bluuebunny/crossref_metadata_2025 huggingface dataset:
Rat CYP2D2, not 2D1, is functionally conserved with human CYP2D6 in endogenous morphine formation
Authors: Grobe Nadja , Kutchan Toni M. , Zenk Meinhart H.
Published: May 2012

The assumption that CYP2D1 is the corresponding rat cytochrome to human CYP2D6 has been revisited using recombinant proteins in direct enzyme assays. CYP2D1 and 2D2 were incubated with known CYP2D6 substrates, the three morphine precursors thebaine, codeine and (R)‐reticuline. Mass spectrometric analysis showed that rat CYP2D2, not 2D1, catalyzed the 3‐O‐demethylation reaction of thebaine and codeine. In addition, CYP2D2 incubated with (R)‐reticuline generated four products corytuberine, pallidine, salutaridine and isoboldine while rat CYP2D1 was completely inactive. This intramolecular phenol‐coupling reaction follows the same mechanism as observed for CYP2D6. Michaelis–Menten kinetic parameters revealed high catalytic efficiencies for rat CYP2D2. These findings suggest a critical evaluation of other commonly accepted, however untested, CYP2D1 substrates.
Insights in small Heat Shock Protein/client interaction by combined protection analysis of two different client proteins
Authors: Eisenhardt Benjamin D. , Forreiter Christoph
Published: May 2012

MDH and HSP17.6B bind by molecular sieving (View interaction)
Functional analysis of the conserved histidine residue of Bamboo mosaic virus capping enzyme in the activity for the formation of the covalent enzyme–m7GMP intermediate
Authors: Lin Hua-Yang , Yu Chiao-Yuan , Hsu Yau-Heiu , Meng Menghsiao
Published: May 2012

The alphavirus‐like mRNA capping enzyme of Bamboo mosaic virus (BaMV) exhibits an AdoMet‐dependent guanylyltransferase activity by which the methyl group of AdoMet is transferred to GTP, leading to the formation of m7GTP, and the m7GMP moiety is next transferred to the 5′ end of ppRNA via a covalent enzyme–m7GMP intermediate. The function of the conserved H68 of the BaMV capping enzyme in the intermediate formation was analyzed by mutagenesis in this study. The nature of the bond linking the enzyme and m7GMP was changed in the H68C mutant protein, strongly suggesting that H68 covalently binds to m7GMP in the intermediate.
Mechanistic details of the DNA recognition by the Dnmt1 DNA methyltransferase
Authors: Bashtrykov Pavel , Ragozin Sergey , Jeltsch Albert
Published: May 2012

A recently solved Dnmt1‐DNA crystal structure revealed several enzyme–DNA contacts and large structural rearrangements of the DNA at the target site, including the flipping of the non‐target strand base of the base pair flanking the CpG site and formation of a non‐canonical base pair between the non‐target strand Gua and the flanking base pair. Here, we show that the contacts of the enzyme to the target base and the Gua:5mC base pair that are observed in the structure are very important for catalytic activity. The contacts to the non‐target strand Gua are not important since its exchange by Ade stimulated activity. Except target base flipping, we could not find evidence that the DNA rearrangements have a functional role.
Matrix‐dependent perturbation of TGFβ signaling and disease
Authors: Doyle Jefferson J. , Gerber Elizabeth E. , Dietz Harry C.
Published: May 2012

Transforming growth factor beta (TGFβ) is a multipotent cytokine that is sequestered in the extracellular matrix (ECM) through interactions with a number of ECM proteins. The ECM serves to concentrate latent TGFβ at sites of intended function, to influence the bioavailability and/or function of TGFβ activators, and perhaps to regulate the intrinsic performance of cell surface effectors of TGFβ signal propagation. The downstream consequences of TGFβ signaling cascades in turn provide feedback modulation of the ECM. This review covers recent examples of how genetic mutations in constituents of the ECM or TGFβ signaling cascade result in altered ECM homeostasis, cellular performance and ultimately disease, with an emphasis on emerging therapeutic strategies that seek to capitalize on this refined mechanistic understanding.
Balance and Sequence in Online Reviews: How Perceived Usefulness Affects Attitudes and Intentions
Authors: Purnawirawan Nathalia , De Pelsmacker Patrick , Dens Nathalie
Published: May 2012

This paper is the first study that investigates the impact of balance (the ratio of positive and negative reviews) and sequence (the order in which the reviews are presented) of a set of online reviews on the perceived usefulness of these reviews (objective 1). As a second objective, our study attempts to provide more understanding in the gatekeeping role of the perceived usefulness. The results do not only evidence that review balance matters, but also reveal that review sequence has an important effect on the perceived usefulness of a set of reviews. The crucial role of perceived usefulness is demonstrated in that only when reviews are perceived as relatively useful, recall of positive and negative review information affects attitude and intention formation through the impression it creates about the object.
Automorphic Representations and L-Functions for the General Linear Group
Authors: Goldfeld Dorian , Hundley Joseph
Published: May 2012

This graduate-level textbook provides an elementary exposition of the theory of automorphic representations and L-functions for the general linear group in an adelic setting. Definitions are kept to a minimum and repeated when reintroduced so that the book is accessible from any entry point, and with no prior knowledge of representation theory. The book includes concrete examples of global and local representations of GL(n), and presents their associated L-functions. In Volume 1, the theory is developed from first principles for GL(1), then carefully extended to GL(2) with complete detailed proofs of key theorems. Several proofs are presented for the first time, including Jacquet's simple and elegant proof of the tensor product theorem. In Volume 2, the higher rank situation of GL(n) is given a detailed treatment. Containing numerous exercises by Xander Faber, this book will motivate students and researchers to begin working in this fertile field of research.
Note: A flexible light emitting diode-based broadband transient-absorption spectrometer
Authors: Gottlieb Sean M. , Corley Scott C. , Madsen Dorte , Larsen Delmar S.
Published: May 2012

This Note presents a simple and flexible ns-to-ms transient absorption spectrometer based on pulsed light emitting diode (LED) technology that can be incorporated into existing ultrafast transient absorption spectrometers or operate as a stand-alone instrument with fixed-wavelength laser sources. The LED probe pulses from this instrument exhibit excellent stability (∼0.5%) and are capable of producing high signal-to-noise long-time (>100 ns) transient absorption signals either in a broadband multiplexed (spanning 250 nm) or in tunable narrowband (20 ns) operation. The utility of the instrument is demonstrated by measuring the photoinduced ns-to-ms photodynamics of the red/green absorbing fourth GMP phosphodiesterase/adenylyl cyclase/FhlA domain of the NpR6012 locus of the nitrogen-fixing cyanobacterium Nostoc punctiforme.
Feedback control of an azimuthal oscillation in the E × B discharge of Hall thrusters
Authors: Griswold M. E. , Ellison C. L. , Raitses Y. , Fisch N. J.
Published: May 2012

Feedback control of a low-frequency azimuthal wave known as a “rotating spoke” in the E × B discharge of a cylindrical Hall thruster was demonstrated. The rotating spoke is an m = 1 azimuthal variation in density, electron temperature, and potential that rotates at about 10% of the local E × B electron rotation speed. It causes increased electron transport across the magnetic field and is suspected to be an ionization wave. Feedback control of this wave required special consideration because, although it causes a rotating azimuthal variation in the current density to the anode, it does not show up as a signal in the total thruster discharge current. Therefore, an extra source of information was needed to track the oscillation, which was addressed by using a special anode that was split azimuthally into four segments. The current to each segment oscillates as the rotating spoke passes over it, and feedback is accomplished by resistors connected in series with each anode segment which causes the voltage on a segment to decrease in proportion to the current through that segment. The feedback resulted in the disappearance of a coherent azimuthal wave and a decrease in the time-averaged total discharge current by up to 13.2%.
Spherical linear waves in de Sitter spacetime
Authors: Costa João L. , Alho Artur , Natário José
Published: May 2012

We apply Christodoulou's framework, developed to study the Einstein-scalar field equations in spherical symmetry, to the linear wave equation in de Sitter spacetime, as a first step towards the Einstein-scalar field equations with positive cosmological constant. We obtain an integro-differential evolution equation, which we solve by taking initial data on a null cone. As a corollary, we obtain elementary derivations of expected properties of linear waves in de Sitter spacetime: boundedness in terms of (characteristic) initial data, and a Price law establishing uniform exponential decay, in Bondi time, to a constant.
Bacterial effector binds host cell adenylyl cyclase to potentiate Gαs-dependent cAMP production
Authors: Pulliainen Arto T. , Pieles Kathrin , Brand Cameron S. , Hauert Barbara , Böhm Alex , Quebatte Maxime , Wepf Alexander , Gstaiger Matthias , Aebersold Ruedi , Dessauer Carmen W. , Dehio Christoph
Published: May 2012

Subversion of host organism cAMP signaling is an efficient and widespread mechanism of microbial pathogenesis.
Bartonella
effector protein A (BepA) of vasculotumorigenic
Bartonella henselae
protects the infected human endothelial cells against apoptotic stimuli by elevation of cellular cAMP levels by an as yet unknown mechanism. Here, adenylyl cyclase (AC) and the α-subunit of the AC-stimulating G protein (Gαs) were identified as potential cellular target proteins for BepA by gel-free proteomics. Results of the proteomics screen were evaluated for physical and functional interaction by: (
i
) a heterologous in vivo coexpression system, where human AC activity was reconstituted under the regulation of Gαs and BepA in
Escherichia coli
; (
ii
) in vitro AC assays with membrane-anchored full-length human AC and recombinant BepA and Gαs; (
iii
) surface plasmon resonance experiments; and (
iv
) an in vivo fluorescence bimolecular complementation-analysis. The data demonstrate that BepA directly binds host cell AC to potentiate the Gαs-dependent cAMP production. As opposed to the known microbial mechanisms, such as ADP ribosylation of G protein α-subunits by cholera and pertussis toxins, the fundamentally different BepA-mediated elevation of host cell cAMP concentration appears subtle and is dependent on the stimulus of a G protein-coupled receptor-released Gαs. We propose that this mechanism contributes to the persistence of
Bartonella henselae
in the chronically infected vascular endothelium.
Functional modulation of a protein folding landscape via side-chain distortion
Authors: Kelch Brian A. , Salimi Neema L. , Agard David A.
Published: May 2012

Ultrahigh-resolution (< 1.0 
Å
) structures have revealed unprecedented and unexpected details of molecular geometry, such as the deformation of aromatic rings from planarity. However, the functional utility of such energetically costly strain is unknown. The 0.83 Å structure of α-lytic protease (αLP) indicated that residues surrounding a conserved Phe side-chain dictate a rotamer which results in a ∼6° distortion along the side-chain, estimated to cost 4 kcal/mol. By contrast, in the closely related protease Streptomyces griseus Protease B (SGPB), the equivalent Phe adopts a different rotamer and is undistorted. Here, we report that the αLP Phe side-chain distortion is both functional and conserved in proteases with large pro regions. Sequence analysis of the αLP serine protease family reveals a bifurcation separating those sequences expected to induce distortion and those that would not, which correlates with the extent of kinetic stability. Structural and folding kinetics analyses of family members suggest that distortion of this side-chain plays a role in increasing kinetic stability within the αLP family members that use a large Pro region. Additionally, structural and kinetic folding studies of mutants demonstrate that strain alters the folding free energy landscape by destabilizing the transition state (TS) relative to the native state (N). Although side-chain distortion comes at a cost of foldability, it suppresses the rate of unfolding, thereby enhancing kinetic stability and increasing protein longevity under harsh extracellular conditions. This ability of a structural distortion to enhance function is unlikely to be unique to αLP family members and may be relevant in other proteins exhibiting side-chain distortions.
Salience driven value integration explains decision biases and preference reversal
Authors: Tsetsos Konstantinos , Chater Nick , Usher Marius
Published: May 2012

Human choice behavior exhibits many paradoxical and challenging patterns. Traditional explanations focus on how values are represented, but little is known about how values are integrated. Here we outline a psychophysical task for value integration that can be used as a window on high-level, multiattribute decisions. Participants choose between alternative rapidly presented streams of numerical values. By controlling the temporal distribution of the values, we demonstrate that this process underlies many puzzling choice paradoxes, such as temporal, risk, and framing biases, as well as preference reversals. These phenomena can be explained by a simple mechanism based on the integration of values, weighted by their salience. The salience of a sampled value depends on its temporal order and momentary rank in the decision context, whereas the direction of the weighting is determined by the task framing. We show that many known choice anomalies may arise from the microstructure of the value integration process.
Single amino acid mutation in an ATP-binding cassette transporter gene causes resistance to Bt toxin Cry1Ab in the silkworm,
Bombyx mori
Authors: Atsumi Shogo , Miyamoto Kazuhisa , Yamamoto Kimiko , Narukawa Junko , Kawai Sawako , Sezutsu Hideki , Kobayashi Isao , Uchino Keiro , Tamura Toshiki , Mita Kazuei , Kadono-Okuda Keiko , Wada Sanae , Kanda Kohzo , Goldsmith Marian R. , Noda Hiroaki
Published: May 2012

Bt toxins derived from the arthropod bacterial pathogen
Bacillus thuringiensis
are widely used for insect control as insecticides or in transgenic crops. Bt resistance has been found in field populations of several lepidopteran pests and in laboratory strains selected with Bt toxin. Widespread planting of crops expressing Bt toxins has raised concerns about the potential increase of resistance mutations in targeted insects. By using
Bombyx mori
as a model, we identified a candidate gene for a recessive form of resistance to Cry1Ab toxin on chromosome 15 by positional cloning.
BGIBMGA007792-93
, which encodes an ATP-binding cassette transporter similar to human multidrug resistance protein 4 and orthologous to genes associated with recessive resistance to Cry1Ac in
Heliothis virescens
and two other lepidopteran species, was expressed in the midgut. Sequences of 10 susceptible and seven resistant silkworm strains revealed a common tyrosine insertion in an outer loop of the predicted transmembrane structure of resistant alleles. We confirmed the role of this ATP-binding cassette transporter gene in Bt resistance by converting a resistant silkworm strain into a susceptible one by using germline transformation. This study represents a direct demonstration of Bt resistance gene function in insects with the use of transgenesis.
A thermodynamic definition of protein domains
Authors: Porter Lauren L. , Rose George D.
Published: May 2012

Protein domains are conspicuous structural units in globular proteins, and their identification has been a topic of intense biochemical interest dating back to the earliest crystal structures. Numerous disparate domain identification algorithms have been proposed, all involving some combination of visual intuition and/or structure-based decomposition. Instead, we present a rigorous, thermodynamically-based approach that redefines domains as cooperative chain segments. In greater detail, most small proteins fold with high cooperativity, meaning that the equilibrium population is dominated by completely folded and completely unfolded molecules, with a negligible subpopulation of partially folded intermediates. Here, we redefine structural domains in thermodynamic terms as cooperative folding units, based on
m
-values, which measure the cooperativity of a protein or its substructures. In our analysis, a domain is equated to a contiguous segment of the folded protein whose
m
-value is largely unaffected when that segment is excised from its parent structure. Defined in this way, a domain is a self-contained cooperative unit; i.e., its cooperativity depends primarily upon intrasegment interactions, not intersegment interactions. Implementing this concept computationally, the domains in a large representative set of proteins were identified; all exhibit consistency with experimental findings. Specifically, our domain divisions correspond to the experimentally determined equilibrium folding intermediates in a set of nine proteins. The approach was also proofed against a representative set of 71 additional proteins, again with confirmatory results. Our reframed interpretation of a protein domain transforms an indeterminate structural phenomenon into a quantifiable molecular property grounded in solution thermodynamics.
Quantitative nanoscale visualization of heterogeneous electron transfer rates in 2D carbon nanotube networks
Authors: Güell Aleix G. , Ebejer Neil , Snowden Michael E. , McKelvey Kim , Macpherson Julie V. , Unwin Patrick R.
Published: May 2012

Carbon nanotubes have attracted considerable interest for electrochemical, electrocatalytic, and sensing applications, yet there remains uncertainty concerning the intrinsic electrochemical (EC) activity. In this study, we use scanning electrochemical cell microscopy (SECCM) to determine local heterogeneous electron transfer (HET) kinetics in a random 2D network of single-walled carbon nanotubes (SWNTs) on an Si/SiO
2
substrate. The high spatial resolution of SECCM, which employs a mobile nanoscale EC cell as a probe for imaging, enables us to sample the responses of individual portions of a wide range of SWNTs within this complex arrangement. Using two redox processes, the oxidation of ferrocenylmethyl trimethylammonium and the reduction of ruthenium (III) hexaamine, we have obtained conclusive evidence for the high intrinsic EC activity of the sidewalls of the large majority of SWNTs in networks. Moreover, we show that the ends of SWNTs and the points where two SWNTs cross do not show appreciably different HET kinetics relative to the sidewall. Using finite element method modeling, we deduce standard rate constants for the two redox couples and demonstrate that HET based solely on characteristic defects in the SWNT side wall is highly unlikely. This is further confirmed by the analysis of individual line profiles taken as the SECCM probe scans over an SWNT. More generally, the studies herein demonstrate SECCM to be a powerful and versatile method for activity mapping of complex electrode materials under conditions of high mass transport, where kinetic assignments can be made with confidence.
Lysine-specific demethylase 2A (KDM2A) normalizes human embryonic stem cell derived keratinocytes
Authors: Iuchi Shiro , Green Howard
Published: May 2012

Studies on human lysine-specific demethylase 2A (KDM2A) by others have recently begun. To date, the demethylase activity has been known to reduce expression of genes and eventually inhibit proliferation of cells. However, while attempting to improve proliferation of hES-cell–derived Nod keratinocytes, which grow poorly and have a short life span, we found that high expression of the KDM2A gene improves the poor proliferation of the cells. Of the four isomer cDNAs that we prepared from alternatively spliced KDM2A transcripts, only one stimulates the proliferation. This (KDM2A-N782) encodes the 782AA protein containing the JmjC, CXXC, and Ring domains, but not the F-box and AMN1 domains, unlike KDM2A, which has been studied by other groups. Our results not only show that differently spliced transcripts from a gene result in totally opposite outcomes, but also present critical evidence of the complicated activities of KDM2A, which contains all of the five domains.
Escapement of eel (Anguilla anguilla) in coastal areas in Sweden over a 50-year period
Authors: Andersson Jan , Florin Ann-Britt , Petersson Erik
Published: May 2012

Andersson, J., Florin, A.-B., and Petersson, E. 2012. Escapement of eel (Anguilla anguilla) in coastal areas in Sweden over a 50-year period – ICES Journal of Marine Science, 69: 991–999. The escapement of eel from coastal areas in Sweden during the last 50 years was assessed using data from voluntary fishery journals and fishery-independent coastal fish monitoring programmes. It was evident that the level of escapement, determined as catch per unit of effort in numbers, from the Baltic Sea decreased over time, with the most rapid decline occurring in the 1960s and early 1970s, but also in recent years. There were, however, differences in the temporal variability in escapement between areas. Escapement from the northernmost studied site did not change significantly during the last 50 years, while there was a rapid decline in the southern areas. Escapement remained relatively stable between the late 1970s and 2000 however, and escapement at the Swedish west coast, inferred from yellow eel catch per unit of effort, generally increased during the same time. The loss in numbers has to some extent been compensated by an increase in mean weight of silver eel. Possible explanations for the retained level of escapement during the last decades despite the continued reduction in recruitment are discussed. Favourable environmental conditions in combination with a lower fishing effort are suggested as the most probable reasons why the escapement decline has not been more dramatic, but stocking and density-dependent effects cannot be ruled out.
Bacillus gottheilii sp. nov., isolated from a pharmaceutical manufacturing site
Authors: Seiler Herbert , Wenning Mareike , Schmidt Verena , Scherer Siegfried
Published: May 2012

A novel Gram-staining-positive, rod-shaped, motile, strictly aerobic, endospore-forming bacterium, designated WCC 4585T, was isolated from a pharmaceutical production line. The organism grew optimally at 30 °C, at pH 8 and in the presence of 0.5 % (w/v) NaCl. Oval endospores were formed subterminally and terminally in swollen sporangia. The cell-wall diamino acid was meso-diaminopimelic acid (type A1γ) and the genomic DNA G+C content was 38.7 mol%. The major menaquinone was MK-7. The cellular fatty acid profile contained major amounts of iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0, and the cellular phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and aminophospholipid. The isolate was most closely related to

Bacillus oceanisediminis

H2T,

Bacillus infantis

SMC 4352-1T,

Bacillus firmus

NCIMB 9366T,

Bacillus circulans

ATCC 4513T and

Bacillus horneckiae

DSM 23495T with which it shared less than 98.0 % 16S rRNA gene sequence similarity. DNA–DNA relatedness values between strain WCC 4585T and five type strains of related species were ≤27 % and sequence similarity values based on groEL sequences were ≤88.7 %. On the basis of the characteristics presented, strain WCC 4585T is proposed to represent a novel species, Bacillus gottheilii sp. nov. The type strain is WCC 4585T( = DSM 23668T = CCUG 59876T = LMG 25856T).
Pseudonocardia antitumoralis sp. nov., a deoxynyboquinone-producing actinomycete isolated from a deep-sea sediment
Authors: Tian Xin-Peng , Long Li-Juan , Li Su-Mei , Zhang Jing , Xu Ying , He Jie , Li Jie , Wang Fa-Zuo , Li Wen-Jun , Zhang Chang-Sheng , Zhang Si
Published: May 2012

An aerobic actinomycete, designated SCSIO 01299T, was isolated from a deep-sea sediment collected from the northern South China Sea at a depth of 3258 m. The isolate was found to be a natural producer of the synthesized antitumour agent deoxynyboquinone and its three new derivatives, pseudonocardians A, B and C. A blast search based on almost-complete 16S rRNA gene sequences showed that strain SCSIO 01299T had high sequence similarities with members of the genus

Pseudonocardia

. The 16S rRNA gene sequence phylogenetic tree revealed that strain SCSIO 01299T was a member of the genus

Pseudonocardia

. Phenotypic analysis, chemotaxonomy and DNA–DNA relatedness could readily distinguish the isolate from established members in this genus. It was concluded that strain SCSIO 01299T represents a novel species, for which the name Pseudonocardia antitumoralis sp. nov. is proposed. The type strain is SCSIO 01299T ( = DSM 45322T  = CCTCC M 2011255T).
Sediminibacterium ginsengisoli sp. nov., isolated from soil of a ginseng field, and emended descriptions of the genus

Sediminibacterium

and of

Sediminibacterium salmoneum
Authors: Kim Yeon-Ju , Nguyen Ngoc-Lan , Weon Hang-Yeon , Yang Deok-Chun
Published: May 2012

A Gram-negative bacterium, designated DCY13T, was isolated from soil of a ginseng field in South Korea. Comparative analysis of 16S rRNA gene sequences showed that strain DCY13T shared the highest sequence similarity (95.0 %) with

Sediminibacterium salmoneum

NBRC 103935T and 87.6–91.4 % sequence similarity with other members of the family

Chitinophagaceae

. Cells were non-spore-forming rods, catalase- and oxidase-positive, motile by gliding and facultatively anaerobic. The only respiratory quinone was menaquinone 7 (MK-7) and the major fatty acids were iso-C17 : 0 3-OH, iso-C15 : 0 and iso-C15 : 1 G. The G+C content of the genomic DNA was 47.5±1.0 mol%. In addition to phosphatidylethanolamine, the major polar lipids were two unidentified aminophospholipids, one unidentified aminolipid and three unidentified polar lipids. The major cell-wall sugars were ribose, xylose and galactose. It is proposed that strain DCY13T represents a novel species in the genus

Sediminibacterium

, for which the name Sediminibacterium ginsengisoli sp. nov. is proposed. The type strain is DCY13T ( = KCTC 12833T  = JCM 15794T  = DSM 22335T). Emended descriptions of the genus

Sediminibacterium

and of

Sediminibacterium salmoneum

are also proposed.
Flavobacterium enshiense sp. nov., isolated from soil, and emended descriptions of the genus

Flavobacterium

and

Flavobacterium cauense

,

Flavobacterium saliperosum

and

Flavobacterium suncheonense
Authors: Dong Kun , Chen Fang , Du Yan , Wang Gejiao
Published: May 2012

A Gram-negative, strictly aerobic, yellow-pigmented rod, designated DK69T, was isolated from soil collected from the waste liquid treatment facility of Bafeng Pharmaceutical Company in the city of Enshi, Hubei Province, China. Phylogenetic analysis based on 16S rRNA gene sequences placed strain DK69T in the genus

Flavobacterium

of the family

Flavobacteriaceae

. The highest 16S rRNA gene sequence similarities were found with

Flavobacterium cauense

R2A-7T (96.9 %),

Flavobacterium saliperosum

AS 1.3801T (96.3 %) and

Flavobacterium suncheonense

GH29-5T (95.7 %). The major fatty acids (≥5 %) were iso-C15 : 0, iso-C17 : 1ω9c, C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The major respiratory quinone was menaquinone-6. The genomic DNA G+C content was 34.4 mol%. Strain DK69T represents a novel species of the genus

Flavobacterium

, for which the name Flavobacterium enshiense sp. nov. is proposed. The type strain is DK69T ( = CCTCC AB 2011144T  = KCTC 23775T). Emended descriptions of the genus

Flavobacterium

and

Flavobacterium cauense

,

Flavobacterium saliperosum

and

Flavobacterium suncheonense

are also proposed.
Chryseobacterium taihuense sp. nov., isolated from a eutrophic lake, and emended descriptions of the genus

Chryseobacterium

,

Chryseobacterium taiwanense

,

Chryseobacterium jejuense

and

Chryseobacterium indoltheticum
Authors: Wu Yu-Fan , Wu Qing-Long , Liu Shuang-Jiang
Published: May 2012

Bacterial strain THMBM1T was isolated from decomposing algal scum that was collected during an algal bloom in Lake Taihu, Wuxi City, Jiangsu Province, China. Cells of strain THMBM1T were Gram-negative, facultatively anaerobic, non-motile rods. Colonies on tryptic soy agar were translucent and shiny with entire edges; yellow flexirubin-type pigments were produced. Growth was observed at 15–45 °C (optimum 30–37 °C), at pH 5.0–9.0 (optimum pH 8.0) and in the presence of 0–4.0 % (w/v) NaCl (optimum 0–1.0 %). Strain THMBM1T contained MK-6 as the sole respiratory quinone and sym-homospermidine as the predominant polyamine. The predominant cellular fatty acids were iso-C15 : 0 (53.2 %), iso-C17 : 0 3-OH (15.6 %) and iso-C17 : 1ω9c (11.9 %). The polar lipid profile consisted of phosphatidylethanolamine and five unidentified lipids. The DNA G+C content was 36.8 mol% (T
m). Strain THMBM1T was closely related to members of the genus

Chryseobacterium

, with 16S rRNA gene sequence similarities ranging from 92.9 to 97.2 %, the highest sequence similarities being with

Chryseobacterium taiwanense

BCRC 17412T (97.2 %) and

C. gambrini

5-1St1aT (97.1 %). DNA–DNA relatedness between strain THMBM1T and

C. taiwanense

JCM 21767T and

C. gambrini

DSM 18014T was 34.1  and 23.0 %, respectively. Based on these results, it is concluded that strain THMBM1T represents a novel species, for which the name Chryseobacterium taihuense sp. nov. is proposed. The type strain is THMBM1T ( = CGMCC 1.10941T  = NBRC 108747T). Emended descriptions of the genus

Chryseobacterium

and

C. taiwanense

,

C. jejuense

and

C. indoltheticum

are also proposed.
Thauera humireducens sp. nov., a humus-reducing bacterium isolated from a microbial fuel cell
Authors: Yang Gui-Qin , Zhang Jun , Kwon Soon-Wo , Zhou Shun-Gui , Han Lu-Chao , Chen Ming , Ma Chen , Zhuang Li
Published: May 2012

A Gram-negative, rod-shaped, non-spore-forming bacterium, designated SgZ-1T, was isolated from the anode biofilm of a microbial fuel cell. The strain had the ability to grow under anaerobic condition via the oxidation of various organic compounds coupled to the reduction of anthraquione-2,6-disulfonate (AQDS) to anthrahydroquinone-2,6-disulfonate (AHQDS). Growth occurred in TSB in the presence of 0–5.5 % (w/v) NaCl (optimum 0–1 %), at 10–45 °C (optimum 25–37 °C) and at pH 6.0–10.0 (optimum 8.0–8.5). Based on 16S rRNA gene sequence similarity, strain SgZ-1T belonged to the genus

Thauera

. The highest level of 16S rRNA gene sequences similarity (96.7 %) was found to be with

Thauera aminoaromatica

S2
T and

Thauera selenatis

AXT, and lower values were obtained when compared with other recognized

Thauera

species. Chemotaxonomic analysis revealed that strain SgZ-1T contained Q-8 as the predominant quinone, and putrescine and 2-hydroxyputrescine as the major polyamines. The major cellular fatty acids (>5 %) were C16 : 1ω6c and/or C16 : 1ω7c (44.6 %), C16 : 0 (18.8 %), and C18 : 1ω6c and/or C18 : 1ω7c (12.7 %). Based on its phenotypic and phylogenetic properties, chemotaxonomic analysis and the results of physiological and biochemical tests, strain SgZ-1T ( = KACC 16524T = CCTCC M 2011497T) was designated the type strain of a novel species of the genus

Thauera

, for which the name Thauera humireducens sp. nov. was proposed.
Allonocardiopsis opalescens gen. nov., sp. nov., a new member of the suborder

Streptosporangineae

, from the surface-sterilized fruit of a medicinal plant
Authors: Du Hui-Jing , Zhang Yu-Qin , Liu Hong-Yu , Su Jing , Wei Yu-Zhen , Ma Bai-Ping , Guo Bao-Lin , Yu Li-Yan
Published: May 2012

An endophytic actinomycete, designated strain I10A-01259T, was isolated from a surface-sterilized fruit of Lonicera maackii (Rupr.) Maxim., a medicinal plant, which was collected from a suburb of Beijing, China. Whole-cell hydrolysates of the isolate contained galactose and meso-diaminopimelic acid. The predominant phospholipids were phosphatidylglycerol and diphosphatidylglycerol; the menaquinones consisted mainly of MK-9, MK-11 and MK-12, with a minor amount of MK-10. The major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and iso-C15 : 0. Comparative analysis of 16S rRNA gene sequences indicated that strain I10A-01259T was most closely related to

Nocardiopsis arabia

S186T (93.2 % sequence similarity),

Thermobifida halotolerans

YIM 90462T (93.0 %) and other strains of genera within the families

Nocardiopsaceae

and

Thermomonosporaceae

. On the phylogenetic tree based on 16S rRNA gene sequences, strain I10A-01259T fell within the radius of the suborder

Streptosporangineae

, in which the strain formed a distinct lineage next to the genera of the families

Nocardiopsaceae

and

Thermomonosporaceae

. Based on the data from our polyphasic taxonomic study, a novel genus and species, Allonocardiopsis opalescens gen. nov., sp. nov., are proposed within the suborder

Streptosporangineae

. The type strain of Allonocardiopsis opalescens is strain I10A-01259T ( = CPCC 203428T  = DSM 45601T  = KCTC 19844T).
Micromonospora equina sp. nov., isolated from soil from a racecourse
Authors: Everest Gareth J. , Meyers Paul R.
Published: May 2012

Two actinomycete strains were isolated from within the fynbos-rich area surrounded by the horseracing track at Kenilworth Racecourse in Cape Town, South Africa. Rapid molecular identification indicated that the isolates belonged to the family

Micromonosporaceae

. Based on 16S rRNA gene sequence blast analysis, the isolates were identified as members of the genus

Micromonospora

. Phylogenetic analysis showed that the isolates clustered with each other and were most closely related to

Micromonospora viridifaciens

DSM 43909T. Further 16S rRNA gene sequence analysis using EzTaxon revealed that the isolates are closely related to

Micromonospora auratinigra

TT1-11T,

Micromonospora chaiyaphumensis

MC5-1T,

Micromonospora eburnea

LK2-10T,

Micromonospora nigra

DSM 43818T and

Micromonospora olivasterospora

DSM 43868T. DNA–DNA hybridization and physiological tests allowed genotypic and phenotypic differentiation of both isolates from related species; however, their high DNA–DNA relatedness showed that they belong to the same genomic species. Strain Y22T ( = DSM 45644T = NRRL B-24859T) was selected as the type strain to represent this novel species, for which the name Micromonospora equina sp. nov. is proposed.
Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer
Authors: Ha Gavin , Roth Andrew , Lai Daniel , Bashashati Ali , Ding Jiarui , Goya Rodrigo , Giuliany Ryan , Rosner Jamie , Oloumi Arusha , Shumansky Karey , Chin Suet-Feung , Turashvili Gulisa , Hirst Martin , Caldas Carlos , Marra Marco A. , Aparicio Samuel , Shah Sohrab P.
Published: May 2012

Loss of heterozygosity (LOH) and copy number alteration (CNA) feature prominently in the somatic genomic landscape of tumors. As such, karyotypic aberrations in cancer genomes have been studied extensively to discover novel oncogenes and tumor-suppressor genes. Advances in sequencing technology have enabled the cost-effective detection of tumor genome and transcriptome mutation events at single-base-pair resolution; however, computational methods for predicting segmental regions of LOH in this context are not yet fully explored. Consequently, whole transcriptome, nucleotide-level resolution analysis of monoallelic expression patterns associated with LOH has not yet been undertaken in cancer. We developed a novel approach for inference of LOH from paired tumor/normal sequence data and applied it to a cohort of 23 triple-negative breast cancer (TNBC) genomes. Following extensive benchmarking experiments, we describe the nucleotide-resolution landscape of LOH in TNBC and assess the consequent effect of LOH on the transcriptomes of these tumors using RNA-seq-derived measurements of allele-specific expression. We show that the majority of monoallelic expression in the transcriptomes of triple-negative breast cancer can be explained by genomic regions of LOH and establish an upper bound for monoallelic expression that may be explained by other tumor-specific modifications such as epigenetics or mutations. Monoallelically expressed genes associated with LOH reveal that cell cycle, homologous recombination and actin-cytoskeletal functions are putatively disrupted by LOH in TNBC. Finally, we show how inference of LOH can be used to interpret allele frequencies of somatic mutations and postulate on temporal ordering of mutations in the evolutionary history of these tumors.
Implications of rising groundwater level on structural integrity of underground structures – investigations and retrofit of a large building complex
Authors: Tariq Amin Chaudhary Muhammad
Published: May 2012

Purpose

Groundwater levels (GWL) are rising in many cities in the world. The purpose of this study is to present the multi‐faceted approach adopted for examining the impact of a 3 m rise in GWL on the durability, stability and strength of the structural components of a building complex with 40,000 m2 basement. It also reports on the retrofit measures adopted to remedy the situation.

Design/methodology/approach

The overall stability of the building complex was examined for the revised loading conditions as well as the need to strengthen the structurally deficient components to satisfy owner's requirement of a dry and operational basement without the dewatering operation. Structural conditions of the basement walls and a slab of the building complex were assessed based on code guidelines, visual observations, site investigations, analytical finite element model (FEM) studies and sound engineering judgement.

Findings

About 25 percent of the existing basement slab was found to be structrally deficient to resist the applied hydrostatic load. A number of articulation and construction details were also found to be inadequate. Various options for retrofit for the deficient structural components and articulation details were examined and design details were presented for a cost‐effective solution.

Research limitations/implications

The presented methodology is general and can be adopted for similar situations. However, the presented solutions and conclusions are specific to the problem presented herein and modifications will be required for adoption to other situations.

Practical implications

Practising engineers are made aware of the problem of rising GWL for underground structures. Practical information is presented for practising engineers to solve the problem of water leakage in a large basement.

Originality/value

This paper presents an integrated approach for addressing the structural implications of rising groundwater level in an operational basement of a large building complex.
Cracks and stains on façade‐cladding made of carbonate rock thin panels
Authors: Hébert Ronan , Beouch Layla , Fichet Odile , Bigas Jean‐Philippe , Teyssié Dominique , Berthier Benoit , Prichystal Jean‐Baptiste
Published: May 2012

Purpose

This paper aims to present a case study of some current disorders affecting the stone‐panels of façade claddings, i.e. cracking, spalling close to anchorage systems and staining. The purpose of this study is to identify the origin of the mechanical and chemical disorders of the carbonate rock thin panels of the “Les Chênes 1” building of the University of Cergy‐Pontoise (France).

Design/methodology/approach

Mapping of the disorders, anchorage system investigation at spallings, chemical analyses of oil‐like stains were performed in order to characterize both disorders. Porosity and capillarity properties of the rock were measured and compared between samples collected outside and within a stain.

Findings

Mechanical disorders result from vandalism or poor implementation. Spallings are disorders very likely in evolution. Their occurrence may increase through time. Stains are made of silicone destabilization products.

Originality/value

A model is proposed for the formation of oil‐like stains. Water is required to destabilize silicone sealant and to drive the migration of the degradation products through the porous media and towards the surface of the plate exposed to rainfall.
Exploration of management practices for LEED projects
Authors: Ofori‐Boadu Andrea , Owusu‐Manu De‐Graft , Edwards David , Holt Gary
Published: May 2012

Purpose

Traditional management systems sometimes struggle to meet the unique demands of Leadership in Energy and Environmental Design (LEED) projects. Consequently, contractors have to modify their management practices. The purpose of this paper is to explore the management practices necessary to achieve successful implementation of LEED projects.

Design/methodology/approach

LEED project management practices implemented by six US contractors from the Top 100 Green Contractors list published by the Engineering News and Record, were analysed using structured case study interviews. An additional case study probed management practices implemented on a LEED‐GOLD project.

Findings

Findings support the implementation of management practices classified using the six Malcolm Baldrige National Quality Award criteria of leadership, strategic planning, customer focus, measurement, analysis and knowledge management, workforce focus and operation focus.

Research limitations/implications

The qualitative study was based on a limited number of participant organizations. A subsequent quantitative study might provide generalizeable metrics for the green building industry. Further research on the cost effectiveness of the identified management practices is recommended.

Practical implications

This study provides an intuitive framework in the form of discourse on management practices to enhance the success of LEED projects. Contractors may consider the study's recommendations in order to increase their success on such projects.

Originality/value

The need to harmonize management practices with sustainable development has sparked the interest of researchers and practitioners. The study should be of utility to LEED contractors, environmental agencies, governments, educators, and other relevant stakeholders.
External para‐aramid fibre – concrete reinforcement
Authors: Richardson Alan , Galloway Caroline
Published: May 2012

Purpose

This research seeks to investigate the potential of using para‐aramid fibre fabric and yarn as an external reinforcement to existing structures. The purpose of this paper is to improve existing structural performance or to return the original design performance, during refurbishment. The research aims to investigate the potential for enhanced flexural strength and toughness in concrete beams, which may be required for change of use of buildings, where loadings may be subject to change. Buildings in earthquake zones may also benefit from additional toughness provided with external fabric/yarn reinforcement as a means of providing additional time for escape, for the occupants.

Design/methodology/approach

The test compared four types of concrete beams with different reinforcement material compositions and each set consisted of three beams. The beams were: plain reinforced concrete without any external form of reinforcement (RC), plain unreinforced beams with a para aramid sheet (KF), plain unreinforced beams with para aramid strips of yarn attached longitudinally (KY) and plain reinforced concrete beams with sheet fabric (RCKF). All of the para‐aramid material (fabric and yarn) was externally bonded to the samples, using a two part epoxy resin adhesive applied to a prepared surface. To determine the flexural strength and toughness a three point loading test was used to provide load and deflection data on the 12 (500 mm×100 mm×100 mm) concrete beams.

Findings

An increase in flexural strength and toughness was observed when para‐aramid was used in conjunction with steel reinforcement bar (re‐bar). The para‐aramid fabric and yarn produced similar results to the plain reinforced concrete beam in terms of flexural strength but not toughness.

Originality/value

An advantage of using para‐aramid as an external reinforcement, would be to utilise the large deflection the beam sustains under loading, whilst the fabric/yarn holds the beam together across the rupture plane. Although the testing did not prove that para‐aramid would be a viable alternative to steel re‐bar it did show that the material has the potential as an additional reinforcement that may be particularly useful where concrete structures are subject to large deformations or in need of repair.
The international commitment of late‐internationalizing Brazilian entrepreneurial firms
Authors: da Rocha Angela , Cotta de Mello Renato , Pacheco Henrique , de Abreu Farias Isabel
Published: May 2012

Purpose

The purpose of this paper is to contribute to the understanding of international commitment of entrepreneurial firms from an emerging economy to their foreign operations. Specifically, it intends to help bridge an existing gap in the literature by focusing on the international commitment of established small entrepreneurial firms, a topic that has been largely overlooked; investigating small‐firm commitment to foreign investments whereas most studies focus on exporting; combining the different research streams that studied international commitment; and using the resource‐based view (RBV) to explore the interplay between resource allocation and commitment in the foreign investments of small entrepreneurial firms.

Design/methodology/approach

The study adopts an abductive approach to theory development and uses the case method of investigation. Three case studies were developed from primary and secondary sources. A total of 153 pieces of documentation were used to reconstruct past events, in addition to the interviews and information from company sites, permitting triangulation. Pattern‐matching logic was employed as case development progressed, continuously comparing with the theoretical background used in the study.

Findings

The interplay between resource availability, goal congruence, entrepreneur's desire to internationalize and family attitude seem to have a combined impact on the arousal and initial development of international commitment. The relative importance of managerial over financial resources in the early stages and the impact of preparatory activities on the speed and scope of internationalization seem to be specific manifestations of commitment among emerging market firms. As to the outcomes of commitment, performance appears both as an outcome and an antecedent, and, knowledge acquisition and opportunity development seem to increase pari passu with international commitment of emerging market firms.

Practical implications

The findings can be useful to emerging market firms by pointing out the potential negative impact of low international commitment on a firm's internationalization process. Since most firms from emerging markets cannot count on previous internationalization knowledge accumulated by other firms in their (domestic) institutional environment to be used as guides to international expansion, this type of research can provide some guidelines to help their internationalization efforts.

Originality/value

While certain results agreed with the extant literature, new findings generated a set of theoretical propositions regarding international commitment of late‐internationalizing entrepreneurial firms from an emerging Latin American market.