bluuebunny/crossref_metadata_2025 huggingface dataset:
Laser oscillations of whispering gallery modes in thiophene/phenylene co-oligomer microrings
Authors: Fujiwara Seiji , Bando Kazuki , Masumoto Yasuaki , Sasaki Fumio , Kobayashi Shunsuke , Haraichi Satoshi , Hotta Shu
Published: July 2007

Laser oscillation of whispering gallery modes was observed in microring structures of semiconducting thiophene/phenylene co-oligomer (TPCO) crystals at room temperature. Microring structures were formed by dry etching from thin film crystals of TPCO. The thresholds for the laser oscillation of a microring and a thin film crystal are 200 and 1400μJ∕cm2 for picosecond excitation, respectively. Therefore, the threshold for the microring was reduced to 1∕7 of that for the thin film crystal. The dramatic reduction of threshold clearly demonstrates the importance of microcavity in making efficient organic semiconductor lasers.
Large-scale reorganization of the tonotopic map in mouse auditory midbrain revealed by MRI
Authors: Yu Xin , Sanes Dan H. , Aristizabal Orlando , Wadghiri Youssef Zaim , Turnbull Daniel H.
Published: July 2007

The cortex is thought to be the primary site of sensory plasticity, particularly during development. Here, we report that large-scale reorganization of the mouse auditory midbrain tonotopic map is induced by a specific sound-rearing environment consisting of paired low- (16 kHz) and high-frequency (40 kHz) tones. To determine the potential for plasticity in the mouse auditory midbrain, we used manganese-enhanced MRI to analyze the midbrain tonotopic maps of control mice during normal development and mice reared in the two-tone (16 + 40 kHz) environment. We found that the tonotopic map emerged during the third postnatal week in normal mice. Before 3 weeks, a larger percentage of auditory midbrain responded to each of the suprathreshold test frequencies, despite the fact that the primary afferent projections are in place even before hearing onset. By 3 weeks, the midbrain tonotopic map of control mice was established, and manganese-enhanced MRI showed a clear separation between the 16- and 40-kHz responses. Two-tone rearing dramatically altered the appearance of these discrete frequency-specific responses. A significant volume of the auditory midbrain became responsive to both rearing frequencies, resulting in a large-scale reorganization of the tonotopic map. These results indicate that developmental plasticity occurs on a much greater scale than previously appreciated in the mammalian auditory midbrain.
Filopodia act as phagocytic tentacles and pull with discrete steps and a load-dependent velocity
Authors: Kress Holger , Stelzer Ernst H. K. , Holzer Daniela , Buss Folma , Griffiths Gareth , Rohrbach Alexander
Published: July 2007

Filopodia are thin, spike-like cell surface protrusions containing bundles of parallel actin filaments. So far, filopodial dynamics has mainly been studied in the context of cell motility on coverslip-adherent filopodia by using fluorescence and differential interference contrast (DIC) microscopy. In this study, we used an optical trap and interferometric particle tracking with nanometer precision to measure the three-dimensional dynamics of macrophage filopodia, which were not attached to flat surfaces. We found that filopodia act as cellular tentacles: a few seconds after binding to a particle, filopodia retract and pull the bound particle toward the cell. We observed F-actin-dependent stepwise retraction of filopodia with a mean step size of 36 nm, suggesting molecular motor activity during filopodial pulling. Remarkably, this intracellular stepping motion, which was measured at counteracting forces of up to 19 pN, was transmitted to the extracellular tracked particle via the filopodial F-actin bundle and the cell membrane. The pulling velocity depended strongly on the counteracting force and ranged between 600 nm/s at forces <1 pN and ≈40 nm/s at forces >15 pN. This result provides an explanation of the significant differences in filopodial retraction velocities previously reported in the literature. The measured filopodial retraction force–velocity relationship is in agreement with a model for force-dependent multiple motor kinetics.
Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth
Authors: Marcy Yann , Ouverney Cleber , Bik Elisabeth M. , Lösekann Tina , Ivanova Natalia , Martin Hector Garcia , Szeto Ernest , Platt Darren , Hugenholtz Philip , Relman David A. , Quake Stephen R.
Published: July 2007

We have developed a microfluidic device that allows the isolation and genome amplification of individual microbial cells, thereby enabling organism-level genomic analysis of complex microbial ecosystems without the need for culture. This device was used to perform a directed survey of the human subgingival crevice and to isolate bacteria having rod-like morphology. Several isolated microbes had a 16S rRNA sequence that placed them in candidate phylum TM7, which has no cultivated or sequenced members. Genome amplification from individual TM7 cells allowed us to sequence and assemble >1,000 genes, providing insight into the physiology of members of this phylum. This approach enables single-cell genetic analysis of any uncultivated minority member of a microbial community.
Essential role for MFG-E8 as ligand for αvβ5 integrin in diurnal retinal phagocytosis
Authors: Nandrot Emeline F. , Anand Monika , Almeida Dena , Atabai Kamran , Sheppard Dean , Finnemann Silvia C.
Published: July 2007

The integrin receptor αvβ5 controls two independent forms of interactions of the retinal pigment epithelium (RPE) with adjacent photoreceptor outer segments that are essential for vision. αvβ5 localizes specifically to apical microvilli of the RPE and contributes to retinal adhesion that maintains RPE contacts with intact outer segments at all times. Additionally, αvβ5 synchronizes diurnal bursts of RPE phagocytosis that clear photoreceptor outer segment fragments (POS) shed in a circadian rhythm. Dependence of retinal phagocytosis and adhesion on αvβ5 receptors suggests that the extracellular matrix ensheathing RPE microvilli contains ligands for this integrin. Here we studied mice lacking expression of functional MFG-E8 to test the contribution of this integrin ligand to αvβ5 functions in the retina. Lack of MFG-E8 only minimally reduced retinal adhesion. In contrast, lack of MFG-E8, like lack of αvβ5 receptor, eliminated αvβ5 downstream signaling involving the engulfment receptor MerTK and peak POS phagocytosis, both of which follow light onset in wild-type retina. MFG-E8-deficient RPE in primary culture retained normal epithelial morphology and levels of apical αvβ5 receptors, but showed impaired binding and engulfment of isolated POS. Soluble or POS-bound recombinant MFG-E8 was sufficient to fully restore phagocytosis by MFG-E8-deficient RPE. Furthermore, MFG-E8 supplementation strongly increased POS binding by wild-type and MerTK-deficient RPE, but did not affect POS binding by RPE lacking αvβ5. Thus, MFG-E8 stimulates rhythmic POS phagocytosis by ligating apical αvβ5 receptors of the RPE. These results identify MFG-E8 as the first extracellular ligand in the retina that is essential for diurnal POS phagocytosis.
Protein roadblocks and helix discontinuities are barriers to the initiation of mismatch repair
Authors: Pluciennik Anna , Modrich Paul
Published: July 2007

The hemimethylated d(GATC) sequence that directs
Escherichia coli
mismatch repair can reside on either side of a mismatch at a separation distance of 1,000 bp or more. Initiation of repair involves the mismatch-, MutS-, and MutL-dependent activation of MutH endonuclease, which incises the unmethylated strand at the d(GATC) sequence, with the ensuing strand break serving as the loading site for the appropriate 3′-to-5′ or 5′-to-3′ excision system. However, the mechanism responsible for the coordinated recognition of the mismatch and a hemimodified d(GATC) site is uncertain. We show that a protein roadblock (EcoRI
E111Q
, a hydrolytically defective form of EcoRI endonuclease) placed on the helix between the two DNA sites inhibits MutH activation by 70–80% and that events that escape inhibition are attributable, at least in part, to diffusion of EcoRI
E111Q
away from its recognition site. We also demonstrate that a double-strand break located within the shorter path linking the mismatch and a d(GATC) site in a circular heteroduplex abolishes MutH activation, whereas a double-strand break within the longer path is without effect. These findings support the idea that initiation of mismatch repair involves signaling along the helix contour.
Making polymeric micro- and nanoparticles of complex shapes
Authors: Champion Julie A. , Katare Yogesh K. , Mitragotri Samir
Published: July 2007

Polymeric micro- and nanoparticles play a central role in varied applications such as drug delivery, medical imaging, and advanced materials, as well as in fundamental studies in fields such as microfluidics and nanotechnology. Functional behavior of polymeric particles in these fields is strongly influenced by their shape. However, the availability of precisely shaped polymeric particles has been a major bottleneck in understanding and capitalizing on the role of shape in particle function. Here we report a method that directly addresses this need. Our method uses routine laboratory chemicals and equipment to make particles with >20 distinct shapes and characteristic features ranging in size from 60 nm to 30 μm. This method offers independent control over important particle properties such as size and shape, which is crucial to the development of nonspherical particles both as tools and products for a variety of fields.
A CD8+ T cell immune evasion protein specific to Epstein-Barr virus and its close relatives in Old World primates
Authors: Hislop Andrew D. , Ressing Maaike E. , van Leeuwen Daphne , Pudney Victoria A. , Horst Daniëlle , Koppers-Lalic Danijela , Croft Nathan P. , Neefjes Jacques J. , Rickinson Alan B. , Wiertz Emmanuel J.H.J.
Published: July 2007

γ1-Herpesviruses such as Epstein-Barr virus (EBV) have a unique ability to amplify virus loads in vivo through latent growth-transforming infection. Whether they, like α- and β-herpesviruses, have been driven to actively evade immune detection of replicative (lytic) infection remains a moot point. We were prompted to readdress this question by recent work (Pudney, V.A., A.M. Leese, A.B. Rickinson, and A.D. Hislop. 2005. J. Exp. Med. 201:349–360; Ressing, M.E., S.E. Keating, D. van Leeuwen, D. Koppers-Lalic, I.Y. Pappworth, E.J.H.J. Wiertz, and M. Rowe. 2005. J. Immunol. 174:6829–6838) showing that, as EBV-infected cells move through the lytic cycle, their susceptibility to EBV-specific CD8+ T cell recognition falls dramatically, concomitant with a reductions in transporter associated with antigen processing (TAP) function and surface human histocompatibility leukocyte antigen (HLA) class I expression. Screening of genes that are unique to EBV and closely related γ1-herpesviruses of Old World primates identified an early EBV lytic cycle gene, BNLF2a, which efficiently blocks antigen-specific CD8+ T cell recognition through HLA-A–, HLA-B–, and HLA-C–restricting alleles when expressed in target cells in vitro. The small (60–amino acid) BNLF2a protein mediated its effects through interacting with the TAP complex and inhibiting both its peptide- and ATP-binding functions. Furthermore, this targeting of the major histocompatibility complex class I pathway appears to be conserved among the BNLF2a homologues of Old World primate γ1-herpesviruses. Thus, even the acquisition of latent cycle genes endowing unique growth-transforming ability has not liberated these agents from evolutionary pressure to evade CD8+ T cell control over virus replicative foci.
Small intestine lamina propria dendritic cells promote de novo generation of Foxp3 T reg cells via retinoic acid
Authors: Sun Cheng-Ming , Hall Jason A. , Blank Rebecca B. , Bouladoux Nicolas , Oukka Mohamed , Mora J. Rodrigo , Belkaid Yasmine
Published: July 2007

To maintain immune homeostasis, the intestinal immune system has evolved redundant regulatory strategies. In this regard, the gut is home to a large number of regulatory T (T reg) cells, including the Foxp3+ T reg cell. Therefore, we hypothesized that the gut environment preferentially supports extrathymic T reg cell development. We show that peripheral conversion of CD4+ T cells to T reg cells occurs primarily in gut-associated lymphoid tissue (GALT) after oral exposure to antigen and in a lymphopenic environment. Dendritic cells (DCs) purified from the lamina propria (Lp; LpDCs) of the small intestine were found to promote a high level of T reg cell conversion relative to lymphoid organ–derived DCs. This enhanced conversion by LpDCs was dependent on TGF-β and retinoic acid (RA), which is a vitamin A metabolite highly expressed in GALT. Together, these data demonstrate that the intestinal immune system has evolved a self-contained strategy to promote T reg cell neoconversion.
Quantum algebras and parity-dependent spectra
Authors: Sukumar C.V , Hodges Andrew
Published: July 2007

We study the structure of a quantum algebra in which a parity-violating term modifies the standard commutation relation between the creation and annihilation operators of the simple harmonic oscillator. We discuss several useful applications of the modified algebra. We show that the Bernoulli and Euler numbers arise naturally in a special case. We also show a connection with Gaussian and non-Gaussian squeezed states of the simple harmonic oscillator. Such states have been considered in quantum optics. The combinatorial theory of Bernoulli and Euler numbers is developed and used to calculate matrix elements for squeezed states.
How to look like a mallow: evidence of floral mimicry between Turneraceae and Malvaceae
Authors: Benitez-Vieyra Santiago , de Ibarra Natalie Hempel , Wertlen Anna M , Cocucci Andrea A
Published: July 2007

Abundant, many-flowered plants represent reliable and rich food sources for animal pollinators, and may even sustain guilds of specialized pollinators. Contrastingly, rare plants need alternative strategies to ensure pollinators' visitation and faithfulness. Flower mimicry, i.e. the sharing of a similar flower colour and display pattern by different plant species, is a means by which a rare species can exploit a successful model and increase its pollination services. The relationship between two or more rewarding flower mimic species, or Müllerian mimicry, has been proposed as mutualistic, in contrast to the unilaterally beneficial Batesian floral mimicry. In this work, we show that two different geographical colour phenotypes ofTurnera sidoidesssp.pinnatifidaresemble co-flowering Malvaceae in colour as seen by bees' eyes, and that these pollinators do not distinguish between them when approaching flowers in choice tests. Main pollinators ofT. sidoidesare bees specialized for collecting pollen in Malvaceae. We demonstrate that the similarity between at least one of the geographical colour phenotypes ofT. sidoidesand co-flowering Malvaceae is adaptive, since the former obtains more pollination services when growing together with its model than when growing alone. Instead of the convergent evolution pattern attributed to Müllerian mimicry, our data rather suggest an advergent evolution pattern, because onlyT. sidoidesseems to have evolved to be more similar to its malvaceous models.
Behavioural syndromes in Merriam's kangaroo rats (
Dipodomys merriami
): a test of competing hypotheses
Authors: Dochtermann Ned A , Jenkins Stephen H
Published: July 2007

Behavioural syndromes, correlations of behaviours conceptually analogous to personalities, have been a topic of recent attention due to their potential to explain trade-offs in behavioural responses, apparently maladaptive behaviour and limits to plasticity. Using Merriam's kangaroo rats (
Dipodomys merriami
), we assessed the explanatory power and generality of hypothesized syndrome structures derived from the literature and the natural history of the species. Several aspects of functionally distinct behavioural responses of
D. merriami
were quantified. Syndrome structures were compared using structural equation modelling and model selection procedures. A domain-general behavioural syndrome incorporating cross-functional relationships between measures of boldness, agonistic behaviour, flexibility and food hoarding best explained the data. This pattern suggests that
D. merriami
behaviours should not be viewed as discrete elements but as components of a multivariate landscape. Our results support arguments that a lack of independence between behaviours may be a general aspect of behavioural phenotypes and suggest that the ability of
D. merriami
's behaviour to respond to selection may be constrained by underlying connections.
Orang-like manual adaptations in the fossil hominoid
Hispanopithecus laietanus
: first steps towards great ape suspensory behaviours
Authors: Almécija S , Alba D.M , Moyà-Solà S , Köhler M
Published: July 2007

Morphological and biometrical analyses of the partial hand IPS18800 of the fossil great ape
Hispanopithecus laietanus
(=
Dryopithecus laietanus
), from the Late Miocene (about 9.5 Ma) of Can Llobateres (Catalonia, Spain), reveal many similarities with extant orang-utans (
Pongo
). These similarities are interpreted as adaptations to below-branch suspensory behaviours, including arm-swinging and clambering/postural feeding on slender arboreal supports, due to an orang-like double-locking mechanism. This is confirmed by the long and highly curved phalanges of
Hispanopithecus
. The short and stout metacarpals with dorsally constricted heads, together with the dorsally extended articular facets on proximal phalanges, indicate the persistence of significant degrees of palmigrady. A powerful grasping capability is indicated by the great development of basal phalangeal tubercles, the marked insertions for the flexors on phalangeal shafts and the large pits for the collateral ligaments. The morphology of the
Hispanopithecus
long bones of the hand indicates a unique positional repertoire, combining orthogrady with suspensory behaviours and palmigrade quadrupedalism. The retention of powerful grasping and palmigrady suggests that the last common ancestor of hominids might have been more primitive than what can be inferred on the basis of extant taxa, suggesting that pronograde behaviours are compatible with an orthograde bodyplan suitable for climbing and suspension.
Genetic rescue persists beyond first-generation outbreeding in small populations of a rare plant
Authors: Willi Yvonne , Kleunen Mark van , Dietrich Stefan , Fischer Markus
Published: July 2007

Habitat fragmentation commonly causes genetic problems and reduced fitness when populations become small. Stocking small populations with individuals from other populations may enrich genetic variation and alleviate inbreeding, but such artificial gene flow is not commonly used in conservation owing to potential outbreeding depression. We addressed the role of long-term population size, genetic distance between populations and test environment for the performance of two generations of offspring from between-population crosses of the locally rare plant
Ranunculus reptans
L. Interpopulation outbreeding positively affected an aggregate measure of fitness, and the fitness superiority of interpopulation hybrids was maintained in the second offspring (F2) generation. Small populations benefited more strongly from interpopulation outbreeding. Genetic distance between crossed populations in neutral markers or quantitative characters was not important. These results were consistent under near-natural competition-free and competitive conditions. We conclude that the benefits of interpopulation outbreeding are likely to outweigh potential drawbacks, especially for populations that suffer from inbreeding.
Analysis of two human parvovirus PARV4 genotypes identified in human plasma for fractionation
Authors: Fryer Jacqueline F. , Delwart Eric , Bernardin Flavien , Tuke Philip W. , Lukashov Vladimir V. , Baylis Sally A.
Published: July 2007

The presence of the novel parvovirus PARV4 and a related variant, PARV5, was recently demonstrated in pooled plasma used in the manufacture of blood and plasma-derived medicinal products. DNA sequence analysis of nearly full-length genomes of four PARV4 and two PARV5 strains from manufacturing plasma pools is now presented. Like PARV4, PARV5 encodes two non-overlapping open reading frames (ORF1 and ORF2), homologous to the non-structural and capsid proteins of other parvoviruses, respectively. A highly conserved region in ORF2 contains phospholipase A2 motifs involved in parvovirus infectivity. Hybridization of strand-specific probes to DNA extracted from high-titre, PARV4-positive plasma revealed that the positive and negative strands are packaged into PARV4 virions in similar quantities. This extended analysis of nearly full-length PARV4 and PARV5 sequences suggests that they are closely related genotypes and the use of a single virus name, PARV4, comprising genotypes 1 and 2 (previously termed PARV5) is proposed.
Stimulation of baculovirus transcriptome expression in mammalian cells by baculoviral transcriptional activators
Authors: Liu Catherine Y. Y. , Wang Chia Hung , Wang Jui Ching , Chao Yu Chan
Published: July 2007

Autographa californica
multiple nucleopolyhedrovirus (AcMNPV), the type species of the family Baculoviridae, is an insect-specific virus that can enter a variety of mammalian cells. The potential of this versatile virus for protein expression or gene therapy in mammalian cells has become the focus of many studies. In most mammalian cells, transduced AcMNPV genes are either not expressed or expressed at an extremely low level. Here, we studied the effects of the two major AcMNPV trans-activators, IE1 and IE2, on the activation of AcMNPV genome in Vero E6 cells. Microarray analysis showed that when IE1 was overexpressed, it significantly activated genes gp64 and pe38, and upregulated ie2, he65, pcna, orf16, orf17 and orf25. Although, there were only two genes, pe38 and orf17, that were activated by IE2, we discovered interestingly that the combination of IE1 and IE2 factors had a synergistic effect on activation of the AcMNPV genome in mammalian cells, and activated around 38 %, or 59 out of the 155 genes placed on the microarray. This is the first detailed study of baculoviral transcription regulation in mammalian cells, and it shows that the baculoviral genome can be activated in a mammalian system, and also that the two major trans-activators, IE1 and IE2, play a central role in this activation.
Crystal structure of the Murray Valley encephalitis virus NS5 methyltransferase domain in complex with cap analogues
Authors: Assenberg René , Ren Jingshan , Verma Anil , Walter Thomas S. , Alderton David , Hurrelbrink Robert J. , Fuller Stephen D. , Bressanelli Stéphane , Owens Raymond J. , Stuart David I. , Grimes Jonathan M.
Published: July 2007

We have determined the high resolution crystal structure of the methyltransferase domain of the NS5 polypeptide from the Murray Valley encephalitis virus. This domain is unusual in having both the N7 and 2′-O methyltransferase activity required for Cap 1 synthesis. We have also determined structures for complexes of this domain with nucleotides and cap analogues providing information on cap binding, based on which we suggest a model of how the sequential methylation of the N7 and 2′-O groups of the cap may be coordinated.
Complete protein linkage map between the P2 and P3 non-structural proteins of poliovirus
Authors: Yin Jiang , Liu Ying , Wimmer Eckard , Paul Aniko V.
Published: July 2007

All of the non-structural proteins of poliovirus, including their processing precursors, are involved in the replication of the viral RNA genome. These proteins assemble into a replication complex, which also contains the viral RNA and cellular factors. An understanding of how these viral proteins interact with each other would enhance our understanding of the molecular events occurring during poliovirus infection of the cell. Previously, we have employed the yeast two-hybrid system to construct two separate linkage maps for the polioviral P2 and P3 proteins, respectively. In the present study, we have searched for interacting pairs between the P2 and P3 proteins in a similar inducible yeast two-hybrid system. Although, the primary functions of the proteolytic products of the P2 and P3 domains of the polyprotein in the viral life cycle are different, we observed significant interactions between 2CATPaseand 3AB; 2Aproand 3A, 3Cproor 3Dpol; 2B and 3A or 3AB. All of the interactions were measured in the yeast two-hybrid system by exchanging the interacting pairs on the transcription-activation and DNA-binding constructs.In vitroGST pull-down assay suggested that the 2CATPase/3AB interaction involves both ionic and hydrophobic contacts between the two proteins. The possible biological implication of the interactions observed in the yeast two-hybrid system will be discussed.
Experimental scrapie in ‘plt’ mice: an assessment of the role of dendritic-cell migration in the pathogenesis of prion diseases
Authors: Levavasseur Etienne , Metharom Pat , Dorban Gauthier , Nakano Hideki , Kakiuchi Terutaka , Carnaud Claude , Sarradin Pierre , Aucouturier Pierre
Published: July 2007

Peripherally acquired transmissible spongiform encephalopathies display strikingly long incubation periods, during which increasing amounts of prions can be detected in lymphoid tissues. While precise sites of peripheral accumulation have been described, the mechanisms of prion transport from mucosa and skin to lymphoid and nervous tissues remain unknown. Because of unique functional abilities, dendritic cells (DCs) have been suspected to participate in prion pathogenesis. In mice inoculated subcutaneously with scrapie-infected DCs, the incubation was shorter when cells were alive as compared with killed cells, suggesting that DC functions may facilitate prion neuroinvasion. However, early propagation in lymphoid tissues seemed not importantly affected by DC vitality. Mutant (plt) mice that have deficient CCL19/CCL21 expression and DC migration displayed similar infection of secondary lymphoid organs as normal mice, regardless of the route of inoculation and scrapie strain. Under certain conditions of transcutaneous inoculation, the incubation and duration of disease were moderately prolonged inpltmice. This was not related to a milder neuropathogenesis, sincepltand normal mice were equally susceptible to intracerebral prion challenge. We conclude that peripheral spreading of prions appears poorly dependent on cell migration through the chemokine/receptor system CCL19/CCL21/CCR7, although DCs might be able to help prions reach sites of neuroinvasion.
Phylogenetic relationships among sandfly fever group viruses (Phlebovirus: Bunyaviridae) based on the small genome segment
Authors: Xu Fangling , Chen Hongli , Travassos da Rosa Amelia P. A. , Tesh Robert B. , Xiao Shu-Yuan
Published: July 2007

The phleboviruses are more diverse in terms of arthropod vectors and antigenic relationships than most other genera of arthropod-borne viruses. In this study, 30 sandfly fever group viruses from the Naples, Sicilian, Punta Toro, Icoaraci and Frijoles serocomplexes were sequenced. Phylogenetic analyses were performed based on the sequence of the open reading frame for the nucleoprotein (N) and non-structural (NSs) protein genes of the small (S) segment. The five resultant genotypic lineages correlated with the serological grouping and were similar to analysis of M segment sequences. The sequence identity for N and NSs genes within the Sicilian, Naples, Punta Toro, Icoaraci and Frijoles serocomplexes was determined. The results indicated that genetic divergence for the S segment is lower than that for the M segment, suggesting that the S segment is more stable during evolution.
Complete genome characterization of Rocio virus (Flavivirus: Flaviviridae), a Brazilian flavivirus isolated from a fatal case of encephalitis during an epidemic in São Paulo state
Authors: Medeiros Daniele B. A. , Nunes Márcio R. T. , Vasconcelos Pedro F. C. , Chang Gwong-Jen J. , Kuno Goro
Published: July 2007

The flaviviruses of major medical importance in South American countries are yellow fever, dengue, Saint Louis encephalitis, West Nile and Rocio viruses. Rocio virus (ROCV) has been responsible for epidemics of severe encephalitis in Brazil with a case-fatality rate of 10 % and development of sequelae in 20 % of the survivors. We have sequenced and characterized the entire genome of ROCV for the first time, by determining the general traits of the open reading frame and the characteristics of viral genes including the potential cleavage sites, conserved or unique motifs, cysteine residues and potential glycosylation sites. The conserved sequences in the 3′-non-coding region were identified, and the predicted secondary structures during cyclization between 5′- and 3′-non-coding regions were studied. Multiple protein and phylogenetic analyses based on antigenically important and phylogenetically informative genes confirmed a close relationship between ROCV and Ilheus virus (ILHV), together constituting a unique and distinct phylogenetic subgroup as well as the genetic relationship of ROCV with several members of the Japanese encephalitis group. Although ROCV is phylogenetically related to ILHV, our study shows that it is still a virus distinct from the latter virus. This is the first flavivirus uniquely indigenous to Brazil that has been sequenced completely and the genome characterized. The data should be useful for further studies at the molecular level, including construction of infectious clone, identification of gene function, improved disease surveillance based on molecular diagnostic tools and vaccine development.
Disrupting the association of hepatitis C virus core protein with lipid droplets correlates with a loss in production of infectious virus
Authors: Boulant Steeve , Targett-Adams Paul , McLauchlan John
Published: July 2007

In infected cells, hepatitis C virus (HCV) core protein is targeted to lipid droplets, which serve as intracellular storage organelles. Using a tissue culture system to generate infectious HCV, we have shown that the coating of lipid droplets by the core protein occurs in a time-dependent manner and coincides with higher rates of virus production. At earlier times, the protein was located at punctate sites in close proximity to the edge of lipid droplets. Investigations by using Z-stack analysis have shown that many lipid droplets contained a single punctate site that could represent positions where core transfers from the endoplasmic reticulum membrane to droplets. The effects of lipid droplet association on virus production were studied by introducing mutations into the domain D2, the C-terminal region of the core protein necessary for droplet attachment. Alteration of a phenylalanine residue that was crucial for lipid droplet association generated an unstable form of the protein that could only be detected in the presence of a proteasome inhibitor. Moreover, converting two proline residues in D2 to alanines blocked coating of lipid droplets by core, although the protein was directed to punctate sites that were indistinguishable from those observed at early times for wild-type core protein. Neither of these virus mutants gave rise to virus progeny. By contrast, mutation at a cysteine residue positioned 2 aa upstream of the phenylalanine residue did not affect lipid droplet localization and produced wild-type levels of infectious progeny. Taken together, our findings indicate that lipid droplet association by core is connected to virus production.
Binding of tobamovirus replication protein with small RNA duplexes
Authors: Kurihara Yukio , Inaba Naoko , Kutsuna Natsumaro , Takeda Atsushi , Tagami Yuko , Watanabe Yuichiro
Published: July 2007

The sequence profiles of small interfering RNAs (siRNAs) in Arabidopsis infected with the crucifer tobamovirus tobacco mosaic virus (TMV)-Cg were determined by using a small RNA cloning technique. The majority of TMV-derived siRNAs were 21 nt in length. The size of the most abundant endogenous small RNAs in TMV-infected plants was 21 nt, whilst in mock-inoculated plants, it was 24 nt. Northern blot analysis revealed that some microRNAs (miRNAs) accumulated more in TMV-infected plants than in mock-inoculated plants. The question of whether the TMV-Cg-encoded 126K replication protein, an RNA-silencing suppressor, caused small RNA enrichment was examined. Transient expression of the replication protein did not change the pattern of miRNA processing. However, miRNA, miRNA* (the opposite strand of the miRNA duplex) and hairpin-derived siRNA all co-immunoprecipitated with the replication protein. Gel mobility-shift assays indicated that the replication protein binds small RNA duplexes. These results suggest that the tobamovirus replication protein functions as a silencing suppressor by binding small RNA duplexes, changing the small RNA profile in infected plants.
Assessment of two biotypes ofSolanum ptycanthumthat differ in resistance levels to imazamox
Authors: VOLENBERG D S , TRANEL P J , HOLT J F , SIMMONS F W , WELLER S C , SHARKHUU A , RIECHERS D E
Published: July 2007

Glasshouse and laboratory experiments were conducted on acetolactate synthase (ALS) homozygous resistantSolanum ptycanthumbiotypes from Illinois (IL‐R) and Indiana (IN‐R), and homozygous susceptible biotypes from Illinois (IL‐S) and Indiana (IN‐S). Genetic similarity of biotypes was assessed by random amplified polymorphic DNA (RAPD) markers, which determined that the Illinois biotypes are more similar to each other than to the IN‐R biotype. ALS enzyme activity from the IL‐R and IN‐R biotypes had I50values of 362 and 352 μM imazamox respectively. Dose–response experiments using three‐ to four‐leaf‐stage plants of the IL‐R and IN‐R biotypes had GR50values of 242 and 69 g ae ha−1imazamox respectively. Whole‐plant and ALS enzyme results are different than previously reported values in the literature, which was attributed in the current study to the original IN‐R population having individuals that were segregating for ALS resistance. Metabolism studies showed no difference in percentage [14C]imazamox remaining between the IL‐R and IN‐R biotypes up to 72 h after treatment. The IL‐S biotype metabolised [14C]imazamox approximately two times faster than the IL‐R and IN‐R biotypes and this trait was heritable. Response of F3plants containing homozygous ALS‐resistant alleles from the IL‐R biotype in a genetic background of 50% Illinois and 50% Indiana biotypes suggests that genetic factors other than an altered target site or metabolism may also contribute to the magnitude of resistance at the whole‐plant level in resistant biotypes.
Herbicide research and development: challenges and opportunities
Authors: RÜEGG W T , QUADRANTI M , ZOSCHKE A
Published: July 2007

The high adoption of chemical weed control and the broad range of solutions already available to manage most weed problems are significant hurdles to the development and launch of new herbicides. Business potentials are influenced by the high technical and biological standards provided by existing herbicides, as well as the intense competition in the marketplace. Other factors adding complexity are agronomic, structural and technological changes, including the introduction of herbicide‐tolerant crops, and the high costs of development for new active ingredients, mainly due to increasing regulatory requirements. In the light of increasing weed resistance to widely used herbicides, securing diversity in agronomy as well as weed management is a key to efficient crop production in future. In order to support this objective, new herbicides, preferably with new modes‐of‐action, will need to be discovered and developed.
A modelling approach using seedbank and soil properties to predict the relative weed density in organic fields of an Italian pre‐alpine valley
Authors: OTTO S , ZUIN M C , CHISTÈ G , ZANIN G
Published: July 2007

In 1996, a study was conducted on the seedbanks of a pre‐alpine valley in northern Italy which had been organically farmed since 1986. The seedbanks were evaluated using soil cores taken from 16 organic fields located at various altitudes and seed numbers were determined using the ‘seedling emergence method’. Thirteen soil properties were also evaluated. In 2003, the germinable seedbank was assessed in five other fields chosen at random. Soil properties were evaluated by the same method as in 1996. Using the data of the first 16 fields as the analysis data set and those of the latter five as an independent validation data set, a quadratic weed seedbank‐soil properties model was built with partial least square regression analysis. The model estimates the relative abundance of the various species as the sum of the contribution of individual soil properties and has a high predictive capacity. With a novel graphic approach, it is possible to describe the nonlinear relationship between each soil property and weed species relative abundance, giving a rational, quantitative, explanation as to why some species are widespread (e.g. Chenopodium album, Galinsoga parviflora and Chenopodium polyspermum), whereas others tend to concentrate in specific fields (e.g. Spergula arvensis). The approach can, when some hypotheses hold, give a rational basis for the explanation of the relative abundance of species in a weed community and constitutes a useful methodology for study and research.
Variability in immunization guidelines in children before and after lung transplantation
Authors: Benden Christian , Danziger‐Isakov Lara A. , Astor Todd , Aurora Paul , Bluemchen Katharina , Boyer Debra , Conrad Carol , Eichler Irmgard , Elidemir Okan , Goldfarb Samuel , Michaels Marian G. , Mogayzel Peter J. , Mueller Carsten , Parakininkas Daiva , Oberkfell Donna , Solomon Melinda , Boehler Annette
Published: July 2007

Abstract:  Lung transplant candidates and recipients are at high risk of infections from vaccine‐preventable diseases. However, well‐established guidelines neither exist for pre‐ and post‐transplant vaccination nor do monitoring guidelines for pediatric lung transplant recipients. To ascertain the current vaccination and monitoring practices of pediatric lung transplant centers, a self‐administered questionnaire was distributed to the 18 pediatric lung transplant centers within the International Pediatric Lung Transplant Collaborative in April 2006. Sixteen of 18 centers (89%) surveyed responded. Pretransplant, national vaccination guidelines are followed. Eleven centers reported following standardized vaccination guidelines post‐transplant. Vaccines were more commonly provided by the primary‐care physician pretransplant (69%) rather than post‐transplant (38%). Post‐transplant, 50% of the centers recommend live vaccines for household contacts but not for the transplant recipient. Pretransplant monitoring of response to prior vaccination was performed inconsistently except for varicella (88%). Only 44% of the transplant centers measure for response to vaccination post‐transplant, mostly hepatitis B. Current vaccination practices of pediatric lung transplant centers are heterogeneous. The lung transplant community would be well served by studies designed to evaluate the efficacy of vaccinations in this population.
Molecular marker analysis of genetic variation characterizing a grasspea (Lathyrus sativus) collection from central Italy
Authors: Tavoletti S. , Iommarini L.
Published: July 2007

Levels of genetic similarity characterizing 20 grasspea (Lathyrus sativus L.) populations collected in central Italy (17 populations in the Marche region and three populations in the Abruzzo region) were analysed with amplified fragment length polymorphism (AFLP) molecular markers. Two main clusters were found: one included large‐seeded populations from farms that were not market‐oriented (named Household populations) and the second, small‐seeded populations, cultivated in market‐oriented farms (named Commercial populations). Relationships among populations collected in different regions were found, although one population of the Abruzzo region was placed between the two main clusters, suggesting a possible further genetic differentiation within this grasspea germplasm collection. Principal component analysis based on AFLP marker frequency was effective in identifying polymorphic markers showing high discriminating ability between clusters H and C. In particular, seven markers showing high positive and three markers with low negative PC1 scores showed an almost cluster‐specific distribution. These results will be useful for enhancing Italian grasspea germplasm use in plant‐breeding programmes and for extending grasspea cultivation within the sustainable agricultural systems of central Italy.
Mapping of the apple powdery mildew resistance gene Pl1 and its genetic association with an NBS‐LRR candidate resistance gene
Authors: Dunemann F. , Peil A. , Urbanietz A. , Garcia‐Libreros T.
Published: July 2007

Molecular markers for the major apple powdery mildew resistance gene Pl1 were identified and are presently used in marker‐assisted selection in apple breeding. However, the precise map position of the Pl1 gene in the apple genome was not known. The objectives of this investigation were the identification of the Malus linkage group (LG) carrying the Pl1 locus, mapping of the resistance gene by simple sequence repeat (SSR) markers, and the analysis of genetic associations between the Pl1 gene and the numerous NBS‐LRR resistance gene candidates already mapped in the apple genome. A two‐step linkage mapping was used, based on two different apple families. The identification of LG 12 carrying Pl1 was performed indirectly by mapping the SCAR marker AT20 in an apple progeny for which there was a core genetic map but no mildew data available. Then, the position of Pl1 on LG 12 was determined by SSR markers in a second population which has been scored for mildew over 6 years in a greenhouse and in the field. The SSR Hi07f01, previously mapped on LG 12 [Tree Genet. Genomes, 2 (2006), 202] cosegregated with AT20 and was closely linked (∼1 cM) to the Pl1 gene. The TIR‐NBS‐LRR resistance gene analogue 15G11 mapped by the SSCP technique was also closely linked to the Pl1 resistance locus and might be a candidate for Pl1 itself, a second powdery mildew major resistance gene (Pld, [Theor. Appl. Genet., 110 (2004), 175]), or two scab resistance genes (Vg, [IOBC/WPRS Bull., 23 (2000), 245]; Vb, [Genome, 49 (2006), 1238]) which all seem to be located in a common R gene cluster at the distal end of apple LG 12.
EFFECTS OF AGAR AND PECTIN ON GASTRIC EMPTYING AND POST‐PRANDIAL GLYCAEMIC PROFILES IN HEALTHY HUMAN VOLUNTEERS
Authors: Sanaka Masaki , Yamamoto Takatsugu , Anjiki Hajime , Nagasawa Kunitaka , Kuyama Yasushi
Published: July 2007

Dietary fibre, such as pectin, delays gastric emptying and may enhance post‐prandial glucose tolerance. Agar, which is high in fibre content, is widely used in the traditional Japanese diet. Although long‐term diet therapy with agar decreases fasting plasma glucose levels in diabetes, knowledge is lacking about the acute effects of agar on gastric emptying and the post‐prandial glycaemic profiles. The present study was designed to investigate the acute effects of agar.

Ten healthy male volunteers were studied on three occasions with three different test meals (450 kcal/500 mL): (i) a fibre‐free meal; (ii) a meal with 2.0 g agar; or (iii) a meal with 5.2 g pectin. On each occasion, participants underwent a [13C]‐acetate breath test along with serial blood sampling. To quantify gastric emptying, the half [13CO2] excretion time () and the time for maximal [13CO2] excretion rate (tlag) were determined. The post‐prandial glycaemic response was expressed as an incremental change from the fasting value at each sampling time. Data were analysed using repeated‐measures analysis of variance (anova), followed by a post hoc paired Student's t‐test with Bonferroni adjustment.

The time‐course for respiratory [13CO2] excretion differed significantly among the three test meals (P = 0.0004, anova). Compared with the control meal, [13CO2] excretion was significantly lower following consumption of the agar meal (between 40 and 105 min post‐prandially; P < 0.025, Student's t‐test) and the pectin meal (between 40 and 180 min post‐prandially; P < 0.025, Student's t‐test). Among the three meals, significant differences were found in (P = 0.002, anova) and tlag (P = 0.011, anova). Compared with the control meal, the agar and pectin meals exhibited a significantly prolonged (P = 0.007 and P < 0.0001, respectively, Student's t‐test) and tlag (P = 0.006 and P = 0.002, respectively, Student's t‐test). Neither the agar nor pectin meal affected the post‐prandial glucose profile.

In healthy adults, agar and pectin delay gastric emptying but have no impact on the post‐prandial glucose response.
Different transfer of nociceptive sensitivity from rats with postnatal hippocampal lesions to control rats
Authors: Yamamotová Anna , Franĕk Miloslav , Vaculín Šimon , Št'astný František , Bubeníková‐Valešová Vĕra , Rokyta Richard
Published: July 2007

Hippocampal lesions in newborn rats alter the development of mechanisms involved in the processing of nociception. The hippocampal lesion was induced by the bilateral infusion, into the lateral cerebral ventricles, of 0.25 μL of saline containing either 0.25 μmol quinolinic acid (QUIN) and/or 0.25 μmol N‐acetyl‐l‐aspartyl‐l‐glutamate (NAAG) on postnatal day 12. The same amount of sterile saline was injected into the sham‐operated animals (group SHAM). It was expected that the QUIN‐ and NAAG‐lesioned rats would exhibit some differences in thermal pain perception; however, we wanted to know if the control rats would exhibit, at least in part, similar changes in pain perception as their chemically lesioned siblings with which they were housed. Young adult NAAG‐injured rats exhibited increased withdrawal latencies in the tail‐flick and plantar tests, whereas young adult QUIN‐injured animals exhibited only marginally decreased latencies. Nociceptive responses in the SHAM rats paralleled the littermates that had been neonatally treated with QUIN or NAAG, i.e. the responses in the SHAM(QUIN) group decreased, whereas the responses in the SHAM(NAAG) group increased. No significant changes in nociception were observed in intact animals, regardless of which group they were housed with. Our results show that social factors, which were originally demonstrated only for the pain behavior, may also influence basal nociceptive sensitivity in rats. We concluded that the ’sham operation’ may have had a long‐term, nonspecific impact on nociceptive behavior by inducing behavioral mimicry of other animals.
Working with child sexual abuse: a systemic perspective on whether children need to tell their therapist details of the abuse for healing to take place
Authors: Jones Fiona , Morris Mary
Published: July 2007

As clinicians working with children who have been sexually abused we have observed that many children choose not to give the therapist a detailed account of their abuse.1 Our hypothesis is that whether or not children tell their story to the therapist hinges upon several factors: whether they have been believed by their significant (non‐abusing) carer(s); their developmental stage; the therapeutic context; and whether they feel their therapist is available to hear the distressing details of the abuse. We explore this through two case studies and conclude that while children's ability to use therapy is affected by multiple factors – societal, cultural, personal, life histories and beliefs about the value of therapy – telling their therapist the details of their abusive experiences is not necessarily a part of effective therapy.