bluuebunny/crossref_metadata_2025 huggingface dataset:
Rab8A and Rab13 are activated by insulin and regulate GLUT4 translocation in muscle cells
Authors: Sun Yi , Bilan Philip J. , Liu Zhi , Klip Amira
Published: November 2010

Skeletal muscle is the primary site of dietary glucose disposal, a function that depends on insulin-mediated exocytosis of GLUT4 vesicles to its cell surface. In skeletal muscle and adipocytes, this response involves Akt signaling to the Rab-GAP (GTPase-activating protein) AS160/TBC1D4. Intriguingly, the AS160-targeted Rabs appear to differ, with Rab8A participating in GLUT4 exocytosis in muscle cells and Rab10 in adipocytes, and their activation by insulin is unknown. Rabs 8A, 10, and 13 belong to the same subfamily of Rab-GTPases. Here we show that insulin promotes GTP loading of Rab13 and Rab8A but not Rab10 in rat L6 muscle cells, Rab8A activation preceding that of Rab13. siRNA-mediated Rab13 knockdown blocked the insulin-induced increase of GLUT4 at the muscle cell surface that was rescued by a Rab13 ortholog but not by Rab8A. Constitutively active AS160 lowered basal and insulin-stimulated levels of surface GLUT4, effects that were reversed by overexpressing Rab8A or Rab13, suggesting that both Rabs are targets of AS160-GAP activity in the context of GLUT4 traffic. Rab13 had a broader intracellular distribution compared with the perinuclear restriction of Rab8A, and insulin promoted Rab13 colocalization with GLUT4 at the cell periphery. We conclude that Rab13 and Rab8A are Rab-GTPases activated by insulin, and that downstream of AS160 they regulate traffic of GLUT4 vesicles, possibly acting at distinct steps and sites. These findings close in on the series of events regulating muscle GLUT4 traffic in response to insulin, crucial for whole-body glucose homeostasis.
Role of tyrosyl-DNA phosphodiesterase (TDP1) in mitochondria
Authors: Das Benu Brata , Dexheimer Thomas S. , Maddali Kasthuraiah , Pommier Yves
Published: November 2010

Human tyrosyl-DNA phosphodiesterase (TDP1) hydrolyzes the phosphodiester bond at a DNA 3′-end linked to a tyrosyl moiety and has been implicated in the repair of topoisomerase I (Top1)-DNA covalent complexes. TDP1 can also hydrolyze other 3′-end DNA alterations including 3′-phosphoglycolate and 3′-abasic sites, and exhibits 3′-nucleosidase activity indicating it may function as a general 3′-end-processing DNA repair enzyme. Here, using laser confocal microscopy, subcellular fractionation and biochemical analyses we demonstrate that a fraction of the TDP1 encoded by the nuclear TDP1 gene localizes to mitochondria. We also show that mitochondrial base excision repair depends on TDP1 activity and provide evidence that TDP1 is required for efficient repair of oxidative damage in mitochondrial DNA. Together, our findings provide evidence for TDP1 as a novel mitochondrial enzyme.
Metal-organic charge transfer can produce biradical states and is mediated by conical intersections
Authors: Tishchenko Oksana , Li Ruifang , Truhlar Donald G.
Published: October 2010

The present paper illustrates key features of charge transfer between calcium atoms and prototype conjugated hydrocarbons (ethylene, benzene, and coronene) as elucidated by electronic structure calculations. One- and two-electron charge transfer is controlled by two sequential conical intersections. The two lowest electronic states that undergo a conical intersection have closed-shell and open-shell dominant configurations correlating with the 4
s
2
and 4
s
1
3
d
1
states of Ca, respectively. Unlike the neutral-ionic state crossing in, for example, hydrogen halides or alkali halides, the path from separated reactants to the conical intersection region is uphill and the charge-transferred state is a biradical. The lowest-energy adiabatic singlet state shows at least two minima along a single approach path of Ca to the π system: (
i
) a van der Waals complex with a doubly occupied highest molecular orbital, denoted

, and a small negative charge on Ca and (
ii
) an open-shell singlet (biradical) at intermediate approach (Ca⋯C distance ≈2.5–2.7 
Å
) with molecular orbital structure
ϕ
1
ϕ
2
, where
ϕ
2
is an orbital showing significant charge transfer form Ca to the π-system, leading to a one-electron multicentered bond. A third minimum (
iii
) at shorter distances along the same path corresponding to a closed-shell state with molecular orbital structure

has also been found; however, it does not necessarily represent the ground state at a given Ca⋯C distance in all three systems. The topography of the lowest adiabatic singlet potential energy surface is due to the one- and two-electron bonding patterns in Ca-π complexes.
Trading carbon for food: Global comparison of carbon stocks vs. crop yields on agricultural land
Authors: West Paul C. , Gibbs Holly K. , Monfreda Chad , Wagner John , Barford Carol C. , Carpenter Stephen R. , Foley Jonathan A.
Published: November 2010

Expanding croplands to meet the needs of a growing population, changing diets, and biofuel production comes at the cost of reduced carbon stocks in natural vegetation and soils. Here, we present a spatially explicit global analysis of tradeoffs between carbon stocks and current crop yields. The difference among regions is striking. For example, for each unit of land cleared, the tropics lose nearly two times as much carbon (∼120 tons·ha−1vs. ∼63 tons·ha−1) and produce less than one-half the annual crop yield compared with temperate regions (1.71 tons·ha−1·y−1vs. 3.84 tons·ha−1·y−1). Therefore, newly cleared land in the tropics releases nearly 3 tons of carbon for every 1 ton of annual crop yield compared with a similar area cleared in the temperate zone. By factoring crop yield into the analysis, we specify the tradeoff between carbon stocks and crops for all areas where crops are currently grown and thereby, substantially enhance the spatial resolution relative to previous regional estimates. Particularly in the tropics, emphasis should be placed on increasing yields on existing croplands rather than clearing new lands. Our high-resolution approach can be used to determine the net effect of local land use decisions.
Structural basis for the one-pot formation of the diarylheptanoid scaffold by curcuminoid synthase from
Oryza sativa
Authors: Morita Hiroyuki , Wanibuchi Kiyofumi , Nii Hirohiko , Kato Ryohei , Sugio Shigetoshi , Abe Ikuro
Published: November 2010

Curcuminoid synthase (CUS) from
Oryza sativa
is a plant-specific type III polyketide synthase (PKS) that catalyzes the remarkable one-pot formation of the C
6
-C
7
-C
6
diarylheptanoid scaffold of bisdemethoxycurcumin, by the condensation of two molecules of 4-coumaroyl-CoA and one molecule of malonyl-CoA. The crystal structure of
O. sativa
CUS was solved at 2.5-Å resolution, which revealed a unique, downward expanding active-site architecture, previously unidentified in the known type III PKSs. The large active-site cavity is long enough to accommodate the two C
6
-C
3
coumaroyl units and one malonyl unit. Furthermore, the crystal structure indicated the presence of a putative nucleophilic water molecule, which forms hydrogen bond networks with Ser351-Asn142-H
2
O-Tyr207-Glu202, neighboring the catalytic Cys174 at the active-site center. These observations suggest that CUS employs unique catalytic machinery for the one-pot formation of the C
6
-C
7
-C
6
scaffold. Thus, CUS utilizes the nucleophilic water to terminate the initial polyketide chain elongation at the diketide stage. Thioester bond cleavage of the enzyme-bound intermediate generates 4-coumaroyldiketide acid, which is then kept within the downward expanding pocket for subsequent decarboxylative condensation with the second 4-coumaroyl-CoA starter, to produce bisdemethoxycurcumin. The structure-based site-directed mutants, M265L and G274F, altered the substrate and product specificities to accept 4-hydroxyphenylpropionyl-CoA as the starter to produce tetrahydrobisdemethoxycurcumin. These findings not only provide a structural basis for the catalytic machinery of CUS but also suggest further strategies toward expanding the biosynthetic repertoire of the type III PKS enzymes.
Interactions between internal forces, body stiffness, and fluid environment in a neuromechanical model of lamprey swimming
Authors: Tytell Eric D. , Hsu Chia-Yu , Williams Thelma L. , Cohen Avis H. , Fauci Lisa J.
Published: October 2010

Animal movements result from a complex balance of many different forces. Muscles produce force to move the body; the body has inertial, elastic, and damping properties that may aid or oppose the muscle force; and the environment produces reaction forces back on the body. The actual motion is an emergent property of these interactions. To examine the roles of body stiffness, muscle activation, and fluid environment for swimming animals, a computational model of a lamprey was developed. The model uses an immersed boundary framework that fully couples the Navier–Stokes equations of fluid dynamics with an actuated, elastic body model. This is the first model at a Reynolds number appropriate for a swimming fish that captures the complete fluid-structure interaction, in which the body deforms according to both internal muscular forces and external fluid forces. Results indicate that identical muscle activation patterns can produce different kinematics depending on body stiffness, and the optimal value of stiffness for maximum acceleration is different from that for maximum steady swimming speed. Additionally, negative muscle work, observed in many fishes, emerges at higher tail beat frequencies without sensory input and may contribute to energy efficiency. Swimming fishes that can tune their body stiffness by appropriately timed muscle contractions may therefore be able to optimize the passive dynamics of their bodies to maximize peak acceleration or swimming speed.
Mechanism of ligand-gated potassium efflux in bacterial pathogens
Authors: Roosild Tarmo P. , Castronovo Samantha , Healy Jess , Miller Samantha , Pliotas Christos , Rasmussen Tim , Bartlett Wendy , Conway Stuart J. , Booth Ian R.
Published: November 2010

Gram negative pathogens are protected against toxic electrophilic compounds by glutathione-gated potassium efflux systems (Kef) that modulate cytoplasmic pH. We have elucidated the mechanism of gating through structural and functional analysis of
Escherichia coli
KefC. The revealed mechanism can explain how subtle chemical differences in glutathione derivatives can produce opposite effects on channel function. Kef channels are regulated by potassium transport and NAD-binding (KTN) domains that sense both reduced glutathione, which inhibits Kef activity, and glutathione adducts that form during electrophile detoxification and activate Kef. We find that reduced glutathione stabilizes an interdomain association between two KTN folds, whereas large adducts sterically disrupt this interaction. F441 is identified as the pivotal residue discriminating between reduced glutathione and its conjugates. We demonstrate a major structural change on the binding of an activating ligand to a KTN-domain protein. Analysis of the regulatory interactions suggests strategies to disrupt pathogen potassium and pH homeostasis.
Cell division cycle 6, a mitotic substrate of polo-like kinase 1, regulates chromosomal segregation mediated by cyclin-dependent kinase 1 and separase
Authors: Yim Hyungshin , Erikson Raymond L.
Published: November 2010

Defining the links between cell division and DNA replication is essential for understanding normal cell cycle progression and tumorigenesis. In this report we explore the effect of phosphorylation of cell division cycle 6 (Cdc6), a DNA replication initiation factor, by polo-like kinase 1 (Plk1) on the regulation of chromosomal segregation. In mitosis, the phosphorylation of Cdc6 was highly increased, in correlation with the level of Plk1, and conversely, Cdc6 is hypophosphorylated in Plk1-depleted cells, although cyclin A- and cyclin B1-dependent kinases are active. Binding between Cdc6 and Plk1 occurs through the polo-box domain of Plk1, and Cdc6 is phosphorylated by Plk1 on T37. Immunohistochemistry studies reveal that Cdc6 and Plk1 colocalize to the central spindle in anaphase. Expression of T37V mutant of Cdc6 (Cdc6-TV) induces binucleated cells and incompletely separated nuclei. Wild-type Cdc6 but not Cdc6-TV binds cyclin-dependent kinase 1 (Cdk1). Expression of wild-type Plk1 but not kinase-defective mutant promotes the binding of Cdc6 to Cdk1. Cells expressing wild-type Cdc6 display lower Cdk1 activity and higher separase activity than cells expressing Cdc6-TV. These results suggest that Plk1-mediated phosphorylation of Cdc6 promotes the interaction of Cdc6 and Cdk1, leading to the attenuation of Cdk1 activity, release of separase, and subsequent anaphase progression.
Selective inhibition of histone deacetylase 6 (HDAC6) induces DNA damage and sensitizes transformed cells to anticancer agents
Authors: Namdar Mandana , Perez Gisela , Ngo Lang , Marks Paul A.
Published: October 2010

Histone deacetylase 6 (HDAC6) is structurally and functionally unique among the 11 human zinc-dependent histone deacetylases. Here we show that chemical inhibition with the HDAC6-selective inhibitor tubacin significantly enhances cell death induced by the topoisomerase II inhibitors etoposide and doxorubicin and the pan-HDAC inhibitor SAHA (vorinostat) in transformed cells (LNCaP, MCF-7), an effect not observed in normal cells (human foreskin fibroblast cells). The inactive analogue of tubacin, nil-tubacin, does not sensitize transformed cells to these anticancer agents. Further, we show that down-regulation of HDAC6 expression by shRNA in LNCaP cells enhances cell death induced by etoposide, doxorubicin, and SAHA. Tubacin in combination with SAHA or etoposide is more potent than either drug alone in activating the intrinsic apoptotic pathway in transformed cells, as evidenced by an increase in PARP cleavage and partial inhibition of this effect by the pan-caspase inhibitor Z-VAD-fmk. HDAC6 inhibition with tubacin induces the accumulation of γH2AX, an early marker of DNA double-strand breaks. Tubacin enhances DNA damage induced by etoposide or SAHA as indicated by increased accumulation of γH2AX and activation of the checkpoint kinase Chk2. Tubacin induces the expression of DDIT3 (CHOP/GADD153), a transcription factor up-regulated in response to cellular stress. DDIT3 induction is further increased when tubacin is combined with SAHA. These findings point to mechanisms by which HDAC6-selective inhibition can enhance the efficacy of certain anti-cancer agents in transformed cells.
Tumor necrosis factor-α triggers a cytokine cascade yielding postoperative cognitive decline
Authors: Terrando Niccolò , Monaco Claudia , Ma Daqing , Foxwell Brian M. J. , Feldmann Marc , Maze Mervyn
Published: November 2010

Cognitive decline following surgery in older individuals is a major clinical problem of uncertain mechanism; a similar cognitive decline also follows severe infection, chemotherapy, or trauma and is currently without effective therapy. A variety of mechanisms have been proposed, and exploring the role of inflammation, we recently reported the role of IL-1β in the hippocampus after surgery in mice with postoperative cognitive dysfunction. Here, we show that TNF-α is upstream of IL-1 and provokes its production in the brain. Peripheral blockade of TNF-α is able to limit the release of IL-1 and prevent neuroinflammation and cognitive decline in a mouse model of surgery-induced cognitive decline. TNF-α appears to synergize withMyD88, the IL-1/TLR superfamily common signaling pathway, to sustain postoperative cognitive decline. Taken together, our results suggest a unique therapeutic potential for preemptive treatment with anti-TNF antibody to prevent surgery-induced cognitive decline.
Tokamak equilibria with nearly zero central current: the current hole
Authors: Fujita Takaaki
Published: November 2010

The observation of stable sustainment of the ‘current hole’, namely the nearly zero current density region in the central part of a tokamak plasma, has opened a new class of configurations in tokamak plasmas, and a variety of research from the viewpoints of equilibrium, magnetohydrodynamics (MHD) stability, particle orbits and radial transport has been generated. Some theories and codes have been tested and extended by being applied to extreme conditions in the current hole with very weak poloidal field. The current hole is generated due to a transient negative toroidal electric field established when a large off-axis non-inductive current is rapidly formed. It has been observed in high confinement plasmas with a large fraction of bootstrap current in advanced tokamak operation. The current hole is very stiff against current drive, which suggests that it is a saturated or self-organized system. Appearance of the current hole in ITER and DEMO would be expected in some of the operation scenarios, and its influence and its control methods have been studied. Results of experimental and theoretical studies on the current hole are reviewed.
A variable selection method for genome-wide association studies
Authors: He Qianchuan , Lin Dan-Yu
Published: October 2010

Motivation: Genome-wide association studies (GWAS) involving half a million or more single nucleotide polymorphisms (SNPs) allow genetic dissection of complex diseases in a holistic manner. The common practice of analyzing one SNP at a time does not fully realize the potential of GWAS to identify multiple causal variants and to predict risk of disease. Existing methods for joint analysis of GWAS data tend to miss causal SNPs that are marginally uncorrelated with disease and have high false discovery rates (FDRs).

Results: We introduce GWASelect, a statistically powerful and computationally efficient variable selection method designed to tackle the unique challenges of GWAS data. This method searches iteratively over the potential SNPs conditional on previously selected SNPs and is thus capable of capturing causal SNPs that are marginally correlated with disease as well as those that are marginally uncorrelated with disease. A special resampling mechanism is built into the method to reduce false positive findings. Simulation studies demonstrate that the GWASelect performs well under a wide spectrum of linkage disequilibrium patterns and can be substantially more powerful than existing methods in capturing causal variants while having a lower FDR. In addition, the regression models based on the GWASelect tend to yield more accurate prediction of disease risk than existing methods. The advantages of the GWASelect are illustrated with the Wellcome Trust Case-Control Consortium (WTCCC) data.

Availability: The software implementing GWASelect is available at http://www.bios.unc.edu/~lin.

Access to WTCCC data: http://www.wtccc.org.uk/

Contact:  lin@bios.unc.edu

Supplementary information:  Supplementary data are available at Bioinformatics Online.
Benchmarking the performance of human antibody gene alignment utilities using a 454 sequence dataset
Authors: Jackson Katherine J. L. , Boyd Scott , Gaëta Bruno A. , Collins Andrew M.
Published: October 2010

Motivation: Immunoglobulin heavy chain genes are formed by recombination of genes randomly selected from sets of IGHV, IGHD and IGHJ genes. Utilities have been developed to identify genes that contribute to observed VDJ rearrangements, but in the absence of datasets of known rearrangements, the evaluation of these utilities is problematic. We have analyzed thousands of VDJ rearrangements from an individual (S22) whose IGHV, IGHD and IGHJ genotype can be inferred from the dataset. Knowledge of this genotype means that the Stanford_S22 dataset can serve to benchmark the performance of IGH alignment utilities.

Results: We evaluated the performance of seven utilities. Failure to partition a sequence into genes present in the S22 genome was considered an error, and error rates for different utilities ranged from 7.1% to 13.7%.

Availability:  Supplementary data includes the S22 genotypes and alignments. The Stanford_S22 dataset and an evaluation tool is available at http://www.emi.unsw.edu.au/~ihmmune/IGHUtilityEval/.

Contact:  katherine.jackson@unsw.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
Submaximal exercise gas exchange is an important prognostic tool to predict adverse outcomes in heart failure
Authors: Woods Paul R. , Bailey Kent R. , Wood Christina M. , Johnson Bruce D.
Published: October 2010

Aims

Traditionally, VO2peak has been used to determine prognosis in heart failure; however, this measure has limitations. Hence, other exercise and gas exchange parameters measured submaximally, e.g. breathing efficiency (VE/VCO2), end‐tidal CO2 (PETCO2), oxygen uptake efficiency slope (OUES), and circulatory power [ systolic blood pressure (SBP)], have been investigated. The aim of this study was to investigate the prognostic relevance of submaximal exercise gas exchange in heart failure patients.

Method and results

One hundred and thirty‐two consecutive heart failure patients (mean age 56 ± 12 years, ejection fraction 29 ± 11%) performed peak treadmill testing. Gas exchange and haemodynamic variables were measured continuously. Gas exchange data obtained from the first 2 min of exercise and at a respiratory exchange ratio (RER) of 0.9 were the measurements of interest. Over a median follow‐up period of 62.4 (range 0–114) months, there were 44 endpoints (death or transplant). Univariate analysis demonstrated submaximal predictors of survival, which included VE/VCO2 slope and ratio, PETCO2, OUES, and circulatory power (P≤ 0.01). When these and additional submaximal variables were included together in the multivariable analysis, the strongest submaximal exercise predictive model (C‐statistic 0.75) comprised data from the first stage of exercise (VE and circulatory power) and at an RER of 0.9 (VE/VCO2 ratio). The inclusion of VO2peak and demographic data, with submaximal data (VE/VCO2 ratio at an RER = 0.9), increased the predictiveness of the model (C‐statistic 0.78).

Conclusion

Submaximal exercise measures provide useful prognostic information for predicting survival in heart failure. This form of testing is logistically easier, cheaper, and safer for patients compared with maximal exercise.
Use of B‐type natriuretic peptide in the management of hypoxaemic respiratory failure
Authors: Noveanu Markus , Pargger Hans , Breidthardt Tobias , Reichlin Tobias , Schindler Christian , Heise Antje , Schoenenberger Ronald , Manndorff Patricia , Siegemund Martin , Mebazaa Alexandre , Marsch Stephan , Mueller Christian
Published: October 2010

Aims

Evaluation and management of patients with hypoxaemic respiratory failure in the intensive care unit (ICU) are difficult. The use of B‐type natriuretic peptide (BNP), a quantitative marker of cardiac stress and heart failure (HF), may be helpful. The purpose of this study is to describe the prevalence of causative disorders of hypoxaemic respiratory failure in the ICU and to determine the impact of a BNP‐guided diagnostic strategy.

Methods and results

This prospective, multi‐centre, randomized, single‐blind, controlled trial included 314 ICU patients with hypoxaemic respiratory failure: 159 patients were randomly assigned to a diagnostic strategy involving the measurement of BNP and 155 were assessed in a standard manner. The time to discharge and the total cost of treatment were the primary endpoints. Hypoxaemic respiratory failure was multi‐causal in 27% of the patients. Heart failure was the most common diagnosis in both groups. The use of BNP levels, in conjunction with other clinical information, significantly increased the detection of HF in combination with an additional diagnosis (32 vs. 16%, P = 0.001) and also increased the application of HF‐specific medical therapy (nitrates: 32 vs. 23%, P < 0.05 and diuretics: 65 vs. 50%, P < 0.01). Time to discharge (median, 13 vs.14 days, P = 0.50) and total cost of treatment (median, US‐$6190 vs. 7155, P = 0.24) were comparable in both groups.

Conclusion

Hypoxaemic respiratory failure in the ICU is often a multi‐causal disorder. The use of BNP increased the detection of HF, but did not significantly improve patient management as quantified by time to discharge or treatment cost. ClinicalTrials.gov Identifier: NCT00130559.
Regulation and Symbiotic Role of nirK and norC Expression in Rhizobium etli
Authors: Gómez-Hernández Nicolás , Reyes-González Alma , Sánchez Cristina , Mora Yolanda , Delgado María J. , Girard Lourdes
Published: November 2010

Rhizobium etli CFN42 is unable to use nitrate for respiration and lacks nitrate reductase activity as well as the nap or nar genes encoding respiratory nitrate reductase. However, genes encoding proteins closely related to denitrification enzymes, the norCBQD gene cluster and a novel nirKnirVnnrRnnrU operon are located on pCFN42f. In this study, we carried out a genetic and functional characterization of the reductases encoded by the R. etli nirK and norCB genes. By gene fusion expression analysis in free-living conditions, we determined that R. etli regulates its response to nitric oxide through NnrR via the microaerobic expression mediated by FixKf. Interestingly, expression of the norC and nirK genes displays a different level of dependence for NnrR. A null mutation in nnrR causes a drastic drop in the expression of norC, while nirK still exhibits significant expression. A thorough analysis of the nirK regulatory region revealed that this gene is under both positive and negative regulation. Functional analysis carried out in this work demonstrated that reduction of nitrite and nitric oxide in R. etli requires the reductase activities encoded by the norCBQD and nirK genes. Levels of nitrosylleghemoglobin complexes in bean plants exposed to nitrate are increased in a norC mutant but decreased in a nirK mutant. The nitrate-induced decline in nitrogenase-specific activity observed in both the wild type and the norC mutant was not detected in the nirK mutant. This data indicate that bacterial nitrite reductase is an important contributor to the formation of NO in bean nodules in response to nitrate.
A Further Examination of the Relation Between Trait Anger and Alcohol‐Related Aggression: The Role of Anger Control
Authors: Parrott Dominic J. , Giancola Peter R.
Published: November 2010

Background: Trait anger has been identified as a risk factor for alcohol‐related aggression. However, to develop a more accurate risk profile, it is necessary to examine the interactive relations between trait anger and other key personality variables. The present study examined the influence of anger control on alcohol‐related aggression.

Methods: Participants were 164 social drinking men age 21–35 years old. Trait anger and anger control were assessed with the State‐Trait Anger Expression Inventory (Spielberger, 1996). Following consumption of an alcoholic or placebo beverage, participants competed in an aggression paradigm in which electric shocks were received from and administered to a fictitious opponent during a competitive reaction time task. Aggression was operationalized as shock intensities administered to the opponent under conditions of low and high provocation.

Results: Analyses indicated that trait anger significantly predicted aggression, but only among men who were intoxicated and reported low levels of anger control.

Conclusions: The present findings suggest that anger control may be a crucial risk factor in determining whether one's anger proneness will lead to intoxicated aggression following provocation.
Controlled and Behaviorally Relevant Levels of Oral Ethanol Intake in Rhesus Macaques Using a Flavorant‐Fade Procedure
Authors: Katner Simon N. , Flynn Claudia T. , Von Huben Stefani N. , Kirsten Amber J. , Davis Sophia A. , Lay Christopher C. , Cole Maury , Roberts Amanda J. , Fox Howard S. , Taffe Michael A.
Published: November 2010

Background: Flavorant‐fading procedures can initiate and maintain oral ethanol intake in rodents. The present study developed a similar procedure to achieve controlled and behaviorally relevant levels of ethanol intake in monkeys.

Methods: Male rhesus macaques (N= 13) were initially given the opportunity to consume 0.5 g/kg of a 1% (w/v) ethanol plus 4% (w/v) Tang solution in 1‐hr limited‐access sessions without the requirement of an operant response. Once consumption was stable at a particular concentration (%) and/or amount (g/kg), animals were given access to higher concentrations and/or amounts of ethanol. Animals were tested on a bimanual motor skill (BMS) task 20 and 90 min after consumption to assess behavioral impairment. Blood alcohol levels (BALs) were assessed after a session in which animals had the opportunity to consume up to 3.0 g/kg of 6% (w/v) ethanol.

Results: The gradual fading up of higher concentrations and amounts of ethanol resulted in controlled and robust levels (>2.0 g/kg) of ethanol intake in half of the subjects. Increasing the concentration of the sweetener from 4 to 6% (w/v) was effective in initiating consumption in three animals. Two monkeys required the additional step of presenting the increased‐sweetener solutions after a meal (postprandial consumption) to initiate significant ethanol intake. Animals were significantly impaired on the BMS task after consumption of 2.0, 2.5, and 3.0 g/kg of ethanol. Individual consumption ranging from 0.8 to 3.0 g/kg of ethanol produced BALs of 18 to 269 mg/dl.

Conclusions: The flavorant‐fading procedure was effective in producing behaviorally relevant levels of ethanol consumption in rhesus macaques. This model facilitated a randomized‐dose procedure to determine the behavioral effects of 0.5 to 3.0 g/kg of ethanol. This procedure therefore is of significant utility in determining behavioral or physiologic effects of specific doses of consumed ethanol in monkeys.
Interactions of Alcohol Dehydrogenase to p‐Hydroxyacetophenone–sepharose and p‐Acetamidophenol‐sepharose
Authors: Negoro Munetaka , Wakabayashi Ichiro
Published: November 2010

Abstract: Background: p‐Hydroxyacetophenone (HAP)‐sepharose is known to be an effective ligand for isolation of aldehyde dehydrogenase and chloramphenicol acetyltransferase. In this study, we investigated ligand specificities to alcohol dehydrogenase (ADH) using p‐HAP‐sepharose and p‐acetamidophenol (AAP)‐sepharose.

Methods: p‐HAP and p‐AAP were coupled to epoxy‐activated sepharose and used as ligands for affinity chromatography to detect binding proteins. Fractions of affinity chromatography were collected and separated by SDS‐PAGE. Commassie brilliant blue staining was carried out for detecting proteins. For determining protein sequences, polypeptide was separated by HPLC after cleavage of Lys‐specific protease digestion.

Results: p‐HAP ligands have the ability to bind to seven proteins, including class I ADH extracted from a rat cytosolic fraction as well as HLADH (horse liver ADH). p‐HAP, p‐AAP and benzaldehyde (10 mM each) could elute HLADH from the complex of HLADH‐pHAP‐sepharose column. On the other hand, p‐AAP‐sepharose has no ability to bind to HLADH, although three proteins from a rat liver cytosolic fraction were found to be able to bind to p‐AAP‐sepharose.

Conclusions: p‐HAP binds to ADH in a structure‐specific manner and this binding is nonspecific to species of origin of ADH.
High-performance spider webs: integrating biomechanics, ecology and behaviour
Authors: Harmer Aaron M. T. , Blackledge Todd A. , Madin Joshua S. , Herberstein Marie E.
Published: October 2010

Spider silks exhibit remarkable properties, surpassing most natural and synthetic materials in both strength and toughness. Orb-web spider dragline silk is the focus of intense research by material scientists attempting to mimic these naturally produced fibres. However, biomechanical research on spider silks is often removed from the context of web ecology and spider foraging behaviour. Similarly, evolutionary and ecological research on spiders rarely considers the significance of silk properties. Here, we highlight the critical need to integrate biomechanical and ecological perspectives on spider silks to generate a better understanding of (i) how silk biomechanics and web architectures interacted to influence spider web evolution along different structural pathways, and (ii) how silks function in an ecological context, which may identify novel silk applications. An integrative, mechanistic approach to understanding silk and web function, as well as the selective pressures driving their evolution, will help uncover the potential impacts of environmental change and species invasions (of both spiders and prey) on spider success. Integrating these fields will also allow us to take advantage of the remarkable properties of spider silks, expanding the range of possible silk applications from single threads to two- and three-dimensional thread networks.
Yersinia pekkanenii sp. nov.
Authors: Murros-Kontiainen Anna , Johansson Per , Niskanen Taina , Fredriksson-Ahomaa Maria , Korkeala Hannu , Björkroth Johanna
Published: October 2010

The taxonomic position of three strains from water, soil and lettuce samples was studied by using a polyphasic taxonomic approach. The strains were reported to lack the virulence-encoding genes inv and virF in a previous study. Controversially, API 20 E and some other phenotypic tests suggested that the strains belong to Yersinia pseudotuberculosis, which prompted this polyphasic taxonomic study. In both the phylogenetic analyses of four housekeeping genes (glnA, gyrB, recA and HSP60) and numerical analyses of HindIII and EcoRI ribopatterns, the strains formed a separate group within the genus Yersinia. Analysis of the 16S rRNA gene sequences showed that the strains were related to Yersinia aldovae and Yersinia mollaretii, but DNA–DNA hybridization analysis differentiated them from these species. Based on the results of the phylogenetic and DNA–DNA hybridization analyses, a novel species, Yersinia pekkanenii sp. nov., is proposed. The type strain is ÅYV7.1KOH2T ( = DSM 22769T  = LMG 25369T).
Proposal that Mycobacterium massiliense and Mycobacterium bolletii be united and reclassified as Mycobacterium abscessus subsp. bolletii comb. nov., designation of Mycobacterium abscessus subsp. abscessus subsp. nov. and emended description of Mycobacterium abscessus
Authors: Leao Sylvia Cardoso , Tortoli Enrico , Euzéby Jean Paul , Garcia Maria Jesus
Published: October 2010

The names ‘Mycobacterium abscessus subsp. abscessus’ and ‘Mycobacterium abscessus subsp. massiliense’, proposed by Leao et al. (2009, J Clin Microbiol
47, 2691–2698), cannot be validly published. The purpose of this report is to provide a description in accordance with the Rules of the Bacteriological Code (1990 Revision). Moreover, the proposal of the name ‘Mycobacterium abscessus subsp. massiliense’ is contrary to Rule 38 and the correct name of this taxon, at the rank of subspecies, is Mycobacterium abscessus subsp. bolletii comb. nov. A description of Mycobacterium abscessus subsp. abscessus subsp. nov. and an emended description of Mycobacterium abscessus are also given.
Yersinia nurmii sp. nov.
Authors: Murros-Kontiainen Anna , Fredriksson-Ahomaa Maria , Korkeala Hannu , Johansson Per , Rahkila Riitta , Björkroth Johanna
Published: October 2010

This study was set up to identify three Gram-negative, rod-shaped strains originating from broiler meat packaged under a modified atmosphere. A polyphasic taxonomic approach, including multilocus sequence analysis (MLSA) of five genes (16S rRNA, glnA, gyrB, recA and HSP60), DNA–DNA reassociation between the closest phylogenetic neighbours and determination of relevant phenotypic properties, was applied. Phylogenetic analysis of the 16S rRNA gene sequences grouped these strains together and within the genus Yersinia. MLSA of the 16S rRNA gene and four housekeeping genes showed that the strains formed a monophyletic group separate from other Yersinia species in all phylogenetic trees constructed. The strains had a phenotypic profile different from those of other representatives of the genus Yersinia, but most similar to that of Yersinia ruckeri. Typical virulence markers for pathogenic Yersinia were not detected. Based on phylogenetic, phenotypic and DNA–DNA reassociation data, a novel species, Yersinia nurmii sp. nov., is proposed for the isolated strains. The type strain is APN3a-cT ( = DSM 22296T  = LMG 25213T).
Pseudomonas bauzanensis sp. nov., isolated from soil
Authors: Zhang De-Chao , Liu Hong-Can , Zhou Yu-Guang , Schinner Franz , Margesin Rosa
Published: October 2010

A Gram-negative, aerobic, motile rod, designated BZ93T, was isolated from soil from an industrial site. The strain grew at 5–30 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ93T was related to members of the genus Pseudomonas and was related most closely to Pseudomonas xiamenensis C10-2T (97.8 % 16S rRNA gene sequence similarity) and Pseudomonas pertucinogena IFO 14163T (97.4 %). The predominant cellular fatty acids of strain BZ93T were C18 : 1ω7c (54.8 %), summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH; 10.3 %), C16 : 0 (9.9 %) and C17 : 0 cyclo (7.4 %). The major quinone was ubiquinone 9. The major phospholipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unknown phospholipid. The genomic DNA G+C content was 61.8 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness, a novel species, Pseudomonas bauzanensis sp. nov., is proposed. The type strain is BZ93T ( = DSM 22558T  = CGMCC 1.9095T = LMG 26048T).
Leucobacter celer sp. nov., isolated from Korean fermented seafood
Authors: Shin Na-Ri , Kim Min-Soo , Jung Mi-Ja , Roh Seong Woon , Nam Young-Do , Park Eun-Jin , Bae Jin-Woo
Published: October 2010

A novel, Gram-reaction-positive, aerobic, rod-shaped, non-motile bacterial strain, designated NAL101T, was isolated from gajami-sikhae, a traditional Korean fermented seafood made of flatfish. Growth occurred at 4–45 °C, at pH 5–10 and in 0–12 % (w/v) NaCl. Optimum growth occurred at 30–37 °C, at pH 8 and in 0–1 % (w/v) NaCl. The cell-wall amino acids were 2,4-diaminobutyric acid, alanine, glycine, threonine and glutamic acid and the major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The predominant menaquinone was MK-11. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid. The 16S rRNA gene sequence of strain NAL101T showed 97.7 % similarity to that of Leucobacter chironomi MM2LBT, its closest relative. The DNA G+C content was 68.8 mol% and DNA–DNA hybridization values with closely related strains were <22 %. Phylogenetic analyses based on 16S rRNA gene sequences as well as differences in its physiological and biochemical characteristics indicated that strain NAL101T represents a novel species of the genus Leucobacter in the family Microbacteriaceae, for which the name Leucobacter celer sp. nov. is proposed. The type strain is NAL101T ( = KACC 14220T  = JCM 16465T).
Glaciecola arctica sp. nov., isolated from Arctic marine sediment
Authors: Zhang Yan-Jiao , Zhang Xi-Ying , Mi Zi-Hao , Chen Chun-Xiao , Gao Zhao-Ming , Chen Xiu-Lan , Yu Yong , Chen Bo , Zhang Yu-Zhong
Published: October 2010

A Gram-negative, motile, psychrotolerant, oxidase- and catalase-positive bacterium, designated BSs20135T, was isolated from Arctic marine sediment. Cells were straight or slightly curved rods and formed circular, convex and yellowish-brown colonies. Buds and prosthecae could be produced. The strain grew at 4–28 °C (optimum 25 °C) and with 1–5 % (w/v) NaCl (optimum 2 %) and hydrolysed aesculin and DNA, but did not reduce nitrate to nitrite. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain BSs20135T belonged to the genus Glaciecola and shared 93.6–97.7 % sequence similarity with the type strains of known species of the genus Glaciecola. The major cellular fatty acids of strain BSs20135T were summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C17 : 1ω8c and C18 : 1ω7c. The genomic DNA G+C content was 40.3 mol%. Based on 16S rRNA gene sequence analysis, DNA–DNA hybridization data and phenotypic and chemotaxonomic characterization, strain BSs20135T represents a novel species, for which the name Glaciecola arctica sp. nov. is proposed. The type strain is BSs20135T ( = CCTCC AB 209161T  = KACC 14537T).
Salinicoccus sesuvii sp. nov., isolated from the rhizosphere of Sesuvium portulacastrum
Authors: Kämpfer P. , Arun A. B. , Busse H.-J. , Young Chiu-Chung , Lai W.-A. , Rekha P. D. , Chen Wen-Ming
Published: October 2010

A Gram-staining-positive coccus, designated CC-SPL15-2T, was isolated from the rhizosphere of Sesuvium portulacastrum. By 16S rRNA gene sequence analysis, it was shown that strain CC-SPL15-2T belonged to the genus Salinicoccus. The isolate was most closely related to Salinicoccus hispanicus DSM 5352T (98.3 % 16S rRNA gene sequence similarity) and Salinicoccus roseus DSM 5351T (96.7 %); similarities to all other members of the genus Salinicoccus were <96.5 %. In accordance with characteristics of the genus Salinicoccus, the quinone system was mainly composed of menaquinone MK-6. The polar lipid profile exhibited the major components diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. In the polyamine pattern, spermidine was the predominant compound. The fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, which supported the affiliation of strain CC-SPL15-2T to the genus Salinicoccus. DNA–DNA relatedness between strain CC-SPL15-2T and S. hispanicus CCUG 43288T was 42 and 32 % (reciprocal analysis). From these data as well as from physiological and biochemical tests, a clear differentiation of strain CC-SPL15-2T from S. hispanicus and other members of the genus Salinicoccus was possible. We propose that strain CC-SPL15-2T be assigned to a novel species, with the name Salinicoccus sesuvii sp. nov. The type strain is CC-SPL15-2T ( = DSM 23267T  = CCM 7756T).
Aureibacter tunicatorum gen. nov., sp. nov., a marine bacterium isolated from a coral reef sea squirt, and description of Flammeovirgaceae fam. nov.
Authors: Yoon Jaewoo , Adachi Kyoko , Park Sanghwa , Kasai Hiroaki , Yokota Akira
Published: October 2010

Two aerobic, Gram-reaction-negative, golden-yellow pigmented and rod-shaped bacteria, designated strains A5Q-118T and A5Q-27, were isolated from an unidentified sea squirt that thrives in the coral reefs off the coast of Okinawa, Japan. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolates were affiliated with the family ‘Flammeovirgaceae’ of the phylum Bacteroidetes. Strains A5Q-118T and A5Q-27 shared 100 % sequence similarity with each other and showed <92 % similarity with other cultivated members of the family ‘Flammeovirgaceae’. The novel isolates were phenotypically and physiologically different from strains described previously. The DNA G+C content was 35.5–36.2 mol%, MK-7 was the major menaquinone and iso-C15 : 0 and C16 : 1ω5c were the major fatty acids. Based on the results of this polyphasic taxonomic study, it was concluded that strains A5Q-118T and A5Q-27 represent a novel species in a new genus of the family ‘Flammeovirgaceae’, for which the name Aureibacter tunicatorum gen. nov., sp. nov. is proposed. Proposal for designation of the Flammeovirgaceae fam. nov. is also presented. The type strain of Aureibacter tunicatorum is A5Q-118T ( = KCTC 23232T  = NBRC 107587T).
Dactylosporangium tropicum sp. nov., isolated from soil
Authors: Thawai Chitti , Tanasupawat Somboon , Kudo Takuji
Published: October 2010

Two novel actinomycete strains, designated KB2-4T and KB9-2, were isolated from soil samples. Both isolates formed finger-shaped sporangia on short sporangiophores that emerged directly from substrate hyphae. The cell-wall peptidoglycan contained glutamic acid, glycine, alanine and meso-diaminopimelic acid; the whole-cell sugars were galactose, glucose, mannose, rhamnose, ribose and xylose. The diagnostic phospholipid was phosphatidylethanolamine. The predominant menaquinones were MK-9(H8) and MK-9(H6). Mycolic acids were not detected. The predominant cellular fatty acids (>20 %) were iso-C16 : 0 and anteiso-C17 : 0. For both strains, the G+C content of the genomic DNA was about 72 mol%. The morphological and chemotaxonomic characteristics of the two strains were typical of members of the genus Dactylosporangium. Phylogenetic analysis using 16S rRNA gene sequences also indicated that these strains should be classified in the genus Dactylosporangium and showed that the closest relative was Dactylosporangium salmoneum NRRL B-16294T (99.1 % 16S rRNA gene sequence similarity). DNA–DNA relatedness and some physiological and biochemical properties indicated that the isolates could be readily distinguished from their closest phylogenetic relatives. On the basis of these phenotypic and genotypic data, the isolates represent a novel species, for which the name Dactylosporangium tropicum sp. nov. is proposed. The type strain is strain KB2-4T ( = BCC 34760T  = JCM 15673T).
Trichosporon xylopini sp. nov., a hemicellulose-degrading yeast isolated from the wood-inhabiting beetle Xylopinus saperdioides
Authors: Gujjari Pushpa , Suh Sung-Oui , Lee Ching-Fu , Zhou Jianlong J.
Published: October 2010

Four arthroconidium-producing yeasts were isolated from the gut of wood-inhabiting tenebrionid and passalid beetles. The rRNA genes of these yeast strains were sequenced, compared and analysed. The sequence results and other taxonomic characterizations placed two of the strains into Trichosporon porosum, and the remaining strains, EH024T and EH026 which were isolated from Xylopinus saperdioides (Coleoptera: Tenebrionidae), into a novel species of the genus Trichosporon in the Porosum clade. Strain EN6S23 was independently isolated from forest soil in Taiwan and was identified as the same novel species based on identical sequences in the internal transcribed spacers (ITS) and the D1/D2 region of the LSU rRNA gene and similar physiological characteristics to those of strains EH024T and EH026. The three strains can assimilate cellulose and xylan as sole carbon source, and are clearly distinguished from their closest taxon, T. porosum, by 14 nt differences in the ITS and D1/D2 region. These strains did not reproduce sexually under the laboratory conditions tested. The novel species is proposed as Trichosporon xylopini sp. nov. (type strain EH024T  = ATCC MYA-4670T  = CBS 11841T).