bluuebunny/crossref_metadata_2025 huggingface dataset:
Ultrafast imaging of in vivo muscle contraction using ultrasound
Authors: Deffieux Thomas , Gennisson Jean-Luc , Tanter Mickaël , Fink Mathias , Nordez Antoine
Published: November 2006

In this letter, an innovative way of imaging transient and local shear vibrations of an in vivo contracting muscle is proposed. The principle is to use an ultrafast ultrasound scanner (up to 5000framess−1) able to follow with a submillimeter resolution the motion of the muscle tissue in a two dimensional plane. This ultrafast echographic imaging technique leads to both local and transient in vivo studies of the contraction of a muscle as reported by these first experiments done on the biceps brachii.
Time reversal of photoacoustic waves
Authors: Bossy Emmanuel , Daoudi Khalid , Boccara Albert-Claude , Tanter Mickael , Aubry Jean-François , Montaldo Gabriel , Fink Mathias
Published: November 2006

In this work, the authors use the photoacoustic effect to create a source for ultrasonic time-reversal experiments. Photoacoustic waves were generated by an optically absorbing gel sphere excited by a laser pulse in a highly optically diffusive solution and recorded with an ultrasound array controlled by a time-reversal electronics. The emission of the time-reversed photoacoustic waves allowed the refocusing of the ultrasound towards the optical absorber, in particular, in the presence of a strongly acoustically defocusing medium. The authors illustrate how the technique can be applied to perform acoustical imaging in the presence of a strong acoustical aberration.
Electrical transport and quasipersistent photocurrent in vanadium oxide nanowire networks
Authors: Park Jitae , Lee Eunmo , Lee Kyu Won , Lee Cheol Eui
Published: November 2006

Electrical conductivity and photoconductivity measurements were carried out on semiconducting vanadium oxide nanowire networks synthesized through the polycondensation of vanadic acid. The temperature-dependent conductivity was described well by Mott’s optical multiphonon assisted hopping model at high temperatures and by the variable-range hopping mechanism at low temperatures. The photoconductivity showed a weak temperature dependence. Besides, quasipersistent photocurrent with a single-exponential decay behavior was observed right after switching off the light and was explained in terms of the random local-potential fluctuation model.
Experimental evaluation of impact ionization coefficients in AlxGa1−xN based avalanche photodiodes
Authors: Tut Turgut , Gokkavas Mutlu , Butun Bayram , Butun Serkan , Ulker Erkin , Ozbay Ekmel
Published: November 2006

The authors report on the metal-organic chemical vapor deposition growth, fabrication, and characterization of high performance solar-blind avalanche photodetectors and the experimental evaluation of the impact ionization coefficients that are obtained from the photomultiplication data. A Schottky barrier, suitable for back and front illuminations, is used to determine the impact ionization coefficients of electrons and holes in an AlGaN based avalanche photodiode.
Effects of conical lids on vortex breakdown in an enclosed cylindrical chamber
Authors: Yu Peng , Lee Thong See , Zeng Yan , Low Hong Tong
Published: November 2006

The effects of the conical lids on vortex breakdown have been investigated numerically. The boundaries for the onset of vortex breakdown are plotted in terms of the Reynolds number, the aspect ratio H1∕R, where H1 is the height of the side wall, and the height ratio H2∕H1, where H2 is the height of the axis. The concave-cone lid (H2∕H1>1) delays or even completely suppresses vortex breakdown, while the convex-cone lid (H2∕H1<1) precipitates the onset of vortex breakdown. The attached bubbles were found in the chamber with the convex-cone lid at a smaller height ratio. The critical aspect ratio, below which vortex breakdown cannot occur, decreases with the increase of the height ratio. The results indicate that a conical lid can enlarge the vortex breakdown boundaries and this might be of practical interest when using this device for mixing. The results also suggest that the actual shape of the lid has an influence on suppressing or intensifying vortex breakdown.
Regulation of Endothelial Cell Barrier Function by Store‐Operated Calcium Entry
Authors: CIOFFI DONNA L. , STEVENS TROY
Published: November 2006

Transient receptor potential (TRP) channels fulfill important and diverse signaling functions, and are generally conserved among species. The canonical subfamily of TRP proteins, TRPC channels, possesses 7 isoforms that combine in various ways to form heteromultimers. In endothelium, TRPC1 and TRPC4 form subunits of a channel that selectively conducts calcium. This channel is activated by calcium depletion in the endoplasmic reticulum, and thus TRPC1/TRPC4 forms the molecular basis of a store operated calcium entry pathway. TRPC4 interacts with protein 4.1, which tethers the channel to the membrane skeleton and represents a gating mechanism required for calcium permeation. In response to inflammatory agonists such as thrombin and bradykinin, the generation of inositol 1,4,5‐trisphosphate transiently depletes endoplasmic reticulum calcium and activates the TRPC1/TRPC4 channel. Calcium permeation through this channel triggers cytoskeletal reorganization that is necessary to disrupt the endothelial cell barrier and increase permeability. Thus, inhibition of the TRPC1/TRPC4 channel provides a putative anti‐inflammatory strategy.
Plasma rotation and momentum transport studies at JET
Authors: de Vries P C , Rantamäki K M , Giroud C , Asp E , Corrigan G , Eriksson A , de Greef M , Jenkins I , Knoops H C M , Mantica P , Nordman H , Strand P , Tala T , Weiland J , Zastrow K-D
Published: November 2006

An experimental study in plasma rotation and momentum transport was carried out at JET. The toroidal rotation profile was found to scale approximately with that of the ion temperature. However, significant deviations from this were found in high density ELMy H-mode discharges, which had broader rotation profiles. A rotation database analysis showed the variation of the dimensionless Mach number with respect to the plasma scenario. For predominantly NBI heated discharges the Mach number was found to be in the range of 0.3–0.45. Larger Mach numbers were observed in type I ELMy H-modes, while scenarios exhibiting type III ELMs or L-mode had lower Mach numbers. Advanced scenarios often showed a significant increase in the central Mach number when an internal transport barrier formed. A detailed study was done to investigate the Prandtl number,Pr, defined as the ratio between momentum and ion heat diffusivity. Generally the Prandtl number was found to be significantly below unity, e.g. 0.18 <Pr< 0.35. Although it is often predicted that momentum and heat diffusivity are equal in ITG dominated plasma, also for high density ELMy H-mode discharges with temperature profiles close and above the ITG threshold, the Prandtl number wasPr∼ 0.3.
Efficacy of Static Magnetic Field for Locomotor Activity of Experimental Osteopenia
Authors: Taniguchi Norimasa , Kanai Shigeyuki
Published: November 2006

In order to examine the effectiveness of applying a static magnetic field (SMF) for increasing bone mineral density (BMD), we assessed the degree of osteopenia by dual‐energy X‐ray absorptiometry (DEXA), the metabolism measuring system, and histological examination of bone tissue in an ovariectomized (OVX) rat model. Thirty‐six female Wistar rats (8 weeks old, 160–180 g) were divided into three groups. The rats in the OVX‐M group were exposed to SMF for 12 weeks after ovariectomy. The ovariectomized rats in the OVX‐D group were not exposed to SMF as a control. The rats in the normal group received neither ovariectomy nor exposure to SMF. Twelve‐week exposure to SMF in the OVX‐M group inhibited the reduction in BMD that was observed in the OVX‐D group. Moreover, in the OVX rats, before exposure to SMF, there was no clear difference in the level of locomotor activity between the active and resting phases, and the pattern of locomotor activity was irregular. After exposure of OVX rats to SMF, the pattern of locomotor activity became diphasic with clear active and resting phases, as was observed in the normal group. In the OVX‐M group, the continuity of the trabecular bone was maintained more favorably and bone mass was higher than the respective parameters in the OVX‐D group. These results demonstrate that exposure to SMF increased the level of locomotor activity in OVX rats, thereby increasing BMD.
Quantitative measure of sexual selection with respect to the operational sex ratio: a comparison of selection indices
Authors: Mills Suzanne C , Grapputo Alessandro , Koskela Esa , Mappes Tapio
Published: November 2006

Despite numerous indices proposed to predict the evolution of mating systems, a unified measure of sexual selection has remained elusive. Three previous studies have compared indices of sexual selection under laboratory conditions. Here, we use a genetic study to compare the most widely used measures of sexual selection in natural populations. We explored the mating and reproductive successes of male and female bank voles,Clethrionomys glareolus, across manipulated operational sex ratios (OSRs) by genotyping all adult and pup bank voles on 13 islands using six microsatellite loci. We used Bateman's principles (IsandIand Bateman gradients) and selection coefficients (s′ andβ′) to evaluate, for the first time, the genetic mating system of bank voles and compared these measures with alternative indices of sexual selection (index of monopolization and Morisita's index) across the OSRs. We found that all the sexual selection indices show significant positive intercorrelations for both males and females, suggesting that Bateman's principles are an accurate and a valid measure of the mating system. The Bateman gradient, in particular, provides information over and above that of other sexual selection indices. Male bank voles show a greater potential for sexual selection than females, and Bateman gradients indicate a polygynandrous mating system. Selection coefficients reveal strong selection gradients on male bank vole plasma testosterone level rather than body size.
Spatial ability is impaired and hippocampal mineralocorticoid receptor mRNA expression reduced in zebra finches (
Taeniopygia guttata
) selected for acute high corticosterone response to stress
Authors: Hodgson Zoë G , Meddle Simone L , Roberts Mark L , Buchanan Katherine L , Evans Matthew R , Metzdorf Reinhold , Gahr Manfred , Healy Susan D
Published: November 2006

In mammals, stress hormones have profound influences on spatial learning and memory. Here, we investigated whether glucocorticoids influence cognitive abilities in birds by testing a line of zebra finches selectively bred to respond to an acute stressor with high plasma corticosterone (CORT) levels. Cognitive performance was assessed by spatial and visual one-trial associative memory tasks. Task performance in the high CORT birds was compared with that of the random-bred birds from a control breeding line. The birds selected for high CORT in response to an acute stressor performed less well than the controls in the spatial task, but there were no significant differences between the lines in performance during the visual task. The birds from the two lines did not differ in their plasma CORT levels immediately after the performance of the memory tasks; nevertheless, there were significant differences in peak plasma CORT between the lines. The high CORT birds also had significantly lower mineralocorticoid receptor mRNA expression in the hippocampus than the control birds. There was no measurable difference between the lines in glucocorticoid receptor mRNA density in either the hippocampus or the paraventricular nucleus. Together, these findings provide evidence to suggest that stress hormones have important regulatory roles in avian spatial cognition.
Spread of arbitrary conventions among chimpanzees: a controlled experiment
Authors: Bonnie Kristin E , Horner Victoria , Whiten Andrew , de Waal Frans B.M
Published: November 2006

Wild chimpanzees (Pan troglodytes) have a rich cultural repertoire—traditions common in some communities are not present in others. The majority of reports describe functional, material traditions, such as tool use. Arbitrary conventions have received far less attention. In the same way that observations of material culture in wild apes led to experiments to confirm social transmission and identify underlying learning mechanisms, experiments investigating how arbitrary habits or conventions arise and spread within a group are also required. The few relevant experimental studies reported thus far have relied on cross-species (i.e. human–ape) interaction offering limited ecological validity, and no study has successfully generated a tradition not involving tool use in an established group. We seeded one of two rewarded alternative endpoints to a complex sequence of behaviour in each of two chimpanzee groups. Each sequence spread in the group in which it was seeded, with many individuals unambiguously adopting the sequence demonstrated by a group member. In one group, the alternative sequence was discovered by a low ranking female, but was not learned by others. Since the action-sequences lacked meaning before the experiment and had no logical connection with reward, chimpanzees must have extracted both the form and benefits of these sequences through observation of others.
Foetal age determination and development in elephants
Authors: Hildebrandt Thomas , Drews Barbara , Gaeth Ann P , Goeritz Frank , Hermes Robert , Schmitt Dennis , Gray Charlie , Rich Peter , Streich Wolf Juergen , Short Roger V , Renfree Marilyn B
Published: November 2006

Elephants have the longest pregnancy of all mammals, with an average gestation of around 660 days, so their embryonic and foetal development have always been of special interest. Hitherto, it has only been possible to estimate foetal ages from theoretical calculations based on foetal mass. The recent development of sophisticated ultrasound procedures for elephants has now made it possible to monitor the growth and development of foetuses of known gestational age conceived in captivity from natural matings or artificial insemination. We have studied the early stages of pregnancy in 10 captive Asian and 9 African elephants by transrectal ultrasound. Measurements of foetal crown–rump lengths have provided the first accurate growth curves, which differ significantly from the previous theoretical estimates based on the cube root of foetal mass. We have used these to age 22 African elephant foetuses collected during culling operations. Pregnancy can be first recognized ultrasonographically by day 50, the presumptive yolk sac by about day 75 and the zonary placenta by about day 85. The trunk is first recognizable by days 85–90 and is distinct by day 104, while the first heartbeats are evident from around day 80. By combining ultrasonography and morphology, we have been able to produce the first reliable criteria for estimating gestational age and ontological development of Asian and African elephant foetuses during the first third of gestation.
Flavobacterium indicum sp. nov., isolated from warm spring water in Assam, India
Authors: Saha P. , Chakrabarti T.
Published: November 2006

A polyphasic taxonomic approach was employed to characterize a strain designated GPTSA100-9T, which was isolated from water sampled from a warm spring. The micro-organism, comprising Gram-negative, strictly aerobic rods, could not grow on nutritionally rich media such as tryptic soy broth. Analysis of the 16S rRNA gene sequence (1396 nt) of strain GPTSA100-9Trevealed that it is a member of the genusFlavobacterium, sharing 99.8 % sequence similarity with the CFB group bacterium strain A0653 (AF236016), 93.4 % with ‘[Flexibacter]aurantiacussubsp.excathedrus’ and 93.2–92.0 % withFlavobacterium saliperosum,Flavobacterium soli,Flavobacterium aquatileandFlavobacterium columnare. The G+C content of the genomic DNA was 31.0 mol%. The major fatty acids of the strain grown on modified R2A agar were iso-C15 : 0(18.5 %), iso-C15 : 1G (18.0 %), summed feature 3 (iso-C15 : 02-OH and/or C16 : 1ω7c, 16.6 %) and iso-C17 : 03-OH (9.0 %). On the basis of phenotypic and genotypic characteristics, strain GPTSA100-9Trepresents a novel species of the genusFlavobacterium, for which the nameFlavobacterium indicumsp. nov. is proposed. The type strain is GPTSA100-9T(=MTCC 6936T=DSM 17447T).
Burkholderia ginsengisoli sp. nov., a β-glucosidase-producing bacterium isolated from soil of a ginseng field
Authors: Kim Ho-Bin , Park Min-Ju , Yang Hee-Chan , An Dong-Shan , Jin Hai-Zhu , Yang Deok-Chun
Published: November 2006

A bacterial strain (designated KMY03T) that possesses β-glucosidase activity was isolated from soil from a ginseng field in South Korea and was characterized in order to determine its taxonomic position. The bacterium was found to comprise Gram-negative, rod-shaped, motile cells with unipolar polytrichous flagella. On the basis of 16S rRNA gene sequence similarity, strain KMY03T was shown to belong to the family Burkholderiaceae of the Betaproteobacteria, being most closely related to Burkholderia caledonica LMG 19076T (97.8 %), Burkholderia terricola LMG 20594T (97.5 %), Burkholderia xenovorans LMG 21463T (97.4 %) and Burkholderia phytofirmans LMG 22146T (97.3 %). Chemotaxonomic data (major ubiquinone, Q-8; major fatty acids, C17 : 0 cyclo, C16 : 0, C19 : 0 cyclo ω8c and summed feature 2) supported the affiliation of the novel strain with the genus Burkholderia. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed the strain to be differentiated genotypically and phenotypically from Burkholderia species with validly published names. On the basis of these data, strain KMY03T represents a novel species of the genus Burkholderia, for which the name Burkholderia ginsengisoli sp. nov. is proposed. The type strain is KMY03T (=KCTC 12389T=NBRC 100965T).
Ferrimonas futtsuensis sp. nov. and Ferrimonas kyonanensis sp. nov., selenate-reducing bacteria belonging to the Gammaproteobacteria isolated from Tokyo Bay
Authors: Nakagawa Tatsunori , Iino Takao , Suzuki Ken-ichiro , Harayama Shigeaki
Published: November 2006

Two novel mesophilic, facultatively anaerobic, selenate-reducing bacteria, designated strains FUT3661T and Asr22-7T, were isolated from a sediment sample and the alimentary tract of littleneck clams, respectively. Both sources of the samples were collected from the coast of Tokyo Bay, Japan. Cells were Gram-negative rods and motile by means of a polar flagellum. The strains reduced selenate to elemental selenium (Se0) and also reduced iron(III) oxyhydroxide, iron(III) citrate, arsenate, manganese(IV) oxide, elemental sulfur and oxygen and used lactate, pyruvate, yeast extract, tryptone and Casamino acids as electron donors and carbon sources. The strains contained both menaquinone (MK-7) and ubiquinones (Q-7 and Q-8) as isoprenoid quinones. The major fatty acids were C16 : 0 and C16 : 1
ω9c. The G+C content of the genomic DNA was 58.1 mol% for strain FUT3661T and 57.2 mol% for strain Asr22-7T. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strains were related to members of the genus Ferrimonas (<94.0 % similarities), although the two novel strains formed a separate lineage. 16S rRNA gene sequence similarity between strains FUT3661T and Asr22-7T was 96 %. On the basis of this polyphasic analysis, it was concluded that strains FUT3661T and Asr22-7T represent two novel species within the genus Ferrimonas, for which the names Ferrimonas futtsuensis sp. nov. (type strain FUT3661T=NBRC 101558T=DSM 18154T) and Ferrimonas kyonanensis sp. nov. (type strain Asr22-7T=NBRC 101286T=DSM 18153T) are proposed.
Rhizobium lusitanum sp. nov. a bacterium that nodulates Phaseolus vulgaris
Authors: Valverde Angel , Igual José M. , Peix Alvaro , Cervantes Emilio , Velázquez Encarna
Published: November 2006

The species Phaseolus vulgaris is a promiscuous legume nodulated by several species of the family Rhizobiaceae. During a study of rhizobia nodulating this legume in Portugal, we isolated several strains that nodulate P. vulgaris effectively and also Macroptilium atropurpureum and Leucaena leucocephala, but they form ineffective nodules in Medicago sativa. According to phylogenetic analysis of the 16S rRNA gene sequence, the strains from this study belong to the genus Rhizobium, with Rhizobium rhizogenes and Rhizobium tropici as the closest related species, with 99.9 and 99.2 % similarity, respectively, between the type strains of these species and strain P1-7T. The nodD and nifH genes carried by strain P1-7T are phylogenetically related to those of other species nodulating Phaseolus. This strain does not carry virulence genes present in the type strain of R. rhizogenes, ATCC 11325T. Analysis of the recA and atpD genes confirms this phylogenetic arrangement, showing low similarity with respect to those of R. rhizogenes ATCC 11325T (91.9 and 94.1 % similarity, respectively) and R. tropici IIB CIAT 899T (90.6 % and 91.8 % similarity, respectively). The intergenic spacer (ITS) of the strains from this study is phylogenetically divergent from those of R. rhizogenes ATCC 11235T and R. tropici CIAT 899T, with 85.9 and 82.8 % similarity, respectively, with respect to strain P1-7T. The tRNA profile and two-primer random amplified polymorphic DNA pattern of strain P1-7T are also different from those of R. rhizogenes ATCC 11235T and R. tropici CIAT 899T. The strains isolated in this study can be also differentiated from R. rhizogenes and R. tropici by several phenotypic characteristics. The results of DNA–DNA hybridization showed means of 28 and 25 % similarity between strain P1-7T and R. rhizogenes ATCC 11235T and R. tropici CIAT 899T, respectively. All these data showed that the strains isolated in this study belong to a novel species of the genus Rhizobium, for which we propose the name Rhizobium lusitanum sp. nov.; the type strain is P1-7T (=LMG 22705T=CECT 7016T).
Pedobacter ginsengisoli sp. nov., a DNase-producing bacterium isolated from soil of a ginseng field in South Korea
Authors: Ten Leonid N. , Liu Qing-Mei , Im Wan-Taek , Lee Myungjin , Yang Deok-Chun , Lee Sung-Taik
Published: November 2006

A Gram-negative, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated Gsoil 104T, was isolated from a soil sample from a ginseng field in Pocheon Province (South Korea) and was characterized taxonomically by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities, strain Gsoil 104Twas shown to belong to the familySphingobacteriaceae, being related toPedobacter africanusDSM 12126T(97.0 %),Pedobacter caeniLMG 22862T(96.9 %),Pedobacter cryoconitisDSM 14825T(96.8 %) andPedobacter heparinusDSM 2366T(96.6 %). The phylogenetic distance from any otherPedobacterspecies with a validly published name was greater than 3.4 % (i.e. <96.6 % 16S rRNA gene sequence similarity). DNA–DNA hybridization experiments showed that values for DNA–DNA relatedness between strain Gsoil 104Tand its phylogenetically closest neighbours were below 37 %. The G+C content of the genomic DNA was 43.6 mol%. The predominant respiratory quinone was MK-7. The major fatty acids were C16 : 1ω7c, iso-C15 : 0, C16 : 0, iso-C17 : 03-OH and iso-C15 : 02-OH. These chemotaxonomic data support the affiliation of strain Gsoil 104Tto the genusPedobacter. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 104Trepresents a novel species in the genusPedobacter, for which the namePedobacter ginsengisolisp. nov. is proposed. The type strain is Gsoil 104T(=KCTC 12576T=LMG 23399T).
Desulfotomaculum thermosubterraneum sp. nov., a thermophilic sulfate-reducer isolated from an underground mine located in a geothermally active area
Authors: Kaksonen Anna H. , Spring Stefan , Schumann Peter , Kroppenstedt Reiner M. , Puhakka Jaakko A.
Published: November 2006

A thermophilic, Gram-positive, endospore-forming, sulfate-reducing bacterium was isolated from an underground mine in a geothermally active area in Japan. Cells of this strain, designated RL50JIIIT, were rod-shaped and motile. The temperature range for growth was 50–72 °C (optimum growth at 61–66 °C) and the pH range was 6.4–7.8 (optimum at pH 7.2–7.4). Strain RL50JIIITtolerated up to 1.5 % NaCl, but optimum growth occurred in the presence of 0–1 % NaCl. Electron acceptors utilized were sulfate, sulfite, thiosulfate and elemental sulfur. Electron donors utilized were H2in the presence of CO2, alanine, various carboxylic acids and alcohols. Fermentative growth occurred on lactate and pyruvate. The cell wall contained mesodiaminopimelic acid and the major respiratory isoprenoid quinone was menaquinone 7 (MK-7). Major whole-cell fatty acids were iso-C15 : 0, iso-C17 : 0DMA (dimethyl acetal), iso-C15 : 0DMA and iso-C17 : 0. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed 98.7 % similarity withDesulfotomaculum solfataricumDSM 14956T. However, DNA–DNA hybridization experiments withDesulfotomaculum kuznetsovii,Desulfotomaculum luciaeandD. solfataricumand the G+C content of the DNA (54.4 mol%) allowed the differentiation of strain RL50JIIITfrom the recognized species of the genusDesulfotomaculum. Strain RL50JIIITtherefore represents a novel species, for which the nameDesulfotomaculum thermosubterraneumsp. nov. is proposed. The type strain is RL50JIIIT(=DSM 16057T=JCM 13837T).
Salicola salis sp. nov., an extremely halophilic bacterium isolated from Ezzemoul sabkha in Algeria
Authors: Kharroub Karima , Aguilera Margarita , Quesada Teresa , Morillo José Antonio , Ramos-Cormenzana Alberto , Boulharouf Abdrahmane , Monteoliva-Sánchez Mercedes
Published: November 2006

A novel, extremely halophilic bacterium was isolated from brine samples collected from Ezzemoul sabkha in north-east Algeria. Cells of this isolate, designated B2T, were Gram-negative, rod-shaped and motile. Growth occurred between 10 and 25 % (w/v) NaCl and the isolate grew optimally at 15–20 % (w/v) NaCl. The pH range for growth was 6.0–9.0 with an optimum at pH 7.0–7.5. The predominant fatty acids were C16 : 0 and C18 : 1
ω9c. Other fatty acids present were C16 : 1
ω9c, C18 : 0 10-methyl, C12 : 0 3-OH, C10 : 0 and C12 : 0. The G+C content of the genomic DNA was 56.0 mol%. 16S rRNA gene sequence analysis indicated that strain B2T was closely related to Salicola marasensis in the Gammaproteobacteria. The level of 16S rRNA gene sequence similarity between strain B2T and the type strain of Salicola marasensis was 99 %. DNA–DNA hybridization experiments between strain B2T and Salicola marasensis indicated a level of relatedness of 52 %. The phenotypic characteristics of strain B2T allowed its differentiation from recognized species of the genus Salicola. Strain B2T was able to hydrolyse starch but not aesculin. It was unable to use carbohydrates and could not use citrate, pyruvate or succinate as sole carbon and energy sources. On the basis of the polyphasic data presented, strain B2T is considered to represent a novel species of the genus Salicola, for which the name Salicola salis sp. nov. is proposed. The type strain is B2T (=CECT 7106T=LMG 23122T).
Fluorescent Reagents for Live Cell Imaging and Their Introduction into Cells
Authors: Davis Ilan , Parton Richard M.
Published: November 2006

INTRODUCTION

Most biological specimens, including Drosophila tissues, are relatively transparent, so details of internal and intracellular morphology are difficult to image in untreated living specimens using simple bright-field techniques. Although there are methods for improving contrast in bright-field imaging, fluorescence microscopy offers greater advantages and possibilities for increasing contrast and determining the specific localization of molecules in cells. Fluorescence microscopy has proven to be particularly well suited to the study of live material, now that an ever-increasing and bewildering array of different “vital” probes are available for tracking cellular components and activities, including some that have been applied to Drosophila. Here we outline the three methods most commonly used to introduce an appropriate label into Drosophila tissue without unduly perturbing the process.
Imaging Protein Interactions by FRET Microscopy: FRET Measurements by Sensitized Emission
Authors: Verveer Peter J. , Rocks Oliver , Harpur Ailsa G. , Bastiaens Philippe I.H.
Published: November 2006

INTRODUCTION

This protocol describes a method for measuring fluorescence resonance energy transfer (FRET) by the detection of acceptor-sensitized emission. This approach is useful in situations where donor intensities are low and/or there is contamination with high background (auto) fluorescence in the donor channel. However, absorption spectra characteristically exhibit long tails in the higher-energy, shorter-wavelength (blue) region, which may result in the direct excitation of the acceptor molecule in addition to that of the donor, thus resulting in mixing of direct and sensitized emission. Conversely, fluorescence emission tends to tail into the red part of the spectrum, causing donor fluorescence bleed-through into the acceptor detection channel. Corrections for these effects involve the acquisition of fluorescence images of samples containing the donor, the acceptor, and both of these for three different filter settings. The result is an estimation of the sensitized emission, i.e., the emission induced by FRET from the donor to the acceptor alone. Excitation of a donor fluorophore in a FRET pair leads to quenching of the donor fluorescence and increased emission from the acceptor (sensitized emission). This can be normalized using the acceptor emission, measured after specific excitation of the acceptor, to define apparent energy transfer efficiency in each pixel of the image. It is also proportional to the fraction of acceptor molecules that is bound to a donor-tagged molecule. Alternatively, an apparent energy transfer efficiency can also be defined that is proportional to the bound fraction of donor-tagged molecules.
Imaging of Organelle Membrane Systems and Membrane Traffic in Living Cells: Figure 1.
Authors: Lippincott-Schwartz Jennifer , Snapp Erik Lee
Published: November 2006

INTRODUCTION

Eukaryotic cells are composed of an intricate system of internal membranes that are organized into different compartments, including the endoplasmic reticulum, the nucleus, the Golgi apparatus, lysosomes, endosomes, mitochondria, and peroxisomes, with specialized roles within the cell. Only recently have the localization and dynamics of these organelles been studied in the context of the living cell because of the availability of green fluorescent protein (GFP) fusion proteins and recent advances in fluorescent microscope imaging systems.

In this protocol, a confocal laser-scanning microscope (CLSM) and GFP fusion proteins are used in time-lapse imaging to visualize the behavior of organelles and to track membrane-bound transport intermediates that bud off from organelles. Practical issues related to the construction and expression of GFP fusion proteins are also discussed. These are essential for optimizing the brightness and expression levels of GFP fusion proteins so that intracellular membrane-bound structures containing these fusion proteins can be readily visualized.
Song is a reliable signal of bill morphology in Darwin's small tree finch Camarhynchus parvulus, and vocal performance predicts male pairing success
Authors: Christensen Rebekah , Kleindorfer Sonia , Robertson Jeremy
Published: November 2006

The shape and movement of the vocal tract are known to influence bird song. Current theory predicts that large bill and body size are correlated with low frequency song and slow trill rate. It is also widely accepted that song characteristics are important for mate choice by females. We investigated the relationship between bill morphology, song characteristics, and pairing success in Darwin's small tree finch Camarhynchus parvulus, on the Galapagos Islands. Contrary to predictions from a previous cross‐species study on Darwin's finches, we found that individuals with larger bill size produced songs with slow trill rate, high dominant frequency, and broad frequency bandwidth, indicating that song is a reliable signal of bill morphology. Vocal performance as indicated by the deviation from an upper performance limit was higher in paired than unpaired males. Pairing was not skewed in favour of a particular bill size, and both small and large billed males that sang high performance song had high pairing success. The reliable signalling function of song has implications for female choice and territorial defence, given that both females and conspecific competitors can assess the relative size of males’ bills through song, while females may use vocal performance as a signal of male quality.
The flight speed of parent birds feeding young
Authors: I. Houston Alasdair
Published: November 2006

I review previous models of the speed at which parent birds should fly when delivering food to their young. Norberg gives a graphical method of finding a parent's best flight speed. This speed maximizes the overall rate at which energy is delivered to the young. An alternative assumption is that a parent maximizes the net rate of delivery of energy. I suggest that in general we cannot distinguish between net rate and overall rate on the basis of whether the parent feeds itself. The best way to distinguish between these currencies may be to use qualitative predictions. I present new results on the effect of a constraint on energy expenditure on the parent's optimal speed. I show that the optimal speed when foraging should be less than the optimal speed when traveling. I also analyse the advantage to a parent of flying faster than the maximum range speed and evaluate previous empirical studies of the speed at which parent birds fly. Only one study claims that parent birds fly at the speed identified by Norberg, but I raise doubts about this claim.
Application of molecular clocks in ornithology revisited
Authors: Peterson A. Townsend
Published: November 2006

Molecular clocks have seen many applications in ornithology, but many applications are uncritical. In this commentary, I point out logical inconsistencies in many uses of clocks in avian molecular systematics. I call for greater rigor in application of molecular clocks – clocks should only be used when clocklike behavior has been tested and confirmed, and when appropriate calibrations are available. Authors and reviewers should insist on such rigor to assure that systematics is indeed scientific, and not just storytelling.
Due to low infection rates no routine anti‐infective prophylaxis is required in younger patients with chronic lymphocytic leukaemia during fludarabine‐based first line therapy
Authors: Eichhorst Barbara F. , Busch Raymonde , Schweighofer Carmen , Wendtner Clemens M. , Emmerich Berthold , Hallek Michael ,   the German CLL Study Group (GCLLSG)
Published: November 2006

The impact of the combination therapy fludarabine plus cyclophosphamide (FC) in comparison with fludarabine alone regarding the incidence and severity of infections among previously untreated patients with chronic lymphocytic leukaemia (CLL) was evaluated within a multicentre phase III study. A total of 375 patients, up to 65 years old, were randomised between fludarabine or FC for first line therapy. No routine anti‐infective prophylaxis was provided. A total of 196 infectious episodes, including 33 severe infections, were documented. In the fludarabine arm, 32·9% of the patients developed an infectious complication compared with 39·9% in the FC arm (P = 0·2). No difference was observed in the rate of severe infections (Common Toxicity Crtieria grades III and IV) between both treatment arms. Dose reductions were performed more frequently in FC‐treated patients. Granulocyte colony‐stimulating factor (G‐CSF) was administered due to leucopenia in 5% of all patients. A multivariate regression model identified only elevated thymidine kinase, but not the treatment arm, as a statistically independent risk factor for infections. In summary, FC was not associated with a higher rate of infections compared with fludarabine alone. No routine antibiotic or virostatic prophylaxis, or pre‐emptive treatment with G‐CSF, is necessary in first line therapy with fludarabine‐based regimens in younger patients with CLL, if adequate dose reduction is performed. The combination therapy FC is not associated with a higher rate of infections compared with fludarabine alone. No routine antibiotic or virostatic prophylaxis as well as pre‐emptive treatment with G‐CSF is necessary in first line therapy with fludarabine‐based regimen in younger patients with CLL, if adequate dose reductions due to cytopenia or previous infections are performed.
Sea surface shape derivation above the seismic streamer
Authors: Laws Robert , Kragh Ed
Published: November 2006

The rough sea surface causes perturbations in the seismic data that can be significant for time‐lapse studies. The perturbations arise because the reflection response of the non‐flat sea perturbs the seismic wavelet. In order to remove these perturbations from the received seismic data, special deconvolution methods can be used, but these methods require, as input, the time varying wave elevation above each hydrophone in the streamer. In addition, the vertical displacement of the streamer itself must also be known at the position of each hydrophone and at all times. This information is not available in conventional seismic acquisition. However, it can be obtained from the hydrophone measurements provided that the hydrophones are recorded individually (not grouped), that the recording bandwidth is extended down to 0.05 Hz and that data are recorded without gaps between the shot records.

The sea surface elevation, and also the wave‐induced vertical displacement of the streamer, can be determined from the time‐varying pressure that the sea waves cause in the hydrophone measurements. When this was done experimentally, using a single sensor seismic streamer without a conventional low cut filter, the wave induced pressure variations were easily detected. The inversion of these experimental data gives results for the sea surface elevation that are consistent with the weather and sea state at the time of acquisition. A high tension approximation allows a simplified solution of the equations that does not demand a knowledge of the streamer tension. However, best results at the tail end of the streamer are obtained using the general equation.
Proteasomal chymotrypsin‐like peptidase activity is required for essential functions of human monocyte‐derived dendritic cells
Authors: Naujokat Cord , Berges Carsten , Höh Alexandra , Wieczorek Hubert , Fuchs Dominik , Ovens Jörg , Miltz Marion , Sadeghi Mahmoud , Opelz Gerhard , Daniel Volker
Published: November 2006

The ubiquitin–proteasome pathway is the principal system for extralysosomal protein degradation in eukaryotic cells, and is essential for the regulation and maintenance of basic cellular processes, including differentiation, proliferation, cell cycling, gene transcription and apoptosis. The 26S proteasome, a large multicatalytic protease complex, constitutes the system's proteolytic core machinery that exhibits different proteolytic activities residing in defined proteasomal subunits. We have identified proteasome inhibitors – bortezomib, epoxomicin and lactacystin – which selectively inhibit the proteasomal β5 subunit‐located chymotrypsin‐like peptidase activity in human monocyte‐derived dendritic cells (DCs). Inhibition of proteasomal chymotrypsin‐like peptidase activity in immature and mature DCs impairs the cell‐surface expression of CD40, CD86, CD80, human leucocyte antigen (HLA)‐DR, CD206 and CD209, induces apoptosis, and impairs maturation of DCs, as demonstrated by decreased cell‐surface expression of CD83 and lack of nuclear translocation of RelA and RelB. Inhibition of chymotrypsin‐like peptidase activity abrogates macropinocytosis and receptor‐mediated endocytosis of macromolecular antigens in immature DCs, and inhibits the synthesis of interleukin (IL)‐12p70 and IL‐12p40 in mature DCs. As a functional consequence, DCs fail to stimulate allogeneic CD4+ and CD8+ T cells and autologous CD4+ T cells sufficiently in response to inhibition of chymotrypsin‐like peptidase activity. Thus, proteasomal chymotrypsin‐like peptidase activity is required for essential functions of human DCs, and inhibition of proteasomal chymotrypsin‐like peptidase activity by selective inhibitors, or by targeting β5 subunit expression, may provide a novel therapeutic strategy for suppression of deregulated and unwanted immune responses.
The in vitro influences of neurotensin on the motility characteristics of human U373 glioblastoma cells
Authors: Servotte S. , Camby I. , Debeir O. , Deroanne C. , Lambert C. A. , Lapière C. M. , Kiss R. , Nusgens B. , Decaestecker C.
Published: November 2006

Astrocytic tumours are associated with dismal prognoses due to their pronounced ability to diffusely invade the brain parenchyma. Various neuropeptides, including gastrin, are able to modulate tumour astrocyte migration. While neurotensin has been shown to influence the proliferation of glioma cells and the migratory ability of a large set of other cell types, its role in glioma cell migration has never been investigated. Neurotensin‐induced modifications to the motility features of human U373 glioblastoma cells therefore constitute the topic of the present study. We evidenced that three subtypes of neurotensin receptors (NTR1, NTR2 and NTR3) are expressed in U373 glioblastoma cells, at least as far as their mRNAs are concerned. Treating U373 tumour cells with 10 nM neurotensin markedly modified the morphological patterns of these cells and also profoundly altered the organization of their actin cytoskeletons. Pull‐down assays revealed that neurotensin induced the activation in U373 cells of both Rac1 and Cdc42 but not RhoA. Scratch wound assays evidenced that neurotensin (0.1 and 10 nM) very significantly inhibited wound colonization by U373 cells cultured in the absence of serum. In addition, quantitative phase‐contrast videomicroscopy analyses showed that neurotensin decreases the motility levels of U373 glioblastoma cells when these cells are cultured on plastic. In sharp contrast, neurotensin stimulates the motility of U373 cells when they are cultured on laminin, which is a pro‐adhesive extracellular matrix component ubiquitously secreted by glioma cells. Our data thus strongly suggest that, in addition to gastrin, neurotensin is a neuropeptide capable of modulating tumour astrocyte migration into the brain parenchyma.
Effects of RNA Interference on CD80 and CD86 Expression in Bone Marrow‐derived Murine Dendritic Cells
Authors: Gu X. , Xiang J. , Yao Y. , Chen Z.
Published: November 2006

To investigate whether RNA interference (RNAi) induced by small interfering RNA (siRNA) could suppress CD80 and CD86 expression in bone marrow‐derived murine dendritic cells (DC). The bone marrow‐derived DC of mice were separated and cultured in vitro, chemically synthesized siRNA were then transferred into the cells by LipofectAMINE 2000, and the siRNA transfection efficacy was assessed by both fluorescence microscope and flow cytometry. The mRNA expression and protein synthesis were analysed by real‐time RT‐PCR and flow cytometry. The cell viability of transfected DC was determined by annexin V and propidium iodine staining. Transfection of bone marrow‐derived murine DC with a non‐silencing FITC‐labelled control siRNA demonstrated a high (71.86%) transfection efficiency without affecting cellular viability. CD80‐1 siRNA was the most effective siRNA to block CD80 expression in three candidates. Similarly, CD86‐3 siRNA was extraordinarily effective in repressing the expression of CD86. Cotransfection of siRNA specific to CD80 and CD86 can enhance gene silencing that is not affected by DC activation‐inducing signals. CD80 and CD86 siRNA suppressed the expression of CD80 and CD86 to 31.05 ± 2.41% and 25.43 ± 0.85%, respectively, of the level in untreated cells (P < 0.05). siRNA is capable of triggering RNAi in bone marrow‐derived DC; it can specifically and effectively knock down CD80 and CD86 gene expression. This approach is a useful tool by which costimulatory molecules of DC can be studied as well as a potential therapeutic option for allograft rejection.
Strain Differences and the Role for HSP47 and HSP70 in Adjuvant Arthritis in Rats
Authors: Miletić T. , Kovačević‐Jovanović V. , Stanojević S. , Vujić V. , Kosec D. , Mitić K. , Dimitrijević M.
Published: November 2006

Because of high sequence homology between microbial and endogenous heat shock proteins (HSP), immunological cross‐reactivity to microbial HSP has been suggested as a possible cause of the development of autoimmune diseases, such as rheumatoid arthritis. The present study aimed to determine a potential role of HSP47, a molecular chaperone involved in the synthesis and assembly of collagen molecules, and microbial HSP71 (mHSP71) in adjuvant arthritis (AA) in two rat strains: Dark Agouti (DA), susceptible to AA induction and Albino Oxford (AO), which is resistant to AA induction. Immunization with complete Freund's adjuvant (CFA) induced an increased expression of HSP47 in joints of DA rats, which exhibited severe clinical signs of AA at the time of disease peak, while this protein was not detectable in joints of AO rats. In contrast, no strain differences in HSP72 (rat analogue of mHSP71) expressions in joints were observed. The increased levels of anti‐HSP47 antibodies were detected in sera of DA rats during the AA peak, while the immunization with CFA increased levels of anti‐mHSP71 antibodies in sera of AO rats. HSP47 and mHSP71 reduced proliferation of draining inguinal lymph node cells (LNC) in resistant AO rat strain, leading to a hypothesis that both HSP participated in AA control. Finally, mHSP71 potentiated the apoptotic response of LNC in susceptible DA rat strain. In conclusion, our findings indicate involvement of HSP47 in the development of AA in the rat, and point out to the regulatory role for both HSP47 and mHSP71.
Acute Suppression of Serum IgM and IgA in Tank Workers Exposed to Benzene
Authors: Kirkeleit J. , Ulvestad E. , Riise T. , Bråtveit M. , Moen B. E.
Published: November 2006

We investigated associations between benzene exposure and alterations of proteins and cells of the immune system among workers maintaining cargo tanks containing crude oil residues. Individual exposure to benzene, benzene in blood and urine, peripheral blood lymphocytes (total lymphocytes, lymphocytes in subpopulations CD3, CD4, CD8, CD19, CD56 and CD4/CD8 ratio), complement factors C3 and C4 and serum concentration of immunoglobulins (IgG, IgA, IgM and IgE) were analysed among 13 tank workers and nine unexposed referents (catering section). Benzene exposure was measured during three consecutive 12‐h work days. Blood and urine samples were collected pre‐shift on the first day (baseline), post‐shift on the third day, and pre–next shift on the following morning. The time spent in the cargo tank was logged. The individual geometric mean benzene exposure in the breathing zone of tank workers over 3 days was 0.15 p.p.m. (range 0.01–0.62 p.p.m.) (n = 26). The geometric mean benzene concentration in blood post‐shift was 12.3 nmol/l among tank workers versus 0.7 nmol/l among the referents. Tank workers showed a decline (versus referents) in IgM from baseline to post‐shift (t‐test, P = 0.04) and IgA from baseline to pre–next shift (t‐test, P = 0.01). They also showed a decline in CD4 T cells from baseline to post‐shift (t‐test, P = 0.04). Suppression correlated with benzene exposure, benzene concentrations in blood and urine and time spent in the tank. The groups did not differ significantly in the change in other immune parameters. The clinical significance is unknown and warrants further studies.