Mimicking an Enzyme-Based Colorimetric Aptasensor for Antibiotic Residue Detection in Milk Combining Magnetic Loop-DNA Probes and CHA-Assisted Target Recycling Amplification.

PubMed

Luan, Qian; Gan, Ning; Cao, Yuting; Li, Tianhua

2017-07-19

A mimicking-enzyme-based colorimetric aptasensor was developed for the detection of kanamycin (KANA) in milk using magnetic loop-DNA-NMOF-Pt (m-L-DNA) probes and catalytic hairpin assembly (CHA)-assisted target recycling for signal amplification. The m-L-DNA probes were constructed via hybridization of hairpin DNA H1 (containing aptamer sequence) immobilized magnetic beads (m-H1) and signal DNA (sDNA, partial hybridization with H1) labeled nano Fe-MIL-88NH 2 -Pt (NMOF-Pt-sDNA). In the presence of KANA and complementary hairpin DNA H2, the m-L-DNA probes decomposed and formed an m-H1/KANA intermediate, which triggered the CHA reaction to form a stable duplex strand (m-H1-H2) while releasing KANA again for recycling. Consequently, numerous NMOF-Pt-sDNA as mimicking enzymes can synergistically catalyze 3,3',5,5'-tetramethylbenzidine (TMB) for color development. The aptasensor exhibited high selectivity and sensitivity for KANA in milk with a detection limit of 0.2 pg mL -1 within 30 min. The assay can be conveniently extended for on-site screening of other antibiotics in foods by simply changing the base sequence of the probes.

Intractable Polyuria Mimicking Diabetes Insipidus-Source Traced to Vecuronium Infusion.

PubMed

Haldar, Rudrashish; Samanta, Sukhen; Singla, Ankush

2016-01-01

Continuous infusion of vecuronium is a commonly used technique for patients requiring prolonged neuromuscular blockade for mechanical ventilation. As compared with older neuromuscular blocking agents, it confers the advantages of rapid excretion and intermediate duration of action. Prolongation of neuromuscular blockade and muscle weakness are the known complications of continuous vecuronium infusion. This report attempts to describe polyuria, as a hitherto unknown complication of vecuronium infusion, which can occur due to the mannitol present in commercially available preparation of vecuronium bromide.

Molecular mechanism of DNA replication-coupled inactivation of the initiator protein in Escherichia coli: interaction of DnaA with the sliding clamp-loaded DNA and the sliding clamp-Hda complex.

PubMed

Su'etsugu, Masayuki; Takata, Makoto; Kubota, Toshio; Matsuda, Yusaku; Katayama, Tsutomu

2004-06-01

In Escherichia coli, the ATP-DnaA protein initiates chromosomal replication. After the DNA polymerase III holoenzyme is loaded on to DNA, DnaA-bound ATP is hydrolysed in a manner depending on Hda protein and the DNA-loaded form of the DNA polymerase III sliding clamp subunit, which yields ADP-DnaA, an inactivated form for initiation. This regulatory DnaA-inactivation represses extra initiation events. In this study, in vitro replication intermediates and structured DNA mimicking replicational intermediates were first used to identify structural prerequisites in the process of DnaA-ATP hydrolysis. Unlike duplex DNA loaded with sliding clamps, primer RNA-DNA heteroduplexes loaded with clamps were not associated with DnaA-ATP hydrolysis, and duplex DNA provided in trans did not rescue this defect. At least 40-bp duplex DNA is competent for the DnaA-ATP hydrolysis when a single clamp was loaded. The DnaA-ATP hydrolysis was inhibited when ATP-DnaA was tightly bound to a DnaA box-bearing oligonucleotide. These results imply that the DnaA-ATP hydrolysis involves the direct interaction of ATP-DnaA with duplex DNA flanking the sliding clamp. Furthermore, Hda protein formed a stable complex with the sliding clamp. Based on these, we suggest a mechanical basis in the DnaA-inactivation that ATP-DnaA interacts with the Hda-clamp complex with the aid of DNA binding. Copyright Blackwell Publishing Limited

Mimicking bug-like surface structures and their fluid transport produced by ultrashort laser pulse irradiation of steel

NASA Astrophysics Data System (ADS)

Kirner, S. V.; Hermens, U.; Mimidis, A.; Skoulas, E.; Florian, C.; Hischen, F.; Plamadeala, C.; Baumgartner, W.; Winands, K.; Mescheder, H.; Krüger, J.; Solis, J.; Siegel, J.; Stratakis, E.; Bonse, J.

2017-12-01

Ultrashort laser pulses with durations in the fs-to-ps range were used for large area surface processing of steel aimed at mimicking the morphology and extraordinary wetting behaviour of bark bugs (Aradidae) found in nature. The processing was performed by scanning the laser beam over the surface of polished flat sample surfaces. A systematic variation of the laser processing parameters (peak fluence and effective number of pulses per spot diameter) allowed the identification of different regimes associated with characteristic surface morphologies (laser-induced periodic surface structures, i.e., LIPSS, grooves, spikes, etc.). Moreover, different laser processing strategies, varying laser wavelength, pulse duration, angle of incidence, irradiation atmosphere, and repetition rates, allowed to achieve a range of morphologies that resemble specific structures found on bark bugs. For identifying the ideal combination of parameters for mimicking bug-like structures, the surfaces were inspected by scanning electron microscopy. In particular, tilted micrometre-sized spikes are the best match for the structure found on bark bugs. Complementary to the morphology study, the wetting behaviour of the surface structures for water and oil was examined in terms of philic/phobic nature and fluid transport. These results point out a route towards reproducing complex surface structures inspired by nature and their functional response in technologically relevant materials.

Generation of functional podocytes from human induced pluripotent stem cells.

PubMed

Ciampi, Osele; Iacone, Roberto; Longaretti, Lorena; Benedetti, Valentina; Graf, Martin; Magnone, Maria Chiara; Patsch, Christoph; Xinaris, Christodoulos; Remuzzi, Giuseppe; Benigni, Ariela; Tomasoni, Susanna

2016-07-01

Generating human podocytes in vitro could offer a unique opportunity to study human diseases. Here, we describe a simple and efficient protocol for obtaining functional podocytes in vitro from human induced pluripotent stem cells. Cells were exposed to a three-step protocol, which induced their differentiation into intermediate mesoderm, then into nephron progenitors and, finally, into mature podocytes. After differentiation, cells expressed the main podocyte markers, such as synaptopodin, WT1, α-Actinin-4, P-cadherin and nephrin at the protein and mRNA level, and showed the low proliferation rate typical of mature podocytes. Exposure to Angiotensin II significantly decreased the expression of podocyte genes and cells underwent cytoskeleton rearrangement. Cells were able to internalize albumin and self-assembled into chimeric 3D structures in combination with dissociated embryonic mouse kidney cells. Overall, these findings demonstrate the establishment of a robust protocol that, mimicking developmental stages, makes it possible to derive functional podocytes in vitro. Copyright © 2016. Published by Elsevier B.V.

Rhodanine hydrolysis leads to potent thioenolate mediated metallo-β-lactamase inhibition

NASA Astrophysics Data System (ADS)

Brem, Jürgen; van Berkel, Sander S.; Aik, Weishen; Rydzik, Anna M.; Avison, Matthew B.; Pettinati, Ilaria; Umland, Klaus-Daniel; Kawamura, Akane; Spencer, James; Claridge, Timothy D. W.; McDonough, Michael A.; Schofield, Christopher J.

2014-12-01

The use of β-lactam antibiotics is compromised by resistance, which is provided by β-lactamases belonging to both metallo (MBL)- and serine (SBL)-β-lactamase subfamilies. The rhodanines are one of very few compound classes that inhibit penicillin-binding proteins (PBPs), SBLs and, as recently reported, MBLs. Here, we describe crystallographic analyses of the mechanism of inhibition of the clinically relevant VIM-2 MBL by a rhodanine, which reveal that the rhodanine ring undergoes hydrolysis to give a thioenolate. The thioenolate is found to bind via di-zinc chelation, mimicking the binding of intermediates in β-lactam hydrolysis. Crystallization of VIM-2 in the presence of the intact rhodanine led to observation of a ternary complex of MBL, a thioenolate fragment and rhodanine. The crystallographic observations are supported by kinetic and biophysical studies, including 19F NMR analyses, which reveal the rhodanine-derived thioenolate to be a potent broad-spectrum MBL inhibitor and a lead structure for the development of new types of clinically useful MBL inhibitors.

High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer.

PubMed Central

Abele, U.; Schulz, G. E.

1995-01-01

The structure of adenylate kinase from yeast ligated with the two-substrate-mimicking inhibitor Ap5A and Mg2+ has been refined to 1.96 A resolution. In addition, the refined structure of the same complex with a bound imidazole molecule replacing Mg2+ has been determined at 1.63 A. These structures indicate that replacing Mg2+ by imidazole disturbs the water structure and thus the complex. A comparison with the G-proteins shows that Mg2+ is exactly at the same position with respect to the phosphates. However, although the Mg2+ ligand sphere of the G-proteins is a regular octahedron containing peptide ligands, the reported adenylate kinase has no such ligands and an open octahedron leaving space for the Mg2+ to accompany the transferred phosphoryl group. A superposition of the known crystalline and therefore perturbed phosphoryl transfer geometries in the adenylate kinases demonstrates that all of them are close to the start of the forward reaction with bound ATP and AMP. Averaging all observed perturbed structures gives rise to a close approximation of the transition state, indicating in general how to establish an elusive transition state geometry. The average shows that the in-line phosphoryl transfer is associative, because there is no space for a dissociative metaphosphate intermediate. As a side result, the secondary dipole interaction in the alpha-helices of both protein structures has been quantified. PMID:7670369

Crystal Structure of Heart 6-Phosphofructo-2-Kinase/Fructose-2,6-Bisphosphatase (PFKFB2) and the Inhibitory Influence of Citrate on Substrate Binding

PubMed Central

Crochet, Robert B.; Kim, Jeong-Do; Lee, Herie; Yim, Young-Sun; Kim, Song-Gun; Neau, David; Lee, Yong-Hwan

2016-01-01

The heart-specific isoform of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFKFB2) is an important regulator of glycolytic flux in cardiac cells. Here, we present the crystal structures of two PFKFB2 orthologues, human and bovine, at resolutions of 2.0 and 1.8Å, respectively. Citrate, a TCA cycle intermediate and well-known inhibitor of PFKFB2, co-crystallized in the 2-kinase domains of both orthologues, occupying the fructose-6-phosphate binding-site and extending into the γ-phosphate binding pocket of ATP. This steric and electrostatic occlusion of the γ-phosphate site by citrate proved highly consequential to the binding of co-complexed ATP analogues. The bovine structure, which co-crystallized with ADP, closely resembled the overall structure of other PFKFB isoforms, with ADP mimicking the catalytic binding mode of ATP. The human structure, on the other hand, co-complexed with AMPPNP, which, unlike ADP, contains a γ-phosphate. The presence of this γ-phosphate made adoption of the catalytic ATP binding mode impossible for AMPPNP, forcing the analogue to bind atypically with concomitant conformational changes to the ATP binding-pocket. Inhibition kinetics were used to validate the structural observations, confirming citrate’s inhibition mechanism as competitive for F6P and noncompetitive for ATP. Together, these structural and kinetic data establish a molecular basis for citrate’s negative feed-back loop of the glycolytic pathway via PFKFB2. PMID:27802586

Self-assembling, protein-based intracellular bacterial organelles: emerging vehicles for encapsulating, targeting and delivering therapeutical cargoes

PubMed Central

2011-01-01

Many bacterial species contain intracellular nano- and micro-compartments consisting of self-assembling proteins that form protein-only shells. These structures are built up by combinations of a reduced number of repeated elements, from 60 repeated copies of one unique structural element self-assembled in encapsulins of 24 nm to 10,000-20,000 copies of a few protein species assembled in a organelle of around 100-150 nm in cross-section. However, this apparent simplicity does not correspond to the structural and functional sophistication of some of these organelles. They package, by not yet definitely solved mechanisms, one or more enzymes involved in specific metabolic pathways, confining such reactions and sequestering or increasing the inner concentration of unstable, toxics or volatile intermediate metabolites. From a biotechnological point of view, we can use the self assembling properties of these particles for directing shell assembling and enzyme packaging, mimicking nature to design new applications in biotechnology. Upon appropriate engineering of the building blocks, they could act as a new family of self-assembled, protein-based vehicles in Nanomedicine to encapsulate, target and deliver therapeutic cargoes to specific cell types and/or tissues. This would provide a new, intriguing platform of microbial origin for drug delivery. PMID:22046962

Charge Transfer from n-Doped Nanocrystals: Mimicking Intermediate Events in Multielectron Photocatalysis.

PubMed

Wang, Junhui; Ding, Tao; Wu, Kaifeng

2018-06-12

In multielectron photocatalytic reactions, an absorbed photon triggers charge transfer from the light-harvester to the attached catalyst, leaving behind a charge of the opposite sign in the light-harvester. If this charge is not scavenged before the absorption of the following photons, photoexcitation generates not neutral but charged excitons from which the extraction of charges should become more difficult. This is potentially an efficiency-limiting intermediate event in multielectron photocatalysis. To study the charge dynamics in this event, we doped CdS nanocrystal quantum dots (QDs) with an extra electron and measured hole transfer from n-doped QDs to attached acceptors. We find that the Auger decay of charged excitons lowers the charge separation yield to 68.6% from 98.4% for neutral excitons. In addition, the hole transfer rate in the presence of two electrons (1290 ps) is slower than that in the presence one electron (776 ps), and the recombination rate of charge separated states is about 2 times faster in the former case. This model study provides important insights into possible efficiency-limiting intermediate events involved in photocatalysis.

Peroxidase-Mimicking Nanozyme with Enhanced Activity and High Stability Based on Metal-Support Interactions.

PubMed

Li, Zhihao; Yang, Xiangdong; Yang, Yanbing; Tan, Yaning; He, Yue; Liu, Meng; Liu, Xinwen; Yuan, Quan

2018-01-09

Peroxidase-mimicking nanozymes offer unique advantages in terms of high stability and low cost over natural peroxidase for applications in bioanalysis, biomedicine, and the treatment of pollution. However, the design of high-efficiency peroxidase-mimicking nanozymes remains a great challenge. In this study, we adopted a structural-design approach through hybridization of cube-CeO 2 and Pt nanoparticles to create a new peroxidase-mimicking nanozyme with high efficiency and excellent stability. Relative to pure cube-CeO 2 and Pt nanoparticles, the as-hybridized Pt/cube-CeO 2 nanocomposites display much improved activities because of the strong metal-support interaction. Meanwhile, the nanocomposites also maintain high catalytic activity after long-term storage and multiple recycling. Based on their excellent properties, Pt/cube-CeO 2 nanocomposites were used to construct high-performance colorimetric biosensors for the sensitive detection of metabolites, including H 2 O 2 and glucose. Our findings highlight opportunities for the development of high-efficiency peroxidase-mimicking nanozymes with potential applications such as diagnostics, biomedicine, and the treatment of pollution. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis of Polylactide-Based Core-Shell Interface Cross-Linked Micelles for Anticancer Drug Delivery.

PubMed

Chen, Chih-Kuang; Lin, Wei-Jen; Hsia, Yu; Lo, Leu-Wei

2017-03-01

Well-defined poly(ethylene glycol)-b-allyl functional polylactide-b-polylactides (PEG-APLA-PLAs) are synthesized through sequential ring-opening polymerization. PEG-APLA-PLAs that have amphiphilic properties and reactive allyl side chains on their intermediate blocks are successfully transferred to core-shell interface cross-linked micelles (ICMs) by micellization and UV-initiated irradiation. ICMs have demonstrated enhanced colloidal stability in physiological-mimicking media. Hydrophobic molecules such as Nile Red or doxorubicin (Dox) are readily loaded into ICMs; the resulting drug-ICM formulations possess slow and sustained drug release profiles under physiological-mimicking conditions. ICMs exhibit negligible cytotoxicity in human uterine sarcoma cancer cells by using biodegradable aliphatic polyester as the hydrophobic segments. Relative to free Dox, Dox-loaded ICMs show a reduced cytotoxicity due to the late intracellular release of Dox from ICMs. Overall, ICMs represent a new type of biodegradable cross-linked micelle and can be employed as a promising platform for delivering a broad variety of hydrophobic drugs. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The fission yeast meiosis-specific Dmc1 recombinase mediates formation and branch migration of Holliday junctions by preferentially promoting strand exchange in a direction opposite to that of Rad51

PubMed Central

Murayama, Yasuto; Tsutsui, Yasuhiro; Iwasaki, Hiroshi

2011-01-01

Homologous recombination proceeds via the formation of several intermediates including Holliday junctions (HJs), which are important for creating crossover products. DNA strand exchange is a core reaction that produces these intermediates that is directly catalyzed by RecA family recombinases, of which there are two types in eukaryotes: universal Rad51 and meiosis-specific Dmc1. We demonstrated previously that Rad51 promotes four-strand exchange, mimicking the formation and branch migration of HJs. Here we show that Dmc1 from fission yeast has a similar activity, which requires ATP hydrolysis and is independent of an absolute requirement for the Swi5–Sfr1 complex. These features are critically different from three-strand exchange mediated by Dmc1, but similar to those of four-strand exchange mediated by Rad51, suggesting that strand exchange reactions between duplex–duplex and single-duplex DNAs are mechanistically different. Interestingly, despite similarities in protein structure and in reaction features, the preferential polarities of Dmc1 and Rad51 strand exchange are different (Dmc1 promotes exchange in the 5′-to-3′ direction and Rad51 promotes exchange in the 3′-to-5′ direction relative to the ssDNA region of the DNA substrate). The significance of the Dmc1 polarity is discussed within the context of the necessity for crossover production. PMID:21363965

Neuromuscular synapse integrity requires linkage of acetylcholine receptors to postsynaptic intermediate filament networks via rapsyn–plectin 1f complexes

PubMed Central

Mihailovska, Eva; Raith, Marianne; Valencia, Rocio G.; Fischer, Irmgard; Banchaabouchi, Mumna Al; Herbst, Ruth; Wiche, Gerhard

2014-01-01

Mutations in the cytolinker protein plectin lead to grossly distorted morphology of neuromuscular junctions (NMJs) in patients suffering from epidermolysis bullosa simplex (EBS)-muscular dystrophy (MS) with myasthenic syndrome (MyS). Here we investigated whether plectin contributes to the structural integrity of NMJs by linking them to the postsynaptic intermediate filament (IF) network. Live imaging of acetylcholine receptors (AChRs) in cultured myotubes differentiated ex vivo from immortalized plectin-deficient myoblasts revealed them to be highly mobile and unable to coalesce into stable clusters, in contrast to wild-type cells. We found plectin isoform 1f (P1f) to bridge AChRs and IFs via direct interaction with the AChR-scaffolding protein rapsyn in an isoform-specific manner; forced expression of P1f in plectin-deficient cells rescued both compromised AChR clustering and IF network anchoring. In conditional plectin knockout mice with gene disruption in muscle precursor/satellite cells (Pax7-Cre/cKO), uncoupling of AChRs from IFs was shown to lead to loss of postsynaptic membrane infoldings and disorganization of the NMJ microenvironment, including its invasion by microtubules. In their phenotypic behavior, mutant mice closely mimicked EBS-MD-MyS patients, including impaired body balance, severe muscle weakness, and reduced life span. Our study demonstrates that linkage to desmin IF networks via plectin is crucial for formation and maintenance of AChR clusters, postsynaptic NMJ organization, and body locomotion. PMID:25318670

Huyghens Engines--a new concept and its embodiment for nano-micro interlevel information processing.

PubMed

Santoli, Salvatore

2009-02-01

Current criteria in Bionanotechnology based on software and sensor/actuator hardware of Artificial Intelligence for bioinspired nanostructured systems lack the nanophysical background and key mathematics to describe and mimick the biological hierarchies of nano-to-micro-integrated informational/energetic levels. It is argued that bionanoscale hardware/software undividable solidarity can be mimicked by artificial nanostructured systems featuring intra/interlevel information processing through the emerging organization principle of quantum holography, described by the Heisenberg group G and by harmonic analysis on G. From a property of G as a Lie group, quantum holography is shown to merge the quantum/classical dynamic-symbolic ongoings into the structure-function unity of biological sensing-information processing-actuating, while by Ch. Huyghens' principles about wave motion and coupled oscillators synchronization it applies to environmental waves of any kind, so embodying a universal information processing engine, dubbed Huyghens Engine, that mimicks the holistic nanobiological structure-function solidarity and the kinetics/thermodynamics of nano/micro interface information transfer.

β-Amino acid catalyzed asymmetric Michael additions: design of organocatalysts with catalytic acid/base dyad inspired by serine proteases.

PubMed

Yang, Hui; Wong, Ming Wah

2011-09-16

A new type of chiral β-amino acid catalyst has been computationally designed, mimicking the enzyme catalysis of serine proteases. Our catalyst approach is based on the bioinspired catalytic acid/base dyad, namely, a carboxyl and imidazole pair. DFT calculations predict that this designed organocatalyst catalyzes Michael additions of aldehydes to nitroalkenes with excellent enantioselectivities and remarkably high anti diastereoselectivities. The unusual stacked geometry of the enamine intermediate, hydrogen bonding network, and the adoption of an exo transition state are the keys to understand the stereoselectivity. © 2011 American Chemical Society

Amplified biosensing using the horseradish peroxidase-mimicking DNAzyme as an electrocatalyst.

PubMed

Pelossof, Gilad; Tel-Vered, Ran; Elbaz, Johann; Willner, Itamar

2010-06-01

The hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme is assembled on Au electrodes. It reveals bioelectrocatalytic properties and electrocatalyzes the reduction of H(2)O(2). The bioelectrocatalytic functions of the hemin/G-quadruplex DNAzyme are used to develop electrochemical sensors that follow the activity of glucose oxidase and biosensors for the detection of DNA or low-molecular-weight substrates (adenosine monophosphate, AMP). Hairpin nucleic structures that include the G-quadruplex sequence in a caged configuration and the nucleic acid sequence complementary to the analyte DNA, or the aptamer sequence for AMP, are immobilized on Au-electrode surfaces. In the presence of the DNA analyte, or AMP, the hairpin structures are opened, and the hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme structures are generated on the electrode surfaces. The bioelectrocatalytic cathodic currents generated by the functionalized electrodes, upon the electrochemical reduction of H(2)O(2), provide a quantitative measure for the detection of the target analytes. The DNA target was analyzed with a detection limit of 1 x 10(-12) M, while the detection limit for analyzing AMP was 1 x 10(-6) M. Methods to regenerate the sensing surfaces are presented.

Chronic Pancreatitis in the 21st Century - Research Challenges and Opportunities

PubMed Central

Uc, Aliye; Andersen, Dana K.; Bellin, Melena D.; Bruce, Jason I.; Drewes, Asbjørn M.; Engelhardt, John F.; Forsmark, Christopher E.; Lerch, Markus M.; Lowe, Mark E.; Neuschwander-Tetri, Brent A.; O’Keefe, Stephen J.; Palermo, Tonya M.; Pasricha, Pankaj; Saluja, Ashok K.; Singh, Vikesh K.; Szigethy, Eva M.; Whitcomb, David C.; Yadav, Dhiraj; Conwell, Darwin L.

2016-01-01

A workshop was sponsored by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) to focus on research gaps and opportunities in chronic pancreatitis (CP) and its sequelae. This conference marked the 20th year anniversary of the discovery of the cationic trypsinogen (PRSS1) gene mutation for hereditary pancreatitis. The event was held on July 27, 2016, and structured into 4 sessions: (1) pathophysiology; (2) exocrine complications; (3) endocrine complications; and (4) pain. The current state of knowledge was reviewed; many knowledge gaps and research needs were identified that require further investigation. Common themes included the need to design better tools to diagnose CP and its sequelae early and reliably, identify predisposing risk factors for disease progression, develop standardized protocols to distinguish type 3c diabetes mellitus from other types of diabetes and design effective therapeutic strategies through novel cell culture technologies, animal models mimicking human disease, and pain management tools. Gene therapy and cystic fibrosis conductance regulator (CFTR) potentiators as possible treatments for CP were discussed. Importantly, the need for chronic pancreatitis endpoints and intermediate targets for future drug trials was emphasized. PMID:27748719

Virus based Full Colour Pixels using a Microheater

NASA Astrophysics Data System (ADS)

Kim, Won-Geun; Kim, Kyujung; Ha, Sung-Hun; Song, Hyerin; Yu, Hyun-Woo; Kim, Chuntae; Kim, Jong-Man; Oh, Jin-Woo

2015-09-01

Mimicking natural structures has been received considerable attentions, and there have been a few practical advances. Tremendous efforts based on a self-assembly technique have been contributed to the development of the novel photonic structures which are mimicking nature’s inventions. We emulate the photonic structures from an origin of colour generation of mammalian skins and avian skin/feathers using M13 phage. The structures can be generated a full range of RGB colours that can be sensitively switched by temperature and substrate materials. Consequently, we developed an M13 phage-based temperature-dependent actively controllable colour pixels platform on a microheater chip. Given the simplicity of the fabrication process, the low voltage requirements and cycling stability, the virus colour pixels enable us to substitute for conventional colour pixels for the development of various implantable, wearable and flexible devices in future.

Roles of glutamates and metal ions in a rationally designed nitric oxide reductase based on myoglobin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Y.W.; Robinson, H.; Yeung, N.

2010-05-11

A structural and functional model of bacterial nitric oxide reductase (NOR) has been designed by introducing two glutamates (Glu) and three histidines (His) in sperm whale myoglobin. X-ray structural data indicate that the three His and one Glu (V68E) residues bind iron, mimicking the putative FeB site in NOR, while the second Glu (I107E) interacts with a water molecule and forms a hydrogen bonding network in the designed protein. Unlike the first Glu (V68E), which lowered the heme reduction potential by {approx}110 mV, the second Glu has little effect on the heme potential, suggesting that the negatively charged Glu hasmore » a different role in redox tuning. More importantly, introducing the second Glu resulted in a {approx}100% increase in NOR activity, suggesting the importance of a hydrogen bonding network in facilitating proton delivery during NOR reactivity. In addition, EPR and X-ray structural studies indicate that the designed protein binds iron, copper, or zinc in the FeB site, each with different effects on the structures and NOR activities, suggesting that both redox activity and an intermediate five-coordinate heme-NO species are important for high NOR activity. The designed protein offers an excellent model for NOR and demonstrates the power of using designed proteins as a simpler and more well-defined system to address important chemical and biological issues.« less

Roles of Glutamates and Metal ions in a Rationally Designed Nitric Oxide Reductase Based on Myoglobin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Y Lin; N Yeung; Y Gao

2011-12-31

A structural and functional model of bacterial nitric oxide reductase (NOR) has been designed by introducing two glutamates (Glu) and three histidines (His) in sperm whale myoglobin. X-ray structural data indicate that the three His and one Glu (V68E) residues bind iron, mimicking the putative FeB site in NOR, while the second Glu (I107E) interacts with a water molecule and forms a hydrogen bonding network in the designed protein. Unlike the first Glu (V68E), which lowered the heme reduction potential by {approx}110 mV, the second Glu has little effect on the heme potential, suggesting that the negatively charged Glu hasmore » a different role in redox tuning. More importantly, introducing the second Glu resulted in a {approx}100% increase in NOR activity, suggesting the importance of a hydrogen bonding network in facilitating proton delivery during NOR reactivity. In addition, EPR and X-ray structural studies indicate that the designed protein binds iron, copper, or zinc in the FeB site, each with different effects on the structures and NOR activities, suggesting that both redox activity and an intermediate five-coordinate heme-NO species are important for high NOR activity. The designed protein offers an excellent model for NOR and demonstrates the power of using designed proteins as a simpler and more well-defined system to address important chemical and biological issues.« less

Plume Splitting in a Two-layer Stratified Ambient Fluid

NASA Astrophysics Data System (ADS)

Ma, Yongxing; Flynn, Morris; Sutherland, Bruce

2017-11-01

A line-source plume descending into a two-layer stratified ambient fluid in a finite sized tank is studied experimentally. Although the total volume of ambient fluid is fixed, lower- and upper-layer fluids are respectively removed and added at a constant rate mimicking marine outfall through diffusers and natural and hybrid ventilated buildings. The influence of the plume on the ambient depends on the value of λ, defined as the ratio of the plume buoyancy to the buoyancy loss of the plume as it crosses the ambient interface. Similar to classical filling-box experiments, the plume can always reach the bottom of the tank if λ > 1 . By contrast, if λ < 1 , an intermediate layer eventually forms as a result of plume splitting. Eventually all of the plume fluid spreads within the intermediate layer. The starting time, tv, and the ending time, tt, of the transition process measured from experiments correlate with the value of λ. A three-layer ambient fluid is observed after transition, and the mean value of the measured densities of the intermediate layer fluid is well predicted using plume theory. Acknowledgments: Funding for this study was provided by NSERC.

Efficient near-field wireless energy transfer using adiabatic system variations

DOEpatents

Hamam, Rafif E.; Karalis, Aristeidis; Joannopoulos, John D.; Soljacic, Marin

2013-01-29

Disclosed is a method for transferring energy wirelessly including transferring energy wirelessly from a first resonator structure to an intermediate resonator structure, wherein the coupling rate between the first resonator structure and the intermediate resonator structure is .kappa..sub.1B, transferring energy wirelessly from the intermediate resonator structure to a second resonator structure, wherein the coupling rate between the intermediate resonator structure and the second resonator structure is .kappa..sub.B2, and during the wireless energy transfers, adjusting at least one of the coupling rates .kappa..sub.1B and .kappa..sub.B2 to reduce energy accumulation in the intermediate resonator structure and improve wireless energy transfer from the first resonator structure to the second resonator structure through the intermediate resonator structure.

Efficient near-field wireless energy transfer using adiabatic system variations

DOEpatents

Hamam, Rafif E; Karalis, Aristeidis; Joannopoulos, John D; Soljacic, Marin

2014-09-16

Disclosed is a method for transferring energy wirelessly including transferring energy wirelessly from a first resonator structure to an intermediate resonator structure, wherein the coupling rate between the first resonator structure and the intermediate resonator structure is .kappa..sub.1B, transferring energy wirelessly from the intermediate resonator structure to a second resonator structure, wherein the coupling rate between the intermediate resonator structure and the second resonator structure is .kappa..sub.B2, and during the wireless energy transfers, adjusting at least one of the coupling rates .kappa..sub.1B and .kappa..sub.B2 to reduce energy accumulation in the intermediate resonator structure and improve wireless energy transfer from the first resonator structure to the second resonator structure through the intermediate resonator structure.

Tetra(p-tolyl)borate-functionalized solvent polymeric membrane: a facile and sensitive sensing platform for peroxidase and peroxidase mimetics.

PubMed

Wang, Xuewei; Qin, Wei

2013-07-22

The determination of peroxidase activities is the basis for enzyme-labeled bioaffinity assays, peroxidase-mimicking DNAzymes- and nanoparticles-based assays, and characterization of the catalytic functions of peroxidase mimetics. Here, a facile, sensitive, and cost-effective solvent polymeric membrane-based peroxidase detection platform is described that utilizes reaction intermediates with different pKa values from those of substrates and final products. Several key but long-debated intermediates in the peroxidative oxidation of o-phenylenediamine (o-PD) have been identified and their charge states have been estimated. By using a solvent polymeric membrane functionalized by an appropriate substituted tetraphenylborate as a receptor, those cationic intermediates could be transferred into the membrane from the aqueous phase to induce a large cationic potential response. Thus, the potentiometric indication of the o-PD oxidation catalyzed by peroxidase or its mimetics can be fulfilled. Horseradish peroxidase has been detected with a detection limit at least two orders of magnitude lower than those obtained by spectrophotometric techniques and traditional membrane-based methods. As an example of peroxidase mimetics, G-quadruplex DNAzymes were probed by the intermediate-sensitive membrane and a label-free thrombin detection protocol was developed based on the catalytic activity of the thrombin-binding G-quadruplex aptamer. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficient near-field wireless energy transfer using adiabatic system variations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamam, Rafif E.; Karalis, Aristeidis; Joannopoulos, John D.

Disclosed is a method for transferring energy wirelessly including transferring energy wirelessly from a first resonator structure to an intermediate resonator structure, wherein the coupling rate between the first resonator structure and the intermediate resonator structure is .kappa..sub.1B, transferring energy wirelessly from the intermediate resonator structure to a second resonator structure, wherein the coupling rate between the intermediate resonator structure and the second resonator structure is .kappa..sub.B2, and during the wireless energy transfers, adjusting at least one of the coupling rates .kappa..sub.1B and .kappa..sub.B2 to reduce energy accumulation in the intermediate resonator structure and improve wireless energy transfer from themore » first resonator structure to the second resonator structure through the intermediate resonator structure.« less

The Effects of Molecular Crowding on the Structure and Stability of G-Quadruplexes with an Abasic Site

PubMed Central

Fujimoto, Takeshi; Nakano, Shu-ichi; Miyoshi, Daisuke; Sugimoto, Naoki

2011-01-01

Both cellular environmental factors and chemical modifications critically affect the properties of nucleic acids. However, the structure and stability of DNA containing abasic sites under cell-mimicking molecular crowding conditions remain unclear. Here, we investigated the molecular crowding effects on the structure and stability of the G-quadruplexes including a single abasic site. Structural analysis by circular dichroism showed that molecular crowding by PEG200 did not affect the topology of the G-quadruplex structure with or without an abasic site. Thermodynamic analysis further demonstrated that the degree of stabilization of the G-quadruplex by molecular crowding decreased with substitution of an abasic site for a single guanine. Notably, we found that the molecular crowding effects on the enthalpy change for G-quadruplex formation had a linear relationship with the abasic site effects depending on its position. These results are useful for predicting the structure and stability of G-quadruplexes with abasic sites in the cell-mimicking conditions. PMID:21949901

MIMICKING COUNTERFACTUAL OUTCOMES TO ESTIMATE CAUSAL EFFECTS.

PubMed

Lok, Judith J

2017-04-01

In observational studies, treatment may be adapted to covariates at several times without a fixed protocol, in continuous time. Treatment influences covariates, which influence treatment, which influences covariates, and so on. Then even time-dependent Cox-models cannot be used to estimate the net treatment effect. Structural nested models have been applied in this setting. Structural nested models are based on counterfactuals: the outcome a person would have had had treatment been withheld after a certain time. Previous work on continuous-time structural nested models assumes that counterfactuals depend deterministically on observed data, while conjecturing that this assumption can be relaxed. This article proves that one can mimic counterfactuals by constructing random variables, solutions to a differential equation, that have the same distribution as the counterfactuals, even given past observed data. These "mimicking" variables can be used to estimate the parameters of structural nested models without assuming the treatment effect to be deterministic.

Incubation under fluid dynamic conditions markedly improves the structural preservation in vitro of explanted skeletal muscles.

PubMed

Carton, Flavia; Calderan, Laura; Malatesta, Manuela

2017-11-28

Explanted organs and tissues represent suitable experimental systems mimicking the functional and structural complexity of the living organism, with positive ethical and economic impact on research activities. However, their preservation in culture is generally limited, thus hindering their application as experimental models for biomedical research. In the present study, we investigated the potential of an innovative fluid dynamic culture system to improve the structural preservation in vitro of explanted mouse skeletal muscles (soleus). We used light and transmission electron microscopy to compare the morphological features of muscles maintained either in multiwell plates under conventional conditions or in a bioreactor mimicking the flow of physiological fluids. Our results demonstrate that fluid dynamic conditions markedly slowed the progressive structural deterioration of the muscle tissue occurring during the permanence in the culture medium, prolonging the preservation of some organelles such as mitochondria up to 48 h.

Incubation under fluid dynamic conditions markedly improves the structural preservation in vitro of explanted skeletal muscles

PubMed Central

Carton, Flavia; Calderan, Laura; Malatesta, Manuela

2017-01-01

Explanted organs and tissues represent suitable experimental systems mimicking the functional and structural complexity of the living organism, with positive ethical and economic impact on research activities. However, their preservation in culture is generally limited, thus hindering their application as experimental models for biomedical research. In the present study, we investigated the potential of an innovative fluid dynamic culture system to improve the structural preservation in vitro of explanted mouse skeletal muscles (soleus). We used light and transmission electron microscopy to compare the morphological features of muscles maintained either in multiwell plates under conventional conditions or in a bioreactor mimicking the flow of physiological fluids. Our results demonstrate that fluid dynamic conditions markedly slowed the progressive structural deterioration of the muscle tissue occurring during the permanence in the culture medium, prolonging the preservation of some organelles such as mitochondria up to 48 h. PMID:29313601

Replication of Leaf Surface Structures for Light Harvesting

PubMed Central

Huang, Zhongjia; Yang, Sai; Zhang, Hui; Zhang, Meng; Cao, Wei

2015-01-01

As one of the most important hosts of natural light harvesting, foliage normally has complicated surface structures to capture solar radiances. Bio-mimicking leaf surface structures can provide novel designs of covers in photovoltaic systems. In this article, we reported on replicating leaf surface structures on poly-(methyl methacrylate) polymers to prompt harvesting efficiencies. Prepared via a double transfer process, the polymers were found to have high optical transparencies and transmission hazes, with both values exceeding 80% in some species. Benefiting from optical properties and wrinkled surfaces, the biomimetic polymers brought up to 17% gains to photovoltaic efficiencies. Through Monte-Carlo simulations of light transport, ultrahigh haze values and low reflections were attributed to lightwave guidance schemes lead by the nano- and micro-morphologies which are inherited from master leaves. Thus, leaf surface bio-mimicking can be considered as a strategic direction to design covers of light harvesting systems. PMID:26381702

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Q.; Hu, X; Wang, X

Water-insoluble regenerated silk materials are normally produced by increasing the {beta}-sheet content (silk II). In the present study water-insoluble silk films were prepared by controlling the very slow drying of Bombyx mori silk solutions, resulting in the formation of stable films with a predominant silk I instead of silk II structure. Wide angle X-ray scattering indicated that the silk films stabilized by slow drying were mainly composed of silk I rather than silk II, while water- and methanol-annealed silk films had a higher silk II content. The silk films prepared by slow drying had a globule-like structure at the coremore » surrounded by nano-filaments. The core region was composed of silk I and silk II, surrounded by hydrophilic nano-filaments containing random turns and {alpha}-helix secondary structures. The insoluble silk films prepared by slow drying had unique thermal, mechanical and degradative properties. Differential scanning calorimetry results revealed that silk I crystals had stable thermal properties up to 250 C, without crystallization above the T{sub g}, but degraded at lower temperatures than silk II structure. Compared with water- and methanol-annealed films the films prepared by slow drying had better mechanical ductility and were more rapidly enzymatically degraded, reflecting the differences in secondary structure achieved via differences in post processing of the cast silk films. Importantly, the silk I structure, a key intermediate secondary structure for the formation of mechanically robust natural silk fibers, was successfully generated by the present approach of very slow drying, mimicking the natural process. The results also point to a new mode of generating new types of silk biomaterials with enhanced mechanical properties and increased degradation rates, while maintaining water insolubility, along with a low {beta}-sheet content.« less

Beyond the Periodic Table of Elements: The Role of Superatoms.

PubMed

Jena, Puru

2013-05-02

Atomic clusters composed of homo or heteroatomic species constitute an intermediate phase of matter where every atom counts and whose properties depend on their size, shape, composition, and charge. If specific clusters mimicking the chemistry of atoms can be produced, they can be thought of as man-made superatoms forming the building blocks of a new three-dimensional periodic table. Novel materials with tailored properties can then be synthesized by assembling these superatoms. This invited Perspective presents a brief summary of the pioneering works that led to this concept, and highlights the recent breakthroughs that hold promise for a new era in materials science.

Description of the topographical changes associated to the different stages of the DsbA catalytic cycle

PubMed Central

Vinci, Floriana; Couprie, Joël; Pucci, Piero; Quéméneur, Eric; Moutiez, Mireille

2002-01-01

This paper provides a description of the surface topography of DsbA, the bacterial disulfide-bond forming enzyme, in the different phases of its catalytic cycle. Three representative states, that is, oxidized and reduced protein and a covalent complex mimicking the DsbA-substrate disulfide intermediate, have been investigated by a combination of limited proteolysis experiments and mass spectrometry methodologies. Protease-accessible sites are largely distributed in the oxidized form with a small predominance inside the thioredoxin domain. Proteolysis occurs even in secondary structure elements, revealing a significant mobility of the protein. Many cleavage sites disappear in the reduced form and most of the remaining ones appear with strongly reduced kinetics. The protein within the complex shows an intermediate behavior. This variation of flexibility in DsbA is probably the determining factor for the course of its catalytic cycle. In particular, the great mobility of the oxidized protein might facilitate the accommodation of its various substrates, whereas the increasing rigidity from the complexed to the reduced form could help the release of oxidized products. The formation of the complex between PID peptide and DsbA does not significantly protect the enzyme against proteolysis, reinforcing the results previously obtained by calorimetry concerning the weakness of their interaction. The few cleavage sites observed, however, are in favor of the presence of the peptide in the binding site postulated from crystallographic studies. As for the peptide itself, the proteolytic pattern and the protection effect exerted by DsbA could be explained by a preferential orientation within the binding site. PMID:12070313

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumaran Nair, C; Hoffman, D; Wright, C

Purpose: We aim to evaluate a new commercial dose mimicking inverse-planning application that was designed to provide cross-platform treatment planning, for its dosimetric quality and efficiency. The clinical benefit of this application allows patients treated on O-shaped linac to receive an equivalent plan on conventional L-shaped linac as needed for workflow or machine downtime. Methods: The dose mimicking optimization process seeks to create a similar DVH of an O-shaped linac-based plans with an alternative treatment technique (IMRT or VMAT), by maintaining target conformity, and penalizing dose falloff outside the target. Ten head and neck (HN) helical delivery plans, including simplemore » and complex cases were selected for re-planning with the dose mimicking application. All plans were generated for a 6 MV beam model, using 7-field/ 9-field IMRT and VMAT techniques. PTV coverage (D1, D99 and homogeneity index [HI]), and OARs avoidance (Dmean / Dmax) were compared. Results: The resulting dose mimicked HN plans achieved acceptable PTV coverage for HI (VMAT 7.0±2.3, 7-fld 7.3±2.4, and 9-fld 7.0±2.4), D99 (98.0%±0.7%, 97.8%±0.7%, and 98.0%±0.7%), as well as D1 (106.4%±2.1%, 106.5%±2.2%, and 106.4%±2.1%), respectively. The OAR dose discrepancy varied: brainstem (2% to 4%), cord (3% to 6%), esophagus (−4% to −8%), larynx (−4% to 2%), and parotid (4% to 14%). Mimicked plans would typically be needed for 1–5 fractions of a treatment course, and we estimate <1% variance would be introduced in target coverage while maintaining comparable low dose to OARs. All mimicked plans were approved by independent physician and passed patient specific QA within our established tolerance. Conclusion: Dose mimicked plans provide a practical alternative for responding to clinical workflow issues, and provide reliability for patient treatment. The quality of dose mimicking for HN patients highly depends on the delivery technique, field numbers and angles, as well as user selection of structures.« less

A Three-Dimensional Computational Model of Collagen Network Mechanics

PubMed Central

Lee, Byoungkoo; Zhou, Xin; Riching, Kristin; Eliceiri, Kevin W.; Keely, Patricia J.; Guelcher, Scott A.; Weaver, Alissa M.; Jiang, Yi

2014-01-01

Extracellular matrix (ECM) strongly influences cellular behaviors, including cell proliferation, adhesion, and particularly migration. In cancer, the rigidity of the stromal collagen environment is thought to control tumor aggressiveness, and collagen alignment has been linked to tumor cell invasion. While the mechanical properties of collagen at both the single fiber scale and the bulk gel scale are quite well studied, how the fiber network responds to local stress or deformation, both structurally and mechanically, is poorly understood. This intermediate scale knowledge is important to understanding cell-ECM interactions and is the focus of this study. We have developed a three-dimensional elastic collagen fiber network model (bead-and-spring model) and studied fiber network behaviors for various biophysical conditions: collagen density, crosslinker strength, crosslinker density, and fiber orientation (random vs. prealigned). We found the best-fit crosslinker parameter values using shear simulation tests in a small strain region. Using this calibrated collagen model, we simulated both shear and tensile tests in a large linear strain region for different network geometry conditions. The results suggest that network geometry is a key determinant of the mechanical properties of the fiber network. We further demonstrated how the fiber network structure and mechanics evolves with a local formation, mimicking the effect of pulling by a pseudopod during cell migration. Our computational fiber network model is a step toward a full biomechanical model of cellular behaviors in various ECM conditions. PMID:25386649

Structural analysis of substrate-mimicking inhibitors in complex with Neisseria meningitidis 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase - The importance of accommodating the active site water.

PubMed

Heyes, Logan C; Reichau, Sebastian; Cross, Penelope J; Jameson, Geoffrey B; Parker, Emily J

2014-12-01

3-Deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS) catalyses the first committed step of the shikimate pathway, which produces the aromatic amino acids as well as many other aromatic metabolites. DAH7PS catalyses an aldol-like reaction between phosphoenolpyruvate and erythrose 4-phosphate. Three phosphoenolpyruvate mimics, (R)-phospholactate, (S)-phospholactate and vinyl phosphonate [(E)-2-methyl-3-phosphonoacrylate], were found to competitively inhibit DAH7PS from Neisseria meningitidis, which is the pathogen responsible for bacterial meningitis. The most potent inhibitor was the vinyl phosphonate with a Ki value of 3.9±0.4μM. We report for the first time crystal structures of these compounds bound in the active site of a DAH7PS enzyme which reveals that the inhibitors bind to the active site of the enzyme in binding modes that mimic those of the predicted oxocarbenium and tetrahedral intermediates of the enzyme-catalysed reaction. Furthermore, the inhibitors accommodate the binding of a key active site water molecule. Together, these observations provide strong evidence that this active site water participates directly in the DAH7PS reaction, enabling the facial selectivity of the enzyme-catalysed reaction sequence to be delineated. Copyright © 2014 Elsevier Inc. All rights reserved.

Real-Time Dynamics of Emerging Actin Networks in Cell-Mimicking Compartments

PubMed Central

Deshpande, Siddharth; Pfohl, Thomas

2015-01-01

Understanding the cytoskeletal functionality and its relation to other cellular components and properties is a prominent question in biophysics. The dynamics of actin cytoskeleton and its polymorphic nature are indispensable for the proper functioning of living cells. Actin bundles are involved in cell motility, environmental exploration, intracellular transport and mechanical stability. Though the viscoelastic properties of actin-based structures have been extensively probed, the underlying microstructure dynamics, especially their disassembly, is not fully understood. In this article, we explore the rich dynamics and emergent properties exhibited by actin bundles within flow-free confinements using a microfluidic set-up and epifluorescence microscopy. After forming entangled actin filaments within cell-sized quasi two-dimensional confinements, we induce their bundling using three different fundamental mechanisms: counterion condensation, depletion interactions and specific protein-protein interactions. Intriguingly, long actin filaments form emerging networks of actin bundles via percolation leading to remarkable properties such as stress generation and spindle-like intermediate structures. Simultaneous sharing of filaments in different links of the network is an important parameter, as short filaments do not form networks but segregated clusters of bundles instead. We encounter a hierarchical process of bundling and its subsequent disassembly. Additionally, our study suggests that such percolated networks are likely to exist within living cells in a dynamic fashion. These observations render a perspective about differential cytoskeletal responses towards numerous stimuli. PMID:25785606

Azaglycomimetics: Natural Occurrence, Biological Activity, and Application

NASA Astrophysics Data System (ADS)

Asano, Naoki

A large number of alkaloids mimicking the structures of monosaccharides or oligosaccharides have been isolated from plants and microorganisms. The sugar mimicking alkaloids with a nitrogen in the ring are called azasugars or iminosugars. Naturally occurring azasugars are classified into five structural classes: polyhydroxylated piperidines, pyrrolidines, indolizidines, pyrrolizidines, and nortropanes. They are easily soluble in water because of their polyhydroxylated structures and inhibit glycosidases because of a structural resemblance to the sugar moiety of the natural substrate. Glycosidases are involved in a wide range of anabolic and catabolic processes, such as digestion, lysosomal catabolism of glycoconjugates, biosynthesis of glycoproteins, and the endoplasmic reticulum (ER) quality control and ER-associated degradation of glycoproteins. Hence, modifying or blocking these processes in vivo by inhibitors is of great interest from a therapeutic point of view. Azasugars are an important class of glycosidase inhibitors and are arousing great interest for instance as antidiabetics, antiobesity drugs, antivirals, and therapeutic agents for some genetic disorders. This review describes the recent studies on isolation, characterization, glycosidase inhibitory activity, and therapeutic application of azaglycomimetics.

Chronic Pancreatitis in the 21st Century - Research Challenges and Opportunities: Summary of a National Institute of Diabetes and Digestive and Kidney Diseases Workshop.

PubMed

Uc, Aliye; Andersen, Dana K; Bellin, Melena D; Bruce, Jason I; Drewes, Asbjørn M; Engelhardt, John F; Forsmark, Christopher E; Lerch, Markus M; Lowe, Mark E; Neuschwander-Tetri, Brent A; OʼKeefe, Stephen J; Palermo, Tonya M; Pasricha, Pankaj; Saluja, Ashok K; Singh, Vikesh K; Szigethy, Eva M; Whitcomb, David C; Yadav, Dhiraj; Conwell, Darwin L

2016-11-01

A workshop was sponsored by the National Institute of Diabetes and Digestive and Kidney Diseases to focus on research gaps and opportunities in chronic pancreatitis (CP) and its sequelae. This conference marked the 20th year anniversary of the discovery of the cationic trypsinogen (PRSS1) gene mutation for hereditary pancreatitis. The event was held on July 27, 2016, and structured into 4 sessions: (1) pathophysiology, (2) exocrine complications, (3) endocrine complications, and (4) pain. The current state of knowledge was reviewed; many knowledge gaps and research needs were identified that require further investigation. Common themes included the need to design better tools to diagnose CP and its sequelae early and reliably, identify predisposing risk factors for disease progression, develop standardized protocols to distinguish type 3c diabetes mellitus from other types of diabetes, and design effective therapeutic strategies through novel cell culture technologies, animal models mimicking human disease, and pain management tools. Gene therapy and cystic fibrosis conductance regulator potentiators as possible treatments of CP were discussed. Importantly, the need for CP end points and intermediate targets for future drug trials was emphasized.

Binding and Inactivation Mechanism of a Humanized Fatty Acid Amide Hydrolase by [alpha]-Ketoheterocycle Inhibitors Revealed from Cocrystal Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mileni, Mauro; Garfunkle, Joie; DeMartino, Jessica K.

The cocrystal X-ray structures of two isomeric {alpha}-ketooxazole inhibitors (1 (OL-135) and 2) bound to fatty acid amide hydrolase (FAAH), a key enzymatic regulator of endocannabinoid signaling, are disclosed. The active site catalytic Ser241 is covalently bound to the inhibitors electrophilic carbonyl groups, providing the first structures of FAAH bound to an inhibitor as a deprotonated hemiketal mimicking the enzymatic tetrahedral intermediate. The work also offers a detailed view of the oxyanion hole and an exceptional 'in-action' depiction of the unusual Ser-Ser-Lys catalytic triad. These structures capture the first picture of inhibitors that span the active site into the cytosolicmore » port providing new insights that help to explain FAAH's interaction with substrate leaving groups and their role in modulating inhibitor potency and selectivity. The role for the activating central heterocycle is clearly defined and distinguished from that observed in prior applications with serine proteases, reconciling the large electronic effect of attached substituents found unique to this class of inhibitors with FAAH. Additional striking active site flexibility is seen upon binding of the inhibitors, providing insights into the existence of a now well-defined membrane access channel with the disappearance of a spatially independent portion of the acyl chain-binding pocket. Finally, comparison of the structures of OL-135 (1) and its isomer 2 indicates that they bind identically to FAAH, albeit with reversed orientations of the central activating heterocycle, revealing that the terminal 2-pyridyl substituent and the acyl chain phenyl group provide key anchoring interactions and confirming the distinguishing role of the activating oxazole.« less

De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks.

PubMed

Schneider, G; Lee, M L; Stahl, M; Schneider, P

2000-07-01

An evolutionary algorithm was developed for fragment-based de novo design of molecules (TOPAS, TOPology-Assigning System). This stochastic method aims at generating a novel molecular structure mimicking a template structure. A set of approximately 25,000 fragment structures serves as the building block supply, which were obtained by a straightforward fragmentation procedure applied to 36,000 known drugs. Eleven reaction schemes were implemented for both fragmentation and building block assembly. This combination of drug-derived building blocks and a restricted set of reaction schemes proved to be a key for the automatic development of novel, synthetically tractable structures. In a cyclic optimization process, molecular architectures were generated from a parent structure by virtual synthesis, and the best structure of a generation was selected as the parent for the subsequent TOPAS cycle. Similarity measures were used to define 'fitness', based on 2D-structural similarity or topological pharmacophore distance between the template molecule and the variants. The concept of varying library 'diversity' during a design process was consequently implemented by using adaptive variant distributions. The efficiency of the design algorithm was demonstrated for the de novo construction of potential thrombin inhibitors mimicking peptide and non-peptide template structures.

Bioinspired design and macroscopic assembly of poly(vinyl alcohol)-coated graphene into kilometers-long fibers.

PubMed

Kou, Liang; Gao, Chao

2013-05-21

Nacre is characterized by its excellent mechanical performance due to the well-recognized "brick and mortar" structure. Many efforts have been applied to make nacre-mimicking materials, but it is still a big challenge to realize their continuous production. Here, we prepared sandwich-like building blocks of poly(vinyl alcohol) (PVA)-coated graphene, and achieved high-nanofiller-content kilometers-long fibers by continuous wet-spinning assembly technology. The fibers have a strict "brick and mortar" layered structure, with graphene sheet as rigid brick and PVA as soft mortar. The mortar thickness can be precisely tuned from 2.01 to 3.31 nm by the weight feed ratio of PVA to graphene, as demonstrated by both atomic force microscopy and X-ray diffraction measurements. The mechanical strength of the nacre-mimicking fibers increases with increasing the content of PVA, and it rises gradually from 81 MPa for the fiber with 53.1 wt% PVA to 161 MPa for the fiber with 65.8 wt% PVA. The mechanical performance of our fibers was independent of the molecular weight (MW) of PVA in the wide range of 2-100 kDa, indicating that low MW polymers can also be used to make strong nanocomposites. The tensile stress of fibers immersed in PVA 5 wt% solution reached ca. 200 MPa, surpassing the values of nacre and most of other nacre-mimicking materials. The nacre-mimicking fibers are highly electrically conductive (∼350 S m(-1)) after immersing in hydroiodic acid, enabling them to connect a circuit to illuminate an LED lamp.

An α‐Helix‐Mimicking 12,13‐Helix: Designed α/β/γ‐Foldamers as Selective Inhibitors of Protein–Protein Interactions

PubMed Central

Grison, Claire M.; Miles, Jennifer A.; Robin, Sylvie

2016-01-01

Abstract A major current challenge in bioorganic chemistry is the identification of effective mimics of protein secondary structures that act as inhibitors of protein–protein interactions (PPIs). In this work, trans‐2‐aminocyclobutanecarboxylic acid (tACBC) was used as the key β‐amino acid component in the design of α/β/γ‐peptides to structurally mimic a native α‐helix. Suitably functionalized α/β/γ‐peptides assume an α‐helix‐mimicking 12,13‐helix conformation in solution, exhibit enhanced proteolytic stability in comparison to the wild‐type α‐peptide parent sequence from which they are derived, and act as selective inhibitors of the p53/hDM2 interaction. PMID:27467859

An α-Helix-Mimicking 12,13-Helix: Designed α/β/γ-Foldamers as Selective Inhibitors of Protein-Protein Interactions.

PubMed

Grison, Claire M; Miles, Jennifer A; Robin, Sylvie; Wilson, Andrew J; Aitken, David J

2016-09-05

A major current challenge in bioorganic chemistry is the identification of effective mimics of protein secondary structures that act as inhibitors of protein-protein interactions (PPIs). In this work, trans-2-aminocyclobutanecarboxylic acid (tACBC) was used as the key β-amino acid component in the design of α/β/γ-peptides to structurally mimic a native α-helix. Suitably functionalized α/β/γ-peptides assume an α-helix-mimicking 12,13-helix conformation in solution, exhibit enhanced proteolytic stability in comparison to the wild-type α-peptide parent sequence from which they are derived, and act as selective inhibitors of the p53/hDM2 interaction. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Bioinspired design and macroscopic assembly of poly(vinyl alcohol)-coated graphene into kilometers-long fibers

NASA Astrophysics Data System (ADS)

Kou, Liang; Gao, Chao

2013-05-01

Nacre is characterized by its excellent mechanical performance due to the well-recognized ``brick and mortar'' structure. Many efforts have been applied to make nacre-mimicking materials, but it is still a big challenge to realize their continuous production. Here, we prepared sandwich-like building blocks of poly(vinyl alcohol) (PVA)-coated graphene, and achieved high-nanofiller-content kilometers-long fibers by continuous wet-spinning assembly technology. The fibers have a strict ``brick and mortar'' layered structure, with graphene sheet as rigid brick and PVA as soft mortar. The mortar thickness can be precisely tuned from 2.01 to 3.31 nm by the weight feed ratio of PVA to graphene, as demonstrated by both atomic force microscopy and X-ray diffraction measurements. The mechanical strength of the nacre-mimicking fibers increases with increasing the content of PVA, and it rises gradually from 81 MPa for the fiber with 53.1 wt% PVA to 161 MPa for the fiber with 65.8 wt% PVA. The mechanical performance of our fibers was independent of the molecular weight (MW) of PVA in the wide range of 2-100 kDa, indicating that low MW polymers can also be used to make strong nanocomposites. The tensile stress of fibers immersed in PVA 5 wt% solution reached ca. 200 MPa, surpassing the values of nacre and most of other nacre-mimicking materials. The nacre-mimicking fibers are highly electrically conductive (~350 S m-1) after immersing in hydroiodic acid, enabling them to connect a circuit to illuminate an LED lamp.Nacre is characterized by its excellent mechanical performance due to the well-recognized ``brick and mortar'' structure. Many efforts have been applied to make nacre-mimicking materials, but it is still a big challenge to realize their continuous production. Here, we prepared sandwich-like building blocks of poly(vinyl alcohol) (PVA)-coated graphene, and achieved high-nanofiller-content kilometers-long fibers by continuous wet-spinning assembly technology. The fibers have a strict ``brick and mortar'' layered structure, with graphene sheet as rigid brick and PVA as soft mortar. The mortar thickness can be precisely tuned from 2.01 to 3.31 nm by the weight feed ratio of PVA to graphene, as demonstrated by both atomic force microscopy and X-ray diffraction measurements. The mechanical strength of the nacre-mimicking fibers increases with increasing the content of PVA, and it rises gradually from 81 MPa for the fiber with 53.1 wt% PVA to 161 MPa for the fiber with 65.8 wt% PVA. The mechanical performance of our fibers was independent of the molecular weight (MW) of PVA in the wide range of 2-100 kDa, indicating that low MW polymers can also be used to make strong nanocomposites. The tensile stress of fibers immersed in PVA 5 wt% solution reached ca. 200 MPa, surpassing the values of nacre and most of other nacre-mimicking materials. The nacre-mimicking fibers are highly electrically conductive (~350 S m-1) after immersing in hydroiodic acid, enabling them to connect a circuit to illuminate an LED lamp. Electronic supplementary information (ESI) available: More AFM and SEM images and electrical conductivities of CRG@PVA with different feed ratios, FTIR spectra, Raman and XPS results of GO, CRG and CRG@PVA, SEM images of CRG@PVA fibers with different diameters, SEM images and conductivity of CRG@PVA fibers with different MW of PVA, the tensile curve of CRG@PVA paper, and videos of graphene knot and spring. See DOI: 10.1039/c3nr00455d

Optimized mid-infrared thermal emitters for applications in aircraft countermeasures

NASA Astrophysics Data System (ADS)

Lorenzo, Simón G.; You, Chenglong; Granier, Christopher H.; Veronis, Georgios; Dowling, Jonathan P.

2017-12-01

We introduce an optimized aperiodic multilayer structure capable of broad angle and high temperature thermal emission over the 3 μm to 5 μm atmospheric transmission band. This aperiodic multilayer structure composed of alternating layers of silicon carbide and graphite on top of a tungsten substrate exhibits near maximal emittance in a 2 μm wavelength range centered in the mid-wavelength infrared band traditionally utilized for atmospheric transmission. We optimize the layer thicknesses using a hybrid optimization algorithm coupled to a transfer matrix code to maximize the power emitted in this mid-infrared range normal to the structure's surface. We investigate possible applications for these structures in mimicking 800-1000 K aircraft engine thermal emission signatures and in improving countermeasure effectiveness against hyperspectral imagers. We find these structures capable of matching the Planck blackbody curve in the selected infrared range with relatively sharp cutoffs on either side, leading to increased overall efficiency of the structures. Appropriately optimized multilayer structures with this design could lead to matching a variety of mid-infrared thermal emissions. For aircraft countermeasure applications, this method could yield a flare design capable of mimicking engine spectra and breaking the lock of hyperspectral imaging systems.

Solution structure of a DNA mimicking motif of an RNA aptamer against transcription factor AML1 Runt domain.

PubMed

Nomura, Yusuke; Tanaka, Yoichiro; Fukunaga, Jun-ichi; Fujiwara, Kazuya; Chiba, Manabu; Iibuchi, Hiroaki; Tanaka, Taku; Nakamura, Yoshikazu; Kawai, Gota; Kozu, Tomoko; Sakamoto, Taiichi

2013-12-01

AML1/RUNX1 is an essential transcription factor involved in the differentiation of hematopoietic cells. AML1 binds to the Runt-binding double-stranded DNA element (RDE) of target genes through its N-terminal Runt domain. In a previous study, we obtained RNA aptamers against the AML1 Runt domain by systematic evolution of ligands by exponential enrichment and revealed that RNA aptamers exhibit higher affinity for the Runt domain than that for RDE and possess the 5'-GCGMGNN-3' and 5'-N'N'CCAC-3' conserved motif (M: A or C; N and N' form Watson-Crick base pairs) that is important for Runt domain binding. In this study, to understand the structural basis of recognition of the Runt domain by the aptamer motif, the solution structure of a 22-mer RNA was determined using nuclear magnetic resonance. The motif contains the AH(+)-C mismatch and base triple and adopts an unusual backbone structure. Structural analysis of the aptamer motif indicated that the aptamer binds to the Runt domain by mimicking the RDE sequence and structure. Our data should enhance the understanding of the structural basis of DNA mimicry by RNA molecules.

Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy.

PubMed

Baird, Nathan J; Ludtke, Steven J; Khant, Htet; Chiu, Wah; Pan, Tao; Sosnick, Tobin R

2010-11-24

RNA folding occurs via a series of transitions between metastable intermediate states. It is unknown whether folding intermediates are discrete structures folding along defined pathways or heterogeneous ensembles folding along broad landscapes. We use cryo-electron microscopy and single-particle image reconstruction to determine the structure of the major folding intermediate of the specificity domain of a ribonuclease P ribozyme. Our results support the existence of a discrete conformation for this folding intermediate.

Cryo-EM structures of two bovine adenovirus type 3 intermediates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Lingpeng; Huang, Xiaoxing; Li, Xiaomin

2014-02-15

Adenoviruses (Ads) infect hosts from all vertebrate species and have been investigated as vaccine vectors. We report here near-atomic structures of two bovine Ad type 3 (BAd3) intermediates obtained by cryo-electron microscopy. A comparison between the two intermediate structures reveals that the differences are localized in the fivefold vertex region, while their facet structures are identical. The overall facet structure of BAd3 exhibits a similar structure to human Ads; however, BAd3 protein IX has a unique conformation. Mass spectrometry and cryo-electron tomography analyses indicate that one intermediate structure represents the stage during DNA encapsidation, whilst the other intermediate structure representsmore » a later stage. These results also suggest that cleavage of precursor protein VI occurs during, rather than after, the DNA encapsidation process. Overall, our results provide insights into the mechanism of Ad assembly, and allow the first structural comparison between human and nonhuman Ads at backbone level. - Highlights: • First structure of bovine adenovirus type 3. • Some channels are located at the vertex of intermediate during DNA encapsidation. • Protein IX exhibits a unique conformation of trimeric coiled–coiled structure. • Cleavage of precursor protein VI occurs during the DNA encapsidation process.« less

Mimicking the photosynthetic triplet energy-transfer relay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gust, D.; Moore, T.A.; Moore, A.L.

1993-06-30

In the reaction centers of photosynthetic organisms, chlorophyll triplet states are sometimes formed by recombination of charge-separated intermediates. These triplets are excellent sensitizers for singlet oxygen formation. Carotenoid polyenes can provide photoprotection from singlet oxygen generation by rapidly quenching chlorophyll triplet states via triplet-triplet energy transfer. Because in bacteria the reaction center carotenoid is not located adjacent to the bacteriochlorophyll special pair, which is the origin of the charge separation, it has been postulated that quenching may occur via a triplet relay involving an intermediate chlorophyll monomer. We now report the synthesis and spectroscopic study of a covalently linked carotenoidmore » (C)-porphyrin (P)-pyropheophorbide (Ppd) triad molecule which mimics this triplet relay. The pyropheophorbide singlet-state C-P-[sup 1]Ppd (generated by direct excitation or energy transfer from the attached porphyrin) undergoes intersystem crossing to the triplet C-P-[sup 3]Ppd. In oxygen-free solutions, this triplet decays to [sup 3]C-p-Ppd through a triplet-transfer relay involving an intermediate C-[sup 3]P-Ppd species. In aerated solutions, quenching of C-P-[sup 3]Ppd by the attached carotenoid competes with singlet oxygen sensitization and thus provides a degree of photoprotection. In a similar traid containing a zinc porphyrin moiety, triplet transfer is slow due to the higher energy of the C-[sup 3]P[sub Zn]-Ppd intermediate, and photoprotection via the relay is nonexistent. The triplet relay ceases to function at low temperatures in both the natural and biomimetic cases due to the endergonicity of the first step. 37 refs., 6 figs., 1 tab.« less

Nanofabrication and coloration study of artificial Morpho butterfly wings with aligned lamellae layers

PubMed Central

Zhang, Sichao; Chen, Yifang

2015-01-01

The bright and iridescent blue color from Morpho butterfly wings has attracted worldwide attentions to explore its mysterious nature for long time. Although the physics of structural color by the nanophotonic structures built on the wing scales has been well established, replications of the wing structure by standard top-down lithography still remains a challenge. This paper reports a technical breakthrough to mimic the blue color of Morpho butterfly wings, by developing a novel nanofabrication process, based on electron beam lithography combined with alternate PMMA/LOR development/dissolution, for photonic structures with aligned lamellae multilayers in colorless polymers. The relationship between the coloration and geometric dimensions as well as shapes is systematically analyzed by solving Maxwell’s Equations with a finite domain time difference simulator. Careful characterization of the mimicked blue by spectral measurements under both normal and oblique angles are carried out. Structural color in blue reflected by the fabricated wing scales, is demonstrated and further extended to green as an application exercise of the new technique. The effects of the regularity in the replicas on coloration are analyzed. In principle, this approach establishes a starting point for mimicking structural colors beyond the blue in Morpho butterfly wings. PMID:26577813

Nanofabrication and coloration study of artificial Morpho butterfly wings with aligned lamellae layers.

PubMed

Zhang, Sichao; Chen, Yifang

2015-11-18

The bright and iridescent blue color from Morpho butterfly wings has attracted worldwide attentions to explore its mysterious nature for long time. Although the physics of structural color by the nanophotonic structures built on the wing scales has been well established, replications of the wing structure by standard top-down lithography still remains a challenge. This paper reports a technical breakthrough to mimic the blue color of Morpho butterfly wings, by developing a novel nanofabrication process, based on electron beam lithography combined with alternate PMMA/LOR development/dissolution, for photonic structures with aligned lamellae multilayers in colorless polymers. The relationship between the coloration and geometric dimensions as well as shapes is systematically analyzed by solving Maxwell's Equations with a finite domain time difference simulator. Careful characterization of the mimicked blue by spectral measurements under both normal and oblique angles are carried out. Structural color in blue reflected by the fabricated wing scales, is demonstrated and further extended to green as an application exercise of the new technique. The effects of the regularity in the replicas on coloration are analyzed. In principle, this approach establishes a starting point for mimicking structural colors beyond the blue in Morpho butterfly wings.

Nanofabrication and coloration study of artificial Morpho butterfly wings with aligned lamellae layers

NASA Astrophysics Data System (ADS)

Zhang, Sichao; Chen, Yifang

2015-11-01

The bright and iridescent blue color from Morpho butterfly wings has attracted worldwide attentions to explore its mysterious nature for long time. Although the physics of structural color by the nanophotonic structures built on the wing scales has been well established, replications of the wing structure by standard top-down lithography still remains a challenge. This paper reports a technical breakthrough to mimic the blue color of Morpho butterfly wings, by developing a novel nanofabrication process, based on electron beam lithography combined with alternate PMMA/LOR development/dissolution, for photonic structures with aligned lamellae multilayers in colorless polymers. The relationship between the coloration and geometric dimensions as well as shapes is systematically analyzed by solving Maxwell’s Equations with a finite domain time difference simulator. Careful characterization of the mimicked blue by spectral measurements under both normal and oblique angles are carried out. Structural color in blue reflected by the fabricated wing scales, is demonstrated and further extended to green as an application exercise of the new technique. The effects of the regularity in the replicas on coloration are analyzed. In principle, this approach establishes a starting point for mimicking structural colors beyond the blue in Morpho butterfly wings.

Autoimmunity to Tropomyosin-Specific Peptides Induced by Mycobacterium leprae in Leprosy Patients: Identification of Mimicking Proteins.

PubMed

Singh, Itu; Yadav, Asha Ram; Mohanty, Keshar Kunja; Katoch, Kiran; Sharma, Prashant; Pathak, Vinay Kumar; Bisht, Deepa; Gupta, Umesh D; Sengupta, Utpal

2018-01-01

It has been shown earlier that there is a rise in the levels of autoantibodies and T cell response to cytoskeletal proteins in leprosy. Our group recently demonstrated a rise in both T and B cell responses to keratin and myelin basic protein in all types of leprosy patients and their associations in type 1 reaction (T1R) group of leprosy. In this study, we investigated the association of levels of autoantibodies and lymphoproliferation against myosin in leprosy patients across the spectrum and tried to find out the mimicking proteins or epitopes between host protein and protein/s of Mycobacterium leprae . One hundred and sixty-nine leprosy patients and 55 healthy controls (HC) were enrolled in the present study. Levels of anti-myosin antibodies and T-cell responses against myosin were measured by ELISA and lymphoproliferation assay, respectively. Using 2-D gel electrophoresis, western blot and MALDI-TOF/TOF antibody-reactive spots were identified. Three-dimensional structure of mimicking proteins was modeled by online server. B cell epitopes of the proteins were predicted by BCPREDS server 1.0 followed by identification of mimicking epitopes. Mice of inbred BALB/c strain were hyperimmunized with M. leprae soluble antigen (MLSA) and splenocytes and lymph node cells of these animals were adoptively transferred to naïve mice. Highest level of anti-myosin antibodies was noted in sera of T1R leprosy patients. We observed significantly higher levels of lymphoproliferative response ( p  < 0.05) with myosin in all types of leprosy patients compared to HC. Further, hyperimmunization of inbred BALB/c strain of female mice and rabbit with MLSA revealed that both hyperimmunized rabbit and mice evoked heightened levels of antibodies against myosin and this autoimmune response could be adoptively transferred from hyperimmunized to naïve mice. Tropomyosin was found to be mimicking with ATP-dependent Clp protease ATP-binding subunit of M. leprae . We found four mimicking epitopes between these sequences. These data suggest that these mimicking proteins tropomyosin and ATP-dependent Clp protease ATP-binding subunit of M. leprae or more precisely mimicking epitopes (four B cell epitopes) might be responsible for extensive tissue damage during type1 reaction in leprosy.

Evolutionary origins of hepatitis A virus in small mammals.

PubMed

Drexler, Jan Felix; Corman, Victor M; Lukashev, Alexander N; van den Brand, Judith M A; Gmyl, Anatoly P; Brünink, Sebastian; Rasche, Andrea; Seggewiβ, Nicole; Feng, Hui; Leijten, Lonneke M; Vallo, Peter; Kuiken, Thijs; Dotzauer, Andreas; Ulrich, Rainer G; Lemon, Stanley M; Drosten, Christian

2015-12-08

Hepatitis A virus (HAV) is an ancient and ubiquitous human pathogen recovered previously only from primates. The sole species of the genus Hepatovirus, existing in both enveloped and nonenveloped forms, and with a capsid structure intermediate between that of insect viruses and mammalian picornaviruses, HAV is enigmatic in its origins. We conducted a targeted search for hepatoviruses in 15,987 specimens collected from 209 small mammal species globally and discovered highly diversified viruses in bats, rodents, hedgehogs, and shrews, which by pairwise sequence distance comprise 13 novel Hepatovirus species. Near-complete genomes from nine of these species show conservation of unique hepatovirus features, including predicted internal ribosome entry site structure, a truncated VP4 capsid protein lacking N-terminal myristoylation, a carboxyl-terminal pX extension of VP1, VP2 late domains involved in membrane envelopment, and a cis-acting replication element within the 3D(pol) sequence. Antibodies in some bat sera immunoprecipitated and neutralized human HAV, suggesting conservation of critical antigenic determinants. Limited phylogenetic cosegregation among hepatoviruses and their hosts and recombination patterns are indicative of major hepatovirus host shifts in the past. Ancestral state reconstructions suggest a Hepatovirus origin in small insectivorous mammals and a rodent origin of human HAV. Patterns of infection in small mammals mimicked those of human HAV in hepatotropism, fecal shedding, acute nature, and extinction of the virus in a closed host population. The evolutionary conservation of hepatovirus structure and pathogenesis provide novel insight into the origins of HAV and highlight the utility of analyzing animal reservoirs for risk assessment of emerging viruses.

Evolutionary origins of hepatitis A virus in small mammals

PubMed Central

Drexler, Jan Felix; Corman, Victor M.; Lukashev, Alexander N.; van den Brand, Judith M. A.; Gmyl, Anatoly P.; Brünink, Sebastian; Rasche, Andrea; Seggewiβ, Nicole; Feng, Hui; Leijten, Lonneke M.; Vallo, Peter; Kuiken, Thijs; Dotzauer, Andreas; Ulrich, Rainer G.; Lemon, Stanley M.; Drosten, Christian

2015-01-01

Hepatitis A virus (HAV) is an ancient and ubiquitous human pathogen recovered previously only from primates. The sole species of the genus Hepatovirus, existing in both enveloped and nonenveloped forms, and with a capsid structure intermediate between that of insect viruses and mammalian picornaviruses, HAV is enigmatic in its origins. We conducted a targeted search for hepatoviruses in 15,987 specimens collected from 209 small mammal species globally and discovered highly diversified viruses in bats, rodents, hedgehogs, and shrews, which by pairwise sequence distance comprise 13 novel Hepatovirus species. Near-complete genomes from nine of these species show conservation of unique hepatovirus features, including predicted internal ribosome entry site structure, a truncated VP4 capsid protein lacking N-terminal myristoylation, a carboxyl-terminal pX extension of VP1, VP2 late domains involved in membrane envelopment, and a cis-acting replication element within the 3Dpol sequence. Antibodies in some bat sera immunoprecipitated and neutralized human HAV, suggesting conservation of critical antigenic determinants. Limited phylogenetic cosegregation among hepatoviruses and their hosts and recombination patterns are indicative of major hepatovirus host shifts in the past. Ancestral state reconstructions suggest a Hepatovirus origin in small insectivorous mammals and a rodent origin of human HAV. Patterns of infection in small mammals mimicked those of human HAV in hepatotropism, fecal shedding, acute nature, and extinction of the virus in a closed host population. The evolutionary conservation of hepatovirus structure and pathogenesis provide novel insight into the origins of HAV and highlight the utility of analyzing animal reservoirs for risk assessment of emerging viruses. PMID:26575627

A hot-spot-active magnetic graphene oxide substrate for microRNA detection based on cascaded chemiluminescence resonance energy transfer

NASA Astrophysics Data System (ADS)

Bi, Sai; Chen, Min; Jia, Xiaoqiang; Dong, Ying

2015-02-01

Herein, a cascaded chemiluminescence resonance energy transfer (C-CRET) process was demonstrated from horseradish peroxidase (HRP)-mimicking DNAzyme-catalyzed luminol-H2O2 to fluorescein and further to graphene oxide (GO) when HRP-mimicking DNAzyme/fluorescein was in close proximity to the GO surface. The proposed C-CRET system was successfully implemented to construct three modes of C-CRET hot-spot-active substrates (modes I, II and III) by covalently immobilizing HRP-mimicking DNAzyme/fluorescein-labeled hairpin DNAs (hot-spot-generation probes) on magnetic GO (MGO), resulting in a signal ``off'' state due to the quenching of the luminol/H2O2/HRP-mimicking DNAzyme/fluorescein CRET system by GO. Upon the introduction of microRNA-122 (miRNA-122), the targets (mode I) or the new triggers that were generated through a strand displacement reaction (SDR) initiated by miRNA-122 (modes II and III) hybridized with the loop domains of hairpin probes on MGO to form double-stranded (modes I and II) or triplex-stem structures (mode III), causing an ``open'' configuration of the hairpin probe and a CRET signal ``on'' state, thus achieving sensitive and selective detection of miRNA-122. More importantly, the substrate exhibited excellent controllability, reversibility and reproducibility through SDR and magnetic separation (modes II and III), especially sequence-independence for hairpin probes in mode III, holding great potential for the development of a versatile platform for optical biosensing.Herein, a cascaded chemiluminescence resonance energy transfer (C-CRET) process was demonstrated from horseradish peroxidase (HRP)-mimicking DNAzyme-catalyzed luminol-H2O2 to fluorescein and further to graphene oxide (GO) when HRP-mimicking DNAzyme/fluorescein was in close proximity to the GO surface. The proposed C-CRET system was successfully implemented to construct three modes of C-CRET hot-spot-active substrates (modes I, II and III) by covalently immobilizing HRP-mimicking DNAzyme/fluorescein-labeled hairpin DNAs (hot-spot-generation probes) on magnetic GO (MGO), resulting in a signal ``off'' state due to the quenching of the luminol/H2O2/HRP-mimicking DNAzyme/fluorescein CRET system by GO. Upon the introduction of microRNA-122 (miRNA-122), the targets (mode I) or the new triggers that were generated through a strand displacement reaction (SDR) initiated by miRNA-122 (modes II and III) hybridized with the loop domains of hairpin probes on MGO to form double-stranded (modes I and II) or triplex-stem structures (mode III), causing an ``open'' configuration of the hairpin probe and a CRET signal ``on'' state, thus achieving sensitive and selective detection of miRNA-122. More importantly, the substrate exhibited excellent controllability, reversibility and reproducibility through SDR and magnetic separation (modes II and III), especially sequence-independence for hairpin probes in mode III, holding great potential for the development of a versatile platform for optical biosensing. Electronic supplementary information (ESI) available: Sequences of RNA and DNA used in this study, relationship of the proposed three modes, CRET mechanism of the luminol/H2O2/HRP-mimicking DNAzyme/fluorescein system, calculation of the surface coverage of hairpin probe I-1 on MGO, control experiment, comparison between different modes for microRNA detection, and advantages of the proposed strategy. See DOI: 10.1039/c4nr06603k

Preparation and Exceptional Mechanical Properties of Bone-Mimicking Size-Tuned Graphene Oxide@Carbon Nanotube Hybrid Paper.

PubMed

Oh, Jun Young; Kim, Yern Seung; Jung, Yeonsu; Yang, Seung Jae; Park, Chong Rae

2016-02-23

The self-assembled nanostructures of carbon nanomaterials possess a damage-tolerable architecture crucial for the inherent mechanical properties at both micro- and macroscopic levels. Bone, or "natural composite," has been known to have superior energy dissipation and fracture resistance abilities due to its unique load-bearing hybrid structure. However, few approaches have emulated the desirable structure using carbon nanomaterials. In this paper, we present an approach in fabricating a hybrid composite paper based on graphene oxide (GO) and carbon nanotube (CNT) that mimicks the natural bone structure. The size-tuning strategy enables smaller GO sheets to have more cross-linking reactions with CNTs and be homogeneously incorporated into CNT-assembled paper, which is advantageous for effective stress transfer. The resultant hybrid composite film has enhanced mechanical strength, modulus, toughness, and even electrical conductivity compared to previously reported CNT-GO based composites. We further demonstrate the usefulness of the size-tuned GOs as the "stress transfer medium" by performing in situ Raman spectroscopy during the tensile test.

Critical Intermediate Structure That Directs the Crystalline Texture and Surface Morphology of Organo-Lead Trihalide Perovskite.

PubMed

Chia, Hao-Chung; Sheu, Hwo-Shuenn; Hsiao, Yu-Yun; Li, Shao-Sian; Lan, Yi-Kang; Lin, Chung-Yao; Chang, Je-Wei; Kuo, Yen-Chien; Chen, Chia-Hao; Weng, Shih-Chang; Su, Chun-Jen; Su, An-Chung; Chen, Chun-Wei; Jeng, U-Ser

2017-10-25

We have identified an often observed yet unresolved intermediate structure in a popular processing with dimethylformamide solutions of lead chloride and methylammonium iodide for perovskite solar cells. With subsecond time-resolved grazing-incidence X-ray scattering and X-ray photoemission spectroscopy, supplemental with ab initio calculation, the resolved intermediate structure (CH 3 NH 3 ) 2 PbI 2 Cl 2 ·CH 3 NH 3 I features two-dimensional (2D) perovskite bilayers of zigzagged lead-halide octahedra and sandwiched CH 3 NH 3 I layers. Such intermediate structure reveals a hidden correlation between the intermediate phase and the composition of the processing solution. Most importantly, the 2D perovskite lattice of the intermediate phase is largely crystallographically aligned with the [110] planes of the three-dimensional perovskite cubic phase; consequently, with sublimation of Cl ions from the organo-lead octahedral terminal corners in prolonged annealing, the zigzagged octahedral layers of the intermediate phase can merge with the intercalated methylammonium iodide layers for templated growth of perovskite crystals. Regulated by annealing temperature and the activation energies of the intermediate and perovskite, deduced from analysis of temperature-dependent structural kinetics, the intermediate phase is found to selectively mature first and then melt along the layering direction for epitaxial conversion into perovskite crystals. The unveiled epitaxial conversion under growth kinetics controls might be general for solution-processed and intermediate-templated perovskite formation.

Mimicking lizard-like surface structures upon ultrashort laser pulse irradiation of inorganic materials

NASA Astrophysics Data System (ADS)

Hermens, U.; Kirner, S. V.; Emonts, C.; Comanns, P.; Skoulas, E.; Mimidis, A.; Mescheder, H.; Winands, K.; Krüger, J.; Stratakis, E.; Bonse, J.

2017-10-01

Inorganic materials, such as steel, were functionalized by ultrashort laser pulse irradiation (fs- to ps-range) to modify the surface's wetting behavior. The laser processing was performed by scanning the laser beam across the surface of initially polished flat sample material. A systematic experimental study of the laser processing parameters (peak fluence, scan velocity, line overlap) allowed the identification of different regimes associated with characteristic surface morphologies (laser-induced periodic surface structures, grooves, spikes, etc.). Analyses of the surface using optical as well as scanning electron microscopy revealed morphologies providing the optimum similarity to the natural skin of lizards. For mimicking skin structures of moisture-harvesting lizards towards an optimization of the surface wetting behavior, additionally a two-step laser processing strategy was established for realizing hierarchical microstructures. In this approach, micrometer-scaled capillaries (step 1) were superimposed by a laser-generated regular array of small dimples (step 2). Optical focus variation imaging measurements finally disclosed the three dimensional topography of the laser processed surfaces derived from lizard skin structures. The functionality of these surfaces was analyzed in view of wetting properties.

Bilateral Non-arteritic Anterior Ischaemic Optic Neuropathy as the Presentation of Systemic Amyloidosis.

PubMed

Kanaan, M Z; Lorenzi, A R; Thampy, N; Pandit, R; Dayan, Margaret

2017-12-01

A 75-year-old hypertensive female with stable idiopathic intermediate uveitis presented with bilateral sequential optic neuropathy with optic disc swelling. The optic neuropathy in the first affected eye (right) was thought to be due to non-arteritic anterior ischaemic optic neuropathy (NAION). Asymptomatic left optic disc swelling was found at routine review 2 months later, and a diagnosis of giant cell arteritis (GCA) was sought. Temporal artery duplex ultrasound showed the "halo sign," but a subsequent temporal artery biopsy showed light-chain (AL) amyloidosis with no signs of giant cell arteritis. In this case, bilateral sequential ischaemic optic neuropathy mimicking non-arteritic anterior ischaemic optic neuropathy was the presenting sign of systemic amyloidosis involving the temporal arteries.

Mechanotransduction across the cell surface and through the cytoskeleton

NASA Technical Reports Server (NTRS)

Wang, N.; Butler, J. P.; Ingber, D. E.

1993-01-01

Mechanical stresses were applied directly to cell surface receptors with a magnetic twisting device. The extracellular matrix receptor, integrin beta 1, induced focal adhesion formation and supported a force-dependent stiffening response, whereas nonadhesion receptors did not. The cytoskeletal stiffness (ratio of stress to strain) increased in direct proportion to the applied stress and required intact microtubules and intermediate filaments as well as microfilaments. Tensegrity models that incorporate mechanically interdependent struts and strings that reorient globally in response to a localized stress mimicked this response. These results suggest that integrins act as mechanoreceptors and transmit mechanical signals to the cytoskeleton. Mechanotransduction, in turn, may be mediated simultaneously at multiple locations inside the cell through force-induced rearrangements within a tensionally integrated cytoskeleton.

Super-Anticoagulant Heparin-Mimicking Hydrogel Thin Film Attached Substrate Surfaces to Improve Hemocompatibility.

PubMed

He, Min; Cui, Xiaofei; Jiang, Huiyi; Huang, Xuelian; Zhao, Weifeng; Zhao, Changsheng

2017-02-01

In this study, heparin-mimicking hydrogel thin films are covalently attached onto poly(ether sulfone) membrane surfaces to improve anticoagulant property. The hydrogel films display honeycomb-like porous structure with well controlled thickness and show long-term stability. After immobilizing the hydrogel films, the membranes show excellent anticoagulant property confirmed by the activated partial thromboplastin time values exceeding 600 s. Meanwhile, the thrombin time values increase from 20 to 61 s as the sodium allysulfonate proportions increase from 0 to 80 mol%. In vitro investigations of protein adsorption and blood-related complement activation also confirm that the membranes exhibit super-anticoagulant property. Furthermore, gentamycin sulfate is loaded into the hydrogel films, and the released drug shows significant inhibition toward E. coli bacteria. It is believed that the surface attached heparin-mimicking hydrogel thin films may show high potential for the applications in various biological fields, such as blood contacting materials and drug loading materials. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fibronectin-based multilayer thin films.

PubMed

Gand, Adeline; Tabuteau, Maud; Chat, Coline; Ladam, Guy; Atmani, Hassan; Van Tassel, Paul R; Pauthe, Emmanuel

2017-08-01

Thin films mimicking the structure and composition of the extra-cellular matrix (ECM) are potentially attractive as biomaterials for cell contacting applications. Layer-by-layer (LbL) assembly of a biological polycation, poly(l-lysine) (PLL), and a common ECM protein, fibronectin (Fn), was employed here to construct nanoscale, ECM mimicking films. Incremental film thickness and interfacial charge magnitude are observed to diminish with layer number, resulting in sub-linear film growth scaling and saturation after about 10 layers. Infrared spectroscopy and electron microscopy together reveal the formation of Fn containing aggregates, whose presence correlates with diminished charge reversal and suppressed LbL assembly. PLL-Fn films induce a significantly greater murine MC3T3-E1 pre-osteoblastic cell proliferation, while maintaining a much higher proportion of Fn in the molecular (as opposed to fibrillar) state, compared to a Fn monolayer, suggesting the enhanced Fn content of these ECM-mimicking films to significantly, and positively, affect cell behavior. Copyright © 2017 Elsevier B.V. All rights reserved.

Realistic full wave modeling of focal plane array pixels

DOE PAGES

Campione, Salvatore; Warne, Larry K.; Jorgenson, Roy E.; ...

2017-11-01

Here, we investigate full-wave simulations of realistic implementations of multifunctional nanoantenna enabled detectors (NEDs). We focus on a 2x2 pixelated array structure that supports two wavelengths of operation. We design each resonating structure independently using full-wave simulations with periodic boundary conditions mimicking the whole infinite array. We then construct a supercell made of a 2x2 pixelated array with periodic boundary conditions mimicking the full NED; in this case, however, each pixel comprises 10-20 antennas per side. In this way, the cross-talk between contiguous pixels is accounted for in our simulations. We observe that, even though there are finite extent effects,more » the pixels work as designed, each responding at the respective wavelength of operation. This allows us to stress that realistic simulations of multifunctional NEDs need to be performed to verify the design functionality by taking into account finite extent and cross-talk effects.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Campione, Salvatore; Warne, Larry K.; Jorgenson, Roy E.

Here, we investigate full-wave simulations of realistic implementations of multifunctional nanoantenna enabled detectors (NEDs). We focus on a 2x2 pixelated array structure that supports two wavelengths of operation. We design each resonating structure independently using full-wave simulations with periodic boundary conditions mimicking the whole infinite array. We then construct a supercell made of a 2x2 pixelated array with periodic boundary conditions mimicking the full NED; in this case, however, each pixel comprises 10-20 antennas per side. In this way, the cross-talk between contiguous pixels is accounted for in our simulations. We observe that, even though there are finite extent effects,more » the pixels work as designed, each responding at the respective wavelength of operation. This allows us to stress that realistic simulations of multifunctional NEDs need to be performed to verify the design functionality by taking into account finite extent and cross-talk effects.« less

Synthetic RNAs Mimicking Structural Domains in the Foot-and-Mouth Disease Virus Genome Elicit a Broad Innate Immune Response in Porcine Cells Triggered by RIG-I and TLR Activation.

PubMed

Borrego, Belén; Rodríguez-Pulido, Miguel; Revilla, Concepción; Álvarez, Belén; Sobrino, Francisco; Domínguez, Javier; Sáiz, Margarita

2015-07-17

The innate immune system is the first line of defense against viral infections. Exploiting innate responses for antiviral, therapeutic and vaccine adjuvation strategies is being extensively explored. We have previously described, the ability of small in vitro RNA transcripts, mimicking the sequence and structure of different domains in the non-coding regions of the foot-and-mouth disease virus (FMDV) genome (ncRNAs), to trigger a potent and rapid innate immune response. These synthetic non-infectious molecules have proved to have a broad-range antiviral activity and to enhance the immunogenicity of an FMD inactivated vaccine in mice. Here, we have studied the involvement of pattern-recognition receptors (PRRs) in the ncRNA-induced innate response and analyzed the antiviral and cytokine profiles elicited in swine cultured cells, as well as peripheral blood mononuclear cells (PBMCs).

The creation of a biomimetic interface between boron-doped diamond and immobilized proteins.

PubMed

Hoffmann, René; Kriele, Armin; Obloh, Harald; Tokuda, Norio; Smirnov, Waldemar; Yang, Nianjun; Nebel, Christoph E

2011-10-01

Immobilization of proteins on a solid electrode is to date done by chemical cross-linking or by addition of an adjustable intermediate. In this paper we introduce a concept where a solid with variable surface properties is optimized to mediate binding of the electron-transfer protein Cytochrome c (Cyt c) by mimicking the natural binding environment. It is shown that, as a carbon-based material, boron-doped diamond can be adjusted by simple electrochemical surface treatments to the specific biochemical requirements of Cyt c. The structure and functionality of passively adsorbed Cyt c on variously terminated diamond surfaces were characterized in detail using a combination of electrochemical techniques and atomic force microscopy with single-molecule resolution. Partially oxidized diamond allowed stable immobilization of Cyt c together with high electron transfer activity, driven by a combination of electrostatic and hydrophobic interactions. This surface mimics the natural binding partner, where coarse orientation is governed by electrostatic interaction of the protein's dipole and hydrophobic interactions assist in formation of the electron transfer complex. The optimized surface mediated electron transfer kinetics around 100 times faster than those reported for other solids and even faster kinetics than on self-assembled monolayers of alkanethiols. Copyright © 2011 Elsevier Ltd. All rights reserved.

Dye-ligand affinity systems.

PubMed

Denizli, A; Pişkin, E

2001-10-30

Dye-ligands have been considered as one of the important alternatives to natural counterparts for specific affinity chromatography. Dye-ligands are able to bind most types of proteins, in some cases in a remarkably specific manner. They are commercially available, inexpensive, and can easily be immobilized, especially on matrices bearing hydroxyl groups. Although dyes are all synthetic in nature, they are still classified as affinity ligands because they interact with the active sites of many proteins mimicking the structure of the substrates, cofactors, or binding agents for those proteins. A number of textile dyes, known as reactive dyes, have been used for protein purification. Most of these reactive dyes consist of a chromophore (either azo dyes, anthraquinone, or phathalocyanine), linked to a reactive group (often a mono- or dichlorotriazine ring). The interaction between the dye ligand and proteins can be by complex combination of electrostatic, hydrophobic, hydrogen bonding. Selection of the supporting matrix is the first important consideration in dye-affinity systems. There are several methods for immobilization of dye molecules onto the support matrix, in which usually several intermediate steps are followed. Both the adsorption and elution steps should carefully be optimized/designed for a successful separation. Dye-affinity systems in the form of spherical sorbents or as affinity membranes have been used in protein separation.

Multimodal, 3D pathology-mimicking bladder phantom for evaluation of cystoscopic technologies (Conference Presentation)

NASA Astrophysics Data System (ADS)

Smith, Gennifer T.; Lurie, Kristen L.; Zlatev, Dimitar V.; Liao, Joseph C.; Ellerbee, Audrey K.

2016-02-01

Optical coherence tomography (OCT) and blue light cystoscopy (BLC) have shown significant potential as complementary technologies to traditional white light cystoscopy (WLC) for early bladder cancer detection. Three-dimensional (3D) organ-mimicking phantoms provide realistic imaging environments for testing new technology designs, the diagnostic potential of systems, and novel image processing algorithms prior to validation in real tissue. Importantly, the phantom should mimic features of healthy and diseased tissue as they appear under WLC, BLC, and OCT, which are sensitive to tissue color and structure, fluorescent contrast, and optical scattering of subsurface layers, respectively. We present a phantom posing the hollow shape of the bladder and fabricated using a combination of 3D-printing and spray-coating with Dragon Skin (DS) (Smooth-On Inc.), a highly elastic polymer to mimic the layered structure of the bladder. Optical scattering of DS was tuned by addition of titanium dioxide, resulting in scattering coefficients sufficient to cover the human bladder range (0.49 to 2.0 mm^-1). Mucosal vasculature and tissue coloration were mimicked with elastic cord and red dye, respectively. Urethral access was provided through a small hole excised from the base of the phantom. Inserted features of bladder pathology included altered tissue color (WLC), fluorescence emission (BLC), and variations in layered structure (OCT). The phantom surface and underlying material were assessed on the basis of elasticity, optical scattering, layer thicknesses, and qualitative image appearance. WLC, BLC, and OCT images of normal and cancerous features in the phantom qualitatively matched corresponding images from human bladders.

Observing a late folding intermediate of Ubiquitin at atomic resolution by NMR

PubMed Central

Surana, Parag

2016-01-01

Abstract The study of intermediates in the protein folding pathway provides a wealth of information about the energy landscape. The intermediates also frequently initiate pathogenic fibril formations. While observing the intermediates is difficult due to their transient nature, extreme conditions can partially unfold the proteins and provide a glimpse of the intermediate states. Here, we observe the high resolution structure of a hydrophobic core mutant of Ubiquitin at an extreme acidic pH by nuclear magnetic resonance (NMR) spectroscopy. In the structure, the native secondary and tertiary structure is conserved for a major part of the protein. However, a long loop between the beta strands β3 and β5 is partially unfolded. The altered structure is supported by fluorescence data and the difference in free energies between the native state and the intermediate is reflected in the denaturant induced melting curves. The unfolded region includes amino acids that are critical for interaction with cofactors as well as for assembly of poly‐Ubiquitin chains. The structure at acidic pH resembles a late folding intermediate of Ubiquitin and indicates that upon stabilization of the protein's core, the long loop converges on the core in the final step of the folding process. PMID:27111887

71. Meadow Creek Culvert. This is an example of a ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

71. Meadow Creek Culvert. This is an example of a triple arch concrete box culvert with stone facing mimicking rigid frame structures. - Blue Ridge Parkway, Between Shenandoah National Park & Great Smoky Mountains, Asheville, Buncombe County, NC

Tough Ceramic Mimics Mother of Pearl

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ritchie, Robert

2008-12-05

Berkeley Lab scientists have mimicked the structure of mother of pearl to create what may well be the toughest ceramic ever produced. http://newscenter.lbl.gov/press-releases/2008/12/05/scientists-create-tough-ceramic-that-mimics-mother-of-pearl/

Tough Ceramic Mimics Mother of Pearl

ScienceCinema

Ritchie, Robert

2017-12-12

Berkeley Lab scientists have mimicked the structure of mother of pearl to create what may well be the toughest ceramic ever produced. http://newscenter.lbl.gov/press-releases/2008/12/05/scientists-create-tough-ceramic-that-mimics-mother-of-pearl/

Fabrication and characterization of biotissue-mimicking phantoms in the THz frequency range

NASA Astrophysics Data System (ADS)

Liakhov, E.; Smolyanskaya, O.; Popov, A.; Odlyanitskiy, E.; Balbekin, N.; Khodzitsky, M.

2016-08-01

The study revealed the most promising candidates for phantoms mimicking different biological tissues in the terahertz frequency range. Closest to biological tissues in terms of the refractive index appeared to be gelatin-based gels; in terms of the absorption coefficient they were agar-based gels. Gelatin is more stable in time, but requires special storage conditions to limit water evaporation. The dense structure of the agar-based phantom allows its use without mold and risk of damage. However, agar is a nutrient medium for bacteria and its parameters degrade even when the phantom form and water content are retained. Use of liquid suspensions of lecithin and milk powder are found to be extremely limited.

Conformational study of bovine lactoferricin in membrane-micking conditions by molecular dynamics simulation and circular dichroism.

PubMed

Daidone, Isabella; Magliano, Alessandro; Di Nola, Alfredo; Mignogna, Giuseppina; Clarkson, Matilda Manuela; Lizzi, Anna Rita; Oratore, Arduino; Mazza, Fernando

2011-04-01

Lactoferricins are potent antimicrobial peptides released by pepsin cleavage of Lactoferrins. Bovine Lactoferricin (LfcinB) has higher activity than the intact bovine Lactoferrin, and is the most active among the other Lactoferricins of human, murine and caprine origin. In the intact protein the fragment corresponding to LfcinB is in an helical conformation, while in water LfcinB adopts an amphipathic β-hairpin structure. However, whether any of these structural motifs is the antibacterial active conformation, i.e., the one interacting with bacterial membrane components, remains to be seen. Here we present Circular Dichroism (CD) spectra and Molecular Dynamics (MD) simulations indicating that in membrane-mimicking solvents the LfcinB adopts an amphipathic β-hairpin structure similar to that observed in water, but differing in the dynamic behavior of the side-chains of the two tryptophan residues. In the membrane-mimicking solvent these side-chains show a high propensity to point towards the hydrophobic environment, rather than being in the hydrophobic core as seen in water, while the backbone preserves the hairpin conformation as found in water. These results suggest that the tryptophans might act as anchors pulling the stable, solvent-invariant hairpin structure into the membrane.

Cyclic Boronates Inhibit All Classes of β-Lactamases

PubMed Central

Cain, Ricky; Wang, David Y.; Lohans, Christopher T.; Wareham, David W.; Oswin, Henry P.; Mohammed, Jabril; Spencer, James; Fishwick, Colin W. G.; McDonough, Michael A.

2017-01-01

ABSTRACT β-Lactamase-mediated resistance is a growing threat to the continued use of β-lactam antibiotics. The use of the β-lactam-based serine-β-lactamase (SBL) inhibitors clavulanic acid, sulbactam, and tazobactam and, more recently, the non-β-lactam inhibitor avibactam has extended the utility of β-lactams against bacterial infections demonstrating resistance via these enzymes. These molecules are, however, ineffective against the metallo-β-lactamases (MBLs), which catalyze their hydrolysis. To date, there are no clinically available metallo-β-lactamase inhibitors. Coproduction of MBLs and SBLs in resistant infections is thus of major clinical concern. The development of “dual-action” inhibitors, targeting both SBLs and MBLs, is of interest, but this is considered difficult to achieve due to the structural and mechanistic differences between the two enzyme classes. We recently reported evidence that cyclic boronates can inhibit both serine- and metallo-β-lactamases. Here we report that cyclic boronates are able to inhibit all four classes of β-lactamase, including the class A extended spectrum β-lactamase CTX-M-15, the class C enzyme AmpC from Pseudomonas aeruginosa, and class D OXA enzymes with carbapenem-hydrolyzing capabilities. We demonstrate that cyclic boronates can potentiate the use of β-lactams against Gram-negative clinical isolates expressing a variety of β-lactamases. Comparison of a crystal structure of a CTX-M-15:cyclic boronate complex with structures of cyclic boronates complexed with other β-lactamases reveals remarkable conservation of the small-molecule binding mode, supporting our proposal that these molecules work by mimicking the common tetrahedral anionic intermediate present in both serine- and metallo-β-lactamase catalysis. PMID:28115348

Case Report of Myeloid Sarcoma Masquerading as In-Transit Metastasis at a Previous Melanoma Site: Avoiding a Diagnostic Pitfall.

PubMed

Curry, Jonathan L; Tetzlaff, Michael T; Wang, Sa A; Landon, Gene; Alouch, Nail; Patel, Sapna P; Nagarajan, Priyadharsini; Gupta, Shiva; Aung, Phyu P; Devine, Catherine E; Khoury, Joseph D; Loghavi, Sanam; Prieto, Victor G; DiNardo, Courtney D; Gershenwald, Jeffrey E

2018-06-01

Myeloid sarcoma is a rare extramedullary hematologic malignancy. Accurate and timely diagnosis may be challenging because myeloid sarcoma is known to mimic solid tumors, including hepatobiliary, nasopharyngeal, and breast carcinomas. We report a case of myeloid sarcoma that developed in the primary tumor lymphatic drainage field of a previously treated intermediate-thickness cutaneous melanoma, clinically and radiographically mimicking an in-transit metastasis, in a patient with myelodysplastic syndrome. The diagnosis of myeloid sarcoma was achieved after surgical excision of the mass and pathological examination that included extensive immunohistochemical studies. Awareness of such an unusual clinical presentation can help reduce diagnostic delay and ensure that adequate tissue is obtained for pathological examination and ancillary studies that are critical for accurate diagnosis and appropriate patient management.

Cluster Analysis of Time-Dependent Crystallographic Data: Direct Identification of Time-Independent Structural Intermediates

PubMed Central

Kostov, Konstantin S.; Moffat, Keith

2011-01-01

The initial output of a time-resolved macromolecular crystallography experiment is a time-dependent series of difference electron density maps that displays the time-dependent changes in underlying structure as a reaction progresses. The goal is to interpret such data in terms of a small number of crystallographically refinable, time-independent structures, each associated with a reaction intermediate; to establish the pathways and rate coefficients by which these intermediates interconvert; and thereby to elucidate a chemical kinetic mechanism. One strategy toward achieving this goal is to use cluster analysis, a statistical method that groups objects based on their similarity. If the difference electron density at a particular voxel in the time-dependent difference electron density (TDED) maps is sensitive to the presence of one and only one intermediate, then its temporal evolution will exactly parallel the concentration profile of that intermediate with time. The rationale is therefore to cluster voxels with respect to the shapes of their TDEDs, so that each group or cluster of voxels corresponds to one structural intermediate. Clusters of voxels whose TDEDs reflect the presence of two or more specific intermediates can also be identified. From such groupings one can then infer the number of intermediates, obtain their time-independent difference density characteristics, and refine the structure of each intermediate. We review the principles of cluster analysis and clustering algorithms in a crystallographic context, and describe the application of the method to simulated and experimental time-resolved crystallographic data for the photocycle of photoactive yellow protein. PMID:21244840

Chitosan microspheres with an extracellular matrix-mimicking nanofibrous structure as cell-carrier building blocks for bottom-up cartilage tissue engineering

NASA Astrophysics Data System (ADS)

Zhou, Yong; Gao, Huai-Ling; Shen, Li-Li; Pan, Zhao; Mao, Li-Bo; Wu, Tao; He, Jia-Cai; Zou, Duo-Hong; Zhang, Zhi-Yuan; Yu, Shu-Hong

2015-12-01

Scaffolds for tissue engineering (TE) which closely mimic the physicochemical properties of the natural extracellular matrix (ECM) have been proven to advantageously favor cell attachment, proliferation, migration and new tissue formation. Recently, as a valuable alternative, a bottom-up TE approach utilizing cell-loaded micrometer-scale modular components as building blocks to reconstruct a new tissue in vitro or in vivo has been proved to demonstrate a number of desirable advantages compared with the traditional bulk scaffold based top-down TE approach. Nevertheless, micro-components with an ECM-mimicking nanofibrous structure are still very scarce and highly desirable. Chitosan (CS), an accessible natural polymer, has demonstrated appealing intrinsic properties and promising application potential for TE, especially the cartilage tissue regeneration. According to this background, we report here the fabrication of chitosan microspheres with an ECM-mimicking nanofibrous structure for the first time based on a physical gelation process. By combining this physical fabrication procedure with microfluidic technology, uniform CS microspheres (CMS) with controlled nanofibrous microstructure and tunable sizes can be facilely obtained. Especially, no potentially toxic or denaturizing chemical crosslinking agent was introduced into the products. Notably, in vitro chondrocyte culture tests revealed that enhanced cell attachment and proliferation were realized, and a macroscopic 3D geometrically shaped cartilage-like composite can be easily constructed with the nanofibrous CMS (NCMS) and chondrocytes, which demonstrate significant application potential of NCMS as the bottom-up cell-carrier components for cartilage tissue engineering.Scaffolds for tissue engineering (TE) which closely mimic the physicochemical properties of the natural extracellular matrix (ECM) have been proven to advantageously favor cell attachment, proliferation, migration and new tissue formation. Recently, as a valuable alternative, a bottom-up TE approach utilizing cell-loaded micrometer-scale modular components as building blocks to reconstruct a new tissue in vitro or in vivo has been proved to demonstrate a number of desirable advantages compared with the traditional bulk scaffold based top-down TE approach. Nevertheless, micro-components with an ECM-mimicking nanofibrous structure are still very scarce and highly desirable. Chitosan (CS), an accessible natural polymer, has demonstrated appealing intrinsic properties and promising application potential for TE, especially the cartilage tissue regeneration. According to this background, we report here the fabrication of chitosan microspheres with an ECM-mimicking nanofibrous structure for the first time based on a physical gelation process. By combining this physical fabrication procedure with microfluidic technology, uniform CS microspheres (CMS) with controlled nanofibrous microstructure and tunable sizes can be facilely obtained. Especially, no potentially toxic or denaturizing chemical crosslinking agent was introduced into the products. Notably, in vitro chondrocyte culture tests revealed that enhanced cell attachment and proliferation were realized, and a macroscopic 3D geometrically shaped cartilage-like composite can be easily constructed with the nanofibrous CMS (NCMS) and chondrocytes, which demonstrate significant application potential of NCMS as the bottom-up cell-carrier components for cartilage tissue engineering. Electronic supplementary information (ESI) available: Additional figures and table. See DOI: 10.1039/c5nr06876b

Characterization of two distinct beta2-microglobulin unfolding intermediates that may lead to amyloid fibrils of different morphology.

PubMed

Armen, Roger S; Daggett, Valerie

2005-12-13

The self-assembly of beta(2)-microglobulin into fibrils leads to dialysis-related amyloidosis. pH-mediated partial unfolding is required for the formation of the amyloidogenic intermediate that then self-assembles into amyloid fibrils. Two partially folded intermediates of beta(2)-microglobulin have been identified experimentally and linked to the formation of fibrils of distinct morphology, yet it remains difficult to characterize these partially unfolded states at high resolution using experimental approaches. Consequently, we have performed molecular dynamics simulations at neutral and low pH to determine the structures of these partially unfolded amyloidogenic intermediates. In the low-pH simulations, we observed the formation of alpha-sheet structure, which was first proposed by Pauling and Corey. Multiple simulations were performed, and two distinct intermediate state ensembles were identified that may account for the different fibril morphologies. The predominant early unfolding intermediate was nativelike in structure, in agreement with previous NMR studies. The late unfolding intermediate was significantly disordered, but it maintained an extended elongated structure, with hydrophobic clusters and residual alpha-extended chain strands in specific regions of the sequence that map to amyloidogenic peptides. We propose that the formation of alpha-sheet facilitates self-assembly into partially unfolded prefibrillar amyloidogenic intermediates.

Crystallographic and spectroscopic snapshots reveal a dehydrogenase in action

DOE PAGES

Huo, Lu; Davis, Ian; Liu, Fange; ...

2015-01-07

Aldehydes are ubiquitous intermediates in metabolic pathways and their innate reactivity can often make them quite unstable. There are several aldehydic intermediates in the metabolic pathway for tryptophan degradation that can decay into neuroactive compounds that have been associated with numerous neurological diseases. An enzyme of this pathway, 2-aminomuconate-6-semialdehyde dehydrogenase, is responsible for ‘disarming’ the final aldehydic intermediate. Here we show the crystal structures of a bacterial analogue enzyme in five catalytically relevant forms: resting state, one binary and two ternary complexes, and a covalent, thioacyl intermediate. We also report the crystal structures of a tetrahedral, thiohemiacetal intermediate, a thioacylmore » intermediate and an NAD +-bound complex from an active site mutant. These covalent intermediates are characterized by single-crystal and solution-state electronic absorption spectroscopy. The crystal structures reveal that the substrate undergoes an E/Z isomerization at the enzyme active site before an sp 3-to-sp 2 transition during enzyme-mediated oxidation.« less

Programmed Nanomaterial Assemblies in Large Scales: Applications of Synthetic and Genetically- Engineered Peptides to Bridge Nano-Assemblies and Macro-Assemblies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matsui, Hiroshi

Work is reported in these areas: Large-scale & reconfigurable 3D structures of precise nanoparticle assemblies in self-assembled collagen peptide grids; Binary QD-Au NP 3D superlattices assembled with collagen-like peptides and energy transfer between QD and Au NP in 3D peptide frameworks; Catalytic peptides discovered by new hydrogel-based combinatorial phage display approach and their enzyme-mimicking 2D assembly; New autonomous motors of metal-organic frameworks (MOFs) powered by reorganization of self-assembled peptides at interfaces; Biomimetic assembly of proteins into microcapsules on oil-in-water droplets with structural reinforcement via biomolecular recognition-based cross-linking of surface peptides; and Biomimetic fabrication of strong freestanding genetically-engineered collagen peptide filmsmore » reinforced by quantum dot joints. We gained the broad knowledge about biomimetic material assembly from nanoscale to microscale ranges by coassembling peptides and NPs via biomolecular recognition. We discovered: Genetically-engineered collagen-like peptides can be self-assembled with Au NPs to generate 3D superlattices in large volumes (> μm{sup 3}); The assembly of the 3D peptide-Au NP superstructures is dynamic and the interparticle distance changes with assembly time as the reconfiguration of structure is triggered by pH change; QDs/NPs can be assembled with the peptide frameworks to generate 3D superlattices and these QDs/NPs can be electronically coupled for the efficient energy transfer; The controlled assembly of catalytic peptides mimicking the catalytic pocket of enzymes can catalyze chemical reactions with high selectivity; and, For the bacteria-mimicking swimmer fabrication, peptide-MOF superlattices can power translational and propellant motions by the reconfiguration of peptide assembly at the MOF-liquid interface.« less

Structure of a low-population intermediate state in the release of an enzyme product.

PubMed

De Simone, Alfonso; Aprile, Francesco A; Dhulesia, Anne; Dobson, Christopher M; Vendruscolo, Michele

2015-01-09

Enzymes can increase the rate of biomolecular reactions by several orders of magnitude. Although the steps of substrate capture and product release are essential in the enzymatic process, complete atomic-level descriptions of these steps are difficult to obtain because of the transient nature of the intermediate conformations, which makes them largely inaccessible to standard structure determination methods. We describe here the determination of the structure of a low-population intermediate in the product release process by human lysozyme through a combination of NMR spectroscopy and molecular dynamics simulations. We validate this structure by rationally designing two mutations, the first engineered to destabilise the intermediate and the second to stabilise it, thus slowing down or speeding up, respectively, product release. These results illustrate how product release by an enzyme can be facilitated by the presence of a metastable intermediate with transient weak interactions between the enzyme and product.

Determination of an ensemble of structures representing the intermediate state of the bacterial immunity protein Im7.

PubMed

Gsponer, Joerg; Hopearuoho, Harri; Whittaker, Sara B-M; Spence, Graham R; Moore, Geoffrey R; Paci, Emanuele; Radford, Sheena E; Vendruscolo, Michele

2006-01-03

We present a detailed structural characterization of the intermediate state populated during the folding and unfolding of the bacterial immunity protein Im7. We achieve this result by incorporating a variety of experimental data available for this species in molecular dynamics simulations. First, we define the structure of the exchange-competent intermediate state of Im7 by using equilibrium hydrogen-exchange protection factors. Second, we use this ensemble to predict Phi-values and compare the results with the experimentally determined Phi-values of the kinetic refolding intermediate. Third, we predict chemical-shift measurements and compare them with the measured chemical shifts of a mutational variant of Im7 for which the kinetic folding intermediate is the most stable state populated at equilibrium. Remarkably, we found that the properties of the latter two species are predicted with high accuracy from the exchange-competent intermediate that we determined, suggesting that these three states are characterized by a similar architecture in which helices I, II, and IV are aligned in a native-like, but reorganized, manner. Furthermore, the structural ensemble that we obtained enabled us to rationalize the results of tryptophan fluorescence experiments in the WT protein and a series of mutational variants. The results show that the integration of diverse sets of experimental data at relatively low structural resolution is a powerful approach that can provide insights into the structural organization of this conformationally heterogeneous three-helix intermediate with unprecedented detail and highlight the importance of both native and non-native interactions in stabilizing its structure.

Design and structure of an equilibrium protein folding intermediate: a hint into dynamical regions of proteins.

PubMed

Ayuso-Tejedor, Sara; Angarica, Vladimir Espinosa; Bueno, Marta; Campos, Luis A; Abián, Olga; Bernadó, Pau; Sancho, Javier; Jiménez, M Angeles

2010-07-23

Partly unfolded protein conformations close to the native state may play important roles in protein function and in protein misfolding. Structural analyses of such conformations which are essential for their fully physicochemical understanding are complicated by their characteristic low populations at equilibrium. We stabilize here with a single mutation the equilibrium intermediate of apoflavodoxin thermal unfolding and determine its solution structure by NMR. It consists of a large native region identical with that observed in the X-ray structure of the wild-type protein plus an unfolded region. Small-angle X-ray scattering analysis indicates that the calculated ensemble of structures is consistent with the actual degree of expansion of the intermediate. The unfolded region encompasses discontinuous sequence segments that cluster in the 3D structure of the native protein forming the FMN cofactor binding loops and the binding site of a variety of partner proteins. Analysis of the apoflavodoxin inner interfaces reveals that those becoming destabilized in the intermediate are more polar than other inner interfaces of the protein. Natively folded proteins contain hydrophobic cores formed by the packing of hydrophobic surfaces, while natively unfolded proteins are rich in polar residues. The structure of the apoflavodoxin thermal intermediate suggests that the regions of natively folded proteins that are easily responsive to thermal activation may contain cores of intermediate hydrophobicity. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Stability, denaturation and refolding of Mycobacterium tuberculosis MfpA, a DNA mimicking protein that confers antibiotic resistance

PubMed Central

Khrapunov, Sergei; Brenowitz, Michael

2011-01-01

MfpA from Mycobacterium tuberculosis is a founding member of the pentapeptide repeat class of proteins (PRP) that is believed to confer bacterial resistance to the drug fluoroquinolone by mimicking the size, shape and surface charge of duplex DNA. We show that phenylalanine side chain stacking stabilizes the N-terminus of MfpA’s pentapeptide thus extending the DNA mimicry analogy. The Lumry-Eyring model was applied to multiple spectral measures of MfpA denaturation revealing that the MfpA dimer dissociates to monomers which undergo a structural transition that leads to aggregation. MfpA retains high secondary and tertiary structure content under denaturing conditions. Dimerization stabilizes MfpA’s pentapeptide repeat fold. The high Arrhenius activation energy of the barrier to aggregate formation rationalizes its stability. The mechanism of MfpA denaturation and refolding is a ‘double funnel’ energy landscape where the ‘native’ and ‘aggregate’ funnels are separated by the high barrier that is not overcome during in vitro refolding. PMID:21605934

Organelle-mimicking liposome dissociates G-quadruplexes and facilitates transcription

PubMed Central

Pramanik, Smritimoy; Tateishi-Karimata, Hisae; Sugimoto, Naoki

2014-01-01

Important biological reactions involving nucleic acids occur near the surface of membranes such as the nuclear membrane (NM) and rough endoplasmic reticulum (ER); however, the interactions between biomembranes and nucleic acids are poorly understood. We report here that transcription was facilitated in solution with liposomes, which mimic a biomembrane surface, relative to the reaction in a homogeneous aqueous solution when the template was able to form a G-quadruplex. The G-quadruplex is known to be an inhibitor of transcription, but the stability of the G-quadruplex was decreased at the liposome surface because of unfavourable enthalpy. The destabilization of the G-quadruplex was greater at the surface of NM- and ER-mimicking liposomes than at the surfaces of liposomes designed to mimic other organelles. Thermodynamic analyses revealed that the G-rich oligonucleotides adopted an extended structure at the liposome surface, whereas in solution the compact G-quadruplex was formed. Our data suggest that changes in structure and stability of nucleic acids regulate biological reactions at membrane surfaces. PMID:25336617

The cytopathology of Actinomyces, Nocardia, and their mimickers.

PubMed

McHugh, Kelsey E; Sturgis, Charles D; Procop, Gary W; Rhoads, Daniel D

2017-12-01

Nocardia species and Actinomyces species are 2 of the most commonly diagnosed filamentous bacteria in routine cytopathology practice. These genera share many overlapping cytomorphologic features, including their thin, beaded, branching, Gram-positive, GMS-positive filamentous structures that fragment at their peripheries into bacillary- and coccoid-appearing forms. Features that help distinguish between these 2 microorganisms include the width of their filamentous structures, the angles at which they branch, and their ability or lack thereof to retain a modified acid-fast stain. In addition to cytomorphologic overlap, overlap in clinical presentation is frequent with pulmonary and mucocutaneous presentations seen in both. Differentiating between Nocardia and Actinomyces is essential because patients with these infections require different approaches to medical management. Both antibiotic susceptibilities and the need for early surgical intervention as part of the treatment plan vary greatly among these 2 groups. This review focuses on the clinical presentation, cytomorphology and staining characteristics that can be useful in identifying and distinguishing between Nocardia and Actinomyces infections, as well as their mimickers. © 2017 Wiley Periodicals, Inc.

A hot-spot-active magnetic graphene oxide substrate for microRNA detection based on cascaded chemiluminescence resonance energy transfer.

PubMed

Bi, Sai; Chen, Min; Jia, Xiaoqiang; Dong, Ying

2015-02-28

Herein, a cascaded chemiluminescence resonance energy transfer (C-CRET) process was demonstrated from horseradish peroxidase (HRP)-mimicking DNAzyme-catalyzed luminol-H2O2 to fluorescein and further to graphene oxide (GO) when HRP-mimicking DNAzyme/fluorescein was in close proximity to the GO surface. The proposed C-CRET system was successfully implemented to construct three modes of C-CRET hot-spot-active substrates (modes I, II and III) by covalently immobilizing HRP-mimicking DNAzyme/fluorescein-labeled hairpin DNAs (hot-spot-generation probes) on magnetic GO (MGO), resulting in a signal "off" state due to the quenching of the luminol/H2O2/HRP-mimicking DNAzyme/fluorescein CRET system by GO. Upon the introduction of microRNA-122 (miRNA-122), the targets (mode I) or the new triggers that were generated through a strand displacement reaction (SDR) initiated by miRNA-122 (modes II and III) hybridized with the loop domains of hairpin probes on MGO to form double-stranded (modes I and II) or triplex-stem structures (mode III), causing an "open" configuration of the hairpin probe and a CRET signal "on" state, thus achieving sensitive and selective detection of miRNA-122. More importantly, the substrate exhibited excellent controllability, reversibility and reproducibility through SDR and magnetic separation (modes II and III), especially sequence-independence for hairpin probes in mode III, holding great potential for the development of a versatile platform for optical biosensing.

A Matter of Contrast: Yellow Flower Colour Constrains Style Length in Crocus species.

PubMed

Lunau, Klaus; Konzmann, Sabine; Bossems, Jessica; Harpke, Doerte

2016-01-01

Most flowers display distinct colour patterns comprising two different areas. The peripheral large-area component of floral colour patterns attracts flower visitors from some distance and the central small-area component guides flower visitors towards landing sites. Whereas the peripheral colour is largely variable among species, the central colour, produced mostly by anthers and pollen or pollen mimicking floral guides, is predominantly yellow and UV-absorbing. This holds also for yellow flowers that regularly display a UV bull's eye pattern. Here we show that yellow-flowering Crocus species are a noticeable exception, since yellow-flowering Crocus species-being entirely UV-absorbing-exhibit low colour contrast between yellow reproductive organs and yellow tepals. The elongated yellow or orange-yellow style of Crocus flowers is a stamen-mimicking structure promoting cross-pollination by facilitating flower visitors' contact with the apical stigma before the flower visitors are touching the anthers. Since Crocus species possess either yellow, violet or white tepals, the colour contrast between the stamen-mimicking style and the tepals varies among species. In this study comprising 106 Crocus species, it was tested whether the style length of Crocus flowers is dependent on the corolla colour. The results show that members of the genus Crocus with yellow tepals have evolved independently up to twelve times in the genus Crocus and that yellow-flowering Crocus species possess shorter styles as compared to violet- and white-flowering ones. The manipulation of flower visitors by anther-mimicking elongated styles in Crocus flowers is discussed.

Micro-scale finite element modeling of ultrasound propagation in aluminum trabecular bone-mimicking phantoms: A comparison between numerical simulation and experimental results.

PubMed

Vafaeian, B; Le, L H; Tran, T N H T; El-Rich, M; El-Bialy, T; Adeeb, S

2016-05-01

The present study investigated the accuracy of micro-scale finite element modeling for simulating broadband ultrasound propagation in water-saturated trabecular bone-mimicking phantoms. To this end, five commercially manufactured aluminum foam samples as trabecular bone-mimicking phantoms were utilized for ultrasonic immersion through-transmission experiments. Based on micro-computed tomography images of the same physical samples, three-dimensional high-resolution computational samples were generated to be implemented in the micro-scale finite element models. The finite element models employed the standard Galerkin finite element method (FEM) in time domain to simulate the ultrasonic experiments. The numerical simulations did not include energy dissipative mechanisms of ultrasonic attenuation; however, they expectedly simulated reflection, refraction, scattering, and wave mode conversion. The accuracy of the finite element simulations were evaluated by comparing the simulated ultrasonic attenuation and velocity with the experimental data. The maximum and the average relative errors between the experimental and simulated attenuation coefficients in the frequency range of 0.6-1.4 MHz were 17% and 6% respectively. Moreover, the simulations closely predicted the time-of-flight based velocities and the phase velocities of ultrasound with maximum relative errors of 20 m/s and 11 m/s respectively. The results of this study strongly suggest that micro-scale finite element modeling can effectively simulate broadband ultrasound propagation in water-saturated trabecular bone-mimicking structures. Copyright © 2016 Elsevier B.V. All rights reserved.

Biomimicry as a basis for drug discovery.

PubMed

Kolb, V M

1998-01-01

Selected works are discussed which clearly demonstrate that mimicking various aspects of the process by which natural products evolved is becoming a powerful tool in contemporary drug discovery. Natural products are an established and rich source of drugs. The term "natural product" is often used synonymously with "secondary metabolite." Knowledge of genetics and molecular evolution helps us understand how biosynthesis of many classes of secondary metabolites evolved. One proposed hypothesis is termed "inventive evolution." It invokes duplication of genes, and mutation of the gene copies, among other genetic events. The modified duplicate genes, per se or in conjunction with other genetic events, may give rise to new enzymes, which, in turn, may generate new products, some of which may be selected for. Steps of the inventive evolution can be mimicked in several ways for purpose of drug discovery. For example, libraries of chemical compounds of any imaginable structure may be produced by combinatorial synthesis. Out of these libraries new active compounds can be selected. In another example, genetic system can be manipulated to produce modified natural products ("unnatural natural products"), from which new drugs can be selected. In some instances, similar natural products turn up in species that are not direct descendants of each other. This is presumably due to a horizontal gene transfer. The mechanism of this inter-species gene transfer can be mimicked in therapeutic gene delivery. Mimicking specifics or principles of chemical evolution including experimental and test-tube evolution also provides leads for new drug discovery.

Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation

PubMed Central

Nasedkin, Alexandr; Marcellini, Moreno; Religa, Tomasz L.; Freund, Stefan M.; Menzel, Andreas; Fersht, Alan R.; Jemth, Per; van der Spoel, David; Davidsson, Jan

2015-01-01

The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un)folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un)folding reaction has often been questioned. One of the most well studied (un)folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un)folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un)folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution. PMID:25946337

Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation.

PubMed

Nasedkin, Alexandr; Marcellini, Moreno; Religa, Tomasz L; Freund, Stefan M; Menzel, Andreas; Fersht, Alan R; Jemth, Per; van der Spoel, David; Davidsson, Jan

2015-01-01

The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un)folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un)folding reaction has often been questioned. One of the most well studied (un)folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un)folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un)folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution.

Kinetically trapped metastable intermediate of a disulfide-deficient mutant of the starch-binding domain of glucoamylase.

PubMed

Sugimoto, Hayuki; Nakaura, Miho; Nishimura, Shigenori; Karita, Shuichi; Miyake, Hideo; Tanaka, Akiyoshi

2009-08-01

Refolding of a thermally unfolded disulfide-deficient mutant of the starch-binding domain of glucoamylase was investigated using differential scanning calorimetry, isothermal titration calorimetry, CD, and (1)H NMR. When the protein solution was rapidly cooled from a higher temperature, a kinetic intermediate was formed during refolding. The intermediate was unexpectedly stable compared with typical folding intermediates that have short half-lives. It was shown that this intermediate contained substantial secondary structure and tertiary packing and had the same binding ability with beta-cyclodextrin as the native state, suggesting that the intermediate is highly-ordered and native-like on the whole. These characteristics differ from those of partially folded intermediates such as molten globule states. Far-UV CD spectra showed that the secondary structure was once disrupted during the transition from the intermediate to the native state. These results suggest that the intermediate could be an off-pathway type, possibly a misfolded state, that has to undergo unfolding on its way to the native state.

Reciprocal uniparental disomy in yeast.

PubMed

Andersen, Sabrina L; Petes, Thomas D

2012-06-19

In the diploid cells of most organisms, including humans, each chromosome is usually distinguishable from its partner homolog by multiple single-nucleotide polymorphisms. One common type of genetic alteration observed in tumor cells is uniparental disomy (UPD), in which a pair of homologous chromosomes are derived from a single parent, resulting in loss of heterozygosity for all single-nucleotide polymorphisms while maintaining diploidy. Somatic UPD events are usually explained as reflecting two consecutive nondisjunction events. Here we report a previously undescribed mode of chromosome segregation in Saccharomyces cerevisiae in which one cell division produces daughter cells with reciprocal UPD for the same pair of chromosomes without an aneuploid intermediate. One pair of sister chromatids is segregated into one daughter cell and the other pair is segregated into the other daughter cell, mimicking a meiotic chromosome segregation pattern. We term this process "reciprocal uniparental disomy."

Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR

PubMed Central

NISHIMURA, Chiaki

2017-01-01

The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H. The improved strategy for the analysis of the kinetic intermediate was developed to include (1) the dimethyl sulfoxide method, (2) data processing with the various labeling times, and (3) a new in-house mixer. Particularly, the rapid mixing revealed that helices A and G were significantly more protected at the earlier stage (400 µs) of the intermediate (former-phase intermediate) than the other helices. Mutation studies, where each hydrophobic residue was replaced with an alanine in helices A, B, E, F, G and H, indicated that both non-native and native-like structures exist in the latter-phase folding intermediate. The N-terminal part of helix B is a weak point in the intermediate, and the docking of helix E residues to the core of the A, B, G and H helices was interrupted by a premature helix B, resulting in the accumulation of the intermediate composed of helices A, B, G and H. The prediction-based protein engineering produced important mutants: Helix F in a P88K/A90L/S92K/A94L mutant folded in the latter-phase intermediate, although helix F in the wild type does not fold even at the native state. Furthermore, in the L11G/W14G/A70L/G73W mutant, helix A did not fold but helix E did, which is similar to what was observed in the kinetic intermediate of apoleghemoglobin. Thus, this protein engineering resulted in a changed structure for the apomyoglobin folding intermediate. PMID:28077807

Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR.

PubMed

Nishimura, Chiaki

2017-01-01

The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H. The improved strategy for the analysis of the kinetic intermediate was developed to include (1) the dimethyl sulfoxide method, (2) data processing with the various labeling times, and (3) a new in-house mixer. Particularly, the rapid mixing revealed that helices A and G were significantly more protected at the earlier stage (400 µs) of the intermediate (former-phase intermediate) than the other helices. Mutation studies, where each hydrophobic residue was replaced with an alanine in helices A, B, E, F, G and H, indicated that both non-native and native-like structures exist in the latter-phase folding intermediate. The N-terminal part of helix B is a weak point in the intermediate, and the docking of helix E residues to the core of the A, B, G and H helices was interrupted by a premature helix B, resulting in the accumulation of the intermediate composed of helices A, B, G and H. The prediction-based protein engineering produced important mutants: Helix F in a P88K/A90L/S92K/A94L mutant folded in the latter-phase intermediate, although helix F in the wild type does not fold even at the native state. Furthermore, in the L11G/W14G/A70L/G73W mutant, helix A did not fold but helix E did, which is similar to what was observed in the kinetic intermediate of apoleghemoglobin. Thus, this protein engineering resulted in a changed structure for the apomyoglobin folding intermediate.

Cooperative alpha-helix formation of beta-lactoglobulin induced by sodium n-alkyl sulfates.

PubMed

Chamani, J; Moosavi-Movahedi, A A; Rajabi, O; Gharanfoli, M; Momen-Heravi, M; Hakimelahi, G H; Neamati-Baghsiah, A; Varasteh, A R

2006-01-01

It is generally assumed that folding intermediates contain partially formed native-like secondary structures. However, if we consider the fact that the conformational stability of the intermediate state is simpler than that of the native state, it would be expected that the secondary structures in a folding intermediate would not necessarily be similar to those of the native state. beta-Lactoglobulin is a predominantly beta-sheet protein, although it has a markedly high intrinsic preference for alpha-helical structure. The formation of non-native alpha-helical intermediate of beta-lactoglobulin was induced by n-alkyl sulfates including sodium octyl sulfate, SOS; sodium decyl sulfate, SDeS; sodium dodecyl sulfate, SDS; and sodium tetradecyl sulfate, STS at special condition. The effect of n-alkyl sulfates on the structure of native beta-lactoglobulin at pH 2 was utilized to investigate the contribution of hydrophobic interactions to the stability of non-native alpha-helical intermediate. The addition of various concentrations of n-alkyl sulfates to the native state of beta-lactoglobulin (pH 2) appears to support the stabilized form of non-native alpha-helical intermediate at pH 2. The m values of the intermediate state of beta-lactoglobulin by SOS, SDeS, SDS and STS showed substantial variation. The enhancement of m values as the stability criterion of non-native alpha-helical intermediate state corresponded with increasing chain length of the cited n-alkyl sulfates. The present results suggest that the folding reaction of beta-lactoglobulin follows a non-hierarchical mechanism and hydrophobic interactions play important roles in stabilizing the non-native alpha-helical intermediate state.

Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase

DOE PAGES

Knoot, Cory J.; Purpero, Vincent M.; Lipscomb, John D.

2014-12-29

Intradiol aromatic ring-cleaving dioxygenases use an active site, nonheme Fe 3+ to activate O 2 and catecholic substrates for reaction. The inability of Fe 3+ to directly bind O 2 presents a mechanistic conundrum. The reaction mechanism of protocatechuate 3,4-dioxygenase is investigated in this paper using the alternative substrate 4-fluorocatechol. This substrate is found to slow the reaction at several steps throughout the mechanistic cycle, allowing the intermediates to be detected in solution studies. When the reaction was initiated in an enzyme crystal, it was found to halt at one of two intermediates depending on the pH of the surroundingmore » solution. The X-ray crystal structure of the intermediate at pH 6.5 revealed the key alkylperoxo-Fe 3+ species, and the anhydride-Fe 3+ intermediate was found for a crystal reacted at pH 8.5. Intermediates of these types have not been structurally characterized for intradiol dioxygenases, and they validate four decades of spectroscopic, kinetic, and computational studies. In contrast to our similar in crystallo crystallographic studies of an Fe 2+-containing extradiol dioxygenase, no evidence for a superoxo or peroxo intermediate preceding the alkylperoxo was found. This observation and the lack of spectroscopic evidence for an Fe 2+ intermediate that could bind O 2 are consistent with concerted formation of the alkylperoxo followed by Criegee rearrangement to yield the anhydride and ultimately ring-opened product. Finally, structural comparison of the alkylperoxo intermediates from the intra- and extradiol dioxygenases provides a rationale for site specificity of ring cleavage.« less

A virtual library of constrained cyclic tetrapeptides that mimics all four side-chain orientations for over half the reverse turns in the protein data bank.

PubMed

Arbor, Sage; Marshall, Garland R

2009-02-01

Reverse turns are often recognition sites for protein/protein interactions and, therefore, valuable potential targets for determining recognition motifs in development of potential therapeutics. A virtual combinatorial library of cyclic tetrapeptides (CTPs) was generated and the bonds in the low-energy structures were overlapped with canonical reverse-turn Calpha-Cbeta bonds (Tran et al., J Comput Aided Mol Des 19(8):551-566, 2005) to determine the utility of CTPs as reverse-turn peptidomimetics. All reverse turns in the Protein Data Bank (PDB) with a crystal structures resolution < or = 3.0 A were classified into the same known canonical reverse-turn Calpha-Cbeta bond clusters (Tran et al., J Comput Aided Mol Des 19(8):551-566, 2005). CTP reverse-turn mimics were compiled that mimicked both the relative orientations of three of the four as well as all four Calpha-Cbeta bonds in the reverse turns of the PDB. 54% of reverse turns represented in the PDB had eight or more CTPs structures that mimicked the orientation of all four of the Calpha-Cbeta bonds in the reverse turn.

Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: application in the refinement of de novo models.

PubMed

Fan, Hao; Periole, Xavier; Mark, Alan E

2012-07-01

The efficiency of using a variant of Hamiltonian replica-exchange molecular dynamics (Chaperone H-replica-exchange molecular dynamics [CH-REMD]) for the refinement of protein structural models generated de novo is investigated. In CH-REMD, the interaction between the protein and its environment, specifically, the electrostatic interaction between the protein and the solvating water, is varied leading to cycles of partial unfolding and refolding mimicking some aspects of folding chaperones. In 10 of the 15 cases examined, the CH-REMD approach sampled structures in which the root-mean-square deviation (RMSD) of secondary structure elements (SSE-RMSD) with respect to the experimental structure was more than 1.0 Å lower than the initial de novo model. In 14 of the 15 cases, the improvement was more than 0.5 Å. The ability of three different statistical potentials to identify near-native conformations was also examined. Little correlation between the SSE-RMSD of the sampled structures with respect to the experimental structure and any of the scoring functions tested was found. The most effective scoring function tested was the DFIRE potential. Using the DFIRE potential, the SSE-RMSD of the best scoring structures was on average 0.3 Å lower than the initial model. Overall the work demonstrates that targeted enhanced-sampling techniques such as CH-REMD can lead to the systematic refinement of protein structural models generated de novo but that improved potentials for the identification of near-native structures are still needed. Copyright © 2012 Wiley Periodicals, Inc.

CONSIDERATION OF REACTION INTERMEDIATES IN STRUCTURE-ACTIVITY RELATIONSHIPS: A KEY TO UNDERSTANDING AND PREDICTION

EPA Science Inventory

Consideration of Reaction Intermediates in Structure- Activity Relationships: A Key to Understanding and Prediction

A structure-activity relationship (SAR) represents an empirical means for generalizing chemical information relative to biological activity, and is frequent...

Mild and Selective Hydrozirconation of Amides to Aldehydes Using Cp2Zr(H)Cl

PubMed Central

Spletstoser, Jared T.; White, Jonathan M.; Tunoori, Ashok Rao; Georg, Gunda I.

2008-01-01

An investigation of the use of Cp2Zr(H)Cl (Schwartz’s reagent) to reduce a variety of amides to the corresponding aldehydes under very mild reaction conditions and in high yields is reported. A range of tertiary amides, including Weinreb’s amide, can be converted directly to the corresponding aldehydes with remarkable chemoselectivity. Primary and secondary amides proved to be viable substrates for reduction as well, although the yields were somewhat diminished compared to the corresponding tertiary amides. Results from NMR experiments suggested the presence of a stable, 18-electron zirconacycle intermediate that presumably affords the aldehyde upon water or silica gel workup. A series of competition experiments revealed a preference of the reagent for substrates in which the lone pair of the nitrogen is electron releasing and thus more delocalized across the amide bond by resonance. This trend accounts for the observed excellent selectivity for tertiary amides versus esters. Experiments regarding the solvent dependence of the reaction suggested a kinetic profile similar to that postulated for the hydrozirconation of alkenes and alkynes. Addition of p-anisidine to the reaction intermediate resulted in the formation of the corresponding imine mimicking the addition of water that forms the aldehyde. PMID:17315870

The stability of monomeric intermediates controls amyloid formation: Abeta25-35 and its N27Q mutant.

PubMed

Ma, Buyong; Nussinov, Ruth

2006-05-15

The structure and stabilities of the intermediates affect protein folding as well as misfolding and amyloid formation. By applying Kramer's theory of barrier crossing and a Morse-function-like energy landscape, we show that intermediates with medium stability dramatically increase the rate of amyloid formation; on the other hand, very stable and very unstable intermediates sharply decrease amyloid formation. Remarkably, extensive molecular dynamics simulations and conformational energy landscape analysis of Abeta25-35 and its N27Q mutant corroborate the mathematical description. Both experimental and current simulation results indicate that the core of the amyloid structure of Abeta25-35 formed from residues 28-35. A single mutation of N27Q of Abeta25-35 makes the Abeta25-35 N27Q amyloid-free. Energy landscape calculations show that Abeta25-35 has extended intermediates with medium stability that are prone to form amyloids, whereas the extended intermediates for Abeta25-35 N27Q split into stable and very unstable species that are not disposed to form amyloids. The results explain the contribution of both alpha-helical and beta-strand intermediates to amyloid formation. The results also indicate that the structure and stability of the intermediates, as well as of the native folded and the amyloid states can be targeted in drug design. One conceivable approach is to stabilize the intermediates to deter amyloid formation.

Malignant mesenchymal neoplasms of the dermis and subcutis mimicking benign lesions: a case-based review.

PubMed

Mentzel, Thomas; Brenn, Thomas

2017-11-01

In this short review, malignant mesenchymal neoplasms of the dermis and subcutis mimicking benign lesions and their differential diagnoses are discussed. These include plaque-like dermatofibrosarcoma protuberans, superficial low-grade fibromyxoid sarcoma, low-grade superficial malignant peripheral nerve sheath tumour, epithelioid sarcoma, pseudomyogenic haemangioendothelioma, Kaposi sarcoma mimicking cavernous haemangioma and benign lymphangioendothelioma, and rare forms of angiosarcoma mimicking a benign vascular lesion.

Clear cell carcinoma of the ovary mimicking struma ovarii and carcinoid tumor.

PubMed

Alduaij, Ahmad; Quddus, M Ruhul

2011-04-01

Clear cell carcinomas are considered as high-grade tumor often with poor prognosis. We describe 2 cases of clear cell carcinomas of the ovary mimicking benign or less aggressive tumors encountered in the female genital track. The first case is mimicking a benign monodermal teratoma, the so-called struma ovarii, and the second mimicking a carcinoid tumor. Copyright © 2011 Elsevier Inc. All rights reserved.

A highly sensitive and selective immunoassay for the detection of tetrabromobisphenol A in soil and sediment

USDA-ARS?s Scientific Manuscript database

Tetrabromobisphenol A (TBBPA) is the most widely used brominated flame retardant. A sensitive and selective enzyme-linked immunosorbent assay (ELISA) for the detection of TBBPA was developed. Six haptens (T1-T6) mimicking different structural elements of TBBPA were synthesized and coupled to keyhole...

Survey of beaver-related restoration practices in rangeland streams of the western USA

Treesearch

David S. Pilliod; Ashley T. Rohde; Susan Charnley; Rachael R. Davee; Jason B. Dunham; Hannah Gosnell; Gordon E. Grant; Mark B. Hausner; Justin L. Huntington; Caroline Nash

2018-01-01

Poor condition of many streams and concerns about future droughts in the arid and semi-arid western USA have motivated novel restoration strategies aimed at accelerating recovery and increasing water resources. Translocation of beavers into formerly occupied habitats, restoration activities encouraging beaver recolonization, and instream structures mimicking the...

New Protein Mimetics: The Zinc Finger Motif as a Locked-In Tertiary Fold.

PubMed

Tuchscherer, Gabriele; Lehmann, Christian; Mathieu, Marc

1998-11-16

The principle of a molecular kit is used for the covalent assembly of secondary structure forming peptide blocks to predetermined packing topologies. The resulting locked-in folds (LIFs; depicted schematically) are readily accessible and bypass the intriguing folding problem of linear peptide chains. This strategy allows, for example, mimicking of the essential structural and functional features of zinc finger proteins. © 1998 WILEY-VCH Verlag GmbH, Weinheim, Fed. Rep. of Germany.

Theoretical model for the discrete flexoelectric effect and a description for the sequence of intermediate smectic phases with increasing periodicity.

PubMed

Emelyanenko, A V; Osipov, M A

2003-11-01

A general phenomenological description and a simple molecular model is proposed for the "discrete" flexoelectric effect in tilted smectic liquid crystal phases. This effect defines a polarization in a smectic layer induced by a difference of director orientations in the two smectic layers adjacent to it. It is shown that the "discrete" flexoelectric effect is determined by electrostatic dipole-quadrupole interaction between positionally correlated molecules located in adjacent smectic layers, while the corresponding dipole-dipole interaction is responsible for a coupling between polarization vectors in neighboring layers. It is shown that a simple phenomenological model of a ferrielectric smectic liquid crystal, which has recently been proposed in the literature, can be used to describe the whole sequence of intermediate chiral smectic C* phases with increasing periods, and to determine the nonplanar structure of each phase without additional assumptions. In this sequence the phases with three- and four-layer periodicities have the same structure, as observed in the experiment. The theory predicts also the structure of intermediate phases with longer periods that have not been studied experimentally so far. The structures of intermediate phases with periodicities of up to nine layers are presented together with the phase diagrams, and a relationship between molecular chirality and the three-dimensional structure of intermediate phases is discussed. It is considered also how the coupling between the spontaneous polarization determined by molecular chirality and the induced polarization determined by the discrete flexoelectric effect stabilizes the nonplanar structure of intermediate phases.

An anthropomorphic phantom for quantitative evaluation of breast MRI.

PubMed

Freed, Melanie; de Zwart, Jacco A; Loud, Jennifer T; El Khouli, Riham H; Myers, Kyle J; Greene, Mark H; Duyn, Jeff H; Badano, Aldo

2011-02-01

In this study, the authors aim to develop a physical, tissue-mimicking phantom for quantitative evaluation of breast MRI protocols. The objective of this phantom is to address the need for improved standardization in breast MRI and provide a platform for evaluating the influence of image protocol parameters on lesion detection and discrimination. Quantitative comparisons between patient and phantom image properties are presented. The phantom is constructed using a mixture of lard and egg whites, resulting in a random structure with separate adipose- and glandular-mimicking components. T1 and T2 relaxation times of the lard and egg components of the phantom were estimated at 1.5 T from inversion recovery and spin-echo scans, respectively, using maximum-likelihood methods. The image structure was examined quantitatively by calculating and comparing spatial covariance matrices of phantom and patient images. A static, enhancing lesion was introduced by creating a hollow mold with stereolithography and filling it with a gadolinium-doped water solution. Measured phantom relaxation values fall within 2 standard errors of human values from the literature and are reasonably stable over 9 months of testing. Comparison of the covariance matrices of phantom and patient data demonstrates that the phantom and patient data have similar image structure. Their covariance matrices are the same to within error bars in the anterior-posterior direction and to within about two error bars in the right-left direction. The signal from the phantom's adipose-mimicking material can be suppressed using active fat-suppression protocols. A static, enhancing lesion can also be included with the ability to change morphology and contrast agent concentration. The authors have constructed a phantom and demonstrated its ability to mimic human breast images in terms of key physical properties that are relevant to breast MRI. This phantom provides a platform for the optimization and standardization of breast MRI imaging protocols for lesion detection and characterization.

German Basic Course. Volume II, Lessons 16-25. Revised.

ERIC Educational Resources Information Center

Defense Language Inst., Monterey, CA.

This is the second volume of the intermediate phase of the German Basic Course. The objective of the intermediate phase is mastery of the structural elements of the German language. Accordingly, each lesson contains the following elements: (1) introduction of new structure through "structure perception drills"; (2) a basic dialog dealing with a…

3D-Printed Ultratough Hydrogel Structures with Titin-like Domains.

PubMed

Zhu, Fengbo; Cheng, Libo; Wang, Zhi Jian; Hong, Wei; Wu, Zi Liang; Yin, Jun; Qian, Jin; Zheng, Qiang

2017-04-05

Titin is composed of repeated modular domains which unfold and dissipate energy upon loading. Here we employed such molecular-level paradigm to fabricate macroscopic ultratough hydrogel structures with titin-like domains, enabled by three-dimensional printing with multiple nozzles. Under stretch, the relatively thin and weak gel fibers in the printed structures break first and the hidden lengths postpone the failure of the main structures, mimicking the toughening principle in titin. These titin-like folded domains have been incorporated into a synthetic spider-web, which shows significantly enhanced extensibility and toughness. This work provides a new avenue of topological design for materials/structures with desired properties.

Reversible wavefront shaping between Gaussian and Airy beams by mimicking gravitational field

NASA Astrophysics Data System (ADS)

Wang, Xiangyang; Liu, Hui; Sheng, Chong; Zhu, Shining

2018-02-01

In this paper, we experimentally demonstrate reversible wavefront shaping through mimicking gravitational field. A gradient-index micro-structured optical waveguide with special refractive index profile was constructed whose effective index satisfying a gravitational field profile. Inside the waveguide, an incident broad Gaussian beam is firstly transformed into an accelerating beam, and the generated accelerating beam is gradually changed back to a Gaussian beam afterwards. To validate our experiment, we performed full-wave continuum simulations that agree with the experimental results. Furthermore, a theoretical model was established to describe the evolution of the laser beam based on Landau’s method, showing that the accelerating beam behaves like the Airy beam in the small range in which the linear potential approaches zero. To our knowledge, such a reversible wavefront shaping technique has not been reported before.

Peroxide Activation for Electrophilic Reactivity by the Binuclear Non-heme Iron Enzyme AurF

DOE PAGES

Park, Kiyoung; Li, Ning; Kwak, Yeonju; ...

2017-05-01

Binuclear non-heme iron enzymes activate O 2 for diverse chemistries that include oxygenation of organic substrates and hydrogen atom abstraction. This process often involves the formation of peroxo-bridged biferric intermediates, only some of which can perform electrophilic reactions. To elucidate the geometric and electronic structural requirements to activate peroxo reactivity, the active peroxo intermediate in 4-aminobenzoate N-oxygenase (AurF) has been characterized spectroscopically and computationally. A magnetic circular dichroism study of reduced AurF shows that its electronic and geometric structures are poised to react rapidly with O 2. Nuclear resonance vibrational spectroscopic definition of the peroxo intermediate formed in this reactionmore » shows that the active intermediate has a protonated peroxo bridge. Density functional theory computations on the structure established here show that the protonation activates peroxide for electrophilic/single-electron-transfer reactivity. As a result, this activation of peroxide by protonation is likely also relevant to the reactive peroxo intermediates in other binuclear non-heme iron enzymes.« less

Structure of a low-population binding intermediate in protein-RNA recognition

PubMed Central

Bardaro, Michael F.; Aprile, Francesco A.; Varani, Gabriele; Vendruscolo, Michele

2016-01-01

The interaction of the HIV-1 protein transactivator of transcription (Tat) and its cognate transactivation response element (TAR) RNA transactivates viral transcription and represents a paradigm for the widespread occurrence of conformational rearrangements in protein-RNA recognition. Although the structures of free and bound forms of TAR are well characterized, the conformations of the intermediates in the binding process are still unknown. By determining the free energy landscape of the complex using NMR residual dipolar couplings in replica-averaged metadynamics simulations, we observe two low-population intermediates. We then rationally design two mutants, one in the protein and another in the RNA, that weaken specific nonnative interactions that stabilize one of the intermediates. By using surface plasmon resonance, we show that these mutations lower the release rate of Tat, as predicted. These results identify the structure of an intermediate for RNA-protein binding and illustrate a general strategy to achieve this goal with high resolution. PMID:27286828

Peroxide Activation for Electrophilic Reactivity by the Binuclear Non-heme Iron Enzyme AurF

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Kiyoung; Li, Ning; Kwak, Yeonju

Binuclear non-heme iron enzymes activate O 2 for diverse chemistries that include oxygenation of organic substrates and hydrogen atom abstraction. This process often involves the formation of peroxo-bridged biferric intermediates, only some of which can perform electrophilic reactions. To elucidate the geometric and electronic structural requirements to activate peroxo reactivity, the active peroxo intermediate in 4-aminobenzoate N-oxygenase (AurF) has been characterized spectroscopically and computationally. A magnetic circular dichroism study of reduced AurF shows that its electronic and geometric structures are poised to react rapidly with O 2. Nuclear resonance vibrational spectroscopic definition of the peroxo intermediate formed in this reactionmore » shows that the active intermediate has a protonated peroxo bridge. Density functional theory computations on the structure established here show that the protonation activates peroxide for electrophilic/single-electron-transfer reactivity. As a result, this activation of peroxide by protonation is likely also relevant to the reactive peroxo intermediates in other binuclear non-heme iron enzymes.« less

Multiple stellar populations in Magellanic Cloud clusters - III. The first evidence of an extended main sequence turn-off in a young cluster: NGC 1856

NASA Astrophysics Data System (ADS)

Milone, A. P.; Bedin, L. R.; Piotto, G.; Marino, A. F.; Cassisi, S.; Bellini, A.; Jerjen, H.; Pietrinferni, A.; Aparicio, A.; Rich, R. M.

2015-07-01

Recent studies have shown that the extended main-sequence turn-off (eMSTO) is a common feature of intermediate-age star clusters in the Magellanic Clouds (MCs). The most simple explanation is that these stellar systems harbour multiple generations of stars with an age difference of a few hundred million years. However, while an eMSTO has been detected in a large number of clusters with ages between ˜1-2 Gyr, several studies of young clusters in both MCs and in nearby galaxies do not find any evidence for a prolonged star formation history, i. e. for multiple stellar generations. These results have suggested alternative interpretation of the eMSTOs observed in intermediate-age star clusters. The eMSTO could be due to stellar rotation mimicking an age spread or to interacting binaries. In these scenarios, intermediate-age MC clusters would be simple stellar populations, in close analogy with younger clusters. Here, we provide the first evidence for an eMSTO in a young stellar cluster. We exploit multiband Hubble Space Telescope photometry to study the ˜300-Myr old star cluster NGC 1856 in the Large Magellanic Cloud and detected a broadened MSTO that is consistent with a prolonged star formation which had a duration of about 150 Myr. Below the turn-off, the main sequence (MS) of NGC 1856 is split into a red and blue component, hosting 33 ± 5 and 67 ± 5 per cent of the total number of MS stars, respectively. We discuss these findings in the context of multiple-stellar-generation, stellar-rotation, and interacting-binary hypotheses.

The effect of illumination and electrode adjustment on the carrier behavior in special multilayer devices

NASA Astrophysics Data System (ADS)

Deng, Yanhong; Ou, Qingdong; Wang, Jinjiang; Zhang, Dengyu; Chen, Liezun; Li, Yanqing

2017-08-01

Intermediate connectors play an important role in semiconductor devices, especially in tandem devices. In this paper, four types of different intermediate connectors (e.g. Mg:Alq3/MoO3, MoO3, Mg:Alq3, and none) and two kinds of modified electrode materials (LiF and MoO3) integrated into the special multilayer devices are proposed, with the aim of studying the impact of light illumination and electrode adjustment on the carrier behavior of intermediate connectors through the current density-voltage characteristics, interfacial electronic structures, and capacitance-voltage characteristics. The results show that the illumination enhances the charge generation and separation in intermediate connectors, and further electrode interface modifications enhance the functionality of intermediate connectors. In addition, the device with an efficient intermediate connector structure shows a photoelectric effect, which paves the way for organic photovoltaic devices to realize optical-electrical integration transformation.

Programmable Control in Extracellular Matrix-mimicking Polymer Hydrogels.

PubMed

Hof, Kevin S; Bastings, Maartje M C

2017-06-28

The extracellular matrix (ECM) and cells have a reciprocal relationship, one shapes the other and vice versa. One of the main challenges of synthetic material systems for developmental cell culturing, organoid and stem cell work includes the implementation of this reciprocal nature. The largest hurdle to achieve true cell-instructive materials in biomaterials engineering is a lack of spatial and temporal control over material properties and the display of bioactive signals compared to the natural cell environment. ECM-mimicking hydrogels have been developed using a wide range of polymers, assembly and cross-linking strategies. While our synthetic toolbox is larger than nature, often our systems underperform when compared to ECM systems with natural components like Matrigel. Material properties and three-dimensional structure ill-represent the three-dimensional ECM reciprocal nature and ligand presentation is an oversimplified version of the complexity found in nature. We hypothesize that the lack of programmable control in properties and ligand presentation forms the basis of this mismatch in performance and analyze the presence of control in current state of the art ECM-mimicking systems based on covalent, supramolecular and recombinant polymers. We conclude that through combining the dynamics of supramolecular materials, robustness from covalent systems and the programmable spatial control of bio-activation in recombinant ECM materials, the optimal synthetic artificial ECM could be assembled.

Structures of two intermediate phases between the B1 and B2 phases of PbS under high pressure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Yanchun, E-mail: liyc@ihep.ac.cn, E-mail: liuj@ihep.ac.cn; Lin, Chuanlong; Li, Xiaodong

2014-12-15

The structural transitions of PbS were investigated at pressures up to 50 GPa using synchrotron powder and single crystal X-ray diffraction (XRD) methods in diamond anvil cells. We found two intermediate phases between the B1 phase under atmospheric pressure and the B2 phase at 21.1 GPa, which is different to previous reports. The structures of these two intermediate phases were indexed as B27 and B33, respectively. Their structural parameters were investigated using density functional theory (DFT) calculations. Our results provide a new insight into understanding the transition pathway between the B1 and B2 phases in PbS.

Bio-mimicking nano and micro-structured surface fabrication for antibacterial properties in medical implants.

PubMed

Jaggessar, Alka; Shahali, Hesam; Mathew, Asha; Yarlagadda, Prasad K D V

2017-10-02

Orthopaedic and dental implants have become a staple of the medical industry and with an ageing population and growing culture for active lifestyles, this trend is forecast to continue. In accordance with the increased demand for implants, failure rates, particularly those caused by bacterial infection, need to be reduced. The past two decades have led to developments in antibiotics and antibacterial coatings to reduce revision surgery and death rates caused by infection. The limited effectiveness of these approaches has spurred research into nano-textured surfaces, designed to mimic the bactericidal properties of some animal, plant and insect species, and their topographical features. This review discusses the surface structures of cicada, dragonfly and butterfly wings, shark skin, gecko feet, taro and lotus leaves, emphasising the relationship between nano-structures and high surface contact angles on self-cleaning and bactericidal properties. Comparison of these surfaces shows large variations in structure dimension and configuration, indicating that there is no one particular surface structure that exhibits bactericidal behaviour against all types of microorganisms. Recent bio-mimicking fabrication methods are explored, finding hydrothermal synthesis to be the most commonly used technique, due to its environmentally friendly nature and relative simplicity compared to other methods. In addition, current proposed bactericidal mechanisms between bacteria cells and nano-textured surfaces are presented and discussed. These models could be improved by including additional parameters such as biological cell membrane properties, adhesion forces, bacteria dynamics and nano-structure mechanical properties. This paper lastly reviews the mechanical stability and cytotoxicity of micro and nano-structures and materials. While the future of nano-biomaterials is promising, long-term effects of micro and nano-structures in the body must be established before nano-textures can be used on orthopaedic implant surfaces as way of inhibiting bacterial adhesion.

Invasive Pulmonary Aspergillosis-mimicking Tuberculosis.

PubMed

Kim, Sung-Han; Kim, Mi Young; Hong, Sun In; Jung, Jiwon; Lee, Hyun Joo; Yun, Sung-Cheol; Lee, Sang-Oh; Choi, Sang-Ho; Kim, Yang Soo; Woo, Jun Hee

2015-07-01

Pulmonary tuberculosis is occasionally confused with invasive pulmonary aspergillosis (IPA) in transplant recipients, since clinical suspicion and early diagnosis of pulmonary tuberculosis and IPA rely heavily on imaging modes such as computed tomography (CT). We therefore investigated IPA-mimicking tuberculosis in transplant recipients. All adult transplant recipients who developed tuberculosis or IPA at a tertiary hospital in an intermediate tuberculosis-burden country during a 6-year period were enrolled. First, we tested whether experienced radiologists could differentiate pulmonary tuberculosis from IPA. Second, we determined which radiologic findings could help us differentiate them. During the study period, 28 transplant recipients developed pulmonary tuberculosis after transplantation, and 80 patients developed IPA after transplantation. Two experienced radiologists scored blindly 28 tuberculosis and 50 randomly selected IPA cases. The sensitivities of radiologists A and B for IPA were 78% and 68%, respectively (poor agreement, kappa value = 0.25). The sensitivities of radiologists A and B for tuberculosis were 64% and 61%, respectively (excellent agreement, kappa value = 0.77). We then compared the CT findings of the 28 patients with tuberculosis and 80 patients with IPA. Infarct-shaped consolidations and smooth bronchial wall thickening were more frequent in IPA, and mass-shaped consolidations and centrilobular nodules (<10 mm, clustered) were more frequent in tuberculosis. Certain CT findings appear to be helpful in differentiating between IPA and tuberculosis. Nevertheless, the CT findings of about one-third of pulmonary tuberculosis cases in transplant recipients are very close to those of IPA. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

In Silico Identification of Mimicking Molecules as Defense Inducers Triggering Jasmonic Acid Mediated Immunity against Alternaria Blight Disease in Brassica Species

PubMed Central

Pathak, Rajesh K.; Baunthiyal, Mamta; Shukla, Rohit; Pandey, Dinesh; Taj, Gohar; Kumar, Anil

2017-01-01

Alternaria brassicae and Alternaria brassicicola are two major phytopathogenic fungi which cause Alternaria blight, a recalcitrant disease on Brassica crops throughout the world, which is highly destructive and responsible for significant yield losses. Since no resistant source is available against Alternaria blight, therefore, efforts have been made in the present study to identify defense inducer molecules which can induce jasmonic acid (JA) mediated defense against the disease. It is believed that JA triggered defense response will prevent necrotrophic mode of colonization of Alternaria brassicae fungus. The JA receptor, COI1 is one of the potential targets for triggering JA mediated immunity through interaction with JA signal. In the present study, few mimicking compounds more efficient than naturally occurring JA in terms of interaction with COI1 were identified through virtual screening and molecular dynamics simulation studies. A high quality structural model of COI1 was developed using the protein sequence of Brassica rapa. This was followed by virtual screening of 767 analogs of JA from ZINC database for interaction with COI1. Two analogs viz. ZINC27640214 and ZINC43772052 showed more binding affinity with COI1 as compared to naturally occurring JA. Molecular dynamics simulation of COI1 and COI1-JA complex, as well as best screened interacting structural analogs of JA with COI1 was done for 50 ns to validate the stability of system. It was found that ZINC27640214 possesses efficient, stable, and good cell permeability properties. Based on the obtained results and its physicochemical properties, it is capable of mimicking JA signaling and may be used as defense inducers for triggering JA mediated resistance against Alternaria blight, only after further validation through field trials. PMID:28487711

Contingency Table Browser - prediction of early stage protein structure.

PubMed

Kalinowska, Barbara; Krzykalski, Artur; Roterman, Irena

2015-01-01

The Early Stage (ES) intermediate represents the starting structure in protein folding simulations based on the Fuzzy Oil Drop (FOD) model. The accuracy of FOD predictions is greatly dependent on the accuracy of the chosen intermediate. A suitable intermediate can be constructed using the sequence-structure relationship information contained in the so-called contingency table - this table expresses the likelihood of encountering various structural motifs for each tetrapeptide fragment in the amino acid sequence. The limited accuracy with which such structures could previously be predicted provided the motivation for a more indepth study of the contingency table itself. The Contingency Table Browser is a tool which can visualize, search and analyze the table. Our work presents possible applications of Contingency Table Browser, among them - analysis of specific protein sequences from the point of view of their structural ambiguity.

MurD ligase from E. coli: Tetrahedral intermediate formation study by hybrid quantum mechanical/molecular mechanical replica path method.

PubMed

Perdih, Andrej; Hodoscek, Milan; Solmajer, Tom

2009-02-15

MurD (UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase), a three-domain bacterial protein, catalyses a highly specific incorporation of D-glutamate to the cytoplasmic intermediate UDP-N-acetyl-muramoyl-L-alanine (UMA) utilizing ATP hydrolysis to ADP and P(i). This reaction is part of a biosynthetic path yielding bacterial peptidoglycan. On the basis of structural studies of MurD complexes, a stepwise catalytic mechanism was proposed that commences with a formation of the acyl-phosphate intermediate, followed by a nucleophilic attack of D-glutamate that, through the formation of a tetrahedral reaction intermediate and subsequent phosphate dissociation, affords the final product, UDP-N-acetyl-muramoyl-L-alanine-D-glutamate (UMAG). A hybrid quantum mechanical/molecular mechanical (QM/MM) molecular modeling approach was utilized, combining the B3LYP QM level of theory with empirical force field simulations to evaluate three possible reaction pathways leading to tetrahedral intermediate formation. Geometries of the starting structures based on crystallographic experimental data and tetrahedral intermediates were carefully examined together with a role of crucial amino acids and water molecules. The replica path method was used to generate the reaction pathways between the starting structures and the corresponding tetrahedral reaction intermediates, offering direct comparisons with a sequential kinetic mechanism and the available structural data for this enzyme. The acquired knowledge represents new and valuable information to assist in the ongoing efforts leading toward novel inhibitors of MurD as potential antibacterial drugs. (c) 2008 Wiley-Liss, Inc.

Capturing a flavivirus pre-fusion intermediate.

PubMed

Kaufmann, Bärbel; Chipman, Paul R; Holdaway, Heather A; Johnson, Syd; Fremont, Daved H; Kuhn, Richard J; Diamond, Michael S; Rossmann, Michael G

2009-11-01

During cell entry of flaviviruses, low endosomal pH triggers the rearrangement of the viral surface glycoproteins to a fusion-active state that allows the release of the infectious RNA into the cytoplasm. In this work, West Nile virus was complexed with Fab fragments of the neutralizing mAb E16 and was subsequently exposed to low pH, trapping the virions in a pre-fusion intermediate state. The structure of the complex was studied by cryo-electron microscopy and provides the first structural glimpse of a flavivirus fusion intermediate near physiological conditions. A radial expansion of the outer protein layer of the virion was observed compared to the structure at pH 8. The resulting approximately 60 A-wide shell of low density between lipid bilayer and outer protein layer is likely traversed by the stem region of the E glycoprotein. By using antibody fragments, we have captured a structural intermediate of a virus that likely occurs during cell entry. The trapping of structural transition states by antibody fragments will be applicable for other processes in the flavivirus life cycle and delineating other cellular events that involve conformational rearrangements.

Rapid time-resolved diffraction studies of protein structures using synchrotron radiation

NASA Astrophysics Data System (ADS)

Bartunik, Hans D.; Bartunik, Lesley J.

1992-07-01

The crystal structure of intermediate states in biological reactions of proteins of multi-protein complexes may be studied by time-resolved X-ray diffraction techniques which make use of the high spectral brilliance, continuous wavelength distribution and pulsed time structure of synchrotron radiation. Laue diffraction methods provide a means of investigating intermediate structures with lifetimes in the millisecond time range at presently operational facilities. Third-generation storage rings which are under construction may permit one to reach a time resolution of one microsecond for non-cyclic and one nanosecond for cyclic reactions. The number of individual exposures required for exploring reciprocal space and hence the total time scale strongly depend on the lattice order that may be affected, e.g., by conformational changes. Time-resolved experiments require high population of a specific intermediate which has to be homogeneous over the crystal volume. A number of external excitation techniques have been developed including in situ liberation of active metabolites by laser pulse photolysis of photolabile inactive precursors. First applications to crystal structure analysis of catalytic intermediates of enzymes demonstrate the potential of time-resolved protein crystallography.

Structural fingerprints and their evolution during oligomeric vs. oligomer-free amyloid fibril growth

PubMed Central

Foley, Joseph; Hill, Shannon E.; Miti, Tatiana; Mulaj, Mentor; Ciesla, Marissa; Robeel, Rhonda; Persichilli, Christopher; Raynes, Rachel; Westerheide, Sandy; Muschol, Martin

2013-01-01

Deposits of fibrils formed by disease-specific proteins are the molecular hallmark of such diverse human disorders as Alzheimer's disease, type II diabetes, or rheumatoid arthritis. Amyloid fibril formation by structurally and functionally unrelated proteins exhibits many generic characteristics, most prominently the cross β-sheet structure of their mature fibrils. At the same time, amyloid formation tends to proceed along one of two separate assembly pathways yielding either stiff monomeric filaments or globular oligomers and curvilinear protofibrils. Given the focus on oligomers as major toxic species, the very existence of an oligomer-free assembly pathway is significant. Little is known, though, about the structure of the various intermediates emerging along different pathways and whether the pathways converge towards a common or distinct fibril structures. Using infrared spectroscopy we probed the structural evolution of intermediates and late-stage fibrils formed during in vitro lysozyme amyloid assembly along an oligomeric and oligomer-free pathway. Infrared spectroscopy confirmed that both pathways produced amyloid-specific β-sheet peaks, but at pathway-specific wavenumbers. We further found that the amyloid-specific dye thioflavin T responded to all intermediates along either pathway. The relative amplitudes of thioflavin T fluorescence responses displayed pathway-specific differences and could be utilized for monitoring the structural evolution of intermediates. Pathway-specific structural features obtained from infrared spectroscopy and Thioflavin T responses were identical for fibrils grown at highly acidic or at physiological pH values and showed no discernible effects of protein hydrolysis. Our results suggest that late-stage fibrils formed along either pathway are amyloidogenic in nature, but have distinguishable structural fingerprints. These pathway-specific fingerprints emerge during the earliest aggregation events and persist throughout the entire cascade of aggregation intermediates formed along each pathway. PMID:24089713

Structural fingerprints and their evolution during oligomeric vs. oligomer-free amyloid fibril growth

NASA Astrophysics Data System (ADS)

Foley, Joseph; Hill, Shannon E.; Miti, Tatiana; Mulaj, Mentor; Ciesla, Marissa; Robeel, Rhonda; Persichilli, Christopher; Raynes, Rachel; Westerheide, Sandy; Muschol, Martin

2013-09-01

Deposits of fibrils formed by disease-specific proteins are the molecular hallmark of such diverse human disorders as Alzheimer's disease, type II diabetes, or rheumatoid arthritis. Amyloid fibril formation by structurally and functionally unrelated proteins exhibits many generic characteristics, most prominently the cross β-sheet structure of their mature fibrils. At the same time, amyloid formation tends to proceed along one of two separate assembly pathways yielding either stiff monomeric filaments or globular oligomers and curvilinear protofibrils. Given the focus on oligomers as major toxic species, the very existence of an oligomer-free assembly pathway is significant. Little is known, though, about the structure of the various intermediates emerging along different pathways and whether the pathways converge towards a common or distinct fibril structures. Using infrared spectroscopy we probed the structural evolution of intermediates and late-stage fibrils formed during in vitro lysozyme amyloid assembly along an oligomeric and oligomer-free pathway. Infrared spectroscopy confirmed that both pathways produced amyloid-specific β-sheet peaks, but at pathway-specific wavenumbers. We further found that the amyloid-specific dye thioflavin T responded to all intermediates along either pathway. The relative amplitudes of thioflavin T fluorescence responses displayed pathway-specific differences and could be utilized for monitoring the structural evolution of intermediates. Pathway-specific structural features obtained from infrared spectroscopy and Thioflavin T responses were identical for fibrils grown at highly acidic or at physiological pH values and showed no discernible effects of protein hydrolysis. Our results suggest that late-stage fibrils formed along either pathway are amyloidogenic in nature, but have distinguishable structural fingerprints. These pathway-specific fingerprints emerge during the earliest aggregation events and persist throughout the entire cascade of aggregation intermediates formed along each pathway.

Structural fingerprints and their evolution during oligomeric vs. oligomer-free amyloid fibril growth.

PubMed

Foley, Joseph; Hill, Shannon E; Miti, Tatiana; Mulaj, Mentor; Ciesla, Marissa; Robeel, Rhonda; Persichilli, Christopher; Raynes, Rachel; Westerheide, Sandy; Muschol, Martin

2013-09-28

Deposits of fibrils formed by disease-specific proteins are the molecular hallmark of such diverse human disorders as Alzheimer's disease, type II diabetes, or rheumatoid arthritis. Amyloid fibril formation by structurally and functionally unrelated proteins exhibits many generic characteristics, most prominently the cross β-sheet structure of their mature fibrils. At the same time, amyloid formation tends to proceed along one of two separate assembly pathways yielding either stiff monomeric filaments or globular oligomers and curvilinear protofibrils. Given the focus on oligomers as major toxic species, the very existence of an oligomer-free assembly pathway is significant. Little is known, though, about the structure of the various intermediates emerging along different pathways and whether the pathways converge towards a common or distinct fibril structures. Using infrared spectroscopy we probed the structural evolution of intermediates and late-stage fibrils formed during in vitro lysozyme amyloid assembly along an oligomeric and oligomer-free pathway. Infrared spectroscopy confirmed that both pathways produced amyloid-specific β-sheet peaks, but at pathway-specific wavenumbers. We further found that the amyloid-specific dye thioflavin T responded to all intermediates along either pathway. The relative amplitudes of thioflavin T fluorescence responses displayed pathway-specific differences and could be utilized for monitoring the structural evolution of intermediates. Pathway-specific structural features obtained from infrared spectroscopy and Thioflavin T responses were identical for fibrils grown at highly acidic or at physiological pH values and showed no discernible effects of protein hydrolysis. Our results suggest that late-stage fibrils formed along either pathway are amyloidogenic in nature, but have distinguishable structural fingerprints. These pathway-specific fingerprints emerge during the earliest aggregation events and persist throughout the entire cascade of aggregation intermediates formed along each pathway.

Copper-Hydroperoxo Mediated N-Debenzylation Chemistry Mimicking Aspects of Copper Monoxygenases

PubMed Central

Maiti, Debabrata; Narducci Sarjeant, Amy A.; Karlin, Kenneth D.

2008-01-01

Substantial oxidative N-debenzylation reaction along with PhCH=O formation occurs from a hydroperoxo copper(II) complex which has a dibenzylamino substrate (-N(CH2Ph)2 appended as a substituent on one pyridyl group of its tripodal tetradentate TMPA {≡ TPA ≡ tris(2-pyridylmethyl)amine)} ligand framework. During the course of the (LN(CH2Ph)2)CuII(−OOH) reactivity, formation of a substrate and −OOH (an oxygen atom) derived alkoxo CuII(−OR) complex occurs. The observation that the same CuII(−OR) species occurs from CuI/PhIO chemistry suggests the possibility that a copper-oxo (cupryl) reactive intermediate forms during alkoxo species formation, and new ESI-MS data obtained provides some further support for this high-valent intermediate. Net H-atom abstraction chemistry is proposed, based on kinetic isotope effect studies provided here and that previously published for a closely related CuII(−OOH) species incorporating dimethylamine (-N(CH3)2) as the internal substrate (J. Am. Chem. Soc. 2007, 129, 6720-6721); the CuI/PhIO reactivity, with similar isotope effect results, provides further support. The reactivity of these chemical systems closely resembles proposed oxidative N-dealkylation mechanisms effected by the copper-monooxygenases dopamine β-monooxygenase (DβM) or peptidylglycine-α-hydroxylating monooxygenase (PHM). PMID:18783212

Poverty eradication: a new paradigm.

PubMed

Pethe, V P

1998-08-01

This article offers a new paradigm for eradicating poverty in India. It was assumed incorrectly by Mahatma Gandhi that a good society without mass poverty would follow after independence. India copied Western models of development and developed giant factories, big dams, and megacities. Agriculture did not expand the number of jobs for people. The Western paradigm failed in India because of the false assumption of "trickle down" of income to the masses. The targeted programs to the poor did not directly benefit enough of the poor. Mega-industrialization led to reduced employment and higher skill needs. The model failed mainly because it was a proxy and relied on indirect ways of reaching the poor. The models failed to be adapted to conditions in India. The Swadeshi paradigm is a direct model for addressing mass poverty. Poverty is affected by immediate, intermediate, and ultimate determinants. Poverty begets social and economic problems, such as ignorance, ill health, high fertility, unemployment, and crime. In India and developing countries, mass poverty results from under use of human resources; lack of equal opportunities; and an outdated non-egalitarian social structure, an unjust global economic order, human cruelty, and erosion of ethical values. Indians are squandering their precious resources mimicking Western consumerism. Poverty leads to rapid population growth. People become productive assets with universal literacy, compulsory and free education, health services and sanitation, vocational training, and work ethics. India needs people-oriented policies with less emphasis on capital accumulation.

Evidence for close side-chain packing in an early protein folding intermediate previously assumed to be a molten globule

PubMed Central

Rosen, Laura E.; Connell, Katelyn B.; Marqusee, Susan

2014-01-01

The molten globule, a conformational ensemble with significant secondary structure but only loosely packed tertiary structure, has been suggested to be a ubiquitous intermediate in protein folding. However, it is difficult to assess the tertiary packing of transiently populated species to evaluate this hypothesis. Escherichia coli RNase H is known to populate an intermediate before the rate-limiting barrier to folding that has long been thought to be a molten globule. We investigated this hypothesis by making mimics of the intermediate that are the ground-state conformation at equilibrium, using two approaches: a truncation to generate a fragment mimic of the intermediate, and selective destabilization of the native state using point mutations. Spectroscopic characterization and the response of the mimics to further mutation are consistent with studies on the transient kinetic intermediate, indicating that they model the early intermediate. Both mimics fold cooperatively and exhibit NMR spectra indicative of a closely packed conformation, in contrast to the hypothesis of molten tertiary packing. This result is important for understanding the nature of the subsequent rate-limiting barrier to folding and has implications for the assumption that many other proteins populate molten globule folding intermediates. PMID:25258414

Evidence for close side-chain packing in an early protein folding intermediate previously assumed to be a molten globule.

PubMed

Rosen, Laura E; Connell, Katelyn B; Marqusee, Susan

2014-10-14

The molten globule, a conformational ensemble with significant secondary structure but only loosely packed tertiary structure, has been suggested to be a ubiquitous intermediate in protein folding. However, it is difficult to assess the tertiary packing of transiently populated species to evaluate this hypothesis. Escherichia coli RNase H is known to populate an intermediate before the rate-limiting barrier to folding that has long been thought to be a molten globule. We investigated this hypothesis by making mimics of the intermediate that are the ground-state conformation at equilibrium, using two approaches: a truncation to generate a fragment mimic of the intermediate, and selective destabilization of the native state using point mutations. Spectroscopic characterization and the response of the mimics to further mutation are consistent with studies on the transient kinetic intermediate, indicating that they model the early intermediate. Both mimics fold cooperatively and exhibit NMR spectra indicative of a closely packed conformation, in contrast to the hypothesis of molten tertiary packing. This result is important for understanding the nature of the subsequent rate-limiting barrier to folding and has implications for the assumption that many other proteins populate molten globule folding intermediates.

Direct Observation of Cooperative Protein Structural Dynamics of Homodimeric Hemoglobin from 100 ps to 10 ms with Pump-Probe X-ray Solution Scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Kyung Hwan; Muniyappan, Srinivasan; Oang, Key Young

2012-05-29

Proteins serve as molecular machines in performing their biological functions, but the detailed structural transitions are difficult to observe in their native aqueous environments in real time. For example, despite extensive studies, the solution-phase structures of the intermediates along the allosteric pathways for the transitions between the relaxed (R) and tense (T) forms have been elusive. In this work, we employed picosecond X-ray solution scattering and novel structural analysis to track the details of the structural dynamics of wild-type homodimeric hemoglobin (HbI) from the clam Scapharca inaequivalvis and its F97Y mutant over a wide time range from 100 ps tomore » 56.2 ms. From kinetic analysis of the measured time-resolved X-ray solution scattering data, we identified three structurally distinct intermediates (I 1, I 2, and I 3) and their kinetic pathways common for both the wild type and the mutant. The data revealed that the singly liganded and unliganded forms of each intermediate share the same structure, providing direct evidence that the ligand photolysis of only a single subunit induces the same structural change as the complete photolysis of both subunits does. In addition, by applying novel structural analysis to the scattering data, we elucidated the detailed structural changes in the protein, including changes in the heme-heme distance, the quaternary rotation angle of subunits, and interfacial water gain/loss. The earliest, R-like I 1 intermediate is generated within 100 ps and transforms to the R-like I 2 intermediate with a time constant of 3.2 ± 0.2 ns. Subsequently, the late, T-like I 3 intermediate is formed via subunit rotation, a decrease in the heme-heme distance, and substantial gain of interfacial water and exhibits ligation-dependent formation kinetics with time constants of 730 ± 120 ns for the fully photolyzed form and 5.6 ± 0.8 μs for the partially photolyzed form. For the mutant, the overall kinetics are accelerated, and the formation of the T-like I 3 intermediate involves interfacial water loss (instead of water entry) and lacks the contraction of the heme-heme distance, thus underscoring the dramatic effect of the F97Y mutation. The ability to keep track of the detailed movements of the protein in aqueous solution in real time provides new insights into the protein structural dynamics.« less

Electrospun Fibrous Scaffolds for Tissue Engineering: Viewpoints on Architecture and Fabrication.

PubMed

Jun, Indong; Han, Hyung-Seop; Edwards, James R; Jeon, Hojeong

2018-03-06

Electrospinning has been used for the fabrication of extracellular matrix (ECM)-mimicking fibrous scaffolds for several decades. Electrospun fibrous scaffolds provide nanoscale/microscale fibrous structures with interconnecting pores, resembling natural ECM in tissues, and showing a high potential to facilitate the formation of artificial functional tissues. In this review, we summarize the fundamental principles of electrospinning processes for generating complex fibrous scaffold geometries that are similar in structural complexity to the ECM of living tissues. Moreover, several approaches for the formation of three-dimensional fibrous scaffolds arranged in hierarchical structures for tissue engineering are also presented.

A biomimetic projector with high subwavelength directivity based on dolphin biosonar

NASA Astrophysics Data System (ADS)

Zhang, Yu; Gao, Xiaowei; Zhang, Sai; Cao, Wenwu; Tang, Liguo; Wang, Ding; Li, Yan

2014-09-01

Based on computed tomography of a Yangtze finless porpoise's biosonar system, a biomimetic structure was designed to include air cavity, gradient-index material, and steel outer-structure mimicking air sacs, melon, and skull, respectively. The mainlobe pressure was about three times higher, the angular resolution was one order of magnitude higher, and the effective source size was orders of magnitude larger than those of the subwavelength source without the biomimetic structure. The superior subwavelength directivity over a broad bandwidth suggests potential applications of this biomimetic projector in underwater sonar, medical ultrasonography, and other related applications.

State-of-the-art and outlook for biomimetic materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Richman, R.H.; Bond, G.M.; McNaughton, W.P.

1994-11-01

A remarkable diversity of structures and molecular functions has evolved in plants and animals. Many of these natural substances have properties or capabilities that belie their origins in humble, everyday, starting materials. Consequently, there is a growing awareness among scientists and engineers that biological systems can be a valuable source of inspiration for man-made materials. Emphasis in this assessment is on biomimetics; that is, the achievement of unusual materials properties or processes by mimicking novel aspects of biological systems. Five broad areas are selected for detailed investigation: Mimicking of Natural Material Designs; Biomimetic Materials Processing; Artificial Photosynthesis; Biomimetic Molecular Electronics;more » and Biomimetic Catalysis. Each of these topics is examined in terms of current activities and approaches, key aspects, unresolved issues, and implications for the power industry. Finally, the researchers, their organizations, the main thrusts of investigation, achievements, and funding agencies are summarized in tabular form.« less

Single helically folded aromatic oligoamides that mimic the charge surface of double-stranded B-DNA

NASA Astrophysics Data System (ADS)

Ziach, Krzysztof; Chollet, Céline; Parissi, Vincent; Prabhakaran, Panchami; Marchivie, Mathieu; Corvaglia, Valentina; Bose, Partha Pratim; Laxmi-Reddy, Katta; Godde, Frédéric; Schmitter, Jean-Marie; Chaignepain, Stéphane; Pourquier, Philippe; Huc, Ivan

2018-05-01

Numerous essential biomolecular processes require the recognition of DNA surface features by proteins. Molecules mimicking these features could potentially act as decoys and interfere with pharmacologically or therapeutically relevant protein-DNA interactions. Although naturally occurring DNA-mimicking proteins have been described, synthetic tunable molecules that mimic the charge surface of double-stranded DNA are not known. Here, we report the design, synthesis and structural characterization of aromatic oligoamides that fold into single helical conformations and display a double helical array of negatively charged residues in positions that match the phosphate moieties in B-DNA. These molecules were able to inhibit several enzymes possessing non-sequence-selective DNA-binding properties, including topoisomerase 1 and HIV-1 integrase, presumably through specific foldamer-protein interactions, whereas sequence-selective enzymes were not inhibited. Such modular and synthetically accessible DNA mimics provide a versatile platform to design novel inhibitors of protein-DNA interactions.

Compensatory Evolution of Intrinsic Transcription Terminators in Bacillus Cereus

PubMed Central

Safina, Ksenia R.; Mironov, Andrey A.

2017-01-01

Many RNA molecules possess complicated secondary structure critical to their function. Mutations in double-helical regions of RNA may disrupt Watson–Crick (WC) interactions causing structure destabilization or even complete loss of function. Such disruption can be compensated by another mutation restoring base pairing, as has been shown for mRNA, rRNA and tRNA. Here, we investigate the evolution of intrinsic transcription terminators between closely related strains of Bacillus cereus. While the terminator structure is maintained by strong natural selection, as evidenced by the low frequency of disrupting mutations, we observe multiple instances of pairs of disrupting-compensating mutations in RNA structure stems. Such two-step switches between different WC pairs occur very fast, consistent with the low fitness conferred by the intermediate non-WC variant. Still, they are not instantaneous, and probably involve transient fixation of the intermediate variant. The GU wobble pair is the most frequent intermediate, and remains fixed longer than other intermediates, consistent with its less disruptive effect on the RNA structure. Double switches involving non-GU intermediates are more frequent at the ends of RNA stems, probably because they are associated with smaller fitness loss. Together, these results show that the fitness landscape of bacterial transcription terminators is rather rugged, but that the fitness valleys associated with unpaired stem nucleotides are rather shallow, facilitating evolution. PMID:28201729

Structural Properties of Human IAPP Dimer in Membrane Environment Studied by All-Atom Molecular Dynamics Simulations.

PubMed

Liu, Na; Duan, Mojie; Yang, Minghui

2017-08-11

The aggregation of human islet amyloid polypeptide (hIAPP) can damage the membrane of the β-cells in the pancreatic islets and induce type 2 diabetes (T2D). Growing evidences indicated that the major toxic species are small oligomers of IAPP. Due to the fast aggregation nature, it is hard to characterize the structures of IAPP oligomers by experiments, especially in the complex membrane environment. On the other side, molecular dynamics simulation can provide atomic details of the structure and dynamics of the aggregation of IAPP. In this study, all-atom bias-exchange metadynamics (BE-Meta) and unbiased molecular dynamics simulations were employed to study the structural properties of IAPP dimer in the membranes environments. A number of intermediates, including α-helical states, β-sheet states, and fully disordered states, are identified. The formation of N-terminal β-sheet structure is prior to the C-terminal β-sheet structure towards the final fibril-like structures. The α-helical intermediates have lower propensity in the dimeric hIAPP and are off-pathway intermediates. The simulations also demonstrate that the β-sheet intermediates induce more perturbation on the membrane than the α-helical and disordered states and thus pose higher disruption ability.

An ABA-mimicking ligand that reduces water loss and promotes drought resistance in plants

PubMed Central

Cao, Minjie; Liu, Xue; Zhang, Yan; Xue, Xiaoqian; Zhou, X Edward; Melcher, Karsten; Gao, Pan; Wang, Fuxing; Zeng, Liang; Zhao, Yang; Zhao, Yang; Deng, Pan; Zhong, Dafang; Zhu, Jian-Kang; Xu, H Eric; Xu, Yong

2013-01-01

Abscisic acid (ABA) is the most important hormone for plants to resist drought and other abiotic stresses. ABA binds directly to the PYR/PYL family of ABA receptors, resulting in inhibition of type 2C phosphatases (PP2C) and activation of downstream ABA signaling. It is envisioned that intervention of ABA signaling by small molecules could help plants to overcome abiotic stresses such as drought, cold and soil salinity. However, chemical instability and rapid catabolism by plant enzymes limit the practical application of ABA itself. Here we report the identification of a small molecule ABA mimic (AM1) that acts as a potent activator of multiple members of the family of ABA receptors. In Arabidopsis, AM1 activates a gene network that is highly similar to that induced by ABA. Treatments with AM1 inhibit seed germination, prevent leaf water loss, and promote drought resistance. We solved the crystal structure of AM1 in complex with the PYL2 ABA receptor and the HAB1 PP2C, which revealed that AM1 mediates a gate-latch-lock interacting network, a structural feature that is conserved in the ABA-bound receptor/PP2C complex. Together, these results demonstrate that a single small molecule ABA mimic can activate multiple ABA receptors and protect plants from water loss and drought stress. Moreover, the AM1 complex crystal structure provides a structural basis for designing the next generation of ABA-mimicking small molecules. PMID:23835477

Stream Nitrate Response to Different Burning Treatments in Southern Appalachian Forests

Treesearch

Barton D. Clinton; James M. Vose; Jennifer D. Knoepp; Katherine J. Elliott

2003-01-01

Southern Appalachian forests are undergoing considerable change due to altered disturbance regimes. For example, fire exclusion has had a major impact on the structure and function of pine-hardwood ecosystems. Recently, fire has been prescribed for a variety of applications: 1) stand-replacement in the form of a mimicked wildfire, 2) site-preparation as part of a fell-...

Retrieval Capabilities of Hierarchical Networks: From Dyson to Hopfield

NASA Astrophysics Data System (ADS)

Agliari, Elena; Barra, Adriano; Galluzzi, Andrea; Guerra, Francesco; Tantari, Daniele; Tavani, Flavia

2015-01-01

We consider statistical-mechanics models for spin systems built on hierarchical structures, which provide a simple example of non-mean-field framework. We show that the coupling decay with spin distance can give rise to peculiar features and phase diagrams much richer than their mean-field counterpart. In particular, we consider the Dyson model, mimicking ferromagnetism in lattices, and we prove the existence of a number of metastabilities, beyond the ordered state, which become stable in the thermodynamic limit. Such a feature is retained when the hierarchical structure is coupled with the Hebb rule for learning, hence mimicking the modular architecture of neurons, and gives rise to an associative network able to perform single pattern retrieval as well as multiple-pattern retrieval, depending crucially on the external stimuli and on the rate of interaction decay with distance; however, those emergent multitasking features reduce the network capacity with respect to the mean-field counterpart. The analysis is accomplished through statistical mechanics, Markov chain theory, signal-to-noise ratio technique, and numerical simulations in full consistency. Our results shed light on the biological complexity shown by real networks, and suggest future directions for understanding more realistic models.

Tissue mimicking simulations for temporal enhanced ultrasound-based tissue typing

NASA Astrophysics Data System (ADS)

Bayat, Sharareh; Imani, Farhad; Gerardo, Carlos D.; Nir, Guy; Azizi, Shekoofeh; Yan, Pingkun; Tahmasebi, Amir; Wilson, Storey; Iczkowski, Kenneth A.; Lucia, M. Scott; Goldenberg, Larry; Salcudean, Septimiu E.; Mousavi, Parvin; Abolmaesumi, Purang

2017-03-01

Temporal enhanced ultrasound (TeUS) is an imaging approach where a sequence of temporal ultrasound data is acquired and analyzed for tissue typing. Previously, in a series of in vivo and ex vivo studies we have demonstrated that, this approach is effective for detecting prostate and breast cancers. Evidences derived from our experiments suggest that both ultrasound-signal related factors such as induced heat and tissue-related factors such as the distribution and micro-vibration of scatterers lead to tissue typing information in TeUS. In this work, we simulate mechanical micro-vibrations of scatterers in tissue-mimicking phantoms that have various scatterer densities reflecting benign and cancerous tissue structures. Finite element modeling (FEM) is used for this purpose where the vertexes are scatterers representing cell nuclei. The initial positions of scatterers are determined by the distribution of nuclei segmented from actual digital histology scans of prostate cancer patients. Subsequently, we generate ultrasound images of the simulated tissue structure using the Field II package resulting in a temporal enhanced ultrasound. We demonstrate that the micro-vibrations of scatterers are captured by temporal ultrasound data and this information can be exploited for tissue typing.

Traction force microscopy of engineered cardiac tissues.

PubMed

Pasqualini, Francesco Silvio; Agarwal, Ashutosh; O'Connor, Blakely Bussie; Liu, Qihan; Sheehy, Sean P; Parker, Kevin Kit

2018-01-01

Cardiac tissue development and pathology have been shown to depend sensitively on microenvironmental mechanical factors, such as extracellular matrix stiffness, in both in vivo and in vitro systems. We present a novel quantitative approach to assess cardiac structure and function by extending the classical traction force microscopy technique to tissue-level preparations. Using this system, we investigated the relationship between contractile proficiency and metabolism in neonate rat ventricular myocytes (NRVM) cultured on gels with stiffness mimicking soft immature (1 kPa), normal healthy (13 kPa), and stiff diseased (90 kPa) cardiac microenvironments. We found that tissues engineered on the softest gels generated the least amount of stress and had the smallest work output. Conversely, cardiomyocytes in tissues engineered on healthy- and disease-mimicking gels generated significantly higher stresses, with the maximal contractile work measured in NRVM engineered on gels of normal stiffness. Interestingly, although tissues on soft gels exhibited poor stress generation and work production, their basal metabolic respiration rate was significantly more elevated than in other groups, suggesting a highly ineffective coupling between energy production and contractile work output. Our novel platform can thus be utilized to quantitatively assess the mechanotransduction pathways that initiate tissue-level structural and functional remodeling in response to substrate stiffness.

Electrochemical aptasensor based on the dual-amplification of G-quadruplex horseradish peroxidase-mimicking DNAzyme and blocking reagent-horseradish peroxidase.

PubMed

Yuan, Yali; Gou, Xuxu; Yuan, Ruo; Chai, Yaqin; Zhuo, Ying; Mao, Li; Gan, Xianxue

2011-06-15

A simple electrochemical aptasensor for sensitive detection of thrombin was fabricated with G-quadruplex horseradish peroxidase-mimicking DNAzyme (hemin/G-quadruplex system) and blocking reagent-horseradish peroxidase as dual signal-amplification scheme. Gold nanoparticles (nano-Au) were firstly electrodeposited onto single wall nanotube (SWNT)-graphene modified electrode surface for the immobilization of electrochemical probe of nickel hexacyanoferrates nanoparticles (NiHCFNPs). Subsequently, another nano-Au layer was electrodeposited for further immobilization of thrombin aptamer (TBA), which later formed hemin/G-quadruplex system with hemin. Horseradish peroxidases (HRP) then served as blocking reagent to block possible remaining active sites and avoided the non-specific adsorption. In the presence of thrombin, the TBA binded to thrombin and the hemin released from the hemin/G-quadruplex electrocatalytic structure, increasing steric hindrance of the aptasensor and decomposing hemin/G-quadruplex electrocatalytic structure, which finally decreased the electrocatalytic efficiency of aptasensor toward H(2)O(2) in the presence of NiHCFNPs with a decreased electrochemical signal. On the basis of the synergistic amplifying action, a detection limit as low as 2 pM for thrombin was obtained. Copyright © 2011 Elsevier B.V. All rights reserved.

Pathogenesis of Human Enterovirulent Bacteria: Lessons from Cultured, Fully Differentiated Human Colon Cancer Cell Lines

PubMed Central

Liévin-Le Moal, Vanessa

2013-01-01

SUMMARY Hosts are protected from attack by potentially harmful enteric microorganisms, viruses, and parasites by the polarized fully differentiated epithelial cells that make up the epithelium, providing a physical and functional barrier. Enterovirulent bacteria interact with the epithelial polarized cells lining the intestinal barrier, and some invade the cells. A better understanding of the cross talk between enterovirulent bacteria and the polarized intestinal cells has resulted in the identification of essential enterovirulent bacterial structures and virulence gene products playing pivotal roles in pathogenesis. Cultured animal cell lines and cultured human nonintestinal, undifferentiated epithelial cells have been extensively used for understanding the mechanisms by which some human enterovirulent bacteria induce intestinal disorders. Human colon carcinoma cell lines which are able to express in culture the functional and structural characteristics of mature enterocytes and goblet cells have been established, mimicking structurally and functionally an intestinal epithelial barrier. Moreover, Caco-2-derived M-like cells have been established, mimicking the bacterial capture property of M cells of Peyer's patches. This review intends to analyze the cellular and molecular mechanisms of pathogenesis of human enterovirulent bacteria observed in infected cultured human colon carcinoma enterocyte-like HT-29 subpopulations, enterocyte-like Caco-2 and clone cells, the colonic T84 cell line, HT-29 mucus-secreting cell subpopulations, and Caco-2-derived M-like cells, including cell association, cell entry, intracellular lifestyle, structural lesions at the brush border, functional lesions in enterocytes and goblet cells, functional and structural lesions at the junctional domain, and host cellular defense responses. PMID:24006470

Bone tumor mimickers: A pictorial essay

PubMed Central

Mhuircheartaigh, Jennifer Ni; Lin, Yu-Ching; Wu, Jim S

2014-01-01

Focal lesions in bone are very common and many of these lesions are not bone tumors. These bone tumor mimickers can include numerous normal anatomic variants and non-neoplastic processes. Many of these tumor mimickers can be left alone, while others can be due to a significant disease process. It is important for the radiologist and clinician to be aware of these bone tumor mimickers and understand the characteristic features which allow discrimination between them and true neoplasms in order to avoid unnecessary additional workup. Knowing which lesions to leave alone or which ones require workup can prevent misdiagnosis and reduce patient anxiety. PMID:25114385

Human beta-globin mRNAs that harbor a nonsense codon are degraded in murine erythroid tissues to intermediates lacking regions of exon I or exons I and II that have a cap-like structure at the 5' termini.

PubMed Central

Lim, S K; Maquat, L E

1992-01-01

Previous studies have demonstrated that nonsense codons within beta zero-thalassemic or in vitro-mutagenized human beta-globin transgenes result in the production of mRNAs that are degraded abnormally rapidly in the cytoplasm of murine erythroid cells. As a consequence, three RNA degradative intermediates are formed that lack sequences from either exon I or exons I and II. We show here that the intermediates, like the full-length mRNA from which they derive and the endogenous murine beta maj-globin mRNA, bind to the anticap monoclonal antibody H-20 in a way that is competed by the cap analogue m7G and eliminated by prior exposure to tobacco acid pyrophosphatase. Furthermore, the intermediates, like the two full-length mRNAs, are resistant to a 5'----3' exonuclease activity isolated from HeLa cell nuclei that degrades uncapped but not capped ribopolymers. Based on these observations, the intermediates appear to possess a structure that is indistinguishable from the cap at the 5' end of mRNA, i.e. a methylated nucleoside that is linked to the RNA by a 5'-5' phosphodiester bond. Detection of the intermediates during murine development was concomitant with detection of full-length thalassemic mRNA. Intermediate production appears to be influenced by RNA structure as indicated by the products that derive from a beta zero-thalassemic beta-globin transgene harboring a structural alteration (a 4 bp deletion) that was larger than any of those previously studied. Images PMID:1324170

Enhanced picture of protein-folding intermediates using organic solvents in H/D exchange and quench-flow experiments

PubMed Central

Nishimura, Chiaki; Dyson, H. Jane; Wright, Peter E.

2005-01-01

Hydrogen/deuterium exchange followed by trapping of the labeled species in the aprotic solvent DMSO has been used to elucidate structure in both the burst-phase molten globule-folding intermediate of apomyoglobin and in an equilibrium intermediate that models the kinetic intermediate. Precise estimates can be made of exchange times in an interrupted exchange-out experiment at pH 4 followed by analysis in DMSO solution, giving extensive sequence-specific information about the structure of the equilibrium intermediate. In addition, the use of DMSO as a solvent for NMR measurements after quench-flow pH-pulse labeling experiments gives a greatly increased data set for the elucidation of the kinetic folding pathway. Interestingly, differences are observed in some regions of apomyoglobin between the equilibrium and kinetic intermediates. These differences are quantitative rather than qualitative; that is, the overall patterns of labeling and secondary structure formation remain similar between the two species. However, local differences are observed, which probably reflect the difference in the solution conditions for the equilibrium experiment (pH 4) vs. the kinetic experiment (pH 6) and the change in the status of the stabilizing hydrogen bond between the side chains of His-24 and His-119. PMID:15769860

Agarose Gel Electrophoresis Reveals Structural Fluidity of a Phage T3 DNA Packaging Intermediate

PubMed Central

Serwer, Philip; Wright, Elena T.

2012-01-01

We find a new aspect of DNA packaging-associated structural fluidity for phage T3 capsids. The procedure is (1) glutaraldehyde cross-linking of in vivo DNA packaging intermediates for stabilization of structure and then (2) determining of effective radius by two-dimensional agarose gel electrophoresis (2d-AGE). The intermediates are capsids with incompletely packaged DNA (ipDNA) and without an external DNA segment; these intermediates are called ipDNA-capsids. We initially increase production of ipDNA-capsids by raising NaCl concentration during in vivo DNA packaging. By 2d-AGE, we find a new state of contracted shell for some particles of one previously identified ipDNA-capsid. The contracted shell-state is found when ipDNA length/mature DNA length (F) is above 0.17, but not at lower F. Some contracted-shell ipDNA-capsids have the phage tail; others do not. The contracted-shell ipDNA-capsids are explained by premature DNA maturation cleavage that makes accessible a contracted-shell intermediate of a cycle of the T3 DNA packaging motor. The analysis of ipDNA-capsids, rather than intermediates with uncleaved DNA, provides a simplifying strategy for a complete biochemical analysis of in vivo DNA packaging. PMID:22222979

Structure of Mandelate Racemase with Bound Intermediate Analogues Benzohydroxamate and Cupferron†

PubMed Central

Lietzan, Adam D.; Nagar, Mitesh; Pellmann, Elise A.; Bourque, Jennifer R.; Bearne, Stephen L.; St Maurice, Martin

2012-01-01

Mandelate racemase (MR, EC 5.1.2.2) from Pseudomonas putida catalyzes the Mg2+-dependent interconversion of the enantiomers of mandelate, stabilizing the altered substrate in the transition state by 26 kcal/mol relative to the substrate in the ground state. To understand the origins of this binding discrimination, we solved the X-ray crystal structures of wild-type MR complexed with two analogues of the putative aci-carboxylate intermediate, benzohydroxamate and cupferron, to 2.2-Å resolution. Benzohydroxamate is shown to be a reasonable mimic of the transition state/intermediate since its binding affinity to 21 MR variants correlates well with changes in the free energy of transition state stabilization afforded by these variants. Both benzohydroxamate and cupferron chelate the active site divalent metal ion and are bound in a conformation with the phenyl ring coplanar with the hydroxamate and diazeniumdiolate moieties, respectively. Structural overlays of MR complexed with benzohydroxamate, cupferron, and the ground state analogue (S)-atrolacatate reveal that the para-carbon of the substrate phenyl ring moves by 0.8–1.2 Å between the ground state and intermediate state, consistent with the proposal that the phenyl ring moves during MR catalysis while the polar groups remain relatively fixed. Although the overall protein structure of MR with bound intermediate analogues is very similar to MR with bound (S)-atrolactate, the intermediate-Mg2+ distance shortens, suggesting a tighter complex with the catalytic Mg2+. In addition, Tyr 54 moves nearer to the phenyl ring of the bound intermediate analogues, contributing to an overall constriction of the active site cavity. However, site-directed mutagenesis experiments revealed that the role of Tyr 54 in MR catalysis is relatively minor, suggesting that alterations in enzyme structure that contribute to discrimination between the altered substrate in the transition state and the ground state by this proficient enzyme are extremely subtle. PMID:22264153

Reduced reward-related neural response to mimicry in individuals with autism.

PubMed

Hsu, Chun-Ting; Neufeld, Janina; Chakrabarti, Bhismadev

2018-03-01

Mimicry is a facilitator of social bonds in humans, from infancy. This facilitation is made possible through changing the reward value of social stimuli; for example, we like and affiliate more with people who mimic us. Autism spectrum disorders (ASD) are marked by difficulties in forming social bonds. In this study, we investigate whether the reward-related neural response to being mimicked is altered in individuals with ASD, using a simple conditioning paradigm. Multiple studies in humans and nonhuman primates have established a crucial role for the ventral striatal (VS) region in responding to rewards. In this study, adults with ASD and matched controls first underwent a conditioning task outside the scanner, where they were mimicked by one face and 'anti-mimicked' by another. In the second part, participants passively viewed the conditioned faces in a 3T MRI scanner using a multi-echo sequence. The differential neural response towards mimicking vs. anti-mimicking faces in the VS was tested for group differences as well as an association with self-reported autistic traits. Multiple regression analysis revealed lower left VS response to mimicry (mimicking > anti-mimicking faces) in the ASD group compared to controls. The VS response to mimicry was negatively correlated with autistic traits across the whole sample. Our results suggest that for individuals with ASD and high autistic traits, being mimicked is associated with lower reward-related neural response. This result points to a potential mechanism underlying the difficulties reported by many of individuals with ASD in building social rapport. © 2017 The Authors. European Journal of Neuroscience published by Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Imparting albumin-binding affinity to a human protein by mimicking the contact surface of a bacterial binding protein.

PubMed

Oshiro, Satoshi; Honda, Shinya

2014-04-18

Attachment of a bacterial albumin-binding protein module is an attractive strategy for extending the plasma residence time of protein therapeutics. However, a protein fused with such a bacterial module could induce unfavorable immune reactions. To address this, we designed an alternative binding protein by imparting albumin-binding affinity to a human protein using molecular surface grafting. The result was a series of human-derived 6 helix-bundle proteins, one of which specifically binds to human serum albumin (HSA) with adequate affinity (KD = 100 nM). The proteins were designed by transferring key binding residues of a bacterial albumin-binding module, Finegoldia magna protein G-related albumin-binding domain (GA) module, onto the human protein scaffold. Despite 13-15 mutations, the designed proteins maintain the original secondary structure by virtue of careful grafting based on structural informatics. Competitive binding assays and thermodynamic analyses of the best binders show that the binding mode resembles that of the GA module, suggesting that the contacting surface of the GA module is mimicked well on the designed protein. These results indicate that the designed protein may act as an alternative low-risk binding module to HSA. Furthermore, molecular surface grafting in combination with structural informatics is an effective approach for avoiding deleterious mutations on a target protein and for imparting the binding function of one protein onto another.

Interwoven Aligned Conductive Nanofiber Yarn/Hydrogel Composite Scaffolds for Engineered 3D Cardiac Anisotropy.

PubMed

Wu, Yaobin; Wang, Ling; Guo, Baolin; Ma, Peter X

2017-06-27

Mimicking the anisotropic cardiac structure and guiding 3D cellular orientation play a critical role in designing scaffolds for cardiac tissue regeneration. Significant advances have been achieved to control cellular alignment and elongation, but it remains an ongoing challenge for engineering 3D cardiac anisotropy using these approaches. Here, we present a 3D hybrid scaffold based on aligned conductive nanofiber yarns network (NFYs-NET, composition: polycaprolactone, silk fibroin, and carbon nanotubes) within a hydrogel shell for mimicking the native cardiac tissue structure, and further demonstrate their great potential for engineering 3D cardiac anisotropy for cardiac tissue engineering. The NFYs-NET structures are shown to control cellular orientation and enhance cardiomyocytes (CMs) maturation. 3D hybrid scaffolds were then fabricated by encapsulating NFYs-NET layers within hydrogel shell, and these 3D scaffolds performed the ability to promote aligned and elongated CMs maturation on each layer and individually control cellular orientation on different layers in a 3D environment. Furthermore, endothelialized myocardium was constructed by using this hybrid strategy via the coculture of CMs on NFYs-NET layer and endothelial cells within hydrogel shell. Therefore, these 3D hybrid scaffolds, containing NFYs-NET layer inducing cellular orientation, maturation, and anisotropy and hydrogel shell providing a suitable 3D environment for endothelialization, has great potential in engineering 3D cardiac anisotropy.

Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase

NASA Astrophysics Data System (ADS)

Minges, Alexander; Ciupka, Daniel; Winkler, Christian; Höppner, Astrid; Gohlke, Holger; Groth, Georg

2017-03-01

Pyruvate phosphate dikinase (PPDK) is a vital enzyme in cellular energy metabolism catalyzing the ATP- and Pi-dependent formation of phosphoenolpyruvate from pyruvate in C4 -plants, but the reverse reaction forming ATP in bacteria and protozoa. The multi-domain enzyme is considered an efficient molecular machine that performs one of the largest single domain movements in proteins. However, a comprehensive understanding of the proposed swiveling domain motion has been limited by not knowing structural intermediates or molecular dynamics of the catalytic process. Here, we present crystal structures of PPDKs from Flaveria, a model genus for studying the evolution of C4 -enzymes from phylogenetic ancestors. These structures resolve yet unknown conformational intermediates and provide the first detailed view on the large conformational transitions of the protein in the catalytic cycle. Independently performed unrestrained MD simulations and configurational free energy calculations also identified these intermediates. In all, our experimental and computational data reveal strict coupling of the CD swiveling motion to the conformational state of the NBD. Moreover, structural asymmetries and nucleotide binding states in the PPDK dimer support an alternate binding change mechanism for this intriguing bioenergetic enzyme.

Identification and characterization of the intermediate phase in hybrid organic-inorganic MAPbI3 perovskite.

PubMed

Guo, Xin; McCleese, Christopher; Kolodziej, Charles; Samia, Anna C S; Zhao, Yixin; Burda, Clemens

2016-03-07

Perovskite films were prepared using single step solution deposition at different annealing temperatures and annealing times. The crystal structure, phases and grain size were investigated with XRD, XPS and SEM/EDX. The prepared films show a typical orientation of tetragonal perovskite phase and a gradual transition at room temperature from the yellow intermediate phase to the black perovskite phase. Films with high purity were obtained by sintering at 100 °C. In addition, the chemical composition and crystal structure of intermediate phase were investigated in detail. FTIR, UV-vis and NMR spectra revealed the occurance of DMF complexes. Interestingly, the intermediate phase could be transformed to the black perovskite phase upon X-ray irradiation. In addition, the recovery of the aged perovskite films from a yellow intermediate phase back to the black perovskite was shown to be viable via heating and X-ray irradiation.

Characterization of a transient +2 sulfur oxidation state intermediate from the oxidation of aqueous sulfide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vairavmurthy, M.A.; Zhou, Weiqing

1995-04-01

The oxidation H{sub 2}S to sulfate involves a net transfer of eight electrons and occurs through the formation of several partially oxidized intermediates with oxidation states ranging from {minus}1 to +5. Known intermediates include elemental sulfur (oxidation state 0), polysulfides (outer sulfur: {minus}1, inner sulfur: 0), sulfite (+4) and thiosulfate (outer sulfur: {minus}1, inner sulfur: +5). A noticeable gap in this series of intermediates is that of a +2 sulfur oxidation state oxoacid/oxoanion species, which was never detected experimentally. Here, we present evidence of the transient existence of +2 oxidation state intermediate in the Ni(II)-catalyzed oxidation of aqueous sulfide. X-raymore » absorption near-edge structure (XANES) spectroscopy and Fourier-transform-infrared (FT-IR) spectroscopy were used to characterize this species; they suggest that it has a sulfoxylate ion (SO{sub 2}{sup 2{minus}}) structure.« less

Enzyme-mimicking polymer brush-functionalized surface for combating biomaterial-associated infections

NASA Astrophysics Data System (ADS)

Jiang, Rujian; Xin, Zhirong; Xu, Shiai; Shi, Hengchong; Yang, Huawei; Song, Lingjie; Yan, Shunjie; Luan, Shifang; Yin, Jinghua; Khan, Ather Farooq; Li, Yonggang

2017-11-01

Biomaterial-associated infections critically compromise the functionality and performance of the medical devices, and pose a serious threat to human healthcare. Recently, natural DNase enzyme has been recognized as a potent material to prevent bacterial adhesion and biofilm formation. However, the vulnerability of DNase dramatically limits its long-term performance in antibacterial applications. In this work, DNase-mimicking polymer brushes were constructed to mimic the DNA-cleavage activity as well as the macromolecular scaffold of the natural DNase. The bacteria repellent efficacy of DNase-mimicking polymer brush-functionalized surface was comparable to that of the DNase-functionalized surface. More importantly, due to their inherent stability, DNase-mimicking polymer brushes presented the much better performance in inhibiting bacterial biofilm development for prolonged periods of time, as compared to the natural DNase. The as-developed DNase-mimicking polymer brush-functionalized surface presents a promising approach to combat biomaterial-associated infections.

Multi-modality gellan gum-based tissue-mimicking phantom with targeted mechanical, electrical, and thermal properties.

PubMed

Chen, Roland K; Shih, A J

2013-08-21

This study develops a new class of gellan gum-based tissue-mimicking phantom material and a model to predict and control the elastic modulus, thermal conductivity, and electrical conductivity by adjusting the mass fractions of gellan gum, propylene glycol, and sodium chloride, respectively. One of the advantages of gellan gum is its gelling efficiency allowing highly regulable mechanical properties (elastic modulus, toughness, etc). An experiment was performed on 16 gellan gum-based tissue-mimicking phantoms and a regression model was fit to quantitatively predict three material properties (elastic modulus, thermal conductivity, and electrical conductivity) based on the phantom material's composition. Based on these material properties and the regression model developed, tissue-mimicking phantoms of porcine spinal cord and liver were formulated. These gellan gum tissue-mimicking phantoms have the mechanical, thermal, and electrical properties approximately equivalent to those of the spinal cord and the liver.

The Mechanism of Viral Replication. Structure of Replication Complexes of Encephalomyocarditis Virus

PubMed Central

Thach, Sigrid S.; Dobbertin, Darrell; Lawrence, Charles; Golini, Fred; Thach, Robert E.

1974-01-01

The structure of the purified replicative intermediate of encephalomyocarditis virus was determined by electron microscopy. Approximately 80% of the replicative intermediate complexes were characterized by a filament of double-stranded RNA of widely variable length, which had a “bush” of single-stranded RNA at one end. In many examples one or more additional single-stranded bushes were appended internally to the double-stranded RNA filament. These results support the view that before deproteinization, replicative intermediate contains little if any double-stranded RNA. Images PMID:4366773

Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds

PubMed Central

Popolan-Vaida, Denisia M.; Chen, Bingjie; Moshammer, Kai; Mohamed, Samah Y.; Wang, Heng; Sioud, Salim; Raji, Misjudeen A.; Kohse-Höinghaus, Katharina; Hansen, Nils; Dagaut, Philippe; Leone, Stephen R.

2017-01-01

Decades of research on the autooxidation of organic compounds have provided fundamental and practical insights into these processes; however, the structure of many key autooxidation intermediates and the reactions leading to their formation still remain unclear. This work provides additional experimental evidence that highly oxygenated intermediates with one or more hydroperoxy groups are prevalent in the autooxidation of various oxygenated (e.g., alcohol, aldehyde, keto compounds, ether, and ester) and nonoxygenated (e.g., normal alkane, branched alkane, and cycloalkane) organic compounds. These findings improve our understanding of autooxidation reaction mechanisms that are routinely used to predict fuel ignition and oxidative stability of liquid hydrocarbons, while also providing insights relevant to the formation mechanisms of tropospheric aerosol building blocks. The direct observation of highly oxygenated intermediates for the autooxidation of alkanes at 500–600 K builds upon prior observations made in atmospheric conditions for the autooxidation of terpenes and other unsaturated hydrocarbons; it shows that highly oxygenated intermediates are stable at conditions above room temperature. These results further reveal that highly oxygenated intermediates are not only accessible by chemical activation but also by thermal activation. Theoretical calculations on H-atom migration reactions are presented to rationalize the relationship between the organic compound’s molecular structure (n-alkane, branched alkane, and cycloalkane) and its propensity to produce highly oxygenated intermediates via extensive autooxidation of hydroperoxyalkylperoxy radicals. Finally, detailed chemical kinetic simulations demonstrate the influence of these additional reaction pathways on the ignition of practical fuels. PMID:29183984

Engineering Human TMJ Discs with Protein-Releasing 3D-Printed Scaffolds.

PubMed

Legemate, K; Tarafder, S; Jun, Y; Lee, C H

2016-07-01

The temporomandibular joint (TMJ) disc is a heterogeneous fibrocartilaginous tissue positioned between the mandibular condyle and glenoid fossa of the temporal bone, with important roles in TMJ functions. Tissue engineering TMJ discs has emerged as an alternative approach to overcoming limitations of current treatments for TMJ disorders. However, the anisotropic collagen orientation and inhomogeneous fibrocartilaginous matrix distribution present challenges in the tissue engineering of functional TMJ discs. Here, we developed 3-dimensional (3D)-printed anatomically correct scaffolds with region-variant microstrand alignment, mimicking anisotropic collagen alignment in the TMJ disc and corresponding mechanical properties. Connective tissue growth factor (CTGF) and transforming growth factor beta 3 (TGFβ3) were then delivered in the scaffolds by spatially embedding CTGF- or TGFβ3-encapsulated microspheres (µS) to reconstruct the regionally variant fibrocartilaginous matrix in the native TMJ disc. When cultured with human mesenchymal stem/progenitor cells (MSCs) for 6 wk, 3D-printed scaffolds with CTGF/TGFβ3-µS resulted in a heterogeneous fibrocartilaginous matrix with overall distribution of collagen-rich fibrous structure in the anterior/posterior (AP) bands and fibrocartilaginous matrix in the intermediate zone, reminiscent of the native TMJ disc. High dose of CTGF/TGFβ3-µS (100 mg µS/g of scaffold) showed significantly more collagen II and aggrecan in the intermediate zone than a low dose (50 mg µS/g of scaffold). Similarly, a high dose of CTGF/TGFβ3-µS yielded significantly higher collagen I expression in the AP bands compared with the low-dose and empty µS. From stress relaxation tests, the ratio of relaxation modulus to instantaneous modulus was significantly smaller with CTGF/TGFβ3-µS than empty µS. Similarly, a significantly higher coefficient of viscosity was achieved with the high dose of CTGF/TGFβ3-µS compared with the low-dose and empty µS, suggesting the dose effect of CTGF and TGFβ3 on fibrocartilage formation. Together, our findings may represent an efficient approach to engineering the TMJ disc graft with anisotropic scaffold microstructure, heterogeneous fibrocartilaginous matrix, and region-dependent viscoelastic properties. © International & American Associations for Dental Research 2016.

Structure determination of a key intermediate of the enantioselective Pd complex catalyzed allylic substitution reaction

PubMed

Junker; Reif; Steinhagen; Junker; Felli; Reggelin; Griesinger

2000-09-01

The structure of a catalytic intermediate with important implications for the interpretation of the stereochemical outcome of the palladium complex catalyzed allylic substitution with phosphino-oxazoline (PHOX) ligands is determined by liquid state NMR. The complex displays a novel structure that is highly distorted compared with other palladium eta2-olefin complexes known so far. The structure has been determined from nuclear overhauser data (NOE), scalar coupling constants, and long range projection angle restraints derived from dipole dipole cross-correlated relaxation of multiple quantum coherence. The latter restraints have been implemented into a distance geometry protocol. The projection angle restraints yield a higher precision in the determination of the relative orientation of the two molecular moieties and are essential to provide an exact structural definition of the olefinic part of the catalytic intermediate with respect to the ligand.

Combined PDF and Rietveld studies of ADORable zeolites and the disordered intermediate IPC-1P.

PubMed

Morris, Samuel A; Wheatley, Paul S; Položij, Miroslav; Nachtigall, Petr; Eliášová, Pavla; Čejka, Jiří; Lucas, Tim C; Hriljac, Joseph A; Pinar, Ana B; Morris, Russell E

2016-09-28

The disordered intermediate of the ADORable zeolite UTL has been structurally confirmed using the pair distribution function (PDF) technique. The intermediate, IPC-1P, is a disordered layered compound formed by the hydrolysis of UTL in 0.1 M hydrochloric acid solution. Its structure is unsolvable by traditional X-ray diffraction techniques. The PDF technique was first benchmarked against high-quality synchrotron Rietveld refinements of IPC-2 (OKO) and IPC-4 (PCR) - two end products of IPC-1P condensation that share very similar structural features. An IPC-1P starting model derived from density functional theory was used for the PDF refinement, which yielded a final fit of Rw = 18% and a geometrically reasonable structure. This confirms the layers do stay intact throughout the ADOR process and shows PDF is a viable technique for layered zeolite structure determination.

Bio-mimicking galactose oxidase and hemocyanin, two dioxygen-processing copper proteins.

PubMed

Gamez, Patrick; Koval, Iryna A; Reedijk, Jan

2004-12-21

The modelling of the active sites of metalloproteins is one of the most challenging tasks in bio-inorganic chemistry. Copper proteins form part of this stimulating field of research as copper enzymes are mainly involved in oxidation bio-reactions. Thus, the understanding of the structure-function relationship of their active sites will allow the design of effective and environmental friendly oxidation catalysts. This perspective illustrates some outstanding structural and functional synthetic models of the active site of copper proteins, with special attention given to models of galactose oxidase and hemocyanin.

Structure and dynamics of human vimentin intermediate filament dimer and tetramer in explicit and implicit solvent models.

PubMed

Qin, Zhao; Buehler, Markus J

2011-01-01

Intermediate filaments, in addition to microtubules and microfilaments, are one of the three major components of the cytoskeleton in eukaryotic cells, and play an important role in mechanotransduction as well as in providing mechanical stability to cells at large stretch. The molecular structures, mechanical and dynamical properties of the intermediate filament basic building blocks, the dimer and the tetramer, however, have remained elusive due to persistent experimental challenges owing to the large size and fibrillar geometry of this protein. We have recently reported an atomistic-level model of the human vimentin dimer and tetramer, obtained through a bottom-up approach based on structural optimization via molecular simulation based on an implicit solvent model (Qin et al. in PLoS ONE 2009 4(10):e7294, 9). Here we present extensive simulations and structural analyses of the model based on ultra large-scale atomistic-level simulations in an explicit solvent model, with system sizes exceeding 500,000 atoms and simulations carried out at 20 ns time-scales. We report a detailed comparison of the structural and dynamical behavior of this large biomolecular model with implicit and explicit solvent models. Our simulations confirm the stability of the molecular model and provide insight into the dynamical properties of the dimer and tetramer. Specifically, our simulations reveal a heterogeneous distribution of the bending stiffness along the molecular axis with the formation of rather soft and highly flexible hinge-like regions defined by non-alpha-helical linker domains. We report a comparison of Ramachandran maps and the solvent accessible surface area between implicit and explicit solvent models, and compute the persistence length of the dimer and tetramer structure of vimentin intermediate filaments for various subdomains of the protein. Our simulations provide detailed insight into the dynamical properties of the vimentin dimer and tetramer intermediate filament building blocks, which may guide the development of novel coarse-grained models of intermediate filaments, and could also help in understanding assembly mechanisms.

Crystal structure and magnetic properties of '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' containing residual {alpha}-Fe prepared by low-temperature ammonia nitridation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamashita, S.; Masubuchi, Y.; Nakazawa, Y.

2012-10-15

Slight enhancement of saturation magnetization to 219 A m{sup 2} kg{sup -1} was observed from 199 A m{sup 2} kg{sup -1} for the original {alpha}-Fe on the intermediate nitrided mixture of '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' with residual {alpha}-Fe among the low temperature ammonia nitridation products under 5 T magnetic field at room temperature. The value changed not linearly against the yield as had been expected. Crystal structure refinement indicated that the phase similar to {alpha} Prime Prime -Fe{sub 16}N{sub 2} had deviations on its lattice constants and positional parameters, compared to previously reported values for {alpha} Prime Primemore » -Fe{sub 16}N{sub 2}. Spin-polarized total energy calculations were performed using the projector-augmented wave method as implemented in the Vienna ab-initio simulation package (VASP) to calculate magnetic moment on the refined crystal structure of the intermediate '{alpha} Prime Prime -Fe{sub 16}N{sub 2}'. The calculations supported the observed magnetization enhancement in the intermediate nitridation product. - Graphical abstract: Crystal structural parameters slightly change in the intermediate nitrided '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' from those in {alpha} Prime Prime -Fe{sub 16}N{sub 2} to show the magnetization maxima in the mixture of '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' and the residual {alpha}-F. Highlights: Black-Right-Pointing-Pointer Larger magnetization was observed than the value of Fe{sub 16}N{sub 2} on its intermediate nitrided mixture with residual {alpha}-Fe. Black-Right-Pointing-Pointer The enhancement was related to the crystal structural deviation from Fe{sub 16}N{sub 2} on the intermediate nitride. Black-Right-Pointing-Pointer It was supported by spin-polarized total energy calculation using the deviated structure.« less

A thiamin-bound, pre-decarboxylation reaction intermediate analogue in the pyruvate dehydrogenase E1 subunit induces large scale disorder-to-order transformations in the enzyme and reveals novel structural features in the covalently bound adduct.

PubMed

Arjunan, Palaniappa; Sax, Martin; Brunskill, Andrew; Chandrasekhar, Krishnamoorthy; Nemeria, Natalia; Zhang, Sheng; Jordan, Frank; Furey, William

2006-06-02

The crystal structure of the E1 component from the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDHc) has been determined with phosphonolactylthiamin diphosphate (PLThDP) in its active site. PLThDP serves as a structural and electrostatic analogue of the natural intermediate alpha-lactylthiamin diphosphate (LThDP), in which the carboxylate from the natural substrate pyruvate is replaced by a phosphonate group. This represents the first example of an experimentally determined, three-dimensional structure of a thiamin diphosphate (ThDP)-dependent enzyme containing a covalently bound, pre-decarboxylation reaction intermediate analogue and should serve as a model for the corresponding intermediates in other ThDP-dependent decarboxylases. Regarding the PDHc-specific reaction, the presence of PLThDP induces large scale conformational changes in the enzyme. In conjunction with the E1-PLThDP and E1-ThDP structures, analysis of a H407A E1-PLThDP variant structure shows that an interaction between His-407 and PLThDP is essential for stabilization of two loop regions in the active site that are otherwise disordered in the absence of intermediate analogue. This ordering completes formation of the active site and creates a new ordered surface likely involved in interactions with the lipoyl domains of E2s within the PDHc complex. The tetrahedral intermediate analogue is tightly held in the active site through direct hydrogen bonds to residues His-407, Tyr-599, and His-640 and reveals a new, enzyme-induced, strain-related feature that appears to aid in the decarboxylation process. This feature is almost certainly present in all ThDP-dependent decarboxylases; thus its inclusion in our understanding of general thiamin catalysis is important.

Dysfunctions at human intestinal barrier by water-borne protozoan parasites: lessons from cultured human fully differentiated colon cancer cell lines.

PubMed

Liévin-Le Moal, Vanessa

2013-06-01

Some water-borne protozoan parasites induce diseases through their membrane-associated functional structures and virulence factors that hijack the host cellular molecules and signalling pathways leading to structural and functional lesions in the intestinal barrier. In this Microreview we analyse the insights on the mechanisms of pathogenesis of Entamoeba intestinalis, Giardia and Cryptosporidium observed in the human colon carcinoma fully differentiated colon cancer cell lines, cell subpopulations and clones expressing the structural and functional characteristics of highly specialized fully differentiated epithelial cells lining the intestinal epithelium and mimicking structurally and functionally an intestinal barrier. © 2013 John Wiley & Sons Ltd.

Uncoupling protein 2 deficiency mimics the effects of hypoxia and endoplasmic reticulum stress on mitochondria and triggers pseudohypoxic pulmonary vascular remodeling and pulmonary hypertension.

PubMed

Dromparis, Peter; Paulin, Roxane; Sutendra, Gopinath; Qi, Andrew C; Bonnet, Sébastien; Michelakis, Evangelos D

2013-07-05

Mitochondrial signaling regulates both the acute and the chronic response of the pulmonary circulation to hypoxia, and suppressed mitochondrial glucose oxidation contributes to the apoptosis-resistance and proliferative diathesis in the vascular remodeling in pulmonary hypertension. Hypoxia directly inhibits glucose oxidation, whereas endoplasmic reticulum (ER)-stress can indirectly inhibit glucose oxidation by decreasing mitochondrial calcium (Ca²⁺m levels). Both hypoxia and ER stress promote proliferative pulmonary vascular remodeling. Uncoupling protein 2 (UCP2) has been shown to conduct calcium from the ER to mitochondria and suppress mitochondrial function. We hypothesized that UCP2 deficiency reduces Ca²⁺m in pulmonary artery smooth muscle cells (PASMCs), mimicking the effects of hypoxia and ER stress on mitochondria in vitro and in vivo, promoting normoxic hypoxia inducible factor-1α activation and pulmonary hypertension. Ucp2 knockout (KO)-PASMCs had lower mitochondrial calcium than Ucp2 wildtype (WT)-PASMCs at baseline and during histamine-stimulated ER-Ca²⁺ release. Normoxic Ucp2KO-PASMCs had mitochondrial hyperpolarization, lower Ca²⁺-sensitive mitochondrial enzyme activity, reduced levels of mitochondrial reactive oxygen species and Krebs' cycle intermediates, and increased resistance to apoptosis, mimicking the hypoxia-induced changes in Ucp2WT-PASMC. Ucp2KO mice spontaneously developed pulmonary vascular remodeling and pulmonary hypertension and exhibited a pseudohypoxic state with pulmonary vascular and systemic hypoxia inducible factor-1α activation (increased hematocrit), not exacerbated further by chronic hypoxia. This first description of the role of UCP2 in oxygen sensing and in pulmonary hypertension vascular remodeling may open a new window in biomarker and therapeutic strategies.

Intermediate phases in some rare earth-ruthenium systems

NASA Technical Reports Server (NTRS)

Sharifrazi, P.; Raman, A.; Mohanty, R. C.

1984-01-01

The phase equilibria and crystal structures of intermediate phases were investigated in eight representative RE-Ru systems using powder X-ray diffraction and metallographic techniques. The Fe3C, Mn5C2 and Er5Ru3 structures occur in all but the Ce-Ru systems. Phases analogous to Er5Ru3 possess an unknown crystal structure similar to Er5Rh3(I). MgCu2 and MgZn2 type Laves phases are encountered in the light rare earth and heavy rare earth systems, respectively, and RERu2 phases, where RE = Nd and Sm, possess both the Laves phase structures. An intermediate phase, NdRu, with an unknown structure, occurs only in the Nd-Ru system. A bcc structure with 40 atoms per unit cell is encountered in the phases Er3Ru2 and Y3Ru2. The behavior of cerium in Ce-Ru alloys is unique in that four unidentified structures, not encountered in other RE-Ru systems, have been encountered. Also a phase designated as Ce3Ru is found with the Th7Fe3 type structure.

Non-harmful insertion of data mimicking computer network attacks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neil, Joshua Charles; Kent, Alexander; Hash, Jr, Curtis Lee

Non-harmful data mimicking computer network attacks may be inserted in a computer network. Anomalous real network connections may be generated between a plurality of computing systems in the network. Data mimicking an attack may also be generated. The generated data may be transmitted between the plurality of computing systems using the real network connections and measured to determine whether an attack is detected.

Solution structures and backbone dynamics of Escherichia coli rhodanese PspE in its sulfur-free and persulfide-intermediate forms: implications for the catalytic mechanism of rhodanese.

PubMed

Li, Hongwei; Yang, Fan; Kang, Xue; Xia, Bin; Jin, Changwen

2008-04-15

Rhodanese catalyzes the sulfur-transfer reaction that transfers sulfur from thiosulfate to cyanide by a double-displacement mechanism, in which an active cysteine residue plays a central role. Previous studies indicated that the phage-shock protein E (PspE) from Escherichia coli is a rhodanese composed of a single active domain and is the only accessible rhodanese among the three single-domain rhodaneses in E. coli. To understand the catalytic mechanism of rhodanese at the molecular level, we determined the solution structures of the sulfur-free and persulfide-intermediate forms of PspE by nuclear magnetic resonance (NMR) spectroscopy and identified the active site by NMR titration experiments. To obtain further insights into the catalytic mechanism, we studied backbone dynamics by NMR relaxation experiments. Our results demonstrated that the overall structures in both sulfur-free and persulfide-intermediate forms are highly similar, suggesting that no significant conformational changes occurred during the catalytic reaction. However, the backbone dynamics revealed that the motional properties of PspE in its sulfur-free form are different from the persulfide-intermediate state. The conformational exchanges are largely enhanced in the persulfide-intermediate form of PspE, especially around the active site. The present structural and biochemical studies in combination with backbone dynamics provide further insights in understanding the catalytic mechanism of rhodanese.

Underwater flight by the planktonic sea butterfly.

PubMed

Murphy, David W; Adhikari, Deepak; Webster, Donald R; Yen, Jeannette

2016-02-01

In a remarkable example of convergent evolution, we show that the zooplanktonic sea butterfly Limacina helicina 'flies' underwater in the same way that very small insects fly in the air. Both sea butterflies and flying insects stroke their wings in a characteristic figure-of-eight pattern to produce lift, and both generate extra lift by peeling their wings apart at the beginning of the power stroke (the well-known Weis-Fogh 'clap-and-fling' mechanism). It is highly surprising to find a zooplankter 'mimicking' insect flight as almost all zooplankton swim in this intermediate Reynolds number range (Re=10-100) by using their appendages as paddles rather than wings. The sea butterfly is also unique in that it accomplishes its insect-like figure-of-eight wing stroke by extreme rotation of its body (what we call 'hyper-pitching'), a paradigm that has implications for micro aerial vehicle (MAV) design. No other animal, to our knowledge, pitches to this extent under normal locomotion. © 2016. Published by The Company of Biologists Ltd.

Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans

PubMed Central

Watson, Emma; Olin-Sandoval, Viridiana; Hoy, Michael J; Li, Chi-Hua; Louisse, Timo; Yao, Victoria; Mori, Akihiro; Holdorf, Amy D; Troyanskaya, Olga G; Ralser, Markus; Walhout, Albertha JM

2016-01-01

Metabolic network rewiring is the rerouting of metabolism through the use of alternate enzymes to adjust pathway flux and accomplish specific anabolic or catabolic objectives. Here, we report the first characterization of two parallel pathways for the breakdown of the short chain fatty acid propionate in Caenorhabditis elegans. Using genetic interaction mapping, gene co-expression analysis, pathway intermediate quantification and carbon tracing, we uncover a vitamin B12-independent propionate breakdown shunt that is transcriptionally activated on vitamin B12 deficient diets, or under genetic conditions mimicking the human diseases propionic- and methylmalonic acidemia, in which the canonical B12-dependent propionate breakdown pathway is blocked. Our study presents the first example of transcriptional vitamin-directed metabolic network rewiring to promote survival under vitamin deficiency. The ability to reroute propionate breakdown according to B12 availability may provide C. elegans with metabolic plasticity and thus a selective advantage on different diets in the wild. DOI: http://dx.doi.org/10.7554/eLife.17670.001 PMID:27383050

Cystic echinococcosis: a disease mimicking cancer in a non-endemic country report of two cases.

PubMed

Comrnejo-Juárez, P; Espinosa-Altamirano, A; Ibarra-del-Río, M; Pacheco-Bravo, I; Volkow-Fernández, P

2013-03-01

Echinococcosis is a parasitic disease that involves dogs as definitive host and sheep as intermediate host. Humans become infected incidentally through fecal-oral contact, particularly in the course of playful and close contact with an infected dog. Mexico is considered a region that is virtually free of cystic echinoccocosis. This manuscript describes two cases that were referred to a tertiary-care oncology hospital with a diagnosis of cancer. In one case, the presumptive diagnosis was liver cancer because abdominal ultrasonography revealed a low-density mass in the right hepatic lobe. Drainage was performed and cytologic examination of the fluid showed multiple Echinococcus cyst as well as prostoscolex. The case was resolved with percutaneous drainage and administration of albendazole for two months. In the second case, the patient was referred with a diagnosis of disseminated cervical cancer A cyst was identified in the upper right lung lobe; a diagnostic puncture was performed showing an Echinococcus cyst. This resolved solely with two months of albendazole administration.

Chitosan derivatives targeting lipid bilayers: Synthesis, biological activity and interaction with model membranes.

PubMed

Martins, Danubia Batista; Nasário, Fábio Domingues; Silva-Gonçalves, Laiz Costa; de Oliveira Tiera, Vera Aparecida; Arcisio-Miranda, Manoel; Tiera, Marcio José; Dos Santos Cabrera, Marcia Perez

2018-02-01

The antimicrobial activity of chitosan and derivatives to human and plant pathogens represents a high-valued prospective market. Presently, two low molecular weight derivatives, endowed with hydrophobic and cationic character at different ratios were synthesized and characterized. They exhibit antimicrobial activity and increased performance in relation to the intermediate and starting compounds. However, just the derivative with higher cationic character showed cytotoxicity towards human cervical carcinoma cells. Considering cell membranes as targets, the mode of action was investigated through the interaction with model lipid vesicles mimicking bacterial, tumoral and erythrocyte membranes. Intense lytic activity and binding are demonstrated for both derivatives in anionic bilayers. The less charged compound exhibits slightly improved selectivity towards bacterial model membranes, suggesting that balancing its hydrophobic/hydrophilic character may improve efficiency. Observing the aggregation of vesicles, we hypothesize that the "charge cluster mechanism", ascribed to some antimicrobial peptides, could be applied to these chitosan derivatives. Copyright © 2017 Elsevier Ltd. All rights reserved.

Induced responses to herbivory and jasmonate in three milkweed species.

PubMed

Rasmann, Sergio; Johnson, M Daisy; Agrawal, Anurag A

2009-11-01

We studied constitutive and induced defensive traits (latex exudation, cardenolides, proteases, and C/N ratio) and resistance to monarch caterpillars (Danaus plexippus) in three closely related milkweed species (Asclepias angustifolia, A. barjoniifolia and A. fascicularis). All traits showed significant induction in at least one of the species. Jasmonate application only partially mimicked the effect of monarch feeding. We found some correspondence between latex and cardenolide content and reduced larval growth. Larvae fed cut leaves of A. angustifolia grew better than larvae fed intact plants. Addition of the cardenolide digitoxin to cut leaves reduced larval growth but ouabain (at the same concentration) had no effect. We, thus, confirm that latex and cardenolides are major defenses in milkweeds, effective against a specialist herbivore. Other traits such as proteases and C/N ratio additionally may be integrated in the defense scheme of those plants. Induction seems to play an important role in plants that have an intermediate level of defense, and we advocate incorporating induction as an additional axis of the plant defense syndrome hypothesis.

Time-resolved distance determination by tryptophan fluorescence quenching: probing intermediates in membrane protein folding.

PubMed

Kleinschmidt, J H; Tamm, L K

1999-04-20

The mechanism of insertion and folding of an integral membrane protein has been investigated with the beta-barrel forming outer membrane protein A (OmpA) of Escherichia coli. This work describes a new approach to this problem by combining structural information obtained from tryptophan fluorescence quenching at different depths in the lipid bilayer with the kinetics of the refolding process. Experiments carried out over a temperature range between 2 and 40 degrees C allowed us to detect, trap, and characterize previously unidentified folding intermediates on the pathway of OmpA insertion and folding into lipid bilayers. Three membrane-bound intermediates were found in which the average distances of the Trps were 14-16, 10-11, and 0-5 A, respectively, from the bilayer center. The first folding intermediate is stable at 2 degrees C for at least 1 h. A second intermediate has been isolated at temperatures between 7 and 20 degrees C. The Trps move 4-5 A closer to the center of the bilayer at this stage. Subsequently, in an intermediate that is observable at 26-28 degrees C, the Trps move another 5-10 A closer to the center of the bilayer. The final (native) structure is observed at higher temperatures of refolding. In this structure, the Trps are located on average about 9-10 A from the bilayer center. Monitoring the evolution of Trp fluorescence quenching by a set of brominated lipids during refolding at various temperatures therefore allowed us to identify and characterize intermediate states in the folding process of an integral membrane protein.

Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds.

PubMed

Wang, Zhandong; Popolan-Vaida, Denisia M; Chen, Bingjie; Moshammer, Kai; Mohamed, Samah Y; Wang, Heng; Sioud, Salim; Raji, Misjudeen A; Kohse-Höinghaus, Katharina; Hansen, Nils; Dagaut, Philippe; Leone, Stephen R; Sarathy, S Mani

2017-12-12

Decades of research on the autooxidation of organic compounds have provided fundamental and practical insights into these processes; however, the structure of many key autooxidation intermediates and the reactions leading to their formation still remain unclear. This work provides additional experimental evidence that highly oxygenated intermediates with one or more hydroperoxy groups are prevalent in the autooxidation of various oxygenated (e.g., alcohol, aldehyde, keto compounds, ether, and ester) and nonoxygenated (e.g., normal alkane, branched alkane, and cycloalkane) organic compounds. These findings improve our understanding of autooxidation reaction mechanisms that are routinely used to predict fuel ignition and oxidative stability of liquid hydrocarbons, while also providing insights relevant to the formation mechanisms of tropospheric aerosol building blocks. The direct observation of highly oxygenated intermediates for the autooxidation of alkanes at 500-600 K builds upon prior observations made in atmospheric conditions for the autooxidation of terpenes and other unsaturated hydrocarbons; it shows that highly oxygenated intermediates are stable at conditions above room temperature. These results further reveal that highly oxygenated intermediates are not only accessible by chemical activation but also by thermal activation. Theoretical calculations on H-atom migration reactions are presented to rationalize the relationship between the organic compound's molecular structure ( n -alkane, branched alkane, and cycloalkane) and its propensity to produce highly oxygenated intermediates via extensive autooxidation of hydroperoxyalkylperoxy radicals. Finally, detailed chemical kinetic simulations demonstrate the influence of these additional reaction pathways on the ignition of practical fuels. Copyright © 2017 the Author(s). Published by PNAS.

Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Zhandong; Popolan-Vaida, Denisia M.; Chen, Bingjie

Decades of research on the autooxidation of organic compounds have provided fundamental and practical insights into these processes; however, the structure of many key autooxidation intermediates and the reactions leading to their formation still remain unclear. This work provides additional experimental evidence that highly oxygenated intermediates with one or more hydroperoxy groups are prevalent in the autooxidation of various oxygenated (e.g., alcohol, aldehyde, keto compounds, ether, and ester) and nonoxygenated (e.g., normal alkane, branched alkane, and cycloalkane) organic compounds. These findings improve our understanding of autooxidation reaction mechanisms that are routinely used to predict fuel ignition and oxidative stability ofmore » liquid hydrocarbons, while also providing insights relevant to the formation mechanisms of tropospheric aerosol building blocks. The direct observation of highly oxygenated intermediates for the autooxidation of alkanes at 500–600 K builds upon prior observations made in atmospheric conditions for the autooxidation of terpenes and other unsaturated hydrocarbons; it shows that highly oxygenated intermediates are stable at conditions above room temperature. These results further reveal that highly oxygenated intermediates are not only accessible by chemical activation but also by thermal activation. Theoretical calculations on H-atom migration reactions are presented to rationalize the relationship between the organic compound’s molecular structure (n-alkane, branched alkane, and cycloalkane) and its propensity to produce highly oxygenated intermediates via extensive autooxidation of hydroperoxyalkylperoxy radicals. In conclusion, detailed chemical kinetic simulations demonstrate the influence of these additional reaction pathways on the ignition of practical fuels.« less

Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds

DOE PAGES

Wang, Zhandong; Popolan-Vaida, Denisia M.; Chen, Bingjie; ...

2017-11-28

Decades of research on the autooxidation of organic compounds have provided fundamental and practical insights into these processes; however, the structure of many key autooxidation intermediates and the reactions leading to their formation still remain unclear. This work provides additional experimental evidence that highly oxygenated intermediates with one or more hydroperoxy groups are prevalent in the autooxidation of various oxygenated (e.g., alcohol, aldehyde, keto compounds, ether, and ester) and nonoxygenated (e.g., normal alkane, branched alkane, and cycloalkane) organic compounds. These findings improve our understanding of autooxidation reaction mechanisms that are routinely used to predict fuel ignition and oxidative stability ofmore » liquid hydrocarbons, while also providing insights relevant to the formation mechanisms of tropospheric aerosol building blocks. The direct observation of highly oxygenated intermediates for the autooxidation of alkanes at 500–600 K builds upon prior observations made in atmospheric conditions for the autooxidation of terpenes and other unsaturated hydrocarbons; it shows that highly oxygenated intermediates are stable at conditions above room temperature. These results further reveal that highly oxygenated intermediates are not only accessible by chemical activation but also by thermal activation. Theoretical calculations on H-atom migration reactions are presented to rationalize the relationship between the organic compound’s molecular structure (n-alkane, branched alkane, and cycloalkane) and its propensity to produce highly oxygenated intermediates via extensive autooxidation of hydroperoxyalkylperoxy radicals. In conclusion, detailed chemical kinetic simulations demonstrate the influence of these additional reaction pathways on the ignition of practical fuels.« less

Quantum Chemical Mass Spectrometry: Verification and Extension of the Mobile Proton Model for Histidine

NASA Astrophysics Data System (ADS)

Cautereels, Julie; Blockhuys, Frank

2017-06-01

The quantum chemical mass spectrometry for materials science (QCMS2) method is used to verify the proposed mechanism for proton transfer - the Mobile Proton Model (MPM) - by histidine for ten XHS tripeptides, based on quantum chemical calculations at the DFT/B3LYP/6-311+G* level of theory. The fragmentations of the different intermediate structures in the MPM mechanism are studied within the QCMS2 framework, and the energetics of the proposed mechanism itself and those of the fragmentations of the intermediate structures are compared, leading to the computational confirmation of the MPM. In addition, the calculations suggest that the mechanism should be extended from considering only the formation of five-membered ring intermediates to include larger-ring intermediates. [Figure not available: see fulltext.

Peroxo and Oxo Intermediates in Mononuclear Non-heme Iron Enzymes and Related Active Sites

PubMed Central

Wong, Shaun D.; Liu, Lei V.; Decker, Andrea; Chow, Marina S.

2009-01-01

Summary FeIII–OOH and FeIV=O intermediates have now been documented in a number of non-heme iron active sites. In this Opinion we use spectroscopy combined with electronic structure calculations to define the frontier molecular orbitals (FMOs) of these species and their contributions to reactivity. For the low-spin FeIII–OOH species in activated bleomycin we show that the reactivity of this non-heme iron intermediate is very different from that of the analogous Compound 0 of cytochrome P450. For FeIV=O S = 1 model species we experimentally define the electronic structure and its contribution to reactivity, and computationally evaluate how this would change for the FeIV=O S = 2 intermediates found in non-heme iron enzymes. PMID:19278895

Advances in Fabrication Materials of Honeycomb Structure Films by the Breath-Figure Method

PubMed Central

Heng, Liping; Wang, Bin; Li, Muchen; Zhang, Yuqi; Jiang, Lei

2013-01-01

Creatures in nature possess almost perfect structures and properties, and exhibit harmonization and unification between structure and function. Biomimetics, mimicking nature for engineering solutions, provides a model for the development of functional surfaces with special properties. Recently, honeycomb structure materials have attracted wide attention for both fundamental research and practical applications and have become an increasingly hot research topic. Though progress in the field of breath-figure formation has been reviewed, the advance in the fabrication materials of bio-inspired honeycomb structure films has not been discussed. Here we review the recent progress of honeycomb structure fabrication materials which were prepared by the breath-figure method. The application of breath figures for the generation of all kinds of honeycomb is discussed. PMID:28809319

The impact of intermediate care services on job satisfaction, skills and career development opportunities.

PubMed

Nancarrow, Susan

2007-07-01

The purpose of this study was to examine, in depth, the impact of intermediate care services on staff job satisfaction, skills development and career development opportunities. Recruitment and retention difficulties present a major barrier to the effective delivery of intermediate care services in the UK. The limited existing literature is contradictory, but points to the possibility of staff deskilling and suggests that intermediate care is poorly understood and may be seen by other practitioners as being of lower status than hospital work. These factors have the potential to reduce staff morale and limit the possibilities of recruiting staff. The research is based on interviews with 26 staff from case studies of two intermediate care services in South Yorkshire. Participants reported high levels of job satisfaction, which was because of the enabling philosophy of care, increased autonomy, the setting of care and the actual teams within which the workers were employed. For most disciplines, intermediate care facilitated the application of existing skills in a different way; enhancing some skills, while restricting the use of others. Barriers to career development opportunities were attributed to the relative recency of intermediate care services, small size of the services and lack of clear career structures. Career development opportunities in intermediate care could be improved through staff rotations through acute, community and intermediate care to increase their awareness of the roles of intermediate care staff. The non-hierarchical management structures limits management career development opportunities, instead, there is a need to enhance professional growth opportunities through the use of consultant posts and specialization within intermediate care. This study provides insight into the impact of an increasingly popular model of care on the roles and job satisfaction of workers and highlights the importance of this learning for recruitment and retention of staff.

Characterization of reaction intermediate aggregates in aniline oxidative polymerization at low proton concentration.

PubMed

Ding, Zhongfen; Sanchez, Timothy; Labouriau, Andrea; Iyer, Srinivas; Larson, Toti; Currier, Robert; Zhao, Yusheng; Yang, Dali

2010-08-19

Aggregates of reaction intermediates form during the early stages of aniline oxidative polymerization whenever the initial mole ratio of proton concentration to aniline monomer concentration is low ([H(+)](0)/[An](0)

Role of Intermediate Filaments in Vesicular Traffic.

PubMed

Margiotta, Azzurra; Bucci, Cecilia

2016-04-25

Intermediate filaments are an important component of the cellular cytoskeleton. The first established role attributed to intermediate filaments was the mechanical support to cells. However, it is now clear that intermediate filaments have many different roles affecting a variety of other biological functions, such as the organization of microtubules and microfilaments, the regulation of nuclear structure and activity, the control of cell cycle and the regulation of signal transduction pathways. Furthermore, a number of intermediate filament proteins have been involved in the acquisition of tumorigenic properties. Over the last years, a strong involvement of intermediate filament proteins in the regulation of several aspects of intracellular trafficking has strongly emerged. Here, we review the functions of intermediate filaments proteins focusing mainly on the recent knowledge gained from the discovery that intermediate filaments associate with key proteins of the vesicular membrane transport machinery. In particular, we analyze the current understanding of the contribution of intermediate filaments to the endocytic pathway.

Structure based aggregation studies reveal the presence of helix-rich intermediate during α-Synuclein aggregation

PubMed Central

Ghosh, Dhiman; Singh, Pradeep K.; Sahay, Shruti; Jha, Narendra Nath; Jacob, Reeba S.; Sen, Shamik; Kumar, Ashutosh; Riek, Roland; Maji, Samir K.

2015-01-01

Mechanistic understanding of nucleation dependent polymerization by α-synuclein (α-Syn) into toxic oligomers and amyloids is important for the drug development against Parkinson's disease. However the structural and morphological characterization during nucleation and subsequent fibrillation process of α-Syn is not clearly understood. Using a variety of complementary biophysical techniques monitoring entire pathway of nine different synucleins, we found that transition of unstructured conformation into β-sheet rich fibril formation involves helix-rich intermediates. These intermediates are common for all aggregating synucleins, contain high solvent-exposed hydrophobic surfaces, are cytotoxic to SHSY-5Y cells and accelerate α-Syn aggregation efficiently. A multidimensional NMR study characterizing the intermediate accompanied with site-specific fluorescence study suggests that the N-terminal and central portions mainly participate in the helix-rich intermediate formation while the C-terminus remained in an extended conformation. However, significant conformational transitions occur at the middle and at the C-terminus during helix to β-sheet transition as evident from Trp fluorescence study. Since partial helix-rich intermediates were also observed for other amyloidogenic proteins such as Aβ and IAPP, we hypothesize that this class of intermediates may be one of the important intermediates for amyloid formation pathway by many natively unstructured protein/peptides and represent a potential target for drug development against amyloid diseases. PMID:25784353

Differential diagnosis of jaw pain using informatics technology.

PubMed

Nam, Y; Kim, H-G; Kho, H-S

2018-05-21

This study aimed to deduce evidence-based clinical clues that differentiate temporomandibular disorders (TMD)-mimicking conditions from genuine TMD by text mining using natural language processing (NLP) and recursive partitioning. We compared the medical records of 29 patients diagnosed with TMD-mimicking conditions and 290 patients diagnosed with genuine TMD. Chief complaints and medical histories were preprocessed via NLP to compare the frequency of word usage. In addition, recursive partitioning was used to deduce the optimal size of mouth opening, which could differentiate TMD-mimicking from genuine TMD groups. The prevalence of TMD-mimicking conditions was more evenly distributed across all age groups and showed a nearly equal gender ratio, which was significantly different from genuine TMD. TMD-mimicking conditions were caused by inflammation, infection, hereditary disease and neoplasm. Patients with TMD-mimicking conditions frequently used "mouth opening limitation" (P < .001), but less commonly used words such as "noise" (P < .001) and "temporomandibular joint" (P < .001) than patients with genuine TMD. A diagnostic classification tree on the basis of recursive partitioning suggested that 12.0 mm of comfortable mouth opening and 26.5 mm of maximum mouth opening were deduced as the most optimal mouth-opening cutoff sizes. When the combined analyses were performed based on both the text mining and clinical examination data, the predictive performance of the model was 96.6% with 69.0% sensitivity and 99.3% specificity in predicting TMD-mimicking conditions. In conclusion, this study showed that AI technology-based methods could be applied in the field of differential diagnosis of orofacial pain disorders. © 2018 John Wiley & Sons Ltd.

Structural analysis of kinetic folding intermediates for a TIM barrel protein, indole-3-glycerol phosphate synthase, by hydrogen exchange mass spectrometry and Gō-model simulation

PubMed Central

Gu, Zhenyu; Rao, Maithreyi K.; Forsyth, William R.

2009-01-01

The structures of partially-folded states appearing during the folding of a (βα)8 TIM barrel protein, the indole-3-glycerol phosphate synthase from S. solfataricus (sIGPS), was assessed by hydrogen exchange mass spectrometry (HX-MS) and Gō-model simulations. HX-MS analysis of the peptic peptides derived from the pulse-labeled product of the sub-millisecond folding reaction from the urea-denatured state revealed strong protection in the (βα)4 region, modest protection in the neighboring (βα)1–3 and (βα)5β6 segments and no significant protection in the remaining N- and C-terminal segments. These results demonstrate that this species is not a collapsed form of the unfolded state under native-favoring conditions nor is it the native state formed via fast-track folding. However, the striking contrast of these results with the strong protection observed in the (βα)2–5β6 region after 5 s of folding demonstrates that these species represent kinetically-distinct folding intermediates that are not identical as previously thought. A re-examination of the kinetic folding mechanism by chevron analysis of fluorescence data confirmed distinct roles for these two species: the burst-phase intermediate is predicted to be a misfolded, off-pathway intermediate while the subsequent 5 s intermediate corresponds to an on-pathway equilibrium intermediate. Comparison with the predictions using a Cα Gō-model simulation of the kinetic folding reaction for sIGPS shows good agreement with the core of structure offering protection against exchange in the on-pathway intermediate(s). Because the native-centric Gō-model simulations do not explicitly include sequence-specific information, the simulation results support the hypothesis that the topology of TIM barrel proteins is a primary determinant of the folding free energy surface for the productive folding reaction. The early misfolding reaction must involve aspects of non-native structure not detected by the Gō-model simulation. PMID:17942114

The Effects of Focused/Unfocused Audio-Appended Reading Tasks on Intermediate Female EFL Learners' Written Accuracy

ERIC Educational Resources Information Center

Alavinia, Parviz; Shafaei, Ali; Salimi, Asghar

2018-01-01

The current research study was conducted to examine the impacts of focused and unfocused audio-appended reading tasks on female EFL learners' acquisition of a rule-bound structure (passive voice) and a non-rule-bound structure (prepositions). The participants of this study involved ninety intermediate female English learners. They were assigned…

Folding thermodynamics of pseudoknotted chain conformations

PubMed Central

Kopeikin, Zoia; Chen, Shi-Jie

2008-01-01

We develop a statistical mechanical framework for the folding thermodynamics of pseudoknotted structures. As applications of the theory, we investigate the folding stability and the free energy landscapes for both the thermal and the mechanical unfolding of pseudoknotted chains. For the mechanical unfolding process, we predict the force-extension curves, from which we can obtain the information about structural transitions in the unfolding process. In general, a pseudoknotted structure unfolds through multiple structural transitions. The interplay between the helix stems and the loops plays an important role in the folding stability of pseudoknots. For instance, variations in loop sizes can lead to the destabilization of some intermediate states and change the (equilibrium) folding pathways (e.g., two helix stems unfold either cooperatively or sequentially). In both thermal and mechanical unfolding, depending on the nucleotide sequence, misfolded intermediate states can emerge in the folding process. In addition, thermal and mechanical unfoldings often have different (equilibrium) pathways. For example, for certain sequences, the misfolded intermediates, which generally have longer tails, can fold, unfold, and refold again in the pulling process, which means that these intermediates can switch between two different average end-end extensions. PMID:16674261

Serial Femtosecond Crystallography and Ultrafast Absorption Spectroscopy of the Photoswitchable Fluorescent Protein IrisFP.

PubMed

Colletier, Jacques-Philippe; Sliwa, Michel; Gallat, François-Xavier; Sugahara, Michihiro; Guillon, Virginia; Schirò, Giorgio; Coquelle, Nicolas; Woodhouse, Joyce; Roux, Laure; Gotthard, Guillaume; Royant, Antoine; Uriarte, Lucas Martinez; Ruckebusch, Cyril; Joti, Yasumasa; Byrdin, Martin; Mizohata, Eiichi; Nango, Eriko; Tanaka, Tomoyuki; Tono, Kensuke; Yabashi, Makina; Adam, Virgile; Cammarata, Marco; Schlichting, Ilme; Bourgeois, Dominique; Weik, Martin

2016-03-03

Reversibly photoswitchable fluorescent proteins find growing applications in cell biology, yet mechanistic details, in particular on the ultrafast photochemical time scale, remain unknown. We employed time-resolved pump-probe absorption spectroscopy on the reversibly photoswitchable fluorescent protein IrisFP in solution to study photoswitching from the nonfluorescent (off) to the fluorescent (on) state. Evidence is provided for the existence of several intermediate states on the pico- and microsecond time scales that are attributed to chromophore isomerization and proton transfer, respectively. Kinetic modeling favors a sequential mechanism with the existence of two excited state intermediates with lifetimes of 2 and 15 ps, the second of which controls the photoswitching quantum yield. In order to support that IrisFP is suited for time-resolved experiments aiming at a structural characterization of these ps intermediates, we used serial femtosecond crystallography at an X-ray free electron laser and solved the structure of IrisFP in its on state. Sample consumption was minimized by embedding crystals in mineral grease, in which they remain photoswitchable. Our spectroscopic and structural results pave the way for time-resolved serial femtosecond crystallography aiming at characterizing the structure of ultrafast intermediates in reversibly photoswitchable fluorescent proteins.

Epithelial structure revealed by chemical dissection and unembedded electron microscopy.

PubMed

Fey, E G; Capco, D G; Krochmalnic, G; Penman, S

1984-07-01

Cytoskeletal structures obtained after extraction of Madin-Darby canine kidney epithelial cell monolayers with Triton X-100 were examined in transmission electron micrographs of cell whole mounts and unembedded thick sections. The cytoskeleton, an ordered structure consisting of a peripheral plasma lamina, a complex network of filaments, and chromatin-containing nuclei, was revealed after extraction of intact cells with a nearly physiological buffer containing Triton X-100. The cytoskeleton was further fractionated by extraction with (NH4)2SO4, which left a structure enriched in intermediate filaments and desmosomes around the nuclei. A further digestion with nuclease and elution with (NH4)2SO4 removed the chromatin. The stable structure that remained after this procedure retained much of the epithelial morphology and contained essentially all of the cytokeratin filaments and desmosomes and the chromatin-depleted nuclear matrices. This structural network may serve as a scaffold for epithelial organization. The cytoskeleton and the underlying nuclear matrix intermediate filament scaffold, when examined in both conventional embedded thin sections and in unembedded whole mounts and thick sections, showed the retention of many of the detailed morphological aspects of the intact cells, which suggests a structural continuum linking the nuclear matrix, the intermediate filament network, and the intercellular desmosomal junctions. Most importantly, the protein composition of each of the four fractions obtained by this sequential procedure was essentially unique. Thus, the proteins constituting the soluble fraction, the cytoskeleton, the chromatin fraction, and the underlying nuclear matrix-intermediate filament scaffold are biochemically distinct.

Epithelial structure revealed by chemical dissection and unembedded electron microscopy

PubMed Central

Fey, E. G.; Capco, D. G.; Krochmalnic, G.; Penman, S.

1984-01-01

Cytoskeletal structures obtained after extraction of Madin-Darby canine kidney epithelial cell monolayers with Triton X-100 were examined in transmission electron micrographs of cell whole mounts and unembedded thick sections. The cytoskeleton, an ordered structure consisting of a peripheral plasma lamina, a complex network of filaments, and chromatin-containing nuclei, was revealed after extraction of intact cells with a nearly physiological buffer containing Triton X-100. The cytoskeleton was further fractionated by extraction with (NH4)2SO4, which left a structure enriched in intermediate filaments and desmosomes around the nuclei. A further digestion with nuclease and elution with (NH4)2SO4 removed the chromatin. The stable structure that remained after this procedure retained much of the epithelial morphology and contained essentially all of the cytokeratin filaments and desmosomes and the chromatin-depleted nuclear matrices. This structural network may serve as a scaffold for epithelial organization. The cytoskeleton and the underlying nuclear matrix intermediate filament scaffold, when examined in both conventional embedded thin sections and in unembedded whole mounts and thick sections, showed the retention of many of the detailed morphological aspects of the intact cells, which suggests a structural continuum linking the nuclear matrix, the intermediate filament network, and the intercellular desmosomal junctions. Most importantly, the protein composition of each of the four fractions obtained by this sequential procedure was essentially unique. Thus, the proteins constituting the soluble fraction, the cytoskeleton, the chromatin fraction, and the underlying nuclear matrix-intermediate filament scaffold are biochemically distinct. PMID:6540264

Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair.

PubMed

Zhang, Yuchen; Alsop, Richard J; Soomro, Asfia; Yang, Fei-Chi; Rheinstädter, Maikel C

2015-01-01

The hair is a filamentous biomaterial consisting of the cuticle, the cortex and the medulla, all held together by the cell membrane complex. The cortex mostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3-90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of the α-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers.

Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair

PubMed Central

Zhang, Yuchen; Alsop, Richard J.; Soomro, Asfia; Yang, Fei-Chi

2015-01-01

The hair is a filamentous biomaterial consisting of the cuticle, the cortex and the medulla, all held together by the cell membrane complex. The cortex mostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3–90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of the α-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers. PMID:26557428

Development of a monoclonal antibody-based, congener-specific and solvent-tolerable direct enzyme-linked immunosorbgent assay for the detection of 2,2',4,4'-tetrabromodiphenyl ether in environmental samples

USDA-ARS?s Scientific Manuscript database

A sensitive direct enzyme-linked immunosorbent assay (ELISA) for the detection of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) in environmental samples was developed. A hapten mimicking the whole structure of BDE-47 was synthesized by introducing a butyric acid spacer to 5-hydroxy-BDE-47 and coupled ...

Crystal structure of group II intron domain 1 reveals a template for RNA assembly

DOE PAGES

Zhao, Chen; Rajashankar, Kanagalaghatta R.; Marcia, Marco; ...

2015-10-26

Although the importance of large noncoding RNAs is increasingly appreciated, our understanding of their structures and architectural dynamics remains limited. In particular, we know little about RNA folding intermediates and how they facilitate the productive assembly of RNA tertiary structures. In this paper, we report the crystal structure of an obligate intermediate that is required during the earliest stages of group II intron folding. Composed of domain 1 from the Oceanobacillus iheyensis group II intron (266 nucleotides), this intermediate retains native-like features but adopts a compact conformation in which the active site cleft is closed. Transition between this closed andmore » the open (native) conformation is achieved through discrete rotations of hinge motifs in two regions of the molecule. Finally, the open state is then stabilized by sequential docking of downstream intron domains, suggesting a 'first come, first folded' strategy that may represent a generalizable pathway for assembly of large RNA and ribonucleoprotein structures.« less

Structural and Mechanical Properties of Intermediate Filaments under Extreme Conditions and Disease

NASA Astrophysics Data System (ADS)

Qin, Zhao

Intermediate filaments are one of the three major components of the cytoskeleton in eukaryotic cells. It was discovered during the recent decades that intermediate filament proteins play key roles to reinforce cells subjected to large-deformation as well as participate in signal transduction. However, it is still poorly understood how the nanoscopic structure, as well as the biochemical properties of these protein molecules contribute to their biomechanical functions. In this research we investigate the material function of intermediate filaments under various extreme mechanical conditions as well as disease states. We use a full atomistic model and study its response to mechanical stresses. Learning from the mechanical response obtained from atomistic simulations, we build mesoscopic models following the finer-trains-coarser principles. By using this multiple-scale model, we present a detailed analysis of the mechanical properties and associated deformation mechanisms of intermediate filament network. We reveal the mechanism of a transition from alpha-helices to beta-sheets with subsequent intermolecular sliding under mechanical force, which has been inferred previously from experimental results. This nanoscale mechanism results in a characteristic nonlinear force-extension curve, which leads to a delocalization of mechanical energy and prevents catastrophic fracture. This explains how intermediate filament can withstand extreme mechanical deformation of > 1 00% strain despite the presence of structural defects. We combine computational and experimental techniques to investigate the molecular mechanism of Hutchinson-Gilford progeria syndrome, a premature aging disease. We find that the mutated lamin tail .domain is more compact and stable than the normal one. This altered structure and stability may enhance the association of intermediate filaments with the nuclear membrane, providing a molecular mechanism of the disease. We study the nuclear membrane association with intermediate filaments by focusing on the effect of calcium on the maturation process of lamin A. Our result shows that calcium plays a regulatory role in the post-translational processing of lam in A by tuning its molecular conformation and mechanics. Based on these findings we demonstrate that multiple-scale computational modeling provides a useful tool in understanding the biomechanical property and disease mechanism of intermediate filaments. We provide a perspective on research opportunities to improve the foundation for engineering the mechanical and biochemical functions of biomaterials. (Copies available exclusively from MIT Libraries, libraries.mit.edu/docs - docs@mit.edu)

Mimicking the extracellular matrix with functionalized, metal-assembled collagen peptide scaffolds.

PubMed

Hernandez-Gordillo, Victor; Chmielewski, Jean

2014-08-01

Natural and synthetic three-dimensional (3-D) scaffolds that mimic the microenvironment of the extracellular matrix (ECM), with growth factor storage/release and the display of cell adhesion signals, offer numerous advantages for regenerative medicine and in vitro morphogenesis and oncogenesis modeling. Here we report the design of collagen mimetic peptides (CMPs) that assemble into a highly crosslinked 3-D matrix in response to metal ion stimuli, that may be functionalized with His-tagged cargoes, such as green fluorescent protein (GFP-His8) and human epidermal growth factor (hEGF-His6). The bound hEGF-His6 was found to gradually release from the matrix in vitro and induce cell proliferation in the EGF-dependent cell line MCF10A. The additional incorporation of a cell adhesion sequence (RGDS) at the N-terminus of the CMP creates an environment that facilitated the organization of matrix-encapsulated MCF10A cells into spheroid structures, thus mimicking the ECM environment. Copyright © 2014 Elsevier Ltd. All rights reserved.

Increased NIH 3T3 fibroblast functions on cell culture dishes which mimic the nanometer fibers of natural tissues.

PubMed

Bhardwaj, Garima; Webster, Thomas J

2015-01-01

Traditional flat tissue cell culture dishes have consisted of polystyrene treated with plasma gases for growing, subculturing, and studying cell behavior in vitro. However, increasingly it has been observed that mimicking natural tissue properties (such as chemistry, three-dimensional structure, mechanical properties, etc) in vitro can lead to a better correlation of in vitro to in vivo cellular functions. The following studies compared traditional NIH 3T3 fibroblasts' functions on XanoMatrix scaffolds to standard tissue culture polystyrene. Results found significantly greater fibroblast adhesion and proliferation on XanoMatrix cell culture dishes which mimic the nanoscale geometry of natural tissue fibers with true, tortuous fiber beds creating a robust, consistent, and versatile growth platform. In this manner, this study supports that cell culture dishes which mimic features of natural tissues should be continually studied for a wide range of applications in which mimicking natural cellular functions are important.

Artifact Reduction in X-Ray CT Images of Al-Steel-Perspex Specimens Mimicking a Hip Prosthesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Madhogarhia, Manish; Munshi, P.; Lukose, Sijo

2008-09-26

X-ray Computed Tomography (CT) is a relatively new technique developed in the late 1970's, which enables the nondestructive visualization of the internal structure of objects. Beam hardening caused by the polychromatic spectrum is an important problem in X-ray computed tomography (X-CT). It leads to various artifacts in reconstruction images and reduces image quality. In the present work we are considering the Artifact Reduction in Total Hip Prosthesis CT Scan which is a problem of medical imaging. We are trying to reduce the cupping artifact induced by beam hardening as well as metal artifact as they exist in the CT scanmore » of a human hip after the femur is replaced by a metal implant. The correction method for beam hardening used here is based on a previous work. Simulation study for the present problem includes a phantom consisting of mild steel, aluminium and perspex mimicking the photon attenuation properties of a hum hip cross section with metal implant.« less

Spatiotemporally Controlled Microchannels of Periodontal Mimic Scaffolds

PubMed Central

Park, C.H.; Kim, K.H.; Rios, H.F.; Lee, Y.M.; Giannobile, W.V.; Seol, Y.J.

2014-01-01

Physiologic bioengineering of the oral, dental, and craniofacial complex requires optimized geometric organizations of fibrous connective tissues. A computer-designed, fiber-guiding scaffold has been developed to promote tooth-supporting periodontal tissue regeneration and functional restoration despite limited printing resolution for the manufacture of submicron-scaled features. Here, we demonstrate the use of directional freeze-casting techniques to control pore directional angulations and create mimicked topographies to alveolar crest, horizontal, oblique, and apical fibers of natural periodontal ligaments. For the differing anatomic positions, the gelatin displayed varying patterns of ice growth, determined via internal pore architectures. Regardless of the freezing coordinates, the longitudinal pore arrangements resulted in submicron-scaled diameters (~50 µm), along with corresponding high biomaterial porosity (~90%). Furthermore, the horizontal + coronal ((x→−y→) freezing orientation facilitated the creation of similar structures to major fibers in the periodontal ligament interface. This periodontal tissue-mimicking microenvironment is a potential tissue platform for the generation of naturally oriented ligamentous tissues consistent with periodontal ligament neogenesis. PMID:25216511

Fabrication of High-Sensitivity Skin-Attachable Temperature Sensors with Bioinspired Microstructured Adhesive.

PubMed

Oh, Ju Hyun; Hong, Soo Yeong; Park, Heun; Jin, Sang Woo; Jeong, Yu Ra; Oh, Seung Yun; Yun, Junyeong; Lee, Hanchan; Kim, Jung Wook; Ha, Jeong Sook

2018-02-28

In this study, we demonstrate the fabrication of a highly sensitive flexible temperature sensor with a bioinspired octopus-mimicking adhesive. A resistor-type temperature sensor consisting of a composite of poly(N-isopropylacrylamide) (pNIPAM)-temperature sensitive hydrogel, poly(3,4-ethylenedioxythiophene) polystyrene sulfonate, and carbon nanotubes exhibits a very high thermal sensitivity of 2.6%·°C -1 between 25 and 40 °C so that the change in skin temperature of 0.5 °C can be accurately detected. At the same time, the polydimethylsiloxane adhesive layer of octopus-mimicking rim structure coated with pNIPAM is fabricated through the formation of a single mold by utilizing undercut phenomenon in photolithography. The fabricated sensor shows stable and reproducible detection of skin temperature under repeated attachment/detachment cycles onto skin without any skin irritation for a long time. This work suggests a high potential application of our skin-attachable temperature sensor to wearable devices for medical and health-care monitoring.

A Thermally Insulating Textile Inspired by Polar Bear Hair.

PubMed

Cui, Ying; Gong, Huaxin; Wang, Yujie; Li, Dewen; Bai, Hao

2018-04-01

Animals living in the extremely cold environment, such as polar bears, have shown amazing capability to keep warm, benefiting from their hollow hairs. Mimicking such a strategy in synthetic fibers would stimulate smart textiles for efficient personal thermal management, which plays an important role in preventing heat loss and improving efficiency in house warming energy consumption. Here, a "freeze-spinning" technique is used to realize continuous and large-scale fabrication of fibers with aligned porous structure, mimicking polar bear hairs, which is difficult to achieve by other methods. A textile woven with such biomimetic fibers shows an excellent thermal insulation property as well as good breathability and wearability. In addition to passively insulating heat loss, the textile can also function as a wearable heater, when doped with electroheating materials such as carbon nanotubes, to induce fast thermal response and uniform electroheating while maintaining its soft and porous nature for comfortable wearing. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mimicking the colourful wing scale structure of the Papilio blumei butterfly.

PubMed

Kolle, Mathias; Salgard-Cunha, Pedro M; Scherer, Maik R J; Huang, Fumin; Vukusic, Pete; Mahajan, Sumeet; Baumberg, Jeremy J; Steiner, Ullrich

2010-07-01

The brightest and most vivid colours in nature arise from the interaction of light with surfaces that exhibit periodic structure on the micro- and nanoscale. In the wings of butterflies, for example, a combination of multilayer interference, optical gratings, photonic crystals and other optical structures gives rise to complex colour mixing. Although the physics of structural colours is well understood, it remains a challenge to create artificial replicas of natural photonic structures. Here we use a combination of layer deposition techniques, including colloidal self-assembly, sputtering and atomic layer deposition, to fabricate photonic structures that mimic the colour mixing effect found on the wings of the Indonesian butterfly Papilio blumei. We also show that a conceptual variation to the natural structure leads to enhanced optical properties. Our approach offers improved efficiency, versatility and scalability compared with previous approaches.

Subependymal Heterotopia Mimicking Mass in Conventional Magnetic Resonance Imaging: Demonstration With 3T Advanced Neuroimages.

PubMed

Aktas, Filiz; Ogul, Hayri

2017-10-01

The authors reported a rare patient with large subependymal heterotopia mimicking cerebral neoplasia. A 22-year-old female was admitted with a history of right-sided paresthesia accompanied by progressive headache. Cerebral magnetic resonance (MR) imaging showed a large solid lesion in the left frontal lobe. Advanced MR images proved that the lesion was compatible with subependymal heterotopia. Large subependymal heterotopia may mimick cerebral neoplasia.

Unique fluorophores in the dimeric archaeal histones hMfB and hPyA1 reveal the impact of nonnative structure in a monomeric kinetic intermediate

PubMed Central

Stump, Matthew R.; Gloss, Lisa M.

2008-01-01

Homodimeric archaeal histones and heterodimeric eukaryotic histones share a conserved structure but fold through different kinetic mechanisms, with a correlation between faster folding/association rates and the population of kinetic intermediates. Wild-type hMfB (from Methanothermus fervidus) has no intrinsic fluorophores; Met35, which is Tyr in hyperthermophilic archaeal histones such as hPyA1 (from Pyrococcus strain GB-3A), was mutated to Tyr and Trp. Two Tyr-to-Trp mutants of hPyA1 were also characterized. All fluorophores were introduced into the long, central α-helix of the histone fold. Far-UV circular dichroism (CD) indicated that the fluorophores did not significantly alter the helical content of the histones. The equilibrium unfolding transitions of the histone variants were two-state, reversible processes, with ΔG°(H2O) values within 1 kcal/mol of the wild-type dimers. The hPyA1 Trp variants fold by two-state kinetic mechanisms like wild-type hPyA1, but with increased folding and unfolding rates, suggesting that the mutated residues (Tyr-32 and Tyr-36) contribute to transition state structure. Like wild-type hMfB, M35Y and M35W hMfB fold by a three-state mechanism, with a stopped-flow CD burst-phase monomeric intermediate. The M35 mutants populate monomeric intermediates with increased secondary structure and stability but exhibit decreased folding rates; this suggests that nonnative interactions occur from burial of the hydrophobic Tyr and Trp residues in this kinetic intermediate. These results implicate the long central helix as a key component of the structure in the kinetic monomeric intermediates of hMfB as well as the dimerization transition state in the folding of hPyA1. PMID:18096639

Molecular dynamics simulation of β₂-microglobulin in denaturing and stabilizing conditions.

PubMed

Fogolari, Federico; Corazza, Alessandra; Varini, Nicola; Rotter, Matteo; Gumral, Devrim; Codutti, Luca; Rennella, Enrico; Viglino, Paolo; Bellotti, Vittorio; Esposito, Gennaro

2011-03-01

β₂-Microglobulin has been a model system for the study of fibril formation for 20 years. The experimental study of β₂-microglobulin structure, dynamics, and thermodynamics in solution, at atomic detail, along the pathway leading to fibril formation is difficult because the onset of disorder and aggregation prevents signal resolution in Nuclear Magnetic Resonance experiments. Moreover, it is difficult to characterize conformers in exchange equilibrium. To gain insight (at atomic level) on processes for which experimental information is available at molecular or supramolecular level, molecular dynamics simulations have been widely used in the last decade. Here, we use molecular dynamics to address three key aspects of β₂-microglobulin, which are known to be relevant to amyloid formation: (1) 60 ns molecular dynamics simulations of β₂-microglobulin in trifluoroethanol and in conditions mimicking low pH are used to study the behavior of the protein in environmental conditions that are able to trigger amyloid formation; (2) adaptive biasing force molecular dynamics simulation is used to force cis-trans isomerization at Proline 32 and to calculate the relative free energy in the folded and unfolded state. The native-like trans-conformer (known as intermediate 2 and determining the slow phase of refolding), is simulated for 10 ns, detailing the possible link between cis-trans isomerization and conformational disorder; (3) molecular dynamics simulation of highly concentrated doxycycline (a molecule able to suppress fibril formation) in the presence of β₂-microglobulin provides details of the binding modes of the drug and a rationale for its effect. Copyright © 2010 Wiley-Liss, Inc.

Lactate Racemase Nickel-Pincer Cofactor Operates by a Proton-Coupled Hydride Transfer Mechanism.

PubMed

Rankin, Joel A; Mauban, Robert C; Fellner, Matthias; Desguin, Benoît; McCracken, John; Hu, Jian; Varganov, Sergey A; Hausinger, Robert P

2018-03-09

Lactate racemase (LarA) of Lactobacillus plantarum contains a novel organometallic cofactor with nickel coordinated to a covalently tethered pincer ligand, pyridinium-3-thioamide-5-thiocarboxylic acid mononucleotide, but its function in the enzyme mechanism has not been elucidated. This study presents direct evidence that the nickel-pincer cofactor facilitates a proton-coupled hydride transfer (PCHT) mechanism during LarA-catalyzed lactate racemization. No signal was detected by electron paramagnetic resonance spectroscopy for LarA in the absence or presence of substrate, consistent with a +2 metal oxidation state and inconsistent with a previously proposed proton-coupled electron transfer mechanism. Pyruvate, the predicted intermediate for a PCHT mechanism, was observed in quenched solutions of LarA. A normal substrate kinetic isotope effect ( k H / k D of 3.11 ± 0.17) was established using 2-α- 2 H-lactate, further supporting a PCHT mechanism. UV-visible spectroscopy revealed a lactate-induced perturbation of the cofactor spectrum, notably increasing the absorbance at 340 nm, and demonstrated an interaction of the cofactor with the inhibitor sulfite. A crystal structure of LarA provided greater resolution (2.4 Å) than previously reported and revealed sulfite binding to the pyridinium C4 atom of the reduced pincer cofactor, mimicking hydride reduction during a PCHT catalytic cycle. Finally, computational modeling supports hydride transfer to the cofactor at the C4 position or to the nickel atom, but with formation of a nickel-hydride species requiring dissociation of the His200 metal ligand. In aggregate, these studies provide compelling evidence that the nickel-pincer cofactor acts by a PCHT mechanism.

Emerging Biomimetic Applications of DNA Nanotechnology.

PubMed

Shen, Haijing; Wang, Yingqian; Wang, Jie; Li, Zhihao; Yuan, Quan

2018-06-25

Re-engineering cellular components and biological processes has received great interest and promised compelling advantages in applications ranging from basic cell biology to biomedicine. With the advent of DNA nanotechnology, the programmable self-assembly ability makes DNA an appealing candidate for rational design of artificial components with different structures and functions. This Forum Article summarizes recent developments of DNA nanotechnology in mimicking the structures and functions of existing cellular components. We highlight key successes in the achievements of DNA-based biomimetic membrane proteins and discuss the assembly behavior of these artificial proteins. Then, we focus on the construction of higher-order structures by DNA nanotechnology to recreate cell-like structures. Finally, we explore the current challenges and speculate on future directions of DNA nanotechnology in biomimetics.

Layered chalcogenide glass structures for IR lenses

NASA Astrophysics Data System (ADS)

Gibson, Daniel; Bayya, Shyam; Sanghera, Jas; Nguyen, Vinh; Scribner, Dean; Maksimovic, Velimir; Gill, John; Yi, Allen; Deegan, John; Unger, Blair

2014-07-01

A technique for fabricating novel infrared (IR) lenses can enable a reduction in the size and weight of IR imaging optics through the use of layered glass structures. These structures can range from having a few thick glass layers, mimicking cemented doublets and triplets, to having many thin glass layers approximating graded index (GRIN) lenses. The effectiveness of these structures relies on having materials with diversity in refractive index (large Δn) and dispersion and similar thermo-viscous behavior (common glass transition temperature, ΔTg = 10°C). A library of 13 chalcogenide glasses with broad IR transmission (NIR through LWIR bands) was developed to satisfy these criteria. The lens fabrication methodology, including glass design and synthesis, sheet fabrication, preform making, lens molding and surface finishing are presented.

Biomimicry of optical microstructures of Papilio palinurus

NASA Astrophysics Data System (ADS)

Crne, Matija; Sharma, Vivek; Blair, John; Park, Jung Ok; Summers, Christopher J.; Srinivasarao, Mohan

2011-01-01

The brilliant coloration of animals in nature is sometimes based on their structure rather than on pigments. The green colour on the wings of a butterfly Papilio palinurus originates from the hierarchical microstructure of individual wing scales that are tiled on the wing. The hierarchical structure gives rise to two coloured reflections of visible light, blue and yellow which when additively mixed, produce the perception of green colour on the wing scales. We used breath figure templated assembly as the starting point for the structure and, combining it with atomic layer deposition for the multilayers necessary for the production of interference colors, we have faithfully mimicked the structure and the optical effects found on the wing scale of the butterfly Papilio palinurus.

[Elaboration of Pseudo-natural Products Using Artificial In Vitro Biosynthesis Systems].

PubMed

Goto, Yuki

2018-01-01

 Peptidic natural products often consist of not only proteinogenic building blocks but also unique non-proteinogenic structures such as macrocyclic scaffolds and N-methylated backbones. Since such non-proteinogenic structures are important structural motifs that contribute to diverse bioactivity, we have proposed that peptides with non-proteinogenic structures should be attractive candidates as artificial bioactive peptides mimicking natural products, or so-called pseudo-natural products. We previously devised an engineered translation system for pseudo-natural peptides, referred to as the flexible in vitro translation (FIT) system. This system enabled "one-pot" synthesis of highly diverse pseudo-natural peptide libraries, which can be rapidly screened by mRNA display technology for the discovery of pseudo-natural peptides with diverse bioactivities.

The investigation of order–disorder transition process of ZSM-5 induced by spark plasma sintering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Liang; Wang, Lianjun, E-mail: wanglj@dhu.edu.cn; Jiang, Wan

2014-04-01

Based on the amorphization of zeolites, an order–disorder transition method was used to prepare silica glass via Spark Plasma Sintering (SPS). In order to get a better understanding about the mechanism of amorphization induced by SPS, the intermediate products in this process were prepared and characterized by different characterization techniques. X-ray diffraction and High-energy synchrotron X-ray scattering show a gradual transformation from ordered crystal to glass. Local structural changes in glass network including Si–O bond length, O–Si–O bond angle, size of rings, coordination were detected by Infrared spectroscopy and {sup 29}Si magic-angle spinning nuclear magnetic resonance (NMR) spectroscopy. Topologically ordered,more » amorphous material with a different intermediate-range structure can be obtained by precise control of intermediate process which can be expected to optimize and design material. - Graphical abstract: Low-density, ordered zeolites collapse to the rigid amorphous glass through spark plasma sintering. The intermediate-range structure formed in the process of order–disorder transition may give rise to specific property. - Highlights: • Order–disorder transition process of ZSM-5 induced by spark plasma sintering was investigated using several methods including XRD, High-energy synchrotron X-ray scattering, SAXS, IR, NMR, ect. • Order–disorder transition induced by SPS was compared with TIA and PIA. • Three stages has been divided during the whole process. • The collapse temperature range which may give rise to intermediate-range structure has been located.« less

Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments.

PubMed

Mizukami, Takuya; Abe, Yukiko; Maki, Kosuke

2015-01-01

In this study, the equivalence of the kinetic mechanisms of the formation of urea-induced kinetic folding intermediates and non-native equilibrium states was investigated in apomyoglobin. Despite having similar structural properties, equilibrium and kinetic intermediates accumulate under different conditions and via different mechanisms, and it remains unknown whether their formation involves shared or distinct kinetic mechanisms. To investigate the potential mechanisms of formation, the refolding and unfolding kinetics of horse apomyoglobin were measured by continuous- and stopped-flow fluorescence over a time range from approximately 100 μs to 10 s, along with equilibrium unfolding transitions, as a function of urea concentration at pH 6.0 and 8°C. The formation of a kinetic intermediate was observed over a wider range of urea concentrations (0-2.2 M) than the formation of the native state (0-1.6 M). Additionally, the kinetic intermediate remained populated as the predominant equilibrium state under conditions where the native and unfolded states were unstable (at ~0.7-2 M urea). A continuous shift from the kinetic to the equilibrium intermediate was observed as urea concentrations increased from 0 M to ~2 M, which indicates that these states share a common kinetic folding mechanism. This finding supports the conclusion that these intermediates are equivalent. Our results in turn suggest that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding, which further supports the structural equivalence of transient and equilibrium intermediates. An additional folding intermediate accumulated within ~140 μs of refolding and an unfolding intermediate accumulated in <1 ms of unfolding. Finally, by using quantitative modeling, we showed that a five-state sequential scheme appropriately describes the folding mechanism of horse apomyoglobin.

Gas turbine engine adapted for use in combination with an apparatus for separating a portion of oxygen from compressed air

DOEpatents

Bland, Robert J [Oviedo, FL; Horazak, Dennis A [Orlando, FL

2012-03-06

A gas turbine engine is provided comprising an outer shell, a compressor assembly, at least one combustor assembly, a turbine assembly and duct structure. The outer shell includes a compressor section, a combustor section, an intermediate section and a turbine section. The intermediate section includes at least one first opening and at least one second opening. The compressor assembly is located in the compressor section to define with the compressor section a compressor apparatus to compress air. The at least one combustor assembly is coupled to the combustor section to define with the combustor section a combustor apparatus. The turbine assembly is located in the turbine section to define with the turbine section a turbine apparatus. The duct structure is coupled to the intermediate section to receive at least a portion of the compressed air from the compressor apparatus through the at least one first opening in the intermediate section, pass the compressed air to an apparatus for separating a portion of oxygen from the compressed air to produced vitiated compressed air and return the vitiated compressed air to the intermediate section via the at least one second opening in the intermediate section.

Freeze-quench (57)Fe-Mössbauer spectroscopy: trapping reactive intermediates.

PubMed

Krebs, Carsten; Bollinger, J Martin

2009-01-01

(57)Fe-Mössbauer spectroscopy is a method that probes transitions between the nuclear ground state (I=1/2) and the first nuclear excited state (I=3/2). This technique provides detailed information about the chemical environment and electronic structure of iron. Therefore, it has played an important role in studies of the numerous iron-containing proteins and enzymes. In conjunction with the freeze-quench method, (57)Fe-Mössbauer spectroscopy allows for monitoring changes of the iron site(s) during a biochemical reaction. This approach is particularly powerful for detection and characterization of reactive intermediates. Comparison of experimentally determined Mössbauer parameters to those predicted by density functional theory for hypothetical model structures can then provide detailed insight into the structures of reactive intermediates. We have recently used this methodology to study the reactions of various mononuclear non-heme-iron enzymes by trapping and characterizing several Fe(IV)-oxo reaction intermediates. In this article, we summarize these findings and demonstrate the potential of the method. © Springer Science+Business Media B.V. 2009

Trapped in imidazole: how to accumulate multiple photoelectrons on a black-absorbing ruthenium complex.

PubMed

Zedler, Linda; Kupfer, Stephan; de Moraes, Inês Rabelo; Wächtler, Maria; Beckert, Rainer; Schmitt, Michael; Popp, Jürgen; Rau, Sven; Dietzek, Benjamin

2014-03-24

Ruthenium dyes incorporating a 4H-imidazole chromophore as a ligand exhibit a spectrally broad absorption in the UV/Vis region. Furthermore, they show the ability to store two electrons within the 4H-imidazole ligand. These features render them promising molecular systems, for example, as inter- or intramolecular electron relays. To optimize the structures with respect to their electron-storage capability, it is crucial to understand the impact of structural changes accompanying photoinduced charge transfer in the electronic intermediates of multistep electron-transfer processes. The photophysical properties of these (reactive) intermediates might impact the function of the molecular systems quite substantially. However, the spectroscopic study of short-lived intermediates in stepwise multielectron-transfer processes is experimentally challenging. To this end, this contribution reports on the electrochemical generation of anions identical to intermediate structures and their spectroscopic characterization by in situ resonance Raman and UV/Vis spectroelectrochemistry and computational methods. Thereby, an efficient two-electron pathway to the 4H-imidazole electron-accepting ligand is identified. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Intermediates and the folding of proteins L and G

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, Scott; Head-Gordon, Teresa

We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G that are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted {beta}-1 and {beta}-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contactsmore » involving the third {beta}-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment.« less

Intermediates and the folding of proteins L and G

PubMed Central

Brown, Scott; Head-Gordon, Teresa

2004-01-01

We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G, which are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted β-1 and β-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding, and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third β-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally, the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first-order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment. PMID:15044729

Structural analysis of vimentin and keratin intermediate filaments by cryo-electron tomography.

PubMed

Norlén, Lars; Masich, Sergej; Goldie, Kenneth N; Hoenger, Andreas

2007-06-10

Intermediate filaments are a large and structurally diverse group of cellular filaments that are classified into five different groups. They are referred to as intermediate filaments (IFs) because they are intermediate in diameter between the two other cytoskeletal filament systems that is filamentous actin and microtubules. The basic building block of IFs is a predominantly alpha-helical rod with variable length globular N- and C-terminal domains. On the ultra-structural level there are two major differences between IFs and microtubules or actin filaments: IFs are non-polar, and they do not exhibit large globular domains. IF molecules associate via a coiled-coil interaction into dimers and higher oligomers. Structural investigations into the molecular building plan of IFs have been performed with a variety of biophysical and imaging methods such as negative staining and metal-shadowing electron microscopy (EM), mass determination by scanning transmission EM, X-ray crystallography on fragments of the IF stalk and low-angle X-ray scattering. The actual packing of IF dimers into a long filament varies between the different families. Typically the dimers form so called protofibrils that further assemble into a filament. Here we introduce new cryo-imaging methods for structural investigations of IFs in vitro and in vivo, i.e., cryo-electron microscopy and cryo-electron tomography, as well as associated techniques such as the preparation and handling of vitrified sections of cellular specimens.

Photo-oxidation of tyrosine in a bio-engineered bacterioferritin 'reaction centre'-a protein model for artificial photosynthesis.

PubMed

Hingorani, Kastoori; Pace, Ron; Whitney, Spencer; Murray, James W; Smith, Paul; Cheah, Mun Hon; Wydrzynski, Tom; Hillier, Warwick

2014-10-01

The photosynthetic reaction centre (RC) is central to the conversion of solar energy into chemical energy and is a model for bio-mimetic engineering approaches to this end. We describe bio-engineering of a Photosystem II (PSII) RC inspired peptide model, building on our earlier studies. A non-photosynthetic haem containing bacterioferritin (BFR) from Escherichia coli that expresses as a homodimer was used as a protein scaffold, incorporating redox-active cofactors mimicking those of PSII. Desirable properties include: a di-nuclear metal binding site which provides ligands for bivalent metals, a hydrophobic pocket at the dimer interface which can bind a photosensitive porphyrin and presence of tyrosine residues proximal to the bound cofactors, which can be utilised as efficient electron-tunnelling intermediates. Light-induced electron transfer from proximal tyrosine residues to the photo-oxidised ZnCe6(•+), in the modified BFR reconstituted with both ZnCe6 and Mn(II), is presented. Three site-specific tyrosine variants (Y25F, Y58F and Y45F) were made to localise the redox-active tyrosine in the engineered system. The results indicate that: presence of bound Mn(II) is necessary to observe tyrosine oxidation in all BFR variants; Y45 the most important tyrosine as an immediate electron donor to the oxidised ZnCe6(•+) and that Y25 and Y58 are both redox-active in this system, but appear to function interchangebaly. High-resolution (2.1Å) crystal structures of the tyrosine variants show that there are no mutation-induced effects on the overall 3-D structure of the protein. Small effects are observed in the Y45F variant. Here, the BFR-RC represents a protein model for artificial photosynthesis. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

Thermal decomposition of ammonium hexachloroosmate.

PubMed

Asanova, T I; Kantor, I; Asanov, I P; Korenev, S V; Yusenko, K V

2016-12-07

Structural changes of (NH 4 ) 2 [OsCl 6 ] occurring during thermal decomposition in a reduction atmosphere have been studied in situ using combined energy-dispersive X-ray absorption spectroscopy (ED-XAFS) and powder X-ray diffraction (PXRD). According to PXRD, (NH 4 ) 2 [OsCl 6 ] transforms directly to metallic Os without the formation of any crystalline intermediates but through a plateau where no reactions occur. XANES and EXAFS data by means of Multivariate Curve Resolution (MCR) analysis show that thermal decomposition occurs with the formation of an amorphous intermediate {OsCl 4 } x with a possible polymeric structure. Being revealed for the first time the intermediate was subjected to determine the local atomic structure around osmium. The thermal decomposition of hexachloroosmate is much more complex and occurs within a minimum two-step process, which has never been observed before.

Biomolecular Materials. Report of the January 13-15, 2002 Workshop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alper, M. D.; Stupp, S. I.

2002-01-15

Twenty-two scientists from around the nation and the world met to discuss the way that the molecules, structures, processes and concepts of the biological world could be used or mimicked in designing novel materials, processes or devices of potential practical significance. The emphasis was on basic research, although the long-term goal is, in addition to increased knowledge, the development of applications to further the mission of the Department of Energy.

Intermediate Traces and Intermediate Learners: Evidence for the Use of Intermediate Structure during Sentence Processing in Second Language French

ERIC Educational Resources Information Center

Miller, A. Kate

2015-01-01

This study reports on a sentence processing experiment in second language (L2) French that looks for evidence of trace reactivation at clause edge and in the canonical object position in indirect object cleft sentences with complex embedding and cyclic movement. Reaction time (RT) asymmetries were examined among low (n = 20) and high (n = 20)…

The Unfolding and Refolding Reactions of Triosephosphate Isomerase from Trypanosoma Cruzi Follow Similar Pathways. Guanidinium Hydrochloride Studies

NASA Astrophysics Data System (ADS)

Vázquez-Contreras, Edgar; Pérez Hernández, Gerardo; Sánchez-Rebollar, Brenda Guadalupe; Chánez-Cárdenas, María Elena

2005-04-01

The unfolding and refolding reactions of Trypanosoma cruzi triosephosphate isomerase (TcTIM) was studied under equilibrium conditions at increasing guanidinium hydrochloride concentrations. The changes in activity intrinsic fluorescence and far-ultraviolet circular dichroism as a function of denaturant were used as a quaternary, tertiary and secondary structural probes respectively. The change in extrinsic ANS fluorescence intensity was also investigated. The results show that the transition between the homodimeric native enzyme to the unfolded monomers (unfolding), and its inverse reaction (refolding) are described by similar pathways and two equilibrium intermediates were detected in both reactions. The mild denaturant concentrations intermediate is active and contains significant amount of secondary and tertiary structures. The medium denaturant concentrations intermediate is inactive and able to bind the fluorescent dye. This intermediates are maybe related with those observed in the denaturation pattern of TIMs from other species; the results are discussed in this context.

Capillary electrophoretic study of dibasic acids of different structures: Relation to separation of oxidative intermediates in remediation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Z.; Cocke, D.L.

Dicarboxylic acids are important in environmental chemistry because they are intermediates in oxidative processes involved in natural remediation and waste management processes such as oxidative detoxification and advanced oxidation. Capillary electrophoresis (CE), a promising technique for separating and analyzing these intermediates, has been used to examine a series of dibasic acids of different structures and conformations. This series includes malonic acid, succinic acid, glutaric acid, adipic acid, pimelic acid, maleic acid, fumaric acid, phthalic acid, and trans, trans-muconic acid. The CE parameters as well as structural variations (molecular structure and molecular isomers, buffer composition, pH, applied voltage, injection mode, current,more » temperature, and detection wavelength) that affect the separations and analytical results have been examined in this study. Those factors that affect the separation have been delineated. Among these parameters, the pH has been found to be the most important, which affects the double-layer of the capillary wall, the electro-osmotic flow and analyte mobility. The optimum pH for separating these dibasic acids, as well as the other parameters are discussed in detail and related to the development of methods for analyzing oxidation intermediates in oxidative waste management procedures.« less

Characterization of folding intermediates during urea-induced denaturation of human carbonic anhydrase II.

PubMed

Wahiduzzaman; Dar, Mohammad Aasif; Haque, Md Anzarul; Idrees, Danish; Hassan, Md Imtaiyaz; Islam, Asimul; Ahmad, Faizan

2017-02-01

Knowledge of folding/unfolding pathway is fundamental basis to study protein structure and stability. Human carbonic anhydrase II (HCAII) is a ∼29kDa, β-sheet dominated monomeric protein of 259 amino acid residues. In the present study, the urea-induced denaturation of HCAII was carried out which was a tri-phasic process, i.e., N (native) ↔ X I ↔ X II ↔ D (denatured) with stable intermediates X I and X II populated around 2 and 4M urea, respectively. The far-UV CD was used to characterize the intermediate states (X I and X II ) for secondary structural content, near-UV CD for tertiary structure, dynamic light scattering for hydrodynamic radius and ANS fluorescence spectroscopy for the presence of exposed hydrophobic patches. Based on these experiments, we concluded that urea-induced X I state has characteristics of molten globule state while X II state bears characteristics features of pre-molten globule state. Characterization of the intermediates on the folding pathway will contribute to a deeper understanding of the structure-function relationship of HCAII. Furthermore, this system may provide an excellent model to study urea stress and the strategies adopted by the organisms to combat such a stress. Copyright © 2016 Elsevier B.V. All rights reserved.

Exploring the relevance of gas-phase structures to biology: cold ion spectroscopy of the decapeptide neurokinin A.

PubMed

Pereverzev, A Y; Boyarkin, O V

2017-02-01

Linking the intrinsic tertiary structures of biomolecules to their native geometries is a central prerequisite for making gas-phase studies directly relevant to biology. The isolation of molecules in the gas phase eliminates hydrophilic interactions with solvents, to some extent mimicking a hydrophobic environment. Intrinsic structures therefore may resemble native ones for peptides that in vivo reside in a hydrophobic environment (e.g., binding pockets of receptors). In this study, we investigate doubly protonated neurokinin A (NKA) using IR-UV double resonance cold ion spectroscopy and find only five conformers of this decapeptide in the gas phase. In contrast, NMR data show that in aqueous solutions, NKA exhibits high conformational heterogeneity, which reduces to a few well-defined structures in hydrophobic micelles. Do the gas-phase structures of NKA resemble these native structures? The IR spectra reported here allow the validation of future structural calculations that may answer this question.

Nuclear Resonance Vibrational Spectroscopic Definition of Peroxy Intermediates in Nonheme Iron Sites

DOE PAGES

Sutherlin, Kyle D.; Liu, Lei V.; Lee, Yong-Min; ...

2016-11-02

Fe III-(hydro)peroxy intermediates have been isolated in two classes of mononuclear nonheme Fe enzymes that are important in bioremediation: the Rieske dioxygenases and the extradiol dioxygenases. The binding mode and protonation state of the peroxide moieties in these intermediates are not well-defined, due to a lack of vibrational structural data. Nuclear resonance vibrational spectroscopy (NRVS) is an important technique for obtaining vibrational information on these and other intermediates, as it is sensitive to all normal modes with Fe displacement. Here in this paper, we present the NRVS spectra of side-on Fe III-peroxy and end-on Fe III-hydroperoxy model complexes and assignmore » these spectra using calibrated DFT calculations. We then use DFT calculations to define and understand the changes in the NRVS spectra that arise from protonation and from opening the Fe–O–O angle. This study identifies four spectroscopic handles that will enable definition of the binding mode and protonation state of Fe III-peroxy intermediates in mononuclear nonheme Fe enzymes. These structural differences are important in determining the frontier molecular orbitals available for reactivity.« less

Nuclear Resonance Vibrational Spectroscopic Definition of Peroxy Intermediates in Nonheme Iron Sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sutherlin, Kyle D.; Liu, Lei V.; Lee, Yong-Min

Fe III-(hydro)peroxy intermediates have been isolated in two classes of mononuclear nonheme Fe enzymes that are important in bioremediation: the Rieske dioxygenases and the extradiol dioxygenases. The binding mode and protonation state of the peroxide moieties in these intermediates are not well-defined, due to a lack of vibrational structural data. Nuclear resonance vibrational spectroscopy (NRVS) is an important technique for obtaining vibrational information on these and other intermediates, as it is sensitive to all normal modes with Fe displacement. Here in this paper, we present the NRVS spectra of side-on Fe III-peroxy and end-on Fe III-hydroperoxy model complexes and assignmore » these spectra using calibrated DFT calculations. We then use DFT calculations to define and understand the changes in the NRVS spectra that arise from protonation and from opening the Fe–O–O angle. This study identifies four spectroscopic handles that will enable definition of the binding mode and protonation state of Fe III-peroxy intermediates in mononuclear nonheme Fe enzymes. These structural differences are important in determining the frontier molecular orbitals available for reactivity.« less

Nuclear Resonance Vibrational Spectroscopic Definition of Peroxy Intermediates in Nonheme Iron Sites.

PubMed

Sutherlin, Kyle D; Liu, Lei V; Lee, Yong-Min; Kwak, Yeonju; Yoda, Yoshitaka; Saito, Makina; Kurokuzu, Masayuki; Kobayashi, Yasuhiro; Seto, Makoto; Que, Lawrence; Nam, Wonwoo; Solomon, Edward I

2016-11-02

Fe III -(hydro)peroxy intermediates have been isolated in two classes of mononuclear nonheme Fe enzymes that are important in bioremediation: the Rieske dioxygenases and the extradiol dioxygenases. The binding mode and protonation state of the peroxide moieties in these intermediates are not well-defined, due to a lack of vibrational structural data. Nuclear resonance vibrational spectroscopy (NRVS) is an important technique for obtaining vibrational information on these and other intermediates, as it is sensitive to all normal modes with Fe displacement. Here, we present the NRVS spectra of side-on Fe III -peroxy and end-on Fe III -hydroperoxy model complexes and assign these spectra using calibrated DFT calculations. We then use DFT calculations to define and understand the changes in the NRVS spectra that arise from protonation and from opening the Fe-O-O angle. This study identifies four spectroscopic handles that will enable definition of the binding mode and protonation state of Fe III -peroxy intermediates in mononuclear nonheme Fe enzymes. These structural differences are important in determining the frontier molecular orbitals available for reactivity.

[Establishment of sprouting embryoid body model mimicking early embryonic vasculogenesis in human embryo].

PubMed

Jiang, Hua; Feng, You-Ji; Xie, Yi; Han, Jin-Lan; Wang, Zack; Chen, Tong

2008-10-14

To establish a sprouting embryoid body model mimicking early embryonic vasculogenesis in human embryo. Human embryonic stem were (hESCs) were cultured on the mouse embryo fibroblasts and then were induced to differentiate to form three-dimensional EB. The hEBs were cultured in media containing various angiogenesis-related factors: vascular endothelial growth factor (VEGF), fibroblast growth factor (FGF), endostatin, angiostatin, and platelet factor (PF)-4 of different concentrations for 3 days to observe the sprouting of the hEBs. 3, 3, 3', 3'-tetramethylindo-carbocyanine perchlorate labeled acetylated low density lipoprotein (Dil-AcLDL) was added onto the hEBs foe 4 h Immunofluorescence assay was used to observe if Dil-AcLDL was absorbed and if CD31 was expressed so as to determine the existence of embryonic endothelial cells in the sprouting structures. The ideal culturing condition was analyzed. The differentiated EBs formed sprouting structures in the collagen I matrix containing VEGF and FGF. The sprouts among individual EBs were able to link to each other and form vascular network-like structures. In the presence of VEGF and FGF, the sprouts branching from the EBs assimilated Dil-AcLDL, expressed CD31 and formed a 3-dimensional cylindrical organization. The concentrations of growth factors ideally stimulating sprouting growth were 100 ng/ml of VEGF and 50 ng/ml of FGF. The networks among the EBs were abolished by the angiostatin, endostatin, and PF4. The sprouting from hEBs accumulates embryonic endothelial cells and the sprouting network-like structures are indeed endothelial in nature. Inducing of sprouting EBs is an ideal model that mimics early embryonic vasculogenesis in humans.

Large-Area Direct Laser-Shock Imprinting of a 3D Biomimic Hierarchical Metal Surface for Triboelectric Nanogenerators.

PubMed

Jin, Shengyu; Wang, Yixiu; Motlag, Maithilee; Gao, Shengjie; Xu, Jin; Nian, Qiong; Wu, Wenzhuo; Cheng, Gary J

2018-03-01

Ongoing efforts in triboelectric nanogenerators (TENGs) focus on enhancing power generation, but obstacles concerning the economical and cost-effective production of TENGs continue to prevail. Micro-/nanostructure engineering of polymer surfaces has been dominantly utilized for boosting the contact triboelectrification, with deposited metal electrodes for collecting the scavenged energy. Nevertheless, this state-of-the-art approach is limited by the vague potential for producing 3D hierarchical surface structures with conformable coverage of high-quality metal. Laser-shock imprinting (LSI) is emerging as a potentially scalable approach for directly surface patterning of a wide range of metals with 3D nanoscale structures by design, benefiting from the ultrahigh-strain-rate forming process. Here, a TENG device is demonstrated with LSI-processed biomimetic hierarchically structured metal electrodes for efficient harvesting of water-drop energy in the environment. Mimicking and transferring hierarchical microstructures from natural templates, such as leaves, into these water-TENG devices is effective regarding repelling water drops from the device surface, since surface hydrophobicity from these biomicrostructures maximizes the TENG output. Among various leaves' microstructures, hierarchical microstructures from dried bamboo leaves are preferable regarding maximizing power output, which is attributed to their unique structures, containing both dense nanostructures and microscale features, compared with other types of leaves. Also, the triboelectric output is significantly improved by closely mimicking the hydrophobic nature of the leaves in the LSI-processed metal surface after functionalizing it with low-surface-energy self-assembled-monolayers. The approach opens doors to new manufacturable TENG technologies for economically feasible and ecologically friendly production of functional devices with directly patterned 3D biomimic metallic surfaces in energy, electronics, and sensor applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Deep Granuloma Annulare Mimicking Inflamed Cysts in a Teenager.

PubMed

Guo, Emily L; Degesys, Catherine A; Jahan-Tigh, Richard; Chan, Audrey

2017-07-01

We describe deep granuloma annulare (DGA) of the forehead mimicking inflamed cysts. Reactive inflammation and sterile purulent drainage may be an underrecognized feature of DGA. © 2017 Wiley Periodicals, Inc.

Elucidation of the iron(IV)–oxo intermediate in the non-haem iron halogenase SyrB2

PubMed Central

Wong, Shaun D.; Srnec, Martin; Matthews, Megan L.; Liu, Lei V.; Kwak, Yeonju; Park, Kiyoung; Bell, Caleb B.; Alp, E. Ercan; Zhao, Jiyong; Yoda, Yoshitaka; Kitao, Shinji; Seto, Makoto; Krebs, Carsten; Bollinger, J. Martin; Solomon, Edward I.

2013-01-01

SUMMARY Mononuclear non-haem iron (NHFe) enzymes catalyse a wide variety of oxidative reactions including halogenation, hydroxylation, ring closure, desaturation, and aromatic ring cleavage. These are highly important for mammalian somatic processes such as phenylalanine metabolism, production of neurotransmitters, hypoxic response, and the biosynthesis of natural products.1–3 The key reactive intermediate in the catalytic cycles of these enzymes is an S = 2 FeIV=O species, which has been trapped for a number of NHFe enzymes4–8 including the halogenase SyrB2, the subject of this study. Computational studies to understand the reactivity of the enzymatic NHFe FeIV=O intermediate9–13 are limited in applicability due to the paucity of experimental knowledge regarding its geometric and electronic structures, which determine its reactivity. Synchrotron-based nuclear resonance vibrational spectroscopy (NRVS) is a sensitive and effective method that defines the dependence of the vibrational modes of Fe on the nature of the FeIV=O active site.14–16 Here we present the first NRVS structural characterisation of the reactive FeIV=O intermediate of a NHFe enzyme. This FeIV=O intermediate reacts via an initial H-atom abstraction step, with its subsquent halogenation (native) or hydroxylation (non-native) rebound reactivity being dependent on the substrate.17 A correlation of the experimental NRVS data to electronic structure calculations indicates that the substrate is able to direct the orientation of the FeIV=O intermediate, presenting specific frontier molecular orbitals (FMOs) which can activate the selective halogenation versus hydroxylation reactivity. PMID:23868262

Examination of key intermediates in the catalytic cycle of aspartate-beta-semialdehyde dehydrogenase from a gram-positive infectious bacteria.

PubMed

Faehnle, Christopher R; Le Coq, Johanne; Liu, Xuying; Viola, Ronald E

2006-10-13

Aspartate-beta-semialdehyde dehydrogenase (ASADH) catalyzes a critical branch point transformation in amino acid bio-synthesis. The products of the aspartate pathway are essential in microorganisms, and this entire pathway is absent in mammals, making this enzyme an attractive target for antibiotic development. The first structure of an ASADH from a Gram-positive bacterium, Streptococcus pneumoniae, has now been determined. The overall structure of the apoenzyme has a similar fold to those of the Gram-negative and archaeal ASADHs but contains some interesting structural variations that can be exploited for inhibitor design. Binding of the coenzyme NADP, as well as a truncated nucleotide analogue, into an alternative conformation from that observed in Gram-negative ASADHs causes an enzyme domain closure that precedes catalysis. The covalent acyl-enzyme intermediate was trapped by soaking the substrate into crystals of the coenzyme complex, and the structure of this elusive intermediate provides detailed insights into the catalytic mechanism.

Application of MCR-ALS to reveal intermediate conformations in the thermally induced α-β transition of poly-L-lysine monitored by FT-IR spectroscopy

NASA Astrophysics Data System (ADS)

Alcaráz, Mirta R.; Schwaighofer, Andreas; Goicoechea, Héctor; Lendl, Bernhard

2017-10-01

Temperature-induced conformational transitions of poly-L-lysine were monitored with Fourier-transform infrared (FT-IR) spectroscopy between 10 °C and 70 °C. Chemometric analysis of dynamic IR spectra was performed by multivariate curve analysis-alternating least squares (MCR-ALS) of the amide I‧ and amide II‧ spectral region. With this approach, the pure spectral and concentration profiles of the conformational transition were obtained. Beside the initial α-helical, the intermediate random coil/extended helices and the final β-sheet structure, an additional intermediate PLL conformation was identified and attributed to a transient β-sheet structure.

NMR analysis of a kinetically trapped intermediate of a disulfide-deficient mutant of the starch-binding domain of glucoamylase.

PubMed

Sugimoto, Hayuki; Noda, Yasuo; Segawa, Shin-ichi

2011-09-16

A thermally unfolded disulfide-deficient mutant of the starch-binding domain of glucoamylase refolds into a kinetically trapped metastable intermediate when subjected to a rapid lowering of temperature. We attempted to characterise this intermediate using multidimensional NMR spectroscopy. The (1)H-(15)N heteronuclear single quantum coherence spectrum after a rapid temperature decrease (the spectrum of the intermediate) showed good chemical shift dispersion but was significantly different from that of the native state, suggesting that the intermediate adopts a nonnative but well-structured conformation. Large chemical shift changes for the backbone amide protons between the native and the intermediate states were observed for residues in the β-sheet consisting of strands 2, 3, 5, 6, and 7 as well as in the C-terminal region. These residues were found to be in close proximity to aromatic residues, suggesting that the chemical shift changes are mainly due to ring current shifts caused by the aromatic residues. The two-dimensional nuclear Overhauser enhancement (NOE) spectroscopy experiments showed that the intermediate contained substantial, native-like NOE connectivities, although there were fewer cross peaks in the spectrum of the intermediate compared with that of the native state. It was also shown that there were native-like interresidue NOEs for residues buried in the protein, whereas many of the NOE cross peaks were lost for the residues involved in a surface-exposed aromatic cluster. These results suggest that, in the intermediate, the aromatic cluster at the surface is structurally less organised, whereas the interior of the protein has relatively rigid, native-like side-chain packing. Copyright © 2011 Elsevier Ltd. All rights reserved.

Intermediate introns in nuclear genes of euglenids - are they a distinct type?

PubMed

Milanowski, Rafał; Gumińska, Natalia; Karnkowska, Anna; Ishikawa, Takao; Zakryś, Bożena

2016-02-29

Nuclear genes of euglenids contain two major types of introns: conventional spliceosomal and nonconventional introns. The latter are characterized by variable non-canonical borders, RNA secondary structure that brings intron ends together, and an unknown mechanism of removal. Some researchers also distinguish intermediate introns, which combine features of both types. They form a stable RNA secondary structure and are classified into two subtypes depending on whether they contain one (intermediate/nonconventional subtype) or both (conventional/intermediate subtype) canonical spliceosomal borders. However, it has been also postulated that most introns classified as intermediate could simply be special cases of conventional or nonconventional introns. Sequences of tubB, hsp90 and gapC genes from six strains of Euglena agilis were obtained. They contain four, six, and two or three introns, respectively (the third intron in the gapC gene is unique for just one strain). Conventional introns were present at three positions: two in the tubB gene (at one position conventional/intermediate introns were also found) and one in the gapC gene. Nonconventional introns are present at ten positions: two in the tubB gene (at one position intermediate/nonconventional introns were also found), six in hsp90 (at four positions intermediate/nonconventional introns were also found), and two in the gapC gene. Sequence and RNA secondary structure analyses of nonconventional introns confirmed that their most strongly conserved elements are base pairing nucleotides at positions +4, +5 and +6/ -8, -7 and -6 (in most introns CAG/CTG nucleotides were observed). It was also confirmed that the presence of the 5' GT/C end in intermediate/nonconventional introns is not the result of kinship with conventional introns, but is due to evolutionary pressure to preserve the purine at the 5' end. However, an example of a nonconventional intron with GC-AG ends was shown, suggesting the possibility of intron type conversion between nonconventional and conventional. Furthermore, an analysis of conventional introns revealed that the ability to form a stable RNA secondary structure by some introns is probably not a result of their relationship with nonconventional introns. It was also shown that acquisition of new nonconventional introns is an ongoing process and can be observed at the level of a single species. In the recently acquired intron in the gapC gene an extended direct repeats at the intron-exon junctions are present, suggesting that double-strand break repair process could be the source of new nonconventional introns.

Protein vivisection reveals elusive intermediates in folding

PubMed Central

Zheng, Zhongzhou; Sosnick, Tobin R.

2010-01-01

Although most folding intermediates escape detection, their characterization is crucial to the elucidation of folding mechanisms. Here we outline a powerful strategy to populate partially unfolded intermediates: A buried aliphatic residue is substituted with a charged residue (e.g., Leu→Glu−) to destabilize and unfold a specific region of the protein. We apply this strategy to Ubiquitin, reversibly trapping a folding intermediate in which the β5 strand is unfolded. The intermediate refolds to a native-like structure upon charge neutralization under mildly acidic conditions. Characterization of the trapped intermediate using NMR and hydrogen exchange methods identifies a second folding intermediate and reveals the order and free energies of the two major folding events on the native side of the rate-limiting step. This general strategy may be combined with other methods and have broad applications in the study of protein folding and other reactions that require trapping of high energy states. PMID:20144618

Intermediate states and structure evolution in the free-falling process of the dislocation in graphene

NASA Astrophysics Data System (ADS)

Wang, Shaofeng; Yao, Yin; Bai, Jianhui; Wang, Rui

2017-04-01

This paper investigated the intermediate states and the structure evolution of the dislocation in graphene when it falls freely from the saddle point of the energy landscape. The O-type dislocation, an unstable equilibrium structure located at the saddle point, is obtained from the lattice theory of the dislocation structure and improved by the ab initio calculation to take the buckling into account. Intermediate states along the kinetics path in the falling process are obtained from the ab initio simulation. Once the dislocation falls from the saddle point to the energy valley, this O-type dislocation transforms into the stable structure that is referred to as the B-type dislocation, and in the meantime, it moves a distance that equals half a Burgers vector. The structure evolution and the energy variation in the free-falling process are revealed explicitly. It is observed that rather than smooth change, a platform manifests itself in the energy curve. The unusual behaviour in the energy curve is mainly originated from symmetry breaking and bond formation in the dislocation core. The results can provide deep insight in the mechanism of the brittle feature of covalent materials.

Structure and mechanical behavior of bird beaks

NASA Astrophysics Data System (ADS)

Seki, Yasuaki

The structure and mechanical behavior of Toco toucan (Ramphastos toco) and Wreathed hornbill (Rhyticeros undulatus) beaks were examined. The structure of Toco toucan and Wreathed hornbill beak was found to be a sandwich composite with an exterior of keratin and a fibrous bony network of closed cells made of trabeculae. A distinctive feature of the hornbill beak is its casque formed from cornified keratin layers. The casque is believed to have an acoustic function due to the complex internal structure. The toucan and hornbill beaks have a hollow region that extends from proximal to mid-section. The rhamphotheca is comprised of super-posed polygonal scales (45 mum diameter and 1 mum thickness) fixed by some organic adhesive. The branched intermediate filaments embedded in keratin matrix were discovered by transmission electron microscopy (TEM). The diameter of intermediate laments was ~10 nm. The orientation of intermediate filaments was examined with TEM tomography and the branched filaments were homogeneously distributed. The closed-cell foam is comprised of the fibrous structure of bony struts with an edge connectivity of three or four and the cells are sealed off by the thin membranes. The volumetric structure of bird beak foam was reproduced by computed tomography for finite element modeling.

The physical chemistry of Criegee intermediates in the gas phase

DOE PAGES

Osborn, David L.; Taatjes, Craig A.

2015-07-24

Here, carbonyl oxides, also known as Criegee intermediates, are key intermediates in both gas phase ozonolysis of unsaturated hydrocarbons in the troposphere and solution phase organic synthesis via ozonolysis. Although the study of Criegee intermediates in both arenas has a long history, direct studies in the gas phase have only recently become possible through new methods of generating stabilised Criegee intermediates in sufficient quantities. This advance has catalysed a large number of new experimental and theoretical investigations of Criegee intermediate chemistry. In this article we review the physical chemistry of Criegee intermediates, focusing on their molecular structure, spectroscopy, unimolecular andmore » bimolecular reactions. These recent results have overturned conclusions from some previous studies, while confirming others, and have clarified areas of investigation that will be critical targets for future studies. In addition to expanding our fundamental understanding of Criegee intermediates, the rapidly expanding knowledge base will support increasingly predictive models of their impacts on society.« less

Super-Planckian Thermophotovoltaics Without Vacuum Gaps

NASA Astrophysics Data System (ADS)

Mirmoosa, M. S.; Biehs, S.-A.; Simovski, C. R.

2017-11-01

We introduce the concept of a thermophotovoltaic system whose emitter is separated from the photovoltaic cell by an intermediate thick slab of gallium arsenide. Owing to the engineered structure of the emitter (a multilayer structure of negative- and positive-ɛ layers) together with a high refractiveindex and transparency of the intermediate slab, we achieve a super-Planckian and frequency-selective spectrum of radiative heat transfer which is desirable for the efficient performance of thermophotovoltaic systems.

The evolution of intermediate castration virulence and ant coexistence in a spatially structured environment.

PubMed

Szilágyi, András; Scheuring, István; Edwards, David P; Orivel, Jerome; Yu, Douglas W

2009-12-01

Theory suggests that spatial structuring should select for intermediate levels of virulence in parasites, but empirical tests are rare and have never been conducted with castration (sterilizing) parasites. To test this theory in a natural landscape, we construct a spatially explicit model of the symbiosis between the ant-plant Cordia nodosa and its two, protecting ant symbionts, Allomerus and Azteca. Allomerus is also a castration parasite, preventing fruiting to increase colony fecundity. Limiting the dispersal of Allomerus and host plant selects for intermediate castration virulence. Increasing the frequency of the mutualist, Azteca, selects for higher castration virulence in Allomerus, because seeds from Azteca-inhabited plants are a public good that Allomerus exploits. These results are consistent with field observations and, to our knowledge, provide the first empirical evidence supporting the hypothesis that spatial structure can reduce castration virulence and the first such evidence in a natural landscape for either mortality or castration virulence.

Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes.

PubMed

Lin, Milo M; Meinhold, Lars; Shorokhov, Dmitry; Zewail, Ahmed H

2008-08-07

A 2D free-energy landscape model is presented to describe the (un)folding transition of DNA/RNA hairpins, together with molecular dynamics simulations and experimental findings. The dependence of the (un)folding transition on the stem sequence and the loop length is shown in the enthalpic and entropic contributions to the free energy. Intermediate structures are well defined by the two coordinates of the landscape during (un)zipping. Both the free-energy landscape model and the extensive molecular dynamics simulations totaling over 10 mus predict the existence of temperature-dependent kinetic intermediate states during hairpin (un)zipping and provide the theoretical description of recent ultrafast temperature-jump studies which indicate that hairpin (un)zipping is, in general, not a two-state process. The model allows for lucid prediction of the collapsed state(s) in simple 2D space and we term it the kinetic intermediate structure (KIS) model.

A Springloaded Metal-Ligand Mesocate Allows Access to Trapped Intermediates of Self-Assembly.

PubMed

Bogie, Paul M; Holloway, Lauren R; Lyon, Yana; Onishi, Nicole C; Beran, Gregory J O; Julian, Ryan R; Hooley, Richard J

2018-04-02

A strained, "springloaded" Fe 2 L 3 iminopyridine mesocate shows highly variable reactivity upon postassembly reaction with competitive diamines. The strained assembly is reactive toward transimination in minutes at ambient temperature and allows observation of kinetically trapped intermediates in the self-assembly pathway. When diamines are used that can only form less favored cage products upon full equilibration, trapped ML 3 fragments with pendant, "hanging" NH 2 groups are selectively formed instead. Slight variations in diamine structure have large effects on the product outcome: less rigid diamines convert the mesocate to more favored self-assembled cage complexes under mild conditions and allow observation of heterocomplex intermediates in the displacement pathway. The mesocate allows control of equilibrium processes and direction of product outcomes via small, iterative changes in added subcomponent structure and provides a method of accessing metal-ligand cage structures not normally observed in multicomponent Fe-iminopyridine self-assembly.

Interrogating viral capsid assembly with ion mobility-mass spectrometry

NASA Astrophysics Data System (ADS)

Uetrecht, Charlotte; Barbu, Ioana M.; Shoemaker, Glen K.; van Duijn, Esther; Heck, Albert J. R.

2011-02-01

Most proteins fulfil their function as part of large protein complexes. Surprisingly, little is known about the pathways and regulation of protein assembly. Several viral coat proteins can spontaneously assemble into capsids in vitro with morphologies identical to the native virion and thus resemble ideal model systems for studying protein complex formation. Even for these systems, the mechanism for self-assembly is still poorly understood, although it is generally thought that smaller oligomeric structures form key intermediates. This assembly nucleus and larger viral assembly intermediates are typically low abundant and difficult to monitor. Here, we characterised small oligomers of Hepatitis B virus (HBV) and norovirus under equilibrium conditions using native ion mobility mass spectrometry. This data in conjunction with computational modelling enabled us to elucidate structural features of these oligomers. Instead of more globular shapes, the intermediates exhibit sheet-like structures suggesting that they are assembly competent. We propose pathways for the formation of both capsids.

Resonance-Raman spectro-electrochemistry of intermediates in molecular artificial photosynthesis of bimetallic complexes.

PubMed

Zedler, Linda; Guthmuller, Julien; Rabelo de Moraes, Inês; Kupfer, Stephan; Krieck, Sven; Schmitt, Michael; Popp, Jürgen; Rau, Sven; Dietzek, Benjamin

2014-05-25

The sequential order of photoinduced charge transfer processes and accompanying structure changes were analyzed by UV-vis and resonance-Raman spectroscopy of intermediates of a Ru(ii) based photocatalytic hydrogen evolving system obtained by electrochemical reduction.

Microengineered 3D cell-laden thermoresponsive hydrogels for mimicking cell morphology and orientation in cartilage tissue engineering.

PubMed

Mellati, Amir; Fan, Chia-Ming; Tamayol, Ali; Annabi, Nasim; Dai, Sheng; Bi, Jingxiu; Jin, Bo; Xian, Cory; Khademhosseini, Ali; Zhang, Hu

2017-01-01

Mimicking the zonal organization of native articular cartilage, which is essential for proper tissue functions, has remained a challenge. In this study, a thermoresponsive copolymer of chitosan-g-poly(N-isopropylacrylamide) (CS-g-PNIPAAm) was synthesized as a carrier of mesenchymal stem cells (MSCs) to provide a support for their proliferation and differentiation. Microengineered three-dimensional (3D) cell-laden CS-g-PNIPAAm hydrogels with different microstripe widths were fabricated to control cellular alignment and elongation in order to mimic the superficial zone of natural cartilage. Biochemical assays showed six- and sevenfold increment in secretion of glycosaminoglycans (GAGs) and total collagen from MSCs encapsulated within the synthesized hydrogel after 28 days incubation in chondrogenic medium. Chondrogenic differentiation was also verified qualitatively by histological and immunohistochemical assessments. It was found that 75 ± 6% of cells encapsulated within 50 μm wide microstripes were aligned with an aspect ratio of 2.07 ± 0.16 at day 5, which was more organized than those observed in unpatterned constructs (12 ± 7% alignment and a shape index of 1.20 ± 0.07). The microengineered constructs mimicked the cell shape and organization in the superficial zone of cartilage whiles the unpatterned one resembled the middle zone. Our results suggest that microfabrication of 3D cell-laden thermosensitive hydrogels is a promising platform for creating biomimetic structures leading to more successful multi-zonal cartilage tissue engineering. Biotechnol. Bioeng. 2017;114: 217-231. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

The Effects of Hsp90α1 Mutations on Myosin Thick Filament Organization.

PubMed

He, Qiuxia; Liu, Kechun; Tian, Zhenjun; Du, Shao Jun

2015-01-01

Heat shock protein 90α plays a key role in myosin folding and thick filament assembly in muscle cells. To assess the structure and function of Hsp90α and its potential regulation by post-translational modification, we developed a combined knockdown and rescue assay in zebrafish embryos to systematically analyze the effects of various mutations on Hsp90α function in myosin thick filament organization. DNA constructs expressing the Hsp90α1 mutants with altered putative ATP binding, phosphorylation, acetylation or methylation sites were co-injected with Hsp90α1 specific morpholino into zebrafish embryos. Myosin thick filament organization was analyzed in skeletal muscles of the injected embryos by immunostaining. The results showed that mutating the conserved D90 residue in the Hsp90α1 ATP binding domain abolished its function in thick filament organization. In addition, phosphorylation mimicking mutations of T33D, T33E and T87E compromised Hsp90α1 function in myosin thick filament organization. Similarly, K287Q acetylation mimicking mutation repressed Hsp90α1 function in myosin thick filament organization. In contrast, K206R and K608R hypomethylation mimicking mutations had not effect on Hsp90α1 function in thick filament organization. Given that T33 and T87 are highly conserved residues involved post-translational modification (PTM) in yeast, mouse and human Hsp90 proteins, data from this study could indicate that Hsp90α1 function in myosin thick filament organization is potentially regulated by PTMs involving phosphorylation and acetylation.

The Effects of Hsp90α1 Mutations on Myosin Thick Filament Organization

PubMed Central

He, Qiuxia; Liu, Kechun; Tian, Zhenjun; Du, Shao Jun

2015-01-01

Heat shock protein 90α plays a key role in myosin folding and thick filament assembly in muscle cells. To assess the structure and function of Hsp90α and its potential regulation by post-translational modification, we developed a combined knockdown and rescue assay in zebrafish embryos to systematically analyze the effects of various mutations on Hsp90α function in myosin thick filament organization. DNA constructs expressing the Hsp90α1 mutants with altered putative ATP binding, phosphorylation, acetylation or methylation sites were co-injected with Hsp90α1 specific morpholino into zebrafish embryos. Myosin thick filament organization was analyzed in skeletal muscles of the injected embryos by immunostaining. The results showed that mutating the conserved D90 residue in the Hsp90α1 ATP binding domain abolished its function in thick filament organization. In addition, phosphorylation mimicking mutations of T33D, T33E and T87E compromised Hsp90α1 function in myosin thick filament organization. Similarly, K287Q acetylation mimicking mutation repressed Hsp90α1 function in myosin thick filament organization. In contrast, K206R and K608R hypomethylation mimicking mutations had not effect on Hsp90α1 function in thick filament organization. Given that T33 and T87 are highly conserved residues involved post-translational modification (PTM) in yeast, mouse and human Hsp90 proteins, data from this study could indicate that Hsp90α1 function in myosin thick filament organization is potentially regulated by PTMs involving phosphorylation and acetylation. PMID:26562659

Electrocardiogram artifact caused by rigors mimicking narrow complex tachycardia: a case report.

PubMed

Matthias, Anne Thushara; Indrakumar, Jegarajah

2014-02-04

The electrocardiogram (ECG) is useful in the diagnosis of cardiac and non-cardiac conditions. Rigors due to shivering can cause electrocardiogram artifacts mimicking various cardiac rhythm abnormalities. We describe an 80-year-old Sri Lankan man with an abnormal electrocardiogram mimicking narrow complex tachycardia during the immediate post-operative period. Electrocardiogram changes caused by muscle tremor during rigors could mimic a narrow complex tachycardia. Identification of muscle tremor as a cause of electrocardiogram artifact can avoid unnecessary pharmacological and non-pharmacological intervention to prevent arrhythmias.

Mesalamine treatment mimicking relapse in a child with ulcerative colitis.

PubMed

Hojsak, Iva; Pavić, Ana M; Kolaček, Sanja

2014-11-01

There are reports on mesalamine-induced bloody diarrhea mimicking ulcerative colitis (UC) relapse, mostly in adults. Herein we present a case of a child with UC who developed relapse of hemorrhagic colitis related to mesalamine. A 10-year-old girl developed severe symptoms mimicking UC relapse 3 weeks after introduction of mesalamine therapy. After mesalamine was withdrawn, her symptoms improved, but deteriorated again during the challenge of mesalamine despite concomitant use of corticosteroids. This is the first case report on such a young child during the concomitant use of corticosteroids.

Magnetic Ordering of Erbium and Uranium NICKEL(2) SILICON(2) by Neutron Scattering

NASA Astrophysics Data System (ADS)

Lin, Hong

The magnetic ordering has been studied in UNi _2Si_2 and erbium single crystals by elastic neutron scattering. Abundant results are given regarding the magnetic structure, magnetic phase transitions, and the effect of a magnetic field on these properties. Three ordered phases are observed in UNi _2Si_2. They have been determined to be an incommensurate longitudinal spin density wave with a magnetic wave vector around q = 0.74c ^* in the high temperature phase, a simple body-centred antiferromagnet in the intermediate temperature phase, and a square wave in the low temperature phase. This square wave can be viewed equivalently as a longitudinal spin density wave with q = 2/3c ^* superimposed on a ferromagnetic component. Hysteresis and sample dependence are observed in the low-temperature phase transition. The two lower temperature phase transitions are both first order. The transition to paramagnetism is second order with a critical exponent beta = 0.35 +/- 0.03. When a magnetic field is applied along the c axis, the intermediate temperature phase is destabilised and disappears above a field of 3.5T. Although there is no new phase induced by the field, there exists a reentrant point where the three ordered phases can coexist. Erbium has three distinct ordered phases: the cone phase at low temperatures, the c-axis modulated (CAM) phase at higher temperatures, and the intermediate phase with moments modulated both along c and perpendicular to c. Within these phases the modulation of the moments may lock in to the lattice. The observed weak harmonics of the wave vector q in the basal plane for the cone phase and the q = 1/4c^* structure in the intermediate phase can be explained by a basal-plane spin slip model. The effect of magnetic field along the c axis on the magnetic structure is to stabilise the cone phase and to destabilise the intermediate phase. A new lock-in structure with q = 1/4c^* in the cone phase is induced by fields above 1.8T. The presence of the field also stabilises the lock-in structure with q = 2/7c^* in both the intermediate and the CAM phases.

Recent Progress of Microfluidics in Translational Applications

PubMed Central

Liu, Zongbin; Han, Xin

2016-01-01

Microfluidics, featuring microfabricated structures, is a technology for manipulating fluids at the micrometer scale. The small dimension and flexibility of microfluidic systems are ideal for mimicking molecular and cellular microenvironment, and show great potential in translational research and development. Here, the recent progress of microfluidics in biological and biomedical applications, including molecular analysis, cellular analysis, and chip-based material delivery and biomimetic design is presented. The potential future developments in the translational microfluidics field are also discussed. PMID:27091777

Modular heat exchanger

DOEpatents

Giardina, A.R.

1981-03-03

A shell and tube heat exchanger is described having a plurality of individually removable tube bundle modules. A lattice of structural steel forming rectangular openings therein is placed at each end of a cylindrical shell. Longitudinal structural members are placed in the shell between corners of the rectangular openings situated on opposite ends of the shell. Intermediate support members interconnect the longitudinal supports so as to increase the longitudinal supports rigidity. Rectangular parallelepiped tube bundle modules occupy the space defined by the longitudinal supports and end supports and each include a rectangular tube sheet situated on each end of a plurality of tubes extending there through, a plurality of rectangular tube supports located between the tube sheets, and a tube bundle module stiffening structure disposed about the bundle's periphery and being attached to the tube sheets and tube supports. The corners of each tube bundle module have longitudinal framework members which are mateable with and supported by the longitudinal support members. Intermediate support members constitute several lattices, each of which is situated in a plane between the end support members. The intermediate support members constituting the several lattices extend horizontally and vertically between longitudinal supports of adjacent tube module voids. An alternative embodiment for intermediate support members constitute a series of structural plates situated at the corners of the module voids and having recesses therein for receiving the respective longitudinal support members adjacent thereto, protrusions separating the recesses, and a plurality of struts situated between protrusions of adjacent structural plates. 12 figs.

Modular heat exchanger

DOEpatents

Giardina, Angelo R. [Marple Township, Delaware County, PA

1981-03-03

A shell and tube heat exchanger having a plurality of individually removable tube bundle modules. A lattice of structural steel forming rectangular openings therein is placed at each end of a cylindrical shell. Longitudinal structural members are placed in the shell between corners of the rectangular openings situated on opposite ends of the shell. Intermediate support members interconnect the longitudinal supports so as to increase the longitudinal supports rigidity. Rectangular parallelpiped tube bundle moldules occupy the space defined by the longitudinal supports and end supports and each include a rectangular tube sheet situated on each end of a plurality of tubes extending therethrough, a plurality of rectangular tube supports located between the tube sheets, and a tube bundle module stiffening structure disposed about the bundle's periphery and being attached to the tube sheets and tube supports. The corners of each tube bundle module have longitudinal framework members which are mateable with and supported by the longitudinal support members. Intermediate support members constitute several lattice, each of which is situate d in a plane between the end support members. The intermediate support members constituting the several lattice extend horizontally and vertically between longitudinal supports of adjacent tube module voids. An alternative embodiment for intermediate support members constitute a series of structural plates situated at the corners of the module voids and having recesses therein for receiving the respective longitudinal support members adjacent thereto, protrusions separating the recesses, and a plurality of struts situated between protrusions of adjacent structural plates.

Common structural features of toxic intermediates from α-synuclein and GroES fibrillogenesis detected using cryogenic coherent X-ray diffraction imaging.

PubMed

Kameda, Hiroshi; Usugi, Sayaka; Kobayashi, Mana; Fukui, Naoya; Lee, Seki; Hongo, Kunihiro; Mizobata, Tomohiro; Sekiguchi, Yuki; Masaki, Yu; Kobayashi, Amane; Oroguchi, Tomotaka; Nakasako, Masayoshi; Takayama, Yuki; Yamamoto, Masaki; Kawata, Yasushi

2017-01-01

The aggregation and deposition of α-synuclein (αSyn) in neuronal cells is correlated to pathogenesis of Parkinson's disease. Although the mechanism of αSyn aggregation and fibril formation has been studied extensively, the structural hallmarks that are directly responsible for toxicity toward cells are still under debate. Here, we have compared the structural characteristics of the toxic intermediate molecular species of αSyn and similar toxic species of another protein, GroES, using coherent X-ray diffraction analysis. Using coherent X-ray free electron laser pulses of SACLA, we analysed αSyn and GroES fibril intermediate species and characterized various aggregate structures. Unlike previous studies where an annular oligomeric form of αSyn was identified, particle reconstruction from scattering traces suggested that the specific forms of the toxic particles were varied, with the sizes of the particles falling within a specific range. We did however discover a common structural feature in both αSyn and GroES samples; the edges of the detected particles were nearly parallel and produced a characteristic diffraction pattern in the diffraction experiments. The presence of parallel-edged particles in toxic intermediates of αSyn and GroES fibrillogenesis pointed towards a plausible common molecular interface that leads to the formation of mature fibrils. © The Authors 2016. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

SU-F-T-433: Evaluation of a New Dose Mimicking Application for Clinical Flexibility and Reliability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoffman, D; Nair, C Kumaran; Wright, C

2016-06-15

Purpose: Clinical workflow and machine down time occasionally require patients to be temporarily treated on a system other than the initial treatment machine. A new commercial dose mimicking application provides automated cross-platform treatment planning to expedite this clinical flexibility. The aim of this work is to evaluate the feasibility of automatic plan creation and establish a robust clinical workflow for prostate and pelvis patients. Methods: Five prostate and five pelvis patients treated with helical plans were selected for re-planning with the dose mimicking application, covering both simple and complex scenarios. Two-arc VMAT and 7- and 9-field IMRT plans were generatedmore » for each case, with the objective function of achieving similar dose volume histogram from the initial helical plans. Dosimetric comparisons include target volumes and organs at risk (OARs) (rectum, bladder, small bowel, femoral heads, etc.). Dose mimicked plans were evaluated by a radiation oncologist, and patient-specific QAs were performed to validate delivery. Results: Overall plan generation and transfer required around 30 minutes of dosimetrist’s time once the dose-mimicking protocol is setup for each site. The resulting VMAT and 7- and 9-field IMRT plans achieved equivalent PTV coverage and homogeneity (D99/DRx = 97.3%, 97.2%, 97.2% and HI = 6.0, 5.8, and 5.9, respectively), compared to helical plans (97.6% and 4.6). The OAR dose discrepancies were up to 6% in rectum Dmean, but generally lower in bladder, femoral heads, bowel and penile bulb. In the context of 1–5 fractions, the radiation oncologist evaluated the dosimetric changes as not clinically significant. All delivery QAs achieved >90% pass with a 3%/3mm gamma criteria. Conclusion: The automated dose-mimicking workflow offers a strategy to avoid missing treatment fractions due to machine down time with non-clinically significant changes in dosimetry. Future work will further optimize dose mimicking plans and investigate other cross-platform treatment delivery options.« less

High-Rate Charging Induced Intermediate Phases and Structural Changes of Layer-Structured Cathode for Lithium-Ion Batteries

DOE PAGES

Zhou, Yong-Ning; Yue, Ji-Li; Hu, Enyuan; ...

2016-08-08

Using fast time-resolved in situ X-ray diffraction, charge-rate dependent phase transition processes of layer structured cathode material LiNi 1/3Mn 1/3Co 1/3O 2 for lithium-ion batteries are studied. During first charge, intermediate phases emerge at high rates of 10C, 30C, and 60C, but not at low rates of 0.1C and 1C. These intermediate phases can be continuously observed during relaxation after the charging current is switched off. After half-way charging at high rate, sample studied by scanning transmission electron microscopy shows Li-rich and Li-poor phases' coexistence with tetrahedral occupation of Li in Li-poor phase. Also, the high rate induced overpotential ismore » thought to be the driving force for the formation of this intermediate Li-poor phase. The in situ quick X-ray absorption results show that the oxidation of Ni accelerates with increasing charging rate and the Ni 4+ state can be reached at the end of charge with 30C rate. Finally, these results give new insights in the understanding of the layered cathodes during high-rate charging.« less

The large-scale structure of the Universe.

PubMed

Springel, Volker; Frenk, Carlos S; White, Simon D M

2006-04-27

Research over the past 25 years has led to the view that the rich tapestry of present-day cosmic structure arose during the first instants of creation, where weak ripples were imposed on the otherwise uniform and rapidly expanding primordial soup. Over 14 billion years of evolution, these ripples have been amplified to enormous proportions by gravitational forces, producing ever-growing concentrations of dark matter in which ordinary gases cool, condense and fragment to make galaxies. This process can be faithfully mimicked in large computer simulations, and tested by observations that probe the history of the Universe starting from just 400,000 years after the Big Bang.

Cystic Benign Metastasizing Leiomyoma of the Lung Mimicking Hydatid Cyst.

PubMed

Alimi, Faouzi; El Hadj Sidi, Chighali; Ghannouchi, Chams

2016-12-01

A 60-year-old woman, with history of a resected uterine benign leiomyoma, is operated for a cystic lesion in the left lung, mimicking an hydatid cyst, and confirmed histologically as Cystic Benign Metastasizing Leiomyoma.

Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments

PubMed Central

Mizukami, Takuya; Abe, Yukiko; Maki, Kosuke

2015-01-01

In this study, the equivalence of the kinetic mechanisms of the formation of urea-induced kinetic folding intermediates and non-native equilibrium states was investigated in apomyoglobin. Despite having similar structural properties, equilibrium and kinetic intermediates accumulate under different conditions and via different mechanisms, and it remains unknown whether their formation involves shared or distinct kinetic mechanisms. To investigate the potential mechanisms of formation, the refolding and unfolding kinetics of horse apomyoglobin were measured by continuous- and stopped-flow fluorescence over a time range from approximately 100 μs to 10 s, along with equilibrium unfolding transitions, as a function of urea concentration at pH 6.0 and 8°C. The formation of a kinetic intermediate was observed over a wider range of urea concentrations (0–2.2 M) than the formation of the native state (0–1.6 M). Additionally, the kinetic intermediate remained populated as the predominant equilibrium state under conditions where the native and unfolded states were unstable (at ~0.7–2 M urea). A continuous shift from the kinetic to the equilibrium intermediate was observed as urea concentrations increased from 0 M to ~2 M, which indicates that these states share a common kinetic folding mechanism. This finding supports the conclusion that these intermediates are equivalent. Our results in turn suggest that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding, which further supports the structural equivalence of transient and equilibrium intermediates. An additional folding intermediate accumulated within ~140 μs of refolding and an unfolding intermediate accumulated in <1 ms of unfolding. Finally, by using quantitative modeling, we showed that a five-state sequential scheme appropriately describes the folding mechanism of horse apomyoglobin. PMID:26244984

Well, slap my thigh: expression of surprise facilitates memory of surprising material.

PubMed

Parzuchowski, Michal; Szymkow-Sudziarska, Aleksandra

2008-06-01

Two studies examined the general prediction that one's emotional expression should facilitate memory for material that matches the expression. The authors focused on specific facial expressions of surprise. In the first study, participants who were mimicking a surprised expression showed better recall for the surprising words and worse recall for neutral words, relative to those who were mimicking a neutral expression. Study 2 replicated the results of Study 1, showing that participants who mimicked a surprised expression recalled more words spoken in a surprising manner compared with those that sounded neutral or sad. Conversely, participants who mimicked sad facial expressions showed greater recall for sad than neutral or surprising words. The results provide evidence of the importance of matching the emotional valence of the recall content to the facial expression of the recaller during the memorization period. (PsycINFO Database Record (c) 2008 APA, all rights reserved). (Copyright) 2008 APA, all rights reserved.

A Metal Bump Bonding Method Using Ag Nanoparticles as Intermediate Layer

NASA Astrophysics Data System (ADS)

Fu, Weixin; Nimura, Masatsugu; Kasahara, Takashi; Mimatsu, Hayata; Okada, Akiko; Shoji, Shuichi; Ishizuka, Shugo; Mizuno, Jun

2015-11-01

The future development of low-temperature and low-pressure bonding technology is necessary for fine-pitch bump application. We propose a bump structure using Ag nanoparticles as an intermediate layer coated on a fine-pitch Cu pillar bump. The intermediate layer is prepared using an efficient and cost-saving squeegee-coating method followed by a 100°C baking process. This bump structure can be easily flattened before the bonding process, and the low-temperature sinterability of the nanoparticles is retained. The bonding experiment was successfully performed at 250°C and 39.8 MPa and the bonding strength was comparable to that achieved via other bonding technology utilizing metal particles or porous material as bump materials.

DNA-Mediated Self-Organization of Polymeric Nanocompartments Leads to Interconnected Artificial Organelles.

PubMed

Liu, Juan; Postupalenko, Viktoriia; Lörcher, Samuel; Wu, Dalin; Chami, Mohamed; Meier, Wolfgang; Palivan, Cornelia G

2016-11-09

Self-organization of nanocomponents was mainly focused on solid nanoparticles, quantum dots, or liposomes to generate complex architectures with specific properties, but intrinsically limited or not developed enough, to mimic sophisticated structures with biological functions in cells. Here, we present a biomimetic strategy to self-organize synthetic nanocompartments (polymersomes) into clusters with controlled properties and topology by exploiting DNA hybridization to interconnect polymersomes. Molecular and external factors affecting the self-organization served to design clusters mimicking the connection of natural organelles: fine-tune of the distance between tethered polymersomes, different topologies, no fusion of clustered polymersomes, and no aggregation. Unexpected, extended DNA bridges that result from migration of the DNA strands inside the thick polymer membrane (about 12 nm) represent a key stability and control factor, not yet exploited for other synthetic nano-object networks. The replacement of the empty polymersomes with artificial organelles, already reported for single polymersome architecture, will provide an excellent platform for the development of artificial systems mimicking natural organelles or cells and represents a fundamental step in the engineering of molecular factories.

Polyclonal antibodies against a structure mimicking the covalent linkage unit between picornavirus RNA and VPg: an immunochemical study.

PubMed

Ivanova, O A; Venyaminova, A G; Repkova, M N; Drygin, Yu F

2005-09-01

We propose that therapy of patients with anticancer drugs that poison DNA topoisomerases induces formation of covalent complexes of cellular RNAs and DNA topoisomerases. The appearance of these complexes can be detected with antibodies against a synthetic hapten mimicking the covalent linkage unit Tyr-pU(p) of picornavirus RNA and VPg. We synthesized hapten [N(Ac),CO(NH2)]Tyr-(5 P --> O)Up-O-(CH2)6NH2, conjugated it with BSA, and immunized rabbits with the antigen obtained. The raised polyclonal antibodies were purified by successive affinity chromatography on BSA-Sepharose and hapten-Sepharose columns. Target antibodies recognized hapten and encephalomyocarditis virus RNA-VPg complex specifically as found using the dot-immunogold method. We believe that these antibodies might be useful to study mechanism of picorna and similar virus RNA synthesis. The discovery and qualitative determination of the cellular RNA-DNA topoisomerases covalent complexes with these antibodies might be useful to monitor therapy efficacy by drugs "freezing" dead-end complexes of DNA topoisomerases and nucleic acids and to understand the mechanism of DNA topoisomerase poisoning in situ.

Unfolding Kinetics of β-Lactoglobulin Induced by Surfactant and Denaturant: A Stopped-Flow/Fluorescence Study

PubMed Central

Viseu, Maria Isabel; Melo, Eduardo P.; Carvalho, Teresa Isabel; Correia, Raquel F.; Costa, Sílvia M. B.

2007-01-01

The β→α transition of β-lactoglobulin, a globular protein abundant in the milk of several mammals, is investigated in this work. This transition, induced by the cationic surfactant dodecyltrimethylammonium chloride (DTAC), is accompanied by partial unfolding of the protein. In this work, unfolding of bovine β-lactoglobulin in DTAC is compared with its unfolding induced by the chemical denaturant guanidine hydrochloride (GnHCl). The final protein states attained in the two media have quite different secondary structure: in DTAC the α-helical content increases, leading to the so-called α-state; in GnHCl the amount of ordered secondary-structure decreases, resulting in a random coil-rich final state (denatured, or D, state). To obtain information on both mechanistic routes, in DTAC and GnHCl, and to characterize intermediates, the kinetics of unfolding were investigated in the two media. Equilibrium and kinetic data show the partial accumulation of an on-pathway intermediate in each unfolding route: in DTAC, an intermediate (I1) with mostly native secondary structure but loose tertiary structure appears between the native (β) and α-states; in GnHCl, another intermediate (I2) appears between states β and D. Kinetic rate constants follow a linear Chevron-plot representation in GnHCl, but show a more complex mechanism in DTAC, which acts like a stronger binding species. PMID:17693475

Acute Fulminant Uremic Neuropathy Following Coronary Angiography Mimicking Guillain-Barre Syndrome.

PubMed

Priti, Kumari; Ranwa, Bhanwar

2017-01-01

A 55-year-old diabetic woman suffered a posterior wall ST-elevation myocardial infarction. She developed contrast-induced nephropathy following coronary angiography. Acute fulminant uremic neuropathy was precipitated which initially mimicked Guillan-Barre Syndrome, hence reported.

Ring system-based chemical graph generation for de novo molecular design

NASA Astrophysics Data System (ADS)

Miyao, Tomoyuki; Kaneko, Hiromasa; Funatsu, Kimito

2016-05-01

Generating chemical graphs in silico by combining building blocks is important and fundamental in virtual combinatorial chemistry. A premise in this area is that generated structures should be irredundant as well as exhaustive. In this study, we develop structure generation algorithms regarding combining ring systems as well as atom fragments. The proposed algorithms consist of three parts. First, chemical structures are generated through a canonical construction path. During structure generation, ring systems can be treated as reduced graphs having fewer vertices than those in the original ones. Second, diversified structures are generated by a simple rule-based generation algorithm. Third, the number of structures to be generated can be estimated with adequate accuracy without actual exhaustive generation. The proposed algorithms were implemented in structure generator Molgilla. As a practical application, Molgilla generated chemical structures mimicking rosiglitazone in terms of a two dimensional pharmacophore pattern. The strength of the algorithms lies in simplicity and flexibility. Therefore, they may be applied to various computer programs regarding structure generation by combining building blocks.

Activation of chronic toxoplasmosis by transportation stress in a mouse model.

PubMed

Shen, Bang; Yuan, Yuan; Cheng, Jianxi; Pan, Ming; Xia, Ningbo; Zhang, Weichao; Wang, Yifan; Zhou, Yanqin; Zhao, Junlong

2016-12-27

Toxoplasma gondii is an obligate intracellular parasite infecting 25% of the world population and enormous number of animals. It can exist in two forms in intermediate hosts: the fast replicating tachyzoites responsible for acute infection and the slowly replicating bradyzoites responsible for life-long chronic infection. The interconversion between tachyzoites and bradyzoites plays critical roles in the transmission and pathogenesis of T. gondii. However, the molecular mechanisms that govern the interconversion are largely unknown. In this study, we established a chronic infection model in mice and examined the impact of transportation stress on the status of chronic infection. Our results demonstrated that, treating chronically infected mice with conditions mimicking transportation stress reduced the levels of several key cytokines that restrict the infection at chronic stage. Increased expression of the tachyzoite specific gene SAG1 (surface antigen 1) was detected in brain cysts of stress treated mice, indicating activation and conversion of bradyzoites to tachyzoites. Using this model, we identified fifteen toxoplasmic proteins that had significant abundance changes during stress induced cysts reactivation. These proteins serve as a basis for further investigation of the mechanisms governing bradyzoite conversion.

COX16 promotes COX2 metallation and assembly during respiratory complex IV biogenesis

PubMed Central

Aich, Abhishek; Wang, Cong; Chowdhury, Arpita; Ronsör, Christin; Pacheu-Grau, David; Richter-Dennerlein, Ricarda; Dennerlein, Sven

2018-01-01

Cytochrome c oxidase of the mitochondrial oxidative phosphorylation system reduces molecular oxygen with redox equivalent-derived electrons. The conserved mitochondrial-encoded COX1- and COX2-subunits are the heme- and copper-center containing core subunits that catalyze water formation. COX1 and COX2 initially follow independent biogenesis pathways creating assembly modules with subunit-specific, chaperone-like assembly factors that assist in redox centers formation. Here, we find that COX16, a protein required for cytochrome c oxidase assembly, interacts specifically with newly synthesized COX2 and its copper center-forming metallochaperones SCO1, SCO2, and COA6. The recruitment of SCO1 to the COX2-module is COX16- dependent and patient-mimicking mutations in SCO1 affect interaction with COX16. These findings implicate COX16 in CuA-site formation. Surprisingly, COX16 is also found in COX1-containing assembly intermediates and COX2 recruitment to COX1. We conclude that COX16 participates in merging the COX1 and COX2 assembly lines. PMID:29381136

Transient intermediates are populated in the folding pathways of single-domain two-state folding protein L

NASA Astrophysics Data System (ADS)

Maity, Hiranmay; Reddy, Govardhan

2018-04-01

Small single-domain globular proteins, which are believed to be dominantly two-state folders, played an important role in elucidating various aspects of the protein folding mechanism. However, recent single molecule fluorescence resonance energy transfer experiments [H. Y. Aviram et al. J. Chem. Phys. 148, 123303 (2018)] on a single-domain two-state folding protein L showed evidence for the population of an intermediate state and it was suggested that in this state, a β-hairpin present near the C-terminal of the native protein state is unfolded. We performed molecular dynamics simulations using a coarse-grained self-organized-polymer model with side chains to study the folding pathways of protein L. In agreement with the experiments, an intermediate is populated in the simulation folding pathways where the C-terminal β-hairpin detaches from the rest of the protein structure. The lifetime of this intermediate structure increased with the decrease in temperature. In low temperature conditions, we also observed a second intermediate state, which is globular with a significant fraction of the native-like tertiary contacts satisfying the features of a dry molten globule.

Direct Structural and Chemical Characterization of the Photolytic Intermediates of Methylcobalamin Using Time-Resolved X-ray Absorption Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Subramanian, Ganesh; Zhang, Xiaoyi; Kodis, Gerdenis

Cobalt-carbon bond cleavage is crucial to most natural and synthetic applications of the cobalamin class of compounds, and here we present the first direct electronic and geometric structural characteristics of intermediates formed following photoexcitation of methylcobalamin (MeCbl) using time-resolved X-ray absorption spectroscopy (XAS). We catch transients corresponding to two intermediates, in the hundreds of picoseconds and a few microseconds. Highlights of the picosecond intermediate, which is reduced in comparison to the ground state, are elongation of the upper axial Co-C bond and relaxation of the corrin ring. This is not so with the recombining photocleaved products captured at a fewmore » microseconds, where the Co-C bond almost (yet not entirely) reverts to its ground state configuration and a substantially elongated lower axial Co-NIm bond is observed. The reduced cobalt site here confirms formation of methyl radical as the photoproduct.« less

Thiamin diphosphate-dependent enzymes: from enzymology to metabolic regulation, drug design and disease models.

PubMed

Bunik, Victoria I; Tylicki, Adam; Lukashev, Nikolay V

2013-12-01

Bringing a knowledge of enzymology into research in vivo and in situ is of great importance in understanding systems biology and metabolic regulation. The central metabolic significance of thiamin (vitamin B1 ) and its diphosphorylated derivative (thiamin diphosphate; ThDP), and the fundamental differences in the ThDP-dependent enzymes of metabolic networks in mammals versus plants, fungi and bacteria, or in health versus disease, suggest that these enzymes are promising targets for biotechnological and medical applications. Here, the in vivo action of known regulators of ThDP-dependent enzymes, such as synthetic structural analogs of the enzyme substrates and thiamin, is analyzed in light of the enzymological data accumulated during half a century of research. Mimicking the enzyme-specific catalytic intermediates, the phosphonate analogs of 2-oxo acids selectively inhibit particular ThDP-dependent enzymes. Because of their selectivity, use of these compounds in cellular and animal models of ThDP-dependent enzyme malfunctions improves the validity of the model and its predictive power when compared with the nonselective and enzymatically less characterized oxythiamin and pyrithiamin. In vitro studies of the interaction of thiamin analogs and their biological derivatives with potential in vivo targets are necessary to identify and attenuate the analog selectivity. For both the substrate and thiamin synthetic analogs, in vitro reactivities with potential targets are highly relevant in vivo. However, effective concentrations in vivo are often higher than in vitro studies would suggest. The significance of specific inihibition of the ThDP-dependent enzymes for the development of herbicides, antibiotics, anticancer and neuroprotective strategies is discussed. © 2013 FEBS.

Role of the lens in controlling physical dormancy break and germination of Delonix regia (Fabaceae: Caesalpinioideae).

PubMed

Jaganathan, G K; Wu, G-R; Han, Y-Y; Liu, B L

2017-01-01

Physical dormancy occurs in all three subfamilies of Fabaceae, namely Mimosoideae, Papilionoideae and Caesalpinioideae, making it one of the largest plant families in terms of number of species with physical dormancy. However, little is known about the water gap structure and germination ecology of species in Caesalpinioideae. Freshly collected seeds of Delonix regia (Caesalpinioideae) did not imbibe water, thus they had physical dormancy. Both dry heat and wet heat were effective in breaking dormancy, however, longer duration was required at 80 °C and shorter duration at 90 °C. Seeds buried in the field for 2 years germinated to 21% and 42% after the first and second summer, respectively, compared with 3% germination in seeds at the time of maturity. Seeds incubated at 15/60 °C in the laboratory (mimicking summer conditions) for 3 months supported this conclusion, as dormancy was relieved in 18% and 24% of seeds stored dry and watered intermediately, respectively. All the dormancy breaking treatments resulted in lifting of palisade layers in the lens region to form a circular lid-like opening, i.e. water gap (Type II simple). Blocking experiments confirmed that water entered only through the lens and no secondary water entry point was observed. No apparent changes in morphology/anatomy of the hilum region were noted in dormant and non-dormant (water permeable) seeds. These results suggest that summer temperatures could open the lens in a proportion of seeds every year and that germination occurs during the subsequent wet season in the tropics. © 2016 German Botanical Society and The Royal Botanical Society of the Netherlands.

Acute Fulminant Uremic Neuropathy Following Coronary Angiography Mimicking Guillain–Barre Syndrome

PubMed Central

Priti, Kumari; Ranwa, Bhanwar

2017-01-01

A 55-year-old diabetic woman suffered a posterior wall ST-elevation myocardial infarction. She developed contrast-induced nephropathy following coronary angiography. Acute fulminant uremic neuropathy was precipitated which initially mimicked Guillan–Barre Syndrome, hence reported. PMID:28706599

Calvarial sarcoid mimicking metastatic disease.

PubMed

Bodie, B F; Kheir, S M; Omura, E F

1980-10-01

A 61-year-old white woman presented with localized cutaneous Boeck's sarcoid and multiple lytic skull lesions mimicking metastatic carcinoma. Complete workup revealed no neoplastic process; biopsy of the skull lesions showed noncaseating granulomas consistent with sarcoid. Although rare, calvarial sarcoid can occur.

Tissue mimicking materials for dental ultrasound

PubMed Central

Singh, Rahul S.; Culjat, Martin O.; Grundfest, Warren S.; Brown, Elliott R.; White, Shane N.

2008-01-01

While acoustic tissue mimicking materials have been explored for a variety of soft and hard biological tissues, no dental hard tissue mimicking materials have been characterized. Tooth phantoms are necessary to better understand acoustic phenomenology within the tooth environment and to accelerate the advancement of dental ultrasound imaging systems. In this study, soda lime glass and dental composite were explored as surrogates for human enamel and dentin, respectively, in terms of compressional velocity, attenuation, and acoustic impedance. The results suggest that a tooth phantom consisting of glass and composite can effectively mimic the acoustic behavior of a natural human tooth. PMID:18396919

Melorheostosis mimicking synovial osteochondromatosis.

PubMed

Wadhwa, Vibhor; Chhabra, Avneesh; Samet, Jonathan D

2014-01-01

Melorheostosis is an uncommon, sporadic, sclerosing bone lesion that may affect the adjacent soft tissues. It has been associated with many entities such as osteopoikilosis, soft tissue vascular malformations, bone and soft tissue tumors, nephrotic syndrome, segmental limb contractures, osteosarcoma, desmoid tumor, and mesenteric fibromatosis. Synovial osteochondromatosis is a benign neoplasia of the hyaline cartilage presenting as nodules in the subsynovial tissue of a joint or tendon sheath. The intra-articular extension of melorheostosis mimicking synovial osteochondromatosis has not been reported before. In this article, the authors describe an unusual case mimicking synovial chondromatosis arising as a result of melorheostosis and their characteristic imaging findings.

The E. coli thioredoxin folding mechanism: the key role of the C-terminal helix.

PubMed

Vazquez, Diego S; Sánchez, Ignacio E; Garrote, Ana; Sica, Mauricio P; Santos, Javier

2015-02-01

In this work, the unfolding mechanism of oxidized Escherichia coli thioredoxin (EcTRX) was investigated experimentally and computationally. We characterized seven point mutants distributed along the C-terminal α-helix (CTH) and the preceding loop. The mutations destabilized the protein against global unfolding while leaving the native structure unchanged. Global analysis of the unfolding kinetics of all variants revealed a linear unfolding route with a high-energy on-pathway intermediate state flanked by two transition state ensembles TSE1 and TSE2. The experiments show that CTH is mainly unfolded in TSE1 and the intermediate and becomes structured in TSE2. Structure-based molecular dynamics are in agreement with these experiments and provide protein-wide structural information on transient states. In our model, EcTRX folding starts with structure formation in the β-sheet, while the protein helices coalesce later. As a whole, our results indicate that the CTH is a critical module in the folding process, restraining a heterogeneous intermediate ensemble into a biologically active native state and providing the native protein with thermodynamic and kinetic stability. Copyright © 2014 Elsevier B.V. All rights reserved.

Natural lipid extracts and biomembrane-mimicking lipid compositions are disposed to form nonlamellar phases, and they release DNA from lipoplexes most efficiently

PubMed Central

Koynova, Rumiana; MacDonald, Robert C.

2007-01-01

A viewpoint now emerging is that a critical factor in lipid-mediated transfection (lipofection) is the structural evolution of lipoplexes upon interacting and mixing with cellular lipids. Here we report our finding that lipid mixtures mimicking biomembrane lipid compositions are superior to pure anionic liposomes in their ability to release DNA from lipoplexes (cationic lipid/DNA complexes), even though they have a much lower negative charge density (and thus lower capacity to neutralize the positive charge of the lipoplex lipids). Flow fluorometry revealed that the portion of DNA released after a 30 min incubation of the cationic O-ethylphosphatidylcholine lipoplexes with the anionic phosphatidylserine or phosphatidylglycerol was 19% and 37%, respectively, whereas a mixture mimicking biomembranes (MM: phosphatidylcholine/phosphatidylethanolamine/ phosphatidylserine/cholesterol 45:20:20:15 w/w) and polar lipid extract from bovine liver released 62% and 74%, respectively, of the DNA content. A possible reason for this superior power in releasing DNA by the natural lipid mixtures was suggested by structural experiments: while pure anionic lipids typically form lamellae, the natural lipid mixtures exhibited a surprising predilection to form nonlamellar phases. Thus, the MM mixture arranged into lamellar arrays at physiological temperature, but began to convert to the hexagonal phase at a slightly higher temperature, ∼40-45°C. A propensity to form nonlamellar phases (hexagonal, cubic, micellar) at close to physiological temperatures was also found with the lipid extracts from natural tissues (from bovine liver, brain, and heart). This result reveals that electrostatic interactions are only one of the factors involved in lipid-mediated DNA delivery. The tendency of lipid bilayers to form nonlamellar phases has been described in terms of bilayer “frustration” which imposes a nonzero intrinsic curvature of the two opposing monolayers. Because the stored curvature elastic energy in a “frustrated” bilayer seems to be comparable to the binding energy between cationic lipid and DNA, the balance between these two energies could play a significant role in the lipoplex-membrane interactions and DNA release energetics. PMID:17559800

Natural lipid extracts and biomembrane-mimicking lipid compositions are disposed to form nonlamellar phases, and they release DNA from lipoplexes most efficiently

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koynova, Rumiana; MacDonald, Robert C.

2010-01-18

A viewpoint now emerging is that a critical factor in lipid-mediated transfection (lipofection) is the structural evolution of lipoplexes upon interacting and mixing with cellular lipids. Here we report our finding that lipid mixtures mimicking biomembrane lipid compositions are superior to pure anionic liposomes in their ability to release DNA from lipoplexes (cationic lipid/DNA complexes), even though they have a much lower negative charge density (and thus lower capacity to neutralize the positive charge of the lipoplex lipids). Flow fluorometry revealed that the portion of DNA released after a 30-min incubation of the cationic O-ethylphosphatidylcholine lipoplexes with the anionic phosphatidylserinemore » or phosphatidylglycerol was 19% and 37%, respectively, whereas a mixture mimicking biomembranes (MM: phosphatidylcholine/phosphatidylethanolamine/phosphatidylserine /cholesterol 45:20:20:15 w/w) and polar lipid extract from bovine liver released 62% and 74%, respectively, of the DNA content. A possible reason for this superior power in releasing DNA by the natural lipid mixtures was suggested by structural experiments: while pure anionic lipids typically form lamellae, the natural lipid mixtures exhibited a surprising predilection to form nonlamellar phases. Thus, the MM mixture arranged into lamellar arrays at physiological temperature, but began to convert to the hexagonal phase at a slightly higher temperature, {approx} 40-45 C. A propensity to form nonlamellar phases (hexagonal, cubic, micellar) at close to physiological temperatures was also found with the lipid extracts from natural tissues (from bovine liver, brain, and heart). This result reveals that electrostatic interactions are only one of the factors involved in lipid-mediated DNA delivery. The tendency of lipid bilayers to form nonlamellar phases has been described in terms of bilayer 'frustration' which imposes a nonzero intrinsic curvature of the two opposing monolayers. Because the stored curvature elastic energy in a 'frustrated' bilayer seems to be comparable to the binding energy between cationic lipid and DNA, the balance between these two energies could play a significant role in the lipoplex-membrane interactions and DNA release energetics.« less

Towards 4th generation biomaterials: a covalent hybrid polymer-ormoglass architecture

NASA Astrophysics Data System (ADS)

Sachot, N.; Mateos-Timoneda, M. A.; Planell, J. A.; Velders, A. H.; Lewandowska, M.; Engel, E.; Castaño, O.

2015-09-01

Hybrid materials are being extensively investigated with the aim of mimicking the ECM microenvironment to develop effective solutions for bone tissue engineering. However, the common drawbacks of a hybrid material are the lack of interactions between the scaffold's constituents and the masking of its bioactive phase. Conventional hybrids often degrade in a non-homogeneous manner and the biological response is far from optimal. We have developed a novel material with strong interactions between constituents. The bioactive phase is directly exposed on its surface mimicking the structure of the ECM of bone. Here, polylactic acid electrospun fibers have been successfully and reproducibly coated with a bioactive organically modified glass (ormoglass, Si-Ca-P2 system) covalently. In comparison with the pure polymeric mats, the fibers obtained showed improved hydrophilicity and mechanical properties, bioactive ion release, exhibited a nanoroughness and enabled good cell adhesion and spreading after just one day of culture (rMSCs and rEPCs). The fibers were coated with different ormoglass compositions to tailor their surface properties (roughness, stiffness, and morphology) by modifying the experimental parameters. Knowing that cells modulate their behavior according to the exposed physical and chemical signals, the development of this instructive material is a valuable advance in the design of functional regenerative biomaterials.Hybrid materials are being extensively investigated with the aim of mimicking the ECM microenvironment to develop effective solutions for bone tissue engineering. However, the common drawbacks of a hybrid material are the lack of interactions between the scaffold's constituents and the masking of its bioactive phase. Conventional hybrids often degrade in a non-homogeneous manner and the biological response is far from optimal. We have developed a novel material with strong interactions between constituents. The bioactive phase is directly exposed on its surface mimicking the structure of the ECM of bone. Here, polylactic acid electrospun fibers have been successfully and reproducibly coated with a bioactive organically modified glass (ormoglass, Si-Ca-P2 system) covalently. In comparison with the pure polymeric mats, the fibers obtained showed improved hydrophilicity and mechanical properties, bioactive ion release, exhibited a nanoroughness and enabled good cell adhesion and spreading after just one day of culture (rMSCs and rEPCs). The fibers were coated with different ormoglass compositions to tailor their surface properties (roughness, stiffness, and morphology) by modifying the experimental parameters. Knowing that cells modulate their behavior according to the exposed physical and chemical signals, the development of this instructive material is a valuable advance in the design of functional regenerative biomaterials. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr04275e

A novel method for a multi-level hierarchical composite with brick-and-mortar structure

PubMed Central

Brandt, Kristina; Wolff, Michael F. H.; Salikov, Vitalij; Heinrich, Stefan; Schneider, Gerold A.

2013-01-01

The fascination for hierarchically structured hard tissues such as enamel or nacre arises from their unique structure-properties-relationship. During the last decades this numerously motivated the synthesis of composites, mimicking the brick-and-mortar structure of nacre. However, there is still a lack in synthetic engineering materials displaying a true hierarchical structure. Here, we present a novel multi-step processing route for anisotropic 2-level hierarchical composites by combining different coating techniques on different length scales. It comprises polymer-encapsulated ceramic particles as building blocks for the first level, followed by spouted bed spray granulation for a second level, and finally directional hot pressing to anisotropically consolidate the composite. The microstructure achieved reveals a brick-and-mortar hierarchical structure with distinct, however not yet optimized mechanical properties on each level. It opens up a completely new processing route for the synthesis of multi-level hierarchically structured composites, giving prospects to multi-functional structure-properties relationships. PMID:23900554

A novel method for a multi-level hierarchical composite with brick-and-mortar structure.

PubMed

Brandt, Kristina; Wolff, Michael F H; Salikov, Vitalij; Heinrich, Stefan; Schneider, Gerold A

2013-01-01

The fascination for hierarchically structured hard tissues such as enamel or nacre arises from their unique structure-properties-relationship. During the last decades this numerously motivated the synthesis of composites, mimicking the brick-and-mortar structure of nacre. However, there is still a lack in synthetic engineering materials displaying a true hierarchical structure. Here, we present a novel multi-step processing route for anisotropic 2-level hierarchical composites by combining different coating techniques on different length scales. It comprises polymer-encapsulated ceramic particles as building blocks for the first level, followed by spouted bed spray granulation for a second level, and finally directional hot pressing to anisotropically consolidate the composite. The microstructure achieved reveals a brick-and-mortar hierarchical structure with distinct, however not yet optimized mechanical properties on each level. It opens up a completely new processing route for the synthesis of multi-level hierarchically structured composites, giving prospects to multi-functional structure-properties relationships.

A novel method for a multi-level hierarchical composite with brick-and-mortar structure

NASA Astrophysics Data System (ADS)

Brandt, Kristina; Wolff, Michael F. H.; Salikov, Vitalij; Heinrich, Stefan; Schneider, Gerold A.

2013-07-01

The fascination for hierarchically structured hard tissues such as enamel or nacre arises from their unique structure-properties-relationship. During the last decades this numerously motivated the synthesis of composites, mimicking the brick-and-mortar structure of nacre. However, there is still a lack in synthetic engineering materials displaying a true hierarchical structure. Here, we present a novel multi-step processing route for anisotropic 2-level hierarchical composites by combining different coating techniques on different length scales. It comprises polymer-encapsulated ceramic particles as building blocks for the first level, followed by spouted bed spray granulation for a second level, and finally directional hot pressing to anisotropically consolidate the composite. The microstructure achieved reveals a brick-and-mortar hierarchical structure with distinct, however not yet optimized mechanical properties on each level. It opens up a completely new processing route for the synthesis of multi-level hierarchically structured composites, giving prospects to multi-functional structure-properties relationships.

Recent Progress of Microfluidics in Translational Applications.

PubMed

Liu, Zongbin; Han, Xin; Qin, Lidong

2016-04-20

Microfluidics, featuring microfabricated structures, is a technology for manipulating fluids at the micrometer scale. The small dimension and flexibility of microfluidic systems are ideal for mimicking molecular and cellular microenvironment, and show great potential in translational research and development. Here, the recent progress of microfluidics in biological and biomedical applications, including molecular analysis, cellular analysis, and chip-based material delivery and biomimetic design is presented. The potential future developments in the translational microfluidics field are also discussed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multiple-probe analysis of folding and unfolding pathways of human serum albumin. Evidence for a framework mechanism of folding.

PubMed

Santra, Manas Kumar; Banerjee, Abhijit; Krishnakumar, Shyam Sundar; Rahaman, Obaidur; Panda, Dulal

2004-05-01

The changes in the far-UV CD signal, intrinsic tryptophan fluorescence and bilirubin absorbance showed that the guanidine hydrochloride (GdnHCl)-induced unfolding of a multidomain protein, human serum albumin (HSA), followed a two-state process. However, using environment sensitive Nile red fluorescence, the unfolding and folding pathways of HSA were found to follow a three-state process and an intermediate was detected in the range 0.25-1.5 m GdnHCl. The intermediate state displayed 45% higher fluorescence intensity than that of the native state. The increase in the Nile red fluorescence was found to be due to an increase in the quantum yield of the HSA-bound Nile red. Low concentrations of GdnHCl neither altered the binding affinity of Nile red to HSA nor induced the aggregation of HSA. In addition, the secondary structure of HSA was not perturbed during the first unfolding transition (<1.5 m GdnHCl); however, the secondary structure was completely lost during the second transition. The data together showed that the half maximal loss of the tertiary structure occurred at a lower GdnHCl concentration than the loss of the secondary structure. Further kinetic studies of the refolding process of HSA using multiple spectroscopic techniques showed that the folding occurred in two phases, a burst phase followed by a slow phase. An intermediate with native-like secondary structure but only a partial tertiary structure was found to form in the burst phase of refolding. Then, the intermediate slowly folded into the native state. An analysis of the refolding data suggested that the folding of HSA could be best explained by the framework model.

The nature of intermediate-range order in Ge-As-S glasses : results from reverse Monte Carlo modeling.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soyer-Uzun, S.; Benmore, C. J.; Siewenie, J. E.

2010-01-01

The experimental neutron and x-ray diffraction data for stoichiometric and S-deficient Ge{sub x}As{sub x}S{sub 100-2x} glasses with x = 18.2, 25.0, and 33.3 at.% have been modeled simultaneously using the reverse Monte Carlo (RMC) technique. Nearest-neighbor coordination environments, as obtained in previous x-ray absorption spectroscopy and diffraction experiments, have been employed as short-range order constraints in these simulations. The large scale three-dimensional structural models thus obtained from RMC simulation are used to investigate the nature and compositional evolution of intermediate-range structural order in these ternary glasses. The intermediate-range structural order is controlled by (1) a corner-shared three-dimensional network of AsS{submore » 3} pyramids and GeS{sub 4} tetrahedra in the stoichiometric Ge{sub 18.2}As{sub 18.2}S{sub 63.6} glass, (2) a heterogeneous structure that consists of homopolar bonded As-rich regions coexisting with a GeS{sub 2} network in the S-deficient Ge{sub 25}As{sub 25}S{sub 50} glass, and (3) a homogeneous structure resulting from the disruption of the topological continuity of the GeS{sub 2} network and As-rich clusters regions due to the formation of Ge-As bonds in the most S-deficient Ge{sub 33.3}As{sub 33.3}S{sub 33.3} glass. This scenario of the compositional evolution of intermediate-range structural order is consistent with and provides an atomistic explanation of the corresponding evolution in the position, width and intensity of the first sharp diffraction peak and the magnitude of small angle scattering in these glasses.« less

Structure, bonding, and reactivity of reactant complexes and key intermediates.

PubMed

Soriano, Elena; Marco-Contelles, José

2011-01-01

Complexes of Pt and Au (gold(III) and cationic gold(I)) have shown an exceptional ability to promote a variety of organic transformations of unsaturated precursors due to their peculiar Lewis acid properties: the alkynophilic character of these soft metals and the π-acid activation of unsaturated groups promotes the intra- or intermolecular attack of a nucleophile. In this chapter we summarize the computational data reported on the structure, bonding, and reactivity of the reactant π-complexes and also on the key intermediate species.

NHC-catalysed benzoin condensation - is it all down to the Breslow intermediate?

PubMed

Rehbein, Julia; Ruser, Stephanie-M; Phan, Jenny

2015-10-01

The Breslow catalytic cycle describing the benzoin condensation promoted by N-heterocyclic carbenes (NHC) as proposed in the late 1950s has since then been tried by generations of physical organic chemists. Emphasis has been laid on proofing the existence of an enaminol like structure (Breslow intermediate) that explains the observed umpolung of an otherwise electrophilic aldehyde. The present study is not focusing on spectroscopic elucidation of a thiazolydene based Breslow intermediate but rather tries to clarify if this key-intermediate is indeed directly linked with the product side of the overall reaction. The here presented EPR-spectroscopic and computational data provide a fundamentally different view on how the benzoin condensation may proceed: a radical pair could be identified as a second key-intermediate that is derived from the Breslow-intermediate via an SET process. These results highlight the close relationship to the Cannizarro reaction and oxidative transformations of aldehydes under NHC catalysis.

The Mr 140,000 Intermediate Chain of Chlamydomonas Flagellar Inner Arm Dynein Is a WD-Repeat Protein Implicated in Dynein Arm Anchoring

PubMed Central

Yang, Pinfen; Sale, Winfield S.

1998-01-01

Previous structural and biochemical studies have revealed that the inner arm dynein I1 is targeted and anchored to a unique site located proximal to the first radial spoke in each 96-nm axoneme repeat on flagellar doublet microtubules. To determine whether intermediate chains mediate the positioning and docking of dynein complexes, we cloned and characterized the 140-kDa intermediate chain (IC140) of the I1 complex. Sequence and secondary structural analysis, with particular emphasis on β-sheet organization, predicted that IC140 contains seven WD repeats. Reexamination of other members of the dynein intermediate chain family of WD proteins indicated that these polypeptides also bear seven WD/β-sheet repeats arranged in the same pattern along each intermediate chain protein. A polyclonal antibody was raised against a 53-kDa fusion protein derived from the C-terminal third of IC140. The antibody is highly specific for IC140 and does not bind to other dynein intermediate chains or proteins in Chlamydomonas flagella. Immunofluorescent microscopy of Chlamydomonas cells confirmed that IC140 is distributed along the length of both flagellar axonemes. In vitro reconstitution experiments demonstrated that the 53-kDa C-terminal fusion protein binds specifically to axonemes lacking the I1 complex. Chemical cross-linking indicated that IC140 is closely associated with a second intermediate chain in the I1 complex. These data suggest that IC140 contains domains responsible for the assembly and docking of the I1 complex to the doublet microtubule cargo. PMID:9843573

The development of quick, robust, quantitative phenotypic assays for describing the host–nonhost landscape to stripe rust

PubMed Central

Dawson, Andrew M.; Bettgenhaeuser, Jan; Gardiner, Matthew; Green, Phon; Hernández-Pinzón, Inmaculada; Hubbard, Amelia; Moscou, Matthew J.

2015-01-01

Nonhost resistance is often conceptualized as a qualitative separation from host resistance. Classification into these two states is generally facile, as they fail to fully describe the range of states that exist in the transition from host to nonhost. This poses a problem when studying pathosystems that cannot be classified as either host or nonhost due to their intermediate status relative to these two extremes. In this study, we investigate the efficacy of the Poaceae-stripe rust (Puccinia striiformis Westend.) interaction for describing the host–nonhost landscape. First, using barley (Hordeum vulgare L.) and Brachypodium distachyon (L.) P. Beauv. We observed that macroscopic symptoms of chlorosis and leaf browning were associated with hyphal colonization by P. striiformis f. sp. tritici, respectively. This prompted us to adapt a protocol for visualizing fungal structures into a phenotypic assay that estimates the percent of leaf colonized. Use of this assay in intermediate host and intermediate nonhost systems found the frequency of infection decreases with evolutionary divergence from the host species. Similarly, we observed that the pathogen’s ability to complete its life cycle decreased faster than its ability to colonize leaf tissue, with no incidence of pustules observed in the intermediate nonhost system and significantly reduced pustule formation in the intermediate host system as compared to the host system, barley-P. striiformis f. sp. hordei. By leveraging the stripe rust pathosystem in conjunction with macroscopic and microscopic phenotypic assays, we now hope to dissect the genetic architecture of intermediate host and intermediate nonhost resistance using structured populations in barley and B. distachyon. PMID:26579142

Heparin-mimicking multilayer coating on polymeric membrane via LbL assembly of cyclodextrin-based supramolecules.

PubMed

Deng, Jie; Liu, Xinyue; Ma, Lang; Cheng, Chong; Shi, Wenbin; Nie, Chuanxiong; Zhao, Changsheng

2014-12-10

In this study, multifunctional and heparin-mimicking star-shaped supramolecules-deposited 3D porous multilayer films with improved biocompatibility were fabricated via a layer-by-layer (LbL) self-assembly method on polymeric membrane substrates. Star-shaped heparin-mimicking polyanions (including poly(styrenesulfonate-co-sodium acrylate; Star-PSS-AANa) and poly(styrenesulfonate-co-poly(ethylene glycol)methyl ether methacrylate; Star-PSS-EGMA)) and polycations (poly(methyl chloride-quaternized 2-(dimethylamino)ethyl methacrylate; Star-PMeDMA) were first synthesized by atom transfer radical polymerization (ATRP) from β-cyclodextrin (β-CD) based cores. Then assembly of 3D porous multilayers onto polymeric membrane surfaces was carried out by alternating deposition of the polyanions and polycations via electrostatic interaction. The surface morphology and composition, water contact angle, blood activation, and thrombotic potential as well as cell viability for the coated heparin-mimicking films were systematically investigated. The results of surface ATR-FTIR spectra and XPS spectra verified successful deposition of the star-shaped supramolecules onto the biomedical membrane surfaces; scanning electron microscopy (SEM) and atomic force microscopy (AFM) observations revealed that the modified substrate had 3D porous surface morphology, which might have a great biological influence on the biointerface. Furthermore, systematic in vitro investigation of protein adsorption, platelet adhesion, human platelet factor 4 (PF4, indicates platelet activation), activate partial thromboplastin time (APTT), thrombin time (TT), coagulation activation (thrombin-antithrombin III complex (TAT, indicates blood coagulant)), and blood-related complement activation (C3a and C5a, indicates inflammation potential) confirmed that the heparin-mimicking multilayer coated membranes exhibited ultralow blood component activations and excellent hemocompatibility. Meanwhile, after surface coating, endothelial cell viability was also promoted, which indicated that the heparin-mimicking multilayer coating might extend the application fields of polymeric membranes in biomedical fields.

Time-multiplexed two-channel capacitive radiofrequency hyperthermia with nanoparticle mediation.

PubMed

Kim, Ki Soo; Hernandez, Daniel; Lee, Soo Yeol

2015-10-24

Capacitive radiofrequency (RF) hyperthermia suffers from excessive temperature rise near the electrodes and poorly localized heat transfer to the deep-seated tumor region even though it is known to have potential to cure ill-conditioned tumors. To better localize heat transfer to the deep-seated target region in which electrical conductivity is elevated by nanoparticle mediation, two-channel capacitive RF heating has been tried on a phantom. We made a tissue-mimicking phantom consisting of two compartments, a tumor-tissue-mimicking insert against uniform background agarose. The tumor-tissue-mimicking insert was made to have higher electrical conductivity than the normal-tissue-mimicking background by applying magnetic nanoparticle suspension to the insert. Two electrode pairs were attached on the phantom surface by equal-angle separation to apply RF electric field to the phantom. To better localize heat transfer to the tumor-tissue-mimicking insert, RF power with a frequency of 26 MHz was delivered to the two channels in a time-multiplexed way. To monitor the temperature rise inside the phantom, MR thermometry was performed at a 3T MRI intermittently during the RF heating. Finite-difference-time-domain (FDTD) electromagnetic and thermal simulations on the phantom model were also performed to verify the experimental results. As compared to the one-channel RF heating, the two-channel RF heating with time-multiplexed driving improved the spatial localization of heat transfer to the tumor-tissue-mimicking region in both the simulation and experiment. The two-channel RF heating also reduced the temperature rise near the electrodes significantly. Time-multiplexed two-channel capacitive RF heating has the capability to better localize heat transfer to the nanoparticle-mediated tumor region which has higher electrical conductivity than the background normal tissues.

Carbonate-mediated Mars-van Krevelen mechanism for CO oxidation on cobalt-doped ceria catalysts: facet-dependence and coordination-dependence.

PubMed

Liu, Bing; Li, Wenping; Song, Weiyu; Liu, Jian

2018-06-13

Carbonate intermediates have been reported to play an active role in CO oxidation over ceria-based catalysts in recent experimental studies. However, the detailed CO oxidation mechanism involving carbonate intermediates over ceria-based catalysts remains obscure. In this work, we carried out systematic density functional theory calculations corrected by on-site Coulomb interactions (DFT+U) to investigate the complete CO oxidation mechanism involving carbonate intermediates over cobalt-doped CeO2 catalysts, aiming to unravel how the carbonate participates in CO oxidation and shed light on the underlying factors that control the carbonate-mediated reaction mechanism. A novel carbonate-mediated Mars-van Krevelen (M-vK) mechanism was proposed, in which the carbonate acts as an active intermediate rather than a spectator and can react with CO to form CO2. This carbonate-mediated M-vK mechanism is facet-dependent because it is predominant on the (110) surface whereas the conventional M-vK mechanism is more favorable on (111) and (100) surfaces. The origin of facet-dependence was discussed by analyzing the geometric and electronic structures. It is found that the negatively charged bent CO2- intermediate formed on the (110) surface plays a critical role in the carbonate-mediated M-vK mechanism, whereas the formation of a neutral linear CO2 intermediate on (111) and (100) surfaces hinders the carbonate-mediated M-vK mechanism. The surface oxygen vacancy hinders the formation of carbonate intermediates, indicating that the carbonate-mediated M-vK mechanism is also vacancy-dependent. The formation of carbonate intermediates on different metal (Ti, V, W, Mo and Re) doped CeO2(110) surfaces was studied and the results indicate that the coordination environment of the dopant species is a key factor that determines the carbonate-mediated M-vK mechanism. This study provides atomic-scale insights into the reaction mechanism involving carbonate intermediates and the structure-mechanism relationship for CO oxidation over cobalt-ceria catalysts.

Structure of Leishmania major Methionyl-tRNA Synthetase in Complex with Intermediate Products Methionyladenylate and Pyrophosphate

PubMed Central

Larson, Eric T.; Kim, Jessica E.; Zucker, Frank H.; Kelley, Angela; Mueller, Natascha; Napuli, Alberto J.; Verlinde, Christophe L.M.J.; Fan, Erkang; Buckner, Frederick S.; Van Voorhis, Wesley C.; Merritt, Ethan A.; Hol, Wim G.J.

2011-01-01

Leishmania parasites cause two million new cases of leishmaniasis each year with several hundreds of millions people at risk. Due to the paucity and shortcomings of available drugs, we have undertaken the crystal structure determination of a key enzyme from Leishmania major in hopes of creating a platform for the rational design of new therapeutics. Crystals of the catalytic core of methionyl-tRNA synthetase from L. major (LmMetRS) were obtained with the substrates MgATP and methionine present in the crystallization medium. These crystals yielded the 2.0 Å resolution structure of LmMetRS in complex with two products, methionyladenylate and pyrophosphate, along with a Mg2+ ion that bridges them. This is the first class I aminoacyl-tRNA synthetase (aaRS) structure with pyrophosphate bound. The residues of the class I aaRS signature sequence motifs, KISKS and HIGH, make numerous contacts with the pyrophosphate. Substantial differences between the LmMetRS structure and previously reported complexes of E. coli MetRS (EcMetRS) with analogs of the methionyladenylate intermediate product are observed, even though one of these analogs only differs by one atom from the intermediate. The source of these structural differences is attributed to the presence of the product pyrophosphate in LmMetRS. Analysis of the LmMetRS structure in light of the Aquifex aeolicus MetRS-tRNAMet complex shows that major rearrangements of multiple structural elements of enzyme and/or tRNA are required to allow the CCA acceptor triplet to reach the methionyladenylate intermediate in the active site. Comparison with sequences of human cytosolic and mitochondrial MetRS reveals interesting differences near the ATP- and methionine-binding regions of LmMetRS, suggesting that it should be possible to obtain compounds that selectively inhibit the parasite enzyme. PMID:21144880

Phase portrait analysis of super solitary waves and flat top solutions

NASA Astrophysics Data System (ADS)

Steffy, S. V.; Ghosh, S. S.

2018-06-01

The phase portrait analysis of super solitary waves has revealed a new kind of intermediate solution which defines the boundary between the two types of super solitary waves, viz., Type I and Type II. A Type I super solitary wave is known to be associated with an intermediate double layer while a Type II solution has no such association. The intermediate solution at the boundary has a flat top structure and is called a flat top solitary wave. Its characteristics resemble an amalgamation of a solitary wave and a double layer. It was found that, mathematically, such kinds of structures may emerge due to the presence of an extra nonlinearity. Although they are relatively unfamiliar in the realm of plasma physics, they have much wider applications in other physical systems.

The Finance of Non Government Schools in Bangladesh.

ERIC Educational Resources Information Center

Puttick, Edwin B.; And Others

The educational system in Bangladesh is unique in its finance and management structure. Elementary and higher education are mostly publicly financed, while secondary and intermediate education are mainly private organized. This study concentrates on private schools at the secondary, intermediate, and college level; and the difference in access…

Identification of early fumonisin biosynthetic intermediates by inactivation of the FUM6 gene in Fusarium verticillioides

USDA-ARS?s Scientific Manuscript database

Fumonisins are polyketide mycotoxins produced by the maize pathogen Fusarium verticillioides and are associated with multiple human and animal diseases. A fumonisin biosynthetic pathway has been proposed, but structures of early pathway intermediates have not been demonstrated. The F. verticillioide...

Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations

NASA Astrophysics Data System (ADS)

Orellana, Laura; Yoluk, Ozge; Carrillo, Oliver; Orozco, Modesto; Lindahl, Erik

2016-08-01

Protein conformational changes are at the heart of cell functions, from signalling to ion transport. However, the transient nature of the intermediates along transition pathways hampers their experimental detection, making the underlying mechanisms elusive. Here we retrieve dynamic information on the actual transition routes from principal component analysis (PCA) of structurally-rich ensembles and, in combination with coarse-grained simulations, explore the conformational landscapes of five well-studied proteins. Modelling them as elastic networks in a hybrid elastic-network Brownian dynamics simulation (eBDIMS), we generate trajectories connecting stable end-states that spontaneously sample the crystallographic motions, predicting the structures of known intermediates along the paths. We also show that the explored non-linear routes can delimit the lowest energy passages between end-states sampled by atomistic molecular dynamics. The integrative methodology presented here provides a powerful framework to extract and expand dynamic pathway information from the Protein Data Bank, as well as to validate sampling methods in general.

Anatomy of an amyloidogenic intermediate: conversion of beta-sheet to alpha-sheet structure in transthyretin at acidic pH.

PubMed

Armen, Roger S; Alonso, Darwin O V; Daggett, Valerie

2004-10-01

The homotetramer of transthyretin (TTR) dissociates into a monomeric amyloidogenic intermediate that self-assembles into amyloid fibrils at low pH. We have performed molecular dynamics simulations of monomeric TTR at neutral and low pH at physiological (310 K) and very elevated temperature (498 K). In the low-pH simulations at both temperatures, one of the two beta-sheets (strands CBEF) becomes disrupted, and alpha-sheet structure forms in the other sheet (strands DAGH). alpha-sheet is formed by alternating alphaL and alphaR residues, and it was first proposed by Pauling and Corey. Overall, the simulations are in agreement with the available experimental observations, including solid-state NMR results for a TTR-peptide amyloid. In addition, they provide a unique explanation for the results of hydrogen exchange experiments of the amyloidogenic intermediate-results that are difficult to explain with beta-structure. We propose that alpha-sheet may represent a key pathological conformation during amyloidogenesis. Copyright 2004 Elsevier Ltd.

The small heat shock protein Hsp27 affects assembly dynamics and structure of keratin intermediate filament networks.

PubMed

Kayser, Jona; Haslbeck, Martin; Dempfle, Lisa; Krause, Maike; Grashoff, Carsten; Buchner, Johannes; Herrmann, Harald; Bausch, Andreas R

2013-10-15

The mechanical properties of living cells are essential for many processes. They are defined by the cytoskeleton, a composite network of protein fibers. Thus, the precise control of its architecture is of paramount importance. Our knowledge about the molecular and physical mechanisms defining the network structure remains scarce, especially for the intermediate filament cytoskeleton. Here, we investigate the effect of small heat shock proteins on the keratin 8/18 intermediate filament cytoskeleton using a well-controlled model system of reconstituted keratin networks. We demonstrate that Hsp27 severely alters the structure of such networks by changing their assembly dynamics. Furthermore, the C-terminal tail domain of keratin 8 is shown to be essential for this effect. Combining results from fluorescence and electron microscopy with data from analytical ultracentrifugation reveals the crucial role of kinetic trapping in keratin network formation. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

[Artificial Cysteine Bridges on the Surface of Green Fluorescent Protein Affect Hydration of Its Transition and Intermediate States].

PubMed

Melnik, T N; Nagibina, G S; Surin, A K; Glukhova, K A; Melnik, B S

2018-01-01

Studying the effect of cysteine bridges on different energy levels of multistage folding proteins will enable a better understanding of the process of folding and functioning of globular proteins. In particular, it will create prospects for directed change in the stability and rate of protein folding. In this work, using the method of differential scanning microcalorimetry, we have studied the effect of three cysteine bridges introduced in different structural elements of the green fluorescent protein on the denaturation enthalpies, activation energies, and heat-capacity increments when this protein passes from native to intermediate and transition states. The studies have allowed us to confirm that, with this protein denaturation, the process hardly damages the structure initially, but then changes occur in the protein structure in the region of 4-6 beta sheets. The cysteine bridge introduced in this region decreases the hydration of the second transition state and increases the hydration of the second intermediate state during the thermal denaturation of the green fluorescent protein.

ATP-induced noncooperative thermal unfolding of hen lysozyme

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Honglin; Yin, Peidong; He, Shengnan

To understand the role of ATP underlying the enhanced amyloidosis of hen egg white lysozyme (HEWL), the synchrotron radiation circular dichroism, combined with tryptophan fluorescence, dynamic light-scattering, and differential scanning calorimetry, is used to examine the alterations of the conformation and thermal unfolding pathway of the HEWL in the presence of ATP, Mg{sup 2+}-ATP, ADP, AMP, etc. It is revealed that the binding of ATP to HEWL through strong electrostatic interaction changes the secondary structures of HEWL and makes the exposed residue W62 move into hydrophobic environments. This alteration of W62 decreases the {beta}-domain stability of HEWL, induces a noncooperativemore » unfolding of the secondary structures, and produces a partially unfolded intermediate. This intermediate containing relatively rich {alpha}-helix and less {beta}-sheet structures has a great tendency to aggregate. The results imply that the ease of aggregating of HEWL is related to the extent of denaturation of the amyloidogenic region, rather than the electrostatic neutralizing effect or monomeric {beta}-sheet enriched intermediate.« less

Intermediate- and short-range order in phosphorus-selenium glasses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bytchkov, Aleksei; Hennet, Louis; Price, David L.

2011-04-01

State-of-the-art neutron and x-ray diffraction measurements have been performed to provide a definitive picture of the intermediate- and short-range structures of P{sub x}Se{sub 1-x} glasses spanning two glass regions, x 0.025-0.54 and 0.64-0.84. Liquid P{sub 4}Se{sub 3} and amorphous red P and Se were also measured. Detailed information was obtained about the development with increasing phosphorous concentration of intermediate-range order on the length scale {approx}6 A ring , based on the behavior of the first sharp diffraction peak. Attention is also paid to the feature in the structure factor at 7.5 A ring {sup -1}, identified in earlier numerical simulations,more » provides further evidence of the existence of molecular units. The real-space transforms yield a reliable statistical picture of the changing short-range order as x increases, using the information about types and concentrations of local structural units provided by previous NMR measurements to interpret the trends observed.« less

[Graft-versus-host disease as the cause of symptoms mimicking Sjögren's syndrome].

PubMed

Tuchocka-Piotrowska, Aleksandra; Puszczewicz, Mariusz; Kołczewska, Aleksandra; Majewski, Dominik

2006-01-01

A case of chronic graft-versus-host disease (chronic GvHD) mimicking symptoms associated with idiopathic Sjögren's syndrome is presented. Hypotheses on the pathophysiological origin of clinical syndromes associated with graft-versus-host disease are discussed.

Hydrothermal synthesis for new multifunctional materials: A few examples of phosphates and phosphonate-based hybrid materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rueff, Jean-Michel, E-mail: jean-michel.rueff@ensicaen.fr; Poienar, Maria; Guesdon, Anne

Novel physical or chemical properties are expected in a great variety of materials, in connection with the dimensionality of their structures and/or with their nanostructures, hierarchical superstructures etc. In the search of new advanced materials, the hydrothermal technique plays a crucial role, mimicking the nature able to produce fractal, hyperbranched, urchin-like or snow flake structures. In this short review including new results, this will be illustrated by examples selected in two types of materials, phosphates and phosphonates, prepared by this method. The importance of the synthesis parameters will be highlighted for a magnetic iron based phosphates and for hybrids containingmore » phosphonates organic building units crystallizing in different structural types. - Graphical abstract: Phosphate dendrite like and phosphonate platelet crystals.« less

A Remarkably Simple Class of Imidazolium-Based Lipids and Their Biological Properties.

PubMed

Wang, Da; Richter, Christian; Rühling, Andreas; Drücker, Patrick; Siegmund, Daniel; Metzler-Nolte, Nils; Glorius, Frank; Galla, Hans-Joachim

2015-10-19

A series of imidazolium salts bearing two alkyl chains in the backbone of the imidazolium core were synthesized, resembling the structure of lipids. Their antibacterial activity and cytotoxicity were evaluated using Gram-positive and Gram-negative bacteria and eukaryotic cell lines including tumor cells. It is shown that the length of alkyl chains in the backbone is vital for the antibiofilm activities of these lipid-mimicking components. In addition to their biological activity, their surface activity and their membrane interactions are shown by film balance and quartz crystal microbalance (QCM) measurements. The structure-activity relationship indicates that the distinctive chemical structure contributes considerably to the biological activities of this novel class of lipids. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The fine structure of human germ layers in vivo: clues to the early differentiation of embryonic stem cells in vitro.

PubMed

Sathananthan, Henry; Selvaraj, Kamala; Clark, Joan

2011-08-01

The fine structure of the three germ layers in human ectopic embryos (stage 7) have been documented by digital light and electron microscopy. The formation of ectoderm, endoderm and mesoderm and notochordal cells, and also the extraembryonic membranes, amnion and yolk sac, are imaged. The germ layers give rise to all the cells and tissues of the human body. Possible clues to the early differentiation of embryonic stem cells (ESC) in vitro were obtained, since these events are more or less mimicked in cultures of ESC derived from the inner cell mass of human blastocysts. The findings are discussed with reference to previous studies on the fine structure of ESC using the same technique. Copyright © 2011. Published by Elsevier Ltd.

Helix formation in arrestin accompanies recognition of photoactivated rhodopsin.

PubMed

Feuerstein, Sophie E; Pulvermüller, Alexander; Hartmann, Rudolf; Granzin, Joachim; Stoldt, Matthias; Henklein, Peter; Ernst, Oliver P; Heck, Martin; Willbold, Dieter; Koenig, Bernd W

2009-11-17

Binding of arrestin to photoactivated phosphorylated rhodopsin terminates the amplification of visual signals in photoreceptor cells. Currently, there is no crystal structure of a rhodopsin-arrestin complex available, although structures of unbound rhodopsin and arrestin have been determined. High-affinity receptor binding is dependent on distinct arrestin sites responsible for recognition of rhodopsin activation and phosphorylation. The loop connecting beta-strands V and VI in rod arrestin has been implicated in the recognition of active rhodopsin. We report the structure of receptor-bound arrestin peptide Arr(67-77) mimicking this loop based on solution NMR data. The peptide binds photoactivated rhodopsin in the unphosphorylated and phosphorylated form with similar affinities and stabilizes the metarhodopsin II photointermediate. A largely alpha-helical conformation of the receptor-bound peptide is observed.

Bioprinting a cardiac valve.

PubMed

Jana, Soumen; Lerman, Amir

2015-12-01

Heart valve tissue engineering could be a possible solution for the limitations of mechanical and biological prostheses, which are commonly used for heart valve replacement. In tissue engineering, cells are seeded into a 3-dimensional platform, termed the scaffold, to make the engineered tissue construct. However, mimicking the mechanical and spatial heterogeneity of a heart valve structure in a fabricated scaffold with uniform cell distribution is daunting when approached conventionally. Bioprinting is an emerging technique that can produce biological products containing matrix and cells, together or separately with morphological, structural and mechanical diversity. This advance increases the possibility of fabricating the structure of a heart valve in vitro and using it as a functional tissue construct for implantation. This review describes the use of bioprinting technology in heart valve tissue engineering. Copyright © 2015 Elsevier Inc. All rights reserved.

Enhancement of DNaseI Salt Tolerance by Mimicking the Domain Structure of DNase from an Extremely Halotolerant Bacterium Thioalkalivibrio sp. K90mix

PubMed Central

Alzbutas, Gediminas; Kaniusaite, Milda; Lagunavicius, Arunas

2016-01-01

In our previous work we showed that DNaseI-like protein from an extremely halotolerant bacterium Thioalkalivibrio sp. K90mix retained its activity at salt concentrations as high as 4 M NaCl and the key factor allowing this was the C-terminal DNA-binding domain, which comprised two HhH (helix-hairpin-helix) motifs. The further investigations revealed that this domain originated from proteins related to bacterial competence ComEA/ComE proteins. It is likely that in the course of evolution the DNA-binding domain from these proteins was fused to a metallo-β-lactamase superfamily domain. Very likely such domain organization having proteins subsequently “donated” the DNA-binding domain to bacterial DNases. In this study we have mimicked this evolutionary step by fusing bovine DNaseI and DNA-binding domains. We have created two fusions: one harboring the DNA-binding domain of DNaseI-like protein from Thioalkalivibrio sp. K90mix and the second one harboring the DNA-binding domain of bacterial competence protein ComEA from Bacillus subtilis. Both domains enhanced salt tolerance of DNaseI, albeit to different extent. Molecular modeling revealed the essential differences between their interaction with DNA shedding some light on the differences in salt tolerance. In this study we have enhanced salt tolerance of bovine DNaseI; thus, we successfully mimicked the Nature’s evolutionary engineering that created the extremely halotolerant bacterial DNase. We have demonstrated that the newly engineered DNaseI variants can be successfully used in applications where activity of the wild type bovine DNaseI is impeded by buffers used. PMID:26939122

Engineering zonal cartilaginous tissue by modulating oxygen levels and mechanical cues through the depth of infrapatellar fat pad stem cell laden hydrogels.

PubMed

Luo, Lu; O'Reilly, Adam R; Thorpe, Stephen D; Buckley, Conor T; Kelly, Daniel J

2017-09-01

Engineering tissues with a structure and spatial composition mimicking those of native articular cartilage (AC) remains a challenge. This study examined if infrapatellar fat pad-derived stem cells (FPSCs) can be used to engineer cartilage grafts with a bulk composition and a spatial distribution of matrix similar to the native tissue. In an attempt to mimic the oxygen gradients and mechanical environment within AC, FPSC-laden hydrogels (either 2 mm or 4 mm in height) were confined to half of their thickness and/or subjected to dynamic compression (DC). Confining FPSC-laden hydrogels was predicted to accentuate the gradient in oxygen tension through the depth of the constructs (higher in the top and lower in the bottom), leading to enhanced glycosaminoglycan (GAG) and collagen synthesis in 2 mm high tissues. When subjected to DC alone, both GAG and collagen accumulation increased within 2 mm high unconfined constructs. Furthermore, the dynamic modulus of constructs increased from 0.96 MPa to 1.45 MPa following the application of DC. There was no synergistic benefit of coupling confinement and DC on overall levels of matrix accumulation; however in all constructs, irrespective of their height, the combination of these boundary conditions led to the development of engineered tissues that spatially best resembled native AC. The superficial region of these constructs mimicked that of native tissue, staining weakly for GAG, strongly for type II collagen, and in 4 mm high tissues more intensely for proteoglycan 4 (lubricin). This study demonstrated that FPSCs respond to joint-like environmental conditions by producing cartilage tissues mimicking native AC. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Self-organization of human iPS cells into trophectoderm mimicking cysts induced by adhesion restriction using microstructured mesh scaffolds.

PubMed

Okeyo, Kennedy O; Tanabe, Maiko; Kurosawa, Osamu; Oana, Hidehiro; Washizu, Masao

2018-04-01

Cellular dynamics leading to the formation of the trophectoderm in humans remain poorly understood owing to limited accessibility to human embryos for research into early human embryogenesis. Compared to animal models, organoids formed by self-organization of stem cells in vitro may provide better insights into differentiation and complex morphogenetic processes occurring during early human embryogenesis. Here we demonstrate that modulating the cell culture microenvironment alone can trigger self-organization of human induced pluripotent stem cells (hiPSCs) to yield trophectoderm-mimicking cysts without chemical induction. To modulate the adhesion microenvironment, we used the mesh culture technique recently developed by our group, which involves culturing hiPSCs on suspended micro-structured meshes with limited surface area for cell adhesion. We show that this adhesion-restriction strategy can trigger a two-stage self-organization of hiPSCs; first into stem cell sheets, which express pluripotency signatures until around day 8-10, then into spherical cysts following differentiation and self-organization of the sheet-forming cells. Detailed morphological analysis using immunofluorescence microscopy with both confocal and two-photon microscopes revealed the anatomy of the cysts as consisting of a squamous epithelial wall richly expressing E-cadherin and CDX2. We also confirmed that the cysts exhibit a polarized morphology with basal protrusions, which show migratory behavior when anchored. Together, our results point to the formation of cysts which morphologically resemble the trophectoderm at the late-stage blastocyst. Thus, the mesh culture microenvironment can initiate self-organization of hiPSCs into trophectoderm-mimicking cysts as organoids with potential application in the study of early embryogenesis and also in drug development. © 2018 Japanese Society of Developmental Biologists.

Partially filled intermediate band of Cr-doped GaN films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sonoda, S.

2012-05-14

We investigated the band structure of sputtered Cr-doped GaN (GaCrN) films using optical absorption, photoelectron yield spectroscopy, and charge transport measurements. It was found that an additional energy band is formed in the intrinsic band gap of GaN upon Cr doping, and that charge carriers in the material move in the inserted band. Prototype solar cells showed enhanced short circuit current and open circuit voltage in the n-GaN/GaCrN/p-GaN structure compared to the GaCrN/p-GaN structure, which validates the proposed concept of an intermediate-band solar cell.

XAFS of short-lived reduction products of structural and functional models of the [Fe Fe] hydrogenase H-cluster

NASA Astrophysics Data System (ADS)

Bondin, Mark I.; Borg, Stacey J.; Cheah, Mun-Hon; Best, Stephen P.

2006-11-01

Thiolate-bridged diiron compounds that are related to the active site of the [Fe-Fe] hydrogenase enzyme have been shown to act as electrocatalysts for reduction of protons. The use of XAFS for clarification of the structures of intermediates formed following reduction of related diiron carbonyl compounds is described. These measurements allow the determination of Fe-Fe and Fe-S bond lengths with good reliability and when used in conjunction with the standard bonding models this provides a means of validating the structures proposed for longer-lived ( t>20 s at -50 °C) reaction intermediates.

Controlling the intermediate structure of an ionic liquid for f-block element separations

DOE PAGES

Abney, Carter W.; Do, Changwoo; Luo, Huimin; ...

2017-04-19

Recent research has revealed molecular structure beyond the inner coordination sphere is essential in defining the performance of separations processes, but nevertheless remains largely unexplored. Here we apply small angle neutron scattering (SANS) and x-ray absorption fine structure (XAFS) spectroscopy to investigate the structure of an ionic liquid system studied for f-block element separations. SANS data reveal dramatic changes in the ionic liquid microstructure (~150 Å) which we demonstrate can be controlled by judicious selection of counter ion. Mesoscale structural features (> 500 Å) are also observed as a function of metal concentration. XAFS analysis supports formation of extended aggregatemore » structures, similar to those observed in traditional solvent extraction processes, and suggest additional parallels may be drawn from further study. As a result, achieving precise tunability over the intermediate features is an important development in controlling mesoscale structure and realizing advanced new forms of soft matter.« less

Crystal structure of a β-aminopeptidase from an Australian Burkholderia sp.

PubMed

John-White, Marietta; Dumsday, Geoff J; Johanesen, Priscilla; Lyras, Dena; Drinkwater, Nyssa; McGowan, Sheena

2017-07-01

β-Aminopeptidases are a unique group of enzymes that have the unusual capability to hydrolyze N-terminal β-amino acids from synthetic β-peptides. β-Peptides can form secondary structures mimicking α-peptide-like structures that are resistant to degradation by most known proteases and peptidases. These characteristics of β-peptides give them great potential as peptidomimetics. Here, the X-ray crystal structure of BcA5-BapA, a β-aminopeptidase from a Gram-negative Burkholderia sp. that was isolated from activated sludge from a wastewater-treatment plant in Australia, is reported. The crystal structure of BcA5-BapA was determined to a resolution of 2.0 Å and showed a tetrameric assembly typical of the β-aminopeptidases. Each monomer consists of an α-subunit (residues 1-238) and a β-subunit (residues 239-367). Comparison of the structure of BcA5-BapA with those of other known β-aminopeptidases shows a highly conserved structure and suggests a similar proteolytic mechanism of action.

Fibromatosis of the breast mimicking an abscess: case report of unusual sonographic features.

PubMed

Lee, So Min; Lee, Ji Young; Lee, Byung Hoon; Kim, Su Young; Joo, Mee; Kim, Jae Il

2015-01-01

Fibromatosis of the breast, also known as a desmoid tumor, is extremely rare and most often appears as an aggressive lesion mimicking breast carcinoma. It lacks metastatic potential but can grow aggressively in a localized area. Ultrasonography often shows an irregular spiculated hypoechoic mass with posterior acoustic shadowing. We discuss a case of breast fibromatosis that presented as a painful palpable breast mass in a 32-year-old woman and mimicked an abscess in the sonogram. We found that this lesion displayed atypical sonographic features such as a heterogeneous echoic mass with an internal anechoic area. Copyright © 2015 Elsevier Inc. All rights reserved.

Controlled transport of latex beads through vertically aligned carbon nanofiber membranes

NASA Astrophysics Data System (ADS)

Zhang, L.; Melechko, A. V.; Merkulov, V. I.; Guillorn, M. A.; Simpson, M. L.; Lowndes, D. H.; Doktycz, M. J.

2002-07-01

Stripes of vertically aligned carbon nanofibers (VACNFs) have been used to form membranes for size selectively controlling the transport of latex beads. Fluidic structures were created in poly(dimethylsiloxane) (PDMS) and interfaced to the VACNF structures for characterization of the membrane pore size. Solutions of fluorescently labeled latex beads were introduced into the PDMS channels and characterized by fluorescence and scanning electron microscopy. Results show that the beads size selectively pass through the nanofiber barriers and the size restriction limit correlates with the interfiber spacing. The results suggest that altering VACNF array density can alter fractionation properties of the membrane. Such membranes may be useful for molecular sorting and for mimicking the properties of natural membranes.

Viruses, Artificial Viruses and Virus-Based Structures for Biomedical Applications.

PubMed

van Rijn, Patrick; Schirhagl, Romana

2016-06-01

Nanobiomaterials such as virus particles and artificial virus particles offer tremendous opportunities to develop new biomedical applications such as drug- or gene-delivery, imaging and sensing but also improve understanding of biological mechanisms. Recent advances within the field of virus-based systems give insights in how to mimic viral structures and virus assembly processes as well as understanding biodistribution, cell/tissue targeting, controlled and triggered disassembly or release and circulation times. All these factors are of high importance for virus-based functional systems. This review illustrates advances in mimicking and enhancing or controlling these aspects to a high degree toward delivery and imaging applications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure of the Protease Domain of Memapsin 2 (β-Secretase) Complexed with Inhibitor

NASA Astrophysics Data System (ADS)

Hong, Lin; Koelsch, Gerald; Lin, Xinli; Wu, Shili; Terzyan, Simon; Ghosh, Arun K.; Zhang, Xuenjun C.; Tang, Jordan

2000-10-01

Memapsin 2 (β-secretase) is a membrane-associated aspartic protease involved in the production of β-amyloid peptide in Alzheimer's disease and is a major target for drug design. We determined the crystal structure of the protease domain of human memapsin 2 complexed to an eight-residue inhibitor at 1.9 angstrom resolution. The active site of memapsin 2 is more open and less hydrophobic than that of other human aspartic proteases. The subsite locations from S4 to S2' are well defined. A kink of the inhibitor chain at P2' and the change of chain direction of P3' and P4' may be mimicked to provide inhibitor selectivity.

Structural Changes Associated with Transthyretin Misfolding and Amyloid Formation Revealed by Solution and Solid-State NMR

DOE PAGES

Lim, Kwang Hun; Dasari, Anvesh K. R.; Hung, Ivan; ...

2016-03-21

Elucidation of structural changes involved in protein misfolding and amyloid formation is crucial for unraveling the molecular basis of amyloid formation. We report structural analyses of the amyloidogenic intermediate and amyloid aggregates of transthyretin using solution and solid-state nuclear magnetic resonance (NMR) spectroscopy. These NMR solution results show that one of the two main β-sheet structures (CBEF β-sheet) is maintained in the aggregation-competent intermediate, while the other DAGH β-sheet is more flexible on millisecond time scales. Magic-angle-spinning solid-state NMR revealed that AB loop regions interacting with strand A in the DAGH β-sheet undergo conformational changes, leading to the destabilized DAGHmore » β-sheet.« less

Structure and antimicrobial activity of platypus 'intermediate' defensin-like peptide.

PubMed

Torres, Allan M; Bansal, Paramjit; Koh, Jennifer M S; Pagès, Guilhem; Wu, Ming J; Kuchel, Philip W

2014-05-02

The three-dimensional structure of a chemically synthesized peptide that we have called 'intermediate' defensin-like peptide (Int-DLP), from the platypus genome, was determined by nuclear magnetic resonance (NMR) spectroscopy; and its antimicrobial activity was investigated. The overall structural fold of Int-DLP was similar to that of the DLPs and β-defensins, however the presence of a third antiparallel β-strand makes its structure more similar to the β-defensins than the DLPs. Int-DLP displayed potent antimicrobial activity against Staphylococcus aureus and Pseudomonas aeruginosa. The four arginine residues at the N-terminus of Int-DLP did not affect the overall fold, but were important for its antimicrobial potency. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

Lipid-protein nanodiscs for cell-free production of integral membrane proteins in a soluble and folded state: comparison with detergent micelles, bicelles and liposomes.

PubMed

Lyukmanova, E N; Shenkarev, Z O; Khabibullina, N F; Kopeina, G S; Shulepko, M A; Paramonov, A S; Mineev, K S; Tikhonov, R V; Shingarova, L N; Petrovskaya, L E; Dolgikh, D A; Arseniev, A S; Kirpichnikov, M P

2012-03-01

Production of integral membrane proteins (IMPs) in a folded state is a key prerequisite for their functional and structural studies. In cell-free (CF) expression systems membrane mimicking components could be added to the reaction mixture that promotes IMP production in a soluble form. Here lipid-protein nanodiscs (LPNs) of different lipid compositions (DMPC, DMPG, POPC, POPC/DOPG) have been compared with classical membrane mimicking media such as detergent micelles, lipid/detergent bicelles and liposomes by their ability to support CF synthesis of IMPs in a folded and soluble state. Three model membrane proteins of different topology were used: homodimeric transmembrane (TM) domain of human receptor tyrosine kinase ErbB3 (TM-ErbB3, 1TM); voltage-sensing domain of K(+) channel KvAP (VSD, 4TM); and bacteriorhodopsin from Exiguobacterium sibiricum (ESR, 7TM). Structural and/or functional properties of the synthesized proteins were analyzed. LPNs significantly enhanced synthesis of the IMPs in a soluble form regardless of the lipid composition. A partial disintegration of LPNs composed of unsaturated lipids was observed upon co-translational IMP incorporation. Contrary to detergents the nanodiscs resulted in the synthesis of ~80% active ESR and promoted correct folding of the TM-ErbB3. None of the tested membrane mimetics supported CF synthesis of correctly folded VSD, and the protocol of the domain refolding was developed. The use of LPNs appears to be the most promising approach to CF production of IMPs in a folded state. NMR analysis of (15)N-Ile-TM-ErbB3 co-translationally incorporated into LPNs shows the great prospects of this membrane mimetics for structural studies of IMPs produced by CF systems. Copyright © 2011 Elsevier B.V. All rights reserved.

Adefovir-Induced Hypophosphatemic Osteomalacia Mimicking Bone Metastases From Primary Hepatocarcinoma.

PubMed

Wei, Wei-Jun; Sun, Zhen-Kui; Shen, Chen-Tian; Qiu, Zhong-Ling; Luo, Quan-Yong

2017-09-01

Adefovir-induced hypophosphatemic osteomalacia in the context of hepatocarcinoma is rare and needs to be differentiated from metastatic hepatocarcinoma. We here report a case of severe osteomalacia whose focal uptakes of radiotracer on the Tc-MDP SPECT/CT images mimicked that of metastatic hepatocarcinoma.

Geometric and electronic structure contributions to function in non-heme iron enzymes.

PubMed

Solomon, Edward I; Light, Kenneth M; Liu, Lei V; Srnec, Martin; Wong, Shaun D

2013-11-19

Mononuclear non-heme Fe (NHFe) enzymes play key roles in DNA repair, the biosynthesis of antibiotics, the response to hypoxia, cancer therapy, and many other biological processes. These enzymes catalyze a diverse range of oxidation reactions, including hydroxylation, halogenation, ring closure, desaturation, and electrophilic aromatic substitution (EAS). Most of these enzymes use an Fe(II) site to activate dioxygen, but traditional spectroscopic methods have not allowed researchers to insightfully probe these ferrous active sites. We have developed a methodology that provides detailed geometric and electronic structure insights into these NHFe(II) active sites. Using these data, we have defined a general mechanistic strategy that many of these enzymes use: they control O2 activation (and limit autoxidation and self-hydroxylation) by allowing Fe(II) coordination unsaturation only in the presence of cosubstrates. Depending on the type of enzyme, O2 activation either involves a 2e(-) reduced Fe(III)-OOH intermediate or a 4e(-) reduced Fe(IV)═O intermediate. Nuclear resonance vibrational spectroscopy (NRVS) has provided the geometric structure of these intermediates, and magnetic circular dichroism (MCD) has defined the frontier molecular orbitals (FMOs), the electronic structure that controls reactivity. This Account emphasizes that experimental spectroscopy is critical in evaluating the results of electronic structure calculations. Therefore these data are a key mechanistic bridge between structure and reactivity. For the Fe(III)-OOH intermediates, the anticancer drug activated bleomycin (BLM) acts as the non-heme Fe analog of compound 0 in heme (e.g., P450) chemistry. However BLM shows different reactivity: the low-spin (LS) Fe(III)-OOH can directly abstract a H atom from DNA. The LS and high-spin (HS) Fe(III)-OOHs have fundamentally different transition states. The LS transition state goes through a hydroxyl radical, but the HS transition state is activated for EAS without O-O cleavage. This activation is important in one class of NHFe enzymes that utilizes a HS Fe(III)-OOH intermediate in dioxygenation. For Fe(IV)═O intermediates, the LS form has a π-type FMO activated for attack perpendicular to the Fe-O bond. However, the HS form (present in the NHFe enzymes) has a π FMO activated perpendicular to the Fe-O bond and a σ FMO positioned along the Fe-O bond. For the NHFe enzymes, the presence of π and σ FMOs enables enzymatic control in determining the type of reactivity: EAS or H-atom extraction for one substrate with different enzymes and halogenation or hydroxylation for one enzyme with different substrates.

Insights into the carboxyltransferase reaction of pyruvate carboxylase from the structures of bound product and intermediate analogues

PubMed Central

Lietzan, Adam D.; St. Maurice, Martin

2014-01-01

Pyruvate carboxylase (PC) is a biotin-dependent enzyme that catalyzes the MgATP- and bicarbonate-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in central metabolism. The carboxyltransferase (CT) domain of PC catalyzes the transfer of a carboxyl group from carboxybiotin to the accepting substrate, pyruvate. It has been hypothesized that the reactive enolpyruvate intermediate is stabilized through a bidentate interaction with the metal ion in the CT domain active site. Whereas bidentate ligands are commonly observed in enzymes catalyzing reactions proceeding through an enolpyruvate intermediate, no bidentate interaction has yet been observed in the CT domain of PC. Here, we report three X-ray crystal structures of the Rhizobium etli PC CT domain with the bound inhibitors oxalate, 3-hydroxypyruvate, and 3-bromopyruvate. Oxalate, a stereoelectronic mimic of the enolpyruvate intermediate, does not interact directly with the metal ion. Instead, oxalate is buried in a pocket formed by several positively charged amino acid residues and the metal ion. Furthermore, both 3-hydroxypyruvate and 3-bromopyruvate, analogs of the reaction product oxaloacetate, bind in an identical manner to oxalate suggesting that the substrate maintains its orientation in the active site throughout catalysis. Together, these structures indicate that the substrates, products and intermediates in the PC-catalyzed reaction are not oriented in the active site as previously assumed. The absence of a bidentate interaction with the active site metal appears to be a unique mechanistic feature among the small group of biotin-dependent enzymes that act on α-keto acid substrates. PMID:24157795

Mechanistic insight into the hydrazine decomposition on Rh(111): effect of reaction intermediate on catalytic activity.

PubMed

Deng, Zhigang; Lu, Xiaoqing; Wen, Zengqiang; Wei, Shuxian; Liu, Yunjie; Fu, Dianling; Zhao, Lianming; Guo, Wenyue

2013-10-14

Periodic density functional theory (DFT) calculations have been performed to systematically investigate the effect of reaction intermediate on catalytic activity for hydrazine (N2H4) decomposition on Rh(111). Reaction mechanisms via intramolecular and NH2-assisted N2H4 decompositions are comparatively analyzed, including adsorption configuration, reaction energy and barrier of elementary step, and reaction network. Our results show that the most favorable N2H4 decomposition pathway starts with the initial N-N bond scission to the NH2 intermediate, followed by stepwise H stripping from adsorbed N2Hx (x = 1-4) species, and finally forms the N2 and NH3 products. Comparatively, the stepwise intramolecular dehydrogenation via N2H4→ N2H3→ N2H2→ N2H → N2, and N2H4→ NH2→ NH → N with or without NH2 promotion effect, are unfavorable due to higher energy barriers encountered. Energy barrier analysis, reaction rate constants, and electronic structures are used to identify the crucial competitive route. The promotion effect of the NH2 intermediate is structurally reflected in the weakening of the N-H bond and strengthening of the N-N bond in N2Hx in the coadsorption system; it results intrinsically from the less structural deformation of the adsorbate, and weakening of the interaction between dehydrogenated fragment and departing H in transition state. Our results highlight the crucial effect of reaction intermediate on catalytic activity and provide a theoretical approach to analyze the effect.

A molten globule-like intermediate state detected in the thermal transition of cytochrome c under low salt concentration.

PubMed

Nakamura, Shigeyoshi; Baba, Takayuki; Kidokoro, Shun-Ichi

2007-04-01

To understand the stabilization mechanism of the transient intermediate state in protein folding, it is very important to understand the structure and stability of the molten globule state under a native condition, in which the native state exists stably. The thermal transitions of horse cytochrome c were thermodynamically evaluated by highly precise differential scanning calorimetry (DSC) at pH 3.8-5.0. The heat capacity functions were analyzed using double deconvolution and the nonlinear least-squares method. An intermediate (I) state is clearly confirmed in the thermal native (N)-to-denatured (D) transition of horse cytochrome c. The mole fraction of the intermediate state shows the largest value, 0.4, at nearly 70 degrees C at pH 4.1. This intermediate state was also detected by the circular dichroism (CD) method and was found to have the properties of the molten globule-like structure by three-state analysis of the CD data. The Gibbs free-energy change between N and I, DeltaG(NI), and that between N and D, DeltaG(ND), were evaluated to be 9-22 kJ mol(-1) and 41-45 kJ mol(-1), respectively at 15( ) degrees C and pH 4.1.

Spectroscopic Characterization of the Water Oxidation Intermediates in the Blue Dimer Ru-Based Catalyst for Artificial Photosynthesis

NASA Astrophysics Data System (ADS)

Moonshiram, Dooshaye; Pushkar, Yulia; Jurss, Jonah; Concepcion, Javier; Meyer, Thomas; Zakharova, Taisiya; Alperovich, Igor

2012-02-01

Utilization of sunlight requires solar capture, light-to-energy conversion and storage. One effective way to store energy is to convert it into chemical energy by fuel-forming reactions, such as water splitting into hydrogen and oxygen. Ruthenium complexes are among few molecular-defined catalysts capable of water splitting. Mechanistic insights about such catalysts can be acquired by spectroscopic analysis of short-lived intermediates of catalytic water oxidation. Use of techniques such as EPR and X-ray absorption spectroscopy (XAS) are used to determine electronic requirements of catalytic water oxidation. About 30 years ago Meyer and coworkers reported first ruthenium-based catalyst for water oxidation, the ``blue dimer''. We performed EPR studies and characterized structures and electronic configurations of intermediates of water oxidation by the ``blue dimer''. Intermediates were prepared chemically by oxidation of Ru-complexes with defined number of Ce (IV) equivalents and freeze-quenched at controlled times. Changes in oxidation state of Ru atom were detected by XANES at Ru K-edges. K-edges are sensitive to changes in Ru oxidation state for Blue Dimer [3,3]^4+, [3,4]^4+, [3,4]'^4+ and [4,5]^3+ allowing a clear assignment of Ru oxidation state in intermediates. EXAFS demonstrated structural changes.

Intermediate-phase method for computing the natural band offset between two materials with dissimilar structures

NASA Astrophysics Data System (ADS)

Gu, Hui-Jun; Zhang, Yue-Yu; Chen, Shi-You; Xiang, Hong-Jun; Gong, Xin-Gao

2018-06-01

The band offset between different semiconductors is an important physical quantity determining carrier transport properties near the interface in heterostructure devices. Computation of the natural band offset is a longstanding challenge. We propose an intermediate-phase method to predict the natural band offset between two structures with different symmetry, for which the superlattice model cannot be directly constructed. With this method and the intermediate phases obtained by our searching algorithm, we successfully calculate the natural band offsets for two representative systems: (i) zinc-blende CdTe and wurtzite CdS and (ii) diamond and graphite. The calculation shows that the valence band maximum (VBM) of zinc-blende CdTe lies 0.71 eV above that of wurtzite CdS, close to the result 0.76 eV obtained by the three-step method. For the natural band offset between diamond and graphite which could not be computed reliably with any superlattice methods, our calculation shows that the Fermi level of graphite lies 1.51 eV above the VBM of diamond using an intermediate phase. This method, under the assumption that the transitivity rule is valid, can be used to calculate the band offsets between any semiconductors with different symmetry on condition that the intermediate phase is reasonably designed.

Development of Vibrational Culture Model Mimicking Vocal Fold Tissues.

PubMed

Kim, Dongjoo; Lim, Jae-Yol; Kwon, Soonjo

2016-10-01

The vocal folds (VFs) are connective tissues with complex matrix structures that provide the required mechanical properties for voice generation. VF injury leads to changes in tissue structure and properties, resulting in reduced voice quality. However, injury-induced biochemical changes and repair in scarred VF tissues have not been well characterized to date. To treat scarred VFs, it is essential to understand how physiological characteristics of VFs tissue change in response to external perturbation. In this study, we designed a simple vibrational culture model to mimic vibratory microenvironments observed in vivo. This model consists of a flexible culture plate, three linear actuators, a stereo splitter, and a function generator. Human vocal fold fibroblast (hVFF) monolayers were established on the flexible membrane, to which normal phonatory vibrations were delivered from linear actuators and a function generator. The hVFF monolayers were exposed to the vibrational stresses at a frequency of 205 Hz for 2, 6, and 10 h with maximum displacement of 47.1 μm, followed by a 6 h rest. We then observed the changes in cell morphology, cell viability, and gene expression related to extracellular matrix components. In our dynamic culture device mimicking normal phonatory frequencies, cell proliferation increased and expression of hyaluronic acid synthase 2 was downregulated in response to vibrational stresses. The results presented herein will be useful for evaluating cellular responses following VF injuries in the presence or absence of vibrational stresses.

Spatial and temporal profile of cisplatin delivery by ultrasound-assisted intravesical chemotherapy in a bladder cancer model.

PubMed

Sasaki, Noboru; Ishi, Kazuhiro; Kudo, Nobuki; Nakayama, Shouta M M; Nakamura, Kensuke; Morishita, Keitaro; Ohta, Hiroshi; Ishizuka, Mayumi; Takiguchi, Mitsuyoshi

2017-01-01

Non-muscle invasive bladder cancer is one of the most common tumors of the urinary tract. Despite the current multimodal therapy, recurrence and progression of disease have been challenging problems. We hereby introduced a new approach, ultrasound-assisted intravesical chemotherapy, intravesical instillation of chemotherapeutic agents and microbubbles followed by ultrasound exposure. We investigated the feasibility of the treatment for non-muscle invasive bladder cancer. In order to evaluate intracellular delivery and cytotoxic effect as a function to the thickness, we performed all experiments using a bladder cancer mimicking 3D culture model. Ultrasound-triggered microbubble cavitation increased both the intracellular platinum concentration and the cytotoxic effect of cisplatin at the thickness of 70 and 122 μm of the culture model. The duration of enhanced cytotoxic effect of cisplatin by ultrasound-triggered microbubble cavitation was approximately 1 hr. Based on the distance and duration of delivery, we further tested the feasibility of repetition of the treatment. Triple treatment increased the effective distance by 1.6-fold. Our results clearly showed spatial and temporal profile of delivery by ultrasound-triggered microbubble cavitation in a tumor-mimicking structure. Furthermore, we demonstrated that the increase in intracellular concentration results in the enhancement of the cytotoxic effect in a structure with the certain thickness. Repetition of ultrasound exposure would be treatment of choice in future clinical application. Our results suggest ultrasound-triggered microbubble cavitation can be repeatable and is promising for the local control of non-muscle invasive bladder cancer.

Synonymies of wasp-mimicking species within the katydid genus Aganacris (Orthoptera: Tettigoniidae: Phaneropterinae)

USDA-ARS?s Scientific Manuscript database

Five neotropical wasp-mimicking species of the genus Aganacris—two known from females only and three from males only—are reviewed. Based on observations of interspecific interactions and morphological comparisons, sexual dimorphism is shown to occur within species, and that female species are consp...

Primary Papillary Mucinous Adenocarcinoma of the Ureter Mimicking Genitourinary Tuberculosis

PubMed Central

Gulwani, Hanni; Jain, Aruna

2010-01-01

Primary adenocarcinomas of the renal pelvis and ureter are rare and account for less than 1% of all malignancies at this site. We report a case of primary papillary mucinous adenocarcinoma of the ureter that clinically mimicked genitourinary tuberculosis. Early diagnosis is important for the better outcome. PMID:21151719

Minimal Mimicry: Mere Effector Matching Induces Preference

ERIC Educational Resources Information Center

Sparenberg, Peggy; Topolinski, Sascha; Springer, Anne; Prinz, Wolfgang

2012-01-01

Both mimicking and being mimicked induces preference for a target. The present experiments investigate the minimal sufficient conditions for this mimicry-preference link to occur. We argue that mere effector matching between one's own and the other person's movement is sufficient to induce preference, independent of which movement is actually…

Neoplastic stomach lesions and their mimickers: spectrum of imaging manifestations

PubMed Central

Virmani, Vivek; Sethi, Vineeta; Fraser-Hill, Margret; Fasih, Najla; Kielar, Ania

2012-01-01

Abstract This review illustrates a wide spectrum of gastric neoplasms with emphasis on imaging findings helpful in characterizing various gastric neoplasms. Both the malignant and benign neoplasms along with focal gastric masses mimicking tumour are illustrated. Moreover, imaging clues to reach an accurate diagnosis are emphasized. PMID:22935192

Stimulating Creative Writing Through Literature: A Guide for Teachers of the Intermediate Grades.

ERIC Educational Resources Information Center

Pilon, Alice Barbara Cummings

A structured writing program for the intermediate grades was designed, utilizing such children's literature as poems, legends, fairy tales, tall tales, and books to stimulate elementary school children to write creatively. Chapters in the teacher's guide for the program present many specific suggestions and activities to help children (1) use…

NMR spectra of 3β-hydroxy-5α-cholane derivatives, zymosterol synthesis intermediates

NASA Astrophysics Data System (ADS)

Baranovsky, A. V.; Bolotin, A. A.; Kiselev, V. P.

2011-05-01

Proton and carbon resonances in NMR spectra of a number of derivatives of 3β-hydroxy-5α-cholanes, zymosterol synthesis intermediates, have been completely assigned using 2D NMR spectroscopy methods. The stereochemistry of the chiral centers and the structures of the molecules have been confirmed.

Ecological importance of intermediate windstorms rivals large, infrequent disturbances in the northern Great Lakes

Treesearch

Kirk M. Stueve; Charles H. (Hobie) Perry; Mark D. Nelson; Sean P. Healey; Andrew D. Hill; Gretchen G. Moisen; Warren B. Cohen; Dale D. Gormanson; Chengquan Huang

2011-01-01

Exogenous disturbances are critical agents of change in temperate forests capable of damaging trees and influencing forest structure, composition, demography, and ecosystem processes. Forest disturbances of intermediate magnitude and intensity receive relatively sparse attention, particularly at landscape scales, despite influencing most forests at least once per...

LC/MS/MS structure elucidation of reaction intermediates formed during the TiO2 photocatalysis of microcystin-LR

EPA Science Inventory

Microcystin-LR (MC-LR), a cyanotoxin and emerging drinking water contaminant, was treated with TiO(2) photocatalysts immobilized on stainless steel plates as an alternative to nanoparticles in slurry. The reaction intermediates of MC-LR were identified with mass spectrometry (MS)...

Structural relaxation in supercooled orthoterphenyl.

PubMed

Chong, S-H; Sciortino, F

2004-05-01

We report molecular-dynamics simulation results performed for a model of molecular liquid orthoterphenyl in supercooled states, which we then compare with both experimental data and mode-coupling-theory (MCT) predictions, aiming at a better understanding of structural relaxation in orthoterphenyl. We pay special attention to the wave number dependence of the collective dynamics. It is shown that the simulation results for the model share many features with experimental data for real system, and that MCT captures the simulation results at the semiquantitative level except for intermediate wave numbers connected to the overall size of the molecule. Theoretical results at the intermediate wave number region are found to be improved by taking into account the spatial correlation of the molecule's geometrical center. This supports the idea that unusual dynamical properties at the intermediate wave numbers, reported previously in simulation studies for the model and discernible in coherent neutron-scattering experimental data, are basically due to the coupling of the rotational motion to the geometrical-center dynamics. However, there still remain qualitative as well as quantitative discrepancies between theoretical prediction and corresponding simulation results at the intermediate wave numbers, which call for further theoretical investigation.

The novel asymmetric entry intermediate of a picornavirus captured with nanodiscs

PubMed Central

Lee, Hyunwook; Shingler, Kristin L.; Organtini, Lindsey J.; Ashley, Robert E.; Makhov, Alexander M.; Conway, James F.; Hafenstein, Susan

2016-01-01

Many nonenveloped viruses engage host receptors that initiate capsid conformational changes necessary for genome release. Structural studies on the mechanisms of picornavirus entry have relied on in vitro approaches of virus incubated at high temperatures or with excess receptor molecules to trigger the entry intermediate or A-particle. We have induced the coxsackievirus B3 entry intermediate by triggering the virus with full-length receptors embedded in lipid bilayer nanodiscs. These asymmetrically formed A-particles were reconstructed using cryo-electron microscopy and a direct electron detector. These first high-resolution structures of a picornavirus entry intermediate captured at a membrane with and without imposing icosahedral symmetry (3.9 and 7.8 Å, respectively) revealed a novel A-particle that is markedly different from the classical A-particles. The asymmetric receptor binding triggers minimal global capsid expansion but marked local conformational changes at the site of receptor interaction. In addition, viral proteins extrude from the capsid only at the site of extensive protein remodeling adjacent to the nanodisc. Thus, the binding of the receptor triggers formation of a unique site in preparation for genome release. PMID:27574701

Combustor assembly in a gas turbine engine

DOEpatents

Wiebe, David J; Fox, Timothy A

2015-04-28

A combustor assembly in a gas turbine engine includes a combustor device, a fuel injection system, a transition duct, and an intermediate duct. The combustor device includes a flow sleeve for receiving pressurized air and a liner surrounded by the flow sleeve. The fuel injection system provides fuel to be mixed with the pressurized air and ignited in the liner to create combustion products. The intermediate duct is disposed between the liner and the transition duct so as to define a path for the combustion products to flow from the liner to the transition duct. The intermediate duct is associated with the liner such that movement may occur therebetween, and the intermediate duct is associated with the transition duct such that movement may occur therebetween. The flow sleeve includes structure that defines an axial stop for limiting axial movement of the intermediate duct.

Method to synthesize dense crystallized sodalite pellet for immobilizing halide salt radioactive waste

DOEpatents

Koyama, Tadafumi

1994-01-01

A method for immobilizing waste chloride salts containing radionuclides such as cesium and strontium and hazardous materials such as barium. A sodalite intermediate is prepared by mixing appropriate amounts of silica, alumina and sodium hydroxide with respect to sodalite and heating the mixture to form the sodalite intermediate and water. Heating is continued to drive off the water to form a water-free intermediate. The water-free intermediate is mixed with either waste salt or waste salt which has been contacted with zeolite to concentrate the radionuclides and hazardous material. The waste salt-intermediate mixture is then compacted and heated under conditions of heat and pressure to form sodalite with the waste salt, radionuclides and hazardous material trapped within the sodalite cage structure. This provides a final product having excellent leach resistant capabilities.

Method to synthesize dense crystallized sodalite pellet for immobilizing halide salt radioactive waste

DOEpatents

Koyama, Tadafumi.

1994-08-23

A method is described for immobilizing waste chloride salts containing radionuclides such as cesium and strontium and hazardous materials such as barium. A sodalite intermediate is prepared by mixing appropriate amounts of silica, alumina and sodium hydroxide with respect to sodalite and heating the mixture to form the sodalite intermediate and water. Heating is continued to drive off the water to form a water-free intermediate. The water-free intermediate is mixed with either waste salt or waste salt which has been contacted with zeolite to concentrate the radionuclides and hazardous material. The waste salt-intermediate mixture is then compacted and heated under conditions of heat and pressure to form sodalite with the waste salt, radionuclides and hazardous material trapped within the sodalite cage structure. This provides a final product having excellent leach resistant capabilities.

Method to synthesize dense crystallized sodalite pellet for immobilizing halide salt radioactive waste

DOEpatents

Koyama, T.

1992-01-01

This report describes a method for immobilizing waste chloride salts containing radionuclides such as cesium and strontium and hazardous materials such as barium. A sodalite intermediate is prepared by mixing appropriate amounts of silica, alumina and sodium hydroxide with respect to sodalite and heating the mixture to form the sodalite intermediate and water. Heating is continued to drive off the water to form a water-free intermediate. The water-free intermediate is mixed with either waste salt or waste salt which has been contacted with zeolite to concentrate the radionuclides and hazardous material. The waste salt-intermediate mixture is then compacted and heated under conditions of heat and pressure to form sodalite with the waste salt, radionuclides and hazardous material trapped within the sodalite cage structure. This provides a final product having excellent leach resistant capabilities.

Sorptive fractionation of organic matter and formation of organo-hydroxy-aluminum complexes during litter biodegradation in the presence of gibbsite

NASA Astrophysics Data System (ADS)

Heckman, K.; Grandy, A. S.; Gao, X.; Keiluweit, M.; Wickings, K.; Carpenter, K.; Chorover, J.; Rasmussen, C.

2013-11-01

Solid and aqueous phase Al species are recognized to affect organic matter (OM) stabilization in forest soils. However, little is known about the dynamics of formation, composition and dissolution of organo-Al hydroxide complexes in microbially-active soil systems, where plant litter is subject to microbial decomposition in close proximity to mineral weathering reactions. We incubated gibbsite-quartz mineral mixtures in the presence of forest floor material inoculated with a native microbial consortium for periods of 5, 60 and 154 days. At each time step, samples were density separated into light (<1.6 g cm-3), intermediate (1.6-2.0 g cm-3), and heavy (>2.0 g cm-3) fractions. The light fraction was mainly comprised of particulate organic matter, while the intermediate and heavy density fractions contained moderate and large amounts of Al-minerals, respectively. Multi-method interrogation of the fractions indicated the intermediate and heavy fractions differed both in mineral structure and organic compound composition. X-ray diffraction analysis and SEM/EDS of the mineral component of the intermediate fractions indicated some alteration of the original gibbsite structure into less crystalline Al hydroxide and possibly proto-imogolite species, whereas alteration of the gibbsite structure was not evident in the heavy fraction. DRIFT, Py-GC/MS and STXM/NEXAFS results all showed that intermediate fractions were composed mostly of lignin-derived compounds, phenolics, and polysaccharides. Heavy fraction organics were dominated by polysaccharides, and were enriched in proteins, N-bearing compounds, and lipids. The source of organics appeared to differ between the intermediate and heavy fractions. Heavy fractions were enriched in 13C with lower C/N ratios relative to intermediate fractions, suggesting a microbial origin. The observed differential fractionation of organics among hydroxy-Al mineral types suggests that microbial activity superimposed with abiotic mineral-surface-mediated fractionation leads to strong density differentiation of organo-mineral complex composition even over the short time scales probed in these incubation experiments. The data highlight the strong interdependency of mineral transformation, microbial community activity, and organic matter stabilization during biodegradation.

The Tautomeric Half-reaction of BphD, a C-C Bond Hydrolase Kinetic and Structural Evidence Supporting a Key Role for Histidine 265 of the Catalytic triad

DOE Office of Scientific and Technical Information (OSTI.GOV)

Horsman, Geoff P.; Bhowmik, Shiva; Seah, Stephen Y.K.

2010-01-07

BphD of Burkholderia xenovorans LB400 catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to afford benzoic acid and 2-hydroxy-2,4-pentadienoic acid (HPD). An enol-keto tautomerization has been proposed to precede hydrolysis via a gem-diol intermediate. The role of the canonical catalytic triad (Ser-112, His-265, Asp-237) in mediating these two half-reactions remains unclear. We previously reported that the BphD-catalyzed hydrolysis of HOPDA ({lambda}{sub max} is 434 nm for the free enolate) proceeds via an unidentified intermediate with a red-shifted absorption spectrum ({lambda}{sub max} is 492 nm) (Horsman, G. P., Ke, J., Dai, S., Seah, S. Y. K., Bolin, J. T.,more » and Eltis, L. D. (2006) Biochemistry 45, 11071-11086). Here we demonstrate that the S112A variant generates and traps a similar intermediate ({lambda}{sub max} is 506 nm) with a similar rate, 1/{tau} {approx} 500 s{sup -1}. The crystal structure of the S112A:HOPDA complex at 1.8-{angstrom} resolution identified this intermediate as the keto tautomer, (E)-2,6-dioxo-6-phenyl-hex-3-enoate. This keto tautomer did not accumulate in either the H265A or the S112A/H265A double variants, indicating that His-265 catalyzes tautomerization. Consistent with this role, the wild type and S112A enzymes catalyzed tautomerization of the product HPD, whereas H265A variants did not. This study thus identifies a keto intermediate, and demonstrates that the catalytic triad histidine catalyzes the tautomerization half-reaction, expanding the role of this residue from its purely hydrolytic function in other serine hydrolases. Finally, the S112A:HOPDA crystal structure is more consistent with hydrolysis occurring via an acyl-enzyme intermediate than a gem-diol intermediate as solvent molecules have poor access to C6, and the closest ordered water is 7{angstrom} away.« less

Superoxide Dismutase 1 In Vivo Ameliorates Maternal Diabetes Mellitus-Induced Apoptosis and Heart Defects Through Restoration of Impaired Wnt Signaling.

PubMed

Wang, Fang; Fisher, Steven A; Zhong, Jianxiang; Wu, Yanqing; Yang, Peixin

2015-10-01

Oxidative stress is manifested in embryos exposed to maternal diabetes mellitus, yet specific mechanisms for diabetes mellitus-induced heart defects are not defined. Gene deletion of intermediates of Wingless-related integration (Wnt) signaling causes heart defects similar to those observed in embryos from diabetic pregnancies. We tested the hypothesis that diabetes mellitus-induced oxidative stress impairs Wnt signaling, thereby causing heart defects, and that these defects can be rescued by transgenic overexpression of the reactive oxygen species scavenger superoxide dismutase 1 (SOD1). Wild-type (WT) and SOD1-overexpressing embryos from nondiabetic WT control dams and nondiabetic/diabetic WT female mice mated with SOD1 transgenic male mice were analyzed. No heart defects were observed in WT and SOD1 embryos under nondiabetic conditions. WT embryos of diabetic dams had a 26% incidence of cardiac outlet defects that were suppressed by SOD1 overexpression. Insulin treatment reduced blood glucose levels and heart defects. Diabetes mellitus increased superoxide production, canonical Wnt antagonist expression, caspase activation, and apoptosis and suppressed cell proliferation. Diabetes mellitus suppressed Wnt signaling intermediates and Wnt target gene expression in the embryonic heart, each of which were reversed by SOD1 overexpression. Hydrogen peroxide and peroxynitrite mimicked the inhibitory effect of high glucose on Wnt signaling, which was abolished by the SOD1 mimetic, tempol. The oxidative stress of diabetes mellitus impairs Wnt signaling and causes cardiac outlet defects that are rescued by SOD1 overexpression. This suggests that targeting of components of the Wnt5a signaling pathway may be a viable strategy for suppression of congenital heart defects in fetuses of diabetic pregnancies. © 2015 American Heart Association, Inc.

A DFT investigation of a bulky biomimetic model catalyzing the 5'-outer ring deiodination of thyroxine.

PubMed

Fortino, Mariagrazia; Marino, Tiziana; Russo, Nino; Sicilia, Emilia

2016-12-01

This paper illustrates the outcomes of a density functional theory investigation aimed at unraveling mechanistic aspects of the 5'-outer ring deiodination process of thyroxine (T4) assisted by the sterically protected organoselenol compound BpqSeH. BpqSeH, which was previously synthesized and tested for its deiodinase activity, is able to afford the active hormone 3,5,3'-tetraiodothyronine (T3) by selective outer-ring deiodination of T4, and to protect the SeH moiety inside the nano-sized molecular cavity from further reactivity, allowing its isolation and characterization. Calculations were also performed including an imidazole ring that, mimicking a His residue in the active site of the original enzyme, plays an crucial role in deprotonating the selenol moiety. Both the suggested enol/keto tautomerization and the previously proven formation of an intermediate whose main characteristic is the presence of a Se⋯I⋯C halogen bond, were examined along the pathway leading to 5'-outer ring deiodination. The calculated potential energy surface showed that neither the pathway encompassing enol/keto tautomerism nor the formation of a halogen bond paving the way to C-I bond breaking and chalcogen-I bond forming is viable. The exergonic formation of the final selenenyl iodide product confirms the stabilization effect of the molecular cavity. Graphical Abstract Computed free energy profile describing the 5'-outer deiodination of thyroxine assisted by the steric hindered organoselenol BpqSH compound. The molecular electrostatic potential map reoported for the INT1 intermediate shows the non-covalent Se-I interaction, due to the attraction between charges of opposite sign, that weakens the C-I bond and prepares the formation of the new Se-I bond.

Ab initio electronic structure calculations for metallic intermediate band formation in photovoltaic materials

NASA Astrophysics Data System (ADS)

Wahnón, P.; Tablero, C.

2002-04-01

A metallic isolated band in the middle of the band gap of several III-V semiconductors has been predicted as photovoltaic materials with the possibility of providing substantially enhanced efficiencies. We have investigated the electronic band structures and lattice constants of GanAsmM and GanPmM with M=Sc, Ti, V, and Cr, to identify whether this isolated band is likely to exist by means of accurate calculations. For this task, we use the SIESTA program, an ab initio periodic density-functional method, fully self consistent in the local-density approximation. Norm-conserving, nonlocal pseudopotentials and confined linear combination of atomic orbitals have been used. We have carried out a case study of GanAsmTi and GanPmTi energy-band structure including analyses of the effect of the basis set, fine k-point mesh to ensure numerical convergence, structural parameters, and generalized gradient approximation for exchange and correlation corrections. We find the isolated intermediate band when one Ti atom replaces the position of one As (or P) atom in the crystal structure. For this kind of compound we show that the intermediate band relative position inside the band gap and width are sensitive to the dynamic relaxation of the crystal and the size of the basis set.

Structural Characterization of a Human-Type Corrinoid Adenosyltransferase Confirms That Coenzyme B[subscript 12] Is Synthesized through a Four-Coordinate Intermediate

DOE Office of Scientific and Technical Information (OSTI.GOV)

St. Maurice, Martin; Mera, Paola; Park, Kiyoung

ATP:cob(I)alamin adenosyltransferases (ACAs) catalyze the transfer of the 5{prime}-deoxyadenosyl moiety from ATP to the upper axial ligand position of cobalamin in the synthesis of coenzyme B{sub 12}. For the ACA-catalyzed reaction to proceed, cob(II)alamin must be reduced to cob(I)alamin in the enzyme active site. This reduction is facilitated through the generation of a four-coordinate cob(II)alamin intermediate on the enzyme. We have determined the high-resolution crystal structure of a human-type ACA from Lactobacillus reuteri with a four-coordinate cob(II)alamin bound in the enzyme active site and with the product, adenosylcobalamin, partially occupied in the active site. The assembled structures represent snapshots ofmore » the steps in the ACA-catalyzed formation of the cobalt-carbon bond of coenzyme B{sub 12}. The structures define the corrinoid binding site and provide visual evidence for a base-off, four-coordinate cob(II)alamin intermediate. The complete structural description of ACA-mediated catalysis reveals the molecular features of four-coordinate cob(II)alamin stabilization and provides additional insights into the molecular basis for dysfunction in human patients suffering from methylmalonic aciduria.« less

R-Matrix Analysis of Structures in Economic Indices: from Nuclear Reactions to High-Frequency Trading

NASA Astrophysics Data System (ADS)

Firk, Frank W. K.

2014-03-01

It is shown that the R-matrix theory of nuclear reactions is a viable mathematical theory for the description of the fine, intermediate and gross structure observed in the time-dependence of economic indices in general, and the daily Dow Jones Industrial Average in particular. A Lorentzian approximation to R-matrix theory is used to analyze the complex structures observed in the Dow Jones Industrial Average on a typical trading day. Resonant structures in excited nuclei are characterized by the values of their fundamental strength function, (average total width of the states)/(average spacing between adjacent states). Here, values of the ratios (average lifetime of individual states of a given component of the daily Dow Jones Industrial Average)/(average interval between the adjacent states) are determined. The ratios for the observed fine and intermediate structure of the index are found to be essentially constant throughout the trading day. These quantitative findings are characteristic of the highly statistical nature of many-body, strongly interacting systems, typified by daily trading. It is therefore proposed that the values of these ratios, determined in the first hour-or-so of trading, be used to provide valuable information concerning the likely performance of the fine and intermediate components of the index for the remainder of the trading day.

Pauling and Corey's alpha-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease.

PubMed

Armen, Roger S; DeMarco, Mari L; Alonso, Darwin O V; Daggett, Valerie

2004-08-10

Transthyretin, beta(2)-microglobulin, lysozyme, and the prion protein are four of the best-characterized proteins implicated in amyloid disease. Upon partial acid denaturation, these proteins undergo conformational change into an amyloidogenic intermediate that can self-assemble into amyloid fibrils. Many experiments have shown that pH-mediated changes in structure are required for the formation of the amyloidogeneic intermediate, but it has proved impossible to characterize these conformational changes at high resolution using experimental means. To probe these conformational changes at atomic resolution, we have performed molecular dynamics simulations of these proteins at neutral and low pH. In low-pH simulations of all four proteins, we observe the formation of alpha-pleated sheet secondary structure, which was first proposed by L. Pauling and R. B. Corey [(1951) Proc. Natl. Acad. Sci. USA 37, 251-256]. In all beta-sheet proteins, transthyretin and beta(2)-microglobulin, alpha-pleated sheet structure formed over the strands that are highly protected in hydrogen-exchange experiments probing amyloidogenic conditions. In lysozyme and the prion protein, alpha-sheets formed in the specific regions of the protein implicated in the amyloidogenic conversion. We propose that the formation of alpha-pleated sheet structure may be a common conformational transition in amyloidosis.

Pauling and Corey's α-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease

PubMed Central

Armen, Roger S.; DeMarco, Mari L.; Alonso, Darwin O. V.; Daggett, Valerie

2004-01-01

Transthyretin, β2-microglobulin, lysozyme, and the prion protein are four of the best-characterized proteins implicated in amyloid disease. Upon partial acid denaturation, these proteins undergo conformational change into an amyloidogenic intermediate that can self-assemble into amyloid fibrils. Many experiments have shown that pH-mediated changes in structure are required for the formation of the amyloidogeneic intermediate, but it has proved impossible to characterize these conformational changes at high resolution using experimental means. To probe these conformational changes at atomic resolution, we have performed molecular dynamics simulations of these proteins at neutral and low pH. In low-pH simulations of all four proteins, we observe the formation of α-pleated sheet secondary structure, which was first proposed by L. Pauling and R. B. Corey [(1951) Proc. Natl. Acad. Sci. USA 37, 251–256]. In all β-sheet proteins, transthyretin and β2-microglobulin, α-pleated sheet structure formed over the strands that are highly protected in hydrogen-exchange experiments probing amyloidogenic conditions. In lysozyme and the prion protein, α-sheets formed in the specific regions of the protein implicated in the amyloidogenic conversion. We propose that the formation of α-pleated sheet structure may be a common conformational transition in amyloidosis. PMID:15280548

GFP's Mechanical Intermediate States

PubMed Central

Saeger, John; Hytönen, Vesa P.; Klotzsch, Enrico; Vogel, Viola

2012-01-01

Green fluorescent protein (GFP) mutants have become the most widely used fluorescence markers in the life sciences, and although they are becoming increasingly popular as mechanical force or strain probes, there is little direct information on how their fluorescence changes when mechanically stretched. Here we derive high-resolution structural models of the mechanical intermediate states of stretched GFP using steered molecular dynamics (SMD) simulations. These structures were used to produce mutants of EGFP and EYFP that mimic GFP's different mechanical intermediates. A spectroscopic analysis revealed that a population of EGFP molecules with a missing N-terminal α-helix was significantly dimmed, while the fluorescence lifetime characteristic of the anionic chromophore state remained unaffected. This suggests a mechanism how N-terminal deletions can switch the protonation state of the chromophore, and how the fluorescence of GFP molecules in response to mechanical disturbance might be turned off. PMID:23118864

On the origin of regio- and stereoselectivity in the rhodium-catalyzed vinylarenes hydroboration reaction.

PubMed

Daura-Oller, Elias; Segarra, Anna M; Poblet, Josep M; Claver, Carmen; Fernández, Elena; Bo, Carles

2004-04-16

We studied the hydroboration of vinylarenes using rhodium complexes bearing atropoisomeric ligands. For the first time, an NMR spectroscopy study of the styrene and catecholborane addition to the precursor of catalyst [Rh(COD)(L-L)]BF(4), where L-L = (R)-BINAP and (R)-QUINAP, showed evidence of the structure of intermediates involved in the catalytic cycle. On the basis of this evidence, and using DFT calculations and QM/MM strategies, we investigated the origin of regio- and stereoselectivity. We determined the structure and stability of the key intermediates for several ligands and substrates and found excellent agreement between the relative stability of the intermediates and the experimentally observed trends. Using model systems, we analyzed the role of the steric and electronic features of the ligands and the substrates in detail.

Theoretical and experimental analysis of the structural pattern responsible for the iridescence of Morpho butterflies.

PubMed

Siddique, Radwanul Hasan; Diewald, Silvia; Leuthold, Juerg; Hölscher, Hendrik

2013-06-17

Morpho butterflies are well-known for their iridescence originating from nanostructures in the scales of their wings. These optical active structures integrate three design principles leading to the wide angle reflection: alternating lamellae layers, "Christmas tree" like shape, and offsets between neighboring ridges. We study their individual effects rigorously by 2D FEM simulations of the nanostructures of the Morpho sulkowskyi butterfly and show how the reflection spectrum can be controlled by the design of the nanostructures. The width of the spectrum is broad (≈ 90 nm) for alternating lamellae layers (or "brunches") of the structure while the "Christmas tree" pattern together with a height offset between neighboring ridges reduces the directionality of the reflectance. Furthermore, we fabricated the simulated structures by e-beam lithography. The resulting samples mimicked all important optical features of the original Morpho butterfly scales and feature the intense blue iridescence with a wide angular range of reflection.

Fibrillar assembly of bacterial cellulose in the presence of wood-based hemicelluloses.

PubMed

Penttilä, Paavo A; Imai, Tomoya; Sugiyama, Junji

2017-09-01

Composite materials mimicking the plant cell wall structure were made by culturing cellulose-producing bacteria together with secondary-wall hemicelluloses from wood. The effects of spruce galactoglucomannan (GGM) and beech xylan on the nanoscale morphology of bacterial cellulose were studied in the original, hydrated state with small-angle X-ray scattering (SAXS). The SAXS intensities were fitted with a model covering multiple levels of the hierarchical structure. Additional information on the structure of dried samples was obtained using scanning and transmission electron microscopy and infra-red spectroscopy. Both hemicelluloses induced a partial conversion of the cellulose crystal structure from I α to I β and a reduction of the cross-sectional dimensions of the cellulose microfibrils, thereby affecting also their packing into bundles. The differences were more pronounced in samples with xylan instead of GGM, and they became more significant with higher hemicellulose concentrations. Copyright © 2017 Elsevier B.V. All rights reserved.

Zeolite-like liquid crystals

NASA Astrophysics Data System (ADS)

Poppe, Silvio; Lehmann, Anne; Scholte, Alexander; Prehm, Marko; Zeng, Xiangbing; Ungar, Goran; Tschierske, Carsten

2015-10-01

Zeolites represent inorganic solid-state materials with porous structures of fascinating complexity. Recently, significant progress was made by reticular synthesis of related organic solid-state materials, such as metal-organic or covalent organic frameworks. Herein we go a step further and report the first example of a fluid honeycomb mimicking a zeolitic framework. In this unique self-assembled liquid crystalline structure, transverse-lying π-conjugated rod-like molecules form pentagonal channels, encircling larger octagonal channels, a structural motif also found in some zeolites. Additional bundles of coaxial molecules penetrate the centres of the larger channels, unreachable by chains attached to the honeycomb framework. This creates a unique fluid hybrid structure combining positive and negative anisotropies, providing the potential for tuning the directionality of anisotropic optical, electrical and magnetic properties. This work also demonstrates a new approach to complex soft-matter self-assembly, by using frustration between space filling and the entropic penalty of chain extension.

Confinement in F4 Exceptional Gauge Group Using Domain Structures

NASA Astrophysics Data System (ADS)

Rafibakhsh, Shahnoosh; Shahlaei, Amir

2017-03-01

We calculate the potential between static quarks in the fundamental representation of the F4 exceptional gauge group using domain structures of the thick center vortex model. As non-trivial center elements are absent, the asymptotic string tension is lost while an intermediate linear potential is observed. SU(2) is a subgroup of F4. Investigating the decomposition of the 26 dimensional representation of F4 to the SU(2) representations, might explain what accounts for the intermediate linear potential, in the exceptional groups with no center element.

Building polyhedra by self-assembly: theory and experiment.

PubMed

Kaplan, Ryan; Klobušický, Joseph; Pandey, Shivendra; Gracias, David H; Menon, Govind

2014-01-01

We investigate the utility of a mathematical framework based on discrete geometry to model biological and synthetic self-assembly. Our primary biological example is the self-assembly of icosahedral viruses; our synthetic example is surface-tension-driven self-folding polyhedra. In both instances, the process of self-assembly is modeled by decomposing the polyhedron into a set of partially formed intermediate states. The set of all intermediates is called the configuration space, pathways of assembly are modeled as paths in the configuration space, and the kinetics and yield of assembly are modeled by rate equations, Markov chains, or cost functions on the configuration space. We review an interesting interplay between biological function and mathematical structure in viruses in light of this framework. We discuss in particular: (i) tiling theory as a coarse-grained description of all-atom models; (ii) the building game-a growth model for the formation of polyhedra; and (iii) the application of these models to the self-assembly of the bacteriophage MS2. We then use a similar framework to model self-folding polyhedra. We use a discrete folding algorithm to compute a configuration space that idealizes surface-tension-driven self-folding and analyze pathways of assembly and dominant intermediates. These computations are then compared with experimental observations of a self-folding dodecahedron with side 300 μm. In both models, despite a combinatorial explosion in the size of the configuration space, a few pathways and intermediates dominate self-assembly. For self-folding polyhedra, the dominant intermediates have fewer degrees of freedom than comparable intermediates, and are thus more rigid. The concentration of assembly pathways on a few intermediates with distinguished geometric properties is biologically and physically important, and suggests deeper mathematical structure.

SSR and morphological trait based population structure analysis of 130 diverse flax (Linum usitatissimum L.) accessions.

PubMed

Choudhary, Shashi Bhushan; Sharma, Hariom Kumar; Kumar, Arroju Anil; Maruthi, Rangappa Thimmaiah; Mitra, Jiban; Chowdhury, Isholeena; Singh, Binay Kumar; Karmakar, Pran Gobinda

2017-02-01

A total of 130 flax accessions of diverse morphotypes and worldwide origin were assessed for genetic diversity and population structure using 11 morphological traits and microsatellite markers (15 gSSRs and 7 EST-SSRs). Analysis performed after classifying these accessions on the basis of plant height, branching pattern, seed size, Indian/foreign origin into six categories called sub-populations viz. fibre type exotic, fibre type indigenous, intermediate type exotic, intermediate type indigenous, linseed type exotic and linseed type indigenous. The study assessed different diversity indices, AMOVA, population structure and included a principal coordinate analysis based on different marker systems. The highest diversity was exhibited by gSSR markers (SI=0.46; He=0.31; P=85.11). AMOVA based on all markers explained significant difference among fibre type, intermediate type and linseed type populations of flax. In terms of variation explained by different markers, EST-SSR markers (12%) better differentiated flax populations compared to morphological (9%) and gSSR (6%) markers at P=0.01. The maximum Nei's unbiased genetic distance (D=0.11) was observed between fibre type and linseed type exotic sub-populations based on EST-SSR markers. The combined structure analysis by using all markers grouped Indian fibre type accessions (63.4%) in a separate cluster along with the Indian intermediate type (48.7%), whereas Indian accessions (82.16%) of linseed type constituted an independent cluster. These findings were supported by the results of the principal coordinate analysis. Morphological markers employed in the study found complementary with microsatellite based markers in deciphering genetic diversity and population structure of the flax germplasm. Copyright © 2016 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

Nickel-aluminum alloy clusters -- structural and dynamical properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jellinek, J.; Krissinel, E.B.

1997-08-01

Structural and dynamical properties of mixed Ni{sub n}Al{sub m} alloy clusters mimicked by a many-body potential are studied computationally for all the possible compositions n and m such that n + m = 13. It is shown that the manifold of the usually very large number of the different possible structural forms can be systematized by introducing classes of structures corresponding to the same concentration of the components, geometry and type of the central atom. General definitions of mixing energy and mixing coefficient are introduced, and it is shown that the energy ordering of the structural forms within each classmore » is governed by the mixing coefficient. The peculiarities of the solid-to-liquid-like transition are described as a function of the concentration of the two types of atoms. These peculiarities are correlated with and explained in terms of the energy spectra of the structural forms. Class-dependent features of the dynamics are described and analyzed.« less

Natural product-like virtual libraries: recursive atom-based enumeration.

PubMed

Yu, Melvin J

2011-03-28

A new molecular enumerator is described that allows chemically and architecturally diverse sets of natural product-like and drug-like structures to be generated from a core structure as simple as a single carbon atom or as complex as a polycyclic ring system. Integrated with a rudimentary machine-learning algorithm, the enumerator has the ability to assemble biased virtual libraries enriched in compounds predicted to meet target criteria. The ability to dynamically generate relatively small focused libraries in a recursive manner could reduce the computational time and infrastructure necessary to construct and manage extremely large static libraries. Depending on enumeration conditions, natural product-like structures can be produced with a wide range of heterocyclic and alicyclic ring assemblies. Because natural products represent a proven source of validated structures for identifying and designing new drug candidates, mimicking the structural and topological diversity found in nature with a dynamic set of virtual natural product-like compounds may facilitate the creation of new ideas for novel, biologically relevant lead structures in areas of uncharted chemical space.

Binuclear Cu A formation in biosynthetic models of Cu A in azurin proceeds via a novel Cu(Cys) 2His mononuclear copper intermediate

DOE PAGES

Chakraborty, Saumen; Polen, Michael J.; Chacon, Kelly N.; ...

2015-09-09

Cu A is a binuclear electron transfer (ET) center found in cytochrome c oxidases (C cOs), nitrous oxide reductases (N 2ORs), and nitric oxide reductase (NOR). In these proteins, the Cu A centers facilitate efficient ET ( k ET > 10 4 s –1) under low thermodynamic driving forces (10–90 mV). While the structure and functional properties of Cu A are well understood, a detailed mechanism of the incorporation of copper into the protein and the identity of the intermediates formed during the Cu A maturation process are still lacking. Previous studies of the Cu A assembly mechanism in vitromore » using a biosynthetic model Cu A center in azurin (Cu AAz) identified a novel intermediate X (I x) during reconstitution of the binuclear site. However, because of the instability of I x and the coexistence of other Cu centers, such as Cu A' and type 1 copper centers, the identity of this intermediate could not be established. In this paper, we report the mechanism of Cu A assembly using variants of Glu114XCu AAz (X = Gly, Ala, Leu, or Gln), the backbone carbonyl of which acts as a ligand to the Cu A site, with a major focus on characterization of the novel intermediate I x. We show that Cu A assembly in these variants proceeds through several types of Cu centers, such as mononuclear red type 2 Cu, the novel intermediate I x, and blue type 1 Cu. Our results show that the backbone flexibility of the Glu114 residue is an important factor in determining the rates of T2Cu → I x formation, suggesting that Cu A formation is facilitated by swinging of the ligand loop, which internalizes the T2Cu capture complex to the protein interior. The kinetic data further suggest that the nature of the Glu114 side chain influences the time scales on which these intermediates are formed, the wavelengths of the absorption peaks, and how cleanly one intermediate is converted to another. Through careful understanding of these mechanisms and optimization of the conditions, we have obtained I x in ~80–85% population in these variants, which allowed us to employ ultraviolet–visible, electron paramagnetic resonance, and extended X-ray absorption fine structure spectroscopic techniques to identify the I x as a mononuclear Cu(Cys) 2(His) complex. Finally, because some of the intermediates have been proposed to be involved in the assembly of native Cu A, these results shed light on the structural features of the important intermediates and mechanism of Cu A formation.« less

X-ray Absorption Spectroscopy Reveals an Organometallic Ni–C Bond in the CO-Treated Form of Acetyl-CoA Synthase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Can, Mehmet; Giles, Logan J.; Ragsdale, Stephen W.

Acetyl-CoA synthase (ACS) is a key enzyme in the Wood–Ljungdahl pathway of anaerobic CO 2 fixation, which has long been proposed to operate by a novel mechanism involving a series of protein-bound organometallic (Ni–CO, methyl–Ni, and acetyl–Ni) intermediates. Here we report the first direct structural evidence of the proposed metal–carbon bond. We describe the preparation of the highly active metal-replete enzyme and near-quantitative generation of the kinetically competent carbonylated intermediate. This advance has allowed a combination of Ni and Fe K-edge X-ray absorption spectroscopy and extended X-ray absorption fine structure experiments along with density functional theory calculations. The data revealmore » that CO binds to the proximal Ni of the six-metal metallocenter at the active site and undergoes dramatic structural and electronic perturbation in forming this organometallic Ni–CO intermediate. This direct identification of a Ni–carbon bond in the catalytically competent CO-bound form of the In conclusion, a cluster of ACS provides definitive experimental structural evidence supporting the proposed organometallic mechanism of anaerobic acetyl-CoA synthesis.« less

The dual-basin landscape in GFP folding

PubMed Central

Andrews, Benjamin T.; Gosavi, Shachi; Finke, John M.; Onuchic, José N.; Jennings, Patricia A.

2008-01-01

Recent experimental studies suggest that the mature GFP has an unconventional landscape composed of an early folding event with a typical funneled landscape, followed by a very slow search and rearrangement step into the locked, active chromophore-containing structure. As we have shown previously, the substantial difference in time scales is what generates the observed hysteresis in thermodynamic folding. The interconversion between locked and the soft folding structures at intermediate denaturant concentrations is so slow that it is not observed under the typical experimental observation time. Simulations of a coarse-grained model were used to describe the fast folding event as well as identify native-like intermediates on energy landscapes enroute to the fluorescent native fold. Interestingly, these simulations reveal structural features of the slow dynamic transition to chromophore activation. Experimental evidence presented here shows that the trapped, native-like intermediate has structural heterogeneity in residues previously linked to chromophore formation. We propose that the final step of GFP folding is a “locking” mechanism leading to chromophore formation and high stability. The combination of previous experimental work and current simulation work is explained in the context of a dual-basin folding mechanism described above. PMID:18713871

X-ray Absorption Spectroscopy Reveals an Organometallic Ni–C Bond in the CO-Treated Form of Acetyl-CoA Synthase

DOE PAGES

Can, Mehmet; Giles, Logan J.; Ragsdale, Stephen W.; ...

2017-02-10

Acetyl-CoA synthase (ACS) is a key enzyme in the Wood–Ljungdahl pathway of anaerobic CO 2 fixation, which has long been proposed to operate by a novel mechanism involving a series of protein-bound organometallic (Ni–CO, methyl–Ni, and acetyl–Ni) intermediates. Here we report the first direct structural evidence of the proposed metal–carbon bond. We describe the preparation of the highly active metal-replete enzyme and near-quantitative generation of the kinetically competent carbonylated intermediate. This advance has allowed a combination of Ni and Fe K-edge X-ray absorption spectroscopy and extended X-ray absorption fine structure experiments along with density functional theory calculations. The data revealmore » that CO binds to the proximal Ni of the six-metal metallocenter at the active site and undergoes dramatic structural and electronic perturbation in forming this organometallic Ni–CO intermediate. This direct identification of a Ni–carbon bond in the catalytically competent CO-bound form of the In conclusion, a cluster of ACS provides definitive experimental structural evidence supporting the proposed organometallic mechanism of anaerobic acetyl-CoA synthesis.« less

Heterogeneity of Equilibrium Molten Globule State of Cytochrome c Induced by Weak Salt Denaturants under Physiological Condition

PubMed Central

Rahaman, Hamidur; Alam Khan, Md. Khurshid; Hassan, Md. Imtaiyaz; Islam, Asimul; Moosavi-Movahedi, Ali Akbar; Ahmad, Faizan

2015-01-01

While many proteins are recognized to undergo folding via intermediate(s), the heterogeneity of equilibrium folding intermediate(s) along the folding pathway is less understood. In our present study, FTIR spectroscopy, far- and near-UV circular dichroism (CD), ANS and tryptophan fluorescence, near IR absorbance spectroscopy and dynamic light scattering (DLS) were used to study the structural and thermodynamic characteristics of the native (N), denatured (D) and intermediate state (X) of goat cytochorme c (cyt-c) induced by weak salt denaturants (LiBr, LiCl and LiClO4) at pH 6.0 and 25°C. The LiBr-induced denaturation of cyt-c measured by Soret absorption (Δε 400) and CD ([θ]409), is a three-step process, N ↔ X ↔ D. It is observed that the X state obtained along the denaturation pathway of cyt-c possesses common structural and thermodynamic characteristics of the molten globule (MG) state. The MG state of cyt-c induced by LiBr is compared for its structural and thermodynamic parameters with those found in other solvent conditions such as LiCl, LiClO4 and acidic pH. Our observations suggest: (1) that the LiBr-induced MG state of cyt-c retains the native Met80-Fe(III) axial bond and Trp59-propionate interactions; (2) that LiBr-induced MG state of cyt-c is more compact retaining the hydrophobic interactions in comparison to the MG states induced by LiCl, LiClO4 and 0.5 M NaCl at pH 2.0; and (3) that there exists heterogeneity of equilibrium intermediates along the unfolding pathway of cyt-c as highly ordered (X1), classical (X2) and disordered (X3), i.e., D ↔ X3 ↔ X2 ↔ X1 ↔ N. PMID:25849212

Heterogeneity of equilibrium molten globule state of cytochrome c induced by weak salt denaturants under physiological condition.

PubMed

Rahaman, Hamidur; Alam Khan, Md Khurshid; Hassan, Md Imtaiyaz; Islam, Asimul; Moosavi-Movahedi, Ali Akbar; Ahmad, Faizan

2015-01-01

While many proteins are recognized to undergo folding via intermediate(s), the heterogeneity of equilibrium folding intermediate(s) along the folding pathway is less understood. In our present study, FTIR spectroscopy, far- and near-UV circular dichroism (CD), ANS and tryptophan fluorescence, near IR absorbance spectroscopy and dynamic light scattering (DLS) were used to study the structural and thermodynamic characteristics of the native (N), denatured (D) and intermediate state (X) of goat cytochorme c (cyt-c) induced by weak salt denaturants (LiBr, LiCl and LiClO4) at pH 6.0 and 25°C. The LiBr-induced denaturation of cyt-c measured by Soret absorption (Δε400) and CD ([θ]409), is a three-step process, N ↔ X ↔ D. It is observed that the X state obtained along the denaturation pathway of cyt-c possesses common structural and thermodynamic characteristics of the molten globule (MG) state. The MG state of cyt-c induced by LiBr is compared for its structural and thermodynamic parameters with those found in other solvent conditions such as LiCl, LiClO4 and acidic pH. Our observations suggest: (1) that the LiBr-induced MG state of cyt-c retains the native Met80-Fe(III) axial bond and Trp59-propionate interactions; (2) that LiBr-induced MG state of cyt-c is more compact retaining the hydrophobic interactions in comparison to the MG states induced by LiCl, LiClO4 and 0.5 M NaCl at pH 2.0; and (3) that there exists heterogeneity of equilibrium intermediates along the unfolding pathway of cyt-c as highly ordered (X1), classical (X2) and disordered (X3), i.e., D ↔ X3 ↔ X2 ↔ X1 ↔ N.

Use of a biosynthetic intermediate to explore the chemical diversity of pseudo-natural fungal polyketides.

PubMed

Asai, Teigo; Tsukada, Kento; Ise, Satomi; Shirata, Naoki; Hashimoto, Makoto; Fujii, Isao; Gomi, Katsuya; Nakagawara, Kosuke; Kodama, Eiichi N; Oshima, Yoshiteru

2015-09-01

The structural complexity and diversity of natural products make them attractive sources for potential drug discovery, with their characteristics being derived from the multi-step combination of enzymatic and non-enzymatic conversions of intermediates in each biosynthetic pathway. Intermediates that exhibit multipotent behaviour have great potential for use as starting points in diversity-oriented synthesis. Inspired by the biosynthetic pathways that form complex metabolites from simple intermediates, we developed a semi-synthetic process that combines heterologous biosynthesis and artificial diversification. The heterologous biosynthesis of fungal polyketide intermediates led to the isolation of novel oligomers and provided evidence for ortho-quinonemethide equivalency in their isochromene form. The intrinsic reactivity of the isochromene polyketide enabled us to access various new chemical entities by modifying and remodelling the polyketide core and through coupling with indole molecules. We thus succeeded in generating exceptionally diverse pseudo-natural polyketides through this process and demonstrated an advanced method of using biosynthetic intermediates.

Use of a biosynthetic intermediate to explore the chemical diversity of pseudo-natural fungal polyketides

NASA Astrophysics Data System (ADS)

Asai, Teigo; Tsukada, Kento; Ise, Satomi; Shirata, Naoki; Hashimoto, Makoto; Fujii, Isao; Gomi, Katsuya; Nakagawara, Kosuke; Kodama, Eiichi N.; Oshima, Yoshiteru

2015-09-01

The structural complexity and diversity of natural products make them attractive sources for potential drug discovery, with their characteristics being derived from the multi-step combination of enzymatic and non-enzymatic conversions of intermediates in each biosynthetic pathway. Intermediates that exhibit multipotent behaviour have great potential for use as starting points in diversity-oriented synthesis. Inspired by the biosynthetic pathways that form complex metabolites from simple intermediates, we developed a semi-synthetic process that combines heterologous biosynthesis and artificial diversification. The heterologous biosynthesis of fungal polyketide intermediates led to the isolation of novel oligomers and provided evidence for ortho-quinonemethide equivalency in their isochromene form. The intrinsic reactivity of the isochromene polyketide enabled us to access various new chemical entities by modifying and remodelling the polyketide core and through coupling with indole molecules. We thus succeeded in generating exceptionally diverse pseudo-natural polyketides through this process and demonstrated an advanced method of using biosynthetic intermediates.

Hydroxyacetone production from C 3 Criegee intermediates

DOE PAGES

Taatjes, Craig A.; Liu, Fang; Rotavera, Brandon; ...

2016-12-21

Hydroxyacetone (CH 3C(O)CH 2OH) is observed as a stable end product from reactions of the (CH 3) 2COO Criegee intermediate, acetone oxide, in a flow tube coupled with multiplexed photoionization mass spectrometer detection. In the experiment, the isomers at m/z = 74 are distinguished by their different photoionization spectra and reaction times. Hydroxyacetone is observed as a persistent signal at longer reaction times at a higher photoionization threshold of ca. 9.7 eV than Criegee intermediate and definitively identified by comparison with the known photoionization spectrum. Complementary electronic structure calculations reveal multiple possible reaction pathways for hydroxyacetone formation, including unimolecular isomerizationmore » via hydrogen atom transfer and –OH group migration as well as self-reaction of Criegee intermediates. Varying the concentration of Criegee intermediates suggests contributions from both unimolecular and self-reaction pathways to hydroxyacetone. As a result, the hydroxyacetone end product can provide an effective, stable marker for the production of transient Criegee intermediates in future studies of alkene ozonolysis.« less

Rare extraskeletal Ewing's sarcoma mimicking as adenocarcinoma of the sigmoid.

PubMed

Mertens, Michelle; Haenen, Filip W N; Siozopoulou, Vasiliki; Van Cleemput, Marc

2017-06-01

Extraskeletal Ewing's sarcoma (EES) is a rare finding in comparison with Ewing's sarcoma of bone and usually manifests in young patients. However, even in older patients, one must consider the diagnosis. In this case, we describe a 52-year-old woman diagnosed with EES, mimicking as adenocarcinoma of the sigmoid. The tumor was not visualized by a multi-slice spiral computed tomography of the abdomen and pelvis with intravenous contrast, and eventually the diagnosis was made by positive immunohistochemical staining for CD99 and by molecular testing for EWSR1 translocation. This combination of the patient's age and the localization of the tumor mimicking an adenocarcinoma of the sigmoid has never been described before.

Creutzfeldt-Jakob Disease Mimicking Alzheimer Disease and Dementia With Lewy Bodies-Findings of FDG PET With 3-Dimensional Stereotactic Surface Projection.

PubMed

Miyazawa, Nobuhiko

2017-05-01

A 78-year-old man received a diagnosis of sporadic Creutzfeldt-Jakob disease based on symptoms and findings of MRI, FDG PET, and cerebrospinal fluid markers. PET with 3-dimensional stereotactic surface projection (3D-SSP) showed that the distribution of hypometabolism mimicked that of Alzheimer disease. A 68-year-old woman was treated under a diagnosis of convulsion. Findings of MRI, PET, familial history, and cerebrospinal fluid markers revealed familial Creutzfeldt-Jakob disease. FDG PET with 3D-SSP disclosed that the hypometabolic pattern mimicked that of dementia with Lewy bodies. FDG PET with 3D-SSP can demonstrate similar patterns in various neurodegenerative disorders.

Mechanism for circularization of linear DNAs: circular parvovirus MVM DNA is formed by a "noose" sliding in a "lasso"-like DNA structure.

PubMed

Bratosin, S; Laub, O; Tal, J; Aloni, Y

1979-09-01

During an electron-microscopic survey with the aim of identifying the parvovirus MVM transcription template, we observed previously unidentified structures of MVM DNA in lysates of virus-infected cells. These included double-stranded "lasso"-like structures and relaxed circles. Both structures were of unit length MVM DNA, indicating that they were not intermediates formed during replication; they each represented about 5% of the total nuclear MVM DNA. The proportion of these structures was unchanged after digestion with sodium dodecyl sulfate/Pronase and RNase and after mild denaturation treatment. Cleavage of the "lasso" structures with EcoRI restriction endonuclease indicated that the "noose" part of the "lasso" structure is located on the 5' side of the genomic single-stranded MVM DNA. A model is presented for the molecular nature of the circularization process of MVM DNA in which the "lasso" structures are identified as intermediates during circle formation. This model proposes a mechanism for circularization of linear DNAs.

Consequences of localized frustration for the folding mechanism of the IM7 protein

PubMed Central

Sutto, Ludovico; Lätzer, Joachim; Hegler, Joseph A.; Ferreiro, Diego U.; Wolynes, Peter G.

2007-01-01

In the laboratory, IM7 has been found to have an unusual folding mechanism in which an “on-pathway” intermediate with nonnative interactions is formed. We show that this intermediate is a consequence of an unusual cluster of highly frustrated interactions in the native structure. This cluster is involved in the binding of IM7 to its target, Colicin E7. Redesign of residues in this cluster to eliminate frustration is predicted by simulations to lead to faster folding without the population of an intermediate ensemble. PMID:18077415

Yuji Tonomura: a pioneer in the field of energy transduction in muscle contraction.

PubMed

Onishi, Hirofumi

2009-07-01

Late Professor Yuji Tonomura has made a great contribution in the study of energy transduction in muscle contraction. He was the investigator who first proposed that a myosin-phosphate intermediate is produced subsequently to the Michaelis-Menten complex in the pre-steady state of the myosin ATPase reaction and that it is a key intermediate for muscle contraction. Here, his proposed intermediate will be viewed from the prospective of today's understanding of actomyosin ATPase kinetics and in the context of myosin motor domain crystal structures.

Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins

PubMed Central

Kurkcuoglu, Zeynep; Doruker, Pemra

2016-01-01

Incorporating receptor flexibility in small ligand-protein docking still poses a challenge for proteins undergoing large conformational changes. In the absence of bound structures, sampling conformers that are accessible by apo state may facilitate docking and drug design studies. For this aim, we developed an unbiased conformational search algorithm, by integrating global modes from elastic network model, clustering and energy minimization with implicit solvation. Our dataset consists of five diverse proteins with apo to complex RMSDs 4.7–15 Å. Applying this iterative algorithm on apo structures, conformers close to the bound-state (RMSD 1.4–3.8 Å), as well as the intermediate states were generated. Dockings to a sequence of conformers consisting of a closed structure and its “parents” up to the apo were performed to compare binding poses on different states of the receptor. For two periplasmic binding proteins and biotin carboxylase that exhibit hinge-type closure of two dynamics domains, the best pose was obtained for the conformer closest to the bound structure (ligand RMSDs 1.5–2 Å). In contrast, the best pose for adenylate kinase corresponded to an intermediate state with partially closed LID domain and open NMP domain, in line with recent studies (ligand RMSD 2.9 Å). The docking of a helical peptide to calmodulin was the most challenging case due to the complexity of its 15 Å transition, for which a two-stage procedure was necessary. The technique was first applied on the extended calmodulin to generate intermediate conformers; then peptide docking and a second generation stage on the complex were performed, which in turn yielded a final peptide RMSD of 2.9 Å. Our algorithm is effective in producing conformational states based on the apo state. This study underlines the importance of such intermediate states for ligand docking to proteins undergoing large transitions. PMID:27348230

A dianionic phosphorane intermediate and transition states in an associative A(N)+D(N) mechanism for the ribonucleaseA hydrolysis reaction.

PubMed

Elsässer, Brigitta; Valiev, Marat; Weare, John H

2009-03-25

The RNaseA enzyme efficiently cleaves phosphodiester bonds in the RNA backbone. Phosphoryl transfer plays a central role in many biochemical reactions, and this is one of the most studied enzymes. However, there remains considerable controversy about the reaction mechanism. Most of this debate centers around the roles of the conserved residues, structures of the transition state or states, the possibility of a stable intermediate, and the charge and structure of this intermediate. In this communication we report calculations of the mechanism of the hydrolysis step in this reaction using a comprehensive QM/MM theoretical approach that includes a high level calculation of the interactions in the QM region, free energy estimates along an NEB optimized reaction path, and the inclusion of the interaction of the protein surroundings and solvent. Contrary to prior calculations we find a stable pentacoordinated dianionic phosphorane intermediate in the reaction path supporting an A(N)+D(N) reaction mechanism. In the transition state in the path from the reactant to the intermediate state (with barrier of 3.96 kcal/mol and intermediate stability of 2.21 kcal/mol) a proton from the attacking water is partially transferred to the His119 residue and the PO bond only partially formed from the remaining nucleophilic OH(-) species (bond order (BO) 0.11). In passing from the intermediate to the product state (barrier 13.22 kcal/mol) the PO bond on the cyclic phosphorane intermediate is nearly broken (BO 0.28) and the transfer of the proton from the Lys41 is almost complete (Lys41-H BO 0.87). In the product state a proton has been transferred from Lys41 to the O2' position of the sugar. The role of Lys41 as the catalytic acid is a result of the relative positioning of the Lys41 and His12 in the catalytic site. This configuration is supported by calculations and docking studies.

Paracoccidioidomycosis mimicking squamous cell carcinoma on the dorsum of the tongue and review of published literature.

PubMed

Pedreira, Renato do Prado Gomes; Guimarães, Eduardo Pereira; de Carli, Marina Lara; Magalhães, Evandro Monteiro de Sá; Pereira, Alessandro Antônio Costa; Hanemann, João Adolfo Costa

2014-06-01

Paracoccidioidomycosis is a disease that is endemic to southern and southeastern Brazil, caused by the fungus Paracoccidioides brasiliensis. The most common clinical oral manifestation is the presence of multiple granulomatous ulcers with hemorrhagic dots, located mainly on the lips, palate, and buccal mucosa. However, the disease can manifest atypically as a single ulcer, mimicking oral squamous cell carcinoma (SCC) or tuberculosis. A 65-year-old male patient presented with a complaint of a single ulcerated lesion on the dorsum of the tongue; the lesion had evolved over 6 months. The diagnostic hypotheses were SCC and oral manifestation of tuberculosis. An incisional biopsy was performed, and histopathological analysis of the specimen revealed pseudoepitheliomatous hyperplasia, a granulomatous structure of epithelioid histiocytes, multinucleated giant cells, and lymphocytes in the connective tissue. Grocott staining confirmed the presence of the fungus in the lesion, and a diagnosis was made of paracoccidioidomycosis. The patient was treated with 200 mg/day of itraconazole for 12 months and now shows no signs or symptoms of recurrence of the disease. Correct diagnosis is essential for a successful therapeutic approach and resolution of the lesion.

Short-term plasticity and long-term potentiation mimicked in single inorganic synapses

NASA Astrophysics Data System (ADS)

Ohno, Takeo; Hasegawa, Tsuyoshi; Tsuruoka, Tohru; Terabe, Kazuya; Gimzewski, James K.; Aono, Masakazu

2011-08-01

Memory is believed to occur in the human brain as a result of two types of synaptic plasticity: short-term plasticity (STP) and long-term potentiation (LTP; refs , , , ). In neuromorphic engineering, emulation of known neural behaviour has proven to be difficult to implement in software because of the highly complex interconnected nature of thought processes. Here we report the discovery of a Ag2S inorganic synapse, which emulates the synaptic functions of both STP and LTP characteristics through the use of input pulse repetition time. The structure known as an atomic switch, operating at critical voltages, stores information as STP with a spontaneous decay of conductance level in response to intermittent input stimuli, whereas frequent stimulation results in a transition to LTP. The Ag2S inorganic synapse has interesting characteristics with analogies to an individual biological synapse, and achieves dynamic memorization in a single device without the need of external preprogramming. A psychological model related to the process of memorizing and forgetting is also demonstrated using the inorganic synapses. Our Ag2S element indicates a breakthrough in mimicking synaptic behaviour essential for the further creation of artificial neural systems that emulate characteristics of human memory.

Ex vivo detection of macrophages in atherosclerotic plaques using intravascular ultrasonic-photoacoustic imaging

NASA Astrophysics Data System (ADS)

Quang Bui, Nhat; Hlaing, Kyu Kyu; Lee, Yong Wook; Kang, Hyun Wook; Oh, Junghwan

2017-01-01

Macrophages are excellent imaging targets for detecting atherosclerotic plaques as they are involved in all the developmental stages of atherosclerosis. However, no imaging technique is currently capable of visualizing macrophages inside blood vessel walls. The current study develops an intravascular ultrasonic-photoacoustic (IVUP) imaging system combined with indocyanine green (ICG) as a contrast agent to provide morphological and compositional information about the targeted samples. Both tissue-mimicking vessel phantoms and atherosclerotic plaque-mimicking porcine arterial tissues are used to demonstrate the feasibility of mapping macrophages labeled with ICG by endoscopically applying the proposed hybrid technique. A delay pulse triggering technique is able to sequentially acquire photoacoustic (PA) and ultrasound (US) signals from a single scan without using any external devices. The acquired PA and US signals are used to reconstruct 2D cross-sectional and 3D volumetric images of the entire tissue with the ICG-loaded macrophages injected. Due to high imaging contrast and sensitivity, the IVUP imaging vividly reveals structural information and detects the spatial distribution of the ICG-labeled macrophages inside the samples. ICG-assisted IVUP imaging can be a feasible imaging modality for the endoscopic detection of atherosclerotic plaques.

An Extracranial Metastasis of Glioblastoma Mimicking Mucoepidermoid Carcinoma.

PubMed

Jie, Wei-Ping; Bai, Jia-Ying; Li, Bin-Bin

2018-05-28

Glioblastoma (GBM) is the most common and aggressive primary malignant tumor of the brain and central nervous system. Extracranial metastases of GBM are very rare, with few case reports published to date. The tumor cells of GBM show strong immunopositivity for glial fibrillary acid protein (GFAP). A 47-year-old man without comorbidities presented with a 1-year history of an augmenting right parotid lump. A right total parotidectomy with selective neck dissection was performed. The hematoxylin-eosin stained slice of a parotid lymph node collected intraoperatively revealed destruction of normal lymph node structure by medium-sized pleomorphic cells scattered in groups; their cytoplasm was lightly stained and pale. There were abundant myxoid stroma in the interstitial tissue. This characteristic mimicked mucoepidermoid carcinoma (MEC). Immunohistochemistry test demonstrated that the cells were positive for GFAP. A diagnosis of extracranial metastasis of GBM was made after confirmation with postoperative pathological examination of the intracranial resection specimen. We believe that this is the first reported case of extracranial metastasis of GBM resembling MEC in the microscope features. Pathologists and clinicians should be alert to this rare lesion and consider this differential diagnosis after excluding other common parotid lesions. Copyright © 2018 Elsevier Inc. All rights reserved.

Biomimetic and Bioinspired Synthesis of Nanomaterials/Nanostructures.

PubMed

Zan, Guangtao; Wu, Qingsheng

2016-03-16

In recent years, due to its unparalleled advantages, the biomimetic and bioinspired synthesis of nanomaterials/nanostructures has drawn increasing interest and attention. Generally, biomimetic synthesis can be conducted either by mimicking the functions of natural materials/structures or by mimicking the biological processes that organisms employ to produce substances or materials. Biomimetic synthesis is therefore divided here into "functional biomimetic synthesis" and "process biomimetic synthesis". Process biomimetic synthesis is the focus of this review. First, the above two terms are defined and their relationship is discussed. Next different levels of biological processes that can be used for process biomimetic synthesis are compiled. Then the current progress of process biomimetic synthesis is systematically summarized and reviewed from the following five perspectives: i) elementary biomimetic system via biomass templates, ii) high-level biomimetic system via soft/hard-combined films, iii) intelligent biomimetic systems via liquid membranes, iv) living-organism biomimetic systems, and v) macromolecular bioinspired systems. Moreover, for these five biomimetic systems, the synthesis procedures, basic principles, and relationships are discussed, and the challenges that are encountered and directions for further development are considered. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural Diversification of Lyngbyatoxin A by Host-Dependent Heterologous Expression of the tleABC Biosynthetic Gene Cluster.

PubMed

Zhang, Lihan; Hoshino, Shotaro; Awakawa, Takayoshi; Wakimoto, Toshiyuki; Abe, Ikuro

2016-08-03

Natural products have enormous structural diversity, yet little is known about how such diversity is achieved in nature. Here we report the structural diversification of a cyanotoxin-lyngbyatoxin A-and its biosynthetic intermediates by heterologous expression of the Streptomyces-derived tleABC biosynthetic gene cluster in three different Streptomyces hosts: S. lividans, S. albus, and S. avermitilis. Notably, the isolated lyngbyatoxin derivatives, including four new natural products, were biosynthesized by crosstalk between the heterologous tleABC gene cluster and the endogenous host enzymes. The simple strategy described here has expanded the structural diversity of lyngbyatoxin A and its biosynthetic intermediates, and provides opportunities for investigation of the currently underestimated hidden biosynthetic crosstalk. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A partially folded structure of amyloid-beta(1-40) in an aqueous environment.

PubMed

Vivekanandan, Subramanian; Brender, Jeffrey R; Lee, Shirley Y; Ramamoorthy, Ayyalusamy

2011-07-29

Aggregation of the Aβ(1-40) peptide is linked to the development of extracellular plaques characteristic of Alzheimer's disease. While previous studies commonly show the Aβ(1-40) is largely unstructured in solution, we show that Aβ(1-40) can adopt a compact, partially folded structure. In this structure (PDB ID: 2LFM), the central hydrophobic region of the peptide forms a 3(10) helix from H13 to D23 and the N- and C-termini collapse against the helix due to the clustering of hydrophobic residues. Helical intermediates have been predicted to be crucial on-pathway intermediates in amyloid fibrillogenesis, and the structure presented here presents a new target for investigation of early events in Aβ(1-40) fibrillogenesis. Copyright © 2011 Elsevier Inc. All rights reserved.

Complete Structure of an Epithelial Keratin Dimer: Implications for Intermediate Filament Assembly.

PubMed

Bray, David J; Walsh, Tiffany R; Noro, Massimo G; Notman, Rebecca

2015-01-01

Keratins are cytoskeletal proteins that hierarchically arrange into filaments, starting with the dimer sub-unit. They are integral to the structural support of cells, in skin, hair and nails. In skin, keratin is thought to play a critical role in conferring the barrier properties and elasticity of skin. In general, the keratin dimer is broadly described by a tri-domain structure: a head, a central rod and a tail. As yet, no atomistic-scale picture of the entire dimer structure exists; this information is pivotal for establishing molecular-level connections between structure and function in intermediate filament proteins. The roles of the head and tail domains in facilitating keratin filament assembly and function remain as open questions. To address these, we report results of molecular dynamics simulations of the entire epithelial human K1/K10 keratin dimer. Our findings comprise: (1) the first three-dimensional structural models of the complete dimer unit, comprising of the head, rod and tail domains; (2) new insights into the chirality of the rod-domain twist gained from analysis of the full domain structure; (3) evidence for tri-subdomain partitioning in the head and tail domains; and, (4) identification of the residue characteristics that mediate non-covalent contact between the chains in the dimer. Our findings are immediately applicable to other epithelial keratins, such as K8/K18 and K5/K14, and to intermediate filament proteins in general.

Customizing clinical narratives for the electronic medical record interface using cognitive methods.

PubMed

Sharda, Pallav; Das, Amar K; Cohen, Trevor A; Patel, Vimla

2006-05-01

As healthcare practice transitions from paper-based to computer-based records, there is increasing need to determine an effective electronic format for clinical narratives. Our research focuses on utilizing a cognitive science methodology to guide the conversion of medical texts to a more structured, user-customized presentation in the electronic medical record (EMR). We studied the use of discharge summaries by psychiatrists with varying expertise-experts, intermediates, and novices. Experts were given two hypothetical emergency care scenarios with narrative discharge summaries and asked to verbalize their clinical assessment. Based on the results, the narratives were presented in a more structured form. Intermediate and novice subjects received a narrative and a structured discharge summary, and were asked to verbalize their assessments of each. A qualitative comparison of the interview transcripts of all subjects was done by analysis of recall and inference made with respect to level of expertise. For intermediate and novice subjects, recall was greater with the structured form than with the narrative. Novices were also able to make more inferences (not always accurate) from the structured form than with the narrative. Errors occurred in assessments using the narrative form but not the structured form. Our cognitive methods to study discharge summary use enabled us to extract a conceptual representation of clinical narratives from end-users. This method allowed us to identify clinically relevant information that can be used to structure medical text for the EMR and potentially improve recall and reduce errors.

An Unusual Foreign Body in the Urinary Bladder Mimicking a Parasitic Worm

PubMed Central

Schmitt, Bryan H.; Feder, Marc T.; Rokke, Denise L.; Moyer, Thomas P.

2012-01-01

We report an unusual case of a foreign body removed from the urinary bladder of a 63-year-old male which mimicked a parasitic worm. The foreign body was identified as an artificial fishing worm by morphological comparison to a similar commercially produced product and by infrared spectrum analysis. PMID:22535991

Being Mimicked Increases Prosocial Behavior in 18-Month-Old Infants

ERIC Educational Resources Information Center

Carpenter, Malinda; Uebel, Johanna; Tomasello, Michael

2013-01-01

Most previous research on imitation in infancy has focused on infants' learning of instrumental actions on objects. This study focused instead on the more social side of imitation, testing whether being mimicked increases prosocial behavior in infants, as it does in adults (van Baaren, Holland, Kawakami, & van Knippenberg, 2004).…

The cutaneous manifestations and common mimickers of physical child abuse.

PubMed

Mudd, Shawna S; Findlay, Jeanne S

2004-01-01

The cutaneous manifestations of physical child abuse are some of the most common and easily recognized forms of injury. To make an accurate assessment and diagnosis, it is important to differentiate between inflicted cutaneous injuries and mimickers of physical abuse. Likewise, an understanding of reporting guidelines helps guide practitioners in their decision making.

Abdominal Wall Endometriosis Mimicking Metastases.

PubMed

Nambiar, Rakul; Anoop, T M; Mony, Rari P

2018-06-01

Abdominal wall lesions can be broadly divided into nontumorous and tumorous conditions. Nontumorous lesions include congenital lesion, abdominal wall hernia, inflammation and infection, vascular lesions, and miscellaneous conditions like hematoma. Tumorous lesions include benign and malignant neoplasms. Here, we report an unusual case of abdominal wall endometriosis mimicking metastases in a patient with breast carcinoma.

Heparin-Mimicking Polymers: Synthesis and Biological Applications

PubMed Central

2016-01-01

Heparin is a naturally occurring, highly sulfated polysaccharide that plays a critical role in a range of different biological processes. Therapeutically, it is mostly commonly used as an injectable solution as an anticoagulant for a variety of indications, although it has also been employed in other forms such as coatings on various biomedical devices. Due to the diverse functions of this polysaccharide in the body, including anticoagulation, tissue regeneration, anti-inflammation, and protein stabilization, and drawbacks of its use, analogous heparin-mimicking materials are also widely studied for therapeutic applications. This review focuses on one type of these materials, namely, synthetic heparin-mimicking polymers. Utilization of these polymers provides significant benefits compared to heparin, including enhancing therapeutic efficacy and reducing side effects as a result of fine-tuning heparin-binding motifs and other molecular characteristics. The major types of the various polymers are summarized, as well as their applications. Because development of a broader range of heparin-mimicking materials would further expand the impact of these polymers in the treatment of various diseases, future directions are also discussed. PMID:27739666

Heparin-Mimicking Polymers: Synthesis and Biological Applications.

PubMed

Paluck, Samantha J; Nguyen, Thi H; Maynard, Heather D

2016-11-14

Heparin is a naturally occurring, highly sulfated polysaccharide that plays a critical role in a range of different biological processes. Therapeutically, it is mostly commonly used as an injectable solution as an anticoagulant for a variety of indications, although it has also been employed in other forms such as coatings on various biomedical devices. Due to the diverse functions of this polysaccharide in the body, including anticoagulation, tissue regeneration, anti-inflammation, and protein stabilization, and drawbacks of its use, analogous heparin-mimicking materials are also widely studied for therapeutic applications. This review focuses on one type of these materials, namely, synthetic heparin-mimicking polymers. Utilization of these polymers provides significant benefits compared to heparin, including enhancing therapeutic efficacy and reducing side effects as a result of fine-tuning heparin-binding motifs and other molecular characteristics. The major types of the various polymers are summarized, as well as their applications. Because development of a broader range of heparin-mimicking materials would further expand the impact of these polymers in the treatment of various diseases, future directions are also discussed.

Quantifying Vocal Mimicry in the Greater Racket-Tailed Drongo: A Comparison of Automated Methods and Human Assessment

PubMed Central

Agnihotri, Samira; Sundeep, P. V. D. S.; Seelamantula, Chandra Sekhar; Balakrishnan, Rohini

2014-01-01

Objective identification and description of mimicked calls is a primary component of any study on avian vocal mimicry but few studies have adopted a quantitative approach. We used spectral feature representations commonly used in human speech analysis in combination with various distance metrics to distinguish between mimicked and non-mimicked calls of the greater racket-tailed drongo, Dicrurus paradiseus and cross-validated the results with human assessment of spectral similarity. We found that the automated method and human subjects performed similarly in terms of the overall number of correct matches of mimicked calls to putative model calls. However, the two methods also misclassified different subsets of calls and we achieved a maximum accuracy of ninety five per cent only when we combined the results of both the methods. This study is the first to use Mel-frequency Cepstral Coefficients and Relative Spectral Amplitude - filtered Linear Predictive Coding coefficients to quantify vocal mimicry. Our findings also suggest that in spite of several advances in automated methods of song analysis, corresponding cross-validation by humans remains essential. PMID:24603717

Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal A Novel Type IA Topoisomerase-DNA Conformational Intermediate

PubMed Central

Changela, Anita; DiGate, Russell J.; Mondragón, Alfonso

2007-01-01

Summary E. coli DNA topoisomerase III belongs to the type IA family of DNA topoisomerases, which transiently cleave single-stranded DNA (ssDNA) via a 5′ phosphotyrosine intermediate. We have solved crystal structures of wild-type E. coli topoisomerase III bound to an 8-base ssDNA molecule in three different pH environments. The structures reveal the enzyme in three distinct conformational states while bound to DNA. One conformation resembles the one observed previously with a DNA-bound, catalytically inactive mutant of topoisomerase III where DNA binding realigns catalytic residues to form a functional active site. Another conformation represents a novel intermediate in which DNA is bound along the ssDNA-binding groove but does not enter the active site, which remains in a catalytically inactive, closed state. A third conformation shows an intermediate state where the enzyme is still in a closed state, but the ssDNA is starting to invade the active site. For the first time, the active site region in the presence of both the catalytic tyrosine and ssDNA substrate is revealed for a type IA DNA topoisomerase, although there is no evidence of ssDNA cleavage. Comparative analysis of the various conformational states suggests a sequence of domain movements undertaken by the enzyme upon substrate binding. PMID:17331537

Identification of an Unfolding Intermediate for a DNA Lesion Bypass Polymerase

PubMed Central

Sherrer, Shanen M.; Maxwell, Brian A.; Pack, Lindsey R.; Fiala, Kevin A.; Fowler, Jason D.; Zhang, Jun; Suo, Zucai

2012-01-01

Sulfolobus solfataricusDNA Polymerase IV (Dpo4), a prototype Y-family DNA polymerase, has been well characterized biochemically and biophysically at 37 °C or lower temperatures. However, the physiological temperature of the hyperthermophile S. solfataricus is approximately 80 °C. With such a large discrepancy in temperature, the in vivo relevance of these in vitro studies of Dpo4 has been questioned. Here, we employed circular dichroism spectroscopy and fluorescence-based thermal scanning to investigate the secondary structural changes of Dpo4 over a temperature range from 26 to 119 °C. Dpo4 was shown to display a high melting temperature characteristic of hyperthermophiles. Unexpectedly, the Little Finger domain of Dpo4, which is only found in the Y-family DNA polymerases, was shown to be more thermostable than the polymerase core. More interestingly, Dpo4 exhibited a three-state cooperative unfolding profile with an unfolding intermediate. The linker region between the Little Finger and Thumb domains of Dpo4 was found to be a source of structural instability. Through site-directed mutagenesis, the interactions between the residues in the linker region and the Palm domain were identified to play a critical role in the formation of the unfolding intermediate. Notably, the secondary structure of Dpo4 was not altered when the temperature was increased from 26 to 87.5 °C. Thus, in addition to providing structural insights into the thermal stability and an unfolding intermediate of Dpo4, our work also validated the relevance of the in vitro studies of Dpo4 performed at temperatures significantly lower than 80 °C. PMID:22667759

Competing Pathways and Multiple Folding Nuclei in a Large Multidomain Protein, Luciferase.

PubMed

Scholl, Zackary N; Yang, Weitao; Marszalek, Piotr E

2017-05-09

Proteins obtain their final functional configuration through incremental folding with many intermediate steps in the folding pathway. If known, these intermediate steps could be valuable new targets for designing therapeutics and the sequence of events could elucidate the mechanism of refolding. However, determining these intermediate steps is hardly an easy feat, and has been elusive for most proteins, especially large, multidomain proteins. Here, we effectively map part of the folding pathway for the model large multidomain protein, Luciferase, by combining single-molecule force-spectroscopy experiments and coarse-grained simulation. Single-molecule refolding experiments reveal the initial nucleation of folding while simulations corroborate these stable core structures of Luciferase, and indicate the relative propensities for each to propagate to the final folded native state. Both experimental refolding and Monte Carlo simulations of Markov state models generated from simulation reveal that Luciferase most often folds along a pathway originating from the nucleation of the N-terminal domain, and that this pathway is the least likely to form nonnative structures. We then engineer truncated variants of Luciferase whose sequences corresponded to the putative structure from simulation and we use atomic force spectroscopy to determine their unfolding and stability. These experimental results corroborate the structures predicted from the folding simulation and strongly suggest that they are intermediates along the folding pathway. Taken together, our results suggest that initial Luciferase refolding occurs along a vectorial pathway and also suggest a mechanism that chaperones may exploit to prevent misfolding. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Hexafluoroisopropanol-induced helix-sheet transition of stem bromelain: correlation to function.

PubMed

Dave, Sandeep; Dkhar, H Kitdorlang; Singh, Manvendra Pratap; Gupta, Garima; Chandra, Vemika; Mahajan, Sahil; Gupta, Pawan

2010-06-01

Stem bromelain is a proteolytic phytoprotein with a variety of therapeutic effects. Understanding its structural properties could provide insight into the mechanisms underlying its clinical utility. Stem bromelain was evaluated for its conformational and folding properties at the pH conditions it encounters when administered orally. It exists as a partially folded intermediate at pH 2.0. The conformational changes to this intermediate state were evaluated using fluorinated alcohols known to induce changes similar to those seen in vivo. Studies using circular dichroism, fluorescence emission spectroscopy, binding of the hydrophobic dye 1-anilino-8-naphthalene sulfonic acid and mass spectrometry indicate that treatment with 10-30% hexafluoroisopropanol induces the partially folded intermediate to adopt much of the native protein's secondary structure, but only a rudimentary tertiary structure, characteristic of the molten globule state. Addition of slightly higher concentrations of hexafluoroisopropanol caused transformation from an alpha-helix to a beta-sheet and induced formation of a compact nonnative structure. This nonnative form was more inhibitory of cell survival than either the native or the partially folded intermediate forms, as measured by enhanced suppression of proliferative cues (e.g., extracellular-signal-regulated kinase) and initiation of apoptotic events. The nonnative form also showed better antitumorigenic properties, as evaluated using an induced two-stage mouse skin papilloma model. In contrast, the nonnative state showed only a fraction of the proteolytic activity of the native form. This study demonstrates that hexafluoroisopropanol can induce a conformational change in stem bromelain to a form with potentially useful therapeutic properties different from those of the native protein. Copyright 2010 Elsevier Ltd. All rights reserved.

Topological Ordering and Viscosity in the Glassy Ge-Se System: The Search for a Structural or Dynamical Signature of the Intermediate Phase

NASA Astrophysics Data System (ADS)

Zeidler, Anita; Salmon, Philip S.; Whittaker, Dean A. J.; Pizzey, Keiron J.; Hannon, Alex C.

2017-11-01

The topological ordering of the network structure in vitreous Ge_xSe_{1-x} was investigated across most of the glass-forming region (0 ≤ x ≤ 0.4) by using high-resolution neutron diffraction to measure the Bhatia-Thornton number-number partial structure factor. This approach gives access to the composition dependence of the mean coordination number \\bar{n} and correlation lengths associated with the network ordering. The thermal properties of the samples were also measured by using temperature-modulated differential scanning calorimetry. The results do not point to a structural origin of the so-called intermediate phase, which in our work is indicated for the composition range 0.175(8) ≤ x ≤ 0.235(8) by a vanishingly-small non-reversing enthalpy near the glass transition. The midpoint of this range coincides with the mean-field expectation of a floppy-to-rigid transition at x = 0.20. The composition dependence of the liquid viscosity, as taken from the literature, was also investigated to look for a dynamical origin of the intermediate phase, using the Mauro-Yue-Ellison-Gupta-Allan (MYEGA) model to estimate the viscosity at the liquidus temperature. The evidence points to a maximum in the viscosity at the liquidus temperature, and a minimum in the fragility index, for the range 0.20 ≤ x ≤ 0.22. The utility of the intermediate phase as a predictor of the material properties in network glass-forming systems is discussed.

Probabilistic generation of random networks taking into account information on motifs occurrence.

PubMed

Bois, Frederic Y; Gayraud, Ghislaine

2015-01-01

Because of the huge number of graphs possible even with a small number of nodes, inference on network structure is known to be a challenging problem. Generating large random directed graphs with prescribed probabilities of occurrences of some meaningful patterns (motifs) is also difficult. We show how to generate such random graphs according to a formal probabilistic representation, using fast Markov chain Monte Carlo methods to sample them. As an illustration, we generate realistic graphs with several hundred nodes mimicking a gene transcription interaction network in Escherichia coli.

Probabilistic Generation of Random Networks Taking into Account Information on Motifs Occurrence

PubMed Central

Bois, Frederic Y.

2015-01-01

Abstract Because of the huge number of graphs possible even with a small number of nodes, inference on network structure is known to be a challenging problem. Generating large random directed graphs with prescribed probabilities of occurrences of some meaningful patterns (motifs) is also difficult. We show how to generate such random graphs according to a formal probabilistic representation, using fast Markov chain Monte Carlo methods to sample them. As an illustration, we generate realistic graphs with several hundred nodes mimicking a gene transcription interaction network in Escherichia coli. PMID:25493547

Damage Evaluation for Ti Alloys in Creep based on Incompatibility Field Measurement via EBSD Technique and Micro-Pillar Experiments Toward Identification of Roles of Dislocation Substructures on Fatigue Crack Initiation

DTIC Science & Technology

2011-02-07

Reproduction of a slip band with a PSB -ladder-like internal structure is attempted assuming initial conditions with and without corresponding strain...into heat at the PSB region, the present study extensively examined possible transition mechanisms toward the growth of grooves thereabout and that...arrangements even with the same dislocation density. (2)A slip band-like region having a substructure mimicking PSB ladder is demonstrated to be

Learning to generate combinatorial action sequences utilizing the initial sensitivity of deterministic dynamical systems.

PubMed

Nishimoto, Ryu; Tani, Jun

2004-09-01

This study shows how sensory-action sequences of imitating finite state machines (FSMs) can be learned by utilizing the deterministic dynamics of recurrent neural networks (RNNs). Our experiments indicated that each possible combinatorial sequence can be recalled by specifying its respective initial state value and also that fractal structures appear in this initial state mapping after the learning converges. We also observed that the sequences of mimicking FSMs are encoded utilizing the transient regions rather than the invariant sets of the evolved dynamical systems of the RNNs.

Study of local currents in low dimension materials using complex injecting potentials

NASA Astrophysics Data System (ADS)

He, Shenglai; Covington, Cody; Varga, Kálmán

2018-04-01

A complex potential is constructed to inject electrons into the conduction band, mimicking electron currents in nanoscale systems. The injected electrons are time propagated until a steady state is reached. The local current density can then be calculated to show the path of the conducting electrons on an atomistic level. The method allows for the calculation of the current density vectors within the medium as a function of energy of the conducting electron. Using this method, we investigate the electron pathway of graphene nanoribbons in various structures, molecular junctions, and black phosphorus nanoribbons. By analyzing the current flow through the structures, we find strong dependence on the structural geometry and the energy of the injected electrons. This method may be of general use in the study of nano-electronic materials and interfaces.

Highly deformable bones: unusual deformation mechanisms of seahorse armor.

PubMed

Porter, Michael M; Novitskaya, Ekaterina; Castro-Ceseña, Ana Bertha; Meyers, Marc A; McKittrick, Joanna

2013-06-01

Multifunctional materials and devices found in nature serve as inspiration for advanced synthetic materials, structures and robotics. Here, we elucidate the architecture and unusual deformation mechanisms of seahorse tails that provide prehension as well as protection against predators. The seahorse tail is composed of subdermal bony plates arranged in articulating ring-like segments that overlap for controlled ventral bending and twisting. The bony plates are highly deformable materials designed to slide past one another and buckle when compressed. This complex plate and segment motion, along with the unique hardness distribution and structural hierarchy of each plate, provide seahorses with joint flexibility while shielding them against impact and crushing. Mimicking seahorse armor may lead to novel bio-inspired technologies, such as flexible armor, fracture-resistant structures or prehensile robotics. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Electrospun nanofibres to mimic natural hierarchical structure of tissues: application in musculoskeletal regeneration.

PubMed

Sankar, Sharanya; Sharma, Chandra S; Rath, Subha N; Ramakrishna, Seeram

2018-01-01

Biomimetic scaffolds mimicking the natural hierarchical structure of tissues have recently attracted the interest of researchers and provide a promising strategy to resemble the nonhomogeneous property of tissues. This review provides an overview of the various hierarchical length scales in the native tissues of the musculoskeletal system. It further focuses on electrospinning as a technique to mimic the tissue structures with specific emphasis on bone. The effect of cellular alignment, infiltration, vascularisation, and differentiation in these nanostructures has also been discussed. An outline of the various additive manufacturing techniques in combination with electrospinning has been elaborated. The review concludes with the challenges and future directions to understand the intricacies of bottom-up approach to engineer the systems at a macroscale. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Intermediate stage of sleep and acute cerveau isolé preparation in the rat.

PubMed

User, P; Gioanni, H; Gottesmann, C

1980-01-01

The acute cerveau isole rat shows spindle bursts of large amplitude alternating with low voltage activity in the frontal cortex and continuous theta rhythm in the dorsal hippocampus. These patterns closely resemble an "intermediate" stage of sleep-waking cycle, when the forebrain structures seem to be functionally disconnected from the brainstem.

French Basic Course. Volume 8, Lessons 76-85.

ERIC Educational Resources Information Center

Defense Language Inst., Monterey, CA.

Volume 8 of the Basic Course in French contains 10 lessons, one for each day of the sixteenth and seventeenth weeks of the intermediate phase. Every fifth lesson is a review. The objective of the intermediate phase is to enable the student to distinguish and use the most essential structures of French. The approach is audio-lingual and…

Whereas Short-Term Facilitation Is Presynaptic, Intermediate-Term Facilitation Involves Both Presynaptic and Postsynaptic Protein Kinases and Protein Synthesis

ERIC Educational Resources Information Center

Jin, Iksung; Kandel, Eric R.; Hawkins, Robert D.

2011-01-01

Whereas short-term plasticity involves covalent modifications that are generally restricted to either presynaptic or postsynaptic structures, long-term plasticity involves the growth of new synapses, which by its nature involves both pre- and postsynaptic alterations. In addition, an intermediate-term stage of plasticity has been identified that…

Synthesis and reversible hydration behavior of the thiosulfate intercalated layered double hydroxide of Zn and Al

DOE Office of Scientific and Technical Information (OSTI.GOV)

Radha, S.; Milius, Wolfgang; Breu, Josef, E-mail: josef.breu@uni-bayreuth.de

2013-08-15

The thiosulfate-intercalated layered double hydroxide of Zn and Al undergoes reversible hydration with a variation in the relative humidity of the ambient. The hydrated and dehydrated phases, which represent the end members of the hydration cycle, both adopt the structure of the 3R{sub 1} polytype. In the intermediate range of relative humidity values (40–60%), the hydrated and dehydrated phases coexist. The end members of the hydration cycle adopt the structure of the same polytype, and vary only in their basal spacings. This points to the possibility that all the intermediate phases have a kinetic origin. - Graphical abstract: Basal spacingmore » evolution of the thiosulfate ion intercalated [Zn–Al] LDH during one complete hydration–dehydration cycle as a function of relative humidity. Display Omitted - Highlights: • Thiosulfate intercalated [Zn–Al] LDHs were synthesized by co-precipitation. • The LDH exhibits reversible hydration with variation in humidity. • Both the end members of the hydration cycle adopt the same polytype structure. • The interstratified intermediates observed are kinetic in origin.« less

Metabolic and functional diversity of saponins, biosynthetic intermediates and semi-synthetic derivatives

PubMed Central

Moses, Tessa; Papadopoulou, Kalliope K.

2014-01-01

Saponins are widely distributed plant natural products with vast structural and functional diversity. They are typically composed of a hydrophobic aglycone, which is extensively decorated with functional groups prior to the addition of hydrophilic sugar moieties, to result in surface-active amphipathic compounds. The saponins are broadly classified as triterpenoids, steroids or steroidal glycoalkaloids, based on the aglycone structure from which they are derived. The saponins and their biosynthetic intermediates display a variety of biological activities of interest to the pharmaceutical, cosmetic and food sectors. Although their relevance in industrial applications has long been recognized, their role in plants is underexplored. Recent research on modulating native pathway flux in saponin biosynthesis has demonstrated the roles of saponins and their biosynthetic intermediates in plant growth and development. Here, we review the literature on the effects of these molecules on plant physiology, which collectively implicate them in plant primary processes. The industrial uses and potential of saponins are discussed with respect to structure and activity, highlighting the undoubted value of these molecules as therapeutics. PMID:25286183

Featured Image: Structures in the Interstellar Medium

NASA Astrophysics Data System (ADS)

Kohler, Susanna

2017-02-01

This beautiful false-color image (which covers 57 degrees2; click for the full view!) reveals structures in the hydrogen gas that makes up the diffuse atomic interstellar medium at intermediate latitudes in our galaxy. The imagewas created by representing three velocity channels with colors red for gas moving at 7.59 km/s, green for 5.12 km/s, and blue for 2.64 km/s and it shows the dramatically turbulent and filamentary structure of this gas. This image is one of many stunning, high-resolution observations that came out of the DRAO HI Intermediate Galactic Latitude Survey, a program that used the Synthesis Telescope at the Dominion Radio Astrophysical Observatory in British Columbia to map faint hydrogen emission at intermediate latitudes in the Milky Way. The findings from the program were recently published in a study led by Kevin Blagrave (Canadian Institute for Theoretical Astrophysics, University of Toronto); to find out more about what they learned, check out the paper below!CitationK. Blagrave et al 2017 ApJ 834 126. doi:10.3847/1538-4357/834/2/126

Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation.

PubMed

Glyde, Robert; Ye, Fuzhou; Darbari, Vidya Chandran; Zhang, Nan; Buck, Martin; Zhang, Xiaodong

2017-07-06

Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DNA is delivered to the RNAP active site. Using a bacterial RNAP containing the alternative σ 54 factor and cryoelectron microscopy, we determined structures of RPc and the activator-bound intermediate complex en route to RPo at 3.8 and 5.8 Å. Our structures show how RNAP-σ 54 interacts with promoter DNA to initiate the DNA distortions required for transcription bubble formation, and how the activator interacts with RPc, leading to significant conformational changes in RNAP and σ 54 that promote RPo formation. We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Observations of an Intermediate Layer During the Coqui II Campaign

NASA Technical Reports Server (NTRS)

Bishop, R. L.; Earle, G. D.; Herrero, F. A.; Bateman, T. T.

2000-01-01

NASA sounding rocket 21.114, launched March 7, 1998, during the Coqui II campaign, provided neutral wind and plasma density measurements of a weak intermediate layer. The layer was centered near 140 km and had an approximate peak plasma density of 2200 cc. The measured winds were typically less than 40 m/s, in agreement with wind shear formation theory and coincident density observations. The data obtained during the flight allow us to explore the plasma density structure and wind field morphology of the intermediate layer. Coupled with simultaneous data from Arecibo Observatory, the upleg and downleg density profiles provide three spatially separated measurements that enable the first detailed investigation of the horizontal extent and variation of an intermediate layer.

Pathophysiology of keratinization

PubMed Central

Deo, Priya Nimish; Deshmukh, Revati

2018-01-01

Cytoskeleton of a cell is made up of microfilaments, microtubules and intermediate filaments. Keratins are diverse proteins. These intermediate filaments maintain the structural integrity of the keratinocytes. The word keratin covers these intermediate filament-forming proteins within the keratinocytes. They are expressed in a specific pattern and according to the stage of cellular differentiation. They always occur in pairs. Mutations in the genes which regulate the expression of keratin proteins are associated with a number of disorders which show defects in both skin and mucosa. In addition, there are a number of disorders which are seen because of abnormal keratinization. These keratins and keratin-associated proteins have become important markers in diagnostic pathology. This review article discusses the classification, structure, functions, the stains used for the demonstration of keratin and associated pathology. The review describes the physiology of keratinization, pathology behind abnormal keratin formation and various keratin disorders. PMID:29731562

One-year follow-up of persons discharged from a locked intermediate care facility.

PubMed

Lamb, H Richard; Weinberger, Linda E

2005-02-01

This study examined outcomes during a one-year follow-up for persons who were discharged from a locked intermediate care facility in an urban area in California. The purpose of this study was to determine the extent to which persons with severe mental illness can be successfully transferred from an intermediate care facility to lower levels of care. A total of 101 persons consecutively discharged were studied by record review and by obtaining information from facility staff members, therapists, case managers, and other community caretakers. During the follow-up period 56 percent of the patients who were discharged from the intermediate care facility were not able to demonstrate even minimal functioning in the community. These persons spent 90 or more days in locked or highly structured institutions that provided 24-hour care (including jail) or had five or more acute hospitalizations. However, 44 percent spent less than 90 days in these institutions and had fewer than five acute hospitalizations. Thirty-three percent were not known to have spent any time in an institution or hospital. The high rate of recidivism shown in this cohort suggests that the current emphasis on transferring patients from more structured, intermediate inpatient services to lower levels of care is not effective for a majority of patients. Furthermore, the poor clinical outcomes found in this cohort did not seem to be offset by any reduction in overall governmental costs because of the high use of acute and intermediate hospitalization and the costs of the criminal justice system.

Robustness of atomistic Gō models in predicting native-like folding intermediates

NASA Astrophysics Data System (ADS)

Estácio, S. G.; Fernandes, C. S.; Krobath, H.; Faísca, P. F. N.; Shakhnovich, E. I.

2012-08-01

Gō models are exceedingly popular tools in computer simulations of protein folding. These models are native-centric, i.e., they are directly constructed from the protein's native structure. Therefore, it is important to understand up to which extent the atomistic details of the native structure dictate the folding behavior exhibited by Gō models. Here we address this challenge by performing exhaustive discrete molecular dynamics simulations of a Gō potential combined with a full atomistic protein representation. In particular, we investigate the robustness of this particular type of Gō models in predicting the existence of intermediate states in protein folding. We focus on the N47G mutational form of the Spc-SH3 folding domain (x-ray structure) and compare its folding pathway with that of alternative native structures produced in silico. Our methodological strategy comprises equilibrium folding simulations, structural clustering, and principal component analysis.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ren, Jingli; Chen, Cun; Wang, Gang

This study explores the temporal scaling behavior induced shear-branching structure in response to variant temperatures and strain rates during plastic deformation of Zr-based bulk metallic glass (BMG). The data analysis based on the compression tests suggests that there are two states of shear-branching structures: the fractal structure with a long-range order at an intermediate temperature of 223 K and a larger strain rate of 2.5 × 10 –2 s –1; the disordered structure dominated at other temperature and strain rate. It can be deduced from the percolation theory that the compressive ductility, ec, can reach the maximum value at themore » intermediate temperature. Furthermore, a dynamical model involving temperature is given for depicting the shear-sliding process, reflecting the plastic deformation has fractal structure at the temperature of 223 K and strain rate of 2.5 × 10 –2 s –1.« less

Folding of the four-helix bundle FF domain from a compact on-pathway intermediate state is governed predominantly by water motion.

PubMed

Sekhar, Ashok; Vallurupalli, Pramodh; Kay, Lewis E

2012-11-20

Friction plays a critical role in protein folding. Frictional forces originating from random solvent and protein fluctuations both retard motion along the folding pathway and activate protein molecules to cross free energy barriers. Studies of friction thus may provide insights into the driving forces underlying protein conformational dynamics. However, the molecular origin of friction in protein folding remains poorly understood because, with the exception of the native conformer, there generally is little detailed structural information on the other states participating in the folding process. Here, we study the folding of the four-helix bundle FF domain that proceeds via a transiently formed, sparsely populated compact on-pathway folding intermediate whose structure was elucidated previously. Because the intermediate is stabilized by both native and nonnative interactions, friction in the folding transition between intermediate and folded states is expected to arise from intrachain reorganization in the protein. However, the viscosity dependencies of rates of folding from or unfolding to the intermediate, as established by relaxation dispersion NMR spectroscopy, clearly indicate that contributions from internal friction are small relative to those from solvent, so solvent frictional forces drive the folding process. Our results emphasize the importance of solvent dynamics in mediating the interconversion between protein configurations, even those that are highly compact, and in equilibrium folding/unfolding fluctuations in general.

Near-field interference for the unidirectional excitation of electromagnetic guided modes.

PubMed

Rodríguez-Fortuño, Francisco J; Marino, Giuseppe; Ginzburg, Pavel; O'Connor, Daniel; Martínez, Alejandro; Wurtz, Gregory A; Zayats, Anatoly V

2013-04-19

Wave interference is a fundamental manifestation of the superposition principle with numerous applications. Although in conventional optics, interference occurs between waves undergoing different phase advances during propagation, we show that the vectorial structure of the near field of an emitter is essential for controlling its radiation as it interferes with itself on interaction with a mediating object. We demonstrate that the near-field interference of a circularly polarized dipole results in the unidirectional excitation of guided electromagnetic modes in the near field, with no preferred far-field radiation direction. By mimicking the dipole with a single illuminated slit in a gold film, we measured unidirectional surface-plasmon excitation in a spatially symmetric structure. The surface wave direction is switchable with the polarization.

Mimicking/extracting structure and functions of natural products: synthetic approaches that address unexplored needs in chemical biology.

PubMed

Hirai, Go

2015-04-01

Natural products are often attractive and challenging targets for synthetic chemists, and many have interesting biological activities. However, synthetic chemists need to be more than simply suppliers of compounds to biologists. Therefore, we have been seeking ways to actively apply organic synthetic methods to chemical biology studies of natural products and their activities. In this personal review, I would like to introduce our work on the development of new biologically active compounds inspired by, or extracted from, the structures of natural products, focusing on enhancement of functional activity and specificity and overcoming various drawbacks of the parent natural products. Copyright © 2014 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure of FGFR3 transmembrane domain dimer: implications for signaling and human pathologies.

PubMed

Bocharov, Eduard V; Lesovoy, Dmitry M; Goncharuk, Sergey A; Goncharuk, Marina V; Hristova, Kalina; Arseniev, Alexander S

2013-11-05

Fibroblast growth factor receptor 3 (FGFR3) transduces biochemical signals via lateral dimerization in the plasma membrane, and plays an important role in human development and disease. Eight different pathogenic mutations, implicated in cancers and growth disorders, have been identified in the FGFR3 transmembrane segment. Here, we describe the dimerization of the FGFR3 transmembrane domain in membrane-mimicking DPC/SDS (9/1) micelles. In the solved NMR structure, the two transmembrane helices pack into a symmetric left-handed dimer, with intermolecular stacking interactions occurring in the dimer central region. Some pathogenic mutations fall within the helix-helix interface, whereas others are located within a putative alternative interface. This implies that although the observed dimer structure is important for FGFR3 signaling, the mechanism of FGFR3-mediated transduction across the membrane is complex. We propose an FGFR3 signaling mechanism that is based on the solved structure, available structures of isolated soluble FGFR domains, and published biochemical and biophysical data. Copyright © 2013 Elsevier Ltd. All rights reserved.

Water Hydrogen-Bonding Network Structure and Dynamics at Phospholipid Multibilayer Surface: Femtosecond Mid-IR Pump-Probe Spectroscopy.

PubMed

Kundu, Achintya; Błasiak, Bartosz; Lim, Joon-Hyung; Kwak, Kyungwon; Cho, Minhaeng

2016-03-03

The water hydrogen-bonding network at a lipid bilayer surface is crucial to understanding membrane structures and its functional activities. With a phospholipid multibilayer mimicking a biological membrane, we study the temperature dependence of water hydrogen-bonding structure, distribution, and dynamics at a lipid multibilayer surface using femtosecond mid-IR pump-probe spectroscopy. We observe two distinguished vibrational lifetime components. The fast component (0.6 ps) is associated with water interacting with a phosphate part, whereas the slow component (1.9 ps) is with bulk-like choline-associated water. With increasing temperature, the vibrational lifetime of phosphate-associated water remains constant though its relative fraction dramatically increases. The OD stretch vibrational lifetime of choline-bound water slows down in a sigmoidal fashion with respect to temperature, indicating a noticeable change of the water environment upon the phase transition. The water structure and dynamics are thus shown to be in quantitative correlation with the structural change of liquid multibilayer upon the gel-to-liquid crystal phase transition.

A case of imported tungiasis in Scotland initially mimicking verrucae vulgaris.

PubMed

Wardhaugh, A D; Norris, J F

1994-10-01

A case is described of Tunga penetrans infection in the feet of a tourist returning from South America to Scotland. The condition had initially mimicked verrucae vulgaris, but microscopic examination of the lesions together with the travel history allowed the diagnosis of tungiasis to be made. This is the first case reported in Scotland.

Thermodynamic stability of Hoogsteen and Watson-Crick base pairs in the presence of histone H3-mimicking peptide.

PubMed

Pramanik, Smritimoy; Nakamura, Kaori; Usui, Kenji; Nakano, Shu-ichi; Saxena, Sarika; Matsui, Jun; Miyoshi, Daisuke; Sugimoto, Naoki

2011-03-14

We found that Hoogsteen base pairs were stabilized by molecular crowding and a histone H3-mimicking peptide, which was not observed for Watson-Crick base pairs. Our findings demonstrate that the type of DNA base pair is critical for the interaction between DNA and histones.

Focal Nodulary Hyperplasia of the Liver Due to Congenital Portosystemic Shunt: A Rare Condition Mimicking Hepatocellulary Carcinoma.

PubMed

Yazal Erdem, Arzu; Emir, Suna; Demir, Haci A; Özyörük, Derya; Çetin, İlker; Turan, Aynur; Karakuş, Esra

2017-01-01

Congenital portosystemic shunts are rare vascular malformations that lead to several complications including liver tumors, pulmonary hypertension, and metabolic encephalopathy. We describe a rare case of a 17-year-old girl with an extrahepatic portosystemic shunt presenting recurrent syncope episodes and a liver mass mimicking hepatocellulary carcinoma.

Traumatic Axillary Artery Dissection with Radial Artery Embolism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chung, Hwan-Hoon; Cha, Sang Hoon, E-mail: shcha123@naver.com; Cho, Sung Bum

This report describes a case of pathologically proven traumatic arterial dissection, presenting as complete occlusion of the axillary artery with radial artery embolism. Occlusion of the axillary artery by traumatic dissection mimicked transection and radial artery embolism mimicked congenital absence of the radial artery on the initial angiogram, but these were correctly diagnosed with the following sonogram.

A multimodal instrument for real-time in situ study of ultrasound and cavitation mediated drug delivery.

PubMed

Bian, Shuning; Seth, Anjali; Daly, Dan; Carlisle, Robert; Stride, Eleanor

2017-03-01

The development of a multimodal instrument capable of real-time in situ measurements of cavitation activity and effect in tissue mimicking phantoms during ultrasound and cavitation mediated drug delivery experiments is described here. The instrument features an acoustic arm that can expose phantoms to high-intensity focused-ultrasound while measuring cavitation activity and an optical arm that monitors cavitation effect using confocal microscopy. This combination of modalities allows real-time in situ characterisation of drug delivery in tissue and tissue mimicking phantoms during ultrasound and cavitation mediated drug delivery experiments. A representative result, obtained with a tissue mimicking phantom and acoustically activated droplets, is presented here as a demonstration of the instrument's capabilities and potential applications.

Structural Characterization of β-Agostic Bonds in Pd-Catalyzed Polymerization

DOE PAGES

Xu, Hongwei; Hu, Chunhua Tony; Wang, Xiaoping; ...

2017-10-23

β-agostic Pd complexes are critical intermediates in catalytic reactions, such as olefin polymerization and Heck reactions. Pd β-agostic complexes, however, have eluded structural characterization, due to the fact that these highly unstable molecules are difficult to isolate. In this paper, we report the single-crystal X-ray and neutron diffraction characterization of β-agostic (α-diimine)Pd–ethyl intermediates in polymerization. Short C α–C β distances and acute Pd–C α–C β bond angles combined serve as unambiguous evidence for the β-agostic interaction. Finally, characterization of the agostic structure and the kinetic barrier for β-H elimination offer important insight into the fundamental understanding of agostic bonds andmore » the mechanism of polymerization.« less

The structure of molten CuCl: Reverse Monte Carlo modeling with high-energy X-ray diffraction data and molecular dynamics of a polarizable ion model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alcaraz, Olga; Trullàs, Joaquim, E-mail: quim.trullas@upc.edu; Tahara, Shuta

2016-09-07

The results of the structural properties of molten copper chloride are reported from high-energy X-ray diffraction measurements, reverse Monte Carlo modeling method, and molecular dynamics simulations using a polarizable ion model. The simulated X-ray structure factor reproduces all trends observed experimentally, in particular the shoulder at around 1 Å{sup −1} related to intermediate range ordering, as well as the partial copper-copper correlations from the reverse Monte Carlo modeling, which cannot be reproduced by using a simple rigid ion model. It is shown that the shoulder comes from intermediate range copper-copper correlations caused by the polarized chlorides.

Structural Characterization of β-Agostic Bonds in Pd-Catalyzed Polymerization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Hongwei; Hu, Chunhua Tony; Wang, Xiaoping

β-agostic Pd complexes are critical intermediates in catalytic reactions, such as olefin polymerization and Heck reactions. Pd β-agostic complexes, however, have eluded structural characterization, due to the fact that these highly unstable molecules are difficult to isolate. In this paper, we report the single-crystal X-ray and neutron diffraction characterization of β-agostic (α-diimine)Pd–ethyl intermediates in polymerization. Short C α–C β distances and acute Pd–C α–C β bond angles combined serve as unambiguous evidence for the β-agostic interaction. Finally, characterization of the agostic structure and the kinetic barrier for β-H elimination offer important insight into the fundamental understanding of agostic bonds andmore » the mechanism of polymerization.« less

Intermediate orthorhombic phases in Ba-122 Iron Arsenides

NASA Astrophysics Data System (ADS)

Ruff, J. P. C.; Islam, Z.; Das, R. K.; Kuo, H.-H.; Fisher, I. R.

2013-03-01

Despite widespread interest, there are details of the tetragonal-orthorhombic structural phase transition in the iron arsenide superconductors that remain controversial. We have revisited the transition in three characteristic compositions of the canonical ``122'' family Ba(Fe/Co)2(As/P)2 using single crystal synchrotron x-ray diffraction. In the parent compound, we confirm previous observations of a sequence of structural transitions which are closely spaced in temperature, and uncover pronounced magnetoelastic effects in the intermediate orthorhombic phase. Modification of the structural transitions by doping is observed to differ significantly depending on whether the dopant is Co or P. Work performed at the Advanced Photon Source was supported by the DOE, under Contract No. DE-AC02-06CH11357.

Intermediate type excitons in Schottky barriers of A3B6 layer semiconductors and UV photodetectors

NASA Astrophysics Data System (ADS)

Alekperov, O. Z.; Guseinov, N. M.; Nadjafov, A. I.

2006-09-01

Photoelectric and photovoltaic spectra of Schottky barrier (SB) structures of InSe, GaSe and GaS layered semiconductors (LS) are investigated at quantum energies from the band edge excitons of corresponding materials up to 6.5eV. Spectral dependences of photoconductivity (PC) of photo resistors and barrier structures are strongly different at the quantum energies corresponding to the intermediate type excitons (ITE) observed in these semiconductors. It was suggested that high UV photoconductivity of A3B6 LS is due to existence of high mobility light carriers in the depth of the band structure. It is shown that SB of semitransparent Au-InSe is high sensitive photo detector in UV region of spectra.

UV absorption spectrum and photodissociation channels of the simplest Criegee intermediate (CH2OO).

PubMed

Dawes, Richard; Jiang, Bin; Guo, Hua

2015-01-14

The lowest-lying singlet states of the simplest Criegee intermediate (CH2OO) have been characterized along the O-O dissociation coordinate using explicitly correlated MRCI-F12 electronic structure theory and large active spaces. It is found that a high-level treatment of dynamic electron-correlation is essential to accurately describe these states. A significant well on the B-state is identified at the MRCI-F12 level with an equilibrium structure that differs substantially from that of the ground X-state. This well is presumably responsible for the apparent vibrational structure in some experimental UV absorption spectra, analogous to the structured Huggins band of the iso-electronic ozone. The B-state potential in the Franck-Condon region is sufficiently accurate that an absorption spectrum calculated with a one-dimensional model agrees remarkably well with experiment.

Structure of a fungal form of aspartate semialdehyde dehydrogenase from Cryptococcus neoformans

PubMed Central

Dahal, Gopal; Viola, Ronald E.

2015-01-01

Aspartate semialdehyde dehydrogenase (ASADH) functions at a critical junction in the aspartate-biosynthetic pathway and represents a valid target for antimicrobial drug design. This enzyme catalyzes the NADPH-dependent reductive dephosphorylation of β-aspartyl phosphate to produce the key intermediate aspartate semialdehyde. Production of this intermediate represents the first committed step in the biosynthesis of the essential amino acids methionine, isoleucine and threonine in fungi, and also the amino acid lysine in bacteria. The structure of a new fungal form of ASADH from Cryptococcus neoformans has been determined to 2.6 Å resolution. The overall structure of CnASADH is similar to those of its bacterial orthologs, but with some critical differences both in biological assembly and in secondary-structural features that can potentially be exploited for the development of species-selective drugs. PMID:26527262

Structural Changes Correlated with Magnetic Spin State Isomorphism in the S2 State of the Mn4CaO5 Cluster in the Oxygen-Evolving Complex of Photosystem II

PubMed Central

Chatterjee, Ruchira; Han, Guangye; Kern, Jan; Gul, Sheraz; Fuller, Franklin D.; Garachtchenko, Anna; Young, Iris; Weng, Tsu-Chien; Nordlund, Dennis; Alonso-Mori, Roberto; Bergmann, Uwe; Sokaras, Dimosthenis; Hatakeyama, Makoto; Yachandra, Vittal K.; Yano, Junko

2016-01-01

The Mn4CaO5 cluster in Photosystem II catalyzes the four-electron redox reaction of water oxidation in natural photosynthesis. This catalytic reaction cycles through four intermediate states (Si, i = 0 to 4), involving changes in the redox state of the four Mn atoms in the cluster. Recent studies suggest the presence and importance of isomorphous structures within the same redox/intermediate S-state. It is highly likely that geometric and electronic structural flexibility play a role in the catalytic mechanism. Among the catalytic intermediates that have been identified experimentally thus far, there is clear evidence of such isomorphism in the S2 state, with a high-spin (5/2) (HS) and a low spin (1/2) (LS) form, identified and characterized by their distinct electron paramagnetic resonance (EPR spectroscopy) signals. We studied these two S2 isomers with Mn extended X-ray absorption fine structure (EXAFS) and absorption and emission spectroscopy (XANES/XES) to characterize the structural and electronic structural properties. The geometric and electronic structure of the HS and LS S2 states are different as determined using Mn EXAFS and XANES/XES, respectively. The Mn K-edge XANES and XES for the HS form are different from the LS and indicate a slightly lower positive charge on the Mn atoms compared to the LS form. Based on the EXAFS results which are clearly different, we propose possible structural differences between the two spin states. Such structural and magnetic redox-isomers if present at room temperature, will likely play a role in the mechanism for water-exchange/oxidation in photosynthesis. PMID:28044099

Structural changes correlated with magnetic spin state isomorphism in the S 2 state of the Mn 4CaO 5 cluster in the oxygen-evolving complex of photosystem II

DOE PAGES

Chatterjee, Ruchira; Han, Guangye; Kern, Jan; ...

2016-05-09

The Mn 4CaO 5 cluster in photosystem II catalyzes the four-electron redox reaction of water oxidation in natural photosynthesis. This catalytic reaction cycles through four intermediate states (S i, i = 0 to 4), involving changes in the redox state of the four Mn atoms in the cluster. Recent studies suggest the presence and importance of isomorphous structures within the same redox/intermediate S-state. It is highly likely that geometric and electronic structural flexibility play a role in the catalytic mechanism. Among the catalytic intermediates that have been identified experimentally thus far, there is clear evidence of such isomorphism in themore » S2 state, with a high-spin (5/2) (HS) and a low spin (1/2) (LS) form, identified and characterized by their distinct electron paramagnetic resonance (EPR spectroscopy) signals. We studied these two S2 isomers with Mn extended X-ray absorption fine structure (EXAFS) and absorption and emission spectroscopy (XANES/XES) to characterize the structural and electronic structural properties. The geometric and electronic structure of the HS and LS S2 states are different as determined using Mn EXAFS and XANES/XES, respectively. The Mn K-edge XANES and XES for the HS form are different from the LS and indicate a slightly lower positive charge on the Mn atoms compared to the LS form. Based on the EXAFS results which are clearly different, we propose possible structural differences between the two spin states. As a result, such structural and magnetic redox-isomers if present at room temperature, will likely play a role in the mechanism for water-exchange/oxidation in photosynthesis.« less

A Curriculum Guide for Primary and Intermediate Special Education in the Opelika City Schools. Revised Edition.

ERIC Educational Resources Information Center

Opelika City Schools, AL.

Presented is a curriculum guide for primary and intermediate special education in the areas of communication skills, arithmetic, science, and physical education. The guide, prepared by the Opelika (Alabama) schools, is said to be based on assumptions such as the values of structured individualized learning, use of materials which do not require…

Simultaneous modelling of X-ray emission and optical polarization of intermediate polars: the case of V405 Aur

NASA Astrophysics Data System (ADS)

J. Lima, I.; Vilega Rodrigues, C.; Medeiros Gomes Silva, K.; Luna, G.; D Amico, F.; Goulart Coelho, J.

2017-10-01

Intermediate polars are compact binaries in which mass transfer occurs from a low-mass star onto a magnetic white dwarf. A shock structure is formed in the magnetic accretion column nearby the white-dwarf surface. High-energy emission is produced in the post-shock region and the main physical process envolved is bremsstrahlung and line emission. Some systems show optical polarization, which may be also originated in the post-shock region. Our main goal is to study the magnetic structure of intermediate polars by simultaneously modelling optical polarimetry and X-ray data using the CYCLOPS code. This code was developed by our group to peform multi-wavelength fitting of the accretion column flux. It considers cyclotron and free-free emission from a 3D post-shock region, which is non-homogeneous in terms of density, temperature, and magnetic field. In this study, we present our modelling of the optical polarization and X-ray emission of V405 Aurigae, the intermediate polar that has the highest magnetic field. Previous studies of this system were not successful in proposing a geometry that explains both the optical and X-ray emissions.

Microwave-assisted rapid photocatalytic degradation of malachite green in TiO2 suspensions: mechanism and pathways.

PubMed

Ju, Yongming; Yang, Shaogui; Ding, Youchao; Sun, Cheng; Zhang, Aiqian; Wang, Lianhong

2008-11-06

Microwave-assisted photocatalytic (MPC) degradation of malachite green (MG) in aqueous TiO2 suspensions was investigated. A 20 mg/L sample of MG was rapidly and completely decomposed in 3 min with the corresponding TOC removal efficiency of about 85%. To gain insight into the degradation mechanism, both GC-MS and LC-ESI-MS/MS techniques were employed to identify the major intermediates of MG degradation, including N-demethylation intermediates [(p-dimethylaminophenyl)(p-methylaminophenyl)phenylmethylium (DM-PM), (p-methylaminophenyl)(p-methylaminophenyl)phenylmethylium (MM-PM), (p-methylaminophenyl)(p-aminophenyl)phenylmethylium (M-PM)]; a decomposition compound of the conjugated structure (4-dimethylaminobenzophenone (DLBP)); products resulting from the adduct reaction of hydroxyl radical; products of benzene removal; and other open-ring intermediates such as phenol, terephthalic acid, adipic acid, benzoic acid, etc. The possible degradation mechanism of MG included five processes: the N-demethylation process, adduct products of the hydroxyl radical, the breakdown of chromophores such as destruction of the conjugated structure intermediate, removal of benzene, and an open-ring reaction. To the best of our knowledge, it is the first time the whole MG photodegradation processes have been reported.

Evaluation of the Molecular Structural Parameters of Normal Rice Starch and Their Relationships with Its Thermal and Digestion Properties.

PubMed

Lin, Lingshang; Zhang, Qing; Zhang, Long; Wei, Cunxu

2017-09-12

The molecular structural parameters of six normal rice starches with different amylose contents were investigated through their iodine absorption spectra and gel permeation chromatography of fully branched and debranched starches. The thermal and digestion properties of starches were also determined and their relationships with molecular structural parameters were analyzed. Results showed that the molecular structural parameters of maximum absorption wavelength, blue value (BV), optical density 620 nm/550 nm (OD 620/550), amylose, intermediate component, and amylopectin, including its short branch-chains, long branch-chains, and branching degree, had high correlation in different determining methods. The intermediate component of starch was significantly positively related to amylose and negatively related to amylopectin, and the amylopectin branching degree was significantly positively related to amylopectin content and negatively related to amylose content. The gelatinization temperatures and enthalpy of native starch were significantly positively related to BV, OD 620/550, and amylose content and negatively related to amylopectin short branch-chains. The gelatinization temperatures and enthalpy of retrograded starch were significantly negatively related to amylopectin branching degree. The digestions of gelatinized and retrograded starches were significantly negatively related to the BV, OD 620/550, amylose, and intermediate component and positively related to amylopectin and its short branch-chains and branching degree.

Photovoltaic efficiency of intermediate band solar cells based on CdTe/CdMnTe coupled quantum dots

NASA Astrophysics Data System (ADS)

Prado, Silvio J.; Marques, Gilmar E.; Alcalde, Augusto M.

2017-11-01

In this work we show the calculation of optimized efficiencies of intermediate band solar cells (IBSCs) based on Mn-doped II-VI CdTe/CdMnTe coupled quantum dot (QD) structures. We focus our attention on the combined effects of geometrical and Mn-doping parameters on optical properties and solar cell efficiency. In the framework of {k \\cdot p} theory, we accomplish detailed calculations of electronic structure, transition energies, optical selection rules and their corresponding intra- and interband oscillator strengths. With these results and by following the intermediate band model, we have developed a strategy which allows us to find optimal photovoltaic efficiency values. We also show that the effects of band admixture which can lead to degradation of optical transitions and reduction of efficiency can be partly minimized by a careful selection of the structural parameters and Mn-concentration. Thus, the improvement of band engineering is mandatory for any practical implementation of QD systems as IBSC hardware. Finally, our calculations show that it is possible to reach significant efficiency, up to  ∼26%, by selecting a restricted space of parameters such as quantum dot size and shape and Mn-concentration effects, to improve the modulation of optical absorption in the structures.

Photovoltaic efficiency of intermediate band solar cells based on CdTe/CdMnTe coupled quantum dots.

PubMed

Prado, Silvio J; Marques, Gilmar E; Alcalde, Augusto M

2017-11-08

In this work we show the calculation of optimized efficiencies of intermediate band solar cells (IBSCs) based on Mn-doped II-VI CdTe/CdMnTe coupled quantum dot (QD) structures. We focus our attention on the combined effects of geometrical and Mn-doping parameters on optical properties and solar cell efficiency. In the framework of [Formula: see text] theory, we accomplish detailed calculations of electronic structure, transition energies, optical selection rules and their corresponding intra- and interband oscillator strengths. With these results and by following the intermediate band model, we have developed a strategy which allows us to find optimal photovoltaic efficiency values. We also show that the effects of band admixture which can lead to degradation of optical transitions and reduction of efficiency can be partly minimized by a careful selection of the structural parameters and Mn-concentration. Thus, the improvement of band engineering is mandatory for any practical implementation of QD systems as IBSC hardware. Finally, our calculations show that it is possible to reach significant efficiency, up to  ∼26%, by selecting a restricted space of parameters such as quantum dot size and shape and Mn-concentration effects, to improve the modulation of optical absorption in the structures.

Structure of GroEL in Complex with an Early Folding Intermediate of Alanine Glyoxylate Aminotransferase*

PubMed Central

Albert, Armando; Yunta, Cristina; Arranz, Rocío; Peña, Álvaro; Salido, Eduardo; Valpuesta, José María; Martín-Benito, Jaime

2010-01-01

Primary hyperoxaluria type 1 is a rare autosomal recessive disease caused by mutations in the alanine glyoxylate aminotransferase gene (AGXT). We have previously shown that P11L and I340M polymorphisms together with I244T mutation (AGXT-LTM) represent a conformational disease that could be amenable to pharmacological intervention. Thus, the study of the folding mechanism of AGXT is crucial to understand the molecular basis of the disease. Here, we provide biochemical and structural data showing that AGXT-LTM is able to form non-native folding intermediates. The three-dimensional structure of a complex between the bacterial chaperonin GroEL and a folding intermediate of AGXT-LTM mutant has been solved by cryoelectron microscopy. The electron density map shows the protein substrate in a non-native extended conformation that crosses the GroEL central cavity. Addition of ATP to the complex induces conformational changes on the chaperonin and the internalization of the protein substrate into the folding cavity. The structure provides a three-dimensional picture of an in vivo early ATP-dependent step of the folding reaction cycle of the chaperonin and supports a GroEL functional model in which the chaperonin promotes folding of the AGXT-LTM mutant protein through forced unfolding mechanism. PMID:20056599

Structure of GroEL in complex with an early folding intermediate of alanine glyoxylate aminotransferase.

PubMed

Albert, Armando; Yunta, Cristina; Arranz, Rocío; Peña, Alvaro; Salido, Eduardo; Valpuesta, José María; Martín-Benito, Jaime

2010-02-26

Primary hyperoxaluria type 1 is a rare autosomal recessive disease caused by mutations in the alanine glyoxylate aminotransferase gene (AGXT). We have previously shown that P11L and I340M polymorphisms together with I244T mutation (AGXT-LTM) represent a conformational disease that could be amenable to pharmacological intervention. Thus, the study of the folding mechanism of AGXT is crucial to understand the molecular basis of the disease. Here, we provide biochemical and structural data showing that AGXT-LTM is able to form non-native folding intermediates. The three-dimensional structure of a complex between the bacterial chaperonin GroEL and a folding intermediate of AGXT-LTM mutant has been solved by cryoelectron microscopy. The electron density map shows the protein substrate in a non-native extended conformation that crosses the GroEL central cavity. Addition of ATP to the complex induces conformational changes on the chaperonin and the internalization of the protein substrate into the folding cavity. The structure provides a three-dimensional picture of an in vivo early ATP-dependent step of the folding reaction cycle of the chaperonin and supports a GroEL functional model in which the chaperonin promotes folding of the AGXT-LTM mutant protein through forced unfolding mechanism.

Structure-guided Mutational Analysis of the Nucleotidyltransferase Domain of Escherichia coli DNA Ligase (LigA).

PubMed

Wang, Li Kai; Zhu, Hui; Shuman, Stewart

2009-03-27

NAD(+)-dependent DNA ligases (LigA) are ubiquitous in bacteria, where they are essential for growth and present attractive targets for antimicrobial drug discovery. LigA has a distinctive modular structure in which a nucleotidyltransferase catalytic domain is flanked by an upstream NMN-binding module and by downstream OB-fold, zinc finger, helix-hairpin-helix, and BRCT domains. Here we conducted a structure-function analysis of the nucleotidyltransferase domain of Escherichia coli LigA, guided by the crystal structure of the LigA-DNA-adenylate intermediate. We tested the effects of 29 alanine and conservative mutations at 15 amino acids on ligase activity in vitro and in vivo. We thereby identified essential functional groups that coordinate the reactive phosphates (Arg(136)), contact the AMP adenine (Lys(290)), engage the phosphodiester backbone flanking the nick (Arg(218), Arg(308), Arg(97) plus Arg(101)), or stabilize the active domain fold (Arg(171)). Finer analysis of the mutational effects revealed step-specific functions for Arg(136), which is essential for the reaction of LigA with NAD(+) to form the covalent ligase-AMP intermediate (step 1) and for the transfer of AMP to the nick 5'-PO(4) to form the DNA-adenylate intermediate (step 2) but is dispensable for phosphodiester formation at a preadenylylated nick (step 3).

The crystal structure of xanthine oxidoreductase during catalysis: Implications for reaction mechanism and enzyme inhibition

PubMed Central

Okamoto, Ken; Matsumoto, Koji; Hille, Russ; Eger, Bryan T.; Pai, Emil F.; Nishino, Takeshi

2004-01-01

Molybdenum is widely distributed in biology and is usually found as a mononuclear metal center in the active sites of many enzymes catalyzing oxygen atom transfer. The molybdenum hydroxylases are distinct from other biological systems catalyzing hydroxylation reactions in that the oxygen atom incorporated into the product is derived from water rather than molecular oxygen. Here, we present the crystal structure of the key intermediate in the hydroxylation reaction of xanthine oxidoreductase with a slow substrate, in which the carbon–oxygen bond of the product is formed, yet the product remains complexed to the molybdenum. This intermediate displays a stable broad charge–transfer band at ≈640 nm. The crystal structure of the complex indicates that the catalytically labile Mo—OH oxygen has formed a bond with a carbon atom of the substrate. In addition, the Mo⋕S group of the oxidized enzyme has become protonated to afford Mo—SH on reduction of the molybdenum center. In contrast to previous assignments, we find this last ligand at an equatorial position in the square-pyramidal metal coordination sphere, not the apical position. A water molecule usually seen in the active site of the enzyme is absent in the present structure, which probably accounts for the stability of this intermediate toward ligand displacement by hydroxide. PMID:15148401

Manipulating the structure and mechanical properties of thermoplastic polyurethane/polycaprolactone hybrid small diameter vascular scaffolds fabricated via electrospinning using an assembled rotating collector.

PubMed

Mi, Hao-Yang; Jing, Xin; Yu, Emily; Wang, Xiaofeng; Li, Qian; Turng, Lih-Sheng

2018-02-01

The success of blood vessel transplants with vascular scaffolds (VSs) highly depends on their structure and mechanical properties. The fabrication of small diameter vascular scaffolds (SDVSs) mimicking the properties of native blood vessels has been a challenge. Herein, we propose a facile method to fabricate thermoplastic polyurethane (TPU)/polycaprolactone (PCL) hybrid SDVSs via electrospinning using a modified rotating collector. By varying the ratio between the TPU and the PCL, and changing the electrospinning volume, SDVSs with a wavy configuration and different properties could be obtained. Detailed investigation revealed that certain TPU/PCL hybrid SDVSs closely resembled the mechanical behaviors of blood vessels due to the presence of a wavy region and the combination of flexible TPU and rigid PCL, which mimicked the properties of elastin and collagen in blood vessels. The fabricated TPU/PCL SDVSs achieved lumen diameters of 1-3mm, wall thicknesses of 100-570µm, circumferential moduli of 1-6MPa, ultimate strengths of 2-8MPa, over 250% elongation-at-break values, toe regions of 5.3-9.4%, high recoverability, and compliances close to those of human veins. Moreover, these TPU/PCL SDVSs possessed sufficient suture retention strength and burst pressure to fulfill transplantation requirements and maintain normal blood flow. Human endothelial cell culture revealed good biocompatibility of the scaffolds, and cells were able to grow on the inner surface of the tubular scaffolds, indicating promising prospects for use as tissue-engineered vascular grafts. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evidence of proteolipid domain formation in an inner mitochondrial membrane mimicking model.

PubMed

Cheniour, Mouhedine; Brewer, Jonathan; Bagatolli, Luis; Marcillat, Olivier; Granjon, Thierry

2017-05-01

Mitochondrial creatine kinase (mtCK) is highly abundant in mitochondria; its quantity is equimolecular to the Adenylic Nucleotide Translocator and represents 1% of the mitochondrial proteins. It is a multitask protein localized in the mitochondria intermembrane space where it binds to the specific cardiolipin (CL) phospholipid. If mtCK was initially thought to be exclusively implicated in energy transfer between mitochondria and cytosol through a mechanism referred to as the phosphocreatine shuttle, several recent studies suggested an additional role in maintaining mitochondria membrane structure. To further characterized mtCK binding process we used multiphoton excitation fluorescence microscopy coupled with Giant Unilamellar Vesicles (GUV) and laurdan as fluorescence probe. We gathered structural and dynamical information on the molecular events occurring during the binding of mtCK to the mitochondria inner membrane. We present the first visualization of mtCK-induced CL segregation on a bilayer model forming micrometer-size proteolipid domains at the surface of the GUV. Those microdomains, which only occurred when CL is included in the lipid mixture, were accompanied by the formation of protein multimolecular assembly, vesicle clamping, and changes in both vesicle curvature and membrane fluidity CONCLUSION: Those results highlighted the importance of the highly abundant mtCK in the lateral organization of the mitochondrial inner membrane. Microdomains were induced in mitochondria-mimicking membranes composed of natural phospholipids without cholesterol and/or sphingolipids differing from the proposed cytoplasmic membrane rafts. Those findings as well as membrane curvature modification were discussed in relation with protein-membrane interaction and protein cluster involvement in membrane morphology. Copyright © 2017 Elsevier B.V. All rights reserved.

Catecholaminergic contributions to vocal communication signals.

PubMed

Matheson, Laura E; Sakata, Jon T

2015-05-01

Social context affects behavioral displays across a variety of species. For example, social context acutely influences the acoustic and temporal structure of vocal communication signals such as speech and birdsong. Despite the prevalence and importance of such social influences, little is known about the neural mechanisms underlying the social modulation of communication. Catecholamines are implicated in the regulation of social behavior and motor control, but the degree to which catecholamines influence vocal communication signals remains largely unknown. Using a songbird, the Bengalese finch, we examined the extent to which the social context in which song is produced affected immediate early gene expression (EGR-1) in catecholamine-synthesising neurons in the midbrain. Further, we assessed the degree to which administration of amphetamine, which increases catecholamine concentrations in the brain, mimicked the effect of social context on vocal signals. We found that significantly more catecholaminergic neurons in the ventral tegmental area and substantia nigra (but not the central grey, locus coeruleus or subcoeruleus) expressed EGR-1 in birds that were exposed to females and produced courtship song than in birds that produced non-courtship song in isolation. Furthermore, we found that amphetamine administration mimicked the effects of social context and caused many aspects of non-courtship song to resemble courtship song. Specifically, amphetamine increased the stereotypy of syllable structure and sequencing, the repetition of vocal elements and the degree of sequence completions. Taken together, these data highlight the conserved role of catecholamines in vocal communication across species, including songbirds and humans. © 2015 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

InxAl1-xN chiral nanorods mimicking the polarization features of scarab beetles

NASA Astrophysics Data System (ADS)

Magnusson, R.; Birch, J.; Hsiao, C.-L.; Sandström, P.; Arwin, H.; Järrendahl, K.

2015-03-01

The scarab beetle Cetonia aurata is known to reflect light with brilliant colors and a high degree of circular polarization. Both color and polarization effects originate from the beetles exoskeleton and have been attributed to a Bragg reflection of the incident light due to a twisted laminar structure. Our strategy for mimicking the optical properties of the Cetonia aurata was therefore to design and fabricate transparent, chiral films. A series of films with tailored transparent structures of helicoidal InxAl1-xN nanorods were grown on sapphire substrates using UHV magnetron sputtering. The value of x is tailored to gradually decrease from one side to the other in each nanorod normal to its growth direction. This introduces an in-plane anisotropy with different refractive indices in the direction of the gradient and perpendicular to it. By rotating the sample during film growth the in-plane optical axis will be rotated from bottom to top and thereby creating a chiral film. Based on Muellermatrix ellipsometry, optical modeling has been done suggesting that both the exoskeleton of Cetonia aurata and our artificial material can be modeled by an anisotropic film made up of a stack of thin layers, each one with its in-plane optical axis slightly rotated with respect to the previous layer. Simulations based on the optical modeling were used to investigate how pitch and thickness of the film together with the optical properties of the constitutive materials affects the width and spectral position of the Bragg reflection band.

Biomimetic photo-actuation: progress and challenges

NASA Astrophysics Data System (ADS)

Dicker, Michael P. M.; Weaver, Paul M.; Rossiter, Jonathan M.; Bond, Ian P.; Faul, Charl F. J.

2016-04-01

Photo-actuation, such as that observed in the reversible sun-tracking movements of heliotropic plants, is produced by a complex, yet elegant series of processes. In the heliotropic leaf movements of the Cornish Mallow, photo-actuation involves the generation, transport and manipulation of chemical signals from a distributed network of sensors in the leaf veins to a specialized osmosis driven actuation region in the leaf stem. It is theorized that such an arrangement is both efficient in terms of materials use and operational energy conversion, as well as being highly robust. We concern ourselves with understanding and mimicking these light driven, chemically controlled actuating systems with the aim of generating intelligent structures which share the properties of efficiency and robustness that are so important to survival in Nature. In this work we present recent progress in mimicking these photo-actuating systems through remote light exposure of a metastable state photoacid and the resulting signal and energy transfer through solution to a pH-responsive hydrogel actuator. Reversible actuation strains of 20% were achieved from this arrangement, with modelling then employed to reveal the critical influence hydrogel pKa has on this result. Although the strong actuation achieved highlights the progress that has been made in replicating the principles of biomimetic photo-actuation, challenges such as photoacid degradation were also revealed. It is anticipated that current work can directly lead to the development of high-performance and low-cost solartrackers for increased photovoltaic energy capture and to the creation of new types of intelligent structures employing chemical control systems.

Cardioprotection by a nonerythropoietic, tissue-protective peptide mimicking the 3D structure of erythropoietin

PubMed Central

Ueba, Hiroto; Brines, Michael; Yamin, Michael; Umemoto, Tomio; Ako, Junya; Momomura, Shin-ichi; Cerami, Anthony; Kawakami, Masanobu

2010-01-01

Erythropoietin (EPO), originally identified for its critical hormonal role in regulating production and survival of erythrocytes, is a member of the type 1 cytokine superfamily. Recent studies have shown that EPO has cytoprotective effects in a wide variety of tissues, including the heart, by preventing apoptosis. However, EPO also has undesirable effects, such as thrombogenesis. In the present study, we investigated whether a helix B-surface peptide (HBSP), a nonerythropoietic, tissue-protective peptide mimicking the 3D structure of erythropoietin, protects cardiomyocytes from apoptosis in vitro and in vivo. In cultured neonatal rat cardiomyocytes, HBSP clearly inhibited apoptosis (≈80%) induced by TNF-α, which was comparable with the effect of EPO, and activated critical signaling pathways of cell survival, including Akt, ERK1/2, and STAT3. Among these pathways, Akt was shown to play an essential role in HBSP-induced prevention of apoptosis, as assessed by using a small interfering RNA approach. In the dilated cardiomyopathic hamster (J2N-k), whose cardiac tissues diffusely expressed TNF-α, HBSP also inhibited apoptosis (≈70%) and activated Akt in cardiomyocytes. Furthermore, the levels of serum creatine kinase activity and of cardiac expression of atrial natriuretic peptide, a marker of chronic heart failure, were down-regulated in animals treated with HBSP. These data demonstrate that HBSP protects cardiomyocytes from apoptosis and leads to a favorable outcome in failing hearts through an Akt-dependent pathway. Because HBSP does not have the undesirable effects of EPO, it could be a promising alternative for EPO to treat cardiovascular diseases, such as myocardial infarction and heart failure. PMID:20660739

Correlation and nuclear distortion effects of Cr-substituted ZnSe.

PubMed

Tablero, C

2007-04-28

There is a great deal of interest in the effect of the correlation and effect of the atomic distortion in materials with a metallic intermediate band. This band, situated within the semiconductor band gaps, would be split, thus creating two bands, a full one below the Fermi energy and an empty one above it, i.e., a metal-insulator transition. This basic electronic band structure corresponds to intermediate band materials and is characteristic of transparent-conducting oxides, up and down converters, and intermediate band solar cells. A sufficiently high density of Cr in ZnSe substituting the Zn atoms leads to a microscopic intermediate band, in which these effects will be analyzed. A Hubbard term has been included to improve the description of the many-body effect. This term modifies the bandwidth of the intermediate band, the Fermi energy, and breaks the orbital-occupation degeneracy. From the results, the intermediate band is not split within the range of Hubbard term values analyzed and for Cr substituting Zn from 0.463% to 3.125% of Cr atomic concentration.

Tiopronin Gold Nanoparticle Precursor Forms Aurophilic Ring Tetramer

PubMed Central

Simpson, Carrie A.; Farrow, Christopher L.; Tian, Peng; Billinge, Simon J.L.; Huffman, Brian J.; Harkness, Kellen M.; Cliffel, David E.

2010-01-01

In the two step synthesis of thiolate-monolayer protected clusters (MPCs), the first step of the reaction is a mild reduction of gold(III) by thiols that generates gold(I) thiolate complexes as intermediates. Using tiopronin (Tio) as the thiol reductant, the characterization of the intermediate Au4Tio4 complex was accomplished with various analytical and structural techniques. Nuclear magnetic resonance (NMR), elemental analysis, thermogravimetric analysis (TGA), and matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) were all consistent with a cyclic gold(I)-thiol tetramer structure, and final structural analysis was gathered through the use of powder diffraction and pair distribution functions (PDF). Crystallographic data has proved challenging for almost all previous gold(I)-thiolate complexes. Herein, a novel characterization technique when combined with standard analytical assessment to elucidate structure without crystallographic data proved invaluable to the study of these complexes. This in conjunction with other analytical techniques, in particular mass spectrometry, can elucidate a structure when crystallographic data is unavailable. In addition, luminescent properties provided evidence of aurophilicity within the molecule. The concept of aurophilicity has been introduced to describe a select group of gold-thiolate structures, which possess unique characteristics, mainly red photoluminescence and a distinct Au-Au intramolecular distance indicating a weak metal-metal bond as also evidenced by the structural model of the tetramer. Significant features of both the tetrameric and aurophilic properties of the intermediate gold(I) tiopronin complex are retained after borohydride reduction to form the MPC, including gold(I) tiopronin partial rings as capping motifs, or “staples”, and weak red photoluminescence that extends into the Near Infrared region. PMID:21067183

Structural characterization of proteins in wheat flour doughs enriched with intermediate wheatgrass (Thinopyrum intermedium) flour.

PubMed

Marti, Alessandra; Bock, Jayne E; Pagani, Maria Ambrogina; Ismail, Baraem; Seetharaman, Koushik

2016-03-01

The high protein and fiber content of intermediate wheatgrass (IWG) - together with its interesting agronomic traits and environment-related benefits - make this perennial crop attractive also for human consumption. Structural characteristics of the proteins in IWG/hard wheat flour (HWF) doughs (at IWG:HWF ratios of 0:100, 50:50, 75:25 and 100:0) - including aggregate formation, thiols availability, and secondary structure changes during dough mixing - were investigated. Proteins in IWG-doughs had higher solubility and thiol content - as function of IWG content - suggesting that protein network was mostly based on non-covalent interactions. While 50% IWG-enrichment gave an increase in random structures, enrichment at ⩾75% resulted in a decrease in β-sheets with an increase in random structures, indicating a decrease in structural order. The observed differences in protein molecular configuration and interactions in HWF compared to IWG doughs necessitate further investigation to establish their impact on the quality of IWG-enriched bread. Copyright © 2015 Elsevier Ltd. All rights reserved.

Transition of temporal scaling behavior in percolation assisted shear-branching structure during plastic deformation

DOE PAGES

Ren, Jingli; Chen, Cun; Wang, Gang; ...

2017-03-22

This study explores the temporal scaling behavior induced shear-branching structure in response to variant temperatures and strain rates during plastic deformation of Zr-based bulk metallic glass (BMG). The data analysis based on the compression tests suggests that there are two states of shear-branching structures: the fractal structure with a long-range order at an intermediate temperature of 223 K and a larger strain rate of 2.5 × 10 –2 s –1; the disordered structure dominated at other temperature and strain rate. It can be deduced from the percolation theory that the compressive ductility, ec, can reach the maximum value at themore » intermediate temperature. Furthermore, a dynamical model involving temperature is given for depicting the shear-sliding process, reflecting the plastic deformation has fractal structure at the temperature of 223 K and strain rate of 2.5 × 10 –2 s –1.« less

Hydrogen-bonded intermediates and transition states during spontaneous and acid-catalyzed hydrolysis of the carcinogen (+)-anti-BPDE.

PubMed

Palenik, Mark C; Rodriguez, Jorge H

2014-07-07

Understanding mechanisms of (+)-anti-BPDE detoxification is crucial for combating its mutagenic and potent carcinogenic action. However, energetic-structural correlations of reaction intermediates and transition states during detoxification via hydrolysis are poorly understood. To gain mechanistic insight we have computationally characterized intermediate and transition species associated with spontaneous and general-acid catalyzed hydrolysis of (+)-anti-BPDE. We studied the role of cacodylic acid as a proton donor in the rate limiting step. The computed activation energy (ΔG‡) is in agreement with the experimental value for hydrolysis in a sodium cacodylate buffer. Both types of, spontaneous and acid catalyzed, BPDE hydrolysis can proceed through low-entropy hydrogen bonded intermediates prior to formation of transition states whose energies determine reaction activation barriers and rates.

Friedreich's ataxia mimicking hereditary motor and sensory neuropathy.

PubMed

Panas, Marios; Kalfakis, Nikolaos; Karadima, Georgia; Davaki, Panagiota; Vassilopoulos, Demetris

2002-11-01

Four patients from three unrelated families, with clinical and electrophysiological findings compatible with the diagnosis of hereditary motor and sensory neuropathy, are presented. The molecular analysis showed that the affected individuals were homozygous for the mutation in the X25 gene, characteristic of Friedreich's ataxia. These patients seem to represent a form of Friedreich's ataxia mimicking Charcot-Marie-Tooth disease.

A rare case of primary bone lymphoma mimicking a pelvic abscess

PubMed Central

Al Wattar, BH; Mohanty, K

2011-01-01

Primary bone lymphoma (PBL) is a rare, malignant, neoplastic disorder of the skeleton that accounts for less than 5% of all primary bone tumours. We present an extremely rare case of PBL mimicking a pelvic abscess around the sacroiliac joint, which has never been reported in the medical literature, and discuss learning points highlighted from this case. PMID:22004625

Central nervous system borreliosis mimicking a pontine tumour.

PubMed

Latsch, Kirsten; Tappe, Dennis; Warmuth-Metz, Monika; Hebestreit, Helge

2006-11-01

In childhood, facial nerve palsy and headache are typical symptoms of second and third stage neuroborreliosis. While focal demyelination is occasionally observed on MRI scans, the appearance of a tumorous lesion is extremely rare. The case of a 10-year-old girl with neuroborreliosis mimicking a space-occupying lesion in the brainstem, without any previously recognized manifestations of borreliosis, is reported.

Antimicrobial Peptide Mimicking Primary Amine and Guanidine Containing Methacrylamide Copolymers Prepared by Raft Polymerization

PubMed Central

Exley, Sarah E.; Paslay, Lea C.; Sahukhal, Gyan S.; Abel, Brooks A.; Brown, Tyler D.; McCormick, Charles L.; Heinhorst, Sabine; Koul, Veena; Choudhary, Veena; Elasri, Mohamed O.; Morgan, Sarah E.

2016-01-01

Naturally occurring antimicrobial peptides (AMPs) display the ability to eliminate a wide variety of bacteria, without toxicity to the host eukaryotic cells. Synthetic polymers containing moieties mimicking lysine and arginine components found in AMPs have been reported to show effectiveness against specific bacteria, with the mechanism of activity purported to depend on the nature of the amino acid mimic. In an attempt to incorporate the antimicrobial activity of both amino acids into a single water-soluble copolymer, a series of copolymers containing lysine mimicking aminopropyl methacrylamide (APMA) and arginine mimicking guanadinopropyl methacrylamide (GPMA) were prepared via aqueous RAFT polymerization. Copolymers were prepared with varying ratios of the comonomers, with degree of polymerization of 35–40 and narrow molecular weight distribution to simulate naturally occurring AMPs. Antimicrobial activity was determined against Gram-negative and Gram-positive bacteria under conditions with varying salt concentration. Toxicity to mammalian cells was assessed by hemolysis of red blood cells and MTT assays of MCF-7 cells. Antimicrobial activity was observed for APMA homopolymer and copolymers with low concentrations of GPMA against all bacteria tested, with low toxicity toward mammalian cells. PMID:26558609