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Sample records for distribution driving protein

  1. Intrinsically disordered proteins drive membrane curvature

    NASA Astrophysics Data System (ADS)

    Busch, David J.; Houser, Justin R.; Hayden, Carl C.; Sherman, Michael B.; Lafer, Eileen M.; Stachowiak, Jeanne C.

    2015-07-01

    Assembly of highly curved membrane structures is essential to cellular physiology. The prevailing view has been that proteins with curvature-promoting structural motifs, such as wedge-like amphipathic helices and crescent-shaped BAR domains, are required for bending membranes. Here we report that intrinsically disordered domains of the endocytic adaptor proteins, Epsin1 and AP180 are highly potent drivers of membrane curvature. This result is unexpected since intrinsically disordered domains lack a well-defined three-dimensional structure. However, in vitro measurements of membrane curvature and protein diffusivity demonstrate that the large hydrodynamic radii of these domains generate steric pressure that drives membrane bending. When disordered adaptor domains are expressed as transmembrane cargo in mammalian cells, they are excluded from clathrin-coated pits. We propose that a balance of steric pressure on the two surfaces of the membrane drives this exclusion. These results provide quantitative evidence for the influence of steric pressure on the content and assembly of curved cellular membrane structures.

  2. Intrinsically disordered proteins drive membrane curvature

    PubMed Central

    Busch, David J.; Houser, Justin R.; Hayden, Carl C.; Sherman, Michael B.; Lafer, Eileen M.; Stachowiak, Jeanne C.

    2015-01-01

    Assembly of highly curved membrane structures is essential to cellular physiology. The prevailing view has been that proteins with curvature-promoting structural motifs, such as wedge-like amphipathic helices and crescent-shaped BAR domains, are required for bending membranes. Here we report that intrinsically disordered domains of the endocytic adaptor proteins, Epsin1 and AP180 are highly potent drivers of membrane curvature. This result is unexpected since intrinsically disordered domains lack a well-defined three-dimensional structure. However, in vitro measurements of membrane curvature and protein diffusivity demonstrate that the large hydrodynamic radii of these domains generate steric pressure that drives membrane bending. When disordered adaptor domains are expressed as transmembrane cargo in mammalian cells, they are excluded from clathrin-coated pits. We propose that a balance of steric pressure on the two surfaces of the membrane drives this exclusion. These results provide quantitative evidence for the influence of steric pressure on the content and assembly of curved cellular membrane structures. PMID:26204806

  3. Intrinsically disordered proteins drive membrane curvature.

    PubMed

    Busch, David J; Houser, Justin R; Hayden, Carl C; Sherman, Michael B; Lafer, Eileen M; Stachowiak, Jeanne C

    2015-07-24

    Assembly of highly curved membrane structures is essential to cellular physiology. The prevailing view has been that proteins with curvature-promoting structural motifs, such as wedge-like amphipathic helices and crescent-shaped BAR domains, are required for bending membranes. Here we report that intrinsically disordered domains of the endocytic adaptor proteins, Epsin1 and AP180 are highly potent drivers of membrane curvature. This result is unexpected since intrinsically disordered domains lack a well-defined three-dimensional structure. However, in vitro measurements of membrane curvature and protein diffusivity demonstrate that the large hydrodynamic radii of these domains generate steric pressure that drives membrane bending. When disordered adaptor domains are expressed as transmembrane cargo in mammalian cells, they are excluded from clathrin-coated pits. We propose that a balance of steric pressure on the two surfaces of the membrane drives this exclusion. These results provide quantitative evidence for the influence of steric pressure on the content and assembly of curved cellular membrane structures.

  4. Driving DNA transposition by lentiviral protein transduction

    PubMed Central

    Cai, Yujia; Mikkelsen, Jacob Giehm

    2014-01-01

    Gene vectors derived from DNA transposable elements have become powerful molecular tools in biomedical research and are slowly moving into the clinic as carriers of therapeutic genes. Conventional uses of DNA transposon-based gene vehicles rely on the intracellular production of the transposase protein from transfected nucleic acids. The transposase mediates mobilization of the DNA transposon, which is typically provided in the context of plasmid DNA. In recent work, we established lentiviral protein transduction from Gag precursors as a new strategy for direct delivery of the transposase protein. Inspired by the natural properties of infecting viruses to carry their own enzymes, we loaded lentivirus-derived particles not only with vector genomes carrying the DNA transposon vector but also with hundreds of transposase subunits. Such particles were found to drive efficient transposition of the piggyBac transposable element in a range of different cell types, including primary cells, and offer a new transposase delivery approach that guarantees short-term activity and limits potential cytotoxicity. DNA transposon vectors, originally developed and launched as a non-viral alternative to viral integrating vectors, have truly become viral. Here, we briefly review our findings and speculate on the perspectives and potential advantages of transposase delivery by lentiviral protein transduction. PMID:25057443

  5. How the hydrophobic factor drives protein folding.

    PubMed

    Baldwin, Robert L; Rose, George D

    2016-11-01

    How hydrophobicity (HY) drives protein folding is studied. The 1971 Nozaki-Tanford method of measuring HY is modified to use gases as solutes, not crystals, and this makes the method easy to use. Alkanes are found to be much more hydrophobic than rare gases, and the two different kinds of HY are termed intrinsic (rare gases) and extrinsic (alkanes). The HY values of rare gases are proportional to solvent-accessible surface area (ASA), whereas the HY values of alkanes depend on special hydration shells. Earlier work showed that hydration shells produce the hydration energetics of alkanes. Evidence is given here that the transfer energetics of alkanes to cyclohexane [Wolfenden R, Lewis CA, Jr, Yuan Y, Carter CW, Jr (2015) Proc Natl Acad Sci USA 112(24):7484-7488] measure the release of these shells. Alkane shells are stabilized importantly by van der Waals interactions between alkane carbon and water oxygen atoms. Thus, rare gases cannot form this type of shell. The very short (approximately picoseconds) lifetime of the van der Waals interaction probably explains why NMR efforts to detect alkane hydration shells have failed. The close similarity between the sizes of the opposing energetics for forming or releasing alkane shells confirms the presence of these shells on alkanes and supports Kauzmann's 1959 mechanism of protein folding. A space-filling model is given for the hydration shells on linear alkanes. The model reproduces the n values of Jorgensen et al. [Jorgensen WL, Gao J, Ravimohan C (1985) J Phys Chem 89:3470-3473] for the number of waters in alkane hydration shells.

  6. How the hydrophobic factor drives protein folding

    PubMed Central

    Baldwin, Robert L.; Rose, George D.

    2016-01-01

    How hydrophobicity (HY) drives protein folding is studied. The 1971 Nozaki–Tanford method of measuring HY is modified to use gases as solutes, not crystals, and this makes the method easy to use. Alkanes are found to be much more hydrophobic than rare gases, and the two different kinds of HY are termed intrinsic (rare gases) and extrinsic (alkanes). The HY values of rare gases are proportional to solvent-accessible surface area (ASA), whereas the HY values of alkanes depend on special hydration shells. Earlier work showed that hydration shells produce the hydration energetics of alkanes. Evidence is given here that the transfer energetics of alkanes to cyclohexane [Wolfenden R, Lewis CA, Jr, Yuan Y, Carter CW, Jr (2015) Proc Natl Acad Sci USA 112(24):7484–7488] measure the release of these shells. Alkane shells are stabilized importantly by van der Waals interactions between alkane carbon and water oxygen atoms. Thus, rare gases cannot form this type of shell. The very short (approximately picoseconds) lifetime of the van der Waals interaction probably explains why NMR efforts to detect alkane hydration shells have failed. The close similarity between the sizes of the opposing energetics for forming or releasing alkane shells confirms the presence of these shells on alkanes and supports Kauzmann's 1959 mechanism of protein folding. A space-filling model is given for the hydration shells on linear alkanes. The model reproduces the n values of Jorgensen et al. [Jorgensen WL, Gao J, Ravimohan C (1985) J Phys Chem 89:3470–3473] for the number of waters in alkane hydration shells. PMID:27791131

  7. Conformation Distributions in Adsorbed Proteins.

    NASA Astrophysics Data System (ADS)

    Meuse, Curtis W.; Hubbard, Joseph B.; Vrettos, John S.; Smith, Jackson R.; Cicerone, Marcus T.

    2007-03-01

    While the structural basis of protein function is well understood in the biopharmaceutical and biotechnology industries, few methods for the characterization and comparison of protein conformation distributions are available. New methods capable of measuring the stability of protein conformations and the integrity of protein-protein, protein-ligand and protein-surface interactions both in solution and on surfaces are needed to help the development of protein-based products. We are developing infrared spectroscopy methods for the characterization and comparison of molecular conformation distributions in monolayers and in solutions. We have extracted an order parameter describing the orientational and conformational variations of protein functional groups around the average molecular values from a single polarized spectrum. We will discuss the development of these methods and compare them to amide hydrogen/deuterium exchange methods for albumin in solution and on different polymer surfaces to show that our order parameter is related to protein stability.

  8. What drives the translocation of proteins?

    PubMed Central

    Simon, S M; Peskin, C S; Oster, G F

    1992-01-01

    We propose that protein translocation across membranes is driven by biased random thermal motion. This "Brownian ratchet" mechanism depends on chemical asymmetries between the cis and trans sides of the membrane. Several mechanisms could contribute to rectifying the thermal motion of the protein, such as binding and dissociation of chaperonins to the translocating chain, chain coiling induced by pH and/or ionic gradients, glycosylation, and disulfide bond formation. This helps explain the robustness and promiscuity of these transport systems. Images PMID:1349170

  9. Toward understanding driving forces in membrane protein folding.

    PubMed

    Hong, Heedeok

    2014-12-15

    α-Helical membrane proteins are largely composed of nonpolar residues that are embedded in the lipid bilayer. An enigma in the folding of membrane proteins is how a polypeptide chain can be condensed into the compact folded state in the environment where the hydrophobic effect cannot strongly drive molecular interactions. Probably other forces such as van der Waals packing, hydrogen bonding, and weakly polar interactions, which are regarded less important in the folding of water-soluble proteins, should emerge. However, it is not clearly understood how those individual forces operate and how they are balanced for stabilizing membrane proteins. Studying this problem is not a trivial task mainly because of the methodological challenges in controlling the reversible folding of membrane proteins in the lipid bilayer. Overcoming the hurdles, meaningful progress has been made in the field in the last few decades. This review will focus on recent studies tackling the problem of driving forces in membrane protein folding.

  10. Intrinsically Disordered Proteins Drive Emergence and Inheritance of Biological Traits.

    PubMed

    Chakrabortee, Sohini; Byers, James S; Jones, Sandra; Garcia, David M; Bhullar, Bhupinder; Chang, Amelia; She, Richard; Lee, Laura; Fremin, Brayon; Lindquist, Susan; Jarosz, Daniel F

    2016-10-06

    Prions are a paradigm-shifting mechanism of inheritance in which phenotypes are encoded by self-templating protein conformations rather than nucleic acids. Here, we examine the breadth of protein-based inheritance across the yeast proteome by assessing the ability of nearly every open reading frame (ORF; ∼5,300 ORFs) to induce heritable traits. Transient overexpression of nearly 50 proteins created traits that remained heritable long after their expression returned to normal. These traits were beneficial, had prion-like patterns of inheritance, were common in wild yeasts, and could be transmitted to naive cells with protein alone. Most inducing proteins were not known prions and did not form amyloid. Instead, they are highly enriched in nucleic acid binding proteins with large intrinsically disordered domains that have been widely conserved across evolution. Thus, our data establish a common type of protein-based inheritance through which intrinsically disordered proteins can drive the emergence of new traits and adaptive opportunities.

  11. Opportunities drive the global distribution of protected areas

    PubMed Central

    Texeira, Marcos; Martin, Osvaldo A.; Grau, H. Ricardo; Jobbágy, Esteban G.

    2017-01-01

    Background Protected areas, regarded today as a cornerstone of nature conservation, result from an array of multiple motivations and opportunities. We explored at global and regional levels the current distribution of protected areas along biophysical, human, and biological gradients, and assessed to what extent protection has pursued (i) a balanced representation of biophysical environments, (ii) a set of preferred conditions (biological, spiritual, economic, or geopolitical), or (iii) existing opportunities for conservation regardless of any representation or preference criteria. Methods We used histograms to describe the distribution of terrestrial protected areas along biophysical, human, and biological independent gradients and linear and non-linear regression and correlation analyses to describe the sign, shape, and strength of the relationships. We used a random forest analysis to rank the importance of different variables related to conservation preferences and opportunity drivers, and an evenness metric to quantify representativeness. Results We find that protection at a global level is primarily driven by the opportunities provided by isolation and a low population density (variable importance = 34.6 and 19.9, respectively). Preferences play a secondary role, with a bias towards tourism attractiveness and proximity to international borders (variable importance = 12.7 and 3.4, respectively). Opportunities shape protection strongly in “North America & Australia–NZ” and “Latin America & Caribbean,” while the importance of the representativeness of biophysical environments is higher in “Sub-Saharan Africa” (1.3 times the average of other regions). Discussion Environmental representativeness and biodiversity protection are top priorities in land conservation agendas. However, our results suggest that they have been minor players driving current protection at both global and regional levels. Attempts to increase their relevance will necessarily

  12. Enhanced Recovery Utilizing Variable Frequency Drives and a Distributed Power System

    SciTech Connect

    Randy Peden; Sanjiv Shah

    2005-07-26

    This report describes complete results of the project entitled ''Enhanced Recovery Utilizing Variable Frequency Drives and a Distributed Power System''. This demonstration project was initiated in July 2003 and completed in March 2005. The objective of the project was to develop an integrated power production/variable frequency drive system that could easily be deployed in the oil field that would increase production and decrease operating costs. This report describes all the activities occurred and documents results of the demonstration.

  13. Distribution and Evolution of Yersinia Leucine-Rich Repeat Proteins

    PubMed Central

    Hu, Yueming; Huang, He; Hui, Xinjie; Cheng, Xi; White, Aaron P.

    2016-01-01

    Leucine-rich repeat (LRR) proteins are widely distributed in bacteria, playing important roles in various protein-protein interaction processes. In Yersinia, the well-characterized type III secreted effector YopM also belongs to the LRR protein family and is encoded by virulence plasmids. However, little has been known about other LRR members encoded by Yersinia genomes or their evolution. In this study, the Yersinia LRR proteins were comprehensively screened, categorized, and compared. The LRR proteins encoded by chromosomes (LRR1 proteins) appeared to be more similar to each other and different from those encoded by plasmids (LRR2 proteins) with regard to repeat-unit length, amino acid composition profile, and gene expression regulation circuits. LRR1 proteins were also different from LRR2 proteins in that the LRR1 proteins contained an E3 ligase domain (NEL domain) in the C-terminal region or an NEL domain-encoding nucleotide relic in flanking genomic sequences. The LRR1 protein-encoding genes (LRR1 genes) varied dramatically and were categorized into 4 subgroups (a to d), with the LRR1a to -c genes evolving from the same ancestor and LRR1d genes evolving from another ancestor. The consensus and ancestor repeat-unit sequences were inferred for different LRR1 protein subgroups by use of a maximum parsimony modeling strategy. Structural modeling disclosed very similar repeat-unit structures between LRR1 and LRR2 proteins despite the different unit lengths and amino acid compositions. Structural constraints may serve as the driving force to explain the observed mutations in the LRR regions. This study suggests that there may be functional variation and lays the foundation for future experiments investigating the functions of the chromosomally encoded LRR proteins of Yersinia. PMID:27217422

  14. Thermal denaturation of Bungarus fasciatus acetylcholinesterase: Is aggregation a driving force in protein unfolding?

    PubMed Central

    Shin, I.; Wachtel, E.; Roth, E.; Bon, C.; Silman, I.; Weiner, L.

    2002-01-01

    A monomeric form of acetylcholinesterase from the venom of Bungarus fasciatus is converted to a partially unfolded molten globule species by thermal inactivation, and subsequently aggregates rapidly. To separate the kinetics of unfolding from those of aggregation, single molecules of the monomeric enzyme were encapsulated in reverse micelles of Brij 30 in 2,2,4-trimethylpentane, or in large unilamellar vesicles of egg lecithin/cholesterol at various protein/micelle (vesicle) ratios. The first-order rate constant for thermal inactivation at 45°C, of single molecules entrapped within the reverse micelles (0.031 min−1), was higher than in aqueous solution (0.007 min−1) or in the presence of normal micelles (0.020 min−1). This clearly shows that aggregation does not provide the driving force for thermal inactivation of BfAChE. Within the large unilamellar vesicles, at average protein/vesicle ratios of 1:1 and 10:1, the first-order rate constants for thermal inactivation of the encapsulated monomeric acetylcholinesterase, at 53°C, were 0.317 and 0.342 min−1, respectively. A crosslinking technique, utilizing the photosensitive probe, hypericin, showed that thermal denaturation produces a distribution of species ranging from dimers through to large aggregates. Consequently, at a protein/vesicle ratio of 10:1, aggregation can occur upon thermal denaturation. Thus, these experiments also demonstrate that aggregation does not drive the thermal unfolding of Bungarus fasciatus acetylcholinesterase. Our experimental approach also permitted monitoring of recovery of enzymic activity after thermal denaturation in the absence of a competing aggregation process. Whereas no detectable recovery of enzymic activity could be observed in aqueous solution, up to 23% activity could be obtained for enzyme sequestered in the reverse micelles. PMID:12142456

  15. A traction control strategy with an efficiency model in a distributed driving electric vehicle.

    PubMed

    Lin, Cheng; Cheng, Xingqun

    2014-01-01

    Both active safety and fuel economy are important issues for vehicles. This paper focuses on a traction control strategy with an efficiency model in a distributed driving electric vehicle. In emergency situation, a sliding mode control algorithm was employed to achieve antislip control through keeping the wheels' slip ratios below 20%. For general longitudinal driving cases, an efficiency model aiming at improving the fuel economy was built through an offline optimization stream within the two-dimensional design space composed of the acceleration pedal signal and the vehicle speed. The sliding mode control strategy for the joint roads and the efficiency model for the typical drive cycles were simulated. Simulation results show that the proposed driving control approach has the potential to apply to different road surfaces. It keeps the wheels' slip ratios within the stable zone and improves the fuel economy on the premise of tracking the driver's intention.

  16. A Traction Control Strategy with an Efficiency Model in a Distributed Driving Electric Vehicle

    PubMed Central

    Lin, Cheng

    2014-01-01

    Both active safety and fuel economy are important issues for vehicles. This paper focuses on a traction control strategy with an efficiency model in a distributed driving electric vehicle. In emergency situation, a sliding mode control algorithm was employed to achieve antislip control through keeping the wheels' slip ratios below 20%. For general longitudinal driving cases, an efficiency model aiming at improving the fuel economy was built through an offline optimization stream within the two-dimensional design space composed of the acceleration pedal signal and the vehicle speed. The sliding mode control strategy for the joint roads and the efficiency model for the typical drive cycles were simulated. Simulation results show that the proposed driving control approach has the potential to apply to different road surfaces. It keeps the wheels' slip ratios within the stable zone and improves the fuel economy on the premise of tracking the driver's intention. PMID:25197697

  17. X-ray analysis of nonMaxwellian distributions (current drive)

    SciTech Connect

    von Goeler, S.; Stevens, J.; Stodiek, W.

    1983-06-01

    The plasma bremsstrahlung emission is utilized to determine the shape of the electron velocity distribution in situations where it deviates strongly from a Maxwellian distribution. The instrumentation used to measure the hard x-ray emission is briefly discussed. Model calculations show that polarization measurements give best results for unrelativistic tails with tail temperatures T/sub b/ < 50 keV, whereas measurements of the angular distribution of the x-ray emission based on the forward scattering of bremsstrahlung for relativistic electrons yields the best information for T/sub b/ > 50 keV. The techniques were originally developed in order to analyze runaway discharges. Recently, they found new interest because of the formation of energetic electron tails during current drive. The first x-ray results from the current drive during LH heating on PLT are discussed.

  18. Optimal investment and scheduling of distributed energy resources with uncertainty in electric vehicles driving schedules

    SciTech Connect

    Cardoso, Goncalo; Stadler, Michael; Bozchalui, Mohammed C.; Sharma, Ratnesh; Marnay, Chris; Barbosa-Povoa, Ana; Ferrao, Paulo

    2013-12-06

    The large scale penetration of electric vehicles (EVs) will introduce technical challenges to the distribution grid, but also carries the potential for vehicle-to-grid services. Namely, if available in large enough numbers, EVs can be used as a distributed energy resource (DER) and their presence can influence optimal DER investment and scheduling decisions in microgrids. In this work, a novel EV fleet aggregator model is introduced in a stochastic formulation of DER-CAM [1], an optimization tool used to address DER investment and scheduling problems. This is used to assess the impact of EV interconnections on optimal DER solutions considering uncertainty in EV driving schedules. Optimization results indicate that EVs can have a significant impact on DER investments, particularly if considering short payback periods. Furthermore, results suggest that uncertainty in driving schedules carries little significance to total energy costs, which is corroborated by results obtained using the stochastic formulation of the problem.

  19. Study of Solid State Drives performance in PROOF distributed analysis system

    NASA Astrophysics Data System (ADS)

    Panitkin, S. Y.; Ernst, M.; Petkus, R.; Rind, O.; Wenaus, T.

    2010-04-01

    Solid State Drives (SSD) is a promising storage technology for High Energy Physics parallel analysis farms. Its combination of low random access time and relatively high read speed is very well suited for situations where multiple jobs concurrently access data located on the same drive. It also has lower energy consumption and higher vibration tolerance than Hard Disk Drive (HDD) which makes it an attractive choice in many applications raging from personal laptops to large analysis farms. The Parallel ROOT Facility - PROOF is a distributed analysis system which allows to exploit inherent event level parallelism of high energy physics data. PROOF is especially efficient together with distributed local storage systems like Xrootd, when data are distributed over computing nodes. In such an architecture the local disk subsystem I/O performance becomes a critical factor, especially when computing nodes use multi-core CPUs. We will discuss our experience with SSDs in PROOF environment. We will compare performance of HDD with SSD in I/O intensive analysis scenarios. In particular we will discuss PROOF system performance scaling with a number of simultaneously running analysis jobs.

  20. Quasistationary distributions of dissipative nonlinear quantum oscillators in strong periodic driving fields

    PubMed

    Breuer; Huber; Petruccione

    2000-05-01

    The dynamics of periodically driven quantum systems coupled to a thermal environment is investigated. The interaction of the system with the external coherent driving field is taken into account exactly by making use of the Floquet picture. Treating the coupling to the environment within the Born-Markov approximation one finds a Pauli-type master equation for the diagonal elements of the reduced density matrix in the Floquet representation. The stationary solution of the latter yields a quasistationary, time-periodic density matrix which describes the long-time behavior of the system. Taking the example of a periodically driven particle in a box, the stationary solution is determined numerically for a wide range of driving amplitudes and temperatures. It is found that the quasistationary distribution differs substantially from a Boltzmann-type distribution at the temperature of the environment. For large driving fields it exhibits a plateau region describing a nearly constant population of a certain number of Floquet states. This number of Floquet states turns out to be nearly independent of the temperature. The plateau region is sharply separated from an exponential tail of the stationary distribution which expresses a canonical Boltzmann-type distribution over the mean energies of the Floquet states. These results are explained in terms of the structure of the matrix of transition rates for the dissipative quantum system. Investigating the corresponding classical, nonlinear Hamiltonian system, one finds that in the semiclassical range essential features of the quasistationary distribution can be understood from the structure of the underlying classical phase space.

  1. Spatiotemporal dataset on Chinese population distribution and its driving factors from 1949 to 2013

    PubMed Central

    Wang, Lizhe; Chen, Lajiao

    2016-01-01

    Spatio-temporal data on human population and its driving factors is critical to understanding and responding to population problems. Unfortunately, such spatio-temporal data on a large scale and over the long term are often difficult to obtain. Here, we present a dataset on Chinese population distribution and its driving factors over a remarkably long period, from 1949 to 2013. Driving factors of population distribution were selected according to the push-pull migration laws, which were summarized into four categories: natural environment, natural resources, economic factors and social factors. Natural environment and natural resources indicators were calculated using Geographic Information System (GIS) and Remote Sensing (RS) techniques, whereas economic and social factors from 1949 to 2013 were collected from the China Statistical Yearbook and China Compendium of Statistics from 1949 to 2008. All of the data were quality controlled and unified into an identical dataset with the same spatial scope and time period. The dataset is expected to be useful for understanding how population responds to and impacts environmental change. PMID:27377410

  2. Spatiotemporal dataset on Chinese population distribution and its driving factors from 1949 to 2013.

    PubMed

    Wang, Lizhe; Chen, Lajiao

    2016-07-05

    Spatio-temporal data on human population and its driving factors is critical to understanding and responding to population problems. Unfortunately, such spatio-temporal data on a large scale and over the long term are often difficult to obtain. Here, we present a dataset on Chinese population distribution and its driving factors over a remarkably long period, from 1949 to 2013. Driving factors of population distribution were selected according to the push-pull migration laws, which were summarized into four categories: natural environment, natural resources, economic factors and social factors. Natural environment and natural resources indicators were calculated using Geographic Information System (GIS) and Remote Sensing (RS) techniques, whereas economic and social factors from 1949 to 2013 were collected from the China Statistical Yearbook and China Compendium of Statistics from 1949 to 2008. All of the data were quality controlled and unified into an identical dataset with the same spatial scope and time period. The dataset is expected to be useful for understanding how population responds to and impacts environmental change.

  3. Spatiotemporal dataset on Chinese population distribution and its driving factors from 1949 to 2013

    NASA Astrophysics Data System (ADS)

    Wang, Lizhe; Chen, Lajiao

    2016-07-01

    Spatio-temporal data on human population and its driving factors is critical to understanding and responding to population problems. Unfortunately, such spatio-temporal data on a large scale and over the long term are often difficult to obtain. Here, we present a dataset on Chinese population distribution and its driving factors over a remarkably long period, from 1949 to 2013. Driving factors of population distribution were selected according to the push-pull migration laws, which were summarized into four categories: natural environment, natural resources, economic factors and social factors. Natural environment and natural resources indicators were calculated using Geographic Information System (GIS) and Remote Sensing (RS) techniques, whereas economic and social factors from 1949 to 2013 were collected from the China Statistical Yearbook and China Compendium of Statistics from 1949 to 2008. All of the data were quality controlled and unified into an identical dataset with the same spatial scope and time period. The dataset is expected to be useful for understanding how population responds to and impacts environmental change.

  4. Fruit availability drives the distribution of a folivorous-frugivorous primate within a large forest remnant.

    PubMed

    Camaratta, Danielle; Chaves, Óscar M; Bicca-Marques, Júlio César

    2017-03-01

    Understanding the ecological factors that influence the presence, abundance, and distribution of species within their habitats is critical for ensuring their long-term conservation. In the case of primary consumers, such as most primates, the availability and richness of plant foods are considered key drivers of population density at these variables influence the spatial distribution of social units within a finer, habitat patch level scale. We tested the hypothesis that the spatiotemporal availability and richness of plant foods, drive the spatial distribution of brown howler monkeys (Alouatta guariba clamitans) at a fine spatial scale. We established five line transects (2.6-4.3 km long) to census the population of brown howlers in Morro São Pedro, a 1,200 ha Atlantic forest remnant in southern Brazil, every 2 weeks from January to June 2015. We used data from tree inventories performed in sighting and control plots, and phenological surveys of 17 top food tree species to estimate bi-weekly food availability. We recorded a total of 95 sightings. The number of sightings per sampling period ranged from 2 to 12. The availability of fruit (ripe and unripe) was higher in sighting than in control plots, whereas leaf availability and the richness of food tree species was similar. We conclude that the spatial distribution of fruiting trees and the availability of fruit drive the pattern of habitat use, and spacing of brown howler groups in Morro São Pedro.

  5. Equilibrium distribution from distributed computing (simulations of protein folding).

    PubMed

    Scalco, Riccardo; Caflisch, Amedeo

    2011-05-19

    Multiple independent molecular dynamics (MD) simulations are often carried out starting from a single protein structure or a set of conformations that do not correspond to a thermodynamic ensemble. Therefore, a significant statistical bias is usually present in the Markov state model generated by simply combining the whole MD sampling into a network whose nodes and links are clusters of snapshots and transitions between them, respectively. Here, we introduce a depth-first search algorithm to extract from the whole conformation space network the largest ergodic component, i.e., the subset of nodes of the network whose transition matrix corresponds to an ergodic Markov chain. For multiple short MD simulations of a globular protein (as in distributed computing), the steady state, i.e., stationary distribution determined using the largest ergodic component, yields more accurate free energy profiles and mean first passage times than the original network or the ergodic network obtained by imposing detailed balance by means of symmetrization of the transition counts.

  6. Adult activity and temperature preference drives region-wide damselfly (Zygoptera) distributions under a warming climate

    PubMed Central

    Corser, Jeffrey D.; White, Erin L.; Schlesinger, Matthew D.

    2015-01-01

    We analysed a recently completed statewide odonate Atlas using multivariate linear models. Within a phylogenetically explicit framework, we developed a suite of data-derived traits to assess the mechanistic distributional drivers of 59 species of damselflies in New York State (NYS). We found that length of the flight season (adult breeding activity period) mediated by thermal preference drives regional distributions at broad (105 km2) scales. Species that had longer adult flight periods, in conjunction with longer growing seasons, had significantly wider distributions. These intrinsic traits shape species' responses to changing climates and the mechanisms behind such range shifts are fitness-based metapopulation processes that adjust phenology to the prevailing habitat and climate regime through a photoperiod filter. PMID:25878048

  7. Direct yaw moment control for distributed drive electric vehicle handling performance improvement

    NASA Astrophysics Data System (ADS)

    Yu, Zhuoping; Leng, Bo; Xiong, Lu; Feng, Yuan; Shi, Fenmiao

    2016-05-01

    For a distributed drive electric vehicle (DDEV) driven by four in-wheel motors, advanced vehicle dynamic control methods can be realized easily because motors can be controlled independently, quickly and precisely. And direct yaw-moment control (DYC) has been widely studied and applied to vehicle stability control. Good vehicle handling performance: quick yaw rate transient response, small overshoot, high steady yaw rate gain, etc, is required by drivers under normal conditions, which is less concerned, however. Based on the hierarchical control methodology, a novel control system using direct yaw moment control for improving handling performance of a distributed drive electric vehicle especially under normal driving conditions has been proposed. The upper-loop control system consists of two parts: a state feedback controller, which aims to realize the ideal transient response of yaw rate, with a vehicle sideslip angle observer; and a steering wheel angle feedforward controller designed to achieve a desired yaw rate steady gain. Under the restriction of the effect of poles and zeros in the closed-loop transfer function on the system response and the capacity of in-wheel motors, the integrated time and absolute error (ITAE) function is utilized as the cost function in the optimal control to calculate the ideal eigen frequency and damper coefficient of the system and obtain optimal feedback matrix and feedforward matrix. Simulations and experiments with a DDEV under multiple maneuvers are carried out and show the effectiveness of the proposed method: yaw rate rising time is reduced, steady yaw rate gain is increased, vehicle steering characteristic is close to neutral steer and drivers burdens are also reduced. The control system improves vehicle handling performance under normal conditions in both transient and steady response. State feedback control instead of model following control is introduced in the control system so that the sense of control intervention to

  8. Competition with stone crabs drives juvenile spiny lobster abundance and distribution.

    PubMed

    Behringer, Donald C; Hart, John E

    2017-02-28

    Interspecific competition is assumed to have a strong influence on the population dynamics of competing species, but is not easily demonstrated for mobile species in the wild. In the Florida Keys (USA), anecdotal observations have long pointed to an inverse relationship in abundance of two large decapod crustaceans found co-occurring in hard-bottom habitat, the stone crab Menippe mercenaria and the Caribbean spiny lobster Panulirus argus. We used them to explicitly test whether competition for a renewable resource (shelter) can drive the abundance and distribution of the inferior competitor. We first explored this relationship in shelter competition mesocosm experiments to determine the competitively dominant species. Results showed that stone crabs are clearly the dominant competitors regardless of the number of lobsters present, the presence of co-sheltering species such as the spider crab, Damithrax spinosissimus, or the order of introduction of competitors into the mesocosm. We also found that lobsters use chemical cues from stone crabs to detect and avoid them. We then tested the ramifications of this competitive dominance in the field by manipulating stone crab abundance and then tracking the abundance and distribution of spiny lobsters through time. Increased stone crab abundance immediately resulted in decreased lobster abundance and increased aggregation. The opposite occurred on sites where stone crabs were removed. When we stopped removing stone crabs from these sites, they soon returned and lobster abundance decreased. This study explicitly demonstrated that interspecific competition can drive population dynamics between these species, and ultimately, community composition in these shallow water habitats.

  9. A polymer physics perspective on driving forces and mechanisms for protein aggregation.

    PubMed

    Pappu, Rohit V; Wang, Xiaoling; Vitalis, Andreas; Crick, Scott L

    2008-01-01

    Protein aggregation is a commonly occurring problem in biology. Cells have evolved stress-response mechanisms to cope with problems posed by protein aggregation. Yet, these quality control mechanisms are overwhelmed by chronic aggregation-related stress and the resultant consequences of aggregation become toxic to cells. As a result, a variety of systemic and neurodegenerative diseases are associated with various aspects of protein aggregation and rational approaches to either inhibit aggregation or manipulate the pathways to aggregation might lead to an alleviation of disease phenotypes. To develop such approaches, one needs a rigorous and quantitative understanding of protein aggregation. Much work has been done in this area. However, several unanswered questions linger, and these pertain primarily to the actual mechanism of aggregation as well as to the types of inter-molecular associations and intramolecular fluctuations realized at low protein concentrations. It has been suggested that the concepts underlying protein aggregation are similar to those used to describe the aggregation of synthetic polymers. Following this suggestion, the relevant concepts of polymer aggregation are introduced. The focus is on explaining the driving forces for polymer aggregation and how these driving forces vary with chain length and solution conditions. It is widely accepted that protein aggregation is a nucleation-dependent process. This view is based mainly on the presence of long times for the accumulation of aggregates and the elimination of these lag times with "seeds". In this sense, protein aggregation is viewed as being analogous to the aggregation of colloidal particles. The theories for polymer aggregation reviewed in this work suggest an alternative mechanism for the origin of long lag times in protein aggregation. The proposed mechanism derives from the recognition that polymers have unique dynamics that distinguish them from other aggregation-prone systems such as

  10. A polymer physics perspective on driving forces and mechanisms for protein aggregation

    PubMed Central

    Pappu, Rohit V.; Wang, Xiaoling; Vitalis, Andreas; Crick, Scott L.

    2008-01-01

    Protein aggregation is a commonly occurring problem in biology. Cells have evolved stress-response mechanisms to cope with problems posed by protein aggregation. Yet, these quality control mechanisms are overwhelmed by chronic aggregation-related stress and the resultant consequences of aggregation become toxic to cells. As a result, a variety of systemic and neurodegenerative diseases are associated with various aspects of protein aggregation and rational approaches to either inhibit aggregation or manipulate the pathways to aggregation might lead to an alleviation of disease phenotypes. To develop such approaches, one needs a rigorous and quantitative understanding of protein aggregation. Much work has been done in this area. However, several unanswered questions linger, and these pertain primarily to the actual mechanism of aggregation as well as to the types of intermolecular associations and intramolecular fluctuations realized at low protein concentrations. It has been suggested that the concepts underlying protein aggregation are similar to those used to describe the aggregation of synthetic polymers. Following this suggestion, the relevant concepts of polymer aggregation are introduced. The focus is on explaining the driving forces for polymer aggregation and how these driving forces vary with chain length and solution conditions. It is widely accepted that protein aggregation is a nucleation-dependent process. This view is based mainly on the presence of long times for the accumulation of aggregates and the elimination of these lag times with “seeds”. In this sense, protein aggregation is viewed as being analogous to the aggregation of colloidal particles. The theories for polymer aggregation reviewed in this work suggest an alternative mechanism for the origin of long lag times in protein aggregation. The proposed mechanism derives from the recognition that polymers have unique dynamics that distinguish them from other aggregation-prone systems such

  11. The driving forces of membrane remodeling by non-intrinsically curved proteins

    NASA Astrophysics Data System (ADS)

    Ryan, Christopher J.; Stachowiak, Jeanne C.; Schmid, Eva M.; Fletcher, Daniel A.; Geissler, Phillip L.

    2011-03-01

    Membranes are dynamically remodeled during numerous processes essential to cells. Among the most well-studied effectors of this remodeling are BAR family proteins, which are small and have a banana-like intrinsic curvature that senses, forms, and stabilizes curved membranes without expending energy as ATP or GTP. Recent experiments in reduced systems have shown, however, that small proteins that feature no such intrinsic curvature can similarly cluster at and dramatically remodel membranes. These proteins have no distinguishing features other than their size and their membrane-binding sites, and the dominant effect that is driving curvature is not well understood. Here, we present a coarse-grained simulation study that captures protein steric and binding effects as well as membrane fluctuations at large scales. We use this model to systematically test for the role that such attributes play in the resulting dynamics and equilibrium structures of remodeling processes that feature this motif.

  12. Host trait combinations drive abundance and canopy distribution of atmospheric bromeliad assemblages

    PubMed Central

    Chaves, Cleber Juliano Neves; Dyonisio, Júlio César; Rossatto, Davi Rodrigo

    2016-01-01

    Epiphytes are strongly dependent on the conditions created by their host's traits and a certain degree of specificity is expected between them, even if these species are largely abundant in a series of tree hosts of a given environment, as in the case of atmospheric bromeliads. Despite their considerable abundance in these environments, we hypothesize that stochasticity alone cannot explain the presence and abundance of atmospheric bromeliads on host trees, since host traits could have a greater influence on the establishment of these bromeliads. We used secondary and reforested seasonal forests and three distinct silvicultures to test whether species richness, phylogenetic diversity and functional diversity of trees can predict the differential presence, abundance and distribution of atmospheric bromeliads on hosts. We compared the observed parameters of their assemblage with null models and performed successive variance hierarchic partitions of abundance and distribution of the assemblage to detect the influence of multiple traits of the tree hosts. Our results do not indicate direct relationships between the abundance of atmospheric bromeliads and phylogenetic or functional diversity of trees, but instead indicate that bromeliads occurred on fewer tree species than expected by chance. We distinguished functional tree patterns that can improve or reduce the abundance of atmospheric bromeliads, and change their distribution on branches and trunk. While individual tree traits are related to increased abundance, species traits are related to the canopy distribution of atmospheric bromeliad assemblages. A balance among these tree functional patterns drives the atmospheric bromeliad assemblage of the forest patches. PMID:26888951

  13. Effectively explore metastable states of proteins by adaptive nonequilibrium driving simulations

    NASA Astrophysics Data System (ADS)

    Wan, Biao; Xu, Shun; Zhou, Xin

    2017-03-01

    Nonequilibrium drivings applied in molecular dynamics (MD) simulations can efficiently extend the visiting range of protein conformations, but might compel systems to go far away from equilibrium and thus mainly explore irrelevant conformations. Here we propose a general method, called adaptive nonequilibrium simulation (ANES), to automatically adjust the external driving on the fly, based on the feedback of the short-time average response of system. Thus, the ANES approximately keeps the local equilibrium but efficiently accelerates the global motion. We illustrate the capability of the ANES in highly efficiently exploring metastable conformations in the deca-alanine peptide and find that the 0.2 -μ s ANES approximately captures the important states and folding and unfolding pathways in the HP35 solution by comparing with the result of the recent 398 -μ s equilibrium MD simulation on Anton [S. Piana et al., Proc. Natl. Acad. Sci. USA 109, 17845 (2012), 10.1073/pnas.1201811109].

  14. Physical factors driving intertidal macroalgae distribution: physiological stress of a dominant fucoid at its southern limit.

    PubMed

    Martínez, Brezo; Arenas, F; Rubal, M; Burgués, S; Esteban, R; García-Plazaola, I; Figueroa, F L; Pereira, R; Saldaña, L; Sousa-Pinto, I; Trilla, A; Viejo, R M

    2012-10-01

    Climate change is driving species range shifts worldwide. However, physiological responses related to distributional changes are not fully understood. Oceanographers have reported an increase in ocean temperature in the northwest Iberian Peninsula that is potentially related to the decline in some cold-temperate intertidal macroalgae in the Cantabrian Sea, namely Fucus serratus. Low tide stress could also play a role in this decline. We performed one mensurative (in situ) and two manipulative (in culture) experiments designed to evaluate the interactive effects of some physical factors. The first experiment analysed field response to low tide stress in marginal (mid-Cantabrian Sea and northern Portugal) versus central (Galicia) populations of F. serratus. Then a second experiment was performed that utilized either harsh or mild summer conditions of atmospheric temperature, irradiance, humidity, and wind velocity to compare the responses of individuals from one marginal and one central population to low tide stress. Finally, the combined effect of sea temperature and the other factors was evaluated to detect interactive effects. Changes in frond growth, maximal photosynthetic quantum yield (F(v)/F(m)), temperature, and desiccation were found. Three additive factors (solar irradiation, ocean and air temperatures) were found to drive F. serratus distribution, except under mildly humid conditions that ameliorated atmospheric thermal stress (two additive factors). Mid-Cantabrian Sea temperatures have recently increased, reaching the inhibitory levels suggested in this study of F. serratus. We also expect an additive secondary contribution of low tide stress to this species decline. On the northern Portugal coast, ocean warming plus low tide stress has not reached this species' inhibition threshold. No significant differential responses attributed to the population of origin were found. Mechanistic approaches that are designed to analyse the interactive effects of

  15. Ring of Change: CDC48/p97 Drives Protein Dynamics at Chromatin

    PubMed Central

    Franz, André; Ackermann, Leena; Hoppe, Thorsten

    2016-01-01

    The dynamic composition of proteins associated with nuclear DNA is a fundamental property of chromosome biology. In the chromatin compartment dedicated protein complexes govern the accurate synthesis and repair of the genomic information and define the state of DNA compaction in vital cellular processes such as chromosome segregation or transcription. Unscheduled or faulty association of protein complexes with DNA has detrimental consequences on genome integrity. Consequently, the association of protein complexes with DNA is remarkably dynamic and can respond rapidly to cellular signaling events, which requires tight spatiotemporal control. In this context, the ring-like AAA+ ATPase CDC48/p97 emerges as a key regulator of protein complexes that are marked with ubiquitin or SUMO. Mechanistically, CDC48/p97 functions as a segregase facilitating the extraction of substrate proteins from the chromatin. As such, CDC48/p97 drives molecular reactions either by directed disassembly or rearrangement of chromatin-bound protein complexes. The importance of this mechanism is reflected by human pathologies linked to p97 mutations, including neurodegenerative disorders, oncogenesis, and premature aging. This review focuses on the recent insights into molecular mechanisms that determine CDC48/p97 function in the chromatin environment, which is particularly relevant for cancer and aging research. PMID:27200082

  16. Widespread Positive Selection Drives Differentiation of Centromeric Proteins in the Drosophila melanogaster subgroup

    PubMed Central

    Beck, Emily A.; Llopart, Ana

    2015-01-01

    Rapid evolution of centromeric satellite repeats is thought to cause compensatory amino acid evolution in interacting centromere-associated kinetochore proteins. Cid, a protein that mediates kinetochore/centromere interactions, displays particularly high amino acid turnover. Rapid evolution of both Cid and centromeric satellite repeats led us to hypothesize that the apparent compensatory evolution may extend to interacting partners in the Condensin I complex (i.e., SMC2, SMC4, Cap-H, Cap-D2, and Cap-G) and HP1s. Missense mutations in these proteins often result in improper centromere formation and aberrant chromosome segregation, thus selection for maintained function and coevolution among proteins of the complex is likely strong. Here, we report evidence of rapid evolution and recurrent positive selection in seven centromere-associated proteins in species of the Drosophila melanogaster subgroup, and further postulate that positive selection on these proteins could be a result of centromere drive and compensatory changes, with kinetochore proteins competing for optimal spindle attachment. PMID:26603658

  17. Widespread Positive Selection Drives Differentiation of Centromeric Proteins in the Drosophila melanogaster subgroup.

    PubMed

    Beck, Emily A; Llopart, Ana

    2015-11-25

    Rapid evolution of centromeric satellite repeats is thought to cause compensatory amino acid evolution in interacting centromere-associated kinetochore proteins. Cid, a protein that mediates kinetochore/centromere interactions, displays particularly high amino acid turnover. Rapid evolution of both Cid and centromeric satellite repeats led us to hypothesize that the apparent compensatory evolution may extend to interacting partners in the Condensin I complex (i.e., SMC2, SMC4, Cap-H, Cap-D2, and Cap-G) and HP1s. Missense mutations in these proteins often result in improper centromere formation and aberrant chromosome segregation, thus selection for maintained function and coevolution among proteins of the complex is likely strong. Here, we report evidence of rapid evolution and recurrent positive selection in seven centromere-associated proteins in species of the Drosophila melanogaster subgroup, and further postulate that positive selection on these proteins could be a result of centromere drive and compensatory changes, with kinetochore proteins competing for optimal spindle attachment.

  18. Spatial Analysis and Quantification of the Thermodynamic Driving Forces in Protein-Ligand Binding: Binding Site Variability

    PubMed Central

    Raman, E. Prabhu; MacKerell, Alexander D.

    2015-01-01

    The thermodynamic driving forces behind small molecule-protein binding are still not well understood, including the variability of those forces associated with different types of ligands in different binding pockets. To better understand these phenomena we calculate spatially resolved thermodynamic contributions of the different molecular degrees of freedom for the binding of propane and methanol to multiple pockets on the proteins Factor Xa and p38 MAP kinase. Binding thermodynamics are computed using a statistical thermodynamics based end-point method applied on a canonical ensemble comprising the protein-ligand complexes and the corresponding free states in an explicit solvent environment. Energetic and entropic contributions of water and ligand degrees of freedom computed from the configurational ensemble provides an unprecedented level of detail into the mechanisms of binding. Direct protein-ligand interaction energies play a significant role in both non-polar and polar binding, which is comparable to water reorganization energy. Loss of interactions with water upon binding strongly compensates these contributions leading to relatively small binding enthalpies. For both solutes, the entropy of water reorganization is found to favor binding in agreement with the classical view of the “hydrophobic effect”. Depending on the specifics of the binding pocket, both energy-entropy compensation and reinforcement mechanisms are observed. Notable is the ability to visualize the spatial distribution of the thermodynamic contributions to binding at atomic resolution showing significant differences in the thermodynamic contributions of water to the binding of propane versus methanol. PMID:25625202

  19. Links between critical proteins drive the controllability of protein interaction networks.

    PubMed

    Wuchty, Stefan; Boltz, Toni; Küçük-McGinty, Hande

    2017-04-10

    Focusing on the interactomes of H. sapiens, S. cerevisiae, and E. coli, we investigated interactions between controlling proteins. In particular, we determined critical, intermittent, and redundant proteins based on their tendency to participate in minimum dominating sets (MDSets). Independently of the organisms considered, we found that interactions that involved critical nodes had the most prominent effects on the topology of their corresponding networks. Furthermore, we observed that phosphorylation and regulatory events were considerably enriched when the corresponding transcription factors and kinases were critical proteins, while such interactions were depleted when they were redundant proteins. Moreover, interactions involving critical proteins were enriched with essential genes, disease genes and drug targets, suggesting that such characteristics may be key for the detection of novel drug targets as well as assess their efficacy. This article is protected by copyright. All rights reserved.

  20. Driving Cells to the Desired State in a Bimodal Distribution through Manipulation of Internal Noise with Biologically Practicable Approaches.

    PubMed

    Shu, Che-Chi; Yeh, Chen-Chao; Jhang, Wun-Sin; Lo, Shih-Chiang

    2016-01-01

    The stochastic nature of gene regulatory networks described by Chemical Master Equation (CME) leads to the distribution of proteins. A deterministic bistability is usually reflected as a bimodal distribution in stochastic simulations. Within a certain range of the parameter space, a bistable system exhibits two stable steady states, one at the low end and the other at the high end. Consequently, it appears to have a bimodal distribution with one sub-population (mode) around the low end and the other around the high end. In most cases, only one mode is favorable, and guiding cells to the desired state is valuable. Traditionally, the population was redistributed simply by adjusting the concentration of the inducer or the stimulator. However, this method has limitations; for example, the addition of stimulator cannot drive cells to the desired state in a common bistable system studied in this work. In fact, it pushes cells only to the undesired state. In addition, it causes a position shift of the modes, and this shift could be as large as the value of the mode itself. Such a side effect might damage coordination, and this problem can be avoided by applying a new method presented in this work. We illustrated how to manipulate the intensity of internal noise by using biologically practicable methods and utilized it to prompt the population to the desired mode. As we kept the deterministic behavior untouched, the aforementioned drawback was overcome. Remarkably, more than 96% of cells has been driven to the desired state. This method is genetically applicable to biological systems exhibiting a bimodal distribution resulting from bistability. Moreover, the reaction network studied in this work can easily be extended and applied to many other systems.

  1. Driving Cells to the Desired State in a Bimodal Distribution through Manipulation of Internal Noise with Biologically Practicable Approaches

    PubMed Central

    Shu, Che-Chi; Yeh, Chen-Chao; Jhang, Wun-Sin; Lo, Shih-Chiang

    2016-01-01

    The stochastic nature of gene regulatory networks described by Chemical Master Equation (CME) leads to the distribution of proteins. A deterministic bistability is usually reflected as a bimodal distribution in stochastic simulations. Within a certain range of the parameter space, a bistable system exhibits two stable steady states, one at the low end and the other at the high end. Consequently, it appears to have a bimodal distribution with one sub-population (mode) around the low end and the other around the high end. In most cases, only one mode is favorable, and guiding cells to the desired state is valuable. Traditionally, the population was redistributed simply by adjusting the concentration of the inducer or the stimulator. However, this method has limitations; for example, the addition of stimulator cannot drive cells to the desired state in a common bistable system studied in this work. In fact, it pushes cells only to the undesired state. In addition, it causes a position shift of the modes, and this shift could be as large as the value of the mode itself. Such a side effect might damage coordination, and this problem can be avoided by applying a new method presented in this work. We illustrated how to manipulate the intensity of internal noise by using biologically practicable methods and utilized it to prompt the population to the desired mode. As we kept the deterministic behavior untouched, the aforementioned drawback was overcome. Remarkably, more than 96% of cells has been driven to the desired state. This method is genetically applicable to biological systems exhibiting a bimodal distribution resulting from bistability. Moreover, the reaction network studied in this work can easily be extended and applied to many other systems. PMID:27911933

  2. Rapid evolution of a Y-chromosome heterochromatin protein underlies sex chromosome meiotic drive

    PubMed Central

    Helleu, Quentin; Gérard, Pierre R.; Dubruille, Raphaëlle; Ogereau, David; Prud’homme, Benjamin; Loppin, Benjamin; Montchamp-Moreau, Catherine

    2016-01-01

    Sex chromosome meiotic drive, the non-Mendelian transmission of sex chromosomes, is the expression of an intragenomic conflict that can have extreme evolutionary consequences. However, the molecular bases of such conflicts remain poorly understood. Here, we show that a young and rapidly evolving X-linked heterochromatin protein 1 (HP1) gene, HP1D2, plays a key role in the classical Paris sex-ratio (SR) meiotic drive occurring in Drosophila simulans. Driver HP1D2 alleles prevent the segregation of the Y chromatids during meiosis II, causing female-biased sex ratio in progeny. HP1D2 accumulates on the heterochromatic Y chromosome in male germ cells, strongly suggesting that it controls the segregation of sister chromatids through heterochromatin modification. We show that Paris SR drive is a consequence of dysfunctional HP1D2 alleles that fail to prepare the Y chromosome for meiosis, thus providing evidence that the rapid evolution of genes controlling the heterochromatin structure can be a significant source of intragenomic conflicts. PMID:26979956

  3. CPI-17 drives oncogenic Ras signaling in human melanomas via Ezrin-Radixin-Moesin family proteins

    PubMed Central

    Riecken, Lars Björn; Zoch, Ansgar; Wiehl, Ulrike; Reichert, Sabine; Scholl, Ingmar; Cui, Yan; Ziemer, Mirjana; Anderegg, Ulf; Hagel, Christian; Morrison, Helen

    2016-01-01

    Hyperactive Ras signaling has strong oncogenic effects causing several different forms of cancer. Hyperactivity is frequently induced by mutations within Ras itself, which account for up to 30% of all human cancers. In addition, hyperactive Ras signaling can also be triggered independent of Ras by either mutation or by misexpression of various upstream regulators and immediate downstream effectors. We have previously reported that C-kinase potentiated protein phosphatase-1 inhibitor of 17 kDa (CPI-17) can drive Ras activity and promote tumorigenic transformation by inhibition of the tumor suppressor Merlin. We now describe an additional element of this oncogenic mechanism in the form of the ezrin-radixin-moesin (ERM) protein family, which exhibits opposing roles in Ras activity control. Thus, CPI-17 drives Ras activity and tumorigenesis in a two-fold way; inactivation of the tumor suppressor merlin and activation of the growth promoting ERM family. The in vivo significance of this oncogenic switch is highlighted by demonstrating CPI-17's involvement in human melanoma pathogenesis. PMID:27793041

  4. Positive Selection Pressure Drives Variation on the Surface-Exposed Variable Proteins of the Pathogenic Neisseria

    PubMed Central

    Hill, Stuart

    2016-01-01

    Pathogenic species of Neisseria utilize variable outer membrane proteins to facilitate infection and proliferation within the human host. However, the mechanisms behind the evolution of these variable alleles remain largely unknown due to analysis of previously limited datasets. In this study, we have expanded upon the previous analyses to substantially increase the number of analyzed sequences by including multiple diverse strains, from various geographic locations, to determine whether positive selective pressure is exerted on the evolution of these variable genes. Although Neisseria are naturally competent, this analysis indicates that only intrastrain horizontal gene transfer among the pathogenic Neisseria principally account for these genes exhibiting linkage equilibrium which drives the polymorphisms evidenced within these alleles. As the majority of polymorphisms occur across species, the divergence of these variable genes is dependent upon the species and is independent of geographical location, disease severity, or serogroup. Tests of neutrality were able to detect strong selection pressures acting upon both the opa and pil gene families, and were able to locate the majority of these sites within the exposed variable regions of the encoded proteins. Evidence of positive selection acting upon the hypervariable domains of Opa contradicts previous beliefs and provides evidence for selection of receptor binding. As the pathogenic Neisseria reside exclusively within the human host, the strong selection pressures acting upon both the opa and pil gene families provide support for host immune system pressure driving sequence polymorphisms within these variable genes. PMID:27532335

  5. Positive Selection Pressure Drives Variation on the Surface-Exposed Variable Proteins of the Pathogenic Neisseria.

    PubMed

    Wachter, Jenny; Hill, Stuart

    2016-01-01

    Pathogenic species of Neisseria utilize variable outer membrane proteins to facilitate infection and proliferation within the human host. However, the mechanisms behind the evolution of these variable alleles remain largely unknown due to analysis of previously limited datasets. In this study, we have expanded upon the previous analyses to substantially increase the number of analyzed sequences by including multiple diverse strains, from various geographic locations, to determine whether positive selective pressure is exerted on the evolution of these variable genes. Although Neisseria are naturally competent, this analysis indicates that only intrastrain horizontal gene transfer among the pathogenic Neisseria principally account for these genes exhibiting linkage equilibrium which drives the polymorphisms evidenced within these alleles. As the majority of polymorphisms occur across species, the divergence of these variable genes is dependent upon the species and is independent of geographical location, disease severity, or serogroup. Tests of neutrality were able to detect strong selection pressures acting upon both the opa and pil gene families, and were able to locate the majority of these sites within the exposed variable regions of the encoded proteins. Evidence of positive selection acting upon the hypervariable domains of Opa contradicts previous beliefs and provides evidence for selection of receptor binding. As the pathogenic Neisseria reside exclusively within the human host, the strong selection pressures acting upon both the opa and pil gene families provide support for host immune system pressure driving sequence polymorphisms within these variable genes.

  6. Two distinct membrane potential-dependent steps drive mitochondrial matrix protein translocation.

    PubMed

    Schendzielorz, Alexander Benjamin; Schulz, Christian; Lytovchenko, Oleksandr; Clancy, Anne; Guiard, Bernard; Ieva, Raffaele; van der Laan, Martin; Rehling, Peter

    2017-01-02

    Two driving forces energize precursor translocation across the inner mitochondrial membrane. Although the membrane potential (Δψ) is considered to drive translocation of positively charged presequences through the TIM23 complex (presequence translocase), the activity of the Hsp70-powered import motor is crucial for the translocation of the mature protein portion into the matrix. In this study, we show that mitochondrial matrix proteins display surprisingly different dependencies on the Δψ. However, a precursor's hypersensitivity to a reduction of the Δψ is not linked to the respective presequence, but rather to the mature portion of the polypeptide chain. The presequence translocase constituent Pam17 is specifically recruited by the receptor Tim50 to promote the transport of hypersensitive precursors into the matrix. Our analyses show that two distinct Δψ-driven translocation steps energize precursor passage across the inner mitochondrial membrane. The Δψ- and Pam17-dependent import step identified in this study is positioned between the two known energy-dependent steps: Δψ-driven presequence translocation and adenosine triphosphate-driven import motor activity.

  7. Modeling how reproductive ecology can drive protein diversification and result in linkage disequilibrium between sperm and egg proteins.

    PubMed

    Tomaiuolo, Maurizio; Levitan, Don R

    2010-07-01

    Gamete-recognition proteins determine whether sperm and eggs are compatible at fertilization, and they often evolve rapidly. The source of selection driving the evolution of these proteins is still debated. It has been suggested that sexual conflict can result in proliferation of genetic variation and possibly linkage disequilibrium between sperm and egg proteins. Empirical evidence suggests that both male and female reproductive success can be predicted by their sperm ligand genotype, but why female success can be predicted by a protein expressed only in males is unknown. Here we use mathematical modeling to investigate the interaction between reproductive behavior and sperm availability on the evolution of sperm ligands and egg receptors. We consider haploid and diploid expression in gametes in two possible ecological scenarios, monogamous spawning and competitive spawning. Reproductive behavior plays an important role in determining possible outcomes resulting from sexual conflict. Sperm limitation selects for common genotypes regardless of mating behavior. Under conditions of sperm abundance, competitive spawning provides conditions for the persistence of allelic variation and gametic disequilibrium. With monogamous spawning, such conditions are more restrictive.

  8. Duplication and Adaptive Evolution of a Key Centromeric Protein in Mimulus, a Genus with Female Meiotic Drive.

    PubMed

    Finseth, Findley R; Dong, Yuzhu; Saunders, Arpiar; Fishman, Lila

    2015-10-01

    The fundamental asymmetry of female meiosis creates an arena for genetic elements to compete for inclusion in the egg, promoting the selfish evolution of centromere variants that maximize their transmission to the future egg. Such "female meiotic drive" has been hypothesized to explain the paradoxically complex and rapidly evolving nature of centromeric DNA and proteins. Although theoretically widespread, few cases of active drive have been observed, thereby limiting the opportunities to directly assess the impact of centromeric drive on molecular variation at centromeres and binding proteins. Here, we characterize the molecular evolutionary patterns of CENH3, the centromere-defining histone variant, in Mimulus monkeyflowers, a genus with one of the few known cases of active centromere-associated female meiotic drive. First, we identify a novel duplication of CENH3 in diploid Mimulus, including in lineages with actively driving centromeres. Second, we demonstrate long-term adaptive evolution at several sites in the N-terminus of CENH3, a region with some meiosis-specific functions that putatively interacts with centromeric DNA. Finally, we infer that the paralogs evolve under different selective regimes; some sites in the N-terminus evolve under positive selection in the pro-orthologs or only one paralog (CENH3_B) and the paralogs exhibit significantly different patterns of polymorphism within populations. Our finding of long-term, adaptive evolution at CENH3 in the context of centromere-associated meiotic drive supports an antagonistic, coevolutionary battle for evolutionary dominance between centromeric DNA and binding proteins.

  9. Identification of a Protein Network Driving Neuritogenesis of MGE-Derived GABAergic Interneurons

    PubMed Central

    Franchi, Sira A.; Astro, Veronica; Macco, Romina; Tonoli, Diletta; Barnier, Jean-Vianney; Botta, Martina; de Curtis, Ivan

    2016-01-01

    Interneurons are essential modulators of brain activity and their abnormal maturation may lead to neural and intellectual disabilities. Here we show that cultures derived from murine medial ganglionic eminences (MGEs) produce virtually pure, polarized γ-aminobutyric acid (GABA)-ergic interneurons that can form morphologically identifiable inhibitory synapses. We show that Rac GTPases and a protein complex including the GIT family scaffold proteins are expressed during maturation in vitro, and are required for the normal development of neurites. GIT1 promotes neurite extension in a conformation-dependent manner, while affecting its interaction with specific partners reduces neurite branching. Proteins of the GIT network are concentrated at growth cones, and interaction mutants may affect growth cone behavior. Our findings identify the PIX/GIT1/liprin-α1/ERC1 network as critical for the regulation of interneuron neurite differentiation in vitro, and show that these cultures represent a valuable system to identify the molecular mechanisms driving the maturation of cortical/hippocampal interneurons. PMID:28066185

  10. Protein kinase D1 drives pancreatic acinar cell reprogramming and progression to intraepithelial neoplasia

    NASA Astrophysics Data System (ADS)

    Liou, Geou-Yarh; Döppler, Heike; Braun, Ursula B.; Panayiotou, Richard; Scotti Buzhardt, Michele; Radisky, Derek C.; Crawford, Howard C.; Fields, Alan P.; Murray, Nicole R.; Wang, Q. Jane; Leitges, Michael; Storz, Peter

    2015-02-01

    The transdifferentiation of pancreatic acinar cells to a ductal phenotype (acinar-to-ductal metaplasia, ADM) occurs after injury or inflammation of the pancreas and is a reversible process. However, in the presence of activating Kras mutations or persistent epidermal growth factor receptor (EGF-R) signalling, cells that underwent ADM can progress to pancreatic intraepithelial neoplasia (PanIN) and eventually pancreatic cancer. In transgenic animal models, ADM and PanINs are initiated by high-affinity ligands for EGF-R or activating Kras mutations, but the underlying signalling mechanisms are not well understood. Here, using a conditional knockout approach, we show that protein kinase D1 (PKD1) is sufficient to drive the reprogramming process to a ductal phenotype and progression to PanINs. Moreover, using 3D explant culture of primary pancreatic acinar cells, we show that PKD1 acts downstream of TGFα and Kras, to mediate formation of ductal structures through activation of the Notch pathway.

  11. The Lymphocytic Choriomeningitis Virus Matrix Protein PPXY Late Domain Drives the Production of Defective Interfering Particles

    PubMed Central

    Ziegler, Christopher M.; Eisenhauer, Philip; Bruce, Emily A.; Weir, Marion E.; King, Benjamin R.; Klaus, Joseph P.; Krementsov, Dimitry N.; Shirley, David J.; Ballif, Bryan A.; Botten, Jason

    2016-01-01

    Arenaviruses cause severe diseases in humans but establish asymptomatic, lifelong infections in rodent reservoirs. Persistently-infected rodents harbor high levels of defective interfering (DI) particles, which are thought to be important for establishing persistence and mitigating virus-induced cytopathic effect. Little is known about what drives the production of DI particles. We show that neither the PPXY late domain encoded within the lymphocytic choriomeningitis virus (LCMV) matrix protein nor a functional endosomal sorting complex transport (ESCRT) pathway is absolutely required for the generation of standard infectious virus particles. In contrast, DI particle release critically requires the PPXY late domain and is ESCRT-dependent. Additionally, the terminal tyrosine in the PPXY motif is reversibly phosphorylated and our findings indicate that this posttranslational modification may regulate DI particle formation. Thus we have uncovered a new role for the PPXY late domain and a possible mechanism for its regulation. PMID:27010636

  12. Nesprins anchor kinesin-1 motors to the nucleus to drive nuclear distribution in muscle cells.

    PubMed

    Wilson, Meredith H; Holzbaur, Erika L F

    2015-01-01

    During skeletal muscle development, nuclei move dynamically through myotubes in a microtubule-dependent manner, driven by the microtubule motor protein kinesin-1. Loss of kinesin-1 leads to improperly positioned nuclei in culture and in vivo. Two models have been proposed to explain how kinesin-1 functions to move nuclei in myotubes. In the cargo model, kinesin-1 acts directly from the surface of the nucleus, whereas in an alternative model, kinesin-1 moves nuclei indirectly by sliding anti-parallel microtubules. Here, we test the hypothesis that an ensemble of Kif5B motors acts from the nuclear envelope to distribute nuclei throughout the length of syncytial myotubes. First, using an inducible dimerization system, we show that controlled recruitment of truncated, constitutively active kinesin-1 motors to the nuclear envelope is sufficient to prevent the nuclear aggregation resulting from depletion of endogenous kinesin-1. Second, we identify a conserved kinesin light chain (KLC)-binding motif in the nuclear envelope proteins nesprin-1 and nesprin-2, and show that recruitment of the motor complex to the nucleus via this LEWD motif is essential for nuclear distribution. Together, our findings demonstrate that the nucleus is a kinesin-1 cargo in myotubes and that nesprins function as nuclear cargo adaptors. The importance of achieving and maintaining proper nuclear position is not restricted to muscle fibers, suggesting that the nesprin-dependent recruitment of kinesin-1 to the nuclear envelope through the interaction of a conserved LEWD motif with kinesin light chain might be a general mechanism for cell-type-specific nuclear positioning during development.

  13. Ribosome Dwell Times and the Protein Copy Number Distribution

    NASA Astrophysics Data System (ADS)

    Gorissen, Mieke; Vanderzande, Carlo

    2012-09-01

    Translation is the cellular process in which ribosomes make proteins from information encoded on messenger RNA (mRNA). We model translation with an exclusion process taking into account the experimentally determined, non-exponential, waiting time between steps of a ribosome. From numerical simulations using realistic parameter values, we determine the distribution P( E) of the number of proteins E produced by one mRNA. We find that for small E this distribution is not geometric. We present a simplified and analytically solvable model that relates P( E) to the distributions of the times to produce the first E proteins.

  14. Measuring dendritic distribution of membrane proteins.

    PubMed

    Ballou, Edmund W; Smith, W Bryan; Anelli, Roberta; Heckman, C J

    2006-09-30

    Neurons perform much of their integrative work in the dendritic tree, and spinal motoneurons have the largest tree of any cell. Electrical excitability is strongly influenced by dendrite membrane properties, which are difficult to measure directly. We describe a method to measure the distribution of ion channel membrane densities along dendritic trajectories. The method combines standard immunohistochemistry with reconstruction procedures for both large-scale and small-scale optical microscopy. Software written for Matlab then extracts the colocalization of the target ion channel with the target dye injected cell, and calculates the relative channel density per square micron of cell surface area, as a function of distance from the cell body. The technique can be used to quantify the localization and distribution of any immunoreactive moiety, and the software provides a flexible vehicle for sensitivity analysis, to validate heuristics for selecting thresholds.

  15. Direct activation of Shroom3 transcription by Pitx proteins drives epithelial morphogenesis in the developing gut

    PubMed Central

    Chung, Mei-I; Nascone-Yoder, Nanette M.; Grover, Stephanie A.; Drysdale, Thomas A.; Wallingford, John B.

    2010-01-01

    Individual cell shape changes are essential for epithelial morphogenesis. A transcriptional network for epithelial cell shape change is emerging in Drosophila, but this area remains largely unexplored in vertebrates. The distinction is important as so far, key downstream effectors of cell shape change in Drosophila appear not to be conserved. Rather, Shroom3 has emerged as a central effector of epithelial morphogenesis in vertebrates, driving both actin- and microtubule-based cell shape changes. To date, the morphogenetic role of Shroom3 has been explored only in the neural epithelium, so the broad expression of this gene raises two important questions: what are the requirements for Shroom3 in non-neural tissues and what factors control Shroom3 transcription? Here, we show in Xenopus that Shroom3 is essential for cell shape changes and morphogenesis in the developing vertebrate gut and that Shroom3 transcription in the gut requires the Pitx1 transcription factor. Moreover, we show that Pitx proteins directly activate Shroom3 transcription, and we identify Pitx-responsive regulatory elements in the genomic DNA upstream of Shroom3. Finally, we show that ectopic expression of Pitx proteins is sufficient to induce Shroom3-dependent cytoskeletal reorganization and epithelial cell shape change. These data demonstrate new breadth to the requirements for Shroom3 in morphogenesis, and they also provide a cell-biological basis for the role of Pitx transcription factors in morphogenesis. More generally, these results provide a foundation for deciphering the transcriptional network that underlies epithelial cell shape change in developing vertebrates. PMID:20332151

  16. Divergent androgen regulation of unfolded protein response pathways drives prostate cancer

    PubMed Central

    Sheng, Xia; Arnoldussen, Yke Jildouw; Storm, Margrethe; Tesikova, Martina; Nenseth, Hatice Zeynep; Zhao, Sen; Fazli, Ladan; Rennie, Paul; Risberg, Bjørn; Wæhre, Håkon; Danielsen, Håvard; Mills, Ian G; Jin, Yang; Hotamisligil, Gökhan; Saatcioglu, Fahri

    2015-01-01

    The unfolded protein response (UPR) is a homeostatic mechanism to maintain endoplasmic reticulum (ER) function. The UPR is activated by various physiological conditions as well as in disease states, such as cancer. As androgens regulate secretion and development of the normal prostate and drive prostate cancer (PCa) growth, they may affect UPR pathways. Here, we show that the canonical UPR pathways are directly and divergently regulated by androgens in PCa cells, through the androgen receptor (AR), which is critical for PCa survival. AR bound to gene regulatory sites and activated the IRE1α branch, but simultaneously inhibited PERK signaling. Inhibition of the IRE1α arm profoundly reduced PCa cell growth in vitro as well as tumor formation in preclinical models of PCa in vivo. Consistently, AR and UPR gene expression were correlated in human PCa, and spliced XBP-1 expression was significantly upregulated in cancer compared with normal prostate. These data establish a genetic switch orchestrated by AR that divergently regulates the UPR pathways and suggest that targeting IRE1α signaling may have therapeutic utility in PCa. PMID:25864123

  17. Rhbdf2 mutations increase its protein stability and drive EGFR hyperactivation through enhanced secretion of amphiregulin

    PubMed Central

    Hosur, Vishnu; Johnson, Kenneth R.; Burzenski, Lisa M.; Stearns, Timothy M.; Maser, Richard S.; Shultz, Leonard D.

    2014-01-01

    The rhomboid 5 homolog 2 (Rhbdf2) gene encodes an inactive rhomboid (iRhom) protease, iRhom2, one of a family of enzymes containing a long cytosolic N terminus and a dormant peptidase domain of unknown function. iRhom2 has been implicated in epithelial regeneration and cancer growth through constitutive activation of epidermal growth factor receptor (EGFR) signaling. However, little is known about the physiological substrates for iRhom2 or the molecular mechanisms underlying these functions. We show that iRhom2 is a short-lived protein whose stability can be increased by select mutations in the N-terminal domain. In turn, these stable variants function to augment the secretion of EGF family ligands, including amphiregulin, independent of metalloprotease a disintegrin and metalloproteinase 17 (ADAM17) activity. In vivo, N-terminal iRhom2 mutations induce accelerated wound healing as well as accelerated tumorigenesis, but they do not drive spontaneous tumor development. This work underscores the physiological prominence of iRhom2 in controlling EGFR signaling events involved in wound healing and neoplastic growth, and yields insight into the function of key iRhom2 domains. PMID:24825892

  18. Dynamic hydration shell restores Kauzmann's 1959 explanation of how the hydrophobic factor drives protein folding.

    PubMed

    Baldwin, Robert L

    2014-09-09

    Kauzmann's explanation of how the hydrophobic factor drives protein folding is reexamined. His explanation said that hydrocarbon hydration shells are formed, possibly of clathrate water, and they explain why hydrocarbons have uniquely low solubilities in water. His explanation was not universally accepted because of skepticism about the clathrate hydration shell. A revised version is given here in which a dynamic hydration shell is formed by van der Waals (vdw) attraction, as proposed in 1985 by Jorgensen et al. [Jorgensen WL, Gao J, Ravimohan C (1985) J Phys Chem 89:3470-3473]. The vdw hydration shell is implicit in theories of hydrophobicity that contain the vdw interaction between hydrocarbon C and water O atoms. To test the vdw shell model against the known hydration energetics of alkanes, the energetics should be based on the Ben-Naim standard state (solute transfer between fixed positions in the gas and liquid phases). Then the energetics are proportional to n, the number of water molecules correlated with an alkane by vdw attraction, given by the simulations of Jorgensen et al. The energetics show that the decrease in entropy upon hydration is the root cause of hydrophobicity; it probably results from extensive ordering of water molecules in the vdw shell. The puzzle of how hydrophobic free energy can be proportional to nonpolar surface area when the free energy is unfavorable and the only known interaction (the vdw attraction) is favorable, is resolved by finding that the unfavorable free energy is produced by the vdw shell.

  19. Rhbdf2 mutations increase its protein stability and drive EGFR hyperactivation through enhanced secretion of amphiregulin.

    PubMed

    Hosur, Vishnu; Johnson, Kenneth R; Burzenski, Lisa M; Stearns, Timothy M; Maser, Richard S; Shultz, Leonard D

    2014-05-27

    The rhomboid 5 homolog 2 (Rhbdf2) gene encodes an inactive rhomboid (iRhom) protease, iRhom2, one of a family of enzymes containing a long cytosolic N terminus and a dormant peptidase domain of unknown function. iRhom2 has been implicated in epithelial regeneration and cancer growth through constitutive activation of epidermal growth factor receptor (EGFR) signaling. However, little is known about the physiological substrates for iRhom2 or the molecular mechanisms underlying these functions. We show that iRhom2 is a short-lived protein whose stability can be increased by select mutations in the N-terminal domain. In turn, these stable variants function to augment the secretion of EGF family ligands, including amphiregulin, independent of metalloprotease a disintegrin and metalloproteinase 17 (ADAM17) activity. In vivo, N-terminal iRhom2 mutations induce accelerated wound healing as well as accelerated tumorigenesis, but they do not drive spontaneous tumor development. This work underscores the physiological prominence of iRhom2 in controlling EGFR signaling events involved in wound healing and neoplastic growth, and yields insight into the function of key iRhom2 domains.

  20. Protein surface-distribution and protein-protein interactions in the binding of peripheral proteins to charged lipid membranes.

    PubMed Central

    Heimburg, T; Marsh, D

    1995-01-01

    The binding of native cytochrome c to negatively charged lipid dispersions of dioleoyl phosphatidylglycerol has been studied over a wide range of ionic strengths. Not only is the strength of protein binding found to decrease rapidly with increasing ionic strength, but also the binding curves reach an apparent saturation level that decreases rapidly with increasing ionic strength. Analysis of the binding isotherms with a general statistical thermodynamic model that takes into account not only the free energy of the electrostatic double layer, but also the free energy of the surface distribution of the protein, demonstrates that the apparent saturation effects could arise from a competition between the out-of-plane binding reaction and the lateral in-plane interactions between proteins at the surface. It is found that association with nonlocalized sites results in binding isotherms that display the apparent saturation effect to a much more pronounced extent than does the Langmuir adsorption isotherm for binding to localized sites. With the model for nonlocalized sites, the binding isotherms of native cytochrome c can be described adequately by taking into account only the entropy of the surface distribution of the protein, without appreciable enthalpic interactions between the bound proteins. The binding of cytochrome c to dioleoyl phosphatidylglycerol dispersions at a temperature at which the bound protein is denatured on the lipid surface, but is nondenatured when free in solution, has also been studied. The binding curves for the surface-denatured protein differ from those for the native protein in that the apparent saturation at high ionic strength is less pronounced. This indicates the tendency of the denatured protein to aggregate on the lipid surface, and can be described by the binding isotherms for nonlocalized sites only if attractive interactions between the surface-bound proteins are included in addition to the distributional entropic terms. Additionally

  1. The Liverwort, Marchantia, Drives Alternative Electron Flow Using a Flavodiiron Protein to Protect PSI1[OPEN

    PubMed Central

    Tsukamoto, Shigeyuki; Sejima, Takehiro

    2017-01-01

    The diffusion efficiency of oxygen in the atmosphere, like that of CO2, is approximately 104 times greater than that in aqueous environments. Consequently, terrestrial photosynthetic organisms need mechanisms to protect against potential oxidative damage. The liverwort Marchantia polymorpha, a basal land plant, has habitats where it is exposed to both water and the atmosphere. Furthermore, like cyanobacteria, M. polymorpha has genes encoding flavodiiron proteins (FLV). In cyanobacteria, FLVs mediate oxygen-dependent alternative electron flow (AEF) to suppress the production of reactive oxygen species. Here, we investigated whether FLVs are required for the protection of photosynthesis in M. polymorpha. A mutant deficient in the FLV1 isozyme (ΔMpFlv1) sustained photooxidative damage to photosystem I (PSI) following repetitive short-saturation pulses of light. Compared with the wild type (Takaragaike-1), ΔMpFlv1 showed the same photosynthetic oxygen evolution rate but a lower electron transport rate during the induction phase of photosynthesis. Additionally, the reaction center chlorophyll in PSI, P700, was highly reduced in ΔMpFlv1 but not in Takaragaike-1. These results indicate that the gene product of MpFlv1 drives AEF to oxidize PSI, as in cyanobacteria. Furthermore, FLV-mediated AEF supports the production of a proton motive force to possibly induce the nonphotochemical quenching of chlorophyll fluorescence and suppress electron transport in the cytochrome b6/f complex. After submerging the thalli, a decrease in photosystem II operating efficiency was observed, particularly in ΔMpFlv1, which implies that species living in these sorts of habitats require FLV-mediated AEF. PMID:28153920

  2. When is an ecological network complex? Connectance drives degree distribution and emerging network properties

    PubMed Central

    Gravel, Dominique

    2014-01-01

    Connectance and degree distributions are important components of the structure of ecological networks. In this contribution, we use a statistical argument and simple network generating models to show that properties of the degree distribution are driven by network connectance. We discuss the consequences of this finding for (1) the generation of random networks in null-model analyses, and (2) the interpretation of network structure and ecosystem properties in relationship with degree distribution. PMID:24688835

  3. PHEV Energy Use Estimation: Validating the Gamma Distribution for Representing the Random Daily Driving Distance

    SciTech Connect

    Lin, Zhenhong; Dong, Jing; Liu, Changzheng; Greene, David L

    2012-01-01

    The petroleum and electricity consumptions of plug-in hybrid electric vehicles (PHEVs) are sensitive to the variation of daily vehicle miles traveled (DVMT). Some studies assume DVMT to follow a Gamma distribution, but such a Gamma assumption is yet to be validated. This study finds the Gamma assumption valid in the context of PHEV energy analysis, based on continuous GPS travel data of 382 vehicles, each tracked for at least 183 days. The validity conclusion is based on the found small prediction errors, resulting from the Gamma assumption, in PHEV petroleum use, electricity use, and energy cost. The finding that the Gamma distribution is valid and reliable is important. It paves the way for the Gamma distribution to be assumed for analyzing energy uses of PHEVs in the real world. The Gamma distribution can be easily specified with very few pieces of driver information and is relatively easy for mathematical manipulation. Given the validation in this study, the Gamma distribution can now be used with better confidence in a variety of applications, such as improving vehicle consumer choice models, quantifying range anxiety for battery electric vehicles, investigating roles of charging infrastructure, and constructing online calculators that provide personal estimates of PHEV energy use.

  4. Distribution of Tight Junction Proteins in Adult Human Salivary Glands

    PubMed Central

    Maria, Ola M.; Kim, Jung-Wan Martin; Gerstenhaber, Jonathan A.; Baum, Bruce J.; Tran, Simon D.

    2008-01-01

    Tight junctions (TJs) are an essential structure of fluid-secreting cells, such as those in salivary glands. Three major families of integral membrane proteins have been identified as components of the TJ: claudins, occludin, and junctional adhesion molecules (JAMs), plus the cytosolic protein zonula occludens (ZO). We have been working to develop an orally implantable artificial salivary gland that would be suitable for treating patients lacking salivary parenchymal tissue. To date, little is known about the distribution of TJ proteins in adult human salivary cells and thus what key molecular components might be desirable for the cellular component of an artificial salivary gland device. Therefore, the aim of this study was to determine the distribution of TJ proteins in human salivary glands. Salivary gland samples were obtained from 10 patients. Frozen and formalin-fixed paraffin-embedded sections were stained using IHC methods. Claudin-1 was expressed in ductal, endothelial, and ∼25% of serous cells. Claudins-2, -3, and -4 and JAM-A were expressed in both ductal and acinar cells, whereas claudin-5 was expressed only in endothelial cells. Occludin and ZO-1 were expressed in acinar, ductal, and endothelial cells. These results provide new information on TJ proteins in two major human salivary glands and should serve as a reference for future studies to assess the presence of appropriate TJ proteins in a tissue-engineered human salivary gland. (J Histochem Cytochem 56:1093–1098, 2008) PMID:18765838

  5. Ecological gradients driving the distribution of four Ericaceae in boreal Quebec, Canada

    PubMed Central

    Thiffault, Nelson; Grondin, Pierre; Noël, Jean; Poirier, Véronique

    2015-01-01

    Understory species play a significant role in forest ecosystem dynamics. As such, species of the Ericaceae family have a major effect on the regeneration of tree species in boreal ecosystems. It is thus imperative to understand the ecological gradients controlling their distribution and abundance, so that their impacts can be taken into account in sustainable forest management. Using innovative analytical techniques from landscape ecology, we aimed to position, along ecological gradients, four Ericaceae found in the boreal forest of Quebec (Canada) (Rhododendron groenlandicum, Kalmia angustifolia, Chamaedaphne calyculata, and Vaccinium spp), to regionalize these species into landscape units relevant to forest management, and to estimate the relative importance of several ecological drivers (climate, disturbances, stand attributes, and physical environment) that control the species distribution and abundance. We conducted our study in boreal Quebec, over a study area covering 535,355 km2. We used data from 15,339 ecological survey plots and forest maps to characterize 1422 ecological districts covering the study region. We evaluated the relative proportion of each ericaceous species and explanatory variables at the district level. Vegetation and explanatory variables matrices were used to conduct redundancy, cluster, and variation partitioning analyses. We observed that ericaceous species are mainly distributed in the western part of the study area and each species has a distinct latitudinal and longitudinal gradient distribution. On the basis of these gradients, we delimited 10 homogeneous landscape units distinct in terms of ericaceous species abundance and environmental drivers. The distribution of the ericaceous species along ecological gradients is closely related to the overlaps between the four sets of explanatory variables considered. We conclude that the studied Ericaceae occupy specific positions along ecological gradients and possess a specific abundance

  6. Examination of the CLIC drive beam pipe design for thermal distortion caused by distributed beam line

    SciTech Connect

    C. Johnson; K. Kloeppel

    1997-01-01

    Beam transport programs are widely used to estimate the distribution of power deposited in accelerator structures by particle beams, either intentionally as for targets or beam dumps or accidentally owing the beam loss incidents. While this is usually adequate for considerations of radiation safety, it does not reveal the expected temperature rise and its effect on structural integrity. To find this, thermal diffusion must be taken into account, requiring another step in the analysis. The method that has been proposed is to use the output of a transport program, perhaps modified, as input for a finite element analysis program that can solve the thermal diffusion equation. At Cern, the design of the CLIC beam pipe has been treated in this fashion. The power distribution produced in the walls by a distributed beam loss was found according to the widely-used electron shower code EGS4. The distribution of power density was then used to form the input for the finite element analysis pro gram ANSYS, which was able to find the expected temperature rise and the resulting thermal distortion. As a result of these studies, the beam pipe design can be modified to include features that will counteract such distortion.

  7. Driving forces of organic carbon spatial distribution in the tropical seascape

    NASA Astrophysics Data System (ADS)

    Gillis, L. G.; Belshe, F. E.; Ziegler, A. D.; Bouma, T. J.

    2017-02-01

    An important ecosystem service of tropical coastal vegetation including seagrass beds and mangrove forests is their ability to accumulate carbon. Here we attempt to establish the driving forces for the accumulation of surface organic carbon in southern Thailand coastal systems. Across 12 sites we found that in line with expectations, seagrass beds (0.6 ± 0.09%) and mangrove forests (0.9 ± 0.3%) had higher organic carbon in the surface (top 5 cm) sediment than un-vegetated mudflats (0.4 ± 0.04%). Unexpectedly, however, mangrove forests in this region retained organic carbon, rather than outwell it, under normal tidal conditions. No relationship was found between organic carbon and substrate grain size. The most interesting finding of our study was that climax and pioneer seagrass species retained more carbon than mixed-species meadows, suggesting that plant morphology and meadow characteristics can be important factors in organic carbon accumulation. Insights such as these are important in developing carbon management strategies involving coastal ecosystems such as offsetting of carbon emissions. The ability of tropical coastal vegetation to sequester carbon is an important aspect for valuing the ecosystems. Our results provide some initial insight into the factors affecting carbon sequestration in these ecosystems, but also highlight the need for further research on a global scale.

  8. Extensive Positive Selection Drives the Evolution of Nonstructural Proteins in Lineage C Betacoronaviruses

    PubMed Central

    Cagliani, Rachele; Mozzi, Alessandra; Pozzoli, Uberto; Al-Daghri, Nasser; Clerici, Mario; Sironi, Manuela

    2016-01-01

    ABSTRACT Middle East respiratory syndrome-related coronavirus (MERS-CoV) spreads to humans via zoonotic transmission from camels. MERS-CoV belongs to lineage C of betacoronaviruses (betaCoVs), which also includes viruses isolated from bats and hedgehogs. A large portion of the betaCoV genome consists of two open reading frames (ORF1a and ORF1b) that are translated into polyproteins. These are cleaved by viral proteases to generate 16 nonstructural proteins (nsp1 to nsp16) which compose the viral replication-transcription complex. We investigated the evolution of ORF1a and ORF1b in lineage C betaCoVs. Results indicated widespread positive selection, acting mostly on ORF1a. The proportion of positively selected sites in ORF1a was much higher than that previously reported for the surface-exposed spike protein. Selected sites were unevenly distributed, with nsp3 representing the preferential target. Several pairs of coevolving sites were also detected, possibly indicating epistatic interactions; most of these were located in nsp3. Adaptive evolution at nsp3 is ongoing in MERS-CoV strains, and two selected sites (G720 and R911) were detected in the protease domain. While position 720 is variable in camel-derived viruses, suggesting that the selective event does not represent a specific adaptation to humans, the R911C substitution was observed only in human-derived MERS-CoV isolates, including the viral strain responsible for the recent South Korean outbreak. It will be extremely important to assess whether these changes affect host range or other viral phenotypes. More generally, data herein indicate that CoV nsp3 represents a major selection target and that nsp3 sequencing should be envisaged in monitoring programs and field surveys. IMPORTANCE Both severe acute respiratory syndrome coronavirus (SARS-CoV) and MERS-CoV originated in bats and spread to humans via an intermediate host. This clearly highlights the potential for coronavirus host shifting and the relevance

  9. Composition and molecular weight distribution of carob germ protein fractions.

    PubMed

    Smith, Brennan M; Bean, Scott R; Schober, Tilman J; Tilley, Michael; Herald, Thomas J; Aramouni, Fadi

    2010-07-14

    Biochemical properties of carob germ proteins were analyzed using a combination of selective extraction, reversed-phase high-performance liquid chromatography (RP-HPLC), size exclusion chromatography (SEC) coupled with multiangle laser light scattering (SEC-MALS), and electrophoretic analysis. Using a modified Osborne extraction procedure, carob germ flour proteins were found to contain approximately 32% albumin and globulin and approximately 68% glutelin with no prolamins detected. The albumin and globulin fraction was found to contain low amounts of disulfide-bonded polymers with relatively low M(w) ranging up to 5 x 10(6) Da. The glutelin fraction, however, was found to contain large amounts of high molecular weight disulfide-bonded polymers with M(w) up to 8 x 10(7) Da. When extracted under nonreducing conditions and divided into soluble and insoluble proteins as typically done for wheat gluten, carob germ proteins were found to be almost entirely ( approximately 95%) in the soluble fraction with only ( approximately 5%) in the insoluble fraction. As in wheat, SEC-MALS analysis showed that the insoluble proteins had a greater M(w) than the soluble proteins and ranged up to 8 x 10(7) Da. The lower M(w) distribution of the polymeric proteins of carob germ flour may account for differences in functionality between wheat and carob germ flour.

  10. Chromosomal Distribution of PcG Proteins during Drosophila Development

    PubMed Central

    Nègre, Nicolas; Hennetin, Jérôme; Sun, Ling V; Lavrov, Sergey; Bellis, Michel; White, Kevin P

    2006-01-01

    Polycomb group (PcG) proteins are able to maintain the memory of silent transcriptional states of homeotic genes throughout development. In Drosophila, they form multimeric complexes that bind to specific DNA regulatory elements named PcG response elements (PREs). To date, few PREs have been identified and the chromosomal distribution of PcG proteins during development is unknown. We used chromatin immunoprecipitation (ChIP) with genomic tiling path microarrays to analyze the binding profile of the PcG proteins Polycomb (PC) and Polyhomeotic (PH) across 10 Mb of euchromatin. We also analyzed the distribution of GAGA factor (GAF), a sequence-specific DNA binding protein that is found at most previously identified PREs. Our data show that PC and PH often bind to clustered regions within large loci that encode transcription factors which play multiple roles in developmental patterning and in the regulation of cell proliferation. GAF co-localizes with PC and PH to a limited extent, suggesting that GAF is not a necessary component of chromatin at PREs. Finally, the chromosome-association profile of PC and PH changes during development, suggesting that the function of these proteins in the regulation of some of their target genes might be more dynamic than previously anticipated. PMID:16613483

  11. Factors driving the seasonal distribution of zooplankton in a eutrophicated Mediterranean Lagoon.

    PubMed

    Ziadi, Boutheina; Dhib, Amel; Turki, Souad; Aleya, Lotfi

    2015-08-15

    The distribution of the zooplankton community was studied along with environmental factors at five sampling stations in Ghar El Melh Lagoon (GML) (Mediterranean Sea, northern Tunisia). GML is characterized by specific following properties: broad and shallow, freshwater supply (Station 1); connection to the sea (S2); stagnation (S3 especially), and eutrophic conditions with enhanced nutrient concentrations (S4 and S5). Samples were taken twice monthly from February 2011 to January 2012. Twenty-three zooplankton groups comprising 10 larval stages were identified. Zooplankton assemblages were largely dominated by copepods (37.25%), followed respectively by ciliates (21.09%), bivalve larvae (14.88%) and gastropod veligers (12.53%). Redundancy analysis indicated that while no significant difference was found in the distribution of zooplankton at any station, a strong difference was observed according to season. Both temporal and physicochemical fluctuations explain more than 50% of changes in zooplankton abundances.

  12. Spatial scale modulates the strength of ecological processes driving disease distributions

    PubMed Central

    Cohen, Jeremy M.; Civitello, David J.; Brace, Amber J.; Feichtinger, Erin M.; Ortega, C. Nicole; Richardson, Jason C.; Sauer, Erin L.; Liu, Xuan; Rohr, Jason R.

    2016-01-01

    Humans are altering the distribution of species by changing the climate and disrupting biotic interactions and dispersal. A fundamental hypothesis in spatial ecology suggests that these effects are scale dependent; biotic interactions should shape distributions at local scales, whereas climate should dominate at regional scales. If so, common single-scale analyses might misestimate the impacts of anthropogenic modifications on biodiversity and the environment. However, large-scale datasets necessary to test these hypotheses have not been available until recently. Here we conduct a cross-continental, cross-scale (almost five orders of magnitude) analysis of the influence of biotic and abiotic processes and human population density on the distribution of three emerging pathogens: the amphibian chytrid fungus implicated in worldwide amphibian declines and West Nile virus and the bacterium that causes Lyme disease (Borrelia burgdorferi), which are responsible for ongoing human health crises. In all three systems, we show that biotic factors were significant predictors of pathogen distributions in multiple regression models only at local scales (∼102–103 km2), whereas climate and human population density always were significant only at relatively larger, regional scales (usually >104 km2). Spatial autocorrelation analyses revealed that biotic factors were more variable at smaller scales, whereas climatic factors were more variable at larger scales, as is consistent with the prediction that factors should be important at the scales at which they vary the most. Finally, no single scale could detect the importance of all three categories of processes. These results highlight that common single-scale analyses can misrepresent the true impact of anthropogenic modifications on biodiversity and the environment. PMID:27247398

  13. Floral abundance, richness, and spatial distribution drive urban garden bee communities.

    PubMed

    Plascencia, M; Philpott, S M

    2017-03-01

    In urban landscapes, gardens provide refuges for bee diversity, but conservation potential may depend on local and landscape features. Foraging and population persistence of bee species, as well as overall pollinator community structure, may be supported by the abundance, richness, and spatial distribution of floral resources. Floral resources strongly differ in urban gardens. Using hand netting and pan traps to survey bees, we examined whether abundance, richness, and spatial distribution of floral resources, as well as ground cover and garden landscape surroundings influence bee abundance, species richness, and diversity on the central coast of California. Differences in floral abundance and spatial distribution, as well as urban cover in the landscape, predicted different bee community variables. Abundance of all bees and of honeybees (Apis mellifera) was lower in sites with more urban land cover surrounding the gardens. Honeybee abundance was higher in sites with patchy floral resources, whereas bee species richness and bee diversity was higher in sites with more clustered floral resources. Surprisingly, bee species richness and bee diversity was lower in sites with very high floral abundance, possibly due to interactions with honeybees. Other studies have documented the importance of floral abundance and landscape surroundings for bees in urban gardens, but this study is the first to document that the spatial arrangement of flowers strongly predicts bee abundance and richness. Based on these findings, it is likely that garden managers may promote bee conservation by managing for floral connectivity and abundance within these ubiquitous urban habitats.

  14. Protein distribution in lupin protein isolates from Lupinus angustifolius L. prepared by various isolation techniques.

    PubMed

    Muranyi, Isabel S; Volke, Daniela; Hoffmann, Ralf; Eisner, Peter; Herfellner, Thomas; Brunnbauer, Markus; Koehler, Peter; Schweiggert-Weisz, Ute

    2016-09-15

    Differences in the protein distribution of various protein isolates from Lupinus angustifolius L. Vitabor were identified as affected by the isolation procedure (alkaline and/or salt-induced extraction followed by isoelectric and/or dilutive precipitation). Protein isolates extracted in alkaline solution showed higher protein yields (26.4-31.7%) compared to salt-induced extraction (19.8-30.0%) or combined alkaline and salt-induced extraction (23.3-25.6%). Chemical variations among the protein isolates especially occurred within the albumins. Protein isolates precipitated isoelectrically showed the highest contents, whereas protein isolates precipitated by dilutive showed the lowest contents of conglutin δ. Furthermore, the alkaline subunits of conglutin α and conglutin γ decreased during alkaline extraction compared to salt-induced extraction. A decrease in protein-bound polar and basic amino acids was shown after protein isolation. In contrast, the amounts of nonpolar, aliphatic, aromatic, hydroxylated and sulfur-rich amino acids were higher in the lupin protein isolates compared to the lupin flakes. However, the functional side chains could not be related to the specific molecular arrangements of the protein isolates, as a similar amino acid composition was found among the protein isolates.

  15. Pineapple translation factor SUI1 and ribosomal protein L36 promoters drive constitutive transgene expression patterns in Arabidopsis thaliana.

    PubMed

    Koia, Jonni; Moyle, Richard; Hendry, Caroline; Lim, Lionel; Botella, José Ramón

    2013-03-01

    The availability of a variety of promoter sequences is necessary for the genetic engineering of plants, in basic research studies and for the development of transgenic crops. In this study, the promoter and 5' untranslated regions of the evolutionally conserved protein translation factor SUI1 gene and ribosomal protein L36 gene were isolated from pineapple and sequenced. Each promoter was translationally fused to the GUS reporter gene and transformed into the heterologous plant system Arabidopsis thaliana. Both the pineapple SUI1 and L36 promoters drove GUS expression in all tissues of Arabidopsis at levels comparable to the CaMV35S promoter. Transient assays determined that the pineapple SUI1 promoter also drove GUS expression in a variety of climacteric and non-climacteric fruit species. Thus the pineapple SUI1 and L36 promoters demonstrate the potential for using translation factor and ribosomal protein genes as a source of promoter sequences that can drive constitutive transgene expression patterns.

  16. Temperature drives global patterns in forest biomass distribution in leaves, stems, and roots

    USGS Publications Warehouse

    Reich, Peter B.; Lou, Yunjian; Bradford, John B.; Poorter, Hendrik; Perry, Charles H.; Oleksyn, Jacek

    2014-01-01

    Whether the fraction of total forest biomass distributed in roots, stems, or leaves varies systematically across geographic gradients remains unknown despite its importance for understanding forest ecology and modeling global carbon cycles. It has been hypothesized that plants should maintain proportionally more biomass in the organ that acquires the most limiting resource. Accordingly, we hypothesize greater biomass distribution in roots and less in stems and foliage in increasingly arid climates and in colder environments at high latitudes. Such a strategy would increase uptake of soil water in dry conditions and of soil nutrients in cold soils, where they are at low supply and are less mobile. We use a large global biomass dataset (>6,200 forests from 61 countries, across a 40 °C gradient in mean annual temperature) to address these questions. Climate metrics involving temperature were better predictors of biomass partitioning than those involving moisture availability, because, surprisingly, fractional distribution of biomass to roots or foliage was unrelated to aridity. In contrast, in increasingly cold climates, the proportion of total forest biomass in roots was greater and in foliage was smaller for both angiosperm and gymnosperm forests. These findings support hypotheses about adaptive strategies of forest trees to temperature and provide biogeographically explicit relationships to improve ecosystem and earth system models. They also will allow, for the first time to our knowledge, representations of root carbon pools that consider biogeographic differences, which are useful for quantifying whole-ecosystem carbon stocks and cycles and for assessing the impact of climate change on forest carbon dynamics.

  17. Temperature drives global patterns in forest biomass distribution in leaves, stems, and roots

    PubMed Central

    Reich, Peter B.; Luo, Yunjian; Bradford, John B.; Poorter, Hendrik; Perry, Charles H.; Oleksyn, Jacek

    2014-01-01

    Whether the fraction of total forest biomass distributed in roots, stems, or leaves varies systematically across geographic gradients remains unknown despite its importance for understanding forest ecology and modeling global carbon cycles. It has been hypothesized that plants should maintain proportionally more biomass in the organ that acquires the most limiting resource. Accordingly, we hypothesize greater biomass distribution in roots and less in stems and foliage in increasingly arid climates and in colder environments at high latitudes. Such a strategy would increase uptake of soil water in dry conditions and of soil nutrients in cold soils, where they are at low supply and are less mobile. We use a large global biomass dataset (>6,200 forests from 61 countries, across a 40 °C gradient in mean annual temperature) to address these questions. Climate metrics involving temperature were better predictors of biomass partitioning than those involving moisture availability, because, surprisingly, fractional distribution of biomass to roots or foliage was unrelated to aridity. In contrast, in increasingly cold climates, the proportion of total forest biomass in roots was greater and in foliage was smaller for both angiosperm and gymnosperm forests. These findings support hypotheses about adaptive strategies of forest trees to temperature and provide biogeographically explicit relationships to improve ecosystem and earth system models. They also will allow, for the first time to our knowledge, representations of root carbon pools that consider biogeographic differences, which are useful for quantifying whole-ecosystem carbon stocks and cycles and for assessing the impact of climate change on forest carbon dynamics. PMID:25225412

  18. Temperature drives global patterns in forest biomass distribution in leaves, stems, and roots.

    PubMed

    Reich, Peter B; Luo, Yunjian; Bradford, John B; Poorter, Hendrik; Perry, Charles H; Oleksyn, Jacek

    2014-09-23

    Whether the fraction of total forest biomass distributed in roots, stems, or leaves varies systematically across geographic gradients remains unknown despite its importance for understanding forest ecology and modeling global carbon cycles. It has been hypothesized that plants should maintain proportionally more biomass in the organ that acquires the most limiting resource. Accordingly, we hypothesize greater biomass distribution in roots and less in stems and foliage in increasingly arid climates and in colder environments at high latitudes. Such a strategy would increase uptake of soil water in dry conditions and of soil nutrients in cold soils, where they are at low supply and are less mobile. We use a large global biomass dataset (>6,200 forests from 61 countries, across a 40 °C gradient in mean annual temperature) to address these questions. Climate metrics involving temperature were better predictors of biomass partitioning than those involving moisture availability, because, surprisingly, fractional distribution of biomass to roots or foliage was unrelated to aridity. In contrast, in increasingly cold climates, the proportion of total forest biomass in roots was greater and in foliage was smaller for both angiosperm and gymnosperm forests. These findings support hypotheses about adaptive strategies of forest trees to temperature and provide biogeographically explicit relationships to improve ecosystem and earth system models. They also will allow, for the first time to our knowledge, representations of root carbon pools that consider biogeographic differences, which are useful for quantifying whole-ecosystem carbon stocks and cycles and for assessing the impact of climate change on forest carbon dynamics.

  19. What drives the aerosol distribution in Guangdong - the most developed province in Southern China?

    PubMed Central

    Li, Lili; Wang, Yunpeng

    2014-01-01

    This paper uses Moderate Resolution Imaging Spectroradiometer (MODIS) data to investigate the spatial and temporal variations of aerosol optical thickness (AOT) over Guangdong, the most developed province in China, during 2010–2012. Linear regression and self-organizing maps (SOM) are used to investigate the relationship between AOT and its affecting factors, including Normalized Difference Vegetation Index (NDVI), elevation, urbanized land fraction, and several socio-economic variables. Results show that the highest values of τ0.55 mainly occur over the rapidly-developing Pearl River Delta (PRD) region and the eastern coast. Seasonal averaged AOT is highest in summer (0.416), followed by spring (0.351), winter (0.292), and autumn (0.254). From unary linear regression and SOM analysis, AOT is shown to be strongly negatively correlated to NDVI (R2 = 0.782) and elevation (R2 = 0.731), and positively correlated with socio-economic factors, especially GDP, industry and vehicle density (R2 above 0.73), but not primary industry. Multiple linear regression between AOT and the contributing factors shows much higher R2 values (>0.8), indicative of the clear relationships between AOT and variables. This study illustrates that human activities have strong impacts on aerosols distribution in Guangdong Province. Economic and industrial developments, as well as vehicle density, are the main controlling factors on aerosol distribution. PMID:25096216

  20. Ecology Drives the Distribution of Specialized Tyrosine Metabolism Modules in Fungi

    PubMed Central

    Greene, George H.; McGary, Kriston L.; Rokas, Antonis; Slot, Jason C.

    2014-01-01

    Gene clusters encoding accessory or environmentally specialized metabolic pathways likely play a significant role in the evolution of fungal genomes. Two such gene clusters encoding enzymes associated with the tyrosine metabolism pathway (KEGG #00350) have been identified in the filamentous fungus Aspergillus fumigatus. The l-tyrosine degradation (TD) gene cluster encodes a functional module that facilitates breakdown of the phenolic amino acid, l-tyrosine through a homogentisate intermediate, but is also involved in the production of pyomelanin, a fungal pathogenicity factor. The gentisate catabolism (GC) gene cluster encodes a functional module likely involved in phenolic compound degradation, which may enable metabolism of biphenolic stilbenes in multiple lineages. Our investigation of the evolution of the TD and GC gene clusters in 214 fungal genomes revealed spotty distributions partially shaped by gene cluster loss and horizontal gene transfer (HGT). Specifically, a TD gene cluster shows evidence of HGT between the extremophilic, melanized fungi Exophiala dermatitidis and Baudoinia compniacensis, and a GC gene cluster shows evidence of HGT between Sordariomycete and Dothideomycete grass pathogens. These results suggest that the distribution of specialized tyrosine metabolism modules is influenced by both the ecology and phylogeny of fungal species. PMID:24391152

  1. Cellular localization and tissue distribution of endogenous DFCP1 protein.

    PubMed

    Nanao, Tomohisa; Koike, Masato; Yamaguchi, Junji; Sasaki, Mitsuho; Uchiyama, Yasuo

    2015-01-01

    Autophagy is essential for the maintenance of cellular metabolism. Once autophagy is induced in cells, the isolation membrane forms a so-called phagophore. The endoplasmic reticulum (ER) is one of several candidates for the membrane source for phagophores. Recently, LC3-positive isolation membranes were found to emerge from a DFCP1 (double FYVE domain-containing protein)-positive, ER-associated compartment called the omegasome. Although the GFP-tagged DFCP1 protein has been examined in cultured cells, little is known about the precise cellular and tissue distribution of this endogenous protein. To determine the expression of the endogenous DFCP1 protein, we produced antibodies specific to mouse DFCP1 protein. The antibody recognized both human and mouse DFCP1 proteins, both of which have molecular masses of approximately 87 kDa. In HeLa cells under normal conditions, immunoreactivity for DFCP1 was found dotted or tubular along Tom20-positive filamentous mitochondria and was only partially co-localized in the ER or Golgi apparatus. Moreover, under starved conditions, distinct DFCP1-positive structures became more dotted and scattered in the cytoplasm, while one part of the LC3-positive autophagosomes were immunopositive for DFCP1. These results indicate that an antibody raised against DFCP1 could be a useful tool in explaining the mechanism of phagophore formation from omegasome compartments.

  2. Ecological segregation drives fine-scale cytotype distribution of Senecio carniolicus in the Eastern Alps

    PubMed Central

    Hülber, Karl; Sonnleitner, Michaela; Flatscher, Ruth; Berger, Andreas; Dobrovsky, Rainer; Niessner, Sophie; Nigl, Thomas; Schneeweiss, Gerald M.; Kubešová, Magdalena; Rauchová, Jana; Suda, Jan; Schönswetter, Peter

    2011-01-01

    In order to uncover patterns and processes of segregation of co-existing cytotypes, we investigated a zone in the eastern Alps (Austria) where diploid and hexaploid individuals of the alpine herb Senecio carniolicus Willd. (Asteraceae) co-occur. Linking the fine-scale distribution of cytotypes to environmental and spatial factors revealed segregation along an ecological gradient, which was also reflected in the cytotype-associated plant assemblages. Compared to diploids, hexaploids are found in more species-rich and denser communities. This may be due to their better competitive ability and lower tolerance of abiotic stress compared to the diploids. The lack of any intermediate cytotypes suggests the presence of strong reproductive isolation mechanisms, whose nature is, however, elusive. PMID:22318659

  3. Factors driving changes in freshwater mussel (Bivalvia, Unionida) diversity and distribution in Peninsular Malaysia.

    PubMed

    Zieritz, Alexandra; Lopes-Lima, Manuel; Bogan, Arthur E; Sousa, Ronaldo; Walton, Samuel; Rahim, Khairul Adha A; Wilson, John-James; Ng, Pei-Yin; Froufe, Elsa; McGowan, Suzanne

    2016-11-15

    Freshwater mussels (Bivalvia, Unionida) fulfil important ecosystem functions and are one of the most threatened freshwater taxa globally. Knowledge of freshwater mussel diversity, distribution and ecology in Peninsular Malaysia is extremely poor, and the conservation status of half of the species presumed to occur in the region has yet to be assessed. We conducted the first comprehensive assessment of Peninsular Malaysia's freshwater mussels based on species presence/absence and environmental data collected from 155 sites spanning all major river catchments and diverse habitat types. Through an integrative morphological-molecular approach we recognised nine native and one widespread non-native species, i.e. Sinanodonta woodiana. Two species, i.e. Pilsbryoconcha compressa and Pseudodon cambodjensis, had not been previously recorded from Malaysia, which is likely a result of morphological misidentifications of historical records. Due to their restriction to single river catchments and declining distributions, Hyriopsis bialata, possibly endemic to Peninsular Malaysia, Ensidens ingallsianus, possibly already extinct in the peninsula, and Rectidens sumatrensis, particularly require conservation attention. Equally, the Pahang, the Perak and the north-western river catchments are of particular conservation value due to the presence of a globally unique freshwater mussel fauna. Statistical relationships of 15 water quality parameters and mussel presence/absence identified acidification and nutrient pollution (eutrophication) as the most important anthropogenic factors threatening freshwater mussel diversity in Peninsular Malaysia. These factors can be linked to atmospheric pollution, deforestation, oil-palm plantations and a lack of functioning waste water treatment, and could be mitigated by establishing riparian buffers and improving waste water treatment for rivers running through agricultural and residential land.

  4. An Overview of Practical Applications of Protein Disorder Prediction and Drive for Faster, More Accurate Predictions

    PubMed Central

    Deng, Xin; Gumm, Jordan; Karki, Suman; Eickholt, Jesse; Cheng, Jianlin

    2015-01-01

    Protein disordered regions are segments of a protein chain that do not adopt a stable structure. Thus far, a variety of protein disorder prediction methods have been developed and have been widely used, not only in traditional bioinformatics domains, including protein structure prediction, protein structure determination and function annotation, but also in many other biomedical fields. The relationship between intrinsically-disordered proteins and some human diseases has played a significant role in disorder prediction in disease identification and epidemiological investigations. Disordered proteins can also serve as potential targets for drug discovery with an emphasis on the disordered-to-ordered transition in the disordered binding regions, and this has led to substantial research in drug discovery or design based on protein disordered region prediction. Furthermore, protein disorder prediction has also been applied to healthcare by predicting the disease risk of mutations in patients and studying the mechanistic basis of diseases. As the applications of disorder prediction increase, so too does the need to make quick and accurate predictions. To fill this need, we also present a new approach to predict protein residue disorder using wide sequence windows that is applicable on the genomic scale. PMID:26198229

  5. An Overview of Practical Applications of Protein Disorder Prediction and Drive for Faster, More Accurate Predictions.

    PubMed

    Deng, Xin; Gumm, Jordan; Karki, Suman; Eickholt, Jesse; Cheng, Jianlin

    2015-07-07

    Protein disordered regions are segments of a protein chain that do not adopt a stable structure. Thus far, a variety of protein disorder prediction methods have been developed and have been widely used, not only in traditional bioinformatics domains, including protein structure prediction, protein structure determination and function annotation, but also in many other biomedical fields. The relationship between intrinsically-disordered proteins and some human diseases has played a significant role in disorder prediction in disease identification and epidemiological investigations. Disordered proteins can also serve as potential targets for drug discovery with an emphasis on the disordered-to-ordered transition in the disordered binding regions, and this has led to substantial research in drug discovery or design based on protein disordered region prediction. Furthermore, protein disorder prediction has also been applied to healthcare by predicting the disease risk of mutations in patients and studying the mechanistic basis of diseases. As the applications of disorder prediction increase, so too does the need to make quick and accurate predictions. To fill this need, we also present a new approach to predict protein residue disorder using wide sequence windows that is applicable on the genomic scale.

  6. Persistent natural acidification drives major distribution shifts in marine benthic ecosystems.

    PubMed

    Linares, C; Vidal, M; Canals, M; Kersting, D K; Amblas, D; Aspillaga, E; Cebrián, E; Delgado-Huertas, A; Díaz, D; Garrabou, J; Hereu, B; Navarro, L; Teixidó, N; Ballesteros, E

    2015-11-07

    Ocean acidification is receiving increasing attention because of its potential to affect marine ecosystems. Rare CO2 vents offer a unique opportunity to investigate the response of benthic ecosystems to acidification. However, the benthic habitats investigated so far are mainly found at very shallow water (less than or equal to 5 m depth) and therefore are not representative of the broad range of continental shelf habitats. Here, we show that a decrease from pH 8.1 to 7.9 observed in a CO2 vent system at 40 m depth leads to a dramatic shift in highly diverse and structurally complex habitats. Forests of the kelp Laminaria rodriguezii usually found at larger depths (greater than 65 m) replace the otherwise dominant habitats (i.e. coralligenous outcrops and rhodolith beds), which are mainly characterized by calcifying organisms. Only the aragonite-calcifying algae are able to survive in acidified waters, while high-magnesium-calcite organisms are almost completely absent. Although a long-term survey of the venting area would be necessary to fully understand the effects of the variability of pH and other carbonate parameters over the structure and functioning of the investigated mesophotic habitats, our results suggest that in addition of significant changes at species level, moderate ocean acidification may entail major shifts in the distribution and dominance of key benthic ecosystems at regional scale, which could have broad ecological and socio-economic implications.

  7. Persistent natural acidification drives major distribution shifts in marine benthic ecosystems

    PubMed Central

    Linares, C.; Vidal, M.; Canals, M.; Kersting, D. K.; Amblas, D.; Aspillaga, E.; Cebrián, E.; Delgado-Huertas, A.; Díaz, D.; Garrabou, J.; Hereu, B.; Navarro, L.; Teixidó, N.; Ballesteros, E.

    2015-01-01

    Ocean acidification is receiving increasing attention because of its potential to affect marine ecosystems. Rare CO2 vents offer a unique opportunity to investigate the response of benthic ecosystems to acidification. However, the benthic habitats investigated so far are mainly found at very shallow water (less than or equal to 5 m depth) and therefore are not representative of the broad range of continental shelf habitats. Here, we show that a decrease from pH 8.1 to 7.9 observed in a CO2 vent system at 40 m depth leads to a dramatic shift in highly diverse and structurally complex habitats. Forests of the kelp Laminaria rodriguezii usually found at larger depths (greater than 65 m) replace the otherwise dominant habitats (i.e. coralligenous outcrops and rhodolith beds), which are mainly characterized by calcifying organisms. Only the aragonite-calcifying algae are able to survive in acidified waters, while high-magnesium-calcite organisms are almost completely absent. Although a long-term survey of the venting area would be necessary to fully understand the effects of the variability of pH and other carbonate parameters over the structure and functioning of the investigated mesophotic habitats, our results suggest that in addition of significant changes at species level, moderate ocean acidification may entail major shifts in the distribution and dominance of key benthic ecosystems at regional scale, which could have broad ecological and socio-economic implications. PMID:26511045

  8. Selection on Network Dynamics Drives Differential Rates of Protein Domain Evolution

    PubMed Central

    Mannakee, Brian K.; Gutenkunst, Ryan N.

    2016-01-01

    The long-held principle that functionally important proteins evolve slowly has recently been challenged by studies in mice and yeast showing that the severity of a protein knockout only weakly predicts that protein’s rate of evolution. However, the relevance of these studies to evolutionary changes within proteins is unknown, because amino acid substitutions, unlike knockouts, often only slightly perturb protein activity. To quantify the phenotypic effect of small biochemical perturbations, we developed an approach to use computational systems biology models to measure the influence of individual reaction rate constants on network dynamics. We show that this dynamical influence is predictive of protein domain evolutionary rate within networks in vertebrates and yeast, even after controlling for expression level and breadth, network topology, and knockout effect. Thus, our results not only demonstrate the importance of protein domain function in determining evolutionary rate, but also the power of systems biology modeling to uncover unanticipated evolutionary forces. PMID:27380265

  9. Cellular Proteomes Have Broad Distributions of Protein Stability

    PubMed Central

    Ghosh, Kingshuk; Dill, Ken

    2010-01-01

    Biological cells are extremely sensitive to temperature. What is the mechanism? We compute the thermal stabilities of the whole proteomes of Escherichia coli, yeast, and Caenorhabditis elegans using an analytical model and an extensive database of stabilities of individual proteins. Our results support the hypothesis that a cell's thermal sensitivities arise from the collective instability of its proteins. This model shows a denaturation catastrophe at temperatures of 49–55°C, roughly the thermal death point of mesophiles. Cells live on the edge of a proteostasis catastrophe. According to the model, it is not that the average protein is problematic; it is the tail of the distribution. About 650 of E. coli's 4300 proteins are less than 4 kcal mol−1 stable to denaturation. And upshifting by only 4° from 37° to 41°C is estimated to destabilize an average protein by nearly 20%. This model also treats effects of denaturants, osmolytes, and other physical stressors. In addition, it predicts the dependence of cellular growth rates on temperature. This approach may be useful for studying physical forces in biological evolution and the role of climate change on biology. PMID:21156142

  10. What factors drive copepod community distribution in the Gulf of Gabes, Eastern Mediterranean Sea?

    PubMed

    Drira, Zaher; Bel Hassen, Malika; Ayadi, Habib; Aleya, Lotfi

    2014-02-01

    The spatial and temporal variations in copepod communities were investigated during four oceanographic cruises conducted between July 2005 and March 2007 aboard the R/V Hannibal. A close relationship was observed between the temperature, salinity, hydrographic properties and water masses characterising the Gulf of Gabes. Indeed, water thermal stratification began in May-June, and a thermocline was established at a 20-m depth, but ranged from 25 m in July to more than 30 m in September. The zooplankton community is dominated by copepods representing 69 % to 83 % of total zooplankton. Spatial and temporal variation of copepods in relation to environmental factors shows their close relationship with the hydrodynamic features of the water column. Thermal stratification in the column, established in summer, supports copepod development. In fact, copepod abundance increases gradually with rising water temperature and salinity, starting from the beginning of thermal stratification (May-June 2006) and lasting until its completion (July 2005 and September 2006). When the water column is well mixed (March 2007), copepod abundance decreased. Our finding shows that temperature and salinity seem to be the most important physical factors and thus strongly influence the taxonomic diversity and distribution of the copepod population. They are characterised by the dominance of Oithona nana, representing 75-86 % of total cyclopoid abundance. The most abundant species during the stratification period were O. nana, Acartia clausi and Stephos marsalensis in July 2005 and September 2006. However, during the mixing period, Euterpina acutifrons was more abundant, representing 21 % of the total. Unlike the copepod community, which is more abundant during the period of high stratification, phytoplankton proliferates during semi-mixed conditions.

  11. Stability enhancement and fuel economy of the 4-wheel-drive hybrid electric vehicles by optimal tyre force distribution

    NASA Astrophysics Data System (ADS)

    Goodarzi, Avesta; Mohammadi, Masoud

    2014-04-01

    In this paper, vehicle stability control and fuel economy for a 4-wheel-drive hybrid vehicle are investigated. The integrated controller is designed within three layers. The first layer determines the total yaw moment and total lateral force made by using an optimal controller method to follow the desired dynamic behaviour of a vehicle. The second layer determines optimum tyre force distribution in order to optimise tyre usage and find out how the tyres should share longitudinal and lateral forces to achieve a target vehicle response under the assumption that all four wheels can be independently steered, driven, and braked. In the third layer, the active steering, wheel slip, and electrical motor torque controllers are designed. In the front axle, internal combustion engine (ICE) is coupled to an electric motor (EM). The control strategy has to determine the power distribution between ICE and EM to minimise fuel consumption and allowing the vehicle to be charge sustaining. Finally, simulations performed in MATLAB/SIMULINK environment show that the proposed structure could enhance the vehicle stability and fuel economy in different manoeuvres.

  12. Human influence and biotic homogenization drive the distribution of Escherichia coli virulence genes in natural habitats.

    PubMed

    Cabal, Adriana; Vicente, Joaquin; Alvarez, Julio; Barasona, Jose Angel; Boadella, Mariana; Dominguez, Lucas; Gortazar, Christian

    2017-02-18

    Cattle are the main reservoirs for Shiga-toxin-producing Escherichia coli (STEC), the only known zoonotic intestinal E. coli pathotype. However, there are other intestinal pathotypes that can cause disease in humans, whose presence has been seldom investigated. Thus, our aim was to identify the effects of anthropic pressure and of wild and domestic ungulate abundance on the distribution and diversity of the main human E. coli pathotypes and nine of their representative virulence genes (VGs). We used a quantitative real-time PCR (qPCR) for the direct detection and quantification of the genus-specific gene uidA, nine E. coli VGs (stx1, sxt2, eae, ehxA, aggR, est, elt, bfpA, invA), as well as four genes related to O157:H7 (rfbO157 , fliCH7 ) and O104:H4 (wzxO104 , fliCH4 ) serotypes in animals (feces from deer, cattle, and wild boar) and water samples collected in three areas of Doñana National Park (DNP), Spain. Eight of the nine VGs were detected, being invA, eae, and stx2 followed by stx1, aggR, and ehxA the most abundant ones. In quantitative terms (gene copies per mg of sample), stx1 and stx2 gave the highest values. Significant differences were seen regarding VGs in the three animal species in the three sampled areas. The serotype-related genes were found in all but one sample types. In general, VGs were more diverse and abundant in the northern part of the Park, where the surface waters are more contaminated by human waste and farms. In the current study, we demonstrated that human influence is more relevant than host species in shaping the E. coli VGs spatial pattern and diversity in DNP. In addition, wildlife could be potential reservoirs for other pathotypes different from STEC, however further isolation steps would be needed to completely characterize those E. coli.

  13. Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer.

    PubMed

    Engin, H Billur; Guney, Emre; Keskin, Ozlem; Oliva, Baldo; Gursoy, Attila

    2013-01-01

    Blocking specific protein interactions can lead to human diseases. Accordingly, protein interactions and the structural knowledge on interacting surfaces of proteins (interfaces) have an important role in predicting the genotype-phenotype relationship. We have built the phenotype specific sub-networks of protein-protein interactions (PPIs) involving the relevant genes responsible for lung and brain metastasis from primary tumor in breast cancer. First, we selected the PPIs most relevant to metastasis causing genes (seed genes), by using the "guilt-by-association" principle. Then, we modeled structures of the interactions whose complex forms are not available in Protein Databank (PDB). Finally, we mapped mutations to interface structures (real and modeled), in order to spot the interactions that might be manipulated by these mutations. Functional analyses performed on these sub-networks revealed the potential relationship between immune system-infectious diseases and lung metastasis progression, but this connection was not observed significantly in the brain metastasis. Besides, structural analyses showed that some PPI interfaces in both metastasis sub-networks are originating from microbial proteins, which in turn were mostly related with cell adhesion. Cell adhesion is a key mechanism in metastasis, therefore these PPIs may be involved in similar molecular pathways that are shared by infectious disease and metastasis. Finally, by mapping the mutations and amino acid variations on the interface regions of the proteins in the metastasis sub-networks we found evidence for some mutations to be involved in the mechanisms differentiating the type of the metastasis.

  14. Distribution of protein D, an immunoglobulin D-binding protein, in Haemophilus strains.

    PubMed Central

    Akkoyunlu, M; Ruan, M; Forsgren, A

    1991-01-01

    Protein D, a novel surface protein of the bacterial species Haemophilus influenzae with specific affinity for human immunoglobulin (Ig) D was detected in all 127 H. influenzae strains studied. All strains representing different serotypes of encapsulated strains and different biotypes of nonencapsulated strains bound 125I-labeled IgD to a high degree (38 to 74%). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot (immunoblot) analysis showed that protein D from all H. influenzae strains had the same apparent molecular weight (i.e., 42,000) and reacted with all three different anti-protein D monoclonal antibodies. By Scatchard analysis, the number of protein D residues on a nontypeable H. influenzae strain was estimated to be approximately 2,800 per organism. The equilibrium constant for the reaction between a human IgD myeloma protein and IgD was found to be 5.8 x 10(8) M-1. Also, all strains of H. haemolyticus and H. aegypticus strains tested bound IgD, 21 to 28% and 41 to 48%, respectively. In extracts of those bacteria, a 42,000-molecular-weight protein reactive with IgD and all three anti-protein D monoclonal antibodies was found. In H. parainfluenzae, H. aphrophilus, H. paraphrophilus, and Actinobacillus actinomycetemcomitans, a 42,000-molecular-weight protein that was reactive with one to three of three anti-protein D monoclonal antibodies but not reactive with human IgD was detected with Western blot analysis. Other Haemophilus species (H. ducreyi, H. parasuis, H. parahaemolyticus, H. segnis, and H. haemoglobinophilus) did not react with human monoclonal IgD or anti-protein D antibodies. On the basis of the wide distribution of protein D among H. influenzae strains, we suggest that protein D could be a vaccine candidate. Images PMID:1900807

  15. The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics

    PubMed Central

    Elbaum-Garfinkle, Shana; Kim, Younghoon; Szczepaniak, Krzysztof; Chen, Carlos Chih-Hsiung; Eckmann, Christian R.; Myong, Sua; Brangwynne, Clifford P.

    2015-01-01

    P granules and other RNA/protein bodies are membrane-less organelles that may assemble by intracellular phase separation, similar to the condensation of water vapor into droplets. However, the molecular driving forces and the nature of the condensed phases remain poorly understood. Here, we show that the Caenorhabditis elegans protein LAF-1, a DDX3 RNA helicase found in P granules, phase separates into P granule-like droplets in vitro. We adapt a microrheology technique to precisely measure the viscoelasticity of micrometer-sized LAF-1 droplets, revealing purely viscous properties highly tunable by salt and RNA concentration. RNA decreases viscosity and increases molecular dynamics within the droplet. Single molecule FRET assays suggest that this RNA fluidization results from highly dynamic RNA–protein interactions that emerge close to the droplet phase boundary. We demonstrate than an N-terminal, arginine/glycine rich, intrinsically disordered protein (IDP) domain of LAF-1 is necessary and sufficient for both phase separation and RNA–protein interactions. In vivo, RNAi knockdown of LAF-1 results in the dissolution of P granules in the early embryo, with an apparent submicromolar phase boundary comparable to that measured in vitro. Together, these findings demonstrate that LAF-1 is important for promoting P granule assembly and provide insight into the mechanism by which IDP-driven molecular interactions give rise to liquid phase organelles with tunable properties. PMID:26015579

  16. Using Local States To Drive the Sampling of Global Conformations in Proteins

    PubMed Central

    2016-01-01

    Conformational changes associated with protein function often occur beyond the time scale currently accessible to unbiased molecular dynamics (MD) simulations, so that different approaches have been developed to accelerate their sampling. Here we investigate how the knowledge of backbone conformations preferentially adopted by protein fragments, as contained in precalculated libraries known as structural alphabets (SA), can be used to explore the landscape of protein conformations in MD simulations. We find that (a) enhancing the sampling of native local states in both metadynamics and steered MD simulations allows the recovery of global folded states in small proteins; (b) folded states can still be recovered when the amount of information on the native local states is reduced by using a low-resolution version of the SA, where states are clustered into macrostates; and (c) sequences of SA states derived from collections of structural motifs can be used to sample alternative conformations of preselected protein regions. The present findings have potential impact on several applications, ranging from protein model refinement to protein folding and design. PMID:26808351

  17. Ensemble models of proteins and protein domains based on distance distribution restraints.

    PubMed

    Jeschke, Gunnar

    2016-04-01

    Conformational ensembles of intrinsically disordered peptide chains are not fully determined by experimental observations. Uncertainty due to lack of experimental restraints and due to intrinsic disorder can be distinguished if distance distributions restraints are available. Such restraints can be obtained from pulsed dipolar electron paramagnetic resonance (EPR) spectroscopy applied to pairs of spin labels. Here, we introduce a Monte Carlo approach for generating conformational ensembles that are consistent with a set of distance distribution restraints, backbone dihedral angle statistics in known protein structures, and optionally, secondary structure propensities or membrane immersion depths. The approach is tested with simulated restraints for a terminal and an internal loop and for a protein with 69 residues by using sets of sparse restraints for underlying well-defined conformations and for published ensembles of a premolten globule-like and a coil-like intrinsically disordered protein.

  18. Reconstitution of a nanomachine driving the assembly of proteins into bacterial outer membranes

    PubMed Central

    Shen, Hsin-Hui; Belousoff, Matthew J.; Noinaj, Nicholas; Lu, Jingxiong; Holt, Stephen A.; Tan, Khershing; Selkrig, Joel; Webb, Chaille T.; Buchanan, Susan K.; Martin, Lisandra L.; Lithgow, Trevor

    2015-01-01

    In biological membranes, various protein secretion devices function as nanomachines, and measuring the internal movements of their component parts is a major technological challenge. The translocation assembly module (the TAM) is a nanomachine required for virulence of bacterial pathogens. We have reconstituted a membrane containing the TAM onto a gold surface for characterization by Quartz Crystal Microbalance with Dissipation (QCM-D) and Magnetic Contrast Neutron Reflectrometry (MCNR). The MCNR studies provided structural resolution down to 1Å, enabling accurate measurement of protein domains projecting from the membrane layer. Here, we show that dynamic movements within the TamA component of the TAM are initiated in the presence of a substrate protein, Ag43, and that these movements recapitulate an initial stage in membrane protein assembly. The reconstituted system provides a powerful new means to study molecular movements in biological membranes, and the technology is widely applicable to studying the dynamics of diverse cellular nanomachines. PMID:25341963

  19. Reconstitution of a nanomachine driving the assembly of proteins into bacterial outer membranes

    NASA Astrophysics Data System (ADS)

    Shen, Hsin-Hui; Leyton, Denisse L.; Shiota, Takuya; Belousoff, Matthew J.; Noinaj, Nicholas; Lu, Jingxiong; Holt, Stephen A.; Tan, Khershing; Selkrig, Joel; Webb, Chaille T.; Buchanan, Susan K.; Martin, Lisandra L.; Lithgow, Trevor

    2014-10-01

    In biological membranes, various protein secretion devices function as nanomachines, and measuring the internal movements of their component parts is a major technological challenge. The translocation and assembly module (TAM) is a nanomachine required for virulence of bacterial pathogens. We have reconstituted a membrane containing the TAM onto a gold surface for characterization by quartz crystal microbalance with dissipation (QCM-D) and magnetic contrast neutron reflectrometry (MCNR). The MCNR studies provided structural resolution down to 1 Å, enabling accurate measurement of protein domains projecting from the membrane layer. Here we show that dynamic movements within the TamA component of the TAM are initiated in the presence of a substrate protein, Ag43, and that these movements recapitulate an initial stage in membrane protein assembly. The reconstituted system provides a powerful new means to study molecular movements in biological membranes, and the technology is widely applicable to studying the dynamics of diverse cellular nanomachines.

  20. Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals

    PubMed Central

    Swanson, Willie J.; Yang, Ziheng; Wolfner, Mariana F.; Aquadro, Charles F.

    2001-01-01

    Rapid evolution driven by positive Darwinian selection is a recurrent theme in male reproductive protein evolution. In contrast, positive selection has never been demonstrated for female reproductive proteins. Here, we perform phylogeny-based tests on three female mammalian fertilization proteins and demonstrate positive selection promoting their divergence. Two of these female fertilization proteins, the zona pellucida glycoproteins ZP2 and ZP3, are part of the mammalian egg coat. Several sites identified in ZP3 as likely to be under positive selection are located in a region previously demonstrated to be involved in species-specific sperm-egg interaction, suggesting the selective pressure is related to male-female interaction. The results provide long-sought evidence for two evolutionary hypotheses: sperm competition and sexual conflict. PMID:11226269

  1. Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein

    NASA Astrophysics Data System (ADS)

    Gruszka, Dominika T.; Whelan, Fiona; Farrance, Oliver E.; Fung, Herman K. H.; Paci, Emanuele; Jeffries, Cy M.; Svergun, Dmitri I.; Baldock, Clair; Baumann, Christoph G.; Brockwell, David J.; Potts, Jennifer R.; Clarke, Jane

    2015-06-01

    Bacteria exploit surface proteins to adhere to other bacteria, surfaces and host cells. Such proteins need to project away from the bacterial surface and resist significant mechanical forces. SasG is a protein that forms extended fibrils on the surface of Staphylococcus aureus and promotes host adherence and biofilm formation. Here we show that although monomeric and lacking covalent cross-links, SasG maintains a highly extended conformation in solution. This extension is mediated through obligate folding cooperativity of the intrinsically disordered E domains that couple non-adjacent G5 domains thermodynamically, forming interfaces that are more stable than the domains themselves. Thus, counterintuitively, the elongation of the protein appears to be dependent on the inherent instability of its domains. The remarkable mechanical strength of SasG arises from tandemly arrayed `clamp' motifs within the folded domains. Our findings reveal an elegant minimal solution for the assembly of monomeric mechano-resistant tethers of variable length.

  2. Structure-function analysis of SAP97, a modular scaffolding protein that drives dendrite growth.

    PubMed

    Zhang, L; Hsu, F-C; Mojsilovic-Petrovic, J; Jablonski, A M; Zhai, J; Coulter, D A; Kalb, R G

    2015-03-01

    Activation of AMPA receptors assembled with the GluA1 subunit can promote dendrite growth in a manner that depends on its direct binding partner, SAP97. SAP97 is a modular scaffolding protein that has at least seven recognizable protein-protein interaction domains. Several complementary approaches were employed to show that the dendrite branching promoting action of full length SAP97 depends on ligand(s) that bind to the PDZ3 domain. Ligand(s) to PDZ1, PDZ2 and I3 domains also contribute to dendrite growth. The ability of PDZ3 ligand(s) to promote dendrite growth depends on localization at the plasma membrane along with GluA1 and SAP97. These results suggest that the assembly of a multi-protein complex at or near synapses is vital for the translation of AMPA-R activity into dendrite growth.

  3. Yeast and Mammals Utilize Similar Cytosolic Components to Drive Protein Transport through the Golgi Complex

    NASA Astrophysics Data System (ADS)

    Dunphy, William G.; Pfeffer, Suzanne R.; Clary, Douglas O.; Wattenberg, Binks W.; Glick, Benjamin S.; Rothman, James E.

    1986-03-01

    Vesicular transport between successive compartments of the mammalian Golgi apparatus has recently been reconstituted in a cell-free system. In addition to ATP, transport requires both membrane-bound and cytosolic proteins. Here we report that the cytosol fraction from yeast will efficiently substitute for mammalian cytosol. Mammalian cytosol contains several distinct transport factors, which we have distinguished on the basis of gel filtration and ion-exchange chromatography. Yeast cytosol appears to contain the same collection of transport factors. Resolved cytosol factors from yeast and mammals complement each other in a synergistic manner. These findings suggest that the molecular mechanisms of intracellular protein transport have been conserved throughout evolution. Moreover, this hybrid cell-free system will enable the application of yeast genetics to the identification and isolation of cytosolic proteins that sustain intracellular protein transport.

  4. Distribution, Transition and Thermodynamic Stability of Protein Conformations in the Denaturant-Induced Unfolding of Proteins

    PubMed Central

    Bian, Liujiao; Ji, Xu

    2014-01-01

    Background Extensive and intensive studies on the unfolding of proteins require appropriate theoretical model and parameter to clearly illustrate the feature and characteristic of the unfolding system. Over the past several decades, four approaches have been proposed to describe the interaction between proteins and denaturants, but some ambiguity and deviations usually occur in the explanation of the experimental data. Methodology/Principal Findings In this work, a theoretical model was presented to show the dependency of the residual activity ratio of the proteins on the molar denaturant concentration. Through the characteristic unfolding parameters ki and Δmi in this model, the distribution, transition and thermodynamic stability of protein conformations during the unfolding process can be quantitatively described. This model was tested with the two-state unfolding of bovine heart cytochrome c and the three-state unfolding of hen egg white lysozyme induced by both guanidine hydrochloride and urea, the four-state unfolding of bovine carbonic anhydrase b induced by guanidine hydrochloride and the unfolding of some other proteins induced by denaturants. The results illustrated that this model could be used accurately to reveal the distribution and transition of protein conformations in the presence of different concentrations of denaturants and to evaluate the unfolding tendency and thermodynamic stability of different conformations. In most denaturant-induced unfolding of proteins, the unfolding became increasingly hard in next transition step and the proteins became more unstable as they attained next successive stable conformation. Conclusions/Significance This work presents a useful method for people to study the unfolding of proteins and may be used to describe the unfolding and refolding of other biopolymers induced by denaturants, inducers, etc. PMID:24603868

  5. The scaffold protein Atg11 recruits fission machinery to drive selective mitochondria degradation by autophagy.

    PubMed

    Mao, Kai; Wang, Ke; Liu, Xu; Klionsky, Daniel J

    2013-07-15

    As the cellular power plant, mitochondria play a significant role in homeostasis. To maintain the proper quality and quantity of mitochondria requires both mitochondrial degradation and division. A selective type of autophagy, mitophagy, drives the degradation of excess or damaged mitochondria, whereas division is controlled by a specific fission complex; however, the relationship between these two processes, especially the role of mitochondrial fission during mitophagy, remains unclear. In this study, we report that mitochondrial fission is important for the progression of mitophagy. When mitophagy is induced, the fission complex is recruited to the degrading mitochondria through an interaction between Atg11 and Dnm1; interfering with this interaction severely blocks mitophagy. These data establish a paradigm for selective organelle degradation.

  6. Small surfactant-like peptides can drive soluble proteins into active aggregates

    PubMed Central

    2012-01-01

    Background Inactive protein inclusion bodies occur commonly in Escherichia coli (E. coli) cells expressing heterologous proteins. Previously several independent groups have found that active protein aggregates or pseudo inclusion bodies can be induced by a fusion partner such as a cellulose binding domain from Clostridium cellulovorans (CBDclos) when expressed in E. coli. More recently we further showed that a short amphipathic helical octadecapeptide 18A (EWLKAFYEKVLEKLKELF) and a short beta structure peptide ELK16 (LELELKLKLELELKLK) have a similar property. Results In this work, we explored a third type of peptides, surfactant-like peptides, for performing such a "pulling-down" function. One or more of three such peptides (L6KD, L6K2, DKL6) were fused to the carboxyl termini of model proteins including Aspergillus fumigatus amadoriase II (AMA, all three peptides were used), Bacillus subtilis lipase A (LipA, only L6KD was used, hereinafter the same), Bacillus pumilus xylosidase (XynB), and green fluorescent protein (GFP), and expressed in E. coli. All fusions were found to predominantly accumulate in the insoluble fractions, with specific activities ranging from 25% to 92% of the native counterparts. Transmission electron microscopic (TEM) and confocal fluorescence microscopic analyses confirmed the formation of protein aggregates in the cell. Furthermore, binding assays with amyloid-specific dyes (thioflavin T and Cong red) to the AMA-L6KD aggregate and the TEM analysis of the aggregate following digestion with protease K suggested that the AMA-L6KD aggregate may contain structures reminiscent of amyloids, including a fibril-like structure core. Conclusions This study shows that the surfactant-like peptides L6KD and it derivatives can act as a pull-down handler for converting soluble proteins into active aggregates, much like 18A and ELK16. These peptide-mediated protein aggregations might have important implications for protein aggregation in vivo, and can be

  7. Molecular crowding drives active Pin1 into nonspecific complexes with endogenous proteins prior to substrate recognition.

    PubMed

    Luh, Laura M; Hänsel, Robert; Löhr, Frank; Kirchner, Donata K; Krauskopf, Katharina; Pitzius, Susanne; Schäfer, Birgit; Tufar, Peter; Corbeski, Ivan; Güntert, Peter; Dötsch, Volker

    2013-09-18

    Proteins and nucleic acids maintain the crowded interior of a living cell and can reach concentrations in the order of 200-400 g/L which affects the physicochemical parameters of the environment, such as viscosity and hydrodynamic as well as nonspecific strong repulsive and weak attractive interactions. Dynamics, structure, and activity of macromolecules were demonstrated to be affected by these parameters. However, it remains controversially debated, which of these factors are the dominant cause for the observed alterations in vivo. In this study we investigated the globular folded peptidyl-prolyl isomerase Pin1 in Xenopus laevis oocytes and in native-like crowded oocyte extract by in-cell NMR spectroscopy. We show that active Pin1 is driven into nonspecific weak attractive interactions with intracellular proteins prior to substrate recognition. The substrate recognition site of Pin1 performs specific and nonspecific attractive interactions. Phosphorylation of the WW domain at Ser16 by PKA abrogates both substrate recognition and the nonspecific interactions with the endogenous proteins. Our results validate the hypothesis formulated by McConkey that the majority of globular folded proteins with surface charge properties close to neutral under physiological conditions reside in macromolecular complexes with other sticky proteins due to molecular crowding. In addition, we demonstrate that commonly used synthetic crowding agents like Ficoll 70 are not suitable to mimic the intracellular environment due to their incapability to simulate biologically important weak attractive interactions.

  8. Positive and strongly relaxed purifying selection drive the evolution of repeats in proteins

    PubMed Central

    Persi, Erez; Wolf, Yuri I.; Koonin, Eugene V

    2016-01-01

    Protein repeats are considered hotspots of protein evolution, associated with acquisition of new functions and novel phenotypic traits, including disease. Paradoxically, however, repeats are often strongly conserved through long spans of evolution. To resolve this conundrum, it is necessary to directly compare paralogous (horizontal) evolution of repeats within proteins with their orthologous (vertical) evolution through speciation. Here we develop a rigorous methodology to identify highly periodic repeats with significant sequence similarity, for which evolutionary rates and selection (dN/dS) can be estimated, and systematically characterize their evolution. We show that horizontal evolution of repeats is markedly accelerated compared with their divergence from orthologues in closely related species. This observation is universal across the diversity of life forms and implies a biphasic evolutionary regime whereby new copies experience rapid functional divergence under combined effects of strongly relaxed purifying selection and positive selection, followed by fixation and conservation of each individual repeat. PMID:27857066

  9. Protein folding by distributed computing and the denatured state ensemble.

    PubMed

    Marianayagam, Neelan J; Fawzi, Nicolas L; Head-Gordon, Teresa

    2005-11-15

    The distributed computing (DC) paradigm in conjunction with the folding@home (FH) client server has been used to study the folding kinetics of small peptides and proteins, giving excellent agreement with experimentally measured folding rates, although pathways sampled in these simulations are not always consistent with the folding mechanism. In this study, we use a coarse-grain model of protein L, whose two-state kinetics have been characterized in detail by using long-time equilibrium simulations, to rigorously test a FH protocol using approximately 10,000 short-time, uncoupled folding simulations starting from an extended state of the protein. We show that the FH results give non-Poisson distributions and early folding events that are unphysical, whereas longer folding events experience a correct barrier to folding but are not representative of the equilibrium folding ensemble. Using short-time, uncoupled folding simulations started from an equilibrated denatured state ensemble (DSE), we also do not get agreement with the equilibrium two-state kinetics because of overrepresented folding events arising from higher energy subpopulations in the DSE. The DC approach using uncoupled short trajectories can make contact with traditionally measured experimental rates and folding mechanism when starting from an equilibrated DSE, when the simulation time is long enough to sample the lowest energy states of the unfolded basin and the simulated free-energy surface is correct. However, the DC paradigm, together with faster time-resolved and single-molecule experiments, can also reveal the breakdown in the two-state approximation due to observation of folding events from higher energy subpopulations in the DSE.

  10. Distribution of adenosine deaminase complexing protein (ADCP) in human tissues.

    PubMed

    Dinjens, W N; ten Kate, J; van der Linden, E P; Wijnen, J T; Khan, P M; Bosman, F T

    1989-12-01

    The normal distribution of adenosine deaminase complexing protein (ADCP) in the human body was investigated quantitatively by ADCP-specific radioimmunoassay (RIA) and qualitatively by immunohistochemistry. In these studies we used a specific rabbit anti-human ADCP antiserum. In all 19 investigated tissues, except erythrocytes, ADCP was found by RIA in the soluble and membrane fractions. From all tissues the membrane fractions contained more ADCP (expressed per mg protein) than the soluble fractions. High membrane ADCP concentrations were found in skin, renal cortex, gastrointestinal tract, and prostate. Immunoperoxidase staining confirmed the predominant membrane-associated localization of the protein. In serous sweat glands, convoluted tubules of renal cortex, bile canaliculi, gastrointestinal tract, lung, pancreas, prostate gland, salivary gland, gallbladder, mammary gland, and uterus, ADCP immunoreactivity was found confined to the luminal membranes of the epithelial cells. These data demonstrate that ADCP is present predominantly in exocrine glands and absorptive epithelia. The localization of ADCP at the secretory or absorptive apex of the cells suggests that the function of ADCP is related to the secretory and/or absorptive process.

  11. Cooperation of two mRNA-binding proteins drives metabolic adaptation to iron deficiency

    PubMed Central

    Puig, Sergi; Vergara, Sandra V.; Thiele, Dennis J.

    2008-01-01

    Summary Iron (Fe) is an essential co-factor for a wide range of cellular processes. We have previously demonstrated that during Fe-deficiency yeast Cth2 is expressed and promotes degradation of a battery of mRNAs leading to reprogramming of Fe-dependent metabolism and Fe-storage. We report that the Cth2-homologous protein, Cth1, is transiently expressed during Fe-deprivation and participates in the response to Fe-deficiency through the degradation of mRNAs primarily involved in mitochondrially-localized activities including respiration and amino acid biosynthesis. In parallel, wild type but not cth1Δ cth2Δ cells accumulate mRNAs encoding proteins that function in glucose import and storage and store high levels of glycogen. In addition, Fe-deficiency leads to Snf1 phosphorylation, a member of the AMP-activated protein kinase family required for the cellular response to glucose starvation. These studies demonstrate a metabolic reprogramming as a consequence of Fe-starvation that is dependent on the coordinated activities of two mRNA-binding proteins. PMID:18522836

  12. Reproductive Aging Drives Protein Accumulation in the Uterus and Limits Lifespan in C. elegans

    PubMed Central

    Zimmerman, Stephanie M.; Hinkson, Izumi V.; Elias, Joshua E.; Kim, Stuart K.

    2015-01-01

    Aging in Caenorhabditis elegans is characterized by widespread physiological and molecular changes, but the mechanisms that determine the rate at which these changes occur are not well understood. In this study, we identify a novel link between reproductive aging and somatic aging in C. elegans. By measuring global age-related changes in the proteome, we identify a previously uncharacterized group of secreted proteins in the adult uterus that dramatically increase in abundance with age. This accumulation is blunted in animals with an extended reproductive period and accelerated in sterile animals lacking a germline. Uterine proteins are not removed in old post-reproductive animals or in young vulvaless worms, indicating that egg-laying is necessary for their rapid removal in wild-type young animals. Together, these results suggest that age-induced infertility contributes to extracellular protein accumulation in the uterus with age. Finally, we show that knocking down multiple age-increased proteins simultaneously extends lifespan. These results provide a mechanistic example of how the cessation of reproduction contributes to detrimental changes in the soma, and demonstrate how the timing of reproductive decline can influence the rate of aging. PMID:26656270

  13. FAM83 proteins: Fostering new interactions to drive oncogenic signaling and therapeutic resistance

    PubMed Central

    Bartel, Courtney A.; Parameswaran, Neetha; Cipriano, Rocky; Jackson, Mark W.

    2016-01-01

    The FAM83 proteins were recently identified as novel transforming oncogenes that function as intermediaries in EGFR/RAS signaling. Using two distinct forward genetics screens, the Bissell and Jackson laboratories uncovered the importance of the FAM83 proteins in promoting resistance to EGFR tyrosine kinase inhibitors and therapies targeting downstream EGFR signaling effectors. The discovery of this novel oncogene family using distinct genetic screens provides compelling evidence that the FAM83 proteins are key oncogenic players in cancer-associated signaling when they are overexpressed or dysregulated. Consistent with a role in oncogenic transformation, the FAM83 genes are frequently overexpressed in diverse human cancer specimens. Importantly, ablation of numerous FAM83 members results in a marked suppression of cancer-associated signaling and loss of tumorigenic potential. Here, we review the current knowledge of the FAM83 proteins’ involvement in cancer signaling and discuss the potential mechanisms by which they contribute to tumorigenesis. Both redundant activities shared by all 8 FAM83 members and non-redundant activities unique to each member are highlighted. We discuss the promise and challenges of the FAM83 proteins as novel points of attack for future cancer therapies. PMID:27221039

  14. Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes.

    PubMed

    Wang, Jinhua; Smith, Philip J; Krainer, Adrian R; Zhang, Michael Q

    2005-01-01

    Exonic splicing enhancers (ESEs) are pre-mRNA cis-acting elements required for splice-site recognition. We previously developed a web-based program called ESEfinder that scores any sequence for the presence of ESE motifs recognized by the human SR proteins SF2/ASF, SRp40, SRp55 and SC35 (http://rulai.cshl.edu/tools/ESE/). Using ESEfinder, we have undertaken a large-scale analysis of ESE motif distribution in human protein-coding genes. Significantly higher frequencies of ESE motifs were observed in constitutive internal protein-coding exons, compared with both their flanking intronic regions and with pseudo exons. Statistical analysis of ESE motif frequency distributions revealed a complex relationship between splice-site strength and increased or decreased frequencies of particular SR protein motifs. Comparison of constitutively and alternatively spliced exons demonstrated slightly weaker splice-site scores, as well as significantly fewer ESE motifs, in the alternatively spliced group. Our results underline the importance of ESE-mediated SR protein function in the process of exon definition, in the context of both constitutive splicing and regulated alternative splicing.

  15. Epithelial-to-mesenchymal transition drives a pro-metastatic Golgi compaction process through scaffolding protein PAQR11

    PubMed Central

    Tan, Xiaochao; Banerjee, Priyam; Guo, Hou-Fu; Ireland, Stephen; Pankova, Daniela; Ahn, Young-ho; Nikolaidis, Irodotos Michail; Liu, Xin; Zhao, Yanbin; Burns, Alan R.; Gibbons, Don L.; Zal, Tomasz; Creighton, Chad J.; Wang, Yanzhuang; Kurie, Jonathan M.

    2016-01-01

    Tumor cells gain metastatic capacity through a Golgi phosphoprotein 3–dependent (GOLPH3-dependent) Golgi membrane dispersal process that drives the budding and transport of secretory vesicles. Whether Golgi dispersal underlies the pro-metastatic vesicular trafficking that is associated with epithelial-to-mesenchymal transition (EMT) remains unclear. Here, we have shown that, rather than causing Golgi dispersal, EMT led to the formation of compact Golgi organelles with improved ribbon linking and cisternal stacking. Ectopic expression of the EMT-activating transcription factor ZEB1 stimulated Golgi compaction and relieved microRNA-mediated repression of the Golgi scaffolding protein PAQR11. Depletion of PAQR11 dispersed Golgi organelles and impaired anterograde vesicle transport to the plasma membrane as well as retrograde vesicle tethering to the Golgi. The N-terminal scaffolding domain of PAQR11 was associated with key regulators of Golgi compaction and vesicle transport in pull-down assays and was required to reconstitute Golgi compaction in PAQR11-deficient tumor cells. Finally, high PAQR11 levels were correlated with EMT and shorter survival in human cancers, and PAQR11 was found to be essential for tumor cell migration and metastasis in EMT-driven lung adenocarcinoma models. We conclude that EMT initiates a PAQR11-mediated Golgi compaction process that drives metastasis. PMID:27869652

  16. ATP hydrolysis by a domain related to translation factor GTPases drives polymerization of a static bacterial morphogenetic protein.

    PubMed

    Castaing, Jean-Philippe; Nagy, Attila; Anantharaman, Vivek; Aravind, L; Ramamurthi, Kumaran S

    2013-01-08

    The assembly of static supramolecular structures is a culminating event of developmental programs. One such structure, the proteinaceous shell (called the coat) that surrounds spores of the bacterium Bacillus subtilis, is composed of about 70 different proteins and represents one of the most durable biological structures known. The coat is built atop a basement layer that contains an ATPase (SpoIVA) that forms a platform required for coat assembly. Here, we show that SpoIVA belongs to the translation factors class of P-loop GTPases and has evolutionarily lost the ability to bind GTP; instead, it uses ATP hydrolysis to drive its self-assembly into static filaments. We demonstrate that ATP hydrolysis is required by every subunit for incorporation into the growing polymer by inducing a conformational change that drives polymerization of a nucleotide-free filament. SpoIVA therefore differs from other self-organizing polymers (dynamic cytoskeletal structures and static intermediate filaments) in that it uses ATP hydrolysis to self-assemble, not disassemble, into a static polymer. We further show that polymerization requires a critical concentration that we propose is only achieved once SpoIVA is recruited to the surface of the developing spore, thereby ensuring that SpoIVA polymerization only occurs at the correct subcellular location during spore morphogenesis.

  17. Multivesicular Bodies in Neurons: Distribution, Protein Content, and Trafficking Functions

    PubMed Central

    VON BARTHELD, CHRISTOPHER S.; ALTICK, AMY L.

    2011-01-01

    Summary Multivesicular bodies (MVBs) are intracellular endosomal organelles characterized by multiple internal vesicles that are enclosed within a single outer membrane. MVBs were initially regarded as purely prelysosomal structures along the degradative endosomal pathway of internalized proteins. MVBs are now known to be involved in numerous endocytic and trafficking functions, including protein sorting, recycling, transport, storage, and release. This review of neuronal MVBs summarizes their research history, morphology, distribution, accumulation of cargo and constitutive proteins, transport, and theories of functions of MVBs in neurons and glia. Due to their complex morphologies, neurons have expanded trafficking and signaling needs, beyond those of “geometrically simpler” cells, but it is not known whether neuronal MVBs perform additional transport and signaling functions. This review examines the concept of compartment-specific MVB functions in endosomal protein trafficking and signaling within synapses, axons, dendrites and cell bodies. We critically evaluate reports of the accumulation of neuronal MVBs based on evidence of stress-induced MVB formation. Furthermore, we discuss potential functions of neuronal and glial MVBs in development, in dystrophic neuritic syndromes, injury, disease, and aging. MVBs may play a role in Alzheimer’s, Huntington’s, and Niemann-Pick diseases, some types of frontotemporal dementia, prion and virus trafficking, as well as in adaptive responses of neurons to trauma and toxin or drug exposure. Functions of MVBs in neurons have been much neglected, and major gaps in knowledge currently exist. Developing truly MVB-specific markers would help to elucidate the roles of neuronal MVBs in intra- and intercellular signaling of normal and diseased neurons. PMID:21216273

  18. Staphylococcus aureus FepA and FepB proteins drive heme iron utilization in Escherichia coli.

    PubMed

    Turlin, Evelyne; Débarbouillé, Michel; Augustyniak, Katarzyna; Gilles, Anne-Marie; Wandersman, Cécile

    2013-01-01

    EfeUOB-like tripartite systems are widespread in bacteria and in many cases they are encoded by genes organized into iron-regulated operons. They consist of: EfeU, a protein similar to the yeast iron permease Ftrp1; EfeO, an extracytoplasmic protein of unknown function and EfeB, also an extracytoplasmic protein with heme peroxidase activity, belonging to the DyP family. Many bacterial EfeUOB systems have been implicated in iron uptake, but a prefential iron source remains undetermined. Nevertheless, in the case of Escherichia coli, the EfeUOB system has been shown to recognize heme and to allow extracytoplasmic heme iron extraction via a deferrochelation reaction. Given the high level of sequence conservations between EfeUOB orthologs, we hypothesized that heme might be the physiological iron substrate for the other orthologous systems. To test this hypothesis, we undertook characterization of the Staphylococcus aureus FepABC system. Results presented here indicate: i) that the S. aureus FepB protein binds both heme and PPIX with high affinity, like EfeB, the E. coli ortholog; ii) that it has low peroxidase activity, comparable to that of EfeB; iii) that both FepA and FepB drive heme iron utilization, and both are required for this activity and iv) that the E. coli FepA ortholog (EfeO) cannot replace FepA in FepB-driven iron release from heme indicating protein specificity in these activities. Our results show that the function in heme iron extraction is conserved in the two orthologous systems.

  19. Sequential domain assembly of ribosomal protein S3 drives 40S subunit maturation

    PubMed Central

    Mitterer, Valentin; Murat, Guillaume; Réty, Stéphane; Blaud, Magali; Delbos, Lila; Stanborough, Tamsyn; Bergler, Helmut; Leulliot, Nicolas; Kressler, Dieter; Pertschy, Brigitte

    2016-01-01

    Eukaryotic ribosomes assemble by association of ribosomal RNA with ribosomal proteins into nuclear precursor particles, which undergo a complex maturation pathway coordinated by non-ribosomal assembly factors. Here, we provide functional insights into how successive structural re-arrangements in ribosomal protein S3 promote maturation of the 40S ribosomal subunit. We show that S3 dimerizes and is imported into the nucleus with its N-domain in a rotated conformation and associated with the chaperone Yar1. Initial assembly of S3 with 40S precursors occurs via its C-domain, while the N-domain protrudes from the 40S surface. Yar1 is replaced by the assembly factor Ltv1, thereby fixing the S3 N-domain in the rotated orientation and preventing its 40S association. Finally, Ltv1 release, triggered by phosphorylation, and flipping of the S3 N-domain into its final position results in the stable integration of S3. Such a stepwise assembly may represent a new paradigm for the incorporation of ribosomal proteins. PMID:26831757

  20. Electrostatic Interactions between Elongated Monomers Drive Filamentation of Drosophila Shrub, a Metazoan ESCRT-III Protein.

    PubMed

    McMillan, Brian J; Tibbe, Christine; Jeon, Hyesung; Drabek, Andrew A; Klein, Thomas; Blacklow, Stephen C

    2016-08-02

    The endosomal sorting complex required for transport (ESCRT) is a conserved protein complex that facilitates budding and fission of membranes. It executes a key step in many cellular events, including cytokinesis and multi-vesicular body formation. The ESCRT-III protein Shrub in flies, or its homologs in yeast (Snf7) or humans (CHMP4B), is a critical polymerizing component of ESCRT-III needed to effect membrane fission. We report the structural basis for polymerization of Shrub and define a minimal region required for filament formation. The X-ray structure of the Shrub core shows that individual monomers in the lattice interact in a staggered arrangement using complementary electrostatic surfaces. Mutations that disrupt interface salt bridges interfere with Shrub polymerization and function. Despite substantial sequence divergence and differences in packing interactions, the arrangement of Shrub subunits in the polymer resembles that of Snf7 and other family homologs, suggesting that this intermolecular packing mechanism is shared among ESCRT-III proteins.

  1. The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA.

    PubMed

    Wittmann, Sina; Renner, Max; Watts, Beth R; Adams, Oliver; Huseyin, Miles; Baejen, Carlo; El Omari, Kamel; Kilchert, Cornelia; Heo, Dong-Hyuk; Kecman, Tea; Cramer, Patrick; Grimes, Jonathan M; Vasiljeva, Lidia

    2017-04-03

    Termination of RNA polymerase II (Pol II) transcription is an important step in the transcription cycle, which involves the dislodgement of polymerase from DNA, leading to release of a functional transcript. Recent studies have identified the key players required for this process and showed that a common feature of these proteins is a conserved domain that interacts with the phosphorylated C-terminus of Pol II (CTD-interacting domain, CID). However, the mechanism by which transcription termination is achieved is not understood. Using genome-wide methods, here we show that the fission yeast CID-protein Seb1 is essential for termination of protein-coding and non-coding genes through interaction with S2-phosphorylated Pol II and nascent RNA. Furthermore, we present the crystal structures of the Seb1 CTD- and RNA-binding modules. Unexpectedly, the latter reveals an intertwined two-domain arrangement of a canonical RRM and second domain. These results provide important insights into the mechanism underlying eukaryotic transcription termination.

  2. Subcellular distribution of mutant movement proteins of Cucumber mosaic virus fused to green fluorescent proteins.

    PubMed

    Canto, Tomas; Palukaitis, Peter

    2005-04-01

    The subcellular distribution of the movement proteins (MPs) of nine alanine-scanning mutants of Cucumber mosaic virus (CMV), fused to the green fluorescent protein (GFP) and expressed from CMV, was determined by confocal microscopy of infected epidermal cells of Nicotiana tabacum and Nicotiana benthamiana, as well as infected N. benthamiana protoplasts. Only those mutant MPs that were functional for movement in all host species tested localized to plasmodesmata of infected epidermal cells and to tubules extending from the surface of infected protoplasts, as for wild-type CMV 3a MP. Various mutant MPs that were either conditionally functional for movement or dysfunctional for movement did not localize to plasmodesmata and did not form tubules on the surface of infected protoplasts. Rather, they showed distribution to different extents throughout the infected cells, including the cytoplasm, nucleus or the plasma membrane. The CMV 3a MP also did not associate with microtubules.

  3. Driving Calmodulin Protein towards Conformational Shift by Changing Ionization States of Select Residues

    NASA Astrophysics Data System (ADS)

    Negi, Sunita; Rana Atilgan, Ali; Atilgan, Canan

    2012-12-01

    Proteins are complex systems made up of many conformational sub-states which are mainly determined by the folded structure. External factors such as solvent type, temperature, pH and ionic strength play a very important role in the conformations sampled by proteins. Here we study the conformational multiplicity of calmodulin (CaM) which is a protein that plays an important role in calcium signaling pathways in the eukaryotic cells. CaM can bind to a variety of other proteins or small organic compounds, and mediates different physiological processes by activating various enzymes. Binding of calcium ions and proteins or small organic molecules to CaM induces large conformational changes that are distinct to each interacting partner. In particular, we discuss the effect of pH variation on the conformations of CaM. By using the pKa values of the charged residues as a basis to assign protonation states, the conformational changes induced in CaM by reducing the pH are studied by molecular dynamics simulations. Our current view suggests that at high pH, barrier crossing to the compact form is prevented by repulsive electrostatic interactions between the two lobes. At reduced pH, not only is barrier crossing facilitated by protonation of residues, but also conformations which are on average more compact are attained. The latter are in accordance with the fluorescence resonance energy transfer experiment results of other workers. The key events leading to the conformational change from the open to the compact conformation are (i) formation of a salt bridge between the N-lobe and the linker, stabilizing their relative motions, (ii) bending of the C-lobe towards the N-lobe, leading to a lowering of the interaction energy between the two-lobes, (iii) formation of a hydrophobic patch between the two lobes, further stabilizing the bent conformation by reducing the entropic cost of the compact form, (iv) sharing of a Ca+2 ion between the two lobes.

  4. CROSS DRIVE: A Collaborative and Distributed Virtual Environment for Exploitation of Atmospherical and Geological Datasets of Mars

    NASA Astrophysics Data System (ADS)

    Cencetti, Michele

    2016-07-01

    European space exploration missions have produced huge data sets of potentially immense value for research as well as for planning and operating future missions. For instance, Mars Exploration programs comprise a series of missions with launches ranging from the past to beyond present, which are anticipated to produce exceptional volumes of data which provide prospects for research breakthroughs and advancing further activities in space. These collected data include a variety of information, such as imagery, topography, atmospheric, geochemical datasets and more, which has resulted in and still demands, databases, versatile visualisation tools and data reduction methods. Such rate of valuable data acquisition requires the scientists, researchers and computer scientists to coordinate their storage, processing and relevant tools to enable efficient data analysis. However, the current position is that expert teams from various disciplines, the databases and tools are fragmented, leaving little scope for unlocking its value through collaborative activities. The benefits of collaborative virtual environments have been implemented in various industrial fields allowing real-time multi-user collaborative work among people from different disciplines. Exploiting the benefits of advanced immersive virtual environments (IVE) has been recognized as an important interaction paradigm to facilitate future space exploration. The current work is mainly aimed towards the presentation of the preliminary results coming from the CROSS DRIVE project. This research received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 607177 and is mainly aimed towards the implementation of a distributed virtual workspace for collaborative scientific discovery, mission planning and operations. The purpose of the CROSS DRIVE project is to lay foundations of collaborative European workspaces for space science. It will demonstrate the feasibility and

  5. Heterogeneous distribution of dye-labelled biomineralizaiton proteins in calcite crystals.

    PubMed

    Liu, Chuang; Xie, Liping; Zhang, Rongqing

    2015-12-17

    Biominerals are highly ordered crystals mediated by organic matters especially proteins in organisms. However, how specific proteins are distributed inside biominerals are not well understood. In the present study, we use fluorescein isothiocyanate (FITC) to label extracted proteins from the shells of bivalve Pinctada fucata. By confocal laser scanning microscopy (CLSM), we observe a heterogeneous distribution of dye-labelled proteins inside synthetic calcite at the microscale. Proteins from the prismatic calcite layers accumulate at the edge of crystals while proteins from the nacreous aragonite layers accumulate at the center of crystals. Raman and X-ray powder diffraction show that both the proteins cannot alter the crystal phase. Scanning electron microscope demonstrates both proteins are able to affect the crystal morphology. This study may provide a direct approach for the visualization of protein distributions in crystals by small-molecule dye-labelled proteins as the additives in the crystallization process and improve our understanding of intracrystalline proteins distribution in biogenic calcites.

  6. PROTEINS IN NUCLEOCYTOPLASMIC INTERACTIONS : II. Turnover and Changes in Nuclear Protein Distribution with Time and Growth.

    PubMed

    Goldstein, L; Prescott, D M

    1968-01-01

    In previous studies, we showed that essentially all the proteins of the Amoeba proteus nucleus could be classified either as Rapidly Migrating Proteins (RMP), which shuttle between nucleus and cytoplasm continuously at a relatively rapid rate during interphase, or as Slow Turnover Proteins (STP), which seem to move hardly at all during interphase. In this paper, we report on the kinetics and direction of the movement of both classes of protein, as well as on aspects of their localization, with and without growth. The effects of growth were observed with and without cell division. These nuclear proteins have been studied in several ways: by transplantation of labeled nuclei into unlabeled cells and noting the rate of distribution to cytoplasm and host cell nuclei; by repeated amputation of cytoplasm from labeled cells-with and without initially labeled cytoplasm-each amputation being followed by refeeding on unlabeled food; by noting the redistribution of the various protein classes following growth and cell division. The data show (a) labeled RMP equilibrate between a grafted labeled nucleus and an unlabeled host nucleus in ca. 3 hr, but are detectable in the latter less than 30 min after the operation; (b) STP label does, indeed, leave the nucleus and does so at a rate of ca. 25% of the nuclear total per cell generation (ca. 36-40 hr at 23 degrees C); (c) the cytoplasm appears to have a reserve of material that is converted to RMP; (d) when labeled cells are amputated just before they would have divided and are refed unlabeled food after each amputation, there is a loss of 20-25% of the nuclear protein label with each amputation; (e) under the latter circumstances, an essentially complete turnover of all nuclear protein can be demonstrated.

  7. Single molecule compression reveals intra-protein forces drive cytotoxin pore formation

    PubMed Central

    Czajkowsky, Daniel M; Sun, Jielin; Shen, Yi; Shao, Zhifeng

    2015-01-01

    Perfringolysin O (PFO) is a prototypical member of a large family of pore-forming proteins that undergo a significant reduction in height during the transition from the membrane-assembled prepore to the membrane-inserted pore. Here, we show that targeted application of compressive forces can catalyze this conformational change in individual PFO complexes trapped at the prepore stage, recapitulating this critical step of the spontaneous process. The free energy landscape determined from these measurements is in good agreement with that obtained from molecular dynamics simulations showing that an equivalent internal force is generated by the interaction of the exposed hydrophobic residues with the membrane. This hydrophobic force is transmitted across the entire structure to produce a compressive stress across a distant, otherwise stable domain, catalyzing its transition from an extended to compact conformation. Single molecule compression is likely to become an important tool to investigate conformational transitions in membrane proteins. DOI: http://dx.doi.org/10.7554/eLife.08421.001 PMID:26652734

  8. Calpain-mediated cleavage of collapsin response mediator protein-2 drives acute axonal degeneration

    PubMed Central

    Zhang, Jian-Nan; Michel, Uwe; Lenz, Christof; Friedel, Caroline C.; Köster, Sarah; d’Hedouville, Zara; Tönges, Lars; Urlaub, Henning; Bähr, Mathias; Lingor, Paul; Koch, Jan C.

    2016-01-01

    Axonal degeneration is a key initiating event in many neurological diseases. Focal lesions to axons result in a rapid disintegration of the perilesional axon by acute axonal degeneration (AAD) within several hours. However, the underlying molecular mechanisms of AAD are only incompletely understood. Here, we studied AAD in vivo through live-imaging of the rat optic nerve and in vitro in primary rat cortical neurons in microfluidic chambers. We found that calpain is activated early during AAD of the optic nerve and that calpain inhibition completely inhibits axonal fragmentation on the proximal side of the crush while it attenuates AAD on the distal side. A screening of calpain targets revealed that collapsin response mediator protein-2 (CRMP2) is a main downstream target of calpain activation in AAD. CRMP2-overexpression delayed bulb formation and rescued impairment of axonal mitochondrial transport after axotomy in vitro. In vivo, CRMP2-overexpression effectively protected the proximal axon from fragmentation within 6 hours after crush. Finally, a proteomic analysis of the optic nerve was performed at 6 hours after crush, which identified further proteins regulated during AAD, including several interactors of CRMP2. These findings reveal CRMP2 as an important mediator of AAD and define it as a putative therapeutic target. PMID:27845394

  9. Short-lived Her proteins drive robust synchronized oscillations in the zebrafish segmentation clock.

    PubMed

    Ay, Ahmet; Knierer, Stephan; Sperlea, Adriana; Holland, Jack; Özbudak, Ertuğrul M

    2013-08-01

    Oscillations are prevalent in natural systems. A gene expression oscillator, called the segmentation clock, controls segmentation of precursors of the vertebral column. Genes belonging to the Hes/her family encode the only conserved oscillating genes in all analyzed vertebrate species. Hes/Her proteins form dimers and negatively autoregulate their own transcription. Here, we developed a stochastic two-dimensional multicellular computational model to elucidate how the dynamics, i.e. period, amplitude and synchronization, of the segmentation clock are regulated. We performed parameter searches to demonstrate that autoregulatory negative-feedback loops of the redundant repressor Her dimers can generate synchronized gene expression oscillations in wild-type embryos and reproduce the dynamics of the segmentation oscillator in different mutant conditions. Our model also predicts that synchronized oscillations can be robustly generated as long as the half-lives of the repressor dimers are shorter than 6 minutes. We validated this prediction by measuring, for the first time, the half-life of Her7 protein as 3.5 minutes. These results demonstrate the importance of building biologically realistic stochastic models to test biological models more stringently and make predictions for future experimental studies.

  10. The Respiratory Syncytial Virus Phosphoprotein, Matrix Protein, and Fusion Protein Carboxy-Terminal Domain Drive Efficient Filamentous Virus-Like Particle Formation.

    PubMed

    Meshram, Chetan D; Baviskar, Pradyumna S; Ognibene, Cherie M; Oomens, Antonius G P

    2016-12-01

    Virus-like particles (VLPs) are attractive as a vaccine concept. For human respiratory syncytial virus (hRSV), VLP assembly is poorly understood and appears inefficient. Hence, hRSV antigens are often incorporated into foreign VLP systems to generate anti-RSV vaccine candidates. To better understand the assembly, and ultimately to enable efficient production, of authentic hRSV VLPs, we examined the associated requirements and mechanisms. In a previous analysis in HEp-2 cells, the nucleoprotein (N), phosphoprotein (P), matrix protein (M), and fusion protein (F) were required for formation of filamentous VLPs, which, similar to those of wild-type virus, were associated with the cell surface. Using fluorescence and electron microscopy combined with immunogold labeling, we examined the surfaces of transfected HEp-2 cells and further dissected the process of filamentous VLP formation. Our results show that N is not required. Coexpression of P plus M plus F, but not P plus M, M plus F, or P plus F, induced both viral protein coalescence and formation of filamentous VLPs that resembled wild-type virions. Despite suboptimal coalescence in the absence of P, the M and F proteins, when coexpressed, formed cell surface-associated filaments with abnormal morphology, appearing longer and thinner than wild-type virions. For F, only the carboxy terminus (Fstem) was required, and addition of foreign protein sequences to Fstem allowed incorporation into VLPs. Together, the data show that P, M, and the F carboxy terminus are sufficient for robust viral protein coalescence and filamentous VLP formation and suggest that M-F interaction drives viral filament formation, with P acting as a type of cofactor facilitating the process and exerting control over particle morphology.

  11. Carbohydrate-protein interactions that drive processive polysaccharide translocation in enzymes revealed from a computational study of cellobiohydrolase processivity.

    PubMed

    Knott, Brandon C; Crowley, Michael F; Himmel, Michael E; Ståhlberg, Jerry; Beckham, Gregg T

    2014-06-18

    Translocation of carbohydrate polymers through protein tunnels and clefts is a ubiquitous biochemical phenomenon in proteins such as polysaccharide synthases, glycoside hydrolases, and carbohydrate-binding modules. Although static snapshots of carbohydrate polymer binding in proteins have long been studied via crystallography and spectroscopy, the molecular details of polysaccharide chain processivity have not been elucidated. Here, we employ simulation to examine how a cellulose chain translocates by a disaccharide unit during the processive cycle of a glycoside hydrolase family 7 cellobiohydrolase. Our results demonstrate that these biologically and industrially important enzymes employ a two-step mechanism for chain threading to form a Michaelis complex and that the free energy barrier to chain threading is significantly lower than the hydrolysis barrier. Taken with previous studies, our findings suggest that the rate-limiting step in enzymatic cellulose degradation is the glycosylation reaction, not chain processivity. Based on the simulations, we find that strong electrostatic interactions with polar residues that are conserved in GH7 cellobiohydrolases, but not in GH7 endoglucanases, at the leading glucosyl ring provide the thermodynamic driving force for polysaccharide chain translocation. Also, we consider the role of aromatic-carbohydrate interactions, which are widespread in carbohydrate-active enzymes and have long been associated with processivity. Our analysis suggests that the primary role for these aromatic residues is to provide tunnel shape and guide the carbohydrate chain to the active site. More broadly, this work elucidates the role of common protein motifs found in carbohydrate-active enzymes that synthesize or depolymerize polysaccharides by chain translocation mechanisms coupled to catalysis.

  12. A Direct-Push Sample-Freezing Drive Shoe for Collecting Sediment Cores with Intact Pore Fluid, Microbial, and Sediment Distributions

    NASA Astrophysics Data System (ADS)

    Bekins, B. A.; Trost, J.; Christy, T. M.; Mason, B.

    2015-12-01

    Abiotic and biological reactions in shallow groundwater and bottom sediments are central to understanding groundwater contaminant attenuation and biogeochemical cycles. The laminar flow regime in unconsolidated surficial aquifers creates narrow reaction zones. Studying these reaction zones requires fine-scale sampling of water together with adjacent sediment in a manner that preserves in situ redox conditions. Collecting representative samples of these narrow zones with traditional subsurface sampling equipment is challenging. For example, use of a basket type core catcher for saturated, non-cohesive sediments results in loss of fluid and sediments during retrieval. A sample-freezing drive shoe designed for a wire line piston core sampler allowed collection of cores with intact sediment, microbial, and pore fluid distributions and has been the basis for studies documenting centimeter-scale variations in aquifer microbial populations (Murphy and Herkelrath, 1996). However, this freezing drive shoe design is not compatible with modern-day direct push sampling rigs. A re-designed sample-freezing drive shoe compatible with a direct-push dual-tube coring system was developed and field-tested. The freezing drive shoe retained sediment and fluid distributions in saturated sediment core samples by freezing a 10 centimeter plug below the core sample with liquid CO­2. Core samples collected across the smear zone at a crude oil spill site near Bemidji, Minnesota, were successfully extracted without loss of fluid or sediment. Multiple core sections from different depths in the aquifer were retrieved from a single hole. This new design makes a highly effective sampling technology available on modern-day direct push sampling equipment to inform myriad questions about subsurface biogeochemistry processes. The re-design of the freezing drive shoe was supported by the USGS Innovation Center for Earth Sciences. References: Murphy, Fred, and W. N. Herkelrath. "A sample

  13. Inflammatory stress of pancreatic beta cells drives release of extracellular heat shock protein 90α.

    PubMed

    Ocaña, Gail J; Pérez, Liliana; Guindon, Lynette; Deffit, Sarah N; Evans-Molina, Carmella; Thurmond, Debbie C; Blum, Janice S

    2017-02-11

    A major obstacle in predicting and preventing the development of autoimmune type 1 diabetes (T1D) in at-risk individuals is the lack of well-established early biomarkers indicative of ongoing beta cell stress during the pre-clinical phase of disease. Recently, serum levels of the alpha cytoplasmic isoform of heat shock protein (HSP) 90 were shown to be elevated in individuals with new-onset T1D. We therefore hypothesized HSP90α could be released from beta cells in response to cellular stress and inflammation associated with the earliest stages of T1D. Here, human beta cell lines and cadaveric islets released HSP90α in response to stress induced by treatment with a combination of pro-inflammatory cytokines including IL-1β, TNF-α, and IFN-γ. Mechanistically, HSP90α release was found to be driven by cytokine-induced endoplasmic reticulum (ER) stress mediated by c-Jun N-terminal kinase (JNK), a pathway that can eventually lead to beta cell apoptosis. Cytokine-induced beta cell HSP90α release and JNK activation were significantly reduced by pre-treating cells with the ER stress-mitigating chemical chaperone tauroursodeoxycholic acid (TUDCA). HSP90α release by cells may thus be a sensitive indicator of stress during inflammation and a useful tool in assessing therapeutic mitigation of cytokine-induced cell damage linked to autoimmunity. This article is protected by copyright. All rights reserved.

  14. Acquisition of an oncogenic fusion protein serves as an initial driving mutation by inducing aneuploidy and overriding proliferative defects

    PubMed Central

    Maggi, Elaine C.; Vijayaraghavan, Jyothi; Zabaleta, Jovanny; Taylor, Christopher M.; Tsien, Fern; Crabtree, Judy S.; Hollenbach, Andrew D.

    2016-01-01

    While many solid tumors are defined by the presence of a particular oncogene, the role that this oncogene plays in driving transformation through the acquisition of aneuploidy and overcoming growth arrest are often not known. Further, although aneuploidy is present in many solid tumors, it is not clear whether it is the cause or effect of malignant transformation. The childhood sarcoma, Alveolar Rhabdomyosarcoma (ARMS), is primarily defined by the t(2;13)(q35;q14) translocation, creating the PAX3-FOXO1 fusion protein. It is unclear what role PAX3-FOXO1 plays in the initial stages of tumor development through the acquisition and persistence of aneuploidy. In this study we demonstrate that PAX3-FOXO1 serves as a driver mutation to initiate a cascade of mRNA and miRNA changes that ultimately reprogram proliferating myoblasts to induce the formation of ARMS. We present evidence that cells containing PAX3-FOXO1 have changes in the expression of mRNA and miRNA essential for maintaining proper chromosome number and structure thereby promoting aneuploidy. Further, we demonstrate that the presence of PAX3-FOXO1 alters the expression of growth factor related mRNA and miRNA, thereby overriding aneuploid-dependent growth arrest. Finally, we present evidence that phosphorylation of PAX3-FOXO1 contributes to these changes. This is one of the first studies describing how an oncogene and post-translational modifications drive the development of a tumor through the acquisition and persistence of aneuploidy. This mechanism has implications for other solid tumors where large-scale genomics studies may elucidate how global alterations contribute to tumor phenotypes allowing the development of much needed multi-faceted tumor-specific therapeutic regimens. PMID:27588498

  15. Evolutionary mechanisms driving the evolution of a large polydnavirus gene family coding for protein tyrosine phosphatases

    PubMed Central

    2012-01-01

    Background Gene duplications have been proposed to be the main mechanism involved in genome evolution and in acquisition of new functions. Polydnaviruses (PDVs), symbiotic viruses associated with parasitoid wasps, are ideal model systems to study mechanisms of gene duplications given that PDV genomes consist of virulence genes organized into multigene families. In these systems the viral genome is integrated in a wasp chromosome as a provirus and virus particles containing circular double-stranded DNA are injected into the parasitoids’ hosts and are essential for parasitism success. The viral virulence factors, organized in gene families, are required collectively to induce host immune suppression and developmental arrest. The gene family which encodes protein tyrosine phosphatases (PTPs) has undergone spectacular expansion in several PDV genomes with up to 42 genes. Results Here, we present strong indications that PTP gene family expansion occurred via classical mechanisms: by duplication of large segments of the chromosomally integrated form of the virus sequences (segmental duplication), by tandem duplications within this form and by dispersed duplications. We also propose a novel duplication mechanism specific to PDVs that involves viral circle reintegration into the wasp genome. The PTP copies produced were shown to undergo conservative evolution along with episodes of adaptive evolution. In particular recently produced copies have undergone positive selection in sites most likely involved in defining substrate selectivity. Conclusion The results provide evidence about the dynamic nature of polydnavirus proviral genomes. Classical and PDV-specific duplication mechanisms have been involved in the production of new gene copies. Selection pressures associated with antagonistic interactions with parasitized hosts have shaped these genes used to manipulate lepidopteran physiology with evidence for positive selection involved in adaptation to host targets. PMID

  16. Note: On the Universality of Proximal Radial Distribution Functions of Proteins

    SciTech Connect

    Lin, Bin; Pettitt, Bernard M.

    2011-03-10

    Protein hydration is important to protein structure and function. Molecular distribution functions have been an invaluable tool to study protein hydration. Proximal radial distribution functions (pRDFs) have been postulated as being transferable across proteins based on evidence collected from two proteins [V. A. Makarov, B. K. Andrews, and B. M. Pettitt, Biopolymers 45(7), 469 (1998)]. Here we selected nine proteins with different sizes as well as different secondary topologies. We show that pRDFs are universal for proteins with compact structures. We further compare these pRDFs with those calculated from polyglycines that have no defined structures to consider the extent of the validity of this approach.

  17. Application of Maximum Entropy principle to modeling torsion angle probability distribution in proteins

    NASA Astrophysics Data System (ADS)

    Rowicka, Małgorzata; Otwinowski, Zbyszek

    2004-04-01

    Using the Maximum Entropy principle, we find probability distribution of torsion angles in proteins. We estimate parameters of this distribution numerically, by implementing the conjugate gradient method in Polak-Ribiere variant. We investigate practical approximations of the theoretical distribution. We discuss the information content of these approximations and compare them with standard histogram method. Our data are pairs of main chain torsion angles for a selected subset of high resolution non-homologous protein structures from Protein Data Bank.

  18. Coagulation factor Xa drives tumor cells into apoptosis through BH3-only protein Bim up-regulation

    SciTech Connect

    Borensztajn, Keren S. . E-mail: K.S.Borensztajn@amc.uva.nl; Bijlsma, Maarten F.; Groot, Angelique P.; Brueggemann, Lois W.; Versteeg, Henri H.; Reitsma, Pieter H.; Peppelenbosch, Maikel P.; Spek, C. Arnold

    2007-07-15

    Coagulation Factor (F)Xa is a serine protease that plays a crucial role during blood coagulation by converting prothrombin into active thrombin. Recently, however, it emerged that besides this role in coagulation, FXa induces intracellular signaling leading to different cellular effects. Here, we show that coagulation factor (F)Xa drives tumor cells of epithelial origin, but not endothelial cells or monocytes, into apoptosis, whereas it even enhances fibroblast survival. FXa signals through the protease activated receptor (PAR)-1 to activate extracellular-signal regulated kinase (ERK) 1/2 and p38. This activation is associated with phosphorylation of the transcription factor CREB, and in tumor cells with up-regulation of the BH3-only pro-apoptotic protein Bim, leading to caspase-3 cleavage, the main hallmark of apoptosis. Transfection of tumor cells with dominant negative forms of CREB or siRNA for either PAR-1, Bim, ERK1 and/or p38 inhibited the pro-apoptotic effect of FXa. In fibroblasts, FXa-induced PAR-1 activation leads to down-regulation of Bim and pre-treatment with PAR-1 or Bim siRNA abolishes proliferation. We thus provide evidence that beyond its role in blood coagulation, FXa plays a key role in cellular processes in which Bim is the central player in determining cell survival.

  19. Electrostatic Contributions Drive the Interaction Between Staphylococcus aureus Protein Efb-C and its Complement Target C3d

    SciTech Connect

    Haspel, N.; Ricklin, D.; Geisbrecht, B.V.; Kavraki, L.E.; Lambris, J.D.

    2008-11-13

    The C3-inhibitory domain of Staphylococcus aureus extracellular fibrinogen-binding protein (Efb-C) defines a novel three-helix bundle motif that regulates complement activation. Previous crystallographic studies of Efb-C bound to its cognate subdomain of human C3 (C3d) identified Arg-131 and Asn-138 of Efb-C as key residues for its activity. In order to characterize more completely the physical and chemical driving forces behind this important interaction, we employed in this study a combination of structural, biophysical, and computational methods to analyze the interaction of C3d with Efb-C and the single-point mutants R131A and N138A. Our results show that while these mutations do not drastically affect the structure of the Efb-C/C3d recognition complex, they have significant adverse effects on both the thermodynamic and kinetic profiles of the resulting complexes. We also characterized other key interactions along the Efb-C/C3d binding interface and found an intricate network of salt bridges and hydrogen bonds that anchor Efb-C to C3d, resulting in its potent complement inhibitory properties.

  20. Electrostatic contributions drive the interaction between Staphylococcus aureus protein Efb-C and its complement target C3d.

    PubMed

    Haspel, Nurit; Ricklin, Daniel; Geisbrecht, Brian V; Kavraki, Lydia E; Lambris, John D

    2008-11-01

    The C3-inhibitory domain of Staphylococcus aureus extracellular fibrinogen-binding protein (Efb-C) defines a novel three-helix bundle motif that regulates complement activation. Previous crystallographic studies of Efb-C bound to its cognate subdomain of human C3 (C3d) identified Arg-131 and Asn-138 of Efb-C as key residues for its activity. In order to characterize more completely the physical and chemical driving forces behind this important interaction, we employed in this study a combination of structural, biophysical, and computational methods to analyze the interaction of C3d with Efb-C and the single-point mutants R131A and N138A. Our results show that while these mutations do not drastically affect the structure of the Efb-C/C3d recognition complex, they have significant adverse effects on both the thermodynamic and kinetic profiles of the resulting complexes. We also characterized other key interactions along the Efb-C/C3d binding interface and found an intricate network of salt bridges and hydrogen bonds that anchor Efb-C to C3d, resulting in its potent complement inhibitory properties.

  1. Cerebral vascular amyloid seeds drive amyloid β-protein fibril assembly with a distinct anti-parallel structure

    PubMed Central

    Xu, Feng; Fu, Ziao; Dass, Sharmila; Kotarba, AnnMarie E.; Davis, Judianne; Smith, Steven O.; Van Nostrand, William E.

    2016-01-01

    Cerebrovascular accumulation of amyloid β-protein (Aβ), a condition known as cerebral amyloid angiopathy (CAA), is a common pathological feature of patients with Alzheimer's disease. Familial Aβ mutations, such as Dutch-E22Q and Iowa-D23N, can cause severe cerebrovascular accumulation of amyloid that serves as a potent driver of vascular cognitive impairment and dementia. The distinctive features of vascular amyloid that underlie its unique pathological properties remain unknown. Here, we use transgenic mouse models producing CAA mutants (Tg-SwDI) or overproducing human wild-type Aβ (Tg2576) to demonstrate that CAA-mutant vascular amyloid influences wild-type Aβ deposition in brain. We also show isolated microvascular amyloid seeds from Tg-SwDI mice drive assembly of human wild-type Aβ into distinct anti-parallel β-sheet fibrils. These findings indicate that cerebrovascular amyloid can serve as an effective scaffold to promote rapid assembly and strong deposition of Aβ into a unique structure that likely contributes to its distinctive pathology. PMID:27869115

  2. The DEG/ENaC cation channel protein UNC-8 drives activity-dependent synapse removal in remodeling GABAergic neurons

    PubMed Central

    Miller-Fleming, Tyne W; Petersen, Sarah C; Manning, Laura; Matthewman, Cristina; Gornet, Megan; Beers, Allison; Hori, Sayaka; Mitani, Shohei; Bianchi, Laura; Richmond, Janet; Miller, David M

    2016-01-01

    Genetic programming and neural activity drive synaptic remodeling in developing neural circuits, but the molecular components that link these pathways are poorly understood. Here we show that the C. elegans Degenerin/Epithelial Sodium Channel (DEG/ENaC) protein, UNC-8, is transcriptionally controlled to function as a trigger in an activity-dependent mechanism that removes synapses in remodeling GABAergic neurons. UNC-8 cation channel activity promotes disassembly of presynaptic domains in DD type GABA neurons, but not in VD class GABA neurons where unc-8 expression is blocked by the COUP/TF transcription factor, UNC-55. We propose that the depolarizing effect of UNC-8-dependent sodium import elevates intracellular calcium in a positive feedback loop involving the voltage-gated calcium channel UNC-2 and the calcium-activated phosphatase TAX-6/calcineurin to initiate a caspase-dependent mechanism that disassembles the presynaptic apparatus. Thus, UNC-8 serves as a link between genetic and activity-dependent pathways that function together to promote the elimination of GABA synapses in remodeling neurons. DOI: http://dx.doi.org/10.7554/eLife.14599.001 PMID:27403890

  3. Protein Kinase Cδ Upregulation in Microglia Drives Neuroinflammatory Responses and Dopaminergic Neurodegeneration in Experimental Models of Parkinson's Disease

    PubMed Central

    Gordon, Richard; Singh, Neeraj; Lawana, Vivek; Ghosh, Anamitra; Harischandra, Dilshan S.; Jin, Huajun; Hogan, Colleen; Sarkar, Souvarish; Rokad, Dharmin; Panicker, Nikhil; Anantharam, Vellareddy; Kanthasamy, Anumantha G.; Kanthasamy, Arthi

    2016-01-01

    Chronic microglial activation has been linked to the progressive degeneration of the nigrostriatal dopaminergic neurons evidenced in Parkinson's disease (PD) pathogenesis. The exact etiology of PD remains poorly understood. Although both oxidative stress and neuroinflammation are identified as co-contributors in PD pathogenesis, signaling mechanisms underlying neurodegenerative processes have yet to be defined. Indeed, we recently identified that protein kinase C delta (PKCδ) activation is critical for induction of dopaminergic neuronal loss in response to neurotoxic stressors. However, it remains to be defined whether PKCδ activation contributes to immune signaling events driving microglial neurotoxicity. In the present study, we systematically investigated whether PKCδ contributes to the heightened microglial activation response following exposure to major proinflammatory stressors, including α-synuclein, tumor necrosis factor α (TNFα), and lipopolysaccharide (LPS). We report that exposure to the aforementioned inflammatory stressors dramatically upregulated PKCδ with a concomitant increase in its kinase activity and nuclear translocation in both BV-2 microglial cells and primary microglia. Importantly, we also observed a marked upregulation of PKCδ in the microglia of the ventral midbrain region of PD patients when compared to age-matched controls, suggesting a role for microglial PKCδ in neurodegenerative processes. Further, shRNA-mediated knockdown and genetic ablation of PKCδ in primary microglia blunted the microglial proinflammatory response elicited by the inflammogens, including ROS generation, nitric oxide production, and proinflammatory cytokine and chemokine release. Importantly, we found that PKCδ activated NFκB, a key mediator of inflammatory signaling events, after challenge with inflammatory stressors, and that transactivation of NFκB led to translocation of the p65 subunit to the nucleus, IκBα degradation and phosphorylation of p65

  4. Involvement of PCH family proteins in cytokinesis and actin distribution.

    PubMed

    Lippincott, J; Li, R

    2000-04-15

    Pombe Cdc15 homology (PCH) proteins constitute an extensive protein family whose members have been found in diverse eukaryotic organisms. These proteins are characterized by the presence of several conserved sequence and structural motifs. Recent studies in yeast and mammalian cultured cells have implicated these proteins in actin-based processes, in particular, cytokinesis. Here we review the recent findings on the in vivo localization, function, and binding partners of PCH family members. We also provide new microscopy data regarding the in vivo dynamics of a budding yeast PCH protein involved in cytokinesis.

  5. Subcellular distribution of tail-anchored proteins in Arabidopsis.

    PubMed

    Kriechbaumer, Verena; Shaw, Rowena; Mukherjee, Joy; Bowsher, Caroline G; Harrison, Anne-Marie; Abell, Ben M

    2009-12-01

    Tail-anchored (TA) proteins function in key cellular processes in eukaryotic cells, such as vesicle trafficking, protein translocation and regulation of transcription. They anchor to internal cell membranes by a C-terminal transmembrane domain, which also serves as a targeting sequence. Targeting occurs post-translationally, via pathways that are specific to the precursor, which makes TA proteins a model system for investigating post-translational protein targeting. Bioinformatics approaches have previously been used to identify potential TA proteins in yeast and humans, yet little is known about TA proteins in plants. The identification of plant TA proteins is important for extending the post-translational model system to plastids, in addition to general proteome characterization, and the identification of functional homologues characterized in other organisms. We identified 454 loci that potentially encode TA proteins in Arabidopsis, and combined published data with new localization experiments to assign localizations to 130 proteins, including 29 associated with plastids. By analysing the tail anchor sequences of characterized proteins, we have developed a tool for predicting localization and estimate that 138 TA proteins are localized to plastids.

  6. Quantitative characterization of the lateral distribution of membrane proteins within the lipid bilayer.

    PubMed Central

    Freire, E; Snyder, B

    1982-01-01

    The dependence of the lateral distribution of membrane proteins on the size, protein/lipoid molar ratio, and the magnitude of the interaction potentials has been investigated by computer modeling protein-lipid distributions with Monte Carlo calculations. These results have allowed us to develop a quantitative characterization of the distribution of membrane proteins and to correlate these distributions with experimental observables. The topological arrangement of protein domains, protein plus annular lipid domains, and free lipid domains is described in terms of radial distribution, pair connectedness, and cluster distribution functions. The radial distribution functions are used to measure the distribution of intermolecular distances between protein molecules, whereas the pair connectedness functions are used to estimate the physical extension of compositional domains. It is shown that, at characteristic protein/lipid molar ratios, previously isolated domains become connected, forming domain networks that extend over the entire membrane surface. These changes in the lateral connectivity of compositional domains are paralleled by changes in the calculated lateral diffusion coefficients and might have important implications for the regulation of diffusion controlled processes within the membrane. PMID:7074188

  7. Spatial distribution of proteins in the quagga mussel adhesive apparatus.

    PubMed

    Rees, David J; Hanifi, Arash; Manion, Joseph; Gantayet, Arpita; Sone, Eli D

    2016-01-01

    The invasive freshwater mollusc Dreissena bugensis (quagga mussel) sticks to underwater surfaces via a proteinacious 'anchor' (byssus), consisting of a series of threads linked to adhesive plaques. This adhesion results in the biofouling of crucial underwater industry infrastructure, yet little is known about the proteins responsible for the adhesion. Here the identification of byssal proteins extracted from freshly secreted byssal material is described. Several new byssal proteins were observed by gel electrophoresis. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to characterize proteins in different regions of the byssus, particularly those localized to the adhesive interface. Byssal plaques and threads contain in common a range of low molecular weight proteins, while several proteins with higher mass were observed only in the plaque. At the adhesive interface, a plaque-specific ~8.1 kDa protein had a relative increase in signal intensity compared to the bulk of the plaque, suggesting it may play a direct role in adhesion.

  8. Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions.

    PubMed

    Najibi, Seyed Morteza; Maadooliat, Mehdi; Zhou, Lan; Huang, Jianhua Z; Gao, Xin

    2017-01-01

    Recently, the study of protein structures using angular representations has attracted much attention among structural biologists. The main challenge is how to efficiently model the continuous conformational space of the protein structures based on the differences and similarities between different Ramachandran plots. Despite the presence of statistical methods for modeling angular data of proteins, there is still a substantial need for more sophisticated and faster statistical tools to model the large-scale circular datasets. To address this need, we have developed a nonparametric method for collective estimation of multiple bivariate density functions for a collection of populations of protein backbone angles. The proposed method takes into account the circular nature of the angular data using trigonometric spline which is more efficient compared to existing methods. This collective density estimation approach is widely applicable when there is a need to estimate multiple density functions from different populations with common features. Moreover, the coefficients of adaptive basis expansion for the fitted densities provide a low-dimensional representation that is useful for visualization, clustering, and classification of the densities. The proposed method provides a novel and unique perspective to two important and challenging problems in protein structure research: structure-based protein classification and angular-sampling-based protein loop structure prediction.

  9. CARd-3D: Carbon Distribution in 3D Structure Program for Globular Proteins.

    PubMed

    Ekambaram, Rajasekaran; Kannaiyan, Akila; Marimuthu, Vijayasarathy; Swaminathan, Vinobha Chinnaiah; Renganathan, Senthil; Perumal, Ananda Gopu

    2014-01-01

    Spatial arrangement of carbon in protein structure is analyzed here. Particularly, the carbon fractions around individual atoms are compared. It is hoped that it follows the principle of 31.45% carbon around individual atoms. The results reveal that globular protein's atoms follow this principle. A comparative study on monomer versus dimer reveal that carbon is better distributed in dimeric form than in its monomeric form. Similar study on solid versus liquid structures reveals that the liquid (NMR) structure has better carbon distribution over the corresponding solid (X-Ray) structure. The carbon fraction distributions in fiber and toxin protein are compared. Fiber proteins follow the principle of carbon fraction distribution. At the same time it has another broad spectrum of carbon distribution than in globular proteins. The toxin protein follows an abnormal carbon fraction distribution. The carbon fraction distribution plays an important role in deciding the structure and shape of proteins. It is hoped to help in understanding the protein folding and function.

  10. Species and tissue distribution of the regulatory protein of glucokinase.

    PubMed

    Vandercammen, A; Van Schaftingen, E

    1993-09-01

    Rat liver is known to contain a regulatory protein that inhibits glucokinase (hexokinase IV or D) competitively versus glucose. This inhibition is greatly reinforced by the presence of fructose 6-phosphate and antagonized by fructose 1-phosphate and by KCl. This protein was now measured in various rat tissues and in the livers of various species by the inhibition it exerts on rat liver glucokinase. Rat, mouse, rabbit, guinea-pig and pig liver, all of which contain glucokinase, also contained between 60 and 200 units/g of tissue of a regulatory protein displaying the properties mentioned above. By contrast, this protein could not be detected in cat, goat, chicken or trout liver, or in rat brain, heart, skeletal muscle, kidney and spleen, all tissues from which glucokinase is missing. Fructose 1-phosphate stimulated glucokinase in extracts of human liver, indicating the presence of regulatory protein. In addition, antibodies raised against rat regulatory protein allowed the detection of an approximately 60 kDa polypeptide in rat, guinea pig, rabbit and human liver. The livers of the toad Bufo marinus, of Xenopus laevis and of the turtle Pseudemys scripta elegans contained a regulatory protein similar to that of the rat, with, however, the major difference that it was not sensitive to fructose 6-phosphate or fructose 1-phosphate. In rat liver, the regulatory protein was detectable 4 days before birth. Its concentration increased afterwards to reach the adult level at day 30 of extrauterine life, whereas glucokinase only appeared after day 15. In the liver of the adult rat, starvation and streptozotocin-diabetes caused a 50-60% decrease in the concentration of regulatory protein after 7 days, whereas glucokinase activity fell to about 20% of its initial level. When 4-day-starved rats were refed, or when diabetic rats were treated with insulin, the concentration of regulatory protein slowly increased to reach about 85% of the control level after 3 days, whereas the

  11. iDriving (Intelligent Driving)

    SciTech Connect

    Malikopoulos, Andreas

    2012-09-17

    iDriving identifies the driving style factors that have a major impact on fuel economy. An optimization framework is used with the aim of optimizing a driving style with respect to these driving factors. A set of polynomial metamodels is constructed to reflect the responses produced in fuel economy by changing the driving factors. The optimization framework is used to develop a real-time feedback system, including visual instructions, to enable drivers to alter their driving styles in responses to actual driving conditions to improve fuel efficiency.

  12. [Distribution of Bt protein in transgenic cotton soils].

    PubMed

    Fu, Qing-Ling; Chen, Su-Wan; Hu, Hong-Qing; Li, Zhen; Han, Xiao-Fang; Wang, Pu

    2011-06-01

    A pot experiment with red soil, yellow brown soil, and yellow cinnamon soil was conducted to detect the Bt protein content in rhizosphere and non-rhizosphere soils at different growth stages of transgenic Bt cotton and common cotton by using enzyme linked immunosorbent assay (ELISA). With the planting of transgenic Bt cotton, the Bt protein content in rhizosphere soil was significantly higher than that in non-rhizosphere soil; while in common cotton soils, there was no significant difference in the Bt protein content between rhizosphere soil and non-rhizosphere soil. At bud stage of transgenic Bt cotton, the Bt protein content in rhizosphere soil was in the order of yellow cinnamon soil > yellow brown soil > red soil, being 144% 121%, and 238% of that in common cotton rhizosphere soil; at florescence stage of transgenic Bt cotton, the Bt protein content in rhizosphere soil was in the order of yellow brown soil > yellow cinnamon soil > red soil, being 156% , 116% , and 197% of that in common cotton rhizosphere soil, respectively. Regardless of planting Bt cotton or common cotton, the Bt protein content in rhizosphere and non-rhizosphere soils had an initial increase with the growth of cotton, peaked at florescence stage, and then decreased. Throughout the whole cotton growth period, the Bt protein content in transgenic Bt cotton rhizosphere soil was higher than that in Bt cotton non-rhizosphere soil, and also, higher than that in common cotton rhizosphere soil, indicating that transgenic Bt cotton could release its Bt protein to rhizosphere soil.

  13. Heterogeneous distribution of dye-labelled biomineralizaiton proteins in calcite crystals

    PubMed Central

    Liu, Chuang; Xie, Liping; Zhang, Rongqing

    2015-01-01

    Biominerals are highly ordered crystals mediated by organic matters especially proteins in organisms. However, how specific proteins are distributed inside biominerals are not well understood. In the present study, we use fluorescein isothiocyanate (FITC) to label extracted proteins from the shells of bivalve Pinctada fucata. By confocal laser scanning microscopy (CLSM), we observe a heterogeneous distribution of dye-labelled proteins inside synthetic calcite at the microscale. Proteins from the prismatic calcite layers accumulate at the edge of crystals while proteins from the nacreous aragonite layers accumulate at the center of crystals. Raman and X-ray powder diffraction show that both the proteins cannot alter the crystal phase. Scanning electron microscope demonstrates both proteins are able to affect the crystal morphology. This study may provide a direct approach for the visualization of protein distributions in crystals by small-molecule dye-labelled proteins as the additives in the crystallization process and improve our understanding of intracrystalline proteins distribution in biogenic calcites. PMID:26675363

  14. Link protein N-terminal peptide binds to bone morphogenetic protein (BMP) type II receptor and drives matrix protein expression in rabbit intervertebral disc cells.

    PubMed

    Wang, Zili; Weitzmann, M Neale; Sangadala, Sreedhara; Hutton, William C; Yoon, S Tim

    2013-09-27

    Intervertebral disc (IVD) degeneration and associated spinal disorders are leading sources of morbidity, and they can be responsible for chronic low back pain. Treatments for degenerative disc diseases continue to be a challenge. Intensive research is now focusing on promoting regeneration of degenerated discs by stimulating production of the disc matrix. Link protein N-terminal peptide (LPP) is a proteolytic fragment of link protein, an important cross-linker and stabilizer of the major structural components of cartilage, aggrecan and hyaluronan. In this study we investigated LPP action in rabbit primary intervertebral disc cells cultured ex vivo in a three-dimensional alginate matrix. Our data reveal that LPP promotes disc matrix production, which was evidenced by increased expression of the chondrocyte-specific transcription factor SOX9 and the extracellular matrix macromolecules aggrecan and collagen II. Using colocalization and pulldown studies we further document a noggin-insensitive direct peptide-protein association between LPP and BMP-RII. This association mediated Smad signaling that converges on BMP genes leading to expression of BMP-4 and BMP-7. Furthermore, through a cell-autonomous loop BMP-4 and BMP-7 intensified Smad1/5 signaling though a feedforward circuit involving BMP-RI, ultimately promoting expression of SOX9 and downstream aggrecan and collagen II genes. Our data define a complex regulatory signaling cascade initiated by LPP and suggest that LPP may be a useful therapeutic substitute for direct BMP administration to treat IVD degeneration and to ameliorate IVD-associated chronic low back pain.

  15. Link Protein N-terminal Peptide Binds to Bone Morphogenetic Protein (BMP) Type II Receptor and Drives Matrix Protein Expression in Rabbit Intervertebral Disc Cells*

    PubMed Central

    Wang, Zili; Weitzmann, M. Neale; Sangadala, Sreedhara; Hutton, William C.; Yoon, S. Tim

    2013-01-01

    Intervertebral disc (IVD) degeneration and associated spinal disorders are leading sources of morbidity, and they can be responsible for chronic low back pain. Treatments for degenerative disc diseases continue to be a challenge. Intensive research is now focusing on promoting regeneration of degenerated discs by stimulating production of the disc matrix. Link protein N-terminal peptide (LPP) is a proteolytic fragment of link protein, an important cross-linker and stabilizer of the major structural components of cartilage, aggrecan and hyaluronan. In this study we investigated LPP action in rabbit primary intervertebral disc cells cultured ex vivo in a three-dimensional alginate matrix. Our data reveal that LPP promotes disc matrix production, which was evidenced by increased expression of the chondrocyte-specific transcription factor SOX9 and the extracellular matrix macromolecules aggrecan and collagen II. Using colocalization and pulldown studies we further document a noggin-insensitive direct peptide-protein association between LPP and BMP-RII. This association mediated Smad signaling that converges on BMP genes leading to expression of BMP-4 and BMP-7. Furthermore, through a cell-autonomous loop BMP-4 and BMP-7 intensified Smad1/5 signaling though a feedforward circuit involving BMP-RI, ultimately promoting expression of SOX9 and downstream aggrecan and collagen II genes. Our data define a complex regulatory signaling cascade initiated by LPP and suggest that LPP may be a useful therapeutic substitute for direct BMP administration to treat IVD degeneration and to ameliorate IVD-associated chronic low back pain. PMID:23940040

  16. Dietary Protein in Older Adults: Adequate Daily Intake but Potential for Improved Distribution

    PubMed Central

    Cardon-Thomas, Danielle K.; Riviere, Timothy; Tieges, Zoë; Greig, Carolyn A.

    2017-01-01

    Daily distribution of dietary protein may be important in protecting against sarcopenia, specifically in terms of per meal amounts relative to a proposed threshold for maximal response. The aims of this study were to determine total and per meal protein intake in older adults, as well as identifying associations with physical activity and sedentary behavior. Three-day food diaries recorded protein intake in 38 participants. Protein distribution, coefficient of variation (CV), and per meal amounts were calculated. Accelerometry was used to collect physical activity data as well as volume and patterns of sedentary time. Average intake was 1.14 g·kg−1·day−1. Distribution was uneven (CV = 0.67), and 79% of participants reported <0.4 g·kg−1 protein content in at least 2/3 daily meals. Protein intake was significantly correlated with step count (r = 0.439, p = 0.007) and negatively correlated with sedentary time (r = −0.456, p = 0.005) and Gini index G, which describes the pattern of accumulation of sedentary time (r = −0.421, p = 0.011). Total daily protein intake was sufficient; however, distribution did not align with the current literature; increasing protein intake may help to facilitate optimization of distribution. Associations between protein and other risk factors for sarcopenia may also inform protective strategies. PMID:28241469

  17. Drugged Driving

    MedlinePlus

    ... Alerts Alcohol Club Drugs Cocaine Hallucinogens Heroin Inhalants Marijuana MDMA (Ecstasy/Molly) Methamphetamine Opioids Prescription Drugs & Cold ... in the past year. Middle Figure: Driving after marijuana use is more common than driving after alcohol ...

  18. Impaired Driving

    MedlinePlus

    Impaired driving is dangerous. It's the cause of more than half of all car crashes. It means operating a ... texting Having a medical condition which affects your driving For your safety and the safety of others, ...

  19. Dietary Protein Intake and Distribution Patterns of Well-Trained Dutch Athletes.

    PubMed

    Gillen, Jenna B; Trommelen, Jorn; Wardenaar, Floris C; Brinkmans, Naomi Y J; Versteegen, Joline J; Jonvik, Kristin L; Kapp, Christoph; de Vries, Jeanne; van den Borne, Joost J G C; Gibala, Martin J; van Loon, Luc J C

    2016-10-06

    Dietary protein intake should be optimized in all athletes to ensure proper recovery and enhance the skeletal muscle adaptive response to exercise training. In addition to total protein intake, the use of specific protein-containing food sources and the distribution of protein throughout the day are relevant for optimizing protein intake in athletes. In the present study, we examined the daily intake and distribution of various protein-containing food sources in a large cohort of strength, endurance and team-sport athletes. Well-trained male (n=327) and female (n=226) athletes completed multiple web-based 24-h dietary recalls over a 2-4 wk period. Total energy intake, the contribution of animal- and plant-based proteins to daily protein intake, and protein intake at six eating moments were determined. Daily protein intake averaged 108±33 and 90±24 g in men and women, respectively, which corresponded to relative intakes of 1.5±0.4 and 1.4±0.4 g/kg. Dietary protein intake was correlated with total energy intake in strength (r=0.71, p<0.001), endurance (r=0.79, p<0.001) and team-sport (r=0.77, p<0.001) athletes. Animal and plant-based sources of protein intake was 57% and 43%, respectively. The distribution of protein intake was 19% (19±8 g) at breakfast, 24% (25±13 g) at lunch and 38% (38±15 g) at dinner. Protein intake was below the recommended 20 g for 58% of athletes at breakfast, 36% at lunch and 8% at dinner. In summary, this survey of athletes revealed they habitually consume > 1.2 g protein/kg/d, but the distribution throughout the day may be suboptimal to maximize the skeletal muscle adaptive response to training.

  20. Composition and Molecular Weight Distribution of Carob Germ Proteins Fractions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biochemical properties of carob germ proteins were analyzed using a combination of selective extraction, reversed-phase high performance liquid chromatography (RP-HPLC), size exclusion chromatography coupled with multi-angle laser light scattering (SEC-MALS) and electrophoretic analysis. Using a mo...

  1. Physical distribution and characteristics of meat & bone meal protein

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Meat & bone meal (MBM) is a high-protein commodity produced by the rendering of fat from unmarketable animal tissue. Concerns related to bovine spongiform encephalopathy have progressively restricted MBM’s conventional use as a feed ingredient. Consequently, significant attention has focused on th...

  2. Hyperdimensional Analysis of Amino Acid Pair Distributions in Proteins

    PubMed Central

    Henriksen, Svend B.; Arnason, Omar; Söring, Jón; Petersen, Steffen B.

    2011-01-01

    Our manuscript presents a novel approach to protein structure analyses. We have organized an 8-dimensional data cube with protein 3D-structural information from 8706 high-resolution non-redundant protein-chains with the aim of identifying packing rules at the amino acid pair level. The cube contains information about amino acid type, solvent accessibility, spatial and sequence distance, secondary structure and sequence length. We are able to pose structural queries to the data cube using program ProPack. The response is a 1, 2 or 3D graph. Whereas the response is of a statistical nature, the user can obtain an instant list of all PDB-structures where such pair is found. The user may select a particular structure, which is displayed highlighting the pair in question. The user may pose millions of different queries and for each one he will receive the answer in a few seconds. In order to demonstrate the capabilities of the data cube as well as the programs, we have selected well known structural features, disulphide bridges and salt bridges, where we illustrate how the queries are posed, and how answers are given. Motifs involving cysteines such as disulphide bridges, zinc-fingers and iron-sulfur clusters are clearly identified and differentiated. ProPack also reveals that whereas pairs of Lys residues virtually never appear in close spatial proximity, pairs of Arg are abundant and appear at close spatial distance, contrasting the belief that electrostatic repulsion would prevent this juxtaposition and that Arg-Lys is perceived as a conservative mutation. The presented programs can find and visualize novel packing preferences in proteins structures allowing the user to unravel correlations between pairs of amino acids. The new tools allow the user to view statistical information and visualize instantly the structures that underpin the statistical information, which is far from trivial with most other SW tools for protein structure analysis. PMID:22174733

  3. Amino acid composition, molecular weight distribution and gel electrophoresis of walnut (Juglans regia L.) proteins and protein fractionations.

    PubMed

    Mao, Xiaoying; Hua, Yufei; Chen, Guogang

    2014-01-27

    As a by-product of oil production, walnut proteins are considered as an additional source of plant protein for human food. To make full use of the protein resource, a comprehensive understanding of composition and characteristics of walnut proteins are required. Walnut proteins have been fractionated and characterized in this study. Amino acid composition, molecular weight distribution and gel electrophoresis of walnut proteins and protein fractionations were analyzed. The proteins were sequentially separated into four fractions according to their solubility. Glutelin was the main component of the protein extract. The content of glutelin, albumin, globulin and prolamin was about 72.06%, 7.54%, 15.67% and 4.73% respectively. Glutelin, albumin and globulin have a balanced content of essential amino acids, except for methionine, with respect to the FAO pattern recommended for adults. SDS-PAGE patterns of albumin, globulin and glutelin showed several polypeptides with molecular weights 14.4 to 66.2 kDa. The pattern of walnut proteins in two-dimension electrophoresis (2-DE) showed that the isoelectric point was mainly in the range of 4.8-6.8. The results of size exclusion chromatogram indicated molecular weight of the major components of walnut proteins were between 3.54 and 81.76 kDa.

  4. Universal protein distributions in a model of cell growth and division

    NASA Astrophysics Data System (ADS)

    Brenner, Naama; Newman, C. M.; Osmanović, Dino; Rabin, Yitzhak; Salman, Hanna; Stein, D. L.

    2015-10-01

    Protein distributions measured under a broad set of conditions in bacteria and yeast were shown to exhibit a common skewed shape, with variances depending quadratically on means. For bacteria these properties were reproduced by temporal measurements of protein content, showing accumulation and division across generations. Here we present a stochastic growth-and-division model with feedback which captures these observed properties. The limiting copy number distribution is calculated exactly, and a single parameter is found to determine the distribution shape and the variance-to-mean relation. Estimating this parameter from bacterial temporal data reproduces the measured distribution shape with high accuracy and leads to predictions for future experiments.

  5. Amount and distribution of dietary protein affects clinical response to levodopa in Parkinson's disease.

    PubMed

    Carter, J H; Nutt, J G; Woodward, W R; Hatcher, L F; Trotman, T L

    1989-04-01

    Reducing dietary protein improves the effectiveness of levodopa (LD) but the most effective distribution of a low-protein diet (0.8 g/kg) is unclear. We compared a 1.6 g/kg protein diet, a 0.8 g/kg diet with protein evenly distributed between meals, and a 0.8 g/kg diet with protein restricted to the evening meal in 5 parkinsonian patients with motor fluctuations. We monitored clinical response, plasma LD, and plasma large amino acids (LNAAs) hourly throughout the day. Mean "on" times were 51% (1.6 g/kg diet), 67% (0.8 g/kg evenly distributed), and 77% (0.8 g/kg restricted). Hourly averages of plasma LD did not differ between the diets. The mean plasma LNAAs were 732 nmol/ml (1.6 g/kg diet), 640 (0.8 g/kg distributed), and 542 (0.8 g/kg restricted), and the diurnal pattern reflected the distribution of protein intake. In conclusion, the amount and distribution of dietary protein affect clinical response to LD. These effects are not related to LD absorption but are explained by the variation in plasma LNAAs.

  6. Universal distribution of mutational effects on protein stability, uncoupling of protein robustness from sequence evolution and distinct evolutionary modes of prokaryotic and eukaryotic proteins

    NASA Astrophysics Data System (ADS)

    Faure, Guilhem; Koonin, Eugene V.

    2015-05-01

    Robustness to destabilizing effects of mutations is thought of as a key factor of protein evolution. The connections between two measures of robustness, the relative core size and the computationally estimated effect of mutations on protein stability (ΔΔG), protein abundance and the selection pressure on protein-coding genes (dN/dS) were analyzed for the organisms with a large number of available protein structures including four eukaryotes, two bacteria and one archaeon. The distribution of the effects of mutations in the core on protein stability is universal and indistinguishable in eukaryotes and bacteria, centered at slightly destabilizing amino acid replacements, and with a heavy tail of more strongly destabilizing replacements. The distribution of mutational effects in the hyperthermophilic archaeon Thermococcus gammatolerans is significantly shifted toward strongly destabilizing replacements which is indicative of stronger constraints that are imposed on proteins in hyperthermophiles. The median effect of mutations is strongly, positively correlated with the relative core size, in evidence of the congruence between the two measures of protein robustness. However, both measures show only limited correlations to the expression level and selection pressure on protein-coding genes. Thus, the degree of robustness reflected in the universal distribution of mutational effects appears to be a fundamental, ancient feature of globular protein folds whereas the observed variations are largely neutral and uncoupled from short term protein evolution. A weak anticorrelation between protein core size and selection pressure is observed only for surface residues in prokaryotes but a stronger anticorrelation is observed for all residues in eukaryotic proteins. This substantial difference between proteins of prokaryotes and eukaryotes is likely to stem from the demonstrable higher compactness of prokaryotic proteins.

  7. Universal distribution of mutational effects on protein stability, uncoupling of protein robustness from sequence evolution and distinct evolutionary modes of prokaryotic and eukaryotic proteins.

    PubMed

    Faure, Guilhem; Koonin, Eugene V

    2015-04-30

    Robustness to destabilizing effects of mutations is thought of as a key factor of protein evolution. The connections between two measures of robustness, the relative core size and the computationally estimated effect of mutations on protein stability (ΔΔG), protein abundance and the selection pressure on protein-coding genes (dN/dS) were analyzed for the organisms with a large number of available protein structures including four eukaryotes, two bacteria and one archaeon. The distribution of the effects of mutations in the core on protein stability is universal and indistinguishable in eukaryotes and bacteria, centered at slightly destabilizing amino acid replacements, and with a heavy tail of more strongly destabilizing replacements. The distribution of mutational effects in the hyperthermophilic archaeon Thermococcus gammatolerans is significantly shifted toward strongly destabilizing replacements which is indicative of stronger constraints that are imposed on proteins in hyperthermophiles. The median effect of mutations is strongly, positively correlated with the relative core size, in evidence of the congruence between the two measures of protein robustness. However, both measures show only limited correlations to the expression level and selection pressure on protein-coding genes. Thus, the degree of robustness reflected in the universal distribution of mutational effects appears to be a fundamental, ancient feature of globular protein folds whereas the observed variations are largely neutral and uncoupled from short term protein evolution. A weak anticorrelation between protein core size and selection pressure is observed only for surface residues in prokaryotes but a stronger anticorrelation is observed for all residues in eukaryotic proteins. This substantial difference between proteins of prokaryotes and eukaryotes is likely to stem from the demonstrable higher compactness of prokaryotic proteins.

  8. Haemophilus influenzae stores and distributes hemin by using protein E.

    PubMed

    Al Jubair, Tamim; Singh, Birendra; Fleury, Christophe; Blom, Anna M; Mörgelin, Matthias; Thunnissen, Marjolein M; Riesbeck, Kristian

    2014-07-01

    The human pathogen Haemophilus influenzae causes mainly respiratory tract infections such as acute otitis media in children and exacerbations in patients with chronic obstructive pulmonary disease. We recently revealed the crystal structure of H. influenzeae protein E (PE), a multifunctional adhesin that is involved in direct interactions with lung epithelial cells and host proteins. Based upon the PE structure we here suggest a hypothetical binding pocket that is compatible in size with a hemin molecule. An H. influenzae mutant devoid of PE bound significantly less hemin in comparison to the PE-expressing wild type counterpart. In addition, E. coli expressing PE at the surface resulted in a hemin-binding phenotype. An interaction between hemin and recombinant soluble PE was also demonstrated by native-PAGE and UV-visible spectrophotometry. Surface plasmon resonance revealed an affinity (Kd) of 1.6 × 10(-6)M for the hemin-PE interaction. Importantly, hemin that was bound to PE at the H. influenzae surface, was donated to co-cultured luciferase-expressing H. influenzae that were starved of hemin. When hemin is bound to PE it thus may serve as a storage pool for H. influenzae. To our knowledge this is the first report showing that H. influenzae can share hemin via a surface-located outer membrane protein.

  9. Lattice models, packing density, and Boltzmann-like distribution of cavities in proteins.

    PubMed

    Rashin, Alexander A; Rashin, Abraham H L

    2005-02-15

    A model reproducing the experimental Boltzmann-like distribution of empty cavity sizes in proteins is introduced. Proteins are represented by lattices of different dimensionalities, corresponding to different numbers of nearest neighbor contacts. Small cavities emerge and join into larger ones in a random process that can be related to random mutations. Simulations of cavity creation are performed under the constraint of a limiting total packing density. Cavities sufficiently large (20 A(3) or more), that they might accommodate at least one additional methyl group produced by a mutation, are counted and compared to the distribution of cavities according to their sizes from protein statistics. The distributions calculated with this very simple model within a realistic range of packing densities are in good agreement with the empirical cavity distribution. The results suggest that the Boltzmann-like distribution of cavities in proteins might be affected by a mechanism controlled by limiting packing density and maximum allowed protein destabilization. This supports an earlier suggestion that the agreement between the free energies of cavity formation from the mutational experiments and from the statistics of the empty cavity distribution in X-ray protein structures is nonfortuitous. A possible relation of the suggested model to the Boltzmann hypothesis is discussed.

  10. Mia40 is a trans-site receptor that drives protein import into the mitochondrial intermembrane space by hydrophobic substrate binding

    PubMed Central

    Peleh, Valentina; Cordat, Emmanuelle; Herrmann, Johannes M

    2016-01-01

    Many proteins of the mitochondrial IMS contain conserved cysteines that are oxidized to disulfide bonds during their import. The conserved IMS protein Mia40 is essential for the oxidation and import of these proteins. Mia40 consists of two functional elements: an N-terminal cysteine-proline-cysteine motif conferring substrate oxidation, and a C-terminal hydrophobic pocket for substrate binding. In this study, we generated yeast mutants to dissect both Mia40 activities genetically and biochemically. Thereby we show that the substrate-binding domain of Mia40 is both necessary and sufficient to promote protein import, indicating that trapping by Mia40 drives protein translocation. An oxidase-deficient Mia40 mutant is inviable, but can be partially rescued by the addition of the chemical oxidant diamide. Our results indicate that Mia40 predominantly serves as a trans-site receptor of mitochondria that binds incoming proteins via hydrophobic interactions thereby mediating protein translocation across the outer membrane by a ‘holding trap’ rather than a ‘folding trap’ mechanism. DOI: http://dx.doi.org/10.7554/eLife.16177.001 PMID:27343349

  11. Effect of mahlep on molecular weight distribution of cookie flour gluten proteins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Size Exclusion-High performance Chromatography (SE-HPLC) has been extensively used in molecular weight distribution analysis of wheat proteins. In this study the protein analysis was conducted on different cookie dough blends with different percentages of some ingredients. The mean chromatography ...

  12. The Measurement and Interpretation of Dietary Protein Distribution During a Rugby Preseason.

    PubMed

    MacKenzie, Kristen; Slater, Gary; King, Neil; Byrne, Nuala

    2015-08-01

    Evidence suggests that increasing protein distribution may be desirable to promote muscle protein synthesis (MPS) in combination with resistance exercise. However, there is a threshold above which additional protein consumption has limited benefit for MPS and may promote protein loss due to increased oxidation. This study aimed to measure daily protein intake and protein distribution in a cohort of rugby players. Twenty-five developing elite rugby union athletes (20.5 ± 2.3 years, 100.2 ± 13.3 kg, 184.4 ± 7.4 cm) were assessed at the start and end of a rugby preseason. Using a 7-day food diary the reported daily protein intake was 2.2 ± 0.7 g · kg · day(-1) which exceeds daily recommendations. The reported carbohydrate intake was 3.6 ± 1.3 g · kg · day(-1) which may reflect a suboptimal intake or dietary underreporting. In general, the rugby athletes were regularly consuming more than 20 g of protein; 3.8 ± 0.9 times per day (68 ± 18% of eating occasions). In addition to documenting current dietary intakes, an excess protein estimation score was calculated to determine how frequently the rugby athletes consumed protein above a known effective dose with a margin of error. 2.0 ± 0.9 eating occasions contained protein in excess of doses (20 g) known to promote MPS. Therefore, it is currently unclear whether the consumption of regular large doses of protein will benefit rugby athletes via increasing protein distribution, or whether high protein intakes may have unintended effects including a reduction in carbohydrate and/or energy intake.

  13. Stone former urine proteome demonstrates a cationic shift in protein distribution compared to normal.

    PubMed

    Kolbach-Mandel, Ann M; Mandel, Neil S; Hoffmann, Brian R; Kleinman, Jack G; Wesson, Jeffrey A

    2017-03-17

    Many urine proteins are found in calcium oxalate stones, yet decades of research have failed to define the role of urine proteins in stone formation. This urine proteomic study compares the relative amounts of abundant urine proteins between idiopathic calcium oxalate stone forming and non-stone forming (normal) cohorts to identify differences that might correlate with disease. Random mid-morning urine samples were collected following informed consent from 25 stone formers and 14 normal individuals. Proteins were isolated from urine using ultrafiltration. Urine proteomes for each sample were characterized using label-free spectral counting mass spectrometry, so that urine protein relative abundances could be compared between the two populations. A total of 407 unique proteins were identified with the 38 predominant proteins accounting for >82% of all sample spectral counts. The most highly abundant proteins were equivalent in stone formers and normals, though significant differences were observed in a few moderate abundance proteins (immunoglobulins, transferrin, and epidermal growth factor), accounting for 13 and 10% of the spectral counts, respectively. These proteins contributed to a cationic shift in protein distribution in stone formers compared to normals (22% vs. 18%, p = 0.04). Our data showing only small differences in moderate abundance proteins suggest that no single protein controls stone formation. Observed increases in immunoglobulins and transferrin suggest increased inflammatory activity in stone formers, but cannot distinguish cause from effect in stone formation. The observed cationic shift in protein distribution would diminish protein charge stabilization, which could lead to protein aggregation and increased risk for crystal aggregation.

  14. Analysis of temperature factor distribution in high-resolution protein structures.

    PubMed Central

    Parthasarathy, S.; Murthy, M. R.

    1997-01-01

    The temperature factors obtained from X-ray refinement of proteins at high resolution show large variations from one structure to another. However, the B-values expressed in units of standard deviation about their mean value (B'-factor) at the C alpha atoms show remarkably characteristic frequency distribution. In all of the 110 proteins examined in this study, the frequency distribution exhibited a bimodal distribution. The peaks in the B'-factor frequency distribution occur at -1.1 and 0.4 for a bin size of 0.5. The peak at lower temperature factor corresponds largely to buried residues, whereas the peak at larger value corresponds to exposed residues. The distribution could be accurately described as a superposition of two Gaussian functions. The parameters describing the distribution are therefore characteristic of protein structures. The frequency distribution for a given amino acid over all the proteins also shows a similar bimodal distribution, although the areas under the two Gaussians differ from one amino acid to another. The area under the frequency distribution curve for any interval in B'-factor represents the propensity of the amino acid to occur in that interval. This propensity is related both to the hydrophilicity/hydrophobicity of the residue and the tendency of the residue to impose a different degree of rigidity on the polypeptide chain. The frequency distribution of stretches of high B'-factors departs appreciably from that expected for a random distribution. The correlation in the B-values of sequentially proximal residues is probably responsible for the bimodal distribution. PMID:9416605

  15. Geochemistry and Mixing Drive the Spatial Distribution of Free-Living Archaea and Bacteria in Yellowstone Lake

    PubMed Central

    Kan, Jinjun; Clingenpeel, Scott; Dow, Charles L.; McDermott, Timothy R.; Macur, Richard E.; Inskeep, William P.; Nealson, Kenneth H.

    2016-01-01

    Yellowstone Lake, the largest subalpine lake in the United States, harbors great novelty and diversity of Bacteria and Archaea. Size-fractionated water samples (0.1–0.8, 0.8–3.0, and 3.0–20 μm) were collected from surface photic zone, deep mixing zone, and vent fluids at different locations in the lake by using a remotely operated vehicle (ROV). Quantification with real-time PCR indicated that Bacteria dominated free-living microorganisms with Bacteria/Archaea ratios ranging from 4037:1 (surface water) to 25:1 (vent water). Microbial population structures (both Bacteria and Archaea) were assessed using 454-FLX sequencing with a total of 662,302 pyrosequencing reads for V1 and V2 regions of 16S rRNA genes. Non-metric multidimensional scaling (NMDS) analyses indicated that strong spatial distribution patterns existed from surface to deep vents for free-living Archaea and Bacteria in the lake. Along with pH, major vent-associated geochemical constituents including CH4, CO2, H2, DIC (dissolved inorganic carbon), DOC (dissolved organic carbon), SO42-, O2 and metals were likely the major drivers for microbial population structures, however, mixing events occurring in the lake also impacted the distribution patterns. Distinct Bacteria and Archaea were present among size fractions, and bigger size fractions included particle-associated microbes (> 3 μm) and contained higher predicted operational taxonomic unit richness and microbial diversities (genus level) than free-living ones (<0.8 μm). Our study represents the first attempt at addressing the spatial distribution of Bacteria and Archaea in Yellowstone Lake, and our results highlight the variable contribution of Archaea and Bacteria to the hydrogeochemical-relevant metabolism of hydrogen, carbon, nitrogen, and sulfur. PMID:26973602

  16. Geochemistry and Mixing Drive the Spatial Distribution of Free-Living Archaea and Bacteria in Yellowstone Lake.

    PubMed

    Kan, Jinjun; Clingenpeel, Scott; Dow, Charles L; McDermott, Timothy R; Macur, Richard E; Inskeep, William P; Nealson, Kenneth H

    2016-01-01

    Yellowstone Lake, the largest subalpine lake in the United States, harbors great novelty and diversity of Bacteria and Archaea. Size-fractionated water samples (0.1-0.8, 0.8-3.0, and 3.0-20 μm) were collected from surface photic zone, deep mixing zone, and vent fluids at different locations in the lake by using a remotely operated vehicle (ROV). Quantification with real-time PCR indicated that Bacteria dominated free-living microorganisms with Bacteria/Archaea ratios ranging from 4037:1 (surface water) to 25:1 (vent water). Microbial population structures (both Bacteria and Archaea) were assessed using 454-FLX sequencing with a total of 662,302 pyrosequencing reads for V1 and V2 regions of 16S rRNA genes. Non-metric multidimensional scaling (NMDS) analyses indicated that strong spatial distribution patterns existed from surface to deep vents for free-living Archaea and Bacteria in the lake. Along with pH, major vent-associated geochemical constituents including CH4, CO2, H2, DIC (dissolved inorganic carbon), DOC (dissolved organic carbon), SO4 (2-), O2 and metals were likely the major drivers for microbial population structures, however, mixing events occurring in the lake also impacted the distribution patterns. Distinct Bacteria and Archaea were present among size fractions, and bigger size fractions included particle-associated microbes (> 3 μm) and contained higher predicted operational taxonomic unit richness and microbial diversities (genus level) than free-living ones (<0.8 μm). Our study represents the first attempt at addressing the spatial distribution of Bacteria and Archaea in Yellowstone Lake, and our results highlight the variable contribution of Archaea and Bacteria to the hydrogeochemical-relevant metabolism of hydrogen, carbon, nitrogen, and sulfur.

  17. Pile Driving

    NASA Technical Reports Server (NTRS)

    1987-01-01

    Machine-oriented structural engineering firm TERA, Inc. is engaged in a project to evaluate the reliability of offshore pile driving prediction methods to eventually predict the best pile driving technique for each new offshore oil platform. Phase I Pile driving records of 48 offshore platforms including such information as blow counts, soil composition and pertinent construction details were digitized. In Phase II, pile driving records were statistically compared with current methods of prediction. Result was development of modular software, the CRIPS80 Software Design Analyzer System, that companies can use to evaluate other prediction procedures or other data bases.

  18. Monte Carlo calculations of energy deposition distributions of electrons below 20 keV in protein.

    PubMed

    Tan, Zhenyu; Liu, Wei

    2014-05-01

    The distributions of energy depositions of electrons in semi-infinite bulk protein and the radial dose distributions of point-isotropic mono-energetic electron sources [i.e., the so-called dose point kernel (DPK)] in protein have been systematically calculated in the energy range below 20 keV, based on Monte Carlo methods. The ranges of electrons have been evaluated by extrapolating two calculated distributions, respectively, and the evaluated ranges of electrons are compared with the electron mean path length in protein which has been calculated by using electron inelastic cross sections described in this work in the continuous-slowing-down approximation. It has been found that for a given energy, the electron mean path length is smaller than the electron range evaluated from DPK, but it is large compared to the electron range obtained from the energy deposition distributions of electrons in semi-infinite bulk protein. The energy dependences of the extrapolated electron ranges based on the two investigated distributions are given, respectively, in a power-law form. In addition, the DPK in protein has also been compared with that in liquid water. An evident difference between the two DPKs is observed. The calculations presented in this work may be useful in studies of radiation effects on proteins.

  19. Further evidence that interfacial water is the main "driving force" of protein dynamics: a neutron scattering study on perdeuterated C-phycocyanin.

    PubMed

    Combet, Sophie; Zanotti, Jean-Marc

    2012-04-14

    The fundamental role of hydration water (also called interfacial water) is widely recognized in protein flexibility, especially in the existence of the so-called protein "dynamical transition" at around 220 K. In the present study, we take advantage of perdeuterated C-phycocyanin (CPC) and elastic incoherent neutron scattering (EINS) to distinguish between protein dynamics and interfacial water dynamics. Powders of hydrogenated (hCPC) and perdeuterated (dCPC) CPC protein have been hydrated, respectively, with D(2)O or H(2)O and measured by EINS to separately probe protein dynamics (hCPC/D(2)O) and water dynamics (dCPC/H(2)O) at different time- and length-scales. We find that "fast" (<20 ps) local mean-square displacements (MSD) of both protein and interfacial water coincide all along the temperature range, with the same dynamical transition temperature at ~220 K. On higher resolution (<400 ps), two different types of motions can be separated: (i) localized motions with the same amplitude for CPC and hydration water and two transitions at ~170 and ~240 K for both; (ii) large scale fluctuations exhibiting for both water molecules and CPC protein a single transition at ~240 K, with a significantly higher amplitude for the interfacial water than for CPC. Moreover, by comparing these motions with bulk water MSD measured under the same conditions, we show no coupling between bulk water dynamics and protein dynamics all along the temperature range. These results show that interfacial water is the main "driving force" governing both local and large scale motions in proteins.

  20. Fast wave current drive

    SciTech Connect

    Goree, J.; Ono, M.; Colestock, P.; Horton, R.; McNeill, D.; Park, H.

    1985-07-01

    Fast wave current drive is demonstrated in the Princeton ACT-I toroidal device. The fast Alfven wave, in the range of high ion-cyclotron harmonics, produced 40 A of current from 1 kW of rf power coupled into the plasma by fast wave loop antenna. This wave excites a steady current by damping on the energetic tail of the electron distribution function in the same way as lower-hybrid current drive, except that fast wave current drive is appropriate for higher plasma densities.

  1. Effect of pH on protein distribution in electrospun PVA/BSA composite nanofibers.

    PubMed

    Tang, Christina; Ozcam, A Evren; Stout, Brendon; Khan, Saad A

    2012-05-14

    We examine the protein distribution within an electrospun polymer nanofiber using polyvinyl alcohol and bovine serum albumin as a model system. We hypothesize that the location of the protein within the nanofiber can be controlled by carefully selecting the pH and the applied polarity of the electric field as the pH affects the net charge on the proteins. Using fluorescently labeled BSA and surface analysis, we observe that the distribution of BSA is affected by the pH of the electrospinning solution. Therefore, we further probe the relevant forces on the protein in solution during electrospinning. The role of hydrodynamic friction was assessed using glutaraldehyde and HCl as a tool to modify the viscosity of the solution during electrospinning. By varying the pH and the polarity of the applied electric field, we evaluated the effects of electrostatic forces and dielectrophoresis on the protein during fiber formation. We surmise that electrostatic forces and hydrodynamic friction are insignificant relative to dielectrophoretic forces; therefore, it is possible to separate species in a blend using polarizability contrast. A coaxial distribution of protein in the core can be obtained by electrospinning at the isoelectric point of the protein, whereas surface enrichment can be obtained when the protein carries a net charge.

  2. Distribution of PASTA domains in penicillin-binding proteins and serine/threonine kinases of Actinobacteria.

    PubMed

    Ogawara, Hiroshi

    2016-09-01

    PASTA domains (penicillin-binding protein and serine/threonine kinase-associated domains) have been identified in penicillin-binding proteins and serine/threonine kinases of Gram-positive Firmicutes and Actinobacteria. They are believed to bind β-lactam antibiotics, and be involved in peptidoglycan metabolism, although their biological function is not definitively clarified. Actinobacteria, especially Streptomyces species, are distinct in that they undergo complex cellular differentiation and produce various antibiotics including β-lactams. This review focuses on the distribution of PASTA domains in penicillin-binding proteins and serine/threonine kinases in Actinobacteria. In Actinobacteria, PASTA domains are detectable exclusively in class A but not in class B penicillin-binding proteins, in sharp contrast to the cases in other bacteria. In penicillin-binding proteins, PASTA domains distribute independently from taxonomy with some distribution bias. Particularly interesting thing is that no Streptomyces species have penicillin-binding protein with PASTA domains. Protein kinases in Actinobacteria possess 0 to 5 PASTA domains in their molecules. Protein kinases in Streptomyces can be classified into three groups: no PASTA domain, 1 PASTA domain and 4 PASTA domain-containing groups. The 4 PASTA domain-containing groups can be further divided into two subgroups. The serine/threonine kinases in different groups may perform different functions. The pocket region in one of these subgroup is more dense and extended, thus it may be involved in binding of ligands like β-lactams more efficiently.

  3. Distracted driving

    MedlinePlus

    ... the road Your hands on the wheel Your mind on driving Distracted driving occurs when something gets in the way of you doing all 3 things. Examples include: Talking on a cell phone Reading or sending text messages Eating and drinking Grooming ( ...

  4. Methods for developing time-series climate surfaces to drive topographically distributed energy- and water-balance models

    USGS Publications Warehouse

    Susong, D.; Marks, D.; Garen, D.

    1999-01-01

    Topographically distributed energy- and water-balance models can accurately simulate both the development and melting of a seasonal snowcover in the mountain basins. To do this they require time-series climate surfaces of air temperature, humidity, wind speed, precipitation, and solar and thermal radiation. If data are available, these parameters can be adequately estimated at time steps of one to three hours. Unfortunately, climate monitoring in mountain basins is very limited, and the full range of elevations and exposures that affect climate conditions, snow deposition, and melt is seldom sampled. Detailed time-series climate surfaces have been successfully developed using limited data and relatively simple methods. We present a synopsis of the tools and methods used to combine limited data with simple corrections for the topographic controls to generate high temporal resolution time-series images of these climate parameters. Methods used include simulations, elevational gradients, and detrended kriging. The generated climate surfaces are evaluated at points and spatially to determine if they are reasonable approximations of actual conditions. Recommendations are made for the addition of critical parameters and measurement sites into routine monitoring systems in mountain basins.Topographically distributed energy- and water-balance models can accurately simulate both the development and melting of a seasonal snowcover in the mountain basins. To do this they require time-series climate surfaces of air temperature, humidity, wind speed, precipitation, and solar and thermal radiation. If data are available, these parameters can be adequately estimated at time steps of one to three hours. Unfortunately, climate monitoring in mountain basins is very limited, and the full range of elevations and exposures that affect climate conditions, snow deposition, and melt is seldom sampled. Detailed time-series climate surfaces have been successfully developed using limited

  5. Interfacial protein engineering for spray-dried emulsions - part I: effects on protein distribution and physical properties.

    PubMed

    Moisio, Timo; Damerau, Annelie; Lampi, Anna-Maija; Piironen, Vieno; Forssell, Pirkko; Partanen, Riitta

    2014-02-01

    Distribution of protein and oil in aqueous and spray-dried emulsions and the effect of protein cross-linking on emulsion properties and matrix-water interactions were investigated. Sodium caseinate and sunflower oil were used to make emulsions which were spray dried using maltodextrin as a wall material. 3% Na-caseinate concentration showed optimum emulsion and process stability as observed in CLSM images, droplet size data and in the amount of heptane-extractable oil from spray-dried emulsions. Transglutaminase cross-linking prior to emulsification slightly increased the amount of protein both on the oil droplet interface and on the particle surface as confirmed by analysis of continuous phase protein in the feed emulsion and by XPS measurements from the powder surface. DSC and water sorption measurements were used to study the physical state of the matrix. Glass transition occurred between RH 54% and 75% at room temperature and it was not affected by cross-linking.

  6. What do metabolic rates tell us about thermal niches? Mechanisms driving crayfish distributions along an altitudinal gradient.

    PubMed

    Stoffels, Rick J; Richardson, Adam J; Vogel, Matthew T; Coates, Simon P; Müller, Warren J

    2016-01-01

    Humans are rapidly altering thermal landscapes, so a central challenge to organismal ecologists is to better understand the thermal niches of ectotherms. However, there is much disagreement over how we should go about this. Some ecologists assume that a statistical model of abundance as a function of habitat temperature provides a sufficient approximation of the thermal niche, but ecophysiologists have shown that the relationship between fitness and temperature can be complicated, and have stressed the need to elucidate the causal mechanisms underlying the response of species to thermal change. Towards this end, we studied the distribution of two crayfishes, Euastacus woiwuru and Euastacus armatus, along an altitudinal gradient, and for both species conducted experiments to determine the temperature-dependence of: (1) aerobic scope (the difference between maximum and basal metabolic rate; purported to be a proxy of the thermal niche); and (2) burst locomotor performance (primarily fuelled using anaerobic pathways). E. woiwuru occupied cooler habitats than E. armatus, but we found no difference in aerobic scope between these species. In contrast, locomotor performance curves differed significantly and strongly between species, with peak locomotor performances of E. woiwuru and E. armatus occurring at ~10 and ~18 °C, respectively. Crayfish from different thermal landscapes may have similar aerobic thermal performance curves but different anaerobic thermal performance curves. Our results support a growing body of literature implying different components of ectotherm fitness have different thermal performance curves, and further challenge our understanding of the ecology and evolution of thermal niches.

  7. Rim formation is not a prerequisite for distribution of cone photoreceptor outer segment proteins

    PubMed Central

    Conley, Shannon M.; Al-Ubaidi, Muayyad R.; Han, Zongchao; Naash, Muna I.

    2014-01-01

    Retinal degeneration slow (RDS/PRPH2) is critical for the formation of the disc/lamella rim in photoreceptor outer segments (OSs), but plays a different role in rods vs. cones. Without RDS, rods fail to form OSs, however, cones lacking RDS (in the rds−/−/Nrl−/−) exhibit balloon-like OSs devoid of lamellae. We show that distribution of most proteins in the lamella and PM domains is preserved even in the absence of RDS, rim, and lamella structures. However, the rim protein prominin-1 exhibits altered trafficking and OS localization, suggesting that proper targeting and distribution of rim proteins may require RDS. Our ultrastructural studies show that in cones, OS formation is initiated by the growth of opsin-containing membrane with RDS-mediated rim formation as a secondary step. This is directly opposite to rods and significantly advances our understanding of the role of the rim in cone OS morphogenesis. Furthermore, our results suggest that the unique folded lamella architecture of the cone OS may maximize density or proximity of phototransduction proteins, but is not required for OS function or for protein distribution and retention in different membrane domains.—Conley, S. M., Al-Ubaidi, M. R., Han, Z., Naash, M. I. Rim formation is not a prerequisite for distribution of cone photoreceptor outer segment proteins. PMID:24736412

  8. c-myc protein in normal tissue. Effects of fixation on its apparent subcellular distribution.

    PubMed Central

    Loke, S. L.; Neckers, L. M.; Schwab, G.; Jaffe, E. S.

    1988-01-01

    The c-myc protein is thought to be a DNA-associated nuclear protein. However, immunohistochemical studies on normal or tumor tissues have shown conflicting findings on its subcellular distribution. By using various fixation procedures on cytospin preparations of HL60 cells, the authors found the subcellular distribution of the c-myc protein to be dependent on the method of fixation. When studying mouse tissues in frozen sections using a biotinylated monoclonal antibody against the c-myc protein, they found the protein to be widely distributed in various normal adult mouse tissues, in most cases localized to the nucleus. However, when these tissues were studied after formalin fixation and paraffin embedding, a loss of nuclear staining was observed concurrent with the appearance of c-myc protein immunoreactivity in the cytoplasm. It is concluded that immunohistochemical studies on the expression of this oncogene should take into consideration the effects of fixation when its subcellular distribution is being examined. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 PMID:3281469

  9. Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins.

    PubMed

    Nguyen, Bao Linh; Pettitt, B Montgomery

    2015-04-14

    The proximal distribution of water around proteins is a convenient method of quantifying solvation. We consider the effect of charged and sulfur-containing amino acid side-chain atoms on the proximal radial distribution function (pRDF) of water molecules around proteins using side-chain analogs. The pRDF represents the relative probability of finding any solvent molecule at a distance from the closest or surface perpendicular protein atom. We consider the near-neighbor distribution. Previously, pRDFs were shown to be universal descriptors of the water molecules around C, N, and O atom types across hundreds of globular proteins. Using averaged pRDFs, a solvent density around any globular protein can be reconstructed with controllable relative error. Solvent reconstruction using the additional information from charged amino acid side-chain atom types from both small models and protein averages reveals the effects of surface charge distribution on solvent density and improves the reconstruction errors relative to simulation. Solvent density reconstructions from the small-molecule models are as effective and less computationally demanding than reconstructions from full macromolecular models in reproducing preferred hydration sites and solvent density fluctuations.

  10. The promoter of brain-specific angiogenesis inhibitor 1-associated protein 4 drives developmentally targeted transgene expression mainly in adult cerebral cortex and hippocampus.

    PubMed

    Kim, Mi-Young; Ahn, Kyu Youn; Lee, Seon Min; Koh, Jeong Tae; Chun, Byeong Jo; Bae, Choon Sang; Lee, Kee Sook; Kim, Kyung Keun

    2004-05-21

    Restricting transgene expression to specific cell types and maintaining long-term expression are major goals for gene therapy. Previously, we cloned brain-specific angiogenesis inhibitor 1-associated protein 4 (BAI1-AP4), a novel brain-specific protein that interacts with BAI1, and found that it was developmentally upregulated in the adult brain. In this report, we isolated 5 kb of the 5' upstream sequence of the mouse BAI1-AP4 gene and analyzed its promoter activity. Functional analyses demonstrated that an Sp1 site was the enhancer, and the region containing the transcription initiation site and an AP2-binding site was the basal promoter. We examined the ability of the BAI1-AP4 promoter to drive adult brain-specific expression by using it to drive lacZ expression in transgenic (TG) mice. Northern blot analyses showed a unique pattern of beta-galactosidase expression in TG brain, peaking at 1 month after birth, like endogenous BAI1-AP4. Histological analyses demonstrated the same localization and developmental expression of beta-galactosidase and BAI1-AP4 in most neurons of the cerebral cortex and hippocampus. Our data indicate that TG mice carrying the BAI1-AP4 promoter could be a valuable model system for region-specific brain diseases.

  11. Effect of driving frequency on the electron-sheath interaction and electron energy distribution function in a low pressure capacitively coupled plasmas

    NASA Astrophysics Data System (ADS)

    Sharma, Sarveshwar; Sirse, Nishant; Kaw, Predhiman; Turner, Miles; Ellingboe, Albert R.; InstitutePlasma Research, Gandhinagar, Gujarat Team; School Of Physical Sciences; Ncpst, Dublin City University, Dublin 9, Ireland Collaboration

    2016-09-01

    The effect of driving frequency (27.12-70 MHz) on the electron-sheath interaction and electron energy distribution function (EEDF) is investigated in a low pressure capacitive discharges using a self-consistent particle-in-cell simulation. At a fixed discharge voltage the EEDF evolves from a strongly bi-Maxwellian at low frequency, 27.12 MHz, to a convex type distribution at an intermediate frequency, 50 MHz, and finally becomes a weak biMaxwellian above 50 MHz. The EEDF evolution leads to a two-fold increase in the effective electron temperature up to 50 MHz, whereas the electron density remains constant in this range. After 50MHz, the electron density increases rapidly and the electron temperature decreases. The transition is caused by the transient electric field excited by bursts of high energy electrons interacting strongly with the sheath edge. Above the transition frequency, high energy electrons are confined between two sheaths which increase the ionization probability and thus the plasma density increases.

  12. Novel activation domain derived from Che-1 cofactor coupled with the artificial protein Jazz drives utrophin upregulation.

    PubMed

    Desantis, Agata; Onori, Annalisa; Di Certo, Maria Grazia; Mattei, Elisabetta; Fanciulli, Maurizio; Passananti, Claudio; Corbi, Nicoletta

    2009-02-01

    Our aim is to upregulate the expression level of the dystrophin related gene utrophin in Duchenne muscular dystrophy, thus complementing the lack of dystrophin functions. To this end, we have engineered synthetic zinc finger based transcription factors. We have previously shown that the artificial three-zinc finger protein named Jazz fused with the Vp16 activation domain, is able to bind utrophin promoter A and to increase the endogenous level of utrophin in transgenic mice. Here, we report on an innovative artificial protein, named CJ7, that consists of Jazz DNA binding domain fused to a novel activation domain derived from the regulatory multivalent adaptor protein Che-1/AATF. This transcriptional activation domain is 100 amino acids in size and it is very powerful as compared to the Vp16 activation domain. We show that CJ7 protein efficiently promotes transcription and accumulation of the acetylated form of histone H3 on the genomic utrophin promoter locus.

  13. [Protein fraction distribution in milling and screened physical fractions of grain amaranth].

    PubMed

    Búcaro Segura, María Ester; Bressani, Ricardo

    2002-06-01

    The purpose of the study was to establish the protein distribution based on solubility in physical fractions of amaranth flour, in particular between the flour from the germ and that from the perisperm. The protein distribution was obtained applying a series of solvents sequentially utilized in the classical methodology of Osborne & Mendel. The sample of A. cruentus weighing 2000 g was divided into 4 subsamples of 500 g each. One was left as the control while the other 3 were ground individually with a mill. Each flour was screened through 18, 20, 30 and 40 mesh screens, so that 5 fractions were obtained from each of the whole grain flours. Samples of each screened fractions were observed by stereoscopy and analyzed for moisture, fat and protein. This characterization suggested that the fraction above the 30 mesh screen and the flour which passed the 40 mesh screen probably were the perisperm and germ respectively. The 30 mesh sample contained 2.34 fat and 9.05% protein while the 40 mesh contained 16.18% fat and 26.46% protein. The extraction and partitioning of the proteins indicated that the most important fractions in germ and perisperm were the water soluble and glutelins measured by Kjeldahl. The relationship of the water soluble + globulin to glutelins ratio was 2.1 to 1 in the whole grain, 1.9 to 1 in the perisperm and 1.7 to 1 in the germ. The distribution of proteins was very much alike between germ and perisperm. The levels of prolamines were quite low. The protein extraction of the perisperm proteins retained on the 30 mesh screen was low (71.1%) measured by Kjeldahl and 47.4% with the Bradford method to measure protein.

  14. Study of the protein distribution in the pig lens cross section by Raman spectroscopy.

    PubMed

    Medina-Gutiérrez, C; Frausto-Reyes, C; Quintanar-Stephano, J L; Sato-Berrú, R; Barbosa-García, O

    2004-06-01

    The distribution of proteins in the cross section of a normal pig lens was studied by near-infrared Raman spectroscopy. The Raman spectra were measured in the visual and equatorial axes of this cross section and the protein peak intensities were determined. It was found that along each axis the protein intensities fluctuate. They have a considerable increment along the visual axis with the exception of the C-N bond peak intensities at 1087.2 cm(-1), which decrease, and along the equatorial axis the increment is slight. This increment in protein distribution along the visual axis is related with the refractive gradient of the lens. The classification of pig lens spectra in these axes was performed using principal component analysis (PCA) and linear discriminant analysis (LDA). Cross-validation shows an excellent group separation.

  15. Parameters of the proteome evolution from the distribution of sequence identities of paralogous proteins

    NASA Astrophysics Data System (ADS)

    Yan, Koon-Kiu; Axelsen, Jacob; Maslov, Sergei

    2006-03-01

    The evolution of the full repertoire of proteins encoded in a given genome is driven by gene duplications, deletions and modifications of amino-acid sequences of already existing proteins. The information about relative rates and other intrinsic parameters of these three basic processes is contained in the distribution of sequence identities of pairs of paralogous proteins. We introduced a simple mathematical framework that allows one to extract some of this hidden information. It was then applied to the proteome-wide set of paralogous proteins in H. pylori, E. coli, S. cerevisiae, C. elegans, D. melanogaster and H. sapiens. We estimated the stationary per-gene deletion and duplication rates, the distribution of amino-acid substitution rate of these organisms. The validity of our mathematical framework was further confirmed by numerical simulations of a simple evolutionary model of a fixed-size proteome.

  16. Similarity and difference of global reanalysis datasets (WFD and APHRODITE) in driving lumped and distributed hydrological models in a humid region of China

    NASA Astrophysics Data System (ADS)

    Xu, Hongliang; Xu, Chong-Yu; Chen, Sidian; Chen, Hua

    2016-11-01

    Different conclusions have been drawn in literature as using reanalysis rainfall products to drive hydrological models for the simulation of streamflow, which warrant a need of further investigation before a generalised conclusion can be drawn. This paper assesses the utility of two widely used reanalysis rainfall datasets (WFD (developed by the WATCH project) and APHRODITE (Asian Precipitation-Highly-Resolved Observational Data Integration Towards Evaluation of the water resources)) against the gauged rainfall in terms of flood simulation in lumped (Xinanjiang Model) and distributed (SWAT Model) hydrological models in a tributary basin of Yangtze River with 94,660 km2 drainage area in humid region of southern China. Differences in terms of rainfall accumulation, number of rainy days, spatial patterns of the rainfall amount and frequency distribution of the rain rates are evaluated. The APHRODITE product shows high consistency with the gauged rainfall while WFD data gives large errors in various statistical indices in the study region. Simulated discharges from the gauged and reanalysis rainfall data, respectively, are analysed and compared with the observed discharge in basin outlet over the period 1991-2005. The APHRODITE data show relatively high ability in modelling hydrological responses while the WFD data based models give large error in simulating the discharge. For the assessment of the high flows, both datasets exhibit some skills in flood prediction, however, APHRODITE data perform better than the WFD data when forcing into the lumped Xinanjiang Model than into the distributed SWAT Model in terms of flood duration, Probability of Detection, False Alarm Rate, regressions of annual peaks and partial duration series.

  17. Distribution of Flagella Secreted Protein and Integral Membrane Protein Among Campylobacter jejuni Isolated from Thailand

    DTIC Science & Technology

    2011-01-01

    significant high isolation rate of C. jejuni in Thai- land and potential role of the FspA protein as one of vaccine candidate lead us to further...foreigners and Thai adults at Bumrungrad Hospital in Bangkok. All C. jejuni isolates were kept at -70 oc in glycerol medium and later were

  18. Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules.

    PubMed

    Matsuoka, Rei; Shimada, Atsushi; Komuro, Yasuaki; Sugita, Yuji; Kohda, Daisuke

    2016-03-01

    Contacts with neighboring molecules in protein crystals inevitably restrict the internal motions of intrinsically flexible proteins. The resultant clear electron densities permit model building, as crystallographic snapshot structures. Although these still images are informative, they could provide biased pictures of the protein motions. If the mobile parts are located at a site lacking direct contacts in rationally designed crystals, then the amplitude of the movements can be experimentally analyzed. We propose a fusion protein method, to create crystal contact-free space (CCFS) in protein crystals and to place the mobile parts in the CCFS. Conventional model building fails when large amplitude motions exist. In this study, the mobile parts appear as smeared electron densities in the CCFS, by suitable processing of the X-ray diffraction data. We applied the CCFS method to a highly mobile presequence peptide bound to the mitochondrial import receptor, Tom20, and a catalytically relevant flexible segment in the oligosaccharyltransferase, AglB. These two examples demonstrated the general applicability of the CCFS method to the analysis of the spatial distribution of motions within protein molecules.

  19. Distribution of regulatory subunits of protein kinase A and A kinase anchor proteins (AKAP 95, 150) in rat pinealocytes.

    PubMed

    Koch, M; Korf, H-W

    2002-12-01

    The rat pineal organ is an established model to study signal transduction cascades that are activated by norepinephrine (NE) and cause increases in cAMP levels and stimulation of protein kinase A (PKA). PKA type II catalyzes the phosphorylation of the transcription factor cAMP-response-element-binding protein (CREB) which is essential for the transcriptional induction of the arylalkylamine- N-acetyltransferase (AANAT), the rate limiting enzyme of melatonin biosynthesis. Moreover, PKA may control protein levels and enzyme activity via two PKA-dependent phosphorylation sites in the AANAT molecule. Despite the functional importance of PKA very little is known about the distribution of its isoenzymes and of A-kinase anchor proteins (AKAPs) that target the PKA to specific membrane areas and organelles by binding to the regulatory (R) subunits of PKA. We have addressed this problem by demonstrating the R subunits alpha and beta of PKA type I and II and two AKAPs (150 and 95) in NE-stimulated and untreated rat pinealocytes by immunoblot and immunocytochemistry. The immunoreactions (IR) of all four R subunits were confined to granules evenly distributed in the pinealocyte cytoplasm. Immunoreactions of RIIalpha and RIIbeta were stronger than those of RIalpha and RIbeta. AKAP 150-IR was concentrated at the cell periphery; AKAP 95-IR was restricted to the nucleus. Amount and subcellular distribution of the immunoreactions of all proteins investigated did not change upon NE stimulation. A substantial colocalization was observed between RII-subunits and AKAP 150-IR, suggesting that, in rat pinealocytes, AKAP 150 primarily anchors the R subunits of PKA II.

  20. Cancer-associated mutations are preferentially distributed in protein kinase functional sites.

    PubMed

    Izarzugaza, Jose M G; Redfern, Oliver C; Orengo, Christine A; Valencia, Alfonso

    2009-12-01

    Protein kinases are a superfamily involved in many crucial cellular processes, including signal transmission and regulation of cell cycle. As a consequence of this role, kinases have been reported to be associated with many types of cancer and are considered as potential therapeutic targets. We analyzed the distribution of pathogenic somatic point mutations (drivers) in the protein kinase superfamily with respect to their location in the protein, such as in structural, evolutionary, and functionally relevant regions. We find these driver mutations are more clearly associated with key protein features than other somatic mutations (passengers) that have not been directly linked to tumor progression. This observation fits well with the expected implication of the alterations in protein kinase function in cancer pathogenicity. To explain the relevance of the detected association of cancer driver mutations at the molecular level in the human kinome, we compare these with genetically inherited mutations (SNPs). We find that the subset of nonsynonymous SNPs that are associated to disease, but sufficiently mild to the point of being widespread in the population, tend to avoid those key protein regions, where they could be more detrimental for protein function. This tendency contrasts with the one detected for cancer associated-driver-mutations, which seems to be more directly implicated in the alteration of protein function. The detailed analysis of protein kinase groups and a number of relevant examples, confirm the relation between cancer associated-driver-mutations and key regions for protein kinase structure and function.

  1. Dementia & Driving

    MedlinePlus

    ... Caregiver Resource Center Family Care Navigator Research Registry Support Groups Caregiver Stories Connections e-Newsletter FCA+(plus) Services ... be like if you could no longer drive. Support groups provide a good venue for both the caregivers ...

  2. Alcohol drives S-nitrosylation and redox activation of protein phosphatase 1, causing bovine airway cilia dysfunction.

    PubMed

    Price, Michael E; Pavlik, Jacqueline A; Liu, Miao; Ding, Shi-Jian; Wyatt, Todd A; Sisson, Joseph H

    2017-03-01

    Individuals with alcohol (ethanol)-use disorders are at increased risk for lung infections, in part, due to defective mucociliary clearance driven by motile cilia in the airways. We recently reported that isolated, demembranated bovine cilia (axonemes) are capable of producing nitric oxide ((∙)NO) when exposed to biologically relevant concentrations of alcohol. This increased presence of (∙)NO can lead to protein S-nitrosylation, a posttranslational modification signaling mechanism involving reversible adduction of nitrosonium cations or (∙)NO to thiolate or thiyl radicals, respectively, of proteins forming S-nitrosothiols (SNOs). We quantified and compared SNO content between isolated, demembranated axonemes extracted from bovine tracheae, with or without in situ alcohol exposure (100 mM × 24 h). We demonstrate that relevant concentrations of alcohol exposure shift the S-nitrosylation status of key cilia regulatory proteins, including 20-fold increases in S-nitrosylation of proteins that include protein phosphatase 1 (PP1). With the use of an ATP-reactivated axoneme motility system, we demonstrate that alcohol-driven S-nitrosylation of PP1 is associated with PP1 activation and dysfunction of axoneme motility. These new data demonstrate that alcohol can shift the S-nitrothiol balance at the level of the cilia organelle and highlight S-nitrosylation as a novel signaling mechanism to regulate PP1 and cilia motility.

  3. Isotopomer distributions in amino acids from a highly expressed protein as a proxy for those from total protein

    SciTech Connect

    Shaikh, Afshan; Shaikh, Afshan S.; Tang, Yinjie; Mukhopadhyay, Aindrila; Keasling, Jay D.

    2008-06-27

    {sup 13}C-based metabolic flux analysis provides valuable information about bacterial physiology. Though many biological processes rely on the synergistic functions of microbial communities, study of individual organisms in a mixed culture using existing flux analysis methods is difficult. Isotopomer-based flux analysis typically relies on hydrolyzed amino acids from a homogeneous biomass. Thus metabolic flux analysis of a given organism in a mixed culture requires its separation from the mixed culture. Swift and efficient cell separation is difficult and a major hurdle for isotopomer-based flux analysis of mixed cultures. Here we demonstrate the use of a single highly-expressed protein to analyze the isotopomer distribution of amino acids from one organism. Using the model organism E. coli expressing a plasmid-borne, his-tagged Green Fluorescent Protein (GFP), we show that induction of GFP does not affect E. coli growth kinetics or the isotopomer distribution in nine key metabolites. Further, the isotopomer labeling patterns of amino acids derived from purified GFP and total cell protein are indistinguishable, indicating that amino acids from a purified protein can be used to infer metabolic fluxes of targeted organisms in a mixed culture. This study provides the foundation to extend isotopomer-based flux analysis to study metabolism of individual strains in microbial communities.

  4. Maximum occurrence analysis of protein conformations for different distributions of paramagnetic metal ions within flexible two-domain proteins.

    PubMed

    Luchinat, Claudio; Nagulapalli, Malini; Parigi, Giacomo; Sgheri, Luca

    2012-02-01

    Multidomain proteins are composed of rigid domains connected by (flexible) linkers. Therefore, the domains may experience a large degree of reciprocal reorientation. Pseudocontact shifts and residual dipolar couplings arising from one or more paramagnetic metals successively placed in a single metal binding site in the protein can be used as restraints to assess the degree of mobility of the different domains. They can be used to determine the maximum occurrence (MO) of each possible protein conformation, i.e. the maximum weight that such conformations can have independently of the real structural ensemble, in agreement with the provided restraints. In the case of two-domain proteins, the metal ions can be placed all in the same domain, or distributed between the two domains. It has been demonstrated that the quantity of independent information for the characterization of the system is larger when all metals are bound in the same domain. At the same time, it has been shown that there are practical advantages in placing the metals in different domains. Here, it is shown that distributing the metals between the domains provides a tool for defining a coefficient of compatibility among the restraints obtained from different metals, without a significant decrease of the capability of the MO values to discriminate among conformations with different weights.

  5. LDRD Final Report (08-ERD-037): Important Modes to Drive Protein MD Simulations to the Next Conformational Level

    SciTech Connect

    Sadigh, B

    2011-04-07

    Every action in biology is performed by dynamic proteins that convert between multiple states in order to engage their functions. Often binding to various ligands is essential for the rates of desired transitions to be enhanced. The goal of computational biology is to study these transitions and discover the different states to fully understand the protein's normal and diseased function, design drugs to target/bias specific states, and understand all of the interactions in between. We have developed a new methodology that is capable of calculating the absolute free energy of proteins while taking into account all the interactions with the solvent molecules. The efficiency of the new scheme is an order of magnitude greater than any existing technique. This method is now implemented in the massively parallel popular MD program package NAMD. This now makes it possible to calculate the relative stability of different conformational states of biological macromolecules as well as their binding free energies to various ligands.

  6. A method for determination of the in situ distribution of chromosomal proteins.

    PubMed

    Silver, L M; Elgin, S C

    1976-02-01

    A technique has been developed for "staining" cytological preparations by indirect immunofluorescent methods that permits determination of the in situ distribution of chromosomal proteins. The method is particularly oriented to the use of polytene chromosome squashes from Drosophila salivary glands. Control experiments indicate that the fixation methods used allow little or no extraction or rearrangement of the chromosomal proteins. The results obtained demonstrate the specific in vivo chromosomal locations of nonhistone proteins purified from isolated chromatin. The technique is apparently capable of resolution at the level of the chromomere or band, the unit of genetic organization in Drosophila.

  7. Effect of surface charge distribution on the adsorption orientation of proteins to lipid monolayers.

    PubMed

    Tiemeyer, Sebastian; Paulus, Michael; Tolan, Metin

    2010-09-07

    The adsorption orientation of the proteins lysozyme and ribonuclease A (RNase A) to a neutral 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and a negatively charged stearic acid lipid film was investigated by means of X-ray reflectivity. Both proteins adsorbed to the negatively charged lipid monolayer, whereas at the neutral monolayer, no adsorption was observed. For acquiring comprehensive information on the proteins' adsorption, X-ray reflectivity data were combined with electron densities obtained from crystallographic data. With this method, it is possible to determine the orientation of adsorbed proteins in solution underneath lipid monolayers. While RNase A specifically coupled with its positively charged active site to the negatively charged lipid monolayer, lysozyme prefers an orientation with its long axis parallel to the Langmuir film. In comparison to the electrostatic maps of the proteins, our results can be explained by the discriminative surface charge distribution of lysozyme and RNase A.

  8. Assortative mating drives linkage disequilibrium between sperm and egg recognition protein loci in the sea urchin Strongylocentrotus purpuratus.

    PubMed

    Stapper, Andres Plata; Beerli, Peter; Levitan, Don R

    2015-04-01

    Sperm and eggs have interacting proteins on their surfaces that influence their compatibility during fertilization. These proteins are often polymorphic within species, producing variation in gamete affinities. We first demonstrate the fitness consequences of various sperm bindin protein (Bindin) variants in the sea urchin Strongylocentrotus purpuratus, and assortative mating between males and females based on their sperm Bindin genotype. This empirical finding of assortative mating based on sperm Bindin genotype could arise by linkage disequilibrium (LD) between interacting sperm and egg recognition loci. We then examine sequence variation in eight exons of the sea urchin egg receptor for sperm Bindin (EBR1). We find little evidence of LD among the eight exons of EBR1, yet strong evidence for LD between sperm Bindin and EBR1 overall, and varying degrees of LD between sperm Bindin among the eight exons. We reject the alternate hypotheses of LD driven by shared evolutionary histories, population structure, or close physical linkage between these interacting loci on the genome. The most parsimonious explanation for this pattern of LD is that it represents selection driven by assortative mating based on interactions among these sperm and egg loci. These findings indicate the importance of ongoing sexual selection in the maintenance of protein polymorphisms and LD, and more generally highlight how LD can be used as an indication of current mate choice, as opposed to historic selection.

  9. The ticking tail: daily oscillations in mRNA poly(A) tail length drive circadian cycles in protein synthesis.

    PubMed

    Gotic, Ivana; Schibler, Ueli

    2012-12-15

    In this issue of Genes & Development, Kojima and colleagues (pp. 2724-2736) examined the impact of mRNA poly(A) tail length on circadian gene expression. Their study demonstrates how dynamic changes in transcript poly(A) tail length can lead to rhythmic protein expression, irrespective of whether mRNA accumulation is circadian or constitutive.

  10. Thermal drift is enough to drive a single microtubule along its axis even in the absence of motor proteins.

    PubMed Central

    Nakata, T; Sato-Yoshitake, R; Okada, Y; Noda, Y; Hirokawa, N

    1993-01-01

    One-dimensional diffusion of microtubules (MTs), a back-and-forth motion of MTs due to thermal diffusion, was reported in dynein motility assay. The interaction between MTs and dynein that allows such motion was implicated in its importance in the force generating cycle of dynein ATPase cycle. However, it was not known whether the phenomenon is special to motor proteins. Here we show two independent examples of one-dimensional diffusion of MTs in the absence of motor proteins. Dynamin, a MT-activated GTPase, causes a nucleotide dependent back-and-forth movement of single MT up to 1 micron along the longitudinal axes, although the MT never showed unidirectional consistent movement. Quantitative analysis of the motion and its nucleotide condition indicates that the motion is due to a thermal driven diffusion, restricted to one dimension, under the weak interaction between MT and dynamin. However, specific protein-protein interaction is not essential for the motion, because similar back-and-forth movement of MT was achieved on coverslips coated with only 0.8% methylcellulose. Both cases demonstrate that thermal diffusion could provide a considerable sliding of MTs only if MTs are restricted on the surface appropriately. Images FIGURE 1 FIGURE 2 FIGURE 3 PMID:7906153

  11. Single-point single-molecule FRAP distinguishes inner and outer nuclear membrane protein distribution

    PubMed Central

    Mudumbi, Krishna C; Schirmer, Eric C; Yang, Weidong

    2016-01-01

    The normal distribution of nuclear envelope transmembrane proteins (NETs) is disrupted in several human diseases. NETs are synthesized on the endoplasmic reticulum and then transported from the outer nuclear membrane (ONM) to the inner nuclear membrane (INM). Quantitative determination of the distribution of NETs on the ONM and INM is limited in available approaches, which moreover provide no information about translocation rates in the two membranes. Here we demonstrate a single-point single-molecule FRAP microscopy technique that enables determination of distribution and translocation rates for NETs in vivo. PMID:27558844

  12. Distribution of Misfolded Prion Protein Seeding Activity Alone Does Not Predict Regions of Neurodegeneration

    PubMed Central

    Alibhai, James; Blanco, Richard A.; Barria, Marcelo A.; Piccardo, Pedro; Caughey, Byron; Perry, V. Hugh; Freeman, Tom C.; Manson, Jean C.

    2016-01-01

    Protein misfolding is common across many neurodegenerative diseases, with misfolded proteins acting as seeds for "prion-like" conversion of normally folded protein to abnormal conformations. A central hypothesis is that misfolded protein accumulation, spread, and distribution are restricted to specific neuronal populations of the central nervous system and thus predict regions of neurodegeneration. We examined this hypothesis using a highly sensitive assay system for detection of misfolded protein seeds in a murine model of prion disease. Misfolded prion protein (PrP) seeds were observed widespread throughout the brain, accumulating in all brain regions examined irrespective of neurodegeneration. Importantly, neither time of exposure nor amount of misfolded protein seeds present determined regions of neurodegeneration. We further demonstrate two distinct microglia responses in prion-infected brains: a novel homeostatic response in all regions and an innate immune response restricted to sites of neurodegeneration. Therefore, accumulation of misfolded prion protein alone does not define targeting of neurodegeneration, which instead results only when misfolded prion protein accompanies a specific innate immune response. PMID:27880767

  13. Distribution of DNA-condensing protein complexes in the adenovirus core

    PubMed Central

    Pérez-Berná, Ana J.; Marion, Sanjin; Chichón, F. Javier; Fernández, José J.; Winkler, Dennis C.; Carrascosa, José L.; Steven, Alasdair C.; Šiber, Antonio; San Martín, Carmen

    2015-01-01

    Genome packing in adenovirus has long evaded precise description, since the viral dsDNA molecule condensed by proteins (core) lacks icosahedral order characteristic of the virus protein coating (capsid). We show that useful insights regarding the organization of the core can be inferred from the analysis of spatial distributions of the DNA and condensing protein units (adenosomes). These were obtained from the inspection of cryo-electron tomography reconstructions of individual human adenovirus particles. Our analysis shows that the core lacks symmetry and strict order, yet the adenosome distribution is not entirely random. The features of the distribution can be explained by modeling the condensing proteins and the part of the genome in each adenosome as very soft spheres, interacting repulsively with each other and with the capsid, producing a minimum outward pressure of ∼0.06 atm. Although the condensing proteins are connected by DNA in disrupted virion cores, in our models a backbone of DNA linking the adenosomes is not required to explain the experimental results in the confined state. In conclusion, the interior of an adenovirus infectious particle is a strongly confined and dense phase of soft particles (adenosomes) without a strictly defined DNA backbone. PMID:25820430

  14. Relative Roles of Deterministic and Stochastic Processes in Driving the Vertical Distribution of Bacterial Communities in a Permafrost Core from the Qinghai-Tibet Plateau, China

    PubMed Central

    Tian, Tian; Li, Dingyao; Cheng, Gang; Mu, Jing; Wu, Qingbai; Niu, Fujun; Stegen, James C.; An, Lizhe; Feng, Huyuan

    2015-01-01

    Understanding the processes that influence the structure of biotic communities is one of the major ecological topics, and both stochastic and deterministic processes are expected to be at work simultaneously in most communities. Here, we investigated the vertical distribution patterns of bacterial communities in a 10-m-long soil core taken within permafrost of the Qinghai-Tibet Plateau. To get a better understanding of the forces that govern these patterns, we examined the diversity and structure of bacterial communities, and the change in community composition along the vertical distance (spatial turnover) from both taxonomic and phylogenetic perspectives. Measures of taxonomic and phylogenetic beta diversity revealed that bacterial community composition changed continuously along the soil core, and showed a vertical distance-decay relationship. Multiple stepwise regression analysis suggested that bacterial alpha diversity and phylogenetic structure were strongly correlated with soil conductivity and pH but weakly correlated with depth. There was evidence that deterministic and stochastic processes collectively drived bacterial vertically-structured pattern. Bacterial communities in five soil horizons (two originated from the active layer and three from permafrost) of the permafrost core were phylogenetically random, indicator of stochastic processes. However, we found a stronger effect of deterministic processes related to soil pH, conductivity, and organic carbon content that were structuring the bacterial communities. We therefore conclude that the vertical distribution of bacterial communities was governed primarily by deterministic ecological selection, although stochastic processes were also at work. Furthermore, the strong impact of environmental conditions (for example, soil physicochemical parameters and seasonal freeze-thaw cycles) on these communities underlines the sensitivity of permafrost microorganisms to climate change and potentially subsequent

  15. Relative Roles of Deterministic and Stochastic Processes in Driving the Vertical Distribution of Bacterial Communities in a Permafrost Core from the Qinghai-Tibet Plateau, China.

    PubMed

    Hu, Weigang; Zhang, Qi; Tian, Tian; Li, Dingyao; Cheng, Gang; Mu, Jing; Wu, Qingbai; Niu, Fujun; Stegen, James C; An, Lizhe; Feng, Huyuan

    2015-01-01

    Understanding the processes that influence the structure of biotic communities is one of the major ecological topics, and both stochastic and deterministic processes are expected to be at work simultaneously in most communities. Here, we investigated the vertical distribution patterns of bacterial communities in a 10-m-long soil core taken within permafrost of the Qinghai-Tibet Plateau. To get a better understanding of the forces that govern these patterns, we examined the diversity and structure of bacterial communities, and the change in community composition along the vertical distance (spatial turnover) from both taxonomic and phylogenetic perspectives. Measures of taxonomic and phylogenetic beta diversity revealed that bacterial community composition changed continuously along the soil core, and showed a vertical distance-decay relationship. Multiple stepwise regression analysis suggested that bacterial alpha diversity and phylogenetic structure were strongly correlated with soil conductivity and pH but weakly correlated with depth. There was evidence that deterministic and stochastic processes collectively drived bacterial vertically-structured pattern. Bacterial communities in five soil horizons (two originated from the active layer and three from permafrost) of the permafrost core were phylogenetically random, indicator of stochastic processes. However, we found a stronger effect of deterministic processes related to soil pH, conductivity, and organic carbon content that were structuring the bacterial communities. We therefore conclude that the vertical distribution of bacterial communities was governed primarily by deterministic ecological selection, although stochastic processes were also at work. Furthermore, the strong impact of environmental conditions (for example, soil physicochemical parameters and seasonal freeze-thaw cycles) on these communities underlines the sensitivity of permafrost microorganisms to climate change and potentially subsequent

  16. Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre

    NASA Astrophysics Data System (ADS)

    Zhang, Lu; Silva, Daniel-Adriano; Zhang, Houdao; Yue, Alexander; Yan, Yijing; Huang, Xuhui

    2014-06-01

    One longstanding puzzle concerning photosystem II, a core component of photosynthesis, is that only one of the two symmetric branches in its reaction centre is active in electron transfer. To investigate the effect of the photosystem II environment on the preferential selection of the energy transfer pathway (a prerequisite for electron transfer), we have constructed an exciton model via extensive molecular dynamics simulations and quantum mechanics/molecular mechanics calculations based on a recent X-ray structure. Our results suggest that it is essential to take into account an ensemble of protein conformations to accurately compute the site energies. We identify the cofactor CLA606 of active chain as the most probable site for the energy excitation. We further pinpoint a number of charged protein residues that collectively lower the CLA606 site energy. Our work provides insights into the understanding of molecular mechanisms of the core machinery of the green-plant photosynthesis.

  17. Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre.

    PubMed

    Zhang, Lu; Silva, Daniel-Adriano; Zhang, Houdao; Yue, Alexander; Yan, YiJing; Huang, Xuhui

    2014-06-23

    One longstanding puzzle concerning photosystem II, a core component of photosynthesis, is that only one of the two symmetric branches in its reaction centre is active in electron transfer. To investigate the effect of the photosystem II environment on the preferential selection of the energy transfer pathway (a prerequisite for electron transfer), we have constructed an exciton model via extensive molecular dynamics simulations and quantum mechanics/molecular mechanics calculations based on a recent X-ray structure. Our results suggest that it is essential to take into account an ensemble of protein conformations to accurately compute the site energies. We identify the cofactor CLA606 of active chain as the most probable site for the energy excitation. We further pinpoint a number of charged protein residues that collectively lower the CLA606 site energy. Our work provides insights into the understanding of molecular mechanisms of the core machinery of the green-plant photosynthesis.

  18. Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre

    PubMed Central

    Zhang, Lu; Silva, Daniel-Adriano; Zhang, Houdao; Yue, Alexander; Yan, YiJing; Huang, Xuhui

    2014-01-01

    One longstanding puzzle concerning photosystem II, a core component of photosynthesis, is that only one of the two symmetric branches in its reaction centre is active in electron transfer. To investigate the effect of the photosystem II environment on the preferential selection of the energy transfer pathway (a prerequisite for electron transfer), we have constructed an exciton model via extensive molecular dynamics simulations and quantum mechanics/molecular mechanics calculations based on a recent X-ray structure. Our results suggest that it is essential to take into account an ensemble of protein conformations to accurately compute the site energies. We identify the cofactor CLA606 of active chain as the most probable site for the energy excitation. We further pinpoint a number of charged protein residues that collectively lower the CLA606 site energy. Our work provides insights into the understanding of molecular mechanisms of the core machinery of the green-plant photosynthesis. PMID:24954746

  19. Role of flippases, scramblases and transfer proteins in phosphatidylserine subcellular distribution.

    PubMed

    Hankins, Hannah M; Baldridge, Ryan D; Xu, Peng; Graham, Todd R

    2015-01-01

    It is well known that lipids are heterogeneously distributed throughout the cell. Most lipid species are synthesized in the endoplasmic reticulum (ER) and then distributed to different cellular locations in order to create the distinct membrane compositions observed in eukaryotes. However, the mechanisms by which specific lipid species are trafficked to and maintained in specific areas of the cell are poorly understood and constitute an active area of research. Of particular interest is the distribution of phosphatidylserine (PS), an anionic lipid that is enriched in the cytosolic leaflet of the plasma membrane. PS transport occurs by both vesicular and non-vesicular routes, with members of the oxysterol-binding protein family (Osh6 and Osh7) recently implicated in the latter route. In addition, the flippase activity of P4-ATPases helps build PS membrane asymmetry by preferentially translocating PS to the cytosolic leaflet. This asymmetric PS distribution can be used as a signaling device by the regulated activation of scramblases, which rapidly expose PS on the extracellular leaflet and play important roles in blood clotting and apoptosis. This review will discuss recent advances made in the study of phospholipid flippases, scramblases and PS-specific lipid transfer proteins, as well as how these proteins contribute to subcellular PS distribution.

  20. A Pleiotropic RNA-Binding Protein Controls Distinct Cell Cycle Checkpoints to Drive Resistance of p53-Defective Tumors to Chemotherapy.

    PubMed

    Cannell, Ian G; Merrick, Karl A; Morandell, Sandra; Zhu, Chang-Qi; Braun, Christian J; Grant, Robert A; Cameron, Eleanor R; Tsao, Ming-Sound; Hemann, Michael T; Yaffe, Michael B

    2015-11-09

    In normal cells, p53 is activated by DNA damage checkpoint kinases to simultaneously control the G1/S and G2/M cell cycle checkpoints through transcriptional induction of p21(cip1) and Gadd45α. In p53-mutant tumors, cell cycle checkpoints are rewired, leading to dependency on the p38/MK2 pathway to survive DNA-damaging chemotherapy. Here we show that the RNA binding protein hnRNPA0 is the "successor" to p53 for checkpoint control. Like p53, hnRNPA0 is activated by a checkpoint kinase (MK2) and simultaneously controls both cell cycle checkpoints through distinct target mRNAs, but unlike p53, this is through the post-transcriptional stabilization of p27(Kip1) and Gadd45α mRNAs. This pathway drives cisplatin resistance in lung cancer, demonstrating the importance of post-transcriptional RNA control to chemotherapy response.

  1. Simulation of porosity decrease with protein adsorption using the distributed pore model.

    PubMed

    Coquebert de Neuville, Bertrand; Thomas, Helen; Morbidelli, Massimo

    2013-11-01

    Chromatographic stationary phases such as Fractogel EMD SO3 (M) have a pore size distribution that is close to the size of proteins. The accessible porosity and the mass transfer inside the particles are therefore strongly affected by the pore to solute size ratio. This effect was simulated using the distributed pore model for three media: Base Fractogel SO3, Fractogel EMD SO3 (M) and (S). This model was extended so as to be able to account for the effect of pore shrinkage due to protein loading on the chromatographic behavior of other proteins. Pulse chromatographic experiments using dextrans of various sizes on column pre-loaded with antibodies have been conducted to test the model reliability.

  2. Dystroglycan protein distribution coincides with basement membranes and muscle differentiation during mouse embryogenesis.

    PubMed

    Anderson, Claire; Winder, Steven J; Borycki, Anne-Gaëlle

    2007-09-01

    Using immunohistochemistry, we have examined beta-Dystroglycan protein distribution in the mouse embryo at embryonic stages E9.5 to E11.5. Our data show that Dystroglycan expression correlates with basement membranes in many tissues, such as the notochord, neural tube, promesonephros, and myotome. In the myotome, we describe the timing of Dystroglycan protein re-distribution at the surface of myogenic precursor cells as basement membrane assembles into a continuous sheet. We also report on non-basement-membrane-associated Dystroglycan expression in the floor plate and the myocardium. This distribution often corresponds to sites of expression previously reported in adults, suggesting that Dystroglycan is continuously produced during development.

  3. Cellular distribution of calmodulin and calmodulin-binding proteins in Vicia faba L

    NASA Technical Reports Server (NTRS)

    Ling, V.; Assmann, S. M.

    1992-01-01

    The distribution of calmodulin (CaM) and CaM-binding proteins within Vicia faba was investigated. Both CaM and CaM-binding proteins were found to be differentially distributed among organs, tissues, and protoplast types. CaM levels, on a per protein basis, were found to be the highest in leaf epidermis, containing 3-fold higher levels of CaM than in total leaf. Similarly, guard cell and epidermal cell protoplasts were also found to have higher levels of CaM than mesophyll cell protoplasts. 125I-CaM blot overlay assays were performed to qualitatively examine CaM-binding proteins in these protoplast types as well as in whole tissues and organs. CaM-binding proteins with Mr 52,000, 78,000, and 115,000 were common in all metabolically active plant parts. Unique CaM-binding protein bands were detected in guard cell protoplasts (Mr 39,000, 88,000), stems (Mr 45,000, 60,000, 64,000), and roots (Mr 62,000), suggesting the presence of specialized CaM-dependent processes in these cells and organs.

  4. Active Degradation Explains the Distribution of Nuclear Proteins during Cellular Senescence

    PubMed Central

    Giampieri, Enrico; De Cecco, Marco; Remondini, Daniel; Sedivy, John; Castellani, Gastone

    2015-01-01

    The amount of cellular proteins is a crucial parameter that is known to vary between cells as a function of the replicative passages, and can be important during physiological aging. The process of protein degradation is known to be performed by a series of enzymatic reactions, ranging from an initial step of protein ubiquitination to their final fragmentation by the proteasome. In this paper we propose a stochastic dynamical model of nuclear proteins concentration resulting from a balance between a constant production of proteins and their degradation by a cooperative enzymatic reaction. The predictions of this model are compared with experimental data obtained by fluorescence measurements of the amount of nuclear proteins in murine tail fibroblast (MTF) undergoing cellular senescence. Our model provides a three-parameter stationary distribution that is in good agreement with the experimental data even during the transition to the senescent state, where the nuclear protein concentration changes abruptly. The estimation of three parameters (cooperativity, saturation threshold, and maximal velocity of the reaction), and their evolution during replicative passages shows that only the maximal velocity varies significantly. Based on our modeling we speculate the reduction of functionality of the protein degradation mechanism as a possible competitive inhibition of the proteasome. PMID:26115222

  5. Disk Drives

    NASA Technical Reports Server (NTRS)

    1994-01-01

    A new material known as AlBeMet, developed by Brush Wellman for research applications in the National Aero-Space Plane (NASP) program, is now used for high performance disk drives. AlBeMet is a compression of aluminum, beryllium metal matrix composite. It reduces system weight and its high thermal conductivity can effectively remove heat and increase an electrical system's lifetime. The lighter, stiffer AlBeMet (AlBeMet 160) used in the disk drive means heads can be moved faster, improving disk performance.

  6. Differential distribution of G-protein beta-subunits in brain: an immunocytochemical analysis.

    PubMed

    Brunk, I; Pahner, I; Maier, U; Jenner, B; Veh, R W; Nürnberg, B; Ahnert-Hilger, G

    1999-05-01

    Heterotrimeric G proteins play central roles in signal transduction of neurons and other cells. The variety of their alpha-, beta-, and gamma-subunits allows numerous combinations thereby confering specificity to receptor-G-protein-effector interactions. Using antisera against individual G-protein beta-subunits we here present a regional and subcellular distribution of Gbeta1, Gbeta2, and Gbeta5 in rat brain. Immunocytochemical specificity of the subtype-specific antisera is revealed in Sf9 cells infected with various G-protein beta-subunits. Since Gbeta-subunits together with a G-protein gamma-subunit affect signal cascades we include a distribution of the neuron-specific Ggamma2- and Ggamma3-subunits in selected brain areas. Gbeta1, Gbeta2, and Gbeta5 are preferentially distributed in the neuropil of hippocampus, cerebellum and spinal cord. Gbeta2 is highly concentrated in the mossy fibres of dentate gyrus neurons ending in the stratum lucidum of hippocampal CA3-area. High amounts of Gbeta2 also occur in interneurons innervating spinal cord alpha-motoneurons. Gbeta5 is differentially distributed in all brain areas studied. It is found in the pyramidal cells of hippocampal CA1-CA3 as well as in the granule cell layer of dentate gyrus and in some interneurons. In the spinal cord Gbeta5 in contrast to Gbeta2 concentrates around alpha-motoneurons. In cultivated mouse hippocampal and hypothalamic neurons Gbeta2 and Gbeta5 are found in different subcellular compartments. Whereas Gbeta5 is restricted to the perikarya, Gbeta2 is also found in processes and synaptic contacts where it partially colocalizes with the synaptic vesicle protein synaptobrevin. An antiserum recognizing Ggamma2 and Ggamma3 reveals that these subunits are less expressed in hippocampus and cerebellum. Presumably this antiserum specifically recognizes Ggamma2 and Ggamma3 in combinations with certain G alphas and/or Gbetas. The widespread but regionally and cellularly rather different distribution of

  7. iTRAQ-based protein profiling provides insights into the central metabolism changes driving grape berry development and ripening

    PubMed Central

    2013-01-01

    Background Grapevine (Vitis vinifera L.) is an economically important fruit crop. Quality-determining grape components such as sugars, acids, flavors, anthocyanins, tannins, etc., accumulate in the different grape berry development stages. Thus, correlating the proteomic profiles with the biochemical and physiological changes occurring in grape is of paramount importance to advance in our understanding of berry development and ripening processes. Results We report the developmental analysis of Vitis vinifera cv. Muscat Hamburg berries at the protein level from fruit set to full ripening. An iTRAQ-based bottom-up proteomic approach followed by tandem mass spectrometry led to the identification and quantitation of 411 and 630 proteins in the green and ripening phases, respectively. Two key points in development relating to changes in protein level were detected: end of the first growth period (7 mm-to-15 mm) and onset of ripening (15 mm-to-V100, V100-to-110). A functional analysis was performed using the Blast2GO software based on the enrichment of GO terms during berry growth. Conclusions The study of the proteome contributes to decipher the biological processes and metabolic pathways involved in the development and quality traits of fruit and its derived products. These findings lie mainly in metabolism and storage of sugars and malate, energy-related pathways such as respiration, photosynthesis and fermentation, and the synthesis of polyphenolics as major secondary metabolites in grape berry. In addition, some key steps in carbohydrate and malate metabolism have been identified in this study, i.e., PFP-PFK or SuSy-INV switches among others, which may influence the final sugar and acid balance in ripe fruit. In conclusion, some proteins not reported to date have been detected to be deregulated in specific tissues and developmental stages, leading to formulate new hypotheses on the metabolic processes underlying grape berry development. These results open up

  8. Distribution of neurofilament protein and calcium-binding proteins parvalbumin, calbindin, and calretinin in the canine hippocampus.

    PubMed

    Hof, P R; Rosenthal, R E; Fiskum, G

    1996-07-01

    Neurofilament protein and calcium-binding proteins parvalbumin, calbindin, and calretinin are present in morphologically distinct neuronal subpopulations in the mammalian cerebral cortex. Immunohistochemical studies of the hippocampal formation and neocortex have demonstrated that while neurofilament protein and calbindin are localized in subsets of pyramidal neurons, the three calcium-binding proteins are useful markers to differentiate non-overlapping populations of interneurons. To date, most studies have been performed in rodents and primates. In the present analysis, we analyzed the distribution of these proteins in the canine hippocampus. Neurofilament protein was present in large multipolar neurons in the hilus and in pyramidal neurons in the CA3 field, whereas pyramidal neurons in the CA1 field and subiculum were less intensely immunoreactive. Parvalbumin immunoreactivity was observed in large multipolar neurons in the hilus and throughout the CA3-CA1 fields, in a few pyramidal-shaped neurons in the CA1 field and subiculum, and had a distinct neuropil staining pattern in the granule cell layer and stratum pyramidale of the Ammon's horn. Calbindin immunoreactivity displayed a strong labeling of the granule cells and mossy fibers and was also observed in a population of moderately immunoreactive neurons in the CA1 field and subiculum. Calretinin immunoreactivity was relatively weaker overall. The inner molecular layer in the dentate gyrus had a distinct band of labeling, the stratum lacunosum/moleculare contained a punctate neuropil staining, and there were a few small multipolar neurons in the hilus, CA3-CA1 fields, and subiculum. Comparison of the staining patterns observed in the dog hippocampus with those in human, macaque monkeys and rats revealed that although there are some subregional differences among these taxa, the dog may constitute a valuable large animal model for the study of certain neurological conditions that affect humans, in spite of the

  9. Fidelity drive: a mechanism for chaperone proteins to maintain stable mutation rates in prokaryotes over evolutionary time.

    PubMed

    Xue, Julian Z; Kaznatcheev, Artem; Costopoulos, Andre; Guichard, Frederic

    2015-01-07

    We show a mechanism by which chaperone proteins can play a key role in maintaining the long-term evolutionary stability of mutation rates in prokaryotes with perfect genetic linkage. Since chaperones can reduce the phenotypic effects of mutations, higher mutation rate, by affecting chaperones, can increase the phenotypic effects of mutations. This in turn leads to greater mutation effect among the proteins that control mutation repair and DNA replication, resulting in large changes in mutation rate. The converse of this is that when mutation rate is low and chaperones are functioning well, then the rate of change in mutation rate will also be low, leading to low mutation rates being evolutionarily frozen. We show that the strength of this recursion is critical to determining the long-term evolutionary patterns of mutation rate among prokaryotes. If this recursion is weak, then mutation rates can grow without bound, leading to the extinction of the lineage. However, if this recursion is strong, then we can reproduce empirical patterns of prokaryotic mutation rates, where mutation rates remain stable over evolutionary time, and where most mutation rates are low, but with a significant fraction of high mutators.

  10. Direct Membrane Association Drives Mitochondrial Fission by the Parkinson Disease-associated Protein α-Synuclein*♦

    PubMed Central

    Nakamura, Ken; Nemani, Venu M.; Azarbal, Farnaz; Skibinski, Gaia; Levy, Jon M.; Egami, Kiyoshi; Munishkina, Larissa; Zhang, Jue; Gardner, Brooke; Wakabayashi, Junko; Sesaki, Hiromi; Cheng, Yifan; Finkbeiner, Steven; Nussbaum, Robert L.; Masliah, Eliezer; Edwards, Robert H.

    2011-01-01

    The protein α-synuclein has a central role in Parkinson disease, but the mechanism by which it contributes to neural degeneration remains unknown. We now show that the expression of α-synuclein in mammalian cells, including neurons in vitro and in vivo, causes the fragmentation of mitochondria. The effect is specific for synuclein, with more fragmentation by α- than β- or γ-isoforms, and it is not accompanied by changes in the morphology of other organelles or in mitochondrial membrane potential. However, mitochondrial fragmentation is eventually followed by a decline in respiration and neuronal death. The fragmentation does not require the mitochondrial fission protein Drp1 and involves a direct interaction of synuclein with mitochondrial membranes. In vitro, synuclein fragments artificial membranes containing the mitochondrial lipid cardiolipin, and this effect is specific for the small oligomeric forms of synuclein. α-Synuclein thus exerts a primary and direct effect on the morphology of an organelle long implicated in the pathogenesis of Parkinson disease. PMID:21489994

  11. Effect of the surface charge distribution on the fluid phase behavior of charged colloids and proteins

    NASA Astrophysics Data System (ADS)

    Blanco, Marco A.; Shen, Vincent K.

    2016-10-01

    A generic but simple model is presented to evaluate the effect of the heterogeneous surface charge distribution of proteins and zwitterionic nanoparticles on their thermodynamic phase behavior. By considering surface charges as continuous "patches," the rich set of surface patterns that is embedded in proteins and charged patchy particles can readily be described. This model is used to study the fluid phase separation of charged particles where the screening length is of the same order of magnitude as the particle size. In particular, two types of charged particles are studied: dipolar fluids and protein-like fluids. The former represents the simplest case of zwitterionic particles, whose charge distribution can be described by their dipole moment. The latter system corresponds to molecules/particles with complex surface charge arrangements such as those found in biomolecules. The results for both systems suggest a relation between the critical region, the strength of the interparticle interactions, and the arrangement of charged patches, where the critical temperature is strongly correlated to the magnitude of the dipole moment. Additionally, competition between attractive and repulsive charge-charge interactions seems to be related to the formation of fluctuating clusters in the dilute phase of dipolar fluids, as well as to the broadening of the binodal curve in protein-like fluids. Finally, a variety of self-assembled architectures are detected for dipolar fluids upon small changes to the charge distribution, providing the groundwork for studying the self-assembly of charged patchy particles.

  12. Altered distribution of tight junction proteins after intestinal ischaemia/reperfusion injury in rats

    PubMed Central

    Li, Qiurong; Zhang, Qiang; Wang, Chenyang; Liu, Xiaoxiang; Qu, Linlin; Gu, Lili; Li, Ning; Li, Jieshou

    2009-01-01

    Tight junction (TJ) disruptions have been demonstrated both in vitro and more recently in vivo in infection. However, the molecular basis for changes of TJ during ischaemia-reperfusion (I/R) injury is poorly understood. In the present study, intestinal damage was induced by I/R in an animal model. As assessed by TUNEL and propidium iodide uptake, we showed that I/R injury induced apoptosis as well as necrosis in rat colon, and the frequency of apoptotic and necrotic cells reached the maximum at 5 hrs of reperfusion. Immunofluorescence microscopy revealed that claudins 1, 3 and 5 are strongly expressed in the surface epithelial cells of the colon; however, labelling of all three proteins was present diffusely within cells and no longer focused at the lateral cell boundaries after I/R. Using Western blot analysis, we found that distribution of TJ proteins in membrane microdomains of TJ was markedly affected in I/R injury rats. Occludin, ZO-1, claudin-1 and claudin-3 were completely displaced from TX-100 insoluble fractions to TX-100 soluble fractions, and claudin-5 was partly displaced. The distribution of lipid raft marker protein caveolin-1 was also changed after I/R. I/R injury results in the disruption of TJs, which characterized by relocalization of the claudins 1, 3 and 5 and an increase in intestinal permeability using molecular tracer measurement. I/R injury altered distribution of TJ proteins in vivo that was associated with functional TJ deficiencies. PMID:19929946

  13. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing.

    PubMed

    Pande, Vijay S; Baker, Ian; Chapman, Jarrod; Elmer, Sidney P; Khaliq, Siraj; Larson, Stefan M; Rhee, Young Min; Shirts, Michael R; Snow, Christopher D; Sorin, Eric J; Zagrovic, Bojan

    2003-01-01

    Atomistic simulations of protein folding have the potential to be a great complement to experimental studies, but have been severely limited by the time scales accessible with current computer hardware and algorithms. By employing a worldwide distributed computing network of tens of thousands of PCs and algorithms designed to efficiently utilize this new many-processor, highly heterogeneous, loosely coupled distributed computing paradigm, we have been able to simulate hundreds of microseconds of atomistic molecular dynamics. This has allowed us to directly simulate the folding mechanism and to accurately predict the folding rate of several fast-folding proteins and polymers, including a nonbiological helix, polypeptide alpha-helices, a beta-hairpin, and a three-helix bundle protein from the villin headpiece. Our results demonstrate that one can reach the time scales needed to simulate fast folding using distributed computing, and that potential sets used to describe interatomic interactions are sufficiently accurate to reach the folded state with experimentally validated rates, at least for small proteins.

  14. Distribution of protein poly(ADP-ribosyl)ation systems across all domains of life

    PubMed Central

    Perina, Dragutin; Mikoč, Andreja; Ahel, Josip; Ćetković, Helena; Žaja, Roko; Ahel, Ivan

    2014-01-01

    Poly(ADP-ribosyl)ation is a post-translational modification of proteins involved in regulation of many cellular pathways. Poly(ADP-ribose) (PAR) consists of chains of repeating ADP-ribose nucleotide units and is synthesized by the family of enzymes called poly(ADP-ribose) polymerases (PARPs). This modification can be removed by the hydrolytic action of poly(ADP-ribose) glycohydrolase (PARG) and ADP-ribosylhydrolase 3 (ARH3). Hydrolytic activity of macrodomain proteins (MacroD1, MacroD2 and TARG1) is responsible for the removal of terminal ADP-ribose unit and for complete reversion of protein ADP-ribosylation. Poly(ADP-ribosyl)ation is widely utilized in eukaryotes and PARPs are present in representatives from all six major eukaryotic supergroups, with only a small number of eukaryotic species that do not possess PARP genes. The last common ancestor of all eukaryotes possessed at least five types of PARP proteins that include both mono and poly(ADP-ribosyl) transferases. Distribution of PARGs strictly follows the distribution of PARP proteins in eukaryotic species. At least one of the macrodomain proteins that hydrolyse terminal ADP-ribose is also always present. Therefore, we can presume that the last common ancestor of all eukaryotes possessed a fully functional and reversible PAR metabolism and that PAR signalling provided the conditions essential for survival of the ancestral eukaryote in its ancient environment. PARP proteins are far less prevalent in bacteria and were probably gained through horizontal gene transfer. Only eleven bacterial species possess all proteins essential for a functional PAR metabolism, although it is not known whether PAR metabolism is truly functional in bacteria. Several dsDNA viruses also possess PARP homologues, while no PARP proteins have been identified in any archaeal genome. Our analysis of the distribution of enzymes involved in PAR metabolism provides insight into the evolution of these important signalling systems, as well as

  15. Central Nodes in Protein Interaction Networks Drive Critical Functions in Transforming Growth Factor Beta-1 Stimulated Kidney Cells

    PubMed Central

    Gheisari, Yousof

    2017-01-01

    Objective Despite the huge efforts, chronic kidney disease (CKD) remains as an unsolved problem in medicine. Many studies have shown a central role for transforming growth factor beta-1 (TGFβ-1) and its downstream signaling cascades in the pathogenesis of CKD. In this study, we have reanalyzed a microarray dataset to recognize critical signaling pathways controlled by TGFβ-1. Materials and Methods This study is a bioinformatics reanalysis for a microarray data. The GSE23338 dataset was downloaded from the gene expression omnibus (GEO) database which assesses the mRNA expression profile of TGFβ-1 treated human kidney cells after 24 and 48 hours incubation. The protein interaction networks for differentially expressed (DE) genes in both time points were constructed and enriched. In addition, by network topology analysis, genes with high centrality were identified and then pathway enrichment analysis was performed with either the total network genes or with the central nodes. Results We found 110 and 170 genes differentially expressed in the time points 24 and 48 hours, respectively. As the genes in each time point had few interactions, the networks were enriched by adding previously known genes interacting with the differentially expressed ones. In terms of degree, betweenness, and closeness centrality parameters 62 and 60 nodes were considered to be central in the enriched networks of 24 hours and 48 hours treatment, respectively. Pathway enrichment analysis with the central nodes was more informative than those with all network nodes or even initial DE genes, revealing key signaling pathways. Conclusion We here introduced a method for the analysis of microarray data that integrates the expression pattern of genes with their topological properties in protein interaction networks. This holistic novel approach allows extracting knowledge from raw bulk omics data. PMID:28042536

  16. Phenotype Clustering of Breast Epithelial Cells in Confocal Imagesbased on Nuclear Protein Distribution Analysis

    SciTech Connect

    Long, Fuhui; Peng, Hanchuan; Sudar, Damir; Levievre, Sophie A.; Knowles, David W.

    2006-09-05

    Background: The distribution of the chromatin-associatedproteins plays a key role in directing nuclear function. Previously, wedeveloped an image-based method to quantify the nuclear distributions ofproteins and showed that these distributions depended on the phenotype ofhuman mammary epithelial cells. Here we describe a method that creates ahierarchical tree of the given cell phenotypes and calculates thestatistical significance between them, based on the clustering analysisof nuclear protein distributions. Results: Nuclear distributions ofnuclear mitotic apparatus protein were previously obtained fornon-neoplastic S1 and malignant T4-2 human mammary epithelial cellscultured for up to 12 days. Cell phenotype was defined as S1 or T4-2 andthe number of days in cultured. A probabilistic ensemble approach wasused to define a set of consensus clusters from the results of multipletraditional cluster analysis techniques applied to the nucleardistribution data. Cluster histograms were constructed to show how cellsin any one phenotype were distributed across the consensus clusters.Grouping various phenotypes allowed us to build phenotype trees andcalculate the statistical difference between each group. The resultsshowed that non-neoplastic S1 cells could be distinguished from malignantT4-2 cells with 94.19 percent accuracy; that proliferating S1 cells couldbe distinguished from differentiated S1 cells with 92.86 percentaccuracy; and showed no significant difference between the variousphenotypes of T4-2 cells corresponding to increasing tumor sizes.Conclusion: This work presents a cluster analysis method that canidentify significant cell phenotypes, based on the nuclear distributionof specific proteins, with high accuracy.

  17. Study of selenium distribution in the protein fractions of the Brazil nut, Bertholletia excelsa.

    PubMed

    Chunhieng, Thavarith; Pétritis, Konstantinos; Elfakir, Claire; Brochier, José; Goli, Thierry; Montet, Didier

    2004-06-30

    The high selenium content of the Brazil nut, Bertholletia excelsa, makes this seed a healthy food qualified as an antiradical protector. The studied nut contained 126 ppm of selenium. Selenium was found to be distributed in the nut protein fractions. The water-extracted fraction, which represented 17.7% of the cake protein, was the richest in selenium with 153 ppm. Analysis by HPLC-MS showed that selenium was linked by a covalent bond to two amino acids to form selenomethionine and selenocystine. The selenomethionine represented a little less than 1% of the total amount of methionine.

  18. Distinct distribution of specific members of protein 4.1 genefamily in the mouse nephron

    SciTech Connect

    Ramez, Mohamed; Blot-Chabaud, Marcel; Cluzeaud, Francoise; Chanan, Sumita; Patterson, Michael; Walensky, Loren D.; Marfatia, Shirin; Baines, Anthony J.; Chasis, Joel A.; Conboy, John G.; Mohandas, Narla; Gascard, Philippe

    2002-12-11

    Background: Protein 4.1 is an adapter protein which linksthe actin cytoskeleton to various transmembrane proteins. 4.1 proteinsare encoded by four homologous genes, 4.1R, 4.1G, 4.1N, and 4.1B, whichundergo complex alternative splicing. Here we performed a detailedcharacterization of the expression of specific 4.1 proteins in the mousenephron. Methods: Distribution of renal 4.1 proteins was investigated bystaining of paraformaldehyde fixed mouse kidney sections with antibodieshighly specific for each 4.1 protein. Major 4.1 splice forms, amplifiedfrom mouse kidney marathon cDNA, were expressed in transfected COS-7cells in order to assign species of known exon composition to proteinsdetected in kidney. Results: A 105kDa4.1R splice form, initiating atATG-2 translation initiation site and lacking exon 16, but including exon17B, was restricted to thick ascending limb of Henle's loop. A 95kDa 4.1Nspliceform,lacking exons 15 and 17D, was expressed in either descendingor ascending thin limb of Henle'sloop, distal convoluted tubule and allregions of the collecting duct system. A major 108kDa 4.1B spliceform,initiating at a newly characterized ATG translation initiation site, andlacking exons 15, 17B, and 21, was present only in Bowman's capsule andproximal convoluted tubule (PCT). There was no expression of 4.1G inkidney. Conclusion: Distinct distribution of 4.1 proteins along thenephron suggests their involvement in targeting of selected transmembraneproteins in kidney epithelium andtherefore in regulation of specifickidney functions.

  19. The human SKA complex drives the metaphase-anaphase cell cycle transition by recruiting protein phosphatase 1 to kinetochores

    PubMed Central

    Sivakumar, Sushama; Janczyk, Paweł Ł; Qu, Qianhui; Brautigam, Chad A; Stukenberg, P Todd; Yu, Hongtao; Gorbsky, Gary J

    2016-01-01

    The spindle- and kinetochore-associated (Ska) complex is essential for normal anaphase onset in mitosis. The C-terminal domain (CTD) of Ska1 binds microtubules and was proposed to facilitate kinetochore movement on depolymerizing spindle microtubules. Here, we show that Ska complex recruits protein phosphatase 1 (PP1) to kinetochores. This recruitment requires the Ska1 CTD, which binds PP1 in vitro and in human HeLa cells. Ska1 lacking its CTD fused to a PP1-binding peptide or fused directly to PP1 rescues mitotic defects caused by Ska1 depletion. Ska1 fusion to catalytically dead PP1 mutant does not rescue and shows dominant negative effects. Thus, the Ska complex, specifically the Ska1 CTD, recruits PP1 to kinetochores to oppose spindle checkpoint signaling kinases and promote anaphase onset. Microtubule binding by Ska, rather than acting in force production for chromosome movement, may instead serve to promote PP1 recruitment to kinetochores fully attached to spindle microtubules at metaphase. DOI: http://dx.doi.org/10.7554/eLife.12902.001 PMID:26981768

  20. CROSS DRIVE: A New Interactive and Immersive Approach for Exploring 3D Time-Dependent Mars Atmospheric Data in Distributed Teams

    NASA Astrophysics Data System (ADS)

    Gerndt, Andreas M.; Engelke, Wito; Giuranna, Marco; Vandaele, Ann C.; Neary, Lori; Aoki, Shohei; Kasaba, Yasumasa; Garcia, Arturo; Fernando, Terrence; Roberts, David; CROSS DRIVE Team

    2016-10-01

    Atmospheric phenomena of Mars can be highly dynamic and have daily and seasonal variations. Planetary-scale wavelike disturbances, for example, are frequently observed in Mars' polar winter atmosphere. Possible sources of the wave activity were suggested to be dynamical instabilities and quasi-stationary planetary waves, i.e. waves that arise predominantly via zonally asymmetric surface properties. For a comprehensive understanding of these phenomena, single layers of altitude have to be analyzed carefully and relations between different atmospheric quantities and interaction with the surface of Mars have to be considered. The CROSS DRIVE project tries to address the presentation of those data with a global view by means of virtual reality techniques. Complex orbiter data from spectrometer and observation data from Earth are combined with global circulation models and high-resolution terrain data and images available from Mars Express or MRO instruments. Scientists can interactively extract features from those dataset and can change visualization parameters in real-time in order to emphasize findings. Stereoscopic views allow for perception of the actual 3D behavior of Mars's atmosphere. A very important feature of the visualization system is the possibility to connect distributed workspaces together. This enables discussions between distributed working groups. The workspace can scale from virtual reality systems to expert desktop applications to web-based project portals. If multiple virtual environments are connected, the 3D position of each individual user is captured and used to depict the scientist as an avatar in the virtual world. The appearance of the avatar can also scale from simple annotations to complex avatars using tele-presence technology to reconstruct the users in 3D. Any change of the feature set (annotations, cutplanes, volume rendering, etc.) within the VR is immediately exchanged between all connected users. This allows that everybody is always

  1. Taxonomic distribution and origins of the extended LHC (light-harvesting complex) antenna protein superfamily

    PubMed Central

    2010-01-01

    Background The extended light-harvesting complex (LHC) protein superfamily is a centerpiece of eukaryotic photosynthesis, comprising the LHC family and several families involved in photoprotection, like the LHC-like and the photosystem II subunit S (PSBS). The evolution of this complex superfamily has long remained elusive, partially due to previously missing families. Results In this study we present a meticulous search for LHC-like sequences in public genome and expressed sequence tag databases covering twelve representative photosynthetic eukaryotes from the three primary lineages of plants (Plantae): glaucophytes, red algae and green plants (Viridiplantae). By introducing a coherent classification of the different protein families based on both, hidden Markov model analyses and structural predictions, numerous new LHC-like sequences were identified and several new families were described, including the red lineage chlorophyll a/b-binding-like protein (RedCAP) family from red algae and diatoms. The test of alternative topologies of sequences of the highly conserved chlorophyll-binding core structure of LHC and PSBS proteins significantly supports the independent origins of LHC and PSBS families via two unrelated internal gene duplication events. This result was confirmed by the application of cluster likelihood mapping. Conclusions The independent evolution of LHC and PSBS families is supported by strong phylogenetic evidence. In addition, a possible origin of LHC and PSBS families from different homologous members of the stress-enhanced protein subfamily, a diverse and anciently paralogous group of two-helix proteins, seems likely. The new hypothesis for the evolution of the extended LHC protein superfamily proposed here is in agreement with the character evolution analysis that incorporates the distribution of families and subfamilies across taxonomic lineages. Intriguingly, stress-enhanced proteins, which are universally found in the genomes of green plants

  2. Ceramic vane drive joint

    DOEpatents

    Smale, Charles H.

    1981-01-01

    A variable geometry gas turbine has an array of ceramic composition vanes positioned by an actuating ring coupled through a plurality of circumferentially spaced turbine vane levers to the outer end of a metallic vane drive shaft at each of the ceramic vanes. Each of the ceramic vanes has an end slot of bow tie configuration including flared end segments and a center slot therebetween. Each of the vane drive shafts has a cross head with ends thereof spaced with respect to the sides of the end slot to define clearance for free expansion of the cross head with respect to the vane and the cross head being configured to uniformly distribute drive loads across bearing surfaces of the vane slot.

  3. The distribution and query systems of the RCSB Protein Data Bank

    PubMed Central

    Bourne, Philip E.; Addess, Kenneth J.; Bluhm, Wolfgang F.; Chen, Li; Deshpande, Nita; Feng, Zukang; Fleri, Ward; Green, Rachel; Merino-Ott, Jeffrey C.; Townsend-Merino, Wayne; Weissig, Helge; Westbrook, John; Berman, Helen M.

    2004-01-01

    The Protein Data Bank (PDB; http://www.pdb.org) is the primary source of information on the 3D structure of biological macromolecules. The PDB’s mandate is to disseminate this information in the most usable form and as widely as possible. The current query and distribution system is described and an alpha version of the future re-engineered system introduced. PMID:14681399

  4. Monomeric C-reactive protein-a key molecule driving development of Alzheimer’s disease associated with brain ischaemia?

    PubMed Central

    Slevin, M.; Matou, S.; Zeinolabediny, Y.; Corpas, R.; Weston, R.; Liu, D.; Boras, E.; Di Napoli, M.; Petcu, E.; Sarroca, S.; Popa-Wagner, A.; Love, S.; Font, M. A.; Potempa, L. A.; Al-baradie, R.; Sanfeliu, C.; Revilla, S.; Badimon, L.; Krupinski, J.

    2015-01-01

    Alzheimer’s disease (AD) increases dramatically in patients with ischaemic stroke. Monomeric C-reactive protein (mCRP) appears in the ECM of ischaemic tissue after stroke, associating with microvasculature, neurons and AD-plaques, Aβ, also, being able to dissociate native-CRP into inflammatory, mCRP in vivo. Here, mCRP injected into the hippocampal region of mice was retained within the retrosplenial tract of the dorsal 3rd ventrical and surrounding major vessels. Mice developed behavioural/cognitive deficits within 1 month, concomitant with mCRP staining within abnormal looking neurons expressing p-tau and in beta-amyloid 1-42-plaque positive regions. mCRP co-localised with CD105 in microvessels suggesting angiogenesis. Phospho-arrays/Western blotting identified signalling activation in endothelial cells and neurons through p-IRS-1, p-Tau and p-ERK1/2-which was blocked following pre-incubation with mCRP-antibody. mCRP increased vascular monolayer permeability and gap junctions, increased NCAM expression and produced haemorrhagic angiogenesis in mouse matrigel implants. mCRP induced tau244–372 aggregation and assembly in vitro. IHC study of human AD/stroke patients revealed co-localization of mCRP with Aβ plaques, tau-like fibrils and IRS-1/P-Tau positive neurons and high mCRP-levels spreading from infarcted core regions matched reduced expression of Aβ/Tau. mCRP may be responsible for promoting dementia after ischaemia and mCRP clearance could inform therapeutic avenues to reduce the risk of future dementia. PMID:26335098

  5. Point mutations in the major outer membrane protein drive hypervirulence of a rapidly expanding clone of Campylobacter jejuni

    PubMed Central

    Wu, Zuowei; Periaswamy, Balamurugan; Sahin, Orhan; Yaeger, Michael; Plummer, Paul; Zhai, Weiwei; Shen, Zhangqi; Dai, Lei; Zhang, Qijing

    2016-01-01

    Infections due to clonal expansion of highly virulent bacterial strains are clear and present threats to human and animal health. Association of genetic changes with disease is now a routine, but identification of causative mutations that enable disease remains difficult. Campylobacter jejuni is an important zoonotic pathogen transmitted to humans mainly via the foodborne route. C. jejuni typically colonizes the gut, but a hypervirulent and rapidly expanding clone of C. jejuni recently emerged, which is able to translocate across the intestinal tract, causing systemic infection and abortion in pregnant animals. The genetic basis responsible for this hypervirulence is unknown. Here, we developed a strategy, termed “directed genome evolution,” by using hybridization between abortifacient and nonabortifacient strains followed by selection in an animal disease model and whole-genome sequence analysis. This strategy successfully identified SNPs in porA, encoding the major outer membrane protein, are responsible for the hypervirulence. Defined mutagenesis verified that these mutations were both necessary and sufficient for causing abortion. Furthermore, sequence analysis identified porA as the gene with the top genome-wide signal of adaptive evolution using Fu’s Fs, a population genetic metric for recent population size changes, which is consistent with the recent expansion of clone “sheep abortion.” These results identify a key virulence factor in Campylobacter and a potential target for the control of this zoonotic pathogen. Furthermore, this study provides general, unbiased experimental and computational approaches that are broadly applicable for efficient elucidation of disease-causing mutations in bacterial pathogens. PMID:27601641

  6. Distribution of Polycyclic Aromatic Hydrocarbons (PAHs) in sludge organic matter pools as a driving force of their fate during anaerobic digestion.

    PubMed

    Aemig, Quentin; Chéron, Claire; Delgenès, Nadine; Jimenez, Julie; Houot, Sabine; Steyer, Jean-Philippe; Patureau, Dominique

    2016-02-01

    The fate of organic matter during anaerobic digestion of sewage sludge was studied in batch systems thanks to a sequential chemical fractionation of the particulate phase coupled to fluorescence spectroscopy. Polycyclic Aromatic Hydrocarbons (PAHs) distribution within the organic pools was characterized from their analysis in the residual fraction after each extraction. Both methods were combined to understand the link between PAHs presence in organic pools and their spectral characterization after extraction. Two batch systems (sludge and inoculum mixture) were set up to study the impact of PAHs spiking on their fate and distribution. The sequential fractionation allowed us to extract and characterize about 50% of total Chemical Oxygen Demand. Moreover, fluorescence spectroscopy helped us to understand the organic pools evolution: the most easily extracted pools composed of protein-like molecules were highly degraded meaning that chemical accessibility mimics the bioaccessibility to degrading microorganisms. PAHs were present in all pools of organic matter but native PAHs were mainly present in low accessible (hardly extractable) fractions and during anaerobic digestion, they accumulated in the non-accessible (non extractable) fraction. Spiked PAHs were more dissipated during anaerobic digestion since spiking made them present in more accessible fractions. During the anaerobic digestion, contrary to native PAHs, spiked ones relocated toward less accessible organic fractions confirming the ageing phenomenon. PCA analysis showed that, in spiked mixture, PAHs presence in organic pools is linked to both PAHs physical-chemical properties and quality/quantity of the associated organic pools.

  7. Nanosecond Motions in Proteins Impose Bounds on the Timescale Distributions of Local Dynamics

    PubMed Central

    Okan, Osman Burak; Atilgan, Ali Rana; Atilgan, Canan

    2009-01-01

    Abstract We elucidate the physics of protein dynamical transition via 10–100-ns molecular dynamics simulations at temperatures spanning 160–300 K. By tracking the energy fluctuations, we show that the protein dynamical transition is marked by a crossover from nonstationary to stationary processes that underlie the dynamics of protein motions. A two-timescale function captures the nonexponential character of backbone structural relaxations. One timescale is attributed to the collective segmental motions and the other to local relaxations. The former is well defined by a single-exponential, nanosecond decay, operative at all temperatures. The latter is described by a set of processes that display a distribution of timescales. Although their average remains on the picosecond timescale, the distribution is markedly contracted at the onset of the transition. It is shown that the collective motions impose bounds on timescales spanned by local dynamical processes. The nonstationary character below the transition implicates the presence of a collection of substates whose interactions are restricted. At these temperatures, a wide distribution of local-motion timescales, extending beyond that of nanoseconds, is observed. At physiological temperatures, local motions are confined to timescales faster than nanoseconds. This relatively narrow window makes possible the appearance of multiple channels for the backbone dynamics to operate. PMID:19804740

  8. The neuronal extracellular matrix restricts distribution and internalization of aggregated Tau-protein.

    PubMed

    Suttkus, A; Holzer, M; Morawski, M; Arendt, T

    2016-01-28

    Alzheimer's disease (AD) is a chronic degenerative disorder characterized by fibrillary aggregates of Aß and Tau-protein. Formation and progression of these pathological hallmarks throughout the brain follow a specific spatio-temporal pattern which provides the basis for neuropathological staging. Previously, we could demonstrate that cortical and subcortical neurons are less frequently affected by neurofibrillary degeneration if they are enwrapped by a specialized form of the hyaluronan-based extracellular matrix (ECM), the so called 'perineuronal net' (PN). PNs are composed of large aggregating chondroitin sulfate proteoglycans connected to a hyaluronan backbone, stabilized by link proteins and cross-linked via tenascin-R. Recently, PN-associated neurons were shown to be better protected against iron-induced neurodegeneration compared to neurons without PN, indicating a neuroprotective function. Here, we investigated the role of PNs in distribution and internalization of exogenous Tau-protein by using organotypic slice cultures of wildtype mice as well as mice lacking the ECM-components aggrecan, HAPLN1 or tenascin-R. We could demonstrate that PNs restrict both distribution and internalization of Tau. Accordingly, PN-ensheathed neurons were less frequently affected by Tau-internalization, than neurons without PN. Finally, the PNs as well as their three investigated components were shown to modulate the processes of distribution as well as internalization of Tau.

  9. Arabinogalactan proteins in root and pollen-tube cells: distribution and functional aspects

    PubMed Central

    Nguema-Ona, Eric; Coimbra, Sílvia; Vicré-Gibouin, Maïté; Mollet, Jean-Claude; Driouich, Azeddine

    2012-01-01

    Background Arabinogalactan proteins (AGPs) are complex proteoglycans of the cell wall found in the entire plant kingdom and in almost all plant organs. AGPs encompass a large group of heavily glycosylated cell-wall proteins which share common features, including the presence of glycan chains especially enriched in arabinose and galactose and a protein backbone particularly rich in hydroxyproline residues. However, AGPs also exhibit strong heterogeneities among their members in various plant species. AGP ubiquity in plants suggests these proteoglycans are fundamental players for plant survival and development. Scope In this review, we first present an overview of current knowledge and specific features of AGPs. A section devoted to major tools used to study AGPs is also presented. We then discuss the distribution of AGPs as well as various aspects of their functional properties in root tissues and pollen tubes. This review also suggests novel directions of research on the role of AGPs in the biology of roots and pollen tubes. PMID:22786747

  10. cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design.

    PubMed

    Pan, Yuchao; Dong, Yuxi; Zhou, Jingtian; Hallen, Mark; Donald, Bruce R; Zeng, Jianyang; Xu, Wei

    2016-09-01

    Finding the global minimum energy conformation (GMEC) of a huge combinatorial search space is the key challenge in computational protein design (CPD) problems. Traditional algorithms lack a scalable and efficient distributed design scheme, preventing researchers from taking full advantage of current cloud infrastructures. We design cloud OSPREY (cOSPREY), an extension to a widely used protein design software OSPREY, to allow the original design framework to scale to the commercial cloud infrastructures. We propose several novel designs to integrate both algorithm and system optimizations, such as GMEC-specific pruning, state search partitioning, asynchronous algorithm state sharing, and fault tolerance. We evaluate cOSPREY on three different cloud platforms using different technologies and show that it can solve a number of large-scale protein design problems that have not been possible with previous approaches.

  11. Distributions of experimental protein structures on coarse-grained free energy landscapes

    NASA Astrophysics Data System (ADS)

    Sankar, Kannan; Liu, Jie; Wang, Yuan; Jernigan, Robert L.

    2015-12-01

    Predicting conformational changes of proteins is needed in order to fully comprehend functional mechanisms. With the large number of available structures in sets of related proteins, it is now possible to directly visualize the clusters of conformations and their conformational transitions through the use of principal component analysis. The most striking observation about the distributions of the structures along the principal components is their highly non-uniform distributions. In this work, we use principal component analysis of experimental structures of 50 diverse proteins to extract the most important directions of their motions, sample structures along these directions, and estimate their free energy landscapes by combining knowledge-based potentials and entropy computed from elastic network models. When these resulting motions are visualized upon their coarse-grained free energy landscapes, the basis for conformational pathways becomes readily apparent. Using three well-studied proteins, T4 lysozyme, serum albumin, and sarco-endoplasmic reticular Ca2+ adenosine triphosphatase (SERCA), as examples, we show that such free energy landscapes of conformational changes provide meaningful insights into the functional dynamics and suggest transition pathways between different conformational states. As a further example, we also show that Monte Carlo simulations on the coarse-grained landscape of HIV-1 protease can directly yield pathways for force-driven conformational changes.

  12. Dynamic measurement of fluorescent proteins spectral distribution on virus infected cells

    NASA Astrophysics Data System (ADS)

    Lee, Ja-Yun; Wu, Ming-Xiu; Kao, Chia-Yun; Wu, Tzong-Yuan; Hsu, I.-Jen

    2006-09-01

    We constructed a dynamic spectroscopy system that can simultaneously measure the intensity and spectral distributions of samples with multi-fluorophores in a single scan. The system was used to monitor the fluorescence distribution of cells infected by the virus, which is constructed by a recombinant baculoviruses, vAcD-Rhir-E, containing the red and green fluorescent protein gene that can simultaneously produce dual fluorescence in recombinant virus-infected Spodoptera frugiperda 21 cells (Sf21) under the control of a polyhedrin promoter. The system was composed of an excitation light source, a scanning system and a spectrometer. We also developed an algorithm and fitting process to analyze the pattern of fluorescence distribution of the dual fluorescence produced in the recombinant virus-infected cells. All the algorithm and calculation are automatically processed in a visualized scanning program and can monitor the specific region of sample by calculating its intensity distribution. The spectral measurement of each pixel was performed at millisecond range and the two dimensional distribution of full spectrum was recorded within several seconds. We have constructed a dynamic spectroscopy system to monitor the process of virus-infection of cells. The distributions of the dual fluorescence were simultaneously measured at micrometer resolution.

  13. Distribution of language-related Cntnap2 protein in neural circuits critical for vocal learning.

    PubMed

    Condro, Michael C; White, Stephanie A

    2014-01-01

    Variants of the contactin associated protein-like 2 (Cntnap2) gene are risk factors for language-related disorders including autism spectrum disorder, specific language impairment, and stuttering. Songbirds are useful models for study of human speech disorders due to their shared capacity for vocal learning, which relies on similar cortico-basal ganglia circuitry and genetic factors. Here we investigate Cntnap2 protein expression in the brain of the zebra finch, a songbird species in which males, but not females, learn their courtship songs. We hypothesize that Cntnap2 has overlapping functions in vocal learning species, and expect to find protein expression in song-related areas of the zebra finch brain. We further expect that the distribution of this membrane-bound protein may not completely mirror its mRNA distribution due to the distinct subcellular localization of the two molecular species. We find that Cntnap2 protein is enriched in several song control regions relative to surrounding tissues, particularly within the adult male, but not female, robust nucleus of the arcopallium (RA), a cortical song control region analogous to human layer 5 primary motor cortex. The onset of this sexually dimorphic expression coincides with the onset of sensorimotor learning in developing males. Enrichment in male RA appears due to expression in projection neurons within the nucleus, as well as to additional expression in nerve terminals of cortical projections to RA from the lateral magnocellular nucleus of the nidopallium. Cntnap2 protein expression in zebra finch brain supports the hypothesis that this molecule affects neural connectivity critical for vocal learning across taxonomic classes.

  14. Protein fluorescence decay: discrete components or distribution of lifetimes? Really no way out of the dilemma?

    PubMed Central

    Vix, A; Lami, H

    1995-01-01

    A new methodology of fluorescence decay analysis by iterative reconvolution is presented. It is based on the recent finding that the statistics of single-photon time-correlated data are best described by a compound Poisson law and requires the recording of a sample of at least 20 decays. Application of multivariate statistical methods to the analysis of the recovered decay parameters results in improved accuracy and better estimation of the uncertainties of mono- and multiexponential decays. If it is, of course, not possible to distinguish unambiguously between discrete components and a continuous distribution of lifetimes, it is, however, possible to determine a higher limit of the width of such a distribution should it be present. With our methodology, the presence of a distribution of lifetimes with a width of approximately 20% of its center value inevitably leads to a failure in the deconvolution procedure, a fact of crucial importance in protein conformational studies, for example. PMID:7756534

  15. Basement membrane protein distribution in LYVE-1-immunoreactive lymphatic vessels of normal tissues and ovarian carcinomas.

    PubMed

    Vainionpää, Noora; Bützow, Ralf; Hukkanen, Mika; Jackson, David G; Pihlajaniemi, Taina; Sakai, Lynn Y; Virtanen, Ismo

    2007-05-01

    The endothelial cells of blood vessels assemble basement membranes that play a role in vessel formation, maintenance and function, and in the migration of inflammatory cells. However, little is known about the distribution of basement membrane constituents in lymphatic vessels. We studied the distribution of basement membrane proteins in lymphatic vessels of normal human skin, digestive tract, ovary and, as an example of tumours with abundant lymphatics, ovarian carcinomas. Basement membrane proteins were localized by immunohistochemistry with monoclonal antibodies, whereas lymphatic capillaries were detected with antibodies to the lymphatic vessel endothelial hyaluronan receptor-1, LYVE-1. In skin and ovary, fibrillar immunoreactivity for the laminin alpha4, beta1, beta2 and gamma1 chains, type IV and XVIII collagens and nidogen-1 was found in the basement membrane region of the lymphatic endothelium, whereas also heterogeneous reactivity for the laminin alpha5 chain was detected in the digestive tract. Among ovarian carcinomas, intratumoural lymphatic vessels were found especially in endometrioid carcinomas. In addition to the laminin alpha4, beta1, beta2 and gamma1 chains, type IV and XVIII collagens and nidogen-1, carcinoma lymphatics showed immunoreactivity for the laminin alpha5 chain and Lutheran glycoprotein, a receptor for the laminin alpha5 chain. In normal lymphatic capillaries, the presence of primarily alpha4 chain laminins may therefore compromise the formation of endothelial basement membrane, as these truncated laminins lack one of the three arms required for efficient network assembly. The localization of basement membrane proteins adjacent to lymphatic endothelia suggests a role for these proteins in lymphatic vessels. The distribution of the laminin alpha5 chain and Lutheran glycoprotein proposes a difference between normal and carcinoma lymphatic capillaries.

  16. The Arabidopsis COPT6 transport protein functions in copper distribution under copper-deficient conditions.

    PubMed

    Garcia-Molina, Antoni; Andrés-Colás, Nuria; Perea-García, Ana; Neumann, Ulla; Dodani, Sheel C; Huijser, Peter; Peñarrubia, Lola; Puig, Sergi

    2013-08-01

    Copper (Cu), an essential redox active cofactor, participates in fundamental biological processes, but it becomes highly cytotoxic when present in excess. Therefore, living organisms have established suitable mechanisms to balance cellular and systemic Cu levels. An important strategy to maintain Cu homeostasis consists of regulating uptake and mobilization via the conserved family of CTR/COPT Cu transport proteins. In the model plant Arabidopsis thaliana, COPT1 protein mediates root Cu acquisition, whereas COPT5 protein functions in Cu mobilization from intracellular storage organelles. The function of these transporters becomes critical when environmental Cu bioavailability diminishes. However, little is know about the mechanisms that mediate plant Cu distribution. In this report, we present evidence supporting an important role for COPT6 in Arabidopsis Cu distribution. Similarly to COPT1 and COPT2, COPT6 fully complements yeast mutants defective in high-affinity Cu uptake and localizes to the plasma membrane of Arabidopsis cells. Whereas COPT2 mRNA is only up-regulated upon severe Cu deficiency, COPT6 transcript is expressed under Cu excess conditions and displays a more gradual increase in response to decreases in environmental Cu levels. Consistent with COPT6 expression in aerial vascular tissues and reproductive organs, copt6 mutant plants exhibit altered Cu distribution under Cu-deficient conditions, including increased Cu in rosette leaves but reduced Cu levels in seeds. This altered Cu distribution is fully rescued when the wild-type COPT6 gene is reintroduced into the copt6 mutant line. Taken together, these findings highlight the relevance of COPT6 in shoot Cu redistribution when environmental Cu is limited.

  17. Distribution of crossing over on mouse synaptonemal complexes using immunofluorescent localization of MLH1 protein.

    PubMed Central

    Anderson, L K; Reeves, A; Webb, L M; Ashley, T

    1999-01-01

    We have used immunofluorescent localization to examine the distribution of MLH1 (MutL homolog) foci on synaptonemal complexes (SCs) from juvenile male mice. MLH1 is a mismatch repair protein necessary for meiotic recombination in mice, and MLH1 foci have been proposed to mark crossover sites. We present evidence that the number and distribution of MLH1 foci on SCs closely correspond to the number and distribution of chiasmata on diplotene-metaphase I chromosomes. MLH1 foci were typically excluded from SC in centromeric heterochromatin. For SCs with one MLH1 focus, most foci were located near the middle of long SCs, but near the distal end of short SCs. For SCs with two MLH1 foci, the distribution of foci was bimodal regardless of SC length, with most foci located near the proximal and distal ends. The distribution of MLH1 foci indicated interference between foci. We observed a consistent relative distance (percent of SC length in euchromatin) between two foci on SCs of different lengths, suggesting that positive interference between MLH1 foci is a function of relative SC length. The extended length of pachytene SCs, as compared to more condensed diplotene-metaphase I bivalents, makes mapping crossover events and interference distances using MLH1 foci more accurate than using chiasmata. PMID:10101178

  18. Distribution of a GABAB-like receptor protein in the rat central nervous system.

    PubMed

    Charles, K J; Calver, A R; Jourdain, S; Pangalos, M N

    2003-11-07

    Using a homology-based bioinformatics approach we have identified the human and rodent orthologues of a novel putative seven transmembrane G protein coupled receptor, termed GABA(BL). The amino acid sequence homology of these cDNAs compared to GABA(B1) and GABA(B2) led us to postulate that GABA(BL) may be a putative novel GABA(B) receptor subunit. We have developed a rabbit polyclonal antisera specific to the GABA(BL) protein and assessed the distribution of GABA(BL) in the rat CNS by immunohistochemistry. Protein expression was particularly dense in regions previously shown to contain known GABA(B) receptor subunits. Dense immunoreactivity was observed in the cortex, major subfields of the hippocampus and the dentate gyrus. GABA(BL) labelling was very conspicuous in the cerebellum, both in the granule cell layer and in Purkinje cells, and was also observed in the substantia gelatinosa and ventral horn motor neurons of the spinal cord. GABA(BL) immunoreactivity was also noted in a subset of parvalbumin positive hippocampal interneurons. Our data suggest a widespread distribution of GABA(BL) throughout the rat CNS.

  19. Pharmacokinetics, Tissue Distribution and Protein Binding Studies of Chrysocauloflavone I in Rats.

    PubMed

    Yang, Sufang; Shi, Peiying; Huang, Xiaomei; Zhao, Meifeng; Li, Shaoguang; Wu, Youjia; Lin, Xinhua; Yao, Hong

    2016-02-01

    Chrysocauloflavone I, an unfrequent biflavonoid, was purified from Selaginella doederleinii in this study. It showed cytotoxic effects on three human cancer cells, NCI-H1975, A549, and HepG-2, in vitro. In silico assessment of the physicochemical properties was performed for predicting the permeability and intestinal absorption of the tested compound. Subsequently, a rapid, sensitive, and specific high-performance liquid chromatography method was developed for determination of the compound in different biological samples to ascertain the pharmacokinetics, tissue distribution, and protein binding profiles of this active ingredient in rats. After intravenous dosing of chrysocauloflavone I at different levels (10 and 20 mg/kg), the elimination half-life was approximately 85 min, and the AUC0-∞ increased with the dose from 148.52 mg/L × min for 10 mg/kg to 399.01 mg/L × min for 20 mg/kg. After single intravenous dosing (20 mg/kg), chrysocauloflavone I was detected in all tissues studied with higher levels in the heart, blood, and lungs. The results of equilibrium dialysis indicated a very high protein binding degree (over 97%) for chrysocauloflavone I. After intragastric administration of 100 mg/kg chrysocauloflavone I to rats, no parent drug was detected in the rat plasma. This is the first report of the favorable bioactivities, plasma pharmacokinetics, tissue distribution, and protein binding profiles of the rare biflavone chrysocauloflavone I.

  20. Shaping protein distributions in stochastic self-regulated gene expression networks

    NASA Astrophysics Data System (ADS)

    Pájaro, Manuel; Alonso, Antonio A.; Vázquez, Carlos

    2015-09-01

    In this work, we study connections between dynamic behavior and network parameters, for self-regulatory networks. To that aim, a method to compute the regions in the space of parameters that sustain bimodal or binary protein distributions has been developed. Such regions are indicative of stochastic dynamics manifested either as transitions between absence and presence of protein or between two positive protein levels. The method is based on the continuous approximation of the chemical master equation, unlike other approaches that make use of a deterministic description, which as will be shown can be misleading. We find that bimodal behavior is a ubiquitous phenomenon in cooperative gene expression networks under positive feedback. It appears for any range of transcription and translation rate constants whenever leakage remains below a critical threshold. Above such a threshold, the region in the parameters space which sustains bimodality persists, although restricted to low transcription and high translation rate constants. Remarkably, such a threshold is independent of the transcription or translation rates or the proportion of an active or inactive promoter and depends only on the level of cooperativity. The proposed method can be employed to identify bimodal or binary distributions leading to stochastic dynamics with specific switching properties, by searching inside the parameter regions that sustain such behavior.

  1. Cytokinetic investigations in human breast cancer by flow cytometrically recorded DNA/protein distributions.

    PubMed

    Weiss, H; Görlich, M; Frege, J; Granetzny, A; Streller, B; Nitschke, U; Weiher, U

    1996-01-01

    This prospective study characterizes T1-T2 breast carcinomas (N = 114) and fibroadenomas (N = 16) by cell kinetic parameters derived from flow cytometrically recorded DNA/protein histograms. Ploidy level, cell cycle distribution and the number of cell subpopulations (SP) characterized by correlating DNA and protein values were assessed. The subpopulations were derived from the three-dimensional plot. The estrogen receptor (ER) status was determined biochemically (N = 61). Within the G1/0 cell peak 1-6 SP were evident in principle. Depending on the number of SP, two subsets were established: subset 1 with < or = 2 SP, subset 2 with > or = 3 SP. They differed significantly in proliferative activity expressed in the percentage of cells in the G2M phase. Subset 2 showed the higher activity. Analysis of subset distributions revealed that subset 1 prevails in favourable prognostic cases as ER positive cases (P < 0.03), lobular carcinomas (P < 0.01) and LN- cases (P < 0.03), whereas subset 2 prevails in the unfavourable counterparts. Analysis of variance showed that the main effect on proliferative activity indicated by G2M% is due to subpopulation composition rather than histologic type, nodal status or ER status (P < 0.01, P < 0.002, P < 0.05), not even due to ploidy level (P < 0.0001). The rationale for subset stratification may be cytogenetic variability connected with protein content heterogeneity accounting for kinetic SP.

  2. Distributions in Protein Conformation Space: Implications for Structure Prediction and Entropy

    PubMed Central

    Sullivan, David C.; Kuntz, Irwin D.

    2004-01-01

    By considering how polymer structures are distributed in conformation space, we show that it is possible to quantify the difficulty of structural prediction and to provide a measure of progress for prediction calculations. The critical issue is the probability that a conformation is found within a specified distance of another conformer. We address this question by constructing a cumulative distribution function (CDF) for the average probability from observations about its limiting behavior at small displacements and numerical simulations of polyalanine chains. We can use the CDF to estimate the likelihood that a structure prediction is better than random chance. For example, the chance of randomly predicting the native backbone structure of a 150-amino-acid protein to low resolution, say within 6 Å, is 10−14. A high-resolution structural prediction, say to 2 Å, is immensely more difficult (10−57). With additional assumptions, the CDF yields the conformational entropy of protein folding from native-state coordinate variance. Or, using values of the conformational entropy change on folding, we can estimate the native state's conformational span. For example, for a 150-mer protein, equilibrium α-carbon displacements in the native ensemble would be 0.3–0.5 Å based on TΔS of 1.42 kcal/(mol residue). PMID:15240450

  3. The subcellular distribution of chromosome 6-encoded dystrophin-related protein in the brain

    PubMed Central

    1992-01-01

    Chromosome 6-encoded dystrophin-related-protein (DRP) shows significant structural similarities to dystrophin at the carboxyl terminus, though the two proteins are encoded on different chromosomes. Both DRP and dystrophin are expressed in muscle and brain and show some similarity in their subcellular localization. For example, in skeletal muscle both are expressed at neuromuscular and myotendinous junctions. However, while dystrophin is absent or severely reduced in Duchenne/Becker muscular dystrophy, DRP continues to be expressed. Within the brain, dystrophin is enriched at the postsynaptic regions of specific subsets of neurons, while the distribution of DRP is yet to be described. In this study we demonstrate a distinct though highly specific pattern of distribution of DRP in the brain. DRP is enriched in the choroid plexus, pia mater, intracerebral vasculature, and ependymal lining. Within the parenchyma proper, DRP is located at the inner plasma face of astrocytic foot processes at the abluminal aspect of the blood-brain barrier. The distribution of DRP is conserved across a large evolutionary distance, from mammals to elasmobranchs, suggesting that DRP may play a role in the maintenance of regional specializations in the brain. PMID:1400579

  4. Statistical Studies on Protein Polymorphism in Natural Populations I. Distribution of Single Locus Heterozygosity

    PubMed Central

    Fuerst, Paul A.; Chakraborty, Ranajit; Nei, Masatoshi

    1977-01-01

    Surveying the literature, the frequency distribution of single-locus heterozygosity among protein loci was examined in 95 vertebrate and 34 invertebrate species with the aim of testing the validity of the mutation-drift hypothesis. This distribution did not differ significantly from that expected under the mutation-drift hypothesis for any of the species examined when tested by the Kolmogorov-Smirnov goodness-of-fit statistic. The agreement between the observed interlocus variance of heterozygosity and its theoretical expectation was also satisfactory. There was an indication that variation in the mutation rate among loci inflates the interlocus variance of heterozygosity. The variance of heterozygosity for a homologous locus among different species was also studied. This variance generally agreed with the theoretical value very well, though in some groups of Drosophila species there was a significant discrepancy. The observed relationship between average heterozygosity and the proportion of polymorphic loci was in good agreement with the theoretical relationship. It was concluded that, with respect to the pattern of distribution of heterozygosity, the majority of data on protein polymorphisms are consistent with the mutation-drift hypothesis. After examining alternative possible explanations involving selection, it was concluded that the present data cannot be explained adequately without considering a large effect of random genetic drift, whether there is selection or not. PMID:881122

  5. Subcellular distribution of folate and folate binding protein in renal proximal tubules

    SciTech Connect

    Sharkey, C.; Hjelle, J.T.; Selhub, J.

    1986-03-01

    High affinity folate binding protein (FBP) found in brush border membranes derived from renal cortices is thought to be involved in the renal conservation of folate. To examine the mechanisms of folate recovery, the subcellular distribution of FBP and /sup 3/H-folate in rabbit renal proximal tubules (PT) was examined using analytical cell fractionation techniques. Tubules contain 3.41 +/- 0.32 picomoles FBP/mg protein (X +/- S.D.; n = 5). Postnuclear supernates (PNS) of PT were layered atop Percoll-sucrose gradients, centrifuged, fractions collected and assayed for various marker enzymes and FBP. Pooled fractions from such gradients were subsequently treated with digitonin and centrifuged in a stoichiometric manner with the activity of the microvillar enzyme, alanylaminopeptidase (AAP); excess FBP distributed with more buoyant particles. Infusion of /sup 3/H-folate into rabbit kidneys followed by tubule isolation and fractionation revealed a time dependent shift in distribution of radiolabel from the AAP-rich gradient fractions to a region containing more buoyant particles; radiolevel was not associated with lysosomal markers. EM-radioautography revealed grains over intracellular vesicles. These results are consistent with the hypothesis that folate is recovered by a process involving receptor-mediated endocytosis or transcytosis.

  6. Integrative omics analysis reveals differentially distributed proteins in dimorphic euspermatozoa of the squid, Loligo bleekeri.

    PubMed

    Yoshida, Masa-aki; Yamada, Lixy; Ochi, Hiroe; Iwata, Yoko; Tamura-Nakano, Miwa; Sawada, Hitoshi; Sauer, Warwick H H; Ogura, Atsushi; Hirohashi, Noritaka

    2014-08-01

    In the coastal squid Loligo bleekeri, each male produces one of two types of fertilization-competent spermatozoa (eusperm) that exhibit morphological and behavioral differences. Large "consort" males produce short-tailed spermatozoa that display free-swimming behavior when ejaculated into seawater. Small "sneaker" males, on the other hand, produce long-tailed spermatozoa that exhibit a self-swarming trait after ejaculation. To understand the molecular basis for adaptive traits employed by alternative male mating tactics, we performed the transcriptome deep sequencing (RNA-seq) and proteome analyses to search for differences in testicular mRNAs and sperm proteins, respectively. From mature male testes we identified a total of 236,455 contigs (FPKM ≧1) where 3789 and 2789 were preferentially (≧10-fold) expressed in consort and sneaker testes, respectively. A proteomic analysis detected 4302 proteins in the mature sperm as post-translational products. A strongly biased (≧10-fold) distribution occurred in 55 consort proteins and 61 sneaker proteins. There was no clear mRNA-protein correlation, making a ballpark estimate impossible for not only overall protein abundance but also the degree of biased sperm type expressed in the spermatozoa. A family encoding dynein heavy chain gene, however, was found to be biased towards sneakers, whereas many enzymes involving energy metabolism were heavily biased towards consort spermatozoa. The difference in flagellar length matched exactly the different amount of tubulins. From these results we hypothesize that discrete differential traits in dimorphic eusperm arose from a series of innovative alterations in the intracellular components of spermatozoa.

  7. A New Distributed Algorithm for Side-Chain Positioning in the Process of Protein Docking*

    PubMed Central

    Moghadasi, Mohammad; Kozakov, Dima; Vakili, Pirooz; Vajda, Sandor; Paschalidis, Ioannis Ch.

    2014-01-01

    Side-chain positioning (SCP) is an important component of computational protein docking methods. Existing SCP methods and available software have been designed for protein folding applications where side-chain positioning is also important. As a result they do not take into account significant special structure that SCP for docking exhibits. We propose a new algorithm which poses SCP as a Maximum Weighted Independent Set (MWIS) problem on an appropriately constructed graph. We develop an approximate algorithm which solves a relaxation of the MWIS and then rounds the solution to obtain a high-quality feasible solution to the problem. The algorithm is fully distributed and can be executed on a large network of processing nodes requiring only local information and message-passing between neighboring nodes. Motivated by the special structure in docking, we establish optimality guarantees for a certain class of graphs. Our results on a benchmark set of enzyme-inhibitor protein complexes show that our predictions are close to the native structure and are comparable to the ones obtained by a state-of-the-art method. The results are substantially improved if rotamers from unbound protein structures are included in the search. We also establish that the use of our SCP algorithm substantially improves docking results. PMID:24844567

  8. Ubiquitous distribution of salts and proteins in spider glue enhances spider silk adhesion

    NASA Astrophysics Data System (ADS)

    Amarpuri, Gaurav; Chaurasia, Vishal; Jain, Dharamdeep; Blackledge, Todd A.; Dhinojwala, Ali

    2015-03-01

    Modern orb-weaving spiders use micron-sized glue droplets on their viscid silk to retain prey in webs. A combination of low molecular weight salts and proteins makes the glue viscoelastic and humidity responsive in a way not easily achieved by synthetic adhesives. Optically, the glue droplet shows a heterogeneous structure, but the spatial arrangement of its chemical components is poorly understood. Here, we use optical and confocal Raman microscopy to show that salts and proteins are present ubiquitously throughout the droplet. The distribution of adhesive proteins in the peripheral region explains the superior prey capture performance of orb webs as it enables the entire surface area of the glue droplet to act as a site for prey capture. The presence of salts throughout the droplet explains the recent Solid-State NMR results that show salts directly facilitate protein mobility. Understanding the function of individual glue components and the role of the droplet's macro-structure can help in designing better synthetic adhesives for humid environments.

  9. The evolution of proteins from random amino acid sequences: II. Evidence from the statistical distributions of the lengths of modern protein sequences.

    PubMed

    White, S H

    1994-04-01

    This paper continues an examination of the hypothesis that modern proteins evolved from random heteropeptide sequences. In support of the hypothesis, White and Jacobs (1993, J Mol Evol 36:79-95) have shown that any sequence chosen randomly from a large collection of nonhomologous proteins has a 90% or better chance of having a lengthwise distribution of amino acids that is indistinguishable from the random expectation regardless of amino acid type. The goal of the present study was to investigate the possibility that the random-origin hypothesis could explain the lengths of modern protein sequences without invoking specific mechanisms such as gene duplication or exon splicing. The sets of sequences examined were taken from the 1989 PIR database and consisted of 1,792 "super-family" proteins selected to have little sequence identity, 623 E. coli sequences, and 398 human sequences. The length distributions of the proteins could be described with high significance by either of two closely related probability density functions: The gamma distribution with parameter 2 or the distribution for the sum of two exponential random independent variables. A simple theory for the distributions was developed which assumes that (1) protoprotein sequences had exponentially distributed random independent lengths, (2) the length dependence of protein stability determined which of these protoproteins could fold into compact primitive proteins and thereby attain the potential for biochemical activity, (3) the useful protein sequences were preserved by the primitive genome, and (4) the resulting distribution of sequence lengths is reflected by modern proteins. The theory successfully predicts the two observed distributions which can be distinguished by the functional form of the dependence of protein stability on length. The theory leads to three interesting conclusions. First, it predicts that a tetra-nucleotide was the signal for primitive translation termination. This prediction is

  10. Accurate protein crystallography at ultra-high resolution: Valence electron distribution in crambin

    PubMed Central

    Jelsch, Christian; Teeter, Martha M.; Lamzin, Victor; Pichon-Pesme, Virginie; Blessing, Robert H.; Lecomte, Claude

    2000-01-01

    The charge density distribution of a protein has been refined experimentally. Diffraction data for a crambin crystal were measured to ultra-high resolution (0.54 Å) at low temperature by using short-wavelength synchrotron radiation. The crystal structure was refined with a model for charged, nonspherical, multipolar atoms to accurately describe the molecular electron density distribution. The refined parameters agree within 25% with our transferable electron density library derived from accurate single crystal diffraction analyses of several amino acids and small peptides. The resulting electron density maps of redistributed valence electrons (deformation maps) compare quantitatively well with a high-level quantum mechanical calculation performed on a monopeptide. This study provides validation for experimentally derived parameters and a window into charge density analysis of biological macromolecules. PMID:10737790

  11. Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin.

    PubMed

    Jelsch, C; Teeter, M M; Lamzin, V; Pichon-Pesme, V; Blessing, R H; Lecomte, C

    2000-03-28

    The charge density distribution of a protein has been refined experimentally. Diffraction data for a crambin crystal were measured to ultra-high resolution (0.54 A) at low temperature by using short-wavelength synchrotron radiation. The crystal structure was refined with a model for charged, nonspherical, multipolar atoms to accurately describe the molecular electron density distribution. The refined parameters agree within 25% with our transferable electron density library derived from accurate single crystal diffraction analyses of several amino acids and small peptides. The resulting electron density maps of redistributed valence electrons (deformation maps) compare quantitatively well with a high-level quantum mechanical calculation performed on a monopeptide. This study provides validation for experimentally derived parameters and a window into charge density analysis of biological macromolecules.

  12. Multiphase Simulated Annealing Based on Boltzmann and Bose-Einstein Distribution Applied to Protein Folding Problem

    PubMed Central

    Liñán-García, Ernesto; Sánchez-Hernández, Juan Paulo; González-Barbosa, J. Javier; González-Flores, Carlos

    2016-01-01

    A new hybrid Multiphase Simulated Annealing Algorithm using Boltzmann and Bose-Einstein distributions (MPSABBE) is proposed. MPSABBE was designed for solving the Protein Folding Problem (PFP) instances. This new approach has four phases: (i) Multiquenching Phase (MQP), (ii) Boltzmann Annealing Phase (BAP), (iii) Bose-Einstein Annealing Phase (BEAP), and (iv) Dynamical Equilibrium Phase (DEP). BAP and BEAP are simulated annealing searching procedures based on Boltzmann and Bose-Einstein distributions, respectively. DEP is also a simulated annealing search procedure, which is applied at the final temperature of the fourth phase, which can be seen as a second Bose-Einstein phase. MQP is a search process that ranges from extremely high to high temperatures, applying a very fast cooling process, and is not very restrictive to accept new solutions. However, BAP and BEAP range from high to low and from low to very low temperatures, respectively. They are more restrictive for accepting new solutions. DEP uses a particular heuristic to detect the stochastic equilibrium by applying a least squares method during its execution. MPSABBE parameters are tuned with an analytical method, which considers the maximal and minimal deterioration of problem instances. MPSABBE was tested with several instances of PFP, showing that the use of both distributions is better than using only the Boltzmann distribution on the classical SA. PMID:27413369

  13. Multiphase Simulated Annealing Based on Boltzmann and Bose-Einstein Distribution Applied to Protein Folding Problem.

    PubMed

    Frausto-Solis, Juan; Liñán-García, Ernesto; Sánchez-Hernández, Juan Paulo; González-Barbosa, J Javier; González-Flores, Carlos; Castilla-Valdez, Guadalupe

    2016-01-01

    A new hybrid Multiphase Simulated Annealing Algorithm using Boltzmann and Bose-Einstein distributions (MPSABBE) is proposed. MPSABBE was designed for solving the Protein Folding Problem (PFP) instances. This new approach has four phases: (i) Multiquenching Phase (MQP), (ii) Boltzmann Annealing Phase (BAP), (iii) Bose-Einstein Annealing Phase (BEAP), and (iv) Dynamical Equilibrium Phase (DEP). BAP and BEAP are simulated annealing searching procedures based on Boltzmann and Bose-Einstein distributions, respectively. DEP is also a simulated annealing search procedure, which is applied at the final temperature of the fourth phase, which can be seen as a second Bose-Einstein phase. MQP is a search process that ranges from extremely high to high temperatures, applying a very fast cooling process, and is not very restrictive to accept new solutions. However, BAP and BEAP range from high to low and from low to very low temperatures, respectively. They are more restrictive for accepting new solutions. DEP uses a particular heuristic to detect the stochastic equilibrium by applying a least squares method during its execution. MPSABBE parameters are tuned with an analytical method, which considers the maximal and minimal deterioration of problem instances. MPSABBE was tested with several instances of PFP, showing that the use of both distributions is better than using only the Boltzmann distribution on the classical SA.

  14. Pharmacokinetics of warfarin in rats: role of serum protein binding and tissue distribution

    SciTech Connect

    Cheung, W.K.

    1985-01-01

    The purpose of this study was to explore the role of serum protein binding and tissue distribution in the non-linear pharmacokinetics of warfarin in rats. The first phase of the research was an attempt to elucidate the causes of intersubject differences in serum protein binding of warfarin in rats. It was found that the distribution of S-warfarin between blood and liver, kidneys, muscle, or fatty tissue was non-linear. Based on the tissue distribution data obtained, a physiologically-based pharmacokinetic model was developed to describe the time course of S-warfarin concentrations in the serum and tissues of rats. The proposed model was able to display the dose-dependent pharmacokinetics of warfarin in rats. Namely a lower clearance and a smaller apparent volume of distribution with increasing dose, which appear to be due to the presence of capacity-limited, high-affinity binding sites for warfarin in various tissues. To determine if the binding of warfarin to the high-affinity binding sites in the liver of rats is reversible, concentrations of S-warfarin in the liver and serum of rats were monitored for a very long time after an intravenous injection of a 1 mg/kg dose. In another study in rats, non-radioactive warfarin was found to be able to displace tissue-bound C/sup 14/-warfarin which was administered about 200 hours before the i.v. injection of the non-radioactive warfarin, showing that the binding of warfarin to the high-affinity binding sites in the body is persistent and reversible.

  15. Intracellular and surface distribution of a membrane protein (CD8) derived from a single nucleus in multinucleated myotubes

    PubMed Central

    1989-01-01

    We have investigated the contribution of an individual nucleus to intracellular and surface membranes in multinucleated muscle fibers. Using a retroviral vector, we introduced the gene encoding the human T- lymphocyte antigen CD8 into C2 mouse muscle cells to form a stable line expressing the human protein on its surface. The intracellular and surface distributions of the protein were then investigated by immunocytochemistry in hybrid myotubes containing a single nucleus expressing CD8. We show that the intracellular distribution of CD8 is limited to a local area surrounding the nucleus encoding it and several neighboring nuclei. On the cell surface, however, the protein is distributed over the entire myotube. Widespread distribution of a surface membrane protein in multinucleated myotubes can thus result from localized synthesis and processing. PMID:2509483

  16. Distribution of keratin and associated proteins in the epidermis of monotreme, marsupial, and placental mammals.

    PubMed

    Alibardi, Lorenzo; Maderson, Paul F A

    2003-10-01

    The expression of acidic and basic keratins, and of some keratinization marker proteins such as filaggrin, loricrin, involucrin, and trichohyalin, is known for the epidermis of only a few eutherian species. Using light and high-resolution immunocytochemistry, the presence of these proteins has been studied in two monotreme and five marsupial species and compared to that in eutherians. In both monotreme and marsupial epidermis lamellar bodies occur in the upper spinosus and granular layers. Development of the granular layer varies between species and regionally within species. There is great interspecific variation in the size (0.1-3.0 microm) of keratohyalin granules (KHGs) associated with production of orthokeratotic corneous tissues. Those skin regions lacking hairs (platypus web), or showing reduced pelage density (wombat) have, respectively, minute or indiscernible KHGs, associated with patchy, or total, parakeratosis. Ultrastructural analysis shows that monotreme and marsupial KHGs comprise irregular coarse filaments of 25-40 nm that contact keratin filaments. Except for parakeratotic tissues of platypus web, distribution of acidic and basic proteins in monotreme and marsupial epidermis as revealed by anti-keratin antibodies AE1, AE2, and AE3 resembles that of eutherian epidermis. Antibodies against human or rat filaggrins have little or no cross-reactivity with epidermal proteins of other mammals: only sparse areas of wombat and rabbit epidermis show a weak immunofluorescence in transitional cells and in the deepest corneous tissues. Of the available, eutherian-derived antibodies, that against involucrin shows no cross-reactivity with any monotreme and marsupial epidermal tissues and that against trichohyalin cross-reacts only with cells in the inner root sheath and medulla of hairs. These results suggest that if involucrin and trichohyalin are present throughout noneutherian epidermis, they may have species-specific molecular structures. By contrast

  17. Aquareovirus NS80 recruits viral proteins to its inclusions, and its C-terminal domain is the primary driving force for viral inclusion formation.

    PubMed

    Shao, Ling; Guo, Hong; Yan, Li-Ming; Liu, Huan; Fang, Qin

    2013-01-01

    Cytoplasmic inclusion bodies formed in reovirus-infected cells are the sites of viral replication and assembly. Previous studies have suggested that the NS80 protein of aquareovirus may be involved in the formation of viral inclusion bodies. However, it remains unknown whether other viral proteins are involved in the process, and what regions of NS80 may act coordinately in mediating inclusion formation. Here, we observed that globular cytoplasmic inclusions were formed in virus-infected cells and viral proteins NS80 and NS38 colocalized in the inclusions. During transfection, singly expressed NS80 could form cytoplasmic inclusions and recruit NS38 and GFP-tagged VP4 to these structures. Further treatment of cells with nocodazole, a microtubule inhibitor, did not disrupt the inclusion, suggesting that inclusion formation does not rely on microtubule network. Besides, we identified that the region 530-742 of NS80 was likely the minimal region required for inclusion formation, and the C-tail, coiled-coil region as well as the conserved linker region were essential for inclusion phenotype. Moreover, with series deletions from the N-terminus, a stepwise conversion occurred from large condensed cytoplasmic to small nuclear inclusions, then to a diffused intracellular distribution. Notablely, we found that the nuclear inclusions, formed by NS80 truncations (471 to 513-742), colocalized with cellular protein β-catenin. These data indicated that NS80 could be a major mediator in recruiting NS38 and VP4 into inclusion structures, and the C-terminus of NS80 is responsible for inclusion formation.

  18. Ras and GTPase-activating protein (GAP) drive GTP into a precatalytic state as revealed by combining FTIR and biomolecular simulations.

    PubMed

    Rudack, Till; Xia, Fei; Schlitter, Jürgen; Kötting, Carsten; Gerwert, Klaus

    2012-09-18

    Members of the Ras superfamily regulate many cellular processes. They are down-regulated by a GTPase reaction in which GTP is cleaved into GDP and P(i) by nucleophilic attack of a water molecule. Ras proteins accelerate GTP hydrolysis by a factor of 10(5) compared to GTP in water. GTPase-activating proteins (GAPs) accelerate hydrolysis by another factor of 10(5) compared to Ras alone. Oncogenic mutations in Ras and GAPs slow GTP hydrolysis and are a factor in many cancers. Here, we elucidate in detail how this remarkable catalysis is brought about. We refined the protein-bound GTP structure and protein-induced charge shifts within GTP beyond the current resolution of X-ray structural models by combining quantum mechanics and molecular mechanics simulations with time-resolved Fourier-transform infrared spectroscopy. The simulations were validated by comparing experimental and theoretical IR difference spectra. The reactant structure of GTP is destabilized by Ras via a conformational change from a staggered to an eclipsed position of the nonbridging oxygen atoms of the γ- relative to the β-phosphates and the further rotation of the nonbridging oxygen atoms of α- relative to the β- and γ-phosphates by GAP. Further, the γ-phosphate becomes more positive although two of its oxygen atoms remain negative. This facilitates the nucleophilic attack by the water oxygen at the phosphate and proton transfer to the oxygen. Detailed changes in geometry and charge distribution in the ligand below the resolution of X-ray structure analysis are important for catalysis. Such high resolution appears crucial for the understanding of enzyme catalysis.

  19. Statistical prediction of protein structural, localization and functional properties by the analysis of its fragment mass distributions after proteolytic cleavage

    NASA Astrophysics Data System (ADS)

    Bogachev, Mikhail I.; Kayumov, Airat R.; Markelov, Oleg A.; Bunde, Armin

    2016-02-01

    Structural, localization and functional properties of unknown proteins are often being predicted from their primary polypeptide chains using sequence alignment with already characterized proteins and consequent molecular modeling. Here we suggest an approach to predict various structural and structure-associated properties of proteins directly from the mass distributions of their proteolytic cleavage fragments. For amino-acid-specific cleavages, the distributions of fragment masses are determined by the distributions of inter-amino-acid intervals in the protein, that in turn apparently reflect its structural and structure-related features. Large-scale computer simulations revealed that for transmembrane proteins, either α-helical or β -barrel secondary structure could be predicted with about 90% accuracy after thermolysin cleavage. Moreover, 3/4 intrinsically disordered proteins could be correctly distinguished from proteins with fixed three-dimensional structure belonging to all four SCOP structural classes by combining 3–4 different cleavages. Additionally, in some cases the protein cellular localization (cytosolic or membrane-associated) and its host organism (Firmicute or Proteobacteria) could be predicted with around 80% accuracy. In contrast to cytosolic proteins, for membrane-associated proteins exhibiting specific structural conformations, their monotopic or transmembrane localization and functional group (ATP-binding, transporters, sensors and so on) could be also predicted with high accuracy and particular robustness against missing cleavages.

  20. Statistical prediction of protein structural, localization and functional properties by the analysis of its fragment mass distributions after proteolytic cleavage

    PubMed Central

    Bogachev, Mikhail I.; Kayumov, Airat R.; Markelov, Oleg A.; Bunde, Armin

    2016-01-01

    Structural, localization and functional properties of unknown proteins are often being predicted from their primary polypeptide chains using sequence alignment with already characterized proteins and consequent molecular modeling. Here we suggest an approach to predict various structural and structure-associated properties of proteins directly from the mass distributions of their proteolytic cleavage fragments. For amino-acid-specific cleavages, the distributions of fragment masses are determined by the distributions of inter-amino-acid intervals in the protein, that in turn apparently reflect its structural and structure-related features. Large-scale computer simulations revealed that for transmembrane proteins, either α-helical or β -barrel secondary structure could be predicted with about 90% accuracy after thermolysin cleavage. Moreover, 3/4 intrinsically disordered proteins could be correctly distinguished from proteins with fixed three-dimensional structure belonging to all four SCOP structural classes by combining 3–4 different cleavages. Additionally, in some cases the protein cellular localization (cytosolic or membrane-associated) and its host organism (Firmicute or Proteobacteria) could be predicted with around 80% accuracy. In contrast to cytosolic proteins, for membrane-associated proteins exhibiting specific structural conformations, their monotopic or transmembrane localization and functional group (ATP-binding, transporters, sensors and so on) could be also predicted with high accuracy and particular robustness against missing cleavages. PMID:26924271

  1. Mapping the prion protein distribution in marsupials: insights from comparing opossum with mouse CNS.

    PubMed

    Poggiolini, Ilaria; Legname, Giuseppe

    2012-01-01

    The cellular form of the prion protein (PrP(C)) is a sialoglycoprotein widely expressed in the central nervous system (CNS) of mammalian species during neurodevelopment and in adulthood. The location of the protein in the CNS may play a role in the susceptibility of a species to fatal prion diseases, which are also known as the transmissible spongiform encephalopathies (TSEs). To date, little is known about PrP(C) distribution in marsupial mammals, for which no naturally occurring prion diseases have been reported. To extend our understanding of varying PrP(C) expression profiles in different mammals we carried out a detailed expression analysis of PrP(C) distribution along the neurodevelopment of the metatherian South American short-tailed opossum (Monodelphis domestica). We detected lower levels of PrP(C) in white matter fiber bundles of opossum CNS compared to mouse CNS. This result is consistent with a possible role for PrP(C) in the distinct neurodevelopment and neurocircuitry found in marsupials compared to other mammalian species.

  2. Quantitative predictions on auxin-induced polar distribution of PIN proteins during vein formation in leaves.

    PubMed

    Alim, K; Frey, E

    2010-10-01

    The dynamic patterning of the plant hormone auxin and its efflux facilitator the PIN protein are the key regulators for the spatial and temporal organization of plant development. In particular auxin induces the polar localization of its own efflux facilitator. Due to this positive feedback, auxin flow is directed and patterns of auxin and PIN arise. During the earliest stage of vein initiation in leaves auxin accumulates in a single cell in a rim of epidermal cells from which it flows into the ground meristem tissue of the leaf blade. There the localized auxin supply yields the successive polarization of PIN distribution along a strand of cells. We model the auxin and PIN dynamics within cells with a minimal canalization model. Solving the model analytically we uncover an excitable polarization front that triggers a polar distribution of PIN proteins in cells. As polarization fronts may extend to opposing directions from their initiation site, we suggest a possible resolution to the puzzling occurrence of bipolar cells, thus we offer an explanation for the development of closed, looped veins. Employing non-linear analysis, we identify the role of the contributing microscopic processes during polarization. Furthermore, we deduce quantitative predictions on polarization fronts establishing a route to determine the up to now largely unknown kinetic rates of auxin and PIN dynamics.

  3. Topographic distribution of bcl-2 protein in feline tissues in health and neoplasia.

    PubMed

    Madewell, B R; Gandour-Edwards, R; Edwards, B F; Walls, J E; Griffey, S M

    1999-11-01

    The bcl-2 family of genes encodes proteins that influence apoptosis. In the present immunohistochemical study, the topographic distribution of bcl-2 protein was examined in healthy feline fetal, neonatal, and adult tissues, a feline renal cell line, and feline tumors obtained from a veterinary hospital. The topographic distribution of bcl-2 in healthy tissues was similar to that described in human tissues. In lymphoid tissues, follicular mantle cells strongly expressed bcl-2. In complex and differentiating epithelium, bcl-2 expression was detected in stem cell and proliferation zones. Bcl-2 expression was also detected in lower crypts of the intestine and in skin basal layers. The feline Crandell kidney cells expressed bcl-2 diffusely throughout the cytoplasm. Of 180 tumors examined, bcl-2 was expressed almost uniformly in cutaneous basal cell tumors, thyroid adenomas, and mammary carcinomas and in 50% of the lymphomas examined. Bcl-2 may play a role in blocking apoptotic cell death in a broad range of normal feline tissues, whereas dysregulated bcl-2 may extend the life of certain tumors or render certain tumors resistant to therapy because most chemotherapeutic and radiotherapeutic agents eliminate tumor cells by triggering apoptosis.

  4. Variable content and distribution of arabinogalactan proteins in banana (Musa spp.) under low temperature stress.

    PubMed

    Yan, Yonglian; Takáč, Tomáš; Li, Xiaoquan; Chen, Houbin; Wang, Yingying; Xu, Enfeng; Xie, Ling; Su, Zhaohua; Šamaj, Jozef; Xu, Chunxiang

    2015-01-01

    Information on the spatial distribution of arabinogalactan proteins (AGPs) in plant organs and tissues during plant reactions to low temperature (LT) is limited. In this study, the extracellular distribution of AGPs in banana leaves and roots, and their changes under LT stress were investigated in two genotypes differing in chilling tolerance, by immuno-techniques using 17 monoclonal antibodies against different AGP epitopes. Changes in total classical AGPs in banana leaves were also tested. The results showed that AGP epitopes recognized by JIM4, JIM14, JIM16, and CCRC-M32 antibodies were primarily distributed in leaf veins, while those recognized by JIM8, JIM13, JIM15, and PN16.4B4 antibodies exhibited predominant sclerenchymal localization. Epitopes recognized by LM2, LM14, and MAC207 antibodies were distributed in both epidermal and mesophyll cells. Both genotypes accumulated classical AGPs in leaves under LT treatment, and the chilling tolerant genotype contained higher classical AGPs at each temperature treatment. The abundance of JIM4 and JIM16 epitopes in the chilling-sensitive genotype decreased slightly after LT treatment, and this trend was opposite for the tolerant one. LT induced accumulation of LM2- and LM14-immunoreactive AGPs in the tolerant genotype compared to the sensitive one, especially in phloem and mesophyll cells. These epitopes thus might play important roles in banana LT tolerance. Different AGP components also showed differential distribution patterns in banana roots. In general, banana roots started to accumulate AGPs under LT treatment earlier than leaves. The levels of AGPs recognized by MAC207 and JIM13 antibodies in the control roots of the tolerant genotype were higher than in the chilling sensitive one. Furthermore, the chilling tolerant genotype showed high immuno-reactivity against JIM13 antibody. These results indicate that several AGPs are likely involved in banana tolerance to chilling injury.

  5. Variable content and distribution of arabinogalactan proteins in banana (Musa spp.) under low temperature stress

    PubMed Central

    Yan, Yonglian; Takáč, Tomáš; Li, Xiaoquan; Chen, Houbin; Wang, Yingying; Xu, Enfeng; Xie, Ling; Su, Zhaohua; Šamaj, Jozef; Xu, Chunxiang

    2015-01-01

    Information on the spatial distribution of arabinogalactan proteins (AGPs) in plant organs and tissues during plant reactions to low temperature (LT) is limited. In this study, the extracellular distribution of AGPs in banana leaves and roots, and their changes under LT stress were investigated in two genotypes differing in chilling tolerance, by immuno-techniques using 17 monoclonal antibodies against different AGP epitopes. Changes in total classical AGPs in banana leaves were also tested. The results showed that AGP epitopes recognized by JIM4, JIM14, JIM16, and CCRC-M32 antibodies were primarily distributed in leaf veins, while those recognized by JIM8, JIM13, JIM15, and PN16.4B4 antibodies exhibited predominant sclerenchymal localization. Epitopes recognized by LM2, LM14, and MAC207 antibodies were distributed in both epidermal and mesophyll cells. Both genotypes accumulated classical AGPs in leaves under LT treatment, and the chilling tolerant genotype contained higher classical AGPs at each temperature treatment. The abundance of JIM4 and JIM16 epitopes in the chilling-sensitive genotype decreased slightly after LT treatment, and this trend was opposite for the tolerant one. LT induced accumulation of LM2- and LM14-immunoreactive AGPs in the tolerant genotype compared to the sensitive one, especially in phloem and mesophyll cells. These epitopes thus might play important roles in banana LT tolerance. Different AGP components also showed differential distribution patterns in banana roots. In general, banana roots started to accumulate AGPs under LT treatment earlier than leaves. The levels of AGPs recognized by MAC207 and JIM13 antibodies in the control roots of the tolerant genotype were higher than in the chilling sensitive one. Furthermore, the chilling tolerant genotype showed high immuno-reactivity against JIM13 antibody. These results indicate that several AGPs are likely involved in banana tolerance to chilling injury. PMID:26074928

  6. Expression and distribution of the duck enteritis virus UL51 protein in experimentally infected ducks.

    PubMed

    Shen, Chanjuan; Cheng, Anchun; Wang, Mingshu; Xu, Chao; Jia, Renyong; Chen, Xiaoyue; Zhu, Dekang; Luo, Qihui; Cui, Hengmin; Zhou, Yi; Wang, Yin; Xu, Zhiwen; Chen, Zhengli; Wang, Xiaoyu

    2010-06-01

    To determine the expression and distribution of tegument proteins encoded by duck enteritis virus (DEV) UL51 gene in tissues of experimentally infected ducks, for the first time, an immunoperoxidase staining method to detect UL51 protein (UL51p) in paraffin-embedded tissues is reported. A rabbit anti-UL51 polyclonal serum, raised against a recombinant 6-His-UL51 fusion protein expressed in Escherichia coli, was prepared, purified, and used as primary antibodies. Fifty-eight 30-day-old DEV-free ducks were intramuscularly inoculated with the pathogenic DEV CHv strain as infection group, and two ducks were selected as preinfection group. The tissues were collected at sequential time points between 2 and 480 hr postinoculation (PI) and prepared for immunoperoxidase staining. DEV UL51p was first found in the spleen and liver at 8 hr PI; in the bursa of Fabricius and thymus at 12 hr PI; in the Harders glands, esophagus, small intestine (including the duodenum, jejunum, and ileum), and large intestine (including the caecum and rectum) at 24 hr PI; in the glandularis ventriculus at 48 hr PI; and in the pancreas, cerebrum, kidney, lung, and myocardium at 72 hr PI. Throughout the infection process, the UL51p was not seen in the muscle. Furthermore, the intensity of positive staining of DEV UL51p antigen in various tissues increased sharply from 8 to 96 hr PI, peaked during 120-144 hr PI, and then decreased steadily from 216 to 480 hr PI, suggesting that the expressional levels of DEV UL51p in systemic organs have a close correlation with the progression of duck virus enteritis (DVE) disease. A number of DEV UL51p was distributed in the bursa of Fabricius, thymus, spleen, liver, esophagus, small intestine, and large intestine of DEV-infected ducks, whereas less DEV UL51p was distributed in the Harders glands, glandularis ventriculus, cerebrum, kidney, lung, pancreas, and myocardium of DEV-infected ducks. Moreover, DEV UL51p can be expressed in the cytoplasm of various types

  7. Phylogenetic distributions and histories of proteins involved in anaerobic pyruvate metabolism in eukaryotes.

    PubMed

    Hug, Laura A; Stechmann, Alexandra; Roger, Andrew J

    2010-02-01

    Protists that live in low oxygen conditions often oxidize pyruvate to acetate via anaerobic ATP-generating pathways. Key enzymes that commonly occur in these pathways are pyruvate:ferredoxin oxidoreductase (PFO) and [FeFe]-hydrogenase (H(2)ase) as well as the associated [FeFe]-H(2)ase maturase proteins HydE, HydF, and HydG. Determining the origins of these proteins in eukaryotes is of key importance to understanding the origins of anaerobic energy metabolism in microbial eukaryotes. We conducted a comprehensive search for genes encoding these proteins in available whole genomes and expressed sequence tag data from diverse eukaryotes. Our analyses of the presence/absence of eukaryotic PFO, [FeFe]-H(2)ase, and H(2)ase maturase sequences across eukaryotic diversity reveal orthologs of these proteins encoded in the genomes of a variety of protists previously not known to contain them. Our phylogenetic analyses revealed: 1) extensive lateral gene transfers of both PFO and [FeFe]-H(2)ase in eubacteria, 2) decreased support for the monophyly of eukaryote PFO domains, and 3) that eukaryotic [FeFe]-H(2)ases are not monophyletic. Although there are few eukaryote [FeFe]-H(2)ase maturase orthologs characterized, phylogenies of these proteins do recover eukaryote monophyly, although a consistent eubacterial sister group for eukaryotic homologs could not be determined. An exhaustive search for these five genes in diverse genomes from two representative eubacterial groups, the Clostridiales and the alpha-proteobacteria, shows that although these enzymes are nearly universally present within the former group, they are very rare in the latter. No alpha-proteobacterial genome sequenced to date encodes all five proteins. Molecular phylogenies and the extremely restricted distribution of PFO, [FeFe]-H(2)ases, and their associated maturases within the alpha-proteobacteria do not support a mitochondrial origin for these enzymes in eukaryotes. However, the unexpected prevalence of PFO

  8. Distribution of the amelogenin protein in developing, injured and carious human teeth

    PubMed Central

    Mitsiadis, Thimios A.; Filatova, Anna; Papaccio, Gianpaolo; Goldberg, Michel; About, Imad; Papagerakis, Petros

    2014-01-01

    Amelogenin is the major enamel matrix protein with key roles in amelogenesis. Although for many decades amelogenin was considered to be exclusively expressed by ameloblasts, more recent studies have shown that amelogenin is also expressed in other dental and no-dental cells. However, amelogenin expression in human tissues remains unclear. Here, we show that amelogenin protein is not only expressed during human embryonic development but also in pathological conditions such as carious lesions and injuries after dental cavity preparation. In developing embryonic teeth, amelogenin stage-specific expression is found in all dental epithelia cell populations but with different intensities. In the different layers of enamel matrix, waves of positive vs. negative immunostaining for amelogenin are detected suggesting that the secretion of amelogenin protein is orchestrated by a biological clock. Amelogenin is also expressed transiently in differentiating odontoblasts during predentin formation, but was absent in mature functional odontoblasts. In intact adult teeth, amelogenin was not present in dental pulp, odontoblasts, and dentin. However, in injured and carious adult human teeth amelogenin is strongly re-expressed in newly differentiated odontoblasts and is distributed in the dentinal tubuli under the lesion site. In an in vitro culture system, amelogenin is expressed preferentially in human dental pulp cells that start differentiating into odontoblast-like cells and form mineralization nodules. These data suggest that amelogenin plays important roles not only during cytodifferentiation, but also during tooth repair processes in humans. PMID:25540624

  9. HUMMR, a hypoxia- and HIF-1α–inducible protein, alters mitochondrial distribution and transport

    PubMed Central

    Li, Yan; Lim, Seung; Hoffman, David; Aspenstrom, Pontus; Federoff, Howard J.

    2009-01-01

    Mitochondrial transport is critical for maintenance of normal neuronal function. Here, we identify a novel mitochondria protein, hypoxia up-regulated mitochondrial movement regulator (HUMMR), which is expressed in neurons and is markedly induced by hypoxia-inducible factor 1 α (HIF-1α). Interestingly, HUMMR interacts with Miro-1 and Miro-2, mitochondrial proteins that are critical for mediating mitochondrial transport. Interestingly, knockdown of HUMMR or HIF-1 function in neurons exposed to hypoxia markedly reduces mitochondrial content in axons. Because mitochondrial transport and distribution are inextricably linked, the impact of reduced HUMMR function on the direction of mitochondrial transport was also explored. Loss of HUMMR function in hypoxia diminished the percentage of motile mitochondria moving in the anterograde direction and enhanced the percentage moving in the retrograde direction. Thus, HUMMR, a novel mitochondrial protein induced by HIF-1 and hypoxia, biases mitochondria transport in the anterograde direction. These findings have broad implications for maintenance of neuronal viability and function during physiological and pathological states. PMID:19528298

  10. Charge density distributions derived from smoothed electrostatic potential functions: design of protein reduced point charge models.

    PubMed

    Leherte, Laurence; Vercauteren, Daniel P

    2011-10-01

    To generate reduced point charge models of proteins, we developed an original approach to hierarchically locate extrema in charge density distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential (MEP) functions. A charge fitting program was used to assign charge values to the so-obtained reduced representations. In continuation to a previous work, the Amber99 force field was selected. To easily generate reduced point charge models for protein structures, a library of amino acid templates was designed. Applications to four small peptides, a set of 53 protein structures, and four KcsA ion channel models, are presented. Electrostatic potential and solvation free energy values generated by the reduced models are compared with the corresponding values obtained using the original set of atomic charges. Results are in closer agreement with the original all-atom electrostatic properties than those obtained with a previous reduced model that was directly built from the smoothed MEP functions [Leherte and Vercauteren in J Chem Theory Comput 5:3279-3298, 2009].

  11. Distribution of G/sub o. cap alpha. / mRNA and protein in bovine tissues

    SciTech Connect

    Price, S.R.; Tsai, S.C.; Adamik, R.; Angus, C.W.; Van Meurs, K.P.; Czarnecki, S.; Bruckwick, E.C.; Moss, J.; Vaughan, M.

    1987-05-01

    G/sub o..cap alpha../ is a 39 kDa guanyl nucleotide-binding protein similar in structure and function to G/sub s..cap alpha../ and G/sub i..cap alpha../ in the adenylate cyclase complex and transducin (G/sub t..cap alpha../) in the retinal photon receptor system. A bovine retinal cDNA clone, lambdaG09, that encodes the complete amino acid sequence of G/sub o..cap alpha../ has been isolated. Nick-translated lambdaG09 cDNA and a 5' end-labeled oligonucleotide probe complementary to a 24 base sequence unique to G/sub o..cap alpha../ were used as probes for Northern analysis of poly(A)/sup +/ RNA from bovine tissues. A major 4.0 kb mRNA was detected in brain and retina and in lesser amounts in heart. Several smaller mRNAs also hybridized with both probes in these tissues and in liver and lung. G/sub o..cap alpha../ protein was identified using rabbit polyclonal antibodies directed against purified bovine G/sub o..cap alpha../ and pertussis toxin-catalyzed (/sup 32/P)ADP-ribosylation. Soluble and membrane proteins were incubated with toxin and (/sup 32/P)NAD and then separated by gel electrophoresis before transfer to nitrocellulose for immunoreaction and subsequent autoradiography. A radiolabeled and immunoreactive 39 kDa membrane protein was found principally in retina and brain, and to a lesser extent, in heart. Thus, in the tissues examined, distribution of the 4.0 kb mRNA parallels that of the immunoreactive G/sub o..cap alpha../ with relatively small amounts in heart and larger amounts in brain and retina.

  12. Mathematical modeling and comparison of protein size distribution in different plant, animal, fungal and microbial species reveals a negative correlation between protein size and protein number, thus providing insight into the evolution of proteomes

    PubMed Central

    2012-01-01

    Background The sizes of proteins are relevant to their biochemical structure and for their biological function. The statistical distribution of protein lengths across a diverse set of taxa can provide hints about the evolution of proteomes. Results Using the full genomic sequences of over 1,302 prokaryotic and 140 eukaryotic species two datasets containing 1.2 and 6.1 million proteins were generated and analyzed statistically. The lengthwise distribution of proteins can be roughly described with a gamma type or log-normal model, depending on the species. However the shape parameter of the gamma model has not a fixed value of 2, as previously suggested, but varies between 1.5 and 3 in different species. A gamma model with unrestricted shape parameter described best the distributions in ~48% of the species, whereas the log-normal distribution described better the observed protein sizes in 42% of the species. The gamma restricted function and the sum of exponentials distribution had a better fitting in only ~5% of the species. Eukaryotic proteins have an average size of 472 aa, whereas bacterial (320 aa) and archaeal (283 aa) proteins are significantly smaller (33-40% on average). Average protein sizes in different phylogenetic groups were: Alveolata (628 aa), Amoebozoa (533 aa), Fornicata (543 aa), Placozoa (453 aa), Eumetazoa (486 aa), Fungi (487 aa), Stramenopila (486 aa), Viridiplantae (392 aa). Amino acid composition is biased according to protein size. Protein length correlated negatively with %C, %M, %K, %F, %R, %W, %Y and positively with %D, %E, %Q, %S and %T. Prokaryotic proteins had a different protein size bias for %E, %G, %K and %M as compared to eukaryotes. Conclusions Mathematical modeling of protein length empirical distributions can be used to asses the quality of small ORFs annotation in genomic releases (detection of too many false positive small ORFs). There is a negative correlation between average protein size and total number of proteins among

  13. Simulating the Distance Distribution between Spin-Labels Attached to Proteins

    PubMed Central

    2016-01-01

    EPR/DEER spectroscopy is playing an increasingly important role in the characterization of the conformational states of proteins. In this study, force field parameters for the bifunctional spin-label (RX) used in EPR/DEER are parametrized and tested with molecular dynamics (MD) simulations. The dihedral angles connecting the Cα atom of the backbone to the nitroxide ring moiety of the RX spin-label attached to i and i + 4 positions in a polyalanine α-helix agree very well with those observed in the X-ray crystallography. Both RXi,i+4 and RXi,i+3 are more rigid than the monofunctional spin-label (R1) commonly used in EPR/DEER, while RXi,i+4 is more rigid and causes less distortion in a protein backbone than RXi,i+3. Simplified dummy spin-label models with a single effective particle representing the RXi,i+3 and RXi,i+4 are also developed and parametrized from the all-atom simulations. MD simulations with dummy spin-labels (MDDS) provide distance distributions that can be directly compared to distance distributions obtained from EPR/DEER to rapidly assess if a hypothetical three-dimensional (3D) structural model is consistent with experiment. The dummy spin-labels can also be used in the restrained-ensemble MD (re-MD) simulations to carry out structural refinement of 3D models. Applications of this methodology to T4 lysozyme, KCNE1, and LeuT are shown to provide important insights about their conformational dynamics. PMID:25645890

  14. Gene expression and protein distribution of orexins and orexin receptors in rat retina.

    PubMed

    Liu, F; Xu, G Z; Wang, L; Jiang, S X; Yang, X L; Zhong, Y M

    2011-08-25

    Orexins, composed of orexin A and orexin B, are identified as endogenous ligands of two orphan G-protein-coupled receptors: orexin 1 and orexin 2 receptors (OX1R and OX2R). Orexins are implicated in regulating wake/sleep states, feeding behaviors, etc. Using reverse transcription-polymerase chain reactive (RT-PCR) analysis and immunofluorescence double labeling, we investigated the distributions of orexin A, orexin B, OX1R and OX2R in rat retina. RT-PCR analysis revealed the presence of mRNAs of prepro-orexin, OX1R and OX2R in rat retina. Immunostaining for orexin A and orexin B was observed in many cells in the inner nuclear layer and the ganglion cell layer. In the outer retina, horizontal cells, labeled by calbindin, and bipolar cells, labeled by homeobox protein Chx10, were orexin A- and orexin B-positive. In the inner retina, two orexins were both found in GABAergic amacrine cells (ACs), including dopaminergic and cholinergic ones, stained by tyrosine hydroxylase and choline acetyltransferase respectively. Glycinergic ACs, including AII ACs, also expressed orexins. Weak to moderate labeling for orexin A and orexin B was diffusely distributed in the inner plexiform layer. Additionally, orexins were expressed in almost all ganglion cells (GCs) retrogradely labeled by cholera toxin B subunit. Specifically, double-labeling experiments demonstrated that melanopsin-positive GCs (intrinsically photosensitive retinal GCs, ipRGCs) were labeled by two orexins. Morever, OX1R immunoreactivity was observed in most of GCs and all dopaminergic ACs, as well as in both outer and inner plexiform layers. In contrast, no obvious OX2R immunostaining was detectable in the rat retina. These results suggest that orexins may modulate the function of neurons, especially in the inner retina. We further hypothesize that the orexin signaling via ipRGCs may be involved in setting the suprachiasmatic nucleus (SCN) circadian clock.

  15. Aberrant distributions of nuclear pore complex proteins in ALS mice and ALS patients.

    PubMed

    Shang, Jingwei; Yamashita, Toru; Nakano, Yumiko; Morihara, Ryuta; Li, Xianghong; Feng, Tian; Liu, Xia; Huang, Yong; Fukui, Yusuke; Hishikawa, Nozomi; Ohta, Yasuyuki; Abe, Koji

    2017-03-24

    Nuclear pore complexes (NPCs) play important roles in traffic of molecules between the nucleus and cytoplasm, aberrant distributions of components of NPCs were demonstrated in C9orf72 amyotrophic lateral sclerosis (C9-ALS) patients, but it is elusive whether such abnormities are also the case with other cause of ALS disease. In the present study, we investigated the spatiotemporal distributions of RanGAP1 and 4 representative nucleoporins (GP210, NUP205, NUP107 and NUP50) of NPCs in human Cu/Zn superoxide dismutase-1 mutation transgenic (SOD1-Tg) mice and sporadic ALS patients. Compared with wild type (WT), these proteins displayed age-dependent and progressive nuclear precipitations, and cytoplasmic aberrant expressions in motor neurons of lumbar cord in SOD1-Tg mice from 10 to 18weeks (W). Double immunofluorescent analysis showed abnormal nuclear retention and apparent co-localizations of RanGAPl with NUP205 and NUP205 with NUPl07, meanwhile, GP210 with NUP205 mainly co-localized in the nuclear envelope (NE) of motor neurons. Furthermore, RanGAP1, GP210 and NUP50 showed similarly abnormal nuclear precipitations and cytoplasmic upregulations in SOD1-Tg mice and ALS patients, moreover, aberrant co-localizations of RanGAP1 with TDP-43 and NUP205 with TDP-43 were also observed in motor neurons. The present study indicated that the mislocalization of these proteins of NPCs may underlie the pathogenesis of ALS both in SOD1-Tg mice and human sporadic ALS patients, and these dysfunctions may be a fundamental pathway for ALS that is not specific only in C9-ALS but also in SOD1-ALS, which may be amenable to pharmacotherapeutic intervention.

  16. Tissue distribution of PEBBLE RNA and pebble protein during Drosophila embryonic development.

    PubMed

    Prokopenko, S N; Saint, R; Bellen, H J

    2000-02-01

    pebble (pbl) is required for cytokinesis during postblastoderm mitoses (Hime, G., Saint, R., 1992. Zygotic expression of the pebble locus is required for cytokinesis during the postblastoderm mitoses of Drosophila. Development 114, 165-171; Lehner, C.F., 1992. The pebble gene is required for cytokinesis in Drosophila. J. Cell Sci. 103, 1021-1030) and encodes a putative guanine nucleotide exchange factor (RhoGEF) for Rho1 GTPase (Prokopenko, S.N., Brumby, A., O'Keefe, L., Prior, L., He, Y., Saint, R., Bellen, H.J., 1999. A putative exchange factor for Rho1 GTPase is required for initiation of cytokinesis in Drosophila. Genes Dev. 13, 2301-2314). Mutations in pbl result in the absence of a contractile ring leading to a failure of cytokinesis and formation of polyploid multinucleate cells. Analysis of the subcellular distribution of PBL demonstrated that during mitosis, PBL accumulates at the cleavage furrow at the anaphase to telophase transition when assembly of a contractile ring is initiated (Prokopenko, S.N., Brumby, A., O'Keefe, L., Prior, L., He, Y., Saint, R., Bellen, H.J., 1999. A putative exchange factor for Rho1 GTPase is required for initiation of cytokinesis in Drosophila. Genes Dev. 13, 2301-2314). In addition, levels of PBL protein cycle during each round of cell division with the highest levels of PBL found in telophase and interphase nuclei. Here, we report the expression pattern of pbl during embryonic development. We show that PEBBLE RNA and PBL protein have a similar tissue distribution and are expressed in a highly dynamic pattern throughout embryogenesis. We show that PBL is strongly enriched in dividing nuclei in syncytial embryos and in pole cells as well as in nuclei of dividing cells in postblastoderm embryos. Our expression data correlate well with the phenotypes observed in pole cells and, particularly, with the absence of cytokinesis after cellular blastoderm formation in pbl mutants.

  17. Visualizing the mobility and distribution of chlorophyll proteins in higher plant thylakoid membranes: effects of photoinhibition and protein phosphorylation.

    PubMed

    Goral, Tomasz K; Johnson, Matthew P; Brain, Anthony P R; Kirchhoff, Helmut; Ruban, Alexander V; Mullineaux, Conrad W

    2010-06-01

    The diffusion of proteins in chloroplast thylakoid membranes is believed to be important for processes including the photosystem-II repair cycle and the regulation of light harvesting. However, to date there is very little direct information on the mobility of thylakoid proteins. We have used fluorescence recovery after photobleaching in a laser-scanning confocal microscope to visualize in real time the exchange of chlorophyll proteins between grana in intact spinach (Spinacia oleracea L.) and Arabidopsis chloroplasts. Most chlorophyll proteins in the grana appear immobile on the 10-min timescale of our measurements. However, a limited population of chlorophyll proteins (accounting for around 15% of chlorophyll fluorescence) can exchange between grana on this timescale. In intact, wild-type chloroplasts this mobile population increases significantly after photoinhibition, consistent with a role for protein diffusion in the photosystem-II repair cycle. No such increase in mobility is seen in isolated grana membranes, or in the Arabidopsis stn8 and stn7 stn8 mutants, which lack the protein kinases required for phosphorylation of photosystem II core proteins and light-harvesting complexes. Furthermore, mobility under low-light conditions is significantly lower in stn8 and stn7 stn8 plants than in wild-type Arabidopsis. The changes in protein mobility correlate with changes in the packing density and size of thylakoid protein complexes, as observed by freeze-fracture electron microscopy. We conclude that protein phosphorylation switches the membrane system to a more fluid state, thus facilitating the photosystem-II repair cycle.

  18. Relationship of molecular weight distribution profile of unreduced gluten protein extracts with quality characteristics of bread.

    PubMed

    Chaudhary, Nisha; Dangi, Priya; Khatkar, B S

    2016-11-01

    A statistical correlation was established among the molecular weight distribution patterns of unreduced gluten proteins and physicochemical, rheological and bread-making quality characteristics of wheat varieties. Size exclusion chromatography fractionated the gluten proteins apparently into five peaks. Peak I signified glutenins (30-130kDa), peak II as gliadins (20-55kDa), peak III as very low molecular weight monomeric gliadins (10-28kDa), peak IV and V, collectively, as albumins and globulins (<10kDa). Peaks I and II had appreciable effects on dough development time (r=0.830(∗∗) and r=-0.930(∗∗)) and dough stability (r=0.901(∗∗) and r=-0.979(∗∗)). Peak I was associated with R/E ratio (r=0.745(∗∗)), gluten index (r=0.959(∗∗)), and gliadin/glutenin ratio (r=-0.952(∗∗)), while peak II influenced inversely as expected. Peak I exhibited positive statistical significance with bread loaf volume (r=0.848(∗∗)); however, peak II had negative (r=-0.818(∗∗)) impact. Bread firmness increased with increment in peak II (r=0.625(∗∗)), and decreased with accretion in peak I (r=-0.623(∗∗)).

  19. The spatial distribution of fixed mutations within genes coding for proteins

    NASA Technical Reports Server (NTRS)

    Holmquist, R.; Goodman, M.; Conroy, T.; Czelusniak, J.

    1983-01-01

    An examination has been conducted of the extensive amino acid sequence data now available for five protein families - the alpha crystallin A chain, myoglobin, alpha and beta hemoglobin, and the cytochromes c - with the goal of estimating the true spatial distribution of base substitutions within genes that code for proteins. In every case the commonly used Poisson density failed to even approximate the experimental pattern of base substitution. For the 87 species of beta hemoglobin examined, for example, the probability that the observed results were from a Poisson process was the minuscule 10 to the -44th. Analogous results were obtained for the other functional families. All the data were reasonably, but not perfectly, described by the negative binomial density. In particular, most of the data were described by one of the very simple limiting forms of this density, the geometric density. The implications of this for evolutionary inference are discussed. It is evident that most estimates of total base substitutions between genes are badly in need of revision.

  20. The SUN protein Mps3 controls Ndc1 distribution and function on the nuclear membrane.

    PubMed

    Chen, Jingjing; Smoyer, Christine J; Slaughter, Brian D; Unruh, Jay R; Jaspersen, Sue L

    2014-02-17

    In closed mitotic systems such as Saccharomyces cerevisiae, nuclear pore complexes (NPCs) and the spindle pole body (SPB) must assemble into an intact nuclear envelope (NE). Ndc1 is a highly conserved integral membrane protein involved in insertion of both complexes. In this study, we show that Ndc1 interacts with the SUN domain-containing protein Mps3 on the NE in live yeast cells using fluorescence cross-correlation spectroscopy. Genetic and molecular analysis of a series of new ndc1 alleles allowed us to understand the role of Ndc1-Mps3 binding at the NE. We show that the ndc1-L562S allele is unable to associate specifically with Mps3 and find that this mutant is lethal due to a defect in SPB duplication. Unlike other ndc1 alleles, the growth and Mps3 binding defect of ndc1-L562S is fully suppressed by deletion of POM152, which encodes a NPC component. Based on our data we propose that the Ndc1-Mps3 interaction is important for controlling the distribution of Ndc1 between the NPC and SPB.

  1. On the simulation of protein folding by short time scale molecular dynamics and distributed computing.

    PubMed

    Fersht, Alan R

    2002-10-29

    There are proposals to overcome the current incompatibilities between the time scales of protein folding and molecular dynamics simulation by using a large number of short simulations of only tens of nanoseconds (distributed computing). According to the principles of first-order kinetic processes, a sufficiently large number of short simulations will include, de facto, a small number of long time scale events that have proceeded to completion. But protein folding is not an elementary kinetic step: folding has a series of early conformational steps that lead to lag phases at the beginning of the kinetics. The presence of these lag phases can bias short simulations toward selecting minor pathways that have fewer or faster lag steps and so miss the major folding pathways. Attempts to circumvent the lags by using loosely coupled parallel simulations that search for first-order transitions are also problematic because of the difficulty of detecting transitions in molecular dynamics simulations. Nevertheless, the procedure of using parallel independent simulations is perfectly valid and quite feasible once the time scale of simulation proceeds past the lag phases into a single exponential region.

  2. Distribution of the cellular prion protein in the central nervous system of the chicken.

    PubMed

    Atoji, Yasuro; Ishiguro, Naotaka

    2009-12-01

    The cellular prion protein (PrP), a cell membrane-bound glycoprotein mainly located in the dendrites and axons of the central nervous system (CNS), is responsible for transmissible spongiform encephalopathies in mammals. PrP genes are widely conserved in vertebrates. In birds, the presence of PrP mRNA has been confirmed in neurons of the chicken brain, but localization of the protein remains to be determined. In the present study, we demonstrated the regional distribution of PrP in the CNS of adult chickens by immunohistochemical staining with a monoclonal antibody that recognizes chicken PrP 161-164. Immunoreactivity was observed in the neuropil, but not in neuronal somata or glial cells. It was preferentially intense in the olfactory bulb, the dorsal thalamus, the hypothalamus, and most regions of the telencephalon. Immunostaining became less intense toward the brainstem, but many nuclei were immunoreactive. Among brainstem nuclei, moderate immunostaining was observed in the nucleus of the solitary tract, dorsal motor nucleus of the vagus nerve, and substantia gelatinosa Rolandi. The cerebellar cortex was devoid of PrP immunoreactivity. The dorsal horn in the spinal cord was strongly immunoreactive. In situ hybridization with two probes of the C-terminal portion demonstrated localization of PrP mRNA in neurons of the brain and spinal cord. These findings suggest that PrP in the chicken CNS is localized in the dendrites and axons of neurons and that it is associated with certain sensory systems.

  3. Distribution, structure and diversity of "bacterial" genes encoding two-component proteins in the Euryarchaeota.

    PubMed

    Ashby, Mark K

    2006-08-01

    The publicly available annotated archaeal genome sequences (23 complete and three partial annotations, October 2005) were searched for the presence of potential two-component open reading frames (ORFs) using gene category lists and BLASTP. A total of 489 potential two-component genes were identified from the gene category lists and BLASTP. Two-component genes were found in 14 of the 21 Euryarchaeal sequences (October 2005) and in neither the Crenarchaeota nor the Nanoarchaeota. A total of 20 predicted protein domains were identified in the putative two-component ORFs that, in addition to the histidine kinase and receiver domains, also includes sensor and signalling domains. The detailed structure of these putative proteins is shown, as is the distribution of each class of two-component genes in each species. Potential members of orthologous groups have been identified, as have any potential operons containing two or more two-component genes. The number of two-component genes in those Euryarchaeal species which have them seems to be linked more to lifestyle and habitat than to genome complexity, with most examples being found in Methanospirillum hungatei, Haloarcula marismortui, Methanococcoides burtonii and the mesophilic Methanosarcinales group. The large numbers of two-component genes in these species may reflect a greater requirement for internal regulation. Phylogenetic analysis of orthologous groups of five different protein classes, three probably involved in regulating taxis, suggests that most of these ORFs have been inherited vertically from an ancestral Euryarchaeal species and point to a limited number of key horizontal gene transfer events.

  4. Differential Protein Distribution between the Nucleus and Mitochondria: Implications in Aging

    PubMed Central

    Lionaki, Eirini; Gkikas, Ilias; Tavernarakis, Nektarios

    2016-01-01

    The coordination of nuclear and mitochondrial genomes plays a pivotal role in maintenance of mitochondrial biogenesis and functionality during stress and aging. Environmental and cellular inputs signal to nucleus and/or mitochondria to trigger interorganellar compensatory responses. Loss of this tightly orchestrated coordination results in loss of cellular homeostasis and underlies various pathologies and age-related diseases. Several signaling cascades that govern interorganellar communication have been revealed up to now, and have been classified as part of the anterograde (nucleus to mitochondria) or retrograde (mitochondrial to nucleus) response. Many of these molecular pathways rely on the dual distribution of nuclear or mitochondrial components under basal or stress conditions. These dually localized components usually engage in specific tasks in their primary organelle of function, whilst upon cellular stimuli, they appear in the other organelle where they engage in the same or a different task, triggering a compensatory stress response. In this review, we focus on protein factors distributed between the nucleus and mitochondria and activated to exert their functions upon basal or stress conditions. We further discuss implications of bi-organellar targeting in the context of aging. PMID:27695477

  5. Distribution and Morphology of Calcium-Binding Proteins Immunoreactive Neurons following Chronic Tungsten Multielectrode Implants.

    PubMed

    Freire, Marco Aurelio M; Faber, Jean; Lemos, Nelson Alessandretti M; Santos, Jose Ronaldo; Cavalcanti, Pedro França; Lima, Ramon Hypolito; Morya, Edgard

    2015-01-01

    The development of therapeutic approaches to improve the life quality of people suffering from different types of body paralysis is a current major medical challenge. Brain-machine interface (BMI) can potentially help reestablishing lost sensory and motor functions, allowing patients to use their own brain activity to restore sensorimotor control of paralyzed body parts. Chronic implants of multielectrodes, employed to record neural activity directly from the brain parenchyma, constitute the fundamental component of a BMI. However, before this technique may be effectively available to human clinical trials, it is essential to characterize its long-term impact on the nervous tissue in animal models. In the present study we evaluated how chronic implanted tungsten microelectrode arrays impact the distribution and morphology of interneurons reactive to calcium-binding proteins calbindin (CB), calretinin (CR) and parvalbumin (PV) across the rat's motor cortex. Our results revealed that chronic microelectrode arrays were well tolerated by the nervous tissue, with recordings remaining viable for up to 6 months after implantation. Furthermore, neither the morphology nor the distribution of inhibitory neurons were broadly impacted. Moreover, restricted microglial activation was observed on the implanted sites. On the whole, our results confirm and expand the notion that tungsten multielectrodes can be deemed as a feasible candidate to future human BMI studies.

  6. Revising the Taxonomic Distribution, Origin and Evolution of Ribosome Inactivating Protein Genes

    PubMed Central

    Lapadula, Walter J.; Sánchez Puerta, María Virginia; Juri Ayub, Maximiliano

    2013-01-01

    Ribosome inactivating proteins are enzymes that depurinate a specific adenine residue in the alpha-sarcin-ricin loop of the large ribosomal RNA, being ricin and Shiga toxins the most renowned examples. They are widely distributed in plants and their presence has also been confirmed in a few bacterial species. According to this taxonomic distribution, the current model about the origin and evolution of RIP genes postulates that an ancestral RIP domain was originated in flowering plants, and later acquired by some bacteria via horizontal gene transfer. Here, we unequivocally detected the presence of RIP genes in fungi and metazoa. These findings, along with sequence and phylogenetic analyses, led us to propose an alternative, more parsimonious, hypothesis about the origin and evolutionary history of the RIP domain, where several paralogous RIP genes were already present before the three domains of life evolved. This model is in agreement with the current idea of the Last Universal Common Ancestor (LUCA) as a complex, genetically redundant organism. Differential loss of paralogous genes in descendants of LUCA, rather than multiple horizontal gene transfer events, could account for the complex pattern of RIP genes across extant species, as it has been observed for other genes. PMID:24039805

  7. Selenium proteins in ovine tissues: III. Distribution of selenium and glutathione peroxidases in tissue cytosols.

    PubMed

    Black, R S; Tripp, M J; Whanger, P D; Weswig, P H

    1978-01-01

    Three 6 week-old lambs were injected with carrier-free selenium-75 as sodium selenite initially and again after 6 days. One lamb received no further injections whereas the other two received injections of either vitamin E or unlabeled Na2SeO3 when the first selenium-75 injection was given. Selected tissues were removed at autopsy 10 days after the first injection. The cytosol from homogenates of these tissues was subjected to gel chromatography, and the elution profiles determined for radioactivity, protein content, and glutathione peroxidase activity using either hydrogen peroxide or cumene hydroperoxide as substrates. The selenium-75 was found to be distributed mainly between 2 different MW peaks. The larger MW seleno-peak (90,000) possessed both glutathione:hydrogen peroxide oxidoreductase, and glutathione:cumene hydroperoxide oxidoreductase activities, but the smaller MW seleno-peak (about 10,000) possessed no glutathione peroxidase activity. A peak of about 60,000 daltons containing only glutathione:cumene hydroperoxide oxidoreductase activity and no selenium-75 was found primarily in the liver and kidney. Vitamin E had no effect on the elution profiles. Selenium status of the animal had only a minor effect on the selenium-75 distribution in the cytosol, but had a marked effect on the absolute amount of the label taken up by tissues.

  8. Immunocytochemical distribution of WARP (von Willebrand A domain-related protein) in the inner ear.

    PubMed

    Duong, Trac; Lopez, Ivan A; Ishiyama, Akira; Ishiyama, Gail

    2011-01-07

    The basic components of the epithelial, perineural, and perivascular basement membranes in the inner ear have been well-documented in several animal models and in the human inner ear. The von Willebrand A domain-related protein (WARP) is an extracellular matrix molecule with restricted expression in cartilage, and a subset of basement membranes in peripheral nerves, muscle, and central nervous system vasculature. It has been suggested that WARP has an important role in maintaining the blood-brain barrier. To date no studies on WARP distribution have been performed in the inner ear, which is equipped with an intricate vasculature network. In the present study, we determined the distribution of WARP by immunocytochemistry in the human inner ear using auditory and vestibular endorgans microdissected from human temporal bones obtained at autopsy. All subjects (n=5, aged 55-87years old) had documented normal auditory and vestibular function. We also determined the WARP immunolocalization in the mouse inner ear. WARP immunoreactivity localized to the vasculature throughout the stroma of the cristae ampullaris, the maculae utricle, and saccule in the human and mouse. In the human and mouse inner ear, WARP immunoreactivity delineated blood vessels located in the stria vascularis, spiral ligament, sub-basilar region, stromal tissue, and the spiral and vestibular ganglia. The distinct localization of WARP in the inner ear vasculature suggests an important role in maintaining its integrity. In addition, WARP allows delineation of microvessels in the inner ear allowing the study of vascular pathology in the development of otological diseases.

  9. The involvement of multidrug and toxin extrusion protein 1 in the distribution and excretion of berberine.

    PubMed

    Xiao, Ling; Xue, Yaru; Zhang, Cuifeng; Wang, Le; Lin, Yunfei; Pan, Guoyu

    2017-03-16

    1. Berberine (BBR), an isoquinoline alkaloid, has demonstrated multiple clinical pharmacological actions. As a substrate of multiple transporters in the liver, BBR is rarely excreted into the bile but can be found in the urine. The purpose of the present study was to investigate the role of multidrug and toxin extrusion protein 1 (MATE1) in the transport of BBR in the liver and kidney. 2. Using human MATE1 (hMATE1)-transfected HEK293 cells, BBR was shown to be a substrate of hMATE1 (Km = 4.28 ± 2.18 μM). In primary rat hepatocytes, pH-dependent uptake and efflux studies suggested that the transport of BBR was driven by the exchange of H(+) and involved Mate1. In rats, we found that pyrimethamine (PYR), an inhibitor of Mate1, increased hepatic and renal distribution of BBR and decreased systematic excretion of BBR. 3. These findings indicated that BBR is a substrate of MATE1 and that hepatic and renal Mate1 promote excretion of BBR into bile and urine, respectively. In conclusion, Mate1 plays a key role in the distribution and excretion of BBR, and we speculate that drug-drug interactions (DDIs) caused by MATE1 may occur between BBR and other co-administered drugs.

  10. Pharmacokinetics, tissue distribution, and plasma protein binding study of chicoric acid by HPLC-MS/MS.

    PubMed

    Wang, Yutang; Xie, Guo; Liu, Qian; Duan, Xiang; Liu, Zhigang; Liu, Xuebo

    2016-09-15

    Chicoric acid is a major active constituent of Echinacea purpurea and has a variety of biological functions. In this study, a liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS) approach was developed and validated for the determination of chicoric acid in rat plasma and various tissues using ferulic acid as an internal standard (IS). This method was successfully applied to pharmacokinetics, tissue distribution, and plasma protein binding (PPB) study of chicoric acid in Sprague-Dawley (SD) rats dosed with 50mg/kg by gastric gavage. The pharmacokinetic parameters were determined and showed a half-life (t1/2) of 4.53±1.44h, an apparent volume of mean residual time (MRT) of 18.58±4.43h, and an area under the curve (AUC) of 26.14 mghL(-1). The tissue distribution of chicoric acid in rats after gavage administration showed a decreasing tendency in different tissues (liver>lung>kidney>heart>spleen>brain). The PPB rates in rat plasma, human plasma, and bovine serum albumin were 98.3, 96.9, and 96.6%, respectively. These results provide insight for the further pharmacological investigation of chicoric acid.

  11. Current Gaps in the Understanding of the Subcellular Distribution of Exogenous and Endogenous Protein TorsinA

    PubMed Central

    Harata, N. Charles

    2014-01-01

    Background An in-frame deletion leading to the loss of a single glutamic acid residue in the protein torsinA (ΔE-torsinA) results in an inherited movement disorder, DYT1 dystonia. This autosomal dominant disease affects the function of the brain without causing neurodegeneration, by a mechanism that remains unknown. Methods We evaluated the literature regarding the subcellular localization of torsinA. Results Efforts to elucidate the pathophysiological basis of DYT1 dystonia have relied partly on examining the subcellular distribution of the wild-type and mutated proteins. A typical approach is to introduce the human torsinA gene (TOR1A) into host cells and overexpress the protein therein. In both neurons and non-neuronal cells, exogenous wild-type torsinA introduced in this manner has been found to localize mainly to the endoplasmic reticulum, whereas exogenous ΔE-torsinA is predominantly in the nuclear envelope or cytoplasmic inclusions. Although these outcomes are relatively consistent, findings for the localization of endogenous torsinA have been variable, leaving its physiological distribution a matter of debate. Discussion As patients’ cells do not overexpress torsinA proteins, it is important to understand why the reported distributions of the endogenous proteins are inconsistent. We propose that careful optimization of experimental methods will be critical in addressing the causes of the differences among the distributions of endogenous (non-overexpressed) vs. exogenously introduced (overexpressed) proteins. PMID:25279252

  12. Effects of kernel vitreousness and protein level on protein molecular weight distribution, milling quality, and breadmaking quality in hard red spring wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dark, hard, and vitreous kernel content is an important grading characteristic for hard red spring (HRS) wheat in the U.S. This research aimed to determine the associations of kernel vitreousness (KV) with protein molecular weight distribution (MWD) and quality traits that were not biased by quanti...

  13. Quantitative autoradiographic evaluation of the influence of protein dose on monoclonal antibody distribution in human ovarian adenocarcinoma xenografts.

    PubMed

    Yang, F E; Brown, R S; Koral, K F; Clavo, A C; Jackson, G A; Wahl, R L

    1992-01-01

    We studied the effect of monoclonal antibody protein dose on the uniformity of radioiodinated antibody distribution within tumor masses using quantitative autoradiography. Groups (n = 11-13/group) of athymic nude mice with subcutaneous HTB77 human ovarian carcinoma xenografts were injected intraperitoneally with an 125I-labeled anticarcinoma-associated antigen murine monoclonal antibody, 5G6.4 using a high or a low protein dose (500 micrograms or 5 micrograms). At 6 days post-injection the macroscopic and microscopic intratumoral biodistribution of radiolabeled antibody was determined. The degree of heterogeneity of the labeled antibody distribution within each tumor was quantified and expressed as the coefficient of variation (CV) of the activity levels in serial histological sections. Tumors from mice given the 500-micrograms protein doses had substantially lower CV values, 0.327 +/- 0.027, than did tumors from animals given 5-micrograms protein doses, 0.458 +/- 0.041, (P = 0.0078), indicating that the higher protein dose resulted in more homogeneous distribution of radioactivity in tumors than did the lower dose. While the percentage of the injected dose reaching the tumor was comparable between groups, injecting the higher dose of protein resulted in significantly lower tumor to non-tumor uptake ratios than those obtained for the lower protein dose. These data indicate, in this system, that to achieve more uniform intratumoral antibody (and radiation for radioimmunotherapy) delivery, a relatively high protein dose must be administered. However, to obtain this increased uniformity, a substantial drop in tumor/background uptake ratios was seen. Quantitative autoradiographic evaluation of human tumor xenografts is a useful method to assess the intratumoral distribution of antibodies.

  14. Burst analysis spectroscopy: a versatile single-particle approach for studying distributions of protein aggregates and fluorescent assemblies.

    PubMed

    Puchalla, Jason; Krantz, Kelly; Austin, Robert; Rye, Hays

    2008-09-23

    Many essential cellular functions depend on the assembly and disassembly of macromolecular complexes. The size, form, and distribution of these assemblies can be heterogeneous and complex, rendering their detailed characterization difficult. Here we describe a simple non-correlation-based method capable of directly measuring population distributions at very low sample concentrations. Specifically, we exploit the highest signal-to-noise light bursts from single fluorescent particles transiting a confocal excitation spot to recursively determine the brightness and size distribution of complex mixtures of fluorescent objects. We refer to this method as burst analysis spectroscopy (BAS) and demonstrate the sensitivity of this technique by examining the free-solution, time-resolved distribution of assembled protein aggregates by using two fluorescently labeled proteins: the aggregation-prone, chaperonin-dependent, folding model protein ribulose-bisphosphate carboxylase/oxygenase (RuBisCO), and an amyloidogenic fragment of the yeast prion protein Sup35. We find that the assembly kinetics of both proteins display complex multimodal behavior not readily quantifiable with other methods.

  15. Burst analysis spectroscopy: A versatile single-particle approach for studying distributions of protein aggregates and fluorescent assemblies

    PubMed Central

    Puchalla, Jason; Krantz, Kelly; Austin, Robert; Rye, Hays

    2008-01-01

    Many essential cellular functions depend on the assembly and disassembly of macromolecular complexes. The size, form, and distribution of these assemblies can be heterogeneous and complex, rendering their detailed characterization difficult. Here we describe a simple non-correlation-based method capable of directly measuring population distributions at very low sample concentrations. Specifically, we exploit the highest signal-to-noise light bursts from single fluorescent particles transiting a confocal excitation spot to recursively determine the brightness and size distribution of complex mixtures of fluorescent objects. We refer to this method as burst analysis spectroscopy (BAS) and demonstrate the sensitivity of this technique by examining the free-solution, time-resolved distribution of assembled protein aggregates by using two fluorescently labeled proteins: the aggregation-prone, chaperonin-dependent, folding model protein ribulose-bisphosphate carboxylase/oxygenase (RuBisCO), and an amyloidogenic fragment of the yeast prion protein Sup35. We find that the assembly kinetics of both proteins display complex multimodal behavior not readily quantifiable with other methods. PMID:18780782

  16. Characterisation of the protein corona using tunable resistive pulse sensing: determining the change and distribution of a particle's surface charge.

    PubMed

    Blundell, Emma L C J; Healey, Matthew J; Holton, Elizabeth; Sivakumaran, Muttuswamy; Manstana, Sarabjit; Platt, Mark

    2016-08-01

    The zeta potential of the protein corona around carboxyl particles has been measured using tunable resistive pulse sensing (TRPS). A simple and rapid assay for characterising zeta potentials within buffer, serum and plasma is presented monitoring the change, magnitude and distribution of proteins on the particle surface. First, we measure the change in zeta potential of carboxyl-functionalised nanoparticles in solutions that contain biologically relevant concentrations of individual proteins, typically constituted in plasma and serum, and observe a significant difference in distributions and zeta values between room temperature and 37 °C assays. The effect is protein dependent, and the largest difference between the two temperatures is recorded for the γ-globulin protein where the mean zeta potential changes from -16.7 to -9.0 mV for 25 and 37 °C, respectively. This method is further applied to monitor particles placed into serum and/or plasma. A temperature-dependent change is again observed with serum showing a 4.9 mV difference in zeta potential between samples incubated at 25 and 37 °C; this shift was larger than that observed for samples in plasma (0.4 mV). Finally, we monitor the kinetics of the corona reorientation for particles initially placed into serum and then adding 5 % (V/V) plasma. The technology presented offers an interesting insight into protein corona structure and kinetics of formation measured in biologically relevant solutions, i.e. high protein, high salt levels, and its particle-by-particle analysis gives a measure of the distribution of particle zeta potential that may offer a better understanding of the behaviour of nanoparticles in solution. Graphical Abstract The relative velocity of a nanoparticle as it traverses a nanopore can be used to determine its zeta potential. Monitoring the changes in translocation speeds can therefore be used to follow changes to the surface chemistry/composition of 210 nm particles that were placed

  17. Antibodies to the Core Proteins of Nairobi Sheep Disease Virus/Ganjam Virus Reveal Details of the Distribution of the Proteins in Infected Cells and Tissues

    PubMed Central

    Lasecka, Lidia; Bin-Tarif, Abdelghani; Bridgen, Anne; Juleff, Nicholas; Waters, Ryan A.; Baron, Michael D.

    2015-01-01

    Nairobi sheep disease virus (NSDV; also called Ganjam virus in India) is a bunyavirus of the genus Nairovirus. It causes a haemorrhagic gastroenteritis in sheep and goats with mortality up to 90%. The virus is closely related to the human pathogen Crimean-Congo haemorrhagic fever virus (CCHFV). Little is currently known about the biology of NSDV. We have generated specific antibodies against the virus nucleocapsid protein (N) and polymerase (L) and used these to characterise NSDV in infected cells and to study its distribution during infection in a natural host. Due to its large size and the presence of a papain-like protease (the OTU-like domain) it has been suggested that the L protein of nairoviruses undergoes an autoproteolytic cleavage into polymerase and one or more accessory proteins. Specific antibodies which recognise either the N-terminus or the C-terminus of the NSDV L protein showed no evidence of L protein cleavage in NSDV-infected cells. Using the specific anti-N and anti-L antibodies, it was found that these viral proteins do not fully colocalise in infected cells; the N protein accumulated near the Golgi at early stages of infection while the L protein was distributed throughout the cytoplasm, further supporting the multifunctional nature of the L protein. These antibodies also allowed us to gain information about the organs and cell types targeted by the virus in vivo. We could detect NSDV in cryosections prepared from various tissues collected post-mortem from experimentally inoculated animals; the virus was found in the mucosal lining of the small and large intestine, in the lungs, and in mesenteric lymph nodes (MLN), where NSDV appeared to target monocytes and/or macrophages. PMID:25905707

  18. Antibodies to the core proteins of Nairobi sheep disease virus/Ganjam virus reveal details of the distribution of the proteins in infected cells and tissues.

    PubMed

    Lasecka, Lidia; Bin-Tarif, Abdelghani; Bridgen, Anne; Juleff, Nicholas; Waters, Ryan A; Baron, Michael D

    2015-01-01

    Nairobi sheep disease virus (NSDV; also called Ganjam virus in India) is a bunyavirus of the genus Nairovirus. It causes a haemorrhagic gastroenteritis in sheep and goats with mortality up to 90%. The virus is closely related to the human pathogen Crimean-Congo haemorrhagic fever virus (CCHFV). Little is currently known about the biology of NSDV. We have generated specific antibodies against the virus nucleocapsid protein (N) and polymerase (L) and used these to characterise NSDV in infected cells and to study its distribution during infection in a natural host. Due to its large size and the presence of a papain-like protease (the OTU-like domain) it has been suggested that the L protein of nairoviruses undergoes an autoproteolytic cleavage into polymerase and one or more accessory proteins. Specific antibodies which recognise either the N-terminus or the C-terminus of the NSDV L protein showed no evidence of L protein cleavage in NSDV-infected cells. Using the specific anti-N and anti-L antibodies, it was found that these viral proteins do not fully colocalise in infected cells; the N protein accumulated near the Golgi at early stages of infection while the L protein was distributed throughout the cytoplasm, further supporting the multifunctional nature of the L protein. These antibodies also allowed us to gain information about the organs and cell types targeted by the virus in vivo. We could detect NSDV in cryosections prepared from various tissues collected post-mortem from experimentally inoculated animals; the virus was found in the mucosal lining of the small and large intestine, in the lungs, and in mesenteric lymph nodes (MLN), where NSDV appeared to target monocytes and/or macrophages.

  19. Climate change and habitat fragmentation drive the occurrence of Borrelia burgdorferi, the agent of Lyme disease, at the northeastern limit of its distribution.

    PubMed

    Simon, Julie A; Marrotte, Robby R; Desrosiers, Nathalie; Fiset, Jessica; Gaitan, Jorge; Gonzalez, Andrew; Koffi, Jules K; Lapointe, Francois-Joseph; Leighton, Patrick A; Lindsay, Lindsay R; Logan, Travis; Milord, Francois; Ogden, Nicholas H; Rogic, Anita; Roy-Dufresne, Emilie; Suter, Daniel; Tessier, Nathalie; Millien, Virginie

    2014-08-01

    Lyme borreliosis is rapidly emerging in Canada, and climate change is likely a key driver of the northern spread of the disease in North America. We used field and modeling approaches to predict the risk of occurrence of Borrelia burgdorferi, the bacteria causing Lyme disease in North America. We combined climatic and landscape variables to model the current and future (2050) potential distribution of the black-legged tick and the white-footed mouse at the northeastern range limit of Lyme disease and estimated a risk index for B. burgdorferi from these distributions. The risk index was mostly constrained by the distribution of the white-footed mouse, driven by winter climatic conditions. The next factor contributing to the risk index was the distribution of the black-legged tick, estimated from the temperature. Landscape variables such as forest habitat and connectivity contributed little to the risk index. We predict a further northern expansion of B. burgdorferi of approximately 250-500 km by 2050 - a rate of 3.5-11 km per year - and identify areas of rapid rise in the risk of occurrence of B. burgdorferi. Our results will improve understanding of the spread of Lyme disease and inform management strategies at the most northern limit of its distribution.

  20. Climate change and habitat fragmentation drive the occurrence of Borrelia burgdorferi, the agent of Lyme disease, at the northeastern limit of its distribution

    PubMed Central

    Simon, Julie A; Marrotte, Robby R; Desrosiers, Nathalie; Fiset, Jessica; Gaitan, Jorge; Gonzalez, Andrew; Koffi, Jules K; Lapointe, Francois-Joseph; Leighton, Patrick A; Lindsay, Lindsay R; Logan, Travis; Milord, Francois; Ogden, Nicholas H; Rogic, Anita; Roy-Dufresne, Emilie; Suter, Daniel; Tessier, Nathalie; Millien, Virginie

    2014-01-01

    Lyme borreliosis is rapidly emerging in Canada, and climate change is likely a key driver of the northern spread of the disease in North America. We used field and modeling approaches to predict the risk of occurrence of Borrelia burgdorferi, the bacteria causing Lyme disease in North America. We combined climatic and landscape variables to model the current and future (2050) potential distribution of the black-legged tick and the white-footed mouse at the northeastern range limit of Lyme disease and estimated a risk index for B. burgdorferi from these distributions. The risk index was mostly constrained by the distribution of the white-footed mouse, driven by winter climatic conditions. The next factor contributing to the risk index was the distribution of the black-legged tick, estimated from the temperature. Landscape variables such as forest habitat and connectivity contributed little to the risk index. We predict a further northern expansion of B. burgdorferi of approximately 250–500 km by 2050 – a rate of 3.5–11 km per year – and identify areas of rapid rise in the risk of occurrence of B. burgdorferi. Our results will improve understanding of the spread of Lyme disease and inform management strategies at the most northern limit of its distribution. PMID:25469157

  1. Protein Copy Number Distributions for a Self-Regulating Gene in the Presence of Decoy Binding Sites

    PubMed Central

    Bokes, Pavol; Singh, Abhyudai

    2015-01-01

    A single transcription factor may interact with a multitude of targets on the genome, some of which are at gene promoters, others being part of DNA repeat elements. Being sequestered at binding sites, protein molecules can be prevented from partaking in other pathways, specifically, from regulating the expression of the very gene that encodes them. Acting as decoys at the expense of the autoregulatory loop, the binding sites can have a profound impact on protein abundance—on its mean as well as on its cell-to-cell variability. In order to quantify this impact, we study in this paper a mathematical model for pulsatile expression of a transcription factor that autoregulates its expression and interacts with decoys. We determine the exact stationary distribution for protein abundance at the single-cell level, showing that in the case of non-cooperative positive autoregulation, the distribution can be bimodal, possessing a basal expression mode and a distinct, up-regulated, mode. Bimodal protein distributions are more feasible if the rate of degradation is the same irrespective of whether protein is bound or not. Contrastingly, the presence of decoy binding sites which protect the protein from degradation reduces the availability of the bimodal scenario. PMID:25811868

  2. Lipid and protein distribution in epithelial cells assessed with confocal microscopy

    NASA Astrophysics Data System (ADS)

    Peterson, Kajsa H.; Randen, Michael; Hays, Richard M.; Magnusson, Karl-Eric

    1992-06-01

    Confocal laser scanning microscopy, image processing, and volume visualization were used to characterize the 3-D distribution of lectin receptors, lipid probes, and actin cytoskeleton in epithelial cells. Small intestine-like cells were grown on glass or filter supports and apically labelled with different fluorescent lipid and lectin probes. The restriction of the probes by the tight junctions was studied in living cells. Series of confocal x-y sections were transferred to an image processing system for analysis. The fluorescence intensity within a specified area of all x-y sections was plotted as a function of the vertical position of the sections. The curve inclination was used to describe the degree of restriction to the probes. It was found that lectins were more confined to the apical part than the lipids, which showed varying degree of redistribution to the basolateral membrane. Volume rendering, and specifically animated sequences with varying viewpoint and opacity mapping, were used to visualize the structure of actin cytoskeleton and distribution of lipid and lectin probes. In toad bladder epithelial cells, actin was labelled before and after treatment with the antidiuretic hormone vasopressin. The hormone-induced redistribution of actin in the apical and lateral portion of the cells was measured on x-z scanned images. Ratios of apical-to-lateral intensity were calculated. It was found that the decrease in the ratios after vasopressin treatment was around 30%. The decrease was due to loss of actin apically. This is supposed to facilitate apical fusion of vesicles containing the water-channel forming proteins, being important in water homeostasis.

  3. Cellular distribution of the fragile X mental retardation protein in the mouse brain.

    PubMed

    Zorio, Diego A R; Jackson, Christine M; Liu, Yong; Rubel, Edwin W; Wang, Yuan

    2017-03-01

    The fragile X mental retardation protein (FMRP) plays an important role in normal brain development. Absence of FMRP results in abnormal neuronal morphologies in a selected manner throughout the brain, leading to intellectual deficits and sensory dysfunction in the fragile X syndrome (FXS). Despite FMRP importance for proper brain function, its overall expression pattern in the mammalian brain at the resolution of individual neuronal cell groups is not known. In this study we used FMR1 knockout and isogenic wildtype mice to systematically map the distribution of FMRP expression in the entire mouse brain. Using immunocytochemistry and cellular quantification analyses, we identified a large number of prominent cell groups expressing high levels of FMRP at the subcortical levels, in particular sensory and motor neurons in the brainstem and thalamus. In contrast, many cell groups in the midbrain and hypothalamus exhibit low FMRP levels. More important, we describe differential patterns of FMRP distribution in both cortical and subcortical brain regions. Almost all major brain areas contain high and low levels of FMRP cell groups adjacent to each other or between layers of the same cortical areas. These differential patterns indicate that FMRP expression appears to be specific to individual neuronal cell groups instead of being associated with all neurons in distinct brain regions, as previously considered. Taken together, these findings support the notion of FMRP differential neuronal regulation and strongly implicate the contribution of fundamental sensory and motor processing at subcortical levels to FXS pathology. J. Comp. Neurol. 525:818-849, 2017. © 2016 Wiley Periodicals, Inc.

  4. Differential distribution of proteins expressed in companion cells in the sieve element-companion cell complex of rice plants.

    PubMed

    Fukuda, Akari; Fujimaki, Syu; Mori, Tomoko; Suzui, Nobuo; Ishiyama, Keiki; Hayakawa, Toshihiko; Yamaya, Tomoyuki; Fujiwara, Toru; Yoneyama, Tadakatsu; Hayashi, Hiroaki

    2005-11-01

    Sieve tubes are comprised of sieve elements, enucleated cells that are incapable of RNA and protein synthesis. The proteins in sieve elements are supplied from the neighboring companion cells through plasmodesmata. In rice plants, it was unclear whether or not all proteins produced in companion cells had the same distribution pattern in the sieve element-companion cell complex. In this study, the distribution pattern of four proteins, beta-glucuronidase (GUS), green fluorescent protein (GFP), thioredoxin h (TRXh) and glutathione S-transferase (GST) were analyzed. The foreign proteins GUS and GFP were expressed in transgenic rice plants under the control of the TRXh gene promoter (PTRXh), a companion cell-specific promoter. Analysis of leaf cross-sections of PTRXh-GUS and PTRXh-GFP plants indicated high accumulation of GUS and GFP, respectively, in companion cells rather than in sieve elements. GUS and GFP were also detected in phloem sap collected from leaf sheaths of the transgenic rice plants, suggesting these proteins could enter sieve elements. Relative amounts of GFP and endogenous phloem proteins, TRXh and GST, in phloem sap and total leaf extracts were compared. Compared to TRXh and GST, GFP content was higher in total leaf extracts, but lower in phloem sap, suggesting that GFP accumulated mainly in companion cells rather than in sieve elements. On the other hand, TRXh and GST appeared to accumulate in sieve elements rather than in companion cells. These results indicate the evidence for differential distribution of proteins between sieve elements and companion cells in rice plants.

  5. Distributions.

    ERIC Educational Resources Information Center

    Bowers, Wayne A.

    This monograph was written for the Conference of the New Instructional Materials in Physics, held at the University of Washington in summer, 1965. It is intended for students who have had an introductory college physics course. It seeks to provide an introduction to the idea of distributions in general, and to some aspects of the subject in…

  6. The C-terminal tail of protein kinase D2 and protein kinase D3 regulates their intracellular distribution

    SciTech Connect

    Papazyan, Romeo; Rozengurt, Enrique; Rey, Osvaldo . E-mail: orey@mednet.ucla.edu

    2006-04-14

    We generated a set of GFP-tagged chimeras between protein kinase D2 (PKD2) and protein kinase D3 (PKD3) to examine in live cells the contribution of their C-terminal region to their intracellular localization. We found that the catalytic domain of PKD2 and PKD3 can localize to the nucleus when expressed without other kinase domains. However, when the C-terminal tail of PKD2 was added to its catalytic domain, the nuclear localization of the resulting protein was inhibited. In contrast, the nuclear localization of the CD of PKD3 was not inhibited by its C-terminal tail. Furthermore, the exchange of the C-terminal tail of PKD2 and PKD3 in the full-length proteins was sufficient to exchange their intracellular localization. Collectively, these data demonstrate that the short C-terminal tail of these kinases plays a critical role in determining their cytoplasmic/nuclear localization.

  7. Regional distribution and subcellular associations of Type II calcium and calmodulin-dependent protein kinase in rat brain

    SciTech Connect

    Erondu, N.E.

    1986-01-01

    Four monoclonal antibodies generated against the Type II CaM kinase have been characterized. Two of these antibodies were used to confirm that both alpha and beta subunits were part of the holoenzyme complex. I also developed liquid phase and solid phase radioimmunoassays for the kinase. With the solid phase radioimmunoassay, the distribution of the kinase in rat brain was examined. This study revealed that the concentration of the kinase varies markedly in different brain regions. It is most highly concentrated in the telencephalon where it comprises approximately 2% of total hippocampal protein, 1.3% of cortical protein and 0.7% of striatal protein. It is less concentrated in lower brain regions ranging from 0.3% of hypothalamic protein to 0.1% of protein in the pons/medulla.

  8. Distribution of abnormal prion protein in a sheep affected with L-type bovine spongiform encephalopathy.

    PubMed

    Matsuura, Y; Iwamaru, Y; Masujin, K; Imamura, M; Mohri, S; Yokoyama, T; Okada, H

    2013-07-01

    To investigate the topographical distribution and patterns of deposition of immunolabelled abnormal prion protein (PrP(Sc)), interspecies transmission of atypical L-type bovine spongiform encephalopathy (BSE) to Cheviot ewes (ARQ/ARQ genotype) was performed. L-type BSE was successfully transmitted via the intracerebral route to a ewe, with an incubation period of 1,562 days. Minimal vacuolar change was detected in the basal ganglia, thalamus and brainstem, and PrP(Sc) accumulated throughout the brain. The L-type BSE-affected sheep was characterized by conspicuous fine particulate deposits in the neuropil, particulate and/or granular intraneuronal and intraglial deposits, and the absence of PrP(Sc) plaques or stellate deposits. In addition, immunohistochemical and western blot analyses revealed that PrP(Sc) accumulation was present in peripheral nervous tissues (including the trigeminal ganglia and dorsal root ganglion) and adrenal glands, but was absent in lymphoid tissues. These results suggest that L-type BSE has distinct and distinguishable characteristics as well as PrP(Sc) tissue tropism in sheep.

  9. Distribution and evolution of stable single α-helices (SAH domains) in myosin motor proteins

    PubMed Central

    Simm, Dominic; Hatje, Klas

    2017-01-01

    Stable single-alpha helices (SAHs) are versatile structural elements in many prokaryotic and eukaryotic proteins acting as semi-flexible linkers and constant force springs. This way SAH-domains function as part of the lever of many different myosins. Canonical myosin levers consist of one or several IQ-motifs to which light chains such as calmodulin bind. SAH-domains provide flexibility in length and stiffness to the myosin levers, and may be particularly suited for myosins working in crowded cellular environments. Although the function of the SAH-domains in human class-6 and class-10 myosins has well been characterised, the distribution of the SAH-domain in all myosin subfamilies and across the eukaryotic tree of life remained elusive. Here, we analysed the largest available myosin sequence dataset consisting of 7919 manually annotated myosin sequences from 938 species representing all major eukaryotic branches using the SAH-prediction algorithm of Waggawagga, a recently developed tool for the identification of SAH-domains. With this approach we identified SAH-domains in more than one third of the supposed 79 myosin subfamilies. Depending on the myosin class, the presence of SAH-domains can range from a few to almost all class members indicating complex patterns of independent and taxon-specific SAH-domain gain and loss. PMID:28369123

  10. Coaxial Redundant Drives

    NASA Technical Reports Server (NTRS)

    Brissette, R.

    1983-01-01

    Harmonic drives allow redundancy and high out put torque in small package. If main drive fails, standby drive takes over and produces torque along same axis as main drive. Uses include power units in robot for internal pipeline inspection, manipulators in deep submersible probes or other applications in which redundancy protects against costly failures.

  11. Canine distemper virus matrix protein influences particle infectivity, particle composition, and envelope distribution in polarized epithelial cells and modulates virulence.

    PubMed

    Dietzel, Erik; Anderson, Danielle E; Castan, Alexandre; von Messling, Veronika; Maisner, Andrea

    2011-07-01

    In paramyxoviruses, the matrix (M) protein mediates the interaction between the envelope and internal proteins during particle assembly and egress. In measles virus (MeV), M mutations, such as those found in subacute sclerosing panencephalitis (SSPE) strains, and differences in vaccine and wild-type M proteins can affect the strength of interaction with the envelope glycoproteins, assembly efficiency, and spread. However, the contribution of the M protein to the replication and pathogenesis of the closely related canine distemper virus (CDV) has not been characterized. To this end this, we generated a recombinant wild-type CDV carrying a vaccine strain M protein. The recombinant virus retained the parental growth phenotype in VerodogSLAMtag cells, but displayed an increased particle-to-infectivity ratio very similar to that of the vaccine strain, likely due to inefficient H protein incorporation. Even though infectious virus was released only from the apical surface, consistent with the release polarity of the wild-type CDV strain, envelope protein distribution in polarized epithelial cells reproduced the bipolar pattern seen in vaccine strain-infected cells. Most notably, the chimeric virus was completely attenuated in ferrets and caused only a mild and transient leukopenia, indicating that the differences in particle infectivity and envelope protein sorting mediated by the vaccine M protein contribute importantly to vaccine strain attenuation.

  12. Prediction of FMN-binding residues with three-dimensional probability distributions of interacting atoms on protein surfaces.

    PubMed

    Mahalingam, Rajasekaran; Peng, Hung-Pin; Yang, An-Suei

    2014-02-21

    Flavin mono-nucleotide (FMN) is a cofactor which is involved in many biological reactions. The insights on protein-FMN interactions aid the protein functional annotation and also facilitate in drug design. In this study, we have established a new method, making use of an encoding scheme of the three-dimensional probability density maps that describe the distributions of 40 non-covalent interacting atom types around protein surfaces, to predict FMN-binding sites on protein surfaces. One machine learning model was trained for each of the 30 protein atom types to predict tentative FMN-binding sites on protein structures. The method's capability was evaluated by five-fold cross-validation on a dataset containing 81 non-redundant FMN-binding protein structures and further tested on independent datasets of 30 and 15 non-redundant protein structures respectively. These predictions achieved an accuracy of 0.94, 0.94 and 0.96 with the Matthews correlation coefficient (MCC) of 0.53, 0.53 and 0.65 respectively for the three protein structure sets. The prediction capability is superior to the existing method. This is the first structure-based approach that does not rely on evolutionary information for predicting FMN-interacting residues. The webserver for the prediction is available at http://ismblab.genomics.sinica.edu.tw/.

  13. Prediction of carbohydrate binding sites on protein surfaces with 3-dimensional probability density distributions of interacting atoms.

    PubMed

    Tsai, Keng-Chang; Jian, Jhih-Wei; Yang, Ei-Wen; Hsu, Po-Chiang; Peng, Hung-Pin; Chen, Ching-Tai; Chen, Jun-Bo; Chang, Jeng-Yih; Hsu, Wen-Lian; Yang, An-Suei

    2012-01-01

    Non-covalent protein-carbohydrate interactions mediate molecular targeting in many biological processes. Prediction of non-covalent carbohydrate binding sites on protein surfaces not only provides insights into the functions of the query proteins; information on key carbohydrate-binding residues could suggest site-directed mutagenesis experiments, design therapeutics targeting carbohydrate-binding proteins, and provide guidance in engineering protein-carbohydrate interactions. In this work, we show that non-covalent carbohydrate binding sites on protein surfaces can be predicted with relatively high accuracy when the query protein structures are known. The prediction capabilities were based on a novel encoding scheme of the three-dimensional probability density maps describing the distributions of 36 non-covalent interacting atom types around protein surfaces. One machine learning model was trained for each of the 30 protein atom types. The machine learning algorithms predicted tentative carbohydrate binding sites on query proteins by recognizing the characteristic interacting atom distribution patterns specific for carbohydrate binding sites from known protein structures. The prediction results for all protein atom types were integrated into surface patches as tentative carbohydrate binding sites based on normalized prediction confidence level. The prediction capabilities of the predictors were benchmarked by a 10-fold cross validation on 497 non-redundant proteins with known carbohydrate binding sites. The predictors were further tested on an independent test set with 108 proteins. The residue-based Matthews correlation coefficient (MCC) for the independent test was 0.45, with prediction precision and sensitivity (or recall) of 0.45 and 0.49 respectively. In addition, 111 unbound carbohydrate-binding protein structures for which the structures were determined in the absence of the carbohydrate ligands were predicted with the trained predictors. The overall

  14. Variation and correlations between protein MW distribution and semolina quality parameters for durum wheat genotypes grown in North Dakota

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This research assessed the associations between protein molecular weight distribution (MWD) and quality characteristics for durum semolina samples that were obtained from thirteen durum genotypes grown at seven locations for two years in North Dakota. Sodium dodecyl sulfate (SDS) extractable and un...

  15. Driving factors behind the distribution of dinocyst composition and abundance in surface sediments in a western Mediterranean coastal lagoon: report from a high resolution mapping study.

    PubMed

    Fertouna-Bellakhal, Mouna; Dhib, Amel; Béjaoui, Béchir; Turki, Souad; Aleya, Lotfi

    2014-07-15

    Species composition and abundance of dinocysts in relation to environmental factors were studied at 123 stations of surface sediment in Bizerte Lagoon. Forty-eight dinocyst types were identified, mainly dominated by Brigantidinium simplex, Votadinum spinosum, Alexandrium pseudogonyaulax, Alexandrium catenella, and Lingulodinum machaerophorum along with many round brown cysts and spiny round brown cysts. Cysts ranged from 1276 to 20126 cysts g(-1)dry weight sediment. Significant differences in cyst distribution pattern were recorded among the zones, with a higher cyst abundance occurring in the lagoon's inner areas. Redundancy analyses showed two distinct associations of dinocysts according to location and environmental variables. Ballast water discharges are potential introducers of non-indigenous species, especially harmful ones such as A. catenella and Polysphaeridium zoharyi, with currents playing a pivotal role in cyst distribution. Findings concerning harmful cyst species indicate potential seedbeds for initiation of future blooms and outbreaks of potentially toxic species in the lagoon.

  16. Satellite-derived NDVI, LST, and climatic factors driving the distribution and abundance of Anopheles mosquitoes in a former malarious area in northwest Argentina.

    PubMed

    Dantur Juri, María Julia; Estallo, Elizabet; Almirón, Walter; Santana, Mirta; Sartor, Paolo; Lamfri, Mario; Zaidenberg, Mario

    2015-06-01

    Distribution and abundance of disease vectors are directly related to climatic conditions and environmental changes. Remote sensing data have been used for monitoring environmental conditions influencing spatial patterns of vector-borne diseases. The aim of this study was to analyze the effect of the Normalized Difference Vegetation Index (NDVI) and Land Surface Temperature (LST) obtained from the Moderate Resolution Imaging Spectroradiometer (MODIS), and climatic factors (temperature, humidity, wind velocity, and accumulated rainfall) on the distribution and abundance of Anopheles species in northwestern Argentina using Poisson regression analyses. Samples were collected from December, 2001 to December, 2005 at three localities, Aguas Blancas, El Oculto and San Ramón de la Nueva Orán. We collected 11,206 adult Anopheles species, with the major abundance observed at El Oculto (59.11%), followed by Aguas Blancas (22.10%) and San Ramón de la Nueva Orán (18.79%). Anopheles pseudopunctipennis was the most abundant species at El Oculto, Anopheles argyritarsis predominated in Aguas Blancas, and Anopheles strodei in San Ramón de la Nueva Orán. Samples were collected throughout the sampling period, with the highest peaks during the spring seasons. LST and mean temperature appear to be the most important variables determining the distribution patterns and major abundance of An. pseudopunctipennis and An. argyritarsis within malarious areas.

  17. Protein repair L-isoaspartyl methyltransferase in plants. Phylogenetic distribution and the accumulation of substrate proteins in aged barley seeds.

    PubMed Central

    Mudgett, M B; Lowenson, J D; Clarke, S

    1997-01-01

    Protein L-isoaspartate (D-aspartate) O-methyltransferases (MTs; EC 2.1.1.77) can initiate the conversion of detrimental L-isoaspartyl residues in spontaneously damaged proteins to normal L-aspartyl residues. We detected this enzyme in 45 species from 23 families representing most of the divisions of the plant kingdom. MT activity is often localized in seeds, suggesting that it has a role in their maturation, quiescence, and germination. The relationship among MT activity, the accumulation of abnormal protein L-isoaspartyl residues, and seed viability was explored in barley (Hordeum vulgare cultivar Himalaya) seeds, which contain high levels of MT. Natural aging of barley seeds for 17 years resulted in a significant reduction in MT activity and in seed viability, coupled with increased levels of "unrepaired" L-isoaspartyl residues. In seeds heated to accelerate aging, we found no reduction of MT activity, but we did observe decreased seed viability and the accumulation of isoaspartyl residues. Among populations of accelerated aged seed, those possessing the highest levels of L-isoaspartyl-containing proteins had the lowest germination percentages. These results suggest that the MT present in seeds cannot efficiently repair all spontaneously damaged proteins containing altered aspartyl residues, and their accumulation during aging may contribute to the loss of seed viability. PMID:9414558

  18. Electrophoretic pattern and distribution of cytoskeletal proteins in flat-epitheloid and stellate process-bearing astrocytes in primary culture.

    PubMed

    Ciesielski-Treska, J; Ulrich, G; Mensch, C; Aunis, D

    1984-01-01

    One- and two-dimensional electrophoresis patterns and distribution of major cytoskeletal proteins were studied in primary astrocytes with either flat-epitheloid or stellate appearance. No major differences in the electrophoretic patterns of actin, tubulin, glial fibrillary acidic protein (GFAP) and vimentin were detected between flat-epitheloid and stellate process-bearing astrocytes produced by the exposure of cultures to dibutyryl cyclic AMP (dBcAMP). However the morphological changes of astrocytes were accompanied by marked changes in the quantitative distribution of cytoskeletal proteins. The most prominent change was a large and specific decrease in the amount of actin, detected by [(35)S]methionine incorporation, densitometric scanning of one-dimensional gels and DNase inhibition assay. In stellate astrocytes produced by a 4 day treatment with dibutyryl cyclic AMP, the amount of actin decreased by 50%. This decrease was not apparently related to the depolymerization of actin.

  19. Using Theoretical Protein Isotopic Distributions to Parse Small-Mass-Difference Post-Translational Modifications via Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Rhoads, Timothy W.; Williams, Jared R.; Lopez, Nathan I.; Morré, Jeffrey T.; Bradford, C. Samuel; Beckman, Joseph S.

    2013-01-01

    Small-mass-difference modifications to proteins are obscured in mass spectrometry by the natural abundance of stable isotopes such as 13C that broaden the isotopic distribution of an intact protein. Using a ZipTip (Millipore, Billerica, MA, USA) to remove salt from proteins in preparation for high-resolution mass spectrometry, the theoretical isotopic distribution intensities calculated from the protein's empirical formula could be fit to experimentally acquired data and used to differentiate between multiple low-mass modifications to proteins. We could readily distinguish copper from zinc bound to a single-metal superoxide dismutase (SOD1) species; copper and zinc only differ by an average mass of 1.8 Da and have overlapping stable isotope patterns. In addition, proteins could be directly modified while bound to the ZipTip. For example, washing 11 mM S-methyl methanethiosulfonate over the ZipTip allowed the number of free cysteines on proteins to be detected as S-methyl adducts. Alternatively, washing with the sulfhydryl oxidant diamide could quickly reestablish disulfide bridges. Using these methods, we could resolve the relative contributions of copper and zinc binding, as well as disulfide reduction to intact SOD1 protein present from <100 μg of the lumbar spinal cord of a transgenic, SOD1 overexpressing mouse. Although techniques like ICP-MS can measure total metal in solution, this is the first method able to assess the metal-binding and sulfhydryl reduction of SOD1 at the individual subunit level and is applicable to many other proteins.

  20. Modeling angles in proteins and circular genomes using multivariate angular distributions based on multiple nonnegative trigonometric sums.

    PubMed

    Fernández-Durán, Juan José; Gregorio-Domínguez, María Mercedes

    2014-02-01

    Fernández-Durán, J. J. (2004): "Circular distributions based on nonnegative trigonometric sums," Biometrics, 60, 499-503, developed a family of univariate circular distributions based on nonnegative trigonometric sums. In this work, we extend this family of distributions to the multivariate case by using multiple nonnegative trigonometric sums to model the joint distribution of a vector of angular random variables. Practical examples of vectors of angular random variables include the wind direction at different monitoring stations, the directions taken by an animal on different occasions, the times at which a person performs different daily activities, and the dihedral angles of a protein molecule. We apply the proposed new family of multivariate distributions to three real data-sets: two for the study of protein structure and one for genomics. The first is related to the study of a bivariate vector of dihedral angles in proteins. In the second real data-set, we compare the fit of the proposed multivariate model with the bivariate generalized von Mises model of [Shieh, G. S., S. Zheng, R. A. Johnson, Y.-F. Chang, K. Shimizu, C.-C. Wang, and S.-L. Tang (2011): "Modeling and comparing the organization of circular genomes," Bioinformatics, 27(7), 912-918.] in a problem related to orthologous genes in pairs of circular genomes. The third real data-set consists of observed values of three dihedral angles in γ-turns in a protein and serves as an example of trivariate angular data. In addition, a simulation algorithm is presented to generate realizations from the proposed multivariate angular distribution.

  1. SNX27 and SORLA Interact to Reduce Amyloidogenic Subcellular Distribution and Processing of Amyloid Precursor Protein

    PubMed Central

    Huang, Timothy Y.; Zhao, Yingjun; Li, Xiaoguang; Wang, Xin; Tseng, I-Chu; Thompson, Robert; Tu, Shichun; Willnow, Thomas E.; Zhang, Yun-wu

    2016-01-01

    Proteolytic generation of amyloidogenic amyloid β (Aβ) fragments from the amyloid precursor protein (APP) significantly contributes to Alzheimer's disease (AD). Although amyloidogenic APP proteolysis can be affected by trafficking through genetically associated AD components such as SORLA, how SORLA functionally interacts with other trafficking components is yet unclear. Here, we report that SNX27, an endosomal trafficking/recycling factor and a negative regulator of the γ-secretase complex, binds to the SORLA cytosolic tail to form a ternary complex with APP. SNX27 enhances cell surface SORLA and APP levels in human cell lines and mouse primary neurons, and depletion of SNX27 or SORLA reduces APP endosome-to-cell surface recycling kinetics. SNX27 overexpression enhances the generation of cell surface APP cleavage products such as soluble alpha-APP C-terminal fragment (CTFα) in a SORLA-dependent manner. SORLA-mediated Aβ reduction is attenuated by downregulation of SNX27. This indicates that an SNX27/SORLA complex functionally interacts to limit APP distribution to amyloidogenic compartments, forming a non-amyloidogenic shunt to promote APP recycling to the cell surface. SIGNIFICANCE STATEMENT Many genes have been identified as risk factors for Alzheimer's disease (AD), and a large proportion of these genes function to limit production or toxicity of the AD-associated amyloid β (Aβ) peptide. Whether and how these genes precisely operate to limit AD onset remains an important question. We identify binding and trafficking interactions between two of these factors, SORLA and SNX27, and demonstrate that SNX27 can direct trafficking of SORLA and the Aβ precursor APP to the cell surface to limit the production of Aβ. Diversion APP to the cell surface through modulation of this molecular complex may represent a complimentary strategy for future development in AD treatment. PMID:27466343

  2. Self-assembled monolayers improve protein distribution on holey carbon cryo-EM supports

    PubMed Central

    Meyerson, Joel R.; Rao, Prashant; Kumar, Janesh; Chittori, Sagar; Banerjee, Soojay; Pierson, Jason; Mayer, Mark L.; Subramaniam, Sriram

    2014-01-01

    Poor partitioning of macromolecules into the holes of holey carbon support grids frequently limits structural determination by single particle cryo-electron microscopy (cryo-EM). Here, we present a method to deposit, on gold-coated carbon grids, a self-assembled monolayer whose surface properties can be controlled by chemical modification. We demonstrate the utility of this approach to drive partitioning of ionotropic glutamate receptors into the holes, thereby enabling 3D structural analysis using cryo-EM methods. PMID:25403871

  3. Power semiconductor controlled drives

    NASA Astrophysics Data System (ADS)

    Dubey, Gopal K.

    This book presents power semiconductor controlled drives employing dc motors, induction motors, and synchronous motors. The dynamics of motor and load systems are covered. Open-loop and closed-loop drives are considered, and thyristor, power transistor, and GTO converters are discussed. In-depth coverage is given to ac drives, particularly those fed by voltage and current source inverters and cycloconverters. Full coverage is given to brushless and commutatorless dc drives, including load-commuted synchronous motor drives. Rectifier-controlled dc drives are presented in detail.

  4. Spatial distributions of phosphorylated membrane proteins aquaporin 0 and MP20 across young and aged human lenses.

    PubMed

    Gutierrez, Danielle B; Garland, Donita L; Schwacke, John H; Hachey, David L; Schey, Kevin L

    2016-08-01

    In the human ocular lens it is now realized that post-translational modifications can alter protein function and/or localization in fiber cells that no longer synthesize proteins. The specific sites of post-translational modification to the abundant ocular lens membrane proteins AQP0 and MP20 have been previously identified and their functional effects are emerging. To further understand how changes in protein function and/or localization induced by these modifications alter lens homeostasis, it is necessary to determine the spatial distributions of these modifications across the lens. In this study, a quantitative LC-MS approach was used to determine the spatial distributions of phosphorylated AQP0 and MP20 peptides from manually dissected, concentric layers of fiber cells from young and aged human lenses. The absolute amounts of phosphorylation were determined for AQP0 Ser235 and Ser229 and for MP20 Ser170 in fiber cells from the lens periphery to the lens center. Phosphorylation of AQP0 Ser229 represented a minor portion of the total phosphorylated AQP0. Changes in spatial distributions of phosphorylated APQ0 Ser235 and MP20 Ser170 correlated with regions of physiological interest in aged lenses, specifically, where barriers to water transport and extracellular diffusion form.

  5. Spatial distribution of protein kinase A activity during cell migration is mediated by A-kinase anchoring protein AKAP Lbc.

    PubMed

    Paulucci-Holthauzen, Adriana A; Vergara, Leoncio A; Bellot, Larry J; Canton, David; Scott, John D; O'Connor, Kathleen L

    2009-02-27

    Protein kinase A (PKA) has been suggested to be spatially regulated in migrating cells due to its ability to control signaling events that are critical for polarized actin cytoskeletal dynamics. Here, using the fluorescence resonance energy transfer-based A-kinase activity reporter (AKAR1), we find that PKA activity gradients form with the strongest activity at the leading edge and are restricted to the basal surface in migrating cells. The existence of these gradients was confirmed using immunocytochemistry using phospho-PKA substrate antibodies. This observation holds true for carcinoma cells migrating randomly on laminin-1 or stimulated to migrate on collagen I with lysophosphatidic acid. Phosphodiesterase inhibition allows the formation of PKA activity gradients; however, these gradients are no longer polarized. PKA activity gradients are not detected when a non-phosphorylatable mutant of AKAR1 is used, if PKA activity is inhibited with H-89 or protein kinase inhibitor, or when PKA anchoring is perturbed. We further find that a specific A-kinase anchoring protein, AKAP-Lbc, is a major contributor to the formation of these gradients. In summary, our data show that PKA activity gradients are generated at the leading edge of migrating cells and provide additional insight into the mechanisms of PKA regulation of cell motility.

  6. Spatial Distribution of Protein Kinase A Activity during Cell Migration Is Mediated by A-kinase Anchoring Protein AKAP Lbc*

    PubMed Central

    Paulucci-Holthauzen, Adriana A.; Vergara, Leoncio A.; Bellot, Larry J.; Canton, David; Scott, John D.; O'Connor, Kathleen L.

    2009-01-01

    Protein kinase A (PKA) has been suggested to be spatially regulated in migrating cells due to its ability to control signaling events that are critical for polarized actin cytoskeletal dynamics. Here, using the fluorescence resonance energy transfer-based A-kinase activity reporter (AKAR1), we find that PKA activity gradients form with the strongest activity at the leading edge and are restricted to the basal surface in migrating cells. The existence of these gradients was confirmed using immunocytochemistry using phospho-PKA substrate antibodies. This observation holds true for carcinoma cells migrating randomly on laminin-1 or stimulated to migrate on collagen I with lysophosphatidic acid. Phosphodiesterase inhibition allows the formation of PKA activity gradients; however, these gradients are no longer polarized. PKA activity gradients are not detected when a non-phosphorylatable mutant of AKAR1 is used, if PKA activity is inhibited with H-89 or protein kinase inhibitor, or when PKA anchoring is perturbed. We further find that a specific A-kinase anchoring protein, AKAP-Lbc, is a major contributor to the formation of these gradients. In summary, our data show that PKA activity gradients are generated at the leading edge of migrating cells and provide additional insight into the mechanisms of PKA regulation of cell motility. PMID:19106088

  7. Are Charge-State Distributions a Reliable Tool Describing Molecular Ensembles of Intrinsically Disordered Proteins by Native MS?

    NASA Astrophysics Data System (ADS)

    Natalello, Antonino; Santambrogio, Carlo; Grandori, Rita

    2017-01-01

    Native mass spectrometry (MS) has become a central tool of structural proteomics, but its applicability to the peculiar class of intrinsically disordered proteins (IDPs) is still object of debate. IDPs lack an ordered tridimensional structure and are characterized by high conformational plasticity. Since they represent valuable targets for cancer and neurodegeneration research, there is an urgent need of methodological advances for description of the conformational ensembles populated by these proteins in solution. However, structural rearrangements during electrospray-ionization (ESI) or after the transfer to the gas phase could affect data obtained by native ESI-MS. In particular, charge-state distributions (CSDs) are affected by protein conformation inside ESI droplets, while ion mobility (IM) reflects protein conformation in the gas phase. This review focuses on the available evidence relating IDP solution ensembles with CSDs, trying to summarize cases of apparent consistency or discrepancy. The protein-specificity of ionization patterns and their responses to ligands and buffer conditions suggests that CSDs are imprinted to protein structural features also in the case of IDPs. Nevertheless, it seems that these proteins are more easily affected by electrospray conditions, leading in some cases to rearrangements of the conformational ensembles.

  8. Conformational distributions of denatured and unstructured proteins are similar to those of 20 × 20 blocked dipeptides.

    PubMed

    Oh, Kwang-Im; Jung, Young-Sang; Hwang, Geum-Sook; Cho, Minhaeng

    2012-05-01

    Understanding intrinsic conformational preferences of amino-acids in unfolded proteins is important for elucidating the underlying principles of their stability and re-folding on biological timescales. Here, to investigate the neighbor interaction effects on the conformational propensities of amino-acids, we carried out (1)H NMR experiments for a comprehensive set of blocked dipeptides and measured the scalar coupling constants between alpha protons and amide protons as well as their chemical shifts. Detailed inspection of these NMR properties shows that, irrespective of amino-acid side-chain properties, the distributions of the measured coupling constants and chemical shifts of the dipeptides are comparatively narrow, indicating small variances of their conformation distributions. They are further compared with those of blocked amino-acids (Ac-X-NHMe), oligopeptides (Ac-GGXGG-NH(2)), and native (lysozyme), denatured (lysozyme and outer membrane protein X from Escherichia coli), unstructured (Domain 2 of the protein 5A of Hepatitis C virus), and intrinsically disordered (hNlg3cyt: intracellular domain of human NL3) proteins. These comparative investigations suggest that the conformational preferences and local solvation environments of the blocked dipeptides are quite similar to not only those of other short oligopeptides but also those of denatured and natively unfolded proteins.

  9. Neurofilament protein is differentially distributed in subpopulations of corticocortical projection neurons in the macaque monkey visual pathways

    NASA Technical Reports Server (NTRS)

    Hof, P. R.; Ungerleider, L. G.; Webster, M. J.; Gattass, R.; Adams, M. M.; Sailstad, C. A.; Morrison, J. H.; Bloom, F. E. (Principal Investigator)

    1996-01-01

    Previous studies of the primate cerebral cortex have shown that neurofilament protein is present in pyramidal neuron subpopulations displaying specific regional and laminar distribution patterns. In order to characterize further the neurochemical phenotype of the neurons furnishing feedforward and feedback pathways in the visual cortex of the macaque monkey, we performed an analysis of the distribution of neurofilament protein in corticocortical projection neurons in areas V1, V2, V3, V3A, V4, and MT. Injections of the retrogradely transported dyes Fast Blue and Diamidino Yellow were placed within areas V4 and MT, or in areas V1 and V2, in 14 adult rhesus monkeys, and the brains of these animals were processed for immunohistochemistry with an antibody to nonphosphorylated epitopes of the medium and heavy molecular weight subunits of the neurofilament protein. Overall, there was a higher proportion of neurons projecting from areas V1, V2, V3, and V3A to area MT that were neurofilament protein-immunoreactive (57-100%), than to area V4 (25-36%). In contrast, feedback projections from areas MT, V4, and V3 exhibited a more consistent proportion of neurofilament protein-containing neurons (70-80%), regardless of their target areas (V1 or V2). In addition, the vast majority of feedback neurons projecting to areas V1 and V2 were located in layers V and VI in areas V4 and MT, while they were observed in both supragranular and infragranular layers in area V3. The laminar distribution of feedforward projecting neurons was heterogeneous. In area V1, Meynert and layer IVB cells were found to project to area MT, while neurons projecting to area V4 were particularly dense in layer III within the foveal representation. In area V2, almost all neurons projecting to areas MT or V4 were located in layer III, whereas they were found in both layers II-III and V-VI in areas V3 and V3A. These results suggest that neurofilament protein identifies particular subpopulations of

  10. Predicting the behaviour of proteins in hydrophobic interaction chromatography. 2. Using a statistical description of their surface amino acid distribution.

    PubMed

    Salgado, J Cristian; Rapaport, Ivan; Asenjo, Juan A

    2006-02-24

    This paper focuses on the prediction of the dimensionless retention time (DRT) of proteins in hydrophobic interaction chromatography (HIC) by means of mathematical models based on the statistical description of the amino acid surface distribution. Previous models characterises the protein surface as a whole. However, most of the time it is not the whole protein but some of its specific regions that interact with the environment. It seems much more natural to use local measurements of the characteristics of the surface. Therefore, the statistical characterisation of the distribution of an amino acid property on the protein surface was carried out from the systematic calculation of the local average of this property in a neighbourhood placed sequentially on each of the amino acids on the protein surface. This process allowed us to characterise the distribution of this property quantitatively using three main statistics: average, standard deviation and maximum. In particular, if the property considered is a hydrophobicity scale, these statistics allowed us to characterise the average hydrophobicity and the hydrophobic content of the most hydrophobic cluster or hotspot, as well as the heterogeneity of the hydrophobicity distribution on the protein surface. We tested the performance of the DRT predictive models based on these statistics on a set of 15 proteins. We obtained better predictive results with respect to the models previously reported. The best predictive model was a linear model based on the maximum. This statistic was calculated using an index of the mobilities of amino acids in chromatography. The predictive performance of this model (measured as the Jack Knife MSE) was 26.9% better than those obtained by the best model which does not consider the amino acid distribution and 19.5% better than the model based on the hydrophobic imbalance (HI). In addition, the best performance was obtained by a linear multivariable model based on the HI and the maximum. The

  11. Differential distribution of non-structural proteins of foot-and-mouth disease virus in BHK-21 cells

    SciTech Connect

    Garcia-Briones, Mercedes; Rosas, Maria F.; Gonzalez-Magaldi, Monica; Martin-Acebes, Miguel A.; Sobrino, Francisco . E-mail: fsobrino@cbm.uam.es; Armas-Portela, Rosario . E-mail: rarmas@cbm.uam.es

    2006-06-05

    Differences in the kinetics of expression and cell distribution among FMDV non-structural proteins (NSPs) have been observed in BHK-21-infected cells. 3D{sup pol} was the first protein detected by immunofluorescence (1.5 h p.i.), showing a perinuclear distribution. At 2-2.5 h p.i., 2B, 2C, 3B and 3C were detected, mostly exhibiting a punctuated, scattered pattern, while 3A and 3D{sup pol} appeared concentrated at one side of the nucleus. This distribution was exhibited by all the NSPs from 3 h p.i., being 2C and, to a lesser extent, precursors 2BC and 3ABBB, the only proteins detected by Western blotting at that infection time. From 4 h p.i., all mature NSPs as well as precursors 2BC, 3ABBB, 3ABB, 3AB and 3CD{sup pol} were detected by this technique. In spite of their similar immunofluorescence patterns, 2C and 3A co-localized partially by confocal microscopy at 3.5 h p.i., and 3A, but not 2C, co-localized with the ER marker calreticulin, suggesting differences in the distribution of these proteins and/or their precursors as infection proceeded. Transient expression of 2C and 3AB resulted in punctuated fluorescence patterns similar to those found in early infected cells, while 3A showed a more diffuse distribution. A shift towards a fibrous pattern was noticed for 3ABB, while a major change was observed in cells expressing 3ABBB, which displayed a perinuclear fibrous distribution. Interestingly, when co-expressed with 3D{sup pol}, the pattern observed for 3ABBB fluorescence was altered, resembling that exhibited by cells transfected with 3AB. Transient expression of 3D{sup pol} showed a homogeneous cell distribution that included, as determined by confocal microscopy, the nucleus. This was confirmed by the detection of 3D{sup pol} in nuclear fractions of transfected cells. 3D{sup pol} and its precursor 3CD{sup pol} were also detected in nuclear fractions of infected cells, suggesting that these proteins can directly interact with the nucleus during FMDV infection.

  12. Ocular disease and driving.

    PubMed

    Wood, Joanne M; Black, Alex A

    2016-09-01

    As the driving population ages, the number of drivers with visual impairment resulting from ocular disease will increase given the age-related prevalence of ocular disease. The increase in visual impairment in the driving population has a number of implications for driving outcomes. This review summarises current research regarding the impact of common ocular diseases on driving ability and safety, with particular focus on cataract, glaucoma, age-related macular degeneration, hemianopia and diabetic retinopathy. The evidence considered includes self-reported driving outcomes, driving performance (on-road and simulator-based) and various motor vehicle crash indices. Collectively, this review demonstrates that driving ability and safety are negatively affected by ocular disease; however, further research is needed in this area. Older drivers with ocular disease need to be aware of the negative consequences of their ocular condition and in the case where treatment options are available, encouraged to seek these earlier for optimum driving safety and quality of life benefits.

  13. Dementia and driving

    MedlinePlus

    ... medlineplus.gov/ency/patientinstructions/000028.htm Dementia and driving To use the sharing features on this page, ... their independence is being taken away. Signs That Driving May No Longer be Safe People with signs ...

  14. Safe driving for teens

    MedlinePlus

    ... gov/pubmed/25837240 . Simons-Morton B, Ouimet MC. Parent involvement in novice teen driving: a review of the ... nlm.nih.gov/pubmed/16788109 . Simons-Morton B. Parent involvement in novice teen driving: rationale, evidence of effects, ...

  15. Spatial and Temporal Dynamics in the Ionic Driving Force for GABAA Receptors

    PubMed Central

    Wright, R.; Raimondo, J. V.; Akerman, C. J.

    2011-01-01

    It is becoming increasingly apparent that the strength of GABAergic synaptic transmission is dynamic. One parameter that can establish differences in the actions of GABAergic synapses is the ionic driving force for the chloride-permeable GABAA receptor (GABAAR). Here we review some of the sophisticated ways in which this ionic driving force can vary within neuronal circuits. This driving force for GABAARs is subject to tight spatial control, with the distribution of Cl− transporter proteins and channels generating regional variation in the strength of GABAAR signalling across a single neuron. GABAAR dynamics can result from short-term changes in their driving force, which involve the temporary accumulation or depletion of intracellular Cl−. In addition, activity-dependent changes in the expression and function of Cl− regulating proteins can result in long-term shifts in the driving force for GABAARs. The multifaceted regulation of the ionic driving force for GABAARs has wide ranging implications for mature brain function, neural circuit development, and disease. PMID:21766044

  16. Gear bearing drive

    NASA Technical Reports Server (NTRS)

    Weinberg, Brian (Inventor); Mavroidis, Constantinos (Inventor); Vranish, John M. (Inventor)

    2011-01-01

    A gear bearing drive provides a compact mechanism that operates as an actuator providing torque and as a joint providing support. The drive includes a gear arrangement integrating an external rotor DC motor within a sun gear. Locking surfaces maintain the components of the drive in alignment and provide support for axial loads and moments. The gear bearing drive has a variety of applications, including as a joint in robotic arms and prosthetic limbs.

  17. Zea mays Taxilin protein negatively regulates opaque-2 transcriptional activity by causing a change in its sub-cellular distribution.

    PubMed

    Zhang, Nan; Qiao, Zhenyi; Liang, Zheng; Mei, Bing; Xu, Zhengkai; Song, Rentao

    2012-01-01

    Zea mays (maize) Opaque-2 (ZmO2) protein is an important bZIP transcription factor that regulates the expression of major storage proteins (22-kD zeins) and other important genes during maize seed development. ZmO2 is subject to functional regulation through protein-protein interactions. To unveil the potential regulatory network associated with ZmO2, a protein-protein interaction study was carried out using the truncated version of ZmO2 (O2-2) as bait in a yeast two-hybrid screen with a maize seed cDNA library. A protein with homology to Taxilin was found to have stable interaction with ZmO2 in yeast and was designated as ZmTaxilin. Sequence analysis indicated that ZmTaxilin has a long coiled-coil domain containing three conserved zipper motifs. Each of the three zipper motifs is individually able to interact with ZmO2 in yeast. A GST pull-down assay demonstrated the interaction between GST-fused ZmTaxilin and ZmO2 extracted from developing maize seeds. Using onion epidermal cells as in vivo assay system, we found that ZmTaxilin could change the sub-cellular distribution of ZmO2. We also demonstrated that this change significantly repressed the transcriptional activity of ZmO2 on the 22-kD zein promoter. Our study suggests that a Taxilin-mediated change in sub-cellular distribution of ZmO2 may have important functional consequences for ZmO2 activity.

  18. Maize opaque10 Encodes a Cereal-Specific Protein That Is Essential for the Proper Distribution of Zeins in Endosperm Protein Bodies

    PubMed Central

    Yao, Dongsheng; Qi, Weiwei; Li, Xia; Yang, Qing; Yan, Shumei; Ling, Huiling; Wang, Gang; Wang, Guifeng; Song, Rentao

    2016-01-01

    Cereal storage proteins are major nitrogen sources for humans and livestock. Prolamins are the most abundant storage protein in most cereals. They are deposited into protein bodies (PBs) in seed endosperm. The inner structure and the storage mechanism for prolamin PBs is poorly understood. Maize opaque10 (o10) is a classic opaque endosperm mutant with misshapen PBs. Through positional cloning, we found that O10 encodes a novel cereal-specific PB protein. Its middle domain contains a seven-repeat sequence that is responsible for its dimerization. Its C terminus contains a transmembrane motif that is required for its ER localization and PB deposition. A cellular fractionation assay indicated that O10 is initially synthesized in the cytoplasm and then anchored to the ER and eventually deposited in the PB. O10 can interact with 19-kD and 22-kD α-zeins and 16-kD and 50-kD γ-zeins through its N-terminal domain. An immunolocalization assay indicated that O10 co-localizes with 16-kD γ-zein and 22-kD α-zein in PBs, forming a ring-shaped structure at the interface between the α-zein-rich core and the γ-zein-rich peripheral region. The loss of O10 function disrupts this ring-shaped distribution of 22-kD and 16-kD zeins, resulting in misshapen PBs. These results showed that O10, as a newly evolved PB protein, is essential for the ring-shaped distribution of 22-kD and 16-kD zeins and controls PB morphology in maize endosperm. PMID:27541862

  19. Sequential Dependencies in Driving

    ERIC Educational Resources Information Center

    Doshi, Anup; Tran, Cuong; Wilder, Matthew H.; Mozer, Michael C.; Trivedi, Mohan M.

    2012-01-01

    The effect of recent experience on current behavior has been studied extensively in simple laboratory tasks. We explore the nature of sequential effects in the more naturalistic setting of automobile driving. Driving is a safety-critical task in which delayed response times may have severe consequences. Using a realistic driving simulator, we find…

  20. Magnetic drive coupling

    NASA Technical Reports Server (NTRS)

    Carter, Edward L. (Inventor)

    1987-01-01

    The driving and driven members of a magnetic drive are separated by en enlarged gap to provide clearance for a conduit or other member. Flux pins in the gap maintain the torque transmitting capability of the drive. The spacing between two of the flux pins is increased to provide space for the conduit.

  1. Grieving while Driving

    ERIC Educational Resources Information Center

    Rosenblatt, Paul C.

    2004-01-01

    Secondary analysis of data from 84 people in 2 interview studies shows that some bereaved people grieve actively while driving. The grief can be intense, even years after a death. Grief while driving may erupt spontaneously or be set off by a wide range of reminders. Some bereaved people seem to save their grieving for times when they drive,…

  2. Influence of protein or cystein deficiency on hepatic subcellular distribution of methyl mercury in two rat strains.

    PubMed

    Beije, B; Arrhenius, E

    1978-02-01

    The influence of protein deprivation and cystein deficiency on the distribution of methyl mercury between 4 subcellular fractions of liver was studied in 2 rat strains (Wistar, strain R and Sprague-Dawley). Kept on a standard diet, the 2 strains showed a similar distribution pattern, with the highest mercury level found in the cytosol, followed by the mitochondrial, microsomal and nuclei fractions. The protein free diet caused on increase in the total amount of bound mercury in both strains, the greatest increase, being found in livers from strain R rats. The cystein deficient diet, on the other hand, gave rise to diverging results. Whereas the level of mercury bound to the subcellular fractions was increased in livers from strain R rats, it was markedly reduced in livers from Sprague-Dawley rats.

  3. Molecular dynamics studies on the NMR structures of rabbit prion protein wild type and mutants: surface electrostatic charge distributions.

    PubMed

    Zhang, Jiapu; Wang, Feng; Zhang, Yuanli

    2015-01-01

    Prion diseases are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species such as sheep and goats, cattle, deer and elk, and humans. But for rabbits, studies have shown that they have a low susceptibility to be infected by prion diseases. This paper does molecular dynamics (MD) studies of rabbit NMR structures (of the wild type and its two mutants of two surface residues), in order to understand the specific mechanism of rabbit prion proteins (RaPrP(C)). Protein surface electrostatic charge distributions are specially focused to analyze the MD trajectories. This paper can conclude that surface electrostatic charge distributions indeed contribute to the structural stability of wild-type RaPrP(C); this may be useful for the medicinal treatment of prion diseases.

  4. Distribution of precursor amyloid-. beta. -protein messenger RNA in human cerebral cortex: relationship to neurofibrillary tangles and neuritic plaques

    SciTech Connect

    Lewis, D.A.; Higgins, G.A.; Young, W.G.; Goldgaber, D.; Gajdusek, D.C.; Wilson, M.C.; Morrison, J.H.

    1988-03-01

    Neurofibrillary tangles (NFT) and neuritic plaques (NP), two neuropathological markers of Alzheimer disease, may both contain peptide fragments derived from the human amyloid ..beta.. protein. However, the nature of the relationship between NFT and NP and the source of the amyloid ..beta.. proteins found in each have remained unclear. The authors used in situ hybridization techniques to map the anatomical distribution of precursor amyloid-..beta..-protein mRNA in the neocortex of brains from three subjects with no known neurologic disease and from five patients with Alzheimer disease. In brains from control subjects, positively hybridizing neurons were present in cortical regions and layers that contain a high density of neuropathological markers in Alzheimer disease, as well as in those loci that contain NP but few NFT. Quantitative analyses of in situ hybridization patterns within layers III and V of the superior frontal cortex revealed that the presence of high numbers of NFT in Alzheimer-diseased brains was associated with a decrease in the number of positively hybridizing neurons compared to controls and Alzheimer-diseased brains with few NFT. These findings suggest that the expression of precursor amyloid-..beta..-protein mRNA may be a necessary but is clearly not a sufficient prerequisite for NFT formation. In addition, these results may indicate that the amyloid ..beta.. protein, present in NP in a given region or layer of cortex, is not derived from the resident neuronal cell bodies that express the mRNA for the precursor protein.

  5. Mycobacterium tuberculosis PE25/PPE41 protein complex induces activation and maturation of dendritic cells and drives Th2-biased immune responses.

    PubMed

    Chen, Wei; Bao, Yige; Chen, Xuerong; Burton, Jeremy; Gong, Xueli; Gu, Dongqing; Mi, Youjun; Bao, Lang

    2016-04-01

    Mycobacterium tuberculosis evades innate host immune responses by parasitizing macrophages and causes significant morbidity and mortality around the world. A mycobacterial antigen that can activate dendritic cells (DCs) and elicit effective host innate immune responses will be vital to the development of an effective TB vaccine. The M. tuberculosis genes PE25/PPE41 encode proteins which have been associated with evasion of the host immune response. We constructed a PE25/PPE41 complex gene via splicing by overlapping extension and expressed it successfully in E. coli. We investigated whether this protein complex could interact with DCs to induce effective host immune responses. The PE25/PPE41 protein complex induced maturation of isolated mouse DCs in vitro, increasing expression of cell surface markers (CD80, CD86 and MHC-II), thereby promoting Th2 polarization via secretion of pro-inflammatory cytokines IL-4 and IL-10. In addition, PE25/PPE41 protein complex-activated DCs induced proliferation of mouse CD4(+) and CD8(+) T cells, and a strong humoral response in immunized mice. The sera of five TB patients were also highly reactive to this antigen. These findings suggest that interaction of the PE25/PPE41 protein complex with DCs may be of great immunological significance.

  6. Syncope and Driving.

    PubMed

    Guzman, Juan C; Morillo, Carlos A

    2015-08-01

    The occurrence of syncope while driving has obvious implications for personal and public safety. Neurally mediated syncope is the most common type of syncope in general and, thereby, also while driving. The presence of structural heart disease (reduced ejection fraction, previous myocardial infarction, significant congenital heart disease) potentially leads to high risk and should determine driving restrictions pending clarification of underlying heart disease and etiology of syncope. The clinical approach to syncope evaluation and recommendations for driving should not differ, whether or not the syncopal spell occurred while driving.

  7. Simple Method of Synthesizing Nickel-Nitrilotriacetic Acid Gold Nanoparticles with a Narrow Size Distribution for Protein Labeling

    NASA Astrophysics Data System (ADS)

    Kitai, Toshiyuki; Watanabe, Yuta; Toyoshima, Yoko Y.; Kobayashi, Takuya; Murayama, Takashi; Sakaue, Hiroyuki; Suzuki, Hitoshi; Takahagi, Takayuki

    2011-09-01

    We developed a simple method to synthesize nickel-nitrilotriacetic acid gold nanoparticles (Ni-NTA Au NPs) with a narrow size distribution for site-specific labeling in protein complexes. Au NPs were synthesized by the reduction of HAuCl4 using trisodium citrate and tannin acid. Then, the nanoparticle surfaces were modified with NTA and subsequent complexation with Ni2+. The mean diameter of the synthesized Ni-NTA Au NPs was 4.3 nm, and the coefficient of variation was 9%. The specific binding of the Ni-NTA Au NPs to polyhistidine-tagged (His-tagged) proteins was determined by transmission electron microscopy using kinesin and the p62 subunit of dynactin. Consequently, our method is useful for analyzing the substructures of protein complexes.

  8. Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms

    PubMed Central

    Jian, Jhih-Wei; Elumalai, Pavadai; Pitti, Thejkiran; Wu, Chih Yuan; Tsai, Keng-Chang; Chang, Jeng-Yih; Peng, Hung-Pin; Yang, An-Suei

    2016-01-01

    Predicting ligand binding sites (LBSs) on protein structures, which are obtained either from experimental or computational methods, is a useful first step in functional annotation or structure-based drug design for the protein structures. In this work, the structure-based machine learning algorithm ISMBLab-LIG was developed to predict LBSs on protein surfaces with input attributes derived from the three-dimensional probability density maps of interacting atoms, which were reconstructed on the query protein surfaces and were relatively insensitive to local conformational variations of the tentative ligand binding sites. The prediction accuracy of the ISMBLab-LIG predictors is comparable to that of the best LBS predictors benchmarked on several well-established testing datasets. More importantly, the ISMBLab-LIG algorithm has substantial tolerance to the prediction uncertainties of computationally derived protein structure models. As such, the method is particularly useful for predicting LBSs not only on experimental protein structures without known LBS templates in the database but also on computationally predicted model protein structures with structural uncertainties in the tentative ligand binding sites. PMID:27513851

  9. Kinetics of Formation and Asymmetrical Distribution of Hsp104-Bound Protein Aggregates in Yeast.

    PubMed

    Paoletti, Camille; Quintin, Sophie; Matifas, Audrey; Charvin, Gilles

    2016-04-12

    Budding yeast cells have a finite replicative life span; that is, a mother cell produces only a limited number of daughter cells before it slows division and dies. Despite the gradual aging of the mother cell, all daughters are born rejuvenated and enjoy a full replicative lifespan. It has been proposed that entry of mother cells into senescence is driven by the progressive accumulation and retention of damaged material, including protein aggregates. This additionally allows the daughter cells to be born damage free. However, the mechanism underlying such asymmetrical segregation of protein aggregates by mother and daughter cells remains controversial, in part because of the difficulties inherent in tracking the dynamics and fate of protein aggregates in vivo. To overcome such limitations, we have developed single-cell real-time imaging methodology to track the formation of heat-induced protein aggregates in otherwise unperturbed dividing cells. By combining the imaging data with a simple computational model of protein aggregation, we show that the establishment of asymmetrical partitioning of protein aggregates upon division is driven by the large bud-specific dilution rate associated with polarized growth and the absence of significant mother/bud exchange of protein aggregates during the budded phase of the cell cycle. To our knowledge, this study sheds new light on the mechanism of establishment of a segregation bias, which can be accounted for by simple physical arguments.

  10. Subcellular distribution of the 18kDa translocator protein and transcript variant PBR-S in human cells.

    PubMed

    Liu, Guo-Jun; Middleton, Ryan J; Banati, Richard B

    2017-05-20

    Despite continued interest in the 18kDa translocator protein (PBR/TSPO) as a biomarker and a therapeutic target for a range of diseases, its functional role, such as in the steroid synthesis pathway and energy metabolism has either become contentious or remains to be described more precisely. The PBR/TSPO gene consists of four exons, while a shorter isoform termed PBR-S lacks exon 2. The PBR-S 102-codon open reading frame differs to that of PBR/TSPO, resulting in a protein that is completely unrelated to PBR/TSPO. To our knowledge, PBR-S protein has never been described and has no known or proposed function. To obtain possible clues on the role of this uncharacterised protein, we compared the subcellular distribution of PBR-S to that of PBR/TSPO. By expressing fluorescently tagged PBR/TSPO, we confirmed that full-length PBR/TSPO co-localises with mitochondria in HeLa, HEK-293, MDA-MB-231, BJ and U87-MG human cell lines. Unlike the strictly mitochondrial localisation of PBR/TSPO, PBR-S has a punctate distribution throughout the cytosol that co-localises with lysosomes in HeLa, HEK-293, MDA-MB-231, BJ and U87-MG cells. In summary, within the cell lines examined we confirm mitochondria rather than occasionally reported other localisations, such as the cell nucleus, to be the only site where PBR/TSPO resides. Due to the lack of any shared protein sequences and the different subcellular locations, we suggest that the previously uncharacterised PBR-S protein variant of the PBR/TSPO gene is likely to serve a different yet to be discovered function compared to PBR/TSPO.

  11. Structure, tissue distribution and genomic organization of the murine RRM-type RNA binding proteins TIA-1 and TIAR.

    PubMed

    Beck, A R; Medley, Q G; O'Brien, S; Anderson, P; Streuli, M

    1996-10-01

    TIA-1 and TIAR are RNA binding proteins of the RNA recognition motif (RRM)/ribonucleoprotein (RNP) family that have been implicated as effectors of apoptotic cell death. We report the structures of murine TIA-1 and TIAR (mTIA-1 and mTIAR) deduced from cDNA cloning, the mRNA and protein tissue distribution of mTIA-1 and mTIAR, and the exon-intron structures of the mTIA-1 and mTIAR genes. Both mTIA-1 and mTIAR are comprised of three approximately 100 amino acid N-terminal RRM domains and a approximately 90 amino acid C-terminal auxiliary domain. This subfamily of RRM proteins is evolutionarily well conserved; mTIA-1 and mTIAR are 80% similar to each other, and 96 and 99% similar to hTIA-1 and hTIAR, respectively. The overall exon-intron structures of the mTIA-1 and mTIAR genes are also similar to each other, as well as to the human TIA-1 gene structure. While Northern blot analysis reveals that mTIA-1 and mTIAR mRNAs have a broad tissue distribution, mTIA-1 and mTIAR proteins are predominantly expressed in brain, testis and spleen. At least two isoforms of both mTIA-1 and mTIAR are generated by alternative splicing. Murine TIA-1 isoforms including or lacking the exon 5 encoded sequences are expressed at a ratio of approximately 1:1, whereas mTIAR isoforms including or lacking the 5'-end of exon 3 sequences are expressed in a approximately 1:6 ratio. Molecular characterization of murine TIA-1 and TIAR RNA binding proteins provides the basis for a genetic analysis of the functional roles of these proteins during mammalian development.

  12. In situ localization and tissue distribution of ostreid herpesvirus 1 proteins in infected Pacific oyster, Crassostrea gigas.

    PubMed

    Martenot, Claire; Segarra, Amélie; Baillon, Laury; Faury, Nicole; Houssin, Maryline; Renault, Tristan

    2016-05-01

    Immunohistochemistry (IHC) assays were conducted on paraffin sections from experimentally infected spat and unchallenged spat produced in hatchery to determine the tissue distribution of three viral proteins within the Pacific oyster, Crassostrea gigas. Polyclonal antibodies were produced from recombinant proteins corresponding to two putative membrane proteins and one putative apoptosis inhibitor encoded by ORF 25, 72, and 87, respectively. Results were then compared to those obtained by in situ hybridization performed on the same individuals, and showed a substantial agreement according to Landis and Koch numeric scale. Positive signals were mainly observed in connective tissue of gills, mantle, adductor muscle, heart, digestive gland, labial palps, and gonads of infected spat. Positive signals were also reported in digestive epithelia. However, few positive signals were also observed in healthy appearing oysters (unchallenged spat) and could be due to virus persistence after a primary infection. Cellular localization of staining seemed to be linked to the function of the viral protein targeted. A nucleus staining was preferentially observed with antibodies targeting the putative apoptosis inhibitor protein whereas a cytoplasmic localization was obtained using antibodies recognizing putative membrane proteins. The detection of viral proteins was often associated with histopathological changes previously reported during OsHV-1 infection by histology and transmission electron microscopy. Within the 6h after viral suspension injection, positive signals were almost at the maximal level with the three antibodies and all studied organs appeared infected at 28h post viral injection. Connective tissue appeared to be a privileged site for OsHV-1 replication even if positive signals were observed in the epithelium cells of different organs which may be interpreted as a hypothetical portal of entry or release for the virus. IHC constitutes a suited method for analyzing the

  13. Drill drive mechanism

    DOEpatents

    Dressel, Michael O.

    1979-01-01

    A drill drive mechanism is especially adapted to provide both rotational drive and axial feed for a drill of substantial diameter such as may be used for drilling holes for roof bolts in mine shafts. The drill shaft is made with a helical pattern of scroll-like projections on its surface for removal of cuttings. The drill drive mechanism includes a plurality of sprockets carrying two chains of drive links which are arranged to interlock around the drill shaft with each drive link having depressions which mate with the scroll-like projections. As the chain links move upwardly or downwardly the surfaces of the depressions in the links mate with the scroll projections to move the shaft axially. Tangs on the drive links mate with notch surfaces between scroll projections to provide a means for rotating the shaft. Projections on the drive links mate together at the center to hold the drive links tightly around the drill shaft. The entire chain drive mechanism is rotated around the drill shaft axis by means of a hydraulic motor and gear drive to cause rotation of the drill shaft. This gear drive also connects with a differential gearset which is interconnected with a second gear. A second motor is connected to the spider shaft of the differential gearset to produce differential movement (speeds) at the output gears of the differential gearset. This differential in speed is utilized to drive said second gear at a speed different from the speed of said gear drive, this speed differential being utilized to drive said sprockets for axial movement of said drill shaft.

  14. Calcium, phosphorus and protein levels as factors in the distribution of the pheasant

    USGS Publications Warehouse

    Dale, F.H.; DeWitt, J.B.

    1958-01-01

    Summary of work on pheasant nutrition conducted since 1949 at the Patuxent Research Refuge. Pheasant chicks fed experimental diets failed to develop normally on protein levels of 15 and 18%. With 22% protein they grew at a reduced rate as compared to those on 28%. Protein level of the reproductive diet was shown to be important; low production of eggs and young resulted from levels below 25%. Calcium was found to be even more critical than protein level for reproduction; birds on a winter diet that furnished 145 mg./kg. per day had poor reproductive success the following spring. About 600 mg./kg. of Ca per day was necessary in the reproduction diet. Birds on an intermediate level of Ca (about 0.5% of diet) showed evidence of cumulative deficiency. It was concluded that pheasants receiving levels of Ca no higher than 0.5% in nature might display 'straggling failure' such as has been observed in several midwestern areas.

  15. Distributed control of protein crystallography beamline 5.0 using CORBA

    SciTech Connect

    Timossi, Chris

    1999-09-24

    The Protein Crystallography Beamline at Berkeley Lab's Advanced Light Source is a facility that is being used to solve the structure of proteins. The software that is being used to control this beamline uses Java for user interface applications which communicate via CORBA with workstations that control the beamline hardware. We describe the software architecture for the beamline and our experiences after two years of operation.

  16. Organ distribution and molecular forms of human xanthine dehydrogenase/xanthine oxidase protein.

    PubMed

    Sarnesto, A; Linder, N; Raivio, K O

    1996-01-01

    Xanthine dehydrogenase/xanthine oxidase (XDH/XO) is a major cytoplasmic source of superoxide radicals and hydrogen peroxide, and it is considered important in the pathogenesis of ischemia-reperfusion damage. Because little is known about the enzyme in human tissues, the aims of this study were to purify human XDH/XO and to produce Ab for detection of the protein in Western blots and for quantification by ELISA. We purified human milk XDH/XO, produced Ab for Western blotting and ELISA of the protein, and evaluated the molecular forms and activity-protein relationships in human tissues. The molecular size of the purified protein under nondenaturing conditions was approximately 300 kd. On SDS-PAGE, it was fragmented into four main bands of 143, 125, 87, and 59 kd. Ab recognized bands of similar size in Western blots of the purified preparation and human milk. In fresh liver homogenates treated with anti-proteases, the three largest bands were observed; in the intestine, only the two largest were observed. Serum, brain, heart, and skeletal muscle were negative, whereas some lung and kidney samples showed one faint band of 143 kd. Trypsin treatment of the enzyme converted the large molecular-weight bands into smaller bands, as did incubation of a liver homogenate without anti-proteases. XDH/XO protein concentrations (ng/mg total protein) were 146 +/- 70 in liver and 556 +/- 320 in intestine and less than 5 ng/ml in serum. The relationship of activity to protein (2.7-3.0 mumol/min/mg XDH/XO protein) was constant in liver and intestine during development. We conclude that 1) human XDH/XO has molecular size and subunit structure similar to other mammalian enzymes; 2) the polypeptide chain is unstable, also in the intact cell, despite retained activity; and 3) the amount of inactive XDH/XO in human liver and intestine is apparently small.

  17. Expression and Subcellular Distribution of GFP-Tagged Human Tetraspanin Proteins in Saccharomyces cerevisiae

    PubMed Central

    Skaar, Karin; Korza, Henryk J.; Tarry, Michael; Sekyrova, Petra; Högbom, Martin

    2015-01-01

    Tetraspanins are integral membrane proteins that function as organizers of multimolecular complexes and modulate function of associated proteins. Mammalian genomes encode approximately 30 different members of this family and remotely related eukaryotic species also contain conserved tetraspanin homologs. Tetraspanins are involved in a number of fundamental processes such as regulation of cell migration, fusion, immunity and signaling. Moreover, they are implied in numerous pathological states including mental disorders, infectious diseases or cancer. Despite the great interest in tetraspanins, the structural and biochemical basis of their activity is still largely unknown. A major bottleneck lies in the difficulty of obtaining stable and homogeneous protein samples in large quantities. Here we report expression screening of 15 members of the human tetraspanin superfamily and successful protocols for the production in S. cerevisiae of a subset of tetraspanins involved in human cancer development. We have demonstrated the subcellular localization of overexpressed tetraspanin-green fluorescent protein fusion proteins in S. cerevisiae and found that despite being mislocalized, the fusion proteins are not degraded. The recombinantly produced tetraspanins are dispersed within the endoplasmic reticulum membranes or localized in granule-like structures in yeast cells. The recombinantly produced tetraspanins can be extracted from the membrane fraction and purified with detergents or the poly (styrene-co-maleic acid) polymer technique for use in further biochemical or biophysical studies. PMID:26218426

  18. Protein and Metalloprotein Distribution in Different Varieties of Beans (Phaseolus vulgaris L.): Effects of Cooking.

    PubMed

    Oliveira, Aline P; Andrade, Geyssa Ferreira; Mateó, Bianca S O; Naozuka, Juliana

    2017-01-01

    Beans (Phaseolus vulgaris L.) are among the main sources of protein and minerals. The cooking of the grains is imperative, due to reduction of the effect of some toxic and antinutritional substances, as well as increase of protein digestibility. In this study, the effects of cooking on albumins, globulins, prolamins, and glutelins concentration and determination of Fe associated with proteins for different beans varieties and on phaseolin concentration in common and black beans were evaluated. Different extractant solutions (water, NaCl, ethanol, and NaOH) were used for extracting albumins, globulins, prolamins, and glutelins, respectively. For the phaseolin separation NaOH, HCl, and NaCl were used. The total concentration of proteins was determined by Bradford method; Cu and Fe associated with phaseolin and other proteins were obtained by graphite furnace atomic absorption spectrometry and by flame atomic absorption spectrometry, respectively. Cooking promoted a negative effect on (1) the proteins concentrations (17 (glutelin) to 95 (albumin) %) of common beans and (2) phaseolin concentration (90%) for common and black beans. Fe associated with albumin, prolamin, and glutelin was not altered. In Fe and Cu associated with phaseolin there was an increase of 20 and 37% for the common and black varieties, respectively.

  19. Protein and Metalloprotein Distribution in Different Varieties of Beans (Phaseolus vulgaris L.): Effects of Cooking

    PubMed Central

    Oliveira, Aline P.; Andrade, Geyssa Ferreira; Mateó, Bianca S. O.

    2017-01-01

    Beans (Phaseolus vulgaris L.) are among the main sources of protein and minerals. The cooking of the grains is imperative, due to reduction of the effect of some toxic and antinutritional substances, as well as increase of protein digestibility. In this study, the effects of cooking on albumins, globulins, prolamins, and glutelins concentration and determination of Fe associated with proteins for different beans varieties and on phaseolin concentration in common and black beans were evaluated. Different extractant solutions (water, NaCl, ethanol, and NaOH) were used for extracting albumins, globulins, prolamins, and glutelins, respectively. For the phaseolin separation NaOH, HCl, and NaCl were used. The total concentration of proteins was determined by Bradford method; Cu and Fe associated with phaseolin and other proteins were obtained by graphite furnace atomic absorption spectrometry and by flame atomic absorption spectrometry, respectively. Cooking promoted a negative effect on (1) the proteins concentrations (17 (glutelin) to 95 (albumin) %) of common beans and (2) phaseolin concentration (90%) for common and black beans. Fe associated with albumin, prolamin, and glutelin was not altered. In Fe and Cu associated with phaseolin there was an increase of 20 and 37% for the common and black varieties, respectively. PMID:28326316

  20. Size-distribution analysis of proteins by analytical ultracentrifugation: strategies and application to model systems.

    PubMed Central

    Schuck, Peter; Perugini, Matthew A; Gonzales, Noreen R; Howlett, Geoffrey J; Schubert, Dieter

    2002-01-01

    Strategies for the deconvolution of diffusion in the determination of size-distributions from sedimentation velocity experiments were examined and developed. On the basis of four different model systems, we studied the differential apparent sedimentation coefficient distributions by the time-derivative method, g(s*), and by least-squares direct boundary modeling, ls-g*(s), the integral sedimentation coefficient distribution by the van Holde-Weischet method, G(s), and the previously introduced differential distribution of Lamm equation solutions, c(s). It is shown that the least-squares approach ls-g*(s) can be extrapolated to infinite time by considering area divisions analogous to boundary divisions in the van Holde-Weischet method, thus allowing the transformation of interference optical data into an integral sedimentation coefficient distribution G(s). However, despite the model-free approach of G(s), for the systems considered, the direct boundary modeling with a distribution of Lamm equation solutions c(s) exhibited the highest resolution and sensitivity. The c(s) approach requires an estimate for the size-dependent diffusion coefficients D(s), which is usually incorporated in the form of a weight-average frictional ratio of all species, or in the form of prior knowledge of the molar mass of the main species. We studied the influence of the weight-average frictional ratio on the quality of the fit, and found that it is well-determined by the data. As a direct boundary model, the calculated c(s) distribution can be combined with a nonlinear regression to optimize distribution parameters, such as the exact meniscus position, and the weight-average frictional ratio. Although c(s) is computationally the most complex, it has the potential for the highest resolution and sensitivity of the methods described. PMID:11806949

  1. Butter making from caprine creams: effect of washing treatment on phospholipids and milk fat globule membrane proteins distribution.

    PubMed

    Lamothe, Sophie; Robitaille, Gilles; St-Gelais, Daniel; Britten, Michel

    2008-11-01

    A washing treatment was applied to caprine cream before churning in order to improve phospholipids and MFGM protein purification from buttermilk and butter serum. Cream obtained from a first separation was diluted with water and separated a second time using pilot plant equipment. Regular and washed creams were churned to produce buttermilk and butter, from which butter serum was extracted. The washing treatment allowed a significant decrease of the casein content. As a result, the phospholipids-to-protein ratios in washed buttermilk and butter serum were markedly increased by 2.1 and 1.7-folds respectively, which represents an advantage for the production of phospholipids concentrates. However, when compared with bovine cream, lower phospholipids-to-protein ratios were observed when the washing treatment was applied to caprine cream. A higher concentration of MFGM protein and a lower retention of phospholipids during washing treatment are responsible for the lower phospholipids-to-protein ratios in buttermilk and butter serum obtained from caprine cream. The phospholipids distribution in the butter making process was similar to the one obtained from bovine regular and washed cream. Phospholipids were preferentially concentrated in the butter serum rather than the buttermilk fraction. This simple approach permitted the production of caprine and bovine butter sera extracts containing up to 180 and 240 g phospholipids/kg sera, respectively, on a dry basis.

  2. Alterations in photosynthetic pigments and amino acid composition of D1 protein change energy distribution in photosystem II.

    PubMed

    Yokono, Makio; Tomo, Tatsuya; Nagao, Ryo; Ito, Hisashi; Tanaka, Ayumi; Akimoto, Seiji

    2012-05-01

    The marine cyanobacterium Prochlorococcus marinus accumulates divinyl chlorophylls instead of monovinyl chlorophylls to harvest light energy. As well as this difference in its chromophore composition, some amino acid residues in its photosystem II D1 protein were different from the conserved amino acid residues in other photosynthetic organisms. We examined PSII complexes isolated from mutants of Synechocystis sp. PCC 6803, in which chromophore and D1 protein were altered (Hisashi Ito and Ayumi Tanaka, 2011) to clarify the effects of chromophores/D1 protein composition on the excitation energy distribution. We prepared the mutants accumulating divinyl chlorophyll (DV mutant). The amino acid residues of V205 and G282 in the D1 protein were substituted with M205 and C282 in the DV mutant to mimic Prochlorococcus D1 protein (DV-V205M/G282C mutant). Isolated PSII complexes were analyzed by time-resolved fluorescence spectroscopy. Energy transfer in CP47 was interrupted in PSII containing divinyl chlorophylls. The V205M/G282C mutation did not recover the energy transfer pathway in CP47, instead, the mutation allowed the excitation energy transfer from CP43 to CP47, which neighbors in the PSII dimer. Mutual orientation of the subcomplexes of PSII might be affected by the substitution. The changes of the energy transfer pathways would reduce energy transfer from antennae to the PSII reaction center, and allow Prochlorococcus to acquire light tolerance.

  3. Depicting the Spatial Distribution of Proteins in Human Tumor Tissue Combining SELDI and MALDI Imaging and Immunohistochemistry

    PubMed Central

    Wehder, Liane; Ernst, Günther; Crecelius, Anna C.; Guntinas-Lichius, Orlando; Melle, Christian; Schubert, Ulrich S.; von Eggeling, Ferdinand

    2010-01-01

    Carcinoma tissue consists of not only tumor cells but also fibroblasts, endothelial cells or vascular structures, and inflammatory cells forming the supportive tumor stroma. Therefore, the spatial distribution of proteins that promote growth and proliferation in these complex functional units is of high interest. Matrix-assisted laser desorption/ionization imaging mass spectrometry is a newly developed technique that generates spatially resolved profiles of protein signals directly from thin tissue sections. Surface-enhanced laser desorption/ionization mass spectrometry (MS)combined with tissue microdissection allows analysis of defined parts of the tissue with a higher sensitivity and a broader mass range. Nevertheless, both MS-based techniques have a limited spatial resolution. IHC is a technique that allows a resolution down to the subcellular level. However, the detection and measurement of a specific protein expression level is possible only by semiquantitative methods. Moreover, prior knowledge about the identity of the proteins of interest is necessary. In this study, we combined all three techniques to gain highest spatial resolution, sensitivity, and quantitative information. We used frozen tissue from head and neck tumors and chose two exemplary proteins (HNP1–3 and S100A8) to highlight the advantages and disadvantages of each technique. It could be shown that the combination of these three techniques results in congruent but also synergetic data. (J Histochem Cytochem 58:929–937, 2010) PMID:20644210

  4. Non-random distribution of amino acids in the transmembrane segments of human type I single span membrane proteins.

    PubMed

    Landolt-Marticorena, C; Williams, K A; Deber, C M; Reithmeier, R A

    1993-02-05

    The distribution of amino acids in the transmembrane segments and flanking regions of 115 human type I single span (amino terminus extracellular and carboxyl terminus cytosolic) plasma membrane proteins was found to be non-random. In this sample, Ile was preferentially localized to the amino-terminal region of the hydrophobic transmembrane segments, followed by Val, while Leu predominated in the carboxyl-terminal half of the segment. Although Gly residues were preferentially located in the transmembrane segment, this residue was excluded from the carboxyl-terminal and adjacent boundary regions. Aromatic residues (Tyr, Trp and Phe) occurred preferentially at the cytoplasmic boundary, with Trp also favored at the extracellular boundary. The extracellular flanking sequence amino-terminal to the transmembrane segment was enriched in residues predicted to initiate helix formation (Pro, Asn and Ser), while Arg and Lys were enriched in the cytoplasmic flank where they may function as topological determinants. The positional preferences of these particular amino acids within the transmembrane segment and flanking regions suggests that, in addition to lipid-protein interactions, these residues may participate in specific protein-protein interactions. A consensus sequence motif for type I membrane proteins is proposed and its role in the biosynthesis, folding, assembly and function of these segments is discussed.

  5. Impact of Proteins on the Uptake, Distribution, and Excretion of Phenolics in the Human Body

    PubMed Central

    Draijer, Richard; van Dorsten, Ferdi A.; Zebregs, Yvonne E.; Hollebrands, Boudewijn; Peters, Sonja; Duchateau, Guus S.; Grün, Christian H.

    2016-01-01

    Polyphenols, a complex group of secondary plant metabolites, including flavonoids and phenolic acids, have been studied in depth for their health-related benefits. The activity of polyphenols may, however, be hampered when consumed together with protein-rich food products, due to the interaction between polyphenols and proteins. To that end we have tested the bioavailability of representatives of a range of polyphenol classes when consumed for five days in different beverage matrices. In a placebo-controlled, randomized, cross-over study, 35 healthy males received either six placebo gelatine capsules consumed with 200 mL of water, six capsules with 800 mg polyphenols derived from red wine and grape extracts, or the same dose of polyphenols incorporated into 200 mL of either pasteurized dairy drink, soy drink (both containing 3.4% proteins) or fruit-flavoured protein-free drink . At the end of the intervention urine and blood was collected and analysed for a broad range of phenolic compounds using Gas Chromatography–Mass Spectrometry (GC-MS), Liquid Chromatography–Multiple Reaction Monitoring–Mass Spectrometry (LC-MRM-MS), and Nuclear Magnetic Resonance (NMR) spectroscopy techniques. The plasma and urine concentrations of the polyphenols identified increased with all formats, including the protein-rich beverages. Compared to capsule ingestion, consumption of polyphenol-rich beverages containing either dairy, soy or no proteins had minor to no effect on the bioavailability and excretion of phenolic compounds in plasma (118% ± 9%) and urine (98% ± 2%). We conclude that intake of polyphenols incorporated in protein-rich drinks does not have a major impact on the bioavailability of a range of different polyphenols and phenolic metabolites. PMID:27983686

  6. Reovirus FAST Proteins Drive Pore Formation and Syncytiogenesis Using a Novel Helix-Loop-Helix Fusion-Inducing Lipid Packing Sensor.

    PubMed

    Read, Jolene; Clancy, Eileen K; Sarker, Muzaddid; de Antueno, Roberto; Langelaan, David N; Parmar, Hiren B; Shin, Kyungsoo; Rainey, Jan K; Duncan, Roy

    2015-06-01

    Pore formation is the most energy-demanding step during virus-induced membrane fusion, where high curvature of the fusion pore rim increases the spacing between lipid headgroups, exposing the hydrophobic interior of the membrane to water. How protein fusogens breach this thermodynamic barrier to pore formation is unclear. We identified a novel fusion-inducing lipid packing sensor (FLiPS) in the cytosolic endodomain of the baboon reovirus p15 fusion-associated small transmembrane (FAST) protein that is essential for pore formation during cell-cell fusion and syncytiogenesis. NMR spectroscopy and mutational studies indicate the dependence of this FLiPS on a hydrophobic helix-loop-helix structure. Biochemical and biophysical assays reveal the p15 FLiPS preferentially partitions into membranes with high positive curvature, and this partitioning is impeded by bis-ANS, a small molecule that inserts into hydrophobic defects in membranes. Most notably, the p15 FLiPS can be functionally replaced by heterologous amphipathic lipid packing sensors (ALPS) but not by other membrane-interactive amphipathic helices. Furthermore, a previously unrecognized amphipathic helix in the cytosolic domain of the reptilian reovirus p14 FAST protein can functionally replace the p15 FLiPS, and is itself replaceable by a heterologous ALPS motif. Anchored near the cytoplasmic leaflet by the FAST protein transmembrane domain, the FLiPS is perfectly positioned to insert into hydrophobic defects that begin to appear in the highly curved rim of nascent fusion pores, thereby lowering the energy barrier to stable pore formation.

  7. Global Analysis of Condition-specific Subcellular Protein Distribution and Abundance*

    PubMed Central

    Jung, Sunhee; Smith, Jennifer J.; von Haller, Priska D.; Dilworth, David J.; Sitko, Katherine A.; Miller, Leslie R.; Saleem, Ramsey A.; Goodlett, David R.; Aitchison, John D.

    2013-01-01

    Cellular control of protein activities by modulation of their abundance or compartmentalization is not easily measured on a large scale. We developed and applied a method to globally interrogate these processes that is widely useful for systems-level analyses of dynamic cellular responses in many cell types. The approach involves subcellular fractionation followed by comprehensive proteomic analysis of the fractions, which is enabled by a data-independent acquisition mass spectrometry approach that samples every available mass to charge channel systematically to maximize sensitivity. Next, various fraction-enrichment ratios are measured for all detected proteins across different environmental conditions and used to group proteins into clusters reflecting changes in compartmentalization and relative conditional abundance. Application of the approach to characterize the response of yeast proteins to fatty acid exposure revealed dynamics of peroxisomes and novel dynamics of MCC/eisosomes, specialized plasma membrane domains comprised of membrane compartment occupied by Can1 (MCC) and eisosome subdomains. It also led to the identification of Fat3, a fatty acid transport protein of the plasma membrane, previously annotated as Ykl187. PMID:23349476

  8. Fluorescent Tagging and Cellular Distribution of the Kaposi's Sarcoma-Associated Herpesvirus ORF45 Tegument Protein

    PubMed Central

    Bergson, Shir; Kalt, Inna; Itzhak, Inbal; Brulois, Kevin F.; Jung, Jae U.

    2014-01-01

    ABSTRACT Kaposi's sarcoma-associated herpesvirus (KSHV), also known as human herpesvirus 8 (HHV-8), is a cancer-related human virus, classified as a member of the Gammaherpesvirinae subfamily. We report here the construction of a dual fluorescent-tagged KSHV genome (BAC16-mCherry-ORF45), which constitutively expresses green fluorescent protein (GFP) and contains the tegument multifunctional ORF45 protein as a fusion protein with monomeric Cherry fluorescent protein (mCherry). We confirmed that this virus is properly expressed and correctly replicates and that the mCherry-ORF45 protein is incorporated into the virions. Using this labeled virus, we describe the dynamics of mCherry-ORF45 expression and localization in newly infected cells as well as in latently infected cells undergoing lytic induction and show that mCherry can be used to monitor cells undergoing the lytic viral cycle. This virus is likely to enable future studies monitoring the dynamics of viral trafficking and tegumentation during viral ingress and egress. IMPORTANCE The present study describes the construction and characterization of a new recombinant KSHV genome BAC16 clone which expresses mCherry-tagged ORF45. This virus enables the tracking of cells undergoing lytic infection and can be used to address issues related to the trafficking and maturation pathways of KSHV virions. PMID:25165104

  9. The actin cytoskeleton may control the polar distribution of an auxin transport protein

    NASA Technical Reports Server (NTRS)

    Muday, G. K.; Hu, S.; Brady, S. R.; Davies, E. (Principal Investigator)

    2000-01-01

    The gravitropic bending of plants has long been linked to the changes in the transport of the plant hormone auxin. To understand the mechanism by which gravity alters auxin movement, it is critical to know how polar auxin transport is initially established. In shoots, polar auxin transport is basipetal (i.e., from the shoot apex toward the base). It is driven by the basal localization of the auxin efflux carrier complex. One mechanism for localizing this efflux carrier complex to the basal membrane may be through attachment to the actin cytoskeleton. The efflux carrier protein complex is believed to consist of several polypeptides, including a regulatory subunit that binds auxin transport inhibitors, such as naphthylphthalamic acid (NPA). Several lines of experimentation have been used to determine if the NPA binding protein interacts with actin filaments. The NPA binding protein has been shown to partition with the actin cytoskeleton during detergent extraction. Agents that specifically alter the polymerization state of the actin cytoskeleton change the amount of NPA binding protein and actin recovered in these cytoskeletal pellets. Actin-affinity columns were prepared with polymers of actin purified from zucchini hypocotyl tissue. NPA binding activity was eluted in a single peak from the actin filament column. Cytochalasin D, which fragments the actin cytoskeleton, was shown to reduce polar auxin transport in zucchini hypocotyls. The interaction of the NPA binding protein with the actin cytoskeleton may localize it in one plane of the plasma membrane, and thereby control the polarity of auxin transport.

  10. Analysis of cache for streaming tape drive

    NASA Technical Reports Server (NTRS)

    Chinnaswamy, V.

    1993-01-01

    A tape subsystem consists of a controller and a tape drive. Tapes are used for backup, data interchange, and software distribution. The backup operation is addressed. During a backup operation, data is read from disk, processed in CPU, and then sent to tape. The processing speeds of a disk subsystem, CPU, and a tape subsystem are likely to be different. A powerful CPU can read data from a fast disk, process it, and supply the data to the tape subsystem at a faster rate than the tape subsystem can handle. On the other hand, a slow disk drive and a slow CPU may not be able to supply data fast enough to keep a tape drive busy all the time. The backup process may supply data to tape drive in bursts. Each burst may be followed by an idle period. Depending on the nature of the file distribution in the disk, the input stream to the tape subsystem may vary significantly during backup. To compensate for these differences and optimize the utilization of a tape subsystem, a cache or buffer is introduced in the tape controller. Most of the tape drives today are streaming tape drives. A streaming tape drive goes into reposition when there is no data from the controller. Once the drive goes into reposition, the controller can receive data, but it cannot supply data to the tape drive until the drive completes its reposition. A controller can also receive data from the host and send data to the tape drive at the same time. The relationship of cache size, host transfer rate, drive transfer rate, reposition, and ramp up times for optimal performance of the tape subsystem are investigated. Formulas developed will also show the advantages of cache watermarks to increase the streaming time of the tape drive, maximum loss due to insufficient cache, tradeoffs between cache and reposition times and the effectiveness of cache on a streaming tape drive due to idle times or interruptions due in host transfers. Several mathematical formulas are developed to predict the performance of the tape

  11. The Alternative Splicing of Cytoplasmic Polyadenylation Element Binding Protein 2 Drives Anoikis Resistance and the Metastasis of Triple Negative Breast Cancer.

    PubMed

    Johnson, Ryan M; Vu, Ngoc T; Griffin, Brian P; Gentry, Amanda E; Archer, Kellie J; Chalfant, Charles E; Park, Margaret A

    2015-10-16

    Triple negative breast cancer (TNBC) represents an anomalous subset of breast cancer with a greatly reduced (30%) 5-year survival rate. The enhanced mortality and morbidity of TNBC arises from the high metastatic rate, which requires the acquisition of AnR, a process whereby anchorage-dependent cells become resistant to cell death induced by detachment. In this study TNBC cell lines were selected for AnR, and these cell lines demonstrated dramatic enhancement in the formation of lung metastases as compared with parental cells. Genetic analysis of the AnR subclones versus parental cells via next generation sequencing and analysis of global alternative RNA splicing identified that the mRNA splicing of cytoplasmic polyadenylation element binding 2 (CPEB2), a translational regulator, was altered in AnR TNBC cells. Specifically, increased inclusion of exon 4 into the mature mRNA to produce the CPEB2B isoform was observed in AnR cell lines. Molecular manipulations of CPEB2 splice variants demonstrated a key role for this RNA splicing event in the resistance of cells to anoikis. Specifically, down-regulation of the CPEB2B isoform using siRNA re-sensitized the AnR cell lines to detachment-induced cell death. The ectopic expression of CPEB2B in parental TNBC cell lines induced AnR and dramatically increased metastatic potential. Importantly, alterations in the alternative splicing of CPEB2 were also observed in human TNBC and additional subtypes of human breast cancer tumors linked to a high metastatic rate. Our findings demonstrate that the regulation of CPEB2 mRNA splicing is a key mechanism in AnR and a driving force in TNBC metastasis.

  12. Distinct cellular and subcellular distributions of G protein-coupled receptor kinase and arrestin isoforms in the striatum.

    PubMed

    Bychkov, Evgeny; Zurkovsky, Lilia; Garret, Mika B; Ahmed, Mohamed R; Gurevich, Eugenia V

    2012-01-01

    G protein-coupled receptor kinases (GRKs) and arrestins mediate desensitization of G protein-coupled receptors (GPCR). Arrestins also mediate G protein-independent signaling via GPCRs. Since GRK and arrestins demonstrate no strict receptor specificity, their functions in the brain may depend on their cellular complement, expression level, and subcellular targeting. However, cellular expression and subcellular distribution of GRKs and arrestins in the brain is largely unknown. We show that GRK isoforms GRK2 and GRK5 are similarly expressed in direct and indirect pathway neurons in the rat striatum. Arrestin-2 and arrestin-3 are also expressed in neurons of both pathways. Cholinergic interneurons are enriched in GRK2, arrestin-3, and GRK5. Parvalbumin-positive interneurons express more of GRK2 and less of arrestin-2 than medium spiny neurons. The GRK5 subcellular distribution in the human striatal neurons is altered by its phosphorylation: unphosphorylated enzyme preferentially localizes to synaptic membranes, whereas phosphorylated GRK5 is found in plasma membrane and cytosolic fractions. Both GRK isoforms are abundant in the nucleus of human striatal neurons, whereas the proportion of both arrestins in the nucleus was equally low. However, overall higher expression of arrestin-2 yields high enough concentration in the nucleus to mediate nuclear functions. These data suggest cell type- and subcellular compartment-dependent differences in GRK/arrestin-mediated desensitization and signaling.

  13. Distinct Cellular and Subcellular Distributions of G Protein-Coupled Receptor Kinase and Arrestin Isoforms in the Striatum

    PubMed Central

    Bychkov, Evgeny; Zurkovsky, Lilia; Garret, Mika B.; Ahmed, Mohamed R.; Gurevich, Eugenia V.

    2012-01-01

    G protein-coupled receptor kinases (GRKs) and arrestins mediate desensitization of G protein-coupled receptors (GPCR). Arrestins also mediate G protein-independent signaling via GPCRs. Since GRK and arrestins demonstrate no strict receptor specificity, their functions in the brain may depend on their cellular complement, expression level, and subcellular targeting. However, cellular expression and subcellular distribution of GRKs and arrestins in the brain is largely unknown. We show that GRK isoforms GRK2 and GRK5 are similarly expressed in direct and indirect pathway neurons in the rat striatum. Arrestin-2 and arrestin-3 are also expressed in neurons of both pathways. Cholinergic interneurons are enriched in GRK2, arrestin-3, and GRK5. Parvalbumin-positive interneurons express more of GRK2 and less of arrestin-2 than medium spiny neurons. The GRK5 subcellular distribution in the human striatal neurons is altered by its phosphorylation: unphosphorylated enzyme preferentially localizes to synaptic membranes, whereas phosphorylated GRK5 is found in plasma membrane and cytosolic fractions. Both GRK isoforms are abundant in the nucleus of human striatal neurons, whereas the proportion of both arrestins in the nucleus was equally low. However, overall higher expression of arrestin-2 yields high enough concentration in the nucleus to mediate nuclear functions. These data suggest cell type- and subcellular compartment-dependent differences in GRK/arrestin-mediated desensitization and signaling. PMID:23139825

  14. Optimization of an immunohistochemical method to assess distribution of tight junction proteins in canine epidermis and adnexae.

    PubMed

    Roussel, A J J; Knol, A C; Bourdeau, P J; Bruet, V

    2014-01-01

    Epidermal tight junctions (TJs) have been well characterized in human medicine. Abnormality of these structures is involved in skin diseases such as atopic dermatitis. There is little information about the expression and distribution of TJ proteins in the canine skin. The aim of this study was to develop an optimal immunohistochemical method for assessment of the expression of TJ proteins in the skin of healthy dogs. Formalin-fixed and paraffin wax-embedded skin biopsy samples from healthy human and canine patients were used. Canine skin samples were from the inguinal region and the nasal planum. Immunohistochemistry was used to study the expression of zonula occludens-1 (ZO-1), occludin and claudin-1, -4 and -7. Heat-induced antigen retrieval with EDTA (pH 9.0) yielded the best labelling of TJ proteins. ZO-1 and occludin were expressed in the cytoplasm and along the keratinocyte membrane, while claudin-1 and -4 were mainly membrane in distribution. ZO-1, occludin and claudin-1 were detected in all epidermal layers with the exception of the stratum corneum, while claudin-4 expression was restricted to the stratum granulosum. Expression of claudin-7 was difficult to evaluate. There was no difference in labelling pattern between inguinal and nasal planum skin.

  15. Stable Allele Frequency Distribution of the Plasmodium falciparum clag Genes Encoding Components of the High Molecular Weight Rhoptry Protein Complex

    PubMed Central

    Alexandre, Jean Semé Fils; Xangsayarath, Phonepadith; Kaewthamasorn, Morakot; Yahata, Kazuhide; Sattabongkot, Jetsumon; Udomsangpetch, Rachanee; Kaneko, Osamu

    2012-01-01

    Plasmodium falciparum Clag protein is a candidate component of the plasmodial surface anion channel located on the parasite-infected erythrocyte. This protein is encoded by 5 separated clag genes and forms a RhopH complex with the other components. Previously, a signature of positive diversifying selection was detected on the hypervariable region of clag2 and clag8 by population-based analyses using P. falciparum originating from Thailand in 1988–1989. In this study, we obtained the sequence of this region of 3 clag genes (clag2, clag8, and clag9) in 2005 and evaluated the changes over time in the frequency distribution of the polymorphism of these gene products by comparison with the sequences obtained in 1988–1989. We found no difference in the frequency distribution of 18 putatively neutral loci between the 2 groups, evidence that the background of the parasite population structure has remained stable over 14 years. Although the frequency distribution of most of the polymorphic sites in the hypervariable region of Clag2, Clag8, and Clag9 was stable over 14 years, we found that a proportion of the major Clag2 group and one amino acid position of Clag8 changed significantly. This may be a response to a certain type of pressure. PMID:23264726

  16. Stable Allele Frequency Distribution of the Plasmodium falciparum clag Genes Encoding Components of the High Molecular Weight Rhoptry Protein Complex.

    PubMed

    Alexandre, Jean Semé Fils; Xangsayarath, Phonepadith; Kaewthamasorn, Morakot; Yahata, Kazuhide; Sattabongkot, Jetsumon; Udomsangpetch, Rachanee; Kaneko, Osamu

    2012-09-01

    Plasmodium falciparum Clag protein is a candidate component of the plasmodial surface anion channel located on the parasite-infected erythrocyte. This protein is encoded by 5 separated clag genes and forms a RhopH complex with the other components. Previously, a signature of positive diversifying selection was detected on the hypervariable region of clag2 and clag8 by population-based analyses using P. falciparum originating from Thailand in 1988-1989. In this study, we obtained the sequence of this region of 3 clag genes (clag2, clag8, and clag9) in 2005 and evaluated the changes over time in the frequency distribution of the polymorphism of these gene products by comparison with the sequences obtained in 1988-1989. We found no difference in the frequency distribution of 18 putatively neutral loci between the 2 groups, evidence that the background of the parasite population structure has remained stable over 14 years. Although the frequency distribution of most of the polymorphic sites in the hypervariable region of Clag2, Clag8, and Clag9 was stable over 14 years, we found that a proportion of the major Clag2 group and one amino acid position of Clag8 changed significantly. This may be a response to a certain type of pressure.

  17. Early turn formation and chain collapse drive fast folding of the major cold shock protein CspA of Escherichia coli.

    PubMed

    Vu, Dung M; Brewer, Scott H; Dyer, R Brian

    2012-11-13

    The folding mechanism of the β-sheet protein CspA, the major cold shock protein of Escherichia coli, was previously reported to be a concerted, two-state process. We have reexamined the folding of CspA using multiple spectroscopic probes of the equilibrium transition and laser-induced temperature jump (T-jump) to achieve better time resolution of the kinetics. Equilibrium temperature-dependent Fourier transform infrared (1634 cm(-1)) and tryptophan fluorescence measurements reveal probe-dependent thermal transitions with midpoints (T(m)) of 66 ± 1 and 61 ± 1 °C, respectively. Singular-value decomposition analysis with global fitting of the temperature-dependent infrared (IR) difference spectra reveals two spectral components with distinct melting transitions with different midpoints. T-jump relaxation measurements of CspA probed by IR and fluorescence spectroscopy show probe-dependent multiexponential kinetics characteristic of non-two-state folding. The frequency-dependent IR transients all show biphasic relaxation with average time constants of 50 ± 7 and 225 ± 25 μs at a T(f) of 77 °C and almost equal amplitudes. Similar biphasic kinetics are observed using Trp fluorescence of the wild-type protein and the Y42W and T68W mutants, with comparable lifetimes. All of these observations support a model for the folding of CspA through a compact intermediate state. The transient IR and fluorescence spectra are consistent with a diffuse intermediate having β-turns and substantial β-sheet structure. The loop β3-β4 structure is likely not folded in the intermediate state, allowing substantial solvent penetration into the barrel structure.

  18. Early Turn Formation and Chain Collapse Drive Fast Folding of the Major Cold Shock Protein CspA of Escherichia coli

    PubMed Central

    Vu, Dung M.; Brewer, Scott H.; Dyer, R. Brian

    2012-01-01

    The folding mechanism of the β-sheet protein CspA, the major cold shock protein of Escherichia coli, was previously reported to be a concerted, two-state process. We have reexamined the folding of CspA using multiple spectroscopic probes of the equilibrium transition and laser-induced temperature jump (T-jump) to achieve better time resolution of the kinetics. Equilibrium temperature-dependent Fourier transform infrared (1634 cm–1) and tryptophan fluorescence measurements reveal probe-dependent thermal transitions with midpoints (Tm) of 66 ± 1 and 61 ± 1 °C, respectively. Singular-value decomposition analysis with global fitting of the temperature-dependent infrared (IR) difference spectra reveals two spectral components with distinct melting transitions with different midpoints. T-Jump relaxation measurements of CspA probed by IR and fluorescence spectroscopy show probe-dependent multiexponential kinetics characteristic of non-two-state folding. The frequency-dependent IR transients all show biphasic relaxation with average time constants of 50 ± 7 and 225 ± 25 μs at a Tf of 77 °C and almost equal amplitudes. Similar biphasic kinetics are observed using Trp fluorescence of the wild-type protein and the Y42W and T68W mutants, with comparable lifetimes. All of these observations support a model for the folding of CspA through a compact intermediate state. The transient IR and fluorescence spectra are consistent with a diffuse intermediate having β-turns and substantial β-sheet structure. The loop β3–β4 structure is likely not folded in the intermediate state, allowing substantial solvent penetration into the barrel structure. PMID:23098216

  19. Marihuana and driving.

    PubMed

    Moskowitz, H

    1985-08-01

    A review was performed of the marihuana and driving literature, both epidemiological and experimental. It was noted that epidemiological studies face considerable difficulties in obtaining estimates of risks involved for drivers utilizing marihuana due to the rapid decline in blood levels of tetrahydrocannabinol. On the other hand, experimental studies examining the relationship between administered marihuana dose and performance have identified many driving-related areas as exhibiting impairment. Areas impaired include coordination, tracking, perception, vigilance and performance in both driving simulators and on the road. Other behavioral areas of lesser importance for driving also exhibited evidence of impairment by marihuana. Areas for further research are suggested.

  20. Distribution of the SynDIG4/proline-rich transmembrane protein 1 in rat brain.

    PubMed

    Kirk, Lyndsey M; Ti, Shu W; Bishop, Hannah I; Orozco-Llamas, Mayra; Pham, Michelle; Trimmer, James S; Díaz, Elva

    2016-08-01

    The modulation of AMPA receptor (AMPAR) content at synapses is thought to be an underlying molecular mechanism of memory and learning. AMPAR content at synapses is highly plastic and is regulated by numerous AMPAR accessory transmembrane proteins such as TARPs, cornichons, and CKAMPs. SynDIG (synapse differentiation-induced gene) defines a family of four genes (SynDIG1-4) expressed in distinct and overlapping patterns in the brain. SynDIG1 was previously identified as a novel transmembrane AMPAR-associated protein that regulates synaptic strength. The related protein SynDIG4 [also known as Prrt1 (proline-rich transmembrane protein 1)] has recently been identified as a component of AMPAR complexes. In this study, we show that SynDIG1 and SynDIG4 have distinct yet overlapping patterns of expression in the central nervous system, with SynDIG4 having especially prominent expression in the hippocampus and particularly within CA1. In contrast to SynDIG1 and other traditional AMPAR auxiliary subunits, SynDIG4 is de-enriched at the postsynaptic density and colocalizes with extrasynaptic GluA1 puncta in primary dissociated neuron culture. These results indicate that, although SynDIG4 shares sequence similarity with SynDIG1, it might act through a unique mechanism as an auxiliary factor for extrasynaptic GluA1-containing AMPARs. J. Comp. Neurol. 524:2266-2280, 2016. © 2015 Wiley Periodicals, Inc.

  1. [Distribution and environmental function of glomalin-related soil protein: A review].

    PubMed

    Wang, Jian; Zhou, Zi-yan; Ling, Wan-ting

    2016-02-01

    Glomalin-related soil protein (GRSP), a glycoprotein secreted by arbuscular mycorrhizal fungi (AMF), is abundant in soil. GRSP can be fractionated into total glomalin-related soil protein (TG), easily extracted glomalin-related soil protein (EEG), immunoreactive total glomalin (IRTG) and immunoreactive easily extracted glomalin (IREEG). The content of GRSP in soil differed with different soil use type, fertilization condition, AMF and host plant species, and environmental conditions. GRSP significantly positively correlates to the aggregate water stability. GRSP may reduce the release of CO2 in agro-ecosystem, benefit the soil carbon fixation, and reduce the bioavailability and plant toxicity of heavy metals in soil. The extraction and characterization of GRSP are of great importance to understanding the basic behaviors of GRSP in soil environments. Further studies are needed to clarify the molecular biology function of GRSP in agro-ecosystem based on the knowledge of proteins and related genes, and impacts of GRSP on the environmental behavior of organic pollutants in soil.

  2. Vitamin D-dependent rat renal calcium-binding protein: development of a radioimmunoassay, tissue distribution, and immunologic identification

    SciTech Connect

    Sonnenberg, J.; Pansini, A.R.; Christakos, S.

    1984-08-01

    A sensitive double antibody RIA has been developed for the 28,000 mol wt rat renal vitamin D-dependent calcium-binding protein. Using this assay, concentrations of calcium-binding protein (CaBP) as low as 30 ng can be measured. The assay is precise (intraassay variability, 5.0%) and reproductible (interassay variability, 8.2%). Measurements of renal CaBP by RIA showed a good correlation with measurements of CaBP by the chelex resin assay and by polyacrylamide gel analysis by densitometric tracing using a purified CaBP marker. The concentration of CaBP in the vitamin D-replete rat kidney is 7.3 +/- 1.0 (mean +/- SEM) micrograms/mg protein. In vitamin D-deficient rats the level of renal CaBP is 2.6 +/- 0.3 micrograms/mg protein. Tissue distribution of immunoreactive rat renal CaBP showed the highest concentration of CaBP in the rat cerebellum (38.3 +/- 5.1 micrograms/mg protein). Lower concentrations of immunoreactive CaBP were detected in several other rat tissues. No immunoreactive CaBP was detected in rat or human serum. In necropsy human kidney and cerebellum, high levels of immunoreactive CaBP were also detected (1.5 +/- 0.1 and 27.3 +/- 2.1 micrograms/mg protein, respectively). When extracts of rat kidney and brain and human cerebellum and kidney were assayed at several dilutions, immunodisplacement curves parallel to that of pure renal CaBP were observed, indicating immunochemical similarity. Fractionation of extracts of rat cerebellum, human kidney, and human cerebellum on Sephadex G-100 revealed immunoreactivity and calcium-binding activity in the 28,000 mol wt region similar to rat kidney.

  3. ISWI proteins participate in the genome-wide nucleosome distribution in Arabidopsis.

    PubMed

    Li, Guang; Liu, Shujing; Wang, Jiawei; He, Jianfeng; Huang, Hai; Zhang, Yijing; Xu, Lin

    2014-05-01

    Chromatin is a highly organized structure with repetitive nucleosome subunits. Nucleosome distribution patterns, which contain information on epigenetic controls, are dynamically affected by ATP-dependent chromatin remodeling factors (remodelers). However, whether plants have specific nucleosome distribution patterns and how plant remodelers contribute to the pattern formation are not clear. In this study we used the micrococcal nuclease digestion followed by deep sequencing (MNase-seq) assay to show the genome-wide nucleosome pattern in Arabidopsis thaliana. We demonstrated that the nucleosome distribution patterns of Arabidopsis are associated with the gene expression level, and have several specific characteristics that are different from those of animals and yeast. In addition, we found that remodelers in the A. thaliana imitation switch (AtISWI) subfamily are important for the formation of the nucleosome distribution pattern. Double mutations in the AtISWI genes, CHROMATIN REMODELING 11 (CHR11) and CHR17, resulted in the loss of the evenly spaced nucleosome pattern in gene bodies, but did not affect nucleosome density, supporting a previous idea that the primary role of ISWI is to slide nucleosomes in gene bodies for pattern formation.

  4. Multiple interactions drive adaptor-mediated recruitment of the ubiquitin ligase rsp5 to membrane proteins in vivo and in vitro.

    PubMed

    Sullivan, James A; Lewis, Michael J; Nikko, Elina; Pelham, Hugh R B

    2007-07-01

    Recognition of membrane proteins by the Nedd4/Rsp5 ubiquitin ligase family is a critical step in their targeting to the multivesicular body pathway. Some substrates contain "PY" motifs (PPxY), which bind to WW domains in the ligase. Others lack PY motifs and instead rely on adaptors that recruit the ligase to them. To investigate the mechanism of adaptor-mediated ubiquitination, we have characterized the interactions between the adaptor Bsd2, the ubiquitin ligase Rsp5, and the membrane proteins Cps1, Tre1, and Smf1 from Saccharomyces cerevisiae. We have reconstituted adaptor-mediated modification of Cps1 and Tre1 in vitro, and we show that two PY motifs in Bsd2 and two WW domains (WW2 and WW3) in Rsp5 are crucial for this. The binding of a weak noncanonical DMAPSY motif in Bsd2 to WW3 is an absolute requirement for Bsd2 adaptor function. We show that sorting of the manganese transporter Smf1, which requires both Bsd2 and Tre1, depends upon two PY motifs in Bsd2 and one motif in Tre1 but only two WW domains in Rsp5. We suggest that sequential assembly of first a Bsd2/Rsp5 complex, then a Tre1/Bsd2/Rsp5 complex followed by a rearrangement of PY-WW interactions is required for the ubiquitination of Smf1.

  5. Aurora A and NF-κB Survival Pathway Drive Chemoresistance in Acute Myeloid Leukemia via the TRAF-Interacting Protein TIFA.

    PubMed

    Wei, Tong-You Wade; Wu, Pei-Yu; Wu, Ting-Jung; Hou, Hsin-An; Chou, Wen-Chien; Teng, Chieh-Lin Jerry; Lin, Chih-Ru; Chen, Jo-Mei Maureen; Lin, Ting-Yang; Su, Hsiang-Chun; Huang, Chia-Chi Flora; Yu, Chang-Tze Ricky; Hsu, Shih-Lan; Tien, Hwei-Fang; Tsai, Ming-Daw

    2017-01-15

    Aurora A-dependent NF-κB signaling portends poor prognosis in acute myeloid leukemia (AML) and other cancers, but the functional basis underlying this association is unclear. Here, we report that Aurora A is essential for Thr9 phosphorylation of the TRAF-interacting protein TIFA, triggering activation of the NF-κB survival pathway in AML. TIFA protein was overexpressed concurrently with Aurora A and NF-κB signaling factors in patients with de novo AML relative to healthy individuals and also correlated with poor prognosis. Silencing TIFA in AML lines and primary patient cells decreased leukemic cell growth and chemoresistance via downregulation of prosurvival factors Bcl-2 and Bcl-XL that support NF-κB-dependent antiapoptotic events. Inhibiting TIFA perturbed leukemic cytokine secretion and reduced the IC50 of chemotherapeutic drug treatments in AML cells. Furthermore, in vivo delivery of TIFA-inhibitory fragments potentiated the clearance of myeloblasts in the bone marrow of xenograft-recipient mice via enhanced chemotoxicity. Collectively, our results showed that TIFA supports AML progression and that its targeting can enhance the efficacy of AML treatments. Cancer Res; 77(2); 494-508. ©2016 AACR.

  6. Comparative distribution of protein components of the A20 ubiquitin-editing complex in normal human brain

    PubMed Central

    Pranski, Elaine L.; Van Sanford, Carson D.; Dalal, Nirjari V.; Orr, Adam L.; Karmali, Dipan; Cooper, Deborah S.; Costa, Nicole; Heilman, Craig J.; Gearing, Marla; Lah, James J.; Levey, Allan I.; Betarbet, Ranjita S.

    2012-01-01

    Activation of innate and adaptive immune responses is tightly regulated, as insufficient activation could result in defective clearance of pathogens, while excessive activation might lead to lethal systemic inflammation or autoimmunity. A20 functions as a negative regulator of innate and adaptive immunity by inhibiting NF-κB activation. A20 mediates its inhibitory function in a complex with other proteins including RNF11 and Itch, both E3 ubiquitin ligases and TAX1BP1, an adaptor protein. Since NF-κB has been strongly implicated in various neuronal functions, we predict that its inhibitor, the A20 complex, is also present in the nervous system. In efforts to better understand the role of A20 complex and NF-κB signaling pathway, we determined regional distribution of A20 mRNA as well as protein expression levels and distribution of RNF11, TAX1BP1 and Itch, in different brain regions. The distribution of TRAF6 was also investigated since TRAF6, also an E3 ligase, has an important role in NF-κB signaling pathway. Our investigations, for the first time, describe and demonstrate that the essential components of the A20 ubiquitin-editing complex are present and mainly expressed in neurons. The A20 complex components are also differentially expressed throughout the human brain. This study provides useful information about region specific expression of the A20 complex components that will be invaluable while determining the role of NF-κB signaling pathway in neuronal development and degeneration. PMID:22634524

  7. Use of granzyme B-based fluorescent protein reporters to monitor granzyme distribution and granule integrity in live cells.

    PubMed

    Bird, Catherina H; Rizzitelli, Alexandra; Harper, Ian; Prescott, Mark; Bird, Phillip I

    2010-08-01

    Reporter proteins comprising granzyme B (GrB) fused to eGFP, ecliptic pHluorin or mCherry, were generated and used to study granule (lysosome) distribution and properties in COS-1 cells and natural killer cells. The reporters resembled native GrB in biosynthesis and localization, and accumulated in granules. In live cells both the eGFP and pHluorin reporters were dark in lysosomes, but fluoresced when the granule integrity or pH was perturbed by Leu-Leu methyl ester, hydrogen peroxide, naphthazarin, or sphingosine treatment. By contrast, fluorescence of the mCherry reporter was not pH-dependent. The quenching of eGFP within granules indicates that this commonly-used fluorescent protein is not appropriate as a vital intra-lysosomal marker.

  8. Starch digestibility and molecular weight distribution of proteins in rice grains subjected to heat-moisture treatment.

    PubMed

    Silva, Wyller Max Ferreira; Biduski, Bárbara; Lima, Karina Oliveira; Pinto, Vânia Zanella; Hoffmann, Jéssica Fernanda; Vanier, Nathan Levien; Dias, Alvaro Renato Guerra

    2017-03-15

    The objective of this study was to evaluate the effects of the heat-moisture treatment (HMT) applied to paddy rice grains on the physicochemical properties, in vitro starch digestibility, and molecular weight distribution of proteins in rice flour. The paddy rice grains were adjusted to 13%, 16%, and 18% moisture and autoclaved at 121°C for 30 and 60min. The HMT promoted a reduction of the amylose content, the swelling power, and the solubility of the rice flour. Changes in the relative crystallinity and molecular weight of the proteins extracted with a sodium phosphate buffer containing 2.0% sodium dodecyl sulfate (SDDS) were observed in HMT samples. The different methods for the quantification of resistant starch resulted in distinct resistant starch contents. The HMT (18%-60min) promoted an increase in resistant starch content and the HMT (16%-60min) caused an increase in the slowly digestible starch in the rice flour.

  9. Sequence, tissue distribution, and chromosomal localization of mRNA encoding a human glucose transporter-like protein

    SciTech Connect

    Fukumoto, Hirofumi; Seino, Susumu; Imura, Hiroo; Seino, Yutaka; Eddy, R.L.; Fukushima, Yoshimitsu; Byers, M.G.; Shows, T.B.; Bell, G.I. )

    1988-08-01

    Recombinant DNA clones encoding a glucose transporter-like protein have been isolated from adult human liver and kidney cDNA libraries by cross-hybridization with the human HepG2/erythrocyte glucose transporter cDNA. Analysis of the sequence of this 524-amino acid glucose transporter-like protein indicates that is has 55.5% identity with the HepG2/erythrocyte glucose transporter as well as a similar structural organization. Studies of the tissue distribution of the mRNA coding for this glucose transporter-like protein in adult human tissues indicate that the highest amounts are present in liver with lower amounts in kidney and small intestine. The amounts of glucose transporter-like mRNA in other tissues, including colon, stomach, cerebrum, skeletal muscle, and adipose tissue, were below the level of sensitivity of our assay. The single-copy gene encoding this glucose transporter-like protein has been localized to the q26.1{yields}q26.3 region of chromosome 3.

  10. Fast revelation of the motif mode for a yeast protein interaction network through intelligent agent-based distributed computing.

    PubMed

    Lee, Wei-Po; Tzou, Wen-Shyong

    2010-09-01

    In the yeast protein-protein interaction network, motif mode, a collection of motifs of special combinations of protein nodes annotated by the molecular function terms of the Gene Ontology, has revealed differences in the conservation constraints within the same topology. In this study, by employing an intelligent agent-based distributed computing method, we are able to discover motif modes in a fast and adaptive manner. Moreover, by focusing on the highly evolutionarily conserved motif modes belonging to the same biological function, we find a large downshift in the distance between nodes belonging to the same motif mode compared with the whole, suggesting that nodes with the same motif mode tend to congregate in a network. Several motif modes with a high conservation of the motif constituents were revealed, but from a new perspective, including that with a three-node motif mode engaged in the protein fate and that with three four-node motif modes involved in the genome maintenance, cellular organization, and transcription. The network motif modes discovered from this method can be linked to the wealth of biological data which require further elucidation with regard to biological functions.

  11. Independent-Trajectory Thermodynamic Integration: a practical guide to protein-drug binding free energy calculations using distributed computing.

    PubMed

    Lawrenz, Morgan; Baron, Riccardo; Wang, Yi; McCammon, J Andrew

    2012-01-01

    The Independent-Trajectory Thermodynamic Integration (IT-TI) approach for free energy calculation with distributed computing is described. IT-TI utilizes diverse conformational sampling obtained from multiple, independent simulations to obtain more reliable free energy estimates compared to single TI predictions. The latter may significantly under- or over-estimate the binding free energy due to finite sampling. We exemplify the advantages of the IT-TI approach using two distinct cases of protein-ligand binding. In both cases, IT-TI yields distributions of absolute binding free energy estimates that are remarkably centered on the target experimental values. Alternative protocols for the practical and general application of IT-TI calculations are investigated. We highlight a protocol that maximizes predictive power and computational efficiency.

  12. Discovering Mercury Protein Modifications in Whole Proteomes Using Natural Isotope Distributions Observed in Liquid Chromatography-Tandem Mass Spectrometry

    SciTech Connect

    Polacco, Benjamin J.; Purvine, Samuel O.; Zink, Erika M.; LaVoie, Stephen P.; Lipton, Mary S.; Summers, Anne O.; Miller, Susan M.

    2011-08-01

    The identification of peptides that result from post-translational modifications is critical for understanding normal pathways of cellular regulation as well as identifying damage from, or exposures to xenobiotics, i.e. the exposome. However, because of their low abundance in proteomes, effective detection of modified peptides by mass spectrometry (MS) typically requires enrichment to eliminate false identifications. We present a new method for confidently identifying peptides with mercury (Hg)-containing adducts that is based on the influence of mercury’s seven stable isotopes on peptide isotope distributions detected by high-resolution MS. Using a pure protein and E. coli cultures exposed to phenyl mercuric acetate, we show the pattern of peak heights in isotope distributions from primary MS single scans efficiently identified Hg adducts in data from chromatographic separation coupled with tandem mass spectrometry with sensitivity and specificity greater than 90%. Isotope distributions are independent of peptide identifications based on peptide fragmentation (e.g. by SEQUEST), so both methods can be combined to eliminate false positives. Summing peptide isotope distributions across multiple scans improved specificity to 99.4% and sensitivity above 95%, affording identification of an unexpected Hg modification. We also illustrate the theoretical applicability of the method for detection of several less common elements including the essential element, selenium, as selenocysteine in peptides.

  13. Opiate agonist-induced re-distribution of Wntless, a mu-opioid receptor interacting protein, in rat striatal neurons.

    PubMed

    Reyes, B A S; Vakharia, K; Ferraro, T N; Levenson, R; Berrettini, W H; Van Bockstaele, E J

    2012-01-01

    Wntless (WLS), a mu-opioid receptor (MOR) interacting protein, mediates Wnt protein secretion that is critical for neuronal development. We investigated whether MOR agonists induce re-distribution of WLS within rat striatal neurons. Adult male rats received either saline, morphine or [d-Ala2, N-Me-Phe4, Gly-ol5]-enkephalin (DAMGO) directly into the lateral ventricles. Following thirty minutes, brains were extracted and tissue sections were processed for immunogold silver detection of WLS. In saline-treated rats, WLS was distributed along the plasma membrane and within the cytoplasmic compartment of striatal dendrites as previously described. The ratio of cytoplasmic to total dendritic WLS labeling was 0.70±0.03 in saline-treated striatal tissue. Morphine treatment decreased this ratio to 0.48±0.03 indicating a shift of WLS from the intracellular compartment to the plasma membrane. However, following DAMGO treatment, the ratio was 0.85±0.05 indicating a greater distribution of WLS intracellularly. The difference in the re-distribution of the WLS following different agonist exposure may be related to DAMGO's well known ability to induce internalization of MOR in contrast to morphine, which is less effective in producing receptor internalization. Furthermore, these data are consistent with our hypothesis that MOR agonists promote dimerization of WLS and MOR, thereby preventing WLS from mediating Wnt secretion. In summary, our findings indicate differential agonist-induced trafficking of WLS in striatal neurons following distinct agonist exposure. Adaptations in WLS trafficking may represent a novel pharmacological target in the treatment of opiate addiction and/or pain.

  14. Dynamics of energy distribution in three channel alpha helix protein based on Davydov’s ansatz

    SciTech Connect

    Ahmad, Faozan; Alatas, Husin

    2015-04-16

    An important aspect of many biological processes at molecular level is the transfer and storage mechanism of bioenergy released in the reaction of the hydrolysis of Adenosinetriphosphate (ATP) by biomacromolecule especially protein. Model of Soliton Davydov is a new break-through that could describe that mechanism. Here we have reformulated quantum mechanical the Davydov theory, using least action principle. Dynamical aspect of the model is analyzed by numerical calculation. We found two dynamical cases: the traveling and pinning soliton that we suggest they are related to the energy transfer and storage mechanism in the protein. Traveling and pinning soliton can be controlled by strength of coupling. In 3- channel approach, we found the breather phenomena in which its frequency is determined by interchannel coupling parameter.

  15. Effects of altered gravity on a distribution of rDNA and nucleolar proteins and the expression of nucleolar proteins in plants

    NASA Astrophysics Data System (ADS)

    Sobol, Margaryta; Kordyum, Elizabeth; Medina, Francisco Javier

    The nucleolus is an inner nuclear organelle originated from the activity of hundreds of rRNA genes, typically spanning several megabases. It morphologically reflects the functional events leading to ribosome biogenesis, from the transcription of rDNA through the processing of nascent pre-rRNA to the assembly of pre-ribosomes. A typical nucleolus consists of three major elements, namely fibrillar centers (FCs), the dense fibrillar component (DFC), and granular component (GC). The rate of ribosome biosynthesis and the subnucleolar structure are reliable monitors of the general level of cell metabolism and, consequently, of the rate of cellular growth, being influenced with many external factors, among which altered gravity could be included. Thus, we can hypothesize that the structural organization of the nucleolar subcomponents and the level, distribution and quantitative/qualitative characteristics of the nucleolar proteins would be changed under conditions of altered gravity. To confirm our hypothesis, we applied parallel procedures, such as cytochemistry, immunofluorescence, confocal laser microscopy, immunogold electron microscopy, monoand bi-dimensional electrophoresis and immunoblotting in root meristematic cells from two-day cress seedlings grown under slow horizontal clinorotation (2 rpm) and in stationary control. The complex model of the ultrastructural organization and functions of the nucleolus was created based on the location of rDNA and the nucleolar proteins fibrillarin, NhL90 and NhL68, these latter being cress nucleolin homologues. The principal stages of ribosome biogenesis, namely ribosomal gene activation, rDNA transcription and pre-rRNA processing were reflected in this model. Compared to the pattern shown in control ground gravity conditions, we found firstly a redistribution of both rDNA and nucleolar proteins in nucleolar subcomponents, induced by clinorotation. Under the conditions of altered gravity, nucleolar DNA concentrated

  16. The Distribution of Circumsporozoite Protein (CS) in Anopheles Stephensi Mosquitoes Infected with Plasmodium Falciparum Malaria

    DTIC Science & Technology

    1990-01-01

    389 in differentiating oocysts, on remnant membranes left on the midgut Roitt IM, BrostoffJ, Male DK (1985): Immunology. St Louis, CV Mosby wall after...Plasmodium falciparum; Anopheles stephensi; Cir- on the mosquito midgut. As oocysts differentiated to ma- cumsporozoite protein; Fuchsin/naphthol AS-BI...and sporogony in the mosquito. During a blood meal, microscopy and an indirect fluorescent antibody test (IFAT). These the mosquito ingests the male

  17. Driving force behind adsorption-induced protein unfolding: a time-resolved X-ray reflectivity study on lysozyme adsorbed at an air/water interface.

    PubMed

    Yano, Yohko F; Uruga, Tomoya; Tanida, Hajime; Toyokawa, Hidenori; Terada, Yasuko; Takagaki, Masafumi; Yamada, Hironari

    2009-01-06

    Time-resolved X-ray reflectivity measurements for lysozyme (LSZ) adsorbed at an air/water interface were performed to study the mechanism of adsorption-induced protein unfolding. The time dependence of the density profile at the air/water interface revealed that the molecular conformation changed significantly during adsorption. Taking into account previous work using Fourier transform infrared (FTIR) spectroscopy, we propose that the LSZ molecules initially adsorbed on the air/water interface have a flat unfolded structure, forming antiparallel beta-sheets as a result of hydrophobic interactions with the gas phase. In contrast, as adsorption continues, a second layer forms in which the molecules have a very loose structure having random coils as a result of hydrophilic interactions with the hydrophilic groups that protrude from the first layer.

  18. Implications of exercise training and distribution of protein intake on molecular processes regulating skeletal muscle plasticity.

    PubMed

    Margolis, Lee M; Rivas, Donato A

    2015-03-01

    To optimize its function, skeletal muscle exhibits exceptional plasticity and possesses the fundamental capacity to adapt its metabolic and contractile properties in response to various external stimuli (e.g., external loading, nutrient availability, and humoral factors). The adaptability of skeletal muscle, along with its relatively large mass and high metabolic rate, makes this tissue an important contributor to whole body health and mobility. This adaptational process includes changes in the number, size, and structural/functional properties of the myofibers. The adaptations of skeletal muscle to exercise are highly interrelated with dietary intake, particularly dietary protein, which has been shown to further potentiate exercise training-induced adaptations. Understanding the molecular adaptation of skeletal muscle to exercise and protein consumption is vital to elicit maximum benefit from exercise training to improve human performance and health. In this review, we will provide an overview of the molecular pathways regulating skeletal muscle adaptation to exercise and protein, and discuss the role of subsequent timing of nutrient intake following exercise.

  19. Intracellular distributions and putative functions of calcium-binding proteins in the bullfrog vestibular otolith organs

    NASA Technical Reports Server (NTRS)

    Baird, R. A.; Steyger, P. S.; Schuff, N. R.

    1997-01-01

    Hair cells in the bullfrog vestibular otolith organs were immunolabeled by monoclonal and polyclonal antisera against calbindin (CaB), calmodulin (CaM), calretinin (CaR), and parvalbumin (PA). S-100, previously shown to immunolabel striolar hair cells in fish vestibular organs, only weakly immunolabeled hair cells in the bullfrog vestibular otolith organs. Immunolabeling was not detected in supporting cells. With the exception of CaR, myelinated axons and unmyelinated nerve terminals were immunolabeled by all of the above antisera. Immunolabeling was seen in all saccular hair cells, although hair cells at the macular margins were immunolabeled more intensely for CaB, CaM, and PA than more centrally located hair cells. As the macula margins are known to be a growth zone, this labeling pattern suggests that marginal hair cells up-regulate their calcium-binding proteins during hair cell development. In the utriculus, immunolabeling for CaM and PA was generally restricted to striolar hair cells. CaR immunolabeling was restricted to the stereociliary array. Immunolabeling for other calcium-binding proteins was generally seen in both the cell body and hair bundles of hair cells, although this labeling was often localized to the stereociliary array and the apical portion of the cell body. CaM and PA immunolabeling in the stereociliary array in saccular and utricular striolar cells suggests a functional role for these proteins in mechanoelectric transduction and adaptation.

  20. An Improved Immunostaining and Imaging Methodology to Determine Cell and Protein Distributions within the Bone Environment

    PubMed Central

    Akkiraju, Hemanth; Bonor, Jeremy; Nohe, Anja

    2015-01-01

    Bone is a dynamic tissue that undergoes multiple changes throughout its lifetime. Its maintenance requires a tight regulation between the cells embedded within the bone matrix, and an imbalance among these cells may lead to bone diseases such as osteoporosis. Identifying cell populations and their proteins within bone is necessary for understanding bone biology. Immunolabeling is one approach used to visualize proteins in tissues. Efficient immunolabeling of bone samples often requires decalcification, which may lead to changes in the structural morphology of the bone. Recently, methyl-methacrylate embedding of non-decalcified tissue followed by heat-induced antigen retrieval has been used to process bone sections for immunolabeling. However, this technique is applicable for bone slices below 50-µm thickness while fixed on slides. Additionally, enhancing epitope exposure for immunolabeling is still a challenge. Moreover, imaging bone cells within the bone environment using standard confocal microscopy is difficult. Here we demonstrate for the first time an improved methodology for immunolabeling non-decalcified bone using a testicular hyaluronidase enzyme-based antigen retrieval technique followed by two-photon fluorescence laser microscopy (TPLM) imaging. This procedure allowed us to image key intracellular proteins in bone cells while preserving the structural morphology of the cells and the bone. PMID:26718242

  1. Piezoelectric drive circuit

    DOEpatents

    Treu, C.A. Jr.

    1999-08-31

    A piezoelectric motor drive circuit is provided which utilizes the piezoelectric elements as oscillators and a Meacham half-bridge approach to develop feedback from the motor ground circuit to produce a signal to drive amplifiers to power the motor. The circuit automatically compensates for shifts in harmonic frequency of the piezoelectric elements due to pressure and temperature changes. 7 figs.

  2. Piezoelectric drive circuit

    DOEpatents

    Treu, Jr., Charles A.

    1999-08-31

    A piezoelectric motor drive circuit is provided which utilizes the piezoelectric elements as oscillators and a Meacham half-bridge approach to develop feedback from the motor ground circuit to produce a signal to drive amplifiers to power the motor. The circuit automatically compensates for shifts in harmonic frequency of the piezoelectric elements due to pressure and temperature changes.

  3. Electric vehicles: Driving range

    NASA Astrophysics Data System (ADS)

    Kempton, Willett

    2016-09-01

    For uptake of electric vehicles to increase, consumers' driving-range needs must be fulfilled. Analysis of the driving patterns of personal vehicles in the US now shows that today's electric vehicles can meet all travel needs on almost 90% of days from a single overnight charge.

  4. Observation of DNA and protein distributions in mammalian cell nuclei using STXM

    NASA Astrophysics Data System (ADS)

    Ohigashi, Takuji; Ito, Atsushi; Shinohara, Kunio; Tone, Shigenobu; Kado, Masataka; Inagaki, Yuichi; Wang, Yu-Fu; Kosugi, Nobuhiro

    2016-01-01

    A whole A549 cell and isolated nuclei of HeLa S3 cells in the apoptotic process were investigated by using a scanning transmission X-ray microscope (STXM) in the UVSOR Synchrotron (Okazaki, Japan). Near edge X-ray absorption fine structures (NEXAFS) of DNA and histone in the N K-edge region were measured as reference and their distribution in the nuclei was determined by using these reference spectra. The four stages of the apoptosis were successfully distinguished.

  5. Experiment K-6-10. Effects of zero gravity on myofibril protein content and isomyosin distribution in rodent skeletal muscle

    NASA Technical Reports Server (NTRS)

    Baldwin, K.; Herrick, R.; Oganov, V.

    1990-01-01

    The purpose of this experiment was to investigate the effects of 12 days of zero gravity (0G) exposure (Cosmos 1887 Biosputnik) on the enzymatic properties, protein content, and isomyosin distribution of the myofibril fraction of the slow-twitch vastus intermedius (VI) and the fast-twitch vastus lateralis (VL) muscles of adult male rats. Measurements were obtained on three experimental groups (n=5 each group) designated as flight-group (FG), vivarium-control (VC), and synchronous-control (SC). Body weight of the FG was significantly lower than the two control groups (p less than 0.05). Compared to the two control groups, VI weight was lower by 23 percent (p less than 0.10); whereas no such reduction was observed for the VL muscle. Myofibril yields (mg protein/g of muscle) in the VI were 35 percent lower in the FG compared to the controls (p less than 0.05); whereas, no such pattern was apparent for the VL muscle. When myofibril yields were expressed on a muscle basis (mg/g x muscle weight), the loss of myofibril protein was more exaggerated and suggests that myofibril protein degradation is an early event in the muscle atrophy response to 0G. Analysis of myosin isoforms indicated that slow-myosin was the primary isoform lost in the calculated degradation of total myosin. No evidence of loss of the fast isomyosins was apparent for either muscle following space flight. Myofibril ATPase activity of the VI was increased in the FG compared to controls, which is consistent with the observation of preferential slow-myosin degradation. These data suggest that muscles containing a high percent of slow-twitch fibers undergo greater degrees of myofibril protein degradation than do muscles containing predominantly fast-twitch fibers in response to a relatively short period of 0G exposure, and the primary target appears to be the slow-myosin molecule.

  6. The Distribution of Prion Protein Allotypes Differs Between Sporadic and Iatrogenic Creutzfeldt-Jakob Disease Patients.

    PubMed

    Moore, Roger A; Head, Mark W; Ironside, James W; Ritchie, Diane L; Zanusso, Gianluigi; Choi, Young Pyo; Pyo Choi, Young; Priola, Suzette A

    2016-02-01

    Sporadic Creutzfeldt-Jakob disease (sCJD) is the most prevalent of the human prion diseases, which are fatal and transmissible neurodegenerative diseases caused by the infectious prion protein (PrP(Sc)). The origin of sCJD is unknown, although the initiating event is thought to be the stochastic misfolding of endogenous prion protein (PrP(C)) into infectious PrP(Sc). By contrast, human growth hormone-associated cases of iatrogenic CJD (iCJD) in the United Kingdom (UK) are associated with exposure to an exogenous source of PrP(Sc). In both forms of CJD, heterozygosity at residue 129 for methionine (M) or valine (V) in the prion protein gene may affect disease phenotype, onset and progression. However, the relative contribution of each PrP(C) allotype to PrP(Sc) in heterozygous cases of CJD is unknown. Using mass spectrometry, we determined that the relative abundance of PrP(Sc) with M or V at residue 129 in brain specimens from MV cases of sCJD was highly variable. This result is consistent with PrP(C) containing an M or V at residue 129 having a similar propensity to misfold into PrP(Sc) thus causing sCJD. By contrast, PrP(Sc) with V at residue 129 predominated in the majority of the UK human growth hormone associated iCJD cases, consistent with exposure to infectious PrP(Sc) containing V at residue 129. In both types of CJD, the PrP(Sc) allotype ratio had no correlation with CJD type, age at clinical onset, or disease duration. Therefore, factors other than PrP(Sc) allotype abundance must influence the clinical progression and phenotype of heterozygous cases of CJD.

  7. The Distribution of Prion Protein Allotypes Differs Between Sporadic and Iatrogenic Creutzfeldt-Jakob Disease Patients

    PubMed Central

    Moore, Roger A.; Head, Mark W.; Ironside, James W.; Ritchie, Diane L.; Zanusso, Gianluigi; Pyo Choi, Young; Priola, Suzette A.

    2016-01-01

    Sporadic Creutzfeldt-Jakob disease (sCJD) is the most prevalent of the human prion diseases, which are fatal and transmissible neurodegenerative diseases caused by the infectious prion protein (PrPSc). The origin of sCJD is unknown, although the initiating event is thought to be the stochastic misfolding of endogenous prion protein (PrPC) into infectious PrPSc. By contrast, human growth hormone-associated cases of iatrogenic CJD (iCJD) in the United Kingdom (UK) are associated with exposure to an exogenous source of PrPSc. In both forms of CJD, heterozygosity at residue 129 for methionine (M) or valine (V) in the prion protein gene may affect disease phenotype, onset and progression. However, the relative contribution of each PrPC allotype to PrPSc in heterozygous cases of CJD is unknown. Using mass spectrometry, we determined that the relative abundance of PrPSc with M or V at residue 129 in brain specimens from MV cases of sCJD was highly variable. This result is consistent with PrPC containing an M or V at residue 129 having a similar propensity to misfold into PrPSc thus causing sCJD. By contrast, PrPSc with V at residue 129 predominated in the majority of the UK human growth hormone associated iCJD cases, consistent with exposure to infectious PrPSc containing V at residue 129. In both types of CJD, the PrPSc allotype ratio had no correlation with CJD type, age at clinical onset, or disease duration. Therefore, factors other than PrPSc allotype abundance must influence the clinical progression and phenotype of heterozygous cases of CJD. PMID:26840342

  8. Allosteric Regulation and Spatial Distribution of Kainate Receptors Bound to Ancillary Proteins

    PubMed Central

    Bowie, Derek; Garcia, Elizabeth P; Marshall, John; Traynelis, Stephen F; Lange, G David

    2003-01-01

    A diverse range of accessory proteins regulates the behaviour of most ligand- and voltage-gated ion channels. For glutamate receptor 6 (GluR6) kainate receptors, two unrelated proteins, concanavalin-A (Con-A) and postsynaptic density protein 95 (PSD-95), bind to extra- and intracellular domains, respectively, but are reported to exert similar effects on GluR6 desensitization behaviour. We have tested the hypothesis that distinct allosteric binding sites control GluR6 receptors via a common transduction pathway. Rapid agonist application to excised patches revealed that neither Con-A nor PSD-95 affect the onset of desensitization. The rate of desensitization elicited by 10 mm l-glutamate was similar in control (τfast= 5.5 ± 0.4 ms), Con-A-treated patches (τfast= 6.1 ± 0.5 ms) and patches containing PSD-95 and GluR6 receptors (τfast= 4.7 ± 0.6 ms). Likewise, the time course of recovery from GluR6 desensitization was similar in both control and Con-A conditions, whereas PSD-95 accelerated recovery almost twofold. Peak and steady-state (SS) dose-response relationships to glutamate were unchanged by lectin treatment (e.g. control, EC50(SS)= 31 ± 28 μmvs Con-A, EC50(SS)= 45 ± 9 μm, n= 6), suggesting that Con-A does not convert non-conducting channels with high agonist affinity into an open conformation. Instead, we demonstrate that the effects of Con-A on macroscopic responses reflect a shift in the relative contribution of different open states of the channel. In contrast, the effect of PSD-95 on recovery behaviour suggests that the association between kainate receptors and cytoskeletal proteins regulates signalling at glutamatergic synapses. Our results show that Con-A and PSD-95 regulate kainate receptors via distinct allosteric mechanisms targeting selective molecular steps in the transduction pathway. PMID:12562952

  9. The nucleotide exchange factor MGE exerts a key function in the ATP-dependent cycle of mt-Hsp70-Tim44 interaction driving mitochondrial protein import.

    PubMed Central

    Schneider, H C; Westermann, B; Neupert, W; Brunner, M

    1996-01-01

    Import of preproteins into the mitochondrial matrix is driven by the ATP-dependent interaction of mt-Hsp70 with the peripheral inner membrane import protein Tim44 and the preprotein in transit. We show that Mge1p, a co-chaperone of mt-Hsp70, plays a key role in the ATP-dependent import reaction cycle in yeast. Our data suggest a cycle in which the mt-Hsp70-Tim44 complex forms with ATP: Mge1p promotes assembly of the complex in the presence of ATP. Hydrolysis of ATP by mt-Hsp70 occurs in complex with Tim44. Mge1p is then required for the dissociation of the ADP form of mt-Hsp70 from Tim44 after release of inorganic phosphate but before release of ADP. ATP hydrolysis and complex dissociation are accompanied by tight binding of mt-Hsp70 to the preprotein in transit. Subsequently, the release of mt-Hsp70 from the polypeptide chain is triggered by Mge1p which promotes release of ADP from mt-Hsp70. Rebinding of ATP to mt-Hsp70 completes the reaction cycle. Images PMID:8918457

  10. Distribution of the receptor-anchoring protein gephyrin in the rat dentate gyrus and changes following entorhinal cortex lesion.

    PubMed

    Simbürger, E; Plaschke, M; Kirsch, J; Nitsch, R

    2000-04-01

    We analyzed the distribution of the receptor-anchoring protein gephyrin in the normal and deafferented rat dentate gyrus to investigate whether the expression of this postsynaptic protein is altered in response to the formation of new synaptic contacts. Confocal microscopy and digital image analysis revealed that in normal dentate gyrus immunolabeling was most prominent in the outer molecular layer and decreased successively in the direction of the granule cell layer. Simultaneous immunolabeling for gephyrin and cell-specific markers showed that granule cells and parvalbumin-positive interneurons express gephyrin. Large, intensely stained, gephyrin-positive clusters were distributed along distinct dendrites, and most of them were positive for parvalbumin. Calbindin-immunostained dendrites were associated with smaller, gephyrin-positive clusters. Lesion of the medial entorhinal cortex leads to deafferentiation of the middle molecular layer which resulted in an increased gephyrin immunoreactivity. These changes were due to a significantly increased concentration of the very small gephyrin-positive clusters. Parvalbumin-positive dendrites did not display any increase in co-localizing gephyrin-positive structures. The altered immunolabeling pattern persisted until 12 weeks after lesion, a time when the process of synaptic reorganization is complete. Our findings suggest that synaptogenesis following deafferentiation results in a cell-specific redistribution of gephyrin immunoreactivity at specific inhibitory synapses.

  11. Polarized Distribution of IQGAP Proteins in Gastric Parietal Cells and Their Roles in Regulated Epithelial Cell Secretion

    PubMed Central

    Zhou, Rihong; Guo, Zhen; Watson, Charles; Chen, Emily; Kong, Rong; Wang, Wenxian; Yao, Xuebiao

    2003-01-01

    Actin cytoskeleton plays an important role in the establishment of epithelial cell polarity. Cdc42, a member of Rho GTPase family, modulates actin dynamics via its regulators, such as IQGAP proteins. Gastric parietal cells are polarized epithelial cells in which regulated acid secretion occurs in the apical membrane upon stimulation. We have previously shown that actin isoforms are polarized to different membrane domains and that the integrity of the actin cytoskeleton is essential for acid secretion. Herein, we show that Cdc42 is preferentially distributed to the apical membrane of gastric parietal cells. In addition, we revealed that two Cdc42 regulators, IQGAP1 and IQGAP2, are present in gastric parietal cells. Interestingly, IQGAP2 is polarized to the apical membrane of the parietal cells, whereas IQGAP1 is mainly distributed to the basolateral membrane. An IQGAP peptide that competes with full-length IQGAP proteins for Cdc42-binding in vitro also inhibits acid secretion in streptolysin-O-permeabilized gastric glands. Furthermore, this peptide disrupts the association of IQGAP and Cdc42 with the apical actin cytoskeleton and prevents the apical membrane remodeling upon stimulation. We propose that IQGAP2 forms a link that associates Cdc42 with the apical cytoskeleton and thus allows for activation of polarized secretion in gastric parietal cells. PMID:12631726

  12. Agouti signalling protein (ASIP) gene: molecular cloning, sequence characterisation and tissue distribution in domestic goose.

    PubMed

    Zhang, J; Wang, C; Liu, Y; Liu, J; Wang, H Y; Liu, A F; He, D Q

    2016-06-01

    Agouti signalling protein (ASIP) is an endogenous antagonist of melanocortin-1 receptor (MC1R) and is involved in the regulation of pigmentation in mammals. The objective of this study was to identify and characterise the ASIP gene in domestic goose. The goose ASIP cDNA consisted of a 44-nucleotide 5'-terminal untranslated region (UTR), a 390-nucleotide open-reading frame (ORF) and a 45-nucleotide 3'-UTR. The length of goose ASIP genomic DNA was 6176 bp, including three coding exons and two introns. Bioinformatic analysis indicated that the ORF encodes a protein of 130 amino-acid residues with a molecular weight of 14.88 kDa and an isoelectric point of 9.73. Multiple sequence alignments and phylogenetic analysis showed that the amino-acid sequence of ASIP was conserved in vertebrates, especially in the avian species. RT-qPCR showed that the goose ASIP mRNA was differentially expressed in the pigment deposition tissues, including eye, foot, feather follicle, skin of the back, as well as in skin of the abdomen. The expression level of the ASIP gene in skin of the abdomen was higher than that in skin of the back. Those findings will contribute to further understanding the functions of the ASIP gene in geese plumage colouring.

  13. Mercury distribution and lipid oxidation in fish muscle: Effects of washing and isoelectric protein precipitation

    USGS Publications Warehouse

    Gong, Y.; Krabbenhoft, D.P.; Ren, L.; Egelandsdal, B.; Richards, M.P.

    2011-01-01

    Nearly all the mercury (Hg) in whole muscle from whitefish (Coregonus clupeaformis) and walleye (Sander vitreus) was present as methyl mercury (MeHg). The Hg content in whole muscle from whitefish and walleye was 0.04-0.09 and 0.14-0.81 ppm, respectively. The myofibril fraction contained approximately three-fourths of the Hg in whitefish and walleye whole muscle. The sarcoplasmic protein fraction (e.g., press juice) was the next most abundant source of Hg. Isolated myosin, triacylglycerols, and cellular membranes contained the least Hg. Protein isolates prepared by pH shifting in the presence of citric acid did not decrease Hg levels. Addition of cysteine during washing decreased the Hg content in washed muscle probably through the interaction of the sulfhydryl group in cysteine with MeHg. Primary and secondary lipid oxidation products were lower during 2 ??C storage in isolates prepared by pH shifting compared to those of washed or unwashed mince from whole muscle. This was attributed to removing some of the cellular membranes by pH shifting. Washing the mince accelerated lipid peroxide formation but decreased secondary lipid oxidation products compared to that of the unwashed mince. This suggested that there was a lipid hydroperoxide generating system that was active upon dilution of aqueous antioxidants and pro-oxidants. ?? 2011 American Chemical Society.

  14. Targeting a novel cancer-driving protein (LAPTM4B-35) by a small molecule (ETS) to inhibit cancer growth and metastasis

    PubMed Central

    Li, Maojin; Zhou, Rouli; Shan, Yi; Li, Li; Wang, Lin; Liu, Gang

    2016-01-01

    Our previous studies demonstrated that LAPTM4B-35 is overexpressed in a variety of solid cancers including hepatocellular carcinoma (HCC), and is an independent factor for prognosis. LAPTM4B-35 overexpression causes carcinogenesis and enhances cancer growth, metastasis and multidrug resistance, and thus may be a candidate for therapeutic targeting. The present study shows ethylglyoxal bisthiosemicarbazon (ETS) has effective anticancer activity through LAPTM4B-35 targeting. Bel-7402 and HepG2 cell lines from human HCC were used as cell models in which LAPTM4B-35 is highly expressed, and a human fetal liver cell line was used as a control. The results showed ETS has a specific and pronounced lethal effect on HCC cells, but not on fetal liver cells in culture. ETS also attenuated growth and metastasis of human HCC xenograft in nude mice, and extended the life span of mice with HCC. ETS induced HCC cell apoptosis, and upregulated a large number of proapoptotic genes and downregulated antiapoptotic genes. When endogenous overexpression of LAPTM4B-35 was knocked down with RNAi, the killing effect of ETS on HepG2 cells was significantly attenuated. ETS also inhibited phosphorylation of LAPTM4B-35 Tyr285, which involves in activation of the PI3K/Akt signaling pathway induced by LAPTM4B-35 overexpression. In addition, the induction of alterations in quantity of c-Myc, Bcl-2, Bax, cyclinD1 and Akt-p molecules in HepG2 cells by LAPTM4B-35 overexpression could be reversed by ETS. Conclusion: ETS is a promising candidate for treatment of HCC through LAPTM4B-35 protein targeting. PMID:27542271

  15. Protein–Protein Interfaces from Cytochrome c Oxidase I Evolve Faster than Nonbinding Surfaces, yet Negative Selection Is the Driving Force

    PubMed Central

    Aledo, Juan Carlos; Valverde, Héctor; Ruíz-Camacho, Manuel; Morilla, Ian; López, Francisco Demetrio

    2014-01-01

    Respiratory complexes are encoded by two genomes (mitochondrial DNA [mtDNA] and nuclear DNA [nDNA]). Although the importance of intergenomic coadaptation is acknowledged, the forces and constraints shaping such coevolution are largely unknown. Previous works using cytochrome c oxidase (COX) as a model enzyme have led to the so-called “optimizing interaction” hypothesis. According to this view, mtDNA-encoded residues close to nDNA-encoded residues evolve faster than the rest of positions, favoring the optimization of protein–protein interfaces. Herein, using evolutionary data in combination with structural information of COX, we show that failing to discern the effects of interaction from other structural and functional effects can lead to deceptive conclusions such as the “optimizing hypothesis.” Once spurious factors have been accounted for, data analysis shows that mtDNA-encoded residues engaged in contacts are, in general, more constrained than their noncontact counterparts. Nevertheless, noncontact residues from the surface of COX I subunit are a remarkable exception, being subjected to an exceptionally high purifying selection that may be related to the maintenance of a suitable heme environment. We also report that mtDNA-encoded residues involved in contacts with other mtDNA-encoded subunits are more constrained than mtDNA-encoded residues interacting with nDNA-encoded polypeptides. This differential behavior cannot be explained on the basis of predicted thermodynamic stability, as interactions between mtDNA-encoded subunits contribute more weakly to the complex stability than those interactions between subunits encoded by different genomes. Therefore, the higher conservation observed among mtDNA-encoded residues involved in intragenome interactions is likely due to factors other than structural stability. PMID:25359921

  16. Distribution of phospholipid transfer protein in human plasma: presence of two forms of phospholipid transfer protein, one catalytically active and the other inactive.

    PubMed

    Oka, T; Kujiraoka, T; Ito, M; Egashira, T; Takahashi, S; Nanjee, M N; Miller, N E; Metso, J; Olkkonen, V M; Ehnholm, C; Jauhiainen, M; Hattori, H

    2000-10-01

    Plasma phospholipid transfer protein (PLTP) plays an important role in the maintenance of plasma high-density lipoprotein (HDL) content and remodeling of HDL in the circulation. In the present study we have used different fractionation methods to investigate the distribution of PLTP in human plasma. A novel enzyme-linked immunosorbent assay developed during the study allowed for simultaneous assessment of both PLTP mass and activity in the fractions obtained. Size-exclusion chromatography and plasma fractionation by nondenaturing polyacrylamide gel electrophoresis (PAGE) yielded similar results demonstrating that PLTP associates in native plasma with two distinct particle populations, while ultracentrifugation with high salt leads to detachment of PLTP from lipoprotein particles and loss of a majority of its phospholipid transfer activity. Interestingly, analysis of the size-exclusion chromatography fractions demonstrated that PLTP exists in the circulation as an active population that elutes in the position of HDL corresponding to an average molecular mass of 160+/-40 kDa and an inactive form with an average mass of 520+/-120 kDa. The inactive fraction containing approximately 70% of the total PLTP protein eluted between HDL and low density lipoprotein (LDL). Thus, the two PLTP pools are associated with different types of lipoprotein particles, suggesting that the PLTP activity in circulation is modulated by the plasma lipoprotein profile and lipid composition.

  17. Driving and dementia

    PubMed Central

    Lee, Linda; Molnar, Frank

    2017-01-01

    Abstract Objective To provide primary care physicians with an approach to driving safety concerns when older persons present with memory difficulties. Sources of information The approach is based on an accredited memory clinic training program developed by the Centre for Family Medicine Primary Care Collaborative Memory Clinic. Main message One of the most challenging aspects of dementia care is the assessment of driving safety. Drivers with dementia are at higher risk of motor vehicle collisions, yet many drivers with mild dementia might be safely able to continue driving for several years. Because safe driving is dependent on multiple cognitive and functional skills, clinicians should carefully consider many factors when determining if cognitive concerns affect driving safety. Specific findings on corroborated history and office-based cognitive testing might aid in the physician’s decisions to refer for comprehensive on-road driving evaluation and whether to notify transportation authorities in accordance with provincial reporting requirements. Sensitive communication and a person-centred approach are essential. Conclusion Primary care physicians must consider many factors when determining if cognitive concerns might affect driving safety in older drivers. PMID:28115437

  18. A novel protein quality control mechanism contributes to heat shock resistance of worldwide-distributed Pseudomonas aeruginosa clone C strains.

    PubMed

    Lee, Changhan; Wigren, Edvard; Trček, Janja; Peters, Verena; Kim, Jihong; Hasni, Muhammad Sharif; Nimtz, Manfred; Lindqvist, Ylva; Park, Chankyu; Curth, Ute; Lünsdorf, Heinrich; Römling, Ute

    2015-11-01

    Pseudomonas aeruginosa is a highly successful nosocomial pathogen capable of causing a wide variety of infections with clone C strains most prevalent worldwide. In this study, we initially characterize a molecular mechanism of survival unique to clone C strains. We identified a P. aeruginosa clone C-specific genomic island (PACGI-1) that contains the highly expressed small heat shock protein sHsp20c, the founding member of a novel subclass of class B bacterial small heat shock proteins. sHsp20c and adjacent gene products are involved in resistance against heat shock. Heat stable sHsp20c is unconventionally expressed in stationary phase in a wide temperature range from 20 to 42°C. Purified sHsp20c has characteristic features of small heat shock protein class B as it is monodisperse, forms sphere-like 24-meric oligomers and exhibits significant chaperone activity. As the P. aeruginosa clone C population is significantly more heat shock resistant than genetically unrelated P. aeruginosa strains without sHsp20c, the horizontally acquired shsp20c operon might contribute to the survival of worldwide-distributed clone C strains.

  19. Prediction of fatty acid-binding residues on protein surfaces with three-dimensional probability distributions of interacting atoms.

    PubMed

    Mahalingam, Rajasekaran; Peng, Hung-Pin; Yang, An-Suei

    2014-08-01

    Protein-fatty acid interaction is vital for many cellular processes and understanding this interaction is important for functional annotation as well as drug discovery. In this work, we present a method for predicting the fatty acid (FA)-binding residues by using three-dimensional probability density distributions of interacting atoms of FAs on protein surfaces which are derived from the known protein-FA complex structures. A machine learning algorithm was established to learn the characteristic patterns of the probability density maps specific to the FA-binding sites. The predictor was trained with five-fold cross validation on a non-redundant training set and then evaluated with an independent test set as well as on holo-apo pair's dataset. The results showed good accuracy in predicting the FA-binding residues. Further, the predictor developed in this study is implemented as an online server which is freely accessible at the following website, http://ismblab.genomics.sinica.edu.tw/.

  20. Laminin isoforms: biological roles and effects on the intracellular distribution of nuclear proteins in intestinal epithelial cells

    SciTech Connect

    Turck, Natacha; Gross, Isabelle; Gendry, Patrick; Stutzmann, Jeanne; Freund, Jean-Noel; Kedinger, Michele; Simon-Assmann, Patricia; Launay, Jean-Francois . E-mail: Jean-Francois.Launay@inserm.u-strasbg.fr

    2005-02-15

    Laminins are structurally and functionally major components of the extracellular matrix. Four isoforms of laminins (laminin-1, -2, -5 and -10) are expressed in a specific pattern along the crypt-villus axis of the intestine. Previous works indicated that expression of these isoforms is developmentally regulated and that laminins could modulate the behaviour of intestinal cells, but the exact role of each isoform remained unclear. Here, we report the first systematic analysis of the cellular functions of the four isoforms using the human colon adenocarcinoma Caco2/TC7 cell line as a model. We compared the respective abilities of each isoform to modulate adhesion, proliferation and differentiation of intestinal epithelial cells. We found that the isoforms were functionally distinct, with laminin-10 being the most adhesive substratum, laminin-2, laminin-5 and laminin-10 enhancing cellular proliferation and at the opposite, laminin-1 stimulating intestinal cell differentiation. To begin to characterise the molecular events induced by the different isoforms, we examined by immunofluorescence the intracellular distribution of several nuclear proteins, recently highlighted by a nuclear proteomic approach. We observed clear nucleocytoplasmic redistribution of these proteins, which depended on the laminin isoform. These results provide evidence for a distinct functional role of laminins in intestinal cell functions characterised by specific localisation of nuclear proteins.

  1. Effect of FCCP on tight junction permeability and cellular distribution of ZO-1 protein in epithelial (MDCK) cells.

    PubMed

    Li, C X; Poznansky, M J

    1990-12-14

    The effect of the uncoupler of oxidative phosphorylation, FCCP (carbonylcyanide p-trifluoromethoxyphenylhydrazone), on the tight junction of Madin-Darby canine kidney cells was examined. FCCP induced an abrupt decrease in the transepithelial electrical resistance of the confluent monolayers over a period of 20 s. When FCCP was withdrawn from the incubation medium, the monolayer resistance recovered to close to the original level in less than 2 h. Staining of the tight junction-associated protein ZO-1 showed that the changes in transepithelial electrical resistance were accompanied by a diffusing of the protein away from cell peripheries and a reconcentration to the tight junction areas following resistance recovery. Intracellular pH was decreased by FCCP on a similar time-scale with no obvious changes in ATP levels over this time-course. These data suggest that the uncoupler FCCP has a profound effect on tight junction permeability and cellular distribution of the tight junction protein ZO-1 in the epithelial cells and that it probably acts by breaking down proton gradients and altering intracellular pH.

  2. Effect of sterol carrier protein-2 expression on sphingolipid distribution in plasma membrane lipid rafts/caveolae.

    PubMed

    Atshaves, Barbara P; Jefferson, John R; McIntosh, Avery L; Gallegos, Adalberto; McCann, Bonnie M; Landrock, Kerstin K; Kier, Ann B; Schroeder, Friedhelm

    2007-10-01

    Although sphingolipids are highly important signaling molecules enriched in lipid rafts/caveolae, relatively little is known regarding factors such as sphingolipid binding proteins that may regulate the distribution of sphingolipids to lipid rafts/caveolae of living cells. Since early work demonstrated that sterol carrier protein-2 (SCP-2) enhanced glycosphingolipid transfer from membranes in vitro, the effect of SCP-2 expression on sphingolipid distribution to lipid rafts/caveolae in living cells was examined. Using a non-detergent affinity chromatography method to isolate lipid rafts/caveolae and non-rafts from purified L-cell plasma membranes, it was shown that lipid rafts/caveolae were highly enriched in multiple sphingolipid species including ceramides, acidic glycosphingolipids (ganglioside GM1); neutral glycosphingolipids (monohexosides, dihexosides, globosides), and sphingomyelin as compared to non-raft domains. SCP-2 overexpression further enriched the content of total sphingolipids and select sphingolipid species in the lipid rafts/caveolae domains. Analysis of fluorescence binding and displacement data revealed that purified human recombinant SCP-2 exhibited high binding affinity (nanomolar range) for all sphingolipid classes tested. The binding affinity decreased in the following order: ceramides > acidic glycosphingolipid (ganglioside GM1) > neutral glycosphingolipid (monohexosides, hexosides, globosides) > sphingomyelin. Enrichment of individual sphingolipid classes to lipid rafts/caveolae versus non-rafts in SCP-2 expressing plasma membranes followed closely with those classes most strongly bound to SCP-2 (ceramides, GM1 > the neutral glycosphingolipids (monohexosides, dihexosides, and globosides) > sphingomyelin). Taken together these data suggested that SCP-2 acts to selectively regulate sphingolipid distribution to lipid rafts/caveolae in living cells.

  3. Crude protein, ash, phosphorus, neutral detergent fiber and starch concentrations in particle size distributions of corn steam flaked to varying bulk densities

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The particle size distribution that results from steam flaking cereal grains could be related to differences in the chemical composition of steam-flaked (SF) vs. unprocessed grain. Particle size distribution and associated crude protein (CP), phosphorus (P), neutral detergent fiber (NDF), and starch...

  4. Chemical composition, molecular weight distribution, secondary structure and effect of NaCl on functional properties of walnut (Juglans regia L) protein isolates and concentrates.

    PubMed

    Mao, Xiao-Ying; Hua, Yu-Fei

    2014-08-01

    Chemical composition, molecular weight distribution, secondary structure and effect of sodium chloride concentration on functional properties of walnut protein isolates, concentrates and defatted walnut flour were study. Compared with walnut protein concentrates (75.6%) and defatted walnut flour (52.5%), walnut protein isolates contain a relatively high amount of protein (90.5%). The yield of walnut protein isolates and concentrates was 43.2% and 76.6%, respectively. In molecular weight distribution study, Walnut protein isolates showed one peak with molecular weight of 106.33 KDa (100%) and walnut protein concentrates showed four peaks with molecular weight of 16,725 KDa (0.8%),104.943 KDa(63.9%), 7.3 KDa (11.4%), 2.6 KDa (23.9%). The secondary structure of walnut protein isolates was similar to that of walnut protein concentrates, but was differ from that of defatted walnut flour. The addition of sodium chloride (0 ~ 1 M) could improve the functionality of walnut protein concentrates, isolates and defatted walnut flour. The maximum solubility, water absorption capacity, emulsifying properties and foaming properties of walnut protein isolates, concentrates and defatted walnut flour were at sodium chloride solutions of 1.0 M, 0.6 M, 0.4 M, 0.6 M, respectively. The solubility of walnut protein concentrates (32.5%) in distilled water with 0 M sodium chloride was lower than that of walnut protein isolates (35.2%). The maximum solubility of walnut protein isolates, concentrates and defatted walnut flour in solution were 36.8%, 33.7% and 9.6% at 1.0 M sodium chloride solutions, respectively. As compared with other vegetable proteins, walnut protein isolates and concentrates exhibited better emulsifying properties and foam stability.

  5. High sensitivity C-reactive protein distribution in the elderly: the Bambuí Cohort Study, Brazil

    PubMed Central

    Assunção, L.G.S.; Eloi-Santos, S.M.; Peixoto, S.V.; Lima-Costa, M.F.; Vidigal, P.G.

    2012-01-01

    The measurement of the serum concentration of the acute-phase reactant C-reactive protein (CRP) provides a useful marker in clinical practice. However, the distribution of CRP is not available for all age and population groups. This study assessed the distribution of high sensitivity CRP (hs-CRP) by gender and age in 1470 elderly individuals from a Brazilian community that participates in the Bambuí Cohort Study. Blood samples were collected after 12 h of fasting and serum samples were stored at -70°C. Measurements were made with a commercial hs-CRP immunonephelometric instrument. More than 50% of the results were above 3.0 mg/L for both genders. Mean hs-CRP was higher in women (3.62 ± 2.58 mg/L) than in men (3.03 ± 2.50 mg/L). This difference was observed for all ages, except for the over-80 age group. This is the first population-based study to describe hs-CRP values in Latin American elderly subjects. Our results indicate that significant gender differences exist in the distribution of hs-CRP, and suggest that gender-specific cut-off points for hs-CRP would be necessary for the prediction of cardiovascular risks. PMID:23011406

  6. Detecting seasonal variation of antifreeze protein distribution in Rhagium mordax using immunofluorescence and high resolution microscopy.

    PubMed

    Buch, J L; Ramløv, H

    2017-02-01

    Larvae of the blackspotted pliers support beetle, Rhagium mordax, were collected monthly, for the duration of 2012 and fixed. The larvae were embedded in paraffin wax and sectioned. Using fluorophore-coupled antibodies specific to the R. mordax antifreeze protein, RmAFP1, sections were visualised with UV reflected light microscopy. An automated software analysis method was developed in order to discard autofluorescence, and quantify fluorescence from bound antibodies. The results show that R. mordax cuticle and gut exhibit a higher degree of fluorophore-bound fluorescence during summer, than in the cold months. It is hypothesised that R. mordax stores RmAFP1 in, or near, the fat body during times when freeze avoidance is not needed.

  7. Drive System Research

    NASA Technical Reports Server (NTRS)

    Handschuh, Robert F.

    2007-01-01

    An overview of the NASA Glenn Research Center Drive Systems Research will be presented. The primary purpose of this research is to improve performance, reliability, and integrity of aerospace drive systems and space mechanisms. The research is conducted through a combination of in-house, academia, and through contractors. Research is conducted through computer code development and validated through component and system testing. The drive system activity currently has four major thrust areas including: thermal behavior of high speed gearing, health and usage monitoring, advanced components, and space mechanisms.

  8. Vision and Driving

    PubMed Central

    Owsley, Cynthia; McGwin, Gerald

    2010-01-01

    Driving is the primary means of personal travel in many countries and is relies heavily on vision for its successful execution. Research over the past few decades has addressed the role of vision in driver safety (motor vehicle collision involvement) and in driver performance (both on-road and using interactive simulators in the laboratory). Here we critically review what is currently known about the role of various aspects of visual function in driving. We also discuss translational research issues on vision screening for licensure and re-licensure and rehabilitation of visually impaired persons who want to drive. PMID:20580907

  9. The Test Drive

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This image taken at NASA's Jet Propulsion Laboratory shows engineers rehearsing the sol 133 (June 8, 2004) drive into 'Endurance' crater by NASA's Mars Exploration Rover Opportunity. Engineers and scientists have recreated the martian surface and slope the rover will encounter using a combination of bare and thinly sand-coated rocks, simulated martian 'blueberries' and a platform tilted at a 25-degree angle. The results of this test convinced engineers that the rover was capable of driving up and down a straight slope before it attempted the actual drive on Mars.

  10. Distribution of adenylate cyclase and GTP-binding proteins in hepatic plasma membranes.

    PubMed

    Dixon, B S; Sutherland, E; Alexander, A; Nibel, D; Simon, F R

    1993-10-01

    Hepatic membrane subfractions prepared from control rats demonstrated forskolin (FSK)-stimulated adenylate cyclase activity in the basolateral (sinusoidal) but not apical (canalicular) plasma membrane. After bile duct ligation (BDL) for 12 or 24 h, there was an increase in FSK-stimulated adenylate cyclase activity in the apical membrane (54.2 +/- 3.9 pmol.mg-1 x min-1). The mechanism for this increase was explored further. ATP hydrolysis was found to be much higher in the apical than the basolateral membrane. Increasing the ATP levels in the assay enhanced apical membrane adenylate cyclase activity (10.5 +/- 0.2 pmol.mg-l.min-1); however, total adenosinetriphosphatase (ATPase) activity was not altered after BDL. Extraction of the apical membrane with bile acids or other detergents resulted in a two- to threefold increase in adenylate cyclase activity (30.6 +/- 3.6 pmol.mg-1 x min-1; detergent C12E8) This suggested that bile duct ligation was acting via the detergent-like action of bile acids to uncover latent adenylate cyclase activity on apical membranes. Further studies demonstrated that both BDL and detergent extraction also enhanced toxin-directed ADP-ribosylation of Gs alpha (cholera toxin) and Gi alpha (pertussis toxin) in the apical but not the basolateral membrane. After BDL, Gi alpha was found to be twofold greater in the apical membrane than the basolateral membrane. Immunoblotting using specific G protein antibodies further confirmed that apical membranes from control rats had a higher concentration of Gi1, 2 alpha and beta and slightly elevated levels of Gi3 alpha and Gs alpha compared with the basolateral membrane. The results demonstrate that adenylate cyclase and heterotrimeric GTP-binding proteins are present on the apical membrane, but measurement of their functional activity requires detergent permeabilization of apical membrane vesicles and is limited by the presence of high ATPase activity.

  11. Matrix Gla protein in Xenopus laevis: molecular cloning, tissue distribution, and evolutionary considerations.

    PubMed

    Cancela, M L; Ohresser, M C; Reia, J P; Viegas, C S; Williamson, M K; Price, P A

    2001-09-01

    Matrix Gla protein (MGP) belongs to the family of vitamin K-dependent, Gla-containing proteins and in higher vertebrates, is found in the extracellular matrix of mineralized tissues and soft tissues. MGP synthesis is highly regulated at the transcription and posttranscription levels and is now known to be involved in the regulation of extracellular matrix calcification and maintenance of cartilage and soft tissue integrity during growth and development. However, its mode of action at the molecular level remains unknown. Because there is a large degree of conservation between amino acid sequences of shark and human MGP, the function of MGP probably has been conserved throughout evolution. Given the complexity of the mammalian system, the study of MGP in a lower vertebrate might be advantageous to relate the onset of MGP expression with specific events during development. Toward this goal, MGP was purified from Xenopus long bones and its N-terminal amino acid sequence was determined and used to clone the Xenopus MGP complementary DNA (cDNA) by a mixture of reverse-transcription (RT)- and 5'- rapid amplification of cDNA ends (RACE)-polymerase chain reaction (PCR). MGP messenger RNA (mRNA) was present in all tissues analyzed although predominantly expressed in Xenopus bone and heart and its presence was detected early in development at the onset of chondrocranium development and long before the appearance of the first calcified structures and metamorphosis. These results show that in this system, as in mammals, MGP may be required to delay or prevent mineralization of cartilage and soft tissues during the early stages of development and indicate that Xenopus is an adequate model organism to further study MGP function during growth and development.

  12. Distribution and concentration of cholesteryl ester transfer protein in plasma of normolipemic subjects.

    PubMed

    Marcel, Y L; McPherson, R; Hogue, M; Czarnecka, H; Zawadzki, Z; Weech, P K; Whitlock, M E; Tall, A R; Milne, R W

    1990-01-01

    A MAb (TP-2) directed against human cholesteryl ester transfer protein (CETP) has been applied to the development of a competitive solid-phase RIA. Experiments with immobilized CETP have shown that upon incubation with plasma or HDL in the presence of Tween (0.05%) apo A-I (but not apo A-II) binds to CETP while TP-2 binding to CETP is concomitantly decreased. With high detergent concentration (0.5% Triton), the interference is eliminated and a specific RIA in which all plasma CETP fractions have the same affinity can be obtained. Plasma levels of CETP, apo A-I, lipids, and lipoproteins were measured in 50 normolipemic, healthy subjects of both sexes. CETP levels varied nearly fourfold with a mean value of 1.7 micrograms/ml. CETP was positively correlated only with apo A-I (r = 0.38) and HDL-triglyceride (r = 0.39). In 29 other normolipemic subjects, where several apolipoproteins were also measured, significant correlations of CETP with apo A-I (0.41), apo E (0.43), and HDL-cholesterol (0.41) were observed, but there was no significant relationship between CETP and either apo A-II, B, or D. In other experiments CETP was shown to be present mostly in HDL3 and VHDL, to display exclusively an alpha 2-electrophoretic migration, and to occur within discrete particles ranging in size from 129 to 154 kD. In conclusion, the association of CETP with apo A-I-containing lipoproteins probably explains the correlation between CETP and apo A-I levels. The relationship between CETP and apo E suggests either a common metabolism or a specific cooperative role in cholesterol ester transport for these proteins.

  13. Distribution of carbon isotopes in amino acids of protein fraction of micro-organisms as a means of studying the mechanisms of their biosynthesis in the cell

    SciTech Connect

    Ivlev, A.A.

    1986-04-10

    The intramolecular distribution of carbon isotopes in the amino acids of the protein fraction of a number of photosynthesizing microorganisms was analyzed using the previously proposed model of carbon isotope fractionation in the cell. A correlation was found between the distributions of the isotopes in the amino acids and the pathways and sequence of their synthesis in the cell cycle. The feasibility of using the isotopic distributions of metabolites for a study of the temporal organization of metabolism in the cell is illustrated.

  14. Uneven HAK/KUP/KT Protein Diversity Among Angiosperms: Species Distribution and Perspectives

    PubMed Central

    Nieves-Cordones, Manuel; Ródenas, Reyes; Chavanieu, Alain; Rivero, Rosa M.; Martinez, Vicente; Gaillard, Isabelle; Rubio, Francisco

    2016-01-01

    HAK/KUP/KT K+ transporters have been widely associated with K+ transport across membranes in bacteria, fungi, and plants. Indeed some members of the plant HAK/KUP/KT family contribute to root K+ uptake, notably at low external concentrations. Besides such role in acquisition, several studies carried out in Arabidopsis have shown that other members are also involved in developmental processes. With the publication of new plant genomes, a growing interest on plant species other than Arabidopsis has become evident. In order to understand HAK/KUP/KT diversity in these new plant genomes, we discuss the evolutionary trends of 913 HAK/KUP/KT sequences identified in 46 genomes revealing five major groups with an uneven distribution among angiosperms, notably between dicotyledonous and monocotyledonous species. This information evidenced the richness of crop genomes in HAK/KUP/KT transporters and supports their study for unraveling novel physiological roles of such transporters in plants. PMID:26904084

  15. Uneven HAK/KUP/KT Protein Diversity Among Angiosperms: Species Distribution and Perspectives.

    PubMed

    Nieves-Cordones, Manuel; Ródenas, Reyes; Chavanieu, Alain; Rivero, Rosa M; Martinez, Vicente; Gaillard, Isabelle; Rubio, Francisco

    2016-01-01

    HAK/KUP/KT K(+) transporters have been widely associated with K(+) transport across membranes in bacteria, fungi, and plants. Indeed some members of the plant HAK/KUP/KT family contribute to root K(+) uptake, notably at low external concentrations. Besides such role in acquisition, several studies carried out in Arabidopsis have shown that other members are also involved in developmental processes. With the publication of new plant genomes, a growing interest on plant species other than Arabidopsis has become evident. In order to understand HAK/KUP/KT diversity in these new plant genomes, we discuss the evolutionary trends of 913 HAK/KUP/KT sequences identified in 46 genomes revealing five major groups with an uneven distribution among angiosperms, notably between dicotyledonous and monocotyledonous species. This information evidenced the richness of crop genomes in HAK/KUP/KT transporters and supports their study for unraveling novel physiological roles of such transporters in plants.

  16. Solvent viscosity dependence of the folding rate of a small protein: distributed computing study.

    PubMed

    Zagrovic, Bojan; Pande, Vijay

    2003-09-01

    By using distributed computing techniques and a supercluster of more than 20,000 processors we simulated folding of a 20-residue Trp Cage miniprotein in atomistic detail with implicit GB/SA solvent at a variety of solvent viscosities (gamma). This allowed us to analyze the dependence of folding rates on viscosity. In particular, we focused on the low-viscosity regime (values below the viscosity of water). In accordance with Kramers' theory, we observe approximately linear dependence of the folding rate on 1/gamma for values from 1-10(-1)x that of water viscosity. However, for the regime between 10(-4)-10(-1)x that of water viscosity we observe power-law dependence of the form k approximately gamma(-1/5). These results suggest that estimating folding rates from molecular simulations run at low viscosity under the assumption of linear dependence of rate on inverse viscosity may lead to erroneous results.

  17. Light-sheet fluorescence imaging to localize cardiac lineage and protein distribution