bluuebunny/crossref_metadata_2025 huggingface dataset:
A comparison of rigid and flexible water models in collisions of monomers and small clusters
Authors: Napari Ismo , Vehkamäki Hanna
Published: September 2006

In this study we have investigated the dynamics of small water clusters using microcanonical molecular dynamics simulations. The clusters are formed by colliding vapor monomers with target clusters of two and five molecules. The monomers are sampled from a thermal ensemble at T=300K and target clusters with several total energies are considered. We compare rigid extended simple point charge water with flexible counterparts having intramolecular harmonic bonds with force constants 103 and 105kcal∕(molÅ2). We show that the lifetimes of the clusters formed via collision process are similar for the rigid model and the flexible model with the bigger force constant, if the translational temperatures of the target cluster molecules are equal. The model with the smaller force constant results in much longer lifetimes due to the stabilizing effect caused by the kinetic energy transfer into internal vibration of the molecules. This process may take several hundreds of picoseconds, giving rise to time-dependent decay rates of constant-energy clusters. A study of binary collisions of water molecules shows that the introduction of flexibility to the molecules increases the possibility of dimer formation and thus offers an alternative route for dimer production in vapors. Our results imply that allowing for internal degrees of freedom is likely to enhance gas-liquid nucleation rates in water simulations.
Direct-bonded GaAs∕InGaAs tandem solar cell
Authors: Tanabe Katsuaki , Fontcuberta i Morral Anna , Atwater Harry A. , Aiken Daniel J. , Wanlass Mark W.
Published: September 2006

A direct-bonded GaAs∕InGaAs solar cell is demonstrated. The direct-bonded interconnect between subcells of this two-junction cell enables monolithic interconnection without threading dislocations and planar defects that typically arise during lattice-mismatched epitaxial heterostructure growth. The bonded interface is a metal-free n+GaAs∕n+InP tunnel junction. The tandem cell open-circuit voltage is approximately the sum of the subcell open-circuit voltages. The internal quantum efficiency is 0.8 for the GaAs subcell compared to 0.9 for an unbonded GaAs subcell near the band gap energy and is 0.7 for both of the InGaAs subcell and an unbonded InGaAs subcell, with bonded and unbonded subcells similar in spectral response.
Diverse responses of phenology to global changes in a grassland ecosystem
Authors: Cleland Elsa E. , Chiariello Nona R. , Loarie Scott R. , Mooney Harold A. , Field Christopher B.
Published: September 2006

Shifting plant phenology (i.e., timing of flowering and other developmental events) in recent decades establishes that species and ecosystems are already responding to global environmental change. Earlier flowering and an extended period of active plant growth across much of the northern hemisphere have been interpreted as responses to warming. However, several kinds of environmental change have the potential to influence the phenology of flowering and primary production. Here, we report shifts in phenology of flowering and canopy greenness (Normalized Difference Vegetation Index) in response to four experimentally simulated global changes: warming, elevated CO
2
, nitrogen (N) deposition, and increased precipitation. Consistent with previous observations, warming accelerated both flowering and greening of the canopy, but phenological responses to the other global change treatments were diverse. Elevated CO
2
and N addition delayed flowering in grasses, but slightly accelerated flowering in forbs. The opposing responses of these two important functional groups decreased their phenological complementarity and potentially increased competition for limiting soil resources. At the ecosystem level, timing of canopy greenness mirrored the flowering phenology of the grasses, which dominate primary production in this system. Elevated CO
2
delayed greening, whereas N addition dampened the acceleration of greening caused by warming. Increased precipitation had no consistent impacts on phenology. This diversity of phenological changes, between plant functional groups and in response to multiple environmental changes, helps explain the diversity in large-scale observations and indicates that changing temperature is only one of several factors reshaping the seasonality of ecosystem processes.
Foraging biology predicts food web complexity
Authors: Beckerman Andrew P. , Petchey Owen L. , Warren Philip H.
Published: September 2006

Food webs, the networks of feeding links between species, are central to our understanding of ecosystem structure, stability, and function. One of the key aspects of food web structure is complexity, or connectance, the number of links expressed as a proportion of the total possible number of links. Connectance (complexity) is linked to the stability of webs and is a key parameter in recent models of other aspects of web structure. However, there is still no fundamental biological explanation for connectance in food webs. Here, we propose that constraints on diet breadth, driven by optimal foraging, provide such an explanation. We show that a simple diet breadth model predicts highly constrained values of connectance as an emergent consequence of individual foraging behavior. When combined with features of real food web data, such as taxonomic and trophic aggregation and cumulative sampling of diets, the model predicts well the levels of connectance and scaling of connectance with species richness, seen in real food webs. This result is a previously undescribed synthesis of foraging theory and food web theory, in which network properties emerge from the behavior of individuals and, as such, provides a mechanistic explanation of connectance currently lacking in food web models.
Host defenses againstStaphylococcus aureusinfection require recognition of bacterial lipoproteins
Authors: Bubeck Wardenburg Juliane , Williams Wade A. , Missiakas Dominique
Published: September 2006

Toll-like receptors and other immune-signaling pathways play important roles as sensors of bacterial pattern molecules, such as peptidoglycan, lipoprotein, or teichoic acid, triggering innate host immune responses that prevent infection. Immune recognition of multiple bacterial products has been viewed as a safeguard against stealth infections; however, this hypothesis has never been tested forStaphylococcus aureus, a frequent human pathogen. By generating mutations that block the diacylglycerol modification of lipoprotein precursors, we show here thatS. aureusvariants lacking lipoproteins escape immune recognition and cause lethal infections with disseminated abscess formation, failing to elicit an adequate host response. Thus, lipoproteins appear to play distinct, nonredundant roles in pathogen recognition and host innate defense mechanisms againstS. aureusinfections.
Structural basis for ligand promiscuity in cytochrome P450 3A4
Authors: Ekroos Marika , Sjögren Tove
Published: September 2006

Cytochrome P450 (CYP) 3A4 is the most promiscuous of the human CYP enzymes and contributes to the metabolism of ≈50% of marketed drugs. It is also the isoform most often involved in unwanted drug–drug interactions. A better understanding of the molecular mechanisms governing CYP3A4–ligand interaction therefore would be of great importance to any drug discovery effort. Here, we present crystal structures of human CYP3A4 in complex with two well characterized drugs: ketoconazole and erythromycin. In contrast to previous reports, the protein undergoes dramatic conformational changes upon ligand binding with an increase in the active site volume by >80%. The structures represent two distinct open conformations of CYP3A4 because ketoconazole and erythromycin induce different types of coordinate shifts. The binding of two molecules of ketoconazole to the CYP3A4 active site and the clear indication of multiple binding modes for erythromycin has implications for the interpretation of the atypical kinetic data often displayed by CYP3A4. The extreme flexibility revealed by the present structures also challenges any attempt to apply computational design tools without the support of relevant experimental data.
Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics
Authors: Zimmermann Jörg , Oakman Erin L. , Thorpe Ian F. , Shi Xinghua , Abbyad Paul , Brooks Charles L. , Boxer Steven G. , Romesberg Floyd E.
Published: September 2006

The evolution of proteins with novel function is thought to start from precursor proteins that are conformationally heterogeneous. The corresponding genes may be duplicated and then mutated to select and optimize a specific conformation. However, testing this idea has been difficult because of the challenge of quantifying protein flexibility and conformational heterogeneity as a function of evolution. Here, we report the characterization of protein heterogeneity and dynamics as a function of evolution for the antifluorescein antibody 4-4-20. Using nonlinear laser spectroscopy, surface plasmon resonance, and molecular dynamics simulations, we demonstrate that evolution localized the Ab-combining site from a heterogeneous ensemble of conformations to a single conformation by introducing mutations that act cooperatively and over significant distances to rigidify the protein. This study demonstrates how protein dynamics may be tailored by evolution and has important implications for our understanding of how novel protein functions are evolved.
Realization of a four-step molecular switch in scanning tunneling microscope manipulation of single chlorophyll-a molecules
Authors: Iancu Violeta , Hla Saw-Wai
Published: September 2006

Single chlorophyll-a molecules, a vital resource for the sustenance of life on Earth, have been investigated by using scanning tunneling microscope manipulation and spectroscopy on a gold substrate at 4.6 K. Chlorophyll-a binds on Au(111) via its porphyrin unit while the phytyl-chain is elevated from the surface by the support of four CH3groups. By injecting tunneling electrons from the scanning tunneling microscope tip, we are able to bend the phytyl-chain, which enables the switching of four molecular conformations in a controlled manner. Statistical analyses and structural calculations reveal that all reversible switching mechanisms are initiated by a single tunneling-electron energy-transfer process, which induces bond rotation within the phytyl-chain.
Helix-packing motifs in membrane proteins
Authors: Walters R. F. S. , DeGrado W. F.
Published: September 2006

The fold of a helical membrane protein is largely determined by interactions between membrane-imbedded helices. To elucidate recurring helix–helix interaction motifs, we dissected the crystallographic structures of membrane proteins into a library of interacting helical pairs. The pairs were clustered according to their three-dimensional similarity (rmsd ≤1.5 Å), allowing 90% of the library to be assigned to clusters consisting of at least five members. Surprisingly, three quarters of the helical pairs belong to one of five tightly clustered motifs whose structural features can be understood in terms of simple principles of helix–helix packing. Thus, the universe of common transmembrane helix-pairing motifs is relatively simple. The largest cluster, which comprises 29% of the library members, consists of an antiparallel motif with left-handed packing angles, and it is frequently stabilized by packing of small side chains occurring every seven residues in the sequence. Right-handed parallel and antiparallel structures show a similar tendency to segregate small residues to the helix–helix interface but spaced at four-residue intervals. Position-specific sequence propensities were derived for the most populated motifs. These structural and sequential motifs should be quite useful for the design and structural prediction of membrane proteins.
Genetic analysis of β1 integrin “activation motifs” in mice
Authors: Czuchra Aleksandra , Meyer Hannelore , Legate Kyle R. , Brakebusch Cord , Fässler Reinhard
Published: September 2006

Akey feature of integrins is their ability to regulate the affinity for ligands, a process termed integrin activation. The final step in integrin activation is talin binding to the NPXY motif of the integrin β cytoplasmic domains. Talin binding disrupts the salt bridge between the α/β tails, leading to tail separation and integrin activation. We analyzed mice in which we mutated the tyrosines of the β1 tail and the membrane-proximal aspartic acid required for the salt bridge. Tyrosine-to-alanine substitutions abolished β1 integrin functions and led to a β1 integrin–null phenotype in vivo. Surprisingly, neither the substitution of the tyrosines with phenylalanine nor the aspartic acid with alanine resulted in an obvious defect. These data suggest that the NPXY motifs of the β1 integrin tail are essential for β1 integrin function, whereas tyrosine phosphorylation and the membrane-proximal salt bridge between α and β1 tails have no apparent function under physiological conditions in vivo.
Three-dimensional reconstruction of the membrane skeleton at the plasma membrane interface by electron tomography
Authors: Morone Nobuhiro , Fujiwara Takahiro , Murase Kotono , Kasai Rinshi S. , Ike Hiroshi , Yuasa Shigeki , Usukura Jiro , Kusumi Akihiro
Published: September 2006

Three-dimensional images of the undercoat structure on the cytoplasmic surface of the upper cell membrane of normal rat kidney fibroblast (NRK) cells and fetal rat skin keratinocytes were reconstructed by electron tomography, with 0.85-nm–thick consecutive sections made ∼100 nm from the cytoplasmic surface using rapidly frozen, deeply etched, platinum-replicated plasma membranes. The membrane skeleton (MSK) primarily consists of actin filaments and associated proteins. The MSK covers the entire cytoplasmic surface and is closely linked to clathrin-coated pits and caveolae. The actin filaments that are closely apposed to the cytoplasmic surface of the plasma membrane (within 10.2 nm) are likely to form the boundaries of the membrane compartments responsible for the temporary confinement of membrane molecules, thus partitioning the plasma membrane with regard to their lateral diffusion. The distribution of the MSK mesh size as determined by electron tomography and that of the compartment size as determined from high speed single-particle tracking of phospholipid diffusion agree well in both cell types, supporting the MSK fence and MSK-anchored protein picket models.
Luminal particles within cellular microtubules
Authors: Garvalov Boyan K. , Zuber Benoît , Bouchet-Marquis Cédric , Kudryashev Mikhail , Gruska Manuela , Beck Martin , Leis Andrew , Frischknecht Friedrich , Bradke Frank , Baumeister Wolfgang , Dubochet Jacques , Cyrklaff Marek
Published: September 2006

The regulation of microtubule dynamics is attributed to microtubule-associated proteins that bind to the microtubule outer surface, but little is known about cellular components that may associate with the internal side of microtubules. We used cryoelectron tomography to investigate in a quantitative manner the three dimensional structure of microtubules in intact mammalian cells. We show that the lumen of microtubules in this native state is filled with discrete, globular particles with a diameter of 7 nm and spacings between 8 and 20 nm in neuronal cells. Cross-sectional views of microtubules confirm the presence of luminal material in vitreous sections of brain tissue. Most of the luminal particles had connections to the microtubule wall, as revealed in tomograms. A higher accumulation of particles was seen near the retracting plus ends of microtubules. The luminal particles were abundant in neurons, but were also observed in other cells, such as astrocytes and stem cells.
Probalign: multiple sequence alignment using partition function posterior probabilities
Authors: Roshan Usman , Livesay Dennis R.
Published: September 2006

Motivation: The maximum expected accuracy optimization criterion for multiple sequence alignment uses pairwise posterior probabilities of residues to align sequences. The partition function methodology is one way of estimating these probabilities. Here, we combine these two ideas for the first time to construct maximal expected accuracy sequence alignments.

Results: We bridge the two techniques within the program Probalign. Our results indicate that Probalign alignments are generally more accurate than other leading multiple sequence alignment methods (i.e. Probcons, MAFFT and MUSCLE) on the BAliBASE 3.0 protein alignment benchmark. Similarly, Probalign also outperforms these methods on the HOMSTRAD and OXBENCH benchmarks. Probalign ranks statistically highest (P-value < 0.005) on all three benchmarks. Deeper scrutiny of the technique indicates that the improvements are largest on datasets containing N/C-terminal extensions and on datasets containing long and heterogeneous length proteins. These points are demonstrated on both real and simulated data. Finally, our method also produces accurate alignments on long and heterogeneous length datasets containing protein repeats. Here, alignment accuracy scores are at least 10% and 15% higher than the other three methods when standard deviation of length is >300 and 400, respectively.

Availability: Open source code implementing Probalign as well as for producing the simulated data, and all real and simulated data are freely available from

Contact:  usman@cs.njit.edu
Burkholderia oklahomensis sp. nov., a Burkholderia pseudomallei-like species formerly known as the Oklahoma strain of Pseudomonas pseudomallei
Authors: Glass Mindy B. , Steigerwalt Arnold G. , Jordan Jean G. , Wilkins Patricia P. , Gee Jay E.
Published: September 2006

C6786, the clinical isolate of the ‘Oklahoma’ strain of Pseudomonas (now Burkholderia) pseudomallei, was originally isolated in 1973 from a wound infection resulting from a farming accident in Oklahoma, USA. Environmental isolates C7532 and C7533 from the Oklahoma accident site were found to match C6786. These three isolates and a clinical isolate originally identified as B. pseudomallei that was recovered from a person in Georgia, USA, involved in an automobile accident were characterized by biochemical, 16S rRNA gene sequencing, multilocus sequence typing and DNA–DNA hybridization analyses. Results indicated that these strains comprise a novel species. The name Burkholderia oklahomensis sp. nov. is proposed, with strain C6786T (=LMG 23618T=NCTC 13387T=CCUG 51349T) as the type strain.
Aquimarina intermedia sp. nov., reclassification of Stanierella latercula (Lewin 1969) as Aquimarina latercula comb. nov. and Gaetbulimicrobium brevivitae Yoon et al. 2006 as Aquimarina brevivitae comb. nov. and emended description of the genus Aquimarina
Authors: Nedashkovskaya Olga I. , Vancanneyt Marc , Christiaens Leentje , Kalinovskaya Natalia I. , Mikhailov Valery V. , Swings Jean
Published: September 2006

A heterotrophic, aerobic, Gram-negative, pigmented and gliding bacterium, strain KMM 6258T, was isolated from the sea urchin Strongylocentrotus intermedius and investigated using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis revealed that the closest relatives of the novel strain are Aquimarina muelleri, Stanierella latercula and Gaetbulimicrobium brevivitae, members of the family Flavobacteriaceae, with sequence similarities of 96.3, 96.4 and 96.2 %, respectively. Phylogenetic evidence, supported by chemotaxonomic and phenotypic data, assigned strain KMM 6258T to the genus Aquimarina as Aquimarina intermedia sp. nov. (type strain KMM 6258T=DSM 17527T=JCM 13506T=LMG 23204T). The reclassification of Stanierella latercula as Aquimarina latercula comb. nov. and Gaetbulimicrobium brevivitae as Aquimarina brevivitae comb. nov. is proposed.
Nocardia harenae sp. nov., an actinomycete isolated from beach sand
Authors: Seo Jae Pyo , Lee Soon Dong
Published: September 2006

A novel actinomycete, strain WS-26T, was isolated from beach sand on the coast of Jeju Island, Republic of Korea, and subjected to a polyphasic taxonomic characterization. The organism produced reddish orange-coloured substrate mycelium and white aerial mycelium, both of which fragmented into rod-shaped elements. A neighbour-joining tree, based on 16S rRNA gene sequence studies, revealed that the isolate formed a distinct branch at the base of a cluster that included Nocardia carnea, N. flavorosea, N. pigrifrangens, N. sienata and N. testacea. This branching pattern was also found in a tree constructed using the maximum-likelihood method, but was not supported by the maximum-parsimony method. Levels of 16S rRNA gene sequence similarity between the isolate and its phylogenetic neighbours ranged from 96.5 to 97.8 %. Chemotaxonomic properties, such as the principal amino acid of peptidoglycan, predominant menaquinone and polar lipids, supported its assignment to the genus Nocardia. On the basis of phenotypic and phylogenetic data, the organism was different from Nocardia species with validly published names. The name Nocardia harenae sp. nov. is proposed, with WS-26T (=KCCM 42317T=NRRL B-24459T) as the type strain.
New insights into the phylogeny of Entamoeba species provided by analysis of four new small-subunit rRNA genes
Authors: Clark C. Graham , Kaffashian Farrokh , Tawari Blessing , Windsor Jeffrey J. , Twigg-Flesner Anke , Davies-Morel Mina C. G. , Blessmann Joerg , Ebert Frank , Peschel Babett , Van An Le , Jackson Colin J. , Macfarlane Lorna , Tannich Egbert
Published: September 2006

Sequences of small-subunit rRNA genes have been obtained for four new isolates of Entamoeba. Phylogenetic analyses give new insights into the evolution of these organisms. A novel Entamoeba from pigs in Vietnam that produces uninucleate cysts proved to be unrelated to other uninucleated cyst-producing species. Revival of the name Entamoeba suis for this organism is proposed. Instead of being related to Entamoeba polecki, it shares a recent common ancestor with the non-encysting Entamoeba gingivalis in a lineage that is basal to the tetranucleate cyst-producing clade. This suggests that species producing cysts with four nuclei are descended from an ancestor that produced cysts with a single nucleus. An Entamoeba from a horse was isolated in culture. No cysts were observed in the original stool sample but the sequence is placed unequivocally within the clade of tetranucleate cyst-producing species with no other sequences being specifically related. Revival of the name Entamoeba equi for this organism is proposed. The Entamoeba ecuadoriensis sequence was found to be the most closely related to Entamoeba histolytica and Entamoeba dispar, as predicted, despite the organism having been an environmental isolate originally assigned to Entamoeba moshkovskii. Finally, a partial E. polecki gene sequence from a pig proved to be virtually identical to that of Entamoeba struthionis from an ostrich, suggesting that the latter name is a synonym.
Microbacterium deminutum sp. nov., Microbacterium pumilum sp. nov. and Microbacterium aoyamense sp. nov.
Authors: Kageyama Akiko , Takahashi Yoko , Ōmura Satoshi
Published: September 2006

Three novel bacterial strains were isolated from a soil sample collected in Japan by culture on a GPM agar plate supplemented with superoxide dismutase and catalase. The strains were Gram-positive, catalase-positive, non-motile bacteria with l-ornithine as a diagnostic diamino acid of the peptidoglycan. The acyl type of the peptidoglycan was N-glycolyl. The major menaquinones were MK-12, 13 and 14. Mycolic acids were not detected. G+C contents of the DNA were in the range 69–71 mol%. Comparative 16S rRNA gene sequence analysis revealed that the isolates belonged to the genus Microbacterium and were closely related to Microbacterium terregens, Microbacterium aurum, Microbacterium koreense, Microbacterium schleiferi and Microbacterium lacticum. However, M. aurum, M. koreense and M. lacticum clearly differed from the isolated strains based on the presence of l-lysine as the cell-wall diamino acid and various other chemotaxonomic characteristics. Levels of DNA–DNA relatedness showed that the isolated strains represented three separate genomic species. Based on both phenotypic and genotypic data, the following novel species of the genus Microbacterium are proposed: Microbacterium deminutum sp. nov. (type strain KV-483T=NRRL B-24453T=NBRC 101278T), Microbacterium pumilum sp. nov. (type strain KV-488T=NRRL B-24452T=NBRC 101279T) and Microbacterium aoyamense sp. nov. (type strain KV-492T=NRRL B-24451T=NBRC 101280T).
Pseudomonas pohangensis sp. nov., isolated from seashore sand in Korea
Authors: Weon Hang-Yeon , Kim Byung-Yong , Yoo Seung-Hee , Baek Youn-Kyung , Lee Seon-Young , Kwon Soon-Wo , Go Seung-Joo , Stackebrandt Erko
Published: September 2006

A novel bacterium, designated strain H3-R18T, was isolated from seashore sand collected from Homi cape, Pohang city, Korea. Cells were Gram-negative, aerobic, non-motile, cream-coloured, mesophilic and slightly halotolerant. 16S rRNA gene sequence analysis indicated that the organism was a member of the genus Pseudomonas, but the sequence showed ⩽96.3 % sequence similarity to that of the type strains of all recognized Pseudomonas species. Highest sequence similarities were to Pseudomonas brenneri CFML 97-391T (96.3 %) and Pseudomonas migulae CIP 105470T (96.3 %). The major fatty acids were summed feature 3 and C16 : 0, with lesser amounts of C12 : 0, C12 : 0 3-OH, C18 : 1ω7c and C14 : 0. The major isoprenoid quinone was Q-9. The DNA G+C content was 64.0 mol%. The phylogenetic, phenotypic and genetic properties of strain H3-R18T suggest that it represents a novel species, for which the name Pseudomonas pohangensis sp. nov. is proposed. The type strain is H3-R18T (=KACC 11517T=DSM 17875T).
Idiomarina homiensis sp. nov., isolated from seashore sand in Korea
Authors: Kwon Soon-Wo , Kim Byung-Yong , Weon Hang-Yeon , Baek Youn-Kyung , Koo Bon-Sung , Go Seung-Joo
Published: September 2006

A halophilic, aerobic bacterium, designated PO-M2T, was isolated from seashore sand, from Pohang, Korea and characterized on the basis of physiological and biochemical features. Phylogenetic analysis of 16S rRNA gene sequences revealed a clear affiliation of the novel strain with members of the genus Idiomarina. Sequence similarities between strain PO-M2T and the type strains of species belonging to the genus Idiomarina ranged from 94.3 to 95.5 %. Cells of strain PO-M2T were straight or slightly curved rods and formed light-yellow colonies on marine agar medium. The major isoprenoid quinone was ubiquinone (Q-8) and the predominant cellular fatty acids were C15 : 0 iso (19.3 %), C17 : 1
ω9c iso (11.9 %), C17 : 0 iso (10.9 %), C18 : 1
ω7c (10.4 %), C16 : 0 (9.0 %) and C16 : 1
ω7c and/or C15 : 0 iso 2-OH (7.2 %). The G+C content of the DNA was 45.1 mol%. Based on physiological, biochemical and chemotaxonomic traits and comparative 16S rRNA gene sequence analysis, it is demonstrated that the isolate represents a novel species of the genus Idiomarina, for which the name Idiomarina homiensis sp. nov. is proposed. The type strain is PO-M2T (=KACC 11514T=DSM 17923T).
Glaciecola nitratireducens sp. nov., isolated from seawater
Authors: Baik Keun Sik , Park Yoon-Dong , Seong Chi Nam , Kim Eun Mi , Bae Kyung Sook , Chun Jongsik
Published: September 2006

A marine bacterial strain, FR1064T, was isolated from a surface seawater sample collected off Jeju Island, South Korea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the Gammaproteobacteria and was related to the genus Glaciecola with 97.6 % sequence similarity to Glaciecola pallidula, its nearest phylogenetic neighbour. DNA–DNA relatedness between strain FR1064T and G. pallidula ACAM 615T was 55 %. Cells of the novel isolate were Gram-negative, aerobic, rod-shaped, motile and halophilic, with an optimum sea salts concentration of 4–7 %. The major fatty acids were straight-chain saturated (C16 : 0), summed feature 3 and monounsaturated fatty acid C18 : 1. The DNA G+C content was 44 mol%. Several phenotypic characteristics differentiated the novel isolate from all previously described members of the genus Glaciecola. The polyphasic data obtained in this study clearly demonstrate that strain FR1064T represents a novel species of the genus Glaciecola. The name Glaciecola nitratireducens sp. nov. is therefore proposed, with strain FR1064T (=KCTC 12276T=JCM 12485T) as the type strain.
Cryptococcus mujuensis sp. nov. and Cryptococcus cuniculi sp. nov., basidiomycetous yeasts isolated from wild rabbit faeces
Authors: Shin Kee-Sun , Oh Hee-Mock , Park Yong-Ha , Lee Kang Hyun , Poo Haryoung , Kwon Gi-Seok , Kwon O-Yu
Published: September 2006

Two previously undescribed anamorphic yeasts, strains T-11T and T-26T, recovered from wild rabbit faecal pellets collected in Muju, Korea, were identified using phenotypic and molecular taxonomic methods. The isolates were characterized by the proliferation of budding cells, positive diazonium blue B and urease reactions, the presence of Q-10 as the major ubiquinone, the presence of xylose in whole-cell hydrolysates and the inability to ferment sugars. Phylogenetic analyses based on 26S rRNA gene partial sequences revealed that strain T-11T was located in the Bulleromyces clade and was related to Sirobasidium intermedium, Tremella exigua, Cryptococcus cellulolyticus and Bullera pseudoalba. Strain T-26T was located in the Mesenterica clade and was closely related to Cryptococcus sp. F6 and Cryptococcus heveanensis CBS 8976. Sequence divergence values of more than 4 % from other described Cryptococcus species, together with the phenotypic differences, showed that the isolated yeasts represent previously unrecognized members of this genus. Therefore, two novel yeast species are proposed: Cryptococcus mujuensis sp. nov., with strain T-11T (=KCTC 17231T=CBS 10308T) as the type strain, and Cryptococcus cuniculi sp. nov., with strain T-26T (=KCTC 17232T=CBS 10309T) as the type strain.
Sphingobacterium daejeonense sp. nov., isolated from a compost sample
Authors: Kim Kyoung-Ho , Ten Leonid N. , Liu Qing-Mei , Im Wan-Taek , Lee Sung-Taik
Published: September 2006

A Gram-negative, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated TR6-04T, was isolated from compost and characterized taxonomically by using a polyphasic approach. The organism grew optimally at 30 °C and at pH 6.5–7.0. The isolate was positive for catalase and oxidase tests but negative for gelatinase, indole and H2S production. Comparative 16S rRNA gene sequence analysis showed that strain TR6-04T fell within the radiation of the cluster comprising Sphingobacterium species and clustered with Sphingobacterium mizutaii ATCC 33299T (96.7 % sequence similarity); the similarity to sequences of other species within the family Sphingobacteriaceae was less than 92.0 %. The G+C content of the genomic DNA was 38.7 mol%. The predominant respiratory quinone was MK-7. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1
ω7c). These chemotaxonomic data supported the affiliation of strain TR6-04T to the genus Sphingobacterium. However, on the basis of its phenotypic properties and phylogenetic distinctiveness, strain TR6-04T (=KCTC 12579T=LMG 23402T=CCUG 52468T) should be classified as the type strain of a novel species, for which the name Sphingobacterium daejeonense sp. nov. is proposed.
Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis
Authors: Berezikov Eugene , van Tetering Geert , Verheul Mark , van de Belt Jose , van Laake Linda , Vos Joost , Verloop Robert , van de Wetering Marc , Guryev Victor , Takada Shuji , van Zonneveld Anton Jan , Mano Hiroyuki , Plasterk Ronald , Cuppen Edwin
Published: September 2006

icroRNAs are 20- to 23-nucleotide RNA molecules that can regulate gene expression. Currently >400 microRNAs have been experimentally identified in mammalian genomes, whereas estimates go up to 1000 and beyond. Here we show that many more mammalian microRNAs exist. We discovered novel microRNA candidates using two approaches: testing of computationally predicted microRNAs by a modified microarray-based detection system, and cloning and sequencing of large numbers of small RNAs from different human and mouse tissues. Together these efforts experimentally identified 348 novel mouse and 81 novel human microRNA candidate genes. Most novel microRNAs candidates are not conserved beyond mammals, and ~10% are taxon-specific. Our analyses indicate that the entire microRNA repertoire is not remotely exhausted.
Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium
Authors: Hawkins Jennifer S. , Kim HyeRan , Nason John D. , Wing Rod A. , Wendel Jonathan F.
Published: September 2006

The DNA content of eukaryotic nuclei (C-value) varies ∼200,000-fold, but there is only a ∼20-fold variation in the number of protein-coding genes. Hence, most C-value variation is ascribed to the repetitive fraction, although little is known about the evolutionary dynamics of the specific components that lead to genome size variation. To understand the modes and mechanisms that underlie variation in genome composition, we generated sequence data from whole genome shotgun (WGS) libraries for three representative diploid (n = 13) members of Gossypium that vary in genome size from 880 to 2460 Mb (1C) and from a phylogenetic outgroup, Gossypioides kirkii, with an estimated genome size of 588 Mb. Copy number estimates including all dispersed repetitive sequences indicate that 40%–65% of each genome is composed of transposable elements. Inspection of individual sequence types revealed differential, lineage-specific expansion of various families of transposable elements among the different plant lineages. Copia-like retrotransposable element sequences have differentially accumulated in the Gossypium species with the smallest genome, G. raimondii, while gypsy-like sequences have proliferated in the lineages with larger genomes. Phylogenetic analyses demonstrated a pattern of lineage-specific amplification of particular subfamilies of retrotransposons within each species studied. One particular group of gypsy-like retrotransposon sequences, Gorge3 (Gossypium retrotransposable gypsy-like element), appears to have undergone a massive proliferation in two plant lineages, accounting for a major fraction of genome-size change. Like maize, Gossypium has undergone a threefold increase in genome size due to the accumulation of LTR retrotransposons over the 5–10 Myr since its origin.
Common fragile sites are conserved features of human and mouse chromosomes and relate to large active genes
Authors: Helmrich Anne , Stout-Weider Karen , Hermann Klaus , Schrock Evelin , Heiden Thomas
Published: September 2006

Common fragile sites (CFSs) are seen as chromosomal gaps and breaks brought about by inhibition of replication, and it is thought that they cluster with tumor breakpoints. This study presents a comprehensive analysis using conventional and molecular cytogenetic mapping of CFSs and their expression frequencies in two mouse strains, BALB/c and C57BL/6, and in human probands. Here we show that induced mouse CFSs relate to sites of spontaneous gaps and breaks and that CFS expression levels in chromosome bands are conserved between the two mouse strains and between syntenic mouse and human DNA segments. Furthermore, four additional mouse CFSs were found to be homologous to human CFSs on the molecular cytogenetic level (Fra2D-FRA2G, Fra4C2-FRA9E, Fra6A3.1-FRA7G, and Fra6B1-FRA7H), increasing the number of such CFSs already described in the literature to eight. Contrary to previous reports, DNA helix flexibility is not increased in the 15 human and eight mouse CFSs molecularly defined so far, compared to large nonfragile control regions. Our findings suggest that the mechanisms that provoke instability at CFSs are evolutionarily conserved. The role that large transcriptionally active genes may play in CFS expression is discussed.
Inference of population genetic parameters in metagenomics: A clean look at messy data
Authors: Johnson Philip L.F. , Slatkin Montgomery
Published: September 2006

Metagenomic projects generate short, overlapping fragments of DNA sequence, each deriving from a different individual. We report a new method for inferring the scaled mutation rate, θ = 2Neu, and the scaled exponential growth rate, R= Ner, from the site-frequency spectrum of these data while accounting for sequencing error via Phred quality scores. After obtaining maximum likelihood parameter estimates for θ and R, we calculate empirical Bayes quality scores reflecting the posterior probability that each apparently polymorphic site is truly polymorphic; these scores can then be used for other applications such as SNP discovery. For realistic parameter ranges, analytic and simulation results show our estimates to be essentially unbiased with tight confidence intervals. In contrast, choosing an arbitrary quality score cutoff (e.g., trimming reads) and ignoring further quality information during inference yields biased estimates with greater variance. We illustrate the use of our technique on a new project analyzing activated sludge from a lab-scale bioreactor seeded by a wastewater treatment plant.
Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements
Authors: Dostie Josée , Richmond Todd A. , Arnaout Ramy A. , Selzer Rebecca R. , Lee William L. , Honan Tracey A. , Rubio Eric D. , Krumm Anton , Lamb Justin , Nusbaum Chad , Green Roland D. , Dekker Job
Published: September 2006

Physical interactions between genetic elements located throughout the genome play important roles in gene regulation and can be identified with the Chromosome Conformation Capture (3C) methodology. 3C converts physical chromatin interactions into specific ligation products, which are quantified individually by PCR. Here we present a high-throughput 3C approach, 3C-Carbon Copy (5C), that employs microarrays or quantitative DNA sequencing using 454-technology as detection methods. We applied 5C to analyze a 400-kb region containing the human β-globin locus and a 100-kb conserved gene desert region. We validated 5C by detection of several previously identified looping interactions in the β-globin locus. We also identified a new looping interaction in K562 cells between the β-globin Locus Control Region and the γ–β-globin intergenic region. Interestingly, this region has been implicated in the control of developmental globin gene switching. 5C should be widely applicable for large-scale mapping of cis- and trans- interaction networks of genomic elements and for the study of higher-order chromosome structure.
Health and quality of life of ventilator‐dependent children
Authors: Noyes Jane
Published: September 2006

Aim.  This paper reports a qualitative study with ventilator‐dependent children and their parents, describing their experiences and meanings concerning the children's health and quality of life.

Background.  Recent medical advances have enabled children to survive premature birth, congenital anomalies, critical illness and accidents with long‐term use of mechanical ventilation to support breathing. In economically developed countries, the number of ventilator‐dependent children is increasing and many require nurse‐led home healthcare services. Debate has been polarized as to whether life on a ventilator is in the best interests of all children. The perspectives of ventilator‐dependent children are largely absent in the literature.

Methods.  Principles derived from Heideggerian phenomenology were used to describe how children and their parents interpreted and rationalized the quality of the child's ‘ventilator‐dependent’ life and their health. The study had two phases with data collection commencing in 1998 and completed in 2004.

Results.  The participants were 35 ventilator‐dependent children, and 50 mothers and 17 fathers of 53 children. Emergent themes revealed some common features across this heterogeneous group. Ventilation made the children feel better and if they had sufficient breath, they experienced better quality of life. It was not possible to delineate the magnitude of health gain or benefit, especially amongst preverbal children and those with profound sensory impairments. Quality of life equated to quality of life experiences, but some children experienced negative social impacts and low self‐esteem. Home healthcare services were not designed to bring about the desired social outcomes that children identified. Parent's accounts showed subtle more negative differences.

Conclusion.  The acceptance of children's dependence on machines to live has brought about the need for nursing, medical, social and biological boundaries to be redefined, especially around children's meanings of their health, what they understand to be good quality of life, and what they need to achieve it. Flexible, high quality child‐focused homecare is likely to improve children's outcomes.
Enrofloxacin and marbofloxacin in horses: comparison of pharmacokinetic parameters, use of urinary and metabolite data to estimate first‐pass effect and absorbed fraction
Authors: PEYROU M. , BOUSQUET‐MELOU A. , LAROUTE V. , VRINS A. , DOUCET M. Y.
Published: September 2006

Enrofloxacin and marbofloxacin are two veterinary fluoroquinolones used to treat severe bacterial infections in horses. A repeated measures study has been designed to compare their pharmacokinetic parameters, to investigate their bioavailability and to estimate their absorbed fraction and first‐pass effect by using plasma, urinary and metabolite data collected from five healthy mares. Clearance and Vd(ss)were greater for enrofloxacin (mean ± SD = 6.34 ± 1.5 mL/min/kg and 2.32 ± 0.32 L/kg, respectively) than for marbofloxacin (4.62  ±  0.67 mL/min/kg and 1.6 ± 0.25 L/kg, respectively). Variance of theAUC0‐infof marbofloxacin was lower than that for enrofloxacin, with, respectively, a CV = 15% and 26% intravenously and a CV = 31% and 55% after oral administration. Mean oral bioavailability was not significantly different between marbofloxacin (59%) and enrofloxacin (55%). The mean percentage of the dose eliminated unchanged in urine was significantly higher for marbofloxacin (39.7%) than that for enrofloxacin (3.4%). Absorbed fraction and first‐pass effect were only determinable for enrofloxacin, whereas the percentage of the dose absorbed in the portal circulation was estimated to be 78% and the fraction not extracted during the first pass through the liver was 65%. Consequently, the moderate observed bioavailability of enrofloxacin appears to be mainly caused by hepatic first‐pass effect.
Qualitative assessment of human exposure to consumption of injection site residues
Authors: SANQUER A. , WACKOWIEZ G. , HAVRILECK B.
Published: September 2006

The recent adoption of the guideline on injection site residues in food producing animals by the Committee for Medicinal Products for Veterinary Use (CVMP) raised the question on the risk specifically related to injection site consumption. As noted in this guideline, residues at injection sites commonly deplete erratically. For the calculation of withdrawal time, treating residues at the injection site like those that occur in other tissues is questionable. An assessment of the risk related to the consumption of a whole or part of an injection site during a year was performed using a probabilistic approach. The risk assessment was modelled on the regimen of a 7‐day antibiotic treatment, and was calculated on the scale of the European Union (EU) as a whole or of each European country. Our analysis indicated a maximal risk of 4 days of injection site consumption during a year in the EU. It also indicated that 37% of consumers would never eat an injection site in the same period. These results suggest that the risk of injection site consumption belongs more appropriately to an acute exposure risk than to a chronic one which is usually posed by the residues present in other edible tissues.
Enrofloxacin assay validation and pharmacokinetics following a single oral dose in chickens
Authors: DA SILVA R. G. , REYES F. G. R. , SARTORI J. R. , RATH S.
Published: September 2006

The pharmacokinetics of enrofloxacin (ENRO), a fluoroquinolone antimicrobial agent, was studied in male broiler chickens (Cobb) after single oral administration of 10 mg of ENRO/kg b.w. A high‐performance liquid chromatography‐photodiode array detector (DAD) (HPLC‐DAD) method was developed and validated and used for quantitation of ENRO and its major metabolite ciprofloxacin in plasma. The HPLC analyses were carried out using a cationic‐octadecyl mixed column and 0.05 mol/L phosphate buffer (pH 2.5)/acetonitrile as mobile phase. The sample preparation of plasma consisted of the precipitation of proteins followed by solid phase extraction on cationic‐octadecyl mixed cartridges. The method was validated considering linear range, linearity, selectivity, sensitivity, limit of detection (LOD), limit of quantitation (LOQ), intra‐ and inter‐day precisions and accuracy. The LOD and LOQ for both fluoroquinolones were 60 and 200 ng/mL for plasma. The plasma concentration vs. time graph was characteristic of a two‐compartment open model. The maximal plasma concentration of 1.5 ± 0.2 mg/mL was achieved at 9 ± 2 h. The elimination half‐life and the mean residence time of ENRO were 1.5 ± 0.2 and 15.64 h, respectively. The area under the concentration–time curve was calculated as 35 ± 4 mg·h/mL.
The complete analysis of oxytetracycline pharmacokinetics in farmed Pacific white shrimp (Litopenaeus vannamei)
Authors: CHIAYVAREESAJJA S. , CHANDUMPAI A. , THEAPPARAT Y. , FAROONGSARNG D.
Published: September 2006

Lack of dosing information of the major antibiotics known as oxytetracycline (OTC) for the Pacific white shrimp (Litopenaeus vannamei) could have harmful impact on aquaculture in Thailand. The aim of this study was to detail complete pharmacokinetic information of OTC in the Pacific white shrimp. Sixty‐four male L. vannamei weighing 14–22 g with carapace length of 2.30–3.00 cm in the standardized moulting stage of C–D0 were used for the investigations. Single dose, 10 μg/g body weight OTC solution was administered intra‐sinusally (i.s.), and the shrimps were then sampled in three replicates at time intervals of 0.25, 0.5, 2, 4, 6, 9, 12, 24, 48, 72, 170, 336 and 504 h postdose. OTC levels with time intervals in biological matrices including the hemolymph, abdominal muscle, and digestive gland of each sample were determined by validated high‐performance liquid chromatography, and were analyzed with noncompartment and compartment models. A simplified two‐compartment model was employed rather than a more complicated model, with additional digestive compartment if necessary. A significant portion of the OTC was found in the digestive glands, even though the OTC was administered i.s. The model indicated that the OTC was thus not only distributed into the tissue compartment, but also to the digestive gland, from where it was eliminated from the shrimp's body. The dispositional half‐lives of all compartments was found to be 14–21 h. Approximately 60% of the drug elimination took place in digestive gland, which is proposed to be the major route of elimination.