bluuebunny/crossref_metadata_2025_split huggingface dataset:
Truths and myths about the determination of molar mass distribution of synthetic and natural polymers by size exclusion chromatography
Authors: Podzimek Stepan 
Published: November 2013

ABSTRACTThis article discusses various aspects of the determination of molar mass distribution by means of size exclusion chromatography (SEC) in various application modes. The effects of erroneous specific refractive index increment (dn/dc), branching, column performance, and enthalpic interactions on the results obtained by different SEC techniques are discussed. Combination of SEC and a light scattering detector represents the most direct way to the molar mass distribution of all natural and synthetic polymers as it completely eliminates the need for column calibration and to a certain extent eliminates the dependence of the obtained results on some operational variables such as flow rate, temperature, or injected mass. A multiangle light scattering (MALS) photometer has become the most frequently used light scattering detector capable of determination of molecular size as another important polymer characteristic. This article contrasts SEC‐MALS method with other application modes of SEC from the viewpoint of some frequent confusions and misunderstandings. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 40111.
Estimation of sea level pressure fields during Cyclone Nilam from Oceansat‐2 scatterometer winds
Authors: Purna Chand Ch. , Rao M. V. , Ramana I. V. , Ali M. M. , Patoux J. , Bourassa M. A. 
Published: November 2013

AbstractSea level pressure observations are rarely available over most of the oceans and no remote sensing instrument can measure it directly. Here, we explore the estimation of sea level pressure fields using surface wind observations from OSCAT, the scatterometer onboard Oceansat‐2, during the 27 October–2 November 2012 passage of Cyclone Nilam over the Bay of Bengal. The estimated pressure is validated with moored‐buoy observations. Scatterometer‐derived pressure differences are closer to in situ observations than those in examined numerical model estimations. The estimated pressure is more accurate than European Centre for Medium‐range Weather Forecasting re‐analysis values in location, track, and intensity.
Spatial organization of cell‐adhesive ligands for advanced cell culture
Authors: Ekerdt Barbara L. , Segalman Rachel A. , Schaffer David V. 
Published: November 2013

AbstractInteraction between biomaterials and cells is a critical aspect for successful application of tissue engineering research. Technological advances within the past decade have enabled a number of studies to investigate how the spatial organization of cell‐adhesive ligands impacts complex and rich cell behaviors ranging from adhesion to differentiation. Cells in their native environment are surrounded by chemical and physical factors spanning a range of length scales from nanometers to hundreds of microns. Furthermore, signals in the form of cell‐adhesive ligands presented from this environment in different size scales and/or geometrical arrangements can change how a cell senses and responds to its surroundings. Biology can thus convey information not only in the concentration of a ligand but through its ability to change the spatial organization of these cues, raising questions both on the mechanisms by which it patterns such information and on the means by which a cell interprets it. This review discusses major findings associated with various systems developed to study cell‐adhesive ligand presentation as well as an overview of the important material systems used in these studies. Promising material systems to further investigations in this field are also examined. Future directions will likely include determining how cells sense local and global ligand concentrations, understanding underlying mechanisms that regulate cell behaviors, and investigating the function of more complex cell types and diverse ligands.
Design of affinity peptides from natural protein ligands: A study of the cardiac troponin complex
Authors: Chandra Divya , Sankalia Nitesh , Arcibal Imee , Banta Scott , Cropek Donald , Karande Pankaj 
Published: November 2013

ABSTRACTWe describe a general strategy for the design and discovery of affinity peptides for a protein from its natural ligands. Our approach is guided by protein–protein interactions in natural systems and focuses on the hetero‐trimeric complex of cardiac troponin I (cTnI), C (cTnC) and T (cTnT). A key premise of this work is that cTnC and cTnT, owing to their innate ability to bind cTnI, are potential templates for the design and discovery of cTnI‐binding peptides. Relying only on the knowledge of primary sequences of cTnC and cTnT, we designed a library of short overlapping peptides that span the entirety of cTnC and cTnT and tested them for binding to cTnI. We were successful in identifying several peptides that display high affinity (1–100 nM) for cTnI. The specific implication of this work is that mimicking natural protein‐protein interactions is an excellent starting point for the discovery and rational design of peptide ligands. The knowledge of secondary or tertiary structures of the proteins involved is not a necessary precondition for this approach. Nevertheless, we show that structural information can be used to validate the results of a fragment‐based peptide design, and can be potentially beneficial for refining the lead candidates. Our approach is broadly applicable to any protein with at least one natural binding ligand with known primary sequence. For protein targets with multiple natural ligands, this approach can potentially yield several distinct affinity peptides capable of simultaneously binding the target protein via orthogonal modes or at complementary interfaces. © 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 102: 97–106, 2014.
Translation of structure‐activity relationships from cyclic mixed efficacy opioid peptides to linear analogues
Authors: Anand Jessica P. , Porter‐Barrus Vanessa R. , Waldschmidt Helen V. , Yeomans Larisa , Pogozheva Irina D. , Traynor John R. , Mosberg Henry I. 
Published: November 2013

ABSTRACTMost opioid analgesics used in the treatment of pain are mu opioid receptor (MOR) agonists. While effective, there are significant drawbacks to opioid use, including the development of tolerance and dependence. However, the coadministration of a MOR agonist with a delta opioid receptor (DOR) antagonist slows the development of MOR‐related side effects, while maintaining analgesia. We have previously reported a series of cyclic mixed efficacy MOR agonist/DOR antagonist ligands. Here we describe the transfer of key features from these cyclic analogs to linear sequences. Using the linear MOR/DOR agonist, Tyr‐DThr‐Gly‐Phe‐Leu‐Ser‐NH2 (DTLES), as a lead scaffold, we replaced Phe4 with bulkier and/or constrained aromatic residues shown to confer DOR antagonism in our cyclic ligands. These replacements failed to confer DOR antagonism in the DTLES analogs, presumably because the more flexible linear ligands can adopt binding poses that will fit in the narrow binding pocket of the active conformations of both MOR and DOR. Nonetheless, the pharmacological profile observed in this series, high affinity and efficacy for MOR and DOR with selectivity relative to KOR, has also been shown to reduce the development of unwanted side effects. We further modified our lead MOR/DOR agonist with a C‐terminal glucoserine to improve bioavailability. The resulting ligand displayed high efficacy and potency at both MOR and DOR and no efficacy at KOR. © 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 102: 107–114, 2014.
Enzyme‐driven bacillus spore coat degradation leading to spore killing
Authors: Mundra Ruchir V. , Mehta Krunal K. , Wu Xia , Paskaleva Elena E. , Kane Ravi S. , Dordick Jonathan S. 
Published: November 2013

ABSTRACTThe bacillus spore coat confers chemical and biological resistance, thereby protecting the core from harsh environments. The primarily protein‐based coat consists of recalcitrant protein crosslinks that endow the coat with such functional protection. Proteases are present in the spore coat, which play a putative role in coat degradation in the environment. However these enzymes are poorly characterized. Nonetheless given the potential for proteases to catalyze coat degradation, we screened 10 commercially available proteases for their ability to degrade the spore coats of B. cereus and B. anthracis. Proteinase K and subtilisin Carlsberg, for B. cereus and B. anthracis spore coats, respectively, led to a morphological change in the otherwise impregnable coat structure, increasing coat permeability towards cortex lytic enzymes such as lysozyme and SleB, thereby initiating germination. Specifically in the presence of lysozyme, proteinase K resulted in 14‐fold faster enzyme induced germination and exhibited significantly shorter lag times, than spores without protease pretreatment. Furthermore, the germinated spores were shown to be vulnerable to a lytic enzyme (PlyPH) resulting in effective spore killing. The spore surface in response to proteolytic degradation was probed using scanning electron microscopy (SEM), which provided key insights regarding coat degradation. The extent of coat degradation and spore killing using this enzyme‐based pretreatment approach is similar to traditional, yet far harsher, chemical decoating methods that employ detergents and strong denaturants. Thus the enzymatic route reduces the environmental burden of chemically mediated spore killing, and demonstrates that a mild and environmentally benign biocatalytic spore killing is achievable. Biotechnol. Bioeng. 2014;111: 654–663. © 2013 Wiley Periodicals, Inc.
Enhancing E. coli isobutanol tolerance through engineering its global transcription factor cAMP receptor protein (CRP)
Authors: Chong Huiqing , Geng Hefang , Zhang Hongfang , Song Hao , Huang Lei , Jiang Rongrong 
Published: November 2013

ABSTRACTThe limited isobutanol tolerance of Escherichia coli is a major drawback during fermentative isobutanol production. Different from classical strain engineering approaches, this work was initiated to improve E. coli isobutanol tolerance from its transcriptional level by engineering its global transcription factor cAMP receptor protein (CRP). Random mutagenesis libraries were generated by error‐prone PCR of crp, and the libraries were subjected to isobutanol stress for selection. Variant IB2 (S179P, H199R) was isolated and exhibited much better growth (0.18 h−1) than the control (0.05 h−1) in 1.2% (v/v) isobutanol (9.6 g/L). Genome‐wide DNA microarray analysis revealed that 58 and 308 genes in IB2 had differential expression (>2‐fold, p < 0.05) in the absence and presence of 1% (v/v) isobutanol, respectively. When challenged with isobutanol, genes related to acid resistance (gadABCE, hdeABD), nitrate reduction (narUZYWV), flagella and fimbrial activity (lfhA, yehB, ycgR, fimCDF), and sulfate reduction and transportation (cysIJH, cysC, cysN) were the major functional groups that were up‐regulated, whereas most of the down‐regulated genes were enzyme (tnaA) and transporters (proVWX, manXYZ). As demonstrated by single‐gene knockout experiments, gadX, nirB, rhaS, hdeB, and ybaS were found associated with strain isobutanol resistance. The intracellular reactive oxygen species (ROS) level in IB2 was only half of that of the control when facing stress, indicating that IB2 can withstand toxic isobutanol much better than the control. Biotechnol. Biotechnol. Bioeng. 2014;111: 700–708. © 2013 Wiley Periodicals, Inc.
Initial experience with the glidesheath slender for transradial coronary angiography and intervention: A feasibility study with prospective radial ultrasound follow‐up
Authors: Aminian Adel , Dolatabadi Dariouch , Lefebvre Pascal , Zimmerman Robert , Brunner Philippe , Michalakis Georges , Lalmand Jacques 
Published: November 2013

ObjectiveThe aim of this study is to evaluate the feasibility and safety of the Glidesheath Slender in routine transradial (TR) coronary angiography and intervention.BackgroundIn recent years, The TR approach has gained in popularity because of several advantages such as reduced vascular access site complications and immediate patient mobilization. Procedural success has been further improved through technological innovations and the development of less invasive devices. The Glidesheath Slender (Terumo, Tokyo, Japan) is a new dedicated radial sheath with a thinner wall and hydrophilic coating. It combines an inner diameter compatible with 6Fr guiding catheter with an outer diameter close to current 5Fr sheaths. Its use has the potential to decrease invasiveness and access site complications during TR procedures.MethodsA total of 114 consecutive patients undergoing TR coronary angiography and/or PCI using the Gidesheath Slender were included in a prospective single‐center feasibility and safety study.ResultsProcedural success was 99.1% with only one case requiring conversion to femoral access. There were six minor hematomas but none of the patients experienced major vascular complications. The rate of symptomatic radial spasm was 4.4%. No case of major sheath kinking was noted. Doppler ultrasound examination of the radial artery at 1 month follow‐up was available in 113/114 patients with only one case of radial artery occlusion (RAO) (0.88%).ConclusionsRoutine use of the Glidesheath Slender for TR coronary angiography and interventions is safe and feasible with a high rate of procedural success and a low rate of RAO. © 2013 Wiley Periodicals, Inc.
Transesterifications and Peracid‐Assisted Oxidations in Aqueous Media Catalyzed by Mycobacterium smegmatis Acyl Transferase
Authors: Wiermans Lotte , Hofzumahaus Sebastian , Schotten Christiane , Weigand Lisa , Schallmey Marcus , Schallmey Anett , Domínguez de María Pablo 
Published: November 2013

AbstractHydrolases catalyze synthetic reactions in nonaqueous media, whereas they perform hydrolysis under aqueous solutions. An acyl transferase from Mycobacterium smegmatis (MsAcT) is able to catalyze synthetic reactions in buffer because of its highly hydrophobic active site, which enables efficient transesterification reactions even at 99.9 % v/v buffer solution. This unique feature of MsAcT among hydrolases may open new opportunities to conduct synthetic (bio)catalysis in aqueous media. With these goals in mind, this paper explores some evidence of such potential: MsAcT can perform enantioselective transesterifications (e.g., (S)‐2‐octanol), which could be combined with other aqueous multistep (asymmetric) reactions; 5‐hydroxymethylfurfural (HMF) can be esterified to produce more hydrophobic and easily extractable HMF esters (e.g., for downstream processing or wastewater treatment); and upon addition of dilute H2O2, MsAcT works efficiently as a perhydrolase to form in situ peracids—in bulk water—that can be used for oxidations (e.g., furfural to furoic acid oxidation). Overall, these and many other new applications can be envisaged by using MsAcT in aqueous solutions.
Ruthenium(II)‐catalysed Functionalisation of CH Bonds via a Six‐membered Cyclometallate: Monoarylation of Aryl 2‐pyridyl Ketones
Authors: Li Bin , Darcel Christophe , Dixneuf Pierre H. 
Published: November 2013

AbstractSelective monoarylation of aryl 2‐pyridyl ketones with a variety of arylbromides via arene sp2 CH bond activation/functionalisation is achieved with a [RuCl2(p‐cymene)]2/ p‐CF3C6H4CO2H catalytic system. The reaction via a 6‐membered ruthenacycle is more difficult to perform than via a 5‐membered cyclometallate but the activation of only one ortho CH bond is unprecedentedly highly selective. A variety of functional 2‐pyridine derivatives are easily obtained. It is shown via H/D exchange that the carboxylic acid favours the reversible CH bond activation.
Fourier‐Transformed Large‐Amplitude AC Voltammetric Study of Tetrathiafulvalene (TTF): Electrode Kinetics of the TTF0/TTF.+ and TTF.+/TTF2+ Processes
Authors: Bond Alan M. , Bano Kiran , Adeel Shaimaa , Martin Lisandra L. , Zhang Jie 
Published: November 2013

AbstractLarge‐amplitude Fourier‐transformed (FT) AC voltammetry was used at high frequency to study the electrode kinetics of tetrathiafulvalene (TTF), its radical cation TTF.+ and that of the dication TTF2+ in acetonitrile (0.1 M Bu4NPF6). The two oxidized forms were prepared by quantitative bulk electrolysis of TTF under dry‐box conditions. A high frequency of 233 Hz was used at glassy carbon (GC) and platinum (Pt) macro disk electrodes to enhance the kinetic sensitivity and hence upper limit of the measurable heterogeneous charge transfer rate constant (k0). Difficulties associated with the use of high frequencies at macro disk electrodes are discussed. Comparison of experimental data with simulations is used to extract k0 and other parameters for each of the TTF0/.+ and TTF.+/2+ processes from both reduction and oxidation perspectives. k0 values for TTF0/.+and TTF.+/0 processes are ≥1.0 cm s−1 and consequently regarded as reversible under the AC conditions used. However, the significantly slower quasi‐reversible behaviour observed for the TTF.+/2+ redox couple, with k0 being 0.3±0.05 cm s−1, can be precisely estimated.
Instant Visual Detection of Picogram Levels of Trinitrotoluene by Using Luminescent Metal–Organic Framework Gel‐Coated Filter Paper
Authors: Lee Ji Ha , Kang Sunwoo , Lee Jin Yong , Jaworski Justyn , Jung Jong Hwa 
Published: November 2013

AbstractThere is an ongoing need for explosive detection strategies to uncover threats to human security including illegal transport and terrorist activities. The widespread military use of the explosive trinitrotoluene (TNT) for landmines poses another particular threat to human health in the form of contamination of the surrounding environment and groundwater. The detection of explosives, particularly at low picogram levels, by using a molecular sensor is seen as an important challenge. Herein, we report on the use of a fluorescent metal–organic framework hydrogel that exhibits a higher detection capability for TNT in the gel state compared with that in the solution state. A portable sensor prepared from filter paper coated by the hydrogel was able to detect TNT at the picogram level with a detection limit of 1.82 ppt (parts per trillon). Our results present a simple and new means to provide selective detection of TNT on a surface or in aqueous solution, as afforded by the unique molecular packing through the metal–organic framework structure in the gel formation and the associated photophysical properties. Furthermore, the rheological properties of the MOF‐based gel were similar to those of a typical hydrogel.
Spectroscopic Elucidation of the Inhibitory Mechanism of Cys2His2 Zinc Finger Transcription Factors by Cobalt(III) Schiff Base Complexes
Authors: Heffern Marie C. , Kurutz Josh W. , Meade Thomas J. 
Published: November 2013

AbstractTranscription factors are key regulators in both normal and pathological cell processes. Affecting the activity of these proteins is a promising strategy for understanding gene regulation and developing effective therapeutics. CoIII Schiff base complexes ([Co(acacen)(L)2]+ where L=labile axial ligands) have been shown to be potent inhibitors of a number of zinc metalloproteins including Cys2His2 zinc finger transcription factors. Inhibition by [Co(acacen)(L)2]+ of the target protein is believed to occur through a dissociative exchange of the labile axial ligands for histidine (His) residues essential for function. Here, we report a series of spectroscopic investigations with model peptides of zinc fingers that elucidate the interaction between [Co(acacen)(L)2]+ complexes and zinc finger transcription factors. Observed changes in NMR chemical shifts and 2D 1H‐1H NOESY NMR spectra demonstrate the preference of [Co(acacen)(L)2]+ complexes to coordinate His residues over other amino acids. The conformation of [Co(acacen)(L)2]+ upon His coordination was characterized by 1H NMR spectroscopy, near‐UV CD, and electronic absorption. These studies reveal that the resulting His‐coordinated [Co(acacen)(L)2]+ complex possesses an octahedral structure. The effects of [Co(acacen)(L)2]+ complexes on the zinc‐finger structure were assessed by the degree of hydrogen bonding (probed by 2D NMR spectroscopy) and secondary‐structure profiles measured by far‐UV CD. These structural studies demonstrate the ability of [Co(acacen)(L)2]+ complexes to disrupt the ββα structure of zinc fingers, resulting in primarily random‐coil conformations. A mechanism is described wherein [Co(acacen)(L)2]+ complexes inhibit zinc finger transcription factor activity through selectively coordinating His residues in the zinc finger by dissociative ligand exchange and disrupting the ββα structural motif required for gene regulation.
Conformational Change from a Twisted Figure‐Eight to an Open‐Extended Structure in Doubly Fused 36π Core‐Modified Octaphyrins Triggered by Protonation: Implication on Photodynamics and Aromaticity
Authors: Karthik Ganesan , Lim Jong Min , Srinivasan A. , Suresh C. H. , Kim Dongho , Chandrashekar Tavarekere K. 
Published: November 2013

AbstractTwo examples of core‐modified 36π doubly fused octaphyrins that undergo a conformational change from a twisted figure‐eight to an open‐extended structure induced by protonation are reported. Syntheses of the two octaphyrins (in which Ar=mesityl or tolyl) were achieved by a simple acid‐catalyzed condensation of dipyrrane unit containing an electron‐rich, rigid dithienothiophene (DTT) core with pentafluorobenzaldehyde followed by oxidation with 2,3‐dichloro‐5,6‐dicyano‐1,4‐benzoquinone (DDQ). The single‐crystal X‐ray structure of the octaphyrin (in which Ar=mesityl) shows a figure‐eight twisted conformation of the expanded porphyrin skeleton with two DTT moieties oriented in a staggered conformation with a π‐cloud distance of 3.7 Å. Spectroscopic and quantum mechanical calculations reveal that both octaphyrins conform to a [4n]π nonaromatic electronic structure. Protonation of the pyrrole nitrogen atoms of the octaphyrins results in dramatic structural change, which led to 1) a large redshift and sharpening of absorption bands in electronic absorption spectrum, 2) a large change in chemical shift of pyrrole β‐CH and NH protons in the 1H NMR spectrum, 3) a small increase in singlet lifetimes, and 4) a moderate increase in two‐photon absorption cross‐section values. Furthermore, nucleus‐independent chemical shift (NICS) values calculated at various geometrical positions show positive values and anisotropy‐induced current density (AICD) plots indicate paratropic ring‐currents for the diprotonated form of the octaphyrin (in which Ar=tolyl); the single‐crystal X‐ray structure of the diprotonated form of the octaphyrin shows an extended structure in which one of the pyrrole ring of each dipyrrin subunit undergoes a 180 ° ring‐flip. Four trifluoroacetic acid (TFA) molecules are bound above and below the molecular plane defined by meso‐carbon atoms and are held by NH⋅⋅⋅O, NH⋅⋅⋅F, and CH⋅⋅⋅F intermolecular hydrogen‐bonding interactions. The extended‐open structure upon protonation allows π‐delocalization and the electronic structure conforms to a [4n]π Hückel antiaromatic in the diprotonated state.