bluuebunny/crossref_metadata_2025 huggingface dataset:
Regulation of S100A2 expression by TGF-β-induced MEK/ERK signalling and its role in cell migration/invasion
Authors: Naz Sarwat , Ranganathan Prathibha , Bodapati Priyanka , Shastry Arun H. , Mishra Laxmi N. , Kondaiah Paturu
Published: July 2012

S100A2, an EF hand calcium-binding protein, is a potential biomarker in several cancers and is also a TGF-β (transforming growth factor-β)-regulated gene in melanoma and lung cancer cells. However, the mechanism of S100A2 regulation by TGF-β and its significance in cancer progression remains largely unknown. In the present study we report the mechanism of S100A2 regulation by TGF-β and its possible role in TGF-β-mediated tumour promotion. Characterization of the S100A2 promoter revealed an AP-1 (activator protein-1) element at positions −1161 to −1151 as being the most critical factor for the TGF-β1 response. Chromatin immunoprecipitation and electrophoretic mobility-shift assays confirmed the functional binding of the AP-1 complex, predominantly JunB, to the S100A2 promoter in response to TGF-β1 in HaCaT keratinocytes. JunB overexpression markedly stimulated the S100A2 promoter which was blocked by the dominant–negative JunB and MEK1 [MAPK (mitogen-activated protein kinase)/ERK (extracellular-signal-regulated kinase) kinase 1] inhibitor, PD98059. Intriguingly, despite the presence of a putative SMAD-binding element, S100A2 regulation by TGF-β1 was found to be SMAD3 independent. Interestingly, p53 protein and TGF-β1 show synergistic regulation of the S100A2 promoter. Finally, knockdown of S100A2 expression compromised TGF-β1-induced cell migration and invasion of Hep3B cells. Together our findings highlight an important link between the TGF-β1-induced MAPK and p53 signalling pathways in the regulation of S100A2 expression and pro-tumorigenic actions.
Metal bioavailability dynamics during a two-year trial using ryegrass (Lolium perenne L.) grown in soils treated with biosolids and metal salts
Authors: Black Amanda , McLaren Ronald G. , Reichman Suzanne M. , Speir Thomas W. , Condron Leo M. , Houliston Gary
Published: July 2012

A 24-month field lysimeter experiment using ryegrass (Lolium perenne L.) grown in three soil types was used to investigate metal bioavailability dynamics following amendment with biosolids and metal salts (Cd, Cu, Ni, Zn). Common surrogates of soil metal bioavailability (total soil metal, EDTA, Ca(NO3)2, total dissolved, diffusive gradient in thin film, and modelled free ion activity) were determined on soil samples taken every 6 months. Ryegrass was also harvested every 6 months and analysed for metal concentrations. Across soils and treatments dissolved organic carbon (DOC) and pH decreased, whereas dissolved Ca and Mg increased with time. The free ion activity concentrations of each metal also increased over 24 months, whereas Ca(NO3)2-extracted metals were unchanged. Zinc presented the most changes in bioavailability status, with total Zn concentration decreasing over time, and EDTA-extractable and soil solution Zn increasing significantly by 1.82 mg kg–1 (1.1%) and 1.52 mg L–1 (29%), respectively. Shoot concentration of Zn increased by 1.32 mg kg–1 (2.7%), whereas shoot Ni concentration decreased by 0.65 mg kg–1 (4%). The findings of this study clearly demonstrated that over 24 months, soil metal bioavailability and shoot metal concentrations register only minor changes and appear to be unaffected by soil DOC and pH fluctuations.
Fate of the nitrification inhibitor dicyandiamide (DCD) sprayed on a grazed pasture: effect of rate and time of application
Authors: Kim Dong-Gill , Giltrap Donna , Saggar Surinder , Palmada Thilak , Berben Peter , Drysdale Doug
Published: July 2012

The objectives of this study were to improve our understanding of seasonal variation in the biophysical disappearance of the nitrification inhibitor dicyandiamide (DCD) in soil and the key regulatory factors. Changes in DCD concentrations in the soil and plant canopy were measured following application to dairy-grazed pasture soil and non-grazed pasture soil. Treatments included two levels of DCD alone (10 and 20 kg ha–1) applied to non-grazed pasture field plots, and DCD (10 kg ha–1) applied with urine and with urea fertiliser. DCD (10 kg ha–1) was also applied in grazed farmlets following grazing. About 4–40% of the DCD applied was intercepted and stayed on the plant canopy from <6 and up to 16 days, depending on the subsequent timing and intensity of rainfall. In this poorly drained soil, <10% of applied DCD leached below 10 cm depth. Neither the level of DCD nor the N source had any significant effect on the half-life of DCD in soil. The half-life of DCD did vary with season, ranging from 7 to 13 days in March to November respectively, and showed a linear decrease with observed increase in soil temperature between 10.7 and 16.5°C. The results suggest that to maintain an optimum effective DCD concentration in soil, different DCD application rates and frequency may be required in different seasons.
Marine protected areas and the value of spatially optimized fishery management
Authors: Rassweiler Andrew , Costello Christopher , Siegel David A.
Published: July 2012

There is a growing focus around the world on marine spatial planning, including spatial fisheries management. Some spatial management approaches are quite blunt, as when marine protected areas (MPAs) are established to restrict fishing in specific locations. Other management tools, such as zoning or spatial user rights, will affect the distribution of fishing effort in a more nuanced manner. Considerable research has focused on the ability of MPAs to increase fishery returns, but the potential for the broader class of spatial management approaches to outperform MPAs has received far less attention. We use bioeconomic models of seven nearshore fisheries in Southern California to explore the value of optimized spatial management in which the distribution of fishing is chosen to maximize profits. We show that fully optimized spatial management can substantially increase fishery profits relative to optimal nonspatial management but that the magnitude of this increase depends on characteristics of the fishing fleet and target species. Strategically placed MPAs can also increase profits substantially compared with nonspatial management, particularly if fishing costs are low, although profit increases available through optimal MPA-based management are roughly half those from fully optimized spatial management. However, if the same total area is protected by randomly placing MPAs, starkly contrasting results emerge: most random MPA designs reduce expected profits. The high value of spatial management estimated here supports continued interest in spatially explicit fisheries regulations but emphasizes that predicted increases in profits can only be achieved if the fishery is well understood and the regulations are strategically designed.
Cardiomyocyte-specific IκB kinase (IKK)/NF-κB activation induces reversible inflammatory cardiomyopathy and heart failure
Authors: Maier Harald J. , Schips Tobias G. , Wietelmann Astrid , Krüger Marcus , Brunner Cornelia , Sauter Martina , Klingel Karin , Böttger Thomas , Braun Thomas , Wirth Thomas
Published: July 2012

Inflammation is a major factor in heart disease. IκB kinase (IKK) and its downstream target NF-κB are regulators of inflammation and are activated in cardiac disorders, but their precise contributions and targets are unclear. We analyzed IKK/NF-κB function in the heart by a gain-of-function approach, generating an inducible transgenic mouse model with cardiomyocyte-specific expression of constitutively active IKK2. In adult animals, IKK2 activation led to inflammatory dilated cardiomyopathy and heart failure. Transgenic hearts showed infiltration with CD11b
+
cells, fibrosis, fetal reprogramming, and atrophy of myocytes with strong constitutively active IKK2 expression. Upon transgene inactivation, the disease was reversible even at an advanced stage. IKK-induced cardiomyopathy was dependent on NF-κB activation, as in vivo expression of IκBα superrepressor, an inhibitor of NF-κB, prevented the development of disease. Gene expression and proteomic analyses revealed enhanced expression of inflammatory cytokines, and an IFN type I signature with activation of the IFN-stimulated gene 15 (ISG15) pathway. In that respect, IKK-induced cardiomyopathy resembled Coxsackievirus-induced myocarditis, during which the NF-κB and ISG15 pathways were also activated. Vice versa, in cardiomyocytes lacking the regulatory subunit of IKK (IKKγ/NEMO), the induction of ISG15 was attenuated. We conclude that IKK/NF-κB activation in cardiomyocytes is sufficient to cause cardiomyopathy and heart failure by inducing an excessive inflammatory response and myocyte atrophy.
On the origin of long-range correlations in texts
Authors: Altmann Eduardo G. , Cristadoro Giampaolo , Esposti Mirko Degli
Published: July 2012

The complexity of human interactions with social and natural phenomena is mirrored in the way we describe our experiences through natural language. In order to retain and convey such a high dimensional information, the statistical properties of our linguistic output has to be highly correlated in time. An example are the robust observations, still largely not understood, of correlations on arbitrary long scales in literary texts. In this paper we explain how long-range correlations flow from highly structured linguistic levels down to the building blocks of a text (words, letters, etc..). By combining calculations and data analysis we show that correlations take form of a bursty sequence of events once we approach the semantically relevant topics of the text. The mechanisms we identify are fairly general and can be equally applied to other hierarchical settings.
Highly efficient and robust molecular ruthenium catalysts for water oxidation
Authors: Duan Lele , Araujo Carlos Moyses , Ahlquist Mårten S.G. , Sun Licheng
Published: July 2012

Water oxidation catalysts are essential components of light-driven water splitting systems, which could convert water to H
2
driven by solar radiation (H
2
O + 
h
ν → 1/2O
2
 + H
2
). The oxidation of water (H
2
O → 1/2O
2
 + 2H
+
 + 2e
-
) provides protons and electrons for the production of dihydrogen (2H
+
 + 2e
-
 → H
2
), a clean-burning and high-capacity energy carrier. One of the obstacles now is the lack of effective and robust water oxidation catalysts. Aiming at developing robust molecular Ru-bda (H
2
bda = 2,2
′
-bipyridine-6,6′-dicarboxylic acid) water oxidation catalysts, we carried out density functional theory studies, correlated the robustness of catalysts against hydration with the highest occupied molecular orbital levels of a set of ligands, and successfully directed the synthesis of robust Ru-bda water oxidation catalysts. A series of mononuclear ruthenium complexes [Ru(bda)L
2
] (L = pyridazine, pyrimidine, and phthalazine) were subsequently synthesized and shown to effectively catalyze Ce
IV
-driven [Ce
IV
 = Ce(NH
4
)
2
(NO
3
)
6
] water oxidation with high oxygen production rates up to 286 s
-1
and high turnover numbers up to 55,400.
Wnt pathway inhibition via the targeting of Frizzled receptors results in decreased growth and tumorigenicity of human tumors
Authors: Gurney Austin , Axelrod Fumiko , Bond Christopher J. , Cain Jennifer , Chartier Cecile , Donigan Lucas , Fischer Marcus , Chaudhari Aurélie , Ji May , Kapoun Ann M. , Lam Andrew , Lazetic Sasha , Ma Shirley , Mitra Satyajit , Park In-Kyung , Pickell Kellie , Sato Aaron , Satyal Sanjeev , Stroud Michelle , Tran Hoang , Yen Wan-Ching , Lewicki John , Hoey Timothy
Published: July 2012

The Wnt/β-catenin pathway, which signals through the Frizzled (Fzd) receptor family and several coreceptors, has long been implicated in cancer. Here we demonstrate a therapeutic approach to targeting the Wnt pathway with a monoclonal antibody, OMP-18R5. This antibody, initially identified by binding to Frizzled 7, interacts with five Fzd receptors through a conserved epitope within the extracellular domain and blocks canonical Wnt signaling induced by multiple Wnt family members. In xenograft studies with minimally passaged human tumors, this antibody inhibits the growth of a range of tumor types, reduces tumor-initiating cell frequency, and exhibits synergistic activity with standard-of-care chemotherapeutic agents.
Structure of the surface layer of the methanogenic archaean
Methanosarcina acetivorans
Authors: Arbing Mark A. , Chan Sum , Shin Annie , Phan Tung , Ahn Christine J. , Rohlin Lars , Gunsalus Robert P.
Published: July 2012

Archaea have a self-assembling proteinaceous surface (S-) layer as the primary and outermost boundary of their cell envelopes. The S-layer maintains structural rigidity, protects the organism from adverse environmental elements, and yet provides access to all essential nutrients. We have determined the crystal structure of one of the two “homologous” tandem polypeptide repeats that comprise the
Methanosarcina acetivorans
S-layer protein and propose a high-resolution model for a microbial S-layer. The molecular features of our hexameric S-layer model recapitulate those visualized by medium resolution electron microscopy studies of microbial S-layers and greatly expand our molecular view of S-layer dimensions, porosity, and symmetry. The S-layer model reveals a negatively charged molecular sieve that presents both a charge and size barrier to restrict access to the cell periplasmic-like space. The β-sandwich folds of the S-layer protein are structurally homologous to eukaryotic virus envelope proteins, suggesting that Archaea and viruses have arrived at a common solution for protective envelope structures. These results provide insight into the evolutionary origins of primitive cell envelope structures, of which the S-layer is considered to be among the most primitive: it also provides a platform for the development of self-assembling nanomaterials with diverse functional and structural properties.
1,500 year quantitative reconstruction of winter precipitation in the Pacific Northwest
Authors: Steinman Byron A. , Abbott Mark B. , Mann Michael E. , Stansell Nathan D. , Finney Bruce P.
Published: July 2012

Multiple paleoclimate proxies are required for robust assessment of past hydroclimatic conditions. Currently, estimates of drought variability over the past several thousand years are based largely on tree-ring records. We produced a 1,500-y record of winter precipitation in the Pacific Northwest using a physical model-based analysis of lake sediment oxygen isotope data. Our results indicate that during the Medieval Climate Anomaly (MCA) (900–1300 AD) the Pacific Northwest experienced exceptional wetness in winter and that during the Little Ice Age (LIA) (1450–1850 AD) conditions were drier, contrasting with hydroclimatic anomalies in the desert Southwest and consistent with climate dynamics related to the El Niño Southern Oscillation (ENSO) and the Pacific Decadal Oscillation (PDO). These findings are somewhat discordant with drought records from tree rings, suggesting that differences in seasonal sensitivity between the two proxies allow a more compete understanding of the climate system and likely explain disparities in inferred climate trends over centennial timescales.
Calcium-dependent folding of single calmodulin molecules
Authors: Stigler Johannes , Rief Matthias
Published: July 2012

Calmodulin is the primary calcium binding protein in living cells. Its function and structure depend strongly on calcium concentration. We used single molecule force spectroscopy by optical tweezers to study the folding of calmodulin in the physiologically relevant range. We find that full-length calmodulin switches from a rich and complex folding behavior at high calcium to a simple folding pathway at apo conditions. Using truncation mutants, we studied the individual domains separately. Folding and stability of the individual domains differ significantly at low calcium concentrations. With increasing calcium, the folding rate constants increase while unfolding rate constants decrease. The complete kinetic as well as energetic behavior of both domains could be modeled using a calcium-dependent three-pathway model. We find that the dominant folding pathway at high calcium concentrations proceeds via a transition state capable of binding one calcium ion. The folding of calmodulin seems to be designed to occur fast robustly over a large range of calcium concentrations and hence energetic stabilities.
Imaging electronic quantum motion with light
Authors: Dixit Gopal , Vendrell Oriol , Santra Robin
Published: July 2012

Imaging the quantum motion of electrons not only in real-time, but also in real-space is essential to understand for example bond breaking and formation in molecules, and charge migration in peptides and biological systems. Time-resolved imaging interrogates the unfolding electronic motion in such systems. We find that scattering patterns, obtained by X-ray time-resolved imaging from an electronic wavepacket, encode spatial and temporal correlations that deviate substantially from the common notion of the instantaneous electronic density as the key quantity being probed. Surprisingly, the patterns provide an unusually visual manifestation of the quantum nature of light. This quantum nature becomes central only for non-stationary electronic states and has profound consequences for time-resolved imaging.
Heat shock protein 90α (HSP90α), a substrate and chaperone of DNA-PK necessary for the apoptotic response
Authors: Solier Stéphanie , Kohn Kurt W. , Scroggins Bradley , Xu Wanping , Trepel Jane , Neckers Leonard , Pommier Yves
Published: July 2012

The “apoptotic ring” is characterized by the phosphorylation of histone H2AX at serine 139 (γ-H2AX) by DNA-dependent protein kinase (DNA-PK). The γ-H2AX apoptotic ring differs from the nuclear foci patterns observed in response to DNA-damaging agents. It contains phosphorylated DNA damage response proteins including activated Chk2, activated ATM, and activated DNA-PK itself but lacks MDC1 and 53BP1, which are required to initiate DNA repair. Because DNA-PK can phosphorylate heat shock protein 90α (HSP90α) in biochemical assays, we investigated whether HSP90α is involved in the apoptotic ring. Here we show that HSP90α is phosphorylated by DNA-PK on threonines 5 and 7 early during apoptosis and that both phosphorylated HSP90α and DNA-PK colocalize in the apoptotic ring. We also show that DNA-PK is a client of HSP90α and that HSP90α is required for full DNA-PK activation, γ-H2AX formation, DNA fragmentation, and apoptotic body formation. In contrast, HSP90 inhibition by geldanamycin markedly enhances TRAIL-induced DNA-PK and H2AX activation. Together, our results reveal that HSP90α is a substrate and chaperone of DNA-PK in the apoptotic response. The response of phosphorylated HSP90α to TRAIL and its localization to the γ-H2AX ring represent epigenetic features of apoptosis that offer insights for studying and monitoring nuclear apoptosis.
Photochemical oxidation of water and reduction of polyoxometalate anions at interfaces of water with ionic liquids or diethylether
Authors: Bernardini Gianluca , Wedd Anthony G. , Zhao Chuan , Bond Alan M.
Published: July 2012

Photoreduction of [P2W18O62]6-, [S2Mo18O62]4-, and [S2W18O62]4-polyoxometalate anions (POMs) and oxidation of water occurs when water–ionic liquid and water–diethylether interfaces are irradiated with white light (275–750 nm) or sunlight. The ionic liquids (ILs) employed were aprotic ([Bmim]X; Bmim = (1-butyl-3-methylimidazolium,X = BF4,PF6) and protic (DEAS = diethanolamine hydrogen sulphate; DEAP = diethanolamine hydrogen phosphate). Photochemical formation of reduced POMs at both thermodynamically stable and unstable water–IL interfaces led to their initial diffusion into the aqueous phase and subsequent extraction into the IL phase. The mass transport was monitored visually by color change and by steady-state voltammetry at microelectrodes placed near the interface and in the bulk solution phases. However, no diffusion into the organic phase was observed when [P2W18O62]6-was photo-reduced at the water–diethylether interface. In all cases, water acted as the electron donor to give the overall process: 4POM + 2H2O + hν → 4POM- + 4H+ + O2. However, more highly reduced POM species are likely to be generated as intermediates. The rate of diffusion of photo-generated POM-was dependent on the initial concentration of oxidized POM and the viscosity of the IL (or mixed phase system produced in cases in which the interface is thermodynamically unstable). In the water-DEAS system, the evolution of dioxygen was monitored in situ in the aqueous phase by using a Clark-type oxygen sensor. Differences in the structures of bulk and interfacial water are implicated in the activation of water. An analogous series of reactions occurred upon irradiation of solid POM salts in the presence of water vapor.
Work and information processing in a solvable model of Maxwell’s demon
Authors: Mandal Dibyendu , Jarzynski Christopher
Published: July 2012

We describe a minimal model of an autonomous Maxwell demon, a device that delivers work by rectifying thermal fluctuations while simultaneously writing information to a memory register. We solve exactly for the steady-state behavior of our model, and we construct its phase diagram. We find that our device can also act as a “Landauer eraser”, using externally supplied work to remove information from the memory register. By exposing an explicit, transparent mechanism of operation, our model offers a simple paradigm for investigating the thermodynamics of information processing by small systems.
α4βδ GABA
A
receptors are high-affinity targets for γ-hydroxybutyric acid (GHB)
Authors: Absalom Nathan , Eghorn Laura F. , Villumsen Inge S. , Karim Nasiara , Bay Tina , Olsen Jesper V. , Knudsen Gitte M. , Bräuner-Osborne Hans , Frølund Bente , Clausen Rasmus P. , Chebib Mary , Wellendorph Petrine
Published: July 2012

γ-Hydroxybutyric acid (GHB) binding to brain-specific high-affinity sites is well-established and proposed to explain both physiological and pharmacological actions. However, the mechanistic links between these lines of data are unknown. To identify molecular targets for specific GHB high-affinity binding, we undertook photolinking studies combined with proteomic analyses and identified several GABA
A
receptor subunits as possible candidates. A subsequent functional screening of various recombinant GABA
A
receptors in
Xenopus laevis
oocytes using the two-electrode voltage clamp technique showed GHB to be a partial agonist at αβδ- but not αβγ-receptors, proving that the δ-subunit is essential for potency and efficacy. GHB showed preference for α4 over α(1,2,6)-subunits and preferably activated α4β1δ (EC
50
= 140 nM) over α4β(2/3)δ (EC
50
= 8.41/1.03 mM). Introduction of a mutation, α4F71L, in α4β1(δ)-receptors completely abolished GHB but not GABA function, indicating nonidentical binding sites. Radioligand binding studies using the specific GHB radioligand [
3
H](
E
,
RS
)-(6,7,8,9-tetrahydro-5-hydroxy-5
H
-benzocyclohept-6-ylidene)acetic acid showed a 39% reduction (
P
= 0.0056) in the number of binding sites in α4 KO brain tissue compared with WT controls, corroborating the direct involvement of the α4-subunit in high-affinity GHB binding. Our data link specific GHB forebrain binding sites with α4-containing GABA
A
receptors and postulate a role for extrasynaptic α4δ-containing GABA
A
receptors in GHB pharmacology and physiology. This finding will aid in elucidating the molecular mechanisms behind the proposed function of GHB as a neurotransmitter and its unique therapeutic effects in narcolepsy and alcoholism.
Arrangement of subunits in intact mammalian mitochondrial ATP synthase determined by cryo-EM
Authors: Baker Lindsay A. , Watt Ian N. , Runswick Michael J. , Walker John E. , Rubinstein John L.
Published: July 2012

Mitochondrial ATP synthase is responsible for the synthesis of ATP, a universal energy currency in cells. Whereas X-ray crystallography has revealed the structure of the soluble region of the complex and the membrane-intrinsic c-subunits, little is known about the structure of the six other proteins (a, b, f, A6L, e, and g) that comprise the membrane-bound region of the complex in animal mitochondria. Here, we present the structure of intact bovine mitochondrial ATP synthase at ∼18 Å resolution by electron cryomicroscopy of single particles in amorphous ice. The map reveals that the a-subunit and c
8
-ring of the complex interact with a small contact area and that the b-subunit spans the membrane without contacting the c
8
-ring. The e- and g-subunits extend from the a-subunit density distal to the c
8
-ring. The map was calculated from images of a preparation of the enzyme solubilized with the detergent dodecyl maltoside, which is visible in electron cryomicroscopy maps. The structure shows that the micelle surrounding the complex is curved. The observed bend in the micelle of the detergent-solubilized complex is consistent with previous electron tomography experiments and suggests that monomers of ATP synthase are sufficient to produce curvature in lipid bilayers.
Transcriptional regulation of juvenile hormone-mediated induction of Krüppel homolog 1, a repressor of insect metamorphosis
Authors: Kayukawa Takumi , Minakuchi Chieka , Namiki Toshiki , Togawa Toru , Yoshiyama Michiyo , Kamimura Manabu , Mita Kazuei , Imanishi Shigeo , Kiuchi Makoto , Ishikawa Yukio , Shinoda Tetsuro
Published: July 2012

The Krüppel homolog 1 gene (Kr-h1) has been proposed to play a key role in the repression of insect metamorphosis.Kr-h1is assumed to be induced by juvenile hormone (JH) via a JH receptor, methoprene-tolerant (Met), but the mechanism of induction is unclear. To elucidate the molecular mechanism ofKr-h1induction, we first cloned cDNAs encodingKr-h1(BmKr-h1) andMet(BmMet1andBmMet2) homologs fromBombyx mori. In aB. moricell line,BmKr-h1was rapidly induced by subnanomolar levels of natural JHs. Reporter assays identified a JH response element (kJHRE), comprising 141 nucleotides, located ∼2 kb upstream from theBmKr-h1transcription start site. The core region ofkJHRE (GGCCTCCACGTG) contains a canonical E-box sequence to which Met, a basic helix–loop–helix Per-ARNT-Sim (bHLH–PAS) transcription factor, is likely to bind. In mammalian HEK293 cells, which lack an intrinsic JH receptor, ectopic expression of BmMet2 fused with Gal4DBD induced JH-dependent activity of an upstream activation sequence reporter. Meanwhile, thekJHRE reporter was activated JH-dependently in HEK293 cells only when cotransfected with BmMet2 and BmSRC, another bHLH–PAS family member, suggesting that BmMet2 and BmSRC jointly interact withkJHRE. We also found that the interaction between BmMet2 and BmSRC is dependent on JH. Therefore, we propose the following hypothesis for the mechanism of JH-mediated induction ofBmKr-h1: BmMet2 accepts JH as a ligand, JH-liganded BmMet2 interacts with BmSRC, and the JH/BmMet2/BmSRC complex activatesBmKr-h1by interacting withkJHRE.
Avibactam is a covalent, reversible, non–β-lactam β-lactamase inhibitor
Authors: Ehmann David E. , Jahić Haris , Ross Philip L. , Gu Rong-Fang , Hu Jun , Kern Gunther , Walkup Grant K. , Fisher Stewart L.
Published: July 2012

Avibactam is a β-lactamase inhibitor that is in clinical development, combined with β-lactam partners, for the treatment of bacterial infections comprising Gram-negative organisms. Avibactam is a structural class of inhibitor that does not contain a β-lactam core but maintains the capacity to covalently acylate its β-lactamase targets. Using the TEM-1 enzyme, we characterized avibactam inhibition by measuring the on-rate for acylation and the off-rate for deacylation. The deacylation off-rate was 0.045 min
−1
, which allowed investigation of the deacylation route from TEM-1. Using NMR and MS, we showed that deacylation proceeds through regeneration of intact avibactam and not hydrolysis. Other than TEM-1, four additional clinically relevant β-lactamases were shown to release intact avibactam after being acylated. We showed that avibactam is a covalent, slowly reversible inhibitor, which is a unique mechanism of inhibition among β-lactamase inhibitors.
Structural and functional characterization of the two phosphoinositide binding sites of PROPPINs, a β-propeller protein family
Authors: Krick Roswitha , Busse Ricarda A. , Scacioc Andreea , Stephan Milena , Janshoff Andreas , Thumm Michael , Kühnel Karin
Published: July 2012

β-propellers that bind polyphosphoinositides (PROPPINs), a eukaryotic WD-40 motif-containing protein family, bind via their predicted β-propeller fold the polyphosphoinositides PtdIns3P and PtdIns(3,5)P
2
using a conserved FRRG motif. PROPPINs play a key role in macroautophagy in addition to other functions. We present the 3.0-Å crystal structure of
Kluyveromyces lactis
Hsv2, which shares significant sequence homologies with its three
Saccharomyces cerevisiae
homologs Atg18, Atg21, and Hsv2. It adopts a seven-bladed β-propeller fold with a rare nonvelcro propeller closure. Remarkably, in the crystal structure, the two arginines of the FRRG motif are part of two distinct basic pockets formed by a set of highly conserved residues. In comprehensive in vivo and in vitro studies of ScAtg18 and ScHsv2, we define within the two pockets a set of conserved residues essential for normal membrane association, phosphoinositide binding, and biological activities. Our experiments show that PROPPINs contain two individual phosphoinositide binding sites. Based on docking studies, we propose a model for phosphoinositide binding of PROPPINs.
Emergence of neural encoding of auditory objects while listening to competing speakers
Authors: Ding Nai , Simon Jonathan Z.
Published: July 2012

A visual scene is perceived in terms of visual objects. Similar ideas have been proposed for the analogous case of auditory scene analysis, although their hypothesized neural underpinnings have not yet been established. Here, we address this question by recording from subjects selectively listening to one of two competing speakers, either of different or the same sex, using magnetoencephalography. Individual neural representations are seen for the speech of the two speakers, with each being selectively phase locked to the rhythm of the corresponding speech stream and from which can be exclusively reconstructed the temporal envelope of that speech stream. The neural representation of the attended speech dominates responses (with latency near 100 ms) in posterior auditory cortex. Furthermore, when the intensity of the attended and background speakers is separately varied over an 8-dB range, the neural representation of the attended speech adapts only to the intensity of that speaker but not to the intensity of the background speaker, suggesting an object-level intensity gain control. In summary, these results indicate that concurrent auditory objects, even if spectrotemporally overlapping and not resolvable at the auditory periphery, are neurally encoded individually in auditory cortex and emerge as fundamental representational units for top-down attentional modulation and bottom-up neural adaptation.
The genome of melon (
Cucumis melo
L.)
Authors: Garcia-Mas Jordi , Benjak Andrej , Sanseverino Walter , Bourgeois Michael , Mir Gisela , González Víctor M. , Hénaff Elizabeth , Câmara Francisco , Cozzuto Luca , Lowy Ernesto , Alioto Tyler , Capella-Gutiérrez Salvador , Blanca Jose , Cañizares Joaquín , Ziarsolo Pello , Gonzalez-Ibeas Daniel , Rodríguez-Moreno Luis , Droege Marcus , Du Lei , Alvarez-Tejado Miguel , Lorente-Galdos Belen , Melé Marta , Yang Luming , Weng Yiqun , Navarro Arcadi , Marques-Bonet Tomas , Aranda Miguel A. , Nuez Fernando , Picó Belén , Gabaldón Toni , Roma Guglielmo , Guigó Roderic , Casacuberta Josep M. , Arús Pere , Puigdomènech Pere
Published: July 2012

We report the genome sequence of melon, an important horticultural crop worldwide. We assembled 375 Mb of the double-haploid line DHL92, representing 83.3% of the estimated melon genome. We predicted 27,427 protein-coding genes, which we analyzed by reconstructing 22,218 phylogenetic trees, allowing mapping of the orthology and paralogy relationships of sequenced plant genomes. We observed the absence of recent whole-genome duplications in the melon lineage since the ancient eudicot triplication, and our data suggest that transposon amplification may in part explain the increased size of the melon genome compared with the close relative cucumber. A low number of nucleotide-binding site–leucine-rich repeat disease resistance genes were annotated, suggesting the existence of specific defense mechanisms in this species. The DHL92 genome was compared with that of its parental lines allowing the quantification of sequence variability in the species. The use of the genome sequence in future investigations will facilitate the understanding of evolution of cucurbits and the improvement of breeding strategies.
Mirror neurons encode the subjective value of an observed action
Authors: Caggiano Vittorio , Fogassi Leonardo , Rizzolatti Giacomo , Casile Antonino , Giese Martin A. , Thier Peter
Published: July 2012

Objects grasped by an agent have a value not only for the acting agent, but also for an individual observing the grasping act. The value that the observer attributes to the object that is grasped can be pivotal for selecting a possible behavioral response. Mirror neurons in area F5 of the monkey premotor cortex have been suggested to play a crucial role in the understanding of action goals. However, it has not been addressed if these neurons are also involved in representing the value of the grasped object. Here we report that observation-related neuronal responses of F5 mirror neurons are indeed modulated by the value that the monkey associates with the grasped object. These findings suggest that during action observation F5 mirror neurons have access to key information needed to shape the behavioral responses of the observer.
High-frequency self-aligned graphene transistors with transferred gate stacks
Authors: Cheng Rui , Bai Jingwei , Liao Lei , Zhou Hailong , Chen Yu , Liu Lixin , Lin Yung-Chen , Jiang Shan , Huang Yu , Duan Xiangfeng
Published: July 2012

Graphene has attracted enormous attention for radio-frequency transistor applications because of its exceptional high carrier mobility, high carrier saturation velocity, and large critical current density. Herein we report a new approach for the scalable fabrication of high-performance graphene transistors with transferred gate stacks. Specifically, arrays of gate stacks are first patterned on a sacrificial substrate, and then transferred onto arbitrary substrates with graphene on top. A self-aligned process, enabled by the unique structure of the transferred gate stacks, is then used to position precisely the source and drain electrodes with minimized access resistance or parasitic capacitance. This process has therefore enabled scalable fabrication of self-aligned graphene transistors with unprecedented performance including a record-high cutoff frequency up to 427 GHz. Our study defines a unique pathway to large-scale fabrication of high-performance graphene transistors, and holds significant potential for future application of graphene-based devices in ultra–high-frequency circuits.
Molecular mechanism of proton transport in CLC Cl
-
/H
+
exchange transporters
Authors: Feng Liang , Campbell Ernest B. , MacKinnon Roderick
Published: July 2012

CLC proteins underlie muscle, kidney, bone, and other organ system function by catalyzing the transport of Cl
-
ions across cell and organellar membranes. Some CLC proteins are ion channels while others are pumps that exchange Cl
-
for H
+
. The pathway through which Cl
-
ions cross the membrane has been characterized, but the transport of H
+
and the principle by which their movement is coupled to Cl
-
movement is not well understood. Here we show that H
+
transport depends not only on the presence of a specific glutamate residue but also the presence of Cl
-
ions. H
+
transport, however, can be isolated and analyzed in the absence of Cl
-
by mutating the glutamate to alanine and adding carboxylate-containing molecules to solution, consistent with the notion that H
+
transfer is mediated through the entry of a carboxylate group into the anion pathway. Cl
-
ions and carboxylate interact with each other strongly. These data support a mechanism in which the glutamate carboxylate functions as a surrogate Cl
-
ion, but it can accept a H
+
and transfer it between the external solution and the central Cl
-
binding site, coupled to the movement of 2 Cl
-
ions.
Synthesis of substituted isoquinolines utilizing palladium-catalyzed α-arylation of ketones
Authors: Donohoe Timothy J. , Pilgrim Ben S. , Jones Geraint R. , Bassuto José A.
Published: July 2012

The utilization of sequential palladium-catalyzed α-arylation and cyclization reactions provides a general approach to an array of isoquinolines and their corresponding
N
-oxides. This methodology allows the convergent combination of readily available precursors in a regioselective manner and in excellent overall yields. This powerful route to polysubstituted isoquinolines, which is not limited to electron rich moieties, also allows rapid access to analogues of biologically active compounds.
Evolution of insect arylalkylamine
N
-acetyltransferases: Structural evidence from the yellow fever mosquito,
Aedes aegypti
Authors: Han Qian , Robinson Howard , Ding Haizhen , Christensen Bruce M. , Li Jianyong
Published: July 2012

Arylalkylamine
N
-acetyltransferase (aaNAT) catalyzes the transacetylation from acetyl-CoA to arylalkylamines. aaNATs are involved in sclerotization and neurotransmitter inactivation in insects. Phyletic distribution analysis confirms three clusters of aaNAT-like sequences in insects: typical insect aaNAT, polyamine NAT-like aaNAT, and mosquito unique putative aaNAT (paaNAT). Here we studied three proteins: aaNAT2, aaNAT5b, and paaNAT7, each from a different cluster. aaNAT2, a protein from the typical insect aaNAT cluster, uses histamine as a substrate as well as the previously identified arylalkylamines. aaNAT5b, a protein from polyamine NAT -like aaNAT cluster, uses hydrazine and histamine as substrates. The crystal structure of aaNAT2 was determined using single-wavelength anomalous dispersion methods, and that of native aaNAT2, aaNAT5b and paaNAT7 was detected using molecular replacement techniques. All three aaNAT structures have a common fold core of GCN5-related
N
-acetyltransferase superfamily proteins, along with a unique structural feature: helix/helices between β3 and β4 strands. Our data provide a start toward a more comprehensive understanding of the structure–function relationship and physiology of aaNATs from the mosquito
Aedes aegypti
and serve as a reference for studying the aaNAT family of proteins from other insect species. The structures of three different types of aaNATs may provide targets for designing insecticides for use in mosquito control.
Augmenting muscle diacylglycerol and triacylglycerol content by blocking fatty acid oxidation does not impede insulin sensitivity
Authors: Timmers Silvie , Nabben Miranda , Bosma Madeleen , van Bree Bianca , Lenaers Ellen , van Beurden Denis , Schaart Gert , Westerterp-Plantenga Margriet S. , Langhans Wolfgang , Hesselink Matthijs K. C. , Schrauwen-Hinderling Vera B. , Schrauwen Patrick
Published: July 2012

A low fat oxidative capacity has been linked to muscle diacylglycerol (DAG) accumulation and insulin resistance. Alternatively, a low fat oxidation rate may stimulate glucose oxidation, thereby enhancing glucose disposal. Here, we investigated whether an ethyl-2-[6-(4-chlorophenoxy)hexyl]-oxirane-2-carboxylate (etomoxir)-induced inhibition of fat oxidation leads to muscle fat storage and insulin resistance. An intervention in healthy male subjects was combined with studies in human primary myotubes. Furthermore, muscle DAG and triacylglycerol (TAG), mitochondrial function, and insulin signaling were examined in etomoxir-treated C57bl6 mice. In humans, etomoxir administration increased glucose oxidation at the expense of fat oxidation. This effect was accompanied by an increased abundance of GLUT4 at the sarcolemma and a lowering of plasma glucose levels, indicative of improved glucose homeostasis. In mice, etomoxir injections resulted in accumulation of muscle TAG and DAG, yet improved insulin-stimulated GLUT4 translocation. Also in human myotubes, insulin signaling was improved by etomoxir, in the presence of increased intramyocellular lipid accumulation. These insulin-sensitizing effects in mice and human myotubes were accompanied by increased phosphorylation of AMP-activated protein kinase (AMPK). Our results show that a reduction in fat oxidation leading to accumulation of muscle DAG does not necessarily lead to insulin resistance, as the reduction in fat oxidation may activate AMPK.
Dynamics, transition states, and timing of bond formation in Diels–Alder reactions
Authors: Black Kersey , Liu Peng , Xu Lai , Doubleday Charles , Houk Kendall N.
Published: July 2012

The time-resolved mechanisms for eight Diels–Alder reactions have been studied by quasiclassical trajectories at 298 K, with energies and derivatives computed by UB3LYP/6-31G(d). Three of these reactions were also simulated at high temperature to compare with experimental results. The reaction trajectories require 50–150 fs on average to transverse the region near the saddle point where bonding changes occur. Even with symmetrical reactants, the trajectories invariably involve unequal bond formation in the transition state. Nevertheless, the time gap between formation of the two new bonds is shorter than a C─C vibrational period. At 298 K, most Diels–Alder reactions are concerted and stereospecific, but at high temperatures (approximately 1,000 K) a small fraction of trajectories lead to diradicals. The simulations illustrate and affirm the bottleneck property of the transition state and the close connection between dynamics and the conventional analysis based on saddle point structure.
Melanoregulin regulates a shedding mechanism that drives melanosome transfer from melanocytes to keratinocytes
Authors: Wu Xufeng S. , Masedunskas Andreas , Weigert Roberto , Copeland Neal G. , Jenkins Nancy A. , Hammer John A.
Published: July 2012

Mammalian pigmentation is driven by the intercellular transfer of pigment-containing melanosomes from the tips of melanocyte dendrites to surrounding keratinocytes. Tip accumulation of melanosomes requires myosin Va, because melanosomes concentrate in the center of melanocytes from myosin Va-null (
dilute
) mice. This distribution defect results in inefficient melanosome transfer and a dilution of coat color.
Dilute
mice that simultaneously lack melanoregulin, the product of the
dilute suppressor
locus, exhibit a nearly complete restoration of coat color, but, surprisingly, melanosomes remain concentrated in the center of their melanocytes. Here we show that
dilute/dsu
melanocytes, but not
dilute
melanocytes, readily transfer the melanosomes concentrated in their center to surrounding keratinocytes in situ. Using time-lapse imaging of WT melanocyte/keratinocyte cocultures in which the plasma membranes of the two cells are marked with different colors, we define an intercellular melanosome transfer pathway that involves the shedding by the melanocyte of melanosome-rich packages, which subsequently are phagocytosed by the keratinocyte. Shedding, which occurs primarily at dendritic tips but also from more central regions, involves adhesion to the keratinocyte, thinning behind the forming package, and apparent self-abscission. Finally, we show that shedding from the cell center is sixfold more frequent in cultured
dilute/dsu
melanocytes than in
dilute
melanocytes, consistent with the in situ data. Together, these results explain how
dsu
restores the coat color of
dilute
mice without restoring intracellular melanosome distribution, indicate that melanoregulin is a negative regulator of melanosome transfer, and provide insight into the mechanism of intercellular melanosome transfer.
Brain and muscle Arnt-like protein-1 (BMAL1) controls circadian cell proliferation and susceptibility to UVB-induced DNA damage in the epidermis
Authors: Geyfman Mikhail , Kumar Vivek , Liu Qiang , Ruiz Rolando , Gordon William , Espitia Francisco , Cam Eric , Millar Sarah E. , Smyth Padhraic , Ihler Alexander , Takahashi Joseph S. , Andersen Bogi
Published: July 2012

The role of the circadian clock in skin and the identity of genes participating in its chronobiology remain largely unknown, leading us to define the circadian transcriptome of mouse skin at two different stages of the hair cycle, telogen and anagen. The circadian transcriptomes of telogen and anagen skin are largely distinct, with the former dominated by genes involved in cell proliferation and metabolism. The expression of many metabolic genes is antiphasic to cell cycle-related genes, the former peaking during the day and the latter at night. Consistently, accumulation of reactive oxygen species, a byproduct of oxidative phosphorylation, and S-phase are antiphasic to each other in telogen skin. Furthermore, the circadian variation in S-phase is controlled by BMAL1 intrinsic to keratinocytes, because keratinocyte-specific deletion of
Bmal1
obliterates time-of-day–dependent synchronicity of cell division in the epidermis leading to a constitutively elevated cell proliferation. In agreement with higher cellular susceptibility to UV-induced DNA damage during S-phase, we found that mice are most sensitive to UVB-induced DNA damage in the epidermis at night. Because in the human epidermis maximum numbers of keratinocytes go through S-phase in the late afternoon, we speculate that in humans the circadian clock imposes regulation of epidermal cell proliferation so that skin is at a particularly vulnerable stage during times of maximum UV exposure, thus contributing to the high incidence of human skin cancers.
Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal
Authors: Fietz Simone A. , Lachmann Robert , Brandl Holger , Kircher Martin , Samusik Nikolay , Schröder Roland , Lakshmanaperumal Naharajan , Henry Ian , Vogt Johannes , Riehn Axel , Distler Wolfgang , Nitsch Robert , Enard Wolfgang , Pääbo Svante , Huttner Wieland B.
Published: July 2012

The expansion of the neocortex during mammalian brain evolution results primarily from an increase in neural progenitor cell divisions in its two principal germinal zones during development, the ventricular zone (VZ) and the subventricular zone (SVZ). Using mRNA sequencing, we analyzed the transcriptomes of fetal human and embryonic mouse VZ, SVZ, and cortical plate. In mouse, the transcriptome of the SVZ was more similar to that of the cortical plate than that of the VZ, whereas in human the opposite was the case, with the inner and outer SVZ being highly related to each other despite their cytoarchitectonic differences. We describe sets of genes that are up- or down-regulated in each germinal zone. These data suggest that cell adhesion and cell–extracellular matrix interactions promote the proliferation and self-renewal of neural progenitors in the developing human neocortex. Notably, relevant extracellular matrix-associated genes include distinct sets of collagens, laminins, proteoglycans, and integrins, along with specific sets of growth factors and morphogens. Our data establish a basis for identifying novel cell-type markers and open up avenues to unravel the molecular basis of neocortex expansion during evolution.