bluuebunny/crossref_metadata_2025 huggingface dataset:
Atomic-level imaging of Mo-V-O complex oxide phase intergrowth, grain boundaries, and defects using HAADF-STEM
Authors: Pyrz William D. , Blom Douglas A. , Sadakane Masahiro , Kodato Katsunori , Ueda Wataru , Vogt Thomas , Buttrey Douglas J.
Published: March 2010

In this work, we structurally characterize defects, grain boundaries, and intergrowth phases observed in various Mo-V-O materials using aberration-corrected high-angle annular dark-field (HAADF) imaging within a scanning transmission electron microscope (STEM). Atomic-level imaging of these preparations clearly shows domains of the orthorhombic M1-type phase intergrown with the trigonal phase. Idealized models based on HAADF imaging indicate that atomic-scale registry at the domain boundaries can be seamless with several possible trigonal and M1-type unit cell orientation relationships. The alignment of two trigonal domains separated by an M1-type domain or vice versa can be predicted by identifying the number of rows/columns of parallel symmetry operators. Intergrowths of the M1 catalyst with the M2 phase or with the Mo
5
O
14
-type phase have not been observed. The resolution enhancements provided by aberration-correction have provided new insights to the understanding of phase equilibria of complex Mo-V-O materials. This study exemplifies the utility of STEM for the characterization of local structure at crystalline phase boundaries.
Association of RIG-I with innate immunity of ducks to influenza
Authors: Barber Megan R. W. , Aldridge Jerry R. , Webster Robert G. , Magor Katharine E.
Published: March 2010

Ducks and wild waterfowl perpetuate all strains of influenza viruses in nature. In their natural host, influenza viruses typically cause asymptomatic infection and little pathology. Ducks are often resistant to influenza viruses capable of killing chickens. Here, we show that the influenza virus sensor, RIG-I, is present in ducks and plays a role in clearing an influenza infection. We show evidence suggesting that RIG-I may be absent in chickens, providing a plausible explanation for their increased susceptibility to influenza viruses compared with ducks. RIG-I detects RNA ligands derived from uncapped viral transcripts and initiates the IFN response. In this study, we show that the chicken embryonic fibroblast cell line, DF-1, cannot respond to a RIG-I ligand. However, transfection of duck RIG-I into DF-1 cells rescues the detection of ligand and induces IFN-β promoter activity. Additionally, DF-1 cells expressing duck RIG-I have an augmented IFN response resulting in decreased influenza replication after challenge with either low or highly pathogenic avian influenza virus. Implicating RIG-I in the antiviral response to an infection in vivo, we found that
RIG-I
expression is induced 200 fold, early in an innate immune response in ducks challenged with the H5N1 virus A/Vietnam/1203/04. Finding this natural disease resistance gene in ducks opens the possibility of increasing influenza resistance through creation of a transgenic chicken.
One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue
Authors: Nury Hugues , Poitevin Frédéric , Van Renterghem Catherine , Changeux Jean-Pierre , Corringer Pierre-Jean , Delarue Marc , Baaden Marc
Published: March 2010

Recently discovered bacterial homologues of eukaryotic pentameric ligand-gated ion channels, such as the
Gloeobacter violaceus
receptor (GLIC), are increasingly used as structural and functional models of signal transduction in the nervous system. Here we present a one-microsecond-long molecular dynamics simulation of the GLIC channel pH stimulated gating mechanism. The crystal structure of GLIC obtained at acidic pH in an open-channel form is equilibrated in a membrane environment and then instantly set to neutral pH. The simulation shows a channel closure that rapidly takes place at the level of the hydrophobic furrow and a progressively increasing quaternary twist. Two major events are captured during the simulation. They are initiated by local but large fluctuations in the pore, taking place at the top of the M2 helix, followed by a global tertiary relaxation. The two-step transition of the first subunit starts within the first 50 ns of the simulation and is followed at 450 ns by its immediate neighbor in the pentamer, which proceeds with a similar scenario. This observation suggests a possible two-step domino-like tertiary mechanism that takes place between adjacent subunits. In addition, the dynamical properties of GLIC described here offer an interpretation of the paradoxical properties of a permeable A13′F mutant whose crystal structure determined at 3.15 Å shows a pore too narrow to conduct ions.
Progressive renal injury from transgenic expression of human carbonic anhydrase IV folding mutants is enhanced by deficiency of p58
IPK
Authors: Datta Rupak , Shah Gul N. , Rubbelke Timothy S. , Waheed Abdul , Rauchman Michael , Goodman Alan G. , Katze Michael G. , Sly William S.
Published: March 2010

Mutations in the human carbonic anhydrase IV (hCAIV) have been associated with retinal degeneration in an autosomal-dominant form of retinitis pigmentosa (RP17). Prior in vitro cell culture studies confirmed that all of the RP17-associated hCAIV mutations cause protein misfolding, leading to endoplasmic reticulum (ER) stress–induced apoptosis in cells expressing the mutant proteins. To evaluate the physiological impacts of these folding mutants in other carbonic anhydrase IV–producing tissues, we generated two transgenic mouse lines expressing R219S or R14W hCAIV under control of the endogenous hCAIV promoter. Expression of either of these mutant proteins in kidneys caused progressive renal injury in male transgenic mice as evidenced by an age-dependent increase in the tubule cell apoptosis starting at approximately 20 weeks of age and vacuolization throughout the renal cortex in older mice. Up-regulation of the ER chaperone, BiP, was observed in the cells of the renal cortex of the male transgenic mice, suggesting ER stress as a causal factor for the renal injury. The renal injury inflicted by expression of the folding mutants was markedly enhanced by haploinsufficiency of the ER cochaperone p58
IPK
. The transgenic mice expressing the hCAIV folding mutants on a p58
IPK
heterozygous background showed extensive renal tubular apoptosis by approximately 10 weeks of age in both male and female mice. These data indicate that expression of the RP17-associated folding mutants of hCAIV can adversely affect tissues beyond the retina and their in vivo proteotoxicity is sensitive to modulation of the protein folding environment of the ER.
Transcriptome and metabolome profiling of field-grown transgenic barley lack induced differences but show cultivar-specific variances
Authors: Kogel Karl-Heinz , Voll Lars M. , Schäfer Patrick , Jansen Carin , Wu Yongchun , Langen Gregor , Imani Jafargholi , Hofmann Jörg , Schmiedl Alfred , Sonnewald Sophia , von Wettstein Diter , Cook R. James , Sonnewald Uwe
Published: March 2010

The aim of the present study was to assess possible adverse effects of transgene expression in leaves of field-grown barley relative to the influence of genetic background and the effect of plant interaction with arbuscular mycorrhizal fungi. We conducted transcript profiling, metabolome profiling, and metabolic fingerprinting of wild-type accessions and barley transgenics with seed-specific expression of (1,3-1, 4)-β-glucanase (GluB) in Baronesse (B) as well as of transgenics in Golden Promise (GP) background with ubiquitous expression of codon-optimized
Trichoderma harzianum
endochitinase (ChGP). We found more than 1,600 differential transcripts between varieties GP and B, with defense genes being strongly overrepresented in B, indicating a divergent response to subclinical pathogen challenge in the field. In contrast, no statistically significant differences between ChGP and GP could be detected based on transcriptome or metabolome analysis, although 22 genes and 4 metabolites were differentially abundant when comparing GluB and B, leading to the distinction of these two genotypes in principle component analysis. The coregulation of most of these genes in GluB and GP, as well as simple sequence repeat-marker analysis, suggests that the distinctive alleles in GluB are inherited from GP. Thus, the effect of the two investigated transgenes on the global transcript profile is substantially lower than the effect of a minor number of alleles that differ as a consequence of crop breeding. Exposing roots to the spores of the mycorrhizal
Glomus
sp. had little effect on the leaf transcriptome, but central leaf metabolism was consistently altered in all genotypes.
Cerebral cavernous malformations proteins inhibit Rho kinase to stabilize vascular integrity
Authors: Stockton Rebecca A. , Shenkar Robert , Awad Issam A. , Ginsberg Mark H.
Published: March 2010

Endothelial cell–cell junctions regulate vascular permeability, vasculogenesis, and angiogenesis. Familial cerebral cavernous malformations (CCMs) in humans result from mutations of CCM2 (malcavernin, OSM, MGC4607), PDCD10 (CCM3), or KRIT1 (CCM1), a Rap1 effector which stabilizes endothelial cell–cell junctions. Homozygous loss of KRIT1 or CCM2 produces lethal vascular phenotypes in mice and zebrafish. We report that the physical interaction of KRIT1 and CCM2 proteins is required for endothelial cell–cell junctional localization, and lack of either protein destabilizes barrier function by sustaining activity of RhoA and its effector Rho kinase (ROCK). Protein haploinsufficient Krit1+/− or Ccm2+/− mouse endothelial cells manifested increased monolayer permeability in vitro, and both Krit1+/− and Ccm2+/− mice exhibited increased vascular leak in vivo, reversible by fasudil, a ROCK inhibitor. Furthermore, we show that ROCK hyperactivity occurs in sporadic and familial human CCM endothelium as judged by increased phosphorylation of myosin light chain. These data establish that KRIT1–CCM2 interaction regulates vascular barrier function by suppressing Rho/ROCK signaling and that this pathway is dysregulated in human CCM endothelium, and they suggest that fasudil could ameliorate both CCM disease and vascular leak.
Lymph node–resident lymphatic endothelial cells mediate peripheral tolerance via Aire-independent direct antigen presentation
Authors: Cohen Jarish N. , Guidi Cynthia J. , Tewalt Eric F. , Qiao Hui , Rouhani Sherin J. , Ruddell Alanna , Farr Andrew G. , Tung Kenneth S. , Engelhard Victor H.
Published: March 2010

Peripheral immune tolerance is generally thought to result from cross-presentation of tissue-derived proteins by quiescent tissue-resident dendritic cells to self-reactive T cells that have escaped thymic negative selection, leading to anergy or deletion. Recently, we and others have implicated the lymph node (LN) stroma in mediating CD8 T cell peripheral tolerance. We demonstrate that LN-resident lymphatic endothelial cells express multiple peripheral tissue antigens (PTAs) independent of the autoimmune regulator (Aire). They directly present an epitope derived from one of these, the melanocyte-specific protein tyrosinase, to tyrosinase-specific CD8 T cells, leading to their deletion. We also show that other LN stromal subpopulations express distinct PTAs by mechanisms that vary in their Aire dependence. These results establish lymphatic endothelial cells, and potentially other LN-resident cells, as systemic mediators of peripheral immune tolerance.
Antagonism of the complement component C4 by flavivirus nonstructural protein NS1
Authors: Avirutnan Panisadee , Fuchs Anja , Hauhart Richard E. , Somnuke Pawit , Youn Soonjeon , Diamond Michael S. , Atkinson John P.
Published: March 2010

The complement system plays an essential protective role in the initial defense against many microorganisms. Flavivirus NS1 is a secreted nonstructural glycoprotein that accumulates in blood, is displayed on the surface of infected cells, and has been hypothesized to have immune evasion functions. Herein, we demonstrate that dengue virus (DENV), West Nile virus (WNV), and yellow fever virus (YFV) NS1 attenuate classical and lectin pathway activation by directly interacting with C4. Binding of NS1 to C4 reduced C4b deposition and C3 convertase (C4b2a) activity. Although NS1 bound C4b, it lacked intrinsic cofactor activity to degrade C4b, and did not block C3 convertase formation or accelerate decay of the C3 and C5 convertases. Instead, NS1 enhanced C4 cleavage by recruiting and activating the complement-specific protease C1s. By binding C1s and C4 in a complex, NS1 promotes efficient degradation of C4 to C4b. Through this mechanism, NS1 protects DENV from complement-dependent neutralization in solution. These studies define a novel immune evasion mechanism for restricting complement control of microbial infection.
Lymph node fibroblastic reticular cells directly present peripheral tissue antigen under steady-state and inflammatory conditions
Authors: Fletcher Anne L. , Lukacs-Kornek Veronika , Reynoso Erika D. , Pinner Sophie E. , Bellemare-Pelletier Angelique , Curry Mark S. , Collier Ai-Ris , Boyd Richard L. , Turley Shannon J.
Published: March 2010

Lymph node stromal cells (LNSCs) can induce potent, antigen-specific T cell tolerance under steady-state conditions. Although expression of various peripheral tissue–restricted antigens (PTAs) and presentation to naive CD8+ T cells has been demonstrated, the stromal subsets responsible have not been identified. We report that fibroblastic reticular cells (FRCs), which reside in the T cell zone of the LN, ectopically express and directly present a model PTA to naive T cells, inducing their proliferation. However, we found that no single LNSC subset was responsible for PTA expression; rather, each subset had its own characteristic antigen display. Studies to date have concentrated on PTA presentation under steady-state conditions; however, because LNs are frequently inflammatory sites, we assessed whether inflammation altered stromal cell–T cell interactions. Strikingly, FRCs showed reduced stimulation of T cells after Toll-like receptor 3 ligation. We also characterize an LNSC subset expressing the highest levels of autoimmune regulator, which responds potently to bystander inflammation by up-regulating PTA expression. Collectively, these data show that diverse stromal cell types have evolved to constitutively express PTAs, and that exposure to viral products alters the interaction between T cells and LNSCs.
Selenium incorporation using recombinant techniques
Authors: Walden Helen
Published: March 2010

Using selenomethionine to phase macromolecular structures is common practice in structure determination, along with the use of selenocysteine. Selenium is consequently the most commonly used heavy atom for MAD. In addition to the well established recombinant techniques for the incorporation of selenium in prokaryal expression systems, there have been recent advances in selenium labelling in eukaryal expression, which will be discussed. Tips and things to consider for the purification and crystallization of seleno-labelled proteins are also included.
Carrying out an optimal experiment
Authors: Dauter Zbigniew
Published: March 2010

Diffraction data collection is the last experimental stage in structural crystallography. It has several technical and theoretical aspects and a compromise usually has to be found between various parameters in order to achieve optimal data quality. The influence and importance of various experimental parameters and their consequences are discussed in the context of different data applications, such as molecular replacement, anomalous phasing, high-resolution refinement or searching for ligands.
Recent developments in classical density modification
Authors: Cowtan Kevin
Published: March 2010

Classical density-modification techniques (as opposed to statistical approaches) offer a computationally cheap method for improving phase estimates in order to provide a good electron-density map for model building. The rise of statistical methods has lead to a shift in focus away from the classical approaches; as a result, some recent developments have not made their way into classical density-modification software. This paper describes the application of some recent techniques, including most importantly the use of prior phase information in the likelihood estimation of phase errors within a classical density-modification framework. The resulting software gives significantly better results than comparable classical methods, while remaining nearly two orders of magnitude faster than statistical methods.
Progress in rational methods of cryoprotection in macromolecular crystallography
Authors: Alcorn Thomas , Juers Douglas H.
Published: March 2010

Cryogenic cooling of macromolecular crystals is commonly used for X-ray data collection both to reduce crystal damage from radiation and to gather functional information by cryogenically trapping intermediates. However, the cooling process can damage the crystals. Limiting cooling-induced crystal damage often requires cryoprotection strategies, which can involve substantial screening of solution conditions and cooling protocols. Here, recent developments directed towards rational methods for cryoprotection are described. Crystal damage is described in the context of the temperature response of the crystal as a thermodynamic system. As such, the internal and external parts of the crystal typically have different cryoprotection requirements. A key physical parameter, the thermal contraction, of 26 different cryoprotective solutions was measured between 294 and 72 K. The range of contractions was 2–13%, with the more polar cryosolutions contracting less. The potential uses of these results in the development of cryocooling conditions, as well as recent developments in determining minimum cryosolution soaking times, are discussed.
Diffraction data analysis in the presence of radiation damage
Authors: Borek Dominika , Cymborowski Marcin , Machius Mischa , Minor Wladek , Otwinowski Zbyszek
Published: March 2010

In macromolecular crystallography, the acquisition of a complete set of diffraction intensities typically involves a high cumulative dose of X-ray radiation. In the process of data acquisition, the irradiated crystal lattice undergoes a broad range of chemical and physical changes. These result in the gradual decay of diffraction intensities, accompanied by changes in the macroscopic organization of crystal lattice order and by localized changes in electron density that, owing to complex radiation chemistry, are specific for a particular macromolecule. The decay of diffraction intensities is a well defined physical process that is fully correctable during scaling and merging analysis and therefore, while limiting the amount of diffraction, it has no other impact on phasing procedures. Specific chemical changes, which are variable even between different crystal forms of the same macromolecule, are more difficult to predict, describe and correct in data. Appearing during the process of data collection, they result in gradual changes in structure factors and therefore have profound consequences in phasing procedures. Examples of various combinations of radiation-induced changes are presented and various considerations pertinent to the determination of the best strategies for handling diffraction data analysis in representative situations are discussed.
The magic triangle goes MAD: experimental phasing with a bromine derivative
Authors: Beck Tobias , Gruene Tim , Sheldrick George M.
Published: March 2010

Experimental phasing is an essential technique for the solution of macromolecular structures. Since many heavy-atom ion soaks suffer from nonspecific binding, a novel class of compounds has been developed that combines heavy atoms with functional groups for binding to proteins. The phasing tool 5-amino-2,4,6-tribromoisophthalic acid (B3C) contains three functional groups (two carboxylate groups and one amino group) that interact with proteins via hydrogen bonds. Three Br atoms suitable for anomalous dispersion phasing are arranged in an equilateral triangle and are thus readily identified in the heavy-atom substructure. B3C was incorporated into proteinase K and a multiwavelength anomalous dispersion (MAD) experiment at the Br K edge was successfully carried out. Radiation damage to the bromine–carbon bond was investigated. A comparison with the phasing tool I3C that contains three I atoms for single-wavelength anomalous dispersion (SAD) phasing was also carried out.
A rational approach to heavy-atom derivative screening
Authors: Joyce M. Gordon , Radaev Sergei , Sun Peter D.
Published: March 2010

Despite the development in recent times of a range of techniques for phasing macromolecules, the conventional heavy-atom derivatization method still plays a significant role in protein structure determination. However, this method has become less popular in modern high-throughput oriented crystallography, mostly owing to its trial-and-error nature, which often results in lengthy empirical searches requiring large numbers of well diffracting crystals. In addition, the phasing power of heavy-atom derivatives is often compromised by lack of isomorphism or even loss of diffraction. In order to overcome the difficulties associated with the `classical' heavy-atom derivatization procedure, an attempt has been made to develop a rational crystal-free heavy-atom derivative-screening method and a quick-soak derivatization procedure which allows heavy-atom compound identification. The method includes three basic steps: (i) the selection of likely reactive compounds for a given protein and specific crystallization conditions based on pre-defined heavy-atom compound reactivity profiles, (ii) screening of the chosen heavy-atom compounds for their ability to form protein adducts using mass spectrometry and (iii) derivatization of crystals with selected heavy-metal compounds using the quick-soak method to maximize diffraction quality and minimize non-isomorphism. Overall, this system streamlines the process of heavy-atom compound identification and minimizes the problem of non-isomorphism in phasing.
Radiation damage in macromolecular crystallography: what is it and why should we care?
Authors: Garman Elspeth F.
Published: March 2010

Radiation damage inflicted during diffraction data collection in macromolecular crystallography has re-emerged in the last decade as a major experimental and computational challenge, as even for crystals held at 100 K it can result in severe data-quality degradation and the appearance in solved structures of artefacts which affect biological interpretations. Here, the observable symptoms and basic physical processes involved in radiation damage are described and the concept of absorbed dose as the basic metric against which to monitor the experimentally observed changes is outlined. Investigations into radiation damage in macromolecular crystallography are ongoing and the number of studies is rapidly increasing. The current literature on the subject is compiled as a resource for the interested researcher.
Circulating vitamin D and colorectal adenomas in Japanese men
Authors: Takahashi Ryota , Mizoue Tetsuya , Otake Toshie , Fukumoto Jin , Tajima Osamu , Tabata Shinji , Abe Hiroshi , Ohnaka Keizo , Kono Suminori
Published: March 2010

Accumulating evidence suggests that vitamin D has anticarcinogenic effects. However, it is unclear whether the nutrient is involved in the early stage of colorectal carcinogenesis. We examined the association between circulating vitamin D concentrations and colorectal adenomas in Japanese men. The study subjects comprised 656 cases of colorectal adenomas and 648 controls with normal colonoscopy among male self defense officials receiving a pre‐retirement health examination between 1997 and 2004. Plasma or serum levels of 25‐hydroxyvitamin D [25(OH)D] were measured using a radioimmunoassay method. Logistic regression analysis was used to obtain odds ratios (OR) and 95% confidence intervals (CI) with adjustment for potential confounding variables. Overall, there was no measurable association between circulating 25(OH)D concentrations and colorectal adenomas. When the analysis was restricted to subjects whose blood was taken during the winter season (November–April), the prevalence odds of colorectal adenomas for the highest versus lowest quartile of 25(OH)D was statistically significantly decreased (OR = 0.58; 95% CI = 0.34–0.99). The reduction was more pronounced for the rectum (OR = 0.22) and distal colon (OR = 0.47) than for proximal colon (OR = 0.70). During the summer season (May–October), higher levels of 25(OH)D were associated with an increased odds of small, but not large, adenomas. The present study adds to evidence that high levels of circulating vitamin D measured during darker season is associated with decreased prevalence of adenomas in the distal sites of the colorectum. (Cancer Sci 2010)
Genetic diversity within and among Atlantic cod (Gadus morhua) farmed in marine cages: a proof‐of‐concept study for the identification of escapees
Authors: Glover K. A. , Dahle G. , Westgaard J. I. , Johansen T. , Knutsen H. , Jørstad K. E.
Published: March 2010

This study presents a molecular genetic characterization of Atlantic cod reared in commercial marine farms. Samples consisted of approximately 47 fish collected from nine cages located on four farms throughout Norway. In addition, 28 farmed escapees were recaptured in the sea (443 fish in total). Nine microsatellite loci and the Pan I gene were analysed, revealing a total of 181 alleles. Each sample contained 43–63% of total allelic variation. Comparing variation with published data for wild cod indicates that lower genetic variation exists within single cages than in wild populations. Significant linkage disequilibrium was observed amongst pairs of loci in all samples, suggesting a low number of contributing parental fish. Global FST was 0.049, and the highest pairwise FST value (pooled loci) was 0.085. For single loci, the Pan I gene was the most diagnostic, displaying a global FST of 0.203. Simulations amongst the samples collected on farms revealed an overall correct self‐assignment percentage of 75%, demonstrating a high probability of identifying individuals to their farm of origin. Identification of the 28 escapees revealed a single cage as the most likely source of origin for half of the escapees, whilst the remaining fish were assigned to a mixture of samples, suggesting more than one source of escapees.
Impact of cutting frequency on the vigour of Rumex obtusifolius
Authors: Stilmant D. , Bodson B. , Vrancken C. , Losseau C.
Published: March 2010

The control of Rumex obtusifolius, even with the use of herbicides, is difficult in permanent grasslands where R. obtusifolius reduces both productivity and nutritive value of herbage. It is important to find alternative approaches to managing R. obtusifolius. Two greenhouse experiments were conducted to compare the impact of different cutting frequencies, which simulated grazing (three cuts), silage making (two cuts) and hay making (one cut) on shoot and root measurements of the vigour of R. obtusifolius. In both experiments the same cutting frequencies were imposed but in Experiment 1 the treatments were imposed for 2 years and in Experiment 2 for 1 year. Compared to the silage‐making and hay‐making treatments, there was a reduction in the vigour of the aerial parts of R. obtusifolius on the grazing treatment, associated with a reduction in the number of leaves (Experiment 1), in the size of the largest leaf (Experiment 1) and in the herbage mass of dry matter (Experiments 1 and 2). Roots had higher concentrations of total soluble sugar and lower concentrations of starch in the grazing treatment than in the other treatments. These results showed that a reduction in the vigour of R. obtusifolius in permanent grasslands is possible only if the plants are submitted to a high frequency of defoliation under cutting or grazing.
Biogeographical contingency and the evolution of tropical anchovies (genus Cetengraulis) from temperate anchovies (genus Engraulis)
Authors: Grant W. S. , Lecomte Frédéric , Bowen Brian W.
Published: March 2010

Aim  Similar regimes of selection in different geographical settings can deterministically produce similar adaptive morphologies. We tested the hypothesis that the evolutionary trajectories of fish in upwelling zones can be altered by biogeographic contingencies in the biological and physical environment.

Location  Eastern Pacific and western Atlantic oceans.

Methods  We estimated phylogenetic relationships among eastern Pacific temperate anchovies (genus Engraulis) and tropical anchovies (genus Cetengraulis) with neighbour‐joining and Bayesian tree analysis of a 521‐bp segment of mitochondrial DNA cytochrome b. Available sequences for five additional engraulid taxa were included to establish polarity of the tree. Bayesian estimates (BEAST) of time to most recent common ancestor (TMRCA) for the nodes in the phylogeny were calibrated with divergence between Cetengraulis edentulus and Cetengraulis mysticetus precipitated by the rise of the Panama Isthmus 2.8–3.2 Ma.

Results  Neighbour‐joining and Bayesian trees indicate that South American Engraulis anchoita (Argentina) and Engraulis ringens (Chile) together are basal sister taxa to the California anchovy (Engraulis mordax) and Old World anchovies (Engraulis japonicas, Engraulis australis, Engraulis capensis and Engraulis encrasicolus). The two tropical species of Cetengraulis are sister‐taxa to Californian E. mordax, even though their phenotypes and ecologies differ markedly. A relaxed molecular clock indicates a TMRCA between Californian E. mordax and Cetengraulis at about 4.2 Ma (3.0–6.3 Ma 95% highest probability density).

Main conclusions  The TMRCA between the California anchovy, E. mordax, and tropical Cetengraulis coincides with the formation of the Gulf of California, which provided opportunities for allopatric isolation during climate oscillations. Mid‐Pliocene warming (3.1–2.9 Ma) may have trapped ancestors of Cetengraulis in the Gulf of California, where they evolved digestive tract morphologies to exploit inshore tropical habitats with low plankton productivities. While populations of several other temperate fishes have become isolated in the Gulf of California, few of these derived species show strong adaptive shifts from temperate sister taxa or range expansions into the tropical provinces of the western Atlantic and eastern Pacific.
The endemic plant families and the palms of New Caledonia: a biogeographical analysis
Authors: Heads Michael
Published: March 2010

This paper provides a panbiogeographical analysis of the endemic plant families and the palms of New Caledonia. There are three endemic plant families in New Caledonia and several genera that were previously recognized as endemic families. Of these taxa, some are sister to widespread Northern Hemisphere or global groups (Canacomyrica, Austrotaxus, Amborella). The others belong to trans‐Indian Ocean groups (Strasburgeria), trans‐tropical Pacific groups (Oncotheca) or Tasman Sea/Coral Sea groups (Phelline, Paracryphia) that are sister to widespread Northern Hemisphere or global groups. In palms, the four clades show allopatric regional connections in, respectively: (1) western Indonesia, Malaysia and Thailand; (2) Vanuatu/Fiji and the southern Ryukyu Islands near Taiwan; (3) the western Tasman/Coral Sea (eastern Australia, New Guinea and the Solomon Islands); and (4) the eastern Tasman/Coral Sea (Lord Howe and Norfolk Islands, New Zealand, Vanuatu, Fiji and the Solomon Islands). The four clades thus belong to different centres of endemism that overlap in New Caledonia. The patterns are attributed not to chance dispersal and adaptive radiation but to the different histories of the eight terranes that fused to produce modern New Caledonia. Trans‐tropical Pacific connections can be related to the Cretaceous igneous plateaus that formed in the central Pacific and were carried, with plate movement, west to the Solomon Islands and New Zealand, and east to Colombia and the Caribbean.
Characterization of bovine neutrophil β2‐adrenergic receptor function
Authors: LaBRANCHE T. P. , EHRICH M. F. , EYRE P.
Published: March 2010

LaBranche, T. P., Ehrich, M. F., Eyre, P. Characterization of bovine neutrophil β2‐adrenergic receptor function.J. vet. Pharmacol. Therap.doi: 10.1111/j.1365‐2885.2009.01143.x.

This study compares bovine leukocyte β‐adrenergic receptor densities to that of the rat, demonstrates for the first time a functional β2‐adrenergic receptor signaling pathway in steer neutrophils, and investigates the effect of an inflammatory stimulus on that signaling pathway. The β1‐/β2‐adrenergic antagonist[3H]CGP‐12177 demonstrated that rat lymphocyte specific binding‐site density was highest, followed by steer and dairy cow lymphocytes, and lastly steer and dairy cow neutrophils. The β2‐adrenergic agonist terbutaline stimulated steer neutrophil adenosine 3,5‐cyclic monophosphate (cAMP) production, an effect increased by inclusion of ≥1 × 10−8 mphorbol 12‐myristate 13‐acetate (PMA), an activator of protein kinase C. Both terbutaline and the nonselective phosphodiesterase inhibitor 3‐isobutyl‐1‐methylxanthine (IBMX) independently decreased steer neutrophil superoxide anion production in a concentration‐dependent manner, with 1 × 10−4 mIBMX enhancing both the potency and efficacy of the terbutaline effect (up to 74% reduction in superoxide anion production). Superoxide anion production was also reduced by the synthetic cAMP analog 8‐bromo‐cAMP, which increased the potency of the IBMX effect on superoxide anion production. Taken together, these data demonstrate the presence of a β2‐adrenergic receptor signaling pathway in bovine neutrophils much like that described in other animal species, as well as the potential for an inflammatory stimulus to alter its function.
Benzydamine as a useful substrate of hepatic flavin‐containing monooxygenase activity in veterinary species
Authors: CAPOLONGO F. , SANTI A. , ANFOSSI P. , MONTESISSA C.
Published: March 2010

Capolongo, F., Santi, A., Anfossi, P., Montesissa, C. Benzydamine as a useful substrate of hepatic flavin‐containing monooxygenase activity in veterinary species.J. vet. Pharmacol. Therap. doi: 10.1111/j.1365‐2885.2009.01145.x.

Benzydamine (BZ), a weak base and an indazole derivative with analgesic and antipyretic properties used in human and veterinary medicine, is metabolized in human, rat, cattle and rabbit to a wide range of metabolites. One of the main metabolites, BZN‐oxide (BZ‐NO), is produced in the liver and brain by flavin‐containing monooxigenases (FMOs), by liver and brain enzymes. To evaluate the suitability of BZ as an FMO probe in veterinary species, BZ metabolism was studiedin vitrousing liver microsomes from bovine, rabbit and swine. Kinetic parameters,KmandVmax, of BZ‐NO production, were evaluated to corroborate the pivotal role of FMOs. Inhibition studies were carried out by heat inactivation and by specific FMO chemical inhibitors: trimethylamine and methimazole. The results confirmed the presence of FMO activity in the liver and the role of BZ as a suitable marker of FMO enzyme activities for the veterinary species considered.
Pharmacokinetics of intrarectal omeprazole in alpacas
Authors: MARMULAK T. , STANLEY S. , KASS P. H. , WIEBE V. , McKEMIE D. , PUSTERLA N.
Published: March 2010

Marmulak, T., Stanley, S., Kass, P.H., Wiebe, V., McKemie, D., Pusterla, N. Pharmacokinetics of intrarectal omeprazole in alpacas. J. vet. Pharmacol. Therap. doi: 10.1111/j.1365‐2885.2009.00149.x.

The purpose of this study was to evaluate the pharmacokinetics of omeprazole in three different vehicles when administered rectally to six alpacas. Alpacas were given single doses of omeprazole (4 mg/kg) in a double‐blinded, randomized cross‐over design with a 1 week washout period. Omeprazole formulations consisted of (1) Treatment A: omeprazole paste mixed in surgical lubricant (2) Treatment B: omeprazole capsule contents in 8.4% sodium bicarbonate and (3) Treatment C: omeprazole capsule contents in surgical lubricant and 8.4% sodium bicarbonate solution. Plasma samples were drawn at 0, 5, 10, 15, 30, 45, 60, 90, 120, 180, 300 and 480 min. Omeprazole plasma concentrations were determined by high‐pressure liquid chromatography‐mass spectrometry. Pharmacokinetic results demonstrated median peak plasma concentrations (Cmax) of 7.35 (3.2–15.2), 7.30 (1.7–10.9) and 8.65 (1.8–19.3) ng/mL and median area under the concentration curve (AUC(0–180)) of 747 (237–1681) min·ng/mL, 552.9 (39–1063) min·ng/mL, and 972 (107–1841) min·ng/mL for treatments A, B and C, respectively. The median half‐lives were similar between groups: 38, 50, and 53 min. As a result of the low measured omeprazole plasma concentrations, it is assumed that rectal absorption of omeprazole is poor in alpacas and not an effective route of administration.
IL‐10 and TGF‐β Immunoregulatory Cytokines rather than Natural Regulatory T Cells are Associated with the Resolution Phase of Vogt‐Koyanagi‐Harada (VKH) Syndrome
Authors: Commodaro A. G. , Peron J. P. S. , Genre J. , Arslanian C. , Sanches L. , Muccioli C. , Rizzo L. V. , Belfort Jr R.
Published: March 2010

The pro‐inflammatory cytokines play a critical role in the initiation and propagation of ocular autoimmune diseases. Regulation of these cytokines is generally mediated by the immunoregulatory cytokine such as IL‐10 or TGF‐β. In this study, we investigated the immunoregulatory cytokine profile and frequency of natural regulatory T cells (nTregs) in patients with Vogt‐Koyanagi‐Harada (VKH). We obtained the peripheral blood mononuclear cells (PBMC) from patients with VKH and healthy controls. The cytokine profile from supernatants of PBMC cultured with or without phytohaemagglutinin (PHA) was measured by ELISA, the percentage of CD4+ Foxp3+ and CD25highFoxp3+ T regulatory cells were analysed by flow cytometry, and the transcriptional level of Foxp3 expression was analysed by real‐time quantitative PCR. The immunoregulatory cytokines, TGF‐β and IL‐10, increased in patients with VKH in the inactive stage of the disease. We observed no significant difference in the CD4+ Foxp3+ and CD25highFoxp3+ T cells as well as no reduction in FOXP3 mRNA expression in the patients with VKH when compared to healthy controls. We showed in our work, an increase in IFN‐γ secretion by PBMC of patients with VKH in the active stage of the disease when compared to healthy controls and patients in the inactive stage. Our data suggest that IL‐10 and TGF‐β cytokines, rather than nTregs are associated with the resolution phase of the disease and may have a more relevant role in controlling this disease.
Perioperative management of combined heart–liver transplantation in patients with cirrhosis, renal insufficiency, or pulmonary hypertension
Authors: Eyraud D. , Ben Menna M. , Vaillant J. C. , Kitajima K. , Lebray P. , Pavie A. , Poynard T. , Coriat P. , Hannoun L.
Published: March 2010

Eyraud D, Ben Menna M, Vaillant JC, Kitajima K, Lebray P, Pavie A, Poynard T, Coriat P, Hannoun L. Perioperative management of combined heart–liver transplantation in patients with cirrhosis, renal insufficiency, or pulmonary hypertension.  Clin Transplant 2011: 25: 228–234. © 2010 John Wiley & Sons A/S.

Abstract:  Stating the main problem:  Only few reports have detailed perioperative management and outcome of combined heart and liver transplantation (CHLT), and none describe the long‐term renal function.

Methods:  Three patients presented clinical signs of cardiomyopathy with reduced ejection fraction and proven cirrhosis with evidence of portal hypertension. Two of them presented renal failure, and the other pulmonary hypertension. After cardiac transplantation and closure of the sternum, liver transplantation was performed using systematically venovenous double‐limb (portal and caval) bypass.

Results:  Mean cold ischemic time for heart and liver was 2 h 46 min and 12 h 47 min, respectively. Intraoperative hemodynamics remained grossly stable during surgery. Mean transfusions were 12 red blood cell packs. All three patients received anti‐R‐Il2 antibodies at post‐operative day 1 and 4. Mean plasma creatinine concentration was 90 ± 8 μmol/L one yr post‐CHLT, vs 160 ± 62 μmol/L pre‐CHLT. All three patients are alive with functional grafts after a mean follow‐up of 26 months (12–38).

Conclusion:  CHLT could be performed safely through two consecutive and independent usual procedures. Perioperative hemodynamic stability, minimal blood loss, and routine splanchnic decompression are probably major determinants of a favorable outcome and good long‐term renal function.
NADPH‐Diaphorase Activity and NO Synthase Expression in the Olfactory Epithelium of the Bovine
Authors: Wenisch S. , Arnhold S.
Published: March 2010

With 2 figures

NADPH‐diaphorase (NADPH‐d) staining of the bovine olfactory epithelium was compared with the immunohistochemical localization of nitric oxide synthase (NOS), soluble guanylyl cyclase, and cGMP (cyclic guanosine 3′,5′‐monophosphate). Out of the three isoforms, only the inducible NOS (NOS‐II) was found at the epithelial surface correlating with the strong labelling for NADPH‐d. In contrast, light diaphorase staining associated with deeper epithelial regions did not coincide with any NOS immunoreactivity. As there is overlapping expression of NOS‐II, soluble guanylyl cyclase and cGMP at the luminal surface morphologically occupied by dendritic knobs of olfactory receptor neurons and microvillar endings of supporting cells, the nitric oxide (NO)/cGMP pathway is likely to be involved in modulating the odour signals during olfactory transduction.
Isolation and Differentiation of Mesenchymal Stem Cells From Bovine Umbilical Cord Blood
Authors: Raoufi MF , Tajik P , Dehghan MM , Eini F , Barin A
Published: March 2010

Contents

Currently, mesenchymal stem cells (MSCs) are used in veterinary clinical applications. Bone marrow and adipose tissue are the most common sources of stem cells derived from adult animals. However, cord blood which is collected non‐invasively is an alternative source of stem cells other than bone marrow and adipose tissue. Moreover, high availability and lower immunogenicity of umbilical cord blood (UCB) haematopoietic stem cells compared to other sources of stem cell therapy such as bone marrow have made them a considerable source for cell therapy, but MSCs is not highly available in cord blood and their immunogenicity is poorly understood. In this study, the cells with spindle morphology from 7 of 9 bovine UCB samples were isolated and cultured. These mesenchymal stromal cells were successfully differentiated to osteocytes, chondrocytes and adipocytes. In addition, Oct‐4 and SH3 were determined by RT‐PCR assay. It is the first report of isolation, culture, characterization and differentiation of bovine umbilical stem cells.
Anti‐inflammatory effect of an insulin infusion in patients on maintenance haemodialysis: A randomized controlled pilot study
Authors: VOS FREDERIEK E , MANNING PATRICK J , SUTHERLAND WAYNE HF , SCHOLLUM JOHN B , WALKER ROBERT J
Published: March 2010

Aim:  A pilot study to investigate the anti‐inflammatory effect of insulin in patients on maintenance haemodialysis.

Background:  Elevated concentrations of pro‐inflammatory and oxidative mediators are thought to contribute to the increased cardiovascular risk in haemodialysis. Insulin has been demonstrated to have anti‐inflammatory properties and a continuous low‐dose insulin infusion in critically ill patients is associated with improved outcomes. The anti‐inflammatory effects of insulin in haemodialysis have not been investigated.

Methods:  In a single‐blind cross‐over study, 11 stable, non‐diabetic, haemodialysis patients received a continuous insulin infusion (Actrapid 2 IU/h) during a dialysis of 4 h or a conventional dialysis in random order. Normoglycaemia was maintained by a modified glucose dialysate and glucose infusion. Blood samples were collected at baseline, 1, 4, 6 and 24 h. C‐reactive protein (CRP), tumour necrosis factor‐α, interleukin‐6, neopterin, vascular cell adhesion molecule 1, protein thiols, dityrosine and peroxides were measured.

Results:  Insulin produced a significant reduction in median CRP over the immediate dialysis phase (confidence interval) by 6% (2–9% (95% CI), P = 0.006) and an even greater decline at 24 h (19% (8–28%, 95% CI), P = 0.001) compared with values of the conventional dialysis. No significant changes were observed in the other markers. Median glucose levels were comparable during both dialysis sessions.

Conclusions:  During haemodialysis, insulin may have a modest anti‐inflammatory effect as evident by a reduction in CRP that appears to have a persistent effect over the next 24 h post dialysis. More studies are required to examine longer‐term benefits as well as the potential role in more high‐risk individuals.
Effect of pediatric advanced life support course on pediatric residents' intubation success
Authors: Kendirli Tanıl , Çaltık Aysun , Duman Murat , Yılmaz Hayri Levent , Yıldızdaş Dinçer , Boşnak Mehmet , Tekin Deniz , Atay Nilgün
Published: March 2010

Background:  The Pediatric Advanced Life Support Program (PALS) course very important for teaching about intubation, resuscitation, shock, trauma, respiratory failure and rhythm disturbances. The aim of the present study was to evaluate the effect of the PALS course on pediatric residents' intubation success during their rotation, daytime and night‐time practice in the pediatric intensive care unit (PICU).

Methods:  The study was carried out from 1 March 2005 to 28 February 2007. The study period had two parts, in that the number of attempts and successful intubations performed by pediatric residents, and the pediatric intensivist successful intubation ratio were evaluated in two different periods: before the PALS course, 1 March 2005–28 February 2006, and after the PALS course, 5 March 2006–28 February 2007. The participating residents' pediatric levels (PL) were classed as PL‐1, PL‐2, PL‐3, PL‐4, and all had first experience in the PICU at the PL‐1 level. The PALS instructor was a pediatric emergency or intensive care doctor. We evaluated whether the PALS course influenced intubation success or not.

Results:  Sixteen residents participated in the study. The proportion of successful intubations was 110 (53.3%) and 104 (65.4%) attempts before and after the PALS course, respectively. The proportion of intubations done by intensivists decreased from 49.1% to 31.7% before and after PALS. The most frequently used endotracheal tube (ETT) internal diameter (ID) was 4.0 mm, and cuffed ETT was used 16% and 21% before and after the course, respectively. Appropriate placing of ETT tip occurred 70.4% and 82.2% of the time before and after the PALS course, respectively. Proportion of successful intubations by residents increased in all levels, except for PL‐1. The most important reason for unsuccessful attempts was inappropriate patient position. Only one patient could not be intubated, and laryngeal mask airway was used in that case. During intubation, complications were broken teeth in two patients before the course, and subglottic stenosis developed in only one patient due to cuffed ETT.

Conclusion:  Successful intubation is a life‐saving intervention during resuscitation, ETT revision for extubation or obstruction for extubation or obstruction during mechanical ventilation. This skill can be developed in the PALS course and by clinical study in PICU and pediatric emergency services. The PALS course must be given to pediatric residents especially within the first year. Also, cuffed ETT can be used for infants and children.