bluuebunny/crossref_metadata_2025 huggingface dataset:
Binding of Kinetically Inert Metal Ions to RNA: The Case of Platinum(II)
Authors: Chapman Erich G. , Hostetter Alethia A. , Osborn Maire F. , Miller Amanda L. , DeRose Victoria J.
Published: June 2011

In this chapter several aspects of Pt(II) are highlighted that focus on the properties of Pt(II)-RNA adducts and the possibility that they influence RNA-based processes in cells. Cellular distribution of Pt(II) complexes results in significant platination of RNA, and localization studies find Pt(II) in the nucleus, nucleolus, and a distribution of other sites in cells. Treatment with Pt(II) compounds disrupts RNA-based processes including enzymatic processing, splicing, and translation, and this disruption may be indicative of structural changes to RNA or RNA-protein complexes. Several RNA-Pt(II) adducts have been characterized in vitro by biochemical and other methods. Evidence for Pt(II) binding in non-helical regions and for Pt(II) cross-linking of internal loops has been found. Although platinated sites have been identified, there currently exists very little in the way of detailed structural characterization of RNA-Pt(II) adducts. Some insight into the details of Pt(II) coordination to RNA, especially RNA helices, can be gained from DNA model systems. Many RNA structures, however, contain complex tertiary folds and common, purine-rich structural elements that present suitable Pt(II) nucleophiles in unique arrangements which may hold the potential for novel types of platinum-RNA adducts. Future research aimed at structural characterization of platinum-RNA adducts may provide further insights into platinum-nucleic acid binding motifs, and perhaps provide a rationale for the observed inhibition by Pt(II) complexes of splicing, translation, and enzymatic processing.
Repression of the RHOH gene by JunD
Authors: Delestré Laure , Berthon Céline , Quesnel Bruno , Figeac Martin , Kerckaert Jean-Pierre , Galiègue-Zouitina Sylvie , Shelley Carl Simon
Published: June 2011

RhoH is a member of the Rho family of small GTP-binding proteins that lacks GTPase activity. Since RhoH is constantly bound by GTP, it is thought to be constitutively active and controlled predominantly by changes in quantitative expression. RhoH is produced specifically in haematopoietic cells and aberrant expression has been linked to various forms of leukaemia. Transcription of the RHOH gene is the first level at which the quantitative levels of the RhoH protein are regulated. Previous studies have demonstrated that RHOH gene transcription is initiated by three distinct promoter regions designated P1, P2 and P3 that define the 5′ end of exons 1, 2 and 4 respectively. In the present study we report that the P3 promoter is largely responsible for RHOH gene transcription in the B-lymphocytic cell line Raji. The P3 promoter contains a minimal promoter region and a repressor region extending from −236 to +67 and +68 to +245 respectively, relative to the 5′ end of exon 4. Chromatin immunoprecipitation demonstrated that two AP1 (activator protein 1) sites in the minimal promoter region bind JunD. When JUND is overexpressed, the endogenous RHOH gene is repressed; however, when JUND is inhibited, expression of endogenous RHOH is induced both in the Raji cell line and AML (acute myeloid leukaemia) cells. In the HCL (hairy cell leukaemia) cell line JOK-1, induction of RHOH increases expression of the α isoform of protein kinase C. This downstream target of RHOH is also induced in AML cells by JUND inhibition. Collectively, these data indicate that JunD is an inhibitor of RHOH gene expression.
Diverse mechanisms for activation of Wnt signalling in the ovarian tumour microenvironment
Authors: Barbolina Maria V. , Burkhalter Rebecca J. , Stack M. Sharon
Published: June 2011

Wnt signalling pathways have been shown to play key roles in both normal development and tumorigenesis. Progression of many human cancers is associated with defined mutations in Wnt pathway components that result in dysregulated β-catenin-mediated gene transcription. Although Wnt pathway mutations are rare in epithelial ovarian cancer (with the exception of the endometrioid histotype), accumulating evidence supports a role for Wnt signalling in ovarian tumorigenesis in the absence of genetic mutations. The present review summarizes evidence in support of activated Wnt signalling in ovarian tumours and discusses alternative mechanisms for Wnt pathway activation in the ovarian tumour microenvironment.
Enhanced cooling capacities of ferroelectric materials at morphotropic phase boundaries
Authors: Chukka Rami , Cheah Jun Wei , Chen Zuhuang , Yang P. , Shannigrahi S. , Wang Junling , Chen Lang
Published: June 2011

The electrocaloric properties of PbZr0.52Ti0.48O3 (PZT) epitaxial films and 0.7Pb(Mg1/3Nb2/3)O3-0.3PbTiO3 (0.7PMN-0.3PT) single crystals are measured and demonstrated enhanced low temperature refrigeration at morphotropic phase boundary compositions. The results reveal large adiabatic cooling figures in ∼260 nm PZT films (11 K in 15 V) and 200 μm thick 0.7PMN-0.3PT single crystals (2.7 K in 240 V) at Curie transition temperatures and secondary cooling peaks at lower temperatures, near critical points. This is a very useful aspect of ferroelectric cooling elements to attain effective cooling over wide range of working temperatures in solid-state devices.
Subwavelength plasmonic lens patterned on a composite optical fiber facet for quasi-one-dimensional Bessel beam generation
Authors: Kang Sehun , Joe Hang-Eun , Kim Jongki , Jeong Yoonseob , Min Byung-Kwon , Oh Kyunghwan
Published: June 2011

We demonstrate a beam shaping method by engraving plasmonic lens consisted of subwavelength slit-metallic groove structure on the cleaved end facet of a composite optical fiber. The fiber consisted of a single mode optical fiber serially concatenated with a coreless silica fiber segment to expand the beam diameter. The subwavelength slit-groove structure on a gold film was fabricated using focused ion beam milling process. Plasmonic interaction in the film generated a quasi-one-dimensional Bessel-like beam with a beam width of 0.8 μm at the focal length of 2 μm. Detailed two- and three-dimensional finite-difference time-domain analyses showed beam characteristics consistent with experimental observations.
The hydrostatic pressure dependence of the piezoelectric properties for the barium titanate and lead titanate crystals: Thermodynamic analysis
Authors: Gao Junjie , Xu Zhuo , Li Fei , Zhang Chonghui , Liu Yi , Liu Gaomin , He Hongliang
Published: June 2011

The influence of the hydrostatic pressure on the piezoelectric response for tetragonal BaTiO3 and PbTiO3 monodomain crystals is investigated using Landau–Ginzburg–Devonshire phenomenological approach. It is shown that hydrostatic pressure could enhance the piezoelectric properties in some directions of crystals. The piezoelectricy enhancement is attributed to the hydrostatic pressure-induced flattening of the elastic Gibbs free-energy profile and its corresponding dielectric softening. For BaTiO3 at 285 K, with increasing pressure, the free-energy profile tends to become flat along the polar [001]c direction, facilitating the dilatation and contraction of polarization. So the dielectric softens and the d33 obviously increases in the [001]c direction. But in the direction perpendicular to the polarization, the free-energy profile goes to steepen, which restrains the polarization rotation away from the [001]c polar axis and in turn makes the shear piezoelectric coefficient d15 decreased. As a result, the maximum longitudinal piezoelectric coefficient d33*(θ) initially going along [111]c axis finally turns to be along [001]c axis with pressure increasing. Whereas for PbTiO3 at room temperature, both along and perpendicular to the polar axis, the free-energy profile tends to flatten, but the flattening along the polar axis predominates all the time. That is to say, the hydrostatic pressure facilitates the polarization dilatation and contraction along the polar axis as well as the polarization rotation in (100)c plane, d33 and d15 both increase, but longitudinal piezoelectric coefficient d33*(θ) for PbTiO3 always displays its maximum value along the polar [001]c direction and increases continuously with pressure in the computational pressure range.
Dynamics of H+ + N2 at E
Lab = 30 eV
Authors: Stopera Christopher , Maiti Buddhadev , Grimes Thomas V. , McLaurin Patrick M. , Morales Jorge A.
Published: June 2011

The H+ + N2 system at ELab = 30 eV, relevant in astrophysics, is investigated with the simplest-level electron nuclear dynamics (SLEND) method. SLEND is a time-dependent, direct, variational, non-adiabatic method that employs a classical-mechanics description for the nuclei and a single-determinantal wavefunction for the electrons. A canonical coherent-states procedure, intrinsic to SLEND, is used to reconstruct quantum vibrational properties from the SLEND classical mechanics. Present simulations employ three basis sets: STO-3G, 6-31G, and 6-31G**, to determine their effect on the results, which include reaction visualizations, product predictions, and scattering properties. Present simulations predict non-charge-transfer scattering and N2 collision-induced dissociation as the main reactions. Average vibrational energy transfer, H+ energy-loss spectra, rainbow angle, and elastic vibrational differential cross sections at the SLEND/6-31G** level agree well with available experimental data. SLEND/6-31G** results are comparable to those calculated with the vibrational close-coupling rotational infinite-order sudden approximation and the quasi-classical trajectory method.
L
1
FePt based exchange coupled composite bit patterned films
Authors: McCallum A. T. , Krone P. , Springer F. , Brombacher C. , Albrecht M. , Dobisz E. , Grobis M. , Weller D. , Hellwig O.
Published: June 2011

We demonstrate a 2.5-fold coercivity reduction in FePt based exchange coupled composite bit patterned media (ECC-BPM) by coupling a lower anisotropy Co/Pd–Co/Ni-multilayer system to the top of a high anisotropy FePt L10 film. Furthermore the tight switching field distribution (SFD) of the lower anisotropy system reduces the SFD of the ECC-BPM composite system compared to a single layer FePt film. The relative amount of switching field and SFD reduction in these ECC-BPM arrays agree with corresponding micromagnetic simulations.
Optimized micromirrors for three-dimensional single-particle tracking in living cells
Authors: Hajjoul Houssam , Mathon Julien , Viero Yannick , Bancaud Aurélien
Published: June 2011

In this letter we describe and fabricate an optimized version of micromirrors for three-dimensional (3D) single-particle tracking in living cells. Our technology is based on parallel arrays of single facet mirrors, which are introduced into the field of view of an optical microscope to provide one tilted view projected alongside the direct fluorescent sample image. Our method outperforms previously published V-shaped micromirrors technologies, as demonstrated by a ten-fold enhanced 3D positioning accuracy and a 1.7-fold reduced bleaching rate. We envision that our technology will be particularly useful for high-throughput 3D live cell imaging.
Design and fabrication of high efficiency power coupler between different photonic crystal waveguides
Authors: Jia Wei , Deng Jun , Sahadevan Ajeesh M. , Wu Hong , Jiang Liyong , Li Xiangyin , Bhatia Charanjit S. , Yang Hyunsoo , Danner Aaron J.
Published: June 2011

Based on inspiration from an inverse optimization strategy and theoretical finite-difference time-domain method simulations, an ultralow loss power coupler between two different photonic crystal waveguides was designed, fabricated and characterized. The experimental results showed that the loss was less than 1 dB for transverse electric polarized light at a wavelength of 1550 nm, which is consistent with expectations from numerical modeling. High efficiency optical couplers are critical for development of integrated optical circuit functionality.
Labeling, Identification, and Recognition of Wine-Relevant Odorants in Expert Sommeliers, Intermediates, and Untrained Wine Drinkers
Authors: Zucco Gesualdo M , Carassai Aurelio , Baroni Maria Rosa , Stevenson Richard J
Published: June 2011

In this study we examined the development of wine expertise. We asked four groups—untrained wine drinkers, second- and third-level trainee sommeliers, and professional sommeliers—to engage in a range of olfactory tasks to assess perceptual and semantic aspects of expertise. These tasks included identification, recognition, and description of a range of domain-specific and common odour stimuli, including wines. Trainee sommeliers were significantly poorer at identification of wine-relevant odours than untrained wine drinkers and professional sommeliers. Trainee and professional sommeliers were, however, significantly better than untrained wine drinkers in a delayed matching-to-sample wine-recognition task, but not in the case of other odorous stimuli. The wine-description task demonstrated a degree of skill, in terms of specificity and quantity of wine-relevant descriptors, as a function of expertise. These results, of one of the first studies of examining wine expertise by a cross-sectional developmental approach, indicate that perceptual aspects of expertise are probably rapidly acquired, being present even in the second-and third-level trainees, while semantic expertise is slower to develop, and may incur time for the identification of wine-specific odorants during training.
Mitochondrial complex II has a key role in mitochondrial-derived reactive oxygen species influence on plant stress gene regulation and defense
Authors: Gleason Cynthia , Huang Shaobai , Thatcher Louise F. , Foley Rhonda C. , Anderson Carol R. , Carroll Adam J. , Millar A. Harvey , Singh Karam B.
Published: June 2011

Mitochondria are both a source of ATP and a site of reactive oxygen species (ROS) production. However, there is little information on the sites of mitochondrial ROS (mROS) production or the biological role of such mROS in plants. We provide genetic proof that mitochondrial complex II (Complex II) of the electron transport chain contributes to localized mROS that regulates plant stress and defense responses. We identify an
Arabidopsis
mutant in the Complex II subunit, SDH1-1, through a screen for mutants lacking
GSTF8
gene expression in response to salicylic acid (SA).
GSTF8
is an early stress-responsive gene whose transcription is induced by biotic and abiotic stresses, and its expression is commonly used as a marker of early stress and defense responses. Transcriptional analysis of this mutant, disrupted in stress responses 1 (
dsr1
), showed that it had altered SA-mediated gene expression for specific downstream stress and defense genes, and it exhibited increased susceptibility to specific fungal and bacterial pathogens. The
dsr1
mutant also showed significantly reduced succinate dehydrogenase activity. Using in vivo fluorescence assays, we demonstrated that root cell ROS production occurred primarily from mitochondria and was lower in the mutant in response to SA. In addition, leaf ROS production was lower in the mutant after avirulent bacterial infection. This mutation, in a conserved region of SDH1-1, is a unique plant mitochondrial mutant that exhibits phenotypes associated with lowered mROS production. It provides critical insights into Complex II function with implications for understanding Complex II's role in mitochondrial diseases across eukaryotes.
Genetic calibration of species diversity among North America's freshwater fishes
Authors: April Julien , Mayden Richard L. , Hanner Robert H. , Bernatchez Louis
Published: June 2011

Freshwater ecosystems are being heavily exploited and degraded by human activities all over the world, including in North America, where fishes and fisheries are strongly affected. Despite centuries of taxonomic inquiry, problems inherent to species identification continue to hamper the conservation of North American freshwater fishes. Indeed, nearly 10% of species diversity is thought to remain undescribed. To provide an independent calibration of taxonomic uncertainty and to establish a more accessible molecular identification key for its application, we generated a standard reference library of mtDNA sequences (DNA barcodes) derived from expert-identified museum specimens for 752 North American freshwater fish species. This study demonstrates that 90% of known species can be delineated using barcodes. Moreover, it reveals numerous genetic discontinuities indicative of independently evolving lineages within described species, which points to the presence of morphologically cryptic diversity. From the 752 species analyzed, our survey flagged 138 named species that represent as many as 347 candidate species, which suggests a 28% increase in species diversity. In contrast, several species of parasitic and nonparasitic lampreys lack such discontinuity and may represent alternative life history strategies within single species. Therefore, it appears that the current North American freshwater fish taxonomy at the species level significantly conceals diversity in some groups, although artificially creating diversity in others. In addition to providing an easily accessible digital identification system, this study identifies 151 fish species for which taxonomic revision is required.
Wnt7a signaling promotes dendritic spine growth and synaptic strength through Ca
2+
/Calmodulin-dependent protein kinase II
Authors: Ciani Lorenza , Boyle Kieran A. , Dickins Ellen , Sahores Macarena , Anane Derek , Lopes Douglas M. , Gibb Alasdair J. , Salinas Patricia C.
Published: June 2011

The balance between excitatory and inhibitory synapses is crucial for normal brain function. Wnt proteins stimulate synapse formation by increasing synaptic assembly. However, it is unclear whether Wnt signaling differentially regulates the formation of excitatory and inhibitory synapses. Here, we demonstrate that Wnt7a preferentially stimulates excitatory synapse formation and function. In hippocampal neurons, Wnt7a increases the number of excitatory synapses, whereas inhibitory synapses are unaffected. Wnt7a or postsynaptic expression of Dishevelled-1 (Dvl1), a core Wnt signaling component, increases the frequency and amplitude of miniature excitatory postsynaptic currents (mEPSCs), but not miniature inhibitory postsynaptic currents (mIPSCs). Wnt7a increases the density and maturity of dendritic spines, whereas Wnt7a-Dvl1–deficient mice exhibit defects in spine morphogenesis and mossy fiber-CA3 synaptic transmission in the hippocampus. Using a postsynaptic reporter for Ca
2+
/Calmodulin-dependent protein kinase II (CaMKII) activity, we demonstrate that Wnt7a rapidly activates CaMKII in spines. Importantly, CaMKII inhibition abolishes the effects of Wnt7a on spine growth and excitatory synaptic strength. These data indicate that Wnt7a signaling is critical to regulate spine growth and synaptic strength through the local activation of CaMKII at dendritic spines. Therefore, aberrant Wnt7a signaling may contribute to neurological disorders in which excitatory signaling is disrupted.
Boundary cap cells are peripheral nervous system stem cells that can be redirected into central nervous system lineages
Authors: Zujovic Violetta , Thibaud Julie , Bachelin Corinne , Vidal Marie , Deboux Cyrille , Coulpier Fanny , Stadler Nicolas , Charnay Patrick , Topilko Piotr , Baron-Van Evercooren Anne
Published: June 2011

Boundary cap cells (BC), which express the transcription factor Krox20, participate in the formation of the boundary between the central nervous system and the peripheral nervous system. To study BC stemness, we developed a method to purify and amplify BC in vitro from

Krox20
Cre/+
, R26R
YFP/+

mouse embryos. We show that BC progeny are EGF/FGF2-responsive, form spheres, and express neural crest markers. Upon growth factor withdrawal, BC progeny gave rise to multiple neural crest and CNS lineages. Transplanted into the developing murine forebrain, they successfully survived, migrated, and integrated within the host environment. Surprisingly, BC progeny generated exclusively CNS cells, including neurons, astrocytes, and myelin-forming oligodendrocytes. In vitro experiments indicated that a sequential combination of ventralizing morphogens and glial growth factors was necessary to reprogram BC into oligodendrocytes. Thus, BC progeny are endowed with differentiation plasticity beyond the peripheral nervous system. The demonstration that CNS developmental cues can reprogram neural crest-derived stem cells into CNS derivatives suggests that BC could serve as a source of cell type-specific lineages, including oligodendrocytes, for cell-based therapies to treat CNS disorders.
Coarse to fine dynamics of monocular and binocular processing in human pattern vision
Authors: Neri Peter
Published: June 2011

Biological image processing has been hypothesized to adopt a coarse to fine strategy: the image is initially analyzed at a coarse spatial scale, and this analysis is then used to guide subsequent inspection at a finer scale. Neurons in visual cortex often display response characteristics that are consistent with this hypothesis for both monocular and binocular signals. Puzzlingly, measurements in human observers have failed to expose similar coarse to fine dynamics for human pattern vision, questioning the applicability of direct parallels between single neurons and perception. We performed a series of measurements using experimental protocols that were specifically designed to examine this question in more detail. We were able to confirm that, when the analysis is restricted to the linear properties of the perceptual process, no coarse to fine dynamics were evident in the data. However, when the analysis was extended to nonlinear descriptors, a clear coarse to fine structure emerged that consisted of two processes: an early nonlinear process operating on a coarse spatial scale followed by a linear process operating on a fine spatial scale. These results potentially serve to reduce the gap between the electrophysiological and behavioral findings.
Methionine sulfoxide reductase A is a stereospecific methionine oxidase
Authors: Lim Jung Chae , You Zheng , Kim Geumsoo , Levine Rodney L.
Published: June 2011

Methionine sulfoxide reductase A (MsrA) catalyzes the reduction of methionine sulfoxide to methionine and is specific for the S epimer of methionine sulfoxide. The enzyme participates in defense against oxidative stresses by reducing methionine sulfoxide residues in proteins back to methionine. Because oxidation of methionine residues is reversible, this covalent modification could also function as a mechanism for cellular regulation, provided there exists a stereospecific methionine oxidase. We show that MsrA itself is a stereospecific methionine oxidase, producing S-methionine sulfoxide as its product. MsrA catalyzes its own autooxidation as well as oxidation of free methionine and methionine residues in peptides and proteins. When functioning as a reductase, MsrA fully reverses the oxidations which it catalyzes.
Disentangling pleasure from incentive salience and learning signals in brain reward circuitry
Authors: Smith Kyle S. , Berridge Kent C. , Aldridge J. Wayne
Published: June 2011

Multiple signals for reward—hedonic impact, motivation, and learned associative prediction—are funneled through brain mesocorticolimbic circuits involving the nucleus accumbens and ventral pallidum. Here, we show how the hedonic “liking” and motivation “wanting” signals for a sweet reward are distinctly modulated and tracked in this circuit separately from signals for Pavlovian predictions (learning). Animals first learned to associate a fixed sequence of Pavlovian cues with sucrose reward. Subsequent intraaccumbens microinjections of an opioid-stimulating drug increased the hedonic liking impact of sucrose in behavior and firing signals of ventral pallidum neurons, and likewise, they increased incentive salience signals in firing to the reward-proximal incentive cue (but did not alter firing signals to the learned prediction value of a reward-distal cue). Microinjection of a dopamine-stimulating drug instead enhanced only the motivation component but did not alter hedonic impact or learned prediction signals. Different dedicated neuronal subpopulations in the ventral pallidum tracked signal enhancements for hedonic impact vs. incentive salience, and a faster firing pattern also distinguished incentive signals from slower hedonic signals, even for a third overlapping population. These results reveal separate neural representations of wanting, liking, and prediction components of the same reward within the nucleus accumbens to ventral pallidum segment of mesocorticolimbic circuitry.
Serine-threonine kinase with-no-lysine 4 (WNK4) controls blood pressure via transient receptor potential canonical 3 (TRPC3) in the vasculature
Authors: Park Hyun Woo , Kim Joo Young , Choi Soo-Kyoung , Lee Young-Ho , Zeng Weizhong , Kim Kyung Hwan , Muallem Shmuel , Lee Min Goo
Published: June 2011

Mutations in the serine-threonine kinase with-no-lysine 4 (WNK4) cause pseudohypoaldosteronism type 2 (PHAII), a Mendelian form of human hypertension. WNK4 regulates diverse ion transporters in the kidney, and dysregulation of renal transporters is considered the main cause of the WNK4 mutation-associated hypertension. Another determinant of hypertension is vascular tone that is regulated by Ca
2+
-dependent blood vessel constriction. However, the role of WNK4 in vasoconstriction as part of its function to regulate blood pressure is not known. Here, we report that WNK4 is a unique modulator of blood pressure by restricting Ca
2+
influx via the transient receptor potential canonical 3 (TRPC3) channel in the vasculature. Loss of WNK4 markedly augmented TRPC3-mediated Ca
2+
influx in vascular smooth muscle cells (VSMCs) in response to α-adrenoreceptor stimulation, which is the pathological hallmark of hypertension in resistance arteries. Notably, WNK4 depletion induced hypertrophic cell growth in VSMCs and increased vasoconstriction in small mesenteric arteries via TRPC3-mediated Ca
2+
influx. In addition, WNK4 mutants harboring the Q562E PHAII-causing or the D318A kinase-inactive mutation failed to mediate TRPC3 inhibition. These results define a previously undescribed function of WNK4 and reveal a unique therapeutic target to control blood pressure in WNK4-related hypertension.
Crystal structure of mouse coronavirus receptor-binding domain complexed with its murine receptor
Authors: Peng Guiqing , Sun Dawei , Rajashankar Kanagalaghatta R. , Qian Zhaohui , Holmes Kathryn V. , Li Fang
Published: June 2011

Coronaviruses have evolved diverse mechanisms to recognize different receptors for their cross-species transmission and host-range expansion. Mouse hepatitis coronavirus (MHV) uses the N-terminal domain (NTD) of its spike protein as its receptor-binding domain. Here we present the crystal structure of MHV NTD complexed with its receptor murine carcinoembryonic antigen-related cell adhesion molecule 1a (mCEACAM1a). Unexpectedly, MHV NTD contains a core structure that has the same β-sandwich fold as human galectins (S-lectins) and additional structural motifs that bind to the N-terminal Ig-like domain of mCEACAM1a. Despite its galectin fold, MHV NTD does not bind sugars, but instead binds mCEACAM1a through exclusive protein–protein interactions. Critical contacts at the interface have been confirmed by mutagenesis, providing a structural basis for viral and host specificities of coronavirus/CEACAM1 interactions. Sugar-binding assays reveal that galectin-like NTDs of some coronaviruses such as human coronavirus OC43 and bovine coronavirus bind sugars. Structural analysis and mutagenesis localize the sugar-binding site in coronavirus NTDs to be above the β-sandwich core. We propose that coronavirus NTDs originated from a host galectin and retained sugar-binding functions in some contemporary coronaviruses, but evolved new structural features in MHV for mCEACAM1a binding.
Axon regeneration requires coordinate activation of p38 and JNK MAPK pathways
Authors: Nix Paola , Hisamoto Naoki , Matsumoto Kunihiro , Bastiani Michael
Published: June 2011

Signaling pathways essential for axon regeneration, but not for neuron development or function, are particularly well suited targets for therapeutic intervention. We find that the parallel PMK-3(p38) and KGB-1(JNK) MAPK pathways must be coordinately activated to promote axon regeneration. Axon regeneration fails if the activity of either pathway is absent. These two MAPKs are coregulated by the E3 ubiquitin ligase RPM-1(Phr1) via targeted degradation of the MAPKKKs DLK-1 and MLK-1 and by the MAPK phosphatase VHP-1(MKP7), which negatively regulates both PMK-3(p38) and KGB-1(JNK).
Punishment sustains large-scale cooperation in prestate warfare
Authors: Mathew Sarah , Boyd Robert
Published: June 2011

Understanding cooperation and punishment in small-scale societies is crucial for explaining the origins of human cooperation. We studied warfare among the Turkana, a politically uncentralized, egalitarian, nomadic pastoral society in East Africa. Based on a representative sample of 88 recent raids, we show that the Turkana sustain costly cooperation in combat at a remarkably large scale, at least in part, through punishment of free-riders. Raiding parties comprised several hundred warriors and participants are not kin or day-to-day interactants. Warriors incur substantial risk of death and produce collective benefits. Cowardice and desertions occur, and are punished by community-imposed sanctions, including collective corporal punishment and fines. Furthermore, Turkana norms governing warfare benefit the ethnolinguistic group, a population of a half-million people, at the expense of smaller social groupings. These results challenge current views that punishment is unimportant in small-scale societies and that human cooperation evolved in small groups of kin and familiar individuals. Instead, these results suggest that cooperation at the larger scale of ethnolinguistic units enforced by third-party sanctions could have a deep evolutionary history in the human species.
Fundamental relationship between operon organization and gene expression
Authors: Lim Han N. , Lee Yeong , Hussein Razika
Published: June 2011

Half a century has passed since the discovery of operons (groups of genes that are transcribed together as a single mRNA). Despite the importance of operons in bacterial gene networks, the relationship between their organization and gene expression remains poorly understood. Here we show using synthetic operons in
Escherichia coli
that the expression of a given gene increases with the length of the operon and as its position moves farther from the end of the operon. These findings can be explained by a common mechanism; increasing the distance from the start of a gene to the end of the operon (termed the “transcription distance”) provides more time for translation to occur during transcription, resulting in increased expression. We confirmed experimentally that the increased expression is indeed due to increased translation. Furthermore our analysis indicates the translation initiation rate for an mRNA is sixfold greater during transcription than after its release, which amplifies the impact of the transcription distance on gene expression. As a result of these mechanisms, gene expression increases by ∼40% for each 1,000 nucleotides of transcription distance. In summary, we demonstrate that a fundamental relationship exists between gene expression and the number, length, and order of the genes in an operon. This relationship has important implications for understanding the functional basis of genome organization and practical applications for synthetic biology.
The transcriptional repressor Blimp1/Prdm1 regulates postnatal reprogramming of intestinal enterocytes
Authors: Harper James , Mould Arne , Andrews Robert M. , Bikoff Elizabeth K. , Robertson Elizabeth J.
Published: June 2011

Female mammals produce milk to feed their newborn offspring before teeth develop and permit the consumption of solid food. Intestinal enterocytes dramatically alter their biochemical signature during the suckling-to-weaning transition. The transcriptional repressor Blimp1 is strongly expressed in immature enterocytes in utero, but these are gradually replaced by Blimp1
−
crypt-derived adult enterocytes. Here we used a conditional inactivation strategy to eliminate Blimp1 function in the developing intestinal epithelium. There was no noticeable effect on gross morphology or formation of mature cell types before birth. However, survival of mutant neonates was severely compromised. Transcriptional profiling experiments reveal global changes in gene expression patterns. Key components of the adult enterocyte biochemical signature were substantially and prematurely activated. In contrast, those required for processing maternal milk were markedly reduced. Thus, we conclude Blimp1 governs the developmental switch responsible for postnatal intestinal maturation.
A cascade of coregulating enhancer binding proteins initiates and propagates a multicellular developmental program
Authors: Giglio Krista M. , Caberoy Nora , Suen Garret , Kaiser Dale , Garza Anthony G.
Published: June 2011

The signal transduction networks that initiate multicellular development in bacteria remain largely undefined. Here, we report that
Myxococcus xanthus
regulates entry into its multicellular developmental program using a novel strategy: a cascade of transcriptional activators known as enhancer binding proteins (EBPs). The EBPs in the cascade function in sequential stages of early development, and several lines of evidence indicate that the cascade is propagated when EBPs that function at one stage of development directly regulate transcription of an EBP gene important for the next developmental stage. We also show that the regulatory cascade is designed in a novel way that extensively expands on the typical use of EBPs: Instead of using only one EBP to regulate a particular gene or group of genes, which is the norm in other bacterial systems, the cascade uses multiple EBPs to regulate EBP genes that are positioned at key transition points in early development. Based on the locations of the putative EBP promoter binding sites, several different mechanisms of EBP coregulation are possible, including the formation of coregulating EBP transcriptional complexes. We propose that
M
.
xanthus
uses an EBP coregulation strategy to make expression of EBP genes that modulate stage-stage transitions responsive to multiple signal transduction pathways, which provide information that is important for a coordinated decision to advance the developmental process.
Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome
Authors: Flynn Ryan A. , Almada Albert E. , Zamudio Jesse R. , Sharp Phillip A.
Published: June 2011

Divergent transcription occurs at the majority of RNA polymerase II (RNAPII) promoters in mouse embryonic stem cells (mESCs), and this activity correlates with CpG islands. Here we report the characterization of upstream antisense transcription in regions encoding transcription start site associated RNAs (TSSa-RNAs) at four divergent CpG island promoters: Isg20l1, Tcea1, Txn1, and Sf3b1. We find that upstream antisense RNAs (uaRNAs) have distinct capped 5′ termini and heterogeneous nonpolyadenylated 3′ ends. uaRNAs are short-lived with average half-lives of 18 minutes and are present at 1–4 copies per cell, approximately one RNA per DNA template. Exosome depletion stabilizes uaRNAs. These uaRNAs are probably initiation products because their capped termini correlate with peaks of paused RNAPII. The pausing factors NELF and DSIF are associated with these antisense polymerases and their sense partners. Knockdown of either NELF or DSIF results in an increase in the levels of uaRNAs. Consistent with P-TEFb controlling release from pausing, treatment with its inhibitor, flavopiridol, decreases uaRNA and nascent mRNA transcripts with similar kinetics. Finally, Isg20l1 induction reveals equivalent increases in transcriptional activity in sense and antisense directions. Together these data show divergent polymerases are regulated after P-TEFb recruitment with uaRNA levels controlled by the exosome.
An analysis of the relationships between subthreshold electrical properties and excitability in skeletal muscle
Authors: Pedersen Thomas H. , L.-H. Huang Christopher , Fraser James A.
Published: June 2011

Skeletal muscle activation requires action potential (AP) initiation followed by its sarcolemmal propagation and tubular excitation to trigger Ca2+ release and contraction. Recent studies demonstrate that ion channels underlying the resting membrane conductance (GM) of fast-twitch mammalian muscle fibers are highly regulated during muscle activity. Thus, onset of activity reduces GM, whereas prolonged activity can markedly elevate GM. Although these observations implicate GM regulation in control of muscle excitability, classical theoretical studies in un-myelinated axons predict little influence of GM on membrane excitability. However, surface membrane morphologies differ markedly between un-myelinated axons and muscle fibers, predominantly because of the tubular (t)-system of muscle fibers. This study develops a linear circuit model of mammalian muscle fiber and uses this to assess the role of subthreshold electrical properties, including GM changes during muscle activity, for AP initiation, AP propagation, and t-system excitation. Experimental observations of frequency-dependent length constant and membrane-phase properties in fast-twitch rat fibers could only be replicated by models that included t-system luminal resistances. Having quantified these resistances, the resulting models showed enhanced conduction velocity of passive current flow also implicating elevated AP propagation velocity. Furthermore, the resistances filter passive currents such that higher frequency current components would determine sarcolemma AP conduction velocity, whereas lower frequency components excite t-system APs. Because GM modulation affects only the low-frequency membrane impedance, the GM changes in active muscle would predominantly affect neuromuscular transmission and low-frequency t-system excitation while exerting little influence on the high-frequency process of sarcolemmal AP propagation. This physiological role of GM regulation was increased by high Cl− permeability, as in muscle endplate regions, and by increased extracellular [K+], as observed in working muscle. Thus, reduced GM at the onset of exercise would enhance t-system excitation and neuromuscular transmission, whereas elevated GM after sustained activity would inhibit these processes and thereby accentuate muscle fatigue.
The pathway and spatial scale for MscS inactivation
Authors: Kamaraju Kishore , Belyy Vladislav , Rowe Ian , Anishkin Andriy , Sukharev Sergei
Published: June 2011

The mechanosensitive channel of small conductance (MscS) is a bacterial tension-driven osmolyte release valve with homologues in many walled eukaryotic organisms. When stimulated by steps of tension in excised patches, Escherichia coli MscS exhibits transient opening followed by reversible adaptation and then complete inactivation. Here, we study properties of the inactivation transition, which renders MscS nonconductive and tension insensitive. Using special pressure protocols we demonstrate that adaptation and inactivation are sequential processes with opposite tension dependencies. In contrast to many eukaryotic channels, which inactivate from the open state, MscS inactivates primarily from the closed state because full openings by preconditioning pulses do not influence the degree of inactivation, and saturating tensions keeping channels open prevent inactivation. The easily opened A98S mutant lacks inactivation completely, whereas the L111S mutant with a right-shifted activation curve inactivates silently before reaching the threshold for opening. This suggests that opening and inactivation are two independent tension-driven pathways, both starting from the closed state. Analysis of tension dependencies for inactivation and recovery rates estimated the in-plane expansion (ΔA) associated with inactivation as 8.5 nm2, which is about half of the area change for opening. Given that the interhelical contact between the outer TM1–TM2 pairs and the core TM3s is the force-transmitting path from the periphery to the gate, the determined ΔA now can be used as a constraining parameter for the models of the inactivated state in which the lipid-facing TM1–TM2 pairs are displaced and uncoupled from the gate.
Influence of charge accumulation of photogenerated carriers in the vicinity of donor/acceptor interface on the open-circuit voltage of zinc-porphyrin/C60 heterojunction organic photovoltaic cells
Authors: Ryuzaki Sou , Onoe Jun
Published: June 2011

The correlation between open-circuit voltage (V
OC) and built-in potential (V
bi) upon photo-irradiation in the vicinity of the donor/acceptor (D/A) interface in zinc-octaethylporphyrin [Zn(OEP)]/C60 heterojunction photovoltaic (OPV) cells is investigated by examining the capacitance–voltage (C–V) characteristics. Charge accumulation of photogenerated carriers in the vicinity of the D/A interface is found to enlarge V
bi of both D [Zn(OEP)] and A (C60) films in the vicinity of the interface. In addition, it is noted that V
OC is in good agreement with the sum of V
bi of each film in the vicinity of the D/A interface. This suggests that charge accumulation of photogenerated carriers in the vicinity of the D/A interface plays a key role in determining V
OC for solar cells.
Gas temperature effects in micrometre-scale dielectric barrier discharges
Authors: Sitaraman H , Raja L L
Published: June 2011

A numerical modelling study of micrometre-length-scale (gap distances of ∼50–100 µm) dielectric barrier discharges (micro-DBDs) is reported. A comparison of micro-DBDs with classical large-scale DBDs (gap distances of ∼ mm) reveals the principal effect of downscaling DBD gap dimensions on the gas heating in these discharges. A one-dimensional, self-consistent, multi-species, multi-temperature continuum model is used in the simulations. For a constant pd (pressure × discharge gap distance) and applied voltage waveform (500 V, 10 MHz), a larger cycle-averaged gas temperature rise is seen in the micro-DBDs ∼hundreds of kelvin compared with much smaller rise ∼tens of kelvin in the classic DBDs. The gas temperature increase in micro-DBDs is mainly due to the rapid increase in the power densities as the gap dimensions are decreased compared with the increase in the wall loss with decreasing gap distances. For conditions studied in this work, the power densities in micro-DBDs are about four orders of magnitude larger than classic DBDs. Operation at higher frequencies, with other conditions remaining constant, is observed to favour larger gas temperatures in micro-DBDs. Micro-DBDs are therefore excellent device candidates to provide controllable gas heating in a variety of micro-electro mechanical systems; small spacecraft electrothermal micropropulsion devices being an example.
Synthesis of hollow carbon sphere/ZnO@C composite as a light-weight microwave absorber
Authors: Liu Rui , Lun Ning , Qi Yong-Xin , Zhu Hui-Ling , Bai Yu-Jun , Bi Jian-Qiang
Published: June 2011

Hollow carbon spheres (HCSs) and HCS/ZnO@C composite are synthesized by the reaction of zinc with sucrose and glycerol, respectively. The electromagnetic parameters of the HCSs and HCS/ZnO@C composite are measured by a coaxial line method. Both the real and imaginary complex permittivities and the loss tangent for the HCS/ZnO@C composite are larger than those for the HCSs. The electromagnetic absorption properties of the HCS/ZnO@C composite are advantageous over those of the HCSs, not only in band width but also in absorber thickness.
Non-vanishing of derivatives of 𝐺𝐿(3)×𝐺𝐿(2) 𝐿-functions
Authors: Sun Qingfeng
Published: June 2011

Let

f
f

be a fixed self-dual Hecke-Maass cusp form for

S

L
3

(

Z

)

SL_3(\mathbb {Z})

and let

B

k

\mathcal {B}_k

be an orthogonal basis of holomorphic cusp forms of weight

k
≡
2
(

m
o
d

4
)

k \equiv 2(\mathrm {mod} \,4)

for

S

L
2

(

Z

)

SL_2(\mathbb {Z})

. We prove an asymptotic formula for the first moment of the first derivative of

L

(
s
,
f
×
g
)

L\left (s,f\times g\right )

at the central point

s
=
1

/

2

s=1/2

, where

g
g

runs over

B

k

\mathcal {B}_k

,

K
≤
k
≤
2
K

K\leq k\leq 2K

,

K
K

large enough. This implies that for each

K
K

large enough there exists

g
∈

B

k

g\in \mathcal {B}_k

with

K
≤
k
≤
2
K

K\leq k\leq 2K

such that

L
′

(
1

/

2
,
f
×
g
)
≠
0

L’(1/2,f\times g)\neq 0

.
What influences European plaice (Pleuronectes platessa) distribution in the eastern English Channel? Using habitat modelling and GIS to predict habitat utilization
Authors: Lauria Valentina , Vaz Sandrine , Martin Corinne S. , Mackinson Steve , Carpentier André
Published: June 2011

Lauria, V., Vaz, S., Martin, C. S., Mackinson, S., and Carpentier, A. 2011. What influences European plaice (Pleuronectes platessa) distribution in the eastern English Channel? Using habitat modelling and GIS to predict habitat utilization. – ICES Journal of Marine Science, 68: 1500–1510. Conservation of fish habitat requires knowledge of how spatial distributions of species are related to environmental factors. Habitat modelling and mapping are useful in predicting species–environment relationships. Species abundance is modelled as a function of environmental parameters to understand species habitat utilization better. The influence of environmental factors on plaice (Pleuronectes platessa) distribution was investigated for two life stages and over two seasons. Generalized linear modelling and quantile regression modelling were used to relate the relative abundance of (juvenile and adult) fish to environmental predictors (seawater temperature, salinity, water column depth, bed-shear stress, and sediment type) in autumn and summer. The resulting regression parameters were used to map preferential and potential habitat distributions within a geographic information system. Models were evaluated by comparing predicted against observed abundances. Seabed sediment type was the main significant predictor of plaice preferential and potential habitats, whereas other factors did not show such a clear influence. The results contribute to a better understanding of the spatial ecology of the species.