bluuebunny/crossref_metadata_2025_split huggingface dataset:
The BOHR effect before Perutz
Authors: Brunori Maurizio 
Published: August 2012

AbstractBefore the outbreak of World War II, Jeffries Wyman postulated that the Bohr effect in hemoglobin demanded the oxygen linked dissociation of the imidazole of two histidines of the polypeptide. This proposal emerged from a rigorous analysis of the acid–base titration curves of oxy‐ and deoxy‐hemoglobin, at a time when the information on the chemistry and structure of the protein was essentially nil. The magnetochemical properties of hemoglobin led Linus Pauling to hypothesize that the (so called) Bohr histidines were coordinated to the heme iron in the fifth and sixth positions; and Wyman shared this opinion. However, this structural hypothesis was abandoned in 1951 when J. Wyman and D. W. Allen proposed the pK shift of the oxygen linked histidines to be the result of “…a change of configuration of the hemoglobin molecule as a whole accompanying oxygenation.” This shift in paradigm, that was published well before the 3D structure of hemoglobin was solved by M.F. Perutz, paved the way to the concept of allostery. After 1960 the availability of the crystallographic structure opened new horizons to the interpretation of the allosteric properties of hemoglobin.
Hydroxynitrile Lyases with α/β‐Hydrolase Fold: Two Enzymes with Almost Identical 3D Structures but Opposite Enantioselectivities and Different Reaction Mechanisms
Authors: Andexer Jennifer N. , Staunig Nicole , Eggert Thorsten , Kratky Christoph , Pohl Martina , Gruber Karl 
Published: August 2012

AbstractHydroxynitrile lyases (HNLs) catalyze the cleavage of cyanohydrins to yield hydrocyanic acid (HCN) and the respective carbonyl compound and are key enzymes in the process of cyanogenesis in plants. In organic syntheses, HNLs are used as biocatalysts for the formation of enantiopure cyanohydrins. We determined the structure of the recently identified, R‐selective HNL from Arabidopsis thaliana (AtHNL) at a crystallographic resolution of 2.5 Å. The structure exhibits an α/β‐hydrolase fold, very similar to the homologous, but S‐selective, HNL from Hevea brasiliensis (HbHNL). The similarities also extend to the active sites of these enzymes, with a Ser‐His‐Asp catalytic triad present in all three cases. In order to elucidate the mode of substrate binding and to understand the unexpected opposite enantioselectivity of AtHNL, complexes of the enzyme with both (R)‐ and (S)‐mandelonitrile were modeled using molecular docking simulations. Compared to the complex of HbHNL with (S)‐mandelonitrile, the calculations produced an approximate mirror image binding mode of the substrate with the phenyl rings located at very similar positions, but with the cyano groups pointing in opposite directions. A catalytic mechanism for AtHNL is proposed, in which His236 from the catalytic triad acts as a general base and the emerging negative charge on the cyano group is stabilized by main‐chain amide groups and an α‐helix dipole very similar to α/β‐hydrolases. This mechanistic proposal is additionally supported by mutagenesis studies.
Direct Cloning, Genetic Engineering, and Heterologous Expression of the Syringolin Biosynthetic Gene Cluster in E. coli through Red/ET Recombineering
Authors: Bian Xiaoying , Huang Fan , Stewart Francis A. , Xia Liqiu , Zhang Youming , Müller Rolf 
Published: August 2012

AbstractThe reconstruction of a natural product biosynthetic pathway from bacteria in a vector and subsequent heterologous expression in a technically amenable microbial system represents an efficient alternative to empirical traditional methods for functional discovery, yield improvement, and genetic engineering to produce “unnatural” derivatives. However, the traditional cloning procedure based on genomic library construction and screening are complicated due to the large size (>10 kb) of most biosynthetic pathways. Here, we describe the direct cloning of a partial syringolin biosynthetic gene cluster (sylCDE, 19 kb) from a digested genomic DNA mixture of Pseudomonas syringae into a plasmid in which sylCDE is under the control of an inducible promoter by one step linear‐plus‐linear homologous recombination (LLHR) in Escherichia coli. After expression in E. coli GB05‐MtaA, two new syringolin derivatives were discovered. The complete syringolin gene cluster was assembled by addition of sylAB and exchange of a synthetic bidirectional promoter against the native promoter to drive sylB and sylC expression by using Red/ET recombineering. The varying production distribution of syringolin derivatives showed the different efficiencies of native and synthetic promoters in E. coli. The successful reconstitution and expression of the syringolin biosynthetic pathway shows that Red/ET recombineering is an efficient tool to clone and engineer secondary metabolite biosynthetic pathways.
Synthesis, Characterization, and Use of NbV/CeIV‐Mixed Oxides in the Direct Carboxylation of Ethanol by using Pervaporation Membranes for Water Removal
Authors: Dibenedetto Angela , Aresta Michele , Angelini Antonella , Ethiraj Jayashree , Aresta Brunella Maria 
Published: August 2012

AbstractNew catalytic systems based on ceria have been used in the direct carboxylation of ethanol. The catalytic behavior of Al2O3and Nb2O5loaded ceria is compared, the latter showing a better performance. A morphological and structural study has been carried out on Nb2O5/CeO2catalysts in order to explain their behavior in catalysis. Pervaporation membranes have been used for water separation. The synthesis of diethylcarbonate (DEC) has been carried out either in a liquid phase (ethanol) pressurized with CO2or in supercritical conditions. A set‐up has been developed that allows the production of quite pure DEC (>90 %) with recycling of CO2and ethanol.
β‐D‐Glucosyl Conjugates of Highly Potent Inhibitors of Blood Coagulation Factor Xa Bearing 2‐Chorothiophene as a P1 Motif
Authors: Lopopolo Gianfranco , de Candia Modesto , Panza Luigi , Romano Maria Rosaria , Lograno Marcello Diego , Campagna Francesco , Altomare Cosimo 
Published: August 2012

AbstractWe synthesized a novel O‐glucoside of the recently reported potent factor Xa (fXa) inhibitor 1, which bears a 5‐chlorothien‐2‐yl moiety and 1‐isopropylpiperidine as fragments that bind the S1 and S4 enzyme pockets, respectively. A β‐D‐glucosyl unit was conjugated through an ether‐linked C3‐alkyl spacer to the central phenyl ring of 1. The synthesized β‐D‐glucose‐based compound 16 achieved picomolar inhibitory potency against human fXa (Ki=60 pM) and high selectivity over thrombin and other serine proteases. In addition to the chlorothienyl S1 binder, a large gain in ΔG resulted from the addition of protonated 1‐isopropylpiperidine (ΔΔG=29.7–30.5 kJ mol−1), which should bind to the aromatic S4 pocket through efficient cation–π and CH⋅⋅⋅π interactions. Instead, the C3‐alkyl‐linked glucose fragment, which is likely directed toward the solvent outside the enzyme binding site, improves ΔG by an average of 2.9–3.8 kJ mol−1. Compound 16 showed sub‐micromolar in vitro anticoagulant activity, as assessed by prothrombin time (PT) and activated thromboplastin time (aPTT) clotting assays in pooled human plasma (PT2 and aPTT2 equal to 0.135 and 0.389 μM, respectively). Although compound 16 was 1.4‐fold less active than parent compound 1 in the ex vivo anticoagulant assay in mice, it showed a significant (1.6‐fold) prolongation of PT relative to controls (P<0.05) 60 min after oral dosing (75 mg kg−1).
Molecular Organization of Various Collagen Fragments as Revealed by Atomic Force Microscopy and Diffusion‐Ordered NMR Spectroscopy
Authors: Stötzel Sabine , Schurink Marloes , Wienk Hans , Siebler Uschi , Burg‐Roderfeld Monika , Eckert Thomas , Kulik Bianca , Wechselberger Rainer , Sewing Judith , Steinmeyer Jürgen , Oesser Steffen , Boelens Rolf , Siebert Hans‐Christian 
Published: August 2012

AbstractHeterogeneous mixtures of collagen fragments can be used as nutrition supplement or as key ingredients for ointments with therapeutic relevance in wound healing. Some mixtures of collagen fragments are referred to as collagen hydrolysates owing to the production process with hydrolytic enzymes. Since the precise composition of collagen hydrolysates is generally unknown, it is of interest to analyze samples containing various collagen fragments with appropriate biophysical methods. Any product optimization without a profound knowledge concerning the size and the molecular weight distribution of its components is nearly impossible. It turned out that a combination of AFM methods with NMR techniques is exceptionally suited to examine the size range and the aggregation behavior of the collagen fragments in the hydrolysates of fish, jellyfish, chicken, porcine and bovine collagen. Supported by molecular modeling calculations, the AFM and NMR experiments provide a detailed knowledge about the composition of collagen hydrolysates and collagen ointments. Furthermore, the data allow a correlation between the size of the fragments and their potential bioactivity.
Bicarbonate efflux via GABAA receptors depolarizes membrane potential and inhibits two‐pore domain potassium channels of astrocytes in rat hippocampal slices
Authors: Ma Bao‐Feng , Xie Min‐Jie , Zhou Min 
Published: August 2012

AbstractIncreasing evidence indicates the functional expression of ionotropic γ‐aminobutyric acid receptor (GABAA‐R) in astrocytes. However, it remains controversial in regard to the intracellular Cl− concentration ([Cl−]i) and the functional role of anion‐selective GABAA‐R in astrocytes. In gramicidin perforated‐patch recordings from rat hippocampal CA1 astrocytes, GABA and GABAA‐R‐specific agonist THIP depolarized astrocyte membrane potential (Vm), and the THIP‐induced currents reversed at the voltages between −75.3 and −78.3 mV, corresponding to a [Cl−]i of 3.1–3.9 mM that favored a passive distribution of Cl− anions across astrocyte membrane. Further analysis showed that GABAA‐R‐induced Vm depolarization was ascribed to HCO3− efflux, while a passively distributed Cl− mediated no net flux or influx of Cl− that leads to an unchanged or hyperpolarized Vm. In addition to a rapidly activated GABAA‐R current component, GABA and THIP also induced a delayed inward current (DIC) in 63% of astrocytes. The DIC became manifest after agonist withdrawal and enhanced in amplitude with increasing agonist application duration or concentrations. Astrocytic two‐pore domain K+ channels (K2Ps), especially TWIK‐1, appeared to underlie the DIC, because (1) acidic intracellular pH, as a result of HCO3− efflux, inhibited TWIK‐1, (2) the DIC remained in the Cs+ recording solutions that inhibited conventional K+ channels, and (3) the DIC was completely inhibited by 1 mM quinine but not by blockers for other cation/anion channels. Altogether, HCO3− efflux through activated GABAA‐R depolarizes astrocyte Vm and induces a delayed inhibition of K2Ps K+ channels via intracellular acidification. © 2012 Wiley Periodicals, Inc.
Efficient 18F‐Labeling of Synthetic Exendin‐4 Analogues for Imaging Beta Cells
Authors: Keliher Edmund J. , Reiner Thomas , Thurber Greg M. , Upadhyay Rabi , Weissleder Ralph 
Published: August 2012

AbstractA number of exendin derivatives have been developed to target glucagon‐like peptide 1 (GLP‐1) receptors on beta cells in vivo. Modifications of exendin analogues have been shown to have significant effects on pharmacokinetics and, as such, have been used to develop a variety of therapeutic compounds. Here, we show that an exendin‐4, modified at position 12 with a cysteine conjugated to a tetrazine, can be labeled with 18F‐trans‐cyclooctene and converted into a PET imaging agent at high yields and with good selectivity. The agent accumulates in beta cells in vivo and has sufficiently high accumulation in mouse models of insulinomas to enable in vivo imaging.
Embryonic NANOG Activity Defines Colorectal Cancer Stem Cells and Modulates through AP1- and TCF-dependent Mechanisms
Authors: Ibrahim Elsayed E. , Babaei-Jadidi Roya , Saadeddin Anas , Spencer-Dene Bradley , Hossaini Sina , Abuzinadah Mohammed , Li Ningning , Fadhil Wakkas , Ilyas Mohammad , Bonnet Dominique , Nateri Abdolrahman S. 
Published: August 2012

Abstract
Embryonic NANOG (NANOG1) is considered as an important regulator of pluripotency while NANOGP8 (NANOG-pseudogene) plays a role in tumorigenesis. Herein, we show NANOG is expressed from both NANOG1 and NANOGP8 in human colorectal cancers (CRC). Enforced NANOG1-expression increases clonogenic potential and tumor formation in xenograft models, although it is expressed only in a small subpopulation of tumor cells and is colocalized with endogenous nuclear β-cateninHigh. Moreover, single NANOG1-CRCs form spherical aggregates, similar to the embryoid body of embryonic stem cells (ESCs), and express higher levels of stem-like Wnt-associated target genes. Furthermore, we show that NANOG1-expression is positively regulated by c-JUN and β-catenin/TCF4. Ectopic expression of c-Jun in murine ApcMin/+-ESCs results in the development of larger xenograft tumors with higher cell density compared to controls. Chromatin immunoprecipitation assays demonstrate that c-JUN binds to the NANOG1-promoter via the octamer M1 DNA element. Collectively, our data suggest that β-Catenin/TCF4 and c-JUN together drive a subpopulation of CRC tumor cells that adopt a stem-like phenotype via the NANOG1-promoter.
Tracing Synaptic Connectivity onto Embryonic Stem Cell-Derived Neurons
Authors: Garcia Isabella , Huang Longwen , Ung Kevin , Arenkiel Benjamin R. 
Published: August 2012

Abstract
Transsynaptic circuit tracing using genetically modified rabies virus (RV) is an emerging technology for identifying synaptic connections between neurons. Complementing this methodology, it is now possible to assay the basic molecular and cellular properties of neuronal lineages derived from embryonic stem cells (ESCs) in vitro, and these properties are under intense investigation toward devising cell replacement therapies. Here, we report the generation of a novel mouse ESC (mESC) line that harbors the genetic elements to allow RV-mediated transsynaptic circuit tracing in ESC-derived neurons and their synaptic networks. To facilitate transsynaptic tracing, we have engineered a new reporter allele by introducing cDNA encoding tdTomato, the Rabies-G glycoprotein, and the avian TVA receptor into the ROSA26 locus by gene targeting. We demonstrate high-efficiency differentiation of these novel mESCs into functional neurons, show their capacity to synaptically connect with primary neuronal cultures as evidenced by immunohistochemistry and electrophysiological recordings, and show their ability to act as source cells for presynaptic tracing of neuronal networks in vitro and in vivo. Together, our data highlight the potential for using genetically engineered stem cells to investigate fundamental mechanisms of synapse and circuit formation with unambiguous identification of presynaptic inputs onto neuronal populations of interest.
Measuring the invisible Higgs width at the 7 and 8 TeV LHC
Authors: Bai Yang , Draper Patrick , Shelton Jessie 
Published: August 2012

Abstract

The LHC is well on track toward the discovery or exclusion of a light Standard Model (SM)-like Higgs boson. Such a Higgs has a very small SM width and can easily have large branching fractions to physics beyond the SM, making Higgs decays an excellent opportunity to observe new physics. Decays into collider-invisible particles are particularly interesting as they are theoretically well motivated and relatively clean experimentally. In this work we estimate the potential of the 7 and 8 TeV LHC to observe an invisible Higgs branching fraction. We analyze three channels that can be used to directly study the invisible Higgs branching ratio at the 7 TeV LHC: an invisible Higgs produced in association with (i) a hard jet; (ii) a leptonic Z; and (iii) forward tagging jets. We find that the last channel, where the Higgs is produced via weak boson fusion, is the most sensitive, allowing branching fractions as small as 40 % to be probed at 20 inverse fb for masses in the range between 120 and 170 GeV, including in particular the interesting region around 125 GeV. We provide an estimate of the 8 TeV LHC sensitivity to an invisibly-decaying Higgs produced via weak boson fusion and find that the reach is comparable to but not better than the reach at the 7 TeV LHC. We further estimate the discovery potential at the 8 TeV LHC for cases where the Higgs has substantial branching fractions to both visible and invisible final states.
The dietary flavonoids naringenin and quercetin acutely impair glucose metabolism in rodents possibly via inhibition of hypothalamic insulin signalling
Authors: Koch Christiane E. , Ganjam Goutham K. , Steger Juliane , Legler Karen , Stöhr Sigrid , Schumacher Daniela , Hoggard Nigel , Heldmaier Gerhard , Tups Alexander 
Published: August 2012

Secondary metabolites of herbs and spices are widely used as an alternative strategy in the therapy of various diseases. The polyphenols naringenin, quercetin and curcumin have been characterised as anti-diabetic agents. Conversely,in vitro,naringenin and quercetin are described to inhibit phosphoinositide-3-kinase (PI3K), an enzyme that is essential for the neuronal control of whole body glucose homoeostasis. Using bothin vitroandin vivoexperiments, we tested whether the inhibitory effect on PI3K occurs in neurons and if it might affect whole body glucose homoeostasis. Quercetin was found to inhibit basal and insulin-induced phosphorylation of Akt (Ser473), a downstream target of PI3K, in HT-22 cells, whereas naringenin and curcumin had no effect. In Djungarian hamsters (Phodopus sungorus) naringenin and quercetin (10 mg/kg administered orally) diminished insulin-induced phosphorylation of Akt (Ser473) in the arcuate nucleus, indicating a reduction in hypothalamic PI3K activity. In agreement with this finding, glucose tolerance in naringenin-treated hamsters (oral) and mice (oral and intracerebroventricular) was reduced compared with controls. Dietary quercetin also impaired glucose tolerance, whereas curcumin was ineffective. Circulating levels of insulin and insulin-like growth factor-binding protein were not affected by the polyphenols. Oral quercetin reduced the respiratory quotient, suggesting that glucose utilisation was impaired after treatment. These data demonstrate that low doses of naringenin and quercetin acutely and potently impair glucose homoeostasis. This effect may be mediated by inhibition of hypothalamic PI3K signalling. Whether chronic impairments in glucose homoeostasis occur after long-term application remains to be identified.
Conceptual distance and word learning: Patterns of acquisition in Samoan–English bilingual children
Authors: HEMSLEY GAYLE , HOLM ALISON , DODD BARBARA 
Published: August 2012

ABSTRACTThis study investigated cross-linguistic influence in acquisition of a second lexicon, evaluating Samoan–English sequentially bilingual children (initial mean age 4 ; 9) during their first 18 months of school. Receptive and Expressive Vocabulary tasks evaluated acquisition of four word types: cognates, matched nouns, phrasal nouns and holonyms. Each word type had varying phonological and conceptual difference between Samoan (L1) and English (L2). Results highlighted conceptual distance between L1 and L2 as a key factor in L2 lexical acquisition. The children acquired L2 lexical items earlier if their conceptual representation was similar to that of L1. Words with greater conceptual distance between L1 and L2 emerged more slowly. This suggests that L1 knowledge influences L2 lexical consolidation for sequential bilinguals. Words that require a conceptual shift from L1 take longer to consolidate and strengthen within the L2 lexicon.
Upper ocean manifestations of a reducing meridional overturning circulation
Authors: Thomas M. D. , de Boer A. M. , Stevens D. P. , Johnson H. L. 
Published: August 2012

Most climate models predict a slowing down of the Atlantic Meridional Overturning Circulation during the 21st century. Using a 100 year climate change integration of a high resolution coupled climate model, we show that a 5.3 Sv reduction in the deep southward transport in the subtropical North Atlantic is balanced solely by a weakening of the northward surface western boundary current, and not by an increase in the southward transport integrated across the interior ocean away from the western boundary. This is consistent with Sverdrup balance holding to a good approximation outside of the western boundary region on decadal time scales, and may help to spatially constrain past and future change in the overturning circulation. The subtropical gyre weakens by 3.4 Sv over the same period due to a weakened wind stress curl. These changes combine to give a net 8.7 Sv reduction in upper western boundary transport.
Optically stimulated luminescence (OSL) as a chronometer for surface exposure dating
Authors: Sohbati Reza , Murray Andrew S. , Chapot Melissa S. , Jain Mayank , Pederson Joel 
Published: August 2012

We pioneer a technique of surface‐exposure dating based upon the characteristic form of an optically stimulated luminescence (OSL) bleaching profile beneath a rock surface; this evolves as a function of depth and time. As a field illustration of this new method, the maximum age of a premier example of Barrier Canyon Style (BCS) rock art in Canyonlands National Park, Utah, USA, is constrained. The natural OSL signal from quartz grains is measured from the surface to a depth of >10 mm in three different rock samples of the Jurassic Navajo Sandstone. Two samples are from talus with unknown daylight exposure histories; one of these samples was exposed at the time of sampling and one was buried and no longer light exposed. A third sample is known to have been first exposed 80 years ago and was still exposed at the time of sampling. First, the OSL‐depth profile of the known‐age sample is modeled to estimate material‐dependent and environmental parameters. These parameters are then used to fit the model to the corresponding data for the samples of unknown exposure history. From these fits we calculate that the buried sample was light exposed for ∼700 years before burial and that the unburied sample has been exposed for ∼120 years. The shielded surface of the buried talus sample is decorated with rock art; this rock fell from the adjacent Great Gallery panel. Related research using conventional OSL dating suggests that this rockfall event occurred ∼900 years ago, and so we deduce that the rock art must have been created between ∼1600 and 900 years ago. Our results are the first credible estimates of exposure ages based on luminescence bleaching profiles. The strength of this novel OSL method is its ability to establish both ongoing and prior exposure times, at decadal to millennial timescales or perhaps longer (depending on the environmental dose rate) even for material subsequently buried. This has considerable potential in many archeological, geological and geo‐hazard applications.