bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural and kinetic mapping of side-chain exposure onto the protein energy landscape
Authors: Bernstein Rachel , Schmidt Kierstin L. , Harbury Pehr B. , Marqusee Susan
Published: June 2011

Identification and characterization of structural fluctuations that occur under native conditions is crucial for understanding protein folding and function, but such fluctuations are often rare and transient, making them difficult to study. Native-state hydrogen exchange (NSHX) has been a powerful tool for identifying such rarely populated conformations, but it generally reveals no information about the placement of these species along the folding reaction coordinate or the barriers separating them from the folded state and provides little insight into side-chain packing. To complement such studies, we have performed native-state alkyl-proton exchange, a method analogous to NSHX that monitors cysteine modification rather than backbone amide exchange, to examine the folding landscape of
Escherichia coli
ribonuclease H, a protein well characterized by hydrogen exchange. We have chosen experimental conditions such that the rate-limiting barrier acts as a kinetic partition: residues that become exposed only upon crossing the unfolding barrier are modified in the EX1 regime (alkylation rates report on the rate of unfolding), while those exposed on the native side of the barrier are modified predominantly in the EX2 regime (alkylation rates report on equilibrium populations). This kinetic partitioning allows for identification and placement of partially unfolded forms along the reaction coordinate. Using this approach we detect previously unidentified, rarely populated conformations residing on the native side of the barrier and identify side chains that are modified only upon crossing the unfolding barrier. Thus, in a single experiment under native conditions, both sides of the rate-limiting barrier are investigated.
Solid-state NMR of proteins sedimented by ultracentrifugation
Authors: Bertini Ivano , Luchinat Claudio , Parigi Giacomo , Ravera Enrico , Reif Bernd , Turano Paola
Published: June 2011

Relatively large proteins in solution, spun in NMR rotors for solid samples at typical ultracentrifugation speeds, sediment at the rotor wall. The sedimented proteins provide high-quality solid-state-like NMR spectra suitable for structural investigation. The proteins fully revert to the native solution state when spinning is stopped, allowing one to study them in both conditions. Transiently sedimented proteins can be considered a novel phase as far as NMR is concerned. NMR of transiently sedimented molecules under fast magic angle spinning has the advantage of overcoming protein size limitations of solution NMR without the need of sample crystallization/precipitation required by solid-state NMR.
Calculated vibrational properties of pigments in protein binding sites
Authors: Lamichhane Hari Prasad , Hastings Gary
Published: June 2011

FTIR difference spectroscopy is widely used to probe molecular bonding interactions of protein-bound electron transfer cofactors. The technique is particularly attractive because it provides information on both neutral and radical cofactor states. Such dual information is not easily obtainable using other techniques. Although FTIR difference spectroscopy has been used to study cofactors in biological protein complexes, in nearly all cases interpretation of the spectra has been purely qualitative. Virtually no computational work has been undertaken in an attempt to model the spectra. To address this problem we have developed the use of ONIOM (our own N-layered integrated molecular Orbital + Molecular mechanics package) (quantum mechanical:molecular mechanics) methods to calculate FTIR difference spectra associated with protein-bound cofactors. As a specific example showing the utility of the approach we have calculated isotope edited FTIR difference spectra associated with unlabeled and labeled ubiquinones in the QAbinding site inRhodobacter sphaeroidesphotosynthetic reaction centers. The calculated spectra are in remarkable agreement with experiment. Such agreement cannot be obtained by considering ubiquinone molecules in the gas phase or in solution. A calculation including the protein environment is required. The ONIOM calculated spectra agree well with experiment but indicate a very different interpretation of the experimental data compared to that proposed previously. In particular the calculations do not predict that one of the carbonyl groups of QAis very strongly hydrogen bonded. We show that a computational-based interpretation of FTIR difference spectra associated with protein-bound cofactors is now possible. This approach will be applicable to FTIR studies of many cofactor-containing proteins.
Impaired protein conformational landscapes as revealed in anomalous Arrhenius prefactors
Authors: Nagel Zachary D. , Dong Ming , Bahnson Brian J. , Klinman Judith P.
Published: June 2011

A growing body of data supports a role for protein motion in enzyme catalysis. In particular, the ability of enzymes to sample catalytically relevant conformational substates has been invoked to model kinetic and spectroscopic data. However, direct experimental links between rapidly interconverting conformations and the chemical steps of catalysis remain rare. We report here on the kinetic analysis and characterization of the hydride transfer step catalyzed by a series of mutant thermophilic alcohol dehydrogenases (ht-ADH), presenting evidence for Arrhenius prefactor values that become enormously elevated above an expected value of approximately 10
13
 s
-1
when the enzyme operates below its optimal temperature range. Restoration of normal Arrhenius behavior in the ht-ADH reaction occurs at elevated temperatures. A simple model, in which reduced temperature alters the ability of the ht-ADH variants to sample the catalytically relevant region of conformational space, can reproduce the available data. These findings indicate an impaired landscape that has been generated by the combined condition of reduced temperature and mutation at a single, active-site hydrophobic side chain. The broader implication is that optimal enzyme function requires the maintenance of a relatively smooth landscape that minimizes low energy traps.
Site-specific protein modifications through pyrroline-carboxy-lysine residues
Authors: Ou Weijia , Uno Tetsuo , Chiu Hsien-Po , Grünewald Jan , Cellitti Susan E. , Crossgrove Tiffany , Hao Xueshi , Fan Qian , Quinn Lisa L. , Patterson Paula , Okach Linda , Jones David H. , Lesley Scott A. , Brock Ansgar , Geierstanger Bernhard H.
Published: June 2011

Pyrroline-carboxy-lysine (Pcl) is a demethylated form of pyrrolysine that is generated by the pyrrolysine biosynthetic enzymes when the growth media is supplemented with
D-ornithine
. Pcl is readily incorporated by the unmodified pyrrolysyl-tRNA/tRNA synthetase pair into proteins expressed in
Escherichia coli
and in mammalian cells. Here, we describe a broadly applicable conjugation chemistry that is specific for Pcl and orthogonal to all other reactive groups on proteins. The reaction of Pcl with 2-amino-benzaldehyde or 2-amino-acetophenone reagents proceeds to near completion at neutral pH with high efficiency. We illustrate the versatility of the chemistry by conjugating Pcl proteins with poly(ethylene glycol)s, peptides, oligosaccharides, oligonucleotides, fluorescence, and biotin labels and other small molecules. Because Pcl is genetically encoded by TAG codons, this conjugation chemistry enables enhancements of the pharmacology and functionality of proteins through site-specific conjugation.
Retrograde nuclear import of tRNA precursors is required for modified base biogenesis in yeast
Authors: Ohira Takayuki , Suzuki Tsutomu
Published: June 2011

The retrograde movement of tRNAs from the cytoplasm to the nucleus occurs constitutively in eukaryotic cells but its functional significance remains unclear. We show evidence suggesting that in
Saccharomyces cerevisiae
, a spliced tRNA precursor must be imported into the nucleus before the biogenesis of a modified base can occur. Wybutosine (yW) is a modified base adjacent to the anticodon of tRNA
Phe
and is required for accurate decoding. Glucose starvation or overexpression of the nuclear tRNA binding protein Trz1p both caused nuclear retention of cytoplasmic tRNAs, impaired the yW synthesis, and induced the accumulation of its intermediate,
N
1
-methylgunanosine (m
1
G), showing that the postspliced tRNA
Phe
is imported to the nucleus, where m
1
G is formed by Trm5p, after which it is reexported to the cytoplasm, where the yW synthesis is completed by cytoplasmic enzymes.
MicroRNA-mediated posttranscriptional regulation is required for maintaining undifferentiated properties of blastoderm and primordial germ cells in chickens
Authors: Lee Sang In , Lee Bo Ram , Hwang Young Sun , Lee Hyung Chul , Rengaraj Deivendran , Song Gwonhwa , Park Tae Sub , Han Jae Yong
Published: June 2011

MicroRNAs (miRNAs) play a critical role in determining the differentiation fate of pluripotent stem cells and germ cells in mammals. However, the mechanism(s) of miRNA-mediated posttranscriptional regulation with regard to lineage specification and differentiation in chick development require further investigation. Therefore, we conducted miRNA expression profiling to explore specific miRNA signatures in undifferentiated blastoderm and primordial germ cells (PGCs). We identified seven miRNAs that are highly expressed in blastoderm and 10 that are highly expressed in PGCs. In this study, miR-302a and miR-456 for blastoderm and miR-181a* for PGCs were analyzed further for their target transcripts and regulatory pathways. Both miR-302a and miR-456 bound directly to the sex-determining region Y box 11 transcript and could act as posttranscriptional coregulators to maintain the undifferentiated state of the chicken blastoderm through the suppression of somatic gene expression and differentiation. Moreover, miR-181a* showed a bifunctional role in PGCs by binding to two different transcripts. miR-181a* inhibited the somatic differentiation of PGCs by silencing homeobox A1 expression. Additionally, miR-181a* prevented PGCs from entering meiosis through the repression of the nuclear receptor subfamily 6, group A, member 1 transcript. Collectively, our data demonstrate that in chickens miRNAs intrinsically regulate the differentiation fate of blastoderms and PGCs and that the specific timing of germ cell meiosis is controlled through miRNA expression.
Discriminating between climate observations in terms of their ability to improve an ensemble of climate predictions
Authors: Huang Yi , Leroy Stephen , Goody Richard M.
Published: June 2011

In view of the cost and complexity of climate-observing systems, it is a matter of concern to know which measurements, by satellite or in situ, can best improve the accuracy and precision of long-term ensembles of climate projections. We follow a statistical procedure to evaluate the relative capabilities of a wide variety of observable data types for improving the accuracy and precision of an ensemble of Intergovernmental Panel on Climate Change (IPCC) models. Thirty-two data types are evaluated for their potential for improving a 50-y surface air temperature trend prediction with data from earlier periods, with an emphasis on 20 y. Data types can be ordered in terms of their ability to increase the precision of a forecast. Results show that important conclusions can follow from this ordering. The small size of the IPCC model ensemble (20 members) creates uncertainties in these conclusions, which need to be substantiated with the larger ensembles expected in the future. But the larger issue of whether the methodology can provide useful answers is demonstrated.
Pressure-induced reversible amorphization and an amorphous–amorphous transition in Ge
2
Sb
2
Te
5
phase-change memory material
Authors: Sun Zhimei , Zhou Jian , Pan Yuanchun , Song Zhitang , Mao Ho-Kwang , Ahuja Rajeev
Published: June 2011

Ge
2
Sb
2
Te
5
(GST) is a technologically very important phase-change material that is used in digital versatile disks-random access memory and is currently studied for the use in phase-change random access memory devices. This type of data storage is achieved by the fast reversible phase transition between amorphous and crystalline GST upon heat pulse. Here we report pressure-induced reversible crystalline-amorphous and polymorphic amorphous transitions in NaCl structured GST by ab initio molecular dynamics calculations. We have showed that the onset amorphization of GST starts at approximately 18 GPa and the system become completely random at approximately 22 GPa. This amorphous state has a cubic framework (
c
-amorphous) of sixfold coordinations. With further increasing pressure, the
c
-amorphous transforms to a high-density amorphous structure with trigonal framework (
t
-amorphous) and an average coordination number of eight. The pressure-induced amorphization is investigated to be due to large displacements of Te atoms for which weak Te–Te bonds exist or vacancies are nearby. Upon decompressing to ambient conditions, the original cubic crystalline structure is restored for
c
-amorphous, whereas
t
-amorphous transforms to another amorphous phase that is similar to the melt-quenched amorphous GST.
In vitro assembly of physiological cohesin/DNA complexes
Authors: Onn Itay , Koshland Douglas
Published: June 2011

Cohesin is a member of the Smc family of protein complexes that mediates higher-order chromosome structure by tethering different regions of chromatin. We present a new in vitro system that assembles cohesin-DNA complexes with in vivo properties. The assembly of these physiological salt-resistant complexes requires the cohesin holo-complex, its ability to bind ATP, the cohesin loader Scc2p and a closed DNA topology. Both the number of cohesin molecules bound to the DNA substrate and their distribution on the DNA substrate are limited. Cohesin and Scc2p bind preferentially to cohesin associated regions (CARs), DNA sequences with enriched cohesin binding in vivo. A subsequence of CARC1 promotes cohesin binding to neighboring sequences within CARC1. The enhancer-like function of this sequence is validated by in vivo deletion analysis. By demonstrating the physiological relevance of these in vitro assembled cohesin-DNA complexes, we establish our in vitro system as a powerful tool to elucidate the mechanism of cohesin and other Smc complexes.
Endoplasmic reticulum stress enhances fibrotic remodeling in the lungs
Authors: Lawson William E. , Cheng Dong-Sheng , Degryse Amber L. , Tanjore Harikrishna , Polosukhin Vasiliy V. , Xu Xiaochuan C. , Newcomb Dawn C. , Jones Brittany R. , Roldan Juan , Lane Kirk B. , Morrisey Edward E. , Beers Michael F. , Yull Fiona E. , Blackwell Timothy S.
Published: June 2011

Evidence of endoplasmic reticulum (ER) stress has been found in lungs of patients with familial and sporadic idiopathic pulmonary fibrosis. We tested whether ER stress causes or exacerbates lung fibrosis by (
i
) conditional expression of a mutant form of surfactant protein C (L188Q
SFTPC
) found in familial interstitial pneumonia and (
ii
) intratracheal treatment with the protein misfolding agent tunicamycin. We developed transgenic mice expressing L188Q
SFTPC
exclusively in type II alveolar epithelium by using the Tet-On system. Expression of L188Q
SFTPC
induced ER stress, as determined by increased expression of heavy-chain Ig binding protein (BiP) and splicing of X-box binding protein 1 (XBP1) mRNA, but no lung fibrosis was identified in the absence of a second profibrotic stimulus. After intratracheal bleomycin, L188Q
SFTPC
-expressing mice developed exaggerated lung fibrosis and reduced static lung compliance compared with controls. Bleomycin-treated L188Q
SFTPC
mice also demonstrated increased apoptosis of alveolar epithelial cells and greater numbers of fibroblasts in the lungs. With a complementary model, intratracheal tunicamycin treatment failed to induce lung remodeling yet resulted in augmentation of bleomycin-induced fibrosis. These data support the concept that ER stress produces a dysfunctional epithelial cell phenotype that facilitates fibrotic remodeling. ER stress pathways may serve as important therapeutic targets in idiopathic pulmonary fibrosis.
Metabolic principles of river basin organization
Authors: Rodriguez-Iturbe Ignacio , Caylor Kelly K. , Rinaldo Andrea
Published: June 2011

The metabolism of a river basin is defined as the set of processes through which the basin maintains its structure and responds to its environment. Green (or biotic) metabolism is measured via transpiration and blue (or abiotic) metabolism through runoff. A principle of equal metabolic rate per unit area throughout the basin structure is developed and tested in a river basin characterized by large heterogeneities in precipitation, vegetation, soil, and geomorphology. This principle is suggested to have profound implications for the spatial organization of river basin hydrologic dynamics, including the minimization of energy expenditure known to control the scale-invariant characteristics of river networks over several orders of magnitude. Empirically derived, remarkably constant rates of average transpiration per unit area through the basin structure lead to a power law for the probability distribution of transpiration from a randomly chosen subbasin. The average runoff per unit area, evaluated for subbasins of a wide range of topological magnitudes, is also shown to be remarkably constant independently of size. A similar result is found for the rainfall after accounting for canopy interception. Allometric scaling of metabolic rates with size, variously addressed in the biological literature and network theory under the label of Kleiber’s law, is similarly derived. The empirical evidence suggests that river basin metabolic activity is linked with the spatial organization that takes place around the drainage network and therefore with the mechanisms responsible for the fractal geometry of the network, suggesting a new coevolutionary framework for biological, geomorphological, and hydrologic dynamics.
ATF6β is a host cellular target of the Toxoplasma gondii virulence factor ROP18
Authors: Yamamoto Masahiro , Ma Ji Su , Mueller Christina , Kamiyama Naganori , Saiga Hiroyuki , Kubo Emi , Kimura Taishi , Okamoto Toru , Okuyama Megumi , Kayama Hisako , Nagamune Kisaburo , Takashima Seiji , Matsuura Yoshiharu , Soldati-Favre Dominique , Takeda Kiyoshi
Published: June 2011

The ROP18 kinase has been identified as a key virulence determinant conferring a high mortality phenotype characteristic of type I Toxoplasma gondii strains. This major effector molecule is secreted by the rhoptries into the host cells during invasion; however, the molecular mechanisms by which this kinase exerts its pathogenic action remain poorly understood. In this study, we show that ROP18 targets the host endoplasmic reticulum–bound transcription factor ATF6β. Disruption of the ROP18 gene severely impairs acute toxoplasmosis by the type I RH strain. Because another virulence factor ROP16 kinase modulates immune responses through its N-terminal portion, we focus on the role of the N terminus of ROP18 in the subversion of host cellular functions. The N-terminal extension of ROP18 contributes to ATF6β-dependent pathogenicity by interacting with ATF6β and destabilizing it. The kinase activity of ROP18 is essential for proteasome-dependent degradation of ATF6β and for parasite virulence. Consistent with a key role for ATF6β in resistance against this intracellular pathogen, ATF6β-deficient mice exhibit a high susceptibility to infection by ROP18-deficient parasites. The results reveal that interference with ATF6β-dependent immune responses is a novel pathogenic mechanism induced by ROP18.
Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation
Authors: Fabbri Giulia , Rasi Silvia , Rossi Davide , Trifonov Vladimir , Khiabanian Hossein , Ma Jing , Grunn Adina , Fangazio Marco , Capello Daniela , Monti Sara , Cresta Stefania , Gargiulo Ernesto , Forconi Francesco , Guarini Anna , Arcaini Luca , Paulli Marco , Laurenti Luca , Larocca Luigi M. , Marasca Roberto , Gattei Valter , Oscier David , Bertoni Francesco , Mullighan Charles G. , Foá Robin , Pasqualucci Laura , Rabadan Raul , Dalla-Favera Riccardo , Gaidano Gianluca
Published: June 2011

The pathogenesis of chronic lymphocytic leukemia (CLL), the most common leukemia in adults, is still largely unknown. The full spectrum of genetic lesions that are present in the CLL genome, and therefore the number and identity of dysregulated cellular pathways, have not been identified. By combining next-generation sequencing and copy number analysis, we show here that the typical CLL coding genome contains <20 clonally represented gene alterations/case, including predominantly nonsilent mutations, and fewer copy number aberrations. These analyses led to the discovery of several genes not previously known to be altered in CLL. Although most of these genes were affected at low frequency in an expanded CLL screening cohort, mutational activation of NOTCH1, observed in 8.3% of CLL at diagnosis, was detected at significantly higher frequency during disease progression toward Richter transformation (31.0%), as well as in chemorefractory CLL (20.8%). Consistent with the association of NOTCH1 mutations with clinically aggressive forms of the disease, NOTCH1 activation at CLL diagnosis emerged as an independent predictor of poor survival. These results provide initial data on the complexity of the CLL coding genome and identify a dysregulated pathway of diagnostic and therapeutic relevance.
Functional properties and toxin pharmacology of a dorsal root ganglion sodium channel viewed through its voltage sensors
Authors: Bosmans Frank , Puopolo Michelino , Martin-Eauclaire Marie-France , Bean Bruce P. , Swartz Kenton J.
Published: June 2011

The voltage-activated sodium (Nav) channel Nav1.9 is expressed in dorsal root ganglion (DRG) neurons where it is believed to play an important role in nociception. Progress in revealing the functional properties and pharmacological sensitivities of this non-canonical Nav channel has been slow because attempts to express this channel in a heterologous expression system have been unsuccessful. Here, we use a protein engineering approach to dissect the contributions of the four Nav1.9 voltage sensors to channel function and pharmacology. We define individual S3b–S4 paddle motifs within each voltage sensor, and show that they can sense changes in membrane voltage and drive voltage sensor activation when transplanted into voltage-activated potassium channels. We also find that the paddle motifs in Nav1.9 are targeted by animal toxins, and that these toxins alter Nav1.9-mediated currents in DRG neurons. Our results demonstrate that slowly activating and inactivating Nav1.9 channels have functional and pharmacological properties in common with canonical Nav channels, but also show distinctive pharmacological sensitivities that can potentially be exploited for developing novel treatments for pain.
An investigation on InxGa1−xN/GaN multiple quantum well solar cells
Authors: Deng Qingwen , Wang Xiaoliang , Xiao Hongling , Wang Cuimei , Yin Haibo , Chen Hong , Hou Qifeng , Lin Defeng , Li Jinmin , Wang Zhanguo , Hou Xun
Published: June 2011

The conversion efficiency of InxGa1−xN/GaN multiple quantum well solar cells is originally investigated in theory based on the ideal diode model and the ideal unity quantum well model. The results reveal that the conversion efficiency partially depends on the width of the quantum well and the thickness of the barrier region but is dominated by the number of quantum wells and indium content of InxGa1−xN. The calculated results are found to be basically trustworthy by comparing with reported experimental results. An In0.15Ga0.85N/GaN multiple quantum well solar cell is successfully fabricated with a conversion efficiency of 0.2%. The main discrepancy between calculated and experimental results is the material quality and manufacturing technology which need to be improved.
Laser-assisted plasma coating at atmospheric pressure: production of yttria-stabilized zirconia thermal barriers
Authors: Ouyang Zihao , Meng Liang , Raman Priya , Cho Tae S , Ruzic D N
Published: June 2011

A laser-assisted plasma-coating technique at atmospheric pressure (LAPCAP) has been investigated. The electron temperature, electron density and gas temperature of the atmospheric-pressure plasma have been measured using optical emission spectroscopy (OES). LAPCAP utilizes laser ablation of 3 mol% yttria-stabilized zirconia into an atmospheric helium/nitrogen plasma to deposit thermal barrier coatings on a nickel-based substrate. The deposited film shows columnar structures similar to films prepared by high-vacuum deposition methods, such as physical vapour deposition and conventional pulsed-laser deposition. However, the LAPCAP films have smaller columns and higher porosity, compared with the films deposited by other techniques. The morphology and characteristics of the films have been analysed by scanning electron microscope, focused ion beam and x-ray diffraction.
Effective permittivity of a metamaterial from coated wires
Authors: Tyukhtin Andrey V , Doilnitsina Emma G
Published: June 2011

We present a method to determine the effective parameters of a periodic structure with small spacing. This technique is analogous to the averaged boundary condition method applied to planar periodic structures. The effective permittivity of a structure from parallel wires with dielectric and magnetic coating was obtained. It contains an effective plasma frequency and some parameter that is responsible for the spatial dispersion. The dependences of these parameters on electromagnetic and geometric characteristics of structure were analysed. Particularly, it was shown that the role of spatial dispersion decreases if we increase both the coating permittivity and the coating permeability. The magnetic coating is more effective for the taming of spatial dispersion. However, the dielectric coating provides essential taming as well, and it is simpler to fabricate than the magnetic coating. Further, different types of plane waves in the metamaterial under consideration were analysed. In particular, it was shown that, in contrast to the ordinary crystal, there are three types of waves: an ordinary wave and two types of extraordinary waves.
Metamaterial analogue of electromagnetically induced transparency in two orthogonal directions
Authors: Meng F-Y , Fu J-H , Zhang K , Wu Q , Kim J-Y , Choi J-J , Lee B , Lee J-C
Published: June 2011

We demonstrate theoretically that the analogue of electromagnetically induced transparency (EIT) in two orthogonal directions can be achieved in a planar metamaterial consisting of spiral resonators and split ring resonators in the same plane. The metamaterial can exhibit EIT-like effect to both normally and laterally incident electromagnetic waves because of its electric and magnetic response, respectively. Full-wave numerical simulations are carried out to validate the EIT-like effect of the planar metamaterial. Absorption curves, transmission spectra, surface current distributions and effective constitutive parameters of the metamaterial illuminated by normally and laterally incident EM waves are presented. These results, showing a transparency window with extremely low absorption and strong dispersion, are in good agreement with each other.
Picard number, holomorphic sectional curvature, and ampleness
Authors: Wong Pit-Mann , Wu Damin , Yau Shing-Tung
Published: June 2011

We prove that for a projective manifold with Picard number equal to one, if the manifold admits a Kähler metric whose holomorphic sectional curvature is quasi-negative, then the canonical bundle of the manifold is ample.
Using acoustics to estimate the fish-length selectivity of trawl mesh
Authors: Somerton David A. , Williams Kresimir , von Szalay Paul G. , Rose Craig S.
Published: June 2011

Somerton, D. A., Williams, K., von Szalay, P. G., and Rose, C. S. 2011. Using acoustics to estimate the fish-length selectivity of trawl mesh. – ICES Journal of Marine Science, 68: 1558–1565. Estimation of the retention probability of a trawlnet traditionally involves conducting experiments during which the fish escaping through the meshes are recaptured using either small-mesh pocketnets attached to the outside of the net or by enclosing the entire trawlnet in a small-mesh net. A new method of estimating the length selectivity of trawl mesh is demonstrated; it does not require the recapture of escaping fish but instead uses standard acoustic methods to estimate the abundance of fish entering the net before mesh selection. The method was applied to the 83–112 eastern otter trawl used by the Alaska Fisheries Science Center (AFSC) to conduct bottom-trawl surveys in the eastern Bering Sea (EBS), and the Aleutian wing trawl used by the AFSC to collect midwater biological samples of walleye pollock (Theragra chalcogramma) during fishery acoustic surveys of the EBS and Gulf of Alaska. The length selectivities of both trawls were also estimated using standard recapture experiments. For both, the estimated lengths at 50% selection (L50) from the acoustic method were similar to the estimates from the recapture experiments, but the estimated selection ranges were narrower. The advantages of the acoustic method are that it is simpler to use than traditional fish-recapture methods and it does not alter normal trawl performance.
Evaluating the effect of real-time closures on cod targeting
Authors: Needle Coby L. , Catarino Rui
Published: June 2011

Needle, C. L., and Catarino, R. 2011. Evaluating the effect of real-time closures on cod targeting. – ICES Journal of Marine Science, 68: 1647–1655. Under its Conservation Credits scheme to reduce cod mortality, the Scottish Government has implemented a system of real-time closures (RTCs) since 2008. These are relatively small, temporarily closed areas (50–225 square nautical miles per RTC, closed for 21 d) that are triggered by high cod catches. An important step in evaluating their effectiveness is to determine the response of vessels to RTCs, because the conservation benefit would be reduced if vessels moved to areas of greater cod abundance following closures. Abundance indices from research-vessel surveys and commercial-vessel observer trips are combined to create a time- and space-dependent relative cod-importance index (RCII). Vessel monitoring system data from Scottish vessels fishing during 2008/2009 are used to construct RCII profiles for each vessel, which are then used to determine whether the areas to which vessels move have a higher or a lower RCII, and how far away they move when an RTC is activated. We show that the RCII of the areas moved to tends to be lower than that of the RTC and that vessels travel farther when moving away from a closure than when moving back after reopening. Although not conclusive, this result indicates that RTCs may impact beneficially on cod mortality.
Quota allocation in mixed fisheries: a bioeconomic modelling approach applied to the Channel flatfish fisheries
Authors: Marchal Paul , Little L. Richard , Thébaud Olivier
Published: June 2011

Marchal, P., Little, L. R., and Thébaud, O. 2011. Quota allocation in mixed fisheries: a bioeconomic modelling approach applied to the Channel flatfish fisheries. – ICES Journal of Marine Science, 68: 1580–1591. A simulation modelling approach is used to assess the respective performances of different regimes of quota allocation (fixed or transferable), quota ownership (owned or not by fishers), and taxation for catching fish above quota. The simulations account for a variety of fleet behaviours (ranging from fixed by tradition to dynamic economics-driven). The modelling framework is applied to the Channel flatfish mixed fisheries. Transferable quota allocation regimes would particularly benefit small netters and beam trawlers, which would achieve a profit of €50–150 million without compromising the conservation of eastern Channel sole, but it could impair the sustainability of other stocks. If quota is owned by fishers, the least fishing-efficient fleet stops fishing, but makes substantial profit from leasing quotas to beam trawlers and to small and large netters, which remain actively fishing. The highest economic return for quota owners (€200–300 million) is achieved when effort allocation is fixed by tradition. The profit achieved by small netters is greatest when fleets are almost entirely economics-driven. Increasing overquota landing taxes generally leads to conservation benefits for all stocks, but at the expense of lower profitability for the fishery overall.
Phenylobacterium
muchangponense sp. nov., isolated from beach soil, and emended description of the genus Phenylobacterium
Authors: Oh Yong-Sik , Roh Dong-Hyun
Published: June 2011

A Gram-staining-negative, non-motile, aerobic bacterium, designated strain A8T, was isolated from the beach soil of Muchangpo, Korea. Cells were rod-shaped (0.5–0.6×0.7–1.3 µm) and colonies were colourless, circular with entire edges and had a glistening surface. The isolate grew optimally at 25–35 °C and did not require NaCl for growth. Strain A8T could not assimilate acetate, dl-lactate, succinate, antipyrine or chloridazon, but weakly assimilated l-phenylalanine. Major fatty acids were summed feature 7 (comprising C18 : 1ω7c/ω9t/ω12t), C16 : 0 and summed feature 4 (comprising C16 : 1ω7c/ iso-C15 : 0 2-OH). The major isoprenoid quinone was ubiquinone-10 and the DNA G+C content was 72.3 mol%. Comparative 16S rRNA gene sequence studies showed that strain A8T belonged to the family

Caulobacteraceae

, class

Alphaproteobacteria

and was most closely related to type strains of members of the genus

Phenylobacterium

(95.7–97.1 % similarity). Signature nucleotides and phylogenetic analysis of the 16S rRNA gene sequence also suggested that strain A8T was affiliated with the genus

Phenylobacterium

. Low DNA–DNA relatedness values (3.0±1.8–11.5±3.2 %) indicated that strain A8T represented a distinct species that was separated from other type strains in the genus

Phenylobacterium

. On the basis of evidence from a polyphasic study, it is proposed that strain A8T ( = KACC 15042T  = LMG 25973T) represents the type strain of a novel species,
Phenylobacterium

muchangponense sp. nov. An emended description of the genus

Phenylobacterium

is also presented.
Erwinia

typographi sp. nov., isolated from bark beetle (Ips typographus) gut
Authors: Skrodenytė-Arbačiauskienė V. , Radžiutė S. , Stunžėnas V. , Būda V.
Published: June 2011

Gram-negative-staining bacteria that were resistant to monoterpene myrcene (7-methyl-3-methylene-1.6-octadiene, C10H16, at concentrations of up to 10 µl ml−1 in TSB) were isolated from the gut contents of adult bark beetles Ips typographus (Coleoptera, Scolytidae). The beetles were collected from the bark of Norway spruce (Picea abies) in Lithuania. Bark beetles feed on conifers, which produce myrcene among many other defensive compounds. It has been suggested that the micro-organisms present within the beetles’ guts could be involved in their resistance towards this plant defensive compound. The most resistant bacterial strains were isolated and characterized by phenotypic assays as well as fatty acid analysis, 16S rRNA gene sequencing, multilocus sequence analyses (MLSA) based on the rpoB, atpD and infB genes and DNA–DNA hybridization. Biochemical characterization indicated that the bacteria belonged to the family

Enterobacteriaceae

. Phylogenetic analyses of the 16S rRNA gene sequences and MLSA of the novel strains revealed that they belonged to the genus

Erwinia

, but represented a novel species. The dominant cellular fatty acids were C16 : 0 and C17 : 0 cyclo. The DNA G+C content was 49.1 mol%. The results obtained in this study indicated that these bacteria from the bark beetle gut represented a novel species, for which the name
Erwinia typographi sp. nov. is proposed, with the type strain DSM 22678T ( = Y1T = LMG 25347T).
Flammeovirga pacifica sp. nov., isolated from deep-sea sediment
Authors: Xu Hui , Fu Yuanyuan , Yang Ning , Ding Zhixin , Lai Qiliang , Zeng Runying
Published: June 2011

Strain WPAGA1T was isolated from marine sediment of the west Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the genus

Flammeovirga

. Strain WPAGA1T exhibited highest 16S rRNA gene sequence similarity with

Flammeovirga yaeyamensis

NBRC 100898T (98.1 %) and lower sequence similarity with

Flammeovirga arenaria

IFO 15982T (94.6 %) and other members of the genus

Flammeovirga

(<94.2 %). DNA–DNA relatedness studies showed that strain WPAGA1T was distinct from

F. yaeyamensis

NBRC 100898T and

F. arenaria

NBRC 15982T (43±4 % and 32±2 % relatedness values, respectively). Strain WPAGA1T could be distinguished from all known members of the genus

Flammeovirga

by a number of phenotypic features. However, the dominant fatty acids of strain WPAGA1T (iso-C15 : 0, C16 : 0 and C20 : 4ω6,9,12,15c), the major polyamine (cadaverine) and the G+C content of the chromosomal DNA (32.9 mol%) were consistent with those of members of the genus

Flammeovirga

. Based on phenotypic and chemotaxonomic features and 16S rRNA gene sequences, strain WPAGA1T can be assigned to the genus

Flammeovirga

as a representative of a novel species, for which the name Flammeovirga pacifica sp. nov. is proposed; the type strain is WPAGA1T ( = CCTCC AB 2010364T = LMG 26175T = DSM 24597T = MCCC 1A06425T).
Salinactinospora qingdaonensis gen. nov., sp. nov., a halophilic actinomycete isolated from a salt pond
Authors: Chang Xianbo , Liu Wenzheng , Zhang Xiao-Hua
Published: June 2011

A novel halophilic, filamentous, actinomycete strain, designated CXB832T, was isolated from a salt pond in Qingdao, China. Optimal growth occurred at 37 °C, pH 7.0–8.0 and 9–12 % (w/v) NaCl. Strain CXB832T formed pale yellow to deep yellow branched substrate mycelium without fragmentation. Abundant white aerial mycelium differentiated into long chains of spores and the spores were rod-shaped with smooth surfaces. Strain CXB832T contained meso-diaminopimelic acid as the diagnostic diamino acid of the cell-wall peptidoglycan, and glucose and xylose as the major whole-cell sugars. The phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipids, glycolipid and unidentified lipids. MK-10(H8), MK-9(H8), MK-10(H2) and MK-10(H6) were the predominant menaquinones. The major fatty acids were i-C16 : 0 (30.71 %), ai-C17 : 0 (13.31 %) and C16 : 0 (11.28 %). The G+C content of the DNA was 60.1 mol%. Comparative analysis of 16S rRNA gene sequences showed that the novel strain was most closely related to genera within the family

Nocardiopsaceae

, but formed a separate lineage. The highest sequence similarities were to

Nocardiopsis arabia

DSM 45083T (95.4 %) and

Haloactinospora alba

DSM 45015T (94.9 %). On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain CXB832T represents a new genus and novel species in the family

Nocardiopsaceae

, for which the name Salinactinospora qingdaonensis gen. nov., sp. nov. is proposed. The type strain of the type species is CXB832T ( = DSM 45442T = LMG 25567T).
Simiduia areninigrae sp. nov., an agarolytic bacterium isolated from sea sand
Authors: Kim Byung-Chun , Poo Haryoung , Lee Kang Hyun , Kim Mi Na , Park Doo-Sang , Oh Hyun Woo , Lee Jin Man , Shin Kee-Sun
Published: June 2011

During a study intended to screen for agar-degrading bacteria, strain M2-5T was isolated from black sand off the shore of Jeju Island, Republic of Korea. Strain M2-5T exhibited agarase activity; the β-agarase gene of the isolate had 62 % amino acid sequence identity to the β-agarase gene of

Microbulbifer thermotolerans

JAMB A94T. The isolate was closely related to members of the genus

Simiduia

but was clearly discernible from reported

Simiduia

species, based on a polyphasic analysis. Cells of strain M2-5T were Gram-negative, catalase- and oxidase-positive, motile rods. The DNA G+C content was 53.3 mol%. The predominant isoprenoid quinone was Q-8. The major cellular fatty acids were C17 : 1ω8c (25.9 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c; 17.2 %) and C17 : 0 (15.0 %). Phylogenetic analysis using 16S rRNA gene sequences showed that strain M2-5T had 96.6 % gene sequence similarity to

Simiduia agarivorans

SA1T, the most closely related type strain of the genus

Simiduia

. These results suggest that strain M2-5T represents a novel species in the genus

Simiduia

, for which the name
Simiduia

areninigrae sp. nov. is proposed; the type strain is M2-5T ( = KCTC 23293T = NCAIM B 02424T).
Bacillus daliensis sp. nov., an alkaliphilic, Gram-positive bacterium isolated from a soda lake
Authors: Zhai Lei , Liao Tingting , Xue Yanfen , Ma Yanhe
Published: June 2011

A Gram-positive, alkaliphilic bacterium, designated strain DLS13T, was isolated from Dali Lake in Inner Mongolia Autonomous Region, China. The isolate was able to grow at pH 7.5–11.0 (optimum at pH 9), in 0–8 % (w/v) NaCl (optimum at 2 %, w/v) and at 10–45 °C (optimum at 30 °C). Cells of the isolate were facultatively anaerobic, spore-forming rods with peritrichous flagella. The predominant isoprenoid quinone was MK-7 and its cell wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0. The genomic DNA G+C content of the isolate was 43.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain DLS13T was a member of the genus

Bacillus

and most closely related to

Bacillus saliphilus

DSM 15402T (96.9 % similarity). The DNA–DNA relatedness value between strain DLS13T and

B. saliphilus

DSM 15402T was 38.7±1.9 %. Comparative analysis of genotypic and phenotypic features indicated that strain DLS13T represents a novel species of the genus

Bacillus

, for which the name Bacillus daliensis sp. nov. is proposed; the type strain is DLS13T ( = CGMCC 1.10369T = JCM 17097T = NBRC 107572T).
Roseovarius halocynthiae sp. nov., isolated from the sea squirt Halocynthia roretzi
Authors: Kim Young-Ok , Kong Hee Jeong , Park Sooyeon , Kang So-Jung , Kim Woo-Jin , Kim Kyung-Kil , Oh Tae-Kwang , Yoon Jung-Hoon
Published: June 2011

A Gram-negative, motile, ovoid- to rod-shaped bacterial strain, designated MA1-10T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea, Korea. Strain MA1-10T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain MA1-10T clustered with

Roseovarius crassostreae

CV919-312T, with which it exhibited 97.1 % sequence similarity, at a bootstrap resampling value of 96.2 %. It exhibited 93.3–95.8 % 16S rRNA gene sequence similarity to the type strains of other recognized

Roseovarius

species. Strain MA1-10T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid, which is consistent with data for the genus

Roseovarius

. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and an unidentified lipid. The DNA G+C content of strain MA1-10T was 55.4 mol%. Mean DNA–DNA relatedness between strain MA1-10T and

R. crassostreae

DSM 16950T was 13 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, demonstrated that strain MA1-10T could be distinguished from all recognized

Roseovarius

species. On the basis of the data presented, strain MA1-10T is considered to represent a novel species of the genus

Roseovarius

, for which the name Roseovarius halocynthiae sp. nov. is proposed; the type strain is MA1-10T ( = KCTC 23462T = CCUG 60745T).
Actinoplanes abujensis sp. nov., isolated from Nigerian arid soil
Authors: Sazak Anil , Sahin Nevzat , Camas Mustafa
Published: June 2011

A novel actinobacterial strain, A4029T, isolated from arid soil of Abuja, Nigeria, and provisionally assigned to the genus

Actinoplanes

, was subjected to a polyphasic taxonomic study. 16S rRNA gene sequence similarity studies showed that strain A4029T belonged to the genus

Actinoplanes

, being most closely related to

Actinoplanes brasiliensis

DSM 43805T (98.9 %) and

Actinoplanes deccanensis

DSM 43806T (98.0 %); similarity to other type strains of the genus

Actinoplanes

ranged from 96.2 to 97.9 %. Chemotaxonomic data [major menaquinone MK-9(H4); major polar lipids phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol; characteristic sugars arabinose and xylose; major fatty acids iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, C17 : 1ω9c
and iso-C14 : 0] confirmed the affiliation of strain A4029T to the genus

Actinoplanes

. The results of DNA–DNA hybridizations and phylogenetic analysis, together with phenotypic and biochemical test data, allowed strain A4029T to be differentiated from strains of other

Actinoplanes

species. Therefore, strain A4029T represents a novel species, for which the name Actinoplanes abujensis sp. nov. is proposed, with A4029T ( = DSM 45518T = NRRL B-24835T = KCTC 19984T) as the type strain.
Streptomyces
staurosporininus sp. nov., a staurosporine-producing actinomycete
Authors: Kim Byung-Yong , Zucchi Tiago Domingues , Fiedler Hans-Peter , Goodfellow Michael
Published: June 2011

The taxonomic position of a staurosporine-producing actinomycete isolated from a hay meadow soil was determined using a polyphasic approach. The organism had chemical and morphological characteristics consistent with its classification in the genus

Streptomyces

and formed a distinct branch between the

Streptomyces lydicus

and

Streptomyces noursei

clades in the 16S rRNA

Streptomyces

gene tree. DNA–DNA relatedness values between the isolate and its nearest phylogenetic neighbours, namely

Streptomyces lydicus

NBRC 13058T and

Streptomyces chattanoogensis

NBRC 12754T, were 53 % and 40 %, respectively. The isolate was also readily distinguished from the type strains of these species using a combination of morphological and other phenotypic properties. On the basis of these results, it is proposed that isolate BK179T ( = KACC 20912T  = NRRL B-24850T) be classified as the type strain of
Streptomyces

staurosporininus sp. nov.
Isoptericola nanjingensis sp. nov., a mineral-weathering bacterium
Authors: Huang Zhi , Sheng Xia-Fang , Zhao Fei , He Lin-Yan , Huang Jing , Wang Qi
Published: June 2011

A Gram-positive-staining, non-motile, rod- or coccoid-shaped actinobacterium, designated strain H17T, was isolated from a soil sample from Nanjing, Jiangsu Province, PR China. The organism grew optimally at 30 °C, pH 7.0 and with 3 % NaCl (w/v). Strain H17T contained l-Lys–d-Asp as the cell-wall peptidoglycan type and galactose, xylose and mannose as the whole-cell sugars. The major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The total polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipids, phosphatidylinositol, phosphoglycolipid, one unidentified glycolipid and one unidentified lipid. The menaquinone was MK9(H4). Mycolic acids were not detected. The DNA G+C content was 72.4 mol%. Phylogenetic analysis of this strain based on 16S rRNA gene sequences revealed 97.8–99.6 % similarity to recognized species of the genus

Isoptericola

. The low level of DNA–DNA relatedness to other species of the genus

Isoptericola

and the many phenotypic properties that distinguished strain H17T from recognized species of this genus demonstrated that isolate H17T should be classified as representing a novel species of the genus

Isoptericola

. The name Isoptericola nanjingensis sp. nov. is proposed for this novel species. The type strain is H17T ( = DSM 24300T = CCTCC AB 2011005T).