bluuebunny/crossref_metadata_2025 huggingface dataset:
Ethanol potently and competitively inhibits binding of the alcohol antagonist Ro15-4513 to α
4/6
β
3
δ GABA
A
receptors
Authors: Hanchar H. Jacob , Chutsrinopkun Panida , Meera Pratap , Supavilai Porntip , Sieghart Werner , Wallner Martin , Olsen Richard W.
Published: April 2006

Although GABA
A
receptors have long been implicated in mediating ethanol (EtOH) actions, receptors containing the “nonsynaptic” δ subunit only recently have been shown to be uniquely sensitive to EtOH. Here, we show that δ subunit-containing receptors bind the imidazo-benzodiazepines (BZs) flumazenil and Ro15-4513 with high affinity (
K
d
< 10 nM), contrary to the widely held belief that these receptors are insensitive to BZs. In immunopurified native cerebellar and recombinant δ subunit-containing receptors, binding of the alcohol antagonist [
3
H]Ro15-4513 is inhibited by low concentrations of EtOH (
K
i
≈ 8 mM). Also, Ro15-4513 binding is inhibited by BZ-site ligands that have been shown to reverse the behavioral alcohol antagonism of Ro15-4513 (i.e., flumazenil, β-carbolinecarboxylate ethyl ester (β-CCE), and
N
-methyl-β-carboline-3-carboxamide (FG7142), but not including any classical BZ agonists like diazepam). Experiments that were designed to distinguish between a competitive and allosteric mechanism suggest that EtOH and Ro15-4513 occupy a mutually exclusive binding site. The fact that only Ro15-4513, but not flumazenil, can inhibit the EtOH effect, and that Ro15-4513 differs from flumazenil by only a single group in the molecule (an azido group at the C7 position of the BZ ring) suggest that this azido group in Ro15-4513 might be the area that overlaps with the alcohol-binding site. Our findings, combined with previous observations that Ro15-4513 is a behavioral alcohol antagonist, suggest that many of the behavioral effects of EtOH at relevant physiological concentrations are mediated by EtOH/Ro15-4513-sensitive GABA
A
receptors.
A chemokine-binding domain in the tumor necrosis factor receptor from variola (smallpox) virus
Authors: Alejo Alí , Ruiz-Argüello M. Begoña , Ho Yin , Smith Vincent P. , Saraiva Margarida , Alcami Antonio
Published: April 2006

Variola virus (VaV) is the causative agent of smallpox, one of the most devastating diseases encountered by man, that was eradicated in 1980. The deliberate release of VaV would have catastrophic consequences on global public health. However, the mechanisms that contribute to smallpox pathogenesis are poorly understood at the molecular level. The ability of viruses to evade the host defense mechanisms is an important determinant of viral pathogenesis. Here we show that the tumor necrosis factor receptor (TNFR) homologue CrmB encoded by VaV functions not only as a soluble decoy TNFR but also as a highly specific binding protein for several chemokines that mediate recruitment of immune cells to mucosal surfaces and the skin, sites of virus entry and viral replication at late stages of smallpox. CrmB binds chemokines through its C-terminal domain, which is unrelated to TNFRs, was named smallpox virus-encoded chemokine receptor (SECRET) domain and uncovers a family of poxvirus chemokine inhibitors. An active SECRET domain was found in another viral TNFR (CrmD) and three secreted proteins encoded by orthopoxviruses. These findings identify a previously undescribed chemokine-binding and inhibitory domain unrelated to host chemokine receptors and a mechanism of immune modulation in VaV that may influence smallpox pathogenesis.
Comparative promoter analysis allows
de novo
identification of specialized cell junction-associated proteins
Authors: Cohen Clemens D. , Klingenhoff Andreas , Boucherot Anissa , Nitsche Almut , Henger Anna , Brunner Bodo , Schmid Holger , Merkle Monika , Saleem Moin A. , Koller Klaus-Peter , Werner Thomas , Gröne Hermann-Josef , Nelson Peter J. , Kretzler Matthias
Published: April 2006

Shared transcription factor binding sites that are conserved in distance and orientation help control the expression of gene products that act together in the same biological context. New bioinformatics approaches allow the rapid characterization of shared promoter structures and can be used to find novel interacting molecules. Here, these principles are demonstrated by using molecules linked to the unique functional unit of the glomerular slit diaphragm. An evolutionarily conserved promoter model was generated by comparative genomics in the proximal promoter regions of the slit diaphragm-associated molecule nephrin. Phylogenetic promoter fingerprints of known elements of the slit diaphragm complex identified the nephrin model in the promoter region of zonula occludens-1 (ZO-1). Genome-wide scans using this promoter model effectively predicted a previously unrecognized slit diaphragm molecule, cadherin-5. Nephrin, ZO-1, and cadherin-5 mRNA showed stringent coexpression across a diverse set of human glomerular diseases. Comparative promoter analysis can identify regulatory pathways at work in tissue homeostasis and disease processes.
Severe urinary concentrating defect in renal collecting duct-selective AQP2 conditional-knockout mice
Authors: Rojek Aleksandra , Füchtbauer Ernst-Martin , Kwon Tae-Hwan , Frøkiær Jørgen , Nielsen Søren
Published: April 2006

Aquaporin-2 (AQP2) is the predominant vasopressin-regulated water channel in kidney connecting tubule (CNT) and collecting duct (CD) and is essential for renal regulation of body water balance. However, the relative role of AQP2 to urinary concentration in the CNT and CD segments is unknown. To examine this directly, transgenic mice expressing AQP2 selectively in CNT but lacking AQP2 expression in CD (AQP2-CD-KO) and mice lacking AQP2 globally (AQP2-total-KO) were generated by exploiting the Cre/loxP technology. LoxP sites were inserted into AQP2 introns 2 and 3, and transgenic mice were bred with strains expressing Cre recombinase under the control of CD-specific Hoxb7− or global EIIa promoter. Mice lacking AQP2 globally died postnatally (days 5–12). AQP2-CD-KO mice were viable to adulthood and showed decreased body weight, 10-fold increased urine production (0.96 ± 0.11 vs. 0.10 ± 0.01 ml/g of body weight), and decreased urinary osmolality (170 ± 19 vs. 1,630 ± 135 milliosmoles/kg of H
2
O). Immunohistochemical staining of AQP2-CD-KO kidneys (
n
= 12) revealed sustained, strong AQP2 expression in CNT cells, whereas >95% of CD principal cells were completely AQP2-negative. Water deprivation for 3 hours caused only marginal decreased urine output (87 ± 7% of levels when mice had free water access;
P
= 0.04) with no change in urine osmolality, revealing an absence of compensatory mechanisms. These results demonstrate that AQP2 in CNT is sufficient for postnatal survival and that AQP2 in CD is essential for regulation of body water balance and cannot be compensated for by other mechanisms.
Reactivation by exon shuffling of a conservedHLA-DR3-like pseudogene segment in a New World primate species
Authors: Doxiadis Gaby G. M. , van der Wiel Marit K. H. , Brok Herbert P. M. , de Groot Natasja G. , Otting Nel , ’t Hart Bert A. , van Rood Jon J. , Bontrop Ronald E.
Published: April 2006

The common marmoset (Callithrix jacchus), a New World monkey species with a limited MHC class II repertoire, is highly susceptible to certain bacterial infections. Genomic analysis of exon 2 sequences documented the existence of only oneDRBregion configuration harboring three loci. Two of these loci display moderate levels of allelic polymorphism, whereas the-DRB*W12gene appears to be monomorphic. This study shows that only theCaja-DRB*W16and-DRB*W12loci produce functional transcripts. TheCaja-DRB1*03locus is occupied by a pseudogene, given that most of the transcripts, if detected at all, show imperfections and are present at low levels. Moreover, two hybrid transcripts were identified that feature the evolutionarily conserved peptide-binding motif characteristic for theCaja-DRB1*03gene. Thus, the severely reduced MHC class II repertoire in common marmosets has been expanded by reactivation of a pseudogene segment as a result of exon shuffling.
Symmetry-, time-, and temperature-dependent strength of carbon nanotubes
Authors: Dumitrica Traian , Hua Ming , Yakobson Boris I.
Published: April 2006

Although the strength of carbon nanotubes has been of great interest, their ideal value has remained elusive both experimentally and theoretically. Here, we present a comprehensive analysis of underlying atomic mechanisms and evaluate the yield strain for arbitrary nanotubes at realistic conditions. For this purpose, we combine detailed quantum mechanical computations of failure nucleation and transition-state barriers with the probabilistic approach of the rate theory. The numerical results are then summarized in a concise set of equations for the breaking strain. We reveal a competition between two alternative routes of brittle bond breaking and plastic relaxation, determine the domains of their dominance, and map the nanotube strength as a function of chiral symmetry, tensile test time, and temperature.
Presence/absence polymorphism for alternative pathogenicity islands in
Pseudomonas viridiflava
, a pathogen of
Arabidopsis
Authors: Araki Hitoshi , Tian Dacheng , Goss Erica M. , Jakob Katrin , Halldorsdottir Solveig S. , Kreitman Martin , Bergelson Joy
Published: April 2006

The contribution of arms race dynamics to plant–pathogen coevolution has been called into question by the presence of balanced polymorphisms in resistance genes of
Arabidopsis thaliana
, but less is known about the pathogen side of the interaction. Here we investigate structural polymorphism in pathogenicity islands (PAIs) in
Pseudomonas viridiflava
, a prevalent bacterial pathogen of
A. thaliana
. PAIs encode the type III secretion system along with its effectors and are essential for pathogen recognition in plants.
P. viridiflava
harbors two structurally distinct and highly diverged PAI paralogs (T- and S-PAI) that are integrated in different chromosome locations in the
P. viridiflava
genome. Both PAIs are segregating as presence/absence polymorphisms such that only one PAI ([T-PAI, ∇S-PAI] and [∇T-PAI, S-PAI]) is present in any individual cell. A worldwide population survey identified no isolate with neither or both PAI. T-PAI and S-PAI genotypes exhibit virulence differences and a host-specificity tradeoff. Orthologs of each PAI can be found in conserved syntenic locations in other
Pseudomonas
species, indicating vertical phylogenetic transmission in this genus. Molecular evolutionary analysis of PAI sequences also argues against “recent” horizontal transfer. Spikes in nucleotide divergence in flanking regions of PAI and ∇-PAI alleles suggest that the dual PAI polymorphism has been maintained in this species under some form of balancing selection. Virulence differences and host specificities are hypothesized to be responsible for the maintenance of the dual PAI system in this bacterial pathogen.
Chinese academic journals: quality, issues and solutions
Authors: Shuhua Wang , Weldon Paul R.
Published: April 2006

Twelve Chinese academic journals, indexed by SCI and financed by the National Natural Science Foundation (NNSF), were analysed using the 2000–2003 Total Citations and Impact Factor data from JCR. It is concluded that the quality of Chinese journals is generally low and has remained so despite recent government measures aimed at improvement. Several factors are influential – particularly the Chinese government's policy of encouraging submission to foreign journals. Finance, management, and the academic degree policy are also obstacles. It is suggested that the Chinese government should reconsider its current policies so as to encourage higher quality in domestic periodicals and thus a greater recognition of Chinese journals by the international academic community.
Self‐archiving practice and the influence of publisher policies in the social sciences
Authors: Antelman Kristin
Published: April 2006

Authors in different disciplines exhibit very different behaviours on the so‐called ‘green’ road to open access, i.e. self‐archiving. This study looks at the self‐archiving behaviour of authors publishing in leading journals in six social science disciplines. It tests the hypothesis that authors are self‐archiving according to the norms of their respective disciplines rather than following self‐archiving policies of publishers, and that, as a result, they are self‐archiving significant numbers of publisher PDF versions. It finds significant levels of self‐archiving, as well as significant self‐archiving of the publisher PDF version, in all the disciplines investigated. Publishers' self‐archiving policies have no influence on author self‐archiving practice.
Book Reviews
Authors: Oppenheim Charles , Oppenheim Charles
Published: April 2006

Digital Copyright by Paul Pedley Facet Publishing, 2005, 134 pp. Electronic book. Available for single user (ISBN 1‐85604‐573‐0; £34.95 plus VAT) or single‐site licence for a single geographical location (ISBN 1‐85604‐559‐5; £175.00 plus VAT).

The Access Principle: The Case for Open Access to Research and Scholarship by John Willinsky MIT Press 2005, ISBN 0 262 23242 1, £22.95 hardback, 290pp
The past, present and future of scientific and technical journals of China
Authors: Xian Jia
Published: April 2006

The early days of the People's Republic of China saw the development of science and technology at home with an accompanying development of scientific and technical journals. A succession of natural disasters then weakened the economy and many journals had to cease publication. The disruption of the Great Proletarian Cultural Revolution followed and only twenty journals survived. Since the opening up of the economy the Chinese government has supported scientific and technical journals and these have developed rapidly. There are now a large number of journals but many of them are still of low quality and little impact, and too few are in English. The number in English will now increase considerably, as will their international influence.
Using digital libraries to provide online access to social science journals in Latin America
Authors: Babini Dominique , Smart Pippa
Published: April 2006

There is a strong history of social science research within Latin America, but its visibility (both within and outside the region) has been low for reasons of language and print distribution. The introduction of the Internet and online publication makes this information potentially more visible to the global research community, and within Latin America several organizations have undertaken to exploit this opportunity. The approaches taken show how collaboration between countries, and particularly between librarians and publishers, can provide innovative solutions. The CLACSO project uses a digital library model as a publishing platform for its member journals and this has provided a successful – and hopefully sustainable – model.
Paperless workflows in journal production: a management perspective
Authors: Markwood Priscilla
Published: April 2006

This article discusses the development of production technologies with emphasis on where efficiencies and cost‐effectiveness are most commonly gained and lost in today's production workflows.
MedBiquitous and journal publishers: scholarly content and online medical communities
Authors: Smothers Valerie , Clarke Michael , Van Dyck Craig
Published: April 2006

MedBiquitous is a consortium whose members are working to develop a common technology framework that will support reforms in healthcare education and competence assessment. The mission of MedBiquitous is to advance healthcare education through technology standards that promote professional competence, collaboration, and better patient care. The consortium members include professional medical associations, technology companies, e‐learning firms, and publishers, among others. Two publishers actively working within MedBiquitous are John Wiley & Sons, Inc., and the American Academy of Pediatrics, who are pursuing their own objectives to help to create improved online medical communities.
Core issues in pricing models for scholarly journals: a qualitative overview
Authors: Chesler Adam
Published: April 2006

Rhetoric about the ideal pricing model for scholarly content is often both strident and ill‐informed. Recognition of the nature of the business model is sometimes overlooked in favour of slogans or blanket accusations. This paper reviews qualitatively some of the core issues surrounding the creation of a sustainable pricing model that will enable authors, readers, and publishers to coexist. No particular examples are recommended or rejected; what is important is that interested parties explore thoroughly the available options and make decisions based on available facts, instead of emotion or trends.
Selling the Sewing Machine Around the World: Singer’s International Marketing Strategies, 1850–1920
Authors: Godley Andrew
Published: April 2006

The sewing machine was one of the first standardized and mass-marketed complex consumer durables to have been diffused widely around the world before 1920. This global diffusion was almost the sole responsibility of one firm, Singer. Despite its American origins, Singer’s success lay principally overseas. New data provide insight into the company’s international marketing strategies. Although the firm had a reputation for marketing sophistication, Singer did not depend on price discrimination, extensive advertising, or loss-leading expansion of retail networks in its overseas markets. Rather, its success was due to the characteristics of consumer demand for sewing machines, features that combined with its strategic investments in market support services and in its selling organization to create Singer’s enormous competitive advantages in foreign markets.
Sporacetigenium mesophilum gen. nov., sp. nov., isolated from an anaerobic digester treating municipal solid waste and sewage
Authors: Chen Shuangya , Song Lei , Dong Xiuzhu
Published: April 2006

Two mesophilic, anaerobic bacterial strains (ZLJ115Tand L4-2) were isolated from the sludge of an anaerobic digester treating municipal solid waste and sewage in Fujian province, China. The strains were Gram-positive, spore-forming, motile rods (0·9–1·0×3·6–7·3 μm). Growth of the strains was observed at 20–42 °C and pH 6·0–9·5. Both strains fermented several mono- and disaccharides. The main fermentation products from glucose were acetate, ethanol, hydrogen and carbon dioxide. Optimal hydrogen production by the new isolates was observed at pH 8·8 and 39 °C, and 1·4 mol H2was detected from fermentation of 1 mol glucose. The DNA G+C contents of strains ZLJ115Tand L4-2 were 53·9 and 54·3 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates represented a novel phyletic sublineage within cluster XI of the clostridia, clustering with four thermophilic species, with <93·8 % 16S rRNA gene sequence similarity to previously described species. Phenotypically, the new isolates were distinguished from their phylogenetic relatives by growing mesophilically and by fermenting a variety of pentoses, as well as their higher genome DNA G+C content. On the basis of polyphasic evidence from this study, a novel genus and species are proposed,Sporacetigenium mesophilumgen. nov., sp. nov.; strain ZLJ115T(=DSM 16796T=AS 1.5019T) is the type strain ofSporacetigenium mesophilum.
Megasphaera paucivorans sp. nov., Megasphaera sueciensis sp. nov. and Pectinatus haikarae sp. nov., isolated from brewery samples, and emended description of the genus Pectinatus
Authors: Juvonen Riikka , Suihko Maija-Liisa
Published: April 2006

Seven unidentified strictly anaerobic, Gram-negative, non-spore-forming bacteria from spoiled beer or the brewery environment were characterized. Based on 16S rRNA gene sequence analyses, all strains were affiliated to theSporomusasub-branch of the class ‘Clostridia’. Three of the strains were non-motile cocci, on average 1·5×1·2 μm or 1·2×1·0 μm, occurring mainly singly or in pairs. They shared nearly identical (>99 %) 16S rRNA gene sequences, being most closely related to the species of theMegasphaera–Anaeroglobusgroup (⩽93·9 % similarity). According to DNA–DNA hybridization results, the coccoid strains represented two genospecies, neither of which was related to any of the recognizedMegasphaeraspecies. Several phenotypic characteristics and/or DNA G+C content also differentiated the strains from each other and from their closest relatives. The other four novel strains were motile, slightly curved to helical rods, 0·6−0·8×3−50 μm or more in size. They shared identical 16S rRNA gene sequences and ribofragment patterns. The highest 16S rRNA gene similarity was found between these isolates andPectinatus cerevisiiphilusATCC 29359T(95·6 %) andPectinatus frisingensisATCC 33332T(93·6 %). The novel strains also differed from recognizedPectinatusspecies in their sugar utilization, proteolytic activity, catalase activity, antibiotic resistance and temperature tolerance. The results suggest that the bacteria belong to three novel species, for which the namesMegasphaera paucivoranssp. nov. (type strain VTT E-032341T=DSM 16981T),Megasphaera sueciensissp. nov. (type strain VTT E-97791T=DSM 17042T) andPectinatus haikaraesp. nov. (type strain VTT E-88329T=DSM 16980T) are proposed.
Sphingomonas soli sp. nov., a β-glucosidase-producing bacterium in the family Sphingomonadaceae in the α-4 subgroup of the Proteobacteria
Authors: Yang Deok-Chun , Im Wan-Taek , Kim Myung Kyum , Ohta Hiroyuki , Lee Sung-Taik
Published: April 2006

Strain T5-04T, a Gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from soil of a ginseng field in South Korea and characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain T5-04Tbelongs to theα-4 subgroup of theProteobacteria, and the highest degrees of sequence similarity determined were toSphingomonas asaccharolyticaIFO 10564T(97·5 %),Sphingomonas koreensisJSS26T(97·1 %),Sphingomonas maliIFO 15500T(96·7 %) andSphingomonas pruniIFO 15498T(96·6 %). Chemotaxonomic data revealed that strain T5-04Tpossesses ubiquinone Q-10 predominantly, C18 : 1as the predominant fatty acid and sphingoglycolipids, all of which corroborate its assignment to the genusSphingomonas. The results of DNA–DNA hybridization and physiological and biochemical tests clearly demonstrated that strain T5-04Trepresents a distinct species. Based on polyphasic evidence, T5-04T(=KCTC 12210T=NBRC 100801T=IAM 15213T) should be classified as the type strain of a novelSphingomonasspecies, for which the nameSphingomonas solisp. nov. is proposed.
Emended description of the genus Phyllobacterium and description of four novel species associated with plant roots: Phyllobacterium bourgognense sp. nov., Phyllobacterium ifriqiyense sp. nov., Phyllobacterium leguminum sp. nov. and Phyllobacterium brassicacearum sp. nov.
Authors: Mantelin Sophie , Saux Marion Fischer-Le , Zakhia Frédéric , Béna Gilles , Bonneau Sophie , Jeder Habib , de Lajudie Philippe , Cleyet-Marel Jean-Claude
Published: April 2006

Gram-negative bacteria were isolated from the rhizoplane ofBrassica napusin France and from root nodules ofArgyrolobium uniflorum,Astragalus algerianusandLathyrus numidicusgrowing in the infra-arid zone of southern Tunisia. Based on phylogenetic analysis of the 16S rRNA gene sequences, the seven isolates belong to theAlphaproteobacteriaand are related toPhyllobacterium myrsinacearumstrains. The isolates formed three clusters; clusters A and C consist of Tunisian strains, whereas cluster B consists of two strains fromBrassica napusfrom France. Phylogenetic reconstruction based on theatpDgene strongly supports their affiliation to the genusPhyllobacterium. DNA–DNA hybridizations revealed that (i) none of the isolates belong to the speciesP. myrsinacearum, (ii) clusters A and C represent two distinct genomospecies and (iii) the two strains of cluster B represent two separate genomospecies. Distinctive phenotypic features were deduced from numerical analysis of phenotypic data. Based on this polyphasic approach, four novel species are proposed:Phyllobacterium leguminumsp. nov. (type strain ORS 1419T=CFBP 6745T=LMG 22833T),Phyllobacterium ifriqiyensesp. nov. (type strain STM 370T=CFBP 6742T=LMG 22831T),Phyllobacterium brassicacearumsp. nov. (type strain STM 196T=CFBP 5551T=LMG 22836T) andPhyllobacterium bourgognensesp. nov. (type strain STM 201T=CFBP 5553T=LMG 22837T). The description of the genusPhyllobacteriumis emended accordingly.
Cohnella thermotolerans gen. nov., sp. nov., and classification of ‘Paenibacillus hongkongensis’ as Cohnella hongkongensis sp. nov.
Authors: Kämpfer Peter , Rosselló-Mora Ramon , Falsen Enevold , Busse Hans-Jürgen , Tindall Brian J.
Published: April 2006

A Gram-positive, rod-shaped, endospore-forming organism, strain CCUG 47242T, was isolated from a sample of industrial starch production in Sweden. 16S rRNA gene sequence analysis demonstrated that this isolate was moderately related to species of the genusPaenibacillus, with <94·4 % sequence similarity to all other hitherto describedPaenibacillusspecies. Strain CCUG 47242Tshowed the greatest sequence similarity (96·5 %) to ‘Paenibacillus hongkongensis’ HKU3, a strain with a name that has not yet been validly published. Chemotaxonomic data [major menaquinone, MK-7 (98 %); major polar lipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, lysyl-phosphatidylglycerol, two unknown phospholipids, four unknown aminophospholipids; major fatty acids, iso-C16 : 0 and anteiso-C15 : 0] showed some significant differences when compared with the type species of the genusPaenibacillus,Paenibacillus polymyxa. Physiological and biochemical tests allowed clear phenotypic differentiation of strain CCUG 47242Tfrom strain HKU3. On the basis of 16S rRNA gene sequence analysis, in combination with chemotaxonomic data, strains CCUG 47242Tand HKU3 represent two novel species of a new genus of endospore-forming bacteria for which we propose the namesCohnella thermotoleransgen. nov., sp. nov. (type strain CCUG 47242T=CIP 108492T=DSM 17683T) andCohnella hongkongensissp. nov. (type strain HKU3T=CCUG 49571T=CIP 107898T=DSM 17642T).
Castellaniella gen. nov., to accommodate the phylogenetic lineage of Alcaligenes defragrans, and proposal of Castellaniella defragrans gen. nov., comb. nov. and Castellaniella denitrificans sp. nov.
Authors: Kämpfer P. , Denger K. , Cook A. M. , Lee S.-T. , Jäckel U. , Denner E. B. M. , Busse H.-J.
Published: April 2006

Comparative 16S rRNA gene sequence analysis indicates that two distinct sublineages exist within the genus Alcaligenes: the Alcaligenes faecalis lineage, comprising Alcaligenes aquatilis and A. faecalis (with the three subspecies A. faecalis subsp. faecalis, A. faecalis subsp. parafaecalis and A. faecalis subsp. phenolicus), and the Alcaligenes defragrans lineage, comprising A. defragrans. This phylogenetic discrimination is supported by phenotypic and chemotaxonomic differences. It is proposed that the A. defragrans lineage constitutes a distinct genus, for which the name Castellaniella gen. nov. is proposed. The type strain for Castellaniella defragrans gen. nov., comb. nov. is 54PinT (=CCUG 39790T=CIP 105602T=DSM 12141T). Finally, on the basis of data from the literature and new DNA–DNA hybridization and phenotypic data, the novel species Castellaniella denitrificans sp. nov. (type strain NKNTAUT=DSM 11046T=CCUG 39541T) is proposed for two strains previously identified as strains of A. defragrans.
Oceanisphaera donghaensis sp. nov., a halophilic bacterium from the East Sea, Korea
Authors: Park Soo-Je , Kang Cheol-Hee , Nam Young-Do , Bae Jin-Woo , Park Yong-Ha , Quan Zhe-Xue , Moon Deok-Soo , Kim Hyeon-Ju , Roh Dong-Hyun , Rhee Sung-Keun
Published: April 2006

A taxonomic study was carried out on two isolates, strains BL1Tand BL11, from marine sediment collected from the East Sea, Korea. Comparative 16S rRNA gene sequence studies showed that these isolates clearly affiliated with theGammaproteobacteria. BL1Tand BL11 were most closely related toOceanisphaera litoralisKMM 3654T(97·6 and 97·7 % 16S rRNA gene sequence similarity, respectively). The level of 16S rRNA gene sequence similarity between strains BL1Tand BL11 was 99·7 %. The two isolates were Gram-negative, aerobic, moderately halophilic, and grew in 0·5–8·0 % NaCl and at 4–42 °C. Strains BL1Tand BL11 shared some physiological and biochemical properties withO. litoralisKMM 3654T, although they differed in that BL1Tand BL11 were able to utilize ethanol, proline and alanine. The G+C contents of the genomic DNA of strains BL1Tand BL11 were 56·6 and 57·1 mol%, respectively. Both strains possessed C16 : 1ω7cand/or iso-C15 : 02-OH, C16 : 0and C18 : 1ω7cas the major fatty acids. DNA–DNA relatedness data indicated that strains BL1Tand BL11 represent a genomic species that is separate fromO. litoralisKMM 3654T. On the basis of polyphasic evidence, it is proposed that strain BL1T(=KCTC 12522T=DSM 17589T) represents the type strain of a novel species,Oceanisphaera donghaensissp. nov.
Alu-mediated 100-kb deletion in the primate genome: The loss of the agouti signaling protein gene in the lesser apes
Authors: Nakayama Kazuhiro , Ishida Takafumi
Published: April 2006

Agouti signaling protein (ASIP) is an endogenous antagonist of melanocortin receptors that controls a wide range of physiological functions. Its central role in regulation of the melanocortin system implied that ASIP has been relevant to the evolution of various physiological traits in primates. In this study, we have tried to determine DNA sequences of the ASIP gene (ASIP) of various simian species to find molecular evolutionary aspects of ASIP. Unexpectedly, we found that the whole coding region of ASIP was missing only from the gibbon genome; gibbons constitute a large group of hominoid species in Southeast Asia. Our analyses revealed that unequal homologous recombination mediated by two AluSx elements erased a ∼100-kb region including ASIP from the gibbon genome. The data provide new evidence for the significant roles of Alu elements in the dynamic evolution of the primate genome.
An isochore map of human chromosomes
Authors: Costantini Maria , Clay Oliver , Auletta Fabio , Bernardi Giorgio
Published: April 2006

Isochores are large DNA segments (≫300 kb on average) that are characterized by an internal variation in GC well below the full variation seen in the mammalian genome. Precisely defining in terms of size and composition as well as mapping the isochores on human chromosomes have, however, remained largely unsolved problems. Here we used a very simple approach to segment the human chromosomes de novo, based on assessments of GC and its variation within and between adjacent regions. We obtain a complete coverage of the human genome (neglecting the remaining gaps) by ∼3200 isochores, which may be visualized as the ultimate chromosomal bands. Isochores visibly belong to five families characterized by different GC levels, as expected from previous investigations. Since we previously showed that isochores are tightly linked to basic biological properties such as gene density, replication timing, and recombination, the new level of detail provided by the isochore map will help the understanding of genome structure, function, and evolution.
Dopamine transporter blockade increases LTP in the CA1 region of the rat hippocampus via activation of the D3 dopamine receptor
Authors: Swant Jarod , Wagner John J.
Published: April 2006

Dopamine has been demonstrated to be involved in the modulation of long-term potentiation (LTP) in the CA1 region of the hippocampus. As monoamine transporter blockade will increase the actions of endogenous monoamine neurotransmitters, the effect of a dopamine transporter (DAT) antagonist on LTP was assessed using field excitatory postsynaptic potentials recorded in the CA1 region of the rat hippocampal slice preparation. Application of the DAT-specific blocker GBR 12,935 produced a significant enhancement in LTP of Schaffer collateral synapses in the CA1 at concentrations as low as 100 nM. A selective D1/D5 dopamine receptor antagonist (SCH 23,390, 1 μM) did not affect the ability of GBR 12,935 to enhance LTP, whereas application of the D3 dopamine receptor antagonist U 99,194 (1 μM) blocked the GBR 12,935-induced enhancement in LTP. In addition, a D3 dopamine receptor agonist (7-OH-DPAT, 1 μM) caused a significant increase in LTP, an effect that was also blocked by U 99,194 (3 μM). These results suggest that either endogenously released dopamine (facilitated by DAT blockade) or exogenously applied dopamine agonist can act to increase LTP in the CA1 of the hippocampus via activation of the D3 subtype of dopamine receptor.
Simultaneous training on two hippocampus-dependent tasks facilitates acquisition of trace eyeblink conditioning
Authors: Kuo Amy G. , Lee Grace , Disterhoft John F.
Published: April 2006

A common cellular alteration, reduced post-burst afterhyperpolarization (AHP) in CA1 neurons, is associated with acquisition of the hippocampus-dependent tasks trace eyeblink conditioning and the Morris water maze. As a similar increase in excitability is correlated with these two learning paradigms, we sought to determine the interactive behavioral effects of training animals on both tasks by using either a consecutive or simultaneous training design. In the consecutive design, animals were trained first on either the trace eyeblink conditioning task for six sessions, followed by training on the water maze task for six sessions, or vice versa. The simultaneous design consisted of six or 11 training days; animals received one session/day of both trace eyeblink conditioning and water maze training. Separate groups were used for consecutive and simultaneous training. Animals trained on both tasks simultaneously were significantly facilitated in their ability to acquire the trace eyeblink conditioning task; no effect of simultaneous training was seen on the water maze task. No effect was seen on acquisition for either task when using the consecutive training design. Taken together, these findings provide insight into how the hippocampus processes information when animals learn multiple hippocampus-dependent tasks.
The Shoot-Specific Expression of γ-Glutamylcysteine Synthetase Directs the Long-Distance Transport of Thiol-Peptides to Roots Conferring Tolerance to Mercury and Arsenic
Authors: Li Yujing , Dankher Om Parkash , Carreira Laura , Smith Aaron P. , Meagher Richard B.
Published: April 2006

Thiol-peptides synthesized as intermediates in phytochelatin (PC) biosynthesis confer cellular tolerance to toxic elements like arsenic, mercury, and cadmium, but little is known about their long-distance transport between plant organs. A modified bacterial γ-glutamylcysteine synthetase (ECS) gene, S1pt∷ECS, was expressed in the shoots of the ECS-deficient, heavy-metal-sensitive cad2-1 mutant of Arabidopsis (Arabidopsis thaliana). S1pt∷ECS directed strong ECS protein expression in the shoots, but no ECS was detected in the roots of transgenic plant lines. The S1pt∷ECS gene restored full mercury tolerance and partial cadmium tolerance to the mutant and enhanced arsenate tolerance significantly beyond wild-type levels. After arsenic treatment, the root concentrations of γ-glutamylcysteine (EC), PC2, and PC3 peptides in a S1pt∷ECS-complemented cad2-1 line increased 6- to 100-fold over the mutant levels and were equivalent to wild-type concentrations. The shoot and root levels of glutathione were 2- to 5-fold above those in wild-type plants, with or without treatment with toxicants. Thus, EC and perhaps glutathione are efficiently transported from shoots to roots. The possibility that EC or other PC pathway intermediates may act as carriers for the long-distance phloem transport and subsequent redistribution of thiol-reactive toxins and nutrients in plants is discussed.
Maize cDNAs Expressed in Endosperm Encode Functional Farnesyl Diphosphate Synthase with Geranylgeranyl Diphosphate Synthase Activity
Authors: Cervantes-Cervantes Miguel , Gallagher Cynthia E. , Zhu Changfu , Wurtzel Eleanore T.
Published: April 2006

Isoprenoids are the most diverse and abundant group of natural products. In plants, farnesyl diphosphate (FPP) and geranylgeranyl diphosphate (GGPP) are precursors to many isoprenoids having essential functions. Terpenoids and sterols are derived from FPP, whereas gibberellins, carotenoids, casbenes, taxenes, and others originate from GGPP. The corresponding synthases (FPP synthase [FPPS] and GGPP synthase [GGPPS]) catalyze, respectively, the addition of two and three isopentenyl diphosphate molecules to dimethylallyl diphosphate. Maize (Zea mays L. cv B73) endosperm cDNAs encoding isoprenoid synthases were isolated by functional complementation of Escherichia coli cells carrying a bacterial gene cluster encoding all pathway enzymes needed for carotenoid biosynthesis, except for GGPPS. This approach indicated that the maize gene products were functional GGPPS enzymes. Yet, the predicted enzyme sequences revealed FPPS motifs and homology with FPPS enzymes. In vitro assays demonstrated that indeed these maize enzymes produced both FPP and GGPP and that the N-terminal sequence affected the ratio of FPP to GGPP. Their functionality in E. coli demonstrated that these maize enzymes can be coupled with a metabolon to provide isoprenoid substrates for pathway use, and suggests that enzyme bifunctionality can be harnessed. The maize cDNAs are encoded by a small gene family whose transcripts are prevalent in endosperm beginning mid development. These maize cDNAs will be valuable tools for assessing the critical structural properties determining prenyl transferase specificity and in metabolic engineering of isoprenoid pathways, especially in cereal crops.
G-Protein Complex Mutants Are Hypersensitive to Abscisic Acid Regulation of Germination and Postgermination Development
Authors: Pandey Sona , Chen Jin-Gui , Jones Alan M. , Assmann Sarah M.
Published: April 2006

Abscisic acid (ABA) plays regulatory roles in a host of physiological processes throughout plant growth and development. Seed germination, early seedling development, stomatal guard cell functions, and acclimation to adverse environmental conditions are key processes regulated by ABA. Recent evidence suggests that signaling processes in both seeds and guard cells involve heterotrimeric G proteins. To assess new roles for the Arabidopsis (Arabidopsis thaliana) Gα subunit (GPA1), the Gβ subunit (AGB1), and the candidate G-protein-coupled receptor (GCR1) in ABA signaling during germination and early seedling development, we utilized knockout mutants lacking one or more of these components. Our data show that GPA1, AGB1, and GCR1 each negatively regulates ABA signaling in seed germination and early seedling development. Plants lacking AGB1 have greater ABA hypersensitivity than plants lacking GPA1, suggesting that AGB1 is the predominant regulator of ABA signaling and that GPA1 affects the efficacy of AGB1 execution. GCR1 acts upstream of GPA1 and AGB1 for ABA signaling pathways during germination and early seedling development: gcr1 gpa1 double mutants exhibit a gpa1 phenotype and agb1 gcr1 and agb1 gcr1 gpa1 mutants exhibit an agb1 phenotype. Contrary to the scenario in guard cells, where GCR1 and GPA1 have opposite effects on ABA signaling during stomatal opening, GCR1 acts in concert with GPA1 and AGB1 in ABA signaling during germination and early seedling development. Thus, cell- and tissue-specific functional interaction in response to a given signal such as ABA may determine the distinct pathways regulated by the individual members of the G-protein complex.
Plant Retromer, Localized to the Prevacuolar Compartment and Microvesicles inArabidopsis, May Interact with Vacuolar Sorting Receptors
Authors: Oliviusson Peter , Heinzerling Oliver , Hillmer Stefan , Hinz Giselbert , Tse Yu Chung , Jiang Liwen , Robinson David G.
Published: April 2006

Receptors for acid hydrolases destined for the lytic compartment in yeast and mammalian cells are retrieved from intermediate, endosomal organelles with the help of a pentameric protein complex called the retromer. We cloned the Arabidopsis thaliana homologs of the three yeast proteins (Vps35, Vps29, and Vps26) constituting the larger subunit of retromer and prepared antisera against them. With these antibodies, we demonstrated the presence of a retromer-like protein complex in salt extracts prepared from Arabidopsis microsomes. This complex is associated with membranes that coequilibrate with prevacuolar compartment markers and with high-density sedimenting membranes. Immunogold negative staining identified these membranes as 90-nm-diameter coated microvesicles. Confocal laser scanning immunofluorescence studies performed on tobacco (Nicotiana tabacum) BY-2 cells revealed high degrees of colabeling between all three retromer antisera and the prevacuolar compartment (PVC) markers PEP12 and vacuolar sorting receptor VSRAt-1. The presence of plant retromer at the surface of multivesicular bodies was also demonstrated by immunogold labeling of sections obtained from high-pressure frozen/freeze-substituted specimens. Treatment of BY-2 cells with wortmannin led to swelling of the PVC and a separation of the VPS35 and VSR signals. Preliminary data suggesting that retromer interacts with the cytosolic domain of a VSR were obtained by immunoprecipitation experiments performed on detergent-solubilized microsomes with Vps35 antibodies.
The Plastid Protein THYLAKOID FORMATION1 and the Plasma Membrane G-Protein GPA1 Interact in a Novel Sugar-Signaling Mechanism inArabidopsis
Authors: Huang Jirong , Taylor J. Philip , Chen Jin-Gui , Uhrig Joachim F. , Schnell Danny J. , Nakagawa Tsuyoshi , Korth Kenneth L. , Jones Alan M.
Published: April 2006

Mutations in genes encoding components of the heterotrimeric G-protein complex were previously shown to confer altered sensitivity to increased levels of d-glucose. This suggests that G-protein coupling may be a novel sugar-signaling mechanism in Arabidopsis thaliana. THYLAKOID FORMATION1 (THF1) is here demonstrated in vivo as a Gα interaction partner that functions downstream of the plasma membrane–delimited heterotrimeric G-protein (GPA1) in a d-glucose signaling pathway. THF1 is a plastid protein localized to both the outer plastid membrane and the stroma. Contact between root plastidic THF1 and GPA1 at the plasma membrane occurs at sites where the plastid membrane abuts the plasma membrane, as demonstrated by Förster resonance energy transfer (FRET). A probable role for THF1 in sugar signaling is demonstrated by both biochemical and genetic evidence. Root growth in the thf1-1 null mutant is hypersensitive to exogenous d-glucose, and THF1-overexpressing roots are resistant to inhibition of growth rate by high d-glucose. Additionally, THF1 levels are rapidly degraded by d-glucose but not l-glucose. The interaction between THF1 and GPA1 has been confirmed by in vitro and in vivo coimmunoprecipitation, FRET analysis, and genetic epistasis and provides evidence of a sugar-signaling mechanism between plastids and the plasma membrane.
Locus-Specific Control of DNA Methylation by theArabidopsisSUVH5 Histone Methyltransferase
Authors: Ebbs Michelle L. , Bender Judith
Published: April 2006

In Arabidopsis thaliana, heterochromatin formation is guided by double-stranded RNA (dsRNA), which triggers methylation of histone H3 at Lys-9 (H3 mK9) and CG plus non-CG methylation on identical DNA sequences. At heterochromatin targets including transposons and centromere repeats, H3 mK9 mediated by the Su(var)3-9 homologue 4 (SUVH4)/KYP histone methyltransferase (MTase) is required for the maintenance of non-CG methylation by the CMT3 DNA MTase. Here, we show that although SUVH4 is the major H3 K9 MTase, the SUVH5 protein also has histone MTase activity in vitro and contributes to the maintenance of H3 mK9 and CMT3-mediated non-CG methylation in vivo. Strikingly, the relative contributions of SUVH4, SUVH5, and a third related histone MTase, SUVH6, to non-CG methylation are locus-specific. For example, SUVH4 and SUVH5 together control transposon sequences with only a minor contribution from SUVH6, whereas SUVH4 and SUVH6 together control a transcribed inverted repeat source of dsRNA with only a minor contribution from SUVH5. This locus-specific variation suggests different mechanisms for recruiting or activating SUVH enzymes at different heterochromatic sequences. The suvh4 suvh5 suvh6 triple mutant loses both monomethyl and dimethyl H3 K9 at target loci. The suvh4 suvh5 suvh6 mutant also displays a loss of non-CG methylation similar to a cmt3 mutant, indicating that SUVH4, SUVH5, and SUVH6 together control CMT3 activity.
Evaluation of the epidermal refractive index measured by optical coherence tomography
Authors: Sand M. , Gambichler T. , Moussa G. , Bechara F. G. , Sand D. , Altmeyer P. , Hoffmann K.
Published: April 2006

Background/aims: It has recently been proposed that the refractive index (RI) measured by means of optical coherence tomography (OCT) may be a valid measure for hydration of skin. In this pilot study, using OCT in vivo, we aimed to investigate the interday variability of RI measurements and acute changes of RI following the application of a moisturizer.

Methods: Twenty healthy Caucasian volunteers were investigated on their forearms using a commercially available OCT system (SkinDex 300®, ISIS optronics GmbH, Mannheim, Germany) fitted with an integrated algorithm for the evaluation of the RI. The interday repeatability of the OCT method was determined performing symmetrical measurements on both forearms on day 1, 5, 9, and 13. In order to investigate the acute effect of a moisturizer on RI, OCT assessments were performed before and 10 min after the application of an aqueous lotion with a lipophilic phase. As a control, the contralateral site was investigated in the same way, except for the use of distilled water instead of the lotion.

Results: Assessments of interday variability revealed insignificant (P>0.05) variances between the four measurement times as expressed in very small repeatability coefficients (right arm: 0.039; left arm 0.053) and small coefficients of variance (right arm: 1.02%; left arm: 1.38%). With regard to the RIs measured over time, we could not observe significant (P>0.05) differences between the two symmetrical anatomic sites (mean±SD of RI: 1.3893±0.0142 (right arm); 1.3875±0.0192 (left arm)). The acute effect of the moisturizer was indicated by a significant decrease of the RI 5 min after the application of the lotion (1.399±0.01 vs. 1.387±0.02; difference between means: 0.012; P=0.033; 95% confidence interval: 0.001–0.0023). However the control site treated with distilled water did not show significant differences between the two measurement times (1.387±0.013 vs. 1.391±0.023; difference between means: −0.004; P=0.57; 95% confidence interval: −0.019–0.011).

Conclusions: In this pilot study, we have demonstrated that RI evaluation via OCT is a promising technique that may be used for the assessment of skin hydration in vivo. However, the direct comparison of OCT with standard methods, ideally such as nuclear magnetic resonance spectroscopy, is necessary.
Capacitance imaging of the skin surface
Authors: Batisse Dominique , Giron Franck , Lévêque Jean Luc
Published: April 2006

Background/aims: A new device allowing recording capacitance images of the skin surface was recently presented. Parameters, extracted from the gray‐level histogram of the images, are tested for a new approach of skin surface hydration measurement in comparison with the classical capacitance method. Illustration of the interest of having both images and parameters for studying the homogeneity and the level of skin surface hydration are presented.

Methods: Software for selecting a region of interest from an image and measuring the parameters derived from its gray‐level histogram was used to characterize skin hydration.

Results: There is a very close correlation between a Corneometer and the parameters extracted from the SkinChip measurements. The importance of having capacitance images of skin is demonstrated in case of non‐homogeneity of the skin hydration, either because of photoaging or following an inflammation process.

Conclusion: Capacitance imaging is a necessary tool for both completely describing and quantifying skin surface hydration.