Defect induced plasticity and failure mechanism of boron nitride nanotubes under tension

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

Anoop Krishnan, N. M., E-mail: anoopnm@civil.iisc.ernet.in; Ghosh, Debraj

2014-07-28

The effects of Stone-Wales (SW) and vacancy defects on the failure behavior of boron nitride nanotubes (BNNTs) under tension are investigated using molecular dynamics simulations. The Tersoff-Brenner potential is used to model the atomic interaction and the temperature is maintained close to 300 K. The effect of a SW defect is studied by determining the failure strength and failure mechanism of nanotubes with different radii. In the case of a vacancy defect, the effect of an N-vacancy and a B-vacancy is studied separately. Nanotubes with different chiralities but similar diameter is considered first to evaluate the chirality dependence. The variation ofmore » failure strength with the radius is then studied by considering nanotubes of different diameters but same chirality. It is observed that the armchair BNNTs are extremely sensitive to defects, whereas the zigzag configurations are the least sensitive. In the case of pristine BNNTs, both armchair and zigzag nanotubes undergo brittle failure, whereas in the case of defective BNNTs, only the zigzag ones undergo brittle failure. An interesting defect induced plastic behavior is observed in defective armchair BNNTs. For this nanotube, the presence of a defect triggers mechanical relaxation by bond breaking along the closest zigzag helical path, with the defect as the nucleus. This mechanism results in a plastic failure.« less

Leigh syndrome associated with mitochondrial complex I deficiency due to a novel mutation in the NDUFS1 gene.

PubMed

Martín, Miguel A; Blázquez, Alberto; Gutierrez-Solana, Luis G; Fernández-Moreira, Daniel; Briones, Paz; Andreu, Antoni L; Garesse, Rafael; Campos, Yolanda; Arenas, Joaquín

2005-04-01

Mutations in the nuclear-encoded subunits of complex I of the mitochondrial respiratory chain are a recognized cause of Leigh syndrome (LS). Recently, 6 mutations in the NDUFS1 gene were identified in 3 families. To describe a Spanish family with LS, complex I deficiency in muscle, and a novel mutation in the NDUFS1 gene. Using molecular genetic approaches, we identified the underlying molecular defect in a patient with LS with a complex I defect. The proband was a child who displayed the clinical features of LS. Muscle biochemistry results showed a complex I defect of the mitochondrial respiratory chain. Sequencing analysis of the mitochondrial DNA-encoded ND genes, the nuclear DNA-encoded NDUFV1, NDUFS1, NDUFS2, NDUFS4, NDUFS6, NDUFS7, NDUFS8, and NDUFAB1 genes, and the complex I assembly factor CIA30 gene revealed a novel homozygous L231V mutation (c.691C-->G) in the NDUFS1 gene. The parents were heterozygous carriers of the L231V mutation. Identifying nuclear mutations as a cause of respiratory chain disorders will enhance the possibility of prenatal diagnosis and help us understand how molecular defects can lead to complex I deficiency.

Defects in middle ear cavitation cause conductive hearing loss in the Tcof1 mutant mouse.

PubMed

Richter, Carol A; Amin, Susan; Linden, Jennifer; Dixon, Jill; Dixon, Michael J; Tucker, Abigail S

2010-04-15

Conductive hearing loss (CHL) is one of the most common forms of human deafness. Despite this observation, a surprising gap in our understanding of the mechanisms underlying CHL remains, particularly with respect to the molecular mechanisms underlying middle ear development and disease. Treacher Collins syndrome (TCS) is an autosomal dominant disorder of facial development that results from mutations in the gene TCOF1. CHL is a common feature of TCS but the causes of the hearing defect have not been studied. In this study, we have utilized Tcof1 mutant mice to dissect the developmental mechanisms underlying CHL. Our results demonstrate that effective cavitation of the middle ear is intimately linked to growth of the auditory bulla, the neural crest cell-derived structure that encapsulates all middle ear components, and that defects in these processes have a profoundly detrimental effect on hearing. This research provides important insights into a poorly characterized cause of human deafness, and provides the first mouse model for the study of middle ear cavity defects, while also being of direct relevance to a human genetic disorder.

Topological defects in liquid crystals and molecular self-assembly (Conference Presentation)

NASA Astrophysics Data System (ADS)

Abbott, Nicholas L.

2017-02-01

Topological defects in liquid crystals (LCs) have been widely used to organize colloidal dispersions and template polymerizations, leading to a range of elastomers and gels with complex mechanical and optical properties. However, little is understood about molecular-level assembly processes within defects. This presentation will describe an experimental study that reveals that nanoscopic environments defined by LC topological defects can selectively trigger processes of molecular self-assembly. By using fluorescence microscopy, cryogenic transmission electron microscopy and super-resolution optical microscopy, key signatures of molecular self-assembly of amphiphilic molecules in topological defects are observed - including cooperativity, reversibility, and controlled growth of the molecular assemblies. By using polymerizable amphiphiles, we also demonstrate preservation of molecular assemblies templated by defects, including nanoscopic "o-rings" synthesized from "Saturn-ring" disclinations. Our results reveal that topological defects in LCs are a versatile class of three-dimensional, dynamic and reconfigurable templates that can direct processes of molecular self-assembly in a manner that is strongly analogous to other classes of macromolecular templates (e.g., polymer—surfactant complexes). Opportunities for the design of exquisitely responsive soft materials will be discussed using bacterial endotoxin as an example.

Molecular-Level Study of the Effect of Prior Axial Compression/Torsion on the Axial-Tensile Strength of PPTA Fibers

NASA Astrophysics Data System (ADS)

Grujicic, M.; Yavari, R.; Ramaswami, S.; Snipes, J. S.; Yen, C.-F.; Cheeseman, B. A.

2013-11-01

A comprehensive all-atom molecular-level computational investigation is carried out in order to identify and quantify: (i) the effect of prior longitudinal-compressive or axial-torsional loading on the longitudinal-tensile behavior of p-phenylene terephthalamide (PPTA) fibrils/fibers; and (ii) the role various microstructural/topological defects play in affecting this behavior. Experimental and computational results available in the relevant open literature were utilized to construct various defects within the molecular-level model and to assign the concentration to these defects consistent with the values generally encountered under "prototypical" PPTA-polymer synthesis and fiber fabrication conditions. When quantifying the effect of the prior longitudinal-compressive/axial-torsional loading on the longitudinal-tensile behavior of PPTA fibrils, the stochastic nature of the size/potency of these defects was taken into account. The results obtained revealed that: (a) due to the stochastic nature of the defect type, concentration/number density and size/potency, the PPTA fibril/fiber longitudinal-tensile strength is a statistical quantity possessing a characteristic probability density function; (b) application of the prior axial compression or axial torsion to the PPTA imperfect single-crystalline fibrils degrades their longitudinal-tensile strength and only slightly modifies the associated probability density function; and (c) introduction of the fibril/fiber interfaces into the computational analyses showed that prior axial torsion can induce major changes in the material microstructure, causing significant reductions in the PPTA-fiber longitudinal-tensile strength and appreciable changes in the associated probability density function.

Nanoscale rotary motors driven by electron tunneling.

PubMed

Wang, Boyang; Vuković, Lela; Král, Petr

2008-10-31

We examine by semiclassical molecular dynamics simulations the possibility of driving nanoscale rotary motors by electron tunneling. The model systems studied have a carbon nanotube shaft with covalently attached "isolating" molecular stalks ending with "conducting" blades. Periodic charging and discharging of the blades at two metallic electrodes maintains an electric dipole on the blades that is rotated by an external electric field. Our simulations demonstrate that these molecular motors can be efficient under load and in the presence of noise and defects.

Impurity distribution and microstructure of Ga-doped ZnO films grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Kvit, A. V.; Yankovich, A. B.; Avrutin, V.; Liu, H.; Izyumskaya, N.; Özgür, Ü.; Morkoç, H.; Voyles, P. M.

2012-12-01

We report microstructural characterization of heavily Ga-doped ZnO (GZO) thin films on GaN and sapphire by aberration-corrected scanning transmission electron microscopy. Growth under oxygen-rich and metal-rich growth conditions leads to changes in the GZO polarity and different extended defects. For GZO layers on sapphire, the primary extended defects are voids, inversion domain boundaries, and low-angle grain boundaries. Ga doping of ZnO grown under metal-rich conditions causes a switch from pure oxygen polarity to mixed oxygen and zinc polarity in small domains. Electron energy loss spectroscopy and energy dispersive spectroscopy spectrum imaging show that Ga is homogeneous, but other residual impurities tend to accumulate at the GZO surface and at extended defects. GZO grown on GaN on c-plane sapphire has Zn polarity and no voids. There are misfit dislocations at the interfaces between GZO and an undoped ZnO buffer layer and at the buffer/GaN interface. Low-angle grain boundaries are the only threading microstructural defects. The potential effects of different extended defects and impurity distributions on free carrier scattering are discussed.

Molecular-dynamics simulation of polymethylene chain confined in cylindrical potentials. I. Nature of the conformational defects

NASA Astrophysics Data System (ADS)

Yamamoto, Takashi; Kimikawa, Yuichi

1992-10-01

The conformational motion of a polymethylene molecule constrained by a cylindrical potential is simulated up to 100 ps. The molecule consists of 60 CH2 groups and has variable bond lengths, bond angles, and dihedral angles. Our main concern here is the excitation and the dynamics of the conformational defects: kinks, jogs, etc. Under weaker constraint a number of gauche bonds are excited; they mostly form pairs such as gtḡ kinks or gtttḡ jogs. These conformational defects show no continuous drift in space. Instead they often annihilate and then recreate at different sites showing apparently random positional changes. The conformational defects produce characteristic strain fields around them. It seems that the conformational defects interact attractively through these strain fields. This is evidenced by remarkably correlated spatial distributions of the gauche bonds.

Ectodermal Wnt signaling regulates abdominal myogenesis during ventral body wall development.

PubMed

Zhang, Lingling; Li, Hanjun; Yu, Jian; Cao, Jingjing; Chen, Huihui; Zhao, Haixia; Zhao, Jianzhi; Yao, Yiyun; Cheng, Huihui; Wang, Lifang; Zhou, Rujiang; Yao, Zhengju; Guo, Xizhi

2014-03-01

Defects of the ventral body wall are prevalent birth anomalies marked by deficiencies in body wall closure, hypoplasia of the abdominal musculature and multiple malformations across a gamut of organs. However, the mechanisms underlying ventral body wall defects remain elusive. Here, we investigated the role of Wnt signaling in ventral body wall development by inactivating Wls or β-catenin in murine abdominal ectoderm. The loss of Wls in the ventral epithelium, which blocks the secretion of Wnt proteins, resulted in dysgenesis of ventral musculature and genito-urinary tract during embryonic development. Molecular analyses revealed that the dermis and myogenic differentiation in the underlying mesenchymal progenitor cells was perturbed by the loss of ectodermal Wls. The activity of the Wnt-Pitx2 axis was impaired in the ventral mesenchyme of the mutant body wall, which partially accounted for the defects in ventral musculature formation. In contrast, epithelial depletion of β-catenin or Wnt5a did not resemble the body wall defects in the ectodermal Wls mutant. These findings indicate that ectodermal Wnt signaling instructs the underlying mesodermal specification and abdominal musculature formation during ventral body wall development, adding evidence to the theory that ectoderm-mesenchyme signaling is a potential unifying mechanism for the origin of ventral body wall defects. Copyright © 2013 Elsevier Inc. All rights reserved.

Molecular dynamics simulations of fluoropolymers in the solid state

NASA Astrophysics Data System (ADS)

Holt, David Bryan

1998-10-01

Molecular mechanics and dynamics simulations have been utilized to address the behavior of helix reversal defects in fluoropolymers. The results of the simulations confirm that helix reversals do form and migrate in PTFE crystals. The most important defect structure is a helix reversal band: two helix reversals which bracker a small chain segment (typically 6-7 backbone atoms) having the opposite helical sense from the parent molecule. Small reversal bands had velocities ranging between 100 m/s (low temperature)-250 m/s (high temperature). The size of this reversal band defect is dependent upon the helical conformation and is equal to approximately half of the helical repeat unit in the low and intermediate temperature phases. In the high temperature phase where intermolecular effects are diminished, a wider distribution of reversal band sizes was observed during the simulations. A mechanism is identified by which significant reorientation of a chain segment about the molecular axis can occur when it is bracketed by two helix reversal bands. Simulations with a model containing a perfluoromethyl (PFM) group at low temperature showed that the presence of the PFM group significantly restricts chain mobility locally. However, a significant reduction in the helix reversal defect density was observed on neighboring chains as well. During simulations in which a shear deformation was applied to the models with and without a PFM group, an increase in reversal defect density was observed. However, the helix reversal density in the sheared model containing the PFM branch was less than that in the model without a PFM branch under no shear. These data implicate helix reversal defects and associated chain segment motions in the mechanical behavior of fluoropolymer materials.

Simulation of Rutherford backscattering spectrometry from arbitrary atom structures.

PubMed

Zhang, S; Nordlund, K; Djurabekova, F; Zhang, Y; Velisa, G; Wang, T S

2016-10-01

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop here a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.

Simulation of Rutherford backscattering spectrometry from arbitrary atom structures

NASA Astrophysics Data System (ADS)

Zhang, S.; Nordlund, K.; Djurabekova, F.; Zhang, Y.; Velisa, G.; Wang, T. S.

2016-10-01

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop here a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.

Molecular dynamical simulations of melting Al nanoparticles using a reaxff reactive force field

NASA Astrophysics Data System (ADS)

Liu, Junpeng; Wang, Mengjun; Liu, Pingan

2018-06-01

Molecular dynamics simulations were performed to study thermal properties and melting points of Al nanoparticles by using a reactive force field under canonical (NVT) ensembles. Al nanoparticles (particle size 2–4 nm) were considered in simulations. A combination of structural and thermodynamic parameters such as the Lindemann index, heat capacities, potential energy and radial-distribution functions was employed to decide melting points. We used annealing technique to obtain the initial Al nanoparticle model. Comparison was made between ReaxFF results and other simulation results. We found that ReaxFF force field is reasonable to describe Al cluster melting behavior. The linear relationship between particle size and melting points was found. After validating the ReaxFF force field, more attention was paid on thermal properties of Al nanoparticles with different defect concentrations. 4 nm Al nanoparticles with different defect concentrations (5%–20%) were considered in this paper. Our results revealed that: the melting points are irrelevant with defect concentration at a certain particle size. The extra storage energy of Al nanoparticles is proportional to nanoparticles’ defect concentration, when defect concentration is 5%–15%. While the particle with 20% defect concentration is similar to the cluster with 10% defect concentration. After melting, the extra energy of all nanoparticles decreases sharply, and the extra storage energy is nearly zero at 600 K. The centro-symmetry parameter analysis shows structure evolution of different models during melting processes.

Mechanical properties of highly defective graphene: from brittle rupture to ductile fracture.

PubMed

Xu, Lanqing; Wei, Ning; Zheng, Yongping

2013-12-20

Defects are generally believed to deteriorate the superlative performance of graphene-based devices but may also be useful when carefully engineered to tailor the local properties and achieve new functionalities. Central to most defect-associated applications is the defect coverage and arrangement. In this work, we investigate, by molecular dynamics simulations, the mechanical properties and fracture dynamics of graphene sheets with randomly distributed vacancies or Stone-Wales defects under tensile deformations over a wide defect coverage range. With defects presented, an sp-sp(2) bonding network and an sp-sp(2)-sp(3) bonding network are observed in vacancy-defected and Stone-Wales-defected graphene, respectively. The ultimate strength degrades gradually with increasing defect coverage and saturates in the high-ratio regime, whereas the fracture strain presents an unusual descending-saturating-improving trend. In the dense vacancy defect situation, the fracture becomes more plastic and super-ductility is observed. Further fracture dynamics analysis reveals that the crack trapping by sp-sp(2) and sp-sp(2)-sp(3) rings and the crack-tip blunting account for the ductile fracture, whereas geometric rearrangement on the entire sheet for vacancy defects and geometric rearrangement on the specific defect sites for Stone-Wales defects account for their distinctive rules of the evolution of the fracture strain.

Selection, Design and Applications of Solid Binding Peptides for Controlled Biomineralization

NASA Astrophysics Data System (ADS)

Gungormus, Mustafa

The regulated formation of inorganic minerals in living systems is called biomineralization. The mineralization processes of biogenic minerals are strictly regulated by a specific set of biomolecules, typically by proteins. Biologically formed calcium phosphates (hydroxyapatite (HA) in particular) are almost always nano-dimensional and nano-crystalline and are formed in vivo under mild conditions. The importance of understanding the molecular mechanisms underlying biological mineralization is underscored by the diseases associated with ectopic calcification or defects of skeletal mineralization. Proteins that mediate the mineralization process offer us a template for understanding how to potentially enhance the treatment of calcified tissue defects. However, the complexity and the number of proteins involved even in a rather simple biomineralization process can be daunting. The goal of this research was to identify short peptides through peptide-display libraries and demonstrate the utility of these peptides in better understanding the molecular mechanisms underlying biomineralization and as potential therapeutic agents in repairing calcified tissue defects. Using the phage-peptide display library, we have identified peptides that have affinity to HA and can regulate the formation of HA crystals. Utilizing the sequence knowledge obtained, we have identified putative functional domains within amelogenin; a naturally existing mineralization related protein, which, in turn, may provide a better understanding of the formation of dental enamel. These peptides also have the potential to be used to repair calcified tissue defects. To investigate this, we have developed and tested in vitro a hydrogel scaffold with pre-determined functionalities. We have also demonstrated the feasibility of obtaining significant re-mineralization of incipient dental root lesions ex vivo in a relatively short time using the mineralization-directing peptides. The approaches developed through this research may offer clinically acceptable novel procedures to treat calcified tissue defects because the developed peptide is safe to use and promotes the mineralization in a short period of time offered by none of the existing treatment options.

Defect silicene and graphene as applied to the anode of lithium-ion batteries: Numerical experiment

NASA Astrophysics Data System (ADS)

Galashev, A. E.; Rakhmanova, O. R.; Zaikov, Yu. P.

2016-09-01

Mechanical properties and stability of two layers of defect silicene supported by graphene sheets, between which the lithium ion passes under an electrostatic field, are studied by the molecular dynamics method. Defects are mono-, di-, tri-, and hexavacansies. Graphene and silicene edges are rigidly fixed. Graphene sheets contacting with silicene take a convex shape, deflecting outward. Mono- and divacancies in silicene tend to a size decrease; larger vacancies exhibit better stability. The ion motion control using an electric field becomes possible only using perfect silicene or silicene with mono- and divacancies. The ion penetrated through larger defects, and its motion in the silicene channel becomes uncontrolled. When the ion moves in the channel, the most strong stress spikes appear in silicene containing monovacancies. In the case of fixed edges, perfect silicene intercalated with a lithium ion is inclined to accumulate larger stresses than silicene containing defects.

Molecular dynamics simulation of the evolution of hydrophobic defects in one monolayer of a phosphatidylcholine bilayer: relevance for membrane fusion mechanisms.

PubMed Central

Tieleman, D Peter; Bentz, Joe

2002-01-01

The spontaneous formation of the phospholipid bilayer underlies the permeability barrier function of the biological membrane. Tears or defects that expose water to the acyl chains are spontaneously healed by lipid lateral diffusion. However, mechanical barriers, e.g., protein aggregates held in place, could sustain hydrophobic defects. Such defects have been postulated to occur in processes such as membrane fusion. This gives rise to a new question in bilayer structure: What do the lipids do in the absence of lipid lateral diffusion to minimize the free energy of a hydrophobic defect? As a first step to understand this rather fundamental question about bilayer structure, we performed molecular dynamic simulations of up to 10 ns of a planar bilayer from which lipids have been deleted randomly from one monolayer. In one set of simulations, approximately one-half of the lipids in the defect monolayer were restrained to form a mechanical barrier. In the second set, lipids were free to diffuse around. The question was simply whether the defects caused by removing a lipid would aggregate together, forming a large hydrophobic cavity, or whether the membrane would adjust in another way. When there are no mechanical barriers, the lipids in the defect monolayer simply spread out and thin with little effect on the other intact monolayer. In the presence of a mechanical barrier, the behavior of the lipids depends on the size of the defect. When 3 of 64 lipids are removed, the remaining lipids adjust the lower one-half of their chains, but the headgroup structure changes little and the intact monolayer is unaffected. When 6 to 12 lipids are removed, the defect monolayer thins, lipid disorder increases, and lipids from the intact monolayer move toward the defect monolayer. Whereas this is a highly simplified model of a fusion site, this engagement of the intact monolayer into the fusion defect is strikingly consistent with recent results for influenza hemagglutinin mediated fusion. PMID:12202375

Defining the molecular pathologies in cloaca malformation: similarities between mouse and human

PubMed Central

Runck, Laura A.; Method, Anna; Bischoff, Andrea; Levitt, Marc; Peña, Alberto; Collins, Margaret H.; Gupta, Anita; Shanmukhappa, Shiva; Wells, James M.; Guasch, Géraldine

2014-01-01

Anorectal malformations are congenital anomalies that form a spectrum of disorders, from the most benign type with excellent functional prognosis, to very complex, such as cloaca malformation in females in which the rectum, vagina and urethra fail to develop separately and instead drain via a single common channel into the perineum. The severity of this phenotype suggests that the defect occurs in the early stages of embryonic development of the organs derived from the cloaca. Owing to the inability to directly investigate human embryonic cloaca development, current research has relied on the use of mouse models of anorectal malformations. However, even studies of mouse embryos lack analysis of the earliest stages of cloaca patterning and morphogenesis. Here we compared human and mouse cloaca development and retrospectively identified that early mis-patterning of the embryonic cloaca might underlie the most severe forms of anorectal malformation in humans. In mouse, we identified that defective sonic hedgehog (Shh) signaling results in early dorsal-ventral epithelial abnormalities prior to the reported defects in septation. This is manifested by the absence of Sox2 and aberrant expression of keratins in the embryonic cloaca of Shh knockout mice. Shh knockout embryos additionally develop a hypervascular stroma, which is defective in BMP signaling. These epithelial and stromal defects persist later, creating an indeterminate epithelium with molecular alterations in the common channel. We then used these animals to perform a broad comparison with patients with mild-to-severe forms of anorectal malformations including cloaca malformation. We found striking parallels with the Shh mouse model, including nearly identical defective molecular identity of the epithelium and surrounding stroma. Our work strongly suggests that early embryonic cloacal epithelial differentiation defects might be the underlying cause of severe forms of anorectal malformations in humans. Moreover, deranged Shh and BMP signaling is correlated with severe anorectal malformations in both mouse and humans. PMID:24524909

Single Molecule Investigation of Kinesin-1 Motility Using Engineered Microtubule Defects

NASA Astrophysics Data System (ADS)

Gramlich, Michael W.; Conway, Leslie; Liang, Winnie H.; Labastide, Joelle A.; King, Stephen J.; Xu, Jing; Ross, Jennifer L.

2017-03-01

The structure of the microtubule is tightly regulated in cells via a number of microtubule associated proteins and enzymes. Microtubules accumulate structural defects during polymerization, and defect size can further increase under mechanical stresses. Intriguingly, microtubule defects have been shown to be targeted for removal via severing enzymes or self-repair. The cell’s control in defect removal suggests that defects can impact microtubule-based processes, including molecular motor-based intracellular transport. We previously demonstrated that microtubule defects influence cargo transport by multiple kinesin motors. However, mechanistic investigations of the observed effects remained challenging, since defects occur randomly during polymerization and are not directly observable in current motility assays. To overcome this challenge, we used end-to-end annealing to generate defects that are directly observable using standard epi-fluorescence microscopy. We demonstrate that the annealed sites recapitulate the effects of polymerization-derived defects on multiple-motor transport, and thus represent a simple and appropriate model for naturally-occurring defects. We found that single kinesins undergo premature dissociation, but not preferential pausing, at the annealed sites. Our findings provide the first mechanistic insight to how defects impact kinesin-based transport. Preferential dissociation on the single-molecule level has the potential to impair cargo delivery at locations of microtubule defect sites in vivo.

Pathophysiology of B-cell intrinsic immunoglobulin class switch recombination deficiencies.

PubMed

Durandy, Anne; Taubenheim, Nadine; Peron, Sophie; Fischer, Alain

2007-01-01

B-cell intrinsic immunoglobulin class switch recombination (Ig-CSR) deficiencies, previously termed hyper-IgM syndromes, are genetically determined conditions characterized by normal or elevated serum IgM levels and an absence or very low levels of IgG, IgA, and IgE. As a function of the molecular mechanism, the defective CSR is variably associated to a defect in the generation of somatic hypermutations (SHMs) in the Ig variable region. The study of Ig-CSR deficiencies contributed to a better delineation of the mechanisms underlying CSR and SHM, the major events of antigen-triggered antibody maturation. Four Ig-CSR deficiency phenotypes have been so far reported: the description of the activation-induced cytidine deaminase (AID) deficiency (Ig-CSR deficiency 1), caused by recessive mutations of AICDA gene, characterized by a defect in CSR and SHM, clearly established the role of AID in the induction of the Ig gene rearrangements underlying CSR and SHM. A CSR-specific function of AID has, however, been detected by the observation of a selective CSR defect caused by mutations affecting the C-terminus of AID. Ig-CSR deficiency 2 is the consequence of uracil-N-glycosylase (UNG) deficiency. Because UNG, a molecule of the base excision repair machinery, removes uracils from DNA and AID deaminates cytosines into uracils, that observation indicates that the AID-UNG pathway directly targets DNA of switch regions from the Ig heavy-chain locus to induce the CSR process. Ig-CSR deficiencies 3 and 4 are characterized by a selective CSR defect resulting from blocks at distinct steps of CSR. A further understanding of the CSR machinery is expected from their molecular definition.

Electronic structure of oxygen-vacancy defects in amorphous In-Ga-Zn-O semiconductors

NASA Astrophysics Data System (ADS)

Noh, Hyeon-Kyun; Chang, K. J.; Ryu, Byungki; Lee, Woo-Jin

2011-09-01

We perform first-principles density functional calculations to investigate the atomic and electronic properties of various O-vacancy (VO) defects in amorphous indium gallium zinc oxides (a-IGZO). The formation energies of VO have a tendency to increase with increasing number of neighboring Ga atoms, whereas they are generally low in the environment surrounded with In atoms. Thus, adding Ga atoms suppresses the formation of O-deficiency defects, which are considered as the origin of device instability in a-IGZO-based thin film transistors. The conduction band edge state is characterized by the In s orbital and insensitive to disorder, in good agreement with the experimental finding that increasing the In content enhances the carrier density and mobility. In a-IGZO, while most VO defects are deep donors, some of the defects act as shallow donors due to local environments different from those in crystalline oxides. As ionized O vacancies can capture electrons, it is suggested that these defects are responsible for positive shifts of the threshold voltage observed under positive gate bias stress. Under light illumination stress, VO defects can be ionized, becoming VO2+ defects due to the negative-U behavior. When electrons are captured by applying a negative bias voltage, ionized VO2+ defects return to the original neutral charge state. Through molecular dynamics simulations, we find that the initial neutral state is restored by annealing, in good agreement with experiments, although the annealing temperature depends on the local environment. Our calculations show that VO defects play an important role in the instability of a-IGZO-based devices.

Effect of Defects on Mechanisms of Initiation and Energy Release in Energetic Molecular Crystals

DTIC Science & Technology

2011-02-10

dynamics of NEEMs ," Aberdeen, MD, Mar. 2010. 60. Dana Dlott (invited) American Chemical Society Annual Meeting, "Vibrational Energy in Molecules with High...hydrocarbons to ascertain their stability under extreme conditions. Also, HEs are often mixed with fuel oils as well so we sought to separately...dependence of the EOS. Ab initio calculations were performed to extract the complete equation of state for an organic molecular crystal over a

Natural killer cell biology illuminated by primary immunodeficiency syndromes in humans.

PubMed

Voss, Matthias; Bryceson, Yenan T

2017-04-01

Natural killer (NK) cells are innate immune cytotoxic effector cells well known for their role in antiviral immunity and tumor immunosurveillance. In parts, this knowledge stems from rare inherited immunodeficiency disorders in humans that abrogate NK cell function leading to immune impairments, most notably associated with a high susceptibility to viral infections. Phenotypically, these disorders range from deficiencies selectively affecting NK cells to complex general immune defects that affect NK cells but also other immune cell subsets. Moreover, deficiencies may be associated with reduced NK cell numbers or rather impair specific NK cell effector functions. In recent years, genetic defects underlying the various NK cell deficiencies have been uncovered and have triggered investigative efforts to decipher the molecular mechanisms underlying these disorders. Here we review the associations between inherited human diseases and NK cell development as well as function, with a particular focus on defects in NK cell exocytosis and cytotoxicity. Furthermore we outline how reports of diverse genetic defects have shaped our understanding of NK cell biology. Copyright © 2015. Published by Elsevier Inc.

Therapeutic Approaches for Shankopathies

PubMed Central

Wang, Xiaoming; Bey, Alexandra; Chang, Leeyup; Krystal, Andrew D.; Jiang, Yong-hui

2013-01-01

Despite recent advances in understanding the molecular mechanisms of autism spectrum disorders (ASD), the current treatments for these disorders are mostly focused on behavioral and educational approaches. The considerable clinical and molecular heterogeneity of ASD present a significant challenge to the development of an effective treatment targeting underlying molecular defects. Deficiency of SHANK family genes causing ASD represent an exciting opportunity for developing molecular therapies because of strong genetic evidence for SHANKs as causative genes in ASD and the availability of a panel of Shank mutant mouse models. In this article we review the literature suggesting the potential for developing therapies based on molecular characteristics and discuss several exciting themes that are emerging from studying Shank mutant mice at the molecular level and in terms of synaptic function. PMID:23536326

Simulation of Rutherford backscattering spectrometry from arbitrary atom structures

DOE PAGES

Zhang, S.; Univ. of Helsinki; Nordlund, Kai; ...

2016-10-25

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop in this paper a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms,more » Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Finally, comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.« less

Molecular dynamics study of structural damage in amorphous silica induced by swift heavy-ion radiation

NASA Astrophysics Data System (ADS)

Zhen, J. S.; Yang, Q.; Yan, Y. H.; Jiang, X. W.; Yan, S. A.; Chen, W.; Guo, X. Q.

2016-03-01

In this paper, the radiation defects induced by the swift heavy ions and the recoil atoms in amorphous SiO2 were studied. The energy of recoil atoms induced by the incident Au ions in SiO2 was calculated by using Monte Carlo method. Results show that the average energies of recoils reach the maximum (200 eV for Si and 130 eV for O, respectively) when the incident energy of Au ion is 100 MeV. Using Tersoff/zbl potential with the newly built parameters, the defects formation processes in SiO2 induced by the recoils were studied by using molecular dynamics method. The displacement threshold energies (Ed) for Si and O atoms are found to be 33.5 and 16.3 eV, respectively. Several types of under- and over-coordinated Si and O defects were analyzed. The results demonstrate that Si3, Si5, and O1 are the mainly defects in SiO2 after radiation. Besides, the size of cylindrical damage region produced by a single recoil atom was calculated. The calculation shows that the depth and the radius are up to 2.0 and 1.4 nm when the energy of recoils is 200 eV. Finally, it is estimated that the Au ion would induce a defected track with a diameter of 4 nm in SiO2.

Nonlinear effects in defect production by atomic and molecular ion implantation

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

David, C., E-mail: david@igcar.gov.in; Dholakia, Manan; Chandra, Sharat

This report deals with studies concerning vacancy related defects created in silicon due to implantation of 200 keV per atom aluminium and its molecular ions up to a plurality of 4. The depth profiles of vacancy defects in samples in their as implanted condition are carried out by Doppler broadening spectroscopy using low energy positron beams. In contrast to studies in the literature reporting a progressive increase in damage with plurality, implantation of aluminium atomic and molecular ions up to Al{sub 3}, resulted in production of similar concentration of vacancy defects. However, a drastic increase in vacancy defects is observed duemore » to Al{sub 4} implantation. The observed behavioural trend with respect to plurality has even translated to the number of vacancies locked in vacancy clusters, as determined through gold labelling experiments. The impact of aluminium atomic and molecular ions simulated using MD showed a monotonic increase in production of vacancy defects for cluster sizes up to 4. The trend in damage production with plurality has been explained on the basis of a defect evolution scheme in which for medium defect concentrations, there is a saturation of the as-implanted damage and an increase for higher defect concentrations.« less

Electronic excitations in shocked nitromethane

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

Reed, Evan J.; Joannopoulos, J. D.; Fried, Laurence E.

2000-12-15

The nature of electronic excitations in crystalline solid nitromethane under conditions of shock loading and static compression are examined. Density-functional theory calculations are used to determine the crystal bandgap under hydrostatic stress, uniaxial strain, and shear strain. Bandgap lowering under uniaxial strain due to molecular defects and vacancies is considered. Ab initio molecular-dynamics simulations are done of all possible nearest-neighbor collisions at a shock front, and of crystal shearing along a sterically hindered slip plane. In all cases, the bandgap is not lowered enough to produce a significant population of excited states in the crystal. The nearly free rotation ofmore » the nitromethane methyl group and localized nature of the highest occupied molecular orbital and lowest unoccupied molecular orbital states play a role in this result. Dynamical effects have a more significant effect on the bandgap than static effects, but relative molecule velocities in excess of 6 km/s are required to produce a significant thermal population of excited states.« less

Molecular dynamics simulations of the structure evolutions of Cu-Zr metallic glasses under irradiation

NASA Astrophysics Data System (ADS)

Lang, Lin; Tian, Zean; Xiao, Shifang; Deng, Huiqiu; Ao, Bingyun; Chen, Piheng; Hu, Wangyu

2017-02-01

Molecular dynamics simulations have been performed to investigate the structural evolution of Cu64.5Zr35.5 metallic glasses under irradiation. The largest standard cluster analysis (LSCA) method was used to quantify the microstructure within the collision cascade regions. It is found that the majority of clusters within the collision cascade regions are full and defective icosahedrons. Not only the smaller structures (common neighbor subcluster) but also primary clusters greatly changed during the collision cascades; while most of these radiation damages self-recover quickly in the following quench states. These findings indicate the Cu-Zr metallic glasses have excellent irradiation-resistance properties.

Ab initio molecular dynamics simulations of ion-solid interactions in zirconate pyrochlores

DOE PAGES

Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; ...

2015-01-31

In this paper, an ab initio molecular dynamics method is employed to study low energy recoil events in zirconate pyrochlores (A 2Zr 2O 7, A = La, Nd and Sm). It shows that both cations and anions in Nd 2Zr 2O 7 and Sm 2Zr 2O 7 are generally more likely to be displaced than those in La 2Zr 2O 7. The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd 2Zr 2O 7 and Sm 2Zr 2O 7 are lower than those in La 2Zr 2O 7. These results suggest thatmore » the order–disorder structural transition more easily occurs in Nd 2Zr 2O 7 and Sm 2Zr 2O 7 resulting in a defect-fluorite structure, which agrees well with experimental observations. Our calculations indicate that oxygen migration from 48f and 8b to 8a sites is dominant under low energy irradiation. A number of new defects, including four types of cation Frenkel pairs and six types of anion Frenkel pairs, are revealed by ab initio molecular dynamics simulations. The present findings may help to advance the fundamental understanding of the irradiation response behavior of zirconate pyrochlores.« less

CO2 packing polymorphism under pressure: Mechanism and thermodynamics of the I-III polymorphic transition

NASA Astrophysics Data System (ADS)

Gimondi, Ilaria; Salvalaglio, Matteo

2017-09-01

In this work, we describe the thermodynamics and mechanism of CO2 polymorphic transitions under pressure from form I to form III combining standard molecular dynamics, well-tempered metadynamics, and committor analysis. We find that the phase transformation takes place through a concerted rearrangement of CO2 molecules, which unfolds via an anisotropic expansion of the CO2 supercell. Furthermore, at high pressures, we find that defected form I configurations are thermodynamically more stable with respect to form I without structural defects. Our computational approach shows the capability of simultaneously providing an extensive sampling of the configurational space, estimates of the thermodynamic stability, and a suitable description of a complex, collective polymorphic transition mechanism.

CO2 packing polymorphism under pressure: Mechanism and thermodynamics of the I-III polymorphic transition.

PubMed

Gimondi, Ilaria; Salvalaglio, Matteo

2017-09-21

In this work, we describe the thermodynamics and mechanism of CO 2 polymorphic transitions under pressure from form I to form III combining standard molecular dynamics, well-tempered metadynamics, and committor analysis. We find that the phase transformation takes place through a concerted rearrangement of CO 2 molecules, which unfolds via an anisotropic expansion of the CO 2 supercell. Furthermore, at high pressures, we find that defected form I configurations are thermodynamically more stable with respect to form I without structural defects. Our computational approach shows the capability of simultaneously providing an extensive sampling of the configurational space, estimates of the thermodynamic stability, and a suitable description of a complex, collective polymorphic transition mechanism.

Endocrine profile and phenotype-(epi)genotype correlation in Spanish patients with pseudohypoparathyroidism.

PubMed

Fernández-Rebollo, Eduardo; Lecumberri, Beatriz; Gaztambide, Sonia; Martinez-Indart, Lorea; Perez de Nanclares, Guiomar; Castaño, Luis

2013-05-01

Recent advances in genetics and epigenetics have revealed an overlap between molecular and clinical features of pseudohypoparathyroidism (PHP) subtypes, broadening the previous spectrum of PHP genotype-phenotype correlations and indicating limitations of the current classification of the disease. The aim of the study was to screen patients with clinical diagnoses of PHP type I or pseudo-PHP for underlying molecular defects and explore possible correlations between molecular findings and clinical features. We investigated the GNAS locus at the molecular level in 72 affected patients (46 women and 26 men) from 56 nonrelated families. Clinical data were obtained for 63 of these patients (38 women and 25 men). The molecular analysis showed that 35 patients carried structural mutations, 32 had loss of methylation, and 2 had a 2q37 deletion but did not reveal any (epi)mutation for 3 patients. Comparing these results and the clinical data, we observed that a younger age at diagnosis was associated with structural defects at the GNAS gene and epigenetic defects with a diagnosis later in life (9.19 ± 1.64 vs 24.57 ± 2.28 years, P < .0001). This first global review of PHP in Spain highlights the importance of a detailed clinical and genetic study of each patient and the integrated analysis of the findings from the two approaches. It may also help geneticists and clinicians to raise the suspicion of PHP earlier, reach more accurate diagnoses, and provide patients with PHP and their families with useful genetic information and counseling, thereby improving outcomes and quality of life.

Amorphization driven by defect-induced mechanical instability.

PubMed

Jiang, Chao; Zheng, Ming-Jie; Morgan, Dane; Szlufarska, Izabela

2013-10-11

Using ab initio molecular dynamics simulations, we perform a comparative study of the defect accumulation process in silicon carbide (SiC) and zirconium carbide (ZrC). Interestingly, we find that the fcc Si sublattice in SiC spontaneously and gradually collapses following the continuous introduction of C Frenkel pairs (FPs). Above a critical amorphization dose of ~0.33 displacements per atom (dpa), the pair correlation function exhibits no long-range order. In contrast, the fcc Zr sublattice in ZrC remains structurally stable against C sublattice displacements up to the highest dose of 1.0 dpa considered. Consequently, ZrC cannot be amorphized by the accumulation of C FPs. We propose defect-induced mechanical instability as the key mechanism driving the amorphization of SiC under electron irradiation.

Electronic excitations and chemistry in Nitromethane and HMX

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

Reed, E J; Manaa, M R; Joannopoulos, J D

2001-06-19

The nature of electronic excitations in crystalline solid nitromethane under conditions of shock loading and static compression are examined. Density functional theory calculations are used to determine the crystal bandgap under hydrostatic stress, uniaxial strain, and shear strain. Bandgap lowering under uniaxial strain due to molecular defects and vacancies is considered. In all cases, the bandgap is not lowered enough to produce a significant population of excited states in the crystal. Preliminary simulations on the formation of detonation product molecules from HMX are discussed.

Role of topographical defects in organic film growth of 4,4' -biphenyldicarboxylic acid on graphene: A low-energy electron microscopy study

NASA Astrophysics Data System (ADS)

Khokhar, Fawad S.; van Gastel, Raoul; Poelsema, Bene

2010-11-01

We have used low-energy electron microscopy (LEEM) to study the formation of self-assembled molecular networks on graphene sheets. 4,4' -biphenyldicarboxylic acid (BDA) molecular networks were grown using organic molecular beam epitaxy. LEEM images provide direct insight in the growth dynamics and show that defects in the graphene play a crucial role in the final morphology of the molecular film that forms. BDA is demonstrated to form hydrogen bond-stabilized chains on graphene. Dark-field LEEM images reveal that the same defects that determine the morphology of the film, also direct the orientation of the domains, highlighting the importance of understanding the role of defects in epitaxial processes on graphene.

Failure to Deliver and Translate-New Insights into RNA Dysregulation in ALS.

PubMed

Coyne, Alyssa N; Zaepfel, Benjamin L; Zarnescu, Daniela C

2017-01-01

Amyotrophic Lateral Sclerosis (ALS) is a progressive and fatal neurodegenerative disease affecting both upper and lower motor neurons. The molecular mechanisms underlying disease pathogenesis remain largely unknown. Multiple genetic loci including genes involved in proteostasis and ribostasis have been linked to ALS providing key insights into the molecular mechanisms underlying disease. In particular, the identification of the RNA binding proteins TDP-43 and fused in sarcoma (FUS) as causative factors of ALS resulted in a paradigm shift centered on the study of RNA dysregulation as a major mechanism of disease. With wild-type TDP-43 pathology being found in ~97% of ALS cases and the identification of disease causing mutations within its sequence, TDP-43 has emerged as a prominent player in ALS. More recently, studies of the newly discovered C9orf72 repeat expansion are lending further support to the notion of defects in RNA metabolism as a key factor underlying ALS. RNA binding proteins are involved in all aspects of RNA metabolism ranging from splicing, transcription, transport, storage into RNA/protein granules, and translation. How these processes are affected by disease-associated mutations is just beginning to be understood. Considerable work has gone into the identification of splicing and transcription defects resulting from mutations in RNA binding proteins associated with disease. More recently, defects in RNA transport and translation have been shown to be involved in the pathomechanism of ALS. A central hypothesis in the field is that disease causing mutations lead to the persistence of RNA/protein complexes known as stress granules. Under times of prolonged cellular stress these granules sequester specific mRNAs preventing them from translation, and are thought to evolve into pathological aggregates. Here we will review recent efforts directed at understanding how altered RNA metabolism contributes to ALS pathogenesis.

Novel ITGB6 mutation in autosomal recessive amelogenesis imperfecta.

PubMed

Seymen, F; Lee, K-E; Koruyucu, M; Gencay, K; Bayram, M; Tuna, E B; Lee, Z H; Kim, J-W

2015-05-01

Hereditary defects in tooth enamel formation, amelogenesis imperfecta (AI), can be non-syndromic or syndromic phenotype. Integrins are signaling proteins that mediate cell-cell and cell-extracellular matrix communication, and their involvement in tooth development is well known. The purposes of this study were to identify genetic cause of an AI family and molecular pathogenesis underlying defective enamel formation. We recruited a Turkish family with isolated AI and performed mutational analyses to clarify the underlying molecular genetic etiology. Autozygosity mapping and exome sequencing identified a novel homozygous ITGB6 transversion mutation in exon 4 (c.517G>C, p.Gly173Arg). The glycine at this position in the middle of the βI-domain is conserved among a wide range of vertebrate orthologs and human paralogs. Clinically, the enamel was generally thin and pitted with pigmentation. Thicker enamel was noted at the cervical area of the molars. In this study, we identified a novel homozygous ITGB6 mutation causing isolated AI, and this advances the understanding of normal and pathologic enamel development. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Novel ITGB6 mutation in autosomal recessive amelogenesis imperfecta

PubMed Central

Seymen, F; Lee, K-E; Koruyucu, M; Gencay, K; Bayram, M; Tuna, EB; Lee, ZH; Kim, J-W

2015-01-01

Objective Hereditary defects in tooth enamel formation, amelogenesis imperfecta (AI), can be non-syndromic or syndromic phenotype. Integrins are signaling proteins that mediate cell–cell and cell–extracellular matrix communication, and their involvement in tooth development is well known. The purposes of this study were to identify genetic cause of an AI family and molecular pathogenesis underlying defective enamel formation. Materials and Methods We recruited a Turkish family with isolated AI and performed mutational analyses to clarify the underlying molecular genetic etiology. Results Autozygosity mapping and exome sequencing identified a novel homozygous ITGB6 transversion mutation in exon 4 (c.517G>C, p.Gly173Arg). The glycine at this position in the middle of the βI-domain is conserved among a wide range of vertebrate orthologs and human paralogs. Clinically, the enamel was generally thin and pitted with pigmentation. Thicker enamel was noted at the cervical area of the molars. Conclusions In this study, we identified a novel homozygous ITGB6 mutation causing isolated AI, and this advances the understanding of normal and pathologic enamel development. PMID:25431241

Novel insights into FAS defects underlying autoimmune lymphoproliferative syndrome revealed by studies in consanguineous patients.

PubMed

Ben-Mustapha, Imen; Agrebi, Nourhen; Barbouche, Mohamed-Ridha

2018-03-01

Autoimmune lymphoproliferative syndrome (ALPS) is a primary immunodeficiency disease due to impaired Fas-Fas ligand apoptotic pathway. It is characterized by chronic nonmalignant, noninfectious lymphadenopathy and/or splenomegaly associated with autoimmune manifestations primarily directed against blood cells. Herein, we review the heterogeneous ALPS molecular bases and discuss recent findings revealed by the study of consanguineous patients. Indeed, this peculiar genetic background favored the identification of a novel form of AR ALPS-FAS associated with normal or residual protein expression, expanding the spectrum of ALPS types. In addition, rare mutational mechanisms underlying the splicing defects of FAS exon 6 have been identified in AR ALPS-FAS with lack of protein expression. These findings will help decipher critical regions required for the tight regulation of FAS exon 6 splicing. We also discuss the genotype-phenotype correlation and disease severity in AR ALPS-FAS. Altogether, the study of ALPS molecular bases in endogamous populations helps to better classify the disease subgroups and to unravel the Fas pathway functioning. ©2017 Society for Leukocyte Biology.

Grain boundary resistance to amorphization of nanocrystalline silicon carbide

PubMed Central

Chen, Dong; Gao, Fei; Liu, Bo

2015-01-01

Under the C displacement condition, we have used molecular dynamics simulation to examine the effects of grain boundaries (GBs) on the amorphization of nanocrystalline silicon carbide (nc-SiC) by point defect accumulation. The results show that the interstitials are preferentially absorbed and accumulated at GBs that provide the sinks for defect annihilation at low doses, but also driving force to initiate amorphization in the nc-SiC at higher doses. The majority of surviving defects are C interstitials, as either C-Si or C-C dumbbells. The concentration of defect clusters increases with increasing dose, and their distributions are mainly observed along the GBs. Especially these small clusters can subsequently coalesce and form amorphous domains at the GBs during the accumulation of carbon defects. A comparison between displacement amorphized nc-SiC and melt-quenched single crystal SiC shows the similar topological features. At a dose of 0.55 displacements per atom (dpa), the pair correlation function lacks long range order, demonstrating that the nc-SiC is fully amorphilized. PMID:26558694

Mobility and coalescence of stacking fault tetrahedra in Cu

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

Martínez, Enrique; Uberuaga, Blas P.

Stacking fault tetrahedra (SFTs) are ubiquitous defects in face-centered cubic metals. They are produced during cold work plastic deformation, quenching experiments or under irradiation. From a dislocation point of view, the SFTs are comprised of a set of stair-rod dislocations at the (110) edges of a tetrahedron bounding triangular stacking faults. These defects are extremely stable, increasing their energetic stability as they grow in size. At the sizes visible within transmission electron microscope they appear nearly immobile. Contrary to common belief, we show in this report, using a combination of molecular dynamics and temperature accelerated dynamics, how small SFTs canmore » diffuse by temporarily disrupting their structure through activated thermal events. More over, we demonstrate that the diffusivity of defective SFTs is several orders of magnitude higher than perfect SFTs, and can be even higher than isolated vacancies. Finally, we show how SFTs can coalesce, forming a larger defect in what is a new mechanism for the growth of these omnipresent defects.« less

Mobility and coalescence of stacking fault tetrahedra in Cu

DOE PAGES

Martínez, Enrique; Uberuaga, Blas P.

2015-03-13

Stacking fault tetrahedra (SFTs) are ubiquitous defects in face-centered cubic metals. They are produced during cold work plastic deformation, quenching experiments or under irradiation. From a dislocation point of view, the SFTs are comprised of a set of stair-rod dislocations at the (110) edges of a tetrahedron bounding triangular stacking faults. These defects are extremely stable, increasing their energetic stability as they grow in size. At the sizes visible within transmission electron microscope they appear nearly immobile. Contrary to common belief, we show in this report, using a combination of molecular dynamics and temperature accelerated dynamics, how small SFTs canmore » diffuse by temporarily disrupting their structure through activated thermal events. More over, we demonstrate that the diffusivity of defective SFTs is several orders of magnitude higher than perfect SFTs, and can be even higher than isolated vacancies. Finally, we show how SFTs can coalesce, forming a larger defect in what is a new mechanism for the growth of these omnipresent defects.« less

Mobility and coalescence of stacking fault tetrahedra in Cu

PubMed Central

Martínez, Enrique; Uberuaga, Blas P.

2015-01-01

Stacking fault tetrahedra (SFTs) are ubiquitous defects in face-centered cubic metals. They are produced during cold work plastic deformation, quenching experiments or under irradiation. From a dislocation point of view, the SFTs are comprised of a set of stair-rod dislocations at the (110) edges of a tetrahedron bounding triangular stacking faults. These defects are extremely stable, increasing their energetic stability as they grow in size. At the sizes visible within transmission electron microscope they appear nearly immobile. Contrary to common belief, we show in this report, using a combination of molecular dynamics and temperature accelerated dynamics, how small SFTs can diffuse by temporarily disrupting their structure through activated thermal events. More over, we demonstrate that the diffusivity of defective SFTs is several orders of magnitude higher than perfect SFTs, and can be even higher than isolated vacancies. Finally, we show how SFTs can coalesce, forming a larger defect in what is a new mechanism for the growth of these omnipresent defects. PMID:25765711

Grain boundary resistance to amorphization of nanocrystalline silicon carbide.

PubMed

Chen, Dong; Gao, Fei; Liu, Bo

2015-11-12

Under the C displacement condition, we have used molecular dynamics simulation to examine the effects of grain boundaries (GBs) on the amorphization of nanocrystalline silicon carbide (nc-SiC) by point defect accumulation. The results show that the interstitials are preferentially absorbed and accumulated at GBs that provide the sinks for defect annihilation at low doses, but also driving force to initiate amorphization in the nc-SiC at higher doses. The majority of surviving defects are C interstitials, as either C-Si or C-C dumbbells. The concentration of defect clusters increases with increasing dose, and their distributions are mainly observed along the GBs. Especially these small clusters can subsequently coalesce and form amorphous domains at the GBs during the accumulation of carbon defects. A comparison between displacement amorphized nc-SiC and melt-quenched single crystal SiC shows the similar topological features. At a dose of 0.55 displacements per atom (dpa), the pair correlation function lacks long range order, demonstrating that the nc-SiC is fully amorphilized.

Hydrogen defects in α-Al2O3 and water weakening of sapphire and alumina ceramics between 600 and 1000°C: I. Infrared characterization of defects

USGS Publications Warehouse

Kronenberg, A.K.; Castaing, J.; Mitchell, T.E.; Kirby, S.H.

2000-01-01

Hydrogen impurities in materials influence their properties, including flow strength. α-Al2O3 single crystals and polycrystalline ceramics were annealed in supercritical water between 850 and 1025°C, under pressures in the range 1500–2000 MPa. A few specimens were further subjected to plastic deformation. Hydrogen penetration was examined using infrared absorption measurements of O–H bond vibrations, which revealed two kinds of hydrogen defects. In single crystals, defects are characterized by sharp O–H absorption bands assigned to interstitial protons. Hydrogen impurities of hydrothermally annealed ceramics and of all hydrothermally deformed specimens are characterized by broad O–H bands assigned to molecular water. The grain boundaries of hydrothermally annealed ceramics are severely damaged. The kinetics of hydrogen penetration is consistent with diffusion data.

A Matter of the Heart: The African Clawed Frog Xenopus as a Model for Studying Vertebrate Cardiogenesis and Congenital Heart Defects

PubMed Central

Hempel, Annemarie; Kühl, Michael

2016-01-01

The African clawed frog, Xenopus, is a valuable non-mammalian model organism to investigate vertebrate heart development and to explore the underlying molecular mechanisms of human congenital heart defects (CHDs). In this review, we outline the similarities between Xenopus and mammalian cardiogenesis, and provide an overview of well-studied cardiac genes in Xenopus, which have been associated with congenital heart conditions. Additionally, we highlight advantages of modeling candidate genes derived from genome wide association studies (GWAS) in Xenopus and discuss commonly used techniques. PMID:29367567

Defect phase diagram for doping of Ga2O3

NASA Astrophysics Data System (ADS)

Lany, Stephan

2018-04-01

For the case of n-type doping of β-Ga2O3 by group 14 dopants (C, Si, Ge, Sn), a defect phase diagram is constructed from defect equilibria calculated over a range of temperatures (T), O partial pressures (pO2), and dopant concentrations. The underlying defect levels and formation energies are determined from first-principles supercell calculations with GW bandgap corrections. Only Si is found to be a truly shallow donor, C is a deep DX-like (lattice relaxed donor) center, and Ge and Sn have defect levels close to the conduction band minimum. The thermodynamic modeling includes the effect of association of dopant-defect pairs and complexes, which causes the net doping to decline when exceeding a certain optimal dopant concentration. The optimal doping levels are surprisingly low, between about 0.01% and 1% of cation substitution, depending on the (T, pO2) conditions. Considering further the stability constraints due to sublimation of molecular Ga2O, specific predictions of optimized pO2 and Si dopant concentrations are given. The incomplete passivation of dopant-defect complexes in β-Ga2O3 suggests a design rule for metastable doping above the solubility limit.

Mapping strain rate dependence of dislocation-defect interactions by atomistic simulations

PubMed Central

Fan, Yue; Osetskiy, Yuri N.; Yip, Sidney; Yildiz, Bilge

2013-01-01

Probing the mechanisms of defect–defect interactions at strain rates lower than 106 s−1 is an unresolved challenge to date to molecular dynamics (MD) techniques. Here we propose an original atomistic approach based on transition state theory and the concept of a strain-dependent effective activation barrier that is capable of simulating the kinetics of dislocation–defect interactions at virtually any strain rate, exemplified within 10−7 to 107 s−1. We apply this approach to the problem of an edge dislocation colliding with a cluster of self-interstitial atoms (SIAs) under shear deformation. Using an activation–relaxation algorithm [Kushima A, et al. (2009) J Chem Phys 130:224504], we uncover a unique strain-rate–dependent trigger mechanism that allows the SIA cluster to be absorbed during the process, leading to dislocation climb. Guided by this finding, we determine the activation barrier of the trigger mechanism as a function of shear strain, and use that in a coarse-graining rate equation formulation for constructing a mechanism map in the phase space of strain rate and temperature. Our predictions of a crossover from a defect recovery at the low strain-rate regime to defect absorption behavior in the high strain-rate regime are validated against our own independent, direct MD simulations at 105 to 107 s−1. Implications of the present approach for probing molecular-level mechanisms in strain-rate regimes previously considered inaccessible to atomistic simulations are discussed. PMID:24114271

The impact of substrate selection for the controlled growth of graphene by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Schumann, T.; Lopes, J. M. J.; Wofford, J. M.; Oliveira, M. H.; Dubslaff, M.; Hanke, M.; Jahn, U.; Geelhaar, L.; Riechert, H.

2015-09-01

We examine how substrate selection impacts the resulting film properties in graphene growth by molecular beam epitaxy (MBE). Graphene growth on metallic as well as dielectric templates was investigated. We find that MBE offers control over the number of atomic graphene layers regardless of the substrate used. High structural quality could be achieved for graphene prepared on Ni (111) films which were epitaxially grown on MgO (111). For growth either on Al2O3 (0001) or on (6√3×6√3)R30°-reconstructed SiC (0001) surfaces, graphene with a higher density of defects is obtained. Interestingly, despite their defective nature, the layers possess a well defined epitaxial relation to the underlying substrate. These results demonstrate the feasibility of MBE as a technique for realizing the scalable synthesis of this two-dimensional crystal on a variety of substrates.

Classical Molecular Dynamics Simulation of Nuclear Fuel

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

Devanathan, Ram; Krack, Matthias; Bertolus, Marjorie

2015-10-10

Molecular dynamics simulation is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermo-mechanical properties. In these simulations, the forces on the ions are dictated by interaction potentials generated by fitting properties of interest to experimental data. The results obtained from the present generation of potentials are qualitatively similar, but quantitatively different. There is a need to refine existing potentials to provide a better representation of the performance of polycrystalline fuel under a varietymore » of operating conditions, and to develop models that are equipped to handle deviations from stoichiometry. In addition to providing insights into fundamental mechanisms governing the behaviour of nuclear fuel, MD simulations can also provide parameters that can be used as inputs for mesoscale models.« less

Molecular genetic studies in a case series of isolated hypoaldosteronism due to biosynthesis defects or aldosterone resistance.

PubMed

Turan, Ihsan; Kotan, Leman Damla; Tastan, Mehmet; Gurbuz, Fatih; Topaloglu, Ali Kemal; Yuksel, Bilgin

2018-06-01

Hypoaldosteronism is associated with either insufficient aldosterone production or aldosterone resistance (pseudohypoaldosteronism). Patients with aldosterone defects typically present with similar symptoms and findings, which include failure to thrive, vomiting, hyponatremia, hyperkalemia and metabolic acidosis. Accurate diagnosis of these clinical conditions therefore can be challenging. Molecular genetic analyses can help to greatly clarify this complexity. The aim of this study was to obtain an overview of the clinical and genetic characteristics of patients with aldosterone defects due to biosynthesis defects or aldosterone resistance. We investigated the clinical and molecular genetic features of 8 consecutive patients with a clinical picture of aldosterone defects seen in our clinics during the period of May 2015 through October 2017. We screened CYP11B2 for aldosterone synthesis defects and NR3C2 and the three EnaC subunits (SCNN1A, SCNN1B and SCNN1G) for aldosterone resistance. We found 4 novel and 2 previously reported mutations in the genes CYP11B2, NR3C2, SCNN1A and SCNN1G in 9 affected individuals from 7 unrelated families. Molecular genetic investigations can help confidently diagnose these conditions and clarify the pathogenicity of aldosterone defects. This study may expand the clinical and genetic correlations of defects in aldosterone synthesis or resistance. © 2018 John Wiley & Sons Ltd.

Effect of strain field on displacement cascade in tungsten studied by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Wang, D.; Gao, N.; Wang, Z. G.; Gao, X.; He, W. H.; Cui, M. H.; Pang, L. L.; Zhu, Y. B.

2016-10-01

Using atomistic methods, the coupling effect of strain field and displacement cascade in body-centered cubic (BCC) tungsten is directly simulated by molecular dynamics (MD) simulations at different temperatures. The values of the hydrostatic and uniaxial (parallel or perpendicular to primary knock-on atom (PKA) direction) strains are from -2% to 2% and the temperature is from 100 to 1000 K. Because of the annealing effect, the influence of strain on radiation damage at low temperature has been proved to be more significant than that at high temperature. When the cascade proceeds under the hydrostatic strain, the Frenkel Pair (FP) production, the fraction of defect in cluster and the average size of the defect cluster, all increase at tensile state and decrease at compressive state. When the cascade is under uniaxial strain, the effect of strain parallel to PKA direction is less than the effect of hydrostatic strain, while the effect of strain perpendicular to PKA direction can be negligible. Under the uniaxial strain along <1 1 1> direction, the SIA and SIA cluster is observed to orientate along the strain direction at tensile state and the uniaxial compressive strain with direction perpendicular to <1 1 1> has led to the similar preferred nucleation. All these results indicate that under irradiation, the tensile state should be avoided for materials used in nuclear power plants.

Structural evolution dynamics in fusion of sumanenes and corannulenes: defects formation and self-healing mechanism

NASA Astrophysics Data System (ADS)

Sorkin, Anastassia; Su, Haibin

2018-06-01

The fusion processes of structures consisting of various combinations between sumanene and corannulene, leading to the formation of graphene nanoribbons (GNRs) under heating are simulated by density-functional-based tight-binding molecular dynamics. Distinct stages are unraveled in the course of GNR formation. Firstly, the carbon fragments coalescence into highly strained framework. Secondly, structural reconstruction invokes breaking most strained bonds to form a GNR structure containing numerous defects. Lastly, defects are remedied by the delicate ‘edge-facilitated self-healing’ process through two synergized edge-related effects: elevated mobility of defects and promoted structure reconstructions owing to the remarkable dynamics associated with edges. Importantly, detailed dynamics in the course of forming GNRs with defects and grain boundaries simulated in this work is valuable to provide better understanding at the atomistic scale of defect formation as well as self-healing in the context of the sp2 carbon network. In particular, edges play important roles in not only generating Stone–Wales (SW), 5-8-5 types of defects, 8-5-5-8 and pentagon–heptagon grain boundaries. In addition, our simulations predict the existence of one novel defect, coined as the Inverse SW defect, which is to be confirmed in future experimental studies. This study of dynamic structural evolution reveals that edges are prone to intrinsic and extrinsic modifications such as atomic-scale defects, structural distortions and inhomogeneity.

Adipose Tissue as a Strategic Source of Mesenchymal Stem Cells in Bone Regeneration: A Topical Review on the Most Promising Craniomaxillofacial Applications

PubMed Central

Marrelli, Massimo; Amantea, Massimiliano; Rengo, Carlo; Rengo, Sandro; Goldberg, Michel; Spagnuolo, Gianrico

2017-01-01

Bone regeneration in craniomaxillofacial surgery represents an issue that involves both surgical and aesthetic aspects. The most recent studies on bone tissue engineering involving adipose-derived stromal/stem cells (ASCs) have clearly demonstrated that such cells can play a crucial role in the treatment of craniomaxillofacial defects, given their strong commitment towards the osteogenic phenotype. A deeper knowledge of the molecular mechanisms underlying ASCs is crucial for a correct understanding of the potentialities of ASCs-based therapies in the most complex maxillofacial applications. In this topical review, we analyzed the molecular mechanisms of ASCs related to their support toward angiogenesis and osteogenesis, during bone regeneration. Moreover, we analyzed both case reports and clinical trials reporting the most promising clinical applications of ASCs in the treatment of craniomaxillofacial defects. Our study aimed to report the main molecular and clinical features shown by ASCs, used as a therapeutic support in bone engineering, as compared to the use of conventional autologous and allogeneic bone grafts. PMID:29027958

Accuracy of existing atomic potentials for the CdTe semiconductor compound

NASA Astrophysics Data System (ADS)

Ward, D. K.; Zhou, X. W.; Wong, B. M.; Doty, F. P.; Zimmerman, J. A.

2011-06-01

CdTe and CdTe-based Cd1-xZnxTe (CZT) alloys are important semiconductor compounds that are used in a variety of technologies including solar cells, radiation detectors, and medical imaging devices. Performance of such systems, however, is limited due to the propensity of nano- and micro-scale defects that form during crystal growth and manufacturing processes. Molecular dynamics simulations offer an effective approach to study the formation and interaction of atomic scale defects in these crystals, and provide insight on how to minimize their concentrations. The success of such a modeling effort relies on the accuracy and transferability of the underlying interatomic potential used in simulations. Such a potential must not only predict a correct trend of structures and energies of a variety of elemental and compound lattices, defects, and surfaces but also capture correct melting behavior and should be capable of simulating crystalline growth during vapor deposition as these processes sample a variety of local configurations. In this paper, we perform a detailed evaluation of the performance of two literature potentials for CdTe, one having the Stillinger-Weber form and the other possessing the Tersoff form. We examine simulations of structures and the corresponding energies of a variety of elemental and compound lattices, defects, and surfaces compared to those obtained from ab initio calculations and experiments. We also perform melting temperature calculations and vapor deposition simulations. Our calculations show that the Stillinger-Weber parameterization produces the correct lowest energy structure. This potential, however, is not sufficiently transferrable for defect studies. Origins of the problems of these potentials are discussed and insights leading to the development of a more transferrable potential suitable for molecular dynamics simulations of defects in CdTe crystals are provided.

Update on Foregut Molecular Embryology and Role of Regenerative Medicine Therapies

PubMed Central

Perin, Silvia; McCann, Conor J.; Borrelli, Osvaldo; De Coppi, Paolo; Thapar, Nikhil

2017-01-01

Esophageal atresia (OA) represents one of the commonest and most severe developmental disorders of the foregut, the most proximal segment of the gastrointestinal (GI) tract (esophagus and stomach) in embryological terms. Of intrigue is the common origin from this foregut of two very diverse functional entities, the digestive and respiratory systems. OA appears to result from incomplete separation of the ventral and dorsal parts of the foregut during development, resulting in disruption of esophageal anatomy and frequent association with tracheo-oesophageal fistula. Not surprisingly, and likely inherent to OA, are associated abnormalities in components of the enteric neuromusculature and ultimately loss of esophageal functional integrity. An appreciation of such developmental processes and associated defects has not only enhanced our understanding of the etiopathogenesis underlying such devastating defects but also highlighted the potential of novel corrective therapies. There has been considerable progress in the identification and propagation of neural crest stem cells from the GI tract itself or derived from pluripotent cells. Such cells have been successfully transplanted into models of enteric neuropathy confirming their ability to functionally integrate and replenish missing or defective enteric nerves. Combinatorial approaches in tissue engineering hold significant promise for the generation of organ-specific scaffolds such as the esophagus with current initiatives directed toward their cellularization to facilitate optimal function. This chapter outlines the most current understanding of the molecular embryology underlying foregut development and OA, and also explores the promise of regenerative medicine. PMID:28503544

Update on Foregut Molecular Embryology and Role of Regenerative Medicine Therapies.

PubMed

Perin, Silvia; McCann, Conor J; Borrelli, Osvaldo; De Coppi, Paolo; Thapar, Nikhil

2017-01-01

Esophageal atresia (OA) represents one of the commonest and most severe developmental disorders of the foregut, the most proximal segment of the gastrointestinal (GI) tract (esophagus and stomach) in embryological terms. Of intrigue is the common origin from this foregut of two very diverse functional entities, the digestive and respiratory systems. OA appears to result from incomplete separation of the ventral and dorsal parts of the foregut during development, resulting in disruption of esophageal anatomy and frequent association with tracheo-oesophageal fistula. Not surprisingly, and likely inherent to OA, are associated abnormalities in components of the enteric neuromusculature and ultimately loss of esophageal functional integrity. An appreciation of such developmental processes and associated defects has not only enhanced our understanding of the etiopathogenesis underlying such devastating defects but also highlighted the potential of novel corrective therapies. There has been considerable progress in the identification and propagation of neural crest stem cells from the GI tract itself or derived from pluripotent cells. Such cells have been successfully transplanted into models of enteric neuropathy confirming their ability to functionally integrate and replenish missing or defective enteric nerves. Combinatorial approaches in tissue engineering hold significant promise for the generation of organ-specific scaffolds such as the esophagus with current initiatives directed toward their cellularization to facilitate optimal function. This chapter outlines the most current understanding of the molecular embryology underlying foregut development and OA, and also explores the promise of regenerative medicine.

Defect-Engineered Heat Transport in Graphene: A Route to High Efficient Thermal Rectification

PubMed Central

Zhao, Weiwei; Wang, Yanlei; Wu, Zhangting; Wang, Wenhui; Bi, Kedong; Liang, Zheng; Yang, Juekuan; Chen, Yunfei; Xu, Zhiping; Ni, Zhenhua

2015-01-01

Low-dimensional materials such as graphene provide an ideal platform to probe the correlation between thermal transport and lattice defects, which could be engineered at the molecular level. In this work, we perform molecular dynamics simulations and non-contact optothermal Raman measurements to study this correlation. We find that oxygen plasma treatment could reduce the thermal conductivity of graphene significantly even at extremely low defect concentration (∼83% reduction for ∼0.1% defects), which could be attributed mainly to the creation of carbonyl pair defects. Other types of defects such as hydroxyl, epoxy groups and nano-holes demonstrate much weaker effects on the reduction where the sp2 nature of graphene is better preserved. With the capability of selectively functionalizing graphene, we propose an asymmetric junction between graphene and defective graphene with a high thermal rectification ratio of ∼46%, as demonstrated by our molecular dynamics simulation results. Our findings provide fundamental insights into the physics of thermal transport in defective graphene, and two-dimensional materials in general, which could help on the future design of functional applications such as optothermal and electrothermal devices. PMID:26132747

Single-layer 1T‧-MoS2 under electron irradiation from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Pizzochero, Michele; Yazyev, Oleg V.

2018-04-01

Irradiation with high-energy particles has recently emerged as an effective tool for tailoring the properties of two-dimensional transition metal dichalcogenides. In order to carry out an atomically-precise manipulation of the lattice, a detailed understanding of the beam-induced events occurring at the atomic scale is necessary. Here, we investigate the response of 1T' -MoS2 to the electron irradiation by ab initio molecular dynamics means. Our simulations suggest that an electron beam with energy smaller than 75 keV does not result in any knock-on damage. The displacement threshold energies are different for the two nonequivalent sulfur atoms in 1T' -MoS2 and strongly depend on whether the top or bottom chalcogen layer is considered. As a result, a careful tuning of the beam energy can promote the formation of ordered defects in the sample. We further discuss the effect of the electron irradiation in the neighborhood of a defective site, the mobility of the sulfur vacancies created and their tendency to aggregate. Overall, our work provides useful guidelines for the imaging and the defect engineering of 1T' -MoS2 using electron microscopy.

Radiation damage buildup by athermal defect reactions in nickel and concentrated nickel alloys

DOE PAGES

Zhang, S.; Nordlund, K.; Djurabekova, F.; ...

2017-04-12

We develop a new method using binary collision approximation simulating the Rutherford backscattering spectrometry in channeling conditions (RBS/C) from molecular dynamics atom coordinates of irradiated cells. The approach allows comparing experimental and simulated RBS/C signals as a function of depth without fitting parameters. The simulated RBS/C spectra of irradiated Ni and concentrated solid solution alloys (CSAs, NiFe and NiCoCr) show a good agreement with the experimental results. The good agreement indicates the damage evolution under damage overlap conditions in Ni and CSAs at room temperature is dominated by defect recombination and migration induced by irradiation rather than activated thermally.

Cystic fibrosis.

PubMed

O'Sullivan, Brian P; Freedman, Steven D

2009-05-30

Cystic fibrosis is the most common lethal genetic disease in white populations. The outlook for patients with the disease has improved steadily over many years, largely as a result of earlier diagnosis, more aggressive therapy, and provision of care in specialised centres. Researchers now have a more complete understanding of the molecular-biological defect that underlies cystic fibrosis, which is leading to new approaches to treatment. One of these treatments, hypertonic saline, is already in use, whereas others are in advanced stages of development. We review clinical care for cystic fibrosis and discuss recent advances in the understanding of its pathogenesis, implementation of screening of neonates, and development of therapies aimed at treating the basic defect.

Molecular dynamics simulation of low-energy recoil events in titanate pyrochlores

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

Dong, Liyuan; Setyawan, Wahyu; Li, Yuhong

2017-01-01

Molecular dynamics simulations of low-energy displacements in titanate pyrochlores have been carried out along three main directions, to determineE dfor A, Ti and O, corresponding defect configurations, and defect formation dynamics.

Defect controlled magnetism in FeP/graphene/Ni(111)

PubMed Central

Bhandary, Sumanta; Eriksson, Olle; Sanyal, Biplab

2013-01-01

Spin switching of organometallic complexes by ferromagnetic surfaces is an important topic in the area of molecular nanospintronics. Moreover, graphene has been shown as a 2D surface for physisorption of molecular magnets and strain engineering on graphene can tune the spin state of an iron porphyrin (FeP) molecule from S = 1 to S = 2. Our ab initio density functional calculations suggest that a pristine graphene layer placed between a Ni(111) surface and FeP yields an extremely weak exchange interaction between FeP and Ni whereas the introduction of defects in graphene shows a variety of ferromagnetic and antiferromagnetic exchange interactions. Moreover, these defects control the easy axes of magnetization, strengths of magnetic anisotropy energies and spin-dipolar contributions. Our study suggests a new way of manipulating molecular magnetism by defects in graphene and hence has the potential to be explored in designing spin qubits to realize logic operations in molecular nanospintronics. PMID:24296980

Effects of vacancies on atom displacement threshold energy calculations through Molecular Dynamics Methods in BaTiO3

NASA Astrophysics Data System (ADS)

Gonzalez Lazo, Eduardo; Cruz Inclán, Carlos M.; Rodríguez Rodríguez, Arturo; Guzmán Martínez, Fernando; Abreu Alfonso, Yamiel; Piñera Hernández, Ibrahin; Leyva Fabelo, Antonio

2017-09-01

A primary approach for evaluating the influence of point defects like vacancies on atom displacement threshold energies values Td in BaTiO3 is attempted. For this purpose Molecular Dynamics Methods, MD, were applied based on previous Td calculations on an ideal tetragonal crystalline structure. It is an important issue in achieving more realistic simulations of radiation damage effects in BaTiO3 ceramic materials. It also involves irradiated samples under severe radiation damage effects due to high fluency expositions. In addition to the above mentioned atom displacement events supported by a single primary knock-on atom, PKA, a new mechanism was introduced. It corresponds to the simultaneous excitation of two close primary knock-on atoms in BaTiO3, which might take place under a high flux irradiation. Therefore, two different BaTiO3 Td MD calculation trials were accomplished. Firstly, single PKA excitations in a defective BaTiO3 tetragonal crystalline structure, consisting in a 2×2×2 BaTiO3 perovskite like super cell, were considered. It contains vacancies on Ba and O atomic positions under the requirements of electrical charge balance. Alternatively, double PKA excitations in a perfect BaTiO3 tetragonal unit cell were also simulated. On this basis, the corresponding primary knock-on atom (PKA) defect formation probability functions were calculated at principal crystal directions, and compared with the previous one we calculated and reported at an ideal BaTiO3 tetrahedral crystal structure. As a general result, a diminution of Td values arises in present calculations in comparison with those calculated for single PKA excitation in an ideal BaTiO3 crystal structure.

Wnt signaling in caudal dysgenesis and diabetic embryopathy

PubMed Central

Pavlinkova, Gabriela; Salbaum, J. Michael; Kappen, Claudia

2010-01-01

Congenital defects are a major complication of diabetic pregnancy, and the leading cause of infant death in the first year of life. Caudal dysgenesis, occurring up to 200-fold more frequently in children born to diabetic mothers, is a hallmark of diabetic pregnancy. Given that there is also an at least 3-fold higher risk for heart defects and neural tube defects, it is important to identify the underlying molecular mechanisms for aberrant embryonic development. We have investigated gene expression in a transgenic mouse model of caudal dysgenesis, and in a pharmacological model using situ hybridization and quantitative real-time PCR. We identify altered expression of several molecules that control developmental processes and embryonic growth. The results from our models point towards major implication of altered Wnt signaling in the pathogenesis of developmental anomalies associated with embryonic exposure to maternal diabetes. PMID:18937363

Molecular medicine: a path towards a personalized medicine.

PubMed

Miranda, Debora Marques de; Mamede, Marcelo; Souza, Bruno Rezende de; Almeida Barros, Alexandre Guimarães de; Magno, Luiz Alexandre; Alvim-Soares, Antônio; Rosa, Daniela Valadão; Castro, Célio José de; Malloy-Diniz, Leandro; Gomez, Marcus Vinícius; Marco, Luiz Armando De; Correa, Humberto; Romano-Silva, Marco Aurélio

2012-03-01

Psychiatric disorders are among the most common human illnesses; still, the molecular and cellular mechanisms underlying their complex pathophysiology remain to be fully elucidated. Over the past 10 years, our group has been investigating the molecular abnormalities in major signaling pathways involved in psychiatric disorders. Recent evidences obtained by the Instituto Nacional de Ciência e Tecnologia de Medicina Molecular (National Institute of Science and Technology - Molecular Medicine, INCT-MM) and others using behavioral analysis of animal models provided valuable insights into the underlying molecular alterations responsible for many complex neuropsychiatric disorders, suggesting that "defects" in critical intracellular signaling pathways have an important role in regulating neurodevelopment, as well as in pathophysiology and treatment efficacy. Resources from the INCT have allowed us to start doing research in the field of molecular imaging. Molecular imaging is a research discipline that visualizes, characterizes, and quantifies the biologic processes taking place at cellular and molecular levels in humans and other living systems through the results of image within the reality of the physiological environment. In order to recognize targets, molecular imaging applies specific instruments (e.g., PET) that enable visualization and quantification in space and in real-time of signals from molecular imaging agents. The objective of molecular medicine is to individualize treatment and improve patient care. Thus, molecular imaging is an additional tool to achieve our ultimate goal.

The plastic response of Tantalum in Quasi-Isentropic Compression Ramp and Release

NASA Astrophysics Data System (ADS)

Moore, Alexander; Brown, Justin; Lim, Hojun; Lane, J. Matthew D.

2017-06-01

The mechanical response of various forms of tantalum under extreme pressures and strain rates is studied using dynamic quasi-isentropic compression loading conditions in atomistic simulations. Ramp compression in bcc metals under these conditions tend to show a significant strengthening effect with increasing pressure; however, due to limitations of experimental methods in such regimes, the underlying physics for this phenomenon is not well understood. Molecular dynamics simulations provide important information about the plasticity mechanisms and can be used to investigate this strengthening. MD simulations are performed on nanocrystalline Ta and single crystal defective Ta with dislocations and point defects to uncover how the material responds and the underlying plasticity mechanisms. The different systems of solid Ta are seen to plastically deform through different mechanisms. Fundamental understanding of tantalum plasticity in these high pressure and strain rate regimes is needed to model and fully understand experimental results. Sandia National Labs is a multi program laboratory managed and operated by Sandia Corp., a wholly owned subsidiary of Lockheed Martin Corp., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

A Theoretical Simulation of the Radiation Responses of Si, Ge, and Si/Ge Superlattice to Low-Energy Irradiation.

PubMed

Jiang, Ming; Xiao, Haiyan; Peng, Shuming; Yang, Guixia; Liu, Zijiang; Qiao, Liang; Zu, Xiaotao

2018-05-02

In this study, the low-energy radiation responses of Si, Ge, and Si/Ge superlattice are investigated by an ab initio molecular dynamics method and the origins of their different radiation behaviors are explored. It is found that the radiation resistance of the Ge atoms that are around the interface of Si/Ge superlattice is comparable to bulk Ge, whereas the Si atoms around the interface are more difficult to be displaced than the bulk Si, showing enhanced radiation tolerance as compared with the bulk Si. The mechanisms for defect generation in the bulk and superlattice structures show somewhat different character, and the associated defects in the superlattice are more complex. Defect formation and migration calculations show that in the superlattice structure, the point defects are more difficult to form and the vacancies are less mobile. The enhanced radiation tolerance of the Si/Ge superlattice will benefit for its applications as electronic and optoelectronic devices under radiation environment.

A Theoretical Simulation of the Radiation Responses of Si, Ge, and Si/Ge Superlattice to Low-Energy Irradiation

NASA Astrophysics Data System (ADS)

Jiang, Ming; Xiao, Haiyan; Peng, Shuming; Yang, Guixia; Liu, Zijiang; Qiao, Liang; Zu, Xiaotao

2018-05-01

In this study, the low-energy radiation responses of Si, Ge, and Si/Ge superlattice are investigated by an ab initio molecular dynamics method and the origins of their different radiation behaviors are explored. It is found that the radiation resistance of the Ge atoms that are around the interface of Si/Ge superlattice is comparable to bulk Ge, whereas the Si atoms around the interface are more difficult to be displaced than the bulk Si, showing enhanced radiation tolerance as compared with the bulk Si. The mechanisms for defect generation in the bulk and superlattice structures show somewhat different character, and the associated defects in the superlattice are more complex. Defect formation and migration calculations show that in the superlattice structure, the point defects are more difficult to form and the vacancies are less mobile. The enhanced radiation tolerance of the Si/Ge superlattice will benefit for its applications as electronic and optoelectronic devices under radiation environment.

Flagellar motility is critical for Listeria monocytogenes biofilm formation.

PubMed

Lemon, Katherine P; Higgins, Darren E; Kolter, Roberto

2007-06-01

The food-borne pathogen Listeria monocytogenes attaches to environmental surfaces and forms biofilms that can be a source of food contamination, yet little is known about the molecular mechanisms of its biofilm development. We observed that nonmotile mutants were defective in biofilm formation. To investigate how flagella might function during biofilm formation, we compared the wild type with flagellum-minus and paralyzed-flagellum mutants. Both nonmotile mutants were defective in biofilm development, presumably at an early stage, as they were also defective in attachment to glass during the first few hours of surface exposure. This attachment defect could be significantly overcome by providing exogenous movement toward the surface via centrifugation. However, this centrifugation did not restore mature biofilm formation. Our results indicate that it is flagellum-mediated motility that is critical for both initial surface attachment and subsequent biofilm formation. Also, any role for L. monocytogenes flagella as adhesins on abiotic surfaces appears to be either minimal or motility dependent under the conditions we examined.

Enthalpy Landscape Dictates the Irradiation-Induced Disordering of Quartz

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

Krishnan, N. M. Anoop; Wang, Bu; Yu, Yingtian

Here, under irradiation, minerals tend to experience an accumulation of structural defects, ultimately leading to a disordered atomic network. Despite the critical importance of understanding and predicting irradiation-induced damage, the physical origin of the initiation and saturation of defects remains poorly understood. Here, based on molecular dynamics simulations of α-quartz, we show that the topography of the enthalpy landscape governs irradiation-induced disordering. Specifically, we show that such disordering differs from that observed upon vitrification in that, prior to saturation, irradiated quartz accesses forbidden regions of the enthalpy landscape, i.e., those that are inaccessible by simply heating and cooling. Furthermore, wemore » demonstrate that damage saturates when the system accesses a local region of the enthalpy landscape corresponding to the configuration of an allowable liquid. At this stage, a sudden decrease in the heights of the energy barriers enhances relaxation, thereby preventing any further accumulation of defects and resulting in a defect-saturated disordered state.« less

Enthalpy Landscape Dictates the Irradiation-Induced Disordering of Quartz

DOE PAGES

Krishnan, N. M. Anoop; Wang, Bu; Yu, Yingtian; ...

2017-07-28

Here, under irradiation, minerals tend to experience an accumulation of structural defects, ultimately leading to a disordered atomic network. Despite the critical importance of understanding and predicting irradiation-induced damage, the physical origin of the initiation and saturation of defects remains poorly understood. Here, based on molecular dynamics simulations of α-quartz, we show that the topography of the enthalpy landscape governs irradiation-induced disordering. Specifically, we show that such disordering differs from that observed upon vitrification in that, prior to saturation, irradiated quartz accesses forbidden regions of the enthalpy landscape, i.e., those that are inaccessible by simply heating and cooling. Furthermore, wemore » demonstrate that damage saturates when the system accesses a local region of the enthalpy landscape corresponding to the configuration of an allowable liquid. At this stage, a sudden decrease in the heights of the energy barriers enhances relaxation, thereby preventing any further accumulation of defects and resulting in a defect-saturated disordered state.« less

Field-enhanced route to generating anti-Frenkel pairs in HfO2

NASA Astrophysics Data System (ADS)

Schie, Marcel; Menzel, Stephan; Robertson, John; Waser, Rainer; De Souza, Roger A.

2018-03-01

The generation of anti-Frenkel pairs (oxygen vacancies and oxygen interstitials) in monoclinic and cubic HfO2 under an applied electric field is examined. A thermodynamic model is used to derive an expression for the critical field strength required to generate an anti-Frenkel pair. The critical field strength of EaFcr˜101GVm-1 obtained for HfO2 exceeds substantially the field strengths routinely employed in the forming and switching operations of resistive switching HfO2 devices, suggesting that field-enhanced defect generation is negligible. Atomistic simulations with molecular static (MS) and molecular dynamic (MD) approaches support this finding. The MS calculations indicated a high formation energy of Δ EaF≈8 eV for the infinitely separated anti-Frenkel pair, and only a decrease to Δ EaF≈6 eV for the adjacent anti-Frenkel pair. The MD simulations showed no defect generation in either phase for E <3 GVm-1 , and only sporadic defect generation in the monoclinic phase (at E =3 GVm-1 ) with fast (trec<4 ps ) recombination. At even higher E but below EaFcr both monoclinic and cubic structures became unstable as a result of field-induced deformation of the ionic potential wells. Further MD investigations starting with preexisting anti-Frenkel pairs revealed recombination of all pairs within trec<1 ps , even for the case of neutral vacancies and charged interstitials, for which formally there is no electrostatic attraction between the defects. In conclusion, we find no physically reasonable route to generating point-defects in HfO2 by an applied field.

Pax2 regulates a fadd-dependent molecular switch that drives tissue fusion during eye development.

PubMed

Viringipurampeer, Ishaq A; Ferreira, Todd; DeMaria, Shannon; Yoon, Jookyung J; Shan, Xianghong; Moosajee, Mariya; Gregory-Evans, Kevin; Ngai, John; Gregory-Evans, Cheryl Y

2012-05-15

Tissue fusion is an essential morphogenetic mechanism in development, playing a fundamental role in developing neural tube, palate and the optic fissure. Disruption of genes associated with the tissue fusion can lead to congenital malformations, such as spina bifida, cleft lip/palate and ocular coloboma. For instance, the Pax2 transcription factor is required for optic fissure closure, although the mechanism of Pax2 action leading to tissue fusion remains elusive. This lack of information defining how transcription factors drive tissue morphogenesis at the cellular level is hampering new treatments options. Through loss- and gain-of-function analysis, we now establish that pax2 in combination with vax2 directly regulate the fas-associated death domain (fadd) gene. In the presence of fadd, cell proliferation is restricted in the developing eye through a caspase-dependent pathway. However, the loss of fadd results in a proliferation defect and concomitant activation of the necroptosis pathway through RIP1/RIP3 activity, leading to an abnormal open fissure. Inhibition of RIP1 with the small molecule drug necrostatin-1 rescues the pax2 eye fusion defect, thereby overcoming the underlying genetic defect. Thus, fadd has an essential physiological function in protecting the developing optic fissure neuroepithelium from RIP3-dependent necroptosis. This study demonstrates the molecular hierarchies that regulate a cellular switch between proliferation and the apoptotic and necroptotic cell death pathways, which in combination drive tissue morphogenesis. Furthermore, our data suggest that future therapeutic strategies may be based on small molecule drugs that can bypass the gene defects causing common congenital tissue fusion defects.

Defect phase diagram for doping of Ga 2O 3

DOE PAGES

Lany, Stephan

2018-04-01

For the case of n-type doping of β-Ga 2O 3 by group 14 dopants (C, Si, Ge, Sn), a defect phase diagram is constructed from defect equilibria calculated over a range of temperatures (T), O partial pressures (pO 2), and dopant concentrations. The underlying defect levels and formation energies are determined from first-principles supercell calculations with GW bandgap corrections. Only Si is found to be a truly shallow donor, C is a deep DX-like (lattice relaxed donor) center, and Ge and Sn have defect levels close to the conduction band minimum. The thermodynamic modeling includes the effect of association ofmore » dopant-defect pairs and complexes, which causes the net doping to decline when exceeding a certain optimal dopant concentration. The optimal doping levels are surprisingly low, between about 0.01% and 1% of cation substitution, depending on the (T, pO 2) conditions. Considering further the stability constraints due to sublimation of molecular Ga 2O, specific predictions of optimized pO 2 and Si dopant concentrations are given. To conclude, the incomplete passivation of dopant-defect complexes in β-Ga 2O 3 suggests a design rule for metastable doping above the solubility limit.« less

Direct Observation of Defect Range and Evolution in Ion-Irradiated Single Crystalline Ni and Ni Binary Alloys.

PubMed

Lu, Chenyang; Jin, Ke; Béland, Laurent K; Zhang, Feifei; Yang, Taini; Qiao, Liang; Zhang, Yanwen; Bei, Hongbin; Christen, Hans M; Stoller, Roger E; Wang, Lumin

2016-02-01

Energetic ions have been widely used to evaluate the irradiation tolerance of structural materials for nuclear power applications and to modify material properties. It is important to understand the defect production, annihilation and migration mechanisms during and after collision cascades. In this study, single crystalline pure nickel metal and single-phase concentrated solid solution alloys of 50%Ni50%Co (NiCo) and 50%Ni50%Fe (NiFe) without apparent preexisting defect sinks were employed to study defect dynamics under ion irradiation. Both cross-sectional transmission electron microscopy characterization (TEM) and Rutherford backscattering spectrometry channeling (RBS-C) spectra show that the range of radiation-induced defect clusters far exceed the theoretically predicted depth in all materials after high-dose irradiation. Defects in nickel migrate faster than in NiCo and NiFe. Both vacancy-type stacking fault tetrahedra (SFT) and interstitial loops coexist in the same region, which is consistent with molecular dynamics simulations. Kinetic activation relaxation technique (k-ART) simulations for nickel showed that small vacancy clusters, such as di-vacancies and tri-vacancies, created by collision cascades are highly mobile, even at room temperature. The slower migration of defects in the alloy along with more localized energy dissipation of the displacement cascade may lead to enhanced radiation tolerance.

Direct Observation of Defect Range and Evolution in Ion-Irradiated Single Crystalline Ni and Ni Binary Alloys

PubMed Central

Lu, Chenyang; Jin, Ke; Béland, Laurent K.; Zhang, Feifei; Yang, Taini; Qiao, Liang; Zhang, Yanwen; Bei, Hongbin; Christen, Hans M.; Stoller, Roger E.; Wang, Lumin

2016-01-01

Energetic ions have been widely used to evaluate the irradiation tolerance of structural materials for nuclear power applications and to modify material properties. It is important to understand the defect production, annihilation and migration mechanisms during and after collision cascades. In this study, single crystalline pure nickel metal and single-phase concentrated solid solution alloys of 50%Ni50%Co (NiCo) and 50%Ni50%Fe (NiFe) without apparent preexisting defect sinks were employed to study defect dynamics under ion irradiation. Both cross-sectional transmission electron microscopy characterization (TEM) and Rutherford backscattering spectrometry channeling (RBS-C) spectra show that the range of radiation-induced defect clusters far exceed the theoretically predicted depth in all materials after high-dose irradiation. Defects in nickel migrate faster than in NiCo and NiFe. Both vacancy-type stacking fault tetrahedra (SFT) and interstitial loops coexist in the same region, which is consistent with molecular dynamics simulations. Kinetic activation relaxation technique (k-ART) simulations for nickel showed that small vacancy clusters, such as di-vacancies and tri-vacancies, created by collision cascades are highly mobile, even at room temperature. The slower migration of defects in the alloy along with more localized energy dissipation of the displacement cascade may lead to enhanced radiation tolerance. PMID:26829570

Defect phase diagram for doping of Ga 2O 3

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

Lany, Stephan

For the case of n-type doping of β-Ga 2O 3 by group 14 dopants (C, Si, Ge, Sn), a defect phase diagram is constructed from defect equilibria calculated over a range of temperatures (T), O partial pressures (pO 2), and dopant concentrations. The underlying defect levels and formation energies are determined from first-principles supercell calculations with GW bandgap corrections. Only Si is found to be a truly shallow donor, C is a deep DX-like (lattice relaxed donor) center, and Ge and Sn have defect levels close to the conduction band minimum. The thermodynamic modeling includes the effect of association ofmore » dopant-defect pairs and complexes, which causes the net doping to decline when exceeding a certain optimal dopant concentration. The optimal doping levels are surprisingly low, between about 0.01% and 1% of cation substitution, depending on the (T, pO 2) conditions. Considering further the stability constraints due to sublimation of molecular Ga 2O, specific predictions of optimized pO 2 and Si dopant concentrations are given. To conclude, the incomplete passivation of dopant-defect complexes in β-Ga 2O 3 suggests a design rule for metastable doping above the solubility limit.« less

The intellectual capacity of patients with Laron syndrome (LS) differs with various molecular defects of the growth hormone receptor gene. Correlation with CNS abnormalities.

PubMed

Shevah, O; Kornreich, L; Galatzer, A; Laron, Z

2005-12-01

The correlation between the molecular defects of the GH receptor (R), psychosocial development and brain abnormalities were evaluated in 10 patients with Laron syndrome (LS), in whom all data were available. The findings revealed that the intelligence quotient (IQ) and abnormalities in the brain of the patients with LS differ with various molecular defects of the GH-receptor. The most severe mental deficits and brain pathology occurred in patients with 3, 5, 6 exon deletion. Patients with point mutations in exons 2, 4 and 7 presented various degrees of medium to mild CNS abnormalities that correlated with the IQ. Notably, the patient with the E180 splice mutation in exon 6 had a normal IQ, which fits the report on normal IQ in a large Ecuadorian cohort with the same mutation. This is the first report to support a correlation between IQ, brain abnormalities and localization of the molecular defects in the GH-R gene. As all patients with LS are IGF-I-deficient, it must be assumed that other as yet unknown factors related to the molecular defects in the GH-R are the major cause of the differences in intellect and brain abnormalities.

Microtubule defects influence kinesin-based transport in vitro.

NASA Astrophysics Data System (ADS)

Xu, Jing

Microtubules are protein polymers that form ``molecular highways'' for long-range transport within living cells. Molecular motors actively step along microtubules to shuttle cellular materials between the nucleus and the cell periphery; this transport is critical for the survival and health of all eukaryotic cells. Structural defects in microtubules exist, but whether these defects impact molecular motor-based transport remains unknown. Here, we report a new, to our knowledge, approach that allowed us to directly investigate the impact of such defects. Using a modified optical-trapping method, we examined the group function of a major molecular motor, conventional kinesin, when transporting cargos along individual microtubules. We found that microtubule defects influence kinesin-based transport in vitro. The effects depend on motor number: cargos driven by a few motors tended to unbind prematurely from the microtubule, whereas cargos driven by more motors tended to pause. To our knowledge, our study provides the first direct link between microtubule defects and kinesin function. The effects uncovered in our study may have physiological relevance in vivo. Supported by the UC Merced (to J.X.), NIH (NS048501 to S.J.K.), NSF (EF-1038697 to A.G.), and the James S. McDonnell Foundation (to A.G.). Work carried out at the Aspen Center for Physics was supported by NSF Grant PHY-1066293.

Genetic Testing as a New Standard for Clinical Diagnosis of Color Vision Deficiencies.

PubMed

Davidoff, Candice; Neitz, Maureen; Neitz, Jay

2016-09-01

The genetics underlying inherited color vision deficiencies is well understood: causative mutations change the copy number or sequence of the long (L), middle (M), or short (S) wavelength sensitive cone opsin genes. This study evaluated the potential of opsin gene analyses for use in clinical diagnosis of color vision defects. We tested 1872 human subjects using direct sequencing of opsin genes and a novel genetic assay that characterizes single nucleotide polymorphisms (SNPs) using the MassArray system. Of the subjects, 1074 also were given standard psychophysical color vision tests for a direct comparison with current clinical methods. Protan and deutan deficiencies were classified correctly in all subjects identified by MassArray as having red-green defects. Estimates of defect severity based on SNPs that control photopigment spectral tuning correlated with estimates derived from Nagel anomaloscopy. The MassArray assay provides genetic information that can be useful in the diagnosis of inherited color vision deficiency including presence versus absence, type, and severity, and it provides information to patients about the underlying pathobiology of their disease. The MassArray assay provides a method that directly analyzes the molecular substrates of color vision that could be used in combination with, or as an alternative to current clinical diagnosis of color defects.

Genetic Testing as a New Standard for Clinical Diagnosis of Color Vision Deficiencies

PubMed Central

Davidoff, Candice; Neitz, Maureen; Neitz, Jay

2016-01-01

Purpose The genetics underlying inherited color vision deficiencies is well understood: causative mutations change the copy number or sequence of the long (L), middle (M), or short (S) wavelength sensitive cone opsin genes. This study evaluated the potential of opsin gene analyses for use in clinical diagnosis of color vision defects. Methods We tested 1872 human subjects using direct sequencing of opsin genes and a novel genetic assay that characterizes single nucleotide polymorphisms (SNPs) using the MassArray system. Of the subjects, 1074 also were given standard psychophysical color vision tests for a direct comparison with current clinical methods. Results Protan and deutan deficiencies were classified correctly in all subjects identified by MassArray as having red–green defects. Estimates of defect severity based on SNPs that control photopigment spectral tuning correlated with estimates derived from Nagel anomaloscopy. Conclusions The MassArray assay provides genetic information that can be useful in the diagnosis of inherited color vision deficiency including presence versus absence, type, and severity, and it provides information to patients about the underlying pathobiology of their disease. Translational Relevance The MassArray assay provides a method that directly analyzes the molecular substrates of color vision that could be used in combination with, or as an alternative to current clinical diagnosis of color defects. PMID:27622081

A molecular dynamics study of thermal transport in nanoparticle doped Argon like solid

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

Shahadat, Muhammad Rubayat Bin, E-mail: rubayat37@gmail.com; Ahmed, Shafkat; Morshed, A. K. M. M.

2016-07-12

Interfacial phenomena such as mass and type of the interstitial atom, nano scale material defect influence heat transfer and the effect become very significant with the reduction of the material size. Non Equilibrium Molecular Dynamics (NEMD) simulation was carried out in this study to investigate the effect of the interfacial phenomena on solid. Argon like solid was considered in this study and LJ potential was used for atomic interaction. Nanoparticles of different masses and different molecular defects were inserted inside the solid. From the molecular simulation, it was observed that a large interfacial mismatch due to change in mass inmore » the homogenous solid causes distortion of the phonon frequency causing increase in thermal resistance. Position of the doped nanoparticles have more profound effect on the thermal conductivity of the solid whereas influence of the mass ratio is not very significant. Interstitial atom positioned perpendicular to the heat flow causes sharp reduction in thermal conductivity. Structural defect caused by the molecular defect (void) also observed to significantly affect the thermal conductivity of the solid.« less

Molecular dynamics simulations of high energy cascade in ordered alloys: Defect production and subcascade division

NASA Astrophysics Data System (ADS)

Crocombette, Jean-Paul; Van Brutzel, Laurent; Simeone, David; Luneville, Laurence

2016-06-01

Displacement cascades have been calculated in two ordered alloys (Ni3Al and UO2) in the molecular dynamics framework using the CMDC (Cell Molecular Dynamics for Cascade) code (J.-P. Crocombette and T. Jourdan, Nucl. Instrum. Meth. B 352, 9 (2015)) for energies ranking between 0.1 and 580 keV. The defect production has been compared to the prediction of the NRT (Norgett, Robinson and Torrens) standard. One observes a decrease with energy of the number of defects compared to the NRT prediction at intermediate energies but, unlike what is commonly observed in elemental solids, the number of produced defects does not always turn to a linear variation with ballistic energy at high energies. The fragmentation of the cascade into subcascades has been studied through the analysis of surviving defect pockets. It appears that the common knowledge equivalence of linearity of defect production and subcascades division does not hold in general for alloys. We calculate the average number of subcascades and average number of defects per subcascades as a function of ballistic energy. We find an unexpected variety of behaviors for these two average quantities above the threshold for subcascade formation.

In Situ Electrochemical Synthesis of Oriented and Defect-Free AEL Molecular-Sieve Films Using Ionic Liquids.

PubMed

Yu, Tongwen; Chu, Wenling; Cai, Rui; Liu, Yanchun; Yang, Weishen

2015-10-26

Simply preparing oriented and defect-free molecular-sieve films have been a long-standing challenge both in academia and industry. Most of the early works focus on the careful and multiple controls of the seeds layer or synthesis conditions. Herein, we report a one-step in situ electrochemical ionothermal method that combines a controllable electric field with ionic liquids. We demonstrate that an in-plane oriented and defect-free AEL (one molecular-sieve framework type) molecular-sieve film was obtained using an Al electrode as the Al source. The excellent corrosion-resistant performance of the film makes this technology promising in multiple applications, such as anti-corrosion coatings. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Primary radiation damage characterization of α-iron under irradiation temperature for various PKA energies

NASA Astrophysics Data System (ADS)

Sahi, Qurat-ul-ain; Kim, Yong-Soo

2018-04-01

The understanding of radiation-induced microstructural defects in body-centered cubic (BCC) iron is of major interest to those using advanced steel under extreme conditions in nuclear reactors. In this study, molecular dynamics (MD) simulations were implemented to examine the primary radiation damage in BCC iron with displacement cascades of energy 1, 5, 10, 20, and 30 keV at temperatures ranging from 100 to 1000 K. Statistical analysis of eight MD simulations of collision cascades were carried out along each [110], [112], [111] and a high index [135] direction and the temperature dependence of the surviving number of point defects and the in-cascade clustering of vacancies and interstitials were studied. The peak time and the corresponding number of defects increase with increasing irradiation temperature and primary knock-on atom (PKA) energy. However, the final number of surviving point defects decreases with increasing lattice temperature. This is associated with the increase of thermal spike at high PKA energy and its long timespan at higher temperatures. Defect production efficiency (i.e., surviving MD defects, per Norgett-Robinson-Torrens displacements) also showed a continuous decrease with the increasing irradiation temperature and PKA energy. The number of interstitial clusters increases with both irradiation temperature and PKA energy. However, the increase in the number of vacancy clusters with PKA energy is minimal-to-constant and decreases as the irradiation temperature increases. Similarly, the probability and cluster size distribution for larger interstitials increase with temperature, whereas only smaller size vacancy clusters were observed at higher temperatures.

Low resistivity and low compensation ratio Ga-doped ZnO films grown by plasma-assisted molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Chen, Cheng-Yu; Hsiao, Li-Han; Chyi, Jen-Inn

2015-09-01

In this study, Ga-doped ZnO (GZO) thin films were deposited on GaN templates by using plasma-assisted molecular beam epitaxy. To obtain low resistivity GZO films, in-situ post-annealing under Zn overpressure was carried out to avoid the generation of acceptor-liked Zn vacancies. The resultant films showed optical transparency over 95% in the visible spectral range. By reducing the acceptor-like defects, GZO films with compensation ratio near 0.4 and resistivity simultaneously lower than 1×10-4 Ω cm have been successfully demonstrated.

Molecular defects of the growth hormone receptor gene, including a new mutation, in Laron syndrome patients in Israel: relationship between defects and ethnic groups.

PubMed

Shevah, Orit; Rubinstein, Menachem; Laron, Zvi

2004-10-01

Laron Syndrome, first described in Israel, is a form of dwarfism similar to isolated growth hormone deficiency caused by molecular defects in the GH receptor gene. To characterize the molecular defects of the GH-R in Laron syndrome patients followed in our clinic. Of the 63 patients in the cohort, we investigated 31 patients and 32 relatives belonging to several ethnic origins. Molecular analysis of the GH-R gene was performed using the single strand conformation polymorphism and DNA sequencing techniques. Eleven molecular defects including a novel mutation were found. Twenty-two patients carried mutations in the extracellular domain, one in the transmembrane domain, and 3 siblings with typical Laron syndrome presented a normal GH-R. Of interest are, on one hand, different mutations within the same ethnic groups: W-15X and 5, 6 exon deletion in Jewish-Iraqis, and E180 splice and 5, 6 exon deletion in Jewish-Moroccans; and on the other hand, identical findings in patients from distinct regions: the 785-1 G to T mutation in an Israeli-Druze and a Peruvian patient. A polymorphism in exon 6, Gly168Gly, was found in 15 probands. One typical Laron patient from Greece was heterozygous for R43X in exon 4 and heterozygous for Gly168Gly. In addition, a novel mutation in exon 5: substitution of T to G replacing tyrosine 86 for aspartic acid (Y86D) is described. This study demonstrates: a) an increased focal incidence of Laron syndrome in different ethnic groups from our area with a high incidence of consanguinity; and b) a relationship between molecular defects of the GH-R, ethnic group and geographic area.

Understanding the Role of TSC1/2 in Cerebellar Purkinje Neurons

DTIC Science & Technology

2016-09-01

development of new pharmacotherapy for TSC-patients with autism . 15. SUBJECT TERMS autism , tuberous sclerosis, cerebellum 16. SECURITY CLASSIFICATION...patients with TSC display symptoms of autism spectrum disorder (ASD). Although much research has been conducted, the neural circuitry and molecular...mechanism underlying autism remain unclear. Specific cerebellar defects have been seen in TSC patients, suggesting a crucial role for the cerebellum

Multiscale crystal defect dynamics: A coarse-grained lattice defect model based on crystal microstructure

NASA Astrophysics Data System (ADS)

Lyu, Dandan; Li, Shaofan

2017-10-01

Crystal defects have microstructure, and this microstructure should be related to the microstructure of the original crystal. Hence each type of crystals may have similar defects due to the same failure mechanism originated from the same microstructure, if they are under the same loading conditions. In this work, we propose a multiscale crystal defect dynamics (MCDD) model that models defects by considering its intrinsic microstructure derived from the microstructure or material genome of the original perfect crystal. The main novelties of present work are: (1) the discrete exterior calculus and algebraic topology theory are used to construct a scale-up (coarse-grained) dual lattice model for crystal defects, which may represent all possible defect modes inside a crystal; (2) a higher order Cauchy-Born rule (up to the fourth order) is adopted to construct atomistic-informed constitutive relations for various defect process zones, and (3) an hierarchical strain gradient theory based finite element formulation is developed to support an hierarchical multiscale cohesive (process) zone model for various defects in a unified formulation. The efficiency of MCDD computational algorithm allows us to simulate dynamic defect evolution at large scale while taking into account atomistic interaction. The MCDD model has been validated by comparing of the results of MCDD simulations with that of molecular dynamics (MD) in the cases of nanoindentation and uniaxial tension. Numerical simulations have shown that MCDD model can predict dislocation nucleation induced instability and inelastic deformation, and thus it may provide an alternative solution to study crystal plasticity.

The impact of environmental stress on male reproductive development in plants: biological processes and molecular mechanisms

PubMed Central

de Storme, Nico; Geelen, Danny

2014-01-01

In plants, male reproductive development is extremely sensitive to adverse climatic environments and (a)biotic stress. Upon exposure to stress, male gametophytic organs often show morphological, structural and metabolic alterations that typically lead to meiotic defects or premature spore abortion and male reproductive sterility. Depending on the type of stress involved (e.g. heat, cold, drought) and the duration of stress exposure, the underlying cellular defect is highly variable and either involves cytoskeletal alterations, tapetal irregularities, altered sugar utilization, aberrations in auxin metabolism, accumulation of reactive oxygen species (ROS; oxidative stress) or the ectopic induction of programmed cell death (PCD). In this review, we present the critically stress-sensitive stages of male sporogenesis (meiosis) and male gametogenesis (microspore development), and discuss the corresponding biological processes involved and the resulting alterations in male reproduction. In addition, this review also provides insights into the molecular and/or hormonal regulation of the environmental stress sensitivity of male reproduction and outlines putative interaction(s) between the different processes involved. PMID:23731015

Paracentric Inversion of Chromosome 21 Leading to Disruption of the HLCS Gene in a Family with Holocarboxylase Synthetase Deficiency.

PubMed

Quinonez, Shane C; Seeley, Andrea H; Lam, Cindy; Glover, Thomas W; Barshop, Bruce A; Keegan, Catherine E

2017-01-01

Holocarboxylase synthetase (HLCS) deficiency is a rare autosomal recessive disorder that presents with multiple life-threatening metabolic derangements including metabolic acidosis, ketosis, and hyperammonemia. A majority of HLCS deficiency patients respond to biotin therapy; however, some patients show only a partial or no response to biotin therapy. Here, we report a neonatal presentation of HLCS deficiency with partial response to biotin therapy. Sequencing of HLCS showed a novel heterozygous mutation in exon 5, c.996G>C (p.Gln332His), which likely abolishes the normal intron 6 splice donor site. Cytogenetic analysis revealed that the defect of the other allele is a paracentric inversion on chromosome 21 that disrupts HLCS. This case illustrates that in addition to facilitating necessary family testing, a molecular diagnosis can optimize management by providing a better explanation of the enzyme's underlying defect. It also emphasizes the potential benefit of a karyotype in cases in which molecular genetic testing fails to provide an explanation.

Cockayne syndrome: Clinical features, model systems and pathways

PubMed Central

Karikkineth, Ajoy C.; Scheibye-Knudsen, Morten; Fivenson, Elayne; Croteau, Deborah L.; Bohr, Vilhelm A.

2016-01-01

Cockayne syndrome (CS) is a disorder characterized by a variety of clinical features including cachectic dwarfism, severe neurological manifestations including microcephaly and cognitive deficits, pigmentary retinopathy, cataracts, sensorineural deafness, and ambulatory and feeding difficulties, leading to death by 12 years of age on average. It is an autosomal recessive disorder, with a prevalence of approximately 2.5 per million. There are several phenotypes (1, 2 and 3) and complementation groups (CSA and CSB), and overlaps with xeroderma pigmentosum (XP). It has been considered a progeria, and many of the clinical features resemble accelerated aging. As such, the study of CS affords an opportunity to better understand the underlying mechanisms of aging. The molecular basis of CS has traditionally been considered to be due to defects in transcription and transcription-coupled nucleotide excision repair (TC-NER). However, recent work suggests that defects in base excision DNA repair and mitochondrial functions may also play key roles. This opens up the possibility of molecular interventions in CS, and by extrapolation, possibly in aging. PMID:27507608

Profilin1 activity in cerebellar granule neurons is required for radial migration in vivo

PubMed Central

Kullmann, Jan A; Wickertsheim, Ines; Minnerup, Lara; Costell, Mercedes; Friauf, Eckhard; Rust, Marco B

2015-01-01

Neuron migration defects are an important aspect of human neuropathies. The underlying molecular mechanisms of such migration defects are largely unknown. Actin dynamics has been recognized as an important determinant of neuronal migration, and we recently found that the actin-binding protein profilin1 is relevant for radial migration of cerebellar granule neurons (CGN). As the exploited brain-specific mutants lacked profilin1 in both neurons and glial cells, it remained unknown whether profilin1 activity in CGN is relevant for CGN migration in vivo. To test this, we capitalized on a transgenic mouse line that expresses a tamoxifen-inducible Cre variant in CGN, but no other cerebellar cell type. In these profilin1 mutants, the cell density was elevated in the molecular layer, and ectopic CGN occurred. Moreover, 5-bromo-2′-deoxyuridine tracing experiments revealed impaired CGN radial migration. Hence, our data demonstrate the cell autonomous role of profilin1 activity in CGN for radial migration. PMID:25495756

Oxidation of InP nanowires: a first principles molecular dynamics study.

PubMed

Berwanger, Mailing; Schoenhalz, Aline L; Dos Santos, Cláudia L; Piquini, Paulo

2016-11-16

InP nanowires are candidates for optoelectronic applications, and as protective capping layers of III-V core-shell nanowires. Their surfaces are oxidized under ambient conditions which affects the nanowire physical properties. The majority of theoretical studies of InP nanowires, however, do not take into account the oxide layer at their surfaces. In this work we use first principles molecular dynamics electronic structure calculations to study the first steps in the oxidation process of a non-saturated InP nanowire surface as well as the properties of an already oxidized surface of an InP nanowire. Our calculations show that the O 2 molecules dissociate through several mechanisms, resulting in incorporation of O atoms into the surface layers. The results confirm the experimental observation that the oxidized layers become amorphous but the non-oxidized core layers remain crystalline. Oxygen related bonds at the oxidized layers introduce defective levels at the band gap region, with greater contributions from defects involving In-O and P-O bonds.

Peeling skin syndrome: genetic defects in late terminal differentiation of the epidermis.

PubMed

Bowden, Paul E

2011-03-01

In this issue, Israeli and colleagues confirm that homozygous mutations in corneodesmosin (CDSN) cause type B peeling skin syndrome (PSS), an autosomal recessive skin disorder. The deletion mutation described resulted in a frameshift, producing a downstream premature stop codon and early truncation of the protein. The recently described CDSN nonsense mutation in another PSS family also resulted in protein truncation and nonsense-mediated mRNA decay. Type B generalized PSS can now be clearly distinguished from acral PSS, caused by mutations in transglutaminase 5. This directly affects cornified envelope cross-linking rather than corneodesmosome adherence. These observations provide new insight into the molecular defects underlying two closely related forms of PSS.

Investigating Alkylsilane Monolayer Tribology at a Single-Asperity Contact with Molecular Dynamics Simulation.

PubMed

Summers, Andrew Z; Iacovella, Christopher R; Cummings, Peter T; McCabe, Clare

2017-10-24

Chemisorbed monolayer films are known to possess favorable characteristics for nanoscale lubrication of micro- and nanoelectromechanical systems (MEMS/NEMS). Prior studies have shown that the friction observed for monolayer-coated surfaces features a strong dependence on the geometry of contact. Specifically, tip-like geometries have been shown to penetrate into monolayer films, inducing defects in the monolayer chains and leading to plowing mechanisms during shear, which result in higher coefficients of friction (COF) than those observed for planar geometries. In this work, we use molecular dynamics simulations to examine the tribology of model silica single-asperity contacts under shear with monolayer-coated substrates featuring various film densities. It is observed that lower monolayer densities lead to reduced COFs, in contrast to results for planar systems where COF is found to be nearly independent of monolayer density. This is attributed to a liquid-like response to shear, whereby fewer defects are imparted in monolayer chains from the asperity, and chains are easily displaced by the tip as a result of the higher free volume. This transition in the mechanism of molecular plowing suggests that liquid-like films should provide favorable lubrication at single-asperity contacts.

Semiconductors Under Ion Radiation: Ultrafast Electron-Ion Dynamics in Perfect Crystals and the Effect of Defects

NASA Astrophysics Data System (ADS)

Lee, Cheng-Wei; Schleife, André

Stability and safety issues have been challenging difficulties for materials and devices under radiation such as solar panels in outer space. On the other hand, radiation can be utilized to modify materials and increase their performance via focused-ion beam patterning at nano-scale. In order to grasp the underlying processes, further understanding of the radiation-material and radiation-defect interactions is required and inevitably involves the electron-ion dynamics that was traditionally hard to capture. By applying Ehrenfest dynamics based on time-dependent density functional theory, we have been able to perform real-time simulation of electron-ion dynamics in MgO and InP/GaP. By simulating a high-energy proton penetrating the material, the energy gain of electronic system can be interpreted as electronic stopping power and the result is compared to existing data. We also study electronic stopping in the vicinity of defects: for both oxygen vacancy in MgO and interface of InP/GaP superlattice, electronic stopping shows strong dependence on the velocity of the proton. To study the energy transfer from electronic system to lattice, simulations of about 100 femto-seconds are performed and we analyze the difference between Ehrenfest and Born-Oppenheimer molecular dynamics.

Suppression of planar defects in the molecular beam epitaxy of GaAs/ErAs/GaAs heterostructures

NASA Astrophysics Data System (ADS)

Crook, Adam M.; Nair, Hari P.; Ferrer, Domingo A.; Bank, Seth R.

2011-08-01

We present a growth method that overcomes the mismatch in rotational symmetry of ErAs and conventional III-V semiconductors, allowing for epitaxially integrated semimetal/semiconductor heterostructures. Transmission electron microscopy and reflection high-energy electron diffraction reveal defect-free overgrowth of ErAs layers, consisting of >2× the total amount of ErAs that can be embedded with conventional layer-by-layer growth methods. We utilize epitaxial ErAs nanoparticles, overgrown with GaAs, as a seed to grow full films of ErAs. Growth proceeds by diffusion of erbium atoms through the GaAs spacer, which remains registered to the underlying substrate, preventing planar defect formation during subsequent GaAs growth. This growth method is promising for metal/semiconductor heterostructures that serve as embedded Ohmic contacts to epitaxial layers and epitaxially integrated active plasmonic devices.

Evaluation of Surface Cleaning of Si(211) for Molecular-Beam Epitaxy Deposition of Infrared Detectors

NASA Astrophysics Data System (ADS)

Jaime-Vasquez, M.; Jacobs, R. N.; Benson, J. D.; Stoltz, A. J.; Almeida, L. A.; Bubulac, L. O.; Chen, Y.; Brill, G.

2010-07-01

We report an assessment of the reproducibility of the HF cleaning process and As passivation prior to the nucleation of ZnTe on the Si(211) surface using temperature desorption spectroscopy, ion scattering spectroscopy, and electron spectroscopy. Observations suggest full H coverage of the Si(211) surface with mostly monohydride and small amounts of dihydride states, and that F is uniformly distributed across the top layer as a physisorbed species. Variations in major contaminants are observed across the Si surface and at the CdTe-ZnTe/Si interface. Defects act as getters for impurities present on the Si surface, and some are buried under the CdTe/ZnTe heterostructure. Overall, the data show evidence of localized concentration of major impurities around defects, supporting the hypothesis of a physical model explaining the electrical activation of defects in long-wave infrared (LWIR) HgCdTe/CdTe/Si devices.

Hole generation associated with intrinsic defects in SOI-based SiGe thin films formed by solid-source molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Satoh, Motoki; Arimoto, Keisuke; Yamanaka, Junji; Sawano, Kentarou; Shiraki, Yasuhiro; Nakagawa, Kiyokazu

2018-04-01

The electronic properties of SiGe on insulator (SGOI) structure are under intense investigation due to its importance as an electronic material. In the previous investigations, a p-type conduction was observed in SGOI even in the absence of extrinsic chemical acceptors, which is a serious problem for device applications. In this paper, the electrical properties of intrinsic-defect-related acceptor states generated during the SGOI formation are reported. It is found that freeze-out is hard to be achieved even at temperatures below 10 K, which indicates that the Fermi level lies near the valence band at low temperatures. With an aim to annihilate these defects, thermal annealing at 1050 °C for 12 h in N2 ambient was carried out. It was found that the thermal treatment is effective in reducing the densities of the acceptor states and in improving the crystalline quality.

Interaction of 〈1 0 0〉 dislocation loops with dislocations studied by dislocation dynamics in α-iron

NASA Astrophysics Data System (ADS)

Shi, X. J.; Dupuy, L.; Devincre, B.; Terentyev, D.; Vincent, L.

2015-05-01

Interstitial dislocation loops with Burgers vector of 〈1 0 0〉 type are formed in α-iron under neutron or heavy ion irradiation. As the density and size of these loops increase with radiation dose and temperature, these defects are thought to play a key role in hardening and subsequent embrittlement of iron-based steels. The aim of the present work is to study the pinning strength of the loops on mobile dislocations. Prior to run massive Dislocation Dynamics (DD) simulations involving experimentally representative array of radiation defects and dislocations, the DD code and its parameterization are validated by comparing the individual loop-dislocation reactions with those obtained from direct atomistic Molecular Dynamics (MD) simulations. Several loop-dislocation reaction mechanisms are successfully reproduced as well as the values of the unpinning stress to detach mobile dislocations from the defects.

Defect kinetics and resistance to amorphization in zirconium carbide

NASA Astrophysics Data System (ADS)

Zheng, Ming-Jie; Szlufarska, Izabela; Morgan, Dane

2015-02-01

To better understand the radiation response of zirconium carbide (ZrC), and in particular its excellent resistance to amorphization, we have used density functional theory methods to study the kinetics of point defects in ZrC. The migration barriers and recombination barriers of the simple point defects are calculated using the ab initio molecular dynamics simulation and the nudged elastic band method. These barriers are used to estimate C and Zr interstitial and vacancy diffusion and Frenkel pair recombination rates. A significant barrier for C Frenkel pair recombination is found but it is shown that a large concentration of C vacancies reduces this barrier dramatically, allowing facile healing of radiation damage. The mechanisms underlying high resistance to amorphization of ZrC were analyzed from the perspectives of structural, thermodynamic, chemical and kinetic properties. This study provides insights into the amorphization resistance of ZrC as well as a foundation for understanding general radiation damage in this material.

Primary radiation damage of an FeCr alloy under pressure: Atomistic simulation

NASA Astrophysics Data System (ADS)

Tikhonchev, M. Yu.; Svetukhin, V. V.

2017-05-01

The primary radiation damage of a binary FeCr alloy deformed by applied mechanical loading is studied by an atomistic molecular dynamics simulation. Loading is simulated by specifying an applied pressure of 0.25, 1.0, and 2.5 GPa of both signs. Hydrostatic and uniaxial loading is considered along the [001], [111], [112], and [210] directions. The influence of loading on the energy of point defect formation and the threshold atomic displacement energy in single-component bcc iron is investigated. The 10-keV atomic displacement cascades in a "random" binary Fe-9 at % Cr alloy are simulated at an initial temperature of 300 K. The number of the point defects generated in a cascade is estimated, and the clustering of point defects and the spatial orientation of interstitial configurations are analyzed. Our results agree with the results of other researchers and supplement them.

Protein Crystallization

NASA Technical Reports Server (NTRS)

Chernov, Alexander A.

2005-01-01

Nucleation, growth and perfection of protein crystals will be overviewed along with crystal mechanical properties. The knowledge is based on experiments using optical and force crystals behave similar to inorganic crystals, though with a difference in orders of magnitude in growing parameters. For example, the low incorporation rate of large biomolecules requires up to 100 times larger supersaturation to grow protein, rather than inorganic crystals. Nucleation is often poorly reproducible, partly because of turbulence accompanying the mixing of precipitant with protein solution. Light scattering reveals fluctuations of molecular cluster size, its growth, surface energies and increased clustering as protein ages. Growth most often occurs layer-by-layer resulting in faceted crystals. New molecular layer on crystal face is terminated by a step where molecular incorporation occurs. Quantitative data on the incorporation rate will be discussed. Rounded crystals with molecularly disordered interfaces will be explained. Defects in crystals compromise the x-ray diffraction resolution crucially needed to find the 3D atomic structure of biomolecules. The defects are immobile so that birth defects stay forever. All lattice defects known for inorganics are revealed in protein crystals. Contribution of molecular conformations to lattice disorder is important, but not studied. This contribution may be enhanced by stress field from other defects. Homologous impurities (e.g., dimers, acetylated molecules) are trapped more willingly by a growing crystal than foreign protein impurities. The trapped impurities induce internal stress eliminated in crystals exceeding a critical size (part of mni for ferritin, lysozyme). Lesser impurities are trapped from stagnant, as compared to the flowing, solution. Freezing may induce much more defects unless quickly amorphysizing intracrystalline water.

Motion of Fullerenes around Topological Defects on Metals: Implications for the Progress of Molecular Scale Devices.

PubMed

Nirmalraj, Peter; Daly, Ronan; Martin, Nazario; Thompson, Damien

2017-03-08

Research on motion of molecules in the presence of thermal noise is central for progress in two-terminal molecular scale electronic devices. However, it is still unclear what influence imperfections in bottom metal electrode surface can have on molecular motion. Here, we report a two-layer crowding study, detailing the early stages of surface motion of fullerene molecules on Au(111) with nanoscale pores in a n-tetradecane chemical environment. The motion of the fullerenes is directed by crowding of the underlying n-tetradecane molecules around the pore fringes at the liquid-solid interface. We observe in real-space the growth of molecular populations around different pore geometries. Supported by atomic-scale modeling, our findings extend the established picture of molecular crowding by revealing that trapped solvent molecules serve as prime nucleation sites at nanopore fringes.

Germ cell tumors: Insights from the Drosophila ovary and the mouse testis

PubMed Central

Salz, Helen K.; Dawson, Emily P.; Heaney, Jason D.

2017-01-01

SUMMARY Ovarian and testicular germ cell tumors of young adults are thought to arise from defects in germ cell development, but the molecular mechanisms underlying malignant transformation are poorly understood. In this review, we focus on the biology of germ cell tumor formation in the Drosophila ovary and the mouse testis, for which the evidence supports common underlying mechanisms such as blocking initiation into the differentiation pathway, impaired lineage progression, and sexual identity instability. We then discuss how these concepts inform our understanding of the disease in humans. PMID:28079292

Parent stress across molecular subtypes of children with Angelman syndrome.

PubMed

Miodrag, N; Peters, S

2015-09-01

Parenting stress has been consistently reported among parents of children with developmental disabilities. However, to date, no studies have investigated the impact of a molecular subtype of Angelman syndrome (AS) on parent stress, despite distinct phenotypic differences among subtypes. Data for 124 families of children with three subtypes of AS: class I and II deletions (n = 99), imprinting centre defects (IC defects; n = 11) and paternal uniparental disomy (UPD; n = 14) were drawn from the AS Rare Diseases Clinical Research Network (RDCRN) database and collected from five research sites across the Unites States. The AS study at the RDCRN gathered health information to understand how the syndrome develops and how to treat it. Parents completed questionnaires on their perceived psychological stress, the severity of children's aberrant behaviour and children's sleep patterns. Children's adaptive functioning and developmental levels were clinically evaluated. Child-related stress reached clinical levels for 40% of parents of children with deletions, 100% for IC defects and 64.3% for UPD. Sleep difficulties were similar and elevated across subtypes. There were no differences between molecular subtypes for overall child and parent-related stress. However, results showed greater isolation and lack of perceived parenting skills for parents of children with UPD compared with deletions. Better overall cognition for children with deletions was significantly related to more child-related stress while their poorer adaptive functioning was associated with more child-related stress. For all three groups, the severity of children's inappropriate behaviour was positively related to different aspects of stress. How parents react to stress depends, in part, on children's AS molecular subtype. Despite falling under the larger umbrella term of AS, it is important to acknowledge the unique aspects associated with children's molecular subtype. Identifying these factors can lead to tailored interventions that fit the particular needs of families of children with different AS subtypes. © 2015 MENCAP and International Association of the Scientific Study of Intellectual and Developmental Disabilities and John Wiley & Sons Ltd.

Molecular dynamics of shock loading of metals with defects

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

Belak, J.F.

1997-12-31

The finite rise time of shock waves in metals is commonly attributed to dissipative or viscous behavior of the metal. This viscous or plastic behavior is commonly attributed to the motion of defects such as dislocations. Despite this intuitive understanding, the experimental observation of defect motion or nucleation during shock loading has not been possible due to the short time scales involved. Molecular dynamics modeling with realistic interatomic potentials can provide some insight into defect motion during shock loading. However, until quite recently, the length scale required to accurately represent a metal with defects has been beyond the scope ofmore » even the most powerful supercomputers. Here, the author presents simulations of the shock response of single defects and indicate how simulation might provide some insight into the shock loading of metals.« less

Molecular Dynamics Modeling of PPTA Crystals in Aramid Fibers

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

Mercer, Brian Scott

2016-05-19

In this work, molecular dynamics modeling is used to study the mechanical properties of PPTA crystallites, which are the fundamental microstructural building blocks of polymer aramid bers such as Kevlar. Particular focus is given to constant strain rate axial loading simulations of PPTA crystallites, which is motivated by the rate-dependent mechanical properties observed in some experiments with aramid bers. In order to accommodate the covalent bond rupture that occurs in loading a crystallite to failure, the reactive bond order force eld ReaxFF is employed to conduct the simulations. Two major topics are addressed: The rst is the general behavior ofmore » PPTA crystallites under strain rate loading. Constant strain rate loading simulations of crystalline PPTA reveal that the crystal failure strain increases with increasing strain rate, while the modulus is not a ected by the strain rate. Increasing temperature lowers both the modulus and the failure strain. The simulations also identify the C N bond connecting the aromatic rings as weakest primary bond along the backbone of the PPTA chain. The e ect of chain-end defects on PPTA micromechanics is explored, and it is found that the presence of a chain-end defect transfers load to the adjacent chains in the hydrogen-bonded sheet in which the defect resides, but does not in uence the behavior of any other chains in the crystal. Chain-end defects are found to lower the strength of the crystal when clustered together, inducing bond failure via stress concentrations arising from the load transfer to bonds in adjacent chains near the defect site. The second topic addressed is the nature of primary and secondary bond failure in crystalline PPTA. Failure of both types of bonds is found to be stochastic in nature and driven by thermal uctuations of the bonds within the crystal. A model is proposed which uses reliability theory to model bonds under constant strain rate loading as components with time-dependent failure rate functions. The model is shown to work well for predicting the onset of primary backbone bond failure, as well as the onset of secondary bond failure via chain slippage for the case of isolated non-interacting chain-end defects.« less

Direct Observation of Defect Range and Evolution in Ion-Irradiated Single Crystalline Ni and Ni Binary Alloys

DOE PAGES

Lu, Chenyang; Jin, Ke; Béland, Laurent K.; ...

2016-02-01

We report that energetic ions have been widely used to evaluate the irradiation tolerance of structural materials for nuclear power applications and to modify material properties. It is important to understand the defect production, annihilation and migration mechanisms during and after collision cascades. In this study, single crystalline pure nickel metal and single-phase concentrated solid solution alloys of 50%Ni50%Co (NiCo) and 50%Ni50%Fe (NiFe) without apparent preexisting defect sinks were employed to study defect dynamics under ion irradiation. Both cross-sectional transmission electron microscopy characterization (TEM) and Rutherford backscattering spectrometry channeling (RBS-C) spectra show that the range of radiation-induced defect clusters farmore » exceed the theoretically predicted depth in all materials after high-dose irradiation. Defects in nickel migrate faster than in NiCo and NiFe. Both vacancy-type stacking fault tetrahedra (SFT) and interstitial loops coexist in the same region, which is consistent with molecular dynamics simulations. Kinetic activation relaxation technique (k-ART) simulations for nickel showed that small vacancy clusters, such as di-vacancies and tri-vacancies, created by collision cascades are highly mobile, even at room temperature. The slower migration of defects in the alloy along with more localized energy dissipation of the displacement cascade may lead to enhanced radiation tolerance.« less

Large-Scale Molecular Simulations on the Mechanical Response and Failure Behavior of a defective Graphene: Cases of 5-8-5 Defects

NASA Astrophysics Data System (ADS)

Wang, Shuaiwei; Yang, Baocheng; Yuan, Jinyun; Si, Yubing; Chen, Houyang

2015-10-01

Understanding the effect of defects on mechanical responses and failure behaviors of a graphene membrane is important for its applications. As examples, in this paper, a family of graphene with various 5-8-5 defects are designed and their mechanical responses are investigated by employing molecular dynamics simulations. The dependence of fracture strength and strain as well as Young’s moduli on the nearest neighbor distance and defect types is examined. By introducing the 5-8-5 defects into graphene, the fracture strength and strain become smaller. However, the Young’s moduli of DL (Linear arrangement of repeat unit 5-8-5 defect along zigzag-direction of graphene), DS (a Slope angle between repeat unit 5-8-5 defect and zigzag direction of graphene) and DZ (Zigzag-like 5-8-5 defects) defects in the zigzag direction become larger than those in the pristine graphene in the same direction. A maximum increase of 11.8% of Young’s modulus is obtained. Furthermore, the brittle cracking mechanism is proposed for the graphene with 5-8-5 defects. The present work may provide insights in controlling the mechanical properties by preparing defects in the graphene, and give a full picture for the applications of graphene with defects in flexible electronics and nanodevices.

Defect formation in fluoropolymer films at their condensation from a gas phase

NASA Astrophysics Data System (ADS)

Luchnikov, P. A.

2018-01-01

The questions of radiation defects, factors of influence of electronic high-frequency discharge plasma components on the molecular structure and properties of the fluoropolymer vacuum films synthesized on a substrate from a gas phase are considered. It is established that at sedimentation of fluoropolymer coverings from a gas phase in high-frequency discharge plasma in films there are radiation defects in molecular and supramolecular structure because of the influence of active plasma components which significantly influence their main properties.

Hole defects in molecular beam epitaxially grown p-GaAs introduced by alpha irradiation

NASA Astrophysics Data System (ADS)

Goodman, S. A.; Auret, F. D.; Meyer, W. E.

1994-01-01

Epitaxial aluminum Schottky barrier diodes on molecular beam epitaxially grown p-GaAs with a free carrier density of 2×1016 cm-3 were irradiated with alpha particles at room temperature using an americium-241 (Am-241) radio nuclide. For the first time, the radiation induced hole defects are characterized using conventional deep level transient spectroscopy (DLTS). The introduction rates and DLTS ``signatures'' of three prominent radiation induced defects Hα1, Hα4, and Hα5, situated 0.08, 0.20, and 0.30 eV above the valence band, respectively, are calculated and compared to those of similar defects introduced during electron irradiation.

Atomistic simulations to characterize the influence of applied strain and PKA energy on radiation damage evolution in pure aluminum

NASA Astrophysics Data System (ADS)

Sahi, Qurat-ul-ain; Kim, Yong-Soo

2018-05-01

Knowledge of defects generation, their mobility, growth rate, and spatial distribution is the cornerstone for understanding the surface and structural evolution of a material used under irradiation conditions. In this study, molecular dynamics simulations were used to investigate the coupled effect of primary knock-on atom (PKA) energy and applied strain (uniaxial and hydrostatic) fields on primary radiation damage evolution in pure aluminum. Cascade damage simulations were carried out for PKA energy ranging between 1 and 20 keV and for applied strain values ranging between -2% and 2% at the fixed temperature of 300 K. Simulation results showed that as the atomic displacement cascade proceeds under uniaxial and hydrostatic strains, the peak and surviving number of Frenkel point defects increases with increasing tension; however, these increments were more prominent under larger volume changing deformations (hydrostatic strain). The percentage fraction of point defects that aggregate into clusters increases under tension conditions; compared to the reference conditions with no strain, these increases are around 13% and 7% for interstitials and vacancies, respectively (under 2% uniaxial strain), and 19% and 11% for interstitials and vacancies, respectively (under 2% hydrostatic strain). Clusters formed of vacancies and interstitials were both larger under tensile strain conditions, with increases in both the average and maximum cluster sizes. The rate of increase/decrease in the number of Frenkel pairs, their clustering, and their size distributions under expansion/compression strain conditions were higher for higher PKA energies. Overall, the present results suggest that strain effects should be considered carefully in radiation damage environments, specifically for conditions of low temperature and high radiation energy. Compressive strain conditions could be beneficial for materials used in nuclear reactor power systems.

Simulating irradiation hardening in tungsten under fast neutron irradiation including Re production by transmutation

NASA Astrophysics Data System (ADS)

Huang, Chen-Hsi; Gilbert, Mark R.; Marian, Jaime

2018-02-01

Simulations of neutron damage under fusion energy conditions must capture the effects of transmutation, both in terms of accurate chemical inventory buildup as well as the physics of the interactions between transmutation elements and irradiation defect clusters. In this work, we integrate neutronics, primary damage calculations, molecular dynamics results, Re transmutation calculations, and stochastic cluster dynamics simulations to study neutron damage in single-crystal tungsten to mimic divertor materials. To gauge the accuracy and validity of the simulations, we first study the material response under experimental conditions at the JOYO fast reactor in Japan and the High Flux Isotope Reactor at Oak Ridge National Laboratory, for which measurements of cluster densities and hardening levels up to 2 dpa exist. We then provide calculations under expected DEMO fusion conditions. Several key mechanisms involving Re atoms and defect clusters are found to govern the accumulation of irradiation damage in each case. We use established correlations to translate damage accumulation into hardening increases and compare our results to the experimental measurements. We find hardening increases in excess of 5000 MPa in all cases, which casts doubts about the integrity of W-based materials under long-term fusion exposure.

Self-Healing Composite of Thermoset Polymer and Programmed Super Contraction Fibers

NASA Technical Reports Server (NTRS)

Li, Guoqiang (Inventor); Meng, Harper (Inventor)

2016-01-01

A composition comprising thermoset polymer, shape memory polymer to facilitate macro scale damage closure, and a thermoplastic polymer for molecular scale healing is disclosed; the composition has the ability to resolve structural defects by a bio-mimetic close-then heal process. In use, the shape memory polymer serves to bring surfaces of a structural defect into approximation, whereafter use of the thermoplastic polymer for molecular scale healing allowed for movement of the thermoplastic polymer into the defect and thus obtain molecular scale healing. The thermoplastic can be fibers, particles or spheres which are used by heating to a level at or above the thermoplastic's melting point, then cooling of the composition below the melting temperature of the thermoplastic. Compositions of the invention have the ability to not only close macroscopic defects, but also to do so repeatedly even if another wound/damage occurs in a previously healed/repaired area.

Heterogeneous Diagnoses Underlying Radial Ray Anomalies.

PubMed

Sevilla-Montoya, Rosalba; Aguinaga, Mónica; Martínez, Alejandro; Razo, Guadalupe; Molina, Bertha; Frías, Sara; Grether, Patricia

2017-03-01

To review perinatal Radial Ray Anomaly (RRA) cases born at the National Institute of Perinatology, Mexico, and to reveal the heterogeneous diagnoses of these patients. All patients with RRA over a 18 mo period were included; 4/15 were detected prenatally and 11/15 postnatally. Karyotype was performed for all patients with bilateral RRA; and chromosomal breakage analysis, when the karyotype was normal. Fifteen RRA patients were identified: one with trisomy 18, three with an isolated defect, six with monogenic disease, four with a genetic association and one with diabetic embryopathy. Five were stillborn and two died during the early neonatal period; all of whom presented with multiple defects. Three of the live born patients and one stillborn with multiple defects had Fanconi anemia. RRAs carry a high perinatal mortality rate (47%) when they occur in association with other defects. The assessment of these patients needs to involve the combined use of ultrasound, clinical, genetic, cytogenetic and molecular testing. The present results indicate that the chromosome breakage test should always be performed to rule out Fanconi anemia in this group.

Using molecular diagnostic testing to personalize the treatment of patients with gastrointestinal stromal tumors.

PubMed

Bannon, Amber E; Klug, Lillian R; Corless, Christopher L; Heinrich, Michael C

2017-05-01

The diagnosis and treatment of gastrointestinal stromal tumor (GIST) has emerged as a paradigm for modern cancer treatment ('precision medicine'), as it highlights the importance of matching molecular defects with specific therapies. Over the past two decades, the molecular classification and diagnostic work up of GIST has been radically transformed, accompanied by the development of molecular therapies for specific subgroups of GIST. This review summarizes the developments in the field of molecular diagnosis of GIST, particularly as they relate to optimizing medical therapy. Areas covered: Based on an extensive literature search of the molecular and clinical aspects of GIST, the authors review the most important developments in this field with an emphasis on the differential diagnosis of GIST including mutation testing, therapeutic implications of each molecular subtype, and emerging technologies relevant to the field. Expert commentary: The use of molecular diagnostics to classify GIST has been shown to be successful in optimizing patient treatment, but these methods remain under-utilized. In order to facilitate efficient and comprehensive molecular testing, the authors have developed a decision tree to aid clinicians.

Promoting the Adsorption of Metal Ions on Kaolinite by Defect Sites: A Molecular Dynamics Study

PubMed Central

Li, Xiong; Li, Hang; Yang, Gang

2015-01-01

Defect sites exist abundantly in minerals and play a crucial role for a variety of important processes. Here molecular dynamics simulations are used to comprehensively investigate the adsorption behaviors, stabilities and mechanisms of metal ions on defective minerals, considering different ionic concentrations, defect sizes and contents. Outer-sphere adsorbed Pb2+ ions predominate for all models (regular and defective), while inner-sphere Na+ ions, which exist sporadically only at concentrated solutions for regular models, govern the adsorption for all defective models. Adsorption quantities and stabilities of metal ions on kaolinite are fundamentally promoted by defect sites, thus explaining the experimental observations. Defect sites improve the stabilities of both inner- and outer-sphere adsorption, and (quasi) inner-sphere Pb2+ ions emerge only at defect sites that reinforce the interactions. Adsorption configurations are greatly altered by defect sites but respond weakly by changing defect sizes or contents. Both adsorption quantities and stabilities are enhanced by increasing defect sizes or contents, while ionic concentrations mainly affect adsorption quantities. We also find that adsorption of metal ions and anions can be promoted by each other and proceeds in a collaborative mechanism. Results thus obtained are beneficial to comprehend related processes for all types of minerals. PMID:26403873

Defect-induced solid state amorphization of molecular crystals

NASA Astrophysics Data System (ADS)

Lei, Lei; Carvajal, Teresa; Koslowski, Marisol

2012-04-01

We investigate the process of mechanically induced amorphization in small molecule organic crystals under extensive deformation. In this work, we develop a model that describes the amorphization of molecular crystals, in which the plastic response is calculated with a phase field dislocation dynamics theory in four materials: acetaminophen, sucrose, γ-indomethacin, and aspirin. The model is able to predict the fraction of amorphous material generated in single crystals for a given applied stress. Our results show that γ-indomethacin and sucrose demonstrate large volume fractions of amorphous material after sufficient plastic deformation, while smaller amorphous volume fractions are predicted in acetaminophen and aspirin, in agreement with experimental observation.

Effects of boron-nitride substrates on Stone-Wales defect formation in graphene: An ab initio molecular dynamics study

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

Jin, K.; Xiao, H. Y.; Zhang, Y.

2014-05-19

Ab initio molecular dynamics simulations are performed to investigate the effects of a boron nitride (BN) substrate on Stone-Wales (SW) defect formation and recovery in graphene. It is found that SW defects can be created by an off-plane recoil atom that interacts with the BN substrate. A mechanism with complete bond breakage for formation of SW defects in suspended graphene is also revealed for recoils at large displacement angles. In addition, further irradiation can result in recovery of the SW defects through a bond rotation mechanism in both graphene and graphene/BN, and the substrate has little effect on the recoverymore » process. This study indicates that the BN substrate enhances the irradiation resistance of graphene.« less

Skin symptoms in four ectodermal dysplasia syndromes including two case reports of Rapp-Hodgkin-Syndrome.

PubMed

Knaudt, Björn; Volz, Thomas; Krug, Markus; Burgdorf, Walter; Röcken, Martin; Berneburg, Mark

2012-01-01

The skin, hair and nail changes in four distinct ectodermal dysplasia syndromes are compared and reviewed. These syndromes comprise Christ-Siemens-Touraine syndrome; ectrodactyly, ectodermal dysplasia and cleft lip/palate syndrome; ankyloblepharon-ectodermal defects-cleft lip/palate syndrome and Rapp-Hodgkin syndrome. A comprehensive overview of the dermatological signs and symptoms in these syndromes was generated from the database of the Ectodermal Dysplasia Network Germany, the clinical findings in the patients seen in our department and an extensive review of the literature. The findings included abnormalities of skin, sweating, hair and nails. These clinical findings are discussed in relation to the underlying molecular defects known to play a role in these four ectodermal dysplasia syndromes.

CMV reactivation drives posttransplant T-cell reconstitution and results in defects in the underlying TCRβ repertoire

PubMed Central

Suessmuth, Yvonne; Mukherjee, Rithun; Watkins, Benjamin; Koura, Divya T.; Finstermeier, Knut; Desmarais, Cindy; Stempora, Linda; Horan, John T.; Langston, Amelia; Qayed, Muna; Khoury, Hanna J.; Grizzle, Audrey; Cheeseman, Jennifer A.; Conger, Jason A.; Robertson, Jennifer; Garrett, Aneesah; Kirk, Allan D.; Waller, Edmund K.; Blazar, Bruce R.; Mehta, Aneesh K.; Robins, Harlan S.

2015-01-01

Although cytomegalovirus (CMV) reactivation has long been implicated in posttransplant immune dysfunction, the molecular mechanisms that drive this phenomenon remain undetermined. To address this, we combined multiparameter flow cytometric analysis and T-cell subpopulation sorting with high-throughput sequencing of the T-cell repertoire, to produce a thorough evaluation of the impact of CMV reactivation on T-cell reconstitution after unrelated-donor hematopoietic stem cell transplant. We observed that CMV reactivation drove a >50-fold specific expansion of Granzyme Bhigh/CD28low/CD57high/CD8+ effector memory T cells (Tem) and resulted in a linked contraction of all naive T cells, including CD31+/CD4+ putative thymic emigrants. T-cell receptor β (TCRβ) deep sequencing revealed a striking contraction of CD8+ Tem diversity due to CMV-specific clonal expansions in reactivating patients. In addition to querying the topography of the expanding CMV-specific T-cell clones, deep sequencing allowed us, for the first time, to exhaustively evaluate the underlying TCR repertoire. Our results reveal new evidence for significant defects in the underlying CD8 Tem TCR repertoire in patients who reactivate CMV, providing the first molecular evidence that, in addition to driving expansion of virus-specific cells, CMV reactivation has a detrimental impact on the integrity and heterogeneity of the rest of the T-cell repertoire. This trial was registered at www.clinicaltrials.gov as #NCT01012492. PMID:25852054

Deep level transient spectroscopic investigation of phosphorus-doped silicon by self-assembled molecular monolayers.

PubMed

Gao, Xuejiao; Guan, Bin; Mesli, Abdelmadjid; Chen, Kaixiang; Dan, Yaping

2018-01-09

It is known that self-assembled molecular monolayer doping technique has the advantages of forming ultra-shallow junctions and introducing minimal defects in semiconductors. In this paper, we report however the formation of carbon-related defects in the molecular monolayer-doped silicon as detected by deep-level transient spectroscopy and low-temperature Hall measurements. The molecular monolayer doping process is performed by modifying silicon substrate with phosphorus-containing molecules and annealing at high temperature. The subsequent rapid thermal annealing drives phosphorus dopants along with carbon contaminants into the silicon substrate, resulting in a dramatic decrease of sheet resistance for the intrinsic silicon substrate. Low-temperature Hall measurements and secondary ion mass spectrometry indicate that phosphorus is the only electrically active dopant after the molecular monolayer doping. However, during this process, at least 20% of the phosphorus dopants are electrically deactivated. The deep-level transient spectroscopy shows that carbon-related defects are responsible for such deactivation.

Nanofiltration across Defect-Sealed Nanoporous Monolayer Graphene

DOE PAGES

O'Hern, Sean C.; Jang, Doojoon; Bose, Suman; ...

2015-04-27

Monolayer nanoporous graphene represents an ideal membrane for molecular separations, but its practical realization is impeded by leakage through defects in the ultrathin graphene. Here, we report a multiscale leakage-sealing process that exploits the nonpolar nature and impermeability of pristine graphene to selectively block defects, resulting in a centimeter-scale membrane that can separate two fluid reservoirs by an atomically thin layer of graphene. After introducing subnanometer pores in graphene, the membrane exhibited rejection of multivalent ions and small molecules and water flux consistent with prior molecular dynamics simulations. The results indicate the feasibility of constructing defect-tolerant monolayer graphene membranes formore » nanofiltration, desalination, and other separation processes.« less

MITOCHONDRIAL DISEASES PART III: THERAPEUTIC INTERVENTIONS IN MOUSE MODELS OF OXPHOS DEFICIENCIES

PubMed Central

Peralta, Susana; Torraco, Alessandra; Iommarini, Luisa; Diaz, Francisca

2015-01-01

Mitochondrial defects are the cause of numerous disorders affecting the oxidative phosphorylation system (OXPHOS) in humans leading predominantly to neurological and muscular degeneration. The molecular origin, manifestations, and progression of mitochondrial diseases have a broad spectrum, which makes very challenging to find a globally effective therapy. The study of the molecular mechanisms underlying the mitochondrial dysfunction indicates that there is a wide range of pathways, enzymes and molecules that could be potentially targeted for therapeutic purpose. Therefore, focusing on the pathology of the disease is essential to design new treatments. In this review, we will summarize and discuss the different therapeutic interventions tested in some mouse models of mitochondrial diseases laying emphasis on the molecular mechanisms of action and their potential applications. PMID:25638392

Variation of expression defects in cell surface 190-kDa protein antigen of Streptococcus mutans.

PubMed

Lapirattanakul, Jinthana; Nomura, Ryota; Matsumoto-Nakano, Michiyo; Srisatjaluk, Ratchapin; Ooshima, Takashi; Nakano, Kazuhiko

2015-05-01

Streptococcus mutans, which consists of four serotypes, c, e, f, and k, possesses a 190-kDa cell surface protein antigen (PA) for initial tooth adhesion. We used Western blot analysis to determine PA expression in 750 S. mutans isolates from 150 subjects and found a significantly higher prevalence of the isolates with PA expression defects in serotypes f and k compared to serotypes c and e. Moreover, the defect patterns could be classified into three types; no PA expression on whole bacterial cells and in their supernatant samples (Type N1), PA expression mainly seen in supernatant samples (Type N2), and only low expression of PA in the samples of whole bacterial cells (Type W). The underlying reasons for the defects were mutations in the gene encoding PA as well as in the transcriptional processing of this gene for Type N1, defects in the sortase gene for Type N2, and low mRNA expression of PA for Type W. Since cellular hydrophobicity and phagocytosis susceptibility of the PA-defective isolates were significantly lower than those of the normal expression isolates, the potential implication of such defective isolates in systemic diseases involving bacteremia other than dental caries was suggested. Additionally, multilocus sequence typing was utilized to characterize S. mutans clones that represented a proportion of isolates with PA defects of 65-100%. Therefore, we described the molecular basis for variation defects in PA expression of S. mutans. Furthermore, we also emphasized the strong association between PA expression defects and serotypes f and k as well as the clonal relationships among these isolates. Copyright © 2015 Elsevier GmbH. All rights reserved.

Molecular hierarchy in neurons differentiated from mouse ES cells containing a single human chromosome 21.

PubMed

Wang, Chi Chiu; Kadota, Mitsutaka; Nishigaki, Ryuichi; Kazuki, Yasuhiro; Shirayoshi, Yasuaki; Rogers, Michael Scott; Gojobori, Takashi; Ikeo, Kazuho; Oshimura, Mitsuo

2004-02-06

Defects in neurogenesis and neuronal differentiation in the fetal brain of Down syndrome (DS) patients lead to the apparent neuropathological abnormalities and contribute to the phenotypic characters of mental retardation, and premature development of Alzheimer's disease, those being the most common phenotype in DS. In order to understand the molecular mechanism underlying the cause of phenotypic abnormalities in the DS brain, we have utilized an in vitro model of TT2F mouse embryonic stem cells containing a single human chromosome 21 (hChr21) to study neuron development and neuronal differentiation by microarray containing 15K developmentally expressed cDNAs. Defective neuronal differentiation in the presence of extra hChr21 manifested primarily the post-transcriptional and translational modification, such as Mrpl10, SNAPC3, Srprb, SF3a60 in the early neuronal stem cell stage, and Mrps18a, Eef1g, and Ubce8 in the late differentiated stage. Hierarchical clustering patterned specific expression of hChr21 gene dosage effects on neuron outgrowth, migration, and differentiation, such as Syngr2, Dncic2, Eif3sf, and Peg3.

Various Stone-Wales defects in phagraphene

NASA Astrophysics Data System (ADS)

Openov, L. A.; Podlivaev, A. I.

2016-08-01

Various Stone-Wales defects in phagraphene, which is a graphene allotrope, predicted recently are studied in terms of the nonorthogonal tight-binding model. The energies of the defect formation and the heights of energy barriers preventing the formation and annealing of the defects are found. Corresponding frequency factors in the Arrhenius formula are calculated. The evolution of the defect structure is studied in the real-time mode using the molecular dynamics method.

Direct correlation and strong reduction of native point defects and microwave dielectric loss in air-annealed (Ba,Sr)TiO{sub 3}

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

Zeng, Z. Q.; Podpirka, A.; Kirchoefer, S. W.

2015-05-04

We report on the native defect and microwave properties of 1 μm thick Ba{sub 0.50}Sr{sub 0.50}TiO{sub 3} (BST) films grown on MgO (100) substrates by molecular beam epitaxy (MBE). Depth-resolved cathodoluminescence spectroscopy (DRCLS) showed high densities of native point defects in as-deposited BST films, causing strong subgap emission between 2.0 eV and 3.0 eV due to mixed cation V{sub C} and oxygen Vo vacancies. Post growth air anneals reduce these defects with 2.2, 2.65, and 3.0 eV V{sub O} and 2.4 eV V{sub C} intensities decreasing with increasing anneal temperature and by nearly two orders of magnitude after 950 °C annealing. These low-defect annealed BSTmore » films exhibited high quality microwave properties, including room temperature interdigitated capacitor tunability of 13% under an electric bias of 40 V and tan δ of 0.002 at 10 GHz and 40 V bias. The results provide a feasible route to grow high quality BST films by MBE through post-air annealing guided by DRCLS.« less

Deep level defects in dilute GaAsBi alloys grown under intense UV illumination

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

Mooney, P. M.; Tarun, Marianne; Beaton, D. A.

2016-07-21

Dilute GaAs1-xBix alloys exhibiting narrow band edge photoluminescence (PL) were recently grown by molecular beam epitaxy (MBE) with the growth surface illuminated by intense UV radiation. To investigate whether the improved optical quality of these films results from a reduction in the concentration of deep level defects, p+/n and n+/p junction diodes were fabricated on both the illuminated and dark areas of several samples. Deep Level Transient Spectroscopy (DLTS) measurements show that the illuminated and dark areas of both the n- and p-type GaAs1-xBix epi-layers have similar concentrations of near mid-gap electron and hole traps, in the 1015 cm-3 range.more » Thus the improved PL spectra cannot be explained by a reduction in non-radiative recombination at deep level defects. We note that carrier freeze-out above 35 K is significantly reduced in the illuminated areas of the p-type GaAs1-xBix layers compared to the dark areas, allowing the first DLTS measurements of defect energy levels close to the valence band edge. These defect levels may account for differences in the PL spectra from the illuminated and dark areas of un-doped layers with a similar Bi fraction.« less

Influence of Atomic Hydrogen, Band Bending, and Defects in the Top Few Nanometers of Hydrothermally Prepared Zinc Oxide Nanorods

NASA Astrophysics Data System (ADS)

Al-Saadi, Mubarak J.; Al-Harthi, Salim H.; Kyaw, Htet H.; Myint, Myo T. Z.; Bora, Tanujjal; Laxman, Karthik; Al-Hinai, Ashraf; Dutta, Joydeep

2017-01-01

We report on the surface, sub-surface (top few nanometers) and bulk properties of hydrothermally grown zinc oxide (ZnO) nanorods (NRs) prior to and after hydrogen treatment. Upon treating with atomic hydrogen (H*), upward and downward band bending is observed depending on the availability of molecular H2O within the structure of the NRs. In the absence of H2O, the H* treatment demonstrated a cleaning effect of the nanorods, leading to a 0.51 eV upward band bending. In addition, enhancement in the intensity of room temperature photoluminescence (PL) signals due to the creation of new surface defects could be observed. The defects enhanced the visible light activity of the ZnO NRs which were subsequently used to photocatalytically degrade aqueous phenol under simulated sunlight. On the contrary, in the presence of H2O, H* treatment created an electronic accumulation layer inducing downward band bending of 0.45 eV ( 1/7th of the bulk ZnO band gap) along with the weakening of the defect signals as observed from room temperature photoluminescence spectra. The results suggest a plausible way of tailoring the band bending and defects of the ZnO NRs through control of H2O/H* species.

Configuration of ripple domains and their topological defects formed under local mechanical stress on hexagonal monolayer graphene.

PubMed

Park, Yeonggu; Choi, Jin Sik; Choi, Taekjib; Lee, Mi Jung; Jia, Quanxi; Park, Minwoo; Lee, Hoonkyung; Park, Bae Ho

2015-03-24

Ripples in graphene are extensively investigated because they ensure the mechanical stability of two-dimensional graphene and affect its electronic properties. They arise from spontaneous symmetry breaking and are usually manifested in the form of domains with long-range order. It is expected that topological defects accompany a material exhibiting long-range order, whose functionality depends on characteristics of domains and topological defects. However, there remains a lack of understanding regarding ripple domains and their topological defects formed on monolayer graphene. Here we explore configuration of ripple domains and their topological defects in exfoliated monolayer graphenes on SiO2/Si substrates using transverse shear microscope. We observe three-color domains with three different ripple directions, which meet at a core. Furthermore, the closed domain is surrounded by an even number of cores connected together by domain boundaries, similar to topological vortex and anti-vortex pairs. In addition, we have found that axisymmetric three-color domains can be induced around nanoparticles underneath the graphene. This fascinating configuration of ripple domains may result from the intrinsic hexagonal symmetry of two-dimensional graphene, which is supported by theoretical simulation using molecular dynamics. Our findings are expected to play a key role in understanding of ripple physics in graphene and other two-dimensional materials.

Continuous improvements of defectivity rates in immersion photolithography via functionalized membranes in point-of-use photochemical filtration

NASA Astrophysics Data System (ADS)

D'Urzo, Lucia; Bayana, Hareen; Vandereyken, Jelle; Foubert, Philippe; Wu, Aiwen; Jaber, Jad; Hamzik, James

2017-03-01

Specific "killer-defects", such as micro-line-bridges are one of the key challenges in photolithography's advanced applications, such as multi-pattern. These defects generate from several sources and are very difficult to eliminate. Pointof-use filtration (POU) plays a crucial role on the mitigation, or elimination, of such defects. Previous studies have demonstrated how the contribution of POU filtration could not be studied independently from photoresists design and track hardware settings. Specifically, we investigated how an effective combination of optimized photoresist, filtration rate, filtration pressure, membrane and device cleaning, and single and multilayer filter membranes at optimized pore size could modulate the occurrence of such defects [1, 2, 3 and 4]. However, the ultimate desired behavior for POU filtration is the selective retention of defect precursor molecules contained in commercially available photoresist. This optimal behavior can be achieved via customized membrane functionalization. Membrane functionalization provides additional non-sieving interactions which combined with efficient size exclusion can selectively capture certain defect precursors. The goal of this study is to provide a comprehensive assessment of membrane functionalization applied on an asymmetric ultra-high molecular weight polyethylene (UPE) membrane at different pore size. Defectivity transferred in a 45 nm line 55 nm space (45L/55S) pattern, created through 193 nm immersion (193i) lithography with a positive tone chemically amplified resist (PT-CAR), has been evaluated on organic under-layer coated wafers. Lithography performance, such as critical dimensions (CD), line width roughness (LWR) and focus energy matrix (FEM) is also assessed.

Reduced α-MSH Underlies Hypothalamic ER-Stress-Induced Hepatic Gluconeogenesis.

PubMed

Schneeberger, Marc; Gómez-Valadés, Alicia G; Altirriba, Jordi; Sebastián, David; Ramírez, Sara; Garcia, Ainhoa; Esteban, Yaiza; Drougard, Anne; Ferrés-Coy, Albert; Bortolozzi, Analía; Garcia-Roves, Pablo M; Jones, John G; Manadas, Bruno; Zorzano, Antonio; Gomis, Ramon; Claret, Marc

2015-07-21

Alterations in ER homeostasis have been implicated in the pathophysiology of obesity and type-2 diabetes (T2D). Acute ER stress induction in the hypothalamus produces glucose metabolism perturbations. However, the neurobiological basis linking hypothalamic ER stress with abnormal glucose metabolism remains unknown. Here, we report that genetic and induced models of hypothalamic ER stress are associated with alterations in systemic glucose homeostasis due to increased gluconeogenesis (GNG) independent of body weight changes. Defective alpha melanocyte-stimulating hormone (α-MSH) production underlies this metabolic phenotype, as pharmacological strategies aimed at rescuing hypothalamic α-MSH content reversed this phenotype at metabolic and molecular level. Collectively, our results posit defective α-MSH processing as a fundamental mediator of enhanced GNG in the context of hypothalamic ER stress and establish α-MSH deficiency in proopiomelanocortin (POMC) neurons as a potential contributor to the pathophysiology of T2D. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Thermodynamics of surface defects at the aspirin/water interface

NASA Astrophysics Data System (ADS)

Schneider, Julian; Zheng, Chen; Reuter, Karsten

2014-09-01

We present a simulation scheme to calculate defect formation free energies at a molecular crystal/water interface based on force-field molecular dynamics simulations. To this end, we adopt and modify existing approaches to calculate binding free energies of biological ligand/receptor complexes to be applicable to common surface defects, such as step edges and kink sites. We obtain statistically accurate and reliable free energy values for the aspirin/water interface, which can be applied to estimate the distribution of defects using well-established thermodynamic relations. As a show case we calculate the free energy upon dissolving molecules from kink sites at the interface. This free energy can be related to the solubility concentration and we obtain solubility values in excellent agreement with experimental results.

Photoluminescence of Molecular Beam Epitaxy-Grown Mercury Cadmium Telluride: Comparison of HgCdTe/GaAs and HgCdTe/Si Technologies

NASA Astrophysics Data System (ADS)

Mynbaev, K. D.; Bazhenov, N. L.; Dvoretsky, S. A.; Mikhailov, N. N.; Varavin, V. S.; Marin, D. V.; Yakushev, M. V.

2018-05-01

Properties of HgCdTe films grown by molecular beam epitaxy on GaAs and Si substrates have been studied by performing variable-temperature photoluminescence (PL) measurements. A substantial difference in defect structure between films grown on GaAs (013) and Si (013) substrates was revealed. HgCdTe/GaAs films were mostly free of defect-related energy levels within the bandgap, which was confirmed by PL and carrier lifetime measurements. By contrast, the properties of HgCdTe/Si films are affected by uncontrolled point defects. These could not be always associated with typical "intrinsic" HgCdTe defects, such as mercury vacancies, so consideration of other defects, possibly inherent in HgCdTe/Si structures, was required. The post-growth annealing was found to have a positive effect on the defect structure by reducing the full-widths at half-maximum of excitonic PL lines for both types of films and lowering the concentration of defects specific to HgCdTe/Si.

Graphene defects induced by ion beam

NASA Astrophysics Data System (ADS)

Gawlik, Grzegorz; Ciepielewski, Paweł; Baranowski, Jacek; Jagielski, Jacek

2017-10-01

The CVD graphene deposited on the glass substrate was bombarded by molecular carbon ions C3+ C6+ hydrocarbon ions C3H4+ and atomic ions He+, C+, N+, Ar+, Kr+ Yb+. Size and density of ion induced defects were estimated from evolution of relative intensities of Raman lines D (∼1350 1/cm), G (∼1600 1/cm), and D‧ (∼1620 1/cm) with ion fluence. The efficiency of defect generation by atomic ions depend on ion mass and energy similarly as vacancy generation directly by ion predicted by SRIM simulations. However, efficiency of defect generation in graphene by molecular carbon ions is essentially higher than summarized efficiency of similar group of separate atomic carbon ions of the same energy that each carbon ion in a cluster. The evolution of the D/D‧ ratio of Raman lines intensities with ion fluence was observed. This effect may indicate evolution of defect nature from sp3-like at low fluence to a vacancy-like at high fluence. Observed ion graphene interactions suggest that the molecular ion interacts with graphene as single integrated object and should not be considered as a group of atomic ions with partial energy.

Downregulation of SIRT1 signaling underlies hepatic autophagy impairment in glycogen storage disease type Ia

PubMed Central

Cho, Jun-Ho; Pan, Chi-Jiunn; Anduaga, Javier

2017-01-01

A deficiency in glucose-6-phosphatase-α (G6Pase-α) in glycogen storage disease type Ia (GSD-Ia) leads to impaired glucose homeostasis and metabolic manifestations including hepatomegaly caused by increased glycogen and neutral fat accumulation. A recent report showed that G6Pase-α deficiency causes impairment in autophagy, a recycling process important for cellular metabolism. However, the molecular mechanism underlying defective autophagy is unclear. Here we show that in mice, liver-specific knockout of G6Pase-α (L-G6pc-/-) leads to downregulation of sirtuin 1 (SIRT1) signaling that activates autophagy via deacetylation of autophagy-related (ATG) proteins and forkhead box O (FoxO) family of transcriptional factors which transactivate autophagy genes. Consistently, defective autophagy in G6Pase-α-deficient liver is characterized by attenuated expressions of autophagy components, increased acetylation of ATG5 and ATG7, decreased conjugation of ATG5 and ATG12, and reduced autophagic flux. We further show that hepatic G6Pase-α deficiency results in activation of carbohydrate response element-binding protein, a lipogenic transcription factor, increased expression of peroxisome proliferator-activated receptor-γ (PPAR-γ), a lipid regulator, and suppressed expression of PPAR-α, a master regulator of fatty acid β-oxidation, all contributing to hepatic steatosis and downregulation of SIRT1 expression. An adenovirus vector-mediated increase in hepatic SIRT1 expression corrects autophagy defects but does not rectify metabolic abnormalities associated with G6Pase-α deficiency. Importantly, a recombinant adeno-associated virus (rAAV) vector-mediated restoration of hepatic G6Pase-α expression corrects metabolic abnormalities, restores SIRT1-FoxO signaling, and normalizes defective autophagy. Taken together, these data show that hepatic G6Pase-α deficiency-mediated down-regulation of SIRT1 signaling underlies defective hepatic autophagy in GSD-Ia. PMID:28558013

Lhx6 and Lhx8 promote palate development through negative regulation of a cell cycle inhibitor gene, p57Kip2

PubMed Central

Cesario, Jeffry M.; Landin Malt, Andre; Deacon, Lindsay J.; Sandberg, Magnus; Vogt, Daniel; Tang, Zuojian; Zhao, Yangu; Brown, Stuart; Rubenstein, John L.; Jeong, Juhee

2015-01-01

Cleft palate is a common birth defect in humans. Therefore, understanding the molecular genetics of palate development is important from both scientific and medical perspectives. Lhx6 and Lhx8 encode LIM homeodomain transcription factors, and inactivation of both genes in mice resulted in profound craniofacial defects including cleft secondary palate. The initial outgrowth of the palate was severely impaired in the mutant embryos, due to decreased cell proliferation. Through genome-wide transcriptional profiling, we discovered that p57Kip2 (Cdkn1c), encoding a cell cycle inhibitor, was up-regulated in the prospective palate of Lhx6−/−;Lhx8−/− mutants. p57Kip2 has been linked to Beckwith–Wiedemann syndrome and IMAGe syndrome in humans, which are developmental disorders with increased incidents of palate defects among the patients. To determine the molecular mechanism underlying the regulation of p57Kip2 by the Lhx genes, we combined chromatin immunoprecipitation, in silico search for transcription factor-binding motifs, and in vitro reporter assays with putative cis-regulatory elements. The results of these experiments indicated that LHX6 and LHX8 regulated p57Kip2 via both direct and indirect mechanisms, with the latter mediated by Forkhead box (FOX) family transcription factors. Together, our findings uncovered a novel connection between the initiation of palate development and a cell cycle inhibitor via LHX. We propose a model in which Lhx6 and Lhx8 negatively regulate p57Kip2 expression in the prospective palate area to allow adequate levels of cell proliferation and thereby promote normal palate development. This is the first report elucidating a molecular genetic pathway downstream of Lhx in palate development. PMID:26071365

Glucose-6-phosphate dehydrogenase laboratory assay: How, when, and why?

PubMed

Minucci, Angelo; Giardina, Bruno; Zuppi, Cecilia; Capoluongo, Ettore

2009-01-01

Glucose 6-phosphate dehydrogenase (G6PD) deficiency is the most common defect of red blood cells. Although some different laboratory techniques or methods are employed for the biochemical screening, a strict relationship between biochemists, clinicians, and molecular biologists is necessary for a definitive diagnosis. This article represents an overview on the current laboratory tests finalized to the screening or to the definitive diagnosis of G6PD-deficiency, underlying the problems regarding the biochemical and molecular identification of heterozygote females other than those regarding the standardization of the clinical and laboratory diagnostic procedures. Finally, this review is aimed to give a flow-chart for the complete diagnostic approach of G6PD-deficiency.

Tensile Strength of Carbon Nanotubes Under Realistic Temperature and Strain Rate

NASA Technical Reports Server (NTRS)

Wei, Chen-Yu; Cho, Kyeong-Jae; Srivastava, Deepak; Biegel, Bryan (Technical Monitor)

2002-01-01

Strain rate and temperature dependence of the tensile strength of single-wall carbon nanotubes has been investigated with molecular dynamics simulations. The tensile failure or yield strain is found to be strongly dependent on the temperature and strain rate. A transition state theory based predictive model is developed for the tensile failure of nanotubes. Based on the parameters fitted from high-strain rate and temperature dependent molecular dynamics simulations, the model predicts that a defect free micrometer long single-wall nanotube at 300 K, stretched with a strain rate of 1%/hour, fails at about 9 plus or minus 1% tensile strain. This is in good agreement with recent experimental findings.

Effects of two-temperature model on cascade evolution in Ni and NiFe

DOE PAGES

Samolyuk, German D.; Xue, Haizhou; Bei, Hongbin; ...

2016-07-05

We perform molecular dynamics simulations of Ni ion cascades in Ni and equiatomic NiFe under the following conditions: (a) classical molecular dynamics (MD) simulations without consideration of electronic energy loss, (b) classical MD simulations with the electronic stopping included, and (c) using the coupled two-temperature MD (2T-MD) model that incorporates both the electronic stopping and the electron-phonon interactions. Our results indicate that the electronic effects are more profound in the higher-energy cascades, and that the 2T-MD model results in a smaller amount of surviving damage and smaller defect clusters, while less damage is produced in NiFe than in Ni.

p38 MAPK-Mediated Bmi-1 Down-Regulation and Defective Proliferation in ATM-Deficient Neural Stem Cells Can Be Restored by Akt Activation

PubMed Central

Kim, Jeesun; Hwangbo, Jeon; Wong, Paul K. Y.

2011-01-01

A-T (ataxia telangiectasia) is a genetic disease caused by a mutation in the Atm (A-T mutated) gene that leads to neurodegeneration. Despite an increase in the numbers of studies in this area in recent years, the mechanisms underlying neurodegeneration in human A-T are still poorly understood. Previous studies demonstrated that neural stem cells (NSCs) isolated from the subventricular zone (SVZ) of Atm -/- mouse brains show defective self-renewal and proliferation, which is accompanied by activation of chronic p38 mitogen-activated protein kinase (MAPK) and a lower level of the polycomb protein Bmi-1. However, the mechanism underlying Bmi-1 down-regulation and its relevance to defective proliferation in Atm-/- NSCs remained unclear. Here, we show that over-expression of Bmi-1 increases self-renewal and proliferation of Atm-/- NSCs to normal, indicating that defective proliferation in Atm-/- NSCs is a consequence of down-regulation of Bmi-1. We also demonstrate that epidermal growth factor (EGF)-induced Akt phosphorylation renders Bmi-1 resistant to the proteasomal degradation, leading to its stabilization and accumulation in the nucleus. However, inhibition of the Akt-dependent Bmi-1 stabilizing process by p38 MAPK signaling reduces the levels of Bmi-1. Treatment of the Atm-/- NSCs with a specific p38 MAPK inhibitor SB203580 extended Bmi-1 posttranscriptional turnover and H2A ubiquitination in Atm-/- NSCs. Our observations demonstrate the molecular basis underlying the impairment of self-renewal and proliferation in Atm-/- NSCs through the p38 MAPK-Akt-Bmi-1-p21 signaling pathway. PMID:21305053

Molecular mechanism for lipid flip-flops.

PubMed

Gurtovenko, Andrey A; Vattulainen, Ilpo

2007-12-06

Transmembrane lipid translocation (flip-flop) processes are involved in a variety of properties and functions of cell membranes, such as membrane asymmetry and programmed cell death. Yet, flip-flops are one of the least understood dynamical processes in membranes. In this work, we elucidate the molecular mechanism of pore-mediated transmembrane lipid translocation (flip-flop) acquired from extensive atomistic molecular dynamics simulations. On the basis of 50 successful flip-flop events resolved in atomic detail, we demonstrate that lipid flip-flops may spontaneously occur in protein-free phospholipid membranes under physiological conditions through transient water pores on a time scale of tens of nanoseconds. While the formation of a water pore is induced here by a transmembrane ion density gradient, the particular way by which the pore is formed is irrelevant for the reported flip-flop mechanism: the appearance of a transient pore (defect) in the membrane inevitably leads to diffusive translocation of lipids through the pore, which is driven by thermal fluctuations. Our findings strongly support the idea that the formation of membrane defects in terms of water pores is the rate-limiting step in the process of transmembrane lipid flip-flop, which, on average, requires several hours. The findings are consistent with available experimental and computational data and provide a view to interpret experimental observations. For example, the simulation results provide a molecular-level explanation in terms of pores for the experimentally observed fact that the exposure of lipid membranes to electric field pulses considerably reduces the time required for lipid flip-flops.

A Mitocentric View of Parkinson’s Disease

PubMed Central

Haelterman, Nele A.; Yoon, Wan Hee; Sandoval, Hector; Jaiswal, Manish; Shulman, Joshua M.; Bellen, Hugo J.

2015-01-01

Parkinson’s disease (PD) is a common neurodegenerative disease, yet the underlying causative molecular mechanisms are ill defined. Numerous observations based on drug studies and mutations in genes that cause PD point to a complex set of rather subtle mitochondrial defects that may be causative. Indeed, intensive investigation of these genes in model organisms has revealed roles in the electron transport chain, mitochondrial protein homeostasis, mitophagy, and the fusion and fission of mitochondria. Here, we attempt to synthesize results from experimental studies in diverse systems to define the precise function of these PD genes, as well as their interplay with other genes that affect mitochondrial function. We propose that subtle mitochondrial defects in combination with other insults trigger the onset and progression of disease, in both familial and idiopathic PD. PMID:24821430

Fluoropolymer Dynamics: Effects of Perfluoromethyl Branches

NASA Astrophysics Data System (ADS)

Eby, R. K.; Holt, D. B.; Farmer, B. L.; Adams, D. D.

1997-03-01

Previous simulations of polytetrafluoroethylene (PTFE) in the solid state showed that the interaction and movement of helix reversals plays an important role in the dynamic behavior of this important polymer. Copolymers of TFE and hexafluoropropylene (HFP), which can be viewed as PTFE with perfluoromethyl (PFM) group branch defects, is also widely used. Molecular mechanics and dynamics calculations have been performed with PTFE chain clusters containing PFM branches to investigate the effect of these defects on the local crystalline environment (and vice versa) and on the motions and interactions of helix reversals. Initial results indicate that helix reversals are attracted to sites of PFM branches in a chain. Such an interaction will impede the motions of helix reversals and have an impact on macroscopic mechanical properties such as resistance to plastic deformation under shear.

Glucotoxicity promotes aberrant activation and mislocalization of Ras-related C3 botulinum toxin substrate 1 [Rac1] and metabolic dysfunction in pancreatic islet β-cells: reversal of such metabolic defects by metformin.

PubMed

Baidwan, Sartaj; Chekuri, Anil; Hynds, DiAnna L; Kowluru, Anjaneyulu

2017-11-01

Emerging evidence suggests that long-term exposure of insulin-secreting pancreatic β-cells to hyperglycemic (HG; glucotoxic) conditions promotes oxidative stress, which, in turn, leads to stress kinase activation, mitochondrial dysfunction, loss of nuclear structure and integrity and cell apoptosis. Original observations from our laboratory have proposed that Rac1 plays a key regulatory role in the generation of oxidative stress and downstream signaling events culminating in the onset of dysfunction of pancreatic β-cells under the duress of metabolic stress. However, precise molecular and cellular mechanisms underlying the metabolic roles of hyperactive Rac1 remain less understood. Using pharmacological and molecular biological approaches, we now report mistargetting of biologically-active Rac1 [GTP-bound conformation] to the nuclear compartment in clonal INS-1 cells, normal rat islets and human islets under HG conditions. Our findings also suggest that such a signaling step is independent of post-translational prenylation of Rac1. Evidence is also presented to highlight novel roles for sustained activation of Rac1 in HG-induced expression of Cluster of Differentiation 36 [CD36], a fatty acid transporter protein, which is implicated in cell apoptosis. Finally, our findings suggest that metformin, a biguanide anti-diabetic drug, at a clinically relevant concentration, prevents β-cell defects [Rac1 activation, nuclear association, CD36 expression, stress kinase and caspase-3 activation, and loss in metabolic viability] under the duress of glucotoxicity. Potential implications of these findings in the context of novel and direct regulation of islet β-cell function by metformin are discussed.

Theoretical investigations on the structures and properties of CL-20/TNT cocrystal and its defective models by molecular dynamics simulation.

PubMed

Hang, Gui-Yun; Yu, Wen-Li; Wang, Tao; Wang, Jin-Tao

2018-06-09

"Perfect" and defective models of CL-20/TNT cocrystal explosive were established. Molecular dynamics methods were introduced to determine the structures and predict the comprehensive performances, including stabilities, sensitivity, energy density and mechanical properties, of the different models. The influences of crystal defects on the properties of these explosives were investigated and evaluated. The results show that, compared with the "perfect" model, the rigidity and toughness of defective models are decreased, while the ductility, tenacity and plastic properties are enhanced. The binding energies, interaction energy of the trigger bond, and the cohesive energy density of defective crystals declined, thus implying that stabilities are weakened, the explosive molecule is activated, trigger bond strength is diminished and safety is worsened. Detonation performance showed that, owing to the influence of crystal defects, the density is lessened, detonation pressure and detonation velocity are also declined, i.e., the power of defective explosive is decreased. In a word, the crystal defects may have a favorable effect on the mechanical properties, but have a disadvantageous influence on sensitivity, stability and energy density of CL-20/TNT cocrystal explosive. The results could provide theoretical guidance and practical instructions to estimate the properties of defective crystal models.

Features of primary damage by high energy displacement cascades in concentrated Ni-based alloys

DOE PAGES

Béland, Laurent Karim; Lu, Chenyang; Osetskiy, Yuri N.; ...

2016-02-25

Alloying of Ni with Fe or Co reduces primary damage production under ion irradiation. Similar results have been obtained from classical molecular dynamics simulations of 1, 10, 20, and 40 keV collision cascades in Ni, NiFe, and NiCo. In all cases, a mix of imperfect stacking fault tetrahedra, faulted loops with a 1/3 {111} Burgers vector, and glissile interstitial loops with a 1/2 {110} Burgers vector were formed, along with small sessile point defect complexes and clusters. Primary damage reduction occurs by three mechanisms. First, Ni-Co, Ni-Fe, Co-Co, and Fe-Fe short-distance repulsive interactions are stiffer than Ni-Ni interactions, which leadmore » to a decrease in damage formation during the transition from the supersonic ballistic regime to the sonic regime. This largely controls final defect production. Second, alloying decreases thermal conductivity, leading to a longer thermal spike lifetime. The associated annealing reduces final damage production. These two mechanisms are especially important at cascades energies less than 40 keV. Third, at the higher energies, the production of large defect clusters by subcascades is inhibited in the alloys. A number of challenges and limitations pertaining to predictive atomistic modeling of alloys under high-energy particle irradiation are discussed.« less

Analysis of Craniocardiac Malformations in Xenopus using Optical Coherence Tomography

PubMed Central

Deniz, Engin; Jonas, Stephan; Hooper, Michael; N. Griffin, John; Choma, Michael A.; Khokha, Mustafa K.

2017-01-01

Birth defects affect 3% of children in the United States. Among the birth defects, congenital heart disease and craniofacial malformations are major causes of mortality and morbidity. Unfortunately, the genetic mechanisms underlying craniocardiac malformations remain largely uncharacterized. To address this, human genomic studies are identifying sequence variations in patients, resulting in numerous candidate genes. However, the molecular mechanisms of pathogenesis for most candidate genes are unknown. Therefore, there is a need for functional analyses in rapid and efficient animal models of human disease. Here, we coupled the frog Xenopus tropicalis with Optical Coherence Tomography (OCT) to create a fast and efficient system for testing craniocardiac candidate genes. OCT can image cross-sections of microscopic structures in vivo at resolutions approaching histology. Here, we identify optimal OCT imaging planes to visualize and quantitate Xenopus heart and facial structures establishing normative data. Next we evaluate known human congenital heart diseases: cardiomyopathy and heterotaxy. Finally, we examine craniofacial defects by a known human teratogen, cyclopamine. We recapitulate human phenotypes readily and quantify the functional and structural defects. Using this approach, we can quickly test human craniocardiac candidate genes for phenocopy as a critical first step towards understanding disease mechanisms of the candidate genes. PMID:28195132

Fragile X syndrome: from molecular genetics to therapy.

PubMed

D'Hulst, C; Kooy, R F

2009-09-01

Fragile X syndrome, the main cause of inherited mental retardation, is caused by transcriptional silencing of the fragile X mental retardation gene, FMR1. Absence of the associated protein FMRP leads to the dysregulation of many genes creating a phenotype of ADHD, anxiety, epilepsy and autism. The core aim of this review is to summarise two decades of molecular research leading to the characterisation of cellular and molecular pathways involved in the pathology of this disease and as a consequence to the identification of two new promising targets for rational therapy of fragile X syndrome, namely the group 1 metabotrope glutamate receptors (Gp1 mGluRs) and the gamma-amino butyric acid A receptors (GABA(A)Rs). As no current clinical treatments are directed specifically at the underlying neuronal defect due to absence of FMRP, this might open new powerful therapeutic strategies.

8-Dehydrosterols induce membrane traffic and autophagy defects through V-ATPase dysfunction in Saccharomyces cerevisae.

PubMed

Hernández, Agustín; Serrano-Bueno, Gloria; Perez-Castiñeira, José Román; Serrano, Aurelio

2015-11-01

8-Dehydrosterols are present in a wide range of biologically relevant situations, from human rare diseases to amine fungicide-treated fungi and crops. However, the molecular bases of their toxicity are still obscure. We show here that 8-dehydrosterols, but not other sterols, affect yeast vacuole acidification through V-ATPases. Moreover, erg2Δ cells display reductions in proton pumping rates consistent with ion-transport uncoupling in vitro. Concomitantly, subunit Vph1p shows conformational changes in the presence of 8-dehydrosterols. Expression of a plant vacuolar H(+)-pumping pyrophosphatase as an alternative H(+)-pump relieves Vma(-)-like phenotypes in erg2Δ-derived mutant cells. As a consequence of these acidification defects, endo- and exo-cytic traffic deficiencies that can be alleviated with a H(+)-pumping pyrophosphatase are also observed. Despite their effect on membrane traffic, 8-dehydrosterols do not induce endoplasmic reticulum stress or assembly defects on the V-ATPase. Autophagy is a V-ATPase dependent process and erg2Δ mutants accumulate autophagic bodies under nitrogen starvation similar to Vma(-) mutants. In contrast to classical Atg(-) mutants, this defect is not accompanied by impairment of traffic through the CVT pathway, processing of Pho8Δ60p, GFP-Atg8p localisation or difficulties to survive under nitrogen starvation conditions, but it is concomitant to reduced vacuolar protease activity. All in all, erg2Δ cells are autophagy mutants albeit some of their phenotypic features differ from classical Atg(-) defective cells. These results may pave the way to understand the aetiology of sterol-related diseases, the cytotoxic effect of amine fungicides, and may explain the tolerance to these compounds observed in plants. Copyright © 2015 Elsevier B.V. All rights reserved.

Molecular dynamics studies of defect formation during heteroepitaxial growth of InGaN alloys on (0001) GaN surfaces

DOE PAGES

Gruber, J.; Zhou, X. W.; Jones, R. E.; ...

2017-05-15

Here, we investigate the formation of extended defects during molecular-dynamics (MD) simulations of GaN and InGaN growth on (0001) and (11more » $$\\bar{2}$$0) wurtzite-GaN surfaces. The simulated growths are conducted on an atypically large scale by sequentially injecting nearly a million individual vapor-phase atoms towards a fixed GaN surface; we apply time-and-position-dependent boundary constraints that vary the ensemble treatments of the vapor-phase, the near-surface solid-phase, and the bulk-like regions of the growing layer. The simulations employ newly optimized Stillinger-Weber In-Ga-N-system potentials, wherein multiple binary and ternary structures are included in the underlying density-functional-theory training sets, allowing improved treatment of In-Ga-related atomic interactions. To examine the effect of growth conditions, we study a matrix of >30 different MD-growth simulations for a range of InxGa1-xN-alloy compositions (0 ≤ x ≤ 0.4) and homologous growth temperatures [0.50 ≤ T/T* m(x) ≤ 0.90], where T* m(x) is the simulated melting point. Growths conducted on polar (0001) GaN substrates exhibit the formation of various extended defects including stacking faults/polymorphism, associated domain boundaries, surface roughness, dislocations, and voids. In contrast, selected growths conducted on semi-polar (11$$\\bar{2}$$0) GaN, where the wurtzite-phase stacking sequence is revealed at the surface, exhibit the formation of far fewer stacking faults. We discuss variations in the defect formation with the MD growth conditions, and we compare the resulting simulated films to existing experimental observations in InGaN/GaN. Finally, while the palette of defects observed by MD closely resembles those observed in the past experiments, further work is needed to achieve truly predictive large-scale simulations of InGaN/GaN crystal growth using MD methodologies.« less

Molecular dynamics studies of defect formation during heteroepitaxial growth of InGaN alloys on (0001) GaN surfaces

NASA Astrophysics Data System (ADS)

Gruber, J.; Zhou, X. W.; Jones, R. E.; Lee, S. R.; Tucker, G. J.

2017-05-01

We investigate the formation of extended defects during molecular-dynamics (MD) simulations of GaN and InGaN growth on (0001) and ( 11 2 ¯ 0 ) wurtzite-GaN surfaces. The simulated growths are conducted on an atypically large scale by sequentially injecting nearly a million individual vapor-phase atoms towards a fixed GaN surface; we apply time-and-position-dependent boundary constraints that vary the ensemble treatments of the vapor-phase, the near-surface solid-phase, and the bulk-like regions of the growing layer. The simulations employ newly optimized Stillinger-Weber In-Ga-N-system potentials, wherein multiple binary and ternary structures are included in the underlying density-functional-theory training sets, allowing improved treatment of In-Ga-related atomic interactions. To examine the effect of growth conditions, we study a matrix of >30 different MD-growth simulations for a range of InxGa1-xN-alloy compositions (0 ≤ x ≤ 0.4) and homologous growth temperatures [0.50 ≤ T/T*m(x) ≤ 0.90], where T*m(x) is the simulated melting point. Growths conducted on polar (0001) GaN substrates exhibit the formation of various extended defects including stacking faults/polymorphism, associated domain boundaries, surface roughness, dislocations, and voids. In contrast, selected growths conducted on semi-polar ( 11 2 ¯ 0 ) GaN, where the wurtzite-phase stacking sequence is revealed at the surface, exhibit the formation of far fewer stacking faults. We discuss variations in the defect formation with the MD growth conditions, and we compare the resulting simulated films to existing experimental observations in InGaN/GaN. While the palette of defects observed by MD closely resembles those observed in the past experiments, further work is needed to achieve truly predictive large-scale simulations of InGaN/GaN crystal growth using MD methodologies.

Molecular dynamics studies of defect formation during heteroepitaxial growth of InGaN alloys on (0001) GaN surfaces.

PubMed

Gruber, J; Zhou, X W; Jones, R E; Lee, S R; Tucker, G J

2017-05-21

We investigate the formation of extended defects during molecular-dynamics (MD) simulations of GaN and InGaN growth on (0001) and ([Formula: see text]) wurtzite-GaN surfaces. The simulated growths are conducted on an atypically large scale by sequentially injecting nearly a million individual vapor-phase atoms towards a fixed GaN surface; we apply time-and-position-dependent boundary constraints that vary the ensemble treatments of the vapor-phase, the near-surface solid-phase, and the bulk-like regions of the growing layer. The simulations employ newly optimized Stillinger-Weber In-Ga-N-system potentials, wherein multiple binary and ternary structures are included in the underlying density-functional-theory training sets, allowing improved treatment of In-Ga-related atomic interactions. To examine the effect of growth conditions, we study a matrix of >30 different MD-growth simulations for a range of In x Ga 1-x N-alloy compositions (0 ≤  x  ≤ 0.4) and homologous growth temperatures [0.50 ≤  T/T * m ( x ) ≤ 0.90], where T * m ( x ) is the simulated melting point. Growths conducted on polar (0001) GaN substrates exhibit the formation of various extended defects including stacking faults/polymorphism, associated domain boundaries, surface roughness, dislocations, and voids. In contrast, selected growths conducted on semi-polar ([Formula: see text]) GaN, where the wurtzite-phase stacking sequence is revealed at the surface, exhibit the formation of far fewer stacking faults. We discuss variations in the defect formation with the MD growth conditions, and we compare the resulting simulated films to existing experimental observations in InGaN/GaN. While the palette of defects observed by MD closely resembles those observed in the past experiments, further work is needed to achieve truly predictive large-scale simulations of InGaN/GaN crystal growth using MD methodologies.

Modeling of dislocation channel width evolution in irradiated metals

DOE PAGES

Doyle, Peter J.; Benensky, Kelsa M.; Zinkle, Steven J.

2017-11-08

Defect-free dislocation channel formation has been reported to promote plastic instability during tensile testing via localized plastic flow, leading to a distinct loss of ductility and strain hardening in many low-temperature irradiated materials. In order to study the underlying mechanisms governing dislocation channel width and formation, the channel formation process is modeled via a simple stochastic dislocation-jog process dependent upon grain size, defect cluster density, and defect size. Dislocations traverse a field of defect clusters and jog stochastically upon defect interaction, forming channels of low defect-density. And based upon prior molecular dynamics (MD) simulations and in-situ experimental transmission electron microscopymore » (TEM) observations, each dislocation encounter with a dislocation loop or stacking fault tetrahedron (SFT) is assumed to cause complete absorption of the defect cluster, prompting the dislocation to jog up or down by a distance equal to half the defect cluster diameter. Channels are predicted to form rapidly and are comparable to reported TEM measurements for many materials. Predicted channel widths are found to be most strongly dependent on mean defect size and correlated well with a power law dependence on defect diameter and density, and distance from the dislocation source. Due to the dependence of modeled channel width on defect diameter and density, maximum channel width is predicted to slowly increase as accumulated dose increases. The relatively weak predicted dependence of channel formation width with distance, in accordance with a diffusion analogy, implies that after only a few microns from the source, most channels observed via TEM analyses may not appear to vary with distance because of limitations in the field-of-view to a few microns. Furthermore, examinations of the effect of the so-called “source-broadening” mechanism of channel formation showed that its effect is simply to add a minimum thickness to the channel without affecting channel dependence on the given parameters.« less

Modeling of dislocation channel width evolution in irradiated metals

NASA Astrophysics Data System (ADS)

Doyle, Peter J.; Benensky, Kelsa M.; Zinkle, Steven J.

2018-02-01

Defect-free dislocation channel formation has been reported to promote plastic instability during tensile testing via localized plastic flow, leading to a distinct loss of ductility and strain hardening in many low-temperature irradiated materials. In order to study the underlying mechanisms governing dislocation channel width and formation, the channel formation process is modeled via a simple stochastic dislocation-jog process dependent upon grain size, defect cluster density, and defect size. Dislocations traverse a field of defect clusters and jog stochastically upon defect interaction, forming channels of low defect-density. Based upon prior molecular dynamics (MD) simulations and in-situ experimental transmission electron microscopy (TEM) observations, each dislocation encounter with a dislocation loop or stacking fault tetrahedron (SFT) is assumed to cause complete absorption of the defect cluster, prompting the dislocation to jog up or down by a distance equal to half the defect cluster diameter. Channels are predicted to form rapidly and are comparable to reported TEM measurements for many materials. Predicted channel widths are found to be most strongly dependent on mean defect size and correlated well with a power law dependence on defect diameter and density, and distance from the dislocation source. Due to the dependence of modeled channel width on defect diameter and density, maximum channel width is predicted to slowly increase as accumulated dose increases. The relatively weak predicted dependence of channel formation width with distance, in accordance with a diffusion analogy, implies that after only a few microns from the source, most channels observed via TEM analyses may not appear to vary with distance because of limitations in the field-of-view to a few microns. Further, examinations of the effect of the so-called "source-broadening" mechanism of channel formation showed that its effect is simply to add a minimum thickness to the channel without affecting channel dependence on the given parameters.

Modeling of dislocation channel width evolution in irradiated metals

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

Doyle, Peter J.; Benensky, Kelsa M.; Zinkle, Steven J.

Defect-free dislocation channel formation has been reported to promote plastic instability during tensile testing via localized plastic flow, leading to a distinct loss of ductility and strain hardening in many low-temperature irradiated materials. In order to study the underlying mechanisms governing dislocation channel width and formation, the channel formation process is modeled via a simple stochastic dislocation-jog process dependent upon grain size, defect cluster density, and defect size. Dislocations traverse a field of defect clusters and jog stochastically upon defect interaction, forming channels of low defect-density. And based upon prior molecular dynamics (MD) simulations and in-situ experimental transmission electron microscopymore » (TEM) observations, each dislocation encounter with a dislocation loop or stacking fault tetrahedron (SFT) is assumed to cause complete absorption of the defect cluster, prompting the dislocation to jog up or down by a distance equal to half the defect cluster diameter. Channels are predicted to form rapidly and are comparable to reported TEM measurements for many materials. Predicted channel widths are found to be most strongly dependent on mean defect size and correlated well with a power law dependence on defect diameter and density, and distance from the dislocation source. Due to the dependence of modeled channel width on defect diameter and density, maximum channel width is predicted to slowly increase as accumulated dose increases. The relatively weak predicted dependence of channel formation width with distance, in accordance with a diffusion analogy, implies that after only a few microns from the source, most channels observed via TEM analyses may not appear to vary with distance because of limitations in the field-of-view to a few microns. Furthermore, examinations of the effect of the so-called “source-broadening” mechanism of channel formation showed that its effect is simply to add a minimum thickness to the channel without affecting channel dependence on the given parameters.« less

Molecular Mechanisms Underlying Genomic Instability in Brca-Deficient Cells

DTIC Science & Technology

2014-11-01

breeding of various HR knockouts with 53BP1 nulls. These mice have been generated and drug sensitivity data with these crosses have been included in...overcome the HR defects in BRCA1-defi- cient cells, we crossed PTIPf/f and BRCA1f(D11)/f(D11) mice with CD19 CRE transgenic mice to simultaneously...http://dx. doi.org/10.1073/pnas.1305362110. Bryant, H.E., Schultz, N., Thomas, H.D., Parker, K.M., Flower , D., Lopez, E., Kyle, S., Meuth, M., Curtin

Germ cell tumors: Insights from the Drosophila ovary and the mouse testis.

PubMed

Salz, Helen K; Dawson, Emily P; Heaney, Jason D

2017-03-01

Ovarian and testicular germ cell tumors of young adults are thought to arise from defects in germ cell development, but the molecular mechanisms underlying malignant transformation are poorly understood. In this review, we focus on the biology of germ cell tumor formation in the Drosophila ovary and the mouse testis, for which evidence supports common underlying mechanisms, such as blocking initiation into the differentiation pathway, impaired lineage progression, and sexual identity instability. We then discuss how these concepts inform our understanding of the disease in humans. Mol. Reprod. Dev. 84: 200-211, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Comparative Study of the Effect of Defects on Selective Adsorption of Butanol from Butanol/Water Binary Vapor Mixtures in Silicalite-1 Films

DOE PAGES

Farzaneh, Amirfarrokh; DeJaco, Robert F.; Ohlin, Lindsay; ...

2017-08-02

A promising route for sustainable 1-butanol (butanol) production is ABE (acetone, butanol, ethanol) fermentation. However, recovery of the products is challenging because of the low concentrations obtained in the aqueous solution, thus hampering large-scale production of biobutanol. Membrane and adsorbent-based technologies using hydrophobic zeolites are interesting alternatives to traditional separation techniques (e.g., distillation) for energy-efficient separation of butanol from aqueous mixtures. To maximize the butanol over water selectivity of the material, it is important to reduce the number of hydrophilic adsorption sites. This can, for instance, be achieved by reducing the density of lattice defect sites where polar silanol groupsmore » are found. The density of silanol defects can be reduced by preparing the zeolite at neutral pH instead of using traditional synthesis solutions with high pH. In this work, binary adsorption of butanol and water in two silicalite-1 films was studied using in situ attenuated total reflectance–Fourier transform infrared (ATR-FTIR) spectroscopy under equal experimental conditions. One of the films was prepared in fluoride medium, whereas the other one was prepared at high pH using traditional synthesis conditions. The amounts of water and butanol adsorbed from binary vapor mixtures of varying composition were determined at 35 and 50 °C, and the corresponding adsorption selectivities were also obtained. Both samples showed very high selectivities (100–23 000) toward butanol under the conditions studied. The sample having low density of defects, in general, showed ca. a factor 10 times higher butanol selectivity than the sample having a higher density of defects at the same experimental conditions. This difference was due to a much lower adsorption of water in the sample with low density of internal defects. Analysis of molecular simulation trajectories provides insights on the local selectivities in the zeolite channel network and at the film surface.« less

Comparative Study of the Effect of Defects on Selective Adsorption of Butanol from Butanol/Water Binary Vapor Mixtures in Silicalite-1 Films

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

Farzaneh, Amirfarrokh; DeJaco, Robert F.; Ohlin, Lindsay

A promising route for sustainable 1-butanol (butanol) production is ABE (acetone, butanol, ethanol) fermentation. However, recovery of the products is challenging because of the low concentrations obtained in the aqueous solution, thus hampering large-scale production of biobutanol. Membrane and adsorbent-based technologies using hydrophobic zeolites are interesting alternatives to traditional separation techniques (e.g., distillation) for energy-efficient separation of butanol from aqueous mixtures. To maximize the butanol over water selectivity of the material, it is important to reduce the number of hydrophilic adsorption sites. This can, for instance, be achieved by reducing the density of lattice defect sites where polar silanol groupsmore » are found. The density of silanol defects can be reduced by preparing the zeolite at neutral pH instead of using traditional synthesis solutions with high pH. In this work, binary adsorption of butanol and water in two silicalite-1 films was studied using in situ attenuated total reflectance–Fourier transform infrared (ATR-FTIR) spectroscopy under equal experimental conditions. One of the films was prepared in fluoride medium, whereas the other one was prepared at high pH using traditional synthesis conditions. The amounts of water and butanol adsorbed from binary vapor mixtures of varying composition were determined at 35 and 50 °C, and the corresponding adsorption selectivities were also obtained. Both samples showed very high selectivities (100–23 000) toward butanol under the conditions studied. The sample having low density of defects, in general, showed ca. a factor 10 times higher butanol selectivity than the sample having a higher density of defects at the same experimental conditions. This difference was due to a much lower adsorption of water in the sample with low density of internal defects. Analysis of molecular simulation trajectories provides insights on the local selectivities in the zeolite channel network and at the film surface.« less

Defects in mercury-cadmium telluride heteroepitaxial structures grown by molecular-beam epitaxy on silicon substrates

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

Mynbaev, K. D., E-mail: mynkad@mail.ioffe.ru; Zablotsky, S. V.; Shilyaev, A. V.

Defects in mercury-cadmium-telluride heteroepitaxial structures (with 0.3 to 0.4 molar fraction of cadmium telluride) grown by molecular-beam epitaxy on silicon substrates are studied. The low-temperature photoluminescence method reveals that there are comparatively deep levels with energies of 50 to 60 meV and shallower levels with energies of 20 to 30 meV in the band gap. Analysis of the temperature dependence of the minority carrier lifetime demonstrates that this lifetime is controlled by energy levels with an energy of ∼30 meV. The possible relationship between energy states and crystal-structure defects is discussed.

Effects of electronic excitation on cascade dynamics in nickel–iron and nickel–palladium systems

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

Zarkadoula, Eva; Samolyuk, German; Weber, William J.

Using molecular dynamics simulations and the two-temperature model, we provide in this paper a comparison of the surviving damage from single ion irradiation events in nickel-based alloys, for cascades with and without taking into account the effects of the electronic excitations. We find that including the electronic effects impacts the amount of the resulting damage and the production of isolated defects. Finally, irradiation of nickel–palladium systems results in larger numbers of defects compared to nickel–iron systems, with similar numbers of isolated defects. We additionally investigate the mass effect on the two-temperature model in molecular dynamics simulations of cascades.

Effects of electronic excitation on cascade dynamics in nickel–iron and nickel–palladium systems

DOE PAGES

Zarkadoula, Eva; Samolyuk, German; Weber, William J.

2017-06-10

Using molecular dynamics simulations and the two-temperature model, we provide in this paper a comparison of the surviving damage from single ion irradiation events in nickel-based alloys, for cascades with and without taking into account the effects of the electronic excitations. We find that including the electronic effects impacts the amount of the resulting damage and the production of isolated defects. Finally, irradiation of nickel–palladium systems results in larger numbers of defects compared to nickel–iron systems, with similar numbers of isolated defects. We additionally investigate the mass effect on the two-temperature model in molecular dynamics simulations of cascades.

Fetal Alcohol Spectrum Disorder (FASD) Associated Neural Defects: Complex Mechanisms and Potential Therapeutic Targets

PubMed Central

Muralidharan, Pooja; Sarmah, Swapnalee; Zhou, Feng C.; Marrs, James A.

2013-01-01

Fetal alcohol spectrum disorder (FASD), caused by prenatal alcohol exposure, can result in craniofacial dysmorphism, cognitive impairment, sensory and motor disabilities among other defects. FASD incidences are as high as 2% to 5 % children born in the US, and prevalence is higher in low socioeconomic populations. Despite various mechanisms being proposed to explain the etiology of FASD, the molecular targets of ethanol toxicity during development are unknown. Proposed mechanisms include cell death, cell signaling defects and gene expression changes. More recently, the involvement of several other molecular pathways was explored, including non-coding RNA, epigenetic changes and specific vitamin deficiencies. These various pathways may interact, producing a wide spectrum of consequences. Detailed understanding of these various pathways and their interactions will facilitate the therapeutic target identification, leading to new clinical intervention, which may reduce the incidence and severity of these highly prevalent preventable birth defects. This review discusses manifestations of alcohol exposure on the developing central nervous system, including the neural crest cells and sensory neural placodes, focusing on molecular neurodevelopmental pathways as possible therapeutic targets for prevention or protection. PMID:24961433

Fetal Alcohol Spectrum Disorder (FASD) Associated Neural Defects: Complex Mechanisms and Potential Therapeutic Targets.

PubMed

Muralidharan, Pooja; Sarmah, Swapnalee; Zhou, Feng C; Marrs, James A

2013-06-19

Fetal alcohol spectrum disorder (FASD), caused by prenatal alcohol exposure, can result in craniofacial dysmorphism, cognitive impairment, sensory and motor disabilities among other defects. FASD incidences are as high as 2% to 5 % children born in the US, and prevalence is higher in low socioeconomic populations. Despite various mechanisms being proposed to explain the etiology of FASD, the molecular targets of ethanol toxicity during development are unknown. Proposed mechanisms include cell death, cell signaling defects and gene expression changes. More recently, the involvement of several other molecular pathways was explored, including non-coding RNA, epigenetic changes and specific vitamin deficiencies. These various pathways may interact, producing a wide spectrum of consequences. Detailed understanding of these various pathways and their interactions will facilitate the therapeutic target identification, leading to new clinical intervention, which may reduce the incidence and severity of these highly prevalent preventable birth defects. This review discusses manifestations of alcohol exposure on the developing central nervous system, including the neural crest cells and sensory neural placodes, focusing on molecular neurodevelopmental pathways as possible therapeutic targets for prevention or protection.

Mechanics of neurulation: From classical to current perspectives on the physical mechanics that shape, fold, and form the neural tube.

PubMed

Vijayraghavan, Deepthi S; Davidson, Lance A

2017-01-30

Neural tube defects arise from mechanical failures in the process of neurulation. At the most fundamental level, formation of the neural tube relies on coordinated, complex tissue movements that mechanically transform the flat neural epithelium into a lumenized epithelial tube (Davidson, 2012). The nature of this mechanical transformation has mystified embryologists, geneticists, and clinicians for more than 100 years. Early embryologists pondered the physical mechanisms that guide this transformation. Detailed observations of cell and tissue movements as well as experimental embryological manipulations allowed researchers to generate and test elementary hypotheses of the intrinsic and extrinsic forces acting on the neural tissue. Current research has turned toward understanding the molecular mechanisms underlying neurulation. Genetic and molecular perturbation have identified a multitude of subcellular components that correlate with cell behaviors and tissue movements during neural tube formation. In this review, we focus on methods and conceptual frameworks that have been applied to the study of amphibian neurulation that can be used to determine how molecular and physical mechanisms are integrated and responsible for neurulation. We will describe how qualitative descriptions and quantitative measurements of strain, force generation, and tissue material properties as well as simulations can be used to understand how embryos use morphogenetic programs to drive neurulation. Birth Defects Research 109:153-168, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Strain-Rate Dependence of Deformation-Twinning in Tantalum

NASA Astrophysics Data System (ADS)

Abeywardhana, Jayalath; Germann, Tim; Ravelo, Ramon

2017-06-01

Large-Scale molecular dynamics (MD) simulations are used to model quasi-isentropic compression and expansion (QIC) in tantalum crystals varying the rate of deformation between the range 108 -1012s-1 and compressive pressures up to 100 GPa. The atomic interactions were modeled employing an embedded-atom method (EAM) potential of Ta. Isentropic expansion was done employing samples initially compressed to pressures of 60 and 100 GPa followed by uniaxial and quasi-isentropically expansion to zero pressure. The effect of initial dislocation density on twinning was also examined by varying the initial defect density of the Ta samples (1010 -1012cm-2). At these high-strain rates, a threshold in strain-rate on deformation twining is observed. Under expansion or compression, deformation twinning increases with strain rate for strain-rates >109s-1 . Below this value, small fraction of twins nucleates but anneal out with time. Samples with lower fraction of twins equilibrate to defect states containing higher screw dislocation densities from those with initially higher twinning fractions. This work was supported by the Department of Energy under contract DE-AC52-06NA25396 and by the Air Force Office of Scientific Research under AFOSR Award No. FA9550-12-1-0476.

K-RasV14I recapitulates Noonan syndrome in mice

PubMed Central

Hernández-Porras, Isabel; Fabbiano, Salvatore; Schuhmacher, Alberto J.; Aicher, Alexandra; Cañamero, Marta; Cámara, Juan Antonio; Cussó, Lorena; Desco, Manuel; Heeschen, Christopher; Mulero, Francisca; Bustelo, Xosé R.; Guerra, Carmen; Barbacid, Mariano

2014-01-01

Noonan syndrome (NS) is an autosomal dominant genetic disorder characterized by short stature, craniofacial dysmorphism, and congenital heart defects. NS also is associated with a risk for developing myeloproliferative disorders (MPD), including juvenile myelomonocytic leukemia (JMML). Mutations responsible for NS occur in at least 11 different loci including KRAS. Here we describe a mouse model for NS induced by K-RasV14I, a recurrent KRAS mutation in NS patients. K-RasV14I–mutant mice displayed multiple NS-associated developmental defects such as growth delay, craniofacial dysmorphia, cardiac defects, and hematologic abnormalities including a severe form of MPD that resembles human JMML. Homozygous animals had perinatal lethality whose penetrance varied with genetic background. Exposure of pregnant mothers to a MEK inhibitor rescued perinatal lethality and prevented craniofacial dysmorphia and cardiac defects. However, Mek inhibition was not sufficient to correct these defects when mice were treated after weaning. Interestingly, Mek inhibition did not correct the neoplastic MPD characteristic of these mutant mice, regardless of the timing at which the mice were treated, thus suggesting that MPD is driven by additional signaling pathways. These genetically engineered K-RasV14I–mutant mice offer an experimental tool for studying the molecular mechanisms underlying the clinical manifestations of NS. Perhaps more importantly, they should be useful as a preclinical model to test new therapies aimed at preventing or ameliorating those deficits associated with this syndrome. PMID:25359213

Configuration of ripple domains and their topological defects formed under local mechanical stress on hexagonal monolayer graphene

DOE PAGES

Park, Yeonggu; Choi, Jin Sik; Choi, Taekjib; ...

2015-03-24

Ripples in graphene are extensively investigated because they ensure the mechanical stability of two-dimensional graphene and affect its electronic properties. They arise from spontaneous symmetry breaking and are usually manifested in the form of domains with long-range order. It is expected that topological defects accompany a material exhibiting long-range order, whose functionality depends on characteristics of domains and topological defects. However, there remains a lack of understanding regarding ripple domains and their topological defects formed on monolayer graphene. Here we explore configuration of ripple domains and their topological defects in exfoliated monolayer graphenes on SiO₂/Si substrates using transverse shear microscope.more » We observe three-color domains with three different ripple directions, which meet at a core. Furthermore, the closed domain is surrounded by an even number of cores connected together by domain boundaries, similar to topological vortex and anti-vortex pairs. In addition, we have found that axisymmetric three-color domains can be induced around nanoparticles underneath the graphene. This fascinating configuration of ripple domains may result from the intrinsic hexagonal symmetry of two-dimensional graphene, which is supported by theoretical simulation using molecular dynamics. Our findings are expected to play a key role in understanding of ripple physics in graphene and other two-dimensional materials.« less

Configuration of ripple domains and their topological defects formed under local mechanical stress on hexagonal monolayer graphene

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

Park, Yeonggu; Choi, Jin Sik; Choi, Taekjib

Ripples in graphene are extensively investigated because they ensure the mechanical stability of two-dimensional graphene and affect its electronic properties. They arise from spontaneous symmetry breaking and are usually manifested in the form of domains with long-range order. It is expected that topological defects accompany a material exhibiting long-range order, whose functionality depends on characteristics of domains and topological defects. However, there remains a lack of understanding regarding ripple domains and their topological defects formed on monolayer graphene. Here we explore configuration of ripple domains and their topological defects in exfoliated monolayer graphenes on SiO₂/Si substrates using transverse shear microscope.more » We observe three-color domains with three different ripple directions, which meet at a core. Furthermore, the closed domain is surrounded by an even number of cores connected together by domain boundaries, similar to topological vortex and anti-vortex pairs. In addition, we have found that axisymmetric three-color domains can be induced around nanoparticles underneath the graphene. This fascinating configuration of ripple domains may result from the intrinsic hexagonal symmetry of two-dimensional graphene, which is supported by theoretical simulation using molecular dynamics. Our findings are expected to play a key role in understanding of ripple physics in graphene and other two-dimensional materials.« less

More than a bystander: the contributions of intrinsic skeletal muscle defects in motor neuron diseases

PubMed Central

Boyer, Justin G.; Ferrier, Andrew; Kothary, Rashmi

2013-01-01

Spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS), and spinal-bulbar muscular atrophy (SBMA) are devastating diseases characterized by the degeneration of motor neurons. Although the molecular causes underlying these diseases differ, recent findings have highlighted the contribution of intrinsic skeletal muscle defects in motor neuron diseases. The use of cell culture and animal models has led to the important finding that muscle defects occur prior to and independently of motor neuron degeneration in motor neuron diseases. In SMA for instance, the muscle specific requirements of the SMA disease-causing gene have been demonstrated by a series of genetic rescue experiments in SMA models. Conditional ALS mouse models expressing a muscle specific mutant SOD1 gene develop atrophy and muscle degeneration in the absence of motor neuron pathology. Treating SBMA mice by over-expressing IGF-1 in a skeletal muscle-specific manner attenuates disease severity and improves motor neuron pathology. In the present review, we provide an in depth description of muscle intrinsic defects, and discuss how they impact muscle function in these diseases. Furthermore, we discuss muscle-specific therapeutic strategies used to treat animal models of SMA, ALS, and SBMA. The study of intrinsic skeletal muscle defects is crucial for the understanding of the pathophysiology of these diseases and will open new therapeutic options for the treatment of motor neuron diseases. PMID:24391590

Type 2 diabetes mellitus induces congenital heart defects in murine embryos by increasing oxidative stress, endoplasmic reticulum stress, and apoptosis.

PubMed

Wu, Yanqing; Reece, E Albert; Zhong, Jianxiang; Dong, Daoyin; Shen, Wei-Bin; Harman, Christopher R; Yang, Peixin

2016-09-01

Maternal type 1 and 2 diabetes mellitus are strongly associated with high rates of severe structural birth defects, including congenital heart defects. Studies in type 1 diabetic embryopathy animal models have demonstrated that cellular stress-induced apoptosis mediates the teratogenicity of maternal diabetes leading to congenital heart defect formation. However, the mechanisms underlying maternal type 2 diabetes mellitus-induced congenital heart defects remain largely unknown. We aim to determine whether oxidative stress, endoplasmic reticulum stress, and excessive apoptosis are the intracellular molecular mechanisms underlying maternal type 2 diabetes mellitus-induced congenital heart defects. A mouse model of maternal type 2 diabetes mellitus was established by feeding female mice a high-fat diet (60% fat). After 15 weeks on the high-fat diet, the mice showed characteristics of maternal type 2 diabetes mellitus. Control dams were either fed a normal diet (10% fat) or the high-fat diet during pregnancy only. Female mice from the high-fat diet group and the 2 control groups were mated with male mice that were fed a normal diet. At E12.5, embryonic hearts were harvested to determine the levels of lipid peroxides and superoxide, endoplasmic reticulum stress markers, cleaved caspase 3 and 8, and apoptosis. E17.5 embryonic hearts were harvested for the detection of congenital heart defect formation using India ink vessel patterning and histological examination. Maternal type 2 diabetes mellitus significantly induced ventricular septal defects and persistent truncus arteriosus in the developing heart, along with increasing oxidative stress markers, including superoxide and lipid peroxidation; endoplasmic reticulum stress markers, including protein levels of phosphorylated-protein kinase RNA-like endoplasmic reticulum kinase, phosphorylated-IRE1α, phosphorylated-eIF2α, C/EBP homologous protein, and binding immunoglobulin protein; endoplasmic reticulum chaperone gene expression; and XBP1 messenger RNA splicing, as well as increased cleaved caspase 3 and 8 in embryonic hearts. Furthermore, maternal type 2 diabetes mellitus triggered excessive apoptosis in ventricular myocardium, endocardial cushion, and outflow tract of the embryonic heart. Similar to those observations in type 1 diabetic embryopathy, maternal type 2 diabetes mellitus causes heart defects in the developing embryo manifested with oxidative stress, endoplasmic reticulum stress, and excessive apoptosis in heart cells. Copyright © 2016 Elsevier Inc. All rights reserved.

A mutation in the Norrie disease gene (NDP) associated with X-linked familial exudative vitreoretinopathy.

PubMed

Chen, Z Y; Battinelli, E M; Fielder, A; Bundey, S; Sims, K; Breakefield, X O; Craig, I W

1993-10-01

Familial exudative vitreoretinopathy (FEVR) is a hereditary disorder characterized by an abnormality of the peripheral retina. Both autosomal dominant (adFEVR) and X-linked (XLFEVR) forms have been described, but the biochemical defect(s) underlying the symptoms are unknown. Molecular analysis of the Norrie gene locus (NDP) in a four generation FEVR family (shown previously to exhibit linkage to the X-chromosome markers DXS228 and MAOA (Xp11.4-p11.3)) reveals a missense mutation in the highly conserved region of the NDP gene, which caused a neutral amino acid substitution (Leu124Phe), was detected in all of the affected males, but not in the unaffected family members, nor in normal controls. The observations suggest that phenotypes of both XLFEVR and Norrie disease can result from mutations in the same gene.

CDYL Deficiency Disrupts Neuronal Migration and Increases Susceptibility to Epilepsy.

PubMed

Qin, Rui; Cao, Shuai; Lyu, Tianjie; Qi, Cai; Zhang, Weiguang; Wang, Yun

2017-01-10

During brain development, the correct migration of newborn neurons is one of the determinants of circuit formation, and neuronal migration defects may lead to neurological and psychiatric disorders. The molecular mechanisms underlying neuronal migration and related disorders are poorly understood. Here, we report that Chromodomain Y-like (CDYL) is critical for neuronal migration in mice. Knocking down CDYL caused neuronal migration defects and disrupted both mobility and multipolar-to-bipolar transition of migrating neurons. We find that CDYL regulates neuronal migration by transcriptionally repressing RhoA. In addition, CDYL deficiency increased the excitability of cortical pyramidal neurons and the susceptibility of mice to convulsant-induced seizures. These results demonstrate that CDYL is a regulator of neuronal migration and shed light on the pathogenesis of seizure-related neurodevelopmental disorders. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

The growth of high-Al-content InAlGaN quaternary alloys by RF-MBE

NASA Astrophysics Data System (ADS)

Wang, B. Z.; Wang, X. L.; Wang, X. Y.; Guo, L. C.; Wang, X. H.; Xiao, H. L.; Liu, H. X.

2007-02-01

High-Al-content InxAlyGa1-x-yN (x = 1-10%, y = 34-45%) quaternary alloys were grown on sapphire by radio-frequency plasma-excited molecular beam epitaxy. Rutherford back-scattering spectrometry, high resolution x-ray diffraction and cathodoluminescence were used to characterize the InAlGaN alloys. The experimental results show that InAlGaN with an appropriate Al/In ratio (near 4.7, which is a lattice-match to the GaN under-layer) has better crystal and optical quality than the InAlGaN alloys whose Al/In ratios are far from 4.7. Some cracks and V-defects occur in high-Al/In-ratio InAlGaN alloys. In the CL image, the cracks and V-defect regions are the emission-enhanced regions.

C. elegans model of neuronal aging

PubMed Central

Peng, Chiu-Ying; Chen, Chun-Hao; Hsu, Jiun-Min

2011-01-01

Aging of the nervous system underlies the behavioral and cognitive decline associated with senescence. Understanding the molecular and cellular basis of neuronal aging will therefore contribute to the development of effective treatments for aging and age-associated neurodegenerative disorders. Despite this pressing need, there are surprisingly few animal models that aim at recapitulating neuronal aging in a physiological context. We recently developed a C. elegans model of neuronal aging, and showed that age-dependent neuronal defects are regulated by insulin signaling. We identified electrical activity and epithelial attachment as two critical factors in the maintenance of structural integrity of C. elegans touch receptor neurons. These findings open a new avenue for elucidating the molecular mechanisms that maintain neuronal structures during the course of aging. PMID:22446530

Photochemical Creation of Fluorescent Quantum Defects in Semiconducting Carbon Nanotube Hosts.

PubMed

Wu, Xiaojian; Kim, Mijin; Kwon, Hyejin; Wang, YuHuang

2018-01-15

Quantum defects are an emerging class of synthetic single-photon emitters that hold vast potential for near-infrared imaging, chemical sensing, materials engineering, and quantum information processing. Herein, we show that it is possible to optically direct the synthetic creation of molecularly tunable fluorescent quantum defects in semiconducting single-walled carbon nanotube hosts through photochemical reactions. By exciting the host semiconductor with light that resonates with its electronic transition, we find that halide-containing aryl groups can covalently bond to the sp 2 carbon lattice. The introduced quantum defects generate bright photoluminescence that allows tracking of the reaction progress in situ. We show that the reaction is independent of temperature but correlates strongly with the photon energy used to drive the reaction, suggesting a photochemical mechanism rather than photothermal effects. This type of photochemical reactions opens the possibility to control the synthesis of fluorescent quantum defects using light and may enable lithographic patterning of quantum emitters with electronic and molecular precision. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Semiconducting molecular crystals: Bulk in-gap states modified by structural and chemical defects

NASA Astrophysics Data System (ADS)

Haas, S.; Krellner, C.; Goldmann, C.; Pernstich, K. P.; Gundlach, D. J.; Batlogg, B.

2007-03-01

Charge transport in organic molecular crystals is strongly influenced by the density of localized in-gap states (traps). Thus, a profound knowledge of the defect states' origin is essential. Temperature-dependent space-charge limited current (TD-SCLC) spectroscopy was used as a powerful tool to quantitatively study the density of states (DOS) in high-quality rubrene and pentacene single crystals. In particular, changes of the DOS due to intentionally induced chemical and structural defects were monitored. For instance, the controlled exposure of pentacene and rubrene to x-ray radiation results in a broad over-all increase of the DOS. Namely, the ionizing radiation induces a variety of both chemical and structural defects. On the other hand, exposure of rubrene to UV-excited oxygen is reflected in a sharp peak in the DOS, whereas in a similar experiment with pentacene oxygen acts as a dopant, and possible defects are metastable on the time-scale of the measurement, thus leaving the extracted DOS virtually unchanged.

[Molecular characterization of heterozygous beta-thalassemia in Lanzarote, Spain].

PubMed

Calvo-Villas, José Manuel; de la Iglesia Iñigo, Silvia; Ropero Gradilla, Paloma; Zapata Ramos, María Francisca; Cuesta Tovar, Jorge; Sicilia Guillén, Francisco

2008-04-05

The aim of this study was to determine the molecular defects of heterozygous beta thalassaemia and to ascertain their distribution in Lanzarote. Molecular characterization was achieved by real time polymerase chain reaction (RT-PCR LightCycler, Roche), PCR-ARMS (PCR-amplification reaction mutations system) and DNA sequencing on an automated DNA sequencer. Two hundred forty-three heterozygous beta thalassaemia carriers were included between July 1991 and February 2007. RT-PCR detected the molecular defect in 81% of the beta thalassaemia chromosomes analyzed [113 codon CD 39 (C --> T); 41 IVS-1-nt-110 (G --> A), 25 IVS 1-nt-1 (G --> A) and 19 IVS 1-nt-6 (T --> C)]. The remaining 12 molecular defects included the deletion 619 bp (7.8%) and the mutations -28 (A --> G), IVS1-nt-2 (T --> G), CD 41/42 (-TTCT), CD 8/9 (+G), CD 51 (-C), CD 22 (G --> T) and CD 24 (T --> A), CD 67 (-TG) and the novel mutation CD 20/21-TGGA. The distribution of the mutations is similar to that found in the Mediterranean area. The increasing migratory flow received in the Canary Islands may explain the emergence of new mutations not reported before in our area.

Melt-growth dynamics in CdTe crystals

DOE PAGES

Zhou, X. W.; Ward, D. K.; Wong, B. M.; ...

2012-06-01

We use a new, quantum-mechanics-based bond-order potential (BOP) to reveal melt growth dynamics and fine scale defect formation mechanisms in CdTe crystals. Previous molecular dynamics simulations of semiconductors have shown qualitatively incorrect behavior due to the lack of an interatomic potential capable of predicting both crystalline growth and property trends of many transitional structures encountered during the melt → crystal transformation. Here, we demonstrate successful molecular dynamics simulations of melt growth in CdTe using a BOP that significantly improves over other potentials on property trends of different phases. Our simulations result in a detailed understanding of defect formation during themore » melt growth process. Equally important, we show that the new BOP enables defect formation mechanisms to be studied at a scale level comparable to empirical molecular dynamics simulation methods with a fidelity level approaching quantum-mechanical methods.« less

Osteoblast dysfunctions in bone diseases: from cellular and molecular mechanisms to therapeutic strategies.

PubMed

Marie, Pierre J

2015-04-01

Several metabolic, genetic and oncogenic bone diseases are characterized by defective or excessive bone formation. These abnormalities are caused by dysfunctions in the commitment, differentiation or survival of cells of the osteoblast lineage. During the recent years, significant advances have been made in our understanding of the cellular and molecular mechanisms underlying the osteoblast dysfunctions in osteoporosis, skeletal dysplasias and primary bone tumors. This led to suggest novel therapeutic approaches to correct these abnormalities such as the modulation of WNT signaling, the pharmacological modulation of proteasome-mediated protein degradation, the induction of osteoprogenitor cell differentiation, the repression of cancer cell proliferation and the manipulation of epigenetic mechanisms. This article reviews our current understanding of the major cellular and molecular mechanisms inducing osteoblastic cell abnormalities in age-related bone loss, genetic skeletal dysplasias and primary bone tumors, and discusses emerging therapeutic strategies to counteract the osteoblast abnormalities in these disorders of bone formation.

The Developmental Regulator SEEDSTICK Controls Structural and Mechanical Properties of the Arabidopsis Seed Coat

PubMed Central

Beauzamy, Léna; Caporali, Elisabetta; Koroney, Abdoul-Salam

2016-01-01

Although many transcription factors involved in cell wall morphogenesis have been identified and studied, it is still unknown how genetic and molecular regulation of cell wall biosynthesis is integrated into developmental programs. We demonstrate by molecular genetic studies that SEEDSTICK (STK), a transcription factor controlling ovule and seed integument identity, directly regulates PMEI6 and other genes involved in the biogenesis of the cellulose-pectin matrix of the cell wall. Based on atomic force microscopy, immunocytochemistry, and chemical analyses, we propose that structural modifications of the cell wall matrix in the stk mutant contribute to defects in mucilage release and seed germination under water-stress conditions. Our studies reveal a molecular network controlled by STK that regulates cell wall properties of the seed coat, demonstrating that developmental regulators controlling organ identity also coordinate specific aspects of cell wall characteristics. PMID:27624758

Physiological and molecular determinants of embryo implantation

PubMed Central

Zhang, Shuang; Lin, Haiyan; Kong, Shuangbo; Wang, Shumin; Wang, Hongmei; Wang, Haibin; Armant, D. Randall

2014-01-01

Embryo implantation involves the intimate interaction between an implantation-competent blastocyst and a receptive uterus, which occurs in a limited time period known as the window of implantation. Emerging evidence shows that defects originating during embryo implantation induce ripple effects with adverse consequences on later gestation events, highlighting the significance of this event for pregnancy success. Although a multitude of cellular events and molecular pathways involved in embryo-uterine crosstalk during implantation have been identified through gene expression studies and genetically engineered mouse models, a comprehensive understanding of the nature of embryo implantation is still missing. This review focuses on recent progress with particular attention to physiological and molecular determinants of blastocyst activation, uterine receptivity, blastocyst attachment and uterine decidualization. A better understanding of underlying mechanisms governing embryo implantation should generate new strategies to rectify implantation failure and improve pregnancy rates in women. PMID:23290997

Folate receptor 1 is necessary for neural plate cell apical constriction during Xenopus neural tube formation

PubMed Central

Balashova, Olga A.; Visina, Olesya

2017-01-01

Folate supplementation prevents up to 70% of neural tube defects (NTDs), which result from a failure of neural tube closure during embryogenesis. The elucidation of the mechanisms underlying folate action has been challenging. This study introduces Xenopus laevis as a model to determine the cellular and molecular mechanisms involved in folate action during neural tube formation. We show that knockdown of folate receptor 1 (Folr1; also known as FRα) impairs neural tube formation and leads to NTDs. Folr1 knockdown in neural plate cells only is necessary and sufficient to induce NTDs. Folr1-deficient neural plate cells fail to constrict, resulting in widening of the neural plate midline and defective neural tube closure. Pharmacological inhibition of folate action by methotrexate during neurulation induces NTDs by inhibiting folate interaction with its uptake systems. Our findings support a model in which the folate receptor interacts with cell adhesion molecules, thus regulating the apical cell membrane remodeling and cytoskeletal dynamics necessary for neural plate folding. Further studies in this organism could unveil novel cellular and molecular events mediated by folate and lead to new ways of preventing NTDs. PMID:28255006

Ab initio molecular dynamics simulation of the effects of stacking faults on the radiation response of 3C-SiC

PubMed Central

Jiang, M.; Peng, S. M.; Zhang, H. B.; Xu, C. H.; Xiao, H. Y.; Zhao, F. A.; Liu, Z. J.; Zu, X. T.

2016-01-01

In this study, an ab initio molecular dynamics method is employed to investigate how the existence of stacking faults (SFs) influences the response of SiC to low energy irradiation. It reveals that the C and Si atoms around the SFs are generally more difficult to be displaced than those in unfaulted SiC, and the corresponding threshold displacement energies for them are generally larger, indicative of enhanced radiation tolerance caused by the introduction of SFs, which agrees well with the recent experiment. As compared with the unfaulted state, more localized point defects are generated in faulted SiC. Also, the efficiency of damage production for Si recoils is generally higher than that of C recoils. The calculated potential energy increases for defect generation in SiC with intrinsic and extrinsic SFs are found to be higher than those in unfaulted SiC, due to the stronger screen-Coulomb interaction between the PKA and its neighbors. The presented results provide a fundamental insight into the underlying mechanism of displacement events in faulted SiC and will help to advance the understanding of the radiation response of SiC with and without SFs. PMID:26880027

Ab initio molecular dynamics investigations of low-energy recoil events in Ni and NiCo

DOE PAGES

Liu, Bin; Yuan, Fenglin; Jin, Ke; ...

2015-10-06

Low-energy recoil events in pure Ni and the equiatomic NiCo alloy are studied using ab initio molecular dynamics simulations. We found that the threshold displacement energies are strongly dependent on orientation and weakly dependent on composition. The minimum threshold displacement energies are along the [1 1 0] direction in both pure Ni and the NiCo alloy. Compared to pure Ni, the threshold displacement energies increase slightly in the NiCo alloy due to stronger bonds in the alloy, irrespective of the element type of the PKA. A single Ni interstitial occupying the center of a tetrahedron formed by four Ni atomsmore » and a <1 0 0> split interstitial is produced in pure Ni by the recoils, while only the <1 0 0> split interstitial is formed in the NiCo alloy. Compared to the replacement sequences in pure Ni, anti-site defect sequences are observed in the alloy, which have high efficiency for both producing defects and transporting energy outside of the cascade core. These results provide insights into energy transfer processes occurring in equiatomic alloys under irradiation.« less

Defects in GaAs films grown by MOMBE

NASA Astrophysics Data System (ADS)

Werner, K.; Heinecke, H.; Weyers, M.; Lüth, H.; Balk, P.

1987-02-01

The nature and densities of the defects obtained in MOMBE GaAs films have been studied. In addition to particulate matter deposited on the surface, imperfections in the substrate will lead to defect generation. Furthermore, the rate of generation is strongly affected by the ratio of the pressures of the group III alkyl and the group V hydride in the molecular beams and by the growth temperature, also on defect-free substrates. Doping has no effect on the defect structure of the surface. By proper choice of experimental conditions defect densities below 100 cm -2 may be consistently obtained.

Personalised Medicine: Genome Maintenance Lessons Learned from Studies in Yeast as a Model Organism.

PubMed

Abugable, Arwa A; Awwad, Dahlia A; Fleifel, Dalia; Ali, Mohamed M; El-Khamisy, Sherif; Elserafy, Menattallah

2017-01-01

Yeast research has been tremendously contributing to the understanding of a variety of molecular pathways due to the ease of its genetic manipulation, fast doubling time as well as being cost-effective. The understanding of these pathways did not only help scientists learn more about the cellular functions but also assisted in deciphering the genetic and cellular defects behind multiple diseases. Hence, yeast research not only opened the doors for transforming basic research into applied research, but also paved the roads for improving diagnosis and innovating personalized therapy of different diseases. In this chapter, we discuss how yeast research has contributed to understanding major genome maintenance pathways such as the S-phase checkpoint activation pathways, repair via homologous recombination and non-homologous end joining as well as topoisomerases-induced protein linked DNA breaks repair. Defects in these pathways lead to neurodegenerative diseases and cancer. Thus, the understanding of the exact genetic defects underlying these diseases allowed the development of personalized medicine, improving the diagnosis and treatment and overcoming the detriments of current conventional therapies such as the side effects, toxicity as well as drug resistance.

Embryonic cholecystitis and defective gallbladder contraction in the Sox17-haploinsufficient mouse model of biliary atresia

PubMed Central

Fujino, Ko; Igarashi, Hitomi; Imaimatsu, Kenya; Tsunekawa, Naoki; Hirate, Yoshikazu; Kurohmaru, Masamichi; Saijoh, Yukio; Kanai-Azuma, Masami

2017-01-01

The gallbladder excretes cytotoxic bile acids into the duodenum through the cystic duct and common bile duct system. Sox17 haploinsufficiency causes biliary atresia-like phenotypes and hepatitis in late organogenesis mouse embryos, but the molecular and cellular mechanisms underlying this remain unclear. In this study, transcriptomic analyses revealed the early onset of cholecystitis in Sox17+/− embryos, together with the appearance of ectopic cystic duct-like epithelia in their gallbladders. The embryonic hepatitis showed positive correlations with the severity of cholecystitis in individual Sox17+/− embryos. Embryonic hepatitis could be induced by conditional deletion of Sox17 in the primordial gallbladder epithelia but not in fetal liver hepatoblasts. The Sox17+/− gallbladder also showed a drastic reduction in sonic hedgehog expression, leading to aberrant smooth muscle formation and defective contraction of the fetal gallbladder. The defective gallbladder contraction positively correlated with the severity of embryonic hepatitis in Sox17+/− embryos, suggesting a potential contribution of embryonic cholecystitis and fetal gallbladder contraction in the early pathogenesis of congenital biliary atresia. PMID:28432216

Neural and Synaptic Defects in slytherin a Zebrafish Model for Human Congenital Disorders of Glycosylation

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

Y Song; J Willer; P Scherer

2011-12-31

Congenital disorder of glycosylation type IIc (CDG IIc) is characterized by mental retardation, slowed growth and severe immunodeficiency, attributed to the lack of fucosylated glycoproteins. While impaired Notch signaling has been implicated in some aspects of CDG IIc pathogenesis, the molecular and cellular mechanisms remain poorly understood. We have identified a zebrafish mutant slytherin (srn), which harbors a missense point mutation in GDP-mannose 4,6 dehydratase (GMDS), the rate-limiting enzyme in protein fucosylation, including that of Notch. Here we report that some of the mechanisms underlying the neural phenotypes in srn and in CGD IIc are Notch-dependent, while others are Notch-independent.more » We show, for the first time in a vertebrate in vivo, that defects in protein fucosylation leads to defects in neuronal differentiation, maintenance, axon branching, and synapse formation. Srn is thus a useful and important vertebrate model for human CDG IIc that has provided new insights into the neural phenotypes that are hallmarks of the human disorder and has also highlighted the role of protein fucosylation in neural development.« less

The Molecular Basis of Hereditary Enamel Defects in Humans

PubMed Central

Carrion, I.A.; Morris, C.

2015-01-01

The formation of human enamel is highly regulated at the molecular level and involves thousands of genes. Requisites for development of this highly mineralized tissue include cell differentiation; production of a unique extracellular matrix; processing of the extracellular matrix; altering of cell function during different stages of enamel formation; cell movement and attachment; regulation of ion and protein movement; and regulation of hydration, pH, and other conditions of the microenvironment, to name just a few. Not surprising, there is a plethora of hereditary conditions with an enamel phenotype. The objective of this review was to identify the hereditary conditions listed on Online Mendelian Inheritance in Man (OMIM) that have an associated enamel phenotype and whether a causative gene has been identified. The OMIM database was searched with the terms amelogenesis, enamel, dental, and tooth, and all results were screened by 2 individuals to determine if an enamel phenotype was identified. Gene and gene product function was reviewed on OMIM and from publications identified in PubMed. The search strategy revealed 91 conditions listed in OMIM as having an enamel phenotype, and of those, 71 have a known molecular etiology or linked genetic loci. The purported protein function of those conditions with a known genetic basis included enzymes, regulatory proteins, extracellular matrix proteins, transcription factors, and transmembrane proteins. The most common enamel phenotype was a deficient amount of enamel, or enamel hypoplasia, with hypomineralization defects being reported less frequently. Knowing these molecular defects allows an initial cataloging of molecular pathways that lead to hereditary enamel defects in humans. This knowledge provides insight into the diverse molecular pathways involved in enamel formation and can be useful when searching for the genetic etiology of hereditary conditions that involve enamel. PMID:25389004

The molecular basis of hereditary enamel defects in humans.

PubMed

Wright, J T; Carrion, I A; Morris, C

2015-01-01

The formation of human enamel is highly regulated at the molecular level and involves thousands of genes. Requisites for development of this highly mineralized tissue include cell differentiation; production of a unique extracellular matrix; processing of the extracellular matrix; altering of cell function during different stages of enamel formation; cell movement and attachment; regulation of ion and protein movement; and regulation of hydration, pH, and other conditions of the microenvironment, to name just a few. Not surprising, there is a plethora of hereditary conditions with an enamel phenotype. The objective of this review was to identify the hereditary conditions listed on Online Mendelian Inheritance in Man (OMIM) that have an associated enamel phenotype and whether a causative gene has been identified. The OMIM database was searched with the terms amelogenesis, enamel, dental, and tooth, and all results were screened by 2 individuals to determine if an enamel phenotype was identified. Gene and gene product function was reviewed on OMIM and from publications identified in PubMed. The search strategy revealed 91 conditions listed in OMIM as having an enamel phenotype, and of those, 71 have a known molecular etiology or linked genetic loci. The purported protein function of those conditions with a known genetic basis included enzymes, regulatory proteins, extracellular matrix proteins, transcription factors, and transmembrane proteins. The most common enamel phenotype was a deficient amount of enamel, or enamel hypoplasia, with hypomineralization defects being reported less frequently. Knowing these molecular defects allows an initial cataloging of molecular pathways that lead to hereditary enamel defects in humans. This knowledge provides insight into the diverse molecular pathways involved in enamel formation and can be useful when searching for the genetic etiology of hereditary conditions that involve enamel. © International & American Associations for Dental Research 2014.

Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Human Neuroepithelial Stem Cells and Radial Glia.

PubMed

Onorati, Marco; Li, Zhen; Liu, Fuchen; Sousa, André M M; Nakagawa, Naoki; Li, Mingfeng; Dell'Anno, Maria Teresa; Gulden, Forrest O; Pochareddy, Sirisha; Tebbenkamp, Andrew T N; Han, Wenqi; Pletikos, Mihovil; Gao, Tianliuyun; Zhu, Ying; Bichsel, Candace; Varela, Luis; Szigeti-Buck, Klara; Lisgo, Steven; Zhang, Yalan; Testen, Anze; Gao, Xiao-Bing; Mlakar, Jernej; Popovic, Mara; Flamand, Marie; Strittmatter, Stephen M; Kaczmarek, Leonard K; Anton, E S; Horvath, Tamas L; Lindenbach, Brett D; Sestan, Nenad

2016-09-06

The mechanisms underlying Zika virus (ZIKV)-related microcephaly and other neurodevelopment defects remain poorly understood. Here, we describe the derivation and characterization, including single-cell RNA-seq, of neocortical and spinal cord neuroepithelial stem (NES) cells to model early human neurodevelopment and ZIKV-related neuropathogenesis. By analyzing human NES cells, organotypic fetal brain slices, and a ZIKV-infected micrencephalic brain, we show that ZIKV infects both neocortical and spinal NES cells as well as their fetal homolog, radial glial cells (RGCs), causing disrupted mitoses, supernumerary centrosomes, structural disorganization, and cell death. ZIKV infection of NES cells and RGCs causes centrosomal depletion and mitochondrial sequestration of phospho-TBK1 during mitosis. We also found that nucleoside analogs inhibit ZIKV replication in NES cells, protecting them from ZIKV-induced pTBK1 relocalization and cell death. We established a model system of human neural stem cells to reveal cellular and molecular mechanisms underlying neurodevelopmental defects associated with ZIKV infection and its potential treatment. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Identification of Genetic Defects Underlying FXII Deficiency in Four Unrelated Chinese Patients.

PubMed

Yang, Lihong; Wang, Yingyu; Zhou, Jianpin; Cheng, Xiaoli; Hao, Xiuping; Xie, Haixiao; Jin, Yanhui; Wang, Mingshan

2016-01-01

Congenital factor XII (FXII) dexFB01;ciency is a rare autosomal recessive disorder, characterized by a great variability in its clinical manifestations. In this study, we screened for mutations in the F12 gene of 4 unrelated patients with FXII coagulant activity <10% of that of normal human plasma. To investigate the molecular defects in these FXII-deficient patients, we performed FXII mutation screening. By sequencing all coding exons as well as xFB02;anking intronic regions of the F12 gene, 6 different mutations, including 3 missense mutations (Gly341Arg, Glu502Lys and Gly542 Ser), 1 insertion (7142insertC) and 2 deletions (5741-5742 delCA and 6753-6755delACA), were identixFB01;ed on the F12 gene. Three of them (Gly341Arg, 5741-5742delCA and 6753-6755delACA) are reported here for the first time. Computer-based algorithms predicted these missense mutations to be deleterious. This study has increased our knowledge of the mutational spectrum underlying FXII deficiency. © 2016 S. Karger AG, Basel.

Molecular dynamics simulation of shock induced ejection on fused silica surface

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

Su, Rui; Xiang, Meizhen; Jiang, Shengli

2014-05-21

Shock response and surface ejection behaviors of fused silica are studied by using non-equilibrium molecular dynamics combining with the Tersoff potential. First, bulk structure and Hugoniot curves of fused silica are calculated and compared with experimental results. Then, the dynamical process of surface ejection behavior is simulated under different loading velocities ranging from 3.5 to 5.0 km∕s, corresponding to shock wave velocities from 7.1 to 8.8 km∕s. The local atomistic shear strain parameter is used to describe the local plastic deformation under conditions of shock compression or releasing. Our result shows that the shear strain is localized in the bottom area ofmore » groove under the shock compression. Surface ejection is observed when the loading velocity exceeds 4.0 km∕s. Meanwhile, the temperature of the micro-jet is ∼5574.7 K, which is close to experiment measurement. Several kinds of structural defects including non-bridging oxygen are found in the bulk area of the sample after ejection.« less

On the activation of molecular hydrogen by gold: a theoretical approximation to the nature of potential active sites.

PubMed

Corma, Avelino; Boronat, Mercedes; González, Silvia; Illas, Francesc

2007-08-28

The study of adsorption and dissociation of molecular hydrogen on single crystal Au(111) and Au(001) surfaces, monoatomic rows in an extended line defect and different Au nanoparticles by means of DF calculations allows us to firmly conclude that the necessary and sufficient condition for H2 dissociation is the existence of low coordinated Au atoms, regardless if they are in nanoparticles or at extended line defects.

Percutaneous treatment of atrial septal defects, muscular ventricular septal defects and patent ductus arteriosus in infants under one year of age.

PubMed

Prada, Fredy; Mortera, Carlos; Bartrons, Joaquim; Rissech, Miguel; Jiménez, Lorenzo; Carretero, Juan; Llevadias, Judit; Araica, Mireya

2009-09-01

Amplatzer devices are used for the percutaneous closure of ostium secundum atrial septal defects, muscular ventricular septal defects and patent ductus arteriosus. However, very little experience has been gained in using these devices in infants under 1 year of age. Between January 2001 and January 2008, 22 symptomatic infants aged under 1 year underwent percutaneous treatment: three had an ostium secundum atrial septal defect, 15 had patent ductus arteriosus, and four had a muscular ventricular septal defect. All the procedures were completed successfully. No immediate or medium-term complications were observed. Closure of these types of defect using an Amplatzer device in infants under 1 year of age, who would otherwise require surgery, is a safe and effective procedure.

Effects of Stone-Wales and vacancy defects in atomic-scale friction on defective graphite

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

Sun, Xiao-Yu; Key Laboratory of Hubei Province for Water Jet Theory and New Technology, Wuhan University, Wuhan 430072; Wu, RunNi

2014-05-05

Graphite is an excellent solid lubricant for surface coating, but its performance is significantly weakened by the vacancy or Stone-Wales (SW) defect. This study uses molecular dynamics simulations to explore the frictional behavior of a diamond tip sliding over a graphite which contains a single defect or stacked defects. Our results suggest that the friction on defective graphite shows a strong dependence on defect location and type. The 5-7-7-5 structure of SW defect results in an effectively negative slope of friction. For defective graphite containing a defect in the surface, adding a single vacancy in the interior layer will decreasemore » the friction coefficients, while setting a SW defect in the interior layer may increase the friction coefficients. Our obtained results may provide useful information for understanding the atomic-scale friction properties of defective graphite.« less

Impact of extended defects on recombination in CdTe heterostructures grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Zaunbrecher, Katherine N.; Kuciauskas, Darius; Swartz, Craig H.; Dippo, Pat; Edirisooriya, Madhavie; Ogedengbe, Olanrewaju S.; Sohal, Sandeep; Hancock, Bobby L.; LeBlanc, Elizabeth G.; Jayathilaka, Pathiraja A. R. D.; Barnes, Teresa M.; Myers, Thomas H.

2016-08-01

Heterostructures with CdTe and CdTe1-xSex (x ˜ 0.01) absorbers between two wider-band-gap Cd1-xMgxTe barriers (x ˜ 0.25-0.3) were grown by molecular beam epitaxy to study carrier generation and recombination in bulk materials with passivated interfaces. Using a combination of confocal photoluminescence (PL), time-resolved PL, and low-temperature PL emission spectroscopy, two extended defect types were identified and the impact of these defects on charge-carrier recombination was analyzed. The dominant defects identified by confocal PL were dislocations in samples grown on (211)B CdTe substrates and crystallographic twinning-related defects in samples on (100)-oriented InSb substrates. Low-temperature PL shows that twin-related defects have a zero-phonon energy of 1.460 eV and a Huang-Rhys factor of 1.50, while dislocation-dominated samples have a 1.473-eV zero-phonon energy and a Huang-Rhys factor of 1.22. The charge carrier diffusion length near both types of defects is ˜6 μm, suggesting that recombination is limited by diffusion dynamics. For heterostructures with a low concentration of extended defects, the bulk lifetime was determined to be 2.2 μs with an interface recombination velocity of 160 cm/s and an estimated radiative lifetime of 91 μs.

Impact of extended defects on recombination in CdTe heterostructures grown by molecular beam epitaxy

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

Zaunbrecher, Katherine N.; Kuciauskas, Darius; Swartz, Craig H.

Heterostructures with CdTe and CdTe 1-xSex (x ~ 0.01) absorbers between two wider-band-gap Cd1-xMgxTe barriers (x ~ 0.25-0.3) were grown by molecular beam epitaxy to study carrier generation and recombination in bulk materials with passivated interfaces. Using a combination of confocal photoluminescence (PL), time-resolved PL, and low-temperature PL emission spectroscopy, two extended defect types were identified and the impact of these defects on charge-carrier recombination was analyzed. The dominant defects identified by confocal PL were dislocations in samples grown on (211)B CdTe substrates and crystallographic twinning-related defects in samples on (100)-oriented InSb substrates. Low-temperature PL shows that twin-related defects havemore » a zero-phonon energy of 1.460 eV and a Huang-Rhys factor of 1.50, while dislocation-dominated samples have a 1.473-eV zero-phonon energy and a Huang-Rhys factor of 1.22. The charge carrier diffusion length near both types of defects is ~6 um, suggesting that recombination is limited by diffusion dynamics. For heterostructures with a low concentration of extended defects, the bulk lifetime was determined to be 2.2 us with an interface recombination velocity of 160 cm/s and an estimated radiative lifetime of 91 us.« less

Vacancy-type defects in Mg-doped GaN grown by ammonia-based molecular beam epitaxy probed using a monoenergetic positron beam

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

Uedono, Akira; Malinverni, Marco; Martin, Denis

Vacancy-type defects in Mg-doped GaN were probed using a monoenergetic positron beam. GaN films with a thickness of 0.5–0.7 μm were grown on GaN/sapphire templates using ammonia-based molecular beam epitaxy and characterized by measuring Doppler broadening spectra. Although no vacancies were detected in samples with a Mg concentration [Mg] below 7 × 10{sup 19 }cm{sup −3}, vacancy-type defects were introduced starting at above [Mg] = 1 × 10{sup 20 }cm{sup −3}. The major defect species was identified as a complex between Ga vacancy (V{sub Ga}) and multiple nitrogen vacancies (V{sub N}s). The introduction of vacancy complexes was found to correlate with a decreasemore » in the net acceptor concentration, suggesting that the defect introduction is closely related to the carrier compensation. We also investigated Mg-doped GaN layers grown using In as the surfactant. The formation of vacancy complexes was suppressed in the subsurface region (≤80 nm). The observed depth distribution of defects was attributed to the thermal instability of the defects, which resulted in the introduction of vacancy complexes during the deposition process.« less

Carbon Nanotubes: Molecular Electronic Components

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Saini, Subhash; Menon, Madhu

1997-01-01

The carbon Nanotube junctions have recently emerged as excellent candidates for use as the building blocks in the formation of nanoscale molecular electronic networks. While the simple joint of two dissimilar tubes can be generated by the introduction of a pair of heptagon-pentagon defects in an otherwise perfect hexagonal graphene sheet, more complex joints require other mechanisms. In this work we explore structural characteristics of complex 3-point junctions of carbon nanotubes using a generalized tight-binding molecular-dynamics scheme. The study of pi-electron local densities of states (LDOS) of these junctions reveal many interesting features, most prominent among them being the defect-induced states in the gap.

Many-Body Theory of Proton-Generated Point Defects for Losses of Electron Energy and Photons in Quantum Wells

NASA Astrophysics Data System (ADS)

Huang, Danhong; Iurov, Andrii; Gao, Fei; Gumbs, Godfrey; Cardimona, D. A.

2018-02-01

The effects of point defects on the loss of either energies of ballistic electron beams or incident photons are studied by using a many-body theory in a multi-quantum-well system. This theory includes the defect-induced vertex correction to a bare polarization function of electrons within the ladder approximation, and the intralayer and interlayer screening of defect-electron interactions is also taken into account in the random-phase approximation. The numerical results of defect effects on both energy-loss and optical-absorption spectra are presented and analyzed for various defect densities, numbers of quantum wells, and wave vectors. The diffusion-reaction equation is employed for calculating distributions of point defects in a layered structure. For completeness, the production rate for Frenkel-pair defects and their initial concentration are obtained based on atomic-level molecular-dynamics simulations. By combining the defect-effect, diffusion-reaction, and molecular-dynamics models with an available space-weather-forecast model, it will be possible in the future to enable specific designing for electronic and optoelectronic quantum devices that will be operated in space with radiation-hardening protection and, therefore, effectively extend the lifetime of these satellite onboard electronic and optoelectronic devices. Specifically, this theory can lead to a better characterization of quantum-well photodetectors not only for high quantum efficiency and low dark current density but also for radiation tolerance or mitigating the effects of the radiation.

Distribution of point defects in Si(100)/Si grown by low-temperature molecular-beam epitaxy and solid-phase epitaxy

NASA Astrophysics Data System (ADS)

Asoka-Kumar, P.; Gossmann, H.-J.; Unterwald, F. C.; Feldman, L. C.; Leung, T. C.; Au, H. L.; Talyanski, V.; Nielsen, B.; Lynn, K. G.

1993-08-01

Positron annihilation in Si is a quantitaive, depth-sensitive technique for the detection of vacancylike defects or voids. A sensitivity of 5×1015 cm-3 for voidlike defects is easily achieved. The technique has been applied to a study of point-defect distributions in thin films of Si grown by molecular-beam epitaxy. A special procedure was developed to remove the influence of the native oxide on the positron measurement. 200-nm-thick films grown at temperatures between 475 and 560 °C show no defects below the sensitivity limit and are indistinguishable from the bulk substrate. So are films grown at 220 °C, provided a 2-min high-temperature anneal to a peak temperature of >=500 °C is executed every ~=30 nm during growth. If TRTA=450 °C, part of the film contains vacancylike defects to a concentration of ~=1018 cm-3. These results correlate well with current-voltage characteristics of p-n junctions grown with different rapid thermal anneal (RTA) temperatures. Ion scattering, with a defect sensitivity of ~=1%, shows no difference between films grown with different TRTA. Recrystallization of amorphous films, deposited at room temperature and annealed in situ at 550 °C, always leaves a significant defect concentration of ~=2×1018 cm-3; those defects are reduced but still present even after a 2-h 800 °C furnace anneal.

Non destructive examination of interface of molecular assembly

NASA Astrophysics Data System (ADS)

Perez, Guy; Richard, Isaline; Lecomte, Jean-Claude

2017-11-01

Molecular assembly interfaces can be characterised by mechanical testing and/or the interaction between waves and the interface. The disadvantage of the mechanical approach is that new defects may be produced at the interface, or existing defects may be destroyed. Using the interaction between waves and the interface is a non-destructive approach. But what kind of waves should be used? Electromagnetic waves in the visible range depend on wave attenuation in the material, infrared waves also depend on the thickness and X-ray waves have a too short a wave length to detect interface defects. In this article, the use of acoustic waves is proposed for non-destructive examination of molecular assembly interfaces. Acoustic wave propagation is very sensitive to variations in interface characteristics depending on whether the waves are reflected or transmitted. To improve the sensitivity and resolution of this technique, small wave lengths have been used with a scanning acoustic microscope (S.A.M.) with a band width from 1MHz to 400 MHz. After a short description of the principle of the method, results are given for different types of components. Different applications of acoustic microscopy are proposed for non-destructive examination of interfaces and defect detection in materials.

Rapid screening for nuclear genes mutations in isolated respiratory chain complex I defects.

PubMed

Pagniez-Mammeri, Hélène; Lombes, Anne; Brivet, Michèle; Ogier-de Baulny, Hélène; Landrieu, Pierre; Legrand, Alain; Slama, Abdelhamid

2009-04-01

Complex I or reduced nicotinamide adenine dinucleotide (NADH): ubiquinone oxydoreductase deficiency is the most common cause of respiratory chain defects. Molecular bases of complex I deficiencies are rarely identified because of the dual genetic origin of this multi-enzymatic complex (nuclear DNA and mitochondrial DNA) and the lack of phenotype-genotype correlation. We used a rapid method to screen patients with isolated complex I deficiencies for nuclear genes mutations by Surveyor nuclease digestion of cDNAs. Eight complex I nuclear genes, among the most frequently mutated (NDUFS1, NDUFS2, NDUFS3, NDUFS4, NDUFS7, NDUFS8, NDUFV1 and NDUFV2), were studied in 22 cDNA fragments spanning their coding sequences in 8 patients with a biochemically proved complex I deficiency. Single nucleotide polymorphisms and missense mutations were detected in 18.7% of the cDNA fragments by Surveyor nuclease treatment. Molecular defects were detected in 3 patients. Surveyor nuclease screening is a reliable method for genotyping nuclear complex I deficiencies, easy to interpret, and limits the number of sequence reactions. Its use will enhance the possibility of prenatal diagnosis and help us for a better understanding of complex I molecular defects.

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

Fucharoen, S.; Rowley, P.T.; Paul, N.W.

This book contains papers divided among the following sections: molecular biology and pathogenesis; pathophysiology - molecular and cellular; clinical manifestations and hematologic changes; cardiopulmonary defects and platelet function; hormones and minerals; and infection and immunology.

Nucleic acid-based approaches to investigate microbial-related cheese quality defects

PubMed Central

O'Sullivan, Daniel J.; Giblin, Linda; McSweeney, Paul L. H.; Sheehan, Jeremiah J.; Cotter, Paul D.

2012-01-01

The microbial profile of cheese is a primary determinant of cheese quality. Microorganisms can contribute to aroma and taste defects, form biogenic amines, cause gas and secondary fermentation defects, and can contribute to cheese pinking and mineral deposition issues. These defects may be as a result of seasonality and the variability in the composition of the milk supplied, variations in cheese processing parameters, as well as the nature and number of the non-starter microorganisms which come from the milk or other environmental sources. Such defects can be responsible for production and product recall costs and thus represent a significant economic burden for the dairy industry worldwide. Traditional non-molecular approaches are often considered biased and have inherently slow turnaround times. Molecular techniques can provide early and rapid detection of defects that result from the presence of specific spoilage microbes and, ultimately, assist in enhancing cheese quality and reducing costs. Here we review the DNA-based methods that are available to detect/quantify spoilage bacteria, and relevant metabolic pathways in cheeses and, in the process, highlight how these strategies can be employed to improve cheese quality and reduce the associated economic burden on cheese processors. PMID:23346082

[Genetic diagnostics of cancer diseases].

PubMed

Cobilanschi, Joana

2013-11-27

Cancer is caused by genetic alterations, but only 10% of the cancer diseases are inherited. The probability for an individual or a family of having inherited cancer, individual consequences of the respective results of genetic testing, as well as its costs and reimbursement by the health insurance must be addressed by expert genetic counseling which at-risk requires special expertise. Identification of a germline mutation which may predispose to a variety of different cancer types allows determination of an individual's specific life time risk in symptomatic as well as in a-symptomatic family members. Identification of the underlying defective gene in heritable cancer disorders also enables optimized preventive and novel therapeutic approaches specifically targeting the underlying molecular pathomechanisms.

Kindler syndrome.

PubMed

Ashton, G H S

2004-03-01

Kindler syndrome is a rare, autosomal recessive skin fragility disorder characterized by blistering in infancy, followed by photosensitivity and progressive poikiloderma. Ultrastructural examination reveals marked basement membrane reduplication and variable levels of cleavage at the dermal-epidermal junction. The molecular pathology underlying Kindler syndrome has recently been shown to involve loss-of-function mutations in a novel gene, KIND1, encoding kindlin-1. Immunofluorescence, gene expression and cell biology studies have shown that kindlin-1 is expressed mainly in basal keratinocytes and plays a role in the attachment of the actin cytoskeleton via focal contacts to the extracellular matrix. Thus, Kindler syndrome is the first genodermatosis caused by a defect in actin-extracellular matrix linkage rather than the classic keratin-extracellular matrix linkage underlying the pathology of other inherited skin fragility disorders such as epidermolysis bullosa. This article reviews the clinical features as well as the molecular and cellular pathology of Kindler syndrome and highlights the importance of the new protein, kindlin-1, in cell-matrix adhesion and its intriguing link to photosensitivity.

Multiscale analysis of the correlation of processing parameters on viscidity of composites fabricated by automated fiber placement

NASA Astrophysics Data System (ADS)

Han, Zhenyu; Sun, Shouzheng; Fu, Yunzhong; Fu, Hongya

2017-10-01

Viscidity is an important physical indicator for assessing fluidity of resin that is beneficial to contact resin with the fibers effectively and reduce manufacturing defects during automated fiber placement (AFP) process. However, the effect of processing parameters on viscidity evolution is rarely studied during AFP process. In this paper, viscidities under different scales are analyzed based on multi-scale analysis method. Firstly, viscous dissipation energy (VDE) within meso-unit under different processing parameters is assessed by using finite element method (FEM). According to multi-scale energy transfer model, meso-unit energy is used as the boundary condition for microscopic analysis. Furthermore, molecular structure of micro-system is built by molecular dynamics (MD) method. And viscosity curves are then obtained by integrating stress autocorrelation function (SACF) with time. Finally, the correlation characteristics of processing parameters to viscosity are revealed by using gray relational analysis method (GRAM). A group of processing parameters is found out to achieve the stability of viscosity and better fluidity of resin.

Requirement of the isocitrate lyase gene ICL1 for VPS41-mediated starvation response in Cryptococcus neoformans.

PubMed

Xu, Zhe; Zhi, Yafei; Dong, Jianzhang; Lin, Benfeng; Ye, Di; Liu, Xiaoguang

2016-07-01

Cryptococcus neoformans is a major cause of fungal meningitis in individuals with impaired immunity. Our previous studies have shown that the VPS41 gene plays a critical role in the survival of Cryptococcus neoformans under nitrogen starvation; however, the molecular mechanisms underlying VPS41-mediated starvation response remain to be elucidated. In the present study, we show that, under nitrogen starvation, VPS41 strongly enhanced ICL1 expression in C. neoformans and that overexpression of ICL1 in the vps41 mutant dramatically suppressed its defects in starvation response due to the loss of VPS41 function. Moreover, targeted deletion of ICL1 resulted in a dramatic decline in viability of C. neoformans cells under nitrogen deprivation. Taken together, our data suggest a model in which VPS41 up-regulates ICL1 expression, directly or indirectly, to promote survival of C. neoformans under nitrogen starvation.

Status of therapeutic gene transfer to treat canine dilated cardiomyopathy in dogs.

PubMed

Sleeper, Meg M; Bish, Lawrence T; Sweeney, H Lee

2010-07-01

Therapeutic gene transfer holds promise as a way to treat dilated cardiomyopathy from any underlying cause because the approach attempts to address metabolic disturbances that occur at the molecular level of the failing heart. Calcium-handling abnormalities and increased rates of apoptosis are abnormalities that occur in many types of heart disease, and gene therapies that target these metabolic defects have proven to be beneficial in numerous rodent models of heart disease. The authors are currently evaluating this approach to treat canine idiopathic dilated cardiomyopathy.

The Spectrum of Mitochondrial Ultrastructural Defects in Mitochondrial Myopathy

PubMed Central

Vincent, Amy E.; Ng, Yi Shiau; White, Kathryn; Davey, Tracey; Mannella, Carmen; Falkous, Gavin; Feeney, Catherine; Schaefer, Andrew M.; McFarland, Robert; Gorman, Grainne S.; Taylor, Robert W.; Turnbull, Doug M.; Picard, Martin

2016-01-01

Mitochondrial functions are intrinsically linked to their morphology and membrane ultrastructure. Characterizing abnormal mitochondrial structural features may thus provide insight into the underlying pathogenesis of inherited and acquired mitochondrial diseases. Following a systematic literature review on ultrastructural defects in mitochondrial myopathy, we investigated skeletal muscle biopsies from seven subjects with genetically defined mtDNA mutations. Mitochondrial ultrastructure and morphology were characterized using two complimentary approaches: transmission electron microscopy (TEM) and serial block face scanning EM (SBF-SEM) with 3D reconstruction. Six ultrastructural abnormalities were identified including i) paracrystalline inclusions, ii) linearization of cristae and abnormal angular features, iii) concentric layering of cristae membranes, iv) matrix compartmentalization, v) nanotunelling, and vi) donut-shaped mitochondria. In light of recent molecular advances in mitochondrial biology, these findings reveal novel aspects of mitochondrial ultrastructure and morphology in human tissues with implications for understanding the mechanisms linking mitochondrial dysfunction to disease. PMID:27506553

Generation of an immortalized mouse embryonic palatal mesenchyme cell line

PubMed Central

Soriano, Philippe

2017-01-01

Palatogenesis is a complex morphogenetic process, disruptions in which result in highly prevalent birth defects in humans. In recent decades, the use of model systems such as genetically-modified mice, mouse palatal organ cultures and primary mouse embryonic palatal mesenchyme (MEPM) cultures has provided significant insight into the molecular and cellular defects underlying cleft palate. However, drawbacks in each of these systems have prevented high-throughput, large-scale studies of palatogenesis in vitro. Here, we report the generation of an immortalized MEPM cell line that maintains the morphology, migration ability, transcript expression and responsiveness to exogenous growth factors of primary MEPM cells, with increased proliferative potential over primary cultures. The immortalization method described in this study will facilitate the generation of palatal mesenchyme cells with an unlimited capacity for expansion from a single genetically-modified mouse embryo and enable mechanistic studies of palatogenesis that have not been possible using primary culture. PMID:28582446

Minority carrier diffusion and defects in InGaAsN grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Kurtz, Steven R.; Klem, J. F.; Allerman, A. A.; Sieg, R. M.; Seager, C. H.; Jones, E. D.

2002-02-01

To gain insight into the nitrogen-related defects of InGaAsN, nitrogen vibrational mode spectra, Hall mobilities, and minority carrier diffusion lengths are examined for InGaAsN (1.1 eV band gap) grown by molecular beam epitaxy (MBE). Annealing promotes the formation of In-N bonding, and lateral carrier transport is limited by large scale (≫mean free path) material inhomogeneities. Comparing solar cell quantum efficiencies with our earlier results for devices grown by metalorganic chemical vapor deposition (MOCVD), we find significant electron diffusion in the MBE material (reversed from the hole diffusion in MOCVD material), and minority carrier diffusion in InGaAsN cannot be explained by a "universal," nitrogen-related defect.

Smoking attenuated the association between IκBα rs696 polymorphism and defective spermatogenesis in humans.

PubMed

Yu, B; Ding, Q; Zheng, T; Jiang, L; Li, Q; Sun, X; Bai, C; Huang, Z

2015-11-01

Defective spermatogenesis is prevalent in infertile men, but the molecular mechanisms underlying its aetiology are largely unknown. In this study, a proposed association between IκBα SNPs, smoking-related ROS and sperm quality was investigated. Two polymorphisms in the IκBα gene, rs2233406 and rs696 were genotyped in 342 controls and 338 patients with defective spermatogenesis from a southern Chinese population. The results showed the rs696 AA genotype to be significantly more common (21.60% versus 14.33%, P = 0.013) and the rs696 GG genotype to be significantly rarer (28.99% versus 37.13%, P = 0.024) in the cases than in the controls. After subjects were stratified into smokers and nonsmokers, these differences were only observed in nonsmokers. Further analysis showed the rs696 AA genotype to be significantly closely associated with defective spermatogenesis in all subjects (P = 0.014, OR = 1.647) and in nonsmokers (P = 0.036, OR = 1.889). In a TM3 cell model, exposure to cigarette smoke condensate was found to activate NF-κB luciferase activity and altered transcriptional level of NF-κB pathway genes. In conclusion, this study demonstrates an association between functional polymorphisms of the IκBα rs696 and cigarette smoking with the risk of defective spermatogenesis, suggesting some interaction between the NF-κB signalling pathway and smoking-related ROS in human spermatogenesis. © 2014 Blackwell Verlag GmbH.

Medium-Chain Acyl-CoA Deficiency: Outlines from Newborn Screening, In Silico Predictions, and Molecular Studies

PubMed Central

Catarzi, Serena; Caciotti, Anna; Thusberg, Janita; Tonin, Rodolfo; Malvagia, Sabrina; la Marca, Giancarlo; Pasquini, Elisabetta; Cavicchi, Catia; Ferri, Lorenzo; Donati, Maria A.; Baronio, Federico; Guerrini, Renzo; Mooney, Sean D.; Morrone, Amelia

2013-01-01

Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) is a disorder of fatty acid oxidation characterized by hypoglycemic crisis under fasting or during stress conditions, leading to lethargy, seizures, brain damage, or even death. Biochemical acylcarnitines data obtained through newborn screening by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were confirmed by molecular analysis of the medium-chain acyl-CoA dehydrogenase (ACADM) gene. Out of 324.000 newborns screened, we identified 14 MCADD patients, in whom, by molecular analysis, we found a new nonsense c.823G>T (p.Gly275∗) and two new missense mutations: c.253G>C (p.Gly85Arg) and c.356T>A (p.Val119Asp). Bioinformatics predictions based on both phylogenetic conservation and functional/structural software were used to characterize the new identified variants. Our findings confirm the rising incidence of MCADD whose existence is increasingly recognized due to the efficacy of an expanded newborn screening panel by LC-MS/MS making possible early specific therapies that can prevent possible crises in at-risk infants. We noticed that the “common” p.Lys329Glu mutation only accounted for 32% of the defective alleles, while, in clinically diagnosed patients, this mutation accounted for 90% of defective alleles. Unclassified variants (UVs or VUSs) are especially critical when considering screening programs. The functional and pathogenic characterization of genetic variants presented here is required to predict their medical consequences in newborns. PMID:24294134

Cellular and Molecular Defects Underlying Invasive Fungal Infections—Revelations from Endemic Mycoses

PubMed Central

Lee, Pamela P.; Lau, Yu-Lung

2017-01-01

The global burden of fungal diseases has been increasing, as a result of the expanding number of susceptible individuals including people living with human immunodeficiency virus (HIV), hematopoietic stem cell or organ transplant recipients, patients with malignancies or immunological conditions receiving immunosuppressive treatment, premature neonates, and the elderly. Opportunistic fungal pathogens such as Aspergillus, Candida, Cryptococcus, Rhizopus, and Pneumocystis jiroveci are distributed worldwide and constitute the majority of invasive fungal infections (IFIs). Dimorphic fungi such as Histoplasma capsulatum, Coccidioides spp., Paracoccidioides spp., Blastomyces dermatiditis, Sporothrix schenckii, Talaromyces (Penicillium) marneffei, and Emmonsia spp. are geographically restricted to their respective habitats and cause endemic mycoses. Disseminated histoplasmosis, coccidioidomycosis, and T. marneffei infection are recognized as acquired immunodeficiency syndrome (AIDS)-defining conditions, while the rest also cause high rate of morbidities and mortalities in patients with HIV infection and other immunocompromised conditions. In the past decade, a growing number of monogenic immunodeficiency disorders causing increased susceptibility to fungal infections have been discovered. In particular, defects of the IL-12/IFN-γ pathway and T-helper 17-mediated response are associated with increased susceptibility to endemic mycoses. In this review, we put together the various forms of endemic mycoses on the map and take a journey around the world to examine how cellular and molecular defects of the immune system predispose to invasive endemic fungal infections, including primary immunodeficiencies, individuals with autoantibodies against interferon-γ, and those receiving biologic response modifiers. Though rare, these conditions provide importance insights to host defense mechanisms against endemic fungi, which can only be appreciated in unique climatic and geographical regions. PMID:28702025

Regulation of Neurospora Catalase-3 by global heterochromatin formation and its proximal heterochromatin region.

PubMed

Wang, Yajun; Dong, Qing; Ding, Zhaolan; Gai, Kexin; Han, Xiaoyun; Kaleri, Farah Naz; He, Qun; Wang, Ying

2016-10-01

Catalase-3 (CAT-3) constitutes the main catalase activity in growing hyphae of Neurospora crassa, and its activity increases during exponential growth or is induced under different stress conditions. Although extensive progress has been made to identify catalase regulators, the regulation mechanism of CAT-3 at the chromatin level still remains unclear. Here, we aim at investigating the molecular regulation mechanisms of cat-3 at the chromatin level. We found that CAT-3 protein levels increased in mutants defective in proper global heterochromatin formation. Bioinformatics analysis identified a 5-kb AT-rich sequence adjacent to the cat-3 promoter as a heterochromatin region because of its enrichment of H3K9me3 and HP1. Expression of CAT-3 was induced by H 2 O 2 treatment in wild-type and such change occurred along with the accumulation of histone H3 acetylation at 5-kb heterochromatin boundaries and cat-3 locus, but without alteration of its H3K9me3 repressive modification. Moreover, disruption of 5-kb heterochromatin region results in elevated cat-3 expression, and higher levels of cat-3 expression were promoted by the combination with global heterochromatin defective mutants. Interestingly, the molecular weight and activity bands of CAT-3 protein are different in heterochromatin defective mutants compared with those in wild-type, suggesting that its N-terminal processing and modification may be altered. Our study indicates that the local chromatin structure creates a heterochromatin repressive environment to repress nearby gene expression. Copyright © 2016 Elsevier Inc. All rights reserved.

Synaptic defects associated with s-inclusion body myositis are prevented by copper.

PubMed

Aldunate, R; Minniti, A N; Rebolledo, D; Inestrosa, N C

2012-08-01

Sporadic-inclusion body myositis (s-IBM) is the most common skeletal muscle disorder to afflict the elderly, and is clinically characterized by skeletal muscle degeneration. Its progressive course leads to muscle weakness and wasting, resulting in severe disability. The exact pathogenesis of this disease is unknown and no effective treatment has yet been found. An intriguing aspect of s-IBM is that it shares several molecular abnormalities with Alzheimer's disease, including the accumulation of amyloid-β-peptide (Aβ). Both disorders affect homeostasis of the cytotoxic fragment Aβ(1-42) during aging, but they are clinically distinct diseases. The use of animals that mimic some characteristics of a disease has become important in the search to elucidate the molecular mechanisms underlying the pathogenesis. With the aim of analyzing Aβ-induced pathology and evaluating the consequences of modulating Aβ aggregation, we used Caenorhabditis elegans that express the Aβ human peptide in muscle cells as a model of s-IBM. Previous studies indicate that copper treatment increases the number and size of amyloid deposits in muscle cells, and is able to ameliorate the motility impairments in Aβ transgenic C. elegans. Our recent studies show that neuromuscular synaptic transmission is defective in animals that express the Aβ-peptide and suggest a specific defect at the nicotine acetylcholine receptors level. Biochemical analyses show that copper treatment increases the number of amyloid deposits but decreases Aβ-oligomers. Copper treatment improves motility, synaptic structure and function. Our results suggest that Aβ-oligomers are the toxic Aβ species that trigger neuromuscular junction dysfunction.

Two-temperature model in molecular dynamics simulations of cascades in Ni-based alloys

DOE PAGES

Zarkadoula, Eva; Samolyuk, German; Weber, William J.

2017-01-03

In high-energy irradiation events, energy from the fast moving ion is transferred to the system via nuclear and electronic energy loss mechanisms. The nuclear energy loss results in the creation of point defects and clusters, while the energy transferred to the electrons results in the creation of high electronic temperatures, which can affect the damage evolution. In this paper, we perform molecular dynamics simulations of 30 keV and 50 keV Ni ion cascades in nickel-based alloys without and with the electronic effects taken into account. We compare the results of classical molecular dynamics (MD) simulations, where the electronic effects aremore » ignored, with results from simulations that include the electronic stopping only, as well as simulations where both the electronic stopping and the electron-phonon coupling are incorporated, as described by the two temperature model (2T-MD). Finally, our results indicate that the 2T-MD leads to a smaller amount of damage, more isolated defects and smaller defect clusters.« less

Evolution of Radiation Induced Defects in SiC: A Multiscale Simulation Approach

NASA Astrophysics Data System (ADS)

Jiang, Hao

Because of various excellent properties, SiC has been proposed for many applications in nuclear reactors including cladding layers in fuel rod, fission products container in TRISO fuel, and first wall/blanket in magnetic controlled fusion reactors. Upon exposure to high energy radiation environments, point defects and defect clusters are generated in materials in amounts significantly exceeding their equilibrium concentrations. The accumulation of defects can lead to undesired consequences such as crystalline-to-amorphous transformation1, swelling, and embrittlement, and these phenomena can adversely affect the lifetime of SiC based components in nuclear reactors. It is of great importance to understand the accumulation process of these defects in order to estimate change in properties of this material and to design components with superior ability to withstand radiation damages. Defect clusters are widely in SiC irradiated at the operation temperatures of various reactors. These clusters are believed to cause more than half of the overall swelling of irradiated SiC and can potentially lead to lowered thermal conductivity and mechanical strength. It is critical to understand the formation and growth of these clusters. Diffusion of these clusters is one importance piece to determine the growth rate of clusters; however it is unclear so far due to the challenges in simulating rare events. Using a combination of kinetic Activation Relaxation Technique with empirical potential and ab initio based climbing image nudged elastic band method, I performed an extensive search of the migration paths of the most stable carbon tri-interstitial cluster in SiC. This research reveals paths with the lowest energy barriers to migration, rotation, and dissociation of the most stable cluster. Based on these energy barriers, I concluded defect clusters are thermally immobile at temperatures lower than 1500 K and can dissociate into smaller clusters and single interstitials at temperatures beyond that. Even though clusters cannot diffuse by thermal vibrations, we found they can migrate at room temperature under the influence of electron radiation. This is the first direct observation of radiation-induced diffusion of defect clusters in bulk materials. We show that the underlying mechanism of this athermal diffusion is elastic collision between incoming electrons and cluster atoms. Our findings suggest that defect clusters may be mobile under certain irradiation conditions, changing current understanding of cluster annealing process in irradiated SiC. With the knowledge of cluster diffusion in SiC demonstrated in this thesis, we now become able to predict cluster evolution in SiC with good agreement with experimental measurements. This ability can enable us to estimate changes in many properties of irradiated SiC relevant for its applications in reactors. Internal interfaces such as grain boundaries can behave as sinks to radiation induced defects. The ability of GBs to absorb, transport, and annihilate radiation-induced defects (sink strength) is important to understand radiation response of polycrystalline materials and to better design interfaces for improved resistance to radiation damage. Nowadays, it is established GBs' sink strength is not a static property but rather evolves with many factors, including radiation environments, grain size, and GB microstructure. In this thesis, I investigated the response of small-angle tilt and twist GBs to point defects fluxes in SiC. First of all, I found the pipe diffusion of interstitials in tilt GBs is slower than bulk diffusion. This is because the increased interatomic distance at dislocation cores raises the migration barrier of interstitial dumbbells. Furthermore, I show that both the annihilation of interstitials at jogs and jog nucleation from clusters are diffusion-controlled and can occur under off-stoichiometric interstitial fluxes. Finally, a dislocation line model is developed to predict the role of tilt GBs in annihilating radiation damage. The model predicts the role of tilt GBs in annihilating defects depends on the rate of defects segregation to and diffusion along tilt GBs. Tilt GBs mainly serve as diffusion channel for defects to reach other sinks when defect diffusivity is high at boundaries. When defect diffusivity is low, most of the defects segregated to tilt GBs are annihilated by dislocation climb. Up-to-date, the response of twist GBs under irradiation has been rarely reported in literature and is still unclear. It is important to develop atom scale insight on this question in order to predict twist GBs' sink strength for a better understanding of radiation response of polycrystalline materials. By using a combination of molecular dynamics and grand canonical Monte Carlo, here I demonstrate the defect kinetics in {001} and {111} twist GBs and the microstructural evolution of these GBs under defect fluxes in SiC. I found due to the deep potential well for interstitials at dislocation intersections within the interface, the mobility of defects on dislocation grid is retard and this leads to defect accumulation at GBs for many cases. Furthermore, I conclude both types of twist GBs have to form mixed dislocations with edge component in order to absorb accumulated interstitials at the interface. The formation of mixed dislocation is either by interstitial loop nucleation or by dislocation reactions at the interface. The continuous formation and climb of these mixed dislocations make twist GBs unsaturatable sinks to radiation induced defects.

Length-scale and strain rate-dependent mechanism of defect formation and fracture in carbon nanotubes under tensile loading

NASA Astrophysics Data System (ADS)

Javvaji, Brahmanandam; Raha, S.; Mahapatra, D. Roy

2017-02-01

Electromagnetic and thermo-mechanical forces play a major role in nanotube-based materials and devices. Under high-energy electron transport or high current densities, carbon nanotubes fail via sequential fracture. The failure sequence is governed by certain length scale and flow of current. We report a unified phenomenological model derived from molecular dynamic simulation data, which successfully captures the important physics of the complex failure process. Length-scale and strain rate-dependent defect nucleation, growth, and fracture in single-walled carbon nanotubes with diameters in the range of 0.47 to 2.03 nm and length which is about 6.17 to 26.45 nm are simulated. Nanotubes with long length and small diameter show brittle fracture, while those with short length and large diameter show transition from ductile to brittle fracture. In short nanotubes with small diameters, we observe several structural transitions like Stone-Wales defect initiation, its propagation to larger void nucleation, formation of multiple chains of atoms, conversion to monatomic chain of atoms, and finally complete fracture of the carbon nanotube. Hybridization state of carbon-carbon bonds near the end cap evolves, leading to the formation of monatomic chain in short nanotubes with small diameter. Transition from ductile to brittle fracture is also observed when strain rate exceeds a critical value. A generalized analytical model of failure is established, which correlates the defect energy during the formation of atomic chain with aspect ratio of the nanotube and strain rate. Variation in the mechanical properties such as elastic modulus, tensile strength, and fracture strain with the size and strain rate shows important implications in mitigating force fields and ways to enhance the life of electronic devices and nanomaterial conversion via fracture in manufacturing.

Vesiculation of healthy and defective red blood cells

NASA Astrophysics Data System (ADS)

Li, He; Lykotrafitis, George

2015-07-01

Vesiculation of mature red blood cells (RBCs) contributes to removal of defective patches of the erythrocyte membrane. In blood disorders, which are related to defects in proteins of the RBC membrane, vesiculation of the plasma membrane is intensified. Several hypotheses have been proposed to explain RBC vesiculation but the exact underlying mechanisms and what determines the sizes of the vesicles are still not completely understood. In this work, we apply a two-component coarse-grained molecular dynamics RBC membrane model to study how RBC vesiculation is controlled by the membrane spontaneous curvature and by lateral compression of the membrane. Our simulation results show that the formation of small homogeneous vesicles with a diameter less than 40 nm can be attributed to a large spontaneous curvature of membrane domains. On the other hand, compression on the membrane can cause the formation of vesicles with heterogeneous composition and with sizes comparable with the size of the cytoskeleton corral. When spontaneous curvature and lateral compression are simultaneously considered, the compression on the membrane tends to facilitate formation of vesicles originating from curved membrane domains. We also simulate vesiculation of RBCs with membrane defects connected to hereditary elliptocytosis (HE) and to hereditary spherocytosis (HS). When the vertical connectivity between the lipid bilayer and the membrane skeleton is elevated, as in normal RBCs, multiple vesicles are shed from the compressed membrane with diameters similar to the cytoskeleton corral size. In HS RBCs, where the connectivity between the lipid bilayer and the cytoskeleton is reduced, larger-size vesicles are released under the same compression ratio as in normal RBCs. Lastly, we find that vesicles released from HE RBCs can contain cytoskeletal filaments due to fragmentation of the membrane skeleton while vesicles released from the HS RBCs are depleted of cytoskeletal filaments.

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

Li, Jincheng; Kim, Tong-Ho; Jiao, Wenyuan

Recent work has shown that Bi incorporation increases during molecular beam epitaxy (MBE) when surface processes are kinetically limited through increased growth rate. Herein we explore how the structural and optical properties of GaAs{sub 1−x}Bi{sub x} films are modified when grown under conditions with varying degrees of kinetic limitations realized through growth temperature and growth rate changes. Within the typical window of MBE growth conditions for GaAs{sub 1−x}Bi{sub x}, we compare films with similar (∼3%) compositions grown under conditions of reduced kinetic limitations, i.e., relatively low gallium supersaturation achieved at higher temperatures (∼350 °C) and lower growth rates (∼0.5 μm/h), tomore » those grown farther from equilibrium, specifically, higher supersaturation achieved at lower growth temperatures (∼290 °C) and higher growth rates (∼1.4 μm/h). Both the x-ray diffraction full width at half maximum of the omega-2theta scan and the 300 K photoluminescence intensity increase when samples are grown under less kinetically limited conditions. We interpret these findings in relation to the incorporation of Bi-related microstructural defects that are more readily formed during less kinetically limited growth. These defects lead to enhanced luminescence efficiency due to the spatial localization of carriers.« less

Impact of extended defects on recombination in CdTe heterostructures grown by molecular beam epitaxy

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

Zaunbrecher, Katherine N.; National Renewable Energy Laboratory, Golden, Colorado 80401; Kuciauskas, Darius

Heterostructures with CdTe and CdTe{sub 1-x}Se{sub x} (x ∼ 0.01) absorbers between two wider-band-gap Cd{sub 1-x}Mg{sub x}Te barriers (x ∼ 0.25–0.3) were grown by molecular beam epitaxy to study carrier generation and recombination in bulk materials with passivated interfaces. Using a combination of confocal photoluminescence (PL), time-resolved PL, and low-temperature PL emission spectroscopy, two extended defect types were identified and the impact of these defects on charge-carrier recombination was analyzed. The dominant defects identified by confocal PL were dislocations in samples grown on (211)B CdTe substrates and crystallographic twinning-related defects in samples on (100)-oriented InSb substrates. Low-temperature PL shows that twin-related defects have amore » zero-phonon energy of 1.460 eV and a Huang-Rhys factor of 1.50, while dislocation-dominated samples have a 1.473-eV zero-phonon energy and a Huang-Rhys factor of 1.22. The charge carrier diffusion length near both types of defects is ∼6 μm, suggesting that recombination is limited by diffusion dynamics. For heterostructures with a low concentration of extended defects, the bulk lifetime was determined to be 2.2 μs with an interface recombination velocity of 160 cm/s and an estimated radiative lifetime of 91 μs.« less

Molecular dynamics of oligofluorenes: A dielectric spectroscopy investigation

NASA Astrophysics Data System (ADS)

Papadopoulos, P.; Floudas, G.; Chi, C.; Wegner, G.

2004-02-01

The molecular dynamics were investigated in a series of "defect-free" oligofluorenes up to the polymer by dielectric spectroscopy (DS). The method is very sensitive to the presence of keto "defects" that when incorporated on the backbone give rise to poor optical and electronic properties. Two dielectrically active processes were found (β and α process). The latter process (α) displays strongly temperature dependent relaxation times and temperature- and molecular weight-dependent spectral broadening associated with intramolecular correlations. The glass temperature (Tg) obeys the Fox-Flory equation and the polymer Tg is obtained by DS at 332 K. The effective dipole moment associated with the α process is 0.27±0.03 D.

Translational bypass of nonsense mutations in zebrafish rep1, pax2.1 and lamb1 highlights a viable therapeutic option for untreatable genetic eye disease.

PubMed

Moosajee, Mariya; Gregory-Evans, Kevin; Ellis, Charles D; Seabra, Miguel C; Gregory-Evans, Cheryl Y

2008-12-15

The extensive molecular genetic heterogeneity seen with inherited eye disease is a major barrier to the development of gene-based therapeutics. The underlying molecular pathology in a considerable proportion of these diseases however are nonsense mutations leading to premature termination codons. A therapeutic intervention targeted at this abnormality would therefore potentially be relevant to a wide range of inherited eye diseases. We have taken advantage of the ability of aminoglycoside drugs to suppress such nonsense mutations and partially restore full-length, functional protein in a zebrafish model of choroideraemia (chm(ru848); juvenile chorio-retinal degeneration) and in two models of ocular coloboma (noi(tu29a) and gup(m189); congenital optic fissure closure defects). In vitro cell-based assays showed significant readthrough with two drugs, gentamicin and paromomycin, which was confirmed by western blot and in vitro prenylation assays. The presence of either aminoglycoside during zebrafish development in vivo showed remarkable prevention of mutant ocular phenotypes in each model and a reduction in multisystemic defects leading to a 1.5-1.7-fold increase in survival. We also identified a significant reduction in abnormal cell death shown by TUNEL assay. To test the hypothesis that optic fissure closure was apoptosis-dependent, the anti-apoptotic agents, curcumin and zVAD-fmk, were tested in gup(m189) embryos. Both drugs were found to reduce the size of the coloboma, providing molecular evidence that cell death is required for optic fissure remodelling. These findings draw attention to the value of zebrafish models of eye disease as useful preclinical drug screening tools in studies to identify molecular mechanisms amenable to therapeutic intervention.

Glucose-6-phosphate dehydrogenase deficiency in Tunisia: molecular data and phenotype-genotype association.

PubMed

Laouini, N; Bibi, A; Ammar, H; Kazdaghli, K; Ouali, F; Othmani, R; Amdouni, S; Haloui, S; Sahli, C A; Jouini, L; Hadj Fredj, S; Siala, H; Ben Romdhane, N; Toumi, N E; Fattoum, S; Messsaoud, T

2013-02-01

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common human enzyme defect. In this study, we aimed to perform a molecular investigation of G6PD deficiency in Tunisia and to associate clinical manifestations and the degree of deficiency with the genotype. A total of 161 Tunisian subjects of both sexes were screened by spectrophotometric assay for enzyme activity. Out of these, 54 unrelated subjects were selected for screening of the most frequent mutations in Tunisia by PCR/RFLP, followed by size-based separation of double-stranded fragments under non-denaturing conditions on a denaturing high performance liquid chromatography system. Of the 56 altered chromosomes examined, 75 % had the GdA(-) mutation, 14.28 % showed the GdB(-) mutation and no mutations were identified in 10.72 % of cases. Hemizygous males with GdA(-) mutation were mostly of class III, while those with GdB(-) mutation were mainly of class II. The principal clinical manifestation encountered was favism. Acute hemolytic crises induced by drugs or infections and neonatal jaundice were also noted. Less severe clinical features such as low back pain were present in heterozygous females and in one homozygous female. Asymptomatic individuals were in majority heterozygote females and strangely one hemizygous male. The spectrum of mutations seems to be homogeneous and similar to that of Mediterranean countries; nevertheless 10.72 % of cases remain with undetermined mutation thus suggesting a potential heterogeneity of the deficiency at the molecular level. On the other hand, we note a better association of the molecular defects with the severity of the deficiency than with clinical manifestations.

Molecular dynamics simulations of hydrogen diffusion in aluminum

DOE PAGES

Zhou, X. W.; El Gabaly, F.; Stavila, V.; ...

2016-03-23

In this study, hydrogen diffusion impacts the performance of solid-state hydrogen storage materials and contributes to the embrittlement of structural materials under hydrogen-containing environments. In atomistic simulations, the diffusion energy barriers are usually calculated using molecular statics simulations where a nudged elastic band method is used to constrain a path connecting the two end points of an atomic jump. This approach requires prior knowledge of the “end points”. For alloy and defective systems, the number of possible atomic jumps with respect to local atomic configurations is tremendous. Even when these jumps can be exhaustively studied, it is still unclear howmore » they can be combined to give an overall diffusion behavior seen in experiments. Here we describe the use of molecular dynamics simulations to determine the overall diffusion energy barrier from the Arrhenius equation. This method does not require information about atomic jumps, and it has additional advantages, such as the ability to incorporate finite temperature effects and to determine the pre-exponential factor. As a test case for a generic method, we focus on hydrogen diffusion in bulk aluminum. We find that the challenge of this method is the statistical variation of the results. However, highly converged energy barriers can be achieved by an appropriate set of temperatures, output time intervals (for tracking hydrogen positions), and a long total simulation time. Our results help elucidate the inconsistencies of the experimental diffusion data published in the literature. The robust approach developed here may also open up future molecular dynamics simulations to rapidly study diffusion properties of complex material systems in multidimensional spaces involving composition and defects.« less

Molecular Diagnostics of Copper-Transporting Protein Mutations Allows Early Onset Individual Therapy of Menkes Disease.

PubMed

Králík, L; Flachsová, E; Hansíková, H; Saudek, V; Zeman, J; Martásek, P

2017-01-01

Menkes disease is a severe X-linked recessive disorder caused by a defect in the ATP7A gene, which encodes a membrane copper-transporting ATPase. Deficient activity of the ATP7A protein results in decreased intestinal absorption of copper, low copper level in serum and defective distribution of copper in tissues. The clinical symptoms are caused by decreased activities of copper-dependent enzymes and include neurodegeneration, connective tissue disorders, arterial changes and hair abnormalities. Without therapy, the disease is fatal in early infancy. Rapid diagnosis of Menkes disease and early start of copper therapy is critical for the effectiveness of treatment. We report a molecular biology-based strategy that allows early diagnosis of copper transport defects and implementation of individual therapies before the full development of pathological symptoms. Low serum copper and decreased activity of copperdependent mitochondrial cytochrome c oxidase in isolated platelets found in three patients indicated a possibility of functional defects in copper-transporting proteins, especially in the ATPA7 protein, a copper- transporting P-type ATPase. Rapid mutational screening of the ATP7A gene using high-resolution melting analysis of DNA indicated presence of mutations in the patients. Molecular investigation for mutations in the ATP7A gene revealed three nonsense mutations: c.2170C>T (p.Gln724Ter); c.3745G>T (p.Glu1249Ter); and c.3862C>T (p.Gln1288Ter). The mutation c.3745G>T (p.Glu1249Ter) has not been identified previously. Molecular analysis of the ATOX1 gene as a possible modulating factor of Menkes disease did not reveal presence of pathogenic mutations. Molecular diagnostics allowed early onset of individual therapies, adequate genetic counselling and prenatal diagnosis in the affected families.

Identification and characterization of the elusive mutation causing the historical von Willebrand Disease type IIC Miami.

PubMed

Obser, T; Ledford-Kraemer, M; Oyen, F; Brehm, M A; Denis, C V; Marschalek, R; Montgomery, R R; Sadler, J E; Schneppenheim, S; Budde, U; Schneppenheim, R

2016-09-01

Essentials Von Willebrand disease IIC Miami features high von Willebrand factor (VWF) with reduced function. We aimed to identify and characterize the elusive underlying mutation in the original family. An inframe duplication of VWF exons 9-10 was identified and characterized. The mutation causes a defect in VWF multimerization and decreased VWF clearance from the circulation. Background A variant of von Willebrand disease (VWD) type 2A, phenotype IIC (VWD2AIIC), is characterized by recessive inheritance, low von Willebrand factor antigen (VWF:Ag), lack of VWF high-molecular-weight multimers, absence of VWF proteolytic fragments and mutations in the VWF propeptide. A family with dominantly inherited VWD2AIIC but markedly elevated VWF:Ag of > 2 U L(-1) was described as VWD type IIC Miami (VWD2AIIC-Miami) in 1993; however, the molecular defect remained elusive. Objectives To identify the molecular mechanism underlying the phenotype of the original VWD2AIIC-Miami. Patients and Methods We studied the original family with VWD2AIIC-Miami phenotypically and by genotyping. The identified mutation was recombinantly expressed and characterized by standard techniques, confocal imaging and in a mouse model, respectively. Results By Multiplex ligation-dependent probe amplification we identified an in-frame duplication of VWF exons 9-10 (c.998_1156dup; p.Glu333_385dup) in all patients. Recombinant mutant (rm)VWF only presented as a dimer. Co-expressed with wild-type VWF, the multimer pattern was indistinguishable from patients' plasma VWF. Immunofluorescence studies indicated retention of rmVWF in unusually large intracellular granules in the endoplasmic reticulum. ADAMTS-13 proteolysis of rmVWF under denaturing conditions was normal; however, an aberrant proteolytic fragment was apparent. A decreased ratio of VWF propeptide to VWF:Ag and a 1-desamino-8-d-arginine vasopressin (DDAVP) test in one patient indicated delayed VWF clearance, which was supported by clearance data after infusion of rmVWF into VWF(-/-) mice. Conclusion The unique phenotype of VWD2 type IIC-Miami results from dominant impairment of multimer assembly, an aberrant structure of mutant mature VWF and reduced clearance in vivo. © 2016 International Society on Thrombosis and Haemostasis.

Mutations at the flavin binding site of ETF:QO yield a MADD-like severe phenotype in Drosophila.

PubMed

Alves, Ema; Henriques, Bárbara J; Rodrigues, João V; Prudêncio, Pedro; Rocha, Hugo; Vilarinho, Laura; Martinho, Rui G; Gomes, Cláudio M

2012-08-01

Following a screening on EMS-induced Drosophila mutants defective for formation and morphogenesis of epithelial cells, we have identified three lethal mutants defective for the production of embryonic cuticle. The mutants are allelic to the CG12140 gene, the fly homologue of electron transfer flavoprotein:ubiquinone oxidoreductase (ETF:QO). In humans, inherited defects in this inner membrane protein account for multiple acyl-CoA dehydrogenase deficiency (MADD), a metabolic disease of β-oxidation, with a broad range of clinical phenotypes, varying from embryonic lethal to mild forms. The three mutant alleles carried distinct missense mutations in ETF:QO (G65E, A68V and S104F) and maternal mutant embryos for ETF:QO showed lethal morphogenetic defects and a significant induction of apoptosis following germ-band elongation. This phenotype is accompanied by an embryonic accumulation of short- and medium-chain acylcarnitines (C4, C8 and C12) as well as long-chain acylcarnitines (C14 and C16:1), whose elevation is also found in severe MADD forms in humans under intense metabolic decompensation. In agreement the ETF:QO activity in the mutant embryos is markedly decreased in relation to wild type activity. Amino acid sequence analysis and structural mapping into a molecular model of ETF:QO show that all mutations map at FAD interacting residues, two of which at the nucleotide-binding Rossmann fold. This structural domain is composed by a β-strand connected by a short loop to an α-helix, and its perturbation results in impaired cofactor association via structural destabilisation and consequently enzymatic inactivation. This work thus pinpoints the molecular origins of a severe MADD-like phenotype in the fruit fly and establishes the proof of concept concerning the suitability of this organism as a potential model organism for MADD. © 2012 Elsevier B.V. All rights reserved.

Molecular basis of abnormal red-green color vision: a family with three types of color vision defects.

PubMed Central

Drummond-Borg, M; Deeb, S; Motulsky, A G

1988-01-01

The molecular nature of three different types of X-linked color-vision defects, protanomaly, deuteranomaly, and protanopia, in a large 3-generation family was determined. In the protanomalous and protanopic males the normal red pigment gene was replaced by a 5' red-3' green fusion gene. The protanomalous male had more red pigment DNA in his fusion gene than did the more severely affected protanopic individual. The deuteranomalous individual had four green pigment genes and one 5' green-3' red fusion gene. These results extend those of Nathans et al., who proposed that most red-green color-vision defects arise as a result of unequal crossing-over between the red and green pigment genes. The various data suggest that differences in severity of color-vision defects associated with fusion genes are caused by differences in crossover sites between the red and green pigment genes. Currently used molecular methodology is not sufficiently sensitive to define these fusion points accurately, and the specific color-vision defect within the deutan or protan class cannot be predicted. The DNA patterns for color-vision genes of female heterozygotes have not previously been described. Patterns of heterozygotes may not be distinguishable from those of normals. However, a definite assignment of the various color pigment gene arrays could be carried out by family study. Two compound heterozygotes for color-vision defects who tested as normal by anomaloscopy were found to carry abnormal fusion genes. In addition, a normal red pigment gene was present on one chromosome and at least one normal green pigment gene was present on the other.(ABSTRACT TRUNCATED AT 250 WORDS) Images Figure 3 PMID:2847528

Eukaryote-like Ser/Thr protein kinase PrkA modulates sporulation via regulating the transcriptional factor σ(K) in Bacillus subtilis.

PubMed

Yan, Jinyuan; Zou, Wei; Fang, Juan; Huang, Xiaowei; Gao, Feng; He, Zeying; Zhang, Keqin; Zhao, Ninghui

2015-01-01

Protein kinase A (PrkA), also known as AMP-activated protein kinase, functions as a serine/threonine protein kinase (STPK), has been shown to be involved in a variety of important biologic processes, including pathogenesis of many important diseases in mammals. However, the biological functions of PrkA are less known in prokaryote cells. Here, we explored the function of PrkA as well as its underlying molecular mechanisms using the model bacterium Bacillus subtilis168. When PrkA is inhibited by 9-β-D-arabinofuranosyladenine (ara-A) in the wild type strain or deleted in the ΔprkA mutant strain, we observed sporulation defects in B. subtilis 168, suggesting that PrkA functions as a sporulation-related protein. Transcriptional analysis using the lacZ reporter gene demonstrated that deletion of prkA significantly reduced the expression of the transcriptional factor σ(K) and its downstream genes. Complementation of sigK gene in prkA knockout mutant partially rescued the phenotype of ΔprkA, further supporting the hypothesis that the decreased σ(K) expression should be one of the reasons for the sporulation defect resulting from prkA disruption. Finally, our data confirmed that Hpr (ScoC) negatively controlled the expression of transcriptional factor σ(K), and thus PrkA accelerated sporulation and the expression of σ(K) by suppression of Hpr (ScoC). Taken together, our study discovered a novel function of the eukaryotic-like STPK PrkA in spore development as well as its underlying molecular mechanism in B. subtilis.

First-principles investigations of proton generation in α-quartz

NASA Astrophysics Data System (ADS)

Yue, Yunliang; Song, Yu; Zuo, Xu

2018-03-01

Proton plays a key role in the interface-trap formation that is one of the primary reliability concerns, thus learning how it behaves is key to understand the radiation response of microelectronic devices. The first-principles calculations have been applied to explore the defects and their reactions associated with the proton release in α-quartz, the well-known crystalline isomer of amorphous silica. When a high concentration of molecular hydrogen (H2) is present, the proton generation can be enhanced by cracking the H2 molecules at the positively charged oxygen vacancies in dimer configuration. If the concentration of molecular hydrogen is low, the proton generation mainly depends on the proton dissociation of the doubly-hydrogenated defects. In particular, a fully passivated {E}2^{\\prime } center can dissociate to release a proton barrierlessly by structure relaxation once trapping a hole. This research provides a microscopic insight into the proton release in silicon dioxide, the critical step associated with the interface-trap formation under radiation in microelectronic devices. Project supported by the Science Challenge Project, China (Grant No. TZ2016003-1-105), CAEP Microsystem and THz Science and Technology Foundation, China (Grant No. CAEPMT201501), the National Natural Science Foundation China (Grant No. NSFC 11404300), and the National Basic Research Program of China (Grant No. 2011CB606405).

Defects, strain relaxation, and compositional grading in high indium content InGaN epilayers grown by molecular beam epitaxy

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

Bazioti, C.; Kehagias, Th.; Pavlidou, E.

2015-10-21

We investigate the structural properties of a series of high alloy content InGaN epilayers grown by plasma-assisted molecular beam epitaxy, employing the deposition temperature as variable under invariant element fluxes. Using transmission electron microscopy methods, distinct strain relaxation modes were observed, depending on the indium content attained through temperature adjustment. At lower indium contents, strain relaxation by V-pit formation dominated, with concurrent formation of an indium-rich interfacial zone. With increasing indium content, this mechanism was gradually substituted by the introduction of a self-formed strained interfacial InGaN layer of lower indium content, as well as multiple intrinsic basal stacking faults andmore » threading dislocations in the rest of the film. We show that this interfacial layer is not chemically abrupt and that major plastic strain relaxation through defect introduction commences upon reaching a critical indium concentration as a result of compositional pulling. Upon further increase of the indium content, this relaxation mode was again gradually succeeded by the increase in the density of misfit dislocations at the InGaN/GaN interface, leading eventually to the suppression of the strained InGaN layer and basal stacking faults.« less

Defect Chemistry of " BaCuO2" I. Oxygen Non -Stoichiometry, Cation Molecularity and X-ray Diffraction Determinations

NASA Astrophysics Data System (ADS)

Spinolo, G.; Anselmi-Tamburini, U.; Arimondi, M.; Ghigna, P.; Flor, G.

1995-11-01

"BaCuO2" is the key intermediate in the synthesis of the Ba2YCu3O7-δ superconductor. Its very complex crystal structure is able to accommodate a large change in oxygen content. Oxygen non-stoichiometry of "BaCuO2" materials with 1:1 and 88:90 (Ba :Cu) molecularity has been investigated by polythermal X-ray powder diffraction coupled with isobaric-isothermal gravimetry determinations under different temperature and oxygen partial pressure conditions [300≤ T≤ 820 °C, 1 ≥ P(O2) ≥ 3 • 10-3 atm]. The 1:1 composition does not give well reproducible results, thus suggesting its polyphasic nature, at least in part of the investigated range. The results for the 88:90 ≅ 0.98 (Ba :Cu) composi­ tion are well reproducible and show that the material is single phase. Ba0.98CuO1.98 + δ is oxygen over-stoichiometric in the whole investigated [T, P(O2)] range, with a maximum value δ˜0.21. A Rietveld X-ray profile fitting is in agreement with previous single-crystal data. The trend of δ vs. P(O2) is consistent with the presence of oxygen interstitial defects on (possibly different) crystallographic sites.

Influence of Acute and Chronic Exercise on Glucose Uptake

PubMed Central

Röhling, Martin; Herder, Christian; Stemper, Theodor; Müssig, Karsten

2016-01-01

Insulin resistance plays a key role in the development of type 2 diabetes. It arises from a combination of genetic predisposition and environmental and lifestyle factors including lack of physical exercise and poor nutrition habits. The increased risk of type 2 diabetes is molecularly based on defects in insulin signaling, insulin secretion, and inflammation. The present review aims to give an overview on the molecular mechanisms underlying the uptake of glucose and related signaling pathways after acute and chronic exercise. Physical exercise, as crucial part in the prevention and treatment of diabetes, has marked acute and chronic effects on glucose disposal and related inflammatory signaling pathways. Exercise can stimulate molecular signaling pathways leading to glucose transport into the cell. Furthermore, physical exercise has the potential to modulate inflammatory processes by affecting specific inflammatory signaling pathways which can interfere with signaling pathways of the glucose uptake. The intensity of physical training appears to be the primary determinant of the degree of metabolic improvement modulating the molecular signaling pathways in a dose-response pattern, whereas training modality seems to have a secondary role. PMID:27069930

Growth of defect-free GaAsSbN axial nanowires via self-catalyzed molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Sharma, Manish; Deshmukh, Prithviraj; Kasanaboina, Pavan; Reynolds, C. Lewis, Jr.; Liu, Yang; Iyer, Shanthi

2017-12-01

Bandgap reduction of 10% by incorporation of a dilute amount of N is reported for the first time, in axial GaAsSb nanowires (NWs) grown on Si (111) via Ga-assisted molecular beam epitaxy. Impact of N incorporation on the surface morphology, NW growth kinetics, and their structural and optical properties were examined. Dilute nitride NWs with Sb composition of 7 at% did not exhibit any noticeable planar defects, as revealed by the absence of satellite twin peaks in the selected-area diffraction pattern and high-resolution transmission electron microscopy imaging. Point defects were also minimal in as-grown dilute nitride NWs, as ascertained from the comparison of low-temperature photoluminescence spectra as well as the shape and shift of Raman modes, with in situ annealed NWs in different ambients. Evidence of enhanced incorporation of N was found in the NWs in situ annealed in N ambient, but with deteriorated optical quality due to simultaneous creation of N-induced defects. The lack of any noticeable defects in the as-grown GaAsSbN NWs demonstrates the advantage of the vapor-liquid-solid mechanism responsible for growth of axial configuration over the vapor-solid growth mechanism for core-shell NWs as well as their thin film counterpart, which commonly exhibit N-induced point defects.

Topological defects in electric double layers of ionic liquids at carbon interfaces

DOE PAGES

Black, Jennifer M.; Okatan, Mahmut Baris; Feng, Guang; ...

2015-06-07

The structure and properties of the electrical double layer in ionic liquids is of interest in a wide range of areas including energy storage, catalysis, lubrication, and many more. Theories describing the electrical double layer for ionic liquids have been proposed, however a full molecular level description of the double layer is lacking. To date, studies have been predominantly focused on ion distributions normal to the surface, however the 3D nature of the electrical double layer in ionic liquids requires a full picture of the double layer structure not only normal to the surface, but also in plane. Here wemore » utilize 3D force mapping to probe the in plane structure of an ionic liquid at a graphite interface and report the direct observation of the structure and properties of topological defects. The observation of ion layering at structural defects such as step-edges, reinforced by molecular dynamics simulations, defines the spatial resolution of the method. Observation of defects allows for the establishment of the universality of ionic liquid behavior vs. separation from the carbon surface and to map internal defect structure. In conclusion, these studies offer a universal pathway for probing the internal structure of topological defects in soft condensed matter on the nanometer level in three dimensions.« less

Molecular dynamics simulations of oxygen vacancy diffusion in SrTiO3.

PubMed

Schie, Marcel; Marchewka, Astrid; Müller, Thomas; De Souza, Roger A; Waser, Rainer

2012-12-05

A classical force-field model with partial ionic charges was applied to study the behaviour of oxygen vacancies in the perovskite oxide strontium titanate (SrTiO(3)). The dynamical behaviour of these point defects was investigated as a function of temperature and defect concentration by means of molecular dynamics (MD) simulations. The interaction between oxygen vacancies and an extended defect, here a Σ3(111) grain boundary, was also examined by means of MD simulations. Analysis of the vacancy distribution revealed considerable accumulation of vacancies in the envelope of the grain boundary. The possible clustering of oxygen vacancies in bulk SrTiO(3) was studied by means of static lattice calculations within the Mott-Littleton approach. All binary vacancy-vacancy configurations were found to be energetically unfavourable.

Segmental bone defects: from cellular and molecular pathways to the development of novel biological treatments

PubMed Central

Pneumaticos, Spyros G; Triantafyllopoulos, Georgios K; Basdra, Efthimia K; Papavassiliou, Athanasios G

2010-01-01

Abstract Several conditions in clinical orthopaedic practice can lead to the development of a diaphyseal segmental bone defect, which cannot heal without intervention. Segmental bone defects have been traditionally treated with bone grafting and/or distraction osteogenesis, methods that have many advantages, but also major drawbacks, such as limited availability, risk of disease transmission and prolonged treatment. In order to overcome such limitations, biological treatments have been developed based on specific pathways of bone physiology and healing. Bone tissue engineering is a dynamic field of research, combining osteogenic cells, osteoinductive factors, such as bone morphogenetic proteins, and scaffolds with osteoconductive and osteoinductive attributes, to produce constructs that could be used as bone graft substitutes for the treatment of segmental bone defects. Scaffolds are usually made of ceramic or polymeric biomaterials, or combinations of both in composite materials. The purpose of the present review is to discuss in detail the molecular and cellular basis for the development of bone tissue engineering constructs. PMID:20345845

Modeling of Branched (L, T and Y) Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Han, Jie; Jaffe, Richard; Saini, Subhash (Technical Monitor)

1998-01-01

Models for connecting two or three carbon nanotubes (CNT) using topological defects (i.e., pentagons and heptagons) are presented for the characterization of experimentally observed L, T and Y CNT junctions. The effects of the separation and orientation of the topological defects on the structures and energetics of these junctions are investigated using the nonlocal density function theory (DFT) and semi-empirical molecular orbital (AM1) calculations, and the Brenner empirical potential molecular mechanics simulations. The potential applications of L, Y and T CNT junctions in nanoelectronic devices are also discussed.

Identification of De Novo Copy Number Variants Associated with Human Disorders of Sexual Development

PubMed Central

Tannour-Louet, Mounia; Han, Shuo; Corbett, Sean T.; Louet, Jean-Francois; Yatsenko, Svetlana; Meyers, Lindsay; Shaw, Chad A.; Kang, Sung-Hae L.; Cheung, Sau Wai; Lamb, Dolores J.

2010-01-01

Disorders of sexual development (DSD), ranging in severity from genital abnormalities to complete sex reversal, are among the most common human birth defects with incidence rates reaching almost 3%. Although causative alterations in key genes controlling gonad development have been identified, the majority of DSD cases remain unexplained. To improve the diagnosis, we screened 116 children born with idiopathic DSD using a clinically validated array-based comparative genomic hybridization platform. 8951 controls without urogenital defects were used to compare with our cohort of affected patients. Clinically relevant imbalances were found in 21.5% of the analyzed patients. Most anomalies (74.2%) evaded detection by the routinely ordered karyotype and were scattered across the genome in gene-enriched subtelomeric loci. Among these defects, confirmed de novo duplication and deletion events were noted on 1p36.33, 9p24.3 and 19q12-q13.11 for ambiguous genitalia, 10p14 and Xq28 for cryptorchidism and 12p13 and 16p11.2 for hypospadias. These variants were significantly associated with genitourinary defects (P = 6.08×10−12). The causality of defects observed in 5p15.3, 9p24.3, 22q12.1 and Xq28 was supported by the presence of overlapping chromosomal rearrangements in several unrelated patients. In addition to known gonad determining genes including SRY and DMRT1, novel candidate genes such as FGFR2, KANK1, ADCY2 and ZEB2 were encompassed. The identification of risk germline rearrangements for urogenital birth defects may impact diagnosis and genetic counseling and contribute to the elucidation of the molecular mechanisms underlying the pathogenesis of human sexual development. PMID:21048976

Activation of multiple signaling pathways causes developmental defects in mice with a Noonan syndrome–associated Sos1 mutation

PubMed Central

Chen, Peng-Chieh; Wakimoto, Hiroko; Conner, David; Araki, Toshiyuki; Yuan, Tao; Roberts, Amy; Seidman, Christine E.; Bronson, Roderick; Neel, Benjamin G.; Seidman, Jonathan G.; Kucherlapati, Raju

2010-01-01

Noonan syndrome (NS) is an autosomal dominant genetic disorder characterized by short stature, unique facial features, and congenital heart disease. About 10%–15% of individuals with NS have mutations in son of sevenless 1 (SOS1), which encodes a RAS and RAC guanine nucleotide exchange factor (GEF). To understand the role of SOS1 in the pathogenesis of NS, we generated mice with the NS-associated Sos1E846K gain-of-function mutation. Both heterozygous and homozygous mutant mice showed many NS-associated phenotypes, including growth delay, distinctive facial dysmorphia, hematologic abnormalities, and cardiac defects. We found that the Ras/MAPK pathway as well as Rac and Stat3 were activated in the mutant hearts. These data provide in vivo molecular and cellular evidence that Sos1 is a GEF for Rac under physiological conditions and suggest that Rac and Stat3 activation might contribute to NS phenotypes. Furthermore, prenatal administration of a MEK inhibitor ameliorated the embryonic lethality, cardiac defects, and NS features of the homozygous mutant mice, demonstrating that this signaling pathway might represent a promising therapeutic target for NS. PMID:21041952

Computational Modeling and Simulation of Genital Tubercle ...

EPA Pesticide Factsheets

Hypospadias is a developmental defect of urethral tube closure that has a complex etiology. Here, we describe a multicellular agent-based model of genital tubercle development that simulates urethrogenesis from the urethral plate stage to urethral tube closure in differentiating male embryos. The model, constructed in CompuCell3D, implemented spatially dynamic signals from SHH, FGF10, and androgen signaling pathways. These signals modulated stochastic cell behaviors, such as differential adhesion, cell motility, proliferation, and apoptosis. Urethral tube closure was an emergent property of the model that was quantitatively dependent on SHH and FGF10 induced effects on mesenchymal proliferation and endodermal apoptosis, ultimately linked to androgen signaling. In the absence of androgenization, simulated genital tubercle development defaulted to the female condition. Intermediate phenotypes associated with partial androgen deficiency resulted in incomplete closure. Using this computer model, complex relationships between urethral tube closure defects and disruption of underlying signaling pathways could be probed theoretically in multiplex disturbance scenarios and modeled into probabilistic predictions for individual risk for hypospadias and potentially other developmental defects of the male genital tubercle. We identify the minimal molecular network that determines the outcome of male genital tubercle development in mice.

The clinical maze of mitochondrial neurology

PubMed Central

DiMauro, Salvatore; Schon, Eric A.; Carelli, Valerio; Hirano, Michio

2014-01-01

Mitochondrial diseases involve the respiratory chain, which is under the dual control of nuclear and mitochondrial DNA (mtDNA). The complexity of mitochondrial genetics provides one explanation for the clinical heterogeneity of mitochondrial diseases, but our understanding of disease pathogenesis remains limited. Classification of Mendelian mitochondrial encephalomyopathies has been laborious, but whole-exome sequencing studies have revealed unexpected molecular aetiologies for both typical and atypical mitochondrial disease phenotypes. Mendelian mitochondrial defects can affect five components of mitochondrial biology: subunits of respiratory chain complexes (direct hits); mitochondrial assembly proteins; mtDNA translation; phospholipid composition of the inner mitochondrial membrane; or mitochondrial dynamics. A sixth category—defects of mtDNA maintenance—combines features of Mendelian and mitochondrial genetics. Genetic defects in mitochondrial dynamics are especially important in neurology as they cause optic atrophy, hereditary spastic paraplegia, and Charcot–Marie–Tooth disease. Therapy is inadequate and mostly palliative, but promising new avenues are being identified. Here, we review current knowledge on the genetics and pathogenesis of the six categories of mitochondrial disorders outlined above, focusing on their salient clinical manifestations and highlighting novel clinical entities. An outline of diagnostic clues for the various forms of mitochondrial disease, as well as potential therapeutic strategies, is also discussed. PMID:23835535

PNPLA1 Deficiency in Mice and Humans Leads to a Defect in the Synthesis of Omega-O-Acylceramides

PubMed Central

Grond, Susanne; Eichmann, Thomas O.; Dubrac, Sandrine; Kolb, Dagmar; Schmuth, Matthias; Fischer, Judith; Crumrine, Debra; Elias, Peter M.; Haemmerle, Guenter; Zechner, Rudolf; Lass, Achim; Radner, Franz P.W.

2017-01-01

Mutations in PNPLA1 have been identified as causative for autosomal recessive congenital ichthyosis in humans and dogs. So far, the underlying molecular mechanisms are unknown. In this study, we generated and characterized PNPLA1-deficient mice and found that PNPLA1 is crucial for epidermal sphingolipid synthesis. The absence of functional PNPLA1 in mice impaired the formation of omega-O-acylceramides and led to an accumulation of nonesterified omega-hydroxy-ceramides. As a consequence, PNPLA1-deficient mice lacked a functional corneocyte-bound lipid envelope leading to a severe skin barrier defect and premature death of newborn animals. Functional analyses of differentiated keratinocytes from a patient with mutated PNPLA1 demonstrated an identical defect in omega-O-acylceramide synthesis in human cells, indicating that PNPLA1 function is conserved among mammals and indispensable for normal skin physiology. Notably, topical application of epidermal lipids from wild-type onto Pnpla1-mutant mice promoted rebuilding of the corneocyte-bound lipid envelope, indicating that supplementation of ichthyotic skin with omega-O-acylceramides might be a therapeutic approach for the treatment of skin symptoms in individuals affected by omega-O-acylceramide deficiency. PMID:27751867

Comparative study of displacement cascades simulated with 'magnetic' potentials and Mendelev-type potential in α-Fe

NASA Astrophysics Data System (ADS)

Gao, Chan; Tian, Dongfeng; Li, Maosheng; Qian, Dazhi

2017-04-01

Different interatomic potentials produce displacement cascades with different features, and hence they significantly influence the results obtained from the displacement cascade simulations. The displacement cascade simulations in α-Fe have been carried out by molecular dynamics with three 'magnetic' potentials (MP) and Mendelev-type potential in this paper. Prior to the cascade simulations, the 'magnetic' potentials are hardened to suit for cascade simulations. We find that the peak time, maximum of defects, cascade volume and cascade density with 'magnetic' potentials are smaller than those with Mendelev-type potential. There is no significant difference within statistical uncertainty in the defect production efficiency with Mendelev-type potential and the second 'magnetic' potential at the same cascade energy, but remarkably smaller than those with the first and third 'magnetic' potential. Self interstitial atom (SIA) clustered fractions with 'magnetic' potentials are smaller than that with Mendelev-type potential, especially at the higher energy, due to the larger interstitial formation energies which result from the 'magnetic' potentials. The defect clustered fractions, which are input data for radiation damage accumulation models, may influence the prediction of microstructural evolution under radiation.

The Sulfate Transporter SST1 Is Crucial for Symbiotic Nitrogen Fixation in Lotus japonicus Root Nodules

PubMed Central

Krusell, Lene; Krause, Katja; Ott, Thomas; Desbrosses, Guilhem; Krämer, Ute; Sato, Shusei; Nakamura, Yasukazu; Tabata, Satoshi; James, Euan K.; Sandal, Niels; Stougaard, Jens; Kawaguchi, Masayoshi; Miyamoto, Ai; Suganuma, Norio; Udvardi, Michael K.

2005-01-01

Symbiotic nitrogen fixation (SNF) by intracellular rhizobia within legume root nodules requires the exchange of nutrients between host plant cells and their resident bacteria. Little is known at the molecular level about plant transporters that mediate such exchanges. Several mutants of the model legume Lotus japonicus have been identified that develop nodules with metabolic defects that cannot fix nitrogen efficiently and exhibit retarded growth under symbiotic conditions. Map-based cloning of defective genes in two such mutants, sst1-1 and sst1-2 (for symbiotic sulfate transporter), revealed two alleles of the same gene. The gene is expressed in a nodule-specific manner and encodes a protein homologous with eukaryotic sulfate transporters. Full-length cDNA of the gene complemented a yeast mutant defective in sulfate transport. Hence, the gene was named Sst1. The sst1-1 and sst1-2 mutants exhibited normal growth and development under nonsymbiotic growth conditions, a result consistent with the nodule-specific expression of Sst1. Data from a previous proteomic study indicate that SST1 is located on the symbiosome membrane in Lotus nodules. Together, these results suggest that SST1 transports sulfate from the plant cell cytoplasm to the intracellular rhizobia, where the nutrient is essential for protein and cofactor synthesis, including nitrogenase biosynthesis. This work shows the importance of plant sulfate transport in SNF and the specialization of a eukaryotic transporter gene for this purpose. PMID:15805486

Computational study of hydroxyapatite structures, properties and defects

NASA Astrophysics Data System (ADS)

Bystrov, V. S.; Coutinho, J.; Bystrova, A. V.; Dekhtyar, Yu D.; Pullar, R. C.; Poronin, A.; Palcevskis, E.; Dindune, A.; Alkan, B.; Durucan, C.; Paramonova, E. V.

2015-03-01

Hydroxyapatite (HAp) was studied from a first principle approach using the local density approximation (LDA) method in AIMPRO code, in combination with various quantum mechanical (QM) and molecular mechanical (MM) methods from HypemChem 7.5/8.0. The data obtained were used for studies of HAp structures, the physical properties of HAp (density of electronic states—DOS, bulk modulus etc) and defects in HAp. Computed data confirmed that HAp can co-exist in different phases—hexagonal and monoclinic. Ordered monoclinic structures, which could reveal piezoelectric properties, are of special interest. The data obtained allow us to characterize the properties of the following defects in HAp: O, H and OH vacancies; H and OH interstitials; substitutions of Ca by Mg, Sr, Mn or Se, and P by Si. These properties reveal the appearance of additional energy levels inside the forbidden zone, shifts of the top of the valence band or the bottom of the conduction band, and subsequent changes in the width of the forbidden zone. The data computed are compared with other known data, both calculated and experimental, such as alteration of the electron work functions under different influences of various defects and treatments, obtained by photoelectron emission. The obtained data are very useful, and there is an urgent need for such analysis of modified HAp interactions with living cells and tissues, improvement of implant techniques and development of new nanomedical applications.

Influence of tool shape on lattice rearrangement under loading conditions reproducing friction stir welding

NASA Astrophysics Data System (ADS)

Konovalenko, Ivan S.; Konovalenko, Igor S.

2015-10-01

Metal behavior under loading conditions that reproduce friction stir welding was studied on the atomic scale. Calculations were conducted based on molecular dynamics simulation with potentials calculated within the embedded atom method. The loading of the interface between two crystallites, whose structure corresponded to aluminum alloy 2024, was simulated by the motion of a cone-shaped tool along the interface with constant angular and translational velocities. The motion of the rotating tool causes fracture of the workpiece crystal structure with subsequent mixing of surface atoms of the interfacing crystallites. It is shown that the resistance force acting on the moving tool from the workpiece and the process of structural defect formation in the workpiece depend on the tool shape.

A robust molecular probe for Ångstrom-scale analytics in liquids

PubMed Central

Nirmalraj, Peter; Thompson, Damien; Dimitrakopoulos, Christos; Gotsmann, Bernd; Dumcenco, Dumitru; Kis, Andras; Riel, Heike

2016-01-01

Traditionally, nanomaterial profiling using a single-molecule-terminated scanning probe is performed at the vacuum–solid interface often at a few Kelvin, but is not a notion immediately associated with liquid–solid interface at room temperature. Here, using a scanning tunnelling probe functionalized with a single C60 molecule stabilized in a high-density liquid, we resolve low-dimensional surface defects, atomic interfaces and capture Ångstrom-level bond-length variations in single-layer graphene and MoS2. Atom-by-atom controllable imaging contrast is demonstrated at room temperature and the electronic structure of the C60–metal probe complex within the encompassing liquid molecules is clarified using density functional theory. Our findings demonstrates that operating a robust single-molecular probe is not restricted to ultra-high vacuum and cryogenic settings. Hence the scope of high-precision analytics can be extended towards resolving sub-molecular features of organic elements and gauging ambient compatibility of emerging layered materials with atomic-scale sensitivity under experimentally less stringent conditions. PMID:27516157

Ion transport in pigmentation.

PubMed

Bellono, Nicholas W; Oancea, Elena V

2014-12-01

Skin melanocytes and ocular pigment cells contain specialized organelles called melanosomes, which are responsible for the synthesis of melanin, the major pigment in mammals. Defects in the complex mechanisms involved in melanin synthesis and regulation result in vision and pigmentation deficits, impaired development of the visual system, and increased susceptibility to skin and eye cancers. Ion transport across cellular membranes is critical for many biological processes, including pigmentation, but the molecular mechanisms by which it regulates melanin synthesis, storage, and transfer are not understood. In this review we first discuss ion channels and transporters that function at the plasma membrane of melanocytes; in the second part we consider ion transport across the membrane of intracellular organelles, with emphasis on melanosomes. We discuss recently characterized lysosomal and endosomal ion channels and transporters associated with pigmentation phenotypes. We then review the evidence for melanosomal channels and transporters critical for pigmentation, discussing potential molecular mechanisms mediating their function. The studies investigating ion transport in pigmentation physiology open new avenues for future research and could reveal novel molecular mechanisms underlying melanogenesis.

Ion transport in pigmentation

PubMed Central

Bellono, Nicholas W.; Oancea, Elena V.

2014-01-01

Skin melanocytes and ocular pigment cells contain specialized organelles called melanosomes, which are responsible for the synthesis of melanin, the major pigment in mammals. Defects in the complex mechanisms involved in melanin synthesis and regulation result in vision and pigmentation deficits, impaired development of the visual system,, and increased susceptibility to skin and eye cancers. Ion transport across cellular membranes is critical for many biological processes, including pigmentation, but the molecular mechanisms by which it regulates melanin synthesis, storage, and transfer are not understood. In this review we first discuss ion channels and transporters that function at the plasma membrane of melanocytes; in the second part we consider ion transport across the membrane of intracellular organelles, with emphasis on melanosomes. We discuss recently characterized lysosomal and endosomal ion channels and transporters associated with pigmentation phenotypes. We then review the evidence for melanosomal channels and transporters critical for pigmentation, discussing potential molecular mechanisms mediating their function. The studies investigating ion transport in pigmentation physiology open new avenues for future research and could reveal novel molecular mechanisms underlying melanogenesis. PMID:25034214

The influence of void and porosity on deformation behaviour of nanocrystalline Ni under tensile followed by compressive loading

NASA Astrophysics Data System (ADS)

Meraj, Md.; Nayak, Shradha; Krishanjeet, Kumar; Pal, Snehanshu

2018-03-01

In this paper, we present a lucid understanding about the deformation behaviour of nanocrystalline (NC) Ni with and without defects subjected to tensile followed by compressive loading using molecular dynamic (MD) simulations. The embedded atom method (EAM) potential have been incorporated in the simulation for three kinds of samples-i.e. for NC Ni (without any defect), porous NC Ni and NC Ni containing a centrally located void. All the three samples, which have been prepared by implementing the Voronoi method and using Atom Eye software, consist of 16 uniform grains. The total number of atoms present in NC Ni, porous NC Ni and NC Ni containing a void are 107021, 105968 and 107012 respectively. The stress-strain response of NC Ni under tensile followed by compressive loading are simulated at a high strain rate of 107 s-1 and at a constant temperature of 300K. The stress-strain curves for the NC Ni with and without defects have been plotted for three different types of loading: (a) tensile loading (b) compressive loading (c) forward tensile loading followed by reverse compressive loading. Prominent change in yield strength of the NC Ni is observed due to the introduction of defects. For tensile followed by compressive loading (during forward loading), the yield point for NC Ni with void is lesser than the yield point of NC Ni and porous NC Ni. The saw tooth shape or serration portion of the stress-strain curve is mainly due to three characteristic phenomena, dislocation generation and its movement, dislocation pile-up at the junctions, and dislocation annihilation. Both twins and stacking faults are observed due to plastic deformation as the deformation mechanism progresses. The dislocation density, number of clusters and number of vacancy of the NC sample with and without defects are plotted against the strain developed in the sample. It is seen that introduction of defects brings about change in mechanical properties of the NC Ni. The crystalline nature of NC Ni is found to decrease with introduction of defects. The findings of this work can thus be extended in bringing a whole new insight related to the deformation behaviour and properties of Nano- materials during cyclic deformation at various temperatures.

Using birth defects registry data to evaluate infant and childhood mortality associated with birth defects: an alternative to traditional mortality assessment using underlying cause of death statistics.

PubMed

Copeland, Glenn E; Kirby, Russell S

2007-11-01

Although birth defects are a leading cause of death in infancy and early childhood, the proportion of all deaths to children with clinically diagnosed birth defects is not well documented. The study is intended to measure the proportion of all deaths to infants and children under age 10 occurring to children with birth defects and how and why this proportion differs from the proportion of deaths due to an underlying cause of congenital anomalies using standard mortality statistics. A linked file of Michigan livebirths and deaths was combined with data from a comprehensive multisource birth defects registry of Michigan livebirths born during the years 1992 through 2000. The data were analyzed to determine the mortality rate for infants and children with birth defects and for children with no reported birth defect. Mortality risk ratios were calculated. The underlying causes of death for children with birth defects were also categorized and compared to cause- specific mortality rates for the general population. Congenital anomalies were the underlying cause of death for 17.8% of all infant deaths while infants with birth defects were 33.7% of all infant deaths in the study. Almost half of all Michigan deaths to children aged 1 to 2 were within the birth defects registry, though only 15.0% had an underlying cause of death of a congenital anomaly based upon standard mortality statistics. The mortality experience among children with birth defects was significantly higher than other children throughout the first 9 years of life, ranging from 4.6 for 5 year olds to 12.8 for children 1 to 2. Mortality risk ratios examined by cause of death for infants with birth defects were highest for other endocrine (28.1), other CNS (28.1), and heart (21.9) conditions. For children 1 through 9, the highest differential risk was seen for other perinatal conditions (39.0), other endocrine (29.7), other CNS (24.5), and heart (21.4). Childhood mortality analyses that incorporate birth defects registry data provide a more comprehensive picture of the full burden of birth defects on mortality in infant and children and can provide an effective mechanism for monitoring the survival and mortality risks of children with selected birth defects on a population basis.

The Bradyrhizobium japonicum Ferrous Iron Transporter FeoAB Is Required for Ferric Iron Utilization in Free Living Aerobic Cells and for Symbiosis.

PubMed

Sankari, Siva; O'Brian, Mark R

2016-07-22

The bacterium Bradyrhizobium japonicum USDA110 does not synthesize siderophores for iron utilization in aerobic environments, and the mechanism of iron uptake within symbiotic soybean root nodules is unknown. An mbfA bfr double mutant defective in iron export and storage activities cannot grow aerobically in very high iron medium. Here, we found that this phenotype was suppressed by loss of function mutations in the feoAB operon encoding ferrous (Fe(2+)) iron uptake proteins. Expression of the feoAB operon genes was elevated under iron limitation, but mutants defective in either gene were unable to grow aerobically over a wide external ferric (Fe(3+)) iron (FeCl3) concentration range. Thus, FeoAB accommodates iron acquisition under iron limited and iron replete conditions. Incorporation of radiolabel from either (55)Fe(2+) or (59)Fe(3+) into cells was severely defective in the feoA and feoB strains, suggesting Fe(3+) reduction to Fe(2+) prior to traversal across the cytoplasmic membrane by FeoAB. The feoA or feoB deletion strains elicited small, ineffective nodules on soybean roots, containing few bacteria and lacking nitrogen fixation activity. A feoA(E40K) mutant contained partial iron uptake activity in culture that supported normal growth and established an effective symbiosis. The feoA(E40K) strain had partial iron uptake activity in situ within nodules and in isolated cells, indicating that FeoAB is the iron transporter in symbiosis. We conclude that FeoAB supports iron acquisition under limited conditions of soil and in the iron-rich environment of a symbiotic nodule. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Silicon Carbide Epitaxial Films Studied by Atomic Force Microscopy

NASA Technical Reports Server (NTRS)

1996-01-01

Silicon carbide (SiC) holds great potential as an electronic material because of its wide band gap energy, high breakdown electric field, thermal stability, and resistance to radiation damage. Possible aerospace applications of high-temperature, high-power, or high-radiation SiC electronic devices include sensors, control electronics, and power electronics that can operate at temperatures up to 600 C and beyond. Commercially available SiC devices now include blue light-emitting diodes (LED's) and high-voltage diodes for operation up to 350 C, with other devices under development. At present, morphological defects in epitaxially grown SiC films limit their use in device applications. Research geared toward reducing the number of structural inhomogeneities can benefit from an understanding of the type and nature of problems that cause defects. The Atomic Force Microscope (AFM) has proven to be a useful tool in characterizing defects present on the surface of SiC epitaxial films. The in-house High-Temperature Integrated Electronics and Sensors (HTIES) Program at the NASA Lewis Research Center not only extended the dopant concentration range achievable in epitaxial SiC films, but it reduced the concentration of some types of defects. Advanced structural characterization using the AFM was warranted to identify the type and structure of the remaining film defects and morphological inhomogeneities. The AFM can give quantitative information on surface topography down to molecular scales. Acquired, in part, in support of the Advanced High Temperature Engine Materials Technology Program (HITEMP), the AFM had been used previously to detect partial fiber debonding in composite material cross sections. Atomic force microscopy examination of epitaxial SiC film surfaces revealed molecular-scale details of some unwanted surface features. Growth pits propagating from defects in the substrate, and hillocks due, presumably, to existing screw dislocations in the substrates, were imaged. Away from local defects, step bunching was observed to yield step heights of hundreds of angstroms, with possible implications for the uniformity of dopants incorporated in SiC devices during fabrication. The quantitative topographic data from the AFM allow the relevant defect information to be extracted, such as the size and distribution of step bunching and the Burgers vector of screw dislocations. These atomic force microscopy results have furthered the understanding of the dynamic epitaxial SiC growth process. A model describing the observed hillock step bunching has been proposed. This cooperation between researchers involved in crystal growth, electronic device fabrication, and surface structural characterization is likely to continue as atomic force microscopy is used to improve SiC films for high-temperature electronic devices for NASA's advanced turbine engines and space power devices, as well as for future applications in the automotive industry.

On the origin and elimination of macroscopic defects in MBE films

NASA Astrophysics Data System (ADS)

Wood, C. E. C.; Rathbun, L.; Ohno, H.; DeSimone, D.

1981-02-01

Spitting of group III metal droplets from Knudsen type effusion cells has been found culpable for a genre of problematical macroscopic surface topographical defects observed in the growth of semiconductor films by molecular beam epitaxy. Successful precautions are described which virtually eliminate the problem.

Forty years of research on xeroderma pigmentosum at the US National Institutes of Health.

PubMed

Kraemer, Kenneth H; DiGiovanna, John J

2015-01-01

In 1968, Dr. James Cleaver reported defective DNA repair in cultured cells from patients with xeroderma pigmentosum. This link between clinical disease and molecular pathophysiology has sparked interest in understanding not only the clinical characteristics of sun sensitivity, damage and cancer that occurred in XP patients but also the mechanisms underlying the damage and repair. While affected patients are rare, their exaggerated UV damage provides a window into the workings of DNA repair. These studies have clarified the importance of a functioning DNA repair system to the maintenance of skin and neurologic health in the general population. Understanding the role of damage in causing cancer, neurologic degeneration, hearing loss and internal cancers provides an opportunity for prevention and treatment. Characterizing complementation groups pointed to the importance of different underlying genes. Studying differences in cancer age of onset and underlying molecular signatures in cancers occurring either in XP patients or the general population has led to insights into differences in carcinogenic mechanisms. The accelerated development of cancers in XP has been used as a model to discover new cancer chemopreventive agents. An astute insight can be a "tipping point" triggering decades of productive inquiry. © 2015 The American Society of Photobiology.

Forty Years of Research on Xeroderma Pigmentosum at the US National Institutes of Health†

PubMed Central

Kraemer, Kenneth H.; DiGiovanna, John J.

2014-01-01

In 1968, Dr. James Cleaver reported defective DNA repair in cultured cells from patients with xeroderma pigmentosum. This link between clinical disease and molecular pathophysiology has sparked interest in understanding not only the clinical characteristics of sun sensitivity, damage and cancer that occurred in XP patients but also the mechanisms underlying the damage and repair. While affected patients are rare, their exaggerated UV damage provides a window into the workings of DNA repair. These studies have clarified the importance of a functioning DNA repair system to the maintenance of skin and neurologic health in the general population. Understanding the role of damage in causing cancer, neurologic degeneration, hearing loss and internal cancers provides an opportunity for prevention and treatment. Characterizing complementation groups pointed to the importance of different underlying genes. Studying differences in cancer age of onset and underlying molecular signatures in cancers occurring either in XP patients or the general population has led to insights into differences in carcinogenic mechanisms. The accelerated development of cancers in XP has been used as a model to discover new cancer chemopreventive agents. An astute insight can be a “tipping point” triggering decades of productive inquiry. PMID:25220021

The genetics of normal and defective color vision

PubMed Central

Neitz, Jay; Neitz, Maureen

2011-01-01

The contributions of genetics research to the science of normal and defective color vision over the previous few decades are reviewed emphasizing the developments in the 25 years since the last anniversary issue of Vision Research. Understanding of the biology underlying color vision has been vaulted forward through the application of the tools of molecular genetics. For all their complexity, the biological processes responsible for color vision are more accessible than for many other neural systems. This is partly because of the wealth of genetic variations that affect color perception, both within and across species, and because components of the color vision system lend themselves to genetic manipulation. Mutations and rearrangements in the genes encoding the long, middle, and short wavelength sensitive cone pigments are responsible for color vision deficiencies and mutations have been identified that affect the number of cone types, the absorption spectrum of the pigments, the functionality and viability of the cones, and the topography of the cone mosaic. The addition of an opsin gene, as occurred in the evolution of primate color vision, and has been done in experimental animals can produce expanded color vision capacities and this has provided insight into the underlying neural circuitry. PMID:21167193

Stochastic left-right neuronal asymmetry in Caenorhabditis elegans.

PubMed

Alqadah, Amel; Hsieh, Yi-Wen; Xiong, Rui; Chuang, Chiou-Fen

2016-12-19

Left-right asymmetry in the nervous system is observed across species. Defects in left-right cerebral asymmetry are linked to several neurological diseases, but the molecular mechanisms underlying brain asymmetry in vertebrates are still not very well understood. The Caenorhabditis elegans left and right amphid wing 'C' (AWC) olfactory neurons communicate through intercellular calcium signalling in a transient embryonic gap junction neural network to specify two asymmetric subtypes, AWC OFF (default) and AWC ON (induced), in a stochastic manner. Here, we highlight the molecular mechanisms that establish and maintain stochastic AWC asymmetry. As the components of the AWC asymmetry pathway are highly conserved, insights from the model organism C. elegans may provide a window onto how brain asymmetry develops in humans.This article is part of the themed issue 'Provocative questions in left-right asymmetry'. © 2016 The Author(s).

Stochastic left–right neuronal asymmetry in Caenorhabditis elegans

PubMed Central

Alqadah, Amel; Hsieh, Yi-Wen; Xiong, Rui

2016-01-01

Left–right asymmetry in the nervous system is observed across species. Defects in left–right cerebral asymmetry are linked to several neurological diseases, but the molecular mechanisms underlying brain asymmetry in vertebrates are still not very well understood. The Caenorhabditis elegans left and right amphid wing ‘C’ (AWC) olfactory neurons communicate through intercellular calcium signalling in a transient embryonic gap junction neural network to specify two asymmetric subtypes, AWCOFF (default) and AWCON (induced), in a stochastic manner. Here, we highlight the molecular mechanisms that establish and maintain stochastic AWC asymmetry. As the components of the AWC asymmetry pathway are highly conserved, insights from the model organism C. elegans may provide a window onto how brain asymmetry develops in humans. This article is part of the themed issue ‘Provocative questions in left–right asymmetry’. PMID:27821536

Growth and characterization of molecular beam epitaxial GaAs layers on porous silicon

NASA Technical Reports Server (NTRS)

Lin, T. L.; Liu, J. K.; Sadwick, L.; Wang, K. L.; Kao, Y. C.

1987-01-01

GaAs layers have been grown on porous silicon (PS) substrates with good crystallinity by molecular beam epitaxy. In spite of the surface irregularity of PS substrates, no surface morphology deterioration was observed on epitaxial GaAs overlayers. A 10-percent Rutherford backscattering spectroscopy minimum channeling yield for GaAs-on-PS layers as compared to 16 percent for GaAs-on-Si layers grown under the same condition indicates a possible improvement of crystallinity when GaAs is grown on PS. Transmission electron microscopy reveals that the dominant defects in the GaAs-on-PS layers are microtwins and stacking faults, which originate from the GaAs/PS interface. GaAs is found to penetrate into the PS layers. n-type GaAs/p-type PS heterojunction diodes were fabricated with good rectifying characteristics.

Rab GTPases: The Key Players in the Molecular Pathway of Parkinson’s Disease

PubMed Central

Shi, Meng-meng; Shi, Chang-he; Xu, Yu-ming

2017-01-01

Parkinson’s disease (PD) is a progressive movement disorder with multiple non-motor symptoms. Although family genetic mutations only account for a small proportion of the cases, these mutations have provided several lines of evidence for the pathogenesis of PD, such as mitochondrial dysfunction, protein misfolding and aggregation, and the impaired autophagy-lysosome system. Recently, vesicle trafficking defect has emerged as a potential pathogenesis underlying this disease. Rab GTPases, serving as the core regulators of cellular membrane dynamics, may play an important role in the molecular pathway of PD through the complex interplay with numerous factors and PD-related genes. This might shed new light on the potential therapeutic strategies. In this review, we emphasize the important role of Rab GTPases in vesicle trafficking and summarize the interactions between Rab GTPases and different PD-related genes. PMID:28400718

Jet and flash imprint defectivity: assessment and reduction for semiconductor applications

NASA Astrophysics Data System (ADS)

Malloy, Matt; Litt, Lloyd C.; Johnson, Steve; Resnick, Douglas J.; Lovell, David

2011-04-01

Defectivity has been historically identified as a leading technical roadblock to the implementation of nanoimprint lithography for semiconductor high volume manufacturing. The lack of confidence in nanoimprint's ability to meet defect requirements originates in part from the industry's past experiences with 1X lithography and the shortage in end-user generated defect data. SEMATECH has therefore initiated a defect assessment aimed at addressing these concerns. The goal is to determine whether nanoimprint, specifically Jet and Flash Imprint Lithography from Molecular Imprints, is capable of meeting semiconductor industry defect requirements. At this time, several cycles of learning have been completed in SEMATECH's defect assessment, with promising results. J-FIL process random defectivity of < 0.1 def/cm2 has been demonstrated using a 120nm half-pitch template, providing proof of concept that a low defect nanoimprint process is possible. Template defectivity has also improved significantly as shown by a pre-production grade template at 80nm pitch. Cycles of learning continue on feature sizes down to 22nm.

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

Yuan, Wenjuan, E-mail: ywj-0131148@163.com, E-mail: luojunkink@126.com; Yang, Hongping; Zhu, Jing

Defects are capable of modulating various properties of graphene, and thus controlling defects is useful in the development of graphene-based devices. Here we present first-principles calculations, which reveal a new avenue for defect engineering of graphene: the modulation by defects on the highest occupied molecular orbital (HOMO) energy of a charged monolayer graphene quantum dot (GQD) is discriminative. When the charge of a GQD increases its HOMO energy also increases. Importantly, when the GQD contains one particular class of defects its HOMO energy is sometimes higher and sometimes lower than that of the corresponding GQD without any defects, but whenmore » the GQD contains another class of defects its HOMO energy is always higher or lower than that of the corresponding intact GQD as its excess charge reaches a critical value. This discriminative modulation could allow defect engineering to control secondary electron ejection in graphene, leading to a new way to develop graphene-based devices.« less

UDP-glucose Dehydrogenase Polymorphisms from Patients with Congenital Heart Valve Defects Disrupt Enzyme Stability and Quaternary Assembly*

PubMed Central

Hyde, Annastasia S.; Farmer, Erin L.; Easley, Katherine E.; van Lammeren, Kristy; Christoffels, Vincent M.; Barycki, Joseph J.; Bakkers, Jeroen; Simpson, Melanie A.

2012-01-01

Cardiac valve defects are a common congenital heart malformation and a significant clinical problem. Defining molecular factors in cardiac valve development has facilitated identification of underlying causes of valve malformation. Gene disruption in zebrafish revealed a critical role for UDP-glucose dehydrogenase (UGDH) in valve development, so this gene was screened for polymorphisms in a patient population suffering from cardiac valve defects. Two genetic substitutions were identified and predicted to encode missense mutations of arginine 141 to cysteine and glutamate 416 to aspartate, respectively. Using a zebrafish model of defective heart valve formation caused by morpholino oligonucleotide knockdown of UGDH, transcripts encoding the UGDH R141C or E416D mutant enzymes were unable to restore cardiac valve formation and could only partially rescue cardiac edema. Characterization of the mutant recombinant enzymes purified from Escherichia coli revealed modest alterations in the enzymatic activity of the mutants and a significant reduction in the half-life of enzyme activity at 37 °C. This reduction in activity could be propagated to the wild-type enzyme in a 1:1 mixed reaction. Furthermore, the quaternary structure of both mutants, normally hexameric, was destabilized to favor the dimeric species, and the intrinsic thermal stability of the R141C mutant was highly compromised. The results are consistent with the reduced function of both missense mutations significantly reducing the ability of UGDH to provide precursors for cardiac cushion formation, which is essential to subsequent valve formation. The identification of these polymorphisms in patient populations will help identify families genetically at risk for valve defects. PMID:22815472

Diamond Blackfan Anemia: Diagnosis, Treatment and Molecular Pathogenesis

PubMed Central

Lipton, Jeffrey M.; Ellis, Steven R.

2009-01-01

Synopsis Diamond Blackfan anemia (DBA) is a genetically and clinically heterogeneous disorder characterized by erythroid failure, congenital anomalies and a predisposition to cancer. Faulty ribosome biogenesis, resulting in pro-apoptotic erythropoiesis leading to erythroid failure, is hypothesized to be the underlying defect. The genes identified to date that are mutated in DBA all encode ribosomal proteins associated with either the small (RPS) or large (RPL) subunit and in these cases haploinsufficiency gives rise to the disease. Extraordinarily robust laboratory and clinical investigations have recently led to demonstrable improvements in clinical care for patients with DBA. PMID:19327583

Ineffective Erythropoiesis in β-Thalassemia

PubMed Central

Ribeil, Jean-Antoine; Arlet, Jean-Benoit; Dussiot, Michael; Cruz Moura, Ivan; Courtois, Geneviève; Hermine, Olivier

2013-01-01

In humans, β-thalassemia dyserythropoiesis is characterized by expansion of early erythroid precursors and erythroid progenitors and then ineffective erythropoiesis. This ineffective erythropoiesis is defined as a suboptimal production of mature erythrocytes originating from a proliferating pool of immature erythroblasts. It is characterized by (1) accelerated erythroid differentiation, (2) maturation blockade at the polychromatophilic stage, and (3) death of erythroid precursors. Despite extensive knowledge of molecular defects causing β-thalassemia, less is known about the mechanisms responsible for ineffective erythropoiesis. In this paper, we will focus on the underlying mechanisms leading to premature death of thalassemic erythroid precursors in the bone marrow. PMID:23606813

Molecular dynamics study on splitting of hydrogen-implanted silicon in Smart-Cut® technology

NASA Astrophysics Data System (ADS)

Bing, Wang; Bin, Gu; Rongying, Pan; Sijia, Zhang; Jianhua, Shen

2015-03-01

Defect evolution in a single crystal silicon which is implanted with hydrogen atoms and then annealed is investigated in the present paper by means of molecular dynamics simulation. By introducing defect density based on statistical average, this work aims to quantitatively examine defect nucleation and growth at nanoscale during annealing in Smart-Cut® technology. Research focus is put on the effects of the implantation energy, hydrogen implantation dose and annealing temperature on defect density in the statistical region. It is found that most defects nucleate and grow at the annealing stage, and that defect density increases with the increase of the annealing temperature and the decrease of the hydrogen implantation dose. In addition, the enhancement and the impediment effects of stress field on defect density in the annealing process are discussed. Project supported by the National Natural Science Foundation of China (No. 11372261), the Excellent Young Scientists Supporting Project of Science and Technology Department of Sichuan Province (No. 2013JQ0030), the Supporting Project of Department of Education of Sichuan Province (No. 2014zd3132), the Opening Project of Key Laboratory of Testing Technology for Manufacturing Process, Southwest University of Science and Technology-Ministry of Education (No. 12zxzk02), the Fund of Doctoral Research of Southwest University of Science and Technology (No. 12zx7106), and the Postgraduate Innovation Fund Project of Southwest University of Science and Technology (No. 14ycxjj0121).

Nuclear Pasta: Topology and Defects

NASA Astrophysics Data System (ADS)

da Silva Schneider, Andre; Horowitz, Charles; Berry, Don; Caplan, Matt; Briggs, Christian

2015-04-01

A layer of complex non-uniform phases of matter known as nuclear pasta is expected to exist at the base of the crust of neutron stars. Using large scale molecular dynamics we study the topology of some pasta shapes, the formation of defects and how these may affect properties of neutron star crusts.

Microdialysis Sampling from Wound Fluids Enables Quantitative Assessment of Cytokines, Proteins, and Metabolites Reveals Bone Defect-Specific Molecular Profiles.

PubMed

Förster, Yvonne; Schmidt, Johannes R; Wissenbach, Dirk K; Pfeiffer, Susanne E M; Baumann, Sven; Hofbauer, Lorenz C; von Bergen, Martin; Kalkhof, Stefan; Rammelt, Stefan

2016-01-01

Bone healing involves a variety of different cell types and biological processes. Although certain key molecules have been identified, the molecular interactions of the healing progress are not completely understood. Moreover, a clinical routine for predicting the quality of bone healing after a fracture in an early phase is missing. This is mainly due to a lack of techniques to comprehensively screen for cytokines, growth factors and metabolites at their local site of action. Since all soluble molecules of interest are present in the fracture hematoma, its in-depth assessment could reveal potential markers for the monitoring of bone healing. Here, we describe an approach for sampling and quantification of cytokines and metabolites by using microdialysis, combined with solid phase extractions of proteins from wound fluids. By using a control group with an isolated soft tissue wound, we could reveal several bone defect-specific molecular features. In bone defect dialysates the neutrophil chemoattractants CXCL1, CXCL2 and CXCL3 were quantified with either a higher or earlier response compared to dialysate from soft tissue wound. Moreover, by analyzing downstream adaptions of the cells on protein level and focusing on early immune response, several proteins involved in the immune cell migration and activity could be identified to be specific for the bone defect group, e.g. immune modulators, proteases and their corresponding inhibitors. Additionally, the metabolite screening revealed different profiles between the bone defect group and the control group. In summary, we identified potential biomarkers to indicate imbalanced healing progress on all levels of analysis.

Microdialysis Sampling from Wound Fluids Enables Quantitative Assessment of Cytokines, Proteins, and Metabolites Reveals Bone Defect-Specific Molecular Profiles

PubMed Central

Wissenbach, Dirk K.; Pfeiffer, Susanne E. M.; Baumann, Sven; Hofbauer, Lorenz C.; von Bergen, Martin; Kalkhof, Stefan; Rammelt, Stefan

2016-01-01

Bone healing involves a variety of different cell types and biological processes. Although certain key molecules have been identified, the molecular interactions of the healing progress are not completely understood. Moreover, a clinical routine for predicting the quality of bone healing after a fracture in an early phase is missing. This is mainly due to a lack of techniques to comprehensively screen for cytokines, growth factors and metabolites at their local site of action. Since all soluble molecules of interest are present in the fracture hematoma, its in-depth assessment could reveal potential markers for the monitoring of bone healing. Here, we describe an approach for sampling and quantification of cytokines and metabolites by using microdialysis, combined with solid phase extractions of proteins from wound fluids. By using a control group with an isolated soft tissue wound, we could reveal several bone defect-specific molecular features. In bone defect dialysates the neutrophil chemoattractants CXCL1, CXCL2 and CXCL3 were quantified with either a higher or earlier response compared to dialysate from soft tissue wound. Moreover, by analyzing downstream adaptions of the cells on protein level and focusing on early immune response, several proteins involved in the immune cell migration and activity could be identified to be specific for the bone defect group, e.g. immune modulators, proteases and their corresponding inhibitors. Additionally, the metabolite screening revealed different profiles between the bone defect group and the control group. In summary, we identified potential biomarkers to indicate imbalanced healing progress on all levels of analysis. PMID:27441377

Study on the thermal resistance in secondary particles chain of silica aerogel by molecular dynamics simulation

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

Liu, M.; Department of Physics, University of Chinese Academy of Sciences, Beijing 100049; Qiu, L., E-mail: qiulin111@sina.com, E-mail: jzzhengxinghua@163.com

2014-09-07

In this article, molecular dynamics simulation was performed to study the heat transport in secondary particles chain of silica aerogel. The two adjacent particles as the basic heat transport unit were modelled to characterize the heat transfer through the calculation of thermal resistance and vibrational density of states (VDOS). The total thermal resistance of two contact particles was predicted by non-equilibrium molecular dynamics simulations (NEMD). The defects were formed by deleting atoms in the system randomly first and performing heating and quenching process afterwards to achieve the DLCA (diffusive limited cluster-cluster aggregation) process. This kind of treatment showed a verymore » reasonable prediction of thermal conductivity for the silica aerogels compared with the experimental values. The heat transport was great suppressed as the contact length increased or defect concentration increased. The constrain effect of heat transport was much significant when contact length fraction was in the small range (<0.5) or the defect concentration is in the high range (>0.5). Also, as the contact length increased, the role of joint thermal resistance played in the constraint of heat transport was increasing. However, the defect concentration did not affect the share of joint thermal resistance as the contact length did. VDOS of the system was calculated by numerical method to characterize the heat transport from atomic vibration view. The smaller contact length and greater defect concentration primarily affected the longitudinal acoustic modes, which ultimately influenced the heat transport between the adjacent particles.« less

Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Keller, D. A.; Ornstein, R. L.; Rein, R.

1993-01-01

The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.

Molecular analysis of the NDP gene in two families with Norrie disease.

PubMed

Rivera-Vega, M Refugio; Chiñas-Lopez, Silvet; Vaca, Ana Luisa Jimenez; Arenas-Sordo, M Luz; Kofman-Alfaro, Susana; Messina-Baas, Olga; Cuevas-Covarrubias, Sergio Alberto

2005-04-01

To describe the molecular defects in the Norrie disease protein (NDP) gene in two families with Norrie disease (ND). We analysed two families with ND at molecular level through polymerase chain reaction, DNA sequence analysis and GeneScan. Two molecular defects found in the NDP gene were: a missense mutation (265C > G) within codon 97 that resulted in the interchange of arginine by proline, and a partial deletion in the untranslated 3' region of exon 3 of the NDP gene. Clinical findings were more severe in the family that presented the partial deletion. We also diagnosed the carrier status of one daughter through GeneScan; this method proved to be a useful tool for establishing female carriers of ND. Here we report two novel mutations in the NDP gene in Mexican patients and propose that GeneScan is a viable mean of establishing ND carrier status.

FGFR3 gene mutation plus GRB10 gene duplication in a patient with achondroplasia plus growth delay with prenatal onset.

PubMed

Yuan, Haiming; Huang, Linhuan; Hu, Xizi; Li, Qian; Sun, Xiaofang; Xie, Yingjun; Kong, Shu; Wang, Xiaoman

2016-07-02

Achondroplasia is a well-defined and common bone dysplasia. Genotype- and phenotype-level correlations have been found between the clinical symptoms of achondroplasia and achondroplasia-specific FGFR3 mutations. A 2-year-old boy with clinical features consistent with achondroplasia and Silver-Russell syndrome-like symptoms was found to carry a mutation in the fibroblast growth factor receptor-3 (FGFR3) gene at c.1138G > A (p.Gly380Arg) and a de novo 574 kb duplication at chromosome 7p12.1 that involved the entire growth-factor receptor bound protein 10 (GRB10) gene. Using quantitative real-time PCR analysis, GRB10 was over-expressed, and, using enzyme-linked immunosorbent assays for IGF1 and IGF-binding protein-3 (IGFBP3), we found that IGF1 and IGFBP3 were low-expressed in this patient. We demonstrate that a combination of uncommon, rare and exceptional molecular defects related to the molecular bases of particular birth defects can be analyzed and diagnosed to potentially explain the observed variability in the combination of molecular defects.

Valproic acid silencing of ascl1b/Ascl1 results in the failure of serotonergic differentiation in a zebrafish model of fetal valproate syndrome

PubMed Central

Jacob, John; Ribes, Vanessa; Moore, Steven; Constable, Sean C.; Sasai, Noriaki; Gerety, Sebastian S.; Martin, Darren J.; Sergeant, Chris P.; Wilkinson, David G.; Briscoe, James

2014-01-01

Fetal valproate syndrome (FVS) is caused by in utero exposure to the drug sodium valproate. Valproate is used worldwide for the treatment of epilepsy, as a mood stabiliser and for its pain-relieving properties. In addition to birth defects, FVS is associated with an increased risk of autism spectrum disorder (ASD), which is characterised by abnormal behaviours. Valproate perturbs multiple biochemical pathways and alters gene expression through its inhibition of histone deacetylases. Which, if any, of these mechanisms is relevant to the genesis of its behavioural side effects is unclear. Neuroanatomical changes associated with FVS have been reported and, among these, altered serotonergic neuronal differentiation is a consistent finding. Altered serotonin homeostasis is also associated with autism. Here we have used a chemical-genetics approach to investigate the underlying molecular defect in a zebrafish FVS model. Valproate causes the selective failure of zebrafish central serotonin expression. It does so by downregulating the proneural gene ascl1b, an ortholog of mammalian Ascl1, which is a known determinant of serotonergic identity in the mammalian brainstem. ascl1b is sufficient to rescue serotonin expression in valproate-treated embryos. Chemical and genetic blockade of the histone deacetylase Hdac1 downregulates ascl1b, consistent with the Hdac1-mediated silencing of ascl1b expression by valproate. Moreover, tonic Notch signalling is crucial for ascl1b repression by valproate. Concomitant blockade of Notch signalling restores ascl1b expression and serotonin expression in both valproate-exposed and hdac1 mutant embryos. Together, these data provide a molecular explanation for serotonergic defects in FVS and highlight an epigenetic mechanism for genome-environment interaction in disease. PMID:24135485

Towards precise defect control in layered oxide structures by using oxide molecular beam epitaxy

PubMed Central

Baiutti, Federico; Christiani, Georg

2014-01-01

Summary In this paper we present the atomic-layer-by-layer oxide molecular beam epitaxy (ALL-oxide MBE) which has been recently installed in the Max-Planck Institute for Solid State Research and we report on its present status, providing some examples that demonstrate its successful application in the synthesis of different layered oxides, with particular reference to superconducting La2CuO4 and insulator-to-metal La2− xSrxNiO4. We briefly review the ALL-oxide MBE technique and its unique capabilities in the deposition of atomically smooth single-crystal thin films of various complex oxides, artificial compounds and heterostructures, introducing our goal of pursuing a deep investigation of such systems with particular emphasis on structural defects, with the aim of tailoring their functional properties by precise defects control. PMID:24995148

Avoiding Defect Nucleation during Equilibration in Molecular Dynamics Simulations with ReaxFF

DTIC Science & Technology

2015-04-01

respectively. All simulations are performed using the LAMMPS computer code.12 2 Fig. 1 a) Initial and b) final configurations of the molecular centers...Plimpton S. Fast parallel algorithms for short-range molecular dynamics. Comput J Phys. 1995;117:1–19. (Software available at http:// lammps .sandia.gov

Melt fracture of linear low-density polyethylenes: Die geometry and molecular weight characteristics

NASA Astrophysics Data System (ADS)

Ebrahimi, Marzieh; Tomkovic, Tanja; Liu, Guochang; Doufas, Antonios A.; Hatzikiriakos, Savvas G.

2018-05-01

The melt fracture phenomena of three linear low-density polyethylenes are investigated as a function of die geometry (capillary, slit, and annular) and molecular weight and its distribution. The onset of melt fracture instabilities is determined by using capillary rheometry, mainly studying the extrudate appearance using optical microscopy. It is found that the onset of flow instabilities (melt fracture phenomena) is significantly affected by die geometry and molecular weight characteristics of the polymers. Use of annular die eliminates the stick-slip transition (oscillating melt fracture) and delays the onset of sharkskin to higher values of shear rate and shear stress. Moreover, it is shown that the molecular weight characteristics of the polymers are well correlated with critical conditions for the onset of flow instabilities based on a criterion proposed in the literature [A. Allal et al., "Relationships between molecular structure and sharkskin defect for linear polymers," J. Non-Newtonian Fluid Mech. 134, 127-135 (2006) and A. Allal and B. Vergnes, "Molecular design to eliminate sharkskin defect for linear polymers," J. Non-Newtonian Fluid Mech. 146, 45-50 (2007)].

Improving Bone Formation in a Rat Femur Segmental Defect by Controlling Bone Morphogenetic Protein-2 Release

DTIC Science & Technology

2011-04-01

tissue and polymer: mineralized tissue stained dark green, osteoid and collagen bright red, soft tissue pink to light green, and erythrocytes bright...of bone, soft tissue , and polymer, high-resolution digital images were acquired at 1.25 · or 20 · . The area of interest comprising the bone defect...bone, soft tissue , and polymer (when present) within the defect were quantified using Metamorph software (Molecular Devices, Inc.) and were calculated

Self-evolving atomistic kinetic Monte Carlo simulations of defects in materials

DOE PAGES

Xu, Haixuan; Beland, Laurent K.; Stoller, Roger E.; ...

2015-01-29

The recent development of on-the-fly atomistic kinetic Monte Carlo methods has led to an increased amount attention on the methods and their corresponding capabilities and applications. In this review, the framework and current status of Self-Evolving Atomistic Kinetic Monte Carlo (SEAKMC) are discussed. SEAKMC particularly focuses on defect interaction and evolution with atomistic details without assuming potential defect migration/interaction mechanisms and energies. The strength and limitation of using an active volume, the key concept introduced in SEAKMC, are discussed. Potential criteria for characterizing an active volume are discussed and the influence of active volume size on saddle point energies ismore » illustrated. A procedure starting with a small active volume followed by larger active volumes was found to possess higher efficiency. Applications of SEAKMC, ranging from point defect diffusion, to complex interstitial cluster evolution, to helium interaction with tungsten surfaces, are summarized. A comparison of SEAKMC with molecular dynamics and conventional object kinetic Monte Carlo is demonstrated. Overall, SEAKMC is found to be complimentary to conventional molecular dynamics, especially when the harmonic approximation of transition state theory is accurate. However it is capable of reaching longer time scales than molecular dynamics and it can be used to systematically increase the accuracy of other methods such as object kinetic Monte Carlo. Furthermore, the challenges and potential development directions are also outlined.« less

Radiation damage in cubic ZrO 2 and yttria-stabilized zirconia from molecular dynamics simulations

DOE PAGES

Aidhy, Dilpuneet S.; Zhang, Yanwen; Weber, William J.

2014-11-20

Here, we perform molecular dynamics simulation on cubic ZrO 2 and yttria-stabilized zirconia (YSZ) to elucidate defect cluster formation resulting from radiation damage, and evaluate the impact of Y-dopants. Interstitial clusters composed of split-interstitial building blocks, i.e., Zr-Zr or Y-Zr are formed. Moreover, oxygen vacancies control cation defect migration; in their presence, Zr interstitials aggregate to form split-interstitials whereas in their absence Zr interstitials remain immobile, as isolated single-interstitials. Y-doping prevents interstitial cluster formation due to sequestration of oxygen vacancies.

Defect states and their energetic position and distribution in organic molecular semiconductors

NASA Astrophysics Data System (ADS)

Sharma, Akanksha; Yadav, Sarita; Kumar, Pramod; Ray Chaudhuri, Sumita; Ghosh, Subhasis

2013-04-01

Energetic position and distribution of defect states due to structural disorder in pentacene and copper phthalocyanine have been obtained by capacitance based spectroscopic techniques. It has been shown that capacitance-frequency and capacitance-voltage characteristics exhibit Gaussian distribution of traps with an energetic position at around 0.5 eV above the highest occupied molecular orbital level of the pentacene and CuPc. These traps have been created by varying growth conditions and almost identical trap parameters in pentacene and copper phthalocyanine indicate that similar structural disorder is responsible for these traps.

What choline metabolism can tell us about the underlying mechanisms of fetal alcohol spectrum disorders.

PubMed

Zeisel, Steven H

2011-10-01

The consequences of fetal exposure to alcohol are very diverse and the likely molecular mechanisms involved must be able to explain how so many developmental processes could go awry. If pregnant rat dams are fed alcohol, their pups develop abnormalities characteristic of fetal alcohol spectrum disorders (FASD), but if these rat dams were also treated with choline, the effects from ethanol were attenuated in their pups. Choline is an essential nutrient in humans, and is an important methyl group donor. Alcohol exposure disturbs the metabolism of choline and other methyl donors. Availability of choline during gestation directly influences epigenetic marks on DNA and histones, and alters gene expression needed for normal neural and endothelial progenitor cell proliferation. Maternal diets low in choline alter development of the mouse hippocampus, and decrement memory for life. Women eating low-choline diets have an increased risk of having an infant with a neural tube or orofacial cleft birth defect. Thus, the varied effects of choline could affect the expression of FASD, and studies on choline might shed some light on the underlying molecular mechanisms responsible for FASD.

microRNA-mediated R gene regulation: molecular scabbards for double-edged swords.

PubMed

Deng, Yingtian; Liu, Minglei; Li, Xiaofei; Li, Feng

2018-02-01

Plant resistance (R) proteins are immune receptors that recognize pathogen effectors and trigger rapid defense responses, namely effector-triggered immunity. R protein-mediated pathogen resistance is usually race specific. During plant-pathogen coevolution, plant genomes accumulated large numbers of R genes. Even though plant R genes provide important natural resources for breeding disease-resistant crops, their presence in the plant genome comes at a cost. Misregulation of R genes leads to developmental defects, such as stunted growth and reduced fertility. In the past decade, many microRNAs (miRNAs) have been identified to target various R genes in plant genomes. miRNAs reduce R gene levels under normal conditions and allow induction of R gene expression under various stresses. For these reasons, we consider R genes to be double-edged "swords" and miRNAs as molecular "scabbards". In the present review, we summarize the contributions and potential problems of these "swords" and discuss the features and production of the "scabbards", as well as the mechanisms used to pull the "sword" from the "scabbard" when needed.

Revealing the properties of defects formed by CH3NH2 molecules in organic-inorganic hybrid perovskite MAPbBr3

NASA Astrophysics Data System (ADS)

Wang, Ji; Zhang, Ao; Yan, Jun; Li, Dan; Chen, Yunlin

2017-03-01

The properties of defects in organic-inorganic hybrid perovskite are widely studied from the first-principles calculation. However, the defects of methylamine (methylamine = CH3NH2), which would be easily formed during the preparation of the organic-inorganic hybrid perovskite, are rarely investigated. Thermodynamic properties as well as defect states of methylamine embedded MAPbX3 (MA = methyl-ammonium = CH3NH3, X = Br, I) are studied based on first-principles calculations of density functional theory. It was found that there is a shallow defect level near the highest occupied molecular orbital, which induced by the interstitial methylamine defect in MAPbBr3, will lead to an increase of photoluminescence. The calculation results showed that interstitial defect states of methylamine may move deeper due to the interaction between methylamine molecules and methyl-ammonium cations. It was also showed that the interstitial methylamine defect is stable at room temperature, and the defect can be removed easily by annealing.

Polymer-dielectric molecular interactions in defect-free poly(3-hexylthiophene): dependence and consequences of regioregularity on transistor charge transport properties

NASA Astrophysics Data System (ADS)

Nawaz, Ali; Cruz-Cruz, Isidro; Rego, Jessica S.; Koehler, Marlus; Gopinathan, Sreelekha P.; Kumar, Anil; Hümmelgen, Ivo A.

2017-08-01

We investigate the molecular interaction of poly(3-hexylthiophene-2,5-diyl) (P3HT) molecules with polar functional groups of the dielectric surface, and its dependence on the regioregularity of P3HT. With this aim, we consider thickness-dependent molecular order of 100% regioregular defect-free P3HT (DF-P3HT) and 93% regioregular P3HT (LT-P3HT), deposited on top of cross-linked poly(vinyl alcohol) (cr-PVA) substrates. Intimate contact of P3HT molecules and cr-PVA surface defects affects the molecular order of P3HT differently, depending on the regioregularity. Consequently, these molecular order changes on the charge transport properties of organic field-effect transistors (OFETs) are investigated using four thicknesses (20, 40, 80 and 120 nm) of P3HT. As compared to other thicknesses, μ sat for 20 nm DF-P3HT OFETs shows further improvement, while the opposite occurs for 20 nm LT-P3HT OFETs. Depending on the regioregularity (and thus the chain orientation), P3HT molecules exhibit a difference in dipole moments. Consequently, the interaction of edge-on or face-on P3HT molecules with cr-PVA surface dipoles has different contributions towards the electrostatic energetic disorder at cr-PVA/P3HT interface. This subtle difference of behavior helps one to understand the huge spread of characteristics of P3HT based transistors found in literature.

Study on the intrinsic defects in tin oxide with first-principles method

NASA Astrophysics Data System (ADS)

Sun, Yu; Liu, Tingyu; Chang, Qiuxiang; Ma, Changmin

2018-04-01

First-principles and thermodynamic methods are used to study the contribution of vibrational entropy to defect formation energy and the stability of the intrinsic point defects in SnO2 crystal. According to thermodynamic calculation results, the contribution of vibrational entropy to defect formation energy is significant and should not be neglected, especially at high temperatures. The calculated results indicate that the oxygen vacancy is the major point defect in undoped SnO2 crystal, which has a higher concentration than that of the other point defect. The property of negative-U is put forward in SnO2 crystal. In order to determine the most stable defects much clearer under different conditions, the most stable intrinsic defect as a function of Fermi level, oxygen partial pressure and temperature are described in the three-dimensional defect formation enthalpy diagrams. The diagram visually provides the most stable point defects under different conditions.

Converting ceria polyhedral nanoparticles into single-crystal nanospheres.

PubMed

Feng, Xiangdong; Sayle, Dean C; Wang, Zhong Lin; Paras, M Sharon; Santora, Brian; Sutorik, Anthony C; Sayle, Thi X T; Yang, Yi; Ding, Yong; Wang, Xudong; Her, Yie-Shein

2006-06-09

Ceria nanoparticles are one of the key abrasive materials for chemical-mechanical planarization of advanced integrated circuits. However, ceria nanoparticles synthesized by existing techniques are irregularly faceted, and they scratch the silicon wafers and increase defect concentrations. We developed an approach for large-scale synthesis of single-crystal ceria nanospheres that can reduce the polishing defects by 80% and increase the silica removal rate by 50%, facilitating precise and reliable mass-manufacturing of chips for nanoelectronics. We doped the ceria system with titanium, using flame temperatures that facilitate crystallization of the ceria yet retain the titania in a molten state. In conjunction with molecular dynamics simulation, we show that under these conditions, the inner ceria core evolves in a single-crystal spherical shape without faceting, because throughout the crystallization it is completely encapsulated by a molten 1- to 2-nanometer shell of titania that, in liquid state, minimizes the surface energy. The principle demonstrated here could be applied to other oxide systems.

Regulation of cell protrusions by small GTPases during fusion of the neural folds

PubMed Central

Rolo, Ana; Savery, Dawn; Escuin, Sarah; de Castro, Sandra C; Armer, Hannah EJ; Munro, Peter MG; Molè, Matteo A; Greene, Nicholas DE; Copp, Andrew J

2016-01-01

Epithelial fusion is a crucial process in embryonic development, and its failure underlies several clinically important birth defects. For example, failure of neural fold fusion during neurulation leads to open neural tube defects including spina bifida. Using mouse embryos, we show that cell protrusions emanating from the apposed neural fold tips, at the interface between the neuroepithelium and the surface ectoderm, are required for completion of neural tube closure. By genetically ablating the cytoskeletal regulators Rac1 or Cdc42 in the dorsal neuroepithelium, or in the surface ectoderm, we show that these protrusions originate from surface ectodermal cells and that Rac1 is necessary for the formation of membrane ruffles which typify late closure stages, whereas Cdc42 is required for the predominance of filopodia in early neurulation. This study provides evidence for the essential role and molecular regulation of membrane protrusions prior to fusion of a key organ primordium in mammalian development. DOI: http://dx.doi.org/10.7554/eLife.13273.001 PMID:27114066

Surface structure and structural point defects of liquid and amorphous aluminosilicate nanoparticles.

PubMed

Linh, Nguyen Ngoc; Hoang, Vo Van

2008-07-02

The surface structure of liquid and amorphous aluminosilicate nanoparticles of composition Al(2)O(3)·2SiO(2) has been investigated in a model of different sizes ranging from 2.0 to 5.0 nm with the Born-Mayer type pair potential under non-periodic boundary conditions. Models have been obtained by cooling from the melts at a constant density of 2.6 g cm(-3) via molecular dynamics (MD) simulation. The surface structure has been investigated via the coordination number, bond-angle distributions and structural point defects. Calculations show that surface effects on surface static and thermodynamic properties of models are significant according to the change in the number of Al atoms in the surface layers. Evolution of the local environment of oxygen in the surface shell of nanoparticles upon cooling from the melt toward the glassy state was also found and discussed. In addition, the nanosize dependence of the glass transition temperature was presented.

Surface structure and structural point defects of liquid and amorphous aluminosilicate nanoparticles

NASA Astrophysics Data System (ADS)

Linh, Nguyen Ngoc; Van Hoang, Vo

2008-07-01

The surface structure of liquid and amorphous aluminosilicate nanoparticles of composition Al2O3·2SiO2 has been investigated in a model of different sizes ranging from 2.0 to 5.0 nm with the Born-Mayer type pair potential under non-periodic boundary conditions. Models have been obtained by cooling from the melts at a constant density of 2.6 g cm-3 via molecular dynamics (MD) simulation. The surface structure has been investigated via the coordination number, bond-angle distributions and structural point defects. Calculations show that surface effects on surface static and thermodynamic properties of models are significant according to the change in the number of Al atoms in the surface layers. Evolution of the local environment of oxygen in the surface shell of nanoparticles upon cooling from the melt toward the glassy state was also found and discussed. In addition, the nanosize dependence of the glass transition temperature was presented.

Effects of Defects on the Mechanical Properties of Kinked Silicon Nanowires.

PubMed

Chen, Yun; Zhang, Cheng; Li, Liyi; Tuan, Chia-Chi; Chen, Xin; Gao, Jian; He, Yunbo; Wong, Ching-Ping

2017-12-01

Kinked silicon nanowires (KSiNWs) have many special properties that make them attractive for a number of applications. The mechanical properties of KSiNWs play important roles in the performance of sensors. In this work, the effects of defects on the mechanical properties of KSiNWs are studied using molecular dynamics simulations and indirectly validated by experiments. It is found that kinks are weak points in the nanowire (NW) because of inharmonious deformation, resulting in a smaller elastic modulus than that of straight NWs. In addition, surface defects have more significant effects on the mechanical properties of KSiNWs than internal defects. The effects of the width or the diameter of the defects are larger than those of the length of the defects. Overall, the elastic modulus of KSiNWs is not sensitive to defects; therefore, KSiNWs have a great potential as strain or stress sensors in special applications.

Carotid body chemoreflex: a driver of autonomic abnormalities in sleep apnoea.

PubMed

Prabhakar, Nanduri R

2016-08-01

What is the topic of this review? This article presents emerging evidence for heightened carotid body chemoreflex activity as a major driver of sympathetic activation and hypertension in sleep apnoea patients. What advances does it heighlight? This article discusses the recent advances on cellular, molecular and epigenetic mechanisms underlying the exaggerated chemoreflex in experimental models of sleep apnoea. The carotid bodies are the principal peripheral chemoreceptors for detecting changes in arterial blood oxygen concentration, and the resulting chemoreflex is a potent regulator of the sympathetic tone, blood pressure and breathing. Sleep apnoea is a disease of the respiratory system that affects several million adult humans. Apnoeas occur during sleep, often as a result of obstruction of the upper airway (obstructive sleep apnoea) or because of defective respiratory rhythm generation by the CNS (central sleep apnoea). Patients with sleep apnoea exhibit several co-morbidities, with the most notable among them being heightened sympathetic nerve activity and hypertension. Emerging evidence suggests that intermittent hypoxia resulting from periodic apnoea stimulates the carotid body, and the ensuing chemoreflex mediates the increased sympathetic tone and hypertension in sleep apnoea patients. Rodent models of intermittent hypoxia that simulate the O2 saturation profiles encountered during sleep apnoea have provided important insights into the cellular and molecular mechanisms underlying the heightened carotid body chemoreflex. This article describes how intermittent hypoxia affects the carotid body function and discusses the cellular, molecular and epigenetic mechanisms underlying the exaggerated chemoreflex. © 2016 The Authors. Experimental Physiology © 2016 The Physiological Society.

Influence of tool shape on lattice rearrangement under loading conditions reproducing friction stir welding

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

Konovalenko, Ivan S., E-mail: ivkon@ispms.tsc.ru; Konovalenko, Igor S., E-mail: igkon@ispms.tsc.ru; National Research Tomsk Polytechnic University, Tomsk, 634050

2015-10-27

Metal behavior under loading conditions that reproduce friction stir welding was studied on the atomic scale. Calculations were conducted based on molecular dynamics simulation with potentials calculated within the embedded atom method. The loading of the interface between two crystallites, whose structure corresponded to aluminum alloy 2024, was simulated by the motion of a cone-shaped tool along the interface with constant angular and translational velocities. The motion of the rotating tool causes fracture of the workpiece crystal structure with subsequent mixing of surface atoms of the interfacing crystallites. It is shown that the resistance force acting on the moving toolmore » from the workpiece and the process of structural defect formation in the workpiece depend on the tool shape.« less

7 CFR 1924.258 - Notification of borrowers.

Code of Federal Regulations, 2014 CFR

2014-01-01

... REGULATIONS CONSTRUCTION AND REPAIR Complaints and Compensation for Construction Defects § 1924.258... frames for filing claims under this subpart. FmHA or its successor agency under Public Law 103-354 will also notify and advise borrowers of the construction defects procedure at any time construction defects...

7 CFR 1924.258 - Notification of borrowers.

Code of Federal Regulations, 2012 CFR

2012-01-01

... REGULATIONS CONSTRUCTION AND REPAIR Complaints and Compensation for Construction Defects § 1924.258... frames for filing claims under this subpart. FmHA or its successor agency under Public Law 103-354 will also notify and advise borrowers of the construction defects procedure at any time construction defects...

7 CFR 1924.258 - Notification of borrowers.

Code of Federal Regulations, 2013 CFR

2013-01-01

... REGULATIONS CONSTRUCTION AND REPAIR Complaints and Compensation for Construction Defects § 1924.258... frames for filing claims under this subpart. FmHA or its successor agency under Public Law 103-354 will also notify and advise borrowers of the construction defects procedure at any time construction defects...

7 CFR 1924.258 - Notification of borrowers.

Code of Federal Regulations, 2011 CFR

2011-01-01

... REGULATIONS CONSTRUCTION AND REPAIR Complaints and Compensation for Construction Defects § 1924.258... frames for filing claims under this subpart. FmHA or its successor agency under Public Law 103-354 will also notify and advise borrowers of the construction defects procedure at any time construction defects...

7 CFR 1924.258 - Notification of borrowers.

Code of Federal Regulations, 2010 CFR

2010-01-01

... REGULATIONS CONSTRUCTION AND REPAIR Complaints and Compensation for Construction Defects § 1924.258... frames for filing claims under this subpart. FmHA or its successor agency under Public Law 103-354 will also notify and advise borrowers of the construction defects procedure at any time construction defects...

Human cytomegalovirus infection interferes with the maintenance and differentiation of trophoblast progenitor cells of the human placenta.

PubMed

Tabata, Takako; Petitt, Matthew; Zydek, Martin; Fang-Hoover, June; Larocque, Nicholas; Tsuge, Mitsuru; Gormley, Matthew; Kauvar, Lawrence M; Pereira, Lenore

2015-05-01

Human cytomegalovirus (HCMV) is a major cause of birth defects that include severe neurological deficits, hearing and vision loss, and intrauterine growth restriction. Viral infection of the placenta leads to development of avascular villi, edema, and hypoxia associated with symptomatic congenital infection. Studies of primary cytotrophoblasts (CTBs) revealed that HCMV infection impedes terminal stages of differentiation and invasion by various molecular mechanisms. We recently discovered that HCMV arrests earlier stages involving development of human trophoblast progenitor cells (TBPCs), which give rise to the mature cell types of chorionic villi-syncytiotrophoblasts on the surfaces of floating villi and invasive CTBs that remodel the uterine vasculature. Here, we show that viral proteins are present in TBPCs of the chorion in cases of symptomatic congenital infection. In vitro studies revealed that HCMV replicates in continuously self-renewing TBPC lines derived from the chorion and alters expression and subcellular localization of proteins required for cell cycle progression, pluripotency, and early differentiation. In addition, treatment with a human monoclonal antibody to HCMV glycoprotein B rescues differentiation capacity, and thus, TBPCs have potential utility for evaluation of the efficacies of novel antiviral antibodies in protecting and restoring placental development. Our results suggest that HCMV replicates in TBPCs in the chorion in vivo, interfering with the earliest steps in the growth of new villi, contributing to virus transmission and impairing compensatory development. In cases of congenital infection, reduced responsiveness of the placenta to hypoxia limits the transport of substances from maternal blood and contributes to fetal growth restriction. Human cytomegalovirus (HCMV) is a leading cause of birth defects in the United States. Congenital infection can result in permanent neurological defects, mental retardation, hearing loss, visual impairment, and pregnancy complications, including intrauterine growth restriction, preterm delivery, and stillbirth. Currently, there is neither a vaccine nor any approved treatment for congenital HCMV infection during gestation. The molecular mechanisms underlying structural deficiencies in the placenta that undermine fetal development are poorly understood. Here we report that HCMV replicates in trophoblast progenitor cells (TBPCs)-precursors of the mature placental cells, syncytiotrophoblasts and cytotrophoblasts, in chorionic villi-in clinical cases of congenital infection. Virus replication in TBPCs in vitro dysregulates key proteins required for self-renewal and differentiation and inhibits normal division and development into mature placental cells. Our findings provide insights into the underlying molecular mechanisms by which HCMV replication interferes with placental maturation and transport functions. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

N vacancy, self-interstitial diffusion, and Frenkel-pair formation/dissociation in TiN studied by ab-initio and classical molecular dynamics

NASA Astrophysics Data System (ADS)

Sangiovanni, Davide G.; Alling, Björn; Hultman, Lars; Abrikosov, Igor A.

2015-03-01

We use ab-initio and classical molecular dynamics (AIMD, CMD) to simulate diffusion of N vacancy and N self-interstitial point-defects in B1 TiN. The physical properties of TiN, important material system for thin film and coatings applications, are largely dictated by concentration and mobility of point defects. We determine N dilute-point-defect diffusion pathways, activation energies, attempt frequencies, and diffusion coefficients as a function of temperature. In addition, MD simulations reveal an unanticipated atomistic process, which controls the spontaneous formation of N-self-interstitial/N-vacancy pairs (Frenkel pairs) in defect-free TiN. This entails that a N lattice atom leaves its bulk position and bonds to a neighboring N lattice atom. In most cases, Frenkel-pair NI and NV recombine within a fraction of ns; 50% of these processes result in the exchange of two nitrogen lattice atoms. Occasionally, however, Frenkel-pair N-interstitial atoms permanently escape from the anion vacancy site, thus producing unpaired NI and NV point defects. The Knut and Alice Wallenberg foundation (Isotope Project, 2011.0094), the Swedish Research Council (VR) Linköping Linnaeus Initiative LiLi-NFM (Grant 2008-6572), and the Swedish Government Strategic Research (Grant MatLiU 2009-00971).

Nitrogen vacancy, self-interstitial diffusion, and Frenkel-pair formation/dissociation in B 1 TiN studied by ab initio and classical molecular dynamics with optimized potentials

NASA Astrophysics Data System (ADS)

Sangiovanni, D. G.; Alling, B.; Steneteg, P.; Hultman, L.; Abrikosov, I. A.

2015-02-01

We use ab initio and classical molecular dynamics (AIMD and CMD) based on the modified embedded-atom method (MEAM) potential to simulate diffusion of N vacancy and N self-interstitial point defects in B 1 TiN. TiN MEAM parameters are optimized to obtain CMD nitrogen point-defect jump rates in agreement with AIMD predictions, as well as an excellent description of Ti Nx(˜0.7

A molecular dynamics simulation study of irradiation induced defects in gold nanowire

NASA Astrophysics Data System (ADS)

Liu, Wenqiang; Chen, Piheng; Qiu, Ruizhi; Khan, Maaz; Liu, Jie; Hou, Mingdong; Duan, Jinglai

2017-08-01

Displacement cascade in gold nanowires was studied using molecular dynamics computer simulations. Primary knock-on atoms (PKAs) with different kinetic energies were initiated either at the surface or at the center of the nanowires. We found three kinds of defects that were induced by the cascade, including point defects, stacking faults and crater at the surface. The starting points of PKAs influence the number of residual point defects, and this consequently affect the boundary of anti-radiation window which was proposed by calculation of diffusion of point defects to the free surface of nanowires. Formation of stacking faults that expanded the whole cross-section of gold nanowires was observed when the PKA's kinetic energy was higher than 5 keV. Increasing the PKA's kinetic energy up to more than 10 keV may lead to the formation of crater at the surface of nanowires due to microexplosion of hot atoms. At this energy, PKAs started from the center of nanowires can also result in the creation of crater because length of cascade region is comparable to diameter of nanowires. Both the two factors, namely initial positions of PKAs as well as the craters induced by higher energy irradiation, would influence the ability of radiation resistance of metal nanowires.

Substrate preparation effects on defect density in molecular beam epitaxial growth of CdTe on CdTe (100) and (211)B

DOE PAGES

Burton, George L.; Diercks, David R.; Perkins, Craig L.; ...

2017-07-01

Recent studies have demonstrated that growth of CdTe on CdTe (100) and (211)B substrates via molecular beam epitaxy (MBE) results in planar defect densities 2 and 3 orders of magnitude higher than growth on InSb (100) substrates, respectively. To understand this shortcoming, MBE growth on CdTe substrates with a variety of substrate preparation methods is studied by scanning electron microscopy, secondary ion mass spectrometry, x-ray photoelectron spectroscopy, cross sectional transmission electron microscopy, and atom probe tomography (APT). Prior to growth, carbon is shown to remain on substrate surfaces even after atomic hydrogen cleaning. APT revealed that following the growth ofmore » films, trace amounts of carbon remained at the substrate/film interface. This residual carbon may lead to structural degradation, which was determined as the main cause of higher defect density.« less

Structural properties and defects of GaN crystals grown at ultra-high pressures: A molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Gao, Tinghong; Li, Yidan; Xie, Quan; Tian, Zean; Chen, Qian; Liang, Yongchao; Ren, Lei; Hu, Xuechen

2018-01-01

The growth of GaN crystals at different pressures was studied by molecular dynamics simulation employing the Stillinger-Weber potential, and their structural properties and defects were characterized using the radial distribution function, the Voronoi polyhedron index method, and a suitable visualization technology. Crystal structures formed at 0, 1, 5, 10, and 20 GPa featured an overwhelming number of <4 0 0 0> Voronoi polyhedra, whereas amorphous structures comprising numerous disordered polyhedra were produced at 50 GPa. During quenching, coherent twin boundaries were easily formed between zinc-blende and wurtzite crystal structures in GaN. Notably, point defects usually appeared at low pressure, whereas dislocations were observed at high pressure, since the simultaneous growth of two crystal grains with different crystal orientations and their boundary expansion was hindered in the latter case, resulting in the formation of a dislocation between these grains.

R6G molecule induced modulation of the optical properties of reduced graphene oxide nanosheets for use in ultrasensitive SPR sensing

PubMed Central

Xue, Tianyu; Yu, Shansheng; Zhang, Xiaoming; Zhang, Xinzheng; Wang, Lei; Bao, Qiaoliang; Chen, Caiyun; Zheng, Weitao; Cui, Xiaoqiang

2016-01-01

A proper understanding of the role that molecular doping plays is essential to research on the modulation of the optical and electronic properties of graphene. The adsorption of R6G molecules onto defect-rich reduced graphene oxide nanosheets results in a shift of the Fermi energy and, consequently, a variation in the optical constants. This optical variation in the graphene nanosheets is used to develop an ultrasensitive surface plasmon resonance biosensor with a detection limit of 10−17 M (0.01 fM) at the molecular level. A density functional theory calculation shows that covalent bonds were formed between the R6G molecules and the defect sites on the graphene nanosheets. Our study reveals the important role that defects play in tailoring the properties and sensor device applications of graphene materials. PMID:26887525

Short stature caused by isolated SHOX gene haploinsufficiency: update on the diagnosis and treatment.

PubMed

Jorge, Alexander A L; Funari, Mariana Fa; Nishi, Mirian Y; Mendonca, Berenice B

2010-12-01

Heterozygous SHOX defects are observed in about 50 to 90% of patients with Leri-Weill dyschondrosteosis (LWD), a common dominant inherited skeletal dysplasia; and in 2 to 15% of children with idiopathic short stature (ISS), indicating that SHOX defects are the most important monogenetic cause of short stature. In addition, children selected by disproportionate idiopathic short stature had a higher frequency of SHOX mutations (22%). A careful clinical evaluation of family members with short stature is recommended since it usually revealed LWD patients in families first classified as having ISS or familial short stature. SHOX-molecular analysis is indicated in families with LWD and ISS children with disproportionate short stature. Treatment with recombinant human growth hormone is considered an accepted approach to treat short stature associated with isolated SHOX defect. Here we review clinical, molecular and therapeutic aspects of SHOX haploinsufficiency.

First principles molecular dynamics study of nitrogen vacancy complexes in boronitrene

NASA Astrophysics Data System (ADS)

Ukpong, A. M.; Chetty, N.

2012-07-01

We present the results of first principles molecular dynamics simulations of nitrogen vacancy complexes in monolayer hexagonal boron nitride. The threshold for local structure reconstruction is found to be sensitive to the presence of a substitutional carbon impurity. We show that activated nitrogen dynamics triggers the annihilation of defects in the layer through formation of Stone-Wales-type structures. The lowest energy state of nitrogen vacancy complexes is negatively charged and spin polarized. Using the divacancy complex, we show that their formation induces spontaneous magnetic moments, which is tunable by electron or hole injection. The Fermi level s-resonant defect state is identified as a unique signature of the ground state of the divacancy complex. Due to their ability to enhance structural cohesion, only the divacancy and the nitrogen vacancy carbon-antisite complexes are able to suppress the Fermi level resonant defect state to open a gap between the conduction and valence bands.

An AT-hook protein DEPRESSED PALEA1 physically interacts with the TCP Family transcription factor RETARDED PALEA1 in rice.

PubMed

Yin, Dedong; Liu, Xue; Shi, Zhenying; Li, Dayong; Zhu, Lihuang

2018-01-01

The cereal crops (such as rice and maize) which belong to the grass family, are the most important grain crops for human beings, and the development of their flower and inflorescence architecture has attracted extensive attention. Although multiple genes involved in the regulation of floral and inflorescence organogenesis have been identified, the underlying molecular mechanisms are largely unknown. Previously, we identified rice depressed palea1 (dp1) mutants with defects in main structure of palea and its enhancer RETARDED PALEA1 (REP1). DP1 is an AT-hook protein while REP1 is a TCP transcription factor, both of which are important regulators of palea development. However, the relationship of these two proteins has not been elucidated yet. Here, we demonstrated that DP1 interacts physically with REP1 both in yeast and in rice protoplasts. Considering the close phylogenetic relationship between maize and rice, we further hypothesize that their orthologs in maize, BARREN STALK FASTIGIATE (BAF1) and BRANCH ANGLE DEFECTIVE 1 (BAD1), may interact physically. Subsequently, we verified their physical interaction, indicating that the interaction between AT-hook proteins and TCP proteins is conserved in rice and maize. Our findings may reveal a novel molecular mechanism of floral and inflorescence development in grasses. Copyright © 2017 Elsevier Inc. All rights reserved.

WIND1 Promotes Shoot Regeneration through Transcriptional Activation of ENHANCER OF SHOOT REGENERATION1 in Arabidopsis[OPEN

PubMed Central

Ohnuma, Mariko; Kurata, Tetsuya; Nakata, Masaru; Ohme-Takagi, Masaru

2017-01-01

Many plant species display remarkable developmental plasticity and regenerate new organs after injury. Local signals produced by wounding are thought to trigger organ regeneration but molecular mechanisms underlying this control remain largely unknown. We previously identified an AP2/ERF transcription factor WOUND INDUCED DEDIFFERENTIATION1 (WIND1) as a central regulator of wound-induced cellular reprogramming in plants. In this study, we demonstrate that WIND1 promotes callus formation and shoot regeneration by upregulating the expression of the ENHANCER OF SHOOT REGENERATION1 (ESR1) gene, which encodes another AP2/ERF transcription factor in Arabidopsis thaliana. The esr1 mutants are defective in callus formation and shoot regeneration; conversely, its overexpression promotes both of these processes, indicating that ESR1 functions as a critical driver of cellular reprogramming. Our data show that WIND1 directly binds the vascular system-specific and wound-responsive cis-element-like motifs within the ESR1 promoter and activates its expression. The expression of ESR1 is strongly reduced in WIND1-SRDX dominant repressors, and ectopic overexpression of ESR1 bypasses defects in callus formation and shoot regeneration in WIND1-SRDX plants, supporting the notion that ESR1 acts downstream of WIND1. Together, our findings uncover a key molecular pathway that links wound signaling to shoot regeneration in plants. PMID:28011694

Tailoring Dirac Fermions in Molecular Graphene

NASA Astrophysics Data System (ADS)

Gomes, Kenjiro K.; Mar, Warren; Ko, Wonhee; Camp, Charlie D.; Rastawicki, Dominik K.; Guinea, Francisco; Manoharan, Hari C.

2012-02-01

The dynamics of electrons in solids is tied to the band structure created by a periodic atomic potential. The design of artificial lattices, assembled through atomic manipulation, opens the door to engineer electronic band structure and to create novel quantum states. We present scanning tunneling spectroscopic measurements of a nanoassembled honeycomb lattice displaying a Dirac fermion band structure. The artificial lattice is created by atomic manipulation of single CO molecules with the scanning tunneling microscope on the surface of Cu(111). The periodic potential generated by the assembled CO molecules reshapes the band structure of the two-dimensional electron gas, present as a surface state of Cu(111), into a ``molecular graphene'' system. We create local defects in the lattice to observe the quasiparticle interference patterns that unveil the underlying band structure. We present direct comparison between the tunneling data, first-principles calculations of the band structure, and tight-binding models.

Nanocarbon synthesis by high-temperature oxidation of nanoparticles

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

Nomura, Ken-ichi; Kalia, Rajiv K.; Li, Ying

High-temperature oxidation of silicon-carbide nanoparticles (nSiC) underlies a wide range of technologies from high-power electronic switches for efficient electrical grid and thermal protection of space vehicles to self-healing ceramic nanocomposites. Here, multimillion-atom reactive molecular dynamics simulations validated by ab initio quantum molecular dynamics simulations predict unexpected condensation of large graphene flakes during high-temperature oxidation of nSiC. Initial oxidation produces a molten silica shell that acts as an autocatalytic ‘nanoreactor’ by actively transporting oxygen reactants while protecting the nanocarbon product from harsh oxidizing environment. Percolation transition produces porous nanocarbon with fractal geometry, which consists of mostly sp 2 carbons with pentagonalmore » and heptagonal defects. Furthermore, this work suggests a simple synthetic pathway to high surface-area, low-density nanocarbon with numerous energy, biomedical and mechanical-metamaterial applications, including the reinforcement of self-healing composites.« less

Nanocarbon synthesis by high-temperature oxidation of nanoparticles

DOE PAGES

Nomura, Ken-ichi; Kalia, Rajiv K.; Li, Ying; ...

2016-04-20

High-temperature oxidation of silicon-carbide nanoparticles (nSiC) underlies a wide range of technologies from high-power electronic switches for efficient electrical grid and thermal protection of space vehicles to self-healing ceramic nanocomposites. Here, multimillion-atom reactive molecular dynamics simulations validated by ab initio quantum molecular dynamics simulations predict unexpected condensation of large graphene flakes during high-temperature oxidation of nSiC. Initial oxidation produces a molten silica shell that acts as an autocatalytic ‘nanoreactor’ by actively transporting oxygen reactants while protecting the nanocarbon product from harsh oxidizing environment. Percolation transition produces porous nanocarbon with fractal geometry, which consists of mostly sp 2 carbons with pentagonalmore » and heptagonal defects. Furthermore, this work suggests a simple synthetic pathway to high surface-area, low-density nanocarbon with numerous energy, biomedical and mechanical-metamaterial applications, including the reinforcement of self-healing composites.« less

Noonan syndrome and clinically related disorders

PubMed Central

Tartaglia, Marco; Gelb, Bruce D.; Zenker, Martin

2010-01-01

Noonan syndrome is a relatively common, clinically variable developmental disorder. Cardinal features include postnatally reduced growth, distinctive facial dysmorphism, congenital heart defects and hypertrophic cardiomyopathy, variable cognitive deficit and skeletal, ectodermal and hematologic anomalies. Noonan syndrome is transmitted as an autosomal dominant trait, and is genetically heterogeneous. So far, heterozygous mutations in nine genes (PTPN11, SOS1, KRAS, NRAS, RAF1, BRAF, SHOC2, MEK1 and CBL) have been documented to underlie this disorder or clinically related phenotypes. Based on these recent discoveries, the diagnosis can now be confirmed molecularly in approximately 75% of affected individuals. Affected genes encode for proteins participating in the RAS-mitogen-activated protein kinases (MAPK) signal transduction pathway, which is implicated in several developmental processes controlling morphology determination, organogenesis, synaptic plasticity and growth. Here, we provide an overview of clinical aspects of this disorder and closely related conditions, the molecular mechanisms underlying pathogenesis, and major genotype-phenotype correlations. PMID:21396583

Nanocarbon synthesis by high-temperature oxidation of nanoparticles

PubMed Central

Nomura, Ken-ichi; Kalia, Rajiv K.; Li, Ying; Nakano, Aiichiro; Rajak, Pankaj; Sheng, Chunyang; Shimamura, Kohei; Shimojo, Fuyuki; Vashishta, Priya

2016-01-01

High-temperature oxidation of silicon-carbide nanoparticles (nSiC) underlies a wide range of technologies from high-power electronic switches for efficient electrical grid and thermal protection of space vehicles to self-healing ceramic nanocomposites. Here, multimillion-atom reactive molecular dynamics simulations validated by ab initio quantum molecular dynamics simulations predict unexpected condensation of large graphene flakes during high-temperature oxidation of nSiC. Initial oxidation produces a molten silica shell that acts as an autocatalytic ‘nanoreactor’ by actively transporting oxygen reactants while protecting the nanocarbon product from harsh oxidizing environment. Percolation transition produces porous nanocarbon with fractal geometry, which consists of mostly sp2 carbons with pentagonal and heptagonal defects. This work suggests a simple synthetic pathway to high surface-area, low-density nanocarbon with numerous energy, biomedical and mechanical-metamaterial applications, including the reinforcement of self-healing composites. PMID:27095061

Elucidating the genotype-phenotype relationships and network perturbations of human shared and specific disease genes from an evolutionary perspective.

PubMed

Begum, Tina; Ghosh, Tapash Chandra

2014-10-05

To date, numerous studies have been attempted to determine the extent of variation in evolutionary rates between human disease and nondisease (ND) genes. In our present study, we have considered human autosomal monogenic (Mendelian) disease genes, which were classified into two groups according to the number of phenotypic defects, that is, specific disease (SPD) gene (one gene: one defect) and shared disease (SHD) gene (one gene: multiple defects). Here, we have compared the evolutionary rates of these two groups of genes, that is, SPD genes and SHD genes with respect to ND genes. We observed that the average evolutionary rates are slow in SHD group, intermediate in SPD group, and fast in ND group. Group-to-group evolutionary rate differences remain statistically significant regardless of their gene expression levels and number of defects. We demonstrated that disease genes are under strong selective constraint if they emerge through edgetic perturbation or drug-induced perturbation of the interactome network, show tissue-restricted expression, and are involved in transmembrane transport. Among all the factors, our regression analyses interestingly suggest the independent effects of 1) drug-induced perturbation and 2) the interaction term of expression breadth and transmembrane transport on protein evolutionary rates. We reasoned that the drug-induced network disruption is a combination of several edgetic perturbations and, thus, has more severe effect on gene phenotypes. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The quantum defect: Early history and recent developments

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

Rau, A.R.; Inokuti, M.

1997-03-01

The notion of the quantum defect is important in atomic and molecular spectroscopy and also in unifying spectroscopy with collision theory. In the latter context, the quantum defect may be viewed as an ancestor of the phase shift. However, the origin of the term {open_quotes}quantum defect{close_quotes} does not seem to be explained in standard textbooks. It occurred in a 1921 paper by Schr{umlt o}dinger, preceding quantum mechanics, yet giving the correct meaning as an index of the short-range interactions with the core of an atom. We present the early history of the quantum-defect idea, and sketch its recent developments. {copyright}more » {ital 1997 American Association of Physics Teachers.}« less

Clinical, hormonal, ovarian, and genetic aspects of 46,XX patients with congenital adrenal hyperplasia due to CYP17A1 defects.

PubMed

Carvalho, Luciane Carneiro de; Brito, Vinicius Nahime; Martin, Regina Matsunaga; Zamboni, Aline Machado; Gomes, Larissa Garcia; Inácio, Marlene; Mermejo, Livia Mara; Coeli-Lacchini, Fernanda; Teixeira, Virginia Ribeiro; Gonçalves, Fabrícia Torres; Carrilho, Alexandre José Faria; Del Toro Camargo, Kenny Yelena; Finkielstain, Gabriela Paula; Taboada, Giselle Fernandes; Frade Costa, Elaine Maria; Domenice, Sorahia; Mendonca, Berenice Bilharinho

2016-06-01

To perform a clinical, biochemical, and molecular evaluation of patients with CYP17A1 defects, including ovarian imaging. Retrospective study. Tertiary care center. Sixteen patients with congenital adrenal hyperplasia due to CYP17A1 defects with a median chronological age of 20 years and belonging to 10 unrelated families. None. Clinical and biochemical parameters, molecular diagnosis, ovarian imaging, and therapeutic management. Seventy-one percent of patients presented with primary amenorrhea, 50% had no breast development, and pubic hair was absent or sparse in all patients; 88% had high blood pressure at diagnosis. Basal LH and P levels were high, and androgen levels were low in all patients. Ultrasound revealed ovarian enlargement in 68.7% and ovarian macrocysts in 62.5% of patients before treatment; three patients had a previous surgical correction of ovarian torsion or rupture. Molecular analysis revealed inactivating CYP17A1 mutations in all patients. The most prevalent mutation was p.W406R, and one patient bore a novel p.G478S/p.I223Nfs*10 compound heterozygous mutation. Treatment with dexamethasone, estrogen, and P resulted in reduction of ovarian volume. Amenorrhea, absent/sparse pubic hair, hypertension, and ovarian macrocysts, whichincrease the risk of ovarian torsion, are important elements in the diagnosis of 46,XX patients with CYP17A1 defects. High basal P levels in patients with hypergonadotropic hypogonadism point to the diagnosis of CYP17A1 defects. Fertility can be achieved in these patients with novel reproductive techniques. Copyright © 2016 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

CD22ΔE12 as a molecular target for corrective repair using a RNA trans-splicing strategy: Anti-leukemic activity of a rationally designed RNA trans-splicing molecule

PubMed Central

Uckun, Fatih M.; Qazi, Sanjive; Ma, Hong; Reaman, Gregory H.; Mitchell, Lloyd G.

2015-01-01

Our recent studies have demonstrated that the CD22 exon 12 deletion (CD22ΔE12) is a characteristic genetic defect of therapy-refractory clones in pediatric B-precursor acute lymphoblastic leukemia (BPL) and implicated the CD22ΔE12 genetic defect in the aggressive biology of relapsed or therapy-refractory pediatric BPL. The purpose of the present study was to further evaluate the biologic significance of the CD22ΔE12 molecular lesion and determine if it could serve as a molecular target for corrective repair using RNA trans-splicing therapy. We show that both pediatric and adult B-lineage lymphoid malignancies are characterized by a very high incidence of the CD22ΔE12 genetic defect. We provide experimental evidence that the correction of the CD22ΔE12 genetic defect in human CD22ΔE12+ BPL cells using a rationally designed CD22 RNA trans-splicing molecule (RTM) caused a pronounced reduction of their clonogenicity. The RTM-mediated correction replaced the downstream mutation-rich segment of Intron 12 and remaining segments of the mutant CD22 pre-mRNA with wildtype CD22 Exons 10-14, thereby preventing the generation of the cis-spliced aberrant CD22ΔE12 product. The anti-leukemic activity of this RTM against BPL xenograft clones derived from CD22ΔE12+ leukemia patients provides the preclinical proof-of-concept that correcting the CD22ΔE12 defect with rationally designed CD22 RTMs may provide the foundation for therapeutic innovations that are needed for successful treatment of high-risk and relapsed BPL patients. PMID:25567759

Defects formation and wave emitting from defects in excitable media

NASA Astrophysics Data System (ADS)

Ma, Jun; Xu, Ying; Tang, Jun; Wang, Chunni

2016-05-01

Abnormal electrical activities in neuronal system could be associated with some neuronal diseases. Indeed, external forcing can cause breakdown even collapse in nervous system under appropriate condition. The excitable media sometimes could be described by neuronal network with different topologies. The collective behaviors of neurons can show complex spatiotemporal dynamical properties and spatial distribution for electrical activities due to self-organization even from the regulating from central nervous system. Defects in the nervous system can emit continuous waves or pulses, and pacemaker-like source is generated to perturb the normal signal propagation in nervous system. How these defects are developed? In this paper, a network of neurons is designed in two-dimensional square array with nearest-neighbor connection type; the formation mechanism of defects is investigated by detecting the wave propagation induced by external forcing. It is found that defects could be induced under external periodical forcing under the boundary, and then the wave emitted from the defects can keep balance with the waves excited from external forcing.

Impaired associative taste learning and abnormal brain activation in kinase-defective eEF2K mice.

PubMed

Gildish, Iness; Manor, David; David, Orit; Sharma, Vijendra; Williams, David; Agarwala, Usha; Wang, Xuemin; Kenney, Justin W; Proud, Chris G; Rosenblum, Kobi

2012-02-24

Memory consolidation is defined temporally based on pharmacological interventions such as inhibitors of mRNA translation (molecular consolidation) or post-acquisition deactivation of specific brain regions (systems level consolidation). However, the relationship between molecular and systems consolidation are poorly understood. Molecular consolidation mechanisms involved in translation initiation and elongation have previously been studied in the cortex using taste-learning paradigms. For example, the levels of phosphorylation of eukaryotic elongation factor 2 (eEF2) were found to be correlated with taste learning in the gustatory cortex (GC), minutes following learning. In order to isolate the role of the eEF2 phosphorylation state at Thr-56 in both molecular and system consolidation, we analyzed cortical-dependent taste learning in eEF2K (the only known kinase for eEF2) ki mice, which exhibit reduced levels of eEF2 phosphorylation but normal levels of eEF2 and eEF2K. These mice exhibit clear attenuation of cortical-dependent associative, but not of incidental, taste learning. In order to gain a better understanding of the underlying mechanisms, we compared brain activity as measured by MEMRI (manganese-enhanced magnetic resonance imaging) between eEF2K ki mice and WT mice during conditioned taste aversion (CTA) learning and observed clear differences between the two but saw no differences under basal conditions. Our results demonstrate that adequate levels of phosphorylation of eEF2 are essential for cortical-dependent associative learning and suggest that malfunction of memory processing at the systems level underlies this associative memory impairment. © 2012 Cold Spring Harbor Laboratory Press

Cohesive Energies of Some Transition Metal Compounds Using Embedded Clusters

NASA Astrophysics Data System (ADS)

Press, Mehernosh Rustom

The molecular-clusters approach to electronic structure calculation is especially well-suited to the study of properties that depend primarily on the local environment of a system, especially those with no translational symmetry, e.g. systems with defects and structural deformations. The presence of the rest of the crystal environment can be accounted for approximately by embedding the cluster in a self-consistent crystal potential. This thesis makes a contribution in the area of investigating the capability of embedded molecular-clusters to yield reliable bulk structural properties. To this end, an algorithm for calculating the cohesive energies of clusters within the discrete-variational X(,(alpha)) LCAO-MO formulation is set up and verified on simple solids: Li, Na, Cu and LiF. We then use this formulation to study transition metal compounds, for which the interesting physics lies in local lattice defects, foreign impurities and structural deformations. In a self -consistent calculation of the lattice energies and stability of defect clusters in wustite, Fe(,1-x)O, corner-sharing aggregates of the 4:1 defect are identified as the most stable defect configurations due to efficient compensation of the cluster charge. The intercalation properties of layered-transition-metal-dichalcogenides continues to be a fertile experimental working area, backed by comparatively little theoretical study. We find that intercalation of ZrS(,2) with Na perturbs the valence energy level structure sufficiently to induce a more ionic Zr-S bond, a narrowing of the optical gap and filling of the lowest unoccupied host lattice orbitals with the electron donated by Na. Fe - intercalation in ZrS(,2) is accommodated via a strong Fe-S bond, impurity-like band levels in the optical gap of the host and hybridization-driven compression and lowering of the conduction band energy levels. The piezoelectric cuprous halides, CuCl and CuBr, exhibit a host of intriguing properties due to a filled and very active d('10) shell at the Fermi energy. A self-consistent calculation via energy minimization of the internal strain in these compounds shows both Cu-halide bonds to be very rigid with little charge delocalization under strain. Piezoelectric response is calculated in terms of effective charges and quadrupolar moments, e(,T) and (DELTA)Q.

The molecular mechanism of plant gravitropism.

PubMed

Wu, Di; Huang, Lin-zhou; Gao, Jin; Wang, Yong-hong

2016-07-20

Gravity is an important environmental factor that regulates plant growth and morphogenesis. In response to gravity stimulus, plants can set the optimum angle between the organs and the gravity vector. Plant gravitropism is divided into four sequential steps, including gravity perception, signal transduction, asymmetrical distribution of auxin, and organ curvature. In recent years, large numbers of mutants with defective gravitropism have been identified and genes involved in the regulation of gravitropism have been functionally characterized. In particular, progress has been achieved on elucidating the molecular mechanisms of gravity perception and asymmetrical distribution of auxin. As one of the most important strategies for plant to adapt environmental changes, gravitropism is also involved in the regulation of rice plant architecture and grain yield through modulating rice tiller angle. Therefore, the investigation of plant gravitropism not only contributes to decipher the regulatory mechanisms of plant growth and development, but also helps to guide the genetic improvement of crop architecture. However, the molecular mechanisms and regulatory network of gravitropism remain to be elusive. In this review, we focus on recent progress on elucidating molecular mechanisms underlying gravitropism and its involvement in regulating rice tiller angle, which is an important agronomic trait that determines rice plant architecture and thus grain yields.

Role of pre-existing point defects on primary damage production and amorphization in silicon carbide (β-SiC)

NASA Astrophysics Data System (ADS)

Sahoo, Deepak Ranjan; Szlufarska, Izabela; Morgan, Dane; Swaminathan, Narasimhan

2018-01-01

Molecular dynamics simulations of displacement cascades were conducted to study the effect of point defects on the primary damage production in β-SiC. Although all types of point defects and Frenkel pairs were considered, Si interstitials and Si Frenkel pairs were unstable and hence excluded from the cascade studies. Si (C) vacancies had the maximum influence, enhancing C (Si) antisites and suppressing C interstitial production, when compared to the sample without any defects. The intracascade recombination mechanisms, in the presence of pre-existing defects, is explored by examining the evolution of point defects during the cascade. To ascertain the role of the unstable Si defects on amorphization, simulations involving explicit displacements of Si atoms were conducted. The dose to amorphization with only Si displacements was much lower than what was observed with only C displacements. The release of elastic energy accumulated due to Si defects, is found to be the amorphizing mechanism.

The effects of self-interstitial clusters on cascade defect evolution beyond the primary damage state

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

Heinisch, H.L.

1997-04-01

The intracascade evolution of the defect distributions of cascades in copper is investigated using stochastic annealing simulations applied to cascades generated with molecular dynamics (MD). The temperature and energy dependencies of annihilation, clustering and free defect production are determined for individual cascades. The annealing simulation results illustrate the strong influence on intracascade evolution of the defect configuration existing in the primary damage state. Another factor significantly affecting the evolution of the defect distribution is the rapid one-dimensional diffusion of small, glissile interstitial loops produced directly in cascades. This phenomenon introduces a cascade energy dependence of defect evolution that is apparentmore » only beyond the primary damage state, amplifying the need for further study of the annealing phase of cascade evolution and for performing many more MD cascade simulations at higher energies.« less

Molecular imaging promotes progress in orthopedic research.

PubMed

Mayer-Kuckuk, Philipp; Boskey, Adele L

2006-11-01

Modern orthopedic research is directed towards the understanding of molecular mechanisms that determine development, maintenance and health of musculoskeletal tissues. In recent years, many genetic and proteomic discoveries have been made which necessitate investigation under physiological conditions in intact, living tissues. Molecular imaging can meet this demand and is, in fact, the only strategy currently available for noninvasive, quantitative, real-time biology studies in living subjects. In this review, techniques of molecular imaging are summarized, and applications to bone and joint biology are presented. The imaging modality most frequently used in the past was optical imaging, particularly bioluminescence and near-infrared fluorescence imaging. Alternate technologies including nuclear and magnetic resonance imaging were also employed. Orthopedic researchers have applied molecular imaging to murine models including transgenic mice to monitor gene expression, protein degradation, cell migration and cell death. Within the bone compartment, osteoblasts and their stem cells have been investigated, and the organic and mineral bone phases have been assessed. These studies addressed malignancy and injury as well as repair, including fracture healing and cell/gene therapy for skeletal defects. In the joints, molecular imaging has focused on the inflammatory and tissue destructive processes that cause arthritis. As described in this review, the feasibility of applying molecular imaging to numerous areas of orthopedic research has been demonstrated and will likely result in an increase in research dedicated to this powerful strategy. Molecular imaging holds great promise in the future for preclinical orthopedic research as well as next-generation clinical musculoskeletal diagnostics.

Corrosion Behavior of X80 Steel with Coupled Coating Defects under Alternating Current Interference in Alkaline Environment

PubMed Central

Li, Zhong; Li, Caiyu; Qian, Hongchang; Li, Jun; Huang, Liang; Du, Cuiwei

2017-01-01

The corrosion behavior of X80 steel in the presence of coupled coating defects was simulated and studied under the interference of alternating current (AC) in an alkaline environment. The results from electrochemical measurements showed that the electrode potential of the coating defect with the smaller exposed area was lower than that with the larger area, which indicated that the steel with the smaller coating defect was more prone to corrosion. The result of weight loss tests also showed that the smaller coating defect had induced a higher corrosion rate. However, the corrosion rate of X80 steel at the larger coating defect decreased gradually with the increase of the larger defect area at a constant smaller defect area. The corrosion morphology images showed that the coating defects with smaller areas suffered from more severe pitting corrosion. PMID:28773078

Defect-induced change of temperature-dependent elastic constants in BCC iron

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

Gao, N.; Setyawan, W.; Zhang, S. H.

2017-07-01

The effects of radiation-induced defects (randomly distributed vacancies, voids, and interstitial dislocation loops) on temperature-dependent elastic constants, C11, C12, and C44 in BCC iron, are studied with molecular dynamics method. The elastic constants are found to decrease with increasing temperatures for all cases containing different defects. The presence of vacancies, voids, or interstitial loops further decreases the elastic constants. For a given number of point defects, the randomly distributed vacancies show the strongest effect compared to voids or interstitial loops. All these results are expected to provide useful information to combine with experimental results for further understanding of radiation damage.

Predictive modeling of synergistic effects in nanoscale ion track formation

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

Zarkadoula, Eva; Pakarinen, Olli H.; Xue, Haizhou

Molecular dynamics techniques and the inelastic thermal spike model are used to study the coupled effects of inelastic energy loss due to 21 MeV Ni ion irradiation and pre-existing defects in SrTiO 3. We determine the dependence on pre-existing defect concentration of nanoscale track formation occurring from the synergy between the inelastic energy loss and the pre-existing atomic defects. We show that the nanoscale ion tracks’ size can be controlled by the concentration of pre-existing disorder. This work identifies a major gap in fundamental understanding concerning the role played by defects in electronic energy dissipation and electron–lattice coupling.

Predictive modeling of synergistic effects in nanoscale ion track formation

DOE PAGES

Zarkadoula, Eva; Pakarinen, Olli H.; Xue, Haizhou; ...

2015-08-05

Molecular dynamics techniques and the inelastic thermal spike model are used to study the coupled effects of inelastic energy loss due to 21 MeV Ni ion irradiation and pre-existing defects in SrTiO 3. We determine the dependence on pre-existing defect concentration of nanoscale track formation occurring from the synergy between the inelastic energy loss and the pre-existing atomic defects. We show that the nanoscale ion tracks’ size can be controlled by the concentration of pre-existing disorder. This work identifies a major gap in fundamental understanding concerning the role played by defects in electronic energy dissipation and electron–lattice coupling.

Computational design of surfaces, nanostructures and optoelectronic materials

NASA Astrophysics Data System (ADS)

Choudhary, Kamal

Properties of engineering materials are generally influenced by defects such as point defects (vacancies, interstitials, substitutional defects), line defects (dislocations), planar defects (grain boundaries, free surfaces/nanostructures, interfaces, stacking faults) and volume defects (voids). Classical physics based molecular dynamics and quantum physics based density functional theory can be useful in designing materials with controlled defect properties. In this thesis, empirical potential based molecular dynamics was used to study the surface modification of polymers due to energetic polyatomic ion, thermodynamics and mechanics of metal-ceramic interfaces and nanostructures, while density functional theory was used to screen substituents in optoelectronic materials. Firstly, polyatomic ion-beams were deposited on polymer surfaces and the resulting chemical modifications of the surface were examined. In particular, S, SC and SH were deposited on amorphous polystyrene (PS), and C2H, CH3, and C3H5 were deposited on amorphous poly (methyl methacrylate) (PMMA) using molecular dynamics simulations with classical reactive empirical many-body (REBO) potentials. The objective of this work was to elucidate the mechanisms by which the polymer surface modification took place. The results of the work could be used in tailoring the incident energy and/or constituents of ion beam for obtaining a particular chemistry inside the polymer surface. Secondly, a new Al-O-N empirical potential was developed within the charge optimized many body (COMB) formalism. This potential was then used to examine the thermodynamic stability of interfaces and mechanical properties of nanostructures composed of aluminum, its oxide and its nitride. The potentials were tested for these materials based on surface energies, defect energies, bulk phase stability, the mechanical properties of the most stable bulk phase, its phonon properties as well as with a genetic algorithm based evolution theory of the materials to ensure that no spurious phases had a lower cohesive energy. Thirdly, lanthanide doped and co-doped Y3Al5O 12 were examined using density functional theory (DFT) with semi-local and local functional. Theoretical results were compared and validated with experimental data and new co-doped materials with high efficiency were predicted. Finally, Transition element doped CH3NH3PbI3 were studied with DFT for validation of the model with experimental data and replacement materials for toxic Pb were predicted.

Epstein–Barr Virus Susceptibility in Activated PI3Kδ Syndrome (APDS) Immunodeficiency

PubMed Central

Carpier, Jean-Marie; Lucas, Carrie L.

2018-01-01

Activated PI3Kδ Syndrome (APDS) is an inherited immune disorder caused by heterozygous, gain-of-function mutations in the genes encoding the phosphoinositide 3-kinase delta (PI3Kδ) subunits p110δ or p85δ. This recently described primary immunodeficiency disease (PID) is characterized by recurrent sinopulmonary infections, lymphoproliferation, and susceptibility to herpesviruses, with Epstein–Barr virus (EBV) infection being most notable. A broad range of PIDs having disparate, molecularly defined genetic etiology can cause susceptibility to EBV, lymphoproliferative disease, and lymphoma. Historically, PID patients with loss-of-function mutations causing defective cell-mediated cytotoxicity or antigen receptor signaling were found to be highly susceptible to pathological EBV infection. By contrast, the gain of function in PI3K signaling observed in APDS patients paradoxically renders these patients susceptible to EBV, though the underlying mechanisms are incompletely understood. At a cellular level, APDS patients exhibit deranged B lymphocyte development and defects in class switch recombination, which generally lead to defective immunoglobulin production. Moreover, APDS patients also demonstrate an abnormal skewing of T cells toward terminal effectors with short telomeres and senescence markers. Here, we review APDS with a particular focus on how the altered lymphocyte biology in these patients may confer EBV susceptibility. PMID:29387064

Reliability-Limiting Defects in GaN/AlGaN High Electron Mobility Transistors

DTIC Science & Technology

2011-12-01

GaN grown by plasma-assisted molecular beam epitaxy”, Appl. Phys. Lett., vol. 77, no. 18, pp. 2885- 2887, 2000. [24] A. Hierro , A. R. Arehart, B...defects and impurities: Applications to III-nitrides”, J. Appl. Phys., vol. 95, pp.3851-3879, 2004. [43] A. Hierro , S. A. Ringel, M. Hansen, J. S

Low defect densities in molecular beam epitaxial GaAs achieved by isoelectronic In doping

NASA Technical Reports Server (NTRS)

Bhattacharya, P. K.; Dhar, S.; Berger, P.; Juang, F.-Y.

1986-01-01

A study has been made of the effects of adding small amounts of In (0.2-1.2 pct) to GaAs grown by molecular beam epitaxy. The density of four electron traps decreases in concentration by an order of magnitude, and the peak intensities of prominent emissions in the excitonic spectra are reduced with increase in In content. Based on the higher surface migration rate of In, compared to Ga, at the growth temperatures it is apparent that the traps and the excitonic transitions are related to point defects. This agrees with earlier observations by Briones and Collins (1982) and Skromme et al. (1985).

Stability of vacancy-type defect clusters in Ni based on first-principles and molecular dynamics simulations

DOE PAGES

Zhao, Shijun; Zhang, Yanwen; Weber, William J.

2017-10-17

Using first-principles calculations based on density-functional theory, the energetics of different vacancy-type defects, including voids, stacking fault tetrahedra (SFT) and vacancy loops, in Ni are investigated. It is found that voids are more stable than SFT at 0 K, which is also the case after taking into account the volumetric strains. By carrying out ab initio molecular dynamics simulations at temperatures up to 1000 K, direct transformations from vacancy loops and voids into SFT are observed. Our results suggest the importance of temperature effects in determining thermodynamic stability of vacancy clusters in face-centered cubic metals.

Tuning Interfacial Thermal Conductance of Graphene Embedded in Soft Materials by Vacancy Defects

DOE PAGES

Liu, Ying; Hu, Chongze; Huang, Jingsong; ...

2015-06-23

Nanocomposites based on graphene dispersed in matrices of soft materials are promising thermal management materials. Their effective thermal conductivity depends on both the thermal conductivity of graphene and the conductance of the thermal transport across graphene-matrix interfaces. Here we report on molecular dynamics simulations of the thermal transport across the interfaces between defected graphene and soft materials in two different modes: in the across mode, heat enters graphene from one side of its basal plane and leaves through the other side; in the non-across mode, heat enters or leaves a graphene simultaneously from both sides of its basal plane. Wemore » show that, as the density of vacancy defects in graphene increases from 0 to 8%, the conductance of the interfacial thermal transport in the across mode increases from 160.4 16 to 207.8 11 MW/m2K, while that in the non-across mode increases from 7.2 0.1 to 17.8 0.6 MW/m2K. The molecular mechanisms for these variations of thermal conductance are clarified by using the phonon density of states and structural characteristics of defected graphenes. On the basis of these results and effective medium theory, we show that it is possible to enhance the effective thermal conductivity of thermal nanocomposites by tuning the density of vacancy defects in graphene despite the fact that graphene s thermal conductivity always decreases as vacancy defects are introduced.« less

Molecular dynamic simulation study of plasma etching L10 FePt media in embedded mask patterning (EMP) process

NASA Astrophysics Data System (ADS)

Zhu, Jianxin; Quarterman, P.; Wang, Jian-Ping

2017-05-01

Plasma etching process of single-crystal L10-FePt media [H. Wang et al., Appl. Phys. Lett. 102(5) (2013)] is studied using molecular dynamic simulation. Embedded-Atom Method [M. S. Daw and M. I. Baskes, Phy. Rev. B 29, 6443 (1984); X. W. Zhou, R. A. Johnson and H. N. G. Wadley, Phy. Rev. B 69, 144113 (2004)] is used to calculate the interatomic potential within atoms in FePt alloy, and ZBL potential [J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter," Volume 1, Pergamon,1985] in comparison with conventional Lennard-Jones "12-6" potential is applied to interactions between etching gas ions and metal atoms. It is shown the post-etch structure defects can include amorphized surface layer and lattice interstitial point defects that caused by etchant ions passed through the surface layer. We show that the amorphized or damaged FePt lattice surface layer (or "magnetic dead-layer") thickness after etching increases with ion energy for Ar ion impacts, but significantly small for He ions at up to 250eV ion energy. However, we showed that He sputtering creates more interstitial defects at lower energy levels and defects are deeper below the surface compared to Ar sputtering. We also calculate the interstitial defect level and depth as dependence on ion energy for both Ar and He ions. Media magnetic property loss due to these defects is also discussed.

Adsorption of small inorganic molecules on a defective MoS2 monolayer.

PubMed

González, César; Biel, Blanca; Dappe, Yannick J

2017-04-05

We present a theoretical study of molecular adsorption on defects on a MoS 2 monolayer. Based on Density Functional Theory, our calculations confirm that small inorganic molecules, such as CO 2 , CO, H 2 O, NO, NO 2 , H 2 and N 2 , remain bonded to the pristine monolayer through weak van der Waals interactions, suggesting that the molecules may easily diffuse over the clean monolayer. On the other hand, the introduction of defects can lead to three different situations, depending on the defect and the molecule considered: physisorption, chemical (strong) bonding to the metallic defects, namely the Mo substitutional atoms on the S vacancies, and dissociation, that can take place spontaneously at 0 K in some specific cases or by the effect of thermal agitation in molecules such as CO 2 or NO 2 on the S vacancy. Our energetic and electronic analyses provide an explanation to such bonding possibilities, showing that in the low interacting situations, the molecules tend to adopt a planar configuration parallel to the monolayer, while a molecular rotation is favored in order to facilitate the bond formation on the reactive sites. Finally, the ab initio based Scanning Tunneling Microscopy (STM) simulations show the fingerprint of each molecule adsorbed on the most reactive site. This work opens the way to the possibility of tuning the catalytic properties of MoS 2 by controlling the creation of specific defects in the MoS 2 monolayer.

Growth hormone receptor gene mutations in two Italian patients with Laron Syndrome.

PubMed

Fassone, L; Corneli, G; Bellone, S; Camacho-Hübner, C; Aimaretti, G; Cappa, M; Ubertini, G; Bona, G

2007-05-01

Laron Syndrome (LS) represents a condition characterized by GH insensitivity caused by molecular defects in the GH receptor (GHR) gene or in the post-receptor signalling pathway. We report the molecular characterization of two unrelated Italian girls from Sicily diagnosed with LS. The DNA sequencing of the GHR gene revealed the presence of different nonsense mutations, occurring in the same background haplotype. The molecular defects occurred in the extracellular domain of the GHR leading to a premature termination signal and to a truncated non-functional receptor. In one patient, a homozygous G to T transversion, in exon 6, led to the mutation GAA to TAA at codon 180 (E180X), while in the second patient a homozygous C to T transition in exon 7 was detected, causing the CGA to TAA substitution at codon 217 (R217X). Both probands presented the polymorphisms Gly168Gly and Ile544Leu in a homozygous state in exons 6 and 10, respectively. The E180X represents a novel defect of the GHR gene, while the R217X mutation has been previously reported in several patients from different ethnic backgrounds but all from countries located in the Mediterranean and Middle Eastern region.

Changes in intranuclear mobility of mature snRNPs provide a mechanism for splicing defects in spinal muscular atrophy

PubMed Central

Clelland, Allyson Kara; Bales, Alexandra Beatrice E.; Sleeman, Judith Elizabeth

2012-01-01

It is becoming increasingly clear that defects in RNA metabolism can lead to disease. Spinal muscular atrophy (SMA), a leading genetic cause of infant mortality, results from insufficient amounts of survival motor neuron (SMN) protein. SMN is required for the biogenesis of small nuclear ribonucleoproteins (snRNPs): essential components of the spliceosome. Splicing abnormalities have been detected in models of SMA but it is unclear how lowered SMN affects the fidelity of pre-mRNA splicing. We have examined the dynamics of mature snRNPs in cells depleted of SMN and demonstrated that SMN depletion increases the mobility of mature snRNPs within the nucleus. To dissect the molecular mechanism by which SMN deficiency affects intranuclear snRNP mobility, we employed a panel of inhibitors of different stages of pre-mRNA processing. This in vivo modelling demonstrates that snRNP mobility is altered directly as a result of impaired snRNP maturation. Current models of nuclear dynamics predict that subnuclear structures, including the spliceosome, form by self-organization mediated by stochastic interactions between their molecular components. Thus, alteration of the intranuclear mobility of snRNPs provides a molecular mechanism for splicing defects in SMA. PMID:22393244

Using bayesian models to assess the effects of under-reporting of cannabis use on the association with birth defects, national birth defects prevention study, 1997-2005.

PubMed

van Gelder, Marleen M H J; Donders, A Rogier T; Devine, Owen; Roeleveld, Nel; Reefhuis, Jennita

2014-09-01

Studies on associations between periconceptional cannabis exposure and birth defects have mainly relied on self-reported exposure. Therefore, the results may be biased due to under-reporting of the exposure. The aim of this study was to quantify the potential effects of this form of exposure misclassification. Using multivariable logistic regression, we re-analysed associations between periconceptional cannabis use and 20 specific birth defects using data from the National Birth Defects Prevention Study from 1997-2005 for 13 859 case infants and 6556 control infants. For seven birth defects, we implemented four Bayesian models based on various assumptions concerning the sensitivity of self-reported cannabis use to estimate odds ratios (ORs), adjusted for confounding and under-reporting of the exposure. We used information on sensitivity of self-reported cannabis use from the literature for prior assumptions. The results unadjusted for under-reporting of the exposure showed an association between cannabis use and anencephaly (posterior OR 1.9 [95% credible interval (CRI) 1.1, 3.2]) which persisted after adjustment for potential exposure misclassification. Initially, no statistically significant associations were observed between cannabis use and the other birth defect categories studied. Although adjustment for under-reporting did not notably change these effect estimates, cannabis use was associated with esophageal atresia (posterior OR 1.7 [95% CRI 1.0, 2.9]), diaphragmatic hernia (posterior OR 1.8 [95% CRI 1.1, 3.0]), and gastroschisis (posterior OR 1.7 [95% CRI 1.2, 2.3]) after correction for exposure misclassification. Under-reporting of the exposure may have obscured some cannabis-birth defect associations in previous studies. However, the resulting bias is likely to be limited. © 2014 John Wiley & Sons Ltd.

Process Setting through General Linear Model and Response Surface Method

NASA Astrophysics Data System (ADS)

Senjuntichai, Angsumalin

2010-10-01

The objective of this study is to improve the efficiency of the flow-wrap packaging process in soap industry through the reduction of defectives. At the 95% confidence level, with the regression analysis, the sealing temperature, temperatures of upper and lower crimper are found to be the significant factors for the flow-wrap process with respect to the number/percentage of defectives. Twenty seven experiments have been designed and performed according to three levels of each controllable factor. With the general linear model (GLM), the suggested values for the sealing temperature, temperatures of upper and lower crimpers are 185, 85 and 85° C, respectively while the response surface method (RSM) provides the optimal process conditions at 186, 89 and 88° C. Due to different assumptions between percentage of defective and all three temperature parameters, the suggested conditions from the two methods are then slightly different. Fortunately, the estimated percentage of defectives at 5.51% under GLM process condition and the predicted percentage of defectives at 4.62% under RSM process condition are not significant different. But at 95% confidence level, the percentage of defectives under RSM condition can be much lower approximately 2.16% than those under GLM condition in accordance with wider variation. Lastly, the percentages of defectives under the conditions suggested by GLM and RSM are reduced by 55.81% and 62.95%, respectively.

Temperature dependence of the radiation tolerance of nanocrystalline pyrochlores A 2Ti 2O 7 (A = Gd, Ho and Lu)

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

Wen, J.; Sun, C.; Dholabhai, P. P.

A potentially enhanced radiation resistance of nanocrystalline materials, as a consequence of the high density of interfaces and surfaces, has attracted much attention both to understand the fundamental role of these defect sinks and to develop them for high-radiation environments. Here, irradiation response of nanocrystalline A 2Ti 2O 7 (A = Gd, Ho and Lu) pyrochlore powders with grain sizes of 20–30 nm was investigated by 1-MeV Kr 2+ ion bombardment. In situ transmission electron microscopy (TEM) revealed that the critical amorphization fluence for each nanocrystalline compound at room temperature was greater than that for their coarse-grained counterparts, indicating anmore » enhanced amorphization resistance. The effect of temperature on the irradiation response of one of these compounds, nanocrystalline Lu 2Ti 2O 7, was further examined by performing ion irradiation at an elevated temperature range of 480–600 K. The critical amorphization temperature (T c) was found to be noticeably higher in nanocrystalline Lu 2Ti 2O 7 (610 K) than its coarse-grained counterpart (480 K), revealing that nanocrystalline Lu 2Ti 2O 7 is less resistant to amorphization compared to its coarse-grained phase under high temperatures. We interpret these results with the aid of atomistic simulations. Molecular statics calculations find that cation antisite defects are less energetically costly to form near surfaces than in the bulk, suggesting that the nanocrystalline form of these materials is generally less susceptible to amorphization than coarse-grained counterparts at low temperatures where defect kinetics are negligible. In contrast, at high temperatures, the annealing efficiency of antisite defects by cation interstitials is significantly reduced due to the sink properties of the surfaces in the nanocrystalline pyrochlore, which contributes to the observed higher amorphization temperature in the nano-grained phase than in coarse-grained counterpart. Altogether, these results provide new insight into the behavior of nanocrystalline materials under irradiation.« less

Temperature dependence of the radiation tolerance of nanocrystalline pyrochlores A 2Ti 2O 7 (A = Gd, Ho and Lu)

DOE PAGES

Wen, J.; Sun, C.; Dholabhai, P. P.; ...

2016-03-21

A potentially enhanced radiation resistance of nanocrystalline materials, as a consequence of the high density of interfaces and surfaces, has attracted much attention both to understand the fundamental role of these defect sinks and to develop them for high-radiation environments. Here, irradiation response of nanocrystalline A 2Ti 2O 7 (A = Gd, Ho and Lu) pyrochlore powders with grain sizes of 20–30 nm was investigated by 1-MeV Kr 2+ ion bombardment. In situ transmission electron microscopy (TEM) revealed that the critical amorphization fluence for each nanocrystalline compound at room temperature was greater than that for their coarse-grained counterparts, indicating anmore » enhanced amorphization resistance. The effect of temperature on the irradiation response of one of these compounds, nanocrystalline Lu 2Ti 2O 7, was further examined by performing ion irradiation at an elevated temperature range of 480–600 K. The critical amorphization temperature (T c) was found to be noticeably higher in nanocrystalline Lu 2Ti 2O 7 (610 K) than its coarse-grained counterpart (480 K), revealing that nanocrystalline Lu 2Ti 2O 7 is less resistant to amorphization compared to its coarse-grained phase under high temperatures. We interpret these results with the aid of atomistic simulations. Molecular statics calculations find that cation antisite defects are less energetically costly to form near surfaces than in the bulk, suggesting that the nanocrystalline form of these materials is generally less susceptible to amorphization than coarse-grained counterparts at low temperatures where defect kinetics are negligible. In contrast, at high temperatures, the annealing efficiency of antisite defects by cation interstitials is significantly reduced due to the sink properties of the surfaces in the nanocrystalline pyrochlore, which contributes to the observed higher amorphization temperature in the nano-grained phase than in coarse-grained counterpart. Altogether, these results provide new insight into the behavior of nanocrystalline materials under irradiation.« less

Lipid binding defects and perturbed synaptogenic activity of a Collybistin R290H mutant that causes epilepsy and intellectual disability.

PubMed

Papadopoulos, Theofilos; Schemm, Rudolf; Grubmüller, Helmut; Brose, Nils

2015-03-27

Signaling at nerve cell synapses is a key determinant of proper brain function, and synaptic defects--or synaptopathies--are at the basis of many neurological and psychiatric disorders. In key areas of the mammalian brain, such as the hippocampus or the basolateral amygdala, the clustering of the scaffolding protein Gephyrin and of γ-aminobutyric acid type A receptors at inhibitory neuronal synapses is critically dependent upon the brain-specific guanine nucleotide exchange factor Collybistin (Cb). Accordingly, it was discovered recently that an R290H missense mutation in the diffuse B-cell lymphoma homology domain of Cb, which carries the guanine nucleotide exchange factor activity, leads to epilepsy and intellectual disability in human patients. In the present study, we determined the mechanism by which the Cb(R290H) mutation perturbs inhibitory synapse formation and causes brain dysfunction. Based on a combination of biochemical, cell biological, and molecular dynamics simulation approaches, we demonstrate that the R290H mutation alters the strength of intramolecular interactions between the diffuse B-cell lymphoma homology domain and the pleckstrin homology domain of Cb. This defect reduces the phosphatidylinositol 3-phosphate binding affinity of Cb, which limits its normal synaptogenic activity. Our data indicate that impairment of the membrane lipid binding activity of Cb and a consequent defect in inhibitory synapse maturation represent a likely molecular pathomechanism of epilepsy and mental retardation in humans. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Primordial dwarfism: an update.

PubMed

Alkuraya, Fowzan S

2015-02-01

To review the recent advances in the clinical and molecular characterization of primordial dwarfism, an extreme growth deficiency disorder that has its onset during embryonic development and persists throughout life. The last decade has witnessed an unprecedented acceleration in the discovery of genes mutated in primordial dwarfism, from one gene to more than a dozen genes. These genetic discoveries have confirmed the notion that primordial dwarfism is caused by defects in basic cellular processes, most notably centriolar biology and DNA damage response. Fortunately, the increasing number of reported clinical primordial dwarfism subtypes has been accompanied by more accurate molecular classification. Qualitative defects of centrioles with resulting abnormal mitosis dynamics, reduced proliferation, and increased apoptosis represent the predominant molecular pathogenic mechanism in primordial dwarfism. Impaired DNA damage response is another important mechanism, which we now know is not mutually exclusive to abnormal centrioles. Molecular characterization of primordial dwarfism is helping families by enabling more reproductive choices and may pave the way for the future development of therapeutics.

mRNA localization: an orchestration of assembly, traffic and synthesis.

PubMed

Xing, Lei; Bassell, Gary J

2013-01-01

Asymmetrical mRNA localization and subsequent local translation provide efficient mechanisms for protein sorting in polarized cells. Defects in mRNA localization have been linked to developmental abnormalities and neurological diseases. Thus, it is critical to understand the machineries mediating and mechanisms underlying the asymmetrical distribution of mRNA and its regulation. The goal of this review is to summarize recent advances in the understanding of mRNA transport and localization, including the assembly and sorting of transport messenger ribonucleic protein (mRNP) granules, molecular mechanisms of active mRNP transport, cytoskeletal interactions and regulation of these events by extracellular signals. © 2012 John Wiley & Sons A/S.

Molecular dynamics simulations of ejecta production from sinusoidal tin surfaces under supported and unsupported shocks

NASA Astrophysics Data System (ADS)

Wu, Bao; Wu, FengChao; Zhu, YinBo; Wang, Pei; He, AnMin; Wu, HengAn

2018-04-01

Micro-ejecta, an instability growth process, occurs at metal/vacuum or metal/gas interface when compressed shock wave releases from the free surface that contains surface defects. We present molecular dynamics (MD) simulations to investigate the ejecta production from tin surface shocked by supported and unsupported waves with pressures ranging from 8.5 to 60.8 GPa. It is found that the loading waveforms have little effect on spike velocity while remarkably affect the bubble velocity. The bubble velocity of unsupported shock loading remains nonzero constant value at late time as observed in experiments. Besides, the time evolution of ejected mass in the simulations is compared with the recently developed ejecta source model, indicating the suppressed ejection of unmelted or partial melted materials. Moreover, different reference positions are chosen to characterize the amount of ejecta under different loading waveforms. Compared with supported shock case, the ejected mass of unsupported shock case saturates at lower pressure. Through the analysis on unloading path, we find that the temperature of tin sample increases quickly from tensile stress state to zero pressure state, resulting in the melting of bulk tin under decaying shock. Thus, the unsupported wave loading exhibits a lower threshold pressure causing the solid-liquid phase transition on shock release than the supported shock loading.

Genotype-phenotype relationships in human red/green color-vision defects: molecular and psychophysical studies.

PubMed Central

Deeb, S S; Lindsey, D T; Hibiya, Y; Sanocki, E; Winderickx, J; Teller, D Y; Motulsky, A G

1992-01-01

The relationship between the molecular structure of the X-linked red and green visual pigment genes and color-vision phenotype as ascertained by anomaloscopy was studied in 64 color-defective males. The great majority of red-green defects were associated with either the deletion of the green-pigment gene or the formation of 5' red-green hybrid genes or 5' green-red hybrid genes. A rapid PCR-based method allowed detection of hybrid genes, including those undetectable by Southern blot analysis, as well as more precise localization of the fusion points in hybrid genes. Protan color-vision defects appeared always associated with 5' red-green hybrid genes. Carriers of single red-green hybrid genes with fusion in introns 1-4 were protanopes. However, carriers of hybrid genes with red-green fusions in introns 2, 3, or 4 in the presence of additional normal green genes manifested as either protanopes or protanomalous trichromats, with the majority being protanomalous. Deutan defects were associated with green-pigment gene deletions, with 5' green-red hybrid genes, or, rarely, with 5' green-red-green hybrid genes. Complete green-pigment gene deletions or green-red fusions in intron 1 were usually associated with deuteranopia, although we unexpectedly found three carriers of a single red-pigment gene without any green-pigment genes to be deuteranomalous trichromats. All but one of the other deuteranomalous subjects had green-red hybrid genes with intron 1, 2, 3, or 4 fusions, as well as several normal green-pigment genes. The one exception had a grossly normal gene array, presumably with a more subtle mutation. Amino acid differences in exon 5 largely determine whether a hybrid gene will be more redlike or more greenlike in phenotype. Various discrepancies as to severity (dichromacy or trichromacy) remain unexplained but may arise because of variability of expression, postreceptoral variation, or both. When phenotypic color-vision defects exist, the kind of defect (protan or deutan) can be predicted by molecular analysis. Red-green hybrid genes are probably always associated with protan color-vision defects, while the presence of green-red hybrid genes may not always manifest phenotypically with color-vision defects. Four subjects who were found to have 5' green-red hybrid genes in addition to normal red- and green-pigment genes had normal color vision as determined by anomaloscopy. These were discovered among a group of 129 Caucasian males who had been recruited as volunteers for a vision study.(ABSTRACT TRUNCATED AT 400 WORDS) Images Figure 3 PMID:1415215

Effect of noise on defect chaos in a reaction-diffusion model.

PubMed

Wang, Hongli; Ouyang, Qi

2005-06-01

The influence of noise on defect chaos due to breakup of spiral waves through Doppler and Eckhaus instabilities is investigated numerically with a modified Fitzhugh-Nagumo model. By numerical simulations we show that the noise can drastically enhance the creation and annihilation rates of topological defects. The noise-free probability distribution function for defects in this model is found not to fit with the previously reported squared-Poisson distribution. Under the influence of noise, the distributions are flattened, and can fit with the squared-Poisson or the modified-Poisson distribution. The defect lifetime and diffusive property of defects under the influence of noise are also checked in this model.

Interleukin-4 production by Follicular Helper T cells requires the conserved Il4 enhancer HS V

PubMed Central

Vijayanand, Pandurangan; Seumois, Grégory; Simpson, Laura J.; Abdul-Wajid, Sarah; Baumjohann, Dirk; Panduro, Marisella; Huang, Xiaozhu; Interlandi, Jeneen; Djuretic, Ivana M.; Brown, Daniel R.; Sharpe, Arlene H.; Rao, Anjana; Ansel, K. Mark

2012-01-01

SUMMARY Follicular helper T cells (Tfh cells) are the major producers of interleukin-4 (IL-4) in secondary lymphoid organs where humoral immune responses develop. Il4 regulation in Tfh cells appears distinct from the classical T helper 2 (Th2) cell pathway, but the underlying molecular mechanisms remain largely unknown. We found that HS V (also known as CNS2), a 3’ enhancer in the Il4 locus, is essential for IL-4 production by Tfh cells. Mice lacking HS V display marked defects in Th2 humoral immune responses, as evidenced by abrogated IgE and sharply reduced IgG1 production in vivo. In contrast, effector Th2 cells that are involved in tissue responses were far less dependent on HS V. HS V facilitated removal of repressive chromatin marks during Th2 and Tfh cell differentiation, and increased accessibility of the Il4 promoter. Thus Tfh and Th2 cells utilize distinct but overlapping molecular mechanisms to regulate Il4, a finding with important implications for understanding the molecular basis of Th2 mediated allergic diseases. PMID:22326582

The study of mechanical behavior on the interface between calcar-defect femur and restorations by means of finite element analysis

NASA Astrophysics Data System (ADS)

Shi, X. H.; Jiang, W.; Chen, H. Z.; Zou, W.; Wang, W. D.; Guo, Z.; Luo, J. M.; Gu, Z. W.; Zhang, X. D.

2008-11-01

The mechanical behaviors of calcar-defected femur and restorations under physiological load are the key factors that will greatly influence the success of femur calcar defect repairing, especially the stress distribution on the bone-restoration interface. 3D finite elements analysis (FEA) was used to analyze the mechanical characters on the interfaces between femoral calcar defects and bone cement or HA restorations. Under the load of two times of a human weight (1436.03 N) and with the increase of the defect dimension from 6 mm to 12 mm, the maximal stresses on the surface of restorations are from 7.06 MPa to 11.89 MPa for bone cement and 2.97-9 MPa for HA separately. In this condition, HA restoration will probably be broken on the bone-restoration interface when the defect diameter is beyond 8 mm. Furthermore, under the load of 1.5 times of a human weight, HA restoration would not be safe unless the defect dimension is smaller than 10 mm, because the maximal stress (4.62 MPa) on the restoration is only a little lower than compressive strength of HA, otherwise the bone fixation device should be applied to ensure the safety. It is relatively safe for all restorations under all the tested defect sizes when the load is just the weight of a human body.

Pathogenesis, Epidemiology, Diagnosis and Clinical Aspects of Smith-Lemli-Opitz Syndrome

PubMed Central

Bianconi, Simona E.; Cross, Joanna L.; Wassif, Christopher A.; Porter, Forbes D.

2015-01-01

Introduction Smith-Lemli-Opitz Syndrome (SLOS) is a malformation syndrome inherited in an autosomal recessive fashion. It is due to a metabolic defect in the conversion of 7-dehydrocholesterol to cholesterol, which leads to an accumulation of 7-dehydrocholesterol and frequently a deficiency of cholesterol. The syndrome is characterized by typical dysmorphic facial features, multiple malformations, and intellectual disability. Areas covered In this paper we provide an overview of the clinical phenotype and discuss how the manifestations of the syndrome vary depending on the age of the patients. We then explore the underlying biochemical defect and pathophysiological alterations that may contribute to the many disease manifestations. Subsequently we explore the epidemiology and succinctly discuss population genetics as they relate to SLOS. The next section presents the diagnostic possibilities. Thereafter, the treatment and management as is standard of care are presented. Expert opinion Even though the knowledge of the underlying molecular mutations and the biochemical alterations is being rapidly accumulated, there is currently no efficacious therapy addressing neurological dysfunction. We discuss the difficulty of treating this disorder, which manifests as a combination of a malformation syndrome and an inborn error of metabolism. A very important factor in developing new therapies is the need to rigorously establish efficacy in controlled trials. PMID:25734025

Supramolecular structures of halogenated oligothiophenes on the Si(111)-√3 ×√3-Ag surface

NASA Astrophysics Data System (ADS)

Liu, R.; Fu, C.; Perepichka, D. F.; Gallagher, M. C.

2016-05-01

We have studied the adsorption of brominated tetrathienoanthracene (TBTTA) molecules onto the Si(111)-√3 × √ 3-Ag surface at room temperature. The two-dimensional √ 3 silver adlayer acts to passivate the silicon surface and provides a high-mobility template for TBTTA adsorption. Scanning tunneling microscopy (STM) images reveal that at low coverage, the molecules readily migrate to step edges and defects in the √ 3 overlayer. With increasing coverage, the molecules eventually form compact supramolecular structures. In terms of the hexagonal √ 3 lattice vectors (a√ 3 and b√ 3), the oblique unit cell of these structures can be defined by lattice vectors am = 3a√ 3 + 2b√ 3, and bm = - a√ 3 + b√ 3. The structures are quite fragile and can decompose under repeated STM imaging. This is particularly true at higher bias and suggests an electric field-induced dissociation in these instances. With increasing molecular dose, the size and stability of the structures increases. At higher coverage, the spatial extent of the supramolecular structures is often limited by defects in the underlying √ 3 layer. Our results suggest that the √ 3-Ag surface provides a relatively inert substrate for the adsorption of TBTTA molecules, and that the supramolecular structures are held together by relatively weak intermolecular forces.

The genetics of normal and defective color vision.

PubMed

Neitz, Jay; Neitz, Maureen

2011-04-13

The contributions of genetics research to the science of normal and defective color vision over the previous few decades are reviewed emphasizing the developments in the 25years since the last anniversary issue of Vision Research. Understanding of the biology underlying color vision has been vaulted forward through the application of the tools of molecular genetics. For all their complexity, the biological processes responsible for color vision are more accessible than for many other neural systems. This is partly because of the wealth of genetic variations that affect color perception, both within and across species, and because components of the color vision system lend themselves to genetic manipulation. Mutations and rearrangements in the genes encoding the long, middle, and short wavelength sensitive cone pigments are responsible for color vision deficiencies and mutations have been identified that affect the number of cone types, the absorption spectra of the pigments, the functionality and viability of the cones, and the topography of the cone mosaic. The addition of an opsin gene, as occurred in the evolution of primate color vision, and has been done in experimental animals can produce expanded color vision capacities and this has provided insight into the underlying neural circuitry. Copyright © 2010 Elsevier Ltd. All rights reserved.

NMDA Receptors Mediate Olfactory Learning and Memory in Drosophila

PubMed Central

Xia, Shouzhen; Miyashita, Tomoyuki; Fu, Tsai-Feng; Lin, Wei-Yong; Wu, Chia-Lin; Pyzocha, Lori; Lin, Inn-Ray; Saitoe, Minoru; Tully, Tim; Chiang, Ann-Shyn

2011-01-01

Summary Background Molecular and electrophysiological properties of NMDARs suggest that they may be the Hebbian “coincidence detectors” hypothesized to underlie associative learning. Because of the nonspecificity of drugs that modulate NMDAR function or the relatively chronic genetic manipulations of various NMDAR subunits from mammalian studies, conclusive evidence for such an acute role for NMDARs in adult behavioral plasticity, however, is lacking. Moreover, a role for NMDARs in memory consolidation remains controversial. Results The Drosophila genome encodes two NMDAR homologs, dNR1 and dNR2. When coexpressed in Xenopus oocytes or Drosophila S2 cells, dNR1 and dNR2 form functional NMDARs with several of the distinguishing molecular properties observed for vertebrate NMDARs, including voltage/Mg2+-dependent activation by glutamate. Both proteins are weakly expressed throughout the entire brain but show preferential expression in several neurons surrounding the dendritic region of the mushroom bodies. Hypomorphic mutations of the essential dNR1 gene disrupt olfactory learning, and this learning defect is rescued with wild-type transgenes. Importantly, we show that Pavlovian learning is disrupted in adults within 15 hr after transient induction of a dNR1 antisense RNA transgene. Extended training is sufficient to overcome this initial learning defect, but long-term memory (LTM) specifically is abolished under these training conditions. Conclusions Our study uses a combination of molecular-genetic tools to (1) generate genomic mutations of the dNR1 gene, (2) rescue the accompanying learning deficit with a dNR1+ transgene, and (3) rapidly and transiently knockdown dNR1+ expression in adults, thereby demonstrating an evolutionarily conserved role for the acute involvement of NMDARs in associative learning and memory. PMID:15823532

NMDA receptors mediate olfactory learning and memory in Drosophila.

PubMed

Xia, Shouzhen; Miyashita, Tomoyuki; Fu, Tsai-Feng; Lin, Wei-Yong; Wu, Chia-Lin; Pyzocha, Lori; Lin, Inn-Ray; Saitoe, Minoru; Tully, Tim; Chiang, Ann-Shyn

2005-04-12

Molecular and electrophysiological properties of NMDARs suggest that they may be the Hebbian "coincidence detectors" hypothesized to underlie associative learning. Because of the nonspecificity of drugs that modulate NMDAR function or the relatively chronic genetic manipulations of various NMDAR subunits from mammalian studies, conclusive evidence for such an acute role for NMDARs in adult behavioral plasticity, however, is lacking. Moreover, a role for NMDARs in memory consolidation remains controversial. The Drosophila genome encodes two NMDAR homologs, dNR1 and dNR2. When coexpressed in Xenopus oocytes or Drosophila S2 cells, dNR1 and dNR2 form functional NMDARs with several of the distinguishing molecular properties observed for vertebrate NMDARs, including voltage/Mg(2+)-dependent activation by glutamate. Both proteins are weakly expressed throughout the entire brain but show preferential expression in several neurons surrounding the dendritic region of the mushroom bodies. Hypomorphic mutations of the essential dNR1 gene disrupt olfactory learning, and this learning defect is rescued with wild-type transgenes. Importantly, we show that Pavlovian learning is disrupted in adults within 15 hr after transient induction of a dNR1 antisense RNA transgene. Extended training is sufficient to overcome this initial learning defect, but long-term memory (LTM) specifically is abolished under these training conditions. Our study uses a combination of molecular-genetic tools to (1) generate genomic mutations of the dNR1 gene, (2) rescue the accompanying learning deficit with a dNR1+ transgene, and (3) rapidly and transiently knockdown dNR1+ expression in adults, thereby demonstrating an evolutionarily conserved role for the acute involvement of NMDARs in associative learning and memory.

The 'double headed slug flap': a simple technique to reconstruct large helical rim defects.

PubMed

Masud, D; Tzafetta, K

2012-10-01

Reconstructing partial defects of the ear can be challenging, balancing the creation of the details of the ear with scarring, morbidity and number of surgical stages. Common causes of ear defects are human bites, tumour excision and burn injuries. Reconstructing defects of the ear with tube pedicled flaps and other local flaps requires an accurate measurement of size of the defect with little room for error, particularly under estimation. We present a simple method of reconstruction for partial defects of the ear using a two-stage technique with post auricular transposition flaps. This allows for under or over estimation of size defects permitting accurate tissue usage giving good aesthetic outcomes. Copyright © 2012 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

Expert consensus document: Clinical and molecular diagnosis, screening and management of Beckwith-Wiedemann syndrome: an international consensus statement.

PubMed

Brioude, Frédéric; Kalish, Jennifer M; Mussa, Alessandro; Foster, Alison C; Bliek, Jet; Ferrero, Giovanni Battista; Boonen, Susanne E; Cole, Trevor; Baker, Robert; Bertoletti, Monica; Cocchi, Guido; Coze, Carole; De Pellegrin, Maurizio; Hussain, Khalid; Ibrahim, Abdulla; Kilby, Mark D; Krajewska-Walasek, Malgorzata; Kratz, Christian P; Ladusans, Edmund J; Lapunzina, Pablo; Le Bouc, Yves; Maas, Saskia M; Macdonald, Fiona; Õunap, Katrin; Peruzzi, Licia; Rossignol, Sylvie; Russo, Silvia; Shipster, Caroleen; Skórka, Agata; Tatton-Brown, Katrina; Tenorio, Jair; Tortora, Chiara; Grønskov, Karen; Netchine, Irène; Hennekam, Raoul C; Prawitt, Dirk; Tümer, Zeynep; Eggermann, Thomas; Mackay, Deborah J G; Riccio, Andrea; Maher, Eamonn R

2018-04-01

Beckwith-Wiedemann syndrome (BWS), a human genomic imprinting disorder, is characterized by phenotypic variability that might include overgrowth, macroglossia, abdominal wall defects, neonatal hypoglycaemia, lateralized overgrowth and predisposition to embryonal tumours. Delineation of the molecular defects within the imprinted 11p15.5 region can predict familial recurrence risks and the risk (and type) of embryonal tumour. Despite recent advances in knowledge, there is marked heterogeneity in clinical diagnostic criteria and care. As detailed in this Consensus Statement, an international consensus group agreed upon 72 recommendations for the clinical and molecular diagnosis and management of BWS, including comprehensive protocols for the molecular investigation, care and treatment of patients from the prenatal period to adulthood. The consensus recommendations apply to patients with Beckwith-Wiedemann spectrum (BWSp), covering classical BWS without a molecular diagnosis and BWS-related phenotypes with an 11p15.5 molecular anomaly. Although the consensus group recommends a tumour surveillance programme targeted by molecular subgroups, surveillance might differ according to the local health-care system (for example, in the United States), and the results of targeted and universal surveillance should be evaluated prospectively. International collaboration, including a prospective audit of the results of implementing these consensus recommendations, is required to expand the evidence base for the design of optimum care pathways.

Transforming graphene nanoribbons into nanotubes by use of point defects.

PubMed

Sgouros, A; Sigalas, M M; Papagelis, K; Kalosakas, G

2014-03-26

Using molecular dynamics simulations with semi-empirical potentials, we demonstrate a method to fabricate carbon nanotubes (CNTs) from graphene nanoribbons (GNRs), by periodically inserting appropriate structural defects into the GNR crystal structure. We have found that various defect types initiate the bending of GNRs and eventually lead to the formation of CNTs. All kinds of carbon nanotubes (armchair, zigzag, chiral) can be produced with this method. The structural characteristics of the resulting CNTs, and the dependence on the different type and distribution of the defects, were examined. The smallest (largest) CNT obtained had a diameter of ∼ 5 Å (∼ 39 Å). Proper manipulation of ribbon edges controls the chirality of the CNTs formed. Finally, the effect of randomly distributed defects on the ability of GNRs to transform into CNTs is considered.

Persistence time of charge carriers in defect states of molecular semiconductors.

PubMed

McMahon, David P; Troisi, Alessandro

2011-06-07

Charge carriers in organic crystals are often trapped in point defects. The persistence time of the charge in these defect states is evaluated by computing the escape rate from this state using non-adiabatic rate theory. Two cases are considered (i) the hopping between separate identical defect states and (ii) the hopping between a defect state and the bulk (delocalized) states. We show that only the second process is likely to happen with realistic defect concentrations and highlight that the inclusion of an effective quantum mode of vibration is essential for accurate computation of the rate. The computed persistence time as a function of the trap energy indicates that trap states shallower than ∼0.3 eV cannot be effectively investigated with some slow spectroscopic techniques such as THz spectroscopy or EPR commonly used to study the nature of excess charge in semiconductors.

Ellis-van Creveld syndrome: prenatal diagnosis, molecular analysis and genetic counseling.

PubMed

Chen, Chih-Ping; Su, Yi-Ning; Hsu, Chin-Yuan; Chern, Schu-Rern; Tsai, Fuu-Jen; Wu, Pei-Chen; Chen, Po-Tsang; Wang, Wayseen

2010-12-01

To present the perinatal findings and molecular genetic analysis of two siblings with Ellis-van Creveld (EvC) syndrome. A 33-year-old woman, gravida 3, para 1, was referred for genetic counseling at 18 gestational weeks because of recurrent fetal skeletal dysplasia. Two years previously, she had delivered a 1,316-g dead male baby at 28 gestational weeks with a karyotype of 46,XY, postaxial polydactyly of the hands, thoracic narrowness, endocardial cushion defects, transposition of the great arteries, shortening of the long bones, malposition of the toes, and hypoplastic nails. During this pregnancy, prenatal ultrasound at 18 gestational weeks revealed shortening of the long bones (equivalent to 15 weeks), postaxial polydactyly of both hands, thoracic narrowness, and endocardial cushion defects. The pregnancy was subsequently terminated, and a 236-g female fetus was delivered with a karyotype of 46,XX, postaxial polydactyly of the hands, thoracic dysplasia, endocardial cushion defects, shortening of the long bones, and malposition of the toes and hypoplastic nails. The phenotype of each of the two siblings was consistent with EVC syndrome. Molecular analysis of the EVC and EVC2 genes revealed heterozygous mutations in the EVC2 gene. A heterozygous deletion mutation of a 26-bp deletion of c.871-2_894del26 encompassing the junction between intron 7 and exon 8 of the EVC2 gene was found in the mother and two siblings, and a heterozygous nonsense mutation of c.1195C >T, p.R399X in exon 10 of the EVC2 gene was found in the father and two siblings. Prenatal sonographic identification of endocardial cushion defects in association with shortening of the long bones should alert clinicians to the possibility of EvC syndrome and prompt a careful search of hexadactyly of the hands. Molecular analysis of the EVC and EVC2 genes is helpful in genetic counseling in cases with prenatally detected postaxial polydactyly, thoracic narrowness, short limbs and endocardial cushion defects. Copyright © 2010 Taiwan Association of Obstetric & Gynecology. Published by Elsevier B.V. All rights reserved.

Patterning of leaf vein networks by convergent auxin transport pathways.

PubMed

Sawchuk, Megan G; Edgar, Alexander; Scarpella, Enrico

2013-01-01

The formation of leaf vein patterns has fascinated biologists for centuries. Transport of the plant signal auxin has long been implicated in vein patterning, but molecular details have remained unclear. Varied evidence suggests a central role for the plasma-membrane (PM)-localized PIN-FORMED1 (PIN1) intercellular auxin transporter of Arabidopsis thaliana in auxin-transport-dependent vein patterning. However, in contrast to the severe vein-pattern defects induced by auxin transport inhibitors, pin1 mutant leaves have only mild vein-pattern defects. These defects have been interpreted as evidence of redundancy between PIN1 and the other four PM-localized PIN proteins in vein patterning, redundancy that underlies many developmental processes. By contrast, we show here that vein patterning in the Arabidopsis leaf is controlled by two distinct and convergent auxin-transport pathways: intercellular auxin transport mediated by PM-localized PIN1 and intracellular auxin transport mediated by the evolutionarily older, endoplasmic-reticulum-localized PIN6, PIN8, and PIN5. PIN6 and PIN8 are expressed, as PIN1 and PIN5, at sites of vein formation. pin6 synthetically enhances pin1 vein-pattern defects, and pin8 quantitatively enhances pin1pin6 vein-pattern defects. Function of PIN6 is necessary, redundantly with that of PIN8, and sufficient to control auxin response levels, PIN1 expression, and vein network formation; and the vein pattern defects induced by ectopic PIN6 expression are mimicked by ectopic PIN8 expression. Finally, vein patterning functions of PIN6 and PIN8 are antagonized by PIN5 function. Our data define a new level of control of vein patterning, one with repercussions on other patterning processes in the plant, and suggest a mechanism to select cell files specialized for vascular function that predates evolution of PM-localized PIN proteins.

Hydrogen molecule defect in proton-conductive SrTiO3 Perovskite

NASA Astrophysics Data System (ADS)

Onishi, Taku

2017-11-01

In proton-conductive SrTiO3 perovskite, no hydrogen molecule defect ideally exists. However, the unforeseen chemical reaction is often observed after the use of fuel cell. From the viewpoint of battery safety, we have investigated the effect of hydrogen molecule defect by molecular orbital analysis. When counter cation vacancy exists, the activation energy for hydrogen molecule migration was 1.39 - 1.50 eV, which is much smaller than the dissociation energy of hydrogen molecule. It implies that hydrogen molecule may migrate without its dissociation.

Successful human long-term application of in situ bone tissue engineering.

PubMed

Horch, Raymund E; Beier, Justus P; Kneser, Ulrich; Arkudas, Andreas

2014-07-01

Tissue Engineering (TE) and Regenerative Medicine (RM) have gained much popularity because of the tremendous prospects for the care of patients with tissue and organ defects. To overcome the common problem of donor-site morbidity of standard autologous bone grafts, we successfully combined tissue engineering techniques for the first time with the arteriovenous loop model to generate vascularized large bone grafts. We present two cases of large bone defects after debridement of an osteomyelitis. One of the defects was localized in the radius and one in the tibia. For osseus reconstruction, arteriovenous loops were created as vascular axis, which were placed in the bony defects. In case 1, the bone generation was achieved using cancellous bone from the iliac crest and fibrin glue and in case 2 using a clinically approved β-tricalciumphosphate/hydroxyapatite (HA), fibrin glue and directly auto-transplanted bone marrow aspirate from the iliac crest. The following post-operative courses were uneventful. The final examinations took place after 36 and 72 months after the initial operations. Computer tomogrphy (CT), membrane resonance imaging (MRI) and doppler ultrasound revealed patent arterio-venous (AV) loops in the bone grafts as well as completely healed bone defects. The patients were pain-free with normal ranges of motion. This is the first study demonstrating successfully axially vascularized in situ tissue engineered bone generation in large bone defects in a clinical scenario using the arteriovenous loop model without creation of a significant donor-site defect utilizing TE and RM techniques in human patients with long-term stability. © 2014 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

Molecular mechanisms of riboflavin responsiveness in patients with ETF-QO variations and multiple acyl-CoA dehydrogenation deficiency.

PubMed

Cornelius, Nanna; Frerman, Frank E; Corydon, Thomas J; Palmfeldt, Johan; Bross, Peter; Gregersen, Niels; Olsen, Rikke K J

2012-08-01

Riboflavin-responsive forms of multiple acyl-CoA dehydrogenation deficiency (RR-MADD) have been known for years, but with presumed defects in the formation of the flavin adenine dinucleotide (FAD) co-factor rather than genetic defects of electron transfer flavoprotein (ETF) or electron transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO). It was only recently established that a number of RR-MADD patients carry genetic defects in ETF-QO and that the well-documented clinical efficacy of riboflavin treatment may be based on a chaperone effect that can compensate for inherited folding defects of ETF-QO. In the present study, we investigate the molecular mechanisms and the genotype-phenotype relationships for the riboflavin responsiveness in MADD, using a human HEK-293 cell expression system. We studied the influence of riboflavin and temperature on the steady-state level and the activity of variant ETF-QO proteins identified in patients with RR-MADD, or non- and partially responsive MADD. Our results showed that variant ETF-QO proteins associated with non- and partially responsive MADD caused severe misfolding of ETF-QO variant proteins when cultured in media with supplemented concentrations of riboflavin. In contrast, variant ETF-QO proteins associated with RR-MADD caused milder folding defects when cultured at the same conditions. Decreased thermal stability of the variants showed that FAD does not completely correct the structural defects induced by the variation. This may cause leakage of electrons and increased reactive oxygen species, as reflected by increased amounts of cellular peroxide production in HEK-293 cells expressing the variant ETF-QO proteins. Finally, we found indications of prolonged association of variant ETF-QO protein with the Hsp60 chaperonin in the mitochondrial matrix, supporting indications of folding defects in the variant ETF-QO proteins.

Tight-binding molecular-dynamics study of point defects in GaAs

NASA Astrophysics Data System (ADS)

Seong, Hyangsuk; Lewis, Laurent J.

1995-08-01

Tight-binding molecular-dynamics simulations at 0 K have been performed in order to study the effect of defects (vacancies and antisites) in different states of charge on the electronic and structural properties of GaAs. Relaxations are fully included in the model, and for each defect we calculate the local atomic structure, the volume change upon relaxing, the formation energy (including chemical potential contributions), and the ionization levels. We find Ga vacancies to relax by an amount which is independent of the state of charge, consistent with positron lifetime measurements. Our calculations also predict Ga vacancies to exhibit a negative-U effect, and to assume a triply negative charge state for most values of the electron chemical potential. The relaxation of As vacancies, on the contrary, depends sensitively on the state of charge. The model confirms the two experimentally observed ionization levels for this defect, just below the conduction-band minimum. Likewise, Ga antisites exhibit large relaxations. In fact, in the neutral state, relaxation is so large that it leads to a ``broken-bond'' configuration, in excellent accord with the first-principles calculations of Zhang and Chadi [Phys. Rev. Lett. 64, 1789 (1990)]. This system also exhibits a negative-U effect, for values of the electron chemical potential near midgap. For As antisites, we find only a weak relaxation, independent of the charge. The model predicts the neutral state of the defect to be the ground state for values of the electron chemical potential near and above midgap, which supports the view that the EL2 defect is a neutral As antisite. Upon comparing the formation energies of the various defects we finally find that, for all values of the atomic chemical potentials, antisites are most likely to occur than vacancies.

High power ultraviolet light emitting diodes based on GaN /AlGaN quantum wells produced by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Cabalu, J. S.; Bhattacharyya, A.; Thomidis, C.; Friel, I.; Moustakas, T. D.; Collins, C. J.; Komninou, Ph.

2006-11-01

In this paper, we report on the growth by molecular beam epitaxy and fabrication of high power nitride-based ultraviolet light emitting diodes emitting in the spectral range between 340 and 350nm. The devices were grown on (0001) sapphire substrates via plasma-assisted molecular beam epitaxy. The growth of the light emitting diode (LED) structures was preceded by detailed materials studies of the bottom n-AlGaN contact layer, as well as the GaN /AlGaN multiple quantum well (MQW) active region. Specifically, kinetic conditions were identified for the growth of the thick n-AlGaN films to be both smooth and to have fewer defects at the surface. Transmission-electron microscopy studies on identical GaN /AlGaN MQWs showed good quality and well-defined interfaces between wells and barriers. Large area mesa devices (800×800μm2) were fabricated and were designed for backside light extraction. The LEDs were flip-chip bonded onto a Si submount for better heat sinking. For devices emitting at 340nm, the measured differential on-series resistance is 3Ω with electroluminescence spectrum full width at half maximum of 18nm. The output power under dc bias saturates at 0.5mW, while under pulsed operation it saturates at approximately 700mA to a value of 3mW, suggesting that thermal heating limits the efficiency of these devices. The output power of the investigated devices was found to be equivalent with those produced by the metal-organic chemical vapor deposition and hydride vapor-phase epitaxy methods. The devices emitting at 350nm were investigated under dc operation and the output power saturates at 4.5mW under 200mA drive current.

Method to repair localized amplitude defects in a EUV lithography mask blank

DOEpatents

Stearns, Daniel G.; Sweeney, Donald W.; Mirkarimi, Paul B.; Chapman, Henry N.

2005-11-22

A method and apparatus are provided for the repair of an amplitude defect in a multilayer coating. A significant number of layers underneath the amplitude defect are undamaged. The repair technique restores the local reflectivity of the coating by physically removing the defect and leaving a wide, shallow crater that exposes the underlying intact layers. The particle, pit or scratch is first removed the remaining damaged region is etched away without disturbing the intact underlying layers.

Swelling Mechanisms of UO2 Lattices with Defect Ingrowths

PubMed Central

Günay, Seçkin D.

2015-01-01

The swelling that occurs in uranium dioxide as a result of radiation-induced defect ingrowth is not fully understood. Experimental and theoretical groups have attempted to explain this phenomenon with various complex theories. In this study, experimental lattice expansion and lattice super saturation were accurately reproduced using a molecular dynamics simulation method. Based on their resemblance to experimental data, the simulation results presented here show that fission induces only oxygen Frenkel pairs while alpha particle irradiation results in both oxygen and uranium Frenkel pair defects. Moreover, in this work, defects are divided into two sub-groups, obstruction type defects and distortion type defects. It is shown that obstruction type Frenkel pairs are responsible for both fission- and alpha-particle-induced lattice swelling. Relative lattice expansion was found to vary linearly with the number of obstruction type uranium Frenkel defects. Additionally, at high concentrations, some of the obstruction type uranium Frenkel pairs formed diatomic and triatomic structures with oxygen ions in their octahedral cages, increasing the slope of the linear dependence. PMID:26244777

The effect of crystallographic misorientation and interfacial separation on jump-to-contact behavior and defect generation in aluminum

NASA Astrophysics Data System (ADS)

Khajehvand, Milad; Sepehrband, Panthea

2018-07-01

The jump-to-contact (JC) phenomenon for (111)-oriented surfaces in aluminum at room temperature is studied via molecular dynamics simulations. The effect of crystallographic misorientation and interfacial distance on the JC behavior and distribution of the resultant defects at the interface is investigated. The effect of misorientation on the critical distance for JC is found to be negligible. However, when JC occurs, different distribution of defects is observed for various misorientation angles. The density of defects is shown to be a function of interfacial distance for low misorientation angles, but independent of it for misorientation angles of ∼30 ± 10°.

Molecular pathways for defect annihilation in directed self-assembly

PubMed Central

Hur, Su-Mi; Thapar, Vikram; Ramírez-Hernández, Abelardo; Khaira, Gurdaman; Segal-Peretz, Tamar; Rincon-Delgadillo, Paulina A.; Li, Weihua; Müller, Marcus; Nealey, Paul F.; de Pablo, Juan J.

2015-01-01

Over the last few years, the directed self-assembly of block copolymers by surface patterns has transitioned from academic curiosity to viable contender for commercial fabrication of next-generation nanocircuits by lithography. Recently, it has become apparent that kinetics, and not only thermodynamics, plays a key role for the ability of a polymeric material to self-assemble into a perfect, defect-free ordered state. Perfection, in this context, implies not more than one defect, with characteristic dimensions on the order of 5 nm, over a sample area as large as 100 cm2. In this work, we identify the key pathways and the corresponding free energy barriers for eliminating defects, and we demonstrate that an extraordinarily large thermodynamic driving force is not necessarily sufficient for their removal. By adopting a concerted computational and experimental approach, we explain the molecular origins of these barriers and how they depend on material characteristics, and we propose strategies designed to overcome them. The validity of our conclusions for industrially relevant patterning processes is established by relying on instruments and assembly lines that are only available at state-of-the-art fabrication facilities, and, through this confluence of fundamental and applied research, we are able to discern the evolution of morphology at the smallest relevant length scales—a handful of nanometers—and present a view of defect annihilation in directed self-assembly at an unprecedented level of detail. PMID:26515095

Molecular pathways for defect annihilation in directed self-assembly.

DOE PAGES

Hur, Su-Mi; Thapar, Vikram; Ramirez-Hernandez, Abelardo; ...

2015-11-17

Over the last few years, the directed self-assembly of block copolymers by surface patterns has transitioned from academic curiosity to viable contender for commercial fabrication of next-generation nanocircuits by lithography. Recently, it has become apparent that kinetics, and not only thermodynamics, plays a key role for the ability of a polymeric material to self-assemble into a perfect, defect-free ordered state. Perfection, in this context, implies not more than one defect, with characteristic dimensions on the order of 5 nm, over a sample area as large as 100 cm2. In this work, we identify the key pathways and the corresponding free-energymore » barriers for eliminating defects, and we demonstrate that an extraordinarily large thermodynamic driving force is not necessarily sufficient for their removal. By adopting a concerted computational and experimental approach, we explain the molecular origins of these barriers, how they depend on material characteristics, and we propose strategies designed to over-come them. The validity of our conclusions for industrially-relevant patterning processes is established by relying on instruments and assembly lines that are only available at state-of-the-art fabrication facilities and, through this confluence of fundamental and applied research, we are able to discern the evolution of morphology at the smallest relevant length scales - a handful of nanometers -, and present a view of defect annihilation in directed self-assembly at an unprecedented level of detail.« less

Molecular dynamics modeling of PPTA crystallite mechanical properties in the presence of defects

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

Mercer, Brian; Zywicz, Edward; Papadopoulos, Panayiotis

Here, the mechanical properties of PPTA crystallites, the fundamental building blocks of aramid polymer fibers such as Kevlar® and Twaron®, are studied here using molecular dynamics simulations. The ReaxFF interatomic potential is employed to study crystallite failure via covalent and hydrogen bond rupture in constant strain-rate tensile loading simulations. Emphasis is placed on analyzing how chain-end defects in the crystallite influence its mechanical response and fracture strength. Chain-end defects are found to affect the behavior of nearby chains in a region of the PPTA crystallite that is small relative to the typical crystallite size in manufactured aramid fibers. The centralmore » Csingle bondN bond along the backbone chain is identified as the weakest in the PPTA polymer chain backbone in dynamic strain-to-failure simulations of the crystallite. It is found that clustering of chain-ends leads to reduced crystallite strength and crystallite failure via hydrogen bond rupture and chain sliding, whereas randomly scattered defects impact the strength less and failure is by covalent bond rupture and chain scission. The axial crystallite modulus increases with increasing chain length and is independent of chain-end defect locations. On the basis of these findings, a theoretical model is proposed to predict the axial modulus as a function of chain length.« less

Molecular dynamics modeling of PPTA crystallite mechanical properties in the presence of defects

DOE PAGES

Mercer, Brian; Zywicz, Edward; Papadopoulos, Panayiotis

2017-03-11

Here, the mechanical properties of PPTA crystallites, the fundamental building blocks of aramid polymer fibers such as Kevlar® and Twaron®, are studied here using molecular dynamics simulations. The ReaxFF interatomic potential is employed to study crystallite failure via covalent and hydrogen bond rupture in constant strain-rate tensile loading simulations. Emphasis is placed on analyzing how chain-end defects in the crystallite influence its mechanical response and fracture strength. Chain-end defects are found to affect the behavior of nearby chains in a region of the PPTA crystallite that is small relative to the typical crystallite size in manufactured aramid fibers. The centralmore » Csingle bondN bond along the backbone chain is identified as the weakest in the PPTA polymer chain backbone in dynamic strain-to-failure simulations of the crystallite. It is found that clustering of chain-ends leads to reduced crystallite strength and crystallite failure via hydrogen bond rupture and chain sliding, whereas randomly scattered defects impact the strength less and failure is by covalent bond rupture and chain scission. The axial crystallite modulus increases with increasing chain length and is independent of chain-end defect locations. On the basis of these findings, a theoretical model is proposed to predict the axial modulus as a function of chain length.« less

Current Nomenclature of Pseudohypoparathyroidism: Inactivating Parathyroid Hormone/Parathyroid Hormone-Related Protein Signaling Disorder

PubMed Central

Turan, Serap

2017-01-01

Disorders related to parathyroid hormone (PTH) resistance and PTH signaling pathway impairment are historically classified under the term of pseudohypoparathyroidism (PHP). The disease was first described and named by Fuller Albright and colleagues in 1942. Albright hereditary osteodystrophy (AHO) is described as an associated clinical entity with PHP, characterized by brachydactyly, subcutaneous ossifications, round face, short stature and a stocky build. The classification of PHP is further divided into PHP-Ia, pseudo-PHP (pPHP), PHP-Ib, PHP-Ic and PHP-II according to the presence or absence of AHO, together with an in vivo response to exogenous PTH and the measurement of Gsα protein activity in peripheral erythrocyte membranes in vitro. However, PHP classification fails to differentiate all patients with different clinical and molecular findings for PHP subtypes and classification become more complicated with more recent molecular characterization and new forms having been identified. So far, new classifications have been established by the EuroPHP network to cover all disorders of the PTH receptor and its signaling pathway. Inactivating PTH/PTH-related protein signaling disorder (iPPSD) is the new name proposed for a group of these disorders and which can be further divided into subtypes - iPPSD1 to iPPSD6. These are termed, starting from PTH receptor inactivation mutation (Eiken and Blomstrand dysplasia) as iPPSD1, inactivating Gsα mutations (PHP-Ia, PHP-Ic and pPHP) as iPPSD2, loss of methylation of GNAS DMRs (PHP-Ib) as iPPSD3, PRKAR1A mutations (acrodysostosis type 1) as iPPSD4, PDE4D mutations (acrodysostosis type 2) as iPPSD5 and PDE3A mutations (autosomal dominant hypertension with brachydactyly) as iPPSD6. iPPSDx is reserved for unknown molecular defects and iPPSDn+1 for new molecular defects which are yet to be described. With these new classifications, the aim is to clarify the borders of each different subtype of disease and make the classification according to molecular pathology. The iPPSD group is designed to be expandable and new classifications will readily fit into it as necessary. PMID:29280743

Current Nomenclature of Pseudohypoparathyroidism: Inactivating Parathyroid Hormone/Parathyroid Hormone-Related Protein Signaling Disorder.

PubMed

Turan, Serap

2017-12-30

Disorders related to parathyroid hormone (PTH) resistance and PTH signaling pathway impairment are historically classified under the term of pseudohypoparathyroidism (PHP). The disease was first described and named by Fuller Albright and colleagues in 1942. Albright hereditary osteodystrophy (AHO) is described as an associated clinical entity with PHP, characterized by brachydactyly, subcutaneous ossifications, round face, short stature and a stocky build. The classification of PHP is further divided into PHP-Ia, pseudo-PHP (pPHP), PHP-Ib, PHP-Ic and PHP-II according to the presence or absence of AHO, together with an in vivo response to exogenous PTH and the measurement of Gsα protein activity in peripheral erythrocyte membranes in vitro. However, PHP classification fails to differentiate all patients with different clinical and molecular findings for PHP subtypes and classification become more complicated with more recent molecular characterization and new forms having been identified. So far, new classifications have been established by the EuroPHP network to cover all disorders of the PTH receptor and its signaling pathway. Inactivating PTH/PTH-related protein signaling disorder (iPPSD) is the new name proposed for a group of these disorders and which can be further divided into subtypes - iPPSD1 to iPPSD6. These are termed, starting from PTH receptor inactivation mutation (Eiken and Blomstrand dysplasia) as iPPSD1, inactivating Gsα mutations (PHP-Ia, PHP-Ic and pPHP) as iPPSD2, loss of methylation of GNAS DMRs (PHP-Ib) as iPPSD3, PRKAR1A mutations (acrodysostosis type 1) as iPPSD4, PDE4D mutations (acrodysostosis type 2) as iPPSD5 and PDE3A mutations (autosomal dominant hypertension with brachydactyly) as iPPSD6. iPPSDx is reserved for unknown molecular defects and iPPSDn+1 for new molecular defects which are yet to be described. With these new classifications, the aim is to clarify the borders of each different subtype of disease and make the classification according to molecular pathology. The iPPSD group is designed to be expandable and new classifications will readily fit into it as necessary.

Impaired Associative Taste Learning and Abnormal Brain Activation in Kinase-Defective eEF2K Mice

ERIC Educational Resources Information Center

Gildish, Iness; Manor, David; David, Orit; Sharma, Vijendra; Williams, David; Agarwala, Usha; Wang, Xuemin; Kenney, Justin W.; Proud, Chris G.; Rosenblum, Kobi

2012-01-01

Memory consolidation is defined temporally based on pharmacological interventions such as inhibitors of mRNA translation (molecular consolidation) or post-acquisition deactivation of specific brain regions (systems level consolidation). However, the relationship between molecular and systems consolidation are poorly understood. Molecular…

MgH Rydberg series: Transition energies from electron propagator theory and oscillator strengths from the molecular quantum defect orbital method

NASA Astrophysics Data System (ADS)

Corzo, H. H.; Velasco, A. M.; Lavín, C.; Ortiz, J. V.

2018-02-01

Vertical excitation energies belonging to several Rydberg series of MgH have been inferred from 3+ electron-propagator calculations of the electron affinities of MgH+ and are in close agreement with experiment. Many electronically excited states with n > 3 are reported for the first time and new insight is given on the assignment of several Rydberg series. Valence and Rydberg excited states of MgH are distinguished respectively by high and low pole strengths corresponding to Dyson orbitals of electron attachment to the cation. By applying the Molecular Quantum Defect Orbital method, oscillator strengths for electronic transitions involving Rydberg states also have been determined.

Molecular dynamics modeling of helium bubbles in austenitic steels

NASA Astrophysics Data System (ADS)

Jelea, A.

2018-06-01

The austenitic steel devices from pressurized water reactors are continuously subjected to neutron irradiation that produces crystalline point defects and helium atoms in the steel matrix. These species evolve into large defects such as dislocation loops and helium filled bubbles. This paper analyzes, through molecular dynamics simulations with recently developed interatomic potentials, the impact of the helium/steel interface on the helium behavior in nanosize bubbles trapped in an austenitic steel matrix. It is shown that the repulsive helium-steel interactions induce higher pressures in the bubble compared to bulk helium at the same temperature and average density. A new equation of state for helium is proposed in order to take into account these interface effects.

ATP Synthase Diseases of Mitochondrial Genetic Origin

PubMed Central

Dautant, Alain; Meier, Thomas; Hahn, Alexander; Tribouillard-Tanvier, Déborah; di Rago, Jean-Paul; Kucharczyk, Roza

2018-01-01

Devastating human neuromuscular disorders have been associated to defects in the ATP synthase. This enzyme is found in the inner mitochondrial membrane and catalyzes the last step in oxidative phosphorylation, which provides aerobic eukaryotes with ATP. With the advent of structures of complete ATP synthases, and the availability of genetically approachable systems such as the yeast Saccharomyces cerevisiae, we can begin to understand these molecular machines and their associated defects at the molecular level. In this review, we describe what is known about the clinical syndromes induced by 58 different mutations found in the mitochondrial genes encoding membrane subunits 8 and a of ATP synthase, and evaluate their functional consequences with respect to recently described cryo-EM structures. PMID:29670542

Recognizing defects in carbon-fiber reinforced plastics

NASA Technical Reports Server (NTRS)

Schuetze, R.; Hillger, W.

1982-01-01

The damage tolerance of structures made of carbon-fiber-reinforced plastic is tested under various loads. Test laminate (73/1/1, 24/9/1, 1465 A) specimens of thickness 1.5-3.2 mm with various defects were subjected to static and dynamic loads. Special attention was given to delamination, and ultrasonic C-scans were made on the specimens. It was shown that cracks from even small defects are detected with great accuracy. The same probes were also X rayed; defects that could not be detected under ordinary X rays were bored and studied under vacuum by a contrast technique. The nondestructive ultrasonic and X ray tests were controlled by partially destructive tests, and good agreement was observed.

Displacement cascades and defects annealing in tungsten, Part I: Defect database from molecular dynamics simulations

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

Setyawan, Wahyu; Nandipati, Giridhar; Roche, Kenneth J.

Molecular dynamics simulations have been used to generate a comprehensive database of surviving defects due to displacement cascades in bulk tungsten. Twenty-one data points of primary knock-on atom (PKA) energies ranging from 100 eV (sub-threshold energy) to 100 keV (~780 × Ed, where Ed = 128 eV is the average displacement threshold energy) have been completed at 300 K, 1025 K and 2050 K. Within this range of PKA energies, two regimes of power-law energy-dependence of the defect production are observed. A distinct power-law exponent characterizes the number of Frenkel pairs produced within each regime. The two regimes intersect atmore » a transition energy which occurs at approximately 250 × Ed. The transition energy also marks the onset of the formation of large self-interstitial atom (SIA) clusters (size 14 or more). The observed defect clustering behavior is asymmetric, with SIA clustering increasing with temperature, while the vacancy clustering decreases. This asymmetry increases with temperature such that at 2050 K (~0.5 Tm) practically no large vacancy clusters are formed, meanwhile large SIA clusters appear in all simulations. The implication of such asymmetry on the long-term defect survival and damage accumulation is discussed. In addition, <100> {110} SIA loops are observed to form directly in the highest energy cascades, while vacancy <100> loops are observed to form at the lowest temperature and highest PKA energies, although the appearance of both the vacancy and SIA loops with Burgers vector of <100> type is relatively rare.« less

What Choline Metabolism Can Tell Us About the Underlying Mechanisms of Fetal Alcohol Spectrum Disorders

PubMed Central

2013-01-01

The consequences of fetal exposure to alcohol are very diverse and the likely molecular mechanisms involved must be able to explain how so many developmental processes could go awry. If pregnant rat dams are fed alcohol, their pups develop abnormalities characteristic of fetal alcohol spectrum disorders (FASD), but if these rat dams were also treated with choline, the effects from ethanol were attenuated in their pups. Choline is an essential nutrient in humans, and is an important methyl group donor. Alcohol exposure disturbs the metabolism of choline and other methyl donors. Availability of choline during gestation directly influences epigenetic marks on DNA and histones, and alters gene expression needed for normal neural and endothelial progenitor cell proliferation. Maternal diets low in choline alter development of the mouse hippocampus, and decrement memory for life. Women eating low-choline diets have an increased risk of having an infant with a neural tube or or ofacial cleft birth defect. Thus, the varied effects of choline could affect the expression of FASD, and studies on choline might shed some light on the underlying molecular mechanisms responsible for FASD. PMID:21259123

Molecular mechanism of a COOH-terminal gating determinant in the ROMK channel revealed by a Bartter's disease mutation

PubMed Central

Flagg, Thomas P; Yoo, Dana; Sciortino, Christopher M; Tate, Margaret; Romero, Michael F; Welling, Paul A

2002-01-01

The ROMK subtypes of inward-rectifier K+ channels mediate potassium secretion and regulate NaCl reabsorption in the kidney. Loss-of-function mutations in this pH-sensitive K+ channel cause Bartter's disease, a familial salt wasting nephropathy. One disease-causing mutation truncates the extreme COOH-terminus and induces a closed gating conformation. Here we identify a region within the deleted domain that plays an important role in pH-dependent gating. The domain contains a structural element that functionally interacts with the pH sensor in the cytoplasmic NH2-terminus to set a physiological range of pH sensitivity. Removal of the domain shifts the pKa towards alkaline pH values, causing channel inactivation under physiological conditions. Suppressor mutations within the pH sensor rescued channel gating and trans addition of the cognate peptide restored pH sensitivity. A specific interdomain interaction was revealed in an in vitro protein-protein binding assay between the NH2- and COOH-terminal cytoplasmic domains expressed as bacterial fusion proteins. These results provide new insights into the molecular mechanisms underlying Kir channel regulation and channel gating defects that are associated with Bartter's disease. PMID:12381810

Atomistic investigation on the detachment of oil molecules from defective alumina surface

NASA Astrophysics Data System (ADS)

Xie, W. K.; Sun, Y. Z.; Liu, H. T.

2017-12-01

The mechanism of oil detachment from defective alumina surface in aqueous solution was investigated via atomistic molecular dynamics (MD) simulations. Special attention was focused on the effect of surface defect on the oil detachment. Our simulation results suggest that compared with perfect Al2O3 surface, defective substrate surface provides much more sites for the adsorption of oil molecules, thus it has higher oil adsorption energy. However, higher oil-solid adsorption energy does not mean that oil contaminants are much more difficult to be detached. It is found that surface defect could induce the spontaneous imbibition of water molecules, effectively promoting the detachment of oil molecules. Thus, compared with perfect alumina surface, the detachment of oil molecules from defective alumina surface tends to be much easier. Moreover, surface defect could lead to the oil residues inside surface defect. In water solution, the entire detachment process of oil molecules on defective surface consists of following stages, including the early detachment of oil molecules inside surface defect induced by capillary-driven spontaneous imbibition of water molecules, the following conformational change of oil molecules on topmost surface and the final migration of detached oil molecules from solid surface. These findings may help to sufficiently enrich the removal mechanism of oil molecules adhered onto defective solid surface.

Multiscale simulations of defect dipole-enhanced electromechanical coupling at dilute defect concentrations

NASA Astrophysics Data System (ADS)

Liu, Shi; Cohen, R. E.

2017-08-01

The role of defects in solids of mixed ionic-covalent bonds such as ferroelectric oxides is complex. Current understanding of defects on ferroelectric properties at the single-defect level remains mostly at the empirical level, and the detailed atomistic mechanisms for many defect-mediated polarization-switching processes have not been convincingly revealed quantum mechanically. We simulate the polarization-electric field (P-E) and strain-electric field (ɛ-E) hysteresis loops for BaTiO3 in the presence of generic defect dipoles with large-scale molecular dynamics and provide a detailed atomistic picture of the defect dipole-enhanced electromechanical coupling. We develop a general first-principles-based atomistic model, enabling a quantitative understanding of the relationship between macroscopic ferroelectric properties and dipolar impurities of different orientations, concentrations, and dipole moments. We find that the collective orientation of dipolar defects relative to the external field is the key microscopic structure feature that strongly affects materials hardening/softening and electromechanical coupling. We show that a small concentration (≈0.1 at. %) of defect dipoles dramatically improves electromechanical responses. This offers the opportunity to improve the performance of inexpensive polycrystalline ferroelectric ceramics through defect dipole engineering for a range of applications including piezoelectric sensors, actuators, and transducers.

Photographic guide to selected external defect indicators and associated internal defects in black cherry

Treesearch

Everette D. Rast; John A. Beaton; John A. Beaton

1985-01-01

To properly classify or grade logs or trees, one must be able to correctly identify defect indicators and assess the effect of the underlying defect on possible end products. This guide aids the individual in identifying the surface defect indicator and also shows the progressive stages of the defect throughout its development for black cherry. It illustrates and...

Photographic guide of selected external defect indicators and associated internal defects in yellow birch

Treesearch

Everette D. Rast; John A. Beaton; David L. Sonderman

1991-01-01

To properly classify or grade logs or trees, one must be able to correctly identify defect indicators and assess the effect of the underlying defect on possible end products. This guide assists the individual in identifying the surface defect indicator and shows the progressive stages of the defect throughout its development for yellow birch. Eleven types of external...

Photographic guide of selected external defect indicators and associated internal defects in sugar maple

Treesearch

Everette D. Rast; John A. Beaton; David L. Sonderman

1991-01-01

To properly classify or grade logs or trees, one must be able to correctly identify defect indicators and assess the effect of the underlying defect on possible end products. This guide assists the individual in identifying the surface defect indicator and shows the progressive stages of the defect throughout its development for sugar maple. Eleven types of external...

Photographic guide to selected external defect indicators and associated internal defects in black walnut

Treesearch

Everette D.Beaton John A. Rast; David L. Sonderman; David L. Sonderman

1988-01-01

To properly classify qr grade logs or trees, one must be able to correctly identify defect indicators and assess the effect of the underlying defect on possible end products. This guide aids the individual in identifying the surface defect indicator and also shows the progressive stages of the defect throughout its develqpment for black walnut. It illustrates and...

Photographic guide of selected external defect indicators and associated internal defects in white oak

Treesearch

Everette D. Rast; John A. Beaton; David L. Sonderman; David L. Sonderman

1989-01-01

To properly classify or grade logs or trees, one must be able to correctly identify defect indicators and assess the effect of the underlying defect on possible end products. This guide assists the individual in identifying the surface defect indicator and also shows the progressive stages of the defect throughout its development for white oak. It illustrates and...

Photographic guide of selected external defect indicators and associated internal defects in yellow-poplar

Treesearch

Everette D. Rast; John A. Beaton; David L. Sonderman

1991-01-01

To properly classify or grade logs or trees, one must be able to correctly identify defect indicators and assess the effect of the underlying defect on possible end products. This guide assists the individual in identifying the surface defect indicator and shows the progressive stages of the defect throughout its development for yellow-poplar. Twelve types of external...

Photographic guide of selected external defect indicators and associated internal defects in northern red oak

Treesearch

Everette D. Rast

1982-01-01

To properly classify or grade logs or trees, one must be able to correctly identify defect indicators and assess the effect of the underlying defect on possible end products. This guide aids the individual in identifying the surface defect indicator and also shows the progressive stages of the defect throughout its development. It illustrates and describes eight types...

Laron syndrome (primary growth hormone resistance or insensitivity): the personal experience 1958-2003.

PubMed

Laron, Zvi

2004-03-01

Clinical and laboratory investigations starting in 1958 of a group of dwarfed children resembling isolated GH deficiency but who had very high serum levels of GH led to the description of the syndrome of primary GH resistance or insensitivity (Laron syndrome) and subsequently to the discovery of its molecular defects residing in the GH receptor and leading to an inability of IGF-I generation. With the biosynthesis of IGF-I in 1986, therapeutic trials started. Continuously more and more patients are being diagnosed in many parts of the world with a variety of molecular defects. This syndrome proved to be a unique model that enables the study of the consequences of GH receptor defects, the physiopathology of GH-IGF-I disruption, and comparison of the GH-independent IGF-I effects. This review presents the personal experience gained from the study follow-up and treatment of the 60 patients followed up for many years in the Israeli cohort.

Morphology-induced defects enhance lipid transfer rates

DOE PAGES

Xia, Yan; Charubin, Kamil; Marquardt, Drew; ...

2016-08-25

Molecular transfer between nanoparticles has been considered to have important implications regarding nanoparticle stability. Recently, the interparticle spontaneous lipid transfer rate constant for discoidal bicelles was found to be very different from spherical, unilamellar vesicles (ULVs). Here, we investigate the mechanism responsible for this discrepancy. Analysis of the data indicates that lipid transfer is entropically favorable, but enthalpically unfavorable with an activation energy that is independent of bicelle size and long- to short-chain lipid molar ratio. Moreover, molecular dynamics simulations reveal a lower lipid dissociation energy cost in the vicinity of interfaces (“defects”) induced by the segregation of the long-more » and short-chain lipids in bicelles; these defects are not present in ULVs. Taken together, these results suggest that the enhanced lipid transfer observed in bicelles arises from interfacial defects as a result of the hydrophobic mismatch between the long- and short-chain lipid species. In conclusion, the observed lipid transfer rate is found to be independent of nanoparticle stability.« less

Effect of point defects on the thermal conductivity of UO2: molecular dynamics simulations

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

Liu, Xiang-Yang; Stanek, Christopher Richard; Andersson, Anders David Ragnar

2015-07-21

The thermal conductivity of uranium dioxide (UO 2) fuel is an important materials property that affects fuel performance since it is a key parameter determining the temperature distribution in the fuel, thus governing, e.g., dimensional changes due to thermal expansion, fission gas release rates, etc. [1] The thermal conductivity of UO 2 nuclear fuel is also affected by fission gas, fission products, defects, and microstructural features such as grain boundaries. Here, molecular dynamics (MD) simulations are carried out to determine quantitatively, the effect of irradiation induced point defects on the thermal conductivity of UO 2, as a function of defectmore » concentrations, for a range of temperatures, 300 – 1500 K. The results will be used to develop enhanced continuum thermal conductivity models for MARMOT and BISON by INL. These models express the thermal conductivity as a function of microstructure state-variables, thus enabling thermal conductivity models with closer connection to the physical state of the fuel [2].« less

Molecular dynamics analysis of diffusion of uranium and oxygen ions in uranium dioxide

NASA Astrophysics Data System (ADS)

Arima, T.; Yoshida, K.; Idemitsu, K.; Inagaki, Y.; Sato, I.

2010-03-01

Diffusion behaviours of oxygen and uranium were evaluated for bulk and grain-boundaries of uranium dioxide using the molecular dynamics (MD) simulation. It elucidated that oxygen behaved like liquid in superionic state at high temperatures and migrated on sub-lattice sites accompanying formation of lattice defects such as Frenkel defects at middle temperatures. Formation energies of Frenkel and Shottky defects were compared to literature data, and migration energies of oxygen and uranium were estimated by introducing vacancies into the supercell. For grain-boundaries (GB) modelled by the coincidence-site lattice theory, MD calculations showed that GB energy and diffusivities of oxygen and uranium increased with the misorientation angle. By analysing GB structures such as pair-correlation functions, it also showed that the disordered phase was observed for uranium as well as oxygen in GBs especially for a large misorientation angle such as S5 GB. Hence, GB diffusion was much larger than bulk diffusion for oxygen and uranium.

SHP-2 acts via ROCK to regulate the cardiac actin cytoskeleton

PubMed Central

Langdon, Yvette; Tandon, Panna; Paden, Erika; Duddy, Jennifer; Taylor, Joan M.; Conlon, Frank L.

2012-01-01

Noonan syndrome is one of the most common causes of human congenital heart disease and is frequently associated with missense mutations in the protein phosphatase SHP-2. Interestingly, patients with acute myelogenous leukemia (AML), acute lymphoblastic leukemia (ALL), juvenile myelomonocytic leukemia (JMML) and LEOPARD syndrome frequently carry a second, somatically introduced subset of missense mutations in SHP-2. To determine the cellular and molecular mechanisms by which SHP-2 regulates heart development and, thus, understand how Noonan-associated mutations affect cardiogenesis, we introduced SHP-2 encoding the most prevalent Noonan syndrome and JMML mutations into Xenopus embryos. Resulting embryos show a direct relationship between a Noonan SHP-2 mutation and its ability to cause cardiac defects in Xenopus; embryos expressing Noonan SHP-2 mutations exhibit morphologically abnormal hearts, whereas those expressing an SHP-2 JMML-associated mutation do not. Our studies indicate that the cardiac defects associated with the introduction of the Noonan-associated SHP-2 mutations are coupled with a delay or arrest of the cardiac cell cycle in M-phase and a failure of cardiomyocyte progenitors to incorporate into the developing heart. We show that these defects are a result of an underlying malformation in the formation and polarity of cardiac actin fibers and F-actin deposition. We show that these defects can be rescued in culture and in embryos through the inhibition of the Rho-associated, coiled-coil-containing protein kinase 1 (ROCK), thus demonstrating a direct relationship between SHP-2N308D and ROCK activation in the developing heart. PMID:22278918

Early transcriptional responses of internalization defective Brucella abortus mutants in professional phagocytes, RAW 264.7.

PubMed

Cha, Seung Bin; Lee, Won Jung; Shin, Min Kyoung; Jung, Myung Hwan; Shin, Seung Won; Yoo, An Na; Kim, Jong Wan; Yoo, Han Sang

2013-06-27

Brucella abortus is an intracellular zoonotic pathogen which causes undulant fever, endocarditis, arthritis and osteomyelitis in human and abortion and infertility in cattle. This bacterium is able to invade and replicate in host macrophage instead of getting removed by this defense mechanism. Therefore, understanding the interaction between virulence of the bacteria and the host cell is important to control brucellosis. Previously, we generated internalization defective mutants and analyzed the envelope proteins. The present study was undertaken to evaluate the changes in early transcriptional responses between wild type and internalization defective mutants infected mouse macrophage, RAW 264.7. Both of the wild type and mutant infected macrophages showed increased expression levels in proinflammatory cytokines, chemokines, apoptosis and G-protein coupled receptors (Gpr84, Gpr109a and Adora2b) while the genes related with small GTPase which mediate intracellular trafficking was decreased. Moreover, cytohesin 1 interacting protein (Cytip) and genes related to ubiquitination (Arrdc3 and Fbxo21) were down-regulated, suggesting the survival strategy of this bacterium. However, we could not detect any significant changes in the mutant infected groups compared to the wild type infected group. In summary, it was very difficult to clarify the alterations in host cellular transcription in response to infection with internalization defective mutants. However, we found several novel gene changes related to the GPCR system, ubiquitin-proteosome system, and growth arrest and DNA damages in response to B. abortus infection. These findings may contribute to a better understanding of the molecular mechanisms underlying host-pathogen interactions and need to be studied further.

Early transcriptional responses of internalization defective Brucella abortus mutants in professional phagocytes, RAW 264.7

PubMed Central

2013-01-01

Background Brucella abortus is an intracellular zoonotic pathogen which causes undulant fever, endocarditis, arthritis and osteomyelitis in human and abortion and infertility in cattle. This bacterium is able to invade and replicate in host macrophage instead of getting removed by this defense mechanism. Therefore, understanding the interaction between virulence of the bacteria and the host cell is important to control brucellosis. Previously, we generated internalization defective mutants and analyzed the envelope proteins. The present study was undertaken to evaluate the changes in early transcriptional responses between wild type and internalization defective mutants infected mouse macrophage, RAW 264.7. Results Both of the wild type and mutant infected macrophages showed increased expression levels in proinflammatory cytokines, chemokines, apoptosis and G-protein coupled receptors (Gpr84, Gpr109a and Adora2b) while the genes related with small GTPase which mediate intracellular trafficking was decreased. Moreover, cytohesin 1 interacting protein (Cytip) and genes related to ubiquitination (Arrdc3 and Fbxo21) were down-regulated, suggesting the survival strategy of this bacterium. However, we could not detect any significant changes in the mutant infected groups compared to the wild type infected group. Conclusions In summary, it was very difficult to clarify the alterations in host cellular transcription in response to infection with internalization defective mutants. However, we found several novel gene changes related to the GPCR system, ubiquitin-proteosome system, and growth arrest and DNA damages in response to B. abortus infection. These findings may contribute to a better understanding of the molecular mechanisms underlying host-pathogen interactions and need to be studied further. PMID:23802650

SHP-2 acts via ROCK to regulate the cardiac actin cytoskeleton.

PubMed

Langdon, Yvette; Tandon, Panna; Paden, Erika; Duddy, Jennifer; Taylor, Joan M; Conlon, Frank L

2012-03-01

Noonan syndrome is one of the most common causes of human congenital heart disease and is frequently associated with missense mutations in the protein phosphatase SHP-2. Interestingly, patients with acute myelogenous leukemia (AML), acute lymphoblastic leukemia (ALL), juvenile myelomonocytic leukemia (JMML) and LEOPARD syndrome frequently carry a second, somatically introduced subset of missense mutations in SHP-2. To determine the cellular and molecular mechanisms by which SHP-2 regulates heart development and, thus, understand how Noonan-associated mutations affect cardiogenesis, we introduced SHP-2 encoding the most prevalent Noonan syndrome and JMML mutations into Xenopus embryos. Resulting embryos show a direct relationship between a Noonan SHP-2 mutation and its ability to cause cardiac defects in Xenopus; embryos expressing Noonan SHP-2 mutations exhibit morphologically abnormal hearts, whereas those expressing an SHP-2 JMML-associated mutation do not. Our studies indicate that the cardiac defects associated with the introduction of the Noonan-associated SHP-2 mutations are coupled with a delay or arrest of the cardiac cell cycle in M-phase and a failure of cardiomyocyte progenitors to incorporate into the developing heart. We show that these defects are a result of an underlying malformation in the formation and polarity of cardiac actin fibers and F-actin deposition. We show that these defects can be rescued in culture and in embryos through the inhibition of the Rho-associated, coiled-coil-containing protein kinase 1 (ROCK), thus demonstrating a direct relationship between SHP-2(N308D) and ROCK activation in the developing heart.

19q13.12 microdeletion syndrome fibroblasts display abnormal storage of cholesterol and sphingolipids in the endo-lysosomal system.

PubMed

Zhao, Kexin; van der Spoel, Aarnoud; Castiglioni, Claudia; Gale, Sarah; Fujiwara, Hideji; Ory, Daniel S; Ridgway, Neale D

2018-06-01

Microdeletions in 19q12q13.12 cause a rare and complex haploinsufficiency syndrome characterized by intellectual deficiency, developmental delays, and neurological movement disorders. Variability in the size and interval of the deletions makes it difficult to attribute the complex clinical phenotype of this syndrome to an underlying gene(s). As an alternate approach, we examined the biochemical and metabolic features of fibroblasts from an affected individual to derive clues as to the molecular basis for the syndrome. Immunofluorescence and electron microscopy of affected fibroblasts revealed an abnormal endo-lysosomal compartment that was characterized by rapid accumulation of lysosomotropic dyes, elevated LAMP1 and LAMP2 expression and vacuoles containing membrane whorls, common features of lysosomal lipid storage disorders. The late endosomes-lysosomes (LE/LY) of affected fibroblasts accumulated low-density lipoprotein cholesterol, and displayed reduced cholesterol esterification and increased de novo cholesterol synthesis, indicative of defective cholesterol transport to the endoplasmic reticulum. Affected fibroblasts also had increased ceramide and sphingolipid mass, altered glycosphingolipid species and accumulation of a fluorescent lactosylceramide probe in LE/LY. Autophagosomes also accumulated in affected fibroblasts because of decreased fusion with autolysosomes, a defect associated with other lysosomal storage diseases. Attempts to correct the cholesterol/sphingolipid storage defect in fibroblasts with cyclodextrin, sphingolipid synthesis inhibitors or by altering ion transport were unsuccessful. Our data show that 19q13.12 deletion fibroblasts have abnormal accumulation of cholesterol and sphingolipids in the endo-lysosomal system that compromises organelle function and could be an underlying cause of the clinical features of the syndrome. Copyright © 2018 Elsevier B.V. All rights reserved.

Reduction in interface defect density in p-BaSi2/n-Si heterojunction solar cells by a modified pretreatment of the Si substrate

NASA Astrophysics Data System (ADS)

Yamashita, Yudai; Yachi, Suguru; Takabe, Ryota; Sato, Takuma; Emha Bayu, Miftahullatif; Toko, Kaoru; Suemasu, Takashi

2018-02-01

We have investigated defects that occurred at the interface of p-BaSi2/n-Si heterojunction solar cells that were fabricated by molecular beam epitaxy. X-ray diffraction measurements indicated that BaSi2 (a-axis-oriented) was subjected to in-plane compressive strain, which relaxed when the thickness of the p-BaSi2 layer exceeded 50 nm. Additionally, transmission electron microscopy revealed defects in the Si layer near steps that were present on the Si(111) substrate. Deep level transient spectroscopy revealed two different electron traps in the n-Si layer that were located at 0.33 eV (E1) and 0.19 eV (E2) below the conduction band edge. The densities of E1 and E2 levels in the region close to the heterointerface were approximately 1014 cm-3. The density of these electron traps decreased below the limits of detection following Si pretreatment to remove the oxide layers from the n-Si substrate, which involved heating the substrate to 800 °C for 30 min under ultrahigh vacuum while depositing a layer of Si (1 nm). The remaining traps in the n-Si layer were hole traps located at 0.65 eV (H1) and 0.38 eV (H2) above the valence band edge. Their densities were as low as 1010 cm-3. Following pretreatment, the current versus voltage characteristics of the p-BaSi2/n-Si solar cells under AM1.5 illumination were reproducible with conversion efficiencies beyond 5% when using a p-BaSi2 layer thickness of 100 nm. The origin of the H2 level is discussed.

Characterization of point defects in monolayer arsenene

NASA Astrophysics Data System (ADS)

Liang, Xiongyi; Ng, Siu-Pang; Ding, Ning; Wu, Chi-Man Lawrence

2018-06-01

Topological defects that are inevitably found in 2D materials can dramatically affect their properties. Using density functional theory (DFT) calculations and ab initio molecular dynamics (AIMD) method, the structural, thermodynamic, electronic and magnetic properties of six types of typical point defects in arsenene, i.e. the Stone-Wales defect, single and double vacancies and adatoms, were systemically studied. It was found that these defects were all more easily generated in arsenene with lower formation energies than those with graphene and silicene. Stone-Wales defects can be transformed from pristine arsenene by overcoming a barrier of 2.19 eV and single vacancy defects tend to coalesce into double vacancy defects by diffusion. However, a type of adatom defect does not exhibit kinetic stability at room temperature. In addition, SV defects and another type of adatom defect can remarkably affect the electronic and magnetic properties of arsenene, e.g. they can introduce localized states near the Fermi level, as well as a strongly local magnetic moment due to dangling bond and unpaired electron. Furthermore, the simulated scanning tunneling microscopy (STM) and Raman spectroscopy were computed and the types of point defects can be fully characterized by correlating the STM images and Raman spectra to the defective atomistic structures. The results provide significant insights to the effect of defects in arsenene for potential applications, as well as identifications of two helpful tools (STM and Raman spectroscopy) to distinguish the type of defects in arsenene for future experiments.

Biochemical and genetic analysis of Leigh syndrome patients in Korea.

PubMed

Chae, Jong-Hee; Lee, Jin Sook; Kim, Ki Joong; Hwang, Yong Seung; Hirano, Michio

2008-06-01

Sixteen Korean patients with Leigh syndrome were identified at the Seoul National University Children's Hospital in 2001-2006. Biochemical or molecular defects were identified in 14 patients (87.5%). Thirteen patients had respiratory chain enzyme defects; 9 had complex I deficiency, and 4 had combined defects of complex I+III+IV. Based on the biochemical defects, targeted genetic studies in 4 patients with complex I deficiency revealed two heteroplasmic mitochondrial DNA mutations in ND genes. One patient had the mitochondrial DNA T8993G point mutation. No mitochondrial DNA defects were identified in 11 (68.7%) of our LS patients, who probably have mutations in nuclear DNA. Although a limited study based in a single tertiary medical center, our findings suggest that isolated complex I deficiency may be the most common cause of Leigh syndrome in Korea.

Reactive wetting properties of TiO2 nanoparticles predicted by ab initio molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Brandt, Erik G.; Agosta, Lorenzo; Lyubartsev, Alexander P.

2016-07-01

Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity.Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity. Electronic supplementary information (ESI) available: Simulation data on equilibration of energies and structures (root-mean-square-deviations and coordination numbers); radial distribution functions for all O-Ti pairs over the entire data domain; comparison of coordination number distributions for dry and wet nanoparticles; dynamics of water reactivity; high-resolution electron density for the rutile NP. A movie of the simulation trajectory for the rutile (TiO2)24.30H2O system. See DOI: 10.1039/C6NR02791A

OCT imaging of craniofacial anatomy in xenopus embryos (Conference Presentation)

NASA Astrophysics Data System (ADS)

Deniz, Engin; Jonas, Stephan M.; Griffin, John; Hooper, Michael C.; Choma, Michael A.; Khokha, Mustafa K.

2016-03-01

The etiology of craniofacial defects is incompletely understood. The ability to obtain large amounts of gene sequence data from families affected by craniofacial defects is opening up new ways to understand molecular genetic etiological factors. One important link between gene sequence data and clinical relevance is biological research into candidate genes and molecular pathways. We present our recent research using OCT as a nondestructive phenotyping modality of craniofacial morphology in Xenopus embryos, an important animal model for biological research in gene and pathway discovery. We define 2D and 3D scanning protocols for a standardized approach to craniofacial imaging in Xenopus embryos. We define standard views and planar reconstructions for visualizing normal anatomy and landmarks. We compare these views and reconstructions to traditional histopathology using alcian blue staining. In addition to being 3D, nondestructive, and having much faster throughout, OCT can identify craniofacial features that are lost during traditional histopathological preparation. We also identify quantitative morphometric parameters to define normative craniofacial anatomy. We also note that craniofacial and cardiac defects are not infrequently present in the same patient (e.g velocardiofacial syndrome). Given that OCT excels at certain aspects of cardiac imaging in Xenopus embryos, our work highlights the potential of using OCT and Xenopus to study molecular genetic factors that impact both cardiac and craniofacial development.

High Electrical Conductivity of Single Metal-Organic Chains.

PubMed

Ares, Pablo; Amo-Ochoa, Pilar; Soler, José M; Palacios, Juan José; Gómez-Herrero, Julio; Zamora, Félix

2018-05-01

Molecular wires are essential components for future nanoscale electronics. However, the preparation of individual long conductive molecules is still a challenge. MMX metal-organic polymers are quasi-1D sequences of single halide atoms (X) bridging subunits with two metal ions (MM) connected by organic ligands. They are excellent electrical conductors as bulk macroscopic crystals and as nanoribbons. However, according to theoretical calculations, the electrical conductance found in the experiments should be even higher. Here, a novel and simple drop-casting procedure to isolate bundles of few to single MMX chains is demonstrated. Furthermore, an exponential dependence of the electrical resistance of one or two MMX chains as a function of their length that does not agree with predictions based on their theoretical band structure is reported. This dependence is attributed to strong Anderson localization originated by structural defects. Theoretical modeling confirms that the current is limited by structural defects, mainly vacancies of iodine atoms, through which the current is constrained to flow. Nevertheless, measurable electrical transport along distances beyond 250 nm surpasses that of all other molecular wires reported so far. This work places in perspective the role of defects in 1D wires and their importance for molecular electronics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Computational modelling of ovine critical-sized tibial defects with implanted scaffolds and prediction of the safety of fixator removal.

PubMed

Doyle, Heather; Lohfeld, Stefan; Dürselen, Lutz; McHugh, Peter

2015-04-01

Computational model geometries of tibial defects with two types of implanted tissue engineering scaffolds, β-tricalcium phosphate (β-TCP) and poly-ε-caprolactone (PCL)/β-TCP, are constructed from µ-CT scan images of the real in vivo defects. Simulations of each defect under four-point bending and under simulated in vivo axial compressive loading are performed. The mechanical stability of each defect is analysed using stress distribution analysis. The results of this analysis highlights the influence of callus volume, and both scaffold volume and stiffness, on the load-bearing abilities of these defects. Clinically-used image-based methods to predict the safety of removing external fixation are evaluated for each defect. Comparison of these measures with the results of computational analyses indicates that care must be taken in the interpretation of these measures. Copyright © 2015 Elsevier Ltd. All rights reserved.

(Epi)genotype–phenotype correlations in Beckwith–Wiedemann syndrome

PubMed Central

Mussa, Alessandro; Russo, Silvia; De Crescenzo, Agostina; Freschi, Andrea; Calzari, Luciano; Maitz, Silvia; Macchiaiolo, Marina; Molinatto, Cristina; Baldassarre, Giuseppina; Mariani, Milena; Tarani, Luigi; Bedeschi, Maria Francesca; Milani, Donatella; Melis, Daniela; Bartuli, Andrea; Cubellis, Maria Vittoria; Selicorni, Angelo; Cirillo Silengo, Margherita; Larizza, Lidia; Riccio, Andrea; Ferrero, Giovanni Battista

2016-01-01

Beckwith–Wiedemann syndrome (BWS) is characterized by cancer predisposition, overgrowth and highly variable association of macroglossia, abdominal wall defects, nephrourological anomalies, nevus flammeus, ear malformations, hypoglycemia, hemihyperplasia, and organomegaly. BWS molecular defects, causing alteration of expression or activity of the genes regulated by two imprinting centres (IC) in the 11p15 chromosomal region, are also heterogeneous. In this paper we define (epi)genotype–phenotype correlations in molecularly confirmed BWS patients. The characteristics of 318 BWS patients with proven molecular defect were compared among the main four molecular subclasses: IC2 loss of methylation (IC2-LoM, n=190), IC1 gain of methylation (IC1-GoM, n=31), chromosome 11p15 paternal uniparental disomy (UPD, n=87), and cyclin-dependent kinase inhibitor 1C gene (CDKN1C) variants (n=10). A characteristic growth pattern was found in each group; neonatal macrosomia was almost constant in IC1-GoM, postnatal overgrowth in IC2-LoM, and hemihyperplasia more common in UPD (P<0.001). Exomphalos was more common in IC2/CDKN1C patients (P<0.001). Renal defects were typical of UPD/IC1 patients, uretheral malformations of IC1-GoM cases (P<0.001). Ear anomalies and nevus flammeus were associated with IC2/CDKN1C genotype (P<0.001). Macroglossia was less common among UPD patients (P<0.001). Wilms' tumor was associated with IC1-GoM or UPD and never observed in IC2-LoM patients (P<0.001). Hepatoblastoma occurred only in UPD cases. Cancer risk was lower in IC2/CDKN1C, intermediate in UPD, and very high in IC1 cases (P=0.009). In conclusion, (epi)genotype–phenotype correlations define four different phenotypic BWS profiles with some degree of clinical overlap. These observations impact clinical care allowing to move toward (epi) genotype-based follow-up and cancer screening. PMID:25898929

Fanconi Anemia: A DNA repair disorder characterized by accelerated decline of the hematopoietic stem cell compartment and other features of aging.

PubMed

Brosh, Robert M; Bellani, Marina; Liu, Yie; Seidman, Michael M

2017-01-01

Fanconi Anemia (FA) is a rare autosomal genetic disorder characterized by progressive bone marrow failure (BMF), endocrine dysfunction, cancer, and other clinical features commonly associated with normal aging. The anemia stems directly from an accelerated decline of the hematopoietic stem cell compartment. Although FA is a complex heterogeneous disease linked to mutations in 19 currently identified genes, there has been much progress in understanding the molecular pathology involved. FA is broadly considered a DNA repair disorder and the FA gene products, together with other DNA repair factors, have been implicated in interstrand cross-link (ICL) repair. However, in addition to the defective DNA damage response, altered epigenetic regulation, and telomere defects, FA is also marked by elevated levels of inflammatory mediators in circulation, a hallmark of faster decline in not only other hereditary aging disorders but also normal aging. In this review, we offer a perspective of FA as a monogenic accelerated aging disorder, citing the latest evidence for its multi-factorial deficiencies underlying its unique clinical and cellular features. Published by Elsevier B.V.

Deregulation of calcium fluxes in HTLV-I infected CD4-positive T-cells plays a major role in malignant transformation.

PubMed

Akl, Haidar; Badran, Bassam; El Zein, Nabil; Dobirta, Gratiela; Burny, Arsene; Martiat, Philippe

2009-01-01

The CD4+ T-cell malignancy induced by human T-cell leukemia virus type 1 (HTLV-I) infection and termed; Adult T-cell Leukemia lymphoma (ATLL), is caused by defects in the mechanisms underlying cell proliferation and cell death. In the CD4+ T-cells, calcium ions are central for both phenomena. ATLL is associated with a marked hypercalcemia in many patients. The consequence of a defect in the Ca2+ signaling pathway for lymphocyte activation is characterized by an impaired NFAT activation and transcription of cytokines, chemokines and many other NFAT target genes whose transcription is essential for productive immune defense. Fresh ATLL cells lack the TCR/CD3 and CD7 molecules on their surface. Whereas CD7 is a calcium transporter, reduction in calcium influx in response to T-cell activation was reported as a functional consequence of TCR/CD3 expression deficiency. Understanding these changes and identifying the molecular players involved might provide further insights on how to improve ATLL treatment.

Effects of annulus defects and implantation of poly(lactic-co-glycolic acid) (PLGA)/fibrin gel scaffolds on nerves ingrowth in a rabbit model of annular injury disc degeneration.

PubMed

Xin, Long; Xu, Weixing; Yu, Leijun; Fan, Shunwu; Wang, Wei; Yu, Fang; Wang, Zhenbin

2017-05-12

Growth of nerve fibers has been shown to occur in a rabbit model of intravertebral disc degeneration (IVD) induced by needle puncture. As nerve growth may underlie the process of chronic pain in humans affected by disc degeneration, we sought to investigate the factors underlying nerve ingrowth in a minimally invasive annulotomy rabbit model of IVD by comparing the effects of empty disc defects with those of defects filled with poly(lactic-co-glycolic acid)/fibrin gel (PLGA) plugs. New Zealand white rabbits (n = 24) received annular injuries at three lumbar levels (L3/4, L4/5, and L5/6). The discs were randomly assigned to four groups: (a) annular defect (1.8-mm diameter; 4-mm depth) by mini-trephine, (b) annular defect implanted with a PLGA scaffold containing a fibrin gel, (c) annular puncture by a 16G needle (5-mm depth), and (d) uninjured L2/3 disc (control). Disc degeneration was evaluated by radiography, MRI, histology, real-time PCR, and analysis of proteoglycan (PG) content. Nerve ingrowth into the discs was assessed by immunostaining with the nerve marker protein gene product 9.5. Injured discs showed a progressive disc space narrowing with significant disc degeneration and proteoglycan loss, as confirmed by imaging results, molecular and compositional analysis, and histological examinations. In 16G punctured discs, nerve ingrowth was observed on the surface of scar tissue. In annular defects, nerve fibers were found to be distributed along small fissures within the fibrocartilaginous-like tissue that filled the AF. In discs filled with PLGA/ fibrin gel, more nerve fibers were observed growing deeper into the inner AF along the open annular track.  In addition, innervations scores showed significantly higher than those of punctured discs and empty defects. A limited vascular proliferation was found in the injured sites and regenerated tissues. Nerve ingrowth was significantly higher in PLGA/fibrin-filled discs than in empty defects. Possible explanations include (i) annular fissures along the defect and early loss of proteoglycan may facilitate the ingrowth process and (ii) biodegradable PLGA/fibrin gel may promote adverse growth of nerves and blood vessels into deeper parts of injured disc. The rabbit annular defect model of disc degeneration appears suitable to investigate the effects of nerve ingrowth in relation to pain generation.

Probing Molecular Insights into Zika Virus–Host Interactions

PubMed Central

Lee, Ina; Li, Ge; Wang, Shusheng; Desprès, Philippe; Zhao, Richard Y.

2018-01-01

The recent Zika virus (ZIKV) outbreak in the Americas surprised all of us because of its rapid spread and association with neurologic disorders including fetal microcephaly, brain and ocular anomalies, and Guillain–Barré syndrome. In response to this global health crisis, unprecedented and world-wide efforts are taking place to study the ZIKV-related human diseases. Much has been learned about this virus in the areas of epidemiology, genetic diversity, protein structures, and clinical manifestations, such as consequences of ZIKV infection on fetal brain development. However, progress on understanding the molecular mechanism underlying ZIKV-associated neurologic disorders remains elusive. To date, we still lack a good understanding of; (1) what virologic factors are involved in the ZIKV-associated human diseases; (2) which ZIKV protein(s) contributes to the enhanced viral pathogenicity; and (3) how do the newly adapted and pandemic ZIKV strains alter their interactions with the host cells leading to neurologic defects? The goal of this review is to explore the molecular insights into the ZIKV–host interactions with an emphasis on host cell receptor usage for viral entry, cell innate immunity to ZIKV, and the ability of ZIKV to subvert antiviral responses and to cause cytopathic effects. We hope this literature review will inspire additional molecular studies focusing on ZIKV–host Interactions. PMID:29724036

Probing Molecular Insights into Zika Virus⁻Host Interactions.

PubMed

Lee, Ina; Bos, Sandra; Li, Ge; Wang, Shusheng; Gadea, Gilles; Desprès, Philippe; Zhao, Richard Y

2018-05-02

The recent Zika virus (ZIKV) outbreak in the Americas surprised all of us because of its rapid spread and association with neurologic disorders including fetal microcephaly, brain and ocular anomalies, and Guillain⁻Barré syndrome. In response to this global health crisis, unprecedented and world-wide efforts are taking place to study the ZIKV-related human diseases. Much has been learned about this virus in the areas of epidemiology, genetic diversity, protein structures, and clinical manifestations, such as consequences of ZIKV infection on fetal brain development. However, progress on understanding the molecular mechanism underlying ZIKV-associated neurologic disorders remains elusive. To date, we still lack a good understanding of; (1) what virologic factors are involved in the ZIKV-associated human diseases; (2) which ZIKV protein(s) contributes to the enhanced viral pathogenicity; and (3) how do the newly adapted and pandemic ZIKV strains alter their interactions with the host cells leading to neurologic defects? The goal of this review is to explore the molecular insights into the ZIKV⁻host interactions with an emphasis on host cell receptor usage for viral entry, cell innate immunity to ZIKV, and the ability of ZIKV to subvert antiviral responses and to cause cytopathic effects. We hope this literature review will inspire additional molecular studies focusing on ZIKV⁻host Interactions.

Thermal conductivity of graphene with defects induced by electron beam irradiation

NASA Astrophysics Data System (ADS)

Malekpour, Hoda; Ramnani, Pankaj; Srinivasan, Srilok; Balasubramanian, Ganesh; Nika, Denis L.; Mulchandani, Ashok; Lake, Roger K.; Balandin, Alexander A.

2016-07-01

We investigate the thermal conductivity of suspended graphene as a function of the density of defects, ND, introduced in a controllable way. High-quality graphene layers are synthesized using chemical vapor deposition, transferred onto a transmission electron microscopy grid, and suspended over ~7.5 μm size square holes. Defects are induced by irradiation of graphene with the low-energy electron beam (20 keV) and quantified by the Raman D-to-G peak intensity ratio. As the defect density changes from 2.0 × 1010 cm-2 to 1.8 × 1011 cm-2 the thermal conductivity decreases from ~(1.8 +/- 0.2) × 103 W mK-1 to ~(4.0 +/- 0.2) × 102 W mK-1 near room temperature. At higher defect densities, the thermal conductivity reveals an intriguing saturation-type behavior at a relatively high value of ~400 W mK-1. The thermal conductivity dependence on the defect density is analyzed using the Boltzmann transport equation and molecular dynamics simulations. The results are important for understanding phonon - point defect scattering in two-dimensional systems and for practical applications of graphene in thermal management.We investigate the thermal conductivity of suspended graphene as a function of the density of defects, ND, introduced in a controllable way. High-quality graphene layers are synthesized using chemical vapor deposition, transferred onto a transmission electron microscopy grid, and suspended over ~7.5 μm size square holes. Defects are induced by irradiation of graphene with the low-energy electron beam (20 keV) and quantified by the Raman D-to-G peak intensity ratio. As the defect density changes from 2.0 × 1010 cm-2 to 1.8 × 1011 cm-2 the thermal conductivity decreases from ~(1.8 +/- 0.2) × 103 W mK-1 to ~(4.0 +/- 0.2) × 102 W mK-1 near room temperature. At higher defect densities, the thermal conductivity reveals an intriguing saturation-type behavior at a relatively high value of ~400 W mK-1. The thermal conductivity dependence on the defect density is analyzed using the Boltzmann transport equation and molecular dynamics simulations. The results are important for understanding phonon - point defect scattering in two-dimensional systems and for practical applications of graphene in thermal management. Electronic supplementary information (ESI) available: Additional thermal conductivity measurements data. See DOI: 10.1039/c6nr03470e

Effect of hydrogen adsorption on the formation and annealing of Stone-Wales defects in graphene

NASA Astrophysics Data System (ADS)

Podlivaev, A. I.; Openov, L. A.

2015-12-01

The heights of energy barriers preventing the formation and annealing of Stone-Wales defects in graphene with a hydrogen atom adsorbed on the defect or in its immediate vicinity have been calculated using the atomistic computer simulation. It has been shown that, in the presence of hydrogen, both barriers are significantly lower than those in the absence of hydrogen. Based on the analysis of the potential energy surface, the frequency factors have been calculated for two different paths of the Stone-Wales transformation, and the temperature dependences of the corresponding annealing times of the defects have been found. The results obtained have been compared with the first-principles calculations and molecular dynamics data.

Calnexin Is Essential for Survival under Nitrogen Starvation and Stationary Phase in Schizosaccharomyces pombe

PubMed Central

Rokeach, Luis A.

2015-01-01

Cell fate is determined by the balance of conserved molecular mechanisms regulating death (apoptosis) and survival (autophagy). Autophagy is a process by which cells recycle their organelles and macromolecules through degradation within the vacuole in yeast and plants, and lysosome in metazoa. In the yeast Schizosaccharomyces pombe, autophagy is strongly induced under nitrogen starvation and in aging cells. Previously, we demonstrated that calnexin (Cnx1p), a highly conserved transmembrane chaperone of the endoplasmic reticulum (ER), regulates apoptosis under ER stress or inositol starvation. Moreover, we showed that in stationary phase, Cnx1p is cleaved into two moieties, L_Cnx1p and S_Cnx1p. Here, we show that the processing of Cnx1p is regulated by autophagy, induced by nitrogen starvation or cell aging. The cleavage of Cnx1p involves two vacuolar proteases: Isp6, which is essential for autophagy, and its paralogue Psp3. Blocking autophagy through the knockout of autophagy-related genes (atg) results in inhibition of both, the cleavage and the trafficking of Cnx1p from the ER to the vacuole. We demonstrate that Cnx1p is required for cell survival under nitrogen-starvation and in chronological aging cultures. The death of the mini_cnx1 mutant (overlapping S_cnx1p) cells is accompanied by accumulation of high levels of reactive-oxygen species (ROS), a slowdown in endocytosis and severe cell-wall defects. Moreover, mutant cells expressing only S_Cnx1p showed cell wall defects. Co-expressing mutant overlapping the L_Cnx1p and S_Cnx1p cleavage products reverses the death, ROS phenotype and cell wall defect to wild-type levels. As it is involved in both apoptosis and autophagy, Cnx1p could be a nexus for the crosstalk between these pro-death and pro-survival mechanisms. Ours, and observations in mammalian systems, suggest that the multiple roles of calnexin depend on its sub-cellular localization and on its cleavage. The use of S. pombe should assist in further shedding light on the multiple roles of calnexin. PMID:25803873

The cellular and molecular etiology of the craniofacial defects in the avian ciliopathic mutant talpid2

USDA-ARS?s Scientific Manuscript database

talpid2 is an avian autosomal recessive mutant with a myriad of congenital malformations, including polydactyly and facial clefting. Although phenotypically similar to talpid3, talpid2 has a distinct facial phenotype and an unknown cellular, molecular and genetic basis. We set out to determine the e...

Wide-range simulation of elastoplastic wave fronts and failure of solids under high-speed loading

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

Saveleva, Natalia, E-mail: saveleva@icmm.ru; Bayandin, Yuriy, E-mail: buv@icmm.ru; Naimark, Oleg, E-mail: naimark@icmm.ru

2015-10-27

The aim of this paper is numerical study of deformation processes and failure of vanadium under shock-wave loading. According developed statistical theory of solid with mesoscopic defects the constitutive equations were proposed in terms of two structural variables characterizing behavior of defects ensembles: defect density tensor and structural scaling parameter. On the basis of wide-range constitutive equations the mathematical model of deformation behavior and failure of vanadium was developed taking into account the bond relaxation mechanisms, multistage of fracture and nonlinearity kinetic of defects. Results of numerical simulation allow the description of the major effects of shock wave propagation (elasticmore » precursor decay, grow of spall strength under grow strain rate)« less

Type 2 diabetes mellitus and exercise impairment.

PubMed

Reusch, Jane E B; Bridenstine, Mark; Regensteiner, Judith G

2013-03-01

Limitations in physical fitness, a consistent finding in individuals with both type I and type 2 diabetes mellitus, correlate strongly with cardiovascular and all-cause mortality. These limitations may significantly contribute to the persistent excess cardiovascular mortality affecting this group. Exercise impairments in VO2 peak and VO2 kinetics manifest early on in diabetes, even with good glycemic control and in the absence of clinically apparent complications. Subclinical cardiac dysfunction is often present but does not fully explain the observed defect in exercise capacity in persons with diabetes. In part, the cardiac limitations are secondary to decreased perfusion with exercise challenge. This is a reversible defect. Similarly, in the skeletal muscle, impairments in nutritive blood flow correlate with slowed (or inefficient) exercise kinetics and decreased exercise capacity. Several correlations highlight the likelihood of endothelial-specific impairments as mediators of exercise dysfunction in diabetes, including insulin resistance, endothelial dysfunction, decreased myocardial perfusion, slowed tissue hemoglobin oxygen saturation, and impairment in mitochondrial function. Both exercise training and therapies targeted at improving insulin sensitivity and endothelial function improve physical fitness in subjects with type 2 diabetes. Optimization of exercise functions in people with diabetes has implications for diabetes prevention and reductions in mortality risk. Understanding the molecular details of endothelial dysfunction in diabetes may provide specific therapeutic targets for the remediation of this defect. Rat models to test this hypothesis are under study.

A high proportion of ADA point mutations associated with a specific alanine-to-valine substitution.

PubMed

Markert, M L; Norby-Slycord, C; Ward, F E

1989-09-01

In 15%-20% of children with severe combined immunodeficiency (SCID), the underlying defect is adenosine deaminase (ADA) deficiency. The overall goal of our research has been to identify the precise molecular defects in patients with ADA-deficient SCID. In this study, we focused on a patient whom we found to have normal sized ADA mRNA by Northern analysis and an intact ADA structural gene by Southern analysis. By cloning and sequencing this patient's ADA cDNA, we found a C-to-T point mutation in exon 11. This resulted in the amino acid substitution of a valine for an alanine at position 329 of the ADA protein. Sequence analysis revealed that this mutation created a new BalI restriction site. Using Southern analyses, we were able to directly screen individuals to determine the frequency of this mutation. By combining data on eight families followed at our institution with data on five other families reported in the literature, we established that five of 13 patients (seven of 22 alleles) with known or suspected point mutations have this defect. This mutation was found to be associated with three different ADA haplotypes. This argues against a founder effect and suggests that the mutation is very old. In summary, a conservative amino acid substitution is found in a high proportion of patients with ADA deficiency; this can easily be detected by Southern analysis.

The same IkappaBalpha mutation in two related individuals leads to completely different clinical syndromes.

PubMed

Janssen, Riny; van Wengen, Annelies; Hoeve, Marieke A; ten Dam, Monique; van der Burg, Miriam; van Dongen, Jacques; van de Vosse, Esther; van Tol, Maarten; Bredius, Robbert; Ottenhoff, Tom H; Weemaes, Corry; van Dissel, Jaap T; Lankester, Arjan

2004-09-06

Both innate and adaptive immune responses are dependent on activation of nuclear factor kappaB (NF-kappaB), induced upon binding of pathogen-associated molecular patterns to Toll-like receptors (TLRs). In murine models, defects in NF-kappaB pathway are often lethal and viable knockout mice have severe immune defects. Similarly, defects in the human NF-kappaB pathway described to date lead to severe clinical disease. Here, we describe a patient with a hyper immunoglobulin M-like immunodeficiency syndrome and ectodermal dysplasia. Monocytes did not produce interleukin 12p40 upon stimulation with various TLR stimuli and nuclear translocation of NF-kappaB was impaired. T cell receptor-mediated proliferation was also impaired. A heterozygous mutation was found at serine 32 in IkappaBalpha. Interestingly, his father has the same mutation but displays complex mosaicism. He does not display features of ectodermal dysplasia and did not suffer from serious infections with the exception of a relapsing Salmonella typhimurium infection. His monocyte function was impaired, whereas T cell function was relatively normal. Consistent with this, his T cells almost exclusively displayed the wild-type allele, whereas both alleles were present in his monocytes. We propose that the T and B cell compartment of the mosaic father arose as a result of selection of wild-type cells and that this underlies the widely different clinical phenotype.

Mechanical behavior enhancement of defective graphene sheet employing boron nitride coating via atomistic study

NASA Astrophysics Data System (ADS)

Setoodeh, A. R.; Badjian, H.

2017-12-01

The most stable form of boron nitride polymorph naming hexagonal boron nitride sheet has recently been widely concerned like graphite due to its interesting features such as electrical insulation and high thermal conductivity. In this study, the molecular dynamic simulations are implemented to investigate the mechanical properties of single-layer graphene sheets under tensile and compressive loadings in the absence and presence of boron-nitride coating layers. In this introduced hybrid nanostructure, the benefit of combining both individual interesting features of graphene and boron-nitride sheets such as exceptional mechanical and electrical properties can be simultaneously achieved for future potential application in nano devices. The influences of chiral indices, boundary conditions and presence of mono-atomic vacancy defects as well as coating dimension on the mechanical behavior of the resulted hybrid structure are reported. The interatomic forces between the atoms are modeled by employing the AIREBO and Tersoff-Brenner potentials for carbon-carbon and boron-nitrogen atoms in each layer, respectively. Furthermore, the van der Waal interlayer forces of carbon-boron and carbon-nitrogen are estimated by the Lennard-Jones potential field. Besides the potential improvement in electrical and physical properties of the nanostructure, it is demonstrated that the buckling load capacity of the fully coated graphene sheet with 3% concentration of mono-atomic vacancy defects noticeably enhances by amounts of 24.1%.

Estrogen amelioration of Aβ-induced defects in mitochondria is mediated by mitochondrial signaling pathway involving ERβ, AKAP and Drp1.

PubMed

Sarkar, Saumyendra; Jun, Sujung; Simpkins, James W

2015-08-07

Perturbations in dynamic properties of mitochondria including fission, fusion, and movement lead to disruption of energy supply to synapses contributing to neuropathology and cognitive dysfunction in Alzheimer׳s disease (AD). The molecular mechanisms underlying these defects are still unclear. Previously, we have shown that ERβ is localized in the mitochondria and ERβ knock down disrupts mitochondrial functions. Because a selective ERβ modulator (DPN) can activate PKA, and localized PKA signaling in the mitochondrial membrane regulates mitochondrial structure and functions, we reasoned that ERβ signaling in the mitochondrial membrane rescues many of the mitochondrial defects caused by soluble Aβ oligomer. We now report that DPN treatment in primary hippocampal neurons attenuates soluble Aβ-oligomer induced dendritic mitochondrial fission and reduced mobility. Additionally, Aβ treatment reduced the respiratory reserve capacity of hippocampal neuron and inhibited phosphorylation of Drp1 at its PKA site, which induces excessive mitochondrial fission, and DPN treatment ameliorates these inhibitions. Finally, we discovered a direct interaction of ERβ with a mitochondrial resident protein AKAP1, which induces the PKA-mediated local signaling pathway involved in increased oxidative phosphorylation and inhibition of mitochondrial fission. Taken together, our findings highlight the possibility that ERβ signaling pathway may be a useful mitochondria-directed therapeutic target for AD. Copyright © 2015 Elsevier B.V. All rights reserved.

Sensitivity of thermal transport in thorium dioxide to defects

NASA Astrophysics Data System (ADS)

Park, Jungkyu; Farfán, Eduardo B.; Mitchell, Katherine; Resnick, Alex; Enriquez, Christian; Yee, Tien

2018-06-01

In this research, the reverse non-equilibrium molecular dynamics is employed to investigate the effect of vacancy and substitutional defects on the thermal transport in thorium dioxide (ThO2). Vacancy defects are shown to severely alter the thermal conductivity of ThO2. The thermal conductivity of ThO2 decreases significantly with increasing the defect concentration of oxygen vacancy; the thermal conductivity of ThO2 decreases by 20% when 0.1% oxygen vacancy defects are introduced in the 100 unit cells of ThO2. The effect of thorium vacancy defect on the thermal transport in ThO2 is even more detrimental; ThO2 with 0.1% thorium vacancy defect concentration exhibits a 38.2% reduction in its thermal conductivity and the thermal conductivity becomes only 8.2% of that of the pristine sample when the thorium vacancy defect concentration is increased to 5%. In addition, neutron activation of thorium produces uranium and this uranium substitutional defects in ThO2 are observed to affect the thermal transport in ThO2 marginally when compared to vacancy defects. This indicates that in the thorium fuel cycle, fissile products such as 233U is not likely to alter the thermal transport in ThO2 fuel.

Is high pressure liquid chromatography an effective screening tool for characterization of molecular defects in hemoglobinopathies?

PubMed

Moorchung, Nikhil; Phillip, Joseph; Sarkar, Ravi Shankar; Prasad, Rupesh; Dutta, Vibha

2013-01-01

Hemoglobinopathies constitute entities that are generated by either abnormal hemoglobin or thalassemias. high pressure liquid chromatography (HPLC) is one of the best methods for screening and detection of various hemoglobinopathies but it has intrinsic interpretive problems. The study was designed to evaluate the different mutations seen in cases of hemoglobinopathies and compare the same with screening tests. 68 patients of hemoglobinopathies were screened by HPLC. Mutation studies in the beta globin gene was performed using the polymerase chain reaction (PCR)-based allele-specific Amplification Refractory Mutation System (ARMS). Molecular analysis for the sickle cell mutation was done by standard methods. The IVS 1/5 mutation was the commonest mutation seen and it was seen in 26 (38.23%) of the cases. This was followed by the IVS 1/1, codon 41/42, codon 8/9, del 22 mutation, codon 15 mutation and the -619 bp deletion. No mutation was seen in eight cases. There was a 100% concordance between the sickle cell trait as diagnosed by HPLC and genetic testing. Our study underlies the importance of molecular testing in all cases of hemoglobinopathies. Although HPLC is a useful screening tool, molecular testing is very useful in accurately diagnosing the mutations. Molecular testing is especially applicable in cases with an abnormal hemoglobin (HbD, HbE and HbS) because there may be a concomitant inheritance of a beta thalassemia mutation. Molecular testing is the gold standard when it comes to the diagnosis of hemoglobinopathies.

Diabetes mellitus and the β-cell: the Last Ten Years

PubMed Central

Ashcroft, Frances M; Rorsman, Patrik

2018-01-01

Diabetes is a major global problem. During the past decade, the genetic basis of various monogenic forms of the disease, and their underlying molecular mechanisms, have been elucidated. Many genes that increase type-2 diabetes (T2DM) risk have also been identified but how they do so remains enigmatic. Nevertheless, defective insulin secretion emerges as the main culprit in both monogenic and polygenic diabetes, with environmental and lifestyle factors, via obesity, accounting for the current dramatic increase in T2DM. There also have been significant advances in therapy, particularly for some monogenic disorders. We review here what ails the beta-cell and how its function may be restored. PMID:22424227

Image processing for grazing incidence fast atom diffraction

NASA Astrophysics Data System (ADS)

Debiossac, Maxime; Roncin, Philippe

2016-09-01

Grazing incidence fast atom diffraction (GIFAD, or FAD) has developed as a surface sensitive technique. Compared with thermal energies helium diffraction (TEAS or HAS), GIFAD is less sensitive to thermal decoherence but also more demanding in terms of surface coherence, the mean distance between defects. Such high quality surfaces can be obtained from freshly cleaved crystals or in a molecular beam epitaxy (MBE) chamber where a GIFAD setup has been installed allowing in situ operation. Based on recent publications by Atkinson et al. (2014) and Debiossac et al. (2014), the paper describes in detail the basic steps needed to measure the relative intensities of the diffraction spots. Care is taken to outline the underlying physical assumptions.

A Dynamic Pathway for Stone-Wales Bond Rotation on Carbon Nanotubes through Diamond-Like Bonds

NASA Technical Reports Server (NTRS)

Wei, Chen-Yu; Srivastava, Deepak; Cho, Kyeong-Jae; Menon, Madhu

2003-01-01

A new lower energy barrier with a two-step pathway of Stone-Wales (SW) ,ond rotation on carbon nanotubes (CNTs) is found through molecular dynamics (MD) simulations of CNTs under tension. The first step involves going over to a stable sp3-like metastable configuration with half rotated and partially tilted C-C bond. The second step involves going over to the fully rotated C-C bond with the formation of a SW defect in the nanotube. The energy barrier for this two-step dynamic pathway is significantly lower than the previously known static barrier for in-plane rotation of the C-C bond on a tensile strained (> 4%) CNT.

Processing of Building Binder Materials to Increase their Activation

NASA Astrophysics Data System (ADS)

Fediuk, R. S.; Garmashov, I. S.; Kuzmin, D. E.; Stoyushko, N. Yu; Gladkova, N. A.

2018-01-01

The paper deals modern physical methods of activation of building powder materials. During mechanical activation a composite binder active molecules cement minerals occur in the destruction of the molecular defects in the areas of packaging and breaking metastable phase decompensation intermolecular forces. The process is accompanied by a change in the kinetics of hardening of Portland cement. Activated concrete has a number of features that are used as design characteristics of structures and are due to the structure of the activated binder and its contacts with concrete aggregates. These features also have a significant impact on the nature of the destruction of concrete under load, changing the boundaries of its microcracks and durability.

JAK2 and genomic instability in the myeloproliferative neoplasms: a case of the chicken or the egg?

PubMed Central

Scott, Linda M.; Rebel, Vivienne I.

2012-01-01

The myeloproliferative neoplasms (MPNs) are a particularly useful model for studying mutation accumulation in neoplastic and the mechanisms of the molecular cells, understanding underlying defects our current This review summarizes acquisition. present their in patients with an MPN, and the effects of mutations targeting Janus kinase 2 (JAK2)-mediated intracellular signaling on DNA damage, and on the elimination of mutation-bearing cells by programmed cell death. Moreover, we discuss findings that suggest that the acquisition of disease-initiating mutations in hematopoietic stem cells of some MPN patients may be the consequence of an inherent genomic instability that was not previously appreciated. PMID:22641564

Epitaxial growth mechanisms of graphene and effects of substrates

NASA Astrophysics Data System (ADS)

Özçelik, V. Ongun; Cahangirov, S.; Ciraci, S.

2012-06-01

The growth process of single layer graphene with and without substrate is investigated using ab initio, finite temperature molecular dynamic calculations within density functional theory. An understanding of the epitaxial graphene growth mechanisms in the atomic level is provided by exploring the transient stages which occur at the growing edges of graphene. These stages are formation and collapse of large carbon rings together with the formation and healing of Stone-Wales like pentagon-heptagon defects. The activation barriers for the healing of these growth induced defects on various substrates are calculated using the climbing image nudge elastic band method and compared with that of the Stone-Wales defect. It is found that the healing of pentagon-heptagon defects occurring near the edge in the course of growth is much easier than that of Stone-Wales defect. The role of the substrate in the epitaxial growth and in the healing of defects are also investigated in detail, along with the effects of using carbon dimers as the building blocks of graphene growth.

Effect of vacancy defects on generalized stacking fault energy of fcc metals.

PubMed

Asadi, Ebrahim; Zaeem, Mohsen Asle; Moitra, Amitava; Tschopp, Mark A

2014-03-19

Molecular dynamics (MD) and density functional theory (DFT) studies were performed to investigate the influence of vacancy defects on generalized stacking fault (GSF) energy of fcc metals. MEAM and EAM potentials were used for MD simulations, and DFT calculations were performed to test the accuracy of different common parameter sets for MEAM and EAM potentials in predicting GSF with different fractions of vacancy defects. Vacancy defects were placed at the stacking fault plane or at nearby atomic layers. The effect of vacancy defects at the stacking fault plane and the plane directly underneath of it was dominant compared to the effect of vacancies at other adjacent planes. The effects of vacancy fraction, the distance between vacancies, and lateral relaxation of atoms on the GSF curves with vacancy defects were investigated. A very similar variation of normalized SFEs with respect to vacancy fractions were observed for Ni and Cu. MEAM potentials qualitatively captured the effect of vacancies on GSF.

Adsorption Site of Gas Molecules on Defective Armchair Graphene Nanoribbon Formed Through Ion Bombardment

NASA Astrophysics Data System (ADS)

Auzar, Zuriana; Johari, Zaharah; Sakina, S. H.; Alias, N. Ezaila

2018-02-01

High sensitivity and selectivity is desired in sensing devices. The aim of this study is to investigate the use of the ion bombardment process in creating a defect on graphene nanoribbons (GNR), which significantly affects sensing properties, in particular adsorption energy, charge transfer and sensitivity. A process has been developed to form the defect on the GNR surface using molecular dynamic (MD) with a reactive force field with nitrogen ion. The sensing properties were calculated using the extended Huckel theory when oxygen (O2) and ammonia (NH3) molecules are exposed to different areas on the defective site. Through simulation, it was found that the ion bombardment process formed various types of defects on the GNR surface. Most notably, molecules adsorbed on the ripple area considerably improve the sensitivity by more than 50%. This indicates that the defect on the armchair graphene nanoribbon (AGNR) surface can be a method to enhance graphene-based sensing performance.

Precise annealing of focal plane arrays for optical detection

DOEpatents

Bender, Daniel A.

2015-09-22

Precise annealing of identified defective regions of a Focal Plane Array ("FPA") (e.g., exclusive of non-defective regions of the FPA) facilitates removal of defects from an FPA that has been hybridized and/or packaged with readout electronics. Radiation is optionally applied under operating conditions, such as under cryogenic temperatures, such that performance of an FPA can be evaluated before, during, and after annealing without requiring thermal cycling.

Precise annealing of focal plane arrays for optical detection

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

Bender, Daniel A.

2017-10-17

Precise annealing of identified defective regions of a Focal Plane Array ("FPA") (e.g., exclusive of non-defective regions of the FPA) facilitates removal of defects from an FPA that has been hybridized and/or packaged with readout electronics. Radiation is optionally applied under operating conditions, such as under cryogenic temperatures, such that performance of an FPA can be evaluated before, during, and after annealing without requiring thermal cycling.

Molecular dynamics modeling of atomic displacement cascades in 3C-SiC: Comparison of interatomic potentials

NASA Astrophysics Data System (ADS)

Samolyuk, G. D.; Osetsky, Y. N.; Stoller, R. E.

2015-10-01

We used molecular dynamics modeling of atomic displacement cascades to characterize the nature of primary radiation damage in 3C-SiC. We demonstrated that the most commonly used interatomic potentials are inconsistent with ab initio calculations of defect energetics. Both the Tersoff potential used in this work and a modified embedded-atom method potential reveal a barrier to recombination of the carbon interstitial and carbon vacancy which is much higher than the density functional theory (DFT) results. The barrier obtained with a newer potential by Gao and Weber is closer to the DFT result. This difference results in significant differences in the cascade production of point defects. We have completed both 10 keV and 50 keV cascade simulations in 3C-SiC at a range of temperatures. In contrast to the Tersoff potential, the Gao-Weber potential produces almost twice as many C vacancies and interstitials at the time of maximum disorder (∼0.2 ps) but only about 25% more stable defects at the end of the simulation. Only about 20% of the carbon defects produced with the Tersoff potential recombine during the in-cascade annealing phase, while about 60% recombine with the Gao-Weber potential. The Gao-Weber potential appears to give a more realistic description of cascade dynamics in SiC, but still has some shortcomings when the defect migration barriers are compared to the ab initio results.

Oocyte spindle proteomics analysis leading to rescue of chromosome congression defects in cloned embryos

PubMed Central

Duan, Xunbao; Zhong, Zhisheng; Potireddy, Santhi; Moncada, Camilo; Merali, Salim; Latham, Keith E.

2015-01-01

Embryos produced by somatic cell nuclear transfer (SCNT) display low term developmental potential. This is associated with deficiencies in spindle composition prior to activation and at early mitotic divisions, including failure to assemble certain proteins on the spindle. The protein-deficient spindles are accompanied by chromosome congression defects prior to activation and during the first mitotic divisions of the embryo. The molecular basis for these deficiencies and how they might be avoided are unknown. Proteomic analyses of spindles isolated from normal metaphase II (MII) stage oocytes and SCNT constructs, along with a systematic immunofluorescent survey of known spindle-associated proteins were undertaken. This was the first proteomics study of mammalian oocyte spindles. The study revealed four proteins as being deficient in spindles of SCNT embryos in addition to those previously identified; these were clathrin heavy chain (CLTC), aurora B kinase, dynactin 4, and casein kinase 1 alpha. Due to substantial reduction in CLTC abundance after spindle removal, we undertook functional studies to explore the importance of CLTC in oocyte spindle function and in chromosome congression defects of cloned embryos. Using siRNA knockdown we demonstrated an essential role for CLTC in chromosome congression during oocyte maturation. We also demonstrated rescue of chromosome congression defects in SCNT embryos at the first mitosis using CLTC mRNA injection. These studies are the first to employ proteomics analyses coupled to functional interventions to rescue a specific molecular defect in cloned embryos. PMID:20883044

Atomistic simulation of defect formation and structure transitions in U-Mo alloys in swift heavy ion irradiation

NASA Astrophysics Data System (ADS)

Kolotova, L. N.; Starikov, S. V.

2017-11-01

In irradiation of swift heavy ions, the defects formation frequently takes place in crystals. High energy transfer into the electronic subsystem and relaxations processes lead to the formation of structural defects and cause specific effects, such as the track formation. There is a large interest to understanding of the mechanisms of defects/tracks formation due to the heating of the electron subsystem. In this work, the atomistic simulation of defects formation and structure transitions in U-Mo alloys in irradiation of swift heavy ions has been carried out. We use the two-temperature atomistic model with explicit account of electron pressure and electron thermal conductivity. This two-temperature model describes ionic subsystem by means of molecular dynamics while the electron subsystem is considered in the continuum approach. The various mechanisms of structure changes in irradiation are examined. In particular, the simulation results indicate that the defects formation may be produced without melting and subsequent crystallization. Threshold stopping power of swift ions for the defects formation in irradiation in the various conditions are calculated.

Mitochondrial iron-sulfur cluster biogenesis from molecular understanding to clinical disease

PubMed Central

Alfadhel, Majid; Nashabat, Marwan; Ali, Qais Abu; Hundallah, Khalid

2017-01-01

Iron–sulfur clusters (ISCs) are known to play a major role in various protein functions. Located in the mitochondria, cytosol, endoplasmic reticulum and nucleus, they contribute to various core cellular functions. Until recently, only a few human diseases related to mitochondrial ISC biogenesis defects have been described. Such diseases include Friedreich ataxia, combined oxidative phosphorylation deficiency 19, infantile complex II/III deficiency defect, hereditary myopathy with lactic acidosis and mitochondrial muscle myopathy, lipoic acid biosynthesis defects, multiple mitochondrial dysfunctions syndromes and non ketotic hyperglycinemia due to glutaredoxin 5 gene defect. Disorders of mitochondrial import, export and translation, including sideroblastic anemia with ataxia, EVEN-PLUS syndrome and mitochondrial complex I deficiency due to nucleotide-binding protein-like protein gene defect, have also been implicated in ISC biogenesis defects. With advances in next generation sequencing technologies, more disorders related to ISC biogenesis defects are expected to be elucidated. In this article, we aim to shed the light on mitochondrial ISC biogenesis, related proteins and their function, pathophysiology, clinical phenotypes of related disorders, diagnostic approach, and future implications. PMID:28064324

Average structure and local configuration of excess oxygen in UO(2+x).

PubMed

Wang, Jianwei; Ewing, Rodney C; Becker, Udo

2014-03-19

Determination of the local configuration of interacting defects in a crystalline, periodic solid is problematic because defects typically do not have a long-range periodicity. Uranium dioxide, the primary fuel for fission reactors, exists in hyperstoichiometric form, UO(2+x). Those excess oxygen atoms occur as interstitial defects, and these defects are not random but rather partially ordered. The widely-accepted model to date, the Willis cluster based on neutron diffraction, cannot be reconciled with the first-principles molecular dynamics simulations present here. We demonstrate that the Willis cluster is a fair representation of the numerical ratio of different interstitial O atoms; however, the model does not represent the actual local configuration. The simulations show that the average structure of UO(2+x) involves a combination of defect structures including split di-interstitial, di-interstitial, mono-interstitial, and the Willis cluster, and the latter is a transition state that provides for the fast diffusion of the defect cluster. The results provide new insights in differentiating the average structure from the local configuration of defects in a solid and the transport properties of UO(2+x).

[Cytochrome c oxydase-deficient Leigh syndrome with homozygous mutation in SURF1 gene].

PubMed

Monnot, S; Chabrol, B; Cano, A; Pellissier, J F; Collignon, P; Montfort, M F; Paquis-Flucklinger, V

2005-05-01

Leigh syndrome is a heterogeneous disorder, usually due to a defect in oxidative metabolism. Mutations in SURF1 gene have been identified in patients with cytochrome c oxidase deficiency. We report a homozygous splice site deletion [516-2_516-1delAG] in a young girl presenting with cytochrome c oxidase-deficient Leigh syndrome. Identification of molecular defect is indispensable for genetic counselling and prenatal diagnosis.

Addition of oral iron to plasma transfusion in human congenital hypotransferrinemia: A 10-year observational follow-up with the effects on hematological parameters and growth.

PubMed

Aslan, Deniz

2018-02-01

Congenital hypotransferrinemia (OMIM 209300) is an extremely rare disorder of inherited iron metabolism. Since its description in 1961, only 16 cases have been reported. The defective gene and molecular defect causing this disorder and clinicolaboratory findings seen in the homozygous and heterozygous states have been documented in both humans and mice. However, due to the lack of follow-up studies of the described cases, the long-term prognosis remains unknown. We present a 10-year observational follow-up of a patient previously diagnosed on a molecular basis who was treated with a unique therapy of plasma transfusion fortified with oral iron, with satisfactory clinicolaboratory responses. © 2017 Wiley Periodicals, Inc.

A further case of a Prader-Willi syndrome phenotype in a patient with Angelman syndrome molecular defect.

PubMed

De Molfetta, Greice Andreotti; Felix, Temis Maria; Riegel, Mariluce; Ferraz, Victor Evangelista de Faria; de Pina Neto, João Monteiro

2002-12-01

Angelman syndrome (AS) and Prader-Willi syndrome (PWS) are distinct human neurogenetic disorders; however, a clinical overlap between AS and PWS has been identified. We report on a further case of a patient showing the PWS phenotype with the AS molecular defect. Despite the PWS phenotype, the DNA methylation analysis of SNRPN revealed an AS pattern. Cytogenetic and FISH analysis showed normal chromosomes 15 and microsatellite analysis showed heterozygous loci inside and outside the 15q11-13 region. The presence of these atypical cases could be more frequent than previously expected and we reinforce that the DNA methylation analysis is important for the correct diagnosis of severe mental deficiency, congenital hypotonia and obesity.

A Novel Type of Macrothrombocytopenia Associated with a Defect in α2,3-Sialylation

PubMed Central

Jones, Claire; Denecke, Jonas; Sträter, Ronald; Stölting, Torsten; Schunicht, Yvonne; Zeuschner, Dagmar; Klumperman, Judith; Lefeber, Dirk J.; Spelten, Oliver; Zarbock, Alexander; Kelm, Sørge; Strenge, Karen; Haslam, Stuart M.; Lühn, Kerstin; Stahl, Dorothea; Gentile, Luca; Schreiter, Thomas; Hilgard, Philip; Beck-Sickinger, Annette G.; Marquardt, Thorsten; Wild, Martin K.

2011-01-01

We describe a novel type of human thrombocytopenia characterized by the appearance of giant platelets and variable neutropenia. Searching for the molecular defect, we found that neutrophils had strongly reduced sialyl-Lewis X and increased Lewis X surface expression, pointing to a deficiency in sialylation. We show that the glycosylation defect is restricted to α2,3-sialylation and can be detected in platelets, neutrophils, and monocytes. Platelets exhibited a distorted structure of the open canalicular system, indicating defective platelet generation. Importantly, patient platelets, but not normal platelets, bound to the asialoglycoprotein receptor (ASGP-R), a liver cell-surface protein that removes desialylated thrombocytes from the circulation in mice. Taken together, this is the first type of human thrombocytopenia in which a specific defect of α2,3-sialylation and an induction of platelet binding to the liver ASGP-R could be detected. PMID:21864493

Transformation between divacancy defects induced by an energy pulse in graphene.

PubMed

Xia, Jun; Liu, XiaoYi; Zhou, Wei; Wang, FengChao; Wu, HengAn

2016-07-08

The mutual transformations among the four typical divacancy defects induced by a high-energy pulse were studied via molecular dynamics simulation. Our study revealed all six possible mutual transformations and found that defects transformed by absorbing energy to overcome the energy barrier with bonding, debonding, and bond rotations. The reversibility of defect transformations was also investigated by potential energy analysis. The energy difference was found to greatly influence the transformation reversibility. The direct transformation path was irreversible if the energy difference was too large. We also studied the correlation between the transformation probability and the input energy. It was found that the transformation probability had a local maxima at an optimal input energy. The introduction of defects and their structural evolutions are important for tailoring the exceptional properties and thereby performances of graphene-based devices, such as nanoporous membranes for the filtration and desalination of water.

Repair of massively defected hemi-joints using demineralized osteoarticular allografts with protected cartilage.

PubMed

Li, Siming; Yang, Xiaohong; Tang, Shenghui; Zhang, Xunmeng; Feng, Zhencheng; Cui, Shuliang

2015-08-01

Surgical replacement of massively defected joints necessarily relies on osteochondral grafts effective to both of bone and cartilage. Demineralized bone matrix (DBM) retains the osteoconductivity but destroys viable chondrocytes in the cartilage portion essential for successful restoration of defected joints. This study prepared osteochondral grafts of DBM with protected cartilage. Protected cartilage portions was characterized by cellular and molecular biology and the grafts were allogenically used for grafting. Protected cartilage showed similar histomorphological structure and protected proteins estimated by total proteins and cartilage specific proteins as in those of fresh controls when DBMs were generated in bone portions. Such grafts were successfully used for simultaneously repair of bone and cartilage in massively defected osteoarticular joints within 16 weeks post-surgery. These results present an allograft with clinical potential for simultaneous restoration of bone and cartilage in defected joints.

Structural Analysis on the Pathologic Mutant Glucocorticoid Receptor Ligand-Binding Domains.

PubMed

Hurt, Darrell E; Suzuki, Shigeru; Mayama, Takafumi; Charmandari, Evangelia; Kino, Tomoshige

2016-02-01

Glucocorticoid receptor (GR) gene mutations may cause familial or sporadic generalized glucocorticoid resistance syndrome. Most of the missense forms distribute in the ligand-binding domain and impair its ligand-binding activity and formation of the activation function (AF)-2 that binds LXXLL motif-containing coactivators. We performed molecular dynamics simulations to ligand-binding domain of pathologic GR mutants to reveal their structural defects. Several calculated parameters including interaction energy for dexamethasone or the LXXLL peptide indicate that destruction of ligand-binding pocket (LBP) is a primary character. Their LBP defects are driven primarily by loss/reduction of the electrostatic interaction formed by R611 and T739 of the receptor to dexamethasone and a subsequent conformational mismatch, which deacylcortivazol resolves with its large phenylpyrazole moiety and efficiently stimulates transcriptional activity of the mutant receptors with LBP defect. Reduced affinity of the LXXLL peptide to AF-2 is caused mainly by disruption of the electrostatic bonds to the noncore leucine residues of this peptide that determine the peptide's specificity to GR, as well as by reduced noncovalent interaction against core leucines and subsequent exposure of the AF-2 surface to solvent. The results reveal molecular defects of pathologic mutant receptors and provide important insights to the actions of wild-type GR.

Evaluation of cell sheet application on one wall bone defect in Macaca nemestrina through periostin expression

NASA Astrophysics Data System (ADS)

Tamin, R. Y.; Soeroso, Y.; Amir, L.; Idrus, E.

2017-08-01

Chronic periodontitis is an oral disease in which the destruction of periodontal tissue leads to tooth loss. Regenerative therapy for attachment cannot be applied to one wall bone defects owing to the minimal existing healthy bone. Tissue engineering in the form of cell sheets has been developed to overcome this limitation. In a previous study, cell sheet application to a one wall bone defect in Macaca nemestrina showed good clinical results. To evaluate the effectiveness of cell sheet application histologically, the level of periostin expression in the gingival crevicular fluid (GCF) of M. nemestrina was determined. Periostin is a 90-kDa protein that regulates coordination and interaction for regeneration and tissue repair. A laboratory observation study was performed to see the differences in periostin levels in samples collected from M. nemestrina’s GCF, where a cell sheet was applied to the bone defect. Gel electrophoresis with SDS-PAGE was performed to detect periostin expression based on its molecular weight and to compare the expression band between the cell sheet and the control at 1, 2, and 3 weeks after treatment. The gel electrophoresis result shows different thicknesses of the protein band around the molecular weight of periostin between the cell sheet groups.

Molecular dynamics modeling of atomic displacement cascades in 3C-SiC: Comparison of interatomic potentials

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

Samolyuk, German D.; Osetskiy, Yury N.; Stoller, Roger E.

We used molecular dynamics modeling of atomic displacement cascades to characterize the nature of primary radiation damage in 3C-SiC. We demonstrated that the most commonly used interatomic potentials are inconsistent with ab initio calculations of defect energetics. Both the Tersoff potential used in this work and a modified embedded-atom method potential reveal a barrier to recombination of the carbon interstitial and carbon vacancy which is much higher than the density functional theory (DFT) results. The barrier obtained with a newer potential by Gao and Weber is closer to the DFT result. This difference results in significant differences in the cascademore » production of point defects. We have completed both 10 keV and 50 keV cascade simulations in 3C-SiC at a range of temperatures. In contrast to the Tersoff potential, the Gao-Weber potential produces almost twice as many C vacancies and interstitials at the time of maximum disorder (~0.2 ps) but only about 25% more stable defects at the end of the simulation. Only about 20% of the carbon defects produced with the Tersoff potential recombine during the in-cascade annealing phase, while about 60% recombine with the Gao-Weber potential.« less

Molecular dynamics modeling of atomic displacement cascades in 3C-SiC: Comparison of interatomic potentials

DOE PAGES

Samolyuk, German D.; Osetskiy, Yury N.; Stoller, Roger E.

2015-06-03

We used molecular dynamics modeling of atomic displacement cascades to characterize the nature of primary radiation damage in 3C-SiC. We demonstrated that the most commonly used interatomic potentials are inconsistent with ab initio calculations of defect energetics. Both the Tersoff potential used in this work and a modified embedded-atom method potential reveal a barrier to recombination of the carbon interstitial and carbon vacancy which is much higher than the density functional theory (DFT) results. The barrier obtained with a newer potential by Gao and Weber is closer to the DFT result. This difference results in significant differences in the cascademore » production of point defects. We have completed both 10 keV and 50 keV cascade simulations in 3C-SiC at a range of temperatures. In contrast to the Tersoff potential, the Gao-Weber potential produces almost twice as many C vacancies and interstitials at the time of maximum disorder (~0.2 ps) but only about 25% more stable defects at the end of the simulation. Only about 20% of the carbon defects produced with the Tersoff potential recombine during the in-cascade annealing phase, while about 60% recombine with the Gao-Weber potential.« less

Magnetoencephalography signals are influenced by skull defects.

PubMed

Lau, S; Flemming, L; Haueisen, J

2014-08-01

Magnetoencephalography (MEG) signals had previously been hypothesized to have negligible sensitivity to skull defects. The objective is to experimentally investigate the influence of conducting skull defects on MEG and EEG signals. A miniaturized electric dipole was implanted in vivo into rabbit brains. Simultaneous recording using 64-channel EEG and 16-channel MEG was conducted, first above the intact skull and then above a skull defect. Skull defects were filled with agar gels, which had been formulated to have tissue-like homogeneous conductivities. The dipole was moved beneath the skull defects, and measurements were taken at regularly spaced points. The EEG signal amplitude increased 2-10 times, whereas the MEG signal amplitude reduced by as much as 20%. The EEG signal amplitude deviated more when the source was under the edge of the defect, whereas the MEG signal amplitude deviated more when the source was central under the defect. The change in MEG field-map topography (relative difference measure, RDM(∗)=0.15) was geometrically related to the skull defect edge. MEG and EEG signals can be substantially affected by skull defects. MEG source modeling requires realistic volume conductor head models that incorporate skull defects. Copyright © 2013 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Comparative study of the oxidation of NiAl(100) by molecular oxygen and water vapor using ambient-pressure X-ray photoelectron spectroscopy

DOE PAGES

Liu, Qianqian; Qin, Hailang; Boscoboinik, Jorge Anibal; ...

2016-10-11

The oxidation behavior of NiAl(100) by molecular oxygen and water vapor under a near-ambient pressure of 0.2 Torr is monitored using ambient-pressure X-ray photoelectron spectroscopy. O 2 exposure leads to the selective oxidation of Al at temperatures ranging from 40 to 500 °C. By contrast, H 2O exposure results in the selective oxidation of Al at 40 and 200 °C, and increasing the oxidation temperature above 300 °C leads to simultaneous formation of both Al and Ni oxides. Furthermore, these results demonstrate that the O 2 oxidation forms a nearly stoichiometric Al 2O 3 structure that provides improved protection tomore » the metallic substrate by barring the outward diffusion of metals. By contrast, the H 2O oxidation results in the formation of a defective oxide layer that allows outward diffusion of Ni at elevated temperatures for simultaneous NiO formation.« less

Eye Development Genes and Known Syndromes

PubMed Central

Slavotinek, Anne M.

2011-01-01

Anophthalmia and microphthalmia (A/M) are significant eye defects because they can have profound effects on visual acuity. A/M is associated with non-ocular abnormalities in an estimated 33–95% of cases and around 25% of patients have an underlying genetic syndrome that is diagnosable. Syndrome recognition is important for targeted molecular genetic testing, prognosis and for counseling regarding recurrence risks. This review provides clinical and molecular information for several of the commonest syndromes associated with A/M: Anophthalmia-Esophageal-Genital syndrome, caused by SOX2 mutations, Anophthalmia and pituitary abnormalities caused by OTX2 mutations, Matthew-Wood syndrome caused by STRA6 mutations, Oculocardiafaciodental syndrome and Lenz microphthalmia caused by BCOR mutations, Microphthalmia Linear Skin pigmentation syndrome caused by HCCS mutations, Anophthalmia, pituitary abnormalities, polysyndactyly caused by BMP4 mutations and Waardenburg anophthalmia caused by mutations in SMOC1. In addition, we briefly discuss the ocular and extraocular phenotypes associated with several other important eye developmental genes, including GDF6, VSX2, RAX, SHH, SIX6 and PAX6. PMID:22005280

Homogeneous AlGaN/GaN superlattices grown on free-standing (1100) GaN substrates by plasma-assisted molecular beam epitaxy

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

Shao, Jiayi; Malis, Oana; Physics Department, Purdue University, West Lafayette, Indiana 47907

Two-dimensional and homogeneous growth of m-plane AlGaN by plasma-assisted molecular beam epitaxy has been realized on free-standing (1100) GaN substrates by implementing high metal-to-nitrogen (III/N) flux ratio. AlN island nucleation, often reported for m-plane AlGaN under nitrogen-rich growth conditions, is suppressed at high III/N flux ratio, highlighting the important role of growth kinetics for adatom incorporation. The homogeneity and microstructure of m-plane AlGaN/GaN superlattices are assessed via a combination of scanning transmission electron microscopy and high resolution transmission electron microscopy (TEM). The predominant defects identified in dark field TEM characterization are short basal plane stacking faults (SFs) bounded by eithermore » Frank-Shockley or Frank partial dislocations. In particular, the linear density of SFs is approximately 5 × 10{sup −5} cm{sup −1}, and the length of SFs is less than 15 nm.« less

Identifcation of a Novel Mutation p.I240T in the FRMD7 gene in a Family with Congenital Nystagmus

NASA Astrophysics Data System (ADS)

Zhu, Yihua; Zhuang, Jianfu; Ge, Xianglian; Zhang, Xiao; Wang, Zheng; Sun, Ji; Yang, Juhua; Gu, Feng

2013-10-01

Congenital Nystagmus (CN) is a genetically heterogeneous ocular disease, which causes a significant proportion of childhood visual impairment. To identify the underlying genetic defect of a CN family, twenty-two members were recruited. Genotype analysis showed that affected individuals shared a common haplotype with markers flanking FRMD7 locus. Sequencing FRMD7 revealed a T > C transition in exon 8, causing a conservative substitution of Isoleucine to Tyrosine at codon 240. By protein structural modeling, we found the mutation may disrupt the hydrophobic core and destabilize the protein structure. We reviewed the literature and found that exons 2, 8, and 9 (11.4% of the sequence of FRMD7 mRNA) represent the majority (55.3%) of the reported FRMD7 mutations. In summary, we identified a novel mutation in FRMD7, showed its molecular consequence, and revealed the mutation-rich exons of the FRMD7 gene. Collectively, this provides molecular insights for future CN clinical genetic diagnosis and treatment.

Comparative study of the oxidation of NiAl(100) by molecular oxygen and water vapor using ambient-pressure X-ray photoelectron spectroscopy

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

Liu, Qianqian; Qin, Hailang; Boscoboinik, Jorge Anibal

The oxidation behavior of NiAl(100) by molecular oxygen and water vapor under a near-ambient pressure of 0.2 Torr is monitored using ambient-pressure X-ray photoelectron spectroscopy. O 2 exposure leads to the selective oxidation of Al at temperatures ranging from 40 to 500 °C. By contrast, H 2O exposure results in the selective oxidation of Al at 40 and 200 °C, and increasing the oxidation temperature above 300 °C leads to simultaneous formation of both Al and Ni oxides. Furthermore, these results demonstrate that the O 2 oxidation forms a nearly stoichiometric Al 2O 3 structure that provides improved protection tomore » the metallic substrate by barring the outward diffusion of metals. By contrast, the H 2O oxidation results in the formation of a defective oxide layer that allows outward diffusion of Ni at elevated temperatures for simultaneous NiO formation.« less

Genes, dreams, and cancer.

PubMed Central

Sikora, K.

1994-01-01

There have been tremendous advances in our understanding of cancer from the application of molecular biology over the past decade. The disease is caused by a series of defects in the genes that accelerate growth--oncogenes--and those that slow down cellular turnover--tumour suppressor genes. The proteins they encode provide a promising hunting ground in which to design and test new anticancer drugs. Several treatment strategies are now under clinical trial entailing direct gene transfer. These include the use of gene marking to detect minimal residual disease, the production of novel cancer vaccines by the insertion of genes which uncloak cancer cells so making them visible to the host's immune system, the isolation and coupling of cancer specific molecular switches upstream of drug activating genes, and the correction of aberrant oncogenes or tumour suppressor genes. The issues in these approaches are likely to have a profound impact on the management of cancer patients as we enter the next century. Images p1221-a PMID:8180542

Identifcation of a novel mutation p.I240T in the FRMD7 gene in a family with congenital nystagmus.

PubMed

Zhu, Yihua; Zhuang, Jianfu; Ge, Xianglian; Zhang, Xiao; Wang, Zheng; Sun, Ji; Yang, Juhua; Gu, Feng

2013-10-30

Congenital Nystagmus (CN) is a genetically heterogeneous ocular disease, which causes a significant proportion of childhood visual impairment. To identify the underlying genetic defect of a CN family, twenty-two members were recruited. Genotype analysis showed that affected individuals shared a common haplotype with markers flanking FRMD7 locus. Sequencing FRMD7 revealed a T > C transition in exon 8, causing a conservative substitution of Isoleucine to Tyrosine at codon 240. By protein structural modeling, we found the mutation may disrupt the hydrophobic core and destabilize the protein structure. We reviewed the literature and found that exons 2, 8, and 9 (11.4% of the sequence of FRMD7 mRNA) represent the majority (55.3%) of the reported FRMD7 mutations. In summary, we identified a novel mutation in FRMD7, showed its molecular consequence, and revealed the mutation-rich exons of the FRMD7 gene. Collectively, this provides molecular insights for future CN clinical genetic diagnosis and treatment.

Identifcation of a Novel Mutation p.I240T in the FRMD7 gene in a Family with Congenital Nystagmus

PubMed Central

Zhu, Yihua; Zhuang, Jianfu; Ge, Xianglian; Zhang, Xiao; Wang, Zheng; Sun, Ji; Yang, Juhua; Gu, Feng

2013-01-01

Congenital Nystagmus (CN) is a genetically heterogeneous ocular disease, which causes a significant proportion of childhood visual impairment. To identify the underlying genetic defect of a CN family, twenty-two members were recruited. Genotype analysis showed that affected individuals shared a common haplotype with markers flanking FRMD7 locus. Sequencing FRMD7 revealed a T > C transition in exon 8, causing a conservative substitution of Isoleucine to Tyrosine at codon 240. By protein structural modeling, we found the mutation may disrupt the hydrophobic core and destabilize the protein structure. We reviewed the literature and found that exons 2, 8, and 9 (11.4% of the sequence of FRMD7 mRNA) represent the majority (55.3%) of the reported FRMD7 mutations. In summary, we identified a novel mutation in FRMD7, showed its molecular consequence, and revealed the mutation-rich exons of the FRMD7 gene. Collectively, this provides molecular insights for future CN clinical genetic diagnosis and treatment. PMID:24169426

Mitochondrial AAA proteases--towards a molecular understanding of membrane-bound proteolytic machines.

PubMed

Gerdes, Florian; Tatsuta, Takashi; Langer, Thomas

2012-01-01

Mitochondrial AAA proteases play an important role in the maintenance of mitochondrial proteostasis. They regulate and promote biogenesis of mitochondrial proteins by acting as processing enzymes and ensuring the selective turnover of misfolded proteins. Impairment of AAA proteases causes pleiotropic defects in various organisms including neurodegeneration in humans. AAA proteases comprise ring-like hexameric complexes in the mitochondrial inner membrane and are functionally conserved from yeast to man, but variations are evident in the subunit composition of orthologous enzymes. Recent structural and biochemical studies revealed how AAA proteases degrade their substrates in an ATP dependent manner. Intersubunit coordination of the ATP hydrolysis leads to an ordered ATP hydrolysis within the AAA ring, which ensures efficient substrate dislocation from the membrane and translocation to the proteolytic chamber. In this review, we summarize recent findings on the molecular mechanisms underlying the versatile functions of mitochondrial AAA proteases and their relevance to those of the other AAA+ machines. Copyright © 2011 Elsevier B.V. All rights reserved.

Supercomplexes of the mitochondrial electron transport chain decline in the aging rat heart.

PubMed

Gómez, Luis A; Monette, Jeffrey S; Chavez, Juan D; Maier, Claudia S; Hagen, Tory M

2009-10-01

Accumulation of mitochondrial electron transport chain (ETC) defects is a recognized hallmark of the age-associated decline in cardiac bioenergetics; however, the molecular events involved are only poorly understood. In the present work, we hypothesized that age-related ETC deterioration stemmed partly from disassociation of large solid-state macromolecular assemblies termed "supercomplexes". Mitochondrial proteins from young and old rat hearts were separated by blue native-PAGE, protein bands analyzed by LC-MALDI-MS/MS, and protein levels quantified by densitometry. Results showed that supercomplexes comprised of various stoichiometries of complexes I, III and IV were observed, and declined significantly (p<0.05, n=4) with age. Supercomplexes displaying the highest molecular masses were the most severely affected. Considering that certain diseases (e.g. Barth Syndrome) display similar supercomplex destabilization as our results for aging, the deterioration in ETC supercomplexes may be an important underlying factor for both impaired mitochondrial function and loss of cardiac bioenergetics with age.

MD simulation of plastic deformation nucleation in stressed crystallites under irradiation

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

Korchuganov, A. V., E-mail: avkor@ispms.tsc.ru; Zolnikov, K. P., E-mail: kost@ispms.tsc.ru; Kryzhevich, D. S., E-mail: kryzhev@ispms.tsc.ru

2016-12-15

The investigation of plastic deformation nucleation in metals and alloys under irradiation and mechanical loading is one of the topical issues of materials science. Specific features of nucleation and evolution of the defect system in stressed and irradiated iron, vanadium, and copper crystallites were studied by molecular dynamics simulation. Mechanical loading was performed in such a way that the modeled crystallite volume remained unchanged. The energy of the primary knock-on atom initiating a cascade of atomic displacements in a stressed crystallite was varied from 0.05 to 50 keV. It was found that atomic displacement cascades might cause global structural transformationsmore » in a region far larger than the radiation-damaged area. These changes are similar to the ones occurring in the process of mechanical loading of samples. They are implemented by twinning (in iron and vanadium) or through the formation of partial dislocation loops (in copper).« less

Past, Present and Future Therapeutics for Cerebellar Ataxias

PubMed Central

Marmolino, D; Manto, M

2010-01-01

Cerebellar ataxias are a group of disabling neurological disorders. Patients exhibit a cerebellar syndrome and can also present with extra-cerebellar deficits, namely pigmentary retinopathy, extrapyramidal movement disorders, pyramidal signs, cortical symptoms (seizures, cognitive impairment/behavioural symptoms), and peripheral neuropathy. Recently, deficits in cognitive operations have been unraveled. Cerebellar ataxias are heterogeneous both at the phenotypic and genotypic point of view. Therapeutical trials performed during these last 4 decades have failed in most cases, in particular because drugs were not targeting a deleterious pathway, but were given to counteract putative defects in neurotransmission. The identification of the causative mutations of many hereditary ataxias, the development of relevant animal models and the recent identifications of the molecular mechanisms underlying ataxias are impacting on the development of new drugs. We provide an overview of the pharmacological treatments currently used in the clinical practice and we discuss the drugs under development. PMID:20808545

Single Crystals Grown Under Unconstrained Conditions

NASA Astrophysics Data System (ADS)

Sunagawa, Ichiro

Based on detailed investigations on morphology (evolution and variation in external forms), surface microtopography of crystal faces (spirals and etch figures), internal morphology (growth sectors, growth banding and associated impurity partitioning) and perfection (dislocations and other lattice defects) in single crystals, we can deduce how and by what mechanism the crystal grew and experienced fluctuation in growth parameters through its growth and post-growth history under unconstrained condition. The information is useful not only in finding appropriate way to growing highly perfect and homogeneous single crystals, but also in deciphering letters sent from the depth of the Earth and the Space. It is also useful in discriminating synthetic from natural gemstones. In this chapter, available methods to obtain molecular information are briefly summarized, and actual examples to demonstrate the importance of this type of investigations are selected from both natural minerals (diamond, quartz, hematite, corundum, beryl, phlogopite) and synthetic crystals (SiC, diamond, corundum, beryl).