bluuebunny/crossref_metadata_2025 huggingface dataset:
Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability
Authors: Vaitheeswaran S. , Thirumalai D.
Published: November 2008

Confinement effects on protein stability are relevant in a number of biological applications ranging from encapsulation in the cylindrical cavity of a chaperonin, translocation through pores, and structure formation in the exit tunnel of the ribosome. Consequently, free energies of interaction between amino acid side chains in restricted spaces can provide insights into factors that control protein stability in nanopores. Using all-atom molecular dynamics simulations, we show that 3 pair interactions between side chains—hydrophobic (Ala–Phe), polar (Ser–Asn) and charged (Lys–Glu)—are substantially altered in hydrophobic, water-filled nanopores, relative to bulk water. When the pore holds water at bulk density, the hydrophobic pair is strongly destabilized and is driven to large separations corresponding to the width and the length of the cylindrical pore. As the water density is reduced, the preference of Ala and Phe to be at the boundary decreases, and the contact pair is preferred. A model that accounts for the volume accessible to Phe and Ala in the solvent-depleted region near the pore boundary explains the simulation results. In the pore, the hydrogen-bonded interactions between Ser and Asn have an enhanced dependence on their relative orientations, as compared with bulk water. When the side chains of Lys and Glu are restrained to be side by side, parallel to each other, then salt bridge formation is promoted in the nanopore. Based on these results, we argue and demonstrate that for a generic amphiphilic sequence, cylindrical confinement is likely to enhance thermodynamic stability relative to the bulk.
Toward understanding early Earth evolution: Prescription for approach from terrestrial noble gas and light element records in lunar soils
Authors: Ozima Minoru , Yin Qing-Zhu , Podosek Frank A. , Miura Yayoi N.
Published: November 2008

Because of the almost total lack of geological record on the Earth's surface before 4 billion years ago, the history of the Earth during this period is still enigmatic. Here we describe a practical approach to tackle the formidable problems caused by this lack. We propose that examinations of lunar soils for light elements such as He, N, O, Ne, and Ar would shed a new light on this dark age in the Earth's history and resolve three of the most fundamental questions in earth science: the onset time of the geomagnetic field, the appearance of an oxygen atmosphere, and the secular variation of an Earth–Moon dynamical system.
Enhanced optical properties of chemical vapor deposited single crystal diamond by low-pressure/high-temperature annealing
Authors: Meng Yu-fei , Yan Chih-shiue , Lai Joseph , Krasnicki Szczesny , Shu Haiyun , Yu Thomas , Liang Qi , Mao Ho-kwang , Hemley Russell J.
Published: November 2008

Single crystal diamond produced by chemical vapor deposition (CVD) at very high growth rates (up to 150 μm/h) has been successfully annealed without graphitization at temperatures up to 2200 °C and pressures <300 torr. Crystals were annealed in a hydrogen environment by using microwave plasma techniques for periods of time ranging from a fraction of minute to a few hours. This low-pressure/high-temperature (LPHT) annealing enhances the optical properties of this high-growth rate CVD single crystal diamond. Significant decreases are observed in UV, visible, and infrared absorption and photoluminescence spectra. The decrease in optical absorption after the LPHT annealing arises from the changes in defect structure associated with hydrogen incorporation during CVD growth. There is a decrease in sharp line spectral features indicating a reduction in nitrogen-vacancy-hydrogen (NVH
−
) defects. These measurements indicate an increase in relative concentration of nitrogen-vacancy (NV) centers in nitrogen-containing LPHT-annealed diamond as compared with as-grown CVD material. The large overall changes in optical properties and the specific types of alterations in defect structure induced by this facile LPHT processing of high-growth rate single-crystal CVD diamond will be useful in the creation of diamond for a variety of scientific and technological applications.
The crystal structure of avian CD1 reveals a smaller, more primordial antigen-binding pocket compared to mammalian CD1
Authors: Zajonc Dirk M. , Striegl Harald , Dascher Christopher C. , Wilson Ian A.
Published: November 2008

The molecular details of glycolipid presentation by CD1 antigen-presenting molecules are well studied in mammalian systems. However, little is known about how these non-classical MHC class I (MHCI) molecules diverged from the MHC locus to create a more complex, hydrophobic binding groove that binds lipids rather than peptides. To address this fundamental question, we have determined the crystal structure of an avian CD1 (chCD1–2) that shares common ancestry with mammalian CD1 from ≈310 million years ago. The chCD1–2 antigen-binding site consists of a compact, narrow, central hydrophobic groove or pore rather than the more open, 2-pocket architecture observed in mammalian CD1s. Potential antigens then would be restricted in size to single-chain lipids or glycolipids. An endogenous ligand, possibly palmitic acid, serves to illuminate the mode and mechanism of ligand interaction with chCD1–2. The palmitate alkyl chain is inserted into the relatively shallow hydrophobic pore; its carboxyl group emerges at the receptor surface and is stabilized by electrostatic and hydrogen bond interactions with an arginine residue that is conserved in all known CD1 proteins. In addition, other novel features, such as an A′ loop that interrupts and segments the normally long, continuous α1 helix, are unique to chCD1–2 and contribute to the unusually narrow binding groove, thereby limiting its size. Because birds and mammals share a common ancestor, but the rate of evolution is slower in birds than in mammals, the chCD1–2-binding groove probably represents a more primordial CD1-binding groove.
Highlylanddenantioselective variants of horseradish peroxidase discovered by an ultrahigh-throughput selection method
Authors: Antipov Eugene , Cho Art E. , Wittrup K. Dane , Klibanov Alexander M.
Published: November 2008

A highly efficient selection method for enhanced enzyme enantioselectivity based on yeast surface display and fluorescence-activated cell sorting (FACS) is developed and validated. Its application to horseradish peroxidase has resulted in enzyme variants up to 2 orders of magnitude selective toward either substrate enantiomer at will. These marked improvements in enantioselectivity are demonstrated for the surface-bound and soluble enzymes and rationalized by computational docking studies.
Bionics in Engineering Education Considerations, Experiences and Conclusions
Authors: Neurohr Ralf , Dragomirescu Cristian
Published: November 2008

During recent years bionics, a new discipline which is in charge with the transfer of the principles of construction, regulation, interaction and organisation of biology into innovative technical solutions, has attracted significant interest from various industries. Based on this request for bionic expertise in engineering, the faculty for teaching engineering in foreign languages (FILS) at ‘Politehnica’ University of Bucharest started a course in bionics in SS 2007, which was supported by the expertise of the German ‘Bionik‐Kompetenz‐Netz’, one of the leading organizations in bionics. This is the report on the considerations involved in the course concept, the first experiences with the students′ acceptance, some conclusions and future perspectives for extending bionics activities at ‘Politehnica’. Finally, within the last section, the evaluation of a questionnaire, filled in by the students at the end of the course, will be presented. In order to avoid any confusion, considering overlapping or mixing up with other bio‐disciplines related to technology, the paper starts with a short introduction, explaining the principles of bionics and providing a clear definition of the field.
Tim-3 expression defines a novel population of dysfunctional T cells with highly elevated frequencies in progressive HIV-1 infection
Authors: Jones R. Brad , Ndhlovu Lishomwa C. , Barbour Jason D. , Sheth Prameet M. , Jha Aashish R. , Long Brian R. , Wong Jessica C. , Satkunarajah Malathy , Schweneker Marc , Chapman Joan M. , Gyenes Gabor , Vali Bahareh , Hyrcza Martin D. , Yue Feng Yun , Kovacs Colin , Sassi Aref , Loutfy Mona , Halpenny Roberta , Persad Desmond , Spotts Gerald , Hecht Frederick M. , Chun Tae-Wook , McCune Joseph M. , Kaul Rupert , Rini James M. , Nixon Douglas F. , Ostrowski Mario A.
Published: November 2008

Progressive loss of T cell functionality is a hallmark of chronic infection with human immunodeficiency virus 1 (HIV-1). We have identified a novel population of dysfunctional T cells marked by surface expression of the glycoprotein Tim-3. The frequency of this population was increased in HIV-1–infected individuals to a mean of 49.4 ± SD 12.9% of CD8+ T cells expressing Tim-3 in HIV-1–infected chronic progressors versus 28.5 ± 6.8% in HIV-1–uninfected individuals. Levels of Tim-3 expression on T cells from HIV-1–infected inviduals correlated positively with HIV-1 viral load and CD38 expression and inversely with CD4+ T cell count. In progressive HIV-1 infection, Tim-3 expression was up-regulated on HIV-1–specific CD8+ T cells. Tim-3–expressing T cells failed to produce cytokine or proliferate in response to antigen and exhibited impaired Stat5, Erk1/2, and p38 signaling. Blocking the Tim-3 signaling pathway restored proliferation and enhanced cytokine production in HIV-1–specific T cells. Thus, Tim-3 represents a novel target for the therapeutic reversal of HIV-1–associated T cell dysfunction.
The Slit/Robo System Suppresses Hepatocyte Growth Factor-dependent Invasion and Morphogenesis
Authors: Stella Maria Cristina , Trusolino Livio , Comoglio Paolo M.
Published: November 2008

The Slit protein acts through the Roundabout receptor as a paracrine chemorepellent in axon guidance and as an inhibitor in leukocyte chemotaxis, but its role in epithelial cell motility and morphogenesis remains largely unexplored. We report that nontransformed epithelial cells and cancerous cells empower the Slit-2/Robo1 signaling system to limit outward migration in response to motogenic attractants and to remain positionally confined within their primitive location. Short hairpin RNA-mediated depletion of SLIT-2 or ectopic expression of a soluble decoy Robo enhance hepatocyte growth factor (HGF)-induced migration, matrix invasion, and tubulogenesis, concomitantly with the up-regulation of Cdc-42 and the down-modulation of Rac-1 activities. Accordingly, autocrine overexpression or exogenous administration of Slit-2 prevent HGF-triggered motile responses, reduce Cdc-42 activation, and stimulate Rac-1. This antimigratory activity of Slit-2 derives from the inhibition of actin-based protrusive forces and from an increased adhesive strength of cadherin-mediated intercellular contacts. These results disclose a novel function for Slit and Robo in the inhibition of growth factor-mediated epithelial cell motility and morphogenesis, invoking a critical role for both molecules as natural antagonists of neoplastic invasive growth.
Polarized Traffic of LRP1 Involves AP1B and SNX17 Operating on Y-dependent Sorting Motifs in Different Pathways
Authors: Donoso Maribel , Cancino Jorge , Lee Jiyeon , van Kerkhof Peter , Retamal Claudio , Bu Guojun , Gonzalez Alfonso , Cáceres Alfredo , Marzolo María-Paz
Published: November 2008

Low-density lipoprotein receptor–related protein 1 (LRP1) is an endocytic recycling receptor with two cytoplasmic tyrosine-based basolateral sorting signals. Here we show that during biosynthetic trafficking LRP1 uses AP1B adaptor complex to move from a post-TGN recycling endosome (RE) to the basolateral membrane. Then it recycles basolaterally from the basolateral sorting endosome (BSE) involving recognition by sorting nexin 17 (SNX17). In the biosynthetic pathway, Y29but not N26from a proximal NPXY directs LRP1 basolateral sorting from the TGN. A N26A mutant revealed that this NPXY motif recognized by SNX17 is required for the receptor's exit from BSE. An endocytic Y63ATL66motif also functions in basolateral recycling, in concert with an additional endocytic motif (LL86,87), by preventing LRP1 entry into the transcytotic apical pathway. All this sorting information operates similarly in hippocampal neurons to mediate LRP1 somatodendritic distribution regardless of the absence of AP1B in neurons. LRP1 basolateral distribution results then from spatially and temporally segregation steps mediated by recognition of distinct tyrosine-based motifs. We also demonstrate a novel function of SNX17 in basolateral/somatodendritic recycling from a different compartment than AP1B endosomes.
Genetic association analysis with FAMHAP: a major program update
Authors: Herold Christine , Becker Tim
Published: November 2008

Summary: FAMHAP is an established software for haplotype association analysis of nuclear families. We have released a major update that comprises various new features for case-control data. Furthermore, weprovide an additional program runFamhap that allows users to start the same method repeatedly for varying sets of genetic markers. In addition, a platform-independent graphical user interface (GUI) was developed to simplify the usage of both FAMHAP and runFamhap. The runFamhap program greatly facilitates the application of FAMHAP to genome-wide association studies (GWAS) and supports flexible genome-wide haplotype analysis. As an example, we describe application to HapMap data.

Availability: The software is available at http://famhap.meb.uni-bonn.de

Contact:  herold@imbie.meb.uni-bonn.de; becker@imbie.meb.uni-bonn.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Ingredient Characterization and Hardening of High‐Protein Food Bars: an NMR State Diagram Approach
Authors: Li Yun , Szlachetka Kristin , Chen Paul , Lin Xiangyang , Ruan Roger
Published: November 2008

A second‐degree simplex lattice mixture design was used to study the effects of soy, dairy, and soy‐dairy blends of powdered proteins in three high‐protein food bar models (sugar syrup, polyol syrup, and reduced‐sugar syrup). Overall protein performance was evaluated based on textural changes during accelerated storage, bar integrity, and dough stickiness and was a strong function of the syrup model used (R2 = 92.33%). Nuclear magnetic resonance (NMR) relaxometry was used to measure relaxation times (T2, T2*, and T1) at 20°C and to create state diagrams (temperature, T2* curves) for the individual powdered proteins and syrups over a temperature range of –35 to 50°C. Increases in relaxation times for powdered protein samples were indicative of better overall protein performance, whereas increases in relaxation times for syrup samples were associated with increases in moisture content and concentration of polyols. Increases in water activity (aw) of the bars during accelerated storage suggested an elevated rate of hardening for polyol‐containing bars that was caused by a decrease in the amount of water capable of acting as a plasticizer in the product. Proteins were separated into four types (A, B, C, and D) based on the shape of the state diagram curve. Predicted to be the most stable, type D proteins (SUPRO 313 and SUPRO 430) offered the most versatility and, when blended with other proteins, often induced synergistic softening effects in the nutrition bars which led to an extended product shelf life. The NMR state diagram technique appears to be a valuable tool for predicting overall performance of powdered proteins in sugar‐, polyol‐, and reduced‐sugar syrup based food bars.
Genetic Composition of Pepino mosaic virus Population in North American Greenhouse Tomatoes
Authors: Ling Kai-Shu , Wintermantel William M. , Bledsoe Michael
Published: November 2008

In just a few short years, pepino mosaic disease has quickly become endemic in greenhouse tomatoes around the world. Although three genotypes of Pepino mosaic virus (PepMV) were identified in the United States, genetic composition of PepMV in greenhouse tomato crops in North America has not been determined. In this study, genetic variability and population structure of PepMV were evaluated through nucleotide sequence comparison and phylogenetic analysis of two genomic regions (helicase domain and TGB2-3) derived from 91 cDNA clones that were derived from 31 field-collected samples. These samples were collected from several major greenhouse tomato facilities in five states in the United States and two provinces in Canada. All four major genotypes of PepMV (EU, US1, US2, and CH2) were found in North America. Three distinct genotypes (EU, US1, and US2) were found in mixed infection in samples collected from Arizona and Colorado, two genotypes (EU and CH2) in Texas, and a single genotype (EU) in Alabama and California and the provinces of British Columbia and Ontario in Canada. The complexity of population genetics of PepMV in the United States poses an additional challenge to the greenhouse tomato industry because a tomato cultivar with durable resistance to multiple genotypes of PepMV may be harder to develop.
First Report of Phytophthora cactorum Associated With Beech Decline in Italy
Authors: Vettraino A. M. , Jung T. , Vannini A.
Published: November 2008

During 2006 and 2007, declining mature beech trees (Fagus sylvatica) were recorded in two stands in the Natural Park of Monti Cimini in central Italy. Symptoms included crown thinning and the presence of bleeding lesions on the main roots and lower stem. Incidence of decline was approximately 5%. Samples of necrotic bark tissue were collected, cut into 5 mm long segments, plated on PARPNH, and incubated at 20°C (1). Phytophthora isolates were obtained from necrotic tissues of 25% of the sampled declining trees. Colonies were rosaceous on potato dextrose agar (PDA) and homothallic. Papillate, ovoid-to-obpyriform, caducous sporangia (mean 38 × 26.2 μm) were produced in soil extract. Oospores were plerotic (mean diameter of 22 to 32 μm) and antheridia paragynous. Optimum growth temperature was 23 to 25°C, minimum 6 to 8°C and maximum 30 to 33°C. A portion of the internal transcribed spacer sequence has been deposited in the NCBI database (GenBank Accession No. FJ183724). A BLAST search of the NCBI database revealed Phytophthora cactorum, Accession No. EU194384, as the closest match with 100% sequence similarity. Pathogenicity of two isolates, PFE3 and IFB-CAC 38, collected from distressed beech trees was tested using a soil infestation test (10 beech seedlings per isolate and control) and an under the bark inoculation method (10 twigs per isolate and controls, wounded and noninoculated taken from a declining beech tree) (2). After 2 weeks at 20°C, twigs and seedlings inoculated with each isolate developed extensive necrotic lesions around the inoculation sites and the collar, respectively, and P. cactorum could be reisolated from all lesions. Controls showed no symptoms. P. cactorum is widespread in declining beech forests in central Europe (1). In Italy, P. cactorum occurs in soils of chestnut and oak forests and was isolated from collar and root lesions of declining walnut trees (3). To our knowledge, this is the first report of P. cactorum being associated with declining beech trees in Italy.

References: (1) T. Jung. Forest Pathol. Online publication. doi:10.1111/j.1439-0329.2008.00566.x, 2008. (2) T. Jung et al. Eur. J. For. Pathol. 26:253, 1996. (3) A. M. Vettraino et al. Plant Pathol. 52:491, 2003.
First Report of Crown Gall Caused by Agrobacterium tumefaciens on Euphorbia esula/virgata in Europe
Authors: Caesar A. J. , Lartey R. T.
Published: November 2008

Hypertrophy and hyperplasia resembling crown galls were found on roots of Euphorbia esula/virgata at a single site in east-central Hungary in 2005. E. esula/virgata, known as leafy spurge in North America, is an invasive species causing substantial economic losses to the value of grazing lands in the Northern Great Plains of the United States and is the target of biological control. E. esula/virgata is widely distributed throughout Eurasia and is found on ditch banks, along roadsides, and in other noncultivated areas in its native range. Large galls on roots resembling crown gall were first noted in 1992 on plants collected for phylogenetic studies from three locations in east-central Hungary. One of these sites was relocated during a 2005 survey and galls were collected from infected plants. Galls were diced and incubated overnight in tubes containing 3 ml of sterile water at room temperature (20 to 25°C). The supernatant was streaked onto plates of potato dextrose agar (PDA), medium 1A, medium 2E, and Roy/Sasser medium. After 7 days, colonies were picked and streaked and subsequently purified on PDA. Of 104 isolates used to inoculate three sunflower plants each (by puncturing roots just below the soil line with a sterile dissecting needle holding a drop of fluid matrix containing bacterial cells), 35 caused galls. Thirty-three isolates were randomly selected from the 104 and used to inoculate three tomato plants each at the soil line. Seventeen caused galls, including two isolates that did not cause galls on sunflower. Finally, none of 20 randomly selected isolates caused galls on kalanchoe plants (Kalanchoe blossfeldiana). Three isolates, which formed the largest galls on sunflower, were used to inoculate five plants of E. esula/virgata growing in a 1:1:1 (peat/sand/Bozeman silt loam) potting mix. The tests were repeated. Galls were visible on inoculated plants within 6 weeks. Diagnostic biochemical tests done prior to and after reisolation indicated that the causal agent was Agrobacterium tumefaciens, which differed from A. rhizogenes in the production of alkali from litmus milk, a positive reaction for the ferric ammonium citrate and 3-ketolactose tests, and negative reactions for tests to detect the production of acid from erythritol and alkali from malonic, l-tartaric, and mucic acid. The three isolates of A. tumefaciens from E. esula/virgata had identical sequences and clustered most closely (99.8 to 99.9% similarity) with five isolates of A. tumefaciens from Tibet and Japan on the basis of cluster analysis using 16S rRNA sequences. Crown gall of E. esula/virgata has also been found in Montana and western North Dakota, and isolates were identified as A. tumefaciens biovars 1 and 2 (1) (the latter is now known as A. rhizogenes). To our knowledge, this the first report of crown gall on E. esula/virgata in Europe.

Reference: (1) A. J. Caesar. Plant Dis. 78:796, 1994.
Edge states intermediate between laminar and turbulent dynamics in pipe flow
Authors: Schneider Tobias M , Eckhardt Bruno
Published: November 2008

We studied the dynamics near the boundary between laminar and turbulent dynamics in pipe flow. This boundary contains invariant dynamical states that are attracting when the dynamics is confined to the boundary. These states can be found by controlling a single quantity, in our case the energy content. The edge state is dominated by two downstream vortices and shows intrinsic chaotic dynamics. With increasing Reynolds number the separation between the edge state and turbulence increases. We can track it down to
Re
=1900, where the turbulent lifetimes are short enough that spontaneous decay can also be seen in experiments.
The flow structure of a puff
Authors: van Doorne Casimir W.H , Westerweel Jerry
Published: November 2008

From time-resolved stereoscopic particle image velocimetry measurements over the entire circular cross section of a pipe, a first-of-its-kind quasi-instantaneous three-dimensional velocity field of a turbulent puff at a low Reynolds number is reconstructed. At the trailing edge of the puff, where the laminar flow undergoes transition to turbulence, pairs of counterrotating streamwise vortices are observed that form the legs of large hairpin vortices. At the upstream end of the puff, a quasi-periodic regeneration of streamwise vortices takes place. Initially, the vortex structure resembles a travelling wave solution, but as the vortices propagate into the turbulent region of the puff, they continue to develop into strong hairpin vortices. These hairpin vortices extract so much energy from the mean flow that they cannot be sustained. This structure provides a possible explanation for the intermittent character of the puffs in pipe flow at low Reynolds numbers.
Highly symmetric travelling waves in pipe flow
Authors: Pringle Chris C.T , Duguet Yohann , Kerswell Rich R
Published: November 2008

The recent theoretical discovery of finite-amplitude travelling waves (TWs) in pipe flow has reignited interest in the transitional phenomena that Osborne Reynolds studied 125 years ago. Despite all being unstable, these waves are providing fresh insight into the flow dynamics. We describe two new classes of TWs, which, while possessing more restrictive symmetries than previously found TWs of Faisst & Eckhardt (2003
Phys. Rev. Lett.
91
, 224502) and Wedin & Kerswell (2004
J. Fluid Mech.
508
, 333–371), seem to be more fundamental to the hierarchy of exact solutions. They exhibit much higher wall shear stresses and appear at notably lower Reynolds numbers. The first M-class comprises the various discrete rotationally symmetric analogues of the mirror-symmetric wave found in Pringle & Kerswell (2007
Phys. Rev. Lett.
99
, 074502), and have a distinctive double-layered structure of fast and slow streaks across the pipe radius. The second N-class has the more familiar separation of fast streaks to the exterior and slow streaks to the interior and looks like the precursor to the class of non-mirror-symmetric waves already known.
Immunoglobulin class switch recombination: study through human natural mutants
Authors: Durandy Anne
Published: November 2008

Immunoglobulin class switch recombination deficiencies in humans are exquisite models to analyse the mechanisms of class switch recombination (CSR). Besides defects in CD40L/CD40 interaction, others result from an intrinsic B-cell deficiency. The recent elucidation of the molecular basis of some of them has made it possible to delineate the molecular events involved in antibody maturation. Activation-induced (cytidine) deaminase (AID) and uracil-N-glycosylase deficiencies have demonstrated the role of AID as the inducer of DNA lesions in switch and variable regions. However, most of these CSR deficiencies remain molecularly undefined. Their characterization would lead to a better understanding of the complex machinery involved in CSR.
Non-visual crypsis: a review of the empirical evidence for camouflage to senses other than vision
Authors: Ruxton Graeme D
Published: November 2008

I review the evidence that organisms have adaptations that confer difficulty of detection by predators and parasites that seek their targets primarily using sensory systems other than vision. In other words, I will answer the question of whether crypsis is a concept that can usefully be applied to non-visual sensory perception. Probably because vision is such an important sensory system in humans, research in this field is sparse. Thus, at present we have very few examples of chemical camouflage, and even these contain some ambiguity in deciding whether they are best seen as examples of background matching or mimicry. There are many examples of organisms that are adaptively silent at times or in locations when or where predation risk is higher or in response to detection of a predator. By contrast, evidence that the form (rather than use) of vocalizations and other sound-based signals has been influenced by issues of reducing detectability to unintended receivers is suggestive rather than conclusive. There is again suggestive but not completely conclusive evidence for crypsis against electro-sensing predators. Lastly, mechanoreception is highly understudied in this regard, but there are scattered reports that strongly suggest that some species can be thought of as being adapted to be cryptic in this modality. Hence, I conclude that crypsis is a concept that can usefully be applied to senses other than vision, and that this is a field very much worthy of more investigation.
Chromaticity in the UV/blue range facilitates the search for achromatically background-matching prey in birds
Authors: Stobbe Nina , Dimitrova Marina , Merilaita Sami , Schaefer H. Martin
Published: November 2008

A large variety of predatory species rely on their visual abilities to locate their prey. However, the search for prey may be hampered by prey camouflage. The most prominent example of concealing coloration is background-matching prey coloration characterized by a strong visual resemblance of prey to the background. Even though this principle of camouflage was recognized to efficiently work in predator avoidance a long time ago, the underlying mechanisms are not very well known. In this study, we assessed whether blue tits (Cyanistes caeruleus) use chromatic cues in the search for prey. We used two prey types that were achromatically identical but differed in chromatic properties in the UV/blue range and presented them on two achromatically identical backgrounds. The backgrounds had either the same chromatic properties as the prey items (matching combination) or differed in their chromatic properties (mismatching combination). Our results show that birds use chromatic cues in the search for mismatching prey, whereupon chromatic contrast leads to a ‘pop-out’ of the prey item from the background. When prey was presented on a matching background, search times were significantly higher. Interestingly, search for more chromatic prey on the matching background was easier than search for less chromatic prey on the matching background. Our results indicate that birds use both achromatic and chromatic cues when searching for prey, and that the combination of both cues might be helpful in the search task.
Detection of bovine papillomavirus type 2 in the peripheral blood of cattle with urinary bladder tumours: possible biological role
Authors: Roperto Sante , Brun Roberto , Paolini Francesca , Urraro Chiara , Russo Valeria , Borzacchiello Giuseppe , Pagnini Ugo , Raso Cinzia , Rizzo Consuelo , Roperto Franco , Venuti Aldo
Published: November 2008

Bovine papillomavirus type 2 (BPV-2) infection has been associated with urinary bladder tumours in adult cattle grazing on bracken fern-infested land. In this study, we investigated the simultaneous presence of BPV-2 in whole blood and urinary bladder tumours of adult cattle in an attempt to better understand the biological role of circulating BPV-2. Peripheral blood samples were collected from 78 cattle clinically suffering from a severe chronic enzootic haematuria. Circulating BPV-2 DNA was detected in 61 of them and in two blood samples from healthy cows. Fifty of the affected animals were slaughtered at public slaughterhouses and neoplastic proliferations in the urinary bladder were detected in all of them. BPV-2 DNA was amplified and sequenced in 78 % of urinary bladder tumour samples and in 38.9 % of normal samples as a control. Circulating episomal BPV-2 DNA was detected in 78.2 % of the blood samples. Simultaneous presence of BPV-2 DNA in neoplastic bladder and blood samples was detected in 37 animals. Specific viral E5 mRNA and E5 oncoprotein were also detected in blood by RT-PCR and Western blot/immunocytochemistry, respectively. It is likely that BPV-2 can persist and be maintained in an active status in the bloodstream, in particular in the lymphocytes, as a reservoir of viral infection that, in the presence of co-carcinogens, may cause the development of urinary bladder tumours.
Substitution of the myristoylation signal of human immunodeficiency virus type 1 Pr55Gag with the phospholipase C-δ1 pleckstrin homology domain results in infectious pseudovirion production
Authors: Urano Emiko , Aoki Toru , Futahashi Yuko , Murakami Tsutomu , Morikawa Yuko , Yamamoto Naoki , Komano Jun
Published: November 2008

The matrix domain (MA) of human immunodeficiency virus type 1 Pr55Gagis covalently modified with a myristoyl group that mediates efficient viral production. However, the role of myristoylation, particularly in the viral entry process, remains uninvestigated. This study replaced the myristoylation signal of MA with a well-studied phosphatidylinositol 4,5-biphosphate-binding plasma membrane (PM) targeting motif, the phospholipase C-δ1 pleckstrin homology (PH) domain. PH–Gag–Pol PM targeting and viral production efficiencies were improved compared with Gag–Pol, consistent with the estimated increases in Gag–PM affinity. Both virions were recovered in similar sucrose density-gradient fractions and had similar mature virion morphologies. Importantly, PH–Gag–Pol and Gag–Pol pseudovirions had almost identical infectivity, suggesting a dispensable role for myristoylation in the virus life cycle. PH–Gag–Pol might be useful in separating the myristoylation-dependent processes from the myristoylation-independent processes. This the first report demonstrating infectious pseudovirion production without myristoylated Pr55Gag.
CTA1-DD adjuvant promotes strong immunity against human immunodeficiency virus type 1 envelope glycoproteins following mucosal immunization
Authors: Sundling Christopher , Schön Karin , Mörner Andreas , Forsell Mattias N. E. , Wyatt Richard T. , Thorstensson Rigmor , Hedestam Gunilla B. Karlsson , Lycke Nils Y.
Published: November 2008

Strategies to induce potent and broad antibody responses against the human immunodeficiency virus type 1 (HIV-1) envelope glycoproteins (Env) at both systemic and mucosal sites represent a central goal for HIV-1 vaccine development. Here, we show that the non-toxic CTA1-DD adjuvant promoted mucosal and systemic humoral and cell-mediated immune responses following intranasal (i.n.) immunizations with trimeric or monomeric forms of HIV-1 Env in mice and in non-human primates. Env-specific IgG subclasses in the serum of immunized mice reflected a balanced Th1/Th2 type of response. Strikingly, i.n. immunizations with Env and the CTA1-DD adjuvant induced substantial levels of mucosal anti-Env IgA in bronchial alveolar lavage and also detectable levels in vaginal secretions. By contrast, parenteral immunizations of Env formulated in Ribi did not stimulate mucosal IgA responses, while the two adjuvants induced a similar distribution of Env-specific IgG-subclasses in serum. A single parenteral boost with Env in Ribi adjuvant into mice previously primed i.n. with Env and CTA1-DD, augmented the serum anti-Env IgG levels to similar magnitudes as those observed after three intraperitoneal immunizations with Env in Ribi. The augmenting potency of CTA1-DD was similar to that of LTK63 or CpG oligodeoxynucleotides (ODN). However, in contrast to CpG ODN, the effect of CTA1-DD and LTK63 appeared to be independent of MyD88 and toll-like receptor signalling. This is the first demonstration that CTA1-DD augments specific immune responses also in non-human primates, suggesting that this adjuvant could be explored further as a clinically safe mucosal vaccine adjuvant for humoral and cell-mediated immunity against HIV-1 Env.
The growth–mortality relationship in larval cohorts of Sardinops melanostictus, revealed by using two new approaches to analyse longitudinal data from otoliths
Authors: Plaza G. , Ishida M.
Published: November 2008

The growth–mortality relationship was assessed for larval cohorts of the Japanese sardine Sardinops melanostictus using two new approaches: (1) repeat measures in general linear model (RM‐GLMs) and (2) the autoregressive‐individual method (AIM). Both methods were compared to the traditional approach in which repeat‐measure ANOVA was used to compare the changes in increment width (WI) at age and otolith radii (RO) at age between individuals from an original population and survivors. In RM‐GLMs, both the WI at age and RO at age (i.e. at 5, 10, 15 and 20 days) were used as the dependent variables, and the standardized residuals of both regressions RO and age and RO and total length (LT), age class, and day of the year as independent variables. A significant increase in WI at age and RO at age from younger to older age classes was seen as indicative of growth‐dependent selection. In AIM, the RO‐at‐age relationship for each fish was fitted for the first 20 days, using autoregression, and then the growth traits (i.e. slopes) between the original cohorts and survivors were compared using ANOVA. In the traditional approach, the WI at age and RO at age for the first 20 days of an original population were compared with those of survivors sampled in later stages. GLMs and traditional approaches supported the growth rate (i.e. the faster an individual grows, the higher its probability of survival) and bigger is better (i.e. larger individuals at any given age will have lower probability of mortality than smaller individuals of the same age) mechanisms. Furthermore, AIM showed that individuals from original cohorts had lower otolith growth rates than those from survivors, giving further support for the growth–mortality hypothesis for the larval stage of this clupeid.
Foraging behaviour and prey discrimination in the bluespotted maskray Dasyatis kuhlii
Authors: Tillett B. J. , Tibbetts I. R. , Whithead D. L.
Published: November 2008

A study observing the foraging behaviours and prey discrimination of a common demersal stingray, the bluespotted maskray Dasyatis kuhlii was performed under controlled laboratory conditions. A selection of prey species and masses were offered at depths of 10 and 50 mm in sand. Foraging efficiency and prey selection at both burial depths were compared. Dasyatis kuhlii selected the ghost shrimps, Trypaea australiensis and T. australiensis >2·5 g, range ± 0·2 g though foraging errors represented by prey being excavated and not consumed suggested a limited discriminatory ability at the point of detection. Burial depth did not influence prey species, mass selection or discriminatory ability.
Large and persistent effect of a female steroid pheromone on ejaculate size in goldfish Carassius auratus
Authors: Hoysak D. J. , Stacey N. E.
Published: November 2008

This study determined if ejaculate size in male goldfish Carassius auratus is increased by the female preovulatory steroid pheromone 4‐pregnen‐17,20β‐diol‐3‐one (17,20βP), which previously has been shown to affect male behaviour and to increase sperm motility and stripped sperm number, and also to increase paternity in competitive spawning and competitive in vitro fertilization. Experimental males were exposed overnight to 17,20βP whereas control males were not. The morning following exposure, each male was placed with a reproductively active female and, after one to 20 spawning acts, aquarium water was sampled to quantify released sperm. Although exposure to 17,20βP induced a five‐fold difference in the number of sperm that could be stripped, the median number of sperm in first ejaculates of pheromone‐exposed males was >60 sixty times that of control males, a pheromonal effect on ejaculate size that persisted for at least 20 spawning acts. The magnitude of the pheromone effect on ejaculate size indicates that it is a critical component of C. auratus sperm allocation, and that examining this effect in concert with other factors (e.g. presence of competitors, male and female size and frequency of spawning) will reveal the contribution of the preovulatory pheromone to male fitness in this promiscuous species.
Significant fish predation on zebra mussels Dreissena polymorpha in Lake Champlain, U.S.A.
Authors: Watzin M. C. , Joppe‐Mercure K. , Rowder J. , Lancaster B. , Bronson L.
Published: November 2008

The objectives of this study were to: (1) determine which fishes were consistently eating zebra mussels Dreissena polymorpha in Lake Champlain and document their feeding behaviour and (2) quantify the diet composition of the fish predators that were found to consume zebra mussels. From 2002 to 2005, freshwater drum Aplodinotus grunniens, pumpkinseed Lepomis gibbosus, yellow perch Perca flavescens and rock bass Ambloplites rupestris all consumed zebra mussels at varying frequencies and amounts. Aplodinotusgrunniens and L. gibbosus chewed clumps of zebra mussels, expelling shells, whereas P. flavescens and A. rupestris swallowed small individuals whole. Lepomis gibbosus consumed zebra mussels at the highest frequency (65–89% of prey consumed) and zebra mussels comprised a large part of this fish’s diet (up to 40% by dry mass). Zebra mussels were also an important component of the diet of A. grunniens (up to 59% of the diet by dry mass, 40–63% frequency of consumption). The percentage of the diet comprising zebra mussels in P. flavescens and A. rupestris varied significantly from year to year but never exceeded 10%. Because A. grunniens and L. gibbosus crushed zebra mussels, the nutritional return from consuming zebra mussels would be similar to other prey; for P. flavescens and A. rupestris zebra mussels were only partially digested and the nutritional return would probably be low. As predation on zebra mussels is widespread and significant, it is possible that fish predators could contribute to regulating the population of zebra mussels in Lake Champlain.
Antarctic fish can survive prolonged exposure to elevated temperatures
Authors: Robinson E. , Davison W.
Published: November 2008

The Antarctic notothenioid Pagothenia borchgrevinki was collected from the stenothermal waters of McMurdo Sound in the summers of 2004, 2005 and 2006. Acclimation ability at 4° C was tested in healthy P. borchgrevinki and in individuals infected with x‐cell gill disease. All healthy fish successfully acclimated to 4° C, establishing compensatory changes in resting oxygen consumption rate (Rrest) and critical swimming speed (Ucrit) during a 1 month acclimation period, which were maintained during a longer, 6 month acclimation period. In contrast, individuals infected with x‐cell disease were unable to acclimate to 4° C, demonstrating significantly reduced survival rates compared with healthy individuals at 4° C. Measurements of Rrest suggest that limitations in the ability of x‐cell fish to uptake oxygen from the external milieu may have a negative effect on their survival at 4° C.
The post‐release process of establishing stable home ranges and diel movement patterns of hatchery‐reared black‐spot tuskfish Choerodon schoenleinii
Authors: Kawabata Y. , Okuyama J. , Asami K. , Yoseda K. , Arai N.
Published: November 2008

Post‐release change of home ranges and diel movement patterns of hatchery‐reared black‐spot tuskfish Choerodon schoenleinii were examined using ultrasonic telemetry. Nine hatchery‐reared C. schoenleinii were released in Urasoko Bay, Ishigaki Island, Okinawa, Japan and monitored using ultrasonic telemetry. The fish gradually increased home ranges for c. 3 months before establishing stable home ranges. This pattern of home‐range change might have been associated with the learning process of natural environments and intraspecific and interspecific competition. The fish also showed strong diurnal movement patterns: moving horizontally and vertically during the day and staying in the same place at night. The behaviour observed in this study is highly valuable to determine when, where and how to release the fish as well as how to increase the fitness of the fish before releasing.
Experience of maintenance infliximab therapy for refractory ulcerative colitis from six centres in England
Authors: RUSSO E. A. , HARRIS A. W. , CAMPBELL S. , LINDSAY J. , HART A. , AREBI N. , MILESTONE A. , TSAI H. H. , WALTERS J. , CARPANI M. , WESTABY D. , THILLAINAYAGAM A. , BANSI D. , GHOSH S.
Published: November 2008

Background  Infliximab is used for treatment of Crohn’s disease and, following the Active Ulcerative Colitis Trials (ACT) 1 and 2, it has been used as rescue and maintenance therapy in moderate and severe ulcerative colitis (UC).

Aim  To report on English experience with maintenance infliximab in terms of response and colectomy rates and side‐effect profile in UC.

Methods  A retrospective audit conducted by using a web‐based questionnaire filled in by 12 gastroenterologists from six English centres.

Results  Of the 38 patients receiving induction with infliximab, 28 (73.6%) maintained an ongoing response (8‐weekly infusions 5 mg/kg) for a mean duration of 16.8 months (range 4–59), with 21 (55.3%) being in remission. Three of 38 patients (7.9%) who also responded had a secondary loss of response after an average of 10 months (range 8–13); seven of 38 patients (18.4%) showed no response. The colectomy rate was seven of 38 (18.4%, five non‐responders and two with secondary loss of response). Adverse effects occurred in five patients (13.2%). Two discontinued infliximab (alopecia, invasive breast cancer). The three less‐severe adverse effects were acute and delayed‐type hypersensitivity reactions and one persistent otitis media.

Conclusion  Our experience suggests acceptable response rates, colectomy rates and side‐effect profile of maintenance therapy with infliximab in moderate and severe UC.
The effect of pneumoperitoneum and Trendelenburg position on acute cerebral blood flow–carbon dioxide reactivity under sevoflurane anaesthesia
Authors: Choi S. H. , Lee S. J. , Rha K. H. , Shin S. K. , Oh Y. J.
Published: November 2008

This study compared cerebral blood flow–carbon dioxide (CBF–CO2) reactivities in the supine and modest Trendelenburg position under pnemoperitoneum during sevoflurane anaesthesia. After induction of anaesthesia in 25 patients, mechanical ventilation was adjusted to increase Paco2 from 4.7 (T1) to 6.0 kPa (T2) in the supine position, and the change in jugular bulb oxygen saturation was measured as an index of CBF. Then, after establishment of pneumoperitoneum and 30° Trendelenburg position, the CO2 step and measurement of CBF were repeated. The CBF–CO2 reactivity was 7.5 (3.3) %.kPa−1 (% change in jugular bulb oxygen saturation per unit change in Paco2) in the supine position and 6.8 (2.3) %.kPa−1 in the 30° Trendelenburg‐pneumoperitoneum condition (p = 0.086). We conclude that CBF–CO2 reactivity is unchanged by the modest Trendelenburg position under pneumoperitoneum during sevoflurane anaesthesia.
A mutation in NFκB interacting protein 1 causes cardiomyopathy and woolly haircoat syndrome of Poll Hereford cattle
Authors: Simpson M. A. , Cook R. W. , Solanki P. , Patton M. A. , Dennis J. A. , Crosby A. H.
Published: November 2008

Cardiomyopathy and woolly haircoat syndrome (CWH) of Poll Hereford cattle is a lethal, autosomal recessive disorder. Cardiac and haircoat changes are congenital, neonatal ocular keratitis develops in some cases and death usually occurs within the first 12 weeks of life. We undertook a homozygosity mapping approach to identify the chromosomal location of the causative gene. Seven candidate genes were examined for homozygosity in affected animals: desmoplakin and junction plakoglobin (both previously implicated in human cardiocutaneous syndromes), desmocollin 2, desmoglein 2, plakophilin 2, nuclear factor kappa B (NFKB1) and NFκB interacting protein 1 (PPP1R13L, also known as NKIP1). Homozygosity in 13 affected animals was observed at the PPP1R13L locus, located on bovine chromosome 18. Subsequent sequence analysis revealed a 7‐bp duplication (c.956_962dup7) in exon 6 of this 13‐exon gene. This frameshift variant is predicted to result in the substitution of three amino acids and the introduction of a premature stop codon at position 325 of the protein product (p.Ser322GlnfsX4). PPP1R13L interacts with NFκB, a family of structurally related transcription factors that regulate genes controlling inflammation, immune responses and cell proliferation and survival. CWH represents a large‐animal model for cardiocutaneous disorders caused by a mutation in the PPP1R13L gene. The identification of this bovine mutation also indicates that PPP1R13L and other genes affecting NFκB activity may be candidate genes in the study of human cardiovascular disease.