the plastoquinone pool during the indirect pathway. At variance with this scheme, we report that a mutant lacking starch (defective for sta6) produces similar hydrogen amounts as the parental strain in conditions of sulfur deprivation. However, when PSII is inhibited by 3-(3,4-dichlorophenyl)-1,1-dimethylurea, conditions where hydrogen is produced by the indirect pathway, hydrogen production is strongly reduced in the starch-deficient mutant. We conclude that starch breakdown contributes to the indirect pathway by feeding electrons to the plastoquinone pool but is dispensable for operation of the direct pathway that prevails in the absence of DCMU. While hydrogenase induction was strongly impaired in the starch-deficient mutant under dark anaerobic conditions, wild-type-like induction was observed in the light. Because this light-driven hydrogenase induction is DCMU insensitive and strongly inhibited by carbonyl cyanide-p-trifluoromethoxyphenylhydrazone or 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone, we conclude that this process is regulated by the proton gradient generated by cyclic electron flow around PSI.
A Pair of Allelic WRKY Genes Play Opposite Roles in Rice-Bacteria Interactions
Authors: Tao Zeng , Liu Hongbo , Qiu Deyun , Zhou Yan , Li Xianghua , Xu Caiguo , Wang Shiping 
Published: August 2009

AbstractAlthough allelic diversity of genes has been reported to play important roles in different physiological processes, information on allelic diversity of defense-responsive genes in host-pathogen interactions is limited. Here, we report that a pair of allelic genes, OsWRKY45-1 and OsWRKY45-2, which encode proteins with a 10-amino acid difference, play opposite roles in rice (Oryza sativa) resistance against bacterial pathogens. Bacterial blight caused by Xanthomonas oryzae pv oryzae (Xoo), bacterial streak caused by Xanthomonas oryzae pv oryzicola (Xoc), and fungal blast caused by Magnaporthe grisea are devastating diseases of rice worldwide. OsWRKY45-1-overexpressing plants showed increased susceptibility and OsWRKY45-1-knockout plants showed enhanced resistance to Xoo and Xoc. In contrast, OsWRKY45-2-overexpressing plants showed enhanced resistance and OsWRKY45-2-suppressing plants showed increased susceptibility to Xoo and Xoc. Interestingly, both OsWRKY45-1- and OsWRKY45-2-overexpressing plants showed enhanced resistance to M. grisea. OsWRKY45-1-regulated Xoo resistance was accompanied by increased accumulation of salicylic acid and jasmonic acid and induced expression of a subset of defense-responsive genes, while OsWRKY45-2-regulated Xoo resistance was accompanied by increased accumulation of jasmonic acid but not salicylic acid and induced expression of another subset of defense-responsive genes. These results suggest that both OsWRKY45-1 and OsWRKY45-2 are positive regulators in rice resistance against M. grisea, but the former is a negative regulator and the latter is a positive regulator in rice resistance against Xoo and Xoc. The opposite roles of the two allelic genes in rice-Xoo interaction appear to be due to their mediation of different defense signaling pathways.
Biochemical and Structural Studies of the Large Ycf4-Photosystem I Assembly Complex of the Green AlgaChlamydomonas reinhardtii
Authors: Ozawa Shin-ichiro , Nield Jon , Terao Akihiro , Stauber Einar J. , Hippler Michael , Koike Hiroyuki , Rochaix Jean-David , Takahashi Yuichiro 
Published: August 2009

AbstractYcf4 is a thylakoid protein essential for the accumulation of photosystem I (PSI) in Chlamydomonas reinhardtii. Here, a tandem affinity purification tagged Ycf4 was used to purify a stable Ycf4-containing complex of &gt;1500 kD. This complex also contained the opsin-related COP2 and the PSI subunits PsaA, PsaB, PsaC, PsaD, PsaE, and PsaF, as identified by mass spectrometry (liquid chromatography–tandem mass spectrometry) and immunoblotting. Almost all Ycf4 and COP2 in wild-type cells copurified by sucrose gradient ultracentrifugation and subsequent ion exchange column chromatography, indicating the intimate and exclusive association of Ycf4 and COP2. Electron microscopy revealed that the largest structures in the purified preparation measure 285 × 185 Å; these particles may represent several large oligomeric states. Pulse-chase protein labeling revealed that the PSI polypeptides associated with the Ycf4-containing complex are newly synthesized and partially assembled as a pigment-containing subcomplex. These results indicate that the Ycf4 complex may act as a scaffold for PSI assembly. A decrease in COP2 to 10% of wild-type levels by RNA interference increased the salt sensitivity of the Ycf4 complex stability but did not affect the accumulation of PSI, suggesting that COP2 is not essential for PSI assembly.
Control of Nuclear and Nucleolar Localization of Nuclear Inclusion Protein a of Picorna-LikePotato virus AinNicotianaSpecies
Authors: Rajamäki Minna-Liisa , Valkonen Jari P.T. 
Published: August 2009

AbstractThe multifunctional nuclear inclusion protein a (NIa) of potyviruses (genus Potyvirus; Potyviridae) accumulates in the nucleus of virus-infected cells for unknown reasons. In this study, two regions in the viral genome-linked protein (VPg) domain of NIa in Potato virus A (PVA) were found to constitute nuclear and nucleolar localization signals (NLS) in plant cells (Nicotiana spp). Amino acid substitutions in both NLS I (residues 4 to 9) and NLS II (residues 41 to 50) prevented nuclear localization, whereas mutations in either single NLS did not. Mutations in either NLS, however, prevented nucleolar localization and prevented or diminished virus replication in protoplasts, accumulation in infected plant tissues, and/or systemic movement in plants. One NLS mutant was partially complemented by the wild-type VPg expressed in transgenic plants. Furthermore, NLS I controlled NIa accumulation in Cajal bodies. The VPg domain interacted with fibrillarin, a nucleolar protein, and depletion of fibrillarin reduced PVA accumulation. Overexpression of VPg in leaf tissues interfered with cosuppression of gene expression (i.e., RNA silencing), whereas NLS I and NLS II mutants, which exhibited reduced nuclear and nucleolar localization, showed no such activity. These results demonstrate that some of the most essential viral functions required for completion of the infection cycle are tightly linked to regulation of the NIa nuclear and nucleolar localization.
Nuclear Pore Complex Component MOS7/Nup88 Is Required for Innate Immunity and Nuclear Accumulation of Defense Regulators inArabidopsis
Authors: Cheng Yu Ti , Germain Hugo , Wiermer Marcel , Bi Dongling , Xu Fang , García Ana V. , Wirthmueller Lennart , Després Charles , Parker Jane E. , Zhang Yuelin , Li Xin 
Published: August 2009

AbstractPlant immune responses depend on dynamic signaling events across the nuclear envelope through nuclear pores. Nuclear accumulation of certain resistance (R) proteins and downstream signal transducers are critical for their functions, but it is not understood how these processes are controlled. Here, we report the identification, cloning, and analysis of Arabidopsis thaliana modifier of snc1,7 (mos7-1), a partial loss-of-function mutation that suppresses immune responses conditioned by the autoactivated R protein snc1 (for suppressor of npr1-1, constitutive 1). mos7-1 single mutant plants exhibit defects in basal and R protein–mediated immunity and in systemic acquired resistance but do not display obvious pleiotropic defects in development, salt tolerance, or plant hormone responses. MOS7 is homologous to human and Drosophila melanogaster nucleoporin Nup88 and resides at the nuclear envelope. In animals, Nup88 attenuates nuclear export of activated NF-κB transcription factors, resulting in nuclear accumulation of NF-κB. Our analysis shows that nuclear accumulation of snc1 and the defense signaling components Enhanced Disease Susceptibility 1 and Nonexpresser of PR genes 1 is significantly reduced in mos7-1 plants, while nuclear retention of other tested proteins is unaffected. The data suggest that specifically modulating the nuclear concentrations of certain defense proteins regulates defense outputs.
The phylogeny of the Pantropical genus Arrhipis Bonvouloir (Coleoptera, Eucnemidae)
Authors: Brüstle Lena , Alaruikka Diane , Muona Jyrki , Teräväinen Marianna 
Published: August 2009

AbstractThe phylogeny of the genus Arrhipis Bonvouloir (Coleoptera, Eucnemidae) is clarified with a cladistic analysis based on five molecular markers and morphology. Sixteen species from Africa, America, Asia, and Australia are included in the analysis. Two separate Asian clades are recovered, one of them being the sister group to a clade with the American and African species. With the exception of the continental south‐east Asian species, all Gondwanan regions have monophyletic faunas. According to the present data, the continental south‐east Asian fauna comprises two monophyletic groups, one of which is the sister group to African and American species. Vicariance seems to be the logical explanation for the distribution of these lignicolous beetles.© The Willi Hennig Society 2009.
Risk factors of scabies in psychiatric and long‐term care hospitals: A nationwide mail‐in survey in Japan
Authors: MAKIGAMI Kuniko , OHTAKI Noriko , ISHII Norihisa , YASUMURA Seiji 
Published: August 2009

AbstractDespite the commonness of scabies in Japanese institutional settings, the nationwide prevalence of scabies has not been elucidated. This study was conducted to assess the prevalence of scabies and control measures in Japanese hospitals. A questionnaire on scabies epidemiology (e.g. number of patients and onsets of outbreak) and preventive measures were sent to psychiatric hospitals and long‐term care hospitals nationwide (n = 1795) in January 2005. Seven hundred and forty‐one hospitals responded (41.3%). Three hundred and thirty‐three (44.9%) respondent hospitals had one or more scabies cases in 2004. Among 159 hospitals that had experienced scabies outbreak, only 32 of them reported cases of crusted scabies. Multivariate regression analysis showed that hospitals had a greater number of beds, and that acute‐ and long‐term care wards were more likely to experience scabies onsets. Hospitals that compiled their infection control manuals on scabies, treated suspicious patients with scabicides without confirmed diagnosis, and performed skin checkup of inpatients were more likely to experience scabies cases. Infection control personnel should be aware that unrecognized crusted scabies can cause outbreaks. Higher patient turnover is a risk factor for scabies introduction into a hospital. Preventive measures against scabies, such as patient screening at admission and treating all suspicious patients without confirmed diagnosis, were not effective to avoid scabies introduction.
Enhanced immune response to pneumococcal infection in malnourished mice nasally treated with heat‐killed Lactobacillus casei
Authors: Villena Julio , Barbieri Natalia , Salva Susana , Herrera Matías , Alvarez Susana 
Published: August 2009

ABSTRACTThe present study analyzed whether nasal administration of viable and non‐viable Lactobacillus casei CRL 431 to immunocompromised mice was capable of increasing resistance against Streptococcus pneumoniae. Weaned mice were malnourished after consuming a PFD for 21 days. Malnourished mice were fed a BCD for 7 days or BCD for 7 days with viable or non‐viable L. casei nasal treatments on day 6 and day 7 (BCD+LcV and BCD+LcN, respectively). The MNC group received PFD whereas the WNC mice consumed BCD. MNC mice showed greater lung colonization, more severe lung injuries, impaired leukocyte recruitment and reduced antibodies and cytokine production when compared with WNC mice. Administration of L. casei increased the resistance of malnourished mice to the infection. Both BCD+LcV and BCD+LcN treatments prevented the dissemination of the pathogen to the blood and induced its lung clearance. BCD+LcV or BCD+LcN groups showed improved production of TNF‐α and activity of phagocytes in the respiratory tract, an effect that was not observed in the BCD control group. In addition, IL‐4 and IL‐10 were significantly increased in BCD+LcV and BCD+LcN groups, which correlated with the increase in the levels of specific respiratory IgA. The nasal treatments with L. casei were also effective at stimulating the production of specific IgG at both the systemic and the respiratory levels. The comparative study between the viable and the non‐viable bacteria demonstrated that viability would be an important factor to achieve maximum protective effects. However, the results from this study suggest that heat‐killed lactic acid bacteria are also effective in the immunomodulation of the systemic and respiratory immune system.