bluuebunny/crossref_metadata_2025 huggingface dataset:
Homology modeling and molecular dynamics simulations of the glycine receptor ligand binding domain
Authors: Speranskiy Kirill , Cascio Michael , Kurnikova Maria
Published: March 2007

We present a homology based model of the ligand binding domain (LBD) of the homopentameric alpha1 glycine receptor (GlyR). The model is based on multiple sequence alignment with other members of the nicotinicoid ligand gated ion channel superfamily and two homologous acetylcholine binding proteins (AChBP) from the freshwater (Lymnaea stagnalis) and saltwater (Aplysia californica) snails with known high resolution structure. Using two template proteins with known structure to model three dimensional structure of a target protein is especially advantageous for sequences with low homology as in the case presented in this paper. The final model was cross‐validated by critical evaluation of experimental and published mutagenesis, functional and other biochemical studies. In addition, a complex structure with strychnine antagonist in the putative binding site is proposed based on docking simulation using Autodock program. Molecular dynamics (MD) simulations with simulated annealing protocol are reported on the proposed LBD of GlyR, which is stable in 5 ns simulation in water, as well as for a deformed LBD structure modeled on the corresponding domain determined in low‐resolution cryomicroscopy structure of the alpha subunit of the full‐length acetylcholine receptor (AChR). Our simulations demonstrate that the beta‐sandwich central core of the protein monomer is fairly rigid in the simulations and resistant to deformations in water. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Crystal structure of an archaeal homologue of multidrug resistance repressor protein, EmrR, from hyperthermophilic archaea Sulfolobus tokodaii strain 7
Authors: Miyazono Ken‐ichi , Tsujimura Masanari , Kawarabayasi Yutaka , Tanokura Masaru
Published: March 2007

MarR family proteins, MarR, MexR, and EmrR, are known as bacterial regulators for a phenotype resistant to multiple antibiotic drugs. Genomic data have indicated the presence of bacterial‐type transcriptional regulators, including MarR family proteins in archaea, though the archaeal transcription system is close to that of eukaryote. To elucidate the structural basis of the transcriptional regulation mechanism of archaeal MarR family proteins, the crystal structure of the ST1710 protein, which was identified as an archaeal EmrR homologue, StEmrR, from hyperthermophilic archaeon Sulfolobus tokodaii strain 7 was determined at 1.45‐Åresolution. The protein was composed of two N‐ and C‐terminal dimerization domains, and the DNA‐binding domain consisted of a winged helix motif, as in the case of bacterial MarR family proteins. Despite the relatively low overall structural similarity between StEmrR and bacterial MarR family proteins, the structure of the DNA‐binding domain displayed high structural similarity. A comparison with the crystal structures of bacterial MarR family proteins revealed that structural variation was mainly due to the different orientation of the two helices at the N‐ and C‐termini. Our results indicated that the distance between the two DNA‐binding domains of MarR family proteins would be changed by the rotation of the two terminal helices to interact with the target DNA. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Predicting protein domain interactions from coevolution of conserved regions
Authors: Kann Maricel G. , Jothi Raja , Cherukuri Praveen F. , Przytycka Teresa M.
Published: March 2007

The knowledge of protein and domain interactions provide crucial insights into their function within a cell. Several computational methods have been proposed to detect interactions between proteins and their constitutive domains. In this work, we focus on approaches based on correlated evolution (coevolution) of sequences of interacting proteins. In this type of approach, often referred to as the mirrortree method, a high correlation of evolutionary histories of two proteins is used as an indicator to predict protein interactions. Recently, it has been observed that subtracting the underlying speciation process by separating coevolution due to common speciation divergence from that due to common function of interacting pairs greatly improves the predictive power of the mirrortree approach. In this article, we investigate possible improvements and limitations of this method. In particular, we demonstrate that the performance of the mirrortree method that can be further improved by restricting the coevolution analysis to the relatively conserved regions in the protein domain sequences (disregarding highly divergent regions). We provide a theoretical validation of our results leading to new insights into the interplay between coevolution and speciation of interacting proteins. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Comprehensive statistical analysis of residues interaction specificity at protein–protein interfaces
Authors: Anashkina Anastasya , Kuznetsov Eugene , Esipova Natalia , Tumanyan Vladimir
Published: March 2007

We calculated interchain contacts on the atomic level for nonredundant set of 4602 protein‐protein interfaces using an unbiased Voronoi‐Delaune tessellation method, and made 20×20 residue contact matrixes both for homodimers and heterocomplexes. The area of contacts and the distance distribution for these contacts were calculated on both the residue and the atomic levels. We analyzed residue area distribution and showed the existence of two types of interresidue contacts: stochastic and specific. We also derived formulas describing the distribution of contact area for stochastic and specific interactions in parametric form. Maximum pairing preference index was found for Cys‐Cys contacts and for oppositely charged interactions. A significant difference in residue contacts was observed between homodimers and heterocomplexes. Interfaces in homodimers were enriched with contacts between residues of the same type due to the effects of structure symmetry. Proteins 2007. © 2007 Wiley‐Liss, Inc.
A comparative infrared spectroscopic study of glycoside hydrolases from extremophilic archaea revealed different molecular mechanisms of adaptation to high temperatures
Authors: Ausili Alessio , Cobucci‐Ponzano Beatrice , Di Lauro Barbara , D'Avino Rossana , Perugino Giuseppe , Bertoli Enrico , Scirè Andrea , Rossi Mosè , Tanfani Fabio , Moracci Marco
Published: March 2007

The identification of the determinants of protein thermal stabilization is often pursued by comparing enzymes from hyperthermophiles with their mesophilic counterparts while direct structural comparisons among proteins and enzymes from hyperthermophiles are rather uncommon. Here, oligomeric β‐glycosidases from the hyperthermophilic archaea Sulfolobus solfataricus (Ssβ‐gly), Thermosphaera aggregans (Taβ‐gly), and Pyrococcus furiosus (Pfβ‐gly), have been compared. Studies of FTIR spectroscopy and kinetics of thermal inactivation showed that the three enzymes had similar secondary structure composition, but Ssβ‐gly and Taβ‐gly (temperatures of melting 98.1 and 98.4°C, respectively) were less stable than Pfβ‐gly, which maintained its secondary structure even at 99.5°C. The thermal denaturation of Pfβ‐gly, followed in the presence of SDS, suggested that this enzyme is stabilized by hydrophobic interactions. A detailed inspection of the 3D‐structures of these enzymes supported the experimental results: Ssβ‐gly and Taβ‐gly are stabilized by a combination of ion‐pairs networks and intrasubunit S‐S bridges while the increased stability of Pfβ‐gly resides in a more compact protein core. The different strategies of protein stabilization give experimental support to recent theories on thermophilic adaptation and suggest that different stabilization strategies could have been adopted among archaea. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Human DEAD‐box ATPase DDX3 shows a relaxed nucleoside substrate specificity
Authors: Franca Raffaella , Belfiore Amalia , Spadari Silvio , Maga Giovanni
Published: March 2007

Human DDX3 (hDDX3) is a DEAD‐box protein shown to possess RNA‐unwinding and adenosine triphosphatase (ATPase) activities. The hDDX3 protein has been implicated in nuclear mRNA export, cell growth control, and cancer progression. In addition, a role of this protein in the replication of human immunodeficiency virus Type 1 and in the pathogenesis of hepatitis C virus has been recently proposed. Its enzymological properties, however, are largely unknown. In this work, we characterized its ATPase activity. We show that hDDX3 ATPase activity is stimulated by various ribo‐ and deoxynucleic acids. Comparative analysis with different nucleoside triphosphate analogs showed that the hDDX3 ATPase couples high catalytic efficiency to a rather relaxed substrate specificity, both in terms of base selection and sugar selection. In addition, its ability to recognize the L‐stereoisomers of both 3′ deoxy‐ and 2′,3′ dideoxy‐ribose, points to a relaxed stereoselectivity. On the basis of these results, we hypothesize the presence of structural determinants on both the base and the sugar moieties, critical for nucleoside binding to the enzyme. Our results expand the knowledge about the DEAD‐box RNA helicases in general and can be used for rational design of selective inhibitors of hDDX3, to be tested as potential antitumor and antiviral agents. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Performance comparison of thermal insulated packaging boxes, bags and refrigerants for single‐parcel shipments
Authors: Singh S. P. , Burgess Gary , Singh Jay
Published: March 2007

A range of packaging solutions exists for products that must be kept within a specific temperature range throughout the supply‐and‐distribution chain. This report summarizes the results of studies conducted over a span of 2 years by the Consortium for Distribution Packaging at Michigan State University. Thermal insulation packaging materials such as expanded polystyrene, polyurethane, corrugated fibreboard, ThermalCor® and other composite packaging such as thermal insulating bags were studied. Phase change materials such as gel packs were also evaluated. Properties such as R‐value, melting point and heat absorption were examined and are reported. Copyright © 2007 John Wiley & Sons, Ltd.
Nondestructive Mechanical Release of Ordered Polymer Microfiber Arrays from Porous Templates
Authors: Grimm Silko , Schwirn Kathrin , Göring Petra , Knoll Heiko , Miclea Paul T. , Greiner Andreas , Wendorff Joachim H. , Wehrspohn Ralf B. , Gösele Ulrich , Steinhart Martin
Published: March 2007

The fabrication of one‐dimensional (1D) nanostructures and microstructures inside the pores of porous templates is intensively investigated. The release of these structures is commonly accomplished by etching and destroying the templates. The 1D nanostructures and microstructures tend to condense because of the occurrence of capillary forces during drying of the specimens. It is shown that highly ordered arrays of polymer microfibers can be easily detached from silanized porous templates by mechanical lift‐off. This procedure leaves the templates intact, thus allowing their recycling, and does not involve the use of solutions or solvents, thus circumventing condensation. Therefore, mechanical lift‐off may enable the up‐scaling of template‐based approaches to the fabrication of highly ordered assemblies of 1D nanostructures and microstructures.
Performance of wavelet based Multi‐Chip Rate DS‐CDMA signals over multi‐path Nakagami‐mfading channels
Authors: Öztürk Ertan
Published: March 2007

Multi‐Chip Rate/Direct Sequence‐Code Division Multiple Access (MCR/DS‐CDMA) technique using scaled chip waveforms has been designed as an alternative to multi‐data rate DS‐CDMA techniques having constant chip rates. In this work, the probability of error (Pe) expression for MCR/DS‐CDMA signals is derived over multi‐path Nakagami‐mfading channels to investigate the effects of chip waveforms on it. This paper also proposes the use of orthogonal wavelets as chip waveforms of MCR/DS‐CDMA signals over the considered channel. For numerical calculations, Daubechies‐22 (D22) wavelet is used because its side lobes are 40 dB below its main lobe in frequency domain. D22is compared with a Square Root Raised Cosine (SRRC) chip waveform. In the numerical calculations, only first four scales of the chip waveforms relating to four different chip/data rates are considered. The results for thePeperformance and the capacity (the number of user per Hertz for a samePelevel) show that D22significantly outperforms the SRRC chip waveform at all data rates, due to low cross correlations among different scales of orthogonal wavelets. Besides, by increasing the number of scales, the advantage of the use of orthogonal wavelets will increase furthermore. Copyright © 2007 John Wiley & Sons, Ltd.
Engineering Oilseed Plants for a Sustainable, Land‐Based Source of Long Chain Polyunsaturated Fatty Acids
Authors: Damude Howard G. , Kinney Anthony J.
Published: March 2007

Numerous clinical studies have demonstrated the cardiovascular and mental health benefits of including very long chain omega‐3 polyunsaturated fatty acids, namely eicospentaenoic acid (EPA) and docosohexaenoic acid (DHA) in the human diet. Certain fish oils can be a rich source of omega‐3 long chain polyunsaturated fatty acids although processed marine oils are generally undesirable as food ingredients because of the associated objectionable flavors and contaminants that are difficult and cost‐prohibitive to remove. Oilseed plants rich in omega‐3 fatty acids, such as flax and walnut oils, contain only the 18‐carbon omega‐3 polyunsaturated fatty acid alpha‐linolenic acid, which is poorly converted by the human body to EPA and DHA. It is now possible to engineer common omega‐6 rich oilseeds such as soybean and canola to produce EPA and DHA and this has been the focus of a number of academic and industrial research groups. Recent advances and future prospects in the production of EPA and DHA in oilseed crops are discussed here.
Expression of the halobacterial transducer protein HtrII from Natronomonas pharaonis in Escherichia coli
Authors: Mennes Nadine , Klare Johann P. , Chizhov Igor , Seidel Ralf , Schlesinger Ramona , Engelhard Martin
Published: March 2007

Archaeal phototaxis is mediated by sensory rhodopsins which form complexes with their cognate transducers. Whereas the receptors sensory rhodopsin I and sensory rhodopsin II (SRII) have been expressed in Escherichia coli (E. coli) only shortened fragments of HtrII from Natronomonas pharaonis (NpHtrII) are available. Here we describe the heterologous expression of full length NpHtrII which was achieved in yields of up to 0.9 mg per litre cell culture. Gel filtration analysis reveals the tendency of the transducer to form dimers and higher‐order oligomers which was also observed when complexed to NpSRII. A circular dichroism (CD) spectrum of NpHtrII is comparable to those obtained for the E. coli chemoreceptors indicating a similar folding with predominantly α‐helical structure. NpHtrII dissociates from the NpSRII/HtrII complex with an apparent K
D of about 0.6 μM. Photocycle kinetics of the complex is comparable to that obtained for NpSRII in complex with a truncated transducer with slight differences in the M‐decay. The data indicate that the heterologously expressed NpHtrII adopt a native like structure, providing the means for elucidating transmembrane signal transduction and activation of microbial signalling cascades.
Effects of maternal hyperhomocysteinemia induced by high methionine diet on the learning and memory performance in offspring
Authors: Baydas Giyasettin , Koz Sema T. , Tuzcu Mehmet , Nedzvetsky Victor S. , Etem Ebru
Published: March 2007

In this study, we suggest that chronic maternal hyperhomocysteinemia results in learning deficits in the offspring due to delayed brain maturation and altered expression pattern of neural cell adhesion molecule. Although the deleterious effects of hyperhomocysteinemia were extensively investigated in the adults, there is no clear evidence suggesting its action on the developing fetal rat brain and cognitive functions of the offspring. Therefore, in the present work we aimed to investigate effects of maternal hyperhomocysteinemia on the fetal brain development and on the behavior of the offspring. A group of pregnant rats received daily methionine (1 g/kg body weight) dissolved in drinking water to induce maternal hyperhomocysteinemia, starting in the beginning of gestational day 0. The levels of glial fibrillary acidic protein, S100B protein, and neural cell adhesion molecule were determined in the tissue samples from the pups. Learning and memory performances of the young‐adult offsprings were tested using Morris water maze test. There were significant reductions in the expressions of glial fibrillary acidic protein and S100B protein in the brains of maternally hyperhomocysteinemic pups on postnatal day 1, suggesting that hyperhomocysteinemia delays brain maturation. In conclusion, maternal hyperhomocysteinemia changes the expression pattern of neural cell adhesion molecule and therefore leads to an impairment in the learning performance of the offspring.
Monitoring process quality in off‐shore outsourcing: A model and findings from multi‐country survey
Authors: Aron Ravi , Bandyopadhyay Subhajyoti , Jayanty Siddharth , Pathak Praveen
Published: March 2007

We investigate how recent advances in information technology and telecommunications have led to real‐time monitoring of processes at the site of the provider by a buyer located across the globe. We construct a game‐theoretic model of the dynamics of the buyer–supplier interaction in the presence of moral hazard and incomplete contracting. We derive the Minimum Quality Threshold (MQT) below which the provider's output will certainly be inspected. Our findings show that the buyer can pick a level of monitoring and thereby force the provider to exceed the quality level of the MQT in output quality and avoid costly and wasteful inspection. Finally, our model explains why the production of processes that are complex and more prone to errors are actually monitored less by the buyers. We furnish the results of a comprehensive, multi‐year, multi‐country survey of the efficacy of monitoring in off‐shore outsourcing projects and demonstrate strong empirical support for the findings of the model.
Foundations in Nursing and Health Care: Writing Skills in Health Care
Authors: Harvey Mary Kay
Published: March 2007

Foundations in Nursing and Health Care: Writing Skills in Health Care Philip Burnard 2004, 176 pages £12.50 softcover
A new Middle–Late Jurassic flora and hot spring chert deposit from the Deseado Massif, Santa Cruz province, Argentina
Authors: CHANNING ALAN , ZAMUNER ALBA B. , ZÚÑIGA ADOLFO
Published: March 2007

We present an initial report of a well-preserved and relatively diverse Gondwanan plant assemblage from Bahía Laura Group, Chon Aike Formation strata of the Estancia Flecha Negra area, central-western region of the Deseado Massif, Santa Cruz province, Patagonia, Argentina. The locality contains the first richly fossiliferous chert with a diverse and well-preserved plant assemblage reported from the Mesozoic which is demonstrably associated with hot spring activity. A compression flora and petrified forest contained in associated clastic and volcaniclastic environments provide an indication of regional plant diversity during this as yet poorly represented stratigraphic interval.
Effect ofPlasmodium yoelii nigeriensisinfection on hepatic and splenic glutathione-S-transferase(s) in Swiss albino and db/+ mice: efficacy of mefloquine and menadione in antimalarial chemotherapy
Authors: AHMAD R. , SRIVASTAVA A. K.
Published: March 2007

The present report deals with the status of hepatic and splenic glutathione-S-transferase (GST) activities in mice during experimental infection withPlasmodium yoelii nigeriensisand subsequent treatment of infected mice with mefloquine (Mf) and menadione (Md). The infection caused significant decline in the hepatic and splenic glutathione-S-transferase (GST) activities of albino and db/+ mice. The decline was observed in the levels of both cytosolic and microsomal GST(s) of liver and spleen in both types of mice. Intraperitoneal administration of mefloquine at a dose of 5 mg/kg and menadione at a dose of 100 mg/kg, twice daily from day 1 p.i. (day 0) until day 10, caused restoration in the levels of hepatic as well as splenic GST(s), albeit to varying degrees. Mf was able to suppress parasitaemia by day 5 in the case of albino mice and by day 3 in the case of db/+ mice but was unable to cure both types of mice completely. On the other hand, Md caused a delay in maturation of infection in both cases, but could not cure the mice.
Genetic characterization of members of the genusContracaecum(Nematoda: Anisakidae) from fish-eating birds from west-central Florida, USA, with evidence of new species
Authors: D'AMELIO S. , BARROS N. B. , INGROSSO S. , FAUQUIER D. A. , RUSSO R. , PAGGI L.
Published: March 2007

Specimens ofContracaecumspp. fromPhalacrocorax auritusandPelecanus occidentalisfrom Florida were characterized by sequencing of the small subunit of the mitochondrial ribosomal RNA gene (rrnS) and by PCR-based RFLP analysis of the same gene and of the internal transcribed spacers (ITS) of nuclear ribosomal DNA. Analyses of therrnSsequence data using the MP and UPGMA approaches yielded trees with similar topologies, delineating 3 main clusters. Specimens fromPh. auritus, morphologically assigned toC. rudolphii(s.l.), were part of the cluster comprising also the other 2 species of theC. rudolphiicomplex (A and B), but representing a genetically distinct group, potentially corresponding to a distinct lineage within the complex, provisionally named asC. rudolphiiC. The second cluster comprised 5 individuals fromP. occidentalis, which formed a genetically relatively homogeneous group. TherrnSdata indicate that these specimens (indicated asContracaecumsp. 1) are clearly genetically different from the morphologically most closely related species, i.e.C. rudolphii(s.l.) andC. microcephalum, and could represent a new species. The third cluster comprised 7 specimens fromP. occidentalismorphologically assigned toC. multipapillatum(s.l.). These were shown to be genetically homogeneous and related to but quite distinct fromC. multipapillatumfrom Greece, although additional studies are needed to assess their status. PCR-RFLP based markers for the quick identification of these taxa are provided.
Indigenous peoples: issues of definition
Authors: Sanders DE
Published: March 2007

The progress that has been made by 'indigenous peoples' in international forums has been aided by the political perception that this category of claimants is limited and in some respects unique, and that such claims can properly and safely be treated as a special case. Although the imprecision of the category and the expanding array of groups involved in the 'indigenous peoples movement' could eventually threaten this perception and provoke more sustained demands for precision, such a transformation has not yet occurred.
The Lapps in Finland
Authors: Modeen T
Published: March 2007

The Lapps of Scandinavia constitute a small indigenous ethnic community divided between four states: Norway, Sweden, Finland and Russia. The Lapps used to depend on reindeer farming and lacked their own schools. Because of their low social status and the lack of governmental understanding for their cultural needs, most of the Finnish Lapps had been assimilated with the majority population. Only in recent years an effort has been made by the government to encourage the preservation of the Lapp language and the Lapp civilization. A Lapp parliament has been created and the Lapp Language Act makes it possible for the Lapps to communicate in their own language with the authorities. It is to be hoped that these measures will bring positive results in a situation where only few Lappish speaking people remain in Finland, many of them having difficulties finding a livelihood in their homeland, the northernmost part of Finland.
The Year Bearer's People: repatriation of ethnographic and sacred knowledge to the Jakaltek Maya of Guatemala
Authors: Montejo VD
Published: March 2007

In the early decades of this century, ethnographers who believed that the indigenous cultures of the Americas were in imminent danger of extinction undertook a variety of methods to record the vestiges of these cultures. Often carried out in collaboration with the controlling political powers, these ethnographic nonetheless became both instruments of persecution against traditional religious practices and the last records of these practices. One such ethnography, The Year Bearer's People, recorded by Oliver La Farge in 1927, became the only remaining record of this religious ceremony that commemorated the new year and was central to the life of the Jakaltek Maya in the Kuchumatán highland region of Guatemala. In this article, the author recounts the translation of this ethnography and the return of this sacred knowledge to the Maya community.
The potential of fruit trees to enhance converted habitats for migrating birds in southern Mexico
Authors: FOSTER MERCEDES S.
Published: March 2007

Migration routes used by Nearctic migrant birds can cover great distances; they also differ among species, within species, and between years and seasons. As a result, migration routes for an entire migratory avifauna can encompass broad geographic areas, making it impossible to protect continuous stretches of habitat sufficient to connect the wintering and breeding grounds for most species. Consequently, ways to enhance habitats converted for human use (i.e. for pasture, crop cultivation, human settlement) as stopover sites for migrants are especially important. Shelterbelts around pastures and fields, if planted with species targeted to support migrant (and resident) bird species that naturally occupy mature forest habitats and that are at least partially frugivorous, could be a powerful enhancement tool for such species, if the birds will enter the converted areas to feed. I tested this approach for Nearctic migrant birds during the spring migration through an area in Chiapas, Mexico. Mature forest tree species whose fruits are eaten by birds were surveyed. Based on life form, crop size and fruit characteristics, I selected three tree species for study: Cymbopetalum mayanum (Annonaceae), Bursera simaruba (Burseraceae) and Trophis racemosa (Moraceae). I compared the use of fruits of these species by migrants and residents in forest with their use of the fruits of isolated individuals of the same species in pasture and cropland. All three plant species were useful for enhancing converted habitats for forest-occupying spring migrants, although species differed in the degree to which they entered disturbed areas to feed on the fruits. These tree species could probably enhance habitats for migrants at sites throughout the natural geographic ranges of the plants; in other geographic areas for other target bird groups, other tree species might be more appropriate.
An update on the distribution of the ‘Endangered’ White-eared Night Heron Gorsachius magnificus in China
Authors: HE FEN-QI , FELLOWES JOHN R. , CHAN BOSCO P. L. , LAU MICHAEL W. N. , LIN JIAN-SHENG , SHING LEE KWOK
Published: March 2007

The literature on the past distribution and status of the White-eared Night Heron in China is reviewed, and updated based on recent field investigations and reports from Hubei, Jiangxi, Guangxi, Guangdong and Hainan. Recent records reveal the species to be more widespread than previously thought, but there remain many uncertainties about the area of occupancy and connectivity between known populations. The rate of discovery of new sites suggests the species may be under-recorded, but a number of recent sites have been lost, and no truly secure populations are known. There thus remains an urgent need for better information from throughout the species' range, especially from historical sites, as well as increased protection.
Selecting priority areas to conserve Psittacines in the Brazilian cerrado: minimizing human–conservation conflicts
Authors: PINTO MÍRIAM PLAZA , MATHIAS PABLO VINÍCIUS CLEMENTE , BLAMIRES DANIEL , DINIZ-FILHO JOSÉ ALEXANDRE FELIZOLA , BINI LUIS MAURICIO
Published: March 2007

The rapid destruction of habitat in biodiversity hotspots calls for the urgent formulation of conservation strategies. In this study, macro-scale biogeographical data for 33 species of Psittacines were used to select networks of priority areas, using an algorithm based on the complementarity concept. Human population size was also incorporated as a cost in the selection process, and the two networks of priority areas (with and without cost) were compared. In the comparison the number of cells selected to represent all species did not differ, but a rearrangement occurred between them. Two of the four cells were located in the same place, and the others changed location but stayed aggregated within the same regions. The study shows that it is possible to minimize human population size and represent all species in a network of priority areas.
The effects of using different species conservation priority lists on the evaluation of habitat importance within Hungarian grasslands
Authors: BATÁRY PÉTER , BÁLDI ANDRÁS , ERDŐS SAROLTA
Published: March 2007

Many bird species of conservation importance inhabit the grasslands of the Hungarian Great Plain. Although extensive grazing management usually supports more bird species than intensive management, the conservation priority is to protect rare or declining species. Therefore, the conservation status of species must also be included in assessments of the value of different habitats. We used territory mapping to count birds in 21 extensively and intensively grazed field pairs on the Hungarian Great Plain, and subsequently adjusted site scores depending on which species appeared on various lists of priority taxa. We investigated differences in conservation scores of two global conservation lists (the Bonn Convention and another based on values of eight biological characteristics), two West Europe based lists (Bird Directive and CORINE), three continental lists (European Threat Status, SPEC and Bern Convention) and two Hungarian lists (protected species of Hungary and an alternative based on the specifics of Hungarian populations). Extensively managed fields had higher conservation values under seven of the nine priority lists: only the two West Europe based lists showed opposite trends in more than half the study areas. Since both West Europe based lists cover many central and eastern European countries, there is an urgent need to revise these lists, especially the Bird Directive list that gives serious legal responsibilities to countries.
Surveys of wintering Little Bustards Tetrax tetrax in central Spain: distribution and population estimates at a regional scale
Authors: DE LA MORENA ELADIO L. GARCÍA , MORALES MANUEL B. , DE JUANA EDUARDO , SUÁREZ FRANCISCO
Published: March 2007

Developing a standardized survey methodology to census and estimate the size of wintering populations is a main conservation priority for the endangered Little Bustard. We present a standard and repeatable methodology to census wintering Little Bustard populations at a regional scale, and the first statistically reliable population estimate of a Little Bustard wintering population in Spain. We carried out two surveys, in 2003 and 2004, using UTM 10 km × 10 km squares as census units, which were subjected to stratified sampling over the species' potential distribution range in the region of Madrid (Central Spain). Only the areas of potentially suitable habitat within squares of known winter presence of the species were considered. The species' winter distribution in Madrid was fairly constant between years, showing a fragmented pattern in three main nuclei. The number of Little Bustards observed was consistent between surveys (752 and 786 birds, respectively), with birds grouped in an average of 32 flocks (1 to 350 birds, mean = 27.9 birds). No between-winter differences in flock size were observed, although differences between sectors were significant. The highest densities were observed in the Tagus valley (mean density = 2.9 birds km−2, 293 birds), followed by north-eastern farmland (mean density = 0.6 bird km−2, 269 birds). The estimated size of the Little Bustard population wintering in the Madrid region was 1,051 (95% CI = 1,043–1,231). This calculation was based on recorded population density, measured as the number of birds per square kilometre, and considers the potential habitats available in each sector. We propose this methodology as adequate for surveying any Little Bustard wintering area, at both regional and smaller spatial scales. Survey results are consistent with previous tentative estimates for the region of Madrid, and with available information on Little Bustard movements. Sixty-five per cent of squares with Little Bustard presence were outside any protected area, which makes the wintering Little Bustard population of Madrid highly vulnerable to habitat disappearance and may affect the viability of breeding nuclei whose individuals winter in the region.
Vines and canopy contact: a route for snake predation on parrot nests
Authors: KOENIG SUSAN E. , WUNDERLE, JR JOSEPH M. , ENKERLIN-HOEFLICH ERNESTO C.
Published: March 2007

Ornithologists have hypothesized that some tropical forest birds avoid snake predation by nesting in isolated trees that do not have vines and canopy contact with neighbouring trees. Here we review two complementary studies that support this hypothesis by demonstrating (1) that an abundance of vines and an interlocking canopy characterized Jamaican Black-billed Parrot Amazona agilis nest-trees that failed due to chick loss, presumably to snakes, and (2) that such trees were used preferentially by an arboreal snake congeneric to the snake implicated in the parrot losses. Evidence strongly suggested that losses of nestling Black-billed Parrots were due in substantial part to predation by the Jamaican (yellow) Boa Epicrates subflavus (Boidae). Studies of the closely related Epicrates inornatus on Puerto Rico revealed that trees used by boas had more vine cover and more crown or canopy contact with neighbouring trees than did randomly selected trees. Moreover, the boas had relatively large home ranges and were most active during March to July, which corresponds with the breeding season of parrots as well as other bird species. We suggest that nest failure due to snakes may be reduced in endangered bird species through isolating the nest-tree by eliminating vines and canopy contact with neighbouring trees and shrubs and by placing barriers on the nest-tree trunk.
Effects of Lycopene Supplementation on Plasma and Tissue Lycopene Levels in Various Rodent Strains
Authors: Huang  , Chuang  , Hu
Published: March 2007

Lycopene has been shown to have various biologic effects, and rats and mice are often used for elucidating its in vivo effects and mechanisms. Here, we compared plasma and tissue lycopene levels in F344 rats, BALB/c mice, nude mice, and gerbils by oral supplementation with lycopene (20 mg/kg BW · 2d) every other morning for 10 days. We found that livers accumulated substantially more lycopene than kidneys and that the hepatic lycopene contents varied greatly in these animals, with gerbils being most efficient (1432 ± 235 nmol/g), followed by nude mice (524 ± 133 nmol/g), F344 rats (28 ± 11 nmol/g), and BALB/c mice (5 ± 2 nmol/g). Plasma lycopene concentrations also varied greatly, of which the highest was found in gerbils (667 ± 160 nmol/L), followed by nude mice (224 ± 51 nmol/L), then by BALB/c mice and F344 rats (198 ± 52 and 139 ± 41 nmol/L, respectively). Interestingly, plasma and tissue β-carotene concentrations in these animals were markedly decreased by lycopene supplementation. To determine the steady-state levels of plasma lycopene, we fed 10 gerbils with lycopene (20 mg/kg BW · 2d) for 20 days, and we found a steady-state level of plasma lycopene between 597 to 722 nmol/L. Our results demonstrate that gerbils and nude mice are better accumulators than F344 rats and BALB/c mice, and that the former species may be more useful for studying the in vivo effects of lycopene.
A Preliminary Assessment of Vitamin K1 Intakes and Serum Undercarboxylated Osteocalcin Levels in 11–13 Year Old Irish Girls
Authors: Collins  , Cashman  , Kiely
Published: March 2007

Low vitamin K1 intakes have been associated with low bone mineral density in women and reduced bone turnover in girls. No European data exist on the relationship between vitamin K1 and serum undercarboxylated osteocalcin (ucOC), an indicator of K1 status in adolescents. The aim of the current study was to assess intakes of vitamin K1 in relation to serum ucOC status in Irish girls. A detailed dietary history method, which measured habitual intakes from a typical 14-day period, was used to estimate vitamin K1 intakes in 18 girls aged 11–13 years. Recently compiled and validated food composition data for vitamin K1 were used to determine vitamin K1 intakes. An enzyme immunoassay was used to measure ucOC in fasting serum samples. The mean (± SD) intake of vitamin K1 in the girls was 72.4 μg/day (SD 34.4). Vegetables (particularly broccoli, composite dishes, and lettuce) contributed 53% of total vitamin K1 intakes. Thirty-Seven percent of the girls failed to meet the current U.S. adequate intake for adolescents of 60 μg/day vitamin K1. Serum ucOC levels were inversely related to body weight-adjusted vitamin K1 intakes, controlling for energy intake (partial correlation r = –0.538; p = 0.026). The data indicate that large-scale studies to examine relationships between vitamin K1 (and green vegetable) intakes and bone growth and development in adolescents are warranted.
Research Paper Effects of 13-HPODE on Expression of Genes Involved in Thyroid Hormone Synthesis, Iodide Uptake and Formation of Hydrogen Peroxide in Porcine Thyrocytes
Authors: Luci  , Bettzieche  , Eder
Published: March 2007

It has been shown that dietary oxidized fats influence thyroid function in rats and pigs. Mechanisms underlying this phenomenon are unknown. This study was performed to investigate whether 13-hydroperoxy-9,11-octadecadienic acid (13-HPODE), a primary oxidation product of linoleic acid, affects expression of genes involved in thyroid hormone synthesis and formation of hydrogen peroxide in primary porcine thyrocytes. Thyrocytes were treated with 13-HPODE in concentrations between 20 and 100 μM. Cells treated with vehicle alone ("control cells") or with equivalent concentrations of linoleic acid were considered as controls. Treatment of cells with 13-HPODE did not affect cell viability but increased the activities of the antioxidant enzymes superoxide dismutase and glutathione peroxidase (p < 0.05) compared to control cells or cells treated with linoleic acid. Relative mRNA concentrations of genes involved in thyroid hormone synthesis like sodium iodide symporter, thyrotropin receptor, and thyroid peroxidase, as well as iodide uptake, did not differ between cells treated with 13-HPODE and control cells or cells treated with linoleic acid. Treatment of cells with 13-HPODE, however, reduced the relative mRNA concentrations of dual oxidase-2 and the formation of hydrogen peroxide compared to control cells or cells treated with linoleic acid (p < 0.05). Because the production of hydrogen peroxide is rate-limiting for the synthesis of thyroid hormones, it is suggested that 13-HPODE could have an impact on the formation of thyroid hormones in the thyroid gland.
Grad‐Shafranov reconstruction with field‐aligned flow: First results
Authors: Teh W.‐L. , Sonnerup B. U. Ö. , Hau L.‐N.
Published: March 2007

Grad‐Shafranov (GS) reconstruction is a novel tool for recovering steady two‐dimensional (2‐D) coherent magnetic field structures from data taken by a single spacecraft. We present first results from a recently developed version of GS reconstruction that incorporates the effects of dynamically significant field‐aligned plasma flow. A new GS solver for this case has been developed and is benchmarked with an exact analytical solution. It is then applied to a magnetopause encounter by Cluster 1 (C1) and Cluster 3 (C3) on July 5, 2001. In the C1 crossing, a field‐aligned plasma flow, in the frame co‐moving with the local magnetopause structures, is present at approximately 57% of the Alfvén speed; in the C3 event the local flow is nearly Alfvénic. We find the following: (1) The recovered field maps are qualitatively similar to those obtained from magneto‐hydrostatic GS reconstruction, indicating that the latter can be fairly robust. (2) Our code provides new information about plasma structure and supersonic field‐aligned flow effects during reconnection. (3) We confirm results from the previous GS studies of the event, which indicated that significant time evolution occurred in the 30 s time lapse between the two crossings, owing to developing reconnection at a site close to the spacecraft. We provide an estimate of 0.47 mV/m for the reconnection electric field.
Rapid volume loss from two East Greenland outlet glaciers quantified using repeat stereo satellite imagery
Authors: Stearns Leigh A. , Hamilton Gordon S.
Published: March 2007

The coastal portions of Kangerdlugssuaq and Helheim glaciers in southeast Greenland lost at least 51 ± 8 km3 yr−1 of ice between 2001–2006 due to thinning and retreat, according to an analysis of sequential digital elevation models (DEMs) derived from stereo ASTER satellite imagery. The dominant contribution to this ice loss was dynamic thinning caused by the acceleration in flow of both glaciers. Peak rates of change, including thinning rates of ∼90 m yr−1, coincided with the rapid increases in flow speed. Extrapolation of the measured data to the ice divides yields an estimated combined catchment volume loss of ∼122 ± 30 km3 yr−1, which accounts for half the total mass loss from the ice sheet reported in recent studies. These catchment‐wide volume losses contributed ∼0.31 ± 0.07 mm yr−1 to global sea level rise over the 5‐year observation period with the coastal regions alone contributing at least 0.1 ± 0.02 mm yr−1.
Prediction of cloud condensation nucleus number concentration using measurements of aerosol size distributions and composition and light scattering enhancement due to humidity
Authors: Ervens Barbara , Cubison Michael , Andrews Elisabeth , Feingold Graham , Ogren John A. , Jimenez Jose L. , DeCarlo Peter , Nenes Athanasios
Published: March 2007

A cloud condensation nucleus (CCN) closure experiment is carried out using data from the Chebogue Point, Nova Scotia, ground site during the International Consortium for Atmospheric Research on Transport and Transformation (ICARTT) field experiment in 2004. The number concentration of CCN at five supersaturations (∼0.07% to ∼0.5%) is predicted from measurements of aerosol size distribution, composition, and hygroscopic growth and is compared to measured CCN concentrations. It is shown that CCN can be predicted quite reliably using measured size distributions, a simple aerosol model to derive the solute‐to‐water mole ratio, and the diameter growth factor g(RH) or the optical growth factor f(RH). The mean error ranges from an overestimate in CCN of ≤5% at high supersaturation to a factor of 2.4 at low supersaturation with regression coefficients r2 of 0.90 and 0.53, respectively. The poor agreement at low supersaturation is primarily a result of high flow rates in the CCN counter that prevented small particles from growing to detectable sizes. Precise knowledge of the temperature gradient, and flow rates of the instrument, is essential to establish the correct supersaturation, particularly at low supersaturation, where errors translate into a large percentage of the activated number. There may also be some contribution from simplified composition assumptions, e.g., neglecting variability with size and/or mixing state. The mostly oxygenated organic aerosol could be modeled as insoluble, within the above uncertainties, from the point of view of hygroscopicity and activation. The generality of these conclusions will have to be tested at other locations.
Trans‐Pacific transport of black carbon and fine aerosols (D < 2.5 μm) into North America
Authors: Hadley O. L. , Ramanathan V. , Carmichael G. R. , Tang Y. , Corrigan C. E. , Roberts G. C. , Mauger G. S.
Published: March 2007

This study presents estimates of long‐range transport of black carbon (BC) and aerosol fine mass (diameter less than 2.5 μm) across the Pacific Ocean into North America during April 2004. These transport estimates are based on simulations by the Chemical Weather Forecast System (CFORS) model and evaluated across 130°W, (30°N–60°N) from 26 March through 25 April 2004. CFORS calculates BC transport into North America at 25–32 Gg of which over 75% originates from Asia. Modeled fine aerosol mass transport is between 900 and 1100 Gg. The BC transport amounts to about 77% of the published estimates of North American BC emissions. Approximately 78% of the BC and 82% of the fine aerosol mass transport occur in the midtroposphere above 2 km. Given the relatively large magnitude of the estimated BC transport, we undertake a detailed validation of the model simulations of fine aerosol mass and BC over the west coast of North America. In situ aircraft data were available for the month of April 2004 to assess the accuracy of model simulations of aerosols in the lower troposphere. Aircraft data for aerosol mass collected in the eastern Pacific Ocean during April 2004 as part of the Cloud Indirect Forcing Experiment, as well as surface measurements of fine mass and BC at 30 west coast locations, are compared to CFORS predictions. These surface sites are part of the Interagency Monitoring of Protected Visual Environments (IMPROVE) network. Both the aircraft and the IMPROVE data sets reveal similar patterns of good agreement near and above the boundary layer accompanied by large overprediction within the boundary layer. The observational data validate the CFORS simulations of BC and fine aerosol mass above the boundary layer. The near‐surface overprediction does not impair the major conclusions of this study regarding long‐range aerosol and BC transport, as most of the long‐range transport occurs above 2 km. From this we conclude that the transport of BC from Asia and other regions west is a major source of BC at high elevations over North America. The simulated concentrations of BC between 1 and 3 km, as well as the measured BC concentrations over the elevated IMPROVE sites, range from 0.1 to 0.3 μg/m3. Direct radiative forcing over North America due to the modeled BC concentration between 1 and 15 km is estimated at an additional 2.04–2.55 W/m2 absorbed in the atmosphere and a dimming of −1.45 to −1.47 W/m2 at the surface. The impact of transported BC on the regional radiation budget through direct and indirect effects of the transported BC and other aerosols warrants further study.