bluuebunny/crossref_metadata_2025 huggingface dataset:
Single-molecule inhibition of human kinesin by adociasulfate-13 and -14 from the spongeCladocroce aculeata
Authors: Smith Thomas E. , Hong Weili , Zachariah Malcolm M. , Harper Mary Kay , Matainaho Teatulohi K. , Van Wagoner Ryan M. , Ireland Chris M. , Vershinin Michael
Published: November 2013

Significance

Kinesin motor proteins are central to cellular processes and considered good drug targets, but very few reported kinesin inhibitors exhibit potential as drugs. Adociasulfates uniquely inhibit kinesins by competing with microtubules for binding. A declining interest in these compounds resulted from a report of large aggregates of adociasulfate-2 responsible for kinesin inhibition, poor cell permeability, and broad kinesin inhibition, limiting potential therapeutic applications. In this study, we show that kinesin inhibition is likely a 1:1 interaction and does not involve aggregates. We suggest a means by which cell permeability may be improved and show that adociasulfates inhibit kinesin-1 and -5 families of motors to a significantly different extent. These results collectively bring adociasulfates back to the foreground of chemical biology.
NMR reveals the allosteric opening and closing of Abelson tyrosine kinase by ATP-site and myristoyl pocket inhibitors
Authors: Skora Lukasz , Mestan Jürgen , Fabbro Doriano , Jahnke Wolfgang , Grzesiek Stephan
Published: November 2013

Significance

Current understanding of the interactions of Abelson tyrosine kinase (c-Abl) and other kinases with inhibitors is largely based on crystallographic structures. These present frozen snapshots of molecules and may not always reflect physiologically relevant conformations and dynamics. Our solution NMR study of various c-Abl complexes with allosteric and ATP-competitive inhibitors reveals a dynamic equilibrium between several c-Abl conformations that is distinctly modulated by both types of inhibitors. The observation of a hitherto unknown open state of the c-Abl•imatinib complex can explain an unusual dose–response in cellular inhibition assays. Our data provide detailed insight into the combined effect of the two inhibitor types, which is able to overcome drug resistance. This may have important implications for the development of new drugs.
Structural basis of ATG3 recognition by the autophagic ubiquitin-like protein ATG12
Authors: Metlagel Zoltan , Otomo Chinatsu , Takaesu Giichi , Otomo Takanori
Published: November 2013

Significance

Autophagy-related (ATG)12 is a ubiquitin-like protein essential to autophagy. It has been known for years that ATG12 is conjugated to the structural protein ATG5 and that the resulting protein–protein conjugate acts like an E3 enzyme that facilitates the attachment of the LC3 ubiquitin-like protein to a lipid molecule, phosphatidylethanolamine. However, the exact role of ATG12 in the E3 complex and the significance of ATG12 being a ubiquitin-like protein have remained elusive. We show that ATG12 binds to a short peptide region of the E2 enzyme ATG3 and describe the structural details of this interaction. This work establishes ATG12 as the ATG3 recruitment factor and explains how ATG12 uses its ubiquitin-like fold for binding to the ATG3 peptide.
Intracellular ATP binding is required to activate the slowly activating K
+
channel I
Ks
Authors: Li Yang , Gao Junyuan , Lu Zhongju , McFarland Kelli , Shi Jingyi , Bock Kevin , Cohen Ira S. , Cui Jianmin
Published: November 2013

Significance

We show that intracellular ATP at physiological concentrations acts as a signaling molecule to activate the slowly activating K
+
channel I
Ks
that regulates heart rate adaptation. ATP binding to the pore-forming α-subunit of I
Ks
, KCNQ1, allows the channel to open. Congenital mutations that reduce ATP binding or subsequent opening of the I
Ks
channel are associated with cardiac arrhythmias in human patients. Electrical abnormalities are often the cause of fatality in cardiovascular diseases, including ischemia and heart failure, in which ATP level is reduced in cardiac cells. Our results open up new possibilities to study and manage these diseases, and the ATP site provides a unique target for therapies.
Long-term depression triggers the selective elimination of weakly integrated synapses
Authors: Wiegert J. Simon , Oertner Thomas G.
Published: November 2013

Significance

Long-term plasticity, the ability of synapses to change their strength, is considered a possible basis of learning and memory. Extending the study of individual synapses to timescales relevant for behavior has been challenging: although rats can retain specific memories for several weeks, intracellular recordings that monitor the strength of individual synapses are typically limited to 1 h. Here we introduce an all-optical approach to stimulate and monitor synaptic function for 7 d. We show that long-term depression of hippocampal synapses significantly shortens their lifetime. While synapses with a high probability of transmitter release often recovered from depression, unreliable synapses were selectively removed from the circuit. Thus, specific activity patterns not only modulate synaptic weights but alter hippocampal connectivity.
Phytoplasmal infection derails genetically preprogrammed meristem fate and alters plant architecture
Authors: Wei Wei , Davis Robert Edward , Nuss Donald L. , Zhao Yan
Published: November 2013

Significance

In higher plants, the destiny of apical meristems (stem cells) is specific organogenesis, which determines the pattern of plant growth, and therefore morphotype and fertility. We found that bacterial infection can derail the meristems from their genetically preprogrammed destiny, altering plant morphogenesis. We identified four abnormal growth patterns, symptoms, in tomato infected with a cell wall-less bacterium, and found that each symptom corresponds to a distinct phase in meristem fate derailment. We unveiled molecular events that underlie the pathogen-induced meristem fate derailment and proposed a model to explain the phenomenon. Through probing the pathologically altered destiny of stem cells, our findings contribute to understanding plant growth and development under both normal and pathological conditions.
Regulation of glutamate receptor internalization by the spine cytoskeleton is mediated by its PKA-dependent association with CPG2
Authors: Loebrich Sven , Djukic Biljana , Tong Zachary J. , Cottrell Jeffrey R. , Turrigiano Gina G. , Nedivi Elly
Published: November 2013

Significance

Clathrin-mediated endocytosis (CME) of glutamate receptors from the postsynaptic membrane is central for adjusting synaptic strength and is thought to be the substrate for various forms of synaptic plasticity. The role of the actin cytoskeleton in CME is recognized as fundamental but remains poorly understood, and we lack a mechanistic understanding of the cytoskeletal/CME association, its functional consequences, and its regulation. Here we identify the activity-regulated
synaptic nuclear envelope 1
gene product candidate plasticity gene 2 (CPG2) as a direct functional link between the cytoskeleton and postsynaptic endocytosis, and as a nexus for the interaction of signaling pathways with the endocytic process. CPG2 reversibly associates with F-actin, and this association is positively regulated by PKA and is an important regulator of both glutamate receptor internalization and postsynaptic strength.
Epileptic baboons have lower numbers of neurons in specific areas of cortex
Authors: Young Nicole A. , Szabó C. Ákos , Phelix Clyde F. , Flaherty David K. , Balaram Pooja , Foust-Yeoman Kallie B. , Collins Christine E. , Kaas Jon H.
Published: November 2013

Significance

We examined the variability of neuron packing densities across cortical regions and areas in two baboons with spontaneous, untreated epilepsy and two baboons without epilepsy. The two baboons without epilepsy had the distribution of neocortical neurons expected for Old World monkeys and baboons, whereas the baboons with untreated epilepsy had reduced numbers of cortical neurons overall, with the greatest reductions in motor and frontal areas of the cortex, and with little or no reduction in the primary visual cortex. The results suggest that neuron loss may follow untreated seizure activity, and this loss is greatest in areas of the cortex related to motor functions.
Drosophila
switch gene
Sex-lethal
can bypass its switch-gene target
transformer
to regulate aspects of female behavior
Authors: Evans Daniel S. , Cline Thomas W.
Published: November 2013

Significance

The
Drosophila
master sex-determination switch gene,
Sex-lethal
(
Sxl
), was thought to elicit all aspects of female-specific somatic differentiation other than size dimorphism by acting on the gene
transformer
(
tra
) alone. Here we show that at least one aspect of
Drosophila
female-specific behavior, ovulation, is controlled by
Sxl
acting developmentally on some target(s) other than
tra
in a small subset of neurons in which, surprisingly, the
tra
target gene
fruitless
may function also. This minor branch in the sex-determination pathway should be useful for understanding how genes control behavior and perhaps also how, during evolution,
Sxl
managed to usurp the role of
tra
as the master regulator of sex determination relatively quickly in
Drosophila's
insect ancestors.
Focal targeting by human β-defensin 2 disrupts localized virulence factor assembly sites in
Enterococcus faecalis
Authors: Kandaswamy Kumaravel , Liew Tze Horng , Wang Charles Y. , Huston-Warren Emily , Meyer-Hoffert Ulf , Hultenby Kjell , Schröder Jens M. , Caparon Michael G. , Normark Staffan , Henriques-Normark Birgitta , Hultgren Scott J. , Kline Kimberly A.
Published: November 2013

Significance

In Gram-positive bacteria, many virulence factors are assembled and attached to the growing cell wall by sortase enzymes, which are localized to one or two sites in the cell membrane. Mislocalization of sortase enzymes negatively impacts their function. We demonstrate that β-defensins target
Enterococcus faecalis
at discrete sites, resulting in the mislocalization of sortase and associated secretion enzymes. The multiple peptide resistance factor protein, which adds cationic residues to anionic lipids as a general cationic peptide resistance strategy, limits focal defensin targeting in
E. faecalis
. This work suggests that focal targeting by defensins is important for efficient bacterial killing, and that pathogens have evolved mechanisms to balance focal localization of secretion and sortase enzymes with modification of these localization sites to combat defensins.
Dysregulation of synaptogenesis genes antecedes motor neuron pathology in spinal muscular atrophy
Authors: Zhang Zhenxi , Pinto Anna Maria , Wan Lili , Wang Wei , Berg Michael G. , Oliva Isabela , Singh Larry N. , Dengler Christopher , Wei Zhi , Dreyfuss Gideon
Published: November 2013

Significance

Spinal muscular atrophy (SMA), a common genetic motor neuron (MN) degenerative disease and leading hereditary cause of infant mortality, results from survival of motor neuron (SMN) protein deficiency. However, SMN’s ubiquitous expression and housekeeping functions in biogenesis of snRNPs, the spliceosome’s subunits, seems difficult to reconcile with SMA’s MN selective pathology. Here, we sequenced transcriptomes of MNs and adjacent white matter microdissected from spinal cords of presymptomatic SMA mice. This process revealed selective and MN-specific splicing and expression-level perturbations of mRNAs, including those essential for establishing neuromuscular junctions, the first structures that degenerate in SMA. We suggest that SMN’s central role in transcriptome regulation explains the gene-expression perturbations that impair MN function and survival in SMA.
Synaptic NMDA receptor stimulation activates PP1 by inhibiting its phosphorylation by Cdk5
Authors: Hou Hailong , Sun Lu , Siddoway Benjamin A. , Petralia Ronald S. , Yang Hongtian , Gu Hua , Nairn Angus C. , Xia Houhui
Published: November 2013

The serine/threonine protein phosphatase protein phosphatase 1 (PP1) is known to play an important role in learning and memory by mediating local and downstream aspects of synaptic signaling, but how PP1 activity is controlled in different forms of synaptic plasticity remains unknown. We find that synaptic N-methyl-d-aspartate (NMDA) receptor stimulation in neurons leads to activation of PP1 through a mechanism involving inhibitory phosphorylation at Thr320 by Cdk5. Synaptic stimulation led to proteasome-dependent degradation of the Cdk5 regulator p35, inactivation of Cdk5, and increased auto-dephosphorylation of Thr320 of PP1. We also found that neither inhibitor-1 nor calcineurin were involved in the control of PP1 activity in response to synaptic NMDA receptor stimulation. Rather, the PP1 regulatory protein, inhibitor-2, formed a complex with PP1 that was controlled by synaptic stimulation. Finally, we found that inhibitor-2 was critical for the induction of long-term depression in primary neurons. Our work fills a major gap regarding the regulation of PP1 in synaptic plasticity.
A biosensor of local kinesin activity reveals roles of PKC and EB1 in KIF17 activation
Authors: Espenel Cedric , Acharya Bipul R. , Kreitzer Geri
Published: November 2013

We showed previously that the kinesin-2 motor KIF17 regulates microtubule (MT) dynamics and organization to promote epithelial differentiation. How KIF17 activity is regulated during this process remains unclear. Several kinesins, including KIF17, adopt compact and extended conformations that reflect autoinhibited and active states, respectively. We designed biosensors of KIF17 to monitor its activity directly in single cells using fluorescence lifetime imaging to detect Förster resonance energy transfer. Lifetime data are mapped on a phasor plot, allowing us to resolve populations of active and inactive motors in individual cells. Using this biosensor, we demonstrate that PKC contributes to the activation of KIF17 and that this is required for KIF17 to stabilize MTs in epithelia. Furthermore, we show that EB1 recruits KIF17 to dynamic MTs, enabling its accumulation at MT ends and thus promoting MT stabilization at discrete cellular domains.
Modulation of NKG2D ligand expression and metastasis in tumors by spironolactone via RXRγ activation
Authors: Leung Wai-Hang , Vong Queenie P. , Lin Wenwei , Janke Laura , Chen Taosheng , Leung Wing
Published: November 2013

Tumor metastasis and lack of NKG2D ligand (NKG2DL) expression are associated with poor prognosis in patients with colon cancer. Here, we found that spironolactone (SPIR), an FDA-approved diuretic drug with a long-term safety profile, can up-regulate NKG2DL expression in multiple colon cancer cell lines by activating the ATM–Chk2-mediated checkpoint pathway, which in turn enhances tumor elimination by natural killer cells. SPIR can also up-regulate the expression of metastasis-suppressor genes TIMP2 and TIMP3, thereby reducing tumor cell invasiveness. Although SPIR is an aldosterone antagonist, its antitumor effects are independent of the mineralocorticoid receptor pathway. By screening the human nuclear hormone receptor siRNA library, we identified retinoid X receptor γ (RXRγ) instead as being indispensable for the antitumor functions of SPIR. Collectively, our results strongly support the use of SPIR or other RXRγ agonists with minimal side effects for colon cancer prevention and therapy.
A molecular basis for the association of the HLA-DRB1 locus, citrullination, and rheumatoid arthritis
Authors: Scally Stephen W. , Petersen Jan , Law Soi Cheng , Dudek Nadine L. , Nel Hendrik J. , Loh Khai Lee , Wijeyewickrema Lakshmi C. , Eckle Sidonia B.G. , van Heemst Jurgen , Pike Robert N. , McCluskey James , Toes Rene E. , La Gruta Nicole L. , Purcell Anthony W. , Reid Hugh H. , Thomas Ranjeny , Rossjohn Jamie
Published: November 2013

Rheumatoid arthritis (RA) is strongly associated with the human leukocyte antigen (HLA)-DRB1 locus that possesses the shared susceptibility epitope (SE) and the citrullination of self-antigens. We show how citrullinated aggrecan and vimentin epitopes bind to HLA-DRB1*04:01/04. Citrulline was accommodated within the electropositive P4 pocket of HLA-DRB1*04:01/04, whereas the electronegative P4 pocket of the RA-resistant HLA-DRB1*04:02 allomorph interacted with arginine or citrulline-containing epitopes. Peptide elution studies revealed P4 arginine–containing peptides from HLA-DRB1*04:02, but not from HLA-DRB1*04:01/04. Citrullination altered protease susceptibility of vimentin, thereby generating self-epitopes that are presented to T cells in HLA-DRB1*04:01+ individuals. Using HLA-II tetramers, we observed citrullinated vimentin- and aggrecan-specific CD4+ T cells in the peripheral blood of HLA-DRB1*04:01+ RA-affected and healthy individuals. In RA patients, autoreactive T cell numbers correlated with disease activity and were deficient in regulatory T cells relative to healthy individuals. These findings reshape our understanding of the association between citrullination, the HLA-DRB1 locus, and T cell autoreactivity in RA.
StochDecomp—Matlab package for noise decomposition in stochastic biochemical systems
Authors: Jetka Tomasz , Charzyńska Agata , Gambin Anna , Stumpf Michael P.H. , Komorowski Michał
Published: November 2013

Motivation: Stochasticity is an indispensable aspect of biochemical processes at the cellular level. Studies on how the noise enters and propagates in biochemical systems provided us with non-trivial insights into the origins of stochasticity, in total, however, they constitute a patchwork of different theoretical analyses.

Results: Here we present a flexible and widely applicable noise decomposition tool that allows us to calculate contributions of individual reactions to the total variability of a system’s output. With the package it is, therefore, possible to quantify how the noise enters and propagates in biochemical systems. We also demonstrate and exemplify using the JAK-STAT signalling pathway that the noise contributions resulting from individual reactions can be inferred from data experimental data along with Bayesian parameter inference. The method is based on the linear noise approximation, which is assumed to provide a reasonable representation of analyzed systems.

Availability and implementation:  http://sourceforge.net/p/stochdecomp/

Contact:  mkomor@ippt.gov.pl or m.stumpf@imperial.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Simulation-based Assessment to Identify Critical Gaps in Safe Anesthesia Resident Performance
Authors: Blum Richard H. , Boulet John R. , Cooper Jeffrey B. , Muret-Wagstaff Sharon L.
Published: November 2013

Background:

Valid methods are needed to identify anesthesia resident performance gaps early in training. However, many assessment tools in medicine have not been properly validated. The authors designed and tested use of a behaviorally anchored scale, as part of a multiscenario simulation-based assessment system, to identify high- and low-performing residents with regard to domains of greatest concern to expert anesthesiology faculty.

Methods:

An expert faculty panel derived five key behavioral domains of interest by using a Delphi process (1) Synthesizes information to formulate a clear anesthetic plan; (2) Implements a plan based on changing conditions; (3) Demonstrates effective interpersonal and communication skills with patients and staff; (4) Identifies ways to improve performance; and (5) Recognizes own limits. Seven simulation scenarios spanning pre-to-postoperative encounters were used to assess performances of 22 first-year residents and 8 fellows from two institutions. Two of 10 trained faculty raters blinded to trainee program and training level scored each performance independently by using a behaviorally anchored rating scale. Residents, fellows, facilitators, and raters completed surveys.

Results:

Evidence supporting the reliability and validity of the assessment scores was procured, including a high generalizability coefficient (ρ2 = 0.81) and expected performance differences between first-year resident and fellow participants. A majority of trainees, facilitators, and raters judged the assessment to be useful, realistic, and representative of critical skills required for safe practice.

Conclusion:

The study provides initial evidence to support the validity of a simulation-based performance assessment system for identifying critical gaps in safe anesthesia resident performance early in training.
Improving Faculty Feedback to Resident Trainees during a Simulated Case
Authors: Minehart Rebecca D. , Rudolph Jenny , Pian-Smith May C. M. , Raemer Daniel B.
Published: November 2013

Background:

Although feedback conversations are an essential component of learning, three challenges make them difficult: the fear that direct task feedback will harm the relationship with the learner, overcoming faculty cognitive biases that interfere with their eliciting the frames that drive trainees’ performances, and time pressure. Decades of research on developmental conversations suggest solutions to these challenges: hold generous inferences about learners, subject one’s own thinking to test by making it public, and inquire directly about learners’ cognitive frames.

Methods:

The authors conducted a randomized, controlled trial to determine whether a 1-h educational intervention for anesthesia faculty improved feedback quality in a simulated case. The primary outcome was an analysis of the feedback conversation between faculty and a simulated resident (actor) by using averages of six elements of a Behaviorally Anchored Rating Scale and an objective structured assessment of feedback. Seventy-one Harvard faculty anesthesiologists from five academic hospitals participated.

Results:

The intervention group scored higher when averaging all ratings. Scores for individual elements showed that the intervention group performed better in maintaining a psychologically safe environment (4.3 ± 1.21 vs. 3.8 ± 1.16; P = 0.001), identifying and exploring performance gaps (4.1 ± 1.38 vs. 3.7 ± 1.34; P = 0.048), and they more frequently emphasized the professionalism error of failing to call for help over the clinical topic of anaphylaxis (66 vs. 41%; P = 0.008).

Conclusions:

Quality of faculty feedback to a simulated resident was improved in the interventional group in a number of areas after a 1-h educational intervention, and this short intervention allowed a group of faculty to overcome enough discomfort in addressing a professionalism lapse to discuss it directly.
Pattern formation and coarsening dynamics in three-dimensional convective mixing in porous media
Authors: Fu Xiaojing , Cueto-Felgueroso Luis , Juanes Ruben
Published: November 2013

Geological carbon dioxide (CO
2
) sequestration entails capturing and injecting CO
2
into deep saline aquifers for long-term storage. The injected CO
2
partially dissolves in groundwater to form a mixture that is denser than the initial groundwater. The local increase in density triggers a gravitational instability at the boundary layer that further develops into columnar plumes of CO
2
-rich brine, a process that greatly accelerates solubility trapping of the CO
2
. Here, we investigate the pattern-formation aspects of convective mixing during geological CO
2
sequestration by means of high-resolution three-dimensional simulation. We find that the CO
2
concentration field self-organizes as a cellular network structure in the diffusive boundary layer at the top boundary. By studying the statistics of the cellular network, we identify various regimes of finger coarsening over time, the existence of a non-equilibrium stationary state, and a universal scaling of three-dimensional convective mixing.
Stone circles: form and soil kinematics
Authors: Hallet Bernard
Published: November 2013

Distinct surface patterns are ubiquitous and diverse in soils of polar and alpine regions, where the ground temperature oscillates about 0°C. They constitute some of the most striking examples of clearly visible, abiotic self-organization in nature. This paper outlines the interplay of frost-related physical processes that produce these patterns spontaneously and presents unique data documenting subsurface soil rotational motion and surface displacement spanning 20 years in well-developed circles of soil outlined by gravel ridges. These sorted circles are particularly attractive research targets for a number of reasons that provide focus for this paper: (i) their exceptional geometric regularity captures the attention of any observer; (ii) they are currently forming and evolving, hence the underlying processes can be monitored readily, especially because they are localized near the ground surface on a scale of metres, which facilitates comprehensive characterization; and (iii) a recent, highly successful numerical model of sorted circle development helps to draw attention to particular field observations that can be used to assess the model, its assumptions and parameter choices, and to the considerable potential for synergetic field and modelling studies.
Regime shifts in models of dryland vegetation
Authors: Zelnik Yuval R. , Kinast Shai , Yizhaq Hezi , Bel Golan , Meron Ehud
Published: November 2013

Drylands are pattern-forming systems showing self-organized vegetation patchiness, multiplicity of stable states and fronts separating domains of alternative stable states. Pattern dynamics, induced by droughts or disturbances, can result in desertification shifts from patterned vegetation to bare soil. Pattern formation theory suggests various scenarios for such dynamics: an abrupt global shift involving a fast collapse to bare soil, a gradual global shift involving the expansion and coalescence of bare-soil domains and an incipient shift to a hybrid state consisting of stationary bare-soil domains in an otherwise periodic pattern. Using models of dryland vegetation, we address the question of which of these scenarios can be realized. We found that the models can be split into two groups: models that exhibit multiplicity of periodic-pattern and bare-soil states, and models that exhibit, in addition, multiplicity of hybrid states. Furthermore, in all models, we could not identify parameter regimes in which bare-soil domains expand into vegetated domains. The significance of these findings is that, while models belonging to the first group can only exhibit abrupt shifts, models belonging to the second group can also exhibit gradual and incipient shifts. A discussion of open problems concludes the paper.
Local properties of patterned vegetation: quantifying endogenous and exogenous effects
Authors: Penny Gopal G. , Daniels Karen E. , Thompson Sally E.
Published: November 2013

Dryland ecosystems commonly exhibit periodic bands of vegetation, thought to form due to competition between individual plants for heterogeneously distributed water. In this paper, we develop a Fourier method for locally identifying the pattern wavenumber and orientation, and apply it to aerial images from a region of vegetation patterning near Fort Stockton, TX, USA. We find that the local pattern wavelength and orientation are typically coherent, but exhibit both rapid and gradual variation driven by changes in hillslope gradient and orientation, the potential for water accumulation, or soil type. Endogenous pattern dynamics, when simulated for spatially homogeneous topographic and vegetation conditions, predict pattern properties that are much less variable than the orientation and wavelength observed in natural systems. Our local pattern analysis, combined with ancillary datasets describing soil and topographic variation, highlights a largely unexplored correlation between soil depth, pattern coherence, vegetation cover and pattern wavelength. It also, surprisingly, suggests that downslope accumulation of water may play a role in changing vegetation pattern properties.
The possible role of Coriolis forces in structuring large-scale sinuous patterns of submarine channel–levee systems
Authors: Wells Mathew , Cossu Remo
Published: November 2013

Submarine channel–levee systems are among the largest sedimentary structures on the ocean floor. These channels have a sinuous pattern and are the main conduits for turbidity currents to transport sediment to the deep ocean. Recent observations have shown that their sinuosity decreases strongly with latitude, with high-latitude channels being much straighter than similar channels near the Equator. One possible explanation is that Coriolis forces laterally deflect turbidity currents so that at high Northern latitudes both the density interface and the downstream velocity maximum are deflected to the right-hand side of the channel (looking downstream). The shift in the velocity field can change the locations of erosion and deposition and introduce an asymmetry between left- and right-turning bends. The importance of Coriolis forces is defined by two Rossby numbers,
Ro

W

=
U
/
Wf
and
Ro

R

=
U
/
Rf
, where
U
is the mean downstream velocity,
W
is the width of the channel,
R
is the radius of curvature and
f
is the Coriolis parameter. In a bending channel, the density interface is flat when
Ro

R

∼−1, and Coriolis forces start to shift the velocity maximum when |
Ro

W

|<5. We review recent experimental and field observations and describe how Coriolis forces could lead to straighter channels at high latitudes.
Deficiency of BrpB causes major defects in cell division, stress responses and biofilm formation by Streptococcus mutans
Authors: Bitoun Jacob P. , Liao Sumei , Xie Gary G. , Beatty Wandy L. , Wen Zezhang T.
Published: November 2013

Streptococcus mutans, the primary aetiological agent of dental caries, possesses an YjeE-like protein that is encoded by locus SMU.409, herein designated brpB. In this study, a BrpB-deficient mutant, JB409, and a double mutant deficient of BrpB and BrpA (a paralogue of the LytR–CpsA–Psr family of cell wall-associated proteins), JB819, were constructed and characterized using function assays and microscopy analysis. Both JB409 and JB819 displayed extended lag phases and drastically slowed growth rates during growth in brain heart infusion medium as compared to the wild-type, UA159. Relative to UA159, JB409 and JB819 were more than 60- and 10-fold more susceptible to acid killing at pH 2.8, and more than 1 and 2 logs more susceptible to hydrogen peroxide, respectively. Complementation of the deficient mutants with a wild-type copy of the respective gene(s) partly restored the acid and oxidative stress responses to a level similar to the wild-type. As compared to UA159, biofilm formation by JB409 and JB819 was drastically reduced (P<0.001), especially during growth in medium containing sucrose. Under a scanning electron microscope, JB409 had significantly more giant cells with an elongated, rod-like morphology, and JB819 formed marble-like super cells with apparent defects in cell division. As revealed by transmission electron microscopy analysis, BrpB deficiency in both JB409 and JB819 resulted in the development of low electron density patches and formation of a loose nucleoid structure. Taken together, these results suggest that BrpB likely functions together with BrpA in regulating cell envelope biogenesis/homeostasis in Strep. mutans. Further studies are under way to elucidate the mechanism that underlies the BrpA- and BrpB-mediated regulation.
Co-circulation of enteroviruses between apes and humans
Authors: Harvala Heli , Van Nguyen Dung , McIntyre Chloe , Ahuka-Mundeke Steve , Ngole Eitel Mpoudi , Delaporte Eric , Peeters Martine , Simmonds Peter
Published: November 2013

A total of 139 stool samples from wild chimpanzees, gorillas and bonobos in Cameroon and Democratic Republic of Congo (DRC) were screened for enteroviruses (EVs) by reverse transcription PCR. Enterovirus RNA was detected in 10 % of samples, comprising eight from 58 sampled chimpanzees (13.8 %), one from 40 bonobos (2.5 %) and five from 40 gorillas (12.2 %). Three viruses isolated from chimpanzees grouped with human isolate EV-A89 and four (four chimpanzees, one gorilla) represented a newly identified type, EV-A119. These species A virus types overlapped with those circulating in human populations in the same area. The remaining six strains comprised a new species D type, EV-D120, infecting one chimpanzee and four gorillas, and a single EV variant infecting a bonobo that was remarkably divergent from other EVs and potentially constitutes a new enterovirus species. The study demonstrates both the circulation of genetically divergent EV variants in apes and monkeys as well as those shared with local human populations.
Isolation and characterization of a new Staphylococcus epidermidis broad-spectrum bacteriophage
Authors: Melo Luís D. R. , Sillankorva Sanna , Ackermann Hans-Wolfgang , Kropinski Andrew M. , Azeredo Joana , Cerca Nuno
Published: November 2013

Staphylococcus epidermidis is considered an important nosocomial pathogen, being very tolerant to the host immune system and antibiotherapy, particularly when in biofilms. Due to its high resistance, alternative antimicrobial strategies are under development. The use of bacteriophages is seen as an important strategy to combat pathogenic organisms. In this study, a S. epidermidis myovirus, SEP1, was isolated and characterized. The genome of this phage was sequenced and shown to be related peripherally to the genus Twortlikevirus. However, when compared with other phages of this genus, it showed DNA sequence identities no greater than 58.2 %. As opposed to other polyvalent viruses of the genus Twortlikevirus, SEP1 is highly specific to S. epidermidis strains. The good infectivity shown by this phage as well as its high lytic spectrum suggested that it might be a good candidate for therapeutic studies.
A fine-scale recombination map of the human–chimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion
Authors: Munch Kasper , Mailund Thomas , Dutheil Julien Y. , Schierup Mikkel Heide
Published: November 2013

Recombination is a major determinant of adaptive and nonadaptive evolution. Understanding how the recombination landscape has evolved in humans is thus key to the interpretation of human genomic evolution. Comparison of fine-scale recombination maps of human and chimpanzee has revealed large changes at fine genomic scales and conservation over large scales. Here we demonstrate how a fine-scale recombination map can be derived for the ancestor of human and chimpanzee, allowing us to study the changes that have occurred in human and chimpanzee since these species diverged. The map is produced from more than one million accurately determined recombination events. We find that this new recombination map is intermediate to the maps of human and chimpanzee but that the recombination landscape has evolved more rapidly in the human lineage than in the chimpanzee lineage. We use the map to show that recombination rate, through the effect of GC-biased gene conversion, is an even stronger determinant of base composition evolution than previously reported.
5-Bromobenzene-1,3-dicarbonitrile
Authors: Seidel Nadine , Seichter Wilhelm , Weber Edwin
Published: November 2013

The asymmetric unit of the title compound, C8H3BrN2, consists of two molecules. The crystal structure features undulating molecular sheets with the molecules linked by C—H...N hydrogen bonds with one N atom acting as a bifurcated acceptor. N...Br interactions also occur [N...Br = 2.991 (3) and 3.099 (3) Å]. Interlayer association is accomplished by offset face-to-face arene interactions [centroid–centroid distance = 3.768 (4) Å].
13-(Imidazol-1-yl)-11,13-dihydromelampomagnolide B monohydrate
Authors: Janganati Venumadhav , Penthala Narsimha Reddy , Parkin Sean , Crooks Peter A.
Published: November 2013

The title compound, C18H24N2O4·H2O {systematic name: (1aR,7aS,8R,10aS,10bS,E)-5-hydroxymethyl-8-[(1H-imidazol-1-yl)methyl]-1a-methyl-2,3,6,7,7a,8,10a,10b-octahydrooxireno[2′,3′:9,10]cyclodeca[1,2-b]furan-9(1aH)-one monohydrate}, an imidazole derivative of melampomagnolide B was synthesized under Michael addition conditions. The molecule is built up from fused ten-, five- (lactone) and three-membered (epoxide) rings. The internal double bond of the ten-membered ring identifies it as thecisorEisomer. The lactone ring has an envelope-type conformation, with the (chiral) C atom opposite the lactone O atoms as the flap atom. In the crystal, O—H...O, O—H...N and weak C—H...O hydrogen bonds link the molecules (along with water) into sheets parallel to thebcplane.
N-Benzyl-2-hydroxyethanaminium cyanurate
Authors: Contreras-Espejel Carlos Abraham , García-Eleno Marco A. , Santacruz-Juárez Ericka , Reyes-Martínez Reyna , Morales-Morales David
Published: November 2013

In the cation of the title compound C9H14ON+·C3H2O3N3−, the benzylamine C—N bond subtends a dihedral angle of 78.3 (2)° with the phenyl ring. The cyanurate anion is in the usual keto-form and shows an r.m.s. deviation from planarity of 0.010 Å. In the crystal, the cyanurate anions form N—H...O hydrogen-bonded zigzag ribbons along [001]. These ribbons are crosslinked by the organocationsviaO—H...N and N—H...O hydrogen bonds, forming bilayers parallel to (010) which are held together along [010] by slipped π–π interactions between pairs of cyanurate anions [shortest contact distances C...C = 3.479 (2), O...N = 3.400 (2); centroid–centroid distance=4.5946 (9) Å] and between cyanurate and phenyl rings [centroid–centroid distance = 3.7924 (12) Å, ring–ring angle = 11.99 (10)°].
Poly[μ-aqua-μ5-[2-(2,3,6-trichlorophenyl)acetato]-caesium]
Authors: Smith Graham
Published: November 2013

In the structure of the title complex, [Cs(C8H4Cl3O2)(H2O)]n, the caesium salt of the commercial herbicide fenac [(2,3,6-trichlorophenyl)acetic acid], the irregular eight-coordination about Cs+comprises a bidentateO:Cl-chelate interaction involving a carboxylate-O atom and anortho-related ring-substituted Cl atom, which is also bridging, a triple-bridging carboxylate-O atom and a bridging water molecule. A two-dimensional polymer is generated, lying parallel to (100), within which there are water–carboxylate O—H...O hydrogen-bonding interactions.
Di-μ2-acetato-1:2κ2O:O′;2:3κ2O:O′-bis{μ2-4,4′-dichloro-2,2′-[2,2-dimethylpropane-1,3-diylbis(nitrilomethanylylidene)]diphenolato}-1:2κ6O,N,N′,O′:O,O′;2:3κ6O,O′:O,N,N′,O′-tricadmium
Authors: Kubono Koji , Tani Keita , Yokoi Kunihiko , Shinmyozu Teruo , Goto Kenta
Published: November 2013

In the title linear homo-trinuclear complex, [Cd3(C19H18Cl2N2O2)2(C2H3O2)2], the central CdIIatom is located on a centre of inversion and has a distorted octahedral coordination geometry formed by four O atoms from two bidentate/tetradentate Schiff base ligands and two O atoms from two bridging acetate ligands. The coordination geometry of the terminal CdIIatom is square-pyramidal with the tetradentate part of the ligand in the basal plane and one O atom from an acetate ligand occupying the apical site. The six-membered CdN2C3ring adopts a chair conformation. The acetate-bridged Cd...Cd distance is 3.3071 (2) Å. The crystal structure is stabilized by C—H...O hydrogen bonds, which formC(7) chain motifs and give rise to a two-dimensional supramolecular network structure lying parallel to theabplane.
N-(1,5-Dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)-2-phenylacetamide
Authors: Kaur Manpreet , Jasinski Jerry P. , Anderson Brian J. , Yathirajan H. S. , Narayana B.
Published: November 2013

The title compound, C19H19N3O2, crystallizes with two independent molecules (AandB) in the asymmetric unit. In moleculeA, the pyrazole ring adopts a slightly disordered half-chair conformation while inBit is planar [r.m.s. deviation = 0.0386 (15) Å]. The dihedral angle between the mean planes of the two phenyl rings is 56.2 (8) inAand 38.2 (3)° inB. TheN-phenyl substituent on the pyrazole ring is twisted by 46.5 (2) inAand 58.6 (4)° inBwhile the extended phenyl ring is twisted by 82.2 (8) inAand 87.5 (9)° inB. The mean plane of the amide group forms an angle of 74.8 (3) inAand 67.7 (1)° inBwith respect to the phenyl ring. In addition, the amide group is rotated by 51.4 (1) inAand 53.6 (2)° inBfrom the the mean plane of the pyrazole ring. In the crystal, the two molecules are linkedviaN—H...O hydrogen bonds, supported by weak C—H...O interactions, forming dimers enclosing anR22(10) ring motif. The dimers are linkedviaC—H...O interactions, forming a three-dimensional structure.
Ethane-1,2-diaminium 2,2′-[terephthaloylbis(azanediyl)]diacetate tetrahydrate
Authors: Pook Niels-Patrick , Gjikaj Mimoza , Adam Arnold
Published: November 2013

In the title salt hydrate, C2H10N22+·C12H10N2O62−·4H2O, each of the ions is located about a centre of inversion and the asymmetric unit is completed by two water molecules in general positons. In the crystal, the cations, anions and water molecules are connected by O—H...O and N—H...O hydrogen bonding into a three-dimensional network.
{2,2′-[Ethane-1,2-diylbis(nitrilomethanylylidene)]diphenolato}(isopropanolato)aluminium dichloromethane hemisolvate
Authors: Zaitsev Kirill V. , Kuchuk Ekaterina A. , Karlov Sergey S. , Zaitseva Galina S. , Churakov Andrei V.
Published: November 2013

In the title compound, [Al(C16H14N2O2)(C3H7O)]·0.5CH2Cl2, the salen complex is monomeric and the dichlormethane solvent molecule lies on a crystallographic twofold axis. The central Al atom is fivefold coordinated and possesses a square-based pyramidal environment. The Al—OAlk(ipropyl) bond [1.7404 (14) Å] is much shorter than the Al—OAr(salen) bond lengths [1.7974 (15) and 1.8094 (14) Å]. The isopropyloxo group forms an intramolecular C—H...N hydrogen bond. In the crystal, the complex molecules are linked by weak C—H...O interactions.
Revision of the Li13Si4structure
Authors: Zeilinger Michael , Fässler Thomas F.
Published: November 2013

Besides Li17Si4, Li16.42Si4, and Li15Si4, another lithium-rich representative in the Li–Si system is the phase Li13Si4(tridecalithium tetrasilicide), the structure of which has been determined previously [Franket al.(1975).Z. Naturforsch. Teil B,30, 10–13]. A careful analysis of X-ray diffraction patterns of Li13Si4revealed discrepancies between experimentally observed and calculated Bragg positions. Therefore, we redetermined the structure of Li13Si4on the basis of single-crystal X-ray diffraction data. Compared to the previous structure report, decisive differences are (i) the introduction of a split position for one Li site [occupancy ratio 0.838 (7):0.162 (7)], (ii) the anisotropic refinement of atomic displacement parameters for all atoms, and (iii) a high accuracy of atom positions and unit-cell parameters. The asymmetric unit of Li13Si4contains two Si and seven Li atoms. Except for one Li atom situated on a site with symmetry 2/m, all other atoms are on mirror planes. The structure consists of isolated Si atoms as well as Si–Si dumbbells surrounded by Li atoms. Each Si atom is either 12- or 13-coordinated. The isolated Si atoms are situated in theabplane atz= 0 and are strictly separated from the Si–Si dumbbells atz= 0.5.
Towards a theory of social responsibility reporting
Authors: Li Yuanhui , Zhang Jie , Foo Check-Teck
Published: November 2013

Purpose

– Here, the paper aims to model major corporate characteristics associated with corporate social responsibility (CSR) reporting (in particular, its quality). Corporations in China are increasingly expected by the public and government to be more socially responsible. As such, it will be intriguing to ask, what are the characteristics associated with higher quality CSR reporting?

Design/methodology/approach

– CSR report quality scores are hand-gathered from HEXUN (web site) whilst financial and stock market information from the China Stock Market and Accounting Research (CSMAR) database. A total of 613 CSR reports' quality scores were utilized (Rankins CSR ratings) in the process of developing the model. Reports are hand-gathered from corporations listed on both the Shenzhen and Shanghai stock exchanges (SSE).

Findings

– The results suggest most interestingly, the quality of CSR report (mandatory) to be strongly, positively related with corporate financial characteristics: market capitalization (corporate size), shareholders' concentration of powers, corporate financial leverage (implying bondholders/debtors' influence). Surprisingly, CSR reporting is associated neither with corporate profitability nor by state-ownership. The presence of independent directors (at least in China) seems to have negative influences.

Practical implications

– CSR reporting may easily be mandated by government through a regulatory process. However, this does not necessarily lead to reports of a high quality. Instead, orientation towards higher visibility in social responsibility for listed corporations is better explained by financial characteristics: market valuation, ownership and leverage.

Originality/value

– This paper utilizes for the first time, in-depth and multi-faceted quality CSR scores (overall, segregated into macro-social, content and technology) for investigating CSR behavior of listed corporations in China. The findings suggest financial characteristics size (market valuation), ownership (shareholders' concentration of powers) and corporate leverage are better predictors of CSR behavior among listed corporations.
Corporate accidents, media coverage, and stock market responses
Authors: Wei Jiuchang , Wang Han , Fan Jin , Zhang Yujuan
Published: November 2013

Purpose

– This study aims to explore the mutual relation of corporate accidents, stock market responses, and media coverage.

Design/methodology/approach

– This paper empirically investigated 119 listed firms' accidents during the 2005-2012 period using the methods of event study, correlation analysis, and multiple regressions.

Findings

– The stock market response and media response are independent with each other in the following 30 days after accidents. Corporate accidents have significant negative effects on the stock market responses. As time goes by, the market reaction tapers off. In a mediate term period, accident onset has significantly positive effect and firm's ownership has weakly positive effect in addition to factors of asset and number of shareholders.

Originality/value

– This paper first examines the interrelationships among accidents, media coverage, and stock market responses. It is part of the corporate social responsibility to avoid or reduce the stakeholders' nervous behaviors in times of accident. Hence, accident-stricken firms should release sufficient and transparent information to shareholders so that they can trade the share more rationally.