bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anchored clathrate waters bind antifreeze proteins to ice
Authors: Garnham Christopher P. , Campbell Robert L. , Davies Peter L. 
Published: April 2011

The mechanism by which antifreeze proteins (AFPs) irreversibly bind to ice has not yet been resolved. The ice-binding site of an AFP is relatively hydrophobic, but also contains many potential hydrogen bond donors/acceptors. The extent to which hydrogen bonding and the hydrophobic effect contribute to ice binding has been debated for over 30 years. Here we have elucidated the ice-binding mechanism through solving the first crystal structure of an Antarctic bacterial AFP. This 34-kDa domain, the largest AFP structure determined to date, folds as a Ca
2+
-bound parallel beta-helix with an extensive array of ice-like surface waters that are anchored via hydrogen bonds directly to the polypeptide backbone and adjacent side chains. These bound waters make an excellent three-dimensional match to both the primary prism and basal planes of ice and in effect provide an extensive X-ray crystallographic picture of the AFP∶ice interaction. This unobstructed view, free from crystal-packing artefacts, shows the contributions of both the hydrophobic effect and hydrogen bonding during AFP adsorption to ice. We term this mode of binding the “anchored clathrate” mechanism of AFP action.
CO
2
-limitation-inducible Green Recovery of fatty acids from cyanobacterial biomass
Authors: Liu Xinyao , Fallon Sarah , Sheng Jie , Curtiss Roy 
Published: April 2011

Using genetically modified cyanobacterial strains, we engineered a Green Recovery strategy to convert membrane lipids into fatty acids for economical and environmentally sustainable biofuel production. The Green Recovery strategy utilizes lipolytic enzymes under the control of promoters induced by CO
2
limitation. Data indicate that strains of the cyanobacterium
Synechocystis
sp. PCC6803 engineered for Green Recovery underwent degradation of membrane diacylglycerols upon CO
2
limitation, leading to release of fatty acids into the culture medium. Recovered fatty acid yields of 36.1 × 10
-12
mg/cell were measured in one of the engineered strains (SD239). Green Recovery can be incorporated into previously constructed fatty-acid-secretion strains, enabling fatty acid recovery from the remaining cyanobacterial biomass that will be generated during fatty acid biofuel production in photobioreactors.
Influence of planktonic foodweb structure on a system's capacity to support pelagic production: an inverse analysis approach
Authors: Marquis Elise , Niquil Nathalie , Vézina Alain F. , Petitgas Pierre , Dupuy Christine 
Published: April 2011

Abstract
Marquis, E., Niquil, N., Vézina, A. F., Petitgas, P., and Dupuy, C. 2011. Influence of planktonic foodweb structure on a system's capacity to support pelagic production: an inverse analysis approach. – ICES Journal of Marine Science, 68: 803–812. Coupled plankton/small pelagic (SP) fish systems were analysed to assess how foodweb structure influences the export of carbon to pelagic fish during the spring bloom in the Bay of Biscay. The investigation of carbon export flows through inverse analysis was supplemented by estimating the carrying capacity for pelagic fish production by applying linear programming. A planktonic foodweb dominated by microbial pathways had the highest trophic efficiency owing to the tight coupling between planktonic trophic levels and predation pressure on mesozooplankton by fish. Moreover, the magnitude of the gap between carrying capacity and estimated carbon export was related to the size structure of primary producers, with the picophytoplankton-based foodweb having the smallest gap and the microphytoplankton-based one the largest gap. Planktonic foodwebs dominated by small autotrophic cells channelled most of their available carbon to pelagic fish production, whereas foodwebs dominated by large phytoplankton were better suited to benthic communities with a large loss of carbon through sedimentation. Although the total carbon available to higher trophic levels does not vary with the size of the main primary producers, the potential export to SP fish depends on the structure of the planktonic foodweb.
Interesting times: winners, losers, and system shifts under climate change around Australia
Authors: Fulton E. A. 
Published: April 2011

AbstractFulton, E. A. 2011. Interesting times: winners, losers, and system shifts under climate change around Australia. – ICES Journal of Marine Science, 68: 1329–1342. Feedback and change are basic features of ecosystems, something global change has highlighted. Changes in the physical environment will see shifts in species ranges, community compositions, and ultimately the form and function of ecosystem and the human societies that exploit them. What these shifts will be depends on which of the competing (and potentially counteracting) mechanisms dominate through space and time. Moreover, changes are unlikely to be simple or linear; there will be winners, losers, and surprises. It also means that management will be complex and non-stationary, presenting management, scientific, and statistical challenges.
Balancing indigenous and non-indigenous commercial objectives in a coral reef finfish fishery
Authors: Williams Ashley J. , Little L. Richard , Begg Gavin A. 
Published: April 2011

Abstract
Williams, A. J., Little, L. R., and Begg, G. A. 2011. Balancing indigenous and non-indigenous commercial objectives in a coral reef finfish fishery. – ICES Journal of Marine Science, 68: 834–847. Indigenous participation in commercial fisheries is poorly established in Australia, except in Torres Strait where indigenous and non-indigenous commercial fishers participate in the Torres Strait Finfish Fishery (TSFF). TSFF stakeholders helped identify specific objectives and alternative management strategies for the fishery at a time when new management strategies were under consideration. A metapopulation and fishing simulation model was used to evaluate alternative management strategies related to harvest and conservation of coral trout (Plectropomus spp.), the main target species. Stakeholders identified objectives relating to conservation of unfished populations, maintenance of harvestable stock, and economic performance. In terms of management options, spatial closures decreased the prospects of meeting nearly all stakeholder objectives. A seasonal closure and larger minimum capture size increased the probability of meeting conservation and harvest objectives, but decreased the probability of meeting most economic objectives for both sectors. Increasing fishing effort increased harvest but decreased the catch rates for both sectors, so had varied effects on the probability of achieving harvest objectives. The research provides a case study of productive engagement with indigenous and non-indigenous stakeholders to address fisheries management needs and provides a framework for impartial evaluation of performance of alternative management strategies against stakeholder objectives.
Extreme spawning-site fidelity in Atlantic cod
Authors: Skjæraasen Jon Egil , Meager Justin J. , Karlsen Ørjan , Hutchings Jeffrey A. , Fernö Anders 
Published: April 2011

Abstract
Skjæraasen, J. E., Meager, J. J., Karlsen, Ø., Hutchings, J. A., and Fernö, A. 2011. Extreme spawning-site fidelity in Atlantic cod. – ICES Journal of Marine Science, 68: 1472–1477. Based on a 3-year mark-recapture study, evidence is provided of spawning-site fidelity in Atlantic cod (Gadus morhua) at a scale (<1 km) smaller than documented previously. Coastal regions where barriers to dispersal exist may allow for local population dynamics and adaptation to develop in broadcast-spawning marine fish at extremely fine spatial scales.
TheMaGene for Complete-Spectrum Resistance toMeloidogyneSpecies inPrunusIs a TNL with a Huge Repeated C-Terminal Post-LRR Region
Authors: Claverie Michel , Dirlewanger Elisabeth , Bosselut Nathalie , Van Ghelder Cyril , Voisin Roger , Kleinhentz Marc , Lafargue Bernard , Abad Pierre , Rosso Marie-Noëlle , Chalhoub Boulos , Esmenjaud Daniel 
Published: April 2011

AbstractRoot-knot nematode (RKN) Meloidogyne species are major polyphagous pests of most crops worldwide, and cultivars with durable resistance are urgently needed because of nematicide bans. The Ma gene from the Myrobalan plum (Prunus cerasifera) confers complete-spectrum, heat-stable, and high-level resistance to RKN, which is remarkable in comparison with the Mi-1 gene from tomato (Solanum lycopersicum), the sole RKN resistance gene cloned. We report here the positional cloning and the functional validation of the Ma locus present at the heterozygous state in the P.2175 accession. High-resolution mapping totaling over 3,000 segregants reduced the Ma locus interval to a 32-kb cluster of three Toll/Interleukin1 Receptor-Nucleotide Binding Site-Leucine-Rich Repeat (LRR) genes (TNL1–TNL3), including a pseudogene (TNL2) and a truncated gene (TNL3). The sole complete gene in this interval (TNL1) was validated as Ma, as it conferred the same complete-spectrum and high-level resistance (as in P.2175) using its genomic sequence and native promoter region in Agrobacterium rhizogenes-transformed hairy roots and composite plants. The full-length cDNA (2,048 amino acids) of Ma is the longest of all Resistance genes cloned to date. Its TNL structure is completed by a huge post-LRR (PL) sequence (1,088 amino acids) comprising five repeated carboxyl-terminal PL exons with two conserved motifs. The amino-terminal region (213 amino acids) of the LRR exon is conserved between alleles and contrasts with the high interallelic polymorphisms of its distal region (111 amino acids) and of PL domains. The Ma gene highlights the importance of these uncharacterized PL domains, which may be involved in pathogen recognition through the decoy hypothesis or in nuclear signaling.
Isolating and defining cells to engineer human blood vessels
Authors: Critser P. J. , Voytik‐Harbin S. L. , Yoder M. C. 
Published: April 2011

AbstractA great deal of attention has been recently focused on understanding the role that bone marrow‐derived putative endothelial progenitor cells (EPC) may play in the process of neoangiogenesis. However, recent data indicate that many of the putative EPC populations are comprised of various haematopoietic cell subsets with proangiogenic activity, but these marrow‐derived putative EPC fail to display vasculogenic activity. Rather, this property is reserved for a rare population of circulating viable endothelial cells with colony‐forming cell (ECFC) ability. Indeed, human ECFC possess clonal proliferative potential, display endothelial and not haematopoietic cell surface antigens, and display in vivo vasculogenic activity when suspended in an extracellular matrix and implanted into immunodeficient mice. Furthermore, human vessels derived became integrated into the murine circulatory system and eventually were remodelled into arterial and venous vessels. Identification of this population now permits determination of optimal type I collagen matrix microenvironment into which the cells should be embedded and delivered to accelerate and even pattern number and size of blood vessels formed, in vivo. Indeed, altering physical properties of ECFC‐collagen matrix implants changed numerous parameters of human blood vessel formation, in host mice. These recent discoveries may permit a strategy for patterning vascular beds for eventual tissue and organ regeneration.
The umbilical cord: a rich and ethical stem cell source to advance regenerative medicine
Authors: Forraz N. , McGuckin C. P. 
Published: April 2011

AbstractScience and medicine place a lot of hope in the development of stem cell research and regenerative medicine. This review will define the concept of regenerative medicine and focus on an abundant stem cell source – neonatal tissues such as the umbilical cord. Umbilical cord blood has been used clinically for over 20 years as a cell source for haematopoietic stem cell transplantation. Beyond this, cord blood and umbilical cord‐derived stem cells have demonstrated potential for pluripotent lineage differentiation (liver, pancreatic, neural tissues and more)in vitroandin vivo. This promising research has opened up a new era for utilization of neonatal stem cells, now used beyond haematology in clinical trials for autoimmune disorders, cerebral palsy or type I diabetes.
From hepatocytes to stem and progenitor cells for liver regenerative medicine: advances and clinical perspectives
Authors: Sokal E. M. 
Published: April 2011

AbstractThe parenchymal liver cell is a unique fully functional metabolic unit that can be used for liver regenerative medicine to restore function of the diseased organ; the aim of the procedure is to prevent progression of end‐stage disease. The alternative, orthotopic liver transplantation, is highly intrusive, irreversible and limited by general organ shortage. Mature liver cell – hepatocyte – transplantation has been shown to have short‐ to medium‐term efficacy for correction of miscellaneous inborn errors of metabolism. However, although proof of concept has been established, the procedure has not yet achieved full success, due to limited durability of functional benefit. Hepatocyte procurement is also restricted by organ shortage, and their storage is difficult due to poor tolerance of cryopreservation. Alternative cell sources are therefore needed for development and wider accessibility of cell‐based liver regenerative medicine. Besides safety, the main challenge for these alternative cells is to acquire similar levels of functionality once implanted into the target organ. In this respect, liver derived progenitor cells may have some advantages over stem cells derived from other tissues.
Digital pathology: current status and future perspectives
Authors: Al‐Janabi Shaimaa , Huisman André , Van Diest Paul J 
Published: April 2011

Al‐Janabi S, Huisman A & Van Diest P J  (2012) Histopathology 61, 1–9Digital pathology: current status and future perspectivesDuring the last decade pathology has benefited from the rapid progress of image digitizing technology. The improvement in this technology had led to the creation of slide scanners which are able to produce whole slide images (WSI) which can be explored by image viewers in a way comparable to the conventional microscope. The file size of the WSI ranges from a few megabytes to several gigabytes, leading to challenges in the area of image storage and management when they will be used routinely in daily clinical practice. Digital slides are used in pathology for education, diagnostic purposes (clinicopathological meetings, consultations, revisions, slide panels and, increasingly, for upfront clinical diagnostics) and archiving. As an alternative to conventional slides, WSI are generally well accepted, especially in education, where they are available to a large number of students with the full possibilities of annotations without the problem of variation between serial sections. Image processing techniques can also be applied to WSI, providing pathologists with tools assisting in the diagnosis‐making process. This paper will highlight the current status of digital pathology applications and its impact on the field of pathology.
Plasma concentrations of testosterone and nandrolone in racing and nonracing intact male horses
Authors: SOMA L. R. , UBOH C. E. , YOU Y. , GUAN F. , McDONNELL S. 
Published: April 2011

Soma, L. R., Uboh, C. E., You, Y., Guan, F., McDonnell, S. Plasma concentrations of testosterone and nandrolone in racing and nonracing intact male horses. J. vet. Pharmacol. Therap. 35, 132–138.Pennsylvania (PA) State Racing Commissions regulate the endogenous androgenic steroid, testosterone (TES), in racing intact males (RIM) by quantification of TES in post‐race samples. Post‐race plasma samples (2209) collected between March 2008 and November 2010 were analyzed for TES, nandrolone (NAN), and other anabolic steroids (ABS). Of the 2209 plasma samples, 2098 had quantifiable TES ≥25 pg/mL. Plasma (mean ± SD) concentrations of TES and NAN in RIM were 329.2 ± 266.4 and 96.0 ± 67.8 pg/mL, respectively. Only 64.6% of RIM had quantifiable concentration of NAN, and there was no relationship between TES and NAN. Plasma TES concentrations were significantly (P < 0.0001) higher during the months of April, May, June, July, and August. A significantly higher (P < 0.006) plasma TES was observed in Thoroughbred (TB) (347.6 ± 288.5 pg/mL) vs. that in Standardbred (STB) (315.4 ± 247.7 pg/mL). Plasma concentrations of TES from breeding stallions (BS) were 601.6 ± 356.5 pg/mL. Statistically significant (P < 0.0001) lower plasma concentrations of the two steroids were observed in RIM horses. Based on quantile distribution of TES in the RIM and BS populations, 99.5% were at or below 1546.1 and 1778.0 pg/mL, respectively. Based on this population of RIM, the suggested upper threshold plasma concentration of endogenous TES in horses competing in PA should remain at 2000 pg/mL.
Robenacoxib vs. carprofen for the treatment of canine osteoarthritis; a randomized, noninferiority clinical trial
Authors: REYMOND N. , SPERANZA C. , GRUET P. , SEEWALD W. , KING J. N. 
Published: April 2011

Reymond, N., Speranza, C., Gruet, P., Seewald, W., King, J. N. Robenacoxib vs. carprofen for the treatment of canine osteoarthritis; a randomized, noninferiority clinical trial.J. vet. Pharmacol. Therap. 35, 175–183.Robenacoxib is a member of the coxib class of nonsteroidal anti‐inflammatory drugs (NSAID), with high selectivity for the cyclooxygenase (COX)‐2 isoform of COX. In this study, the efficacy and tolerability of robenacoxib were compared with those of carprofen in canine osteoarthritis in a multi‐centre, prospective, randomized, blinded, positive‐controlled noninferiority clinical trial. Both drugs were administered orally once daily at recommended dosages: robenacoxib at 1–2 mg/kg (n = 125 dogs) and racemic carprofen at 2–4 mg/kg (n = 63 dogs) for a total of 12 weeks. The efficacy of the test compounds was assessed by veterinary investigators and owners using numerical rating scales at baseline and days 7, 14, 28, 56 and 84. In both groups, all scores were significantly (P < 0.0001) improved compared with baseline at all time points (days 7–84). Robenacoxib had noninferior efficacy to carprofen for the primary endpoint, the global functional disability, both for all dogs and for the subgroup of dogs in which robenacoxib was not administered during meals. Noninferiority was also demonstrated for three of six veterinary investigator secondary endpoints and four of six owner efficacy endpoints. For haematology and clinical chemistry variables, there were some significant differences from baseline levels but no differences between groups. There were no differences between groups in the frequencies of adverse events, which were reported in 46% dogs with robenacoxib and 52% with carprofen (P = 0.44), which were most frequently mild events affecting the gastrointestinal tract. In conclusion, noninferior efficacy and tolerability of robenacoxib compared with carprofen was demonstrated in dogs with osteoarthritis.
Dating the fungus‐growing termites’ mutualism shows a mixture between ancient codiversification and recent symbiont dispersal across divergent hosts
Authors: NOBRE T. , KONÉ N. A. , KONATÉ S. , LINSENMAIR K. E. , AANEN D. K. 
Published: April 2011

AbstractThe mutualistic symbiosis between fungus‐growing termites and Termitomyces fungi originated in Africa and shows a moderate degree of interaction specificity. Here we estimate the age of the mutualism and test the hypothesis that the major splits have occurred simultaneously in the host and in the symbiont. We present a scenario where fungus‐growing termites originated in the African rainforest just before the expansion of the savanna, about 31 Ma (19–49 Ma). Whereas rough age correspondence is observed for the four main clades of host and symbiont, the analysis reveals several recent events of host switching followed by dispersal of the symbiont throughout large areas and throughout different host genera. The most spectacular of these is a group of closely related fungi (the maximum age of which is estimated to be 2.4 Ma), shared between the divergent genera Microtermes, Ancistrotermes, Acanthotermes and Synacanthotermes (which diverged at least 16.7 Ma), and found throughout the African continent and on Madagascar. The lack of geographical differentiation of fungal symbionts shows that continuous exchange has occurred between regions and across host species.
A lectin‐mediated resistance of higher fungi against predators and parasites
Authors: BLEULER‐MARTÍNEZ S. , BUTSCHI A. , GARBANI M. , WÄLTI M. A. , WOHLSCHLAGER T. , POTTHOFF E. , SABOTIĈ J. , POHLEVEN J. , LÜTHY P. , HENGARTNER M. O. , AEBI M. , KÜNZLER M. 
Published: April 2011

AbstractFruiting body lectins are ubiquitous in higher fungi and characterized by being synthesized in the cytoplasm and up‐regulated during sexual development. The function of these lectins is unclear. A lack of phenotype in sexual development upon inactivation of the respective genes argues against a function in this process. We tested a series of characterized fruiting body lectins from different fungi for toxicity towards the nematode Caenorhabditis elegans, the mosquito Aedes aegypti and the amoeba Acanthamoeba castellanii. Most of the fungal lectins were found to be toxic towards at least one of the three target organisms. By altering either the fungal lectin or the glycans of the target organisms, or by including soluble carbohydrate ligands as competitors, we demonstrate that the observed toxicity is dependent on the interaction between the fungal lectins and specific glycans in the target organisms. The toxicity was found to be dose‐dependent such that low levels of lectin were no longer toxic but still led to food avoidance by C. elegans. Finally, we show, in an ecologically more relevant scenario, that challenging the vegetative mycelium of Coprinopsis cinerea with the fungal‐feeding nematode Aphelenchus avenae induces the expression of the nematotoxic fruiting body lectins CGL1 and CGL2. Based on these findings, we propose that filamentous fungi possess an inducible resistance against predators and parasites mediated by lectins that are specific for glycans of these antagonists.
Gut feelings about the endocannabinoid system
Authors: Di Marzo V. , Piscitelli F. 
Published: April 2011

AbstractStemming from the centuries‐old and well known effects of Cannabis on intestinal motility and secretion, research on the role of the endocannabinoid system in gut function and dysfunction has received ever increasing attention since the discovery of the cannabinoid receptors and their endogenous ligands, the endocannabinoids. In this article, some of the most recent developments in this field are discussed, with particular emphasis on new data, most of which are published in Neurogastroenterology & Motility, on the potential tonic endocannabinoid control of intestinal motility, the function of cannabinoid type‐1 (CB1) receptors in gastric function, visceral pain, inflammation and sepsis, the emerging role of cannabinoid type‐2 (CB2) receptors in the gut, and the pharmacology of endocannabinoid‐related molecules and plant cannabinoids not necessarily acting via cannabinoid CB1 and CB2 receptors. These novel data highlight the multi‐faceted aspects of endocannabinoid function in the GI tract, support the feasibility of the future therapeutic exploitation of this signaling system for the treatment of GI disorders, and leave space for some intriguing new hypotheses on the role of endocannabinoids in the gut.