bluuebunny/crossref_metadata_2025 huggingface dataset:
Anti-cooperative assembly of the SRP19 and SRP68/72 components of the signal recognition particle
Authors: Maity Tuhin Subhra , Fried Howard M. , Weeks Kevin M.
Published: June 2008

The mammalian SRP (signal recognition particle) represents an important model for the assembly and role of inter-domain interactions in complex RNPs (ribonucleoproteins). In the present study we analysed the interdependent interactions between the SRP19, SRP68 and SRP72 proteins and the SRP RNA. SRP72 binds the SRP RNA largely via non-specific electrostatic interactions and enhances the affinity of SRP68 for the RNA. SRP19 and SRP68 both bind directly and specifically to the same two RNA helices, but on opposite faces and at opposite ends. SRP19 binds at the apices of helices 6 and 8, whereas the SRP68/72 heterodimer binds at the three-way junction involving RNA helices 5, 6 and 8. Even though both SRP19 and SRP68/72 stabilize a similar parallel orientation for RNA helices 6 and 8, these two proteins bind to the RNA with moderate anti-cooperativity. Long-range anti-cooperative binding by SRP19 and SRP68/72 appears to arise from stabilization of distinct conformations in the stiff intervening RNA scaffold. Assembly of large RNPs is generally thought to involve either co-operative or energetically neutral interactions among components. By contrast, our findings emphasize that antagonistic interactions can play significant roles in assembly of multi-subunit RNPs.
Viscosity stratification and the horizontal scale of end-driven cellular flow
Authors: Morris S. J. S.
Published: June 2008

We analyze isothermal viscosity-stratified creeping flow in a horizontal semi-infinite slot. The slot top and bottom are traction-free, and a cellular motion is driven by a given uniform shear stress applied at the vertical end. The viscosity is a prescribed function of depth: A thin low-viscosity channel of uniform viscosity mμ and thickness αD overlies a thick sublayer of viscosity μ and thickness D. By coupling a lubrication analysis of the channel to an exact solution for the sublayer, we show that in the limit of α→0, with ε=m∕α3 fixed, the flow has horizontal scale given for ε<5 by ℓ=2D∕3ε. The analysis is motivated by the long-standing suggestion that the presence of a low-viscosity layer could explain the existence of long end-driven cells beneath the Pacific and the Indo-Australian plates. Our formula supports that suggestion; applied to published viscosity profiles, it predicts that viscosity stratification could allow a cell length of up to seven times that for isoviscous flow.
Polymer chain generation for coarse-grained models using radical-like polymerization
Authors: Perez Michel , Lame Olivier , Leonforte Fabien , Barrat Jean-Louis
Published: June 2008

A versatile method is proposed to generate configurations of coarse-grained models for polymer melts. This method, largely inspired by chemical “radical polymerization,” is divided in three stages: (i) nucleation of radicals (reacting molecules caching monomers), (ii) growth of chains within a solvent of monomers and (iii) termination: annihilation of radicals and removal of residual monomers. The main interest of this method is that relaxation is performed while chains are generated. Pure mono and polydisperse polymer melts are generated and compared to the configurations generated by the push off method from Auhl et al. [J. Chem. Phys. 119, 12718 (2003)]. A detailed study of the static properties (radius of gyration, mean square internal distance, entanglement length) confirms that the radical-like polymerization technique is suitable to generate equilibrated melts. Moreover, the method is flexible and can be adapted to generate nanostructured polymers, namely, diblock and triblock copolymers.
Atomic-scale analysis of defect dynamics and strain relaxation mechanisms in biaxially strained ultrathin films of face-centered cubic metals
Authors: Kolluri Kedarnath , Gungor M. Rauf , Maroudas Dimitrios
Published: June 2008

We report results of a detailed systematic computational analysis of strain relaxation mechanisms and the associated defect dynamics in ultrathin, i.e., a few nanometers thick, Cu films subjected to a broad range of biaxial tensile strains. The analysis is based on isothermal-isostrain molecular-dynamics simulations of the response of Cu films that are oriented normal to the [111] crystallographic direction using an embedded-atom-method parametrization for Cu and multimillion-atom slab supercells. Our analysis reveals five regimes in the thin film’s mechanical response with increasing strain. Within the considered strain range, after an elastic response up to a biaxial strain level ε=5.5%, the strain in the metallic thin film is relaxed by plastic deformation. At low levels of the applied biaxial strain above the yield strain (ε∼6%), threading dislocation nucleation at the surface of the thin film in conjunction with vacancy cluster formation in the film leads eventually to the formation of voids that extend across the thickness of the film. For 6%<ε<8%, dislocations are emitted uniformly from the thin-film surface, inhibiting the nucleation of voids. For ε≥8%, in addition to nucleation of dislocations from the film surface, dislocation loops are generated in the bulk of the film and grow to intersect the thin-film surface. For ε≥10%, a high density of point defects in the film leads to nucleation of Frank partial dislocations that dissociate to form stacking fault tetrahedra. In addition, dislocation-dislocation interactions due to the high dislocation density lead to the formation of Lomer–Cottrell dislocation locks and complex stable dislocation junctions that act as obstacles to dislocation glide. As a result of these defect mechanisms, nanoscale domains are formed in the crystalline film with an average domain size of 1.5 nm and low-angle misorientations.
Purely squeezed states for quantum deformed systems
Authors: Aleixo A. N. F. , Balantekin A. B.
Published: June 2008

The generalized purely squeezed states for primary shape-invariant potentials systems, quantum deformed by different models, are constructed by the ladder-operator method within an algebraic approach based on supersymmetric quantum mechanics. The characteristic properties of these states as well as their quantum statistical properties and squeezing effects for generalized quadrature observables are studied and analyzed in terms of the quantum deformation parameter q. An application is given for a quantum deformed Pöschl–Teller potential system, and numerical results are presented and discussed in detail.
Photo- and thermally induced changes in the refractive index and film thickness of amorphous As2S8 film
Authors: Zou L. E. , Chen B. X. , Du L. P. , Hamanaka H. , Iso M.
Published: June 2008

Changes in the refractive index and thickness of amorphous As2S8 semiconductor film are observed under illumination, annealing–illumination, and annealing-illumination cycles. Properties of the As2S8 film are measured using techniques of prism coupler, x-ray diffraction spectra and Raman spectra. After light illumination the refractive index change in an as-deposited As2S8 film is one order of magnitude greater than that of an annealed As2S8 film, corresponding to ∼0.06 and ∼0.0057, respectively. Photoexpansions with a change in the relative film thickness of the as-deposited and annealed As2S8 film are nearly −3.5% and −2.1%, respectively, which exhibit the photodensification. The full reversibility of the photoinduced refractive index change is claimed on an annealed As2S8 film sample.
Approximate homomorphisms and derivations between C∗-ternary algebras
Authors: Rassias John Michael , Kim Hark-Mahn
Published: June 2008

In 1940, Ulam proposed the famous Ulam stability problem. In this paper we introduce a general Cauchy–Jensen functional equation and prove the generalized Ulam stability of C∗-ternary homomorphisms and C∗-ternary derivations in C∗-ternary algebras for the general Cauchy–Jensen equation.
Surface plasmon enhanced transmission and directivity through subwavelength slit in X-band microwaves
Authors: Wang Liang , Cao Jin-Xiang , Liu Lei , Lv You , Zheng Shi-Jian
Published: June 2008

In this letter, we experimentally investigated the transmission of microwaves through a single subwavelength slit surrounded by periodic grooves in metallic aluminum plates. Significant transmission enhancement (16.2-fold) and angular confinement (±18°) were observed at X-band microwave frequencies (8–12GHz). We demonstrated that the coupled surface plasmons were involved in the interesting transmission process. The little angular divergence was attributed to the periodic structures of the exit surface. The experimental results show good agreement with theory and are of relevance not only for further understanding the underlying science but also for enlarging applications based on this phenomenon.
Gain and continuous-wave laser power enhancement with a multiple discharge electric oxygen-iodine laser
Authors: Zimmerman J. W. , Woodard B. S. , Benavides G. F. , Carroll D. L. , Verdeyen J. T. , Palla A. D. , Solomon W. C.
Published: June 2008

Herein the authors report on the demonstration of a 70% enhancement in gain and 98% enhancement in continuous-wave laser power on the 1315nm transition of atomic iodine via an increase in flow rates and pressure using multiple discharges in an electric oxygen-iodine laser. O2(aΔ1) is produced by two parallel radio-frequency-excited electric discharges sustained in an O2–He–NO gas mixture, a secondary discharge predissociated the molecular iodine, and I(P1∕22) is then pumped using energy transferred from O2(aΔ1). A gain of 0.17%cm−1 was obtained and the total laser output power was 12.3W.
Femtosecond time-resolved measurement of LDS698 molecular processes under high pressure
Authors: Liu Bingguo , Jin Mingxing , Liu Hang , He Chunyuan , Jiang Dianwu , Ding Dajun
Published: June 2008

Femtosecond time-resolved measurements provide a means to understand high pressure effects on ultrafast molecular processes. We report here a method of transient absorption spectroscopy in conjunction with diamond anvil cells for investigating molecular energy relaxation of solidified LDS698 (pyridine, C19H23N2O4Cl) molecular solution. The pressure effect on the intermolecular energy relaxation is significant with increasing rate constant. The results are satisfactorily interpreted in terms of the intermolecular harmonic oscillator model with the anharmonic correction through surrounding thermal diffusion. This technique opens an approach to study molecular energy relaxation and other ultrafast processes of matter under high pressure.
Evidence of electron-phonon interaction on transport in n- and p-type silicon nanowires
Authors: Vaurette F. , Leturcq R. , Nys J. P. , Deresmes D. , Grandidier B. , Stiévenard D.
Published: June 2008

The authors studied the transport in n- and p-type silicon nanowires. When the temperature decreases from 325to75K, they observed a variation of the nanowire resistance, consistent with a transport governed by electron-phonon scattering. The lateral size of the nanowire down to 25nm is not found to cause further surface scattering, due to the presence of interface states which create a depleted region in the nanowires. Such depleted region allows thus to keep a carrier mobility in the nanowires similar to the bulk one.
Higher weaning weight improves postweaning growth and survival in young Merino sheep
Authors: Hatcher S. , Eppleston J. , Graham R. P. , McDonald J. , Schlunke S. , Watt B. , Thornberry K. J.
Published: June 2008

Two monitoring projects were conducted to investigate weaner mortality in commercial Merino flocks in the Yass and the Central Tablelands Rural Lands Protection Boards located in the Southern Tablelands agricultural region of New South Wales. The projects were conducted in Yass in 2005 and in the Central Tablelands in 2006. A random sample of weaners from four flocks in the Yass board and 11 flocks in the Central Tablelands board were regularly weighed, growth rates were calculated after weaning and survival was determined by the continuing presence of an individual weaner at subsequent weighing activities. Weaning weight was the most important factor in determining postweaning liveweight, growth rates and survival with the significant impact of weaning weight on liveweight persisting for up to 6 months after weaning. Despite the lightest weaners being capable of considerable compensatory growth given sufficient postweaning nutrition, the lightest 25% of weaners were more than twice as likely to die as heavier weaners. A focus on ewe nutrition and parasite control during late pregnancy and lactation will allow Merino producers to achieve higher weaning weights that will set their weaners up for strong postweaning growth with a decreased likelihood of mortality.
Spectral analysis of feeding patterns of steers divergent in residual feed intake
Authors: Dobos Robin , Herd Robert
Published: June 2008

Spectral analysis was used to quantify differences in feeding patterns of Angus steers genetically divergent in residual feed intake (RFI). Forty-two low RFI (more efficient) and 28 high RFI (less efficient) selection line steers were fed a feedlot diet through electronic feeders for 72 days. Mean (±s.e.) daily feed intake was 11.9 ± 0.076 and 12.7 ± 0.095 kg dry matter/day over the 72-day feeding period for low and high RFI steers, respectively. The high RFI steers exhibited different temporal cycles to the low RFI steers in daily feed intake and time spent feeding. However, patterns of number of eating sessions, feeding rate, the time spent eating and the number of eating sessions were similar. Further analysis of daily (24 h) feeding behaviour is required to help improve our understanding of the association between feeding behaviour and feed efficiency.
Single-molecule measurements of importin α/cargo complex dissociation at the nuclear pore
Authors: Sun Changxia , Yang Weidong , Tu Li-Chun , Musser Siegfried M.
Published: June 2008

Macromolecules are transported between the cytoplasm and the nucleoplasm of eukaryotic cells through nuclear pore complexes (NPCs). Large (more than ≈40 kDa) transport cargoes imported into the nucleus typically form a complex with at least one soluble transport cofactor of the importin (Imp) β superfamily. Many cargoes require an accessory cofactor, Imp α, which binds to Imp β and to the nuclear localization sequence on the cargo. We previously reported the use of narrow-field epifluorescence microscopy to directly monitor cargoes in transit through NPCs in permeabilized cells. We now report an expanded approach in which single-molecule fluorescence resonance energy transfer (FRET) is used to detect the disassembly of Imp α/cargo complexes as they transit through NPCs. We found that CAS, the recycling cofactor for Imp α, and RanGTP are essential for this dissociation process. After Imp α/cargo complex dissociation, most Imp α and cargo molecules entered the nucleoplasm. In contrast, the majority of Imp α/cargo complexes that did not dissociate at the NPC in the presence of CAS and RanGTP returned to the cytoplasm. These data are consistent with a model in which Imp α/cargo complexes are dissociated on the nucleoplasmic side of the NPC, and this dissociation requires both CAS and RanGTP.
Apolipoprotein (apo) E4 enhances HIV-1 cell entry
in vitro
, and the
APOE
ε4/ε4 genotype accelerates HIV disease progression
Authors: Burt Trevor D. , Agan Brian K. , Marconi Vincent C. , He Weijing , Kulkarni Hemant , Mold Jeffrey E. , Cavrois Marielle , Huang Yadong , Mahley Robert W. , Dolan Matthew J. , McCune Joseph M. , Ahuja Sunil K.
Published: June 2008

Originally recognized for their role in lipoprotein metabolism and cardiovascular disease, apolipoprotein (apo) E isoforms (apoE2, apoE3, and apoE4) have also been implicated to play a key role in several biological processes not directly related to their lipid transport function. For example, apoE4 contributes significantly to neurodegeneration in Alzheimer's disease. However, the role of apoE in infectious diseases is less well defined. Here, by examining a large cohort of HIV
+
European and African American subjects, we found that the
APOE
ε4/ε4 genotype is associated with an accelerated disease course and especially progression to death compared with the
APOE
ε3/ε3 genotype. However, an association between the ε4/ε4 genotype and HIV-associated dementia (HAD), a neurological condition with clinicopathological features similar to Alzheimer's disease, was not detected. Consistent with the genotype–phenotype relationships observed, compared with recombinant apoE3, apoE4 enhanced HIV fusion/cell entry of both R5 and X4 HIV strains
in vitro
. These findings establish apoE as a determinant of HIV-AIDS pathogenesis and raise the possibility that current efforts to convert apoE4 to an “apoE3-like” molecule to treat Alzheimer's disease might also have clinical applicability in HIV disease.
Ablation of thymic export causes accelerated decay of naïve CD4 T cells in the periphery because of activation by environmental antigen
Authors: Bourgeois Christine , Hao Zhenyue , Rajewsky Klaus , Potocnik Alexandre J. , Stockinger Brigitta
Published: June 2008

A model of chemical thymectomy by inducible Rag ablation was used to study peripheral T cell homeostasis. Induction of Rag ablation was efficient and complete, leading to cessation of thymic T cell production within 3–4 weeks. The decay of peripheral T cells became apparent with a delay of an additional 2–3 weeks and was entirely accounted for by loss of naïve T cells, whereas numbers of memory phenotype and regulatory T cells were not decreased. Naïve CD4 T cells decayed with an average half-life of 50 days, whereas naïve CD8 T cells exhibited a considerably longer half-life. The rapid decay of naïve CD4 T cells was not caused by intrinsic survival differences compared with naïve CD8 T cells, but was caused by changes in the lymphopenic environment resulting in higher microbial load and consequential activation. This finding suggests that in lymphopenic conditions involving compromised thymic function replenishment and survival of a naïve CD4 T cell repertoire may be severely curtailed because of chronic activation. Such a scenario might play a role in the aging immune system and chronic viral infection, such as HIV infection, and contribute to loss of CD4 T cells and impaired immune function. As our data show, continued replenishment with cells from the thymus seems to be required to maintain efficient gut mucosal defense.
Factors Associated With Diagnostic Evaluation for Tuberculosis Among Adults Hospitalized for Clinical Pneumonia in Thailand
Authors: Weber Ann M. , Areerat Peera , Fischer Julie E. , Thamthitiwat Somsak , Olsen Sonja J. , Varma Jay K.
Published: June 2008

Objective.

Thailand is one of 22 countries designated by the World Health Organization as “high burden” with regard to tuberculosis. Preventing nosocomial tuberculosis transmission remains an important, unmet need. We investigated the adequacy of current practices to evaluate hospitalized patients for tuberculosis, which is critical in preventing delayed diagnosis and nosocomial tuberculosis transmission.

Methods.

Thailand conducts active, population-based surveillance for pneumonia in 2 rural provinces. Case report forms are completed for all persons who are hospitalized and meet a case definition of having clinical pneumonia. We analyzed how frequently patients had an adequate diagnostic evaluation for infectious pulmonary tuberculosis, in accordance with national guidelines. We conducted multivariate analyses to determine patient and health-system factors associated with an inadequate diagnostic evaluation for tuberculosis and with tuberculosis disease.

Results.

Of 8,853 cases of clinical pneumonia between September 2003 and March 2006,73% were in patients not adequately evaluated for tuberculosis. Acid-fast bacilli (AFB)–positive tuberculosis was diagnosed in 188 cases, which was 2% of all pneumonia cases and 12% of pneumonia cases in patients adequately evaluated for tuberculosis. Diagnostic evaluations for tuberculosis were less commonly performed among those who were younger than 25 years of age, were female, and lacked cough, sputum production, hemoptysis, and dyspnea. Among patients adequately evaluated, a clinical syndrome of no cough, no hemoptysis, and normal chest radiography findings had a 95% negative predictive value.

Conclusions.

The prevalence of AFB-positive, pulmonary tuberculosis was high among adults hospitalized with clinical pneumonia in Thailand. Most patients were not adequately evaluated for tuberculosis. Efforts are needed to improve identification and diagnosis of infectious tuberculosis cases in hospitalized patients.
AIM Study on the Reaction of CH2SH Radical with Fluorine Atom
Authors: Sun Cui-hong , Zeng Yan-li , Meng Ling-peng , Zheng Shi-jun
Published: June 2008

The reaction of CH2SH radical with fluorine atom was studied at the levels of B3LYP/6-311G(d, p) and MP2(Full)/6-311G(d, p). The computational results show that the reaction has three channels and proceeds by the addition of fluorine atoms on carbon or sulfur sites of CH2SH, forming initial intermediates. The calculated results show that the channel in which fluorine attaches to the carbon atom to form CH2S and HF, is the most likely reaction pathway. Topological analysis of electron density was carried out for the three channels. The change trends of the chemical bonds on the reaction paths were discussed. The energy transition states and the structure transition regions (states) of the three channels were found. The calculated results show that the structure transition regions are broad in unobvious exothermic reactions or unobvious endothermic reactions, and are narrow in obvious exothermic reactions or obvious endothermic reactions.
Self-assembly of Polyaniline: Mechanism Study
Authors: Song Shi-yan , Pan Li-jia , Li Yun , Shi Yi , Pu Lin , Zhang Rong , Zheng You-dou
Published: June 2008

Anisotropic polyaniline (PAni) plates decorated with self-aligned nanofiber arrays were synthesized under the hydrothermal conditions. The formation mechanism of the self-assembled structures was investigated by studying the effect on PAni micro-structure with additive electrolyte in reaction system, and numerical simulation for dependence of systematic electrostatic energy on cross angles of self-assembled nanofiber arrays in grid textured PAni plates. It is proposed that the electrostatic interaction based on ionic doping charges plays an important role in the formation of the self-assembled PAni structures.
In response to ‘On E-value for tandem MS scoring schemes’
Authors: Khatun Jainab , Giddings Morgan
Published: June 2008

Contact:  giddings@unc.edu
Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models
Authors: Poon Art F. Y. , Lewis Fraser I. , Frost Simon D. W. , Kosakovsky Pond Sergei L.
Published: June 2008

Spidermonkey is a new component of the Datamonkey suite of phylogenetic tools that provides methods for detecting coevolving sites from a multiple alignment of homologous nucleotide or amino acid sequences. It reconstructs the substitution history of the alignment by maximum likelihood-based phylogenetic methods, and then analyzes the joint distribution of substitution events using Bayesian graphical models to identify significant associations among sites.

Availability: Spidermonkey is publicly available both as a web application at http://www.data-monkey.org and as a stand-alone component of the phylogenetic software package HyPhy, which is freely distributed on the web (http://www.hyphy.org) as precompiled binaries and open source.

Contact:  afpoon@ucsd.edu
Fossil oak galls preserve ancient multitrophic interactions
Authors: Stone Graham N , van der Ham Raymond W.J.M , Brewer Jan G
Published: June 2008

Trace fossils of insect feeding have contributed substantially to our understanding of the evolution of insect–plant interactions. The most complex phenotypes of herbivory are galls, whose diagnostic morphologies often allow the identification of the gall inducer. Although fossil insect-induced galls over 300 Myr old are known, most are two-dimensional impressions lacking adequate morphological detail either for the precise identification of the causer or for detection of the communities of specialist parasitoids and inquilines inhabiting modern plant galls. Here, we describe the first evidence for such multitrophic associations in Pleistocene fossil galls from the Eemian interglacial (130 000–115 000 years ago) of The Netherlands. The exceptionally well-preserved fossils can be attributed to extant species ofAndricusgallwasps (Hymenoptera: Cynipidae) galling oaks (Quercus), and provide the first fossil evidence of gall attack by herbivorous inquiline gallwasps. Furthermore, phylogenetic placement of one fossil in a lineage showing obligate host plant alternation implies the presence of a second oak species,Quercus cerris, currently unknown from Eemian fossils in northwestern Europe. This contrasts with the southern European native range ofQ. cerrisin the current interglacial and suggests that gallwasp invasions following human planting ofQ. cerrisin northern Europe may represent a return to preglacial distribution limits.
Insights from the amphioxus genome on the origin of vertebrate neural crest
Authors: Yu Jr-Kai , Meulemans Daniel , McKeown Sonja J. , Bronner-Fraser Marianne
Published: June 2008

The emergence of the neural crest has been proposed to play a key role in early vertebrate evolution by remodeling the chordate head into a “new head” that enabled early vertebrates to shift from filter feeding to active predation. Here we show that the genome of the basal chordate, amphioxus, contains homologs of most vertebrate genes implicated in a putative neural crest gene regulatory network (NC-GRN) for neural crest development. Our survey of gene expression shows that early inducing signals, neural plate border patterning genes, and melanocyte differentiation genes appear conserved. Furthermore, exogenous BMP affects expression of amphioxus neural plate border genes as in vertebrates, suggesting that conserved signals specify the neural plate border throughout chordates. In contrast to this core conservation, many neural crest specifier genes are not expressed at the amphioxus neural plate/tube border, raising the intriguing possibility that this level of the network was co-opted during vertebrate evolution. Consistent with this, the regulatory region of AmphiFoxD, homologous to the vertebrate neural crest specifier FoxD3, drives tissue-specific reporter expression in chick mesoderm, but not neural crest. Thus, evolution of a new regulatory element may have allowed co-option of this gene to the NC-GRN.
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes
Authors: Studer Romain A. , Penel Simon , Duret Laurent , Robinson-Rechavi Marc
Published: June 2008

A stringent branch-site codon model was used to detect positive selection in vertebrate evolution. We show that the test is robust to the large evolutionary distances involved. Positive selection was detected in 77% of 884 genes studied. Most positive selection concerns a few sites on a single branch of the phylogenetic tree: Between 0.9% and 4.7% of sites are affected by positive selection depending on the branches. No functional category was overrepresented among genes under positive selection. Surprisingly, whole genome duplication had no effect on the prevalence of positive selection, whether the fish-specific genome duplication or the two rounds at the origin of vertebrates. Thus positive selection has not been limited to a few gene classes, or to specific evolutionary events such as duplication, but has been pervasive during vertebrate evolution.
Development and validation of a mismatch amplification mutation PCR assay to monitor the dissemination of an emerging variant of Vibrio cholerae O1 biotype El Tor
Authors: Morita Masatomo , Ohnishi Makoto , Arakawa Eiji , Bhuiyan N.A. , Nusrin Suraia , Alam Munirul , Siddique A.K. , Qadri Firdausi , Izumiya Hidemasa , Nair G. Balakrish , Watanabe Haruo
Published: June 2008

A mismatch amplification mutation PCR assay was developed and validated for rapid detection of the biotype specific cholera toxin B subunit of V. cholerae O1. This assay will enable easy monitoring of the spread of a new emerging variant of the El Tor biotype of V. cholerae O1.
Microsatellite analysis reveals high genetic diversity but low genetic structure in Ethiopian indigenous cattle populations
Authors: Dadi H. , Tibbo M. , Takahashi Y. , Nomura K. , Hanada H. , Amano T.
Published: June 2008

Ethiopian cattle are under threat from uncontrolled mating practices and are at high risk of becoming genetically homogeneous. Therefore, to evaluate genetic diversity, population structure and degree of admixture, 30 microsatellite markers were genotyped using 351 DNA samples from 10 Ethiopian cattle populations and the Holstein breed. The mean number of alleles per cattle population ranged from 6.93 ± 2.12 in Sheko to 7.50 ± 2.35 in Adwa. The mean observed and expected heterozygosities were 0.674 ± 0.015 and 0.726 ± 0.019 respectively. Ethiopian cattle populations have maintained a high level of within‐population genetic differentiation (98.7%), the remainder being accounted for by differentiation among populations (1.3%). A highly significant deficiency in heterozygotes was detected within populations (FIS = 0.071; P < 0.001) and total inbreeding (FIT = 0.083; P < 0.001). The study populations were highly admixed but distinct from pure Bos taurus and Bos indicus breeds. The various levels of admixture and high genetic diversity make Ethiopian cattle populations suitable for future genetic improvement and utilization under a wide range of agro‐ecologies in Ethiopia.
A high‐resolution comparative radiation hybrid map of ovine chromosomal regions that are homologous to human chromosome 6 (HSA6)
Authors: Wu C. H. , Nomura K. , Goldammer T. , Hadfield T. , Dalrymple B. P. , McWilliam S. , Maddox J. F. , Womack J. E. , Cockett N. E.
Published: June 2008

In this study, we constructed high‐resolution radiation hybrid (RH) and comparative maps of ovine chromosomes or chromosomal segments that are homologous to human chromosome 6 (HSA6). A total of 251 markers were successfully genotyped across the recently developed USUoRH5000 whole‐genome panel; 208 of these markers were assigned to five RH linkage groups distributed on three ovine chromosomes (OAR8, 9 and 20). The RH maps have good correspondence with previous chromosome painting data, although a small centromeric region on OAR9 that is homologous to HSA6 had not been previously detected using human chromosome paints on ovine chromosomal spreads. High percentages of the ovine markers were identified as orthologues in the bovine (86.3%), dog (85.8%), horse (69.3%) and human (88.7%) genomes. These maps contribute to investigations in mammalian chromosome evolution and the search for economic trait loci in sheep.
Early season herbivore differentially affects plant defence responses to subsequently colonizing herbivores and their abundance in the field
Authors: POELMAN ERIK H. , BROEKGAARDEN COLETTE , VAN LOON JOOP J. A. , DICKE MARCEL
Published: June 2008

Induction of plant defences by early season herbivores can mediate interspecific herbivore competition. We have investigated plant‐mediated competition between three herbivorous insects through studies at different levels of biological integration. We have addressed (i) gene expression; (ii) insect behaviour and performance under laboratory conditions; and (iii) population dynamics under field conditions. We studied the expression of genes encoding a trypsin inhibitor and genes that are involved in glucosinolate biosynthesis in response to early season herbivory by Pieris rapae caterpillars in Brassica oleracea plants. Furthermore, we studied the interaction of these transcriptional responses with responses to secondary herbivory by the two specialist herbivores, P. rapae and Plutella xylostella, and the generalist Mamestra brassicae. P. rapae‐induced responses strongly interacted with plant responses to secondary herbivory. Sequential feeding by specialist herbivores resulted in enhanced or similar expression levels of defence‐related genes compared to primary herbivory by specialists. Secondary herbivory by the generalist M. brassicae resulted in lower gene expression levels than in response to primary herbivory by this generalist. Larval performance of both specialist and generalist herbivores was negatively affected by P. rapae‐induced plant responses. However, in the field the specialist P. xylostella was more abundant on P. rapae‐induced plants and preferred these plants over undamaged plants in oviposition experiments. In contrast, the generalist M. brassicae was more abundant on control plants and preferred undamaged plants for oviposition. P. rapae did not discriminate between plants damaged by conspecifics or undamaged plants. Our study shows that early season herbivory differentially affects transcriptional responses involved in plant defence to secondary herbivores and their population development dependent upon their degree of host plant specialization.
A comparison of grain‐size analysis methods for sand‐dominated fluvial sediments
Authors: CHEETHAM MICHAEL D. , KEENE ANNABELLE F. , BUSH RICHARD T. , SULLIVAN LEIGH A. , ERSKINE WAYNE D.
Published: June 2008

Grain‐size distribution is a fundamental tool for interpreting sedimentary units within depositional systems. The techniques assessed in this study are commonly used to determine grain‐size distributions for sand‐dominated sediments. However, the degree of consistency and differences in interpretation when using a combination of grain‐size methods have not yet been assessed systematically for sand‐dominated fluvial sediments. Results obtained from laser diffraction, X‐ray attenuation and scanning electron microscopy grain‐size analysis techniques were compared with those obtained from the traditional sieve/hydrometer method. Scanning electron microscopy was shown to provide an inaccurate quantitative analysis of grain‐size distributions because of difficulties in obtaining representative samples for examination. The X‐ray attenuation method is unsuitable for sand‐dominated sediments because of its upper size range of only 300 μm. The consistently strong correlation between the laser diffraction results and the sieve/hydrometer results shows that these methods are comparable for sand‐dominated fluvial sediments. Provided that sample preparation is consistent, the latter two methods can be used together within a study of such sediments while maintaining a high degree of accuracy. These results indicate that data for sand‐dominated fluvial sediments gained from the long‐established sieve/hydrometer method can be compared with confidence to those obtained by modern studies using laser diffraction techniques.
The interaction between Cistaceae and a highly specific seed‐harvester ant in a Mediterranean scrubland
Authors: Bastida F. , Talavera S. , Ortiz P. L. , Arista M.
Published: June 2008

We studied the interaction between the ant Goniomma kugleri and Cistaceae in a Cistus ladanifer‐dominated scrubland, in southwestern Spain. We monitored seed harvesting, and studied ant preferences among Cistaceae seeds and their capture efficiencies for preferred seeds. For the stand of C. ladanifer, we estimated seed losses due to the ants. Harvesting was restricted to two seasons: mid‐autumn to late winter, and late spring. Ant diet relied on Cistaceae seeds: during autumn and winter 90% of seeds returned to nests were of C. ladanifer, and the remaining fraction also comprised Cistaceae seeds. At this time, the ants harvested seeds directly from the plants. In late spring, the ant diet consisted of Tuberaria guttata s.l. seeds. Goniomma kugleri selectively collected Cistaceae seeds. For preferred species, seed removal rates at the colony level and seed capture times invested by individual workers were correlated with seed size. Because of shorter capture time and higher success frequency, capture efficiency in terms of number of seeds captured per unit time was higher for small‐seeded species. Although each ant colony collected large numbers (up to 105) of C. ladanifer seeds over the autumn–winter season, the impact of ant removal on the annual seed output was moderate, at around 20%. It is likely that, in C. ladanifer, the staggered seed release period, and the pulsed exposure of seed clumps in capsules through progressive locule dehiscence, effectively minimise seed losses to the ants.
VASCULAR DYSFUNCTION IN THE α‐GALACTOSIDASE A‐KNOCKOUT MOUSE IS AN ENDOTHELIAL CELL‐, PLASMA MEMBRANE‐BASED DEFECT
Authors: Park James L , Whitesall Steven E , D’Alecy Louis G , Shu Liming , Shayman James A
Published: June 2008

Fabry disease results from an X‐linked mutation in the lysosomal α‐galactosidase A (Gla) gene. Defective Gla results in multi‐organ accumulation of neutral glycosphingolipids (GSLs), especially in the vascular endothelium, with the major GSL accumulated being globotriaosylceramide (Gb3). Excessive endothelial Gb3 accumulation is associated with increased thrombosis, atherogenesis and endothelial dysfunction. However, the mechanism(s) by which endothelial dysfunction occurs is unclear. The purpose of the present study was to further characterize the vasculopathy associated with a murine model of Fabry disease.

Vascular reactivity was performed in vessels from wild‐type (Gla+/0) and Gla‐knockout (Gla−/0) mice. Conscious blood pressure and heart rate were measured in Gla+/0 and Gla−/0 mice by telemetry.

The present study demonstrates that vascular smooth muscle (VSM) contractions to phenylephrine and serotonin, but not to U46619, were blunted in Gla−/0 mice. Endothelium‐dependent contraction and receptor‐mediated endothelium‐dependent relaxation to acetylcholine were significantly attenuated in vessels from Gla−/0 mice. However, receptor‐independent endothelium‐dependent relaxation to the calcium ionophore ionomycin remained intact in vessels from Gla−/0 mice. Furthermore, VSM reactivity was normal in aortas from Gla−/0 mice in the absence of endothelium. These changes in vascular function were observed without changes in whole‐animal blood pressure or heart rate.

These results suggest that the vasculopathy associated with Fabry disease is localized to the endothelium, despite the accumulation of GSLs throughout the vasculature.
ASSOCIATION BETWEEN PPARGC1A GENE POLYMORPHISMS AND CORONARY ARTERY DISEASE IN A CHINESE POPULATION
Authors: Zhang Yan , Xu Weiwei , Li Xiaoyu , Tang Yibo , Xie Peng , Ji Yong , Fan Leming , Chen Qi
Published: June 2008

Peroxisome proliferrator‐activated receptor γ coactivator‐1α (PGC‐1α; PPARGC1A) is a coactivator of the nuclear hormone receptor family that participates in the transcriptional programme of lipid metabolism and oxidative stress implicated in atherogenesis. Therefore, in the present study, we investigated PPARGC1A polymorphisms in the prevalence of coronary artery disease (CAD).

A case‐control study comprising 342 patients with CAD and 334 controls was performed in a Chinese population. Two single nucleotide polymorphisms (Gly482Ser and Thr394Thr) in the PPARGC1A gene were genotyped and compared using the polymerase chain reaction–restriction fragment length polymorphism method.

The XA (GA + AA) genotype of Gly482Ser displayed a higher frequency in CAD patients than that in control subjects (P = 0.019; adjusted odds ratio = 1.53; 95% confidence interval 1.06–2.20). No significant difference in Thr394Thr genotype distribution or in Gly482Ser–Thr394Thr haplotype combinations was found between CAD patients and controls. Furthermore, we found that the significantly increased risk of CAD associated with the XA genotypes of Gly482Ser was more evident among subjects who were younger than 64 years of age, female, overweight and with hypertension.

The results indicate that the PPARGC1A Gly482Ser polymorphism may contribute to the risk of CAD in the Chinese population investigated.
A NOVEL HIGH‐THROUGHPUT ASSAY FOR THE QUANTITATIVE ASSESSMENT OF RECEPTOR TRAFFICKING
Authors: Grimsey Natasha L , Narayan Pritika J , Dragunow Mike , Glass Michelle
Published: June 2008

Receptor transport between intracellular compartments has important consequences for receptor function and is an exciting area of current study. Existing methods for studying receptor trafficking often require labour‐intensive techniques or are difficult to quantify reliably. We report a novel high‐throughput method that uses automated imaging and analysis tools to accurately quantify cannabinoid CB1 receptor trafficking.

Haemagglutinin (HA)‐tagged CB1 was stably expressed in HEK‐293 cells and cell surface or total receptors were detected immunocytochemically. Images of receptor and nuclear staining were acquired with an automated fluorescent microscope (Discovery‐1; Molecular Devices, Sunnyvale, CA, USA) and quantified at high throughput with MetaMorph (Molecular Devices) software. The ‘Granularity’ assay measured internalization by counting receptor clusters that appear during receptor endocytosis, a well‐established approach. Our assay, referred to as ‘Total Grey Value per Cell’ (TGVC), measures the total fluorescence above background, normalized to cell count.

Incubation with the cannabinoid agonist HU‐210 (100 nmol/L) resulted in rapid CB1 internalization, reaching a maximum within 20 min. Whether quantified by Granularity or TGVC, the time‐course of endocytosis could be modelled with exponentially derived curves and with similar half‐lives. We demonstrate the sensitivity of our TGVC method by measuring the concentration dependence of CB1 internalization and its versatility by measuring downregulation following chronic agonist exposure, whereby total CB1 was reduced to approximately 55% of basal after 3 h.

The TGVC quantification method described is efficient, accurate and versatile and is likely to provide a valuable tool in receptor trafficking studies.
Lessons from a review of thyroglobulin assays in the management of thyroid cancer
Authors: Wong J. , Lu Z. , Doery J. , Fuller P.
Published: June 2008

Thyroglobulin (Tg) measurement has become increasingly an important and integral part of the follow up and management of patients with differentiated thyroid cancer. Clinicians predominantly rely on Tg for decision‐making for surveillance of patients with differentiated thyroid cancer, but despite this new reliance, issues regarding Tg measurement have not been appropriately addressed especially within a local context. In the process of developing an institutional protocol we have identified that there are significant clinical and technical issues regarding Tg measurement, and surprisingly Tg assessment is currently not part of an external quality control programme. We conducted a small pilot study to specifically emphasize some of the assay issues. We aim to inform endocrinologists, pathologists and nuclear medicine physicians, the need and urgency for these issues to be addressed to improve the ongoing surveillance of differentiated thyroid cancer.
Expression of functional Toll‐like receptors and nucleotide‐binding oligomerization domain proteins in murine cementoblasts and their upregulation during cell differentiation
Authors: Nemoto E. , Honda T. , Kanaya S. , Takada H. , Shimauchi H.
Published: June 2008

Background and Objective:  While the primary role of cementoblasts is to synthesize the components of cementum, we have reported that immortalized murine cementoblasts (OCCM‐30) express functional Toll‐like receptor (TLR)‐2 and ‐4, and these receptors are involved in the alteration of gene expression associated with cementum formation and in the upregulation of osteoclastogenesis‐associated molecules, such as receptor activator of nuclear factor‐κB (NF‐κB) ligand. We hypothesized that cementoblasts express a wide range of pattern recognition receptors in a manner comparable to osteoblasts, which are known to express various functional TLRs and nucleotide‐binding oligomerization domain (NOD) proteins.

Material and Methods:  Murine cementoblasts and pre‐osteoblasts were used. The gene and protein levels of TLRs/NODs were analyzed using real‐time polymerase chain reaction and flow cytometry. Interleukin‐6 (IL‐6) and activated NF‐κB were measured using enzyme‐linked immunosorbent assay.

Results:  The expressions of TLR‐1, ‐2, ‐4, ‐6 and ‐9, CD14, NOD‐1 and ‐2 were detected in cementoblasts and were upregulated upon differentiation induced by ascorbic acid. Similar patterns were observed in the mouse MC3T3‐E1 osteoblast cell line. Synthetic ligands, Pam3CSK4 (TLR‐1/2 agonist), Pam2CGDPKHPKSF (TLR‐2/6 agonist), lipid A (TLR4 agonist), CpG DNA (TLR‐9 agonist), FK565 (NOD1 agonist) and muramyldipeptide (NOD2 agonist), effectively induced NF‐κB activation in cementoblasts and/or ascorbic acid‐treated cementoblasts. Furthermore, these ligands induced IL‐6 production in a NF‐κB‐dependent manner in cementoblasts and/or ascorbic acid‐treated cementoblasts.

Conclusion:  These results indicate that cementoblasts possess functional TLR and NOD signaling systems and have a similar capacity to osteoblasts in responding to a wide variety of pathogens.
Isolation and characterization of microsatellite markers in Oligoryzomys longicaudatus (Muridae, Sigmodontinae, Oryzomini), the natural reservoir of genotype Andes hantavirus
Authors: GONZÁLEZ‐ITTIG RAÚL E. , SALAZAR‐BRAVO JORGE , POLOP JAIME J. , GARDENAL CRISTINA N.
Published: June 2008

The rodent Oligoryzomys longicaudatus or long‐tailed pygmy rice rat is the reservoir of the aetiological agent of the hantavirus pulmonary syndrome in southern Argentina and Chile. We characterize 11 polymorphic microsatellite loci which would be useful for studies on microgeographical population structure in the species. Amplification of these loci in 42 individuals from four natural populations revealed four to 21 alleles per locus, and values of observed heterozygosities ranging from 0.371 to 0.896. Cross‐species amplifications showed that some of the primers designed may be useful for other species of the genus Oligoryzomys.
What is your diagnosis? Muculent pleural effusion from a dog
Authors: Riegel Casey M. , Stockham Steven L. , Patton Kristin M. , Thomas Casey L.
Published: June 2008

Abstract: Pleural effusion was examined from a 5‐year‐old, female Brittany Spaniel with a 7‐day history of dyspnea, anorexia, and diarrhea. The fluid was yellow, cloudy, and slightly gelatinous, and had a total protein concentration of 2.8 g/dL, a total nucleated cell concentration of 1.1 × 103/μL, and a triglyceride concentration of 177 mg/dL. A cytocentrifuged preparation contained a mixed inflammatory cell population with a predominance of small lymphocytes and abundant mucinous material in the background. The dog died 3 days later and a mass was found within the lumen and wall of the right auricle of the heart at necropsy. Histopathologic sections of the mass contained a population of anaplastic spindle cells diffusely suspended in a pale basophilic matrix, consistent with myxosarcoma. The cells were positive for vimentin and negative for cytokeratin, desmin, and von Willebrand factor VIII‐related antigen. A myxoid matrix was confirmed by positive staining with Alcian blue. Myxosarcoma is a rare cardiac tumor in dogs that should be considered, along with mucus‐producing carcinomas and bile, as a cause of muculent effusion.