bluuebunny/crossref_metadata_2025 huggingface dataset:
Real-time measurement of dopamine fluctuations after cocaine in the brain of behaving rats
Authors: Heien Michael L. A. V. , Khan Amina S. , Ariansen Jennifer L. , Cheer Joseph F. , Phillips Paul E. M. , Wassum Kate M. , Wightman R. Mark
Published: July 2005

Dopamine neurotransmission has been implicated in the modulation of many cognitive processes. Both rapid (phasic) and slower (tonic) changes in its extracellular concentration contribute to its complex actions. Fastin vivoelectrochemical techniques can measure extracellular dopamine on a rapid time scale but without the selectivity afforded with slower techniques that use chemical separations. Cyclic voltammetry improves chemical resolution over other electrochemical methods, and it can resolve dopamine changes in the brains of behaving rodents over short epochs (<10 s). With this method, however, selective detection of slower dopamine changes is still elusive. Here we demonstrate that principal component regression of cyclic voltammetry data enables quantification of changes in dopamine and extracellular pH. Using this method, we show that cocaine modifies dopamine release in two ways: dopamine concentration transients increase in frequency and magnitude, whereas a gradual increase in steady-state dopamine concentration occurs over 90 s.
Ratcheting of the substrate from the zymogen to proteinase conformations directs the sequential cleavage of prothrombin by prothrombinase
Authors: Bianchini Elsa P. , Orcutt Steven J. , Panizzi Peter , Bock Paul E. , Krishnaswamy Sriram
Published: July 2005

Prothrombinase catalyzes thrombin formation by the ordered cleavage of two peptide bonds in prothrombin. Although these bonds are likely ≈36 Å apart, sequential cleavage of prothrombin at Arg-320 to produce meizothrombin, followed by its cleavage at Arg-271, are both accomplished by equivalent exosite interactions that tether each substrate to the enzyme and facilitate presentation of the scissile bond to the active site of the catalyst. We show that impairing the conformational transition from zymogen to active proteinase that accompanies the formation of meizothrombin has no effect on initial cleavage at Arg-320 but inhibits subsequent cleavage at Arg-271. Full thermodynamic rescue of this defective mutant was achieved by stabilizing the proteinase-like conformation of the intermediate with a reversible, active site-specific inhibitor. Irreversible stabilization of intact prothrombin in a proteinase-like state, even without prior cleavage at Arg-320, also enhanced cleavage at Arg-271. Our results indicate that the sequential presentation and cleavage of the two scissile bonds in prothrombin activation is accomplished by substrate bound either in the zymogen or proteinase conformations. The ordered cleavage of prothrombin by prothrombinase is driven by ratcheting of the substrate from the zymogen to the proteinase-like states.
Space- and time-resolved spectrophotometry in microsystems
Authors: Damean Nicolae , Sia Samuel K. , Linder Vincent , Narovlyansky Max , Whitesides George M.
Published: July 2005

This work describes a simple optical method for obtaining, in a single still-capture image, the continuous absorbance spectra of samples at multiple locations of microsystems. This technique uses an unmodified bright-field microscope, an array of microlenses, and a diffraction grating to disperse the light transmitted by samples of 10- to 500-μm dimensions. By analyzing in a single image the first-order diffracted light, it is possible to collect the full and continuous absorbance spectra of samples at multiple locations (to a spatial resolution of ≈8 μm) in microwells and microchannels to examine dynamic chemical events (to a time resolution of <10 ms). This article also discusses the optical basis of this method. The simultaneous resolution of wavelength, time, and space at a scale <10 μm provides additional capabilities for chemical and biological analysis.
JNK antagonizes Akt-mediated survival signals by phosphorylating 14-3-3
Authors: Sunayama Jun , Tsuruta Fuminori , Masuyama Norihisa , Gotoh Yukiko
Published: July 2005

Life and death decisions are made by integrating a variety of apoptotic and survival signals in mammalian cells. Therefore, there is likely to be a common mechanism that integrates multiple signals adjudicating between the alternatives. In this study, we propose that 14-3-3 represents such an integration point. Several proapoptotic proteins commonly become associated with 14-3-3 upon phosphorylation by survival-mediating kinases such as Akt. We reported previously that cellular stresses induce c-Jun NH2-terminal kinase (JNK)–mediated 14-3-3ζ phosphorylation at Ser184 (Tsuruta, F., J. Sunayama, Y. Mori, S. Hattori, S. Shimizu, Y. Tsujimoto, K. Yoshioka, N. Masuyama, and Y. Gotoh. 2004. EMBO J. 23:1889–1899). Here, we show that phosphorylation of 14-3-3 by JNK releases the proapoptotic proteins Bad and FOXO3a from 14-3-3 and antagonizes the effects of Akt signaling. As a result of dissociation, Bad is dephosphorylated and translocates to the mitochondria, where it associates with Bcl-2/Bcl-xL. Because Bad and FOXO3a share the 14-3-3–binding motif with other proapoptotic proteins, we propose that this JNK-mediated phosphorylation of 14-3-3 regulates these proapoptotic proteins in concert and makes cells more susceptible to apoptotic signals.
The c-SMAC
Authors: Lin Joseph , Miller Mark J. , Shaw Andrey S.
Published: July 2005

T cells integrate and transduce the key signals necessary to mount an appropriate immune response. To do this, they rely on both secreted factors as well as physical cell–cell contact. Much attention has focused on the organization of proteins at the contact area between a T cell and an antigen-presenting cell, known as the immunological synapse. It has been shown in vitro that proteins segregate into two distinct regions within this contact area, a central area referred to as the c-SMAC, where the T cell receptor and associated signaling molecules are enriched, and a peripheral region called the p-SMAC containing LFA-1 and the scaffolding protein talin. Whether or not these structures form in vivo and how they function in T cell activation remain issues of great interest. Here, we review recently published work and propose several possible functions for the role of the c-SMAC in T cell activation.
A novel role for Gab2 in bFGF-mediated cell survival during retinoic acid–induced neuronal differentiation
Authors: Mao Yingwei , Lee Angel W.-M.
Published: July 2005

Gab proteins amplify and integrate signals stimulated by many growth factors. In culture and animals, retinoic acid (RA) induces neuronal differentiation. We show that Gab2 expression is detected in neurons in three models of neuronal differentiation: embryonic carcinoma (EC) stem cells, embryonic stem cells, and primary neural stem cells (NSCs). RA treatment induces apoptosis, countered by basic FGF (bFGF). In EC cells, Gab2 silencing results in hypersensitivity to RA-induced apoptosis and abrogates the protection by bFGF. Gab2 suppression reduces bFGF-dependent activation of AKT but not ERK, and constitutively active AKT, but not constitutively active MEK1, reverses the hypersensitization. Thus, Gab2-mediated AKT activation is required for bFGF's protection. Moreover, Gab2 silencing impairs the differentiation of EC cells to neurons. Similarly, in NSCs, Gab2 suppression reduces bFGF-dependent proliferation as well as neuronal survival and production upon differentiation. Our findings provide the first evidence that Gab2 is an important player in neural differentiation, partly by acting downstream of bFGF to mediate survival through phosphoinositide 3 kinase–AKT.
The neuropeptide neuromedin U promotes inflammation by direct activation of mast cells
Authors: Moriyama Maiko , Sato Takahiro , Inoue Hiromasa , Fukuyama Satoru , Teranishi Hitoshi , Kangawa Kenji , Kano Tatsuhiko , Yoshimura Akihiko , Kojima Masayasu
Published: July 2005

Neuromedin U (NMU) is a neuropeptide that is expressed in the gastrointestinal tract and central nervous system. NMU interacts with two G protein–coupled receptors, NMU-R1 and NMU-R2. Whereas NMU-R2 localizes predominantly to nerve cells, NMU-R1 is expressed in peripheral tissues including lymphocytes and monocytes, suggesting a role of NMU in immunoregulation. However, the functions of NMU in peripheral tissues have not been clarified. In this study, using NMU-deficient mice, we first demonstrated that NMU plays an important role in mast cell-mediated inflammation. Complete Freund's adjuvant-induced mast cell degranulation as well as edema and neutrophil infiltration, which occurred weakly in mast cell–deficient WBB6F1-W/Wv mice, did not occur in NMU-deficient mice. Moreover, intraplantar injection of NMU into paws induced early inflammatory responses such as mast cell degranulation, vasodilation, and plasma extravasation in WT mice but not in WBB6F1-W/Wv mice. NMU-R1 was highly expressed in primary mast cells, and NMU induced Ca2+ mobilization and degranulation in peritoneal mast cells. These data indicate that NMU promotes mast cell–mediated inflammation; therefore, NMU receptor antagonists could be a novel target for pharmacological inhibition of mast cell–mediated inflammatory diseases.
Potentiation of TRPM7 Inward Currents by Protons
Authors: Jiang Jianmin , Li Mingjiang , Yue Lixia
Published: July 2005

TRPM7 is unique in being both an ion channel and a protein kinase. It conducts a large outward current at +100 mV but a small inward current at voltages ranging from −100 to −40 mV under physiological ionic conditions. Here we show that the small inward current of TRPM7 was dramatically enhanced by a decrease in extracellular pH, with an ∼10-fold increase at pH 4.0 and 1–2-fold increase at pH 6.0. Several lines of evidence suggest that protons enhance TRPM7 inward currents by competing with Ca2+ and Mg2+ for binding sites, thereby releasing blockade of divalent cations on inward monovalent currents. First, extracellular protons significantly increased monovalent cation permeability. Second, higher proton concentrations were required to induce 50% of maximal increase in TRPM7 currents when the external Ca2+ and Mg2+ concentrations were increased. Third, the apparent affinity for Ca2+ and Mg2+ was significantly diminished at elevated external H+ concentrations. Fourth, the anomalous-mole fraction behavior of H+ permeation further suggests that protons compete with divalent cations for binding sites in the TRPM7 pore. Taken together, it appears that at physiological pH (7.4), Ca2+ and Mg2+ bind to TRPM7 and inhibit the monovalent cationic currents; whereas at high H+ concentrations, the affinity of TRPM7 for Ca2+ and Mg2+ is decreased, thereby allowing monovalent cations to pass through TRPM7. Furthermore, we showed that the endogenous TRPM7-like current, which is known as Mg2+-inhibitable cation current (MIC) or Mg nucleotide–regulated metal ion current (MagNuM) in rat basophilic leukemia (RBL) cells was also significantly potentiated by acidic pH, suggesting that MIC/MagNuM is encoded by TRPM7. The pH sensitivity represents a novel feature of TRPM7 and implies that TRPM7 may play a role under acidic pathological conditions.
Structural, interfacial and optical characterization of ultrathin zirconia film grown by in situ thermal oxidation of sputtered metallic Zr films
Authors: He G , Fang Q , Zhang J X , Zhu L Q , Liu M , Zhang L D
Published: July 2005

High dielectric constant ZrO2gate dielectric thin films have been prepared by means ofin situthermal oxidation of sputtered metallic Zr films. XRD reveals that the as-oxidized samples are amorphous, but can be made polycrystalline with a highly ()-preferential orientation by increasing the annealing temperature. AFM measurements confirm that high temperature annealing results in increase of the roughness root mean square value of the films. The growth and properties of the interfacial SiO2layer formed at the ZrO2/Si interface are observed by using Fourier transform infrared spectroscopy. It has been found that the formation of the interfacial layer depends on the post-deposition annealing temperature. On the basis of a parametrized Tauc–Lorentz dispersion model, the optical properties of the as-oxidized and annealed films related to the annealing temperature are systematically investigated by spectroscopic ellipsometry. The increase in the refractive index and decrease in extinction coefficient with increase of the annealing temperature are discussed in detail.
A geometric mechanism for diffusion in Hamiltonian systems overcoming the large gap problem: Announcement of results
Authors: Delshams Amadeu , de la Llave Rafael , Seara Tere
Published: July 2005

We present a geometric mechanism for diffusion in Hamiltonian systems. We also present tools that allow us to verify it in a concrete model. In particular, we verify it in a system which presents thelarge gap problem.
Some presentations for \overline{Γ}₀(𝑁)
Authors: Lascurain Orive Antonio
Published: July 2005

Some presentations of the Fuchsian groups defined by the Hecke congruence subgroups
\[
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="normal upper Gamma 0 left-parenthesis upper N right-parenthesis equals StartSet Start 1 By 3 Matrix 1st Row 1st Column a 2nd Column a m p semicolon b c 3rd Column a m p semicolon d EndMatrix element-of upper S upper L left-parenthesis 2 comma double-struck upper Z right-parenthesis vertical-bar c identical-to 0 mod upper N EndSet">

Γ

0

(
N
)

=

{

(

a

a
m
p
;
b
c

a
m
p
;
d

)

∈
S
L
(
2
,

Z

)

|

c
≡
0

mod

N
}

\Gamma _{0}( N)\;=\; \left \{\begin {pmatrix} a& b c& d \end {pmatrix} \in SL(2,\mathbb {Z})\;\Big {|} \;\; c\equiv 0\;\; \text {mod}\; N \right \}

\]
are given. The first is one obtained by the Reidemeister-Schreier rewriting process, thereby completing and correcting Chuman’s work on the subject. The main result (Theorem 3) is the reduction of this huge presentation into another one which is simple and useful. In the process,

Z

N

\mathbb {Z}_N

is partitioned into three subsets that exhibit many cyclic and dual properties of its ring structure. For some cases, a minimal presentation derived from the Ford domains is given explicitly in terms of the units and its inverses.
Embryonic endothelial progenitor cells expressing a broad range of proangiogenic and remodeling factors enhance vascularization and tissue recovery in acute and chronic ischemia
Authors: Kupatt Christian , Horstkotte Jan , Vlastos Georgios A. , Pfosser Achim , Lebherz Corinna , Semisch Matthias , Thalgott Mark , Büttner Kerstin , Browarzyk Christian , Mages Jörg , Hoffmann Reinhard , Deten Alexander , Lamparter Mathias , Müller Fabian , Beck Heike , Büning Hildegard , Boekstegers Peter , Hatzopoulos Antonis K.
Published: July 2005

Clonal embryonic endothelial progenitor cells (eEPCs) isolated from embryonic day 7.5 mice home specifically to hypoxic areas in mouse tumor metastases but spare normal organs and do not form carcinomas. Based on these results, we assessed the potential of eEPCs to enhance vascularization and limit organ dysfunction after ischemia in syngenic and xenotypic organisms. The angiogenic potential of eEPCs was evaluated in chronic ischemic rabbit hindlimbs after regional application by retroinfusion. eEPC treatment improved limb perfusion, paralleled by an increase in capillary density and collateral blood vessel number. Systemic eEPC infusion into mice after ischemic cardiac insult increased postischemic heart output measured by a marked improvement in left ventricle developed pressure and both systolic and diastolic functions. In vitro, eEPCs strongly induced vascular outgrowths from aortic rings. To address the molecular basis of this intrinsic angiogenic potential, we investigated the eEPC transcriptome. Genomewide Affymetrix GeneChip analysis revealed that the eEPCs express a wealth of secreted factors known to induce angiogenesis, tissue remodeling, and organogenesis that may contribute to the eEPC‐mediated beneficial effects. Our findings show that eEPCs induce blood vessel growth and cardioprotection in severe ischemic conditions providing a readily available source to study the mechanisms of neovascularization and tissue recovery.
Hepatitis C virus envelope proteins regulate CHOP via induction of the unfolded protein response
Authors: Chan Shiu‐Wan , Egan Philip Anthony
Published: July 2005

Unfolded protein response (UPR) is a cellular adaptive response that functions to reduce stress caused by malfolded proteins in the endoplasmic reticulum (ER). UPR can be induced under physiological or pathological conditions and is responsible for the pathogenesis of many human diseases. Hepatitis C virus (HCV) is a single‐stranded, positive‐sense RNA virus causing chronic diseases. Its genome encodes two envelope proteins E1 and E2, which mature in the ER to form a noncovalently bound, native complex and disulfide aggregates and have previously been shown to induce expression of the molecular chaperone immunoglobulin heavy chain binding protein. In this study, we show that HCV envelope protein expression regulates another stress indicator CCAAT/enhancer‐binding protein‐homologous protein (CHOP). The ER‐stress element and the activating transcription factor 4 element in the CHOP promoter were activated to a similar extent by HCV envelope protein expression. Using mouse embryonic fibroblasts deficient in the ER stress kinase RNA‐activated protein kinase‐like ER‐resident kinase (PERK), we showed that PERK was necessary and sufficient for activating the CHOP promoter. Expression of HCV E1 and/or E2 also induced splicing of X‐box binding protein 1 and transactivation of the unfolded protein response element, leading to the speculation that HCV E1 and E2 not only regulate the UPR but also ER‐associated degradation.
The first true obligately syntrophic propionate-oxidizing bacterium, Pelotomaculum schinkii sp. nov., co-cultured with Methanospirillum hungatei, and emended description of the genus Pelotomaculum
Authors: de Bok Frank A. M. , Harmsen Hermie J. M. , Plugge Caroline M. , de Vries Maaike C. , Akkermans Antoon D. L. , de Vos Willem M. , Stams Alfons J. M.
Published: July 2005

A Gram-positive, spore-forming, syntrophic propionate-oxidizing bacterium,Pelotomaculum schinkiisp. nov. strain HHT, was isolated as a co-culture withMethanospirillum hungateiJF-1Tfrom anaerobic, freeze-dried granular sludge obtained from an upflow anaerobic sludge bed reactor treating sugar beet wastewater. The bacterium converted propionate to acetate in co-culture withMethanospirillum hungateiJF-1TorMethanobacterium formicicumMFNT, but not in co-culture withMethanobrevibacter arboriphilusAZ. The organism could not be cultured axenically with any of the substrates tested and therefore can be considered as a (the first) true anaerobic syntrophic bacterium. The bacterium contained two distinct 16S rRNA gene sequences, with 96·8 % sequence similarity, which were both expressed during syntrophic growth on propionate as revealed by fluorescentin situhybridization. The most closely related organisms areCryptanaerobacter phenolicusLR7.2T, a bacterium that transforms phenol into benzoate, andPelotomaculum thermopropionicumSIT, a thermophilic, syntrophic propionate-oxidizing bacterium. Other related species belong to the Gram-positive, sulfate-reducing genusDesulfotomaculum. The type strain ofPelotomaculum schinkiiis strain HHT(=ATCC BAA-615T=DSM 15200T).
Emended description of Pasteuria nishizawae
Authors: Noel Gregory R. , Atibalentja N. , Domier Leslie L.
Published: July 2005

The description of the Gram-positive, obligately parasitic, mycelial and endospore-forming bacterium, Pasteuria nishizawae, is emended to include additional observations on the life cycle, host specificity and endospore morphology. The nucleotide sequence of the 16S rRNA gene is also provided.
Genetic diversity and phylogeny of rhizobia isolated from agroforestry legume species in southern Ethiopia
Authors: Wolde-meskel Endalkachew , Terefework Zewdu , Frostegård Åsa , Lindström Kristina
Published: July 2005

The genetic diversity within 195 rhizobial strains isolated from root nodules of 18 agroforestry species (15 woody and three herbaceous legumes) growing in diverse ecoclimatic zones in southern Ethiopia was investigated by using PCR–RFLP of the ribosomal operon [16S rRNA gene, 23S rRNA gene and the internal transcribed spacer (ITS) region between the 16S rRNA and 23S rRNA genes] and 16S rRNA gene partial sequence (800 and 1350 bp) analyses. All of the isolates and the 28 reference strains could be differentiated by using these methods. The size of the ITS varied among test strains (500–1300 bp), and 58 strains contained double copies. UPGMA dendrograms generated from cluster analyses of the 16S and 23S rRNA gene PCR–RFLP data were in good agreement, and the combined distance matrices delineated 87 genotypes, indicating considerable genetic diversity among the isolates. Furthermore, partial sequence analysis of 67 representative strains revealed 46 16S rRNA gene sequence types, among which 12 were 100 % similar to those of previously described species and 34 were novel sequences with 94–99 % similarity to those of recognized species. The phylogenetic analyses suggested that strains indigenous to Ethiopia belonged to the genera Agrobacterium, Bradyrhizobium, Mesorhizobium, Methylobacterium, Rhizobium and Sinorhizobium. Many of the rhizobia isolated from previously uninvestigated indigenous woody legumes had novel 16S rRNA gene sequences and were phylogenetically diverse. This study clearly shows that the characterization of symbionts of unexplored legumes growing in previously unexplored biogeographical areas will reveal additional diversity.
Paucibacter toxinivorans gen. nov., sp. nov., a bacterium that degrades cyclic cyanobacterial hepatotoxins microcystins and nodularin
Authors: Rapala Jarkko , Berg Katri A. , Lyra Christina , Niemi R. Maarit , Manz Werner , Suomalainen Sini , Paulin Lars , Lahti Kirsti
Published: July 2005

Thirteen bacterial isolates from lake sediment, capable of degrading cyanobacterial hepatotoxins microcystins and nodularin, were characterized by phenotypic, genetic and genomic approaches. Cells of these isolates were Gram-negative, motile by means of a single polar flagellum, oxidase-positive, weakly catalase-positive and rod-shaped. According to phenotypic characteristics (carbon utilization, fatty acid and enzyme activity profiles), the G+C content of the genomic DNA (66·1–68·0 mol%) and 16S rRNA gene sequence analysis (98·9–100 % similarity) the strains formed a single microdiverse genospecies that was most closely related to Roseateles depolymerans (95·7–96·3 % 16S rRNA gene sequence similarity). The isolates assimilated only a few carbon sources. Of the 96 carbon sources tested, Tween 40 was the only one used by all strains. The strains were able to mineralize phosphorus from organic compounds, and they had strong leucine arylamidase and chymotrypsin activities. The cellular fatty acids identified from all strains were C16 : 0 (9·8–19 %) and C17 : 1
ω7c (<1–5·8 %). The other predominant fatty acids comprised three groups: summed feature 3 (<1–2·2 %), which included C14 : 0 3-OH and C16 : 1 iso I, summed feature 4 (54–62 %), which included C16 : 1
ω7c and C15 : 0 iso OH, and summed feature 7 (8·5–28 %), which included ω7c, ω9c and ω12t forms of C18 : 1. A more detailed analysis of two strains indicated that C16 : 1
ω7c was the main fatty acid. The phylogenetic and phenotypic features separating our strains from recognized bacteria support the creation of a novel genus and species, for which the name Paucibacter toxinivorans gen. nov., sp. nov. is proposed. The type strain is 2C20T (=DSM 16998T=HAMBI 2767T=VYH 193597T).
Algoriphagus locisalis sp. nov., isolated from a marine solar saltern
Authors: Yoon Jung-Hoon , Kang So-Jung , Oh Tae-Kwang
Published: July 2005

Two Gram-negative, rod-shaped, non-motile bacterial strains, MSS-170T and MSS-171, were isolated from sea water of a marine solar saltern of the Yellow Sea, Korea, and characterized by using a polyphasic taxonomic approach. The two isolates grew optimally at 30 °C and in the presence of 2 % (w/v) NaCl. They were characterized chemotaxonomically as having MK-7 as the predominant menaquinone and major amounts of fatty acids iso-C15 : 0 and C16 : 1
ω7c and/or iso-C15 : 0 2-OH. The DNA G+C content of each of the two strains was 42 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the two strains fall within the evolutionary radiation enclosed by the genus Algoriphagus. Strains MSS-170T and MSS-171 had identical 16S rRNA gene sequences and exhibited a mean DNA–DNA relatedness level of 93 %. The two strains exhibited 16S rRNA gene sequence similarity levels of 96·4–98·9 % with respect to the type strains of recognized Algoriphagus species. DNA–DNA relatedness levels between the two strains and the type strains of six Algoriphagus species were less than 35 %. On the basis of phenotypic data and phylogenetic and genetic distinctiveness, strains MSS-170T and MSS-171 were classified in the genus Algoriphagus as members of a novel species, for which the name Algoriphagus locisalis sp. nov. is proposed. The type strain is MSS-170T (=KCTC 12310T=JCM 12597T).
Roseovarius crassostreae sp. nov., a member of the Roseobacter clade and the apparent cause of juvenile oyster disease (JOD) in cultured Eastern oysters
Authors: Boettcher Katherine J. , Geaghan Kara K. , Maloy Aaron P. , Barber Bruce J.
Published: July 2005

An α-proteobacterium has been identified which is believed to be the causative agent of juvenile oyster disease (JOD). Since its first isolation in 1997, the bacterium has been recovered as the numerically dominant species from JOD-affected animals throughout the north-eastern United States (Maine, New York and Massachusetts). Colonies are usually beige to pinkish-beige, although the majority of isolates recovered in 2003 from an epizootic in Martha's Vineyard, Massachusetts, produce colonies with a greenish-yellow appearance. The cells are Gram-negative, aerobic, strictly marine and rod or ovoid in appearance. They are actively motile by one or two flagella, but cells are also observed to produce tufts of polar fimbriae. The principal fatty acid in whole cells is C18 : 1
ω7c and other characteristic fatty acids are C16 : 0, C10 : 0 3-OH, 11-methyl C18 : 1
ω7c and C18 : 0. Almost without exception, isolates have 16S rRNA gene sequences that are 100 % identical to each other. Phylogenetic analyses place the organism within the Roseobacter clade of the α-Proteobacteria, with moderate bootstrap support for inclusion in the genus Roseovarius. DNA–DNA relatedness values from pairwise comparisons of this organism with the type species of the genus (Roseovarius tolerans) and the only other described species in this genus, Roseovarius nubinhibens, were 11 and 47 %, respectively. Phenotypic and biochemical dissimilarities also support the assignment of this bacterium to a novel species. The name Roseovarius crassostreae sp. nov. is proposed, with the type strain CV919-312T (=ATCC BAA-1102T=DSM 16950T).
Isoptericola hypogeus sp. nov., isolated from the Roman catacomb of Domitilla
Authors: Groth Ingrid , Schumann Peter , Schütze Barbara , Gonzalez Juan M. , Laiz Leonila , Saiz-Jimenez Cesareo , Stackebrandt Erko
Published: July 2005

In order to clarify the taxonomic position of an actinobacterium from the Roman catacomb of Domitilla, a combination of phenotypic characterization, phylogenetic analysis based on the 16S rRNA gene sequence and DNA–DNA relatedness studies was used. The results from the polyphasic taxonomic study of this organism showed that strain HKI 0342T(=DSM 16849T=NCIMB 14033T) should be considered as the type strain of a novel species of the genusIsoptericola, for which the nameIsoptericola hypogeussp. nov. is proposed.
Saturnispora hagleri sp. nov., a yeast species isolated from Drosophila flies in Atlantic rainforest in Brazil
Authors: Morais Paula B. , Lachance Marc-André , Rosa Carlos A.
Published: July 2005

Six strains representing a novel yeast species belonging to the genus Saturnispora were isolated from two species of the Drosophila fasciola subgroup (Drosophila repleta group) in an Atlantic rainforest site in Rio de Janeiro State, Brazil. Four strains were isolated from crops and one from external parts of Drosophila cardinae. The other strain was isolated from external parts of Drosophila fascioloides. Analysis of the D1/D2 large-subunit rDNA sequences indicated that the novel species is closely related to Saturnispora dispora. The name Saturnispora hagleri sp. nov. is proposed to accommodate these strains. The type strain is UFMG-55T (=CBS 10007T=NRRL Y-27828T).
Munich Information Center for Protein Sequences Plant Genome Resources. A Framework for Integrative and Comparative Analyses
Authors: Schoof Heiko , Spannagl Manuel , Yang Li , Ernst Rebecca , Gundlach Heidrun , Haase Dirk , Haberer Georg , Mayer Klaus F.X.
Published: July 2005

With several plant genomes sequenced, the power of comparative genome analysis can now be applied. However, genome-scale cross-species analyses are limited by the effort for data integration. To develop an integrated cross-species plant genome resource, we maintain comprehensive databases for model plant genomes, including Arabidopsis (Arabidopsis thaliana), maize (Zea mays), Medicago truncatula, and rice (Oryza sativa). Integration of data and resources is emphasized, both in house as well as with external partners and databases. Manual curation and state-of-the-art bioinformatic analysis are combined to achieve quality data. Easy access to the data is provided through Web interfaces and visualization tools, bulk downloads, and Web services for application-level access. This allows a consistent view of the model plant genomes for comparative and evolutionary studies, the transfer of knowledge between species, and the integration with functional genomics data.
The alc-GR System. A Modified alc Gene Switch Designed for Use in Plant Tissue Culture
Authors: Roberts Gethin R. , Garoosi G. Ali , Koroleva Olga , Ito Masaki , Laufs Patrick , Leader David J. , Caddick Mark X. , Doonan John H. , Tomsett A. Brian
Published: July 2005

The ALCR/alcA (alc) two-component, ethanol-inducible gene expression system provides stringent control of transgene expression in genetically modified plants. ALCR is an ethanol-activated transcription factor that can drive expression from the ALCR-responsive promoter (alcA). However, the alc system has been shown to have constitutive expression when used in plant callus or cell suspension cultures, possibly resulting from endogenous inducer produced in response to lowered oxygen availability. To widen the use of the alc system in plant cell culture conditions, the receptor domain of the rat glucocorticoid receptor (GR) was translationally fused to the C terminus of ALCR to produce ALCR-GR, which forms the basis of a glucocorticoid-inducible system (alc-GR). The alc-GR switch system was tested in tobacco (Nicotiana tabacum) Bright Yellow-2 suspension cells using a constitutively expressed ALCR-GR with four alternative alcA promoter-driven reporter genes: β-glucuronidase, endoplasmic reticulum-targeted green fluorescent protein, haemagglutinin, and green fluorescent protein-tagged Arabidopsis (Arabidopsis thaliana) Arath;CDKA;1 cyclin-dependent kinase. Gene expression was shown to be stringently dependent on the synthetic glucocorticoid dexamethasone and, in cell suspensions, no longer required ethanol for induction. Thus, the alc-GR system allows tight control of alcA-driven genes in cell culture and complements the conventional ethanol switch used in whole plants.
Metabolic Engineering of Isoflavonoid Biosynthesis in Alfalfa
Authors: Deavours Bettina E. , Dixon Richard A.
Published: July 2005

The potential health benefits of dietary isoflavones have generated considerable interest in engineering the synthesis of these phytoestrogens into plants. Genistein glucoside production (up to 50 nmol g−1 fresh weight) was engineered in alfalfa (Medicago sativa) leaves by constitutive expression of isoflavone synthase from Medicago truncatula (MtIFS1). Glucosides of biochanin A (4′-O-methylgenistein) and pratensein (3′-hydroxybiochanin A) also accumulated. Although MtIFS1 was highly expressed in all organs examined, genistein accumulation was limited to leaves. MtIFS1-expressing lines accumulated several additional isoflavones, including formononetin and daidzein, in response to UV-B or Phoma medicaginis, whereas the chalcone and flavanone precursors of these compounds accumulated in control lines. Enhanced accumulation of the phytoalexin medicarpin was observed in P. medicaginis-infected leaves of MtIFS1-expressing plants. Microarray profiling indicated that MtIFS1 expression does not significantly alter global gene expression in the leaves. Our results highlight some of the challenges associated with metabolic engineering of plant natural products, including tissue-specific accumulation, potential for further modification by endogenous enzyme activities (hydroxylation, methylation, and glycosylation), and the differential response of engineered plants to environmental factors.
OsPTF1, a Novel Transcription Factor Involved in Tolerance to Phosphate Starvation in Rice
Authors: Yi Keke , Wu Zhongchang , Zhou Jie , Du Liming , Guo Longbiao , Wu Yunrong , Wu Ping
Published: July 2005

We report here on a novel transcription factor with a basic helix-loop-helix domain for tolerance to inorganic phosphate (Pi) starvation in rice (Oryza sativa). The gene is designated OsPTF1. The expression of OsPTF1 is Pi starvation induced in roots while constitutively expressed in shoots, as shown by northern-blot analysis. Overexpression of OsPTF1 enhanced tolerance to Pi starvation in transgenic rice. Tillering ability, root and shoot biomass, and phosphorus content of transgenic rice plants were about 30% higher than those of the wild-type plants in Pi-deficient conditions in hydroponic experiments. In soil pot and field experiments, more than 20% increase in tiller number, panicle weight, and phosphorus content was observed in transgenic plants compared to wild-type plants at low-Pi levels. In Pi-deficient conditions, transgenic rice plants showed significantly higher total root length and root surface area, which results in a higher instantaneous Pi uptake rate over their wild-type counterparts. Microarray analysis for transgenic plants overexpressing OsPTF1 has been performed to investigate the downstream regulation of OsPTF1.
Effects of Calreticulin on Viral Cell-to-Cell Movement
Authors: Chen Min-Huei , Tian Guo-Wei , Gafni Yedidya , Citovsky Vitaly
Published: July 2005

Cell-to-cell tobacco mosaic virus movement protein (TMV MP) mediates viral spread between the host cells through plasmodesmata. Although several host factors have been shown to interact with TMV MP, none of them coresides with TMV MP within plasmodesmata. We used affinity purification to isolate a tobacco protein that binds TMV MP and identified it as calreticulin. The interaction between TMV MP and calreticulin was confirmed in vivo and in vitro, and both proteins were shown to share a similar pattern of subcellular localization to plasmodesmata. Elevation of the intracellular levels of calreticulin severely interfered with plasmodesmal targeting of TMV MP, which, instead, was redirected to the microtubular network. Furthermore, in TMV-infected plant tissues overexpressing calreticulin, the inability of TMV MP to reach plasmodesmata substantially impaired cell-to-cell movement of the virus. Collectively, these observations suggest a functional relationship between calreticulin, TMV MP, and viral cell-to-cell movement.
Control of Root Cap Formation by MicroRNA-Targeted Auxin Response Factors in Arabidopsis
Authors: Wang Jia-Wei , Wang Ling-Jian , Mao Ying-Bo , Cai Wen-Juan , Xue Hong-Wei , Chen Xiao-Ya
Published: July 2005

The plant root cap mediates the direction of root tip growth and protects internal cells. Root cap cells are continuously produced from distal stem cells, and the phytohormone auxin provides position information for root distal organization. Here, we identify the Arabidopsis thaliana auxin response factors ARF10 and ARF16, targeted by microRNA160 (miR160), as the controller of root cap cell formation. The Pro35S:MIR160 plants, in which the expression of ARF10 and ARF16 is repressed, and the arf10-2 arf16-2 double mutants display the same root tip defect, with uncontrolled cell division and blocked cell differentiation in the root distal region and show a tumor-like root apex and loss of gravity-sensing. ARF10 and ARF16 play a role in restricting stem cell niche and promoting columella cell differentiation; although functionally redundant, the two ARFs are indispensable for root cap development, and the auxin signal cannot bypass them to initiate columella cell production. In root, auxin and miR160 regulate the expression of ARF10 and ARF16 genes independently, generating a pattern consistent with root cap development. We further demonstrate that miR160-uncoupled production of ARF16 exerts pleiotropic effects on plant phenotypes, and miR160 plays an essential role in regulating Arabidopsis development and growth.
Actin-Related Protein2/3 Complex Component ARPC1 Is Required for Proper Cell Morphogenesis and Polarized Cell Growth inPhyscomitrella patens
Authors: Harries Phillip A. , Pan Aihong , Quatrano Ralph S.
Published: July 2005

The actin-related protein2/3 (Arp2/3) complex functions as a regulator of actin filament dynamics in a wide array of eukaryotic cells. Here, we focus on the role of the Arp2/3 complex subunit ARPC1 in elongating tip cells of protonemal filaments of the moss Physcomitrella patens. Using RNA interference (RNAi) to generate loss-of-function mutants, we show dramatic defects in cell morphology manifested as short, irregularly shaped cells with abnormal division patterns. The arpc1 RNAi plants lack the rapidly elongating caulonemal cell type found in wild-type protonemal tissue. The absence of this cell type prevents normal bud formation even in response to cytokinin treatment and results in filamentous colonies lacking leafy gametophores. In addition, arpc1 protoplasts show an increased sensitivity to osmotic shock and are defective in their ability to properly establish a polarized outgrowth during regeneration from a single cell. This failure of arpc1 protoplasts to undergo proper tip growth is rescued by ARPC1 overexpression and is phenocopied in wild-type protoplasts treated with Latrunculin B, a potent inhibitor of actin polymerization. We show in moss that ARPC1, and by inference the Arp2/3 complex, plays a critical role in controlling polarized growth and cell division patterning through its regulation of actin dynamics at the cell apex.
The Putative RNA-Dependent RNA PolymeraseRDR6Acts Synergistically withASYMMETRIC LEAVES1and2to RepressBREVIPEDICELLUSand MicroRNA165/166 in Arabidopsis Leaf Development
Authors: Li Hong , Xu Lin , Wang Hua , Yuan Zheng , Cao Xiaofeng , Yang Zhongnan , Zhang Dabing , Xu Yuquan , Huang Hai
Published: July 2005

The Arabidopsis thaliana  ASYMMETRIC LEAVES1 (AS1) and AS2 genes are important for repressing class I KNOTTED1-like homeobox (KNOX) genes and specifying leaf adaxial identity in leaf development. RNA-dependent RNA polymerases (RdRPs) are critical for posttranscriptional and transcriptional gene silencing in eukaryotes; however, very little is known about their functions in plant development. Here, we show that the Arabidopsis RDR6 gene (also called SDE1 and SGS2) that encodes a putative RdRP, together with AS1 and AS2, regulates leaf development. rdr6 single mutant plants displayed only minor phenotypes, whereas rdr6 as1 and rdr6 as2 double mutants showed dramatically enhanced as1 and as2 phenotypes, with severe defects in the leaf adaxial-abaxial polarity and vascular development. In addition, the double mutant plants produced more lobed leaves than the as1 and as2 single mutants and showed leaf-like structures associated on a proportion of leaf blades. The abnormal leaf morphology of the double mutants was accompanied by an extended ectopic expression of a class I KNOX gene BREVIPEDICELLUS (BP) and high levels of microRNA165/166 that may lead to mRNA degradation of genes in the class III HD-ZIP family. Taken together, our data suggest that the Arabidopsis RDR6-associated epigenetic pathway and the AS1-AS2 pathway synergistically repress BP and MIR165/166 for proper plant development.
Safety and tolerability of antagonist anti‐human CD40 Mab ch5D12 in patients with moderate to severe Crohn's disease
Authors: KASRAN A. , BOON L. , WORTEL C. H. , van HOGEZAND R. A. , SCHREIBER S. , GOLDIN E. , DE BOER M. , GEBOES K. , RUTGEERTS P. , CEUPPENS J. L.
Published: July 2005

Background:  The ligation of CD40 by CD154 is a critical step in the interaction between APC and T cells. In animals, antagonizing CD40L‐CD40 has been shown to reduce the severity of several autoimmune and inflammatory disorders, including experimental colitis.

Aim:  To investigate tolerability and safety of an antagonist chimeric monoclonal anti‐human CD40 antibody (ch5D12) for treatment of Crohn's disease.

Method:  ch5D12 was administrated to 18 patients with moderate to severe Crohn's disease in a single dose, open‐label dose‐escalation phase I/IIa study.

Results:  ch5D12 plasma concentrations increased dose‐dependently after infusion. Two patients developed an anti‐ch5D12 antibody response. Overall response and remission rates were 72 and 22%, respectively with no evidence for a dose–response effect. Treatment with ch5D12 reduced microscopic disease activity and intensity of the lamina propria cell infiltrate, but did not alter percentages of circulating T and B cells. ch5D12 was well tolerated, although some patients experienced headache, muscle aches, or joint pains, which may have been related to the study drug.

Conclusions:  Antagonizing CD154–CD40 interactions with ch5D12 is a promising therapeutic approach for remission induction in Crohn's disease.
The impact of major depressive disorder on the short‐ and long‐term outcome of Crohn's disease treatment with infliximab
Authors: PERSOONS P. , VERMEIRE S. , DEMYTTENAERE K. , FISCHLER B. , VANDENBERGHE J. , VAN OUDENHOVE L. , PIERIK M. , HLAVATY T. , VAN ASSCHE G. , NOMAN M. , RUTGEERTS P.
Published: July 2005

Background:  Major depressive disorder is the most common psychiatric diagnosis in Crohn's disease. In other chronic diseases, evidence suggests that depression influences the course of the disease. Strong evidence of such a mediating role of major depressive disorder in Crohn's disease has never been found.

Aim:  To assess the relationship between major depressive disorder and outcome of treatment of luminal Crohn's disease with infliximab.

Methods:  In this prospective study, 100 consecutive unselected patients underwent assessment of psychosocial, demographical disease‐related biological and clinical parameters at baseline and at 4 weeks after infliximab. Major depressive disorder was diagnosed using the Patient Health Questionnaire. Subsequently, the patients were followed up clinically until the next flare or during 9 months.

Results:  The Crohn's disease responded in 75% of the patients, and remission was achieved in 60%. The presence of major depressive disorder at baseline predicted a lower remission rate (OR = 0.166, 95% CI = 0.049–0.567, P = 0.004). At follow‐up, 88% of the patients needed retreatment. At univariate regression analysis, major depressive disorder significantly decreased time to retreatment (P = 0.001). Multivariate Cox regression confirmed major depressive disorder as an independent determinant of active disease both at baseline and at re‐evaluation (hazard ratio = 2.271, 95% CI: 1.36–3.79, P = 0.002).

Conclusion:  Major depressive disorder is a risk factor for failure to achieve remission with infliximab and for earlier retreatment in patients with active luminal Crohn's disease. Assessment and management of major depressive disorder should be part of the clinical approach to patients with Crohn's disease.
Upper gastrointestinal symptoms and therapies in elderly out‐patients, users of non‐selective NSAIDs or coxibs
Authors: PILOTTO A. , FRANCESCHI M. , VITALE D. F. , ZANINELLI A. , MASOTTI G. , RENGO F. ,   ON BEHALF OF F.I.R.I. (FONDAZIONE ITALIANA RICERCA SULL'INVECCHIAMENTO) AND THE SOFIA PROJECT INVESTIGATORS
Published: July 2005

Background:  The association between coxib or non‐steroidal anti‐inflammatory drug use with gastrointestinal symptoms and drug prescriptions in ambulatory elderly patients is not well defined.

Aim:  To evaluate the association between non‐steroidal anti‐inflammatory drug NSAID and coxib use with gastrointestinal symptoms and therapies in elderly subjects managed by their general practitioner.

Materials:  The study was carried out by 133 general practitioners in Italy. By using a structured interview, sex, age, physical function, current medications, new drug prescriptions and upper gastrointestinal symptoms were registered from all elderly subjects who were referred to their general practitioners during a 2‐week period. The numbers of hospitalizations, gastrointestinal bleeding events and gastrointestinal diagnostic procedures occurring during the last 6‐month period were recorded.

Results:  Included in this study were 5515 elderly subjects. The overall prevalence of drug use was 92%. Musculo‐skeletal drugs were taken by 15% of patients; NSAIDs were taken by 6%, and coxibs by 3% of patients. A significantly higher prevalence of upper gastrointestinal symptoms was observed in elderly NSAID users compared with coxib users and non‐users of musculo‐skeletal drugs (44% vs. 33% vs. 32% respectively, P = 0.001). The prescriptions of drugs for acid‐related disorders were significantly higher in patients who were concomitantly taking NSAID rather than coxibs (13% vs. 6%, P < 0.01). The prescriptions of drugs for acid‐related disorders were significantly associated with the presence of upper gastrointestinal symptoms (OR = 1.7, 95% CI = 1.6–1.9), previous gastrointestinal disorders (OR = 1.1, 95% CI = 1.0–1.3) and NSAID use (OR = 1.5, 95% CI = 1.0–2.2), but no coxib use.

Conclusion:  In this elderly population, upper gastrointestinal symptoms and prescriptions for gastroenterological drugs were higher in non‐steroidal anti‐inflammatory drug users than coxib users and non‐users of musculo‐skeletal drugs.
Successful percutaneous coronary intervention in a patient with severe haemophilia A using bivalirudin as the sole procedural anticoagulant
Authors: Krolick M. A.
Published: July 2005

Summary.  This article presents the case of a patient with severe haemophilia A who underwent successful multivessel percutaneous coronary intervention (PCI). Patients with haemophilia who are diagnosed with coronary artery disease (CAD) and require intervention present a challenge to doctors due to the high risks of bleeding. The patient was administered recombinant factor VIII pre‐ and post‐procedure. Anticoagulation during PCI was maintained with bivalirudin, a thrombin‐specific anticoagulant. There were no complications and the patient tolerated the procedure well. This case suggests that bivalirudin as the sole procedural anticoagulant can be safely used in patients with a very high risk of bleeding undergoing PCI.
The molecular analysis of haemophilia B: a guideline from the UK haemophilia centre doctors’ organization haemophilia genetics laboratory network
Authors: Mitchell M. , Keeney S. , Goodeve A.
Published: July 2005

Summary.  Haemophilia B is one of the most common inherited bleeding disorders and has a well understood pathophysiology. Our understanding of the molecular genetics of the disease has allowed the development of comprehensive carrier and prenatal diagnosis for this single gene disorder. Continuing technological developments improve our ability to provide genetic analysis in a rapid and cost‐effective manner. This guideline aims to provide advice on current best laboratory practice when approaching genetic diagnosis of haemophilia B.