Different structures formed at HII boundaries

NASA Astrophysics Data System (ADS)

Miao, Jingqi; Cornwall, Paul; Kinnear, Tim

2015-03-01

Hydrodynamic simulations on the evolution of molecular clouds (MCs) at HII boundaries are used to show that radiation driven implosion (RDI) model can create almost all of the different morphological structures, such as a single bright-rimmed cloud (BRC), fragment structure and multiple elephant trunk (ET) structures.

Fidelity of DNA Replication in Normal and Malignant Human Breast Cells.

DTIC Science & Technology

1997-08-01

enzyme) into the multiple cloning site (MCS). This template will not only replicate inside a mammalian cell (utilizing the E-B virus origin), and...Maniatis, T. Commonly used techniques in molecular cloning . In: Molecular cloning : REFERENCES a laboratory manual, 2nd edition. Cold Spring Harbor...A vatit"Y Of DNA synthesis and the typt of DNA replica~tion Products " celular prca including DNA rsplicatlon. DNA repsair. R~NA formed in experiments

Distributed Circuit Plasticity: New Clues for the Cerebellar Mechanisms of Learning.

PubMed

D'Angelo, Egidio; Mapelli, Lisa; Casellato, Claudia; Garrido, Jesus A; Luque, Niceto; Monaco, Jessica; Prestori, Francesca; Pedrocchi, Alessandra; Ros, Eduardo

2016-04-01

The cerebellum is involved in learning and memory of sensory motor skills. However, the way this process takes place in local microcircuits is still unclear. The initial proposal, casted into the Motor Learning Theory, suggested that learning had to occur at the parallel fiber-Purkinje cell synapse under supervision of climbing fibers. However, the uniqueness of this mechanism has been questioned, and multiple forms of long-term plasticity have been revealed at various locations in the cerebellar circuit, including synapses and neurons in the granular layer, molecular layer and deep-cerebellar nuclei. At present, more than 15 forms of plasticity have been reported. There has been a long debate on which plasticity is more relevant to specific aspects of learning, but this question turned out to be hard to answer using physiological analysis alone. Recent experiments and models making use of closed-loop robotic simulations are revealing a radically new view: one single form of plasticity is insufficient, while altogether, the different forms of plasticity can explain the multiplicity of properties characterizing cerebellar learning. These include multi-rate acquisition and extinction, reversibility, self-scalability, and generalization. Moreover, when the circuit embeds multiple forms of plasticity, it can easily cope with multiple behaviors endowing therefore the cerebellum with the properties needed to operate as an effective generalized forward controller.

Clear relationship between ETF/ETFDH genotype and phenotype in patients with multiple acyl-CoA dehydrogenation deficiency.

PubMed

Olsen, Rikke K J; Andresen, Brage S; Christensen, Ernst; Bross, Peter; Skovby, Flemming; Gregersen, Niels

2003-07-01

Mutations in electron transfer flavoprotein (ETF) and its dehydrogenase (ETFDH) are the molecular basis of multiple acyl-CoA dehydrogenation deficiency (MADD), an autosomal recessively inherited and clinically heterogeneous disease that has been divided into three clinical forms: a neonatal-onset form with congenital anomalies (type I), a neonatal-onset form without congenital anomalies (type II), and a late-onset form (type III). To examine whether these different clinical forms could be explained by different ETF/ETFDH mutations that result in different levels of residual ETF/ETFDH enzyme activity, we have investigated the molecular genetic basis for disease development in nine patients representing the phenotypic spectrum of MADD. We report the genomic structures of the ETFA, ETFB, and ETFDH genes and the identification and characterization of seven novel and three previously reported disease-causing mutations. Our molecular genetic investigations of these nine patients are consistent with three clinical forms of MADD showing a clear relationship between the nature of the mutations and the severity of disease. Interestingly, our data suggest that homozygosity for two null mutations causes fetal development of congenital anomalies resulting in a type I disease phenotype. Even minute amounts of residual ETF/ETFDH activity seem to be sufficient to prevent embryonic development of congenital anomalies giving rise to type II disease. Overexpression studies of an ETFB-D128N missense mutation identified in a patient with type III disease showed that the residual activity of the mutant enzyme could be rescued up to 59% of that of wild-type activity when ETFB-D128N-transformed E. coli cells were grown at low temperature. This indicates that the effect of the ETF/ETFDH genotype in patients with milder forms of MADD, in whom residual enzyme activity allows modulation of the enzymatic phenotype, may be influenced by environmental factors like cellular temperature. Copyright 2003 Wiley-Liss, Inc.

Correlated Heterospectral Lipidomics for Biomolecular Profiling of Remyelination in Multiple Sclerosis

PubMed Central

2017-01-01

Analyzing lipid composition and distribution within the brain is important to study white matter pathologies that present focal demyelination lesions, such as multiple sclerosis. Some lesions can endogenously re-form myelin sheaths. Therapies aim to enhance this repair process in order to reduce neurodegeneration and disability progression in patients. In this context, a lipidomic analysis providing both precise molecular classification and well-defined localization is crucial to detect changes in myelin lipid content. Here we develop a correlated heterospectral lipidomic (HSL) approach based on coregistered Raman spectroscopy, desorption electrospray ionization mass spectrometry (DESI-MS), and immunofluorescence imaging. We employ HSL to study the structural and compositional lipid profile of demyelination and remyelination in an induced focal demyelination mouse model and in multiple sclerosis lesions from patients ex vivo. Pixelwise coregistration of Raman spectroscopy and DESI-MS imaging generated a heterospectral map used to interrelate biomolecular structure and composition of myelin. Multivariate regression analysis enabled Raman-based assessment of highly specific lipid subtypes in complex tissue for the first time. This method revealed the temporal dynamics of remyelination and provided the first indication that newly formed myelin has a different lipid composition compared to normal myelin. HSL enables detailed molecular myelin characterization that can substantially improve upon the current understanding of remyelination in multiple sclerosis and provides a strategy to assess remyelination treatments in animal models. PMID:29392175

MOLECULAR MECHANISMS OF FEAR LEARNING AND MEMORY

PubMed Central

Johansen, Joshua P.; Cain, Christopher K.; Ostroff, Linnaea E.; LeDoux, Joseph E.

2011-01-01

Pavlovian fear conditioning is a useful behavioral paradigm for exploring the molecular mechanisms of learning and memory because a well-defined response to a specific environmental stimulus is produced through associative learning processes. Synaptic plasticity in the lateral nucleus of the amygdala (LA) underlies this form of associative learning. Here we summarize the molecular mechanisms that contribute to this synaptic plasticity in the context of auditory fear conditioning, the form of fear conditioning best understood at the molecular level. We discuss the neurotransmitter systems and signaling cascades that contribute to three phases of auditory fear conditioning: acquisition, consolidation, and reconsolidation. These studies suggest that multiple intracellular signaling pathways, including those triggered by activation of Hebbian processes and neuromodulatory receptors, interact to produce neural plasticity in the LA and behavioral fear conditioning. Together, this research illustrates the power of fear conditioning as a model system for characterizing the mechanisms of learning and memory in mammals, and potentially for understanding fear related disorders, such as PTSD and phobias. PMID:22036561

The c.301_302delAG PROP1 gene mutation in Romanian patients with multiple pituitary hormone deficiency.

PubMed

Lazea, Cecilia; Grigorescu-Sido, Paula; Popp, Radu; Legendre, Marie; Amselem, Serge; Al-Khzouz, Camelia; Bucerzan, Simona; Creţ, Victoria; Crişan, Mirela; Brad, Cristian

2015-09-01

To establish the frequency of the c.301_302 delAG mutation of the PROP1 gene in Romanian patients with multiple pituitary hormone deficiency (MPHD). Somatic assessment, hormonal test, bone age, magnetic resonance imaging of the pituitary gland, and molecular diagnosis were performed in 26 patients with MPHD (7 patients with familial form of MPHD and 19 patients with sporadic form of MPHD). The c.301_302delAG mutation was detected in the homozygous state in 10 patients belonging to 5 unrelated families (7 patients with familial history of MPHD and 3 patients with sporadic form of MPHD). Those 10 patients presented variable pituitary hormone deficiency and pituitary morphology. The c.301_302delAG homozygous genotype had a high frequency of 38% (10/26), reaching 100% (7/7) in group with familial cases of MPHD and 16% (3/19) in group with sporadic forms of MPHD.

Disentangling the multigenic and pleiotropic nature of molecular function

PubMed Central

2015-01-01

Background Biological processes at the molecular level are usually represented by molecular interaction networks. Function is organised and modularity identified based on network topology, however, this approach often fails to account for the dynamic and multifunctional nature of molecular components. For example, a molecule engaging in spatially or temporally independent functions may be inappropriately clustered into a single functional module. To capture biologically meaningful sets of interacting molecules, we use experimentally defined pathways as spatial/temporal units of molecular activity. Results We defined functional profiles of Saccharomyces cerevisiae based on a minimal set of Gene Ontology terms sufficient to represent each pathway's genes. The Gene Ontology terms were used to annotate 271 pathways, accounting for pathway multi-functionality and gene pleiotropy. Pathways were then arranged into a network, linked by shared functionality. Of the genes in our data set, 44% appeared in multiple pathways performing a diverse set of functions. Linking pathways by overlapping functionality revealed a modular network with energy metabolism forming a sparse centre, surrounded by several denser clusters comprised of regulatory and metabolic pathways. Signalling pathways formed a relatively discrete cluster connected to the centre of the network. Genetic interactions were enriched within the clusters of pathways by a factor of 5.5, confirming the organisation of our pathway network is biologically significant. Conclusions Our representation of molecular function according to pathway relationships enables analysis of gene/protein activity in the context of specific functional roles, as an alternative to typical molecule-centric graph-based methods. The pathway network demonstrates the cooperation of multiple pathways to perform biological processes and organises pathways into functionally related clusters with interdependent outcomes. PMID:26678917

XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes

PubMed Central

Blinov, Michael L.; Moraru, Ion I.

2011-01-01

Multi-state molecules and multi-component complexes are commonly involved in cellular signaling. Accounting for molecules that have multiple potential states, such as a protein that may be phosphorylated on multiple residues, and molecules that combine to form heterogeneous complexes located among multiple compartments, generates an effect of combinatorial complexity. Models involving relatively few signaling molecules can include thousands of distinct chemical species. Several software tools (StochSim, BioNetGen) are already available to deal with combinatorial complexity. Such tools need information standards if models are to be shared, jointly evaluated and developed. Here we discuss XML conventions that can be adopted for modeling biochemical reaction networks described by user-specified reaction rules. These could form a basis for possible future extensions of the Systems Biology Markup Language (SBML). PMID:21464833

Intra-amoeba multiplication induces chemotaxis and biofilm colonization and formation for Legionella.

PubMed

Bigot, Renaud; Bertaux, Joanne; Frere, Jacques; Berjeaud, Jean-Marc

2013-01-01

Legionella pneumophila, a facultative intracellular bacterium, is the causative agent of legionellosis. In the environment this pathogenic bacterium colonizes the biofilms as well as amoebae, which provide a rich environment for the replication of Legionella. When seeded on pre-formed biofilms, L. pneumophila was able to establish and survive and was only found at the surface of the biofilms. Different phenotypes were observed when the L. pneumophila, used to implement pre-formed biofilms or to form mono-species biofilms, were cultivated in a laboratory culture broth or had grown intracellulary within the amoeba. Indeed, the bacteria, which developed within the amoeba, formed clusters when deposited on a solid surface. Moreover, our results demonstrate that multiplication inside the amoeba increased the capacity of L. pneumophila to produce polysaccharides and therefore enhanced its capacity to establish biofilms. Finally, it was shown that the clusters formed by L. pneumophila were probably related to the secretion of a chemotaxis molecular agent.

Intra-Amoeba Multiplication Induces Chemotaxis and Biofilm Colonization and Formation for Legionella

PubMed Central

Bigot, Renaud; Bertaux, Joanne; Frere, Jacques; Berjeaud, Jean-Marc

2013-01-01

Legionella pneumophila, a facultative intracellular bacterium, is the causative agent of legionellosis. In the environment this pathogenic bacterium colonizes the biofilms as well as amoebae, which provide a rich environment for the replication of Legionella. When seeded on pre-formed biofilms, L. pneumophila was able to establish and survive and was only found at the surface of the biofilms. Different phenotypes were observed when the L. pneumophila, used to implement pre-formed biofilms or to form mono-species biofilms, were cultivated in a laboratory culture broth or had grown intracellulary within the amoeba. Indeed, the bacteria, which developed within the amoeba, formed clusters when deposited on a solid surface. Moreover, our results demonstrate that multiplication inside the amoeba increased the capacity of L. pneumophila to produce polysaccharides and therefore enhanced its capacity to establish biofilms. Finally, it was shown that the clusters formed by L. pneumophila were probably related to the secretion of a chemotaxis molecular agent. PMID:24205008

Optical properties and carrier dynamics of GaAs/GaInAs multiple-quantum-well shell grown on GaAs nanowire by molecular beam epitaxy

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

Park, Kwangwook; Ravindran, Sooraj; Ju, Gun Wu

GaAs/GaInAs multiple-quantum-well (MQW) shells having different GaInAs shell width formed on the surface of self-catalyzed GaAs core nanowires (NWs) are grown on (100) Si substrate using molecular beam epitaxy. The photoluminescence emission from GaAs/GaInAs MQW shells and the carrier lifetime could be varied by changing the width of GaInAs shell. Time-resolved photoluminescence measurements showed that the carrier lifetime had a fast and slow decay owing to the mixing of wurtzite and zinc-blende structures of the NWs. Furthermore, strain relaxation caused the carrier lifetime to decrease beyond a certain thickness of GaInAs quantum well shells.

Protein Phosphatase 1-Dependent Transcriptional Programs for Long-Term Memory and Plasticity

ERIC Educational Resources Information Center

Graff, Johannes; Koshibu, Kyoko; Jouvenceau, Anne; Dutar, Patrick; Mansuy, Isabelle M.

2010-01-01

Gene transcription is essential for the establishment and the maintenance of long-term memory (LTM) and for long-lasting forms of synaptic plasticity. The molecular mechanisms that control gene transcription in neuronal cells are complex and recruit multiple signaling pathways in the cytoplasm and the nucleus. Protein kinases (PKs) and…

A Nonequilibrium Rate Formula for Collective Motions of Complex Molecular Systems

NASA Astrophysics Data System (ADS)

Yanao, Tomohiro; Koon, Wang Sang; Marsden, Jerrold E.

2010-09-01

We propose a compact reaction rate formula that accounts for a non-equilibrium distribution of residence times of complex molecules, based on a detailed study of the coarse-grained phase space of a reaction coordinate. We take the structural transition dynamics of a six-atom Morse cluster between two isomers as a prototype of multi-dimensional molecular reactions. Residence time distribution of one of the isomers shows an exponential decay, while that of the other isomer deviates largely from the exponential form and has multiple peaks. Our rate formula explains such equilibrium and non-equilibrium distributions of residence times in terms of the rates of diffusions of energy and the phase of the oscillations of the reaction coordinate. Rapid diffusions of energy and the phase generally give rise to the exponential decay of residence time distribution, while slow diffusions give rise to a non-exponential decay with multiple peaks. We finally make a conjecture about a general relationship between the rates of the diffusions and the symmetry of molecular mass distributions.

Molecular interactions in gelatin/chitosan composite films.

PubMed

Qiao, Congde; Ma, Xianguang; Zhang, Jianlong; Yao, Jinshui

2017-11-15

Gelatin and chitosan were mixed at different mass ratios in solution forms, and the rheological properties of these film-forming solutions, upon cooling, were studied. The results indicate that the significant interactions between gelatin and chitosan promote the formation of multiple complexes, reflected by an increase in the storage modulus of gelatin solution. Furthermore, these molecular interactions hinder the formation of gelatin networks, consequently decreasing the storage modulus of polymer gels. Both hydrogen bonds and electrostatic interactions are formed between gelatin and chitosan, as evidenced by the shift of the amide-II bands of polymers. X-ray patterns of composite films indicate that the contents of triple helices decrease with increasing chitosan content. Only one glass transition temperature (T g ) was observed in composite films with different composition ratios, and it decreases gradually with an increase in chitosan proportion, indicating that gelatin and chitosan have good miscibility and form a wide range of blends. Copyright © 2017 Elsevier Ltd. All rights reserved.

Arc in synaptic plasticity: from gene to behavior

PubMed Central

Korb, Erica; Finkbeiner, Steven

2011-01-01

The activity-regulated cytoskeletal (Arc) gene encodes a protein that is critical for memory consolidation. Arc is one of the most tightly regulated molecules known: neuronal activity controls Arc mRNA induction, trafficking, and accumulation, and Arc protein production, localization and stability. Arc regulates synaptic strength through multiple mechanisms and is involved in essentially every known form of synaptic plasticity. It also mediates memory formation and is implicated in multiple neurological diseases. In this review, we will discuss how Arc is regulated and used as a tool to study neuronal activity. We will also attempt to clarify how its molecular functions correspond to its requirement for various forms of plasticity, discuss Arc’s role in behavior and disease, and highlight critical unresolved questions. PMID:21963089

Molecular mechanisms of fear learning and memory.

PubMed

Johansen, Joshua P; Cain, Christopher K; Ostroff, Linnaea E; LeDoux, Joseph E

2011-10-28

Pavlovian fear conditioning is a particularly useful behavioral paradigm for exploring the molecular mechanisms of learning and memory because a well-defined response to a specific environmental stimulus is produced through associative learning processes. Synaptic plasticity in the lateral nucleus of the amygdala (LA) underlies this form of associative learning. Here, we summarize the molecular mechanisms that contribute to this synaptic plasticity in the context of auditory fear conditioning, the form of fear conditioning best understood at the molecular level. We discuss the neurotransmitter systems and signaling cascades that contribute to three phases of auditory fear conditioning: acquisition, consolidation, and reconsolidation. These studies suggest that multiple intracellular signaling pathways, including those triggered by activation of Hebbian processes and neuromodulatory receptors, interact to produce neural plasticity in the LA and behavioral fear conditioning. Collectively, this body of research illustrates the power of fear conditioning as a model system for characterizing the mechanisms of learning and memory in mammals and potentially for understanding fear-related disorders, such as PTSD and phobias. Copyright © 2011 Elsevier Inc. All rights reserved.

High-capacity and security molecular capsule transporters.

PubMed

Visessamit, Jakkapol; Kulsirirat, Kathawut; Yupapin, Preecha P

2015-01-01

Multiwavelength optical capsules can be generated and controlled by using soliton/Gaussian pulses within a nonlinear device system known as a "PANDA" ring circuit and system. The security of molecule/drug transportation can be formed by the strong coupling of soliton-like pulse, where the high-capacity optical capsules can be formed using the multiwavelength solitons, which can be a good advantage and combination of drug delivery to the required targets. Moreover, the multiple access of drug delivery can be formed using the optical networks, which allows the use of various drug molecules with variety of diagnosis and therapeutic applications.

Generalizing genetical genomics: getting added value from environmental perturbation.

PubMed

Li, Yang; Breitling, Rainer; Jansen, Ritsert C

2008-10-01

Genetical genomics is a useful approach for studying the effect of genetic perturbations on biological systems at the molecular level. However, molecular networks depend on the environmental conditions and, thus, a comprehensive understanding of biological systems requires studying them across multiple environments. We propose a generalization of genetical genomics, which combines genetic and sensibly chosen environmental perturbations, to study the plasticity of molecular networks. This strategy forms a crucial step toward understanding why individuals respond differently to drugs, toxins, pathogens, nutrients and other environmental influences. Here we outline a strategy for selecting and allocating individuals to particular treatments, and we discuss the promises and pitfalls of the generalized genetical genomics approach.

Evidence for nucleosynthetic enrichment of the protosolar molecular cloud core by multiple supernova events.

PubMed

Schiller, Martin; Paton, Chad; Bizzarro, Martin

2015-01-15

The presence of isotope heterogeneity of nucleosynthetic origin amongst meteorites and their components provides a record of the diverse stars that contributed matter to the protosolar molecular cloud core. Understanding how and when the solar system's nucleosynthetic heterogeneity was established and preserved within the solar protoplanetary disk is critical for unraveling the earliest formative stages of the solar system. Here, we report calcium and magnesium isotope measurements of primitive and differentiated meteorites as well as various types of refractory inclusions, including refractory inclusions (CAIs) formed with the canonical 26 Al/ 27 Al of ~5 × 10 -5 ( 26 Al decays to 26 Mg with a half-life of ~0.73 Ma) and CAIs that show fractionated and unidentified nuclear effects (FUN-CAIs) to understand the origin of the solar system's nucleosynthetic heterogeneity. Bulk analyses of primitive and differentiated meteorites along with canonical and FUN-CAIs define correlated, mass-independent variations in 43 Ca, 46 Ca and 48 Ca. Moreover, sequential dissolution experiments of the Ivuna carbonaceous chondrite aimed at identifying the nature and number of presolar carriers of isotope anomalies within primitive meteorites have detected the presence of multiple carriers of the short-lived 26 Al nuclide as well as carriers of anomalous and uncorrelated 43 Ca, 46 Ca and 48 Ca compositions, which requires input from multiple and recent supernovae sources. We infer that the solar system's correlated nucleosynthetic variability reflects unmixing of old, galactically-inherited homogeneous dust from a new, supernovae-derived dust component formed shortly prior to or during the evolution of the giant molecular cloud parental to the protosolar molecular cloud core. This implies that similarly to 43 Ca, 46 Ca and 48 Ca, the short-lived 26 Al nuclide was heterogeneously distributed in the inner solar system at the time of CAI formation.

Comparative genomics and evolution of eukaryotic phospholipidbiosynthesis

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

Lykidis, Athanasios

2006-12-01

Phospholipid biosynthetic enzymes produce diverse molecular structures and are often present in multiple forms encoded by different genes. This work utilizes comparative genomics and phylogenetics for exploring the distribution, structure and evolution of phospholipid biosynthetic genes and pathways in 26 eukaryotic genomes. Although the basic structure of the pathways was formed early in eukaryotic evolution, the emerging picture indicates that individual enzyme families followed unique evolutionary courses. For example, choline and ethanolamine kinases and cytidylyltransferases emerged in ancestral eukaryotes, whereas, multiple forms of the corresponding phosphatidyltransferases evolved mainly in a lineage specific manner. Furthermore, several unicellular eukaryotes maintain bacterial-type enzymesmore » and reactions for the synthesis of phosphatidylglycerol and cardiolipin. Also, base-exchange phosphatidylserine synthases are widespread and ancestral enzymes. The multiplicity of phospholipid biosynthetic enzymes has been largely generated by gene expansion in a lineage specific manner. Thus, these observations suggest that phospholipid biosynthesis has been an actively evolving system. Finally, comparative genomic analysis indicates the existence of novel phosphatidyltransferases and provides a candidate for the uncharacterized eukaryotic phosphatidylglycerol phosphate phosphatase.« less

Vibration-translation energy transfer in anharmonic diatomic molecules. 2: The vibrational quantum number dependence

NASA Technical Reports Server (NTRS)

Mckenzie, R. L.

1975-01-01

A semiclassical model of the inelastic collision between a vibrationally excited anharmonic oscillator and a structureless atom was used to predict the variation of thermally averaged vibration-translation rate coefficients with temperature and initial-state quantum number. Multiple oscillator states were included in a numerical solution for collinear encounters. The results are compared with CO-He experimental values for both ground and excited initial states using several simplified forms of the interaction potential. The numerical model was also used as a basis for evaluating several less complete but analytic models. Two computationally simple analytic approximations were found that successfully reproduced the numerical rate coefficients for a wide range of molecular properties and collision partners. Their limitations were also identified. The relative rates of multiple-quantum transitions from excited states were evaluated for several molecular types.

On the molecular basis of the receptor mosaic hypothesis of the engram.

PubMed

Agnati, Luigi F; Ferré, Sergi; Leo, Giuseppina; Lluis, Carme; Canela, Enric I; Franco, Rafael; Fuxe, Kjell

2004-08-01

1. This paper revisits the so-called "receptor mosaic hypothesis" for memory trace formation in the light of recent findings in "functional (or interaction) proteomics." The receptor mosaic hypothesis maintains that receptors may form molecular aggregates at the plasma membrane level representing part of the computational molecular networks. 2. Specific interactions between receptors occur as a consequence of the pattern of transmitter release from the source neurons, which release the chemical code impinging on the receptor mosaics of the target neuron. Thus, the decoding of the chemical message depends on the receptors forming the receptor mosaics and on the type of interactions among receptors and other proteins in the molecular network with novel long-term mosaics formed by their stabilization via adapter proteins formed in target neurons through the incoming neurotransmitter code. The internalized receptor heteromeric complexes or parts of them may act as transcription factors for the formation of such adapter proteins. 3. Receptor mosaics are formed both at the pre- and postsynaptic level of the plasma membranes and this phenomenon can play a role in the Hebbian behavior of some synaptic contacts. The appropriate "matching" of the pre- with the postsynaptic receptor mosaic can be thought of as the "clamping of the synapse to the external teaching signal." According to our hypothesis the behavior of the molecular networks at plasma membrane level to which the receptor mosaics belong can be set in a "frozen" conformation (i.e. in a frozen functional state) and this may represent a mechanism to maintain constant the input to a neuron. 4. Thus, we are suggesting that molecular networks at plasma membrane level may display multiple "attractors" each of which stores the memory of a specific neurotransmitter code due to a unique firing pattern. Hence, this mechanism may play a role in learning processes where the input to a neuron is likely to remain constant for a while.

High Molecular Weight Complex Analysis of Epstein-Barr Virus Latent Membrane Protein 1 (LMP-1): Structural Insights into LMP-1’s Homo-Oligomerization and Lipid Raft Association

PubMed Central

Wrobel, Christopher M.; Geiger, Timothy R.; Nix, Rebecca N.; Robitaille, Aaron M.; Balser, Sandra; Cervantes, Alfredo; Gonzalez, Miguel; Martin, Jennifer M.

2013-01-01

LMP-1 is a constitutively active Tumor Necrosis Factor Receptor analog encoded by Epstein-Barr virus. LMP-1 activation correlates with oligomerization and raft localization, but direct evidence of LMP-1 oligomers is limited. We report that LMP-1 forms multiple high molecular weight native LMP-1 complexes when analyzed by BN-PAGE, the largest of which are enriched in detergent resistant membranes. The largest of these high molecular weight complexes are not formed by purified LMP-1 or by loss of function LMP-1 mutants. Consistent with these results we find a dimeric form of LMP-1 that can be stabilized by disulfide crosslinking. We identify cysteine 238 in the C-terminus of LMP-1 as the crosslinked cysteine. Disulfide crosslinking occurs post-lysis but the dimer can be crosslinked in intact cells with membrane permeable crosslinkers. LMP-1/C238A retains wild type LMP-1 NF-κB activity. LMP-1’s TRAF binding, raft association and oligomerization are associated with the dimeric form of LMP-1. Our results suggest the possibility that the observed dimeric species results from inter-oligomeric crosslinking of LMP-1 molecules in adjacent core LMP-1 oligomers. PMID:24075898

Formation of ultra-compact dwarf galaxies from supergiant molecular clouds

NASA Astrophysics Data System (ADS)

Goodman, Morgan; Bekki, Kenji

2018-05-01

The origin of ultra-compact dwarf galaxies (UCDs) is not yet clear. One possible formation path of UCDs is the threshing of a nucleated elliptical dwarf galaxy (dE, N), however, it remains unclear how such massive nuclear stellar systems were formed in dwarf galaxies. To better establish the early history of UCDs, we investigate the formation of UCD progenitor clusters from super giant molecular clouds (SGMCs), using hydrodynamical simulations. In this study we focus on SGMCs with masses 107 - 108 M_{\\odot } that can form massive star clusters that display physical properties similar to UCDs. We find that the clusters have extended star formation histories with two phases, producing multiple distinct stellar populations, and that the star formation rate is dependent on the feedback effects of SNe and AGB stars. The later generations of stars formed in these clusters are more compact, leading to a clearly nested structure, and these stars will be more He-rich than those of the first generation, leading to a slight colour gradient. The simulated clusters demonstrate scaling relations between Reff and M and σv and M consistent with those observed in UCDs and strongly consistent with those of the original SGMC. We discuss whether SGMCs such as these can be formed through merging of self-gravitating molecular clouds in galaxies at high-z.

Technological Innovations for High-Throughput Approaches to In Vitro Allergy Diagnosis.

PubMed

Chapman, Martin D; Wuenschmann, Sabina; King, Eva; Pomés, Anna

2015-07-01

Allergy diagnostics is being transformed by the advent of in vitro IgE testing using purified allergen molecules, combined with multiplex technology and biosensors, to deliver discriminating, sensitive, and high-throughput molecular diagnostics at the point of care. Essential elements of IgE molecular diagnostics are purified natural or recombinant allergens with defined purity and IgE reactivity, planar or bead-based multiplex systems to enable IgE to multiple allergens to be measured simultaneously, and, most recently, nanotechnology-based biosensors that facilitate rapid reaction rates and delivery of test results via mobile devices. Molecular diagnostics relies on measurement of IgE to purified allergens, the "active ingredients" of allergenic extracts. Typically, this involves measuring IgE to multiple allergens which is facilitated by multiplex technology and biosensors. The technology differentiates between clinically significant cross-reactive allergens (which could not be deduced by conventional IgE assays using allergenic extracts) and provides better diagnostic outcomes. Purified allergens are manufactured under good laboratory practice and validated using protein chemistry, mass spectrometry, and IgE antibody binding. Recently, multiple allergens (from dog) were expressed as a single molecule with high diagnostic efficacy. Challenges faced by molecular allergy diagnostic companies include generation of large panels of purified allergens with known diagnostic efficacy, access to flexible and robust array or sensor technology, and, importantly, access to well-defined serum panels form allergic patients for product development and validation. Innovations in IgE molecular diagnostics are rapidly being brought to market and will strengthen allergy testing at the point of care.

Water condensation: a multiscale phenomenon.

PubMed

Jensen, Kasper Risgaard; Fojan, Peter; Jensen, Rasmus Lund; Gurevich, Leonid

2014-02-01

The condensation of water is a phenomenon occurring in multiple situations in everyday life, e.g., when fog is formed or when dew forms on the grass or on windows. This means that this phenomenon plays an important role within the different fields of science including meteorology, building physics, and chemistry. In this review we address condensation models and simulations with the main focus on heterogeneous condensation of water. The condensation process is, at first, described from a thermodynamic viewpoint where the nucleation step is described by the classical nucleation theory. Further, we address the shortcomings of the thermodynamic theory in describing the nucleation and emphasize the importance of nanoscale effects. This leads to the description of condensation from a molecular viewpoint. Also presented is how the nucleation can be simulated by use of molecular models, and how the condensation process is simulated on the macroscale using computational fluid dynamics. Finally, examples of hybrid models combining molecular and macroscale models for the simulation of condensation on a surface are presented.

On the structure and functions of gelatinase B/matrix metalloproteinase-9 in neuroinflammation.

PubMed

Vandooren, Jennifer; Van Damme, Jo; Opdenakker, Ghislain

2014-01-01

The blood-brain barrier (BBB) is a specific structure that is composed of two basement membranes (BMs) and that contributes to the control of neuroinflammation. As long as the BBB is intact, extravasated leukocytes may accumulate between two BMs, generating vascular cuffs. Specific matrix metalloproteinases, MMP-2 and MMP-9, have been shown to cleave BBB beta-dystroglycan and to disintegrate thereby the parenchymal BM, resulting in encephalomyelitis. This knowledge has been added to the molecular basis of the REGA model to understand the pathogenesis of multiple sclerosis, and it gives further ground for the use of MMP inhibitors for the treatment of acute neuroinflammation. MMP-9 is associated with central nervous system inflammation and occurs in various forms: monomers and multimers. None of the various neurological and neuropathologic functions of MMP-9 have been associated with either molecular structure or molecular form, and therefore, in-depth structure-function studies are needed before medical intervention with MMP-9-specific inhibitors is initiated.

GBT Observations of the Star-Forming Regions DR21 and MonR2 with the new Argus Instrument

NASA Astrophysics Data System (ADS)

Linville, Dylan; Frayer, David; Cunningham, Nichol; Maddalena, Ronald

2018-01-01

We present GBT molecular line observations of DR21 and MonR2 with the new 16 element 75--115 GHz Argus instrument. Both molecular cloud complexes are associated with regions of high-mass star formation. We present the results of our 13CO, C18O, and HCO+ observations. Both MonR2 and DR21 show multiple velocity components, and the data suggest that the core of MonR2 is collapsing, while DR21 contains a region with a strong outflow traced by HCO+.

Multifunctional thin film surface

DOEpatents

Brozik, Susan M.; Harper, Jason C.; Polsky, Ronen; Wheeler, David R.; Arango, Dulce C.; Dirk, Shawn M.

2015-10-13

A thin film with multiple binding functionality can be prepared on an electrode surface via consecutive electroreduction of two or more aryl-onium salts with different functional groups. This versatile and simple method for forming multifunctional surfaces provides an effective means for immobilization of diverse molecules at close proximities. The multifunctional thin film has applications in bioelectronics, molecular electronics, clinical diagnostics, and chemical and biological sensing.

Multiple generations of grain aggregation in different environments preceded solar system body formation.

PubMed

Ishii, Hope A; Bradley, John P; Bechtel, Hans A; Brownlee, Donald E; Bustillo, Karen C; Ciston, James; Cuzzi, Jeffrey N; Floss, Christine; Joswiak, David J

2018-06-26

The solar system formed from interstellar dust and gas in a molecular cloud. Astronomical observations show that typical interstellar dust consists of amorphous ( a -) silicate and organic carbon. Bona fide physical samples for laboratory studies would yield unprecedented insight about solar system formation, but they were largely destroyed. The most likely repositories of surviving presolar dust are the least altered extraterrestrial materials, interplanetary dust particles (IDPs) with probable cometary origins. Cometary IDPs contain abundant submicron a- silicate grains called GEMS (glass with embedded metal and sulfides), believed to be carbon-free. Some have detectable isotopically anomalous a- silicate components from other stars, proving they are preserved dust inherited from the interstellar medium. However, it is debated whether the majority of GEMS predate the solar system or formed in the solar nebula by condensation of high-temperature (>1,300 K) gas. Here, we map IDP compositions with single nanometer-scale resolution and find that GEMS contain organic carbon. Mapping reveals two generations of grain aggregation, the key process in growth from dust grains to planetesimals, mediated by carbon. GEMS grains, some with a- silicate subgrains mantled by organic carbon, comprise the earliest generation of aggregates. These aggregates (and other grains) are encapsulated in lower-density organic carbon matrix, indicating a second generation of aggregation. Since this organic carbon thermally decomposes above ∼450 K, GEMS cannot have accreted in the hot solar nebula, and formed, instead, in the cold presolar molecular cloud and/or outer protoplanetary disk. We suggest that GEMS are consistent with surviving interstellar dust, condensed in situ, and cycled through multiple molecular clouds. Copyright © 2018 the Author(s). Published by PNAS.

Investigating charge generation in polymer:non-fullerene acceptor bulk heterojunction films

DOE PAGES

Stoltzfus, Dani M.; Larson, Bryon W.; Zarrabi, Nasim; ...

2018-01-31

Non-fullerene acceptors are now capable of being used in high efficiency bulk heterojunction (BHJ) donor-acceptor organic solar cells. Acceptors comprising single or multiple linked chromophores have been used. We have developed a new non-fullerene molecular acceptor as well as two non-polymeric macromolecular materials that contain four equivalents of a similar chromophore, but can adopt different spatial arrangements of the chromophores. We compare the effect of having single and multiple chromophores within a macromolecule on the charge generation processes in P3HT:non-fullerene acceptor BHJ films using Transient Absorption Spectroscopy (TAS) and Time Resolved Microwave Conductivity (TRMC) measurements. It was found from themore » TAS measurements that at low weight percent (5 wt%) the single chromophore formed more polarons than the acceptors in which chromophores were linked, due to it having a more even distribution within the film. At higher concentrations (50 wt%) the trend was reversed due to the single chromophore forming crystalline domains, which reduced the interface area with the P3HT donor. The TRMC measurements showed that more mobile carriers were formed in the macromolecular acceptors when used at low concentrations in the blend and, independent of concentration, mobile carriers had a longer lifetime when compared to films containing the molecular material, which we ascribe to the charges being able to sample more than one chromophore and thus reduce recombination events.« less

Communication: Dominance of extreme statistics in a prototype many-body Brownian ratchet.

PubMed

Hohlfeld, Evan; Geissler, Phillip L

2014-10-28

Many forms of cell motility rely on Brownian ratchet mechanisms that involve multiple stochastic processes. We present a computational and theoretical study of the nonequilibrium statistical dynamics of such a many-body ratchet, in the specific form of a growing polymer gel that pushes a diffusing obstacle. We find that oft-neglected correlations among constituent filaments impact steady-state kinetics and significantly deplete the gel's density within molecular distances of its leading edge. These behaviors are captured quantitatively by a self-consistent theory for extreme fluctuations in filaments' spatial distribution.

Formation of polycyclic lactones through a ruthenium-catalyzed ring-closing metathesis/hetero-Pauson-Khand reaction sequence.

PubMed

Finnegan, David F; Snapper, Marc L

2011-05-20

Processes that form multiple carbon-carbon bonds in one operation can generate molecular complexity quickly and therefore be used to shorten syntheses of desirable molecules. We selected the hetero-Pauson-Khand (HPK) cycloaddition and ring-closing metathesis (RCM) as two unique carbon-carbon bond-forming reactions that could be united in a tandem ruthenium-catalyzed process. In doing so, complex polycyclic products can be obtained in one reaction vessel from acyclic precursors using a single ruthenium additive that can catalyze sequentially two mechanistically distinct transformations.

Brownian Dynamics and Molecular Dynamics Study of the Association between Hydrogenase and Ferredoxin from Chlamydomonas reinhardtii

PubMed Central

Long, Hai; Chang, Christopher H.; King, Paul W.; Ghirardi, Maria L.; Kim, Kwiseon

2008-01-01

The [FeFe] hydrogenase from the green alga Chlamydomonas reinhardtii can catalyze the reduction of protons to hydrogen gas using electrons supplied from photosystem I and transferred via ferredoxin. To better understand the association of the hydrogenase and the ferredoxin, we have simulated the process over multiple timescales. A Brownian dynamics simulation method gave an initial thorough sampling of the rigid-body translational and rotational phase spaces, and the resulting trajectories were used to compute the occupancy and free-energy landscapes. Several important hydrogenase-ferredoxin encounter complexes were identified from this analysis, which were then individually simulated using atomistic molecular dynamics to provide more details of the hydrogenase and ferredoxin interaction. The ferredoxin appeared to form reasonable complexes with the hydrogenase in multiple orientations, some of which were good candidates for inclusion in a transition state ensemble of configurations for electron transfer. PMID:18621810

Multiple isoelectric forms of poliovirus RNA-dependent RNA polymerase: Evidence for phosphorylation

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

Ransone, L.J.; Dasgupta, A.

1989-11-01

Poliovirus-specific RNA-dependent RNA polymerase (3Dpol) was purified to apparent homogeneity. A single polypeptide of an apparent molecular weight of 63,000 catalyzes the synthesis of dimeric and monomeric RNA products in response to the poliovirion RNA template. Analysis of purified 3Dpol by two-dimensional electrophoresis showed multiple forms of 3Dpol, suggesting posttranslational modification of the protein in virus-infected cells. The two major forms of 3Dpol appear to have approximate pI values of 7.1 and 7.4. Incubation of purified 3Dpol with calf intestinal phosphatase resulted in almost complete disappearance of the pI 7.1 form and a concomitant increase in the intensity of themore » pI 7.4 form of 3Dpol. Addition of 32P-labeled Pi during infection of HeLa cells with poliovirus resulted in specific labeling of 3Dpol and 3CD, a viral protein which contains the entire 3Dpol sequence. Both 3Dpol and 3CD appear to be phosphorylated at serine residues. Ribosomal salt washes prepared from both mock- and poliovirus-infected cells contain phosphatases capable of dephosphorylating quantitatively the phosphorylated form (pI 7.1) of 3Dpol.« less

A Triple Protostar System in L1448 IRS3B Formed via Fragmentation of a Gravitationally Unstable Disk

NASA Astrophysics Data System (ADS)

Tobin, John J.; Kratter, Kaitlin M.; Persson, Magnus; Looney, Leslie; Dunham, Michael; Segura-Cox, Dominique; Li, Zhi-Yun; Chandler, Claire J.; Sadavoy, Sarah; Harris, Robert J.; Melis, Carl; Perez, Laura M.

2017-01-01

Binary and multiple star systems are a frequent outcome of the star formation process; most stars form as part of a binary/multiple protostar system. A possible pathway to the formation of close (< 500 AU) binary/multiple star systems is fragmentation of a massive protostellar disk due to gravitational instability. We observed the triple protostar system L1448 IRS3B with ALMA at 1.3 mm in dust continuum and molecular lines to determine if this triple protostar system, where all companions are separated by < 200 AU, is likely to have formed via disk fragmentation. From the dust continuum emission, we find a massive, 0.39 solar mass disk surrounding the three protostars with spiral structure. The disk is centered on two protostars that are separated by 61 AU and the third protostar is located in the outer disk at 183 AU. The tertiary companion is coincident with a spiral arm, and it is the brightest source of emission in the disk, surrounded by ~0.09 solar masses of disk material. Molecular line observations from 13CO and C18O confirm that the kinematic center of mass is coincident with the two central protostars and that the disk is consistent with being in Keplerian rotation; the combined mass of the two close protostars is ~1 solar mass. We demonstrate that the disk around L1448 IRS3B remains marginally unstable at radii between 150~AU and 320~AU, overlapping with the location of the tertiary protostar. This is consistent with models for a protostellar disk that has recently undergone gravitational instability, spawning the companion stars.

Neuron-Like Networks Between Ribosomal Proteins Within the Ribosome

NASA Astrophysics Data System (ADS)

Poirot, Olivier; Timsit, Youri

2016-05-01

From brain to the World Wide Web, information-processing networks share common scale invariant properties. Here, we reveal the existence of neural-like networks at a molecular scale within the ribosome. We show that with their extensions, ribosomal proteins form complex assortative interaction networks through which they communicate through tiny interfaces. The analysis of the crystal structures of 50S eubacterial particles reveals that most of these interfaces involve key phylogenetically conserved residues. The systematic observation of interactions between basic and aromatic amino acids at the interfaces and along the extension provides new structural insights that may contribute to decipher the molecular mechanisms of signal transmission within or between the ribosomal proteins. Similar to neurons interacting through “molecular synapses”, ribosomal proteins form a network that suggest an analogy with a simple molecular brain in which the “sensory-proteins” innervate the functional ribosomal sites, while the “inter-proteins” interconnect them into circuits suitable to process the information flow that circulates during protein synthesis. It is likely that these circuits have evolved to coordinate both the complex macromolecular motions and the binding of the multiple factors during translation. This opens new perspectives on nanoscale information transfer and processing.

THE REMARKABLE MOLECULAR CONTENT OF THE RED SPIDER NEBULA (NGC 6537)

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

Edwards, J. L.; Ziurys, L. M., E-mail: lziurys@email.arizona.edu

2013-06-10

Millimeter and sub-millimeter molecular-line observations of planetary nebula (PN) NGC 6537 (Red Spider) have been carried out using the Sub-Millimeter Telescope and the 12 m antenna of the Arizona Radio Observatory in the frequency range 86-692 GHz. CN, HCN, HNC, CCH, CS, SO, H{sub 2}CO, HCO{sup +} and N{sub 2}H{sup +}, along with the J = 3 {yields} 2 and 6 {yields} 5 lines of CO and those of several isotopologues, were detected toward the Red Spider, estimated to be {approx}1600 yr old. This extremely high excitation PN evidently fosters a rich molecular environment. The presence of CS and SOmore » suggest that sulfur may be sequestered in molecular form in such nebulae. A radiative transfer analysis of the CO and CS spectra indicate a kinetic temperature of T{sub K} {approx} 60-80 K and gas densities of n(H{sub 2}) {approx} 1-8 Multiplication-Sign 10{sup 5} cm{sup -3} in NGC 6537. Column densities of the molecules in the nebula and their fractional abundances relative to H{sub 2} ranged from N{sub tot} {approx} 10{sup 16} cm{sup -2} and f {approx} 10{sup -4} for CO, to {approx}7 Multiplication-Sign 10{sup 11} cm{sup -2} and f {approx} 8 Multiplication-Sign 10{sup -9} for the least abundant species, N{sub 2}H{sup +}. For SO and CS, N{sub tot} {approx} 2 Multiplication-Sign 10{sup 12} cm{sup -2} and 10{sup 13} cm{sup -2}, respectively, with f {approx} 10{sup -7} and 2 Multiplication-Sign 10{sup -8}. It was also found that HCN/HNC Almost-Equal-To 2. A low {sup 12}C/{sup 13}C ratio of {approx}4 was measured, indicative of hot-bottom burning. These results, coupled with past observations, suggest that molecular abundances in PNe are governed principally by the physical and chemical properties of the individual object and its progenitor star, rather than nebular age.« less

CSO CO (2–1) and Spitzer IRAC observations of a bipolar outflow in high-mass star-forming region IRAS 22506+5944

NASA Astrophysics Data System (ADS)

Xie, Ze-Qiang; Qiu, Ke-Ping

2018-02-01

We present Caltech Submillimeter Observatory CO (2–1) and Spitzer IRAC observations toward IRAS 22506+5944, which is a 104 L ⊙ massive star-forming region. The CO (2–1) maps show an east-west bipolar molecular outflow originating from the 3 mm dust continuum peak. The Spitzer IRAC color-composite image reveals a pair of bow-shaped tips which are prominent in excess 4.5μm emission and are located at the leading fronts of the bipolar outflow, providing compelling evidence for the existence of bow-shocks as the driving agents of the molecular outflow. By comparing our CO (2–1) observations with previously published CO (1–0) data, we find that the CO (2–1)/(1–0) line ratio increases from low (∼5 kms‑1) to moderate (∼8–12 kms‑1) velocities, and then decreases at higher velocities. This is qualitatively consistent with the scenario that the molecular outflow is driven by multiple bow-shocks. We also revisit the position-velocity diagram of the CO (1–0) data, and find two spur structures along the outflow axis, which are further evidence for the presence of multiple jet bowshocks. Finally, power-law fittings to the mass spectrum of the outflow gives power law indexes more consistent with the jet bow-shock model than the wide-angle wind model.

Stacked Metal Silicide/Silicon Far-Infrared Detectors

NASA Technical Reports Server (NTRS)

Maserjian, Joseph

1988-01-01

Selective doping of silicon in proposed metal silicide/silicon Schottky-barrier infrared photodetector increases maximum detectable wavelength. Stacking layers to form multiple Schottky barriers increases quantum efficiency of detector. Detectors of new type enhance capabilities of far-infrared imaging arrays. Grows by molecular-beam epitaxy on silicon waferscontaining very-large-scale integrated circuits. Imaging arrays of detectors made in monolithic units with image-preprocessing circuitry.

Globular cluster formation with multiple stellar populations: self-enrichment in fractal massive molecular clouds

NASA Astrophysics Data System (ADS)

Bekki, Kenji

2017-08-01

Internal chemical abundance spreads are one of fundamental properties of globular clusters (GCs) in the Galaxy. In order to understand the origin of such abundance spreads, we numerically investigate GC formation from massive molecular clouds (MCs) with fractal structures using our new hydrodynamical simulations with star formation and feedback effects of core-collapse supernovae (SNe) and asymptotic giant branch (AGB) stars. We particularly investigate star formation from gas chemically contaminated by SNe and AGB stars ('self-enrichment') in forming GCs within MCs with different initial conditions and environments. The principal results are as follows. GCs with multiple generations of stars can be formed from merging of hierarchical star cluster complexes that are developed from high-density regions of fractal MCs. Feedback effects of SNe and AGB stars can control the formation efficiencies of stars formed from original gas of MCs and from gas ejected from AGB stars. The simulated GCs have strong radial gradients of helium abundances within the central 3 pc. The original MC masses need to be as large as 107 M⊙ for a canonical initial stellar mass function (IMF) so that the final masses of stars formed from AGB ejecta can be ˜105 M⊙. Since star formation from AGB ejecta is rather prolonged (˜108 yr), their formation can be strongly suppressed by SNe of the stars themselves. This result implies that the so-called mass budget problem is much more severe than ever thought in the self-enrichment scenario of GC formation and thus that IMF for the second generation of stars should be 'top-light'.

The Kirkwood{endash}Buckingham variational method and the boundary value problems for the molecular Schr{umlt o}dinger equation

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

Pupyshev, V.I.; Scherbinin, A.V.; Stepanov, N.F.

1997-11-01

The approach based on the multiplicative form of a trial wave function within the framework of the variational method, initially proposed by Kirkwood and Buckingham, is shown to be an effective analytical tool in the quantum mechanical study of atoms and molecules. As an example, the elementary proof is given to the fact that the ground state energy of a molecular system placed into the box with walls of finite height goes to the corresponding eigenvalue of the Dirichlet boundary value problem when the height of the walls is growing up to infinity. {copyright} {ital 1997 American Institute of Physics.}

MOLECULAR VACUUM PUMP

DOEpatents

Eckberg, E.E.

1960-09-27

A multiple molecular vacuum pump capable of producing a vacuum of the order of 10/sup -9/ mm Hg is described. The pump comprises a casing of an aggregate of paired and matched cylindrical plates, a recessed portion on one face of each plate concentrically positioned formed by a radially extending wall and matching the similarly recessed portion of its twin plate of that pair of plates and for all paired and matched plates; a plurality of grooves formed in the radially extending walls of each and all recesses progressing in a spiral manner from their respective starting points out at the periphery of the recess inwardly to the central area; a plurality of rotors rotatably mounted to closely occupy the spaces as presented by the paired and matched recesses between all paired plates; a hollowed drive-shaft perforated at points adjacent to the termini of all spiral grooves; inlet ports at the starting points of all grooves and through all plates at common points to each respectively; and a common outlet passage presented by the hollow portion of the perforated hollowed drive-shaft of the molecular pump. (AEC)

Can small hydrophobic gold nanoparticles inhibit β2-microglobulin fibrillation?

NASA Astrophysics Data System (ADS)

Brancolini, Giorgia; Toroz, Dimitrios; Corni, Stefano

2014-06-01

Inorganic nanoparticles stabilized by a shell of organic ligands can enhance or suppress the natural propensity of proteins to form fibrils. Functionalization facilitates targeted delivery of the nanoparticles to various cell types, bioimaging, drug delivery and other therapeutic and diagnostic applications. In this study, we provide a computational model of the effect of a prototypical thiol-protected gold nanoparticle, Au25L18- (L = S(CH2)2Ph) on the β2-microglobulin natural fibrillation propensity. To reveal the molecular basis of the protein-nanoparticle association process, we performed various simulations at multiple levels (Classical Molecular Dynamics and Brownian Dynamics) that cover multiple length- and timescales. The results provide a model of the ensemble of structures constituting the protein-gold nanoparticle complexes, and insights into the driving forces for the binding of β2-microglobulin to hydrophobic small size gold nanoparticles. We have found that the small nanoparticles can bind the protein to form persistent complexes. This binding of nanoparticles is able to block the active sites of domains from binding to another protein, thus leading to potential inhibition of the fibrillation activity. A comparison with the binding patches identified for the interaction of the protein with a known inhibitor of fibrillation, supports our conclusion.Inorganic nanoparticles stabilized by a shell of organic ligands can enhance or suppress the natural propensity of proteins to form fibrils. Functionalization facilitates targeted delivery of the nanoparticles to various cell types, bioimaging, drug delivery and other therapeutic and diagnostic applications. In this study, we provide a computational model of the effect of a prototypical thiol-protected gold nanoparticle, Au25L18- (L = S(CH2)2Ph) on the β2-microglobulin natural fibrillation propensity. To reveal the molecular basis of the protein-nanoparticle association process, we performed various simulations at multiple levels (Classical Molecular Dynamics and Brownian Dynamics) that cover multiple length- and timescales. The results provide a model of the ensemble of structures constituting the protein-gold nanoparticle complexes, and insights into the driving forces for the binding of β2-microglobulin to hydrophobic small size gold nanoparticles. We have found that the small nanoparticles can bind the protein to form persistent complexes. This binding of nanoparticles is able to block the active sites of domains from binding to another protein, thus leading to potential inhibition of the fibrillation activity. A comparison with the binding patches identified for the interaction of the protein with a known inhibitor of fibrillation, supports our conclusion. Electronic supplementary information (ESI) available: Details on the molecular dynamics simulation results. Table S1 reports results of the MD trajectories with a single NP at different initial velocities (d1, d2, d3, and d4) (three-dimensional structures and contact residues). Table S2 reports results of the MD trajectories with a couple of NPs at different initial velocities (initial orientations, three-dimensional structures, contact residues and root-mean-square deviations). Table S3 reports root-mean-square fluctuations and divergence of the protein structure with respect to the NMR model. Table S4 describes the average energy of the final complexes. See DOI: 10.1039/c4nr01514b

Analysis of Several PLA2 mRNA in Human Meningiomas

PubMed Central

Denizot, Yves; De Armas, Rafael; Durand, Karine; Robert, Sandrine; Moreau, Jean-Jacques; Caire, François; Weinbreck, Nicolas; Labrousse, François

2009-01-01

In view of the important oncogenic action of phospholipase A2(PLA2) we investigated PLA2 transcripts in human meningiomas. Real-time PCR was used to investigate PLA2 transcripts in 26 human meningioma tumors. Results indicated that three Ca2+-dependent high molecular weight PLA2 (PLA2-IVA, PLA2-IVB, PLA2-IVC), one Ca2+-independent high molecular weight PLA2 (PLA2-VI) and five low molecular weight secreted forms of PLA2 (PLA2-IB, PLA2-IIA, PLA2-III, PLA2-V, and PLA2-XII) are expressed with PLA2-IVA, PLA2-IVB, PLA2-VI, and PLA2-XIIA as the major expressed forms. PLA2-IIE, PLA2-IIF, PLA2-IVD, and PLA2-XIIB are not detected. Plasma (PLA2-VIIA) and intracellular (PLA2-VIIB) platelet-activating factor acetylhydrolase transcripts are expressed in human meningiomas. However no difference was found for PLA2 transcript amounts in relation to the tumor grade, the subtype of meningiomas, the presence of inflammatory infiltrated cells, of an associated edema, mitosis, brain invasion, vascularisation or necrosis. In conclusion numerous genes encoding multiples forms of PLA2 are expressed in meningiomas where they might act on the phospholipid remodeling and on the local eicosanoid and/or cytokine networks. PMID:20339511

Cytoskeleton in motion: the dynamics of keratin intermediate filaments in epithelia.

PubMed

Windoffer, Reinhard; Beil, Michael; Magin, Thomas M; Leube, Rudolf E

2011-09-05

Epithelia are exposed to multiple forms of stress. Keratin intermediate filaments are abundant in epithelia and form cytoskeletal networks that contribute to cell type-specific functions, such as adhesion, migration, and metabolism. A perpetual keratin filament turnover cycle supports these functions. This multistep process keeps the cytoskeleton in motion, facilitating rapid and protein biosynthesis-independent network remodeling while maintaining an intact network. The current challenge is to unravel the molecular mechanisms underlying the regulation of the keratin cycle in relation to actin and microtubule networks and in the context of epithelial tissue function.

Cytoskeleton in motion: the dynamics of keratin intermediate filaments in epithelia

PubMed Central

Windoffer, Reinhard; Beil, Michael; Magin, Thomas M.

2011-01-01

Epithelia are exposed to multiple forms of stress. Keratin intermediate filaments are abundant in epithelia and form cytoskeletal networks that contribute to cell type–specific functions, such as adhesion, migration, and metabolism. A perpetual keratin filament turnover cycle supports these functions. This multistep process keeps the cytoskeleton in motion, facilitating rapid and protein biosynthesis–independent network remodeling while maintaining an intact network. The current challenge is to unravel the molecular mechanisms underlying the regulation of the keratin cycle in relation to actin and microtubule networks and in the context of epithelial tissue function. PMID:21893596

Photopolymerization-based fabrication of chemical sensing films

DOEpatents

Yang, Xiaoguang; Swanson, Basil I.; Du, Xian-Xian

2003-12-30

A photopolymerization method is disclosed for attaching a chemical microsensor film to an oxide surface including the steps of pretreating the oxide surface to form a functionalized surface, coating the functionalized surface with a prepolymer solution, and polymerizing the prepolymer solution with ultraviolet light to form the chemical microsensor film. The method also allows the formation of molecular imprinted films by photopolymerization. Formation of multilayer sensing films and patterned films is allowed by the use of photomasking techniques to allow patterning of multiple regions of a selected sensing film, or creating a sensor surface containing several films designed to detect different compounds.

Infectious Multiple Drug Resistance in the Enterobacteriaceae

DTIC Science & Technology

1983-10-01

producing a form of ST that does not Vibrio cholera and Eichernchia co/i. Infect Immun undergo the same posttranslational modification 1974; 10:320-7... cholera toxin. Although there have been numerous reports of the relationship between E. coli LT toxin (and cholera toxin) and a putative enterotoxin...dissect the fine molecular structure of cholera toxin and thereby create a general strategy by which subunit vaccines might be directly synthesized in the

Characteristic Variations and Similarities in Biochemical, Molecular, and Functional Properties of Glyoxalases across Prokaryotes and Eukaryotes.

PubMed

Kaur, Charanpreet; Sharma, Shweta; Hasan, Mohammad Rokebul; Pareek, Ashwani; Singla-Pareek, Sneh L; Sopory, Sudhir K

2017-03-30

The glyoxalase system is the ubiquitous pathway for the detoxification of methylglyoxal (MG) in the biological systems. It comprises two enzymes, glyoxalase I (GLYI) and glyoxalase II (GLYII), which act sequentially to convert MG into d-lactate, thereby helping living systems get rid of this otherwise cytotoxic byproduct of metabolism. In addition, a glutathione-independent GLYIII enzyme activity also exists in the biological systems that can directly convert MG to d-lactate. Humans and Escherichia coli possess a single copy of GLYI (encoding either the Ni- or Zn-dependent form) and GLYII genes, which through MG detoxification provide protection against various pathological and disease conditions. By contrast, the plant genome possesses multiple GLYI and GLYII genes with a role in abiotic stress tolerance. Plants possess both Ni 2+ - and Zn 2+ -dependent forms of GLYI, and studies on plant glyoxalases reveal the various unique features of these enzymes distinguishing them from prokaryotic and other eukaryotic glyoxalases. Through this review, we provide an overview of the plant glyoxalase family along with a comparative analysis of glyoxalases across various species, highlighting similarities as well as differences in the biochemical, molecular, and physiological properties of these enzymes. We believe that the evolution of multiple glyoxalases isoforms in plants is an important component of their robust defense strategies.

Molecular Mechanics of the Moisture Effect on Epoxy/Carbon Nanotube Nanocomposites.

PubMed

Tam, Lik-Ho; Wu, Chao

2017-10-13

The strong structural integrity of polymer nanocomposite is influenced in the moist environment; but the fundamental mechanism is unclear, including the basis for the interactions between the absorbed water molecules and the structure, which prevents us from predicting the durability of its applications across multiple scales. In this research, a molecular dynamics model of the epoxy/single-walled carbon nanotube (SWCNT) nanocomposite is constructed to explore the mechanism of the moisture effect, and an analysis of the molecular interactions is provided by focusing on the hydrogen bond (H-bond) network inside the nanocomposite structure. The simulations show that at low moisture concentration, the water molecules affect the molecular interactions by favorably forming the water-nanocomposite H-bonds and the small cluster, while at high concentration the water molecules predominantly form the water-water H-bonds and the large cluster. The water molecules in the epoxy matrix and the epoxy-SWCNT interface disrupt the molecular interactions and deteriorate the mechanical properties. Through identifying the link between the water molecules and the nanocomposite structure and properties, it is shown that the free volume in the nanocomposite is crucial for its structural integrity, which facilitates the moisture accumulation and the distinct material deteriorations. This study provides insights into the moisture-affected structure and properties of the nanocomposite from the nanoscale perspective, which contributes to the understanding of the nanocomposite long-term performance under the moisture effect.

Molecular Mechanics of the Moisture Effect on Epoxy/Carbon Nanotube Nanocomposites

PubMed Central

2017-01-01

The strong structural integrity of polymer nanocomposite is influenced in the moist environment; but the fundamental mechanism is unclear, including the basis for the interactions between the absorbed water molecules and the structure, which prevents us from predicting the durability of its applications across multiple scales. In this research, a molecular dynamics model of the epoxy/single-walled carbon nanotube (SWCNT) nanocomposite is constructed to explore the mechanism of the moisture effect, and an analysis of the molecular interactions is provided by focusing on the hydrogen bond (H-bond) network inside the nanocomposite structure. The simulations show that at low moisture concentration, the water molecules affect the molecular interactions by favorably forming the water-nanocomposite H-bonds and the small cluster, while at high concentration the water molecules predominantly form the water-water H-bonds and the large cluster. The water molecules in the epoxy matrix and the epoxy-SWCNT interface disrupt the molecular interactions and deteriorate the mechanical properties. Through identifying the link between the water molecules and the nanocomposite structure and properties, it is shown that the free volume in the nanocomposite is crucial for its structural integrity, which facilitates the moisture accumulation and the distinct material deteriorations. This study provides insights into the moisture-affected structure and properties of the nanocomposite from the nanoscale perspective, which contributes to the understanding of the nanocomposite long-term performance under the moisture effect. PMID:29027979

Molecular approaches towards development of purified natural products and their structurally known derivatives as efficient anti-cancer drugs: current trends.

PubMed

Saha, Santu Kumar; Khuda-Bukhsh, Anisur Rahman

2013-08-15

Several natural products and their derivatives, either in purified or structurally identified form, exhibit immense pharmacological and biological properties, some of them showing considerable anticancer potential. Although the molecular mechanisms of action of some of these products are yet to be elucidated, extensive research in this area continues to generate new data that are clinically exploitable. Recent advancement in molecular biology, high throughput screening, biomarker identifications, target selection and genomic approaches have enabled us to understand salient interactions of natural products and their derivatives with cancer cells vis-à-vis normal cells. In this review we highlight the recent approaches and application of innovative technologies made to improve quality as well as efficiency of structurally identified natural products and their derivatives, particularly in small molecular forms capable of being used in "targeted therapies" in oncology. These products preferentially involve multiple mechanistic pathways and overcome chemo-resistance in tumor types with cumulative action. We also mention briefly a few physico-chemical features that compare natural products with drugs in recent natural product discovery approaches. We further report here a few purified natural products as examples that provide molecular interventions in cancer therapeutics to give the reader a glimpse of the current trends of approach for discovering useful anticancer drugs. © 2013 Elsevier B.V. All rights reserved.

Isozymes of lignin peroxidase and manganese(II) peroxidase from the white-rot basidiomycete Trametes versicolor. I. Isolation of enzyme forms and characterization of physical and catalytic properties.

PubMed

Johansson, T; Nyman, P O

1993-01-01

The basidiomycete Trametes versicolor is a white-rot fungus and a potent degrader of lignin. The development of extracellular enzyme activities in the fungal culture under physiological conditions of secondary metabolism was investigated. Using the culture medium as starting material a large number of peroxidase forms were purified by the use of chromatographic techniques. Sixteen forms of lignin peroxidase and five forms of manganese(II) peroxidase were separated and the majority of these enzymes was characterized with respect to isoelectric point, molecular mass, and specific enzyme activity. The manganese(II) peroxidases showed a lower isoelectric point (pI 3.2-2.9) and a slightly higher molecular mass (44-45 kDa) than the lignin peroxidases (pI 3.7-3.1, and 41-43 kDa). Specific enzyme activities for the forms of lignin peroxidase, using veratryl alcohol as the substrate, were found to differ considerably. Certain differences in the specific enzyme activity were also observed among the forms of manganese(II) peroxidase. A multitude of peroxidase forms has previously been encountered in another white-rot fungus, Phanerochaete chrysosporium. The discovery that it also occurs in T. versicolor would suggest that this multiplicity could be a common feature among white-rot fungi and may be essential for the biodegradation of lignin.

Conformational properties of serine proteinase inhibitors (serpins) confer multiple pathophysiological roles.

PubMed

Janciauskiene, S

2001-03-26

Serine proteinase inhibitors (Serpins) are irreversible suicide inhibitors of proteases that regulate diverse physiological processes such as coagulation, fibrinolysis, complement activation, angiogenesis, apoptosis, inflammation, neoplasia and viral pathogenesis. The molecular structure and physical properties of serpins permit these proteins to adopt a number of variant conformations under physiological conditions including the native inhibitory form and several inactive, non-inhibitory forms, such as complexes with protease or other ligands, cleaved, polymerised and oxidised. Alterations of a serpin which affect its structure and/or secretion and thus reduce its functional levels may result in pathology. Serpin dysfunction has been implicated in thrombosis, emphysema, liver cirrhosis, immune hypersensitivity and mental disorders. The loss of inhibitory activity of serpins necessarily results in an imbalance between proteases and their inhibitors, but it may also have other physiological effects through the generation of abnormal concentrations of modified, non-inhibitory forms of serpins. Although these forms of inhibitory serpins are detected in tissues and fluids recovered from inflammatory sites, the important questions of which conditions result in generation of different molecular forms of serpins, what biological function these forms have, and which of them are directly linked to pathologies and/or may be useful markers for characterisation of disease states, remain to be answered. Elucidation of the biological activities of non-inhibitory forms of serpins may provide useful insights into the pathogenesis of diseases and suggest new therapeutic strategies.

Vibrational cross-angles in condensed molecules: a structural tool.

PubMed

Chen, Hailong; Zhang, Yufan; Li, Jiebo; Liu, Hongjun; Jiang, De-En; Zheng, Junrong

2013-09-05

The fluctuations of three-dimensional molecular conformations of a molecule in different environments play critical roles in many important chemical and biological processes. X-ray diffraction (XRD) techniques and nuclear magnetic resonance (NMR) methods are routinely applied to monitor the molecular conformations in condensed phases. However, some special requirements of the methods have prevented them from exploring many molecular phenomena at the current stage. Here, we introduce another method to resolve molecular conformations based on an ultrafast MIR/T-Hz multiple-dimensional vibrational spectroscopic technique. The model molecule (4'-methyl-2'-nitroacetanilide, MNA) is prepared in two of its crystalline forms and liquid samples. Two polarized ultrafast infrared pulses are then used to determine the cross-angles of vibrational transition moment directions by exciting one vibrational band and detecting the induced response on another vibrational band of the molecule. The vibrational cross-angles are then converted into molecular conformations with the aid of calculations. The molecular conformations determined by the method are supported by X-ray diffraction and molecular dynamics simulation results. The experimental results suggest that thermodynamic interactions with solvent molecules are not altering the molecular conformations of MNA in the solutions to control their ultimate conformations in the crystals.

Interaction of multiple biomimetic antimicrobial polymers with model bacterial membranes

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

Baul, Upayan, E-mail: upayanb@imsc.res.in; Vemparala, Satyavani, E-mail: vani@imsc.res.in; Kuroda, Kenichi, E-mail: kkuroda@umich.edu

Using atomistic molecular dynamics simulations, interaction of multiple synthetic random copolymers based on methacrylates on prototypical bacterial membranes is investigated. The simulations show that the cationic polymers form a micellar aggregate in water phase and the aggregate, when interacting with the bacterial membrane, induces clustering of oppositely charged anionic lipid molecules to form clusters and enhances ordering of lipid chains. The model bacterial membrane, consequently, develops lateral inhomogeneity in membrane thickness profile compared to polymer-free system. The individual polymers in the aggregate are released into the bacterial membrane in a phased manner and the simulations suggest that the most probablemore » location of the partitioned polymers is near the 1-palmitoyl-2-oleoyl-phosphatidylglycerol (POPG) clusters. The partitioned polymers preferentially adopt facially amphiphilic conformations at lipid-water interface, despite lacking intrinsic secondary structures such as α-helix or β-sheet found in naturally occurring antimicrobial peptides.« less

Dissociative electron attachment to C{sub 2}F{sub 5} radicals

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

Haughey, Sean A.; Field, Thomas A.; Langer, Judith

Dissociative electron attachment to the reactive C{sub 2}F{sub 5} molecular radical has been investigated with two complimentary experimental methods; a single collision beam experiment and a new flowing afterglow Langmuir probe technique. The beam results show that F{sup -} is formed close to zero electron energy in dissociative electron attachment to C{sub 2}F{sub 5}. The afterglow measurements also show that F{sup -} is formed in collisions between electrons and C{sub 2}F{sub 5} molecules with rate constants of 3.7 Multiplication-Sign 10{sup -9} cm{sup 3} s{sup -1} to 4.7 Multiplication-Sign 10{sup -9} cm{sup 3} s{sup -1} at temperatures of 300-600 K. Themore » rate constant increases slowly with increasing temperature, but the rise observed is smaller than the experimental uncertainty of 35%.« less

Ligand-Receptor Interaction Modulates the Energy Landscape of Enzyme-Instructed Self-Assembly of Small Molecules.

PubMed

Haburcak, Richard; Shi, Junfeng; Du, Xuewen; Yuan, Dan; Xu, Bing

2016-11-30

The concurrence of enzymatic reaction and ligand-receptor interactions is common for proteins, but rare for small molecules and has yet to be explored. Here we show that ligand-receptor interaction modulates the morphology of molecular assemblies formed by enzyme-instructed assembly of small molecules. While the absence of ligand-receptor interaction allows enzymatic dephosphorylation of a precursor to generate the hydrogelator that self-assembles to form long nanofibers, the presence of the ligand-receptor interaction biases the pathway to form precipitous aggregates containing short nanofibers. While the hydrogelators self-assemble to form nanofibers or nanoribbons that are unable to bind with the ligand (i.e., vancomycin), the addition of surfactant breaks up the assemblies to restore the ligand-receptor interaction. In addition, an excess amount of the ligands can disrupt the nanofibers and result in the precipitates. As the first example of the use of ligand-receptor interaction to modulate the kinetics of enzymatic self-assembly, this work not only provides a solution to evaluate the interaction between aggregates and target molecules but also offers new insight for understanding the emergent behavior of sophisticated molecular systems having multiple and parallel processes.

The dependence of stellar properties on initial cloud density

NASA Astrophysics Data System (ADS)

Jones, Michael O.; Bate, Matthew R.

2018-05-01

We investigate the dependence of stellar properties on the initial mean density of the molecular cloud in which stellar clusters form using radiation hydrodynamical simulations that resolve the opacity limit for fragmentation. We have simulated the formation of three star clusters from the gravitational collapse of molecular clouds whose densities vary by a factor of a hundred. As with previous calculations including radiative feedback, we find that the dependence of the characteristic stellar mass, Mc, on the initial mean density of the cloud, ρ, is weaker than the dependence of the thermal Jeans mass. However, unlike previous calculations, which found no statistically significant variation in the median mass with density, we find a weak dependence approximately of the form Mc∝ρ-1/5. The distributions of properties of multiple systems do not vary significantly between the calculations. We compare our results to the result of observational surveys of star-forming regions, and suggest that the similarities between the properties of our lowest density calculation and the nearby Taurus-Auriga region indicate that the apparent excess of solar-type stars observed may be due to the region's low density.

Star formation around supermassive black holes.

PubMed

Bonnell, I A; Rice, W K M

2008-08-22

The presence of young massive stars orbiting on eccentric rings within a few tenths of a parsec of the supermassive black hole in the galactic center is challenging for theories of star formation. The high tidal shear from the black hole should tear apart the molecular clouds that form stars elsewhere in the Galaxy, and transport of stars to the galactic center also appears unlikely during their lifetimes. We conducted numerical simulations of the infall of a giant molecular cloud that interacts with the black hole. The transfer of energy during closest approach allows part of the cloud to become bound to the black hole, forming an eccentric disk that quickly fragments to form stars. Compressional heating due to the black hole raises the temperature of the gas up to several hundred to several thousand kelvin, ensuring that the fragmentation produces relatively high stellar masses. These stars retain the eccentricity of the disk and, for a sufficiently massive initial cloud, produce an extremely top-heavy distribution of stellar masses. This potentially repetitive process may explain the presence of multiple eccentric rings of young stars in the presence of a supermassive black hole.

Biomimetic nanoclay scaffolds for bone tissue engineering

NASA Astrophysics Data System (ADS)

Ambre, Avinash Harishchandra

Tissue engineering offers a significant potential alternative to conventional methods for rectifying tissue defects by evoking natural regeneration process via interactions between cells and 3D porous scaffolds. Imparting adequate mechanical properties to biodegradable scaffolds for bone tissue engineering is an important challenge and extends from molecular to macroscale. This work focuses on the use of sodium montmorillonite (Na-MMT) to design polymer composite scaffolds having enhanced mechanical properties along with multiple interdependent properties. Materials design beginning at the molecular level was used in which Na-MMT clay was modified with three different unnatural amino acids and further characterized using Fourier Transform Infrared (FTIR) spectroscopy, X-ray diffraction (XRD). Based on improved bicompatibility with human osteoblasts (bone cells) and intermediate increase in d-spacing of MMT clay (shown by XRD), 5-aminovaleric acid modified clay was further used to prepare biopolymer (chitosan-polygalacturonic acid complex) scaffolds. Osteoblast proliferation in biopolymer scaffolds containing 5-aminovaleric acid modified clay was similar to biopolymer scaffolds containing hydroxyapatite (HAP). A novel process based on biomineralization in bone was designed to prepare 5-aminovaleric acid modified clay capable of imparting multiple properties to the scaffolds. Bone-like apatite was mineralized in modified clay and a novel nanoclay-HAP hybrid (in situ HAPclay) was obtained. FTIR spectroscopy indicated a molecular level organic-inorganic association between the intercalated 5-aminovaleric acid and mineralized HAP. Osteoblasts formed clusters on biopolymer composite films prepared with different weight percent compositions of in situ HAPclay. Human MSCs formed mineralized nodules on composite films and mineralized extracellular matrix (ECM) in composite scaffolds without the use of osteogenic supplements. Polycaprolactone (PCL), a synthetic polymer, was used for preparing composites (films and scaffolds) containing in situ HAPclay. Composite films showed significantly improved nanomechanical properties. Human MSCs formed mineralized ECM on films in absence of osteogenic supplements and were able to infiltrate the scaffolds. Atomic force microscopy imaging of mineralized ECM formed on composite films showed similarities in dimensions, arrangement of collagen and apatite with their natural bone counterparts. This work indicates the potential of in situ HAPclay to impart polymeric scaffolds with osteoinductive, osteoconductive abilities and improve their mechanical properties besides emphasizing nanoclays as cell-instructive materials.

A molecular imaging analysis of C×43 association with Cdo during skeletal myoblast differentiation

NASA Astrophysics Data System (ADS)

Nosi, Daniele; Mercatelli, Raffaella; Chellini, Flaminia; Soria, Silvia; Pini, Alessandro; Formigli, Lucia; Quercioli, Franco

2014-02-01

Cell-to-cell contacts are crucial for cell differentiation. The promyogenic cell surface protein, Cdo, functions as a component of multiprotein clusters to mediate cell adhesion signaling. Connexin43, the main connexin forming gap junctions, also plays a key role in myogenesis. At least part of its effects are independent of the intercellular channel function, but the mechanisms underlying are unknown. Here, using multiple optical approaches, we provided the first evidence that Cx43 physically interacts with Cdo to form dynamic complexes during myoblast differentiation, offering clues for considering this interaction a structural basis of the channel-independent function of Cx43.

Epistemological issues in the study of microbial life: alternative terran biospheres?

PubMed

Cleland, Carol E

2007-12-01

The assumption that all life on Earth today shares the same basic molecular architecture and biochemistry is part of the paradigm of modern biology. This paper argues that there is little theoretical or empirical support for this widely held assumption. Scientists know that life could have been at least modestly different at the molecular level and it is clear that alternative molecular building blocks for life were available on the early Earth. If the emergence of life is, like other natural phenomena, highly probable given the right chemical and physical conditions then it seems likely that the early Earth hosted multiple origins of life, some of which produced chemical variations on life as we know it. While these points are often conceded, it is nevertheless maintained that any primitive alternatives to familiar life would have been eliminated long ago, either amalgamated into a single form of life through lateral gene transfer (LGT) or alternatively out-competed by our putatively more evolutionarily robust form of life. Besides, the argument continues, if such life forms still existed, we surely would have encountered telling signs of them by now. These arguments do not hold up well under close scrutiny. They reflect a host of assumptions that are grounded in our experience with large multicellular organisms and, most importantly, do not apply to microbial forms of life, which cannot be easily studied without the aid of sophisticated technologies. Significantly, the most powerful molecular biology techniques available-polymerase chain reaction (PCR) amplification of rRNA genes augmented by metagenomic analysis-could not detect such microbes if they existed. Given the profound philosophical and scientific importance that such a discovery would represent, a dedicated search for 'shadow microbes' (heretofore unrecognized 'alien' forms of terran microbial life) seems in order. The best place to start such a search is with puzzling (anomalous) phenomena, such as desert varnish, that resist classification as 'biological' or 'nonbiological'.

Butyrylcholinesterase: K variant, plasma activity, molecular forms and rivastigmine treatment in Alzheimer's disease in a Southern Brazilian population.

PubMed

Bono, G F; Simão-Silva, D P; Batistela, M S; Josviak, N D; Dias, P F R; Nascimento, G A; Souza, R L R; Piovezan, M R; Souza, R K M; Furtado-Alle, L

2015-02-01

Alzheimer's disease (AD) is a neurodegenerative disorder in which there is a decline of cholinergic function. The symptomatic AD treatment involves the use of ChEIs (cholinesterase inhibitors) as rivastigimine, a dual inhibitor. The human butyrylcholinesterase (BChE) is an enzyme that has specific roles in cholinergic neurotransmission and it has been associated with AD. In the serum, BChE is found in four main molecular forms: G1 (monomer); G1-ALB (monomer linked to albumin); G2 (dimer); and G4 (tetramer). The interaction between the products of BCHE gene and CHE2 locus results in CHE2 C5+ and CHE2 C5- phenotypes. CHE2 C5+ phenotype and BChE-K are factors that influence on BChE activity. This work aimed to verify the proportions of BChE molecular forms, total and relative activity in 139 AD patients and 139 elderly controls, taking into account K variant, CHE2 locus, rivastigmine treatment and clinical dementia rating (CDR) of AD patients. Phenotypic frequencies of CHE2 C5+ and frequency of the carriers of the K allele were similar between groups. Total BChE activity in plasma was significantly lower in AD patients than in elderly controls. Furthermore, we found that reduction on plasma BChE activity is associated directly with AD progression in AD patients and that rivastigmine treatment has a stronger effect on BChE activity within the CDR2 group. The reduction in BChE activity did not occur proportionally in all molecular forms. Multiple regression analysis results confirmed that AD acts as the main factor in plasma BChE activity reduction and that severe stages are related with an even greater reduction. These findings suggest that the reduction of total plasma BChE and relative BChE molecular forms activity in AD patients is probably associated with a feedback mechanism and provides a future perspective of using this enzyme as a possible plasmatic secondary marker for AD. Copyright © 2014 Elsevier Ltd. All rights reserved.

Molecular and Cellular Aspects of Calcific Aortic Valve Disease

PubMed Central

Towler, Dwight A.

2014-01-01

Calcific aortic valve disease (CAVD) increasingly afflicts our aging population. One-third of our elderly have echocardiographic or radiological evidence of aortic valve sclerosis (CAVS), an early and subclinical form of CAVD. Age, gender, tobacco use, hypercholesterolemia, hypertension, and type II diabetes all contribute to the risk of disease that has worldwide distribution. Upon progression to its most severe form --- calcific aortic stenosis (CAS) --- CAVD becomes debilitating and devastating, and 2% of individuals over age 60 suffer from CAS to the extent that surgical intervention is required. No effective pharmacotherapies exist for treating those at risk for clinical progression. It is becoming increasingly apparent that a diverse spectrum of cellular and molecular mechanisms converge to regulate valvular calcium load; this is evidenced not only in histopathologic heterogeneity of CAVD but also from the multiplicity of cell types that can participate in valve biomineralization. In this review, we highlight our current understanding of CAVD disease biology, emphasizing molecular and cellular aspects of its regulation. We end by pointing to important biological and clinical questions that must be answered to enable sophisticated disease staging and the development of new strategies to medically treat CAVD. PMID:23833294

Structure and function of archaeal prefoldin, a co-chaperone of group II chaperonin.

PubMed

Ohtaki, Akashi; Noguchi, Keiichi; Yohda, Masafumi

2010-01-01

Molecular chaperones are key cellular components involved in the maintenance of protein homeostasis and other unrelated functions. Prefoldin is a chaperone that acts as a co-factor of group II chaperonins in eukaryotes and archaea. It assists proper folding of protein by capturing nonnative proteins and delivering it to the group II chaperonin. Eukaryotic prefoldin is a multiple subunit complex composed of six different polypeptide chains. Archaeal prefoldin, on the other hand, is a heterohexameric complex composed of two alpha and four beta subunits, and forms a double beta barrel assembly with six long coiled coils protruding from it like a jellyfish with six tentacles. Based on the structural information of the archaeal prefoldin, substrate recognition and prefoldin-chaperonin binding mechanisms have been investigated. In this paper, we review a series of studies on the molecular mechanisms of archaeal PFD function. Particular emphasis will be placed on the molecular structures revealed by X-ray crystallography and molecular dynamics induced by binding to nonnative protein substrates.

Re"CYC"ling molecular regulators in the evolution and development of flower symmetry.

PubMed

Spencer, Victoria; Kim, Minsung

2018-07-01

Flower forms are both highly diverse and multifaceted. As well as varying in colour, size, organ number, and much more, flowers show different types of symmetry. Floral symmetry can be grouped into three main categories: asymmetry, bilateral symmetry and radial symmetry, characterised by zero, one, and multiple planes of symmetry, respectively. This review will first explore floral symmetry from a classical morphological view, then from a modern molecular perspective. The recent molecular work on symmetry in monocots and eudicots will be discussed, followed by an in-depth discussion into the evolution of CYC genes, particularly in the capitulum of the sunflower family (Asteraceae). Whilst recent studies on non-model species are helping to bring new light to this field, more species coverage is required to understand how traits such as bilateral symmetry have evolved so many times, and whether the same molecular regulators were recruited for this function. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Spatially resolved multicomponent gels

NASA Astrophysics Data System (ADS)

Draper, Emily R.; Eden, Edward G. B.; McDonald, Tom O.; Adams, Dave J.

2015-10-01

Multicomponent supramolecular systems could be used to prepare exciting new functional materials, but it is often challenging to control the assembly across multiple length scales. Here we report a simple approach to forming patterned, spatially resolved multicomponent supramolecular hydrogels. A multicomponent gel is first formed from two low-molecular-weight gelators and consists of two types of fibre, each formed by only one gelator. One type of fibre in this ‘self-sorted network’ is then removed selectively by a light-triggered gel-to-sol transition. We show that the remaining network has the same mechanical properties as it would have done if it initially formed alone. The selective irradiation of sections of the gel through a mask leads to the formation of patterned multicomponent networks, in which either one or two networks can be present at a particular position with a high degree of spatial control.

Supramolecular Differentiation for Construction of Anisotropic Fullerene Nanostructures by Time-Programmed Control of Interfacial Growth.

PubMed

Bairi, Partha; Minami, Kosuke; Hill, Jonathan P; Nakanishi, Waka; Shrestha, Lok Kumar; Liu, Chao; Harano, Koji; Nakamura, Eiichi; Ariga, Katsuhiko

2016-09-27

Supramolecular assembly can be used to construct a wide variety of ordered structures by exploiting the cumulative effects of multiple noncovalent interactions. However, the construction of anisotropic nanostructures remains subject to some limitations. Here, we demonstrate the preparation of anisotropic fullerene-based nanostructures by supramolecular differentiation, which is the programmed control of multiple assembly strategies. We have carefully combined interfacial assembly and local phase separation phenomena. Two fullerene derivatives, PhH and C12H, were together formed into self-assembled anisotropic nanostructures by using this approach. This technique is applicable for the construction of anisotropic nanostructures without requiring complex molecular design or complicated methodology.

Resveratrol Neuroprotection in Stroke and Traumatic CNS injury

PubMed Central

Lopez, Mary; Dempsey, Robert J; Vemuganti, Raghu

2015-01-01

Resveratrol, a stilbene formed in many plants in response to various stressors, elicits multiple beneficial effects in vertebrates. Particularly, resveratrol was shown to have therapeutic properties in cancer, atherosclerosis and neurodegeneration. Resveratrol-induced benefits are modulated by multiple synergistic pathways that control oxidative stress, inflammation and cell death. Despite the lack of a definitive mechanism, both in vivo and in vitro studies suggest that resveratrol can induce a neuroprotective state when administered acutely or prior to experimental injury to the CNS. In this review, we discuss the neuroprotective potential of resveratrol in stroke, traumatic brain injury and spinal cord injury, with a focus on the molecular pathways responsible for this protection. PMID:26277384

KinImmerse: Macromolecular VR for NMR ensembles

PubMed Central

Block, Jeremy N; Zielinski, David J; Chen, Vincent B; Davis, Ian W; Vinson, E Claire; Brady, Rachael; Richardson, Jane S; Richardson, David C

2009-01-01

Background In molecular applications, virtual reality (VR) and immersive virtual environments have generally been used and valued for the visual and interactive experience – to enhance intuition and communicate excitement – rather than as part of the actual research process. In contrast, this work develops a software infrastructure for research use and illustrates such use on a specific case. Methods The Syzygy open-source toolkit for VR software was used to write the KinImmerse program, which translates the molecular capabilities of the kinemage graphics format into software for display and manipulation in the DiVE (Duke immersive Virtual Environment) or other VR system. KinImmerse is supported by the flexible display construction and editing features in the KiNG kinemage viewer and it implements new forms of user interaction in the DiVE. Results In addition to molecular visualizations and navigation, KinImmerse provides a set of research tools for manipulation, identification, co-centering of multiple models, free-form 3D annotation, and output of results. The molecular research test case analyzes the local neighborhood around an individual atom within an ensemble of nuclear magnetic resonance (NMR) models, enabling immersive visual comparison of the local conformation with the local NMR experimental data, including target curves for residual dipolar couplings (RDCs). Conclusion The promise of KinImmerse for production-level molecular research in the DiVE is shown by the locally co-centered RDC visualization developed there, which gave new insights now being pursued in wider data analysis. PMID:19222844

Current dichotomy between traditional molecular biological and omic research in cancer biology and pharmacology.

PubMed

Reinhold, William C

2015-12-10

There is currently a split within the cancer research community between traditional molecular biological hypothesis-driven and the more recent "omic" forms or research. While the molecular biological approach employs the tried and true single alteration-single response formulations of experimentation, the omic employs broad-based assay or sample collection approaches that generate large volumes of data. How to integrate the benefits of these two approaches in an efficient and productive fashion remains an outstanding issue. Ideally, one would merge the understandability, exactness, simplicity, and testability of the molecular biological approach, with the larger amounts of data, simultaneous consideration of multiple alterations, consideration of genes both of known interest along with the novel, cross-sample comparisons among cell lines and patient samples, and consideration of directed questions while simultaneously gaining exposure to the novel provided by the omic approach. While at the current time integration of the two disciplines remains problematic, attempts to do so are ongoing, and will be necessary for the understanding of the large cell line screens including the Developmental Therapeutics Program's NCI-60, the Broad Institute's Cancer Cell Line Encyclopedia, and the Wellcome Trust Sanger Institute's Cancer Genome Project, as well as the the Cancer Genome Atlas clinical samples project. Going forward there is significant benefit to be had from the integration of the molecular biological and the omic forms or research, with the desired goal being improved translational understanding and application.

Multiple-collision analysis of characteristic X-rays from low-energy Ar 2+ travelling in solid targets

NASA Astrophysics Data System (ADS)

Cipolla, Sam J.; Mildebrath, Mark E.

1983-12-01

The density of atoms in a solid target fosters a multiple-collision mechanism that leads to the production of an equilibrium fraction of L-shell vacancies in an incident heavy ion. It is then possiblein a subsequent ion-atom collision in the solid for an L-vacancy to be transferred to the K-shell of a target atom via rotational coupling of the 2p π-2p σ molecular orbitals formed in the ion-atom quasimolecule. The vacancy-transfer cross section and the equilibrium fraction and lifetime of the vacancies can be found by using an appropriate multiple-collision analysis of the characteristic target and projectile X-rays. Results will be presented for 160-380 keV Ar 2+ incident of targets of Mg, Al, and Si.

Characteristic Variations and Similarities in Biochemical, Molecular, and Functional Properties of Glyoxalases across Prokaryotes and Eukaryotes

PubMed Central

Kaur, Charanpreet; Sharma, Shweta; Hasan, Mohammad Rokebul; Pareek, Ashwani; Singla-Pareek, Sneh L.; Sopory, Sudhir K.

2017-01-01

The glyoxalase system is the ubiquitous pathway for the detoxification of methylglyoxal (MG) in the biological systems. It comprises two enzymes, glyoxalase I (GLYI) and glyoxalase II (GLYII), which act sequentially to convert MG into d-lactate, thereby helping living systems get rid of this otherwise cytotoxic byproduct of metabolism. In addition, a glutathione-independent GLYIII enzyme activity also exists in the biological systems that can directly convert MG to d-lactate. Humans and Escherichia coli possess a single copy of GLYI (encoding either the Ni- or Zn-dependent form) and GLYII genes, which through MG detoxification provide protection against various pathological and disease conditions. By contrast, the plant genome possesses multiple GLYI and GLYII genes with a role in abiotic stress tolerance. Plants possess both Ni2+- and Zn2+-dependent forms of GLYI, and studies on plant glyoxalases reveal the various unique features of these enzymes distinguishing them from prokaryotic and other eukaryotic glyoxalases. Through this review, we provide an overview of the plant glyoxalase family along with a comparative analysis of glyoxalases across various species, highlighting similarities as well as differences in the biochemical, molecular, and physiological properties of these enzymes. We believe that the evolution of multiple glyoxalases isoforms in plants is an important component of their robust defense strategies. PMID:28358304

Structural and molecular interrogation of intact biological systems

PubMed Central

Chung, Kwanghun; Wallace, Jenelle; Kim, Sung-Yon; Kalyanasundaram, Sandhiya; Andalman, Aaron S.; Davidson, Thomas J.; Mirzabekov, Julie J.; Zalocusky, Kelly A.; Mattis, Joanna; Denisin, Aleksandra K.; Pak, Sally; Bernstein, Hannah; Ramakrishnan, Charu; Grosenick, Logan; Gradinaru, Viviana; Deisseroth, Karl

2014-01-01

Obtaining high-resolution information from a complex system, while maintaining the global perspective needed to understand system function, represents a key challenge in biology. Here we address this challenge with a method (termed CLARITY) for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. Using mouse brains, we show intact-tissue imaging of long-range projections, local circuit wiring, cellular relationships, subcellular structures, protein complexes, nucleic acids and neurotransmitters. CLARITY also enables intact-tissue in situ hybridization, immunohistochemistry with multiple rounds of staining and de-staining in non-sectioned tissue, and antibody labelling throughout the intact adult mouse brain. Finally, we show that CLARITY enables fine structural analysis of clinical samples, including non-sectioned human tissue from a neuropsychiatric-disease setting, establishing a path for the transmutation of human tissue into a stable, intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease. PMID:23575631

Dimer model for Tau proteins bound in microtubule bundles

NASA Astrophysics Data System (ADS)

Hall, Natalie; Kluber, Alexander; Hayre, N. Robert; Singh, Rajiv; Cox, Daniel

2013-03-01

The microtubule associated protein tau is important in nucleating and maintaining microtubule spacing and structure in neuronal axons. Modification of tau is implicated as a later stage process in Alzheimer's disease, but little is known about the structure of tau in microtubule bundles. We present preliminary work on a proposed model for tau dimers in microtubule bundles (dimers are the minimal units since there is one microtubule binding domain per tau). First, a model of tau monomer was created and its characteristics explored using implicit solvent molecular dynamics simulation. Multiple simulations yield a partially collapsed form with separate positively/negatively charged clumps, but which are a factor of two smaller than required by observed microtubule spacing. We argue that this will elongate in dimer form to lower electrostatic energy at a cost of entropic ``spring'' energy. We will present preliminary results on steered molecular dynamics runs on tau dimers to estimate the actual force constant. Supported by US NSF Grant DMR 1207624.

Human Autoantibodies Reveal Titin as a Chromosomal Protein

PubMed Central

Machado, Cristina; Sunkel, Claudio E.; Andrew, Deborah J.

1998-01-01

Assembly of the higher-order structure of mitotic chromosomes is a prerequisite for proper chromosome condensation, segregation and integrity. Understanding the details of this process has been limited because very few proteins involved in the assembly of chromosome structure have been discovered. Using a human autoimmune scleroderma serum that identifies a chromosomal protein in human cells and Drosophila embryos, we cloned the corresponding Drosophila gene that encodes the homologue of vertebrate titin based on protein size, sequence similarity, developmental expression and subcellular localization. Titin is a giant sarcomeric protein responsible for the elasticity of striated muscle that may also function as a molecular scaffold for myofibrillar assembly. Molecular analysis and immunostaining with antibodies to multiple titin epitopes indicates that the chromosomal and muscle forms of titin may vary in their NH2 termini. The identification of titin as a chromosomal component provides a molecular basis for chromosome structure and elasticity. PMID:9548712

W49A: A Massive Molecular Cloud Forming a Massive Star Cluster in the Galactic Disk

NASA Astrophysics Data System (ADS)

Galvan-Madrid, Roberto; Liu, Hauyu Baobab; Pineda, Jaime E.; Zhang, Zhi-Yu; Ginsburg, Adam; Roman-Zuñiga, Carlos; Peters, Thomas

2015-08-01

I summarize our current results of the MUSCLE survey of W49A, the most luminous star formation region in the Milky Way. Our approach emphasizes multi-scale, multi-resolution imaging in dust, ionized-, and molecular gas, to trace the multiple gas components from <0.1 pc (core scale) all the way up to the scale of the entire giant molecular cloud (GMC), ˜100 pc. The 106 M⊙ GMC is structured in a radial network of filaments that converges toward the central 'hub' with ˜2x105 M⊙, which contains within a few pc a deeply embedded young massive cluster (YMC) of stellar mass ~5x104 M⊙. We also discuss the dynamics of the filamentary network, the role of turbulence in the formation of this YMC, and how objects like W49A can link Milky Way and extragalactic star formation relations.

Molecular dynamics study of the encapsulation capability of a PCL-PEO based block copolymer for hydrophobic drugs with different spatial distributions of hydrogen bond donors and acceptors.

PubMed

Patel, Sarthak K; Lavasanifar, Afsaneh; Choi, Phillip

2010-03-01

Molecular dynamics simulation was used to study the potential of using a block copolymer containing three poly(epsilon-caprolactone) (PCL) blocks of equal length connected to one end of a poly(ethylene oxide) (PEO) block, designated as PEO-b-3PCL, to encapsulate two classes of hydrophobic drugs with distinctively different molecular structures. In particular, the first class of drugs consisted of two cucurbitacin drugs (CuB and CuI) that contain multiple hydrogen bond donors and acceptors evenly distributed on their molecules while the other class of drugs (fenofibrate and nimodipine) contain essentially only clustered hydrogen bond acceptors. In the case of cucurbitacin drugs, the results showed that PEO-b-3PCL lowered the Flory-Huggins interaction parameters (chi) considerably (i.e., increased the drug solubility) compared to the linear di-block copolymer PEO-b-PCL with the same PCL/PEO (w/w) ratio of 1.0. However, the opposite effect was observed for fenofibrate and nimodipine. Analysis of the intermolecular interactions indicates that the number of hydrogen bonds formed between the three PCL blocks and cucurbitacin drugs is significantly higher than that of the linear di-block copolymer. On the other hand, owing to the absence of hydrogen bond donors and the clustering of the hydrogen bond acceptors on the fenofibrate and nimodipine molecules, this significantly reduces the number of hydrogen bonds formed in the multi-PCL block environment, leading to unfavourable chi values. The findings of the present work suggest that multi-hydrophobic block architecture could potentially increase the drug loading for hydrophobic drugs with structures containing evenly distributed multiple hydrogen bond donors and acceptors. (c) 2009 Elsevier Ltd. All rights reserved.

The glycoprotein character of multiple forms of Aspergillus polygalacturonase.

PubMed

Stratilová, E; Mislovicová, D; Kacuráková, M; Machová, E; Kolarová, N; Markovic, O; Jörnvall, H

1998-02-01

Comparisons of known primary structures of polygalacturonases show that extent and localization of potential N-glycosylation sites differ. Some sites are similar in position and adjacent to strictly conserved residues at the potential active site. The presence of N-acetylglucosamine and mannose in the molecules of two homogeneous, major Aspergillus sp. polygalacturonase forms was confirmed by IR spectroscopy. The purification method, based on interaction of the carbohydrate part with concanavalin A immobilized on chlorotriazine bead cellulose, was optimized. Deglycosylation with N-glycosidase F under denaturating and nondenaturating conditions led to molecular mass decreases followed by complete inactivation of the polygalacturonase enzyme activity. These results show the importance of glycosylation in these protein forms, while the comparative patterns establish both variability and some similarities in overall glycosylation architectures.

Aqueous self-assembly of poly(ethylene oxide)-block-poly(ε-caprolactone) (PEO-b-PCL) copolymers: disparate diblock copolymer compositions give rise to nano- and meso-scale bilayered vesicles

NASA Astrophysics Data System (ADS)

Qi, Wei; Ghoroghchian, P. Peter; Li, Guizhi; Hammer, Daniel A.; Therien, Michael J.

2013-10-01

Nanoparticles formed from diblock copolymers of FDA approved PEO and PCL have generated considerable interest as in vivo drug delivery vehicles. Herein, we report the synthesis of the most extensive family PEO-b-PCL copolymers that vary over the largest range of number-average molecular weights (Mn: 3.6-57k), PEO weight fractions (fPEO: 0.08-0.33), and PEO chain lengths (0.75-5.8k) reported to date. These polymers were synthesized in order to establish the full range of aqueous phase behaviours of these diblock copolymers and to specifically identify formulations that were able to generate bilayered vesicles (polymersomes). Cryogenic transmission electron microscopy (cryo-TEM) was utilized in order to visualize the morphology of these structures upon aqueous self-assembly of dry polymer films. Nanoscale polymersomes were formed from PEO-b-PCL copolymers over a wide range of PEO weight fractions (fPEO: 0.14-0.27) and PEO molecular weights (0.75-3.8k) after extrusion of aqueous suspensions. Comparative morphology diagrams, which describe the nature of self-assembled structures as a function of diblock copolymer molecular weight and PEO weight fraction, show that in contrast to micron-scale polymersomes, which form only from a limited range of PEO-b-PCL diblock copolymer compositions, a multiplicity of PEO-b-PCL diblock copolymer compositions are able to give rise to nanoscale vesicles. These data underscore that PEO-b-PCL compositions that spontaneously form micron-sized polymersomes, as well as those that have previously been reported to form polymersomes via a cosolvent fabrication system, provide only limited insights into the distribution of PEO-b-PCL diblocks that give rise to nanoscale vesicles. The broad range of polymersome-forming PEO-b-PCL compositions described herein suggest the ability to construct extensive families of nanoscale vesicles of varied bilayer thickness, providing the ability to tune the timescales of vesicle degradation and encapsulant release based on the intended in vivo application.Nanoparticles formed from diblock copolymers of FDA approved PEO and PCL have generated considerable interest as in vivo drug delivery vehicles. Herein, we report the synthesis of the most extensive family PEO-b-PCL copolymers that vary over the largest range of number-average molecular weights (Mn: 3.6-57k), PEO weight fractions (fPEO: 0.08-0.33), and PEO chain lengths (0.75-5.8k) reported to date. These polymers were synthesized in order to establish the full range of aqueous phase behaviours of these diblock copolymers and to specifically identify formulations that were able to generate bilayered vesicles (polymersomes). Cryogenic transmission electron microscopy (cryo-TEM) was utilized in order to visualize the morphology of these structures upon aqueous self-assembly of dry polymer films. Nanoscale polymersomes were formed from PEO-b-PCL copolymers over a wide range of PEO weight fractions (fPEO: 0.14-0.27) and PEO molecular weights (0.75-3.8k) after extrusion of aqueous suspensions. Comparative morphology diagrams, which describe the nature of self-assembled structures as a function of diblock copolymer molecular weight and PEO weight fraction, show that in contrast to micron-scale polymersomes, which form only from a limited range of PEO-b-PCL diblock copolymer compositions, a multiplicity of PEO-b-PCL diblock copolymer compositions are able to give rise to nanoscale vesicles. These data underscore that PEO-b-PCL compositions that spontaneously form micron-sized polymersomes, as well as those that have previously been reported to form polymersomes via a cosolvent fabrication system, provide only limited insights into the distribution of PEO-b-PCL diblocks that give rise to nanoscale vesicles. The broad range of polymersome-forming PEO-b-PCL compositions described herein suggest the ability to construct extensive families of nanoscale vesicles of varied bilayer thickness, providing the ability to tune the timescales of vesicle degradation and encapsulant release based on the intended in vivo application. Electronic supplementary information (ESI) available: Materials and methods, characterization data. See DOI: 10.1039/c3nr03250g

Peptide aptamer-assisted immobilization of green fluorescent protein for creating biomolecule-complexed carbon nanotube device

NASA Astrophysics Data System (ADS)

Nii, Daisuke; Nozawa, Yosuke; Miyachi, Mariko; Yamanoi, Yoshinori; Nishihara, Hiroshi; Tomo, Tatsuya; Shimada, Yuichiro

2017-10-01

Carbon nanotubes are a novel material for next-generation applications. In this study, we generated carbon nanotube and green fluorescent protein (GFP) conjugates using affinity binding peptides. The carbon nanotube-binding motif was introduced into the N-terminus of the GFP through molecular biology methods. Multiple GFPs were successfully aligned on a single-walled carbon nanotube via the molecular recognition function of the peptide aptamer, which was confirmed through transmission electron microscopy and optical analysis. Fluorescence spectral analysis results also suggested that the carbon nanotube-GFP complex was autonomously formed with orientation and without causing protein denaturation during immobilization. This simple process has a widespread potential for fabricating carbon nanotube-biomolecule hybrid devices.

Entering the 'big data' era in medicinal chemistry: molecular promiscuity analysis revisited.

PubMed

Hu, Ye; Bajorath, Jürgen

2017-06-01

The 'big data' concept plays an increasingly important role in many scientific fields. Big data involves more than unprecedentedly large volumes of data that become available. Different criteria characterizing big data must be carefully considered in computational data mining, as we discuss herein focusing on medicinal chemistry. This is a scientific discipline where big data is beginning to emerge and provide new opportunities. For example, the ability of many drugs to specifically interact with multiple targets, termed promiscuity, forms the molecular basis of polypharmacology, a hot topic in drug discovery. Compound promiscuity analysis is an area that is much influenced by big data phenomena. Different results are obtained depending on chosen data selection and confidence criteria, as we also demonstrate.

Method of making molecularly doped composite polymer material

DOEpatents

Affinito, John D [Tucson, AZ; Martin, Peter M [Kennewick, WA; Graff, Gordon L [West Richland, WA; Burrows, Paul E [Kennewick, WA; Gross, Mark E. , Sapochak, Linda S.

2005-06-21

A method of making a composite polymer of a molecularly doped polymer. The method includes mixing a liquid polymer precursor with molecular dopant forming a molecularly doped polymer precursor mixture. The molecularly doped polymer precursor mixture is flash evaporated forming a composite vapor. The composite vapor is cryocondensed on a cool substrate forming a composite molecularly doped polymer precursor layer, and the cryocondensed composite molecularly doped polymer precursor layer is cross linked thereby forming a layer of the composite polymer layer of the molecularly doped polymer.

Brg1 coordinates multiple processes during retinogenesis and is a tumor suppressor in retinoblastoma

DOE PAGES

Aldiri, Issam; Ajioka, Itsuki; Xu, Beisi; ...

2015-12-01

Retinal development requires precise temporal and spatial coordination of cell cycle exit, cell fate specification, cell migration and differentiation. When this process is disrupted, retinoblastoma, a developmental tumor of the retina, can form. Epigenetic modulators are central to precisely coordinating developmental events, and many epigenetic processes have been implicated in cancer. Studying epigenetic mechanisms in development is challenging because they often regulate multiple cellular processes; therefore, elucidating the primary molecular mechanisms involved can be difficult. Here we explore the role of Brg1 (Smarca4) in retinal development and retinoblastoma in mice using molecular and cellular approaches. Brg1 was found to regulatemore » retinal size by controlling cell cycle length, cell cycle exit and cell survival during development. Brg1 was not required for cell fate specification but was required for photoreceptor differentiation and cell adhesion/polarity programs that contribute to proper retinal lamination during development. The combination of defective cell differentiation and lamination led to retinal degeneration in Brg1-deficient retinae. Despite the hypocellularity, premature cell cycle exit, increased cell death and extended cell cycle length, retinal progenitor cells persisted in Brg1-deficient retinae, making them more susceptible to retinoblastoma. In conclusion, ChIP-Seq analysis suggests that Brg1 might regulate gene expression through multiple mechanisms.« less

Molecular Insights into the Effects of Media-Drug and Carrier-Drug Interactions on pH-Responsive Drug Carriers.

PubMed

Katiyar, Ratna S; Jha, Prateek K

2018-05-10

We have performed two sets of all atom molecular dynamics (MD) simulations of poly(acrylic acid) (PAA) oligomers, considered as a model pH-responsive drug carrier. In the first set, multiple oligomers of PAA are simulated in model gastric and intestinal fluids, where the degree of deprotonation of PAA oligomers is varied with the medium pH. Since the gastric fluid has a pH substantially lower than that of intestinal fluid, PAA is relatively lesser ionized in gastric fluid and forms aggregates. In the second set, we simulated multiple oligomers of PAA with multiple molecules of a cationic anticancer drug, doxorubicin (DOX), for a range of pH values representative of various physiological conditions. The diffusion coefficient of DOX decreases with an increase in pH due to an increase in the ionic complexation of PAA with DOX, despite a decrease in PAA aggregation. Our findings are in agreement with recent experimental reports on pH-triggered targeting of tumor cells by the PAA-DOX system. Results of these two sets of studies establish that both carrier aggregation and carrier-drug interactions are competing influences that together determine the drug release from pH-responsive polymers.

Brg1 coordinates multiple processes during retinogenesis and is a tumor suppressor in retinoblastoma

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

Aldiri, Issam; Ajioka, Itsuki; Xu, Beisi

Retinal development requires precise temporal and spatial coordination of cell cycle exit, cell fate specification, cell migration and differentiation. When this process is disrupted, retinoblastoma, a developmental tumor of the retina, can form. Epigenetic modulators are central to precisely coordinating developmental events, and many epigenetic processes have been implicated in cancer. Studying epigenetic mechanisms in development is challenging because they often regulate multiple cellular processes; therefore, elucidating the primary molecular mechanisms involved can be difficult. Here we explore the role of Brg1 (Smarca4) in retinal development and retinoblastoma in mice using molecular and cellular approaches. Brg1 was found to regulatemore » retinal size by controlling cell cycle length, cell cycle exit and cell survival during development. Brg1 was not required for cell fate specification but was required for photoreceptor differentiation and cell adhesion/polarity programs that contribute to proper retinal lamination during development. The combination of defective cell differentiation and lamination led to retinal degeneration in Brg1-deficient retinae. Despite the hypocellularity, premature cell cycle exit, increased cell death and extended cell cycle length, retinal progenitor cells persisted in Brg1-deficient retinae, making them more susceptible to retinoblastoma. In conclusion, ChIP-Seq analysis suggests that Brg1 might regulate gene expression through multiple mechanisms.« less

Identification of molecular markers associated with mite resistance in coconut (Cocos nucifera L.).

PubMed

Shalini, K V; Manjunatha, S; Lebrun, P; Berger, A; Baudouin, L; Pirany, N; Ranganath, R M; Prasad, D Theertha

2007-01-01

Coconut mite (Aceria guerreronis 'Keifer') has become a major threat to Indian coconut (Coçcos nucifera L.) cultivators and the processing industry. Chemical and biological control measures have proved to be costly, ineffective, and ecologically undesirable. Planting mite-resistant coconut cultivars is the most effective method of preventing yield loss and should form a major component of any integrated pest management stratagem. Coconut genotypes, and mite-resistant and -susceptible accessions were collected from different parts of South India. Thirty-two simple sequence repeat (SSR) and 7 RAPD primers were used for molecular analyses. In single-marker analysis, 9 SSR and 4 RAPD markers associated with mite resistance were identified. In stepwise multiple regression analysis of SSRs, a combination of 6 markers showed 100% association with mite infestation. Stepwise multiple regression analysis for RAPD data revealed that a combination of 3 markers accounted for 83.86% of mite resistance in the selected materials. Combined stepwise multiple regression analysis of RAPD and SSR data showed that a combination of 5 markers explained 100% of the association with mite resistance in coconut. Markers associated with mite resistance are important in coconut breeding programs and will facilitate the selection of mite-resistant plants at an early stage as well as mother plants for breeding programs.

Resolution of Site-Specific Conformational Heterogeneity in Proline-Rich Molecular Recognition by Src Homology 3 Domains.

PubMed

Horness, Rachel E; Basom, Edward J; Mayer, John P; Thielges, Megan C

2016-02-03

Conformational heterogeneity and dynamics are increasingly evoked in models of protein molecular recognition but are challenging to experimentally characterize. Here we combine the inherent temporal resolution of infrared (IR) spectroscopy with the spatial resolution afforded by selective incorporation of carbon-deuterium (C-D) bonds, which provide frequency-resolved absorptions within a protein IR spectrum, to characterize the molecular recognition of the Src homology 3 (SH3) domain of the yeast protein Sho1 with its cognate proline-rich (PR) sequence of Pbs2. The IR absorptions of C-D bonds introduced at residues along a peptide of the Pbs2 PR sequence report on the changes in the local environments upon binding to the SH3 domain. Interestingly, upon forming the complex the IR spectra of the peptides labeled with C-D bonds at either of the two conserved prolines of the PXXP consensus recognition sequence show more absorptions than there are C-D bonds, providing evidence for the population of multiple states. In contrast, the NMR spectra of the peptides labeled with (13)C at the same residues show only single resonances, indicating rapid interconversion on the NMR time scale. Thus, the data suggest that the SH3 domain recognizes its cognate peptide with a component of induced fit molecular recognition involving the adoption of multiples states, which have previously gone undetected due to interconversion between the populated states that is too fast to resolve using conventional methods.

Formation and emission mechanisms of Ag nanoclusters in the Ar matrix assembly cluster source

NASA Astrophysics Data System (ADS)

Zhao, Junlei; Cao, Lu; Palmer, Richard E.; Nordlund, Kai; Djurabekova, Flyura

2017-11-01

In this paper, we study the mechanisms of growth of Ag nanoclusters in a solid Ar matrix and the emission of these nanoclusters from the matrix by a combination of experimental and theoretical methods. The molecular dynamics simulations show that the cluster growth mechanism can be described as "thermal spike-enhanced clustering" in multiple sequential ion impact events. We further show that experimentally observed large sputtered metal clusters cannot be formed by direct sputtering of Ag mixed in the Ar. Instead, we describe the mechanism of emission of the metal nanocluster that, at first, is formed in the cryogenic matrix due to multiple ion impacts, and then is emitted as a result of the simultaneous effects of interface boiling and spring force. We also develop an analytical model describing this size-dependent cluster emission. The model bridges the atomistic simulations and experimental time and length scales, and allows increasing the controllability of fast generation of nanoclusters in experiments with a high production rate.

The Physical Origin of Long Gas Depletion Times in Galaxies

NASA Astrophysics Data System (ADS)

Semenov, Vadim A.; Kravtsov, Andrey V.; Gnedin, Nickolay Y.

2017-08-01

We present a model that explains why galaxies form stars on a timescale significantly longer than the timescales of processes governing the evolution of interstellar gas. We show that gas evolves from a non-star-forming to a star-forming state on a relatively short timescale, and thus the rate of this evolution does not limit the star formation rate (SFR). Instead, the SFR is limited because only a small fraction of star-forming gas is converted into stars before star-forming regions are dispersed by feedback and dynamical processes. Thus, gas cycles into and out of a star-forming state multiple times, which results in a long timescale on which galaxies convert gas into stars. Our model does not rely on the assumption of equilibrium and can be used to interpret trends of depletion times with the properties of observed galaxies and the parameters of star formation and feedback recipes in simulations. In particular, the model explains how feedback self-regulates the SFR in simulations and makes it insensitive to the local star formation efficiency. We illustrate our model using the results of an isolated L *-sized galaxy simulation that reproduces the observed Kennicutt-Schmidt relation for both molecular and atomic gas. Interestingly, the relation for molecular gas is almost linear on kiloparsec scales, although a nonlinear relation is adopted in simulation cells. We discuss how a linear relation emerges from non-self-similar scaling of the gas density PDF with the average gas surface density.

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

Semenov, Vadim A.; Kravtsov, Andrey V.; Gnedin, Nickolay Y., E-mail: semenov@uchicago.edu

We present a model that explains why galaxies form stars on a timescale significantly longer than the timescales of processes governing the evolution of interstellar gas. We show that gas evolves from a non-star-forming to a star-forming state on a relatively short timescale, and thus the rate of this evolution does not limit the star formation rate (SFR). Instead, the SFR is limited because only a small fraction of star-forming gas is converted into stars before star-forming regions are dispersed by feedback and dynamical processes. Thus, gas cycles into and out of a star-forming state multiple times, which results inmore » a long timescale on which galaxies convert gas into stars. Our model does not rely on the assumption of equilibrium and can be used to interpret trends of depletion times with the properties of observed galaxies and the parameters of star formation and feedback recipes in simulations. In particular, the model explains how feedback self-regulates the SFR in simulations and makes it insensitive to the local star formation efficiency. We illustrate our model using the results of an isolated L {sub *}-sized galaxy simulation that reproduces the observed Kennicutt–Schmidt relation for both molecular and atomic gas. Interestingly, the relation for molecular gas is almost linear on kiloparsec scales, although a nonlinear relation is adopted in simulation cells. We discuss how a linear relation emerges from non-self-similar scaling of the gas density PDF with the average gas surface density.« less

Mach Cones in a Coulomb Lattice and a Dusty Plasma

NASA Astrophysics Data System (ADS)

Samsonov, D.; Goree, J.; Ma, Z. W.; Bhattacharjee, A.; Thomas, H. M.; Morfill, G. E.

1999-11-01

Mach cones, or V-shaped disturbances created by supersonic objects, have been detected in a two-dimensional Coulomb crystal. Electrically charged microspheres levitated in a glow-discharge plasma formed a dusty plasma, with particles arranged in a hexagonal lattice in a horizontal plane. Beneath this lattice plane, a sphere moved faster than the lattice sound speed. Mach cones were double, first compressive then rarefactive, due to the strongly coupled crystalline state. Molecular dynamics simulations using a Yukawa potential also show multiple Mach cones.

A many-body states picture of electronic friction: The case of multiple orbitals and multiple electronic states

NASA Astrophysics Data System (ADS)

Dou, Wenjie; Subotnik, Joseph E.

2016-08-01

We present a very general form of electronic friction as present when a molecule with multiple orbitals hybridizes with a metal electrode. To develop this picture of friction, we embed the quantum-classical Liouville equation (QCLE) within a classical master equation (CME). Thus, this article extends our previous work analyzing the case of one electronic level, as we may now treat the case of multiple levels and many electronic molecular states. We show that, in the adiabatic limit, where electron transitions are much faster than nuclear motion, the QCLE-CME reduces to a Fokker-Planck equation, such that nuclei feel an average force as well as friction and a random force—as caused by their interaction with the metallic electrons. Finally, we show numerically and analytically that our frictional results agree with other published results calculated using non-equilibrium Green's functions. Numerical recipes for solving this QCLE-CME will be provided in a subsequent paper.

A many-body states picture of electronic friction: The case of multiple orbitals and multiple electronic states

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

Dou, Wenjie; Subotnik, Joseph E.

We present a very general form of electronic friction as present when a molecule with multiple orbitals hybridizes with a metal electrode. To develop this picture of friction, we embed the quantum-classical Liouville equation (QCLE) within a classical master equation (CME). Thus, this article extends our previous work analyzing the case of one electronic level, as we may now treat the case of multiple levels and many electronic molecular states. We show that, in the adiabatic limit, where electron transitions are much faster than nuclear motion, the QCLE-CME reduces to a Fokker-Planck equation, such that nuclei feel an average forcemore » as well as friction and a random force—as caused by their interaction with the metallic electrons. Finally, we show numerically and analytically that our frictional results agree with other published results calculated using non-equilibrium Green’s functions. Numerical recipes for solving this QCLE-CME will be provided in a subsequent paper.« less

Pediatric schwannomatosis, a rare but distinct form of neurofibromatosis.

PubMed

Thomas, Anna K; Egelhoff, John C; Curran, John G; Thomas, Bobby

2016-03-01

Schwannomatosis is the third major form of neurofibromatosis, distinct from neurofibromatosis type 2 (NF2) and type 1 (NF1). This condition is rare with a variable phenotypic presentation and complex molecular and genetic findings. In this case, a previously healthy teenager was found to have multiple spinal lesions and an enhancing right parotid mass on MRI. On extensive further work-up, this patient met the existing clinical criteria for schwannomatosis. This case report aims to review the clinical features and current diagnostic criteria for schwannomatosis and compare it to NF1 and NF2. Special emphasis will be placed on imaging features that should prompt the radiologist to suggest this rare diagnosis.

Nanoscale architecture of the Schizosaccharomyces pombe contractile ring.

PubMed

McDonald, Nathan A; Lind, Abigail L; Smith, Sarah E; Li, Rong; Gould, Kathleen L

2017-09-15

The contractile ring is a complex molecular apparatus which physically divides many eukaryotic cells. Despite knowledge of its protein composition, the molecular architecture of the ring is not known. Here we have applied super-resolution microscopy and FRET to determine the nanoscale spatial organization of Schizosaccharomyces pombe contractile ring components relative to the plasma membrane. Similar to other membrane-tethered actin structures, we find proteins localize in specific layers relative to the membrane. The most membrane-proximal layer (0-80 nm) is composed of membrane-binding scaffolds, formin, and the tail of the essential myosin-II. An intermediate layer (80-160 nm) consists of a network of cytokinesis accessory proteins as well as multiple signaling components which influence cell division. Farthest from the membrane (160-350 nm) we find F-actin, the motor domains of myosins, and a major F-actin crosslinker. Circumferentially within the ring, multiple proteins proximal to the membrane form clusters of different sizes, while components farther from the membrane are uniformly distributed. This comprehensive organizational map provides a framework for understanding contractile ring function.

Nanoscale architecture of the Schizosaccharomyces pombe contractile ring

PubMed Central

McDonald, Nathan A; Lind, Abigail L; Smith, Sarah E; Li, Rong

2017-01-01

The contractile ring is a complex molecular apparatus which physically divides many eukaryotic cells. Despite knowledge of its protein composition, the molecular architecture of the ring is not known. Here we have applied super-resolution microscopy and FRET to determine the nanoscale spatial organization of Schizosaccharomyces pombe contractile ring components relative to the plasma membrane. Similar to other membrane-tethered actin structures, we find proteins localize in specific layers relative to the membrane. The most membrane-proximal layer (0–80 nm) is composed of membrane-binding scaffolds, formin, and the tail of the essential myosin-II. An intermediate layer (80–160 nm) consists of a network of cytokinesis accessory proteins as well as multiple signaling components which influence cell division. Farthest from the membrane (160–350 nm) we find F-actin, the motor domains of myosins, and a major F-actin crosslinker. Circumferentially within the ring, multiple proteins proximal to the membrane form clusters of different sizes, while components farther from the membrane are uniformly distributed. This comprehensive organizational map provides a framework for understanding contractile ring function. PMID:28914606

The Trophic Life Cycle Stage of the Opportunistic Fungal Pathogen Pneumocystis murina Hinders the Ability of Dendritic Cells To Stimulate CD4+ T Cell Responses

PubMed Central

Evans, Heather M.; Simpson, Andrew; Shen, Shu; Stromberg, Arnold J.; Pickett, Carol L.

2017-01-01

ABSTRACT The life cycle of the opportunistic fungal pathogen Pneumocystis murina consists of a trophic stage and an ascus-like cystic stage. Infection with the cyst stage induces proinflammatory immune responses, while trophic forms suppress the cytokine response to multiple pathogen-associated molecular patterns (PAMPs), including β-glucan. A targeted gene expression assay was used to evaluate the dendritic cell response following stimulation with trophic forms alone, with a normal mixture of trophic forms and cysts, or with β-glucan. We demonstrate that stimulation with trophic forms downregulated the expression of multiple genes normally associated with the response to infection, including genes encoding transcription factors. Trophic forms also suppressed the expression of genes related to antigen processing and presentation, including the gene encoding the major histocompatibility complex (MHC) class II transactivator, CIITA. Stimulation of dendritic cells with trophic forms, but not a mixture of trophic forms and cysts, reduced the expression of MHC class II and the costimulatory molecule CD40 on the surface of the cells. These defects in the expression of MHC class II and costimulatory molecules corresponded with a reduced capacity for trophic form-loaded dendritic cells to stimulate CD4+ T cell proliferation and polarization. These data are consistent with the delayed innate and adaptive responses previously observed in immunocompetent mice inoculated with trophic forms compared to responses in mice inoculated with a mixture of trophic forms and cysts. We propose that trophic forms broadly inhibit the ability of dendritic cells to fulfill their role as antigen-presenting cells. PMID:28694293

Mass Spectrometry: A Technique of Many Faces

PubMed Central

Olshina, Maya A.; Sharon, Michal

2016-01-01

Protein complexes form the critical foundation for a wide range of biological process, however understanding the intricate details of their activities is often challenging. In this review we describe how mass spectrometry plays a key role in the analysis of protein assemblies and the cellular pathways which they are involved in. Specifically, we discuss how the versatility of mass spectrometric approaches provides unprecedented information on multiple levels. We demonstrate this on the ubiquitin-proteasome proteolytic pathway, a process that is responsible for protein turnover. We follow the various steps of this degradation route and illustrate the different mass spectrometry workflows that were applied for elucidating molecular information. Overall, this review aims to stimulate the integrated use of multiple mass spectrometry approaches for analyzing complex biological systems. PMID:28100928

Live-cell visualization of gasdermin D-driven pyroptotic cell death.

PubMed

Rathkey, Joseph K; Benson, Bryan L; Chirieleison, Steven M; Yang, Jie; Xiao, Tsan S; Dubyak, George R; Huang, Alex Y; Abbott, Derek W

2017-09-01

Pyroptosis is a form of cell death important in defenses against pathogens that can also result in a potent and sometimes pathological inflammatory response. During pyroptosis, GSDMD (gasdermin D), the pore-forming effector protein, is cleaved, forms oligomers, and inserts into the membranes of the cell, resulting in rapid cell death. However, the potent cell death induction caused by GSDMD has complicated our ability to understand the biology of this protein. Studies aimed at visualizing GSDMD have relied on expression of GSDMD fragments in epithelial cell lines that naturally lack GSDMD expression and also lack the proteases necessary to cleave GSDMD. In this work, we performed mutagenesis and molecular modeling to strategically place tags and fluorescent proteins within GSDMD that support native pyroptosis and facilitate live-cell imaging of pyroptotic cell death. Here, we demonstrate that these fusion proteins are cleaved by caspases-1 and -11 at Asp-276. Mutations that disrupted the predicted p30-p20 autoinhibitory interface resulted in GSDMD aggregation, supporting the oligomerizing activity of these mutations. Furthermore, we show that these novel GSDMD fusions execute inflammasome-dependent pyroptotic cell death in response to multiple stimuli and allow for visualization of the morphological changes associated with pyroptotic cell death in real time. This work therefore provides new tools that not only expand the molecular understanding of pyroptosis but also enable its direct visualization. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Driven and decaying turbulence simulations of low–mass star formation: From clumps to cores to protostars

DOE PAGES

Offner, Stella S. R.; Klein, Richard I.; McKee, Christopher F.

2008-10-20

Molecular clouds are observed to be turbulent, but the origin of this turbulence is not well understood. As a result, there are two different approaches to simulating molecular clouds, one in which the turbulence is allowed to decay after it is initialized, and one in which it is driven. We use the adaptive mesh refinement (AMR) code, Orion, to perform high-resolution simulations of molecular cloud cores and protostars in environments with both driven and decaying turbulence. We include self-gravity, use a barotropic equation of state, and represent regions exceeding the maximum grid resolution with sink particles. We analyze the propertiesmore » of bound cores such as size, shape, line width, and rotational energy, and we find reasonable agreement with observation. At high resolution the different rates of core accretion in the two cases have a significant effect on protostellar system development. Clumps forming in a decaying turbulence environment produce high-multiplicity protostellar systems with Toomre Q unstable disks that exhibit characteristics of the competitive accretion model for star formation. In contrast, cores forming in the context of continuously driven turbulence and virial equilibrium form smaller protostellar systems with fewer low-mass members. Furthermore, our simulations of driven and decaying turbulence show some statistically significant differences, particularly in the production of brown dwarfs and core rotation, but the uncertainties are large enough that we are not able to conclude whether observations favor one or the other.« less

Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations

PubMed Central

Dixit, Anshuman; Verkhivker, Gennady M.

2009-01-01

Structural and functional studies of the ABL and EGFR kinase domains have recently suggested a common mechanism of activation by cancer-causing mutations. However, dynamics and mechanistic aspects of kinase activation by cancer mutations that stimulate conformational transitions and thermodynamic stabilization of the constitutively active kinase form remain elusive. We present a large-scale computational investigation of activation mechanisms in the ABL and EGFR kinase domains by a panel of clinically important cancer mutants ABL-T315I, ABL-L387M, EGFR-T790M, and EGFR-L858R. We have also simulated the activating effect of the gatekeeper mutation on conformational dynamics and allosteric interactions in functional states of the ABL-SH2-SH3 regulatory complexes. A comprehensive analysis was conducted using a hierarchy of computational approaches that included homology modeling, molecular dynamics simulations, protein stability analysis, targeted molecular dynamics, and molecular docking. Collectively, the results of this study have revealed thermodynamic and mechanistic catalysts of kinase activation by major cancer-causing mutations in the ABL and EGFR kinase domains. By using multiple crystallographic states of ABL and EGFR, computer simulations have allowed one to map dynamics of conformational fluctuations and transitions in the normal (wild-type) and oncogenic kinase forms. A proposed multi-stage mechanistic model of activation involves a series of cooperative transitions between different conformational states, including assembly of the hydrophobic spine, the formation of the Src-like intermediate structure, and a cooperative breakage and formation of characteristic salt bridges, which signify transition to the active kinase form. We suggest that molecular mechanisms of activation by cancer mutations could mimic the activation process of the normal kinase, yet exploiting conserved structural catalysts to accelerate a conformational transition and the enhanced stabilization of the active kinase form. The results of this study reconcile current experimental data with insights from theoretical approaches, pointing to general mechanistic aspects of activating transitions in protein kinases. PMID:19714203

Formation of new stellar populations from gas accreted by massive young star clusters.

PubMed

Li, Chengyuan; de Grijs, Richard; Deng, Licai; Geller, Aaron M; Xin, Yu; Hu, Yi; Faucher-Giguère, Claude-André

2016-01-28

Stars in clusters are thought to form in a single burst from a common progenitor cloud of molecular gas. However, massive, old 'globular' clusters--those with ages greater than ten billion years and masses several hundred thousand times that of the Sun--often harbour multiple stellar populations, indicating that more than one star-forming event occurred during their lifetimes. Colliding stellar winds from late-stage, asymptotic-giant-branch stars are often suggested to be triggers of second-generation star formation. For this to occur, the initial cluster masses need to be greater than a few million solar masses. Here we report observations of three massive relatively young star clusters (1-2 billion years old) in the Magellanic Clouds that show clear evidence of burst-like star formation that occurred a few hundred million years after their initial formation era. We show that such clusters could have accreted sufficient gas to form new stars if they had orbited in their host galaxies' gaseous disks throughout the period between their initial formation and the more recent bursts of star formation. This process may eventually give rise to the ubiquitous multiple stellar populations in globular clusters.

Structuring of Hydrogels across Multiple Length Scales for Biomedical Applications.

PubMed

Cooke, Megan E; Jones, Simon W; Ter Horst, Britt; Moiemen, Naiem; Snow, Martyn; Chouhan, Gurpreet; Hill, Lisa J; Esmaeli, Maryam; Moakes, Richard J A; Holton, James; Nandra, Rajpal; Williams, Richard L; Smith, Alan M; Grover, Liam M

2018-04-01

The development of new materials for clinical use is limited by an onerous regulatory framework, which means that taking a completely new material into the clinic can make translation economically unfeasible. One way to get around this issue is to structure materials that are already approved by the regulator, such that they exhibit very distinct physical properties and can be used in a broader range of clinical applications. Here, the focus is on the structuring of soft materials at multiple length scales by modifying processing conditions. By applying shear to newly forming materials, it is possible to trigger molecular reorganization of polymer chains, such that they aggregate to form particles and ribbon-like structures. These structures then weakly interact at zero shear forming a solid-like material. The resulting self-healing network is of particular use for a range of different biomedical applications. How these materials are used to allow the delivery of therapeutic entities (cells and proteins) and as a support for additive layer manufacturing of larger-scale tissue constructs is discussed. This technology enables the development of a range of novel materials and structures for tissue augmentation and regeneration. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

THE EGNoG SURVEY: GAS EXCITATION IN NORMAL GALAXIES AT z Almost-Equal-To 0.3

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

Bauermeister, A.; Blitz, L.; Wright, M.

As observations of molecular gas in galaxies are pushed to lower star formation rate (SFR) galaxies at higher redshifts, it is becoming increasingly important to understand the conditions of the gas in these systems to properly infer their molecular gas content. The rotational transitions of the carbon monoxide (CO) molecule provide an excellent probe of the gas excitation conditions in these galaxies. In this paper, we present the results from the gas excitation sample of the Evolution of molecular Gas in Normal Galaxies (EGNoG) survey at the Combined Array for Research in Millimeter-wave Astronomy (CARMA). This subset of the fullmore » EGNoG sample consists of four galaxies at z Almost-Equal-To 0.3 with SFRs of 40-65 M {sub Sun} yr{sup -1} and stellar masses of Almost-Equal-To 2 Multiplication-Sign 10{sup 11} M {sub Sun }. Using the 3 mm and 1 mm bands at CARMA, we observe both the CO(J = 1 {yields} 0) and CO(J = 3 {yields} 2) transitions in these four galaxies in order to probe the excitation of the molecular gas. We report robust detections of both lines in three galaxies (and an upper limit on the fourth), with an average line ratio, r {sub 31} = L'{sub CO(3-2)}/L'{sub CO(1-0)}, of 0.46 {+-} 0.07 (with systematic errors {approx}< 40%), which implies sub-thermal excitation of the CO(J = 3 {yields} 2) line. We conclude that the excitation of the gas in these massive, highly star-forming galaxies is consistent with normal star-forming galaxies such as local spirals, not starbursting systems like local ultraluminous infrared galaxies. Since the EGNoG gas excitation sample galaxies are selected from the main sequence (MS) of star-forming galaxies, we suggest that this result is applicable to studies of MS galaxies at intermediate and high redshifts, supporting the assumptions made in studies that find molecular gas fractions in star-forming galaxies at z {approx} 1-2 to be an order of magnitude larger than what is observed locally.« less

A new approach to the method of source-sink potentials for molecular conduction

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

Pickup, Barry T., E-mail: B.T.Pickup@sheffield.ac.uk, E-mail: P.W.Fowler@sheffield.ac.uk; Fowler, Patrick W., E-mail: B.T.Pickup@sheffield.ac.uk, E-mail: P.W.Fowler@sheffield.ac.uk; Borg, Martha

2015-11-21

We re-derive the tight-binding source-sink potential (SSP) equations for ballistic conduction through conjugated molecular structures in a form that avoids singularities. This enables derivation of new results for families of molecular devices in terms of eigenvectors and eigenvalues of the adjacency matrix of the molecular graph. In particular, we define the transmission of electrons through individual molecular orbitals (MO) and through MO shells. We make explicit the behaviour of the total current and individual MO and shell currents at molecular eigenvalues. A rich variety of behaviour is found. A SSP device has specific insulation or conduction at an eigenvalue ofmore » the molecular graph (a root of the characteristic polynomial) according to the multiplicities of that value in the spectra of four defined device polynomials. Conduction near eigenvalues is dominated by the transmission curves of nearby shells. A shell may be inert or active. An inert shell does not conduct at any energy, not even at its own eigenvalue. Conduction may occur at the eigenvalue of an inert shell, but is then carried entirely by other shells. If a shell is active, it carries all conduction at its own eigenvalue. For bipartite molecular graphs (alternant molecules), orbital conduction properties are governed by a pairing theorem. Inertness of shells for families such as chains and rings is predicted by selection rules based on node counting and degeneracy.« less

Nucleotide Dependent Switching in Rho GTPase: Conformational Heterogeneity and Competing Molecular Interactions

PubMed Central

Kumawat, Amit; Chakrabarty, Suman; Kulkarni, Kiran

2017-01-01

Ras superfamily of GTPases regulate myriad cellular processes through a conserved nucleotide (GTP/GDP) dependent switching mechanism. Unlike Ras family of GTPases, for the Rho GTPases, there is no clear evidence for the existence of “sub-states” such as state 1 & state 2 in the GTP bound form. To explore the nucleotide dependent conformational space of the Switch I loop and also to look for existence of state 1 like conformations in Rho GTPases, atomistic molecular dynamics and metadynamics simulations on RhoA were performed. These studies demonstrate that both the nucleotide-free state and the GDP bound “OFF” state have very similar conformations, whereas the GTP bound “ON” state has unique conformations with signatures of two intermediate states. The conformational free energy landscape for these systems suggests the presence of multiple intermediate states. Interestingly, the energetic penalty of exposing the non-polar residues in the GTP bound form is counter balanced by the favourable hydrogen bonded interactions between the γ-phosphate group of GTP with the highly conserved Tyr34 and Thr37 residues. These competing molecular interactions lead to a tuneable energy landscape of the Switch I conformation, which can undergo significant changes based on the local environment including changes upon binding to effectors. PMID:28374773

Molecular Evolution of Aralkylamine N-Acetyltransferase in Fish: A Genomic Survey.

PubMed

Li, Jia; You, Xinxin; Bian, Chao; Yu, Hui; Coon, Steven L; Shi, Qiong

2015-12-31

All living organisms synchronize biological functions with environmental changes; melatonin plays a vital role in regulating daily and seasonal variations. Due to rhythmic activity of the timezyme aralkylamine N-acetyltransferase (AANAT), the blood level of melatonin increases at night and decreases during daytime. Whereas other vertebrates have a single form of AANAT, bony fishes possess various isoforms of aanat genes, though the reasons are still unclear. Here, we have taken advantage of multiple unpublished teleost aanat sequences to explore and expand our understanding of the molecular evolution of aanat in fish. Our results confirm that two rounds of whole-genome duplication (WGD) led to the existence of three fish isoforms of aanat, i.e., aanat1a, aanat1b, and aanat2; in addition, gene loss led to the absence of some forms from certain special fish species. Furthermore, we suggest the different roles of two aanat1s in amphibious mudskippers, and speculate that the loss of aanat1a, may be related to terrestrial vision change. Several important sites of AANAT proteins and regulatory elements of aanat genes were analyzed for structural comparison and functional forecasting, respectively, which provides insights into the molecular evolution of the differences between AANAT1 and AANAT2.

More Than Filaments and Cores: Statistical Study of Structure Formation and Dynamics in Nearby Molecular Clouds

NASA Astrophysics Data System (ADS)

Chen, How-Huan; Goodman, Alyssa

2018-01-01

In the past decade, multiple attempts at understanding the connection between filaments and star forming cores have been made using observations across the entire epectrum. However, the filaments and the cores are usually treated as predefined--and well-defined--entities, instead of structures that often come at different sizes, shapes, with substantially different dynamics, and inter-connected at different scales. In my dissertation, I present an array of studies using different statistical methods, including the dendrogram and the probability distribution function (PDF), of structures at different size scales within nearby molecular clouds. These structures are identified using observations of different density tracers, and where possible, in the multi-dimensional parameter space of key dynamic properties--the LSR velocity, the velocity dispersion, and the column density. The goal is to give an overview of structure formation in nearby star-forming clouds, as well as of the dynamics in these structures. I find that the overall statistical properties of a larger structure is often the summation/superposition of sub-structures within, and that there could be significant variations due to local physical processes. I also find that the star formation process within molecular clouds could in fact take place in a non-monolithic manner, connecting potentially merging and/or transient structures, at different scales.

Nucleotide Dependent Switching in Rho GTPase: Conformational Heterogeneity and Competing Molecular Interactions

NASA Astrophysics Data System (ADS)

Kumawat, Amit; Chakrabarty, Suman; Kulkarni, Kiran

2017-04-01

Ras superfamily of GTPases regulate myriad cellular processes through a conserved nucleotide (GTP/GDP) dependent switching mechanism. Unlike Ras family of GTPases, for the Rho GTPases, there is no clear evidence for the existence of “sub-states” such as state 1 & state 2 in the GTP bound form. To explore the nucleotide dependent conformational space of the Switch I loop and also to look for existence of state 1 like conformations in Rho GTPases, atomistic molecular dynamics and metadynamics simulations on RhoA were performed. These studies demonstrate that both the nucleotide-free state and the GDP bound “OFF” state have very similar conformations, whereas the GTP bound “ON” state has unique conformations with signatures of two intermediate states. The conformational free energy landscape for these systems suggests the presence of multiple intermediate states. Interestingly, the energetic penalty of exposing the non-polar residues in the GTP bound form is counter balanced by the favourable hydrogen bonded interactions between the γ-phosphate group of GTP with the highly conserved Tyr34 and Thr37 residues. These competing molecular interactions lead to a tuneable energy landscape of the Switch I conformation, which can undergo significant changes based on the local environment including changes upon binding to effectors.

Anharmonic and Quantum Fluctuations in Molecular Crystals: A First-Principles Study of the Stability of Paracetamol

NASA Astrophysics Data System (ADS)

Rossi, Mariana; Gasparotto, Piero; Ceriotti, Michele

2016-09-01

Molecular crystals often exist in multiple competing polymorphs, showing significantly different physicochemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful form, a real challenge due to the combinatorial search space, and the complex interplay of subtle effects that work together to determine the relative stability of different structures. Here we take a comprehensive approach based on different flavors of thermodynamic integration in order to estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects. We take the two main stable forms of paracetamol as a paradigmatic example. We find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our analysis highlights the many challenges inherent in the development of a quantitative and predictive framework to model molecular crystals. However, it also indicates which of the components of the free energy can benefit from a cancellation of errors that can redeem the predictive power of approximate models, and suggests simple steps that could be taken to improve the reliability of ab initio crystal structure prediction.

Molecular therapy for acute myeloid leukaemia

PubMed Central

Coombs, Catherine C.; Tallman, Martin S.; Levine, Ross L.

2017-01-01

Acute myeloid leukaemia (AML) is a heterogeneous disease that is, in general, associated with a very poor prognosis. Multiple cytogenetic and molecular abnormalities that characterize different forms of AML have been used to better prognosticate patients and inform treatment decisions. Indeed, risk status in patients with this disease has classically been based on cytogenetic findings; however, additional molecular characteristics have been shown to inform risk assessment, including FLT3, NPM1, KIT, and CEBPA mutation status. Advances in sequencing technology have led to the discovery of novel somatic mutations in tissue samples from patients with AML, providing deeper insight into the mutational landscape of the disease. The majority of patients with AML (>97%) are found to have a clonal somatic abnormality on mutational profiling. Nevertheless, our understanding of the utility of mutation profiling in clinical practice remains incomplete and is continually evolving, and evidence-based approaches to application of these data are needed. In this Review, we discuss the evidence-base for integrating mutational data into treatment decisions for patients with AML, and propose novel therapeutic algorithms in the era of molecular medicine. PMID:26620272

A Computational Framework for 3D Mechanical Modeling of Plant Morphogenesis with Cellular Resolution

PubMed Central

Gilles, Benjamin; Hamant, Olivier; Boudaoud, Arezki; Traas, Jan; Godin, Christophe

2015-01-01

The link between genetic regulation and the definition of form and size during morphogenesis remains largely an open question in both plant and animal biology. This is partially due to the complexity of the process, involving extensive molecular networks, multiple feedbacks between different scales of organization and physical forces operating at multiple levels. Here we present a conceptual and modeling framework aimed at generating an integrated understanding of morphogenesis in plants. This framework is based on the biophysical properties of plant cells, which are under high internal turgor pressure, and are prevented from bursting because of the presence of a rigid cell wall. To control cell growth, the underlying molecular networks must interfere locally with the elastic and/or plastic extensibility of this cell wall. We present a model in the form of a three dimensional (3D) virtual tissue, where growth depends on the local modulation of wall mechanical properties and turgor pressure. The model shows how forces generated by turgor-pressure can act both cell autonomously and non-cell autonomously to drive growth in different directions. We use simulations to explore lateral organ formation at the shoot apical meristem. Although different scenarios lead to similar shape changes, they are not equivalent and lead to different, testable predictions regarding the mechanical and geometrical properties of the growing lateral organs. Using flower development as an example, we further show how a limited number of gene activities can explain the complex shape changes that accompany organ outgrowth. PMID:25569615

Multiplicity At Early Stages Of Star Formation, Small Clusters. Observations Overview

NASA Astrophysics Data System (ADS)

Saito, Masao

2017-07-01

The SOLA (Soul of Lupus with ALMA) project is conducting comprehensive studies of the Lupus Molecular Clouds and their star formation processes covering 10-10^4 AU scale. Our goal is to exploit ALMA and other facilities over a wide wavelength range to establish a prototypical low-mass star forming scenario based on the Lupus region. In the presentation, we will focus on angular momentum in dense cores in a filament, molecular outflows from young stars, and Class 0/I binary survey in Lupus as well as overview of our projects. Our binary survey was conducted in ALMA cycle 2 and achieved at 0.2-0.3 arcsec resolution discovering new binary systems in Lupus. At the same time, we obtained EX Lup, EXor type burst source, data in ALMA Cycle 3.

Multiplicity at Early Stages of Star Formation, Small Clusters. Observations Overview

NASA Astrophysics Data System (ADS)

Saito, Masao

2017-06-01

The SOLA (Soul of Lupus with ALMA) project is conducting comprehensive studies of the Lupus Molecular Clouds and their star formation processes covering 10-10^4 AU scale. Our goal is to exploit ALMA and other facilities over a wide wavelength range to establish a prototypical low-mass star forming scenario based on the Lupus region. In the presentation, we will focus on angular momentum in dense cores in a filament, molecular outflows from young stars, and Class 0/I binary survey in Lupus as well as overview of our projects. Our binary survey was conducted in ALMA cycle 2 and achieved at 0.2-0.3 arcsec resolution discovering new binary systems in Lupus. At the same time, we obtained EX Lup, EXor type burst source, data in ALMA Cycle 3.

Nonequilibrium Chromosome Looping via Molecular Slip Links

NASA Astrophysics Data System (ADS)

Brackley, C. A.; Johnson, J.; Michieletto, D.; Morozov, A. N.; Nicodemi, M.; Cook, P. R.; Marenduzzo, D.

2017-09-01

We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site." This emergent collective behavior favors the extrusion of loops which are much larger than the ones formed by single slip links.

Entering the ‘big data’ era in medicinal chemistry: molecular promiscuity analysis revisited

PubMed Central

Hu, Ye; Bajorath, Jürgen

2017-01-01

The ‘big data’ concept plays an increasingly important role in many scientific fields. Big data involves more than unprecedentedly large volumes of data that become available. Different criteria characterizing big data must be carefully considered in computational data mining, as we discuss herein focusing on medicinal chemistry. This is a scientific discipline where big data is beginning to emerge and provide new opportunities. For example, the ability of many drugs to specifically interact with multiple targets, termed promiscuity, forms the molecular basis of polypharmacology, a hot topic in drug discovery. Compound promiscuity analysis is an area that is much influenced by big data phenomena. Different results are obtained depending on chosen data selection and confidence criteria, as we also demonstrate. PMID:28670471

Survey for C-Band High Spectral Lines with the Arecibo Telescope

NASA Astrophysics Data System (ADS)

Tan, Wei Siang

High-mass stars have masses greater than 8 solar masses and are the main source of heavy elements such as iron in the interstellar medium. This type of stars form in giant molecular clouds. Studying the molecular environment in star-forming regions is crucial to understand the physical structure and conditions that lead to the formation of high-mass stars. This thesis presents observations conducted with the 305m Arecibo Telescope in Puerto Rico of twelve high-mass star forming regions. Every source was observed in multiple transitions of molecular species including CH, CH3OH, H2CS, and OH lines, and a radio recombination line. The observations were conducted with the C-Band High receiver of the Arecibo Telescope in the frequency range of 6.0 to 7.4GHz. The goals of the observations were to investigate the detectability of different molecular species (including new possible molecular masers) and obtain high sensitivity observations of the 6.7GHz CH3OH line to detect absorption and use it as a probe of the kinematics of the molecular material with respect to the ionized gas. Among the results of the observations, we report detection of 6.7GHz CH3OH masers toward nine regions, OH masers toward five sources, 6.7GHz CH3OH absorption toward four sources (including tentative detections), and detection of H2CS toward the star forming region G34.26+0.15. We also found a variable and recurrent 6.7GHz CH3OH maser in G45.12+0.13. The 6.7GHz CH 3OH and 6278.65MHz H2CS absorption lines were modeled using the radiative transfer code RADEX to investigate the physical conditions of the molecular clouds responsible for the absorption lines. Our analysis of the absorption lines supports the interpretation that the spectral lines are tracing molecular envelopes of HII regions. In the case of 6.7GHz CH 3OH absorption, our results and data from an extensive literature review indicate that absorption is rare, but that a population of 6.7GHz CH 3OH absorbers may be present at levels below ˜ 100mJy. In the case of the 6278.65MHz H2CS absorption in G34.26+0.15, the data are consistent with infalling gas onto the HII region, which supports the key principle of gravitational collapse of molecular clouds during the process of star formation. However, high angular resolution observations of the H 2CS line are needed to confirm the infall hypothesis.

A Simple and Convenient Method of Multiple Linear Regression to Calculate Iodine Molecular Constants

ERIC Educational Resources Information Center

Cooper, Paul D.

2010-01-01

A new procedure using a student-friendly least-squares multiple linear-regression technique utilizing a function within Microsoft Excel is described that enables students to calculate molecular constants from the vibronic spectrum of iodine. This method is advantageous pedagogically as it calculates molecular constants for ground and excited…

Self-assembly of electronically abrupt borophene/organic lateral heterostructures

PubMed Central

Liu, Xiaolong; Wei, Zonghui; Balla, Itamar; Mannix, Andrew J.; Guisinger, Nathan P.; Luijten, Erik; Hersam, Mark C.

2017-01-01

Two-dimensional boron sheets (that is, borophene) have recently been realized experimentally and found to have promising electronic properties. Because electronic devices and systems require the integration of multiple materials with well-defined interfaces, it is of high interest to identify chemical methods for forming atomically abrupt heterostructures between borophene and electronically distinct materials. Toward this end, we demonstrate the self-assembly of lateral heterostructures between borophene and perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA). These lateral heterostructures spontaneously form upon deposition of PTCDA onto submonolayer borophene on Ag(111) substrates as a result of the higher adsorption enthalpy of PTCDA on Ag(111) and lateral hydrogen bonding among PTCDA molecules, as demonstrated by molecular dynamics simulations. In situ x-ray photoelectron spectroscopy confirms the weak chemical interaction between borophene and PTCDA, while molecular-resolution ultrahigh-vacuum scanning tunneling microscopy and spectroscopy reveal an electronically abrupt interface at the borophene/PTCDA lateral heterostructure interface. As the first demonstration of a borophene-based heterostructure, this work will inform emerging efforts to integrate borophene into nanoelectronic applications. PMID:28261662

Palmitoylation is required for the production of a soluble multimeric Hedgehog protein complex and long-range signaling in vertebrates

PubMed Central

Chen, Miao-Hsueh; Li, Ya-Jun; Kawakami, Takatoshi; Xu, Shan-Mei; Chuang, Pao-Tien

2004-01-01

Hedgehog (Hh) signaling plays a major role in multiple aspects of embryonic development. A key issue in Hh signaling is to elucidate the molecular mechanism by which a Hh protein morphogen gradient is formed despite its membrane association. In this study, we used a combination of genetic, cellular, and biochemical approaches to address the role of lipid modifications in long-range vertebrate Hh signaling. Our molecular analysis of knockout mice deficient in Skn, the murine homolog of the Drosophila ski gene, which catalyzes Hh palmitoylation, and gene-targeted mice producing a nonpalmitoylated form of Shh indicates that Hh palmitoylation is essential for its activity as well as the generation of a protein gradient in the developing embryos. Furthermore, our biochemical data show that Hh lipid modifications are required for producing a soluble multimeric protein complex, which constitutes the major active component for Hh signaling. These results suggest that soluble Hh multimeric complex travels in the morphogenetic field to activate Hh signaling in distant Hh-responsive cells. PMID:15075292

OBSERVATIONS OF MOLECULAR OUTFLOW IN CAR 291.6-01.9

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

Saul, M.; Saul, L., E-mail: msaul@phys.unsw.edu.au, E-mail: luke.saul@space.unibe.ch

We report the first observations of a dense molecular gas nebula and bipolar outflow in Car 291.6-01.9, showing characteristics of an embedded young stellar object (YSO). Using the Mopra radio telescope near Coonabarabaran, Australia, we image the kinematic structure of several emission features to examine physical properties within a molecular clump of mass {approx}3.2 {+-} 0.6 Multiplication-Sign 10{sup 3} M{sub Sun} in which a stellar cluster may be forming. Motivated by acquiring a more thorough understanding of star formation we ask what may have initiated collapse in the clump; observed outflow alignment is suggestive of {approx}1.0 pc distant massive starmore » HD 308280 radiative-driven compression as a formation trigger for the dense core. An outflow derived age of <10{sup 6} years, together with significant C{sup 18}O and SO core depletion, support the case for the core as the host of an extremely YSO cluster.« less

Coherent exciton-vibrational dynamics and energy transfer in conjugated organics

DOE PAGES

Nelson, Tammie R.; Ondarse-Alvarez, Dianelys; Oldani, Nicolas; ...

2018-06-13

Coherence, signifying concurrent electron-vibrational dynamics in complex natural and man-made systems, is currently a subject of intense study. Understanding this phenomenon is important when designing carrier transport in optoelectronic materials. Here, excited state dynamics simulations reveal a ubiquitous pattern in the evolution of photoexcitations for a broad range of molecular systems. Symmetries of the wavefunctions define a specific form of the non-adiabatic coupling that drives quantum transitions between excited states, leading to a collective asymmetric vibrational excitation coupled to the electronic system. This promotes periodic oscillatory evolution of the wavefunctions, preserving specific phase and amplitude relations across the ensemble ofmore » trajectories. The simple model proposed here explains the appearance of coherent exciton-vibrational dynamics due to non-adiabatic transitions, which is universal across multiple molecular systems. The observed relationships between electronic wavefunctions and the resulting functionalities allows us to understand, and potentially manipulate, excited state dynamics and energy transfer in molecular materials.« less

Coherent exciton-vibrational dynamics and energy transfer in conjugated organics

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

Nelson, Tammie R.; Ondarse-Alvarez, Dianelys; Oldani, Nicolas

Coherence, signifying concurrent electron-vibrational dynamics in complex natural and man-made systems, is currently a subject of intense study. Understanding this phenomenon is important when designing carrier transport in optoelectronic materials. Here, excited state dynamics simulations reveal a ubiquitous pattern in the evolution of photoexcitations for a broad range of molecular systems. Symmetries of the wavefunctions define a specific form of the non-adiabatic coupling that drives quantum transitions between excited states, leading to a collective asymmetric vibrational excitation coupled to the electronic system. This promotes periodic oscillatory evolution of the wavefunctions, preserving specific phase and amplitude relations across the ensemble ofmore » trajectories. The simple model proposed here explains the appearance of coherent exciton-vibrational dynamics due to non-adiabatic transitions, which is universal across multiple molecular systems. The observed relationships between electronic wavefunctions and the resulting functionalities allows us to understand, and potentially manipulate, excited state dynamics and energy transfer in molecular materials.« less

Anharmonic and Quantum Fluctuations in Molecular Crystals from Ab Initio Simulations

NASA Astrophysics Data System (ADS)

Rossi, Mariana; Gasparotto, Piero; Ceriotti, Michele

Molecular crystals often exist in multiple competing polymorphs which are challenging to be predicted computationally, but show significantly different physicochemical properties. This challenge is not due only to the combinatorial search space, but also to the complex interplay of subtle effects determine the relative stability of different structures. Here we estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects, by using a series of different flavors of thermodynamic integration. As an example, for the two most stable forms of paracetamol we find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our studies indicate that anharmonic free energies could play an important role for molecular crystals composed by large molecules and opens the way for a systematic inclusion of these effects in order to obtain a predictive screening of structures.

Comparison of (GTG)5-oligonucleotide and ribosomal intergenic transcribed spacer (ITS)-PCR for molecular typing of Klebsiella isolates.

PubMed

Ryberg, Anna; Olsson, Crister; Ahrné, Siv; Monstein, Hans-Jürg

2011-02-01

Molecular typing of Klebsiella species has become important for monitoring dissemination of β-lactamase-producers in hospital environments. The present study was designed to evaluate poly-trinucleotide (GTG)(5)- and rDNA intergenic transcribed spacer (ITS)-PCR fingerprint analysis for typing of Klebsiella pneumoniae and Klebsiella oxytoca isolates. Multiple displacement amplified DNA derived from 19 K. pneumoniae (some with an ESBL-phenotype), 35 K. oxytoca isolates, five K. pneumoniae, two K. oxytoca, three Raoultella, and one Enterobacter aerogenes type and reference strains underwent (GTG)(5) and ITS-PCR analysis. Dendrograms were constructed using cosine coefficient and the Neighbour joining method. (GTG)(5) and ITS-PCR analysis revealed that K. pneumoniae and K. oxytoca isolates, reference and type strains formed distinct cluster groups, and tentative subclusters could be established. We conclude that (GTG)(5) and ITS-PCR analysis combined with automated capillary electrophoresis provides promising tools for molecular typing of Klebsiella isolates. Copyright © 2010 Elsevier B.V. All rights reserved.

Clinical, molecular genetics and therapeutic aspects of syndromic obesity.

PubMed

Geets, E; Meuwissen, M E C; Van Hul, W

2018-04-26

Obesity has become a major health problem worldwide. To date, more than 25 different syndromic forms of obesity are known in which one (monogenic) or multiple (polygenic) genes are involved. This review gives an overview of these forms and focuses more in detail on six syndromes: Prader Willi Syndrome and Prader Willi like phenotype, Bardet Biedl Syndrome, Alström Syndrome, Wilms tumor, Aniridia, Genitourinary malformations and mental Retardation syndrome and 16p11.2 (micro)deletions. Years of research provided plenty of information on the molecular genetics of these disorders and the obesity phenotype leading to a more individualized treatment of the symptoms, however, a lot of questions still remain unanswered. As these obesity syndromes have different signs and symptoms in common, it makes it difficult to accurately diagnose patients which may result in inappropriate treatment of the disease. Therefore, the big challenge for clinicians and scientists is to more clearly differentiate all syndromic forms of obesity to provide conclusive genetic explanations and eventually deliver accurate genetic counseling and treatment. In addition, further delineation of the (functions of the) underlying genes with the use of array- or next generation sequencing-based technology will be helpful to unravel the mechanisms of energy metabolism in the general population. This article is protected by copyright. All rights reserved.

MultiDK: A Multiple Descriptor Multiple Kernel Approach for Molecular Discovery and Its Application to Organic Flow Battery Electrolytes.

PubMed

Kim, Sungjin; Jinich, Adrián; Aspuru-Guzik, Alán

2017-04-24

We propose a multiple descriptor multiple kernel (MultiDK) method for efficient molecular discovery using machine learning. We show that the MultiDK method improves both the speed and accuracy of molecular property prediction. We apply the method to the discovery of electrolyte molecules for aqueous redox flow batteries. Using multiple-type-as opposed to single-type-descriptors, we obtain more relevant features for machine learning. Following the principle of "wisdom of the crowds", the combination of multiple-type descriptors significantly boosts prediction performance. Moreover, by employing multiple kernels-more than one kernel function for a set of the input descriptors-MultiDK exploits nonlinear relations between molecular structure and properties better than a linear regression approach. The multiple kernels consist of a Tanimoto similarity kernel and a linear kernel for a set of binary descriptors and a set of nonbinary descriptors, respectively. Using MultiDK, we achieve an average performance of r 2 = 0.92 with a test set of molecules for solubility prediction. We also extend MultiDK to predict pH-dependent solubility and apply it to a set of quinone molecules with different ionizable functional groups to assess their performance as flow battery electrolytes.

Modeling the action-potential-sensitive nonlinear-optical response of myelinated nerve fibers and short-term memory

NASA Astrophysics Data System (ADS)

Shneider, M. N.; Voronin, A. A.; Zheltikov, A. M.

2011-11-01

The Goldman-Albus treatment of the action-potential dynamics is combined with a phenomenological description of molecular hyperpolarizabilities into a closed-form model of the action-potential-sensitive second-harmonic response of myelinated nerve fibers with nodes of Ranvier. This response is shown to be sensitive to nerve demyelination, thus enabling an optical diagnosis of various demyelinating diseases, including multiple sclerosis. The model is applied to examine the nonlinear-optical response of a three-neuron reverberating circuit—the basic element of short-term memory.

Advances in Nucleophilic Phosphine Catalysis of Alkenes, Allenes, Alkynes, and MBHADs

PubMed Central

Fan, Yi Chiao

2014-01-01

In nucleophilic phosphine catalysis, tertiary phosphines undergo conjugate additions to activated carbon–carbon multiple bonds to form β-phosphonium enolates, β-phosphonium dienolates, β-phosphonium enoates, and vinyl phosphonium ylides as intermediates. When these reactive zwitterionic species react with nucleophiles and electrophiles, they may generate carbo- and heterocycles with multifarious molecular architectures. This Article describes the reactivities of these phosphonium zwitterions, the applications of phosphine catalysis in the syntheses of biologically active compounds and natural products, and recent developments in the enantioselective phosphine catalysis. PMID:24196409

Free energy landscape and transition pathways from Watson–Crick to Hoogsteen base pairing in free duplex DNA

PubMed Central

Yang, Changwon; Kim, Eunae; Pak, Youngshang

2015-01-01

Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson–Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine–thymine (A–T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. PMID:26250116

Study of Electron Gas on a Neutron-Rich Nuclear Pasta

NASA Astrophysics Data System (ADS)

Ramirez-Homs, Enrique

This study used a classical molecular dynamics model to observe the role of electron gas on the formation of nuclear structures at subsaturation densities (rho < 0.015 fm-3) and low temperatures (T < 1MeV ). The simulations were performed by varying the Coulomb interaction strength on systems of isospin symmetric and asymmetric matter with periodic boundary conditions. The effect was quantified on the fragment size multiplicity, the inter-particle distance, the isospin content of the clusters, the nucleon mobility and cluster persistence, and on the nuclear structure shapes. The existence of the nuclear pasta structures was observed even with the absence of the Coulomb interaction but with a modication of the shapes formed. It was found that the presence of the electron gas tends to distribute matter more evenly, forms less compact objects, decreases the isospin content of clusters, modies the nucleon mobility, reduces the persistence and the fragment size multiplicity, but does not alter the inter-particle distance in clusters. The degree of these effects also varied on the nuclear structures and depended on their isospin content, temperature, and density.

Recent research on the growth plate: Advances in fibroblast growth factor signaling in growth plate development and disorders.

PubMed

Xie, Yangli; Zhou, Siru; Chen, Hangang; Du, Xiaolan; Chen, Lin

2014-08-01

Skeletons are formed through two distinct developmental actions, intramembranous ossification and endochondral ossification. During embryonic development, most bone is formed by endochondral ossification. The growth plate is the developmental center for endochondral ossification. Multiple signaling pathways participate in the regulation of endochondral ossification. Fibroblast growth factor (FGF)/FGF receptor (FGFR) signaling has been found to play a vital role in the development and maintenance of growth plates. Missense mutations in FGFs and FGFRs can cause multiple genetic skeletal diseases with disordered endochondral ossification. Clarifying the molecular mechanisms of FGFs/FGFRs signaling in skeletal development and genetic skeletal diseases will have implications for the development of therapies for FGF-signaling-related skeletal dysplasias and growth plate injuries. In this review, we summarize the recent advances in elucidating the role of FGFs/FGFRs signaling in growth plate development, genetic skeletal disorders, and the promising therapies for those genetic skeletal diseases resulting from FGFs/FGFRs dysfunction. Finally, we also examine the potential important research in this field in the future. © 2014 Society for Endocrinology.

Multiple polypeptides immunologically related to beta-poly(L-malate) hydrolase (polymalatase) in the plasmodium of the slime mold Physarum polycephalum.

PubMed

Karl, M; Holler, E

1998-01-15

Plasmodia of Physarum polycephalum contain large amounts of the cell-type-specific polyanion beta-poly(L-malate) and of a corresponding specific hydrolase (polymalatase), both expressed in the plasmodial form of the organism. We have partially purified polymalatase, the preparation consisting of several polypeptides, which could not be separated without destroying the hydrolase activity. Polypeptides of 68 kDa and 97 kDa were identified as polymalatases. Both were glycosylated, the 68-kDa form giving rise to a 54-kDa form when deglycosylated, and the 97-kDa form giving rise to an 88-kDa polypeptide that was indistinguishable from an 88-kDa inactive species also contained in the enzyme preparation. Antisera against each of these proteins were used to detect the intracellular distribution of the proteins. We found that the antisera crossreacted with the three proteins and, furthermore, with a multiplicity of polypeptides ubiquitously distributed over the plasmodium. Results of a two-dimensional non-denaturing in the first dimension and SDS-denaturing polyacrylamide gel electrophoresis in the second dimension suggested that the proteins were derived from a 200-kDa 'precursor' protein by proteolytic fragmentation. Polymalatase activity could be generated from a high molecular-mass precursor. According to several pieces of evidence, the proteolytic nicking occurred within plasmodia. The fragments were sticky and gave rise to preferred sizes of nicked macromolecules. The observed multiplicity varied as a function of the age of the cultures. The cellular distribution and the intracellular pH value were not compatible with an in situ polymalatase activity and suggested other, presently unknown, function(s) such as in the transportation of beta-poly(L-malate) from the nucleus to the culture medium.

Hybrid colored noise process with space-dependent switching rates

NASA Astrophysics Data System (ADS)

Bressloff, Paul C.; Lawley, Sean D.

2017-07-01

A fundamental issue in the theory of continuous stochastic process is the interpretation of multiplicative white noise, which is often referred to as the Itô-Stratonovich dilemma. From a physical perspective, this reflects the need to introduce additional constraints in order to specify the nature of the noise, whereas from a mathematical perspective it reflects an ambiguity in the formulation of stochastic differential equations (SDEs). Recently, we have identified a mechanism for obtaining an Itô SDE based on a form of temporal disorder. Motivated by switching processes in molecular biology, we considered a Brownian particle that randomly switches between two distinct conformational states with different diffusivities. In each state, the particle undergoes normal diffusion (additive noise) so there is no ambiguity in the interpretation of the noise. However, if the switching rates depend on position, then in the fast switching limit one obtains Brownian motion with a space-dependent diffusivity of the Itô form. In this paper, we extend our theory to include colored additive noise. We show that the nature of the effective multiplicative noise process obtained by taking both the white-noise limit (κ →0 ) and fast switching limit (ɛ →0 ) depends on the order the two limits are taken. If the white-noise limit is taken first, then we obtain Itô, and if the fast switching limit is taken first, then we obtain Stratonovich. Moreover, the form of the effective diffusion coefficient differs in the two cases. The latter result holds even in the case of space-independent transition rates, where one obtains additive noise processes with different diffusion coefficients. Finally, we show that yet another form of multiplicative noise is obtained in the simultaneous limit ɛ ,κ →0 with ɛ /κ2 fixed.

Potent New Small-Molecule Inhibitor of Botulinum Neurotoxin Serotype A Endopeptidase Developed by Synthesis-Based Computer-Aided Molecular Design

DTIC Science & Technology

2009-11-01

dynamics of the complex predicted by multiple molecular dynamics simulations , and discuss further structural optimization to achieve better in vivo efficacy...complex with BoNTAe and the dynamics of the complex predicted by multiple molecular dynamics simulations (MMDSs). On the basis of the 3D model, we discuss...is unlimited whereas AHP exhibited 54% inhibition under the same conditions (Table 1). Computer Simulation Twenty different molecular dynamics

Learning surface molecular structures via machine vision

NASA Astrophysics Data System (ADS)

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

2017-08-01

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (`read out') all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.

Collapse and Fragmentation of Molecular Cloud Cores. VII. Magnetic Fields and Multiple Protostar Formation

NASA Astrophysics Data System (ADS)

Boss, Alan P.

2002-04-01

Recent observations of star-forming regions suggest that binary and multiple young stars are the rule rather than the exception and implicate fragmentation as the likely mechanism for their formation. Most numerical hydrodynamic calculations of fragmentation have neglected the possibly deleterious effects of magnetic fields, despite ample evidence for the importance of magnetic support of precollapse clouds. We present here the first numerical hydrodynamic survey of the collapse and fragmentation of initially magnetically supported clouds that takes into account several magnetic field effects in an approximate manner. The models are calculated with a three-dimensional, finite differences code that solves the equations of hydrodynamics, gravitation, and radiative transfer in the Eddington and diffusion approximations. Magnetic field effects are included through two simple approximations: magnetic pressure is added to the gas pressure, and magnetic tension is approximated by gravity dilution once collapse is well underway. Ambipolar diffusion of the magnetic field leading to cloud collapse is treated approximately as well. Models are calculated for a variety of initial cloud density profiles, shapes, and rotation rates. We find that in spite of the inclusion of magnetic field effects, dense cloud cores are capable of fragmenting into binary and multiple protostar systems. Initially prolate clouds tend to fragment into binary protostars, while initially oblate clouds tend to fragment into multiple protostar systems containing a small number (of the order of 4) of fragments. The latter are likely to be subject to rapid orbital evolution, with close encounters possibly leading to the ejection of fragments. Contrary to expectation, magnetic tension effects appear to enhance fragmentation, allowing lower mass fragments to form than would otherwise be possible, because magnetic tension helps to prevent a central density singularity from forming and producing a dominant single object. Magnetically supported dense cloud cores thus seem to be capable of collapsing and fragmenting into sufficient numbers of binary and multiple protostar systems to be compatible with observations of the relative rarity of single protostars.

The Gould’s Belt Distances Survey (GOBELINS) II. Distances and Structure toward the Orion Molecular Clouds

NASA Astrophysics Data System (ADS)

Kounkel, Marina; Hartmann, Lee; Loinard, Laurent; Ortiz-León, Gisela N.; Mioduszewski, Amy J.; Rodríguez, Luis F.; Dzib, Sergio A.; Torres, Rosa M.; Pech, Gerardo; Galli, Phillip A. B.; Rivera, Juana L.; Boden, Andrew F.; Evans, Neal J., II; Briceño, Cesar; Tobin, John J.

2017-01-01

We present the results of the Gould’s Belt Distances Survey of young star-forming regions toward the Orion Molecular Cloud Complex. We detected 36 young stellar objects (YSOs) with the Very Large Baseline Array, 27 of which have been observed in at least three epochs over the course of two years. At least half of these YSOs belong to multiple systems. We obtained parallax and proper motions toward these stars to study the structure and kinematics of the Complex. We measured a distance of 388 ± 5 pc toward the Orion Nebula Cluster, 428 ± 10 pc toward the southern portion L1641, 388 ± 10 pc toward NGC 2068, and roughly ˜420 pc toward NGC 2024. Finally, we observed a strong degree of plasma radio scattering toward λ Ori.

Computational study of a calcium release-activated calcium channel

NASA Astrophysics Data System (ADS)

Talukdar, Keka; Shantappa, Anil

2016-05-01

The naturally occurring proteins that form hole in membrane are commonly known as ion channels. They play multiple roles in many important biological processes. Deletion or alteration of these channels often leads to serious problems in the physiological processes as it controls the flow of ions through it. The proper maintenance of the flow of ions, in turn, is required for normal health. Here we have investigated the behavior of a calcium release-activated calcium ion channel with pdb entry 4HKR in Drosophila Melanogaster. The equilibrium energy as well as molecular dynamics simulation is performed first. The protein is subjected to molecular dynamics simulation to find their energy minimized value. Simulation of the protein in the environment of water and ions has given us important results too. The solvation energy is also found using Charmm potential.

New insights on multiplicity and clustering in Taurus.

NASA Astrophysics Data System (ADS)

Joncour, Isabelle; Duchene, Gaspard; Moraux, Estelle; Mundy, Lee

2018-01-01

Multiplicity and clustering of young stars are critical clues to constraint star formation process. The Taurus molecular complex is the archetype of a quiescent star forming region that may retain primeval signature of star formation.Using statistical and clustering tools such as nearest neighbor statistics, correlation functions and the density-Based Spatial Clustering of Applications with Noise (DBSCAN) algorithm, this work reveals new spatial substructures in Taurus.We have identified unexpected ultra wide pairs (UWPs) candidates of high order multiplicity in Taurus in the 5-60 kAU separation range (Joncour et al 2017), beyond the separation assessed for wide pairs (Kraus & Hillenbrand 2009).Our work reveals 20 local stellar substructures, the Nested Elementary Structures (NESTs). These NESTs contain nearly half the stars of Taurus and 75% of the Class 0/I objects probing that they are the preferred sites of star formation (Joncour et al, sub.). The NESTs size ranges from few kAU up to 80 kAU making a length scale bridge between wide pairs and loose group (few hundreds kAU, Kirk & Myers, 2011). The NESTs mass ranges from 0.5-10 solar mass. The balance between Class I, II and III in NESTs suggests that they may be ordered as an evolutionary temporal scheme, some of them got infertile, while other shelter stars in infancy.The UWPs and the NESTs may be pristine imprints of their spatial configuration at birth. The UWPs population may result from a cascade fragmentation scenario of the natal molecular core. They could be the older counterparts, to the 0.5 Myr prestellar cores/Class 0 multiple objects observed at radio/millimeter wavelengths (Tobin et al 2010, 2016) and the precursors of the large number of UWPs (10–100 kAU) recently identified in older moving groups (Floriano-Alonso et al, 2015 ; Elliot et al 2016). The NESTs may result from the gravitational collapse of a gas clump that fragments to give a tight collection of stars within few millions years.This project has been partly supported by the StarFormMapper project funded by the European Union's Horizon 2020 Research and Innovation Action (RIA) program under grant agreement number 687528.

Impact of oxygen stoichiometry on electroforming and multiple switching modes in TiN/TaOx/Pt based ReRAM

NASA Astrophysics Data System (ADS)

Sharath, S. U.; Joseph, M. J.; Vogel, S.; Hildebrandt, E.; Komissinskiy, P.; Kurian, J.; Schroeder, T.; Alff, L.

2016-10-01

We have investigated the material and electrical properties of tantalum oxide thin films (TaOx) with engineered oxygen contents grown by RF-plasma assisted molecular beam epitaxy. The optical bandgap and the density of the TaOx films change consistently with oxygen contents in the range of 3.63 to 4.66 eV and 12.4 to 9.0 g/cm3, respectively. When exposed to atmosphere, an oxidized Ta2O5-y surface layer forms with a maximal thickness of 1.2 nm depending on the initial oxygen deficiency of the film. X-ray photoelectron spectroscopy studies show that multiple sub-stoichiometric compositions occur in oxygen deficient TaOx thin films, where all valence states of Ta including metallic Ta are possible. Devices of the form Pt/Ta2O5-y/TaOx/TiN exhibit highly tunable forming voltages of 10.5 V to 1.5 V with decreasing oxygen contents in TaOx. While a stable bipolar resistive switching (BRS) occurs in all devices irrespective of oxygen content, unipolar switching was found to coexist with BRS only at higher oxygen contents, which transforms to a threshold switching behaviour in the devices grown under highest oxidation.

Monomeric Ti(IV) homopiperazine complexes and their exploitation for the ring opening polymerisation of rac-lactide

PubMed Central

2013-01-01

Background The area of biodegradable/sustainable polymers is one of increasing importance in the 21st Century due to their positive environmental characteristics. Lewis acidic metal centres are currently one of the most popular choices for the initiator for the polymerisation. Thus, in this paper we report the synthesis and characterisation of a series of monometallic homopiperazine Ti(IV) complexes where we have systematically varied the sterics of the phenol moieties. Results When the ortho substituent of the ligand is either a Me, tBu or amyl then the β-cis isomer is isolated exclusively in the solid-state. Nevertheless, in solution multiple isomers are clearly observed from analysis of the NMR spectra. However, when the ortho substituent is an H-atom then the trans-isomer is formed in the solid-state and solely in solution. The complexes have been screened for the polymerisation of rac-lactide in solution and under the industrially preferred melt conditions. Narrow molecular weight material (PDI 1.07 – 1.23) is formed under melt conditions with controlled molecular weights. Conclusions Six new Ti(IV) complexes are presented which are highly active for the polymerisation. In all cases atactic polymer is prepared with predictable molecular weight control. This shows the potential applicability of Ti(IV) to initiate the polymerisations. PMID:23915921

Anesthetics mechanism on a DMPC lipid membrane model: Insights from molecular dynamics simulations.

PubMed

Saeedi, Marzieh; Lyubartsev, Alexander P; Jalili, Seifollah

2017-07-01

To provide insight into the molecular mechanisms of local anesthetic action, we have carried out an extensive investigation of two amide type local anesthetics, lidocaine and articaine in both charged and uncharged forms, interacting with DMPC lipid membrane. We have applied both standard molecular dynamics simulations and metadynamics simulations to provide a detailed description of the free energy landscape of anesthetics embedded in the lipid bilayer. The global minimum of the free energy surface (equilibrium position of anesthetics in the lipid membrane) occurred around 1nm of the bilayer center. The uncharged anesthetics show more affinity to bind to this region compared to the charged drugs. The binding free energy of uncharged lidocaine in the membrane (-30.3kJ/mol) is higher than uncharged articaine (-24.0kJ/mol), which is in good agreement with higher lipid solubility of lidocaine relative to the articaine. The octanol/water partition coefficient of uncharged drugs was also investigated using expanded ensemble simulations. In addition, complementary standard MD simulations were carried out to study the partitioning behavior of multiple anesthetics inside the lipid bilayer. The results obtained here are in line with previously reported simulations and suggest that the different forms of anesthetics induce different structural modifications in the lipid bilayer, which can provide new insights into their complex membrane translocation phenomena. Copyright © 2017 Elsevier B.V. All rights reserved.

Gadd45a Protein Promotes Skeletal Muscle Atrophy by Forming a Complex with the Protein Kinase MEKK4.

PubMed

Bullard, Steven A; Seo, Seongjin; Schilling, Birgit; Dyle, Michael C; Dierdorff, Jason M; Ebert, Scott M; DeLau, Austin D; Gibson, Bradford W; Adams, Christopher M

2016-08-19

Skeletal muscle atrophy is a serious and highly prevalent condition that remains poorly understood at the molecular level. Previous work found that skeletal muscle atrophy involves an increase in skeletal muscle Gadd45a expression, which is necessary and sufficient for skeletal muscle fiber atrophy. However, the direct mechanism by which Gadd45a promotes skeletal muscle atrophy was unknown. To address this question, we biochemically isolated skeletal muscle proteins that associate with Gadd45a as it induces atrophy in mouse skeletal muscle fibers in vivo We found that Gadd45a interacts with multiple proteins in skeletal muscle fibers, including, most prominently, MEKK4, a mitogen-activated protein kinase kinase kinase that was not previously known to play a role in skeletal muscle atrophy. Furthermore, we found that, by forming a complex with MEKK4 in skeletal muscle fibers, Gadd45a increases MEKK4 protein kinase activity, which is both sufficient to induce skeletal muscle fiber atrophy and required for Gadd45a-mediated skeletal muscle fiber atrophy. Together, these results identify a direct biochemical mechanism by which Gadd45a induces skeletal muscle atrophy and provide new insight into the way that skeletal muscle atrophy occurs at the molecular level. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Systems Biophysics of Gene Expression

PubMed Central

Vilar, Jose M.G.; Saiz, Leonor

2013-01-01

Gene expression is a process central to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular and extracellular changes. This diversity in scales poses fundamental challenges to the use of traditional approaches to fully understand even the simplest gene expression systems. Recent advances in computational systems biophysics have provided promising avenues to reliably integrate the molecular detail of biophysical process into the system behavior. Here, we review recent advances in the description of gene regulation as a system of biophysical processes that extend from specific protein-DNA interactions to the combinatorial assembly of nucleoprotein complexes. There is now basic mechanistic understanding on how promoters controlled by multiple, local and distal, DNA binding sites for transcription factors can actively control transcriptional noise, cell-to-cell variability, and other properties of gene regulation, including precision and flexibility of the transcriptional responses. PMID:23790365

The multiple-hit pathogenesis of non-alcoholic fatty liver disease (NAFLD).

PubMed

Buzzetti, Elena; Pinzani, Massimo; Tsochatzis, Emmanuel A

2016-08-01

Nonalcoholic fatty liver disease (NAFLD) is increasingly prevalent and represents a growing challenge in terms of prevention and treatment. Despite its high prevalence, only a small minority of affected patients develops inflammation and subsequently fibrosis and chronic liver disease, while most of them only exhibit simple steatosis. In this context, the full understanding of the mechanisms underlying the development of NAFLD and non-alcoholic steatohepatitis (NASH) is of extreme importance; despite advances in this field, knowledge on the pathogenesis of NAFLD is still incomplete. The 'two-hit' hypothesis is now obsolete, as it is inadequate to explain the several molecular and metabolic changes that take place in NAFLD. The "multiple hit" hypothesis considers multiple insults acting together on genetically predisposed subjects to induce NAFLD and provides a more accurate explanation of NAFLD pathogenesis. Such hits include insulin resistance, hormones secreted from the adipose tissue, nutritional factors, gut microbiota and genetic and epigenetic factors. In this article, we review the factors that form this hypothesis. Copyright © 2016 Elsevier Inc. All rights reserved.

Pre-examination factors affecting molecular diagnostic test results and interpretation: A case-based approach.

PubMed

Payne, Deborah A; Baluchova, Katarina; Peoc'h, Katell H; van Schaik, Ron H N; Chan, K C Allen; Maekawa, Masato; Mamotte, Cyril; Russomando, Graciela; Rousseau, François; Ahmad-Nejad, Parviz

2017-04-01

Multiple organizations produce guidance documents that provide opportunities to harmonize quality practices for diagnostic testing. The International Organization for Standardization ISO 15189 standard addresses requirements for quality in management and technical aspects of the clinical laboratory. One technical aspect addresses the complexities of the pre-examination phase prior to diagnostic testing. The Committee for Molecular Diagnostics of the International Federation for Clinical Chemistry and Laboratory Medicine (also known as, IFCC C-MD) conducted a survey of international molecular laboratories and determined ISO 15189 to be the most referenced guidance document. In this review, the IFCC C-MD provides case-based examples illustrating the value of select pre-examination processes as these processes relate to molecular diagnostic testing. Case-based examples in infectious disease, oncology, inherited disease and pharmacogenomics address the utility of: 1) providing information to patients and users, 2) designing requisition forms, 3) obtaining informed consent and 4) maintaining sample integrity prior to testing. The pre-examination phase requires extensive and consistent communication between the laboratory, the healthcare provider and the end user. The clinical vignettes presented in this paper illustrate the value of applying select ISO 15189 recommendations for general laboratory to the more specialized area of Molecular Diagnostics. Copyright © 2016 Elsevier B.V. All rights reserved.

High Spectral Resolution Lidar Measurements of Multiple Scattering

NASA Technical Reports Server (NTRS)

Eloranta, E. W.; Piironen, P.

1996-01-01

The University of Wisconsin High Spectral Resolution Lidar (HSRL) provides unambiguous measurements of backscatter cross section, backscatter phase function, depolarization, and optical depth. This is accomplished by dividing the lidar return into separate particulate and molecular contributions. The molecular return is then used as a calibration target. We have modified the HSRL to use an I2 molecular absorption filter to separate aerosol and molecular signals. This allows measurement in dense clouds. Useful profiles extend above the cloud base until the two way optical depth reaches values between 5 and 6; beyond this, photon counting errors become large. In order to observe multiple scattering, the HSRL includes a channel which records the combined aerosol and molecular lidar return simultaneously with the spectrometer channel measurements of optical properties. This paper describes HSRL multiple scattering measurements from both water and ice clouds. These include signal strengths and depolarizations as a function of receiver field of view. All observations include profiles of extinction and backscatter cross sections. Measurements are also compared to predictions of a multiple scattering model based on small angle approximations.

Comparison of biochemical properties of liver arginase from streptozocin-induced diabetic and control mice.

PubMed

Spolarics, Z; Bond, J S

1989-11-01

Arginase activity is elevated in livers of diabetic animals compared to controls and there is evidence that this is due in part to increased specific activity (activity/mg arginase protein). To investigate the molecular basis of this increased activity, the physicochemical and kinetic properties of hepatic arginase from diabetic and control mice were compared. Two types of arginase subunits with molecular weights of 35,000 and 38,000 were found in both the diabetic and control animals and the subunits in these animals had similar, multiple ionic forms. Kinetic parameters of purified preparations of arginase for arginine (apparent Km and Vmax values) and the thermal stability of these preparations from diabetics and controls were also similar. Furthermore, no difference was found in the distribution of arginase activity among different subcellular liver fractions. Separation of basic and acidic oligomeric forms of arginase by fast-protein liquid chromatography resulted in a slightly different distribution of activity among the forms in the normal and diabetic group. The apparent Km values for Mn2+ of the basic form of the enzyme were 25 and 33 microM for the enzyme from normal and diabetic animals, respectively; for acidic forms, for which two apparent Km values were measured, the values were 8 and 197 microM for arginase from controls and 35 and 537 microM from diabetics. These results indicate that in diabetes, while no marked changes in the physicochemical characteristics of arginase are obvious, some changes are found in the interaction of arginase with its cofactor Mn.

A slippery molecular assembly allows water as a self-erasable security marker

PubMed Central

Thirumalai, Rajasekaran; Mukhopadhyay, Rahul Dev; Praveen, Vakayil K.; Ajayaghosh, Ayyappanpillai

2015-01-01

Protection of currency and valuable documents from counterfeit continues to be a challenge. While there are many embedded security features available for document safety, they are not immune to forgery. Fluorescence is a sensitive property, which responds to external stimuli such as solvent polarity, temperature or mechanical stress, however practical use in security applications is hampered due to several reasons. Therefore, a simple and specific stimuli responsive security feature that is difficult to duplicate is of great demand. Herein we report the design of a fluorescent molecular assembly on which water behaves as a self-erasable security marker for checking the authenticity of documents at point of care. The underlying principle involves the disciplined self-assembly of a tailor-made fluorescent molecule, which initially form a weak blue fluorescence (λem = 425 nm, Φf = 0.13) and changes to cyan emission (λem = 488 nm,Φf = 0.18) in contact with water due to a reversible molecular slipping motion. This simple chemical tool, based on the principles of molecular self-assembly and fluorescence modulation, allows creation of security labels and optically masked barcodes for multiple documents authentication. PMID:25940779

Multiple forms of ADP-glucose pyrophosphorylase from tomato fruit

NASA Technical Reports Server (NTRS)

Chen, B. Y.; Janes, H. W.

1997-01-01

ADP-glucose pyrophosphorylase (AGP) was purified from tomato (Lycopersicon esculentum Mill.) fruit to apparent homogeneity. By sodium dodecyl sulfate-polyacrylamide gel electrophoresis the enzyme migrated as two close bands with molecular weights of 50,000 and 51,000. Two-dimensional polyacrylamide gel electrophoresis analysis of the purified enzyme, however, revealed at least five major protein spots that could be distinguished by their slight differences in net charge and molecular weight. Whereas all of the spots were recognized by the antiserum raised against tomato fruit AGP holoenzyme, only three of them reacted strongly with antiserum raised against the potato tuber AGP large subunit, and the other two spots (with lower molecular weights) reacted specifically with antisera raised against spinach leaf AGP holoenzyme and the potato tuber AGP small subunit. The results suggest the existence of at least three isoforms of the AGP large subunit and two isoforms of the small subunit in tomato fruit in vivo. The native molecular mass of the enzyme determined by gel filtration was 220 +/- 10 kD, indicating a tetrameric structure for AGP from tomato fruit. The purified enzyme is very sensitive to 3-phosphoglycerate/inorganic phosphate regulation.

A slippery molecular assembly allows water as a self-erasable security marker.

PubMed

Thirumalai, Rajasekaran; Mukhopadhyay, Rahul Dev; Praveen, Vakayil K; Ajayaghosh, Ayyappanpillai

2015-05-05

Protection of currency and valuable documents from counterfeit continues to be a challenge. While there are many embedded security features available for document safety, they are not immune to forgery. Fluorescence is a sensitive property, which responds to external stimuli such as solvent polarity, temperature or mechanical stress, however practical use in security applications is hampered due to several reasons. Therefore, a simple and specific stimuli responsive security feature that is difficult to duplicate is of great demand. Herein we report the design of a fluorescent molecular assembly on which water behaves as a self-erasable security marker for checking the authenticity of documents at point of care. The underlying principle involves the disciplined self-assembly of a tailor-made fluorescent molecule, which initially form a weak blue fluorescence (λem = 425 nm, Φf = 0.13) and changes to cyan emission (λem = 488 nm,Φf = 0.18) in contact with water due to a reversible molecular slipping motion. This simple chemical tool, based on the principles of molecular self-assembly and fluorescence modulation, allows creation of security labels and optically masked barcodes for multiple documents authentication.

The Geropathology Research Network: An Interdisciplinary Approach for Integrating Pathology Into Research on Aging

PubMed Central

Ikeno, Yuji; Niedernhofer, Laura; McIndoe, Richard A.; Ciol, Marcia A.; Ritchey, Jerry; Liggitt, Denny

2016-01-01

Geropathology is the study of aging and age-related lesions and diseases in the form of whole necropsies/autopsies, surgical biopsies, histology, and molecular biomarkers. It encompasses multiple subspecialties of geriatrics, anatomic pathology, molecular pathology, clinical pathology, and gerontology. In order to increase the consistency and scope of communication in the histologic and molecular pathology assessment of tissues from preclinical and clinical aging studies, a Geropathology Research Network has been established consisting of pathologists and scientists with expertise in the comparative pathology of aging, the design of aging research studies, biostatistical methods for analysis of aging data, and bioinformatics for compiling and annotating large sets of data generated from aging studies. The network provides an environment to promote learning and exchange of scientific information and ideas for the aging research community through a series of symposia, the development of uniform ways of integrating pathology into aging studies, and the statistical analysis of pathology data. The efforts of the network are ultimately expected to lead to a refined set of sentinel biomarkers of molecular and anatomic pathology that could be incorporated into preclinical and clinical aging intervention studies to increase the relevance and productivity of these types of investigations. PMID:26243216

Diversity of Wolbachia pipientis strain wPip in a genetically admixtured, above-ground Culex pipiens (Diptera: Culicidae) population: association with form molestus ancestry and host selection patterns.

PubMed

Morningstar, Rebecca J; Hamer, Gabriel L; Goldberg, Tony L; Huang, Shaoming; Andreadis, Theodore G; Walker, Edward D

2012-05-01

Analysis of molecular genetic diversity in nine marker regions of five genes within the bacteriophage WO genomic region revealed high diversity of the Wolbachia pipentis strain wPip in a population of Culex pipiens L. sampled in metropolitan Chicago, IL. From 166 blood fed females, 50 distinct genetic profiles of wPip were identified. Rarefaction analysis suggested a maximum of 110 profiles out of a possible 512 predicted by combinations of the nine markers. A rank-abundance curve showed that few strains were common and most were rare. Multiple regression showed that markers associated with gene Gp2d, encoding a partial putative capsid protein, were significantly associated with ancestry of individuals either to form molestus or form pipiens, as determined by prior microsatellite allele frequency analysis. None of the other eight markers was associated with ancestry to either form, nor to ancestry to Cx. quinquefasciatus Say. Logistic regression of host choice (mammal vs. avian) as determined by bloodmeal analysis revealed that significantly fewer individuals that had fed on mammals had the Gp9a genetic marker (58.5%) compared with avian-fed individuals (88.1%). These data suggest that certain wPip molecular genetic types are associated with genetic admixturing in the Cx. pipiens complex of metropolitan Chicago, IL, and that the association extends to phenotypic variation related to host preference.

The Physical Origin of Long Gas Depletion Times in Galaxies

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

Semenov, Vadim A.; Kravtsov, Andrey V.; Gnedin, Nickolay Y.

2017-08-18

We present a model that elucidates why gas depletion times in galaxies are long compared to the time scales of the processes driving the evolution of the interstellar medium. We show that global depletion times are not set by any "bottleneck" in the process of gas evolution towards the star-forming state. Instead, depletion times are long because star-forming gas converts only a small fraction of its mass into stars before it is dispersed by dynamical and feedback processes. Thus, complete depletion requires that gas transitions between star-forming and non-star-forming states multiple times. Our model does not rely on the assumption of equilibrium and can be used to interpret trends of depletion times with the properties of observed galaxies and the parameters of star formation and feedback recipes in galaxy simulations. In particular, the model explains the mechanism by which feedback self-regulates star formation rate in simulations and makes it insensitive to the local star formation efficiency. We illustrate our model using the results of an isolatedmore » $$L_*$$-sized disk galaxy simulation that reproduces the observed Kennicutt-Schmidt relation for both molecular and atomic gas. Interestingly, the relation for molecular gas is close to linear on kiloparsec scales, even though a non-linear relation is adopted in simulation cells. This difference is due to stellar feedback, which breaks the self-similar scaling of the gas density PDF with the average gas surface density.« less

Network, cellular, and molecular mechanisms underlying long-term memory formation.

PubMed

Carasatorre, Mariana; Ramírez-Amaya, Víctor

2013-01-01

The neural network stores information through activity-dependent synaptic plasticity that occurs in populations of neurons. Persistent forms of synaptic plasticity may account for long-term memory storage, and the most salient forms are the changes in the structure of synapses. The theory proposes that encoding should use a sparse code and evidence suggests that this can be achieved through offline reactivation or by sparse initial recruitment of the network units. This idea implies that in some cases the neurons that underwent structural synaptic plasticity might be a subpopulation of those originally recruited; However, it is not yet clear whether all the neurons recruited during acquisition are the ones that underwent persistent forms of synaptic plasticity and responsible for memory retrieval. To determine which neural units underlie long-term memory storage, we need to characterize which are the persistent forms of synaptic plasticity occurring in these neural ensembles and the best hints so far are the molecular signals underlying structural modifications of the synapses. Structural synaptic plasticity can be achieved by the activity of various signal transduction pathways, including the NMDA-CaMKII and ACh-MAPK. These pathways converge with the Rho family of GTPases and the consequent ERK 1/2 activation, which regulates multiple cellular functions such as protein translation, protein trafficking, and gene transcription. The most detailed explanation may come from models that allow us to determine the contribution of each piece of this fascinating puzzle that is the neuron and the neural network.

Characterization of a novel alpha-amidated decapeptide derived from proopiomelanocortin-A in the trout pituitary.

PubMed

Tollemer, H; Leprince, J; Bailhache, T; Chauveau, I; Vandesande, F; Tonon, M C; Jego, P; Vaudry, H

1997-01-01

Two complementary DNAs encoding distinct forms of POMC have been characterized in the trout pituitary. One of the POMC variants (POMC-A) possesses a C-terminal extension of 25 amino acids, which has no equivalent in other POMCs described to date. This C-terminal peptide contains three pairs of basic amino acids, suggesting that it may be the precursor of multiple processed peptides. In addition, the presence of a C-terminal glycine residue suggests that some of the processing products may be alpha-amidated. To characterize the molecular forms of the peptides generated from the C-terminal domain of trout POMC-A, we have developed specific antibodies against the C-terminal pentapeptide YHFQG and its alpha-amidated derivative YHFQ-NH2. Immunocytochemical labeling of pituitary sections with antibodies against YHFQ-NH2 revealed the presence of numerous immunoreactive cells in the pars intermedia and the rostral pars distalis. In contrast, the antibodies against YHFQG produced only weak immunostaining. HPLC analysis combined with RIA detection revealed that extracts of the pars intermedia and pars distalis contain several peptides derived from the C-terminal extension of trout POMC-A, with the predominant molecular form exhibiting the same retention time as ALGERKYHFQ-NH2. Tryptic digestion of this major form produced a peptide that coeluted with YHFQ-NH2. These data indicate that the processing of the C-terminal extension of trout POMC-A generates several novel peptides including the decapeptide amide ALGERKYHFQ-NH2.

Protein Arms in the Kinetochore-Microtubule Interface of the Yeast DASH Complex

PubMed Central

Miranda, JJ L.; King, David S.

2007-01-01

The yeast DASH complex is a heterodecameric component of the kinetochore necessary for accurate chromosome segregation. DASH forms closed rings around microtubules with a large gap between the DASH ring and the microtubule cylinder. We characterized the microtubule-binding properties of limited proteolysis products and subcomplexes of DASH, thus identifying candidate polypeptide extensions involved in establishing the DASH-microtubule interface. The acidic C-terminal extensions of tubulin subunits are not essential for DASH binding. We also measured the molecular mass of DASH rings on microtubules with scanning transmission electron microscopy and found that approximately 25 DASH heterodecamers assemble to form each ring. Dynamic association and relocation of multiple flexible appendages of DASH may allow the kinetochore to translate along the microtubule surface. PMID:17460120

Crystallization by Particle Attachment in Synthetic, Biogenic, and Geologic Environments

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

De Yoreo, James J.; Gilbert, Pupa U.; Sommerdijk, Nico

Field and laboratory observations show that crystals commonly form by the addition and attachment of particles that range from multi-ion complexes to fully formed nanoparticles. These non-classical pathways to crystallization are diverse, in contrast to classical models that consider the addition of monomeric chemical species. We review progress toward understanding crystal growth by particle attachment processes and show that multiple pathways result from the interplay of free energy landscapes and reaction dynamics. Much remains unknown about the fundamental aspects; particularly the relationships between solution structure, interfacial forces, and particle motion. Developing a predictive description that connects molecular details to ensemblemore » behavior will require revisiting long-standing interpretations of crystal formation in synthetic systems and patterns of mineralization in natural environments.« less

Hexagonal Nanopyramidal Prisms of Nearly Intrinsic InN on Patterned GaN Nanowire Arrays

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

Golam Sarwar, A. T. M.; Leung, Benjamin; Wang, George T.

By using multiple growth steps that separate the nucleation and growth processes, we show that nearly intrinsic InN single nanocrystals of high optical quality can be formed on patterned GaN nanowire arrays by molecular beam epitaxy. The InN nanostructures form into well-defined hexagonal prisms with pyramidal tops. Micro-photoluminescence (μ-PL) is carried out at low temperature (LT: 28.2 K) and room temperature (RT: 285 K) to gauge the relative material quality of the InN nanostructures. Nanopyramidal prisms grown using a three-step growth method are found to show superior quantum efficiency. In conclusion, excitation and temperature dependent μ-PL demonstrates the very highmore » quality and nearly intrinsic nature of the ordered InN nanostructure arrays.« less

Hexagonal Nanopyramidal Prisms of Nearly Intrinsic InN on Patterned GaN Nanowire Arrays

DOE PAGES

Golam Sarwar, A. T. M.; Leung, Benjamin; Wang, George T.; ...

2018-01-04

By using multiple growth steps that separate the nucleation and growth processes, we show that nearly intrinsic InN single nanocrystals of high optical quality can be formed on patterned GaN nanowire arrays by molecular beam epitaxy. The InN nanostructures form into well-defined hexagonal prisms with pyramidal tops. Micro-photoluminescence (μ-PL) is carried out at low temperature (LT: 28.2 K) and room temperature (RT: 285 K) to gauge the relative material quality of the InN nanostructures. Nanopyramidal prisms grown using a three-step growth method are found to show superior quantum efficiency. In conclusion, excitation and temperature dependent μ-PL demonstrates the very highmore » quality and nearly intrinsic nature of the ordered InN nanostructure arrays.« less

Extracellular Ca2(+)-dependent inducible alkaline phosphatase from extremely halophilic archaebacterium Haloarcula marismortui.

PubMed Central

Goldman, S; Hecht, K; Eisenberg, H; Mevarech, M

1990-01-01

When starved of inorganic phosphate, the extremely halophilic archaebacterium Haloarcula marismortui produces the enzyme alkaline phosphatase and secretes it to the medium. This inducible extracellular enzyme is a glycoprotein whose subunit molecular mass is 160 kDa, as estimated by sodium dodecyl sulfate-gel electrophoresis. The native form of the enzyme is heterogeneous and composed of multiple oligomeric forms. The enzymatic activity of the halophilic alkaline phosphatase is maximal at pH 8.5, and the enzyme is inhibited by phosphate. Unlike most alkaline phosphatases, the halobacterial enzyme requires Ca2+ and not Zn2+ ions for its activity. Both calcium ions (in the millimolar range) and NaCl (in the molar range) are required for the stability of the enzyme. Images PMID:2123861

Fingerprinting of near-homogeneous DNA ligase I and II from human cells. Similarity of their AMP-binding domains.

PubMed

Yang, S W; Becker, F F; Chan, J Y

1990-10-25

DNA ligases play obligatory roles during replication, repair, and recombination. Multiple forms of DNA ligase have been reported in mammalian cells including DNA ligase I, the high molecular mass species which functions during replication, and DNA ligase II, the low molecular mass species which is associated with repair. In addition, alterations in DNA ligase activities have been reported in acute lymphocytic leukemia cells, Bloom's syndrome cells, and cells undergoing differentiation and development. To better distinguish the biochemical and molecular properties of the various DNA ligases from human cells, we have developed a method of purifying multiple species of DNA ligase from HeLa cells by chromatography through DEAE-Bio-Gel, CM-Bio-Gel, hydroxylapatite, Sephacryl S-300, Mono P, and DNA-cellulose. DNA-cellulose chromatography of the partially purified enzymes resolved multiple species of DNA ligase after labeling the enzyme with [alpha-32P]ATP to form the ligase-[32P]AMP adduct. The early eluting enzyme activity (0.25 M NaCl) contained a major 67-kDa-labeled protein, while the late eluting activity (0.48 M NaCl) contained two major labeled proteins of 90 and 78 kDa. Neutralization experiments with antiligase I antibodies indicated that the early and late eluting activity peaks were DNA ligase II and I, respectively. The three major ligase-[32P]AMP polypeptides (90, 78, and 67 kDa) were subsequently purified to near homogeneity by elution from preparative sodium dodecyl sulfate-polyacrylamide gels. All three polypeptides retained DNA ligase activities after gel elution and renaturation. To further reveal the relationship between these enzymes, partial digestion by V8-protease was performed. All three purified polypeptides gave rise to a common 22-kDa-labeled fragment for their AMP-binding domains, indicating that the catalytic sites of ligase I and II are quite similar, if not identical. Similar findings were obtained from the two-dimensional gel electrophoresis of their AMP-binding domains in the trypsin-digested protein fragments. The results also suggested that these isozymes have been derived from the same primordial DNA sequence or from the same precursor protein. The purification scheme and the data obtained will be instrumental for the further elucidation of the biological roles of various DNA ligases from human cells.

A study of MRI-guided diffuse fluorescence molecular tomography for monitoring PDT effects in pancreas cancer

NASA Astrophysics Data System (ADS)

Samkoe, Kimberley S.; Davis, Scott C.; Srinivasan, Subhadra; O'Hara, Julia A.; Hasan, Tayyaba; Pogue, Brian W.

2009-06-01

Over the last several decades little progress has been made in the therapy and treatment monitoring of pancreas adenocarcinoma, a devastating and aggressive form of cancer that has a 5-year patient survival rate of 3%. Currently, investigations for the use of interstitial Verteporfin photodynamic therapy (PDT) are being undertaken in both orthotopic xenograft mouse models and in human clinical trials. In the mouse models, magnetic resonance (MR) imaging has been used as a measure of surrogate response to Verteporfin PDT; however, MR imaging alone lacks the molecular information required to assess the metabolic function and growth rates of the tumor immediately after treatment. We propose the implementation of MR-guided fluorescence tomography in conjunction with a fluorescently labeled (IR-Dye 800 CW, LI-COR) epidermal growth factor (EGF) as a molecular measure of surrogate response. To demonstrate the effectiveness of MR-guided diffuse fluorescence tomography for molecular imaging, we have used the AsPC-1 (+EGFR) human pancreatic adenocarcinoma in an orthotopic mouse model. EGF IRDye 800CW was injected 48 hours prior to imaging. MR image sequences were collected simultaneously with the fluorescence data using a MR-coupled diffuse optical tomography system. Image reconstruction was performed multiple times with varying abdominal organ segmentation in order to obtain a optimal tomographic image. It is shown that diffuse fluorescence tomography of the orthotopic pancreas model is feasible, with consideration of confounding fluorescence signals from the multiple organs and tissues surrounding the pancreas. MR-guided diffuse fluorescence tomography will be used to monitor EGF response after photodynamic therapy. Additionally, it provide the opportunity to individualize subsequent therapies based on response to PDT as well as to evaluate the success of combination therapies, such as PDT with chemotherapy, antibody therapy or even radiation.

Curli mediate bacterial adhesion to fibronectin via tensile multiple bonds

NASA Astrophysics Data System (ADS)

Oh, Yoo Jin; Hubauer-Brenner, Michael; Gruber, Hermann J.; Cui, Yidan; Traxler, Lukas; Siligan, Christine; Park, Sungsu; Hinterdorfer, Peter

2016-09-01

Many enteric bacteria including pathogenic Escherichia coli and Salmonella strains produce curli fibers that bind to host surfaces, leading to bacterial internalization into host cells. By using a nanomechanical force-sensing approach, we obtained real-time information about the distribution of molecular bonds involved in the adhesion of curliated bacteria to fibronectin. We found that curliated E. coli and fibronectin formed dense quantized and multiple specific bonds with high tensile strength, resulting in tight bacterial binding. Nanomechanical recognition measurements revealed that approximately 10 bonds were disrupted either sequentially or simultaneously under force load. Thus the curli formation of bacterial surfaces leads to multi-bond structural components of fibrous nature, which may explain the strong mechanical binding of curliated bacteria to host cells and unveil the functions of these proteins in bacterial internalization and invasion.

Evaluation of the molecular level visualisation approach for teaching and learning chemistry in Thailand

NASA Astrophysics Data System (ADS)

Phenglengdi, Butsari

This research evaluates the use of a molecular level visualisation approach in Thai secondary schools. The goal is to obtain insights about the usefulness of this approach, and to examine possible improvements in how the approach might be applied in the future. The methodology used for this research used both qualitative and quantitative approaches. Data were collected in the form of pre- and post-intervention multiple choice questions, open-ended-questions, drawing exercises, one-to-one interviews and video recordings of class activity. The research was conducted in two phases, involving a total of 261 students from the 11th Grade in Thailand. The use of VisChem animations in three studies was evaluated in Phase I. Study 1 was a pilot study exploring the benefits of incorporating VisChem animations to portray the molecular level. Study 2 compared test results between students exposed to these animations of molecular level events, and those not. Finally, in Study 3, test results were gathered from different types of schools (a rural school, a city school, and a university school). The results showed that students (and teachers) had misconceptions at the molecular level, and VisChem animations could help students understand chemistry concepts at the molecular level across all three types of schools. While the animation treatment group had a better score on the topic of states of water, the non-animation treatment group had a better score on the topic of dissolving sodium chloride in water than the animation group. The molecular level visualisation approach as a learning design was evaluated in Phase II. This approach involved a combination of VisChem animations, pictures, and diagrams together with the seven-step VisChem learning design. The study involved three classes of students, each with a different treatment, described as Class A - Traditional approach; Class B - VisChem animations with traditional approach; and Class C - Molecular level visualisation approach. Pre-test and post-test scores were compared across the three classes. The results from the multiple choice and calculation tests showed that the Class C - molecular level visualisation approach group demonstrated a deeper understanding of chemistry concepts than students in Classes A and B. However, the results showed that all the students were unable to perform satisfactorily on the calculation tests because the students had insufficient prior knowledge about stoichiometry to connect with the new knowledge. In the drawing tests the students exposed to the molecular level visualisation approach had a better mental model than the other classes, albeit with some remaining misconceptions. The findings highlight the intersecting nature of the teacher, student, and modelling in chemistry teaching. Use of a multi-step molecular level visualisation approach that encourages observation, reflection of prior understanding, and multiple opportunities at viewing (and using various visualisation elements), are key elements leading to a deeper understanding of chemistry. Presentation of the multi-step molecular level visualisation approach must be coupled with careful consideration of student prior knowledge, and with adequate guidance from a teacher who understands the topics at a deep level.

Disentangling the Circumnuclear Environs of Centaurus A. III. An Inner Molecular Ring, Nuclear Shocks, and the CO to Warm H{sub 2} Interface

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

Espada, D.; Miura, R. E.; Iono, D.

2017-07-10

We present the distribution and kinematics of the molecular gas in the circumnuclear disk (CND; 400 pc × 200 pc) of Centaurus A with resolutions of ∼5 pc (0.″3) and shed light onto the mechanism feeding the active galactic nucleus (AGN) using CO(3–2), HCO{sup +}(4–3), HCN(4–3), and CO(6–5) observations obtained with ALMA. Multiple filaments or streamers of tens to a hundred parsec scale exist within the CND, which form a ring-like structure with an unprojected diameter of 9″ × 6″ (162 pc × 108 pc) and a position angle P.A. ≃ 155°. Inside the nuclear ring, there are two leadingmore » and straight filamentary structures with lengths of about 30–60 pc at P.A. ≃ 120° on opposite sides of the AGN, with a rotational symmetry of 180° and steeper position–velocity diagrams, which are interpreted as nuclear shocks due to non-circular motions. Along the filaments, and unlike other nearby AGNs, several dense molecular clumps present low HCN/HCO{sup +}(4–3) ratios (≲0.5). The filaments abruptly end in the probed transitions at r ≃ 20 pc from the AGN, but previous near-IR H{sub 2}( J = 1–0)S(1) maps show that they continue in an even warmer gas phase ( T ∼ 1000 K), winding up in the form of nuclear spirals, and forming an inner ring structure with another set of symmetric filaments along the N–S direction and within r ≃ 10 pc. The molecular gas is governed primarily by non-circular motions, being the successive shock fronts at different scales where loss of angular momentum occurs, a mechanism that may feed efficiently powerful radio galaxies down to parsec scales.« less

Eukaryotic membrane tethers revisited using magnetic tweezers.

PubMed

Hosu, Basarab G; Sun, Mingzhai; Marga, Françoise; Grandbois, Michel; Forgacs, Gabor

2007-04-19

Membrane nanotubes, under physiological conditions, typically form en masse. We employed magnetic tweezers (MTW) to extract tethers from human brain tumor cells and compared their biophysical properties with tethers extracted after disruption of the cytoskeleton and from a strongly differing cell type, Chinese hamster ovary cells. In this method, the constant force produced with the MTW is transduced to cells through super-paramagnetic beads attached to the cell membrane. Multiple sudden jumps in bead velocity were manifest in the recorded bead displacement-time profiles. These discrete events were interpreted as successive ruptures of individual tethers. Observation with scanning electron microscopy supported the simultaneous existence of multiple tethers. The physical characteristics, in particular, the number and viscoelastic properties of the extracted tethers were determined from the analytic fit to bead trajectories, provided by a standard model of viscoelasticity. Comparison of tethers formed with MTW and atomic force microscopy (AFM), a technique where the cantilever-force transducer is moved at constant velocity, revealed significant differences in the two methods of tether formation. Our findings imply that extreme care must be used to interpret the outcome of tether pulling experiments performed with single molecular techniques (MTW, AFM, optical tweezers, etc). First, the different methods may be testing distinct membrane structures with distinct properties. Second, as soon as a true cell membrane (as opposed to that of a vesicle) can attach to a substrate, upon pulling on it, multiple nonspecific membrane tethers may be generated. Therefore, under physiological conditions, distinguishing between tethers formed through specific and nonspecific interactions is highly nontrivial if at all possible.

Eukaryotic membrane tethers revisited using magnetic tweezers

NASA Astrophysics Data System (ADS)

Hosu, Basarab G.; Sun, Mingzhai; Marga, Françoise; Grandbois, Michel; Forgacs, Gabor

2007-06-01

Membrane nanotubes, under physiological conditions, typically form en masse. We employed magnetic tweezers (MTW) to extract tethers from human brain tumor cells and compared their biophysical properties with tethers extracted after disruption of the cytoskeleton and from a strongly differing cell type, Chinese hamster ovary cells. In this method, the constant force produced with the MTW is transduced to cells through super-paramagnetic beads attached to the cell membrane. Multiple sudden jumps in bead velocity were manifest in the recorded bead displacement-time profiles. These discrete events were interpreted as successive ruptures of individual tethers. Observation with scanning electron microscopy supported the simultaneous existence of multiple tethers. The physical characteristics, in particular, the number and viscoelastic properties of the extracted tethers were determined from the analytic fit to bead trajectories, provided by a standard model of viscoelasticity. Comparison of tethers formed with MTW and atomic force microscopy (AFM), a technique where the cantilever-force transducer is moved at constant velocity, revealed significant differences in the two methods of tether formation. Our findings imply that extreme care must be used to interpret the outcome of tether pulling experiments performed with single molecular techniques (MTW, AFM, optical tweezers, etc). First, the different methods may be testing distinct membrane structures with distinct properties. Second, as soon as a true cell membrane (as opposed to that of a vesicle) can attach to a substrate, upon pulling on it, multiple nonspecific membrane tethers may be generated. Therefore, under physiological conditions, distinguishing between tethers formed through specific and nonspecific interactions is highly nontrivial if at all possible.

SRY-box-containing Gene 2 Regulation of Nuclear Receptor Tailless (Tlx) Transcription in Adult Neural Stem Cells*

PubMed Central

Shimozaki, Koji; Zhang, Chun-Li; Suh, Hoonkyo; Denli, Ahmet M.; Evans, Ronald M.; Gage, Fred H.

2012-01-01

Adult neurogenesis is maintained by self-renewable neural stem cells (NSCs). Their activity is regulated by multiple signaling pathways and key transcription factors. However, it has been unclear whether these factors interplay with each other at the molecular level. Here we show that SRY-box-containing gene 2 (Sox2) and nuclear receptor tailless (TLX) form a molecular network in adult NSCs. We observed that both Sox2 and TLX proteins bind to the upstream region of Tlx gene. Sox2 positively regulates Tlx expression, whereas the binding of TLX to its own promoter suppresses its transcriptional activity in luciferase reporter assays. Such TLX-mediated suppression can be antagonized by overexpressing wild-type Sox2 but not a mutant lacking the transcriptional activation domain. Furthermore, through regions involved in DNA-binding activity, Sox2 and TLX physically interact to form a complex on DNAs that contain a consensus binding site for TLX. Finally, depletion of Sox2 revealed the potential negative feedback loop of TLX expression that is antagonized by Sox2 in adult NSCs. These data suggest that Sox2 plays an important role in Tlx transcription in cultured adult NSCs. PMID:22194602

SRY-box-containing gene 2 regulation of nuclear receptor tailless (Tlx) transcription in adult neural stem cells.

PubMed

Shimozaki, Koji; Zhang, Chun-Li; Suh, Hoonkyo; Denli, Ahmet M; Evans, Ronald M; Gage, Fred H

2012-02-17

Adult neurogenesis is maintained by self-renewable neural stem cells (NSCs). Their activity is regulated by multiple signaling pathways and key transcription factors. However, it has been unclear whether these factors interplay with each other at the molecular level. Here we show that SRY-box-containing gene 2 (Sox2) and nuclear receptor tailless (TLX) form a molecular network in adult NSCs. We observed that both Sox2 and TLX proteins bind to the upstream region of Tlx gene. Sox2 positively regulates Tlx expression, whereas the binding of TLX to its own promoter suppresses its transcriptional activity in luciferase reporter assays. Such TLX-mediated suppression can be antagonized by overexpressing wild-type Sox2 but not a mutant lacking the transcriptional activation domain. Furthermore, through regions involved in DNA-binding activity, Sox2 and TLX physically interact to form a complex on DNAs that contain a consensus binding site for TLX. Finally, depletion of Sox2 revealed the potential negative feedback loop of TLX expression that is antagonized by Sox2 in adult NSCs. These data suggest that Sox2 plays an important role in Tlx transcription in cultured adult NSCs.

Multiple-locus variable number of tandem repeat analysis as a tool for molecular epidemiology of botulism: The Italian experience.

PubMed

Anniballi, Fabrizio; Fillo, Silvia; Giordani, Francesco; Auricchio, Bruna; Tehran, Domenico Azarnia; di Stefano, Enrica; Mandarino, Giuseppina; De Medici, Dario; Lista, Florigio

2016-12-01

Clostridium botulinum is the bacterial agent of botulism, a rare but severe neuro-paralytic disease. Because of its high impact, in Italy botulism is monitored by an ad hoc surveillance system. The National Reference Centre for Botulism, as part of this system, collects and analyzes all demographic, epidemiologic, microbiological, and molecular data recovered during cases and/or outbreaks occurred in Italy. A panel of 312 C. botulinum strains belonging to group I were submitted to MLVA sub-typing. Strains, isolated from clinical specimens, food and environmental samples collected during the surveillance activities, were representative of all forms of botulism from all Italian regions. Through clustering analysis isolates were grouped into 12 main clusters. No regional or temporal clustering was detected, demonstrating the high heterogeneity of strains circulating in Italy. This study confirmed that MLVA is capable of sub-typing C. botulinum strains. Moreover, MLVA is effective at tracing and tracking the source of contamination and is helpful for the surveillance system in terms of planning and upgrading of procedures, activities and data collection forms. Copyright © 2016 Elsevier B.V. All rights reserved.

The development of psychopathy.

PubMed

Blair, R J R; Peschardt, K S; Budhani, S; Mitchell, D G V; Pine, D S

2006-01-01

The current review focuses on the construct of psychopathy, conceptualized as a clinical entity that is fundamentally distinct from a heterogeneous collection of syndromes encompassed by the term 'conduct disorder'. We will provide an account of the development of psychopathy at multiple levels: ultimate causal (the genetic or social primary cause), molecular, neural, cognitive and behavioral. The following main claims will be made: (1) that there is a stronger genetic as opposed to social ultimate cause to this disorder. The types of social causes proposed (e.g., childhood sexual/physical abuse) should elevate emotional responsiveness, not lead to the specific form of reduced responsiveness seen in psychopathy; (2) The genetic influence leads to the emotional dysfunction that is the core of psychopathy; (3) The genetic influence at the molecular level remains unknown. However, it appears to impact the functional integrity of the amygdala and orbital/ventrolateral frontal cortex (and possibly additional systems); (4) Disruption within these two neural systems leads to impairment in the ability to form stimulus-reinforcement associations and to alter stimulus-response associations as a function of contingency change. These impairments disrupt the impact of standard socialization techniques and increase the risk for frustration-induced reactive aggression respectively.

A structural study of F-actin - filamin networks

NASA Astrophysics Data System (ADS)

Ahrens-Braunstein, Ashley; Nguyen, Lam; Hirst, Linda

2010-03-01

The cell's ability to move and contract is attributed to the semi-flexible filamentous protein, F -actin, one of the three filaments in the cytoskeleton. Actin bundling can be formed by a cross-linking actin binding protein (ABP) filamin. By examining filamin's cross-linking abilities at different concentrations and molar ratios, we can study the flexibility, structure and multiple network formations created when cross-linking F-actin with this protein. We have studied the phase diagram of this protein system using fluorescence microscopy, analyzing the network structures observed in the context of a coarse grained molecular dynamics simulation carried out by our group.

Molecular profiling of multiple myeloma: from gene expression analysis to next-generation sequencing.

PubMed

Agnelli, Luca; Tassone, Pierfrancesco; Neri, Antonino

2013-06-01

Multiple myeloma is a fatal malignant proliferation of clonal bone marrow Ig-secreting plasma cells, characterized by wide clinical, biological, and molecular heterogeneity. Herein, global gene and microRNA expression, genome-wide DNA profilings, and next-generation sequencing technology used to investigate the genomic alterations underlying the bio-clinical heterogeneity in multiple myeloma are discussed. High-throughput technologies have undoubtedly allowed a better comprehension of the molecular basis of the disease, a fine stratification, and early identification of high-risk patients, and have provided insights toward targeted therapy studies. However, such technologies are at risk of being affected by laboratory- or cohort-specific biases, and are moreover influenced by high number of expected false positives. This aspect has a major weight in myeloma, which is characterized by large molecular heterogeneity. Therefore, meta-analysis as well as multiple approaches are desirable if not mandatory to validate the results obtained, in line with commonly accepted recommendation for tumor diagnostic/prognostic biomarker studies.

A role for self-gravity at multiple length scales in the process of star formation.

PubMed

Goodman, Alyssa A; Rosolowsky, Erik W; Borkin, Michelle A; Foster, Jonathan B; Halle, Michael; Kauffmann, Jens; Pineda, Jaime E

2009-01-01

Self-gravity plays a decisive role in the final stages of star formation, where dense cores (size approximately 0.1 parsecs) inside molecular clouds collapse to form star-plus-disk systems. But self-gravity's role at earlier times (and on larger length scales, such as approximately 1 parsec) is unclear; some molecular cloud simulations that do not include self-gravity suggest that 'turbulent fragmentation' alone is sufficient to create a mass distribution of dense cores that resembles, and sets, the stellar initial mass function. Here we report a 'dendrogram' (hierarchical tree-diagram) analysis that reveals that self-gravity plays a significant role over the full range of possible scales traced by (13)CO observations in the L1448 molecular cloud, but not everywhere in the observed region. In particular, more than 90 per cent of the compact 'pre-stellar cores' traced by peaks of dust emission are projected on the sky within one of the dendrogram's self-gravitating 'leaves'. As these peaks mark the locations of already-forming stars, or of those probably about to form, a self-gravitating cocoon seems a critical condition for their existence. Turbulent fragmentation simulations without self-gravity-even of unmagnetized isothermal material-can yield mass and velocity power spectra very similar to what is observed in clouds like L1448. But a dendrogram of such a simulation shows that nearly all the gas in it (much more than in the observations) appears to be self-gravitating. A potentially significant role for gravity in 'non-self-gravitating' simulations suggests inconsistency in simulation assumptions and output, and that it is necessary to include self-gravity in any realistic simulation of the star-formation process on subparsec scales.

Explaining the luminosity spread in young clusters: proto and pre-main sequence stellar evolution in a molecular cloud environment

NASA Astrophysics Data System (ADS)

Jensen, Sigurd S.; Haugbølle, Troels

2018-02-01

Hertzsprung-Russell diagrams of star-forming regions show a large luminosity spread. This is incompatible with well-defined isochrones based on classic non-accreting protostellar evolution models. Protostars do not evolve in isolation of their environment, but grow through accretion of gas. In addition, while an age can be defined for a star-forming region, the ages of individual stars in the region will vary. We show how the combined effect of a protostellar age spread, a consequence of sustained star formation in the molecular cloud, and time-varying protostellar accretion for individual protostars can explain the observed luminosity spread. We use a global magnetohydrodynamic simulation including a sub-scale sink particle model of a star-forming region to follow the accretion process of each star. The accretion profiles are used to compute stellar evolution models for each star, incorporating a model of how the accretion energy is distributed to the disc, radiated away at the accretion shock, or incorporated into the outer layers of the protostar. Using a modelled cluster age of 5 Myr, we naturally reproduce the luminosity spread and find good agreement with observations of the Collinder 69 cluster, and the Orion Nebular Cluster. It is shown how stars in binary and multiple systems can be externally forced creating recurrent episodic accretion events. We find that in a realistic global molecular cloud model massive stars build up mass over relatively long time-scales. This leads to an important conceptual change compared to the classic picture of non-accreting stellar evolution segmented into low-mass Hayashi tracks and high-mass Henyey tracks.

Star-Formation in Free-Floating Evaporating Gaseous Globules

NASA Astrophysics Data System (ADS)

Sahai, Raghvendra

2017-08-01

We propose to study the stellar embryos in select members of a newly recognized class of Free-floating Evaporating Gaseous Globules (frEGGS) embedded in HII regions and having head-tail shapes. We discovered two of these in the Cygnus massive star-forming region (MSFR) with HST, including one of the most prominent members of this class (IRAS20324). Subsequent archival searches of Spitzer imaging of MSFRs has allowed us to build a statistical sample of frEGGs. Our molecular-line observations show the presence of dense molecular cores with total gas masses of (0.5-few) Msun in these objects, and our radio continuum images and Halpha images (from the IPHAS survey) reveal bright photo-ionized peripheries around these objects. We hypothesize that frEGGs are density concentrations originating in giant molecular clouds, that, when subject to the sculpting and compression by strong winds and UV radiation from massive stars, become active star-forming cores. For the 4 frEGGs with HST or near-IR AO images showing young stars and bipolar cavities produced by their jets or collimated outflows, the symmetry axis points roughly toward the external ionizing star or star cluster - exciting new evidence for our overpressure-induced star formation hypothesis. We propose to test this hypothesis by imaging 24 frEGGs in two nearby MSFRs that represent different radiation-dominated environments. Using ACS imaging with filters F606W, F814W, & F658N (Ha+[NII]), we will search for jets and outflow-excavated cavities, investigate the stellar nurseries inside frEGGs, and determine whether the globules are generally forming multiple star systems or small clusters, as in IRAS20324.

Structures and mechanism of dipeptidyl peptidases 8 and 9, important players in cellular homeostasis and cancer.

PubMed

Ross, Breyan; Krapp, Stephan; Augustin, Martin; Kierfersauer, Reiner; Arciniega, Marcelino; Geiss-Friedlander, Ruth; Huber, Robert

2018-02-13

Dipeptidyl peptidases 8 and 9 are intracellular N-terminal dipeptidyl peptidases (preferentially postproline) associated with pathophysiological roles in immune response and cancer biology. While the DPP family member DPP4 is extensively characterized in molecular terms as a validated therapeutic target of type II diabetes, experimental 3D structures and ligand-/substrate-binding modes of DPP8 and DPP9 have not been reported. In this study we describe crystal and molecular structures of human DPP8 (2.5 Å) and DPP9 (3.0 Å) unliganded and complexed with a noncanonical substrate and a small molecule inhibitor, respectively. Similar to DPP4, DPP8 and DPP9 molecules consist of one β-propeller and α/β hydrolase domain, forming a functional homodimer. However, they differ extensively in the ligand binding site structure. In intriguing contrast to DPP4, where liganded and unliganded forms are closely similar, ligand binding to DPP8/9 induces an extensive rearrangement at the active site through a disorder-order transition of a 26-residue loop segment, which partially folds into an α-helix (R-helix), including R160/133, a key residue for substrate binding. As vestiges of this helix are also seen in one of the copies of the unliganded form, conformational selection may contributes to ligand binding. Molecular dynamics simulations support increased flexibility of the R-helix in the unliganded state. Consistently, enzyme kinetics assays reveal a cooperative allosteric mechanism. DPP8 and DPP9 are closely similar and display few opportunities for targeted ligand design. However, extensive differences from DPP4 provide multiple cues for specific inhibitor design and development of the DPP family members as therapeutic targets or antitargets.

Learning surface molecular structures via machine vision

DOE PAGES

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

2017-08-10

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (‘read out’) all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds andmore » thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. Here, the method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.« less

Learning surface molecular structures via machine vision

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

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (‘read out’) all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds andmore » thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. Here, the method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.« less

Flo11p-Independent Control of “Mat” Formation by Hsp70 Molecular Chaperones and Nucleotide Exchange Factors in Yeast

PubMed Central

Martineau, Céline N.; Beckerich, Jean-Marie; Kabani, Mehdi

2007-01-01

The yeast Saccharomyces cerevisiae has been used as a model for fungal biofilm formation due to its ability to adhere to plastic surfaces and to form mats on low-density agar petri plates. Mats are complex multicellular structures composed of a network of cables that form a central hub from which emanate multiple radial spokes. This reproducible and elaborate pattern is indicative of a highly regulated developmental program that depends on specific transcriptional programming, environmental cues, and possibly cell–cell communication systems. While biofilm formation and sliding motility were shown to be strictly dependent on the cell-surface adhesin Flo11p, little is known about the cellular machinery that controls mat formation. Here we show that Hsp70 molecular chaperones play key roles in this process with the assistance of the nucleotide exchange factors Fes1p and Sse1p and the Hsp40 family member Ydj1p. The disruption of these cofactors completely abolished mat formation. Furthermore, complex interactions among SSA genes were observed: mat formation depended mostly on SSA1 while minor defects were observed upon loss of SSA2; additional mutations in SSA3 or SSA4 further enhanced these phenotypes. Importantly, these mutations did not compromise invasive growth or Flo11p expression, suggesting that Flo11p-independent pathways are necessary to form mats. PMID:17947402

Structural insights into the rhabdovirus transcription/replication complex.

PubMed

Ivanov, Ivan; Yabukarski, Filip; Ruigrok, Rob W H; Jamin, Marc

2011-12-01

The rhabdoviruses have a non-segmented single stranded negative-sense RNA genome. Their multiplication in a host cell requires three viral proteins in addition to the viral RNA genome. The nucleoprotein (N) tightly encapsidates the viral RNA, and the N-RNA complex serves as the template for both transcription and replication. The viral RNA-dependent RNA polymerase is a two subunit complex that consists of a large subunit, L, and a non-catalytic cofactor, the phosphoprotein, P. P also acts as a chaperone of nascent RNA-free N by forming a N(0)-P complex that prevents N from binding to cellular RNAs and from polymerizing in the absence of RNA. Here, we discuss the recent molecular and structural studies of individual components and multi-molecular complexes that are involved in the transcription/replication complex of these viruses with regard to their implication in viral transcription and replication. Copyright © 2011 Elsevier B.V. All rights reserved.

Regulators of spindle microtubules and their mechanisms: Living together matters.

PubMed

Lakshmi, R Bhagya; Nair, Vishnu M; Manna, Tapas K

2018-02-01

Development and survival of all eukaryotic organisms depend on equal partitioning of their chromosomes between the two newly formed daughter cells during mitosis. The mitotic spindle performs the task of physically segregating the chromosomes through multiple stages of mitosis. During this process, kinetochore-microtubule attachment requires to be selectively stabilized to hold the chromosomes, but at the same time, it has to be flexible enough to allow kinetochore microtubule dynamicity and chromosome movements. Research during the last decade or so has identified a number of proteins associated with the spindle microtubule plus ends that regulate these processes and orchestrate forces to spatially organize and separate the chromosomes. In this review, we describe the molecular details of those regulators and their mechanisms of action at the kinetochore-microtubule interface. © 2018 IUBMB Life, 70(2):101-111, 2018. © 2018 International Union of Biochemistry and Molecular Biology.

Molecular modeling of the conformational dynamics of the cellular prion protein

NASA Astrophysics Data System (ADS)

Nguyen, Charles; Colling, Ian; Bartz, Jason; Soto, Patricia

2014-03-01

Prions are infectious agents responsible for transmissible spongiform encephalopathies (TSEs), a type of fatal neurodegenerative disease in mammals. Prions propagate biological information by conversion of the non-pathological version of the prion protein to the infectious conformation, PrPSc. A wealth of knowledge has shed light on the nature and mechanism of prion protein conversion. In spite of the significance of this problem, we are far from fully understanding the conformational dynamics of the cellular isoform. To remedy this situation we employ multiple biomolecular modeling techniques such as docking and molecular dynamics simulations to map the free energy landscape and determine what specific regions of the prion protein are most conductive to binding. The overall goal is to characterize the conformational dynamics of the cell form of the prion protein, PrPc, to gain insight into inhibition pathways against misfolding. NE EPSCoR FIRST Award to Patricia Soto.

ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines.

PubMed

Chen, Haochuan; Fu, Haohao; Shao, Xueguang; Chipot, Christophe; Cai, Wensheng

2018-06-18

Extended adaptive biasing force (eABF), a collective variable (CV)-based importance-sampling algorithm, has proven to be very robust and efficient compared with the original ABF algorithm. Its implementation in Colvars, a software addition to molecular dynamics (MD) engines, is, however, currently limited to NAMD and LAMMPS. To broaden the scope of eABF and its variants, like its generalized form (egABF), and make them available to other MD engines, e.g., GROMACS, AMBER, CP2K, and openMM, we present a PLUMED-based implementation, called extended-Lagrangian free energy calculation (ELF). This implementation can be used as a stand-alone gradient estimator for other CV-based sampling algorithms, such as temperature-accelerated MD (TAMD) and extended-Lagrangian metadynamics (MtD). ELF provides the end user with a convenient framework to help select the best-suited importance-sampling algorithm for a given application without any commitment to a particular MD engine.

THE GOULD’S BELT DISTANCES SURVEY (GOBELINS). II. DISTANCES AND STRUCTURE TOWARD THE ORION MOLECULAR CLOUDS

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

Kounkel, Marina; Hartmann, Lee; Loinard, Laurent

We present the results of the Gould’s Belt Distances Survey of young star-forming regions toward the Orion Molecular Cloud Complex. We detected 36 young stellar objects (YSOs) with the Very Large Baseline Array, 27 of which have been observed in at least three epochs over the course of two years. At least half of these YSOs belong to multiple systems. We obtained parallax and proper motions toward these stars to study the structure and kinematics of the Complex. We measured a distance of 388 ± 5 pc toward the Orion Nebula Cluster, 428 ± 10 pc toward the southern portion L1641, 388 ± 10 pc towardmore » NGC 2068, and roughly ∼420 pc toward NGC 2024. Finally, we observed a strong degree of plasma radio scattering toward λ Ori.« less

[Programmed necrosis and necroptosis - molecular mechanisms].

PubMed

Giżycka, Agata; Chorostowska-Wynimko, Joanna

2015-12-16

Programmed necrosis has been proven vital for organism development and homeostasis maintenance. Its regulatory effects on functional activity of the immune system, as well as on pathways regulating the death mechanisms in cells with diminished apoptotic activity, including malignant cells, have been confirmed. There is also increasing evidence indicating necrosis involvement in many human pathologies. Contrary to previous beliefs, necrosis is not only a passive, pathological, gene-independent process. However, the current knowledge regarding molecular regulation of programmed necrosis is scarce. In part this is due to the multiplicity and complexity of signaling pathways involved in programmed necrosis, as well as the absence of specific cellular markers identifying this process, but also the ambiguous and imprecise international terminology. This review presents the current state of the art on molecular mechanisms of programmed necrosis. In particular, its specific and frequent form, necroptosis, is discussed. The role of RIP1 and RIP3 kinases in this process is presented, as well as the diverse pathways induced by ligation of tumor necrosis factor α, to its receptor, TNFR1, i.e. cell survival, apoptosis or necroptosis.

Diverse assessment and active student engagement sustain deep learning: A comparative study of outcomes in two parallel introductory biochemistry courses.

PubMed

Bevan, Samantha J; Chan, Cecilia W L; Tanner, Julian A

2014-01-01

Although there is increasing evidence for a relationship between courses that emphasize student engagement and achievement of student deep learning, there is a paucity of quantitative comparative studies in a biochemistry and molecular biology context. Here, we present a pedagogical study in two contrasting parallel biochemistry introductory courses to compare student surface and deep learning. Surface and deep learning were measured quantitatively by a study process questionnaire at the start and end of the semester, and qualitatively by questionnaires and interviews with students. In the traditional lecture/examination based course, there was a dramatic shift to surface learning approaches through the semester. In the course that emphasized student engagement and adopted multiple forms of assessment, a preference for deep learning was sustained with only a small reduction through the semester. Such evidence for the benefits of implementing student engagement and more diverse non-examination based assessment has important implications for the design, delivery, and renewal of introductory courses in biochemistry and molecular biology. © 2014 The International Union of Biochemistry and Molecular Biology.

"Zip me up, and cool me down": Molar narratives and molecular intensities in 'helicopter' mental health services.

PubMed

McGrath, Laura; Reavey, Paula

2016-03-01

Experiences of the space-time dimensions of contemporary mental health services are shaped according to what we describe here as a 'helicopter service', where professionals drop down into service users' lives for short, often pre-determined bursts of time. This can create a system where users' experiences are observed and assessed from a more distanced and circumscribed perspective. This paper considers the implications of these systemic changes, using interviews with current UK service users. To help in the exploration of the complexities faced by service users', we use Deleuze and Guatarri's (1987) distinction between molar and molecular forms of organisation. A process oriented thematic analysis discusses: a) Affording narratives of distress: Molarity, monitoring and space in service interactions and b) Narratives in therapy: Compartmentalising the distressed self. Multiple aspects of the relationship between space and distress are explored. An understanding of experiences of distress beyond the boundaries of the molar, which considers its intensive, molecular and transformative nature, may help to open up engagement with the affective and emotional dimensions of mental health. Copyright © 2016 Elsevier Ltd. All rights reserved.

Metal-organic molecular device for non-volatile memory storage

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

Radha, B., E-mail: radha.boya@manchester.ac.uk, E-mail: kulkarni@jncasr.ac.in; Sagade, Abhay A.; Kulkarni, G. U., E-mail: radha.boya@manchester.ac.uk, E-mail: kulkarni@jncasr.ac.in

Non-volatile memory devices have been of immense research interest for their use in active memory storage in powered off-state of electronic chips. In literature, various molecules and metal compounds have been investigated in this regard. Molecular memory devices are particularly attractive as they offer the ease of storing multiple memory states in a unique way and also represent ubiquitous choice for miniaturized devices. However, molecules are fragile and thus the device breakdown at nominal voltages during repeated cycles hinders their practical applicability. Here, in this report, a synergetic combination of an organic molecule and an inorganic metal, i.e., a metal-organicmore » complex, namely, palladium hexadecylthiolate is investigated for memory device characteristics. Palladium hexadecylthiolate following partial thermolysis is converted to a molecular nanocomposite of Pd(II), Pd(0), and long chain hydrocarbons, which is shown to exhibit non-volatile memory characteristics with exceptional stability and retention. The devices are all solution-processed and the memory action stems from filament formation across the pre-formed cracks in the nanocomposite film.« less

Investigation into the interaction of losartan with human serum albumin and glycated human serum albumin by spectroscopic and molecular dynamics simulation techniques: A comparison study.

PubMed

Moeinpour, Farid; Mohseni-Shahri, Fatemeh S; Malaekeh-Nikouei, Bizhan; Nassirli, Hooriyeh

2016-09-25

The interaction between losartan and human serum albumin (HSA), as well as its glycated form (gHSA) was studied by multiple spectroscopic techniques and molecular dynamics simulation under physiological conditions. The binding information, including the binding constants, effective quenching constant and number of binding sites showed that the binding partiality of losartan to HSA was higher than to gHSA. The findings of three-dimensional fluorescence spectra demonstrated that the binding of losartan to HSA and gHSA would alter the protein conformation. The distances between Trp residue and the binding sites of the drug were evaluated on the basis of the Förster theory, and it was indicated that non-radiative energy transfer from HSA and gHSA to the losartan happened with a high possibility. According to molecular dynamics simulation, the protein secondary and tertiary structure changes were compared in HSA and gHSA for clarifying the obtained results. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Conformational Transition Pathways of Epidermal Growth Factor Receptor Kinase Domain from Multiple Molecular Dynamics Simulations and Bayesian Clustering.

PubMed

Li, Yan; Li, Xiang; Ma, Weiya; Dong, Zigang

2014-08-12

The epidermal growth factor receptor (EGFR) is aberrantly activated in various cancer cells and an important target for cancer treatment. Deep understanding of EGFR conformational changes between the active and inactive states is of pharmaceutical interest. Here we present a strategy combining multiply targeted molecular dynamics simulations, unbiased molecular dynamics simulations, and Bayesian clustering to investigate transition pathways during the activation/inactivation process of EGFR kinase domain. Two distinct pathways between the active and inactive forms are designed, explored, and compared. Based on Bayesian clustering and rough two-dimensional free energy surfaces, the energy-favorable pathway is recognized, though DFG-flip happens in both pathways. In addition, another pathway with different intermediate states appears in our simulations. Comparison of distinct pathways also indicates that disruption of the Lys745-Glu762 interaction is critically important in DFG-flip while movement of the A-loop significantly facilitates the conformational change. Our simulations yield new insights into EGFR conformational transitions. Moreover, our results verify that this approach is valid and efficient in sampling of protein conformational changes and comparison of distinct pathways.

BiP and Multiple DNAJ Molecular Chaperones in the Endoplasmic Reticulum Are Required for Efficient Simian Virus 40 Infection

PubMed Central

Goodwin, Edward C.; Lipovsky, Alex; Inoue, Takamasa; Magaldi, Thomas G.; Edwards, Anne P. B.; Van Goor, Kristin E. Y.; Paton, Adrienne W.; Paton, James C.; Atwood, Walter J.; Tsai, Billy; DiMaio, Daniel

2011-01-01

ABSTRACT Simian virus 40 (SV40) is a nonenveloped DNA virus that traffics through the endoplasmic reticulum (ER) en route to the nucleus, but the mechanisms of capsid disassembly and ER exit are poorly understood. We conducted an unbiased RNA interference screen to identify cellular genes required for SV40 infection. SV40 infection was specifically inhibited by up to 50-fold by knockdown of four different DNAJ molecular cochaperones or by inhibition of BiP, the Hsp70 partner of DNAJB11. These proteins were not required for the initiation of capsid disassembly, but knockdown markedly inhibited SV40 exit from the ER. In addition, BiP formed a complex with SV40 capsids in the ER in a DNAJB11-dependent fashion. These experiments identify five new cellular proteins required for SV40 infection and suggest that the binding of BiP to the capsid is required for ER exit. Further studies of these proteins will provide insight into the molecular mechanisms of polyomavirus infection and ER function. PMID:21673190

HIV-1 Genetic Variability in Cuba and Implications for Transmission and Clinical Progression.

PubMed

Blanco, Madeline; Machado, Liuber Y; Díaz, Héctor; Ruiz, Nancy; Romay, Dania; Silva, Eladio

2015-10-01

INTRODUCTION Serological and molecular HIV-1 studies in Cuba have shown very low prevalence of seropositivity, but an increasing genetic diversity attributable to introduction of many HIV-1 variants from different areas, exchange of such variants among HIV-positive people with several coinciding routes of infection and other epidemiologic risk factors in the seropositive population. The high HIV-1 genetic variability observed in Cuba has possible implications for transmission and clinical progression. OBJECTIVE Study genetic variability for the HIV-1 env, gag and pol structural genes in Cuba; determine the prevalence of B and non-B subtypes according to epidemiologic and behavioral variables and determine whether a relationship exists between genetic variability and transmissibility, and between genetic variability and clinical disease progression in people living with HIV/AIDS. METHODS Using two molecular assays (heteroduplex mobility assay and nucleic acid sequencing), structural genes were characterized in 590 people with HIV-1 (480 men and 110 women), accounting for 3.4% of seropositive individuals in Cuba as of December 31, 2013. Nonrandom sampling, proportional to HIV prevalence by province, was conducted. Relationships between molecular results and viral factors, host characteristics, and patients' clinical, epidemiologic and behavioral variables were studied for molecular epidemiology, transmission, and progression analyses. RESULTS Molecular analysis of the three HIV-1 structural genes classified 297 samples as subtype B (50.3%), 269 as non-B subtypes (45.6%) and 24 were not typeable. Subtype B prevailed overall and in men, mainly in those who have sex with men. Non-B subtypes were prevalent in women and heterosexual men, showing multiple circulating variants and recombinant forms. Sexual transmission was the predominant form of infection for all. B and non-B subtypes were encountered throughout Cuba. No association was found between subtypes and transmission or clinical progression, although the proportion of deaths was higher for subtype B. Among those who died during the study period, there were no differences between subtypes in the mean time from HIV or AIDS diagnosis to death. CONCLUSIONS Our results suggest that B and non-B HIV-1 subtypes found in Cuba do not differ in transmissibility and in clinical disease progression. KEYWORDS HIV-1, AIDS, molecular epidemiology, transmissibility, clinical progression, subtypes, circulating recombinant forms, pathogenesis, Cuba.

Unprecedented multiplicity of Ig transmembrane and secretory mRNA forms in the cartilaginous fish.

PubMed

Rumfelt, Lynn L; Diaz, Marilyn; Lohr, Rebecca L; Mochon, Evonne; Flajnik, Martin F

2004-07-15

In most jawed vertebrates including cartilaginous fish, membrane-bound IgM is expressed as a five Ig superfamily (Igsf)-domain H chain attached to a transmembrane (Tm) region. Heretofore, bony fish IgM was the one exception with IgM mRNA spliced to produce a four-domain Tm H chain. We now demonstrate that the Tm and secretory (Sec) mRNAs of the novel cartilaginous fish Ig isotypes, IgW and IgNAR, are present in multiple forms, most likely generated by alternative splicing. In the nurse shark, Ginglymostoma cirratum, and horn shark, Heterodontus francisci, alternative splicing of Tm exons to the second or the fourth constant (C(H)) exons produces two distinct IgW Tm cDNAs. Although the seven-domain IgW Sec cDNA form contains a canonical secretory tail shared with IgM, IgNAR, and IgA, we report a three-domain cDNA form of shark IgW (IgW(short)) having an unusual Sec tail, which is orthologous to skate IgX(short) cDNA. The IgW and IgW(short) Sec transcripts are restricted in their tissue distribution and expression levels vary among individual sharks, with all forms expressed early in ontogeny. IgNAR mRNA is alternatively spliced to produce a truncated four-domain Tm cDNA and a second Tm cDNA is expressed identical in Igsf domains as the Sec form. PBL is enriched in the Tm cDNA of these Igs. These molecular data suggest that cartilaginous fish have augmented their humoral immune repertoire by diversifying the sizes of their Ig isotypes. Furthermore, these Tm cDNAs are prototypical and the truncated variants may translate as more stable protein at the cell surface.

Autographa californica Nucleopolyhedrovirus AC141 (Exon0), a Potential E3 Ubiquitin Ligase, Interacts with Viral Ubiquitin and AC66 To Facilitate Nucleocapsid Egress.

PubMed

Biswas, Siddhartha; Willis, Leslie G; Fang, Minggang; Nie, Yingchao; Theilmann, David A

2018-02-01

During the infection cycle of Autographa californica multiple nucleopolyhedrovirus (AcMNPV), two forms of virions are produced, budded virus (BV) and occlusion-derived virus (ODV). Nucleocapsids that form BV have to egress from the nucleus, whereas nucleocapsids that form ODV remain inside the nucleus. The molecular mechanism that determines whether nucleocapsids remain inside or egress from the nucleus is unknown. AC141 (a predicted E3 ubiquitin ligase) and viral ubiquitin (vUbi) have both been shown to be required for efficient BV production. In this study, it was hypothesized that vUbi interacts with AC141, and in addition, that this interaction was required for BV production. Deletion of both ac141 and vubi restricted viral infection to a single cell, and BV production was completely eliminated. AC141 was ubiquitinated by either vUbi or cellular Ubi, and this interaction was required for optimal BV production. Nucleocapsids in BV, but not ODV, were shown to be specifically ubiquitinated by vUbi, including a 100-kDa protein, as well as high-molecular-weight conjugates. The viral ubiquitinated 100-kDa BV-specific nucleocapsid protein was identified as AC66, which is known to be required for BV production and was shown by coimmunoprecipitation and mass spectrometry to interact with AC141. Confocal microscopy also showed that AC141, AC66, and vUbi interact at the nuclear periphery. These results suggest that ubiquitination of nucleocapsid proteins by vUbi functions as a signal to determine if a nucleocapsid will egress from the nucleus and form BV or remain in the nucleus to form ODV. IMPORTANCE Baculoviruses produce two types of virions called occlusion-derived virus (ODV) and budded virus (BV). ODVs are required for oral infection, whereas BV enables the systemic spread of virus to all host tissues, which is critical for killing insects. One of the important steps for BV production is the export of nucleocapsids out of the nucleus. This study investigated the molecular mechanisms that enable the selection of nucleocapsids for nuclear export instead of being retained within the nucleus, where they would become ODV. Our data show that ubiquitination, a universal cellular process, specifically tags nucleocapsids of BV, but not those found in ODV, using a virus-encoded ubiquitin (vUbi). Therefore, ubiquitination may be the molecular signal that determines if a nucleocapsid is destined to form a BV, thus ensuring lethal infection of the host. © Crown copyright 2018.

Gas Flow and Star Formation in the Centre of the Milky Way : Investigations with Smoothed Particle Hydrodynamics

NASA Astrophysics Data System (ADS)

Lucas, William Evan

2015-06-01

The centre of the Milky Way, commonly referred to as the Galactic Centre, is roughly that region within 500 pc of the central black hole, Sagittarius A*. Within the innermost parsec around the supermassive black hole Sagittarius A* are more than a hundred massive young stars whose orbits align to form one or possibly two discs. At about 100 pc is a ring containing more than ten million solar masses of molecular gas which could be the origin of some of the most massive star clusters in the Galaxy. I have performed a number of numerical simulations to help us understand how it is that these structures may have been formed. I firstly describe and test an improvement to the smoothed particle hydrodynamics code I used. This improves conservation of energy and momentum in certain situations such as in strong shocks from supernovae, which were to be included in a later chapter. The discs of massive stars around Sagittarius A* are believed to have been born there within fragmenting gaseous discs. This is problematic, as the formation of two stellar discs would require two gaseous counterparts. A method is described of forming multiple discs around a black hole from a single cloud's infall and subsequent tidal destruction. This is due to its prolate shape providing a naturally large distribution in the direction of the angular momentum vectors within the cloud. The resulting discs may then go on to form stars. Energetically, it would appear that a sequence of supernovae could potentially cause a giant molecular cloud to fall inwards towards the central black hole from an originally large orbit around the Galactic Centre. I simulate the impact on a giant molecular cloud of supernovae originating from a massive stellar cluster located a parsec away. Ultimately, the supernovae are found to have little effect. Finally, I simulate the formation of the dense ring of clouds observed in the Central Molecular Zone at a distance of about 100 pc from Sgr A*. Infalling gas is shown to be subject to such extreme tidal forces that a single cloud of gas is extended to form a long stream. The ribbon grows to the point that it self-intersects and forms a ring-like structure. Its complexity depends on the orbit of the original cloud. The position-velocity data is compared with observations, and similarities are noted.

CASPT2 study of inverse sandwich-type dinuclear Cr(I) and Fe(I) complexes of the dinitrogen molecule: significant differences in spin multiplicity and coordination structure between these two complexes.

PubMed

Nakagaki, Masayuki; Sakaki, Shigeyoshi

2014-02-20

Inverse sandwich-type complexes (ISTCs), (μ-N2)[M(AIP)]2 (AIPH = (Z)-1-amino-3-imino-prop-1-ene; M = Cr and Fe), were investigated with the CASPT2 method. In the ISTC of Cr, the ground state takes a singlet spin multiplicity. However, the singlet to nonet spin states are close in energy to each other. The thermal average of effective magnetic moments (μeff) of these spin multiplicities is close to the experimental value. The η(2)-side-on coordination structure of N2 is calculated to be more stable than the η(1)-end-on coordination one. This is because the d-orbital of Cr forms a strong dπ-π* bonding interaction with the π* orbital of N2 in molecular plane. In the ISTC of Fe, on the other hand, the ground state takes a septet spin multiplicity, which agrees well with the experimentally reported μeff value. The η(1)-end-on structure of N2 is more stable than the η(2)-side-on structure. In the η(1)-end-on structure, two doubly occupied d-orbitals of Fe can form two dπ-π* bonding interactions. The negative spin density is found on the bridging N2 ligand in the Fe complex but is not in the Cr complex. All these interesting differences between ISTCs of Cr and Fe are discussed on the basis of the electronic structure and bonding nature.

Free energy landscape and transition pathways from Watson-Crick to Hoogsteen base pairing in free duplex DNA.

PubMed

Yang, Changwon; Kim, Eunae; Pak, Youngshang

2015-09-18

Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson-Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine-thymine (A-T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Discovery of small molecules binding to the normal conformation of prion by combining virtual screening and multiple biological activity evaluation methods

NASA Astrophysics Data System (ADS)

Li, Lanlan; Wei, Wei; Jia, Wen-Juan; Zhu, Yongchang; Zhang, Yan; Chen, Jiang-Huai; Tian, Jiaqi; Liu, Huanxiang; He, Yong-Xing; Yao, Xiaojun

2017-12-01

Conformational conversion of the normal cellular prion protein, PrPC, into the misfolded isoform, PrPSc, is considered to be a central event in the development of fatal neurodegenerative diseases. Stabilization of prion protein at the normal cellular form (PrPC) with small molecules is a rational and efficient strategy for treatment of prion related diseases. However, few compounds have been identified as potent prion inhibitors by binding to the normal conformation of prion. In this work, to rational screening of inhibitors capable of stabilizing cellular form of prion protein, multiple approaches combining docking-based virtual screening, steady-state fluorescence quenching, surface plasmon resonance and thioflavin T fluorescence assay were used to discover new compounds interrupting PrPC to PrPSc conversion. Compound 3253-0207 that can bind to PrPC with micromolar affinity and inhibit prion fibrillation was identified from small molecule databases. Molecular dynamics simulation indicated that compound 3253-0207 can bind to the hotspot residues in the binding pocket composed by β1, β2 and α2, which are significant structure moieties in conversion from PrPC to PrPSc.

Quantum Chemical and Docking Insights into Bioavailability Enhancement of Curcumin by Piperine in Pepper.

PubMed

Patil, Vaishali M; Das, Sukanya; Balasubramanian, Krishnan

2016-05-26

We combine quantum chemical and molecular docking techniques to provide new insights into how piperine molecule in various forms of pepper enhances bioavailability of a number of drugs including curcumin in turmeric for which it increases its bioavailability by a 20-fold. We have carried out docking studies of quantum chemically optimized piperine structure binding to curcumin, CYP3A4 in cytochrome P450, p-Glycoprotein and UDP-glucuronosyltransferase (UGT), the enzyme responsible for glucuronosylation, which increases the solubility of curcumin. All of these studies establish that piperine binds to multiple sites on the enzymes and also intercalates with curcumin forming a hydrogen bonded complex with curcumin. The conjugated network of double bonds and the presence of multiple charge centers of piperine offer optimal binding sites for piperine to bind to enzymes such as UDP-GDH, UGT, and CYP3A4. Piperine competes for curcumin's intermolecular hydrogen bonding and its stacking propensity by hydrogen bonding with enolic proton of curcumin. This facilitates its metabolic transport, thereby increasing its bioavailability both through intercalation into curcumin layers through intermolecular hydrogen bonding, and by inhibiting enzymes that cause glucuronosylation of curcumin.

The molecular biology of prostate cancer: current understanding and clinical implications.

PubMed

Gandhi, Jason; Afridi, Adil; Vatsia, Sohrab; Joshi, Gargi; Joshi, Gunjan; Kaplan, Steven A; Smith, Noel L; Khan, Sardar Ali

2018-04-01

With continuous progress over the past few decades in understanding diagnosis, treatment, and genetics, much has been learned about the prostate cancer-diagnosed genome. A comprehensive MEDLINE® and Google scholar literature search was conducted using keyword variations relating to the genetics of prostate cancer such as chromosomal alterations, androgen receptor, castration-resistant, inheritance, polymorphisms, oncogenes, metastasis, biomarkers, and immunotherapy. Traditionally, androgen receptors (AR) have been the focus of research. Recently, identification of recurrent chromosomal alterations that lead to either multiplication of regions (gain-of-function) or deletion of regions (loss-of-function) has opened the door to greater genetic accessibility. These chromosomal aberrations lead to variation in copy number and gene expression. Some of these chromosomal alterations are inherited, while others undergo somatic mutations during disease progression. Inherited gene mutations that make one susceptible to prostate cancer have been identified with familial-linked studies. Somatic genes that progress tumorigenesis have also been identified. Research on the molecular biology of prostate cancer has characterized these genes into tumor suppressor genes or oncogenes. Additionally, genome-wide assay studies have identified many high-risk single-nucleotide polymorphisms recurrent throughout the prostate cancer-diagnosed genome. Castration-resistant prostate cancer is the most aggressive form of prostate cancer, and its research has elucidated many types of mutations associated with AR itself, including enhanced expression and amplification, point mutations, and alternative splicing. Understanding the molecular biology of prostate cancer has permitted more accurate identification using advanced biomarkers and therapy for aggressive forms using immunotherapy. An age-related disease, prostate cancer commands profound attention. With increasing life expectancy and the continuous pursuit of it, prostate cancer is a powerful obstacle best defeated using targeted therapies specifically designed for the unique molecular profile of the malignancy.

Quantum dot-based molecular imaging of cancer cell growth using a clone formation assay.

PubMed

Geng, Xia-Fei; Fang, Min; Liu, Shao-Ping; Li, Yan

2016-10-01

This aim of the present study was to investigate clonal growth behavior and analyze the proliferation characteristics of cancer cells. The MCF‑7 human breast cancer cell line, SW480 human colon cancer cell line and SGC7901 human gastric cancer cell line were selected to investigate the morphology of cell clones. Quantum dot‑based molecular targeted imaging techniques (which stained pan‑cytokeratin in the cytoplasm green and Ki67 in the cell nucleus yellow or red) were used to investigate the clone formation rate, cell morphology, discrete tendency, and Ki67 expression and distribution in clones. From the cell clone formation assay, the MCF‑7, SW480 and SGC7901 cells were observed to form clones on days 6, 8 and 12 of cell culture, respectively. These three types of cells had heterogeneous morphology, large nuclear:cytoplasmic ratios, and conspicuous pathological mitotic features. The cells at the clone periphery formed multiple pseudopodium. In certain clones, cancer cells at the borderline were separated from the central cell clusters or presented a discrete tendency. With quantum dot‑based molecular targeted imaging techniques, cells with strong Ki67 expression were predominantly shown to be distributed at the clone periphery, or concentrated on one side of the clones. In conclusion, cancer cell clones showed asymmetric growth behavior, and Ki67 was widely expressed in clones of these three cell lines, with strong expression around the clones, or aggregated at one side. Cell clone formation assay based on quantum dots molecular imaging offered a novel method to study the proliferative features of cancer cells, thus providing a further insight into tumor biology.

Morphology, Ontogenesis and Molecular Phylogeny of Neokeronopsis (Afrokeronopsis) aurea nov. subgen., nov. spec. (Ciliophora: Hypotricha), a New African Flagship Ciliate Confirms the CEUU Hypothesis

PubMed Central

FOISSNER, Wilhelm; STOECK, Thorsten

2010-01-01

Summary Neokeronopsis (Afrokeronopsis) aurea nov. subgen., nov. spec. was discovered in soil from the floodplain of a small river in the Krueger National Park, Republic of South Africa. Its morphology, ontogenesis, and 18S rDNA were studied with standard methods. Furthermore, we supplemented the data on N. (N.) spectabilis by reinvestigating the preparations deposited in the British Museum of Natural History. Neokeronopsis (Afrokeronopsis) aurea is a very conspicuous ciliate because it has an average size of 330 × 120 μm and is golden yellow due to the orange-coloured cytoplasm and citrine cortical granules. Further main characteristics include the semirigid body; the urostylid cirral pattern with a distinct corona of frontal and pseudobuccal cirri both originating from the midventral rows; multiple anterior fragmentation of dorsal kineties 1–3; multiple posterior fragmentation of kinety 3, commencing with an unique whirl of kinetofragments; three caudal cirri; an oxytrichid/cyrtohymenid oral apparatus with polystichad paroral membrane and buccal depression; a single oral primordium developing along the transverse cirral row; and an oxytrichid 18S rDNA. These peculiarities are used to establish the new oxytrichid family Neokeronopsidae, the new subgenus Afrokeronopsis, and the new species N. (A.) aurea. Further, these features confirm the CEUU hypothesis, i.e., convergent evolution of a midventral cirral pattern in urostylid and oxytrichid hypotrichs; additionally, N. (A.) aurea is the first (semi)rigid hypotrich with cortical granules and the second one with midventral rows, breaking the granule and flexibility dogmas. These and other observations show that the phylogeny of the hypotrichs is full of convergences. Thus, only a combined effort of classical and molecular phylogeneticists will provide the data needed for a natural classification. Based on the CEUU hypothesis, the molecular data, and literature evidence, we suggest that midventral oxytrichids should be ranked as distinct families; accordingly, we establish a further new family, the Uroleptidae, which forms a distinct clade within the oxytrichid molecular trees. Neokeronopsis is possibly related to Pattersoniella because it has the same special mode of forming the buccal cirri and possesses a buccal depression found also in Steinia, a close relative of Pattersoniella. The large size and conspicuous colour make N. (A.) aurea a biogeographic flagship possibly confined to Africa or Gondwana, while Neokeronopsis (N.) spectabilis (Kahl, 1932) is an Eurasian flagship. PMID:20700468

SncRNA (microRNA & snoRNA) opposite expression pattern found in multiple sclerosis relapse and remission is sex dependent

PubMed Central

Muñoz-Culla, Maider; Irizar, Haritz; Sáenz-Cuesta, Matías; Castillo-Triviño, Tamara; Osorio-Querejeta, Iñaki; Sepúlveda, Lucía; López de Munain, Adolfo; Olascoaga, Javier; Otaegui, David

2016-01-01

Multiple sclerosis (MS) is a common inflammatory and degenerative disease that causes neurological disability. It affects young adults and its prevalence is higher in women. The most common form is manifested as a series of acute episodes of neurological disability (relapses) followed by a recovery phase (remission). Recently, non-coding RNAs have emerged as new players in transcriptome regulation, and in turn, they could have a significant role in MS pathogenesis. In this context, our aim was to investigate the involvement of microRNAs and snoRNAs in the relapse-remission dynamics of MS in peripheral blood leucocytes, to shed light on the molecular and regulatory mechanisms that underlie this complex process. With this approach, we found that a subset of small non-coding RNAs (sncRNA) is altered in relapse and remission, revealing unexpected opposite changes that are sex dependent. Furthermore, we found that a relapse-related miRNA signature regulated general metabolism processes in leucocytes, and miRNA altered in remission are involved in the regulation of innate immunity. We observed that sncRNA dysregulation is different in relapse and remission leading to differences in transcriptome regulation, and that this process is sex dependent. In conclusion, relapse and remission have a different molecular background in men and women. PMID:26831009

Treating the Synapse in Major Psychiatric Disorders: The Role of Postsynaptic Density Network in Dopamine-Glutamate Interplay and Psychopharmacologic Drugs Molecular Actions

PubMed Central

Tomasetti, Carmine; Iasevoli, Felice; Buonaguro, Elisabetta Filomena; De Berardis, Domenico; Fornaro, Michele; Fiengo, Annastasia Lucia Carmela; Martinotti, Giovanni; Orsolini, Laura; Valchera, Alessandro; Di Giannantonio, Massimo; de Bartolomeis, Andrea

2017-01-01

Dopamine-glutamate interplay dysfunctions have been suggested as pathophysiological key determinants of major psychotic disorders, above all schizophrenia and mood disorders. For the most part, synaptic interactions between dopamine and glutamate signaling pathways take part in the postsynaptic density, a specialized ultrastructure localized under the membrane of glutamatergic excitatory synapses. Multiple proteins, with the role of adaptors, regulators, effectors, and scaffolds compose the postsynaptic density network. They form structural and functional crossroads where multiple signals, starting at membrane receptors, are received, elaborated, integrated, and routed to appropriate nuclear targets. Moreover, transductional pathways belonging to different receptors may be functionally interconnected through postsynaptic density molecules. Several studies have demonstrated that psychopharmacologic drugs may differentially affect the expression and function of postsynaptic genes and proteins, depending upon the peculiar receptor profile of each compound. Thus, through postsynaptic network modulation, these drugs may induce dopamine-glutamate synaptic remodeling, which is at the basis of their long-term physiologic effects. In this review, we will discuss the role of postsynaptic proteins in dopamine-glutamate signals integration, as well as the peculiar impact of different psychotropic drugs used in clinical practice on postsynaptic remodeling, thereby trying to point out the possible future molecular targets of “synapse-based” psychiatric therapeutic strategies. PMID:28085108

Toward fulfilling the promise of molecular medicine in fragile X syndrome.

PubMed

Krueger, Dilja D; Bear, Mark F

2011-01-01

Fragile X syndrome (FXS) is the most common inherited form of mental retardation and a leading known cause of autism. It is caused by loss of expression of the fragile X mental retardation protein (FMRP), an RNA-binding protein that negatively regulates protein synthesis. In neurons, multiple lines of evidence suggest that protein synthesis at synapses is triggered by activation of group 1 metabotropic glutamate receptors (Gp1 mGluRs) and that many functional consequences of activating these receptors are altered in the absence of FMRP. These observations have led to the theory that exaggerated protein synthesis downstream of Gp1 mGluRs is a core pathogenic mechanism in FXS. This excess can be corrected by reducing signaling by Gp1 mGluRs, and numerous studies have shown that inhibition of mGluR5, in particular, can ameliorate multiple mutant phenotypes in animal models of FXS. Clinical trials based on this therapeutic strategy are currently under way. FXS is therefore poised to be the first neurobehavioral disorder in which corrective treatments have been developed from the bottom up: from gene identification to pathophysiology in animals to novel therapeutics in humans. The insights gained from FXS and other autism-related single-gene disorders may also assist in identifying molecular mechanisms and potential treatment approaches for idiopathic autism.

IONIZED GAS KINEMATICS AT HIGH RESOLUTION. V. [Ne ii], MULTIPLE CLUSTERS, HIGH EFFICIENCY STAR FORMATION, AND BLUE FLOWS IN HE 2–10

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

Beck, Sara; Turner, Jean; Lacy, John

2015-11-20

We measured the 12.8 μm [Ne ii] line in the dwarf starburst galaxy He 2–10 with the high-resolution spectrometer TEXES on the NASA IRTF. The data cube has a diffraction-limited spatial resolution of ∼1″ and a total velocity resolution, including thermal broadening, of ∼5 km s{sup −1}. This makes it possible to compare the kinematics of individual star-forming clumps and molecular clouds in the three dimensions of space and velocity, and allows us to determine star formation efficiencies. The kinematics of the ionized gas confirm that the starburst contains multiple dense clusters. From the M/R of the clusters and themore » ≃30%–40% star formation efficiencies, the clusters are likely to be bound and long lived, like globulars. Non-gravitational features in the line profiles show how the ionized gas flows through the ambient molecular material, as well as a narrow velocity feature, which we identify with the interface of the H ii region and a cold dense clump. These data offer an unprecedented view of the interaction of embedded H ii regions with their environment.« less

Zwitterionic lipid assemblies: Molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field

PubMed Central

Shinoda, Wataru; DeVane, Russell; Klein, Michael L.

2010-01-01

A new coarse-grained (CG) intermolecular force field is presented for a series of zwitterionic lipids. The model is an extension of our previous work on nonionic surfactants and is designed to reproduce experimental surface/interfacial properties as well as distribution functions from all-atom molecular dynamics (MD) simulations. Using simple functional forms, the force field parameters are optimized for multiple lipid molecules, simultaneously. The resulting CG lipid bilayers have reasonable molecular areas, chain order parameters, and elastic properties. The computed surface pressure vs. area (π-A) curve for a DPPC monolayer demonstrates a significant improvement over the previous CG models. The DPPC monolayer has a longer persistence length than a PEG lipid monolayer, exhibiting a long-lived curved monolayer surface under negative tension. The bud ejected from an oversaturated DPPC monolayer has a large bicelle-like structure, which is different from the micellar bud formed from an oversaturated PEG lipid monolayer. We have successfully observed vesicle formation during CG-MD simulations, starting from an aggregate of DMPC molecules. Depending on the aggregate size, the lipid assembly spontaneously transforms into a closed vesicle or a bicelle. None of the various intermediate structures between these extremes seem to be stable. An attempt to observe fusion of two vesicles through the application of an external adhesion force was not successful. The present CG force field also supports stable multi-lamellar DMPC vesicles. PMID:20438090

Inhibition of epidermal growth factor receptor by ferulic acid and 4-vinylguaiacol in human breast cancer cells.

PubMed

Sudhagar, S; Sathya, S; Anuradha, R; Gokulapriya, G; Geetharani, Y; Lakshmi, B S

2018-02-01

To examine the potential of ferulic acid and 4-vinylguaiacol for inhibiting epidermal growth factor receptor (EGFR) in human breast cancer cells in vitro. Ferulic acid and 4-vinylguaiacol limit the EGF (epidermal growth factor)-induced breast cancer proliferation and new DNA synthesis. Western blot analysis revealed both ferulic acid and 4-vinylguaiacol exhibit sustained inhibition of EGFR activation through down-regulation of Tyr 1068 autophosphorylation. Molecular docking analysis shows ferulic acid forming hydrogen bond interaction with Lys 745 and Met 793 whereas, 4-vinylguaiacol forms two hydrogen bonds with Phe 856 and exhibits stronger hydrophobic interactions with multiple amino acid residues at the EGFR kinase domain. Ferulic acid and 4-vinylguaiacol could serve as a potential structure for the development of new small molecule therapeutics against EGFR.

CRYSTAL GROWTH. Crystallization by particle attachment in synthetic, biogenic, and geologic environments.

PubMed

De Yoreo, James J; Gilbert, Pupa U P A; Sommerdijk, Nico A J M; Penn, R Lee; Whitelam, Stephen; Joester, Derk; Zhang, Hengzhong; Rimer, Jeffrey D; Navrotsky, Alexandra; Banfield, Jillian F; Wallace, Adam F; Michel, F Marc; Meldrum, Fiona C; Cölfen, Helmut; Dove, Patricia M

2015-07-31

Field and laboratory observations show that crystals commonly form by the addition and attachment of particles that range from multi-ion complexes to fully formed nanoparticles. The particles involved in these nonclassical pathways to crystallization are diverse, in contrast to classical models that consider only the addition of monomeric chemical species. We review progress toward understanding crystal growth by particle-attachment processes and show that multiple pathways result from the interplay of free-energy landscapes and reaction dynamics. Much remains unknown about the fundamental aspects, particularly the relationships between solution structure, interfacial forces, and particle motion. Developing a predictive description that connects molecular details to ensemble behavior will require revisiting long-standing interpretations of crystal formation in synthetic systems, biominerals, and patterns of mineralization in natural environments. Copyright © 2015, American Association for the Advancement of Science.

Replica Exchange Molecular Dynamics Study of Dimerization in Prion Protein: Multiple Modes of Interaction and Stabilization.

PubMed

Chamachi, Neharika G; Chakrabarty, Suman

2016-08-04

The pathological forms of prions are known to be a result of misfolding, oligomerization, and aggregation of the cellular prion. While the mechanism of misfolding and aggregation in prions has been widely studied using both experimental and computational tools, the structural and energetic characterization of the dimer form have not garnered as much attention. On one hand dimerization can be the first step toward a nucleation-like pathway to aggregation, whereas on the other hand it may also increase the conformational stability preventing self-aggregation. In this work, we have used extensive all-atom replica exchange molecular dynamics simulations of both monomer and dimer forms of a mouse prion protein to understand the structural, dynamic, and thermodynamic stability of dimeric prion as compared to the monomeric form. We show that prion proteins can dimerize spontaneously being stabilized by hydrophobic interactions as well as intermolecular hydrogen bonding and salt bridge formation. We have computed the conformational free energy landscapes for both monomer and dimer forms to compare the thermodynamic stability and misfolding pathways. We observe large conformational heterogeneity among the various modes of interactions between the monomers and the strong intermolecular interactions may lead to as high as 20% β-content. The hydrophobic regions in helix-2, surrounding coil regions, terminal regions along with the natively present β-sheet region appear to actively participate in prion-prion intermolecular interactions. Dimerization seems to considerably suppress the inherent dynamic instability observed in monomeric prions, particularly because the regions of structural frustration constitute the dimer interface. Further, we demonstrate an interesting reversible coupling between the Q160-G131 interaction (which leads to inhibition of β-sheet extension) and the G131-V161 H-bond formation.

Three molecular forms of atrial natriuretic peptides: quantitative analysis and biological characterization.

PubMed

Nagai-Okatani, Chiaki; Kangawa, Kenji; Minamino, Naoto

2017-07-01

Atrial natriuretic peptide (ANP) is primarily produced in the heart tissue and plays a pivotal role in maintaining cardiovascular homeostasis in endocrine and autocrine/paracrine systems and has clinical applications as a biomarker and a therapeutic agent for cardiac diseases. ANP is synthesized by atrial cardiomyocytes as a preprohormone that is processed by a signal peptidase and stored in secretory granules as a prohormone. Subsequent proteolytic processing of ANP by corin during the secretion process results in a bioactive form consisting of 28 amino acid residues. Mechanical stretch of the atrial wall and multiple humoral factors directly stimulates the transcription and secretion of ANP. Secreted ANP elicits natriuretic and diuretic effects via cyclic guanosine monophosphate produced through binding to the guanylyl cyclase-A/natriuretic peptide receptor-A. Circulating ANP is subjected to rapid clearance by a natriuretic peptide receptor-C-mediated mechanism and proteolytic degradation by neutral endopeptidase. In humans, ANP is present as three endogenous molecular forms: bioactive α-ANP, a homodimer of α-ANP designated as β-ANP, and an ANP precursor designated as proANP (also referred to as γ-ANP). The proANP and especially β-ANP, as minor forms in circulation, are notably increased in patients with cardiac diseases, suggesting the utility of monitoring the pathophysiological conditions that result in abnormal proANP processing that cannot be monitored by inactive N-terminal proANP-related fragments. Emerging plate-based sandwich immunoassays for individual quantitation of the three ANP forms enables evaluation of diagnostic implications and net ANP bioactivity. This new tool may provide further understanding in the pathophysiology of cardiac diseases. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

Integrated photoacoustic, ultrasound and fluorescence platform for diagnostic medical imaging-proof of concept study with a tissue mimicking phantom.

PubMed

James, Joseph; Murukeshan, Vadakke Matham; Woh, Lye Sun

2014-07-01

The structural and molecular heterogeneities of biological tissues demand the interrogation of the samples with multiple energy sources and provide visualization capabilities at varying spatial resolution and depth scales for obtaining complementary diagnostic information. A novel multi-modal imaging approach that uses optical and acoustic energies to perform photoacoustic, ultrasound and fluorescence imaging at multiple resolution scales from the tissue surface and depth is proposed in this paper. The system comprises of two distinct forms of hardware level integration so as to have an integrated imaging system under a single instrumentation set-up. The experimental studies show that the system is capable of mapping high resolution fluorescence signatures from the surface, optical absorption and acoustic heterogeneities along the depth (>2cm) of the tissue at multi-scale resolution (<1µm to <0.5mm).

Self-assembly behaviours of peptide-drug conjugates: influence of multiple factors on aggregate morphology and potential self-assembly mechanism

NASA Astrophysics Data System (ADS)

Fan, Qin; Ji, Yujie; Wang, Jingjing; Wu, Li; Li, Weidong; Chen, Rui; Chen, Zhipeng

2018-04-01

Peptide-drug conjugates (PDCs) as self-assembly prodrugs have the unique and specific features to build one-component nanomedicines. Supramolecular structure based on PDCs could form various morphologies ranging from nanotube, nanofibre, nanobelt to hydrogel. However, the assembly process of PDCs is too complex to predict or control. Herein, we investigated the effects of extrinsic factors on assembly morphology and the possible formation of nanostructures based on PDCs. To this end, we designed a PDC consisting of hydrophobic drug (S)-ketoprofen (Ket) and valine-glutamic acid dimeric repeats peptide (L-VEVE) to study their assembly behaviour. Our results showed that the critical assembly concentration of Ket-L-VEVE was 0.32 mM in water to form various nanostructures which experienced from micelle, nanorod, nanofibre to nanoribbon. The morphology was influenced by multiple factors including molecular design, assembly time, pH and hydrogen bond inhibitor. On the basis of experimental results, we speculated the possible assembly mechanism of Ket-L-VEVE. The π-π stacking interaction between Ket molecules could serve as an anchor, and hydrogen bonded-induced β-sheets and hydrophilic/hydrophobic balance between L-VEVE peptide play structure-directing role in forming filament-like or nanoribbon morphology. This work provides a new sight to rationally design and precisely control the nanostructure of PDCs based on aromatic fragment.

Self-assembly behaviours of peptide-drug conjugates: influence of multiple factors on aggregate morphology and potential self-assembly mechanism.

PubMed

Fan, Qin; Ji, Yujie; Wang, Jingjing; Wu, Li; Li, Weidong; Chen, Rui; Chen, Zhipeng

2018-04-01

Peptide-drug conjugates (PDCs) as self-assembly prodrugs have the unique and specific features to build one-component nanomedicines. Supramolecular structure based on PDCs could form various morphologies ranging from nanotube, nanofibre, nanobelt to hydrogel. However, the assembly process of PDCs is too complex to predict or control. Herein, we investigated the effects of extrinsic factors on assembly morphology and the possible formation of nanostructures based on PDCs. To this end, we designed a PDC consisting of hydrophobic drug ( S )-ketoprofen (Ket) and valine-glutamic acid dimeric repeats peptide (L-VEVE) to study their assembly behaviour. Our results showed that the critical assembly concentration of Ket-L-VEVE was 0.32 mM in water to form various nanostructures which experienced from micelle, nanorod, nanofibre to nanoribbon. The morphology was influenced by multiple factors including molecular design, assembly time, pH and hydrogen bond inhibitor. On the basis of experimental results, we speculated the possible assembly mechanism of Ket-L-VEVE. The π-π stacking interaction between Ket molecules could serve as an anchor, and hydrogen bonded-induced β-sheets and hydrophilic/hydrophobic balance between L-VEVE peptide play structure-directing role in forming filament-like or nanoribbon morphology. This work provides a new sight to rationally design and precisely control the nanostructure of PDCs based on aromatic fragment.

Cytogenetic and molecular evidence suggest multiple origins and geographical parthenogenesis in Nothoscordum gracile (Alliaceae).

PubMed

Souza, Luiz Gustavo Rodrigues; Crosa, Orfeo; Speranza, Pablo; Guerra, Marcelo

2012-04-01

Nothoscordum gracile is an apomitic tetraploid widely distributed throughout the Americas and naturalized in many temperate regions of other continents. It has been suggested to form a species complex with sexual and apomictic N. nudicaule and N. macrostemon. Tetraploids of these species also share a structurally heterozygous chromosome complement 2n = 19 (13M + 6A). In this work, the origin of N. gracile and its relationships with its related species was investigated based on cytological and molecular data. Cytogenetic analyses were based on meiotic behaviour, CMA bands, localization of 5S and 45S rDNA sites, and genomic in situ hybridization (GISH). Nuclear ITS and plastidial trnL-trnF sequences were also obtained for most individuals. Proximal CMA bands were observed in the long arms of all acrocentrics of 2x and 4x N. macrostemon but not in diploid and some tetraploid cytotypes of N. nudicaule. Samples of N. gracile showed a variable number of CMA bands in the long arms of acrocentrics. Analysis of ITS sequences, dot-blot, GISH, and 5S and 45S rDNA sites, revealed no differentiation among the three species. The trnL-trnF cpDNA fragment showed variation with a trend to geographical structuring irrespective of morphospecies and fully congruent with karyotype variation. The 2n = 19 karyotype was probably formed by a centric fusion event occurring in N. nudicaule and later transmitted to tetraploid cytotypes of N. macrostemon. Diploids of N. nudicaule and N. macrostemon appeared as consistent recently diverged species, whereas tetraploid apomicts seem to constitute an assemblage of polyploid hybrids originating from multiple independent hybridization events between them, part of which are morphologically recognizable as N. gracile.

Molecular insight into atypical instability behavior of fixed-dose combination containing amlodipine besylate and losartan potassium.

PubMed

Handa, Tarun; Jhajra, Shalu; Bhagat, Shweta; Bharatam, P V; Chakraborti, Asit K; Singh, Saranjit

2017-03-20

Combination therapy with the use of fixed-dose combinations (FDCs) is evincing increasing interest of prescribers, manufacturers and even regulators, evidently due to the primary benefit of improved patient compliance. However, owing to potential of drug-drug interaction, FDCs require closer scrutiny with respect to their physical and chemical stability. Accordingly, the purpose of the present study was to explore stability behavior of a popular antihypertensive combination of amlodipine besylate (AML) and losartan potassium (LST). Physical mixtures of the two drugs and multiple marketed formulations were stored under accelerated conditions of temperature and humidity (40°C/75% RH) in a stability chamber and samples were withdrawn after 1 and 3 months. The physical changes were observed visibly, while chemical changes were monitored by HPLC employing a method that could separate the two drugs and all other components present. The combination revealed strong physical instability and also chemical degradation of AML in the presence of LST. Interestingly, three isomeric interaction products of AML were formed in the combination, which otherwise were reported in the literature to be generated on exposure of AML free base above its melting point. The same unusual products were even formed when multiple marketed FDCs were stored under accelerated conditions outside their storage packs. However, these were absent when AML alone was stored in the same studied conditions. Therefore, reasons for physical and chemical incompatibility and the mechanism of degradation of AML in the presence of LST were duly explored at the molecular level. The outcomes of the study are expected to help in development of stable FDCs of the two drugs. Copyright © 2016 Elsevier B.V. All rights reserved.

Effects of multiple enzyme-substrate interactions in basic units of cellular signal processing

NASA Astrophysics Data System (ADS)

Seaton, D. D.; Krishnan, J.

2012-08-01

Covalent modification cycles are a ubiquitous feature of cellular signalling networks. In these systems, the interaction of an active enzyme with the unmodified form of its substrate is essential for signalling to occur. However, this interaction is not necessarily the only enzyme-substrate interaction possible. In this paper, we analyse the behaviour of a basic model of signalling in which additional, non-essential enzyme-substrate interactions are possible. These interactions include those between the inactive form of an enzyme and its substrate, and between the active form of an enzyme and its product. We find that these additional interactions can result in increased sensitivity and biphasic responses, respectively. The dynamics of the responses are also significantly altered by the presence of additional interactions. Finally, we evaluate the consequences of these interactions in two variations of our basic model, involving double modification of substrate and scaffold-mediated signalling, respectively. We conclude that the molecular details of protein-protein interactions are important in determining the signalling properties of enzymatic signalling pathways.

Iterative reactions of transient boronic acids enable sequential C-C bond formation

NASA Astrophysics Data System (ADS)

Battilocchio, Claudio; Feist, Florian; Hafner, Andreas; Simon, Meike; Tran, Duc N.; Allwood, Daniel M.; Blakemore, David C.; Ley, Steven V.

2016-04-01

The ability to form multiple carbon-carbon bonds in a controlled sequence and thus rapidly build molecular complexity in an iterative fashion is an important goal in modern chemical synthesis. In recent times, transition-metal-catalysed coupling reactions have dominated in the development of C-C bond forming processes. A desire to reduce the reliance on precious metals and a need to obtain products with very low levels of metal impurities has brought a renewed focus on metal-free coupling processes. Here, we report the in situ preparation of reactive allylic and benzylic boronic acids, obtained by reacting flow-generated diazo compounds with boronic acids, and their application in controlled iterative C-C bond forming reactions is described. Thus far we have shown the formation of up to three C-C bonds in a sequence including the final trapping of a reactive boronic acid species with an aldehyde to generate a range of new chemical structures.

Black Widow Nebula Hiding in the Dust

NASA Technical Reports Server (NTRS)

2005-01-01

In this Spitzer image, the two opposing bubbles are being formed in opposite directions by the powerful outflows from massive groups of forming stars. The baby stars can be seen as specks of yellow where the two bubbles overlap.

When individual stars form from molecular clouds of gas and dust they produce intense radiation and very strong particle winds. Both the radiation and the stellar winds blow the dust outward from the star creating a cavity or, bubble.

In the case of the Black Widow Nebula, astronomers suspect that a large cloud of gas and dust condensed to create multiple clusters of massive star formation. The combined winds from these groups of large stars probably blew out bubbles into the direction of least resistance, forming a double bubble.

The infrared image was captured by the Galactic Legacy Infrared Mid-Plane Survey Extraordinaire (GLIMPSE) Legacy project. The Spitzer picture is a four-channel false-color composite, showing emission from wavelengths of 3.6 microns (blue), 4.5 microns (green), 5.8 microns (orange) and 8.0 microns (red).

Analysis of molecular interactions in solid dosage forms; challenge to molecular pharmaceutics.

PubMed

Yamamoto, Keiji; Limwikrant, Waree; Moribe, Kunikazu

2011-01-01

The molecular states of active pharmaceutical ingredients (APIs) in pharmaceutical dosage forms strongly affect the properties and quality of a drug. Various important fundamental physicochemical studies were reviewed from the standpoint of molecular pharmaceutics. Mechanochemical effects were evaluated in mixtures of APIs and pharmaceutical additives. Amorphization, complex formation and nanoparticle formation are observed after grinding process depending on the combination of APIs and pharmaceutical additives. Sealed-heating method and mesoporous materials have been used to investigate drug molecular interactions in dosage forms. Molecular states have been investigated using powder X-ray diffraction, thermal analysis, IR, solid state fluorometry, and NMR. © 2011 Pharmaceutical Society of Japan

Molecular landscape of acute myeloid leukemia in younger adults and its clinical relevance

PubMed Central

Ivey, Adam; Huntly, Brian J. P.

2016-01-01

Recent major advances in understanding the molecular basis of acute myeloid leukemia (AML) provide a double-edged sword. Although defining the topology and key features of the molecular landscape are fundamental to development of novel treatment approaches and provide opportunities for greater individualization of therapy, confirmation of the genetic complexity presents a huge challenge to successful translation into routine clinical practice. It is now clear that many genes are recurrently mutated in AML; moreover, individual leukemias harbor multiple mutations and are potentially composed of subclones with differing mutational composition, rendering each patient’s AML genetically unique. In order to make sense of the overwhelming mutational data and capitalize on this clinically, it is important to identify (1) critical AML-defining molecular abnormalities that distinguish biological disease entities; (2) mutations, typically arising in subclones, that may influence prognosis but are unlikely to be ideal therapeutic targets; (3) mutations associated with preleukemic clones; and (4) mutations that have been robustly shown to confer independent prognostic information or are therapeutically relevant. The reward of identifying AML-defining molecular lesions present in all leukemic populations (including subclones) has been exemplified by acute promyelocytic leukemia, where successful targeting of the underlying PML-RARα oncoprotein has eliminated the need for chemotherapy for disease cure. Despite the molecular heterogeneity and recognizing that treatment options for other forms of AML are limited, this review will consider the scope for using novel molecular information to improve diagnosis, identify subsets of patients eligible for targeted therapies, refine outcome prediction, and track treatment response. PMID:26660431

Proteins from Multiple Metabolic Pathways Associate with Starch Biosynthetic Enzymes in High Molecular Weight Complexes: A Model for Regulation of Carbon Allocation in Maize Amyloplasts1[C][W][OA

PubMed Central

Hennen-Bierwagen, Tracie A.; Lin, Qiaohui; Grimaud, Florent; Planchot, Véronique; Keeling, Peter L.; James, Martha G.; Myers, Alan M.

2009-01-01

Starch biosynthetic enzymes from maize (Zea mays) and wheat (Triticum aestivum) amyloplasts exist in cell extracts in high molecular weight complexes; however, the nature of those assemblies remains to be defined. This study tested the interdependence of the maize enzymes starch synthase IIa (SSIIa), SSIII, starch branching enzyme IIb (SBEIIb), and SBEIIa for assembly into multisubunit complexes. Mutations that eliminated any one of those proteins also prevented the others from assembling into a high molecular mass form of approximately 670 kD, so that SSIII, SSIIa, SBEIIa, and SBEIIb most likely all exist together in the same complex. SSIIa, SBEIIb, and SBEIIa, but not SSIII, were also interdependent for assembly into a complex of approximately 300 kD. SSIII, SSIIa, SBEIIa, and SBEIIb copurified through successive chromatography steps, and SBEIIa, SBEIIb, and SSIIa coimmunoprecipitated with SSIII in a phosphorylation-dependent manner. SBEIIa and SBEIIb also were retained on an affinity column bearing a specific conserved fragment of SSIII located outside of the SS catalytic domain. Additional proteins that copurified with SSIII in multiple biochemical methods included the two known isoforms of pyruvate orthophosphate dikinase (PPDK), large and small subunits of ADP-glucose pyrophosphorylase, and the sucrose synthase isoform SUS-SH1. PPDK and SUS-SH1 required SSIII, SSIIa, SBEIIa, and SBEIIb for assembly into the 670-kD complex. These complexes may function in global regulation of carbon partitioning between metabolic pathways in developing seeds. PMID:19168640

Characterization of interactions of simvastatin, pravastatin, fluvastatin, and pitavastatin with bovine serum albumin: multiple spectroscopic and molecular docking.

PubMed

Shi, Jie-Hua; Wang, Qi; Pan, Dong-Qi; Liu, Ting-Ting; Jiang, Min

2017-05-01

The binding interactions of simvastatin (SIM), pravastatin (PRA), fluvastatin (FLU), and pitavastatin (PIT) with bovine serum albumin (BSA) were investigated for determining the affinity of four statins with BSA through multiple spectroscopic and molecular docking methods. The experimental results showed that SIM, PRA, FLU, and PIT statins quenched the intrinsic fluorescence of BSA through a static quenching process and the stable stains-BSA complexes with the binding constants in the order of 10 4  M -1 at 298 K were formed through intermolecular nonbond interaction. The values of ΔH 0 , ΔS 0 and ΔG 0 in the binding process of SIM, PRA, FLU, and PIT with BSA were negative at the studied temperature range, suggesting that the binding process of four statins and BSA was spontaneous and the main interaction forces were van der Waals force and hydrogen-bonding interactions. Moreover, the binding of four statins with BSA was enthalpy-driven process due to |ΔH°|>|TΔS°| under the studied temperature range. From the results of site marker competitive experiments and molecular docking, subdomain IIIA (site II) was the primary binding site for SIM, PRA, FLU, and PIT on BSA. The results of UV-vis absorption, synchronous fluorescence, 3D fluorescence and FT-IR spectra proved that the slight change in the conformation of BSA, while the significant changes in the conformation of SIM, PRA, FLU, and PIT drug in statin-BSA complexes, indicating that the flexibility of statin molecules plays an important role in increasing the stability of statin-BSA complexes.

Second-Order Nonlinear Optical Properties of a Dithienylethene-Indolinooxazolidine Hybrid: A Joint Experimental and Theoretical Investigation.

PubMed

Bondu, Flavie; Quertinmont, Jean; Rodriguez, Vincent; Pozzo, Jean-Luc; Plaquet, Aurélie; Champagne, Benoît; Castet, Frédéric

2015-12-14

The nonlinear optical (NLO) properties of a double photochrome molecular switch are reported for the first time by considering the four trans forms of a dithienylethene-indolinooxazolidine hybrid. The four forms are characterized by means of hyper-Rayleigh scattering (HRS) experiments and quantum chemical calculations. Experimental measurements provide evidence that the pH- and light-triggered transformations between the different forms of the hybrid are accompanied by large variations of the first hyperpolarizability, which makes this compound an effective multistate NLO switch. Quantum chemical calculations conducted at the time-dependent Hartree-Fock and time-dependent DFT levels agree with the experimental data and allow a complete rationalization of the NLO responses of the different forms. The HRS signal of the forms with an open indolinooxazolidine moiety are more than one order of magnitude larger than that measured for the other forms, whereas the open/closed status of the dithienylethene subunit barely influences the dynamic NLO properties. However, extrapolation of the NLO responses to the static limit leads to univocally distinguishable intrinsic responses for three of the various forms. This hybrid system thus acts as a highly efficient multistate NLO switch for eventual exploitation in optical memory systems with multiple storage and nondestructive readout capacity. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dual Contrast - Magnetic Resonance Fingerprinting (DC-MRF): A Platform for Simultaneous Quantification of Multiple MRI Contrast Agents.

PubMed

Anderson, Christian E; Donnola, Shannon B; Jiang, Yun; Batesole, Joshua; Darrah, Rebecca; Drumm, Mitchell L; Brady-Kalnay, Susann M; Steinmetz, Nicole F; Yu, Xin; Griswold, Mark A; Flask, Chris A

2017-08-16

Injectable Magnetic Resonance Imaging (MRI) contrast agents have been widely used to provide critical assessments of disease for both clinical and basic science imaging research studies. The scope of available MRI contrast agents has expanded over the years with the emergence of molecular imaging contrast agents specifically targeted to biological markers. Unfortunately, synergistic application of more than a single molecular contrast agent has been limited by MRI's ability to only dynamically measure a single agent at a time. In this study, a new Dual Contrast - Magnetic Resonance Fingerprinting (DC - MRF) methodology is described that can detect and independently quantify the local concentration of multiple MRI contrast agents following simultaneous administration. This "multi-color" MRI methodology provides the opportunity to monitor multiple molecular species simultaneously and provides a practical, quantitative imaging framework for the eventual clinical translation of molecular imaging contrast agents.

deltaGseg: macrostate estimation via molecular dynamics simulations and multiscale time series analysis.

PubMed

Low, Diana H P; Motakis, Efthymios

2013-10-01

Binding free energy calculations obtained through molecular dynamics simulations reflect intermolecular interaction states through a series of independent snapshots. Typically, the free energies of multiple simulated series (each with slightly different starting conditions) need to be estimated. Previous approaches carry out this task by moving averages at certain decorrelation times, assuming that the system comes from a single conformation description of binding events. Here, we discuss a more general approach that uses statistical modeling, wavelets denoising and hierarchical clustering to estimate the significance of multiple statistically distinct subpopulations, reflecting potential macrostates of the system. We present the deltaGseg R package that performs macrostate estimation from multiple replicated series and allows molecular biologists/chemists to gain physical insight into the molecular details that are not easily accessible by experimental techniques. deltaGseg is a Bioconductor R package available at http://bioconductor.org/packages/release/bioc/html/deltaGseg.html.

Multiple emulsions as soft templates for the synthesis of multifunctional silicone porous particles.

PubMed

Vilanova, Neus; Kolen'ko, Yury V; Solans, Conxita; Rodríguez-Abreu, Carlos

2015-01-01

Multiple emulsion templating is a versatile strategy for the synthesis of porous particles. The present work addresses the synthesis of multifunctional poly(dimethylsiloxane) porous particles using multiple water-in-oil-in-water emulsions as soft templates with an oil phase constituted by a crosslinkable poly(dimethylsiloxane) (PDMS) oil. Herewith, the impact of the viscosity of PDMS oil (i.e., molecular weight) on the properties of both the emulsion templates and the resulting particles was evaluated. The viscosity of PDMS oil has a strong effect on the size and polydispersity of the emulsion templates as well as on the mechanical properties of the derived particles. The elastic modulus can be tuned by mixing PDMS oils of different viscosities to form bimodal crosslinked networks. Iron oxide nanoparticles can be readily incorporated into the emulsion templates to provide additional functionalities to the silicone particles, such as magnetic separation or magnetic hyperthermia. The synthesized composite magnetic particles were found to be useful as recoverable absorbent materials (e.g., for oil spills) by taking advantage of their high buoyancy and high hydrophobicity. Copyright © 2014 Elsevier Inc. All rights reserved.

The Structure and Evolution of Self-Gravitating Molecular Clouds

NASA Astrophysics Data System (ADS)

Holliman, John Herbert, II

1995-01-01

We present a theoretical formalism to evaluate the structure of molecular clouds and to determine precollapse conditions in star-forming regions. Models consist of pressure-bounded, self-gravitating spheres of a single -fluid ideal gas. We treat the case without rotation. The analysis is generalized to consider states in hydrostatic equilibrium maintained by multiple pressure components. Individual pressures vary with density as P_i(r) ~ rho^{gamma {rm p},i}(r), where gamma_{rm p},i is the polytropic index. Evolution depends additionally on whether conduction occurs on a dynamical time scale and on the adiabatic index gammai of each component, which is modified to account for the effects of any thermal coupling to the environment of the cloud. Special attention is given to properly representing the major contributors to dynamical support in molecular clouds: the pressures due to static magnetic fields, Alfven waves, and thermal motions. Straightforward adjustments to the model allow us to treat the intrinsically anisotropic support provided by the static fields. We derive structure equations, as well as perturbation equations for performing a linear stability analysis. The analysis provides insight on the nature of dynamical motions due to collapse from an equilibrium state and estimates the mass of condensed objects that form in such a process. After presenting a set of general results, we describe models of star-forming regions that include the major pressure components. We parameterize the extent of ambipolar diffusion. The analysis contributes to the physical understanding of several key results from observations of these regions. Commonly observed quantities are explicitly cross-referenced with model results. We theoretically determine density and linewidth profiles on scales ranging from that of molecular cloud cores to that of giant molecular clouds (GMCs). The model offers an explanation of the mean pressures in GMCs, which are observed to be high relative to that in the intercloud medium. We estimate what fraction of a cloud on the verge of gravitational collapse will ultimately form a condensed object, and we predict the qualitative appearance of the collapse. Finally, we simulate fragmentation--a key step in the star-forming process whereby molecular clouds or clumps within more massive clouds break up into substantially less massive cores that can in turn condense into stars. Fragmentation occurs in the context of dynamical collapse--a highly nonlinear process--so it has been difficult to reach a consensus on its specific appearance or on the influence of initial conditions. Increases in density by several orders of magnitude and the unknown, time-dependent positions of the rapidly evolving fragments present difficulties for the simulation of fragmentation. In order to increase the efficiency and effective resolution with which we can model this process, we have assembled can adaptive mesh refinement (AMR) hydrodynamics algorithm and an adaptive elliptical solver for self-gravity. The code is adaptive in the sense that it can dynamically and automatically alter the configuration of a recursively finer mesh in the computational domain. A test suite helps confirm the proper operation of the algorithm. Using initial conditions adopted in previous fragmentation studies, we simulate the collapse of a molecular cloud core. (Abstract shortened by UMI.).

High temperature methods for forming oxidizer fuel

DOEpatents

Bravo, Jose Luis [Houston, TX

2011-01-11

A method of treating a formation fluid includes providing formation fluid from a subsurface in situ heat treatment process. The formation fluid is separated to produce a liquid stream and a first gas stream. The first gas stream includes carbon dioxide, hydrogen sulfide, hydrocarbons, hydrogen or mixtures thereof. Molecular oxygen is separated from air to form a molecular oxygen stream comprising molecular oxygen. The first gas stream is combined with the molecular oxygen stream to form a combined stream comprising molecular oxygen and the first gas stream. The combined stream is provided to one or more downhole burners.

U1 small nuclear RNA variants differentially form ribonucleoprotein particles in vitro.

PubMed

Somarelli, Jason A; Mesa, Annia; Rodriguez, Carol E; Sharma, Shalini; Herrera, Rene J

2014-04-25

The U1 small nuclear (sn)RNA participates in splicing of pre-mRNAs by recognizing and binding to 5' splice sites at exon/intron boundaries. U1 snRNAs associate with 5' splice sites in the form of ribonucleoprotein particles (snRNPs) that are comprised of the U1 snRNA and 10 core components, including U1A, U1-70K, U1C and the 'Smith antigen', or Sm, heptamer. The U1 snRNA is highly conserved across a wide range of taxa; however, a number of reports have identified the presence of expressed U1-like snRNAs in multiple species, including humans. While numerous U1-like molecules have been shown to be expressed, it is unclear whether these variant snRNAs have the capacity to form snRNPs and participate in splicing. The purpose of the present study was to further characterize biochemically the ability of previously identified human U1-like variants to form snRNPs and bind to U1 snRNP proteins. A bioinformatics analysis provided support for the existence of multiple expressed variants. In vitro gel shift assays, competition assays, and immunoprecipitations (IPs) revealed that the variants formed high molecular weight assemblies to varying degrees and associated with core U1 snRNP proteins to a lesser extent than the canonical U1 snRNA. Together, these data suggest that the human U1 snRNA variants analyzed here are unable to efficiently bind U1 snRNP proteins. The current work provides additional biochemical insights into the ability of the variants to assemble into snRNPs. Copyright © 2014 Elsevier B.V. All rights reserved.

Noninvasive imaging of multiple myeloma using near infrared fluorescent molecular probe

NASA Astrophysics Data System (ADS)

Hathi, Deep; Zhou, Haiying; Bollerman-Nowlis, Alex; Shokeen, Monica; Akers, Walter J.

2016-03-01

Multiple myeloma is a plasma cell malignancy characterized by monoclonal gammopathy and osteolytic bone lesions. Multiple myeloma is most commonly diagnosed in late disease stages, presenting with pathologic fracture. Early diagnosis and monitoring of disease status may improve quality of life and long-term survival for multiple myeloma patients from what is now a devastating and fatal disease. We have developed a near-infrared targeted fluorescent molecular probe with high affinity to the α4β1 integrin receptor (VLA-4)overexpressed by a majority of multiple myeloma cells as a non-radioactive analog to PET/CT tracer currently being developed for human diagnostics. A near-infrared dye that emits about 700 nm was conjugated to a high affinity peptidomimmetic. Binding affinity and specificity for multiple myeloma cells was investigated in vitro by tissue staining and flow cytometry. After demonstration of sensitivity and specificity, preclinical optical imaging studies were performed to evaluate tumor specificity in murine subcutaneous and metastatic multiple myeloma models. The VLA-4-targeted molecular probe showed high affinity for subcutaneous MM tumor xenografts. Importantly, tumor cells specific accumulation in the bone marrow of metastatic multiple myeloma correlated with GFP signal from transfected cells. Ex vivo flow cytometry of tumor tissue and bone marrow further corroborated in vivo imaging data, demonstrating the specificity of the novel agent and potential for quantitative imaging of multiple myeloma burden in these models.

Molecular Level Coating of Metal Oxide Particles

NASA Technical Reports Server (NTRS)

McDaniel, Patricia R. (Inventor); St.Clair, Terry L. (Inventor)

2002-01-01

Polymer encapsulated metal oxide particles are prepared by combining a polyamide acid in a polar osmotic solvent with a metal alkoxide solution. The polymer was imidized and the metal oxide formed simultaneously in a refluxing organic solvent. The resulting polymer-metal oxide is an intimately mixed commingled blend, possessing, synergistic properties of both the polymer and preceramic metal oxide. The encapsulated metal oxide particles have multiple uses including, being useful in the production of skin lubricating creams, weather resistant paints, as a filler for paper. making ultraviolet light stable filled printing ink, being extruded into fibers or ribbons, and coatings for fibers used in the production of composite structural panels.

Molecular Level Coating for Metal Oxide Particles

NASA Technical Reports Server (NTRS)

McDaniel, Patricia R. (Inventor); Saint Clair, Terry L. (Inventor)

2000-01-01

Polymer encapsulated metal oxide particles are prepared by combining a polyamide acid in a polar aprotic solvent with a metal alkoxide solution. The polymer was imidized and the metal oxide formed simultaneously in a refluxing organic solvent. The resulting polymer-metal oxide is an intimately mixed commingled blend, possessing synergistic properties of both the polymer and preceramic metal oxide. The encapsulated metal oxide particles have multiple uses including, being useful in the production of skin lubricating creams, weather resistant paints, as a filler for paper, making ultraviolet light stable filled printing ink, being extruded into fibers or ribbons, and coatings for fibers used in the production of composite structural panels.

Microgravity

NASA Image and Video Library

2000-12-15

NASA is looking to biological techniques that are millions of years old to help it develop new materials and technologies for the 21st century. Sponsored by NASA, Jeffrey Brinker of the University of New Mexico is studying how multiple elements can assemble themselves into a composite material that is clear, tough, and impermeable. His research is based on the model of how an abalone builds the nacre, also called mother-of-pearl, inside its shell. Strong thin coatings, or lamellae, in Brinker's research are formed when objects are dip-coated. Evaporation drives the self-assembly of molecular aggregates (micelles) of surfactant, soluble silica, and organic monomers and their further self-organization into layered organic and inorganic assemblies.

Self-Organization in Coordination-Driven Self-Assembly

PubMed Central

Northrop, Brian H.; Zheng, Yao-Rong; Chi, Ki-Whan; Stang, Peter J.

2009-01-01

Conspectus Self-assembly allows for the preparation of highly complex molecular and supramolecular systems from relatively simple starting materials. Typically, self-assembled supramolecules are constructed by combining complementary pairs of two highly symmetric molecular components, thus limiting the chances of forming unwanted side products. Combining asymmetric molecular components or multiple complementary sets of molecules in one complex mixture can produce myriad different ordered and disordered supramolecular assemblies. Alternatively, spontaneous self-organization phenomena can promote the formation of specific product(s) out of a collection of multiple possibilities. Self-organization processes are common throughout much of nature and are especially common in biological systems. Recently, researchers have studied self-organized self-assembly in purely synthetic systems. This Account describes our investigations of self-organization in the coordination-driven self-assembly of platinum(II)-based metallosupramolecules. The modularity of the coordination-driven approach to self-assembly has allowed us to systematically study a wide variety of different factors that can control the extent of supramolecular self-organization. In particular, we have evaluated the effects of the symmetry and polarity of ambidentate donor subunits, differences in geometrical parameters (e.g. the size, angularity, and dimensionality) of Pt(II)-based acceptors and organic donors, the influence of temperature and solvent, and the effects of intermolecular steric interactions and hydrophobic interactions on self-organization. Our studies have shown that the extent of self-organization in the coordination-driven self-assembly of both 2D polygons and 3D polyhedra ranges from no organization (a statistical mixture of multiple products), to amplified organization (wherein a particular product or products are favored over others), and all the way to the absolute self-organization of discrete supramolecular assemblies. In many cases, inputs such as dipolar interactions, steric interactions, and differences in the geometric parameters of subunits—used either alone or as multiple factors simultaneously—can achieve absolute self-organization of discrete supramolecules. We have also observed instances where self-organization is not absolute and varies in its deviation from statistical results. Steric interactions are particularly useful control factors for driving such amplified self-organization because they can be subtly tuned through small structural variations. Having the ability to fully understand and control the self-organization of complex mixtures into specific synthetic supramolecules can provide a better understanding of analogous processes in biological systems. Furthermore, self-organization may allow for the facile synthesis of complex multifunctional, multicomponent systems from simply mixing a collection of much simpler, judiciously designed individual molecular components. PMID:19555073

Imaging mass spectrometry data reduction: automated feature identification and extraction.

PubMed

McDonnell, Liam A; van Remoortere, Alexandra; de Velde, Nico; van Zeijl, René J M; Deelder, André M

2010-12-01

Imaging MS now enables the parallel analysis of hundreds of biomolecules, spanning multiple molecular classes, which allows tissues to be described by their molecular content and distribution. When combined with advanced data analysis routines, tissues can be analyzed and classified based solely on their molecular content. Such molecular histology techniques have been used to distinguish regions with differential molecular signatures that could not be distinguished using established histologic tools. However, its potential to provide an independent, complementary analysis of clinical tissues has been limited by the very large file sizes and large number of discrete variables associated with imaging MS experiments. Here we demonstrate data reduction tools, based on automated feature identification and extraction, for peptide, protein, and lipid imaging MS, using multiple imaging MS technologies, that reduce data loads and the number of variables by >100×, and that highlight highly-localized features that can be missed using standard data analysis strategies. It is then demonstrated how these capabilities enable multivariate analysis on large imaging MS datasets spanning multiple tissues. Copyright © 2010 American Society for Mass Spectrometry. Published by Elsevier Inc. All rights reserved.

Phylogeography of Canada Geese (Branta canadensis) in western North America

USGS Publications Warehouse

Scribner, K.T.; Talbot, S.L.; Pearce, J.M.; Pierson, Barbara J.; Bollinger, K.S.; Derksen, D.V.

2003-01-01

Using molecular genetic markers that differ in mode of inheritance and rate of evolution, we examined levels and partitioning of genetic variation for seven nominal subspecies (11 breeding populations) of Canada Geese (Branta canadensis) in western North America. Gene trees constructed from mtDNA control region sequence data show that subspecies of Canada Geese do not have distinct mtDNA. Large- and small-bodied forms of Canada Geese were highly diverged (0. 077 average sequence divergence) and represent monophyletic groups. A majority (65%) of 20 haplotypes resolved were observed in single breeding locales. However, within both large- and small-bodied forms certain haplotypes occurred across multiple subspecies. Population trees for both nuclear (microsatellites) and mitochondrial markers were generally concordant and provide resolution of population and subspecific relationships indicating incomplete lineage sorting. All populations and subspecies were genetically diverged, but to varying degrees. Analyses of molecular variance, nested-clade and coalescence-based analyses of mtDNA suggest that both historical (past fragmentation) and contemporary forces have been important in shaping current spatial genetic distributions. Gene flow appears to be ongoing though at different rates, even among currently recognized subspecies. The efficacy of current subspecific taxonomy is discussed in light of hypothesized historical vicariance and current demographic trends of management and conservation concern.

The Molecular Architecture for the Intermediate Filaments of Hard α -Keratin Based on the Superlattice Data Obtained from a Study of Mammals Using Synchrotron Fibre Diffraction

DOE PAGES

James, Veronica

2011-01-01

High- and low-angle X-ray diffraction studies of hard α -keratin have been studied, and various models have been proposed over the last 70 years. Most of these studies have been confined to one or two forms of alpha keratin. This high- and low-angle synchrotron fibre diffraction study extends the study to cover all available data for all known forms of hard α -keratin including hairs, fingernails, hooves, horn, and quills from mammals, marsupials, and a monotreme, and it confirms that the model proposed is universally acceptable for all mammals. A complete Bragg analysis of the meridional diffraction patterns, including multiple-timemore » exposures to verify any weak reflections, verified the existence of a superlattice consisting of two infinite lattices and three finite lattices. An analysis of the equatorial patterns establishes the radii of the oligomeric levels of dimers, tetramers, and intermediate filaments (IFs) together with the centre to centre distance for the IFs, thus confirming the proposed helices within helices molecular architecture for hard α -keratin. The results verify that the structure proposed by Feughelman and James meets the criteria for a valid α -keratin structure.« less

The Molecular Architecture for the Intermediate Filaments of Hard [alpha]-Keratin Based on the Superlattice Data Obtained from a Study ofMammals Using Synchrotron Fibre Diffraction

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

James, Veronica

2014-09-24

High- and low-angle X-ray diffraction studies of hard {alpha}-keratin have been studied, and various models have been proposed over the last 70 years. Most of these studies have been confined to one or two forms of alpha keratin. This high- and low-angle synchrotron fibre diffraction study extends the study to cover all available data for all known forms of hard {alpha}-keratin including hairs, fingernails, hooves, horn, and quills from mammals, marsupials, and a monotreme, and it confirms that the model proposed is universally acceptable for all mammals. A complete Bragg analysis of the meridional diffraction patterns, including multiple-time exposures tomore » verify any weak reflections, verified the existence of a superlattice consisting of two infinite lattices and three finite lattices. An analysis of the equatorial patterns establishes the radii of the oligomeric levels of dimers, tetramers, and intermediate filaments (IFs) together with the centre to centre distance for the IFs, thus confirming the proposed helices within helices molecular architecture for hard {alpha}-keratin. The results verify that the structure proposed by Feughelman and James meets the criteria for a valid {alpha}-keratin structure.« less

The Molecular Architecture for the Intermediate Filaments of Hard α -Keratin Based on the Superlattice Data Obtained from a Study of Mammals Using Synchrotron Fibre Diffraction

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

James, Veronica

High- and low-angle X-ray diffraction studies of hard α -keratin have been studied, and various models have been proposed over the last 70 years. Most of these studies have been confined to one or two forms of alpha keratin. This high- and low-angle synchrotron fibre diffraction study extends the study to cover all available data for all known forms of hard α -keratin including hairs, fingernails, hooves, horn, and quills from mammals, marsupials, and a monotreme, and it confirms that the model proposed is universally acceptable for all mammals. A complete Bragg analysis of the meridional diffraction patterns, including multiple-timemore » exposures to verify any weak reflections, verified the existence of a superlattice consisting of two infinite lattices and three finite lattices. An analysis of the equatorial patterns establishes the radii of the oligomeric levels of dimers, tetramers, and intermediate filaments (IFs) together with the centre to centre distance for the IFs, thus confirming the proposed helices within helices molecular architecture for hard α -keratin. The results verify that the structure proposed by Feughelman and James meets the criteria for a valid α -keratin structure.« less

ALMA Observations of Starless Core Substructure in Ophiuchus

NASA Astrophysics Data System (ADS)

Kirk, H.; Dunham, M. M.; Di Francesco, J.; Johnstone, D.; Offner, S. S. R.; Sadavoy, S. I.; Tobin, J. J.; Arce, H. G.; Bourke, T. L.; Mairs, S.; Myers, P. C.; Pineda, J. E.; Schnee, S.; Shirley, Y. L.

2017-04-01

Compact substructure is expected to arise in a starless core as mass becomes concentrated in the central region likely to form a protostar. Additionally, multiple peaks may form if fragmentation occurs. We present Atacama Large Millimeter/submillimeter Array (ALMA) Cycle 2 observations of 60 starless and protostellar cores in the Ophiuchus molecular cloud. We detect eight compact substructures which are > 15\\prime\\prime from the nearest Spitzer young stellar object. Only one of these has strong evidence for being truly starless after considering ancillary data, e.g., from Herschel and X-ray telescopes. An additional extended emission structure has tentative evidence for starlessness. The number of our detections is consistent with estimates from a combination of synthetic observations of numerical simulations and analytical arguments. This result suggests that a similar ALMA study in the Chamaeleon I cloud, which detected no compact substructure in starless cores, may be due to the peculiar evolutionary state of cores in that cloud.

Experimental evidence for a chiral symmetry-breaking mechanism in aspartic acid: Lattice and sub-lattice matching

NASA Astrophysics Data System (ADS)

Teschke, Omar; Soares, David Mendez

2017-10-01

A mother crystal formed from a transient molecular structure of (D+L) aspartic acid in solution is reported. Hexagonal structures with a lattice constant of 1.04 nm were crystallized from a solution in which three aspartic acid species coexist: right- and left-handed enantiomorphs, denoted D-aspartic and L-aspartic, respectively, and transitory (D+L) aspartic acid specie. Atomic force microscopy images of the crystalline deposits reveal domains of the transitory (D+L) aspartic acid crystal forming the substrate deposit on silicon wafers, and on top of this hexagonal lattice only L-aspartic acid is observed to conform and crystallize. A preferential crystallization mechanism is then observed for (D+L) aspartic acid crystals that seed only L-aspartic deposits by the geometrical matching of their multiple hexagonal lattice structures with periodicities of 1.04 nm and 0.52 nm, respectively.

Discovery of black dye crystal structure polymorphs: Implications for dye conformational variation in dye-sensitized solar cells

DOE PAGES

Cole, Jacqueline M.; Low, Kian Sing; Gong, Yun

2015-11-24

Here, we present the discovery of a new crystal structure polymorph (1) and pseudopolymorph (2) of the Black Dye, one of the world’s leading dyes for dye-sensitized solar cells, DSSCs (10.4% device performance efficiency). This reveals that Black Dye molecules can adopt multiple low-energy conformers. This is significant since it challenges existing models of the Black Dye···TiO 2 adsorption process that renders a DSSC working electrode; these have assumed a single molecular conformation that refers to the previously reported Black Dye crystal structure (3). The marked structural differences observed between 1, 2, and 3 make the need for modeling multiplemore » conformations more acute. Additionally, the ordered form of the Black Dye (1) provides a more appropriate depiction of its anionic structure, especially regarding its anchoring group and NCS bonding descriptions. The tendency toward NCS ligand isomerism, evidenced via the disordered form 2, has consequences for electron injection and electron recombination in Black Dye embedded DSSC devices. Dyes 2 and 3 differ primarily by the absence or presence of a solvent of crystallization, respectively; solvent environment effects on the dye are thereby elucidated. This discovery of multiple Black Dye conformers from diffraction, with atomic-level definition, complements recently reported nanoscopic evidence for multiple dye conformations existing at a dye···TiO 2 interface, for a chemically similar DSSC dye; those results emanated from imaging and spectroscopy, but were unresolved at the submolecular level. Taken together, these findings lead to the general notion that multiple dye conformations should be explicitly considered when modeling dye···TiO 2 interfaces in DSSCs, at least for ruthenium-based dye complexes.« less

Evidence for feedback and stellar-dynamically regulated bursty star cluster formation: the case of the Orion Nebula Cluster

NASA Astrophysics Data System (ADS)

Kroupa, Pavel; Jeřábková, Tereza; Dinnbier, František; Beccari, Giacomo; Yan, Zhiqiang

2018-04-01

A scenario for the formation of multiple co-eval populations separated in age by about 1 Myr in very young clusters (VYCs, ages less than 10 Myr) and with masses in the range 600-20 000 M⊙ is outlined. It rests upon a converging inflow of molecular gas building up a first population of pre-main sequence stars. The associated just-formed O stars ionise the inflow and suppress star formation in the embedded cluster. However, they typically eject each other out of the embedded cluster within 106 yr, that is before the molecular cloud filament can be ionised entirely. The inflow of molecular gas can then resume forming a second population. This sequence of events can be repeated maximally over the life-time of the molecular cloud (about 10 Myr), but is not likely to be possible in VYCs with mass <300 M⊙, because such populations are not likely to contain an O star. Stellar populations heavier than about 2000 M⊙ are likely to have too many O stars for all of these to eject each other from the embedded cluster before they disperse their natal cloud. VYCs with masses in the range 600-2000 M⊙ are likely to have such multi-age populations, while VYCs with masses in the range 2000-20 000 M⊙ can also be composed solely of co-eval, mono-age populations. More massive VYCs are not likely to host sub-populations with age differences of about 1 Myr. This model is applied to the Orion Nebula Cluster (ONC), in which three well-separated pre-main sequences in the colour-magnitude diagram of the cluster have recently been discovered. The mass-inflow history is constrained using this model and the number of OB stars ejected from each population are estimated for verification using Gaia data. As a further consequence of the proposed model, the three runaway O star systems, AE Aur, μ Col and ι Ori, are considered as significant observational evidence for stellar-dynamical ejections of massive stars from the oldest population in the ONC. Evidence for stellar-dynamical ejections of massive stars in the currently forming population is also discussed.

3D-liquid chromatography as a complex mixture characterization tool for knowledge-based downstream process development.

PubMed

Hanke, Alexander T; Tsintavi, Eleni; Ramirez Vazquez, Maria Del Pilar; van der Wielen, Luuk A M; Verhaert, Peter D E M; Eppink, Michel H M; van de Sandt, Emile J A X; Ottens, Marcel

2016-09-01

Knowledge-based development of chromatographic separation processes requires efficient techniques to determine the physicochemical properties of the product and the impurities to be removed. These characterization techniques are usually divided into approaches that determine molecular properties, such as charge, hydrophobicity and size, or molecular interactions with auxiliary materials, commonly in the form of adsorption isotherms. In this study we demonstrate the application of a three-dimensional liquid chromatography approach to a clarified cell homogenate containing a therapeutic enzyme. Each separation dimension determines a molecular property relevant to the chromatographic behavior of each component. Matching of the peaks across the different separation dimensions and against a high-resolution reference chromatogram allows to assign the determined parameters to pseudo-components, allowing to determine the most promising technique for the removal of each impurity. More detailed process design using mechanistic models requires isotherm parameters. For this purpose, the second dimension consists of multiple linear gradient separations on columns in a high-throughput screening compatible format, that allow regression of isotherm parameters with an average standard error of 8%. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1283-1291, 2016. © 2016 American Institute of Chemical Engineers.

Molecular mechanisms of protein-cholesterol interactions in plasma membranes: Functional distinction between topological (tilted) and consensus (CARC/CRAC) domains.

PubMed

Fantini, Jacques; Di Scala, Coralie; Baier, Carlos J; Barrantes, Francisco J

2016-09-01

The molecular mechanisms that control the multiple possible modes of protein association with membrane cholesterol are remarkably convergent. These mechanisms, which include hydrogen bonding, CH-π stacking and dispersion forces, are used by a wide variety of extracellular proteins (e.g. microbial or amyloid) and membrane receptors. Virus fusion peptides penetrate the membrane of host cells with a tilted orientation that is compatible with a transient interaction with cholesterol; this tilted orientation is also characteristic of the process of insertion of amyloid proteins that subsequently form oligomeric pores in the plasma membrane of brain cells. Membrane receptors that are associated with cholesterol generally display linear consensus binding motifs (CARC and CRAC) characterized by a triad of basic (Lys/Arg), aromatic (Tyr/phe) and aliphatic (Leu/Val) amino acid residues. In some cases, the presence of both CARC and CRAC within the same membrane-spanning domain allows the simultaneous binding of two cholesterol molecules, one in each membrane leaflet. In this review the molecular basis and the functional significance of the different modes of protein-cholesterol interactions in plasma membranes are discussed. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Sexual polyploidization in plants – cytological mechanisms and molecular regulation

PubMed Central

De Storme, Nico; Geelen, Danny

2013-01-01

In the plant kingdom, events of whole genome duplication or polyploidization are generally believed to occur via alterations of the sexual reproduction process. Thereby, diploid pollen and eggs are formed that contain the somatic number of chromosomes rather than the gametophytic number. By participating in fertilization, these so-called 2n gametes generate polyploid offspring and therefore constitute the basis for the establishment of polyploidy in plants. In addition, diplogamete formation, through meiotic restitution, is an essential component of apomixis and also serves as an important mechanism for the restoration of F1 hybrid fertility. Characterization of the cytological mechanisms and molecular factors underlying 2n gamete formation is therefore not only relevant for basic plant biology and evolution, but may also provide valuable cues for agricultural and biotechnological applications (e.g. reverse breeding, clonal seeds). Recent data have provided novel insights into the process of 2n pollen and egg formation and have revealed multiple means to the same end. Here, we summarize the cytological mechanisms and molecular regulatory networks underlying 2n gamete formation, and outline important mitotic and meiotic processes involved in the ectopic induction of sexual polyploidization. PMID:23421646

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

Kayode, Olumide; Wang, Ruiying; Pendlebury, Devon F.

The molecular basis of enzyme catalytic power and specificity derives from dynamic interactions between enzyme and substrate during catalysis. While considerable effort has been devoted to understanding how conformational dynamics within enzymes affect catalysis, the role of conformational dynamics within protein substrates has not been addressed. Here in this paper, we examine the importance of substrate dynamics in the cleavage of Kunitz-BPTI protease inhibitors by mesotrypsin, finding that the varied conformational dynamics of structurally similar substrates can profoundly impact the rate of catalysis. A 1.4 Å crystal structure of a mesotrypsin-product complex formed with a rapidly cleaved substrate reveals amore » dramatic conformational change in the substrate upon proteolysis. Using long all-atom molecular dynamics simulations of acyl-enzyme intermediates with proteolysis rates spanning three orders of magnitude, we identify global and local dynamic features of substrates on the ns-μs timescale that correlate with enzymatic rates and explain differential susceptibility to proteolysis. By integrating multiple enhanced sampling methods for molecular dynamics, we model a viable conformational pathway between substratelike and product-like states, linking substrate dynamics on the ns-μs timescale with large collective substrate motions on the much slower timescale of catalysis. Our findings implicate substrate flexibility as a critical determinant of catalysis.« less

Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides.

PubMed

Yu, Hua; Wang, Mao-jun; Xuan, Nan-xia; Shang, Zhi-cai; Wu, Jun

2015-10-01

To provide essential information for peptide inhibitor design, the interactions of Eps15 homology domain of Eps15 homology domain-containing protein 1 (EHD1 EH domain) with three peptides containing NPF (asparagine-proline-phenylalanine), DPF (aspartic acid-proline-phenylalanine), and GPF (glycine-proline-phenylalanine) motifs were deciphered at the atomic level. The binding affinities and the underlying structure basis were investigated. Molecular dynamics (MD) simulations were performed on EHD1 EH domain/peptide complexes for 60 ns using the GROMACS package. The binding free energies were calculated and decomposed by molecular mechanics/generalized Born surface area (MM/GBSA) method using the AMBER package. The alanine scanning was performed to evaluate the binding hot spot residues using FoldX software. The different binding affinities for the three peptides were affected dominantly by van der Waals interactions. Intermolecular hydrogen bonds provide the structural basis of contributions of van der Waals interactions of the flanking residues to the binding. van der Waals interactions should be the main consideration when we design peptide inhibitors of EHD1 EH domain with high affinities. The ability to form intermolecular hydrogen bonds with protein residues can be used as the factor for choosing the flanking residues.

Molecular profiling reveals frequent gain of MYCN and anaplasia-specific loss of 4q and 14q in Wilms tumor.

PubMed

Williams, Richard D; Al-Saadi, Reem; Natrajan, Rachael; Mackay, Alan; Chagtai, Tasnim; Little, Suzanne; Hing, Sandra N; Fenwick, Kerry; Ashworth, Alan; Grundy, Paul; Anderson, James R; Dome, Jeffrey S; Perlman, Elizabeth J; Jones, Chris; Pritchard-Jones, Kathy

2011-12-01

Anaplasia in Wilms tumor, a distinctive histology characterized by abnormal mitoses, is associated with poor patient outcome. While anaplastic tumors frequently harbour TP53 mutations, little is otherwise known about their molecular biology. We have used array comparative genomic hybridization (aCGH) and cDNA microarray expression profiling to compare anaplastic and favorable histology Wilms tumors to determine their common and differentiating features. In addition to changes on 17p, consistent with TP53 deletion, recurrent anaplasia-specific genomic loss and under-expression were noted in several other regions, most strikingly 4q and 14q. Further aberrations, including gain of 1q and loss of 16q were common to both histologies. Focal gain of MYCN, initially detected by high resolution aCGH profiling in 6/61 anaplastic samples, was confirmed in a significant proportion of both tumor types by a genomic quantitative PCR survey of over 400 tumors. Overall, these results are consistent with a model where anaplasia, rather than forming an entirely distinct molecular entity, arises from the general continuum of Wilms tumor by the acquisition of additional genomic changes at multiple loci. Copyright © 2011 Wiley Periodicals, Inc.

Sexual polyploidization in plants--cytological mechanisms and molecular regulation.

PubMed

De Storme, Nico; Geelen, Danny

2013-05-01

In the plant kingdom, events of whole genome duplication or polyploidization are generally believed to occur via alterations of the sexual reproduction process. Thereby, diploid pollen and eggs are formed that contain the somatic number of chromosomes rather than the gametophytic number. By participating in fertilization, these so-called 2n gametes generate polyploid offspring and therefore constitute the basis for the establishment of polyploidy in plants. In addition, diplogamete formation, through meiotic restitution, is an essential component of apomixis and also serves as an important mechanism for the restoration of F1 hybrid fertility. Characterization of the cytological mechanisms and molecular factors underlying 2n gamete formation is therefore not only relevant for basic plant biology and evolution, but may also provide valuable cues for agricultural and biotechnological applications (e.g. reverse breeding, clonal seeds). Recent data have provided novel insights into the process of 2n pollen and egg formation and have revealed multiple means to the same end. Here, we summarize the cytological mechanisms and molecular regulatory networks underlying 2n gamete formation, and outline important mitotic and meiotic processes involved in the ectopic induction of sexual polyploidization. © 2013 Ghent University. New Phytologist © 2013 New Phytologist Trust.

Biomimetic Hierarchical Assembly of Helical Supraparticles from Chiral Nanoparticles

DOE PAGES

Zhou, Yunlong; Marson, Ryan L.; van Anders, Greg; ...

2016-02-22

Chiroptical materials found in butterflies, beetles, stomatopod crustaceans, and other creatures are attributed to biocomposites with helical motifs and multiscale hierarchical organization. These structurally sophisticated materials self-assemble from primitive nanoscale building blocks, a process that is simpler and more energy efficient than many top-down methods currently used to produce similarly sized three-dimensional materials. In this paper, we report that molecular-scale chirality of a CdTe nanoparticle surface can be translated to nanoscale helical assemblies, leading to chiroptical activity in the visible electromagnetic range. Chiral CdTe nanoparticles coated with cysteine self-organize around Te cores to produce helical supraparticles. D-/L-Form of the aminomore » acid determines the dominant left/right helicity of the supraparticles. Coarse-grained molecular dynamics simulations with a helical pair-potential confirm the assembly mechanism and the origin of its enantioselectivity, providing a framework for engineering three-dimensional chiral materials by self-assembly. Finally, the helical supraparticles further self-organize into lamellar crystals with liquid crystalline order, demonstrating the possibility of hierarchical organization and with multiple structural motifs and length scales determined by molecular-scale asymmetry of nanoparticle interactions.« less

UV-Vis spectroscopy and density functional study of solvent effect on the charge transfer band of the n → σ* complexes of 2-Methylpyridine and 2-Chloropyridine with molecular iodine

NASA Astrophysics Data System (ADS)

Gogoi, Pallavi; Mohan, Uttam; Borpuzari, Manash Protim; Boruah, Abhijit; Baruah, Surjya Kumar

2017-03-01

UV-Vis spectroscopy has established that Pyridine substitutes form n→σ* charge transfer (CT) complexes with molecular Iodine. This study is a combined approach of purely experimental UV-Vis spectroscopy, Multiple linear regression theory and Computational chemistry to analyze the effect of solvent upon the charge transfer band of 2-Methylpyridine-I2 and 2-Chloropyridine-I2 complexes. Regression analysis verifies the dependence of the CT band upon different solvent parameters. Dielectric constant and refractive index are considered among the bulk solvent parameters and Hansen, Kamlet and Catalan parameters are taken into consideration at the molecular level. Density Functional Theory results explain well the blue shift of the CT bands in polar medium as an outcome of stronger donor acceptor interaction. A logarithmic relation between the bond length of the bridging atoms of the donor and the acceptor with the dielectric constant of the medium is established. Tauc plot and TDDFT study indicates a non-vertical electronic transition in the complexes. Buckingham and Lippert Mataga equations are applied to check the Polarizability effect on the CT band.

Surface induced molecular dynamics of thin lipid films confined to submicron cavities: A 1H multiple-quantum NMR study

NASA Astrophysics Data System (ADS)

Jagadeesh, B.; Prabhakar, A.; Demco, D. E.; Buda, A.; Blümich, B.

2005-03-01

The dynamics and molecular order of thin lipid (lecithin) films confined to 200, 100 and 20 nm cylindrical pores with varying surface coverage, were investigated by 1H multiple-quantum NMR. The results show that the molecular dynamics in the surface controlled layers are less hindered compared to those in the bulk. Dynamic heterogeneity among terminal CH 3 groups is evident. Enhanced dynamic freedom is observed for films with area per molecule, ˜ 128 Å 2. The results are discussed in terms of changes in the lipid molecular organization with respect to surface concentration, its plausible motional modes and dynamic heterogeneity.

Combination therapeutics in complex diseases.

PubMed

He, Bing; Lu, Cheng; Zheng, Guang; He, Xiaojuan; Wang, Maolin; Chen, Gao; Zhang, Ge; Lu, Aiping

2016-12-01

The biological redundancies in molecular networks of complex diseases limit the efficacy of many single drug therapies. Combination therapeutics, as a common therapeutic method, involve pharmacological intervention using several drugs that interact with multiple targets in the molecular networks of diseases and may achieve better efficacy and/or less toxicity than monotherapy in practice. The development of combination therapeutics is complicated by several critical issues, including identifying multiple targets, targeting strategies and the drug combination. This review summarizes the current achievements in combination therapeutics, with a particular emphasis on the efforts to develop combination therapeutics for complex diseases. © 2016 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

From hatching to dispatching: the multiple cellular roles of the Hsp70 molecular chaperone machinery.

PubMed

Meimaridou, Eirini; Gooljar, Sakina B; Chapple, J Paul

2009-01-01

Molecular chaperones are best recognized for their roles in de novo protein folding and the cellular response to stress. However, many molecular chaperones, and in particular the Hsp70 chaperone machinery, have multiple diverse cellular functions. At the molecular level, chaperones are mediators of protein conformational change. To facilitate conformational change of client/substrate proteins, in manifold contexts, chaperone power must be closely regulated and harnessed to specific cellular locales--this is controlled by cochaperones. This review considers specialized functions of the Hsp70 chaperone machinery mediated by its cochaperones. We focus on vesicular trafficking, protein degradation and a potential role in G protein-coupled receptor processing.

Accurate Solution of Multi-Region Continuum Biomolecule Electrostatic Problems Using the Linearized Poisson-Boltzmann Equation with Curved Boundary Elements

PubMed Central

Altman, Michael D.; Bardhan, Jaydeep P.; White, Jacob K.; Tidor, Bruce

2009-01-01

We present a boundary-element method (BEM) implementation for accurately solving problems in biomolecular electrostatics using the linearized Poisson–Boltzmann equation. Motivating this implementation is the desire to create a solver capable of precisely describing the geometries and topologies prevalent in continuum models of biological molecules. This implementation is enabled by the synthesis of four technologies developed or implemented specifically for this work. First, molecular and accessible surfaces used to describe dielectric and ion-exclusion boundaries were discretized with curved boundary elements that faithfully reproduce molecular geometries. Second, we avoided explicitly forming the dense BEM matrices and instead solved the linear systems with a preconditioned iterative method (GMRES), using a matrix compression algorithm (FFTSVD) to accelerate matrix-vector multiplication. Third, robust numerical integration methods were employed to accurately evaluate singular and near-singular integrals over the curved boundary elements. Finally, we present a general boundary-integral approach capable of modeling an arbitrary number of embedded homogeneous dielectric regions with differing dielectric constants, possible salt treatment, and point charges. A comparison of the presented BEM implementation and standard finite-difference techniques demonstrates that for certain classes of electrostatic calculations, such as determining absolute electrostatic solvation and rigid-binding free energies, the improved convergence properties of the BEM approach can have a significant impact on computed energetics. We also demonstrate that the improved accuracy offered by the curved-element BEM is important when more sophisticated techniques, such as non-rigid-binding models, are used to compute the relative electrostatic effects of molecular modifications. In addition, we show that electrostatic calculations requiring multiple solves using the same molecular geometry, such as charge optimization or component analysis, can be computed to high accuracy using the presented BEM approach, in compute times comparable to traditional finite-difference methods. PMID:18567005

Isotopic constraints on the origin of meteoritic organic matter

NASA Technical Reports Server (NTRS)

Kerridge, J. F.

1991-01-01

Salient features of the isotopic distribution of H, C and N in the organic material found in carbonaceous meteorites are noted. Most organic fractions are strongly enriched in D with respect to the D/H ratio characteristic of H2 in the protosolar system; substantial variations in C-13/C-12 ratio are found among different molecular species, with oxidised species tending to be C-13 enriched relative to reduced species; some homologous series reveal systematic decrease in C-13/C-12 with increasing C number; considerable variation in N-15/N-14 ratio is observed within organic matter, though no systematic pattern to its distribution has yet emerged; no interelement correlations have been observed between isotope enrichments for the different biogenic elements. The isotopic complexity echoes the molecular diversity observed in meteoritic organic matter and suggests that the organic matter was formed by multiple processes and/or from multiple sources. However, existence of a few systematic patterns points towards survival of isotopic signatures characteristic of one or more specific processes. The widespread D enrichment implies either survival of many species of interstellar molecule or synthesis from a reservoir containing a significant interstellar component. Several of the questions raised above can be addressed by more detailed determination of the distribution of the H, C and N isotopes among different well-characterized molecular fractions. Thus, the present study is aimed at discovering whether the different amino acids have comparable D enrichments, which would imply local synthesis from a D-enriched reservoir, or very viable D enrichments, which would imply survival of some interstellar amino acids. The same approach is also being applied to polycyclic aromatic hydrocarbons. Because the analytical technique employed (secondary ion mass spectrometry) can acquire data for all three isotopic systems from each molecular fraction, any presently obscured interelement isotopic correlation should also be revealed, which will aid in identifying pertinent synthetic processes.

Micropropagation of tulip: production of virus-free stock plants.

PubMed

Podwyszyńska, Małgorzata; Sochacki, Dariusz

2010-01-01

We describe here a new tulip micropropagation method based on the cyclic shoot multiplication in presence of the thidiazuron (TDZ), which enables the production of virus-free stock plants, speeds up breeding, and provides new genotypes for the market. In our novel protocol, cyclic shoot multiplication can be performed for 2-3 years by using TDZ instead of other cytokinins, as 6-benzylaminopurine (BAP) and N(6)-(-isopentyl)adenine (2iP). It makes possible to produce 500-2,000 microbulbs from one healthy plant. There are six main stages of tulip micropropagation. Stage 0 is the selection of true-to-type and virus-free plants, confirmed by ELISA. Fragments of flower stems isolated from bulbs are used as initial explants. Shoot multiplication is based on the regeneration of adventitious shoots, which are sub-cultured every 8 weeks. In the Stage 3, the specially prepared shoots are induced by low temperature treatment to form bulbs which finally develop on a sucrose-rich medium at 20 degrees C. Bulbs are then dried for 6 weeks and rooted in vivo. The number of multiplication subcultures should be limited to 5-10 cycles in order to lower the risk of mutation. Virus indexing should be repeated 3-4 times, at the initial stage and then during shoot multiplication. Genetic stability of micropropagated shoots can be confirmed using molecular markers.

Molecular study on some antibiotic resistant genes in Salmonella spp. isolates

NASA Astrophysics Data System (ADS)

Nabi, Ari Q.

2017-09-01

Studying the genes related with antimicrobial resistance in Salmonella spp. is a crucial step toward a correct and faster treatment of infections caused by the pathogen. In this work Integron mediated antibiotic resistant gene IntI1 (Class I Integrase IntI1) and some plasmid mediated antibiotic resistance genes (Qnr) were scanned among the isolated non-Typhoid Salmonellae strains with known resistance to some important antimicrobial drugs using Sybr Green real time PCR. The aim of the study was to correlate the multiple antibiotics and antimicrobial resistance of Salmonella spp. with the presence of integrase (IntI1) gene and plasmid mediated quinolone resistant genes. Results revealed the presence of Class I Integrase gene in 76% of the isolates with confirmed multiple antibiotic resistances. Moreover, about 32% of the multiple antibiotic resistant serotypes showed a positive R-PCR for plasmid mediated qnrA gene encoding for nalidixic acid and ciprofloxacin resistance. No positive results could be revealed form R-PCRs targeting qnrB or qnrS. In light of these results we can conclude that the presence of at least one of the qnr genes and/or the presence of Integrase Class I gene were responsible for the multiple antibiotic resistance to for nalidixic acid and ciprofloxacin from the studied Salmonella spp. and further studies required to identify the genes related with multiple antibiotic resistance of the pathogen.

Some Surprising Implications of NMR-directed Simulations of Substrate Recognition and Binding by Cytochrome P450cam (CYP101A1).

PubMed

Asciutto, Eliana K; Pochapsky, Thomas C

2018-04-27

Cytochrome P450 cam (CYP101A1) catalyzes the stereospecific 5-exo hydroxylation of d-camphor by molecular oxygen. Previously, residual dipolar couplings measured for backbone amide 1 H- 15 N correlations in both substrate-free and bound forms of CYP101A1 were used as restraints in soft annealing molecular dynamic simulations in order to identify average conformations of the enzyme with and without substrate bound. Multiple substrate-dependent conformational changes remote from the enzyme active site were identified, and site-directed mutagenesis and activity assays confirmed the importance of these changes in substrate recognition. The current work makes use of perturbation response scanning (PRS) and umbrella sampling molecular dynamic of the residual dipolar coupling-derived CYP101A1 structures to probe the roles of remote structural features in enforcing the regio- and stereospecific nature of the hydroxylation reaction catalyzed by CYP101A1. An improper dihedral angle Ψ was defined and used to maintain substrate orientation in the CYP101A1 active site, and it was observed that different values of Ψ result in different PRS response maps. Umbrella sampling methods show that the free energy of the system is sensitive to Ψ, and bound substrate forms an important mechanical link in the transmission of mechanical coupling through the enzyme structure. Finally, a qualitative approach to interpreting PRS maps in terms of the roles of secondary structural features is proposed. Copyright © 2018 Elsevier Ltd. All rights reserved.

Two γ-ray bursts from dusty regions with little molecular gas.

PubMed

Hatsukade, B; Ohta, K; Endo, A; Nakanishi, K; Tamura, Y; Hashimoto, T; Kohno, K

2014-06-12

Long-duration γ-ray bursts are associated with the explosions of massive stars and are accordingly expected to reside in star-forming regions with molecular gas (the fuel for star formation). Previous searches for carbon monoxide (CO), a tracer of molecular gas, in burst host galaxies did not detect any emission. Molecules have been detected as absorption in the spectra of γ-ray burst afterglows, and the molecular gas is similar to the translucent or diffuse molecular clouds of the Milky Way. Absorption lines probe the interstellar medium only along the line of sight, so it is not clear whether the molecular gas represents the general properties of the regions where the bursts occur. Here we report spatially resolved observations of CO line emission and millimetre-wavelength continuum emission in two galaxies hosting γ-ray bursts. The bursts happened in regions rich in dust, but not particularly rich in molecular gas. The ratio of molecular gas to dust (<9-14) is significantly lower than in star-forming regions of the Milky Way and nearby star-forming galaxies, suggesting that much of the dense gas where stars form has been dissipated by other massive stars.

Pragmatic precision oncology: the secondary uses of clinical tumor molecular profiling

PubMed Central

Thota, Ramya; Staggs, David B; Johnson, Douglas B; Warner, Jeremy L

2016-01-01

Background Precision oncology increasingly utilizes molecular profiling of tumors to determine treatment decisions with targeted therapeutics. The molecular profiling data is valuable in the treatment of individual patients as well as for multiple secondary uses. Objective To automatically parse, categorize, and aggregate clinical molecular profile data generated during cancer care as well as use this data to address multiple secondary use cases. Methods A system to parse, categorize and aggregate molecular profile data was created. A naÿve Bayesian classifier categorized results according to clinical groups. The accuracy of these systems were validated against a published expertly-curated subset of molecular profiling data. Results Following one year of operation, 819 samples have been accurately parsed and categorized to generate a data repository of 10,620 genetic variants. The database has been used for operational, clinical trial, and discovery science research. Conclusions A real-time database of molecular profiling data is a pragmatic solution to several knowledge management problems in the practice and science of precision oncology. PMID:27026612

Deformation of porous molecular networks induced by the exchange of guests in single crystals.

PubMed

Saied, Okba; Maris, Thierry; Wuest, James D

2003-12-10

A strategy for making molecular networks that are porous and deformable is revealed by the behavior of compound 1, in which groups that form hydrogen bonds are attached to a nominally tetrahedral Si core. Compound 1 crystallizes from various carboxylic acids to produce a porous hydrogen-bonded diamondoid network, with up to 65% of the volume available for including guests. Changing the guests expands or contracts the network up to 30% in one direction, and single crystals can accommodate these exchange-induced deformations without loss of crystallinity. This resilience appears to result in part from the incorporation of flexible Si nodes in an otherwise robust network maintained by multiple hydrogen bonds. In certain cases, exchange is faster than deformation of the network, allowing the isolation of metastable structures with a new guest included in an otherwise unchanged network. Such processes can provide new materials that would be difficult or impossible to obtain in other ways.

Plasmid Vectors and Molecular Building Blocks for the Development of Genetic Manipulation Tools for Trypanosoma cruzi

PubMed Central

Bouvier, León A.; Cámara, María de los Milagros; Canepa, Gaspar E.; Miranda, Mariana R.; Pereira, Claudio A.

2013-01-01

The post genomic era revealed the need for developing better performing, easier to use and more sophisticated genetic manipulation tools for the study of Trypanosoma cruzi, the etiological agent of Chagas disease. In this work a series of plasmids that allow genetic manipulation of this protozoan parasite were developed. First of all we focused on useful tools to establish selection strategies for different strains and which can be employed as expression vectors. On the other hand molecular building blocks in the form of diverse selectable markers, modifiable fluorescent protein and epitope-tag coding sequences were produced. Both types of modules were harboured in backbone molecules conceived to offer multiple construction and sub-cloning strategies. These can be used to confer new properties to already available genetic manipulation tools or as starting points for whole novel designs. The performance of each plasmid and building block was determined independently. For illustration purposes, some simple direct practical applications were conducted. PMID:24205392

Tailored protein encapsulation into a DNA host using geometrically organized supramolecular interactions

PubMed Central

Sprengel, Andreas; Lill, Pascal; Stegemann, Pierre; Bravo-Rodriguez, Kenny; Schöneweiß, Elisa-C.; Merdanovic, Melisa; Gudnason, Daniel; Aznauryan, Mikayel; Gamrad, Lisa; Barcikowski, Stephan; Sanchez-Garcia, Elsa; Birkedal, Victoria; Gatsogiannis, Christos; Ehrmann, Michael; Saccà, Barbara

2017-01-01

The self-organizational properties of DNA have been used to realize synthetic hosts for protein encapsulation. However, current strategies of DNA–protein conjugation still limit true emulation of natural host–guest systems, whose formation relies on non-covalent bonds between geometrically matching interfaces. Here we report one of the largest DNA–protein complexes of semisynthetic origin held in place exclusively by spatially defined supramolecular interactions. Our approach is based on the decoration of the inner surface of a DNA origami hollow structure with multiple ligands converging to their corresponding binding sites on the protein surface with programmable symmetry and range-of-action. Our results demonstrate specific host–guest recognition in a 1:1 stoichiometry and selectivity for the guest whose size guarantees sufficient molecular diffusion preserving short intermolecular distances. DNA nanocontainers can be thus rationally designed to trap single guest molecules in their native form, mimicking natural strategies of molecular recognition and anticipating a new method of protein caging. PMID:28205515

Spectroscopic and biological activity studies of the chromium-binding peptide EEEEGDD.

PubMed

Arakawa, Hirohumi; Kandadi, Machender R; Panzhinskiy, Evgeniy; Belmore, Kenneth; Deng, Ge; Love, Ebony; Robertson, Preshus M; Commodore, Juliette J; Cassady, Carolyn J; Nair, Sreejayan; Vincent, John B

2016-06-01

While trivalent chromium has been shown at high doses to have pharmacological effects improving insulin resistance in rodent models of insulin resistance, the mechanism of action of chromium at a molecular level is not known. The chromium-binding and transport agent low-molecular-weight chromium-binding substance (LMWCr) has been proposed to be the biologically active form of chromium. LMWCr has recently been shown to be comprised of a heptapeptide of the sequence EEEEDGG. The binding of Cr(3+) to this heptapeptide has been examined. Mass spectrometric and a variety of spectroscopic studies have shown that multiple chromic ions bind to the peptide in an octahedral fashion through carboxylate groups and potentially small anionic ligands such as oxide and hydroxide. A complex of Cr and the peptide when administered intravenously to mice is able to decrease area under the curve in intravenous glucose tolerance tests. It can also restore insulin-stimulated glucose uptake in myotubes rendered insulin resistant by treating them with a high-glucose media.

Emerging insights into resistance to BRAF inhibitors in melanoma.

PubMed

Bucheit, Amanda D; Davies, Michael A

2014-02-01

Melanoma is the most aggressive form of skin cancer. The treatment of patients with advanced melanoma is rapidly evolving due to an improved understanding of molecular drivers of this disease. Somatic mutations in BRAF are the most common genetic alteration found in these tumors. Recently, two different mutant-selective small molecule inhibitors of BRAF, vemurafenib and dabrafenib, have gained regulatory approval based on positive results in randomized phase III trials. While the development of these agents represents a landmark in the treatment of melanoma, the benefit of these agents is limited by the frequent and rapid onset of resistance. The identification of several molecular mechanisms of resistance to BRAF inhibitors is rapidly leading to the clinical testing of combinatorial strategies to improve the clinical benefit of these agents. These mechanisms, and the lessons learned from the initial testing of the BRAF inhibitors, provide multiple insights that may facilitate the development of targeted therapies against other oncogenic mutations in melanoma, as well as in other cancers. Copyright © 2013 Elsevier Inc. All rights reserved.

Tailored protein encapsulation into a DNA host using geometrically organized supramolecular interactions

NASA Astrophysics Data System (ADS)

Sprengel, Andreas; Lill, Pascal; Stegemann, Pierre; Bravo-Rodriguez, Kenny; Schöneweiß, Elisa-C.; Merdanovic, Melisa; Gudnason, Daniel; Aznauryan, Mikayel; Gamrad, Lisa; Barcikowski, Stephan; Sanchez-Garcia, Elsa; Birkedal, Victoria; Gatsogiannis, Christos; Ehrmann, Michael; Saccà, Barbara

2017-02-01

The self-organizational properties of DNA have been used to realize synthetic hosts for protein encapsulation. However, current strategies of DNA-protein conjugation still limit true emulation of natural host-guest systems, whose formation relies on non-covalent bonds between geometrically matching interfaces. Here we report one of the largest DNA-protein complexes of semisynthetic origin held in place exclusively by spatially defined supramolecular interactions. Our approach is based on the decoration of the inner surface of a DNA origami hollow structure with multiple ligands converging to their corresponding binding sites on the protein surface with programmable symmetry and range-of-action. Our results demonstrate specific host-guest recognition in a 1:1 stoichiometry and selectivity for the guest whose size guarantees sufficient molecular diffusion preserving short intermolecular distances. DNA nanocontainers can be thus rationally designed to trap single guest molecules in their native form, mimicking natural strategies of molecular recognition and anticipating a new method of protein caging.

Irradiation of industrial enzyme preparations. II. Characterization of fungal pectinase by thin-layer isoelectric focusing and gel filtration

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

Delincee, H.

1978-01-01

Industrial dry fungal pectinase from A. niger was irradiated with doses (up to 1 Mrad) of /sup 60/Co-..gamma..rays effective in reducing microbial contamination. The pectinase was characterized by thin-layer isoelectric focusing and gel filtration in order to detect possible radiation-induced structural alterations. Thin-layer isoelectric focusing revealed at least fifteen multiple forms with pectin-depolymerizing activity, with isoelectric points in the range pH 4.5 to 7. Heterogeneity of pectinesterase was also demonstrated, the main band occurring around pH 4. By thin-layer gel filtration the molecular weight of the pectin-depolymerase was estimated as being about 36,000, and that of pectinesterase as about 33,000.more » Radiation-induced changes of the charge properties or molecular size of the irradiated pectinase preparation were not observed. The feasibility of using ionizing radiation for the reduction of microbial contamination of industrial enzyme preparations looks promising.« less

Efficient preconditioning of the electronic structure problem in large scale ab initio molecular dynamics simulations

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

Schiffmann, Florian; VandeVondele, Joost, E-mail: Joost.VandeVondele@mat.ethz.ch

2015-06-28

We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling’s iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filteringmore » small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.« less

An origin of arc structures deeply embedded in dense molecular cloud cores

NASA Astrophysics Data System (ADS)

Matsumoto, Tomoaki; Onishi, Toshikazu; Tokuda, Kazuki; Inutsuka, Shu-ichiro

2015-04-01

We investigated the formation of arc-like structures in the infalling envelope around protostars, motivated by the recent Atacama Large Millimeter/Submillimeter Array (ALMA) observations of the high-density molecular cloud core, MC27/L1521F. We performed self-gravitational hydrodynamical numerical simulations with an adaptive mesh refinement code. A filamentary cloud with a 0.1 pc width fragments into cloud cores because of perturbations due to weak turbulence. The cloud core undergoes gravitational collapse to form multiple protostars, and gravitational torque from the orbiting protostars produces arc structures extending up to a 1000 au scale. As well as on a spatial extent, the velocity ranges of the arc structures, ˜0.5 km s-1, are in agreement with the ALMA observations. We also found that circumstellar discs are often misaligned in triple system. The misalignment is caused by the tidal interaction between the protostars when they undergo close encounters because of a highly eccentric orbit of the tight binary pair.

Copper metallothioneins.

PubMed

Calvo, Jenifer; Jung, Hunmin; Meloni, Gabriele

2017-04-01

Metallothioneins (MTs) are a class of low molecular weight and cysteine-rich metal binding proteins present in all the branches of the tree of life. MTs efficiently bind with high affinity several essential and toxic divalent and monovalent transition metals by forming characteristic polynuclear metal-thiolate clusters within their structure. MTs fulfil multiple biological functions related to their metal binding properties, with essential roles in both Zn(II) and Cu(I) homeostasis as well as metal detoxification. Depending on the organism considered, the primary sequence, and the specific physiological and metabolic status, Cu(I)-bound MT isoforms have been isolated, and their chemistry and biology characterized. Besides the recognized role in the biochemistry of divalent metals, it is becoming evident that unique biological functions in selectively controlling copper levels, its reactivity as well as copper-mediated biochemical processes have evolved in some members of the MT superfamily. Selected examples are reviewed to highlight the peculiar chemical properties and biological functions of copper MTs. © 2016 IUBMB Life, 69(4):236-245, 2017. © 2017 International Union of Biochemistry and Molecular Biology.

Stepwise Nucleation of Aniline: Emergence of Spectroscopic Fingerprints of the Liquid Phase.

PubMed

Leon, Iker; Usabiaga, Imanol; Arnaiz, Pedro Felipe; Lesarri, Alberto; Fernández, Jose Andres

2018-06-11

We deal here with the controlled nucleation of aniline from the isolated molecule until formation of a moderately large aggregate: aniline nonamer. The structure of the cluster at each step of the nucleation was unravelled combining mass-resolved IR spectroscopy and computational chemistry, demonstrating that aggregation is primarily guided by formation of extensive N-H···N hydrogen bond networks that give the aggregates a sort of branched backbone, in clear competition with multiple N-H/C-H···pi and pi···pi interactions. The result is the co-existence of close nucleation paths connecting relational aggregates. The delicate balance of molecular forces makes the aniline clusters a challenge for molecular orbital calculations and an ideal system to refine the present nucleation models. Noticeably, spectroscopic signatures characteristic of the condensed phase are apparent in the nanometer-size aggregates formed in this work. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crystal structure of Bombyx mori arylphorins reveals a 3:3 heterohexamer with multiple papain cleavage sites

PubMed Central

Hou, Yong; Li, Jianwei; Li, Yi; Dong, Zhaoming; Xia, Qingyou; Yuan, Y Adam

2014-01-01

In holometabolous insects, the accumulation and utilization of storage proteins (SPs), including arylphorins and methionine-rich proteins, are critical for the insect metamorphosis. SPs function as amino acids reserves, which are synthesized in fat body, secreted into the larval hemolymph and taken up by fat body shortly before pupation. However, the detailed molecular mechanisms of digestion and utilization of SPs during development are largely unknown. Here, we report the crystal structure of Bombyx mori arylphorins at 2.8 Å, which displays a heterohexameric structural arrangement formed by trimerization of dimers comprising two structural similar arylphorins. Our limited proteolysis assay and microarray data strongly suggest that papain-like proteases are the major players for B. mori arylphorins digestion in vitro and in vivo. Consistent with the biochemical data, dozens of papain cleavage sites are mapped on the surface of the heterohexameric structure of B. mori arylphorins. Hence, our results provide the insightful information to understand the metamorphosis of holometabolous insects at molecular level. PMID:24639361

Comparative systems biology between human and animal models based on next-generation sequencing methods.

PubMed

Zhao, Yu-Qi; Li, Gong-Hua; Huang, Jing-Fei

2013-04-01

Animal models provide myriad benefits to both experimental and clinical research. Unfortunately, in many situations, they fall short of expected results or provide contradictory results. In part, this can be the result of traditional molecular biological approaches that are relatively inefficient in elucidating underlying molecular mechanism. To improve the efficacy of animal models, a technological breakthrough is required. The growing availability and application of the high-throughput methods make systematic comparisons between human and animal models easier to perform. In the present study, we introduce the concept of the comparative systems biology, which we define as "comparisons of biological systems in different states or species used to achieve an integrated understanding of life forms with all their characteristic complexity of interactions at multiple levels". Furthermore, we discuss the applications of RNA-seq and ChIP-seq technologies to comparative systems biology between human and animal models and assess the potential applications for this approach in the future studies.

Molecular dynamics based enhanced sampling of collective variables with very large time steps.

PubMed

Chen, Pei-Yang; Tuckerman, Mark E

2018-01-14

Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

Molecular dynamics based enhanced sampling of collective variables with very large time steps

NASA Astrophysics Data System (ADS)

Chen, Pei-Yang; Tuckerman, Mark E.

2018-01-01

Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

Integrated plasticity at inhibitory and excitatory synapses in the cerebellar circuit.

PubMed

Mapelli, Lisa; Pagani, Martina; Garrido, Jesus A; D'Angelo, Egidio

2015-01-01

The way long-term potentiation (LTP) and depression (LTD) are integrated within the different synapses of brain neuronal circuits is poorly understood. In order to progress beyond the identification of specific molecular mechanisms, a system in which multiple forms of plasticity can be correlated with large-scale neural processing is required. In this paper we take as an example the cerebellar network, in which extensive investigations have revealed LTP and LTD at several excitatory and inhibitory synapses. Cerebellar LTP and LTD occur in all three main cerebellar subcircuits (granular layer, molecular layer, deep cerebellar nuclei) and correspondingly regulate the function of their three main neurons: granule cells (GrCs), Purkinje cells (PCs) and deep cerebellar nuclear (DCN) cells. All these neurons, in addition to be excited, are reached by feed-forward and feed-back inhibitory connections, in which LTP and LTD may either operate synergistically or homeostatically in order to control information flow through the circuit. Although the investigation of individual synaptic plasticities in vitro is essential to prove their existence and mechanisms, it is insufficient to generate a coherent view of their impact on network functioning in vivo. Recent computational models and cell-specific genetic mutations in mice are shedding light on how plasticity at multiple excitatory and inhibitory synapses might regulate neuronal activities in the cerebellar circuit and contribute to learning and memory and behavioral control.

Toward Fulfilling the Promise of Molecular Medicine in Fragile X Syndrome

PubMed Central

Krueger, Dilja D.; Bear, Mark F.

2011-01-01

Fragile X syndrome (FXS) is the most common inherited form of mental retardation and a leading known cause of autism. It is caused by loss of expression of the fragile X mental retardation protein (FMRP), an RNA-binding protein that negatively regulates protein synthesis. In neurons, multiple lines of evidence suggest that protein synthesis at synapses is triggered by activation of group 1 metabotropic glutamate receptors (Gp1 mGluRs) and that many functional consequences of activating these receptors are altered in the absence of FMRP. These observations have led to the theory that exaggerated protein synthesis downstream of Gp1 mGluRs is a core pathogenic mechanism in FXS. This excess can be corrected by reducing signaling by Gp1 mGluRs, and numerous studies have shown that inhibition of mGluR5, in particular, can ameliorate multiple mutant phenotypes in animal models of FXS. Clinical trials based on this therapeutic strategy are currently under way. FXS is therefore poised to be the first neurobehavioral disorder in which corrective treatments have been developed from the bottom up: from gene identification to pathophysiology in animals to novel therapeutics in humans. The insights gained from FXS and other autism-related single-gene disorders may also assist in identifying molecular mechanisms and potential treatment approaches for idiopathic autism. PMID:21090964

Natural Compounds As Modulators of Non-apoptotic Cell Death in Cancer Cells

PubMed Central

Guamán-Ortiz, Luis Miguel; Orellana, Maria Isabel Ramirez; Ratovitski, Edward A.

2017-01-01

Cell death is an innate capability of cells to be removed from microenvironment, if and when they are damaged by multiple stresses. Cell death is often regulated by multiple molecular pathways and mechanism, including apoptosis, autophagy, and necroptosis. The molecular network underlying these processes is often intertwined and one pathway can dynamically shift to another one acquiring certain protein components, in particular upon treatment with various drugs. The strategy to treat human cancer ultimately relies on the ability of anticancer therapeutics to induce tumor-specific cell death, while leaving normal adjacent cells undamaged. However, tumor cells often develop the resistance to the drug-induced cell death, thus representing a great challenge for the anticancer approaches. Numerous compounds originated from the natural sources and biopharmaceutical industries are applied today in clinics showing advantageous results. However, some exhibit serious toxic side effects. Thus, novel effective therapeutic approaches in treating cancers are continued to be developed. Natural compounds with anticancer activity have gained a great interest among researchers and clinicians alike since they have shown more favorable safety and efficacy then the synthetic marketed drugs. Numerous studies in vitro and in vivo have found that several natural compounds display promising anticancer potentials. This review underlines certain information regarding the role of natural compounds from plants, microorganisms and sea life forms, which are able to induce non-apoptotic cell death in tumor cells, namely autophagy and necroptosis. PMID:28367073

Remyelination Therapy in Multiple Sclerosis.

PubMed

Harlow, Danielle E; Honce, Justin M; Miravalle, Augusto A

2015-01-01

Multiple sclerosis (MS) is an immune-mediated disorder of the central nervous system that results in destruction of the myelin sheath that surrounds axons and eventual neurodegeneration. Current treatments approved for the treatment of relapsing forms of MS target the aberrant immune response and successfully reduce the severity of attacks and frequency of relapses. Therapies are still needed that can repair damage particularly for the treatment of progressive forms of MS for which current therapies are relatively ineffective. Remyelination can restore neuronal function and prevent further neuronal loss and clinical disability. Recent advancements in our understanding of the molecular and cellular mechanisms regulating myelination, as well as the development of high-throughput screens to identify agents that enhance myelination, have lead to the identification of many potential remyelination therapies currently in preclinical and early clinical development. One problem that has plagued the development of treatments to promote remyelination is the difficulty in assessing remyelination in patients with current imaging techniques. Powerful new imaging technologies are making it easier to discern remyelination in patients, which is critical for the assessment of these new therapeutic strategies during clinical trials. This review will summarize what is currently known about remyelination failure in MS, strategies to overcome this failure, new therapeutic treatments in the pipeline for promoting remyelination in MS patients, and new imaging technologies for measuring remyelination in patients.

Caspase-1 inhibition prevents glial inflammasome activation and pyroptosis in models of multiple sclerosis.

PubMed

McKenzie, Brienne A; Mamik, Manmeet K; Saito, Leina B; Boghozian, Roobina; Monaco, Maria Chiara; Major, Eugene O; Lu, Jian-Qiang; Branton, William G; Power, Christopher

2018-06-12

Multiple sclerosis (MS) is a progressive inflammatory demyelinating disease of the CNS of unknown cause that remains incurable. Inflammasome-associated caspases mediate the maturation and release of the proinflammatory cytokines IL-1β and IL-18 and activate the pore-forming protein gasdermin D (GSDMD). Inflammatory programmed cell death, pyroptosis, was recently shown to be mediated by GSDMD. Here, we report molecular evidence for GSDMD-mediated inflammasome activation and pyroptosis in both myeloid cells (macrophages/microglia) and, unexpectedly, in myelin-forming oligodendrocytes (ODCs) in the CNS of patients with MS and in the MS animal model, experimental autoimmune encephalomyelitis (EAE). We observed inflammasome activation and pyroptosis in human microglia and ODCs in vitro after exposure to inflammatory stimuli and demonstrate caspase-1 inhibition by the small-molecule inhibitor VX-765 in both cell types. GSDMD inhibition by siRNA transduction suppressed pyroptosis in human microglia. VX-765 treatment of EAE animals reduced the expression of inflammasome- and pyroptosis-associated proteins in the CNS, prevented axonal injury, and improved neurobehavioral performance. Thus, GSDMD-mediated pyroptosis in select glia cells is a previously unrecognized mechanism of inflammatory demyelination and represents a unique therapeutic opportunity for mitigating the disease process in MS and other CNS inflammatory diseases.

On the Split Personality of Penultimate Proline

PubMed Central

Glover, Matthew S.; Shi, Liuqing; Fuller, Daniel R.; Arnold, Randy J.; Radivojac, Predrag; Clemmer, David E.

2014-01-01

The influence of the position of the amino acid proline in polypeptide sequences is examined by a combination of ion mobility spectrometry-mass spectrometry (IMS-MS), amino acid substitutions, and molecular modeling. The results suggest that when proline exists as the second residue from the N-terminus (i.e., penultimate proline), two families of conformers are formed. We demonstrate the existence of these families by a study of a series of truncated and mutated peptides derived from the 11-residue peptide Ser1-Pro2-Glu3-Leu4-Pro5-Ser6-Pro7-Gln8-Ala9-Glu10-Lys11. We find that every peptide from this sequence with a penultimate proline residue has multiple conformations. Substitution of Ala for Pro residues indicates that multiple conformers arise from the cis- trans isomerization of Xaa1–Pro2 peptide bonds as Xaa–Ala peptide bonds are unlikely to adopt the cis isomer, and examination of spectra from a library of 58 peptides indicates that ~80% of sequences show this effect. A simple mechanism suggesting that the barrier between the cis-and trans-proline forms is lowered because of low steric impedance is proposed. This observation may have interesting biological implications as well, and we note that a number of biologically active peptides have penultimate proline residues. PMID:25503299

Senescence and programmed cell death in plants: polyamine action mediated by transglutaminase

PubMed Central

Del Duca, Stefano; Serafini-Fracassini, Donatella; Cai, Giampiero

2014-01-01

Research on polyamines (PAs) in plants laps a long way of about 50 years and many roles have been discovered for these aliphatic cations. PAs regulate cell division, differentiation, organogenesis, reproduction, dormancy-break and senescence, homeostatic adjustments in response to external stimuli and stresses. Nevertheless, the molecular mechanisms of their multiple activities are still matter of research. PAs are present in free and bound forms and interact with several important cell molecules; some of these interactions may occur by covalent linkages catalyzed by transglutaminase (TGase), giving rise to “cationization” or cross-links among specific proteins. Senescence and programmed cell death (PCD) can be delayed by PAs; in order to re-interpret some of these effects and to obtain new insights into their molecular mechanisms, their conjugation has been revised here. The TGase-mediated interactions between proteins and PAs are the main target of this review. After an introduction on the characteristics of this enzyme, on its catalysis and role in PCD in animals, the plant senescence and PCD models in which TGase has been studied, are presented: the corolla of naturally senescing or excised flowers, the leaves senescing, either excised or not, the pollen during self-incompatible pollination, the hypersensitive response and the tuber storage parenchyma during dormancy release. In all the models examined, TGase appears to be involved by a similar molecular mechanism as described during apoptosis in animal cells, even though several substrates are different. Its effect is probably related to the type of PCD, but mostly to the substrate to be modified in order to achieve the specific PCD program. As a cross-linker of PAs and proteins, TGase is an important factor involved in multiple, sometimes controversial, roles of PAs during senescence and PCD. PMID:24778637

Mergeomics: a web server for identifying pathological pathways, networks, and key regulators via multidimensional data integration.

PubMed

Arneson, Douglas; Bhattacharya, Anindya; Shu, Le; Mäkinen, Ville-Petteri; Yang, Xia

2016-09-09

Human diseases are commonly the result of multidimensional changes at molecular, cellular, and systemic levels. Recent advances in genomic technologies have enabled an outpour of omics datasets that capture these changes. However, separate analyses of these various data only provide fragmented understanding and do not capture the holistic view of disease mechanisms. To meet the urgent needs for tools that effectively integrate multiple types of omics data to derive biological insights, we have developed Mergeomics, a computational pipeline that integrates multidimensional disease association data with functional genomics and molecular networks to retrieve biological pathways, gene networks, and central regulators critical for disease development. To make the Mergeomics pipeline available to a wider research community, we have implemented an online, user-friendly web server ( http://mergeomics. idre.ucla.edu/ ). The web server features a modular implementation of the Mergeomics pipeline with detailed tutorials. Additionally, it provides curated genomic resources including tissue-specific expression quantitative trait loci, ENCODE functional annotations, biological pathways, and molecular networks, and offers interactive visualization of analytical results. Multiple computational tools including Marker Dependency Filtering (MDF), Marker Set Enrichment Analysis (MSEA), Meta-MSEA, and Weighted Key Driver Analysis (wKDA) can be used separately or in flexible combinations. User-defined summary-level genomic association datasets (e.g., genetic, transcriptomic, epigenomic) related to a particular disease or phenotype can be uploaded and computed real-time to yield biologically interpretable results, which can be viewed online and downloaded for later use. Our Mergeomics web server offers researchers flexible and user-friendly tools to facilitate integration of multidimensional data into holistic views of disease mechanisms in the form of tissue-specific key regulators, biological pathways, and gene networks.

Molecular Diversity of HIV-1 among People Who Inject Drugs in Kuala Lumpur, Malaysia: Massive Expansion of Circulating Recombinant Form (CRF) 33_01B and Emergence of Multiple Unique Recombinant Clusters

PubMed Central

Chow, Wei Zhen; Ng, Kim Tien; Yong, Yean Kong; Azmel, Azureen; Takebe, Yutaka; Al-Darraji, Haider Abdulrazzaq Abed; Kamarulzaman, Adeeba; Tee, Kok Keng

2013-01-01

Since the discovery of HIV-1 circulating recombinant form (CRF) 33_01B in Malaysia in the early 2000 s, continuous genetic diversification and active recombination involving CRF33_01B and other circulating genotypes in the region including CRF01_AE and subtype B′ of Thai origin, have led to the emergence of novel CRFs and unique recombinant forms. The history and magnitude of CRF33_01B transmission among various risk groups including people who inject drugs (PWID) however have not been investigated despite the high epidemiological impact of CRF33_01B in the region. We update the most recent molecular epidemiology of HIV-1 among PWIDs recruited in Malaysia between 2010 and 2011 by population sequencing and phylogenetic analysis of 128 gag-pol sequences. HIV-1 CRF33_01B was circulating among 71% of PWIDs whilst a lower prevalence of other previously dominant HIV-1 genotypes [subtype B′ (11%) and CRF01_AE (5%)] and CRF01_AE/B′ unique recombinants (13%) were detected, indicating a significant shift in genotype replacement in this population. Three clusters of CRF01_AE/B′ recombinants displaying divergent yet phylogenetically-related mosaic genomes to CRF33_01B were identified and characterized, suggestive of an abrupt emergence of multiple novel CRF clades. Using rigorous maximum likelihood approach and the Bayesian Markov chain Monte Carlo (MCMC) sampling of CRF33_01Bpol sequences to elucidate the past population dynamics, we found that the founder lineages of CRF33_01B were likely to have first emerged among PWIDs in the early 1990 s before spreading exponentially to various high and low-risk populations (including children who acquired infections from their mothers) and later on became endemic around the early 2000 s. Taken together, our findings provide notable genetic evidence indicating the widespread expansion of CRF33_01B among PWIDs and into the general population. The emergence of numerous previously unknown recombinant clades highlights the escalating genetic complexity of HIV-1 in the Southeast Asian region. PMID:23667490

Molecular diversity of HIV-1 among people who inject drugs in Kuala Lumpur, Malaysia: massive expansion of circulating recombinant form (CRF) 33_01B and emergence of multiple unique recombinant clusters.

PubMed

Chow, Wei Zhen; Ong, Lai Yee; Razak, Siti Humaira; Lee, Yeat Mei; Ng, Kim Tien; Yong, Yean Kong; Azmel, Azureen; Takebe, Yutaka; Al-Darraji, Haider Abdulrazzaq Abed; Kamarulzaman, Adeeba; Tee, Kok Keng

2013-01-01

Since the discovery of HIV-1 circulating recombinant form (CRF) 33_01B in Malaysia in the early 2000 s, continuous genetic diversification and active recombination involving CRF33_01B and other circulating genotypes in the region including CRF01_AE and subtype B' of Thai origin, have led to the emergence of novel CRFs and unique recombinant forms. The history and magnitude of CRF33_01B transmission among various risk groups including people who inject drugs (PWID) however have not been investigated despite the high epidemiological impact of CRF33_01B in the region. We update the most recent molecular epidemiology of HIV-1 among PWIDs recruited in Malaysia between 2010 and 2011 by population sequencing and phylogenetic analysis of 128 gag-pol sequences. HIV-1 CRF33_01B was circulating among 71% of PWIDs whilst a lower prevalence of other previously dominant HIV-1 genotypes [subtype B' (11%) and CRF01_AE (5%)] and CRF01_AE/B' unique recombinants (13%) were detected, indicating a significant shift in genotype replacement in this population. Three clusters of CRF01_AE/B' recombinants displaying divergent yet phylogenetically-related mosaic genomes to CRF33_01B were identified and characterized, suggestive of an abrupt emergence of multiple novel CRF clades. Using rigorous maximum likelihood approach and the Bayesian Markov chain Monte Carlo (MCMC) sampling of CRF33_01Bpol sequences to elucidate the past population dynamics, we found that the founder lineages of CRF33_01B were likely to have first emerged among PWIDs in the early 1990 s before spreading exponentially to various high and low-risk populations (including children who acquired infections from their mothers) and later on became endemic around the early 2000 s. Taken together, our findings provide notable genetic evidence indicating the widespread expansion of CRF33_01B among PWIDs and into the general population. The emergence of numerous previously unknown recombinant clades highlights the escalating genetic complexity of HIV-1 in the Southeast Asian region.

[Amplicon density-weighted algorithms for analyzing dissimilarity and dynamic alterations of RAPD polymorphisms of Cordyceps sinensis].

PubMed

Yao, Yi-sang; Gao, Ling; Li, Yu-ling; Ma, Shao-li; Wu, Zi-mei; Tan, Ning-zhi; Wu, Jian-yong; Ni, Lu-qun; Zhu, Jia-shi

2014-08-18

To examine the dynamic maturational alterations of random amplified polymorphic DNA (RAPD) molecular marker polymorphism resulted from differential expressions of multiple fungi in the caterpillar body, stroma and ascocarp portion of Cordyceps sinensis (Cs). Used the fuzzy, integral RAPD molecular marker polymorphism method with 20 random primers; used density-weighted cluster algorithms and ZUNIX similarity equations; compared RAPD polymorphisms of the caterpillar body, stroma and ascocarp of Cs during maturation; and compared RAPD polymorphisms of Cs and Hirsutella sinensis (Hs). Density-unweighted algorithms neglected the differences in density of the DNA amplicons. Use of the density-weighted ZUNIX similarity equations and the clustering method integrated components of the amplicon density differences in similarity computations and clustering construction and prevented from the loss of the information of fungal genomes. An overall similarity 0.42 (< the overall dissimilarity 0.58) was observed for all compartments of Cs at different maturation stages. The similarities for the stromata or caterpillar bodies of Cs at 3 maturational stages were 0.57 or 0.50, respectively. During Cs maturation, there were dynamic Low→High→Low alterations of the RAPD polymorphisms between stromata and caterpillar bodies dissected from the same pieces of Cs. The polymorphic similarity was the highest (0.87) between the ascocarp and mature stroma, forming a clustering clade, while the premature stroma and caterpillar body formed another clade. These 2 clades merged into one cluster. Another clade containing the maturing stroma and caterpillar body merged with mature caterpillar body, forming another cluster. The RAPD polymorphic similarities between Hs and Cs samples were 0.55-0.69. Hs were separated from Cs clusters by the out-group control Paecilomyces militaris. The wealthy RAPD polymorphisms change dynamically in the Cs compartments with maturation. The different RAPD polymorphism for Hs from those for Cs supports the hypothesis of integrated micro-ecosystem Cs with multiple fungi, but does not support the "single fungal species" hypothesis for Cs and the anamorph-teleomorph connection between Hs and Cs.

The proteolytic system of pineapple stems revisited: Purification and characterization of multiple catalytically active forms.

PubMed

Matagne, André; Bolle, Laetitia; El Mahyaoui, Rachida; Baeyens-Volant, Danielle; Azarkan, Mohamed

2017-06-01

Crude pineapple proteases extract (aka stem bromelain; EC 3.4.22.4) is an important proteolytic mixture that contains enzymes belonging to the cysteine proteases of the papain family. Numerous studies have been reported aiming at the fractionation and characterization of the many molecular species present in the extract, but more efforts are still required to obtain sufficient quantities of the various purified protease forms for detailed physicochemical, enzymatic and structural characterization. In this work, we describe an efficient strategy towards the purification of at least eight enzymatic forms. Thus, following rapid fractionation on a SP-Sepharose FF column, two sub-populations with proteolytic activity were obtained: the unbound (termed acidic) and bound (termed basic) bromelain fractions. Following reversible modification with monomethoxypolyethylene glycol (mPEG), both fractions were further separated on Q-Sepharose FF and SP-Sepharose FF, respectively. This procedure yielded highly purified molecular species, all titrating ca. 1 mol of thiol group per mole of enzyme, with distinct biochemical properties. N-terminal sequencing allowed identifying at least eight forms with proteolytic activity. The basic fraction contained previously identified species, i.e. basic bromelain forms 1 and 2, ananain forms 1 and 2, and comosain (MEROPS identifier: C01.027). Furthermore, a new proteolytic species, showing similarities with basic bomelain forms 1 and 2, was discovered and termed bromelain form 3. The two remaining species were found in the acidic bromelain fraction and were arbitrarily named acidic bromelain forms 1 and 2. Both, acidic bromelain forms 1, 2 and basic bromelain forms 1, 2 and 3 are glycosylated, while ananain forms 1 and 2, and comosain are not. The eight protease forms display different amidase activities against the various substrates tested, namely small synthetic chromogenic compounds (DL-BAPNA and Boc-Ala-Ala-Gly-pNA), fluorogenic compounds (like Boc-Gln-Ala-Arg-AMC, Z-Arg-Arg-AMC and Z-Phe-Arg-AMC), and proteins (azocasein and azoalbumin), suggesting a specific organization of their catalytic residues. All forms are completely inhibited by specific cysteine and cysteine/serine protease inhibitors, but not by specific serine and aspartic protease inhibitors, with the sole exception of pepstatin A that significantly affects acidic bromelain forms 1 and 2. For all eight protease forms, inhibition is also observed with 1,10-phenanthrolin, a metalloprotease inhibitor. Metal ions (i.e. Mn 2+ , Mg 2+ and Ca 2+ ) showed various effects depending on the protease under consideration, but all of them are totally inhibited in the presence of Zn 2+ . Mass spectrometry analyses revealed that all forms have a molecular mass of ca. 24 kDa, which is characteristic of enzymes belonging to the papain-like proteases family. Far-UV CD spectra analysis further supported this analysis. Interestingly, secondary structure calculation proves to be highly reproducible for all cysteine proteases of the papain family tested so far (this work; see also Azarkan et al., 2011; Baeyens-Volant et al., 2015) and thus can be used as a test for rapid identification of the classical papain fold. Copyright © 2017 Elsevier Ltd. All rights reserved.

Superoxide dismutase from Trichuris ovis--inhibition by benzimidazoles and pyrimidine derivatives.

PubMed

Sanchez-Moreno, M; Garcia-Rejon, L; Salas, I; Osuna, A; Monteoliva, M

1992-01-01

Three superoxide dismutase isoenzymes of different cellular location were detected in an homogenate of Trichuris ovis. Each of these molecular forms was purified by differential centrifugation and precipitation with ammonium sulphate, followed by chromatography on DEAE-cellulose and Sephadex G-75 columns. The activity levels of the two molecular forms detected in the mitochondrial (one cyanide sensitive Cu-Zn-SOD and the other cyanide insensitive Mn-SOD) were higher than that of the superoxide dismutase detected in the cytoplasmic fraction (cyanide sensitive Cu-Zn-SOD). All molecular forms present evident differences to the SODs contained in the host liver. Molecular mass and some of the physical and chemical properties of the enzyme was determined for all three molecular forms. An inhibitory effect on the SOD of the parasite an the host was detected with a series of compounds, some of which markedly inhibited parasite enzyme but not host enzyme.

Towards the chemometric dissection of peptide - HLA-A*0201 binding affinity: comparison of local and global QSAR models

NASA Astrophysics Data System (ADS)

Doytchinova, Irini A.; Walshe, Valerie; Borrow, Persephone; Flower, Darren R.

2005-03-01

The affinities of 177 nonameric peptides binding to the HLA-A*0201 molecule were measured using a FACS-based MHC stabilisation assay and analysed using chemometrics. Their structures were described by global and local descriptors, QSAR models were derived by genetic algorithm, stepwise regression and PLS. The global molecular descriptors included molecular connectivity χ indices, κ shape indices, E-state indices, molecular properties like molecular weight and log P, and three-dimensional descriptors like polarizability, surface area and volume. The local descriptors were of two types. The first used a binary string to indicate the presence of each amino acid type at each position of the peptide. The second was also position-dependent but used five z-scales to describe the main physicochemical properties of the amino acids forming the peptides. The models were developed using a representative training set of 131 peptides and validated using an independent test set of 46 peptides. It was found that the global descriptors could not explain the variance in the training set nor predict the affinities of the test set accurately. Both types of local descriptors gave QSAR models with better explained variance and predictive ability. The results suggest that, in their interactions with the MHC molecule, the peptide acts as a complicated ensemble of multiple amino acids mutually potentiating each other.

Excitation mechanism in the photoisomerization of a surface-bound azobenzene derivative: Role of the metallic substrate.

PubMed

Hagen, Sebastian; Kate, Peter; Leyssner, Felix; Nandi, Dhananjay; Wolf, Martin; Tegeder, Petra

2008-10-28

Two-photon photoemission spectroscopy is employed to elucidate the electronic structure and the excitation mechanism in the photoinduced isomerization of the molecular switch tetra-tert-butyl-azobenzene (TBA) adsorbed on Au(111). Our results demonstrate that the optical excitation and the mechanism of molecular switching at a metal surface is completely different compared to the corresponding process for the free molecule. In contrast to direct (intramolecular) excitation operative in the isomerization in the liquid phase, the conformational change in the surface-bound TBA is driven by a substrate-mediated charge transfer process. We find that photoexcitation above a threshold hnu approximately 2.2 eV leads to hole formation in the Au d-band followed by a hole transfer to the highest occupied molecular orbital of TBA. This transiently formed positive ion resonance subsequently results in a conformational change. The photon energy dependent photoisomerization cross section exhibit an unusual shape for a photochemical reaction of an adsorbate on a metal surface. It shows a thresholdlike behavior below hnu approximately 2.2 eV and above hnu approximately 4.4 eV. These thresholds correspond to the minimum energy required to create single or multiple hot holes in the Au d-bands, respectively. This study provides important new insights into the use of light to control the structure and function of molecular switches in direct contact with metal electrodes.

Excitation mechanism in the photoisomerization of a surface-bound azobenzene derivative: Role of the metallic substrate

NASA Astrophysics Data System (ADS)

Hagen, Sebastian; Kate, Peter; Leyssner, Felix; Nandi, Dhananjay; Wolf, Martin; Tegeder, Petra

2008-10-01

Two-photon photoemission spectroscopy is employed to elucidate the electronic structure and the excitation mechanism in the photoinduced isomerization of the molecular switch tetra-tert-butyl-azobenzene (TBA) adsorbed on Au(111). Our results demonstrate that the optical excitation and the mechanism of molecular switching at a metal surface is completely different compared to the corresponding process for the free molecule. In contrast to direct (intramolecular) excitation operative in the isomerization in the liquid phase, the conformational change in the surface-bound TBA is driven by a substrate-mediated charge transfer process. We find that photoexcitation above a threshold hν ≈2.2 eV leads to hole formation in the Au d-band followed by a hole transfer to the highest occupied molecular orbital of TBA. This transiently formed positive ion resonance subsequently results in a conformational change. The photon energy dependent photoisomerization cross section exhibit an unusual shape for a photochemical reaction of an adsorbate on a metal surface. It shows a thresholdlike behavior below hν ≈2.2 eV and above hν ≈4.4 eV. These thresholds correspond to the minimum energy required to create single or multiple hot holes in the Au d-bands, respectively. This study provides important new insights into the use of light to control the structure and function of molecular switches in direct contact with metal electrodes.

An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis.

PubMed

Kayode, Olumide; Wang, Ruiying; Pendlebury, Devon F; Cohen, Itay; Henin, Rachel D; Hockla, Alexandra; Soares, Alexei S; Papo, Niv; Caulfield, Thomas R; Radisky, Evette S

2016-12-16

The molecular basis of enzyme catalytic power and specificity derives from dynamic interactions between enzyme and substrate during catalysis. Although considerable effort has been devoted to understanding how conformational dynamics within enzymes affect catalysis, the role of conformational dynamics within protein substrates has not been addressed. Here, we examine the importance of substrate dynamics in the cleavage of Kunitz-bovine pancreatic trypsin inhibitor protease inhibitors by mesotrypsin, finding that the varied conformational dynamics of structurally similar substrates can profoundly impact the rate of catalysis. A 1.4-Å crystal structure of a mesotrypsin-product complex formed with a rapidly cleaved substrate reveals a dramatic conformational change in the substrate upon proteolysis. By using long all-atom molecular dynamics simulations of acyl-enzyme intermediates with proteolysis rates spanning 3 orders of magnitude, we identify global and local dynamic features of substrates on the nanosecond-microsecond time scale that correlate with enzymatic rates and explain differential susceptibility to proteolysis. By integrating multiple enhanced sampling methods for molecular dynamics, we model a viable conformational pathway between substrate-like and product-like states, linking substrate dynamics on the nanosecond-microsecond time scale with large collective substrate motions on the much slower time scale of catalysis. Our findings implicate substrate flexibility as a critical determinant of catalysis. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

First Molecular Characterization of Theileria ornithorhynchi Mackerras, 1959: yet Another Challenge to the Systematics of the Piroplasms.

PubMed

Paparini, Andrea; Macgregor, James; Ryan, Una M; Irwin, Peter J

2015-12-01

Piroplasms, tick-transmitted Apicomplexa of the genera Theileria, Babesia and Cytauxzoon, are blood-borne parasites of clinical and veterinary importance. The order Piroplasmida shows a puzzling systematics characterized by multiple clades, soft polytomies and paraphyletic/polyphyletic genera. In the present study, screening of platypuses (Ornithorhynchus anatinus), was performed to infer the parasite molecular phylogeny. DNA was extracted from blood, ectoparasites and tick eggs and the 18S rRNA- hsp70-genes were used for the phylogenetic reconstructions. Microscopic analyses detected pleomorphic intra-erythrocytic organisms and tetrads consistent with previous descriptions of Theileria ornithorhynchi Mackerras, 1959, but observation of possible schizonts could not be confirmed. DNA sequences obtained from blood and ticks allowed resolving the systematics of the first piroplasm infecting a monotreme host. Molecularly, T. ornithorhynchi formed a novel monophyletic group, basal to most known piroplasms' clades. The ancestral position of this clade, isolated from an ancient lineage of mammalian host appears particularly fascinating. The present paper discusses the inadequacies of the current molecular systematics for the Piroplasmida and the consequences of incomplete sampling, morphology-based classification and ambiguous microscopic identifications. Likely when the current sampling bias is rectified and more sequence data is made available, the phylogenetic position of T. ornithorhynchi will be further contextualized without ambiguity. Copyright © 2015 Elsevier GmbH. All rights reserved.

Implementation of a Multiplex and Quantitative Proteomics Platform for Assessing Protein Lysates Using DNA-Barcoded Antibodies.

PubMed

Lee, Jinho; Geiss, Gary K; Demirkan, Gokhan; Vellano, Christopher P; Filanoski, Brian; Lu, Yiling; Ju, Zhenlin; Yu, Shuangxing; Guo, Huifang; Bogatzki, Lisa Y; Carter, Warren; Meredith, Rhonda K; Krishnamurthy, Savitri; Ding, Zhiyong; Beechem, Joseph M; Mills, Gordon B

2018-06-01

Molecular analysis of tumors forms the basis for personalized cancer medicine and increasingly guides patient selection for targeted therapy. Future opportunities for personalized medicine are highlighted by the measurement of protein expression levels via immunohistochemistry, protein arrays, and other approaches; however, sample type, sample quantity, batch effects, and "time to result" are limiting factors for clinical application. Here, we present a development pipeline for a novel multiplexed DNA-labeled antibody platform which digitally quantifies protein expression from lysate samples. We implemented a rigorous validation process for each antibody and show that the platform is amenable to multiple protocols covering nitrocellulose and plate-based methods. Results are highly reproducible across technical and biological replicates, and there are no observed "batch effects" which are common for most multiplex molecular assays. Tests from basal and perturbed cancer cell lines indicate that this platform is comparable to orthogonal proteomic assays such as Reverse-Phase Protein Array, and applicable to measuring the pharmacodynamic effects of clinically-relevant cancer therapeutics. Furthermore, we demonstrate the potential clinical utility of the platform with protein profiling from breast cancer patient samples to identify molecular subtypes. Together, these findings highlight the potential of this platform for enhancing our understanding of cancer biology in a clinical translation setting. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

The Geropathology Research Network: An Interdisciplinary Approach for Integrating Pathology Into Research on Aging.

PubMed

Ladiges, Warren; Ikeno, Yuji; Niedernhofer, Laura; McIndoe, Richard A; Ciol, Marcia A; Ritchey, Jerry; Liggitt, Denny

2016-04-01

Geropathology is the study of aging and age-related lesions and diseases in the form of whole necropsies/autopsies, surgical biopsies, histology, and molecular biomarkers. It encompasses multiple subspecialties of geriatrics, anatomic pathology, molecular pathology, clinical pathology, and gerontology. In order to increase the consistency and scope of communication in the histologic and molecular pathology assessment of tissues from preclinical and clinical aging studies, a Geropathology Research Network has been established consisting of pathologists and scientists with expertise in the comparative pathology of aging, the design of aging research studies, biostatistical methods for analysis of aging data, and bioinformatics for compiling and annotating large sets of data generated from aging studies. The network provides an environment to promote learning and exchange of scientific information and ideas for the aging research community through a series of symposia, the development of uniform ways of integrating pathology into aging studies, and the statistical analysis of pathology data. The efforts of the network are ultimately expected to lead to a refined set of sentinel biomarkers of molecular and anatomic pathology that could be incorporated into preclinical and clinical aging intervention studies to increase the relevance and productivity of these types of investigations. © The Author 2015. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Sequence Dependent Interactions Between DNA and Single-Walled Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Roxbury, Daniel

It is known that single-stranded DNA adopts a helical wrap around a single-walled carbon nanotube (SWCNT), forming a water-dispersible hybrid molecule. The ability to sort mixtures of SWCNTs based on chirality (electronic species) has recently been demonstrated using special short DNA sequences that recognize certain matching SWCNTs of specific chirality. This thesis investigates the intricacies of DNA-SWCNT sequence-specific interactions through both experimental and molecular simulation studies. The DNA-SWCNT binding strengths were experimentally quantified by studying the kinetics of DNA replacement by a surfactant on the surface of particular SWCNTs. Recognition ability was found to correlate strongly with measured binding strength, e.g. DNA sequence (TAT)4 was found to bind 20 times stronger to the (6,5)-SWCNT than sequence (TAT)4T. Next, using replica exchange molecular dynamics (REMD) simulations, equilibrium structures formed by (a) single-strands and (b) multiple-strands of 12-mer oligonucleotides adsorbed on various SWCNTs were explored. A number of structural motifs were discovered in which the DNA strand wraps around the SWCNT and 'stitches' to itself via hydrogen bonding. Great variability among equilibrium structures was observed and shown to be directly influenced by DNA sequence and SWCNT type. For example, the (6,5)-SWCNT DNA recognition sequence, (TAT)4, was found to wrap in a tight single-stranded right-handed helical conformation. In contrast, DNA sequence T12 forms a beta-barrel left-handed structure on the same SWCNT. These are the first theoretical indications that DNA-based SWCNT selectivity can arise on a molecular level. In a biomedical collaboration with the Mayo Clinic, pathways for DNA-SWCNT internalization into healthy human endothelial cells were explored. Through absorbance spectroscopy, TEM imaging, and confocal fluorescence microscopy, we showed that intracellular concentrations of SWCNTs far exceeded those of the incubation solution, which suggested an energy-dependent pathway. Additionally, by means of pharmacological inhibition and vector-induced gene knockout studies, the DNA-SWCNTs were shown to enter the cells via Rac1-mediated macropinocytosis.

Multiple time step integrators in ab initio molecular dynamics.

PubMed

Luehr, Nathan; Markland, Thomas E; Martínez, Todd J

2014-02-28

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

Simulation of free energies of bicontinuous morphologies formed through block copolymer/homopolymer self-assembly

NASA Astrophysics Data System (ADS)

Padmanabhan, Poornima; Martinez-Veracoechea, Francisco; Escobedo, Fernando

Different types of bicontinuous phases can be formed from A-B diblock copolymers by the addition of A-type homopolymers over a range of compositions and relative chain lengths. Particle-based molecular simulations were used to study three bicontinuous phases - double gyroid (G), double diamond (D) and plumber's nightmare (P) - near their triple point of coexistence. For 3-D ordered phases, the stability of the morphology formed in simulation is highly sensitive to box size whose exact size is unknown a-priori. Accurate free energy estimates are required to ascertain the stable phase, particularly when multiple competing phases spontaneously form at the conditions of interest. A variant of thermodynamic integration was implemented to obtain free energies and hence identify the stable phases and their optimal box sizes by tracing a reversible path that connects the ordered and disordered phases. Clear evidence was found of D-G and D-P phase coexistence, consistent with previous predictions for the same blend using Self-consistent field theory. Our simulations also allowed us to examine the microscopic details of these coexisting bicontinuous phases and detect key differences between the microstructure of their nodes and struts.

Expansion and concatenation of nonmuscle myosin IIA filaments drive cellular contractile system formation during interphase and mitosis

PubMed Central

Fenix, Aidan M.; Taneja, Nilay; Buttler, Carmen A.; Lewis, John; Van Engelenburg, Schuyler B.; Ohi, Ryoma; Burnette, Dylan T.

2016-01-01

Cell movement and cytokinesis are facilitated by contractile forces generated by the molecular motor, nonmuscle myosin II (NMII). NMII molecules form a filament (NMII-F) through interactions of their C-terminal rod domains, positioning groups of N-terminal motor domains on opposite sides. The NMII motors then bind and pull actin filaments toward the NMII-F, thus driving contraction. Inside of crawling cells, NMIIA-Fs form large macromolecular ensembles (i.e., NMIIA-F stacks), but how this occurs is unknown. Here we show NMIIA-F stacks are formed through two non–mutually exclusive mechanisms: expansion and concatenation. During expansion, NMIIA molecules within the NMIIA-F spread out concurrent with addition of new NMIIA molecules. Concatenation occurs when multiple NMIIA-Fs/NMIIA-F stacks move together and align. We found that NMIIA-F stack formation was regulated by both motor activity and the availability of surrounding actin filaments. Furthermore, our data showed expansion and concatenation also formed the contractile ring in dividing cells. Thus interphase and mitotic cells share similar mechanisms for creating large contractile units, and these are likely to underlie how other myosin II–based contractile systems are assembled. PMID:26960797

Unlimited multistability in multisite phosphorylation systems.

PubMed

Thomson, Matthew; Gunawardena, Jeremy

2009-07-09

Reversible phosphorylation on serine, threonine and tyrosine is the most widely studied posttranslational modification of proteins. The number of phosphorylated sites on a protein (n) shows a significant increase from prokaryotes, with n /= 150 sites. Multisite phosphorylation has many roles and site conservation indicates that increasing numbers of sites cannot be due merely to promiscuous phosphorylation. A substrate with n sites has an exponential number (2(n)) of phospho-forms and individual phospho-forms may have distinct biological effects. The distribution of these phospho-forms and how this distribution is regulated have remained unknown. Here we show that, when kinase and phosphatase act in opposition on a multisite substrate, the system can exhibit distinct stable phospho-form distributions at steady state and that the maximum number of such distributions increases with n. Whereas some stable distributions are focused on a single phospho-form, others are more diffuse, giving the phospho-proteome the potential to behave as a fluid regulatory network able to encode information and flexibly respond to varying demands. Such plasticity may underlie complex information processing in eukaryotic cells and suggests a functional advantage in having many sites. Our results follow from the unusual geometry of the steady-state phospho-form concentrations, which we show to constitute a rational algebraic curve, irrespective of n. We thereby reduce the complexity of calculating steady states from simulating 3 x 2(n) differential equations to solving two algebraic equations, while treating parameters symbolically. We anticipate that these methods can be extended to systems with multiple substrates and multiple enzymes catalysing different modifications, as found in posttranslational modification 'codes' such as the histone code. Whereas simulations struggle with exponentially increasing molecular complexity, mathematical methods of the kind developed here can provide a new language in which to articulate the principles of cellular information processing.

A Comparison of Raw-to-Scale Conversion Consistency between Single- and Multiple-Linking Using a Nonequivalent Groups Anchor Test Design. Research Report. ETS RR-14-13

ERIC Educational Resources Information Center

Liu, Jinghua; Guo, Hongwen; Dorans, Neil J.

2014-01-01

Maintaining score interchangeability and scale consistency is crucial for any testing programs that administer multiple forms across years. The use of a multiple linking design, which involves equating a new form to multiple old forms and averaging the conversions, has been proposed to control scale drift. However, the use of multiple linking…

GIANT MOLECULAR CLOUDS AND STAR FORMATION IN THE NON-GRAND DESIGN SPIRAL GALAXY NGC 6946

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

Rebolledo, David; Wong, Tony; Leroy, Adam

We present high spatial resolution observations of giant molecular clouds (GMCs) in the eastern part of the nearby spiral galaxy NGC 6946 obtained with the Combined Array for Research in Millimeter-wave Astronomy (CARMA). We have observed CO(1 {yields} 0), CO(2 {yields} 1) and {sup 13}CO(1 {yields} 0), achieving spatial resolutions of 5.''4 Multiplication-Sign 5.''0, 2.''5 Multiplication-Sign 2.''0, and 5.''6 Multiplication-Sign 5.''4, respectively, over a region of 6 Multiplication-Sign 6 kpc. This region extends from 1.5 kpc to 8 kpc galactocentric radius, thus avoiding the intense star formation in the central kpc. We have recovered short-spacing u-v components by using singlemore » dish observations from the Nobeyama 45 m and IRAM 30 m telescopes. Using the automated CPROPS algorithm, we identified 45 CO cloud complexes in the CO(1 {yields} 0) map and 64 GMCs in the CO(2 {yields} 1) maps. The sizes, line widths, and luminosities of the GMCs are similar to values found in other extragalactic studies. We have classified the clouds into on-arm and inter-arm clouds based on the stellar mass density traced by the 3.6 {mu}m map. Clouds located on-arm present in general higher star formation rates than clouds located in inter-arm regions. Although the star formation efficiency shows no systematic trend with galactocentric radius, some on-arm clouds-which are more luminous and more massive compared to inter-arm GMCs-are also forming stars more efficiently than the rest of the identified GMCs. We find that these structures appear to be located in two specific regions in the spiral arms. One of them shows a strong velocity gradient, suggesting that this region of high star formation efficiency may be the result of gas flow convergence.« less

The Three Forms of Molecular Oxygen.

ERIC Educational Resources Information Center

Laing, Michael

1989-01-01

Finds that a logical application of the simple rules of the molecular orbital bonding theory for diatomic molecules predicted the existence of three spin isomers of the oxygen molecule: one triplet form with two unpaired electrons and two singlet forms with all electrons paired. (MVL)

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.

Unmasking molecular profiles of bladder cancer.

PubMed

Piao, Xuan-Mei; Byun, Young Joon; Kim, Wun-Jae; Kim, Jayoung

2018-03-01

Precision medicine is designed to tailor treatments for individual patients by factoring in each person's specific biology and mechanism of disease. This paradigm shifted from a "one size fits all" approach to "personalized and precision care" requires multiple layers of molecular profiling of biomarkers for accurate diagnosis and prediction of treatment responses. Intensive studies are also being performed to understand the complex and dynamic molecular profiles of bladder cancer. These efforts involve looking bladder cancer mechanism at the multiple levels of the genome, epigenome, transcriptome, proteome, lipidome, metabolome etc. The aim of this short review is to outline the current technologies being used to investigate molecular profiles and discuss biomarker candidates that have been investigated as possible diagnostic and prognostic indicators of bladder cancer.

Structural mechanisms of chaperone mediated protein disaggregation

PubMed Central

Sousa, Rui

2014-01-01

The ClpB/Hsp104 and Hsp70 classes of molecular chaperones use ATP hydrolysis to dissociate protein aggregates and complexes, and to move proteins through membranes. ClpB/Hsp104 are members of the AAA+ family of proteins which form ring-shaped hexamers. Loops lining the pore in the ring engage substrate proteins as extended polypeptides. Interdomain rotations and conformational changes in these loops coupled to ATP hydrolysis unfold and pull proteins through the pore. This provides a mechanism that progressively disrupts local secondary and tertiary structure in substrates, allowing these chaperones to dissociate stable aggregates such as β-sheet rich prions or coiled coil SNARE complexes. While the ClpB/Hsp104 mechanism appears to embody a true power-stroke in which an ATP powered conformational change in one protein is directly coupled to movement or structural change in another, the mechanism of force generation by Hsp70s is distinct and less well understood. Both active power-stroke and purely passive mechanisms in which Hsp70 captures spontaneous fluctuations in a substrate have been proposed, while a third proposed mechanism—entropic pulling—may be able to generate forces larger than seen in ATP-driven molecular motors without the conformational coupling required for a power-stroke. The disaggregase activity of these chaperones is required for thermotolerance, but unrestrained protein complex/aggregate dissociation is potentially detrimental. Disaggregating chaperones are strongly auto-repressed, and are regulated by co-chaperones which recruit them to protein substrates and activate the disaggregases via mechanisms involving either sequential transfer of substrate from one chaperone to another and/or simultaneous interaction of substrate with multiple chaperones. By effectively subjecting substrates to multiple levels of selection by multiple chaperones, this may insure that these potent disaggregases are only activated in the appropriate context. PMID:25988153

Terrestrial Planet Formation in Binary Star Systems

NASA Technical Reports Server (NTRS)

Lissauer, Jack J.; Quintana, Elisa V.; Chambers, John; Duncan, Martin J.; Adams, Fred

2003-01-01

Most stars reside in multiple star systems; however, virtually all models of planetary growth have assumed an isolated single star. Numerical simulations of the collapse of molecular cloud cores to form binary stars suggest that disks will form within such systems. Observations indirectly suggest disk material around one or both components within young binary star systems. If planets form at the right places within such circumstellar disks, they can remain in stable orbits within the binary star systems for eons. We are simulating the late stages of growth of terrestrial planets within binary star systems, using a new, ultrafast, symplectic integrator that we have developed for this purpose. We show that the late stages of terrestrial planet formation can indeed take place in a wide variety of binary systems and we have begun to delineate the range of parameter space for which this statement is true. Results of our initial simulations of planetary growth around each star in the alpha Centauri system and other 'wide' binary systems, as well as around both stars in very close binary systems, will be presented.

Mapping of native inorganic elements and injected nanoparticles in a biological organ with laser-induced plasma

NASA Astrophysics Data System (ADS)

Motto-Ros, V.; Sancey, L.; Ma, Q. L.; Lux, F.; Bai, X. S.; Wang, X. C.; Yu, Jin; Panczer, G.; Tillement, O.

2012-11-01

Emission spectroscopy of laser-induced plasma from a thin section of mouse kidney successfully detected inorganic elements, Na, Ca, Cu, and Gd, naturally contained in the organ or artificially injected in the form of Gd-based nanoparticle. A two-dimensional scan of the sample allowed the laser beam to explore its surface with a resolution of 100 μm, resulting in a quantitative elemental mapping of the organ with sub-mM sensitivity. The compatibility of the setup with standard optical microscopy emphasizes the potential to provide multiple images of a same biological tissue with different types of response which can be elemental, molecular, or cellular.

What's in a name? Y chromosomes, surnames and the genetic genealogy revolution.

PubMed

King, Turi E; Jobling, Mark A

2009-08-01

Heritable surnames are highly diverse cultural markers of coancestry in human populations. A patrilineal surname is inherited in the same way as the non-recombining region of the Y chromosome and there should, therefore, be a correlation between the two. Studies of Y haplotypes within surnames, mostly of the British Isles, reveal high levels of coancestry among surname cohorts and the influence of confounding factors, including multiple founders for names, non-paternities and genetic drift. Combining molecular genetics and surname analysis illuminates population structure and history, has potential applications in forensic studies and, in the form of 'genetic genealogy', is an area of rapidly growing interest for the public.

Molecular characterization of crane Coccidia, Eimeria gruis and E. reichenowi, found in feces of migratory cranes.

PubMed

Matsubayashi, Makoto; Takami, Kazutoshi; Abe, Niichiro; Kimata, Isao; Tani, Hiroyuki; Sasai, Kazumi; Baba, Eiichiroh

2005-08-01

Eimeria gruis and E. reichenowi have lethal pathogenicity to a number of species of cranes. These parasites develop at multiple organs or tissues in infected cranes, thus lacking the specificity of infection sites shown by other Eimeria spp. in spite of morphologic similarity. To date, there have been many reports of crane Eimeria infections, however, genetic examinations of these parasites have never been published. In the present study, we isolated oocysts of E. gruis and E. reichenowi from crane feces at a wintering area in Japan. By phylogenic analysis, we first demonstrated that partial sequences of the isolates formed their own cluster, located separately from other Eimeria spp.

Ancient techniques for new materials

NASA Technical Reports Server (NTRS)

2000-01-01

NASA is looking to biological techniques that are millions of years old to help it develop new materials and technologies for the 21st century. Sponsored by NASA, Jeffrey Brinker of the University of New Mexico is studying how multiple elements can assemble themselves into a composite material that is clear, tough, and impermeable. His research is based on the model of how an abalone builds the nacre, also called mother-of-pearl, inside its shell. Strong thin coatings, or lamellae, in Brinker's research are formed when objects are dip-coated. Evaporation drives the self-assembly of molecular aggregates (micelles) of surfactant, soluble silica, and organic monomers and their further self-organization into layered organic and inorganic assemblies.

Surface ordering of (In,Ga)As quantum dots controlled by GaAs substrate indexes

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

Wang, Zh.M.; Seydmohamadi, Sh.; Lee, J.H.

Self-organized surface ordering of (In,Ga)As quantum dots in a GaAs matrix was investigated using stacked multiple quantum dot layers prepared by molecular-beam epitaxy. While one-dimensional chain-like ordering is formed on singular and slightly misorientated GaAs(100) surfaces, we report on two-dimensional square-like ordering that appears on GaAs(n11)B, where n is 7, 5, 4, and 3. Using a technique to control surface diffusion, the different ordering patterns are found to result from the competition between anisotropic surface diffusion and anisotropic elastic matrix, a similar mechanism suggested before by Solomon [Appl. Phys. Lett. 84, 2073 (2004)].

The Role of TLR2 in Infection and Immunity

PubMed Central

Oliveira-Nascimento, Laura; Massari, Paola; Wetzler, Lee M.

2012-01-01

Toll-like receptors (TLRs) are recognition molecules for multiple pathogens, including bacteria, viruses, fungi, and parasites. TLR2 forms heterodimers with TLR1 and TLR6, which is the initial step in a cascade of events leading to significant innate immune responses, development of adaptive immunity to pathogens and protection from immune sequelae related to infection with these pathogens. This review will discuss the current status of TLR2 mediated immune responses by recognition of pathogen-associated molecular patterns (PAMPS) on these organisms. We will emphasize both canonical and non-canonical responses to TLR2 ligands with emphasis on whether the inflammation induced by these responses contributes to the disease state or to protection from diseases. PMID:22566960

Writing throughout the biochemistry curriculum: Synergistic inquiry-based writing projects for biochemistry students.

PubMed

Mertz, Pamela; Streu, Craig

2015-01-01

This article describes a synergistic two-semester writing sequence for biochemistry courses. In the first semester, students select a putative protein and are tasked with researching their protein largely through bioinformatics resources. In the second semester, students develop original ideas and present them in the form of a research grant proposal. Both projects involve multiple drafts and peer review. The complementarity of the projects increases student exposure to bioinformatics and literature resources, fosters higher-order thinking skills, and develops teamwork and communication skills. Student feedback and responses on perception surveys demonstrated that the students viewed both projects as favorable learning experiences. © 2015 The International Union of Biochemistry and Molecular Biology.

An Overview of Mongenic and Syndromic Obesities in Humans

PubMed Central

Chung, Wendy K.

2011-01-01

Obesity is increasing in prevalence in the United States with over 65% of adults considered overweight and 16% of children with BMI > 95 percentile. The heritability of obesity is estimated between 40 and 70%, but the genetics of obesity for most individuals are complex and involve the interaction of multiple genes and environment. There are however several syndromic and non-syndromic forms of obesity that are monogenic and oligogenic that provide insight into the underlying molecular control of food intake and the neural networks that control ingestive behavior and satiety to regulate body weight and which may interact with treatment exposures to produce or exacerbate obesity in childhood cancer survivors. PMID:21994130

[Changes in molecular forms of sex hormone binding globulin during menstrual cycle and menopause].

PubMed

Fonseca, M E; Masón, M; Ochoa, R; Hernández-V, M; Zárate, A

1996-11-01

Sex hormone binding globulin (SHBG) is a glycoprotein that transports mainly androgens and estrogens regulating the amount of free and bound hormone which in turn plays a role in the metabolic balance. It is also known that estrogens increase the hepatic production of SHBG which circulates in various molecular forms containing different amounts of sialic acid as the main component of carbohydrates. In the present work we studied physiological variations of molecular forms of SHBG during the normal menstrual cycle and the menopause. During the follicular phase the form 54 KD was the predominant variant, in the periovulatory period was isomers 90 KD, and during the luteal phase corresponded to both 54 and 90 KD. In the menopause dimeric form of 90 KD corresponded to the major proportion and was present a higher molecular forms of 115-135 KD. Following estrogen therapy the chromatographic profile changed as to that observed during the menstrual cycle. Important changes in the proportion of sialic acid were observed in each of the phases of menstrual cycle and following estrogen replacement. And increase in the amount of sialic acid corresponded to higher estrogen concentrations. It is concluded that SHBG concentrations varies during the menstrual cycle according the estrogen levels which in addition regulates the proportion of molecular forms and sialic acid containt.

Calcium dynamics regulating the timing of decision-making in C. elegans.

PubMed

Tanimoto, Yuki; Yamazoe-Umemoto, Akiko; Fujita, Kosuke; Kawazoe, Yuya; Miyanishi, Yosuke; Yamazaki, Shuhei J; Fei, Xianfeng; Busch, Karl Emanuel; Gengyo-Ando, Keiko; Nakai, Junichi; Iino, Yuichi; Iwasaki, Yuishi; Hashimoto, Koichi; Kimura, Koutarou D

2017-05-23

Brains regulate behavioral responses with distinct timings. Here we investigate the cellular and molecular mechanisms underlying the timing of decision-making during olfactory navigation in Caenorhabditis elegans . We find that, based on subtle changes in odor concentrations, the animals appear to choose the appropriate migratory direction from multiple trials as a form of behavioral decision-making. Through optophysiological, mathematical and genetic analyses of neural activity under virtual odor gradients, we further find that odor concentration information is temporally integrated for a decision by a gradual increase in intracellular calcium concentration ([Ca 2+ ] i ), which occurs via L-type voltage-gated calcium channels in a pair of olfactory neurons. In contrast, for a reflex-like behavioral response, [Ca 2+ ] i rapidly increases via multiple types of calcium channels in a pair of nociceptive neurons. Thus, the timing of neuronal responses is determined by cell type-dependent involvement of calcium channels, which may serve as a cellular basis for decision-making.

Correlating Polymer Crystals via Self-Induced Nucleation

NASA Astrophysics Data System (ADS)

Reiter, Günter

Crystallizable polymers often form multiple stacks of uniquely oriented lamellae, which have good registry despite being separated by amorphous fold surfaces. These correlations require multiple synchronized, yet unidentified, nucleation events. Here, we demonstrate that in thin films of isotactic polystyrene, the probability of generating correlated lamellae is controlled by the branched morphology of a single primary lamella. The nucleation density ns of secondary lamellae is found to be dependent on the width of the branches of the primary lamella. This relation is independent of molecular weight, crystallization temperature, and film thickness. We propose a nucleation mechanism based on the insertion of polymers into a branched primary lamellar crystal. Even in single crystals, characterized by faceted structures with a well-defined envelope reflecting the underlying crystal unit cell, polymers are folded and thus in a meta-stable state. Annealing such meta-stable single crystals allowed to unveil the initial morphological framework of a dendritic single crystal, i.e. the initial stages of growth.

Calcium dynamics regulating the timing of decision-making in C. elegans

PubMed Central

Tanimoto, Yuki; Yamazoe-Umemoto, Akiko; Fujita, Kosuke; Kawazoe, Yuya; Miyanishi, Yosuke; Yamazaki, Shuhei J; Fei, Xianfeng; Busch, Karl Emanuel; Gengyo-Ando, Keiko; Nakai, Junichi; Iino, Yuichi; Iwasaki, Yuishi; Hashimoto, Koichi; Kimura, Koutarou D

2017-01-01

Brains regulate behavioral responses with distinct timings. Here we investigate the cellular and molecular mechanisms underlying the timing of decision-making during olfactory navigation in Caenorhabditis elegans. We find that, based on subtle changes in odor concentrations, the animals appear to choose the appropriate migratory direction from multiple trials as a form of behavioral decision-making. Through optophysiological, mathematical and genetic analyses of neural activity under virtual odor gradients, we further find that odor concentration information is temporally integrated for a decision by a gradual increase in intracellular calcium concentration ([Ca2+]i), which occurs via L-type voltage-gated calcium channels in a pair of olfactory neurons. In contrast, for a reflex-like behavioral response, [Ca2+]i rapidly increases via multiple types of calcium channels in a pair of nociceptive neurons. Thus, the timing of neuronal responses is determined by cell type-dependent involvement of calcium channels, which may serve as a cellular basis for decision-making. DOI: http://dx.doi.org/10.7554/eLife.21629.001 PMID:28532547

A northward colonisation of the Andes by the potato cyst nematode during geological times suggests multiple host-shifts from wild to cultivated potatoes.

PubMed

Picard, Damien; Sempere, Thierry; Plantard, Olivier

2007-02-01

The cyst nematode Globodera pallida is a major pest of potato in South America where this specialist parasite is native. To investigate its phylogeography, we have genotyped individuals from 42 Peruvian populations using mitochondrial and nuclear molecular markers. A clear south-to-north phylogeographical pattern was revealed with five well-supported clades. The clade containing the southern populations is genetically more diverse and forms the most basal branch. The large divergence among cytochrome b haplotypes suggests that they diverged before human domestication of potato. As the nematodes studied have been sampled on cultivated potato, multiple host-shifts from wild to cultivated potatoes must have occurred independently in each clade. We hypothesise that this south-to-north pattern took place during the uplift of the Andes beginning 20 My ago and following the same direction. To our knowledge, this is the first study of a plant parasite sampled on cultivated plants revealing an ancient phylogeographical pattern.

Photochromic amorphous molecular materials and their applications

NASA Astrophysics Data System (ADS)

Shirota, Yasuhiko; Utsumi, Hisayuki; Ujike, Toshiki; Yoshikawa, Satoru; Moriwaki, Kazuyuki; Nagahama, Daisuke; Nakano, Hideyuki

2003-01-01

Two novel classes of photochromic amorphous molecular materials based on azobenzene and dithienylethene were designed and synthesized. They were found to readily form amorphous glasses with well-defined glass-transition temperatures when the melt samples were cooled on standing in air and to exhibit photochromism in their amorphous films as well as in solution. Photochromic properties of these materials are discussed in relation to their molecular structures. Surface relief grating was formed on the amorphous films of azobenzene-based photochromic amorphous molecular materials by irradiation with two coherent Ar + laser beams. Dual image was formed at the same location of the films of dithienylethene-based photochromic amorphous molecular materials by irradiation with two linearly polarized light beams perpendicular to each other.

Enhanced sampling by multiple molecular dynamics trajectories: carbonmonoxy myoglobin 10 micros A0-->A(1-3) transition from ten 400 picosecond simulations.

PubMed

Loccisano, Anne E; Acevedo, Orlando; DeChancie, Jason; Schulze, Brita G; Evanseck, Jeffrey D

2004-05-01

The utility of multiple trajectories to extend the time scale of molecular dynamics simulations is reported for the spectroscopic A-states of carbonmonoxy myoglobin (MbCO). Experimentally, the A0-->A(1-3) transition has been observed to be 10 micros at 300 K, which is beyond the time scale of standard molecular dynamics simulations. To simulate this transition, 10 short (400 ps) and two longer time (1.2 ns) molecular dynamics trajectories, starting from five different crystallographic and solution phase structures with random initial velocities centered in a 37 A radius sphere of water, have been used to sample the native-fold of MbCO. Analysis of the ensemble of structures gathered over the cumulative 5.6 ns reveals two biomolecular motions involving the side chains of His64 and Arg45 to explain the spectroscopic states of MbCO. The 10 micros A0-->A(1-3) transition involves the motion of His64, where distance between His64 and CO is found to vary up to 8.8 +/- 1.0 A during the transition of His64 from the ligand (A(1-3)) to bulk solvent (A0). The His64 motion occurs within a single trajectory only once, however the multiple trajectories populate the spectroscopic A-states fully. Consequently, multiple independent molecular dynamics simulations have been found to extend biomolecular motion from 5 ns of total simulation to experimental phenomena on the microsecond time scale.

PCR-based karyotyping of Anopheles gambiae inversion 2Rj identifies the BAMAKO chromosomal form.

PubMed

Coulibaly, Mamadou B; Pombi, Marco; Caputo, Beniamino; Nwakanma, Davis; Jawara, Musa; Konate, Lassana; Dia, Ibrahima; Fofana, Abdrahamane; Kern, Marcia; Simard, Frédéric; Conway, David J; Petrarca, Vincenzo; della Torre, Alessandra; Traoré, Sékou; Besansky, Nora J

2007-10-01

The malaria vector Anopheles gambiae is polymorphic for chromosomal inversions on the right arm of chromosome 2 that segregate nonrandomly between assortatively mating populations in West Africa. One such inversion, 2Rj, is associated with the BAMAKO chromosomal form endemic to southern Mali and northern Guinea Conakry near the Niger River. Although it exploits a unique ecology and both molecular and chromosomal data suggest reduced gene flow between BAMAKO and other A. gambiae populations, no molecular markers exist to identify this form. To facilitate study of the BAMAKO form, a PCR assay for molecular karyotyping of 2Rj was developed based on sequences at the breakpoint junctions. The assay was extensively validated using more than 700 field specimens whose karyotypes were determined in parallel by cytogenetic and molecular methods. As inversion 2Rj also occurs in SAVANNA populations outside the geographic range of BAMAKO, samples were tested from Senegal, Cameroon and western Guinea Conakry as well as from Mali. In southern Mali, where 2Rj polymorphism in SAVANNA populations was very low and most of the 2Rj homozygotes were found in BAMAKO karyotypes, the molecular and cytogenetic methods were almost perfectly congruent. Elsewhere agreement between the methods was much poorer, as the molecular assay frequently misclassified 2Rj heterozygotes as 2R+j standard homozygotes. Molecular karyotyping of 2Rj is robust and accurate on 2R+j standard and 2Rj inverted homozygotes. Therefore, the proposed approach overcomes the lack of a rapid tool for identifying the BAMAKO form across developmental stages and sexes, and opens new perspectives for the study of BAMAKO ecology and behaviour. On the other hand, the method should not be applied for molecular karyotyping of j-carriers within the SAVANNA chromosomal form.

The multiple infrared source GL 437

NASA Technical Reports Server (NTRS)

Wynn-Williams, C. G.; Becklin, E. E.; Beichman, C. A.; Capps, R.; Shakeshaft, J. R.

1981-01-01

Infrared and radio continuum observations of the multiple infrared source GL 437 show that it consists of a compact H II region plus two objects which are probably early B stars undergoing rapid mass loss. The group of sources appears to be a multiple system of young stars that have recently emerged from the near side of a molecular cloud. Emission in the unidentified 3.3 micron feature is associated with, but more extended than, the emission from the compact H II region; it probably arises from hot dust grains at the interface between the H II region and the molecular cloud.

Laser isotope separation by multiple photon absorption

DOEpatents

Robinson, C. Paul; Rockwood, Stephen D.; Jensen, Reed J.; Lyman, John L.; Aldridge, III, Jack P.

1987-01-01

Multiple photon absorption from an intense beam of infrared laser light may be used to induce selective chemical reactions in molecular species which result in isotope separation or enrichment. The molecular species must have a sufficient density of vibrational states in its vibrational manifold that, is the presence of sufficiently intense infrared laser light tuned to selectively excite only those molecules containing a particular isotope, multiple photon absorption can occur. By this technique, for example, intense CO.sub.2 laser light may be used to highly enrich .sup.34 S in natural SF.sub.6 and .sup.11 B in natural BCl.sub.3.

Laser isotope separation by multiple photon absorption

DOEpatents

Robinson, C. Paul; Rockwood, Stephen D.; Jensen, Reed J.; Lyman, John L.; Aldridge, III, Jack P.

1977-01-01

Multiple photon absorption from an intense beam of infrared laser light may be used to induce selective chemical reactions in molecular species which result in isotope separation or enrichment. The molecular species must have a sufficient density of vibrational states in its vibrational manifold that, in the presence of sufficiently intense infrared laser light tuned to selectively excite only those molecules containing a particular isotope, multiple photon absorption can occur. By this technique, for example, intense CO.sub.2 laser light may be used to highly enrich .sup.34 S in natural SF.sub.6 and .sup.11 B in natural BCl.sub.3.

Detection method for dissociation of multiple-charged ions

DOEpatents

Smith, Richard D.; Udseth, Harold R.; Rockwood, Alan L.

1991-01-01

Dissociations of multiple-charged ions are detected and analyzed by charge-separation tandem mass spectrometry. Analyte molecules are ionized to form multiple-charged parent ions. A particular charge parent ion state is selected in a first-stage mass spectrometer and its mass-to-charge ratio (M/Z) is detected to determine its mass and charge. The selected parent ions are then dissociated, each into a plurality of fragments including a set of daughter ions each having a mass of at least one molecular weight and a charge of at least one. Sets of daughter ions resulting from the dissociation of one parent ion (sibling ions) vary in number but typically include two to four ions, one or more multiply-charged. A second stage mass spectrometer detects mass-to-charge ratio (m/z) of the daughter ions and a temporal or temporo-spatial relationship among them. This relationship is used to correlate the daughter ions to determine which (m/z) ratios belong to a set of sibling ions. Values of mass and charge of each of the sibling ions are determined simultaneously from their respective (m/z) ratios such that the sibling ion charges are integers and sum to the parent ion charge.

ALMA Observations of Elias 2–24: A Protoplanetary Disk with Multiple Gaps in the Ophiuchus Molecular Cloud

NASA Astrophysics Data System (ADS)

Cieza, Lucas A.; Casassus, Simon; Pérez, Sebastian; Hales, Antonio; Cárcamo, Miguel; Ansdell, Megan; Avenhaus, Henning; Bayo, Amelia; Bertrang, Gesa H.-M.; Cánovas, Hector; Christiaens, Valentin; Dent, William; Ferrero, Gabriel; Gamen, Roberto; Olofsson, Johan; Orcajo, Santiago; Osses, Axel; Peña-Ramirez, Karla; Principe, David; Ruíz-Rodríguez, Dary; Schreiber, Matthias R.; van der Plas, Gerrit; Williams, Jonathan P.; Zurlo, Alice

2017-12-01

We present ALMA 1.3 mm continuum observations at 0\\buildrel{\\prime\\prime}\\over{.} 2 (25 au) resolution of Elias 2–24, one of the largest and brightest protoplanetary disks in the Ophiuchus Molecular Cloud, and we report the presence of three partially resolved concentric gaps located at ∼20, 52, and 87 au from the star. We perform radiative transfer modeling of the disk to constrain its surface density and temperature radial profile and place the disk structure in the context of mechanisms capable of forming narrow gaps such as condensation fronts and dynamical clearing by actively forming planets. In particular, we estimate the disk temperature at the locations of the gaps to be 23, 15, and 12 K (at 20, 52, and 87 au, respectively), very close to the expected snowlines of CO (23–28 K) and N2 (12–15 K). Similarly, by assuming that the widths of the gaps correspond to 4–8× the Hill radii of forming planets (as suggested by numerical simulations), we estimate planet masses in the range of 0.2{--}1.5 {M}{Jup}, 1.0{--}8.0 {M}{Jup}, and 0.02{--}0.15 {M}{Jup} for the inner, middle, and outer gap, respectively. Given the surface density profile of the disk, the amount of “missing mass” at the location of each one of these gaps (between 4 and 20 {M}{Jup}) is more than sufficient to account for the formation of such planets.

The most distant, luminous, dusty star-forming galaxies: redshifts from NOEMA and ALMA spectral scans

NASA Astrophysics Data System (ADS)

Fudamoto, Y.; Ivison, R. J.; Oteo, I.; Krips, M.; Zhang, Z.-Y.; Weiss, A.; Dannerbauer, H.; Omont, A.; Chapman, S. C.; Christensen, L.; Arumugam, V.; Bertoldi, F.; Bremer, M.; Clements, D. L.; Dunne, L.; Eales, S. A.; Greenslade, J.; Maddox, S.; Martinez-Navajas, P.; Michalowski, M.; Pérez-Fournon, I.; Riechers, D.; Simpson, J. M.; Stalder, B.; Valiante, E.; van der Werf, P.

2017-12-01

We present 1.3- and/or 3-mm continuum images and 3-mm spectral scans, obtained using Northern Extended Millimeter Array (NOEMA) and Atacama Large Millimeter Array (ALMA), of 21 distant, dusty, star-forming galaxies. Our sample is a subset of the galaxies selected by Ivison et al. on the basis of their extremely red far-infrared (far-IR) colours and low Herschel flux densities; most are thus expected to be unlensed, extraordinarily luminous starbursts at z ≳ 4, modulo the considerable cross-section to gravitational lensing implied by their redshift. We observed 17 of these galaxies with NOEMA and four with ALMA, scanning through the 3-mm atmospheric window. We have obtained secure redshifts for seven galaxies via detection of multiple CO lines, one of them a lensed system at z = 6.027 (two others are also found to be lensed); a single emission line was detected in another four galaxies, one of which has been shown elsewhere to lie at z = 4.002. Where we find no spectroscopic redshifts, the galaxies are generally less luminous by 0.3-0.4 dex, which goes some way to explaining our failure to detect line emission. We show that this sample contains the most luminous known star-forming galaxies. Due to their extreme star-formation activity, these galaxies will consume their molecular gas in ≲ 100 Myr, despite their high molecular gas masses, and are therefore plausible progenitors of the massive, 'red-and-dead' elliptical galaxies at z ≈ 3.

Loss of laminin alpha 1 results in multiple structural defects and divergent effects on adhesion during vertebrate optic cup morphogenesis

PubMed Central

Bryan, Chase D.; Chien, Chi-Bin; Kwan, Kristen M.

2016-01-01

The vertebrate eye forms via a complex set of morphogenetic events. The optic vesicle evaginates and undergoes transformative shape changes to form the optic cup, in which neural retina and retinal pigmented epithelium enwrap the lens. It has long been known that a complex, glycoprotein-rich extracellular matrix layer surrounds the developing optic cup throughout the process, yet the functions of the matrix and its specific molecular components have remained unclear. Previous work established a role for laminin extracellular matrix in particular steps of eye development, including optic vesicle evagination, lens differentiation, and retinal ganglion cell polarization, yet it is unknown what role laminin might play in the early process of optic cup formation subsequent to the initial step of optic vesicle evagination. Here, we use the zebrafish lama1 mutant (lama1UW1) to determine the function of laminin during optic cup morphogenesis. Using live imaging, we find, surprisingly, that loss of laminin leads to divergent effects on focal adhesion assembly in a spatiotemporally-specific manner, and that laminin is required for multiple steps of optic cup morphogenesis, including optic stalk constriction, invagination, and formation of a spherical lens. Laminin is not required for single cell behaviors and changes in cell shape. Rather, in lama1UW1 mutants, loss of epithelial polarity and altered adhesion lead to defective tissue architecture and formation of a disorganized retina. These results demonstrate that the laminin extracellular matrix plays multiple critical roles regulating adhesion and polarity to establish and maintain tissue structure during optic cup morphogenesis. PMID:27339294

Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins.

PubMed

Pang, Yuan-Ping

2016-09-01

Predicting crystallographic B-factors of a protein from a conventional molecular dynamics simulation is challenging, in part because the B-factors calculated through sampling the atomic positional fluctuations in a picosecond molecular dynamics simulation are unreliable, and the sampling of a longer simulation yields overly large root mean square deviations between calculated and experimental B-factors. This article reports improved B-factor prediction achieved by sampling the atomic positional fluctuations in multiple picosecond molecular dynamics simulations that use uniformly increased atomic masses by 100-fold to increase time resolution. Using the third immunoglobulin-binding domain of protein G, bovine pancreatic trypsin inhibitor, ubiquitin, and lysozyme as model systems, the B-factor root mean square deviations (mean ± standard error) of these proteins were 3.1 ± 0.2-9 ± 1 Å 2 for Cα and 7.3 ± 0.9-9.6 ± 0.2 Å 2 for Cγ, when the sampling was done for each of these proteins over 20 distinct, independent, and 50-picosecond high-mass molecular dynamics simulations with AMBER forcefield FF12MC or FF14SB. These results suggest that sampling the atomic positional fluctuations in multiple picosecond high-mass molecular dynamics simulations may be conducive to a priori prediction of crystallographic B-factors of a folded globular protein.

PM2.5 Characterization for Time Series Studies: Organic Molecular Marker Speciation Methods and Observations from Daily Measurements in Denver

PubMed Central

Dutton, Steven J.; Williams, Daniel E.; Garcia, Jessica K.; Vedal, Sverre; Hannigan, Michael P.

2009-01-01

Particulate matter less than 2.5 microns in diameter (PM2.5) has been shown to have a wide range of adverse health effects and consequently is regulated in accordance with the US-EPA’s National Ambient Air Quality Standards. PM2.5 originates from multiple primary sources and is also formed through secondary processes in the atmosphere. It is plausible that some sources form PM2.5 that is more toxic than PM2.5 from other sources. Identifying the responsible sources could provide insight into the biological mechanisms causing the observed health effects and provide a more efficient approach to regulation. This is the goal of the Denver Aerosol Sources and Health (DASH) study, a multi-year PM2.5 source apportionment and health study. The first step in apportioning the PM2.5 to different sources is to determine the chemical make-up of the PM2.5. This paper presents the methodology used during the DASH study for organic speciation of PM2.5. Specifically, methods are covered for solvent extraction of non-polar and semi-polar organic molecular markers using gas chromatography-mass spectrometry (GC-MS). Vast reductions in detection limits were obtained through the use of a programmable temperature vaporization (PTV) inlet along with other method improvements. Results are presented for the first 1.5 years of the DASH study revealing seasonal and source-related patterns in the molecular markers and their long-term correlation structure. Preliminary analysis suggests that point sources are not a significant contributor to the organic molecular markers measured at our receptor site. Several motor vehicle emission markers help identify a gasoline/diesel split in the ambient data. Findings show both similarities and differences when compared with other cities where similar measurements and assessments have been made. PMID:20161318

Evolution of cytokinesis-related protein localization during the emergence of multicellularity in volvocine green algae.

PubMed

Arakaki, Yoko; Fujiwara, Takayuki; Kawai-Toyooka, Hiroko; Kawafune, Kaoru; Featherston, Jonathan; Durand, Pierre M; Miyagishima, Shin-Ya; Nozaki, Hisayoshi

2017-12-06

The volvocine lineage, containing unicellular Chlamydomonas reinhardtii and differentiated multicellular Volvox carteri, is a powerful model for comparative studies aiming at understanding emergence of multicellularity. Tetrabaena socialis is the simplest multicellular volvocine alga and belongs to the family Tetrabaenaceae that is sister to more complex multicellular volvocine families, Goniaceae and Volvocaceae. Thus, T. socialis is a key species to elucidate the initial steps in the evolution of multicellularity. In the asexual life cycle of C. reinhardtii and multicellular volvocine species, reproductive cells form daughter cells/colonies by multiple fission. In embryogenesis of the multicellular species, daughter protoplasts are connected to one another by cytoplasmic bridges formed by incomplete cytokinesis during multiple fission. These bridges are important for arranging the daughter protoplasts in appropriate positions such that species-specific integrated multicellular individuals are shaped. Detailed comparative studies of cytokinesis between unicellular and simple multicellular volvocine species will help to elucidate the emergence of multicellularity from the unicellular ancestor. However, the cytokinesis-related genes between closely related unicellular and multicellular species have not been subjected to a comparative analysis. Here we focused on dynamin-related protein 1 (DRP1), which is known for its role in cytokinesis in land plants. Immunofluorescence microscopy using an antibody against T. socialis DRP1 revealed that volvocine DRP1 was localized to division planes during cytokinesis in unicellular C. reinhardtii and two simple multicellular volvocine species T. socialis and Gonium pectorale. DRP1 signals were mainly observed in the newly formed division planes of unicellular C. reinhardtii during multiple fission, whereas in multicellular T. socialis and G. pectorale, DRP1 signals were observed in all division planes during embryogenesis. These results indicate that the molecular mechanisms of cytokinesis may be different in unicellular and multicellular volvocine algae. The localization of DRP1 during multiple fission might have been modified in the common ancestor of multicellular volvocine algae. This modification may have been essential for the re-orientation of cells and shaping colonies during the emergence of multicellularity in this lineage.

Fast Molecular Cloud Destruction Requires Fast Cloud Formation

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

Mac Low, Mordecai-Mark; Burkert, Andreas; Ibáñez-Mejía, Juan C., E-mail: mordecai@amnh.org, E-mail: burkert@usm.lmu.de, E-mail: ibanez@ph1.uni-koeln.de

A large fraction of the gas in the Galaxy is cold, dense, and molecular. If all this gas collapsed under the influence of gravity and formed stars in a local free-fall time, the star formation rate in the Galaxy would exceed that observed by more than an order of magnitude. Other star-forming galaxies behave similarly. Yet, observations and simulations both suggest that the molecular gas is indeed gravitationally collapsing, albeit hierarchically. Prompt stellar feedback offers a potential solution to the low observed star formation rate if it quickly disrupts star-forming clouds during gravitational collapse. However, this requires that molecular cloudsmore » must be short-lived objects, raising the question of how so much gas can be observed in the molecular phase. This can occur only if molecular clouds form as quickly as they are destroyed, maintaining a global equilibrium fraction of dense gas. We therefore examine cloud formation timescales. We first demonstrate that supernova and superbubble sweeping cannot produce dense gas at the rate required to match the cloud destruction rate. On the other hand, Toomre gravitational instability can reach the required production rate. We thus argue that, although dense, star-forming gas may last only around a single global free-fall time; the dense gas in star-forming galaxies can globally exist in a state of dynamic equilibrium between formation by gravitational instability and disruption by stellar feedback. At redshift z ≳ 2, the Toomre instability timescale decreases, resulting in a prediction of higher molecular gas fractions at early times, in agreement with the observations.« less

Integration of G protein α (Gα) signaling by the regulator of G protein signaling 14 (RGS14).

PubMed

Brown, Nicole E; Goswami, Devrishi; Branch, Mary Rose; Ramineni, Suneela; Ortlund, Eric A; Griffin, Patrick R; Hepler, John R

2015-04-03

RGS14 contains distinct binding sites for both active (GTP-bound) and inactive (GDP-bound) forms of Gα subunits. The N-terminal regulator of G protein signaling (RGS) domain binds active Gαi/o-GTP, whereas the C-terminal G protein regulatory (GPR) motif binds inactive Gαi1/3-GDP. The molecular basis for how RGS14 binds different activation states of Gα proteins to integrate G protein signaling is unknown. Here we explored the intramolecular communication between the GPR motif and the RGS domain upon G protein binding and examined whether RGS14 can functionally interact with two distinct forms of Gα subunits simultaneously. Using complementary cellular and biochemical approaches, we demonstrate that RGS14 forms a stable complex with inactive Gαi1-GDP at the plasma membrane and that free cytosolic RGS14 is recruited to the plasma membrane by activated Gαo-AlF4(-). Bioluminescence resonance energy transfer studies showed that RGS14 adopts different conformations in live cells when bound to Gα in different activation states. Hydrogen/deuterium exchange mass spectrometry revealed that RGS14 is a very dynamic protein that undergoes allosteric conformational changes when inactive Gαi1-GDP binds the GPR motif. Pure RGS14 forms a ternary complex with Gαo-AlF4(-) and an AlF4(-)-insensitive mutant (G42R) of Gαi1-GDP, as observed by size exclusion chromatography and differential hydrogen/deuterium exchange. Finally, a preformed RGS14·Gαi1-GDP complex exhibits full capacity to stimulate the GTPase activity of Gαo-GTP, demonstrating that RGS14 can functionally engage two distinct forms of Gα subunits simultaneously. Based on these findings, we propose a working model for how RGS14 integrates multiple G protein signals in host CA2 hippocampal neurons to modulate synaptic plasticity. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Method of forming a multiple layer dielectric and a hot film sensor therewith

NASA Technical Reports Server (NTRS)

Hopson, Purnell, Jr. (Inventor); Tran, Sang Q. (Inventor)

1990-01-01

The invention is a method of forming a multiple layer dielectric for use in a hot-film laminar separation sensor. The multiple layer dielectric substrate is formed by depositing a first layer of a thermoelastic polymer such as on an electrically conductive substrate such as the metal surface of a model to be tested under cryogenic conditions and high Reynolds numbers. Next, a second dielectric layer of fused silica is formed on the first dielectric layer of thermoplastic polymer. A resistive metal film is deposited on selected areas of the multiple layer dielectric substrate to form one or more hot-film sensor elements to which aluminum electrical circuits deposited upon the multiple layered dielectric substrate are connected.

Density functional theory calculation of refractive indices of liquid-forming silicon oil compounds

NASA Astrophysics Data System (ADS)

Lee, Sanghun; Park, Sung Soo; Hagelberg, Frank

2012-02-01

A combination of quantum chemical calculation and molecular dynamics simulation is applied to compute refractive indices of liquid-forming silicon oils. The densities of these species are obtained from molecular dynamics simulations based on the NPT ensemble while the molecular polarizabilities are evaluated by density functional theory. This procedure is shown to yield results well compatible with available experimental data, suggesting that it represents a robust and economic route for determining the refractive indices of liquid-forming organic complexes containing silicon.

Direct observation of sequential oxidations of a titania-bound molecular proxy catalyst generated through illumination of molecular sensitizers

NASA Astrophysics Data System (ADS)

Chen, Hsiang-Yun; Ardo, Shane

2018-01-01

Natural photosynthesis uses the energy in sunlight to oxidize or reduce reaction centres multiple times, therefore preparing each reaction centre for a multiple-electron-transfer reaction that will ultimately generate stable reaction products. This process relies on multiple chromophores per reaction centre to quickly generate the active state of the reaction centre and to outcompete deleterious charge recombination. Using a similar design principle, we report spectroscopic evidence for the generation of a twice-oxidized TiO2-bound molecular proxy catalyst after low-intensity visible-light excitation of co-anchored molecular Ru(II)-polypyridyl dyes. Electron transfer from an excited dye to TiO2 generated a Ru(III) state that subsequently and repeatedly reacted with neighbouring Ru(II) dyes via self-exchange electron transfer to ultimately oxidize a distant co-anchored proxy catalyst before charge recombination. The largest yield for twice-oxidized proxy catalysts occurred when they were present at low coverage, suggesting that large dye/electrocatalyst ratios are also desired in dye-sensitized photoelectrochemical cells.

Selenium/Tellurium-Containing Hyperbranched Polymers: Effect of Molecular Weight and Degree of Branching on Glutathione Peroxidase-Like Activity.

PubMed

Thomas, Joice; Dong, Zeyuan; Dehaen, Wim; Smet, Mario

2012-12-21

A series of novel hyperbranched polyselenides and polytellurides with multiple catalytic sites at the branching units has been synthesized via the polycondensation of A2 + B3 monomers. The GPx-like activities of these polymer mimics were assessed and it was found that the polytellurides showed higher GPx-like activities than the corresponding polyselenides. Interestingly, the polymers with higher molecular weights and degree of branching (DB) showed higher GPx-like activities than the analogous lower molecular weight polymer. The enhancement in the catalytical activity of the hyperbranched polymers with increasing molecular weight affirmed the importance of the incorporation of multiple catalytic groups in the macromolecule which increases the local concentration of catalytic sites. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular-specific urokinase antibodies

NASA Technical Reports Server (NTRS)

Atassi, M. Zouhair (Inventor); Morrison, Dennis R. (Inventor)

2009-01-01

Antibodies have been developed against the different molecular forms of urokinase using synthetic peptides as immunogens. The peptides were synthesized specifically to represent those regions of the urokinase molecules which are exposed in the three-dimensional configuration of the molecule and are uniquely homologous to urokinase. Antibodies are directed against the lysine 158-isoleucine 159 peptide bond which is cleaved during activation from the single-chain (ScuPA) form to the bioactive double chain (54 KDa and 33 KDa) forms of urokinase and against the lysine 135 lysine 136 bond that is cleaved in the process of removing the alpha-chain from the 54 KDa form to produce the 33 KDa form of urokinase. These antibodies enable the direct measurement of the different molecular forms of urokinase from small samples of conditioned medium harvested from cell cultures.

Multiple core-hole formation by free-electron laser radiation in molecular nitrogen

NASA Astrophysics Data System (ADS)

Banks, H. I. B.; Little, D. A.; Emmanouilidou, A.

2018-05-01

We investigate the formation of multiple-core-hole states of molecular nitrogen interacting with a free-electron laser pulse. In previous work, we obtained bound and continuum molecular orbitals in the single-center expansion scheme and used these orbitals to calculate photo-ionization and auger decay rates. We extend our formulation to track the proportion of the population that accesses single-site versus two-site double-core-hole (TSDCH) states, before the formation of the final atomic ions. We investigate the pulse parameters that favor the formation of the single-site and TSDCH as well as triple-core-hole states for 525 and 1100 eV photons.

The xyloglucan-cellulose assembly at the atomic scale.

PubMed

Hanus, Jaroslav; Mazeau, Karim

2006-05-01

The assembly of cell wall components, cellulose and xyloglucan (XG), was investigated at the atomistic scale using molecular dynamics simulations. A molecular model of a cellulose crystal corresponding to the allomorph Ibeta and exhibiting a flexible complex external morphology was employed to mimic the cellulose microfibril. The xyloglucan molecules considered were the three typical basic repeat units, differing only in the size of one of the lateral chain. All the investigated XG fragments adsorb nonspecifically onto cellulose fiber; multiple arrangements are equally probable, and every cellulose surface was capable of binding the short XG molecules. The following structural effects emerged: XG molecules that do not have any long side chains tended to adapt themselves nicely to the topology of the microfibril, forming a flat, outstretched conformation with all the sugar residues interacting with the surface. In contrast, the XG molecules, which have long side chains, were not able to adopt a flat conformation that would enable the interaction of all the XG residues with the surface. In addition to revealing the fundamental atomistic details of the XG adsorption on cellulose, the present calculations give a comprehensive understanding of the way the XG molecules can unsorb from cellulose to create a network that forms the cell wall. Our revisited view of the adsorption features of XG on cellulose microfibrils is consistent with experimental data, and a model of the network is proposed. Copyright (c) 2006 Wiley Periodicals, Inc.

Next-Generation of Allergen-Specific Immunotherapies: Molecular Approaches.

PubMed

Curin, Mirela; Khaitov, Musa; Karaulov, Alexander; Namazova-Baranova, Leyla; Campana, Raffaela; Garib, Victoria; Valenta, Rudolf

2018-06-09

The aim of this article is to discuss how allergen-specific immunotherapy (AIT) can be improved through molecular approaches. We provide a summary of next-generation molecular AIT approaches and of their clinical evaluation. Furthermore, we discuss the potential of next generation molecular AIT forms for the treatment of severe manifestations of allergy and mention possible future molecular strategies for the secondary and primary prevention of allergy. AIT has important advantages over symptomatic forms of allergy treatment but its further development is limited by the quality of the therapeutic antigen preparations which are derived from natural allergen sources. The field of allergy diagnosis is currently undergoing a dramatic improvement through the use of molecular testing with defined, mainly recombinant allergens which allows high-resolution diagnosis. Several studies demonstrate that molecular testing in early childhood can predict the development of symptomatic allergy later on in life. Clinical studies indicate that molecular AIT approaches have the potential to improve therapy of allergic diseases and may be used as allergen-specific forms of secondary and eventually primary prevention for allergy.

[Use of multiple locus variable number tandem repeats analysis for the Brucella systematization].

PubMed

Kulakov, Iu K; Kovalev, D A; Misetova, E N; Golovneva, S I; Liapustina, L V; Zheludkov, M M

2012-01-01

The methods of molecular-genetic differentiation to strain level acquire increasing significance in the current system of struggle with brucellosis. MLVA (multiple locus variable number tandem repeats analysis) was selected for molecular-genetic differentiation to strain level and simultaneous establishment of the genetic relationship of investigated Brucella strains. The goal of this work was MLVA typing of three pathogenic Brucella species strains with the analysis of stability of chosen loci, discrimination power and concordance to conventional phenotypic methods of the Brucella differentiation for use in systematization of brucellosis causing agents. Twenty six Brucella strains representing reference (n = 15), vaccine (n = 2) and field strains of three pathogenic Brucella species were tested: B. melitensis (n = 3), B. abortus (n = 2), B. suis (n = 2), and isolates (n = 2) with unidentified taxonomic position using MLVA with 9 pairs primers on known variable loci of Brucella genome. The analysis of the stability of chosen loci, discrimination power on Hunter-Gaston discrimination index (HGDI) and consistency to phenotypic methods of identification was performed. MLVA was confirmed for the results of phenotypic methods of identification, stability of the chosen loci in majority reference, and vaccine strains with a high index of variability HGDI 0.9969 for all loci. A dendrogram was plotted on the basis of MLVA data on distributed Brucella strains in related clusters according to its taxonomic species and biovar positions and construction of 25 genotypes. B. melitensis strains formed cluster related to the reference strain of B. melitensis 63/9 biovar 2. Australian isolates of Brucella 83-4 and Brucella 83-6 isolated from rodents formed a cluster distant from other strains of Brucella. MLVA is a promising method for differentiation of Brucella strains with known and unresolved taxonomic status for their systematization and creation of MLVA genotype catalogue that will promote qualitative improvement of brucellosis surveillance system in Russia.

Multifunctional nanoparticle-protein conjugates with controllable bioactivity and pH responsiveness

NASA Astrophysics Data System (ADS)

Liu, Feng; Xue, Lulu; Yuan, Yuqi; Pan, Jingjing; Zhang, Chenjie; Wang, Hongwei; Brash, John L.; Yuan, Lin; Chen, Hong

2016-02-01

The modulation of protein activity is of significance for disease therapy, molecular diagnostics, and tissue engineering. Nanoparticles offer a new platform for the preparation of protein conjugates with improved protein properties. In the present work, Escherichia coli (E. coli) inorganic pyrophosphatase (PPase) and poly(methacrylic acid) (PMAA) were attached together to gold nanoparticles (AuNPs), forming AuNP-PPase-PMAA conjugates having controllable multi-biofunctionalities and responsiveness to pH. By treating with poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA) and regulating the pH, the bioactivity of the conjugate becomes ``on/off''-switchable. In addition, by taking advantage of the ability of AuNPs to undergo reversible aggregation/dispersion, the conjugates can be recycled and reused multiple times; and due to the shielding effect of the PMAA, the conjugated enzyme has high resistance to protease digestion. This approach has considerable potential in areas such as controlled delivery and release of drugs, biosensing, and biocatalysis.The modulation of protein activity is of significance for disease therapy, molecular diagnostics, and tissue engineering. Nanoparticles offer a new platform for the preparation of protein conjugates with improved protein properties. In the present work, Escherichia coli (E. coli) inorganic pyrophosphatase (PPase) and poly(methacrylic acid) (PMAA) were attached together to gold nanoparticles (AuNPs), forming AuNP-PPase-PMAA conjugates having controllable multi-biofunctionalities and responsiveness to pH. By treating with poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA) and regulating the pH, the bioactivity of the conjugate becomes ``on/off''-switchable. In addition, by taking advantage of the ability of AuNPs to undergo reversible aggregation/dispersion, the conjugates can be recycled and reused multiple times; and due to the shielding effect of the PMAA, the conjugated enzyme has high resistance to protease digestion. This approach has considerable potential in areas such as controlled delivery and release of drugs, biosensing, and biocatalysis. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr07436c

Fragmentation of organic ions bearing fixed multiple charges observed in MALDI MS.

PubMed

Lou, Xianwen; Li, Bao; de Waal, Bas F M; Schill, Jurgen; Baker, Matthew B; Bovee, Ralf A A; van Dongen, Joost L J; Milroy, Lech-Gustav; Meijer, E W

2018-01-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) was used to analyze a series of synthetic organic ions bearing fixed multiple charges. Despite the multiple intrinsic charges, only singly charged ions were recorded in each case. In addition to the pseudo-molecular ions formed by counterion adduction, deprotonation and electron capture, a number of fragment ions were also observed. Charge splitting by fragmentation was found to be a viable route for charge reduction leading to the formation of the observed singly charged fragment ions. Unlike multivalent metal ions, organic ions can rearrange and/or fragment during charge reduction. This fragmentation process will evidently complicate the interpretation of the MALDI MS spectrum. Because MALDI MS is usually considered as a soft ionization technique, the fragment ion peaks can easily be erroneously interpreted as impurities. Therefore, the awareness and understanding of the underlying MALDI-induced fragmentation pathways is essential for a proper interpretation of the corresponding mass spectra. Due to the fragment ions generated during charge reduction, special care should be taken in the MALDI MS analysis of multiply charged ions. In this work, the possible mechanisms by which the organic ions bearing fixed multiple charges fragment are investigated. With an improved understanding of the fragmentation mechanisms, MALDI TOF MS should still be a useful technique for the characterization of organic ions with fixed multiple charges. Copyright © 2017 John Wiley & Sons, Ltd.

Development and application of an algorithm to compute weighted multiple glycan alignments.

PubMed

Hosoda, Masae; Akune, Yukie; Aoki-Kinoshita, Kiyoko F

2017-05-01

A glycan consists of monosaccharides linked by glycosidic bonds, has branches and forms complex molecular structures. Databases have been developed to store large amounts of glycan-binding experiments, including glycan arrays with glycan-binding proteins. However, there are few bioinformatics techniques to analyze large amounts of data for glycans because there are few tools that can handle the complexity of glycan structures. Thus, we have developed the MCAW (Multiple Carbohydrate Alignment with Weights) tool that can align multiple glycan structures, to aid in the understanding of their function as binding recognition molecules. We have described in detail the first algorithm to perform multiple glycan alignments by modeling glycans as trees. To test our tool, we prepared several data sets, and as a result, we found that the glycan motif could be successfully aligned without any prior knowledge applied to the tool, and the known recognition binding sites of glycans could be aligned at a high rate amongst all our datasets tested. We thus claim that our tool is able to find meaningful glycan recognition and binding patterns using data obtained by glycan-binding experiments. The development and availability of an effective multiple glycan alignment tool opens possibilities for many other glycoinformatics analysis, making this work a big step towards furthering glycomics analysis. http://www.rings.t.soka.ac.jp. kkiyoko@soka.ac.jp. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Family matters: The first molecular phylogeny of the Onchidorididae Gray, 1827 (Mollusca, Gastropoda, Nudibranchia).

PubMed

Hallas, Joshua M; Gosliner, Terrence M

2015-07-01

Recent investigations into the evolution of the Onchidorididae using morphological based methods have resulted in low support for relationships among genera. This study aims to determine if molecular data corroborates recent morphological interpretations of the evolution of Onchidorididae. Five genetic markers: 16S, 18S, 28S, cytochrome c oxidase 1 (COI) and histone 3 (H3), were sequenced from 32 species comprising Onchidorididae and five other families, three from Phanerobranchia and two from Cryptobranchia. Phylogenies were estimated using maximum likelihood, and Bayesian inference analyses; with both yielding similar topologies. Molecular analyses resulted in high support for the monophyly of the suctorian clade and the placement of the genera within Onchidorididae. However, the Onchidorididae forms a paraphyletic grouping due to the recovery of the Goniodorididae and the Akiodorididae nested within family. In addition, the placement of Corambe as the most derived member of Onchidorididae is contradicted by the present study. Rather it is sister to a large clade that includes Acanthodoris and the species traditionally placed in Onchidoris and Adalaria, now defined as Onchidorididae. We have chosen to maintain Corambidae as a distinct taxon (including Corambe and Loy), sister to Onchidorididae. We also maintain Goniodorididae, Akiodorididae and Calycidoridae (including Calycidoris and Diaphorodoris), which along with the Onchidorididae and Corambidae comprise the suctorian superfamily Onchidoridoidea. Ancestral character reconstruction also suggests that the formation of a gill pocket, a character that currently defines the Cryptobranchia, may have evolved multiple times from an ancestor that lacked the ability to retract its gills into a fully formed gill pocket. The diversity of gill morphology displayed by the Onchidoridoidea will help give new insight into the evolution of this complex character within the Nudibranchia. Copyright © 2015 Elsevier Inc. All rights reserved.

ALMA observations of atomic carbon in z ˜ 4 dusty star-forming galaxies

NASA Astrophysics Data System (ADS)

Bothwell, M. S.; Aguirre, J. E.; Aravena, M.; Bethermin, M.; Bisbas, T. G.; Chapman, S. C.; De Breuck, C.; Gonzalez, A. H.; Greve, T. R.; Hezaveh, Y.; Ma, J.; Malkan, M.; Marrone, D. P.; Murphy, E. J.; Spilker, J. S.; Strandet, M.; Vieira, J. D.; Weiß, A.

2017-04-01

We present Atacama Large Millimeter Array [C I](1 - 0) (rest frequency 492 GHz) observations for a sample of 13 strongly lensed dusty star-forming galaxies (DSFGs) originally discovered at 1.4 mm in a blank-field survey by the South Pole Telescope (SPT). We compare these new data with available [C I] observations from the literature, allowing a study of the interstellar medium (ISM) properties of ˜30 extreme DSFGs spanning a redshift range 2 < z < 5. Using the [C I] line as a tracer of the molecular ISM, we find a mean molecular gas mass for SPT-DSFGs of 6.6 × 1010 M⊙. This is in tension with gas masses derived via low-J 12CO and dust masses; bringing the estimates into accordance requires either (a) an elevated CO-to-H2 conversion factor for our sample of αCO ˜ 2.5 and a gas-to-dust ratio ˜200, or (b) an high carbon abundance X_{C I} ˜ 7× 10^{-5}. Using observations of a range of additional atomic and molecular lines (including [C I], [C II]and multiple transitions of CO), we use a modern photodissociation region code (3D-PDR) to assess the physical conditions (including the density, UV radiation field strength and gas temperature) within the ISM of the DSFGs in our sample. We find that the ISM within our DSFGs is characterized by dense gas permeated by strong UV fields. We note that previous efforts to characterize photodissociation region regions in DSFGs may have significantly under-estimated the density of the ISM. Combined, our analysis suggests that the ISM of extreme dusty starbursts at high redshift consists of dense, carbon-rich gas not directly comparable to the ISM of starbursts in the local Universe.

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

Bally, John; Ginsburg, Adam; Probst, Ron

We present observations of near-infrared 2.12 μm molecular hydrogen outflows emerging from 1.1 mm dust continuum clumps in the North America and Pelican Nebula (NAP) complex selected from the Bolocam Galactic Plane Survey (BGPS). Hundreds of individual shocks powered by over 50 outflows from young stars are identified, indicating that the dusty molecular clumps surrounding the NGC 7000/IC 5070/W80 H II region are among the most active sites of ongoing star formation in the solar vicinity. A spectacular X-shaped outflow, MHO 3400, emerges from a young star system embedded in a dense clump more than a parsec from the ionizationmore » front associated with the Pelican Nebula (IC 5070). Suspected to be a binary, the source drives a pair of outflows with orientations differing by 80°. Each flow exhibits S-shaped symmetry and multiple shocks indicating a pulsed and precessing jet. The 'Gulf of Mexico', located south of the North America Nebula (NGC 7000), contains a dense cluster of molecular hydrogen objects (MHOs), Herbig-Haro (HH) objects, and over 300 young stellar objects (YSOs), indicating a recent burst of star formation. The largest outflow detected thus far in the North America and Pelican Nebula complex, the 1.6 parsec long MHO 3417 flow, emerges from a 500 M {sub ☉} BGPS clump and may be powered by a forming massive star. Several prominent outflows such as MHO 3427 appear to be powered by highly embedded YSOs only visible at λ > 70 μm. An 'activity index' formed by dividing the number of shocks by the mass of the cloud containing their source stars is used to estimate the relative evolutionary states of Bolocam clumps. Outflows can be used as indicators of the evolutionary state of clumps detected in millimeter and submillimeter dust continuum surveys.« less

Molecular characterization, biological forms and sporozoite rate of Anopheles stephensi in southern Iran

PubMed Central

Chavshin, Ali Reza; Oshaghi, Mohammad Ali; Vatandoost, Hasan; Hanafi-Bojd, Ahmad Ali; Raeisi, Ahmad; Nikpoor, Fatemeh

2014-01-01

Objective To identify the biological forms, sporozoite rate and molecular characterization of the Anopheles stephensi (An. stephensi) in Hormozgan and Sistan-Baluchistan provinces, the most important malarious areas in Iran. Methods Wild live An. stephensi samples were collected from different malarious areas in southern Iran. The biological forms were identified based on number of egg-ridges. Molecular characterization of biological forms was verified by analysis of the mitochondrial cytochrome oxidase subunit I and II (mtDNA-COI/COII). The Plasmodium infection was examined in the wild female specimens by species-specific nested–PCR method. Results Results showed that all three biological forms including mysorensis, intermediate and type are present in the study areas. Molecular investigations revealed no genetic variation between mtDNA COI/COII sequences of the biological forms and no Plasmodium parasites was detected in the collected mosquito samples. Conclusions Presence of three biological forms with identical sequences showed that the known biological forms belong to a single taxon and the various vectorial capacities reported for these forms are more likely corresponded to other epidemiological factors than to the morphotype of the populations. Lack of malaria parasite infection in An. stephensi, the most important vector of malaria, may be partly due to the success and achievement of ongoing active malaria control program in the region. PMID:24144130

Schizophrenia-associated methylomic variation: molecular signatures of disease and polygenic risk burden across multiple brain regions.

PubMed

Viana, Joana; Hannon, Eilis; Dempster, Emma; Pidsley, Ruth; Macdonald, Ruby; Knox, Olivia; Spiers, Helen; Troakes, Claire; Al-Saraj, Safa; Turecki, Gustavo; Schalkwyk, Leonard C; Mill, Jonathan

2017-01-01

Genetic association studies provide evidence for a substantial polygenic component to schizophrenia, although the neurobiological mechanisms underlying the disorder remain largely undefined. Building on recent studies supporting a role for developmentally regulated epigenetic variation in the molecular aetiology of schizophrenia, this study aimed to identify epigenetic variation associated with both a diagnosis of schizophrenia and elevated polygenic risk burden for the disease across multiple brain regions. Genome-wide DNA methylation was quantified in 262 post-mortem brain samples, representing tissue from four brain regions (prefrontal cortex, striatum, hippocampus and cerebellum) from 41 schizophrenia patients and 47 controls. We identified multiple disease-associated and polygenic risk score-associated differentially methylated positions and regions, which are not enriched in genomic regions identified in genetic studies of schizophrenia and do not reflect direct genetic effects on DNA methylation. Our study represents the first analysis of epigenetic variation associated with schizophrenia across multiple brain regions and highlights the utility of polygenic risk scores for identifying molecular pathways associated with aetiological variation in complex disease. © The Author 2016. Published by Oxford University Press.

Altered proteomic polymorphisms in the caterpillar body and stroma of natural Cordyceps sinensis during maturation.

PubMed

Dong, Yun-Zi; Zhang, Li-Juan; Wu, Zi-Mei; Gao, Ling; Yao, Yi-Sang; Tan, Ning-Zhi; Wu, Jian-Yong; Ni, Luqun; Zhu, Jia-Shi

2014-01-01

To examine the maturational changes in proteomic polymorphisms resulting from differential expression by multiple intrinsic fungi in the caterpillar body and stroma of natural Cordyceps sinensis (Cs), an integrated micro-ecosystem. The surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) biochip technique was used to profile the altered protein compositions in the caterpillar body and stroma of Cs during its maturation. The MS chromatograms were analyzed using density-weighted algorithms to examine the similarities and cluster relationships among the proteomic polymorphisms of the Cs compartments and the mycelial products Hirsutella sinensis (Hs) and Paecilomyces hepiali (Ph). SELDI-TOF MS chromatograms displayed dynamic proteomic polymorphism alterations among samples from the different Cs compartments during maturation. More than 1,900 protein bands were analyzed using density-weighted ZUNIX similarity equations and clustering methods, revealing integral polymorphism similarities of 57.4% between the premature and mature stromata and 42.8% between the premature and mature caterpillar bodies. The across-compartment similarity was low, ranging from 10.0% to 18.4%. Consequently, each Cs compartment (i.e., the stroma and caterpillar body) formed a clustering clade, and the 2 clades formed a Cs cluster. The polymorphic similarities ranged from 0.51% to 1.04% between Hs and the Cs compartments and were 2.8- to 4.8-fold higher (1.92%-4.34%) between Ph and the Cs compartments. The Hs and Ph mycelial samples formed isolated clades outside of the Cs cluster. Proteomic polymorphisms in the caterpillar body and stroma of Cs change dynamically during maturation. The proteomic polymorphisms in Hs and Ph differ from those in Cs, suggesting the presence of multiple Cs-associated fungi and multiple Ophiocordyceps sinensis genotypes with altered differential protein expression in the Cs compartments during maturation. In conjunction with prior mycological and molecular observations, the findings from this proteomic study support the integrated micro-ecosystem hypothesis for natural Cs.

Altered Proteomic Polymorphisms in the Caterpillar Body and Stroma of Natural Cordyceps sinensis during Maturation

PubMed Central

Wu, Zi-Mei; Gao, Ling; Yao, Yi-Sang; Tan, Ning-Zhi; Wu, Jian-Yong; Ni, Luqun; Zhu, Jia-Shi

2014-01-01

Objective To examine the maturational changes in proteomic polymorphisms resulting from differential expression by multiple intrinsic fungi in the caterpillar body and stroma of natural Cordyceps sinensis (Cs), an integrated micro-ecosystem. Methods The surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) biochip technique was used to profile the altered protein compositions in the caterpillar body and stroma of Cs during its maturation. The MS chromatograms were analyzed using density-weighted algorithms to examine the similarities and cluster relationships among the proteomic polymorphisms of the Cs compartments and the mycelial products Hirsutella sinensis (Hs) and Paecilomyces hepiali (Ph). Results: SELDI-TOF MS chromatograms displayed dynamic proteomic polymorphism alterations among samples from the different Cs compartments during maturation. More than 1,900 protein bands were analyzed using density-weighted ZUNIX similarity equations and clustering methods, revealing integral polymorphism similarities of 57.4% between the premature and mature stromata and 42.8% between the premature and mature caterpillar bodies. The across-compartment similarity was low, ranging from 10.0% to 18.4%. Consequently, each Cs compartment (i.e., the stroma and caterpillar body) formed a clustering clade, and the 2 clades formed a Cs cluster. The polymorphic similarities ranged from 0.51% to 1.04% between Hs and the Cs compartments and were 2.8- to 4.8-fold higher (1.92%–4.34%) between Ph and the Cs compartments. The Hs and Ph mycelial samples formed isolated clades outside of the Cs cluster. Conclusion Proteomic polymorphisms in the caterpillar body and stroma of Cs change dynamically during maturation. The proteomic polymorphisms in Hs and Ph differ from those in Cs, suggesting the presence of multiple Cs-associated fungi and multiple Ophiocordyceps sinensis genotypes with altered differential protein expression in the Cs compartments during maturation. In conjunction with prior mycological and molecular observations, the findings from this proteomic study support the integrated micro-ecosystem hypothesis for natural Cs. PMID:25310818

A Diagnostic Assessment for Introductory Molecular and Cell Biology

ERIC Educational Resources Information Center

Shi, Jia; Wood, William B.; Martin, Jennifer M.; Guild, Nancy A.; Vicens, Quentin; Knight, Jennifer K.

2010-01-01

We have developed and validated a tool for assessing understanding of a selection of fundamental concepts and basic knowledge in undergraduate introductory molecular and cell biology, focusing on areas in which students often have misconceptions. This multiple-choice Introductory Molecular and Cell Biology Assessment (IMCA) instrument is designed…

Empirical Refinements of a Molecular Genetics Learning Progression: The Molecular Constructs

ERIC Educational Resources Information Center

Todd, Amber; Kenyon, Lisa

2016-01-01

This article describes revisions to four of the eight constructs of the Duncan molecular genetics learning progression [Duncan, Rogat, & Yarden, (2009)]. As learning progressions remain hypothetical models until validated by multiple rounds of empirical studies, these revisions are an important step toward validating the progression. Our…

Star cluster formation in a turbulent molecular cloud self-regulated by photoionization feedback

NASA Astrophysics Data System (ADS)

Gavagnin, Elena; Bleuler, Andreas; Rosdahl, Joakim; Teyssier, Romain

2017-12-01

Most stars in the Galaxy are believed to be formed within star clusters from collapsing molecular clouds. However, the complete process of star formation, from the parent cloud to a gas-free star cluster, is still poorly understood. We perform radiation-hydrodynamical simulations of the collapse of a turbulent molecular cloud using the RAMSES-RT code. Stars are modelled using sink particles, from which we self-consistently follow the propagation of the ionizing radiation. We study how different feedback models affect the gas expulsion from the cloud and how they shape the final properties of the emerging star cluster. We find that the star formation efficiency is lower for stronger feedback models. Feedback also changes the high-mass end of the stellar mass function. Stronger feedback also allows the establishment of a lower density star cluster, which can maintain a virial or sub-virial state. In the absence of feedback, the star formation efficiency is very high, as well as the final stellar density. As a result, high-energy close encounters make the cluster evaporate quickly. Other indicators, such as mass segregation, statistics of multiple systems and escaping stars confirm this picture. Observations of young star clusters are in best agreement with our strong feedback simulation.

Performance Evaluation of NWChem Ab-Initio Molecular Dynamics (AIMD) Simulations on the Intel® Xeon Phi™ Processor

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

Bylaska, Eric J.; Jacquelin, Mathias; De Jong, Wibe A.

2017-10-20

Ab-initio Molecular Dynamics (AIMD) methods are an important class of algorithms, as they enable scientists to understand the chemistry and dynamics of molecular and condensed phase systems while retaining a first-principles-based description of their interactions. Many-core architectures such as the Intel® Xeon Phi™ processor are an interesting and promising target for these algorithms, as they can provide the computational power that is needed to solve interesting problems in chemistry. In this paper, we describe the efforts of refactoring the existing AIMD plane-wave method of NWChem from an MPI-only implementation to a scalable, hybrid code that employs MPI and OpenMP tomore » exploit the capabilities of current and future many-core architectures. We describe the optimizations required to get close to optimal performance for the multiplication of the tall-and-skinny matrices that form the core of the computational algorithm. We present strong scaling results on the complete AIMD simulation for a test case that simulates 256 water molecules and that strong-scales well on a cluster of 1024 nodes of Intel Xeon Phi processors. We compare the performance obtained with a cluster of dual-socket Intel® Xeon® E5–2698v3 processors.« less

High-throughput Molecular Simulations of MOFs for CO2 Separation: Opportunities and Challenges

NASA Astrophysics Data System (ADS)

Erucar, Ilknur; Keskin, Seda

2018-02-01

Metal organic frameworks (MOFs) have emerged as great alternatives to traditional nanoporous materials for CO2 separation applications. MOFs are porous materials that are formed by self-assembly of transition metals and organic ligands. The most important advantage of MOFs over well-known porous materials is the possibility to generate multiple materials with varying structural properties and chemical functionalities by changing the combination of metal centers and organic linkers during the synthesis. This leads to a large diversity of materials with various pore sizes and shapes that can be efficiently used for CO2 separations. Since the number of synthesized MOFs has already reached to several thousand, experimental investigation of each MOF at the lab-scale is not practical. High-throughput computational screening of MOFs is a great opportunity to identify the best materials for CO2 separation and to gain molecular-level insights into the structure-performance relationships. This type of knowledge can be used to design new materials with the desired structural features that can lead to extraordinarily high CO2 selectivities. In this mini-review, we focused on developments in high-throughput molecular simulations of MOFs for CO2 separations. After reviewing the current studies on this topic, we discussed the opportunities and challenges in the field and addressed the potential future developments.

Molecular structure, vibrational spectra, NBO analysis, first hyperpolarizability, and HOMO-LUMO studies of 2-amino-4-hydroxypyrimidine by density functional method

NASA Astrophysics Data System (ADS)

Jeyavijayan, S.

2015-04-01

This study is a comparative analysis of FTIR and FT-Raman spectra of 2-amino-4-hydroxypyrimidine. The total energies of different conformations have been obtained from DFT (B3LYP) method with 6-31+G(d,p) and 6-311++G(d,p) basis sets. The barrier of planarity between the most stable and planar form is also predicted. The molecular structure, vibrational wavenumbers, infrared intensities, Raman scattering activities were calculated for the molecule using the B3LYP density functional theory (DFT) method. The computed values of frequencies are scaled using multiple scaling factors to yield good coherence with the observed values. Reliable vibrational assignments were made on the basis of total energy distribution (TED) along with scaled quantum mechanical (SQM) method. The stability of the molecule arising from hyperconjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Non-linear properties such as electric dipole moment (μ), polarizability (α), and hyperpolarizability (β) values of the investigated molecule have been computed using B3LYP quantum chemical calculation. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Besides, molecular electrostatic potential (MEP), Mulliken's charges analysis, and several thermodynamic properties were performed by the DFT method.

Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides* #

PubMed Central

Yu, Hua; Wang, Mao-Jun; Xuan, Nan-Xia; Shang, Zhi-Cai; Wu, Jun

2015-01-01

Objective: To provide essential information for peptide inhibitor design, the interactions of Eps15 homology domain of Eps15 homology domain-containing protein 1 (EHD1 EH domain) with three peptides containing NPF (asparagine-proline-phenylalanine), DPF (aspartic acid-proline-phenylalanine), and GPF (glycine-proline-phenylalanine) motifs were deciphered at the atomic level. The binding affinities and the underlying structure basis were investigated. Methods: Molecular dynamics (MD) simulations were performed on EHD1 EH domain/peptide complexes for 60 ns using the GROMACS package. The binding free energies were calculated and decomposed by molecular mechanics/generalized Born surface area (MM/GBSA) method using the AMBER package. The alanine scanning was performed to evaluate the binding hot spot residues using FoldX software. Results: The different binding affinities for the three peptides were affected dominantly by van der Waals interactions. Intermolecular hydrogen bonds provide the structural basis of contributions of van der Waals interactions of the flanking residues to the binding. Conclusions: van der Waals interactions should be the main consideration when we design peptide inhibitors of EHD1 EH domain with high affinities. The ability to form intermolecular hydrogen bonds with protein residues can be used as the factor for choosing the flanking residues. PMID:26465136

A highly selective and picomolar level photoelectrochemical sensor for PCB 101 detection in environmental water samples.

PubMed

Shi, Huijie; Zhao, Jinzhi; Wang, Yingling; Zhao, Guohua

2016-07-15

A highly selective and sensitive photoelectrochemical (PEC) sensor was fabricated for fast and convenient detection of PCB 101 in environmental water samples with a low detection limit of 1.0×10(-14)molL(-1) based on single crystalline TiO2 nanorods (NRs). By integration with molecular imprinting (MI) technique, the PEC sensor's selectivity towards PCB 101 was significantly improved, so that the interference caused by 100-fold excess of PCB 126 and PCB 77 which had similar structure with PCB 101 was below 37%, not to mention other coexisted pollutants. This high selectivity could be attributed to the high-quality expression of the molecular imprinting sites on the rigid and smooth surface of single crystalline TiO2 NRs on which PCB 101 could be selectively and preferentially adsorbed. The oriented and multiple halogen bonds formed between PCB 101 and the molecular imprinting sites played a critical role in improving the recognition ability of the PEC sensor. Meanwhile, the one dimensional nanorods structure of TiO2 was beneficial for the efficient separation of photogenerated electrons and holes, leading to enhanced photocurrent response and further improving the sensitivity of the PEC sensor. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular dynamics of alamethicin transmembrane channels from open-channel current noise analysis.

PubMed

Mak, D O; Webb, W W

1995-12-01

Conductance noise measurement of the open states of alamethicin transmembrane channels reveals excess noise attributable to cooperative low-frequency molecular dynamics that can generate fluctuations approximately 1 A rms in the effective channel pore radius. Single-channel currents through both persistent and nonpersistent channels with multiple conductance states formed by purified polypeptide alamethicin in artificial phospholipid bilayers isolated onto micropipettes with gigaohm seals were recorded using a voltage-clamp technique with low background noise (rms noise < 3 pA up to 20 kHz). Current noise power spectra between 100 Hz and 20 kHz of each open channel state showed little frequency dependence. Noise from undetected conductance state transitions was insignificant. Johnson and shot noises were evaluated. Current noise caused by electrolyte concentration fluctuation via diffusion was isolated by its dependence on buffer concentration. After removing these contributions, significant current noise remains in all persistent channel states and increases in higher conductance states. In nonpersistent channels, remaining noise occurs primarily in the lowest two states. These fluctuations of channel conductance are attributed to thermal oscillations of the channel molecular conformation and are modeled as a Langevin translational oscillation of alamethicin molecules moving radially from the channel pore, damped mostly by lipid bilayer viscosity.

An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis*

PubMed Central

Kayode, Olumide; Wang, Ruiying; Pendlebury, Devon F.; Cohen, Itay; Henin, Rachel D.; Hockla, Alexandra; Soares, Alexei S.; Papo, Niv; Caulfield, Thomas R.; Radisky, Evette S.

2016-01-01

The molecular basis of enzyme catalytic power and specificity derives from dynamic interactions between enzyme and substrate during catalysis. Although considerable effort has been devoted to understanding how conformational dynamics within enzymes affect catalysis, the role of conformational dynamics within protein substrates has not been addressed. Here, we examine the importance of substrate dynamics in the cleavage of Kunitz-bovine pancreatic trypsin inhibitor protease inhibitors by mesotrypsin, finding that the varied conformational dynamics of structurally similar substrates can profoundly impact the rate of catalysis. A 1.4-Å crystal structure of a mesotrypsin-product complex formed with a rapidly cleaved substrate reveals a dramatic conformational change in the substrate upon proteolysis. By using long all-atom molecular dynamics simulations of acyl-enzyme intermediates with proteolysis rates spanning 3 orders of magnitude, we identify global and local dynamic features of substrates on the nanosecond-microsecond time scale that correlate with enzymatic rates and explain differential susceptibility to proteolysis. By integrating multiple enhanced sampling methods for molecular dynamics, we model a viable conformational pathway between substrate-like and product-like states, linking substrate dynamics on the nanosecond-microsecond time scale with large collective substrate motions on the much slower time scale of catalysis. Our findings implicate substrate flexibility as a critical determinant of catalysis. PMID:27810896

An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis

DOE PAGES

Kayode, Olumide; Wang, Ruiying; Pendlebury, Devon F.; ...

2016-11-03

The molecular basis of enzyme catalytic power and specificity derives from dynamic interactions between enzyme and substrate during catalysis. While considerable effort has been devoted to understanding how conformational dynamics within enzymes affect catalysis, the role of conformational dynamics within protein substrates has not been addressed. Here in this paper, we examine the importance of substrate dynamics in the cleavage of Kunitz-BPTI protease inhibitors by mesotrypsin, finding that the varied conformational dynamics of structurally similar substrates can profoundly impact the rate of catalysis. A 1.4 Å crystal structure of a mesotrypsin-product complex formed with a rapidly cleaved substrate reveals amore » dramatic conformational change in the substrate upon proteolysis. Using long all-atom molecular dynamics simulations of acyl-enzyme intermediates with proteolysis rates spanning three orders of magnitude, we identify global and local dynamic features of substrates on the ns-μs timescale that correlate with enzymatic rates and explain differential susceptibility to proteolysis. By integrating multiple enhanced sampling methods for molecular dynamics, we model a viable conformational pathway between substratelike and product-like states, linking substrate dynamics on the ns-μs timescale with large collective substrate motions on the much slower timescale of catalysis. Our findings implicate substrate flexibility as a critical determinant of catalysis.« less

Magnetic Behavior of a Dy8 Molecular Nanomagnet

NASA Astrophysics Data System (ADS)

Zhang, Qing; Sarachik, Myriam; Baker, Michael; Chen, Yizhang; Kent, Andrew; Stamatatos, Theocharis

2015-03-01

As part of a study of quantum tunneling in a newly synthesized family of dysprosium-based molecular magnets that exhibit a chiral spin structure, we report initial investigations of the magnetic response of a Dy8 cluster with the formula (Et4N)4[Dy8O(nd)8(NO3)10(H2O)2] .2MeCN. The molecular complex contains triangular arrangements of exchange coupled Dy(III) ions. The compound forms an approximate snub-square Archimedean lattice unit. The measured magnetization of this network of four triangles suggests the presence of multiple spin chiral vortexes. Single crystal susceptibility and magnetization measurements indicate the presence of a hard-axis direction and an easy plane. These principal orientations have been investigated in magnetic fields up to 5 Tesla for temperatures between 1.8 and 100 K using a SQUID-based Quantum Design MPMS magnetometer. Complex easy plane magnetic hysteresis loops emerge at lower temperatures measured using Hall probe magnetometry at sub 1 K temperatures. The analysis of these measurements will be discussed and compared with results of theoretical calculations. Work supported by ARO W911NF-13-1-1025 (CCNY), NSF-DMR-1309202 (NYU); the synthesis of the Dy8 cluster was supported by NSERC (Discovery grant to Th.C.S.).

Observation of ambipolar switching in a silver nanoparticle single-electron transistor with multiple molecular floating gates

NASA Astrophysics Data System (ADS)

Yamamoto, Makoto; Shinohara, Shuhei; Tamada, Kaoru; Ishii, Hisao; Noguchi, Yutaka

2016-03-01

Ambipolar switching behavior was observed in a silver nanoparticle (AgNP)-based single-electron transistor (SET) with tetra-tert-butyl copper phthalocyanine (ttbCuPc) as a molecular floating gate. Depending on the wavelength of the incident light, the stability diagram shifted to the negative and positive directions along the gate voltage axis. These results were explained by the photoinduced charging of ttbCuPc molecules in the vicinity of AgNPs. Moreover, multiple device states were induced by the light irradiation at a wavelength of 600 nm, suggesting that multiple ttbCuPc molecules individually worked as a floating gate.

Laser isotope separation by multiple photon absorption

DOEpatents

Robinson, C.P.; Rockwood, S.D.; Jensen, R.J.; Lyman, J.L.; Aldridge, J.P. III.

1987-04-07

Multiple photon absorption from an intense beam of infrared laser light may be used to induce selective chemical reactions in molecular species which result in isotope separation or enrichment. The molecular species must have a sufficient density of vibrational states in its vibrational manifold that, is the presence of sufficiently intense infrared laser light tuned to selectively excite only those molecules containing a particular isotope, multiple photon absorption can occur. By this technique, for example, intense CO[sub 2] laser light may be used to highly enrich [sup 34]S in natural SF[sub 6] and [sup 11]B in natural BCl[sub 3]. 8 figs.

Rapid Prototyping of Patterned Multifunctional Nanostructures

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

FAN,HONGYOU; LU,YUNFENG; LOPEZ,GABRIEL P.

2000-07-18

The ability to engineer ordered arrays of objects on multiple length scales has potential for applications such as microelectronics, sensors, wave guides, and photonic lattices with tunable band gaps. Since the invention of surfactant templated mesoporous sieves in 1992, great progress has been made in controlling different mesophases in the form of powders, particles, fibers, and films. To date, although there have been several reports of patterned mesostructures, materials prepared have been limited to metal oxides with no specific functionality. For many of the envisioned applications of hierarchical materials in micro-systems, sensors, waveguides, photonics, and electronics, it is necessary tomore » define both form and function on several length scales. In addition, the patterning strategies utilized so far require hours or even days for completion. Such slow processes are inherently difficult to implement in commercial environments. The authors present a series of new methods of producing patterns within seconds. Combining sol-gel chemistry, Evaporation-Induced Self-Assembly (EISA), and rapid prototyping techniques like pen lithography, ink-jet printing, and dip-coating on micro-contact printed substrates, they form hierarchically organized silica structures that exhibit order and function on multiple scales: on the molecular scale, functional organic moieties are positioned on pore surfaces, on the mesoscale, mono-sized pores are organized into 1-, 2-, or 3-dimensional networks, providing size-selective accessibility from the gas or liquid phase, and on the macroscale, 2-dimensional arrays and fluidic or photonic systems may be defined. These rapid patterning techniques establish for the first time a link between computer-aided design and rapid processing of self-assembled nanostructures.« less

Quantum molecular dynamics and multistep-direct analyses of multiple preequilibrium emission

NASA Astrophysics Data System (ADS)

Chadwick, M. B.; Chiba, S.; Niita, K.; Maruyama, T.; Iwamoto, A.

1995-11-01

We study multiple preequilibrium emission in nucleon induced reactions at intermediate energies, and compare quantum molecular dynamics (QMD) calculations with multistep-direct Feshbach-Kerman-Koonin results [M. B. Chadwick, P. G. Young, D. C. George, and Y. Watanabe, Phys. Rev. C 50, 996 (1994)]. When the theoretical expressions of this reference are reformulated so that the definitions of primary and multiple emission correspond to those used in QMD, the two theories yield similar results for primary and multiple preequilibrium emission. We use QMD as a tool to determine the multiplicities of fast preequilibrium nucleons as a function of incident energy. For fast particle cross sections to exceed 5% of the inclusive preequilibrium emission cross sections we find that two particles should be included in reactions above 50 MeV, three above about 180 MeV, and four are only needed when the incident energy exceeds about 400 MeV.

The different molecular forms of urine neutrophil gelatinase-associated lipocalin present in dogs with urinary diseases.

PubMed

Hsu, Wei-Li; Chiou, Hsiao-Chi; Tung, Kwong-Chung; Belot, Guillaume; Virilli, Anais; Wong, Min-Liang; Lin, Fong-Yuan; Lee, Ya-Jane

2014-08-27

Neutrophil gelatinase-associated lipocalin (NGAL) is a useful biomarker for the early prediction of renal diseases. NGAL may exist as monomer, dimer and/or NGAL/MMP-9 complex forms in humans. In this study, the existence of various forms of NGAL in urine (uNGAL) was determined and whether these forms are related to the different urinary diseases found in dogs is further discussed. Eighty-one urine samples from dogs with different forms of renal disease (41), pyuria (19) and a number of non-renal related diseases (10), as well as healthy dogs (11), were collected. uNGAL concentrations and their molecular forms in dogs were measured by ELISA and Western blot analysis, respectively. The uNGAL concentrations of dogs with pyuria (median: 15.35 ng/mL) were significantly higher than those of the healthy control animals (median: 3.92 ng/mL) (p < 0.01), but lower than those of dogs with renal diseases (median: 23.77 ng/mL). Each NGAL molecular form could be detected in dog urine. In particular, monomer was detected more frequently in patients with renal disease than those with non-renal diseases; while the dimer form appeared in a significantly higher percentage of cases with pyuria compared to those without pyuria. The NGAL/MMP-9 complex was found to exist not only in the patients with cystitis, but also in the cases with renal injury. Different molecular forms of uNGAL can indicate different origins of the urinary abnormalities. Determining the molecular forms of uNGAL present in diseased dogs may provide clinical workers with a tool that will help the early and more precise detection of different urinary diseases.

"Multiple partial recognitions in dynamic equilibrium" in the binding sites of proteins form the molecular basis of promiscuous recognition of structurally diverse ligands.

PubMed

Kohda, Daisuke

2018-04-01

Promiscuous recognition of ligands by proteins is as important as strict recognition in numerous biological processes. In living cells, many short, linear amino acid motifs function as targeting signals in proteins to specify the final destination of the protein transport. In general, the target signal is defined by a consensus sequence containing wild-characters, and hence represented by diverse amino acid sequences. The classical lock-and-key or induced-fit/conformational selection mechanism may not cover all aspects of the promiscuous recognition. On the basis of our crystallographic and NMR studies on the mitochondrial Tom20 protein-presequence interaction, we proposed a new hypothetical mechanism based on "a rapid equilibrium of multiple states with partial recognitions". This dynamic, multiple recognition mode enables the Tom20 receptor to recognize diverse mitochondrial presequences with nearly equal affinities. The plant Tom20 is evolutionally unrelated to the animal Tom20 in our study, but is a functional homolog of the animal/fungal Tom20. NMR studies by another research group revealed that the presequence binding by the plant Tom20 was not fully explained by simple interaction modes, suggesting the presence of a similar dynamic, multiple recognition mode. Circumstantial evidence also suggested that similar dynamic mechanisms may be applicable to other promiscuous recognitions of signal peptides by the SRP54/Ffh and SecA proteins.

Molecular Testing in Multiple Synchronous Lung Adenocarcinomas: Case Report and Literature Review.

PubMed

Rafael, Oana C; Lazzaro, Richard; Hasanovic, Adnan

2016-02-01

Discovery of driver mutations in pulmonary adenocarcinoma has revolutionized the field of thoracic oncology with major impact on therapy and diagnosis. Testing for EGFR, ALK, and KRAS mutations has become part of everyday practice. We report a case with multiple synchronous primary pulmonary adenocarcinomas in a 72-year-old female with previous history of smoking. The patient presented with cough and bilateral lung ground glass opacities. A positron emission tomography/computed tomography scan showed no activity in mediastinal lymph nodes. She underwent a left upper lobe biopsy and a right upper lobe wedge resection. Pathology revealed 4 morphologically distinct adenocarcinoma foci, suggestive of synchronous primary lung tumors. Molecular testing demonstrated no mutation in the left tumor. Three different driver mutations were present in the right lung tumors: KRAS codon 12 G12D and G12V and EGFR exon 21 L858R mutation, confirming the initial histologic impression. Subsequently, left upper lobe lobectomy showed 3 additional foci of adenocarcinoma with different morphologies, suggestive of synchronous primaries as well. No additional molecular testing was performed. Synchronous pulmonary adenocarcinomas are not uncommon; however, 4 or more synchronous tumors are rare. Distinguishing multiple primary tumors from intrapulmonary metastases is a common problem in thoracic oncology with major implications for staging, prognosis, and treatment. Lung adenocarcinoma subclassification based on predominant and coexisting histologic patterns can greatly facilitate differentiation between intrapulmonary metastases and multiple synchronous tumors. Use of molecular profiling is recommended since it further increases confidence in the diagnostic workup of multiple pulmonary adenocarcinomas and helps guiding therapy. © The Author(s) 2015.

Diagnostic value of multiple café-au-lait macules for neurofibromatosis 1 in Chinese children.

PubMed

Yao, Ruen; Wang, Lili; Yu, Yongguo; Wang, Jian; Shen, Yiping

2016-05-01

Neurofibromatosis 1 (NF1) is a common autosomal dominant condition caused by mutations in the NF1 gene. The appearance of multiple café-au-lait macules is an early sign of the condition, which often alert physicians to follow up and further examine the patient for the possibility of NF1. In order to determine the predictive value of multiple café-au-lait macules at early age for NF1 in Chinese patients, we recruited 19 children who shared the common sign of multiple café-au-lait macules from a general pediatric clinic in Shanghai. All the patients were clinically evaluated following the National Institutes of Health criteria for NF1 and molecular tested for sequence variants and copy number changes. Nine children met the clinical diagnostic criteria of NF1, and molecular tests confirmed all nine patients with pathogenic variants including two genomic deletions, two novel frame-shift variants, four novel nonsense and a splicing variants. In addition, four children who did not meet the diagnostic criteria were also found to carry pathogenic NF1 variants. Overall, 68.4% (13/19) of children with café-au-lait macules and various other clinical presentations were molecularly confirmed with NF1. This study demonstrated that the majority of Chinese children with multiple café-au-lait macules who came to seek for medical attention had NF1. Molecular testing is necessary to be used as an adjunct and sometimes as the main tool for confirming and diagnosing children of NF1 at early age. © 2015 Japanese Dermatological Association.

Molecular Ultrasound Imaging for the Detection of Neural Inflammation

NASA Astrophysics Data System (ADS)

Volz, Kevin R.

Molecular imaging is a form of nanotechnology that enables the noninvasive examination of biological processes in vivo. Radiopharmaceutical agents are used to selectively target biochemical markers, which permits their detection and evaluation. Early visualization of molecular variations indicative of pathophysiological processes can aid in patient diagnoses and management decisions. Molecular imaging is performed by introducing molecular probes into the body. Molecular probes are often contrast agents that have been nanoengineered to selectively target and tether to molecules, enabling their radiologic identification. Ultrasound contrast agents have been demonstrated as an effective method of detecting perfusion at the tissue level. Through a nanoengineering process, ultrasound contrast agents can be targeted to specific molecules, thereby extending ultrasound's capabilities from the tissue to molecular level. Molecular ultrasound, or targeted contrast enhanced ultrasound (TCEUS), has recently emerged as a popular molecular imaging technique due to its ability to provide real-time anatomical and functional information in the absence of ionizing radiation. However, molecular ultrasound represents a novel form of molecular imaging, and consequently remains largely preclinical. A review of the TCEUS literature revealed multiple preclinical studies demonstrating its success in detecting inflammation in a variety of tissues. Although, a gap was identified in the existing evidence, as TCEUS effectiveness for detection of neural inflammation in the spinal cord was unable to be uncovered. This gap in knowledge, coupled with the profound impacts that this TCEUS application could have clinically, provided rationale for its exploration, and use as contributory evidence for the molecular ultrasound body of literature. An animal model that underwent a contusive spinal cord injury was used to establish preclinical evidence of TCEUS to detect neural inflammation. Imaging was performed while targeting three early inflammatory markers (P-selectin, VCAM-1, ICAM-1). Imaging protocols and outcome measures of previous TCEUS investigations of inflammation were replicated to aid in comparisons of outcomes. Signal intensity data was used to generate time intensity curves for qualitative and quantitative analysis of contrast agent temporal behavior. A proof of principle study established preclinical evidence to support the ability of TCEUS to detect acute neural inflammation. Substantial increases in signal intensities were observed while targeting inflammatory markers compared to controls. Further investigations consisted of examining molecular ultrasound sensitivity, and were accomplished by examining targeted contrast agent dosing parameters, and the ability of TCEUS to longitudinally evaluate neural inflammation. Qualitative analysis of TCEUS imaging performed with both administered doses revealed marked increases in signal intensities during acute inflammation, where inflammatory marker expression was presumably at its highest. This was in comparison to measures obtained in the absence of, and during, chronic inflammation. This research contributes much needed empirical evidence to the molecular ultrasound body of literature, and represents the first steps towards advancing this TCEUS application to clinical practice. Future studies are necessary to further these findings and effectively build upon this evidence. Increasing evidence of TCEUS use for the detection of neural inflammation will aid in its eventual clinical translation, where it will likely have a positive impact on patient care.

Molecular nano-arches on silicon

NASA Astrophysics Data System (ADS)

Dobrin, S.

2007-08-01

The formation of molecular nano-arches on the Si(1 1 1)-7 × 7 surface was modeled using density functional theory (DFT). It has been suggested, based on the calculations, that the arches are formed by molecular dimers of chlorobenzene at near-monolayer coverages. Molecules of the dimer are covalently bound to two silicon adatoms and to each other thereby forming a molecular arch on the surface. The structure of the molecular dimer was calculated at the B3LYP/6-31G(d) level of theory. The dimers were found to be stable at room temperature, and to form a near-monolayer coverage, which has been observed in the experiment [X.H. Chen, Q. Kong, J.C. Polanyi, D. Rogers, S. So, Surf. Sci. 340 (1995) 224; Y. Cao, J.F. Deng, G.Q. Xu, J. Chem. Phys. 112 (2000) 4759].

Dynamics and molecular determinants of cytoplasmic lipid droplet clustering and dispersion.

PubMed

Orlicky, David J; Monks, Jenifer; Stefanski, Adrianne L; McManaman, James L

2013-01-01

Perilipin-1 (Plin1), a prominent cytoplasmic lipid droplet (CLD) binding phosphoprotein and key physiological regulator of triglyceride storage and lipolysis in adipocytes, is thought to regulate the fragmentation and dispersion of CLD that occurs in response to β-adrenergic activation of adenylate cyclase. Here we investigate the dynamics and molecular determinants of these processes using cell lines stably expressing recombinant forms of Plin1 and/or other members of the perilipin family. Plin1 and a C-terminal CLD-binding fragment of Plin1 (Plin1CT) induced formation of single dense CLD clusters near the microtubule organizing center, whereas neither an N-terminal CLD-binding fragment of Plin1, nor Plin2 or Plin3 induced clustering. Clustered CLD coated by Plin1, or Plin1CT, dispersed in response to isoproterenol, or other agents that activate adenylate cyclase, in a process inhibited by the protein kinase A inhibitor, H89, and blocked by microtubule disruption. Isoproterenol-stimulated phosphorylation of CLD-associated Plin1 on serine 492 preceded their dispersion, and live cell imaging showed that cluster dispersion involved initial fragmentation of tight clusters into multiple smaller clusters, which then fragmented into well-dispersed individual CLD. siRNA knockdown of the cortical actin binding protein, moesin, induced disaggregation of tight clusters into multiple smaller clusters, and inhibited the reaggregation of dispersed CLD into tight clusters. Together these data suggest that the clustering and dispersion processes involve a complex orchestration of phosphorylation-dependent, microtubule-dependent and independent, and microfilament dependent steps.

Profiling the array of Ca(v)3.1 variants from the human T-type calcium channel gene CACNA1G: alternative structures, developmental expression, and biophysical variations.

PubMed

Emerick, Mark C; Stein, Rebecca; Kunze, Robin; McNulty, Megan M; Regan, Melissa R; Hanck, Dorothy A; Agnew, William S

2006-08-01

We describe the regulated transcriptome of CACNA1G, a human gene for T-type Ca(v)3.1 calcium channels that is subject to extensive alternative RNA splicing. Fifteen sites of transcript variation include 2 alternative 5'-UTR promoter sites, 2 alternative 3'-UTR polyadenylation sites, and 11 sites of alternative splicing within the open reading frame. A survey of 1580 fetal and adult human brain full-length complementary DNAs reveals a family of 30 distinct transcripts, including multiple functional forms that vary in expression with development. Statistical analyses of fetal and adult transcript populations reveal patterns of linkages among intramolecular splice site configurations that change dramatically with development. A shift from nearly independent, biased splicing in fetal transcripts to strongly concerted splicing in adult transcripts suggests progressive activation of multiple "programs" of splicing regulation that reorganize molecular structures in differentiating cells. Patch-clamp studies of nine selected variants help relate splicing regulation to permutations of the gating parameters most likely to modify T-channel physiology in expressing neurons. Gating behavior reflects combinatorial interactions between variable domains so that molecular phenotype depends on ensembles of coselected domains, consistent with the observed emergence of concerted splicing during development. We conclude that the structural gene and networks of splicing regulatory factors define an integrated system for the phenotypic variation of Ca(v)3.1 biophysics during nervous system development. Copyright 2006 Wiley-Liss, Inc.

Globally intertwined evolutionary history of giant barrel sponges

NASA Astrophysics Data System (ADS)

Swierts, Thomas; Peijnenburg, Katja T. C. A.; de Leeuw, Christiaan A.; Breeuwer, Johannes A. J.; Cleary, Daniel F. R.; de Voogd, Nicole J.

2017-09-01

Three species of giant barrel sponge are currently recognized in two distinct geographic regions, the tropical Atlantic and the Indo-Pacific. In this study, we used molecular techniques to study populations of giant barrel sponges across the globe and assessed whether the genetic structure of these populations agreed with current taxonomic consensus or, in contrast, whether there was evidence of cryptic species. Using molecular data, we assessed whether giant barrel sponges in each oceanic realm represented separate monophyletic lineages. Giant barrel sponges from 17 coral reef systems across the globe were sequenced for mitochondrial (partial CO1 and ATP6 genes) and nuclear (ATPsβ intron) DNA markers. In total, we obtained 395 combined sequences of the mitochondrial CO1 and ATP6 markers, which resulted in 17 different haplotypes. We compared a phylogenetic tree constructed from 285 alleles of the nuclear intron ATPsβ to the 17 mitochondrial haplotypes. Congruent patterns between mitochondrial and nuclear gene trees of giant barrel sponges provided evidence for the existence of multiple reproductively isolated species, particularly where they occurred in sympatry. The species complexes in the tropical Atlantic and the Indo-Pacific, however, do not form separate monophyletic lineages. This rules out the scenario that one species of giant barrel sponge developed into separate species complexes following geographic separation and instead suggests that multiple species of giant barrel sponges already existed prior to the physical separation of the Indo-Pacific and tropical Atlantic.

Basal protein phosphatase 2A activity restrains cytokine expression: role for MAPKs and tristetraprolin.

PubMed

Rahman, Md Mostafizur; Rumzhum, Nowshin N; Morris, Jonathan C; Clark, Andrew R; Verrills, Nicole M; Ammit, Alaina J

2015-05-18

PP2A is a master controller of multiple inflammatory signaling pathways. It is a target in asthma; however the molecular mechanisms by which PP2A controls inflammation warrant further investigation. In A549 lung epithelial cells in vitro we show that inhibition of basal PP2A activity by okadaic acid (OA) releases restraint on MAPKs and thereby increases MAPK-mediated pro-asthmatic cytokines, including IL-6 and IL-8. Notably, PP2A inhibition also impacts on the anti-inflammatory protein - tristetraprolin (TTP), a destabilizing RNA binding protein regulated at multiple levels by p38 MAPK. Although PP2A inhibition increases TTP mRNA expression, resultant TTP protein builds up in the hyperphosphorylated inactive form. Thus, when PP2A activity is repressed, pro-inflammatory cytokines increase and anti-inflammatory proteins are rendered inactive. Importantly, these effects can be reversed by the PP2A activators FTY720 and AAL(s), or more specifically by overexpression of the PP2A catalytic subunit (PP2A-C). Moreover, PP2A plays an important role in cytokine expression in cells stimulated with TNFα; as inhibition of PP2A with OA or PP2A-C siRNA results in significant increases in cytokine production. Collectively, these data reveal the molecular mechanisms of PP2A regulation and highlight the potential of boosting the power of endogenous phosphatases as novel anti-inflammatory strategies to combat asthmatic inflammation.

Short-peptide-based molecular hydrogels: novel gelation strategies and applications for tissue engineering and drug delivery

NASA Astrophysics Data System (ADS)

Wang, Huaimin; Yang, Zhimou

2012-08-01

Molecular hydrogels hold big potential for tissue engineering and controlled drug delivery. Our lab focuses on short-peptide-based molecular hydrogels formed by biocompatible methods and their applications in tissue engineering (especially, 3D cell culture) and controlled drug delivery. This feature article firstly describes our recent progresses of the development of novel methods to form hydrogels, including the strategy of disulfide bond reduction and assistance with specific protein-peptide interactions. We then introduce the applications of our hydrogels in fields of controlled stem cell differentiation, cell culture, surface modifications of polyester materials by molecular self-assembly, and anti-degradation of recombinant complex proteins. A novel molecular hydrogel system of hydrophobic compounds that are only formed by hydrolysis processes was also included in this article. The hydrogels of hydrophobic compounds, especially those of hydrophobic therapeutic agents, may be developed into a carrier-free delivery system for long term delivery of therapeutic agents. With the efforts in this field, we believe that molecular hydrogels formed by short peptides and hydrophobic therapeutic agents can be practically applied for 3D cell culture and long term drug delivery in near future, respectively.

The oxygenating constituent of 3,6-diketocamphane monooxygenase from the CAM plasmid of Pseudomonas putida: the first crystal structure of a type II Baeyer-Villiger monooxygenase.

PubMed

Isupov, Michail N; Schröder, Ewald; Gibson, Robert P; Beecher, Jean; Donadio, Giuliana; Saneei, Vahid; Dcunha, Stephlina A; McGhie, Emma J; Sayer, Christopher; Davenport, Colin F; Lau, Peter C; Hasegawa, Yoshie; Iwaki, Hiroaki; Kadow, Maria; Balke, Kathleen; Bornscheuer, Uwe T; Bourenkov, Gleb; Littlechild, Jennifer A

2015-11-01

The three-dimensional structures of the native enzyme and the FMN complex of the overexpressed form of the oxygenating component of the type II Baeyer-Villiger 3,6-diketocamphane monooxygenase have been determined to 1.9 Å resolution. The structure of this dimeric FMN-dependent enzyme, which is encoded on the large CAM plasmid of Pseudomonas putida, has been solved by a combination of multiple anomalous dispersion from a bromine crystal soak and molecular replacement using a bacterial luciferase model. The orientation of the isoalloxazine ring of the FMN cofactor in the active site of this TIM-barrel fold enzyme differs significantly from that previously observed in enzymes of the bacterial luciferase-like superfamily. The Ala77 residue is in a cis conformation and forms a β-bulge at the C-terminus of β-strand 3, which is a feature observed in many proteins of this superfamily.

The E3 ligase Ubr3 regulates Usher syndrome and MYH9 disorder proteins in the auditory organs of Drosophila and mammals.

PubMed

Li, Tongchao; Giagtzoglou, Nikolaos; Eberl, Daniel F; Jaiswal, Sonal Nagarkar; Cai, Tiantian; Godt, Dorothea; Groves, Andrew K; Bellen, Hugo J

2016-06-22

Myosins play essential roles in the development and function of auditory organs and multiple myosin genes are associated with hereditary forms of deafness. Using a forward genetic screen in Drosophila, we identified an E3 ligase, Ubr3, as an essential gene for auditory organ development. Ubr3 negatively regulates the mono-ubiquitination of non-muscle Myosin II, a protein associated with hearing loss in humans. The mono-ubiquitination of Myosin II promotes its physical interaction with Myosin VIIa, a protein responsible for Usher syndrome type IB. We show that ubr3 mutants phenocopy pathogenic variants of Myosin II and that Ubr3 interacts genetically and physically with three Usher syndrome proteins. The interactions between Myosin VIIa and Myosin IIa are conserved in the mammalian cochlea and in human retinal pigment epithelium cells. Our work reveals a novel mechanism that regulates protein complexes affected in two forms of syndromic deafness and suggests a molecular function for Myosin IIa in auditory organs.

The molecular mechanism of nuclear transport revealed by atomic-scale measurements

PubMed Central

Hough, Loren E; Dutta, Kaushik; Sparks, Samuel; Temel, Deniz B; Kamal, Alia; Tetenbaum-Novatt, Jaclyn; Rout, Michael P; Cowburn, David

2015-01-01

Nuclear pore complexes (NPCs) form a selective filter that allows the rapid passage of transport factors (TFs) and their cargoes across the nuclear envelope, while blocking the passage of other macromolecules. Intrinsically disordered proteins (IDPs) containing phenylalanyl-glycyl (FG)-rich repeats line the pore and interact with TFs. However, the reason that transport can be both fast and specific remains undetermined, through lack of atomic-scale information on the behavior of FGs and their interaction with TFs. We used nuclear magnetic resonance spectroscopy to address these issues. We show that FG repeats are highly dynamic IDPs, stabilized by the cellular environment. Fast transport of TFs is supported because the rapid motion of FG motifs allows them to exchange on and off TFs extremely quickly through transient interactions. Because TFs uniquely carry multiple pockets for FG repeats, only they can form the many frequent interactions needed for specific passage between FG repeats to cross the NPC. DOI: http://dx.doi.org/10.7554/eLife.10027.001 PMID:26371551

Endocytosis-dependent coordination of multiple actin regulators is required for wound healing

PubMed Central

Matsubayashi, Yutaka; Coulson-Gilmer, Camilla

2015-01-01

The ability to heal wounds efficiently is essential for life. After wounding of an epithelium, the cells bordering the wound form dynamic actin protrusions and/or a contractile actomyosin cable, and these actin structures drive wound closure. Despite their importance in wound healing, the molecular mechanisms that regulate the assembly of these actin structures at wound edges are not well understood. In this paper, using Drosophila melanogaster embryos, we demonstrate that Diaphanous, SCAR, and WASp play distinct but overlapping roles in regulating actin assembly during wound healing. Moreover, we show that endocytosis is essential for wound edge actin assembly and wound closure. We identify adherens junctions (AJs) as a key target of endocytosis during wound healing and propose that endocytic remodeling of AJs is required to form “signaling centers” along the wound edge that control actin assembly. We conclude that coordination of actin assembly, AJ remodeling, and membrane traffic is required for the construction of a motile leading edge during wound healing. PMID:26216900

Photoswitchable red fluorescent protein with a large Stokes shift

PubMed Central

Piatkevich, Kiryl D.; English, Brian P.; Malashkevich, Vladimir N.; Xiao, Hui; Almo, Steven C.; Singer, Robert H.; Verkhusha, Vladislav V.

2014-01-01

SUMMARY Subclass of fluorescent proteins, large Stokes shift fluorescent proteins, is characterized by their increased spread between the excitation and emission maxima. Here we report a photoswitchable variant of a red fluorescent protein with a large Stokes shift, PSLSSmKate, which initially exhibits excitation/emission at 445/622 nm, but irradiation with violet light photoswitches PSLSSmKate into a common red form with excitation/emission at 573/621 nm. We characterize spectral, photophysical and biochemical properties of PSLSSmKate in vitro and in mammalian cells, and determine its crystal structure in the large Stokes shift form. Mass-spectrometry, mutagenesis and spectroscopic analysis of PSLSSmKate allow us to propose molecular mechanisms for the large Stokes shift, pH dependence and light-induced chromophore transformation. We demonstrate applicability of PSLSSmKate to superresolution PALM microscopy and protein dynamics in live cells. Given its promising properties, we expect that PSLSSmKate-like phenotype will be further used for photoactivatable imaging and tracking multiple populations of intracellular objects. PMID:25242289

Photoswitchable red fluorescent protein with a large Stokes shift.

PubMed

Piatkevich, Kiryl D; English, Brian P; Malashkevich, Vladimir N; Xiao, Hui; Almo, Steven C; Singer, Robert H; Verkhusha, Vladislav V

2014-10-23

A subclass of fluorescent proteins (FPs), large Stokes shift (LSS) FP, are characterized by increased spread between excitation and emission maxima. We report a photoswitchable variant of a red FP with an LSS, PSLSSmKate, which initially exhibits excitation and emission at 445 and 622 nm, but violet irradiation photoswitches PSLSSmKate into a common red form with excitation and emission at 573 and 621 nm. We characterize spectral, photophysical, and biochemical properties of PSLSSmKate in vitro and in mammalian cells and determine its crystal structure in the LSS form. Mass spectrometry, mutagenesis, and spectroscopy of PSLSSmKate allow us to propose molecular mechanisms for the LSS, pH dependence, and light-induced chromophore transformation. We demonstrate the applicability of PSLSSmKate to superresolution photoactivated localization microscopy and protein dynamics in live cells. Given its promising properties, we expect that PSLSSmKate-like phenotype will be further used for photoactivatable imaging and tracking multiple populations of intracellular objects.

Sampling the multiple folding mechanisms of Trp-cage in explicit solvent

PubMed Central

Juraszek, J.; Bolhuis, P. G.

2006-01-01

We investigate the kinetic pathways of folding and unfolding of the designed miniprotein Trp- cage in explicit solvent. Straightforward molecular dynamics and replica exchange methods both have severe convergence problems, whereas transition path sampling allows us to sample unbiased dynamical pathways between folded and unfolded states and leads to deeper understanding of the mechanisms of (un)folding. In contrast to previous predictions employing an implicit solvent, we find that Trp-cage folds primarily (80% of the paths) via a pathway forming the tertiary contacts and the salt bridge, before helix formation. The remaining 20% of the paths occur in the opposite order, by first forming the helix. The transition states of the rate-limiting steps are solvated native-like structures. Water expulsion is found to be the last step upon folding for each route. Committor analysis suggests that the dynamics of the solvent is not part of the reaction coordinate. Nevertheless, during the transition, specific water molecules are strongly bound and can play a structural role in the folding. PMID:17035504

May Diet and Dietary Supplements Improve the Wellness of Multiple Sclerosis Patients? A Molecular Approach

PubMed Central

Riccio, Paolo; Rossano, Rocco; Liuzzi, Grazia Maria

2010-01-01

Multiple sclerosis is a complex and multifactorial neurological disease, and nutrition is one of the environmental factors possibly involved in its pathogenesis. At present, the role of nutrition is unclear, and MS therapy is not associated to a particular diet. MS clinical trials based on specific diets or dietary supplements are very few and in some cases controversial. To understand how diet can influence the course of MS and improve the wellness of MS patients, it is necessary to identify the dietary molecules, their targets and the molecular mechanisms involved in the control of the disease. The aim of this paper is to provide a molecular basis for the nutritional intervention in MS by evaluating at molecular level the effect of dietary molecules on the inflammatory and autoimmune processes involved in the disease. PMID:21461338

Defining the molecular basis of BubR1 kinetochore interactions and APC/C-CDC20 inhibition.

PubMed

D'Arcy, Sheena; Davies, Owen R; Blundell, Tom L; Bolanos-Garcia, Victor M

2010-05-07

BubR1 is essential for the mitotic checkpoint that prevents aneuploidy in cellular progeny by triggering anaphase delay in response to kinetochores incorrectly/not attached to the mitotic spindle. Here, we define the molecular architecture of the functionally significant N-terminal region of human BubR1 and present the 1.8 A crystal structure of its tetratricopeptide repeat (TPR) domain. The structure reveals divergence from the classical TPR fold and is highly similar to the TPR domain of budding yeast Bub1. Shared distinctive features include a disordered loop insertion, a 3(10)-helix, a tight turn involving glycine positive Phi angles, and noncanonical packing of and between the TPR motifs. We also define the molecular determinants of the interaction between BubR1 and kinetochore protein Blinkin. We identify a shallow groove on the concave surface of the BubR1 TPR domain that forms multiple discrete and potentially cooperative interactions with Blinkin. Finally, we present evidence for a direct interaction between BubR1 and Bub1 mediated by regions C-terminal to their TPR domains. This interaction provides a mechanism for Bub1-dependent kinetochore recruitment of BubR1. We thus present novel molecular insights into the structure of BubR1 and its interactions at the kinetochore-microtubule interface. Our studies pave the way for future structure-directed engineering aimed at dissecting the roles of kinetochore-bound and other pools of BubR1 in vivo.

Role of the protective antigen octamer in the molecular mechanism of anthrax lethal toxin stabilization in plasma

PubMed Central

Kintzer, Alexander F.; Sterling, Harry J.; Tang, Iok I.; Abdul-Gader, Ali; Miles, Andrew J.; Wallace, B. A.; Williams, Evan R.; Krantz, Bryan A.

2010-01-01

Anthrax is caused by strains of Bacillus anthracis that produce two key virulence factors, anthrax toxin (Atx) and a poly-γ-D-glutamic acid capsule. Atx is comprised of three-proteins: protective antigen (PA) and two enzymes, lethal factor (LF) and edema factor (EF). To disrupt cell function, these components must assemble into holotoxin complexes, which contain either a ring-shaped homooctameric or homoheptameric PA oligomer bound to multiple copies of either LF and/or EF, producing lethal toxin (LT), edema toxin, or mixtures thereof. Once a host cell endocytoses these complexes, PA converts into a membrane-inserted channel that translocates LF and EF into the cytosol. LT may assemble on host cell surfaces or extracellularly in plasma. We show that under physiological conditions in bovine plasma that LT complexes containing heptameric PA aggregate and inactivate more readily than LT complexes containing octameric PA. LT complexes containing octameric PA possess enhanced stability, channel forming activity, and macrophage cytotoxicity relative to those containing heptameric PA. Under physiological conditions, multiple biophysical probes reveal that heptameric PA can prematurely adopt the channel conformation, but octameric PA complexes remain in their soluble prechannel configuration allowing them to resist aggregation and inactivation. We conclude that PA may form an octameric oligomeric state as a means to produce a more stable and active LT complex that may circulate freely in the blood. PMID:20433851

Interfacial thiol-ene photoclick reactions for forming multilayer hydrogels.

PubMed

Shih, Han; Fraser, Andrew K; Lin, Chien-Chi

2013-03-13

Interfacial visible light-mediated thiol-ene photoclick reactions were developed for preparing step-growth hydrogels with multilayer structures. The effect of a noncleavage type photoinitiator eosin-Y on visible-light-mediated thiol-ene photopolymerization was first characterized using in situ photorheometry, gel fraction, and equilibrium swelling ratio. Next, spectrophotometric properties of eosin-Y in the presence of various relevant macromer species were evaluated using ultraviolet-visible light (UV-vis) spectrometry. It was determined that eosin-Y was able to reinitiate the thiol-ene photoclick reaction, even after light exposure. Because of its small molecular weight, most eosin-Y molecules readily leached out from the hydrogels. The diffusion of residual eosin-Y from preformed hydrogels was exploited for fabricating multilayer step-growth hydrogels. Interfacial hydrogel coating was formed via the same visible-light-mediated gelation mechanism without adding fresh initiator. The thickness of the thiol-ene gel coating could be easily controlled by adjusting visible light exposure time, eosin-Y concentration initially loaded in the core gel, or macromer concentration in the coating solution. The major benefits of this interfacial thiol-ene coating system include its simplicity and cytocompatibility. The formation of thiol-ene hydrogels and coatings neither requires nor generates any cytotoxic components. This new gelation chemistry may have great utilities in controlled release of multiple sensitive growth factors and encapsulation of multiple cell types for tissue regeneration.

How Does Dense Molecular Gas Contribute to Star Formation in the Starburst Galaxy NGC 2146?

NASA Astrophysics Data System (ADS)

Wofford, Alia

2017-01-01

The starburst galaxy NGC 2146 is believed to have been formed approximately 800 Myr ago, when two galaxies collided with each other possibly leading to a burst of star formation. NGC 2146 is known as a starburst galaxy for the high frequency of star formation going on in its molecular clouds. These clouds serve as nurseries for star formation to occur. Hydrogen Cyanide (HCN) and Carbon monoxide (CO) are molecules found in molecular gas clouds. HCN molecules are tracers for high density star forming gas. Whereas, CO molecules are tracers for low density star forming gas. In this project, we are observing these two molecules and their proximity to where the stars are forming in the galaxy to determine if the star formation is occurring in the same area as the high and low density molecular gas areas in starburst galaxy NGC 2146.

Atomic scale study of nanocontacts

NASA Astrophysics Data System (ADS)

Buldum, A.; Ciraci, S.; Batra, Inder P.; Fong, C. Y.

1998-03-01

Nanocontact and subsequent pulling off a sharp Ni(111) tip on a Cu(110) surface are investigated by using molecular dynamics method with embedded atom model. As the contact is formed, the sharp tip experiences multiple jump to contact in the attractive force range. The contact interface develops discontinuously mainly due to disorder-order transformations which lead to disappearance of a layer and hence abrupt changes in the normal force variation. Atom exchange occurs in the repulsive range. The connective neck is reduced also discontinuously by pulling off the tip. The novel atomic structure of the neck under the tensile force is analyzed. We also presented a comperative study for the contact by a Si(111) tip on Si(111)-(2x1) surface.

Logic-Gate Functions in Chemomechanical Materials.

PubMed

Schneider, Hans-Jörg

2017-09-06

Chemomechanical polymers that change their shape or volume on stimulation by multiple external chemical signals, particularly on the basis of selective molecular recognition, are discussed. Several examples illustrate how such materials, usually in the form of hydrogels, can be used for the design of chemically triggered valves or artificial muscles and applied, for example, in self-healing materials or drug delivery. The most attractive feature of such materials is that they can combine sensor and actuator within single units, from nano- to macrosize. Simultaneous action of a cofactor allows selective response in the sense of AND logic gates by, for example, amino acids and peptides, which without the presence of a second effector do not induce any changes. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Eyes Have It: A Problem-Based Learning Exercise in Molecular Evolution

ERIC Educational Resources Information Center

White, Harold B.

2007-01-01

Molecular evolution provides an interesting context in which to use problem-based learning because it integrates a variety of topics in biology, biochemistry, and molecular biology. This three-stage problem for advanced students deals with the structure, multiple functions, and properties of lactate dehydrogenase isozymes, and the related…

Assessing High School Chemistry Students' Modeling Sub-Skills in a Computerized Molecular Modeling Learning Environment

ERIC Educational Resources Information Center

Dori, Yehudit Judy; Kaberman, Zvia

2012-01-01

Much knowledge in chemistry exists at a molecular level, inaccessible to direct perception. Chemistry instruction should therefore include multiple visual representations, such as molecular models and symbols. This study describes the implementation and assessment of a learning unit designed for 12th grade chemistry honors students. The organic…

A Study on Segmented Multiple-Step Forming of Doubly Curved Thick Plate by Reconfigurable Multi-Punch Dies

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

Ko, Young Ho; Han, Myoung Soo; Han, Jong Man

2007-05-17

Doubly curved thick plate forming in shipbuilding industries is currently performed by a thermal forming process, called as Line Heating by using gas flame torches. Due to the empirical manual work of it, the industries are eager for an alternative way to manufacture curved thick plates for ships. It was envisaged in this study to manufacture doubly curved thick plates by the multi-punch die forming. Experiments and finite element analyses were conducted to evaluate the feasibility of the reconfigurable discrete die forming to the thick plates. Single and segmented multiple step forming procedures were considered from both forming efficiency andmore » accuracy. Configuration of the multi-punch dies suitable for the segmented multiple step forming was also explored. As a result, Segmented multiple step forming with matched dies had a limited formability when the objective shapes become complicate, while a unmatched die configuration provided better possibility to manufacture large curved plates for ships.« less

Pragmatic precision oncology: the secondary uses of clinical tumor molecular profiling.

PubMed

Rioth, Matthew J; Thota, Ramya; Staggs, David B; Johnson, Douglas B; Warner, Jeremy L

2016-07-01

Precision oncology increasingly utilizes molecular profiling of tumors to determine treatment decisions with targeted therapeutics. The molecular profiling data is valuable in the treatment of individual patients as well as for multiple secondary uses. To automatically parse, categorize, and aggregate clinical molecular profile data generated during cancer care as well as use this data to address multiple secondary use cases. A system to parse, categorize and aggregate molecular profile data was created. A naÿve Bayesian classifier categorized results according to clinical groups. The accuracy of these systems were validated against a published expertly-curated subset of molecular profiling data. Following one year of operation, 819 samples have been accurately parsed and categorized to generate a data repository of 10,620 genetic variants. The database has been used for operational, clinical trial, and discovery science research. A real-time database of molecular profiling data is a pragmatic solution to several knowledge management problems in the practice and science of precision oncology. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Computational Insights into the Molecular Mechanism of the High Immunomodulatory Activity of LZ-8 Protein Isolated from the Lingzhi or Reishi Medicinal Mushroom Ganoderma lucidum (Agaricomycetes).

PubMed

Bao, Da-Peng; Bai, Rui; Gao, Ying-Nv; Wu, Ying-Ying; Wang, Ying

2018-01-01

Ling zhi-8 (LZ-8) is the first fungal immunomodulatory protein (FIP) isolated from the lingzhi or reishi medicinal mushroom, Ganoderma lucidum. LZ-8 effectively induces interleukin 2 expression and secretion by forming a stable homodimer, and it is regarded as a good candidate to become a new therapeutic agent and/or functional food supplement. However, the molecular mechanism by which LZ-8 dimerization influences the regulation of interleukin 2 is not clear. In this study we performed structure-based multiple alignment of LZ-8 and an FIP from Volvariella volvacea, compared the electrostatic potential of their protein surfaces, and developed a model summarizing the unique electrostatic interaction in LZ-8 dimerization. In addition, further electrostatic potential and virtual amino acid mutation analyses suggested that L10, W12, and D45 are the key amino acid residues responsible for the protein's high immunomodulatory activity. These findings may provide useful insights into the design and construction of a new FIP mutant for use in treating and preventing autoimmune diseases.

Diffraction-based BioCD biosensor for point-of-care diagnostics

NASA Astrophysics Data System (ADS)

Choi, H.; Chang, C.; Savran, C.; Nolte, D.

2018-02-01

The BioCD platform technology uses spinning-disk interferometry to detect molecular binding to target molecular probes in biological samples. Interferometric configurations have included differential phase contrast and in-line quadrature detection. For the detection of extremely low analyte concentrations, nano- or microparticles can enhance the signal through background-free diffraction detection. Diffraction signal measurements on BioCD biosensors are achieved by forming gratings on a disc surface. The grating pattern was printed with biotinylated bovine serum albumin (BSA) and streptavidin coated beads were deployed. The diameter of the beads was 1 micron and strong protein bonding occurs between BSA and streptavidin-coated beads at the printed location. The wavelength for the protein binding detection was 635 nm. The periodic pattern on the disc amplified scattered light into the first-order diffraction position. The diffracted signal contains Mie scattering and a randomly-distributed-bead noise contributions. Variation of the grating pattern periodicity modulates the diffraction efficiency. To test multiple spatial frequencies within a single scan, we designed a fan-shaped grating to perform frequency filter multiplexing on a diffraction-based BioCD.

Thalidomide‐induced teratogenesis: History and mechanisms

PubMed Central

2015-01-01

Nearly 60 years ago thalidomide was prescribed to treat morning sickness in pregnant women. What followed was the biggest man‐made medical disaster ever, where over 10,000 children were born with a range of severe and debilitating malformations. Despite this, the drug is now used successfully to treat a range of adult conditions, including multiple myeloma and complications of leprosy. Tragically, a new generation of thalidomide damaged children has been identified in Brazil. Yet, how thalidomide caused its devastating effects in the forming embryo remains unclear. However, studies in the past few years have greatly enhanced our understanding of the molecular mechanisms the drug. This review will look at the history of the drug, and the range and type of damage the drug caused, and outline the mechanisms of action the drug uses including recent molecular advances and new findings. Some of the remaining challenges facing thalidomide biologists are also discussed. Birth Defects Research (Part C) 105:140–156, 2015. © 2015 The Authors Birth Defects Research Part C: Embryo Today: Reviews Published by Wiley Periodicals, Inc. PMID:26043938

The evolution, morphology, and development of fern leaves

PubMed Central

Vasco, Alejandra; Moran, Robbin C.; Ambrose, Barbara A.

2013-01-01

Leaves are lateral determinate structures formed in a predictable sequence (phyllotaxy) on the flanks of an indeterminate shoot apical meristem. The origin and evolution of leaves in vascular plants has been widely debated. Being the main conspicuous organ of nearly all vascular plants and often easy to recognize as such, it seems surprising that leaves have had multiple origins. For decades, morphologists, anatomists, paleobotanists, and systematists have contributed data to this debate. More recently, molecular genetic studies have provided insight into leaf evolution and development mainly within angiosperms and, to a lesser extent, lycophytes. There has been recent interest in extending leaf evolutionary developmental studies to other species and lineages, particularly in lycophytes and ferns. Therefore, a review of fern leaf morphology, evolution and development is timely. Here we discuss the theories of leaf evolution in ferns, morphology, and diversity of fern leaves, and experimental results of fern leaf development. We summarize what is known about the molecular genetics of fern leaf development and what future studies might tell us about the evolution of fern leaf development. PMID:24027574

Anomalous length dependence of conductance of aromatic nanoribbons with amine anchoring groups

NASA Astrophysics Data System (ADS)

Bilić, Ante; Sanvito, Stefano

2012-09-01

Two sets of aromatic nanoribbons, based around a common hexagonal scaffolding, with single and dual terminal amine groups have been considered as potential molecular wires in a junction formed by gold leads. Charge transport through the two-terminal device has been modeled using density functional theory (with and without self-interaction correction) and the nonequilibrium Green's function method. The effects of wire length, multiple terminal contacts, and pathways across the junction have been investigated. For nanoribbons with the oligopyrene motif and conventional single amine terminal groups, an increase in the wire length causes an exponential drop in the conductance. In contrast, for the nanoribbons with the oligoperylene motif and dual amine anchoring groups the predicted conductance rises with the wire length over the whole range of investigated lengths. Only when the effects of self-interaction correction are taken into account, the conductance of the oligoperylene ribbons exhibits saturation for longer members of the series. The oligoperylene nanoribbons, with dual amine groups at both terminals, show the potential to fully harness the highly conjugated system of π molecular orbitals across the junction.

Vibrational spectroscopy of the silicate mineral plumbotsumite Pb5(OH)10Si4O8 - An assessment of the molecular structure

NASA Astrophysics Data System (ADS)

López, Andrés; Frost, Ray L.; Scholz, Ricardo; Gobac, Željka Žigovečki; Xi, Yunfei

2013-12-01

We have used scanning electron microscopy with energy dispersive X-ray analysis to determine the precise formula of plumbotsumite, a rare lead silicate mineral of formula Pb5(OH)10Si4O8. This study forms the first systematic study of plumbotsumite from the Bigadic deposits, Turkey. Vibrational spectroscopy was used to assess the molecular structure of plumbotsumite as the structure is not known. The mineral is characterized by sharp Raman bands at 1047, 1055 and 1060 cm-1 assigned to SiO stretching vibrational modes and sharp Raman bands at 673, 683 and 697 cm-1 assigned to OSiO bending modes. The observation of multiple bands offers support for a layered structure with variable SiO3 structural units. Little information may be obtained from the infrared spectra because of broad spectral profiles. Intense Raman bands at 3510, 3546 and 3620 cm-1 are ascribed to OH stretching modes. Evidence for the presence of water in the plumbotsumite structure was inferred from the infrared spectra.

Metabolite identification through multiple kernel learning on fragmentation trees.

PubMed

Shen, Huibin; Dührkop, Kai; Böcker, Sebastian; Rousu, Juho

2014-06-15

Metabolite identification from tandem mass spectrometric data is a key task in metabolomics. Various computational methods have been proposed for the identification of metabolites from tandem mass spectra. Fragmentation tree methods explore the space of possible ways in which the metabolite can fragment, and base the metabolite identification on scoring of these fragmentation trees. Machine learning methods have been used to map mass spectra to molecular fingerprints; predicted fingerprints, in turn, can be used to score candidate molecular structures. Here, we combine fragmentation tree computations with kernel-based machine learning to predict molecular fingerprints and identify molecular structures. We introduce a family of kernels capturing the similarity of fragmentation trees, and combine these kernels using recently proposed multiple kernel learning approaches. Experiments on two large reference datasets show that the new methods significantly improve molecular fingerprint prediction accuracy. These improvements result in better metabolite identification, doubling the number of metabolites ranked at the top position of the candidates list. © The Author 2014. Published by Oxford University Press.

Factors that affect molecular weight distribution of Suwannee river fulvic acid as determined by electrospray ionization/mass spectrometry

USGS Publications Warehouse

Rostad, Colleen E.; Leenheer, Jerry A.

2004-01-01

Effects of methylation, molar response, multiple charging, solvents, and positive and negative ionization on molecular weight distributions of aquatic fulvic acid were investigated by electrospray ionization/mass spectrometry. After preliminary analysis by positive and negative modes, samples and mixtures of standards were derivatized by methylation to minimize ionization sites and reanalyzed.Positive ionization was less effective and produced more complex spectra than negative ionization. Ionization in methanol/water produced greater response than in acetonitrile/water. Molar response varied widely for the selected free acid standards when analyzed individually and in a mixture, but after methylation this range decreased. After methylation, the number average molecular weight of the Suwannee River fulvic acid remained the same while the weight average molecular weight decreased. These differences are probably indicative of disaggregation of large aggregated ions during methylation. Since the weight average molecular weight decreased, it is likely that aggregate formation in the fulvic acid was present prior to derivatization, rather than multiple charging in the mass spectra.

Testing the molecular-hydrogen Kennicutt-Schmidt law in the low-density environments of extended ultraviolet disc galaxies

NASA Astrophysics Data System (ADS)

Watson, Linda C.; Martini, Paul; Lisenfeld, Ute; Böker, Torsten; Schinnerer, Eva

2016-01-01

Studying star formation beyond the optical radius of galaxies allows us to test empirical relations in extreme conditions with low average gas density and low molecular fraction. Previous studies discovered galaxies with extended ultraviolet (XUV) discs, which often contain star-forming regions with lower Hα-to-far-UV (FUV) flux ratios compared to inner disc star-forming regions. However, most previous studies lack measurements of molecular gas, which is presumably the component of the interstellar medium out of which stars form. We analysed published CO measurements and upper limits for 15 star-forming regions in the XUV or outer disc of three nearby spiral galaxies and a new CO upper limit from the IRAM (Institut de Radioastronomie Millimétrique) 30 m telescope in one star-forming region at r = 3.4r25 in the XUV disc of NGC 4625. We found that the star-forming regions are in general consistent with the same molecular-hydrogen Kennicutt-Schmidt law that applies within the optical radius, independent of whether we used Hα or FUV as the star formation rate (SFR) tracer. However, a number of the CO detections are significantly offset towards higher SFR surface density for their molecular-hydrogen surface density. Deeper CO data may enable us to use the presence or absence of molecular gas as an evolutionary probe to break the degeneracy between age and stochastic sampling of the initial mass function as the explanation for the low Hα-to-FUV flux ratios in XUV discs.

Method of assembly of molecular-sized nets and scaffolding

DOEpatents

Michl, Josef; Magnera, Thomas F.; David, Donald E.; Harrison, Robin M.

1999-01-01

The present invention relates to methods and starting materials for forming molecular-sized grids or nets, or other structures based on such grids and nets, by creating molecular links between elementary molecular modules constrained to move in only two directions on an interface or surface by adhesion or bonding to that interface or surface. In the methods of this invention, monomers are employed as the building blocks of grids and more complex structures. Monomers are introduced onto and allowed to adhere or bond to an interface. The connector groups of adjacent adhered monomers are then polymerized with each other to form a regular grid in two dimensions above the interface. Modules that are not bound or adhered to the interface are removed prior to reaction of the connector groups to avoid undesired three-dimensional cross-linking and the formation of non-grid structures. Grids formed by the methods of this invention are useful in a variety of applications, including among others, for separations technology, as masks for forming regular surface structures (i.e., metal deposition) and as templates for three-dimensional molecular-sized structures.

Method of assembly of molecular-sized nets and scaffolding

DOEpatents

Michl, J.; Magnera, T.F.; David, D.E.; Harrison, R.M.

1999-03-02

The present invention relates to methods and starting materials for forming molecular-sized grids or nets, or other structures based on such grids and nets, by creating molecular links between elementary molecular modules constrained to move in only two directions on an interface or surface by adhesion or bonding to that interface or surface. In the methods of this invention, monomers are employed as the building blocks of grids and more complex structures. Monomers are introduced onto and allowed to adhere or bond to an interface. The connector groups of adjacent adhered monomers are then polymerized with each other to form a regular grid in two dimensions above the interface. Modules that are not bound or adhered to the interface are removed prior to reaction of the connector groups to avoid undesired three-dimensional cross-linking and the formation of non-grid structures. Grids formed by the methods of this invention are useful in a variety of applications, including among others, for separations technology, as masks for forming regular surface structures (i.e., metal deposition) and as templates for three-dimensional molecular-sized structures. 9 figs.

ODMSummary: A Tool for Automatic Structured Comparison of Multiple Medical Forms Based on Semantic Annotation with the Unified Medical Language System.

PubMed

Storck, Michael; Krumm, Rainer; Dugas, Martin

2016-01-01

Medical documentation is applied in various settings including patient care and clinical research. Since procedures of medical documentation are heterogeneous and developed further, secondary use of medical data is complicated. Development of medical forms, merging of data from different sources and meta-analyses of different data sets are currently a predominantly manual process and therefore difficult and cumbersome. Available applications to automate these processes are limited. In particular, tools to compare multiple documentation forms are missing. The objective of this work is to design, implement and evaluate the new system ODMSummary for comparison of multiple forms with a high number of semantically annotated data elements and a high level of usability. System requirements are the capability to summarize and compare a set of forms, enable to estimate the documentation effort, track changes in different versions of forms and find comparable items in different forms. Forms are provided in Operational Data Model format with semantic annotations from the Unified Medical Language System. 12 medical experts were invited to participate in a 3-phase evaluation of the tool regarding usability. ODMSummary (available at https://odmtoolbox.uni-muenster.de/summary/summary.html) provides a structured overview of multiple forms and their documentation fields. This comparison enables medical experts to assess multiple forms or whole datasets for secondary use. System usability was optimized based on expert feedback. The evaluation demonstrates that feedback from domain experts is needed to identify usability issues. In conclusion, this work shows that automatic comparison of multiple forms is feasible and the results are usable for medical experts.

Detection of N-acetylated forms of alpha-MSH and beta-endorphin in the intermediate pituitary of the holostean fishes, Lepisosteus spatula, Lepisosteus osseus, and Amia calva.

PubMed

Dores, R M; Keller, H; White, Y; Marra, L E; Youson, J H

1994-01-01

Acid extracts of the intermediate pituitaries of the gars, L. spatula and L. osseus, were fractionated by Sephadex G-50 column chromatography and analyzed by radioimmunoassay. This procedure revealed that immunoreactive forms of N-acetylated beta-endorphin- and alpha-MSH-sized material were present in equimolar amounts and represented the major end products of the POMC biosynthetic pathway in these species. Cation-exchange chromatography indicated that multiple N-acetylated forms of beta-endorphin were present in the intermediate pituitaries of the two species of gar, and that these forms differed in their net positive charge and in their apparent molecular weight. Reversed-phase HPLC analysis of the alpha-MSH-related material indicated that up to 90% of the total MSH in the pituitary of the gar was N-acetylated. Furthermore, the predominant form of alpha-MSH in both species of gar was N,O-diacetyl-ACTH(1-13)-NH2. Nearly identical results were obtained following the analysis of alpha-MSH-related peptides in the intermediate pituitary of the bowfin, A. calva. The pattern of posttranslational processing of POMC observed in the intermediate pituitaries of holostean fishes is very similar to the processing events observed in lungfishes, turtles, and mammals; hence, the processing of POMC has been remarkably conserved during vertebrate evolution.

FIRST OPTICAL AND NEAR-INFRARED POLARIMETRY OF A MOLECULAR CLOUD FORMING A PROTO-BROWN DWARF CANDIDATE

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

Soam, A.; Maheswar, G.; Kwon, Jugmi

2015-04-20

LDN 328 is cited as an example of a fairly isolated clump contracting to form multiple sub-cores, possibly through gravitational fragmentation. In one of these sub-cores, a proto-brown dwarf (L328-IRS) candidate is in the process of formation through the self-gravitating contraction, similar to the formation scenario of a low-mass star. We present results of our optical and near-infrared polarization observations of regions toward LDN 328. This is the first observational attempt to map the magnetic field geometry of a cloud harboring a proto-brown dwarf candidate associated with a sub-parsec-scale molecular outflow. On a parsec scale, the magnetic field is foundmore » to follow the curved structure of the cloud showing a head–tail morphology. The magnetic field is found to be well ordered over a 0.02–0.2 pc scale around L328-IRS. Taking into account the uncertainties in the determination of position angles, the projected angular offset between the magnetic field direction and the outflow axis is found to be in the range of 0°–70°. Considering outflow to be the proxy for the rotation axis, the result obtained in this study implies that the rotation axis in L328 is preferably parallel to the local magnetic field. The magnetic field strength estimated in the close vicinity of L328-IRS is ∼20 μG. Results from the present study suggest that the magnetic field may be playing a vital role even in the cores that are forming sub-stellar sources.« less

Initiation of DNA replication: functional and evolutionary aspects

PubMed Central

Bryant, John A.; Aves, Stephen J.

2011-01-01

Background The initiation of DNA replication is a very important and highly regulated step in the cell division cycle. It is of interest to compare different groups of eukaryotic organisms (a) to identify the essential molecular events that occur in all eukaryotes, (b) to start to identify higher-level regulatory mechanisms that are specific to particular groups and (c) to gain insights into the evolution of initiation mechanisms. Scope This review features a wide-ranging literature survey covering replication origins, origin recognition and usage, modification of origin usage (especially in response to plant hormones), assembly of the pre-replication complex, loading of the replisome, genomics, and the likely origin of these mechanisms and proteins in Archaea. Conclusions In all eukaryotes, chromatin is organized for DNA replication as multiple replicons. In each replicon, replication is initiated at an origin. With the exception of those in budding yeast, replication origins, including the only one to be isolated so far from a plant, do not appear to embody a specific sequence; rather, they are AT-rich, with short tracts of locally bent DNA. The proteins involved in initiation are remarkably similar across the range of eukaryotes. Nevertheless, their activity may be modified by plant-specific mechanisms, including regulation by plant hormones. The molecular features of initiation are seen in a much simpler form in the Archaea. In particular, where eukaryotes possess a number of closely related proteins that form ‘hetero-complexes’ (such as the origin recognition complex and the MCM complex), archaeans typically possess one type of protein (e.g. one MCM) that forms a homo-complex. This suggests that several eukaryotic initiation proteins have evolved from archaeal ancestors by gene duplication and divergence. PMID:21508040

The variable presentations of glycogen storage disease type IV: a review of clinical, enzymatic and molecular studies.

PubMed

Moses, Shimon W; Parvari, Ruti

2002-03-01

Glycogen storage disease type IV (GSD-IV), also known as Andersen disease or amylopectinosis (MIM 23250), is a rare autosomal recessive disorder caused by a deficiency of glycogen branching enzyme (GBE) leading to the accumulation of amylopectin-like structures in affected tissues. The disease is extremely heterogeneous in terms of tissue involvement, age of onset and clinical manifestations. The human GBE cDNA is approximately 3-kb in length and encodes a 702-amino acid protein. The GBE amino acid sequence shows a high degree of conservation throughout species. The human GBE gene is located on chromosome 3p14 and consists of 16 exons spanning at least 118 kb of chromosomal DNA. Clinically the classic Andersen disease is a rapidly progressive disorder leading to terminal liver failure unless liver transplantation is performed. Several mutations have been reported in the GBE gene in patients with classic phenotype. Mutations in the GBE gene have also been identified in patients with the milder non-progressive hepatic form of the disease. Several other variants of GSD-IV have been reported: a variant with multi-system involvement including skeletal and cardiac muscle, nerve and liver; a juvenile polysaccharidosis with multi-system involvement but normal GBE activity; and the fatal neonatal neuromuscular form associated with a splice site mutation in the GBE gene. Other presentations include cardiomyopathy, arthrogryposis and even hydrops fetalis. Polyglucosan body disease, characterized by widespread upper and lower motor neuron lesions, can present with or without GBE deficiency indicating that different biochemical defects could result in an identical phenotype. It is evident that this disease exists in multiple forms with enzymatic and molecular heterogeneity unparalleled in the other types of glycogen storage diseases.

Superoxide dismutase (SOD) in boar spermatozoa: purification, biochemical properties and changes in activity during semen storage (16°C) in different extenders.

PubMed

Orzołek, Aleksandra; Wysocki, Paweł; Strzeżek, Jerzy; Kordan, Władysław

2013-03-01

The antioxidant system in semen is composed of enzymes, low-molecular weight antioxidants and seminal plasma proteins. Loss of enzymatic activity of superoxide dismutase (SOD) during semen preservation may cause insufficient antioxidant defense of boar spermatozoa. The aim of this study was to isolate and characterize SOD molecular forms from spermatozoa and to describe changes in SOD activity in boar sperm during preservation at 16°C. Sperm extracts were prepared from fresh or diluted semen and used for SOD purification or activity measurement. Ion-exchange chromatography and gel filtration was used to purify SOD molecular forms. BTS, Dilu Cell, M III and Vitasem were used as diluents for 5-day storage of semen at +16°C. The molecular form of SOD released from spermatozoa after cold shock and homogenization had a molecular weight of approximately 67kDa. The activity of the SOD form was the highest at pH 10 within the temperature range between 20 and 45°C. The enzymatic activity of form released after cold shock was inhibited by H2O2 and diethyldithiocarbamate (DDC; by 65 and 40%, respectively). The SOD form released by homogenization was inhibited by H2O2 and DDC (40%). The molecular form released after urea treatment was a 30kDa protein with maximum activity at 20°C and pH 10. Enzymatic activity of this form was inhibited by H2O2 by 35%, DDC by 80% and 2-mercaptoethanol by 15%. The antigenic determinants of SOD isolated from boar seminal plasma and spermatozoa were similar to each other. Susceptibility of spermatozoa to cold shock increased during storage, but the differences between extenders were statistically non-significant. Copyright © 2013 Society for Biology of Reproduction & the Institute of Animal Reproduction and Food Research of Polish Academy of Sciences in Olsztyn. Published by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

Wavelet Imaging on Multiple Scales (WIMS) reveals focal adhesion distributions, dynamics and coupling between actomyosin bundle stability

PubMed Central

Toplak, Tim; Palmieri, Benoit; Juanes-García, Alba; Vicente-Manzanares, Miguel; Grant, Martin; Wiseman, Paul W.

2017-01-01

We introduce and use Wavelet Imaging on Multiple Scales (WIMS) as an improvement to fluorescence correlation spectroscopy to measure physical processes and features that occur across multiple length scales. In this study, wavelet transforms of cell images are used to characterize molecular dynamics at the cellular and subcellular levels (i.e. focal adhesions). We show the usefulness of the technique by applying WIMS to an image time series of a migrating osteosarcoma cell expressing fluorescently labelled adhesion proteins, which allows us to characterize different components of the cell ranging from optical resolution scale through to focal adhesion and whole cell size scales. Using WIMS we measured focal adhesion numbers, orientation and cell boundary velocities for retraction and protrusion. We also determine the internal dynamics of individual focal adhesions undergoing assembly, disassembly or elongation. Thus confirming as previously shown, WIMS reveals that the number of adhesions and the area of the protruding region of the cell are strongly correlated, establishing a correlation between protrusion size and adhesion dynamics. We also apply this technique to characterize the behavior of adhesions, actin and myosin in Chinese hamster ovary cells expressing a mutant form of myosin IIB (1935D) that displays decreased filament stability and impairs front-back cell polarity. We find separate populations of actin and myosin at each adhesion pole for both the mutant and wild type form. However, we find these populations move rapidly inwards toward one another in the mutant case in contrast to the cells that express wild type myosin IIB where those populations remain stationary. Results obtained with these two systems demonstrate how WIMS has the potential to reveal novel correlations between chosen parameters that belong to different scales. PMID:29049414

The same pocket in menin binds both MLL and JUND but has opposite effects on transcription

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

Huang, Jing; Gurung, Buddha; Wan, Bingbing

2013-04-08

Menin is a tumour suppressor protein whose loss or inactivation causes multiple endocrine neoplasia 1 (MEN1), a hereditary autosomal dominant tumour syndrome that is characterized by tumorigenesis in multiple endocrine organs. Menin interacts with many proteins and is involved in a variety of cellular processes. Menin binds the JUN family transcription factor JUND and inhibits its transcriptional activity. Several MEN1 missense mutations disrupt the menin-JUND interaction, suggesting a correlation between the tumour-suppressor function of menin and its suppression of JUND-activated transcription. Menin also interacts with mixed lineage leukaemia protein 1 (MLL1), a histone H3 lysine 4 methyltransferase, and functions asmore » an oncogenic cofactor to upregulate gene transcription and promote MLL1-fusion-protein-induced leukaemogenesis. A recent report on the tethering of MLL1 to chromatin binding factor lens epithelium-derived growth factor (LEDGF) by menin indicates that menin is a molecular adaptor coordinating the functions of multiple proteins. Despite its importance, how menin interacts with many distinct partners and regulates their functions remains poorly understood. Here we present the crystal structures of human menin in its free form and in complexes with MLL1 or with JUND, or with an MLL1-LEDGF heterodimer. These structures show that menin contains a deep pocket that binds short peptides of MLL1 or JUND in the same manner, but that it can have opposite effects on transcription. The menin-JUND interaction blocks JUN N-terminal kinase (JNK)-mediated JUND phosphorylation and suppresses JUND-induced transcription. In contrast, menin promotes gene transcription by binding the transcription activator MLL1 through the peptide pocket while still interacting with the chromatin-anchoring protein LEDGF at a distinct surface formed by both menin and MLL1.« less

Multiple orthokeratinized odontogenic cysts: a case report.

PubMed

Cheng, Yi-Shing Lisa; Liang, Hui; Wright, John; Teenier, Tom

2015-03-01

The purpose of this report is to document the clinical, radiographic, pathological and molecular findings of the first case of multiple orthokeratinized odontogenic cysts (OOCs). Multiple odontogenic keratocysts are one of the major features of nevoid basal cell carcinoma syndrome (NBCCS), and loss of heterozygosity in the PTCH gene, the culprit gene for NBCCS, has recently been found in sporadic OOC cases. Therefore, in this presenting case, we also investigated the possibility that this patient might also have NBCCS, by comparing the available clinical information and the molecular findings of this case to the diagnostic criteria for NBCCS (as proposed by the First International Colloquium on NBCCS in 2011). However, this patient with multiple OOCs showed no evidence of having NBCCS. This conclusion supports the findings from previous case series based on sporadic cases that OOC does not appear to be associated with NBCCS.

Microcanonical molecular simulations of methane hydrate nucleation and growth: evidence that direct nucleation to sI hydrate is among the multiple nucleation pathways.

PubMed

Zhang, Zhengcai; Walsh, Matthew R; Guo, Guang-Jun

2015-04-14

The results of six high-precision constant energy molecular dynamics (MD) simulations initiated from methane-water systems equilibrated at 80 MPa and 250 K indicate that methane hydrates can nucleate via multiple pathways. Five trajectories nucleate to an amorphous solid. One trajectory nucleates to a structure-I hydrate template with long-range order which spans the simulation box across periodic boundaries despite the presence of several defects. While experimental and simulation data for hydrate nucleation with different time- and length-scales suggest that there may exist multiple pathways for nucleation, including metastable intermediates and the direct formation of the globally-stable phase, this work provides the most compelling evidence that direct formation to the globally stable crystalline phase is one of the multiple pathways available for hydrate nucleation.

Optima HD Imax: Molecular Implant

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

Tieger, D. R.; Splinter, P. R.; Hsieh, T. J.

2008-11-03

Molecular implantation offers semiconductor device manufacturers multiple advantages over traditional high current ion implanters. The dose multiplication due to implanting more than one atom per molecule and the transport of beams at higher energies relative to the effective particle energies result in significant throughput enhancements without risk of energy contamination. The Optima HD Imax is introduced with molecular implant capability and the ability to reach up to 4.2 keV effective {sup 11}B from octadecaborane (B{sub 18}H{sub 22}). The ion source and beamline are optimized for molecular species ionization and transport. The beamline is coupled to the Optima HD mechanically scannedmore » endstation. The use of spot beam technology with ionized molecules maximizes the throughput potential and produces uniform implants with fast setup time and with superior angle control. The implanter architecture is designed to run multiple molecular species; for example, in addition to B{sub 18}H{sub 22} the system is capable of implanting carbon molecules for strain engineering and shallow junction engineering. Source lifetime data and typical operating conditions are described both for high dose, memory applications such as dual poly gate as well as lower energy implants for source drain extension and contact implants. Throughputs have been achieved in excess of 50 wafers per hour at doses up to 1x10{sup 16} ions/cm{sup 2} and for energies as low as 1 keV.« less

Modeling colorectal cancer using CRISPR-Cas9-mediated engineering of human intestinal organoids.

PubMed

Matano, Mami; Date, Shoichi; Shimokawa, Mariko; Takano, Ai; Fujii, Masayuki; Ohta, Yuki; Watanabe, Toshiaki; Kanai, Takanori; Sato, Toshiro

2015-03-01

Human colorectal tumors bear recurrent mutations in genes encoding proteins operative in the WNT, MAPK, TGF-β, TP53 and PI3K pathways. Although these pathways influence intestinal stem cell niche signaling, the extent to which mutations in these pathways contribute to human colorectal carcinogenesis remains unclear. Here we use the CRISPR-Cas9 genome-editing system to introduce multiple such mutations into organoids derived from normal human intestinal epithelium. By modulating the culture conditions to mimic that of the intestinal niche, we selected isogenic organoids harboring mutations in the tumor suppressor genes APC, SMAD4 and TP53, and in the oncogenes KRAS and/or PIK3CA. Organoids engineered to express all five mutations grew independently of niche factors in vitro, and they formed tumors after implantation under the kidney subcapsule in mice. Although they formed micrometastases containing dormant tumor-initiating cells after injection into the spleen of mice, they failed to colonize in the liver. In contrast, engineered organoids derived from chromosome-instable human adenomas formed macrometastatic colonies. These results suggest that 'driver' pathway mutations enable stem cell maintenance in the hostile tumor microenvironment, but that additional molecular lesions are required for invasive behavior.

Centrosomes are autocatalytic droplets of pericentriolar material organized by centrioles.

PubMed

Zwicker, David; Decker, Markus; Jaensch, Steffen; Hyman, Anthony A; Jülicher, Frank

2014-07-01

Centrosomes are highly dynamic, spherical organelles without a membrane. Their physical nature and their assembly are not understood. Using the concept of phase separation, we propose a theoretical description of centrosomes as liquid droplets. In our model, centrosome material occurs in a form soluble in the cytosol and a form that tends to undergo phase separation from the cytosol. We show that an autocatalytic chemical transition between these forms accounts for the temporal evolution observed in experiments. Interestingly, the nucleation of centrosomes can be controlled by an enzymatic activity of the centrioles, which are present at the core of all centrosomes. This nonequilibrium feature also allows for multiple stable centrosomes, a situation that is unstable in equilibrium phase separation. Our theory explains the growth dynamics of centrosomes for all cell sizes down to the eight-cell stage of the Caenorhabditis elegans embryo, and it also accounts for data acquired in experiments with aberrant numbers of centrosomes and altered cell volumes. Furthermore, the model can describe unequal centrosome sizes observed in cells with perturbed centrioles. We also propose an interpretation of the molecular details of the involved proteins in the case of C. elegans. Our example suggests a general picture of the organization of membraneless organelles.

Effects of Plume Hydrodynamics and Oxidation on the Composition of a Condensing Laser-Induced Plasma

DOE PAGES

Weisz, David G.; Crowhurst, Jonathan C.; Finko, Mikhail S.; ...

2018-02-01

High-temperature chemistry in laser ablation plumes leads to vapor-phase speciation, which can induce chemical fractionation during condensation. In this work, using emission spectroscopy acquired after ablation of a SrZrO 3 target, we have experimentally observed the formation of multiple molecular species (ZrO and SrO) as a function of time as the laser ablation plume evolves. Although the stable oxides SrO and ZrO 2 are both refractory, we observed emission from the ZrO intermediate at earlier times than SrO. We deduced the time-scale of oxygen entrainment into the laser ablation plume using an 18O 2 environment by observing the in-growth ofmore » Zr 18O in the emission spectra relative to Zr 16O, which was formed by reaction of Zr with 16O from the target itself. Using temporally resolved plume-imaging, we determined that ZrO formed more readily at early times, volumetrically in the plume, while SrO formed later in time, around the periphery. Lastly, using a simple temperature-dependent reaction model, we have illustrated that the formation sequence of these oxides subsequent to ablation is predictable to first order.« less

Dscam2 mediates axonal tiling in the Drosophila visual system

PubMed Central

Millard, S. Sean; Flanagan, John J.; Pappu, Kartik S.; Wu, Wei; Zipursky, S. Lawrence

2009-01-01

Sensory processing centres in both the vertebrate and the invertebrate brain are often organized into reiterated columns, thus facilitating an internal topographic representation of the external world. Cells within each column are arranged in a stereotyped fashion and form precise patterns of synaptic connections within discrete layers. These connections are largely confined to a single column, thereby preserving the spatial information from the periphery. Other neurons integrate this information by connecting to multiple columns. Restricting axons to columns is conceptually similar to tiling. Axons and dendrites of neighbouring neurons of the same class use tiling to form complete, yet non-overlapping, receptive fields1-3. It is thought that, at the molecular level, cell-surface proteins mediate tiling through contact-dependent repulsive interactions1,2,4,5, but proteins serving this function have not yet been identified. Here we show that the immunoglobulin superfamily member Dscam2 restricts the connections formed by L1 lamina neurons to columns in the Drosophila visual system. Our data support a model in which Dscam2 homophilic interactions mediate repulsion between neurites of L1 cells in neighbouring columns. We propose that Dscam2 is a tiling receptor for L1 neurons. PMID:17554308

Molecular biological analysis in a patient with multiple lung adenocarcinomas.

PubMed

Wakayama, Tomoshige; Hirata, Hirokuni; Suka, Shunsuke; Sato, Kozo; Tatewaki, Masamitsu; Souma, Ryosuke; Satoh, Hideyuki; Tamura, Motohiko; Matsumura, Yuji; Imada, Hiroki; Sugiyama, Kumiya; Arima, Masafumi; Kurasawa, Kazuhiro; Fukuda, Takeshi; Fukushima, Yasutsugu

2018-05-01

The utility of molecular biological analysis in lung adenocarcinoma has been demonstrated. Herein we report a rare case presenting as multiple lung adenocarcinomas with four different EGFR gene mutations detected in three lung tumors. After opacification was detected by routine chest X-ray, the patient, a 64-year-old woman, underwent chest computed tomography which revealed a right lung segment S4 ground-glass nodule (GGN). Follow-up computed tomography revealed a 42 mm GGN nodule with a 26 mm nodule (S6) and a 20 mm GGN (S10). Histopathology of resected specimens from the right middle and lower lobes revealed all three nodules were adenocarcinomas. Four EGFR mutations were detected; no three tumors had the same mutations. Molecular biological analysis is a promising tool for the diagnosis of primary tumors in patients with multiple lung carcinomas of the same histotype, enabling appropriate treatment. © 2018 The Authors. Thoracic Cancer published by China Lung Oncology Group and John Wiley & Sons Australia, Ltd.

Simultaneous acquisition of differing image types

DOEpatents

Demos, Stavros G

2012-10-09

A system in one embodiment includes an image forming device for forming an image from an area of interest containing different image components; an illumination device for illuminating the area of interest with light containing multiple components; at least one light source coupled to the illumination device, the at least one light source providing light to the illumination device containing different components, each component having distinct spectral characteristics and relative intensity; an image analyzer coupled to the image forming device, the image analyzer decomposing the image formed by the image forming device into multiple component parts based on type of imaging; and multiple image capture devices, each image capture device receiving one of the component parts of the image. A method in one embodiment includes receiving an image from an image forming device; decomposing the image formed by the image forming device into multiple component parts based on type of imaging; receiving the component parts of the image; and outputting image information based on the component parts of the image. Additional systems and methods are presented.

Novel strategies to construct complex synthetic vectors to produce DNA molecular weight standards.

PubMed

Chen, Zhe; Wu, Jianbing; Li, Xiaojuan; Ye, Chunjiang; Wenxing, He

2009-05-01

DNA molecular weight standards (DNA markers, nucleic acid ladders) are commonly used in molecular biology laboratories as references to estimate the size of various DNA samples in electrophoresis process. One method of DNA marker production is digestion of synthetic vectors harboring multiple DNA fragments of known sizes by restriction enzymes. In this article, we described three novel strategies-sequential DNA fragment ligation, screening of ligation products by polymerase chain reaction (PCR) with end primers, and "small fragment accumulation"-for constructing complex synthetic vectors and minimizing the mass differences between DNA fragments produced from restrictive digestion of synthetic vectors. The strategy could be applied to construct various complex synthetic vectors to produce any type of low-range DNA markers, usually available commercially. In addition, the strategy is useful for single-step ligation of multiple DNA fragments for construction of complex synthetic vectors and other applications in molecular biology field.

Cloning Yeast Actin cDNA Leads to an Investigative Approach for the Molecular Biology Laboratory

ERIC Educational Resources Information Center

Black, Michael W.; Tuan, Alice; Jonasson, Erin

2008-01-01

The emergence of molecular tools in multiple disciplines has elevated the importance of undergraduate laboratory courses that train students in molecular biology techniques. Although it would also be desirable to provide students with opportunities to apply these techniques in an investigative manner, this is generally not possible in the…

Lighting the dark molecular gas and a Bok globule

NASA Astrophysics Data System (ADS)

Togi, Aditya G.

Stars are the building blocks of galaxies. The gas present in galaxies is the primary fuel for star formation. Galaxy evolution depends on the amount of gas present in the interstellar medium (ISM). Stars are born mainly from molecular gas in the GMCs. Robust knowledge of the molecular hydrogen H2 gas distribution is necessary to understand star formation in galaxies. Since H2 is not readily observable in the cold interstellar medium (ISM), the molecular gas content has traditionally been inferred using indirect tracers like carbon-monoxide (CO), dust emission, gamma ray interactions, and star formation efficiency. Physical processes resulting in enhancement and reduction of these indirect tracers can result in misleading estimates of molecular gas masses. My dissertation work is based on devising a new temperature power law distribution model for H2, a direct tracer, to calculate the total molecular gas mass in galaxies. The model parameters are estimated using mid infrared (MIR) H2 rotational line fluxes obtained from IRS-Spitzer (Infrared Spectrograph-Spitzer) instrument and the model is extrapolated to a suitable lower temperature to recover the total molecular gas mass. The power law model is able to recover the dark molecular gas, undetected by CO, in galaxies at metallicity as low as one-tenth of our Milky Way value. I have applied the power law model in U/LIRGs and shocks of Stephan's Quintet to understand molecular gas properties, where shocks play an important role in exciting H2. Comparing the molecular gas content derived through our power law model can be useful in studying the application of our model in mergers. The parameters derived by our model is useful in understanding variation in molecular gas properties in shock regions of Stephan's Quintet. Low mass stars are formed in small isolated dense cores known as Bok globules. Multiple star formation events are seen in a Bok globule. In my thesis I also studied a Bok globule, B207, and determined the physical properties and future evolutionary stage of the cloud. My thesis spans studying ISM properties in galaxies from kpc to sub-pc scales. Using the power law model in the coming era of James Webb Space Telescope (JWST) with the high sensitivity MIR Instrument (MIRI) spectrograph we will be able to understand the properties of molecular gas at low and high redshifts.

A Theoretical and Experimental Study of DNA Self-assembly

NASA Astrophysics Data System (ADS)

Chandran, Harish

The control of matter and phenomena at the nanoscale is fast becoming one of the most important challenges of the 21st century with wide-ranging applications from energy and health care to computing and material science. Conventional top-down approaches to nanotechnology, having served us well for long, are reaching their inherent limitations. Meanwhile, bottom-up methods such as self-assembly are emerging as viable alternatives for nanoscale fabrication and manipulation. A particularly successful bottom up technique is DNA self-assembly where a set of carefully designed DNA strands form a nanoscale object as a consequence of specific, local interactions among the different components, without external direction. The final product of the self-assembly process might be a static nanostructure or a dynamic nanodevice that performs a specific function. Over the past two decades, DNA self-assembly has produced stunning nanoscale objects such as 2D and 3D lattices, polyhedra and addressable arbitrary shaped substrates, and a myriad of nanoscale devices such as molecular tweezers, computational circuits, biosensors and molecular assembly lines. In this dissertation we study multiple problems in the theory, simulations and experiments of DNA self-assembly. We extend the Turing-universal mathematical framework of self-assembly known as the Tile Assembly Model by incorporating randomization during the assembly process. This allows us to reduce the tile complexity of linear assemblies. We develop multiple techniques to build linear assemblies of expected length N using far fewer tile types than previously possible. We abstract the fundamental properties of DNA and develop a biochemical system, which we call meta-DNA, based entirely on strands of DNA as the only component molecule. We further develop various enzyme-free protocols to manipulate meta-DNA systems and provide strand level details along with abstract notations for these mechanisms. We simulate DNA circuits by providing detailed designs for local molecular computations that involve spatially contiguous molecules arranged on addressable substrates via enzyme-free DNA hybridization reaction cascades. We use the Visual DSD simulation software in conjunction with localized reaction rates obtained from biophysical modeling to create chemical reaction networks of localized hybridization circuits that are then model checked using the PRISM model checking software. We develop a DNA detection system employing the triggered self-assembly of a novel DNA dendritic nanostructure. Detection begins when a specific, single-stranded target DNA strand triggers a hybridization chain reaction between two distinct DNA hairpins. Each hairpin opens and hybridizes up to two copies of the other, and hence each layer of the growing dendritic nanostructure can in principle accommodate an exponentially increasing number of cognate molecules, generating a nanostructure with high molecular weight. We build linear activatable assemblies employing a novel protection/deprotection strategy to strictly enforce the direction of tiling assembly growth to ensure the robustness of the assembly process. Our system consists of two tiles that can form a linear co-polymer. These tiles, which are initially protected such that they do not react with each other, can be activated to form linear co-polymers via the use of a strand displacing enzyme.

Comprehensive molecular diagnosis of a large cohort of Japanese retinitis pigmentosa and Usher syndrome patients by next-generation sequencing.

PubMed

Oishi, Maho; Oishi, Akio; Gotoh, Norimoto; Ogino, Ken; Higasa, Koichiro; Iida, Kei; Makiyama, Yukiko; Morooka, Satoshi; Matsuda, Fumihiko; Yoshimura, Nagahisa

2014-10-16

Retinitis pigmentosa (RP), a major cause of blindness in developed countries, has multiple causative genes; its prevalence differs by ethnicity. Usher syndrome is the most common form of syndromic RP and is accompanied by hearing impairment. Although molecular diagnosis is challenging, recent technological advances such as targeted high-throughput resequencing are efficient screening tools. We performed comprehensive molecular testing in 329 Japanese RP and Usher syndrome patients by using a custom capture panel that covered the coding exons and exon/intron boundaries of all 193 known inherited eye disease genes combined with Illumina HiSequation 2500. Candidate variants were screened using systematic data analyses, and their potential pathogenicity was assessed according to the frequency of the variants in normal populations, in silico prediction tools, and compatibility with known phenotypes or inheritance patterns. Molecular diagnoses were made in 115/317 RP patients (36.3%) and 6/12 Usher syndrome patients (50%). We identified 104 distinct mutations, including 66 novel mutations. EYS, USH2A, and RHO were common causative genes. In particular, mutations in EYS accounted for 15.0% of the autosomal recessive/simplex RP patients or 10.7% of the entire RP cohort. Among the 189 previously reported mutations detected in the current study, 55 (29.1%) were found commonly in Japanese or other public databases and were excluded from molecular diagnoses. By screening a large cohort of patients, this study catalogued the genetic variations involved in RP and Usher syndrome in a Japanese population and highlighted the different distribution of causative genes among populations. Copyright 2014 The Association for Research in Vision and Ophthalmology, Inc.

Feeling stretched or compressed? The multiple mechanosensitive responses of wood formation to bending.

PubMed

Roignant, Jeanne; Badel, Éric; Leblanc-Fournier, Nathalie; Brunel-Michac, Nicole; Ruelle, Julien; Moulia, Bruno; Decourteix, Mélanie

2018-05-11

Trees constantly experience wind, perceive resulting mechanical cues, and modify their growth and development accordingly. Previous studies have demonstrated that multiple bending treatments trigger ovalization of the stem and the formation of flexure wood in gymnosperms, but ovalization and flexure wood have rarely been studied in angiosperms, and none of the experiments conducted so far has used multidirectional bending treatments at controlled intensities. Assuming that bending involves tensile and compressive strain, we hypothesized that different local strains may generate specific growth and wood differentiation responses. Basal parts of young poplar stems were subjected to multiple transient controlled unidirectional bending treatments during 8 weeks, which enabled a distinction to be made between the wood formed under tensile or compressive flexural strains. This set-up enabled a local analysis of poplar stem responses to multiple stem bending treatments at growth, anatomical, biochemical and molecular levels. In response to multiple unidirectional bending treatments, poplar stems developed significant cross-sectional ovalization. At the tissue level, some aspects of wood differentiation were similarly modulated in the compressed and stretched zones (vessel frequency and diameter of fibres without a G-layer), whereas other anatomical traits (vessel diameter, G-layer formation, diameter of fibres with a G-layer and microfibril angle) and the expression of fasciclin-encoding genes were differentially modulated in the two zones. This work leads us to propose new terminologies to distinguish the 'flexure wood' produced in response to multiple bidirectional bending treatments from wood produced under transient tensile strain (tensile flexure wood; TFW) or under transient compressive strain (compressive flexure wood; CFW). By highlighting similarities and differences between tension wood and TFW and by demonstrating that plants could have the ability to discriminate positive strains from negative strains, this work provides new insight into the mechanisms of mechanosensitivity in plants.

Inner ear development: building a spiral ganglion and an organ of Corti out of unspecified ectoderm.

PubMed

Fritzsch, Bernd; Pan, Ning; Jahan, Israt; Elliott, Karen L

2015-07-01

The mammalian inner ear develops from a placodal thickening into a complex labyrinth of ducts with five sensory organs specialized to detect position and movement in space. The mammalian ear also develops a spiraled cochlear duct containing the auditory organ, the organ of Corti (OC), specialized to translate sound into hearing. Development of the OC from a uniform sheet of ectoderm requires unparalleled precision in the topological developmental engineering of four different general cell types, namely sensory neurons, hair cells, supporting cells, and general otic epithelium, into a mosaic of ten distinctly recognizable cell types in and around the OC, each with a unique distribution. Moreover, the OC receives unique innervation by ear-derived spiral ganglion afferents and brainstem-derived motor neurons as efferents and requires neural-crest-derived Schwann cells to form myelin and neural-crest-derived cells to induce the stria vascularis. This transformation of a sheet of cells into a complicated interdigitating set of cells necessitates the orchestrated expression of multiple transcription factors that enable the cellular transformation from ectoderm into neurosensory cells forming the spiral ganglion neurons (SGNs), while simultaneously transforming the flat epithelium into a tube, the cochlear duct, housing the OC. In addition to the cellular and conformational changes forming the cochlear duct with the OC, changes in the surrounding periotic mesenchyme form passageways for sound to stimulate the OC. We review molecular developmental data, generated predominantly in mice, in order to integrate the well-described expression changes of transcription factors and their actions, as revealed in mutants, in the formation of SGNs and OC in the correct position and orientation with suitable innervation. Understanding the molecular basis of these developmental changes leading to the formation of the mammalian OC and highlighting the gaps in our knowledge might guide in vivo attempts to regenerate this most complicated cellular mosaic of the mammalian body for the reconstitution of hearing in a rapidly growing population of aging people suffering from hearing loss.

FERMI LARGE AREA TELESCOPE STUDY OF COSMIC RAYS AND THE INTERSTELLAR MEDIUM IN NEARBY MOLECULAR CLOUDS

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

Ackermann, M.; Ajello, M.; Allafort, A.

We report an analysis of the interstellar {gamma}-ray emission from the Chamaeleon, R Coronae Australis (R CrA), and Cepheus and Polaris flare regions with the Fermi Large Area Telescope. They are among the nearest molecular cloud complexes, within {approx}300 pc from the solar system. The {gamma}-ray emission produced by interactions of cosmic rays (CRs) and interstellar gas in those molecular clouds is useful to study the CR densities and distributions of molecular gas close to the solar system. The obtained {gamma}-ray emissivities above 250 MeV are (5.9 {+-} 0.1{sub stat}{sup +0.9}{sub -1.0sys}) Multiplication-Sign 10{sup -27} photons s{sup -1} sr{sup -1}more » H-atom{sup -1}, (10.2 {+-} 0.4{sub stat}{sup +1.2}{sub -1.7sys}) Multiplication-Sign 10{sup -27} photons s{sup -1} sr{sup -1} H-atom{sup -1}, and (9.1 {+-} 0.3{sub stat}{sup +1.5}{sub -0.6sys}) Multiplication-Sign 10{sup -27} photons s{sup -1} sr{sup -1} H-atom{sup -1} for the Chamaeleon, R CrA, and Cepheus and Polaris flare regions, respectively. Whereas the energy dependences of the emissivities agree well with that predicted from direct CR observations at the Earth, the measured emissivities from 250 MeV to 10 GeV indicate a variation of the CR density by {approx}20% in the neighborhood of the solar system, even if we consider systematic uncertainties. The molecular mass calibrating ratio, X{sub CO} = N(H{sub 2})/W{sub CO}, is found to be (0.96 {+-} 0.06{sub stat}{sup +0.15}{sub -0.12sys}) Multiplication-Sign 10{sup 20} H{sub 2}-molecule cm{sup -2} (K km s{sup -1}){sup -1}, (0.99 {+-} 0.08{sub stat}{sup +0.18}{sub -0.10sys}) Multiplication-Sign 10{sup 20} H{sub 2}-molecule cm{sup -2} (K km s{sup -1}){sup -1}, and (0.63 {+-} 0.02{sub stat}{sup +0.09}{sub -0.07sys}) Multiplication-Sign 10{sup 20} H{sub 2}-molecule cm{sup -2} (K km s{sup -1}){sup -1} for the Chamaeleon, R CrA, and Cepheus and Polaris flare regions, respectively, suggesting a variation of X{sub CO} in the vicinity of the solar system. From the obtained values of X{sub CO}, the masses of molecular gas traced by W{sub CO} in the Chamaeleon, R CrA, and Cepheus and Polaris flare regions are estimated to be {approx}5 Multiplication-Sign 10{sup 3} M{sub Sun }, {approx}10{sup 3} M{sub Sun }, and {approx}3.3 Multiplication-Sign 10{sup 4} M{sub Sun }, respectively. A comparable amount of gas not traced well by standard H I and CO surveys is found in the regions investigated.« less

Molecular receptors in metal oxide sol-gel materials prepared via molecular imprinting

DOEpatents

Sasaki, Darryl Y.; Brinker, C. Jeffrey; Ashley, Carol S.; Daitch, Charles E.; Shea, Kenneth J.; Rush, Daniel J.

2000-01-01

A method is provided for molecularly imprinting the surface of a sol-gel material, by forming a solution comprised of a sol-gel material, a solvent, an imprinting molecule, and a functionalizing siloxane monomer of the form Si(OR).sub.3-n X.sub.n, wherein n is an integer between zero and three and X is a functional group capable of reacting with the imprinting molecule, evaporating the solvent, and removing the imprinting molecule to form the molecularly imprinted metal oxide sol-gel material. The use of metal oxide sol-gels allows the material porosity, pore size, density, surface area, hardness, electrostatic charge, polarity, optical density, and surface hydrophobicity to be tailored and be employed as sensors and in catalytic and separations operations.

ODMSummary: A Tool for Automatic Structured Comparison of Multiple Medical Forms Based on Semantic Annotation with the Unified Medical Language System

PubMed Central

Krumm, Rainer; Dugas, Martin

2016-01-01

Introduction Medical documentation is applied in various settings including patient care and clinical research. Since procedures of medical documentation are heterogeneous and developed further, secondary use of medical data is complicated. Development of medical forms, merging of data from different sources and meta-analyses of different data sets are currently a predominantly manual process and therefore difficult and cumbersome. Available applications to automate these processes are limited. In particular, tools to compare multiple documentation forms are missing. The objective of this work is to design, implement and evaluate the new system ODMSummary for comparison of multiple forms with a high number of semantically annotated data elements and a high level of usability. Methods System requirements are the capability to summarize and compare a set of forms, enable to estimate the documentation effort, track changes in different versions of forms and find comparable items in different forms. Forms are provided in Operational Data Model format with semantic annotations from the Unified Medical Language System. 12 medical experts were invited to participate in a 3-phase evaluation of the tool regarding usability. Results ODMSummary (available at https://odmtoolbox.uni-muenster.de/summary/summary.html) provides a structured overview of multiple forms and their documentation fields. This comparison enables medical experts to assess multiple forms or whole datasets for secondary use. System usability was optimized based on expert feedback. Discussion The evaluation demonstrates that feedback from domain experts is needed to identify usability issues. In conclusion, this work shows that automatic comparison of multiple forms is feasible and the results are usable for medical experts. PMID:27736972

Molecular Design of Branched and Binary Molecules at Ordered Interfaces

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

Genson, Kirsten Larson

2005-01-01

This study examined five different branched molecular architectures to discern the effect of design on the ability of molecules to form ordered structures at interfaces. Photochromic monodendrons formed kinked packing structures at the air-water interface due to the cross-sectional area mismatch created by varying number of alkyl tails and the hydrophilic polar head group. The lower generations formed orthorhombic unit cell with long range ordering despite the alkyl tails tilted to a large degree. Favorable interactions between liquid crystalline terminal groups and the underlying substrate were observed to compel a flexible carbosilane dendrimer core to form a compressed elliptical conformationmore » which packed stagger within lamellae domains with limited short range ordering. A twelve arm binary star polymer was observed to form two dimensional micelles at the air-water interface attributed to the higher polystyrene block composition. Linear rod-coil molecules formed a multitude of packing structures at the air-water interface due to the varying composition. Tree-like rod-coil molecules demonstrated the ability to form one-dimensional structures at the air-water interface and at the air-solvent interface caused by the preferential ordering of the rigid rod cores. The role of molecular architecture and composition was examined and the influence chemically competing fragments was shown to exert on the packing structure. The amphiphilic balance of the different molecular series exhibited control on the ordering behavior at the air-water interface and within bulk structures. The shell nature and tail type was determined to dictate the preferential ordering structure and molecular reorganization at interfaces with the core nature effect secondary.« less

Can we beat the biotin-avidin pair?: cucurbit[7]uril-based ultrahigh affinity host-guest complexes and their applications.

PubMed

Shetty, Dinesh; Khedkar, Jayshree K; Park, Kyeng Min; Kim, Kimoon

2015-12-07

The design of synthetic, monovalent host-guest molecular recognition pairs is still challenging and of particular interest to inquire into the limits of the affinity that can be achieved with designed systems. In this regard, cucurbit[7]uril (CB[7]), an important member of the host family cucurbit[n]uril (CB[n], n = 5-8, 10, 14), has attracted much attention because of its ability to form ultra-stable complexes with multiple guests. The strong hydrophobic effect between the host cavity and guests, ion-dipole and dipole-dipole interactions of guests with CB portals helps in cooperative and multiple noncovalent interactions that are essential for realizing such strong complexations. These highly selective, strong yet dynamic interactions can be exploited in many applications including affinity chromatography, biomolecule immobilization, protein isolation, biological catalysis, and sensor technologies. In this review, we summarize the progress in the development of high affinity guests for CB[7], factors affecting the stability of complexes, theoretical insights, and the utility of these high affinity pairs in different challenging applications.

Stereoselective HDAC inhibition from cysteine-derived zinc-binding groups.

PubMed

Butler, Kyle V; He, Rong; McLaughlin, Kathryn; Vistoli, Giulio; Langley, Brett; Kozikowski, Alan P

2009-08-01

A series of small-molecule histone deacetylase (HDAC) inhibitors, which feature zinc binding groups derived from cysteine, were synthesized. These inhibitors were tested against multiple HDAC isoforms, and the most potent, compound 10, was determined to have IC(50) values below 1 microM. The compounds were also tested in a cellular assay of oxidative stress-induced neurodegeneration. Many of the inhibitors gave near-complete protection against cell death at 10 microM without the neurotoxicity seen with hydroxamic acid-based inhibitors, and were far more neuroprotective than HDAC inhibitors currently in clinical trials. Both enantiomers of cysteine were used in the synthesis of a variety of novel zinc-binding groups (ZBGs). Derivatives of L-cysteine were active in the HDAC inhibition assays, while the derivatives of D-cysteine were inactive. Notably, the finding that both the D- and L-cysteine derivatives were active in the neuroprotection assays suggests that multiple mechanisms are working to protect the neurons from cell death. Molecular modeling was employed to investigate the differences in inhibitory activity between the HDAC inhibitors generated from the two enantiomeric forms of cysteine.

3D local structure around copper site of rabbit prion-related protein: Quantitative determination by XANES spectroscopy combined with multiple-scattering calculations

NASA Astrophysics Data System (ADS)

Cui, P. X.; Lian, F. L.; Wang, Y.; Wen, Yi; Chu, W. S.; Zhao, H. F.; Zhang, S.; Li, J.; Lin, D. H.; Wu, Z. Y.

2014-02-01

Prion-related protein (PrP), a cell-surface copper-binding glycoprotein, is considered to be responsible for a number of transmissible spongiform encephalopathies (TSEs). The structural conversion of PrP from the normal cellular isoform (PrPC) to the post-translationally modified form (PrPSc) is thought to be relevant to Cu2+ binding to histidine residues. Rabbits are one of the few mammalian species that appear to be resistant to TSEs, because of the structural characteristics of the rabbit prion protein (RaPrPC) itself. Here we determined the three-dimensional local structure around the C-terminal high-affinity copper-binding sites using X-ray absorption near-edge structure combined with ab initio calculations in the framework of the multiple-scattering (MS) theory. Result shows that two amino acid resides, Gln97 and Met108, and two histidine residues, His95 and His110, are involved in binding this copper(II) ion. It might help us understand the roles of copper in prion conformation conversions, and the molecular mechanisms of prion-involved diseases.

Free energy landscape of the Michaelis complex of lactate dehydrogenase: A network analysis of atomistic simulations

NASA Astrophysics Data System (ADS)

Pan, Xiaoliang; Schwartz, Steven

2015-03-01

It has long been recognized that the structure of a protein is a hierarchy of conformations interconverting on multiple time scales. However, the conformational heterogeneity is rarely considered in the context of enzymatic catalysis in which the reactant is usually represented by a single conformation of the enzyme/substrate complex. Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of two forms of the cofactor nicotinamide adenine dinucleotide (NADH and NAD+). Recent experimental results suggest that multiple substates exist within the Michaelis complex of LDH, and they are catalytic competent at different reaction rates. In this study, millisecond-scale all-atom molecular dynamics simulations were performed on LDH to explore the free energy landscape of the Michaelis complex, and network analysis was used to characterize the distribution of the conformations. Our results provide a detailed view of the kinetic network the Michaelis complex and the structures of the substates at atomistic scale. It also shed some light on understanding the complete picture of the catalytic mechanism of LDH.

Trade-offs in osmoregulation and parallel shifts in molecular function follow ecological transitions to freshwater in the Alewife

USGS Publications Warehouse

Velotta, Jonathan P.; McCormick, Stephen; Schultz, Eric T.

2015-01-01

Adaptation to freshwater may be expected to reduce performance in seawater because these environments represent opposing selective regimes. We tested for such a trade-off in populations of the Alewife (Alosa pseudoharengus). Alewives are ancestrally anadromous, and multiple populations have been independently restricted to freshwater (landlocked). We conducted salinity challenge experiments, whereby juvenile Alewives from one anadromous and multiple landlocked populations were exposed to freshwater and seawater on acute and acclimation timescales. In response to acute salinity challenge trials, independently derived landlocked populations varied in the degree to which seawater tolerance has been lost. In laboratory-acclimation experiments, landlocked Alewives exhibited improved freshwater tolerance, which was correlated with reductions in seawater tolerance and hypo-osmotic balance, suggesting that trade-offs in osmoregulation may be associated with local adaptation to freshwater. We detected differentiation between life-history forms in the expression of an ion-uptake gene (NHE3), and in gill Na+/K+-ATPase activity. Trade-offs in osmoregulation, therefore, may be mediated by differentiation in ion-uptake and salt-secreting pathways.

Co-existence of Blau syndrome and NAID? Diagnostic challenges associated with presence of multiple pathogenic variants in NOD2 gene: a case report.

PubMed

Dziedzic, Magdalena; Marjańska, Agata; Bąbol-Pokora, Katarzyna; Urbańczyk, Anna; Grześk, Elżbieta; Młynarski, Wojciech; Kołtan, Sylwia

2017-07-27

Pediatric autoinflammatory diseases are rare and still poorly understood conditions resulting from defective genetic control of innate immune system, inter alia from anomalies of NOD2 gene. The product of this gene is Nod2 protein, taking part in maintenance of immune homeostasis. Clinical form of resultant autoinflammatory condition depends on NOD2 genotype; usually patients with NOD2 defects present with Blau syndrome, NOD2-associated autoinflammatory disease (NAID) or Crohn's disease. We present the case of a 7-year-old girl with co-existing symptoms of two rare diseases, Blau syndrome and NAID. Overlapping manifestations of two syndromes raised a significant diagnostic challenge, until next-generation molecular test (NGS) identified presence of three pathogenic variants of NOD2 gene: P268S, IVS8 +158 , 1007 fs, and established the ultimate diagnosis. Presence of multiple genetical abnormalities resulted in an ambiguous clinical presentation with overlapping symptoms of Blau syndrome and NAID. Final diagnosis of autoinflammatory disease opened new therapeutic possibilities, including the use of biological treatments.

Free energy surface of the Michaelis complex of lactate dehydrogenase: a network analysis of microsecond simulations.

PubMed

Pan, Xiaoliang; Schwartz, Steven D

2015-04-30

It has long been recognized that the structure of a protein creates a hierarchy of conformations interconverting on multiple time scales. The conformational heterogeneity of the Michaelis complex is of particular interest in the context of enzymatic catalysis in which the reactant is usually represented by a single conformation of the enzyme/substrate complex. Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of two forms of the cofactor nicotinamide adenine dinucleotide (NADH and NAD(+)). Recent experimental results suggest that multiple substates exist within the Michaelis complex of LDH, and they show a strong variance in their propensity toward the on-enzyme chemical step. In this study, microsecond-scale all-atom molecular dynamics simulations were performed on LDH to explore the free energy landscape of the Michaelis complex, and network analysis was used to characterize the distribution of the conformations. Our results provide a detailed view of the kinetic network of the Michaelis complex and the structures of the substates at atomistic scales. They also shed light on the complete picture of the catalytic mechanism of LDH.

[Establishment and Management of Multiple Myeloma Specimen Bank Applied for Molecular Biological Researches].

PubMed

Li, Han-Qing; Mei, Jian-Gang; Cao, Hong-Qin; Shao, Liang-Jing; Zhai, Yong-Ping

2017-12-01

To establish a multiple myeloma specimen bank applied for molecular biological researches and to explore the methods of specimen collection, transportation, storage, quality control and the management of specimen bank. Bone marrow and blood samples were collected from multiple myeloma patients, plasma cell sorting were operated after the separation of mononuclear cells from bone marrow specimens. The plasma cells were divided into 2 parts, one was added with proper amount of TRIzol and then kept in -80 °C refrigerator for subsequent RNA extraction, the other was added with proper amount of calf serum cell frozen liquid and then kept in -80 °C refrigerator for subsequent cryopreservation of DNA extraction after numbered respectively. Serum and plasma were separated from peripheral blood, specimens of serum and plasma were then stored at -80 °C refrigerator after registration. Meantime, the myeloma specimen information management system was established, managed and maintained by specially-assigned persons and continuous modification and improvement in the process of use as to facilitate the rapid collection, management, query of the effective samples and clinical data. A total of 244 portions plasma cells, 564 portions of serum, and 1005 portions of plasma were collected, clinical characters were documented. A multiple myeloma specimen bank have been established initially, which can provide quality samples and related clinical information for molecular biological research on multiple myeloma.

Distributed computation: the new wave of synthetic biology devices.

PubMed

Macía, Javier; Posas, Francesc; Solé, Ricard V

2012-06-01

Synthetic biology (SB) offers a unique opportunity for designing complex molecular circuits able to perform predefined functions. But the goal of achieving a flexible toolbox of reusable molecular components has been shown to be limited due to circuit unpredictability, incompatible parts or random fluctuations. Many of these problems arise from the challenges posed by engineering the molecular circuitry: multiple wires are usually difficult to implement reliably within one cell and the resulting systems cannot be reused in other modules. These problems are solved by means of a nonstandard approach to single cell devices, using cell consortia and allowing the output signal to be distributed among different cell types, which can be combined in multiple, reusable and scalable ways. Copyright © 2012 Elsevier Ltd. All rights reserved.

Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) for Conformational Space Search of Peptide and Miniprotein

PubMed Central

Hao, Ge-Fei; Xu, Wei-Fang; Yang, Sheng-Gang; Yang, Guang-Fu

2015-01-01

Protein and peptide structure predictions are of paramount importance for understanding their functions, as well as the interactions with other molecules. However, the use of molecular simulation techniques to directly predict the peptide structure from the primary amino acid sequence is always hindered by the rough topology of the conformational space and the limited simulation time scale. We developed here a new strategy, named Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) to identify the native states of a peptide and miniprotein. A cluster of near native structures could be obtained by using the MSA-MD method, which turned out to be significantly more efficient in reaching the native structure compared to continuous MD and conventional SA-MD simulation. PMID:26492886

Supergenes and their role in evolution.

PubMed

Thompson, M J; Jiggins, C D

2014-07-01

Adaptation is commonly a multidimensional problem, with changes in multiple traits required to match a complex environment. This is epitomized by balanced polymorphisms in which multiple phenotypes co-exist and are maintained in a population by a balance of selective forces. Consideration of such polymorphisms led to the concept of the supergene, where alternative phenotypes in a balanced polymorphism segregate as if controlled by a single genetic locus, resulting from tight genetic linkage between multiple functional loci. Recently, the molecular basis for several supergenes has been resolved. Thus, major chromosomal inversions have been shown to be associated with polymorphisms in butterflies, ants and birds, offering a mechanism for localised reduction in recombination. In several examples of plant self-incompatibility, the functional role of multiple elements within the supergene architecture has been demonstrated, conclusively showing that balanced polymorphism can be maintained at multiple coadapted and tightly linked elements. Despite recent criticism, we argue that the supergene concept remains relevant and is more testable than ever with modern molecular methods.

Simultaneous detection of multiple chemical residues in milk using broad-specifity antibodies in a hybrid immunosorbent assay

USDA-ARS?s Scientific Manuscript database

The wide array of applications using quantum dots (QDs) for detection of multiple analytes reflects the versatility of the technology. In this study, a novel immunoassay using 2 types of sensors (QDs and an enzyme) were simultaneously used for detecting multiple structurally different low-molecular...

Multiple schwannomatosis caused by the recently described INI1 gene--molecular pathology, and implications for prognosis.

PubMed

Brennan, Paul M; Barlow, Antonio; Geraghty, Alistair; Summers, David; Fitzpatrick, Michael M

2011-06-01

The most common genetic predisposition to multiple schwannoma growth is mutation of the neurofibromatosis type 2 gene. We describe a patient with multiple schwannomas and mutation in the recently described INI1 gene, which also predisposes to the disease. We explore the implications for prognosis and outcome.

Method for forming cooperative binary ionic solids

DOEpatents

Shelnutt, John A.; Martin, Kathleen E.; Wang, Zhongchun; Medforth, Craig J.

2013-03-05

A nanostructured molecular unit and method for forming is described where a cationic porphyrin having an ethanolic substituent species and a metal in the porphyrin cavity is combined with an anionic porphyrin having a sulfonate substituent species and a metal in the porphyrin cavity to form by self-assembly a nanostructured molecular unit with a morphology comprising four dendritic elements connected at a central node.

Method for forming cooperative binary ionic solids

DOEpatents

Shelnutt, John A.; Martin, Kathleen E.; Wang, Zhongchun; Medforth, Craig J.

2014-09-09

A nanostructured molecular unit and method for forming is described where a cationic porphyrin having an ethanolic substituent species and a metal in the porphyrin cavity is combined with an anionic porphyrin having a sulfonate substituent species and a metal in the porphyrin cavity to form by self-assembly a nanostructured molecular unit with a morphology comprising four dendritic elements connected at a central node.

The dynamic behavior of a liquid ethanol-water mixture: a perspective from quantum chemical topology.

PubMed

Mejía, Sol M; Mills, Matthew J L; Shaik, Majeed S; Mondragon, Fanor; Popelier, Paul L A

2011-05-07

Quantum Chemical Topology (QCT) is used to reveal the dynamics of atom-atom interactions in a liquid. A molecular dynamics simulation was carried out on an ethanol-water liquid mixture at its azeotropic concentration (X(ethanol)=0.899), using high-rank multipolar electrostatics. A thousand (ethanol)(9)-water heterodecamers, respecting the water-ethanol ratio of the azeotropic mixture, were extracted from the simulation. Ab initio electron densities were computed at the B3LYP/6-31+G(d) level for these molecular clusters. A video shows the dynamical behavior of a pattern of bond critical points and atomic interaction lines, fluctuating over 1 ns. A bond critical point distribution revealed the fluctuating behavior of water and ethanol molecules in terms of O-H···O, C-H···O and H···H interactions. Interestingly, the water molecule formed one to six C-H···O and one to four O-H···O interactions as a proton acceptor. We found that the more localized a dynamical bond critical point distribution, the higher the average electron density at its bond critical points. The formation of multiple C-H···O interactions affected the shape of the oxygen basin of the water molecule, which is shown in three dimensions. The hydrogen atoms of water strongly preferred to form H···H interactions with ethanol's alkyl hydrogen atoms over its hydroxyl hydrogen. This journal is © the Owner Societies 2011

Nonlinear eigen-structures in star-forming gyratory nonthermal complex molecular clouds

NASA Astrophysics Data System (ADS)

Karmakar, Pralay Kumar; Dutta, Pranamika

2018-01-01

This paper deals with the nonlinear gravito-electrostatic fluctuations in star-forming rotating complex partially ionized dust molecular clouds, evolutionarily well-governed by a derived pair of the Korteweg-de Vries (KdV) equations of a unique analytical shape, in a bi-fluidic-model fabric. The lighter constituent species, such as electrons and ions, are considered thermo-statistically as the nonthermal ones in nature, governed by the anti-equilibrium kappa-distribution laws, due to inherent nonlocal gradient effects stemming from large-scale inhomogeneity. The heavier species, such as the constitutive identical neutral and charged dust micro-spheres, are treated as separate turbulent viscous fluids in the Larson logatropic tapestry. Application of a standard technique of multiple scale analysis over the nonlinearly perturbed cloud procedurally yields the pair KdV system. It comprises of the gravitational KdV and electrostatic KdV equations with exclusive constructs of diversified multi-parametric coefficients. A numerical constructive platform is provided to see the excitation and propagatory dynamics of gravitational rarefactive periodic soliton-trains and electrostatic rarefactive aperiodic damped soliton-trains of distinctive patterns as the pair-KdV-supported discrete coherent eigen-mode structures illustratively. The varied key stabilizing and tonality destabilizing factors behind the cloud dynamics are identified. An elaborated contrast of the eigen-mode conjugacy is reconnoitered. The main implications and applications of the semi-analytical results explored here are summarily outlined in the real astro-space-cosmic statuses.

The Dual Origin Of The Nitrogen Deficiency In Comets: Selective Volatile Trapping In The Nebula And Postaccretion Radiogenic Heating

NASA Astrophysics Data System (ADS)

Mousis, Olivier; Guilbert-Lepoutre, A.; Lunine, J. I.; Cochran, A. L.; Waite, J. H.; Petit, J.; Rousselot, P.

2012-10-01

We propose a scenario that explains the apparent nitrogen deficiency in comets in a way consistent with the presence of this molecule in the atmospheres of Pluto and Triton. We use a statistical thermodynamic model to investigate the composition of the successive multiple guest clathrates that may have formed during the cooling of the primordial nebula from the most abundant volatiles present in the gas phase. These clathrates agglomerated with the other ices (pure condensates or stoechiometric hydrates) and formed the building blocks of comets. We report that molecular nitrogen is a poor clathrate former, when we consider a plausible gas phase composition of the primordial nebula. This implies that its trapping into cometesimals requires a low disk temperature (about 20 K) in order to allow the formation of its pure condensate. We find that it is possible to explain the lack of molecular nitrogen in comets as a consequence of their postformation internal heating engendered by the decay of radiogenic nuclides. This scenario is found to be consistent with the presence of nitrogen-rich atmospheres around Pluto and Triton. Our model predicts that comets should present xenon-to-water and krypton-to-water ratios close to solar xenon-to-oxygen and krypton-to-oxygen ratios, respectively. In contrast, the argon-to-water ratio is predicted to be depleted by a factor of about 300 in comets compared to solar argon-to-oxygen, as a consequence of the nitrogen outgassing.

High molecular gas fractions in normal massive star-forming galaxies in the young Universe.

PubMed

Tacconi, L J; Genzel, R; Neri, R; Cox, P; Cooper, M C; Shapiro, K; Bolatto, A; Bouché, N; Bournaud, F; Burkert, A; Combes, F; Comerford, J; Davis, M; Schreiber, N M Förster; Garcia-Burillo, S; Gracia-Carpio, J; Lutz, D; Naab, T; Omont, A; Shapley, A; Sternberg, A; Weiner, B

2010-02-11

Stars form from cold molecular interstellar gas. As this is relatively rare in the local Universe, galaxies like the Milky Way form only a few new stars per year. Typical massive galaxies in the distant Universe formed stars an order of magnitude more rapidly. Unless star formation was significantly more efficient, this difference suggests that young galaxies were much more molecular-gas rich. Molecular gas observations in the distant Universe have so far largely been restricted to very luminous, rare objects, including mergers and quasars, and accordingly we do not yet have a clear idea about the gas content of more normal (albeit massive) galaxies. Here we report the results of a survey of molecular gas in samples of typical massive-star-forming galaxies at mean redshifts of about 1.2 and 2.3, when the Universe was respectively 40% and 24% of its current age. Our measurements reveal that distant star forming galaxies were indeed gas rich, and that the star formation efficiency is not strongly dependent on cosmic epoch. The average fraction of cold gas relative to total galaxy baryonic mass at z = 2.3 and z = 1.2 is respectively about 44% and 34%, three to ten times higher than in today's massive spiral galaxies. The slow decrease between z approximately 2 and z approximately 1 probably requires a mechanism of semi-continuous replenishment of fresh gas to the young galaxies.

Transcriptome profiling of the floral buds and discovery of genes related to sex-differentiation in the dioecious cucurbit Coccinia grandis (L.) Voigt.

PubMed

Mohanty, Jatindra Nath; Nayak, Sanghamitra; Jha, Sumita; Joshi, Raj Kumar

2017-08-30

Dioecious species offer an inclusive structure to study the molecular basis of sexual dimorphism in angiosperms. Despite having a small genome and heteromorphic sex chromosomes, Coccinia grandis is a highly neglected dioecious species with little information available on its physical state, genetic orientation and key sex-defining elements. In the present study, we performed RNA-Seq and DGE analysis of male (MB) and female (FB) buds in C. grandis to gain insights into the molecular basis of sex determination in this plant. De novo assembly of 75 million clean reads resulted in 72,479 unigenes for male library and 63,308 unigenes for female library with a mean length of 736bp. 61,458 (85.57%) unigenes displayed significant similarity with protein sequences from publicly available databases. Comparative transcriptome analyses revealed 1410 unigenes as differentially expressed (DEGs) between MB and FB samples. A consistent correlation between the expression levels of DEGs was observed for the RNA-Seq pattern and qRT-PCR validation. Functional annotation showed high enrichment of DEGs involved in phytohormone biosynthesis, hormone signaling and transduction, transcriptional regulation and methyltransferase activity. High induction of hormone responsive genes such as ARF6, ACC synthase1, SNRK2 and BRI1-associated receptor kinase 1 (BAK1) suggest that multiple phytohormones and their signaling crosstalk play crucial role in sex determination in this species. Beside, the transcription factors such as zinc fingers, homeodomain leucine zippers and MYBs were identified as major determinants of male specific expression. Moreover, the detection of multiple DEGs as the miRNA target site implies that a small RNA mediated gene silencing cascade may also be regulating gender differentiation in C. grandis. Overall, the present transcriptome resources provide us a large number of DEGs involved in sex expression and could form the groundwork for unravelling the molecular mechanism of sex determination in C. grandis. Copyright © 2017 Elsevier B.V. All rights reserved.

Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation

PubMed Central

Ramirez, Samuel A.; Elston, Timothy C.

2018-01-01

Polarity establishment, the spontaneous generation of asymmetric molecular distributions, is a crucial component of many cellular functions. Saccharomyces cerevisiae (yeast) undergoes directed growth during budding and mating, and is an ideal model organism for studying polarization. In yeast and many other cell types, the Rho GTPase Cdc42 is the key molecular player in polarity establishment. During yeast polarization, multiple patches of Cdc42 initially form, then resolve into a single front. Because polarization relies on strong positive feedback, it is likely that the amplification of molecular-level fluctuations underlies the generation of multiple nascent patches. In the absence of spatial cues, these fluctuations may be key to driving polarization. Here we used particle-based simulations to investigate the role of stochastic effects in a Turing-type model of yeast polarity establishment. In the model, reactions take place either between two molecules on the membrane, or between a cytosolic and a membrane-bound molecule. Thus, we developed a computational platform that explicitly simulates molecules at and near the cell membrane, and implicitly handles molecules away from the membrane. To evaluate stochastic effects, we compared particle simulations to deterministic reaction-diffusion equation simulations. Defining macroscopic rate constants that are consistent with the microscopic parameters for this system is challenging, because diffusion occurs in two dimensions and particles exchange between the membrane and cytoplasm. We address this problem by empirically estimating macroscopic rate constants from appropriately designed particle-based simulations. Ultimately, we find that stochastic fluctuations speed polarity establishment and permit polarization in parameter regions predicted to be Turing stable. These effects can operate at Cdc42 abundances expected of yeast cells, and promote polarization on timescales consistent with experimental results. To our knowledge, our work represents the first particle-based simulations of a model for yeast polarization that is based on a Turing mechanism. PMID:29529021

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring

PubMed Central

2012-01-01

Background Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families. Results The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Conclusions Our results demonstrate that the method we present here using a k-modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family. PMID:22793672

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring.

PubMed

Durston, Kirk K; Chiu, David Ky; Wong, Andrew Kc; Li, Gary Cl

2012-07-13

Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families. The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Our results demonstrate that the method we present here using a k-modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family.

Ecological niche partitioning between Anopheles gambiae molecular forms in Cameroon: the ecological side of speciation

PubMed Central

Simard, Frédéric; Ayala, Diego; Kamdem, Guy Colince; Pombi, Marco; Etouna, Joachim; Ose, Kenji; Fotsing, Jean-Marie; Fontenille, Didier; Besansky, Nora J; Costantini, Carlo

2009-01-01

Background Speciation among members of the Anopheles gambiae complex is thought to be promoted by disruptive selection and ecological divergence acting on sets of adaptation genes protected from recombination by polymorphic paracentric chromosomal inversions. However, shared chromosomal polymorphisms between the M and S molecular forms of An. gambiae and insufficient information about their relationship with ecological divergence challenge this view. We used Geographic Information Systems, Ecological Niche Factor Analysis, and Bayesian multilocus genetic clustering to explore the nature and extent of ecological and chromosomal differentiation of M and S across all the biogeographic domains of Cameroon in Central Africa, in order to understand the role of chromosomal arrangements in ecological specialisation within and among molecular forms. Results Species distribution modelling with presence-only data revealed differences in the ecological niche of both molecular forms and the sibling species, An. arabiensis. The fundamental environmental envelope of the two molecular forms, however, overlapped to a large extent in the rainforest, where they occurred in sympatry. The S form had the greatest niche breadth of all three taxa, whereas An. arabiensis and the M form had the smallest niche overlap. Correspondence analysis of M and S karyotypes confirmed that molecular forms shared similar combinations of chromosomal inversion arrangements in response to the eco-climatic gradient defining the main biogeographic domains occurring across Cameroon. Savanna karyotypes of M and S, however, segregated along the smaller-scale environmental gradient defined by the second ordination axis. Population structure analysis identified three chromosomal clusters, each containing a mixture of M and S specimens. In both M and S, alternative karyotypes were segregating in contrasted environments, in agreement with a strong ecological adaptive value of chromosomal inversions. Conclusion Our data suggest that inversions on the second chromosome of An. gambiae are not causal to the evolution of reproductive isolation between the M and S forms. Rather, they are involved in ecological specialization to a similar extent in both genetic backgrounds, and most probably predated lineage splitting between molecular forms. However, because chromosome-2 inversions promote ecological divergence, resulting in spatial and/or temporal isolation between ecotypes, they might favour mutations in other ecologically significant genes to accumulate in unlinked chromosomal regions. When such mutations occur in portions of the genome where recombination is suppressed, such as the pericentromeric regions known as speciation islands in An. gambiae, they would contribute further to the development of reproductive isolation. PMID:19460146

Dual Thermosensitive Hydrogels Assembled from the Conserved C-Terminal Domain of Spider Dragline Silk.

PubMed

Qian, Zhi-Gang; Zhou, Ming-Liang; Song, Wen-Wen; Xia, Xiao-Xia

2015-11-09

Stimuli-responsive hydrogels have great potentials in biomedical and biotechnological applications. Due to the advantages of precise control over molecular weight and being biodegradable, protein-based hydrogels and their applications have been extensively studied. However, protein hydrogels with dual thermosensitive properties are rarely reported. Here we present the first report of dual thermosensitive hydrogels assembled from the conserved C-terminal domain of spider dragline silk. First, we found that recombinant C-terminal domain of major ampullate spidroin 1 (MaSp1) of the spider Nephila clavipes formed hydrogels when cooled to approximately 2 °C or heated to 65 °C. The conformational changes and self-assembly of the recombinant protein were studied to understand the mechanism of the gelation processes using multiple methods. It was proposed that the gelation in the low-temperature regime was dominated by hydrogen bonding and hydrophobic interaction between folded protein molecules, whereas the gelation in the high-temperature regime was due to cross-linking of the exposed hydrophobic patches resulting from partial unfolding of the protein upon heating. More interestingly, genetic fusion of the C-terminal domain to a short repetitive region of N. clavipes MaSp1 resulted in a chimeric protein that formed a hydrogel with significantly improved mechanical properties at low temperatures between 2 and 10 °C. Furthermore, the formation of similar hydrogels was observed for the recombinant C-terminal domains of dragline silk of different spider species, thus demonstrating the conserved ability to form dual thermosensitive hydrogels. These findings may be useful in the design and construction of novel protein hydrogels with tunable multiple thermosensitivity for applications in the future.

Multiple endocrine neoplasia type 1

PubMed Central

Marini, Francesca; Falchetti, Alberto; Monte, Francesca Del; Sala, Silvia Carbonell; Gozzini, Alessia; Luzi, Ettore; Brandi, Maria Luisa

2006-01-01

Multiple Endocrine Neoplasia type 1 (MEN1) is a rare autosomal dominant hereditary cancer syndrome presented mostly by tumours of the parathyroids, endocrine pancreas and anterior pituitary, and characterised by a very high penetrance and an equal sex distribution. It occurs in approximately one in 30,000 individuals. Two different forms, sporadic and familial, have been described. The sporadic form presents with two of the three principal MEN1-related endocrine tumours (parathyroid adenomas, entero-pancreatic tumours and pituitary tumours) within a single patient, while the familial form consists of a MEN1 case with at least one first degree relative showing one of the endocrine characterising tumours. Other endocrine and non-endocrine lesions, such as adrenal cortical tumours, carcinoids of the bronchi, gastrointestinal tract and thymus, lipomas, angiofibromas, collagenomas have been described. The responsible gene, MEN1, maps on chromosome 11q13 and encodes a 610 aminoacid nuclear protein, menin, with no sequence homology to other known human proteins. MEN1 syndrome is caused by inactivating mutations of the MEN1 tumour suppressor gene. This gene is probably involved in the regulation of several cell functions such as DNA replication and repair and transcriptional machinery. The combination of clinical and genetic investigations, together with the improving of molecular genetics knowledge of the syndrome, helps in the clinical management of patients. Treatment consists of surgery and/or drug therapy, often in association with radiotherapy or chemotherapy. Currently, DNA testing allows the early identification of germline mutations in asymptomatic gene carriers, to whom routine surveillance (regular biochemical and/or radiological screenings to detect the development of MEN1-associated tumours and lesions) is recommended. PMID:17014705

The Role of mGlu Receptors in Hippocampal Plasticity Deficits in Neurological and Psychiatric Disorders: Implications for Allosteric Modulators as Novel Therapeutic Strategies

PubMed Central

Senter, Rebecca K.; Ghoshal, Ayan; Walker, Adam G.; Xiang, Zixiu; Niswender, Colleen M.; Conn, P. Jeffrey

2016-01-01

Long-term potentiation (LTP) and long-term depression (LTD) are two distinct forms of synaptic plasticity that have been extensively characterized at the Schaffer collateral-CA1 (SC-CA1) synapse and the mossy fiber (MF)-CA3 synapse within the hippocampus, and are postulated to be the molecular underpinning for several cognitive functions. Deficits in LTP and LTD have been implicated in the pathophysiology of several neurological and psychiatric disorders. Therefore, there has been a large effort focused on developing an understanding of the mechanisms underlying these forms of plasticity and novel therapeutic strategies that improve or rescue these plasticity deficits. Among many other targets, the metabotropic glutamate (mGlu) receptors show promise as novel therapeutic candidates for the treatment of these disorders. Among the eight distinct mGlu receptor subtypes (mGlu1-8), the mGlu1,2,3,5,7 subtypes are expressed throughout the hippocampus and have been shown to play important roles in the regulation of synaptic plasticity in this brain area. However, development of therapeutic agents that target these mGlu receptors has been hampered by a lack of subtype-selective compounds. Recently, discovery of allosteric modulators of mGlu receptors has provided novel ligands that are highly selective for individual mGlu receptor subtypes. The mGlu receptors modulate the multiple forms of synaptic plasticity at both SC-CA1 and MF synapses and allosteric modulators of mGlu receptors have emerged as potential therapeutic agents that may rescue plasticity deficits and improve cognitive function in patients suffering from multiple neurological and psychiatric disorders. PMID:27296640

Design and intestinal mucus penetration mechanism of core-shell nanocomplex.

PubMed

Zhang, Xin; Cheng, Hongbo; Dong, Wei; Zhang, Meixia; Liu, Qiaoyu; Wang, Xiuhua; Guan, Jian; Wu, Haiyang; Mao, Shirui

2018-02-28

The objective of this study was to design intestinal mucus-penetrating core-shell nanocomplex by functionally mimicking the surface of virus, which can be used as the carrier for peroral delivery of macromolecules, and further understand the influence of nanocomplex surface properties on the mucosal permeation capacity. Taking insulin as a model drug, the core was formed by the self-assembly among positively charged chitosan, insulin and negatively charged sodium tripolyphosphate, different types of alginates were used as the shell forming material. The nanocomplex was characterized by dynamic light scattering (DLS), atomic force microscopy (AFM) and FTIR. Nanocomplex movement in mucus was recorded using multiple particle tracking (MPT) method. Permeation and uptake of different nanocomplex were studied in rat intestine. It was demonstrated that alginate coating layer was successfully formed on the core and the core-shell nanocomplex showed a good physical stability and improved enzymatic degradation protection. The mucus penetration and MPT study showed that the mucus penetration capacity of the nanocomplex was surface charge and coating polymer structure dependent, nanocomplex with negative alginate coating had 1.6-2.5 times higher mucus penetration ability than that of positively charged chitosan-insulin nanocomplex. Moreover, the mucus penetration ability of the core-shell nanocomplex was alginate structure dependent, whereas alginate with lower G content and lower molecular weight showed the best permeation enhancing ability. The improvement of intestine permeation and intestinal villi uptake of the core-shell nanocomplex were further confirmed in rat intestine and multiple uptake mechanisms were involved in the transport process. In conclusion, core-shell nanocomplex composed of oppositely charged materials could provide a strategy to overcome the mucus barrier and enhance the mucosal permeability. Copyright © 2018 Elsevier B.V. All rights reserved.

MALDI imaging mass spectrometry analysis-A new approach for protein mapping in multiple sclerosis brain lesions.

PubMed

Maccarrone, Giuseppina; Nischwitz, Sandra; Deininger, Sören-Oliver; Hornung, Joachim; König, Fatima Barbara; Stadelmann, Christine; Turck, Christoph W; Weber, Frank

2017-03-15

Multiple sclerosis is a disease of the central nervous system characterized by recurrent inflammatory demyelinating lesions in the early disease stage. Lesion formation and mechanisms leading to lesion remyelination are not fully understood. Matrix Assisted Laser Desorption Ionisation Mass Spectrometry imaging (MALDI-IMS) is a technology which analyses proteins and peptides in tissue, preserves their spatial localization, and generates molecular maps within the tissue section. In a pilot study we employed MALDI imaging mass spectrometry to profile and identify peptides and proteins expressed in normal-appearing white matter, grey matter and multiple sclerosis brain lesions with different extents of remyelination. The unsupervised clustering analysis of the mass spectra generated images which reflected the tissue section morphology in luxol fast blue stain and in myelin basic protein immunohistochemistry. Lesions with low remyelination extent were defined by compounds with molecular weight smaller than 5300Da, while more completely remyelinated lesions showed compounds with molecular weights greater than 15,200Da. An in-depth analysis of the mass spectra enabled the detection of cortical lesions which were not seen by routine luxol fast blue histology. An ion mass, mainly distributed at the rim of multiple sclerosis lesions, was identified by liquid chromatography and tandem mass spectrometry as thymosin beta-4, a protein known to be involved in cell migration and in restorative processes. The ion mass of thymosin beta-4 was profiled by MALDI imaging mass spectrometry in brain slides of 12 multiple sclerosis patients and validated by immunohistochemical analysis. In summary, our results demonstrate the ability of the MALDI-IMS technology to map proteins within the brain parenchyma and multiple sclerosis lesions and to identify potential markers involved in multiple sclerosis pathogenesis and/or remyelination. Copyright © 2016 Elsevier B.V. All rights reserved.

A Pivotal Role of DELLAs in Regulating Multiple Hormone Signals.

PubMed

Davière, Jean-Michel; Achard, Patrick

2016-01-04

Plant phenotypic plasticity is controlled by diverse hormone pathways, which integrate and convey information from multiple developmental and environmental signals. Moreover, in plants many processes such as growth, development, and defense are regulated in similar ways by multiple hormones. Among them, gibberellins (GAs) are phytohormones with pleiotropic actions, regulating various growth processes throughout the plant life cycle. Previous work has revealed extensive interplay between GAs and other hormones, but the molecular mechanism became apparent only recently. Molecular and physiological studies have demonstrated that DELLA proteins, considered as master negative regulators of GA signaling, integrate multiple hormone signaling pathways through physical interactions with transcription factors or regulatory proteins from different families. In this review, we summarize the latest progress in GA signaling and its direct crosstalk with the main phytohormone signaling, emphasizing the multifaceted role of DELLA proteins with key components of major hormone signaling pathways. Copyright © 2016 The Author. Published by Elsevier Inc. All rights reserved.

MoleculeNet: a benchmark for molecular machine learning† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc02664a

PubMed Central

Wu, Zhenqin; Ramsundar, Bharath; Feinberg, Evan N.; Gomes, Joseph; Geniesse, Caleb; Pappu, Aneesh S.; Leswing, Karl

2017-01-01

Molecular machine learning has been maturing rapidly over the last few years. Improved methods and the presence of larger datasets have enabled machine learning algorithms to make increasingly accurate predictions about molecular properties. However, algorithmic progress has been limited due to the lack of a standard benchmark to compare the efficacy of proposed methods; most new algorithms are benchmarked on different datasets making it challenging to gauge the quality of proposed methods. This work introduces MoleculeNet, a large scale benchmark for molecular machine learning. MoleculeNet curates multiple public datasets, establishes metrics for evaluation, and offers high quality open-source implementations of multiple previously proposed molecular featurization and learning algorithms (released as part of the DeepChem open source library). MoleculeNet benchmarks demonstrate that learnable representations are powerful tools for molecular machine learning and broadly offer the best performance. However, this result comes with caveats. Learnable representations still struggle to deal with complex tasks under data scarcity and highly imbalanced classification. For quantum mechanical and biophysical datasets, the use of physics-aware featurizations can be more important than choice of particular learning algorithm. PMID:29629118

Modeling Stochastic Kinetics of Molecular Machines at Multiple Levels: From Molecules to Modules

PubMed Central

Chowdhury, Debashish

2013-01-01

A molecular machine is either a single macromolecule or a macromolecular complex. In spite of the striking superficial similarities between these natural nanomachines and their man-made macroscopic counterparts, there are crucial differences. Molecular machines in a living cell operate stochastically in an isothermal environment far from thermodynamic equilibrium. In this mini-review we present a catalog of the molecular machines and an inventory of the essential toolbox for theoretically modeling these machines. The tool kits include 1), nonequilibrium statistical-physics techniques for modeling machines and machine-driven processes; and 2), statistical-inference methods for reverse engineering a functional machine from the empirical data. The cell is often likened to a microfactory in which the machineries are organized in modular fashion; each module consists of strongly coupled multiple machines, but different modules interact weakly with each other. This microfactory has its own automated supply chain and delivery system. Buoyed by the success achieved in modeling individual molecular machines, we advocate integration of these models in the near future to develop models of functional modules. A system-level description of the cell from the perspective of molecular machinery (the mechanome) is likely to emerge from further integrations that we envisage here. PMID:23746505