Self-assembled nanogel of hydrophobized dendritic dextrin for protein delivery.

PubMed

Ozawa, Yayoi; Sawada, Shin-Ichi; Morimoto, Nobuyuki; Akiyoshi, Kazunari

2009-07-07

Highly branched cyclic dextrin derivatives (CH-CDex) that are partly substituted with cholesterol groups have been synthesized. The CH-CDex forms monodisperse and stable nanogels with a hydrodynamic radii of approximately 10 nm by the self-assembly of 4-6 CH-CDex macromolecules in water. The CH-CDex nanogels spontaneously trap 10-16 molecules of fluorescein isothiocyanate-labeled insulin (FITC-Ins). The complex shows high colloidal stability: no dissociation of trapped insulin is observed after at least 1 month in phosphate buffer (0.1 M, pH 8.0). In the presence of bovine serum albumin (BSA, 50 mg . mL(-1)), which is a model blood system, the FITC-Ins trapped in the nanogels is continuously released ( approximately 20% at 12 h) without burst release. The high-density nanogel structure derived from the highly branched CDex significantly affects the stability of the nanogel-protein complex.

The sensitivity of gas-phase models of dense interstellar clouds to changes in dissociative recombination branching ratios

NASA Technical Reports Server (NTRS)

Millar, T. J.; Defrees, D. J.; Mclean, A. D.; Herbst, E.

1988-01-01

The approach of Bates to the determination of neutral product branching ratios in ion-electron dissociative recombination reactions has been utilized in conjunction with quantum chemical techniques to redetermine branching ratios for a wide variety of important reactions of this class in dense interstellar clouds. The branching ratios have then been used in a pseudo time-dependent model calculation of the gas phase chemistry of a dark cloud resembling TMC-1 and the results compared with an analogous model containing previously used branching ratios. In general, the changes in branching ratios lead to stronger effects on calculated molecular abundances at steady state than at earlier times and often lead to reductions in the calculated abundances of complex molecules. However, at the so-called 'early time' when complex molecule synthesis is most efficient, the abundances of complex molecules are hardly affected by the newly used branching ratios.

Computational models of airway branching morphogenesis.

PubMed

Varner, Victor D; Nelson, Celeste M

2017-07-01

The bronchial network of the mammalian lung consists of millions of dichotomous branches arranged in a highly complex, space-filling tree. Recent computational models of branching morphogenesis in the lung have helped uncover the biological mechanisms that construct this ramified architecture. In this review, we focus on three different theoretical approaches - geometric modeling, reaction-diffusion modeling, and continuum mechanical modeling - and discuss how, taken together, these models have identified the geometric principles necessary to build an efficient bronchial network, as well as the patterning mechanisms that specify airway geometry in the developing embryo. We emphasize models that are integrated with biological experiments and suggest how recent progress in computational modeling has advanced our understanding of airway branching morphogenesis. Copyright © 2016 Elsevier Ltd. All rights reserved.

The role of branch architecture in assimilate production and partitioning: the example of apple (Malus domestica)

PubMed Central

Fanwoua, Julienne; Bairam, Emna; Delaire, Mickael; Buck-Sorlin, Gerhard

2014-01-01

Understanding the role of branch architecture in carbon production and allocation is essential to gain more insight into the complex process of assimilate partitioning in fruit trees. This mini review reports on the current knowledge of the role of branch architecture in carbohydrate production and partitioning in apple. The first-order carrier branch of apple illustrates the complexity of branch structure emerging from bud activity events and encountered in many fruit trees. Branch architecture influences carbon production by determining leaf exposure to light and by affecting leaf internal characteristics related to leaf photosynthetic capacity. The dynamics of assimilate partitioning between branch organs depends on the stage of development of sources and sinks. The sink strength of various branch organs and their relative positioning on the branch also affect partitioning. Vascular connections between branch organs determine major pathways for branch assimilate transport. We propose directions for employing a modeling approach to further elucidate the role of branch architecture on assimilate partitioning. PMID:25071813

Branched-Chain Amino and Keto Acid Biochemistry and Cellular Biology in Central Nervous System Diseases

DTIC Science & Technology

2009-05-21

pyruvate dehydrogenase complex (PDC) and 2-oxo- glutarate dehydrogenase complex. These dehydrogenase complexes share the same basic structure, perform the...Science 312 (2006) 927-930. [20] J. Dancis, M. Levitz, R.G. Westall, Maple syrup urine disease: branched- chain keto- aciduria , Pediatrics 25 (1960...2127 2128 Dancis J, Levitz M, Westall RG. 1960. Maple syrup urine disease: branched-chain keto- aciduria . Pediatrics 25:72-9. Danner DJ, Lemmon

Branch length estimation and divergence dating: estimates of error in Bayesian and maximum likelihood frameworks.

PubMed

Schwartz, Rachel S; Mueller, Rachel L

2010-01-11

Estimates of divergence dates between species improve our understanding of processes ranging from nucleotide substitution to speciation. Such estimates are frequently based on molecular genetic differences between species; therefore, they rely on accurate estimates of the number of such differences (i.e. substitutions per site, measured as branch length on phylogenies). We used simulations to determine the effects of dataset size, branch length heterogeneity, branch depth, and analytical framework on branch length estimation across a range of branch lengths. We then reanalyzed an empirical dataset for plethodontid salamanders to determine how inaccurate branch length estimation can affect estimates of divergence dates. The accuracy of branch length estimation varied with branch length, dataset size (both number of taxa and sites), branch length heterogeneity, branch depth, dataset complexity, and analytical framework. For simple phylogenies analyzed in a Bayesian framework, branches were increasingly underestimated as branch length increased; in a maximum likelihood framework, longer branch lengths were somewhat overestimated. Longer datasets improved estimates in both frameworks; however, when the number of taxa was increased, estimation accuracy for deeper branches was less than for tip branches. Increasing the complexity of the dataset produced more misestimated branches in a Bayesian framework; however, in an ML framework, more branches were estimated more accurately. Using ML branch length estimates to re-estimate plethodontid salamander divergence dates generally resulted in an increase in the estimated age of older nodes and a decrease in the estimated age of younger nodes. Branch lengths are misestimated in both statistical frameworks for simulations of simple datasets. However, for complex datasets, length estimates are quite accurate in ML (even for short datasets), whereas few branches are estimated accurately in a Bayesian framework. Our reanalysis of empirical data demonstrates the magnitude of effects of Bayesian branch length misestimation on divergence date estimates. Because the length of branches for empirical datasets can be estimated most reliably in an ML framework when branches are <1 substitution/site and datasets are > or =1 kb, we suggest that divergence date estimates using datasets, branch lengths, and/or analytical techniques that fall outside of these parameters should be interpreted with caution.

Mapping and Quantification of Vascular Branching in Plants, Animals and Humans by VESGEN Software

NASA Technical Reports Server (NTRS)

Parsons-Wingerter, Patricia A.; Vickerman, Mary B.; Keith, Patricia A.

2010-01-01

Humans face daunting challenges in the successful exploration and colonization of space, including adverse alterations in gravity and radiation. The Earth-determined biology of humans, animals and plants is significantly modified in such extraterrestrial environments. One physiological requirement shared by humans with larger plants and animals is a complex, highly branching vascular system that is dynamically responsive to cellular metabolism, immunological protection and specialized cellular/tissue function. The VESsel GENeration (VESGEN) Analysis has been developed as a mature beta version, pre-release research software for mapping and quantification of the fractal-based complexity of vascular branching. Alterations in vascular branching pattern can provide informative read-outs of altered vascular regulation. Originally developed for biomedical applications in angiogenesis, VESGEN 2D has provided novel insights into the cytokine, transgenic and therapeutic regulation of angiogenesis, lymphangiogenesis and other microvascular remodeling phenomena. Vascular trees, networks and tree-network composites are mapped and quantified. Applications include disease progression from clinical ophthalmic images of the human retina; experimental regulation of vascular remodeling in the mouse retina; avian and mouse coronary vasculature, and other experimental models in vivo. We envision that altered branching in the leaves of plants studied on ISS such as Arabidopsis thaliana cans also be analyzed.

Mapping and Quantification of Vascular Branching in Plants, Animals and Humans by VESGEN Software

NASA Technical Reports Server (NTRS)

Parsons-Wingerter, P. A.; Vickerman, M. B.; Keith, P. A.

2010-01-01

Humans face daunting challenges in the successful exploration and colonization of space, including adverse alterations in gravity and radiation. The Earth-determined biology of plants, animals and humans is significantly modified in such extraterrestrial environments. One physiological requirement shared by larger plants and animals with humans is a complex, highly branching vascular system that is dynamically responsive to cellular metabolism, immunological protection and specialized cellular/tissue function. VESsel GENeration (VESGEN) Analysis has been developed as a mature beta version, pre-release research software for mapping and quantification of the fractal-based complexity of vascular branching. Alterations in vascular branching pattern can provide informative read-outs of altered vascular regulation. Originally developed for biomedical applications in angiogenesis, VESGEN 2D has provided novel insights into the cytokine, transgenic and therapeutic regulation of angiogenesis, lymphangiogenesis and other microvascular remodeling phenomena. Vascular trees, networks and tree-network composites are mapped and quantified. Applications include disease progression from clinical ophthalmic images of the human retina; experimental regulation of vascular remodeling in the mouse retina; avian and mouse coronary vasculature, and other experimental models in vivo. We envision that altered branching in the leaves of plants studied on ISS such as Arabidopsis thaliana cans also be analyzed.

Ongoing Fixed Wing Research within the NASA Langley Aeroelasticity Branch

NASA Technical Reports Server (NTRS)

Bartels, Robert; Chwalowski, Pawel; Funk, Christie; Heeg, Jennifer; Hur, Jiyoung; Sanetrik, Mark; Scott, Robert; Silva, Walter; Stanford, Bret; Wiseman, Carol

2015-01-01

The NASA Langley Aeroelasticity Branch is involved in a number of research programs related to fixed wing aeroelasticity and aeroservoelasticity. These ongoing efforts are summarized here, and include aeroelastic tailoring of subsonic transport wing structures, experimental and numerical assessment of truss-braced wing flutter and limit cycle oscillations, and numerical modeling of high speed civil transport configurations. Efforts devoted to verification, validation, and uncertainty quantification of aeroelastic physics in a workshop setting are also discussed. The feasibility of certain future civil transport configurations will depend on the ability to understand and control complex aeroelastic phenomena, a goal that the Aeroelasticity Branch is well-positioned to contribute through these programs.

On an Integral with Two Branch Points

ERIC Educational Resources Information Center

de Oliveira, E. Capelas; Chiacchio, Ary O.

2006-01-01

The paper considers a class of real integrals performed by using a convenient integral in the complex plane. A complex integral containing a multi-valued function with two branch points is transformed into another integral containing a pole and a unique branch point. As a by-product we obtain a new class of integrals which can be calculated in a…

BRANCHED FIBERS FROM OLD FAST-TWITCH DYSTROPHIC MUSCLES ARE THE SITES OF TERMINAL DAMAGE IN MUSCULAR DYSTROPHY.

PubMed

Kiriaev, Leonit; Kueh, Sindy; Morley, John W; North, Kathryn N; Houweling, Peter J; Head, Stewart I

2018-02-07

A striking pathological feature of dystrophinopathies is the presence of morphologically abnormal branched skeletal muscle fibers. The deterioration of muscle contractile function in Duchenne muscular dystrophy is accompanied by both an increase in number and complexity of these branched fibers. We propose that when number and complexity of branched fibers reaches a critical threshold, "tipping point" the branches in and of themselves are the site of contraction-induced rupture. In the present study, we use the dystrophic mdx mouse and littermate controls to study the pre-diseased dystrophic fast-twitch EDL muscle at 2-3-weeks, the peak myonecrotic phase at 6-9 weeks and finally "old" at 58-112 weeks. Using a combination of isolated muscle function contractile measurements coupled with single fiber imaging and confocal microscope imaging of cleared whole muscles we identified a distinct pathophysiology; acute fiber rupture at branch nodes, which occurs in "old" fast-twitch EDL muscle approaching the end stage of the dystrophinopathy muscle disease, where the EDL muscles are entirely composed of complexed branched fibers. This evidence supports our concept of "tipping point" where the number and extent of fiber branching reaches a level where the branching itself terminally compromises muscle function, irrespective of the absence of dystrophin.

The activity state of the branched-chain 2-oxo acid dehydrogenase complex in rat tissues.

PubMed Central

Wagenmakers, A J; Schepens, J T; Veldhuizen, J A; Veerkamp, J H

1984-01-01

An assay is described to define the proportion of the branched-chain 2-oxo acid dehydrogenase complex that is present in the active state in rat tissues. Activities are measured in homogenates in two ways: actual activities, present in tissues, by blocking both the kinase and phosphatase of the enzyme complex during homogenization, preincubation, and incubation with 1-14C-labelled branched-chain 2-oxo acid, and total activities by blocking only the kinase during the 5 min preincubation (necessary for activation). The kinase is blocked by 5 mM-ADP and absence of Mg2+ and the phosphatase by the simultaneous presence of 50 mM-NaF. About 6% of the enzyme is active in skeletal muscle of fed rats, 7% in heart, 20% in diaphragm, 47% in kidney, 60% in brain and 98% in liver. An entirely different assay, which measures activities in crude tissue extracts before and after treatment with a broad-specificity protein phosphatase, gave similar results for heart, liver and kidney. Advantages of our assay with homogenates are the presence of intact mitochondria, the simplicity, the short duration and the high sensitivity. The actual activities measured indicate that the degradation of branched-chain 2-oxo acids predominantly occurs in liver and kidney and is limited in skeletal muscle in the fed state. PMID:6430280

The activity state of the branched-chain 2-oxo acid dehydrogenase complex in rat tissues.

PubMed

Wagenmakers, A J; Schepens, J T; Veldhuizen, J A; Veerkamp, J H

1984-05-15

An assay is described to define the proportion of the branched-chain 2-oxo acid dehydrogenase complex that is present in the active state in rat tissues. Activities are measured in homogenates in two ways: actual activities, present in tissues, by blocking both the kinase and phosphatase of the enzyme complex during homogenization, preincubation, and incubation with 1-14C-labelled branched-chain 2-oxo acid, and total activities by blocking only the kinase during the 5 min preincubation (necessary for activation). The kinase is blocked by 5 mM-ADP and absence of Mg2+ and the phosphatase by the simultaneous presence of 50 mM-NaF. About 6% of the enzyme is active in skeletal muscle of fed rats, 7% in heart, 20% in diaphragm, 47% in kidney, 60% in brain and 98% in liver. An entirely different assay, which measures activities in crude tissue extracts before and after treatment with a broad-specificity protein phosphatase, gave similar results for heart, liver and kidney. Advantages of our assay with homogenates are the presence of intact mitochondria, the simplicity, the short duration and the high sensitivity. The actual activities measured indicate that the degradation of branched-chain 2-oxo acids predominantly occurs in liver and kidney and is limited in skeletal muscle in the fed state.

Actin filament curvature biases branching direction

NASA Astrophysics Data System (ADS)

Wang, Evan; Risca, Viviana; Chaudhuri, Ovijit; Chia, Jia-Jun; Geissler, Phillip; Fletcher, Daniel

2012-02-01

Actin filaments are key components of the cellular machinery, vital for a wide range of processes ranging from cell motility to endocytosis. Actin filaments can branch, and essential in this process is a protein complex known as the Arp2/3 complex, which nucleate new ``daughter'' filaments from pre-existing ``mother'' filaments by attaching itself to the mother filament. Though much progress has been made in understanding the Arp2/3-actin junction, some very interesting questions remain. In particular, F-actin is a dynamic polymer that undergoes a wide range of fluctuations. Prior studies of the Arp2/3-actin junction provides a very static notion of Arp2/3 binding. The question we ask is how differently does the Arp2/3 complex interact with a straight filament compared to a bent filament? In this study, we used Monte Carlo simulations of a surface-tethered worm-like chain to explore possible mechanisms underlying the experimental observation that there exists preferential branch formation by the Arp2/3 complex on the convex face of a curved filament. We show that a fluctuation gating model in which Arp2/3 binding to the actin filament is dependent upon a rare high-local-curvature shape fluctuation of the filament is consistent with the experimental data.

Shear zone junctions: Of zippers and freeways

NASA Astrophysics Data System (ADS)

Passchier, Cees W.; Platt, John P.

2017-02-01

Ductile shear zones are commonly treated as straight high-strain domains with uniform shear sense and characteristic curved foliation trails, bounded by non-deforming wall rock. Many shear zones, however, are branched, and if movement on such branches is contemporaneous, the resulting shape can be complicated and lead to unusual shear sense arrangement and foliation geometries in the wall rock. For Y-shaped shear zone triple junctions with three joining branches and transport direction at a high angle to the branchline, only eight basic types of junction are thought to be stable and to produce significant displacement. The simplest type, called freeway junctions, have similar shear sense in all three branches. The other types show joining or separating behaviour of shear zone branches similar to the action of a zipper. Such junctions may have shear zone branches that join to form a single branch (closing zipper junction), or a single shear zone that splits to form two branches, (opening zipper junction). All categories of shear zone junctions show characteristic foliation patterns and deflection of markers in the wall rock. Closing zipper junctions are unusual, since they form a non-active zone with opposite deflection of foliations in the wall rock known as an extraction fault or wake. Shear zipper junctions can form domains of overprinting shear sense along their flanks. A small and large field example are given from NE Spain and Eastern Anatolia. The geometry of more complex, 3D shear zone junctions with slip parallel and oblique to the branchline is briefly discussed.

Structural model of the p14/SF3b155 · branch duplex complex.

PubMed

Schellenberg, Matthew J; Dul, Erin L; MacMillan, Andrew M

2011-01-01

Human p14 (SF3b14), a component of the spliceosomal U2 snRNP, interacts directly with the pre-mRNA branch adenosine within the context of the bulged duplex formed between the pre-mRNA branch region and U2 snRNA. This association occurs early in spliceosome assembly and persists within the fully assembled spliceosome. Analysis of the crystal structure of a complex containing p14 and a peptide derived from p14-associated SF3b155 combined with the results of cross-linking studies has suggested that the branch nucleotide interacts with a pocket on a non-canonical RNA binding surface formed by the complex. Here we report a structural model of the p14 · bulged duplex interaction based on a combination of X-ray crystallography of an adenine p14/SF3b155 peptide complex, biochemical comparison of a panel of disulfide cross-linked protein-RNA complexes, and small-angle X-ray scattering (SAXS). These studies reveal specific recognition of the branch adenosine within the p14 pocket and establish the orientation of the bulged duplex RNA bound on the protein surface. The intimate association of one surface of the bulged duplex with the p14/SF3b155 peptide complex described by this model buries the branch nucleotide at the interface and suggests that p14 · duplex interaction must be disrupted before the first step of splicing.

Structural model of the p14/SF3b155·branch duplex complex

PubMed Central

Schellenberg, Matthew J.; Dul, Erin L.; MacMillan, Andrew M.

2011-01-01

Human p14 (SF3b14), a component of the spliceosomal U2 snRNP, interacts directly with the pre-mRNA branch adenosine within the context of the bulged duplex formed between the pre-mRNA branch region and U2 snRNA. This association occurs early in spliceosome assembly and persists within the fully assembled spliceosome. Analysis of the crystal structure of a complex containing p14 and a peptide derived from p14-associated SF3b155 combined with the results of cross-linking studies has suggested that the branch nucleotide interacts with a pocket on a non-canonical RNA binding surface formed by the complex. Here we report a structural model of the p14•bulged duplex interaction based on a combination of X-ray crystallography of an adenine p14/SF3b155 peptide complex, biochemical comparison of a panel of disulfide cross-linked protein–RNA complexes, and small-angle X-ray scattering (SAXS). These studies reveal specific recognition of the branch adenosine within the p14 pocket and establish the orientation of the bulged duplex RNA bound on the protein surface. The intimate association of one surface of the bulged duplex with the p14/SF3b155 peptide complex described by this model buries the branch nucleotide at the interface and suggests that p14•duplex interaction must be disrupted before the first step of splicing. PMID:21062891

Interaction and formation mechanism of binary complex between zein and propylene glycol alginate.

PubMed

Sun, Cuixia; Dai, Lei; Gao, Yanxiang

2017-02-10

The anti-solvent co-precipitation method was used to fabricate the zein-propylene glycol alginate (PGA) binary complex with different mass ratios of zein to PGA (20:1, 10:1, 5:1, 2:1 and 1:1) at pH 4.0. Results showed that attractive electrostatic interaction between zein and PGA occurred and negatively charged binary complex with large size and high turbidity was formed due to the charge neutralization. Hydrogen bonding and hydrophobic effects were involved in the interactions between zein and PGA, leading to the changed secondary structure and improved thermal stability of zein. Aggregates in the irregular shape with large size were obviously observed in the AFM images. PGA alone exhibited a fine filamentous network structure, while zein-PGA binary complex showed a rough branch-like pattern and the surface of "branch" was closely adsorbed by lots of spherical zein particles. Q in zein-PGA binary complex dispersions presented the improved photochemical and thermal stability. The potential mechanism of a two-step process was proposed to explain the formation of zein-PGA binary complexes. Copyright © 2016 Elsevier Ltd. All rights reserved.

A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response

PubMed Central

Adamson, Britt; Norman, Thomas M.; Jost, Marco; Cho, Min Y.; Nuñez, James K.; Chen, Yuwen; Villalta, Jacqueline E.; Gilbert, Luke A.; Horlbeck, Max A.; Hein, Marco Y.; Pak, Ryan A.; Gray, Andrew N.; Gross, Carol A.; Dixit, Atray; Parnas, Oren; Regev, Aviv; Weissman, Jonathan S.

2016-01-01

SUMMARY Functional genomics efforts face tradeoffs between number of perturbations examined and complexity of phenotypes measured. We bridge this gap with Perturb-seq, which combines droplet-based single-cell RNA-seq with a strategy for barcoding CRISPR-mediated perturbations, allowing many perturbations to be profiled in pooled format. We applied Perturb-seq to dissect the mammalian unfolded protein response (UPR) using single and combinatorial CRISPR perturbations. Two genome-scale CRISPR interference (CRISPRi) screens identified genes whose repression perturbs ER homeostasis. Subjecting ~100 hits to Perturb-seq enabled high-precision functional clustering of genes. Single-cell analyses decoupled the three UPR branches, revealed bifurcated UPR branch activation among cells subject to the same perturbation, and uncovered differential activation of the branches across hits, including an isolated feedback loop between the translocon and IRE1α. These studies provide insight into how the three sensors of ER homeostasis monitor distinct types of stress and highlight the ability of Perturb-seq to dissect complex cellular responses. PMID:27984733

Universal High Energy Anomaly in the Angle-Resolved Photoemission Spectra of High Temperature Superconductors: Possible Evidence of Spinon and Holon Branches

NASA Astrophysics Data System (ADS)

Graf, J.; Gweon, G.-H.; McElroy, K.; Zhou, S. Y.; Jozwiak, C.; Rotenberg, E.; Bill, A.; Sasagawa, T.; Eisaki, H.; Uchida, S.; Takagi, H.; Lee, D.-H.; Lanzara, A.

2007-02-01

A universal high energy anomaly in the single particle spectral function is reported in three different families of high temperature superconductors by using angle-resolved photoemission spectroscopy. As we follow the dispersing peak of the spectral function from the Fermi energy to the valence band complex, we find dispersion anomalies marked by two distinctive high energy scales, E1≈0.38eV and E2≈0.8eV. E1 marks the energy above which the dispersion splits into two branches. One is a continuation of the near parabolic dispersion, albeit with reduced spectral weight, and reaches the bottom of the band at the Γ point at ≈0.5eV. The other is given by a peak in the momentum space, nearly independent of energy between E1 and E2. Above E2, a bandlike dispersion reemerges. We conjecture that these two energies mark the disintegration of the low-energy quasiparticles into a spinon and holon branch in the high Tc cuprates.

Strike-slip linked core complexes: A new kinematic model of basement rock exhumation in a crustal-scale fault system

NASA Astrophysics Data System (ADS)

Meyer, Sven Erik; Passchier, Cees; Abu-Alam, Tamer; Stüwe, Kurt

2014-05-01

Metamorphic core complexes usually develop as extensional features during continental crustal thinning, such as the Basin and Range and the Aegean Terrane. The Najd fault system in Saudi Arabia is a 2000 km-long and 400 km-wide complex network of crustal-scale strike-slip shear zones in a Neoproterozoic collision zone. Locally, the anastomosing shear zones lead to exhumation of lower crustal segments and represent a new kinematic model for the development of core complexes. We report on two such structures: the Qazaz complex in Saudi Arabia and the Hafafit complex in Egypt. The 15 km-wide Qazaz complex is a triangular dome of gently dipping mylonitic foliations within the 140 km-long sinistral strike-slip Qazaz mylonite zone. The gneissic dome consists of high-grade rocks, surrounded by low-grade metasediments and metavolcanics. The main SE-trending strike-slip Qazaz shear zone splits southwards into two branches around the gneiss dome: the western branch is continuous with the shallow dipping mylonites of the dome core, without overprinting, and changes by more than 90 degrees from a NS-trending strike-slip zone to an EW-trending 40 degree south-dipping detachment that bounds the gneiss dome to the south. The eastern SE-trending sinistral strike-slip shear zone branch is slightly younger and transects the central dome fabrics. The gneiss dome appears to have formed along a jog in the strike-slip shear zone during 40 km of horizontal strike-slip motion, which caused local exhumation of lower crustal rocks by 25 km along the detachment. The eastern shear zone branch formed later during exhumation, transacted the gneiss dome and offset the two parts by another 70 km. The Hafafit core complex in Egypt is of similar shape and size to the Qazaz structure, but forms the northern termination of a sinistral strike-slip zone that is at least 100 km in length. This zone may continue into Saudi Arabia as the Ajjaj shear zone for another 100 km. The NW trending strike slip mylonite zone grades into a gently N-dipping detachment to the west which accommodated strike slip by exhumation of high-grade lower crustal rocks. The Qazaz and the Hafafit Domes are similar, mirror-image structures with small differences in the accommodating shear zones. It is likely that these types of strike-slip related oblique core complexes are common in the Arabian Nubian shield, and possibly elsewhere.

Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps

PubMed Central

Rakesh, Ramachandran; Joseph, Agnel Praveen; Bhaskara, Ramachandra M.; Srinivasan, Narayanaswamy

2016-01-01

ABSTRACT Pre-mRNA splicing in eukaryotes is performed by the spliceosome, a highly complex macromolecular machine. SF3b is a multi-protein complex which recognizes the branch point adenosine of pre-mRNA as part of a larger U2 snRNP or U11/U12 di-snRNP in the dynamic spliceosome machinery. Although a cryo-EM map is available for human SF3b complex, the structure and relative spatial arrangement of all components in the complex are not yet known. We have recognized folds of domains in various proteins in the assembly and generated comparative models. Using an integrative approach involving structural and other experimental data, guided by the available cryo-EM density map, we deciphered a pseudo-atomic model of the closed form of SF3b which is found to be a “fuzzy complex” with highly flexible components and multiplicity of folds. Further, the model provides structural information for 5 proteins (SF3b10, SF3b155, SF3b145, SF3b130 and SF3b14b) and localization information for 4 proteins (SF3b10, SF3b145, SF3b130 and SF3b14b) in the assembly for the first time. Integration of this model with the available U11/U12 di-snRNP cryo-EM map enabled elucidation of an open form. This now provides new insights on the mechanistic features involved in the transition between closed and open forms pivoted by a hinge region in the SF3b155 protein that also harbors cancer causing mutations. Moreover, the open form guided model of the 5′ end of U12 snRNA, which includes the branch point duplex, shows that the architecture of SF3b acts as a scaffold for U12 snRNA: pre-mRNA branch point duplex formation with potential implications for branch point adenosine recognition fidelity. PMID:27618338

Regulation of branched-chain amino acid catabolism in rat models for spontaneous type 2 diabetes mellitus.

PubMed

Kuzuya, Teiji; Katano, Yoshiaki; Nakano, Isao; Hirooka, Yoshiki; Itoh, Akihiro; Ishigami, Masatoshi; Hayashi, Kazuhiko; Honda, Takashi; Goto, Hidemi; Fujita, Yuko; Shikano, Rie; Muramatsu, Yuji; Bajotto, Gustavo; Tamura, Tomohiro; Tamura, Noriko; Shimomura, Yoshiharu

2008-08-15

The branched-chain alpha-keto acid dehydrogenase (BCKDH) complex is the most important regulatory enzyme in branched-chain amino acid (BCAA) catabolism. We examined the regulation of hepatic BCKDH complex activity in spontaneous type 2 diabetes Otsuka Long-Evans Tokushima Fatty (OLETF) rats and Zucker diabetic fatty rats. Hepatic BCKDH complex activity in these rats was significantly lower than in corresponding control rats. The amount of BCKDH complex in OLETF rats corresponded to the total activity of the complex. Activity and abundance of the bound form of BCKDH kinase, which is responsible for inactivation of the complex, showed an inverse correlation to BCKDH complex activity in OLETF rats. Dietary supplementation of 5% BCAAs for 10 weeks markedly increased BCKDH complex activity, and decreased the activity and bound form of BCKDH kinase in the rats. These results suggest that BCAA catabolism in type 2 diabetes is downregulated and enhanced by BCAA supplementation.

Architecture, Assembly, and Emerging Applications of Branched Functional Polyelectrolytes and Poly(ionic liquid)s.

PubMed

Xu, Weinan; Ledin, Petr A; Shevchenko, Valery V; Tsukruk, Vladimir V

2015-06-17

Branched polyelectrolytes with cylindrical brush, dendritic, hyperbranched, grafted, and star architectures bearing ionizable functional groups possess complex and unique assembly behavior in solution at surfaces and interfaces as compared to their linear counterparts. This review summarizes the recent developments in the introduction of various architectures and understanding of the assembly behavior of branched polyelectrolytes with a focus on functional polyelectrolytes and poly(ionic liquid)s with responsive properties. The branched polyelectrolytes and poly(ionic liquid)s interact electrostatically with small molecules, linear polyelectrolytes, or other branched polyelectrolytes to form assemblies of hybrid nanoparticles, multilayer thin films, responsive microcapsules, and ion-conductive membranes. The branched structures lead to unconventional assemblies and complex hierarchical structures with responsive properties as summarized in this review. Finally, we discuss prospectives for emerging applications of branched polyelectrolytes and poly(ionic liquid)s for energy harvesting and storage, controlled delivery, chemical microreactors, adaptive surfaces, and ion-exchange membranes.

Early-stage reduction of the dendritic complexity in basolateral amygdala of a transgenic mouse model of Alzheimer's disease

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

Guo, Congdi; Long, Ben; Hu, Yarong

Alzheimer's disease is a representative age-related neurodegenerative disease that could result in loss of memory and cognitive deficiency. However, the precise onset time of Alzheimer's disease affecting neuronal circuits and the mechanisms underlying the changes are not clearly known. To address the neuroanatomical changes during the early pathologic developing process, we acquired the neuronal morphological characterization of AD in APP/PS1 double-transgenic mice using the Micro-Optical Sectioning Tomography system. We reconstructed the neurons in 3D datasets with a resolution of 0.32 × 0.32 × 1 μm and used the Sholl method to analyze the anatomical characterization of the dendritic branches. The results showed that, similar tomore » the progressive change in amyloid plaques, the number of dendritic branches were significantly decreased in 9-month-old mice. In addition, a distinct reduction of dendritic complexity occurred in third and fourth-order dendritic branches of 9-month-old mice, while no significant changes were identified in these parameters in 6-month-old mice. At the branch-level, the density distribution of dendritic arbors in the radial direction decreased in the range of 40–90 μm from the neuron soma in 6-month-old mice. These changes in the dendritic complexity suggest that these reductions contribute to the progressive cognitive impairment seen in APP/PS1 mice. This work may yield insights into the early changes in dendritic abnormality and its relevance to dysfunctional mechanisms of learning, memory and emotion in Alzheimer's disease. - Highlights: • Neuron-level, reduction of dendritic complexity in BLA of 9-month-old AD mice. • Specific range of branch decrease in density of 6-month-old AD mice. • 3D imaging with high resolution will provide insights into brain aging.« less

Binding of the Extracellular Eight-Cysteine Motif of Opy2 to the Putative Osmosensor Msb2 Is Essential for Activation of the Yeast High-Osmolarity Glycerol Pathway

PubMed Central

Yamamoto, Katsuyoshi

2015-01-01

To adapt to environmental high osmolarity, the budding yeast Saccharomyces cerevisiae activates the Hog1 mitogen-activated protein kinase, which regulates diverse osmoadaptive responses. Hog1 is activated through the high-osmolarity glycerol (HOG) pathway, which consists of independent upstream signaling routes termed the SLN1 branch and the SHO1 branch. Here, we report that the extracellular cysteine-rich (CR) domain of the transmembrane-anchor protein Opy2 binds to the Hkr1-Msb2 homology (HMH) domain of the putative osmosensor Msb2 and that formation of the Opy2-Msb2 complex is essential for osmotic activation of Hog1 through the MSB2 subbranch of the SHO1 branch. By analyzing the phenotypes of mutants with Opy2 cysteine-to-alanine mutations, we deduced that the CR domain forms four intramolecular disulfide bonds. To probe for the potential induction of conformational changes in the Opy2-Msb2 complex by osmostress, we constructed mutants with a site-specific Cys-to-Ala mutation of the Opy2 CR domain and mutants with a Cys substitution of the Msb2 HMH domain. Each of these mutants had a reduced cysteine. These mutants were then combinatorially cross-linked using chemical cross-linkers of different lengths. Cross-linking between Opy2 Cys48 and Msb2 Cys1023 was sensitive to osmotic changes, suggesting that osmostress induced a conformational change. We therefore propose that the Opy2-Msb2 complex might serve as an osmosensor. PMID:26598606

Structural Mechanics and Dynamics Branch

NASA Technical Reports Server (NTRS)

Stefko, George

2003-01-01

The 2002 annual report of the Structural Mechanics and Dynamics Branch reflects the majority of the work performed by the branch staff during the 2002 calendar year. Its purpose is to give a brief review of the branch s technical accomplishments. The Structural Mechanics and Dynamics Branch develops innovative computational tools, benchmark experimental data, and solutions to long-term barrier problems in the areas of propulsion aeroelasticity, active and passive damping, engine vibration control, rotor dynamics, magnetic suspension, structural mechanics, probabilistics, smart structures, engine system dynamics, and engine containment. Furthermore, the branch is developing a compact, nonpolluting, bearingless electric machine with electric power supplied by fuel cells for future "more electric" aircraft. An ultra-high-power-density machine that can generate projected power densities of 50 hp/lb or more, in comparison to conventional electric machines, which generate usually 0.2 hp/lb, is under development for application to electric drives for propulsive fans or propellers. In the future, propulsion and power systems will need to be lighter, to operate at higher temperatures, and to be more reliable in order to achieve higher performance and economic viability. The Structural Mechanics and Dynamics Branch is working to achieve these complex, challenging goals.

Early Experience with the Use of Inner Branches in Endovascular Repair of Complex Abdominal and Thoraco-abdominal Aortic Aneurysms.

PubMed

Katsargyris, Athanasios; Marques de Marino, Pablo; Mufty, Hozan; Pedro, Luis Mendes; Fernandes, Ruy; Verhoeven, Eric L G

2018-05-01

Visceral arteries in fenestrated and branched endovascular repair (F/BEVAR) have been addressed by fenestrations or directional side branches. Inner branches, as used in the arch branched device, could provide an extra option for visceral arteries "unsuitable" for fenestrations or directional side branches. Early experience with the use of inner branches for visceral arteries in F/BEVAR is described. All consecutive patients treated by F/BEVAR for complex abdominal aortic aneurysm (AAA) or thoraco-abdominal aneurysm (TAAA) using stent grafts with inner branches were included. Data were collected prospectively. Thirty-two patients (28 male, mean age 71.6 ± 8.3 years) were included. Seven (21.9%) patients had a complex AAA and 25 (78.1%) had a TAAA. A stent graft with inner branches only was used in four (12.5%) patients. The remaining 28 (87.5%) patients received a stent graft with fenestrations and inner branches. In total 52 vessels were targeted with inner branches. Technical success was achieved in all 32 (100%) patients. All 38 inner branch target vessels in grafts including fenestrations and inner branches were instantly catheterised (<1 minute), whereas catheterisation of target vessels in "inner branch only" grafts proved more difficult (<1 minute, n = 3; 1-3 min, n = 4; and >3 min, n = 7). The 30 day operative mortality was 3.1% (1/32). Estimated survival at 1 year was 80.0% ± 8.3%. During follow-up, four renal inner branches occluded in three patients. The estimated inner branch target vessel stent patency at 1 year was 91.9 ± 4.5%. The estimated freedom from re-intervention at 1 year was 78.4% ± 8.9%. Early data suggest that visceral inner branches might represent a feasible third option to address selected target vessels in F/BEVAR. Stent grafts with inner branch(es) in combination with fenestrations seem to be a better configuration than stent grafts with inner branches alone. Durability of the inner branch design needs further investigation. Copyright © 2018 European Society for Vascular Surgery. Published by Elsevier B.V. All rights reserved.

Nature of alpha and beta particles in glycogen using molecular size distributions.

PubMed

Sullivan, Mitchell A; Vilaplana, Francisco; Cave, Richard A; Stapleton, David; Gray-Weale, Angus A; Gilbert, Robert G

2010-04-12

Glycogen is a randomly hyperbranched glucose polymer. Complex branched polymers have two structural levels: individual branches and the way these branches are linked. Liver glycogen has a third level: supramolecular clusters of beta particles which form larger clusters of alpha particles. Size distributions of native glycogen were characterized using size exclusion chromatography (SEC) to find the number and weight distributions and the size dependences of the number- and weight-average masses. These were fitted to two distinct randomly joined reference structures, constructed by random attachment of individual branches and as random aggregates of beta particles. The z-average size of the alpha particles in dimethylsulfoxide does not change significantly with high concentrations of LiBr, a solvent system that would disrupt hydrogen bonding. These data reveal that the beta particles are covalently bonded to form alpha particles through a hitherto unsuspected enzyme process, operative in the liver on particles above a certain size range.

Selecting Surrogates for an Alkylphenol Ethoxylate Analytical Method in Sewage and Soil Matrices

EPA Science Inventory

Alkylphenol ethoxylates (APEs) are nonionic surfactants commonly used in industrial detergents. These products contain complex mixtures of branched and linear chains. APEs and their degradation products, alkylphenols, are highly toxic to aquatic organisms, potentially estrogeni...

Effect of genotype and environment on branching in weedy green millet (Setaria viridis) and domesticated foxtail millet (Setaria italica) (Poaceae).

PubMed

Doust, Andrew N; Kellogg, Elizabeth A

2006-04-01

Many domesticated crops are derived from species whose life history includes weedy characteristics, such as the ability to vary branching patterns in response to environmental conditions. However, domesticated crop plants are characterized by less variable plant architecture, as well as by a general reduction in vegetative branching compared to their progenitor species. Here we examine weedy green millet and its domesticate foxtail millet that differ in the number of tillers (basal branches) and axillary branches along each tiller. Branch number in F(2:3) progeny of a cross between the two species varies with genotype, planting density, and other environmental variables, with significant genotype-environment interactions (GEI). This is shown by a complex pattern of reaction norms and by variation in the pattern of significant quantitative trait loci (QTL) amongst trials. Individual and joint analyses of high and low density trials indicate that most QTL have significant GEI. Dominance and epistasis also explain some variation in branching. Likely candidate genes underlying the QTL (based on map position and phenotypic effect) include teosinte branched1 and barren stalk1. Phytochrome B, which has been found to affect response to shading in other plants, explains little or no variation. Much variation in branching is explained by QTL that do not have obvious candidate genes from maize or rice.

Characterization of branch complexity by fractal analyses

USGS Publications Warehouse

Alados, C.L.; Escos, J.; Emlen, J.M.; Freeman, D.C.

1999-01-01

The comparison between complexity in the sense of space occupancy (box-counting fractal dimension D(c) and information dimension D1) and heterogeneity in the sense of space distribution (average evenness index f and evenness variation coefficient J(cv)) were investigated in mathematical fractal objects and natural branch structures. In general, increased fractal dimension was paired with low heterogeneity. Comparisons between branch architecture in Anthyllis cytisoides under different slope exposure and grazing impact revealed that branches were more complex and more homogeneously distributed for plants on northern exposures than southern, while grazing had no impact during a wet year. Developmental instability was also investigated by the statistical noise of the allometric relation between internode length and node order. In conclusion, our study demonstrated that fractal dimension of branch structure can be used to analyze the structural organization of plants, especially if we consider not only fractal dimension but also shoot distribution within the canopy (lacunarity). These indexes together with developmental instability analyses are good indicators of growth responses to the environment.

Characterization of branch complexity by fractal analyses and detect plant functional adaptations

USGS Publications Warehouse

Alados, C.L.; Escos, J.; Emlen, J.M.; Freeman, D.C.

1999-01-01

The comparison between complexity in the sense of space occupancy (box-counting fractal dimension Dc and information dimension DI ) and heterogeneity in the sense of space distribution (average evenness index and evenness variation coefficient JCV) were investigated in mathematical fractal objects and natural branch ¯ J structures. In general, increased fractal dimension was paired with low heterogeneity. Comparisons between branch architecture in Anthyllis cytisoides under different slope exposure and grazing impact revealed that branches were more complex and more homogeneously distributed for plants on northern exposures than southern, while grazing had no impact during a wet year. Developmental instability was also investigated by the statistical noise of the allometric relation between internode length and node order. In conclusion, our study demonstrated that fractal dimension of branch structure can be used to analyze the structural organization of plants, especially if we consider not only fractal dimension but also shoot distribution within the canopy (lacunarity). These indexes together with developmental instability analyses are good indicators of growth responses to the environment.

Spatial mapping and quantification of developmental branching morphogenesis.

PubMed

Short, Kieran; Hodson, Mark; Smyth, Ian

2013-01-15

Branching morphogenesis is a fundamental developmental mechanism that shapes the formation of many organs. The complex three-dimensional shapes derived by this process reflect equally complex genetic interactions between branching epithelia and their surrounding mesenchyme. Despite the importance of this process to normal adult organ function, analysis of branching has been stymied by the absence of a bespoke method to quantify accurately the complex spatial datasets that describe it. As a consequence, although many developmentally important genes are proposed to influence branching morphogenesis, we have no way of objectively assessing their individual contributions to this process. We report the development of a method for accurately quantifying many aspects of branching morphogenesis and we demonstrate its application to the study of organ development. As proof of principle we have employed this approach to analyse the developing mouse lung and kidney, describing the spatial characteristics of the branching ureteric bud and pulmonary epithelia. To demonstrate further its capacity to profile unrecognised genetic contributions to organ development, we examine Tgfb2 mutant kidneys, identifying elements of both developmental delay and specific spatial dysmorphology caused by haplo-insufficiency for this gene. This technical advance provides a crucial resource that will enable rigorous characterisation of the genetic and environmental factors that regulate this essential and evolutionarily conserved developmental mechanism.

Mechanism of synergistic activation of Arp2/3 complex by cortactin and N-WASP

PubMed Central

Helgeson, Luke A; Nolen, Brad J

2013-01-01

Nucleation promoting factors (NPFs) initiate branched actin network assembly by activating Arp2/3 complex, a branched actin filament nucleator. Cellular actin networks contain multiple NPFs, but how they coordinately regulate Arp2/3 complex is unclear. Cortactin is an NPF that activates Arp2/3 complex weakly on its own, but with WASP/N-WASP, another class of NPFs, potently activates. We dissect the mechanism of synergy and propose a model in which cortactin displaces N-WASP from nascent branches as a prerequisite for nucleation. Single-molecule imaging revealed that unlike WASP/N-WASP, cortactin remains bound to junctions during nucleation, and specifically targets junctions with a ∼160-fold increased on rate over filament sides. N-WASP must be dimerized for potent synergy, and targeted mutations indicate release of dimeric N-WASP from nascent branches limits nucleation. Mathematical modeling shows cortactin-mediated displacement but not N-WASP recycling or filament recruitment models can explain synergy. Our results provide a molecular basis for coordinate Arp2/3 complex regulation. DOI: http://dx.doi.org/10.7554/eLife.00884.001 PMID:24015358

Structural characterization of saturated branched chain fatty acid methyl esters by collisional dissociation of molecular ions generated by electron ionization.

PubMed

Ran-Ressler, Rinat R; Lawrence, Peter; Brenna, J Thomas

2012-01-01

Saturated branched chain fatty acids (BCFA) are present as complex mixtures in numerous biological samples. The traditional method for structure elucidation, electron ionization (EI) mass spectrometry, sometimes does not unambiguously enable assignment of branching in isomeric BCFA. Zirrolli and Murphy (Zirrolli , J. A. , and R. A. Murphy. 1993. Low-energy tandem mass spectrometry of the molecular ion derived from fatty acid methyl esters: a novel method for analysis of branched-chain fatty acids. J. Am. Soc. Mass Spectrom. 4: 223-229.) showed that the molecular ions of four BCFA methyl ester (BCFAME) yield highly characteristic fragments upon collisional dissociation using a triple quadrupole instrument. Here, we confirm and extend these results by analysis using a tabletop 3-D ion trap for activated molecular ion EI-MS/MS to 30 BCFAME. iso-BCFAME produces a prominent ion (30-100% of base peak) for [M-43] (M-C₃H₇), corresponding to the terminal isopropyl moiety in the original iso-BCFAME. Anteiso-FAME yield prominent ions (20-100% of base peak) corresponding to losses on both side of the methyl branch, [M-29] and [M-57], and tend to produce more prominent m/z 115 peaks corresponding to a cyclization product around the ester. Dimethyl and tetramethyl FAME, with branches separated by at least one methylene group, yield fragment on both sides of the sites of methyl branches that are more than 6 C away from the carboxyl carbon. EI-MS/MS yields uniquely specific ions that enable highly confident structural identification and quantification of BCFAME.

Structural characterization of saturated branched chain fatty acid methyl esters by collisional dissociation of molecular ions generated by electron ionization[S

PubMed Central

Ran-Ressler, Rinat R.; Lawrence, Peter; Brenna, J. Thomas

2012-01-01

Saturated branched chain fatty acids (BCFA) are present as complex mixtures in numerous biological samples. The traditional method for structure elucidation, electron ionization (EI) mass spectrometry, sometimes does not unambiguously enable assignment of branching in isomeric BCFA. Zirrolli and Murphy (Zirrolli , J. A. , and R. A. Murphy. 1993. Low-energy tandem mass spectrometry of the molecular ion derived from fatty acid methyl esters: a novel method for analysis of branched-chain fatty acids. J. Am. Soc. Mass Spectrom. 4: 223–229.) showed that the molecular ions of four BCFA methyl ester (BCFAME) yield highly characteristic fragments upon collisional dissociation using a triple quadrupole instrument. Here, we confirm and extend these results by analysis using a tabletop 3-D ion trap for activated molecular ion EI-MS/MS to 30 BCFAME. iso-BCFAME produces a prominent ion (30-100% of base peak) for [M-43] (M-C3H7), corresponding to the terminal isopropyl moiety in the original iso-BCFAME. Anteiso-FAME yield prominent ions (20-100% of base peak) corresponding to losses on both side of the methyl branch, [M-29] and [M-57], and tend to produce more prominent m/z 115 peaks corresponding to a cyclization product around the ester. Dimethyl and tetramethyl FAME, with branches separated by at least one methylene group, yield fragment on both sides of the sites of methyl branches that are more than 6 C away from the carboxyl carbon. EI-MS/MS yields uniquely specific ions that enable highly confident structural identification and quantification of BCFAME. PMID:22021637

Spectroscopy of the Schwarzschild black hole at arbitrary frequencies.

PubMed

Casals, Marc; Ottewill, Adrian

2012-09-14

Linear field perturbations of a black hole are described by the Green function of the wave equation that they obey. After Fourier decomposing the Green function, its two natural contributions are given by poles (quasinormal modes) and a largely unexplored branch cut in the complex frequency plane. We present new analytic methods for calculating the branch cut on a Schwarzschild black hole for arbitrary values of the frequency. The branch cut yields a power-law tail decay for late times in the response of a black hole to an initial perturbation. We determine explicitly the first three orders in the power-law and show that the branch cut also yields a new logarithmic behavior T(-2ℓ-5)lnT for late times. Before the tail sets in, the quasinormal modes dominate the black hole response. For electromagnetic perturbations, the quasinormal mode frequencies approach the branch cut at large overtone index n. We determine these frequencies up to n(-5/2) and, formally, to arbitrary order. Highly damped quasinormal modes are of particular interest in that they have been linked to quantum properties of black holes.

Fort Collins Science Center Ecosystem Dynamics Branch

USGS Publications Warehouse

Wilson, Jim; Melcher, C.; Bowen, Z.

2009-01-01

Complex natural resource issues require understanding a web of interactions among ecosystem components that are (1) interdisciplinary, encompassing physical, chemical, and biological processes; (2) spatially complex, involving movements of animals, water, and airborne materials across a range of landscapes and jurisdictions; and (3) temporally complex, occurring over days, weeks, or years, sometimes involving response lags to alteration or exhibiting large natural variation. Scientists in the Ecosystem Dynamics Branch of the U.S. Geological Survey, Fort Collins Science Center, investigate a diversity of these complex natural resource questions at the landscape and systems levels. This Fact Sheet describes the work of the Ecosystems Dynamics Branch, which is focused on energy and land use, climate change and long-term integrated assessments, herbivore-ecosystem interactions, fire and post-fire restoration, and environmental flows and river restoration.

Coulomb branches with complex singularities

NASA Astrophysics Data System (ADS)

Argyres, Philip C.; Martone, Mario

2018-06-01

We construct 4d superconformal field theories (SCFTs) whose Coulomb branches have singular complex structures. This implies, in particular, that their Coulomb branch coordinate rings are not freely generated. Our construction also gives examples of distinct SCFTs which have identical moduli space (Coulomb, Higgs, and mixed branch) geometries. These SCFTs thus provide an interesting arena in which to test the relationship between moduli space geometries and conformal field theory data. We construct these SCFTs by gauging certain discrete global symmetries of N = 4 superYang-Mills (sYM) theories. In the simplest cases, these discrete symmetries are outer automorphisms of the sYM gauge group, and so these theories have lagrangian descriptions as N = 4 sYM theories with disconnected gauge groups.

Gene Transfer in Eukaryotic Cells Using Activated Dendrimers

NASA Astrophysics Data System (ADS)

Dennig, Jörg

Gene transfer into eukaryotic cells plays an important role in cell biology. Over the last 30 years a number of transfection methods have been developed to mediate gene transfer into eukaryotic cells. Classical methods include co-precipitation of DNA with calcium phosphate, charge-dependent precipitation of DNA with DEAE-dextran, electroporation of nucleic acids, and formation of transfection complexes between DNA and cationic liposomes. Gene transfer technologies based on activated PAMAM-dendrimers provide another class of transfection reagents. PAMAM-dendrimers are highly branched, spherical molecules. Activation of newly synthesized dendrimers involves hydrolytic removal of some of the branches, and results in a molecule with a higher degree of flexibility. Activated dendrimers assemble DNA into compact structures via charge interactions. Activated dendrimer - DNA complexes bind to the cell membrane of eukaryotic cells, and are transported into the cell by non-specific endocytosis. A structural model of the activated dendrimer - DNA complex and a potential mechanism for its uptake into cells will be discussed.

The Coulomb Branch of 3d N= 4 Theories

NASA Astrophysics Data System (ADS)

Bullimore, Mathew; Dimofte, Tudor; Gaiotto, Davide

2017-09-01

We propose a construction for the quantum-corrected Coulomb branch of a general 3d gauge theory with N=4 supersymmetry, in terms of local coordinates associated with an abelianized theory. In a fixed complex structure, the holomorphic functions on the Coulomb branch are given by expectation values of chiral monopole operators. We construct the chiral ring of such operators, using equivariant integration over BPS moduli spaces. We also quantize the chiral ring, which corresponds to placing the 3d theory in a 2d Omega background. Then, by unifying all complex structures in a twistor space, we encode the full hyperkähler metric on the Coulomb branch. We verify our proposals in a multitude of examples, including SQCD and linear quiver gauge theories, whose Coulomb branches have alternative descriptions as solutions to Bogomolnyi and/or Nahm equations.

Rational growth of branched nanowire heterostructures with synthetically encoded properties and function

PubMed Central

Jiang, Xiaocheng; Tian, Bozhi; Xiang, Jie; Qian, Fang; Zheng, Gengfeng; Wang, Hongtao; Mai, Liqiang; Lieber, Charles M.

2011-01-01

Branched nanostructures represent unique, 3D building blocks for the “bottom-up” paradigm of nanoscale science and technology. Here, we report a rational, multistep approach toward the general synthesis of 3D branched nanowire (NW) heterostructures. Single-crystalline semiconductor, including groups IV, III–V, and II–VI, and metal branches have been selectively grown on core or core/shell NW backbones, with the composition, morphology, and doping of core (core/shell) NWs and branch NWs well controlled during synthesis. Measurements made on the different composition branched NW structures demonstrate encoding of functional p-type/n-type diodes and light-emitting diodes (LEDs) as well as field effect transistors with device function localized at the branch/backbone NW junctions. In addition, multibranch/backbone NW structures were synthesized and used to demonstrate capability to create addressable nanoscale LED arrays, logic circuits, and biological sensors. Our work demonstrates a previously undescribed level of structural and functional complexity in NW materials, and more generally, highlights the potential of bottom-up synthesis to yield increasingly complex functional systems in the future. PMID:21730174

Enzymes involved in branched-chain amino acid metabolism in humans.

PubMed

Adeva-Andany, María M; López-Maside, Laura; Donapetry-García, Cristóbal; Fernández-Fernández, Carlos; Sixto-Leal, Cristina

2017-06-01

Branched-chain amino acids (leucine, isoleucine and valine) are structurally related to branched-chain fatty acids. Leucine is 2-amino-4-methyl-pentanoic acid, isoleucine is 2-amino-3-methyl-pentanoic acid, and valine is 2-amino-3-methyl-butanoic acid. Similar to fatty acid oxidation, leucine and isoleucine produce acetyl-coA. Additionally, leucine generates acetoacetate and isoleucine yields propionyl-coA. Valine oxidation produces propionyl-coA, which is converted into methylmalonyl-coA and succinyl-coA. Branched-chain aminotransferase catalyzes the first reaction in the catabolic pathway of branched-chain amino acids, a reversible transamination that converts branched-chain amino acids into branched-chain ketoacids. Simultaneously, glutamate is converted in 2-ketoglutarate. The branched-chain ketoacid dehydrogenase complex catalyzes the irreversible oxidative decarboxylation of branched-chain ketoacids to produce branched-chain acyl-coA intermediates, which then follow separate catabolic pathways. Human tissue distribution and function of most of the enzymes involved in branched-chain amino acid catabolism is unknown. Congenital deficiencies of the enzymes involved in branched-chain amino acid metabolism are generally rare disorders. Some of them are associated with reduced pyruvate dehydrogenase complex activity and respiratory chain dysfunction that may contribute to their clinical phenotype. The biochemical phenotype is characterized by accumulation of the substrate to the deficient enzyme and its carnitine and/or glycine derivatives. It was established at the beginning of the twentieth century that the plasma level of the branched-chain amino acids is increased in conditions associated with insulin resistance such as obesity and diabetes mellitus. However, the potential clinical relevance of this elevation is uncertain.

Computing quantum hashing in the model of quantum branching programs

NASA Astrophysics Data System (ADS)

Ablayev, Farid; Ablayev, Marat; Vasiliev, Alexander

2018-02-01

We investigate the branching program complexity of quantum hashing. We consider a quantum hash function that maps elements of a finite field into quantum states. We require that this function is preimage-resistant and collision-resistant. We consider two complexity measures for Quantum Branching Programs (QBP): a number of qubits and a number of compu-tational steps. We show that the quantum hash function can be computed efficiently. Moreover, we prove that such QBP construction is optimal. That is, we prove lower bounds that match the constructed quantum hash function computation.

Sensory Neuron Fates Are Distinguished by a Transcriptional Switch that Regulates Dendrite Branch Stabilization

PubMed Central

Smith, Cody J.; O’Brien, Timothy; Chatzigeorgiou, Marios; Spencer, W. Clay; Feingold-Link, Elana; Husson, Steven J.; Hori, Sayaka; Mitani, Shohei; Gottschalk, Alexander; Schafer, William R.; Miller, David M.

2013-01-01

SUMMARY Sensory neurons adopt distinct morphologies and functional modalities to mediate responses to specific stimuli. Transcription factors and their downstream effectors orchestrate this outcome but are incompletely defined. Here, we show that different classes of mechanosensory neurons in C. elegans are distinguished by the combined action of the transcription factors MEC-3, AHR-1, and ZAG-1. Low levels of MEC-3 specify the elaborate branching pattern of PVD nociceptors, whereas high MEC-3 is correlated with the simple morphology of AVM and PVM touch neurons. AHR-1 specifies AVM touch neuron fate by elevating MEC-3 while simultaneously blocking expression of nociceptive genes such as the MEC-3 target, the claudin-like membrane protein HPO-30, that promotes the complex dendritic branching pattern of PVD. ZAG-1 exercises a parallel role to prevent PVM from adopting the PVD fate. The conserved dendritic branching function of the Drosophila AHR-1 homolog, Spineless, argues for similar pathways in mammals. PMID:23889932

The Coulomb Branch of 3d $${\\mathcal{N}= 4}$$ N = 4 Theories

DOE PAGES

Bullimore, Mathew; Dimofte, Tudor; Gaiotto, Davide

2017-06-03

We propose a construction for the quantum-corrected Coulomb branch of a general 3d gauge theory with N=4 supersymmetry, in terms of local coordinates associated with an abelianized theory. In a fixed complex structure, the holomorphic functions on the Coulomb branch are given by expectation values of chiral monopole operators. We construct the chiral ring of such operators, using equivariant integration over BPS moduli spaces. We also quantize the chiral ring, which corresponds to placing the 3d theory in a 2d Omega background. Then, by unifying all complex structures in a twistor space, we encode the full hyperkähler metric on themore » Coulomb branch. We verify our proposals in a multitude of examples, including SQCD and linear quiver gauge theories, whose Coulomb branches have alternative descriptions as solutions to Bogomolnyi and/or Nahm equations.« less

A dynamic processes study of PM retention by trees under different wind conditions.

PubMed

Xie, Changkun; Kan, Liyan; Guo, Jiankang; Jin, Sijia; Li, Zhigang; Chen, Dan; Li, Xin; Che, Shengquan

2018-02-01

Particulate matter (PM) is one of the most serious environmental problems, exacerbating respiratory and vascular illnesses. Plants have the ability to reduce non-point source PM pollution through retention on leaves and branches. Studies of the dynamic processes of PM retention by plants and the mechanisms influencing this process will help to improve the efficiency of urban greening for PM reduction. We examined dynamic processes of PM retention and the major factors influencing PM retention by six trees with different branch structure characteristics in wind tunnel experiments at three different wind speeds. The results showed that the changes of PM numbers retained by plant leaves over time were complex dynamic processes for which maximum values could exceed minimum values by over 10 times. The average value of PM measured in multiple periods and situations can be considered a reliable indicator of the ability of the plant to retain PM. The dynamic processes were similar for PM 10 and PM 2.5 . They could be clustered into three groups simulated by continually-rising, inverse U-shaped, and U-shaped polynomial functions, respectively. The processes were the synthetic effect of characteristics such as species, wind speed, period of exposure and their interactions. Continually-rising functions always explained PM retention in species with extremely complex branch structure. Inverse U-shaped processes explained PM retention in species with relatively simple branch structure and gentle wind. The U-shaped processes mainly explained PM retention at high wind speeds and in species with a relatively simple crown. These results indicate that using plants with complex crowns in urban greening and decreasing wind speed in plant communities increases the chance of continually-rising or inverse U-shaped relationships, which have a positive effect in reducing PM pollution. Copyright © 2017 Elsevier Ltd. All rights reserved.

Synthesis and supramolecular assembly of biomimetic polymers

NASA Astrophysics Data System (ADS)

Marciel, Amanda Brittany

A grand challenge in materials chemistry is the synthesis of macromolecules and polymers with precise shapes and architectures. Polymer microstructure and architecture strongly affect the resulting functionality of advanced materials, yet understanding the static and dynamic properties of these complex macromolecules in bulk has been difficult due to their inherit polydispersity. Single molecule studies have provided a wealth of information on linear flexible and semi-flexible polymers in dilute solutions. However, few investigations have focused on industrially relevant complex topologies (e.g., star, comb, hyperbranched polymers) in industrially relevant solution conditions (e.g., semi-dilute, concentrated). Therefore, from this perspective there is a strong need to synthesize precision complex architectures for bulk studies as well as complex architectures compatible with current single molecule techniques to study static and dynamic polymer properties. In this way, we developed a hybrid synthetic strategy to produce branched polymer architectures based on chemically modified DNA. Overall, this approach enables control of backbone length and flexibility, as well as branch grafting density and chemical identity. We utilized a two-step scheme based on enzymatic incorporation of non-natural nucleotides containing bioorthogonal dibenzocyclooctyne (DBCO) functional groups along the main polymer backbone, followed by copper-free "click" chemistry to graft synthetic polymer branches or oligonucleotide branches to the DNA backbone, thereby allowing for the synthesis of a variety of polymer architectures, including three-arm stars, H-polymers, graft block copolymers, and comb polymers for materials assembly and single molecule studies. Bulk materials properties are also affected by industrial processing conditions that alter polymer morphology. Therefore, in an alternative strategy we developed a microfluidic-based approach to assemble highly aligned synthetic oligopeptides nanostructures using microscale extensional flows. This strategy enabled reproducible, reliable fabrication of aligned hierarchical constructs that do not form spontaneously in solution. In this way, fluidic-directed assembly of supramolecular structures allows for unprecedented manipulation at the nano- and mesoscale, which has the potential to provide rapid and efficient control of functional materials properties.

The COMPASS-Like Complex Promotes Flowering and Panicle Branching in Rice1[OPEN

PubMed Central

Wang, Shiliang; Jiang, Haiyang; Cheng, Beijiu

2018-01-01

Flowering time (heading date) and panicle branch number are important agronomic traits that determine yield in rice (Oryza sativa). The activation of flowering requires histone methylation, but the roles of trimethylation of Lys 4 of histone 3 (H3K4me3) in modulating heading date and panicle development are unclear. Here, we showed that the COMPASS-like complex promotes flowering and panicle branching. The rice (Oryza sativa) WD40 protein OsWDR5a interacts with the TRITHORAX-like protein OsTrx1/SET domain group protein 723 (SDG723) to form the core components of the COMPASS-like complex. Plants in which OsWDR5a or OsTrx1 expression was decreased by RNA interference produced fewer secondary branches and less grain and exhibited a delayed heading date under long-day and short-day conditions, whereas loss of OsWDR5a function resulted in embryo lethality. OsWDR5a binds to Early heading date 1 to regulate its H3K4me3 and expression levels. Together, our results show that the COMPASS-like complex promotes flowering and panicle development and suggest that modulation of H3K4me3 levels by the COMPASS-like complex is critical for rice development. PMID:29440594

Controlled growth of novel hyper-branched nanostructures in nanoporous alumina membrane.

PubMed

Zhang, Junping; Day, Cynthia S; Carroll, David L

2009-12-07

This paper proposes a novel approach to fabricate hyper-branched anodic aluminium oxide (AAO) nanostructures with different branches on the vertically-aligned trunk and at the trunk terminal. Silver nanowires with different dimensional and multifunctional complexity have been prepared from this hyper-branched AAO template by varying the electrodeposition time. These kinds of novel nanostructure may be used to build blocks for nanoelectronic and nanophotonic devices.

Accuracy of 1D microvascular flow models in the limit of low Reynolds numbers.

PubMed

Pindera, Maciej Z; Ding, Hui; Athavale, Mahesh M; Chen, Zhijian

2009-05-01

We describe results of numerical simulations of steady flows in tubes with branch bifurcations using fully 3D and reduced 1D geometries. The intent is to delineate the range of validity of reduced models used for simulations of flows in microcapillary networks, as a function of the flow Reynolds number Re. Results from model problems indicate that for Re less than 1 and possibly as high as 10, vasculatures may be represented by strictly 1D Poiseuille flow geometries with flow variation in the axial dimensions only. In that range flow rate predictions in the different branches generated by 1D and 3D models differ by a constant factor, independent of Re. When the cross-sectional areas of the branches are constant these differences are generally small and appear to stem from an uncertainty of how the individual branch lengths are defined. This uncertainty can be accounted for by a simple geometrical correction. For non-constant cross-sections the differences can be much more significant. If additional corrections for the presence of branch junctions and flow area variations are not taken into account in 1D models of complex vasculatures, the resultant flow predictions should be interpreted with caution.

Maple syrup urine disease: The E1{beta} gene of human branched-chain {alpha}-ketoacid dehydrogenase complex has 11 rather than 10 exons, and the 3{prime} UTR in one of the two E1{beta} mRNAs arises from intronic sequences

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

Chuang, J.L.; Chuang, D.T.; Cox, R.P.

1996-06-01

Maple syrup urine disease (MSUD) or branched-chain ketoaciduria is caused by a deficiency in the mitochondrial branched-chain {alpha}-ketoacid dehydrogenase (BCKAD) complex. The clinical manifestations are characterized by accumulation of branched chain amino and {alpha}-ketoacids, which leads to severe cerebral edema with seizures, ketoacidosis, and mental retardation. The BCKAD complex comprises three catalytic components, i.e., a decarboxylase (E1) consisting of two E1{alpha} (M{sub r} = 46,000) and two E1{Beta} (M{sub r} = 37,500) subunits, a transacylase (E2) that contains 24 lipoic acid-bearing subunits, and a dehydrogenase (E3), which is a homodimeric flavoprotein. MSUD is genetically heterogeneous, since mutations in the E1{alpha}more » subunit (type IA MSUD), the E1{Beta} subunit (type IB), the E2 subunit (type II) and the E3 subunit (type III) have been described. The functional consequences of certain mutations in the BCKAD complex have been studied. 23 refs., 3 figs.« less

Optimizing the way kinematical feed chains with great distance between slides are chosen for CNC machine tools

NASA Astrophysics Data System (ADS)

Lucian, P.; Gheorghe, S.

2017-08-01

This paper presents a new method, based on FRISCO formula, for optimizing the choice of the best control system for kinematical feed chains with great distance between slides used in computer numerical controlled machine tools. Such machines are usually, but not limited to, used for machining large and complex parts (mostly in the aviation industry) or complex casting molds. For such machine tools the kinematic feed chains are arranged in a dual-parallel drive structure that allows the mobile element to be moved by the two kinematical branches and their related control systems. Such an arrangement allows for high speed and high rigidity (a critical requirement for precision machining) during the machining process. A significant issue for such an arrangement it’s the ability of the two parallel control systems to follow the same trajectory accurately in order to address this issue it is necessary to achieve synchronous motion control for the two kinematical branches ensuring that the correct perpendicular position it’s kept by the mobile element during its motion on the two slides.

Comparative morphology of stingray lateral line canal and electrosensory systems.

PubMed

Jordan, Laura K

2008-11-01

Elasmobranchs (sharks, skates, and rays) possess a variety of sensory systems including the mechanosensory lateral line and electrosensory systems, which are particularly complex with high levels of interspecific variation in batoids (skates and rays). Rays have dorsoventrally compressed, laterally expanded bodies that prevent them from seeing their mouths and more often than not, their prey. This study uses quantitative image analysis techniques to identify, quantify, and compare structural differences that may have functional consequences in the detection capabilities of three Eastern Pacific stingray species. The benthic round stingray, Urobatis halleri, pelagic stingray, Pteroplatytrygon (Dasyatis) violacea, and benthopelagic bat ray, Myliobatis californica, show significant differences in sensory morphology. Ventral lateral line canals correlate with feeding ecology and differ primarily in the proportion of pored and nonpored canals and the degree of branching complexity. Urobatis halleri shows a high proportion of nonpored canals, while P. violacea has an intermediate proportion of pored and nonpored canals with almost no secondary branching of pored canals. In contrast, M. californica has extensive and highly branched pored ventral lateral line canals that extended laterally toward the wing tips on the anterior edge of the pectoral fins. Electrosensory morphology correlates with feeding habitat and prey mobility; benthic feeders U. halleri and M. californica, have greater electrosensory pore numbers and densities than P. violacea. The percentage of the wing surface covered by these sensory systems appears to be inversely related to swimming style. These methods can be applied to a broader range of species to enable further discussion of the relationship of phylogeny, ecology, and morphology, while the results provide testable predictions of detection capabilities.

Dramatic Increase in the Signal and Sensitivity of Detection via Self-Assembly of Branched DNA

PubMed Central

Kim, Kyung-Tae; Chae, Chi-Bom

2011-01-01

In molecular testing using PCR, the target DNA is amplified via PCR and the sequence of interest is investigated via hybridization with short oligonucleotide capture probes that are either in a solution or immobilized on solid supports such as beads or glass slides. In this report, we report the discovery of assembly of DNA complex(es) between a capture probe and multiple strands of the PCR product. The DNA complex most likely has branched structure. The assembly of branched DNA was facilitated by the product of asymmetric PCR. The amount of branched DNA assembled was increased five fold when the asymmetric PCR product was denatured and hybridized with a capture probe all in the same PCR reaction mixture. The major branched DNA species appeared to contain three reverse strands (the strand complementary to the capture probe) and two forward strands. The DNA was sensitive to S1 nuclease suggesting that it had single-stranded gaps. Branched DNA also appeared to be assembled with the capture probes immobilized on the surface of solid support when the product of asymmetric PCR was hybridized. Assembly of the branched DNA was also increased when hybridization was performed in complete PCR reaction mixture suggesting the requirement of DNA synthesis. Integration of asymmetric PCR, heat denaturation and hybridization in the same PCR reaction mixture with the capture probes immobilized on the surface of solid support achieved dramatic increase in the signal and sensitivity of detection of DNA. Such a system should be advantageously applied for development of automated process for detection of DNA. PMID:21870112

Enhancement of branching efficiency by the actin filament-binding activity of N-WASP/WAVE2.

PubMed

Suetsugu, S; Miki, H; Yamaguchi, H; Obinata, T; Takenawa, T

2001-12-01

The actin-related protein (Arp) 2/3 complex is an essential regulator of de novo actin filament formation. Arp2/3 nucleates the polymerization of actin and creates branched actin filaments when activated by Arp2/3-complex activating domain (VCA) of Wiskott-Aldrich syndrome proteins (WASP family proteins). We found that the branching of actin filaments on pre-existing ADP filaments mediated by the Arp2/3 complex is twice as efficient when Arp2/3 was activated by wild-type neural WASP (N-WASP) or WASP-family verprolin-homologous protein (WAVE) 2 than when activated by the VCA domain alone. By contrast, there was no difference between wild-type N-WASP or WAVE2 and VCA in the branching efficiency on de novo filaments, which are thought to consist mainly of ADP-phosphate filaments. This increased branching efficiency on ADP filaments is due to the basic region located in the center of N-WASP and WAVE2, which was found to associate with ADP actin filaments. Actin filaments and phosphatidylinositol bisphosphate (PIP2) associate with N-WASP at different sites. This association of N-WASP and WAVE2 with actin filaments enhanced recruitment of Arp2/3 to the pre-existing filaments, presumably leading to efficient nucleation and branch formation on pre-existing filaments. These data together suggest that the actin filament binding activity of N-WASP and WAVE2 in the basic region increases the number of barbed ends created on pre-existing filaments. Efficient branching on ADP filaments may be important for initiation of actin-based motility.

Different roles of the small GTPases Rac1, Cdc42, and RhoG in CALEB/NGC-induced dendritic tree complexity.

PubMed

Schulz, Jana; Franke, Kristin; Frick, Manfred; Schumacher, Stefan

2016-10-01

Rho GTPases play prominent roles in the regulation of cytoskeletal reorganization. Many aspects have been elaborated concerning the individual functions of Rho GTPases in distinct signaling pathways leading to cytoskeletal rearrangements. However, major questions have yet to be answered regarding the integration and the signaling hierarchy of different Rho GTPases in regulating the cytoskeleton in fundamental physiological events like neuronal process differentiation. Here, we investigate the roles of the small GTPases Rac1, Cdc42, and RhoG in defining dendritic tree complexity stimulated by the transmembrane epidermal growth factor family member CALEB/NGC. Combining gain-of-function and loss-of-function analysis in primary hippocampal neurons, we find that Rac1 is essential for CALEB/NGC-mediated dendritic branching. Cdc42 reduces the complexity of dendritic trees. Interestingly, we identify the palmitoylated isoform of Cdc42 to adversely affect dendritic outgrowth and dendritic branching, whereas the prenylated Cdc42 isoform does not. In contrast to Rac1, CALEB/NGC and Cdc42 are not directly interconnected in regulating dendritic tree complexity. Unlike Rac1, the Rac1-related GTPase RhoG reduces the complexity of dendritic trees by acting upstream of CALEB/NGC. Mechanistically, CALEB/NGC activates Rac1, and RhoG reduces the amount of CALEB/NGC that is located at the right site for Rac1 activation at the cell membrane. Thus, Rac1, Cdc42, and RhoG perform very specific and non-redundant functions at different levels of hierarchy in regulating dendritic tree complexity induced by CALEB/NGC. Rho GTPases play a prominent role in dendritic branching. CALEB/NGC is a transmembrane member of the epidermal growth factor (EGF) family that mediates dendritic branching, dependent on Rac1. CALEB/NGC stimulates Rac1 activity. RhoG inhibits CALEB/NGC-mediated dendritic branching by decreasing the amount of CALEB/NGC at the plasma membrane. Palmitoylated, but not prenylated form of the GTPase Cdc42 decreases dendritic branching. CALEB/NGC and Cdc42 are not directly interconnected in regulating dendritic branching. Thus, CALEB/NGC organizes a Rho GTPase signaling module at the plasma membrane for shaping dendritic trees. © 2016 International Society for Neurochemistry.

A new method to synthesize complicated multi-branched carbon nanotubes with controlled architecture and composition.

PubMed

Wei, Dacheng; Liu, Yunqi; Cao, Lingchao; Fu, Lei; Li, Xianglong; Wang, Yu; Yu, Gui; Zhu, Daoben

2006-02-01

Here we develop a simple method by using flow fluctuation to synthesize arrays of multi-branched carbon nanotubes (CNTs) that are far more complex than those previously reported. The architectures and compositions can be well controlled, thus avoiding any template or additive. A branching mechanism of fluctuation-promoted coalescence of catalyst particles is proposed. This finding will provide a hopeful approach to the goal of CNT-based integrated circuits and be valuable for applying branched junctions in nanoelectronics and producing branched junctions of other materials.

Plasticity first: molecular signatures of a complex morphological trait in filamentous cyanobacteria.

PubMed

Koch, Robin; Kupczok, Anne; Stucken, Karina; Ilhan, Judith; Hammerschmidt, Katrin; Dagan, Tal

2017-08-31

Filamentous cyanobacteria that differentiate multiple cell types are considered the peak of prokaryotic complexity and their evolution has been studied in the context of multicellularity origins. Species that form true-branching filaments exemplify the most complex cyanobacteria. However, the mechanisms underlying the true-branching morphology remain poorly understood despite of several investigations that focused on the identification of novel genes or pathways. An alternative route for the evolution of novel traits is based on existing phenotypic plasticity. According to that scenario - termed genetic assimilation - the fixation of a novel phenotype precedes the fixation of the genotype. Here we show that the evolution of transcriptional regulatory elements constitutes a major mechanism for the evolution of new traits. We found that supplementation with sucrose reconstitutes the ancestral branchless phenotype of two true-branching Fischerella species and compared the transcription start sites (TSSs) between the two phenotypic states. Our analysis uncovers several orthologous TSSs whose transcription level is correlated with the true-branching phenotype. These TSSs are found in genes that encode components of the septosome and elongasome (e.g., fraC and mreB). The concept of genetic assimilation supplies a tenable explanation for the evolution of novel traits but testing its feasibility is hindered by the inability to recreate and study the evolution of present-day traits. We present a novel approach to examine transcription data for the plasticity first route and provide evidence for its occurrence during the evolution of complex colony morphology in true-branching cyanobacteria. Our results reveal a route for evolution of the true-branching phenotype in cyanobacteria via modification of the transcription level of pre-existing genes. Our study supplies evidence for the 'plasticity-first' hypothesis and highlights the importance of transcriptional regulation in the evolution of novel traits.

Collaborative Research. Damage and Burst Dynamics in Failure of Complex Geomaterials. A Statistical Physics Approach to Understanding the Complex Emergent Dynamics in Near Mean-Field Geological Materials

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

Rundle, John B.; Klein, William

We have carried out research to determine the dynamics of failure in complex geomaterials, specifically focusing on the role of defects, damage and asperities in the catastrophic failure processes (now popularly termed “Black Swan events”). We have examined fracture branching and flow processes using models for invasion percolation, focusing particularly on the dynamics of bursts in the branching process. We have achieved a fundamental understanding of the dynamics of nucleation in complex geomaterials, specifically in the presence of inhomogeneous structures.

A Decision-Oriented Investigation of Air Force Civil Engineering’s Operations Branch and the Implications for a Decision Support System.

DTIC Science & Technology

1984-09-01

information when making a decision [ Szilagyi and Wallace , 1983:3201." Driver and Mock used cognitive complexity ideas to develop this two dimensional...flexible AMOUNT OF INFORMATION USED High hierarchic integrative Figure 6. Cognitive Complexity Model ( Szilagyi and Wallace , 1983:321) Decisive Style. The...large amount of inform- ation. However, he processes this information with a multiple focus approach ( Szilagyi and Wallace , 1983:320-321). 26 McKenney

The ability of multi-site, multi-depth sacral lateral branch blocks to anesthetize the sacroiliac joint complex.

PubMed

Dreyfuss, Paul; Henning, Troy; Malladi, Niriksha; Goldstein, Barry; Bogduk, Nikolai

2009-01-01

To determine the physiologic effectiveness of multi-site, multi-depth sacral lateral branch injections. Double-blind, randomized, placebo-controlled study. Outpatient pain management center. Twenty asymptomatic volunteers. The dorsal innervation to the sacroiliac joint (SIJ) is from the L5 dorsal ramus and the S1-3 lateral branches. Multi-site, multi-depth lateral branch blocks were developed to compensate for the complex regional anatomy that limited the effectiveness of single-site, single-depth lateral branch injections. Bilateral multi-site, multi-depth lateral branch green dye injections and subsequent dissection on two cadavers revealed a 91% accuracy with this technique. Session 1: 20 asymptomatic subjects had a 25-g spinal needle probe their interosseous (IO) and dorsal sacroiliac (DSI) ligaments. The inferior dorsal SIJ was entered and capsular distension with contrast medium was performed. Discomfort had to occur with each provocation maneuver and a contained arthrogram was necessary to continue in the study. Session 2: 1 week later; computer randomized, double-blind multi-site, multi-depth lateral branch blocks injections were performed. Ten subjects received active (bupivicaine 0.75%) and 10 subjects received sham (normal saline) multi-site, multi-depth lateral branch injections. Thirty minutes later, provocation testing was repeated with identical methodology used in session 1. Presence or absence of pain for ligamentous probing and SIJ capsular distension. Seventy percent of the active group had an insensate IO and DSI ligaments, and inferior dorsal SIJ vs 0-10% of the sham group. Twenty percent of the active vs 10% of the sham group did not feel repeat capsular distension. Six of seven subjects (86%) retained the ability to feel repeat capsular distension despite an insensate dorsal SIJ complex. Multi-site, multi-depth lateral branch blocks are physiologically effective at a rate of 70%. Multi-site, multi-depth lateral branch blocks do not effectively block the intra-articular portion of the SIJ. There is physiological evidence that the intra-articular portion of the SIJ is innervated from both ventral and dorsal sources. Comparative multi-site, multi-depth lateral branch blocks should be considered a potentially valuable tool to diagnose extra-articular SIJ pain and determine if lateral branch radiofrequency neurotomy may assist one with SIJ pain.

Purification and properties of two terminal oxidase complexes of Escherichia coli aerobic respiratory chain.

PubMed

Kita, K; Konishi, K; Anraku, Y

1986-01-01

Two terminal oxidase complexes, cytochrome b-562-o complex and cytochrome b-558-d complex, are isolated in highly purified forms which show ubiquinol oxidase activities. From the result of steady-state kinetics of cytochromes in the membrane and E'm values of purified cytochromes, we propose a branched arrangement of the late exponential phase of aerobic growth, as shown in Fig. 10. Cytochrome b-556 is reduced by several dehydrogenases and the gene for this cytochrome (cybA) is located in the sdh gene cluster. Recently, we found another low-potential b-type cytochrome, cytochrome b-561 (Em' = 20 mV), which is also reduced by dehydrogenases. The position of this new cytochrome in the aerobic respiratory chain is under investigation. Two terminal oxidase complexes branch at the site of ubiquinone-8, and the Km value for oxygen of the purified cytochrome b-558-d complex is about 8-fold lower than that of the purified cytochrome b-562-o complex when ubiquinol-1 is used as substrate. This result is consistent with the idea that the cytochrome b-558-d complex is synthesized as an alternative oxidase for more efficient utilization of oxygen at low oxygen concentration. Thus, E. coli cells can maintain efficient oxidative energy conservation over a wide range of oxygen pressures by simply changing the contents of the two terminal oxidases, each of which functions as a coupling site.

Computational and Experimental Evaluation of a Complex Inlet Swirl Pattern Generation System (POSTPRINT)

DTIC Science & Technology

2016-08-01

Sanders, Chase A. Nessler, William W. Copenhaver, Michael G. List, and Timothy J. Janczewski Turbomachinery Branch Turbine Engine Division AUGUST...Branch Turbine Engine Division Turbine Engine Division Aerospace Systems Directorate //Signature// ROBERT D. HANCOCK Principal Scientist Turbine ...ORGANIZATION Turbomachinery Branch Turbine Engine Division Air Force Research Laboratory, Aerospace Systems Directorate Wright-Patterson Air Force

Dissociation of branched-chain alpha-keto acid dehydrogenase kinase (BDK) from branched-chain alpha-keto acid dehydrogenase complex (BCKDC) by BDK inhibitors.

PubMed

Murakami, Taro; Matsuo, Masayuki; Shimizu, Ayako; Shimomura, Yoshiharu

2005-02-01

Branched-chain alpha-keto acid dehydrogenase kinase (BDK) phosphorylates and inactivates the branched-chain alpha-keto acid dehydrogenase complex (BCKDC), which is the rate-limiting enzyme in the branched-chain amino acid catabolism. BDK has been believed to be bound to the BCKDC. However, recent our studies demonstrated that protein-protein interaction between BDK and BCKDC is one of the factors to regulate BDK activity. Furthermore, only the bound form of BDK appears to have its activity. In the present study, we examined effects of BDK inhibitors on the amount of BDK bound to the BCKDC using rat liver extracts. The bound form of BDK in the extracts of liver from low protein diet-fed rats was measured by an immunoprecipitation pull down assay with or without BDK inhibitors. Among the BDK inhibitors. alpha-ketoisocaproate, alpha-chloroisocaproate, and a-ketoisovalerate released the BDK from the complex. Furthermore, the releasing effect of these inhibitors on the BDK appeared to depend on their inhibition constants. On the other hand, clofibric acid and thiamine pyrophosphate had no effect on the protein-protein interaction between two enzymes. These results suggest that the dissociation of the BDK from the BCKDC is one of the mechanisms responsible for the action of some inhibitors to BDK.

Decreased enzyme activity and contents of hepatic branched-chain alpha-keto acid dehydrogenase complex subunits in a rat model for type 2 diabetes mellitus.

PubMed

Bajotto, Gustavo; Murakami, Taro; Nagasaki, Masaru; Sato, Yuzo; Shimomura, Yoshiharu

2009-10-01

The mitochondrial branched-chain alpha-keto acid dehydrogenase complex (BCKDC) is responsible for the committed step in branched-chain amino acid catabolism. In the present study, we examined BCKDC regulation in Otsuka Long-Evans Tokushima Fatty (OLETF) rats both before (8 weeks of age) and after (25 weeks of age) the onset of type 2 diabetes mellitus. Long-Evans Tokushima Otsuka (LETO) rats were used as controls. Plasma branched-chain amino acid and branched-chain alpha-keto acid concentrations were significantly increased in young and middle-aged OLETF rats. Although the hepatic complex was nearly 100% active in all animals, total BCKDC activity and protein abundance of E1alpha, E1beta, and E2 subunits were markedly lower in OLETF than in LETO rats at 8 and 25 weeks of age. In addition, hepatic BCKDC activity and protein amounts were significantly decreased in LETO rats aged 25 weeks than in LETO rats aged 8 weeks. In skeletal muscle, E1beta and E2 proteins were significantly reduced, whereas E1alpha tended to increase in OLETF rats. Taken together, these results suggest that (1) whole-body branched-chain alpha-keto acid oxidation capacity is extremely reduced in OLETF rats independently of diabetes development, (2) the aging process decreases BCKDC activity and protein abundance in the liver of normal rats, and (3) differential posttranscriptional regulation for the subunits of BCKDC may exist in skeletal muscle.

The antagonistic modulation of Arp2/3 activity by N-WASP, WAVE2 and PICK1 defines dynamic changes in astrocyte morphology.

PubMed

Murk, Kai; Blanco Suarez, Elena M; Cockbill, Louisa M R; Banks, Paul; Hanley, Jonathan G

2013-09-01

Astrocytes exhibit a complex, branched morphology, allowing them to functionally interact with numerous blood vessels, neighboring glial processes and neuronal elements, including synapses. They also respond to central nervous system (CNS) injury by a process known as astrogliosis, which involves morphological changes, including cell body hypertrophy and thickening of major processes. Following severe injury, astrocytes exhibit drastically reduced morphological complexity and collectively form a glial scar. The mechanistic details behind these morphological changes are unknown. Here, we investigate the regulation of the actin-nucleating Arp2/3 complex in controlling dynamic changes in astrocyte morphology. In contrast to other cell types, Arp2/3 inhibition drives the rapid expansion of astrocyte cell bodies and major processes. This intervention results in a reduced morphological complexity of astrocytes in both dissociated culture and in brain slices. We show that this expansion requires functional myosin II downstream of ROCK and RhoA. Knockdown of the Arp2/3 subunit Arp3 or the Arp2/3 activator N-WASP by siRNA also results in cell body expansion and reduced morphological complexity, whereas depleting WAVE2 specifically reduces the branching complexity of astrocyte processes. By contrast, knockdown of the Arp2/3 inhibitor PICK1 increases astrocyte branching complexity. Furthermore, astrocyte expansion induced by ischemic conditions is delayed by PICK1 knockdown or N-WASP overexpression. Our findings identify a new morphological outcome for Arp2/3 activation in restricting rather than promoting outwards movement of the plasma membrane in astrocytes. The Arp2/3 regulators PICK1, and N-WASP and WAVE2 function antagonistically to control the complexity of astrocyte branched morphology, and this mechanism underlies the morphological changes seen in astrocytes during their response to pathological insult.

Topological analysis of long-chain branching patterns in polyolefins.

PubMed

Bonchev, D; Markel, E; Dekmezian, A

2001-01-01

Patterns in molecular topology and complexity for long-chain branching are quantitatively described. The Wiener number, the topological complexity index, and a new index of 3-starness are used to quantify polymer structure. General formulas for these indices were derived for the cases of 3-arm star, H-shaped, and B-arm comb polymers. The factors affecting complexity in monodisperse polymer systems are ranked as follows: number of arms > arm length > arm central position approximately equal to arm clustering > total molecular weight approximately equal to backbone molecular weight. Topological indices change rapidly and then plateau as the molecular weight of branches on a polyolefin backbone increases from 0 to 5 kD. Complexity calculations relate 2-arm or 3-arm comb structures to the corresponding 3-arm stars of equivalent complexity but much higher molecular weight. In a subsequent paper, we report the application of topological analysis for developing structure/property relationships for monodisperse polymers. While the focus of the present work is on the description of monodisperse, well-defined architectures, the methods may be extended to the description of polydisperse systems.

Unravelling the nanostructure of strawberry fruit pectins by endo-polygalacturonase digestion and atomic force microscopy.

PubMed

Paniagua, Candelas; Kirby, Andrew R; Gunning, A Patrick; Morris, Victor J; Matas, Antonio J; Quesada, Miguel A; Mercado, José A

2017-06-01

Pectins analysed by AFM are visualized as individual chains, branched or unbranched, and aggregates. To investigate the nature of these structures, sodium carbonate soluble pectins from strawberry fruits were digested with endo-polygalacturonase M2 from Aspergillus aculeatus and visualized by AFM. A gradual decrease in the length of chains was observed as result of the treatment, reaching a minimum L N value of 22nm. The branches were not visible after 2h of enzymatic incubation. The size of complexes also diminished significantly with the enzymatic digestion. A treatment to hydrolyse rhamnogalacturonan II borate diester bonds neither affected chains length or branching nor complex size but reduced the density of aggregates. These results suggest that chains are formed by a mixture of homogalacturonan and more complex molecules composed by a homogalacturonan unit linked to an endo-PG resistant unit. Homogalacturonan is a structural component of the complexes and rhamnogalacturonan II could be involved in their formation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Nanoscale segregation of actin nucleation and elongation factors determines dendritic spine protrusion

PubMed Central

Chazeau, Anaël; Mehidi, Amine; Nair, Deepak; Gautier, Jérémie J; Leduc, Cécile; Chamma, Ingrid; Kage, Frieda; Kechkar, Adel; Thoumine, Olivier; Rottner, Klemens; Choquet, Daniel; Gautreau, Alexis; Sibarita, Jean-Baptiste; Giannone, Grégory

2014-01-01

Actin dynamics drive morphological remodeling of neuronal dendritic spines and changes in synaptic transmission. Yet, the spatiotemporal coordination of actin regulators in spines is unknown. Using single protein tracking and super-resolution imaging, we revealed the nanoscale organization and dynamics of branched F-actin regulators in spines. Branched F-actin nucleation occurs at the PSD vicinity, while elongation occurs at the tip of finger-like protrusions. This spatial segregation differs from lamellipodia where both branched F-actin nucleation and elongation occur at protrusion tips. The PSD is a persistent confinement zone for IRSp53 and the WAVE complex, an activator of the Arp2/3 complex. In contrast, filament elongators like VASP and formin-like protein-2 move outwards from the PSD with protrusion tips. Accordingly, Arp2/3 complexes associated with F-actin are immobile and surround the PSD. Arp2/3 and Rac1 GTPase converge to the PSD, respectively, by cytosolic and free-diffusion on the membrane. Enhanced Rac1 activation and Shank3 over-expression, both associated with spine enlargement, induce delocalization of the WAVE complex from the PSD. Thus, the specific localization of branched F-actin regulators in spines might be reorganized during spine morphological remodeling often associated with synaptic plasticity. PMID:25293574

Whey protein supplementation does not alter plasma branched-chained amino acid profiles but results in unique metabolomics patterns in obese women enrolled in an 8-week weight loss trial

USDA-ARS?s Scientific Manuscript database

Background. Elevations of plasma concentrations of branched-chain amino acids (BCAA) are correlated with insulin resistance. Reduction in the activity of branched-chain ketoacid dehydrogenase complex (BCKDC) activity and impaired complete mitochondrial BCAA catabolism may contribute to this phenoty...

Managing International Branch Campuses: Lessons Learnt from Eight Years on a Branch Campus in Malaysia

ERIC Educational Resources Information Center

Hill, Christopher; Thabet, Rawy Abdelrahman

2018-01-01

Purpose: International branch campuses (IBCs) are complex entities and while much has been written about their expansion and development, the literature is largely from an external perspective. There have been few longitudinal studies examining the development of an IBC over time. The purpose of this paper is to review the development of one IBC…

Gravity driven and in situ fractional crystallization processes in the Centre Hill complex, Abitibi Subprovince, Canada: Evidence from bilaterally-paired cyclic units

NASA Astrophysics Data System (ADS)

Thériault, R. D.; Fowler, A. D.

1996-12-01

The formation of layers in mafic intrusions has been explained by various processes, making it the subject of much controversy. The concept that layering originates from gravitational settling of crystals has been superseded in recent years by models involving in situ fractional crystallization. Here we present evidence from the Centre Hill complex that both processes may be operative simultaneously within the same intrusion. The Centre Hill complex is part of the Munro Lake sill, an Archean layered mafic intrusion emplaced in volcanic rocks of the Abitibi Subprovince. The Centre Hill complex comprises the following lithostratigraphic units: six lower cyclic units of peridotite and clinopyroxenite; a middle unit of leucogabbro; six upper cyclic units of branching-textured gabbro (BTG) and clotted-textured gabbro (CTG), the uppermost of these units being overlain by a marginal zone of fine-grained gabbro. The cyclic units of peridotite/clinopyroxenite and BTG/CTG are interpreted to have formed concurrently through fractional crystallization, associated with periodic replenishment of magma to the chamber. The units of peridotite and clinopyroxenite formed by gravitational accumulation of crystals that grew under the roof. The cyclic units of BTG and CTG formed along the upper margin of the sill by two different mechanisms: (1) layers of BTG crystallized in situ along an inward-growing roof and (2) layers of CTG formed by accumulation of buoyant plagioclase crystals. The layers of BTG are characterized by branching pseudomorphs after fayalite up to 50 cm in length that extend away from the upper margin. The original branching crystals are interpreted to have grown from stagnant intercumulus melt in a high thermal gradient resulting from the injection of new magma to the chamber.

Surgical anatomy of the hypoglossal nerve: A new classification system for selective upper airway stimulation.

PubMed

Heiser, Clemens; Knopf, Andreas; Hofauer, Benedikt

2017-12-01

Selective upper airway stimulation (UAS) has shown effectiveness in treating patients with obstructive sleep apnea (OSA). The terminating branches of the hypoglossal nerve show a wide complexity, requiring careful discernment of a functional breakpoint between branches for inclusion and exclusion from the stimulation cuff electrode. The purpose of this study was to describe and categorize the topographic phenotypes of these branches. Thirty patients who received an implant with selective UAS from July 2015 to June 2016 were included. All implantations were recorded using a microscope and resultant tongue motions were captured perioperatively for comparison. Eight different variations of the branches were encountered and described, both in a tabular numeric fashion and in pictorial schema. The examinations showed the complex phenotypic surgical anatomy of the hypoglossal nerve. A schematic classification system has been developed to help surgeons identify the optimal location for cuff placement in UAS. © 2017 Wiley Periodicals, Inc.

Effects of predation on diel activity and habitat use of the coral-reef shrimp Cinetorhynchus hendersoni (Rhynchocinetidae)

NASA Astrophysics Data System (ADS)

Ory, Nicolas C.; Dudgeon, David; Duprey, Nicolas; Thiel, Martin

2014-09-01

Nonlethal effects of predators on prey behaviour are still poorly understood, although they may have cascading effects through food webs. Underwater observations and experiments were conducted on a shallow fringing coral reef in Malaysia to examine whether predation risks affect diel activity, habitat use, and survival of the rhynchocinetid shrimp Cinetorhynchus hendersoni. The study site was within a protected area where predatory fish were abundant. Visual surveys and tethering experiments were conducted in April-May 2010 to compare the abundance of shrimps and predatory fishes and the relative predation intensity on shrimps during day and night. Shrimps were not seen during the day but came out of refuges at night, when the risk of being eaten was reduced. Shrimp preferences for substrata of different complexities and types were examined at night when they could be seen on the reef; complex substrata were preferred, while simple substrata were avoided. Shrimps were abundant on high-complexity columnar-foliate Porites rus, but tended to make little use of branching Acropora spp. Subsequent tethering experiments, conducted during daytime in June 2013, compared the relative mortality of shrimps on simple (sand-rubble, massive Porites spp.) and complex ( P. rus, branching Acropora spp.) substrata under different predation risk scenarios (i.e., different tether lengths and exposure durations). The mortality of shrimps with short tethers (high risk) was high on all substrata while, under low and intermediate predation risks (long tethers), shrimp mortality was reduced on complex corals relative to that on sand-rubble or massive Porites spp. Overall, mortality was lowest on P. rus. Our study indicates that predation risks constrain shrimp activity and habitat choice, forcing them to hide deep inside complex substrata during the day. Such behavioural responses to predation risks and their consequences for the trophic role of invertebrate mesoconsumers warrant further investigation, especially in areas where predatory fishes have been overexploited.

Secondary motion in three-dimensional branching networks

NASA Astrophysics Data System (ADS)

Guha, Abhijit; Pradhan, Kaustav

2017-06-01

A major aim of the present work is to understand and thoroughly document the generation, the three-dimensional distribution, and the evolution of the secondary motion as the fluid progresses downstream through a branched network. Six generations (G0-G5) of branches (involving 63 straight portions and 31 bifurcation modules) are computed in one go; such computational challenges are rarely taken in the literature. More than 30 × 106 computational elements are employed for high precision of computed results and fine quality of the flow visualization diagrams. The study of co-planar vis-à-vis non-planar space-filling configurations establishes a quantitative evaluation of the dependence of the fluid dynamics on the three-dimensional arrangement of the same individual branches. As compared to the secondary motion in a simple curved pipe, three distinctive features, viz., the change of shape and size of the flow-cross-section, the division of non-uniform primary flow in a bifurcation module, and repeated switchover from clockwise to anticlockwise curvature and vice versa in the flow path, make the present situation more complex. It is shown that the straight portions in the network, in general, attenuate the secondary motion, while the three-dimensionally complex bifurcation modules generate secondary motion and may alter the number, arrangement, and structure of vortices. A comprehensive picture of the evolution of quantitative flow visualizations of the secondary motion is achieved by constructing contours of secondary velocity | v → S | , streamwise vorticity ω S , and λ 2 iso-surfaces. It is demonstrated, for example, that for in-plane configuration, the vortices on any plane appear in pair (i.e., for each clockwise rotating vortex, there is an otherwise identical anticlockwise vortex), whereas the vortices on a plane for the out-of-plane configuration may be dissimilar, and there may even be an odd number of vortices. We have formulated three new parameters (ES/P, δ S F , and δ G n ) for a quantitative description of the overall features of the secondary flow field. δ S F represents a non-uniformity index of the secondary flow in an individual branch, ES/P represents the mass-flow-averaged relative kinetic energy of the secondary motion in an individual branch, and δ G n provides a measure of the non-uniformity of the secondary flow between various branches of the same generation Gn. The repeated enhancement of the secondary kinetic energy in the bifurcation modules is responsible for the occurrence of significant values of ES/P even in generation G5. For both configurations, it is found that for any bifurcation module, the value of ES/P is greater in that daughter branch in which the mass-flow rate is greater. Even though the various contour plots of the complex secondary flow structure appear visually very different from one another, the values of δ S F are found to lie within a small range ( 0.37 ≤ δ S F ≤ 0.66 ) for the six-generation networks studied. It is shown that δ G n grows as the generation number Gn increases. It is established that the out-of-plane configuration, in general, creates more secondary kinetic energy (higher ES/P), a similar level of non-uniformity in the secondary flow in an individual branch (similar δ S F ), and a significantly lower level of non-uniformity in the distribution of secondary motion among various branches of the same generation (much lower δ G n ), as compared to the in-plane arrangement of the same branches.

Secondary motion in three-dimensional branching networks

PubMed Central

Guha, Abhijit; Pradhan, Kaustav

2017-01-01

A major aim of the present work is to understand and thoroughly document the generation, the three-dimensional distribution, and the evolution of the secondary motion as the fluid progresses downstream through a branched network. Six generations (G0-G5) of branches (involving 63 straight portions and 31 bifurcation modules) are computed in one go; such computational challenges are rarely taken in the literature. More than 30 × 106 computational elements are employed for high precision of computed results and fine quality of the flow visualization diagrams. The study of co-planar vis-à-vis non-planar space-filling configurations establishes a quantitative evaluation of the dependence of the fluid dynamics on the three-dimensional arrangement of the same individual branches. As compared to the secondary motion in a simple curved pipe, three distinctive features, viz., the change of shape and size of the flow-cross-section, the division of non-uniform primary flow in a bifurcation module, and repeated switchover from clockwise to anticlockwise curvature and vice versa in the flow path, make the present situation more complex. It is shown that the straight portions in the network, in general, attenuate the secondary motion, while the three-dimensionally complex bifurcation modules generate secondary motion and may alter the number, arrangement, and structure of vortices. A comprehensive picture of the evolution of quantitative flow visualizations of the secondary motion is achieved by constructing contours of secondary velocity v→S, streamwise vorticity ωS, and λ2 iso-surfaces. It is demonstrated, for example, that for in-plane configuration, the vortices on any plane appear in pair (i.e., for each clockwise rotating vortex, there is an otherwise identical anticlockwise vortex), whereas the vortices on a plane for the out-of-plane configuration may be dissimilar, and there may even be an odd number of vortices. We have formulated three new parameters (ES/P, δSF, and δGn) for a quantitative description of the overall features of the secondary flow field. δSF represents a non-uniformity index of the secondary flow in an individual branch, ES/P represents the mass-flow-averaged relative kinetic energy of the secondary motion in an individual branch, and δGn provides a measure of the non-uniformity of the secondary flow between various branches of the same generation Gn. The repeated enhancement of the secondary kinetic energy in the bifurcation modules is responsible for the occurrence of significant values of ES/P even in generation G5. For both configurations, it is found that for any bifurcation module, the value of ES/P is greater in that daughter branch in which the mass-flow rate is greater. Even though the various contour plots of the complex secondary flow structure appear visually very different from one another, the values of δSF are found to lie within a small range (0.37≤δSF≤0.66) for the six-generation networks studied. It is shown that δGn grows as the generation number Gn increases. It is established that the out-of-plane configuration, in general, creates more secondary kinetic energy (higher ES/P), a similar level of non-uniformity in the secondary flow in an individual branch (similar δSF), and a significantly lower level of non-uniformity in the distribution of secondary motion among various branches of the same generation (much lower δGn), as compared to the in-plane arrangement of the same branches. PMID:28713213

Branch length mediates flower production and inflorescence architecture of Fouquieria splendens (ocotillo)

USGS Publications Warehouse

Bowers, Janice E.

2006-01-01

The capacity of individual branches to store water and fix carbon can have profound effects on inflorescence size and architecture, thus on floral display, pollination, and fecundity. Mixed regression was used to investigate the relation between branch length, a proxy for plant resources, and floral display of Fouquieria splendens (ocotillo), a woody, candelabraform shrub of wide distribution in arid North America. Long branches produced three times as many flowers as short branches, regardless of overall plant size. Long branches also had more complex panicles with more cymes and cyme types than short branches; thus, branch length also influenced inflorescence architecture. Within panicles, increasing the number of cymes by one unit added about two flowers, whereas increasing the number of cyme types by one unit added about 21 flowers. Because flower production is mediated by branch length, and because most plants have branches of various lengths, the floral display of individual plants necessarily encompasses a wide range of inflorescence size and structure. ?? Springer 2006.

Regio- and Enantioselective N-Allylations of Imidazole, Benzimidazole, and Purine Heterocycles Catalyzed by Single-Component Metallacyclic Iridium Complexes

PubMed Central

Stanley, Levi M.

2010-01-01

Highly regio- and enantioselective iridium-catalyzed N-allylations of benzimidazoles, imidazoles, and purines have been developed. N-Allylated benzimidazoles and imidazoles were isolated in high yields (up to 97%) with high branched-to-linear selectivity (up to 99:1) and enantioselectivity (up to 98% ee) from the reactions of benzimidazole and imidazole nucleophiles with unsymmetrical allylic carbonates in the presence of single component, ethylene-bound, metallacyclic iridium catalysts. N-Allylated purines were also obtained in high yields (up to 91%) with high N9:N7 selectivity (up to 96:4), high branched-to-linear selectivity (98:2), and high enantioselectivity (up to 98% ee) under similar conditions. The reactions encompass a range of benzimidazole, imidazole, and purine nucleophiles, as well as a variety of unsymmetrical aryl, heteroaryl, and aliphatic allylic carbonates. Competition experiments between common amine nucleophiles and the heterocyclic nitrogen nucleophiles studied in this work illustrate the effect of nucleophile pKa on the rate of iridium-catalyzed N-allylation reactions. Kinetic studies on the allylation of benzimidazole catalyzed by metallacyclic iridium-phosphoramidite complexes, in combination with studies on the deactivation of these catalysts in the presence of heterocyclic nucleophiles, provide insight into the effects of the structure of the phosphoramidite ligands on the stability of the metallacyclic catalysts. The data obtained from these studies has led to the development of N-allylations of benzimidazoles and imidazoles in the absence of an exogenous base. PMID:19480431

A neutral branched platinum-acetylide complex possessing a tetraphenylethylene core: preparation of a luminescent organometallic gelator and its unexpected spectroscopic behaviour during sol-to-gel transition.

PubMed

Ren, Yuan-Yuan; Wu, Nai-Wei; Huang, Junhai; Xu, Zheng; Sun, Dan-Dan; Wang, Cui-Hong; Xu, Lin

2015-10-21

A neutral branched platinum-acetylide complex TPA possessing a tetraphenylethylene core was successfully prepared, which was found to form luminescent organometallic gels in ethyl acetate. Stimulated by temperature or F(-), the reversible gel-sol transition was realized. More interestingly, TPA exhibited an unexpected blue shift of the emission during the sol-to-gel transition.

Neurexin and Neuroligin-based adhesion complexes drive axonal arborisation growth independent of synaptic activity

PubMed Central

Constance, William D; Mukherjee, Amrita; Fisher, Yvette E; Pop, Sinziana; Blanc, Eric; Toyama, Yusuke

2018-01-01

Building arborisations of the right size and shape is fundamental for neural network function. Live imaging in vertebrate brains strongly suggests that nascent synapses are critical for branch growth during development. The molecular mechanisms underlying this are largely unknown. Here we present a novel system in Drosophila for studying the development of complex arborisations live, in vivo during metamorphosis. In growing arborisations we see branch dynamics and localisations of presynaptic proteins very similar to the ‘synaptotropic growth’ described in fish/frogs. These accumulations of presynaptic proteins do not appear to be presynaptic release sites and are not paired with neurotransmitter receptors. Knockdowns of either evoked or spontaneous neurotransmission do not impact arbor growth. Instead, we find that axonal branch growth is regulated by dynamic, focal localisations of Neurexin and Neuroligin. These adhesion complexes provide stability for filopodia by a ‘stick-and-grow’ based mechanism wholly independent of synaptic activity. PMID:29504935

The central branch of the North Anatolian Fault In The Southern Marmara Sea: Evidence for a distributed, Holocene-active fault system

NASA Astrophysics Data System (ADS)

Barın, Burcu; Okay, Seda; Çifçi, Günay; Dondurur, Derman; Cormier, Marie Helene; Sorlien, Christopher; Meriç İlkimen, Elif

2015-04-01

The North Anatolian Fault (NAF) is a major right-lateral transform fault in northern Turkey that branches westward into several strands in the vicinity of the Sea of Marmara. The main northern branch bisects the Marmara Sea from east to west, and seismic reflection profiles acquired over the past 15 years have revealed its complex geometry. Further, the several basins that developed along that branch record stratigraphic sequences that provide the needed framework to interpret the relative timing of tectonic deformation in the Marmara Sea. In contrast, the central branch, which snakes across the shallow southern shelf of the Marmara Sea, has been much less investigated. Here, we analyze a comprehensive dataset of high-resolution multi-channel, sparker, and CHIRP seismic profiles, which were collected with the facilities of Seismic Laboratory (SeisLab) in the Institute of Marine Sciences and Technology and R/V K. Piri Reis belonging to Dokuz Eylül University, along the central branch in 2008 (TAMAM expedition) and in 2013-2014 (SoMAR expedition), within the framework of a bilateral TÜBİTAK - NSF project. In combination with other existing seismic profiles, these new data reveal that the Central Branch consists of multiple faults strands that are distributed across the broad southern shelf. They also reveal that many of these strands are Holocene-active, although they slip at slower rates than the northern branch and are associated with slower basin subsidence or local uplift. Lastly, seismic data image a system of half-grabens across the southern shelf that are associated with the strands of the central branch. Strata within these half-grabens are progressively tilted and consistently dip to the south. Further analysis will be conducted to determine whether the formation of these grabens are controlled by oblique slip on the strands of the central branch, or by slip on detachment faults beneath the southern shelf.

How Often Do They Have Sex? A Comparative Analysis of the Population Structure of Seven Eukaryotic Microbial Pathogens

PubMed Central

Tomasini, Nicolás; Lauthier, Juan José; Ayala, Francisco José; Tibayrenc, Michel; Diosque, Patricio

2014-01-01

The model of predominant clonal evolution (PCE) proposed for micropathogens does not state that genetic exchange is totally absent, but rather, that it is too rare to break the prevalent PCE pattern. However, the actual impact of this “residual” genetic exchange should be evaluated. Multilocus Sequence Typing (MLST) is an excellent tool to explore the problem. Here, we compared online available MLST datasets for seven eukaryotic microbial pathogens: Trypanosoma cruzi, the Fusarium solani complex, Aspergillus fumigatus, Blastocystis subtype 3, the Leishmania donovani complex, Candida albicans and Candida glabrata. We first analyzed phylogenetic relationships among genotypes within each dataset. Then, we examined different measures of branch support and incongruence among loci as signs of genetic structure and levels of past recombination. The analyses allow us to identify three types of genetic structure. The first was characterized by trees with well-supported branches and low levels of incongruence suggesting well-structured populations and PCE. This was the case for the T. cruzi and F. solani datasets. The second genetic structure, represented by Blastocystis spp., A. fumigatus and the L. donovani complex datasets, showed trees with weakly-supported branches but low levels of incongruence among loci, whereby genetic structuration was not clearly defined by MLST. Finally, trees showing weakly-supported branches and high levels of incongruence among loci were observed for Candida species, suggesting that genetic exchange has a higher evolutionary impact in these mainly clonal yeast species. Furthermore, simulations showed that MLST may fail to show right clustering in population datasets even in the absence of genetic exchange. In conclusion, these results make it possible to infer variable impacts of genetic exchange in populations of predominantly clonal micro-pathogens. Moreover, our results reveal different problems of MLST to determine the genetic structure in these organisms that should be considered. PMID:25054834

Disassortativity of random critical branching trees

NASA Astrophysics Data System (ADS)

Kim, J. S.; Kahng, B.; Kim, D.

2009-06-01

Random critical branching trees (CBTs) are generated by the multiplicative branching process, where the branching number is determined stochastically, independent of the degree of their ancestor. Here we show analytically that despite this stochastic independence, there exists the degree-degree correlation (DDC) in the CBT and it is disassortative. Moreover, the skeletons of fractal networks, the maximum spanning trees formed by the edge betweenness centrality, behave similarly to the CBT in the DDC. This analytic solution and observation support the argument that the fractal scaling in complex networks originates from the disassortativity in the DDC.

Directing the Branching Growth of Cuprous Oxide by OH- Ions

NASA Astrophysics Data System (ADS)

Chen, Kunfeng; Si, Yunfei; Xue, Dongfeng

The effect of OH- ions on the branching growth of cuprous oxide microcrystals was systematically studied by a reduction route, where copper-citrate complexes were reduced by glucose under alkaline conditions. Different copper salts including Cu(NO3)2, CuCl2, CuSO4, and Cu(Ac)2 were used in this work. The results indicate that the Cu2O branching growth habit is closely correlated to the concentration of OH- ions, which plays an important role in directing the diffusion-limited branching growth of Cu2O and influencing the reduction power of glucose. A variety of Cu2O branching patterns including 6-pod, 8-pod and 24-pod branches, have been achieved without using template and surfactant. The current method can provide a good platform for studying the growth mechanism of microcrystal branching patterns.

A Research Program on the Asymptotic Description of Electromagnetic Pulse Propagation in Spatially Inhomogeneous Temporally Dispersive, Attenuative Media

DTIC Science & Technology

2007-09-01

the right- half of the complex wo- plane . The Sommerfeld precursor then describes the signal front which arrives at 0 = 1 with...resonance Lorentz model dielectric [18], the complex phase function qO(w, 0) is analytic in the w- plane formed by the two branch cuts in the lower half of... the w,- plane symmetrically located about the imaginary axis. In the right half plane , the branch

A highly accurate analytical solution for the surface fields of a short vertical wire antenna lying on a multilayer ground

NASA Astrophysics Data System (ADS)

Parise, M.

2018-01-01

A highly accurate analytical solution is derived to the electromagnetic problem of a short vertical wire antenna located on a stratified ground. The derivation consists of three steps. First, the integration path of the integrals describing the fields of the dipole is deformed and wrapped around the pole singularities and the two vertical branch cuts of the integrands located in the upper half of the complex plane. This allows to decompose the radiated field into its three contributions, namely the above-surface ground wave, the lateral wave, and the trapped surface waves. Next, the square root terms responsible for the branch cuts are extracted from the integrands of the branch-cut integrals. Finally, the extracted square roots are replaced with their rational representations according to Newton's square root algorithm, and residue theorem is applied to give explicit expressions, in series form, for the fields. The rigorous integration procedure and the convergence of square root algorithm ensure that the obtained formulas converge to the exact solution. Numerical simulations are performed to show the validity and robustness of the developed formulation, as well as its advantages in terms of time cost over standard numerical integration procedures.

Influence of chemical structure of branched and dendritic organosilicon luminophores on their optical and thermal properties

NASA Astrophysics Data System (ADS)

Borshchev, Oleg V.; Kleymyuk, Elena A.; Surin, Nikolay M.; Svidchenko, Evgeniya A.; Fedorov, Yuriy V.; Dmitryakov, Petr V.; Chvalun, Sergei N.; Ponomarenko, Sergei A.

2017-04-01

Synthesis and investigation of optical and thermal properties of a homologous series of highly luminescent nanostructured organosilicon luminophores (NOLs) containing different donor to acceptor ratio (D:A) are reported. Each of the NOL consists of a 1,4-bis(5-phenylthienyl-2-yl)benzene (PTPTP) acceptor unit and four, six or twelve 2,2'-bithienyl donor fragments connected to each other through two or six silicon atoms. These complex molecules show a "molecular antenna" effect with high efficiency of intramolecular energy transfer about 97-98% combined with excellent photoluminescence (PL) quantum yield of 84-91% and fast PL decay time of 0.90-0.95 ns. A significant increase of the molar extinction coefficient from 94 000 to 257 000 M-1cm-1 with increasing the D:A ratio from 4:1 to 12:1 was observed. It was found that increasing the branching extent in the NOLs prohibits their crystallization. Thermal gravimetric analysis (TGA) showed that all the NOLs reported, regardless of their branching extent, are thermally stable up to 455 °C under nitrogen. These characteristics make them promising materials for various organic photonics applications.

Effect of thermal modification on rheological properties of polyethylene blends

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

Siriprumpoonthum, Monchai; Nobukawa, Shogo; Yamaguchi, Masayuki, E-mail: m-yama@jaist.ac.jp

2014-03-15

We examined the effects of thermal modification under flow field on the rheological properties of linear low-density polyethylene (LLDPE) with high molecular weight, low-density polyethylene (LDPE), and their blends, without thermal stabilizer. Although structural changes during processing are not detected by size extrusion chromatography or nuclear magnetic resonance spectroscopy, linear viscoelastic properties changed greatly, especially for the LLDPE. A cross-linking reaction took place, leading to, presumably, star-shaped long-chain branches. Consequently, the modified LLDPE, having high zero-shear viscosity, became a thermorheologically complex melt. Moreover, it should be noted that the drawdown force, defined as the uniaxial elongational force at a constantmore » draw ratio, was significantly enhanced for the blends. Enhancement of elongational viscosity was also detected. The drawdown force and elongational viscosity are marked for the thermally modified blend as compared with those for the blend of thermally modified pure components. Intermolecular cross-linking reactions between LDPE and LLDPE, yielding polymers with more than two branch points per chain, result in marked strain-hardening in the elongational viscosity behavior even at small strain. The recovery curve of the oscillatory modulus after the shear modification is further evidence of a branched structure.« less

Geodynamics branch data base for main magnetic field analysis

NASA Technical Reports Server (NTRS)

Langel, Robert A.; Baldwin, R. T.

1991-01-01

The data sets used in geomagnetic field modeling at GSFC are described. Data are measured and obtained from a variety of information and sources. For clarity, data sets from different sources are categorized and processed separately. The data base is composed of magnetic observatory data, surface data, high quality aeromagnetic, high quality total intensity marine data, satellite data, and repeat data. These individual data categories are described in detail in a series of notebooks in the Geodynamics Branch, GSFC. This catalog reviews the original data sets, the processing history, and the final data sets available for each individual category of the data base and is to be used as a reference manual for the notebooks. Each data type used in geomagnetic field modeling has varying levels of complexity requiring specialized processing routines for satellite and observatory data and two general routines for processing aeromagnetic, marine, land survey, and repeat data.

The antagonistic modulation of Arp2/3 activity by N-WASP, WAVE2 and PICK1 defines dynamic changes in astrocyte morphology

PubMed Central

Murk, Kai; Blanco Suarez, Elena M.; Cockbill, Louisa M. R.; Banks, Paul; Hanley, Jonathan G.

2013-01-01

Summary Astrocytes exhibit a complex, branched morphology, allowing them to functionally interact with numerous blood vessels, neighboring glial processes and neuronal elements, including synapses. They also respond to central nervous system (CNS) injury by a process known as astrogliosis, which involves morphological changes, including cell body hypertrophy and thickening of major processes. Following severe injury, astrocytes exhibit drastically reduced morphological complexity and collectively form a glial scar. The mechanistic details behind these morphological changes are unknown. Here, we investigate the regulation of the actin-nucleating Arp2/3 complex in controlling dynamic changes in astrocyte morphology. In contrast to other cell types, Arp2/3 inhibition drives the rapid expansion of astrocyte cell bodies and major processes. This intervention results in a reduced morphological complexity of astrocytes in both dissociated culture and in brain slices. We show that this expansion requires functional myosin II downstream of ROCK and RhoA. Knockdown of the Arp2/3 subunit Arp3 or the Arp2/3 activator N-WASP by siRNA also results in cell body expansion and reduced morphological complexity, whereas depleting WAVE2 specifically reduces the branching complexity of astrocyte processes. By contrast, knockdown of the Arp2/3 inhibitor PICK1 increases astrocyte branching complexity. Furthermore, astrocyte expansion induced by ischemic conditions is delayed by PICK1 knockdown or N-WASP overexpression. Our findings identify a new morphological outcome for Arp2/3 activation in restricting rather than promoting outwards movement of the plasma membrane in astrocytes. The Arp2/3 regulators PICK1, and N-WASP and WAVE2 function antagonistically to control the complexity of astrocyte branched morphology, and this mechanism underlies the morphological changes seen in astrocytes during their response to pathological insult. PMID:23843614

In situ fenestrations for the aortic arch and visceral segment: advances and challenges.

PubMed

Riga, Celia V; McWilliams, Richard G; Cheshire, Nicholas J W

2011-09-01

The management of complex aortic pathologies remains a major challenge particularly in the emergency setting. Bespoke fenestrated and branch stent graft technology has shown encouraging short- and mid-term results in selected patients. Despite tremendous technological advances in this field however, factors such as the inherent delay in device manufacturing, anatomical and technical challenges, high degree of planning, and cost hinder the wider applications of minimally invasive endovascular therapy. In situ fenestration of aortic stent grafts is an attractive alternative that eliminates the need for preoperative custom tailoring with the potential to widen the therapeutic options available and to offer a bailout option after inadvertent side branch occlusion. This article summarizes the principles of this technique and discusses its current applications.

Objects of Industrial Property as an Instrument for Introducing Technological Innovations in Machine Building

NASA Astrophysics Data System (ADS)

Nikitenko, S. M.; Mesyats, M. A.

2017-10-01

The article is devoted to the investigation of the possibility of applying new credit instruments for the implementation of technological innovations in machine building and other branches of the fuel and energy complex. The possibilities of using the new tool as an element of industrial policy in the program of import substitution of high-tech products have been considered.

Fixman compensating potential for general branched molecules

NASA Astrophysics Data System (ADS)

Jain, Abhinandan; Kandel, Saugat; Wagner, Jeffrey; Larsen, Adrien; Vaidehi, Nagarajan

2013-12-01

The technique of constraining high frequency modes of molecular motion is an effective way to increase simulation time scale and improve conformational sampling in molecular dynamics simulations. However, it has been shown that constraints on higher frequency modes such as bond lengths and bond angles stiffen the molecular model, thereby introducing systematic biases in the statistical behavior of the simulations. Fixman proposed a compensating potential to remove such biases in the thermodynamic and kinetic properties calculated from dynamics simulations. Previous implementations of the Fixman potential have been limited to only short serial chain systems. In this paper, we present a spatial operator algebra based algorithm to calculate the Fixman potential and its gradient within constrained dynamics simulations for branched topology molecules of any size. Our numerical studies on molecules of increasing complexity validate our algorithm by demonstrating recovery of the dihedral angle probability distribution function for systems that range in complexity from serial chains to protein molecules. We observe that the Fixman compensating potential recovers the free energy surface of a serial chain polymer, thus annulling the biases caused by constraining the bond lengths and bond angles. The inclusion of Fixman potential entails only a modest increase in the computational cost in these simulations. We believe that this work represents the first instance where the Fixman potential has been used for general branched systems, and establishes the viability for its use in constrained dynamics simulations of proteins and other macromolecules.

DNA binding and biological studies of some novel water-soluble polymer-copper(II)-phenanthroline complexes.

PubMed

Kumar, Rajendran Senthil; Arunachalam, Sankaralingam; Periasamy, Vaiyapuri Subbarayan; Preethy, Christo Paul; Riyasdeen, Anvarbatcha; Akbarsha, Mohammad Abdulkader

2008-10-01

Some novel water-soluble polymer-copper(II)-phenanthroline complex samples, [Cu(phen)2(BPEI)]Cl(2).4H2O (phen=1,10-phenanthroline, BPEI=branched polyethyleneimine), with different degrees of copper complex content in the polymer chain have been prepared by ligand substitution method in water-ethanol medium and characterized by infrared, UV-visible, EPR spectral and elemental analysis methods. The binding of these complex samples with DNA has been investigated by electronic absorption spectroscopy, emission spectroscopy and gel retardation assay. Electrostatic interactions between DNA molecule and polymer-copper(II) complex molecule containing many high positive charges have been observed. Besides these ionic interactions, van der Waals interactions, hydrogen bonding and other partial intercalation binding modes may also exist in this system. The polymer-copper(II) complex with higher degree of copper complex content was screened for its antimicrobial activity and antitumor activity.

System and method for modeling and analyzing complex scenarios

DOEpatents

Shevitz, Daniel Wolf

2013-04-09

An embodiment of the present invention includes a method for analyzing and solving possibility tree. A possibility tree having a plurality of programmable nodes is constructed and solved with a solver module executed by a processor element. The solver module executes the programming of said nodes, and tracks the state of at least a variable through a branch. When a variable of said branch is out of tolerance with a parameter, the solver disables remaining nodes of the branch and marks the branch as an invalid solution. The valid solutions are then aggregated and displayed as valid tree solutions.

Conservation and Divergence in the Candida Species Biofilm Matrix Mannan-Glucan Complex Structure, Function, and Genetic Control.

PubMed

Dominguez, Eddie; Zarnowski, Robert; Sanchez, Hiram; Covelli, Antonio S; Westler, William M; Azadi, Parastoo; Nett, Jeniel; Mitchell, Aaron P; Andes, David R

2018-04-03

Candida biofilms resist the effects of available antifungal therapies. Prior studies with Candida albicans biofilms show that an extracellular matrix mannan-glucan complex (MGCx) contributes to antifungal sequestration, leading to drug resistance. Here we implement biochemical, pharmacological, and genetic approaches to explore a similar mechanism of resistance for the three most common clinically encountered non- albicans Candida species (NAC). Our findings reveal that each Candida species biofilm synthesizes a mannan-glucan complex and that the antifungal-protective function of this complex is conserved. Structural similarities extended primarily to the polysaccharide backbone (α-1,6-mannan and β-1,6-glucan). Surprisingly, biochemical analysis uncovered stark differences in the branching side chains of the MGCx among the species. Consistent with the structural analysis, similarities in the genetic control of MGCx production for each Candida species also appeared limited to the synthesis of the polysaccharide backbone. Each species appears to employ a unique subset of modification enzymes for MGCx synthesis, likely accounting for the observed side chain diversity. Our results argue for the conservation of matrix function among Candida spp. While biogenesis is preserved at the level of the mannan-glucan complex backbone, divergence emerges for construction of branching side chains. Thus, the MGCx backbone represents an ideal drug target for effective pan- Candida species biofilm therapy. IMPORTANCE Candida species, the most common fungal pathogens, frequently grow as a biofilm. These adherent communities tolerate extremely high concentrations of antifungal agents, due in large part, to a protective extracellular matrix. The present studies define the structural, functional, and genetic similarities and differences in the biofilm matrix from the four most common Candida species. Each species synthesizes an extracellular mannan-glucan complex (MGCx) which contributes to sequestration of antifungal drug, shielding the fungus from this external assault. Synthesis of a common polysaccharide backbone appears conserved. However, subtle structural differences in the branching side chains likely rely upon unique modification enzymes, which are species specific. Our findings identify MGCx backbone synthesis as a potential pan- Candida biofilm therapeutic target. Copyright © 2018 Dominguez et al.

Moving into the paravisceral aorta using fenestrated and branched endografts.

PubMed

Farber, Mark A; Vallabhaneni, Raghuveer

2012-12-01

When one compares the potential advantages of endovascular aortic repair with respect to traditional open repair, it would seem logical that extension into the paravisceral aorta would be easily justified, given the complexity of open aortic repair and its associated complications. Eight years have transpired between trial initiation and Food and Drug Administration approval of the first fenestrated device in the United States for the treatment of juxtarenal aneurysms. While there are only a few centers in the United States with substantial experience performing fenestrated and branched endovascular aortic repair, there is a diverse experience outside the United States that has been gained over the past decade. It is through the experience of these centers that the technical and procedural complexities of complex endovascular aortic repair has been solved and provide the foundation that has allowed aortic specialists to move endovascular therapy into the paravisceral aorta with fenestrated and branched endovascular aortic repairs. Copyright © 2012 Elsevier Inc. All rights reserved.

Measuring the Evolution of Ontology Complexity: The Gene Ontology Case Study

PubMed Central

Dameron, Olivier; Bettembourg, Charles; Le Meur, Nolwenn

2013-01-01

Ontologies support automatic sharing, combination and analysis of life sciences data. They undergo regular curation and enrichment. We studied the impact of an ontology evolution on its structural complexity. As a case study we used the sixty monthly releases between January 2008 and December 2012 of the Gene Ontology and its three independent branches, i.e. biological processes (BP), cellular components (CC) and molecular functions (MF). For each case, we measured complexity by computing metrics related to the size, the nodes connectivity and the hierarchical structure. The number of classes and relations increased monotonously for each branch, with different growth rates. BP and CC had similar connectivity, superior to that of MF. Connectivity increased monotonously for BP, decreased for CC and remained stable for MF, with a marked increase for the three branches in November and December 2012. Hierarchy-related measures showed that CC and MF had similar proportions of leaves, average depths and average heights. BP had a lower proportion of leaves, and a higher average depth and average height. For BP and MF, the late 2012 increase of connectivity resulted in an increase of the average depth and average height and a decrease of the proportion of leaves, indicating that a major enrichment effort of the intermediate-level hierarchy occurred. The variation of the number of classes and relations in an ontology does not provide enough information about the evolution of its complexity. However, connectivity and hierarchy-related metrics revealed different patterns of values as well as of evolution for the three branches of the Gene Ontology. CC was similar to BP in terms of connectivity, and similar to MF in terms of hierarchy. Overall, BP complexity increased, CC was refined with the addition of leaves providing a finer level of annotations but decreasing slightly its complexity, and MF complexity remained stable. PMID:24146805

Atomic temporal interval relations in branching time: calculation and application

NASA Astrophysics Data System (ADS)

Anger, Frank D.; Ladkin, Peter B.; Rodriguez, Rita V.

1991-03-01

A practical method of reasoning about intervals in a branching-time model which is dense, unbounded, future-branching, without rejoining branches is presented. The discussion is based on heuristic constraint- propagation techniques using the relation algebra of binary temporal relations among the intervals over the branching-time model. This technique has been applied with success to models of intervals over linear time by Allen and others, and is of cubic-time complexity. To extend it to branding-time models, it is necessary to calculate compositions of the relations; thus, the table of compositions for the 'atomic' relations is computed, enabling the rapid determination of the composition of arbitrary relations, expressed as disjunctions or unions of the atomic relations.

The macroevolution of size and complexity in insect male genitalia

PubMed Central

Rudoy, Andrey

2016-01-01

The evolution of insect male genitalia has received much attention, but there is still a lack of data on the macroevolutionary origin of its extraordinary variation. We used a calibrated molecular phylogeny of 71 of the 150 known species of the beetle genus Limnebius to study the evolution of the size and complexity of the male genitalia in its two subgenera, Bilimneus, with small species with simple genitalia, and Limnebius s.str., with a much larger variation in size and complexity. We reconstructed ancestral values of complexity (perimeter and fractal dimension of the aedeagus) and genital and body size with Bayesian methods. Complexity evolved more in agreement with a Brownian model, although with evidence of weak directional selection to a decrease or increase in complexity in the two subgenera respectively, as measured with an excess of branches with negative or positive change. On the contrary, aedeagus size, the variable with the highest rates of evolution, had a lower phylogenetic signal, without significant differences between the two subgenera in the average change of the individual branches of the tree. Aedeagus size also had a lower correlation with time and no evidence of directional selection. Rather than to directional selection, it thus seems that the higher diversity of the male genitalia in Limnebius s.str. is mostly due to the larger variance of the phenotypic change in the individual branches of the tree for all measured variables. PMID:27114865

Purification of Ovine Respiratory Complex I Results in a Highly Active and Stable Preparation*

PubMed Central

Letts, James A.; Degliesposti, Gianluca; Fiedorczuk, Karol; Skehel, Mark; Sazanov, Leonid A.

2016-01-01

NADH-ubiquinone oxidoreductase (complex I) is the largest (∼1 MDa) and the least characterized complex of the mitochondrial electron transport chain. Because of the ease of sample availability, previous work has focused almost exclusively on bovine complex I. However, only medium resolution structural analyses of this complex have been reported. Working with other mammalian complex I homologues is a potential approach for overcoming these limitations. Due to the inherent difficulty of expressing large membrane protein complexes, screening of complex I homologues is limited to large mammals reared for human consumption. The high sequence identity among these available sources may preclude the benefits of screening. Here, we report the characterization of complex I purified from Ovis aries (ovine) heart mitochondria. All 44 unique subunits of the intact complex were identified by mass spectrometry. We identified differences in the subunit composition of subcomplexes of ovine complex I as compared with bovine, suggesting differential stability of inter-subunit interactions within the complex. Furthermore, the 42-kDa subunit, which is easily lost from the bovine enzyme, remains tightly bound to ovine complex I. Additionally, we developed a novel purification protocol for highly active and stable mitochondrial complex I using the branched-chain detergent lauryl maltose neopentyl glycol. Our data demonstrate that, although closely related, significant differences exist between the biochemical properties of complex I prepared from ovine and bovine mitochondria and that ovine complex I represents a suitable alternative target for further structural studies. PMID:27672209

Managing Offshore Branch Campuses: An Analytical Framework for Institutional Strategies

ERIC Educational Resources Information Center

Shams, Farshid; Huisman, Jeroen

2012-01-01

The aim of this article is to develop a framework that encapsulates the key managerial complexities of running offshore branch campuses. In the transnational higher education (TNHE) literature, several managerial ramifications and impediments have been addressed by scholars and practitioners. However, the strands of the literature are highly…

Teaching Machines and Programmed Instruction.

ERIC Educational Resources Information Center

Kay, Harry; And Others

The various devices used in programed instruction range from the simple linear programed book to branching and skip branching programs, adaptive teaching machines, and even complex computer based systems. In order to provide a background for the would-be programer, the essential principles of each of these devices is outlined. Different ideas of…

Tree growth visualization

Treesearch

L. Linsen; B.J. Karis; E.G. McPherson; B. Hamann

2005-01-01

In computer graphics, models describing the fractal branching structure of trees typically exploit the modularity of tree structures. The models are based on local production rules, which are applied iteratively and simultaneously to create a complex branching system. The objective is to generate three-dimensional scenes of often many realistic- looking and non-...

Computer program for stress, stability, and vibration of complex branched shells of revolution: BOSOR 4

NASA Technical Reports Server (NTRS)

Bushnell, D.

1974-01-01

Code is easy to use yet is general with respect to: (a) type of analysis to be performed; (b) geometry of shell meridian; (c) type of wall construction; (d) type of boundary conditions, ring supports, and branching configuration; and (e) type of loading.

Developing Structure-Property Relationships in Branched Wormlike Micelles via Advanced Rheological and Neutron Scattering Techniques

NASA Astrophysics Data System (ADS)

Calabrese, Michelle A.

Surfactant wormlike micelles (WLMs) are of particular scientific interest due to their ability to branch, break, and reform under shear, which can lead to shear banding flow instabilities. The tunable self-assembly of WLMs makes them ubiquitous in applications ranging from consumer products to energy recovery fluids. Altering the topology of WLMs by inducing branching provides a microstructural pathway to design and optimize the flow properties for such targeted applications. The goal of this thesis is to understand the role of micellar branching on the resulting equilibrium and non-equilibrium properties, while advancing instrumentation and analysis methods in rheology and neutron scattering. The degree of branching in the mixed cationic/anionic surfactant solutions is controlled by the addition of sodium tosylate. The equilibrium properties are characterized via small angle neutron scattering (SANS), linear viscoelastic rheology, neutron spin echo, and dynamic light scattering. Combining rheology with spatiotemporally-resolved SANS enables unambiguous identification of non-equilibrium rheological and scattering signatures of branching and shear banding. The nonlinear WLM response is characterized via flow-SANS under steady shear, shear startup, and large amplitude oscillatory shear. New methods of time-resolved data analysis are developed, which improve experimental resolution by several-fold. Shear-induced orientation is a complex function of branching level, radial position, and deformation type. The structural mechanisms behind shear band formation are elucidated for steady and dynamic flows, which depend on branching level. Shear banding disappears at high branching levels for all deformation types. These responses are used to validate constitutive modeling predictions of dynamic shear banding for the first time. Finally, quantitative metrics to predict shear banding from rheology or flow-induced orientation are developed. Together, advanced rheological and neutron techniques provide a platform for creating structure-property relationships that predict flow and structural phenomena in WLMs and other soft materials. These methods have enabled characteristic differences in linear versus branched WLMs to be determined. This research is part of a broader effort to characterize branching in polymers and self-assembled systems, and may aid in the formulation of WLMs for specific applications. Finally, this work provides a basis for testing and developing microstructure-based constitutive equations that incorporate micellar breakage and branching.

THE FIRST DISTANCE CONSTRAINT ON THE RENEGADE HIGH-VELOCITY CLOUD COMPLEX WD

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

Peek, J. E. G.; Roman-Duval, Julia; Tumlinson, Jason

2016-09-10

We present medium-resolution, near-ultraviolet Very Large Telescope/FLAMES observations of the star USNO-A0600-15865535. We adapt a standard method of stellar typing to our measurement of the shape of the Balmer ϵ absorption line to demonstrate that USNO-A0600-15865535 is a blue horizontal branch star, residing in the lower stellar halo at a distance of 4.4 kpc from the Sun. We measure the H and K lines of singly ionized calcium and find two isolated velocity components, one originating in the disk, and one associated with the high-velocity cloud complex WD. This detection demonstrated that complex WD is closer than ∼4.4 kpc andmore » is the first distance constraint on the +100 km s{sup −1} Galactic complex of clouds. We find that complex WD is not in corotation with the Galactic disk, which has been assumed for decades. We examine a number of scenarios and find that the most likely scenario is that complex WD was ejected from the solar neighborhood and is only a few kiloparsecs from the Sun.« less

Combination of branched GDGTs and testate amoebae for the reconstruction of past climate change in a French peatland

NASA Astrophysics Data System (ADS)

Huguet, Arnaud; Jassey, Vincent E. J.; Laggoun-Défarge, Fatima; Derenne, Sylvie; Gilbert, Daniel; Delarue, Frédéric; Payne, Richard; Buttler, Alexandre; Mitchell, Edward A. D.

2013-04-01

Peatlands are important archives for the reconstruction of past environmental changes because of their high rates of peat accumulation due to the low rate of plant litter decomposition. Branched glycerol dialkyl glycerol tetraethers (GDGTs) are complex lipids of high molecular weight, recently discovered in soils and suggested to be produced by anaerobic bacteria. The relative distribution of branched GDGTs in soils correlates with environmental variables: the degree of methylation, expressed in the methylation index of branched tetraethers (MBT), depends on mean annual air temperature (MAAT) and to a lesser extent on soil pH, whereas the relative abundance of cyclopentyl rings of branched GDGTs, expressed in the cyclisation ratio of branched tetraethers (CBT), is related to soil pH. The MBT/CBT proxies are increasingly used for the reconstruction of past air temperatures, but have rarely been applied in peatlands. Testate amoebae are common and diverse unicellular eukaryotes in peatlands. They build shells that are preserved in peat. They are good indicators of changing environmental conditions in peatlands and are thus used in both ecological and paleoecological studies, especially for reconstructing surface moisture. The aim of this study was to examine the applicability of branched GDGTs and testate amoebae as indicators of environmental changes (temperature and moisture) in temperate peatlands. Within the PEATWARM project, both GDGTs and testate amoebae were studied at high resolution in a 4 m peat core collected in Frasne mire (French Jura Mountains) and covering the last 7,400 years BP. GDGT-inferred temperatures ranged between 8 and 12 °C until 250 cm depth and were higher than present measured mean annual air temperature (ca. 6 °C). Temperature estimates in the top part of the bog were most consistent with spring and summer mean air temperatures recorded in the peatland (ca. 11.5 °C), suggesting that branched GDGT-producing bacteria might be more active during the warmest months of the year. At 250 cm depth, reconstructed temperature showed a pronounced shift, likely reflecting both a change in climatic conditions but also in the composition of the peat. Indeed, drier conditions were indicated by testate amoebae at the bottom of the peat core, whereas wetter conditions occurred at the top. Interestingly, temperature variations inferred from MBT/CBT proxies were weakly linked with moisture variations inferred from testate amoebae until 150 cm depth (r = -0.41, p = 0.06). Therefore, the distribution of branched GDGTs might also depend on peat moisture level, in addition to air temperature and pH. Our data suggest that the joint use of MBT/CBT and testate amoebae is a promising approach to estimate past climate change, but that more research is required to calibrate and apply with confidence these proxies in peatlands.

Regulation of root morphogenesis in arbuscular mycorrhizae: what role do fungal exudates, phosphate, sugars and hormones play in lateral root formation?

PubMed Central

Fusconi, Anna

2014-01-01

Background Arbuscular mycorrhizae (AMs) form a widespread root–fungus symbiosis that improves plant phosphate (Pi) acquisition and modifies the physiology and development of host plants. Increased branching is recognized as a general feature of AM roots, and has been interpreted as a means of increasing suitable sites for colonization. Fungal exudates, which are involved in the dialogue between AM fungi and their host during the pre-colonization phase, play a well-documented role in lateral root (LR) formation. In addition, the increased Pi content of AM plants, in relation to Pi-starved controls, as well as changes in the delivery of carbohydrates to the roots and modulation of phytohormone concentration, transport and sensitivity, are probably involved in increasing root system branching. Scope This review discusses the possible causes of increased branching in AM plants. The differential root responses to Pi, sugars and hormones of potential AM host species are also highlighted and discussed in comparison with those of the non-host Arabidopsis thaliana. Conclusions Fungal exudates are probably the main compounds regulating AM root morphogenesis during the first colonization steps, while a complex network of interactions governs root development in established AMs. Colonization and high Pi act synergistically to increase root branching, and sugar transport towards the arbusculated cells may contribute to LR formation. In addition, AM colonization and high Pi generally increase auxin and cytokinin and decrease ethylene and strigolactone levels. With the exception of cytokinins, which seem to regulate mainly the root:shoot biomass ratio, these hormones play a leading role in governing root morphogenesis, with strigolactones and ethylene blocking LR formation in the non-colonized, Pi-starved plants, and auxin inducing them in colonized plants, or in plants grown under high Pi conditions. PMID:24227446

Survival of Atlantic salmon Salmo salar smolts through a hydropower complex.

PubMed

Stich, D S; Bailey, M M; Zydlewski, J D

2014-10-01

This study evaluated Atlantic salmon Salmo salar smolt survival through the lower Penobscot River, Maine, U.S.A., and characterized relative differences in proportional use and survival through the main-stem of the river and an alternative migration route, the Stillwater Branch. The work was conducted prior to removal of two main-stem dams and operational changes in hydropower facilities in the Stillwater Branch. Survival and proportional use of migration routes in the lower Penobscot were estimated from multistate (MS) models based on 6 years of acoustic telemetry data from 1669 smolts and 2 years of radio-telemetry data from 190 fish. A small proportion (0·12, 95% c.i. = 0·06-0·25) of smolts used the Stillwater Branch, and mean survival through the two operational dams in this part of the river was relatively high (1·00 and 0·97). Survival at Milford Dam, the dam that will remain in the main-stem of the Penobscot River, was relatively low (0·91), whereas survival through two dams that were removed was relatively high (0·99 and 0·98). Smolt survival could decrease in the Stillwater Branch with the addition of two new powerhouses while continuing to meet fish passage standards. The effects of removing two dams in the main-stem are expected to be negligible for smolt survival based on high survival observed from 2005 to 2012 at those locations. Survival through Milford Dam was been well below current regulatory standards, and thus improvement of passage at this location offers the best opportunity for improving overall smolt survival in the lower river. © 2014 The Fisheries Society of the British Isles.

Survival of Atlantic salmon Salmo salar smolts through a hydropower complex

USGS Publications Warehouse

Stich, D.S.; Bailey, M.M.; Zydlewski, Joseph D.

2014-01-01

This study evaluated Atlantic salmon Salmo salar smolt survival through the lower Penobscot River, Maine, U.S.A., and characterized relative differences in proportional use and survival through the main-stem of the river and an alternative migration route, the Stillwater Branch. The work was conducted prior to removal of two main-stem dams and operational changes in hydropower facilities in the Stillwater Branch. Survival and proportional use of migration routes in the lower Penobscot were estimated from multistate (MS) models based on 6 years of acoustic telemetry data from 1669 smolts and 2 years of radio-telemetry data from 190 fish. A small proportion (0·12, 95% c.i. = 0·06–0·25) of smolts used the Stillwater Branch, and mean survival through the two operational dams in this part of the river was relatively high (1·00 and 0·97). Survival at Milford Dam, the dam that will remain in the main-stem of the Penobscot River, was relatively low (0·91), whereas survival through two dams that were removed was relatively high (0·99 and 0·98). Smolt survival could decrease in the Stillwater Branch with the addition of two new powerhouses while continuing to meet fish passage standards. The effects of removing two dams in the main-stem are expected to be negligible for smolt survival based on high survival observed from 2005 to 2012 at those locations. Survival through Milford Dam was been well below current regulatory standards, and thus improvement of passage at this location offers the best opportunity for improving overall smolt survival in the lower river.

Branched-chain amino acid (BCAA) supplementation enhances adaptability to exercise training of mice with a muscle-specific defect in the control of BCAA catabolism.

PubMed

Xu, Minjun; Kitaura, Yasuyuki; Shindo, Daichi; Shimomura, Yoshiharu

2018-03-01

Branched-chain α-keto acid dehydrogenase (BCKDH) kinase (BDK) suppresses the branched-chain amino acid (BCAA) catabolism by inactivation of the BCKDH complex. The muscle-specific BDK-deficient (BDK-mKO) mice showed accelerated BCAA oxidation in muscle and decreased endurance capacity after training (Xu et al. PLoS One. 12 (2017) e0180989). We here report that BCAA supplementation overcompensated endurance capacity in BDK-mKO mice after training.

Complex coevolution of wing, tail, and vocal sounds of courting male bee hummingbirds.

PubMed

Clark, Christopher J; McGuire, Jimmy A; Bonaccorso, Elisa; Berv, Jacob S; Prum, Richard O

2018-03-01

Phenotypic characters with a complex physical basis may have a correspondingly complex evolutionary history. Males in the "bee" hummingbird clade court females with sound from tail-feathers, which flutter during display dives. On a phylogeny of 35 species, flutter sound frequency evolves as a gradual, continuous character on most branches. But on at least six internal branches fall two types of major, saltational changes: mode of flutter changes, or the feather that is the sound source changes, causing frequency to jump from one discrete value to another. In addition to their tail "instruments," males also court females with sound from their syrinx and wing feathers, and may transfer or switch instruments over evolutionary time. In support of this, we found a negative phylogenetic correlation between presence of wing trills and singing. We hypothesize this transference occurs because wing trills and vocal songs serve similar functions and are thus redundant. There are also three independent origins of self-convergence of multiple signals, in which the same species produces both a vocal (sung) frequency sweep, and a highly similar nonvocal sound. Moreover, production of vocal, learned song has been lost repeatedly. Male bee hummingbirds court females with a diverse, coevolving array of acoustic traits. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Branched Peptide, B2088, Disrupts the Supramolecular Organization of Lipopolysaccharides and Sensitizes the Gram-negative Bacteria

NASA Astrophysics Data System (ADS)

Lakshminarayanan, Rajamani; Tan, Wei Xiang; Aung, Thet Tun; Goh, Eunice Tze Leng; Muruganantham, Nandhakumar; Li, Jianguo; Chang, Jamie Ya Ting; Dikshit, Neha; Saraswathi, Padmanabhan; Lim, Rayne Rui; Kang, Tse Siang; Balamuralidhar, Vanniarajan; Sukumaran, Bindu; Verma, Chandra S.; Sivaraman, Jayaraman; Chaurasia, Shyam Sunder; Liu, Shouping; Beuerman, Roger W.

2016-05-01

Dissecting the complexities of branched peptide-lipopolysaccharides (LPS) interactions provide rationale for the development of non-cytotoxic antibiotic adjuvants. Using various biophysical methods, we show that the branched peptide, B2088, binds to lipid A and disrupts the supramolecular organization of LPS. The disruption of outer membrane in an intact bacterium was demonstrated by fluorescence spectroscopy and checkerboard assays, the latter confirming strong to moderate synergism between B2088 and various classes of antibiotics. The potency of synergistic combinations of B2088 and antibiotics was further established by time-kill kinetics, mammalian cell culture infections model and in vivo model of bacterial keratitis. Importantly, B2088 did not show any cytotoxicity to corneal epithelial cells for at least 96 h continuous exposure or hemolytic activity even at 20 mg/ml. Peptide congeners containing norvaline, phenylalanine and tyrosine (instead of valine in B2088) displayed better synergism compared to other substitutions. We propose that high affinity and subsequent disruption of the supramolecular assembly of LPS by the branched peptides are vital for the development of non-cytotoxic antibiotic adjuvants that can enhance the accessibility of conventional antibiotics to the intracellular targets, decrease the antibiotic consumption and holds promise in averting antibiotic resistance.

High-pressure modulation of the structure of the bacterial photochemical reaction center at physiological and cryogenic temperatures

NASA Astrophysics Data System (ADS)

Timpmann, Kõu; Kangur, Liina; Lõhmus, Ants; Freiberg, Arvi

2017-07-01

The optical absorption and fluorescence response to external high pressure of the reaction center membrane chromoprotein complex from the wild-type non-sulfur photosynthetic bacterium Rhodobacter sphaeroides was investigated using the native pigment cofactors as local molecular probes of the reaction center structure at physiological (ambient) and cryogenic (79 K) temperatures. In detergent-purified complexes at ambient temperature, abrupt blue shift and accompanied broadening of the special pair band was observed at about 265 MPa. These reversible in pressure features were assigned to a pressure-induced rupture of a lone hydrogen bond that binds the photo-chemically active L-branch primary electron donor bacteriochlorophyll cofactor to the surrounding protein scaffold. In native membrane-protected complexes the hydrogen bond rupture appeared significantly restricted and occurred close to about 500 MPa. The free energy change associated with the rupture of the special pair hydrogen bond in isolate complexes was estimated to be equal to about 12 kJ mol-1. In frozen samples at cryogenic temperatures the hydrogen bond remained apparently intact up to the maximum utilized pressure of 600 MPa. In this case, however, heterogeneous spectral response of the cofactors from the L-and M-branches was observed due to anisotropic build-up of the protein structure. While in solid phase, the special pair fluorescence as a function of pressure exactly followed the respective absorption spectrum at a constant Stokes shift, at ambient temperature, the two paths began to deviate strongly from one other at the hydrogen bond rupture pressure. This effect was tentatively interpreted by different emission properties of hydrogen-bound and hydrogen-unbound special pair exciton states.

Programmable growth of branched silicon nanowires using a focused ion beam.

PubMed

Jun, Kimin; Jacobson, Joseph M

2010-08-11

Although significant progress has been made in being able to spatially define the position of material layers in vapor-liquid-solid (VLS) grown nanowires, less work has been carried out in deterministically defining the positions of nanowire branching points to facilitate more complicated structures beyond simple 1D wires. Work to date has focused on the growth of randomly branched nanowire structures. Here we develop a means for programmably designating nanowire branching points by means of focused ion beam-defined VLS catalytic points. This technique is repeatable without losing fidelity allowing multiple rounds of branching point definition followed by branch growth resulting in complex structures. The single crystal nature of this approach allows us to describe resulting structures with linear combinations of base vectors in three-dimensional (3D) space. Finally, by etching the resulting 3D defined wire structures branched nanotubes were fabricated with interconnected nanochannels inside. We believe that the techniques developed here should comprise a useful tool for extending linear VLS nanowire growth to generalized 3D wire structures.

Cecropia peltata Accumulates Starch or Soluble Glycogen by Differentially Regulating Starch Biosynthetic Genes[W][OA

PubMed Central

Bischof, Sylvain; Umhang, Martin; Eicke, Simona; Streb, Sebastian; Qi, Weihong; Zeeman, Samuel C.

2013-01-01

The branched glucans glycogen and starch are the most widespread storage carbohydrates in living organisms. The production of semicrystalline starch granules in plants is more complex than that of small, soluble glycogen particles in microbes and animals. However, the factors determining whether glycogen or starch is formed are not fully understood. The tropical tree Cecropia peltata is a rare example of an organism able to make either polymer type. Electron micrographs and quantitative measurements show that glycogen accumulates to very high levels in specialized myrmecophytic structures (Müllerian bodies), whereas starch accumulates in leaves. Compared with polymers comprising leaf starch, glycogen is more highly branched and has shorter branches—factors that prevent crystallization and explain its solubility. RNA sequencing and quantitative shotgun proteomics reveal that isoforms of all three classes of glucan biosynthetic enzyme (starch/glycogen synthases, branching enzymes, and debranching enzymes) are differentially expressed in Müllerian bodies and leaves, providing a system-wide view of the quantitative programming of storage carbohydrate metabolism. This work will prompt targeted analysis in model organisms and cross-species comparisons. Finally, as starch is the major carbohydrate used for food and industrial applications worldwide, these data provide a basis for manipulating starch biosynthesis in crops to synthesize tailor-made polyglucans. PMID:23632447

A new simple asymmetric hysteresis operator and its application to inverse control of piezoelectric actuators.

PubMed

Badel, A; Qiu, J; Nakano, T

2008-05-01

Piezoelectric actuators (PEAs) are commonly used as micropositioning devices due to their high resolution, high stiffness, and fast frequency response. Because piezoceramic materials are ferroelectric, they fundamentally exhibit hysteresis behavior in their response to an applied electric field. The positioning precision can be significantly reduced due to nonlinear hysteresis effects when PEAs are used in relatively long range applications. This paper describes a new, precise, and simple asymmetric hysteresis operator dedicated to PEAs. The complex hysteretic transfer characteristic has been considered in a purely phenomenological way, without taking into account the underlying physics. This operator is based on two curves. The first curve corresponds to the main ascending branch and is modeled by the function f1. The second curve corresponds to the main reversal branch and is modeled by the function g2. The functions f(1) and g(2) are two very simple hyperbola functions with only three parameters. Particular ascending and reversal branches are deduced from appropriate translations of f(1) and g(2). The efficiency and precision of the proposed approach is demonstrated, in practice, by a real-time inverse feed-forward controller for piezoelectric actuators. Advantages and drawbacks of the proposed approach compared with classical hysteresis operators are discussed.

Method and Apparatus of Multiplexing and Acquiring Data from Multiple Optical Fibers Using a Single Data Channel of an Optical Frequency-Domain Reflectometry (OFDR) System

NASA Technical Reports Server (NTRS)

Parker, Jr., Allen R (Inventor); Chan, Hon Man (Inventor); Piazza, Anthony (Nino) (Inventor); Richards, William Lance (Inventor)

2014-01-01

A method and system for multiplexing a network of parallel fiber Bragg grating (FBG) sensor-fibers to a single acquisition channel of a closed Michelson interferometer system via a fiber splitter by distinguishing each branch of fiber sensors in the spatial domain. On each branch of the splitter, the fibers have a specific pre-determined length, effectively separating each branch of fiber sensors spatially. In the spatial domain the fiber branches are seen as part of one acquisition channel on the interrogation system. However, the FBG-reference arm beat frequency information for each fiber is retained. Since the beat frequency is generated between the reference arm, the effective fiber length of each successive branch includes the entire length of the preceding branch. The multiple branches are seen as one fiber having three segments where the segments can be resolved. This greatly simplifies optical, electronic and computational complexity, and is especially suited for use in multiplexed or branched OFS networks for SHM of large and/or distributed structures which need a lot of measurement points.

Branching, Chain Scission, and Solution Stability of Worm-Like Micelles

NASA Astrophysics Data System (ADS)

Beaucage, Greg; Vogtt, Karsten; Jiang, Hanqui

As salt is added to a simple micelle solution such as SDS or SLES, the zero shear rate specific viscosity rises rapidly followed by a maximum and decay. The rapid rise in viscosity is associated with formation of elliptical and extended chain worm-like micelles, WLMs. Entanglement of these long chain micelles leads to the viscoelastic behavior we associate with shampoo and body wash. The plateau and drop in viscosity at high salt concentrations is caused by a special type of topological branching where the branch points have no energy penalty to motion along the chain according to Cates theory. These have some similarity to catenane crosslinks. Predictive dynamic theories for WLMs rely on structural details; the diameter, persistence length, contour length, branch length, segment length between branch points, and mesh size. Further, since the contour length and other large scale features are in kinetic equilibrium, with frequent chain breakage and formation, the thermodynamics of these long chain structures are of interest both in terms of chain scission as well as in terms of the stability of the colloidal solution as a whole. Recent structural studies of WLMs using static neutron scattering based on new scattering models will be presented demonstrating that these input parameters for dynamic models of complex topological systems are quantitatively and directly available. In this context it is important to consider a comparison between dynamic features, for instance entanglement, and their static analogs, chain overlap.

Branch-pipe-routing approach for ships using improved genetic algorithm

NASA Astrophysics Data System (ADS)

Sui, Haiteng; Niu, Wentie

2016-09-01

Branch-pipe routing plays fundamental and critical roles in ship-pipe design. The branch-pipe-routing problem is a complex combinatorial optimization problem and is thus difficult to solve when depending only on human experts. A modified genetic-algorithm-based approach is proposed in this paper to solve this problem. The simplified layout space is first divided into threedimensional (3D) grids to build its mathematical model. Branch pipes in layout space are regarded as a combination of several two-point pipes, and the pipe route between two connection points is generated using an improved maze algorithm. The coding of branch pipes is then defined, and the genetic operators are devised, especially the complete crossover strategy that greatly accelerates the convergence speed. Finally, simulation tests demonstrate the performance of proposed method.

Molecular rheology of branched polymers: decoding and exploring the role of architectural dispersity through a synergy of anionic synthesis, interaction chromatography, rheometry and modeling.

PubMed

van Ruymbeke, E; Lee, H; Chang, T; Nikopoulou, A; Hadjichristidis, N; Snijkers, F; Vlassopoulos, D

2014-07-21

An emerging challenge in polymer physics is the quantitative understanding of the influence of a macromolecular architecture (i.e., branching) on the rheological response of entangled complex polymers. Recent investigations of the rheology of well-defined architecturally complex polymers have determined the composition in the molecular structure and identified the role of side-products in the measured samples. The combination of different characterization techniques, experimental and/or theoretical, represents the current state-of-the-art. Here we review this interdisciplinary approach to molecular rheology of complex polymers, and show the importance of confronting these different tools for ensuring an accurate characterization of a given polymeric sample. We use statistical tools in order to relate the information available from the synthesis protocols of a sample and its experimental molar mass distribution (typically obtained from size exclusion chromatography), and hence obtain precise information about its structural composition, i.e. enhance the existing sensitivity limit. We critically discuss the use of linear rheology as a reliable quantitative characterization tool, along with the recently developed temperature gradient interaction chromatography. The latter, which has emerged as an indispensable characterization tool for branched architectures, offers unprecedented sensitivity in detecting the presence of different molecular structures in a sample. Combining these techniques is imperative in order to quantify the molecular composition of a polymer and its consequences on the macroscopic properties. We validate this approach by means of a new model asymmetric comb polymer which was synthesized anionically. It was thoroughly characterized and its rheology was carefully analyzed. The main result is that the rheological signal reveals fine molecular details, which must be taken into account to fully elucidate the viscoelastic response of entangled branched polymers. It is important to appreciate that, even optimal model systems, i.e., those synthesized with high-vacuum anionic methods, need thorough characterization via a combination of techniques. Besides helping to improve synthetic techniques, this methodology will be significant in fine-tuning mesoscopic tube-based models and addressing outstanding issues such as the quantitative description of the constraint release mechanism.

Complexity of chemical graphs in terms of size, branching, and cyclicity.

PubMed

Balaban, A T; Mills, D; Kodali, V; Basak, S C

2006-08-01

Chemical graph complexity depends on many factors, but the main ones are size, branching, and cyclicity. Some molecular descriptors embrace together all these three parameters, which cannot then be disentangled. The topological index J (and its refinements that include accounting for bond multiplicity and the presence of heteroatoms) was designed to compensate in a significant measure for graph size and cyclicity, and therefore it contains information mainly on branching. In order to separate these factors, two new indices (F and G) related with J are proposed, which allow to group together graphs with the same size into families of constitutional formulas differing in their branching and cyclicity. A comparison with other topological indices revealed that a few other topological indices vary similarly with index G, notably DN2S4 among the triplet indices, and TOTOP among the indices contained in the Molconn-Z program. This comparison involved all possible chemical graphs (i.e. connected planar graphs with vertex degrees not higher than four) with four through six vertices, and all possible alkanes with four through nine carbon atoms.

Star-shaped PHB-PLA block copolymers: immortal polymerization with dinuclear indium catalysts.

PubMed

Yu, I; Ebrahimi, T; Hatzikiriakos, S G; Mehrkhodavandi, P

2015-08-28

The first example of a one-component precursor to star-shaped polyesters, and its utilization in the synthesis of previously unknown star-shaped poly(hydroxybutyrate)-poly(lactic acid) block copolymers, is reported. A series of such mono- and bis-benzyl alkoxy-bridged complexes were synthesized, fully characterized, and their solvent dependent solution structures and reactivity were examined. These complexes were highly active catalysts for the controlled polymerization of β-butyrolactone to form poly(hydroxybutyrate) at room temperature. Solution studies indicate that a mononuclear propagating species formed in THF and that the dimer-monomer equilibrium affects the rates of BBL polymerization. In the presence of linear and branched alcohols, these complexes catalyze well-controlled immortal polymerization and copolymerization of β-butyrolactone and lactide.

The effect of RNA stiffness on the self-assembly of virus particles

NASA Astrophysics Data System (ADS)

Li, Siyu; Erdemci-Tandogan, Gonca; van der Schoot, Paul; Zandi, Roya

2018-01-01

Under many in vitro conditions, some small viruses spontaneously encapsidate a single stranded (ss) RNA into a protein shell called the capsid. While viral RNAs are found to be compact and highly branched because of long distance base-pairing between nucleotides, recent experiments reveal that in a head-to-head competition between an ssRNA with no secondary or higher order structure and a viral RNA, the capsid proteins preferentially encapsulate the linear polymer! In this paper, we study the impact of genome stiffness on the encapsidation free energy of the complex of RNA and capsid proteins. We show that an increase in effective chain stiffness because of base-pairing could be the reason why under certain conditions linear chains have an advantage over branched chains when it comes to encapsidation efficiency. While branching makes the genome more compact, RNA base-pairing increases the effective Kuhn length of the RNA molecule, which could result in an increase of the free energy of RNA confinement, that is, the work required to encapsidate RNA, and thus less efficient packaging.

Role and structural mechanism of WASP-triggered conformational changes in branched actin filament nucleation by Arp2/3 complex.

PubMed

Rodnick-Smith, Max; Luan, Qing; Liu, Su-Ling; Nolen, Brad J

2016-07-05

The Arp2/3 (Actin-related proteins 2/3) complex is activated by WASP (Wiskott-Aldrich syndrome protein) family proteins to nucleate branched actin filaments that are important for cellular motility. WASP recruits actin monomers to the complex and stimulates movement of Arp2 and Arp3 into a "short-pitch" conformation that mimics the arrangement of actin subunits within filaments. The relative contribution of these functions in Arp2/3 complex activation and the mechanism by which WASP stimulates the conformational change have been unknown. We purified budding yeast Arp2/3 complex held in or near the short-pitch conformation by an engineered covalent cross-link to determine if the WASP-induced conformational change is sufficient for activity. Remarkably, cross-linked Arp2/3 complex bypasses the need for WASP in activation and is more active than WASP-activated Arp2/3 complex. These data indicate that stimulation of the short-pitch conformation is the critical activating function of WASP and that monomer delivery is not a fundamental requirement for nucleation but is a specific requirement for WASP-mediated activation. During activation, WASP limits nucleation rates by releasing slowly from nascent branches. The cross-linked complex is inhibited by WASP's CA region, even though CA potently stimulates cross-linking, suggesting that slow WASP detachment masks the activating potential of the short-pitch conformational switch. We use structure-based mutations and WASP-Arp fusion chimeras to determine how WASP stimulates movement toward the short-pitch conformation. Our data indicate that WASP displaces the autoinhibitory Arp3 C-terminal tail from a hydrophobic groove at Arp3's barbed end to destabilize the inactive state, providing a mechanism by which WASP stimulates the short-pitch conformation and activates Arp2/3 complex.

Structure, function and regulation of the enzymes in the starch biosynthetic pathway.

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

Geiger, Jim

Starch is the major reserve polysaccharide in nature and accounts for the majority of the caloric intact of humans. It is also gaining importance as a renewable and biodegradable industrial material. There is burgeoning interest in increasing the amount and altering the properties of the plant starches by plant genetic modification. A rational approach to this effort will require a detailed, atomic-level understanding of the enzymatic processes that produce the starch granule. The starch granule is a complex particle made up of alternating layers of crystalline and amorphous lamellae. It consists of two types of polymer, amylose, a polymer ofmore » relatively long chains of α-1,4-linked glucans that contain virtually no branches, and amylopectin, which is highly branched and contains much shorter chains. This complex structure is synthesized by the coordinate activities of the starch synthases (SS), which elongate the polysaccharide chain by addition of glucose units via α-1,4 linkages using ADP- glucose as a donor, and branching enzymes (BE), which branch the polysaccharide chain by cleavage of α₋1,4 linkages and subsequent re-attachment via α₋1,6 linkages. Several isoforms of both starch synthase (SS) and branching enzyme (BE) are found in plants, including SSI, SSII, SSIII and granule- bound SS (GBSS), and SBEI, SBEIIa and SBEIIb. These isoforms have different activities and substrate and product specificities and play different roles in creating the granule and determining the properties of the resulting starch. The overarching goal of this proposal is to begin to understand the regulation and specificities of these enzymes at the atomic level. High-resolution X-ray structures of these enzymes bound to substrates and products will be determined to visualize the molecular interactions responsible for the properties of the enzymes. Hypotheses regarding these issues will then be tested using mutagenesis and enzyme assays. To date, we have determined the structure of ADP- Glucose pyrophosphorylase from potato in its inhibited conformation, and bound to both ATP and ADP-glucose. In addition, we have determined the first structure of glycogen synthase in its "closed", catalytically active conformation bound to ADP-glucose. We also determined the structure of glycogen synthase bound to malto-oligosaccharides, showing for the first time that an enzyme in the starch biosynthetic pathway recognizes glucans not just in its active site but on binding sites on the surface of the enzyme ten’s of Angstroms from the active site. In addition our structure of a glycogen branching enzyme bound to malto-oligosaccharides identified seven distinct binding sites distributed about the surface of the enzyme. We will now determine the function of these sites to get a molecular-level picture of exactly how these enzymes interact with their polymeric substrates and confer specificity leading to the complex structure of the starch granule. We will extend our studies to other isoforms of the enzymes, to understand how their structures give rise to their distinct function. Our goal is to understand what accounts for the various functional differences between SS and SBE isoforms at a molecular level.« less

Effects of clofibric acid on the activity and activity state of the hepatic branched-chain 2-oxo acid dehydrogenase complex.

PubMed Central

Zhao, Y; Jaskiewicz, J; Harris, R A

1992-01-01

Feeding clofibric acid to rats caused little or no change in total activity of the liver branched-chain 2-oxo acid dehydrogenase complex (BCODC). No change in mass of liver BCODC was detected by immunoblot analysis in response to dietary clofibric acid. No changes in abundance of mRNAs for the BCODC E1 alpha, E1 beta and E2 subunits were detected by Northern-blot analysis. Likewise, dietary clofibric acid had no effect on the activity state of liver BCODC (percentage of enzyme in the dephosphorylated, active, form) of rats fed on a chow diet. However, dietary clofibric acid greatly increased the activity state of liver BCODC of rats fed on a diet deficient in protein. No stable change in liver BCODC kinase activity was found in response to clofibric acid in either chow-fed or low-protein-fed rats. Clofibric acid had a biphasic effect on flux through BCODC in hepatocytes prepared from low-protein-fed rats. Stimulation of BCODC flux at low concentrations was due to clofibric acid inhibition of BCODC kinase, which in turn allowed activation of BCODC by BCODC phosphatase. Inhibition of BCODC flux at high concentrations was due to direct inhibition of BCODC by clofibric acid. The results suggest that the effects of clofibric acid in vivo on branched-chain amino acid metabolism can be explained by the inhibitory effects of this drug on BCODC kinase. Images Fig. 2. Fig. 3. PMID:1637295

Bioinspired peony-like beta-Ni(OH)2 nanostructures with enhanced electrochemical activity and superhydrophobicity.

PubMed

Cao, Huaqiang; Zheng, He; Liu, Kaiyu; Warner, Jamie H

2010-02-01

Constructing complex nanostructures has become increasingly important in the development of hydrogen storage, self-cleaning materials, and the formation of chiral branched nanowires. Several approaches have been developed to generate complex nanostructures, which have led to novel applications. Combining biology and nanotechnology through the utilization of biomolecules to chemically template the growth of complex nanostructures during synthesis has aroused great interest. Herein, we use a biomolecule-assisted hydrothermal method to synthesize beta-phase Ni(OH)(2) peony-like complex nanostructures with second-order structure nanoplate structure. The novel beta-Ni(OH)(2) nanostructures exhibit high-power Ni/MH battery performance, close to the theoretical capacity of Ni(OH)(2), as well as controlled wetting behavior. We demonstrate that this bioinspired route to generate a complex nanostructure has applications in environmental protection and green secondary cells. This approach opens up opportunities for the synthesis and potential applications of new kinds of nanostructures.

Regulation of hepatic branched-chain alpha-keto acid dehydrogenase kinase in a rat model for type 2 diabetes mellitus at different stages of the disease.

PubMed

Doisaki, Masao; Katano, Yoshiaki; Nakano, Isao; Hirooka, Yoshiki; Itoh, Akihiro; Ishigami, Masatoshi; Hayashi, Kazuhiko; Goto, Hidemi; Fujita, Yuko; Kadota, Yoshihiro; Kitaura, Yasuyuki; Bajotto, Gustavo; Kazama, Shunsuke; Tamura, Tomohiro; Tamura, Noriko; Feng, Guo-Gang; Ishikawa, Naohisa; Shimomura, Yoshiharu

2010-03-05

Branched-chain alpha-keto acid dehydrogenase (BCKDH) kinase (BDK) is responsible for the regulation of BCKDH complex, which is the rate-limiting enzyme in the catabolism of branched-chain amino acids (BCAAs). In the present study, we investigated the expression and activity of hepatic BDK in spontaneous type 2 diabetes using hyperinsulinemic Zucker diabetic fatty rats aged 9weeks and hyperglycemic, but not hyperinsulinemic rats aged 18weeks. The abundance of hepatic BDK mRNA and total BDK protein did not correlate with changes in serum insulin concentrations. On the other hand, the amount of BDK bound to the complex and its kinase activity were correlated with alterations in serum insulin levels, suggesting that hyperinsulinemia upregulates hepatic BDK. The activity of BDK inversely corresponded with the BCKDH complex activity, which was suppressed in hyperinsulinemic rats. These results suggest that insulin regulates BCAA catabolism in type 2 diabetic rats by modulating the hepatic BDK activity. 2010 Elsevier Inc. All rights reserved.

Impact of Branched-Chain Amino Acid Catabolism on Fatty Acid and Alkene Biosynthesis in Micrococcus luteus.

PubMed

Surger, Maximilian J; Angelov, Angel; Stier, Philipp; Übelacker, Maria; Liebl, Wolfgang

2018-01-01

Micrococcus luteus naturally produces alkenes, unsaturated aliphatic hydrocarbons, and represents a promising host to produce hydrocarbons as constituents of biofuels and lubricants. In this work, we identify the genes for key enzymes of the branched-chain amino acid catabolism in M. luteus , whose first metabolic steps lead also to the formation of primer molecules for branched-chain fatty acid and olefin biosynthesis, and demonstrate how these genes can be used to manipulate the production of specific olefins in this organism. We constructed mutants of several gene candidates involved in the branched-chain amino acid metabolism or its regulation and investigated the resulting changes in the cellular fatty acid and olefin profiles by GC/MS. The gene cluster encoding the components of the branched-chain α-keto acid dehydrogenase (BCKD) complex was identified by deletion and promoter exchange mutagenesis. Overexpression of the BCKD gene cluster resulted in about threefold increased olefin production whereas deletion of the cluster led to a drastic reduction in branched-chain fatty acid content and a complete loss of olefin production. The specificities of the acyl-CoA dehydrogenases of the branched amino acid degradation pathways were deduced from the fatty acid and olefin profiles of the respective deletion mutant strains. In addition, growth experiments with branched amino acids as the only nitrogen source were carried out with the mutants in order to confirm our annotations. Both the deletion mutant of the BCKD complex, responsible for the further degradation of all three branched-chain amino acids, as well as the deletion mutant of the proposed isovaleryl-CoA dehydrogenase (specific for leucine degradation) were not able to grow on leucine in contrast to the parental strain. In conclusion, our experiments allow the unambigous assignment of specific functions to the genes for key enzymes of the branched-chain amino acid metabolism of M. luteus . We also show how this knowledge can be used to engineer the isomeric composition and the chain lengths of the olefins produced by this organism.

Expert systems for MSFC power systems

NASA Technical Reports Server (NTRS)

Weeks, David J.

1988-01-01

Future space vehicles and platforms including Space Station will possess complex power systems. These systems will require a high level of autonomous operation to allow the crew to concentrate on mission activities and to limit the number of ground support personnel to a reasonable number. The Electrical Power Branch at NASA-Marshall is developing advanced automation approaches which will enable the necessary levels of autonomy. These approaches include the utilization of knowledge based or expert systems.

Highly branched penta-saccharide-bearing amphiphiles for membrane protein studies

PubMed Central

Ehsan, Muhammad; Du, Yang; Scull, Nicola J.; Tikhonova, Elena; Tarrasch, Jeffrey; Mortensen, Jonas S.; Loland, Claus J.; Skiniotis, Georgios; Guan, Lan; Byrne, Bernadette; Kobilka, Brian K.; Chae, Pil Seok

2016-01-01

Detergents are essential tools for membrane protein manipulation. Micelles formed by detergent molecules have the ability to encapsulate the hydrophobic domains of membrane proteins. The resulting protein-detergent complexes (PDCs) are compatible with the polar environments of aqueous media, making structural and functional analysis feasible. Although a number of novel agents have been developed to overcome the limitations of conventional detergents, most of them have traditional head groups such as glucoside or maltoside. In this study, we introduce a class of amphiphiles, the PSA’Es with a novel highly branched penta-saccharide hydrophilic group. The PSA’Es conferred markedly increased stability to a diverse range of membrane proteins compared to conventional detergents, indicating a positive role for the new hydrophilic group in maintaining the native protein integrity. In addition, PDCs formed by PSA’Es were smaller and more suitable for electron microscopic analysis than those formed by DDM, indicating that the new agents have significant potential for the structure-function studies of membrane proteins. PMID:26966956

Axonal properties determine somatic firing in a model of in vitro CA1 hippocampal sharp wave/ripples and persistent gamma oscillations

PubMed Central

Traub, Roger D.; Schmitz, Dietmar; Maier, Nikolaus; Whittington, Miles A.; Draguhn, Andreas

2012-01-01

Evidence has been presented that CA1 pyramidal cells, during spontaneous in vitro sharp wave/ripple (SPW-R) complexes, generate somatic action potentials that originate in axons. ‘Participating’ (somatically firing) pyramidal cells fire (almost always) at most once during a particular SPW-R whereas non-participating cells virtually never fire during an SPW-R. Somatic spikelets were small or absent, while ripple-frequency EPSCs and IPSCs occurred during the SPW-R in pyramidal neurons. These experimental findings could be replicated with a network model in which electrical coupling was present between small pyramidal cell axonal branches. Here, we explore this model in more depth. Factors that influence somatic participation include: (i) the diameter of axonal branches that contain coupling sites to other axons, because firing in larger branches injects more current into the main axon, increasing antidromic firing probability; (ii) axonal K+ currents; and (iii) somatic hyperpolarization and shunting. We predict that portions of axons fire at high frequency during SPW-R, while somata fire much less. In the model, somatic firing can occur by occasional generation of full action potentials in proximal axonal branches, which are excited by high-frequency spikelets. When the network contains phasic synaptic inhibition, at the axonal gap junction site, gamma oscillations result, again with more frequent axonal firing than somatic firing. Combining the models, so as to generate gamma followed by sharp waves, leads to strong overlap between the population of cells firing during gamma the population of cells firing during a subsequent sharp wave, as observed in vivo. PMID:22697272

Automated feature extraction for retinal vascular biometry in zebrafish using OCT angiography

NASA Astrophysics Data System (ADS)

Bozic, Ivan; Rao, Gopikrishna M.; Desai, Vineet; Tao, Yuankai K.

2017-02-01

Zebrafish have been identified as an ideal model for angiogenesis because of anatomical and functional similarities with other vertebrates. The scale and complexity of zebrafish assays are limited by the need to manually treat and serially screen animals, and recent technological advances have focused on automation and improving throughput. Here, we use optical coherence tomography (OCT) and OCT angiography (OCT-A) to perform noninvasive, in vivo imaging of retinal vasculature in zebrafish. OCT-A summed voxel projections were low pass filtered and skeletonized to create an en face vascular map prior to connectivity analysis. Vascular segmentation was referenced to the optic nerve head (ONH), which was identified by automatically segmenting the retinal pigment epithelium boundary on the OCT structural volume. The first vessel branch generation was identified as skeleton segments with branch points closest to the ONH, and subsequent generations were found iteratively by expanding the search space outwards from the ONH. Biometric parameters, including length, curvature, and branch angle of each vessel segment were calculated and grouped by branch generation. Despite manual handling and alignment of each animal over multiple time points, we observe distinct qualitative patterns that enable unique identification of each eye from individual animals. We believe this OCT-based retinal biometry method can be applied for automated animal identification and handling in high-throughput organism-level pharmacological assays and genetic screens. In addition, these extracted features may enable high-resolution quantification of longitudinal vascular changes as a method for studying zebrafish models of retinal neovascularization and vascular remodeling.

Dendritic Cytoskeletal Architecture Is Modulated by Combinatorial Transcriptional Regulation in Drosophila melanogaster.

PubMed

Das, Ravi; Bhattacharjee, Shatabdi; Patel, Atit A; Harris, Jenna M; Bhattacharya, Surajit; Letcher, Jamin M; Clark, Sarah G; Nanda, Sumit; Iyer, Eswar Prasad R; Ascoli, Giorgio A; Cox, Daniel N

2017-12-01

Transcription factors (TFs) have emerged as essential cell autonomous mediators of subtype specific dendritogenesis; however, the downstream effectors of these TFs remain largely unknown, as are the cellular events that TFs control to direct morphological change. As dendritic morphology is largely dictated by the organization of the actin and microtubule (MT) cytoskeletons, elucidating TF-mediated cytoskeletal regulatory programs is key to understanding molecular control of diverse dendritic morphologies. Previous studies in Drosophila melanogaster have demonstrated that the conserved TFs Cut and Knot exert combinatorial control over aspects of dendritic cytoskeleton development, promoting actin and MT-based arbor morphology, respectively. To investigate transcriptional targets of Cut and/or Knot regulation, we conducted systematic neurogenomic studies, coupled with in vivo genetic screens utilizing multi-fluor cytoskeletal and membrane marker reporters. These analyses identified a host of putative Cut and/or Knot effector molecules, and a subset of these putative TF targets converge on modulating dendritic cytoskeletal architecture, which are grouped into three major phenotypic categories, based upon neuromorphometric analyses: complexity enhancer, complexity shifter, and complexity suppressor. Complexity enhancer genes normally function to promote higher order dendritic growth and branching with variable effects on MT stabilization and F-actin organization, whereas complexity shifter and complexity suppressor genes normally function in regulating proximal-distal branching distribution or in restricting higher order branching complexity, respectively, with spatially restricted impacts on the dendritic cytoskeleton. Collectively, we implicate novel genes and cellular programs by which TFs distinctly and combinatorially govern dendritogenesis via cytoskeletal modulation. Copyright © 2017 by the Genetics Society of America.

Computational complexity of Boolean functions

NASA Astrophysics Data System (ADS)

Korshunov, Aleksei D.

2012-02-01

Boolean functions are among the fundamental objects of discrete mathematics, especially in those of its subdisciplines which fall under mathematical logic and mathematical cybernetics. The language of Boolean functions is convenient for describing the operation of many discrete systems such as contact networks, Boolean circuits, branching programs, and some others. An important parameter of discrete systems of this kind is their complexity. This characteristic has been actively investigated starting from Shannon's works. There is a large body of scientific literature presenting many fundamental results. The purpose of this survey is to give an account of the main results over the last sixty years related to the complexity of computation (realization) of Boolean functions by contact networks, Boolean circuits, and Boolean circuits without branching. Bibliography: 165 titles.

Purification of Ovine Respiratory Complex I Results in a Highly Active and Stable Preparation.

PubMed

Letts, James A; Degliesposti, Gianluca; Fiedorczuk, Karol; Skehel, Mark; Sazanov, Leonid A

2016-11-18

NADH-ubiquinone oxidoreductase (complex I) is the largest (∼1 MDa) and the least characterized complex of the mitochondrial electron transport chain. Because of the ease of sample availability, previous work has focused almost exclusively on bovine complex I. However, only medium resolution structural analyses of this complex have been reported. Working with other mammalian complex I homologues is a potential approach for overcoming these limitations. Due to the inherent difficulty of expressing large membrane protein complexes, screening of complex I homologues is limited to large mammals reared for human consumption. The high sequence identity among these available sources may preclude the benefits of screening. Here, we report the characterization of complex I purified from Ovis aries (ovine) heart mitochondria. All 44 unique subunits of the intact complex were identified by mass spectrometry. We identified differences in the subunit composition of subcomplexes of ovine complex I as compared with bovine, suggesting differential stability of inter-subunit interactions within the complex. Furthermore, the 42-kDa subunit, which is easily lost from the bovine enzyme, remains tightly bound to ovine complex I. Additionally, we developed a novel purification protocol for highly active and stable mitochondrial complex I using the branched-chain detergent lauryl maltose neopentyl glycol. Our data demonstrate that, although closely related, significant differences exist between the biochemical properties of complex I prepared from ovine and bovine mitochondria and that ovine complex I represents a suitable alternative target for further structural studies. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Association mapping in sunflower (Helianthus annuus L.) reveals independent control of apical vs. basal branching.

PubMed

Nambeesan, Savithri U; Mandel, Jennifer R; Bowers, John E; Marek, Laura F; Ebert, Daniel; Corbi, Jonathan; Rieseberg, Loren H; Knapp, Steven J; Burke, John M

2015-03-11

Shoot branching is an important determinant of plant architecture and influences various aspects of growth and development. Selection on branching has also played an important role in the domestication of crop plants, including sunflower (Helianthus annuus L.). Here, we describe an investigation of the genetic basis of variation in branching in sunflower via association mapping in a diverse collection of cultivated sunflower lines. Detailed phenotypic analyses revealed extensive variation in the extent and type of branching within the focal population. After correcting for population structure and kinship, association analyses were performed using a genome-wide collection of SNPs to identify genomic regions that influence a variety of branching-related traits. This work resulted in the identification of multiple previously unidentified genomic regions that contribute to variation in branching. Genomic regions that were associated with apical and mid-apical branching were generally distinct from those associated with basal and mid-basal branching. Homologs of known branching genes from other study systems (i.e., Arabidopsis, rice, pea, and petunia) were also identified from the draft assembly of the sunflower genome and their map positions were compared to those of associations identified herein. Numerous candidate branching genes were found to map in close proximity to significant branching associations. In sunflower, variation in branching is genetically complex and overall branching patterns (i.e., apical vs. basal) were found to be influenced by distinct genomic regions. Moreover, numerous candidate branching genes mapped in close proximity to significant branching associations. Although the sunflower genome exhibits localized islands of elevated linkage disequilibrium (LD), these non-random associations are known to decay rapidly elsewhere. The subset of candidate genes that co-localized with significant associations in regions of low LD represents the most promising target for future functional analyses.

Bundle-branch reentry ventricular tachycardia after transcatheter aortic valve replacement

PubMed Central

de la Rosa Riestra, Adriana; Rubio Caballero, José Amador; Freites Estévez, Alfonso; Alonso Belló, Javier; Botas Rodríguez, Javier

2016-01-01

An 83-year-old male suffering from severe symptomatic aortic valve stenosis received an implant of a biological aortic prosthesis through the femoral artery without complications. Seven days after dischargement he experienced a syncope. The patient was wearing an ECG holter monitor that day, which showed a wide QRS complex tachycardia of 300 beats per minute. The electrophysiological study revealed a bundle-branch reentry ventricular tachycardia as the cause of the syncope. Radio-frequency was applied on the right-bundle branch. Twelve months later, the patient has remained asymptomatic. PMID:27134443

Phase behavior and structure of stable complexes between a long polyanion and a branched polycation

NASA Astrophysics Data System (ADS)

Mengarelli, Valentina; Zeghal, Mehdi; Auvray, Loïc; Clemens, Daniel

2011-08-01

The association between oppositely charged branched polyethylenimine (BPEI) and polymethacrylic acid (PMA) in the dilute regime is investigated using turbidimetric titration and electrophoretic mobility measurements. The complexation is controlled by tuning continuously the pH-sensitive charge of the polyacid in acidic solution. The formation of soluble and stable positively charged complexes is a cooperative process characterized by the existence of two regimes of weak and strong complexation. In the regime of weak complexation, a long PMA chain overcharged by several BPEI molecules forms a binary complex. As the charge of the polyacid increases, these binary complexes condense at a well defined charge ratio of the mixture to form large positively charged aggregates. The overcharging and the existence of two regimes of complexation are analyzed in the light of recent theories. The structure of the polyelectrolytes is investigated at higher polymer concentration by small angle neutron scattering. Binary complexes of finite size present an open structure where the polyacid chains connecting a small number of BPEI molecules have shrunk slightly. In the condensed complexes, BPEI molecules, wrapped by polyacid chains, form networks of stretched necklaces.

Checkpoint repair for high-performance out-of-order execution machines

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

Hwu, W.M.W.; Patt, Y.N.

Out-or-order execution and branch prediction are two mechanisms that can be used profitably in the design of supercomputers to increase performance. Proper exception handling and branch prediction miss handling in an out-of-order execution machine to require some kind of repair mechanism which can restore the machine to a known previous state. In this paper the authors present a class of repair mechanisms using the concept of checkpointing. The authors derive several properties of checkpoint repair mechanisms. In addition, they provide algorithms for performing checkpoint repair that incur little overhead in time and modest cost in hardware, which also require nomore » additional complexity or time for use with write-back cache memory systems than they do with write-through cache memory systems, contrary to statements made by previous researchers.« less

Upper Miocene reef complex of Mallorca, Balearic Islands, Spain

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

Pomar, L.

1988-02-01

The late Tortonian-Messinian coral reef platform of south Mallorca onlaps a folded middle late Miocene carbonate platform on which progradation of up to 20 km occurs. Vertical sea cliffs (up to 100 m high) superbly show the last 5 km of this progradation and complement the numerous water-well cores from the island interior. The Mallorca reef presents the most complete facies zonation of the Miocene reefs of the western Mediterranean. The reef wall framework is up to 20 m thick and shows (1) erosional reef flat with reef breccia and small corals; (2) spur-and-grove zone with large, massive corals; (3)more » deep buttresses and pinnacles with terraces of branching corals; and (4) deep reef wall with flat, laminar coral colonies, branching red algae, and Halimeda sands.« less

Designing Dendrimer and Miktoarm Polymer Based Multi-Tasking Nanocarriers for Efficient Medical Therapy.

PubMed

Sharma, Anjali; Kakkar, Ashok

2015-09-17

To address current complex health problems, there has been an increasing demand for smart nanocarriers that could perform multiple complimentary biological tasks with high efficacy. This has provoked the design of tailor made nanocarriers, and the scientific community has made tremendous effort in meeting daunting challenges associated with synthetically articulating multiple functions into a single scaffold. Branched and hyper-branched macromolecular architectures have offered opportunities in enabling carriers with capabilities including location, delivery, imaging etc. Development of simple and versatile synthetic methodologies for these nanomaterials has been the key in diversifying macromolecule based medical therapy and treatment. This review highlights the advancement from conventional "only one function" to multifunctional nanomedicine. It is achieved by synthetic elaboration of multivalent platforms in miktoarm polymers and dendrimers by physical encapsulation, covalent linking and combinations thereof.

High Throughput Engineering to Revitalize a Vestigial Electron Transfer Pathway in Bacterial Photosynthetic Reaction Centers*

PubMed Central

Faries, Kaitlyn M.; Kressel, Lucas L.; Wander, Marc J.; Holten, Dewey; Laible, Philip D.; Kirmaier, Christine; Hanson, Deborah K.

2012-01-01

Photosynthetic reaction centers convert light energy into chemical energy in a series of transmembrane electron transfer reactions, each with near 100% yield. The structures of reaction centers reveal two symmetry-related branches of cofactors (denoted A and B) that are functionally asymmetric; purple bacterial reaction centers use the A pathway exclusively. Previously, site-specific mutagenesis has yielded reaction centers capable of transmembrane charge separation solely via the B branch cofactors, but the best overall electron transfer yields are still low. In an attempt to better realize the architectural and energetic factors that underlie the directionality and yields of electron transfer, sites within the protein-cofactor complex were targeted in a directed molecular evolution strategy that implements streamlined mutagenesis and high throughput spectroscopic screening. The polycistronic approach enables efficient construction and expression of a large number of variants of a heteroligomeric complex that has two intimately regulated subunits with high sequence similarity, common features of many prokaryotic and eukaryotic transmembrane protein assemblies. The strategy has succeeded in the discovery of several mutant reaction centers with increased efficiency of the B pathway; they carry multiple substitutions that have not been explored or linked using traditional approaches. This work expands our understanding of the structure-function relationships that dictate the efficiency of biological energy-conversion reactions, concepts that will aid the design of bio-inspired assemblies capable of both efficient charge separation and charge stabilization. PMID:22247556

A multiscale model of placental oxygen exchange: The effect of villous tree structure on exchange efficiency.

PubMed

Lin, Mabelle; Mauroy, Benjamin; James, Joanna L; Tawhai, Merryn H; Clark, Alys R

2016-11-07

The placenta is critical to fetal health during pregnancy as it supplies oxygen and nutrients to maintain life. It has a complex structure, and alterations to this structure across spatial scales are associated with several pregnancy complications, including intrauterine growth restriction (IUGR). The relationship between placental structure and its efficiency as an oxygen exchanger is not well understood in normal or pathological pregnancies. Here we present a computational framework that predicts oxygen transport in the placenta which accounts for blood and oxygen transport in the space around a placental functional unit (the villous tree). The model includes the well-defined branching structure of the largest villous tree branches, as well as a smoothed representation of the small terminal villi that comprise the placenta's gas exchange interfaces. The model demonstrates that oxygen exchange is sensitive to villous tree geometry, including the villous branch length and volume, which are seen to change in IUGR. This is because, to be an efficient exchanger, the architecture of the villous tree must provide a balance between maximising the surface area available for exchange, and the opposing condition of allowing sufficient maternal blood flow to penetrate into the space surrounding the tree. The model also predicts an optimum oxygen exchange when the branch angle is 24 °, as villous branches and TBs are spread out sufficiently to channel maternal blood flow deep into the placental tissue for oxygen exchange without being shunted directly into the DVs. Without concurrent change in the branch length and angles, the model predicts that the number of branching generations has a small influence on oxygen exchange. The modelling framework is presented in 2D for simplicity but is extendible to 3D or to incorporate the high-resolution imaging data that is currently evolving to better quantify placental structure. Copyright © 2016 Elsevier Ltd. All rights reserved.

Clofibric acid stimulates branched-chain amino acid catabolism by three mechanisms.

PubMed

Kobayashi, Rumi; Murakami, Taro; Obayashi, Mariko; Nakai, Naoya; Jaskiewicz, Jerzy; Fujiwara, Yoko; Shimomura, Yoshiharu; Harris, Robert A

2002-11-15

Clofibrate promotes catabolism of branched-chain amino acids by increasing the activity of the branched-chain alpha-keto acid dehydrogenase [BCKDH] complex. Depending upon the sex of the rats, nutritional state, and tissue being studied, clofibrate can affect BCKDH complex activity by three different mechanisms. First, by directly inhibiting BCKDH kinase activity, clofibrate can increase the proportion of the BCKDH complex in the active, dephosphorylated state. This occurs in situations in which the BCKDH complex is largely inactive due to phosphorylation, e.g., in the skeletal muscle of chow-fed rats or in the liver of female rats late in the light cycle. Second, by increasing the levels at which the enzyme components of the BCKDH complex are expressed, clofibrate can increase the total enzymatic activity of the BCKDH complex. This is readily demonstrated in livers of rats fed a low-protein diet, a nutritional condition that induces a decrease in the level of expression of the BCKDH complex. Third, by decreasing the amount of BCKDH kinase expressed and therefore its activity, clofibrate induces an increase in the percentage of the BCKDH complex in the active, dephosphorylated state. This occurs in the livers of rats fed a low-protein diet, a nutritional condition that causes inactivation of the BCKDH complex due to upregulation of the amount of BCKDH kinase. WY-14,643, which, like clofibric acid, is a ligand for the peroxisome-proliferator-activated receptor alpha [PPARalpha], does not directly inhibit BCKDH kinase but produces the same long-term effects as clofibrate on expression of the BCKDH complex and its kinase. Thus, clofibrate is unique in its capacity to stimulate BCAA oxidation through inhibition of BCKDH kinase activity, whereas PPARalpha activators in general promote BCAA oxidation by increasing expression of components of the BCKDH complex and decreasing expression of the BCKDH kinase.

Anatomy of the β-branching enzyme of polyketide biosynthesis and its interaction with an acyl-ACP substrate.

PubMed

Maloney, Finn P; Gerwick, Lena; Gerwick, William H; Sherman, David H; Smith, Janet L

2016-09-13

Alkyl branching at the β position of a polyketide intermediate is an important variation on canonical polyketide natural product biosynthesis. The branching enzyme, 3-hydroxy-3-methylglutaryl synthase (HMGS), catalyzes the aldol addition of an acyl donor to a β-keto-polyketide intermediate acceptor. HMGS is highly selective for two specialized acyl carrier proteins (ACPs) that deliver the donor and acceptor substrates. The HMGS from the curacin A biosynthetic pathway (CurD) was examined to establish the basis for ACP selectivity. The donor ACP (CurB) had high affinity for the enzyme (Kd = 0.5 μM) and could not be substituted by the acceptor ACP. High-resolution crystal structures of HMGS alone and in complex with its donor ACP reveal a tight interaction that depends on exquisite surface shape and charge complementarity between the proteins. Selectivity is explained by HMGS binding to an unusual surface cleft on the donor ACP, in a manner that would exclude the acceptor ACP. Within the active site, HMGS discriminates between pre- and postreaction states of the donor ACP. The free phosphopantetheine (Ppant) cofactor of ACP occupies a conserved pocket that excludes the acetyl-Ppant substrate. In comparison with HMG-CoA (CoA) synthase, the homologous enzyme from primary metabolism, HMGS has several differences at the active site entrance, including a flexible-loop insertion, which may account for the specificity of one enzyme for substrates delivered by ACP and the other by CoA.

Three-Dimensional Reconstruction of the Virtual Plant Branching Structure Based on Terrestrial LIDAR Technologies and L-System

NASA Astrophysics Data System (ADS)

Gong, Y.; Yang, Y.; Yang, X.

2018-04-01

For the purpose of extracting productions of some specific branching plants effectively and realizing its 3D reconstruction, Terrestrial LiDAR data was used as extraction source of production, and a 3D reconstruction method based on Terrestrial LiDAR technologies combined with the L-system was proposed in this article. The topology structure of the plant architectures was extracted using the point cloud data of the target plant with space level segmentation mechanism. Subsequently, L-system productions were obtained and the structural parameters and production rules of branches, which fit the given plant, was generated. A three-dimensional simulation model of target plant was established combined with computer visualization algorithm finally. The results suggest that the method can effectively extract a given branching plant topology and describes its production, realizing the extraction of topology structure by the computer algorithm for given branching plant and also simplifying the extraction of branching plant productions which would be complex and time-consuming by L-system. It improves the degree of automation in the L-system extraction of productions of specific branching plants, providing a new way for the extraction of branching plant production rules.

Get a Grip: Substrate Orientation and Digital Grasping Pressures in Strepsirrhines.

PubMed

Congdon, Kimberly A; Ravosa, Matthew J

2016-01-01

Skeletal functional morphology in primates underlies many fossil interpretations. Understanding the functional correlates of arboreal grasping is central to identifying locomotor signatures in extinct primates. We tested 3 predictions linking substrate orientation and digital grasping pressures: (1) below-branch pressures are greater than above-branch and vertical-branch pressures; (2) there is no difference in pressure exerted across digits within autopods at any substrate orientation, and (3) there is no difference in pressure exerted between homologous digits across autopods at any substrate orientation. Adult males and females from 3 strepsirrhine species crossed an artificial arboreal substrate oriented for above-, below- and vertical-branch locomotion. We compared digital pressures within and across behaviors via ANOVA and Tukey's Honest Significant Difference test. Results show limited support for all predictions: below-branch pressures exceeded vertical-branch pressures and above-branch pressures for some digits and species (prediction 1), lateral digits often exerted greater pressures than medial digits (prediction 2), and pedal digits occasionally exerted greater pressures than manual digits during above-branch and vertical orientations but less often for below-branch locomotion (prediction 3). We observed functional variability across autopods, substrate and species that could underlie morphological variation within and across primates. Future work should consider the complexity of arboreality when inferring locomotor modes in fossils. © 2016 S. Karger AG, Basel.

Highly flexible pulse programmer for NMR applications

NASA Technical Reports Server (NTRS)

Dart, J.; Burum, D. P.; Rhim, W. K.

1980-01-01

A pulse generator for NMR application is described. Eighteen output channels are provided to allow use in single and double resonance experiments. Complex pulse sequences may be generated by loading instructions into a 256-word by 16-bit program memory. Features of the pulse generator include programmable time delays from 0.5 micros to 1000 s, branching and looping instructions, and the ability to be loaded and operated either manually or from a PDP-11/10 computer.

Diastereoselective sp2-sp3 coupling of sugar enol ethers with unactivated cycloalkenes: new entries to C-branched sugars.

PubMed

Hussain, Nazar; Tatina, Madhu Babu; Rasool, Faheem; Mukherjee, Debaraj

2016-10-25

Sugar enol ethers undergo efficient coupling at C-2 with unactivated cycloalkenes under a low Pd loading affording allylic substitution products. High diastereoselectivity was observed at the allylic centre with sterically hindered substrates. Generation of a π-allyl complex by the Pd(ii) catalyst via cleavage of the allylic C-H bond of the cycloalkene may be responsible for the formation of sp 2 -sp 3 coupling products.

DNA recombination activity in soybean mitochondria.

PubMed

Manchekar, Medha; Scissum-Gunn, Karyn; Song, Daqing; Khazi, Fayaz; McLean, Stephanie L; Nielsen, Brent L

2006-02-17

Mitochondrial genomes in higher plants are much larger and more complex as compared to animal mitochondrial genomes. There is growing evidence that plant mitochondrial genomes exist predominantly as a collection of linear and highly branched DNA molecules and replicate by a recombination-dependent mechanism. However, biochemical evidence of mitochondrial DNA (mtDNA) recombination activity in plants has previously been lacking. We provide the first report of strand-invasion activity in plant mitochondria. Similar to bacterial RecA, this activity from soybean is dependent on the presence of ATP and Mg(2+). Western blot analysis using an antibody against the Arabidopsis mitochondrial RecA protein shows cross-reaction with a soybean protein of about 44 kDa, indicating conservation of this protein in at least these two plant species. mtDNA structure was analyzed by electron microscopy of total soybean mtDNA and molecules recovered after field-inversion gel electrophoresis (FIGE). While most molecules were found to be linear, some molecules contained highly branched DNA structures and a small but reproducible proportion consisted of circular molecules (many with tails) similar to recombination intermediates. The presence of recombination intermediates in plant mitochondria preparations is further supported by analysis of mtDNA molecules by 2-D agarose gel electrophoresis, which indicated the presence of complex recombination structures along with a considerable amount of single-stranded DNA. These data collectively provide convincing evidence for the occurrence of homologous DNA recombination in plant mitochondria.

A new insight into the three-dimensional architecture of the Golgi complex: Characterization of unusual structures in epididymal principal cells

PubMed Central

Martínez-Martínez, Narcisa; Martínez-Alonso, Emma; Tomás, Mónica; Neumüller, Josef; Pavelka, Margit

2017-01-01

Principal epididymal cells have one of the largest and more developed Golgi complex of mammalian cells. In the present study, we have used this cell as model for the study of the three-dimensional architecture of the Golgi complex of highly secretory and endocytic cells. Electron tomography demonstrated the presence in this cell type of some unknown or very unusual Golgi structures such as branched cisternae, pocket-like cisternal invaginations or tubular connections. In addition, we have used this methodology and immunoelectron microscopy to analyze the close relationship between this organelle and both the endoplasmic reticulum and microtubules, and to describe in detail how these elements interact with compact and non-compact regions of the ribbon. PMID:28957389

Enhancement of the microbial community biomass and diversity during air sparging bioremediation of a soil highly contaminated with kerosene and BTEX.

PubMed

Kabelitz, Nadja; Machackova, Jirina; Imfeld, Gwenaël; Brennerova, Maria; Pieper, Dietmar H; Heipieper, Hermann J; Junca, Howard

2009-03-01

In order to obtain insights in complexity shifts taking place in natural microbial communities under strong selective pressure, soils from a former air force base in the Czech Republic, highly contaminated with jet fuel and at different stages of a bioremediation air sparging treatment, were analyzed. By tracking phospholipid fatty acids and 16S rRNA genes, a detailed monitoring of the changes in quantities and composition of the microbial communities developed at different stages of the bioventing treatment progress was performed. Depending on the length of the air sparging treatment that led to a significant reduction in the contamination level, we observed a clear shift in the soil microbial community being dominated by Pseudomonads under the harsh conditions of high aromatic contamination to a status of low aromatic concentrations, increased biomass content, and a complex composition with diverse bacterial taxonomical branches.

Turing mechanism underlying a branching model for lung morphogenesis.

PubMed

Xu, Hui; Sun, Mingzhu; Zhao, Xin

2017-01-01

The mammalian lung develops through branching morphogenesis. Two primary forms of branching, which occur in order, in the lung have been identified: tip bifurcation and side branching. However, the mechanisms of lung branching morphogenesis remain to be explored. In our previous study, a biological mechanism was presented for lung branching pattern formation through a branching model. Here, we provide a mathematical mechanism underlying the branching patterns. By decoupling the branching model, we demonstrated the existence of Turing instability. We performed Turing instability analysis to reveal the mathematical mechanism of the branching patterns. Our simulation results show that the Turing patterns underlying the branching patterns are spot patterns that exhibit high local morphogen concentration. The high local morphogen concentration induces the growth of branching. Furthermore, we found that the sparse spot patterns underlie the tip bifurcation patterns, while the dense spot patterns underlies the side branching patterns. The dispersion relation analysis shows that the Turing wavelength affects the branching structure. As the wavelength decreases, the spot patterns change from sparse to dense, the rate of tip bifurcation decreases and side branching eventually occurs instead. In the process of transformation, there may exists hybrid branching that mixes tip bifurcation and side branching. Since experimental studies have reported that branching mode switching from side branching to tip bifurcation in the lung is under genetic control, our simulation results suggest that genes control the switch of the branching mode by regulating the Turing wavelength. Our results provide a novel insight into and understanding of the formation of branching patterns in the lung and other biological systems.

Plant root and shoot dynamics during subsurface obstacle interaction

NASA Astrophysics Data System (ADS)

Conn, Nathaniel; Aguilar, Jeffrey; Benfey, Philip; Goldman, Daniel

As roots grow, they must navigate complex underground environments to anchor and retrieve water and nutrients. From gravity sensing at the root tip to pressure sensing along the tip and elongation zone, the complex mechanosensory feedback system of the root allows it to bend towards greater depths and avoid obstacles of high impedance by asymmetrically suppressing cell elongation. Here we investigate the mechanical and physiological responses of roots to rigid obstacles. We grow Maize, Zea mays, plants in quasi-2D glass containers (22cm x 17cm x 1.4cm) filled with photoelastic gel and observe that, regardless of obstacle interaction, smaller roots branch off the primary root when the upward growing shoot (which contains the first leaf) reaches an average length of 40 mm, coinciding with when the first leaf emerges. However, prior to branching, contacts with obstacles result in reduced root growth rates. The growth rate of the root relative to the shoot is sensitive to the angle of the obstacle surface, whereby the relative root growth is greatest for horizontally oriented surfaces. We posit that root growth is prioritized when horizontal obstacles are encountered to ensure anchoring and access to nutrients during later stages of development. NSF Physics of Living Systems.

The evolutionary origin of feathers.

PubMed

Regal, P J

1975-03-01

Previous theories relating the origin of feathers to flight or to heat conservation are considered to be inadequate. There is need for a model of feather evolution that gives attention to the function and adaptive advantage of intermediate structures. The present model attempts to reveal and to deal with, the spectrum of complex questions that must be considered. In several genera of modern lizards, scales are elongated in warm climates. It is argued that these scales act as small shields to solar radiation. Experiments are reported that tend to confirm this. Using lizards as a conceptual model, it is argued that feathers likewise arose as adaptations to intense solar radiation. Elongated scales are assumed to have subdivided into finely branched structures that produced a heat-shield, flexible as well as long and broad. Associated muscles had the function of allowing the organism fine control over rates of heat gain and loss: the specialized scales or early feathers could be moved to allow basking in cool weather or protection in hot weather. Subdivision of the scales also allowed a close fit between the elements of the insulative integument. There would have been mechanical and thermal advantages to having branches that interlocked into a pennaceous structure early in evolution, so the first feathers may have been pennaceous. A versatile insulation of movable, branched scales would have been a preadaptation for endothermy. As birds took to the air they faced cooling problems despite their insulative covering because of high convective heat loss. Short glides may have initially been advantageous in cooling an animal under heat stress, but at some point the problem may have shifted from one of heat exclusion to one of heat retention. Endothermy probably evolved in conjunction with flight. If so, it is an unnecessary assumption to postulate that the climate cooled and made endothermy advantageous. The development of feathers is complex and a model is proposed that gives attention to the fundamental problems of deriving a branched structure with a cylindrical base from an elongated scale.

Physiological and glycomic characterization of N-acetylglucosaminyltransferase-IVa and -IVb double deficient mice

PubMed Central

Takamatsu, Shinji; Antonopoulos, Aristotelis; Ohtsubo, Kazuaki; Ditto, David; Chiba, Yasunori; Le, Dzung T.; Morris, Howard R.; Haslam, Stuart M.; Dell, Anne; Marth, Jamey D.; Taniguchi, Naoyuki

2010-01-01

N-Acetylglucosaminyltransferase-IV (GnT-IV) has two isoenzymes, GnT-IVa and GnT-IVb, which initiate the GlcNAcβ1-4 branch synthesis on the Manα1-3 arm of the N-glycan core thereby increasing N-glycan branch complexity and conferring endogenous lectin binding epitopes. To elucidate the physiological significance of GnT-IV, we engineered and characterized GnT-IVb-deficient mice and further generated GnT-IVa/-IVb double deficient mice. In wild-type mice, GnT-IVa expression is restricted to gastrointestinal tissues, whereas GnT-IVb is broadly expressed among organs. GnT-IVb deficiency induced aberrant GnT-IVa expression corresponding to the GnT-IVb distribution pattern that might be attributed to increased Ets-1, which conceivably activates the Mgat4a promoter, and thereafter preserved apparent GnT-IV activity. The compensative GnT-IVa expression might contribute to amelioration of the GnT-IVb-deficient phenotype. GnT-IVb deficiency showed mild phenotypic alterations in hematopoietic cell populations and hemostasis. GnT-IVa/-IVb double deficiency completely abolished GnT-IV activity that resulted in the disappearance of the GlcNAcβ1-4 branch on the Manα1-3 arm that was confirmed by MALDI-TOF MS and GC-MS linkage analyses. Comprehensive glycomic analyses revealed that the abundance of terminal moieties was preserved in GnT-IVa/-IVb double deficiency that was due to the elevated expression of glycosyltransferases regarding synthesis of terminal moieties. Thereby, this may maintain the expression of glycan ligands for endogenous lectins and prevent cellular dysfunctions. The fact that the phenotype of GnT-IVa/-IVb double deficiency largely overlapped that of GnT-IVa single deficiency can be attributed to the induced glycomic compensation. This is the first report that mammalian organs have highly organized glycomic compensation systems to preserve N-glycan branch complexity. PMID:20015870

In vitro reconstruction of branched tubular structures from lung epithelial cells in high cell concentration gradient environment.

PubMed

Hagiwara, Masaya; Peng, Fei; Ho, Chih-Ming

2015-01-27

We have succeeded in developing hollow branching structure in vitro commonly observed in lung airway using primary lung airway epithelial cells. Cell concentration gradient is the key factor that determines production of the branching cellular structures, as optimization of this component removes the need for heterotypic culture. The higher cell concentration leads to the more production of morphogens and increases the growth rate of cells. However, homogeneous high cell concentration does not make a branching structure. Branching requires sufficient space in which cells can grow from a high concentration toward a low concentration. Simulation performed using a reaction-diffusion model revealed that long-range inhibition prevents cells from branching when they are homogeneously spread in culture environments, while short-range activation from neighboring cells leads to positive feedback. Thus, a high cell concentration gradient is required to make branching structures. Spatial distributions of morphogens, such as BMP-4, play important roles in the pattern formation. This simple yet robust system provides an optimal platform for the further study and understanding of branching mechanisms in the lung airway, and will facilitate chemical and genetic studies of lung morphogenesis programs.

Stability of synchrony against local intermittent fluctuations in tree-like power grids

NASA Astrophysics Data System (ADS)

Auer, Sabine; Hellmann, Frank; Krause, Marie; Kurths, Jürgen

2017-12-01

90% of all Renewable Energy Power in Germany is installed in tree-like distribution grids. Intermittent power fluctuations from such sources introduce new dynamics into the lower grid layers. At the same time, distributed resources will have to contribute to stabilize the grid against these fluctuations in the future. In this paper, we model a system of distributed resources as oscillators on a tree-like, lossy power grid and its ability to withstand desynchronization from localized intermittent renewable infeed. We find a remarkable interplay of the network structure and the position of the node at which the fluctuations are fed in. An important precondition for our findings is the presence of losses in distribution grids. Then, the most network central node splits the network into branches with different influence on network stability. Troublemakers, i.e., nodes at which fluctuations are especially exciting the grid, tend to be downstream branches with high net power outflow. For low coupling strength, we also find branches of nodes vulnerable to fluctuations anywhere in the network. These network regions can be predicted at high confidence using an eigenvector based network measure taking the turbulent nature of perturbations into account. While we focus here on tree-like networks, the observed effects also appear, albeit less pronounced, for weakly meshed grids. On the other hand, the observed effects disappear for lossless power grids often studied in the complex system literature.

Using the Git Software Tool on the Peregrine System | High-Performance

Science.gov Websites

branch workflow. Create a local branch called "experimental" based on the current master... git branch experimental Use your branch (start working on that experimental branch....) git checkout experimental git pull origin experimental # work, work, work, commit.... Send local branch to the repo git push

Stenting complex aorta aneurysms with the Cardiatis multilayer flow modulator: first impressions.

PubMed

Debing, E; Aerden, D; Gallala, S; Vandenbroucke, F; Van den Brande, P

2014-06-01

Our aim was to assess the feasibility and efficacy of the Cardiatis multilayer flow modulator in the treatment of complex aorta aneurysms. This is a single-center prospective registry. Six patients (4 males and 2 females; mean age 74 years) with complex aorta aneurysms (unsuitable for endovascular repair with standard, fenestrated, or branched stent grafts) were treated with the Cardiatis multilayer flow modulator. Clinical success was 100%. Median follow-up was 10 months. One patient died the third postoperative day due to aneurysm rupture. Four aneurysms were completely thrombosed between 1 and 6 months after the procedure. The patency of the covered aortic branches was 100%. At 6 months, the sac volume was decreased in two patients, increased in two patients and remains stable in one patient. There were no stent migrations, retractions, thrombosis, fractures, or reinterventions. The device preserves flow into the covered aortic branches and completed aneurysm thrombosis occurs gradually; however, the stent did not prevent rupture immediately after the implantation. Longer follow-up is mandatory to prove the efficacy of this technology. Copyright © 2014 European Society for Vascular Surgery. Published by Elsevier Ltd. All rights reserved.

[Primary branch size of Pinus koraiensis plantation: a prediction based on linear mixed effect model].

PubMed

Dong, Ling-Bo; Liu, Zhao-Gang; Li, Feng-Ri; Jiang, Li-Chun

2013-09-01

By using the branch analysis data of 955 standard branches from 60 sampled trees in 12 sampling plots of Pinus koraiensis plantation in Mengjiagang Forest Farm in Heilongjiang Province of Northeast China, and based on the linear mixed-effect model theory and methods, the models for predicting branch variables, including primary branch diameter, length, and angle, were developed. Considering tree effect, the MIXED module of SAS software was used to fit the prediction models. The results indicated that the fitting precision of the models could be improved by choosing appropriate random-effect parameters and variance-covariance structure. Then, the correlation structures including complex symmetry structure (CS), first-order autoregressive structure [AR(1)], and first-order autoregressive and moving average structure [ARMA(1,1)] were added to the optimal branch size mixed-effect model. The AR(1) improved the fitting precision of branch diameter and length mixed-effect model significantly, but all the three structures didn't improve the precision of branch angle mixed-effect model. In order to describe the heteroscedasticity during building mixed-effect model, the CF1 and CF2 functions were added to the branch mixed-effect model. CF1 function improved the fitting effect of branch angle mixed model significantly, whereas CF2 function improved the fitting effect of branch diameter and length mixed model significantly. Model validation confirmed that the mixed-effect model could improve the precision of prediction, as compare to the traditional regression model for the branch size prediction of Pinus koraiensis plantation.

Genetic diversity of Burkholderia (Proteobacteria) species from the Caatinga and Atlantic rainforest biomes in Bahia, Brazil.

PubMed

Santini, A C; Santos, H R M; Gross, E; Corrêa, R X

2013-03-11

The genus Burkholderia (β-Proteobacteria) currently comprises more than 60 species, including parasites, symbionts and free-living organisms. Several new species of Burkholderia have recently been described showing a great diversity of phenotypes. We examined the diversity of Burkholderia spp in environmental samples collected from Caatinga and Atlantic rainforest biomes of Bahia, Brazil. Legume nodules were collected from five locations, and 16S rDNA and recA genes of the isolated microorganisms were analyzed. Thirty-three contigs of 16S rRNA genes and four contigs of the recA gene related to the genus Burkholderia were obtained. The genetic dissimilarity of the strains ranged from 0 to 2.5% based on 16S rDNA analysis, indicating two main branches: one distinct branch of the dendrogram for the B. cepacia complex and another branch that rendered three major groups, partially reflecting host plants and locations. A dendrogram designed with sequences of this research and those designed with sequences of Burkholderia-type strains and the first hit BLAST had similar topologies. A dendrogram similar to that constructed by analysis of 16S rDNA was obtained using sequences of the fragment of the recA gene. The 16S rDNA sequences enabled sufficient identification of relevant similarities and groupings amongst isolates and the sequences that we obtained. Only 6 of the 33 isolates analyzed via 16S rDNA sequencing showed high similarity with the B. cepacia complex. Thus, over 3/4 of the isolates have potential for biotechnological applications.

Leaf evolution in early-diverging ferns: insights from a new fern-like plant from the Late Devonian of China

PubMed Central

Wang, De-Ming; Xu, Hong-He; Xue, Jin-Zhuang; Wang, Qi; Liu, Le

2015-01-01

Background and Aims With the exception of angiosperms, the main euphyllophyte lineages (i.e. ferns sensu lato, progymnosperms and gymnosperms) had evolved laminate leaves by the Late Devonian. The evolution of laminate leaves, however, remains unclear for early-diverging ferns, largely represented by fern-like plants. This study presents a novel fern-like taxon with pinnules, which provides new insights into the early evolution of laminate leaves in early-diverging ferns. Methods Macrofossil specimens were collected from the Upper Devonian (Famennian) Wutong Formation of Anhui and Jiangsu Provinces, South China. A standard degagement technique was employed to uncover compressed plant portions within the rock matrix. Key Results A new fern-like taxon, Shougangia bella gen. et sp. nov., is described and represents an early-diverging fern with highly derived features. It has a partially creeping stem with adventitious roots only on one side, upright primary and secondary branches arranged in helices, tertiary branches borne alternately or (sub)oppositely, laminate and usually lobed leaves with divergent veins, and complex fertile organs terminating tertiary branches and possessing multiple divisions and numerous terminal sporangia. Conclusions Shougangia bella provides unequivocal fossil evidence for laminate leaves in early-diverging ferns. It suggests that fern-like plants, along with other euphyllophyte lineages, had independently evolved megaphylls by the Late Devonian, possibly in response to a significant decline in atmospheric CO2 concentration. Among fern-like plants, planate ultimate appendages are homologous with laminate pinnules, and in the evolution of megaphylls, fertile organs tend to become complex. PMID:25979918

Angiographic Structural Differentiation between Native Arteriogenesis and Therapeutic Synangiosis in Intracranial Arterial Steno-Occlusive Disease.

PubMed

Ooi, Y C; Laiwalla, A N; Liou, R; Gonzalez, N R

2016-06-01

Encephaloduroarteriosynangiosis has been shown to generate collateral vessels from the extracranial-to-intracranial circulation in patients with Moyamoya disease and intracranial arterial steno-occlusive disease. The mechanisms involved are not well-understood. We hypothesized that angiogenesis is the leading mechanism forming collaterals after encephaloduroarteriosynangiosis because there are no pre-existing connections. Angiogenesis-generated collaterals should exhibit higher architectural complexity compared with innate collaterals. Pre- and postoperative digital subtraction angiograms were analyzed in patients enrolled in a prospective trial of encephaloduroarteriosynangiosis surgery. Branching angioscore, tortuosity index, and local connected fractal dimension were compared between innate and postoperative collaterals. One hundred one angiograms (50 preoperative, 51 postoperative) were analyzed from 44 patients (22 with intracranial atherosclerosis and 22 with Moyamoya disease). There was a significantly higher median branching angioscore (13 versus 4, P < .001) and a lower median tortuosity index (1.08 versus 1.76, P < .001) in the encephaloduroarteriosynangiosis collaterals compared with innate collaterals. Higher mean local fractal dimension peaks (1.28 ± 0.1 versus 1.16 ± 0.11, P < .001) were observed in the encephaloduroarteriosynangiosis collaterals compared with innate collaterals for both intracranial atherosclerosis (P < .001) and Moyamoya disease (P < .001) groups. The observed increase in high connectivity was greater in the intracranial atherosclerosis group compared with patients with Moyamoya disease (P = .01). The higher median branching angioscore and local connected fractal dimension, along with the lower median tortuosity index of encephaloduroarteriosynangiosis collaterals, are consistent with the greater complexity observed in the process of sprouting and splitting associated with angiogenesis. © 2016 by American Journal of Neuroradiology.

[Application and analysis of abdominal aortic branch malperfusion pattern in thoracic endovascular aortic repair for Stanford B aortic dissection].

PubMed

Han, X F; Guo, X; Li, T Z; Liu, G R; Huang, L J

2017-12-18

To evaluate the efficiency of thoracic endovascular aortic repair (TEVAR) in dealing with abdominal aortic branch malperfusion based on the analysis of aortic computed tomography angiography (CTA) images in pre- and post-TEVAR. Retrospective analysis from September 2015 to March 2016 in single institution to 32 patients, diagnosed as Stanford B aortic dissection with abdominal aortic branch malperfusion, CTA images in pre- and post-TEVAR were collected. Based on the aortic branch malperfusion pattern redefined by Nagamine, we identified and characterized branch malperfusion pattern for four abdominal aortic branches (celiac trunk, superior mesenteric artery, bilateral renal artery) in statistical analysis. In the four abdominal aortic branches (total 128 branches), 86 branches (67.2%) expressed with Class I patterns, in which subtype I-b presented with 0.8%, subtype I-c with 5.5%; 14 branches (10.9%) expressed with Class II patterns, in which subtype II-b-1 with 3.9%, subtype II-b-2 with 3.1%; 16 branches (12.5%) expressed with Class III patterns, all with subtype III-a, no subtype III-b and III-c presented. The remaining 12 branches were normal. The 100% successful rate of TEVAR obtained in 32 patients performed. The mean following-up was 4 months. Aortic CTA showed that among the 14 "high-risk" abdominal aortic branch malperfusion, 13 (92.9%) with obvious branch malperfusion in post-TEVAR were observed to improve, and the remaining one branch malperfusion (7.1%) was observed to change from subtype I-b to I-c. Few ratios in abdominal aortic branches suffered with obvious malperfusion complicated by Stanford B aortic dissection. For branches with "high-risk" malperfusion pattern, optimal changes were observed in abdominal aortic branch without revascularization in post-TEVAR, as well other branches with non-"high-risk" pattern perfusion were mostly stable in post-TEVAR. It could be of profound benefit to extend branch malperfusion patterns redefined by Nagamine in clinical practice to assess aortic dissection and in further guide for revascularization or not.

Fluid Mechanics and Complex Variable Theory: Getting Past the 19th Century

ERIC Educational Resources Information Center

Newton, Paul K.

2017-01-01

The subject of fluid mechanics is a rich, vibrant, and rapidly developing branch of applied mathematics. Historically, it has developed hand-in-hand with the elegant subject of complex variable theory. The Westmont College NSF-sponsored workshop on the revitalization of complex variable theory in the undergraduate curriculum focused partly on…

Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe

PubMed Central

Bonazzi, Marion; Reiter, Ella; Urban, Christian; Taylor, G. Michael; Velemínský, Petr; Marcsik, Antónia; Pálfi, György; Boldsen, Jesper L.; Nebel, Almut; Mays, Simon; Benjak, Andrej

2018-01-01

Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom—a skeleton from the Great Chesterford cemetery with a calibrated age of 415–545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide. PMID:29746563

Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe.

PubMed

Schuenemann, Verena J; Avanzi, Charlotte; Krause-Kyora, Ben; Seitz, Alexander; Herbig, Alexander; Inskip, Sarah; Bonazzi, Marion; Reiter, Ella; Urban, Christian; Dangvard Pedersen, Dorthe; Taylor, G Michael; Singh, Pushpendra; Stewart, Graham R; Velemínský, Petr; Likovsky, Jakub; Marcsik, Antónia; Molnár, Erika; Pálfi, György; Mariotti, Valentina; Riga, Alessandro; Belcastro, M Giovanna; Boldsen, Jesper L; Nebel, Almut; Mays, Simon; Donoghue, Helen D; Zakrzewski, Sonia; Benjak, Andrej; Nieselt, Kay; Cole, Stewart T; Krause, Johannes

2018-05-01

Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide.

Varieties of noise: analogical reasoning in synthetic biology.

PubMed

Knuuttila, Tarja; Loettgers, Andrea

2014-12-01

The picture of synthetic biology as a kind of engineering science has largely created the public understanding of this novel field, covering both its promises and risks. In this paper, we will argue that the actual situation is more nuanced and complex. Synthetic biology is a highly interdisciplinary field of research located at the interface of physics, chemistry, biology, and computational science. All of these fields provide concepts, metaphors, mathematical tools, and models, which are typically utilized by synthetic biologists by drawing analogies between the different fields of inquiry. We will study analogical reasoning in synthetic biology through the emergence of the functional meaning of noise, which marks an important shift in how engineering concepts are employed in this field. The notion of noise serves also to highlight the differences between the two branches of synthetic biology: the basic science-oriented branch and the engineering-oriented branch, which differ from each other in the way they draw analogies to various other fields of study. Moreover, we show that fixing the mapping between a source domain and the target domain seems not to be the goal of analogical reasoning in actual scientific practice.

Programming of the complex logarithm function in the solution of the cracked anisotropic plate loaded by a point force

NASA Astrophysics Data System (ADS)

Zaal, K. J. J. M.

1991-06-01

In programming solutions of complex function theory, the complex logarithm function is replaced by the complex logarithmic function, introducing a discontinuity along the branch cut into the programmed solution which was not present in the mathematical solution. Recently, Liaw and Kamel presented their solution of the infinite anisotropic centrally cracked plate loaded by an arbitrary point force, which they used as Green's function in a boundary element method intended to evaluate the stress intensity factor at the tip of a crack originating from an elliptical home. Their solution may be used as Green's function of many more numerical methods involving anisotropic elasticity. In programming applications of Liaw and Kamel's solution, the standard definition of the logarithmic function with the branch cut at the nonpositive real axis cannot provide a reliable computation of the displacement field for Liaw and Kamel's solution. Either the branch cut should be redefined outside the domain of the logarithmic function, after proving that the domain is limited to a part of the plane, or the logarithmic function should be defined on its Riemann surface. A two dimensional line fractal can provide the link between all mesh points on the plane essential to evaluate the logarithm function on its Riemann surface. As an example, a two dimensional line fractal is defined for a mesh once used by Erdogan and Arin.

Grassroots Activists and the Three Branches of Government: "Key Players in the Civil Rights Movement"

ERIC Educational Resources Information Center

Brown, Elizabeth; Silvestri, Linda

2014-01-01

In order to understand the complex workings of the three branches of American government, young citizens need early exposure in the elementary years to hands-on lessons that include real life examples and opportunities for students to apply what they have learned. To that end, the authors designed a five-day, inquiry-based unit for fourth grade…

Using Principal-Agent Theory as a Framework for Analysis in Evaluating the Multiple Stakeholders Involved in the Accreditation and Quality Assurance of International Medical Branch Campuses

ERIC Educational Resources Information Center

Borgos, Jill E.

2013-01-01

This article applies the theoretical framework of principal-agent theory in order to better understand the complex organisational relationships emerging between entities invested in the establishment and monitoring of cross-border international branch campus medical schools. Using the key constructs of principal-agent theory, information asymmetry…

Role and structural mechanism of WASP-triggered conformational changes in branched actin filament nucleation by Arp2/3 complex

PubMed Central

Rodnick-Smith, Max; Luan, Qing; Liu, Su-Ling; Nolen, Brad J.

2016-01-01

The Arp2/3 (Actin-related proteins 2/3) complex is activated by WASP (Wiskott–Aldrich syndrome protein) family proteins to nucleate branched actin filaments that are important for cellular motility. WASP recruits actin monomers to the complex and stimulates movement of Arp2 and Arp3 into a “short-pitch” conformation that mimics the arrangement of actin subunits within filaments. The relative contribution of these functions in Arp2/3 complex activation and the mechanism by which WASP stimulates the conformational change have been unknown. We purified budding yeast Arp2/3 complex held in or near the short-pitch conformation by an engineered covalent cross-link to determine if the WASP-induced conformational change is sufficient for activity. Remarkably, cross-linked Arp2/3 complex bypasses the need for WASP in activation and is more active than WASP-activated Arp2/3 complex. These data indicate that stimulation of the short-pitch conformation is the critical activating function of WASP and that monomer delivery is not a fundamental requirement for nucleation but is a specific requirement for WASP-mediated activation. During activation, WASP limits nucleation rates by releasing slowly from nascent branches. The cross-linked complex is inhibited by WASP’s CA region, even though CA potently stimulates cross-linking, suggesting that slow WASP detachment masks the activating potential of the short-pitch conformational switch. We use structure-based mutations and WASP–Arp fusion chimeras to determine how WASP stimulates movement toward the short-pitch conformation. Our data indicate that WASP displaces the autoinhibitory Arp3 C-terminal tail from a hydrophobic groove at Arp3′s barbed end to destabilize the inactive state, providing a mechanism by which WASP stimulates the short-pitch conformation and activates Arp2/3 complex. PMID:27325766

Pressure and high-Tc superconductivity in sulfur hydrides.

PubMed

Gor'kov, Lev P; Kresin, Vladimir Z

2016-05-11

The paper discusses fundamentals of record-TC superconductivity discovered under high pressure in sulfur hydride. The rapid increase of TC with pressure in the vicinity of Pcr ≈ 123GPa is interpreted as the fingerprint of a first-order structural transition. Based on the cubic symmetry of the high-TC phase, it is argued that the lower-TC phase has a different periodicity, possibly related to an instability with a commensurate structural vector. In addition to the acoustic branches, the phonon spectrum of H3S contains hydrogen modes with much higher frequencies. Because of the complex spectrum, usual methods of calculating TC are here inapplicable. A modified approach is formulated and shown to provide realistic values for TC and to determine the relative contributions of optical and acoustic branches. The isotope effect (change of TC upon Deuterium for Hydrogen substitution) originates from high frequency phonons and differs in the two phases. The decrease of TC following its maximum in the high-TC phase is a sign of intermixing with pairing at hole-like pockets which arise in the energy spectrum of the cubic phase at the structural transition. On-pockets pairing leads to the appearance of a second gap and is remarkable for its non-adiabatic regime: hydrogen mode frequencies are comparable to the Fermi energy.

Using NASA's GeneLab for VESGEN Systems Analysis of Vascular Phenotypes from Stress and Other Signaling Pathways

NASA Technical Reports Server (NTRS)

Parsons-Wingerter, P.; Weitzel, Alexander; Vyas, R. J.; Murray, M. C.; Vickerman, M. B.; Bhattacharya, S.; Wyatt, S. E.

2016-01-01

One fundamental requirement shared by humans with all higher terrestrial life forms, including other vertebrates, insects, and higher land plants, is a complex, fractally branching vascular system. NASA's VESsel GENeration Analysis (VESGEN) software maps and quantifies vascular trees, networks, and tree-network composites according to weighted physiological rules such as vessel connectivity, tapering and bifurcational branching. According to fluid dynamics, successful vascular transport requires a complex distributed system of highly regulated laminar flow. Microvascular branching rules within vertebrates, dicot leaves and the other organisms therefore display many similarities. A unifying perspective is that vascular patterning offers a useful readout of molecular signaling that necessarily integrates these complex pathways. VESGEN has elucidated changes in vascular pattern resulting from inflammatory, developmental and other signaling within numerous tissues and major model organisms studied for Space Biology. For a new VESGEN systems approach, we analyzed differential gene expression in leaves of Arabidopsis thaliana reported by GeneLab (GLDS-7) for spaceflight. Vascularrelated changes in leaf gene expression were identified that can potentially be phenocopied by mutants in ground-based experiments. To link transcriptional, protein and other molecular change with phenotype, alterations in the spatial and dynamic dimensions of vascular patterns for Arabidopsis leaves and other model species are being co-localized with signaling patterns of single molecular expression analyzed as information dimensions. Previously, Drosophila microarray data returned from space suggested significant changes in genes related to wing venation development that include EGF, Notch, Hedghog, Wingless and Dpp signaling. Phenotypes of increasingly abnormal ectopic wing venation in the (non-spaceflight) Drosophila wing generated by overexpression of a Notch antagonist were analyzed by VESGEN. Other VESGEN research applications include the mouse retina, GI and coronary vessels, avian placental analogs and translational studies in the astronaut retina related to health challenges for long-duration missions.

NASAs VESGEN: Systems Analysis of Vascular Phenotypes from Stress and Other Signaling Pathways Using GeneLab.

NASA Technical Reports Server (NTRS)

Parsons-Wingerter, Patricia A.; Weitzel, Alexander; Vyas, Ruchi J.; Murray, Matthew C.; Wyatt, Sarah E.

2016-01-01

One fundamental requirement shared by humans with all higher terrestrial life forms, including insect wings, higher land plants and other vertebrates, is a complex, fractally branching vascular system. NASA's VESsel GENeration Analysis (VESGEN) software maps and quantifies vascular trees, networks, and tree-network composites according to weighted physiological rules such as vessel connectivity, tapering and bifurcational branching. According to fluid dynamics, successful vascular transport requires a complex distributed system of highly regulated laminar flow. Microvascular branching rules within vertebrates, dicot leaves and the other organisms therefore display many similarities. One unifying perspective is that vascular patterning offers a useful readout that necessarily integrates complex molecular signaling pathways. VESGEN has elucidated changes in vascular pattern resulting from inflammatory, stress response, developmental and other signaling within numerous tissues and major model organisms studied for Space Biology. For a new VESGEN systems approach, we analyzed differential gene expression in leaves of Arabidopsis thaliana reported by GeneLab (GLDS-7) for spaceflight. Vascular-related changes in leaf gene expression were identified that can potentially be phenocopied by mutants in ground-based experiments. To link transcriptional, protein and other molecular change with phenotype, alterations in the Euclidean and dynamic dimensions (x,y,t) of vascular patterns for Arabidopsis leaves and other model species are being co-localized with signaling patterns of single molecular expression analyzed as information dimensions (i,j,k,...). Previously, Drosophila microarray data returned from space suggested significant changes in genes related to wing venation development that include EGF, Notch, Hedghog, Wingless and Dpp signaling. Phenotypes of increasingly abnormal ectopic wing venation in the (non-spaceflight) Drosophila wing generated by overexpression of a Notch antagonist were analyzed by VESGEN. Other VESGEN research applications include the mouse retina, GI and coronary vessels, avian placental analogs and translational studies in the astronaut retina related to health challenges for long-duration missions.

Impaired growth and neurological abnormalities in branched-chain α-keto acid dehydrogenase kinase-deficient mice

PubMed Central

Joshi, Mandar A.; Jeoung, Nam Ho; Obayashi, Mariko; Hattab, Eyas M.; Brocken, Eric G.; Liechty, Edward A.; Kubek, Michael J.; Vattem, Krishna M.; Wek, Ronald C.; Harris, Robert A.

2006-01-01

The BCKDH (branched-chain α-keto acid dehydrogenase complex) catalyses the rate-limiting step in the oxidation of BCAAs (branched-chain amino acids). Activity of the complex is regulated by a specific kinase, BDK (BCKDH kinase), which causes inactivation, and a phosphatase, BDP (BCKDH phosphatase), which causes activation. In the present study, the effect of the disruption of the BDK gene on growth and development of mice was investigated. BCKDH activity was much greater in most tissues of BDK−/− mice. This occurred in part because the E1 component of the complex cannot be phosphorylated due to the absence of BDK and also because greater than normal amounts of the E1 component were present in tissues of BDK−/− mice. Lack of control of BCKDH activity resulted in markedly lower blood and tissue levels of the BCAAs in BDK−/− mice. At 12 weeks of age, BDK−/− mice were 15% smaller than wild-type mice and their fur lacked normal lustre. Brain, muscle and adipose tissue weights were reduced, whereas weights of the liver and kidney were greater. Neurological abnormalities were apparent by hind limb flexion throughout life and epileptic seizures after 6–7 months of age. Inhibition of protein synthesis in the brain due to hyperphosphorylation of eIF2α (eukaryotic translation initiation factor 2α) might contribute to the neurological abnormalities seen in BDK−/− mice. BDK−/− mice show significant improvement in growth and appearance when fed a high protein diet, suggesting that higher amounts of dietary BCAA can partially compensate for increased oxidation in BDK−/− mice. Disruption of the BDK gene establishes that regulation of BCKDH by phosphorylation is critically important for the regulation of oxidative disposal of BCAAs. The phenotype of the BDK−/− mice demonstrates the importance of tight regulation of oxidative disposal of BCAAs for normal growth and neurological function. PMID:16875466

Wolff-Parkinson-White syndrome type B and left bundle-branch block: electrophysiologic and radionuclide study

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

Rakovec, P.; Kranjec, I.; Fettich, J.J.

1985-01-01

Coinciding left bundle-branch block and Wolff-Parkinson-White syndrome type B, a very rare electrocardiographic occurrence, was found in a patient with dilated cardiomyopathy. Electrophysiologic study revealed eccentric retrograde atrial activation during ventricular pacing, suggesting right-sided accessory pathway. At programmed atrial pacing, effective refractory period of the accessory pathway was 310 ms; at shorter pacing coupling intervals, normal atrioventricular conduction with left bundle-branch block was seen. Left bundle-branch block was seen also with His bundle pacing. Radionuclide phase imaging demonstrated right ventricular phase advance and left ventricular phase delay; both right and left ventricular phase images revealed broad phase distribution histograms. Combinedmore » electrophysiologic and radionuclide investigations are useful to disclose complex conduction abnormalities and their mechanical correlates.« less

Modelling of non-equilibrium flow in the branched pipeline systems

NASA Astrophysics Data System (ADS)

Sumskoi, S. I.; Sverchkov, A. M.; Lisanov, M. V.; Egorov, A. F.

2016-09-01

This article presents a mathematical model and a numerical method for solving the task of water hammer in the branched pipeline system. The task is considered in the onedimensional non-stationary formulation taking into account the realities such as the change in the diameter of the pipeline and its branches. By comparison with the existing analytic solution it has been shown that the proposed method possesses good accuracy. With the help of the developed model and numerical method the task has been solved concerning the transmission of the compression waves complex in the branching pipeline system when several shut down valves operate. It should be noted that the offered model and method may be easily introduced to a number of other tasks, for example, to describe the flow of blood in the vessels.

Cell-wall polysaccharides and glycoproteins of parenchymatous tissues of runner bean (Phaseolus coccineus).

PubMed Central

Ryden, P; Selvendran, R R

1990-01-01

1. Polymers were solubilized from the cell walls of parenchyma from mature runner-bean pods with minimum degradation by successive extractions with cyclohexane-trans-1,2-diamine-NNN'N'-tetra-acetate (CDTA), Na2CO3 and KOH to leave the alpha-cellulose residue, which contained cross-linked pectic polysaccharides and Hyp-rich glycoproteins. These were solubilized with chlorite/acetic acid and cellulase. The polymers were fractionated by anion-exchange chromatography, and fractions were subjected to methylation analysis. 2. The pectic polysaccharides differed in their ease of extraction, and a small proportion were highly cross-linked. The bulk of the pectic polysaccharides solubilized by CDTA and Na2CO3 were less branched than those solubilized by KOH. There was good evidence that most of the pectic polysaccharides were not degraded during extraction. 3. The protein-containing fractions included Hyp-rich and Hyp-poor glycoproteins associated with easily extractable pectic polysaccharides, Hyp-rich glycoproteins solubilized with 4M-KOH+borate, the bulk of which were not associated with pectic polysaccharides, and highly cross-linked Hyp-rich glycoproteins. 4. Isodityrosine was not detected, suggesting that it does not have a (major) cross-linking role in these walls. Instead, it is suggested that phenolics, presumably linked to C-5 of 3,5-linked Araf residues of Hyp-rich glycoproteins, serve to cross-link some of the polymers. 5. There were two main types of xyloglucan, with different degrees of branching. The bulk of the less branched xyloglucans were solubilized by more-concentrated alkali. The anomeric configurations of the sugars in one of the highly branched xyloglucans were determined by 13C-n.m.r. spectroscopy. 6. The structural features of the cell-wall polymers and complexes are discussed in relation to the structure of the cell walls of parenchyma tissues. PMID:2167068

Structure-based design and mechanisms of allosteric inhibitors for mitochondrial branched-chain α-ketoacid dehydrogenase kinase

PubMed Central

Qi, Xiangbing; Gui, Wen-Jun; Morlock, Lorraine K.; Wallace, Amy L.; Ahmed, Kamran; Laxman, Sunil; Campeau, Philippe M.; Lee, Brendan H.; Hutson, Susan M.; Tu, Benjamin P.; Williams, Noelle S.; Tambar, Uttam K.; Wynn, R. Max; Chuang, David T.

2013-01-01

The branched-chain amino acids (BCAAs) leucine, isoleucine, and valine are elevated in maple syrup urine disease, heart failure, obesity, and type 2 diabetes. BCAA homeostasis is controlled by the mitochondrial branched-chain α-ketoacid dehydrogenase complex (BCKDC), which is negatively regulated by the specific BCKD kinase (BDK). Here, we used structure-based design to develop a BDK inhibitor, (S)-α-chloro-phenylpropionic acid [(S)-CPP]. Crystal structures of the BDK-(S)-CPP complex show that (S)-CPP binds to a unique allosteric site in the N-terminal domain, triggering helix movements in BDK. These conformational changes are communicated to the lipoyl-binding pocket, which nullifies BDK activity by blocking its binding to the BCKDC core. Administration of (S)-CPP to mice leads to the full activation and dephosphorylation of BCKDC with significant reduction in plasma BCAA concentrations. The results buttress the concept of targeting mitochondrial BDK as a pharmacological approach to mitigate BCAA accumulation in metabolic diseases and heart failure. PMID:23716694

The emerging complexity of ubiquitin architecture.

PubMed

Ohtake, Fumiaki; Tsuchiya, Hikaru

2017-02-01

Ubiquitylation is an essential post-translational modification (PTM) of proteins with diverse cellular functions. Polyubiquitin chains with different topologies have different cellular roles, and are referred to as a 'ubiquitin code'. Recent studies have begun to reveal that more complex ubiquitin architectures function as important signals in several biological pathways. These include PTMs of ubiquitin itself, such as acetylated ubiquitin and phospho-ubiquitin. Moreover, important roles for heterogeneous polyubiquitin chains, such as mixed or branched chains, have been reported, which significantly increase the diversity of the ubiquitin code. In this review, we describe mass spectrometry-based methods to characterize the ubiquitin signal. We also describe recent advances in our understanding of complex ubiquitin architectures, including our own findings concerning ubiquitin acetylation and branching within polyubiquitin chains. © The Authors 2016. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Improved properties of recycled polypropylene by introducing the long chain branched structure through reactive extrusion.

PubMed

Li, Yingchun; Jia, Shuai; Du, Shuanli; Wang, Yafei; Lv, Lida; Zhang, Jianbin

2018-06-01

An approach originated from preparing long chain branched polypropylene (PP) was applied to modify the properties of recycled PP that involved reactive extrusion to introduce a branched chain structure onto recycled PP under the assistance of chemical reaction between maleic anhydride (MAH) monomer and glycidyl methacrylate (GMA) grafts. The results from Fourier transformed infrared spectroscopy (FTIR) indicated the reaction took place during melt mixing, and the intensity of ester increased with increasing amount of MAH. Several rheological plots including complex viscosity, storage modulus, loss modulus, loss tangent and Cole-Cole plot were used to investigate the rheological properties of recycled PP and modified PP with MAH, which indicated an additional longer relaxation time that was not shown in recycled PP. The effects of branched structure on melting and crystallization behaviors were also investigated, demonstrating the branched chains acted as nucleating agent. Moreover, the branched structure of modified samples gave rise to enhance mechanical properties, especially, the higher impact strength compared with recycled PP. Copyright © 2018 Elsevier Ltd. All rights reserved.

Structural analysis of the role of TPX2 in branching microtubule nucleation

PubMed Central

Thawani, Akanksha

2017-01-01

The mitotic spindle consists of microtubules (MTs), which are nucleated by the γ-tubulin ring complex (γ-TuRC). How the γ-TuRC gets activated at the right time and location remains elusive. Recently, it was uncovered that MTs nucleate from preexisting MTs within the mitotic spindle, which requires the protein TPX2, but the mechanism basis for TPX2 action is unknown. Here, we investigate the role of TPX2 in branching MT nucleation. We establish the domain organization of Xenopus laevis TPX2 and define the minimal TPX2 version that stimulates branching MT nucleation, which we find is unrelated to TPX2’s ability to nucleate MTs in vitro. Several domains of TPX2 contribute to its MT-binding and bundling activities. However, the property necessary for TPX2 to induce branching MT nucleation is contained within newly identified γ-TuRC nucleation activator motifs. Separation-of-function mutations leave the binding of TPX2 to γ-TuRC intact, whereas branching MT nucleation is abolished, suggesting that TPX2 may activate γ-TuRC to promote branching MT nucleation. PMID:28264915

Microtubule nucleation and organization in dendrites

PubMed Central

Delandre, Caroline; Amikura, Reiko; Moore, Adrian W.

2016-01-01

ABSTRACT Dendrite branching is an essential process for building complex nervous systems. It determines the number, distribution and integration of inputs into a neuron, and is regulated to create the diverse dendrite arbor branching patterns characteristic of different neuron types. The microtubule cytoskeleton is critical to provide structure and exert force during dendrite branching. It also supports the functional requirements of dendrites, reflected by differential microtubule architectural organization between neuron types, illustrated here for sensory neurons. Both anterograde and retrograde microtubule polymerization occur within growing dendrites, and recent studies indicate that branching is enhanced by anterograde microtubule polymerization events in nascent branches. The polarities of microtubule polymerization events are regulated by the position and orientation of microtubule nucleation events in the dendrite arbor. Golgi outposts are a primary microtubule nucleation center in dendrites and share common nucleation machinery with the centrosome. In addition, pre-existing dendrite microtubules may act as nucleation sites. We discuss how balancing the activities of distinct nucleation machineries within the growing dendrite can alter microtubule polymerization polarity and dendrite branching, and how regulating this balance can generate neuron type-specific morphologies. PMID:27097122

Charged boson stars and black holes with nonminimal coupling to gravity

NASA Astrophysics Data System (ADS)

Verbin, Y.; Brihaye, Y.

2018-02-01

We find new spherically symmetric charged boson star solutions of a complex scalar field coupled nonminimally to gravity by a "John-type" term of Horndeski theory, that is a coupling between the kinetic scalar term and Einstein tensor. We study the parameter space of the solutions and find two distinct families according to their position in parameter space. More widespread is the family of solutions (which we call branch 1) existing for a finite interval of the central value of the scalar field starting from zero and ending at some finite maximal value. This branch contains as a special case the charged boson stars of the minimally coupled theory. In some regions of parameter space we find a new second branch ("branch 2") of solutions which are more massive and more stable than those of branch 1. This second branch exists also in a finite interval of the central value of the scalar field, but its end points (either both or in some cases only one) are extremal Reissner-Nordström black hole solutions.

Physiological remodeling of bifurcation aneurysms: preclinical results of the eCLIPs device.

PubMed

Marotta, Thomas R; Riina, Howard A; McDougall, Ian; Ricci, Donald R; Killer-Oberpfalzer, Monika

2018-02-01

OBJECTIVE Intracranial bifurcation aneurysms are complex lesions for which current therapy, including simple coiling, balloon- or stent-assisted coiling, coil retention, or intrasaccular devices, is inadequate. Thromboembolic complications due to a large burden of intraluminal metal, impedance of access to side branches, and a high recurrence rate, due largely to the unmitigated high-pressure flow into the aneurysm (water hammer effect), are among the limitations imposed by current therapy. The authors describe herein a novel device, eCLIPs, and its use in a preclinical laboratory study that suggests the device's design and functional features may overcome many of these limitations. METHODS A preclinical model of wide-necked bifurcation aneurysms in rabbits was used to assess functional features and efficacy of aneurysm occlusion by the eCLIPs device. RESULTS The eCLIPs device, in bridging the aneurysm neck, allows coil retention, disrupts flow away from the aneurysm, leaves the main vessel and side branches unencumbered by intraluminal metal, and serves as a platform for endothelial growth across the neck, excluding the aneurysm from the circulation. CONCLUSIONS The eCLIPs device permits physiological remodeling of the bifurcation.

Analysis of the LIV System of Campylobacter jejuni Reveals Alternative Roles for LivJ and LivK in Commensalism beyond Branched-Chain Amino Acid Transport ▿

PubMed Central

Ribardo, Deborah A.; Hendrixson, David R.

2011-01-01

Campylobacter jejuni is a leading cause of diarrheal disease in humans and an intestinal commensal in poultry and other agriculturally important animals. These zoonotic infections result in significant amounts of C. jejuni present in the food supply to contribute to disease in humans. We previously found that a transposon insertion in Cjj81176_1038, encoding a homolog of the Escherichia coli LivJ periplasmic binding protein of the leucine, isoleucine, and valine (LIV) branched-chain amino acid transport system, reduced the commensal colonization capacity of C. jejuni 81-176 in chicks. Cjj81176_1038 is the first gene of a six-gene locus that encodes homologous components of the E. coli LIV system. By analyzing mutants with in-frame deletions of individual genes or pairs of genes, we found that this system constitutes a LIV transport system in C. jejuni responsible for a high level of leucine acquisition and, to a lesser extent, isoleucine and valine acquisition. Despite each LIV protein being required for branched-chain amino acid transport, only the LivJ and LivK periplasmic binding proteins were required for wild-type levels of commensal colonization of chicks. All LIV permease and ATPase components were dispensable for in vivo growth. These results suggest that the biological functions of LivJ and LivK for colonization are more complex than previously hypothesized and extend beyond a role for binding and acquiring branched-chain amino acids during commensalism. In contrast to other studies indicating a requirement and utilization of other specific amino acids for colonization, acquisition of branched-chain amino acids does not appear to be a determinant for C. jejuni during commensalism. PMID:21949065

Yersinia pestis strains of ancient phylogenetic branch 0.ANT are widely spread in the high-mountain plague foci of Kyrgyzstan

PubMed Central

Nosov, Nikita Yu; Krasnov, Yaroslav M.; Oglodin, Yevgeny G.; Kukleva, Lyubov M.; Guseva, Natalia P.; Kuznetsov, Alexander A.; Abdikarimov, Sabyrzhan T.; Dzhaparova, Aigul K.; Kutyrev, Vladimir V.

2017-01-01

Fifty six Yersinia pestis strains, isolated over the period of more than 50 years in three high-mountain foci of Kyrgyzstan (Tien Shan, Alai, and Talas), have been characterized by means of PCR and single nucleotide polymorphism (SNP) typing methods. Seven of these strains were also characterized by means of whole genome sequencing and genome-wide SNP phylogenetic analysis. It was found that forty two strains belong to 0.ANT2, 0.ANT3 and 0.ANT5 phylogenetic branches. From these, strains of 0.ANT2 and 0.ANT3 branches were earlier detected in China only, whereas 0.ANT5 phylogenetic branch was identified for Y. pestis phylogeny for the first time. According to the results of genome-wide SNP analysis, 0.ANT5 strains are ones of the most closely related to Y. pestis strain responsible for the Justinianic Plague. We have also found out that four of the studied strains belong to the phylogenetic branch 2.MED1, and ten strains from Talas high-mountain focus belong to the phylogenetic branch 0.PE4 (sub-branch 0.PE4t). Established diversity of Y. pestis strains and extensive dissemination of the strains pertaining to the 0.ANT branch confirm the antiquity of the mentioned above plague foci and suggest that strains of the 0.ANT branch, which serve as precursors for all highly virulent Y. pestis strains, had their origin in the Tien Shan mountains. PMID:29073248

Yersinia pestis strains of ancient phylogenetic branch 0.ANT are widely spread in the high-mountain plague foci of Kyrgyzstan.

PubMed

Eroshenko, Galina A; Nosov, Nikita Yu; Krasnov, Yaroslav M; Oglodin, Yevgeny G; Kukleva, Lyubov M; Guseva, Natalia P; Kuznetsov, Alexander A; Abdikarimov, Sabyrzhan T; Dzhaparova, Aigul K; Kutyrev, Vladimir V

2017-01-01

Fifty six Yersinia pestis strains, isolated over the period of more than 50 years in three high-mountain foci of Kyrgyzstan (Tien Shan, Alai, and Talas), have been characterized by means of PCR and single nucleotide polymorphism (SNP) typing methods. Seven of these strains were also characterized by means of whole genome sequencing and genome-wide SNP phylogenetic analysis. It was found that forty two strains belong to 0.ANT2, 0.ANT3 and 0.ANT5 phylogenetic branches. From these, strains of 0.ANT2 and 0.ANT3 branches were earlier detected in China only, whereas 0.ANT5 phylogenetic branch was identified for Y. pestis phylogeny for the first time. According to the results of genome-wide SNP analysis, 0.ANT5 strains are ones of the most closely related to Y. pestis strain responsible for the Justinianic Plague. We have also found out that four of the studied strains belong to the phylogenetic branch 2.MED1, and ten strains from Talas high-mountain focus belong to the phylogenetic branch 0.PE4 (sub-branch 0.PE4t). Established diversity of Y. pestis strains and extensive dissemination of the strains pertaining to the 0.ANT branch confirm the antiquity of the mentioned above plague foci and suggest that strains of the 0.ANT branch, which serve as precursors for all highly virulent Y. pestis strains, had their origin in the Tien Shan mountains.

Youth Media Literacy Practices: The Possibilities and Complexities of Creating and Distributing Non-Commercial Public Media in a Private and Commercial World

ERIC Educational Resources Information Center

Bach, Amy Jane

2010-01-01

Drawn from more than two years of ethnographic data collection, this dissertation study explores the literacy practices enacted in a youth media organization (the Youth Media Group) that is a branch of a public access television station (Manhattan Media) in New York City. Rooted in New Literacy Studies, a branch of scholarship which explores…

Distinct Bacterial Communities Associated with Massive and Branching Scleractinian Corals and Potential Linkages to Coral Susceptibility to Thermal or Cold Stress

PubMed Central

Liang, Jiayuan; Yu, Kefu; Wang, Yinghui; Huang, Xueyong; Huang, Wen; Qin, Zhenjun; Pan, Ziliang; Yao, Qiucui; Wang, Wenhuan; Wu, Zhengchao

2017-01-01

It is well known that different coral species have different tolerances to thermal or cold stress, which is presumed to be related to the density of Symbiodinium. However, the intrinsic factors between stress-tolerant characteristics and coral-associated bacteria are rarely studied. In this study, 16 massive coral and 9 branching coral colonies from 6 families, 10 genera, and 18 species were collected at the same time and location (Xinyi Reef) in the South China Sea to investigate the bacterial communities. The results of an alpha diversity analysis showed that bacterial diversities associated with massive corals were generally higher than those with branching corals at different taxonomic levels (phylum, class, order, and so on). In addition, hierarchical clustering tree and PCoA analyses showed that coral species were clustered into two large groups according to the similarity of bacterial communities. Group I consisted of massive Goniastrea, Plesiastrea, Leptastrea, Platygyra, Echinopora, Porites, and Leptoria, and group II consisted of branching Acropora and Pocillopora. These findings suggested that both massive corals and branching corals have their own preference for the choice of associated bacteria, which may be involved in observed differences in thermal/cold tolerances. Further analysis found that 55 bacterial phyla, including 43 formally described phyla and 12 candidate phyla, were detected in these coral species. Among them, 52 phyla were recovered from the massive coral group, and 46 phyla were recovered from the branching coral group. Formally described coral pathogens have not been detected in these coral species, suggesting that they are less likely to be threatened by disease in this geographic area. This study highlights a clear relationship between the high complexity of bacterial community associated with coral, skeletal morphology of coral and potentially tolerances to thermal or cold stress. PMID:28642738

Environmental Complexity and Central Nervous System Development and Function

ERIC Educational Resources Information Center

Lewis, Mark H.

2004-01-01

Environmental restriction or deprivation early in development can induce social, cognitive, affective, and motor abnormalities similar to those associated with autism. Conversely, rearing animals in larger, more complex environments results in enhanced brain structure and function, including increased brain weight, dendritic branching,…

A novel branched TAT(47-57) peptide for selective Ni(2+) introduction into the human fibrosarcoma cell nucleus.

PubMed

Szyrwiel, Łukasz; Shimura, Mari; Shirataki, Junko; Matsuyama, Satoshi; Matsunaga, Akihiro; Setner, Bartosz; Szczukowski, Łukasz; Szewczuk, Zbigniew; Yamauchi, Kazuto; Malinka, Wiesław; Chavatte, Laurent; Łobinski, Ryszard

2015-07-01

A TAT47-57 peptide was modified on the N-terminus by elongation with a 2,3-diaminopropionic acid residue and then by coupling of two histidine residues on its N-atoms. This branched peptide could bind to Ni under physiological conditions as a 1 : 1 complex. We demonstrated that the complex was quantitatively taken up by human fibrosarcoma cells, in contrast to Ni(2+) ions. Ni localization (especially at the nuclei) was confirmed by imaging using both scanning X-ray fluorescence microscopy and Newport Green fluorescence. A competitive assay with Newport Green showed that the latter displaced the peptide ligand from the Ni-complex. Ni(2+) delivered as a complex with the designed peptide induced substantially more DNA damage than when introduced as a free ion. The availability of such a construct opens up the way to investigate the importance of the nucleus as a target for the cytotoxicity, genotoxicity or carcinogenicity of Ni(2+).

Analytical and numerical construction of equivalent cables.

PubMed

Lindsay, K A; Rosenberg, J R; Tucker, G

2003-08-01

The mathematical complexity experienced when applying cable theory to arbitrarily branched dendrites has lead to the development of a simple representation of any branched dendrite called the equivalent cable. The equivalent cable is an unbranched model of a dendrite and a one-to-one mapping of potentials and currents on the branched model to those on the unbranched model, and vice versa. The piecewise uniform cable, with a symmetrised tri-diagonal system matrix, is shown to represent the canonical form for an equivalent cable. Through a novel application of the Laplace transform it is demonstrated that an arbitrary branched model of a dendrite can be transformed to the canonical form of an equivalent cable. The characteristic properties of the equivalent cable are extracted from the matrix for the transformed branched model. The one-to-one mapping follows automatically from the construction of the equivalent cable. The equivalent cable is used to provide a new procedure for characterising the location of synaptic contacts on spinal interneurons.

Branched flow and caustics in random media with magnetic fields

NASA Astrophysics Data System (ADS)

Metzger, Jakob; Fleischmann, Ragnar; Geisel, Theo

2009-03-01

Classical particles as well as quantum mechanical waves exhibit complex behaviour when propagating through random media. One of the dominant features of the dynamics in correlated, weak disorder potentials is the branching of the flow. This can be observed in several physical systems, most notably in the electron flow in two-dimensional electron gases [1], and has also been used to describe the formation of freak waves [2]. We present advances in the theoretical understanding and numerical simulation of classical branched flows in magnetic fields. In particular, we study branching statistics and branch density profiles. Our results have direct consequences for experiments which measure transport properties in electronic systems [3].[1] e.g. M. A. Topinka et al., Nature 410, 183 (2001), M. P. Jura et al., Nature Physics 3, 841 (2007)[2] E. J. Heller, L. Kaplan and A. Dahlen, J. Geophys. Res., 113, C09023 (2008)[3] J. J. Metzger, R. Fleischmann and T. Geisel, in preparation

Isolation and determination of absolute configurations of insect-produced methyl-branched hydrocarbons

PubMed Central

Bello, Jan E.; McElfresh, J. Steven; Millar, Jocelyn G.

2015-01-01

Although the effects of stereochemistry have been studied extensively for volatile insect pheromones, little is known about the effects of chirality in the nonvolatile methyl-branched hydrocarbons (MBCHs) used by many insects as contact pheromones. MBCHs generally contain one or more chiral centers and so two or more stereoisomeric forms are possible for each structure. However, it is not known whether insects biosynthesize these molecules in high stereoisomeric purity, nor is it known whether insects can distinguish the different stereoisomeric forms of MBCHs. This knowledge gap is due in part to the lack of methods for isolating individual MBCHs from the complex cuticular hydrocarbon (CHC) blends of insects, as well as the difficulty in determining the absolute configurations of the isolated MBCHs. To address these deficiencies, we report a straightforward method for the isolation of individual cuticular hydrocarbons from the complex CHC blend. The method was used to isolate 36 pure MBCHs from 20 species in nine insect orders. The absolute stereochemistries of the purified MBCHs then were determined by digital polarimetry. The absolute configurations of all of the isolated MBCHs were determined to be (R) by comparison with a library of synthesized, enantiomerically pure standards, suggesting that the biosynthetic pathways used to construct MBCHs are highly conserved within the Insecta. The development of a straightforward method for isolation of specific CHCs will enable determination of their functional roles by providing pure compounds for bioassays. PMID:25583471

Federal budget process: An overview

NASA Astrophysics Data System (ADS)

Frizzell, Virgil A., Jr.

Much geophysical research funding originates from the federal government, and many who obtain federal funding consider the executive branch to be its source. In fact, the federal budget results from a complex ballet between the executive and legislative branches. Because it is both little understood and essential to our work, this report will review the fundamentals of the three-year budgetary process.The Constitution assigns the power of the purse to the Congress. Before the 1920s, executive branch agencies and departments submitted their own separate budgets to Congress, and deliberate planning and priority setting was minimal. In 1921 Congress empowered the president to submit an executive branch budget reflecting his priorities for the next fiscal year. Following this protocol, former President Reagan submitted his budget for Fiscal Year 1990 in January, and President Bush outlined his FY'90 priorities in February.

Distance descending ordering method: An O(n) algorithm for inverting the mass matrix in simulation of macromolecules with long branches

NASA Astrophysics Data System (ADS)

Xu, Xiankun; Li, Peiwen

2017-11-01

Fixman's work in 1974 and the follow-up studies have developed a method that can factorize the inverse of mass matrix into an arithmetic combination of three sparse matrices-one of them is positive definite and needs to be further factorized by using the Cholesky decomposition or similar methods. When the molecule subjected to study is of serial chain structure, this method can achieve O (n) time complexity. However, for molecules with long branches, Cholesky decomposition about the corresponding positive definite matrix will introduce massive fill-in due to its nonzero structure. Although there are several methods can be used to reduce the number of fill-in, none of them could strictly guarantee for zero fill-in for all molecules according to our test, and thus cannot obtain O (n) time complexity by using these traditional methods. In this paper we present a new method that can guarantee for no fill-in in doing the Cholesky decomposition, which was developed based on the correlations between the mass matrix and the geometrical structure of molecules. As a result, the inverting of mass matrix will remain the O (n) time complexity, no matter the molecule structure has long branches or not.

The morphology and classification of α ganglion cells in the rat retinae: a fractal analysis study.

PubMed

Jelinek, Herbert F; Ristanović, Dušan; Milošević, Nebojša T

2011-09-30

Rat retinal ganglion cells have been proposed to consist of a varying number of subtypes. Dendritic morphology is an essential aspect of classification and a necessary step toward understanding structure-function relationships of retinal ganglion cells. This study aimed at using a heuristic classification procedure in combination with the box-counting analysis to classify the alpha ganglion cells in the rat retinae based on the dendritic branching pattern and to investigate morphological changes with retinal eccentricity. The cells could be divided into two groups: cells with simple dendritic pattern (box dimension lower than 1.390) and cells with complex dendritic pattern (box dimension higher than 1.390) according to their dendritic branching pattern complexity. Both were further divided into two subtypes due to the stratification within the inner plexiform layer. In the present study we have shown that the alpha rat RCGs can be classified further by their dendritic branching complexity and thus extend those of previous reports that fractal analysis can be successfully used in neuronal classification, particularly that the fractal dimension represents a robust and sensitive tool for the classification of retinal ganglion cells. A hypothesis of possible functional significance of our classification scheme is also discussed. Copyright © 2011 Elsevier B.V. All rights reserved.

Heterogeneous OH oxidation of motor oil particles causes selective depletion of branched and less cyclic hydrocarbons.

PubMed

Isaacman, Gabriel; Chan, Arthur W H; Nah, Theodora; Worton, David R; Ruehl, Chris R; Wilson, Kevin R; Goldstein, Allen H

2012-10-02

Motor oil serves as a useful model system for atmospheric oxidation of hydrocarbon mixtures typical of anthropogenic atmospheric particulate matter, but its complexity often prevents comprehensive chemical speciation. In this work we fully characterize this formerly "unresolved complex mixture" at the molecular level using recently developed soft ionization gas chromatography techniques. Nucleated motor oil particles are oxidized in a flow tube reactor to investigate the relative reaction rates of observed hydrocarbon classes: alkanes, cycloalkanes, bicycloalkanes, tricycloalkanes, and steranes. Oxidation of hydrocarbons in a complex aerosol is found to be efficient, with approximately three-quarters (0.72 ± 0.06) of OH collisions yielding a reaction. Reaction rates of individual hydrocarbons are structurally dependent: compared to normal alkanes, reaction rates increased by 20-50% with branching, while rates decreased ∼20% per nonaromatic ring present. These differences in rates are expected to alter particle composition as a function of oxidation, with depletion of branched and enrichment of cyclic hydrocarbons. Due to this expected shift toward ring-opening reactions heterogeneous oxidation of the unreacted hydrocarbon mixture is less likely to proceed through fragmentation pathways in more oxidized particles. Based on the observed oxidation-induced changes in composition, isomer-resolved analysis has potential utility for determining the photochemical age of atmospheric particulate matter with respect to heterogeneous oxidation.

Improved deoxyribozymes for synthesis of covalently branched DNA and RNA.

PubMed

Lee, Christine S; Mui, Timothy P; Silverman, Scott K

2011-01-01

A covalently branched nucleic acid can be synthesized by joining the 2'-hydroxyl of the branch-site ribonucleotide of a DNA or RNA strand to the activated 5'-phosphorus of a separate DNA or RNA strand. We have previously used deoxyribozymes to synthesize several types of branched nucleic acids for experiments in biotechnology and biochemistry. Here, we report in vitro selection experiments to identify improved deoxyribozymes for synthesis of branched DNA and RNA. Each of the new deoxyribozymes requires Mn²(+) as a cofactor, rather than Mg²(+) as used by our previous branch-forming deoxyribozymes, and each has an initially random region of 40 rather than 22 or fewer combined nucleotides. The deoxyribozymes all function by forming a three-helix-junction (3HJ) complex with their two oligonucleotide substrates. For synthesis of branched DNA, the best new deoxyribozyme, 8LV13, has k(obs) on the order of 0.1 min⁻¹, which is about two orders of magnitude faster than our previously identified 15HA9 deoxyribozyme. 8LV13 also functions at closer-to-neutral pH than does 15HA9 (pH 7.5 versus 9.0) and has useful tolerance for many DNA substrate sequences. For synthesis of branched RNA, two new deoxyribozymes, 8LX1 and 8LX6, were identified with broad sequence tolerances and substantial activity at pH 7.5, versus pH 9.0 for many of our previous deoxyribozymes that form branched RNA. These experiments provide new, and in key aspects improved, practical catalysts for preparation of synthetic branched DNA and RNA.

Impact of high-performance work systems on individual- and branch-level performance: test of a multilevel model of intermediate linkages.

PubMed

Aryee, Samuel; Walumbwa, Fred O; Seidu, Emmanuel Y M; Otaye, Lilian E

2012-03-01

We proposed and tested a multilevel model, underpinned by empowerment theory, that examines the processes linking high-performance work systems (HPWS) and performance outcomes at the individual and organizational levels of analyses. Data were obtained from 37 branches of 2 banking institutions in Ghana. Results of hierarchical regression analysis revealed that branch-level HPWS relates to empowerment climate. Additionally, results of hierarchical linear modeling that examined the hypothesized cross-level relationships revealed 3 salient findings. First, experienced HPWS and empowerment climate partially mediate the influence of branch-level HPWS on psychological empowerment. Second, psychological empowerment partially mediates the influence of empowerment climate and experienced HPWS on service performance. Third, service orientation moderates the psychological empowerment-service performance relationship such that the relationship is stronger for those high rather than low in service orientation. Last, ordinary least squares regression results revealed that branch-level HPWS influences branch-level market performance through cross-level and individual-level influences on service performance that emerges at the branch level as aggregated service performance.

[Effects of Loquat-Branch Dust Substitution on Ganoderma lucidum Cultivation in Its Main Active Components].

PubMed

Zhang, Ping; Chen, Feng; Lai, Teng-qiang; Jin, Ling-yun; Li, Ye

2015-12-01

To select the best Ganoderma lucidum cultivation medium of replacing sawdust into loquat-branch dust, in order to realize high output and high quality production of Ganoderma lucidum. Loquat-branch dust was added as substitution in Ganoderma lucidum cultivation, its effects on the biomass and the content of Ganoderma polysaccharides, triterpenoids and flavonoids were analyzed. By using loquat-branch dust in culture, Ganoderma lucidum grew well with normal fruiting body obtained and spores released. Compared with control group, the biological efficiency was increased by 11.34%, when the addition of the loquat-branch dust was 80%, while the amount of spore had little difference. When the addition of the loquat-branch dust was 90%, the content of Ganoderma polysaccharides and triterpenoids was increased by 32.29% and 30.58% respectively, while the efficiency of flavonoids had little difference. Using loquat-branch dust cultivation can improve the quality of Ganoderma lucidum. According to the comprehensive score, 80% loquat-branch dust is the most suitable cultivation medium.

Extension of the TDCR model to compute counting efficiencies for radionuclides with complex decay schemes.

PubMed

Kossert, K; Cassette, Ph; Carles, A Grau; Jörg, G; Gostomski, Christroph Lierse V; Nähle, O; Wolf, Ch

2014-05-01

The triple-to-double coincidence ratio (TDCR) method is frequently used to measure the activity of radionuclides decaying by pure β emission or electron capture (EC). Some radionuclides with more complex decays have also been studied, but accurate calculations of decay branches which are accompanied by many coincident γ transitions have not yet been investigated. This paper describes recent extensions of the model to make efficiency computations for more complex decay schemes possible. In particular, the MICELLE2 program that applies a stochastic approach of the free parameter model was extended. With an improved code, efficiencies for β(-), β(+) and EC branches with up to seven coincident γ transitions can be calculated. Moreover, a new parametrization for the computation of electron stopping powers has been implemented to compute the ionization quenching function of 10 commercial scintillation cocktails. In order to demonstrate the capabilities of the TDCR method, the following radionuclides are discussed: (166m)Ho (complex β(-)/γ), (59)Fe (complex β(-)/γ), (64)Cu (β(-), β(+), EC and EC/γ) and (229)Th in equilibrium with its progenies (decay chain with many α, β and complex β(-)/γ transitions). © 2013 Published by Elsevier Ltd.

Ultrafast Spin Crossover in [FeII (bpy)3 ]2+ : Revealing Two Competing Mechanisms by Extreme Ultraviolet Photoemission Spectroscopy.

PubMed

Moguilevski, Alexandre; Wilke, Martin; Grell, Gilbert; Bokarev, Sergey I; Aziz, Saadullah G; Engel, Nicholas; Raheem, Azhr A; Kühn, Oliver; Kiyan, Igor Yu; Aziz, Emad F

2017-03-03

Photoinduced spin-flip in Fe II complexes is an ultrafast phenomenon that has the potential to become an alternative to conventional processing and magnetic storage of information. Following the initial excitation by visible light into the singlet metal-to-ligand charge-transfer state, the electronic transition to the high-spin quintet state may undergo different pathways. Here we apply ultrafast XUV (extreme ultraviolet) photoemission spectroscopy to track the low-to-high spin dynamics in the aqueous iron tris-bipyridine complex, [Fe(bpy) 3 ] 2+ , by monitoring the transient electron density distribution among excited states with femtosecond time resolution. Aided by first-principles calculations, this approach enables us to reveal unambiguously both the sequential and direct de-excitation pathways from singlet to quintet state, with a branching ratio of 4.5:1. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Vibrio parahaemolyticus isolates from southeastern Chinese coast are genetically diverse with circulation of clonal complex 3 strains since 2002.

PubMed

Yu, Ying; Hu, Weizhao; Wu, Beibei; Zhang, Peipei; Chen, Jianshun; Wang, Shuna; Fang, Weihuan

2011-11-01

Multilocus sequence typing (MLST) was used to examine the clonal relationship and genetic diversity of 71 Vibrio parahaemolyticus isolates from clinical and seafood-related sources in southeastern Chinese coast between 2002 and 2009. The tested isolates fell into 61 sequence types (STs). Of 17 clinical isolates, 7 belonged to ST3 of the pandemic clonal complex 3, with 3 strains isolated in 2002. Although there was no apparent clonal relationship found between clinical strains and those from seafood-related sources positive with pathogenic markers, there were clonal relationships between clinical strains from this study and those from environmental sources in other parts of China. Phylogenetic analysis showed that strains of 112 STs (61 STs from this study and 51 retrieved from PUBMLST database covering different continents) could be divided into four branches. The vast majority of our isolates and those from other countries were genetically diverse and clustered into two major branches of mixed distribution (of geographic origins and sample sources), whereas five STs representing six isolates split as two minor branches because of divergence of their recA genes, which had 80%-82% nucleotide identity to typical V. parahaemolyticus strains and 73.3%-76.9% identity to the CDS24 of a Vibrio sp. plasmid p23023, indicating that the recA gene might have recombined by lateral gene transfer. This was further supported by a high ratio of recombination to mutation (3.038) for recA. In conclusion, MLST with fully extractable database is a powerful system for analysis of clonal relationship for strains of a particular region in a national or global scale as well as between clinical and environmental or food-related strains.

Leaf evolution in early-diverging ferns: insights from a new fern-like plant from the Late Devonian of China.

PubMed

Wang, De-Ming; Xu, Hong-He; Xue, Jin-Zhuang; Wang, Qi; Liu, Le

2015-06-01

With the exception of angiosperms, the main euphyllophyte lineages (i.e. ferns sensu lato, progymnosperms and gymnosperms) had evolved laminate leaves by the Late Devonian. The evolution of laminate leaves, however, remains unclear for early-diverging ferns, largely represented by fern-like plants. This study presents a novel fern-like taxon with pinnules, which provides new insights into the early evolution of laminate leaves in early-diverging ferns. Macrofossil specimens were collected from the Upper Devonian (Famennian) Wutong Formation of Anhui and Jiangsu Provinces, South China. A standard degagement technique was employed to uncover compressed plant portions within the rock matrix. A new fern-like taxon, SHOUGANGIA BELLA GEN ET SP NOV: , is described and represents an early-diverging fern with highly derived features. It has a partially creeping stem with adventitious roots only on one side, upright primary and secondary branches arranged in helices, tertiary branches borne alternately or (sub)oppositely, laminate and usually lobed leaves with divergent veins, and complex fertile organs terminating tertiary branches and possessing multiple divisions and numerous terminal sporangia. Shougangia bella provides unequivocal fossil evidence for laminate leaves in early-diverging ferns. It suggests that fern-like plants, along with other euphyllophyte lineages, had independently evolved megaphylls by the Late Devonian, possibly in response to a significant decline in atmospheric CO2 concentration. Among fern-like plants, planate ultimate appendages are homologous with laminate pinnules, and in the evolution of megaphylls, fertile organs tend to become complex. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Hydrothermal growth of cross-linked hyperbranched copper dendrites using copper oxalate complex

NASA Astrophysics Data System (ADS)

Truong, Quang Duc; Kakihana, Masato

2012-06-01

A facile and surfactant-free approach has been developed for the synthesis of cross-linked hyperbranched copper dendrites using copper oxalate complex as a precursor and oxalic acid as a reducing and structure-directing agent. The synthesized particles are composed of highly branched nanostructures with unusual cross-linked hierarchical networks. The formation of copper dendrites can be explained in view of both diffusion control and aggregation-based growth model accompanied by the chelation-assisted assembly. Oxalic acid was found to play dual roles as reducing and structure-directing agent based on the investigation results. The understanding on the crystal growth and the roles of oxalic acid provides clear insight into the formation mechanism of hyperbranched metal dendrites.

Economics of Cancer Medicines: For Whose Benefit?

PubMed

Gyawali, Bishal; Sullivan, Richard

2017-04-01

Although new cancer drugs are continually getting approved and used, the value that these drugs add is very debatable. Because of the skyrocketing cost of the new drugs, each new approval represents a multibillion market. However, unlike other branches of economics, cancer drugs are intricately associated with socio-political issues, emotional overlay, public pressure, industry manipulation and propaganda. In this article, we review the value added by new cancer drugs and examine the socio-political agenda around them with highlights on the increasing gulf between high-income and low-middle income countries regarding the affordability to these drugs. Finally, we also suggest a way forward to address this highly complex issue.

Anatomical study of the left superior mediastinal lymphatics for tracheal branches of left recurrent laryngeal nerve-preserving mediastinoscope-assisted surgery in esophageal cancer.

PubMed

Nakajima, Yutaka; Tokairin, Yutaka; Nakajima, Yasuaki; Kawada, Kenro; Nagai, Kagami; Yamaguchi, Kumiko; Akita, Keiichi; Kawano, Tatsuyuki

2018-03-01

Curative treatment of esophageal cancer requires meticulous superior mediastinal lymphadenectomy, in addition to esophagectomy, because superior mediastinal lymph node metastases are common in esophageal cancer. When preserving the tracheal branches of the left recurrent laryngeal nerve (RLN), good anatomical understanding is required for confirmation of the positional relationships between the courses of lymphatic vessels, lymph node distribution, and the left RLN and its tracheal branches. We performed a detailed anatomical examination of these relationships. Macroscopic anatomical observation and histological examination was performed on cadavers. In addition to hematoxylin and eosin staining, immunostaining using antipodoplanin antibody D2-40 (podoplanin) was performed to identify the lymphatic vessels. The tracheal branches of the left RLN were clearly observed, but no lymphatic vessels crossing the ventral or dorsal side of the branches were identified either macro-anatomically or histologically. No complex lymphatic network structure straddling the plane composed of tracheal branches of the left RLN was found in the left superior mediastinum. This suggests that dissection of the lymph nodes around the left RLN via the pneumomediastinum method using the left cervical approach may allow preservation of the tracheal branches of the left RLN by maintaining dissection accuracy.

Morphodynamics of a growing microbial colony driven by cell death

NASA Astrophysics Data System (ADS)

Ghosh, Pushpita; Levine, Herbert

2017-11-01

Bacterial cells can often self-organize into multicellular structures with complex spatiotemporal morphology. In this work, we study the spatiotemporal dynamics of a growing microbial colony in the presence of cell death. We present an individual-based model of nonmotile bacterial cells which grow and proliferate by consuming diffusing nutrients on a semisolid two-dimensional surface. The colony spreads by growth forces and sliding motility of cells and undergoes cell death followed by subsequent disintegration of the dead cells in the medium. We model cell death by considering two possible situations: In one of the cases, cell death occurs in response to the limitation of local nutrients, while the other case corresponds to an active death process, known as apoptotic or programmed cell death. We demonstrate how the colony morphology is influenced by the presence of cell death. Our results show that cell death facilitates transitions from roughly circular to highly branched structures at the periphery of an expanding colony. Interestingly, our results also reveal that for the colonies which are growing in higher initial nutrient concentrations, cell death occurs much earlier compared to the colonies which are growing in lower initial nutrient concentrations. This work provides new insights into the branched patterning of growing bacterial colonies as a consequence of complex interplay among the biochemical and mechanical effects.

The effects of drought and disturbance on the growth and developmental instability of loblolly pine (Pinus taeda L.)

USGS Publications Warehouse

Graham, John H.; Duda, Jeffrey J.; Brown, Michelle L.; Kitchen, Stanley G.; Emlen, John M.; Malol, Jagadish; Bankstahl, Elizabeth; Krzysik, Anthony J.; Balbach, Harold E.; Freeman, D. Carl

2012-01-01

Ecological indicators provide early warning of adverse environmental change, helping land managers adaptively manage their resources while minimizing costly remediation. In 1999 and 2000, we studied two such indicators, growth and developmental instability, of loblolly pine (Pinus taeda L.) influenced by mechanized infantry training at Fort Benning, Georgia. Disturbed areas were used for military training; tracked and wheeled vehicles damaged vegetation and soils. Highly disturbed sites had fewer trees, diminished ground cover, warmer soils in the summer, and more compacted soils with a shallower A-horizon. We hypothesized that disturbance would decrease the growth of needles, branches, and tree rings, increase the complexity of tree rings, and increase the developmental instability of needles. Contrary to our expectations, however, disturbance enhanced growth in the first year of the study, possibly by reducing competition. In the second year, a drought reduced growth of branches and needles, eliminating the stimulatory effect of disturbance. Growth-ring widths increased with growing-season precipitation, and decreased with growing-season temperature over the last 40 years. Disturbance had no effect on tree-ring complexity, as measured by the Hurst exponent. Within-fascicle variation of current-year needle length, a measure of developmental instability, differed among the study populations, but appeared unrelated to mechanical disturbance or drought.

Overexpression of STARCH BRANCHING ENZYME II increases short-chain branching of amylopectin and alters the physicochemical properties of starch from potato tuber.

PubMed

Brummell, David A; Watson, Lyn M; Zhou, Jun; McKenzie, Marian J; Hallett, Ian C; Simmons, Lyall; Carpenter, Margaret; Timmerman-Vaughan, Gail M

2015-04-29

Starch is biosynthesised by a complex of enzymes including various starch synthases and starch branching and debranching enzymes, amongst others. The role of all these enzymes has been investigated using gene silencing or genetic knockouts, but there are few examples of overexpression due to the problems of either cloning large genomic fragments or the toxicity of functional cDNAs to bacteria during cloning. The aim of this study was to investigate the function of potato STARCH BRANCHING ENZYME II (SBEII) using overexpression in potato tubers. A hybrid SBEII intragene consisting of potato cDNA containing a fragment of potato genomic DNA that included a single intron was used in order to prevent bacterial translation during cloning. A population of 20 transgenic potato plants exhibiting SBEII overexpression was generated. Compared with wild-type, starch from these tubers possessed an increased degree of amylopectin branching, with more short chains of degree of polymerisation (DP) 6-12 and particularly of DP6. Transgenic lines expressing a GRANULE-BOUND STARCH SYNTHASE (GBSS) RNAi construct were also generated for comparison and exhibited post-transcriptional gene silencing of GBSS and reduced amylose content in the starch. Both transgenic modifications did not affect granule morphology but reduced starch peak viscosity. In starch from SBEII-overexpressing lines, the increased ratio of short to long amylopectin branches facilitated gelatinisation, which occurred at a reduced temperature (by up to 3°C) or lower urea concentration. In contrast, silencing of GBSS increased the gelatinisation temperature by 4°C, and starch required a higher urea concentration for gelatinisation. In lines with a range of SBEII overexpression, the magnitude of the increase in SBEII activity, reduction in onset of gelatinisation temperature and increase in starch swollen pellet volume were highly correlated, consistent with reports that starch swelling is greatly dependent upon the amylopectin branching pattern. This work reports the first time that overexpression of SBEII has been achieved in a non-cereal plant. The data show that overexpression of SBEII using a simple single-intron hybrid intragene is an effective way to modify potato starch physicochemical properties, and indicate that an increased ratio of short to long amylopectin branches produces commercially beneficial changes in starch properties such as reduced gelatinisation temperature, reduced viscosity and increased swelling volume.

Frequency analysis of stress relaxation dynamics in model asphalts

NASA Astrophysics Data System (ADS)

Masoori, Mohammad; Greenfield, Michael L.

2014-09-01

Asphalt is an amorphous or semi-crystalline material whose mechanical performance relies on viscoelastic responses to applied strain or stress. Chemical composition and its effect on the viscoelastic properties of model asphalts have been investigated here by computing complex modulus from molecular dynamics simulation results for two different model asphalts whose compositions each resemble the Strategic Highway Research Program AAA-1 asphalt in different ways. For a model system that contains smaller molecules, simulation results for storage and loss modulus at 443 K reach both the low and high frequency scaling limits of the Maxwell model. Results for a model system composed of larger molecules (molecular weights 300-900 g/mol) with longer branches show a quantitatively higher complex modulus that decreases significantly as temperature increases over 400-533 K. Simulation results for its loss modulus approach the low frequency scaling limit of the Maxwell model at only the highest temperature simulated. A Black plot or van Gurp-Palman plot of complex modulus vs. phase angle for the system of larger molecules suggests some overlap among results at different temperatures for less high frequencies, with an interdependence consistent with the empirical Christensen-Anderson-Marasteanu model. Both model asphalts are thermorheologically complex at very high frequencies, where they show a loss peak that appears to be independent of temperature and density.

Study of the techniques feasible for food synthesis aboard a spacecraft

NASA Technical Reports Server (NTRS)

Weiss, A. H.

1972-01-01

Synthesis of sugars by Ca(OH)2 catalyzed formaldehyde condensation (the formose reaction) has produced branched carbohydrates that do not occur in nature. The kinetics and mechanisms of the homogeneously catalyzed autocatalytic condensation were studied and analogies between homogeneous and heterogeneous rate laws have been found. Aldol condensations proceed simultaneously with Cannizzaro and crossed-Cannizzaro reactions and Lobry de Bruyn-Van Eckenstein rearrangements. The separate steps as well as the interactions of this highly complex reaction system were elucidated. The system exhibits instabilities, competitive catalytic, mass action, and equilibrium phenomena, complexing, and parallel and consecutive reactions. Specific finding that have been made on the problem will be of interest for synthesizing sugars, both for sustained space flight and for large scale food manufacture. A contribution to methodology for studying complex catalyzed reactions and to understanding control of reaction selectivity was a broad goal of the project.

Fort Collins Science Center Ecosystem Dynamics branch--interdisciplinary research for addressing complex natural resource issues across landscapes and time

USGS Publications Warehouse

Bowen, Zachary H.; Melcher, Cynthia P.; Wilson, Juliette T.

2013-01-01

The Ecosystem Dynamics Branch of the Fort Collins Science Center offers an interdisciplinary team of talented and creative scientists with expertise in biology, botany, ecology, geology, biogeochemistry, physical sciences, geographic information systems, and remote-sensing, for tackling complex questions about natural resources. As demand for natural resources increases, the issues facing natural resource managers, planners, policy makers, industry, and private landowners are increasing in spatial and temporal scope, often involving entire regions, multiple jurisdictions, and long timeframes. Needs for addressing these issues include (1) a better understanding of biotic and abiotic ecosystem components and their complex interactions; (2) the ability to easily monitor, assess, and visualize the spatially complex movements of animals, plants, water, and elements across highly variable landscapes; and (3) the techniques for accurately predicting both immediate and long-term responses of system components to natural and human-caused change. The overall objectives of our research are to provide the knowledge, tools, and techniques needed by the U.S. Department of the Interior, state agencies, and other stakeholders in their endeavors to meet the demand for natural resources while conserving biodiversity and ecosystem services. Ecosystem Dynamics scientists use field and laboratory research, data assimilation, and ecological modeling to understand ecosystem patterns, trends, and mechanistic processes. This information is used to predict the outcomes of changes imposed on species, habitats, landscapes, and climate across spatiotemporal scales. The products we develop include conceptual models to illustrate system structure and processes; regional baseline and integrated assessments; predictive spatial and mathematical models; literature syntheses; and frameworks or protocols for improved ecosystem monitoring, adaptive management, and program evaluation. The descriptions in this fact sheet provide snapshots of our three research emphases, followed by descriptions of select current projects.

Synthesis of branched iminosugars through a hypervalent iodine(III)-mediated radical-polar crossover reaction.

PubMed

Santana, Andrés G; Paz, Nieves R; Francisco, Cosme G; Suárez, Ernesto; González, Concepción C

2013-08-02

The synthesis of a novel type of branched iminosugars is described. This synthetic strategy is based on two key reactions: first, an aldol reaction with formaldehyde in order to introduce selectively the hydroxymethyl branch, and second, a tandem β-fragmentation-intramolecular cyclization reaction. The combination of both reactions afforded a battery of compounds exhibiting a great structural complexity, with the concomitant formation of a quaternary center, starting from readily available aldoses. With this approach we have demonstrated the usefulness of the fragmentation of anomeric alkoxyl radicals (ARF) promoted by the PhIO/I2 system for the preparation of new compounds with potential interest for both medicinal and synthetic chemists.

Imaging in Classic Form of Maple Syrup Urine Disease: A Rare Metabolic Central Nervous System

PubMed Central

Jain, Aditi; Jagdeesh, K.; Mane, Ranoji; Singla, Saurabh

2013-01-01

Maple syrup urine disease (MSUD) is a rare autosomal recessive disorder of branched-chain amino acid metabolism. The condition gets its name from the distinctive sweet odour of affected infants’ urine. MSUD is caused by a deficiency of the branched-chain α-ketoacid dehydrogenase enzyme complex, leading to accumulation of the branched-chain amino acids (leucine, isoleucine, and valine) and their toxic by-products (ketoacids) in the blood and urine. Imaging is characterestized by MSUD oedema affecting the myelinated white matter. We present a neonate with classic type of MSUD and its imaging features on computed tomography, conventional magnetic resonance imaging, diffusion-weighted imaging, and magnetic resonance spectroscopy. PMID:24049754

Imaging in classic form of maple syrup urine disease: a rare metabolic central nervous system.

PubMed

Jain, Aditi; Jagdeesh, K; Mane, Ranoji; Singla, Saurabh

2013-04-01

Maple syrup urine disease (MSUD) is a rare autosomal recessive disorder of branched-chain amino acid metabolism. The condition gets its name from the distinctive sweet odour of affected infants' urine. MSUD is caused by a deficiency of the branched-chain α-ketoacid dehydrogenase enzyme complex, leading to accumulation of the branched-chain amino acids (leucine, isoleucine, and valine) and their toxic by-products (ketoacids) in the blood and urine. Imaging is characterestized by MSUD oedema affecting the myelinated white matter. We present a neonate with classic type of MSUD and its imaging features on computed tomography, conventional magnetic resonance imaging, diffusion-weighted imaging, and magnetic resonance spectroscopy.

Molecular characterization of maple syrup urine disease patients from Tunisia.

PubMed

Jaafar, N; Moleirinho, A; Kerkeni, E; Monastiri, K; Seboui, H; Amorim, A; Prata, M J; Quental, S

2013-03-15

Maple syrup urine disease (MSUD) is a rare disorder of branched-chain amino acids (BCAA) metabolism caused by the defective function of branched-chain α-ketoacid dehydrogenase complex (BCKD). The disease causal mutations can occur either in BCKDHA, BCKDHB or DBT genes encoding respectively the E1α, E1β and E2 subunits of the complex. In this study we report the molecular characterization of 3 Tunisian patients with the classic form of MSUD. Two novel putative mutations have been identified: the alteration c.716A>G (p.Glu239Gly) in BCKDHB and a small deletion (c.1333_1336delAATG; p.Asn445X) detected in DBT gene. Copyright © 2012 Elsevier B.V. All rights reserved.

Cardiac resynchronization therapy with His bundle pacing as a method of treatment of chronic heart failure in patients with permanent atrial fibrillation and left bundle branch block.

PubMed

Boczar, Krzysztof; Sławuta, Agnieszka; Ząbek, Andrzej; Dębski, Maciej; Gajek, Jacek; Lelakowski, Jacek; Małecka, Barbara

CRT is a therapeutic option for patients with heart failure, sinus rhythm, prolonged QRS complex duration and reduced ejection fraction. We present a case of 71-year-old woman with dilated cardiomyopathy, NYHA functional class III and AF. We implanted CRT combined with direct His-bundle pacing. The indication for such a therapy was a left bundle branch block with a QRS complex of 178ms and a left ventricular EF of 15%, left ventricular end-diastolic diameter (LVEDD) of 75mm. After 8months of follow-up the LVEDD was 60mm with EF 35-40%. Copyright © 2017. Published by Elsevier Inc.

Bundle Branch Block

MedlinePlus

... known cause. Causes can include: Left bundle branch block Heart attacks (myocardial infarction) Thickened, stiffened or weakened ... myocarditis) High blood pressure (hypertension) Right bundle branch block A heart abnormality that's present at birth (congenital) — ...

Automated anatomical labeling of bronchial branches using multiple classifiers and its application to bronchoscopy guidance based on fusion of virtual and real bronchoscopy

NASA Astrophysics Data System (ADS)

Ota, Shunsuke; Deguchi, Daisuke; Kitasaka, Takayuki; Mori, Kensaku; Suenaga, Yasuhito; Hasegawa, Yoshinori; Imaizumi, Kazuyoshi; Takabatake, Hirotsugu; Mori, Masaki; Natori, Hiroshi

2008-03-01

This paper presents a method for automated anatomical labeling of bronchial branches (ALBB) extracted from 3D CT datasets. The proposed method constructs classifiers that output anatomical names of bronchial branches by employing the machine-learning approach. We also present its application to a bronchoscopy guidance system. Since the bronchus has a complex tree structure, bronchoscopists easily tend to get disoriented and lose the way to a target location. A bronchoscopy guidance system is strongly expected to be developed to assist bronchoscopists. In such guidance system, automated presentation of anatomical names is quite useful information for bronchoscopy. Although several methods for automated ALBB were reported, most of them constructed models taking only variations of branching patterns into account and did not consider those of running directions. Since the running directions of bronchial branches differ greatly in individuals, they could not perform ALBB accurately when running directions of bronchial branches were different from those of models. Our method tries to solve such problems by utilizing the machine-learning approach. Actual procedure consists of three steps: (a) extraction of bronchial tree structures from 3D CT datasets, (b) construction of classifiers using the multi-class AdaBoost technique, and (c) automated classification of bronchial branches by using the constructed classifiers. We applied the proposed method to 51 cases of 3D CT datasets. The constructed classifiers were evaluated by leave-one-out scheme. The experimental results showed that the proposed method could assign correct anatomical names to bronchial branches of 89.1% up to segmental lobe branches. Also, we confirmed that it was quite useful to assist the bronchoscopy by presenting anatomical names of bronchial branches on real bronchoscopic views.

Survival affects decision making for fenestrated and branched endovascular aortic repair.

PubMed

Beach, Jocelyn M; Rajeswaran, Jeevanantham; Parodi, F Ezequiel; Kuramochi, Yuki; Brier, Corey; Blackstone, Eugene; Eagleton, Matthew J

2018-03-01

Repair options for complex abdominal and thoracoabdominal aortic aneurysms (TAAAs) are evolving with increased experience and availability of less invasive endovascular techniques. Identifying risk factors for mortality after fenestrated and branched endovascular aortic repair (F/B-EVAR) could improve patient selection and facilitate decision making regarding who may benefit from prophylactic F/B-EVAR. We evaluated 1091 patients in a prospective investigational device exemption trial who underwent F/B-EVAR from August 2001 to June 2015 for complex aortic aneurysms (CAAs). Multivariable analysis of risk factors for death was performed using a nonproportional hazards model and a nonparametric analysis using random survival forest technology. Operative mortality after F/B-EVAR was low (3.7%), with high CAA-related survival at 30 day and 5 years (96.8% and 94.0%, respectively). All-cause 5-year survival, however, was 46.2% and older age, heart failure, chronic obstructive pulmonary disease, renal disease, anemia, and coagulation disorders were risk factors. Risk was highest for those undergoing type I/II TAAA repairs and those with larger aneurysms. Patients with multiple comorbidities and those undergoing type I or II TAAA repair are at greatest risk of mortality; however, in this high-risk population, F/B-EVAR offers greater survival compared with that reported for the natural history of untreated aneurysms. Operative and early mortality is lower than the best-reported open repair outcomes, even in this high-risk population, suggesting a potential benefit in extending the use of F/B-EVAR to low-to-average risk CAA patients. Copyright © 2017 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

Cortactin binding to F-actin revealed by electron microscopy and 3D reconstruction.

PubMed

Pant, Kiran; Chereau, David; Hatch, Victoria; Dominguez, Roberto; Lehman, William

2006-06-16

Cortactin and WASP activate Arp2/3-mediated actin filament nucleation and branching. However, different mechanisms underlie activation by the two proteins, which rely on distinct actin-binding modules and modes of binding to actin filaments. It is generally thought that cortactin binds to "mother" actin filaments, while WASP donates actin monomers to Arp2/3-generated "daughter" filament branches. Interestingly, cortactin also binds WASP in addition to F-actin and the Arp2/3 complex. However, the structural basis for the role of cortactin in filament branching remains unknown, making interpretation difficult. Here, electron microscopy and 3D reconstruction were carried out on F-actin decorated with the actin-binding repeating domain of cortactin, revealing conspicuous density on F-actin attributable to cortactin that is located on a consensus-binding site on subdomain-1 of actin subunits. Strikingly, the binding of cortactin widens the gap between the two long-pitch filament strands. Although other proteins have been found to alter the structure of the filament, the cortactin-induced conformational change appears unique. The results are consistent with a mechanism whereby alterations of the F-actin structure may facilitate recruitment of the Arp2/3 complex to the "mother" filament in the cortex of cells. In addition, cortactin may act as a structural adapter protein, stabilizing nascent filament branches while mediating the simultaneous recruitment of Arp2/3 and WASP.

Artificial intelligence in medicine.

PubMed

Hamet, Pavel; Tremblay, Johanne

2017-04-01

Artificial Intelligence (AI) is a general term that implies the use of a computer to model intelligent behavior with minimal human intervention. AI is generally accepted as having started with the invention of robots. The term derives from the Czech word robota, meaning biosynthetic machines used as forced labor. In this field, Leonardo Da Vinci's lasting heritage is today's burgeoning use of robotic-assisted surgery, named after him, for complex urologic and gynecologic procedures. Da Vinci's sketchbooks of robots helped set the stage for this innovation. AI, described as the science and engineering of making intelligent machines, was officially born in 1956. The term is applicable to a broad range of items in medicine such as robotics, medical diagnosis, medical statistics, and human biology-up to and including today's "omics". AI in medicine, which is the focus of this review, has two main branches: virtual and physical. The virtual branch includes informatics approaches from deep learning information management to control of health management systems, including electronic health records, and active guidance of physicians in their treatment decisions. The physical branch is best represented by robots used to assist the elderly patient or the attending surgeon. Also embodied in this branch are targeted nanorobots, a unique new drug delivery system. The societal and ethical complexities of these applications require further reflection, proof of their medical utility, economic value, and development of interdisciplinary strategies for their wider application. Copyright © 2017. Published by Elsevier Inc.

Some Cenozoic hydrocarbon basins on the continental shelf of Vietnam

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

Dien, P.T.

1994-07-01

The formation of the East Vietnam Sea basins was related to different geodynamic processes. The pre-Oligocene basement consists of igneous, metamorphic, and metasediment complexes. The Cretaceous-Eocene basement formations are formed by convergence of continents after destruction of the Tethys Ocean. Many Jurassic-Eocene fractured magmatic highs of the Cuulong basin basement constitute important reservoirs that are producing good crude oil. The Paleocene-Eocene formations are characterized by intramountain metamolasses, sometimes interbedded volcanic rocks. Interior structures of the Tertiary basins connect with rifted branches of the widened East Vietnam Sea. Bacbo (Song Hong) basin is predominated by alluvial-rhythmic clastics in high-constructive deltas, whichmore » developed on the rifting and sagging structures of the continental branch. Petroleum plays are constituted from Type III source rocks, clastic reservoirs, and local caprocks. Cuulong basin represents sagging structures and is predominated by fine clastics, with tidal-lagoonal fine sandstone and shalestone in high-destructive deltas that are rich in Type II source rocks. The association of the pre-Cenozoic fractured basement reservoirs and the Oligocene-Miocene clastic reservoir sequences with the Oligocene source rocks and the good caprocks is frequently met in petroleum plays of this basin. Nan Conson basin was formed from complicated structures that are related to spreading of the oceanic branch. This basin is characterized by Oligocene epicontinental fine clastics and Miocene marine carbonates that are rich in Types I, II, and III organic matter. There are both pre-Cenozoic fractured basement reservoirs, Miocene buildup carbonate reservoir rocks and Oligocene-Miocene clastic reservoir sequences, in this basin. Pliocene-Quaternary sediments are sand and mud carbonates in the shelf facies of the East Vietnam Sea back-arc basin. Their great thickness provides good conditions for maturation and trapping.« less

Coevolution of patch-type dependent emigration and patch-type dependent immigration.

PubMed

Weigang, Helene C

2017-08-07

The three phases of dispersal - emigration, transfer and immigration - are affecting each other and the former and latter decisions may depend on patch types. Despite the inevitable fact of the complexity of the dispersal process, patch-type dependencies of dispersal decisions modelled as emigration and immigration are usually missing in theoretical dispersal models. Here, I investigate the coevolution of patch-type dependent emigration and patch-type dependent immigration in an extended Hamilton-May model. The dispersing population inhabits a landscape structured into many patches of two types and disperses during a continuous-time season. The trait under consideration is a four dimensional vector consisting of two values for emigration probability from the patches and two values for immigration probability into the patches of each type. Using the adaptive dynamics approach I show that four qualitatively different dispersal strategies may evolve in different parameter regions, including a counterintuitive strategy, where patches of one type are fully dispersed from (emigration probability is one) but individuals nevertheless always immigrate into them during the dispersal season (immigration probability is one). I present examples of evolutionary branching in a wide parameter range, when the patches with high local death rate during the dispersal season guarantee a high expected disperser output. I find that two dispersal strategies can coexist after evolutionary branching: a strategy with full immigration only into the patches with high expected disperser output coexists with a strategy that immigrates into any patch. Stochastic simulations agree with the numerical predictions. Since evolutionary branching is also found when immigration evolves alone, the present study is adding coevolutionary constraints on the emigration traits and hence finds that the coevolution of a higher dimensional trait sometimes hinders evolutionary diversification. Copyright © 2017 Elsevier Ltd. All rights reserved.

Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa.

PubMed

Borowiec, Marek L; Lee, Ernest K; Chiu, Joanna C; Plachetzki, David C

2015-11-23

Understanding the phylogenetic relationships among major lineages of multicellular animals (the Metazoa) is a prerequisite for studying the evolution of complex traits such as nervous systems, muscle tissue, or sensory organs. Transcriptome-based phylogenies have dramatically improved our understanding of metazoan relationships in recent years, although several important questions remain. The branching order near the base of the tree, in particular the placement of the poriferan (sponges, phylum Porifera) and ctenophore (comb jellies, phylum Ctenophora) lineages is one outstanding issue. Recent analyses have suggested that the comb jellies are sister to all remaining metazoan phyla including sponges. This finding is surprising because it suggests that neurons and other complex traits, present in ctenophores and eumetazoans but absent in sponges or placozoans, either evolved twice in Metazoa or were independently, secondarily lost in the lineages leading to sponges and placozoans. To address the question of basal metazoan relationships we assembled a novel dataset comprised of 1080 orthologous loci derived from 36 publicly available genomes representing major lineages of animals. From this large dataset we procured an optimized set of partitions with high phylogenetic signal for resolving metazoan relationships. This optimized data set is amenable to the most appropriate and computationally intensive analyses using site-heterogeneous models of sequence evolution. We also employed several strategies to examine the potential for long-branch attraction to bias our inferences. Our analyses strongly support the Ctenophora as the sister lineage to other Metazoa. We find no support for the traditional view uniting the ctenophores and Cnidaria. Our findings are supported by Bayesian comparisons of topological hypotheses and we find no evidence that they are biased by long-branch attraction. Our study further clarifies relationships among early branching metazoan lineages. Our phylogeny supports the still-controversial position of ctenophores as sister group to all other metazoans. This study also provides a workflow and computational tools for minimizing systematic bias in genome-based phylogenetic analyses. Future studies of metazoan phylogeny will benefit from ongoing efforts to sequence the genomes of additional invertebrate taxa that will continue to inform our view of the relationships among the major lineages of animals.

Molecular evolution accompanying functional divergence of duplicated genes along the plant starch biosynthesis pathway

PubMed Central

2014-01-01

Background Starch is the main source of carbon storage in the Archaeplastida. The starch biosynthesis pathway (sbp) emerged from cytosolic glycogen metabolism shortly after plastid endosymbiosis and was redirected to the plastid stroma during the green lineage divergence. The SBP is a complex network of genes, most of which are members of large multigene families. While some gene duplications occurred in the Archaeplastida ancestor, most were generated during the sbp redirection process, and the remaining few paralogs were generated through compartmentalization or tissue specialization during the evolution of the land plants. In the present study, we tested models of duplicated gene evolution in order to understand the evolutionary forces that have led to the development of SBP in angiosperms. We combined phylogenetic analyses and tests on the rates of evolution along branches emerging from major duplication events in six gene families encoding sbp enzymes. Results We found evidence of positive selection along branches following cytosolic or plastidial specialization in two starch phosphorylases and identified numerous residues that exhibited changes in volume, polarity or charge. Starch synthases, branching and debranching enzymes functional specializations were also accompanied by accelerated evolution. However, none of the sites targeted by selection corresponded to known functional domains, catalytic or regulatory. Interestingly, among the 13 duplications tested, 7 exhibited evidence of positive selection in both branches emerging from the duplication, 2 in only one branch, and 4 in none of the branches. Conclusions The majority of duplications were followed by accelerated evolution targeting specific residues along both branches. This pattern was consistent with the optimization of the two sub-functions originally fulfilled by the ancestral gene before duplication. Our results thereby provide strong support to the so-called “Escape from Adaptive Conflict” (EAC) model. Because none of the residues targeted by selection occurred in characterized functional domains, we propose that enzyme specialization has occurred through subtle changes in affinity, activity or interaction with other enzymes in complex formation, while the basic function defined by the catalytic domain has been maintained. PMID:24884572

Identification of Complex Carbon Nanotube Structures

NASA Technical Reports Server (NTRS)

Han, Jie; Saini, Subhash (Technical Monitor)

1998-01-01

A variety of complex carbon nanotube (CNT) structures have been observed experimentally. These include sharp bends, branches, tori, and helices. They are believed to be formed by using topological defects such as pentagons and heptagons to connect different CNT. The effects of type, number, and arrangement (separation and orientation) of defects on atomic structures and energetics of complex CNT are investigated using topology, quantum mechanics and molecular mechanics calculations. Energetically stable models are derived for identification of observed complex CNT structures.

Experimental investigation of the dynamics of spontaneous pattern formation during dendritic ice crystal growth

NASA Astrophysics Data System (ADS)

Tirmizi, Shakeel H.; Gill, William N.

1989-06-01

The dynamics of spontaneous pattern formation are studied experimentally by observing and recording the evolution of ice crystal patterns which grow freely in a supercooled melt. The sequence of evolution to dendrites is recorded in real time using cine-micrography. In the range of subcoolings from 0.06 to 0.29°C, all the patterns evolved as follows: Smooth disk → Perturbed disk → Disk dendrite → Partially developed dendrite → Fully developed dendrite. The initial smooth disk, the main branch and the side branches all developed perturbations beyond a critical size which depends on the subcooling. The combined effect of the destabilizing thermal gradients ahead of the growing crystal and the stabilizing Gibbs-Thompson capillarity effect dictates the critical size of the unstable structures in terms of the mean curvature of the interface. Detailed analysis of the evolving patterns was done using digital image analysis on the PRIME computer to determine both the manner in which the dendritic growth process replicates itself and the role which the shape and the movement of the interface play in the pattern formation process. Total arc length ST, total area A and the complexity ratio ξ = ST⧸√ A of evolving patterns were computed as a function of time and undercooling for each crystal image. These results permitted us to make some comparisons with theoretical models on pattern evolution. Three distinct phases of evolution were identified: the initial phase when the crystal structure is smooth and free of any perturbations and the complexity ratio is almost a constant, an intermediate phase when the crystal structure develops perturbations which grow quickly in number and in size and the complexity ratio increases rapidly and a final phase when the pattern approaches that of a fully developed dendrite which, on a global scale grows in a shape-perserving manner and has a slowly increasing complexity ratio which seems to approach an asymptote. Two factors were found to be responsible for the symmetric dendritic patterns. These are: first, hexagonal symmetry due to the hexagonal closed packed structure, leads to strong anisotropy in molecular attachment kinetics and in surface free energy; second, the competition among side branches causes smaller side branches to melt when they are trapped between larger ones which generate latent heat and prevent the small branches from gaining access to the fresh cold fluid ahead of them. These two factors lead to a channelling effect which prevents the growth of perturbations from occurring randomly and thus directs the evolving crystal structure into patterns which are regular and reproducible. Theoretical models which are local in nature fail to take into account side branch competition, and this is one of their major weaknesses.

Physical stage of photosynthesis charge separation

NASA Astrophysics Data System (ADS)

Yakovlev, A. G.; Shuvalov, V. A.

2016-06-01

An analytical review is given concerning the biophysical aspects of light-driven primary charge separation in photosynthesis reaction centers (RCs) which are special pigment-protein complexes residing in a cell membrane. The primary (physical) stage of charge separation occurs in the pico- and femtosecond ranges and consists of transferring an electron along the active A-branch of pigments. The review presents vast factual material on both the general issues of primary photosynthesis and some more specific topics, including (1) the role of the inactive B-branch of pigments, (2) the effect of the protein environment on the charge separation, and (3) the participation of monomeric bacteriochlorophyll BA in primary electron acceptance. It is shown that the electron transfer and stabilization are strongly influenced by crystallographic water and tyrosine M210 molecules from the nearest environment of BA. A linkage between collective nuclear motions and electron transfer upon charge separation is demonstrated. The nature of the high quantum efficiency of primary charge separation reactions is discussed.

The Emerging Role of Branched-Chain Amino Acids in Insulin Resistance and Metabolism.

PubMed

Yoon, Mee-Sup

2016-07-01

Insulin is required for maintenance of glucose homeostasis. Despite the importance of insulin sensitivity to metabolic health, the mechanisms that induce insulin resistance remain unclear. Branched-chain amino acids (BCAAs) belong to the essential amino acids, which are both direct and indirect nutrient signals. Even though BCAAs have been reported to improve metabolic health, an increased BCAA plasma level is associated with a high risk of metabolic disorder and future insulin resistance, or type 2 diabetes mellitus (T2DM). The activation of mammalian target of rapamycin complex 1 (mTORC1) by BCAAs has been suggested to cause insulin resistance. In addition, defective BCAA oxidative metabolism might occur in obesity, leading to a further accumulation of BCAAs and toxic intermediates. This review provides the current understanding of the mechanism of BCAA-induced mTORC1 activation, as well as the effect of mTOR activation on metabolic health in terms of insulin sensitivity. Furthermore, the effects of impaired BCAA metabolism will be discussed in detail.

Expression-Linked Patterns of Codon Usage, Amino Acid Frequency, and Protein Length in the Basally Branching Arthropod Parasteatoda tepidariorum

PubMed Central

Whittle, Carrie A.; Extavour, Cassandra G.

2016-01-01

Abstract Spiders belong to the Chelicerata, the most basally branching arthropod subphylum. The common house spider, Parasteatoda tepidariorum, is an emerging model and provides a valuable system to address key questions in molecular evolution in an arthropod system that is distinct from traditionally studied insects. Here, we provide evidence suggesting that codon usage, amino acid frequency, and protein lengths are each influenced by expression-mediated selection in P. tepidariorum. First, highly expressed genes exhibited preferential usage of T3 codons in this spider, suggestive of selection. Second, genes with elevated transcription favored amino acids with low or intermediate size/complexity (S/C) scores (glycine and alanine) and disfavored those with large S/C scores (such as cysteine), consistent with the minimization of biosynthesis costs of abundant proteins. Third, we observed a negative correlation between expression level and coding sequence length. Together, we conclude that protein-coding genes exhibit signals of expression-related selection in this emerging, noninsect, arthropod model. PMID:27017527

Harnessing Electrostatic Forces to Grow Bio-inspired Hierarchical Vascular Networks

NASA Astrophysics Data System (ADS)

Behler, Kristopher; Melrose, Zachary; Schott, Andrew; Wetzel, Eric

2012-02-01

Vascular networks provide a system for fluid distribution. Artificial vascular materials with enhanced properties are currently being developed that could ultimately be integrated into systems reliant upon fluid transport while retaining their structural properties. An uninterrupted and controllable supply of liquid is optimal for many applications such as continual self-healing materials, in-situ delivery of index matched fluids, thermal management and drug delivery systems could benefit from a bio-inspired vascular approach that combines complex network geometries with minimal processing parameters. Two such approaches to induce vascular networks are electrohydrodynamic viscous fingering (EHVF) and electrical treeing (ET). EHVF is a phenomenon that occurs when a low viscosity liquid is forced through a high viscosity fluid or matrix, resulting in branches due to capillary and viscous forces in the high viscosity material. By applying voltages of 0 -- 60 kV, finger diameter is reduced. ET is the result of partial discharges in a dielectric material. In the vicinity of a small diameter electrode, the local electric field is greater than the global dielectric strength, causing a localized, step-wise, breakdown to occur forming a highly branched interconnected structure. ET is a viable method to produce networks on a smaller, micron, scale than the products of the EHVF method.

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

PubMed Central

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

2009-01-01

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

Releasing the brakes while hanging on: Cortactin effects on actin-driven motility.

PubMed

Gov, Nir S; Bernheim-Groswasser, Anne

2012-01-01

Actin polymerization plays a major role in many cellular processes, including cell motility, vesicle trafficking, and pathogen propulsion. The transformation of the (protrusive) polymerization forces into directed motion requires that the growing filaments are positioned next to the surface. This is achieved by localization of surface actin nucleators (WASP), which then activate Arp2/3 complex to form new actin branches. Yet, the same surface-bound WASP molecule which initiates the nucleation of new actin branches, also inherently prevents the translation of the polymerization forces into motion, essentially because the WASP molecule has to be in contact with the network during the formation of the new branch. In our recent paper we show that cortactin relaxes this internal inhibition by enhancing the release of WASP-VCA molecule from the new branching site after nucleation is initiated. We show that this enhanced release has two major effects; it increases the turnover rate of branching per WASP molecule, and it decreases the friction-like force caused by the binding of the moving surface with respect to the growing actin network.

Critical and speculative review of the roles of multi-protein complexes in starch biosynthesis in cereals.

PubMed

Crofts, Naoko; Nakamura, Yasunori; Fujita, Naoko

2017-09-01

Starch accounts for the majority of edible carbohydrate resources generated through photosynthesis. Amylopectin is the major component of starch and is one of highest-molecular-weight biopolymers. Rapid and systematic synthesis of frequently branched hydro-insoluble amylopectin and efficient accumulation into amyloplasts of cereal endosperm is crucial. The functions of multiple starch biosynthetic enzymes, including elongation, branching, and debranching enzymes, must be temporally and spatially coordinated. Accordingly, direct evidence of protein-protein interactions of starch biosynthetic enzymes were first discovered in developing wheat endosperm in 2004, and they have since been shown in the developing seeds of other cereals. This review article describes structural characteristics of starches as well as similarities and differences in protein complex formation among different plant species and among mutant plants that are deficient in specific starch biosynthetic enzymes. In addition, evidence for protein complexes that are involved in the initiation stages of starch biosynthesis is summarized. Finally, we discuss the significance of protein complexes and describe new methods that may elucidate the mechanisms and roles of starch biosynthetic enzyme complexes. Copyright © 2017 Elsevier B.V. All rights reserved.

Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics

PubMed Central

Kolaczkowski, Bryan; Thornton, Joseph W.

2009-01-01

Bayesian inference (BI) of phylogenetic relationships uses the same probabilistic models of evolution as its precursor maximum likelihood (ML), so BI has generally been assumed to share ML's desirable statistical properties, such as largely unbiased inference of topology given an accurate model and increasingly reliable inferences as the amount of data increases. Here we show that BI, unlike ML, is biased in favor of topologies that group long branches together, even when the true model and prior distributions of evolutionary parameters over a group of phylogenies are known. Using experimental simulation studies and numerical and mathematical analyses, we show that this bias becomes more severe as more data are analyzed, causing BI to infer an incorrect tree as the maximum a posteriori phylogeny with asymptotically high support as sequence length approaches infinity. BI's long branch attraction bias is relatively weak when the true model is simple but becomes pronounced when sequence sites evolve heterogeneously, even when this complexity is incorporated in the model. This bias—which is apparent under both controlled simulation conditions and in analyses of empirical sequence data—also makes BI less efficient and less robust to the use of an incorrect evolutionary model than ML. Surprisingly, BI's bias is caused by one of the method's stated advantages—that it incorporates uncertainty about branch lengths by integrating over a distribution of possible values instead of estimating them from the data, as ML does. Our findings suggest that trees inferred using BI should be interpreted with caution and that ML may be a more reliable framework for modern phylogenetic analysis. PMID:20011052

Long-branch attraction bias and inconsistency in Bayesian phylogenetics.

PubMed

Kolaczkowski, Bryan; Thornton, Joseph W

2009-12-09

Bayesian inference (BI) of phylogenetic relationships uses the same probabilistic models of evolution as its precursor maximum likelihood (ML), so BI has generally been assumed to share ML's desirable statistical properties, such as largely unbiased inference of topology given an accurate model and increasingly reliable inferences as the amount of data increases. Here we show that BI, unlike ML, is biased in favor of topologies that group long branches together, even when the true model and prior distributions of evolutionary parameters over a group of phylogenies are known. Using experimental simulation studies and numerical and mathematical analyses, we show that this bias becomes more severe as more data are analyzed, causing BI to infer an incorrect tree as the maximum a posteriori phylogeny with asymptotically high support as sequence length approaches infinity. BI's long branch attraction bias is relatively weak when the true model is simple but becomes pronounced when sequence sites evolve heterogeneously, even when this complexity is incorporated in the model. This bias--which is apparent under both controlled simulation conditions and in analyses of empirical sequence data--also makes BI less efficient and less robust to the use of an incorrect evolutionary model than ML. Surprisingly, BI's bias is caused by one of the method's stated advantages--that it incorporates uncertainty about branch lengths by integrating over a distribution of possible values instead of estimating them from the data, as ML does. Our findings suggest that trees inferred using BI should be interpreted with caution and that ML may be a more reliable framework for modern phylogenetic analysis.

Is Juvenile Hormone a potential mechanism that underlay the "branched Y-model"?

PubMed

Márquez-García, Armando; Canales-Lazcano, Jorge; Rantala, Markus J; Contreras-Garduño, Jorge

2016-05-01

Trade-offs are a central tenet in the life-history evolution and the simplest model to understand it is the "Y" model: the investment of one arm will affect the investment of the other arm. However, this model is by far more complex, and a "branched Y-model" is proposed: trade-offs could exist within each arm of the Y, but the mechanistic link is unknown. Here we used Tenebrio molitor to test if Juvenile Hormone (JH) could be a mechanistic link behind the "branched Y-model". Larvae were assigned to one of the following experimental groups: (1) low, (2) medium and (3) high doses of methoprene (a Juvenile Hormone analogue, JHa), (4) acetone (methoprene diluents; control one) or (5) näive (handled in the same way as other groups; control two). The JHa lengthened the time of development from larvae to pupae and larvae to adults, resulting in adults with a larger size. Males with medium and long JHa treatment doses were favored with female choice, but had smaller testes and fewer viable sperm. There were no differences between groups in regard to the number of spermatozoa of males, or the number of ovarioles or eggs of females. This results suggest that JH: (i) is a mechanistic link of insects "branched Y model", (ii) is a double ended-sword because it may not only provide benefits on reproduction but could also impose costs, and (iii) has a differential effect on each sex, being males more affected than females. Copyright © 2016 Elsevier Inc. All rights reserved.

Morphology-controlled cactus-like branched anatase TiO2 arrays with high light-harvesting efficiency for dye-sensitized solar cells

NASA Astrophysics Data System (ADS)

Wu, Wu-Qiang; Rao, Hua-Shang; Feng, Hao-Lin; Guo, Xin-Dong; Su, Cheng-Yong; Kuang, Dai-Bin

2014-08-01

The present work establishes a facile process for one-step hydrothermal growth of vertically aligned anatase cactus-like branched TiO2 (CBT) arrays on a transparent conducting oxide (TCO) substrate. Various CBT morphologies are obtained by adjusting the potassium titanium oxide oxalate (PTO) reactant concentration (from 0.05 M to 0.15 M) and this yields a morphologically-controllable branched TiO2 arrays geometry. The CBT arrays consist of a vertically oriented nanowire (NW) or nanosheet (NS) stem and a host of short nanorod (NR) branches. The hierarchical CBT arrays demonstrate their excellent candidatures as photoanodes, which are capable of exhibiting high light-harvesting efficiency in dye-sensitized solar cells (DSSCs). Consequently, DSSCs based on 7 μm long optimized CBT arrays (0.05 M PTO), which are assembled with high density and high aspect-ratio NR branches, exhibit an impressive power conversion efficiency of 6.43% under AM 1.5G one sun illumination. The high performance can be attributed to the prominent light-harvesting efficiency, resulting from larger surface area and superior light-scattering capability.

Resource reallocation patterns within Sagittaria trifolia inflorescences following differential pollination.

PubMed

Dai, Can; Luo, Wen-Jie; Gong, Yan-Bing; Liu, Fan; Wang, Zheng-Xiang

2018-04-30

Understanding resource allocation to reproduction, a key factor in life history tradeoffs, has long intrigued plant ecologists. Despite the recognized importance of understanding the movement of resources among flowers following variable pollination, the patterns of resource reallocation to plant reproductive organs have not been thoroughly addressed. In this study, we aimed to empirically explore how resources redistribute within inflorescences in response to differential pollination intensities. Using a common herb, Sagittaria trifolia, we conducted supplemental and controlled pollination for single, some, or all flowers in simple and complex inflorescences, and compared their resulting fruiting probabilities, seed production, and average seed masses. Pollen supplementation of a single flower significantly increased its fruiting probability; however, the same manipulation of an inflorescence did not increase its overall reproduction. Single pollen-supplemented flowers had a higher percentage fruit set than inflorescences receiving supplemental pollination. In complex inflorescences, supplemental pollination had no effect on the reproductive success of flowers on the lateral or main branches. We provided evidence of resource reallocation from controlled to pollen-supplemented flowers in simple inflorescences; however, resources were unlikely to be reallocated between the main and lateral branches in the complex inflorescences, suggesting that flowering branches represent integrated physiological units in S. trifolia. The results also demonstrated that single-flower supplemental pollination would exaggerate pollen limitation and lead to a biased understanding of a plant's reproductive status. © 2018 Botanical Society of America.

Very large cooperative effects in heterobimetallic titanium-chromium catalysts for ethylene polymerization/copolymerization.

PubMed

Liu, Shaofeng; Motta, Alessandro; Mouat, Aidan R; Delferro, Massimiliano; Marks, Tobin J

2014-07-23

The heterobimetallic complexes, (η(5)-indenyl)[1-Me2Si((t)BuN)TiCl2]-3-CnH2n-[N,N-bis(2-(ethylthio)ethyl)amine]CrCl3 (n = 0, Ti-C0-Cr(SNS); n = 2, Ti-C2-Cr(SNS); n = 6, Ti-C6-Cr(SNS)), (η(5)-indenyl)[1-Me2Si((t)BuN)TiCl2]-3-C2H4-[N,N-bis((o-OMe-C6H4)2P)amine]CrCl3 (Ti-C2-Cr(PNP)), and (η(5)-indenyl)[1-Me2Si((t)BuN)TiCl2]-3-C2H4-[N,N-bis((diethylamine)ethyl)-amine]CrCl3 (Ti-C2-Cr(NNN)), are synthesized, fully characterized, and employed as olefin polymerization catalysts. With ethylene as the feed and MAO as cocatalyst/activator, SNS-based complexes Ti-C0-Cr(SNS), Ti-C2-Cr(SNS), and Ti-C6-Cr(SNS) afford linear low-density polyethylenes (LLDPEs) with exclusive n-butyl branches (6.8-25.8 branches/1000 C), while under identical polymerization conditions Ti-C2-Cr(PNP) and Ti-C2-Cr(NNN) produce polyethylenes with heterogeneous branching (C2, C4, and C≥6) or negligible branching, respectively. Under identical ethylene polymerization conditions, Ti-C0-Cr(SNS) produces polyethylenes with higher activity (4.5× and 6.1×, respectively), Mn (1.3× and 1.8×, respectively), and branch density (1.4× and 3.8×, respectively), than Ti-C2-Cr(SNS) and Ti-C6-Cr(SNS). Versus a CGC(Et)Ti + SNSCr tandem catalyst, Ti-C0-Cr(SNS) yields polyethylene with somewhat lower activity, but with 22.6× higher Mn and 4.0× greater branching density under identical conditions. In ethylene +1-pentene competition experiments, Ti-C0-Cr(SNS) yields 5.5% n-propyl branches and 94.5% n-butyl branches at [1-pentene] = 0.1 M, and the estimated effective local concentration of 1-hexene is ∼8.6 M. In contrast, the tandem CGC(Et)Ti + SNSCr system yields 91.0% n-propyl branches under identical reaction conditions. The homopolymerization and 1-pentene competition results argue that close Ti···Cr spatial proximity together with weak C-H···Ti and C-H···S interactions significantly influence relative 1-hexene enchainment and chain transfer rates, supported by DFT computation, and that such effects are conversion insensitive but cocatalyst and solvent sensitive.

Relationships between root diameter, root length and root branching along lateral roots in adult, field-grown maize

PubMed Central

Wu, Qian; Pagès, Loïc; Wu, Jie

2016-01-01

Background and Aims Root diameter, especially apical diameter, plays an important role in root development and function. The variation in diameter between roots, and along roots, affects root structure and thus the root system’s overall foraging performance. However, the effect of diameter variation on root elongation, branching and topological connections has not been examined systematically in a population of high-order roots, nor along the roots, especially for mature plants grown in the field. Methods A method combining both excavation and analysis was applied to extract and quantify root architectural traits of adult, field-grown maize plants. The relationships between root diameter and other root architectural characteristics are analysed for two maize cultivars. Key Results The basal diameter of the lateral roots (orders 1–3) was highly variable. Basal diameter was partly determined by the diameter of the bearing segment. Basal diameter defined a potential root length, but the lengths of most roots fell far short of this. This was explained partly by differences in the pattern of diameter change along roots. Diameter tended to decrease along most roots, with the steepness of the gradient of decrease depending on basal diameter. The longest roots were those that maintained (or sometimes increased) their diameters during elongation. The branching density (cm–1) of laterals was also determined by the diameter of the bearing segment. However, the location of this bearing segment along the mother root was also involved – intermediate positions were associated with higher densities of laterals. Conclusions The method used here allows us to obtain very detailed records of the geometry and topology of a complex root system. Basal diameter and the pattern of diameter change along a root were associated with its final length. These relationships are especially useful in simulations of root elongation and branching in source–sink models. PMID:26744490

High quality draft genome sequences of Pseudomonas fulva DSM 17717 T, Pseudomonas parafulva DSM 17004 T and Pseudomonas cremoricolorata DSM 17059 T type strains

DOE PAGES

Peña, Arantxa; Busquets, Antonio; Gomila, Margarita; ...

2016-09-01

Pseudomonas has the highest number of species out of any genus of Gram-negative bacteria and is phylogenetically divided into several groups. The Pseudomonas putida phylogenetic branch includes at least 13 species of environmental and industrial interest, plant-associated bacteria, insect pathogens, and even some members that have been found in clinical specimens. In the context of the Genomic Encyclopedia of Bacteria and Archaea project, we present the permanent, high-quality draft genomes of the type strains of 3 taxonomically and ecologically closely related species in the Pseudomonas putida phylogenetic branch: Pseudomonas fulva DSM 17717 T, Pseudomonas parafulva DSM 17004 T and Pseudomonasmore » cremoricolorata DSM 17059T. All three genomes are comparable in size (4.6-4.9Mb), with 4,119-4,459 protein-coding genes. Average nucleotide identity based on BLAST comparisons and digital genome-to-genome distance calculations are in good agreement with experimental DNA-DNA hybridization results. The genome sequences presented here will be very helpful in elucidating the taxonomy, phylogeny and evolution of the Pseudomonas putida species complex.« less

A method for evaluating the murine pulmonary vasculature using micro-computed tomography.

PubMed

Phillips, Michael R; Moore, Scott M; Shah, Mansi; Lee, Clara; Lee, Yueh Z; Faber, James E; McLean, Sean E

2017-01-01

Significant mortality and morbidity are associated with alterations in the pulmonary vasculature. While techniques have been described for quantitative morphometry of whole-lung arterial trees in larger animals, no methods have been described in mice. We report a method for the quantitative assessment of murine pulmonary arterial vasculature using high-resolution computed tomography scanning. Mice were harvested at 2 weeks, 4 weeks, and 3 months of age. The pulmonary artery vascular tree was pressure perfused to maximal dilation with a radio-opaque casting material with viscosity and pressure set to prevent capillary transit and venous filling. The lungs were fixed and scanned on a specimen computed tomography scanner at 8-μm resolution, and the vessels were segmented. Vessels were grouped into categories based on lumen diameter and branch generation. Robust high-resolution segmentation was achieved, permitting detailed quantitation of pulmonary vascular morphometrics. As expected, postnatal lung development was associated with progressive increase in small-vessel number and arterial branching complexity. These methods for quantitative analysis of the pulmonary vasculature in postnatal and adult mice provide a useful tool for the evaluation of mouse models of disease that affect the pulmonary vasculature. Copyright © 2016 Elsevier Inc. All rights reserved.

High quality draft genome sequences of Pseudomonas fulva DSM 17717 T, Pseudomonas parafulva DSM 17004 T and Pseudomonas cremoricolorata DSM 17059 T type strains

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

Peña, Arantxa; Busquets, Antonio; Gomila, Margarita

Pseudomonas has the highest number of species out of any genus of Gram-negative bacteria and is phylogenetically divided into several groups. The Pseudomonas putida phylogenetic branch includes at least 13 species of environmental and industrial interest, plant-associated bacteria, insect pathogens, and even some members that have been found in clinical specimens. In the context of the Genomic Encyclopedia of Bacteria and Archaea project, we present the permanent, high-quality draft genomes of the type strains of 3 taxonomically and ecologically closely related species in the Pseudomonas putida phylogenetic branch: Pseudomonas fulva DSM 17717 T, Pseudomonas parafulva DSM 17004 T and Pseudomonasmore » cremoricolorata DSM 17059T. All three genomes are comparable in size (4.6-4.9Mb), with 4,119-4,459 protein-coding genes. Average nucleotide identity based on BLAST comparisons and digital genome-to-genome distance calculations are in good agreement with experimental DNA-DNA hybridization results. The genome sequences presented here will be very helpful in elucidating the taxonomy, phylogeny and evolution of the Pseudomonas putida species complex.« less

Epicormic Branches and Lumber Grade of Bottomland Oak

Treesearch

James S. Meadows

1995-01-01

Epicormic branches can be a serious problem in management of hardwood forests for high-quality sawtimber production. In one study in central Alabama, defects caused by epicormic branches that developed following a partial cutting resulted in a 13 percent reduction in the value of willow oak lumber. Production of epicormic branches along the boles of hardwood trees is...

Fucosylated chondroitin sulfate oligosaccharides exert anticoagulant activity by targeting at intrinsic tenase complex with low FXII activation: Importance of sulfation pattern and molecular size.

PubMed

Li, Junhui; Li, Shan; Yan, Lufeng; Ding, Tian; Linhardt, Robert J; Yu, Yanlei; Liu, Xinyue; Liu, Donghong; Ye, Xingqian; Chen, Shiguo

2017-10-20

Fucosylated chondroitin sulfates (fCSs) are structurally unusual glycosaminoglycans isolated from sea cucumbers that exhibit potent anticoagulant activity. These fCSs were isolated from sea cucumber, Isostichopus badionotus and Pearsonothuria graeffei. Fenton reaction followed by gel filtration chromatography afforded fCS oligosaccharides, with different sulfation patterns identified by mass and NMR spectroscopy, and these were used to clarify the relationship between the structures and the anticoagulant activities of fCSs. In vitro activities were measured by activated partial thromboplastin time (APTT), thrombin time (TT), thrombin and factor Xa inhibition, and activation of FXII. The results showed that free radicals preferentially acted on GlcA residues affording oligosaccharides that were purified from both fCSs. The inhibition of thrombin and factor X activities, mediated through antithrombin III and heparin cofactor II of fCSs oligosaccharides were affected by their molecular weight and fucose branches. Oligosaccharides with different sulfation patterns of the fucose branching had a similar ability to inhibit the FXa by the intrinsic factor Xase (factor IXa-VIIIa complex). Oligosaccharides with 2,4-O-sulfo fucose branches from fCS-Ib showed higher activities than ones with 3,4-O-disulfo branches obtained from fCS-Pg. Furthermore, a heptasaccharide is the minimum size oligosaccharide required for anticoagulation and FXII activation. This activity was absent for fCS oligosaccharides smaller than nonasaccharides. Molecular size and fucose branch sulfation are important for anticoagulant activity and reduction of size can reverse the activation of FXII caused by native fCSs. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Substrate specificities and intracellular distributions of three N-glycan processing enzymes functioning at a key branch point in the insect N-glycosylation pathway.

PubMed

Geisler, Christoph; Jarvis, Donald L

2012-03-02

Man(α1-6)[GlcNAc(β1-2)Man(α1-3)]ManGlcNAc(2) is a key branch point intermediate in the insect N-glycosylation pathway because it can be either trimmed by a processing β-N-acetylglucosaminidase (FDL) to produce paucimannosidic N-glycans or elongated by N-acetylglucosaminyltransferase II (GNT-II) to produce complex N-glycans. N-acetylglucosaminyltransferase I (GNT-I) contributes to branch point intermediate production and can potentially reverse the FDL trimming reaction. However, there has been no concerted effort to evaluate the relationships among these three enzymes in any single insect system. Hence, we extended our previous studies on Spodoptera frugiperda (Sf) FDL to include GNT-I and -II. Sf-GNT-I and -II cDNAs were isolated, the predicted protein sequences were analyzed, and both gene products were expressed and their acceptor substrate specificities and intracellular localizations were determined. Sf-GNT-I transferred N-acetylglucosamine to Man(5)GlcNAc(2), Man(3)GlcNAc(2), and GlcNAc(β1-2)Man(α1-6)[Man(α1-3)]ManGlcNAc(2), demonstrating its role in branch point intermediate production and its ability to reverse FDL trimming. Sf-GNT-II only transferred N-acetylglucosamine to Man(α1-6)[GlcNAc(β1-2)Man(α1-3)]ManGlcNAc(2), demonstrating that it initiates complex N-glycan production, but cannot use Man(3)GlcNAc(2) to produce hybrid or complex structures. Fluorescently tagged Sf-GNT-I and -II co-localized with an endogenous Sf Golgi marker and Sf-FDL co-localized with Sf-GNT-I and -II, indicating that all three enzymes are Golgi resident proteins. Unexpectedly, fluorescently tagged Drosophila melanogaster FDL also co-localized with Sf-GNT-I and an endogenous Drosophila Golgi marker, indicating that it is a Golgi resident enzyme in insect cells. Thus, the substrate specificities and physical juxtapositioning of GNT-I, GNT-II, and FDL support the idea that these enzymes function at the N-glycan processing branch point and are major factors determining the net outcome of the insect cell N-glycosylation pathway.

Precision Branching Ratio Measurement for the Superallowed β+ Emitter Ga62 and Isospin-Symmetry-Breaking Corrections in A≥62 Nuclei

NASA Astrophysics Data System (ADS)

Hyland, B.; Svensson, C. E.; Ball, G. C.; Leslie, J. R.; Achtzehn, T.; Albers, D.; Andreoiu, C.; Bricault, P.; Churchman, R.; Cross, D.; Dombsky, M.; Finlay, P.; Garrett, P. E.; Geppert, C.; Grinyer, G. F.; Hackman, G.; Hanemaayer, V.; Lassen, J.; Lavoie, J. P.; Melconian, D.; Morton, A. C.; Pearson, C. J.; Pearson, M. R.; Phillips, A. A.; Schumaker, M. A.; Smith, M. B.; Towner, I. S.; Valiente-Dobón, J. J.; Wendt, K.; Zganjar, E. F.

2006-09-01

A high-precision branching ratio measurement for the superallowed β+ decay of Ga62 was performed at the Isotope Separator and Accelerator radioactive ion beam facility. Nineteen γ rays emitted following β+ decay of Ga62 were identified, establishing the dominant superallowed branching ratio to be (99.861±0.011)%. Combined with recent half-life and Q-value measurements, this branching ratio yields a superallowed ft value of 3075.6±1.4s for Ga62 decay. These results demonstrate the feasibility of high-precision superallowed branching ratio measurements in the A≥62 mass region and provide the first stringent tests of the large isospin-symmetry-breaking effects predicted for these decays.

Branch-and-Bound algorithm applied to uncertainty quantification of a Boiling Water Reactor Station Blackout

DOE PAGES

Nielsen, Joseph; Tokuhiro, Akira; Hiromoto, Robert; ...

2015-11-13

Evaluation of the impacts of uncertainty and sensitivity in modeling presents a significant set of challenges in particular to high fidelity modeling. Computational costs and validation of models creates a need for cost effective decision making with regards to experiment design. Experiments designed to validate computation models can be used to reduce uncertainty in the physical model. In some cases, large uncertainty in a particular aspect of the model may or may not have a large impact on the final results. For example, modeling of a relief valve may result in large uncertainty, however, the actual effects on final peakmore » clad temperature in a reactor transient may be small and the large uncertainty with respect to valve modeling may be considered acceptable. Additionally, the ability to determine the adequacy of a model and the validation supporting it should be considered within a risk informed framework. Low fidelity modeling with large uncertainty may be considered adequate if the uncertainty is considered acceptable with respect to risk. In other words, models that are used to evaluate the probability of failure should be evaluated more rigorously with the intent of increasing safety margin. Probabilistic risk assessment (PRA) techniques have traditionally been used to identify accident conditions and transients. Traditional classical event tree methods utilize analysts’ knowledge and experience to identify the important timing of events in coordination with thermal-hydraulic modeling. These methods lack the capability to evaluate complex dynamic systems. In these systems, time and energy scales associated with transient events may vary as a function of transition times and energies to arrive at a different physical state. Dynamic PRA (DPRA) methods provide a more rigorous analysis of complex dynamic systems. Unfortunately DPRA methods introduce issues associated with combinatorial explosion of states. This study presents a methodology to address combinatorial explosion using a Branch-and-Bound algorithm applied to Dynamic Event Trees (DET), which utilize LENDIT (L – Length, E – Energy, N – Number, D – Distribution, I – Information, and T – Time) as well as a set theory to describe system, state, resource, and response (S2R2) sets to create bounding functions for the DET. The optimization of the DET in identifying high probability failure branches is extended to create a Phenomenological Identification and Ranking Table (PIRT) methodology to evaluate modeling parameters important to safety of those failure branches that have a high probability of failure. The PIRT can then be used as a tool to identify and evaluate the need for experimental validation of models that have the potential to reduce risk. Finally, in order to demonstrate this methodology, a Boiling Water Reactor (BWR) Station Blackout (SBO) case study is presented.« less

Tandem Carbocupration/Oxygenation of Terminal Alkynes

PubMed Central

Zhang, Donghui; Ready, Joseph M.

2008-01-01

A direct and general synthesis of α-branched aldehydes and their enol derivatives is described. Carbocupration of terminal alkynes and subsequent oxygenation with lithium tert-butyl peroxide generates a metallo-enolate. Trapping with various electrophiles provides α-branched aldehydes or stereo-defined trisubstituted enol esters or silyl ethers. The tandem carbocupration/oxygenation tolerates alkyl and silyl ethers, esters and tertiary amines. The reaction is effective with organocopper complexes derived from primary, secondary and tertiary Grignard reagents and from n-butyllithium. PMID:16321021

[Hybrid operating rooms: only for advanced endovascular procedures?].

PubMed

Verhoeven, E; Katsargyris, A; Töpel, I; Steinbauer, M

2013-10-01

The evolution of endovascular techniques has led to the concept of the "hybrid operating room" (hybrid OR). A hybrid OR combines the sterility of an OR in an operating theatre environment with a high-quality fixed imaging system. On the basis of these advantages it would be desirable that an angio-hybrid OR becomes a standard requirement for endovascular surgery. In Great Britain guidelines have already been published that require a hybrid OR even for normal endovascular management of the infrarenal aorta. However, in Germany there are no guidelines from professional societies or formal rules from the federal joint committee, thus in this article a classification of endovascular procedures according to their complexity and the necessary infrastructures are proposed in order to define particular procedures that should only be performed in an angio-hybrid OR. According to our experience, endovascular procedures can be classified into four categories based on their complexity and the requirements regarding fluoroscopy: level 1: standard EVAR, TEVAR, iliac and popliteal artery procedures; level 2: iliac branched (IBD) and standard (2 fenestrations for the renal arteries and a scallop for the superior mesenteric artery) fenestrated stent-grafting; level 3: more complex fenestrated procedures (three or four fenestrations); and level 4: branched stent-grafting for TAAA. At this moment it is still acceptable to perform level 1 and level 2 procedures outside of a hybrid OR. In our opinion, it is not recommended to perform level 3 and level 4 endovascular procedures without a hybrid OR. Georg Thieme Verlag KG Stuttgart · New York.

Intermittent maple syrup urine disease: two case reports.

PubMed

Axler, Olof; Holmquist, Peter

2014-02-01

The presenting symptoms and clinical course of 2 cases of intermittent maple syrup urine disease (MSUD) are described. Intermittent MSUD is a potentially life-threatening metabolic disorder caused by a deficiency of branched-chain α-keto acid dehydrogenase, the enzyme complex that decarboxylates the 3 branched-chain amino acids. In contrast to classic MSUD, children with the intermittent form show normal development with normal intelligence and, when asymptomatic, normal levels of branched-chain amino acids. Symptoms usually appear between 5 months and 2 years of age, when a trivial infection such as otitis media or viral gastroenteritis triggers catabolism of muscle protein. Intermittent MSUD should be suspected in cases of common infections with a clinically atypical course, especially in children displaying ataxia or marked drowsiness.

Absence of Complex I Implicates Rearrangement of the Respiratory Chain in European Mistletoe.

PubMed

Senkler, Jennifer; Rugen, Nils; Eubel, Holger; Hegermann, Jan; Braun, Hans-Peter

2018-05-21

The mitochondrial oxidative phosphorylation (OXPHOS) system, which is based on the presence of five protein complexes, is in the very center of cellular ATP production. Complexes I to IV are components of the respiratory electron transport chain that drives proton translocation across the inner mitochondrial membrane. The resulting proton gradient is used by complex V (the ATP synthase complex) for the phosphorylation of ADP. Occurrence of complexes I to V is highly conserved in eukaryotes, with exceptions being restricted to unicellular parasites that take up energy-rich compounds from their hosts. Here we present biochemical evidence that the European mistletoe (Viscum album), an obligate semi-parasite living on branches of trees, has a highly unusual OXPHOS system. V. album mitochondria completely lack complex I and have greatly reduced amounts of complexes II and V. At the same time, the complexes III and IV form remarkably stable respiratory supercomplexes. Furthermore, complexome profiling revealed the presence of 150 kDa complexes that include type II NAD(P)H dehydrogenases and an alternative oxidase. Although the absence of complex I genes in mitochondrial genomes of mistletoe species has recently been reported, this is the first biochemical proof that these genes have not been transferred to the nuclear genome and that this respiratory complex indeed is not assembled. As a consequence, the whole respiratory chain is remodeled. Our results demonstrate that, in the context of parasitism, multicellular life can cope with lack of one of the OXPHOS complexes and give new insights into the life strategy of mistletoe species. Copyright © 2018 Elsevier Ltd. All rights reserved.

Overview of the Advanced High Frequency Branch

NASA Technical Reports Server (NTRS)

Miranda, Felix A.

2015-01-01

This presentation provides an overview of the competencies, selected areas of research and technology development activities, and current external collaborative efforts of the NASA Glenn Research Center's Advanced High Frequency Branch.

Coherent Raman and Infrared Studies of Sulfur Trioxide

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

Chrysostom, Engelene; Vulpanovici, Nicolae; Masiello, Anthony

2001-07-02

High resolution (0.001 cm-1) coherent anti-Stokes Raman scattering (CARS) was used to observe the Q-branch structure of the IR-inactive n1 symmetric stretching mode of 32S 16O3 and its various 18O isotopomers. The v1 spectrum of 32S 16O3 reveals two intense Q-branch regions in the 1065-1067 cm-1 region, with surprisingly complex vibrational-rotational structure not resolved in earlier studies. Efforts to simulate this with a simple Fermi-resonance model involving v1 and 2v4 do not reproduce the spectral detail nor yield reasonable spectroscopic parameters. A more subtle combination of Fermi resonance and indirect Coriolis interactions with nearby states; 2v4 (l = 0, ?more » 2), v2+v4 (l = ? 1), 2v2 (l =0) is suspected and a determination of the location of these coupled states by high resolution infrared measurements is underway. At medium resolution (0.125 cm-1), the infrared spectra reveal Q-branch features from which approximate band origins are estimated for the v2, v3, v4 fundamental modes of 32S 18O3, 32S 18O2 16O and 32S 18O 16O2. These and literature data for 32S 16O3 are used to calculate force constants for SO3 and a comparison is made with similar values for SO2 and SO. The frequencies and force constants are in excellent agreement with a recent ab initio calculation by Martin. *In memory of Dr. Nicolae Vulpanovici (1968-2001)« less

Modeling Stepped Leaders Using a Time Dependent Multi-dipole Model and High-speed Video Data

NASA Astrophysics Data System (ADS)

Karunarathne, S.; Marshall, T.; Stolzenburg, M.; Warner, T. A.; Orville, R. E.

2012-12-01

In summer of 2011, we collected lightning data with 10 stations of electric field change meters (bandwidth of 0.16 Hz - 2.6 MHz) on and around NASA/Kennedy Space Center (KSC) covering nearly 70 km × 100 km area. We also had a high-speed video (HSV) camera recording 50,000 images per second collocated with one of the electric field change meters. In this presentation we describe our use of these data to model the electric field change caused by stepped leaders. Stepped leaders of a cloud to ground lightning flash typically create the initial path for the first return stroke (RS). Most of the time, stepped leaders have multiple complex branches, and one of these branches will create the ground connection for the RS to start. HSV data acquired with a short focal length lens at ranges of 5-25 km from the flash are useful for obtaining the 2-D location of these multiple branches developing at the same time. Using HSV data along with data from the KSC Lightning Detection and Ranging (LDAR2) system and the Cloud to Ground Lightning Surveillance System (CGLSS), the 3D path of a leader may be estimated. Once the path of a stepped leader is obtained, the time dependent multi-dipole model [ Lu, Winn,and Sonnenfeld, JGR 2011] can be used to match the electric field change at various sensor locations. Based on this model, we will present the time-dependent charge distribution along a leader channel and the total charge transfer during the stepped leader phase.

Survey of the Influence of the Width of Urban Branch Roads on the Meeting of Two-Way Vehicle Flows

PubMed Central

Chen, Qun; Zhao, Yunan; Pan, Shuangli; Wang, Yan

2016-01-01

Branch roads, which are densely distributed in cities, allow for the flow of local traffic and provide connections between the city and outlying areas. Branch roads are typically narrow, and two-way traffic flows on branch roads are thus affected when vehicles traveling in opposite directions meet. This study investigates the changes in the velocities of vehicles when they meet on two-way branch roads. Various widths of branch roads were selected, and their influence on traffic flows was investigated via a video survey. The results show that, depending on the average vehicle velocity, branch roads require different widths to prevent a large decrease in velocity when vehicles meet. When the velocity on a branch road is not high (e.g., the average velocity without meeting is approximately 6 m/s), appropriately increasing the road width will notably increase the meeting velocity. However, when the velocity is high (e.g., the average velocity without meeting is greater than 10 m/s), there is a large decrease in velocity when meeting even if the road surface is wide (6.5 m). This study provides a basis for selecting the width of urban branch roads and the simulation of bidirectional traffic on such roads. PMID:26881427

Survey of the Influence of the Width of Urban Branch Roads on the Meeting of Two-Way Vehicle Flows.

PubMed

Chen, Qun; Zhao, Yunan; Pan, Shuangli; Wang, Yan

2016-01-01

Branch roads, which are densely distributed in cities, allow for the flow of local traffic and provide connections between the city and outlying areas. Branch roads are typically narrow, and two-way traffic flows on branch roads are thus affected when vehicles traveling in opposite directions meet. This study investigates the changes in the velocities of vehicles when they meet on two-way branch roads. Various widths of branch roads were selected, and their influence on traffic flows was investigated via a video survey. The results show that, depending on the average vehicle velocity, branch roads require different widths to prevent a large decrease in velocity when vehicles meet. When the velocity on a branch road is not high (e.g., the average velocity without meeting is approximately 6 m/s), appropriately increasing the road width will notably increase the meeting velocity. However, when the velocity is high (e.g., the average velocity without meeting is greater than 10 m/s), there is a large decrease in velocity when meeting even if the road surface is wide (6.5 m). This study provides a basis for selecting the width of urban branch roads and the simulation of bidirectional traffic on such roads.

An Efficient Independence Sampler for Updating Branches in Bayesian Markov chain Monte Carlo Sampling of Phylogenetic Trees.

PubMed

Aberer, Andre J; Stamatakis, Alexandros; Ronquist, Fredrik

2016-01-01

Sampling tree space is the most challenging aspect of Bayesian phylogenetic inference. The sheer number of alternative topologies is problematic by itself. In addition, the complex dependency between branch lengths and topology increases the difficulty of moving efficiently among topologies. Current tree proposals are fast but sample new trees using primitive transformations or re-mappings of old branch lengths. This reduces acceptance rates and presumably slows down convergence and mixing. Here, we explore branch proposals that do not rely on old branch lengths but instead are based on approximations of the conditional posterior. Using a diverse set of empirical data sets, we show that most conditional branch posteriors can be accurately approximated via a [Formula: see text] distribution. We empirically determine the relationship between the logarithmic conditional posterior density, its derivatives, and the characteristics of the branch posterior. We use these relationships to derive an independence sampler for proposing branches with an acceptance ratio of ~90% on most data sets. This proposal samples branches between 2× and 3× more efficiently than traditional proposals with respect to the effective sample size per unit of runtime. We also compare the performance of standard topology proposals with hybrid proposals that use the new independence sampler to update those branches that are most affected by the topological change. Our results show that hybrid proposals can sometimes noticeably decrease the number of generations necessary for topological convergence. Inconsistent performance gains indicate that branch updates are not the limiting factor in improving topological convergence for the currently employed set of proposals. However, our independence sampler might be essential for the construction of novel tree proposals that apply more radical topology changes. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Expression and Functional Role of Sprouty-2 in Breast Morphogenesis

PubMed Central

Hilmarsdottir, Bylgja; Gustafsdottir, Sigrun M.; Franzdottir, Sigridur Rut; Arason, Ari Jon; Steingrimsson, Eirikur; Magnusson, Magnus K.; Gudjonsson, Thorarinn

2013-01-01

Branching morphogenesis is a mechanism used by many species for organogenesis and tissue maintenance. Receptor tyrosine kinases (RTKs), including epidermal growth factor receptor (EGFR) and the sprouty protein family are believed to be critical regulators of branching morphogenesis. The aim of this study was to analyze the expression of Sprouty-2 (SPRY2) in the mammary gland and study its role in branching morphogenesis. Human breast epithelial cells, breast tissue and mouse mammary glands were used for expression studies using immunoblotting, real rime PCR and immunohistochemistry. Knockdown of SPRY2 in the breast epithelial stem cell line D492 was done by lentiviral transduction of shRNA constructs targeting SPRY2. Three dimensional culture of D492 with or without endothelial cells was done in reconstituted basement membrane matrix. We show that in the human breast, SPRY2 is predominantly expressed in the luminal epithelial cells of both ducts and lobuli. In the mouse mammary gland, SPRY2 expression is low or absent in the virgin state, while in the pregnant mammary gland SPRY2 is expressed at branching epithelial buds with increased expression during lactation. This expression pattern is closely associated with the activation of the EGFR pathway. Using D492 which generates branching structures in three-dimensional (3D) culture, we show that SPRY2 expression is low during initiation of branching with subsequent increase throughout the branching process. Immunostaining locates expression of phosphorylated SPRY2 and EGFR at the tip of lobular-like, branching ends. SPRY2 knockdown (KD) resulted in increased migration, increased pERK and larger and more complex branching structures indicating a loss of negative feedback control during branching morphogenesis. In D492 co-cultures with endothelial cells, D492 SPRY2 KD generates spindle-like colonies that bear hallmarks of epithelial to mesenchymal transition. These data indicate that SPRY2 is an important regulator of branching morphogenesis and epithelial to mesenchymal transition in the mammary gland. PMID:23573284

Expression and functional role of sprouty-2 in breast morphogenesis.

PubMed

Sigurdsson, Valgardur; Ingthorsson, Saevar; Hilmarsdottir, Bylgja; Gustafsdottir, Sigrun M; Franzdottir, Sigridur Rut; Arason, Ari Jon; Steingrimsson, Eirikur; Magnusson, Magnus K; Gudjonsson, Thorarinn

2013-01-01

Branching morphogenesis is a mechanism used by many species for organogenesis and tissue maintenance. Receptor tyrosine kinases (RTKs), including epidermal growth factor receptor (EGFR) and the sprouty protein family are believed to be critical regulators of branching morphogenesis. The aim of this study was to analyze the expression of Sprouty-2 (SPRY2) in the mammary gland and study its role in branching morphogenesis. Human breast epithelial cells, breast tissue and mouse mammary glands were used for expression studies using immunoblotting, real rime PCR and immunohistochemistry. Knockdown of SPRY2 in the breast epithelial stem cell line D492 was done by lentiviral transduction of shRNA constructs targeting SPRY2. Three dimensional culture of D492 with or without endothelial cells was done in reconstituted basement membrane matrix. We show that in the human breast, SPRY2 is predominantly expressed in the luminal epithelial cells of both ducts and lobuli. In the mouse mammary gland, SPRY2 expression is low or absent in the virgin state, while in the pregnant mammary gland SPRY2 is expressed at branching epithelial buds with increased expression during lactation. This expression pattern is closely associated with the activation of the EGFR pathway. Using D492 which generates branching structures in three-dimensional (3D) culture, we show that SPRY2 expression is low during initiation of branching with subsequent increase throughout the branching process. Immunostaining locates expression of phosphorylated SPRY2 and EGFR at the tip of lobular-like, branching ends. SPRY2 knockdown (KD) resulted in increased migration, increased pERK and larger and more complex branching structures indicating a loss of negative feedback control during branching morphogenesis. In D492 co-cultures with endothelial cells, D492 SPRY2 KD generates spindle-like colonies that bear hallmarks of epithelial to mesenchymal transition. These data indicate that SPRY2 is an important regulator of branching morphogenesis and epithelial to mesenchymal transition in the mammary gland.

High-precision branching-ratio measurement for the superallowed β+ emitter 26Alm

NASA Astrophysics Data System (ADS)

Finlay, P.; Ball, G. C.; Leslie, J. R.; Svensson, C. E.; Andreoiu, C.; Austin, R. A. E.; Bandyopadhyay, D.; Cross, D. S.; Demand, G.; Djongolov, M.; Ettenauer, S.; Garrett, P. E.; Green, K. L.; Grinyer, G. F.; Hackman, G.; Leach, K. G.; Pearson, C. J.; Phillips, A. A.; Rand, E. T.; Sumithrarachchi, C. S.; Triambak, S.; Williams, S. J.

2012-05-01

A high-precision branching-ratio measurement for the superallowed β+ emitter 26Alm was performed at the TRIUMF-ISAC radioactive ion beam facility. An upper limit of ⩽12 ppm at 90% confidence level was found for the second forbidden β+ decay of 26Alm to the 21+ state at 1809 keV in 26Mg. An inclusive upper limit of ⩽15 ppm at 90% confidence level was found when considering all possible nonanalog β+/EC decay branches of 26Alm, resulting in a superallowed branching ratio of 100.0000-0.0015+0%.

Growth habit of the late Paleozoic rhizomorphic tree-lycopsid family Diaphorodendraceae: phylogenetic, evolutionary, and paleoecological significance.

PubMed

Dimichele, William A; Elrick, Scott D; Bateman, Richard M

2013-08-01

Rhizomorphic lycopsids evolved the tree habit independently of all other land plants. Newly discovered specimens allow radical revision of our understanding of the growth architectures of the extinct Paleozoic sister-genera Synchysidendron and Diaphorodendron. Detailed descriptions of six remarkable adpression specimens from the Pennsylvanian of the USA and three casts from the late Mississippian of Scotland are used to revise and reanalyze a previously published morphological cladistic matrix and to reinterpret their remarkable growth forms. Contrary to previous assertions, Synchysidendron resembled Diaphorodendron in having a distinct and relatively complex growth habit that emphasized serially homologous, closely spaced, deciduous lateral branches at the expense of reduced monocarpic crown branches. Lateral branches originated through several strongly anisotomous dichotomies before producing during extended periods large numbers of Achlamydocarpon strobili. The comparatively large diameter of abscission scars remaining on the main trunk and the emergence of branches above the horizontal plane suggest that the lateral branch systems were robust. Lateral branches were borne in two opposite rows on the main trunk and continued upward into an isotomously branched, determinate crown; their striking distichous arrangement caused preferred orientation of fallen trunks on bedding planes. This discovery identifies the plagiotropic growth habit, dominated by serial lateral branches, as ubiquitous in the Diaphorodendraceae and also as unequivocally primitive within Isoetales s.l., a conclusion supported by both the revised morphological cladistic analysis and relative first appearances of taxa in the fossil record. Previously assumed complete homology between crown branching in Lepidodendraceae and that of all earlier-divergent genera requires reassessment. Saltational phenotypic transitions via modification of key developmental switches remains the most credible explanation for architectural evolution in the group. The resulting architecture allowed Diaphorodendraceae to co-dominate disturbed, clastic, equatorial wetlands from the Asbian to the Early Permian.

Evaluation of the cognitive effects of travel technique in complex real and virtual environments.

PubMed

Suma, Evan A; Finkelstein, Samantha L; Reid, Myra; V Babu, Sabarish; Ulinski, Amy C; Hodges, Larry F

2010-01-01

We report a series of experiments conducted to investigate the effects of travel technique on information gathering and cognition in complex virtual environments. In the first experiment, participants completed a non-branching multilevel 3D maze at their own pace using either real walking or one of two virtual travel techniques. In the second experiment, we constructed a real-world maze with branching pathways and modeled an identical virtual environment. Participants explored either the real or virtual maze for a predetermined amount of time using real walking or a virtual travel technique. Our results across experiments suggest that for complex environments requiring a large number of turns, virtual travel is an acceptable substitute for real walking if the goal of the application involves learning or reasoning based on information presented in the virtual world. However, for applications that require fast, efficient navigation or travel that closely resembles real-world behavior, real walking has advantages over common joystick-based virtual travel techniques.

Fast and Accurate Circuit Design Automation through Hierarchical Model Switching.

PubMed

Huynh, Linh; Tagkopoulos, Ilias

2015-08-21

In computer-aided biological design, the trifecta of characterized part libraries, accurate models and optimal design parameters is crucial for producing reliable designs. As the number of parts and model complexity increase, however, it becomes exponentially more difficult for any optimization method to search the solution space, hence creating a trade-off that hampers efficient design. To address this issue, we present a hierarchical computer-aided design architecture that uses a two-step approach for biological design. First, a simple model of low computational complexity is used to predict circuit behavior and assess candidate circuit branches through branch-and-bound methods. Then, a complex, nonlinear circuit model is used for a fine-grained search of the reduced solution space, thus achieving more accurate results. Evaluation with a benchmark of 11 circuits and a library of 102 experimental designs with known characterization parameters demonstrates a speed-up of 3 orders of magnitude when compared to other design methods that provide optimality guarantees.

Computer models of complex multiloop branched pipeline systems

NASA Astrophysics Data System (ADS)

Kudinov, I. V.; Kolesnikov, S. V.; Eremin, A. V.; Branfileva, A. N.

2013-11-01

This paper describes the principal theoretical concepts of the method used for constructing computer models of complex multiloop branched pipeline networks, and this method is based on the theory of graphs and two Kirchhoff's laws applied to electrical circuits. The models make it possible to calculate velocities, flow rates, and pressures of a fluid medium in any section of pipeline networks, when the latter are considered as single hydraulic systems. On the basis of multivariant calculations the reasons for existing problems can be identified, the least costly methods of their elimination can be proposed, and recommendations for planning the modernization of pipeline systems and construction of their new sections can be made. The results obtained can be applied to complex pipeline systems intended for various purposes (water pipelines, petroleum pipelines, etc.). The operability of the model has been verified on an example of designing a unified computer model of the heat network for centralized heat supply of the city of Samara.

Pathogenic bacteria and microbial-source tracking markers in Brandywine Creek Basin, Pennsylvania and Delaware, 2009-10

USGS Publications Warehouse

Duris, Joseph W.; Reif, Andrew G.; Olson, Leif E.; Johnson, Heather E.

2011-01-01

The City of Wilmington, Delaware, is in the downstream part of the Brandywine Creek Basin, on the main stem of Brandywine Creek. Wilmington uses this stream, which drains a mixed-land-use area upstream, for its main drinking-water supply. Because the stream is used for drinking water, Wilmington is in need of information about the occurrence and distribution of specific fecally derived pathogenic bacteria (disease-causing bacteria) and their relations to commonly measured fecal-indicator bacteria (FIB), as well as information regarding the potential sources of the fecal pollution and pathogens in the basin. This study focused on five routinely sampled sites within the basin, one each on the West Branch and the East Branch of Brandywine Creek and at three on the main stem below the confluence of the West and East Branches. These sites were sampled monthly for 1 year. Targeted event samples were collected on two occasions during high flow and two occasions during normal flow. On the basis of this study, high flows in the Brandywine Creek Basin were related to increases in FIB densities, and in the frequency of selected pathogen and source markers, in the West Branch and main stem of Brandywine Creek, but not in the East Branch. Water exceeding the moderate fullbody-contact single-sample recreational water-quality criteria (RWQC) for Escherichia coli (E. coli) was more likely to contain selected markers for pathogenic E. coli (eaeA,stx1, and rfbO157 gene markers) and bovine fecal sources (E. hirae and LTIIa gene markers), whereas samples exceeding the enterococci RWQC were more likely to contain the same pathogenic markers but also were more likely to carry a marker indicative of human source (esp gene marker). On four sample dates, during high flow between October and March, the West Branch was the only observed potential contributor of selected pathogen and bovine source markers to the main stem of Brandywine Creek. Indeed, the stx2 marker, which indicates a highly virulent type of pathogenic E. coli, was found only in the West Branch and main stem at high flow but was not found in the East Branch under similar conditions. However, it must be noted that throughout the entire year of sampling there were occasions, during both high and normal flows, when both the East and West Branches were potential contributors of pathogen and microbial-source tracking markers to the main stem. Therefore, this study indicates that under selected conditions (high flow, October through March), West Branch Brandywine Creek Basin was the most likely source of elevated FIB densities in the main stem. These elevated densities are associated with more frequent detection of selected pathogenic E. coli markers (rfbO157 stx1) and are associated with MST markers of bovine source. However, during other times of the year, both the West Branch and East Branch Basins are acting as potential sources of FIB and fecally derived pathogens.

Structural basis of Arp2/3 complex inhibition by GMF, Coronin, and Arpin

PubMed Central

Sokolova, Olga S.; Chemeris, Angelina; Guo, Siyang; Alioto, Salvatore L.; Gandhi, Meghal; Padrick, Shae; Pechnikova, Evgeniya; David, Violaine; Gautreau, Alexis; Goode, Bruce L.

2017-01-01

The evolutionarily conserved Arp2/3 complex plays a central role in nucleating the branched actin filament arrays that drive cell migration, endocytosis, and other processes. To better understand Arp2/3 complex regulation, we used single particle electron microscopy to compare the structures of Arp2/3 complex bound to three different inhibitory ligands: GMF, Coronin, and Arpin. Although the three inhibitors have distinct binding sites on Arp2/3 complex, they each induced an ‘open’ nucleation-inactive conformation. Coronin promoted a standard (previously described) open conformation of Arp2/3 complex, with the N-terminal β-propeller domain of Coronin positioned near the p35/ARPC2 subunit of Arp2/3 complex. GMF induced two distinct open conformations of Arp2/3 complex, which correlated with two suggested binding sites for GMF. Further, GMF synergized with Coronin in inhibiting actin nucleation by Arp2/3 complex. Arpin, which uses VCA-related acidic (A) motifs to interact with the Arp2/3 complex, induced the standard open conformation, and two new masses appeared at positions near Arp2 and Arp3. Further, Arpin showed additive inhibitory effects on Arp2/3 complex with Coronin and GMF. Together, these data suggest that Arp2/3 complex conformation is highly polymorphic and that its activities can be controlled combinatorially by different inhibitory ligands. PMID:27939292

The three-dimensional feto-maternal vascular interrelationship during early bovine placental development: a scanning electron microscopical study

PubMed Central

PFARRER, CHRISTIANE; EBERT, BRIGITTE; MIGLINO, MARIA ANGELICA; KLISCH, KARL; LEISER, RUDOLF

2001-01-01

Both the fetal and maternal microvasculature of bovine placentomes was examined by scanning electron microscopy of vascular casts. So far the development of the vascular architecture of the bovine placentome in early gestation has only been studied 2-dimensionally due to technical difficulties arising from the fragility of the early placental blood vessels. Repeated experiments led to the selection of the microvascular corrosion casts presented here. The vasculature of the maternal compartment is supplied by large caruncular stalk or spiral arteries, which release short maternal stem arteries. In the 3rd month of gestation, these arteries branch into several arterioles at their base, thus providing the vascular framework for the lower part of the septal walls of the primary crypts. In the 4th month, due to progressive longitudinal growth of the stem arteries, branching into arterioles occurs not only at the base, but over the whole length of the stem arteries. These arterioles supply the capillary complexes of the septa which resemble the major part of the septal vasculature and face the secondary crypts. Further indentation results in the formation of tertiary crypt capillary complexes, encircling the earlier secondary unit. From the 6th month of gestation the architecture resembles the fully developed maternal placenta with stem arteries running directly to the fetal side to branch into 4 to 6 arterioles, which turn back to enter secondary and tertiary septa. Maternal venules, collecting the blood from the capillary bed of secondary and tertiary septa, converge onto stem veins leaving the caruncle via branches of the uterine vein. The fetal part of the placentome is supplied by the cotyledonary arteries, which branch into fetal stem arteries that are the tributary to single villous trees. Over their whole course towards the maternal side, these give off arterioles entering secondary villi. The tertiary or terminal villous vasculature consists of capillaries, which are organised in serial capillary loops. This system is progressively elaborated in the course of gestation. In the 4th month there are only finger-like loops, whereas from the 6th month large fan-like structures can be observed. In early gestation the maternal and fetal blood vessels meet predominantly in a countercurrent fashion, changing to the less efficient crosscurrent exchange when the tertiary unit develops. These results indicate the development of a highly elaborated fetomaternal villous-crypt exchange system, already established in the 1st half of gestation, thus meeting the increasing needs of the fetus. PMID:11430698

Protein-protein interactions among enzymes of starch biosynthesis in high-amylose barley genotypes reveal differential roles of heteromeric enzyme complexes in the synthesis of A and B granules.

PubMed

Ahmed, Zaheer; Tetlow, Ian J; Ahmed, Regina; Morell, Matthew K; Emes, Michael J

2015-04-01

The present study investigated the role of protein phosphorylation, and protein complex formation between key enzymes of amylopectin synthesis, in barley genotypes exhibiting "high amylose" phenotypes. Starch branching enzyme (SBE) down-regulated lines (ΔSBEIIa and ΔSBEIIb), starch synthase (SS)IIa (ssiia(-), sex6) and SSIII (ssiii(-), amo1) mutants were compared to a reference genotype, OAC Baxter. Down-regulation of either SBEIIa or IIb caused pleiotropic effects on SSI and starch phosphorylase (SP) and resulted in formation of novel protein complexes in which the missing SBEII isoform was substituted by SBEI and SP. In the ΔSBEIIb down-regulated line, soluble SP activity was undetectable. Nonetheless, SP was incorporated into a heteromeric protein complex with SBEI and SBEIIa and was readily detected in starch granules. In amo1, unlike other mutants, the data suggest that both SBEIIa and SBEIIb are in a protein complex with SSI and SSIIa. In the sex6 mutant no protein complexes involving SBEIIa or SBEIIb were detected in amyloplasts. Studies with Pro-Q Diamond revealed that GBSS, SSI, SSIIa, SBEIIb and SP are phosphorylated in their granule bound state. Alteration in the granule proteome in ΔSBEIIa and ΔSBEIIb lines, suggests that different protein complexes are involved in the synthesis of A and B granules. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

USSR Report Agriculture.

DTIC Science & Technology

1986-04-24

and its intensification, especially in such branches as poultry raising and swine breeding, have become possible as a result of the rapid development...vitamins and other components are being allocated to large . livestock husbandry complexes and poultry factories mainly for the production of mixed...microelements and other biologically active substances). Analysis has shown that large livestock complexes and poultry factories, owing to the low

Gas-analytic measurement complexes of Baikal atmospheric-limnological observatory

NASA Astrophysics Data System (ADS)

Pestunov, D. A.; Shamrin, A. M.; Shmargunov, V. P.; Panchenko, M. V.

2015-11-01

The paper presents the present-day structure of stationary and mobile hardware-software gas-analytical complexes of Baikal atmospheric-limnological observatory (BALO) Siberian Branch Russian Academy of Sciences (SB RAS), designed to study the processes of gas exchange of carbon-containing gases in the "atmosphere-water" system, which are constantly updated to include new measuring and auxiliary instrumentation.

Impacts of autochthonous marine branched GDGTs on related paleo- environmental proxies: a preliminary study

NASA Astrophysics Data System (ADS)

Dong, L.; Li, L.; Li, Q.; Zhang, C.

2014-12-01

Two proxies derived from branched glycerol dialkyl glycerol tetraethers (brGDGTs)-, the methylation index of branched tetraethers (MBT) and the cyclization ratio of branched tetraethers (CBT), are often used to reconstruct paleo mean annual air temperature (MAAT) and soil pH on the belief of their terrestrial origin. However, mounting evidence indicates the existence of autochthonous brGDGTs in marine environments，which may affect MAAT reconstruction and the use of other related paleoenvironmental proxies. Here we provide high resolution profiles of brGDGTs in a sedimentary core (MD05-2896/7) from the southern South China Sea, which include MBT and CBT indices as well as the branched and isoprenoid tetraether (BIT) index. The BIT results varied systematically with glacial-interglacial cycles, with values distinctly lower (<0.1) during the interglacial periods (MIS 1 and MIS 5) than during the glacial periods (MIS 2, MIS, 3, MIS 4 and MIS 6). Also distinct is the MBT/CBT-derived temperature, which show lower values during the interglacial periods but higher values during the glacial periods. We hypothesize that the lower MBT/CBT-derived temperature during the interglacial periods reflects subsurface water column temperature registered by autochthonous brGDGTs produced in situ marine conditions, whereas the higher MBT/CBT derived-temperature during the glacial periods reflects terrestrial MAAT because of the overwhelming input of brGDGTs from land when sea level was low. Similarly, the CBT-derived pH appears to have been overprinted also by the sea water signal of the interglacials but affected mostly by precipitation during the glacial intervals, showing patterns similar to or as a positive response to the southern hemispheric climate oscillation due to teleconnection. Our study demonstrates the complexity of brGDGT occurrence in marine environments and suggests that the MBT/CBT proxy should not be directly employed for the reconstruction of terrestrial MAAT at marine settings when BIT value is lower than 0.1.

Polyphosphazene Based Star-Branched and Dendritic Molecular Brushes.

PubMed

Henke, Helena; Posch, Sandra; Brüggemann, Oliver; Teasdale, Ian

2016-05-01

A new synthetic procedure is described for the preparation of poly(organo)phosphazenes with star-branched and star dendritic molecular brush type structures, thus describing the first time it has been possible to prepare controlled, highly branched architectures for this type of polymer. Furthermore, as a result of the extremely high-arm density generated by the phosphazene repeat unit, the second-generation structures represent quite unique architectures for any type of polymer. Using two relativity straight forward iterative syntheses it is possible to prepare globular highly branched polymers with up to 30 000 functional end groups, while keeping relatively narrow polydispersities (1.2-1.6). Phosphine mediated polymerization of chlorophosphoranimine is first used to prepare three-arm star polymers. Subsequent substitution with diphenylphosphine moieties gives poly(organo)phosphazenes to function as multifunctional macroinitiators for the growth of a second generation of polyphosphazene arms. Macrosubstitution with Jeffamine oligomers gives a series of large, water soluble branched macromolecules with high-arm density and hydrodynamic diameters between 10 and 70 nm. © 2016 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Developmental Framework for Complex Plasmodesmata Formation Revealed by Large-Scale Imaging of the Arabidopsis Leaf Epidermis[W

PubMed Central

Fitzgibbon, Jessica; Beck, Martina; Zhou, Ji; Faulkner, Christine; Robatzek, Silke; Oparka, Karl

2013-01-01

Plasmodesmata (PD) form tubular connections that function as intercellular communication channels. They are essential for transporting nutrients and for coordinating development. During cytokinesis, simple PDs are inserted into the developing cell plate, while during wall extension, more complex (branched) forms of PD are laid down. We show that complex PDs are derived from existing simple PDs in a pattern that is accelerated when leaves undergo the sink–source transition. Complex PDs are inserted initially at the three-way junctions between epidermal cells but develop most rapidly in the anisocytic complexes around stomata. For a quantitative analysis of complex PD formation, we established a high-throughput imaging platform and constructed PDQUANT, a custom algorithm that detected cell boundaries and PD numbers in different wall faces. For anticlinal walls, the number of complex PDs increased with increasing cell size, while for periclinal walls, the number of PDs decreased. Complex PD insertion was accelerated by up to threefold in response to salicylic acid treatment and challenges with mannitol. In a single 30-min run, we could derive data for up to 11k PDs from 3k epidermal cells. This facile approach opens the door to a large-scale analysis of the endogenous and exogenous factors that influence PD formation. PMID:23371949

Phosphorus and carbon availability regulate structural composition and complexity of AM fungal mycelium.

PubMed

Olsson, Ola; Olsson, Pål Axel; Hammer, Edith C

2014-08-01

The regulation of the structural composition and complexity of the mycelium of arbuscular mycorrhizal (AM) fungi is not well understood due to their obligate biotrophic nature. The aim of this study was to investigate the structure of extraradical mycelium at high and low availability of carbon (C) to the roots and phosphorus (P) to the fungus. We used monoxenic cultures of the AM fungus Rhizophagus irregularis (formerly Glomus intraradices) with transformed carrot roots as the host in a cultivation system including a root-free compartment into which the extraradical mycelium could grow. We found that high C availability increased hyphal length and spore production and anastomosis formation within individual mycelia. High P availability increased the formation of branched absorbing structures and reduced spore production and the overall length of runner hyphae. The complexity of the mycelium, as indicated by its fractal dimensions, increased with both high C and P availability. The results indicate that low P availability induces a growth pattern that reflects foraging for both P and C. Low C availability to AM roots could still support the explorative development of the mycelium when P availability was low. These findings help us to better understand the development of AM fungi in ecosystems with high P input and/or when plants are subjected to shading, grazing or any management practice that reduces the photosynthetic ability of the plant.

Effect of starvation and exercise on actual and total activity of the branched-chain 2-oxo acid dehydrogenase complex in rat tissues.

PubMed Central

Wagenmakers, A J; Schepens, J T; Veerkamp, J H

1984-01-01

Starvation does not change the actual activity per g of tissue of the branched-chain 2-oxo acid dehydrogenase in skeletal muscles, but affects the total activity to a different extent, depending on the muscle type. The activity state (proportion of the enzyme present in the active state) does not change in diaphragm and decreases in quadriceps muscle. Liver and kidney show an increase of both activities, without a change of the activity state. In heart and brain no changes were observed. Related to organ wet weights, the actual activity present in the whole-body muscle mass decreases on starvation, whereas the activities present in liver and kidney do not change, or increase slightly. Exercise (treadmill-running) of untrained rats for 15 and 60 min causes a small increase of the actual activity and the activity state of the branched-chain 2-oxo acid dehydrogenase complex in heart and skeletal muscle. Exercise for 1 h, furthermore, increased the actual and the total activity in liver and kidney, without a change of the activity state. In brain no changes were observed. The actual activity per g of tissue in skeletal muscle was less than 2% of that in liver and kidney, both before and after exercise and starvation. Our data indicate that the degradation of branched-chain 2-oxo acids predominantly occurs in liver and to a smaller extent in kidney and skeletal muscle in fed, starved and exercised rats. PMID:6508743

Branched hybrid vessel: in vitro loaded hydrodynamic forces influence the tissue architecture.

PubMed

Kobashi, T; Matsuda, T

2000-01-01

This study was conducted to investigate how a continuous load of hydrodynamic stresses influences the tissue architecture of a branched hybrid vessel in vitro. Tubular hybrid medial tissue of small (3 mm) and large (6 mm) diameters, prepared by thermal gelation of a cold mixed solution of bovine smooth muscle cells (SMCs) and type I collagen in glass molds, was assembled into a branched hybrid medial tissue by end-to-side anastomosis. After a 2-week culture period, bovine endothelial cells (ECs) were seeded onto the luminal surface. The branched hybrid vessel was connected to a mock circulatory loop system and tested for two modes of flow: 1) low flow rate for 24 h, 2) high flow rate for 24 or 72 h. After exposure to a low flow rate for 24 h, cobblestone appearance of the ECs was dominant. After exposure to a high flow rate, EC alignment in the direction of flow was observed in the branch region, except at the region of predicted flow separation where ECs retained their polygonal configuration. Elongation of SMCs with no preferential orientation was observed in the case of vessels exposed to a high flow rate for 24 h, and circumferential orientation was prominent in those exposed to a high flow rate for 72 h. On the other hand, collagen fibrils exhibited no preferential orientation in either case. After injection of Evans blue-albumin conjugate into the circulating medium, the luminal surface of the hybrid vessel exposed to a high flow rate for 24 h was examined by confocal laser scanning microscopy. The fluorescence intensity was low at the high shear zone in the branch region, while at the flow separation region it was very high, indicating the increased albumin permeability at the latter region. These findings reflect region-specific tissue architecture in the branch region, in response to the local flow pattern, and may provide an in vitro atherosclerosis model as well as a fundamental basis for the development of functional branched hybrid grafts.

A Review of the Scattering-Parameter Extraction Method with Clarification of Ambiguity Issues in Relation to Metamaterial Homogenization

NASA Astrophysics Data System (ADS)

Arslanagic, S.; Hansen, T. V.; Mortensen, N. A.; Gregersen, A. H.; Sigmund, O.; Ziolkowski, R. W.; Breinbjerg, O.

2013-04-01

The scattering parameter extraction method of metamaterial homogenization is reviewed to show that the only ambiguity is the one related to the choice of the branch of the complex logarithmic function (or the complex inverse cosine function), whereas it has no ambiguity for the sign of the wave number and intrinsic impedance. While the method indeed yields two signs of the intrinsic impedance, and thus the wave number, the signs are dependent, and moreover, both sign combinations lead to the same permittivity and permeability, and are thus permissible. This observation is in distinct contrast to a number of statements in the literature where the correct sign of the intrinsic impedance and wave number, resulting from the scattering parameter method, is chosen by imposing additional physical requirements such as passivity. The scattering parameter method is reviewed through an investigation of a uniform plane wave normally incident on a planar slab in free-space, and the severity of the branch ambiguity is illustrated through simulations of a known metamaterial realization. Several approaches for proper branch selection are reviewed and their suitability to metamaterial samples is discussed.

The complex role of branched chain amino acids in diabetes and cancer.

PubMed

O'Connell, Thomas M

2013-10-14

The obesity and diabetes epidemics are continuing to spread across the globe. There is increasing evidence that diabetes leads to a significantly higher risk for certain types of cancer. Both diabetes and cancer are characterized by severe metabolic perturbations and the branched chain amino acids (BCAAs) appear to play a significant role in both of these diseases. These essential amino acids participate in a wide variety of metabolic pathways, but it is now recognized that they are also critical regulators of a number of cell signaling pathways. An elevation in branched chain amino acids has recently been shown to be significantly correlated with insulin resistance and the future development of diabetes. In cancer, the normal demands for BCAAs are complicated by the conflicting needs of the tumor and the host. The severe muscle wasting syndrome experience by many cancer patients, known as cachexia, has motivated the use of BCAA supplementation. The desired improvement in muscle mass must be balanced by the need to avoid providing materials for tumor proliferation. A better understanding of the complex functions of BCAAs could lead to their use as biomarkers of the progression of certain cancers in diabetic patients.

Mechanics of Lamellipodia

NASA Astrophysics Data System (ADS)

Quint, D. A.; Schwarz, J. M.

2008-03-01

The actin cytoskeleton is a morphologically-complex assembly of cross-linked F-actin filaments. The cytoskeleton provides rigidity for the cell within appropriate time scales so that it can change its shape to, for example, crawl along surfaces. In addition to cross-linking proteins, many other proteins are involved in the assembly of the actin cytoskeleton such as branching proteins, capping proteins, and severing proteins. Presumably these proteins work cooperatively toward the dynamic formation of rigidity. We will initially focus on the role of branching proteins. The F-actin filaments in lamellipodia---protrusions of the mobile edge of a crawling cell---have some overall orientation due to the branching. Branched filaments emerge at a 70 degree angle from the mother filament's growing end.^1 This overall orientation is modelled as an anisotropy in an effective medium theory determining the cytoskeleton's elasticity in the static regime. The potential for a splay rigid phase, in addition to a rigid phase, is also investigated. ^1T. M. Svitkina and G. G. Borisy, J. Cell Biol. 145, 1009 (1999).

Tectonic position and geological manifestations of the Mogod (Central Mongolia), January 5, 1967, earthquake (a view after 40 years)

USGS Publications Warehouse

Rogozhin, E.A.; Imaev, V.S.; Smekalin, O.P.; Schwartz, D.P.

2008-01-01

The earthquake source, reaching the surface in the form of an extended system of faults, encompassed the N-S and NW-SE planes of two large faults near their juncture zone. A revised seismotectonic study of the system of coseismic ruptures performed after many years revealed a complex structure of primary coseismic ruptures in the juncture area of fault branches of different directions. In addition to the two major faults, the juncture zone consists of intersecting or parallel branches of both structural directions. The trench study and detailed mapping of the shallow structure of the seismic rupture characterizes it as a right-lateral-thrust fault on the N-S branch and a strike-slip-reverse fault on the NW-SE branch. Results of our paleoseismogeological study indicate that equally strong earthquakes are likely to have occurred in the same seismic source in the past (about 8000 and 160 years ago). ?? Pleiades Publishing, Ltd. 2008.

Force feedback controls motor activity and mechanical properties of self-assembling branched actin networks

PubMed Central

Bieling, Peter; Li, Tai-De; Weichsel, Julian; McGorty, Ryan; Jreij, Pamela; Huang, Bo; Fletcher, Daniel A.; Mullins, R. Dyche

2016-01-01

Branched actin networks–created by the Arp2/3 complex, capping protein, and a nucleation promoting factor– generate and transmit forces required for many cellular processes, but their response to force is poorly understood. To address this, we assembled branched actin networks in vitro from purified components and used simultaneous fluorescence and atomic force microscopy to quantify their molecular composition and material properties under various forces. Remarkably, mechanical loading of these self-assembling materials increases their density, power, and efficiency. Microscopically, increased density reflects increased filament number and altered geometry, but no change in average length. Macroscopically, increased density enhances network stiffness and resistance to mechanical failure beyond those of isotropic actin networks. These effects endow branched actin networks with memory of their mechanical history that shapes their material properties and motor activity. This work reveals intrinsic force feedback mechanisms by which mechanical resistance makes self-assembling actin networks stiffer, stronger, and more powerful. PMID:26771487

Right Cervical Aortic Arch and Pseudocoarctation of the Aorta Associated with Aneurysms and Steal Phenomena: US, CTA, and MRA Findings

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

Tanju, Sumru, E-mail: sumrutanju@yahoo.com; Ustuner, Evren; Erden, Ilhan

A 55-year-old woman presented with right cervical aortic arch with pseudocoarctation of the aorta further complicated by the presence of multiple aneurysms and a high-grade stenosis at the origin of the left subclavian trunk from the aorta causing a discrepancy in blood pressure between the right and left arms. The branching pattern and the resulting complex steal syndromes involving the left carotid and the subclavian system are unique. The computed tomography angiography, magnetic resonance angiography, and Doppler ultrasound findings are described.

Characterization of the highly branched glycogen from the thermoacidophilic red microalga Galdieria sulphuraria and comparison with other glycogens.

PubMed

Martinez-Garcia, Marta; Stuart, Marc C A; van der Maarel, Marc J E C

2016-08-01

The thermoacidophilic red microalga Galdieria sulphuraria synthesizes glycogen when growing under heterotrophic conditions. Structural characterization revealed that G. sulphuraria glycogen is the most highly branched glycogen described to date, with 18% of α-(1→6) linkages. Moreover, it differs from other glycogens because it is composed of short chains only and has a substantially smaller molecular weight and particle size. The physiological role of this highly branched glycogen in G. sulphuraria is discussed. Copyright © 2016 Elsevier B.V. All rights reserved.

Monopodial and sympodial branching architecture in cotton is differentially regulated by the Gossypium hirsutum SINGLE FLOWER TRUSS and SELF-PRUNING orthologs.

PubMed

McGarry, Roisin C; Prewitt, Sarah F; Culpepper, Samantha; Eshed, Yuval; Lifschitz, Eliezer; Ayre, Brian G

2016-10-01

Domestication of upland cotton (Gossypium hirsutum) converted it from a lanky photoperiodic perennial to a day-neutral annual row-crop. Residual perennial traits, however, complicate irrigation and crop management, and more determinate architectures are desired. Cotton simultaneously maintains robust monopodial indeterminate shoots and sympodial determinate shoots. We questioned if and how the FLOWERING LOCUS T/SINGLE FLOWER TRUSS (SFT)-like and TERMINAL FLOWER1/SELF-PRUNING (SP)-like genes control the balance of monopodial and sympodial growth in a woody perennial with complex growth habit. Virus-based manipulation of GhSP and GhSFT expression enabled unprecedented functional analysis of cotton development. GhSP maintains growth in all apices; in its absence, both monopodial and sympodial branch systems terminate precociously. GhSFT encodes a florigenic signal stimulating rapid onset of sympodial branching and flowering in side shoots of wild photoperiodic and modern day-neutral accessions. High florigen concentrations did not alter monopodial apices, implying that once a cotton apex is SP-determined, it cannot be reset by florigen. GhSP is also essential to establish and maintain cambial activity. Dynamic changes in GhSFT and GhSP levels navigate meristems between monopodial and sympodial programs in a single plant. SFT and SP influenced cotton domestication and are ideal targets for further agricultural optimization. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

LSPV+7, a branch-point-tolerant reconstructor for strong turbulence adaptive optics.

PubMed

Steinbock, Michael J; Hyde, Milo W; Schmidt, Jason D

2014-06-20

Optical wave propagation through long paths of extended turbulence presents unique challenges to adaptive optics (AO) systems. As scintillation and branch points develop in the beacon phase, challenges arise in accurately unwrapping the received wavefront and optimizing the reconstructed phase with respect to branch cut placement on a continuous facesheet deformable mirror. Several applications are currently restricted by these capability limits: laser communication, laser weapons, remote sensing, and ground-based astronomy. This paper presents a set of temporally evolving AO simulations comparing traditional least-squares reconstruction techniques to a complex-exponential reconstructor and several other reconstructors derived from the postprocessing congruence operation. The reconstructors' behavior in closed-loop operation is compared and discussed, providing several insights into the fundamental strengths and limitations of each reconstructor type. This research utilizes a self-referencing interferometer (SRI) as the high-order wavefront sensor, driving a traditional linear control law in conjunction with a cooperative point source beacon. The SRI model includes practical optical considerations and frame-by-frame fiber coupling effects to allow for realistic noise modeling. The "LSPV+7" reconstructor is shown to offer the best performance in terms of Strehl ratio and correction stability-outperforming the traditional least-squares reconstructed system by an average of 120% in the studied scenarios. Utilizing a continuous facesheet deformable mirror, these reconstructors offer significant AO performance improvements in strong turbulence applications without the need for segmented deformable mirrors.

Identification of high-mannose and multiantennary complex-type N-linked glycans containing alpha-galactose epitopes from Nurse shark IgM heavy chain.

PubMed

Harvey, David J; Crispin, Max; Moffatt, Beryl E; Smith, Sylvia L; Sim, Robert B; Rudd, Pauline M; Dwek, Raymond A

2009-11-01

MALDI-TOF mass spectrometry, negative ion nano-electrospray MS/MS and exoglycosidase digestion were used to identify 36 N-linked glycans from 19S IgM heavy chain derived from the nurse shark (Ginglymostoma cirratum). The major glycan was the high-mannose compound, Man(6)GlcNAc(2) accompanied by small amounts of Man(5)GlcNAc(2), Man(7)GlcNAc(2) and Man(8)GlcNAc(2). Bi- and tri-antennary (isomer with a branched 3-antenna) complex-type glycans were also abundant, most contained a bisecting GlcNAc residue (beta1-->4-linked to the central mannose) and with varying numbers of alpha-galactose residues capping the antennae. Small amounts of monosialylated glycans were also found. This appears to be the first comprehensive study of glycosylation in this species of animal. The glycosylation pattern has implications for the mechanism of activation of the complement system by nurse shark IgM.

QRS analysis using wavelet transformation for the prediction of response to cardiac resynchronization therapy: a prospective pilot study.

PubMed

Vassilikos, Vassilios P; Mantziari, Lilian; Dakos, Georgios; Kamperidis, Vasileios; Chouvarda, Ioanna; Chatzizisis, Yiannis S; Kalpidis, Panagiotis; Theofilogiannakos, Efstratios; Paraskevaidis, Stelios; Karvounis, Haralambos; Mochlas, Sotirios; Maglaveras, Nikolaos; Styliadis, Ioannis H

2014-01-01

Wider QRS and left bundle branch block morphology are related to response to cardiac resynchronization therapy (CRT). A novel time-frequency analysis of the QRS complex may provide additional information in predicting response to CRT. Signal-averaged electrocardiograms were prospectively recorded, before CRT, in orthogonal leads and QRS decomposition in three frequency bands was performed using the Morlet wavelet transformation. Thirty eight patients (age 65±10years, 31 males) were studied. CRT responders (n=28) had wider baseline QRS compared to non-responders and lower QRS energies in all frequency bands. The combination of QRS duration and mean energy in the high frequency band had the best predicting ability (AUC 0.833, 95%CI 0.705-0.962, p=0.002) followed by the maximum energy in the high frequency band (AUC 0.811, 95%CI 0.663-0.960, p=0.004). Wavelet transformation of the QRS complex is useful in predicting response to CRT. © 2013.

Experimental observations of a complex, supersonic nozzle concept

NASA Astrophysics Data System (ADS)

Magstadt, Andrew; Berry, Matthew; Glauser, Mark; Ruscher, Christopher; Gogineni, Sivaram; Kiel, Barry; Skytop Turbulence Labs, Syracuse University Team; Spectral Energies, LLC. Team; Air Force Research Laboratory Team

2015-11-01

A complex nozzle concept, which fuses multiple canonical flows together, has been experimentally investigated via pressure, schlieren and PIV in the anechoic chamber at Syracuse University. Motivated by future engine designs of high-performance aircraft, the rectangular, supersonic jet under investigation has a single plane of symmetry, an additional shear layer (referred to as a wall jet) and an aft deck representative of airframe integration. Operating near a Reynolds number of 3 ×106 , the nozzle architecture creates an intricate flow field comprised of high turbulence levels, shocks, shear & boundary layers, and powerful corner vortices. Current data suggest that the wall jet, which is an order of magnitude less energetic than the core, has significant control authority over the acoustic power through some non-linear process. As sound is a direct product of turbulence, experimental and analytical efforts further explore this interesting phenomenon associated with the turbulent flow. The authors acknowledge the funding source, a SBIR Phase II project with Spectral Energies, LLC. and AFRL turbine engine branch under the direction of Dr. Barry Kiel.

A Lectin from Platypodium elegans with Unusual Specificity and Affinity for Asymmetric Complex N-Glycans*

PubMed Central

Benevides, Raquel Guimarães; Ganne, Géraldine; Simões, Rafael da Conceição; Schubert, Volker; Niemietz, Mathäus; Unverzagt, Carlo; Chazalet, Valérie; Breton, Christelle; Varrot, Annabelle; Cavada, Benildo Sousa; Imberty, Anne

2012-01-01

Lectin activity with specificity for mannose and glucose has been detected in the seed of Platypodium elegans, a legume plant from the Dalbergieae tribe. The gene of Platypodium elegans lectin A has been cloned, and the resulting 261-amino acid protein belongs to the legume lectin family with similarity with Pterocarpus angolensis agglutinin from the same tribe. The recombinant lectin has been expressed in Escherichia coli and refolded from inclusion bodies. Analysis of specificity by glycan array evidenced a very unusual preference for complex type N-glycans with asymmetrical branches. A short branch consisting of one mannose residue is preferred on the 6-arm of the N-glycan, whereas extensions by GlcNAc, Gal, and NeuAc are favorable on the 3-arm. Affinities have been obtained by microcalorimetry using symmetrical and asymmetrical Asn-linked heptasaccharides prepared by the semi-synthetic method. Strong affinity with Kd of 4.5 μm was obtained for both ligands. Crystal structures of Platypodium elegans lectin A complexed with branched trimannose and symmetrical complex-type Asn-linked heptasaccharide have been solved at 2.1 and 1.65 Å resolution, respectively. The lectin adopts the canonical dimeric organization of legume lectins. The trimannose bridges the binding sites of two neighboring dimers, resulting in the formation of infinite chains in the crystal. The Asn-linked heptasaccharide binds with the 6-arm in the primary binding site with extensive additional contacts on both arms. The GlcNAc on the 6-arm is bound in a constrained conformation that may rationalize the higher affinity observed on the glycan array for N-glycans with only a mannose on the 6-arm. PMID:22692206

Ca2+-Citrate Uptake and Metabolism in Lactobacillus casei ATCC 334

PubMed Central

Mortera, Pablo; Pudlik, Agata; Magni, Christian; Alarcón, Sergio

2013-01-01

The putative citrate metabolic pathway in Lactobacillus casei ATCC 334 consists of the transporter CitH, a proton symporter of the citrate-divalent metal ion family of transporters CitMHS, citrate lyase, and the membrane-bound oxaloacetate decarboxylase complex OAD-ABDH. Resting cells of Lactobacillus casei ATCC 334 metabolized citrate in complex with Ca2+ and not as free citrate or the Mg2+-citrate complex, thereby identifying Ca2+-citrate as the substrate of the transporter CitH. The pathway was induced in the presence of Ca2+ and citrate during growth and repressed by the presence of glucose and of galactose, most likely by a carbon catabolite repression mechanism. The end products of Ca2+-citrate metabolism by resting cells of Lb. casei were pyruvate, acetate, and acetoin, demonstrating the activity of the membrane-bound oxaloacetate decarboxylase complex OAD-ABDH. Following pyruvate, the pathway splits into two branches. One branch is the classical citrate fermentation pathway producing acetoin by α-acetolactate synthase and α-acetolactate decarboxylase. The other branch yields acetate, for which the route is still obscure. Ca2+-citrate metabolism in a modified MRS medium lacking a carbohydrate did not significantly affect the growth characteristics, and generation of metabolic energy in the form of proton motive force (PMF) was not observed in resting cells. In contrast, carbohydrate/Ca2+-citrate cometabolism resulted in a higher biomass yield in batch culture. However, also with these cells, no generation of PMF was associated with Ca2+-citrate metabolism. It is concluded that citrate metabolism in Lb. casei is beneficial when it counteracts acidification by carbohydrate metabolism in later growth stages. PMID:23709502

Qualitative and quantitative analysis of branches in dextran using high-performance anion exchange chromatography coupled to quadrupole time-of-flight mass spectrometry.

PubMed

Yi, Lin; Ouyang, Yilan; Sun, Xue; Xu, Naiyu; Linhardt, Robert J; Zhang, Zhenqing

2015-12-04

Dextran, a family of natural polysaccharides, consists of an α (1→6) linked-glucose main (backbone) chain having a number of branches. The determination of the types and the quantities of branches in dextran is important in understanding its various biological roles. In this study, a hyphenated method using high-performance anion exchange chromatography (HPAEC) in parallel with pulsed amperometric detection (PAD) and mass spectrometry (MS) was applied to qualitative and quantitative analysis of dextran branches. A rotary cation-exchange cartridge array desalter was used for removal of salt from the HPAEC eluent making it MS compatible. MS and MS/MS were used to provide structural information on the enzymatically prepared dextran oligosaccharides. PAD provides quantitative data on the ratio of enzyme-resistant, branched dextran oligosaccharides. Both the types and degree of branching found in a variety of dextrans could be simultaneously determined online using this method. Copyright © 2015 Elsevier B.V. All rights reserved.

PI(3,5)P2 controls endosomal branched actin dynamics by regulating cortactin–actin interactions

PubMed Central

Hong, Nan Hyung; Qi, Aidong

2015-01-01

Branched actin critically contributes to membrane trafficking by regulating membrane curvature, dynamics, fission, and transport. However, how actin dynamics are controlled at membranes is poorly understood. Here, we identify the branched actin regulator cortactin as a direct binding partner of phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) and demonstrate that their interaction promotes turnover of late endosomal actin. In vitro biochemical studies indicated that cortactin binds PI(3,5)P2 via its actin filament-binding region. Furthermore, PI(3,5)P2 competed with actin filaments for binding to cortactin, thereby antagonizing cortactin activity. These findings suggest that PI(3,5)P2 formation on endosomes may remove cortactin from endosome-associated branched actin. Indeed, inhibition of PI(3,5)P2 production led to cortactin accumulation and actin stabilization on Rab7+ endosomes. Conversely, inhibition of Arp2/3 complex activity greatly reduced cortactin localization to late endosomes. Knockdown of cortactin reversed PI(3,5)P2-inhibitor–induced actin accumulation and stabilization on endosomes. These data suggest a model in which PI(3,5)P2 binding removes cortactin from late endosomal branched actin networks and thereby promotes net actin turnover. PMID:26323691

In vivo single branch axotomy induces GAP-43-dependent sprouting and synaptic remodeling in cerebellar cortex.

PubMed

Allegra Mascaro, Anna Letizia; Cesare, Paolo; Sacconi, Leonardo; Grasselli, Giorgio; Mandolesi, Georgia; Maco, Bohumil; Knott, Graham W; Huang, Lieven; De Paola, Vincenzo; Strata, Piergiorgio; Pavone, Francesco S

2013-06-25

Plasticity in the central nervous system in response to injury is a complex process involving axonal remodeling regulated by specific molecular pathways. Here, we dissected the role of growth-associated protein 43 (GAP-43; also known as neuromodulin and B-50) in axonal structural plasticity by using, as a model, climbing fibers. Single axonal branches were dissected by laser axotomy, avoiding collateral damage to the adjacent dendrite and the formation of a persistent glial scar. Despite the very small denervated area, the injured axons consistently reshape the connectivity with surrounding neurons. At the same time, adult climbing fibers react by sprouting new branches through the intact surroundings. Newly formed branches presented varicosities, suggesting that new axons were more than just exploratory sprouts. Correlative light and electron microscopy reveals that the sprouted branch contains large numbers of vesicles, with varicosities in the close vicinity of Purkinje dendrites. By using an RNA interference approach, we found that downregulating GAP-43 causes a significant increase in the turnover of presynaptic boutons. In addition, silencing hampers the generation of reactive sprouts. Our findings show the requirement of GAP-43 in sustaining synaptic stability and promoting the initiation of axonal regrowth.

INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Branch Processes of Vortex Filaments and Hopf Invariant Constraint on Scroll Wave

NASA Astrophysics Data System (ADS)

Zhu, Tao; Ren, Ji-Rong; Mo, Shu-Fan

2009-12-01

In this paper, by making use of Duan's topological current theory, the evolution of the vortex filaments in excitable media is discussed in detail. The vortex filaments are found generating or annihilating at the limit points and encountering, splitting, or merging at the bifurcation points of a complex function Z(vec x, t). It is also shown that the Hopf invariant of knotted scroll wave filaments is preserved in the branch processes (splitting, merging, or encountering) during the evolution of these knotted scroll wave filaments. Furthermore, it also revealed that the “exclusion principle" in some chemical media is just the special case of the Hopf invariant constraint, and during the branch processes the “exclusion principle" is also protected by topology.

Excitation of Continuous and Discrete Modes in Incompressible Boundary Layers

NASA Technical Reports Server (NTRS)

Ashpis, David E.; Reshotko, Eli

1998-01-01

This report documents the full details of the condensed journal article by Ashpis & Reshotko (JFM, 1990) entitled "The Vibrating Ribbon Problem Revisited." A revised formal solution of the vibrating ribbon problem of hydrodynamic stability is presented. The initial formulation of Gaster (JFM, 1965) is modified by application of the Briggs method and a careful treatment of the complex double Fourier transform inversions. Expressions are obtained in a natural way for the discrete spectrum as well as for the four branches of the continuous spectra. These correspond to discrete and branch-cut singularities in the complex wave-number plane. The solutions from the continuous spectra decay both upstream and downstream of the ribbon, with the decay in the upstream direction being much more rapid than that in the downstream direction. Comments and clarification of related prior work are made.

Oxidative phosphorylation in Debaryomyces hansenii: physiological uncoupling at different growth phases.

PubMed

Cabrera-Orefice, Alfredo; Guerrero-Castillo, Sergio; Díaz-Ruíz, Rodrigo; Uribe-Carvajal, Salvador

2014-07-01

Physiological uncoupling of mitochondrial oxidative phosphorylation (OxPhos) was studied in Debaryomyces hansenii. In other species, such as Yarrowia lipolytica and Saccharomyces cerevisiae, OxPhos can be uncoupled through differential expression of branched respiratory chain enzymes or by opening of a mitochondrial unspecific channel (ScMUC), respectively. However D. hansenii mitochondria, which contain both a branched respiratory chain and a mitochondrial unspecific channel (DhMUC), selectively uncouple complex I-dependent rate of oxygen consumption in the stationary growth phase. The uncoupled complex I-dependent respiration was only 20% of the original activity. Inhibition was not due to inactivation of complex I, lack of protein expression or to differential expression of alternative oxidoreductases. Furthermore, all other respiratory chain activities were normal. Decrease of complex I-dependent respiration was due to NAD(+) loss from the matrix, probably through an open of DhMUC. When NAD(+) was added back, coupled complex I-activity was recovered. NAD(+) re-uptake was independent of DhMUC opening and seemed to be catalyzed by a NAD(+)-specific transporter, which was sensitive to bathophenanthroline, bromocresol purple or pyridoxal-5'-phosphate as described for S. cerevisiae mitochondrial NAD(+) transporters. Loss of NAD(+) from the matrix through an open MUC is proposed as an additional mechanism to uncouple OxPhos. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Construction and Commissioning of BL37XU at SPring-8

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

Terada, Yasuko; Goto, Shunji; Takimoto, Naoki

2004-05-12

Trace element analysis beamline (BL37XU) at SPring-8 was designed for application to various X-ray fluorescence analyses such as XRF imaging, XAFS, TXRF and XRF holography. The beamline has of two branches, one being a SPring-8 standard undulator-beamline optics branch (Branch A) and the other a high-energy branch (Branch B). In the experimental hutches, several kinds of experimental device are equipped. The end-stations have been opened to public use since November 2002, and various experiments have been carried out.

In-hospital outcome in patients with ST elevation myocardial infarction and right bundle branch block. A sub-study from RENASICA II, a national multicenter registry.

PubMed

Juárez-Herrera, Ursulo; Jerjes Sánchez, Carlos; González-Pacheco, Héctor; Martínez-Sánchez, Carlos

2010-01-01

Compare in-hospital outcome in patients with ST-elevation myocardial infarction with right versus left bundle branch block. RENASICA II, a national Mexican registry enrolled 8098 patients with final diagnosis of acute coronary syndrome secondary to ischemic heart disease. In 4555 STEMI patients, 545 had bundle branch block, 318 (58.3%) with right and 225 patients with left (41.6%). Both groups were compared in terms of in-hospital outcome through major cardiovascular adverse events; (cardiovascular death, recurrent ischemia and reinfarction). Multivariable analysis was performed to identify in-hospital mortality risk among right and left bundle branch block patients. There were not statistical differences in both groups regarding baseline characteristics, time of ischemia, myocardial infarction location, ventricular dysfunction and reperfusion strategies. In-hospital outcome in bundle branch block group was characterized by a high incidence of major cardiovascular adverse events with a trend to higher mortality in patients with right bundle branch block (OR 1.70, CI 1.19 - 2.42, p < 0.003), compared to left bundle branch block patients. In this sub-study right bundle branch block accompanying ST-elevation myocardial infarction of any location at emergency room presentation was an independent predictor of high in-hospital mortality.

Closer insight into the structure of moderate to densely branched comb polymers by combining modelling and linear rheological measurements.

PubMed

Ahmadi, Mostafa; Pioge, Sandie; Fustin, Charles-Andre; Gohy, Jean-Francois; van Ruymbeke, Evelyne

2017-02-07

Synthesis of combs with well-entangled backbones and long branches with high densities has always been a challenge. Steric hindrance frequently leads to coupling of chains and structural imperfections that cannot be easily distinguished by traditional characterization methods. Research studies have therefore tried to use a combination of different methods to obtain more information on the actual microstructures. In this work, a grafting-from approach is used to synthesize poly(n-butyl acrylate) combs using atom transfer radical polymerization (ATRP) in three steps including the synthesis of a backbone, cleavage of protecting groups and growth of side branches. We have compared the linear viscoelastic properties theoretically predicted by a time marching algorithm (TMA) tube based model with the measured rheological behaviour to provide a better insight into the actual microstructure formed during synthesis. For combs with branches smaller than an entanglement, no discernible hierarchical relaxation can be distinguished, while for those with longer branches, a high frequency plateau made by entangled branches can be separated from backbone's relaxation. Dilution of the backbone, after relaxation of side branches, may accelerate the final relaxation, while extra friction can delay it especially for longer branches. Such a comparison provides a better assessment of the microstructure formed in combs.

Encapsulating fatty acid esters of bioactive compounds in starch

NASA Astrophysics Data System (ADS)

Lay Ma, Ursula Vanesa

Interest in the use of many bioactive compounds in foods is growing in large part because of the apparent health benefits of these molecules. However, many of these compounds can be easily degraded during processing, storage, or their passage through the gastrointestinal tract before reaching the target site. In addition, they can be bitter, acrid, or astringent, which may negatively affect the sensory properties of the product. Encapsulation of these molecules may increase their stability during processing, storage, and in the gastrointestinal tract, while providing controlled release properties. The ability of amylose to form inclusion complexes and spherulites while entrapping certain compounds has been suggested as a potential method for encapsulation of certain molecules. However, complex formation and spherulitic crystallization are greatly affected by the type of inclusion molecules, type of starch, and processing conditions. The objectives of the present investigation were to: (a) study the effect of amylose, amylopectin, and intermediate material on spherulite formation and its microstructure; (b) investigate the formation of amylose and high amylose starch inclusion complexes with ascorbyl palmitate, retinyl palmitate, and phytosterol esters; (c) evaluate the ability of spherulites to form in the presence of fatty acid esters and to entrap ascorbyl palmitate, retinyl palmitate, and phytosterol esters; and (d) evaluate the effect of processing conditions on spherulite formation and fatty acid ester entrapment. Higher ratios of linear to branched molecules resulted in the formation of more and rounder spherulites with higher heat stability. In addition to the presence of branches, it appears that spherulitic crystallization is also affected by other factors, such as degree of branching, chain length, and chain length distribution. Amylose and Hylon VII starch formed inclusion complexes with fatty acid esters of ascorbic acid, retinol, or phytosterols. However, only retinyl palmitate formed a complex with amylopectin. In general, ascorbyl palmitate resulted in the highest complexation, followed by retinyl palmitate and phytosterol ester. The presence of native lipids in Hylon VII starch did not inhibit complex formation. On the contrary, native lipids appear to increase the complexation yield and thermal stability of the starch-fatty acid ester inclusion complexes, possibly due to the formation of ternary complexes. From the three fatty acid esters studied, only ascorbyl palmitate was entrapped in starch spherulites. Various structures including round spherulites, various sizes of torus-shape spherulites, non-spherulitic birefringent and non-birefringent particles, "balloon" morphologies, and gel-like material were formed depending on processing conditions. However, only the torus-shape spherulites, and some non-spherulitic birefringent and non-birefringent particles showed ascorbyl palmitate entrapment. The % yield of the precipitate increased with higher % of added Hylon VII, and decreased with higher heating temperature and faster cooling rates. The amount of entrapped ascorbyl palmitate in the starch precipitate seems to be governed by the amount of this compound added during processing. This study showed that starch can form inclusion complexes with fatty acid esters which may be used for the delivery of certain bioactive molecules. In addition, encapsulation of fatty acid esters in starch spherulites may be a good potential delivery system for water soluble bioactive molecules. However, further research is necessary to gain a better understanding of the type of molecules that can be entrapped in starch spherulites, and the factors affecting spherulitic crystallization and bioactive compound entrapment.

Exploring the structure of fucosylated chondroitin sulfate through bottom-up nuclear magnetic resonance and electrospray ionization-high-resolution mass spectrometry approaches.

PubMed

Santos, Gustavo Rc; Porto, Ana Co; Soares, Paulo Ag; Vilanova, Eduardo; Mourão, Paulo As

2017-07-01

Fucosylated chondroitin sulfate (FCS) from sea cucumbers is composed of a chondroitin sulfate (CS) central core and branches of sulfated fucose. The structure of this complex glycosaminoglycan is usually investigated via nuclear magnetic resonance (NMR) analyses of the intact molecule, ergo through a top-down approach, which often yield spectra with intricate sets of signals. Here we employed a bottom-up approach to analyze the FCSs from the sea cucumbers Isostichopus badionotus and Ludwigothurea grisea from their basic constituents, viz. CS cores and sulfated fucose branches, obtained via systematic fragmentation through mild acid hydrolysis. Oligosaccharides derived from the central CS core were analyzed via NMR spectroscopy and the disaccharides produced using chondroitin sulfate lyase via SAX-HPLC. The CS cores from the two species were similar, showing only slight differences in the proportions of 4- or 6-monosulfated and 4,6-disulfated β-d-GalNAc. Sulfated fucose units released from the FCSs were analyzed via NMR and ESI-HRMS spectroscopies. The fucose units from each species presented extensive qualitative differences, but quantitative assessments of these units were hindered, mostly because of their extensive desulfation during the hydrolysis. The bottom-up analysis performed here has proved useful to explore the structure of FCS through a sum-of-the-parts approach in a qualitative manner. We further demonstrate that under specific acidification conditions particular fucose branches can be removed preferentially from FCS. Preparation of derivatives enriched with particular fucose branches could be useful for studies on "structure vs. biological function" of FCS. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Impaired adiponectin signaling contributes to disturbed catabolism of branched-chain amino acids in diabetic mice.

PubMed

Lian, Kun; Du, Chaosheng; Liu, Yi; Zhu, Di; Yan, Wenjun; Zhang, Haifeng; Hong, Zhibo; Liu, Peilin; Zhang, Lijian; Pei, Haifeng; Zhang, Jinglong; Gao, Chao; Xin, Chao; Cheng, Hexiang; Xiong, Lize; Tao, Ling

2015-01-01

The branched-chain amino acids (BCAA) accumulated in type 2 diabetes are independent contributors to insulin resistance. The activity of branched-chain α-keto acid dehydrogenase (BCKD) complex, rate-limiting enzyme in BCAA catabolism, is reduced in diabetic states, which contributes to elevated BCAA concentrations. However, the mechanisms underlying decreased BCKD activity remain poorly understood. Here, we demonstrate that mitochondrial phosphatase 2C (PP2Cm), a newly identified BCKD phosphatase that increases BCKD activity, was significantly downregulated in ob/ob and type 2 diabetic mice. Interestingly, in adiponectin (APN) knockout (APN(-/-)) mice fed with a high-fat diet (HD), PP2Cm expression and BCKD activity were significantly decreased, whereas BCKD kinase (BDK), which inhibits BCKD activity, was markedly increased. Concurrently, plasma BCAA and branched-chain α-keto acids (BCKA) were significantly elevated. APN treatment markedly reverted PP2Cm, BDK, BCKD activity, and BCAA and BCKA levels in HD-fed APN(-/-) and diabetic animals. Additionally, increased BCKD activity caused by APN administration was partially but significantly inhibited in PP2Cm knockout mice. Finally, APN-mediated upregulation of PP2Cm expression and BCKD activity were abolished when AMPK was inhibited. Collectively, we have provided the first direct evidence that APN is a novel regulator of PP2Cm and systematic BCAA levels, suggesting that targeting APN may be a pharmacological approach to ameliorating BCAA catabolism in the diabetic state. © 2015 by the American Diabetes Association. Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered.

Dynamic pathway modeling of signal transduction networks: a domain-oriented approach.

PubMed

Conzelmann, Holger; Gilles, Ernst-Dieter

2008-01-01

Mathematical models of biological processes become more and more important in biology. The aim is a holistic understanding of how processes such as cellular communication, cell division, regulation, homeostasis, or adaptation work, how they are regulated, and how they react to perturbations. The great complexity of most of these processes necessitates the generation of mathematical models in order to address these questions. In this chapter we provide an introduction to basic principles of dynamic modeling and highlight both problems and chances of dynamic modeling in biology. The main focus will be on modeling of s transduction pathways, which requires the application of a special modeling approach. A common pattern, especially in eukaryotic signaling systems, is the formation of multi protein signaling complexes. Even for a small number of interacting proteins the number of distinguishable molecular species can be extremely high. This combinatorial complexity is due to the great number of distinct binding domains of many receptors and scaffold proteins involved in signal transduction. However, these problems can be overcome using a new domain-oriented modeling approach, which makes it possible to handle complex and branched signaling pathways.

Phosphorylation by CK2 regulates MUS81/EME1 in mitosis and after replication stress.

PubMed

Palma, Anita; Pugliese, Giusj Monia; Murfuni, Ivana; Marabitti, Veronica; Malacaria, Eva; Rinalducci, Sara; Minoprio, Anna; Sanchez, Massimo; Mazzei, Filomena; Zolla, Lello; Franchitto, Annapaola; Pichierri, Pietro

2018-06-01

The MUS81 complex is crucial for preserving genome stability through the resolution of branched DNA intermediates in mitosis. However, untimely activation of the MUS81 complex in S-phase is dangerous. Little is known about the regulation of the human MUS81 complex and how deregulated activation affects chromosome integrity. Here, we show that the CK2 kinase phosphorylates MUS81 at Serine 87 in late-G2/mitosis, and upon mild replication stress. Phosphorylated MUS81 interacts with SLX4, and this association promotes the function of the MUS81 complex. In line with a role in mitosis, phosphorylation at Serine 87 is suppressed in S-phase and is mainly detected in the MUS81 molecules associated with EME1. Loss of CK2-dependent MUS81 phosphorylation contributes modestly to chromosome integrity, however, expression of the phosphomimic form induces DSBs accumulation in S-phase, because of unscheduled targeting of HJ-like DNA intermediates, and generates a wide chromosome instability phenotype. Collectively, our findings describe a novel regulatory mechanism controlling the MUS81 complex function in human cells. Furthermore, they indicate that, genome stability depends mainly on the ability of cells to counteract targeting of branched intermediates by the MUS81/EME1 complex in S-phase, rather than on a correct MUS81 function in mitosis.

Branched-chain amino acids complex inhibits melanogenesis in B16F0 melanoma cells.

PubMed

Cha, Jae-Young; Yang, Hyun-Ju; Moon, Hyung-In; Cho, Young-Su

2012-04-01

Present study was investigated the effect of each or complex of three branched-chain amino acids (BCAAs; isoleucine, leucine, and valine) on melanin production in B16F0 melanoma cells treated with various concentrations (1-16 mM) for 72 h. Among the 20 amino acids, lysine and glycine showed the highest activities of DPPH radical scavenging and mushroom tyrosinase inhibition, respectively. Each and combination of BCAAs reduced melanogenesis in a concentration-dependent manner without any morphological changes and cell viability in melanoma cells. Present study was also investigated the inhibitory effects of each or complex of BCAAs at each 10 mM concentration on the 100 μM IBMX-mediated stimulation of melanogenesis in melanoma cells for 72 h and found that IBMX treatment was stimulated to enhance melanin synthesis and that the complex of BCAAs was the most effectively inhibited in the melanin amounts of cellular and extracellular and the whitening the cell pellet. When the inhibitory effect of BCAAs on tyrosinase was examined by intracellular tyrosinase assay, both isoleucine and valine exhibit slightly inhibition, but leucine and combination of BCAAs did not inhibit the cell-derived tyrosinase activity. Present study demonstrated that complex of BCAAs inhibited melanin production without changes intercellular tyrosinase activity. Thus, the complex of BCAAs may be used in development of safe potentially depigmenting agents.

White Light Used to Enable Enhanced Surface Topography, Geometry, and Wear Characterization of Oil-Free Bearings

NASA Technical Reports Server (NTRS)

Lucero, John M.

2003-01-01

A new optically based measuring capability that characterizes surface topography, geometry, and wear has been employed by NASA Glenn Research Center s Tribology and Surface Science Branch. To characterize complex parts in more detail, we are using a three-dimensional, surface structure analyzer-the NewView5000 manufactured by Zygo Corporation (Middlefield, CT). This system provides graphical images and high-resolution numerical analyses to accurately characterize surfaces. Because of the inherent complexity of the various analyzed assemblies, the machine has been pushed to its limits. For example, special hardware fixtures and measuring techniques were developed to characterize Oil- Free thrust bearings specifically. We performed a more detailed wear analysis using scanning white light interferometry to image and measure the bearing structure and topography, enabling a further understanding of bearing failure causes.

The Complexity of Teacher Questions in Chemistry Classrooms: An Empirical Analysis on the Basis of Two Competence Models

ERIC Educational Resources Information Center

Nehring, Andreas; Päßler, Andreas; Tiemann, Rüdiger

2017-01-01

With regard to the moderate performance of German students in international large-scale assessments, one branch of German science education research is concerned with the construction and evaluation of competence models. Based on the theory-driven definition of competence levels, these models imply a correlation between the complexity of a…

The thoracic muscular system and its innervation in third instar Calliphora vicina Larvae. II. Projection patterns of the nerves associated with the pro- and mesothorax and the pharyngeal complex.

PubMed

Schoofs, Andreas; Hanslik, Ulrike; Niederegger, Senta; Heinzel, Hans-Georg; Spiess, Roland

2010-08-01

We describe the anatomy of the nerves that project from the central nervous system (CNS) to the pro- and mesothoracic segments and the cephalopharyngeal skeleton (CPS) for third instar Calliphora larvae. Due to the complex branching pattern we introduce a nomenclature that labels side branches of first and second order. Two fine nerves that were not yet described are briefly introduced. One paired nerve projects to the ventral arms (VAs) of the CPS. The second, an unpaired nerve, projects to the ventral surface of the cibarial part of the esophagus (ES). Both nerves were tentatively labeled after the structures they innervate. The antennal nerve (AN) innervates the olfactory dorsal organ (DO). It contains motor pathways that project through the frontal connectives (FC) to the frontal nerve (FN) and innervate the cibarial dilator muscles (CDM) which mediate food ingestion. The maxillary nerve (MN) innervates the sensory terminal organ (TO), ventral organ (VO), and labial organ (LO) and comprises the motor pathways to the mouth hook (MH) elevator, MH depressor, and the labial retractor (LR) which opens the mouth cavity. An anastomosis of unknown function exists between the AN and MN. The prothoracic accessory nerve (PaN) innervates a dorsal protractor muscle of the CPS and sends side branches to the aorta and the bolwig organ (BO) (stemmata). In its further course, this nerve merges with the prothoracic nerve (PN). The architecture of the PN is extremely complex. It innervates a set of accessory pharyngeal muscles attached to the CPS and the body wall musculature of the prothorax. Several anastomoses exist between side branches of this nerve which were shown to contain motor pathways. The mesothoracic nerve (MeN) innervates a MH accessor and the longitudinal and transversal body wall muscles of the second segment. J. Morphol. 271:969-979, 2010. (c) 2010 Wiley-Liss, Inc.

Congestion relaxation due to density-dependent junction rules in TASEP network

NASA Astrophysics Data System (ADS)

Tannai, Takahiro; Nishinari, Katsuhiro

2017-09-01

We now consider a small network module of Totally Asymmetric Simple Exclusion Process with branching and aggregation points, and rules of junctions dependent on the densities of segments of the network module. We also focus on the interaction among junctions which are branching and aggregation. The interaction among junctions with density-dependent rules possesses more complexity than those with density-independent rules studied in the previous papers. In conclusion, we confirm the result that density-dependent rules enable vehicles to move more effectively than the density-independent rules.

[Physiology of the urethral sphincteric vesico-prostatic complex].

PubMed

Carmignani, L; Gadda, F; Dell'Orto, P; Ferruti, M; Grisotto, M; Rocco, F

2001-09-01

We propose a review of the literature about innervation and physiology of the urethral sphincteric complex. Parasympathetic innervation of the pelvic viscera comes from ventral branches of the sacral nerves (S2-S4). The orthosympathetic component derives from superior hypogastric plexus and runs down the hypogastric nerves to form the right and left pelvic plexus together with the parasympathetic component. The pelvic plexus is situated inferolaterally with respect to the rectum and runs on the surface of the levator ani muscle down to the prostatic apex. The pelvic plexus gives innervation to the rectum, the bladder, the prostate and the urethral sphincteric complex. The pelvic muscular floor is innervated by the somatic component (pudendal nerve) derived from the sacral branches (S2-S4). Bladder neck and smooth muscle urethral sphincter innervation is given mostly by the orthosympathetic component. The rhabdosphincter innervation comes from the pudendal nerve and from the pelvic plexus; its role in the continence mechanism is probably to give steady tonic urethral compression. Levator ani muscle takes part in the sphincteric complex with its anteromedial pubococcygeal portion. It plays its role strengthening the sphincteric tone during increase of the abdominal pressure or during active quick stop cessation of the urinary stream.

Branched actin networks push against each other at adherens junctions to maintain cell-cell adhesion.

PubMed

Efimova, Nadia; Svitkina, Tatyana M

2018-05-07

Adherens junctions (AJs) are mechanosensitive cadherin-based intercellular adhesions that interact with the actin cytoskeleton and carry most of the mechanical load at cell-cell junctions. Both Arp2/3 complex-dependent actin polymerization generating pushing force and nonmuscle myosin II (NMII)-dependent contraction producing pulling force are necessary for AJ morphogenesis. Which actin system directly interacts with AJs is unknown. Using platinum replica electron microscopy of endothelial cells, we show that vascular endothelial (VE)-cadherin colocalizes with Arp2/3 complex-positive actin networks at different AJ types and is positioned at the interface between two oppositely oriented branched networks from adjacent cells. In contrast, actin-NMII bundles are located more distally from the VE-cadherin-rich zone. After Arp2/3 complex inhibition, linear AJs split, leaving gaps between cells with detergent-insoluble VE-cadherin transiently associated with the gap edges. After NMII inhibition, VE-cadherin is lost from gap edges. We propose that the actin cytoskeleton at AJs acts as a dynamic push-pull system, wherein pushing forces maintain extracellular VE-cadherin transinteraction and pulling forces stabilize intracellular adhesion complexes. © 2018 Efimova and Svitkina.

A Chemical Composition Survey of the Iron-complex Globular Cluster NGC 6273 (M19)

NASA Astrophysics Data System (ADS)

Johnson, Christian I.; Caldwell, Nelson; Rich, R. Michael; Mateo, Mario; Bailey, John I., III; Clarkson, William I.; Olszewski, Edward W.; Walker, Matthew G.

2017-02-01

Recent observations have shown that a growing number of the most massive Galactic globular clusters contain multiple populations of stars with different [Fe/H] and neutron-capture element abundances. NGC 6273 has only recently been recognized as a member of this “iron-complex” cluster class, and we provide here a chemical and kinematic analysis of >300 red giant branch and asymptotic giant branch member stars using high-resolution spectra obtained with the Magellan-M2FS and VLT-FLAMES instruments. Multiple lines of evidence indicate that NGC 6273 possesses an intrinsic metallicity spread that ranges from about [Fe/H] = -2 to -1 dex, and may include at least three populations with different [Fe/H] values. The three populations identified here contain separate first (Na/Al-poor) and second (Na/Al-rich) generation stars, but a Mg-Al anti-correlation may only be present in stars with [Fe/H] ≳ -1.65. The strong correlation between [La/Eu] and [Fe/H] suggests that the s-process must have dominated the heavy element enrichment at higher metallicities. A small group of stars with low [α/Fe] is identified and may have been accreted from a former surrounding field star population. The cluster’s large abundance variations are coupled with a complex, extended, and multimodal blue horizontal branch (HB). The HB morphology and chemical abundances suggest that NGC 6273 may have an origin that is similar to ω Cen and M54. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. These observations are associated with program GO-14197. This paper includes data gathered with the 6.5 m Magellan Telescopes located as Las Campanas Observatory, Chile.

Visualizing anatomical evidences on atrioventricular conduction system for TAVI.

PubMed

Kawashima, Tomokazu; Sato, Fumi

2014-06-01

Visualizing the anatomy of the atrioventricular (AV) conduction axis substantiates that there is remarkable inter-individual variation at the macro- and microscopic levels, and that the atrioventricular bundle and left bundle branch are located more anteriorly, distally, and cranially and much closer to the aortic root complex than previously thought. The AV conduction system may therefore be compromised during implantation of a transcatheter aortic valve prosthesis, which may account for the relatively high incidence of new cardiac conduction abnormalities when conventional prosthetic valves are used. The design of the newer JenaValve® may afford advantages over more conventional valves by avoiding the high-risk implantation area and the potential for coronary ostia obstruction. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Wilson disease: more than meets the eye.

PubMed

Kelly, Claire; Pericleous, Marinos

2018-02-15

Wilson disease is a rare but important disorder of copper metabolism, with a failure to excrete copper appropriately into bile. It is a multisystem condition with presentations across all branches of medicine. Diagnosis can be difficult and requires a high index of suspicion. It should be considered in unexplained liver disease particularly where neuropsychiatric features are also present. Treatments are available for all stages of disease. A particularly important presentation not to overlook is acute liver failure which carries a high mortality risk and may require urgent liver transplantation. Here, we provide an overview of this complex condition. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Sodium channel blockade with QRS widening after an escitalopram overdose.

PubMed

Schreffler, Susan M; Marraffa, Jeanna M; Stork, Christine M; Mackey, Jennifer

2013-09-01

Escitalopram is rarely associated with prolongation of the QTc interval; however, there are no reported cases of QRS complex widening associated with escitalopram overdose. We report a case of a patient who presented with both QRS complex widening and QTc interval prolongation after an escitalopram overdose. A 16-year-old girl presented to the emergency department after ingestion of escitalopram, tramadol/acetaminophen, and hydrocodone/acetaminophen. Laboratory results were significant for 4-hour acetaminophen 21.1 μg/mL. Serum electrolytes including potassium, magnesium, and calcium were all normal. Initial electrocardiogram (ECG) revealed a widened QRS with an incomplete right bundle branch pattern. After administration of 100-mEq sodium bicarbonate, a repeat ECG revealed narrowing of the QRS complex and a prolonged QTc interval. Magnesium sulfate 2 g intravenous and sodium bicarbonate drip were initiated. A repeat ECG, 1 hour after the second, revealed normalization of the QRS complex and QTc interval. Prolongation of the QTc interval is an expected effect of escitalopram. Both escitalopram and citalopram are metabolized to the cardiotoxic metabolite S-didesmethylcitalopram and didesmethylcitalopram, respectively, which have been implicated in numerous cardiac abnormalities including widening of the QRS complex. Although never previously described with escitalopram, this mechanism provides a reasonable explanation for the QRS complex widening and incomplete right bundle branch block that occurred in our patient. Both QRS complex widening and QTc interval prolongation should be monitored in cases of escitalopram and citalopram overdoses.

Petrogenesis of the Pulang porphyry complex, southwestern China: Implications for porphyry copper metallogenesis and subduction of the Paleo-Tethys Oceanic lithosphere

NASA Astrophysics Data System (ADS)

Wang, Peng; Dong, Guo-Chen; Zhao, Guo-Chun; Han, Yi-Gui; Li, Yong-Ping

2018-04-01

The Pulang complex is located in the southern segment of the Yidun Arc in the Sanjiang Tethys belt, southwestern China. It is composed of quartz diorite, quartz monzonite and granodiorite porphyries, and hosts the super-large Pulang deposit. This study presents new U-Pb geochronological, major-trace elemental and Sr-Nd-Hf isotopic data to constrain the petrogenesis of the Pulang complex and to evaluate its significances for porphyric mineralization and tectonic evolution of the Paleo-Tethys Ocean. The zircon U-Pb dating yields ages ranging from 208 Ma to 214 Ma. Geochemically, the Pulang complex has high Sr and MgO contents, and high Sr/Y and La/Yb ratios, but low Yb and Y contents, displaying adakitic affinities. However, it has moderate Sr/Y and La/Yb ratios, and high Rb contents (32 to 202 ppm). The Pulang samples plot into the transitional field between adakites and normal arc rocks, differing from typical adakites. It is attributed to the assimilation of 10-15% crustal components. The zircon εHf(t) (-4.6 to -2.5), whole-rock (87Sr/86Sr)i (0.7052 to 0.7102), εNd(t) (-0.62 to 2.12) values and adakitic affinities suggest that the Pulang complex was derived from a basaltic slab-melt source and reacted with peridotite during ascending through an enriched asthenospheric mantle wedge. The basaltic slab-melts likely resulted from the westward subduction of the Ganzi-Litang oceanic plate (a branch of the Paleo-Tethys). As far as the metallogenesis concerned, three factors in mineralization are proposed in this paper. The country rock, quartz diorite porphyry, has higher Cu contents than the mantle (average 30 ppm), suggesting that ore-forming magma was derived from a Cu-enriched source, which is a crucial contribution to the late mineralization to form the super-large Pulang deposit. In addition, the barren quartz diorite, granodiorite, and ore-bearing quartz monzonite porphyries are all characterized by high oxygen fugacity, which is another important factor for the mineralization. Moreover, the separation/exsolution of the quartz monzonite from the quartz diorite is vital to the enrichment of Cu in the Pulang deposit. The emplacement of the Pulang pluton, posterior to the closure of the Jiangshajiang Ocean (a branch of the paleo-Tethys), is consistent with the igneous rocks associated with the westward subduction of the Ganzi-Litang oceanic plate during late Triassic Time. The Zhongdian Arc in the southern segment of the Yidun Arc was close to the arc front that was conducive to Cu mineralization in the porphyry system.

Molecular basis of branched peptides resistance to enzyme proteolysis.

PubMed

Falciani, Chiara; Lozzi, Luisa; Pini, Alessandro; Corti, Federico; Fabbrini, Monica; Bernini, Andrea; Lelli, Barbara; Niccolai, Neri; Bracci, Luisa

2007-03-01

We found that synthetic peptides in the form of dendrimers become resistant to proteolysis. To determine the molecular basis of this resistance, different bioactive peptides were synthesized in monomeric, two-branched and tetra-branched form and incubated with human plasma and serum. Proteolytic resistance of branched multimeric sequences was compared to that of the same peptides synthesized as multimeric linear molecules. Unmodified peptides and cleaved sequences were detected by high pressure liquid chromatography and mass spectrometry. An increase in peptide copies did not increase peptide resistance in linear multimeric sequences, whereas multimericity progressively enhanced proteolytic stability of branched multimeric peptides. A structure-based hypothesis of branched peptide resistance to proteolysis by metallopeptidases is presented.

Elucidating central metabolic redox obstacles hindering ethanol production in Clostridium thermocellum

DOE PAGES

Thompson, R. Adam; Layton, Donovan S.; Guss, Adam M.; ...

2015-10-21

Clostridium thermocellum is an anaerobic, Gram-positive, thermophilic bacterium that has generated great interest due to its ability to ferment lignocellulosic biomass to ethanol. However, ethanol production is low due to the complex and poorly understood branched metabolism of C. thermocellum, and in some cases overflow metabolism as well. In this work, we developed a predictive stoichiometric metabolic model for C. thermocellum which incorporates the current state of understanding, with particular attention to cofactor specificity in the atypical glycolytic enzymes and the complex energy, redox, and fermentative pathways with the goal of aiding metabolic engineering efforts. We validated the model smore » capability to encompass experimentally observed phenotypes for the parent strain and derived mutants designed for significant perturbation of redox and energy pathways. Metabolic flux distributions revealed significant alterations in key metabolic branch points (e.g., phosphoenol pyruvate, pyruvate, acetyl-CoA, and cofactor nodes) in engineered strains for channeling electron and carbon fluxes for enhanced ethanol synthesis, with the best performing strain doubling ethanol yield and titer compared to the parent strain. In silico predictions of a redox-imbalanced genotype incapable of growth were confirmed in vivo, and a mutant strain was used as a platform to probe redox bottlenecks in the central metabolism that hinder efficient ethanol production. The results highlight the robustness of the redox metabolism of C. thermocellum and the necessity of streamlined electron flux from reduced ferredoxin to NAD(P)H for high ethanol production. The model was further used to design a metabolic engineering strategy to phenotypically constrain C. thermocellum to achieve high ethanol yields while requiring minimal genetic manipulations. Furthermore, the model can be applied to design C. thermocellum as a platform microbe for consolidated bioprocessing to produce ethanol and other reduced metabolites.« less

High yield production of long branched Au nanoparticles characterized by atomic resolution transmission electron microscopy

PubMed Central

Mayoral, Alvaro; Magen, Cesar; Jose-Yacaman, Miguel

2011-01-01

Long multi-branched gold nanoparticles have been synthesized in a very high yield through a facile synthesis combining two different capping agents. The stability of these materials with the time has been tested and their characterization have been performed by diverse advanced electron microscopy techniques, paying special attention to aberration corrected transmission electron microscopy in order to unambiguously analyze the surface structure of the branches and provide insights for the formation of stellated gold nanoparticles. PMID:22125420

A Glycomics Platform for the Analysis of Permethylated Oligosaccharide Alditols

PubMed Central

Costello, Catherine E.; Contado-Miller, Joy May; Cipollo, John F.

2007-01-01

This communication reports the development of an LC/MS platform for the analysis of permethylated oligosaccharide alditols that, for the first time, demonstrates routine online oligosaccharide isomer separation of these compounds prior to introduction into the mass spectrometer. The method leverages a high resolution liquid chromatography system with the superior fragmentation pattern characteristics of permethylated oligosaccharide alditols that are dissociated under low-energy collision conditions using quadrupole orthogonal time-of-flight (QoTOF) instrumentation and up to pseudo MS3 mass spectrometry. Glycoforms, including isomers, are readily identified and their structures assigned. The isomer-specific spectra include highly informative cross-ring and elimination fragments, branch position specific signatures and glycosidic bond fragments, thus facilitating linkage, branch and sequence assignment. The method is sensitive and can be applied using as little as 40 fmol of derivatized oligosaccharide. Because permethylation renders oligosaccharides nearly chemically equivalent in the mass spectrometer, the method is semi-quantitative and, in this regard, is comparable to methods reported using high field NMR and capillary electrophoresis. In this post - genomic age, the importance of glycosylation in biological processes has become clear. The nature of many of the important questions in glycomics is such that sample material is often extremely limited, thus necessitating the development of highly sensitive methods for rigorous structural assignment of the oligosaccharides in complex mixtures. The glycomics platform presented here fulfills these criteria and should lead to more facile glycomics analyses. PMID:17719235

The evolution of hydrocarbons past the asymptotic giant branch: the case of MSX SMC 029

NASA Astrophysics Data System (ADS)

Pauly, Tyler; Sloan, Gregory C.; Kraemer, Kathleen E.; Bernard-Salas, Jeronimo; Lebouteiller, Vianney; Goes, Christopher; Barry, Donald

2015-01-01

We present an optimally extracted high-resolution spectrum of MSX SMC 029 obtained by the Infrared Spectrograph on the Spitzer Space Telescope. MSX SMC 029 is a carbon-rich object in the Small Magellanic Cloud that has evolved past the asymptotic giant branch (AGB). The spectrum reveals a cool carbon-rich dust continuum with emission from polycyclic aromatic hydrocarbons (PAHs) and absorption from simpler hydrocarbons, both aliphatic and aromatic, including acetylene and benzene. The spectrum shows many similarities to the carbon-rich post-AGB objects SMP LMC 011 in the Large Magellanic Cloud and AFGL 618 in the Galaxy. Both of these objects also show infrared absorption features from simple hydrocarbons. All three spectra lack strong atomic emission lines in the infrared, indicating that we are observing the evolution of carbon-rich dust and free hydrocarbons in objects between the AGB and planetary nebulae. These three objects give us a unique view of the elusive phase when hydrocarbons exist both as relatively simple molecules and the much more complex and ubiquitous PAHs. We may be witnessing the assembly of amorphous carbon into PAHs.

Endovascular Management of Thoracic Aortic Aneurysms

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

Fattori, Rossella, E-mail: rossella.fattori@unibo.it; Russo, Vincenzo; Lovato, Luigi

The overall survival of patients with thoracic aortic aneurysm (TAA) has improved significantly in the past few years. Endovascular treatment, proposed as an alternative to surgery, has been considered a therapeutic innovation because of its low degree of invasiveness, which allows the treatment of even high-surgical risk patients with limited complications and mortality. A major limitation is the lack of adequate evidence regarding long-term benefit and durability because follow-up has been limited to just a few years even in the largest series. The combination of endovascular exclusion with visceral branch revascularization for the treatment of thoraco-abdominal aortic aneurysms involving themore » visceral aorta has also been attempted. As an alternative, endografts with branches represent a technological evolution that allows treatment of complex anatomy. Even if only small numbers of patients and short follow-up are available, this technical approach, which has with limited mortality (<10%) and paraplegia rates, to expand endovascular treatment to TAA seems feasible. With improved capability to recognize proper anatomy and select clinical candidates, the choice of endovascular stent-graft placement may offer a strategy to optimize management and improve prognosis.« less

Cryogenic Vibrational Spectroscopy Provides Unique Fingerprints for Glycan Identification.

PubMed

Masellis, Chiara; Khanal, Neelam; Kamrath, Michael Z; Clemmer, David E; Rizzo, Thomas R

2017-10-01

The structural characterization of glycans by mass spectrometry is particularly challenging. This is because of the high degree of isomerism in which glycans of the same mass can differ in their stereochemistry, attachment points, and degree of branching. Here we show that the addition of cryogenic vibrational spectroscopy to mass and mobility measurements allows one to uniquely identify and characterize these complex biopolymers. We investigate six disaccharide isomers that differ in their stereochemistry, attachment point of the glycosidic bond, and monosaccharide content, and demonstrate that we can identify each one unambiguously. Even disaccharides that differ by a single stereogenic center or in the monosaccharide sequence order show distinct vibrational fingerprints that would clearly allow their identification in a mixture, which is not possible by ion mobility spectrometry/mass spectrometry alone. Moreover, this technique can be applied to larger glycans, which we demonstrate by distinguishing isomeric branched and linear pentasaccharides. The creation of a database containing mass, collision cross section, and vibrational fingerprint measurements for glycan standards should allow unambiguous identification and characterization of these biopolymers in mixtures, providing an enabling technology for all fields of glycoscience. Graphical Abstract ᅟ.

Structural features of soluble cereal arabinoxylan fibers associated with a slow rate of in vitro fermentation by human fecal microbiota.

PubMed

Rumpagaporn, Pinthip; Reuhs, Brad L; Kaur, Amandeep; Patterson, John A; Keshavarzian, Ali; Hamaker, Bruce R

2015-10-05

Most soluble dietary fibers ferment rapidly in the proximal colon, potentially causing discomfort and poor tolerability. Alkali-extracted arabinoxylan isolates from corn, wheat, rice and sorghum brans were prepared, through hydrolysis (except sorghum) and ethanol fractionation, to have a broad range of initial fermentation rates, and their linkage patterns were determined to understand structural aspects related to slow fermentation rate. They were all highly branched polymers with degree of substitution greater than 64%. There was no relationship of molecular mass, arabinose:xylose ratio, or degree of substitution to fermentation rate patterns. Slow fermenting wheat and corn arabinoxylans had much higher amount of terminal xylose in branches than fast fermenting rice and sorghum arabinoxylans. The slowest fermenting wheat arabinoxylan additionally contained a complex trisaccharide side chain with two arabinoses linked at the O-2 and O-3 positions of an arabinose that is O-2 linked to the xylan backbone. Structural features were proposed for tolerable slowly fermentable arabinoxylan with possible beneficial fermentation function into the distal colon. Copyright © 2015 Elsevier Ltd. All rights reserved.

Simulation of solute transport through heterogeneous networks: analysis using the method of moments and the statistics of local transport characteristics.

PubMed

Li, Min; Qi, Tao; Bernabé, Yves; Zhao, Jinzhou; Wang, Ying; Wang, Dong; Wang, Zheming

2018-02-28

We used a time domain random walk approach to simulate passive solute transport in networks. In individual pores, solute transport was modeled as a combination of Poiseuille flow and Taylor dispersion. The solute plume data were interpreted via the method of moments. Analysis of the first and second moments showed that the longitudinal dispersivity increased with increasing coefficient of variation of the pore radii CV and decreasing pore coordination number Z. The third moment was negative and its magnitude grew linearly with time, meaning that the simulated dispersion was intrinsically non-Fickian. The statistics of the Eulerian mean fluid velocities [Formula: see text], the Taylor dispersion coefficients [Formula: see text] and the transit times [Formula: see text] were very complex and strongly affected by CV and Z. In particular, the probability of occurrence of negative velocities grew with increasing CV and decreasing Z. Hence, backward and forward transit times had to be distinguished. The high-τ branch of the transit-times probability curves had a power law form associated to non-Fickian behavior. However, the exponent was insensitive to pore connectivity, although variations of Z affected the third moment growth. Thus, we conclude that both the low- and high-τ branches played a role in generating the observed non-Fickian behavior.

Quantification of Short-Chain Chlorinated Paraffins by Deuterodechlorination Combined with Gas Chromatography-Mass Spectrometry.

PubMed

Gao, Yuan; Zhang, Haijun; Zou, Lili; Wu, Ping; Yu, Zhengkun; Lu, Xianbo; Chen, Jiping

2016-04-05

Analysis of short-chain chlorinated paraffins (SCCPs) is extremely difficult because of their complex compositions with thousands of isomers and homologues. A novel analytical method, deuterodechlorination combined with high resolution gas chromatography-high resolution mass spectrometry (HRGC-HRMS), was developed. A protocol is applied in the deuterodechlorination of SCCPs with LiAlD4, and the formed deuterated n-alkanes of different alkane chains can be distinguished readily from each other on the basis of their retention time and fragment mass ([M](+)) by HRGC-HRMS. An internal standard quantification of individual SCCP congeners was achieved, in which branched C10-CPs and branched C12-CPs were used as the extraction and reaction internal standards, respectively. A maximum factor of 1.26 of the target SCCP concentrations were determined by this method, and the relative standard deviations for quantification of total SCCPs were within 10%. This method was applied to determine the congener compositions of SCCPs in commercial chlorinated paraffins and environmental and biota samples after method validation. Low-chlorinated SCCP congeners (Cl1-4) were found to account for 32.4%-62.4% of the total SCCPs. The present method provides an attractive perspective for further studies on the toxicological and environmental characteristics of SCCPs.

A study of the electrical properties of complex resistor network based on NW model

NASA Astrophysics Data System (ADS)

Chang, Yunfeng; Li, Yunting; Yang, Liu; Guo, Lu; Liu, Gaochao

2015-04-01

The power and resistance of two-port complex resistor network based on NW small world network model are studied in this paper. Mainly, we study the dependence of the network power and resistance on the degree of port vertices, the connection probability and the shortest distance. Qualitative analysis and a simplified formula for network resistance are given out. Finally, we define a branching parameter and give out its physical meaning in the analysis of complex resistor network.

Microsurgical anatomy of the extracerebral segment of recurrent artery of Heubner in the Mexican population.

PubMed

Gasca-González, Oscar Octavio; Delgado-Reyes, Luis; Pérez-Cruz, Julio César

2011-01-01

The recurrent artery of Heubner (RAH) is originated commonly from the anterior cerebral artery. Its extracerebral segment is directed toward the anterior perforate substance where it penetrates the cortex. The RAH was dissected from 15 human brains from Mexican population, and the presence, length, branches, course and either RHAs or anterior communicating artery complex variants were reported. The RAH was found in 93% of the hemispheres and duplicated in 39% of the hemispheres. The RAH was duplicated in at least a hemisphere in 46.6% of the brains; 40% of the brains had a RAH in every hemisphere. It was duplicated in every hemisphere in 20%. A single artery at a hemisphere was found in 26.6% and double at the other hemisphere. With a length between 13.6 and 36.7 mm (mean: 24.2 mm) and giving rise to 1-9 branches (mean: 3.9 branches), the RAH originated from the juxtacommunicating segment in 44% of the cases, from A2 in 41%, from A1 in 5% and as a branch of the frontopolar artery in 10%. It had an oblique course in 38%, an L in 31%, sinuous in 18% and an inverted L in 13%. In 53.3% of the brains, some variant of the anterior communicating artery complex was found. Because of the common anatomy of the RAH and its variants, we must consider the probability of finding it duplicated; therefore, it is necessary to make minute dissections of the region to locate or to secure the absence of the RAH.

Extralaryngeal branching of the recurrent laryngeal nerve: a meta-analysis of 28,387 nerves.

PubMed

Henry, Brandon Michael; Vikse, Jens; Graves, Matthew J; Sanna, Silvia; Sanna, Beatrice; Tomaszewska, Iwona M; Tubbs, R Shane; Tomaszewski, Krzysztof A

2016-11-01

The recurrent laryngeal nerves (RLN) are branches of the vagus nerve that go on to innervate most of the intrinsic muscles of the larynx. Historically, the RLN has been considered to branch after it enters the larynx, but numerous studies have demonstrated that it often branches before. The wide variability of this extralaryngeal branching (ELB) has significant implications for the risk of iatrogenic injury. We aimed to assess the anatomical characteristics of ELB comprehensively. Articles on the ELB of the RLN were identified by a comprehensive database search. Relevant data were extracted and pooled into a meta-analysis of the prevalence of branching, branching pattern, distance of ELB point from the larynx, and presence of positive motor signals in anterior and posterior ELB branches. A total of 69 articles (n = 28,387 nerves) from both intraoperative and cadaveric modalities were included in the meta-analysis. The overall pooled prevalence of ELB was 60.0 % (95 % CI 52.0-67.7). Cadaveric and intraoperative subgroups differed with prevalence rates of 73.3 % (95 % CI 61.0-84.0) and 39.2 % (95 % CI 29.0-49.9), respectively. Cadavers most often presented with a ELB pattern of bifurcation, with a prevalence of 61.1 %, followed by no branching at 23.4 %. Branching of the RLN occurred most often at a distance of 1-2 cm (74.8 % of cases) prior to entering the larynx. A positive motor signal was most often noted in anterior RLN branches (99.9 %) but only in 1.5 % of posterior branches. The anatomy of the RLN is highly variable, and ELB is likely to have been underreported in intraoperative studies. Because of its high likelihood, the possibility of ELB needs to be assessed in patients to prevent iatrogenic injury and long-term postoperative complications.

Fractal branching organizations of Ediacaran rangeomorph fronds reveal a lost Proterozoic body plan.

PubMed

Hoyal Cuthill, Jennifer F; Conway Morris, Simon

2014-09-09

The branching morphology of Ediacaran rangeomorph fronds has no exact counterpart in other complex macroorganisms. As such, these fossils pose major questions as to growth patterns, functional morphology, modes of feeding, and adaptive optimality. Here, using parametric Lindenmayer systems, a formal model of rangeomorph morphologies reveals a fractal body plan characterized by self-similar, axial, apical, alternate branching. Consequent morphological reconstruction for 11 taxa demonstrates an adaptive radiation based on 3D space-filling strategies. The fractal body plan of rangeomorphs is shown to maximize surface area, consistent with diffusive nutrient uptake from the water column (osmotrophy). The enigmas of rangeomorph morphology, evolution, and extinction are resolved by the realization that they were adaptively optimized for unique ecological and geochemical conditions in the late Proterozoic. Changes in ocean conditions associated with the Cambrian explosion sealed their fate.

Modeling the Interaction Between Hydraulic and Natural Fractures Using Dual-Lattice Discrete Element Method

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

Zhou, Jing; Huang, Hai; Deo, Milind

The interaction between hydraulic fractures (HF) and natural fractures (NF) will lead to complex fracture networks due to the branching and merging of natural and hydraulic fractures in unconventional reservoirs. In this paper, a newly developed hydraulic fracturing simulator based on discrete element method is used to predict the generation of complex fracture network in the presence of pre-existing natural fractures. By coupling geomechanics and reservoir flow within a dual lattice system, this simulator can effectively capture the poro-elastic effects and fluid leakoff into the formation. When HFs are intercepting single or multiple NFs, complex mechanisms such as direct crossing,more » arresting, dilating and branching can be simulated. Based on the model, the effects of injected fluid rate and viscosity, the orientation and permeability of NFs and stress anisotropy on the HF-NF interaction process are investigated. Combined impacts from multiple parameters are also examined in the paper. The numerical results show that large values of stress anisotropy, intercepting angle, injection rate and viscosity will impede the opening of NFs.« less

Computer analysis of potentiometric data of complexes formation in the solution

NASA Astrophysics Data System (ADS)

Jastrzab, Renata; Kaczmarek, Małgorzata T.; Tylkowski, Bartosz; Odani, Akira

2018-02-01

The determination of equilibrium constants is an important process for many branches of chemistry. In this review we provide the readers with a discussion on computer methods which have been applied for elaboration of potentiometric experimental data generated during complexes formation in solution. The review describes both: general basis of modeling tools and examples of the use of calculated stability constants.

Precision Branching Ratio Measurement for the Superallowed &+circ; Emitter ^62Ga

NASA Astrophysics Data System (ADS)

Finlay, Paul; Svensson, C. E.; Austin, R. A. E.; Ball, G. C.; Bandyopadhyay, D.; Chaffey, A.; Chakrawarthy, R. S.; Garrett, P. E.; Grinyer, G. F.; Hackman, G.; Hyland, B.; Kanungo, R.; Leslie, J. R.; Mattoon, C.; Morton, A. C.; Pearson, C. J.; Ressler, J. J.; Sarazin, F.; Savajols, H.

2007-10-01

A high-precision branching ratio measurement for the superallowed &+circ; emitter ^62Ga has been made using the 8π γ-ray spectrometer in conjunction with the SCintillating Electron-Positron Tagging ARray (SCEPTAR) as part of an ongoing experimental program in superallowed Fermi beta decay studies at the Isotope Separator and Accelerator (ISAC) facility at TRIUMF in Vancouver, Canada, which delivered a high-purity beam of ˜10^4 ^62Ga/s in December 2005. The present work represents the highest statistics measurement of the ^62Ga superallowed branching ratio to date. 25 γ rays emitted following non-superallowed decay branches of ^62Ga have been identified and their intensities determined. These data yield a superallowed branching ratio with 10-4 precision, and our observed branch to the first nonanalogue 0^+ state sets a new upper limit on the isospin-mixing correction δC1^1. By comparing our ft value with the world average Ft, we make stringent tests of the different calculations for the isospin-symmetry-breaking correction δC, which is predicted to be large for ^62Ga.

Selective methylative homologation: an alternate route to alkane upgrading.

PubMed

Bercaw, John E; Hazari, Nilay; Labinger, Jay A; Scott, Valerie J; Sunley, Glenn J

2008-09-10

InI3 catalyzes the reaction of branched alkanes with methanol to produce heavier and more highly branched alkanes, which are more valuable fuels. The reaction of 2,3-dimethylbutane with methanol in the presence of InI3 at 180-200 degrees C affords the maximally branched C7 alkane, 2,2,3-trimethylbutane (triptane). With the addition of catalytic amounts of adamantane the selectivity of this transformation can be increased up to 60%. The lighter branched alkanes isobutane and isopentane also react with methanol to generate triptane, while 2-methylpentane is converted into 2,3-dimethylpentane and other more highly branched species. Observations implicate a chain mechanism in which InI3 activates branched alkanes to produce tertiary carbocations which are in equilibrium with olefins. The latter react with a methylating species generated from methanol and InI3 to give the next-higher carbocation, which accepts a hydride from the starting alkane to form the homologated alkane and regenerate the original carbocation. Adamantane functions as a hydride transfer agent and thus helps to minimize competing side reactions, such as isomerization and cracking, that are detrimental to selectivity.

Loss of Highly Branched Arabinans and Debranching of Rhamnogalacturonan I Accompany Loss of Firm Texture and Cell Separation during Prolonged Storage of Apple1

PubMed Central

Peña, María J.; Carpita, Nicholas C.

2004-01-01

Growth and maturation of the edible cortical cells of apples (Malus domestica Borkh) are accompanied by a selective loss of pectin-associated (1→4)-β-d-galactan from the cell walls, whereas a selective loss of highly branched (1→5)-α-l-arabinans occurs after ripening and in advance of the loss of firm texture. The selective loss of highly branched arabinans occurs during the overripening of apples of four cultivars (Gala, Red Delicious, Firm Gold, and Gold Rush) that varied markedly in storage life, but, in all instances, the loss prestages the loss of firm texture, measured by both breaking strength and compression resistance. The unbranched (1→5)-linked arabinans remain associated with the major pectic polymer, rhamnogalacturonan I, and their content remains essentially unchanged during overripening. However, the degree of rhamnogalacturonan I branching at the rhamnosyl residues also decreases, but only after extensive loss of the highly branched arabinans. In contrast to the decrease in arabinan content, the loss of the rhamnogalacturonan I branching is tightly correlated with loss of firm texture in all cultivars, regardless of storage time. In vitro cell separation assays show that structural proteins, perhaps via their phenolic residues, and homogalacturonans also contribute to cell adhesion. Implications of these cell wall modifications in the mechanisms of apple cortex textural changes and cell separation are discussed. PMID:15247384

High-Precision Half-Life and Branching Ratio Measurements for the Superallowed β+ Emitter 26Alm

NASA Astrophysics Data System (ADS)

Finlay, P.; Svensson, C. E.; Demand, G. A.; Garrett, P. E.; Green, K. L.; Leach, K. G.; Phillips, A. A.; Rand, E. T.; Ball, G.; Bandyopadhyay, D.; Djongolov, M.; Ettenauer, S.; Hackman, G.; Pearson, C. J.; Leslie, J. R.; Andreoiu, C.; Cross, D.; Austin, R. A. E.; Grinyer, G. F.; Sumithrarachchi, C. S.; Williams, S. J.; Triambak, S.

2013-03-01

High-precision half-life and branching-ratio measurements for the superallowed β+ emitter 26Alm were performed at the TRIUMF-ISAC radioactive ion beam facility. An upper limit of ≤ 15 ppm at 90% C.L. was determined for the sum of all possible non-analogue β+/EC decay branches of 26Alm, yielding a superallowed branching ratio of 100.0000+0-0.0015%. A value of T1/2 = 6:34654(76) s was determined for the 26Alm half-life which is consistent with, but 2.5 times more precise than, the previous world average. Combining these results with world-average measurements yields an ft value of 3037.58(60) s, the most precisely determined for any superallowed emitting nucleus to date. This high-precision ft value for 26Alm provides a new benchmark to refine theoretical models of isospin-symmetry-breaking effects in superallowed β decays.

Branching habit and the allocation of reproductive resources in conifers.

PubMed

Leslie, Andrew B

2012-09-01

Correlated relationships between branch thickness, branch density, and twig and leaf size have been used extensively to study the evolution of plant canopy architecture, but fewer studies have explored the impact of these relationships on the allocation of reproductive resources. This study quantifies pollen cone production in conifers, which have similar basic reproductive biology but vary dramatically in branching habit, in order to test how differences in branch diameter influence pollen cone size and the density with which they are deployed in the canopy. Measurements of canopy branch density, the number of cones per branch and cone size were used to estimate the amount of pollen cone tissues produced by 16 species in three major conifer clades. The number of pollen grains produced was also estimated using direct counts from individual pollen cones. The total amount of pollen cone tissues in the conifer canopy varied little among species and clades, although vegetative traits such as branch thickness, branch density and pollen cone size varied over several orders of magnitude. However, branching habit controls the way these tissues are deployed: taxa with small branches produce small pollen cones at a high density, while taxa with large branches produce large cones relatively sparsely. Conifers appear to invest similar amounts of energy in pollen production independent of branching habit. However, similar associations between branch thickness, branch density and pollen cone size are seen across conifers, including members of living and extinct groups not directly studied here. This suggests that reproductive features relating to pollen cone size are in large part a function of the evolution of vegetative morphology and branching habit.

Growth mechanisms of MgO nanocrystals via a sol-gel synthesis using different complexing agents

PubMed Central

2014-01-01

In the preparation of nanostructured materials, it is important to optimize synthesis parameters in order to obtain the desired material. This work investigates the role of complexing agents, oxalic acid and tartaric acid, in the production of MgO nanocrystals. Results from simultaneous thermogravimetric analysis (STA) show that the two different synthesis routes yield precursors with different thermal profiles. It is found that the thermal profiles of the precursors can reveal the effects of crystal growth during thermal annealing. X-ray diffraction confirms that the final products are pure, single phase and of cubic shape. It is also found that complexing agents can affect the rate of crystal growth. The structures of the oxalic acid and tartaric acid as well as the complexation sites play very important roles in the formation of the nanocrystals. The complexing agents influence the rate of growth which affects the final crystallite size of the materials. Surprisingly, it is also found that oxalic acid and tartaric acid act as surfactants inhibiting crystal growth even at a high temperature of 950°C and a long annealing time of 36 h. The crystallite formation routes are proposed to be via linear and branched polymer networks due to the different structures of the complexing agents. PMID:24650322

High-Temperature, Thin-Film Ceramic Thermocouples Developed

NASA Technical Reports Server (NTRS)

Sayir, Ali; Blaha, Charles A.; Gonzalez, Jose M.

2005-01-01

To enable long-duration, more distant human and robotic missions for the Vision for Space Exploration, as well as safer, lighter, quieter, and more fuel efficient vehicles for aeronautics and space transportation, NASA is developing instrumentation and material technologies. The high-temperature capabilities of thin-film ceramic thermocouples are being explored at the NASA Glenn Research Center by the Sensors and Electronics Branch and the Ceramics Branch in partnership with Case Western Reserve University (CWRU). Glenn s Sensors and Electronics Branch is developing thin-film sensors for surface measurement of strain, temperature, heat flux, and surface flow in propulsion system research. Glenn s Ceramics Branch, in conjunction with CWRU, is developing structural and functional ceramic technology for aeropropulsion and space propulsion.

HIV vulnerability and the erasure of sexual and gender diversity in Abidjan, Côte d'Ivoire.

PubMed

Thomann, Matthew

2016-01-01

In the fight against concentrated HIV epidemics, men who have sex with men (MSM) are often framed as a homogeneous population, with little attention paid to sexual and gender diversity and its impact on HIV vulnerability. This article draws on ethnographic research conducted in Abidjan, Côte d'Ivoire among les branchés - a local term encompassing several categories of same-sex desire and practice. In the context of increased HIV prevention programming targeting Ivoirian sexual and gender minorities, such diversity is effectively erased. This obfuscation of difference has particularly negative impacts for travestis, who may be at higher risk for HIV infection, though research and prevention efforts in which they are grouped with 'MSM' render them underrepresented and make their vulnerability difficult to quantify. Branchés whose class and/or ethnic backgrounds compound their stigmatised status as sexual and gender minorities also bear the burden of this exclusion. Furthermore, some branchés deploy 'MSM' as a form of self-identification, further complicating who such categories represent. By highlighting the ways in which constructions of gender and sexuality within HIV/AIDS programming obscure complex social realities, I aim to reorient thinking around the development of purposeful HIV programming that engages the complexity of sexual and gender minority experience.

BCAA Metabolism and NH3 Homeostasis.

PubMed

Conway, M E; Hutson, S M

2016-01-01

The branched chain amino acids (BCAA) are essential amino acids required not only for growth and development, but also as nutrient signals and as nitrogen donors to neurotransmitter synthesis and glutamate/glutamine cycling. Transamination and oxidative decarboxylation of the BCAAs are catalysed by the branched-chain aminotransferase proteins (BCATm, mitochondrial and BCATc, cytosolic) and the branched-chain α-keto acid dehydrogenase enzyme complex (BCKDC), respectively. These proteins show tissue, cell compartmentation, and protein-protein interactions, which call for substrate shuttling or channelling and nitrogen transfer for oxidation to occur. Efficient regulation of these pathways is mediated through the redox environment and phosphorylation in response to dietary and hormonal stimuli. The wide distribution of these proteins allows for effective BCAA utilisation. We discuss how BCAT, BCKDC, and glutamate dehydrogenase operate in supramolecular complexes, allowing for efficient channelling of substrates. The role of BCAAs in brain metabolism is highlighted in rodent and human brain, where differential expression of BCATm indicates differences in nitrogen metabolism between species. Finally, we introduce a new role for BCAT, where a change in function is triggered by oxidation of its redox-active switch. Our understanding of how BCAA metabolism and nitrogen transfer is regulated is important as many studies now point to BCAA metabolic dysregulation in metabolic and neurodegenerative conditions.

Phenotypic, histological and proteomic analyses reveal multiple differences associated with chloroplast development in yellow and variegated variants from Camellia sinensis

PubMed Central

Ma, Chengying; Cao, Junxi; Li, Jianke; Zhou, Bo; Tang, Jinchi; Miao, Aiqing

2016-01-01

Leaf colour variation is observed in several plants. We obtained two types of branches with yellow and variegated leaves from Camellia sinensis. To reveal the mechanisms that underlie the leaf colour variations, combined morphological, histological, ionomic and proteomic analyses were performed using leaves from abnormal branches (variants) and normal branches (CKs). The measurement of the CIE-Lab coordinates showed that the brightness and yellowness of the variants were more intense than the CKs. When chloroplast profiles were analysed, HY1 (branch with yellow leaves) and HY2 (branch with variegated leaves) displayed abnormal chloroplast structures and a reduced number and size compared with the CKs, indicating that the abnormal chloroplast development might be tightly linked to the leaf colour variations. Moreover, the concentration of elemental minerals was different between the variants and the CKs. Furthermore, DEPs (differentially expressed proteins) were identified in the variants and the CKs by a quantitative proteomics analysis using the label-free approach. The DEPs were significantly involved in photosynthesis and included PSI, PSII, cytochrome b6/f complex, photosynthetic electron transport, LHC and F-type ATPase. Our results suggested that a decrease in the abundance of photosynthetic proteins might be associated with the changes of leaf colours in tea plants. PMID:27633059

Structure of a human pulmonary acinus.

PubMed

Berend, N; Rynell, A C; Ward, H E

1991-02-01

The structure of the human pulmonary acinus has been described infrequently. The aim of the study was to determine the branching pattern of respiratory bronchioles and alveolar ducts in a human acinus from the peripheral part of the lung, where space constraints may have affected airway branching patterns. The lungs were obtained from an 18 year old victim of a motor vehicle accident and fixed in inflation under a pressure of 25 cm H2O. A block was cut from the lower edge of the right lower lobe and embedded in plastic. Serial sections were cut and the branching pattern of airways subtended by a terminal bronchiole were followed. The acinus was bounded on two sides by pleura and on the remaining sides by connective tissue septa. The terminal bronchiole divided into two respiratory bronchioles, each of which gave rise to four systems of alveolar ducts. Between successive systems of alveolar ducts the respiratory bronchioles continued as single airways, becoming progressively more alveolated towards the periphery but not subtending further branches of respiratory bronchioles. The duct systems became less complex towards the periphery, near to the edge of the lung. The total volume of the acinus was similar to that found in previous studies. This branching pattern has not been described previously in a human acinus.

SDF1 regulates leading process branching and speed of migrating interneurons

PubMed Central

Lysko, Daniel E.; Putt, Mary; Golden, Jeffrey A.

2011-01-01

Cell migration is required for normal embryonic development, yet how cells navigate complex paths while integrating multiple guidance cues remains poorly understood. During brain development, interneurons migrate from the ventral ganglionic eminence to the cerebral cortex within several migratory streams. They must exit these streams to invade the cortical plate. While SDF1-signaling is necessary for normal interneuron stream migration, how they switch from tangential stream migration to invade the cortical plate is unknown. Here we demonstrate that SDF1-signaling reduces interneuron branching frequency by reducing cAMP levels via a Gi-signaling pathway using an in vitro mouse explant system, resulting in the maintenance of stream migration. Blocking SDF1-signaling, or increasing branching frequency, results in stream exit and cortical plate invasion in mouse brain slices. These data support a novel model to understand how migrating interneurons switch from tangential migration to invade the cortical plate in which reducing SDF1-signaling increases leading process branching and slows the migration rate, permitting migrating interneurons to sense cortically directed guidance cues. PMID:21289183

Towards engineered branch placement: Unreal™ match between vapour-liquid-solid glancing angle deposition nanowire growth and simulation

NASA Astrophysics Data System (ADS)

Taschuk, M. T.; Tucker, R. T.; LaForge, J. M.; Beaudry, A. L.; Kupsta, M. R.; Brett, M. J.

2013-12-01

The vapour-liquid-solid glancing angle deposition (VLS-GLAD) process is capable of producing complex nanotree structures with control over azimuthal branch orientation and height. We have developed a thin film growth simulation including ballistic deposition, simplified surface diffusion, and droplet-mediated cubic crystal growth for the VLS-GLAD process using the UnrealTM Development Kit. The use of a commercial game engine has provided an interactive environment while allowing a custom physics implementation. Our simulation's output is verified against experimental data, including a volumetric film reconstruction produced using focused ion beam and scanning-electron microscopy (SEM), crystallographic texture, and morphological characteristics such as branch orientation. We achieve excellent morphological and texture agreement with experimental data, as well as qualitative agreement with SEM imagery. The simplified physics in our model reproduces the experimental films, indicating that the dominant role flux geometry plays in the VLS-GLAD competitive growth process responsible for azimuthally oriented branches and biaxial crystal texture evolution. The simulation's successful reproduction of experimental data indicates that it should have predictive power in designing novel VLS-GLAD structures.

Tree branch-shaped cupric oxide for highly effective photoelectrochemical water reduction

NASA Astrophysics Data System (ADS)

Jang, Youn Jeong; Jang, Ji-Wook; Choi, Sun Hee; Kim, Jae Young; Kim, Ju Hun; Youn, Duck Hyun; Kim, Won Yong; Han, Suenghoon; Sung Lee, Jae

2015-04-01

Highly efficient tree branch-shaped CuO photocathodes are fabricated using the hybrid microwave annealing process with a silicon susceptor within 10 minutes. The unique hierarchical, one-dimensional structure provides more facile charge transport, larger surface areas, and increased crystallinity and crystal ordering with less defects compared to irregular-shaped CuO prepared by conventional thermal annealing. As a result, the photocathode fabricated with the tree branch-shaped CuO produces an unprecedently high photocurrent density of -4.4 mA cm-2 at 0 VRHE under AM 1.5 G simulated sunlight compared to -1.44 mA cm-2 observed for a photocathode fabricated by thermal annealing. It is also confirmed that stoichiometric hydrogen and oxygen are produced from photoelectrochemical water splitting on the tree branch-shaped CuO photocathode and a platinum anode.Highly efficient tree branch-shaped CuO photocathodes are fabricated using the hybrid microwave annealing process with a silicon susceptor within 10 minutes. The unique hierarchical, one-dimensional structure provides more facile charge transport, larger surface areas, and increased crystallinity and crystal ordering with less defects compared to irregular-shaped CuO prepared by conventional thermal annealing. As a result, the photocathode fabricated with the tree branch-shaped CuO produces an unprecedently high photocurrent density of -4.4 mA cm-2 at 0 VRHE under AM 1.5 G simulated sunlight compared to -1.44 mA cm-2 observed for a photocathode fabricated by thermal annealing. It is also confirmed that stoichiometric hydrogen and oxygen are produced from photoelectrochemical water splitting on the tree branch-shaped CuO photocathode and a platinum anode. Electronic supplementary information (ESI) available: The detailed schematic diagram for the HMA process, XRD results, the temperature profile during HMA, derivative XANES results, TEM images, J-V curves, lists of previously reported copper oxide photocathode, and parameters extracted from EIS. See DOI: 10.1039/c5nr00208g

Cooperative 3D Path Optimization (C3PO) Simulation

DTIC Science & Technology

2015-11-10

is the starting point for the path. As branches are added, they are checked to make sure they meet the requirements that the unmanned vehicle (UV...tune the maximum branch size for the tree to get longer branches. It makes sense that in open space this would lead to smaller (by number of nodes...starting with very high maximum branch size and gradually make it smaller as suitable paths can’t be found. The authors would also like to try this

A Babcock-Leighton Solar Dynamo Model with Multi-cellular Meridional Circulation in Advection- and Diffusion-dominated Regimes

NASA Astrophysics Data System (ADS)

Belucz, Bernadett; Dikpati, Mausumi; Forgács-Dajka, Emese

2015-06-01

Babcock-Leighton type-solar dynamo models with single-celled meridional circulation are successful in reproducing many solar cycle features. Recent observations and theoretical models of meridional circulation do not indicate a single-celled flow pattern. We examine the role of complex multi-cellular circulation patterns in a Babcock-Leighton solar dynamo in advection- and diffusion-dominated regimes. We show from simulations that the presence of a weak, second, high-latitude reverse cell speeds up the cycle and slightly enhances the poleward branch in the butterfly diagram, whereas the presence of a second cell in depth reverses the tilt of the butterfly wing to an antisolar type. A butterfly diagram constructed from the middle of convection zone yields a solar-like pattern, but this may be difficult to realize in the Sun because of magnetic buoyancy effects. Each of the above cases behaves similarly in higher and lower magnetic diffusivity regimes. However, our dynamo with a meridional circulation containing four cells in latitude behaves distinctly differently in the two regimes, producing solar-like butterfly diagrams with fast cycles in the higher diffusivity regime, and complex branches in butterfly diagrams in the lower diffusivity regime. We also find that dynamo solutions for a four-celled pattern, two in radius and two in latitude, prefer to quickly relax to quadrupolar parity if the bottom flow speed is strong enough, of similar order of magnitude as the surface flow speed.

A BABCOCK–LEIGHTON SOLAR DYNAMO MODEL WITH MULTI-CELLULAR MERIDIONAL CIRCULATION IN ADVECTION- AND DIFFUSION-DOMINATED REGIMES

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

Belucz, Bernadett; Forgács-Dajka, Emese; Dikpati, Mausumi, E-mail: bbelucz@astro.elte.hu, E-mail: dikpati@ucar.edu

Babcock–Leighton type-solar dynamo models with single-celled meridional circulation are successful in reproducing many solar cycle features. Recent observations and theoretical models of meridional circulation do not indicate a single-celled flow pattern. We examine the role of complex multi-cellular circulation patterns in a Babcock–Leighton solar dynamo in advection- and diffusion-dominated regimes. We show from simulations that the presence of a weak, second, high-latitude reverse cell speeds up the cycle and slightly enhances the poleward branch in the butterfly diagram, whereas the presence of a second cell in depth reverses the tilt of the butterfly wing to an antisolar type. A butterflymore » diagram constructed from the middle of convection zone yields a solar-like pattern, but this may be difficult to realize in the Sun because of magnetic buoyancy effects. Each of the above cases behaves similarly in higher and lower magnetic diffusivity regimes. However, our dynamo with a meridional circulation containing four cells in latitude behaves distinctly differently in the two regimes, producing solar-like butterfly diagrams with fast cycles in the higher diffusivity regime, and complex branches in butterfly diagrams in the lower diffusivity regime. We also find that dynamo solutions for a four-celled pattern, two in radius and two in latitude, prefer to quickly relax to quadrupolar parity if the bottom flow speed is strong enough, of similar order of magnitude as the surface flow speed.« less

High-yield aqueous synthesis of multi-branched iron oxide core-gold shell nanoparticles: SERS substrate for immobilization and magnetic separation of bacteria

NASA Astrophysics Data System (ADS)

Tamer, Ugur; Onay, Aykut; Ciftci, Hakan; Bozkurt, Akif Göktuğ; Cetin, Demet; Suludere, Zekiye; Hakkı Boyacı, İsmail; Daniel, Philippe; Lagarde, Fabienne; Yaacoub, Nader; Greneche, Jean-Marc

2014-10-01

The high product yield of multi-branched core-shell Fe3- x O4@Au magnetic nanoparticles was synthesized used as magnetic separation platform and surface-enhanced Raman scattering (SERS) substrates. The multi-branched magnetic nanoparticles were prepared by a seed-mediated growth approach using magnetic gold nanospheres as the seeds and subsequent reduction of metal salt with ascorbic acid in the presence of a stabilizing agent chitosan biopolymer and silver ions. The anisotropic growth of nanoparticles was observed in the presence of chitosan polymer matrix resulting in multi-branched nanoparticles with a diameter over 100 nm, and silver ions also play a crucial role on the growth of multi-branched nanoparticles. We propose the mechanism of the formation of multi-branched nanoparticles while the properties of nanoparticles embedded in chitosan matrix are discussed. The surface morphology of nanoparticles was characterized with transmission electron microscopy, scanning electron microscopy, ultraviolet visible spectroscopy (UV-Vis), X-ray diffraction, and fourier transform infrared spectroscopy and 57Fe Mössbauer spectrometry. Additionally, the magnetic properties of the nanoparticles were also examined. We also demonstrated that the synthesized Fe3- x O4@Au multi-branched nanoparticle is capable of targeted separation of pathogens from matrix and sensing as SERS substrates.

Genetic Predisposition to an Impaired Metabolism of the Branched-Chain Amino Acids and Risk of Type 2 Diabetes: A Mendelian Randomisation Analysis.

PubMed

Lotta, Luca A; Scott, Robert A; Sharp, Stephen J; Burgess, Stephen; Luan, Jian'an; Tillin, Therese; Schmidt, Amand F; Imamura, Fumiaki; Stewart, Isobel D; Perry, John R B; Marney, Luke; Koulman, Albert; Karoly, Edward D; Forouhi, Nita G; Sjögren, Rasmus J O; Näslund, Erik; Zierath, Juleen R; Krook, Anna; Savage, David B; Griffin, Julian L; Chaturvedi, Nishi; Hingorani, Aroon D; Khaw, Kay-Tee; Barroso, Inês; McCarthy, Mark I; O'Rahilly, Stephen; Wareham, Nicholas J; Langenberg, Claudia

2016-11-01

Higher circulating levels of the branched-chain amino acids (BCAAs; i.e., isoleucine, leucine, and valine) are strongly associated with higher type 2 diabetes risk, but it is not known whether this association is causal. We undertook large-scale human genetic analyses to address this question. Genome-wide studies of BCAA levels in 16,596 individuals revealed five genomic regions associated at genome-wide levels of significance (p < 5 × 10-8). The strongest signal was 21 kb upstream of the PPM1K gene (beta in standard deviations [SDs] of leucine per allele = 0.08, p = 3.9 × 10-25), encoding an activator of the mitochondrial branched-chain alpha-ketoacid dehydrogenase (BCKD) responsible for the rate-limiting step in BCAA catabolism. In another analysis, in up to 47,877 cases of type 2 diabetes and 267,694 controls, a genetically predicted difference of 1 SD in amino acid level was associated with an odds ratio for type 2 diabetes of 1.44 (95% CI 1.26-1.65, p = 9.5 × 10-8) for isoleucine, 1.85 (95% CI 1.41-2.42, p = 7.3 × 10-6) for leucine, and 1.54 (95% CI 1.28-1.84, p = 4.2 × 10-6) for valine. Estimates were highly consistent with those from prospective observational studies of the association between BCAA levels and incident type 2 diabetes in a meta-analysis of 1,992 cases and 4,319 non-cases. Metabolome-wide association analyses of BCAA-raising alleles revealed high specificity to the BCAA pathway and an accumulation of metabolites upstream of branched-chain alpha-ketoacid oxidation, consistent with reduced BCKD activity. Limitations of this study are that, while the association of genetic variants appeared highly specific, the possibility of pleiotropic associations cannot be entirely excluded. Similar to other complex phenotypes, genetic scores used in the study captured a limited proportion of the heritability in BCAA levels. Therefore, it is possible that only some of the mechanisms that increase BCAA levels or affect BCAA metabolism are implicated in type 2 diabetes. Evidence from this large-scale human genetic and metabolomic study is consistent with a causal role of BCAA metabolism in the aetiology of type 2 diabetes.

mTORC1 Is a Local, Postsynaptic Voltage Sensor Regulated by Positive and Negative Feedback Pathways

PubMed Central

Niere, Farr; Raab-Graham, Kimberly F.

2017-01-01

The mammalian/mechanistic target of rapamycin complex 1 (mTORC1) serves as a regulator of mRNA translation. Recent studies suggest that mTORC1 may also serve as a local, voltage sensor in the postsynaptic region of neurons. Considering biochemical, bioinformatics and imaging data, we hypothesize that the activity state of mTORC1 dynamically regulates local membrane potential by promoting and repressing protein synthesis of select mRNAs. Our hypothesis suggests that mTORC1 uses positive and negative feedback pathways, in a branch-specific manner, to maintain neuronal excitability within an optimal range. In some dendritic branches, mTORC1 activity oscillates between the “On” and “Off” states. We define this as negative feedback. In contrast, positive feedback is defined as the pathway that leads to a prolonged depolarized or hyperpolarized resting membrane potential, whereby mTORC1 activity is constitutively on or off, respectively. We propose that inactivation of mTORC1 increases the expression of voltage-gated potassium alpha (Kv1.1 and 1.2) and beta (Kvβ2) subunits, ensuring that the membrane resets to its resting membrane potential after experiencing increased synaptic activity. In turn, reduced mTORC1 activity increases the protein expression of syntaxin-1A and promotes the surface expression of the ionotropic glutamate receptor N-methyl-D-aspartate (NMDA)-type subunit 1 (GluN1) that facilitates increased calcium entry to turn mTORC1 back on. Under conditions such as learning and memory, mTORC1 activity is required to be high for longer periods of time. Thus, the arm of the pathway that promotes syntaxin-1A and Kv1 protein synthesis will be repressed. Moreover, dendritic branches that have low mTORC1 activity with increased Kv expression would balance dendrites with constitutively high mTORC1 activity, allowing for the neuron to maintain its overall activity level within an ideal operating range. Finally, such a model suggests that recruitment of more positive feedback dendritic branches within a neuron is likely to lead to neurodegenerative disorders. PMID:28611595

Olefin polymerization from single site catalysts confined within porous media

NASA Astrophysics Data System (ADS)

Kasi, Rajeswari M.

Single Site Catalysts (SSCs) have been utilized for olefin polymerization. Altering the metal-ligand architecture in the SSCs, polyolefin properties can be enhanced in a rational manner. This influence of the ligands in the SSC on the property of polyolefins prepared can be referred to as the primary ligand influence. Extending this understanding and subsequent control of the metal-ligand framework to the interaction of SSCs within organic and inorganic supports is vital for the synthesis of polyolefins with tailored properties. The motivation behind this thesis was to explore the support influence on the reactivity of the SSC tethered to a support matrix during ethylene homo and copolymerization. In order to address this question of the support influence on the final polyolefin properties, synthetic routes to covalently bind SSCs on different matrices have been explored. Two distinct supported SSCs have been used to prepare branched polyethylenes. Branched polyethylenes can be prepared by either copolymerization (ethylene and alpha-olefin) or oligomerization/copolymerization processes (ethylene and in situ generated alpha-olefin). Synthetic routes to prepare precursor catalysts to Constrained Geometry Catalysts (CGCs) by silyl elimination chemistry have been developed (Chapter 2). Efficient synthetic protocols to assemble CGCs on aminomethylpolysytrene matrices (Chapter 3) and amine-functionalized mesoporous silica (Chapter 4) are also reported. These supported catalysts, with appropriate cocatalysts have been used to prepare ethylene homo and copolymers, the polymer thermal properties and microstructures were analyzed by various analytical techniques. Branched polyethylenes (LLDPE) can be prepared by copolymerization chemistry. It has been observed is that the influence of the support is seen in the production of lower crystalline forms of high density polyethylene (HDPE, 20--50% crystalline), while homogeneous polymerization of analogous soluble CGCs afford HDPE of higher percent crystallinity (greater than 60% crystalline). High-density polyethylene with crystallinity of 40--60% can be prepared by using cocatalysts tethered to AMPS or silica in conjunction with analogous soluble, homogeneous CGCs (Chapter 6). Preparative methods to assemble piano stool complexes on hydroxy polystyrenes have been designed. These supported catalysts in conjunction with cocatalysts act as both oligomerization and copolymerization catalysts and allow the preparation of branched polyethylenes from ethylene only feed (Chapter 7).

Yleaf: Software for Human Y-Chromosomal Haplogroup Inference from Next-Generation Sequencing Data.

PubMed

Ralf, Arwin; Montiel González, Diego; Zhong, Kaiyin; Kayser, Manfred

2018-05-01

Next-generation sequencing (NGS) technologies offer immense possibilities given the large genomic data they simultaneously deliver. The human Y-chromosome serves as good example how NGS benefits various applications in evolution, anthropology, genealogy, and forensics. Prior to NGS, the Y-chromosome phylogenetic tree consisted of a few hundred branches, based on NGS data, it now contains many thousands. The complexity of both, Y tree and NGS data provide challenges for haplogroup assignment. For effective analysis and interpretation of Y-chromosome NGS data, we present Yleaf, a publically available, automated, user-friendly software for high-resolution Y-chromosome haplogroup inference independently of library and sequencing methods.

Conservation and Divergence in the Candida Species Biofilm Matrix Mannan-Glucan Complex Structure, Function, and Genetic Control

PubMed Central

Dominguez, Eddie; Zarnowski, Robert; Sanchez, Hiram; Covelli, Antonio S.; Westler, William M.; Azadi, Parastoo; Nett, Jeniel

2018-01-01

ABSTRACT Candida biofilms resist the effects of available antifungal therapies. Prior studies with Candida albicans biofilms show that an extracellular matrix mannan-glucan complex (MGCx) contributes to antifungal sequestration, leading to drug resistance. Here we implement biochemical, pharmacological, and genetic approaches to explore a similar mechanism of resistance for the three most common clinically encountered non-albicans Candida species (NAC). Our findings reveal that each Candida species biofilm synthesizes a mannan-glucan complex and that the antifungal-protective function of this complex is conserved. Structural similarities extended primarily to the polysaccharide backbone (α-1,6-mannan and β-1,6-glucan). Surprisingly, biochemical analysis uncovered stark differences in the branching side chains of the MGCx among the species. Consistent with the structural analysis, similarities in the genetic control of MGCx production for each Candida species also appeared limited to the synthesis of the polysaccharide backbone. Each species appears to employ a unique subset of modification enzymes for MGCx synthesis, likely accounting for the observed side chain diversity. Our results argue for the conservation of matrix function among Candida spp. While biogenesis is preserved at the level of the mannan-glucan complex backbone, divergence emerges for construction of branching side chains. Thus, the MGCx backbone represents an ideal drug target for effective pan-Candida species biofilm therapy. PMID:29615504

A Maze Game on Android Using Growing Tree Method

NASA Astrophysics Data System (ADS)

Hendrawan, Y. F.

2018-01-01

A maze is a type of puzzle games where a player moves in complex and branched passages to find a particular target or location. One method to create a maze is the Growing Tree method. The method creates a tree that has branches which are the paths of a maze. This research explored three types of Growing Tree method implementations for maze generation on Android mobile devices. The layouts produced could be played in first and third-person perspectives. The experiment results showed that it took 17.3 seconds on average to generate 20 cells x 20 cells dynamic maze layouts.

The c-axis charge traveling wave in a coupled system of Josephson junctions

NASA Astrophysics Data System (ADS)

Shukrinov, Yu. M.; Hamdipour, M.

2012-05-01

We demonstrate a manifestation of the charge traveling wave along the c axis (TW) in current voltage characteristics of coupled Josephson junctions in high- T c superconductors. The branches related to the TW with different wavelengths are found for the stacks with different number of Josephson junctions at different values of system's parameters. Transitions between the TW branches and the outermost branch are observed. The electric charge in the superconducting layers and charge-charge correlation functions for TW and outermost branches show different behavior with bias current. We propose an experimental testing of the TW branching by microwave irradiation.

Pectin-modifying enzymes and pectin-derived materials: applications and impacts.

PubMed

Bonnin, Estelle; Garnier, Catherine; Ralet, Marie-Christine

2014-01-01

Pectins are complex branched polysaccharides present in primary cell walls. As a distinctive feature, they contain high amount of partly methyl-esterified galacturonic acid and low amount of rhamnose and carry arabinose and galactose as major neutral sugars. Due to their structural complexity, they are modifiable by many different enzymes, including hydrolases, lyases, and esterases. Their peculiar structure is the origin of their physicochemical properties. Among others, their remarkable gelling properties make them a key additive for food industries. Pectin-degrading enzymes and -modifying enzymes may be used in a wide variety of applications to modulate pectin properties or produce pectin derivatives and oligosaccharides with functional as well as nutritional interests. This paper reviews the scientific information available on pectin structure, pectin-modifying enzymes, and the use of enzymes to produce pectin with controlled structure or pectin-derived oligosaccharides, with functional or nutritional interesting properties.

Biosorption: current perspectives on concept, definition and application.

PubMed

Fomina, Marina; Gadd, Geoffrey Michael

2014-05-01

Biosorption is a physico-chemical and metabolically-independent process based on a variety of mechanisms including absorption, adsorption, ion exchange, surface complexation and precipitation. Biosorption processes are highly important in the environment and conventional biotreatment processes. As a branch of biotechnology, biosorption has been aimed at the removal or recovery of organic and inorganic substances from solution by biological material which can include living or dead microorganisms and their components, seaweeds, plant materials, industrial and agricultural wastes and natural residues. For decades biosorption has been heralded as a promising cost-effective clean-up biotechnology. Despite significant progress in our understanding of this complex phenomenon and a dramatic increase in publications in this research area, commercialization of biosorption technologies has been limited so far. This article summarizes existing knowledge on various aspects of the fundamentals and applications of biosorption and critically reviews the obstacles to commercial success and future perspectives. Copyright © 2014 Elsevier Ltd. All rights reserved.

Morphological study of the innervation pattern of the rabbit sinoatrial node

NASA Technical Reports Server (NTRS)

Roberts, L. A.; Slocum, G. R.; Riley, D. A.

1989-01-01

The pattern of sinoatrial (SA) node innervations in rabbit was elucidated using a newly developed highly reproducible cholinesterase/silver impregnation staining procedure which made it possible to delineate large nerves, fine processes, and ganglion cells. The SA node and dominant pacemaker sites were identified by microelectrode recording. A generalized pattern of innnervation was recognized, which includes a large ganglionic complex inferior to the SA node; two or more moderately large nerves traversing the SA node parallel to the crista terminalis; nerves entering the intercaval region from the septum, the superior vena cava, and the inferior vena cava to impinge on the SA node; and a fine network of nerve processes, which was particularly dense in the SA node. From the location and distribution of the nerves and ganglionic branches, it can be inferred that the neural network in the intercaval region is capable of performing complex modulatory and integrative functions among the structures within this region.

Exercise promotes BCAA catabolism: effects of BCAA supplementation on skeletal muscle during exercise.

PubMed

Shimomura, Yoshiharu; Murakami, Taro; Nakai, Naoya; Nagasaki, Masaru; Harris, Robert A

2004-06-01

Branched-chain amino acids (BCAAs) are essential amino acids that can be oxidized in skeletal muscle. It is known that BCAA oxidation is promoted by exercise. The mechanism responsible for this phenomenon is attributed to activation of the branched-chain alpha-keto acid dehydrogenase (BCKDH) complex, which catalyzes the second-step reaction of the BCAA catabolic pathway and is the rate-limiting enzyme in the pathway. This enzyme complex is regulated by a phosphorylation-dephosphorylation cycle. The BCKDH kinase is responsible for inactivation of the complex by phosphorylation, and the activity of the kinase is inversely correlated with the activity state of the BCKDH complex, which suggests that the kinase is the primary regulator of the complex. We found recently that administration of ligands for peroxisome proliferator-activated receptor-alpha (PPARalpha) in rats caused activation of the hepatic BCKDH complex in association with a decrease in the kinase activity, which suggests that promotion of fatty acid oxidation upregulates the BCAA catabolism. Long-chain fatty acids are ligands for PPARalpha, and the fatty acid oxidation is promoted by several physiological conditions including exercise. These findings suggest that fatty acids may be one of the regulators of BCAA catabolism and that the BCAA requirement is increased by exercise. Furthermore, BCAA supplementation before and after exercise has beneficial effects for decreasing exercise-induced muscle damage and promoting muscle-protein synthesis; this suggests the possibility that BCAAs are a useful supplement in relation to exercise and sports.

High-precision half-life and branching-ratio measurements for superallowed Fermi β+ emitters at TRIUMF - ISAC

NASA Astrophysics Data System (ADS)

Laffoley, A. T.; Dunlop, R.; Finlay, P.; Grinyer, G. F.; Andreoiu, C.; Austin, R. A. E.; Ball, G. C.; Bandyopadhyay, D.; Blank, B.; Bouzomita, H.; Chagnon-Lessard, S.; Chester, A.; Cross, D. S.; Demand, G.; Diaz Varela, A.; Djongolov, M.; Ettenauer, S.; Garnsworthy, A. B.; Garrett, P. E.; Giovinazzo, J.; Glister, J.; Green, K. L.; Hackman, G.; Hadinia, B.; Jamieson, D. S.; Ketelhut, S.; Leach, K. G.; Leslie, J. R.; Pearson, C. J.; Phillips, A. A.; Rand, E. T.; Starosta, K.; Sumithrarachchi, C. S.; Svensson, C. E.; Tardiff, E. R.; Thomas, J. C.; Towner, I. S.; Triambak, S.; Unsworth, C.; Williams, S. J.; Wong, J.; Yates, S. W.; Zganjar, E. F.

2014-03-01

A program of high-precision half-life and branching-ratio measurements for superallowed Fermi β emitters is being carried out at TRIUMF's Isotope Separator and Accelerator (ISAC) radioactive ion beam facility. Recent half-life measurements for the superallowed decays of 14O, 18Ne, and 26Alm, as well as branching-ratio measurements for 26Alm and 74Rb are reported. These results provide demanding tests of the Standard Model and the theoretical isospin symmetry breaking (ISB) corrections in superallowed Fermi β decays.

The Intersection of the Extrinsic Hedgehog and WNT/Wingless Signals with the Intrinsic Hox Code Underpins Branching Pattern and Tube Shape Diversity in the Drosophila Airways

PubMed Central

Matsuda, Ryo; Hosono, Chie; Saigo, Kaoru; Samakovlis, Christos

2015-01-01

The tubular networks of the Drosophila respiratory system and our vasculature show distinct branching patterns and tube shapes in different body regions. These local variations are crucial for organ function and organismal fitness. Organotypic patterns and tube geometries in branched networks are typically controlled by variations of extrinsic signaling but the impact of intrinsic factors on branch patterns and shapes is not well explored. Here, we show that the intersection of extrinsic hedgehog(hh) and WNT/wingless (wg) signaling with the tube-intrinsic Hox code of distinct segments specifies the tube pattern and shape of the Drosophila airways. In the cephalic part of the airways, hh signaling induces expression of the transcription factor (TF) knirps (kni) in the anterior dorsal trunk (DTa1). kni represses the expression of another TF spalt major (salm), making DTa1 a narrow and long tube. In DTa branches of more posterior metameres, Bithorax Complex (BX-C) Hox genes autonomously divert hh signaling from inducing kni, thereby allowing DTa branches to develop as salm-dependent thick and short tubes. Moreover, the differential expression of BX-C genes is partly responsible for the anterior-to-posterior gradual increase of the DT tube diameter through regulating the expression level of Salm, a transcriptional target of WNT/wg signaling. Thus, our results highlight how tube intrinsic differential competence can diversify tube morphology without changing availabilities of extrinsic factors. PMID:25615601

Clinical and biochemical profiles of maple syrup urine disease in malaysian children.

PubMed

Yunus, Z Md; Kamaludin, Dp Abg; Mamat, M; Choy, Y S; Ngu, Lh

2012-01-01

Maple Syrup Urine Disease (MSUD) is an autosomal recessive disorder caused by defects in the branched-chain α-ketoacid dehydrogenase complex resulting in accumulation of branched-chain amino acids (BCAAs) and corresponding branched-chain ketoacids (BCKAs) in tissues and plasma, which are neurotoxic. Early diagnosis and subsequent nutritional modification management can reduce the morbidity and mortality. Prior to 1990s, the diagnosis of MSUD and other inborn errors of metabolism (IEM) in Malaysia were merely based on clinical suspicion and qualitative one-dimensional thin layer chromatography technique. We have successfully established specific laboratory diagnostic techniques to diagnose MSUD and other IEM. We described here our experience in performing high-risk screening for IEM in Malaysia from 1999 to 2006. We analysed the clinical and biochemical profiles of 25 patients with MSUD. A total of 12,728 plasma and urine samples from patients suspected of having IEM were received from physicians all over Malaysia. Plasma amino acids quantitation using fully automated amino acid analyzer and identification of urinary organic acids using Gas Chromatography Mass Spectrometry (GCMS). Patients' clinical information were obtained from the request forms and case records Results: Twenty-five patients were diagnosed MSUD. Nineteen patients (76%) were affected by classical MSUD, whereas six patients had non-classical MSUD. Delayed diagnosis was common among our case series, and 80% of patients had survived with treatment with mild-to-moderate learning difficulties. Our findings suggested that MSUD is not uncommon in Malaysia especially among the Malay and early laboratory diagnosis is crucial.

Middle Triassic back-arc basalts from the blocks in the Mersin Mélange, southern Turkey: Implications for the geodynamic evolution of the Northern Neotethys

NASA Astrophysics Data System (ADS)

Sayit, Kaan; Bedi, Yavuz; Tekin, U. Kagan; Göncüoglu, M. Cemal; Okuyucu, Cengiz

2017-01-01

The Mersin Mélange is a tectonostratigraphic unit within the allochthonous Mersin Ophiolitic Complex in the Taurides, southern Turkey. This chaotic structure consists of blocks and tectonic slices of diverse origins and ages set in a clastic matrix of Upper Cretaceous age. In this study, we examine two blocks at two different sections characterized by basaltic lava flows alternating with radiolarian-bearing pelagic sediments. The radiolarian assemblage extracted from the mudstone-chert alternation overlying the lavas yields an upper Anisian age (Middle Triassic). The immobile element geochemistry suggests that the lava flows are predominantly characterized by sub-alkaline basalts. All lavas display pronounced negative Nb anomalies largely coupled with normal mid-ocean basalt (N-MORB)-like high field strength element (HFSE) patterns. On the basis of geochemical modelling, the basalts appear to have dominantly derived from spinel-peridotite and pre-depleted spinel-peridotite sources, while some enriched compositions can be explained by contribution of garnet-facies melts from enriched domains. The overall geochemical characteristics suggest generation of these Middle Triassic lavas at an intra-oceanic back-arc basin within the northern branch of Neotethys. This finding is of significant importance, since these rocks may represent the presence of the oldest subduction zone found thus far from the Neotethyan branches. This, in turn, suggests that the rupturing of the Gondwanan lithosphere responsible for the opening of the northern branch of Neotethys should have occurred during the Lower Triassic or earlier.

(1 + 1) resonant enhanced multiphoton ionization via the A2Sigma(+) state of NO - Ionic rotational branching ratios and their intensity dependence

NASA Technical Reports Server (NTRS)

Rudolph, H.; Mckoy, V.; Dixit, S. N.; Huo, W. M.

1988-01-01

Rotational branching ratios resulting from the (1 + 1) resonant enhanced multiphoton ionization spectroscopy of NO via the 0-0 transition of the A-X band for the four possible branches that can be assigned as R(21.5) are explored using calculation performed in the frozen-core approximation at the Hartree-Fock level. The four different branches, of which three are distinctly different in the perturbative limit, have rather different branching ratios. The mixed R12 + Q22(21.5) branch, which is not intense and has the lowest transition energy, appears to give the best agreement with experimental branching ratio for parallel detection. The agreement is less satisfactory for perpendicular detection. Neither the effect of finite-acceptance angle of the photoelectron detector nor high intensities can explain the discrepancy.

Ideal crop plant architecture is mediated by tassels replace upper ears1, a BTB/POZ ankyrin repeat gene directly targeted by TEOSINTE BRANCHED1.

PubMed

Dong, Zhaobin; Li, Wei; Unger-Wallace, Erica; Yang, Jinliang; Vollbrecht, Erik; Chuck, George

2017-10-10

Axillary branch suppression is a favorable trait bred into many domesticated crop plants including maize compared with its highly branched wild ancestor teosinte. Branch suppression in maize was achieved through selection of a gain of function allele of the teosinte branched1 (tb1) transcription factor that acts as a repressor of axillary bud growth. Previous work indicated that other loci may function epistatically with tb1 and may be responsible for some of its phenotypic effects. Here, we show that tb1 mediates axillary branch suppression through direct activation of the tassels replace upper ears1 ( tru1 ) gene that encodes an ankyrin repeat domain protein containing a BTB/POZ motif necessary for protein-protein interactions. The expression of TRU1 and TB1 overlap in axillary buds, and TB1 binds to two locations in the tru1 gene as shown by chromatin immunoprecipitation and gel shifts. In addition, nucleotide diversity surveys indicate that tru1 , like tb1 , was a target of selection. In modern maize, TRU1 is highly expressed in the leaf trace vasculature of axillary internodes, while in teosinte, this expression is highly reduced or absent. This increase in TRU1 expression levels in modern maize is supported by comparisons of relative protein levels with teosinte as well as by quantitative measurements of mRNA levels. Hence, a major innovation in creating ideal maize plant architecture originated from ectopic overexpression of tru1 in axillary branches, a critical step in mediating the effects of domestication by tb1.

Effective construction of quaternary stereocenters by highly enantioselective α-amination of branched aldehydes.

PubMed

Fu, Ji-Ya; Xu, Xiao-Ying; Li, Yan-Chun; Huang, Qing-Chun; Wang, Li-Xin

2010-10-21

A highly efficient enantioselective α-amination of branched aldehydes with azadicarboxylates promoted by chiral proline-derived amide thiourea bifunctional catalysts was developed for the first time, affording the adducts bearing quaternary stereogenic centers with excellent yields (up to 99%) and enantioselectivities (up to 97% ee).

Purification and characterization of highly branched α-glucan-producing enzymes from Paenibacillus sp. PP710.

PubMed

Tsusaki, Keiji; Watanabe, Hikaru; Yamamoto, Takuo; Nishimoto, Tomoyuki; Chaen, Hiroto; Fukuda, Shigeharu

2012-01-01

Highly branched α-glucan molecules exhibit low digestibility for α-amylase and glucoamylase, and abundant in α-(1→3)-, α-(1→6)-glucosidic linkages and α-(1→6)-linked branch points where another glucosyl chain is initiated through an α-(1→3)-linkage. From a culture supernatant of Paenibacillus sp. PP710, we purified α-glucosidase (AGL) and α-amylase (AMY), which were involved in the production of highly branched α-glucan from maltodextrin. AGL catalyzed the transglucosylation reaction of a glucosyl residue to a nonreducing-end glucosyl residue by α-1,6-, α-1,4-, and α-1,3-linkages. AMY catalyzed the hydrolysis of the α-1,4-linkage and the intermolecular or intramolecular transfer of maltooligosaccharide like cyclodextrin glucanotransferase (CGTase). It also catalyzed the transfer of an α-1,4-glucosyl chain to a C3- or C4-hydroxyl group in the α-1,4- or α-1,6-linked nonreducing-end residue or the α-1,6-linked residue located in the other chains. Hence AMY was regarded as a novel enzyme. We think that the mechanism of formation of highly branched α-glucan from maltodextrin is as follows: α-1,6- and α-1,3-linked residues are generated by the transglucosylation of AGL at the nonreducing ends of glucosyl chains. Then AMY catalyzes the transfer of α-1,4-chains to C3- or C4-hydroxyl groups in the α-1,4- or α-1,6-linked residues generated by AGL. Thus the concerted reactions of both AGL and AMY are necessary to produce the highly branched α-glucan from maltodextrin.

Viewing the Roots of Polynomial Functions in Complex Variable: The Use of Geogebra and the CAS Maple

ERIC Educational Resources Information Center

Alves, Francisco Regis Vieira

2013-01-01

Admittedly, the Fundamental Theorem of Calculus-TFA holds an important role in the Complex Analysis-CA, as well as in other mathematical branches. In this article, we bring a discussion about the TFA, the Rouché's theorem and the winding number with the intention to analyze the roots of a polynomial equation. We propose also a description for a…

Monitoring of Freezing Dynamics in Trees: A Simple Phase Shift Causes Complexity1[OPEN

PubMed Central

Charra-Vaskou, Katline

2017-01-01

During winter, trees have to cope with harsh conditions, including extreme freeze-thaw stress. This study focused on ice nucleation and propagation, related water shifts and xylem cavitation, as well as cell damage and was based on in situ monitoring of xylem (thermocouples) and surface temperatures (infrared imaging), ultrasonic emissions, and dendrometer analysis. Field experiments during late winter on Picea abies growing at the alpine timberline revealed three distinct freezing patterns: (1) from the top of the tree toward the base, (2) from thin branches toward the main stem’s top and base, and (3) from the base toward the top. Infrared imaging showed freezing within branches from their base toward distal parts. Such complex freezing causes dynamic and heterogenous patterns in water potential and probably in cavitation. This study highlights the interaction between environmental conditions upon freezing and thawing and demonstrates the enormous complexity of freezing processes in trees. Diameter shrinkage, which indicated water fluxes within the stem, and acoustic emission analysis, which indicated cavitation events near the ice front upon freezing, were both related to minimum temperature and, upon thawing, related to vapor pressure deficit and soil temperature. These complex patterns, emphasizing the common mechanisms between frost and drought stress, shed new light on winter tree physiology. PMID:28242655

Dynamics driving function: new insights from electron transferring flavoproteins and partner complexes.

PubMed

Toogood, Helen S; Leys, David; Scrutton, Nigel S

2007-11-01

Electron transferring flavoproteins (ETFs) are soluble heterodimeric FAD-containing proteins that function primarily as soluble electron carriers between various flavoprotein dehydrogenases. ETF is positioned at a key metabolic branch point, responsible for transferring electrons from up to 10 primary dehydrogenases to the membrane-bound respiratory chain. Clinical mutations of ETF result in the often fatal disease glutaric aciduria type II. Structural and biophysical studies of ETF in complex with partner proteins have shown that ETF partitions the functions of partner binding and electron transfer between (a) a 'recognition loop', which acts as a static anchor at the ETF-partner interface, and (b) a highly mobile redox-active FAD domain. Together, this enables the FAD domain of ETF to sample a range of conformations, some compatible with fast interprotein electron transfer. This 'conformational sampling' enables ETF to recognize structurally distinct partners, whilst also maintaining a degree of specificity. Complex formation triggers mobility of the FAD domain, an 'induced disorder' mechanism contrasting with the more generally accepted models of protein-protein interaction by induced fit mechanisms. We discuss the implications of the highly dynamic nature of ETFs in biological interprotein electron transfer. ETF complexes point to mechanisms of electron transfer in which 'dynamics drive function', a feature that is probably widespread in biology given the modular assembly and flexible nature of biological electron transfer systems.

Dependency of branch diameter growth in young Acer trees on light availability and shoot elongation.

PubMed

Sone, Kosei; Noguchi, Ko; Terashima, Ichiro

2005-01-01

Many biomechanical and theoretical studies have been based on the pipe-model theory, according to which a tree is regarded as an assemblage of pipes, each having the same amount of leaf area or leaf mass. However, the physiological mechanisms underlying the theory have not been extensively examined, particularly at the branch level. We analyzed how branches and trunks thickened in nine young Acer mono Maxim. var. marmoratum (Nichols) Hara f. dissectum (Wesmael) Rehder. and A. rufinerve (Siebold & Zucc.) trees. In particular, we examined the roles of light, allocation of photosynthates and shoot heterogeneity. The cross-sectional area (A) of a branch was proportional to cumulative leaf mass or leaf area of the branch, and cumulative cross-sectional area of the daughter branches (SigmaA) above a branching point was equal to the A of the mother branch. These results indicate the validity of the pipe-model theory. However, the theory was invalid for current-year growth of branch cross-sectional area (DeltaA). The DeltaA/SigmaDeltaA for a branching point was greatest (nearly equal to 1) at the crown surface, decreased with crown depth, and tended to increase again at the trunk base, and DeltaA strongly depended on light interception and the yearly increment of leaves on the branch. We examined factors that influenced DeltaA with multiple regression analysis. The ratio of DeltaA of a branch to branch leaf area depended on both relative irradiance and mean current-year shoot length of the branch, suggesting that diameter growth of a branch is determined by the balance between supply of photosynthates, which depends on light interception by the branch, and demand for photosynthates, which is created by the high cambial activity associated with vigorous shoot elongation.

Branching habit and the allocation of reproductive resources in conifers

PubMed Central

Leslie, Andrew B.

2012-01-01

Background and Aims Correlated relationships between branch thickness, branch density, and twig and leaf size have been used extensively to study the evolution of plant canopy architecture, but fewer studies have explored the impact of these relationships on the allocation of reproductive resources. This study quantifies pollen cone production in conifers, which have similar basic reproductive biology but vary dramatically in branching habit, in order to test how differences in branch diameter influence pollen cone size and the density with which they are deployed in the canopy. Methods Measurements of canopy branch density, the number of cones per branch and cone size were used to estimate the amount of pollen cone tissues produced by 16 species in three major conifer clades. The number of pollen grains produced was also estimated using direct counts from individual pollen cones. Key Results The total amount of pollen cone tissues in the conifer canopy varied little among species and clades, although vegetative traits such as branch thickness, branch density and pollen cone size varied over several orders of magnitude. However, branching habit controls the way these tissues are deployed: taxa with small branches produce small pollen cones at a high density, while taxa with large branches produce large cones relatively sparsely. Conclusions Conifers appear to invest similar amounts of energy in pollen production independent of branching habit. However, similar associations between branch thickness, branch density and pollen cone size are seen across conifers, including members of living and extinct groups not directly studied here. This suggests that reproductive features relating to pollen cone size are in large part a function of the evolution of vegetative morphology and branching habit. PMID:22782240

BPP: a sequence-based algorithm for branch point prediction.

PubMed

Zhang, Qing; Fan, Xiaodan; Wang, Yejun; Sun, Ming-An; Shao, Jianlin; Guo, Dianjing

2017-10-15

Although high-throughput sequencing methods have been proposed to identify splicing branch points in the human genome, these methods can only detect a small fraction of the branch points subject to the sequencing depth, experimental cost and the expression level of the mRNA. An accurate computational model for branch point prediction is therefore an ongoing objective in human genome research. We here propose a novel branch point prediction algorithm that utilizes information on the branch point sequence and the polypyrimidine tract. Using experimentally validated data, we demonstrate that our proposed method outperforms existing methods. Availability and implementation: https://github.com/zhqingit/BPP. djguo@cuhk.edu.hk. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Service employees give as they get: internal service as a moderator of the service climate-service outcomes link.

PubMed

Ehrhart, Karen Holcombe; Witt, L A; Schneider, Benjamin; Perry, Sara Jansen

2011-03-01

We lend theoretical insight to the service climate literature by exploring the joint effects of branch service climate and the internal service provided to the branch (the service received from corporate units to support external service delivery) on customer-rated service quality. We hypothesized that service climate is related to service quality most strongly when the internal service quality received is high, providing front-line employees with the capability to deliver what the service climate motivates them to do. We studied 619 employees and 1,973 customers in 36 retail branches of a bank. We aggregated employee perceptions of the internal service quality received from corporate units and the local service climate and external customer perceptions of service quality to the branch level of analysis. Findings were consistent with the hypothesis that high-quality internal service is necessary for branch service climate to yield superior external customer service quality. PsycINFO Database Record (c) 2011 APA, all rights reserved.

Engineered short branched-chain acyl-CoA synthesis in E. coli and acylation of chloramphenicol to branched-chain derivatives.

PubMed

Bi, Huiping; Bai, Yanfen; Cai, Tao; Zhuang, Yibin; Liang, Xiaomei; Zhang, Xueli; Liu, Tao; Ma, Yanhe

2013-12-01

Short branched-chain acyl-CoAs are important building blocks for a wide variety of pharmaceutically valuable natural products. Escherichia coli has been used as a heterologous host for the production of a variety of natural compounds for many years. In the current study, we engineered synthesis of isobutyryl-CoA and isovaleryl-CoA from glucose in E. coli by integration of the branched-chain α-keto acid dehydrogenase complex from Streptomyces avermitilis. In the presence of the chloramphenicol acetyltransferase (cat) gene, chloramphenicol was converted to both chloramphenicol-3-isobutyrate and chloramphenicol-3-isovalerate by the recombinant E. coli strains, which suggested successful synthesis of isobutyryl-CoA and isovaleryl-CoA. Furthermore, we improved the α-keto acid precursor supply by overexpressing the alsS gene from Bacillus subtilis and the ilvC and ilvD genes from E. coli and thus enhanced the synthesis of short branched-chain acyl-CoAs. By feeding 25 mg/L chloramphenicol, 2.96 ± 0.06 mg/L chloramphenicol-3-isobutyrate and 3.94 ± 0.06 mg/L chloramphenicol-3-isovalerate were generated by the engineered E. coli strain, which indicated efficient biosynthesis of short branched-chain acyl-CoAs. HPLC analysis showed that the most efficient E. coli strain produced 80.77 ± 3.83 nmol/g wet weight isovaleryl-CoA. To our knowledge, this is the first report of production of short branched-chain acyl-CoAs in E. coli and opens a way to biosynthesize various valuable natural compounds based on these special building blocks from renewable carbon sources.

ADAPT

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

Reynolds, John; Jankovsky, Zachary; Metzroth, Kyle G

2018-04-04

The purpose of the ADAPT code is to generate Dynamic Event Trees (DET) using a user specified set of simulators. ADAPT can utilize any simulation tool which meets a minimal set of requirements. ADAPT is based on the concept of DET which uses explicit modeling of the deterministic dynamic processes that take place during a nuclear reactor plant system (or other complex system) evolution along with stochastic modeling. When DET are used to model various aspects of Probabilistic Risk Assessment (PRA), all accident progression scenarios starting from an initiating event are considered simultaneously. The DET branching occurs at user specifiedmore » times and/or when an action is required by the system and/or the operator. These outcomes then decide how the dynamic system variables will evolve in time for each DET branch. Since two different outcomes at a DET branching may lead to completely different paths for system evolution, the next branching for these paths may occur not only at separate times, but can be based on different branching criteria. The computational infrastructure allows for flexibility in ADAPT to link with different system simulation codes, parallel processing of the scenarios under consideration, on-line scenario management (initiation as well as termination), analysis of results, and user friendly graphical capabilities. The ADAPT system is designed for a distributed computing environment; the scheduler can track multiple concurrent branches simultaneously. The scheduler is modularized so that the DET branching strategy can be modified (e.g. biasing towards the worst-case scenario/event). Independent database systems store data from the simulation tasks and the DET structure so that the event tree can be constructed and analyzed later. ADAPT is provided with a user-friendly client which can easily sort through and display the results of an experiment, precluding the need for the user to manually inspect individual simulator runs.« less

Dynamics of pulsatile flow in fractal models of vascular branching networks.

PubMed

Bui, Anh; Sutalo, Ilija D; Manasseh, Richard; Liffman, Kurt

2009-07-01

Efficient regulation of blood flow is critically important to the normal function of many organs, especially the brain. To investigate the circulation of blood in complex, multi-branching vascular networks, a computer model consisting of a virtual fractal model of the vasculature and a mathematical model describing the transport of blood has been developed. Although limited by some constraints, in particular, the use of simplistic, uniformly distributed model for cerebral vasculature and the omission of anastomosis, the proposed computer model was found to provide insights into blood circulation in the cerebral vascular branching network plus the physiological and pathological factors which may affect its functionality. The numerical study conducted on a model of the middle cerebral artery region signified the important effects of vessel compliance, blood viscosity variation as a function of the blood hematocrit, and flow velocity profile on the distributions of flow and pressure in the vascular network.

[GENETIC AND METABOLIC URGENCIES IN THE NEONATAL INTENSIVE CARE UNIT: MAPLE SYRUP URINE DISEASE].

PubMed

Páez Rojas, Paola Liliana; Suarez Obando, Fernando

2015-07-01

Maple syrup urine disease (MSUD) is a hereditary disorder of branched chain amino/keto acid metabolism, caused by a decreased activity of the branched-chain alpha- ketoacid dehydrogenase complex (BCKAD), which leads to abnormal elevated plasma concentrations of branched-chain amino acids (BCAAs) clinically manifested as a heavy burden for Central Nervous system. The toxic accumulation of substrates promotes the development of a severe and rapidly progressive neonatal encephalopathy if treatment is not immediately given. This disorder has a specific medical management in acute phase in order to minimize mortality and morbidity. For all those reasons, it is important to include the MSUD as a possible diagnosis in a encephalopathic newborn. We present a colombian newborn with classical MSUD with fatal outcome as an example of metabolic emergency and a differential diagnosis in the encephalopathic newborn. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Anomalous origins of the calcarine and parieto-occipital arteries.

PubMed

Madhavan, Karthik; Dlouhy, Brian J; Vogel, Timothy W; Policeni, Bruno A; Smoker, Wendy R K; Hasan, David M

2010-10-01

Understanding cerebrovascular anatomy and its variations is of utmost importance in treating vascular malformations. The two patients presented here demonstrate yet to be reported anomalous origins of the cortical branches of the posterior cerebral artery. In one patient, fetal calcarine arteries were identified arising from the internal carotid arteries bilaterally with no calcarine branches arising from the posterior circulation and the basilar artery giving rise to terminal parieto-occipital arteries. Additionally, with vertebral artery injections, we found the dominant arterial supply to the right parieto-occipital artery arose from the right internal carotid artery and right posterior communicating artery and the dominant arterial supply to the left parieto-occipital artery arose from the right vertebral artery. A second patient demonstrated anomalous origins of the calcarine and parietal occipital branches from the supraclinoid left internal carotid artery. Understanding this complex cerebrovascular anatomy is important in the endovascular treatment of cerebrovascular aneurysms and malformations. Published by Elsevier Ltd.

An Organotypic 3D Assay for Primary Human Mammary Epithelial Cells that Recapitulates Branching Morphogenesis.

PubMed

Linnemann, Jelena R; Meixner, Lisa K; Miura, Haruko; Scheel, Christina H

2017-01-01

We have developed a three-dimensional organotypic culture system for primary human mammary epithelial cells (HMECs) in which the cells are cultured in free floating collagen type I gels. In this assay, luminal cells predominantly form multicellular spheres, while basal/myoepithelial cells form complex branched structures resembling terminal ductal lobular units (TDLUs), the functional units of the human mammary gland in situ. The TDLU-like organoids can be cultured for at least 3 weeks and can then be passaged multiple times. Subsequently, collagen gels can be stained with carmine or by immunofluorescence to allow for the analysis of morphology, protein expression and polarization, and to facilitate quantification of structures. In addition, structures can be isolated for gene expression analysis. In summary, this technique is suitable for studying branching morphogenesis, regeneration, and differentiation of HMECs as well as their dependence on the physical environment.

Fiber tracking of brain white matter based on graph theory.

PubMed

Lu, Meng

2015-01-01

Brain white matter tractography is reconstructed via diffusion-weighted magnetic resonance images. Due to the complex structure of brain white matter fiber bundles, fiber crossing and fiber branching are abundant in human brain. And regular methods with diffusion tensor imaging (DTI) can't accurately handle this problem. the biggest problems of the brain tractography. Therefore, this paper presented a novel brain white matter tractography method based on graph theory, so the fiber tracking between two voxels is transformed into locating the shortest path in a graph. Besides, the presented method uses Q-ball imaging (QBI) as the source data instead of DTI, because QBI can provide accurate information about multiple fiber crossing and branching in one voxel using orientation distribution function (ODF). Experiments showed that the presented method can accurately handle the problem of brain white matter fiber crossing and branching, and reconstruct brain tractograhpy both in phantom data and real brain data.

Brain white matter fiber estimation and tractography using Q-ball imaging and Bayesian MODEL.

PubMed

Lu, Meng

2015-01-01

Diffusion tensor imaging allows for the non-invasive in vivo mapping of the brain tractography. However, fiber bundles have complex structures such as fiber crossings, fiber branchings and fibers with large curvatures that tensor imaging (DTI) cannot accurately handle. This study presents a novel brain white matter tractography method using Q-ball imaging as the data source instead of DTI, because QBI can provide accurate information about multiple fiber crossings and branchings in a single voxel using an orientation distribution function (ODF). The presented method also uses graph theory to construct the Bayesian model-based graph, so that the fiber tracking between two voxels can be represented as the shortest path in a graph. Our experiment showed that our new method can accurately handle brain white matter fiber crossings and branchings, and reconstruct brain tractograhpy both in phantom data and real brain data.

Two consecutive partial liver transplants in a patient with Classic Maple Syrup Urine Disease☆☆☆

PubMed Central

Chin, H.L.; Aw, M.M.; Quak, S.H.; Huang, J.; Hart, C.E.; Prabhakaran, K.; Goh, D.L.

2015-01-01

Maple syrup urine disease is caused by a deficiency in the branched chain ketoacid dehydrogenase (BCKAD) complex. This results in the accumulation of branched chain amino acids (BCAA) and branched chain ketoacids in the body. Even when aggressively treated with dietary restriction of BCAA, patients experience long term cognitive, neurological and psychosocial problems. Liver transplantation from deceased donors has been shown to be an effective modality in introducing adequate BCKAD activity, attaining a metabolic cure for patients. Here, we report the clinical course of the first known patient with classic MSUD who received two consecutive partial liver grafts from two different living non-carrier donors and his five year outcome posttransplant. We also show that despite the failure of the first liver graft, and initial acute cellular rejection of the second liver graft in our patient, his metabolic control remained good without metabolic decompensation. PMID:26937410

Two consecutive partial liver transplants in a patient with Classic Maple Syrup Urine Disease.

PubMed

Chin, H L; Aw, M M; Quak, S H; Huang, J; Hart, C E; Prabhakaran, K; Goh, D L

2015-09-01

Maple syrup urine disease is caused by a deficiency in the branched chain ketoacid dehydrogenase (BCKAD) complex. This results in the accumulation of branched chain amino acids (BCAA) and branched chain ketoacids in the body. Even when aggressively treated with dietary restriction of BCAA, patients experience long term cognitive, neurological and psychosocial problems. Liver transplantation from deceased donors has been shown to be an effective modality in introducing adequate BCKAD activity, attaining a metabolic cure for patients. Here, we report the clinical course of the first known patient with classic MSUD who received two consecutive partial liver grafts from two different living non-carrier donors and his five year outcome posttransplant. We also show that despite the failure of the first liver graft, and initial acute cellular rejection of the second liver graft in our patient, his metabolic control remained good without metabolic decompensation.

Principles of Biomimetic Vascular Network Design Applied to a Tissue-Engineered Liver Scaffold

PubMed Central

Hoganson, David M.; Pryor, Howard I.; Spool, Ira D.; Burns, Owen H.; Gilmore, J. Randall

2010-01-01

Branched vascular networks are a central component of scaffold architecture for solid organ tissue engineering. In this work, seven biomimetic principles were established as the major guiding technical design considerations of a branched vascular network for a tissue-engineered scaffold. These biomimetic design principles were applied to a branched radial architecture to develop a liver-specific vascular network. Iterative design changes and computational fluid dynamic analysis were used to optimize the network before mold manufacturing. The vascular network mold was created using a new mold technique that achieves a 1:1 aspect ratio for all channels. In vitro blood flow testing confirmed the physiologic hemodynamics of the network as predicted by computational fluid dynamic analysis. These results indicate that this biomimetic liver vascular network design will provide a foundation for developing complex vascular networks for solid organ tissue engineering that achieve physiologic blood flow. PMID:20001254

Principles of biomimetic vascular network design applied to a tissue-engineered liver scaffold.

PubMed

Hoganson, David M; Pryor, Howard I; Spool, Ira D; Burns, Owen H; Gilmore, J Randall; Vacanti, Joseph P

2010-05-01

Branched vascular networks are a central component of scaffold architecture for solid organ tissue engineering. In this work, seven biomimetic principles were established as the major guiding technical design considerations of a branched vascular network for a tissue-engineered scaffold. These biomimetic design principles were applied to a branched radial architecture to develop a liver-specific vascular network. Iterative design changes and computational fluid dynamic analysis were used to optimize the network before mold manufacturing. The vascular network mold was created using a new mold technique that achieves a 1:1 aspect ratio for all channels. In vitro blood flow testing confirmed the physiologic hemodynamics of the network as predicted by computational fluid dynamic analysis. These results indicate that this biomimetic liver vascular network design will provide a foundation for developing complex vascular networks for solid organ tissue engineering that achieve physiologic blood flow.

Biomimetic Branched Hollow Fibers Templated by Self-assembled Fibrous Polyvinylpyrrolidone (PVP) Structures in Aqueous Solution

PubMed Central

Qiu, Penghe; Mao, Chuanbin

2010-01-01

Branched hollow fibers are common in nature, but to form artificial fibers with a similar branched hollow structure is still a challenge. We discovered that polyvinylpyrrolidone (PVP) could self-assemble into branched hollow fibers in an aqueous solution after aging the PVP solution for about two weeks. Based on this finding, we demonstrated two approaches by which the self-assembly of PVP into branched hollow fibers could be exploited to template the formation of branched hollow inorganic fibers. First, inorganic material such as silica with high affinity against the PVP could be deposited on the surface of the branched hollow PVP fibers to form branched hollow silica fibers. To extend the application of PVP self-assembly in templating the formation of hollow branched fibers, we then adopted a second approach where the PVP molecules bound to inorganic nanoparticles (using gold nanoparticles as a model) co-self-assemble with the free PVP molecules in an aqueous solution, resulting in the formation of the branched hollow fibers with the nanoparticles embedded in the PVP matrix constituting the walls of the fibers. Heating the resultant fibers above the glass transition temperature of PVP led to the formation of branched hollow gold fibers. Our work suggests that the self-assembly of the PVP molecules in the solution can serve as a general method for directing the formation of branched hollow inorganic fibers. The branched hollow fibers may find potential applications in microfluidics, artificial blood vessel generation, and tissue engineering. PMID:20158250

Volatile profiling reveals intracellular metabolic changes in Aspergillus parasiticus: veA regulates branched chain amino acid and ethanol metabolism

PubMed Central

2010-01-01

Background Filamentous fungi in the genus Aspergillus produce a variety of natural products, including aflatoxin, the most potent naturally occurring carcinogen known. Aflatoxin biosynthesis, one of the most highly characterized secondary metabolic pathways, offers a model system to study secondary metabolism in eukaryotes. To control or customize biosynthesis of natural products we must understand how secondary metabolism integrates into the overall cellular metabolic network. By applying a metabolomics approach we analyzed volatile compounds synthesized by Aspergillus parasiticus in an attempt to define the association of secondary metabolism with other metabolic and cellular processes. Results Volatile compounds were examined using solid phase microextraction - gas chromatography/mass spectrometry. In the wild type strain Aspergillus parasiticus SU-1, the largest group of volatiles included compounds derived from catabolism of branched chain amino acids (leucine, isoleucine, and valine); we also identified alcohols, esters, aldehydes, and lipid-derived volatiles. The number and quantity of the volatiles produced depended on media composition, time of incubation, and light-dark status. A block in aflatoxin biosynthesis or disruption of the global regulator veA affected the volatile profile. In addition to its multiple functions in secondary metabolism and development, VeA negatively regulated catabolism of branched chain amino acids and synthesis of ethanol at the transcriptional level thus playing a role in controlling carbon flow within the cell. Finally, we demonstrated that volatiles generated by a veA disruption mutant are part of the complex regulatory machinery that mediates the effects of VeA on asexual conidiation and sclerotia formation. Conclusions 1) Volatile profiling provides a rapid, effective, and powerful approach to identify changes in intracellular metabolic networks in filamentous fungi. 2) VeA coordinates the biosynthesis of secondary metabolites with catabolism of branched chain amino acids, alcohol biosynthesis, and β-oxidation of fatty acids. 3) Intracellular chemical development in A. parasiticus is linked to morphological development. 4) Understanding carbon flow through secondary metabolic pathways and catabolism of branched chain amino acids is essential for controlling and customizing production of natural products. PMID:20735852

Synthesis, chemical characterization, and economical feasibility of poly-phenolic-branched-chain fatty acids: Synthesis of poly-phenolic-branched-chain fatty acids

USDA-ARS?s Scientific Manuscript database

New poly-phenolic branched-chain fatty acid (poly-PBC-FA) products were synthesized from a combination of soybean fatty acids and phenolic materials through a highly efficient zeolite catalyzed arylation method. These poly-PBC-FAs are liquid at room temperature and do not have the unpleasant odor li...

Crosslinked polybenzimidazoles containing branching structure as membrane materials with excellent cell performance and durability for fuel cell applications

NASA Astrophysics Data System (ADS)

Hu, Meishao; Ni, Jiangpeng; Zhang, Boping; Neelakandan, Sivasubramaniyan; Wang, Lei

2018-06-01

Crosslinking is an effective method to improve the properties of high temperature proton exchange membranes based on polybenzimidazole. However, the compact structure of crosslinked polybenzimidazole hinders the phosphoric acid absorption of the membranes, resulting in a relatively poor fuel cell performance. Recently, we find that branched polymers can absorb more phosphoric acid with a larger free volume, but suffer from deteriorated mechanical strength. In this work, a new method is proposed to obtain excellent over-all properties of high temperature proton exchange membranes. A series of crosslinked polybenzimidazoles containing branching structure as membrane materials are successfully prepared for the first time. Compared with conventional crosslinked membranes, these crosslinked polybenzimidazole membranes containing branching structure exhibit a higher phosphoric acid doping level and proton conductivity, improved durability, lower swelling rate and comparable mechanical strength. In particular, the fuel cell base on the crosslinked and branched membrane with a 10% ratio of crosslinker in non-humidified hydrogen/air at 160 °C achieves a power density of 404 mW cm-2. The results indicate that the combination of crosslinking and branching is an effective approach to improve the properties of polybenzimidazole membrane materials.

Delineating neurotrophin-3 dependent signaling pathways underlying sympathetic axon growth along intermediate targets.

PubMed

Keeler, Austin B; Suo, Dong; Park, Juyeon; Deppmann, Christopher D

2017-07-01

Postganglionic sympathetic neurons detect vascular derived neurotrophin 3 (NT3) via the axonally expressed receptor tyrosine kinase, TrkA, to promote chemo-attraction along intermediate targets. Once axons arrive to their final target, a structurally related neurotrophic factor, nerve growth factor (NGF), also acts through TrkA to promote final target innervation. Does TrkA signal differently at these different locales? We previously found that Coronin-1 is upregulated in sympathetic neurons upon exposure to NGF, thereby endowing the NGF-TrkA complex with new signaling capabilities (i.e. calcium signaling), which dampens axon growth and branching. Based on the notion that axons do not express functional levels of Coronin-1 prior to final target innervation, we developed an in vitro model for axon growth and branching along intermediate targets using Coro1a -/- neurons grown in NT3. We found that, similar to NGF-TrkA, NT3-TrkA is capable of inducing MAPK and PI3K in the presence or absence of Coronin-1. However, unlike NGF, NT3 does not induce calcium release from intracellular stores. Using a combination of pharmacology, knockout neurons and in vitro functional assays, we suggest that the NT3-TrkA complex uses Ras/MAPK and/or PI3K-AKT signaling to induce axon growth and inhibit axon branching along intermediate targets. However, in the presence of Coronin-1, these signaling pathways lose their ability to impact NT3 dependent axon growth or branching. This is consistent with a role for Coronin-1 as a molecular switch for axon behavior and suggests that Coronin-1 suppresses NT3 dependent axon behavior. Copyright © 2017 Elsevier Inc. All rights reserved.

Power of Ultra Performance Liquid Chromatography/Electrospray Ionization-MS Reconstructed Ion Chromatograms in the Characterization of Small Differences in Polymer Microstructure.

PubMed

Epping, Ruben; Panne, Ulrich; Falkenhagen, Jana

2018-03-06

From simple homopolymers to functionalized, 3-dimensional structured copolymers, the complexity of polymeric materials has become more and more sophisticated. With new applications, for instance, in the semiconductor or pharmaceutical industry, the requirements for the characterization have risen with the complexity of the used polymers. For each additional distribution, an additional dimension in analysis is needed. Small, often isomeric heterogeneities in topology or microstructure can usually not be simply separated chromatographically or distinguished by any common detector but affect the properties of materials significantly. For a drug delivery system, for example, the degree of branching and branching distribution is crucial for the formation of micelles. Instead of a complicated, time-consuming, and/or expensive 2D-chromatography or ion mobility spectrometry (IMS) method, that also has its limitations, in this work, a simple approach using size exclusion chromatography (SEC) coupled with electrospray ionization (ESI) mass spectrometry is proposed. The online coupling allows the analysis of reconstructed ion chromatograms (RICs) of each degree of polymerization. While a complete separation often cannot be achieved, the derived retention times and peak widths lead to information on the existence and dispersity of heterogeneities. Although some microstructural heterogeneities like short chain branching can for large polymers be characterized with methods such as light scattering, for oligomers where the heterogeneities just start to form and their influence is at the maximum, they are inaccessible with these methods. It is also shown that with a proper calibration even quantitative information can be obtained. This method is suitable to detect small differences in, e.g., branching, 3D-structure, monomer sequence, or tacticity and could potentially be used in routine analysis to quickly determine deviations.

Supramolecular Properties of Triazole-containing Two Armed Peptidomimetics: From Organogelators to Nucleotide-binding Tweezers

NASA Astrophysics Data System (ADS)

Chui, Tin Ki

This thesis described the development of a new type of branched peptidomimetics using a class of previously reported triazole-containing peptidomimetics as the structural motif. The propensity of these new branched peptiomimetics in being an organogelator, forming supramolecular assemblies and recognizing anions and biomolecules was investigated. The quest began with the preparation of two different series of branched peptidomimetics, namely 69-K-aa3 (aa = V or L) and 70-B-aa3. The former series made use of the flexible L-lysine (K) as the branching unit while the latter series was composed of the relatively rigid 3,5-diminobenzoate (B). In each series, the peptidomimetic arms were composed of solely valine (V) or leucine (L). The effects of the identity of the amino acids and the branching units on the gelation and self-assembling properties of these branched bis(tripeptidomimetic)s were investigated. The 69-K-aa3 series was found to exhibit poor solubility in common organic solvents yet it was able to form strong and stable gels in aromatic solvents. The 70-B-aa3 series, on the other hand, was a poor organogelator despite its excellent solubility. Morphological studies using scanning electron microscopy (SEM) and transmission electron microscopy (TEM) revealed the ability of the former to form a hyperbranched 3D network whereas the latter was only capable of forming isolated spherical lumps. Nevertheless, the latter displayed the ability in forming supramolecular polymers as shown from viscometric studies. Solution-to-gel transition temperature measurement of the gels formed by the 69-K-aa3 series and association constants determination by 1H NMR titration experiments for the supramolecular polymerization of the 70-B-aa3 series both suggested that peptidomimetic arms comprised of valine performed better than those made up of leucine in terms of association strength, and such a difference was attributed to the bulkier nature of the leucine side chain. In order to obtain a clearer picture on the mode of association of these two series of branched peptidomimetics, the length of the tripeptidomimetic arms was truncated to a dipeptide, and the amino acid, valine, was used for further studies. Both the two new candidates, 88-K-V2 and 89-B-V2, were shown to dimerize in chloroform as shown from vapor pressure osmometry (VPO) studies. 1H NMR titration experiments indicated a better dimerization strength for the latter candidate due to the intermolecular pi-pi interactions offered by its benzene ring in addition to the intermolecular hydrogen bonding by the amides and triazole units. H/D exchange and 2D NMR experiments, and molecular modeling revealed that 88-K-V2 dimerized through the formation of antiparallel beta-strands whereas formation of parallel beta-strands took place in 89-B-V2. Compound 88-K-V2 was found to form 1:1 complexes with chloride (Ka 640 M-1) and monobasic diethyl phosphate (DEP) ion (Ka 810 M-1) in chloroform. Interestingly, 89-B-V 2 was shown to form the usual 1:1 complex with the former ion (Ka 970 M-1) while forming an unexpected 2:1 complex with the latter with positive cooperativity. It was observed that both the amides and triazole protons were involved in anion-binding. In the 88-K-V2-DEP complex, the host formed a helix-like structure that wrapped around the anion located at the center of the complex as determined by 2D NMR and molecular modeling studies. Finally, further structural modification of 88-K-V2 gave a water-soluble nucleotide-binding tweezer 93-K-R2·4TFA . This tweezer consisted of four arginines (R), two triazole units, two pyrene probes and a small hydrophilic ethanolamine tail. Fluorescence study showed that this tweezer was able to form 1:1 complexes with different nucleotides in water with similar binding strength regardless of the number of phosphate groups present in the nucleotides. Moleular modeling suggested that such a charge-independent binding behavior was due to the similar number of hydrogen bonds involved in the binding between the nucleotide phosphate moiety and the tweezer amides, triazole protons and guanidinium groups. In summary, this thesis reported a new class of branched peptidomimetics that were constructed from conventional peptide and non-classical triazole linkages. The resulting peptidomimetics exhibited very rich supramolecular chemistry, ranging from gel formation, self-association, host.guest complexation and anion recognition. All these properties were due to the presence of multiple hydrogen bonding units in the form of amide and triazole units along the tweezer backbone. Through hydrogen bonding interaction with various guest molecules, the multiple-arm architecture could fold itself into a complementary conformation that could bind to the guest molecules in a much more efficient manner.

Micro-CT scan reveals an unexpected high-volume and interconnected pore network in a Cretaceous Sanagasta dinosaur eggshell.

PubMed

Hechenleitner, E Martín; Grellet-Tinner, Gerald; Foley, Matthew; Fiorelli, Lucas E; Thompson, Michael B

2016-03-01

The Cretaceous Sanagasta neosauropod nesting site (La Rioja, Argentina) was the first confirmed instance of extinct dinosaurs using geothermal-generated heat to incubate their eggs. The nesting strategy and hydrothermal activities at this site led to the conclusion that the surprisingly 7 mm thick-shelled eggs were adapted to harsh hydrothermal microenvironments. We used micro-CT scans in this study to obtain the first three-dimensional microcharacterization of these eggshells. Micro-CT-based analyses provide a robust assessment of gas conductance in fossil dinosaur eggshells with complex pore canal systems, allowing calculation, for the first time, of the shell conductance through its thickness. This novel approach suggests that the shell conductance could have risen during incubation to seven times more than previously estimated as the eggshell erodes. In addition, micro-CT observations reveal that the constant widening and branching of pore canals form a complex funnel-like pore canal system. Furthermore, the high density of pore canals and the presence of a lateral canal network in the shell reduce the risks of pore obstruction during the extended incubation of these eggs in a relatively highly humid and muddy nesting environment. © 2016 The Author(s).

Effect of double-tailed surfactant architecture on the conformation, self-assembly, and processing in polypeptide-surfactant complexes.

PubMed

Junnila, Susanna; Hanski, Sirkku; Oakley, Richard J; Nummelin, Sami; Ruokolainen, Janne; Faul, Charl F J; Ikkala, Olli

2009-10-12

This work describes the solid-state conformational and structural properties of self-assembled polypeptide-surfactant complexes with double-tailed surfactants. Poly(L-lysine) was complexed with three dialkyl esters of phosphoric acid (i.e., phosphodiester surfactants), where the surfactant tail branching and length was varied to tune the supramolecular architecture in a facile way. After complexation with the branched surfactant bis(2-ethylhexyl) phosphate in an aqueous solution, the polypeptide chains adopted an alpha-helical conformation. These rod-like helices self-assembled into cylindrical phases with the amorphous alkyl tails pointing outward. In complexes with dioctyl phosphate and didodecyl phosphate, which have two linear n-octyl or n-dodecyl tails, respectively, the polypeptide formed antiparallel beta-sheets separated by alkyl layers, resulting in well-ordered lamellar self-assemblies. By heating, it was possible to trigger a partial opening of the beta-sheets and disruption of the lamellar phase. After repeated heating/cooling, all of these complexes also showed a glass transition between 37 and 50 degrees C. Organic solvent treatment and plasticization by overstoichiometric amount of surfactant led to structure modification in poly(L-lysine)-dioctyl phosphate complexes, PLL(diC8)(x) (x = 1.0-3.0). Here, the alpha-helical PLL is surrounded by the surfactants and these bottle-brush-like chains self-assemble in a hexagonal cylindrical morphology. As x is increased, the materials are clearly plasticized and the degree of ordering is improved: The stiff alpha-helical backbones in a softened surfactant matrix give rise to thermotropic liquid-crystalline phases. The complexes were examined by Fourier transform infrared spectroscopy, small- and wide-angle X-ray scattering, transmission electron microscopy, differential scanning calorimetry, polarized optical microscopy, and circular dichroism.

Community detection in complex networks using proximate support vector clustering

NASA Astrophysics Data System (ADS)

Wang, Feifan; Zhang, Baihai; Chai, Senchun; Xia, Yuanqing

2018-03-01

Community structure, one of the most attention attracting properties in complex networks, has been a cornerstone in advances of various scientific branches. A number of tools have been involved in recent studies concentrating on the community detection algorithms. In this paper, we propose a support vector clustering method based on a proximity graph, owing to which the introduced algorithm surpasses the traditional support vector approach both in accuracy and complexity. Results of extensive experiments undertaken on computer generated networks and real world data sets illustrate competent performances in comparison with the other counterparts.

Fluid dynamic study in a femoral artery branch casting of man with upstream main lumen curvature for steady flow

NASA Technical Reports Server (NTRS)

Cho, Y. I.; Back, L. H.; Back, M. R.

1985-01-01

An in-vitro, steady flow investigation was conducted in a hollow, transparent vascular replica of the profunda femoris branch of man for a range of physiological flow conditions. The replica casting tested was obtained from a human cadaver and indicated some plague formation along the main lumen and branch. The flow visualization observations and measured pressure distributions indicated the highly three-dimensional flow characteristics with arterial curvature and branching, and the important role of centrifugal effects in fluid transport mechanisms.

Photofragmentation of Gas-Phase Lanthanide Cyclopentadienyl Complexes: Experimental and Time-Dependent Excited-State Molecular Dynamics

PubMed Central

2015-01-01

Unimolecular gas-phase laser-photodissociation reaction mechanisms of open-shell lanthanide cyclopentadienyl complexes, Ln(Cp)3 and Ln(TMCp)3, are analyzed from experimental and computational perspectives. The most probable pathways for the photoreactions are inferred from photoionization time-of-flight mass spectrometry (PI-TOF-MS), which provides the sequence of reaction intermediates and the distribution of final products. Time-dependent excited-state molecular dynamics (TDESMD) calculations provide insight into the electronic mechanisms for the individual steps of the laser-driven photoreactions for Ln(Cp)3. Computational analysis correctly predicts several key reaction products as well as the observed branching between two reaction pathways: (1) ligand ejection and (2) ligand cracking. Simulations support our previous assertion that both reaction pathways are initiated via a ligand-to-metal charge-transfer (LMCT) process. For the more complex chemistry of the tetramethylcyclopentadienyl complexes Ln(TMCp)3, TMESMD is less tractable, but computational geometry optimization reveals the structures of intermediates deduced from PI-TOF-MS, including several classic “tuck-in” structures and products of Cp ring expansion. The results have important implications for metal–organic catalysis and laser-assisted metal–organic chemical vapor deposition (LCVD) of insulators with high dielectric constants. PMID:24910492

WAVE2 is regulated by multiple phosphorylation events within its VCA domain

PubMed Central

Pocha, Shirin M; Cory, Giles O

2009-01-01

The (Wiskott-Aldrich Syndrome Protein)-family verprolin homologous protein (WAVE) family of proteins occupies a pivotal position in the cell, converting extracellular signals into the formation of branched filamentous (F) actin structures. WAVE proteins contain a verprolin central acidic (VCA) domain at their C-terminus, responsible for binding to and activating the Arp2/3 complex, which in-turn nucleates the formation of new actin filaments. Here we identify five Casein Kinase 2 (CK2) phosphorylation sites within the VCA domain of WAVE2, serines 482, 484, 488, 489, and 497. Phosphorylation of these sites is required for a high affinity interaction with the Arp2/3 complex. Phosphorylation of ser 482 and 484 specifically inhibits the activation of the Arp2/3 complex by the WAVE2 VCA domain, but has no effect on the affinity for the Arp2/3 complex when the other phosphorylation sites are occupied. We demonstrate phosphorylation of all five sites on endogenous WAVE2 and show that their mutation to non-phosphorylatable alanine residues inhibits WAVE2 function in vivo, inhibiting cell ruffling and disrupting the integrity of the leading edge of migrating cells. Cell Motil. Cytoskeleton 2008. © 2008 Wiley-Liss, Inc. PMID:19012317

WAVE2 is regulated by multiple phosphorylation events within its VCA domain.

PubMed

Pocha, Shirin M; Cory, Giles O

2009-01-01

The (Wiskott-Aldrich Syndrome Protein)-family verprolin homologous protein (WAVE) family of proteins occupies a pivotal position in the cell, converting extracellular signals into the formation of branched filamentous (F) actin structures. WAVE proteins contain a verprolin central acidic (VCA) domain at their C-terminus, responsible for binding to and activating the Arp2/3 complex, which in-turn nucleates the formation of new actin filaments. Here we identify five Casein Kinase 2 (CK2) phosphorylation sites within the VCA domain of WAVE2, serines 482, 484, 488, 489, and 497. Phosphorylation of these sites is required for a high affinity interaction with the Arp2/3 complex. Phosphorylation of ser 482 and 484 specifically inhibits the activation of the Arp2/3 complex by the WAVE2 VCA domain, but has no effect on the affinity for the Arp2/3 complex when the other phosphorylation sites are occupied. We demonstrate phosphorylation of all five sites on endogenous WAVE2 and show that their mutation to non-phosphorylatable alanine residues inhibits WAVE2 function in vivo, inhibiting cell ruffling and disrupting the integrity of the leading edge of migrating cells. (c) 2008 Wiley-Liss, Inc.

[Coronary angioplasty with the Monorail system via 6 French diagnostic catheters].

PubMed

Villavicencio, R; González, H; López, J; Zavala, E; Ban Hayashi, E B; Gaspar, J; Gil, M; Martínez Ríos, M A

1994-01-01

We studied the use of "Monorail" system with Express (Scimed) balloon catheters for coronary angioplasty through 6 French (F) "high-flow" diagnostic catheters (Novoste, USCI). Prospectively, from July 1992 to January 1993, angioplasty of 31 lesions in 24 patients was attempted (1.3 lesions/procedure). Twenty procedures were of a single lesion and four were multi-vessel angioplasty. Fourteen lesions were in the left anterior descending or in its branches, 10 in the left circumflex or in its branches, 6 in the right coronary artery, and one in the distal anastomosis of an internal mammary artery graft. Thirteen lesions (42%) were type A, 17 (55%) type B and one (3%) type C. Balloon sizes varied between 2.0 and 3.5 mm. Twenty-nine lesions could be successfully dilated (93.5%); two cases were unsuccessful due to an acute occlusion in one and residual stenosis of more than 50% in the other. For only one case, another balloon catheter different from the "Monorail" system was necessary to complete a multi-vessel angioplasty. Coronary visualization and manipulation of the balloon through the tip of the diagnostic catheter were satisfactory in all cases, except with the 3.5 mm balloon catheter. Coronary angioplasty with "Monorail" system balloon catheters through 6 F "high-flow" diagnostic catheters is feasible and provides a high success rate in simple and moderately complex selected lesions, including multivessel angioplasty with advantages of smaller artery punction and the feasibility of performing coronary angioplasty with the same catheter used for diagnostic angiography.

Preparation and evaluation of multifunctional branched diesters as fuel property enhancers for biodiesel and petroleum diesel fuels

USDA-ARS?s Scientific Manuscript database

A series of eight highly branched diesters were prepared by Fischer esterification of alcohols to acids in high yield that were similar in molecular weight to typical fatty acid methyl esters encountered in biodiesel. Examination of the properties of the synthetic diesters revealed that several poss...

Water-Based Coating Simplifies Circuit Board Manufacturing

NASA Technical Reports Server (NTRS)

2008-01-01

The Structures and Materials Division at Glenn Research Center is devoted to developing advanced, high-temperature materials and processes for future aerospace propulsion and power generation systems. The Polymers Branch falls under this division, and it is involved in the development of high-performance materials, including polymers for high-temperature polymer matrix composites; nanocomposites for both high- and low-temperature applications; durable aerogels; purification and functionalization of carbon nanotubes and their use in composites; computational modeling of materials and biological systems and processes; and developing polymer-derived molecular sensors. Essentially, this branch creates high-performance materials to reduce the weight and boost performance of components for space missions and aircraft engine components. Under the leadership of chemical engineer, Dr. Michael Meador, the Polymers Branch boasts world-class laboratories, composite manufacturing facilities, testing stations, and some of the best scientists in the field.

Adaptation of the Mitochondrial Genome in Cephalopods: Enhancing Proton Translocation Channels and the Subunit Interactions

PubMed Central

Almeida, Daniela; Maldonado, Emanuel; Vasconcelos, Vitor; Antunes, Agostinho

2015-01-01

Mitochondrial protein-coding genes (mt genes) encode subunits forming complexes of crucial cellular pathways, including those involved in the vital process of oxidative phosphorylation (OXPHOS). Despite the vital role of the mitochondrial genome (mt genome) in the survival of organisms, little is known with respect to its adaptive implications within marine invertebrates. The molluscan Class Cephalopoda is represented by a marine group of species known to occupy contrasting environments ranging from the intertidal to the deep sea, having distinct metabolic requirements, varied body shapes and highly advanced visual and nervous systems that make them highly competitive and successful worldwide predators. Thus, cephalopods are valuable models for testing natural selection acting on their mitochondrial subunits (mt subunits). Here, we used concatenated mt genes from 17 fully sequenced mt genomes of diverse cephalopod species to generate a robust mitochondrial phylogeny for the Class Cephalopoda. We followed an integrative approach considering several branches of interest–covering cephalopods with distinct morphologies, metabolic rates and habitats–to identify sites under positive selection and localize them in the respective protein alignment and/or tridimensional structure of the mt subunits. Our results revealed significant adaptive variation in several mt subunits involved in the energy production pathway of cephalopods: ND5 and ND6 from Complex I, CYTB from Complex III, COX2 and COX3 from Complex IV, and in ATP8 from Complex V. Furthermore, we identified relevant sites involved in protein-interactions, lining proton translocation channels, as well as disease/deficiencies related sites in the aforementioned complexes. A particular case, revealed by this study, is the involvement of some positively selected sites, found in Octopoda lineage in lining proton translocation channels (site 74 from ND5) and in interactions between subunits (site 507 from ND5) of Complex I. PMID:26285039

Chemical composition of Tipuana tipu, a source for tropical honey bee products.

PubMed

dos Santos Pereira, Alberto; de Aquino Neto, Francisco Radler

2003-01-01

Tipuana tipu (Benth.) Kuntze is a tree from the leguminosae family (Papilionoideae) indigenous in Argentina and extensively used in urbanism, mainly in Southern Brazil. The epicuticular waxes of leaves and branch, and flower surface were studied by high temperature high resolution gas chromatography. Several compounds were characterized, among which the aliphatic alcohols were predominant in branch, leaves and receptacle. Alkanes were predominant only in the petals and the aliphatic acids were predominant in stamen. In branches and leaf epicuticular surfaces, six long chain wax esters series were characterized, as well as lupeol and b-amyrin hexadecanoates.

Chemical Complexity in the Eu-enhanced Monometallic Globular NGC 5986

NASA Astrophysics Data System (ADS)

Johnson, Christian I.; Caldwell, Nelson; Rich, R. Michael; Mateo, Mario; Bailey, John I., III; Olszewski, Edward W.; Walker, Matthew G.

2017-06-01

NGC 5986 is a poorly studied but relatively massive Galactic globular cluster that shares several physical and morphological characteristics with “iron-complex” clusters known to exhibit significant metallicity and heavy-element dispersions. In order to determine whether NGC 5986 joins the iron-complex cluster class, we investigated the chemical composition of 25 red giant branch and asymptotic giant branch cluster stars using high-resolution spectra obtained with the Magellan-M2FS instrument. Cluster membership was verified using a combination of radial velocity and [Fe/H] measurements, and we found the cluster to have a mean heliocentric radial velocity of +99.76 km s-1 (σ = 7.44 km s-1). We derived a mean metallicity of [Fe/H] = -1.54 dex (σ = 0.08 dex), but the cluster’s small dispersion in [Fe/H] and low [La/Eu] abundance preclude it from being an iron-complex cluster. NGC 5986 has < [{Eu}/{Fe}]> =+0.76 {dex} (σ = 0.08 dex), which is among the highest ratios detected in a Galactic cluster, but the small [Eu/Fe] dispersion is puzzling because such high values near [Fe/H] ˜ -1.5 are typically only found in dwarf galaxies exhibiting large [Eu/Fe] variations. NGC 5986 exhibits classical globular cluster characteristics, such as uniformly enhanced [α/Fe] ratios, a small dispersion in Fe-peak abundances, and (anti)correlated light-element variations. Similar to NGC 2808, we find evidence that NGC 5986 may host at least four to five populations with distinct light-element compositions, and the presence of a clear Mg-Al anticorrelation along with an Al-Si correlation suggests that the cluster gas experienced processing at temperatures ≳65-70 MK. However, the current data do not support burning temperatures exceeding ˜100 MK. We find some evidence that the first- and second-generation stars in NGC 5986 may be fully spatially mixed, which could indicate that the cluster has lost a significant fraction of its original mass. This paper includes data gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile.

Efficacy and durability of the chimney graft technique in urgent and complex thoracic endovascular aortic repair.

PubMed

Bin Jabr, Adel; Lindblad, Bengt; Dias, Nuno; Resch, Timothy; Malina, Martin

2015-04-01

This study reports the early and midterm to long-term experience of chimney grafts (CGs) in urgent endovascular repair of complex lesions in the thoracic aorta. Twenty-nine high-risk patients (20 men) who were unfit for open repair were treated using CG technique for ruptured (n = 14) or symptomatic (n = 15) aortic lesions engaging the aortic arch itself (n = 9), the descending aorta (n = 10), or the thoracoabdominal aorta (n = 10). Twenty-two patients (76%) were treated urgently (≤24 hours) and seven were semiurgent (≤3 days). Of 41 chimneys used, 24 were placed in supra-aortic branches and 17 in visceral branches. Median follow-up (interquartile range) for the entire cohort was 2 years (0.6-3.8 years), 2.5 years (1-4 years) for 30-day survivors, and 3.5 years (1.9-6.4 years) for those who were still alive. Four patients (14%) died ≤30 days of cerebral infarction (n = 1), visceral ischemia secondary to the initial rupture (n = 1), multiple organ failure (n = 1), or heart failure (n = 1). There were 11 late deaths (38%); however, only two deaths were related to the CG technique. The primary and secondary technical success rates were 86% (25 of 29) and 97% (28 of 29), respectively. The secondary patency rate of CGs was 98%. Seventeen (68%) of the aortic lesions shrank significantly. Three patients (10%) had primary type I endoleak and another three (10%) had secondary type I endoleak. The endoleaks were managed with Onyx (ev3 Endovascular, Inc, Plymouth, Minn) or coil embolization (n = 2), restenting (n = 1), and conversion to open repair (n = 2). One secondary endoleak is still under observation after >20 months. All primary endoleaks and one secondary endoleak originated from CGs in the brachiocephalic trunk (4 of 6 [67%]). The midterm to long-term results of the CG technique for urgent and complex lesions of the thoracic aorta in high-risk patients are promising, with low early mortality and long durability of the CGs. More patients with longer follow-up are still needed. Copyright © 2015 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

The 2-Oxoacid Dehydrogenase Complexes in Mitochondria Can Produce Superoxide/Hydrogen Peroxide at Much Higher Rates Than Complex I*

PubMed Central

Quinlan, Casey L.; Goncalves, Renata L. S.; Hey-Mogensen, Martin; Yadava, Nagendra; Bunik, Victoria I.; Brand, Martin D.

2014-01-01

Several flavin-dependent enzymes of the mitochondrial matrix utilize NAD+ or NADH at about the same operating redox potential as the NADH/NAD+ pool and comprise the NADH/NAD+ isopotential enzyme group. Complex I (specifically the flavin, site IF) is often regarded as the major source of matrix superoxide/H2O2 production at this redox potential. However, the 2-oxoglutarate dehydrogenase (OGDH), branched-chain 2-oxoacid dehydrogenase (BCKDH), and pyruvate dehydrogenase (PDH) complexes are also capable of considerable superoxide/H2O2 production. To differentiate the superoxide/H2O2-producing capacities of these different mitochondrial sites in situ, we compared the observed rates of H2O2 production over a range of different NAD(P)H reduction levels in isolated skeletal muscle mitochondria under conditions that favored superoxide/H2O2 production from complex I, the OGDH complex, the BCKDH complex, or the PDH complex. The rates from all four complexes increased at higher NAD(P)H/NAD(P)+ ratios, although the 2-oxoacid dehydrogenase complexes produced superoxide/H2O2 at high rates only when oxidizing their specific 2-oxoacid substrates and not in the reverse reaction from NADH. At optimal conditions for each system, superoxide/H2O2 was produced by the OGDH complex at about twice the rate from the PDH complex, four times the rate from the BCKDH complex, and eight times the rate from site IF of complex I. Depending on the substrates present, the dominant sites of superoxide/H2O2 production at the level of NADH may be the OGDH and PDH complexes, but these activities may often be misattributed to complex I. PMID:24515115

The sensory but not muscular pelvic nerve branch is necessary for parturition in the rat.

PubMed

Martínez-Gómez, M; Cruz, Y; Pacheco, P; Aguilar-Roblero, R; Hudson, R

1998-03-01

In the rat the pelvic nerve consists of a viscerocutaneous (sensory) branch which receives information from pelvic viscera and the midline perineal region, and a somatomotor (muscular) branch which innervates the ilio- and pubococcygeous muscles. To investigate the contribution of these branches to the parturition process, the length of gestation and course of delivery were closely monitored in 43 pregnant, Wistar-strain rats randomly assigned to five groups: untreated control animals, animals in which the somatomotor branch of the pelvic nerve was bilaterally sectioned on Day 14 of gestation, animals in which the viscerocutaneous branch of the pelvic nerve was bilaterally sectioned on Day 14 of gestation, animals treated similarly to the previous group but with young delivered by C-section at term, and sham-operated controls. Sectioning the viscerocutaneous branch seriously disrupted parturition and resulted in major dystocia and a high percentage of stillbirths in all females. In contrast, sectioning the somatomotor branch had no apparent effect on parturition and no significant differences were found between females of this group and sham or control dams on any of the measures recorded. It is concluded that the viscerocutaneous branch of the pelvic nerve is vital for the normal course of parturition in the rat but that the somatomotor branch plays little role, if any.

A Missing Puzzle Piece in Murray's Law: the Optimal Angle of Junctions

NASA Astrophysics Data System (ADS)

Wang, Ruo-Qian; Taylor, Katherine; Winter, Amos G.; Global Engineering; Research Lab Team

2014-11-01

Branching flows are common in biological systems, such as the circulatory and respiratory systems of animals. The optimal radii of parent and daughter branches can be explained with Murray's law, which dictates that the sum of metabolic and pumping costs is minimized. Murray's Law can be used to determine the diameter of cascading channels but misses an important parameter: the angles of the branches. Past hydraulic studies have investigated the angle effect, but have not focused on whether this geometry follows Murray's Law; while a simple network optimization is able to show that at low Reynolds numbers a branch with a parent channel connecting to n equally distant channels obeying Murray's Law has a minimum total head loss with a branching angle θ, such that cos θ =n-2/3 , but it's not valid for high Reynolds number flows, which may experience separation and turbulence at the branches. The present study is focused on determining the optimal branch angle that complies with Murray's Law for moderate Reynolds numbers. Computational studies using Open FOAM and experiments using 3D printed branched channels will be presented. These results will be used to quantify the effect of Reynolds number on optimal branch geometry.

Staff Clinicians | Center for Cancer Research

Cancer.gov

The Neuro-Oncology Branch (NOB), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH) is seeking staff clinicians to provide high-quality patient care for individuals with primary central nervous system (CNS) malignancies.  The NOB is comprised of a multidisciplinary team of physicians, healthcare providers, and scientists who are dedicated to developing new therapies and improving outcomes for patients with primary brain and spinal cord tumors. The NOB is one of the first trans-institutional initiatives at the National Institutes of Health. The Branch is focused on developing an integrated clinical, translational, and basic research program that engages the strengths and resources of the National Cancer Institutes (NCI) and the National Institutes of Neurological Disorders and Stroke (NINDS) for the purpose of developing novel experimental therapeutics for individuals with primary central nervous system (CNS) malignancies. About NCI's Center for Cancer Research The Center for Cancer Research (CCR) is the intramural research component of the National Cancer Institute (NCI).  CCR’s enabling infrastructure facilitates clinical studies at the NIH Clinical Center, the world’s largest dedicated clinical research complex; provides extensive opportunities for collaboration; and allows scientists and clinicians to undertake high-risk, high-impact laboratory- and clinic-based investigations.  Investigators are supported by a wide array of intellectual, technological, and research resources, including surgical and pathology facilities, animal facilities, and dedicated, high-quality technology cores in areas such as imaging/microscopy, chemistry/purification, mass spectrometry, flow cytometry, genomics/DNA sequencing, transgenics and knock-out mice, arrays/molecular profiling, and human genetics/bioinformatics.  For an overview of CCR, please visit http://ccr.cancer.gov/.

Proteomic analysis of etiolated juvenile tetraploid Robinia pseudoacacia branches during different cutting periods.

PubMed

Lu, Nan; Xu, Zhaohe; Meng, Bingnan; Sun, Yuhan; Zhang, Jiangtao; Wang, Shaoming; Li, Yun

2014-04-21

The propagation of hard-branch cuttings of tetraploid Robinia pseudoacacia (black locust) is restricted by the low rooting rate; however, etiolated juvenile tetraploid black locust branches result in a significantly higher rooting rate of cuttings compared with non-etiolated juvenile tetraploid branches. To identify proteins that influence the juvenile tetraploid branch rooting process, two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectra (MALDI-TOF/TOF-MS) were used to analyze proteomic differences in the phloem of tetraploid R. pseudoacacia etiolated and non-etiolated juvenile branches during different cutting periods. A total of 58 protein spots differed in expression level, and 16 protein spots were only expressed in etiolated branches or non-etiolated ones. A total of 40 highly expressed protein spots were identified by mass spectrometry, 14 of which were accurately retrieved. They include nucleoglucoprotein metabolic proteins, signaling proteins, lignin synthesis proteins and phyllochlorin. These results help to reveal the mechanism of juvenile tetraploid R. pseudoacacia etiolated branch rooting and provide a valuable reference for the improvement of tetraploid R. pseudoacacia cutting techniques.

Enhanced cellular transport and drug targeting using dendritic nanostructures

NASA Astrophysics Data System (ADS)

Kannan, R. M.; Kolhe, Parag; Kannan, Sujatha; Lieh-Lai, Mary

2003-03-01

Dendrimers and hyperbranched polymers possess highly branched architectures, with a large number of controllable, tailorable, peripheral' functionalities. Since the surface chemistry of these materials can be modified with relative ease, these materials have tremendous potential in targeted drug delivery. The large density of end groups can also be tailored to create enhanced affinity to targeted cells, and can also encapsulate drugs and deliver them in a controlled manner. We are developing tailor-modified dendritic systems for drug delivery. Synthesis, drug/ligand conjugation, in vitro cellular and in vivo drug delivery, and the targeting efficiency to the cell are being studied systematically using a wide variety of experimental tools. Results on PAMAM dendrimers and polyol hyperbranched polymers suggest that: (1) These materials complex/encapsulate a large number of drug molecules and release them at tailorable rates; (2) The drug-dendrimer complex is transported very rapidly through a A549 lung epithelial cancel cell line, compared to free drug, perhaps by endocytosis. The ability of the drug-dendrimer-ligand complexes to target specific asthma and cancer cells is currently being explored using in vitro and in vivo animal models.

Production of Low-Freezing-Point Highly Branched Alkanes through Michael Addition.

PubMed

Jing, Yaxuan; Xia, Qineng; Liu, Xiaohui; Wang, Yanqin

2017-12-22

A new approach for the production of low-freezing-point, high-quality fuels from lignocellulose-derived molecules was developed with Michael addition as the key step. Among the investigated catalysts, CoCl 2 ⋅6 H 2 O was found most active for the Michael addition of 2,4-pentanedione with FA (single aldol adduct of furfural and acetone, 4-(2-furanyl)-3-butene-2-one). Over CoCl 2 ⋅6 H 2 O, a high carbon yield of C 13 oxygenates (about 75 %) can be achieved under mild conditions (353 K, 20 h). After hydrodeoxygenation, low-freezing-point (<223 K) branched alkanes with 13 carbons within jet fuel ranges were obtained over a Pd/NbOPO 4 catalyst. Furthermore, C 18,23 fuel precursors could be easily synthesized through Michael addition of 2,4-pentanedione with DFA (double-condensation product of furfural and acetone) under mild conditions and the molar ratio of C 18 /C 23 is dependent on the reaction conditions of Michael addition. After hydrodeoxygenation, high density (0.8415 g mL -1 ) and low-freezing-point (<223 K) branched alkanes with 18, 23 carbons within lubricant range were also obtained over a Pd/NbOPO 4 catalyst. These highly branched alkanes can be directly used as transportation fuels or additives. This work opens a new strategy for the synthesis of highly branched alkanes with low freezing point from renewable biomass. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Total synthesis of mycobacterial arabinogalactan containing 92 monosaccharide units

NASA Astrophysics Data System (ADS)

Wu, Yong; Xiong, De-Cai; Chen, Si-Cong; Wang, Yong-Shi; Ye, Xin-Shan

2017-03-01

Carbohydrates are diverse bio-macromolecules with highly complex structures that are involved in numerous biological processes. Well-defined carbohydrates obtained by chemical synthesis are essential to the understanding of their functions. However, synthesis of carbohydrates is greatly hampered by its insufficient efficiency. So far, assembly of long carbohydrate chains remains one of the most challenging tasks for synthetic chemists. Here we describe a highly efficient assembly of a 92-mer polysaccharide by the preactivation-based one-pot glycosylation protocol. Several linear and branched oligosaccharide/polysaccharide fragments ranging from 5-mer to 31-mer in length have been rapidly constructed in one-pot manner, which enables the first total synthesis of a biologically important mycobacterial arabinogalactan through a highly convergent [31+31+30] coupling reaction. Our results show that the preactivation-based one-pot glycosylation protocol may provide access to the construction of long and complicated carbohydrate chains.

Developmental Defects of Caenorhabditis elegans Lacking Branched-chain α-Ketoacid Dehydrogenase Are Mainly Caused by Monomethyl Branched-chain Fatty Acid Deficiency.

PubMed

Jia, Fan; Cui, Mingxue; Than, Minh T; Han, Min

2016-02-05

Branched-chain α-ketoacid dehydrogenase (BCKDH) catalyzes the critical step in the branched-chain amino acid (BCAA) catabolic pathway and has been the focus of extensive studies. Mutations in the complex disrupt many fundamental metabolic pathways and cause multiple human diseases including maple syrup urine disease (MSUD), autism, and other related neurological disorders. BCKDH may also be required for the synthesis of monomethyl branched-chain fatty acids (mmBCFAs) from BCAAs. The pathology of MSUD has been attributed mainly to BCAA accumulation, but the role of mmBCFA has not been evaluated. Here we show that disrupting BCKDH in Caenorhabditis elegans causes mmBCFA deficiency, in addition to BCAA accumulation. Worms with deficiency in BCKDH function manifest larval arrest and embryonic lethal phenotypes, and mmBCFA supplementation suppressed both without correcting BCAA levels. The majority of developmental defects caused by BCKDH deficiency may thus be attributed to lacking mmBCFAs in worms. Tissue-specific analysis shows that restoration of BCKDH function in multiple tissues can rescue the defects, but is especially effective in neurons. Taken together, we conclude that mmBCFA deficiency is largely responsible for the developmental defects in the worm and conceivably might also be a critical contributor to the pathology of human MSUD. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Interactive Design and Visualization of Branched Covering Spaces.

PubMed

Roy, Lawrence; Kumar, Prashant; Golbabaei, Sanaz; Zhang, Yue; Zhang, Eugene

2018-01-01

Branched covering spaces are a mathematical concept which originates from complex analysis and topology and has applications in tensor field topology and geometry remeshing. Given a manifold surface and an -way rotational symmetry field, a branched covering space is a manifold surface that has an -to-1 map to the original surface except at the ramification points, which correspond to the singularities in the rotational symmetry field. Understanding the notion and mathematical properties of branched covering spaces is important to researchers in tensor field visualization and geometry processing, and their application areas. In this paper, we provide a framework to interactively design and visualize the branched covering space (BCS) of an input mesh surface and a rotational symmetry field defined on it. In our framework, the user can visualize not only the BCSs but also their construction process. In addition, our system allows the user to design the geometric realization of the BCS using mesh deformation techniques as well as connecting tubes. This enables the user to verify important facts about BCSs such as that they are manifold surfaces around singularities, as well as the Riemann-Hurwitz formula which relates the Euler characteristic of the BCS to that of the original mesh. Our system is evaluated by student researchers in scientific visualization and geometry processing as well as faculty members in mathematics at our university who teach topology. We include their evaluations and feedback in the paper.

DNA damage in an animal model of maple syrup urine disease.

PubMed

Scaini, Giselli; Jeremias, Isabela C; Morais, Meline O S; Borges, Gabriela D; Munhoz, Bruna P; Leffa, Daniela D; Andrade, Vanessa M; Schuck, Patrícia F; Ferreira, Gustavo C; Streck, Emilio L

2012-06-01

Maple syrup urine disease is an inborn error of metabolism caused by a severe deficiency of the branched chain alpha-ketoacid dehydrogenase complex. Neurological dysfunction is a common finding in patients with maple syrup urine disease. However, the mechanisms underlying the neuropathology of brain damage in this disorder are poorly understood. In this study, we investigated whether acute or chronic administration of a branched chain amino acid pool (leucine, isoleucine and valine) causes transient DNA damage, as determined by the alkaline comet assay, in the brain and blood of rats during development and whether antioxidant treatment prevented the alterations induced by branched chain amino acids. Our results showed that the acute administration of branched chain amino acids increased the DNA damage frequency and damage index in the hippocampus. However, the chronic administration of branched chain amino acids increased the DNA damage frequency and damage index in both the hippocampus and the striatum, and the antioxidant treatment was able to prevent DNA damage in the hippocampus and striatum. The present study demonstrated that metabolite accumulation in MSUD induces DNA damage in the hippocampus and striatum and that it may be implicated in the neuropathology observed in the affected patients. We demonstrated that the effect of antioxidant treatment (N-acetylcysteine plus deferoxamine) prevented DNA damage, suggesting the involvement of oxidative stress in DNA damage. Copyright © 2012 Elsevier Inc. All rights reserved.

Fractal structures and fractal functions as disease indicators

USGS Publications Warehouse

Escos, J.M; Alados, C.L.; Emlen, J.M.

1995-01-01

Developmental instability is an early indicator of stress, and has been used to monitor the impacts of human disturbance on natural ecosystems. Here we investigate the use of different measures of developmental instability on two species, green peppers (Capsicum annuum), a plant, and Spanish ibex (Capra pyrenaica), an animal. For green peppers we compared the variance in allometric relationship between control plants, and a treatment group infected with the tomato spotted wilt virus. The results show that infected plants have a greater variance about the allometric regression line than the control plants. We also observed a reduction in complexity of branch structure in green pepper with a viral infection. Box-counting fractal dimension of branch architecture declined under stress infection. We also tested the reduction in complexity of behavioral patterns under stress situations in Spanish ibex (Capra pyrenaica). Fractal dimension of head-lift frequency distribution measures predator detection efficiency. This dimension decreased under stressful conditions, such as advanced pregnancy and parasitic infection. Feeding distribution activities reflect food searching efficiency. Power spectral analysis proves to be the most powerful tool for character- izing fractal behavior, revealing a reduction in complexity of time distribution activity under parasitic infection.

Habitat preferences of a corallivorous reef fish: predation risk versus food quality

NASA Astrophysics Data System (ADS)

Brooker, R. M.; Munday, P. L.; Mcleod, I. M.; Jones, G. P.

2013-09-01

Many animals preferentially select a habitat from a range of those potentially available. However, the consequences of these preferences for distribution and abundance, and the underlying basis of habitat preferences are often unknown. The present study, conducted at Great Keppel Island, Australia, examined how distribution and abundance of an obligate corallivorous filefish, Oxymonacanthus longirostris, relates to coral architecture and diversity. The main drivers of the distribution and abundance of O. longirostris among reefs were coral species richness and availability of branching coral. Feeding territories had a higher percentage of Acropora coral than surrounding habitat. In addition, feeding territories had a higher percentage of the structurally important branching coral, Acropora nobilis, and a primary prey species, Acropora millepora. A series of pair-wise choice experiments in which both structural complexity and coral tissue quality were independently manipulated showed that habitat choice was primarily based on structural complexity and shelter characteristics. In addition, the choice for the preferred coral ( A. nobilis) was stronger in the presence of a piscivorous fish. These results indicate that species-diverse coral habitats, which provide sufficient structural complexity along with nutritionally important prey, are essential for population persistence of this small, corallivorous reef fish.

Modified parton branching model for multi-particle production in hadronic collisions: Application to SUSY particle branching

NASA Astrophysics Data System (ADS)

Yuanyuan, Zhang

The stochastic branching model of multi-particle productions in high energy collision has theoretical basis in perturbative QCD, and also successfully describes the experimental data for a wide energy range. However, over the years, little attention has been put on the branching model for supersymmetric (SUSY) particles. In this thesis, a stochastic branching model has been built to describe the pure supersymmetric particle jets evolution. This model is a modified two-phase stochastic branching process, or more precisely a two phase Simple Birth Process plus Poisson Process. The general case that the jets contain both ordinary particle jets and supersymmetric particle jets has also been investigated. We get the multiplicity distribution of the general case, which contains a Hypergeometric function in its expression. We apply this new multiplicity distribution to the current experimental data of pp collision at center of mass energy √s = 0.9, 2.36, 7 TeV. The fitting shows the supersymmetric particles haven't participate branching at current collision energy.

Interfacing 3D micro/nanochannels with a branch-shaped reservoir enhances fluid and mass transport

NASA Astrophysics Data System (ADS)

Kumar, Prasoon; Gandhi, Prasanna S.; Majumder, Mainak

2017-01-01

Three-dimensional (3D) micro/nanofluidic devices can accelerate progress in numerous fields such as tissue engineering, drug delivery, self-healing and cooling devices. However, efficient connections between networks of micro/nanochannels and external fluidic ports are key to successful applications of 3D micro/nanofluidic devices. Therefore, in this work, the extent of the role of reservoir geometry in interfacing with vascular (micro/nanochannel) networks, and in the enabling of connections with external fluidic ports while maintaining the compactness of devices, has been experimentally and theoretically investigated. A statistical modelling suggested that a branch-shaped reservoir demonstrates enhanced interfacing with vascular networks when compared to other regular geometries of reservoirs. Time-lapse dye flow experiments by capillary action through fabricated 3D micro/nanofluidic devices confirmed the connectivity of branch-shaped reservoirs with micro/nanochannel networks in fluidic devices. This demonstrated a ~2.2-fold enhancement of the volumetric flow rate in micro/nanofluidic networks when interfaced to branch-shaped reservoirs over rectangular reservoirs. The enhancement is due to a ~2.8-fold increase in the perimeter of the reservoirs. In addition, the mass transfer experiments exhibited a ~1.7-fold enhancement in solute flux across 3D micro/nanofluidic devices that interfaced with branch-shaped reservoirs when compared to rectangular reservoirs. The fabrication of 3D micro/nanofluidic devices and their efficient interfacing through branch-shaped reservoirs to an external fluidic port can potentially enable their use in complex applications, in which enhanced surface-to-volume interactions are desirable.

Environmental control of branching in petunia.

PubMed

Drummond, Revel S M; Janssen, Bart J; Luo, Zhiwei; Oplaat, Carla; Ledger, Susan E; Wohlers, Mark W; Snowden, Kimberley C

2015-06-01

Plants alter their development in response to changes in their environment. This responsiveness has proven to be a successful evolutionary trait. Here, we tested the hypothesis that two key environmental factors, light and nutrition, are integrated within the axillary bud to promote or suppress the growth of the bud into a branch. Using petunia (Petunia hybrida) as a model for vegetative branching, we manipulated both light quality (as crowding and the red-to-far-red light ratio) and phosphate availability, such that the axillary bud at node 7 varied from deeply dormant to rapidly growing. In conjunction with the phenotypic characterization, we also monitored the state of the strigolactone (SL) pathway by quantifying SL-related gene transcripts. Mutants in the SL pathway inhibit but do not abolish the branching response to these environmental signals, and neither signal is dominant over the other, suggesting that the regulation of branching in response to the environment is complex. We have isolated three new putatively SL-related TCP (for Teosinte branched1, Cycloidia, and Proliferating cell factor) genes from petunia, and have identified that these TCP-type transcription factors may have roles in the SL signaling pathway both before and after the reception of the SL signal at the bud. We show that the abundance of the receptor transcript is regulated by light quality, such that axillary buds growing in added far-red light have greatly increased receptor transcript abundance. This suggests a mechanism whereby the impact of any SL signal reaching an axillary bud is modulated by the responsiveness of these cells to the signal. © 2015 American Society of Plant Biologists. All Rights Reserved.

Environmental Control of Branching in Petunia1[OPEN

PubMed Central

Oplaat, Carla; Wohlers, Mark W.

2015-01-01

Plants alter their development in response to changes in their environment. This responsiveness has proven to be a successful evolutionary trait. Here, we tested the hypothesis that two key environmental factors, light and nutrition, are integrated within the axillary bud to promote or suppress the growth of the bud into a branch. Using petunia (Petunia hybrida) as a model for vegetative branching, we manipulated both light quality (as crowding and the red-to-far-red light ratio) and phosphate availability, such that the axillary bud at node 7 varied from deeply dormant to rapidly growing. In conjunction with the phenotypic characterization, we also monitored the state of the strigolactone (SL) pathway by quantifying SL-related gene transcripts. Mutants in the SL pathway inhibit but do not abolish the branching response to these environmental signals, and neither signal is dominant over the other, suggesting that the regulation of branching in response to the environment is complex. We have isolated three new putatively SL-related TCP (for Teosinte branched1, Cycloidia, and Proliferating cell factor) genes from petunia, and have identified that these TCP-type transcription factors may have roles in the SL signaling pathway both before and after the reception of the SL signal at the bud. We show that the abundance of the receptor transcript is regulated by light quality, such that axillary buds growing in added far-red light have greatly increased receptor transcript abundance. This suggests a mechanism whereby the impact of any SL signal reaching an axillary bud is modulated by the responsiveness of these cells to the signal. PMID:25911529

Testing for Independence between Evolutionary Processes.

PubMed

Behdenna, Abdelkader; Pothier, Joël; Abby, Sophie S; Lambert, Amaury; Achaz, Guillaume

2016-09-01

Evolutionary events co-occurring along phylogenetic trees usually point to complex adaptive phenomena, sometimes implicating epistasis. While a number of methods have been developed to account for co-occurrence of events on the same internal or external branch of an evolutionary tree, there is a need to account for the larger diversity of possible relative positions of events in a tree. Here we propose a method to quantify to what extent two or more evolutionary events are associated on a phylogenetic tree. The method is applicable to any discrete character, like substitutions within a coding sequence or gains/losses of a biological function. Our method uses a general approach to statistically test for significant associations between events along the tree, which encompasses both events inseparable on the same branch, and events genealogically ordered on different branches. It assumes that the phylogeny and themapping of branches is known without errors. We address this problem from the statistical viewpoint by a linear algebra representation of the localization of the evolutionary events on the tree.We compute the full probability distribution of the number of paired events occurring in the same branch or in different branches of the tree, under a null model of independence where each type of event occurs at a constant rate uniformly inthephylogenetic tree. The strengths andweaknesses of themethodare assessed via simulations;we then apply the method to explore the loss of cell motility in intracellular pathogens. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Government 101: how an idea becomes law.

PubMed

Griffith, James T

2006-01-01

The passing of a law is frequently accompanied by media attention and citizen apathy. In today's healthcare delivery situation, we should understand how a bill becomes law and what happens to the idea that engenders that process. Laws arise from the recommendations of ordinary citizens, but the recommendations follow a complicated process developed by the writers of our constitution to prevent abuses. Laws begin as ideas, they become bills considered by the legislature, they are expanded and enforced by the executive branch, and they are further interpreted by the judiciary branch. The laws governing healthcare issues are particularly complex, as most arise from the state legislatures.

Multiple Trellis Coded Modulation (MTCM): An MSAT-X report

NASA Technical Reports Server (NTRS)

Divsalar, D.; Simon, M. K.

1986-01-01

Conventional trellis coding outputs one channel symbol per trellis branch. The notion of multiple trellis coding is introduced wherein more than one channel symbol per trellis branch is transmitted. It is shown that the combination of multiple trellis coding with M-ary modulation yields a performance gain with symmetric signal set comparable to that previously achieved only with signal constellation asymmetry. The advantage of multiple trellis coding over the conventional trellis coded asymmetric modulation technique is that the potential for code catastrophe associated with the latter has been eliminated with no additional cost in complexity (as measured by the number of states in the trellis diagram).

Grass meristems II: inflorescence architecture, flower development and meristem fate.

PubMed

Tanaka, Wakana; Pautler, Michael; Jackson, David; Hirano, Hiro-Yuki

2013-03-01

Plant development depends on the activity of various types of meristems that generate organs such as leaves and floral organs throughout the life cycle. Grass species produce complex inflorescences and unique flowers. The grass inflorescence is composed of different types of branches, including a specialized branch called a spikelet. The spikelet is a special unit of the inflorescence and forms one to several florets, depending on the species. In the floret, floral organs such as perianth organs, carpels and stamens are formed. In Arabidopsis, because the inflorescence meristem (IM) forms the floral meristems (FMs) directly on its flanks, the change of meristem fate is relatively simple. In contrast, in grasses, different types of meristem, such as the IM, the branch meristem (BM), the spikelet pair meristem (SPM) in some grasses, the spikelet meristem (SM) and the FM, are responsible for the elaboration of their complex inflorescences and flowers. Therefore, sequential changes of meristem fate are required, and a number of genes involved in the specification of the fate of each meristem have been identified. In this review, we focus on the following issues concerning the fate of the reproductive meristems in two grass species, maize (Zea mays) and rice (Oryza sativa): (i) meristem regulation during inflorescence development; (ii) specification and fate change of the BM and the SM; (iii) determinacy of the FM; and (iv) communication between the meristem and lateral organs.

Protein phosphatase 2Cm is a critical regulator of branched-chain amino acid catabolism in mice and cultured cells.

PubMed

Lu, Gang; Sun, Haipeng; She, Pengxiang; Youn, Ji-Youn; Warburton, Sarah; Ping, Peipei; Vondriska, Thomas M; Cai, Hua; Lynch, Christopher J; Wang, Yibin

2009-06-01

The branched-chain amino acids (BCAA) are essential amino acids required for protein homeostasis, energy balance, and nutrient signaling. In individuals with deficiencies in BCAA, these amino acids can be preserved through inhibition of the branched-chain-alpha-ketoacid dehydrogenase (BCKD) complex, the rate-limiting step in their metabolism. BCKD is inhibited by phosphorylation of its E1alpha subunit at Ser293, which is catalyzed by BCKD kinase. During BCAA excess, phosphorylated Ser293 (pSer293) becomes dephosphorylated through the concerted inhibition of BCKD kinase and the activity of an unknown intramitochondrial phosphatase. Using unbiased, proteomic approaches, we have found that a mitochondrial-targeted phosphatase, PP2Cm, specifically binds the BCKD complex and induces dephosphorylation of Ser293 in the presence of BCKD substrates. Loss of PP2Cm completely abolished substrate-induced E1alpha dephosphorylation both in vitro and in vivo. PP2Cm-deficient mice exhibited BCAA catabolic defects and a metabolic phenotype similar to the intermittent or intermediate types of human maple syrup urine disease (MSUD), a hereditary disorder caused by defects in BCKD activity. These results indicate that PP2Cm is the endogenous BCKD phosphatase required for nutrient-mediated regulation of BCKD activity and suggest that defects in PP2Cm may be responsible for a subset of human MSUD.

HIV Vulnerability and the Erasure of Sexual and Gender Diversity in Abidjan, Côte d'Ivoire

PubMed Central

Thomann, Matthew

2016-01-01

In the fight against concentrated HIV epidemics, men who have sex with men (MSM) are often framed as a homogeneous population, with little attention paid to sexual and gender diversity and its impact on HIV vulnerability. This article draws on ethnographic research conducted in Abidjan, Côte d'Ivoire among les branchés – a local term encompassing several categories of same-sex desire and practice. In the context of increased HIV prevention programming targeting Ivoirian sexual and gender minorities, such diversity is effectively erased. This obfuscation of difference has particularly negative impacts for travestis, who may be at higher risk for HIV infection, though research and prevention efforts in which they are grouped with “MSM” render them underrepresented and make their vulnerability difficult to quantify. Branchés whose class and/or ethnic backgrounds compound their stigmatized status as sexual and gender minorities also bear the burden of this exclusion. Furthermore, some branchés deploy “MSM” as a form of self-identification, further complicating who such categories represent. By highlighting the ways in which constructions of gender and sexuality within HIV/AIDS programming obscure complex social realities, I aim to reorient thinking around the development of purposeful HIV programming that engages the complexity of sexual and gender minority experience. PMID:26894990

Branched-chain amino acids in metabolic signalling and insulin resistance.

PubMed

Lynch, Christopher J; Adams, Sean H

2014-12-01

Branched-chain amino acids (BCAAs) are important nutrient signals that have direct and indirect effects. Frequently, BCAAs have been reported to mediate antiobesity effects, especially in rodent models. However, circulating levels of BCAAs tend to be increased in individuals with obesity and are associated with worse metabolic health and future insulin resistance or type 2 diabetes mellitus (T2DM). A hypothesized mechanism linking increased levels of BCAAs and T2DM involves leucine-mediated activation of the mammalian target of rapamycin complex 1 (mTORC1), which results in uncoupling of insulin signalling at an early stage. A BCAA dysmetabolism model proposes that the accumulation of mitotoxic metabolites (and not BCAAs per se) promotes β-cell mitochondrial dysfunction, stress signalling and apoptosis associated with T2DM. Alternatively, insulin resistance might promote aminoacidaemia by increasing the protein degradation that insulin normally suppresses, and/or by eliciting an impairment of efficient BCAA oxidative metabolism in some tissues. Whether and how impaired BCAA metabolism might occur in obesity is discussed in this Review. Research on the role of individual and model-dependent differences in BCAA metabolism is needed, as several genes (BCKDHA, PPM1K, IVD and KLF15) have been designated as candidate genes for obesity and/or T2DM in humans, and distinct phenotypes of tissue-specific branched chain ketoacid dehydrogenase complex activity have been detected in animal models of obesity and T2DM.

Synthesis of customized petroleum-replica fuel molecules by targeted modification of free fatty acid pools in Escherichia coli

PubMed Central

Howard, Thomas P.; Middelhaufe, Sabine; Moore, Karen; Edner, Christoph; Kolak, Dagmara M.; Taylor, George N.; Parker, David A.; Lee, Rob; Smirnoff, Nicholas; Aves, Stephen J.; Love, John

2013-01-01

Biofuels are the most immediate, practical solution for mitigating dependence on fossil hydrocarbons, but current biofuels (alcohols and biodiesels) require significant downstream processing and are not fully compatible with modern, mass-market internal combustion engines. Rather, the ideal biofuels are structurally and chemically identical to the fossil fuels they seek to replace (i.e., aliphatic n- and iso-alkanes and -alkenes of various chain lengths). Here we report on production of such petroleum-replica hydrocarbons in Escherichia coli. The activity of the fatty acid (FA) reductase complex from Photorhabdus luminescens was coupled with aldehyde decarbonylase from Nostoc punctiforme to use free FAs as substrates for alkane biosynthesis. This combination of genes enabled rational alterations to hydrocarbon chain length (Cn) and the production of branched alkanes through upstream genetic and exogenous manipulations of the FA pool. Genetic components for targeted manipulation of the FA pool included expression of a thioesterase from Cinnamomum camphora (camphor) to alter alkane Cn and expression of the branched-chain α-keto acid dehydrogenase complex and β-keto acyl-acyl carrier protein synthase III from Bacillus subtilis to synthesize branched (iso-) alkanes. Rather than simply reconstituting existing metabolic routes to alkane production found in nature, these results demonstrate the ability to design and implement artificial molecular pathways for the production of renewable, industrially relevant fuel molecules. PMID:23610415

Water availability as an agent of selection in introduced populations of Arabidopsis thaliana: impacts on flowering time evolution

PubMed Central

Stock, Amanda J.; McGoey, Brechann V.

2015-01-01

Flowering is one of the most influential events in the life history of a plant and one of the main determinants of reproductive investment and lifetime fitness. It is also a highly complex trait controlled by dozens of genes. Understanding the selective pressures influencing time to flowering, and being able to reliably predict how it will evolve in novel environments, are unsolved challenges for plant evolutionary geneticists. Using the model plant species, Arabidopsis thaliana, we examined the impact of simulated high and low winter precipitation levels on the flowering time of naturalized lines from across the eastern portion of the introduced North American range, and the fitness consequences of early versus late flowering. Flowering time order was significantly correlated across two environments—in a previous common garden experiment and in environmental chambers set to mimic mid-range photoperiod and temperature conditions. Plants in low water flowered earlier, had fewer basal branches and produced fewer fruits. Selection in both treatments favored earlier flowering and more basal branches. Our analyses revealed an interaction between flowering time and water treatment for fitness, where flowering later was more deleterious for fitness in the low water treatment. Our results are consistent with the hypothesis that differences in winter precipitation levels are one of the selective agents underlying a flowering time cline in introduced A. thaliana populations. PMID:25909038

Evolutionary origins of germline segregation in Metazoa: evidence for a germ stem cell lineage in the coral Orbicella faveolata (Cnidaria, Anthozoa).

PubMed

Barfield, Sarah; Aglyamova, Galina V; Matz, Mikhail V

2016-01-13

The ability to segregate a committed germ stem cell (GSC) lineage distinct from somatic cell lineages is a characteristic of bilaterian Metazoans. However, the occurrence of GSC lineage specification in basally branching Metazoan phyla, such as Cnidaria, is uncertain. Without an independently segregated GSC lineage, germ cells and their precursors must be specified throughout adulthood from continuously dividing somatic stem cells, generating the risk of propagating somatic mutations within the individual and its gametes. To address the potential for existence of a GSC lineage in Anthozoa, the sister-group to all remaining Cnidaria, we identified moderate- to high-frequency somatic mutations and their potential for gametic transfer in the long-lived coral Orbicella faveolata (Anthozoa, Cnidaria) using a 2b-RAD sequencing approach. Our results demonstrate that somatic mutations can drift to high frequencies (up to 50%) and can also generate substantial intracolonial genetic diversity. However, these somatic mutations are not transferable to gametes, signifying the potential for an independently segregated GSC lineage in O. faveolata. In conjunction with previous research on germ cell development in other basally branching Metazoan species, our results suggest that the GSC system may be a Eumetazoan characteristic that evolved in association with the emergence of greater complexity in animal body plan organization and greater specificity of stem cell functions. © 2016 The Author(s).

Evolutionary origins of germline segregation in Metazoa: evidence for a germ stem cell lineage in the coral Orbicella faveolata (Cnidaria, Anthozoa)

PubMed Central

Barfield, Sarah; Aglyamova, Galina V.; Matz, Mikhail V.

2016-01-01

The ability to segregate a committed germ stem cell (GSC) lineage distinct from somatic cell lineages is a characteristic of bilaterian Metazoans. However, the occurrence of GSC lineage specification in basally branching Metazoan phyla, such as Cnidaria, is uncertain. Without an independently segregated GSC lineage, germ cells and their precursors must be specified throughout adulthood from continuously dividing somatic stem cells, generating the risk of propagating somatic mutations within the individual and its gametes. To address the potential for existence of a GSC lineage in Anthozoa, the sister-group to all remaining Cnidaria, we identified moderate- to high-frequency somatic mutations and their potential for gametic transfer in the long-lived coral Orbicella faveolata (Anthozoa, Cnidaria) using a 2b-RAD sequencing approach. Our results demonstrate that somatic mutations can drift to high frequencies (up to 50%) and can also generate substantial intracolonial genetic diversity. However, these somatic mutations are not transferable to gametes, signifying the potential for an independently segregated GSC lineage in O. faveolata. In conjunction with previous research on germ cell development in other basally branching Metazoan species, our results suggest that the GSC system may be a Eumetazoan characteristic that evolved in association with the emergence of greater complexity in animal body plan organization and greater specificity of stem cell functions. PMID:26763699

Quantifying the effect of side branches in endothelial shear stress estimates

PubMed Central

Giannopoulos, Andreas A.; Chatzizisis, Yiannis S.; Maurovich-Horvat, Pal; Antoniadis, Antonios P.; Hoffmann, Udo; Steigner, Michael L.; Rybicki, Frank J.; Mitsouras, Dimitrios

2016-01-01

Background and aims Low and high endothelial shear stress (ESS) is associated with coronary atherosclerosis progression and high-risk plaque features. Coronary ESS is currently assessed via computational fluid dynamic (CFD) simulation in the lumen geometry determined from invasive imaging such as intravascular ultrasound and optical coherence tomography. This process typically omits side branches of the target vessel in the CFD model as invasive imaging of those vessels is not clinically-indicated. The purpose of this study was to determine the extent to which this simplification affects the determination of those regions of the coronary endothelium subjected to pathologic ESS. Methods We determined the diagnostic accuracy of ESS profiling without side branches to detect pathologic ESS in the major coronary arteries of 5 hearts imaged ex vivo with CT angiography. ESS of the three major coronary arteries was calculated both without (test model), and with (reference model) inclusion of all side branches >1.5 mm in diameter, using previously-validated CFD approaches. Diagnostic test characteristics (accuracy, sensitivity, specificity and negative and positive predictive value [NPV/PPV]) with respect to the reference model were assessed for both the entire length as well as only the proximal portion of each major coronary artery, where the majority of high-risk plaques occur. Results Using the model without side branches overall accuracy, sensitivity, specificity, NPV and PPV were 83.4%, 54.0%, 96%, 95.9% and 55.1%, respectively to detect low ESS, and 87.0%, 67.7%, 90.7%, 93.7% and 57.5%, respectively to detect high ESS. When considering only the proximal arteries, test characteristics differed for low and high ESS, with low sensitivity (67.7%) and high specificity (90.7%) to detect low ESS, and low sensitivity (44.7%) and high specificity (95.5%) to detect high ESS. Conclusions The exclusion of side branches in ESS vascular profiling studies greatly reduces the ability to detect regions of the major coronary arteries subjected to pathologic ESS. Single-conduit models can in general only be used to rule out pathologic ESS. PMID:27372207

Quantifying the effect of side branches in endothelial shear stress estimates.

PubMed

Giannopoulos, Andreas A; Chatzizisis, Yiannis S; Maurovich-Horvat, Pal; Antoniadis, Antonios P; Hoffmann, Udo; Steigner, Michael L; Rybicki, Frank J; Mitsouras, Dimitrios

2016-08-01

Low and high endothelial shear stress (ESS) is associated with coronary atherosclerosis progression and high-risk plaque features. Coronary ESS is currently assessed via computational fluid dynamic (CFD) simulation of coronary blood flow in the lumen geometry determined from invasive imaging such as intravascular ultrasound and optical coherence tomography. This process typically omits side branches of the target vessel in the CFD model as invasive imaging of those vessels is not usually clinically-indicated. The purpose of this study was to determine the extent to which this simplification affects the determination of those regions of the coronary endothelium subjected to pathologic ESS. We determined the diagnostic accuracy of ESS profiling without side branches to detect pathologic ESS in the major coronary arteries of 5 hearts imaged ex vivo with computed tomography angiography (CTA). ESS of the three major coronary arteries was calculated both without (test model), and with (reference model) inclusion of all side branches >1.5 mm in diameter, using previously-validated CFD approaches. Diagnostic test characteristics (accuracy, sensitivity, specificity and negative and positive predictive value [NPV/PPV]) with respect to the reference model were assessed for both the entire length as well as only the proximal portion of each major coronary artery, where the majority of high-risk plaques occur. Using the model without side branches overall accuracy, sensitivity, specificity, NPV and PPV were 83.4%, 54.0%, 96%, 95.9% and 55.1%, respectively to detect low ESS, and 87.0%, 67.7%, 90.7%, 93.7% and 57.5%, respectively to detect high ESS. When considering only the proximal arteries, test characteristics differed for low and high ESS, with low sensitivity (67.7%) and high specificity (90.7%) to detect low ESS, and low sensitivity (44.7%) and high specificity (95.5%) to detect high ESS. The exclusion of side branches in ESS vascular profiling studies greatly reduces the ability to detect regions of the major coronary arteries subjected to pathologic ESS. Single-conduit models can in general only be used to rule out pathologic ESS. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Hydrogeology, water quality, and ecology of Anderton Branch near the Quail Hollow Landfill, Bedford County, Tennessee, 1995-99

USGS Publications Warehouse

Farmer, James

2004-01-01

The Quail Hollow Landfill, located in southeastern Bedford County on the Highland Rim overlooking the Central Basin karst region of Tennessee, is constructed on the gravelly, clay-rich residuum of the Fort Payne Formation of Mississippian age. A conceptual hydrologic model of the landfill indicated that Anderton Branch was at risk of being affected by the landfill. Ground water flowing beneath the landfill mixes with percolating rainwater that has passed through the landfill and discharges to the surface from numerous weeps, seeps, and springs present in the area. Anderton Branch, adjacent to the landfill site on the north and east, receives most of the discharge from these weeps, seeps, and springs. Anderton Branch also receives water from the Powell Branch drainage basin to the west and south because of diverted flow of ground water through Harrison Spring Cave. The U.S. Geological Survey, in cooperation with the Bedford County Solid Waste Authority, conducted a study to evaluate the effect of the Quail Hollow Landfill on ground- and surface-water quality. During storm runoff, specific conductance was elevated, and cadmium, iron, manganese, lead, and nickel concentrations in Anderton Branch frequently exceeded maximum contaminant levels for drinking water for the State of Tennessee. High chloride inputs to Anderton Branch were detected at two locations?a barnyard straddling the stream and a tributary draining a pond that receives water directly from the landfill. The chloride inputs probably contribute to chloride load levels that are three times higher for Anderton Branch than for the control stream Anthony Branch. Although toxic volatile organic compounds were detected in water from monitoring wells at the landfill, no organic contaminants were detected in domestic water wells adjacent to the landfill or in Anderton Branch. Sons Spring, a karst spring near the landfill, has been affected by the landfill as indicated by an increase in chloride concentrations from 4 milligrams per liter in 1974 to 59 milligrams per liter in 1996. Analysis of water samples from Sons Spring detected concentrations of nickel that exceeded primary drinking-water standards and Tennessee Department of Environment and Conservation fish and aquatic life chronic standards. Trichloroethene, 1,1-dichloroethene, and 1,1-dichloroethane also were detected at Sons Spring. The presence of these chlorinated solvents imply the landfill origin of the contaminants in Sons Spring. Continuous monitoring at Sons Spring indicated a pattern of decreased specific conductance and lower contaminant concentrations after a storm. Contaminant concentrations increased with specific conductance to pre-storm levels after several days. The benthic macroinvertebrate community in Anderton Branch adjacent to the landfill was not different from the communities at control sites upstream and in Anthony Branch. Sons Spring, however, has low abundance and numbers of benthic macroinvertebrate taxa. Toxicity studies using Ceriodaphnia dubia indicated no toxicity in the base flow or storm water in Anderton Branch or in a tributary draining a pond that receives water from the landfill and Sons Spring; however, water collected from Sons Spring resulted in 100 percent mortality to all organisms within 48 hours. High concentrations of nickel were detected in crayfish tissue from control sites and Anderton Branch. Analysis of sediment samples also indicates nickel concentrations are high at control sites upstream of the landfill. Increased levels of the biomarker metallothionein detected in crayfish from Anderton Branch likely are not caused by nickel or cadmium because the levels present in the tissue are not correlated with metallothionein levels. Despite the high levels of certain metals in Anderton Branch during storm flow, the lack of toxicity and the health of the benthic community imply no detectable negative effect from the landfill to the stream. Sons Spring, howe

On complexity of trellis structure of linear block codes

NASA Technical Reports Server (NTRS)

Lin, Shu

1990-01-01

The trellis structure of linear block codes (LBCs) is discussed. The state and branch complexities of a trellis diagram (TD) for a LBC is investigated. The TD with the minimum number of states is said to be minimal. The branch complexity of a minimal TD for a LBC is expressed in terms of the dimensions of specific subcodes of the given code. Then upper and lower bounds are derived on the number of states of a minimal TD for a LBC, and it is shown that a cyclic (or shortened cyclic) code is the worst in terms of the state complexity among the LBCs of the same length and dimension. Furthermore, it is shown that the structural complexity of a minimal TD for a LBC depends on the order of its bit positions. This fact suggests that an appropriate permutation of the bit positions of a code may result in an equivalent code with a much simpler minimal TD. Boolean polynomial representation of codewords of a LBC is also considered. This representation helps in study of the trellis structure of the code. Boolean polynomial representation of a code is applied to construct its minimal TD. Particularly, the construction of minimal trellises for Reed-Muller codes and the extended and permuted binary primitive BCH codes which contain Reed-Muller as subcodes is emphasized. Finally, the structural complexity of minimal trellises for the extended and permuted, and double-error-correcting BCH codes is analyzed and presented. It is shown that these codes have relatively simple trellis structure and hence can be decoded with the Viterbi decoding algorithm.

Highly-branched anisotropic hybrid nanoparticles at surfaces.

NASA Astrophysics Data System (ADS)

Tsukruk, Vladimir

2009-03-01

We present a brief overview of our recent studies on combined hybrid anisotropic structures composed of inorganic nanoparticles and highly branched molecules such as modified silsesquioxanes polyhedra cores (POSS) with mixed hydrophobic-hydrophilic tails and silver nanowires with functionalized star block copolymer with embedded gold nanoparticles (nanocobs). We demonstrate two-stage melting of that branched POSS and their ability to form monolayer and multilayered LB structures. On the other hand, we observed that silver-BCP-gold nanocobs display extremely bright Raman scattering caused by surface enhanced Raman effect with very different longitudinal and transversal optical properties as revealed by high-resolution confocal Raman microscopy. To study these hybrid nanostructures we applied combined AFM, SEM, TEM, XPS, SERS, UV-vis, and XR techniques.

Synthesis and excellent field emission properties of three-dimensional branched GaN nanowire homostructures

NASA Astrophysics Data System (ADS)

Li, Enling; Sun, Lihe; Cui, Zhen; Ma, Deming; Shi, Wei; Wang, Xiaolin

2016-10-01

Three-dimensional branched GaN nanowire homostructures have been synthesized on the Si substrate via a two-step approach by chemical vapor deposition. Structural characterization reveals that the single crystal GaN nanowire trunks have hexagonal wurtzite characteristics and grow along the [0001] direction, while the homoepitaxial single crystal branches grow in a radial direction from the six-sided surfaces of the trunks. The field emission measurements demonstrate that the branched GaN nanowire homostructures have excellent field emission properties, with low turn-on field at 2.35 V/μm, a high field enhancement factor of 2938, and long emission current stability. This indicates that the present branched GaN nanowire homostructures will become valuable for practical field emission applications.

Thermodynamic characterization of a triple-helical three-way junction containing a Hoogsteen branch point.

PubMed

Hüsler, P L; Klump, H H

1995-09-10

We have designed a Hoogsteen (HG) triple-helical three-way junction (ternary complex) constructed from three 33-mer oligonucleotides based on the same subset of sequences used for the Watson-Crick (WC) triple-helical three-way junction, characterized previously (P. L. Hüsler and H. H. Klump (1994) Arch. Biochem. Biophys., 313, 29-38). The junction differs primarily in the assembly of the branch point and the ends of the arms. The three oligonucleotides can each fold into a WC hairpin, linked by a four-member cytosine loop, each containing a homo-pyrimidine 10-mer single-strand extension. On lowering the pH (between 6 and 4), the extensions mutually associate to one of the other hairpins via Hoogsteen (HG) hydrogen bonding. Collectively, this process results in the formation of the branch point and the triple-helical arms. The HG triple-helical three-way junction is characterized by gel electrophoresis, circular dichroism, uv melting, and differential scanning calorimetry. The junction undergoes thermal unfolding in two distinct temperature regions. In the temperature range 15 to 50 degrees C loss of HG base pairing results in the dissociation of the three-way junction. Between 55 and 95 degrees C the resulting hairpins undergo further successive unfolding. The overall calorimetric unfolding enthalpy and entropy changes associated with the loss of HG base pairing are approximately equal to the sum of the enthalpy and entropy changes associated with the dissociation of the HG base pairing in the isolated arms (170.6 kcal.mol-1; 540.1 cal.mol-1.K-1). It is apparent from these results that in the proximity of the branch point the structure is not perturb or strain. This result is contrary to the results obtained for the WC triple-helical three-way and for three-way junctions constructed from canonical double-helical DNA. Complete folding of the junction requires either high Na+ (600 mM) ion concentrations or 40-60 mM Mg2+.

Anatomic changes of target vessels after fenestrated and branched aortic aneurysm repair.

PubMed

Kalder, J; Keschenau, P; Tamm, M; Jalaie, H; Jacobs, M J; Greiner, A

2014-04-01

Objective of this study was to evaluate the anatomic changes of the stented target vessels after endovascular repair of complex aortic aneurysms. Between July 2011 and December 2013, 53 aortic aneurysms were treated in our department with fenestrated and branched stent-graft devices. Forty-two of these patients were pre- and postoperatively scanned with a high resolution computer tomography (CT) (Cook Zenith® fenestrated or branched, Australia Pty. Ltd., Brisbane, Australia: N.=19; AnacondaTM fenestrated, Vascutek, Glasgow, Scotland, UK: N.=23). The other 11 out of the 53 patients did not receive a CT scan, because of a pre-existing renal failure. In the CT scans we retrospectively evaluated the anatomic vessel deviation at the origin of the target vessel and the vessel shift distal to the stent. For the first measurement the CT scans were loaded into OsiriX MD®, and the pre- and postoperative angles of the target vessels were measured and subtracted. For matching, the CT-scans were normalized at vertebral body lumbar 2. The second measured angle was the maximal measured angle distal to the target vessel stent-graft. Altogether, 113 target vessels were stented (celiac trunk [CT] 15, superior mesenteric arteries [SMA] 26, renal arteries [RA] 72), with 97 balloon-expandable PTFE stents: 90 Atrium V12 (Maquet Getinge group, Hudson, NH, USA), 7 BeGrafts (Bentley InnoMed, Hechingen, Germany) and 16 self-expandable fluency PTFE stents (Bard, Karlsruhe, Germany). The mean anatomic deviation at the target vessel origin was 28±17.3 and the mean vessel shift distal to the stent was 36.3±18.8. There were no significant differences between the main device and the target vessel stent types. Fenestrated and branched stent-graft solutions for aortic aneurysm repair induce changes of the target vessel anatomy. We did not observe significant differences between the several devices.

Zoology: At Last an Exit for Ctenophores.

PubMed

Giribet, Gonzalo

2016-10-24

Ctenophores, one of the most basal branches in the tree of life, have been found to have a through-gut, complete with mouth and anus. Basal animals are surprisingly complex and simplification has been rampant in animal evolution. Copyright © 2016 Elsevier Ltd. All rights reserved.

Shaping highly regular glass architectures: A lesson from nature

PubMed Central

Schoeppler, Vanessa; Reich, Elke; Vacelet, Jean; Rosenthal, Martin; Pacureanu, Alexandra; Rack, Alexander; Zaslansky, Paul; Zolotoyabko, Emil; Zlotnikov, Igor

2017-01-01

Demospongiae is a class of marine sponges that mineralize skeletal elements, the glass spicules, made of amorphous silica. The spicules exhibit a diversity of highly regular three-dimensional branched morphologies that are a paradigm example of symmetry in biological systems. Current glass shaping technology requires treatment at high temperatures. In this context, the mechanism by which glass architectures are formed by living organisms remains a mystery. We uncover the principles of spicule morphogenesis. During spicule formation, the process of silica deposition is templated by an organic filament. It is composed of enzymatically active proteins arranged in a mesoscopic hexagonal crystal-like structure. In analogy to synthetic inorganic nanocrystals that show high spatial regularity, we demonstrate that the branching of the filament follows specific crystallographic directions of the protein lattice. In correlation with the symmetry of the lattice, filament branching determines the highly regular morphology of the spicules on the macroscale. PMID:29057327

Stable dipole solitons and soliton complexes in the nonlinear Schrödinger equation with periodically modulated nonlinearity

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

Lebedev, M. E., E-mail: gloriouslair@gmail.com, E-mail: galfimov@yahoo.com; Alfimov, G. L., E-mail: gloriouslair@gmail.com, E-mail: galfimov@yahoo.com; Malomed, Boris A., E-mail: malomed@post.tau.ac.il

We develop a general classification of the infinite number of families of solitons and soliton complexes in the one-dimensional Gross-Pitaevskii/nonlinear Schrödinger equation with a nonlinear lattice pseudopotential, i.e., periodically modulated coefficient in front of the cubic term, which takes both positive and negative local values. This model finds direct implementations in atomic Bose-Einstein condensates and nonlinear optics. The most essential finding is the existence of two branches of dipole solitons (DSs), which feature an antisymmetric shape, being essentially squeezed into a single cell of the nonlinear lattice. This soliton species was not previously considered in nonlinear lattices. We demonstrate thatmore » one branch of the DS family (namely, which obeys the Vakhitov-Kolokolov criterion) is stable, while unstable DSs spontaneously transform into stable fundamental solitons (FSs). The results are obtained in numerical and approximate analytical forms, the latter based on the variational approximation. Some stable bound states of FSs are found too.« less

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples.

PubMed

Yu, Feiqiao Brian; Blainey, Paul C; Schulz, Frederik; Woyke, Tanja; Horowitz, Mark A; Quake, Stephen R

2017-07-05

Metagenomics and single-cell genomics have enabled genome discovery from unknown branches of life. However, extracting novel genomes from complex mixtures of metagenomic data can still be challenging and represents an ill-posed problem which is generally approached with ad hoc methods. Here we present a microfluidic-based mini-metagenomic method which offers a statistically rigorous approach to extract novel microbial genomes while preserving single-cell resolution. We used this approach to analyze two hot spring samples from Yellowstone National Park and extracted 29 new genomes, including three deeply branching lineages. The single-cell resolution enabled accurate quantification of genome function and abundance, down to 1% in relative abundance. Our analyses of genome level SNP distributions also revealed low to moderate environmental selection. The scale, resolution, and statistical power of microfluidic-based mini-metagenomics make it a powerful tool to dissect the genomic structure of microbial communities while effectively preserving the fundamental unit of biology, the single cell.

A new missense mutation in the BCKDHB gene causes the classic form of maple syrup urine disease (MSUD).

PubMed

Miryounesi, Mohammad; Ghafouri-Fard, Soudeh; Goodarzi, Hamedreza; Fardaei, Majid

2015-05-01

Maple syrup urine disease (MSUD) is an autosomal recessive metabolic disease caused by mutations in the BCKDHA, BCKDHB, DBT and DLD genes, which encode the E1α, E1β, E2 and E3 subunits of the branched chain α ketoacid dehydrogenase (BCKD) complex, respectively. This complex is involved in the metabolism of branched-chain amino acids. In this study, we analyzed the DNA sequences of BCKDHA and BCKDHB genes in an infant who suffered from MSUD and died at the age of 6 months. We found a new missense mutation in exon 5 of BCKDHB gene (c.508C>T). The heterozygosity of the parents for the mentioned nucleotide change was confirmed by direct sequence analysis of the corresponding segment. Another missense mutation has been found in the same codon previously and shown by in silico analyses to be deleterious. This report provides further evidence that this amino acid change can cause classic MSUD.

Antidiarrheal activity of extracts from Maytenus gonoclada and inhibition of Dengue virus by lupeol.

PubMed

Silva, Fernando C; Rodrigues, Vanessa G; Duarte, Lucienir P; Lula, Ivana S; Sinisterra, Ruben D; Vieira-Filho, Sidney A; Rodrigues, Rodrigo A L; Kroon, Erna G; Oliveira, Patrícia L; Farias, Luiz M; Magalhães, Paula P; Silva, Grácia D F

2017-01-01

Diarrhea is an infectious disease caused by bacterial, virus, or protozoan, and dengue is caused by virus, included among the neglected diseases in several underdeveloped and developing countries, with an urgent demand for new drugs. Considering the antidiarrheal potential of species of Maytenus genus, a phytochemical investigation followed by antibacterial activity test with extracts of branches and heartwood and bark of roots from Maytenus gonoclada were conducted. Moreover, due the frequency of isolation of lupeol from Maytenus genus the antiviral activity against Dengue virus and cytotoxicity of lupeol and its complex with β-cyclodextrins were also tested. The results indicated the bioactivity of ethyl acetate extract from branches and ethanol extract from heartwood of roots of M. gonoclada against diarrheagenic bacteria. The lupeol showed potent activity against Dengue virus and low cytotoxicity in LLC-MK2 cells, but its complex with β-cyclodextrin was inactive. Considering the importance of novel and selective antiviral drug candidates the results seem to be promising.

Isolation of a Bacterial Strain Able To Degrade Branched Nonylphenol

PubMed Central

Tanghe, Tom; Dhooge, Willem; Verstraete, Willy

1999-01-01

Conventional enrichment of microorganisms on branched nonylphenol (NP) as only carbon and energy source yielded mixed cultures able to grow on the organic compound. However, plating yielded no single colonies capable, alone or in combination with other isolates, of degrading the NP in liquid culture. Therefore, a special approach was used, referred to as “serial dilution-plate resuspension,” to reduce culture complexity. In this way, one isolate, TTNP3, tentatively identified as a Sphingomonas sp., was found to be able to grow on NP in liquid culture. Remarkably, this isolate was able to be filtered through a 0.45-μm-pore-diameter filter. Moreover, isolate TTNP3 did not form visible colonies on mineral medium with NP, and it formed visible colonies on R2A agar only after a prolonged incubation of 1 week. High-performance liquid chromatography and gas chromatography-mass spectroscopy analysis of the culture media indicated that the strain starts the degradation of NP with a fission of the phenol ring and preferably uses the para isomer of NP and not the ortho isomer. No distinct accumulation of an intermediary product could be observed. PMID:9925611

Giant seismites and megablock uplift in the East African Rift: evidence for Late Pleistocene large magnitude earthquakes.

PubMed

Hilbert-Wolf, Hannah Louise; Roberts, Eric M

2015-01-01

In lieu of comprehensive instrumental seismic monitoring, short historical records, and limited fault trench investigations for many seismically active areas, the sedimentary record provides important archives of seismicity in the form of preserved horizons of soft-sediment deformation features, termed seismites. Here we report on extensive seismites in the Late Quaternary-Recent (≤ ~ 28,000 years BP) alluvial and lacustrine strata of the Rukwa Rift Basin, a segment of the Western Branch of the East African Rift System. We document examples of the most highly deformed sediments in shallow, subsurface strata close to the regional capital of Mbeya, Tanzania. This includes a remarkable, clastic 'megablock complex' that preserves remobilized sediment below vertically displaced blocks of intact strata (megablocks), some in excess of 20 m-wide. Documentation of these seismites expands the database of seismogenic sedimentary structures, and attests to large magnitude, Late Pleistocene-Recent earthquakes along the Western Branch of the East African Rift System. Understanding how seismicity deforms near-surface sediments is critical for predicting and preparing for modern seismic hazards, especially along the East African Rift and other tectonically active, developing regions.

Informatic search strategies to discover analogues and variants of natural product archetypes.

PubMed

Johnston, Chad W; Connaty, Alex D; Skinnider, Michael A; Li, Yong; Grunwald, Alyssa; Wyatt, Morgan A; Kerr, Russell G; Magarvey, Nathan A

2016-03-01

Natural products are a crucial source of antimicrobial agents, but reliance on low-resolution bioactivity-guided approaches has led to diminishing interest in discovery programmes. Here, we demonstrate that two in-house automated informatic platforms can be used to target classes of biologically active natural products, specifically, peptaibols. We demonstrate that mass spectrometry-based informatic approaches can be used to detect natural products with high sensitivity, identifying desired agents present in complex microbial extracts. Using our specialised software packages, we could elaborate specific branches of chemical space, uncovering new variants of trichopolyn and demonstrating a way forward in mining natural products as a valuable source of potential pharmaceutical agents.

Fundamental properties of resonances

PubMed Central

Ceci, S.; Hadžimehmedović, M.; Osmanović, H.; Percan, A.; Zauner, B.

2017-01-01

All resonances, from hydrogen nuclei excited by the high-energy gamma rays in deep space to newly discovered particles produced in Large Hadron Collider, should be described by the same fundamental physical quantities. However, two distinct sets of properties are used to describe resonances: the pole parameters (complex pole position and residue) and the Breit-Wigner parameters (mass, width, and branching fractions). There is an ongoing decades-old debate on which one of them should be abandoned. In this study of nucleon resonances appearing in the elastic pion-nucleon scattering we discover an intricate interplay of the parameters from both sets, and realize that neither set is completely independent or fundamental on its own. PMID:28345595

High Leucine Diets Stimulate Cerebral Branched-Chain Amino Acid Degradation and Modify Serotonin and Ketone Body Concentrations in a Pig Model

PubMed Central

Wessels, Anna G.; Kluge, Holger; Hirche, Frank; Kiowski, Andreas; Schutkowski, Alexandra; Corrent, Etienne; Bartelt, Jörg; König, Bettina; Stangl, Gabriele I.

2016-01-01

In addition to its role as an essential protein component, leucine (Leu) displays several other metabolic functions such as activation of protein synthesis. This property makes it an interesting amino acid for the therapy of human muscle atrophy and for livestock production. However, Leu can stimulate its own degradation via the branched-chain keto acid dehydrogenase complex (BCKDH). To examine the response of several tissues to excessive Leu, pigs were fed diets containing two- (L2) and four-fold (L4) higher Leu contents than the recommended amount (control). We found that the L4 diet led to a pronounced increase in BCKDH activity in the brain (2.5-fold, P < 0.05), liver (1.8-fold, P < 0.05) and cardiac muscle (1.7-fold, P < 0.05), whereas we found no changes in enzyme activity in the pancreas, skeletal muscle, adipose tissue and intestinal mucosa. The L2 diet had only weak effects on BCKDH activity. Both high Leu diets reduced the concentrations of free valine and isoleucine in nearly all tissues. In the brain, high Leu diets modified the amount of tryptophan available: for serotonin synthesis. Compared to the controls, pigs treated with the high Leu diets consumed less food, showed increased plasma concentrations of 3-hydroxybutyrate and reduced levels of circulating serotonin. In conclusion, excessive Leu can stimulate BCKDH activity in several tissues, including the brain. Changes in cerebral tryptophan, along with the changes in amino acid-derived metabolites in the plasma may limit the use of high Leu diets to treat muscle atrophy or to increase muscle growth. PMID:26930301

High Incidence of Pathogenic Streptococcus agalactiae ST485 Strain in Pregnant/Puerperal Women and Isolation of Hyper-Virulent Human CC67 Strain

PubMed Central

Li, Liping; Wang, Rui; Huang, Yan; Huang, Ting; Luo, Fuguang; Huang, Weiyi; Yang, Xiuying; Lei, Aiying; Chen, Ming; Gan, Xi

2018-01-01

Group B streptococcus (GBS) is the major pathogen causing diseases in neonates, pregnant/puerperal women, cows and fish. Recent studies have shown that GBS may be infectious across hosts and some fish GBS strain might originate from human. The purpose of this study is to investigate the genetic relationship of CC103 strains that recently emerged in cows and humans, and explore the pathogenicity of clinical GBS isolates from human to tilapia. Ninety-two pathogenic GBS isolates were identified from 19 patients with different diseases and their evolution and pathogenicity to tilapia were analyzed. The multilocus sequence typing revealed that clonal complex (CC) 103 strain was isolated from 21.74% (20/92) of patients and ST485 strain was from 14.13% (13/92) patients with multiple diseases including neonates. Genomic evolution analysis showed that both bovine and human CC103 strains alternately form independent evolutionary branches. Three CC67 isolates carried gbs2018-C gene and formed one evolutionary branch with ST61 and ST67 strains that specifically infect dairy cows. Studies of interspecies transmission to tilapia found that 21/92 (22.83%) isolates including all ST23 isolates were highly pathogenic to tilapia and demonstrated that streptococci could break through the blood-brain barrier into brain tissue. In conclusions, CC103 strains are highly prevalent among pathogenic GBS from humans and have evolved into the highly pathogenic ST485 strains specifically infecting humans. The CC67 strains isolated from cows are able to infect humans through evolutionary events of acquiring CC17-specific type C gbs2018 gene and others. Human-derived ST23 pathogenic GBS strains are highly pathogenic to tilapia. PMID:29467722

XAS and XMCD studies of magnetic properties modifications of Pt/Co/Au and Pt/Co/Pt trilayers induced by Ga⁺ ions irradiation.

PubMed

Mazalski, Piotr; Sveklo, Iosif; Kurant, Zbigniew; Ollefs, Katharina; Rogalev, Andrei; Wilhelm, Fabrice; Fassbender, Juergen; Baczewski, Lech Tomasz; Wawro, Andrzej; Maziewski, Andrzej

2015-05-01

Magnetic and magneto-optical properties of Pt/Co/Au and Pt/Co/Pt trilayers subjected to 30 keV Ga(+) ion irradiation are compared. In two-dimensional maps of these properties as a function of cobalt thickness and ion fluence, two branches with perpendicular magnetic anisotropy (PMA) for Pt/Co/Pt trilayers are well distinguished. The replacement of the Pt capping layer with Au results in the two branches still being visible but the in-plane anisotropy for the low-fluence branch is suppressed whereas the high-fluence branch displays PMA. The X-ray absorption spectra and X-ray magnetic circular dichroism (XMCD) spectra are discussed and compared with non-irradiated reference samples. The changes of their shapes and peak amplitude, particularly for the high-fluence branch, are related to the modifications of the local environment of Co(Pt) atoms and the etching effects induced by ion irradiation. Additionally, in irradiated trilayers the XMCD measurements at the Pt L2,3-edge reveal an increase of the magnetic moment induced in Pt atoms.

An efficient mechanism for enhancing the thermoelectricity of nanoribbons by blocking phonon transport in 2D materials.

PubMed

Liu, Yue-Yang; Zeng, Yu-Jia; Jia, Pin-Zhen; Cao, Xuan-Hao; Jiang, Xiangwei; Chen, Ke-Qiu

2018-07-11

Inspired by the novel mechanism of reducing thermal conductivity by local phonon resonance instead of by inducing structural defects, we investigate the effect of side branching on the thermoelectric properties of [Formula: see text] nanoribbons, and prove that side branching is a highly efficient mechanism for enhancing the thermoelectricity of different kinds of nanoribbons. For both armchair and zigzag [Formula: see text] nanoribbons, the side branches result in not only significant blocking of phonon transport but also notable increase of the Seebeck coefficient. Consequently, the thermoelectric figure of merit of the armchair [Formula: see text] nanoribbon is boosted from 0.72 to as high as 1.93, and the originally non-thermoelectric metallic zigzag [Formula: see text] nanoribbon is turned into a thermoelectric material due to the appearance of the band gap induced by the side branches. These results mean that the mechanism of branching is not only very efficient, but also takes effect regardless of the original properties of the nanoribbons, and thus will hold great promise for its application in the thermoelectric field.

Planification de trajectoires pour placement automatise de fibres sur surfaces de geometries complexes

NASA Astrophysics Data System (ADS)

Hely, Clement

During the past 50 years, the use of composite materials drastically increase, mainly thanks to the interest of aeronautical industries for these strong and lightweight materials. To improve the productivity of composite materials manufacturing some of the largest aeronautics companies began to develop automated processes such as Automated Fibre Placement (AFP). The AFP workcells currently used by the industry were mainly developed for production of large, nearly flat, plates with low curvatures such as aircraft fuselages. However, the fields of aeronautics and sport goods production begin nowadays to show an interest for manufacturing of smaller and more complex parts. The aim of the project in which this research takes place is to design a new AFP workcell and to develop new techniques allowing production of parts with small size and complex geometry. The work presented in this thesis focuses on the path planning on multi-axial revolution surfaces, e.g. Y-shaped tubes of constant circular cross section. Several path planning algorithms will be presented aiming at the exhaustive coverage of a mandrel with pre-impregnated (prepreg) composite tape. The methodology used in two of these algorithms is to individually cover each branch of the Y-shaped part with paths deriving from a helix. In the first one, the helix will be cut at the boundary between a branch and the junction region (algorithm HD) while in the second (algorithm HA) the pseudo-helix path can be adjusted to follow this boundary. These two methods were shown to have some drawbacks compromising their practical use and possibly leading to parts with diminished mechanical properties. To avoid these drawbacks, two others algorithms were developed with a new methodology. With them, the aim is to cover two branches of the Y-shape with a continuous course (i.e. without cut). The first one uses a well known strategy which defines plies with a constant fibre orientation. Parallel paths are then computed to generate a full and uniform ply covering two branches. Once again this method suffers from a main drawback, namely that it can produce highly curved paths leading to manufacturing defects. To overcome this limitation, a last algorithm is proposed ensuring that the maximal curvature of a trajectory stays below a fixed threshold. However, fulfilling this constraint prevents to predict the complete shape of the path and to ensure a perfectly uniform coverage. It is thus proposed to generate an exhaustive set of trajectories having different shapes and covering all the part. Then, a selection algorithm is used to choose the ones which are best suited according to selection criteria. To help the definition of these criteria, a finite element analysis is conducted to give some insight concerning the best suited shapes for specific loading cases. Finally, simulations were carried out with a workcell constituted by a robotic manipulator associated with a rotary table to verify the feasibility of the paths generated by the different algorithms.

The Role of Echocardiography in the Optimization of Cardiac Resynchronization Therapy: Current Evidence and Future Perspectives.

PubMed

Spartalis, Michael; Tzatzaki, Eleni; Spartalis, Eleftherios; Damaskos, Christos; Athanasiou, Antonios; Livanis, Efthimios; Voudris, Vassilis

2017-01-01

Cardiac resynchronization therapy (CRT) has become a mainstay in the management of heart failure. Up to one-third of patients who received resynchronization devices do not experience the full benefits of CRT. The clinical factors influencing the likelihood to respond to the therapy are wide QRS complex, left bundle branch block, female gender, non-ischaemic cardiomyopathy (highest responders), male gender, ischaemic cardiomyopathy (moderate responders) and narrow QRS complex, non-left bundle branch block (lowest, non-responders). This review provides a conceptual description of the role of echocardiography in the optimization of CRT. A literature survey was performed using PubMed database search to gather information regarding CRT and echocardiography. A total of 70 studies met selection criteria for inclusion in the review. Echocardiography helps in the initial selection of the patients with dyssynchrony, which will benefit the most from optimal biventricular pacing and provides a guide to left ventricular (LV) lead placement during implantation. Different echocardiographic parameters have shown promise and can offer the possibility of patient selection, response prediction, lead placement optimization strategies and optimization of device configurations. LV ejection fraction along with specific electrocardiographic criteria remains the cornerstone of CRT patient selection. Echocardiography is a non-invasive, cost-effective, highly reproducible method with certain limitations and accuracy that is affected by measurement errors. Echocardiography can assist with the identification of the appropriate electromechanical substrate of CRT response and LV lead placement. The targeted approach can improve the haemodynamic response, as also the patient-specific parameters estimation.

The Role of Echocardiography in the Optimization of Cardiac Resynchronization Therapy: Current Evidence and Future Perspectives

PubMed Central

Spartalis, Michael; Tzatzaki, Eleni; Spartalis, Eleftherios; Damaskos, Christos; Athanasiou, Antonios; Livanis, Efthimios; Voudris, Vassilis

2017-01-01

Background: Cardiac resynchronization therapy (CRT) has become a mainstay in the management of heart failure. Up to one-third of patients who received resynchronization devices do not experience the full benefits of CRT. The clinical factors influencing the likelihood to respond to the therapy are wide QRS complex, left bundle branch block, female gender, non-ischaemic cardiomyopathy (highest responders), male gender, ischaemic cardiomyopathy (moderate responders) and narrow QRS complex, non-left bundle branch block (lowest, non-responders). Objective: This review provides a conceptual description of the role of echocardiography in the optimization of CRT. Method: A literature survey was performed using PubMed database search to gather information regarding CRT and echocardiography. Results: A total of 70 studies met selection criteria for inclusion in the review. Echocardiography helps in the initial selection of the patients with dyssynchrony, which will benefit the most from optimal biventricular pacing and provides a guide to left ventricular (LV) lead placement during implantation. Different echocardiographic parameters have shown promise and can offer the possibility of patient selection, response prediction, lead placement optimization strategies and optimization of device configurations. Conclusion: LV ejection fraction along with specific electrocardiographic criteria remains the cornerstone of CRT patient selection. Echocardiography is a non-invasive, cost-effective, highly reproducible method with certain limitations and accuracy that is affected by measurement errors. Echocardiography can assist with the identification of the appropriate electromechanical substrate of CRT response and LV lead placement. The targeted approach can improve the haemodynamic response, as also the patient-specific parameters estimation. PMID:29387277

Diversity in skeletal architecture influences biological heterogeneity and Symbiodinium habitat in corals.

PubMed

Yost, Denise M; Wang, Li-Hsueh; Fan, Tung-Yung; Chen, Chii-Shiarng; Lee, Raymond W; Sogin, Emilia; Gates, Ruth D

2013-10-01

Scleractinian corals vary in response to rapid shifts in the marine environment and changes in reef community structure post-disturbance reveal a clear relationship between coral performance and morphology. With exceptions, massive corals are thought to be more tolerant and branching corals more vulnerable to changing environmental conditions, notably thermal stress. The typical responses of massive and branching coral taxa, respectively, are well documented; however, the biological and functional characteristics that underpin this variation are not well understood. We address this gap by comparing multiple biological attributes that are correlated with skeletal architecture in two perforate (having porous skeletal matrices with intercalating tissues) and two imperforate coral species (Montipora aequituberculata, Porites lobata, Pocillopora damicornis, and Seriatopora hystrix) representing three morphotypes. Our results reveal inherent biological heterogeneity among corals and the potential for perforate skeletons to create complex, three-dimensional internal habitats that impact the dynamics of the symbiosis. Patterns of tissue thickness are correlated with the concentration of symbionts within narrow regions of tissue in imperforate corals versus broad distribution throughout the larger tissue area in perforate corals. Attributes of the perforate and environmentally tolerant P. lobata were notable, with tissues ∼5 times thicker than in the sensitive, imperforate species P. damicornis and S. hystrix. Additionally, P. lobata had the lowest baseline levels of superoxide and Symbiodinium that provisioned high levels of energy. Given our observations, we hypothesize that the complexity of the visually obscured internal environment has an impact on host-symbiont dynamics and ultimately on survival, warranting further scientific investigation. Copyright © 2013 Elsevier GmbH. All rights reserved.

Branched Chain Amino Acid Suppresses Hepatocellular Cancer Stem Cells through the Activation of Mammalian Target of Rapamycin

PubMed Central

Nishitani, Shinobu; Horie, Mayumi; Ishizaki, Sonoko; Yano, Hirohisa

2013-01-01

Differentiation of cancer stem cells (CSCs) into cancer cells causes increased sensitivity to chemotherapeutic agents. Although inhibition of mammalian target of rapamycin (mTOR) leads to CSC survival, the effect of branched chain amino acids (BCAAs), an mTOR complex 1 (mTORC1) activator remains unknown. In this study, we examined the effects of BCAA on hepatocellular carcinoma (HCC) cells expressing a hepatic CSC marker, EpCAM. We examined the effects of BCAA and/or 5-fluorouracil (FU) on expression of EpCAM and other CSC-related markers, as well as cell proliferation in HCC cells and in a xenograft mouse model. We also characterized CSC-related and mTOR signal-related molecule expression and tumorigenicity in HCC cells with knockdown of Rictor or Raptor, or overexpression of constitutively active rheb (caRheb). mTOR signal-related molecule expression was also examined in BCAA-treated HCC cells. In-vitro BCAA reduced the frequency of EpCAM-positive cells and improved sensitivity to the anti-proliferative effect of 5-FU. Combined 5-FU and BCAA provided better antitumor efficacy than 5-FU alone in the xenograft model. Stimulation with high doses of BCAA activated mTORC1. Knockdown and overexpression experiments revealed that inhibition of mTOR complex 2 (mTORC2) or activation of mTORC1 led to decreased EpCAM expression and little or no tumorigenicity. BCAA may enhance the sensitivity to chemotherapy by reducing the population of cscs via the mTOR pathway. This result suggests the utility of BCAA in liver cancer therapy. PMID:24312415

Iron deficiency impairs developing hippocampal neuron gene expression, energy metabolism and dendrite complexity

PubMed Central

Bastian, Thomas W.; von Hohenberg, William C.; Mickelson, Daniel J.; Lanier, Lorene M.; Georgieff, Michael K.

2016-01-01

Iron deficiency (ID), with and without anemia, affects an estimated 2 billion people worldwide. ID is particularly deleterious during early-life brain development, leading to long-term neurological impairments, including deficits in hippocampus-mediated learning and memory. Neonatal rats with fetal/neonatal ID anemia (IDA) have shorter hippocampal CA1 apical dendrites with disorganized branching. ID-induced dendritic structural abnormalities persist into adulthood despite normalization of iron status. However, the specific developmental effects of neuronal iron loss on hippocampal neuron dendrite growth and branching are unknown. Embryonic hippocampal neuron cultures were chronically treated with deferoxamine (DFO, an iron chelator) beginning at 3 days in vitro (DIV). Levels of mRNA for Tfr1 and Slc11a2, iron-responsive genes involved in iron uptake, were significantly elevated in DFO-treated cultures at 11DIV and 18DIV, indicating a similar degree of neuronal ID as seen in rodent ID models. DFO treatment decreased mRNA levels for genes indexing dendritic and synaptic development (i.e., BdnfVI, Camk2a, Vamp1, Psd95, Cfl1, Pfn1, Pfn2, and Gda) and mitochondrial function (i.e., Ucp2, Pink1, and Cox6a1). At 18DIV, DFO reduced key aspects of energy metabolism including basal respiration, maximal respiration, spare respiratory capacity, ATP production, and glycolytic rate, capacity, and reserve. Sholl analysis revealed a significant decrease in distal dendritic complexity in DFO-treated neurons at both 11DIV and 18DIV. At 11DIV, the length of primary dendrites and the number and length of branches in DFO-treated neurons was reduced. By 18DIV, a partial recovery of dendritic branch number in DFO-treated neurons was counteracted by a significant reduction in the number and length of primary dendrites and length of branches. Our findings suggest that early neuronal iron loss, at least partially driven through altered mitochondrial function and neuronal energy metabolism, is responsible for the effects of fetal/neonatal ID and IDA on hippocampal neuron dendritic and synaptic maturation. Impairments in these neurodevelopmental processes likely underlie the negative impact of early life ID and IDA on hippocampus-mediated learning and memory. PMID:27669335

Perforator and secondary branch origin in relation to the neck of saccular, cerebral bifurcation aneurysms.

PubMed

Pritz, Michael B

2014-11-01

Perforator and secondary branch origin in relation to the neck of cerebral, saccular bifurcation aneurysms were analyzed. These two features were considered important for treatment. From a series of microsurgically clipped saccular cerebral aneurysms, 142 bifurcation aneurysms had detailed imaging studies and operative records that could be analyzed. The incidence of perforator origin from the aneurysm neck was as follows: basilar, 1/15 (7%); internal carotid artery bifurcation, 4/23 (17%); main stem of the middle cerebral artery/secondary branch of the middle cerebral artery, 6/52 (12%); anterior communicating artery region, 5/46 (11%); and distal bifurcation vessels, 0/6 (0%). Aneurysms arising from the anterior communicating artery between the anterior cerebral arteries had a high incidence of perforator origin from the aneurysm neck. The location of secondary branch origin from the aneurysm neck varied depending on the aneurysm group. Perforator origin from the aneurysm neck was infrequent. A subgroup of anterior communicating artery region aneurysms had a high incidence of perforator origin from the aneurysm neck. Although protection of these neck perforators will be difficult, their identification may be even more challenging. Secondary branch origin from the aneurysm neck varied depending on the aneurysm group. Advanced endovascular techniques are needed to obliterate aneurysms in which the secondary branch(es) arise from the aneurysm neck. If this is not possible, craniotomy and clip ligation will be required if complete aneurysm obliteration is the goal. Copyright © 2014 Elsevier Inc. All rights reserved.

Expression of Escherichia coli glycogen branching enzyme in an Arabidopsis mutant devoid of endogenous starch branching enzymes induces the synthesis of starch-like polyglucans.

PubMed

Boyer, Laura; Roussel, Xavier; Courseaux, Adeline; Ndjindji, Ofilia M; Lancelon-Pin, Christine; Putaux, Jean-Luc; Tetlow, Ian J; Emes, Michael J; Pontoire, Bruno; D' Hulst, Christophe; Wattebled, Fabrice

2016-07-01

Starch synthesis requires several enzymatic activities including branching enzymes (BEs) responsible for the formation of α(1 → 6) linkages. Distribution and number of these linkages are further controlled by debranching enzymes that cleave some of them, rendering the polyglucan water-insoluble and semi-crystalline. Although the activity of BEs and debranching enzymes is mandatory to sustain normal starch synthesis, the relative importance of each in the establishment of the plant storage polyglucan (i.e. water insolubility, crystallinity and presence of amylose) is still debated. Here, we have substituted the activity of BEs in Arabidopsis with that of the Escherichia coli glycogen BE (GlgB). The latter is the BE counterpart in the metabolism of glycogen, a highly branched water-soluble and amorphous storage polyglucan. GlgB was expressed in the be2 be3 double mutant of Arabidopsis, which is devoid of BE activity and consequently free of starch. The synthesis of a water-insoluble, partly crystalline, amylose-containing starch-like polyglucan was restored in GlgB-expressing plants, suggesting that BEs' origin only has a limited impact on establishing essential characteristics of starch. Moreover, the balance between branching and debranching is crucial for the synthesis of starch, as an excess of branching activity results in the formation of highly branched, water-soluble, poorly crystalline polyglucan. © 2015 John Wiley & Sons Ltd.