FOXC1 modulates MYOC secretion through regulation of the exocytic proteins RAB3GAP1, RAB3GAP2 and SNAP25.

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Alexandra Rasnitsyn

Full Text Available The neurodegenerative disease glaucoma is one of the leading causes of blindness in the world. Glaucoma is characterized by progressive visual field loss caused by retinal ganglion cell (RGC death. Both surgical glaucoma treatments and medications are available, however, they only halt glaucoma progression and are unable to reverse damage. Furthermore, many patients do not respond well to treatments. It is therefore important to better understand the mechanisms involved in glaucoma pathogenesis. Patients with Axenfeld-Rieger syndrome (ARS offer important insight into glaucoma progression. ARS patients are at 50% risk of developing early onset glaucoma and respond poorly to treatments, even when surgical treatments are combined with medications. Mutations in the transcription factor FOXC1 cause ARS. Alterations in FOXC1 levels cause ocular malformations and disrupt stress response in ocular tissues, thereby contributing to glaucoma progression. In this study, using biochemical and molecular techniques, we show that FOXC1 regulates the expression of RAB3GAP1, RAB3GAP2 and SNAP25, three genes with central roles in both exocytosis and endocytosis, responsible for extracellular trafficking. FOXC1 positively regulates RAB3GAP1 and RAB3GAP2, while either increase or decrease in FOXC1 levels beyond its normal range results in decreased SNAP25. In addition, we found that FOXC1 regulation of RAB3GAP1, RAB3GAP2 and SNAP25 affects secretion of Myocilin (MYOC, a protein associated with juvenile onset glaucoma and steroid-induced glaucoma. The present work reveals that FOXC1 is an important regulator of exocytosis and establishes a new link between FOXC1 and MYOC-associated glaucoma.

A vesicle trafficking protein αSNAP regulates Paneth cell differentiation in vivo.

Science.gov (United States)

Lechuga, Susana; Naydenov, Nayden G; Feygin, Alex; Jimenez, Antonio J; Ivanov, Andrei I

2017-05-13

A soluble N-ethylmaleimide-sensitive factor-attachment protein alpha (αSNAP) is a multifunctional scaffolding protein that regulates intracellular vesicle trafficking and signaling. In cultured intestinal epithelial cells, αSNAP has been shown to be essential for cell survival, motility, and adhesion; however, its physiologic functions in the intestinal mucosa remain unknown. In the present study, we used a mouse with a spontaneous hydrocephalus with hop gait (hyh) mutation of αSNAP to examine the roles of this trafficking protein in regulating intestinal epithelial homeostasis in vivo. Homozygous hyh mice demonstrated decreased expression of αSNAP protein in the intestinal epithelium, but did not display gross abnormalities of epithelial architecture in the colon and ileum. Such αSNAP depletion attenuated differentiation of small intestinal epithelial enteroids ex vivo. Furthermore, αSNAP-deficient mutant animals displayed reduced formation of lysozyme granules in small intestinal crypts and decreased expression of lysozyme and defensins in the intestinal mucosa, which is indicative of defects in Paneth cell differentiation. By contrast, development of Goblet cells, enteroendocrine cells, and assembly of enterocyte apical junctions was not altered in hyh mutant mice. Our data revealed a novel role of αSNAP in the intestinal Paneth cell differentiation in vivo. Copyright © 2017 Elsevier Inc. All rights reserved.

Identification and Characterization of Botulinum Neurotoxin A Substrate Binding Pockets and Their Re-Engineering for Human SNAP-23.

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Sikorra, Stefan; Litschko, Christa; Müller, Carina; Thiel, Nadine; Galli, Thierry; Eichner, Timo; Binz, Thomas

2016-01-29

Botulinum neurotoxins (BoNTs) are highly potent bacterial proteins that block neurotransmitter release at the neuromuscular junction by cleaving SNAREs (soluble N-ethyl maleimide sensitive factor attachment protein receptors). However, their serotype A (BoNT/A) that cleaves SNAP-25 (synaptosomal-associated protein of 25 kDa) has also been an established pharmaceutical for treatment of medical conditions that rely on hyperactivity of cholinergic nerve terminals for 25 years. The expansion of its use to a variety of further medical conditions associated with hypersecretion components is prevented partly because the involved SNARE isoforms are not cleaved. Therefore, we examined by mutational analyses the reason for the resistance of human SNAP-23, an isoform of SNAP-25. We show that replacement of 10 SNAP-23 residues with their SNAP-25 counterparts effects SNAP-25-like cleavability. Conversely, transfer of each of the replaced SNAP-23 residues to SNAP-25 drastically decreased the cleavability of SNAP-25. By means of the existing SNAP-25-toxin co-crystal structure, molecular dynamics simulations, and corroborative mutagenesis studies, the appropriate binding pockets for these residues in BoNT/A were characterized. Systematic mutagenesis of two major BoNT/A binding pockets was conducted in order to adapt these pockets to corresponding amino acids of human SNAP-23. Human SNAP-23 cleaving mutants were isolated using a newly established yeast-based screening system. This method may be useful for engineering novel BoNT/A pharmaceuticals for the treatment of diseases that rely on SNAP-23-mediated hypersecretion. Copyright © 2015 Elsevier Ltd. All rights reserved.

Directed supramolecular surface assembly of SNAP-tag fusion proteins

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Uhlenheuer, D.A.; Wasserberg, D.; Haase, C.; Nguyen, H.; Schenkel, J.H.; Huskens, J.; Ravoo, B.J.; Jonkheijm, P.; Brunsveld, L.

2012-01-01

Supramolecular assembly of proteins on surfaces and vesicles was investigated by site-selective incorporation of a supramolecular guest element on proteins. Fluorescent proteins were site-selectively labeled with bisadamantane by SNAP-tag technology. The assembly of the bisadamantane functionalized

Directed Supramolecular Surface Assembly of SNAP-tag Fusion Proteins

NARCIS (Netherlands)

Uhlenheuer, D.A.; Wasserberg, D.; Haase, C.; Nguyen, Hoang D.; Schenkel, J.H.; Huskens, Jurriaan; Ravoo, B.J.; Jonkheijm, Pascal; Brunsveld, Luc

2012-01-01

Supramolecular assembly of proteins on surfaces and vesicles was investigated by site-selective incorporation of a supramolecular guest element on proteins. Fluorescent proteins were site-selectively labeled with bisadamantane by SNAP-tag technology. The assembly of the bisadamantane functionalized

A fluorogenic probe for SNAP-tagged plasma membrane proteins based on the solvatochromic molecule Nile Red.

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Prifti, Efthymia; Reymond, Luc; Umebayashi, Miwa; Hovius, Ruud; Riezman, Howard; Johnsson, Kai

2014-03-21

A fluorogenic probe for plasma membrane proteins based on the dye Nile Red and SNAP-tag is introduced. It takes advantage of Nile Red, a solvatochromic molecule highly fluorescent in an apolar environment, such as cellular membranes, but almost dark in a polar aqueous environment. The probe possesses a tuned affinity for membranes allowing its Nile Red moiety to insert into the lipid bilayer of the plasma membrane, becoming fluorescent, only after its conjugation to a SNAP-tagged plasma membrane protein. The fluorogenic character of the probe was demonstrated for different SNAP-tag fusion proteins, including the human insulin receptor. This work introduces a new approach for generating a powerful turn-on probe for "no-wash" labeling of plasma membrane proteins with numerous applications in bioimaging.

Cleavage of SNAP25 and its shorter versions by the protease domain of serotype A botulinum neurotoxin.

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Rahman M Mizanur

Full Text Available Various substrates, catalysts, and assay methods are currently used to screen inhibitors for their effect on the proteolytic activity of botulinum neurotoxin. As a result, significant variation exists in the reported results. Recently, we found that one source of variation was the use of various catalysts, and have therefore evaluated its three forms. In this paper, we characterize three substrates under near uniform reaction conditions using the most active catalytic form of the toxin. Bovine serum albumin at varying optimum concentrations stimulated enzymatic activity with all three substrates. Sodium chloride had a stimulating effect on the full length synaptosomal-associated protein of 25 kDa (SNAP25 and its 66-mer substrates but had an inhibitory effect on the 17-mer substrate. We found that under optimum conditions, full length SNAP25 was a better substrate than its shorter 66-mer or 17-mer forms both in terms of kcat, Km, and catalytic efficiency kcat/Km. Assay times greater than 15 min introduced large variations and significantly reduced the catalytic efficiency. In addition to characterizing the three substrates, our results identify potential sources of variations in previous published results, and underscore the importance of using well-defined reaction components and assay conditions.

Synaptotagmin-7 is an asynchronous calcium sensor for synaptic transmission in neurons expressing SNAP-23.

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Jens P Weber

Full Text Available Synchronization of neurotransmitter release with the presynaptic action potential is essential for maintaining fidelity of information transfer in the central nervous system. However, synchronous release is frequently accompanied by an asynchronous release component that builds up during repetitive stimulation, and can even play a dominant role in some synapses. Here, we show that substitution of SNAP-23 for SNAP-25 in mouse autaptic glutamatergic hippocampal neurons results in asynchronous release and a higher frequency of spontaneous release events (mEPSCs. Use of neurons from double-knock-out (SNAP-25, synaptotagmin-7 mice in combination with viral transduction showed that SNAP-23-driven release is triggered by endogenous synaptotagmin-7. In the absence of synaptotagmin-7 release became even more asynchronous, and the spontaneous release rate increased even more, indicating that synaptotagmin-7 acts to synchronize release and suppress spontaneous release. However, compared to synaptotagmin-1, synaptotagmin-7 is a both leaky and asynchronous calcium sensor. In the presence of SNAP-25, consequences of the elimination of synaptotagmin-7 were small or absent, indicating that the protein pairs SNAP-25/synaptotagmin-1 and SNAP-23/synaptotagmin-7 might act as mutually exclusive calcium sensors. Expression of fusion proteins between pHluorin (pH-sensitive GFP and synaptotagmin-1 or -7 showed that vesicles that fuse using the SNAP-23/synaptotagmin-7 combination contained synaptotagmin-1, while synaptotagmin-7 barely displayed activity-dependent trafficking between vesicle and plasma membrane, implying that it acts as a plasma membrane calcium sensor. Overall, these findings support the idea of alternative syt∶SNARE combinations driving release with different kinetics and fidelity.

The reduced serum free triiodothyronine and increased dorsal hippocampal SNAP-25 and Munc18-1 had existed in middle-aged CD-1 mice with mild spatial cognitive impairment.

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Cao, Lei; Jiang, Wei; Wang, Fang; Yang, Qi-Gang; Wang, Chao; Chen, Yong-Ping; Chen, Gui-Hai

2013-12-02

Changes of synaptic proteins in highlighted brain regions and decreased serum thyroid hormones (THs) have been implied in age-related learning and memory decline. Previously, we showed significant pairwise correlations among markedly impaired spatial learning and memory ability, decreased serum free triiodothyronine (FT3) and increased hippocampal SNAP-25 and Munc18-1 in old Kunming mice. However, whether these changes and the correlations occur in middle-age mice remains unclear. Since this age is one of the best stages to study age-related cognitive decline, we explored the spatial learning and memory ability, serum THs, cerebral SNAP-25 and Munc18-1 levels and their relationships of middle-aged mice in this study. The learning and memory abilities of 35 CD-1 mice (19 mice aged 6 months and 16 mice aged 12 months) were measured with a radial six-arm water maze (RAWM). The SNAP-25 and Munc18-1 levels were semi-quantified by Western blotting and the serum THs were detected by radioimmunoassay. The results showed the middle-aged mice had decreased serum FT3, increased dorsal hippocampal (DH) SNAP-25 and Munc18-1, and many or long number of errors and latency in both learning and memory phases of the RAWM. The Pearson's correlation test showed that the DH SANP-25 and Munc18-1 levels were positively correlated with the number of errors and latency in learning phases of the RAWM. Meanwhile, the DH SANP-25 and Munc18-1 levels negatively correlated with the serum FT3 level. These results suggested that reduced FT3 with increased DH SNAP-25 and Munc18-1 levels might be involved in the spatial learning ability decline in the middle-aged mice. © 2013 Elsevier B.V. All rights reserved.

The SNARE protein SNAP23 and the SNARE-interacting protein Munc18c in human skeletal muscle are implicated in insulin resistance/type 2 diabetes

DEFF Research Database (Denmark)

Boström, Pontus; Andersson, Linda; Vind, Birgitte

2010-01-01

/cytosolic compartment in the patients with the type 2 diabetes. Expression of the SNARE-interacting protein Munc18c was higher in skeletal muscle from patients with type 2 diabetes. Studies in L6 cells showed that Munc18c promoted the expression of SNAP23. CONCLUSIONS: We have translated our previous in vitro results......OBJECTIVE: Our previous studies suggest that the SNARE protein synaptosomal-associated protein of 23 kDa (SNAP23) is involved in the link between increased lipid levels and insulin resistance in cardiomyocytes. The objective was to determine whether SNAP23 may also be involved in the known...... association between lipid accumulation in skeletal muscle and insulin resistance/type 2 diabetes in humans, as well as to identify a potential regulator of SNAP23. RESEARCH DESIGN AND METHODS: We analyzed skeletal muscle biopsies from patients with type 2 diabetes and healthy, insulin-sensitive control...

Secretory proteins in the reproductive tract of the snapping turtle, Chelhydra serpentina.

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Mahmoud, I Y; Paulson, J R; Dudley, M; Patzlaff, J S; Al-Kindi, A Y A

2004-12-01

SDS-polyacrylamide gel electrophoresis was used to separate the secretory proteins produced by the epithelial and endometrial glands of the uterine tube and uterus in the snapping turtle Chelydra serpentina. The proteins were analyzed throughout the phases of the reproductive cycle from May to August, including preovulatory, ovulatory, postovulatory or luteal, and vitellogenic phases. The pattern of secretory proteins is quite uniform along the length of the uterine tube, and the same is true of the uterus, but the patterns for uterine tube and uterus are clearly different. We identify 13 major proteins in C. serpentina egg albumen. Bands co-migrating with 11 of these are found in the uterine tube, but at most 4 are found in the uterus, suggesting that the majority of the albumen proteins are most likely secreted in the uterine tube, not in the uterus. Although some of the egg albumen proteins are present in the uterine tube only at the time of ovulation, most of the bands corresponding to albumen proteins are present throughout the breeding season even though the snapping turtle is a monoclutch species. These results suggest that the glandular secretory phase in the uterine tube is active and quite homogeneous in function regardless of location or phase of the reproductive cycle.

Synaptosomal-associated protein 25 gene polymorphisms and antisocial personality disorder: association with temperament and psychopathy.

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Basoglu, Cengiz; Oner, Ozgur; Ates, Alpay; Algul, Ayhan; Bez, Yasin; Cetin, Mesut; Herken, Hasan; Erdal, Mehmet Emin; Munir, Kerim M

2011-06-01

The molecular genetic of personality disorders has been investigated in several studies; however, the association of antisocial behaviours with synaptosomal-associated protein 25 (SNAP25) gene polymorphisms has not. This association is of interest as SNAP25 gene polymorphism has been associated with attention-deficit hyperactivity disorder and personality. We compared the distribution of DdeI and MnII polymorphisms in 91 young male offenders and in 38 sex-matched healthy control subjects. We also investigated the association of SNAP25 gene polymorphisms with severity of psychopathy and with temperament traits: novelty seeking, harm avoidance, and reward dependence. The MnII T/T and DdeI T/T genotypes were more frequently present in male subjects with antisocial personality disorder (APD) than in sex-matched healthy control subjects. The association was stronger when the frequency of both DdeI and MnII T/T were taken into account. In the APD group, the genotype was not significantly associated with the Psychopathy Checklist-Revised scores, measuring the severity of psychopathy. However, the APD subjects with the MnII T/T genotype had higher novelty seeking scores; whereas, subjects with the DdeI T/T genotype had lower reward dependence scores. Again, the association between genotype and novelty seeking was stronger when both DdeI and MnII genotypes were taken into account. DdeI and MnII T/T genotypes may be a risk factor for antisocial behaviours. The association of the SNAP25 DdeI T/T and MnII T/T genotypes with lower reward dependence and higher novelty seeking suggested that SNAP25 genotype might influence other personality disorders, as well.

Valor preditivo dos escores de SNAP e SNAP-PE na mortalidade neonatal Predictive value of SNAP and SNAP-PE for neonatal mortality

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Rita C. Silveira

2001-12-01

Full Text Available OBJETIVOS: avaliar os escores SNAP e SNAP-PE como preditores de mortalidade neonatal na nossa UTI neonatal, comparando seus resultados. MÉTODOS: todos os recém-nascidos admitidos na UTI neonatal no período de março de 1997 a dezembro de 1998 foram avaliados prospectivamente quanto ao SNAP e SNAP-PE com 24 horas de vida. Foram critérios de exclusão o óbito ou alta da UTI nas primeiras 24 horas de vida, as malformações congênitas incompatíveis com a vida, e recém-nascidos transferidos de outros hospitais. RESULTADOS: 553 recém-nascidos foram incluídos, 54 faleceram. Os valores das medianas do SNAP e SNAP-PE foram mais elevados naqueles que não sobreviveram. Os recém-nascidos foram divididos em cinco faixas de gravidade crescente de SNAP e SNAP-PE. SNAP: até 6, 7-11, 12-15, 16-24, acima de 24 (mortalidade: 3%, 11%, 29%, 48%, 75%, respectivamente. SNAP-PE: até 11, 12-23, 24-32, 33-50, acima de 50 (mortalidade: 3%, 10%, 53%, 78%, 83%, respectivamente. A partir da Curva ROC, os pontos de corte foram 12 para SNAP e 24 para SNAP-PE, obtendo-se sensibilidade, especificidade, valor preditivo positivo (VPP e valor preditivo negativo (VPN para mortalidade. SNAP 12: sensibilidade 79,6%, especificidade 71,7%, VPP 23,4%, VPN 97%. SNAP-PE 24: sensibilidade 79,6%, especificidade 80%, VPP 30%, VPN 97,3%. A área abaixo da Curva ROC (Az para SNAP foi 81,4% e para SNAP-PE 85,1%, ambas estatisticamente significativas. A comparação entre as áreas das duas curvas não evidenciou diferença estatisticamente significativa. CONCLUSÕES: os escores SNAP e SNAP-PE são excelentes preditores de sobrevida neonatal, recomendamos sua utilização rotineiramente na admissão de recém-nascidos nas Unidades de Tratamento Intensivo Neonatal.OBJECTIVE: to evaluate the Score for Neonatal Acute Physiology and the Score for Neonatal Acute Physiology Perinatal Extension as neonatal mortality predictors in our neonatal intensive care unit, and to compare their

Interactions Between SNAP-25 and Synaptotagmin-1 Are Involved in Vesicle Priming, Clamping Spontaneous and Stimulating Evoked Neurotransmission

DEFF Research Database (Denmark)

Schupp, Melanie; Malsam, Jörg; Ruiter, Marvin

2016-01-01

between region I (vesicle priming) and region II (evoked release). Spontaneous release was disinhibited by region I mutations and found to correlate with defective complexin (Cpx) clamping in an in vitro fusion assay, pointing to an interdependent role of synaptotagmin and Cpx in release clamping...... triggering, depend on direct SNARE complex interaction. SIGNIFICANCE STATEMENT: The function of synaptotagmin-1 (syt-1):soluble NSF attachment protein receptor (SNARE) interactions during neurotransmission remains unclear. We mutated SNAP-25 within the recently identified region I and region II...... was disinhibited by region I mutation and found to correlate with defective complexin (Cpx) clamping in vitro, pointing to an interdependent role of synaptotagmin and Cpx in release clamping. Therefore, vesicle priming, clamping spontaneous release, and eliciting evoked release are three different functions of syt...

Simultaneous isolation of mRNA and native protein from minute samples of cells

DEFF Research Database (Denmark)

Petersen, Tonny Studsgaard; Andersen, Claus Yding

2014-01-01

Precious biological samples often lack a sufficient number of cells for multiple procedures, such as extraction of mRNA while maintaining protein in a non-denatured state suitable for subsequent characterization. Here we present a new method for the simultaneous purification of mRNA and native...... in their native state for traditional protein assays. We validated the procedure using neonatal rat ovaries and small numbers of human granulosa cells, demonstrating the extraction of mRNA suitable for gene expression analysis with simultaneous isolation of native proteins suitable for downstream characterization...... proteins from samples containing small numbers of cells. Our approach utilizes oligodeoxythymidylate [oligo(dT)25]-coated paramagnetic beads in an optimized reaction buffer to isolate mRNA comparable in quantity and quality to mRNA isolated with existing methods, while maintaining the proteins...

Identification of fibroblast growth factor receptor 3 (FGFR3 as a protein receptor for botulinum neurotoxin serotype A (BoNT/A.

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Birgitte P S Jacky

Full Text Available Botulinum neurotoxin serotype A (BoNT/A causes transient muscle paralysis by entering motor nerve terminals (MNTs where it cleaves the SNARE protein Synaptosomal-associated protein 25 (SNAP25206 to yield SNAP25197. Cleavage of SNAP25 results in blockage of synaptic vesicle fusion and inhibition of the release of acetylcholine. The specific uptake of BoNT/A into pre-synaptic nerve terminals is a tightly controlled multistep process, involving a combination of high and low affinity receptors. Interestingly, the C-terminal binding domain region of BoNT/A, HC/A, is homologous to fibroblast growth factors (FGFs, making it a possible ligand for Fibroblast Growth Factor Receptors (FGFRs. Here we present data supporting the identification of Fibroblast Growth Factor Receptor 3 (FGFR3 as a high affinity receptor for BoNT/A in neuronal cells. HC/A binds with high affinity to the two extra-cellular loops of FGFR3 and acts similar to an agonist ligand for FGFR3, resulting in phosphorylation of the receptor. Native ligands for FGFR3; FGF1, FGF2, and FGF9 compete for binding to FGFR3 and block BoNT/A cellular uptake. These findings show that FGFR3 plays a pivotal role in the specific uptake of BoNT/A across the cell membrane being part of a larger receptor complex involving ganglioside- and protein-protein interactions.

Arsenite reduces insulin secretion in rat pancreatic β-cells by decreasing the calcium-dependent calpain-10 proteolysis of SNAP-25

International Nuclear Information System (INIS)

Diaz-Villasenor, Andrea; Burns, Anna L.; Salazar, Ana Maria; Sordo, Monserrat; Hiriart, Marcia; Cebrian, Mariano E.; Ostrosky-Wegman, Patricia

2008-01-01

An increase in the prevalence of type 2 diabetes has been consistently observed among residents of high arsenic exposure areas. We have previously shown that in rat pancreatic β-cells, low arsenite doses impair the secretion of insulin without altering its synthesis. To further study the mechanism by which arsenite reduces insulin secretion, we evaluated the effects of arsenite on the calcium-calpain pathway that triggers insulin exocytosis in RINm5F cells. Cell cycle and proliferation analysis were also performed to complement the characterization. Free [Ca 2+ ]i oscillations needed for glucose-stimulated insulin secretion were abated in the presence of subchronic low arsenite doses (0.5-2 μM). The global activity of calpains increased with 2 μM arsenite. However, during the secretion of insulin stimulated with glucose (15.6 mM), 1 μM arsenite decreased the activity of calpain-10, measured as SNAP-25 proteolysis. Both proteins are needed to fuse insulin granules with the membrane to produce insulin exocytosis. Arsenite also induced a slowdown in the β cell line proliferation in a dose-dependent manner, reflected by a reduction of dividing cells and in their arrest in G2/M. Data obtained showed that one of the mechanisms by which arsenite impairs insulin secretion is by decreasing the oscillations of free [Ca 2+ ]i, thus reducing calcium-dependent calpain-10 partial proteolysis of SNAP-25. The effects in cell division and proliferation observed with arsenite exposure can be an indirect consequence of the decrease in insulin secretion

The Curious Acoustic Behavior of Estuarine Snapping Shrimp: Temporal Patterns of Snapping Shrimp Sound in Sub-Tidal Oyster Reef Habitat.

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DelWayne R Bohnenstiehl

Full Text Available Ocean soundscapes convey important sensory information to marine life. Like many mid-to-low latitude coastal areas worldwide, the high-frequency (>1.5 kHz soundscape of oyster reef habitat within the West Bay Marine Reserve (36°N, 76°W is dominated by the impulsive, short-duration signals generated by snapping shrimp. Between June 2011 and July 2012, a single hydrophone deployed within West Bay was programmed to record 60 or 30 seconds of acoustic data every 15 or 30 minutes. Envelope correlation and amplitude information were then used to count shrimp snaps within these recordings. The observed snap rates vary from 1500-2000 snaps per minute during summer to <100 snaps per minute during winter. Sound pressure levels are positively correlated with snap rate (r = 0.71-0.92 and vary seasonally by ~15 decibels in the 1.5-20 kHz range. Snap rates are positively correlated with water temperatures (r = 0.81-0.93, as well as potentially influenced by climate-driven changes in water quality. Light availability modulates snap rate on diurnal time scales, with most days exhibiting a significant preference for either nighttime or daytime snapping, and many showing additional crepuscular increases. During mid-summer, the number of snaps occurring at night is 5-10% more than predicted by a random model; however, this pattern is reversed between August and April, with an excess of up to 25% more snaps recorded during the day in the mid-winter. Diurnal variability in sound pressure levels is largest in the mid-winter, when the overall rate of snapping is at its lowest, and the percentage difference between daytime and nighttime activity is at its highest. This work highlights our lack of knowledge regarding the ecology and acoustic behavior of one of the most dominant soniforous invertebrate species in coastal systems. It also underscores the necessity of long-duration, high-temporal-resolution sampling in efforts to understand the bioacoustics of animal

[Development of the Human Olfactory Bulbs in the Prenatal Ontogenesis: an Immunochistochemical Study with Markers of Presynaptic Terminals (anti-SNAP-25, -Synapsin-I, -Synaptophysin)].

Science.gov (United States)

Kharlamova, A S; Barabanov, V M; Saveliev, S V

2015-01-01

We provide the data of the olfactory bulbs (OB) development in the human fetuses on the stages from 8 week to birth. Immunochistochemical markers of presynaptic terminals (anti-SNAP-25, -synapsin-I, -synaptophysin) were used to evaluate the maturation of the OB. Differentiation of the OB layers begins from periphery, which implicitly evidences that growth of the olfactory nerves fibers induses not only anatomical differentiation of the OB, but also differentiation of its functional layers. The sites of the developing glomerulus are revealed using the immunochistochemical prosedure on the stage before distinct glomerulus can be identified with common histological procedure. OB conductive system demonstrates immunoreactivity with the antibodies to the presynaptic proteins on the all stages from 10-11 weeks of fetus development. Four stages of the OB development are described. All functional layers of the OB are mature at the 22-weeks stage. Further differentiation of the OB neuroblasts, including lamina formation of the internal granular leyer, glomerular layer development, OB growth continue after 20-22 weeks stage until 38-40 weeks of the fetus develoment. Patterns of the immunoreactivity with antibodies to SNAP-25, synapsin-I and synaptophysin are completely appropriate to those of adult's OB on the 38-40 weeks of the prenatal development. Complete maturity of the human OB is achived at 38-40 weeks of the prenatal development.

Thermally responsive silicon nanowire arrays for native/denatured-protein separation

International Nuclear Information System (INIS)

Wang Hongwei; Wang Yanwei; Yuan Lin; Wang Lei; Yang Weikang; Wu Zhaoqiang; Li Dan; Chen Hong

2013-01-01

We present our findings of the selective adsorption of native and denatured proteins onto thermally responsive, native-protein resistant poly(N-isopropylacrylamide) (PNIPAAm) decorated silicon nanowire arrays (SiNWAs). The PNIPAAm–SiNWAs surface, which shows very low levels of native-protein adsorption, favors the adsorption of denatured proteins. The amount of denatured-protein adsorption is higher at temperatures above the lower critical solution temperature (LCST) of PNIPAAm. Temperature cycling surrounding the LCST, which ensures against thermal denaturation of native proteins, further increases the amount of denatured-protein adsorption. Moreover, the PNIPAAm–SiNWAs surface is able to selectively adsorb denatured protein even from mixtures of different protein species; meanwhile, the amount of native proteins in solution is kept nearly at its original level. It is believed that these results will not only enrich current understanding of protein interactions with PNIPAAm-modified SiNWAs surfaces, but may also stimulate applications of PNIPAAm–SiNWAs surfaces for native/denatured protein separation. (paper)

SnapShot: The Bacterial Cytoskeleton.

Science.gov (United States)

Fink, Gero; Szewczak-Harris, Andrzej; Löwe, Jan

2016-07-14

Most bacteria and archaea contain filamentous proteins and filament systems that are collectively known as the bacterial cytoskeleton, though not all of them are cytoskeletal, affect cell shape, or maintain intracellular organization. To view this SnapShot, open or download the PDF. Copyright © 2016. Published by Elsevier Inc.

AlphaScreen-based homogeneous assay using a pair of 25-residue artificial proteins for high-throughput analysis of non-native IgG.

Science.gov (United States)

Senga, Yukako; Imamura, Hiroshi; Miyafusa, Takamitsu; Watanabe, Hideki; Honda, Shinya

2017-09-29

Therapeutic IgG becomes unstable under various stresses in the manufacturing process. The resulting non-native IgG molecules tend to associate with each other and form aggregates. Because such aggregates not only decrease the pharmacological effect but also become a potential risk factor for immunogenicity, rapid analysis of aggregation is required for quality control of therapeutic IgG. In this study, we developed a homogeneous assay using AlphaScreen and AF.2A1. AF.2A1 is a 25-residue artificial protein that binds specifically to non-native IgG generated under chemical and physical stresses. This assay is performed in a short period of time. Our results show that AF.2A1-AlphaScreen may be used to evaluate the various types of IgG, as AF.2A1 recognizes the non-native structure in the constant region (Fc region) of IgG. The assay was effective for detection of non-native IgG, with particle size up to ca. 500 nm, generated under acid, heat, and stirring conditions. In addition, this technique is suitable for analyzing non-native IgG in CHO cell culture supernatant and mixed with large amounts of native IgG. These results indicate the potential of AF.2A1-AlphaScreen to be used as a high-throughput evaluation method for process monitoring as well as quality testing in the manufacturing of therapeutic IgG.

Defining SNAP by cross-sectional and longitudinal definitions of neurodegeneration.

Science.gov (United States)

Wisse, L E M; Das, S R; Davatzikos, C; Dickerson, B C; Xie, S X; Yushkevich, P A; Wolk, D A

2018-01-01

Suspected non-Alzheimer's pathophysiology (SNAP) is a biomarker driven designation that represents a heterogeneous group in terms of etiology and prognosis. SNAP has only been identified by cross-sectional neurodegeneration measures, whereas longitudinal measures might better reflect "active" neurodegeneration and might be more tightly linked to prognosis. We compare neurodegeneration defined by cross-sectional 'hippocampal volume' only (SNAP/L-) versus both cross-sectional and longitudinal 'hippocampal atrophy rate' (SNAP/L+) and investigate how these definitions impact prevalence and the clinical and biomarker profile of SNAP in Mild Cognitive Impairment (MCI). 276 MCI patients from ADNI-GO/2 were designated amyloid "positive" (A+) or "negative" (A-) based on their florbetapir scan and neurodegeneration 'positive' or 'negative' based on cross-sectional hippocampal volume and longitudinal hippocampal atrophy rate. 74.1% of all SNAP participants defined by the cross-sectional definition of neurodegeneration also met the longitudinal definition of neurodegeneration, whereas 25.9% did not. SNAP/L+ displayed larger white matter hyperintensity volume, a higher conversion rate to dementia over 5 years and a steeper decline on cognitive tasks compared to SNAP/L- and the A- CN group. SNAP/L- had more abnormal values on neuroimaging markers and worse performance on cognitive tasks than the A- CN group, but did not show a difference in dementia conversion rate or longitudinal cognition. Using a longitudinal definition of neurodegeneration in addition to a cross-sectional one identifies SNAP participants with significant cognitive decline and a worse clinical prognosis for which cerebrovascular disease may be an important driver.

SNAP operating system reference manual

International Nuclear Information System (INIS)

Sabuda, J.D.; Polito, J.; Walker, J.L.; Grant, F.H. III.

1982-03-01

The SNAP Operating System (SOS) is a FORTRAN 77 program which provides assistance to the safeguards analyst who uses the Safeguards Automated Facility Evaluation (SAFE) and the Safeguards Network Analysis Procedure (SNAP) techniques. Features offered by SOS are a data base system for storing a library of SNAP applications, computer graphics representation of SNAP models, a computer graphics editor to develop and modify SNAP models, a SAFE-to-SNAP interface, automatic generation of SNAP input data, and a computer graphic post-processor for SNAP. The SOS Reference Manual provides detailed application information concerning SOS as well as a detailed discussion of all SOS components and their associated command input formats. SOS was developed for the US Nuclear Regulatory Commission's Office of Nuclear Regulatory Research and the US Naval Surface Weapons Center by Pritsker and Associates, Inc., under contract to Sandia National Laboratories

SnapShot: Fanconi anemia and associated proteins.

Science.gov (United States)

Wang, Anderson T; Smogorzewska, Agata

2015-01-15

Fanconi anemia is a genetic disorder resulting from biallelic mutations in one of the 17 FANC genes. It is characterized by congenital abnormalities, bone marrow failure, and cancer predisposition. The underlying cause is genomic instability resulting from the deficiency in replication-dependent DNA interstrand crosslink repair pathway commonly referred to as the Fanconi anemia-BRCA pathway. This SnapShot presents the key factors involved. Copyright © 2015 Elsevier Inc. All rights reserved.

Whole Protein Native Fitness Potentials

Science.gov (United States)

Faraggi, Eshel; Kloczkowski, Andrzej

2013-03-01

Protein structure prediction can be separated into two tasks: sample the configuration space of the protein chain, and assign a fitness between these hypothetical models and the native structure of the protein. One of the more promising developments in this area is that of knowledge based energy functions. However, standard approaches using pair-wise interactions have shown shortcomings demonstrated by the superiority of multi-body-potentials. These shortcomings are due to residue pair-wise interaction being dependent on other residues along the chain. We developed a method that uses whole protein information filtered through machine learners to score protein models based on their likeness to native structures. For all models we calculated parameters associated with the distance to the solvent and with distances between residues. These parameters, in addition to energy estimates obtained by using a four-body-potential, DFIRE, and RWPlus were used as training for machine learners to predict the fitness of the models. Testing on CASP 9 targets showed that our method is superior to DFIRE, RWPlus, and the four-body potential, which are considered standards in the field.

Oligomerisation of Synaptobrevin-2 Studied by Native Mass Spectrometry and Chemical Cross-Linking

Science.gov (United States)

Wittig, Sabine; Haupt, Caroline; Hoffmann, Waldemar; Kostmann, Susann; Pagel, Kevin; Schmidt, Carla

2018-06-01

Synaptobrevin-2 is a key player in signal transmission in neurons. It forms, together with SNAP25 and Syntaxin-1A, the neuronal soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex and mediates exocytosis of synaptic vesicles with the pre-synaptic membrane. While Synaptobrevin-2 is part of a four-helix bundle in this SNARE complex, it is natively unstructured in the absence of lipids or other SNARE proteins. Partially folded segments, presumably SNARE complex formation intermediates, as well as formation of Synaptobrevin-2 dimers and oligomers, were identified in previous studies. Here, we employ three Synaptobrevin-2 variants—the full-length protein Syb(1-116), the soluble, cytosolic variant Syb(1-96) as well as a shorter version Syb(49-96) containing structured segments but omitting a trigger site for SNARE complex formation—to study oligomerisation in the absence of interaction partners or when incorporated into the lipid bilayer of liposomes. Combining native mass spectrometry with chemical cross-linking, we find that the truncated versions show increased oligomerisation. Our findings from both techniques agree well and confirm the presence of oligomers in solution while membrane-bound Synaptobrevin-2 is mostly monomeric. Using ion mobility mass spectrometry, we could further show that lower charge states of Syb(49-96) oligomers, which most likely represent solution structures, follow an isotropic growth curve suggesting that they are intrinsically disordered. From a technical point of view, we show that the combination of native ion mobility mass spectrometry with chemical cross-linking is well-suited for the analysis of protein homo-oligomers. [Figure not available: see fulltext.

A SNAP-tagged derivative of HIV-1--a versatile tool to study virus-cell interactions.

Directory of Open Access Journals (Sweden)

Manon Eckhardt

Full Text Available Fluorescently labeled human immunodeficiency virus (HIV derivatives, combined with the use of advanced fluorescence microscopy techniques, allow the direct visualization of dynamic events and individual steps in the viral life cycle. HIV proteins tagged with fluorescent proteins (FPs have been successfully used for live-cell imaging analyses of HIV-cell interactions. However, FPs display limitations with respect to their physicochemical properties, and their maturation kinetics. Furthermore, several independent FP-tagged constructs have to be cloned and characterized in order to obtain spectral variations suitable for multi-color imaging setups. In contrast, the so-called SNAP-tag represents a genetically encoded non-fluorescent tag which mediates specific covalent coupling to fluorescent substrate molecules in a self-labeling reaction. Fusion of the SNAP-tag to the protein of interest allows specific labeling of the fusion protein with a variety of synthetic dyes, thereby offering enhanced flexibility for fluorescence imaging approaches.Here we describe the construction and characterization of the HIV derivative HIV(SNAP, which carries the SNAP-tag as an additional domain within the viral structural polyprotein Gag. Introduction of the tag close to the C-terminus of the matrix domain of Gag did not interfere with particle assembly, release or proteolytic virus maturation. The modified virions were infectious and could be propagated in tissue culture, albeit with reduced replication capacity. Insertion of the SNAP domain within Gag allowed specific staining of the viral polyprotein in the context of virus producing cells using a SNAP reactive dye as well as the visualization of individual virions and viral budding sites by stochastic optical reconstruction microscopy. Thus, HIV(SNAP represents a versatile tool which expands the possibilities for the analysis of HIV-cell interactions using live cell imaging and sub-diffraction fluorescence

Subcellular localization of proteins in the anaerobic sulfate reducer Desulfovibrio vulgaris via SNAP-tag labeling and photoconversion

Energy Technology Data Exchange (ETDEWEB)

Gorur, A.; Leung, C. M.; Jorgens, D.; Tauscher, A.; Remis, J. P.; Ball, D. A.; Chhabra, S.; Fok, V.; Geller, J. T.; Singer, M.; Hazen, T. C.; Juba, T.; Elias, D.; Wall, J.; Biggin, M.; Downing, K. H.; Auer, M.

2010-06-01

Systems Biology studies the temporal and spatial 3D distribution of macromolecular complexes with the aim that such knowledge will allow more accurate modeling of biological function and will allow mathematical prediction of cellular behavior. However, in order to accomplish accurate modeling precise knowledge of spatial 3D organization and distribution inside cells is necessary. And while a number of macromolecular complexes may be identified by its 3D structure and molecular characteristics alone, the overwhelming number of proteins will need to be localized using a reporter tag. GFP and its derivatives (XFPs) have been traditionally employed for subcelllar localization using photoconversion approaches, but this approach cannot be taken for obligate anaerobic bacteria, where the intolerance towards oxygen prevents XFP approaches. As part of the GTL-funded PCAP project (now ENIGMA) genetic tools have been developed for the anaerobe sulfate reducer Desulfovibrio vulgaris that allow the high-throughput generation of tagged-protein mutant strains, with a focus on the commercially available SNAP-tag cell system (New England Biolabs, Ipswich, MA), which is based on a modified O6-alkylguanine-DNA alkyltransferase (AGT) tag, that has a dead-end reaction with a modified O6-benzylguanine (BG) derivative and has been shown to function under anaerobic conditions. After initial challenges with respect to variability, robustness and specificity of the labeling signal we have optimized the labeling. Over the last year, as a result of the optimized labeling protocol, we now obtain robust labeling of 20 out of 31 SNAP strains. Labeling for 13 strains were confirmed at least five times. We have also successfully performed photoconversion on 5 of these 13 strains, with distinct labeling patterns for different strains. For example, DsrC robustly localizes to the periplasmic portion of the inner membrane, where as a DNA-binding protein localizes to the center of the cell, where the

On the radioimmunological determination of native and heat denaturated protein

International Nuclear Information System (INIS)

Menzel, E.J.; Glatz, F.; Technische Univ., Vienna

1981-01-01

Precipitation radioimmunoassay, solid phase radioimmunoassay and passive hemagglutination were examined for their efficiency in the determination of native or denaturated soy proteins. Native as well as autoclaved soy protein could be determined quantitatively in the precipitation radioimmunoassay, using antisera directed against the native product. In the solid phase technique only the autoclaved soy protein could be detected with high sensitivity. In the passive hemagglutination reaction, no agglutination could be observed with erythrocytes coated with autoclaved soy protein. Only antisera against the denaturated (autoclaved) soy protein agglutinated these erythrocytes. (orig.) [de

SNAP Operating System (SOS) user's guide

International Nuclear Information System (INIS)

Sabuda, J.D.; Polito, J.; Walker, J.L.; Grant, F.H. III.

1982-03-01

The SNAP Operating System (SOS) is a FORTRAN 77 program which provides assistance to the safeguards analyst who uses the Safeguards Automated Facility Evaluation (SAFE) and the Safeguards Network Analysis Procedure (SNAP) techniques. Features offered by SOS are a data base system for storing a library of SNAP applications, computer graphics representation of SNAP models, a computer graphics editor to develop and modify SNAP models, a SAFE-to-SNAP interface, automatic generation of SNAP input data, and a computer graphics postprocessor for SNAP. The SOS User's Guide is designed to provide the user with the information necessary to use SOS effectively. Examples are used throughout to illustrate the concepts. The format of the user's guide follows the same sequence as would be used in executing an actual application

Extracellular anti-angiogenic proteins augment an endosomal protein trafficking pathway to reach mitochondria and execute apoptosis in HUVECs.

Science.gov (United States)

Chen, Mo; Qiu, Tao; Wu, Jiajie; Yang, Yang; Wright, Graham D; Wu, Min; Ge, Ruowen

2018-03-09

Classic endocytosis destinations include the recycling endosome returning to the plasma membrane or the late endosome (LE) merging with lysosomes for cargo degradation. However, the anti-angiogenic proteins angiostatin and isthmin, are endocytosed and trafficked to mitochondria (Mito) to execute apoptosis of endothelial cells. How these extracellular proteins reach mitochondria remains a mystery. Through confocal and super-resolution fluorescent microscopy, we demonstrate that angiostatin and isthmin are trafficked to mitochondria through the interaction between LE and Mito. Using purified organelles, the LE-Mito interaction is confirmed through in vitro lipid-fusion assay, as well as single vesicle total internal reflection fluorescent microscopy. LE-Mito interaction enables the transfer of not only lipids but also proteins from LE to Mito. Angiostatin and isthmin augment this endosomal protein trafficking pathway and make use of it to reach mitochondria to execute apoptosis. Cell fractionation and biochemical analysis identified that the cytosolic scaffold protein Na+/H+ exchanger regulatory factor 1 (NHERF1) associated with LE and the t-SNARE protein synaptosome-associated protein 25 kDa (SNAP25) associated with Mito form an interaction complex to facilitate LE-Mito interaction. Proximity ligation assay coupled with fluorescent microscopy showed that both NHERF1 and SNAP25 are located at the contacting face between LE and Mito. RNAi knockdown of either NHERF1 or SNAP25 suppressed not only the mitochondrial trafficking of angiostatin and isthmin but also their anti-angiogenic and pro-apoptotic functions. Hence, this study reveals a previously unrealized endosomal protein trafficking pathway from LE to Mito that allows extracellular proteins to reach mitochondria and execute apoptosis.

α-SNAP prevents docking of the acrosome during sperm exocytosis because it sequesters monomeric syntaxin.

Directory of Open Access Journals (Sweden)

Facundo Rodríguez

Full Text Available α-SNAP has an essential role in membrane fusion that consists of bridging cis SNARE complexes to NSF. α-SNAP stimulates NSF, which releases itself, α-SNAP, and individual SNAREs that subsequently re-engage in the trans arrays indispensable for fusion. α-SNAP also binds monomeric syntaxin and NSF disengages the α-SNAP/syntaxin dimer. Here, we examine why recombinant α-SNAP blocks secretion in permeabilized human sperm despite the fact that the endogenous protein is essential for membrane fusion. The only mammalian organism with a genetically modified α-SNAP is the hyh mouse strain, which bears a M105I point mutation; males are subfertile due to defective sperm exocytosis. We report here that recombinant α-SNAP-M105I has greater affinity for the cytosolic portion of immunoprecipitated syntaxin than the wild type protein and in consequence NSF is less efficient in releasing the mutant. α-SNAP-M105I is a more potent sperm exocytosis blocker than the wild type and requires higher concentrations of NSF to rescue its effect. Unlike other fusion scenarios where SNAREs are subjected to an assembly/disassembly cycle, the fusion machinery in sperm is tuned so that SNAREs progress uni-directionally from a cis configuration in resting cells to monomeric and subsequently trans arrays in cells challenged with exocytosis inducers. By means of functional and indirect immunofluorescense assays, we show that recombinant α-SNAPs--wild type and M105I--inhibit exocytosis because they bind monomeric syntaxin and prevent this SNARE from assembling with its cognates in trans. Sequestration of free syntaxin impedes docking of the acrosome to the plasma membrane assessed by transmission electron microscopy. The N-terminal deletion mutant α-SNAP-(160-295, unable to bind syntaxin, affects neither docking nor secretion. The implications of this study are twofold: our findings explain the fertility defect of hyh mice and indicate that assembly of SNAREs in trans

SAFE/SNAP application to shipboard security

International Nuclear Information System (INIS)

Grady, L.M.; Walker, J.L.; Polito, J.

1981-11-01

An application of the combined Safeguards Automated Facility Evaluation/Safeguards Network Analysis Procedure (SAFE/SNAP) modeling technique to a physical protection system (PPS) aboard a generic ship is described. This application was performed as an example of how the SAFE and SNAP techniques could be used. Estimates of probability of interruption and neutralization for the example shipboard PPS are provided by SAFE as well as an adversary scenario, which serves as input to SNAP. This adversary scenario is analyzed by SNAP through four cases which incorporate increasingly detailed security force tactics. Comparisons between the results of the SAFE and SNAP analyses are made and conclusions drawn on the validity of each technique. Feedback from SNAP to SAFE is described, and recommendations for upgrading the ship based on the results of the SAFE/SNAP application are also discussed

Elementary chaotic snap flows

International Nuclear Information System (INIS)

Munmuangsaen, Buncha; Srisuchinwong, Banlue

2011-01-01

Highlights: → Five new elementary chaotic snap flows and a generalization of an existing chaotic snap flow have been presented. → Three of all are conservative systems whilst three others are dissipative systems. → Four cases need only a single control parameter and a single nonlinearity. → A cubic case in a jerk representation requires only two terms and a single nonlinearity. - Abstract: Hyperjerk systems with 4th-order derivative of the form x .... =f(x ... ,x .. ,x . ,x) have been referred to as snap systems. Five new elementary chaotic snap flows and a generalization of an existing flow are presented through an extensive numerical search. Four of these flows demonstrate elegant simplicity of a single control parameter based on a single nonlinearity of a quadratic, a piecewise-linear or an exponential type. Two others demonstrate elegant simplicity of all unity-in-magnitude parameters based on either a single cubic nonlinearity or three cubic nonlinearities. The chaotic snap flow with a single cubic nonlinearity requires only two terms and can be transformed to its equivalent dynamical form of only five terms which have a single nonlinearity. An advantage is that such a chaotic flow offers only five terms even though the (four) dimension is high. Three of the chaotic snap flows are characterized as conservative systems whilst three others are dissipative systems. Basic dynamical properties are described.

Analysis of Proteins, Protein Complexes, and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis - Native Mass Spectrometry

Science.gov (United States)

Belov, Arseniy M.; Viner, Rosa; Santos, Marcia R.; Horn, David M.; Bern, Marshall; Karger, Barry L.; Ivanov, Alexander R.

2017-12-01

Native mass spectrometry (MS) is a rapidly advancing field in the analysis of proteins, protein complexes, and macromolecular species of various types. The majority of native MS experiments reported to-date has been conducted using direct infusion of purified analytes into a mass spectrometer. In this study, capillary zone electrophoresis (CZE) was coupled online to Orbitrap mass spectrometers using a commercial sheathless interface to enable high-performance separation, identification, and structural characterization of limited amounts of purified proteins and protein complexes, the latter with preserved non-covalent associations under native conditions. The performance of both bare-fused silica and polyacrylamide-coated capillaries was assessed using mixtures of protein standards known to form non-covalent protein-protein and protein-ligand complexes. High-efficiency separation of native complexes is demonstrated using both capillary types, while the polyacrylamide neutral-coated capillary showed better reproducibility and higher efficiency for more complex samples. The platform was then evaluated for the determination of monoclonal antibody aggregation and for analysis of proteomes of limited complexity using a ribosomal isolate from E. coli. Native CZE-MS, using accurate single stage and tandem-MS measurements, enabled identification of proteoforms and non-covalent complexes at femtomole levels. This study demonstrates that native CZE-MS can serve as an orthogonal and complementary technique to conventional native MS methodologies with the advantages of low sample consumption, minimal sample processing and losses, and high throughput and sensitivity. This study presents a novel platform for analysis of ribosomes and other macromolecular complexes and organelles, with the potential for discovery of novel structural features defining cellular phenotypes (e.g., specialized ribosomes). [Figure not available: see fulltext.

Shortening a loop can increase protein native state entropy.

Science.gov (United States)

Gavrilov, Yulian; Dagan, Shlomi; Levy, Yaakov

2015-12-01

Protein loops are essential structural elements that influence not only function but also protein stability and folding rates. It was recently reported that shortening a loop in the AcP protein may increase its native state conformational entropy. This effect on the entropy of the folded state can be much larger than the lower entropic penalty of ordering a shorter loop upon folding, and can therefore result in a more pronounced stabilization than predicted by polymer model for loop closure entropy. In this study, which aims at generalizing the effect of loop length shortening on native state dynamics, we use all-atom molecular dynamics simulations to study how gradual shortening a very long or solvent-exposed loop region in four different proteins can affect their stability. For two proteins, AcP and Ubc7, we show an increase in native state entropy in addition to the known effect of the loop length on the unfolded state entropy. However, for two permutants of SH3 domain, shortening a loop results only with the expected change in the entropy of the unfolded state, which nicely reproduces the observed experimental stabilization. Here, we show that an increase in the native state entropy following loop shortening is not unique to the AcP protein, yet nor is it a general rule that applies to all proteins following the truncation of any loop. This modification of the loop length on the folded state and on the unfolded state may result with a greater effect on protein stability. © 2015 Wiley Periodicals, Inc.

Relation between native ensembles and experimental structures of proteins

DEFF Research Database (Denmark)

Best, R. B.; Lindorff-Larsen, Kresten; DePristo, M. A.

2006-01-01

Different experimental structures of the same protein or of proteins with high sequence similarity contain many small variations. Here we construct ensembles of "high-sequence similarity Protein Data Bank" (HSP) structures and consider the extent to which such ensembles represent the structural...... Data Bank ensembles; moreover, we show that the effects of uncertainties in structure determination are insufficient to explain the results. These results highlight the importance of accounting for native-state protein dynamics in making comparisons with ensemble-averaged experimental data and suggest...... heterogeneity of the native state in solution. We find that different NMR measurements probing structure and dynamics of given proteins in solution, including order parameters, scalar couplings, and residual dipolar couplings, are remarkably well reproduced by their respective high-sequence similarity Protein...

Morphological study on the olfactory systems of the snapping turtle, Chelydra serpentina.

Science.gov (United States)

Nakamuta, Nobuaki; Nakamuta, Shoko; Kato, Hideaki; Yamamoto, Yoshio

2016-06-01

In this study, the olfactory system of a semi-aquatic turtle, the snapping turtle, has been morphologically investigated by electron microscopy, immunohistochemistry, and lectin histochemistry. The nasal cavity of snapping turtle was divided into the upper and lower chambers, lined by the sensory epithelium containing ciliated and non-ciliated olfactory receptor neurons, respectively. Each neuron expressed both Gαolf, the α-subunit of G-proteins coupling to the odorant receptors, and Gαo, the α-subunit of G-proteins coupling to the type 2 vomeronasal receptors. The axons originating from the upper chamber epithelium projected to the ventral part of the olfactory bulb, while those from the lower chamber epithelium to the dorsal part of the olfactory bulb. Despite the identical expression of G-protein α-subunits in the olfactory receptor neurons, these two projections were clearly distinguished from each other by the differential expression of glycoconjugates. In conclusion, these data indicate the presence of two types of olfactory systems in the snapping turtle. Topographic arrangement of the upper and lower chambers and lack of the associated glands in the lower chamber epithelium suggest their possible involvement in the detection of odorants: upper chamber epithelium in the air and the lower chamber epithelium in the water. Copyright © 2016 Elsevier Ltd. All rights reserved.

Structural interface parameters are discriminatory in recognising near-native poses of protein-protein interactions.

Directory of Open Access Journals (Sweden)

Sony Malhotra

Full Text Available Interactions at the molecular level in the cellular environment play a very crucial role in maintaining the physiological functioning of the cell. These molecular interactions exist at varied levels viz. protein-protein interactions, protein-nucleic acid interactions or protein-small molecules interactions. Presently in the field, these interactions and their mechanisms mark intensively studied areas. Molecular interactions can also be studied computationally using the approach named as Molecular Docking. Molecular docking employs search algorithms to predict the possible conformations for interacting partners and then calculates interaction energies. However, docking proposes number of solutions as different docked poses and hence offers a serious challenge to identify the native (or near native structures from the pool of these docked poses. Here, we propose a rigorous scoring scheme called DockScore which can be used to rank the docked poses and identify the best docked pose out of many as proposed by docking algorithm employed. The scoring identifies the optimal interactions between the two protein partners utilising various features of the putative interface like area, short contacts, conservation, spatial clustering and the presence of positively charged and hydrophobic residues. DockScore was first trained on a set of 30 protein-protein complexes to determine the weights for different parameters. Subsequently, we tested the scoring scheme on 30 different protein-protein complexes and native or near-native structure were assigned the top rank from a pool of docked poses in 26 of the tested cases. We tested the ability of DockScore to discriminate likely dimer interactions that differ substantially within a homologous family and also demonstrate that DOCKSCORE can distinguish correct pose for all 10 recent CAPRI targets.

Snapping plicae associated with radiocapitellar chondromalacia.

Science.gov (United States)

Antuna, S A; O'Driscoll, S W

2001-05-01

Painful snapping of the elbow joint is usually attributed to intra-articular loose bodies, instability, or medial dislocation of the triceps muscle over the medial epicondyle. We report our experience with 14 patients who were treated arthroscopically for snapping elbow that was found to be caused by hypertrophic synovial folds associated with radiocapitellar chondromalacia. Case series. The records of 14 patients who were treated arthroscopically for painful snapping elbows caused by intra-articular plicae were reviewed. There were 6 women and 8 men with an average age of 36 years (range, 27 to 48 years). Nine patients had had some type of trauma to the joint. Four patients had been previously diagnosed with lateral epicondylitis and 5 with intra-articular loose bodies. The average time from initial onset of symptoms to treatment was 13 months (range, 8 to 36 months). Average follow-up was 24 months (range, 6 to 66 months). All patients complained of painful snapping in the posterolateral or anterolateral aspect of the elbow. The snapping occurred between 90 degrees and 110 degrees of flexion with the forearm in pronation. In 7 patients, the snapping was reproducible by passively flexing the pronated elbow, which we refer to as the flexion-pronation test. At the time of arthroscopic surgery, all patients had a thickened synovial plica that would snap back and forward over the radial head, usually associated with a chondromalacic area on the radial head. Twelve patients had complete relief of their snapping after surgery. One patient in whom there was associated posterolateral rotatory elbow instability did not improve. One patient became asymptomatic for 4 years but then had recurrence of her symptoms, which persisted despite 2 subsequent arthroscopies. The presence of synovial plicae in the radiocapitellar joint must be considered in the differential diagnosis of painful snapping elbow. Arthroscopy confirms the diagnosis and allows excision of the plica.

Ubuntu Core Snaps for Science

Science.gov (United States)

Wyngaard, J.

2017-12-01

A key challenge in the burgeoning sector of IoT (Internet of Things) is ensuring device and communication security. Ubuntu Core's approach to this is the use of 'snaps'. Along side this growth, scientists are increasingly utilising the many new low cost sensors now available. This work prototypes the use of snaps as a possible avenue to reducing the barrier to entry for scientific use of these low cost sensors while also ensuring proper meta-data is captured. Snaps are contained applications that have been signed. This means that a snap application is unable to read or write to any area of the system beyond its assigned reach, thereby significantly limiting the possible impact of any break in security higher up the stack. Further, application and system updates are automatically verified as authentic before being applied. Additionally, on an embedded system running Ubuntu Core the hardware interface (Gadget), kernel, and OS (Core) are all also snaps and therefore also have acquired these same gains. The result is an architecture that enables: (1) Secure, robust, remote automatic updates of both the OS and applications. (2) A user friendly deployment mechanism.(3) A easy to maintain means of supporting multiple platforms. The above is primarily targeted at non-academic domains, however, it is proposed that the Scientific community can benefit from it too. This work therefore prototypes a snap for sensors on board a small Unmanned Aircraft System (sUAS). For demonstration purposes this snap specifically targets connecting a popular low cost CO2 meter to a Raspberry Pi3 and the popular open source sUAS autopilot Arducopter.

Desalting Protein Ions in Native Mass Spectrometry Using Supercharging Reagents

Science.gov (United States)

Cassou, Catherine A.; Williams, Evan R.

2014-01-01

Effects of the supercharging reagents m-NBA and sulfolane on sodium ion adduction to protein ions formed using native mass spectrometry were investigated. There is extensive sodium adduction on protein ions formed by electrospray ionization from aqueous solutions containing millimolar concentrations of NaCl, which can lower sensitivity by distributing the signal of a given charge state over multiple adducted ions and can reduce mass measuring accuracy for large proteins and non-covalent complexes for which individual adducts cannot be resolved. The average number of sodium ions adducted to the most abundant ion formed from ten small (8.6–29 kDa) proteins for which adducts can be resolved is reduced by 58% or 80% on average, respectively, when 1.5% m-NBA or 2.5% sulfolane are added to aqueous solutions containing sodium compared to without the supercharging reagent. Sulfolane is more effective than m-NBA at reducing sodium ion adduction and at preserving non-covalent protein-ligand and protein-protein interactions. Desalting with 2.5% sulfolane enables detection of several glycosylated forms of 79.7 kDa holo-transferrin and NADH bound to the 146 kDa homotetramer LDH, which are otherwise unresolved due to peak broadening from extensive sodium adduction. Although sulfolane is more effective than m-NBA at protein ion desalting, m-NBA reduces salt clusters at high m/z and can increase the signal-to-noise ratios of protein ions by reducing chemical noise. Desalting is likely a result of these supercharging reagents binding sodium ions in solution, thereby reducing the sodium available to adduct to protein ions. PMID:25133273

Safeguards Network Analysis Procedure (SNAP): overview

International Nuclear Information System (INIS)

Chapman, L.D; Engi, D.

1979-08-01

Nuclear safeguards systems provide physical protection and control of nuclear materials. The Safeguards Network Analysis Procedure (SNAP) provides a convenient and standard analysis methodology for the evaluation of physical protection system effectiveness. This is achieved through a standard set of symbols which characterize the various elements of safeguards systems and an analysis program to execute simulation models built using the SNAP symbology. The outputs provided by the SNAP simulation program supplements the safeguards analyst's evaluative capabilities and supports the evaluation of existing sites as well as alternative design possibilities. This paper describes the SNAP modeling technique and provides an example illustrating its use

Analysis of protein interactions at native chloroplast membranes by ellipsometry.

Directory of Open Access Journals (Sweden)

Verena Kriechbaumer

Full Text Available Membrane bound receptors play vital roles in cell signaling, and are the target for many drugs, yet their interactions with ligands are difficult to study by conventional techniques due to the technical difficulty of monitoring these interactions in lipid environments. In particular, the ability to analyse the behaviour of membrane proteins in their native membrane environment is limited. Here, we have developed a quantitative approach to detect specific interactions between low-abundance chaperone receptors within native chloroplast membranes and their soluble chaperone partners. Langmuir-Schaefer film deposition was used to deposit native chloroplasts onto gold-coated glass slides, and interactions between the molecular chaperones Hsp70 and Hsp90 and their receptors in the chloroplast membranes were detected and quantified by total internal reflection ellipsometry (TIRE. We show that native chloroplast membranes deposited on gold-coated glass slides using Langmuir-Schaefer films retain functional receptors capable of binding chaperones with high specificity and affinity. Taking into account the low chaperone receptor abundance in native membranes, these binding properties are consistent with data generated using soluble forms of the chloroplast chaperone receptors, OEP61 and Toc64. Therefore, we conclude that chloroplasts have the capacity to selectively bind chaperones, consistent with the notion that chaperones play an important role in protein targeting to chloroplasts. Importantly, this method of monitoring by TIRE does not require any protein labelling. This novel combination of techniques should be applicable to a wide variety of membranes and membrane protein receptors, thus presenting the opportunity to quantify protein interactions involved in fundamental cellular processes, and to screen for drugs that target membrane proteins.

Revised SNAP III Training Manual

Energy Technology Data Exchange (ETDEWEB)

Moss, Calvin Elroy [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Gonzales, Samuel M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Myers, William L. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Nelson, Mark Andrew [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Rothrock, Richard Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Salazar, Samuel A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Sorensen, Eric Byron [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Sundby, Gary M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2017-11-21

The Shielded Neutron Assay Probe (SNAP) technique was developed to determine the leakage neutron source strength of a radioactive object. The original system consisted of an Eberline^TM Mini-scaler and discrete neutron detector. The system was operated by obtaining the count rate with the Eberline^TM instrument, determining the absolute efficiency from a graph, and calculating the neutron source strength by hand. In 2003 the SNAP III, shown in Figure 1, was designed and built. It required the operator to position the SNAP, and then measure the source-to-detector and detectorto- reflector distances. Next the operator entered the distance measurements and started the data acquisition. The SNAP acquired the required count rate and then calculated and displayed the leakage neutron source strength (NSS). The original design of the SNAP III is described in SNAP III Training Manual (ER-TRN-PLN-0258, Rev. 0, January 2004, prepared by William Baird) This report describes some changes that have been made to the SNAP III. One important change is the addition of a LEMO connector to provide neutron detection output pulses for input to the MC-15. This feature is useful in active interrogation with a neutron generator because the MC-15 has the capability to only record data when it is not gated off by a pulse from the neutron generator. This avoids recording of a lot of data during the generator pulses that are not useful. Another change was the replacement of the infrared RS-232 serial communication output by a similar output via a 4-pin LEMO connector. The current document includes a more complete explanation of how to estimate the amount of moderation around a neutron-emitting source.

Snapping shrimp sound production patterns on Caribbean coral reefs: relationships with celestial cycles and environmental variables

Science.gov (United States)

Lillis, Ashlee; Mooney, T. Aran

2018-06-01

The rich acoustic environment of coral reefs, including the sounds of a variety of fish and invertebrates, is a reflection of the structural complexity and biological diversity of these habitats. Emerging interest in applying passive acoustic monitoring and soundscape analysis to measure coral reef habitat characteristics and track ecological patterns is hindered by a poor understanding of the most common and abundant sound producers on reefs—the snapping shrimp. Here, we sought to address several basic biophysical drivers of reef sound by investigating acoustic activity patterns of snapping shrimp populations on two adjacent coral reefs using a detailed snap detection analysis routine to a high-resolution 2.5-month acoustic dataset from the US Virgin Islands. The reefs exhibited strong diel and lunar periodicity in snap rates and clear spatial differences in snapping levels. Snap rates peaked at dawn and dusk and were higher overall during daytime versus nighttime, a seldom-reported pattern in earlier descriptions of diel snapping shrimp acoustic activity. Small differences between the sites in snap rate rhythms were detected and illustrate how analyses of specific soundscape elements might reveal subtle between-reef variation. Snap rates were highly correlated with environmental variables, including water temperature and light, and were found to be sensitive to changes in oceanographic forcing. This study further establishes snapping shrimp as key players in the coral reef chorus and provides evidence that their acoustic output reflects a combination of environmental conditions, celestial influences, and spatial habitat variation. Effective application of passive acoustic monitoring in coral reef habitats using snap rates or snapping-influenced acoustic metrics will require a mechanistic understanding of the underlying spatial and temporal variation in snapping shrimp sound production across multiple scales.

45 CFR 670.25 - Designation of specially protected species of native mammals, birds, and plants.

Science.gov (United States)

2010-10-01

... native mammals, birds, and plants. 670.25 Section 670.25 Public Welfare Regulations Relating to Public... Protected Species of Mammals, Birds, and Plants § 670.25 Designation of specially protected species of native mammals, birds, and plants. The following species has been designated as Specially Protected...

Probabilistic Determination of Native State Ensembles of Proteins

DEFF Research Database (Denmark)

Olsson, Simon; Vögeli, Beat Rolf; Cavalli, Andrea

2014-01-01

ensembles of proteins by the combination of physical force fields and experimental data through modern statistical methodology. As an example, we use NMR residual dipolar couplings to determine a native state ensemble of the extensively studied third immunoglobulin binding domain of protein G (GB3...

Application of native signal sequences for recombinant proteins secretion in Pichia pastoris

DEFF Research Database (Denmark)

Borodina, Irina; Do, Duy Duc; Eriksen, Jens C.

Background Methylotrophic yeast Pichia pastoris is widely used for recombinant protein production, largely due to its ability to secrete correctly folded heterologous proteins to the fermentation medium. Secretion is usually achieved by cloning the recombinant gene after a leader sequence, where...... alpha‐mating factor (MF) prepropeptide from Saccharomyces cerevisiae is most commonly used. Our aim was to test whether signal peptides from P. pastoris native secreted proteins could be used to direct secretion of recombinant proteins. Results Eleven native signal peptides from P. pastoris were tested...... by optimization of expression of three different proteins in P. pastoris. Conclusions Native signal peptides from P. pastoris can be used to direct secretion of recombinant proteins. A novel USER‐based P. pastoris system allows easy cloning of protein‐coding gene with the promoter and leader sequence of choice....

Analysis of oligomeric transition of silkworm small heat shock protein sHSP20.8 using high hydrostatic pressure native PAGE

Science.gov (United States)

Fujisawa, Tetsuro; Ueda, Toshifumi; Kameyama, Keiichi; Aso, Yoichi; Ishiguro, Ryo

2013-06-01

The small heat shock proteins (sHSPs) solubilize thermo-denatured proteins without adenosine triphosphate energy consumption to facilitate protein refolding. sHSP20.8 is one of the silkworm (Bombyx mori) sHSPs having only one cystein in the N-terminal domain: Cys43. We report a simple measurement of oligomeric transition of sHSP20.8 using high hydrostatic pressure native polyacrylamide gel electrophoresis (high hydrostatic pressure (HP) native polyacrylamide gel electrophoresis (PAGE)). At ambient pressure under oxydative condition, the native PAGE of thermal transition of sHSP20.8 oligomer displayed a cooperative association. In contrast, HP native PAGE clearly demonstrated that sHSP20.8 dissociated at 80 MPa and 25°C, and the resultant molecular species gradually reassociated with time under that condition. In addition, the reassociation process was suppressed in the presence of the reductant. These results are consistent with the idea that sHSP20.8 oligomer temporally dissociates at the first thermo-sensing step and reassociates with the oxidation of Cys43.

Dynamics of snapping beams and jumping poppers

Science.gov (United States)

Pandey, A.; Moulton, D. E.; Vella, D.; Holmes, D. P.

2014-01-01

We consider the dynamic snapping instability of elastic beams and shells. Using the Kirchhoff rod and Föppl-von Kármán plate equations, we study the stability, deformation modes, and snap-through dynamics of an elastic arch with clamped boundaries and subject to a concentrated load. For parameters typical of everyday and technological applications of snapping, we show that the stretchability of the arch plays a critical role in determining not only the post-buckling mode of deformation but also the timescale of snapping and the frequency of the arch's vibrations about its final equilibrium state. We show that the growth rate of the snap-through instability and its subsequent ringing frequency can both be interpreted physically as the result of a sound wave in the material propagating over a distance comparable to the length of the arch. Finally, we extend our analysis of the ringing frequency of indented arches to understand the “pop” heard when everted shell structures snap-through to their stable state. Remarkably, we find that not only are the scaling laws for the ringing frequencies in these two scenarios identical but also the respective prefactors are numerically close; this allows us to develop a master curve for the frequency of ringing in snapping beams and shells.

Dynamic ultrasound of the external snapping hip syndrome

International Nuclear Information System (INIS)

Choi, Yun Sun; Song, Baek Yong; Paik, Sang Hyun; Lee, Tae Gyu; Yoon, Yong Kyu; Lee, Sung Moon

2002-01-01

Snapping hip syndrome has been described as a hip pain accompanied by an audible snapping during motion of the hip or while walking. The variable causes of its external, internal, and intra-articular origins have been described. The most common extemal snapping hip has been associated with a thickened posterior border of the iliotibial band or of the anterior border of the gluteus maximus muscle slipping over the greater trochanter. The aim of this study was to evaluate the dynamic ultrasound findings of external snapping hip syndrome with review of the literature. We studied 5 patients (7 cases) with external snapping hip and pain over the greater trochanter during walking or hip motion (3 males and 2 females, age range, 14-32 years; mean, 19 years). Two patients reported bilateral snapping hips.

Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.

Directory of Open Access Journals (Sweden)

Nobuyuki Uchikoga

Full Text Available Interaction profile method is a useful method for processing rigid-body docking. After the docking process, the resulting set of docking poses could be classified by calculating similarities among them using these interaction profiles to search for near-native poses. However, there are some cases where the near-native poses are not included in this set of docking poses even when the bound-state structures are used. Therefore, we have developed a method for generating near-native docking poses by introducing a re-docking process. We devised a method for calculating the profile of interaction fingerprints by assembling protein complexes after determining certain core-protein complexes. For our analysis, we used 44 bound-state protein complexes selected from the ZDOCK benchmark dataset ver. 2.0, including some protein pairs none of which generated near-native poses in the docking process. Consequently, after the re-docking process we obtained profiles of interaction fingerprints, some of which yielded near-native poses. The re-docking process involved searching for possible docking poses in a restricted area using the profile of interaction fingerprints. If the profile includes interactions identical to those in the native complex, we obtained near-native docking poses. Accordingly, near-native poses were obtained for all bound-state protein complexes examined here. Application of interaction fingerprints to the re-docking process yielded structures with more native interactions, even when a docking pose, obtained following the initial docking process, contained only a small number of native amino acid interactions. Thus, utilization of the profile of interaction fingerprints in the re-docking process yielded more near-native poses.

Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.

Science.gov (United States)

Uchikoga, Nobuyuki; Matsuzaki, Yuri; Ohue, Masahito; Hirokawa, Takatsugu; Akiyama, Yutaka

2013-01-01

Interaction profile method is a useful method for processing rigid-body docking. After the docking process, the resulting set of docking poses could be classified by calculating similarities among them using these interaction profiles to search for near-native poses. However, there are some cases where the near-native poses are not included in this set of docking poses even when the bound-state structures are used. Therefore, we have developed a method for generating near-native docking poses by introducing a re-docking process. We devised a method for calculating the profile of interaction fingerprints by assembling protein complexes after determining certain core-protein complexes. For our analysis, we used 44 bound-state protein complexes selected from the ZDOCK benchmark dataset ver. 2.0, including some protein pairs none of which generated near-native poses in the docking process. Consequently, after the re-docking process we obtained profiles of interaction fingerprints, some of which yielded near-native poses. The re-docking process involved searching for possible docking poses in a restricted area using the profile of interaction fingerprints. If the profile includes interactions identical to those in the native complex, we obtained near-native docking poses. Accordingly, near-native poses were obtained for all bound-state protein complexes examined here. Application of interaction fingerprints to the re-docking process yielded structures with more native interactions, even when a docking pose, obtained following the initial docking process, contained only a small number of native amino acid interactions. Thus, utilization of the profile of interaction fingerprints in the re-docking process yielded more near-native poses.

Snap evaporation of droplets on smooth topographies.

Science.gov (United States)

Wells, Gary G; Ruiz-Gutiérrez, Élfego; Le Lirzin, Youen; Nourry, Anthony; Orme, Bethany V; Pradas, Marc; Ledesma-Aguilar, Rodrigo

2018-04-11

Droplet evaporation on solid surfaces is important in many applications including printing, micro-patterning and cooling. While seemingly simple, the configuration of evaporating droplets on solids is difficult to predict and control. This is because evaporation typically proceeds as a "stick-slip" sequence-a combination of pinning and de-pinning events dominated by static friction or "pinning", caused by microscopic surface roughness. Here we show how smooth, pinning-free, solid surfaces of non-planar topography promote a different process called snap evaporation. During snap evaporation a droplet follows a reproducible sequence of configurations, consisting of a quasi-static phase-change controlled by mass diffusion interrupted by out-of-equilibrium snaps. Snaps are triggered by bifurcations of the equilibrium droplet shape mediated by the underlying non-planar solid. Because the evolution of droplets during snap evaporation is controlled by a smooth topography, and not by surface roughness, our ideas can inspire programmable surfaces that manage liquids in heat- and mass-transfer applications.

Rupturing Giant Plasma Membrane Vesicles to Form Micron-sized Supported Cell Plasma Membranes with Native Transmembrane Proteins.

Science.gov (United States)

Chiang, Po-Chieh; Tanady, Kevin; Huang, Ling-Ting; Chao, Ling

2017-11-09

Being able to directly obtain micron-sized cell blebs, giant plasma membrane vesicles (GPMVs), with native membrane proteins and deposit them on a planar support to form supported plasma membranes could allow the membrane proteins to be studied by various surface analytical tools in native-like bilayer environments. However, GPMVs do not easily rupture on conventional supports because of their high protein and cholesterol contents. Here, we demonstrate the possibility of using compression generated by the air-water interface to efficiently rupture GPMVs to form micron-sized supported membranes with native plasma membrane proteins. We demonstrated that not only lipid but also a native transmembrane protein in HeLa cells, Aquaporin 3 (AQP3), is mobile in the supported membrane platform. This convenient method for generating micron-sized supported membrane patches with mobile native transmembrane proteins could not only facilitate the study of membrane proteins by surface analytical tools, but could also enable us to use native membrane proteins for bio-sensing applications.

Comparative kinematical analyses of Venus flytrap (Dionaea muscipula snap traps

Directory of Open Access Journals (Sweden)

Simon Poppinga

2016-05-01

Full Text Available Although the Venus flytrap (Dionaea muscipula can be considered as one of the most extensively investigated carnivorous plants, knowledge is still scarce about diversity of the snap-trap motion, the functionality of snap traps under varying environmental conditions, and their opening motion. By conducting simple snap-trap closure experiments in air and under water, we present striking evidence that adult Dionaea snaps similarly fast in aerial and submersed states and, hence, is potentially able to gain nutrients from fast aquatic prey during seasonal inundation. We reveal three snapping modes of adult traps, all incorporating snap buckling, and show that millimeter-sized, much slower seedling traps do not yet incorporate such elastic instabilities. Moreover, opening kinematics of young and adult Dionaea snap traps reveal that reverse snap buckling is not performed, corroborating the assumption that growth takes place on certain trap lobe regions. Our findings are discussed in an evolutionary, biomechanical, functional–morphological and biomimetic context.

Reduced expression of exocytotic proteins caused by anti-cholinesterase pesticides in Brachionus calyciflorus (Rotifera: Monogononta

Directory of Open Access Journals (Sweden)

IA Pérez-Legaspi

Full Text Available AbstractThe organophosphate and carbamate pesticides methyl-parathion and carbaryl have a common action mechanism: they inhibit acetylcholinesterase enzyme by blocking the transmission of nerve impulses. However, they can alter the expression of exocytotic membrane proteins (SNARE, by modifying release of neurotransmitters and other substances. This study evaluated the adverse effects of the pesticides methyl-parathion and carbaryl on expression of SNARE proteins: Syntaxin-1, Syntaxin-4 and SNAP-23 in freshwater rotifer Brachionus calyciflorus. Protein expression of these three proteins was analyzed before and after exposure to these two pesticides by Western Blot. The expression of Syntaxin-1, Syntaxin-4 and SNAP-23 proteins in B. calyciflorussignificantly decreases with increasing concentration of either pesticides. This suggests that organophosphates and carbamates have adverse effects on expression of membrane proteins of exocytosis by altering the recognition, docking and fusion of presynaptic and vesicular membranes involved in exocytosis of neurotransmitters. Our results demonstrate that the neurotoxic effect of anticholinesterase pesticides influences the interaction of syntaxins and SNAP-25 and the proper assembly of the SNARE complex.

Poor Dietary Guidelines Compliance among Low-Income Women Eligible for Supplemental Nutrition Assistance Program-Education (SNAP-Ed

Directory of Open Access Journals (Sweden)

Shinyoung Jun

2018-03-01

Full Text Available The Supplemental Nutrition Assistance Program-Education (SNAP-Ed program aims to improve nutritional intakes of low-income individuals (<185% poverty threshold. The objective of this study was to describe the compliance with Dietary Guidelines for Americans (DGA recommendations for fruits, vegetables, and whole grains among SNAP-Ed eligible (n = 3142 and ineligible (n = 3168 adult women (19–70 years nationwide and SNAP-Ed participating women in Indiana (n = 2623, using the NHANES 2007–2012 and Indiana SNAP-Ed survey data, respectively. Sensitivity analysis further stratified women by race/ethnicity and by current SNAP participation (<130% poverty threshold. Nationally, lower-income women were less likely to meet the fruit (21% vs. 25% and vegetable (11% vs. 19% guidelines than higher-income women, but did not differ on whole grains, which were ~5% regardless of income. The income differences in fruit and vegetable intakes were driven by non-Hispanic whites. Fewer SNAP-Ed-eligible U.S. women met fruit (21% vs. 55% and whole grain (4% vs. 18% but did not differ for vegetable recommendations (11% vs. 9% when compared to Indiana SNAP-Ed women. This same trend was observed among current SNAP participants. Different racial/ethnic group relationships with DGA compliance were found in Indiana compared to the nation. Nevertheless, most low-income women in the U.S. are at risk of not meeting DGA recommendations for fruits (79%, vegetables (89%, and whole grains (96%; SNAP-Ed participants in Indiana had higher compliance with DGA recommendations. Increased consumption of these three critical food groups would improve nutrient density, likely reduce calorie consumption by replacing high calorie choices, and improve fiber intakes.

Snapping Knee Caused by Medial Meniscal Cyst

Directory of Open Access Journals (Sweden)

Tsuyoshi Ohishi

2014-01-01

Full Text Available Snapping phenomenon around the medial aspect of the knee is rare. We present this case of snapping knee caused by the sartorius muscle over a large medial meniscal cyst in a 66-year-old female. Magnetic resonance images demonstrated a large medial meniscal cyst with a horizontal tear of the medial meniscus. Arthroscopic cyst decompression with limited meniscectomy resulted in the disappearance of snapping, and no recurrence of the cyst was observed during a 2-year follow-up period.

Probing the Composition, Assembly and Activity of Protein Molecular Machines using Native Mass Spectrometry

NARCIS (Netherlands)

van de Waterbeemd, M.J.

2017-01-01

Native mass spectrometry and mass spectrometry in general, are powerful analytical tools for studying proteins and protein complexes. Native mass spectrometry may provide accurate mass measurements of large macromolecular assemblies enabling the investigation of their composition and stoichiometry.

Synaptotagmin-7 Is an Asynchronous Calcium Sensor for Synaptic Transmission in Neurons Expressing SNAP-23

DEFF Research Database (Denmark)

Weber, Jens P; Toft-Bertelsen, Trine L; Mohrmann, Ralf

2014-01-01

Synchronization of neurotransmitter release with the presynaptic action potential is essential for maintaining fidelity of information transfer in the central nervous system. However, synchronous release is frequently accompanied by an asynchronous release component that builds up during repetitive...... stimulation, and can even play a dominant role in some synapses. Here, we show that substitution of SNAP-23 for SNAP-25 in mouse autaptic glutamatergic hippocampal neurons results in asynchronous release and a higher frequency of spontaneous release events (mEPSCs). Use of neurons from double-knock-out (SNAP......, while synaptotagmin-7 barely displayed activity-dependent trafficking between vesicle and plasma membrane, implying that it acts as a plasma membrane calcium sensor. Overall, these findings support the idea of alternative syt∶SNARE combinations driving release with different kinetics and fidelity....

Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures

International Nuclear Information System (INIS)

Lammert, Heiko; Noel, Jeffrey K.; Haglund, Ellinor; Onuchic, José N.; Schug, Alexander

2015-01-01

The diversity in a set of protein nuclear magnetic resonance (NMR) structures provides an estimate of native state fluctuations that can be used to refine and enrich structure-based protein models (SBMs). Dynamics are an essential part of a protein’s functional native state. The dynamics in the native state are controlled by the same funneled energy landscape that guides the entire folding process. SBMs apply the principle of minimal frustration, drawn from energy landscape theory, to construct a funneled folding landscape for a given protein using only information from the native structure. On an energy landscape smoothed by evolution towards minimal frustration, geometrical constraints, imposed by the native structure, control the folding mechanism and shape the native dynamics revealed by the model. Native-state fluctuations can alternatively be estimated directly from the diversity in the set of NMR structures for a protein. Based on this information, we identify a highly flexible loop in the ribosomal protein S6 and modify the contact map in a SBM to accommodate the inferred dynamics. By taking into account the probable native state dynamics, the experimental transition state is recovered in the model, and the correct order of folding events is restored. Our study highlights how the shared energy landscape connects folding and function by showing that a better description of the native basin improves the prediction of the folding mechanism

SNAP/SOS: a package for simulating and analyzing safeguards systems

International Nuclear Information System (INIS)

Grant, F.H. III; Polito, J.; Sabuda, J.

1983-01-01

The effective analysis of safeguards systems at nuclear facilities requires significant effort. The Safeguards Network Analysis Procedure (SNAP) and the SNAP Operating System (SOS) reduce that effort to a manageable level. SNAP provides a detailed analysis of site safeguards for tactical evaluation. SOS helps the analyst organize and manage the SNAP effort effectively. SOS provides a database for model storage, automatic model generation, and computer graphics. The SOS/SNAP combination is a working example of a simulation system including executive-level control, database system, and facilities for model creation, editing, and output analysis

LC-MS/MS as an alternative for SDS-PAGE in blue native analysis of protein complexes.

NARCIS (Netherlands)

Wessels, H.C.T.; Vogel, R.O.; Heuvel, L.P.W.J. van den; Smeitink, J.A.M.; Rodenburg, R.J.T.; Nijtmans, L.G.J.; Farhoud, M.H.

2009-01-01

Two-dimensional blue native/SDS-PAGE is widely applied to investigate native protein-protein interactions, particularly those within membrane multi-protein complexes. MS has enabled the application of this approach at the proteome scale, typically by analysis of picked protein spots. Here, we

SNAP Telescope Latest Developments

Science.gov (United States)

Lampton, M.; SNAP Collaboration

2004-12-01

The coming era of precision cosmology imposes new demands on space telescopes with regard to spectrophotometric accuracy and image stability. To meet these requirements for SNAP we have developed an all reflecting two-meter-class space telescope of the three-mirror anastigmat type. Our design features a large flat annular field (1.5 degrees = 580mm diameter) and a telephoto advantage of 6, delivering a 22m focal length within an optical package length of only 3.5 meters. The use of highly stable materials (Corning ULE glass and carbon-fiber reinforced cyanate ester resin for the metering structure) combined with agressive distributed thermal control and an L2 orbit location will lead to unmatched figure stability. Owing to our choice of rigid structure with nondeployable solar panels, finite-element models show no structural resonances below 10Hz. An exhaustive stray light study has been completed. Beginning in 2005, two industry studies will develop plans for fabrication, integration and test, bringing SNAP to a highly realistic level of definition. SNAP is supported by the Office of Science, US DoE, under contract DE-AC03-76SF00098.

Determining Membrane Protein-Lipid Binding Thermodynamics Using Native Mass Spectrometry.

Science.gov (United States)

Cong, Xiao; Liu, Yang; Liu, Wen; Liang, Xiaowen; Russell, David H; Laganowsky, Arthur

2016-04-06

Membrane proteins are embedded in the biological membrane where the chemically diverse lipid environment can modulate their structure and function. However, the thermodynamics governing the molecular recognition and interaction of lipids with membrane proteins is poorly understood. Here, we report a method using native mass spectrometry (MS), to determine thermodynamics of individual ligand binding events to proteins. Unlike conventional methods, native MS can resolve individual ligand binding events and, coupled with an apparatus to control the temperature, determine binding thermodynamic parameters, such as for protein-lipid interactions. We validated our approach using three soluble protein-ligand systems (maltose binding protein, lysozyme, and nitrogen regulatory protein) and obtained similar results to those using isothermal titration calorimetry and surface plasmon resonance. We also determined for the first time the thermodynamics of individual lipid binding to the ammonia channel (AmtB), an integral membrane protein from Escherichia coli. Remarkably, we observed distinct thermodynamic signatures for the binding of different lipids and entropy-enthalpy compensation for binding lipids of variable chain length. Additionally, using a mutant form of AmtB that abolishes a specific phosphatidylglycerol (PG) binding site, we observed distinct changes in the thermodynamic signatures for binding PG, implying these signatures can identify key residues involved in specific lipid binding and potentially differentiate between specific lipid binding sites.

SNAP: Small Next-generation Atmospheric Probe Concept

Science.gov (United States)

Sayanagi, K. M.; Dillman, R. A.; Atkinson, D. H.; Li, J.; Saikia, S.; Simon, A. A.; Spilker, T. R.; Wong, M. H.; Hope, D.

2017-12-01

We present a concept for a small, atmospheric probe that could be flexibly added to future missions that orbit or fly-by a giant planet as a secondary payload, which we call the Small Next-generation Atmospheric Probe (SNAP). SNAP's main scientific objectives are to determine the vertical distribution of clouds and cloud-forming chemical species, thermal stratification, and wind speed as a function of depth. As a case study, we present the advantages, cost and risk of adding SNAP to the future Uranus Orbiter and Probe flagship mission; in combination with the mission's main probe, SNAP would perform atmospheric in-situ measurements at a second location, and thus enable and enhance the scientific objectives recommended by the 2013 Planetary Science Decadal Survey and the 2014 NASA Science Plan to determine atmospheric spatial variabilities. We envision that the science objectives can be achieved with a 30-kg entry probe 0.5m in diameter (less than half the size of the Galileo probe) that reaches 5-bar pressure-altitude and returns data to Earth via the carrier spacecraft. As the baseline instruments, the probe will carry an Atmospheric Structure Instrument (ASI) that measures the temperature, pressure and acceleration, a carbon nanotube-based NanoChem atmospheric composition sensor, and an Ultra-Stable Oscillator (USO) to conduct a Doppler Wind Experiment (DWE). We also catalog promising technologies currently under development that will strengthen small atmospheric entry probe missions in the future. While SNAP is applicable to multiple planets, we examine the feasibility, benefits and impacts of adding SNAP to the Uranus Orbiter and Probe flagship mission. Our project is supported by NASA PSDS3 grant NNX17AK31G.

Analysis of Native-Like Proteins and Protein Complexes Using Cation to Anion Proton Transfer Reactions (CAPTR)

Science.gov (United States)

Laszlo, Kenneth J.; Bush, Matthew F.

2015-12-01

Mass spectra of native-like protein complexes often exhibit narrow charge-state distributions, broad peaks, and contributions from multiple, coexisting species. These factors can make it challenging to interpret those spectra, particularly for mixtures with significant heterogeneity. Here we demonstrate the use of ion/ion proton transfer reactions to reduce the charge states of m/ z-selected, native-like ions of proteins and protein complexes, a technique that we refer to as cation to anion proton transfer reactions (CAPTR). We then demonstrate that CAPTR can increase the accuracy of charge state assignments and the resolution of interfering species in native mass spectrometry. The CAPTR product ion spectra for pyruvate kinase exhibit ~30 peaks and enable unambiguous determination of the charge state of each peak, whereas the corresponding precursor spectra exhibit ~6 peaks and the assigned charge states have an uncertainty of ±3%. 15+ bovine serum albumin and 21+ yeast enolase dimer both appear near m/ z 4450 and are completely unresolved in a mixture. After a single CAPTR event, the resulting product ions are baseline resolved. The separation of the product ions increases dramatically after each subsequent CAPTR event; 12 events resulted in a 3000-fold improvement in separation relative to the precursor ions. Finally, we introduce a framework for interpreting and predicting the figures of merit for CAPTR experiments. More generally, these results suggest that CAPTR strongly complements other mass spectrometry tools for analyzing proteins and protein complexes, particularly those in mixtures.

Extending the accuracy of the SNAP interatomic potential form

Science.gov (United States)

Wood, Mitchell A.; Thompson, Aidan P.

2018-06-01

The Spectral Neighbor Analysis Potential (SNAP) is a classical interatomic potential that expresses the energy of each atom as a linear function of selected bispectrum components of the neighbor atoms. An extension of the SNAP form is proposed that includes quadratic terms in the bispectrum components. The extension is shown to provide a large increase in accuracy relative to the linear form, while incurring only a modest increase in computational cost. The mathematical structure of the quadratic SNAP form is similar to the embedded atom method (EAM), with the SNAP bispectrum components serving as counterparts to the two-body density functions in EAM. The effectiveness of the new form is demonstrated using an extensive set of training data for tantalum structures. Similar to artificial neural network potentials, the quadratic SNAP form requires substantially more training data in order to prevent overfitting. The quality of this new potential form is measured through a robust cross-validation analysis.

Snap-Through Buckling Problem of Spherical Shell Structure

Directory of Open Access Journals (Sweden)

Sumirin Sumirin

2014-12-01

Full Text Available This paper presents results of a numerical study on the nonlinear behavior of shells undergoing snap-through instability. This research investigates the problem of snap-through buckling of spherical shells applying nonlinear finite element analysis utilizing ANSYS Program. The shell structure was modeled by axisymmetric thin shell of finite elements. Shells undergoing snap-through buckling meet with significant geometric change of their physical configuration, i.e. enduring large deflections during their deformation process. Therefore snap-through buckling of shells basically is a nonlinear problem. Nonlinear numerical operations need to be applied in their analysis. The problem was solved by a scheme of incremental iterative procedures applying Newton-Raphson method in combination with the known line search as well as the arc- length methods. The effects of thickness and depth variation of the shell is taken care of by considering their geometrical parameter l. The results of this study reveal that spherical shell structures subjected to pressure loading experience snap-through instability for values of l≥2.15. A form of ‘turn-back’ of the load-displacement curve took place at load levels prior to the achievement of the critical point. This phenomenon was observed for values of l=5.0 to l=7.0.

Combined SAFE/SNAP approach to safeguards evaluation

International Nuclear Information System (INIS)

Engi, D.; Chapman, L.D.; Grant, F.H.; Polito, J.

1980-01-01

Generally, the scope of a safeguards evaluation model can efficiently address one of two issues, (1) global safeguards effectiveness, or (2) vulnerability analysis for individual scenarios. The Safeguards Automated Facility Evaluation (SAFE) focuses on (1) while the Safeguards Network Analysis Procedure (SNAP) is directed at (2). SAFE addresses (1) in that it considers the entire facility, i.e., the composite system of hardware and human components, in one global analysis. SNAP addresses (2) by providing a safeguards modeling symbology sufficiently flexible to represent quite complex scenarios from the standpoint of hardware interfaces while also accounting for a rich variety of human decision making. A combined SAFE/SNAP approach to the problem of safeguards evaluation is described and illustrated through an example

In vivo evaluation of radiotracers targeting the melanin-concentrating hormone receptor 1: [11C]SNAP-7941 and [18F]FE@SNAP reveal specific uptake in the ventricular system.

Science.gov (United States)

Zeilinger, Markus; Dumanic, Monika; Pichler, Florian; Budinsky, Lubos; Wadsak, Wolfgang; Pallitsch, Katharina; Spreitzer, Helmut; Lanzenberger, Rupert; Hacker, Marcus; Mitterhauser, Markus; Philippe, Cécile

2017-08-14

The MCHR1 is involved in the regulation of energy homeostasis and changes of the expression are linked to a variety of associated diseases, such as diabetes and adiposity. The study aimed at the in vitro and in vivo evaluation of [ 11 C]SNAP-7941 and [ 18 F]FE@SNAP as potential PET-tracers for the MCHR1. Competitive binding studies with non-radioactive derivatives and small-animal PET/CT and MRI brain studies were performed under baseline conditions and tracer displacement with the unlabelled MCHR1 antagonist (±)-SNAP-7941. Binding studies evinced high binding affinity of the non-radioactive derivatives. Small-animal imaging of [ 11 C]SNAP-7941 and [ 18 F]FE@SNAP evinced high tracer uptake in MCHR1-rich regions of the ventricular system. Quantitative analysis depicted a significant tracer reduction after displacement with (±)-SNAP-7941. Due to the high binding affinity of the non-labelled derivatives and the high specific tracer uptake of [ 11 C]SNAP-7941 and [ 18 F]FE@SNAP, there is strong evidence that both radiotracers may serve as highly suitable agents for specific MCHR1 imaging.

External Snapping Hip Syndrome: Emphasis on the MR Imaging

International Nuclear Information System (INIS)

Choi, Jung Eun; Lee, Bae Young; Sung, Mi Sook; Lee, Ki Haeng; Yoo, Won Jong; Lim, Hyun Wook; Chung, Myung Hee; Park, Jeong Mi; Kim, Jee Young

2010-01-01

The aim of this study is to evaluate the MR imaging features of patients with external snapping hip syndrome. We retrospectively reviewed 63 hip MR images. The images were analyzed according to the thickness and contour of the iliotibial band and the gluteus maximus, the presence of bone marrow edema, bursitis, joint effusion and other associated findings. The MR imaging of 22 hips with snapping hip syndrome depicted the causes of external snapping hip syndrome in twenty cases (90%). The MR imaging features of the snapping hip included thickening of the iliotibial band in twelve cases (55%) and/or thickening of the anterior band of the gluteus maximus in nineteen (86%), and a wavy contour of the iliotibial band or the anterior band of the gluteus maximus in ten cases (45%). These findings show a significant p value (<0.01). The majority of patients with snapping hip syndrome revealed thickening of the iliotibial band, thickening of the anterior band of the gluteus maximus and wavy contour of the those structures on MR imaging

External Snapping Hip Syndrome: Emphasis on the MR Imaging

Energy Technology Data Exchange (ETDEWEB)

Choi, Jung Eun; Lee, Bae Young [Catholic University St. Paul' s Hospital, Seoul (Korea, Republic of); Sung, Mi Sook; Lee, Ki Haeng; Yoo, Won Jong; Lim, Hyun Wook; Chung, Myung Hee [Catholic University Bucheon St. Mary' s Hospital, Bucheon (Korea, Republic of); Park, Jeong Mi [Catholic University St. Mary' s Hospital, Seoul (Korea, Republic of); Kim, Jee Young [Catholic University St. Vincent' s Hospital, Suwon (Korea, Republic of)

2010-02-15

The aim of this study is to evaluate the MR imaging features of patients with external snapping hip syndrome. We retrospectively reviewed 63 hip MR images. The images were analyzed according to the thickness and contour of the iliotibial band and the gluteus maximus, the presence of bone marrow edema, bursitis, joint effusion and other associated findings. The MR imaging of 22 hips with snapping hip syndrome depicted the causes of external snapping hip syndrome in twenty cases (90%). The MR imaging features of the snapping hip included thickening of the iliotibial band in twelve cases (55%) and/or thickening of the anterior band of the gluteus maximus in nineteen (86%), and a wavy contour of the iliotibial band or the anterior band of the gluteus maximus in ten cases (45%). These findings show a significant p value (<0.01). The majority of patients with snapping hip syndrome revealed thickening of the iliotibial band, thickening of the anterior band of the gluteus maximus and wavy contour of the those structures on MR imaging.

Snapping wrist due to multiple accessory tendon of first extensor compartment

Directory of Open Access Journals (Sweden)

S. Dhiyaneswaran Subramaniyam

2018-01-01

Conclusion: There are various causes for snapping wrist syndrome. Multiple accessory tendon can also cause snapping as shown in this case report. Moreover am presenting this case to highlight the diagnostic failure with non dynamic radiological investigation and to consider multiple accessory tendon as differential diagnosis for snapping wrist syndrome. Also suggest dynamic study could be a better choice of investigation to diagnosis snapping syndrome. First compartment tunnel release with few accessory tendon slip tenotomy gives good result.

A document review to characterize Atomic International SNAP fuels shipped to INEL 1966--1973

International Nuclear Information System (INIS)

Wahnschaffe, S.D.; Lords, R.E.; Kneff, D.W.; Nagel, W.E.; Pearlman, H.; Schaubert, V.J.

1995-09-01

This report provides the results of a document search and review study to obtain information on the spent fuels for the following six Nuclear Auxiliary Power (SNAP) reactor cores now stored at the Idaho National Engineering Laboratory (INEL): SNAP-2 Experimental Reactor, SNAP-2 Development Reactor, SNAP-10A Ground Test Reactor, SNAP-8 Experimental Reactor, SNAP-8 Development Reactor, and Shield Test Reactor. The report also covers documentation on SNAP fuel materials from four in-pile materials tests: NAA-82-1, NAA-115-2, NAA-117-1, and NAA-121. Pieces of these fuel materials are also stored at INEL as part of the SNAP fuel shipments

Analyzing import intermediates of mitochondrial proteins by blue native gel electrophoresis.

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Waizenegger, Thomas; Rapaport, Doron

2007-01-01

Blue native gel electrophoresis (BNGE) is a powerful tool for analyzing native protein complexes from biological membranes as well as water-soluble proteins. It can be used for determining relative molecular masses of protein complexes and their subunit composition and for the detection of subcomplexes. We describe the analysis by BNGE of in vitro import reactions composed of radiolabeled precursor proteins and isolated mitochondria. Such an analysis is a powerful tool to follow import intermediates and to study assembly of protein complexes. Analysis of import reactions by BNGE provides information on the molecular mass of the complex with which the imported precursor is associated. In addition, components of such a complex can be identified by incubating the mitochondrial lysate with either soluble antibodies or antibodies coupled to protein A matrix. The binding of soluble antibodies to specific complexes results in an observed shift in their apparent molecular mass (antibody shift). Alternatively, addition of matrix-bound antibodies followed by removal of the matrix from the mixture will result in depletion of the specific complex from the mitochondrial lysate (antibody depletion). The experimental details of these techniques are described.

A highly compliant protein native state with a spontaneous-like mechanical unfolding pathway

DEFF Research Database (Denmark)

Heiðarsson, Pétur Orri; Valpapuram, Immanuel; Camilloni, Carlo

2012-01-01

The mechanical properties of proteins and their force-induced structural changes play key roles in many biological processes. Previous studies have shown that natively folded proteins are brittle under tension, unfolding after small mechanical deformations, while partially folded intermediate...... states, such as molten globules, are compliant and can deform elastically a great amount before crossing the transition state barrier. Moreover, under tension proteins appear to unfold through a different sequence of events than during spontaneous unfolding. Here, we describe the response to force...... of the four-α-helix acyl-CoA binding protein (ACBP) in the low-force regime using optical tweezers and ratcheted molecular dynamics simulations. The results of our studies reveal an unprecedented mechanical behavior of a natively folded protein. ACBP displays an atypical compliance along two nearly orthogonal...

Unexpected transcellular protein crossover occurs during canonical DNA transfection.

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Arsenault, Jason; Cuijpers, Sabine A G; Niranjan, Dhevahi; Davletov, Bazbek

2014-12-01

Transfection of DNA has been invaluable for biological sciences, yet the effects upon membrane homeostasis are far from negligible. Here, we demonstrate that Neuro2A cells transfected using Lipofectamine LTX with the fluorescently coupled Botulinum serotype A holoenzyme (EGFP-LcA) cDNA express this SNAP25 protease that can, once translated, escape the transfected host cytosol and become endocytosed into untransfected cells, without its innate binding and translocation domains. Fluorescent readouts revealed moderate transfection rates (30-50%) while immunoblotting revealed a surprisingly total enzymatic cleavage of SNAP25; the transgenic protein acted beyond the confines of its host cell. Using intracellular dyes, no important cytotoxic effects were observed from reagent treatment alone, which excluded the possibility of membrane ruptures, though noticeably, intracellular acidic organelles were redistributed towards the plasma membrane. This drastic, yet frequently unobserved, change in protein permeability and endosomal trafficking following reagent treatment highlights important concerns for all studies using transient transfection. © 2014 The Authors. Journal of Cellular Biochemistry Published by Wiley Periodicals, Inc.

SNAP: A General Purpose Network Analysis and Graph Mining Library.

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Leskovec, Jure; Sosič, Rok

2016-10-01

Large networks are becoming a widely used abstraction for studying complex systems in a broad set of disciplines, ranging from social network analysis to molecular biology and neuroscience. Despite an increasing need to analyze and manipulate large networks, only a limited number of tools are available for this task. Here, we describe Stanford Network Analysis Platform (SNAP), a general-purpose, high-performance system that provides easy to use, high-level operations for analysis and manipulation of large networks. We present SNAP functionality, describe its implementational details, and give performance benchmarks. SNAP has been developed for single big-memory machines and it balances the trade-off between maximum performance, compact in-memory graph representation, and the ability to handle dynamic graphs where nodes and edges are being added or removed over time. SNAP can process massive networks with hundreds of millions of nodes and billions of edges. SNAP offers over 140 different graph algorithms that can efficiently manipulate large graphs, calculate structural properties, generate regular and random graphs, and handle attributes and meta-data on nodes and edges. Besides being able to handle large graphs, an additional strength of SNAP is that networks and their attributes are fully dynamic, they can be modified during the computation at low cost. SNAP is provided as an open source library in C++ as well as a module in Python. We also describe the Stanford Large Network Dataset, a set of social and information real-world networks and datasets, which we make publicly available. The collection is a complementary resource to our SNAP software and is widely used for development and benchmarking of graph analytics algorithms.

SNAP-3D: a three-dimensional neutron diffusion code

International Nuclear Information System (INIS)

McCallien, C.W.J.

1975-10-01

A preliminary report is presented describing the data requirements of a one- two- or three-dimensional multi-group diffusion code, SNAP-3D. This code is primarily intended for neutron diffusion calculations but it can also carry out gamma calculations if the diffuse approximation is accurate enough. It is suitable for fast and thermal reactor core calculations and for shield calculations. It is assumed the reader is familiar with the older, two-dimensional code SNAP and can refer to the report [TRG-Report-1990], describing it. The present report concentrates on the enhancements to SNAP that have been made to produce the three-dimensional version, SNAP-3D, and is intended to act a a guide on data preparation until a single, comprehensive report can be published. (author)

Defining SNAP by cross-sectional and longitudinal definitions of neurodegeneration

OpenAIRE

Wisse, L.E.M.; Das, S.R.; Davatzikos, C.; Dickerson, B.C.; Xie, S.X.; Yushkevich, P.A.; Wolk, D.A.

2018-01-01

Introduction: Suspected non-Alzheimer's pathophysiology (SNAP) is a biomarker driven designation that represents a heterogeneous group in terms of etiology and prognosis. SNAP has only been identified by cross-sectional neurodegeneration measures, whereas longitudinal measures might better reflect “active” neurodegeneration and might be more tightly linked to prognosis. We compare neurodegeneration defined by cross-sectional ‘hippocampal volume’ only (SNAP/L−) versus both cross-sectional and ...

SNAP sky background at the north ecliptic pole

International Nuclear Information System (INIS)

Aldering, Greg

2002-01-01

I summarize the extant direct and indirect data on the sky background SNAP will see at the North Ecliptic Pole over the wavelength range 0.4 < λ < 1.7 (micro)m. At the spatial resolution of SNAP the sky background due to stars and galaxies is resolved, so the only source considered is zodiacal light. Several models are explored to provide interpolation in wavelength between the broadband data from HST and COBE observations. I believe the input data are now established well enough that the accuracy of the sky background presented here is sufficient for SNAP simulations, and that it will stand up to scrutiny by reviewers

Long-term exposure to high glucose induces changes in the content and distribution of some exocytotic proteins in cultured hippocampal neurons.

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Gaspar, J M; Castilho, Á; Baptista, F I; Liberal, J; Ambrósio, A F

2010-12-29

A few studies have reported the existence of depletion of synaptic vesicles, and changes in neurotransmitter release and in the content of exocytotic proteins in the hippocampus of diabetic rats. Recently, we found that diabetes alters the levels of synaptic proteins in hippocampal nerve terminals. Hyperglycemia is considered the main trigger of diabetic complications, although other factors, such as low insulin levels, also contribute to diabetes-induced changes. Thus, the aim of this work was to evaluate whether long-term elevated glucose per se, which mimics prolonged hyperglycemia, induces significant changes in the content and localization of synaptic proteins involved in exocytosis in hippocampal neurons. Hippocampal cell cultures were cultured for 14 days and were exposed to high glucose (50 mM) or mannitol (osmotic control; 25 mM plus 25 mM glucose), for 7 days. Cell viability and nuclear morphology were evaluated by MTT and Hoechst assays, respectively. The protein levels of vesicle-associated membrane protein-2 (VAMP-2), synaptosomal-associated protein-25 (SNAP-25), syntaxin-1, synapsin-1, synaptophysin, synaptotagmin-1, rabphilin 3a, and also of vesicular glutamate and GABA transporters (VGluT-1 and VGAT), were evaluated by immunoblotting, and its localization was analyzed by immunocytochemistry. The majority of the proteins were not affected. However, elevated glucose decreased the content of SNAP-25 and increased the content of synaptotagmin-1 and VGluT-1. Moreover, there was an accumulation of syntaxin-1, synaptotagmin-1 and VGluT-1 in the cell body of some hippocampal neurons exposed to high glucose. No changes were detected in mannitol-treated cells. In conclusion, elevated glucose per se did not induce significant changes in the content of the majority of the synaptic proteins studied in hippocampal cultures, with the exception of SNAP-25, synaptotagmin-1 and VGluT-1. However, there was an accumulation of some proteins in cell bodies of hippocampal

Genome-scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins.

Science.gov (United States)

Irani, Zahra Azimzadeh; Kerkhoven, Eduard J; Shojaosadati, Seyed Abbas; Nielsen, Jens

2016-05-01

Pichia pastoris is used for commercial production of human therapeutic proteins, and genome-scale models of P. pastoris metabolism have been generated in the past to study the metabolism and associated protein production by this yeast. A major challenge with clinical usage of recombinant proteins produced by P. pastoris is the difference in N-glycosylation of proteins produced by humans and this yeast. However, through metabolic engineering, a P. pastoris strain capable of producing humanized N-glycosylated proteins was constructed. The current genome-scale models of P. pastoris do not address native nor humanized N-glycosylation, and we therefore developed ihGlycopastoris, an extension to the iLC915 model with both native and humanized N-glycosylation for recombinant protein production, but also an estimation of N-glycosylation of P. pastoris native proteins. This new model gives a better prediction of protein yield, demonstrates the effect of the different types of N-glycosylation of protein yield, and can be used to predict potential targets for strain improvement. The model represents a step towards a more complete description of protein production in P. pastoris, which is required for using these models to understand and optimize protein production processes. © 2015 Wiley Periodicals, Inc.

Can Natural Proteins Designed with ‘Inverted’ Peptide Sequences Adopt Native-Like Protein Folds?

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Sridhar, Settu; Guruprasad, Kunchur

2014-01-01

We have carried out a systematic computational analysis on a representative dataset of proteins of known three-dimensional structure, in order to evaluate whether it would possible to ‘swap’ certain short peptide sequences in naturally occurring proteins with their corresponding ‘inverted’ peptides and generate ‘artificial’ proteins that are predicted to retain native-like protein fold. The analysis of 3,967 representative proteins from the Protein Data Bank revealed 102,677 unique identical inverted peptide sequence pairs that vary in sequence length between 5–12 and 18 amino acid residues. Our analysis illustrates with examples that such ‘artificial’ proteins may be generated by identifying peptides with ‘similar structural environment’ and by using comparative protein modeling and validation studies. Our analysis suggests that natural proteins may be tolerant to accommodating such peptides. PMID:25210740

A cDNA Immunization Strategy to Generate Nanobodies against Membrane Proteins in Native Conformation

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Eden, Thomas; Menzel, Stephan; Wesolowski, Janusz; Bergmann, Philine; Nissen, Marion; Dubberke, Gudrun; Seyfried, Fabienne; Albrecht, Birte; Haag, Friedrich; Koch-Nolte, Friedrich

2018-01-01

Nanobodies (Nbs) are soluble, versatile, single-domain binding modules derived from the VHH variable domain of heavy-chain antibodies naturally occurring in camelids. Nbs hold huge promise as novel therapeutic biologics. Membrane proteins are among the most interesting targets for therapeutic Nbs because they are accessible to systemically injected biologics. In order to be effective, therapeutic Nbs must recognize their target membrane protein in native conformation. However, raising Nbs against membrane proteins in native conformation can pose a formidable challenge since membrane proteins typically contain one or more hydrophobic transmembrane regions and, therefore, are difficult to purify in native conformation. Here, we describe a highly efficient genetic immunization strategy that circumvents these difficulties by driving expression of the target membrane protein in native conformation by cells of the immunized camelid. The strategy encompasses ballistic transfection of skin cells with cDNA expression plasmids encoding one or more orthologs of the membrane protein of interest and, optionally, other costimulatory proteins. The plasmid is coated onto 1 µm gold particles that are then injected into the shaved and depilated skin of the camelid. A gene gun delivers a helium pulse that accelerates the DNA-coated particles to a velocity sufficient to penetrate through multiple layers of cells in the skin. This results in the exposure of the extracellular domains of the membrane protein on the cell surface of transfected cells. Repeated immunization drives somatic hypermutation and affinity maturation of target-specific heavy-chain antibodies. The VHH/Nb coding region is PCR-amplified from B cells obtained from peripheral blood or a lymph node biopsy. Specific Nbs are selected by phage display or by screening of Nb-based heavy-chain antibodies expressed as secretory proteins in transfected HEK cells. Using this strategy, we have successfully generated agonistic

Combined SAFE/SNAP approach to safeguards evaluation

International Nuclear Information System (INIS)

Engi, D.; Chapman, L.D.; Grant, F.H.; Polito, J.

1980-01-01

The scope of a safeguards evaluation model can efficiently address one of two issues: (1) global safeguards effectiveness or (2) vulnerability analysis for individual scenarios. The Safeguards Automated Facility Evaluation (SAFE) focuses on the first issue, while the Safeguards Network Analysis Procedure (SNAP) is directed towards the second. A combined SAFE/SNAP approach to the problem of safeguards evaluation is described and illustrated through an example. 4 refs

Native whey protein with high levels of leucine results in similar post-exercise muscular anabolic responses as regular whey protein: a randomized controlled trial.

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Hamarsland, Håvard; Nordengen, Anne Lene; Nyvik Aas, Sigve; Holte, Kristin; Garthe, Ina; Paulsen, Gøran; Cotter, Matthew; Børsheim, Elisabet; Benestad, Haakon B; Raastad, Truls

2017-01-01

Protein intake is essential to maximally stimulate muscle protein synthesis, and the amino acid leucine seems to possess a superior effect on muscle protein synthesis compared to other amino acids. Native whey has higher leucine content and thus a potentially greater anabolic effect on muscle than regular whey (WPC-80). This study compared the acute anabolic effects of ingesting 2 × 20 g of native whey protein, WPC-80 or milk protein after a resistance exercise session. A total of 24 young resistance trained men and women took part in this double blind, randomized, partial crossover, controlled study. Participants received either WPC-80 and native whey ( n  = 10), in a crossover design, or milk ( n  = 12). Supplements were ingested immediately (20 g) and two hours after (20 g) a bout of heavy-load lower body resistance exercise. Blood samples and muscle biopsies were collected to measure plasma concentrations of amino acids by gas-chromatography mass spectrometry, muscle phosphorylation of p70S6K, 4E-BP1 and eEF-2 by immunoblotting, and mixed muscle protein synthesis by use of [ 2 H 5 ]phenylalanine-infusion, gas-chromatography mass spectrometry and isotope-ratio mass spectrometry. Being the main comparison, differences between native whey and WPC-80 were analysed by a one-way ANOVA and comparisons between the whey supplements and milk were analysed by a two-way ANOVA. Native whey increased blood leucine concentrations more than WPC-80 and milk ( P  whey ingestion induced a greater phosphorylation of p70S6K than milk 180 min after exercise ( P  = 0.03). Muscle protein synthesis rates increased 1-3 h hours after exercise with WPC-80 (0.119%), and 1-5 h after exercise with native whey (0.112%). Muscle protein synthesis rates were higher 1-5 h after exercise with native whey than with milk (0.112% vs. 0.064, P  = 0.023). Despite higher-magnitude increases in blood leucine concentrations with native whey, it was not superior to WPC-80

Functional NifD-K fusion protein in Azotobacter vinelandii is a homodimeric complex equivalent to the native heterotetrameric MoFe protein

International Nuclear Information System (INIS)

Lahiri, Surobhi; Pulakat, Lakshmi; Gavini, Nara

2005-01-01

The MoFe protein of the complex metalloenzyme nitrogenase folds as a heterotetramer containing two copies each of the homologous α and β subunits, encoded by the nifD and the nifK genes respectively. Recently, the functional expression of a fusion NifD-K protein of nitrogenase was demonstrated in Azotobacter vinelandii, strongly implying that the MoFe protein is flexible as it could accommodate major structural changes, yet remain functional [M.H. Suh, L. Pulakat, N. Gavini, J. Biol. Chem. 278 (2003) 5353-5360]. This finding led us to further explore the type of interaction between the fused MoFe protein units. We aimed to determine whether an interaction exists between the two fusion MoFe proteins to form a homodimer that is equivalent to native heterotetrameric MoFe protein. Using the Bacteriomatch Two-Hybrid System, translationally fused constructs of NifD-K (fusion) with the full-length λCI of the pBT bait vector and also NifD-K (fusion) with the N-terminal α-RNAP of the pTRG target vector were made. To compare the extent of interaction between the fused NifD-K proteins to that of the β-β interactions in the native MoFe protein, we proceeded to generate translationally fused constructs of NifK with the α-RNAP of the pTRG vector and λCI protein of the pBT vector. The strength of the interaction between the proteins in study was determined by measuring the β-galactosidase activity and extent of ampicillin resistance of the colonies expressing these proteins. This analysis demonstrated that direct protein-protein interaction exists between NifD-K fusion proteins, suggesting that they exist as homodimers. As the interaction takes place at the β-interfaces of the NifD-K fusion proteins, we propose that these homodimers of NifD-K fusion protein may function in a similar manner as that of the heterotetrameric native MoFe protein. The observation that the extent of protein-protein interaction between the β-subunits of the native MoFe protein in Bacterio

Folding 19 proteins to their native state and stability of large proteins from a coarse-grained model.

Science.gov (United States)

Kapoor, Abhijeet; Travesset, Alex

2014-03-01

We develop an intermediate resolution model, where the backbone is modeled with atomic resolution but the side chain with a single bead, by extending our previous model (Proteins (2013) DOI: 10.1002/prot.24269) to properly include proline, preproline residues and backbone rigidity. Starting from random configurations, the model properly folds 19 proteins (including a mutant 2A3D sequence) into native states containing β sheet, α helix, and mixed α/β. As a further test, the stability of H-RAS (a 169 residue protein, critical in many signaling pathways) is investigated: The protein is stable, with excellent agreement with experimental B-factors. Despite that proteins containing only α helices fold to their native state at lower backbone rigidity, and other limitations, which we discuss thoroughly, the model provides a reliable description of the dynamics as compared with all atom simulations, but does not constrain secondary structures as it is typically the case in more coarse-grained models. Further implications are described. Copyright © 2013 Wiley Periodicals, Inc.

A protein chip membrane-capture assay for botulinum neurotoxin activity

International Nuclear Information System (INIS)

Marconi, Severine; Ferracci, Geraldine; Berthomieu, Maelys; Kozaki, Shunji; Miquelis, Raymond; Boucraut, Jose; Seagar, Michael

2008-01-01

Botulinum neurotoxins A and B (BoNT/A and B) are neuromuscular blocking agents which inhibit neurotransmission by cleaving the intra-cellular presynaptic SNARE proteins SNAP-25 and VAMP2, localized respectively in plasma membrane and synaptic vesicles. These neurotoxins are both dangerous pathogens and powerful therapeutic agents with numerous clinical and cosmetic applications. Consequently there is a need for in vitro assays of their biological activity to screen for potential inhibitors and to replace the widely used in vivo mouse assay. Surface plasmon resonance (SPR) was used to measure membrane vesicle capture by antibodies against SNAP-25 and VAMP2. Substrate cleavage by BoNTs modified capture providing a method to assay toxin activity. Firstly using synaptic vesicles as a substrate, a comparison of the EC 50 s for BoNT/B obtained by SPR, ELISA or flow cytometry indicated similar sensitivity although SPR assays were more rapid. Sonication of brain or neuronal cultures generated plasma membrane fragments with accessible intra-cellular epitopes adapted to measurement of BoNT/A activity. SPR responses were proportional to antigen concentration permitting detection of as little as 4 pM SNAP-25 in crude lysates. BoNT/A activity was assayed using monoclonal antibodies that specifically recognize a SNAP-25 epitope generated by the proteolytic action of the toxin. Incubation of intact primary cultured neurons with BoNT/A yielded an EC 50 of 0.5 pM. The SPR biosensor method was sensitive enough to monitor BoNT/A and B activity in cells cultured in a 96-well format providing an alternative to experimental animals for toxicological assays

Germination of beans and snap beans seed

Directory of Open Access Journals (Sweden)

Zdravković Milan

2000-01-01

Full Text Available The aim of this study was to investigate germination of good bean seed of the variety Galeb and the bad bean seed of the same variety. We were also interested in germination of bean and snap bean seed damaged by grain weevil, and in germination of the seed treated by freezing which was aimed at controlling grain weevil by cold. We also recorded the differences between bean and snap bean seed, which was or was not treated by freezing in laboratory conditions. This investigation was carried out by applying the two factorial block system. The obtained results were evaluated by the variance analysis and x2 test These results suggest that the bean seed of a bad fraction had low levels of germination, but still it was present. Although the seed of good appearance was carefully selected, germination was slightly lower than it should have been. The seed with the large amount of grain weevils performed a high level germination in laboratory conditions. There were no differences in germination between the seed injured by grain weevil either in beans or in snap beans. As for the seed treated or untreated by freezing, there also were no differences between beans and snap beans. .

Territorial aggressiveness and predation: two possible origins of snapping in the ant Plectroctena minor.

Science.gov (United States)

Dejean, Alain; Suzzoni, Jean-Pierre; Schatz, Bertrand; Orivel, Jérôme

2002-07-01

Plectroctena minor workers have long mandibles that can snap and deliver a sharp blow to intruders or prey, stunning or killing them. Encounters between homocolonial P. minor workers separated for 24 h or 15 days never resulted in snapping, while this behaviour was always noted during encounters between heterocolonial workers on neutral arenas or on the territory of a colony. In the latter case, only the aliens, that generally tried to escape, were snapped at. Snapping also occurred during encounters with workers belonging to sympatric ponerine species. During predation, the percentages of snapping varied according to prey nature, suggesting prey discrimination. Termite soldiers were always snapped at, while other prey were more often snapped close to rather than far from the nest entrances, indicating an intermingling of territorial aggressiveness and predatory behaviour. We discuss the adaptive value of snapping for hunting in galleries.

Septin 7 reduces nonmuscle myosin IIA activity in the SNAP23 complex and hinders GLUT4 storage vesicle docking and fusion

Energy Technology Data Exchange (ETDEWEB)

Wasik, Anita A.; Dumont, Vincent [Department of Pathology, University of Helsinki, 00014 Helsinki (Finland); Tienari, Jukka [Department of Pathology, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, 05850 Hyvinkää (Finland); Nyman, Tuula A. [Institute of Biotechnology, University of Helsinki, 00014 Helsinki (Finland); Fogarty, Christopher L.; Forsblom, Carol; Lehto, Markku [Folkhälsan Institute of Genetics, Folkhälsan Research Center, 00290 Helsinki (Finland); Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, 000290 Helsinki (Finland); Diabetes& Obesity Research Program, Research Program´s Unit, 00014 University of Helsinki (Finland); Lehtonen, Eero [Department of Pathology, University of Helsinki, 00014 Helsinki (Finland); Laboratory Animal Centre, University of Helsinki, 00014 Helsinki (Finland); Groop, Per-Henrik [Folkhälsan Institute of Genetics, Folkhälsan Research Center, 00290 Helsinki (Finland); Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, 000290 Helsinki (Finland); Diabetes& Obesity Research Program, Research Program´s Unit, 00014 University of Helsinki (Finland); Baker IDI Heart & Diabetes Institute, 3004 Melbourne (Australia); Lehtonen, Sanna, E-mail: sanna.h.lehtonen@helsinki.fi [Department of Pathology, University of Helsinki, 00014 Helsinki (Finland)

2017-01-15

Glomerular epithelial cells, podocytes, are insulin responsive and can develop insulin resistance. Here, we demonstrate that the small GTPase septin 7 forms a complex with nonmuscle myosin heavy chain IIA (NMHC-IIA; encoded by MYH9), a component of the nonmuscle myosin IIA (NM-IIA) hexameric complex. We observed that knockdown of NMHC-IIA decreases insulin-stimulated glucose uptake into podocytes. Both septin 7 and NM-IIA associate with SNAP23, a SNARE protein involved in GLUT4 storage vesicle (GSV) docking and fusion with the plasma membrane. We observed that insulin decreases the level of septin 7 and increases the activity of NM-IIA in the SNAP23 complex, as visualized by increased phosphorylation of myosin regulatory light chain. Also knockdown of septin 7 increases the activity of NM-IIA in the complex. The activity of NM-IIA is increased in diabetic rat glomeruli and cultured human podocytes exposed to macroalbuminuric sera from patients with type 1 diabetes. Collectively, the data suggest that the activity of NM-IIA in the SNAP23 complex plays a key role in insulin-stimulated glucose uptake into podocytes. Furthermore, we observed that septin 7 reduces the activity of NM-IIA in the SNAP23 complex and thereby hinders GSV docking and fusion with the plasma membrane. - Highlights: • Septin 7, nonmuscle myosin heavy chain IIA (NMHC-IIA) and SNAP23 form a complex. • Knockdown of septin 7 increases NM-IIA activity in the SNAP23 complex. • Insulin decreases septin 7 level and increases NM-IIA activity in the SNAP23 complex. • Septin 7 hinders GSV docking/fusion by reducing NM-IIA activity in the SNAP23 complex.

Septin 7 reduces nonmuscle myosin IIA activity in the SNAP23 complex and hinders GLUT4 storage vesicle docking and fusion

International Nuclear Information System (INIS)

Wasik, Anita A.; Dumont, Vincent; Tienari, Jukka; Nyman, Tuula A.; Fogarty, Christopher L.; Forsblom, Carol; Lehto, Markku; Lehtonen, Eero; Groop, Per-Henrik; Lehtonen, Sanna

2017-01-01

Glomerular epithelial cells, podocytes, are insulin responsive and can develop insulin resistance. Here, we demonstrate that the small GTPase septin 7 forms a complex with nonmuscle myosin heavy chain IIA (NMHC-IIA; encoded by MYH9), a component of the nonmuscle myosin IIA (NM-IIA) hexameric complex. We observed that knockdown of NMHC-IIA decreases insulin-stimulated glucose uptake into podocytes. Both septin 7 and NM-IIA associate with SNAP23, a SNARE protein involved in GLUT4 storage vesicle (GSV) docking and fusion with the plasma membrane. We observed that insulin decreases the level of septin 7 and increases the activity of NM-IIA in the SNAP23 complex, as visualized by increased phosphorylation of myosin regulatory light chain. Also knockdown of septin 7 increases the activity of NM-IIA in the complex. The activity of NM-IIA is increased in diabetic rat glomeruli and cultured human podocytes exposed to macroalbuminuric sera from patients with type 1 diabetes. Collectively, the data suggest that the activity of NM-IIA in the SNAP23 complex plays a key role in insulin-stimulated glucose uptake into podocytes. Furthermore, we observed that septin 7 reduces the activity of NM-IIA in the SNAP23 complex and thereby hinders GSV docking and fusion with the plasma membrane. - Highlights: • Septin 7, nonmuscle myosin heavy chain IIA (NMHC-IIA) and SNAP23 form a complex. • Knockdown of septin 7 increases NM-IIA activity in the SNAP23 complex. • Insulin decreases septin 7 level and increases NM-IIA activity in the SNAP23 complex. • Septin 7 hinders GSV docking/fusion by reducing NM-IIA activity in the SNAP23 complex.

Triggered Snap-Through of Bistable Shells

Science.gov (United States)

Cai, Yijie; Huang, Shicheng; Trase, Ian; Hu, Nan; Chen, Zi

Elastic bistable shells are common structures in nature and engineering, such as the lobes of the Venus flytrap or the surface of a toy jumping poppers. Despite their ubiquity, the parameters that control the bistability of such structures are not well understood. In this study, we explore how the geometrical features of radially symmetric elastic shells affect the shape and potential energy of a shell's stable states, and how to tune certain parameters in order to generate a snap-through transition from a convex semi-stable state to concave stable state. We fabricated a series of elastic shells with varying geometric parameters out of silicone rubber and measured the resulting potential energy in the semi-stable state. Finite element simulations were also conducted in order to determine the deformation and stress in the shells during snap-through. It was found that the energy of the semi-stable state is controlled by only two geometric parameters and a dimensionless ratio. We also noted two distinct transitions during snap-through, one between monostability and semi-bistability (the state a popper toy is in before it snaps-through and jumps), and a second transition between semi-bistability and true bistability. This work shows that it is possible to use a set of simple parameters to tailor the energy landscape of an elastic shell in order to generate complex trigger motions for their potential use in smart applications. Z.C. acknowledge support from Society in Science-Branco Weiss Fellowship, administered by ETH Zurich.

Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes.

Science.gov (United States)

Lu, Jonathan; Trnka, Michael J; Roh, Soung-Hun; Robinson, Philip J J; Shiau, Carrie; Fujimori, Danica Galonic; Chiu, Wah; Burlingame, Alma L; Guan, Shenheng

2015-12-01

Native electrospray-ionization mass spectrometry (native MS) measures biomolecules under conditions that preserve most aspects of protein tertiary and quaternary structure, enabling direct characterization of large intact protein assemblies. However, native spectra derived from these assemblies are often partially obscured by low signal-to-noise as well as broad peak shapes because of residual solvation and adduction after the electrospray process. The wide peak widths together with the fact that sequential charge state series from highly charged ions are closely spaced means that native spectra containing multiple species often suffer from high degrees of peak overlap or else contain highly interleaved charge envelopes. This situation presents a challenge for peak detection, correct charge state and charge envelope assignment, and ultimately extraction of the relevant underlying mass values of the noncovalent assemblages being investigated. In this report, we describe a comprehensive algorithm developed for addressing peak detection, peak overlap, and charge state assignment in native mass spectra, called PeakSeeker. Overlapped peaks are detected by examination of the second derivative of the raw mass spectrum. Charge state distributions of the molecular species are determined by fitting linear combinations of charge envelopes to the overall experimental mass spectrum. This software is capable of deconvoluting heterogeneous, complex, and noisy native mass spectra of large protein assemblies as demonstrated by analysis of (1) synthetic mononucleosomes containing severely overlapping peaks, (2) an RNA polymerase II/α-amanitin complex with many closely interleaved ion signals, and (3) human TriC complex containing high levels of background noise. Graphical Abstract ᅟ.

Aggregation of natively folded proteins: a theoretical approach

International Nuclear Information System (INIS)

Trovato, Antonio; Maritan, Amos; Seno, Flavio

2007-01-01

The reliable identification of β-aggregating stretches in protein sequences is essential for the development of therapeutic agents for Alzheimer's and Parkinson's diseases, as well as other pathological conditions associated with protein deposition. While the list of aggregation related diseases is growing, it has also been shown that many proteins that are normally well behaved can be induced to aggregate in vitro. This fact suggests the existence of a unified framework that could explain both folding and aggregation. By assuming this universal behaviour, we have recently introduced an algorithm (PASTA: prediction of amyloid structure aggregation), which is based on a sequence-specific energy function derived from the propensity of two residue types to be found paired in neighbouring strands within β-sheets in globular proteins. The algorithm is able to predict the most aggregation-prone portions of several proteins initially unfolded, in excellent agreement with experimental results. Here, we apply the method to a set of proteins which are known to aggregate, but which are natively folded. The quality of the prediction is again very high, corroborating the hypothesis that the amyloid structure is stabilized by the same physico-chemical determinants as those operating in folded proteins

A cDNA Immunization Strategy to Generate Nanobodies against Membrane Proteins in Native Conformation

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Thomas Eden

2018-01-01

Full Text Available Nanobodies (Nbs are soluble, versatile, single-domain binding modules derived from the VHH variable domain of heavy-chain antibodies naturally occurring in camelids. Nbs hold huge promise as novel therapeutic biologics. Membrane proteins are among the most interesting targets for therapeutic Nbs because they are accessible to systemically injected biologics. In order to be effective, therapeutic Nbs must recognize their target membrane protein in native conformation. However, raising Nbs against membrane proteins in native conformation can pose a formidable challenge since membrane proteins typically contain one or more hydrophobic transmembrane regions and, therefore, are difficult to purify in native conformation. Here, we describe a highly efficient genetic immunization strategy that circumvents these difficulties by driving expression of the target membrane protein in native conformation by cells of the immunized camelid. The strategy encompasses ballistic transfection of skin cells with cDNA expression plasmids encoding one or more orthologs of the membrane protein of interest and, optionally, other costimulatory proteins. The plasmid is coated onto 1 µm gold particles that are then injected into the shaved and depilated skin of the camelid. A gene gun delivers a helium pulse that accelerates the DNA-coated particles to a velocity sufficient to penetrate through multiple layers of cells in the skin. This results in the exposure of the extracellular domains of the membrane protein on the cell surface of transfected cells. Repeated immunization drives somatic hypermutation and affinity maturation of target-specific heavy-chain antibodies. The VHH/Nb coding region is PCR-amplified from B cells obtained from peripheral blood or a lymph node biopsy. Specific Nbs are selected by phage display or by screening of Nb-based heavy-chain antibodies expressed as secretory proteins in transfected HEK cells. Using this strategy, we have successfully

What determines the structures of native folds of proteins?

International Nuclear Information System (INIS)

Trovato, Antonio; Hoang, Trinh X; Banavar, Jayanth R; Maritan, Amos; Seno, Flavio

2005-01-01

We review a simple physical model (Hoang et al 2004 Proc. Natl Acad. Sci. USA 101 7960, Banavar et al 2004 Phys. Rev. E at press) which captures the essential physico-chemical ingredients that determine protein structure, such as the inherent anisotropy of a chain molecule, the geometrical and energetic constraints placed by hydrogen bonds, sterics, and hydrophobicity. Within this framework, marginally compact conformations resembling the native state folds of proteins emerge as competing minima in the free energy landscape. Here we demonstrate that a hydrophobic-polar (HP) sequence composed of regularly repeated patterns has as its ground state a β-helical structure remarkably similar to a known architecture in the Protein Data Bank

Digital Snaps

DEFF Research Database (Denmark)

Sandbye, Mette; Larsen, Jonas

. Distance as the New Punctum / Mikko Villi -- pt. II. FAMILY ALBUMS IN TRANSITION -- ch. 4. How Digital Technologies Do Family Snaps, Only Better / Gillian Rose -- ch. 5. Friendship Photography: Memory, Mobility and Social Networking / Joanne Garde-Hansen -- ch. 6. Play, Process and Materiality in Japanese...... -- ch. 9. Retouch Yourself: The Pleasures and Politics of Digital Cosmetic Surgery / Tanya Sheehan -- ch. 10. Virtual Selves: Art and Digital Autobiography / Louise Wolthers -- ch. 11. Mobile-Media Photography: New Modes of Engagement / Michael Shanks and Connie Svabo....

Serum biochemistry and native protein electrophoresis in diarrheic calves with arthritis

Directory of Open Access Journals (Sweden)

Pekcan M.

2012-01-01

Full Text Available In this study, serum biochemistry and native protein electrophoresis in newborn calves with diarrhea and arthritis, were performed in order to evaluate the changes along with clinical findings for their possible application in the diagnosis and prognosis of disease. Based on clinical examination, animals were allotied into two groups comprising either diseased or healthy animals. Urea, creatinine, ALT, AST, LDH, albumin, total protein, glucose, total cholesterol, uric acid and iron levels were determined in the sera. Serum protein native polyacrilamide gel electrophoresis (nPAGE was performed followed by protein band ratio estimation supported with densitometry at 596 nm. Differences between the average mean of healthy and diseased animals were compared statistically (Kruskal-Walley test. In this study a decrease in serum glucose and cholesterol values (p<0.001, increase in urea, LDH levels and α1-and α2-globulin levels (p<0.01 and p<0.05 respectively were found to be associated with the disease. As a result, the observed significant changes in biochemical parameters and clinical investigation in calves, suggesting acute inflammation causing the decrease in glucose and increase in α-globulins, may be of prognostic value.

The Classroom Animal: Snapping Turtles.

Science.gov (United States)

Kramer, David C.

1987-01-01

Describes the distinctive features of the common snapping turtle. Discusses facts and misconceptions held about the turtle. Provides guidelines for proper care and treatment of a young snapper in a classroom environment. (ML)

Efficient radiological assessment of the internal snapping hip syndrome

International Nuclear Information System (INIS)

Wunderbaldinger, P.; Bremer, C.; Matuszewski, L.; Marten, K.; Turetschek, K.; Rand, T.

2001-01-01

The aim of this study was to evaluate the diagnostic value/significance of various imaging techniques for demonstrating the underlying causative pathology of clinically suspected internal snapping hip syndrome. We intended to define the most efficient diagnostic imaging algorithm that leads to a specific definite therapy for this rare hip disorder. The imaging studies of 54 patients (43 women, 11 men, average age 58 years) with the clinical suspicion of internal snapping hip syndrome were compared for their diagnostic value/significance for finding the underlying pathology. Radiological workup included plain radiographs of the pelvis and hip joints (n=54), ultrasound (US) of the hip joints (n=29), computed tomography (CT) of the pelvis and proximal femur (n=17), and magnetic resonance imaging (MRI) of the pelvis/hip joint (n=21). In order to establish an efficient diagnostic algorithm we compared the diagnostic value of each imaging technique alone and in combination with the other methods. The underlying causative pathology could be established in 37% of patients (n=20) by the use of conventional radiographs alone and in 46% of the patients (n=25) by US alone, and in combination in 83% of the patients (n=45). By adding CT to the radiological workup, we established final diagnosis in 88% (in combination with X-ray; n=15/17) and 94% (together with X-ray and US; n=16/17) of the patients. Whenever MR imaging was used a causative pathology was found in all patients (100%; n=21). The most efficient radiological algorithm in the assessment of patients with internal snapping hip syndrome is the combination of plain radiography and US. MR imaging can be retained for unresolved and difficult cases. (orig.)

Electrophoretic mobility shift in native gels indicates calcium-dependent structural changes of neuronal calcium sensor proteins.

Science.gov (United States)

Viviano, Jeffrey; Krishnan, Anuradha; Wu, Hao; Venkataraman, Venkat

2016-02-01

In proteins of the neuronal calcium sensor (NCS) family, changes in structure as well as function are brought about by the binding of calcium. In this article, we demonstrate that these structural changes, solely due to calcium binding, can be assessed through electrophoresis in native gels. The results demonstrate that the NCS proteins undergo ligand-dependent conformational changes that are detectable in native gels as a gradual decrease in mobility with increasing calcium but not other tested divalent cations such as magnesium, strontium, and barium. Surprisingly, such a gradual change over the entire tested range is exhibited only by the NCS proteins but not by other tested calcium-binding proteins such as calmodulin and S100B, indicating that the change in mobility may be linked to a unique NCS family feature--the calcium-myristoyl switch. Even within the NCS family, the changes in mobility are characteristic of the protein, indicating that the technique is sensitive to the individual features of the protein. Thus, electrophoretic mobility on native gels provides a simple and elegant method to investigate calcium (small ligand)-induced structural changes at least in the superfamily of NCS proteins. Copyright © 2015 Elsevier Inc. All rights reserved.

The Role of Conformational Flexibility on Protein Supercharging in Native Electrospray Ionization

Science.gov (United States)

Sterling, Harry J.; Cassou, Catherine A.; Trnka, Michael J.; Burlingame, A. L.; Krantz, Bryan A.; Williams, Evan R.

2012-01-01

Effects of covalent intramolecular bonds, either native disulfide bridges or chemical crosslinks, on ESI supercharging of proteins from aqueous solutions were investigated. Chemically modifying cytochrome c with up to seven crosslinks or ubiquitin with up to two crosslinks did not affect the average or maximum charge states of these proteins in the absence of m-nitrobenzyl alcohol (m-NBA), but the extent of supercharging induced by m-NBA increased with decreasing numbers of crosslinks. For the model random coil polypeptide reduced/alkylated RNase A, a decrease in charging with increasing m-NBA concentration attributable to reduced surface tension of the ESI droplet was observed, whereas native RNase A electrosprayed from these same solutions exhibited enhanced charging. The inverse relationship between the extent of supercharging and the number of intramolecular crosslinks for folded proteins, as well as the absence of supercharging for proteins that are random coils in aqueous solution, indicate that conformational restrictions induced by the crosslinks reduce the extent of supercharging. These results provide additional evidence that protein and protein complex supercharging from aqueous solution is primarily due to partial or significant unfolding that occurs as a result of chemical and/or thermal denaturation induced by the supercharging reagent late in the ESI droplet lifetime. PMID:21399817

Screening of mutations affecting protein stability and dynamics of FGFR1—A simulation analysis

Directory of Open Access Journals (Sweden)

C. George Priya Doss

2012-12-01

Full Text Available Single amino acid substitutions in Fibroblast Growth Factor Receptor 1 (FGFR1 destabilize protein and have been implicated in several genetic disorders like various forms of cancer, Kallamann syndrome, Pfeiffer syndrome, Jackson Weiss syndrome, etc. In order to gain functional insight into mutation caused by amino acid substitution to protein function and expression, special emphasis was laid on molecular dynamics simulation techniques in combination with in silico tools such as SIFT, PolyPhen 2.0, I-Mutant 3.0 and SNAP. It has been estimated that 68% nsSNPs were predicted to be deleterious by I-Mutant, slightly higher than SIFT (37%, PolyPhen 2.0 (61% and SNAP (58%. From the observed results, P722S mutation was found to be most deleterious by comparing results of all in silico tools. By molecular dynamics approach, we have shown that P722S mutation leads to increase in flexibility, and deviated more from the native structure which was supported by the decrease in the number of hydrogen bonds. In addition, biophysical analysis revealed a clear insight of stability loss due to P722S mutation in FGFR1 protein. Majority of mutations predicted by these in silico tools were in good concordance with the experimental results.

Snapin mediates insulin secretory granule docking, but not trans-SNARE complex formation

Energy Technology Data Exchange (ETDEWEB)

Somanath, Sangeeta [Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT (United Kingdom); Partridge, Christopher J. [Diabetes Research Laboratories, Oxford Centre for Diabetes, Endocrinology and Churchill Hospital, University of Oxford, Oxford, OX3 7LJ (United Kingdom); Marshall, Catriona [Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT (United Kingdom); Rowe, Tony [CSL Limited, 45 Poplar Road, Parkville, Victoria 3052 (Australia); Turner, Mark D., E-mail: mark.turner@ntu.ac.uk [Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS (United Kingdom)

2016-04-29

Secretory granule exocytosis is a tightly regulated process requiring granule targeting, tethering, priming, and membrane fusion. At the heart of this process is the SNARE complex, which drives fusion through a coiled-coil zippering effect mediated by the granule v-SNARE protein, VAMP2, and the plasma membrane t-SNAREs, SNAP-25 and syntaxin-1A. Here we demonstrate that in pancreatic β-cells the SNAP-25 accessory protein, snapin, C-terminal H2 domain binds SNAP-25 through its N-terminal Sn-1 domain. Interestingly whilst snapin binds SNAP-25, there is only modest binding of this complex with syntaxin-1A under resting conditions. Instead synataxin-1A appears to be recruited in response to secretory stimulation. These results indicate that snapin plays a role in tethering insulin granules to the plasma membrane through coiled coil interaction of snapin with SNAP-25, with full granule fusion competency only resulting after subsequent syntaxin-1A recruitment triggered by secretory stimulation. - Highlights: • Snapin mediates granule docking. • Snapin binds SNAP-25. • SNARE complex forms downstream.

Snapin mediates insulin secretory granule docking, but not trans-SNARE complex formation

International Nuclear Information System (INIS)

Somanath, Sangeeta; Partridge, Christopher J.; Marshall, Catriona; Rowe, Tony; Turner, Mark D.

2016-01-01

Secretory granule exocytosis is a tightly regulated process requiring granule targeting, tethering, priming, and membrane fusion. At the heart of this process is the SNARE complex, which drives fusion through a coiled-coil zippering effect mediated by the granule v-SNARE protein, VAMP2, and the plasma membrane t-SNAREs, SNAP-25 and syntaxin-1A. Here we demonstrate that in pancreatic β-cells the SNAP-25 accessory protein, snapin, C-terminal H2 domain binds SNAP-25 through its N-terminal Sn-1 domain. Interestingly whilst snapin binds SNAP-25, there is only modest binding of this complex with syntaxin-1A under resting conditions. Instead synataxin-1A appears to be recruited in response to secretory stimulation. These results indicate that snapin plays a role in tethering insulin granules to the plasma membrane through coiled coil interaction of snapin with SNAP-25, with full granule fusion competency only resulting after subsequent syntaxin-1A recruitment triggered by secretory stimulation. - Highlights: • Snapin mediates granule docking. • Snapin binds SNAP-25. • SNARE complex forms downstream.

Levels of protein hydroperoxides and carbonyl groups in guinea pigs native of high altitudes (Huancavelica, 3660 m)

OpenAIRE

Huayta, Roxana; Zúñiga, Haydée; Esquerre, Cynthia; Hernández, Luz; Carranza, Elizabeth

2014-01-01

The influence of hypobaric hypoxia on protein oxidation in lungs, heart, liver, kidneys and testicles of high altitude native guinea pigs (Huancavelica, 3660 m) in comparison to sea level (Lima, 150 m) native guinea pigs was evaluated. The concentration of protein hydroperoxides (POOH) and carbonyl groups (GC) as markers of protein oxidation, as well as total thiols (TT) concentration, powerful reducing agents that act as live antioxidants were determined. The results showed low concentration...

78 FR 52899 - Supplemental Nutrition Assistance Program (SNAP) Enhancing Retail Food Store Eligibility...

Science.gov (United States)

2013-08-27

... food choices, access to food, and retailer operations. Listening session attendees will be provided... food, be eligible to participate in SNAP? 10. Restaurants are generally prohibited from being SNAP... in an area where no store meets basic eligibility criteria for SNAP authorization, how should FNS...

Snapping turtles, a biological screen for PCB's

Energy Technology Data Exchange (ETDEWEB)

Olafsson, P.G.; Bryan, A.M.; Bush, B.; Stone, W.

1983-01-01

Snapping turtles are capable of storing extremely high concentration of organochlorine compounds in their fat without any apparent detrimental effect. This tolerance, to high bioconcentration, permits a wide gradation between the extremes in pollution levels and facilitates the detection of extremely toxic substances present in trace amounts. Consequently snapping turtles provide an excellent biological screen for these compounds.

Cutaneous fibroma in a captive common snapping turtle (Chelydra serpentina).

Science.gov (United States)

Gonzales-Viera, O; Bauer, G; Bauer, A; Aguiar, L S; Brito, L T; Catão-Dias, J L

2012-11-01

An adult female common snapping turtle (Chelydra serpentina) had a mass on the plantar surface of the right forelimb that was removed surgically. Microscopical examination revealed many spindle cells with mild anisocytosis and anisokaryosis and a surrounding collagenous stroma. There were no mitoses. Immunohistochemistry showed that the spindle cells expressed vimentin, but not desmin. A diagnosis of cutaneous fibroma was made. Tumours are reported uncommonly in chelonian species. Cutaneous fibroma has been diagnosed in an alligator snapping turtle (Macrochelys temminckii), but not previously in a common snapping turtle. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

Two-step purification of His-tagged Nef protein in native condition using heparin and immobilized metal ion affinity chromatographies.

Science.gov (United States)

Finzi, Andrés; Cloutier, Jonathan; Cohen, Eric A

2003-07-01

The Nef protein encoded by human immunodeficiency virus type 1 (HIV-1) has been shown to be an important factor of progression of viral growth and pathogenesis in both in vitro and in vivo. The lack of a simple procedure to purify Nef in its native conformation has limited molecular studies on Nef function. A two-step procedure that includes heparin and immobilized metal ion affinity chromatographies (IMACs) was developed to purify His-tagged Nef (His(6)-Nef) expressed in bacteria in native condition. During the elaboration of this purification procedure, we identified two closely SDS-PAGE-migrating contaminating bacterial proteins, SlyD and GCHI, that co-eluted with His(6)-Nef in IMAC in denaturing condition and developed purification steps to eliminate these contaminants in native condition. Overall, this study describes a protocol that allows rapid purification of His(6)-Nef protein expressed in bacteria in native condition and that removes metal affinity resin-binding bacterial proteins that can contaminate recombinant His-tagged protein preparation.

Synthetic study on prion protein fragments using a SPPS and native chemical ligation

Czech Academy of Sciences Publication Activity Database

Zawada, Z.; Šebestík, Jaroslav; Bednárová, Lucie; Bouř, Petr; Hlaváček, Jan; Stibor, Ivan

2009-01-01

Roč. 37, Suppl. 1 (2009), s. 44-44 ISSN 0939-4451. [International Congress on Amino Acids, Peptides and Proteins /11./. 03.08.2009-07.08.2009, Vienna] Institutional research plan: CEZ:AV0Z40550506 Keywords : prion protein * SPPS * native chemical ligation * fragments Subject RIV: CC - Organic Chemistry

Recent Developments in the Recovery of SNAP-DYN Technical Data Base

Science.gov (United States)

Determan, William R.; Grimmett, David

2007-01-01

SNAP-DYN was a concept for a multi-kilowatt class (i.e., 10 to 50 kWe) of space nuclear electric power systems based on the SNAP reactor, shield, and liquid metal heat transfer technologies developed in the 1960s and coupled with dynamic power conversion hardware and state of the art space radiator technologies. The basic concept minimized the system's development costs by utilizing established technologies for each of the major components within the power system to reduce its overall development schedule. Three power conversion technologies were evaluated for the SNAP-DYN concept including Organic Rankine Cycle (ORC) with a peak cycle temperature of 672 K, a closed Brayton cycle (CBC) with a peak cycle temperature of 906 K, and a free piston Stirling cycle (FPSC) with a peak cycle temperature of 870 K. Net system conversion efficiencies were estimated to range from 16 to 19 % over the 10 to 50 kWe power range. Specific power levels for these systems were estimated to range from 6.4 to 13 W/kg over the same power range. SNAP-DYN reactor thermal power levels varied from 55 to 260 kWt, but a much longer lifetime (5 to 10 years vs. 1.3 years) was being evaluated for this power system application than had been demonstrated in the 1960s SNAP reactor development program. The last SNAP reactor under development at the end of the program in 1973 was designed for a 5-year mission life at a nominal thermal power level of 110 kWt with a coolant outlet temperature capability of 922 K. This reactor technology formed the basis for the SNAP-DYN reactor concept.

An essential nonredundant role for mycobacterial DnaK in native protein folding.

Directory of Open Access Journals (Sweden)

Allison Fay

2014-07-01

Full Text Available Protein chaperones are essential in all domains of life to prevent and resolve protein misfolding during translation and proteotoxic stress. HSP70 family chaperones, including E. coli DnaK, function in stress induced protein refolding and degradation, but are dispensable for cellular viability due to redundant chaperone systems that prevent global nascent peptide insolubility. However, the function of HSP70 chaperones in mycobacteria, a genus that includes multiple human pathogens, has not been examined. We find that mycobacterial DnaK is essential for cell growth and required for native protein folding in Mycobacterium smegmatis. Loss of DnaK is accompanied by proteotoxic collapse characterized by the accumulation of insoluble newly synthesized proteins. DnaK is required for solubility of large multimodular lipid synthases, including the essential lipid synthase FASI, and DnaK loss is accompanied by disruption of membrane structure and increased cell permeability. Trigger Factor is nonessential and has a minor role in native protein folding that is only evident in the absence of DnaK. In unstressed cells, DnaK localizes to multiple, dynamic foci, but relocalizes to focal protein aggregates during stationary phase or upon expression of aggregating peptides. Mycobacterial cells restart cell growth after proteotoxic stress by isolating persistent DnaK containing protein aggregates away from daughter cells. These results reveal unanticipated essential nonredunant roles for mycobacterial DnaK in mycobacteria and indicate that DnaK defines a unique susceptibility point in the mycobacterial proteostasis network.

Membrane fusion by VAMP3 and plasma membrane t-SNAREs

International Nuclear Information System (INIS)

Hu Chuan; Hardee, Deborah; Minnear, Fred

2007-01-01

Pairing of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins on vesicles (v-SNAREs) and SNARE proteins on target membranes (t-SNAREs) mediates intracellular membrane fusion. VAMP3/cellubrevin is a v-SNARE that resides in recycling endosomes and endosome-derived transport vesicles. VAMP3 has been implicated in recycling of transferrin receptors, secretion of α-granules in platelets, and membrane trafficking during cell migration. Using a cell fusion assay, we examined membrane fusion capacity of the ternary complexes formed by VAMP3 and plasma membrane t-SNAREs syntaxin1, syntaxin4, SNAP-23 and SNAP-25. VAMP3 forms fusogenic pairing with t-SNARE complexes syntaxin1/SNAP-25, syntaxin1/SNAP-23 and syntaxin4/SNAP-25, but not with syntaxin4/SNAP-23. Deletion of the N-terminal domain of syntaxin4 enhanced membrane fusion more than two fold, indicating that the N-terminal domain negatively regulates membrane fusion. Differential membrane fusion capacities of the ternary v-/t-SNARE complexes suggest that transport vesicles containing VAMP3 have distinct membrane fusion kinetics with domains of the plasma membrane that present different t-SNARE proteins

Studies on voltammetric determination of cadmium in samples containing native and digested proteins

Energy Technology Data Exchange (ETDEWEB)

Drozd, Marcin; Pietrzak, Mariusz, E-mail: mariusz@ch.pw.edu.pl; Malinowska, Elżbieta

2014-03-01

Highlights: • Proteins exhibit diverse impact on the DPASV cadmium signals. • Proteins subjected to HNO{sub 3} introduce less interference, than the native ones. • Optimal amount of SDS depends on the kind of protein. • Presence of thiolated coating agents of QDs do not influence the analysis. - Abstract: This work focuses on determination of cadmium ions using anodic stripping voltammetry (ASV) on thin film mercury electrode in conditions corresponding to those obtained after digestion of cadmium-based quantum dots and their conjugates. It presents the impact of selected proteins, including potential receptors and surface blocking agents on the voltammetric determination of cadmium. Experiments regarding elimination of interferences related to proteins presence using sodium dodecyl sulfate (SDS) are also shown. Effect of SDS on selected analytical parameters and simplicity of analyses carried out was investigated in the framework of current studies. The significant differences of influence among tested proteins on ASV cadmium determination, as well as the variability in SDS effectiveness as the antifouling agent were observed and explained. This work is especially important for those, who design new bioassays and biosensors with a use of quantum dots as electrochemical labels, as it shows what problems may arise from presence of native and digested proteins in tested samples.

Binary polypeptide system for permanent and oriented protein immobilization

Directory of Open Access Journals (Sweden)

Bailes Julian

2010-05-01

Full Text Available Abstract Background Many techniques in molecular biology, clinical diagnostics and biotechnology rely on binary affinity tags. The existing tags are based on either small molecules (e.g., biotin/streptavidin or glutathione/GST or peptide tags (FLAG, Myc, HA, Strep-tag and His-tag. Among these, the biotin-streptavidin system is most popular due to the nearly irreversible interaction of biotin with the tetrameric protein, streptavidin. The major drawback of the stable biotin-streptavidin system, however, is that neither of the two tags can be added to a protein of interest via recombinant means (except for the Strep-tag case leading to the requirement for chemical coupling. Results Here we report a new immobilization system which utilizes two monomeric polypeptides which self-assemble to produce non-covalent yet nearly irreversible complex which is stable in strong detergents, chaotropic agents, as well as in acids and alkali. Our system is based on the core region of the tetra-helical bundle known as the SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor complex. This irreversible protein attachment system (IPAS uses either a shortened syntaxin helix and fused SNAP25-synaptobrevin or a fused syntaxin-synaptobrevin and SNAP25 allowing a two-component system suitable for recombinant protein tagging, capture and immobilization. We also show that IPAS is suitable for use with traditional beads and chromatography, planar surfaces and Biacore, gold nanoparticles and for protein-protein interaction in solution. Conclusions IPAS offers an alternative to chemical cross-linking, streptavidin-biotin system and to traditional peptide affinity tags and can be used for a wide range of applications in nanotechnology and molecular sciences.

Scapulothoracic Anatomy and Snapping Scapula Syndrome

Directory of Open Access Journals (Sweden)

Rachel M. Frank

2013-01-01

Full Text Available The scapulothoracic articulation is a sliding junction between the deep aspect of the scapula and thoracic rib cage at the levels of ribs 2 through 7. Motion at this articulation is dynamically stabilized by a variety of muscular attachments, allowing for controlled positioning of the glenoid to assist in glenohumeral joint function. A thorough understanding of the complex anatomic relationships, including the various muscles, and bursa, is critical to the evaluation of patients presenting with scapulothoracic disorders. The snapping scapula syndrome is caused by either osseous lesions or scapulothoracic bursitis and can be difficult to recognize and treat. The purpose of this review is to discuss the anatomy of the scapulothoracic articulation with an emphasis on the pathology associated with snapping scapula syndrome.

A Label Free Colorimetric Assay for the Detection of Active Botulinum Neurotoxin Type A by SNAP-25 Conjugated Colloidal Gold

Directory of Open Access Journals (Sweden)

Christopher Gwenin

2013-08-01

Full Text Available Botulinum neurotoxins are one of the most potent toxins known to man. Current methods of detection involve the quantification of the toxin but do not take into account the percentage of the toxin that is active. At present the assay used for monitoring the activity of the toxin is the mouse bioassay, which is lengthy and has ethical issues due to the use of live animals. This report demonstrates a novel assay that utilises the endopeptidase activity of the toxin to detect Botulinum neurotoxin in a pharmaceutical sample. The cleaving of SNAP-25 is monitored via UV-Visible spectroscopy with a limit of detection of 373 fg/mL and has been further developed into a high throughput method using a microplate reader detecting down to 600 fg/mL of active toxin. The results show clear differences between the toxin product and the placebo, which contains the pharmaceutical excipients human serum albumin and lactose, showing that the assay detects the active form of the toxin.

Effects of environmental contaminants on snapping turtles of a tidal wetland

Energy Technology Data Exchange (ETDEWEB)

Albers, P H; Sileo, L; Mulhern, B M

1986-01-01

Snapping turtles (Chelydra serpentina) were collected from a brackish-water and a nearly freshwater area in the contaminated Hackensack Meadowlands of New Jersey and an uncontaminated freshwater area in Maryland to determine the effects of environmental contaminants on a resident wetland species. No turtles were observed or caught in Meadowlands at two trapping sites that were the most heavily contaminated by metals. Snapping turtles from the brackish-water area had an unusually low lipid content of body fat and reduced growth compared to turtles from the freshwater areas in New Jersey and Maryland. Despite the serious metal contamination of the Hackensack Meadowlands, the metal content of kidneys and livers from New Jersey turtles was low and not greatly different from that of the Maryland turtles. Organochlorine pesticide concentrations in body fat were generally low at all three study areas. Polychlorinated biphenyls (PCBs) concentrations in fat were highest in male turtles from the New Jersey brackish-water area. Analysis of blood for amino-levulinic acid dehydratase, albumin, glucose, hemoglobin, osmolatility, packed cell volume, total protein, triglycerides, and uric acid failed to reveal any differences among groups that would indicated physiological impairment related to contaminants.

Effects of environmental contaminants on snapping turtles of a tidal wetland

Science.gov (United States)

Albers, P.H.; Sileo, L.; Mulhern, B.M.

1986-01-01

Snapping turtles (Chelydra serpentina) were collected from a brackish-water and a nearly freshwater area in the contaminated Hackensack Meadowlands of New Jersey and an uncontaminated freshwater area in Maryland to determine the effects of environmental contaminants on a resident wetland species. No turtles were observed or caught in the Meadowlands at two trapping sites that were the most heavily contaminated by metals. Snapping turtles from the brackish-water area had an unusually low lipid content of body fat and reduced growth compared to turtles from the fresh-water areas in New Jersey and Maryland. Despite the serious metal contamination of the Hackensack Meadowlands, the metal content of kidneys and livers from New Jersey turtles was low and not greatly different from that of the Maryland turtles. Organochlorine pesticide concentrations in body fat were generally low at all three study areas. Polychlorinated biphenyls (PCBs) concentrations in fat were highest in male turtles from the New Jersey brackish-water area. Analysis of blood for amino-levulinic acid dehydratase, albumin, glucose, hemoglobin, osmolality, packed cell volume, total protein, triglycerides, and uric acid failed to reveal any differences among groups that would indicate physiological impairment related to contaminants.

The t-SNAREs syntaxin4 and SNAP23 but not v-SNARE VAMP2 are indispensable to tether GLUT4 vesicles at the plasma membrane in adipocyte

International Nuclear Information System (INIS)

Kawaguchi, Takayuki; Tamori, Yoshikazu; Kanda, Hajime; Yoshikawa, Mari; Tateya, Sanshiro; Nishino, Naonobu; Kasuga, Masato

2010-01-01

SNARE proteins (VAMP2, syntaxin4, and SNAP23) have been thought to play a key role in GLUT4 trafficking by mediating the tethering, docking and subsequent fusion of GLUT4-containing vesicles with the plasma membrane. The precise functions of these proteins have remained elusive, however. We have now shown that depletion of the vesicle SNARE (v-SNARE) VAMP2 by RNA interference in 3T3-L1 adipocytes inhibited the fusion of GLUT4 vesicles with the plasma membrane but did not affect tethering of the vesicles to the membrane. In contrast, depletion of the target SNAREs (t-SNAREs) syntaxin4 or SNAP23 resulted in impairment of GLUT4 vesicle tethering to the plasma membrane. Our results indicate that the t-SNAREs syntaxin4 and SNAP23 are indispensable for the tethering of GLUT4 vesicles to the plasma membrane, whereas the v-SNARE VAMP2 is not required for this step but is essential for the subsequent fusion event.

Insecticide Efficacy and Timing for Control of Western Bean Cutworm (Lepidoptera: Noctuidae) in Dry and Snap Beans.

Science.gov (United States)

Goudis, L A; Trueman, C L; Baute, T S; Hallett, R H; Gillard, C L

2016-02-01

The western bean cutworm, Striacosta albicosta (Smith) (Lepidoptera: Noctuidae), is a recent pest of corn, dry,and snap beans, in the Great Lakes region, and best practices for its management in beans need to be established.Insecticide efficacy and application timing field studies, conducted in 2011–2013, determined that lambda-cyhalothrin and chlorantraniliprole were capable of reducing western bean cutworm feeding damage in dry beans from 2.3 to 0.4% in preharvest samples, and in snap beans from 4.8 to 0.1% of marketable pods, respectively. The best application timing in dry beans was determined to be 4–18 d after 50% egg hatch. No economic benefit was found when products were applied to dry beans, and despite high artificial inoculation rates, damage to marketable yield was relatively low. Thiamethoxam, methoxyfenozide, and spinetoram were also found to be effective at reducing western bean cutworm damage in dry bean to as low as 0.3% compared to an untreated control with 2.5% damaged pods. In snap beans, increased return on investment between CAD$400 and CAD$600 was seen with multiple applications of lambda-cyhalothrin, and with chlorantraniliprole applied 4 d after egg mass infestation.

SNAP: a tool for nuclear physical protection system modeling

International Nuclear Information System (INIS)

Engi, D.; Grant, F.H. III.

1979-10-01

Nuclear safeguards systems are concerned, in part, with the physical protection of nuclear materials. The function of a physical protection system is to define the facility against adversary activities which could lead to theft of nuclear material or sabotage resulting in a radiological release. The Safeguards Network Analysis Procedure (SNAP) provides a convenient and standard analysis methodology for the evaluation of physical protection system analysis. This paper describes a detailed application of SNAP to a hypothetical nuclear facility

Telling our stories: heroin-assisted treatment and SNAP activism in the Downtown Eastside of Vancouver.

Science.gov (United States)

Boyd, Susan; Murray, Dave; MacPherson, Donald

2017-05-18

This article highlights the experiences of a peer-run group, SALOME/NAOMI Association of Patients (SNAP), that meets weekly in the Downtown Eastside of Vancouver, British Columbia, Canada. SNAP is a unique independent peer- run drug user group that formed in 2011 following Canada's first heroin-assisted treatment trial (HAT), North America Opiate Medication Initiative (NAOMI). SNAP's members are now made up of former research participants who participated in two heroin-assisted trials in Vancouver. This article highlights SNAP members' experiences as research subjects in Canada's second clinical trial conducted in Vancouver, Study to Assess Longer-term Opioid Medication Effectiveness (SALOME), that began recruitment of research participants in 2011. This paper draws on one brainstorming session, three focus groups, and field notes, with the SALOME/NAOMI Association of Patients (SNAP) in late 2013 about their experiences as research subjects in Canada's second clinical trial, SALOME in the DTES of Vancouver, and fieldwork from a 6-year period (March 2011 to February 2017) with SNAP members. SNAP's research draws on research principles developed by drug user groups and critical methodological frameworks on community-based research for social justice. The results illuminate how participating in the SALOME clinical trial impacted the lives of SNAP members. In addition, the findings reveal how SNAP member's advocacy for HAT impacts the group in positive ways. Seven major themes emerged from the analysis of the brainstorming and focus groups: life prior to SALOME, the clinic setting and routine, stability, 6-month transition, support, exiting the trial and ethics, and collective action, including their participation in a constitutional challenge in the Supreme Court of BC to continue receiving HAT once the SALOME trial ended. HAT benefits SNAP members. They argue that permanent HAT programs should be established in Canada because they are an effective harm reduction

Snap-top nanocarriers

KAUST Repository

Ambrogio, Michael W.

2010-08-06

(Equation Presented). An approach to the design and fabrication of mechanized mesoporous silica nanoparticles is demonstrated at the proof of principle level. It relies on the reductive cleavage of disulfide bonds within an integrated nanosystem, wherein surface-bound rotaxanes incorporate disulfide bonds in their stalks,-which are encircled by cucurbit[6]uril or α-cyclodextrin rings, until reductive chemistry is performed, resulting in the snapping of the stalks of the rotaxanes, leading to cargo release from the inside of the nanoparticles. © 2010 American Chemical Society.

Snap-top nanocarriers

KAUST Repository

Ambrogio, Michael W.; Pecorelli, Travis A.; Patel, Kaushik I.; Khashab, Niveen M.; Trabolsi, Ali; Khatib, Hussam A.; Botros, Youssry Y.; Zink, Jeffrey I.; Stoddart, Fraser Fraser Raser

2010-01-01

(Equation Presented). An approach to the design and fabrication of mechanized mesoporous silica nanoparticles is demonstrated at the proof of principle level. It relies on the reductive cleavage of disulfide bonds within an integrated nanosystem, wherein surface-bound rotaxanes incorporate disulfide bonds in their stalks,-which are encircled by cucurbit[6]uril or α-cyclodextrin rings, until reductive chemistry is performed, resulting in the snapping of the stalks of the rotaxanes, leading to cargo release from the inside of the nanoparticles. © 2010 American Chemical Society.

Vortex formation with a snapping shrimp claw.

Science.gov (United States)

Hess, David; Brücker, Christoph; Hegner, Franziska; Balmert, Alexander; Bleckmann, Horst

2013-01-01

Snapping shrimp use one oversized claw to generate a cavitating high speed water jet for hunting, defence and communication. This work is an experimental investigation about the jet generation. Snapping shrimp (Alpheus-bellulus) were investigated by using an enlarged transparent model reproducing the closure of the snapper claw. Flow inside the model was studied using both High-Speed Particle Image Velocimetry (HS-PIV) and flow visualization. During claw closure a channel-like cavity was formed between the plunger and the socket featuring a nozzle-type contour at the orifice. Closing the mechanism led to the formation of a leading vortex ring with a dimensionless formation number of approximate ΔT*≈4. This indicates that the claw might work at maximum efficiency, i.e. maximum vortex strength was achieved by a minimum of fluid volume ejected. The subsequent vortex cavitation with the formation of an axial reentrant jet is a reasonable explanation for the large penetration depth of the water jet. That snapping shrimp can reach with their claw-induced flow. Within such a cavitation process, an axial reentrant jet is generated in the hollow cylindrical core of the cavitated vortex that pushes the front further downstream and whose length can exceed the initial jet penetration depth by several times.

Vortex formation with a snapping shrimp claw.

Directory of Open Access Journals (Sweden)

David Hess

Full Text Available Snapping shrimp use one oversized claw to generate a cavitating high speed water jet for hunting, defence and communication. This work is an experimental investigation about the jet generation. Snapping shrimp (Alpheus-bellulus were investigated by using an enlarged transparent model reproducing the closure of the snapper claw. Flow inside the model was studied using both High-Speed Particle Image Velocimetry (HS-PIV and flow visualization. During claw closure a channel-like cavity was formed between the plunger and the socket featuring a nozzle-type contour at the orifice. Closing the mechanism led to the formation of a leading vortex ring with a dimensionless formation number of approximate ΔT*≈4. This indicates that the claw might work at maximum efficiency, i.e. maximum vortex strength was achieved by a minimum of fluid volume ejected. The subsequent vortex cavitation with the formation of an axial reentrant jet is a reasonable explanation for the large penetration depth of the water jet. That snapping shrimp can reach with their claw-induced flow. Within such a cavitation process, an axial reentrant jet is generated in the hollow cylindrical core of the cavitated vortex that pushes the front further downstream and whose length can exceed the initial jet penetration depth by several times.

MAGGIE Component 1: Identification and Purification of Native and Recombinant Multiprotein Complexes and Modified Proteins from Pyrococcus furiosus

Energy Technology Data Exchange (ETDEWEB)

Adams, Michael W. [University of Georgia; W. W. Adams, Michael

2014-01-07

Virtualy all cellular processes are carried out by dynamic molecular assemblies or multiprotein complexes (PCs), the composition of which is largely unknown. Structural genomics efforts have demonstrated that less than 25% of the genes in a given prokaryotic genome will yield stable, soluble proteins when expressed using a one-ORF-at-a-time approach. We proposed that much of the remaining 75% of the genes encode proteins that are part of multiprotein complexes or are modified post-translationally, for example, with metals. The problem is that PCs and metalloproteins (MPs) cannot be accurately predicted on a genome-wide scale. The only solution to this dilemma is to experimentally determine PCs and MPs in biomass of a model organism and to develop analytical tools that can then be applied to the biomass of any other organism. In other words, organisms themselves must be analyzed to identify their PCs and MPs: “native proteomes” must be determined. This information can then be utilized to design multiple ORF expression systems to produce recombinant forms of PCs and MPs. Moreover, the information and utility of this approach can be enhanced by using a hyperthermophile, one that grows optimally at 100°C, as a model organism. By analyzing the native proteome at close to 100 °C below the optimum growth temperature, we will trap reversible and dynamic complexes, thereby enabling their identification, purification, and subsequent characterization. The model organism for the current study is Pyrococcus furiosus, a hyperthermophilic archaeon that grows optimally at 100°C. It is grown up to 600-liter scale and kg quantities of biomass are available. In this project we identified native PCs and MPs using P. furiosus biomass (with MS/MS analyses to identify proteins by component 4). In addition, we provided samples of abundant native PCs and MPs for structural characterization (using SAXS by component 5). We also designed and evaluated generic bioinformatics and

Comparison of a mouse and a novel human scFv-SNAP-auristatin F drug conjugate with potent activity against EGFR-overexpressing human solid tumor cells

Directory of Open Access Journals (Sweden)

Woitok M

2017-07-01

Full Text Available Mira Woitok,1,2 Diana Klose,1 Stefano Di Fiore,1 Wolfgang Richter,3 Christoph Stein,1 Gerrit Gresch,1 Elena Grieger,1 Stefan Barth,1 Rainer Fischer,1,2 Katharina Kolberg,1,* Judith Niesen1,* 1Fraunhofer Institute for Molecular Biology and Applied Ecology (IME, Aachen, Germany; 2Institute of Molecular Biotechnology (Biology VII, RWTH Aachen University, Aachen, Germany; 3Tube Pharmaceuticals GmbH, Vienna, Austria *These authors contributed equally to this work Abstract: Antibody–drug conjugates (ADCs can deliver toxins to specific targets such as tumor cells. They have shown promise in preclinical/clinical development but feature stoichiometrically undefined chemical linkages, and those based on full-size antibodies achieve only limited tumor penetration. SNAP-tag technology can overcome these challenges by conjugating benzylguanine-modified toxins to single-chain fragment variables (scFvs with 1:1 stoichio­metry while preserving antigen binding. Two (human and mouse scFv-SNAP fusion proteins recognizing the epidermal growth factor receptor (EGFR were expressed in HEK 293T cells. The purified fusion proteins were conjugated to auristatin F (AURIF. Binding activity was confirmed by flow cytometry/immunohistochemistry, and cytotoxic activity was confirmed by cell viability/apoptosis and cell cycle arrest assays, and a novel microtubule dynamics disassembly assay was performed. Both ADCs bound specifically to their target cells in vitro and ex vivo, indicating that the binding activity of the scFv-SNAP fusions was unaffected by conjugation to AURIF. Cytotoxic assays confirmed that the ADCs induced apoptosis and cell cycle arrest at nanomolar concentrations and microtubule disassembly. The SNAP-tag technology provides a platform for the development of novel ADCs with defined conjugation sites and stoichiometry. We achieved the stable and efficient linkage of AURIF to human or murine scFvs using the SNAP-tag technology, offering a strategy to

Snap Down Voltage of a Fast-Scanning Micromirror with Vertical Electrostatic Combdrives

Science.gov (United States)

Wada, Hiroyuki; Lee, Daesung; Zappe, Stefan; Krishnamoorthy, Uma; Solgaard, Olav

2004-02-01

The parallel transition mode of the snap down of a fast-scanning mirror with vertical combdrives was analyzed. The snap down voltage of such a mirror significantly decreased when offsets between the ideal and actual upper movable comb teeth were more than 0.1 μm. When gap between the upper and lower comb teeth was decreased to increase torque, snap down voltage significantly decreased. The largest offset is induced by the lithography step in the fabrication process of the mirror. Self-alignment is required to increase the resonant frequency of the scanning mirror.

Why and how does native topology dictate the folding speed of a protein?

Science.gov (United States)

Rustad, Mark; Ghosh, Kingshuk

2012-11-01

Since the pioneering work of Plaxco, Simons, and Baker, it is now well known that the rates of protein folding strongly correlate with the average sequence separation (absolute contact order (ACO)) of native contacts. In spite of multitude of papers, our understanding to the basis of the relation between folding speed and ACO is still lacking. We model the transition state as a Gaussian polymer chain decorated with weak springs between native contacts while the unfolded state is modeled as a Gaussian chain only. Using these hamiltonians, our perturbative calculation explicitly shows folding speed and ACO are linearly related when only the first order term in the series is considered. However, to the second order, we notice the existence of two new topological metrics, termed COC1 and COC2 (COC stands for contact order correction). These additional correction terms are needed to properly account for the entropy loss due to overlapping (nested or linked) loops that are not well described by simple addition of entropies in ACO. COC1 and COC2 are related to fluctuations and correlations among different sequence separations. The new metric combining ACO, COC1, and COC2 improves folding speed dependence on native topology when applied to three different databases: (i) two-state proteins with only α/β and β proteins, (ii) two-state proteins (α/β, β and purely helical proteins all combined), and (iii) master set (multi-state and two-state) folding proteins. Furthermore, the first principle calculation provides us direct physical insights to the meaning of the fit parameters. The coefficient of ACO, for example, is related to the average strength of the contacts, while the constant term is related to the protein folding speed limit. With the new scaling law, our estimate of the folding speed limit is in close agreement with the widely accepted value of 1 μs observed in proteins and RNA. Analyzing an exhaustive set (7367) of monomeric proteins from protein data bank

Decarboxylative alkylation for site-selective bioconjugation of native proteins via oxidation potentials

Science.gov (United States)

Bloom, Steven; Liu, Chun; Kölmel, Dominik K.; Qiao, Jennifer X.; Zhang, Yong; Poss, Michael A.; Ewing, William R.; MacMillan, David W. C.

2018-02-01

The advent of antibody-drug conjugates as pharmaceuticals has fuelled a need for reliable methods of site-selective protein modification that furnish homogeneous adducts. Although bioorthogonal methods that use engineered amino acids often provide an elegant solution to the question of selective functionalization, achieving homogeneity using native amino acids remains a challenge. Here, we explore visible-light-mediated single-electron transfer as a mechanism towards enabling site- and chemoselective bioconjugation. Specifically, we demonstrate the use of photoredox catalysis as a platform to selectivity wherein the discrepancy in oxidation potentials between internal versus C-terminal carboxylates can be exploited towards obtaining C-terminal functionalization exclusively. This oxidation potential-gated technology is amenable to endogenous peptides and has been successfully demonstrated on the protein insulin. As a fundamentally new approach to bioconjugation this methodology provides a blueprint toward the development of photoredox catalysis as a generic platform to target other redox-active side chains for native conjugation.

Decarboxylative alkylation for site-selective bioconjugation of native proteins via oxidation potentials.

Science.gov (United States)

Bloom, Steven; Liu, Chun; Kölmel, Dominik K; Qiao, Jennifer X; Zhang, Yong; Poss, Michael A; Ewing, William R; MacMillan, David W C

2018-02-01

The advent of antibody-drug conjugates as pharmaceuticals has fuelled a need for reliable methods of site-selective protein modification that furnish homogeneous adducts. Although bioorthogonal methods that use engineered amino acids often provide an elegant solution to the question of selective functionalization, achieving homogeneity using native amino acids remains a challenge. Here, we explore visible-light-mediated single-electron transfer as a mechanism towards enabling site- and chemoselective bioconjugation. Specifically, we demonstrate the use of photoredox catalysis as a platform to selectivity wherein the discrepancy in oxidation potentials between internal versus C-terminal carboxylates can be exploited towards obtaining C-terminal functionalization exclusively. This oxidation potential-gated technology is amenable to endogenous peptides and has been successfully demonstrated on the protein insulin. As a fundamentally new approach to bioconjugation this methodology provides a blueprint toward the development of photoredox catalysis as a generic platform to target other redox-active side chains for native conjugation.

A pairwise residue contact area-based mean force potential for discrimination of native protein structure

Directory of Open Access Journals (Sweden)

Pezeshk Hamid

2010-01-01

Full Text Available Abstract Background Considering energy function to detect a correct protein fold from incorrect ones is very important for protein structure prediction and protein folding. Knowledge-based mean force potentials are certainly the most popular type of interaction function for protein threading. They are derived from statistical analyses of interacting groups in experimentally determined protein structures. These potentials are developed at the atom or the amino acid level. Based on orientation dependent contact area, a new type of knowledge-based mean force potential has been developed. Results We developed a new approach to calculate a knowledge-based potential of mean-force, using pairwise residue contact area. To test the performance of our approach, we performed it on several decoy sets to measure its ability to discriminate native structure from decoys. This potential has been able to distinguish native structures from the decoys in the most cases. Further, the calculated Z-scores were quite high for all protein datasets. Conclusions This knowledge-based potential of mean force can be used in protein structure prediction, fold recognition, comparative modelling and molecular recognition. The program is available at http://www.bioinf.cs.ipm.ac.ir/softwares/surfield

Effect of temporary drought at different growth stages on snap bean ...

African Journals Online (AJOL)

High quality snap bean (Phaseolus vulgaris L.) can be produced under rain-fed conditions, provided that adequate moisture is available. However, drought may occur at any stage of growth of snap bean. The objective of this study was to evaluate the effect of drought stress at different growth stages on pod physical quality ...

SNAP - a three dimensional neutron diffusion code

International Nuclear Information System (INIS)

McCallien, C.W.J.

1993-02-01

This report describes a one- two- three-dimensional multi-group diffusion code, SNAP, which is primarily intended for neutron diffusion calculations but can also carry out gamma calculations if the diffusion approximation is accurate enough. It is suitable for fast and thermal reactor core calculations and for shield calculations. SNAP can solve the multi-group neutron diffusion equations using finite difference methods. The one-dimensional slab, cylindrical and spherical geometries and the two-dimensional case are all treated as simple special cases of three-dimensional geometries. Numerous reflective and periodic symmetry options are available and may be used to reduce the number of mesh points necessary to represent the system. Extrapolation lengths can be specified at internal and external boundaries. (Author)

Experimental Snap Loading of Synthetic Ropes

Directory of Open Access Journals (Sweden)

C.M. Hennessey

2005-01-01

Full Text Available Large tensile forces, known as snap loads, can occur when a slack rope becomes taut. Such forces may damage the rope or masses connected to it. Experiments are described in which one end of a rope is attached to the top of a drop tower and the bottom end is attached to a weight. The weight is raised to a certain height and then released. The force at the top of the rope and the acceleration of the weight are recorded during the first snap load that occurs. Repeated drop tests are performed on each rope. The effects of the type of rope, drop height, drop weight, whether the rope has been subjected to static precycling, and the number of previous dynamic tests are examined. A mathematical model is proposed for the rope force as a function of the displacement and velocity of the weight.

Droplet snap-off in fluids with nematic liquid crystalline ordering

International Nuclear Information System (INIS)

Verhoeff, A A; Lekkerkerker, H N W

2012-01-01

We studied the snap-off of nematic liquid crystalline droplets originating from the Rayleigh-Taylor instability at the isotropic-nematic interface in suspensions of charged gibbsite in water and sterically stabilized gibbsite in bromotoluene. We found that droplet snap-off strongly depends on the director field structure inside the thinning neck, which is determined by the ratio of the splay elastic constant and the anchoring strength of the nematic phase to the droplet interface relative to the thickness of the thinning neck. If anchoring is weak, which is the case for aqueous gibbsite, this ratio is comparable to the thickness of the breaking thread. As a result, the thinning neck and pending drop have a uniform director field and droplet snap-off is determined by the viscous properties of the liquid crystal as well as by thermal fluctuations of the interface. On the other hand, in sterically stabilized gibbsite where anchoring is strong, this ratio is significantly smaller than the neck thickness. In this case, the neck has an escaped radial director field and the neck thinning is retarded close to snap-off due to a topological energy barrier involved in the separation of the droplet from the thread. (paper)

Preparing diagnostic data for the SNAP transport code

International Nuclear Information System (INIS)

Murphy, J.A.; Scott, S.D.; Towner, H.H.

1992-01-01

This paper describes the program SNAPIN which is used to prepare data for transport analysis with the SNAP code. The data input to SNAP includes diagnostic profiles [n e (R), T e (R), T i (R), v φ (R), Z eff (R), P rad (R)] and measurements such as total plasma current, R major , beam power, gas puff rate, etc. SNAPIN reads in the necessary TFTR data, allows editing of that data, including graphical editing of profile data and the selection of physics models. SNAPIN allows comparison of profile data from all diagnostics that measure a quantity, for example, electron temperature profiles from Thomson scattering and electron cyclotron emission (ECE). A powerful user interface is important to help the user prepare input data sets quickly and consistently, because hundreds of variables must be specified for each analysis. SNAPIN facilitates this by a careful organization of menus, display of all scalar data and switch settings within the menus, the graphical editing and comparison of profiles, and step-by-step checking for consistent physics controls [J. Murphy, S. Scott, and H. Towner, The SNAP User's Guide, Technical Report PPPL-TM-393, Princeton Plasma Physics Laboratory (1992)

Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?

Science.gov (United States)

Vendruscolo, M; Najmanovich, R; Domany, E

2000-02-01

We present a method to derive contact energy parameters from large sets of proteins. The basic requirement on which our method is based is that for each protein in the database the native contact map has lower energy than all its decoy conformations that are obtained by threading. Only when this condition is satisfied one can use the proposed energy function for fold identification. Such a set of parameters can be found (by perceptron learning) if Mp, the number of proteins in the database, is not too large. Other aspects that influence the existence of such a solution are the exact definition of contact and the value of the critical distance Rc, below which two residues are considered to be in contact. Another important novel feature of our approach is its ability to determine whether an energy function of some suitable proposed form can or cannot be parameterized in a way that satisfies our basic requirement. As a demonstration of this, we determine the region in the (Rc, Mp) plane in which the problem is solvable, i.e., we can find a set of contact parameters that stabilize simultaneously all the native conformations. We show that for large enough databases the contact approximation to the energy cannot stabilize all the native folds even against the decoys obtained by gapless threading.

Examining Internet Access and Social Media Application Use for Online Nutrition Education in SNAP-Ed Participants in Rural Illinois.

Science.gov (United States)

Loehmer, Emily; Smith, Sylvia; McCaffrey, Jennifer; Davis, Jeremy

2018-01-01

To examine Internet access and interest in receiving nutrition education via social media applications among low-income adults participating in the Supplemental Nutrition Assistance Program Education (SNAP-Ed). A cross-sectional survey was distributed during 25 SNAP-Ed classes throughout the 16 southernmost counties of Illinois. From 188 responses, the majority of participants had Internet access (76%). Among participants aged 18-32 years (n = 51), 92% owned a smartphone with Internet access and 57% indicated that they would use online nutrition education, with most interest in e-mail (41%), Facebook (40%), and text messaging (35%). There was little interest in using blogs, Vine, Twitter, Tumblr, and Pinterest. Overall, 49% of middle-aged adults aged 33-64 years and 87% of seniors aged ≥65 years reported they would not use online nutrition education. Results indicated similar Internet accessibility in southern Illinois among low-income populations compared with national rural rates. Interest in using online nutrition education varied among SNAP-Ed participants according to age. Young adults appeared to be the most captive audience regarding online nutrition education. Results may be useful to agencies implementing SNAP-Ed to supplement current curriculum with online nutrition education for audiences aged ≤32 years. Copyright © 2017 Society for Nutrition Education and Behavior. Published by Elsevier Inc. All rights reserved.

SNAP and AI Fuel Summary Report

International Nuclear Information System (INIS)

Lords, R.E.

1994-08-01

The SNAP and AI Fuel Summary Report provides a detailed overview of treatment and storage of these fuels from fabrication through current storage including design parameters and reactor history. Chemical and physical characteristics are described, and potential indicators of as-stored fuel conditions are emphasized

Scapulothoracic bursitis and snapping scapula syndrome: a critical review of current evidence.

Science.gov (United States)

Warth, Ryan J; Spiegl, Ulrich J; Millett, Peter J

2015-01-01

Symptomatic scapulothoracic disorders, such as painful scapular crepitus and/or bursitis, are uncommon; however, they can produce significant pain and disability in many patients. To review the current knowledge pertaining to snapping scapula syndrome and to identify areas of further research that may be helpful to improve clinical outcomes and patient satisfaction. Systematic review. We performed a preliminary search of the PubMed and Embase databases using the search terms "snapping scapula," "scapulothoracic bursitis," "partial scapulectomy," and "superomedial angle resection" in September 2013. All nonreview articles related to the topic of snapping scapula syndrome were included. The search identified a total of 167 unique articles, 81 of which were relevant to the topic of snapping scapula syndrome. There were 36 case series of fewer than 10 patients, 16 technique papers, 11 imaging studies, 9 anatomic studies, and 9 level IV outcomes studies. The level of evidence obtained from this literature search was inadequate to perform a formal systematic review or meta-analysis. Therefore, a critical review of current evidence is presented. Snapping scapula syndrome, a likely underdiagnosed condition, can produce significant shoulder dysfunction in many patients. Because the precise origin is typically unknown, specific treatments that are effective for some patients may not be effective for others. Nevertheless, bursectomy with or without partial scapulectomy is currently the most effective primary method of treatment in patients who fail nonoperative therapy. However, many patients experience continued shoulder disability even after surgical intervention. Future studies should focus on identifying the modifiable factors associated with poor outcomes after operative and nonoperative management for snapping scapula syndrome in an effort to improve clinical outcomes and patient satisfaction. © 2014 The Author(s).

Predictors of natively unfolded proteins: unanimous consensus score to detect a twilight zone between order and disorder in generic datasets

Directory of Open Access Journals (Sweden)

Deiana Antonio

2010-04-01

Full Text Available Abstract Background Natively unfolded proteins lack a well defined three dimensional structure but have important biological functions, suggesting a re-assignment of the structure-function paradigm. To assess that a given protein is natively unfolded requires laborious experimental investigations, then reliable sequence-only methods for predicting whether a sequence corresponds to a folded or to an unfolded protein are of interest in fundamental and applicative studies. Many proteins have amino acidic compositions compatible both with the folded and unfolded status, and belong to a twilight zone between order and disorder. This makes difficult a dichotomic classification of protein sequences into folded and natively unfolded ones. In this work we propose an operational method to identify proteins belonging to the twilight zone by combining into a consensus score good performing single predictors of folding. Results In this methodological paper dichotomic folding indexes are considered: hydrophobicity-charge, mean packing, mean pairwise energy, Poodle-W and a new global index, that is called here gVSL2, based on the local disorder predictor VSL2. The performance of these indexes is evaluated on different datasets, in particular on a new dataset composed by 2369 folded and 81 natively unfolded proteins. Poodle-W, gVSL2 and mean pairwise energy have good performance and stability in all the datasets considered and are combined into a strictly unanimous combination score SSU, that leaves proteins unclassified when the consensus of all combined indexes is not reached. The unclassified proteins: i belong to an overlap region in the vector space of amino acidic compositions occupied by both folded and unfolded proteins; ii are composed by approximately the same number of order-promoting and disorder-promoting amino acids; iii have a mean flexibility intermediate between that of folded and that of unfolded proteins. Conclusions Our results show that

Snap: an integrated SNP annotation platform

DEFF Research Database (Denmark)

Li, Shengting; Ma, Lijia; Li, Heng

2007-01-01

Snap (Single Nucleotide Polymorphism Annotation Platform) is a server designed to comprehensively analyze single genes and relationships between genes basing on SNPs in the human genome. The aim of the platform is to facilitate the study of SNP finding and analysis within the framework of medical...

Wide-field surveys from the SNAP mission

International Nuclear Information System (INIS)

2002-01-01

The Supernova/Acceleration Probe (SNAP) is a proposed space-borne observatory that will survey the sky with a wide-field optical/NIR imager. The images produced by SNAP will have an unprecedented combination of depth, solid-angle, angular resolution, and temporal sampling. Two 7.5 square-degree fields will be observed every four days over 16 months to a magnitude depth of AB = 27.7 in each of nine filters. Co-adding images over all epochs will give an AB = 30.3 per filter. A 300 square-degree field will be surveyed with no repeat visits to AB = 28 per filter. The nine filters span 3500-17000 (angstrom). Although the survey strategy is tailored for supernova and weak gravitational lensing observations, the resulting data supports a broad range of auxiliary science programs

How amide hydrogens exchange in native proteins.

Science.gov (United States)

Persson, Filip; Halle, Bertil

2015-08-18

Amide hydrogen exchange (HX) is widely used in protein biophysics even though our ignorance about the HX mechanism makes data interpretation imprecise. Notably, the open exchange-competent conformational state has not been identified. Based on analysis of an ultralong molecular dynamics trajectory of the protein BPTI, we propose that the open (O) states for amides that exchange by subglobal fluctuations are locally distorted conformations with two water molecules directly coordinated to the N-H group. The HX protection factors computed from the relative O-state populations agree well with experiment. The O states of different amides show little or no temporal correlation, even if adjacent residues unfold cooperatively. The mean residence time of the O state is ∼100 ps for all examined amides, so the large variation in measured HX rate must be attributed to the opening frequency. A few amides gain solvent access via tunnels or pores penetrated by water chains including native internal water molecules, but most amides access solvent by more local structural distortions. In either case, we argue that an overcoordinated N-H group is necessary for efficient proton transfer by Grotthuss-type structural diffusion.

How amide hydrogens exchange in native proteins

Science.gov (United States)

Persson, Filip; Halle, Bertil

2015-01-01

Amide hydrogen exchange (HX) is widely used in protein biophysics even though our ignorance about the HX mechanism makes data interpretation imprecise. Notably, the open exchange-competent conformational state has not been identified. Based on analysis of an ultralong molecular dynamics trajectory of the protein BPTI, we propose that the open (O) states for amides that exchange by subglobal fluctuations are locally distorted conformations with two water molecules directly coordinated to the N–H group. The HX protection factors computed from the relative O-state populations agree well with experiment. The O states of different amides show little or no temporal correlation, even if adjacent residues unfold cooperatively. The mean residence time of the O state is ∼100 ps for all examined amides, so the large variation in measured HX rate must be attributed to the opening frequency. A few amides gain solvent access via tunnels or pores penetrated by water chains including native internal water molecules, but most amides access solvent by more local structural distortions. In either case, we argue that an overcoordinated N–H group is necessary for efficient proton transfer by Grotthuss-type structural diffusion. PMID:26195754

Formative Assessment Using Social Marketing Principles to Identify Health and Nutrition Perspectives of Native American Women Living within the Chickasaw Nation Boundaries in Oklahoma

Science.gov (United States)

Parker, Stephany; Hunter, Toma; Briley, Chiquita; Miracle, Sarah; Hermann, Janice; Van Delinder, Jean; Standridge, Joy

2011-01-01

Objective: To identify health product and promotion channels for development of a Chickasaw Nation Supplemental Nutrition Assistance Education Program (SNAP-Ed) social marketing program. Methods: The study was qualitative and used social marketing principles to assess Native American women's views of health and nutrition. Focus groups (n = 8) and…

Octylphenol (OP) alters the expression of members of the amyloid protein family in the hypothalamus of the snapping turtle, Chelydra serpentina serpentina.

Science.gov (United States)

Trudeau, Vance L; Chiu, Suzanne; Kennedy, Sean W; Brooks, Ronald J

2002-03-01

The gonadal estrogen estradiol-17beta (E(2)) is important for developing and regulating hypothalamic function and many aspects of reproduction in vertebrates. Pollutants such as octylphenol (OP) that mimic the actions of estrogens are therefore candidate endocrine-disrupting chemicals. We used a differential display strategy (RNA-arbitrarily primed polymerase chain reaction) to isolate partial cDNA sequences of neurotransmitter, developmental, and disease-related genes that may be regulated by OP or E(2) in the snapping turtle Chelydra serpentina serpentina hypothalamus. Hatchling and year-old male snapping turtles were exposed to a 10 ng/mL nominal concentration of waterborne OP or E(2) for 17 days. One transcript [421 base pairs (bp)] regulated by OP and E(2) was 93% identical to human APLP-2. APLP-2 and the amyloid precursor protein (APP) regulate neuronal differentiation and are also implicated in the genesis of Alzheimer disease in humans. Northern blot analysis determined that the turtle hypothalamus contains a single APLP-2 transcript of 3.75 kb in length. Exposure to OP upregulated hypothalamic APLP-2 mRNA levels 2-fold (p < 0.05) in month-old and yearling turtles. E(2) did not affect APLP-2 mRNA levels in hatchlings but stimulated a 2-fold increase (p < 0.05) in APLP-2 mRNA levels in yearling males. The protein beta-amyloid, a selectively processed peptide derived from APP, is also involved in neuronal differentiation, and accumulation of this neurotoxic peptide causes neuronal degeneration in the brains of patients with Alzheimer disease. Therefore, we also sought to determine the effects of estrogens on the expression of beta-amyloid. Using homology cloning based on known sequences, we isolated a cDNA fragment (474 bp) from turtle brain with 88% identity to human APP. Northern blot analysis determined that a single 3.5-kb transcript was expressed in the turtle hypothalamus. Waterborne OP also increased the expression of hypothalamic APP after 35 days of

SNAP Participants' Eating Patterns over the Benefit Month: A Time Use Perspective.

Science.gov (United States)

Hamrick, Karen S; Andrews, Margaret

2016-01-01

Individuals receiving monthly benefits through the U.S. Supplemental Nutrition Assistance Program (SNAP) often fall short of food at the end of the month and some report feelings of hunger. To investigate this situation, we used time diaries from the 2006-08 American Time Use Survey and Eating & Health Module to identify the timing of days where respondents reported no eating occurrences. Analysis includes descriptive statistics, a logit model, and a simulated benefit month. We found that SNAP participants were increasingly more likely than nonparticipants to report a day with no eating occurrences over the benefit issuance cycle. This supports the view that there is a monthly cycle in food consumption associated with the SNAP monthly benefit issuance policy.

The development of Version 2 of the AN-SNAP casemix classification system.

Science.gov (United States)

Green, Janette; Gordon, Robert

2007-04-01

This paper presents the results of a recent review of the Australian National Sub-acute and Non-acute Patient (AN-SNAP) classification system. The AN-SNAP system was developed by the Centre for Health Service Development, University of Wollongong in 1997. The review was conducted between August 2005 and September 2006. Four clinical sub-committees comprising more than 50 clinicians from sub-acute services across New South Wales as well as representatives from Queensland and the Australian Capital Territory were established to develop a set of proposals to be considered for incorporation into Version 2 of the classification. It is proposed that the final AN-SNAP Version 2 classification will be available for implementation from 1 July 2007.

Strategies to improve the dietary quality of Supplemental Nutrition Assistance Program (SNAP) beneficiaries: an assessment of stakeholder opinions.

Science.gov (United States)

Blumenthal, Susan J; Hoffnagle, Elena E; Leung, Cindy W; Lofink, Hayley; Jensen, Helen H; Foerster, Susan B; Cheung, Lilian Wy; Nestle, Marion; Willett, Walter C

2014-12-01

To examine the opinions of stakeholders on strategies to improve dietary quality of Supplemental Nutrition Assistance Program (SNAP) participants. Participants answered a thirty-eight-item web-based survey assessing opinions and perceptions of SNAP and programme policy changes. Survey of 522 individuals with stakeholder interest in SNAP, conducted in October through December 2011. The top three barriers to improving dietary quality identified were: (i) unhealthy foods marketed in low-income communities; (ii) the high cost of healthy foods; and (iii) lifestyle challenges faced by low-income individuals. Many respondents (70 %) also disagreed that current SNAP benefit levels were adequate to maintain a healthy diet. Stakeholders believed that vouchers, coupons or monetary incentives for purchasing healthful foods might have the greatest potential for improving the diets of SNAP participants. Many respondents (78 %) agreed that sodas should not be eligible for purchases with SNAP benefits. More than half (55 %) believed retailers could easily implement such restrictions. A majority of respondents (58 %) agreed that stores should stock a minimum quantity of healthful foods in order to be certified as a SNAP retailer, and most respondents (83 %) believed that the US Department of Agriculture should collect data on the foods purchased with SNAP benefits. Results suggest that there is broad stakeholder support for policies that align SNAP purchase eligibility with national public health goals of reducing food insecurity, improving nutrition and preventing obesity.

Evaluación de déficit de atención con hiperactividad: la escala SNAP IV adaptada a la Argentina Assessment of attention deficit hyperactivity: SNAP-IV scale adapted to Argentina

Directory of Open Access Journals (Sweden)

Nora Grañana

2011-05-01

Full Text Available OBJETIVO: Valorar la utilidad de la escala SNAP IV como instrumento de detección de trastorno por déficit de atención con hiperactividad (TDAH en niños argentinos de 4 a 14 años de edad. MÉTODOS: Se adaptó y se administró la escala SNAP IV a un grupo de 1 230 escolares de la provincia de Buenos Aires, Argentina. Se determinó el diagnóstico con el control clínico de acuerdo a los criterios del Manual diagnóstico y estadístico de los trastornos mentales, 4.ª edición. Se determinaron la sensibilidad y especificidad así como los puntajes de corte para la escala SNAP IV en la población estudiada. RESULTADOS: Se estableció el puntaje en la escala SNAP IV que tuviera la mejor correlación entre sensibilidad y especificidad para determinar los casos verdaderos positivos que realmente tuvieran un diagnóstico clínico. Los puntajes de corte obtenidos fueron: un índice de 1,66 (15/27 puntos para la subescala déficit de atención y de 1,77 (16/27 puntos para hiperactividadimpulsividad en la población estudiada. CONCLUSIONES: La escala SNAP IV para detección de TDAH se considera válida en el caso de la población estudiada, siempre y cuando se modifiquen los puntajes de corte para obtener la mejor relación sensibilidad/especificidad, con base en las particularidades culturales y socioeconómicas de dicha población.OBJECTIVE: Assess the usefulness of the SNAP-IV scale as an instrument for detecting attention deficit hyperactivity disorder (ADHD in Argentine children aged 4 to 14 years. METHODS: The SNAP-IV scale was adapted and administered to a group of 1 230 schoolchildren in the province of Buenos Aires, Argentina. The diagnosis was determined with the clinical control, based on the criteria of the Diagnostic and Statistical Manual of Mental Disorders, 4th edition. The sensitivity and specificity, as well as the cut-off scores for the SNAP-IV scale in the population studied, were determined. RESULTS: The score on the SNAP-IV scale

Sensitive Electrochemical Detection of Native and Aggregated x-Synuclein Protein Involved in Parkinson's Disease

NARCIS (Netherlands)

Masarik, Michal; Stobiecka, Agata; Kizek, René; Jelen, Frantisek; Pechan, Zdenk; Hoyer, Wolfgang; Subramaniam, Vinod; Palecek, Emil

2004-01-01

The aggregation of α-synuclein, a 14 kDa protein, is involved in several human neurodegenerative disorders, including Parkinson's disease. We studied native and in vitro aggregated α-synuclein by circular dichroism (CD), atomic force microscopy (AFM) and electrochemical methods. We used constant

SNAP Participants' Eating Patterns over the Benefit Month: A Time Use Perspective.

Directory of Open Access Journals (Sweden)

Karen S Hamrick

Full Text Available Individuals receiving monthly benefits through the U.S. Supplemental Nutrition Assistance Program (SNAP often fall short of food at the end of the month and some report feelings of hunger. To investigate this situation, we used time diaries from the 2006-08 American Time Use Survey and Eating & Health Module to identify the timing of days where respondents reported no eating occurrences. Analysis includes descriptive statistics, a logit model, and a simulated benefit month. We found that SNAP participants were increasingly more likely than nonparticipants to report a day with no eating occurrences over the benefit issuance cycle. This supports the view that there is a monthly cycle in food consumption associated with the SNAP monthly benefit issuance policy.

SNAP Participants’ Eating Patterns over the Benefit Month: A Time Use Perspective

Science.gov (United States)

2016-01-01

Individuals receiving monthly benefits through the U.S. Supplemental Nutrition Assistance Program (SNAP) often fall short of food at the end of the month and some report feelings of hunger. To investigate this situation, we used time diaries from the 2006–08 American Time Use Survey and Eating & Health Module to identify the timing of days where respondents reported no eating occurrences. Analysis includes descriptive statistics, a logit model, and a simulated benefit month. We found that SNAP participants were increasingly more likely than nonparticipants to report a day with no eating occurrences over the benefit issuance cycle. This supports the view that there is a monthly cycle in food consumption associated with the SNAP monthly benefit issuance policy. PMID:27410962

Method for reducing snap in magnetic amplifiers

Science.gov (United States)

Fischer, R. L. E.; Word, J. L.

1968-01-01

Method of reducing snap in magnetic amplifiers uses a degenerative feedback circuit consisting of a resistor and a separate winding on a magnetic core. The feedback circuit extends amplifier range by allowing it to be used at lower values of output current.

Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies

Science.gov (United States)

2018-01-01

Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents. PMID:29488756

Ligand-directed tosyl chemistry for in situ native protein labeling and engineering in living systems: from basic properties to applications.

Science.gov (United States)

Tsukiji, Shinya; Hamachi, Itaru

2014-08-01

The ability to introduce any chemical probe to any endogenous target protein in its native environment, that is in cells and in vivo, is anticipated to provide various new exciting tools for biological and biomedical research. Although still at the prototype stage, the ligand-directed tosyl (LDT) chemistry is a novel type of affinity labeling technique that we developed for such a dream. This chemistry allows for modifying native proteins by various chemical probes with high specificity in various biological settings ranging from in vitro (in test tubes) to in living cells and in vivo. Since the first report, the list of proteins that are successfully labeled by the LDT chemistry has been increasing. A growing number of studies have demonstrated its utility to create semisynthetic proteins directly in cellular contexts. The in situ generated semisynthetic proteins are applicable for various types of analysis and imaging of intracellular biological processes. In this review, we summarize the basic properties of the LDT chemistry and its applications toward in situ engineering and analysis of native proteins in living systems. Current limitations and future challenges of this area are also described. Copyright © 2014 Elsevier Ltd. All rights reserved.

Beyond velocity and acceleration: jerk, snap and higher derivatives

Science.gov (United States)

Eager, David; Pendrill, Ann-Marie; Reistad, Nina

2016-11-01

The higher derivatives of motion are rarely discussed in the teaching of classical mechanics of rigid bodies; nevertheless, we experience the effect not only of acceleration, but also of jerk and snap. In this paper we will discuss the third and higher order derivatives of displacement with respect to time, using the trampolines and theme park roller coasters to illustrate this concept. We will also discuss the effects on the human body of different types of acceleration, jerk, snap and higher derivatives, and how they can be used in physics education to further enhance the learning and thus the understanding of classical mechanics concepts.

Innovative, wearable snap connector technology for improved device networking in electronic garments

Science.gov (United States)

Kostrzewski, Andrew A.; Lee, Kang S.; Gans, Eric; Winterhalter, Carole A.; Jannson, Tomasz P.

2007-04-01

This paper discusses Physical Optics Corporation's (POC) wearable snap connector technology that provides for the transfer of data and power throughout an electronic garment (e-garment). These connectors resemble a standard garment button and can be mated blindly with only one hand. Fully compatible with military clothing, their application allows for the networking of multiple electronic devices and an intuitive method for adding/removing existing components from the system. The attached flexible cabling also permits the rugged snap connectors to be fed throughout the standard webbing found in military garments permitting placement in any location within the uniform. Variations of the snap electronics/geometry allow for integration with USB 2.0 devices, RF antennas, and are capable of transferring high bandwidth data streams such as the 221 Mbps required for VGA video. With the trend towards providing military officers with numerous electronic devices (i.e., heads up displays (HMD), GPS receiver, PDA, etc), POC's snap connector technology will greatly improve cable management resulting in a less cumbersome uniform. In addition, with electronic garments gaining widespread adoption in the commercial marketplace, POC's technology is finding applications in such areas as sporting good manufacturers and video game technology.

Concentration of Tobacco Advertisements at SNAP and WIC Stores, Philadelphia, Pennsylvania, 2012

Science.gov (United States)

Chilton, Mariana; Zhao, Qian-Wei; Szymkowiak, Dorota; Coffman, Ryan; Mallya, Giridhar

2015-01-01

Introduction Tobacco advertising is widespread in urban areas with racial/ethnic minority and low-income households that participate in nutrition assistance programs. Tobacco sales and advertising are linked to smoking behavior, which may complicate matters for low-income families struggling with disparate health risks relating to nutrition and chronic disease. We investigated the relationship between the amount and type of tobacco advertisements on tobacco outlets and the outlet type and location. Methods By using field visits and online images, we inspected all licensed tobacco retail outlets in Philadelphia (N = 4,639). Point pattern analyses were used to identify significant clustering of tobacco outlets and outlets with exterior tobacco advertisements. Logistic regression was used to analyze the relationship between the outlet’s acceptance of Supplemental Nutrition Assistance Program (SNAP) and Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) and the presence of tobacco advertisements. Results Tobacco outlets with exterior tobacco advertisements were significantly clustered in several high-poverty areas. Controlling for racial/ethnic and income composition and land use, SNAP and WIC vendors were significantly more likely to have exterior (SNAP odds ratio [OR], 2.11; WIC OR, 1.59) and interior (SNAP OR, 3.43; WIC OR, 1.69) tobacco advertisements than other types of tobacco outlets. Conclusion Tobacco advertising is widespread at retail outlets, particularly in low-income and racial/ethnic minority neighborhoods. Policy makers may be able to mitigate the effects of this disparate exposure through tobacco retail licensing, local sign control rules, and SNAP and WIC authorization. PMID:25654220

In Situ Blotting : A Novel Method for Direct Transfer of Native Proteins from Sectioned Tissue to Blotting Membrane

NARCIS (Netherlands)

Okabe, Masashi; Nyakas, Csaba; Buwalda, Bauke; Luiten, Paul G.M.

1993-01-01

We describe a novel technique for direct transfer of native proteins from unfixed frozen tissue sections to an immobilizing matrix, e.g., nitrocellulose, polyvinyliden difluoride, or positively charged nylon membranes. Proteins are directly blotted onto the membrane, providing optimal accessibility

Growth In SNAP Retailers Was Associated With Increased Client Enrollment In Georgia During The Great Recession.

Science.gov (United States)

Shannon, Jerry; Shannon, Sarah; Adams, Grace Bagwell; Lee, Jung Sun

2016-11-01

Policies to improve food accessibility in underserved areas often use direct financial incentives to attract new food retailers. Our analysis of data on the Supplemental Nutrition Assistance Program (SNAP) in Georgia before and after the Great Recession suggests that increased program enrollment improves access to food for SNAP beneficiaries by acting as an indirect subsidy to retailers. We divided food stores into four categories: large, midsize, small, and specialty retailers. Between 2008 and 2011 the number of SNAP enrollees increased by 87 percent, and between 2007 and 2014 the number of SNAP retailers in Georgia increased by 82 percent, primarily because of growth in the number of authorized small retailers. Inside metropolitan Atlanta, changes in the numbers of SNAP enrollees and authorized retailers were positively and significantly associated for small retailers. For the areas outside of metropolitan Atlanta, the association between changes in numbers of enrollees and authorized retailers was strongest for small retailers; more modest associations were also seen for large and specialty retailers. Policy makers should consider how retailers' sensitivity to and reliance on SNAP funding can be leveraged to improve not only food availability, but also access to healthy foods. Project HOPE—The People-to-People Health Foundation, Inc.

Biologically Complex Planar Cell Plasma Membranes Supported on Polyelectrolyte Cushions Enhance Transmembrane Protein Mobility and Retain Native Orientation.

Science.gov (United States)

Liu, Han-Yuan; Chen, Wei-Liang; Ober, Christopher K; Daniel, Susan

2018-01-23

Reconstituted supported lipid bilayers (SLB) are widely used as in vitro cell-surface models because they are compatible with a variety of surface-based analytical techniques. However, one of the challenges of using SLBs as a model of the cell surface is the limited complexity in membrane composition, including the incorporation of transmembrane proteins and lipid diversity that may impact the activity of those proteins. Additionally, it is challenging to preserve the transmembrane protein native orientation, function, and mobility in SLBs. Here, we leverage the interaction between cell plasma membrane vesicles and polyelectrolyte brushes to create planar bilayers from cell plasma membrane vesicles that have budded from the cell surface. This approach promotes the direct incorporation of membrane proteins and other species into the planar bilayer without using detergent or reconstitution and preserves membrane constituents. Furthermore, the structure of the polyelectrolyte brush serves as a cushion between the planar bilayer and rigid supporting surface, limiting the interaction of the cytosolic domains of membrane proteins with this surface. Single particle tracking was used to analyze the motion of GPI-linked yellow fluorescent proteins (GPI-YFP) and neon-green fused transmembrane P2X2 receptors (P2X2-neon) and shows that this platform retains over 75% mobility of multipass transmembrane proteins in its native membrane environment. An enzyme accessibility assay confirmed that the protein orientation is preserved and results in the extracellular domain facing toward the bulk phase and the cytosolic side facing the support. Because the platform presented here retains the complexity of the cell plasma membrane and preserves protein orientation and mobility, it is a better representative mimic of native cell surfaces, which may find many applications in biological assays aimed at understanding cell membrane phenomena.

78 FR 12245 - Supplemental Nutrition Assistance Program: Suspension of SNAP Benefit Payments to Retailers

Science.gov (United States)

2013-02-22

..., national origin, gender, age, disability, marital or family status. Regulations at 7 CFR 272.6.... Discrimination in any aspect of the program administration is prohibited by these regulations, according to the... SNAP benefits at the location, store inventory, and the SNAP history of the store owners. For example...

A meniscus causing painful snapping of the elbow joint: MR imaging with arthroscopic and histologic correlation

Energy Technology Data Exchange (ETDEWEB)

Huang, Guo-Shu; Chen, Cheng-Yu [National Defense Medical Center, Department of Radiology, Tri-Service General Hospital, Taipei (Taiwan); Lee, Chian-Her [National Defense Medical Center, Department of Orthopedic Surgery, Tri-Service General Hospital, Taipei (Taiwan); Lee, Herng-Sheng [National Defense Medical Center, Department of Pathology, Tri-Service General Hospital, Taipei (Taiwan)

2005-12-01

Snapping of the elbow joint can cause pain. We report a case of painful snapping elbow produced by an interposed meniscus in the radiohumeral joint in a 20-year-old man. The MR arthrogram demonstrated a meniscus-like tissue interposed between the radial head and humeral capitellum. The MR-arthrographic findings were well correlated with surgical findings. The location and appearance of the meniscus-like tissue was similar to that of meniscus in the knee joint. Histologic findings of the excised meniscus-like tissue showed a typical presentation of fibrocartilage. A meniscus may exist in the elbow joint and can be a rare cause of painful snapping elbow. MR arthrography is helpful for identifying the snapping tissue in the elbow joint. (orig.)

The 'Snap Vote' of 462/1 BCE

DEFF Research Database (Denmark)

Thomsen, Christian Ammitzbøll

2014-01-01

still holds that the absence of 4,000 politically conservative hoplites under the leadership of Kimon paved the way for radical democratic reform - championed by Ephialtes and voted through the Athenian assembly in a ‘snap vote’ by the mass of democratic rowers who remained in the city. This note re...

Distal triceps injuries (including snapping triceps): A systematic review of the literature.

Science.gov (United States)

Shuttlewood, Kimberley; Beazley, James; Smith, Christopher D

2017-06-18

To review current literature on types of distal triceps injury and determine diagnosis and appropriate management. We performed a systematic review in PubMed, Cochrane and EMBASE using the terms distal triceps tears and snapping triceps on the 10 th January 2017. We excluded all animal, review, foreign language and repeat papers. We reviewed all papers for relevance and of the papers left we were able to establish the types of distal triceps injury, how these injuries are diagnosed and investigated and the types of management of these injuries including surgical. The results are then presented in a review paper format. Three hundred and seventy-nine papers were identified of which 65 were relevant to distal triceps injuries. After exclusion we had 47 appropriate papers. The papers highlighted 2 main distal triceps injuries: Distal triceps tears and snapping triceps. Triceps tear are more common in males than females occurring in the 4 th -5 th decade of life and often due to a direct trauma but are also strongly associated with weightlifting and American football. The tears are diagnosed by history and clinically with a palpable gap. Diagnosis can be confirmed with the use of ultrasound (US) and magnetic resonance imaging. Treatment depends on type of tear. Partial tears can be treated conservatively with bracing and physio whereas acute tears need repair either open or arthroscopic using suture anchor or bone tunnel techniques with similar success. Chronic tears often need augmenting with tendon allograft or autograft. Snapping triceps are also seen more in men than women but at a mean age of 32 years. They are characterized by a snapping sensation mostly medially and can be associated with ulna nerve subluxation and ulna nerve symptoms. US is the diagnostic modality of choice due to its dynamic nature and to differentiate between snapping triceps tendon or ulna nerve. Treatment is conservative initially with activity avoidance and if that fails surgical

The sensitivity of graphene “snap-through” to substrate geometry

KAUST Repository

Wagner, Till J. W.

2012-01-01

We study theoretically the deposition of few layer graphene sheets onto a grooved substrate incorporating adhesion between substrate and sheet. We develop a model to understand the equilibrium of the sheet allowing for partial conformation of sheet to substrate. This model gives physical insight into recent observations of snap-through from flat to conforming states and emphasizes the crucial role of substrate shape in determining the nature of this transition. Our analytical results are consistent with numerical simulations using a van der Waals-like interaction. Finally, we propose a substrate shape that should exhibit a continuous, rather than snap-through, transition. © 2012 American Institute of Physics.

Modulation of inflammatory mediators in the trigeminal ganglion by botulinum neurotoxin type A

DEFF Research Database (Denmark)

Edvinsson, Jacob; Warfvinge, Karin; Edvinsson, Lars

2015-01-01

(synaptic vesicle docking protein) or SV2-A (Botulinum toxin receptor element). RESULTS: We report that CGRP, iNOS, IL-1β, SNAP-25 and SV2-A were observed in fresh TG with a differential distribution. Interestingly, NaCl organ culture of the TG resulted in enhanced expression of CGRP and SNAP-25 in neurons...

Native chemical ligation at Asx-Cys, Glx-Cys: chemical synthesis and high-resolution X-ray structure of ShK toxin by racemic protein crystallography.

Science.gov (United States)

Dang, Bobo; Kubota, Tomoya; Mandal, Kalyaneswar; Bezanilla, Francisco; Kent, Stephen B H

2013-08-14

We have re-examined the utility of native chemical ligation at -Gln/Glu-Cys- [Glx-Cys] and -Asn/Asp-Cys- [Asx-Cys] sites. Using the improved thioaryl catalyst 4-mercaptophenylacetic acid (MPAA), native chemical ligation could be performed at -Gln-Cys- and Asn-Cys- sites without side reactions. After optimization, ligation at a -Glu-Cys- site could also be used as a ligation site, with minimal levels of byproduct formation. However, -Asp-Cys- is not appropriate for use as a site for native chemical ligation because of formation of significant amounts of β-linked byproduct. The feasibility of native chemical ligation at -Gln-Cys- enabled a convergent total chemical synthesis of the enantiomeric forms of the ShK toxin protein molecule. The D-ShK protein molecule was ~50,000-fold less active in blocking the Kv1.3 channel than the L-ShK protein molecule. Racemic protein crystallography was used to obtain high-resolution X-ray diffraction data for ShK toxin. The structure was solved by direct methods and showed significant differences from the previously reported NMR structures in some regions of the ShK protein molecule.

A Simple Snap Oscillator with Coexisting Attractors, Its Time-Delayed Form, Physical Realization, and Communication Designs

Science.gov (United States)

Rajagopal, Karthikeyan; Jafari, Sajad; Akgul, Akif; Karthikeyan, Anitha; Çiçek, Serdar; Shekofteh, Yasser

2018-05-01

In this paper, we report a novel chaotic snap oscillator with one nonlinear function. Dynamic analysis of the system shows the existence of bistability. To study the time delay effects on the proposed snap oscillator, we introduce multiple time delay in the fourth state equation. Investigation of dynamical properties of the time-delayed system shows that the snap oscillator exhibits the same multistable properties as the nondelayed system. The new multistable hyperjerk chaotic system has been tested in chaos shift keying and symmetric choc shift keying modulated communication designs for engineering applications. It has been determined that the symmetric chaos shift keying modulated communication system implemented with the new chaotic system is more successful than the chaos shift keying modulation for secure communication. Also, circuit implementation of the chaotic snap oscillator with tangent function is carried out showing its feasibility.

Botulinum toxin's axonal transport from periphery to the spinal cord.

Science.gov (United States)

Matak, Ivica; Riederer, Peter; Lacković, Zdravko

2012-07-01

Axonal transport of enzymatically active botulinum toxin A (BTX-A) from periphery to the CNS has been described in facial and trigeminal nerve, leading to cleavage of synaptosomal-associated protein 25 (SNAP-25) in central nuclei. Aim of present study was to examine the existence of axonal transport of peripherally applied BTX-A to spinal cord via sciatic nerve. We employed BTX-A-cleaved SNAP-25 immunohistochemistry of lumbar spinal cord after intramuscular and subcutaneous hind limb injections, and intraneural BTX-A sciatic nerve injections. Truncated SNAP-25 in ipsilateral spinal cord ventral horns and dorsal horns appeared after single peripheral BTX-A administrations, even at low intramuscular dose applied (5 U/kg). Cleaved SNAP-25 appearance in the spinal cord after BTX-A injection into the sciatic nerve was prevented by proximal intrasciatic injection of colchicine (5 mM, 2 μl). Cleaved SNAP-25 in ventral horn, using choline-acetyltransferase (ChAT) double labeling, was localized within cholinergic neurons. These results extend the recent findings on BTX-A retrograde axonal transport in facial and trigeminal nerve. Appearance of truncated SNAP-25 in spinal cord following low-dose peripheral BTX-A suggest that the axonal transport of BTX-A occurs commonly following peripheral application. Copyright © 2012 Elsevier Ltd. All rights reserved.

Native protein excited by low doses of γ-radiation serves as a source of secondary biogenic radiation

International Nuclear Information System (INIS)

Kuzin, A.M.; Surkenova, G.N.; Revin, A.F.

1996-01-01

In is demonstrated that native protein of egg-white after being γ-irradiated with law doses is able to stimulate transition of cells of remote biological detector from non-cycling state to proliferation even if irradiated protein is separated from detector by quartz-glass. Animal tissues which have a high protein content (freshly cut hair, insect bodies) reveal the same ability. The role of natural background radiation in the maintenance excitation, state of living tissue proteins is discussed. 13 refs.; 1 figs.; 4 tabs

Revealing Abrupt and Spontaneous Ruptures of Protein Native Structure under picoNewton Compressive Force Manipulation.

Science.gov (United States)

Chowdhury, S Roy; Cao, Jin; He, Yufan; Lu, H Peter

2018-03-27

Manipulating protein conformations for exploring protein structure-function relationship has shown great promise. Although protein conformational changes under pulling force manipulation have been extensively studied, protein conformation changes under a compressive force have not been explored quantitatively. The latter is even more biologically significant and relevant in revealing protein functions in living cells associated with protein crowdedness, distribution fluctuations, and cell osmotic stress. Here we report our experimental observations on abrupt ruptures of protein native structures under compressive force, demonstrated and studied by single-molecule AFM-FRET spectroscopic nanoscopy. Our results show that the protein ruptures are abrupt and spontaneous events occurred when the compressive force reaches a threshold of 12-75 pN, a force amplitude accessible from thermal fluctuations in a living cell. The abrupt ruptures are sensitive to local environment, likely a general and important pathway of protein unfolding in living cells.

The snap-back effect of an RC-IGBT and its simulations

International Nuclear Information System (INIS)

Zhang Wenliang; Tian Xiaoli; Zhu Yangjun; Tan Jingfei

2013-01-01

The RC-IGBT (reverse conducting insulated gate bipolar transistor) is a new kind of power semiconductor device which has many advantages such as smaller chip size, higher power density, lower manufacturing cost, softer turn off behavior, and better reliability. However, its performance has a number of drawbacks, such as the snap-back effect. In this paper, an introduction about the snap-back effect of the RC-IGBT is given firstly. Then the physical explanations are presented with two simplified models. After that, some numerical simulations are carried out to verify the correctness of the models. (semiconductor devices)

A Brief Description of the Kokkos implementation of the SNAP potential in ExaMiniMD.

Energy Technology Data Exchange (ETDEWEB)

Thompson, Aidan P. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Trott, Christian Robert [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2017-11-01

Within the EXAALT project, the SNAP [1] approach is being used to develop high accuracy potentials for use in large-scale long-time molecular dynamics simulations of materials behavior. In particular, we have developed a new SNAP potential that is suitable for describing the interplay between helium atoms and vacancies in high-temperature tungsten[2]. This model is now being used to study plasma-surface interactions in nuclear fusion reactors for energy production. The high-accuracy of SNAP potentials comes at the price of increased computational cost per atom and increased computational complexity. The increased cost is mitigated by improvements in strong scaling that can be achieved using advanced algorithms [3].

Protein Domain Analysis of C. botulinum Type A Neurotoxin and Its Relationship with Other Botulinum Serotypes

OpenAIRE

Sharma, Shashi K.; Basavanna, Uma; Shukla, Hem D.

2009-01-01

Botulinum neurotoxins (BoNTs) are highly potent poisons produced by seven serotypes of Clostridium botulinum. The mechanism of neurotoxin action is a multistep process which leads to the cleavage of one of three different SNARE proteins essential for synaptic vesicle fusion and transmission of the nerve signals to muscles: synaptobrevin, syntaxin, or SNAP-25. In order to understand the precise mechanism of neurotoxin in a host, the domain structure of the neurotoxin was analyzed among differe...

SNAP Satellite Focal Plane Development

International Nuclear Information System (INIS)

Bebek, C.; Akerlof, C.; Aldering, G.; Amanullah, R.; Astier, P.; Baltay, C.; Barrelet, E.; Basa, S.; Bercovitz, J.; Bergstrom, L.; Berstein, G.P.; Bester, M.; Bohlin, R.; Bonissent, A.; Bower, C.; Campbell, M.; Carithers, W.; Commins, E.; Day, C.; Deustua, S.; DiGennaro, R.; Ealet, A.; Ellis, R.; Emmett, W.; Eriksson, M.; Fouchez, D.; Fruchter, A.; Genat, J-F.; Goldhaber, G.; Goobar, A.; Groom, D.; Heetderks, H.; Holland, S.; Huterer, D.; Johnson, W.; Kadel, R.; Karcher, A.; Kim, A.; Kolbe, W.; Lafever, R.; Lamoureaux, J.; Lampton, M.; Lefevre, O.; Levi, M.; Levin, D.; Linder, E.; Loken, S.; Malina, R.; Mazure, A.; McKay, T.; McKee, S.; Miquel, R.; Morgan, N.; Mortsell, E.; Mostek, N.; Mufson, S.; Musser, J.; Roe, N.; Nugent, P.; Oluseyi, H.; Pain, R.; Palaio, N.; Pankow, D.; Perlmutter, S.; Prieto, E.; Rabinowitz, D.; Refregier, A.; Rhodes, J.; Schubnell, M.; Sholl, M.; Smadja, G.; Smith, R.; Smoot, G.; Snyder, J.; Spadafora, A.; Szymkowiak, A.; Tarle, G.; Taylor, K.; Tilquin, A.; Tomasch, A.; Vincent, D.; von der Lippe, H.; Walder, J-P.; Wang, G.

2003-01-01

The proposed SuperNova/Acceleration Probe (SNAP) mission will have a two-meter class telescope delivering diffraction-limited images to an instrumented 0.7 square degree field in the visible and near-infrared wavelength regime. The requirements for the instrument suite and the present configuration of the focal plane concept are presented. A two year R and D phase, largely supported by the Department of Energy, is just beginning. We describe the development activities that are taking place to advance our preparedness for mission proposal in the areas of detectors and electronics

The Schedule for Nonadaptive and Adaptive Personality for Youth (SNAP-Y): a new measure for assessing adolescent personality and personality pathology.

Science.gov (United States)

Linde, Jennifer A; Stringer, Deborah; Simms, Leonard J; Clark, Lee Anna

2013-08-01

The Schedule for Nonadaptive and Adaptive Personality-Youth Version (SNAP-Y) is a new, reliable self-report questionnaire that assesses 15 personality traits relevant to both normal-range personality and the alternative DSM-5 model for personality disorder. Community adolescents, 12 to 18 years old (N = 364), completed the SNAP-Y; 347 also completed the Big Five Inventory-Adolescent, 144 provided 2-week retest data, and 128 others completed the Minnesota Multiphasic Personality Inventory-Adolescent. Outpatient adolescents (N = 103) completed the SNAP-Y, and 97 also completed the Minnesota Multiphasic Personality Inventory-Adolescent. The SNAP-Y demonstrated strong psychometric properties, and structural, convergent, discriminant, and external validities. Consistent with the continuity of personality, results paralleled those in adult and college samples using the adult Schedule for Nonadaptive and Adaptive Personality-Second Edition (SNAP-2), from which the SNAP-Y derives and which has established validity in personality-trait assessment across the normal-abnormal continuum. The SNAP-Y thus provides a new, clinically useful instrument to assess personality traits and personality pathology in adolescents.

Identification of unknown protein complex members by radiolocalization and analysis of low-abundance complexes resolved using native polyacrylamide gel electrophoresis.

Science.gov (United States)

Bose, Mahuya; Adams, Brian P; Whittal, Randy M; Bose, Himangshu S

2008-02-01

Identification of unknown binding partners of a protein of interest can be a difficult process. Current strategies to determine protein binding partners result in a high amount of false-positives, requiring use of several different methods to confirm the accuracy of the apparent association. We have developed and utilized a method that is reliable and easily substantiated. Complexes are isolated from cell extract after exposure to the radiolabeled protein of interest, followed by resolution on a native polyacrylamide gel. Native conformations are preserved, allowing the complex members to maintain associations. By radiolabeling the protein of interest, the complex can be easily identified at detection levels below the threshold of Serva Blue, Coomassie, and silver stains. The visualized radioactive band is analyzed by MS to identify binding partners, which can be subsequently verified by antibody shift and immunoprecipitation of the complex. By using this method we have successfully identified binding partners of two proteins that reside in different locations of a cellular organelle.

Combinations of SPR and MS for Characterizations of Native and Recombinant Proteins in Cell Lysates

DEFF Research Database (Denmark)

Borch, Jonas; Roepstorff, Peter

2006-01-01

Surface plasmon resonance and mass spectrometry (SPR-MS) has been combined for quality check of recombinant 6xHis-tagged 14-3-3 proteins expressed in Escherichia coli. Lysates were injected over an SPR sensorchip with immobilized Ni2+ for SPR analysis of the specific Ni2+ binding response...... and stability. To validate the identity, intactness and homogeneity of the captured proteins were eluted for mass spectrometric analysis of intact molecular weight and peptide mass mapping. Additionally, the captured recombinant proteins were investigated for specific binding to known phosphorylated ligands...... of 14-3-3 proteins in order to test their activity. Specific binding of recombinant and native 14-3-3 proteins in complex mixtures to immobilized phosphopeptides and subsequent elution was also tested by SPR-MS. Ammonium sulfate precipitate fractions from lysates of E. coli expressing 14-3-3 protein...

Measuring the Effect of Supplemental Nutrition Assistance Program (SNAP) Participation on Food Security.

OpenAIRE

James Mabli; Jim Ohls; Lisa Dragoset; Laura Castner; Betsy Santos

2013-01-01

The Supplemental Nutrition Assistance Program (SNAP) provides food assistance to more than 47 million low-income Americans every month. It aims to reduce hunger by facilitating beneficiaries’ access to enough food for a healthy, active lifestyle, otherwise known as "food security." Our study conducted for the Food and Nutrition Service of the U.S. Department of Agriculture shows that SNAP participation is associated with improved food security. The study is the largest and most rigorous one...

Immobilised native plant cysteine proteases: packed-bed reactor for white wine protein stabilisation

OpenAIRE

Benucci, Ilaria; Lombardelli, Claudio; Liburdi, Katia; Acciaro, Giuseppe; Zappino, Matteo; Esti, Marco

2015-01-01

This research presents a feasibility study of using a continuous packed-bed reactor (PBR), containing immobilised native plant cysteine proteases, as a specific and mild alternative technique relative to the usual bentonite fining for white wine protein stabilisation. The operational parameters for a PBR containing immobilised bromelain (PBR-br) or immobilised papain (PBR-pa) were optimised using model wine fortified with synthetic substrate (Bz-Phe-Val-Arg-pNA). The effectiveness of PBR-br, ...

Soluble Non-ammonia Nitrogen in Ruminal and Omasal Digesta of Korean Native Steers Supplemented with Soluble Proteins

Directory of Open Access Journals (Sweden)

C. W. Choi

2012-09-01

Full Text Available An experiment was conducted to study the effect of soluble protein supplements on concentration of soluble non-ammonia nitrogen (SNAN in the liquid phase of ruminal (RD and omasal digesta (OD of Korean native steers, and to investigate diurnal pattern in SNAN concentration in RD and OD. Three ruminally cannulated Korean native steers in a 3×3 Latin square design consumed a basal diet of rice straw and corn-based concentrate (control, and that supplemented (kg/d DM basis with intact casein (0.24; IC or acid hydrolyzed casein (0.46; AHC. Ruminal digesta was sampled using a vacuum pump, whereas OD was collected using an omasal sampling system at 2.0 h intervals after a morning feeding. The SNAN fractions (free amino acid (AA, peptide and soluble protein in RD and OD were assessed using the ninhydrin assay. Concentrations of free AA and total SNAN in RD were significantly (p<0.05 lower than those in OD. Although free AA concentration was relatively high, mean peptide was quantitatively the most important fraction of total SNAN in both RD and OD, indicating that degradation of peptide to AA rather than hydrolysis of soluble protein to peptide or deamination may be the most limiting step in rumen proteolysis of Korean native steers. Diurnal variation in peptide concentration in OD for the soluble protein supplemented diets during the feeding cycle peaked 2 h post-feeding and decreased thereafter whereas that for the control was relatively constant during the entire feeding cycle. Diurnal variation in peptide concentration was rather similar between RD and OD.

Polycyclic aromatic hydrocarbons affect survival and development of common snapping turtle (Chelydra serpentina) embryos and hatchlings

Energy Technology Data Exchange (ETDEWEB)

Van Meter, Robin J [School of Environmental Science, Engineering, and Policy and Department of Bioscience and Biotechnology, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104 (United States); Spotila, James R [School of Environmental Science, Engineering, and Policy and Department of Bioscience and Biotechnology, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104 (United States); Avery, Harold W [School of Environmental Science, Engineering, and Policy and Department of Bioscience and Biotechnology, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104 (United States)

2006-08-15

Polycyclic aromatic hydrocarbons (PAHs) are toxic compounds found in the John Heinz National Wildlife Refuge in Philadelphia, Pennsylvania. We assessed the impact of PAHs and crude oil on snapping turtle development and behavior by exposing snapping turtle eggs from the Refuge and from three clean reference sites to individual PAHs or a crude oil mixture at stage 9 of embryonic development. Exposure to PAHs had a significant effect on survival rates in embryos from one clean reference site, but not in embryos from the other sites. There was a positive linear relationship between level of exposure to PAHs and severity of deformities in embryos collected from two of the clean reference sites. Neither righting response nor upper temperature tolerance (critical thermal maximum, CTM) of snapping turtle hatchlings with no or minor deformities was significantly affected by exposure to PAHs. - Exposure to polycyclic aromatic hydrocarbons on the egg reduces survival of snapping turtle embryos and causes developmental abnormalities.

Polycyclic aromatic hydrocarbons affect survival and development of common snapping turtle (Chelydra serpentina) embryos and hatchlings

International Nuclear Information System (INIS)

Van Meter, Robin J.; Spotila, James R.; Avery, Harold W.

2006-01-01

Polycyclic aromatic hydrocarbons (PAHs) are toxic compounds found in the John Heinz National Wildlife Refuge in Philadelphia, Pennsylvania. We assessed the impact of PAHs and crude oil on snapping turtle development and behavior by exposing snapping turtle eggs from the Refuge and from three clean reference sites to individual PAHs or a crude oil mixture at stage 9 of embryonic development. Exposure to PAHs had a significant effect on survival rates in embryos from one clean reference site, but not in embryos from the other sites. There was a positive linear relationship between level of exposure to PAHs and severity of deformities in embryos collected from two of the clean reference sites. Neither righting response nor upper temperature tolerance (critical thermal maximum, CTM) of snapping turtle hatchlings with no or minor deformities was significantly affected by exposure to PAHs. - Exposure to polycyclic aromatic hydrocarbons on the egg reduces survival of snapping turtle embryos and causes developmental abnormalities

Native Mass Spectrometry in Fragment-Based Drug Discovery.

Science.gov (United States)

Pedro, Liliana; Quinn, Ronald J

2016-07-28

The advent of native mass spectrometry (MS) in 1990 led to the development of new mass spectrometry instrumentation and methodologies for the analysis of noncovalent protein-ligand complexes. Native MS has matured to become a fast, simple, highly sensitive and automatable technique with well-established utility for fragment-based drug discovery (FBDD). Native MS has the capability to directly detect weak ligand binding to proteins, to determine stoichiometry, relative or absolute binding affinities and specificities. Native MS can be used to delineate ligand-binding sites, to elucidate mechanisms of cooperativity and to study the thermodynamics of binding. This review highlights key attributes of native MS for FBDD campaigns.

Application of native agarose gel electrophoresis of serum proteins in veterinary diagnostics

Directory of Open Access Journals (Sweden)

Jania Bartosz

2016-12-01

Full Text Available Electrophoretic techniques, used to separate mixtures of electrically charged particles, are widely used in science. One of these techniques, native protein electrophoresis in an agarose gel, is applied in human and veterinary medicine. Changes in the proportions of individual protein fractions correspond to significant changes in the physiology of the body. Although the pattern obtained by electrophoretic separation rarely indicates a specific disease, it provides valuable information for the differential diagnosis. Decades of research on the types of patterns obtained in the case of particular diseases have led to the accumulation of substantial knowledge. The paper presents the available information on this topic. Serum protein electrophoresis is recommended in cases of increased levels of total protein in order to reveal the nature of the process. The basic information which can be obtained from electrophoretic separation includes the immune status of the organism. Both increased antigenic stimulation and immunodeficiency are clearly visible in electropherograms. Moreover, the level of heterogeneity of the corresponding protein fractions can help to distinguish between infectious diseases and cancer - multiple myeloma - the latter producing a homogeneous immunoglobulin fraction. Analysis of other protein fractions helps to detect or confirm an ongoing inflammatory process and provides information regarding liver function. Even when the concentration of total protein is within the reference range, this analysis can be recommended as a basic laboratory test.

Optimization of photoactive protein Z for fast and efficient site-specific conjugation of native IgG.

Science.gov (United States)

Hui, James Z; Tsourkas, Andrew

2014-09-17

Antibody conjugates have been used in a variety of applications from immunoassays to drug conjugates. However, it is becoming increasingly clear that in order to maximize an antibody's antigen binding ability and to produce homogeneous antibody-conjugates, the conjugated molecule should be attached onto IgG site-specifically. We previously developed a facile method for the site-specific modification of full length, native IgGs by engineering a recombinant Protein Z that forms a covalent link to the Fc domain of IgG upon exposure to long wavelength UV light. To further improve the efficiency of Protein Z production and IgG conjugation, we constructed a panel of 13 different Protein Z variants with the UV-active amino acid benzoylphenylalanine (BPA) in different locations. By using this panel of Protein Z to cross-link a range of IgGs from different hosts, including human, mouse, and rat, we discovered two previously unknown Protein Z variants, L17BPA and K35BPA, that are capable of cross-linking many commonly used IgG isotypes with efficiencies ranging from 60% to 95% after only 1 h of UV exposure. When compared to existing site-specific methods, which often require cloning or enzymatic reactions, the Protein Z-based method described here, utilizing the L17BPA, K35BPA, and the previously described Q32BPA variants, represents a vastly more accessible and efficient approach that is compatible with nearly all native IgGs, thus making site-specific conjugation more accessible to the general research community.

Reconceiving SNAP: Is Nutritional Assistance Really Income Support?

Science.gov (United States)

Besharov, Douglas J.

2016-01-01

Since its creation, the Supplemental Nutrition Assistance Program (SNAP) has changed from an antihunger program to an income-supplementation program. Because the program (and its predecessor Food Stamp Program) was not designed for this purpose, the result is a program that has many unintended and, many believe, negative effects. The key challenge…

Molecular Investigation of the Stem Snap Point in Textile Hemp

Directory of Open Access Journals (Sweden)

Marc Behr

2017-12-01

Full Text Available Fibre crops are important natural resources, as they sustainably provide bast fibres, an economically-valuable raw material used in the textile and biocomposite sectors. Among fibre crops, textile hemp (Cannabis sativa L. is appreciated for its long and strong gelatinous bast fibres. The stem of fibre crops is a useful system for cell wall-oriented studies, because it shows a strong tissue polarity with a lignified inner core and a cellulosic hypolignified cortex, as well as a basipetal lignification gradient. Along the stem axis of fibre crops, a specific region, denoted snap point, marks the transition from elongation (above it to fibre thickening (below it. After empirically determining the snap point by tilting the plant, we divided the stem segment containing it into three non-overlapping consecutive regions measuring 1 cm each, and carried out targeted RT-qPCR on cell wall-related genes separately, in outer and inner tissues. Different gene clusters can be observed, two of which are the major gene groups, i.e., one group with members expressed at higher levels in the inner tissues, and one group whose genes are more expressed in the cortex. The present results provide a molecular validation that the snap point is characterised by a gradient of events associated with the shift from fibre elongation to thickening.

Native proteomic analysis of protein complexes in murine intestinal brush border membranes

Czech Academy of Sciences Publication Activity Database

Babušiak, M.; Man, Petr; Petrák, J.; Vyoral, D.

2007-01-01

Roč. 7, č. 1 (2007), s. 121-129 ISSN 1615-9853 R&D Projects: GA ČR(CZ) GD204/03/H066; GA AV ČR KJB500200612; GA MŠk LC545 Grant - others:GA ČR(CZ) GA303/04/0003; GA MZd(CZ) NR8930; GA MŠk(CZ) LC06044; CZ(CZ) 023736; GA MZd(CZ) NR8317 Program:NR Institutional research plan: CEZ:AV0Z50200510 Keywords : blue native electrophoresis * brush border membranes * protein complexes Subject RIV: EE - Microbiology, Virology Impact factor: 5.479, year: 2007

Calcium Regulates Molecular Interactions of Otoferlin with Soluble NSF Attachment Protein Receptor (SNARE) Proteins Required for Hair Cell Exocytosis*

Science.gov (United States)

Ramakrishnan, Neeliyath A.; Drescher, Marian J.; Morley, Barbara J.; Kelley, Philip M.; Drescher, Dennis G.

2014-01-01

Mutations in otoferlin, a C2 domain-containing ferlin family protein, cause non-syndromic hearing loss in humans (DFNB9 deafness). Furthermore, transmitter secretion of cochlear inner hair cells is compromised in mice lacking otoferlin. In the present study, we show that the C2F domain of otoferlin directly binds calcium (KD = 267 μm) with diminished binding in a pachanga (D1767G) C2F mouse mutation. Calcium was found to differentially regulate binding of otoferlin C2 domains to target SNARE (t-SNARE) proteins and phospholipids. C2D–F domains interact with the syntaxin-1 t-SNARE motif with maximum binding within the range of 20–50 μm Ca2+. At 20 μm Ca2+, the dissociation rate was substantially lower, indicating increased binding (KD = ∼10−9) compared with 0 μm Ca2+ (KD = ∼10−8), suggesting a calcium-mediated stabilization of the C2 domain·t-SNARE complex. C2A and C2B interactions with t-SNAREs were insensitive to calcium. The C2F domain directly binds the t-SNARE SNAP-25 maximally at 100 μm and with reduction at 0 μm Ca2+, a pattern repeated for C2F domain interactions with phosphatidylinositol 4,5-bisphosphate. In contrast, C2F did not bind the vesicle SNARE protein synaptobrevin-1 (VAMP-1). Moreover, an antibody targeting otoferlin immunoprecipitated syntaxin-1 and SNAP-25 but not synaptobrevin-1. As opposed to an increase in binding with increased calcium, interactions between otoferlin C2F domain and intramolecular C2 domains occurred in the absence of calcium, consistent with intra-C2 domain interactions forming a “closed” tertiary structure at low calcium that “opens” as calcium increases. These results suggest a direct role for otoferlin in exocytosis and modulation of calcium-dependent membrane fusion. PMID:24478316

multiple disease resistance in snap bean genotypes in kenya

African Journals Online (AJOL)

Prof. Adipala Ekwamu

Department of Plant Science and Crop Protection, University of Nairobi, P. O. Box 29053- ... Agriculture (CIAT), National Agricultural Research Laboratories Institute, ... Climbing snap bean lines had thick pods that could reduce pod quality. ... MATERIALS AND METHODS ... were harvested in sterile distilled water and spore.

Protein Profile in Corpus Luteum during Pregnancy in Korean Native Cows

Directory of Open Access Journals (Sweden)

H. J. Chung

2012-11-01

Full Text Available Steroidogenesis requires coordination of the anabolic and catabolic pathways of lipid metabolism, but the profile of proteins associated with progesterone synthesis in cyclic and pregnant corpus luteum (CL is not well-known in cattle. In Experiment 1, plasma progesterone level was monitored in cyclic cows (n = 5 and pregnant cows (n = 6; until d-90. A significant decline in the plasma progesterone level occurred at d-19 of cyclic cows. Progesterone level in abbatoir-derived luteal tissues was also determined at d 1 to 5, 6 to 13 and 14 to 20 of cyclic cows, and d-60 and -90 of pregnant cows (n = 5 each. Progesterone level in d-60 CL was not different from those in d 6 to 13 CL and d-90 CL, although the difference between d 6 to 13 and d-90 was significant. In Experiment 2, protein expression pattern in CL at d-90 (n = 4 was compared with that in CL of cyclic cows at d 6 to 13 (n = 5. Significant changes in the level of protein expression were detected in 32 protein spots by two-dimensional polyacrylamide gel electrophoresis (2-DE, and 23 of them were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS. Six proteins were found only in pregnant CL, while the other 17 proteins were found only in cyclic CL. Among the above 6 proteins, vimentin which is involved in the regulation of post-implantation development was included. Thus, the protein expression pattern in CL was disorientated from cyclic luteal phase to mid pregnancy, and alterations in specific CL protein expression may contribute to the maintenance of pregnancy in Korean native cows.

INSITU BLOTTING - A NOVEL METHOD FOR DIRECT TRANSFER OF NATIVE PROTEINS FROM SECTIONED TISSUE TO BLOTTING MEMBRANE - PROCEDURE AND SOME APPLICATIONS

NARCIS (Netherlands)

OKABE, M; NYAKAS, C; BUWALDA, B; LUITEN, PGM

We describe a novel technique for direct transfer of native proteins from unfixed frozen tissue sections to an immobilizing matrix, e.g., nitrocellulose, polyvinyliden difluoride, or positively charged nylon membranes. Proteins are directly blotted onto the membrane, providing optimal accessibility

Tuning and switching of band gap of the periodically undulated beam by the snap through buckling

Directory of Open Access Journals (Sweden)

Y. Li

2017-05-01

Full Text Available We propose highly tuning and switching band gaps of phononic crystals through the snap through buckling by investigating wave propagation in a designed tractable undulated beam with single material and periodically arched shape. A series of numerical analyses are conducted to offer a thorough understanding of the evolution of the band gaps as a function of the vertical applied load. We find out that the interesting snap through buckling induced by the vertical load can alter the width of the band gap of the undulated beam dramatically, even switch them on and off. Our researches show an effective strategy to tune the band gaps of phononic crystals through the snap through buckling behavior.

Boundaries of mass resolution in native mass spectrometry.

Science.gov (United States)

Lössl, Philip; Snijder, Joost; Heck, Albert J R

2014-06-01

Over the last two decades, native mass spectrometry (MS) has emerged as a valuable tool to study intact proteins and noncovalent protein complexes. Studied experimental systems range from small-molecule (drug)-protein interactions, to nanomachineries such as the proteasome and ribosome, to even virus assembly. In native MS, ions attain high m/z values, requiring special mass analyzers for their detection. Depending on the particular mass analyzer used, instrumental mass resolution does often decrease at higher m/z but can still be above a couple of thousand at m/z 5000. However, the mass resolving power obtained on charge states of protein complexes in this m/z region is experimentally found to remain well below the inherent instrument resolution of the mass analyzers employed. Here, we inquire into reasons for this discrepancy and ask how native MS would benefit from higher instrumental mass resolution. To answer this question, we discuss advantages and shortcomings of mass analyzers used to study intact biomolecules and biomolecular complexes in their native state, and we review which other factors determine mass resolving power in native MS analyses. Recent examples from the literature are given to illustrate the current status and limitations.

Dynamic and bio-orthogonal protein assembly along a supramolecular polymer

NARCIS (Netherlands)

Petkau - Milroy, K.; Uhlenheuer, D.A.; Spiering, A.J.H.; Vekemans, J.A.J.M.; Brunsveld, L.

2013-01-01

Dynamic protein assembly along supramolecular columnar polymers has been achieved through the site-specific covalent attachment of different SNAP-tag fusion proteins to self-assembled benzylguanine-decorated discotics. The self-assembly of monovalent discotics into supramolecular polymers creates a

The amino acid sequence of snapping turtle (Chelydra serpentina) ribonuclease

NARCIS (Netherlands)

Beintema, Jacob; Broos, Jaap; Meulenberg, Janneke; Schüller, Cornelis

1985-01-01

Snapping turtle (Chelydra serpentina) ribonuclease was isolated from pancreatic tissue. Turtle ribonuclease binds much more weakly to the affinity chromatography matrix used than mammalian ribonucleases. The amino acid sequence was determined from overlapping peptides obtained from three different

SnapShot: Phosphoregulation of Mitosis.

Science.gov (United States)

Burgess, Andrew; Vuong, Jenny; Rogers, Samuel; Malumbres, Marcos; O'Donoghue, Seán I

2017-06-15

During mitosis, a cell divides its duplicated genome into two identical daughter cells. This process must occur without errors to prevent proliferative diseases (e.g., cancer). A key mechanism controlling mitosis is the precise timing of more than 32,000 phosphorylation and dephosphorylation events by a network of kinases and counterbalancing phosphatases. The identity, magnitude, and temporal regulation of these events have emerged recently, largely from advances in mass spectrometry. Here, we show phosphoevents currently believed to be key regulators of mitosis. For an animated version of this SnapShot, please see http://www.cell.com/cell/enhanced/odonoghue2. Copyright © 2017. Published by Elsevier Inc.

Intra-articular lipoma causing snapping in the patellofemoral joint

International Nuclear Information System (INIS)

Yilmaz, E.; Karakurt, L.; Yildirim, H.; Ozercan, R.

2007-01-01

Intra-articular lipoma is an exceedingly rare diagnosis. We identified a lipoma that was seated in the retropatellar are and caused snapping of the patella during flexion of the knee joint. The tumor was easily and totally excised under arthroscopic guidance after the thin pedicle was cut. (author)

Outer Membrane Protein 25 of Brucella Activates Mitogen-Activated Protein Kinase Signal Pathway in Human Trophoblast Cells

Directory of Open Access Journals (Sweden)

Jing Zhang

2017-12-01

Full Text Available Outer membrane protein 25 (OMP25, a virulence factor from Brucella, plays an important role in maintaining the structural stability of Brucella. Mitogen-activated protein kinase (MAPK signal pathway widely exists in eukaryotic cells. In this study, human trophoblast cell line HPT-8 and BALB/c mice were infected with Brucella abortus 2308 strain (S2308 and 2308ΔOmp25 mutant strain. The expression of cytokines and activation of MAPK signal pathway were detected. We found that the expressions of tumor necrosis factor-α, interleukin-1, and interleukin-10 (IL-10 were increased in HPT-8 cells infected with S2308 and 2308ΔOmp25 mutant. S2308 also activated p38 phosphorylation protein, extracellular-regulated protein kinases (ERK, and Jun-N-terminal kinase (JNK from MAPK signal pathway. 2308ΔOmp25 could not activate p38, ERK, and JNK branches. Immunohistochemistry experiments showed that S2308 was able to activate phosphorylation of p38 and ERK in BABL/c mice. However, 2308ΔOmp25 could weakly activate phosphorylation of p38 and ERK. These results suggest that Omp25 played an important role in the process of Brucella activation of the MAPK signal pathway.

cDNA, genomic sequence cloning and overexpression of ribosomal protein S25 gene (RPS25) from the Giant Panda.

Science.gov (United States)

Hao, Yan-Zhe; Hou, Wan-Ru; Hou, Yi-Ling; Du, Yu-Jie; Zhang, Tian; Peng, Zheng-Song

2009-11-01

RPS25 is a component of the 40S small ribosomal subunit encoded by RPS25 gene, which is specific to eukaryotes. Studies in reference to RPS25 gene from animals were handful. The Giant Panda (Ailuropoda melanoleuca), known as a "living fossil", are increasingly concerned by the world community. Studies on RPS25 of the Giant Panda could provide scientific data for inquiring into the hereditary traits of the gene and formulating the protective strategy for the Giant Panda. The cDNA of the RPS25 cloned from Giant Panda is 436 bp in size, containing an open reading frame of 378 bp encoding 125 amino acids. The length of the genomic sequence is 1,992 bp, which was found to possess four exons and three introns. Alignment analysis indicated that the nucleotide sequence of the coding sequence shows a high homology to those of Homo sapiens, Bos taurus, Mus musculus and Rattus norvegicus as determined by Blast analysis, 92.6, 94.4, 89.2 and 91.5%, respectively. Primary structure analysis revealed that the molecular weight of the putative RPS25 protein is 13.7421 kDa with a theoretical pI 10.12. Topology prediction showed there is one N-glycosylation site, one cAMP and cGMP-dependent protein kinase phosphorylation site, two Protein kinase C phosphorylation sites and one Tyrosine kinase phosphorylation site in the RPS25 protein of the Giant Panda. The RPS25 gene was overexpressed in E. coli BL21 and Western Blotting of the RPS25 protein was also done. The results indicated that the RPS25 gene can be really expressed in E. coli and the RPS25 protein fusioned with the N-terminally his-tagged form gave rise to the accumulation of an expected 17.4 kDa polypeptide. The cDNA and the genomic sequence of RPS25 were cloned successfully for the first time from the Giant Panda using RT-PCR technology and Touchdown-PCR, respectively, which were both sequenced and analyzed preliminarily; then the cDNA of the RPS25 gene was overexpressed in E. coli BL21 and immunoblotted, which is the first

Immobilised native plant cysteine proteases: packed-bed reactor for white wine protein stabilisation.

Science.gov (United States)

Benucci, Ilaria; Lombardelli, Claudio; Liburdi, Katia; Acciaro, Giuseppe; Zappino, Matteo; Esti, Marco

2016-02-01

This research presents a feasibility study of using a continuous packed-bed reactor (PBR), containing immobilised native plant cysteine proteases, as a specific and mild alternative technique relative to the usual bentonite fining for white wine protein stabilisation. The operational parameters for a PBR containing immobilised bromelain (PBR-br) or immobilised papain (PBR-pa) were optimised using model wine fortified with synthetic substrate (Bz-Phe-Val-Arg-pNA). The effectiveness of PBR-br, both in terms of hazing potential and total protein decrease, was significantly higher than PBR-pa, in all the seven unfined, white wines used. Among the wines tested, Sauvignon Blanc, given its total protein content as well as its very high intrinsic instability, was selected as a control wine to evaluate the effect of the treatment on wine as to its soluble protein profile, phenolic composition, mineral component, and sensory properties. The treatment in a PBR containing immobilised bromelain appeared effective in decreasing both wine hazing potential and total protein amount, while it did not significantly affect the phenol compounds, the mineral component nor the sensory quality of wine. The enzymatic treatment in PBR was shown to be a specific and mild technique for use as an alternative to bentonite fining for white wine protein stabilisation.

In Situ Cyclization of Native Proteins: Structure-Based Design of a Bicyclic Enzyme.

Science.gov (United States)

Pelay-Gimeno, Marta; Bange, Tanja; Hennig, Sven; Grossmann, Tom N

2018-05-30

Increased tolerance of enzymes towards thermal and chemical stress is required for many applications and can be achieved by macrocyclization of the enzyme resulting in the stabilizing of its tertiary structure. So far, macrocyclization approaches utilize a very limited structural diversity which complicates the design process. Here, we report an approach that enables cyclization via the installation of modular crosslinks into native proteins composed entirely of proteinogenic amino acids. Our stabilization procedure involves the introduction of three surface exposed cysteines which are reacted with a triselectrophile resulting in the in situ cylization of the protein (INCYPRO). A bicyclic version of Sortase A was designed exhibiting increased tolerance towards thermal as well as chemical denaturation, and proved efficient in protein labeling under denaturing conditions. In addition, we applied INCYPRO to the KIX domain resulting in up to 24 °C increased thermal stability. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Reflective Polyethylene Mulch Reduces Mexican Bean Beetle (Coleoptera: Coccinellidae) Densities and Damage in Snap Beans.

Science.gov (United States)

Nottingham, L B; Kuhar, T P

2016-08-01

Mexican bean beetle, Epilachna varivestis Mulsant, is a serious pest of snap beans, Phaseolus vulgaris L., in the eastern United States. These beetles are intolerant to direct sunlight, explaining why individuals are typically found on the undersides of leaves and in the lower portion of the plant canopy. We hypothesized that snap beans grown on reflective, agricultural polyethylene (plastic mulch) would have fewer Mexican bean beetles and less injury than those grown on black plastic or bare soil. In 2014 and 2015, beans were seeded into beds of metallized, white, and black plastic, and bare soil, in field plots near Blacksburg, VA. Mexican bean beetle density, feeding injury, predatory arthropods, and snap bean yield were sampled. Reflected light intensity, temperature, and humidity were monitored using data loggers. Pyranometer readings showed that reflected light intensity was highest over metallized plastic and second highest over white plastic; black plastic and bare soil were similarly low. Temperature and humidity were unaffected by treatments. Significant reductions in Mexican bean beetle densities and feeding injury were observed in both metallized and white plastic plots compared to black plastic and bare soil, with metallized plastic having the fewest Mexican bean beetle life stages and injury. Predatory arthropod densities were not reduced by reflective plastic. Metallized plots produced the highest yields, followed by white. The results of this study suggest that growing snap beans on reflective plastic mulch can suppress the incidence and damage of Mexican bean beetle, and increase yield in snap beans. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Snapping scapular syndrome secondary to rib intramedullary fixation device

Directory of Open Access Journals (Sweden)

Ezequiel E. Zaidenberg

2015-01-01

Conclusion: Surgeons should pay attention to any protrusion of intramedullary rib implants, especially in the evaluation of routine X-rays following surgical treatment. We should be aware of the possibility of this rare cause of snapping scapula syndrome to avoid delayed diagnosis and consider removing the implant will resolve the pain.

Study of an integral field spectrograph for the SNAP satellite. Prototype, simulation and performances

International Nuclear Information System (INIS)

Aumeunier, Marie-Helene

2007-01-01

The SNAP (Supernovae/Acceleration Probe) project plans to measure very precisely the cosmological parameters and to determine the nature of dark energy by observations of type Ia supernovae and weak lensing. The SNAP instrument consists in a 2-meter telescope with a one square-degree imager and a spectrograph in the visible and infrared range. A dedicated optimized integral field spectrograph based on an imager slicer technology has been developed. To test and validate the performances, two approaches have been developed: a complete simulation of the complete instrument at the pixel level and the manufacturing and test of a spectrograph prototype operating at room temperature and in cryogenic environment. In this thesis we will test the optical and functional performances of the SNAP spectrograph: especially diffraction losses, stray-light and spectro-photometric calibration. We present an original approach for the spectro-photometric calibration adapted for the slicer and the optical performances resulting from the first measurement campaign in the visible range. (author) [fr

Structural Basis for Substrate Recognition by the Ankyrin Repeat Domain of Human DHHC17 Palmitoyltransferase

Energy Technology Data Exchange (ETDEWEB)

Verardi, Raffaello; Kim, Jin-Sik; Ghirlando, Rodolfo; Banerjee, Anirban

2017-09-01

DHHC enzymes catalyze palmitoylation, a major post-translational modification that regulates a number of key cellular processes. There are up to 24 DHHCs in mammals and hundreds of substrate proteins that get palmitoylated. However, how DHHC enzymes engage with their substrates is still poorly understood. There is currently no structural information about the interaction between any DHHC enzyme and protein substrates. In this study we have investigated the structural and thermodynamic bases of interaction between the ankyrin repeat domain of human DHHC17 (ANK17) and Snap25b. We solved a high-resolution crystal structure of the complex between ANK17 and a peptide fragment of Snap25b. Through structure-guided mutagenesis, we discovered key residues in DHHC17 that are critically important for interaction with Snap25b. We further extended our finding by showing that the same residues are also crucial for the interaction of DHHC17 with Huntingtin, one of its most physiologically relevant substrates.

The Snapping Elbow Syndrome as a Reason for Chronic Elbow Neuralgia in a Tennis Player - MR, US and Sonoelastography Evaluation.

Science.gov (United States)

Łasecki, Mateusz; Olchowy, Cyprian; Pawluś, Aleksander; Zaleska-Dorobisz, Urszula

2014-01-01

Ulnar neuropathy is the second most common peripheral nerve neuropathy after median neuropathy, with an incidence of 25 cases per 100 000 men and 19 cases per 100 000 women each year. Skipping (snapping) elbow syndrome is an uncommon cause of pain in the posterior-medial elbow area, sometimes complicated by injury of the ulnar nerve. One of the reason is the dislocation of the abnormal insertion of the medial triceps head over the medial epicondyle during flexion and extension movements. Others are: lack of the Osboune fascia leading to ulnar nerve instability and focal soft tissue tumors (fibromas, lipomas, etc). Recurrent subluxation of the nerve at the elbow results in a tractional and frictional neuritis with classical symptoms of peripheral neuralgia. As far as we know snapping triceps syndrome had never been evaluated in sonoelastography. A 28yo semi-professional left handed tennis player was complaining about pain in posterior-medial elbow area. Initial US examination suggest golfers elbow syndrome which occurs quite commonly and has a prevalence of 0.3-0.6% in males and 0-3-1.1% in women and may be associated (approx. 50% of cases) with ulnar neuropathy. However subsequently made MRI revealed unusual distal triceps anatomy, moderate ulnar nerve swelling and lack of medial epicondylitis symptoms. Followed (second) US examination and sonoelastography have detected slipping of the both ulnar nerve and the additional band of the medial triceps head. Snapping elbow syndrome is a poorly known medical condition, sometimes misdiagnosed as the medial epicondylitis. It describes a broad range of pathologies and anatomical abnormalities. One of the most often reasons is the slipping of the ulnar nerve as the result of the Osborne fascia/anconeus epitrochlearis muscle absence. Simultaneously presence of two or more "snapping reasons" is rare but should be always taken under consideration. There are no sonoelastography studies describing golfers elbow syndrome

SnapAnatomy, a computer-based interactive tool for independent learning of human anatomy.

Science.gov (United States)

Yip, George W; Rajendran, Kanagasuntheram

2008-06-01

Computer-aided instruction materials are becoming increasing popular in medical education and particularly in the teaching of human anatomy. This paper describes SnapAnatomy, a new interactive program that the authors designed for independent learning of anatomy. SnapAnatomy is primarily tailored for the beginner student to encourage the learning of anatomy by developing a three-dimensional visualization of human structure that is essential to applications in clinical practice and the understanding of function. The program allows the student to take apart and to accurately put together body components in an interactive, self-paced and variable manner to achieve the learning outcome.

SnapShot: Hormones of the gastrointestinal tract.

Science.gov (United States)

Coate, Katie C; Kliewer, Steven A; Mangelsdorf, David J

2014-12-04

Specialized endocrine cells secrete a variety of peptide hormones all along the gastrointestinal (GI) tract, making it one of the largest endocrine organs in the body. Nutrients and developmental and neural cues trigger the secretion of gastrointestinal (GI) hormones from specialized endocrine cells along the GI tract. These hormones act in target tissues to facilitate digestion and regulate energy homeostasis. This SnapShot summarizes the production and functions of GI hormones. Copyright © 2014 Elsevier Inc. All rights reserved.

A comparison of native tallgrass prairie and plains bluestem forage systems for cow-calf production in the southern great plains.

Science.gov (United States)

Coleman, S W; Phillips, W A; Volesky, J D; Buchanan, D

2001-07-01

The objective of this study was to compare an introduced warm-season perennial grass (plains bluestem, Bothriochloa ischaemum) to native tallgrass prairie for cow-calf production. Three systems were used, two based on tallgrass prairie with two different forms of protein supplementation and one based on plains bluestem as the primary forage. The systems were as follows: 1) native tallgrass prairie with pelleted oilseed meal as the winter protein supplement (native-control); 2) native tallgrass prairie with limited access to wheat pasture as the winter protein supplement (native-wheat); and 3) plains bluestem with limited access to wheat pasture as the protein supplement (bluestem-wheat). Oilseed meal protein supplements were fed twice weekly. Cows grazing wheat pasture were allowed 6 h of grazing twice weekly. Ninety-nine cows per year were used over the 3-yr study. Cows were sired by either Charolais, Gelbvieh, Angus, or Hereford bulls out of commercial Angus-Hereford dams. Calves were sired by Simmental bulls. Calving and weaning rate increased over time but did not differ among systems or breed types. System did not influence the size or body condition score of cows or the performance of calves, but changes in the weight and condition scores of cows were greater on either native system than on the bluestem-wheat system. Cows from Charolais and Gelbvieh bulls were taller (P < 0.05), and heavier (P < 0.05), and weaned heavier (P < 0.05) calves than cows from Angus or Hereford bulls. The weight of cows on the bluestem-wheat system tended to decrease over time, whereas cows grazing on the native systems tended to gain weight over time. The native-control system was the most profitable system based on cow production. If excess hay produced from the bluestem-wheat system was sold as a cash crop, then this system was the most profitable. In general, we conclude that limit-grazing wheat pasture is a viable alternative to oilseed meal as protein supplement for wintering

Rapamycin-binding FKBP25 associates with diverse proteins that form large intracellular entities

International Nuclear Information System (INIS)

Galat, Andrzej; Thai, Robert

2014-01-01

Highlights: • The hFKBP25 interacts with diverse components of macromolecular entities. • We show that the endogenous human FKBP25 is bound to polyribosomes. • The endogenous hFKBP25 co-immunoprecipitated with nucleosomal proteins. • FKBP25 could induce conformational switch in macromolecular complexes. - Abstract: In this paper, we show some evidence that a member of the FK506-binding proteins, FKBP25 is associated to diverse components that are part of several different intracellular large-molecular mass entities. The FKBP25 is a high-affinity rapamycin-binding immunophilin, which has nuclear translocation signals present in its PPIase domain but it was detected both in the cytoplasm compartment and in the nuclear proteome. Analyses of antiFKBP25-immunoprecipitated proteins have revealed that the endogenous FKBP25 is associated to the core histones of the nucleosome, and with several proteins forming spliceosomal complexes and ribosomal subunits. Using polyclonal antiFKBP25 we have detected FKBP25 associated with polyribosomes. Added RNAs or 0.5 M NaCl release FKBP25 that was associated with the polyribosomes indicating that the immunophilin has an intrinsic capacity to form complexes with polyribonucleotides via its charged surface patches. Rapamycin or FK506 treatments of the polyribosomes isolated from porcine brain, HeLa and K568 cells caused a residual release of the endogenous FKBP25, which suggests that the immunophilin also binds to some proteins via its PPIase cavity. Our proteomics study indicates that the nuclear pool of the FKBP25 targets various nuclear proteins that are crucial for packaging of DNA, chromatin remodeling and pre-mRNA splicing whereas the cytosolic pool of this immunophilin is bound to some components of the ribosome

Rapamycin-binding FKBP25 associates with diverse proteins that form large intracellular entities

Energy Technology Data Exchange (ETDEWEB)

Galat, Andrzej, E-mail: galat@dsvidf.cea.fr; Thai, Robert

2014-08-08

Highlights: • The hFKBP25 interacts with diverse components of macromolecular entities. • We show that the endogenous human FKBP25 is bound to polyribosomes. • The endogenous hFKBP25 co-immunoprecipitated with nucleosomal proteins. • FKBP25 could induce conformational switch in macromolecular complexes. - Abstract: In this paper, we show some evidence that a member of the FK506-binding proteins, FKBP25 is associated to diverse components that are part of several different intracellular large-molecular mass entities. The FKBP25 is a high-affinity rapamycin-binding immunophilin, which has nuclear translocation signals present in its PPIase domain but it was detected both in the cytoplasm compartment and in the nuclear proteome. Analyses of antiFKBP25-immunoprecipitated proteins have revealed that the endogenous FKBP25 is associated to the core histones of the nucleosome, and with several proteins forming spliceosomal complexes and ribosomal subunits. Using polyclonal antiFKBP25 we have detected FKBP25 associated with polyribosomes. Added RNAs or 0.5 M NaCl release FKBP25 that was associated with the polyribosomes indicating that the immunophilin has an intrinsic capacity to form complexes with polyribonucleotides via its charged surface patches. Rapamycin or FK506 treatments of the polyribosomes isolated from porcine brain, HeLa and K568 cells caused a residual release of the endogenous FKBP25, which suggests that the immunophilin also binds to some proteins via its PPIase cavity. Our proteomics study indicates that the nuclear pool of the FKBP25 targets various nuclear proteins that are crucial for packaging of DNA, chromatin remodeling and pre-mRNA splicing whereas the cytosolic pool of this immunophilin is bound to some components of the ribosome.

Native sulfur/chlorine SAD phasing for serial femtosecond crystallography

International Nuclear Information System (INIS)

Nakane, Takanori; Song, Changyong; Suzuki, Mamoru; Nango, Eriko; Kobayashi, Jun; Masuda, Tetsuya; Inoue, Shigeyuki; Mizohata, Eiichi; Nakatsu, Toru; Tanaka, Tomoyuki; Tanaka, Rie; Shimamura, Tatsuro; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Yabashi, Makina; Nureki, Osamu; Iwata, So; Sugahara, Michihiro

2015-01-01

Sulfur SAD phasing facilitates the structure determination of diverse native proteins using femtosecond X-rays from free-electron lasers via serial femtosecond crystallography. Serial femtosecond crystallography (SFX) allows structures to be determined with minimal radiation damage. However, phasing native crystals in SFX is not very common. Here, the structure determination of native lysozyme from single-wavelength anomalous diffraction (SAD) by utilizing the anomalous signal of sulfur and chlorine at a wavelength of 1.77 Å is successfully demonstrated. This sulfur SAD method can be applied to a wide range of proteins, which will improve the determination of native crystal structures

Antioxidant and Hypolipidaemic Effect of Raw Green Snap (Phaseolus vulgaris) on Aged Male Rats Exposed to gamma Irradiation

International Nuclear Information System (INIS)

Abed EI-Gawad, E.I.; Aiad, S.K.

2008-01-01

This Study was established to assess the effect of supplemental dietary raw green snap (Phaseolus vulgaris) for three months to overcome gamma-irradiation induced alterations on some oxidant/ antioxidant parameters (Fe 3+ , Cu 2+ , total iron, ferritin, transferrin and ceruloplasmin) and the hyper lipidemic state (triglycerides, cholesterol, high- and low density lipoprotein (HDL-c and LDL-c) in aged male rats. Raw green snap is an indigenous plant used in Unani and Ayurvedic medicine in India. The study also aimed to estimate the effect of dietary raw green snap on general health through the follow up of body weight and mortality during the course of supplementation. Thirty-two aged male rats (24 months, 370-375 g) were divided equally into four groups. 1- Control group, the animals fed on a balanced diet for 3 months. 2- Supplemented group, the animals balanced diet was supplemented with raw green snap (70 g / kg body wt/ day) for 3 months. 3- Irradiated group, the animals fed on a balanced diet for 3 months were then exposed to whole body y-radiation at a dose level of 4 Gy. 4-Supplemented-irradiated group, the animals' balanced diet was supplemented with raw green snap (70 g/ kg/ day) for three months and then exposed to whole body gamma irradiation at a dose level of 4 Gy. The blood samples were taken from orbital venous plexuses after 48 h of stopping green snap supplementation (supplemented group) or after irradiation (irradiated and supplemented gamma-irradiated groups). The results obtained showed reduction in the body wt in green snap supplemented group which increased gradually concomitant with occurrence of animal mortality on week 7 reaching II) maximal values (-32.79 and 33.33 %) respectively, on week 12 of supplementation. Also, the supplemented group showed non significant changes in tested parameters although the level of total iron and triglycerides recorded noticeable changes as compared with controls

Toward the topology design of mechanisms that exhibit snap-through behavior

DEFF Research Database (Denmark)

Burns, T. E.; Sigmund, Ole

2004-01-01

Topology optimization has proven to be a powerful method for the conceptual design of structures and mechanisms. In previously published work, we concentrated on the development of numerical methods that accommodate the finite deformation and incorporated these analyses into the topology...... optimization. We demonstrated by relatively straightforward transversely loaded clamped-clamped beam examples that topology optimization can be used to design structures that experience snap-through behavior. Here, we focus our attention on the design problem formulation where the goal is to develop a general...... approach for the design of mechanisms that experience more complex snap-through behavior. A multiphase design strategy is outlined, numerous significant challenges to this complex design process are discussed, and several examples are presented that demonstrate progress toward this goal. (C) 2004 Elsevier...

Behavior of native microbial populations of WPC-34 and WPC-80 whey protein stored at different temperatures

Science.gov (United States)

Whey protein (WPC34 and 80) has been used as food ingredients and as a base for making biodegradable product. However, there is limited information on the behavior of native microflora associated with these products. WPC 34 and WPC80 were obtained from the manufacturer, and were stored at 5, 10, 15,...

Recombinant proteins incorporating short non-native extensions may display increased aggregation propensity as detected by high resolution NMR spectroscopy

International Nuclear Information System (INIS)

Zanzoni, Serena; D’Onofrio, Mariapina; Molinari, Henriette; Assfalg, Michael

2012-01-01

Highlights: ► Bile acid binding proteins from different constructs retain structural integrity. ► NMR 15 N-T 1 relaxation data of BABPs show differences if LVPR extension is present. ► Deviations from a 15 N-T 1 /molecular-weight calibration curve indicate aggregation. -- Abstract: The use of a recombinant protein to investigate the function of the native molecule requires that the former be obtained with the same amino acid sequence as the template. However, in many cases few additional residues are artificially introduced for cloning or purification purposes, possibly resulting in altered physico-chemical properties that may escape routine characterization. For example, increased aggregation propensity without visible protein precipitation is hardly detected by most analytical techniques but its investigation may be of great importance for optimizing the yield of recombinant protein production in biotechnological and structural biology applications. In this work we show that bile acid binding proteins incorporating the common C-terminal LeuValProArg extension display different hydrodynamic properties from those of the corresponding molecules without such additional amino acids. The proteins were produced enriched in nitrogen-15 for analysis via heteronuclear NMR spectroscopy. Residue-specific spin relaxation rates were measured and related to rotational tumbling time and molecular size. While the native-like recombinant proteins show spin-relaxation rates in agreement with those expected for monomeric globular proteins of their mass, our data indicate the presence of larger adducts for samples of proteins with very short amino acid extensions. The used approach is proposed as a further screening method for the quality assessment of biotechnological protein products.

Recombinant proteins incorporating short non-native extensions may display increased aggregation propensity as detected by high resolution NMR spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Zanzoni, Serena; D' Onofrio, Mariapina; Molinari, Henriette [Department of Biotechnology, University of Verona, 37134 Verona (Italy); Assfalg, Michael, E-mail: michael.assfalg@univr.it [Department of Biotechnology, University of Verona, 37134 Verona (Italy)

2012-10-26

Highlights: Black-Right-Pointing-Pointer Bile acid binding proteins from different constructs retain structural integrity. Black-Right-Pointing-Pointer NMR {sup 15}N-T{sub 1} relaxation data of BABPs show differences if LVPR extension is present. Black-Right-Pointing-Pointer Deviations from a {sup 15}N-T{sub 1}/molecular-weight calibration curve indicate aggregation. -- Abstract: The use of a recombinant protein to investigate the function of the native molecule requires that the former be obtained with the same amino acid sequence as the template. However, in many cases few additional residues are artificially introduced for cloning or purification purposes, possibly resulting in altered physico-chemical properties that may escape routine characterization. For example, increased aggregation propensity without visible protein precipitation is hardly detected by most analytical techniques but its investigation may be of great importance for optimizing the yield of recombinant protein production in biotechnological and structural biology applications. In this work we show that bile acid binding proteins incorporating the common C-terminal LeuValProArg extension display different hydrodynamic properties from those of the corresponding molecules without such additional amino acids. The proteins were produced enriched in nitrogen-15 for analysis via heteronuclear NMR spectroscopy. Residue-specific spin relaxation rates were measured and related to rotational tumbling time and molecular size. While the native-like recombinant proteins show spin-relaxation rates in agreement with those expected for monomeric globular proteins of their mass, our data indicate the presence of larger adducts for samples of proteins with very short amino acid extensions. The used approach is proposed as a further screening method for the quality assessment of biotechnological protein products.

HRR25, a putative protein kinase from budding yeast: Association with repair of damaged DNA

International Nuclear Information System (INIS)

Hoekstra, M.F.; Ou, A.C.; DeMaggio, A.J.; Burbee, D.G.; Liskay, R.M.; Heffron, F.

1991-01-01

In simple eukaryotes, protein kinases regulate mitotic and meiotic cell cycles, the response to polypeptide pheromones, and the initiation of nuclear DNA synthesis. The protein HRR25 from the budding yeast Saccharomyces cerevisiae was defined by the mutation hrr25-1. This mutation resulted in sensitivity to continuous expression of the HO double-strand endonuclease, to methyl methanesulfonate, and to x-irradiation. Homozygotes of hrr25-1 were unable to sporulate and disruption and deletion of HRR25 interfered with mitotic and meiotic cell division. Sequence analysis revealed two distinctive regions in the protein. The NH 2 -terminus of HRR25 contains the hallmark features of protein kinases, whereas the COOH-terminus is rich in proline and glutamine. Mutations in HRR25 at conserved residues found in all protein kinases inactivated the gene, and these mutants exhibited the hrr25 null phenotypes. Taken together, the hrr25 mutant phenotypes and the features of the gene product indicate that HRR25 is a distinctive member of the protein kinase superfamily

A Study of Structural Stress Technique for Fracture Prediction of an Auto-Mobile Clutch Snap-Ring

International Nuclear Information System (INIS)

Kim, Ju Hee; Myeong, Man Sik; Oh, Chang Sik; Kim, Yun Jae

2016-01-01

The endurance reliability assessment of a highly complex mechanism is generally predicted by the fatigue life based on simple stress analysis. This study discusses various fatigue life assessment techniques for an automobile clutch snap ring. Finite element analyses were conducted to determine the structural stress on the snap ring. Structural stress that is insensitive in regards to the mesh size and type definition is presented in this study. The structural stress definition is consistent with elementary structural mechanics theory and provides an effective measure of a stress state that pertains to fatigue behavior of welded joints in the form of both membrane and bending components. Numerical procedures for both solid models and shell or plate element models are presented to demonstrate the mesh-size insensitivity when extracting the structural stress parameters. Conventional finite element models can be used with the structural stress calculations as a post-processing procedure. The two major implications from this research were: (a) structural stresses pertaining to fatigue behavior can be consistently calculated in a mesh-insensitive manner regardless of the types of finite element models; and (b) by comparing with the clutch snap-ring fatigue test data, we should predict the fatigue fractures of an automobile clutch snap ring using this method

Flour mill stream blending affects sugar snap cookie and Japanese sponge cake quality and oxidative cross-linking potential of soft white wheat.

Science.gov (United States)

Ramseyer, Daniel D; Bettge, Arthur D; Morris, Craig F

2011-01-01

The purpose of this research was to study the functional differences between straight grade (75% extraction rate) and patent (60% extraction rate) flour blends from 28 genetically pure soft white and club wheat grain lots, as evidenced by variation in sugar snap cookie and Japanese sponge cake quality. Functional differences were examined relative to arabinoxylan content, protein content, and oxidative cross-linking potential of flour slurries. Oxidative cross-linking measurements were obtained on flour slurries with a low shear Bostwick consistometer and considered endogenous oxidative cross-linking potential (water alone) or enhanced oxidative cross-linking potential (with added hydrogen peroxide-peroxidase). A 2-way ANOVA indicated that flour blend was the greater source of variation compared to grain lot for all response variables except water-extractable arabinoxylan content. Patent flours produced larger sugar snap cookies and Japanese sponge cakes, and contained significantly less total and water-unextractable arabinoxylans, protein, and ash than did straight grade flours. Patent flours produced more viscous slurries for endogenous and enhanced cross-linking measurements compared to the straight grade flours. The functional differences between patent and straight grade flours appear to be related to the particular mill streams that were utilized in the formulation of the 2 flour blends and compositional differences among those streams. Journal of Food Science © 2011 Institute of Food Technologists® No claim to original US government works.

Polycyclic aromatic hydrocarbons affect survival and development of common snapping turtle (Chelydra serpentina) embryos and hatchlings.

Science.gov (United States)

Van Meter, Robin J; Spotila, James R; Avery, Harold W

2006-08-01

Polycyclic aromatic hydrocarbons (PAHs) are toxic compounds found in the John Heinz National Wildlife Refuge in Philadelphia, Pennsylvania. We assessed the impact of PAHs and crude oil on snapping turtle development and behavior by exposing snapping turtle eggs from the Refuge and from three clean reference sites to individual PAHs or a crude oil mixture at stage 9 of embryonic development. Exposure to PAHs had a significant effect on survival rates in embryos from one clean reference site, but not in embryos from the other sites. There was a positive linear relationship between level of exposure to PAHs and severity of deformities in embryos collected from two of the clean reference sites. Neither righting response nor upper temperature tolerance (critical thermal maximum, CTM) of snapping turtle hatchlings with no or minor deformities was significantly affected by exposure to PAHs.

On using the dynamic snap-through motion of MEMS initially curved microbeams for filtering applications

KAUST Repository

Ouakad, Hassen M.; Younis, Mohammad I.

2014-01-01

Numerical and experimental investigations of the dynamics of micromachined shallow arches (initially curved microbeams) and the possibility of using their dynamic snap-through motion for filtering purposes are presented. The considered MEMS arches are actuated by a DC electrostatic load along with an AC harmonic load. Their dynamics is examined numerically using a Galerkin-based reduced-order model when excited near both their first and third natural frequencies. Several simulation results are presented demonstrating interesting jumps and dynamic snap-through behavior of the MEMS arches and their attractive features for uses as band-pass filters, such as their sharp roll-off from pass-bands to stop-bands and their flat response. Experimental work is conducted to test arches realized of curved polysilicon microbeams when excited by DC and AC loads. Experimental data of the micromachined curved beams are shown for the softening and hardening behavior near the first and third natural frequencies, respectively, as well as dynamic snap-through motion. © 2013 Elsevier Ltd.

Experimental investigation of snap-through motion of in-plane MEMS shallow arches under electrostatic excitation

KAUST Repository

Ramini, Abdallah

2015-12-11

We present an experimental investigation for the nonlinear dynamic behaviors of clamped–clamped in-plane MEMS shallow arches when excited by harmonic electrostatic forces. Frequency sweeps are conducted to study the dynamic behaviors in the neighborhoods of the first and third resonance frequencies as well as the super-harmonic resonances. Experimental results show local softening behavior of small oscillations around the first resonance frequency and hardening behavior at the third resonance frequency for small dc and ac loads. Interesting dynamic snap-through cross-well motions are observed experimentally at high voltages for the first time in the micro-scale world. In addition to the dynamic snap-through motion, the MEMS arch exhibits large oscillations of a continuous band of snap-through motion between the super-harmonic resonance regime and the first primary resonance regime. This continuous band is unprecedented experimentally in the micro/macro world, and is promising for a variety of sensing, actuation and communications applications.

Experimental investigation of snap-through motion of in-plane MEMS shallow arches under electrostatic excitation

KAUST Repository

Ramini, Abdallah; Bellaredj, Mohammed L F; Al Hafiz, Md Abdullah; Younis, Mohammad I.

2015-01-01

We present an experimental investigation for the nonlinear dynamic behaviors of clamped–clamped in-plane MEMS shallow arches when excited by harmonic electrostatic forces. Frequency sweeps are conducted to study the dynamic behaviors in the neighborhoods of the first and third resonance frequencies as well as the super-harmonic resonances. Experimental results show local softening behavior of small oscillations around the first resonance frequency and hardening behavior at the third resonance frequency for small dc and ac loads. Interesting dynamic snap-through cross-well motions are observed experimentally at high voltages for the first time in the micro-scale world. In addition to the dynamic snap-through motion, the MEMS arch exhibits large oscillations of a continuous band of snap-through motion between the super-harmonic resonance regime and the first primary resonance regime. This continuous band is unprecedented experimentally in the micro/macro world, and is promising for a variety of sensing, actuation and communications applications.

Diagnosing Snapping Sartorius Tendon Secondary to a Meniscal Cyst Using Dynamic Ultrasound Avoids Incorrect Surgical Procedure

Directory of Open Access Journals (Sweden)

Vipin Asopa

2013-01-01

Full Text Available We describe a case of painful snapping in the medial aspect of the knee of a 40-year-old man, following a knee hyperflexion injury. Dynamic real-time ultrasonography determined that the snapping was due to the distal tendon of sartorius passing over a medial meniscal cyst. The patient subsequently underwent arthroscopic decompression of the cyst instead of an inappropriate hamstring tendon harvest procedure, with complete resolution of symptoms.

2BC Non-Structural Protein of Enterovirus A71 Interacts with SNARE Proteins to Trigger Autolysosome Formation.

Science.gov (United States)

Lai, Jeffrey K F; Sam, I-Ching; Verlhac, Pauline; Baguet, Joël; Eskelinen, Eeva-Liisa; Faure, Mathias; Chan, Yoke Fun

2017-07-04

Viruses have evolved unique strategies to evade or subvert autophagy machinery. Enterovirus A71 (EV-A71) induces autophagy during infection in vitro and in vivo. In this study, we report that EV-A71 triggers autolysosome formation during infection in human rhabdomyosarcoma (RD) cells to facilitate its replication. Blocking autophagosome-lysosome fusion with chloroquine inhibited virus RNA replication, resulting in lower viral titres, viral RNA copies and viral proteins. Overexpression of the non-structural protein 2BC of EV-A71 induced autolysosome formation. Yeast 2-hybrid and co-affinity purification assays showed that 2BC physically and specifically interacted with a N -ethylmaleimide-sensitive factor attachment receptor (SNARE) protein, syntaxin-17 (STX17). Co-immunoprecipitation assay further showed that 2BC binds to SNARE proteins, STX17 and synaptosome associated protein 29 (SNAP29). Transient knockdown of STX17, SNAP29, and microtubule-associated protein 1 light chain 3B (LC3B), crucial proteins in the fusion between autophagosomes and lysosomes) as well as the lysosomal-associated membrane protein 1 (LAMP1) impaired production of infectious EV-A71 in RD cells. Collectively, these results demonstrate that the generation of autolysosomes triggered by the 2BC non-structural protein is important for EV-A71 replication, revealing a potential molecular pathway targeted by the virus to exploit autophagy. This study opens the possibility for the development of novel antivirals that specifically target 2BC to inhibit formation of autolysosomes during EV-A71 infection.

Structural study of the AOT reverse micellar system. Influence of attractive interactions induced by the solubilisation of native and modified proteins

International Nuclear Information System (INIS)

Cassin, Guillaume

1994-01-01

This research thesis reports the study of the influence of intra-micellar attractions on the thermodynamic behaviour of reverse micellar systems, as well as of the effects induced by the solubilisation of natives or modified proteins. The author proposes a model to explain the decrease of attractions between droplets when the volume fraction occupied by reverse micelles increases. This model which highlights the importance of depletion forces between reverse micelles, allows the building up of a theoretical relationship between the bonding parameter and the volume fraction of reverse micelles. In order to understand the appearance of an attractive term related to the solubilisation of native cytochrome-c in these systems, this protein has been chemically modified. The author highlights the role of the charge born by a micellar probe on the thermodynamic behaviour of micro-emulsions. Then, the author applies the model of dimerizing adhesive spheres to reverse micellar systems containing native cytochrome-c. He shows that theoretical predictions of this model are in agreement with obtained experimental results [fr

Effects of environmentally relevant concentrations of atrazine on gonadal development of snapping turtles (Chelydra serpentina).

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de Solla, Shane R; Martin, Pamela A; Fernie, Kimberly J; Park, Brad J; Mayne, Gregory

2006-02-01

The herbicide atrazine has been suspected of affecting sexual development by inducing aromatase, resulting in the increased conversion of androgens to estrogens. We used snapping turtles (Chelydra serpentina), a species in which sex is dependent on the production of estrogen through aromatase activity in a temperature-dependent manner, to investigate if environmentally relevant exposures to atrazine affected gonadal development. Eggs were incubated in soil to which atrazine was applied at a typical field application rate (3.1 L/ha), 10-fold this rate (31 L/ha), and a control rate (no atrazine) for the duration of embryonic development. The incubation temperature (25 degrees C) was selected to produce only males. Although some males with testicular oocytes and females were produced in the atrazine-treated groups (3.3-3.7%) but not in the control group, no statistical differences were found among treatments. Furthermore, snapping turtle eggs collected from natural nests in a corn field were incubated at the pivotal temperature (27.5 degrees C) at which both males and females normally would be produced, and some males had oocytes in the testes (15.4%). The presence of low numbers of males with oocytes may be a natural phenomenon, and we have limited evidence to suggest that the presence of normal males with oocytes may represent a feminizing effect of atrazine. Histological examination of the thyroid gland revealed no effect on thyroid morphology.

A ribonuclease-resistant region of 5S RNA and its relation to the RNA binding sites of proteins L18 and L25

DEFF Research Database (Denmark)

Douthwaite, S; Garrett, R A; Wagner, R

1979-01-01

An RNA fragment, constituting three subfragments of nucleotide sequences 1-11, 69-87 and 89-120, is the most ribonuclease-resistant part of the native 5S RNA of Escherichia coli, at 0 degrees C. A smaller fragment of nucleotide sequence 69-87 and 90-110 is ribonuclease-resistant at 25 degrees....... Degradation of the L25-5S RNA complex with ribonuclease A or T2 yielded RNA fragments similar to those of the free 5S RNA at 0 degrees C and 25 degrees C; moreover L25 remained strongly bound to both RNA fragments and also produced some opening of the RNA structure in at least two positions. Protein L18...... initially protected most of the 5S RNA against ribonuclease digestion, at 0 degrees C, but was then gradually released prior to the formation of the larger RNA fragment. It cannot be concluded, therefore, as it was earlier (Gray et al., 1973), that this RNA fragment contains the primary binding site of L18....

Mapping a nucleolar targeting sequence of an RNA binding nucleolar protein, Nop25

International Nuclear Information System (INIS)

Fujiwara, Takashi; Suzuki, Shunji; Kanno, Motoko; Sugiyama, Hironobu; Takahashi, Hisaaki; Tanaka, Junya

2006-01-01

Nop25 is a putative RNA binding nucleolar protein associated with rRNA transcription. The present study was undertaken to determine the mechanism of Nop25 localization in the nucleolus. Deletion experiments of Nop25 amino acid sequence showed Nop25 to contain a nuclear targeting sequence in the N-terminal and a nucleolar targeting sequence in the C-terminal. By expressing derivative peptides from the C-terminal as GFP-fusion proteins in the cells, a lysine and arginine residue-enriched peptide (KRKHPRRAQDSTKKPPSATRTSKTQRRRR) allowed a GFP-fusion protein to be transported and fully retained in the nucleolus. When the peptide was fused with cMyc epitope and expressed in the cells, a cMyc epitope was then detected in the nucleolus. Nop25 did not localize in the nucleolus by deletion of the peptide from Nop25. Furthermore, deletion of a subdomain (KRKHPRRAQ) in the peptide or amino acid substitution of lysine and arginine residues in the subdomain resulted in the loss of Nop25 nucleolar localization. These results suggest that the lysine and arginine residue-enriched peptide is the most prominent nucleolar targeting sequence of Nop25 and that the long stretch of basic residues might play an important role in the nucleolar localization of Nop25. Although Nop25 contained putative SUMOylation, phosphorylation and glycosylation sites, the amino acid substitution in these sites had no effect on the nucleolar localization, thus suggesting that these post-translational modifications did not contribute to the localization of Nop25 in the nucleolus. The treatment of the cells, which expressed a GFP-fusion protein with a nucleolar targeting sequence of Nop25, with RNase A resulted in a complete dislocation of the protein from the nucleolus. These data suggested that the nucleolar targeting sequence might therefore play an important role in the binding of Nop25 to RNA molecules and that the RNA binding of Nop25 might be essential for the nucleolar localization of Nop25

Formative assessment using social marketing principles to identify health and nutrition perspectives of Native American women living within the Chickasaw Nation boundaries in Oklahoma.

Science.gov (United States)

Parker, Stephany; Hunter, Toma; Briley, Chiquita; Miracle, Sarah; Hermann, Janice; Van Delinder, Jean; Standridge, Joy

2011-01-01

To identify health product and promotion channels for development of a Chickasaw Nation Supplemental Nutrition Assistance Education Program (SNAP-Ed) social marketing program. The study was qualitative and used social marketing principles to assess Native American women's views of health and nutrition. Focus groups (n = 8) and interviews (n = 4) were conducted to identify indigenous views of product, promotion, price, and place related to SNAP-Ed behavioral objectives. The major theme identified for product was diabetes prevention. Participants (n = 42) indicated a preference for family-based education with promotion by elders, tribal leaders, and "everyday people." Participants identified tribe-specific community sites for program implementation at times conducive to work schedules. Culturally appropriate social marketing programs are necessary to address diabetes prevention with a focus on family, heritage, and tribal community. Additional research is necessary to explore the role of elders and tribal leaders in diabetes prevention efforts. Copyright © 2011 Society for Nutrition Education. Published by Elsevier Inc. All rights reserved.

The Vici Syndrome Protein EPG5 Is a Rab7 Effector that Determines the Fusion Specificity of Autophagosomes with Late Endosomes/Lysosomes.

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Wang, Zheng; Miao, Guangyan; Xue, Xue; Guo, Xiangyang; Yuan, Chongzhen; Wang, Zhaoyu; Zhang, Gangming; Chen, Yingyu; Feng, Du; Hu, Junjie; Zhang, Hong

2016-09-01

Mutations in the human autophagy gene EPG5 cause the multisystem disorder Vici syndrome. Here we demonstrated that EPG5 is a Rab7 effector that determines the fusion specificity of autophagosomes with late endosomes/lysosomes. EPG5 is recruited to late endosomes/lysosomes by direct interaction with Rab7 and the late endosomal/lysosomal R-SNARE VAMP7/8. EPG5 also binds to LC3/LGG-1 (mammalian and C. elegans Atg8 homolog, respectively) and to assembled STX17-SNAP29 Qabc SNARE complexes on autophagosomes. EPG5 stabilizes and facilitates the assembly of STX17-SNAP29-VAMP7/8 trans-SNARE complexes, and promotes STX17-SNAP29-VAMP7-mediated fusion of reconstituted proteoliposomes. Loss of EPG5 activity causes abnormal fusion of autophagosomes with various endocytic vesicles, in part due to elevated assembly of STX17-SNAP25-VAMP8 complexes. SNAP25 knockdown partially suppresses the autophagy defect caused by EPG5 depletion. Our study reveals that EPG5 is a Rab7 effector involved in autophagosome maturation, providing insight into the molecular mechanism underlying Vici syndrome. Copyright © 2016 Elsevier Inc. All rights reserved.

Clinical and cognitive trajectories in cognitively healthy elderly individuals with suspected non-Alzheimer's disease pathophysiology (SNAP) or Alzheimer's disease pathology: a longitudinal study.

Science.gov (United States)

Burnham, Samantha C; Bourgeat, Pierrick; Doré, Vincent; Savage, Greg; Brown, Belinda; Laws, Simon; Maruff, Paul; Salvado, Olivier; Ames, David; Martins, Ralph N; Masters, Colin L; Rowe, Christopher C; Villemagne, Victor L

2016-09-01

Brain amyloid β (Aβ) deposition and neurodegeneration have been documented in about 50-60% of cognitively healthy elderly individuals (aged 60 years or older). The long-term cognitive consequences of the presence of Alzheimer's disease pathology and neurodegeneration, and whether they have an independent or synergistic effect on cognition, are unclear. We aimed to characterise the long-term clinical and cognitive trajectories of healthy elderly individuals using a two-marker (Alzheimer's disease pathology and neurodegeneration) imaging construct. Between Nov 3, 2006, and Nov 25, 2014, 573 cognitively healthy individuals in Melbourne and Perth, Australia, (mean age 73·1 years [SD 6·2]; 58% women) were enrolled in the Australian Imaging, Biomarker and Lifestyle (AIBL) study. Alzheimer's disease pathology (A) was determined by measuring Aβ deposition by PET, and neurodegeneration (N) was established by measuring hippocampal volume using MRI. Individuals were categorised as A(-)N(-), A(+)N(-), A(+)N(+), or suspected non-Alzheimer's disease pathophysiology (A(-)N(+), SNAP). Clinical progression, hippocampal volume, standard neuropsychological tests, and domain-specific and global cognitive composite scores were assessed over 6 years of follow-up. Linear mixed effect models and a Cox proportional hazards model of survival were used to evaluate, compare, and contrast the clinical, cognitive, and volumetric trajectories of patients in the four AN categories. 50 (9%) healthy individuals were classified as A(+)N(+), 87 (15%) as A(+)N(-), 310 (54%) as A(-)N(-), and 126 (22%) as SNAP. APOE ε4 was more frequent in participants in the A(+)N(+) (27; 54%) and A(+)N(-) (42; 48%) groups than in the A(-)N(-) (66; 21%) and SNAP groups (23; 18%). The A(+)N(-) and A(+)N(+) groups had significantly faster cognitive decline than the A(-)N(-) group (0·08 SD per year for AIBL-Preclinical AD Cognitive Composite [PACC]; p<0·0001; and 0·25; p<0·0001; respectively). The A (+)N

Capillary electrophoresis hyphenated with UV-native-laser induced fluorescence detection (CE/UV-native-LIF).

Science.gov (United States)

Couderc, François; Ong-Meang, Varravaddheay; Poinsot, Véréna

2017-01-01

Native laser-induced fluorescence using UV lasers associated to CE offers now a large related literature, for now 30 years. The main works have been performed using very expensive Ar-ion lasers emitting at 257 and 275 nm. They are not affordable for routine analyses, but have numerous applications such as protein, catecholamine, and indolamine analysis. Some other lasers such as HeCd 325 nm have been used but only for few applications. Diode lasers, emitting at 266 nm, cheaper, are extensively used for the same topics, even if the obtained sensitivity is lower than the one observed using the costly UV-Ar-ion lasers. This review presents various CE or microchips applications and different UV lasers used for the excitation of native fluorescence. We showed that CE/Native UV laser induced fluorescence detection is very sensitive for detection as well as small aromatic biomolecules than proteins containing Trp and Tyr amino acids. Moreover, it is a simple way to analyze biomolecules without derivatization. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proteomic differences between native and tissue‐engineered tendon and ligament

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Tew, Simon R.; Peffers, Mandy; Canty‐Laird, Elizabeth G.; Comerford, Eithne

2016-01-01

Tendons and ligaments (T/Ls) play key roles in the musculoskeletal system, but they are susceptible to traumatic or age‐related rupture, leading to severe morbidity as well as increased susceptibility to degenerative joint diseases such as osteoarthritis. Tissue engineering represents an attractive therapeutic approach to treating T/L injury but it is hampered by our poor understanding of the defining characteristics of the two tissues. The present study aimed to determine differences in the proteomic profile between native T/Ls and tissue engineered (TE) T/L constructs. The canine long digital extensor tendon and anterior cruciate ligament were analyzed along with 3D TE fibrin‐based constructs created from their cells. Native tendon and ligament differed in their content of key structural proteins, with the ligament being more abundant in fibrocartilaginous proteins. 3D T/L TE constructs contained less extracellular matrix (ECM) proteins and had a greater proportion of cellular‐associated proteins than native tissue, corresponding to their low collagen and high DNA content. Constructs were able to recapitulate native T/L tissue characteristics particularly with regard to ECM proteins. However, 3D T/L TE constructs had similar ECM and cellular protein compositions indicating that cell source may not be an important factor for T/L tissue engineering. PMID:27080496

Towards Lego Snapping; Integration of Carbon Nanotubes and Few-Layer Graphene

Science.gov (United States)

Nasseri, Mohsen; Boland, Mathias; Farrokhi, M. Javad; Strachan, Douglas

Integration of semiconducting, conducting, and insulating nanomaterials into precisely aligned complicated systems is one of the main challenges to the ultimate size scaling of electronic devices, which is a key goal in nanoscience and nanotechnology. This integration could be made more effective through controlled alignment of the crystallographic lattices of the nanoscale components. Of the vast number of materials of atomically-thin materials, two of the sp2 bonded carbon structures, graphene and carbon nanotubes, are ideal candidates for this type of application since they are built from the same backbone carbon lattice. Here we report carbon nanotube and graphene hybrid nanostructures fabricated through their catalytic synthesis and etching. The growth formations we have investigated through various high-resolution microscopy techniques provide evidence of lego-snapped interfaces between nanotubes and graphene into device-relevant orientations. We will finish with a discussion of the various size and energy regimes relevant to these lego-snapped interfaces and their implications on developing these integrated formations.

Multi-crystal native SAD analysis at 6 keV.

Science.gov (United States)

Liu, Qun; Guo, Youzhong; Chang, Yanqi; Cai, Zheng; Assur, Zahra; Mancia, Filippo; Greene, Mark I; Hendrickson, Wayne A

2014-10-01

Anomalous diffraction signals from typical native macromolecules are very weak, frustrating their use in de novo structure determination. Here, native SAD procedures are described to enhance signal to noise in anomalous diffraction by using multiple crystals in combination with synchrotron X-rays at 6 keV. Increased anomalous signals were obtained at 6 keV compared with 7 keV X-ray energy, which was used for previous native SAD analyses. A feasibility test of multi-crystal-based native SAD phasing was performed at 3.2 Å resolution for a known tyrosine protein kinase domain, and real-life applications were made to two novel membrane proteins at about 3.0 Å resolution. The three applications collectively serve to validate the robust feasibility of native SAD phasing at lower energy.

SNAP23-Dependent Surface Translocation of Leukotriene B4 (LTB4) Receptor 1 Is Essential for NOX2-Mediated Exocytotic Degranulation in Human Mast Cells Induced by Trichomonas vaginalis-Secreted LTB4.

Science.gov (United States)

Min, Arim; Lee, Young Ah; Kim, Kyeong Ah; El-Benna, Jamel; Shin, Myeong Heon

2017-01-01

Trichomonas vaginalis is a sexually transmitted parasite that causes vaginitis in women and itself secretes lipid mediator leukotriene B 4 (LTB 4 ). Mast cells are important effector cells of tissue inflammation during infection with parasites. Membrane-bridging SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) complexes are critical for fusion during exocytosis. Although T. vaginalis-derived secretory products (TvSP) have been shown to induce exocytosis in mast cells, information regarding the signaling mechanisms between mast cell activation and TvSP is limited. In this study, we found that SNAP23-dependent surface trafficking of LTB 4 receptor 1 (BLT1) is required for nicotinamide adenine dinucleotide phosphate oxidase 2 (NOX2)-mediated exocytotic degranulation of mast cells induced by TvSP. First, stimulation with TvSP induced exocytotic degranulation and reactive oxygen species (ROS) generation in HMC-1 cells. Next, TvSP-induced ROS generation and exocytosis were strongly inhibited by transfection of BLT1 small interfering RNA (siRNA). TvSP induced trafficking of BLT1 from the cytosol to the plasma membrane. We also found that knockdown of SNAP23 abrogated TvSP-induced ROS generation, exocytosis, and surface trafficking of BLT1 in HMC-1 cells. By coimmunoprecipitation, there was a physical interaction between BLT1 and SNAP23 in TvSP-stimulated HMC-1 cells. Taken together, our results suggest that SNAP23-dependent surface trafficking of BLT1 is essential for exocytosis in human mast cells induced by T. vaginalis-secreted LTB 4 Our data collectively demonstrate a novel regulatory mechanism for SNAP23-dependent mast cell activation of T. vaginalis-secreted LTB 4 involving surface trafficking of BLT1. These results can help to explain how the cross talk mechanism between parasite and host can govern deliberately tissue inflammatory responses. Copyright © 2016 American Society for Microbiology.

Comparative evaluation of the diagnostic potential of recombinant envelope proteins and native cell culture purified viral antigens of Chikungunya virus.

Science.gov (United States)

Khan, Mohsin; Dhanwani, Rekha; Kumar, Jyoti S; Rao, P V Lakshmana; Parida, Manmohan

2014-07-01

Despite the fact that Chikungunya resurgence is associated with epidemic of unprecedented magnitude, there are challenges in the field of its clinical diagnosis. However, serological tests in an ELISA format provide a rapid tool for the diagnosis of Chikungunya infection. Indeed, ELISAs based on recombinant proteins hold a great promise as these methods are cost effective and are free from the risk of handling biohazardous material. In this study, the performance of recombinant CHIKV antigens was compared in various ELISA formats for the diagnosis of Chikungunya. Two recombinant antigens derived from the envelope proteins of Chikungunya virus were prepared and evaluated by comparing their competence for detecting circulating antibodies in serum samples of patients infected with CHIKV using MAC-ELISA and indirect IgM-ELISA. The efficacy of the recombinant antigens was also compared with the native antigen. The indirect antibody capture IgM microplate ELISA revealed ≥90% concordance with the native antigen in detecting the CHIKV specific IgM antibodies whereas the recombinant antigen based MAC-ELISA showed 100% specificity. The recombinant antigens used in this study were effective and reliable targets for the diagnosis of CHIKV infection and also provide an alternative for native antigen use which is potentially biohazardous. © 2013 Wiley Periodicals, Inc.

The unhealthy food environment does not modify the association between obesity and participation in the Supplemental Nutrition Assistance Program (SNAP) in Los Angeles County.

Science.gov (United States)

Chaparro, M Pia; Harrison, Gail G; Wang, May C; Seto, Edmund Y W; Pebley, Anne R

2017-01-14

Participation in the Supplemental Nutrition Assistance Program (SNAP) has been linked to an increased risk of obesity, but not much is known about the mechanisms behind this association. The objective of this study was to determine if the neighborhood density of unhealthy food outlets modifies the association between obesity and participation in SNAP. Data comes from the first wave of the Los Angeles Family and Neighborhood Survey; included are a subsample of adults (18+ years) who were SNAP participants or eligible non-participants (N = 1,176). We carried out multilevel analyses with obesity (BMI ≥ 30 Kg/m 2 ), SNAP participation, and the neighborhood density of unhealthy food outlets as dependent, independent and modifying variables, respectively, controlling for age, gender, race/ethnicity, marital status, working status, mental health, and neighborhood poverty. SNAP participants had double the odds of obesity compared to eligible non-participants (OR = 2.02; 95%CI = 1.44-2.83). However, the neighborhood density of unhealthy food outlets did not modify this association. SNAP participation was associated with higher odds of obesity in our primarily Hispanic sample in Los Angeles County, with no effect modification found for the unhealthy portion of the food environment. More research is needed with additional food environment measures to confirm our null findings. Additional research is needed to elucidate the mechanisms linking SNAP participation and obesity as they remain unclear.

Photoaffinity labeling of serum vitamin D binding protein by 3-deoxy-3-azido-25-hydroxyvitamin D3

International Nuclear Information System (INIS)

Link, R.P.; Kutner, A.; Schnoes, H.K.; DeLuca, H.F.

1987-01-01

3-Deoxy-3-azido-25-hydroxyvitamin D3 was covalently incorporated in the 25-hydroxyvitamin D3 binding site of purified human plasma vitamin D binding protein. Competition experiments showed that 3-deoxy-3-azido-25-hydroxyvitamin D3 and 25-hydroxyvitamin D3 bind at the same site on the protein. Tritiated 3-deoxy-3-azido-25-hydroxyvitamin D3 was synthesized from tritiated 25-hydroxyvitamin D3, retaining the high specific activity of the parent compound. The tritiated azido label bound reversibly to human vitamin D binding protein in the dark and covalently to human vitamin D binding protein after exposure to ultraviolet light. Reversible binding of tritiated 3-deoxy-3-azido-25-hydroxyvitamin D3 was compared to tritiated 25-hydroxyvitamin D3 binding to human vitamin D binding protein. Scatchard analysis of the data indicated equivalent maximum density binding sites with a KD,app of 0.21 nM for 25-hydroxyvitamin D3 and a KD,app of 1.3 nM for the azido derivative. Covalent binding was observed only after exposure to ultraviolet irradiation, with an average of 3% of the reversibly bound label becoming covalently bound to vitamin D binding protein. The covalent binding was reduced 70-80% when 25-hydroxyvitamin D3 was present, indicating strong covalent binding at the vitamin D binding site of the protein. When tritiated 3-deoxy-3-azido-25-hydroxyvitamin D3 was incubated with human plasma in the absence and presence of 25-hydroxyvitamin D3, 12% of the azido derivative was reversibly bound to vitamin D binding protein. After ultraviolet irradiation, four plasma proteins covalently bound the azido label, but vitamin D binding protein was the only protein of the four that was unlabeled in the presence of 25-hydroxyvitamin D3

Algae-Produced Pfs25 Elicits Antibodies That Inhibit Malaria Transmission

Science.gov (United States)

Gregory, James A.; Li, Fengwu; Tomosada, Lauren M.; Cox, Chesa J.; Topol, Aaron B.; Vinetz, Joseph M.; Mayfield, Stephen

2012-01-01

Subunit vaccines are significantly more expensive to produce than traditional vaccines because they are based primarily on recombinant proteins that must be purified from the expression system. Despite the increased cost, subunit vaccines are being developed because they are safe, effective, and can elicit antibodies that confer protection against diseases that are not currently vaccine-preventable. Algae are an attractive platform for producing subunit vaccines because they are relatively inexpensive to grow, genetically tractable, easily scaled to large volumes, have a short generation time, and are devoid of inflammatory, viral, or prion contaminants often present in other systems. We tested whether algal chloroplasts can produce malaria transmission blocking vaccine candidates, Plasmodium falciparum surface protein 25 (Pfs25) and 28 (Pfs28). Antibodies that recognize Pfs25 and Pfs28 disrupt the sexual development of parasites within the mosquito midgut, thus preventing transmission of malaria from one human host to the next. These proteins have been difficult to produce in traditional recombinant systems because they contain tandem repeats of structurally complex epidermal growth factor-like domains, which cannot be produced in bacterial systems, and because they are not glycosylated, so they must be modified for production in eukaryotic systems. Production in algal chloroplasts avoids these issues because chloroplasts can fold complex eukaryotic proteins and do not glycosylate proteins. Here we demonstrate that algae are the first recombinant system to successfully produce an unmodified and aglycosylated version of Pfs25 or Pfs28. These antigens are structurally similar to the native proteins and antibodies raised to these recombinant proteins recognize Pfs25 and Pfs28 from P. falciparum. Furthermore, antibodies to algae-produced Pfs25 bind the surface of in-vitro cultured P. falciparum sexual stage parasites and exhibit transmission blocking activity. Thus

The Snapping Elbow Syndrome as a Reason for Chronic Elbow Neuralgia in a Tennis Player – MR, US and Sonoelastography Evaluation

International Nuclear Information System (INIS)

Łasecki, Mateusz; Olchowy, Cyprian; Pawluś, Aleksander; Zaleska-Dorobisz, Urszula

2014-01-01

Ulnar neuropathy is the second most common peripheral nerve neuropathy after median neuropathy, with an incidence of 25 cases per 100 000 men and 19 cases per 100 000 women each year. Skipping (snapping) elbow syndrome is an uncommon cause of pain in the posterior-medial elbow area, sometimes complicated by injury of the ulnar nerve. One of the reason is the dislocation of the abnormal insertion of the medial triceps head over the medial epicondyle during flexion and extension movements. Others are: lack of the Osboune fascia leading to ulnar nerve instability and focal soft tissue tumors (fibromas, lipomas, etc). Recurrent subluxation of the nerve at the elbow results in a tractional and frictional neuritis with classical symptoms of peripheral neuralgia. As far as we know snapping triceps syndrome had never been evaluated in sonoelastography. A 28yo semi-professional left handed tennis player was complaining about pain in posterior-medial elbow area. Initial US examination suggest golfers elbow syndrome which occurs quite commonly and has a prevalence of 0.3–0.6% in males and 0–3–1.1% in women and may be associated (approx. 50% of cases) with ulnar neuropathy. However subsequently made MRI revealed unusual distal triceps anatomy, moderate ulnar nerve swelling and lack of medial epicondylitis symptoms. Followed (second) US examination and sonoelastography have detected slipping of the both ulnar nerve and the additional band of the medial triceps head. Snapping elbow syndrome is a poorly known medical condition, sometimes misdiagnosed as the medial epicondylitis. It describes a broad range of pathologies and anatomical abnormalities. One of the most often reasons is the slipping of the ulnar nerve as the result of the Osborne fascia/anconeus epitrochlearis muscle absence. Simultaneously presence of two or more “snapping reasons” is rare but should be always taken under consideration. There are no sonoelastography studies describing golfers elbow syndrome

Jojoba seed meal proteins associated with proteolytic and protease inhibitory activities.

Science.gov (United States)

Shrestha, Madan K; Peri, Irena; Smirnoff, Patricia; Birk, Yehudith; Golan-Goldhirsh, Avi

2002-09-25

The jojoba, Simmondsia chinensis, is a characteristic desert plant native to the Sonoran desert. The jojoba meal after oil extraction is rich in protein. The major jojoba proteins were albumins (79%) and globulins (21%), which have similar amino acid compositions and also showed a labile thrombin-inhibitory activity. SDS-PAGE showed two major proteins at 50 kDa and 25 kDa both in the albumins and in the globulins. The 25 kDa protein has trypsin- and chymotrypsin-inhibitory activities. In vitro digestibility of the globulins and albumins resembled that of casein and soybean protein concentrates and was increased after heat treatment. The increased digestibility achieved by boiling may be attributed to inactivation of the protease inhibitors and denaturation of proteins.

On the presence of plutonium in Madagascar following the SNAP-9A satellite failure.

Science.gov (United States)

Rääf, C; Holm, E; Rabesiranana, N; Garcia-Tenorio, R; Chamizo, E

2017-10-01

This study examined the 238 Pu and 239+240 Pu activity concentration and the 240 Pu/ 239 Pu atomic ratio in peat bogs sampled in 2012 from marshlands in central Madagascar. The purpose was to investigate the presence of plutonium isotopes, 238, 239, 240 Pu, from the 1964 satellite failure carrying a SNAP-9A radiothermal generator. With an average 238 Pu/ 239+240 Pu activity ratio of 0.165 ± 0.02 (decay corrected to 1964), the peat bogs in Madagascar exhibit similar values as the ones found in the southeastern African continent, except they are one order of magnitude higher than expected (0.025) from global fallout in the Southern Hemisphere. The 240 Pu/ 239 Pu atomic ratio showed a distinct decrease for layers dating back to the mid-1960s (down to 0.069 compared with an anticipated ratio of 0.17 for global fallout), indicating that the SNAP-9A failure also resulted in an elevated deposition of 239 Pu. The obtained results demonstrate that further Pu analysis in Madagascar and in southeastern continental Africa is necessary to fully account for the regional Pu deposition from the SNAP-9A event. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluation of diamide insecticides co-applied with other agrochemicals at various times to manage Ostrinia nubilalis in processing snap bean.

Science.gov (United States)

Huseth, Anders S; Groves, Russell L; Chapman, Scott A; Nault, Brian A

2015-12-01

Multiple applications of pyrethroid insecticides are used to manage European corn borer, Ostrinia nubilalis Hübner, in snap bean, but new diamide insecticides may reduce application frequency. In a 2 year small-plot study, O. nubilalis control was evaluated by applying cyantraniliprole (diamide) and bifenthrin (pyrethroid) insecticides at one of three phenological stages (bud, bloom and pod formation) of snap bean development. Co-application of these insecticides with either herbicides or fungicides was also examined as a way to reduce the total number of sprays during a season. Cyantraniliprole applications timed either during bloom or during pod formation controlled O. nubilalis better than similar timings of bifenthrin. Co-applications of insecticides with fungicides controlled O. nubilalis as well as insecticide applications alone. Insecticides applied either alone or with herbicides during bud stage did not control this pest. Diamides are an alternative to pyrethroids for the management of O. nubilalis in snap bean. Adoption of diamides by snap bean growers could improve the efficiency of production by reducing the number of sprays required each season. © 2015 Society of Chemical Industry.

A graphene oxide based fluorescence resonance energy transfer (FRET) biosensor for ultrasensitive detection of botulinum neurotoxin A (BoNT/A) enzymatic activity.

Science.gov (United States)

Shi, Jingyu; Guo, Jiubiao; Bai, Gongxun; Chan, Chunyu; Liu, Xuan; Ye, Weiwei; Hao, Jianhua; Chen, Sheng; Yang, Mo

2015-03-15

Botulinum neurotoxins (BoNTs) are among the most potent toxic bacterial proteins for humans, which make them potential agents for bioterrorism. Therefore, an ultrasensitive detection of BoNTs and their active states is in great need as field-deployable systems for anti-terrorism applications. We report the construction of a novel graphene oxide (GO)-peptide based fluorescence resonance energy transfer (FRET) biosensor for ultrasensitive detection of the BoNT serotype A light chain (BoNT-LcA) protease activity. A green fluorescence protein (GFP) modified SNAP-25 peptide substrate (SNAP-25-GFP) was optimally designed and synthesized with the centralized recognition/cleavage sites. This FRET platform was constructed by covalent immobilization of peptide substrate on GO with BSA passivation which have advantages of low non-specific adsorption and high stability in protein abundant solution. BoNT-LcA can specifically cleave SNAP-25-GFP substrate covalently immobilized on GO to release the fragment with GFP. Based on fluorescence signal recovery measurement, the target BoNT-LcA was detected sensitively and selectively with the linear detection range from 1fg/mL to 1pg/mL. The limit of detection (LOD) for BoNT-LcA is around 1fg/mL. Copyright © 2014 Elsevier B.V. All rights reserved.

Proteomic differences between native and tissue-engineered tendon and ligament.

Science.gov (United States)

Kharaz, Yalda A; Tew, Simon R; Peffers, Mandy; Canty-Laird, Elizabeth G; Comerford, Eithne

2016-05-01

Tendons and ligaments (T/Ls) play key roles in the musculoskeletal system, but they are susceptible to traumatic or age-related rupture, leading to severe morbidity as well as increased susceptibility to degenerative joint diseases such as osteoarthritis. Tissue engineering represents an attractive therapeutic approach to treating T/L injury but it is hampered by our poor understanding of the defining characteristics of the two tissues. The present study aimed to determine differences in the proteomic profile between native T/Ls and tissue engineered (TE) T/L constructs. The canine long digital extensor tendon and anterior cruciate ligament were analyzed along with 3D TE fibrin-based constructs created from their cells. Native tendon and ligament differed in their content of key structural proteins, with the ligament being more abundant in fibrocartilaginous proteins. 3D T/L TE constructs contained less extracellular matrix (ECM) proteins and had a greater proportion of cellular-associated proteins than native tissue, corresponding to their low collagen and high DNA content. Constructs were able to recapitulate native T/L tissue characteristics particularly with regard to ECM proteins. However, 3D T/L TE constructs had similar ECM and cellular protein compositions indicating that cell source may not be an important factor for T/L tissue engineering. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Native Mass Spectrometry in Fragment-Based Drug Discovery

Directory of Open Access Journals (Sweden)

Liliana Pedro

2016-07-01

Full Text Available The advent of native mass spectrometry (MS in 1990 led to the development of new mass spectrometry instrumentation and methodologies for the analysis of noncovalent protein–ligand complexes. Native MS has matured to become a fast, simple, highly sensitive and automatable technique with well-established utility for fragment-based drug discovery (FBDD. Native MS has the capability to directly detect weak ligand binding to proteins, to determine stoichiometry, relative or absolute binding affinities and specificities. Native MS can be used to delineate ligand-binding sites, to elucidate mechanisms of cooperativity and to study the thermodynamics of binding. This review highlights key attributes of native MS for FBDD campaigns.

Isolation and characterization of starch from industrial fresh pasta by-product and its potential use in sugar-snap cookie making.

Science.gov (United States)

Ellouzi, Soumaya Zouari; Driss, Dorra; Maktouf, Sameh; Neifar, Mohamed; Kobbi, Ameni; Kamoun, Hounaida; Chaabouni, Semia Ellouze; Ghorbel, Raoudha Ellouze

2015-09-01

In this paper, starch was extracted from fresh pasta by-product (PS) and its chemical composition and physical and microscopic characteristics were determined. Commercial wheat starch (CS) was used as reference. In general, purity was similar between starches studied. However, others compounds such as protein, lipid and ash were significantly different. PS starch granules had large lenticular-shape (25-33 μm) and small spherical-shape (5-8 μm). The pH and color of PS starch were similar to those reported for CS starch. On the other hand, PS had higher water absorption capacity, viscosity and cooking stability than CS. The gelatinization temperature of PS was similar to that of CS (60 and 61 °C). At high temperature (90 °C) both starches had similar rheological behavior. The results achieved suggest that PS starch has potential for application in food systems requiring high processing temperatures such the manufacture of sugar snap cookie. The effects of PS starch addition on the dough making stage and the final cookie quality were analyzed. Improvements in dough cohesiveness (24 %) and springiness (10 %) were significant relative to those of CS dough. Texture profile analysis confirmed the rheological changes.

Developmental regulation of silk protein P25 in the silkworm ...

Indian Academy of Sciences (India)

tribpo

anti-P25 sera were raised in rabbit and mice. The relative ... of B. mori. Couble et al (1983) identified a new mRNA species in the posterior ... quantitative changes in P25 protein level during development in B. mori. 2 . ..... physiology biochemistry and pharmacology (eds) G A Kerkut and L I Gilbert (New York: Pergamon.

Critical homoclinic orbits lead to snap-back repellers

International Nuclear Information System (INIS)

Gardini, Laura; Sushko, Iryna; Avrutin, Viktor; Schanz, Michael

2011-01-01

Highlights: → We consider critical homoclinic orbits in continuous and discontinuous maps. → Unbounded homoclinic orbits in maps on unbounded domains are considered as well. → We show that a snapback-repeller (SBR) with a non-critical homoclinic orbit implies chaos. → We show also that a SBR with a critical homoclinic orbit may or may not imply chaos. - Abstract: When nondegenerate homoclinic orbits to an expanding fixed point of a map f:X→X,X subset or equal R n , exist, the point is called a snap-back repeller. It is known that the relevance of a snap-back repeller (in its original definition) is due to the fact that it implies the existence of an invariant set on which the map is chaotic. However, when does the first homoclinic orbit appear? When can other homoclinic explosions, i.e., appearance of infinitely many new homoclinic orbits, occur? As noticed by many authors, these problems are still open. In this work we characterize these bifurcations, for any kind of map, smooth or piecewise smooth, continuous or discontinuous, defined in a bounded or unbounded closed set. We define a noncritical homoclinic orbit and a homoclinic orbit of an expanding fixed point is structurally stable iff it is noncritical. That is, only critical homoclinic orbits are responsible for the homoclinic explosions. The possible kinds of critical homoclinic orbits will be also investigated, as well as their dynamic role.

Formation of truncated proteins and high-molecular-mass aggregates upon soft illumination of photosynthetic proteins

DEFF Research Database (Denmark)

Rinalducci, Sara; Campostrini, Natascia; Antonioli, Paolo

2005-01-01

Different spot profiles were observed in 2D gel electrophoresis of thylakoid membranes performed either under complete darkness or by leaving the sample for a short time to low visible light. In the latter case, a large number of new spots with lower molecular masses, ranging between 15,000 and 25......,000 Da, were observed, and high-molecular-mass aggregates, seen as a smearing in the upper part of the gel, appeared in the region around 250 kDa. Identification of protein(s) contained in these new spots by MS/MS revealed that most of them are simply truncated proteins deriving from native ones...

Boundaries of mass resolution in native mass spectrometry

NARCIS (Netherlands)

Lössl, Philip|info:eu-repo/dai/nl/371559693; Snijder, Joost|info:eu-repo/dai/nl/338018328; Heck, Albert J R|info:eu-repo/dai/nl/105189332

Over the last two decades, native mass spectrometry (MS) has emerged as a valuable tool to study intact proteins and noncovalent protein complexes. Studied experimental systems range from small-molecule (drug)-protein interactions, to nanomachineries such as the proteasome and ribosome, to even

SNAP 19 Viking RTG mission performance

International Nuclear Information System (INIS)

Brittain, W.M.

1976-01-01

The Viking-75 mission utilized the August/September 1975 opportunity to launch two spacecrafts to Mars for arrival in 1976 after about a one-year transit period. On arrival, each spacecraft, consisting of an orbiter and lander, will be placed in Mars orbit, with each lander subsequently descending from orbit to a soft-landing on the Martian surface. Two SNAP 19 RTG's (radioisotope thermoelectric generators) provide the primary source of electrical power and means of thermal control for each Viking lander. The RTG's will be switched on-load just prior to separation of the lander from the orbiter for checkout of the lander, and will remain on-load during entry and the remainder of the 90-day minimum surface mission

SNAP Participation in Preschool-Aged Children and Prevalence of Overweight and Obesity

Science.gov (United States)

Simmons, Shannon; Alexander, Jeffrey L.; Ewing, Helen; Whetzel, Stephanie

2012-01-01

Background: An increased prevalence of overweight and obesity for adults on government-funded nutrition assistance, such as the Supplemental Nutrition Assistance Program (SNAP), has been observed; however, this association among preschool-aged children is not well understood. Longitudinal research designs tracking changes in body mass…

The Australian National Sub-acute and Non-acute Patient Casemix Classification (AN-SNAP): its application and value in a stroke rehabilitation programme.

Science.gov (United States)

Lowthian, P; Disler, P; Ma, S; Eagar, K; Green, J; de Graaff, S

2000-10-01

To investigate whether the Australian National Sub-acute and Non-acute Patient Casemix Classification (SNAP) and Functional Independence Measure and Functional Related Group (Version 2) (FIM-FRG2) casemix systems can be used to predict functional outcome, and reduce the variance of length of stay (LOS) of patients undergoing rehabilitation after strokes. The study comprised a retrospective analysis of the records of patients admitted to the Cedar Court Healthsouth Rehabilitation Hospital for rehabilitation after stroke. The sample included 547 patients (83.3% of those admitted with stroke during this period). Patient data were stratified for analysis into the five SNAP or nine FIM-FRG2 groups, on the basis of the admission FIM scores and age. The AN-SNAP classification accounted for a 30.7% reduction of the variance of LOS, and 44.2% of motor FIM, and the FIM-FRG2 accounts for 33.5% and 56.4% reduction respectively. Comparison of the Cedar Court with the national AN-SNAP data showed differences in the LOS and functional outcomes of older, severely disabled patients. Intensive rehabilitation in selected patients of this type appears to have positive effects, albeit with a slightly longer period of inpatient rehabilitation. Casemix classifications can be powerful management tools. Although FIM-FRG2 accounts for more reduction in variance than SNAP, division into nine groups meant that some contained few subjects. This paper supports the introduction of AN-SNAP as the standard casemix tool for rehabilitation in Australia, which will hopefully lead to rational, adequate funding of the rehabilitation phase of care.

Experimental exposure of eggs to polybrominated diphenyl ethers BDE-47 and BDE-99 in red-eared sliders (Trachemys scripta elegans) and snapping turtles (Chelydra serpentina) and possible species-specific differences in debromination.

Science.gov (United States)

Eisenreich, Karen M; Rowe, Christopher L

2013-02-01

Polybrominated diphenyl ethers (PBDEs) are a bioaccumulative, persistent, and toxic class of flame retardants that can potentially impact turtles in natural habitats via exposure through maternal transfer. To simulate maternal transfer in the present study, PBDE congeners BDE-47 and BDE-99 were topically applied to the eggshell and were allowed to diffuse into the egg contents of the red-eared slider (Trachemys scripta elegans) and snapping turtle (Chelydra serpentina). Eggs were topically dosed over 8 d to achieve a target concentration of 40 ng/g in the egg contents. Transfer efficiency was higher for BDE-47 than for BDE-99 in the red-eared sliders (25.8 ± 1.9% vs 9.9 ± 1.1%) and snapping turtles (31.3 ± 1.6% vs 12.5 ± 1.4%), resulting in greater BDE-47 and lower BDE-99 egg content concentrations relative to the 40 ng/g target. However, only 25.8 and 31.3% of the total BDE-47 and 9.9 and 12.5% of the total BDE-99 dose applied could be accounted for in the red-eared slider and snapping turtle egg contents, respectively. Additionally, increased BDE-47 in red-eared slider egg contents dosed with only BDE-99 indicate that BDE-99 might have been debrominated to BDE-47. The efficacy of topical dosing for administering desired embryonic exposures is clearly affected by the chemical properties of the applied compounds and was more successful for BDE-47 in both species. Copyright © 2012 SETAC.

Lipid droplets interact with mitochondria using SNAP23

DEFF Research Database (Denmark)

Jägerström, Sara; Polesie, Sam; Wickström, Ylva

2009-01-01

peroxisomes and the endoplasmic reticulum. We have used electron and confocal microscopy to demonstrate that LD form complexes with mitochondria in NIH 3T3 fibroblasts. Using an in vitro system of purified LD and mitochondria, we also show the formation of the LD-mitochondria complex, in which cytosolic...... factors are involved. Moreover, the presence of LD markers in mitochondria isolated by subcellular fractionations is demonstrated. Finally, ablation of SNAP23 using siRNA reduced complex formation and beta oxidation, which suggests that the LD-mitochondria complex is functional in the cell....

Native Liquid Extraction Surface Analysis Mass Spectrometry: Analysis of Noncovalent Protein Complexes Directly from Dried Substrates

Science.gov (United States)

Martin, Nicholas J.; Griffiths, Rian L.; Edwards, Rebecca L.; Cooper, Helen J.

2015-08-01

Liquid extraction surface analysis (LESA) mass spectrometry is a promising tool for the analysis of intact proteins from biological substrates. Here, we demonstrate native LESA mass spectrometry of noncovalent protein complexes of myoglobin and hemoglobin from a range of surfaces. Holomyoglobin, in which apomyoglobin is noncovalently bound to the prosthetic heme group, was observed following LESA mass spectrometry of myoglobin dried onto glass and polyvinylidene fluoride surfaces. Tetrameric hemoglobin [(αβ)2 4H] was observed following LESA mass spectrometry of hemoglobin dried onto glass and polyvinylidene fluoride (PVDF) surfaces, and from dried blood spots (DBS) on filter paper. Heme-bound dimers and monomers were also observed. The `contact' LESA approach was particularly suitable for the analysis of hemoglobin tetramers from DBS.

Sex differences in the effects of pre- and postnatal caffeine exposure on behavior and synaptic proteins in pubescent rats.

Science.gov (United States)

Sallaberry, Cássia; Ardais, Ana Paula; Rocha, Andréia; Borges, Maurício Felisberto; Fioreze, Gabriela T; Mioranzza, Sabrina; Nunes, Fernanda; Pagnussat, Natália; Botton, Paulo Henrique S; Porciúncula, Lisiane O

2018-02-02

Few studies have addressed the effects of caffeine in the puberty and/or adolescence in a sex dependent manner. Considering that caffeine intake has increased in this population, we investigated the behavioral and synaptic proteins changes in pubescent male and female rats after maternal consumption of caffeine. Adult female Wistar rats started to receive water or caffeine (0.1 and 0.3g/L in drinking water; low and moderate dose, respectively) during the active cycle at weekdays, two weeks before mating. The treatment lasted up to weaning and the offspring received caffeine until the onset of puberty (30-34days old). Behavioral tasks were performed to evaluate locomotor activity (open field task), anxious-like behavior (elevated plus maze task) and recognition memory (object recognition task) and synaptic proteins levels (proBDNF, BDNF, GFAP and SNAP-25) were verified in the hippocampus and cerebral cortex. While hyperlocomotion was observed in both sexes after caffeine treatment, anxiety-related behavior was attenuated by caffeine (0.3g/L) only in females. While moderate caffeine worsened recognition memory in females, an improvement in the long-term memory was observed in male rats for both doses. Coincident with memory improvement in males, caffeine increased pro- and BDNF in the hippocampus and cortex. Females presented increased proBDNF levels in both brain regions, with no effects of caffeine. While GFAP was not altered, moderate caffeine intake increased SNAP-25 in the cortex of female rats. Our findings revealed that caffeine promoted cognitive benefits in males associated with increased BDNF levels, while females showed less anxiety. Our findings revealed that caffeine promotes distinct behavioral outcomes and alterations in synaptic proteins during brain development in a sex dependent manner. Copyright © 2017 Elsevier Inc. All rights reserved.

Neutron flux calculations for the Rossendorf research reactor in (hex)- and (hex,z)-geometry using SNAP-3D

International Nuclear Information System (INIS)

Koch, R.; Findeisen, A.

1986-04-01

The multigroup neutron diffusion theory code SNAP-3D has been used to perform time independent neutron flux and power calculations of the 10 MW Rossendorf research reactor of the type WWR-SM. The report describes these calculations, as well as the actual reactor configuration, some details of the code SNAP-3D, and two- and three-dimensional reactor models. For evaluating the calculations some flux values and control rod worths have been compared with those of measurements. (author)

The Schedule for Nonadaptive and Adaptive Personality for Youth (SNAP-Y): A New Measure for Assessing Adolescent Personality and Personality Pathology

Science.gov (United States)

Linde, Jennifer A.; Stringer, Deborah; Simms, Leonard J.; Clark, Lee Anna

2013-01-01

The Schedule for Nonadaptive and Adaptive Personality-Youth Version (SNAP-Y) is a new, reliable self-report questionnaire that assesses 15 personality traits relevant to both normal-range personality and the alternative "DSM"-5 model for personality disorder. Community adolescents, 12 to 18 years old (N = 364), completed the SNAP-Y; 347…

Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements

Directory of Open Access Journals (Sweden)

Sze Sing-Hoi

2008-07-01

Full Text Available Abstract Background Since experimental determination of protein folding pathways remains difficult, computational techniques are often used to simulate protein folding. Most current techniques to predict protein folding pathways are computationally intensive and are suitable only for small proteins. Results By assuming that the native structure of a protein is known and representing each intermediate conformation as a collection of fully folded structures in which each of them contains a set of interacting secondary structure elements, we show that it is possible to significantly reduce the conformation space while still being able to predict the most energetically favorable folding pathway of large proteins with hundreds of residues at the mesoscopic level, including the pig muscle phosphoglycerate kinase with 416 residues. The model is detailed enough to distinguish between different folding pathways of structurally very similar proteins, including the streptococcal protein G and the peptostreptococcal protein L. The model is also able to recognize the differences between the folding pathways of protein G and its two structurally similar variants NuG1 and NuG2, which are even harder to distinguish. We show that this strategy can produce accurate predictions on many other proteins with experimentally determined intermediate folding states. Conclusion Our technique is efficient enough to predict folding pathways for both large and small proteins at the mesoscopic level. Such a strategy is often the only feasible choice for large proteins. A software program implementing this strategy (SSFold is available at http://faculty.cs.tamu.edu/shsze/ssfold.

THE EFFECTS OF OXIDANT AIR POLLUTANTS ON SOYBEANS, SNAP BEANS AND POTATOES

Science.gov (United States)

During the past 5 years the impact of photochemical oxidants on soybeans and snap beans in Maryland and on potatoes in Virginia and Delaware was assessed with open-top chambers. The mean yields of four selected soybean varieties grown in open-top chambers with carbon-filtered air...

25 CFR 163.40 - Indian and Alaska Native forestry education assistance.

Science.gov (United States)

2010-04-01

... professional educator, a personnel specialist, an Indian or Alaska Native who is not employed by the Bureau of...-secondary mathematics and science courses; (ii) Promote forestry career awareness that could include modern...

Diatoms on the carapace of common snapping turtles: Luticola spp. dominate despite spatial variation in assemblages.

Directory of Open Access Journals (Sweden)

Shelly C Wu

Full Text Available Filamentous algae are often visible on the carapaces of freshwater turtles and these algae are dominated by a few species with varying geographic distributions. Compared to filamentous algae, little is known about the much more speciose microalgae on turtles. Our objectives were to compare the diatom flora on a single turtle species (the common snapping turtle, Chelydra serpentina across part of its range to examine spatial patterns and determine whether specific diatom taxa were consistently associated with turtles (as occurs in the filamentous alga Basicladia spp.. Using preserved turtle specimens from museums, we systematically sampled diatoms on the carapaces of 25 snapping turtles across five states. The diverse diatom assemblages formed two groups-the southern Oklahoma group and the northern Illinois/Wisconsin/New York group, with Arkansas not differing from either group. Of the six diatom species found in all five states, four species are widespread, whereas Luticola cf. goeppertiana and L. cf. mutica are undescribed species, known only from turtles in our study. L. cf. goeppertiana comprised 83% of the diatom abundance on Oklahoma turtles and was relatively more abundant on southern turtles (Oklahoma and Arkansas than on northern turtles (where mean abundance/state was > 10%. L. cf. mutica was the most abundant species (40% on New York turtles. Some Luticola species are apparently turtle associates and results support a pattern of spatial variation in Luticola species, similar to that in Basicladia. Using museum specimens is an efficient and effective method to study the distribution of micro-epibionts.

Diatoms on the carapace of common snapping turtles: Luticola spp. dominate despite spatial variation in assemblages

Science.gov (United States)

Wu, Shelly C.; Bergey, Elizabeth A.

2017-01-01

Filamentous algae are often visible on the carapaces of freshwater turtles and these algae are dominated by a few species with varying geographic distributions. Compared to filamentous algae, little is known about the much more speciose microalgae on turtles. Our objectives were to compare the diatom flora on a single turtle species (the common snapping turtle, Chelydra serpentina) across part of its range to examine spatial patterns and determine whether specific diatom taxa were consistently associated with turtles (as occurs in the filamentous alga Basicladia spp.). Using preserved turtle specimens from museums, we systematically sampled diatoms on the carapaces of 25 snapping turtles across five states. The diverse diatom assemblages formed two groups–the southern Oklahoma group and the northern Illinois/Wisconsin/New York group, with Arkansas not differing from either group. Of the six diatom species found in all five states, four species are widespread, whereas Luticola cf. goeppertiana and L. cf. mutica are undescribed species, known only from turtles in our study. L. cf. goeppertiana comprised 83% of the diatom abundance on Oklahoma turtles and was relatively more abundant on southern turtles (Oklahoma and Arkansas) than on northern turtles (where mean abundance/state was > 10%). L. cf. mutica was the most abundant species (40%) on New York turtles. Some Luticola species are apparently turtle associates and results support a pattern of spatial variation in Luticola species, similar to that in Basicladia. Using museum specimens is an efficient and effective method to study the distribution of micro-epibionts. PMID:28192469

Immuno-detection of cleaved SNAP-25 from differentiated mouse embryonic stem cells provides a sensitive assay for determination of botulinum A toxin and antitoxin potency.

Science.gov (United States)

Yadirgi, G; Stickings, P; Rajagopal, S; Liu, Y; Sesardic, D

2017-12-01

Botulinum toxin type A is a causative agent of human botulism. Due to high toxicity and ease of production it is classified by the Centres for Disease Control and Prevention as a category A bioterrorism agent. The same serotype, BoNT/A, is also the most widely used in pharmaceutical preparations for treatment of a diverse range of neuromuscular disorders. Traditionally, animals are used to confirm the presence and activity of toxin and to establish neutralizing capabilities of countermeasures in toxin neutralization tests. Cell based assays for BoNT/A have been reported as the most viable alternative to animal models, since they are capable of reflecting all key steps (binding, translocation, internalization and cleavage of intracellular substrate) involved in toxin activity. In this paper we report preliminary development of a simple immunochemical method for specifically detecting BoNT/A cleaved intracellular substrate, SNAP-25, in cell lysates of neurons derived from mouse embryonic stem cells. The assay offers sensitivity of better than 0.1LD50/ml (3fM) which is not matched by other functional assays, including the mouse bioassay, and provides serotype specificity for quantitative detection of BoNT/A and anti-BoNT/A antitoxin. Subject to formal validation, the method described here could potentially be used as a substitute for the mouse bioassay to measure potency and consistency of therapeutic products. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

The mobility of food retailers: How proximity to SNAP authorized food retailers changed in Atlanta during the Great Recession.

Science.gov (United States)

Shannon, Jerry; Bagwell-Adams, Grace; Shannon, Sarah; Lee, Jung Sun; Wei, Yangjiaxin

2018-07-01

Retailer mobility, defined as the shifting geographic patterns of retail locations over time, is a significant but understudied factor shaping neighborhood food environments. Our research addresses this gap by analyzing changes in proximity to SNAP authorized chain retailers in the Atlanta urban area using yearly data from 2008 to 2013. We identify six demographically similar geographic clusters of census tracts in our study area based on race and economic variables. We use these clusters in exploratory data analysis to identify how proximity to the twenty largest retail food chains changed during this period. We then use fixed effects models to assess how changing store proximity is associated with race, income, participation in SNAP, and population density. Our results show clear differences in geographic distribution between store categories, but also notable variation within each category. Increasing SNAP enrollment predicted decreased distances to almost all small retailers but increased distances to many large retailers. Our chain-focused analysis underscores the responsiveness of small retailers to changes in neighborhood SNAP participation and the value of tracking chain expansion and contraction in markets across time. Better understanding of retailer mobility and the forces that drive it can be a productive avenue for future research. Copyright © 2018 Elsevier Ltd. All rights reserved.

Geometrically controlled snapping transitions in shells with curved creases.

Science.gov (United States)

Bende, Nakul Prabhakar; Evans, Arthur A; Innes-Gold, Sarah; Marin, Luis A; Cohen, Itai; Hayward, Ryan C; Santangelo, Christian D

2015-09-08

Curvature and mechanics are intimately connected for thin materials, and this coupling between geometry and physical properties is readily seen in folded structures from intestinal villi and pollen grains to wrinkled membranes and programmable metamaterials. While the well-known rules and mechanisms behind folding a flat surface have been used to create deployable structures and shape transformable materials, folding of curved shells is still not fundamentally understood. Shells naturally deform by simultaneously bending and stretching, and while this coupling gives them great stability for engineering applications, it makes folding a surface of arbitrary curvature a nontrivial task. Here we discuss the geometry of folding a creased shell, and demonstrate theoretically the conditions under which it may fold smoothly. When these conditions are violated we show, using experiments and simulations, that shells undergo rapid snapping motion to fold from one stable configuration to another. Although material asymmetry is a proven mechanism for creating this bifurcation of stability, for the case of a creased shell, the inherent geometry itself serves as a barrier to folding. We discuss here how two fundamental geometric concepts, creases and curvature, combine to allow rapid transitions from one stable state to another. Independent of material system and length scale, the design rule that we introduce here explains how to generate snapping transitions in arbitrary surfaces, thus facilitating the creation of programmable multistable materials with fast actuation capabilities.

Comparison of CLASS and ITK-SNAP in segmentation of urinary bladder in CT urography

Science.gov (United States)

Cha, Kenny; Hadjiiski, Lubomir; Chan, Heang-Ping; Caoili, Elaine M.; Cohan, Richard H.; Zhou, Chuan

2014-03-01

We are developing a computerized method for bladder segmentation in CT urography (CTU) for computeraided diagnosis of bladder cancer. We have developed a Conjoint Level set Analysis and Segmentation System (CLASS) consisting of four stages: preprocessing and initial segmentation, 3D and 2D level set segmentation, and post-processing. In case the bladder contains regions filled with intravenous (IV) contrast and without contrast, CLASS segments the noncontrast (NC) region and the contrast (C) filled region separately and conjoins the contours. In this study, we compared the performance of CLASS to ITK-SNAP 2.4, which is a publicly available software application for segmentation of structures in 3D medical images. ITK-SNAP performs segmentation by using the edge-based level set on preprocessed images. The level set were initialized by manually placing a sphere at the boundary between the C and NC parts of the bladders with C and NC regions, and in the middle of the bladders that had only C or NC region. Level set parameters and the number of iterations were chosen after experimentation with bladder cases. Segmentation performances were compared using 30 randomly selected bladders. 3D hand-segmented contours were obtained as reference standard, and computerized segmentation accuracy was evaluated in terms of the average volume intersection %, average % volume error, average absolute % volume error, average minimum distance, and average Jaccard index. For CLASS, the values for these performance metrics were 79.0±8.2%, 16.1±16.3%, 19.9±11.1%, 3.5±1.3 mm, 75.7±8.4%, respectively. For ITK-SNAP, the corresponding values were 78.8±8.2%, 8.3±33.1%, 24.2±23.7%, 5.2±2.6 mm, 71.0±15.4%, respectively. CLASS on average performed better and exhibited less variations than ITK-SNAP for bladder segmentation.

Precise determination of protein extinction coefficients under native and denaturing conditions using SV-AUC.

Science.gov (United States)

Hoffmann, Andreas; Grassl, Kerstin; Gommert, Janine; Schlesak, Christian; Bepperling, Alexander

2018-04-17

The accurate determination of protein concentration is an important though non-trivial task during the development of a biopharmaceutical. The fundamental prerequisite for this is the availability of an accurate extinction coefficient. Common approaches for the determination of an extinction coefficient for a given protein are either based on the theoretical prediction utilizing the amino acid sequence or the photometric determination combined with a measurement of absolute protein concentration. Here, we report on an improved SV-AUC based method utilizing an analytical ultracentrifuge equipped with absorbance and Rayleigh interference optics. Global fitting of datasets helped to overcome some of the obstacles encountered with the traditional method employing synthetic boundary cells. Careful calculation of dn/dc values taking glycosylation and solvent composition into account allowed the determination of the extinction coefficients of monoclonal antibodies and an Fc-fusion protein under native as well as under denaturing conditions. An intra-assay precision of 0.9% and an accuracy of 1.8% compared to the theoretical value was achieved for monoclonal antibodies. Due to the large number of data points of a single dataset, no meaningful difference between the ProteomeLab XL-I and the new Optima AUC platform could be observed. Thus, the AUC-based approach offers a precise, convenient and versatile alternative to conventional methods like total amino acid analysis (AAA).

Low dose radiation induced protein and its effect on expression of CD25 molecule in lymphocytes

International Nuclear Information System (INIS)

Lu Duicai; Su Liaoyuan

2001-01-01

Objective: To find the substantial basis for effects of low dose radiation, on development, extraction, and the biogical activity of the low-dose radiation-induced proteins, and the effects of LDR induced proteins on CD25 molecule expression of human lymphocytes. Methods: 1. Healthy Kumning male mice exposed to radiation of 226 Ra γ-rays at 5, 10 and 15 cGy respectively. The mice were killed 2 hours after exposure, the spleen cells were broken with ultrasonic energy and then ultra-centrifugalized at low temperature (4 degree C). The LDR-induced proteins were obtained in the supernatant solution. Then the changes of CD25 molecule was measured by flow cytometry (FCM) with immunofluorescence technique, which was used to reflect the effect of LDR induced proteins on CD25 molecule expression of human lymphocytes. Results: LDR induced proteins were obtained from spleen cells in mice exposed to 5-15 cGy whole body radiation. Conclusion: The expression of CD25 molecule of lymphocytes was increased significantly after use of LDR induced proteins. LDR induced proteins can enhance expression of CD25 molecule of lymphocytes slightly

An improved method to prepare an injectable microemulsion of the galanin-receptor 3 selective antagonist, SNAP 37889, using Kolliphor® HS 15

Science.gov (United States)

Scheller, Karlene J.; Williams, Spencer J.; Lawrence, Andrew J.; Jarrott, Bevyn; Djouma, Elvan

2014-01-01

Research into the galanin-3 (GAL3) receptor has many challenges, including the lack of commercially available selective ligands. While the identification of non-peptidergic GAL3 receptor-selective antagonists, 1-phenyl-3-[3-(trifluoromethyl)phenyl]iminoindol-2-one (SNAP 37889) and 1-[3-(2-pyrrolidin-1-ylethoxy)phenyl]-3-[3-(trifluoromethyl)phenyl]iminoindol-2-one (SNAP 398299) have implicated a role for GAL3 receptors in anxiety, depression and drug-seeking behaviour, a major limitation of their use is poor aqueous solubility. Previously we have used 5% dimethylsulfoxide (DMSO) with 1% hydroxypropylmethyl cellulose in saline to dissolve SNAP 37889 for intraperitoneal (i.p.) injections of rats; however this produced a micro-suspension that was not ideal. The injectable formulation of SNAP 37889 was improved as follows:•30% (w/v) Kolliphor® HS 15 (Solutol HS® 15) and sodium phosphate buffer (0.01 M, pH 7.4) were used as vehicles.•A smooth glass mortar and pestle was used to triturate the Kolliphor® HS 15 and SNAP 37889 into a paste before addition to the sodium phosphate buffer at room temperature (RT).•The resulting mixture was vortexed until the paste was fully dissolved and the microemulsion was allowed to sit for 20 min to allow air bubbles to coalesce. PMID:26150955

Supercharging Protein Complexes from Aqueous Solution Disrupts their Native Conformations

Science.gov (United States)

Sterling, Harry J.; Kintzer, Alexander F.; Feld, Geoffrey K.; Cassou, Catherine A.; Krantz, Bryan A.; Williams, Evan R.

2012-02-01

The effects of aqueous solution supercharging on the solution- and gas-phase structures of two protein complexes were investigated using traveling-wave ion mobility-mass spectrometry (TWIMS-MS). Low initial concentrations of m-nitrobenzyl alcohol ( m-NBA) in the electrospray ionization (ESI) solution can effectively increase the charge of concanavalin A dimers and tetramers, but at higher m-NBA concentrations, the increases in charge are accompanied by solution-phase dissociation of the dimers and up to a ~22% increase in the collision cross section (CCS) of the tetramers. With just 0.8% m-NBA added to the ESI solution of a ~630 kDa anthrax toxin octamer complex, the average charge is increased by only ~4% compared with the "native" complex, but it is sufficiently destabilized so that extensive gas-phase fragmentation occurs in the relatively high pressure regions of the TWIMS device. Anthrax toxin complexes exist in either a prechannel or a transmembrane channel state. With m-NBA, the prechannel state of the complex has the same CCS/charge ratio in the gas phase as the transmembrane channel state of the same complex formed without m-NBA, yet undergoes extensive dissociation, indicating that destabilization from supercharging occurs in the ESI droplet prior to ion formation and is not a result of Coulombic destabilization in the gas phase as a result of higher charging. These results demonstrate that the supercharging of large protein complexes is the result of conformational changes induced by the reagents in the ESI droplets, where enrichment of the supercharging reagent during droplet evaporation occurs.

Sorting of a HaloTag protein that has only a signal peptide sequence into exocrine secretory granules without protein aggregation.

Science.gov (United States)

Fujita-Yoshigaki, Junko; Matsuki-Fukushima, Miwako; Yokoyama, Megumi; Katsumata-Kato, Osamu

2013-11-15

The mechanism involved in the sorting and accumulation of secretory cargo proteins, such as amylase, into secretory granules of exocrine cells remains to be solved. To clarify that sorting mechanism, we expressed a reporter protein HaloTag fused with partial sequences of salivary amylase protein in primary cultured parotid acinar cells. We found that a HaloTag protein fused with only the signal peptide sequence (Met(1)-Ala(25)) of amylase, termed SS25H, colocalized well with endogenous amylase, which was confirmed by immunofluorescence microscopy. Percoll-density gradient centrifugation of secretory granule fractions shows that the distributions of amylase and SS25H were similar. These results suggest that SS25H is transported to secretory granules and is not discriminated from endogenous amylase by the machinery that functions to remove proteins other than granule cargo from immature granules. Another reporter protein, DsRed2, that has the same signal peptide sequence also colocalized with amylase, suggesting that the sorting to secretory granules is not dependent on a characteristic of the HaloTag protein. Whereas Blue Native PAGE demonstrates that endogenous amylase forms a high-molecular-weight complex, SS25H does not participate in the complex and does not form self-aggregates. Nevertheless, SS25H was released from cells by the addition of a β-adrenergic agonist, isoproterenol, which also induces amylase secretion. These results indicate that addition of the signal peptide sequence, which is necessary for the translocation in the endoplasmic reticulum, is sufficient for the transportation and storage of cargo proteins in secretory granules of exocrine cells.

High-level secretion of native recombinant human calreticulin in yeast

DEFF Research Database (Denmark)

Čiplys, Evaldas; Žitkus, Eimantas; Gold, Leslie I.

2015-01-01

, Saccharomyces cerevisiae and Pichia pastoris. RESULTS: Expression of a full-length human CRT precursor including its native signal sequence resulted in high-level secretion of mature recombinant protein into the culture medium by both S. cerevisiae and P. pastoris. To ensure the structural and functional...... by non-denaturing PAGE. Moreover, limited trypsin digestion yielded identical fragment patterns of calcium-binding recombinant and native CRT suggesting that the yeast-derived CRT was correctly folded. Furthermore, both native and recombinant CRT induced cellular proliferation (MTS assay) and migration...... recombinant CRT protein with yields reaching 75 % of total secreted protein and with production levels of 60 and 200 mg/l from S. cerevisiae and P. pastoris, respectively. Finally, cultivation of P. pastoris in a bioreactor yielded CRT secretion titer to exceed 1.5 g/l of culture medium. CONCLUSIONS: Yeasts...

Mercury concentrations in snapping turtles (Chelydra serpentina) correlate with environmental and landscape characteristics.

Science.gov (United States)

Turnquist, Madeline A; Driscoll, Charles T; Schulz, Kimberly L; Schlaepfer, Martin A

2011-10-01

Mercury (Hg) deposited onto the landscape can be transformed into methylmercury (MeHg), a neurotoxin that bioaccumulates up the aquatic food chain. Here, we report on Hg concentrations in snapping turtles (Chelydra serpentina) across New York State, USA. The objectives of this study were to: (1) test which landscape, water, and biometric characteristics correlate with total Hg (THg) concentrations in snapping turtles; and (2) determine whether soft tissue THg concentrations correlate with scute (shell) concentrations. Forty-eight turtles were sampled non-lethally from ten lakes and wetlands across New York to observe patterns under a range of ecosystem variables and water chemistry conditions. THg concentrations ranged from 0.041 to 1.50 μg/g and 0.47 to 7.43 μg/g wet weight of muscle tissue and shell, respectively. The vast majority of mercury (~94%) was in the MeHg form. Sixty-one percent of turtle muscle samples exceeded U.S. Environmental Protection Agency (U.S. EPA) consumption advisory limit of 0.3 μg Hg/g for fish. Muscle THg concentrations were significantly correlated with sulfate in water and the maximum elevation of the watershed. Shell THg concentrations were significantly correlated with the acid neutralizing capacity (ANC) of water, the maximum elevation of the watershed, the percent open water in the watershed, the lake to watershed size, and various forms of atmospheric Hg deposition. Thus, our results demonstrate that THg concentrations in snapping turtles are spatially variable, frequently exceed advisory limits, and are significantly correlated with several landscape and water characteristics.

Restructuring a State Nutrition Education and Obesity Prevention Program: Implications of a Local Health Department Model for SNAP-Ed.

Science.gov (United States)

Wu, Helen W; Backman, Desiree; Kizer, Kenneth W

The US Department of Agriculture Supplemental Nutrition Assistance Program-Education (SNAP-Ed) funds state programs to improve nutrition and physical activity in low-income populations through its Nutrition Education and Obesity Prevention grants. States vary in how they manage and structure these programs. California substantially restructured its program in 2012 to universally position local health departments (LHDs) as the programmatic lead in all jurisdictions. This study sought to determine whether California's reorganization aligned with desirable attributes of decentralized public management. This study conducted 40 in person, semistructured interviews with 57 local, state, and federal SNAP-Ed stakeholders between October 2014 and March 2015. Local respondents represented 15 counties in all 7 of California's SNAP-Ed regions. We identified 3 common themes that outlined advantages or disadvantages of local public management, and we further defined subthemes within: (1) coordination and communication (within local jurisdictions, across regions, between local and state), (2) efficiency (administrative, fiscal, program), and (3) quality (innovation, skills). We conducted qualitative content analysis to evaluate how respondents characterized the California experience for each theme, identifying positive and negative experiences. California's LHD model offers some distinct advantages, but the model does not exhibit all the advantages of decentralized public management. Strategic planning, partnerships, subcontracting, and fiscal oversight are closer to communities than previously. However, administrative burden remains high and LHDs are limited in their ability to customize programs on the basis of community needs because of state and federal constraints. California's use of a universal LHD model for SNAP-Ed is novel. Recent federal SNAP-Ed changes present an opportunity for other states to consider this structure. Employing small-scale approaches initially (eg

The orphan G protein-coupled receptor 25 (GPR25) is activated by Apelin and Apela in non-mammalian vertebrates.

Science.gov (United States)

Zhang, Jiannan; Wan, Yiping; Fang, Chao; Chen, Junan; Ouyang, Wangan; Li, Juan; Wang, Yajun

2018-06-22

G protein-coupled receptor 25 (GPR25) is an orphan G protein-coupled receptor in vertebrates, that has been implicated to be associated with autoimmune diseases and regulate blood pressure in humans. However, the endogenous ligand of GPR25 remains unknown in vertebrates. Here, we reported that in non-mammalian vertebrates (zebrafish, spotted gars, and pigeons), GPR25 could be activated by Apelin and Apela peptides, which are also the two endogenous ligands of vertebrate Apelin receptor (APLNR). Using the pGL3-CRE-luciferase reporter assay and confocal microscopy, we first demonstrated that like APLNR, zebrafish GPR25 expressing in HEK293 cells could be effectively activated by zebrafish Apelin and Apela peptides, leading to the inhibition of forskolin-stimulated cAMP production and receptor internalization. Like zebrafish GPR25, pigeon and spotted gar GPR25 could also be activated by Apelin and Apela, and their activation could inhibit forskolin-induced cAMP accumulation. Interestingly, unlike zebrafish (/spotted gar/pigeon) GPR25, human GPR25 could not be activated by Apelin and Apela under the same experimental conditions. RNA-seq analysis further revealed that GPR25 is expressed in a variety of tissues, including the testes and intestine of zebrafish/spotted gars/humans, implying the potential roles of GPR25 signaling in many physiological processes in vertebrates. Taken together, our data not only provides the first proof that the orphan receptor GPR25 possesses two potential ligands 'Apelin and Apela' and its activation decreases intracellular cAMP levels in non-mammalian vertebrates, but also facilitates to unravel the physiological roles of GPR25 signaling in vertebrates. Copyright © 2018 Elsevier Inc. All rights reserved.

Alga-Produced Cholera Toxin-Pfs25 Fusion Proteins as Oral Vaccines

Science.gov (United States)

Gregory, James A.; Topol, Aaron B.; Doerner, David Z.

2013-01-01

Infectious diseases disproportionately affect indigent regions and are the greatest cause of childhood mortality in developing countries. Practical, low-cost vaccines for use in these countries are paramount to reducing disease burdens and concomitant poverty. Algae are a promising low-cost system for producing vaccines that can be orally delivered, thereby avoiding expensive purification and injectable delivery. We engineered the chloroplast of the eukaryotic alga Chlamydomonas reinhardtii to produce a chimeric protein consisting of the 25-kDa Plasmodium falciparum surface protein (Pfs25) fused to the β subunit of the cholera toxin (CtxB) to investigate an alga-based whole-cell oral vaccine. Pfs25 is a promising malaria transmission-blocking vaccine candidate that has been difficult to produce in traditional recombinant systems due to its structurally complex tandem repeats of epidermal growth factor-like domains. The noncatalytic CtxB domain of the cholera holotoxin assembles into a pentameric structure and acts as a mucosal adjuvant by binding GM1 ganglioside receptors on gut epithelial cells. We demonstrate that CtxB-Pfs25 accumulates as a soluble, properly folded and functional protein within algal chloroplasts, and it is stable in freeze-dried alga cells at ambient temperatures. In mice, oral vaccination using freeze-dried algae that produce CtxB-Pfs25 elicited CtxB-specific serum IgG antibodies and both CtxB- and Pfs25-specific secretory IgA antibodies. These data suggest that algae are a promising system for production and oral delivery of vaccine antigens, but as an orally delivered adjuvant, CtxB is best suited for eliciting secretory IgA antibodies for vaccine antigens against pathogens that invade mucosal surfaces using this strategy. PMID:23603678

SNAP-Ed (Supplemental Nutrition Assistance Program-Education) Increases Long-Term Food Security among Indiana Households with Children in a Randomized Controlled Study.

Science.gov (United States)

Rivera, Rebecca L; Maulding, Melissa K; Abbott, Angela R; Craig, Bruce A; Eicher-Miller, Heather A

2016-11-01

Food insecurity is negatively associated with US children's dietary intake and health. The Supplemental Nutrition Assistance Program-Education (SNAP-Ed) aims to alleviate food insecurity by offering nutrition, budgeting, and healthy lifestyle education to low-income individuals and families. The objective of this study was to evaluate the long-term impact of the Indiana SNAP-Ed on food security among households with children. A randomized, controlled, parallel study design with SNAP-Ed as an intervention was carried out during a 4- to 10-wk intervention period. Intervention group participants received the first 4 Indiana SNAP-Ed curriculum lessons. Study participants (n = 575) were adults aged ≥18 y from low-income Indiana households with ≥1 child living in the household. Both treatment groups completed an assessment before and after the intervention period and 1 y after recruitment. The 18-item US Household Food Security Survey Module was used to classify the primary outcomes of food security for the household and adults and children in the household. A linear mixed model was used to compare intervention with control group effects over time on food security. Mean ± SEM changes in household food security score and food security score among household adults from baseline to 1-y follow-up were 1.2 ± 0.4 and 0.9 ± 0.3 units lower, respectively, in the intervention group than in the control group (P security score from baseline to 1-y follow-up among household children was not significantly different in the intervention group compared with the control group. SNAP-Ed improved food security over a longitudinal time frame among low-income Indiana households with children in this study. SNAP-Ed may be a successful intervention to improve food security. © 2016 American Society for Nutrition.

Development of a mercury electromagnetic centrifugal pump for the SNAP-8 refractory boiler development program

Science.gov (United States)

Fuller, R. A.; Schnacke, A. W.

1974-01-01

An electromagnetic pump, in which pressure is developed in mercury because of the interaction of the magnetic field and current which flows as a result of the voltage induced in the mercury contained in the pump duct, was developed for the SNAP-8 refractory boiler test facility. Pump performance results are presented for ten duct configurations and two stator sizes. These test results were used to design and fabricate a pump which met the SNAP-8 criteria of 530 psi developed pressure at 12,500 lb/hr. The pump operated continuously for over 13,000 hours without failure or performance degradation. Included in this report are descriptions of the experimental equipment, measurement techniques, all experimental data, and an analysis of the electrical losses in the pump.

Integrative demographic modeling reveals population level impacts of PCB toxicity to juvenile snapping turtles

International Nuclear Information System (INIS)

Salice, Christopher J.; Rowe, Christopher L.; Eisenreich, Karen M.

2014-01-01

A significant challenge in ecotoxicology and risk assessment lies in placing observed contaminant effects in a meaningful ecological context. Polychlorinated biphenyls (PCBs) have been shown to affect juvenile snapping turtle survival and growth but the ecological significance of these effects is difficult to discern without a formal, population-level assessment. We used a demographic matrix model to explore the potential population-level effects of PCBs on turtles. Our model showed that effects of PCBs on juvenile survival, growth and size at hatching could translate to negative effects at the population level despite the fact that these life cycle components do not typically contribute strongly to population level processes. This research points to the utility of using integrative demographic modeling approaches to better understand contaminant effects in wildlife. The results indicate that population-level effects are only evident after several years, suggesting that for long-lived species, detecting adverse contaminant effects could prove challenging. -- Highlights: • Previous studies have shown the PCBs can impact juvenile snapping turtles. • We used a demographic model of turtles to evaluate population-level PCB effects. • PCB effects on turtles may translate to negative population responses. • Long-term monitoring is needed to detect contaminant effects on natural turtle populations. • Demographic models can improve our understanding contaminant ecotoxicity. -- A demographic model was used to show that PCB induced effects on young snapping turtles can result in adverse effects at the population level

Native fruit traits may mediate dispersal competition between native and non-native plants

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Clare Aslan

2012-02-01

Full Text Available Seed disperser preferences may mediate the impact of invasive, non-native plant species on their new ecological communities. Significant seed disperser preference for invasives over native species could facilitate the spread of the invasives while impeding native plant dispersal. Such competition for dispersers could negatively impact the fitness of some native plants. Here, we review published literature to identify circumstances under which preference for non-native fruits occurs. The importance of fruit attraction is underscored by several studies demonstrating that invasive, fleshy-fruited plant species are particularly attractive to regional frugivores. A small set of studies directly compare frugivore preference for native vs. invasive species, and we find that different designs and goals within such studies frequently yield contrasting results. When similar native and non-native plant species have been compared, frugivores have tended to show preference for the non-natives. This preference appears to stem from enhanced feeding efficiency or accessibility associated with the non-native fruits. On the other hand, studies examining preference within existing suites of co-occurring species, with no attempt to maximize fruit similarity, show mixed results, with frugivores in most cases acting opportunistically or preferring native species. A simple, exploratory meta-analysis finds significant preference for native species when these studies are examined as a group. We illustrate the contrasting findings typical of these two approaches with results from two small-scale aviary experiments we conducted to determine preference by frugivorous bird species in northern California. In these case studies, native birds preferred the native fruit species as long as it was dissimilar from non-native fruits, while non-native European starlings preferred non-native fruit. However, native birds showed slight, non-significant preference for non-native fruit

Near-native protein loop sampling using nonparametric density estimation accommodating sparcity.

Science.gov (United States)

Joo, Hyun; Chavan, Archana G; Day, Ryan; Lennox, Kristin P; Sukhanov, Paul; Dahl, David B; Vannucci, Marina; Tsai, Jerry

2011-10-01

Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM) has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estimate a continuous joint backbone dihedral angle density at each loop position. The φ,ψ distributions are estimated via a Dirichlet process mixture of hidden Markov models (DPM-HMM). Models are quickly generated based on samples from these distributions and were enriched using an end-to-end distance filter. The performance of the DPM-HMM method was evaluated against a diverse test set in a leave-one-out approach. Candidates as low as 0.45 Å RMSD and with a worst case of 3.66 Å were produced. For the canonical loops like the immunoglobulin complementarity-determining regions (mean RMSD 7.0 Å), this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues. In a direct test of sampling to the Loopy algorithm, our method demonstrates the ability to sample nearer native structures for both the canonical CDRH1 and non-canonical CDRH3 loops. Lastly, in the realistic test conditions of the CASP9 experiment, successful application of DPM-HMM for 90 loops from 45 TBM targets shows the general applicability of our sampling method in loop modeling problem. These results demonstrate that our DPM-HMM produces an advantage by consistently sampling near native loop structure. The software used in this analysis is available for download at http://www.stat.tamu.edu/~dahl/software/cortorgles/.

Near-native protein loop sampling using nonparametric density estimation accommodating sparcity.

Directory of Open Access Journals (Sweden)

Hyun Joo

2011-10-01

Full Text Available Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estimate a continuous joint backbone dihedral angle density at each loop position. The φ,ψ distributions are estimated via a Dirichlet process mixture of hidden Markov models (DPM-HMM. Models are quickly generated based on samples from these distributions and were enriched using an end-to-end distance filter. The performance of the DPM-HMM method was evaluated against a diverse test set in a leave-one-out approach. Candidates as low as 0.45 Å RMSD and with a worst case of 3.66 Å were produced. For the canonical loops like the immunoglobulin complementarity-determining regions (mean RMSD 7.0 Å, this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues. In a direct test of sampling to the Loopy algorithm, our method demonstrates the ability to sample nearer native structures for both the canonical CDRH1 and non-canonical CDRH3 loops. Lastly, in the realistic test conditions of the CASP9 experiment, successful application of DPM-HMM for 90 loops from 45 TBM targets shows the general applicability of our sampling method in loop modeling problem. These results demonstrate that our DPM-HMM produces an advantage by consistently sampling near native loop structure. The software used in this analysis is available for download at http://www.stat.tamu.edu/~dahl/software/cortorgles/.

Near-Native Protein Loop Sampling Using Nonparametric Density Estimation Accommodating Sparcity

Science.gov (United States)

Day, Ryan; Lennox, Kristin P.; Sukhanov, Paul; Dahl, David B.; Vannucci, Marina; Tsai, Jerry

2011-01-01

Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM) has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estimate a continuous joint backbone dihedral angle density at each loop position. The φ,ψ distributions are estimated via a Dirichlet process mixture of hidden Markov models (DPM-HMM). Models are quickly generated based on samples from these distributions and were enriched using an end-to-end distance filter. The performance of the DPM-HMM method was evaluated against a diverse test set in a leave-one-out approach. Candidates as low as 0.45 Å RMSD and with a worst case of 3.66 Å were produced. For the canonical loops like the immunoglobulin complementarity-determining regions (mean RMSD 7.0 Å), this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues. In a direct test of sampling to the Loopy algorithm, our method demonstrates the ability to sample nearer native structures for both the canonical CDRH1 and non-canonical CDRH3 loops. Lastly, in the realistic test conditions of the CASP9 experiment, successful application of DPM-HMM for 90 loops from 45 TBM targets shows the general applicability of our sampling method in loop modeling problem. These results demonstrate that our DPM-HMM produces an advantage by consistently sampling near native loop structure. The software used in this analysis is available for download at http://www.stat.tamu.edu/~dahl/software/cortorgles/. PMID:22028638

Native sulfur/chlorine SAD phasing for serial femtosecond crystallography.

Science.gov (United States)

Nakane, Takanori; Song, Changyong; Suzuki, Mamoru; Nango, Eriko; Kobayashi, Jun; Masuda, Tetsuya; Inoue, Shigeyuki; Mizohata, Eiichi; Nakatsu, Toru; Tanaka, Tomoyuki; Tanaka, Rie; Shimamura, Tatsuro; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Yabashi, Makina; Nureki, Osamu; Iwata, So; Sugahara, Michihiro

2015-12-01

Serial femtosecond crystallography (SFX) allows structures to be determined with minimal radiation damage. However, phasing native crystals in SFX is not very common. Here, the structure determination of native lysozyme from single-wavelength anomalous diffraction (SAD) by utilizing the anomalous signal of sulfur and chlorine at a wavelength of 1.77 Å is successfully demonstrated. This sulfur SAD method can be applied to a wide range of proteins, which will improve the determination of native crystal structures.

Snapping turtles (Chelydra serpentina) as biomonitors of lead contamination of the Big River in Missouri`s Old Lead Belt

Energy Technology Data Exchange (ETDEWEB)

Overmann, S.R.; Krajicek, J.J. [Southeast Missouri State Univ., Cape Girardeau, MO (United States). Dept. of Biology

1995-04-01

The usefulness of common snapping turtles (Chelydra serpentina) as biomonitors of lead (Pb) contamination of aquatic ecosystems was assessed. Thirty-seven snapping turtles were collected from three sites on the Big River, an Ozarkian stream contaminated with Pb mine tailings. Morphometric measurements, tissue Pb concentrations (muscle, blood, bone, carapace, brain, and liver), {delta}-aminolevulinic acid dehydratase ({delta}-ALAD) activity, hematocrit, hemoglobin, plasma glucose, osmolality, and chloride ion content were measured. The data showed no effects of Pb contamination on capture success or morphological measurements. Tissue Pb concentrations were related to capture location. Hematocrit, plasma osmolality, plasma glucose, and plasma chloride ion content were not significantly different with respect to capture location. The {delta}-ALAD activity levels were decreased in turtles taken from contaminated sites. Lead levels in the Big River do not appear to be adversely affecting the snapping turtles of the river. Chelydra serpentina is a useful species for biomonitoring of Pb-contaminated aquatic environments.

Niobium tunnel junction fabrication using e-gun evaporation and SNAP

Science.gov (United States)

Kortlandt, J.; van der Zant, H. S. J.; Schellingerhout, A. J. G.; Mooij, J. E.

1990-11-01

We have fabricated high quality small area Nb-Al-Al 2O 3-Nb junctions with SNAP, making use of e-beam evaporation in a 10 -5 Pa diffusion pumped vacuum system. Nominal dimensions of the junctions are 8x8, 4x4 and 2x2 μm 2. We obtain typical current densities of 5-6 × 10 +2A/cm 2 and (critical current) x (subgap resistance) products of 40 mV.

The analgesic effect on neuropathic pain of retrogradely transported botulinum neurotoxin A involves Schwann cells and astrocytes.

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Sara Marinelli

Full Text Available In recent years a growing debate is about whether botulinum neurotoxins are retrogradely transported from the site of injection. Immunodetection of cleaved SNAP-25 (cl-SNAP-25, the protein of the SNARE complex targeted by botulinum neurotoxin serotype A (BoNT/A, could represent an excellent approach to investigate the mechanism of action on the nociceptive pathways at peripheral and/or central level. After peripheral administration of BoNT/A, we analyzed the expression of cl-SNAP-25, from the hindpaw's nerve endings to the spinal cord, together with the behavioral effects on neuropathic pain. We used the chronic constriction injury of the sciatic nerve in CD1 mice as animal model of neuropathic pain. We evaluated immunostaining of cl-SNAP-25 in the peripheral nerve endings, along the sciatic nerve, in dorsal root ganglia and in spinal dorsal horns after intraplantar injection of saline or BoNT/A, alone or colocalized with either glial fibrillar acidic protein, GFAP, or complement receptor 3/cluster of differentiation 11b, CD11b, or neuronal nuclei, NeuN, depending on the area investigated. Immunofluorescence analysis shows the presence of the cl-SNAP-25 in all tissues examined, from the peripheral endings to the spinal cord, suggesting a retrograde transport of BoNT/A. Moreover, we performed in vitro experiments to ascertain if BoNT/A was able to interact with the proliferative state of Schwann cells (SC. We found that BoNT/A modulates the proliferation of SC and inhibits the acetylcholine release from SC, evidencing a new biological effect of the toxin and further supporting the retrograde transport of the toxin along the nerve and its ability to influence regenerative processes. The present results strongly sustain a combinatorial action at peripheral and central neural levels and encourage the use of BoNT/A for the pathological pain conditions difficult to treat in clinical practice and dramatically impairing patients' quality of life.

Stabilization of Proteins and Noncovalent Protein Complexes during Electrospray Ionization by Amino Acid Additives.

Science.gov (United States)

Zhang, Hua; Lu, Haiyan; Chingin, Konstantin; Chen, Huanwen

2015-07-21

Ionization of proteins and noncovalent protein complexes with minimal disturbance to their native structure presents a great challenge for biological mass spectrometry (MS). In living organisms, the native structure of intracellular proteins is commonly stabilized by solute amino acids (AAs) accumulated in cells at very high concentrations. Inspired by nature, we hypothesized that AAs could also pose a stabilizing effect on the native structure of proteins and noncovalent protein complexes during ionization. To test this hypothesis, here we explored MS response for various protein complexes upon the addition of free AAs at mM concentrations into the electrospray ionization (ESI) solution. Thermal activation of ESI droplets in the MS inlet capillary was employed as a model destabilizing factor during ionization. Our results indicate that certain AAs, in particular proline (Pro), pose considerable positive effect on the stability of noncovalent protein complexes in ESI-MS without affecting the signal intensity of protein ions and original protein-ligand equilibrium, even when added at the 20 mM concentration. The data suggest that the degree of protein stabilization is primarily determined by the osmolytic and ampholytic characteristics of AA solutes. The highest stability and visibility of noncovalent protein complexes in ESI-MS are achieved using AA additives with neutral isoelectric point, moderate proton affinity, and unfavorable interaction with the native protein state. Overall, our results indicate that the simple addition of free amino acids into the working solution can notably improve the stability and accuracy of protein analysis by native ESI-MS.

Preclinical in vitro and in vivo evaluation of [11C]SNAP-7941 – the first PET tracer for the melanin concentrating hormone receptor 1

International Nuclear Information System (INIS)

Philippe, Cécile; Nics, Lukas; Zeilinger, Markus; Kuntner, Claudia; Wanek, Thomas; Mairinger, Severin; Shanab, Karem; Spreitzer, Helmut; Viernstein, Helmut; Wadsak, Wolfgang; Mitterhauser, Markus

2013-01-01

Introduction: Due to its involvement in a variety of pathologies (obesity, diabetes, gut inflammation and depression), the melanin concentrating hormone receptor 1 (MCHR1) is a new target for the treatment of these lifestyle diseases. We previously presented the radiosynthesis of [ 11 C]SNAP-7941, the first potential PET tracer for the MCHR1. Methods: We herein present its in vitro and in vivo evaluation, including binding affinity, plasma stability, stability against liver mircrosomes and carboxylesterase, lipohilicity, biodistribution, in vivo metabolism and small-animal PET. Results: [ 11 C]SNAP-7941 evinced high stability against liver microsomes, carboxylesterase and in human plasma. The first small-animal PET experiments revealed a 5 fold increased brain uptake after Pgp/BCRP inhibition. Therefore, it can be assumed that [ 11 C]SNAP-7941 is a Pgp/BCRP substrate. No metabolites were found in brain. Conclusion: On the basis of these experiments with healthy rats, the suitability of [ 11 C]SNAP-7941 for the visualisation of central and peripheral MCHR1 remains speculative

Research to Understand Milk Consumption Behaviors in a Food-Insecure Low-Income SNAP Population in the US

Directory of Open Access Journals (Sweden)

Karla Jaye Finnell

2017-09-01

Full Text Available Milk, due to its affordability and nutritional value, can fortify the diets of families that experience food insecurity or find a high-quality diet cost-prohibitive. However, it can also be a leading source of excess calories and saturated fat. Yet, little is known about what influences consumer behavior of Supplemental Nutrition Assistance Program (SNAP recipients toward the type of milk used or the prevalence of low-fat milk use among this population. This cross-sectional telephone survey of SNAP recipients (n = 520 documented that 7.5% of this population usually consumes low-fat milk, a prevalence that lags behind national figures (34.4% for the same time-period. There was a weak association between sociodemographic characteristics of SNAP recipients and low-fat milk use. Instead, less low-fat milk consumption was associated with a knowledge gap and misperceptions of the nutritional properties of the different types of milk. Promoting low-fat milk use by correcting these misperceptions can improve the diet of America’s low-income population and reduce food insecurity by maximizing the nutritional value of the foods consumed.

Biochemical characterization of native Usher protein complexes from a vesicular subfraction of tracheal epithelial cells.

Science.gov (United States)

Zallocchi, Marisa; Sisson, Joseph H; Cosgrove, Dominic

2010-02-16

Usher syndrome is the major cause of deaf/blindness in the world. It is a genetic heterogeneous disorder, with nine genes already identified as causative for the disease. We noted expression of all known Usher proteins in bovine tracheal epithelial cells and exploited this system for large-scale biochemical analysis of Usher protein complexes. The dissected epithelia were homogenized in nondetergent buffer and sedimented on sucrose gradients. At least two complexes were evident after the first gradient: one formed by specific isoforms of CDH23, PCDH15, and VLGR-1 and a different one at the top of the gradient that included all of the Usher proteins and rab5, a transport vesicle marker. TEM analysis of these top fractions found them enriched in 100-200 nm vesicles, confirming a vesicular association of the Usher complex(es). Immunoisolation of these vesicles confirmed some of the associations already predicted and identified novel interactions. When the vesicles are lysed in the presence of phenylbutyrate, most of the Usher proteins cosediment into the gradient at a sedimentation coefficient of approximately 50 S, correlating with a predicted molecular mass of 2 x 10(6) Da. Although it is still unclear whether there is only one complex or several independent complexes that are trafficked within distinct vesicular pools, this work shows for the first time that native Usher protein complexes occur in vivo. This complex(es) is present primarily in transport vesicles at the apical pole of tracheal epithelial cells, predicting that Usher proteins may be directionally transported as complexes in hair cells and photoreceptors.

BIOCHEMICAL CHARACTERIZATION OF NATIVE USHER PROTEIN COMPLEXES FROM A VESICULAR SUBFRACTION OF TRACHEAL EPITHELIAL CELLS†

Science.gov (United States)

Zallocchi, Marisa; Sisson, Joseph H.; Cosgrove, Dominic

2010-01-01

Usher syndrome is the major cause of deaf/blindness in the world. It is a genetic heterogeneous disorder, with nine genes already identified as causative for the disease. We noted expression of all known Usher proteins in bovine tracheal epithelial cells, and exploited this system for large-scale biochemical analysis of Usher protein complexes. The dissected epithelia were homogenized in non-detergent buffer, and sedimented on sucrose gradients. At least two complexes were evident after the first gradient: one formed by specific isoforms of CDH23, PCDH15 and VLGR-1, and a different one at the top of the gradient that included all the Usher proteins and rab5, a transport vesicle marker. TEM analysis of these top fractions found them enriched in 100–200 nm vesicles, confirming a vesicular association of the Usher complex(es). Immunoisolation of these vesicles confirmed some of the associations already predicted and identified novel interactions. When the vesicles are lysed in the presence of phenylbutyrate, most of the Usher proteins co-sediment into the gradient at a sedimentation coefficient of approximately 50S, correlating with a predicted molecular mass of 2 × 106 Daltons. Although it is still unclear whether there is only one complex or several independent complexes that are trafficked within distinct vesicular pools, this work shows for the first time that native Usher proteins complexes occur in vivo. This complex(es) is present primarily in transport vesicles at the apical pole of tracheal epithelial cells, predicting that Usher proteins may be directionally transported as complexes in hair cells and photoreceptors. PMID:20058854

Evidence of native α-synuclein conformers in the human brain.

Science.gov (United States)

Gould, Neal; Mor, Danielle E; Lightfoot, Richard; Malkus, Kristen; Giasson, Benoit; Ischiropoulos, Harry

2014-03-14

α-Synuclein aggregation is central to the pathogenesis of several brain disorders. However, the native conformations and functions of this protein in the human brain are not precisely known. The native state of α-synuclein was probed by gel filtration coupled with native gradient gel separation, an array of antibodies with non-overlapping epitopes, and mass spectrometry. The existence of metastable conformers and stable monomer was revealed in the human brain.

SNAP 19 Pioneer F and G. Final Report

Science.gov (United States)

1973-06-01

The generator developed for the Pioneer mission evolved from the SNAP 19 RTG`s launched aboard the NIMBUS III spacecraft. In order to satisfy the power requirements and environment of earth escape trajectory, significant modifications were made to the thermoelectric converter, heat source, and structural configuration. Specifically, a TAGS 2N thermoelectric couple was designed to provide higher efficiency and improved long term power performance, and the electrical circuitry was modified to yield very low magnetic field from current flow in the RTG. A new heat source was employed to satisfy operational requirements and its integration with the generator required alteration to the method of providing support to the fuel capsule.

Resolution of two native monomeric 90 kDa nitrate reductase active proteins from Shewanella gelidimarina and the sequence of two napA genes

International Nuclear Information System (INIS)

Simpson, Philippa J.L.; McKinzie, Audra A.; Codd, Rachel

2010-01-01

Research highlights: → Two monomeric 90 kDa nitrate reductase active proteins from Shewanella gelidimarina. → Sequence of napA from napEDABC-type operon and napA from NapDAGHB-type operon. → Isolation of NAP as NapA or NapAB correlated with NapA P47E amino acid substitution. -- Abstract: The reduction of nitrate to nitrite in the bacterial periplasm occurs in the 90 kDa NapA subunit of the periplasmic nitrate reductase (NAP) system. Most Shewanella genomes contain two nap operons: napEDABC and napDAGHB, which is an unusual feature of this genus. Two native, monomeric, 90 kDa nitrate reductase active proteins were resolved by hydrophobic interaction chromatography from aerobic cultures of Shewanella gelidimarina replete with reduced nitrogen compounds. The 90 kDa protein obtained in higher yield was characterized as NapA by electronic absorption and electron paramagnetic resonance spectroscopies and was identified by LC/MS/MS and MALDI-TOF/TOF MS as NapA from the napEDABC-type operon. The other 90 kDa protein, which was unstable and produced in low yields, was posited as NapA from the napDAGHB-type operon. Two napA genes have been sequenced from the napEDABC-type and napDAGHB-type operons of S. gelidimarina. Native NAP from S. putrefaciens was resolved as one NapA monomer and one NapAB heterodimer. Two amino acid substitutions in NapA correlated with the isolation of NAP as a NapA monomer or a NapAB heterodimer. The resolution of native, redox-active NapA isoforms in Shewanella provides new insight into the respiratory versatility of this genus, which has implications in bioremediation and the assembly of microbial fuel cells.

REGULATED VESICULAR TRAFFICKING OF SPECIFIC PCDH15 AND VLGR1 VARIANTS IN AUDITORY HAIR CELLS

Science.gov (United States)

Zallocchi, Marisa; Delimont, Duane; Meehan, Daniel T.; Cosgrove, Dominic

2012-01-01

Usher syndrome is a genetically heterogeneous disorder characterized by hearing and balance dysfunction and progressive retinitis pigmentosa. Mouse models carrying mutations for the nine Usher-associated genes have splayed stereocilia and some show delayed maturation of ribbon synapses suggesting these proteins may play different roles in terminal differentiation of auditory hair cells. The presence of the Usher proteins at the basal and apical aspects of the neurosensory epithelia suggests the existence of regulated trafficking through specific transport proteins and routes. Immature mouse cochleae and UB/OC-1 cells were used in this work to address whether specific variants of PCDH15 and VLGR1 are being selectively transported to opposite poles of the hair cells. Confocal co-localization studies between apical and basal vesicular markers and the different PCDH15 and VLGR1 variants along with sucrose density gradients and the use of vesicle trafficking inhibitors show the existence of Usher protein complexes in at least two vesicular sub-pools. The apically trafficked pool co-localized with the early endosomal vesicle marker, rab5, while the basally trafficked pool associates with membrane microdomains and SNAP25. Moreover, co-immunoprecipitation experiments between SNAP25 and VLGR1 show a physical interaction of these two proteins in organ of Corti and brain. Collectively, these findings establish the existence of a differential vesicular trafficking mechanism for specific Usher protein variants in mouse cochlear hair cells, with the apical variants playing a potential role in endosomal recycling and stereocilia development/maintenance and the basolateral variants involved in vesicle docking and/or fusion through SNAP25-mediated interactions. PMID:23035094

The Use of Protein-Protein Interactions for the Analysis of the Associations between PM2.5 and Some Diseases.

Science.gov (United States)

Zhang, Qing; Zhang, Pei-Wei; Cai, Yu-Dong

2016-01-01

Nowadays, pollution levels are rapidly increasing all over the world. One of the most important pollutants is PM2.5. It is known that the pollution environment may cause several problems, such as greenhouse effect and acid rain. Among them, the most important problem is that pollutants can induce a number of serious diseases. Some studies have reported that PM2.5 is an important etiologic factor for lung cancer. In this study, we extensively investigate the associations between PM2.5 and 22 disease classes recommended by Goh et al., such as respiratory diseases, cardiovascular diseases, and gastrointestinal diseases. The protein-protein interactions were used to measure the linkage between disease genes and genes that have been reported to be modulated by PM2.5. The results suggest that some diseases, such as diseases related to ear, nose, and throat and gastrointestinal, nutritional, renal, and cardiovascular diseases, are influenced by PM2.5 and some evidences were provided to confirm our results. For example, a total of 18 genes related to cardiovascular diseases are identified to be closely related to PM2.5, and cardiovascular disease relevant gene DSP is significantly related to PM2.5 gene JUP.

Effects of immobilization and aerobic training on proteins related to intramuscular substrate storage and metabolism in young and older men

DEFF Research Database (Denmark)

Vigelsø Hansen, Andreas; Gram, Martin; Wiuff, Caroline

2016-01-01

by aerobic training in young and older men. METHODS: 17 young (23 ± 1 years, 24 ± 1 kg m(-2), and 20 ± 2% body fat) and 15 older men (68 ± 1 years; 27 ± 1 kg m(-2), and 29 ± 2% body fat) underwent 2 weeks' one leg immobilization followed by 6 weeks' cycle training. Biopsies were obtained from m. vastus...... lateralis just before immobilization (at inclusion), after immobilization, and the after 6 weeks' training. The biopsies were analyzed for muscle substrates; muscle perilipin protein (PLIN), glycogen synthase (GS), synaptosomal-associated protein of 23 kDa (SNAP23) protein content, and muscle 3-hydroxyacyl...... GS (74%) protein compared to the older men. Immobilization decreased and training restored HAD activity, GS and SNAP23 protein content in young and older men. CONCLUSION: Evidence of age-related metabolic inflexibility is presented, seen as body fat and IMTG accumulation. The question arises...

Biochemical and pharmacological studies of native and irradiated crotamine with gamma radiation of Co60

International Nuclear Information System (INIS)

Mitake, M.B.

2000-01-01

Ionizing radiation can change the molecular structure and affect the biological properties of biomolecules. This has been employed to attenuate animal toxins. Crotamine is a strongly basic polypeptide from South American rattlesnake venom, composed of 42 amino acid residues. It induces skeletal muscle spasms, leading to a spastic paralysis of hind limbs in mice. The objective was to carry out biochemical and pharmacological studies of native and irradiated crotamine with Co. Crotamine was purified from Crotalus durissus terrificus venom by Sephadex G-100 gel filtration followed by ion exchange chromatography, using a Fast performance Liquid Chromatography (FPLC) system. It was irradiated at 2 mg/ml in 0.15 m NaCl with 2.0 kGy gamma radiation emitted by a Co source. Native and irradiated crotamine were evaluated by biochemical characterization, toxic activity (LD50), and biodistribution. The native and irradiated crotamine were labeled with 29.6 MBq of I using chloramine T method and separated in a Sephadex G-50 column. Male Swiss mice (35 @ 5 g) were injected IP with 0.1 mL (2.4x10 cpm/mouse) of I native crotamine or with 0.4 mL (1.3 x 10 cpm/mouse) of I irradiated crotamine. The animals were sacrificed by ether inhalation at 0.08, 0.25, 0.5,1, 2, 3, 4, 8, 12, and 24 hours. Blood, spleen, liver, kidneys, brain, lungs, heart, and skeletal muscle were collected in order to determine radioactivity content. The results showed that gamma radiation did not change protein concentration, electrophoretic profile, or protein primary structure, although differences could be seen by spectroscopic techniques. Gamma radiation reduced crotamine toxicity, but did not eliminate bioactivity. Biodistribution studies showed that native and irradiated crotamine have hepatic metabolism and renal elimination. Native and irradiated crotamine have an affinity to skeletal muscle and did not cross the blood-brain barrier. (author)

Biochemical and pharmacological studies of native and irradiated crotamine with gamma radiation of 60Co

International Nuclear Information System (INIS)

Mitake, Malvina Boni

2000-01-01

Ionizing radiation can change the molecular structure and affect the biological properties of biomolecules. This has been employed to attenuate animal toxins. Crotamine is a strongly basic polypeptide from the South American rattlesnake venom, composed of 42 amino acid residues. It induces skeletal muscle spasms leading to a spastic paralysis of hind limbs in mice. The objective of this thesis was carry out biochemical and pharmacological studies of native and irradiated crotamine with 60 Co. Crotamine was purified from Crotalus durissus terrificus venom by Sephadex G-100 gel filtration followed by ion exchange chromatography, using a Fast Performance Liquid Chromatography (FPLC) system. It was irradiated at 2 mg/ml in 0.15 M Na Cl with 2.0 kGy gamma radiation emitted by a 60 Co source. The native and irradiated crotamine were evaluated by biochemical characterization, toxic activity (LD 50 and biodistribution. The native and irradiated crotamine were labelled with 29.6 MBq of 125 I using chloramine T method, and separated in a Sephadex G-50 column. Male Swiss mice (35± 5 g), were injected i.p. with o.1 mL (2.4 x 10 6 cpm/mouse) of 125 I native crotamine or with 0.4 mL (1.3 x 10 6 cpm/mouse) of 125 I irradiated crotamine. At 0.08; 0.25; 0.5; 1; 2; 4; 8; 12 and 24 hours the animal were killed by ether inhalation. Blood, spleen, liver, kidneys, brain, lungs, heart, and skeletal muscle were collected in order to determine radioactivity content. The results showed that gamma radiation did not change the protein concentration, the electroforetic profile or the primary structure of the protein, although differences were shown by spectroscopic techniques. The gamma radiation diminished the toxicity of crotamine, but it did not abolish bioactivity. Biodistribution studies showed that native and irradiated crotamine have hepatic metabolism and renal elimination. The native and irradiated crotamine have affinity by skeletal muscle and they did not pass the blood - brain

Prion protein gene polymorphisms in Turkish native goat breeds

Indian Academy of Sciences (India)

HASAN MEYDAN

3The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of ... Eighteen single-nucleotide polymorphisms were detected in the caprine PRNP .... Sampling localities, sample size (n) and sex of Turkish native goat breeds.

The biology of non-native proteins

NARCIS (Netherlands)

Herczenik, E.

2007-01-01

Protein misfolding diseases are linked by common principles of protein aggregation, plaque development and tissue damage. There is no adequate therapy for these highly debilitating diseases. This thesis aims to increase the understanding of protein misfolding diseases, which will hopefully lead to

Ectomycorrhizal fungal communities of native and non-native Pinus and Quercus species in a common garden of 35-year-old trees.

Science.gov (United States)

Trocha, Lidia K; Kałucka, Izabela; Stasińska, Małgorzata; Nowak, Witold; Dabert, Mirosława; Leski, Tomasz; Rudawska, Maria; Oleksyn, Jacek

2012-02-01

Non-native tree species have been widely planted or have become naturalized in most forested landscapes. It is not clear if native trees species collectively differ in ectomycorrhizal fungal (EMF) diversity and communities from that of non-native tree species. Alternatively, EMF species community similarity may be more determined by host plant phylogeny than by whether the plant is native or non-native. We examined these unknowns by comparing two genera, native and non-native Quercus robur and Quercus rubra and native and non-native Pinus sylvestris and Pinus nigra in a 35-year-old common garden in Poland. Using molecular and morphological approaches, we identified EMF species from ectomycorrhizal root tips and sporocarps collected in the monoculture tree plots. A total of 69 EMF species were found, with 38 species collected only as sporocarps, 18 only as ectomycorrhizas, and 13 both as ectomycorrhizas and sporocarps. The EMF species observed were all native and commonly associated with a Holarctic range in distribution. We found that native Q. robur had ca. 120% higher total EMF species richness than the non-native Q. rubra, while native P. sylvestris had ca. 25% lower total EMF species richness than non-native P. nigra. Thus, across genera, there was no evidence that native species have higher EMF species diversity than exotic species. In addition, we found a higher similarity in EMF communities between the two Pinus species than between the two Quercus species. These results support the naturalization of non-native trees by means of mutualistic associations with cosmopolitan and novel fungi.

Mapping Proteoforms and Protein Complexes From King Cobra Venom Using Both Denaturing and Native Top-down Proteomics.

Science.gov (United States)

Melani, Rafael D; Skinner, Owen S; Fornelli, Luca; Domont, Gilberto B; Compton, Philip D; Kelleher, Neil L

2016-07-01

Characterizing whole proteins by top-down proteomics avoids a step of inference encountered in the dominant bottom-up methodology when peptides are assembled computationally into proteins for identification. The direct interrogation of whole proteins and protein complexes from the venom of Ophiophagus hannah (king cobra) provides a sharply clarified view of toxin sequence variation, transit peptide cleavage sites and post-translational modifications (PTMs) likely critical for venom lethality. A tube-gel format for electrophoresis (called GELFrEE) and solution isoelectric focusing were used for protein fractionation prior to LC-MS/MS analysis resulting in 131 protein identifications (18 more than bottom-up) and a total of 184 proteoforms characterized from 14 protein toxin families. Operating both GELFrEE and mass spectrometry to preserve non-covalent interactions generated detailed information about two of the largest venom glycoprotein complexes: the homodimeric l-amino acid oxidase (∼130 kDa) and the multichain toxin cobra venom factor (∼147 kDa). The l-amino acid oxidase complex exhibited two clusters of multiproteoform complexes corresponding to the presence of 5 or 6 N-glycans moieties, each consistent with a distribution of N-acetyl hexosamines. Employing top-down proteomics in both native and denaturing modes provides unprecedented characterization of venom proteoforms and their complexes. A precise molecular inventory of venom proteins will propel the study of snake toxin variation and the targeted development of new antivenoms or other biotherapeutics. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Unique structural modulation of a non-native substrate by cochaperone DnaJ.

Science.gov (United States)

Tiwari, Satyam; Kumar, Vignesh; Jayaraj, Gopal Gunanathan; Maiti, Souvik; Mapa, Koyeli

2013-02-12

The role of bacterial DnaJ protein as a cochaperone of DnaK is strongly appreciated. Although DnaJ unaccompanied by DnaK can bind unfolded as well as native substrate proteins, its role as an individual chaperone remains elusive. In this study, we demonstrate that DnaJ binds a model non-native substrate with a low nanomolar dissociation constant and, more importantly, modulates the structure of its non-native state. The structural modulation achieved by DnaJ is different compared to that achieved by the DnaK-DnaJ complex. The nature of structural modulation exerted by DnaJ is suggestive of a unique unfolding activity on the non-native substrate by the chaperone. Furthermore, we demonstrate that the zinc binding motif along with the C-terminal substrate binding domain of DnaJ is necessary and sufficient for binding and the subsequent binding-induced structural alterations of the non-native substrate. We hypothesize that this hitherto unknown structural alteration of non-native states by DnaJ might be important for its chaperoning activity by removing kinetic traps of the folding intermediates.

Energy landscape of all-atom protein-protein interactions revealed by multiscale enhanced sampling.

Directory of Open Access Journals (Sweden)

Kei Moritsugu

2014-10-01

Full Text Available Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape.

Frontotemporal dysregulation of the SNARE protein interactome is associated with faster cognitive decline in old age.

Science.gov (United States)

Ramos-Miguel, Alfredo; Jones, Andrea A; Sawada, Ken; Barr, Alasdair M; Bayer, Thomas A; Falkai, Peter; Leurgans, Sue E; Schneider, Julie A; Bennett, David A; Honer, William G

2018-06-01

The molecular underpinnings associated with cognitive reserve remain poorly understood. Because animal models fail to fully recapitulate the complexity of human brain aging, postmortem studies from well-designed cohorts are crucial to unmask mechanisms conferring cognitive resistance against cumulative neuropathologies. We tested the hypothesis that functionality of the SNARE protein interactome might be an important resilience factor preserving cognitive abilities in old age. Cognition was assessed annually in participants from the Rush "Memory and Aging Project" (MAP), a community-dwelling cohort representative of the overall aging population. Associations between cognition and postmortem neurochemical data were evaluated in functional assays quantifying various species of the SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) machinery in samples from the inferior temporal (IT, n = 154) and middle-frontal (MF, n = 174) gyri. Using blue-native gel electrophoresis, we isolated and quantified several types of complexes containing the three SNARE proteins (syntaxin-1, SNAP25, VAMP), as well as the GABAergic/glutamatergic selectively expressed complexins-I/II (CPLX1/2), in brain tissue homogenates and reconstitution assays with recombinant proteins. Multivariate analyses revealed significant associations between IT and MF neurochemical data (SNARE proteins and/or complexes), and multiple age-related neuropathologies, as well as with multiple cognitive domains of MAP participants. Controlling for demographic variables, neuropathologic indices and total synapse density, we found that temporal 150-kDa SNARE species (representative of pan-synaptic functionality) and frontal CPLX1/CPLX2 ratio of 500-kDa heteromeric species (representative of inhibitory/excitatory input functionality) were, among all the immunocharacterized complexes, the strongest predictors of cognitive function nearest death. Interestingly, these two neurochemical

Non-Native & Native English Teachers

Directory of Open Access Journals (Sweden)

İrfan Tosuncuoglu

2017-12-01

Full Text Available In many countries the primary (mother tongue language is not English but there is a great demand for English language teachers all over the world. The demand in this field is try to be filled largely by non-native English speaking teachers who have learned English in the country or abroad, or from another non native English peaking teachers. In some countries, particularly those where English speaking is a a sign of status, the students prefer to learn English from a native English speaker. The perception is that a non-native English speaking teacher is a less authentic teacher than a native English speaker and their instruction is not satifactory in some ways. This paper will try to examine the literature to explore whether there is a difference in instructional effectiveness between NNESTs and native English teachers.

The Use of Protein-Protein Interactions for the Analysis of the Associations between PM2.5 and Some Diseases

Directory of Open Access Journals (Sweden)

Qing Zhang

2016-01-01

Full Text Available Nowadays, pollution levels are rapidly increasing all over the world. One of the most important pollutants is PM2.5. It is known that the pollution environment may cause several problems, such as greenhouse effect and acid rain. Among them, the most important problem is that pollutants can induce a number of serious diseases. Some studies have reported that PM2.5 is an important etiologic factor for lung cancer. In this study, we extensively investigate the associations between PM2.5 and 22 disease classes recommended by Goh et al., such as respiratory diseases, cardiovascular diseases, and gastrointestinal diseases. The protein-protein interactions were used to measure the linkage between disease genes and genes that have been reported to be modulated by PM2.5. The results suggest that some diseases, such as diseases related to ear, nose, and throat and gastrointestinal, nutritional, renal, and cardiovascular diseases, are influenced by PM2.5 and some evidences were provided to confirm our results. For example, a total of 18 genes related to cardiovascular diseases are identified to be closely related to PM2.5, and cardiovascular disease relevant gene DSP is significantly related to PM2.5 gene JUP.

Determinatio of Psychometrics Index of SNAP-IV Rating Scale in Parents Execution

Directory of Open Access Journals (Sweden)

Seyyed Jalal Sadrosadat

2008-01-01

Full Text Available Objective: SNAP-IV rating scale to diagnosis Attention Deficit Hyperactivity Disorder (ADHD developed by Swanson, Nolan and Pelham. The aim of this study is determination of psychometrics specifications of this scale. Materials & Methods: This Descriptive research is a methodological, applied and validity assessment study. One thousand students at 7 to 12 age of primary school in Tehran city were selected by cluster sampling. Then the students mothers was asked to complete rating scale to consider behavior of their children.30 staff members of sample group were retest after one mounts. Diagnostic interview was administered at 36 members of sample group. Data were analyzed by using pearsonian correlation coefficient, Kolmogorof – Smirnoff and Behrens – Fisher T test. Results: Criterion validity was 48%, factor analysis was detected 3 factors that explain 56% of the total variance. Reliability coefficient was 82% . internal consistency coefficient was 90% and split –half coefficient was 76%, Cut-off point in scale and subscales was 1.57,1.47 and 1.9 respectively. Conclusion: The SNAP-IV Rating scales have fit psychometrics specifications. Therefore, it is useable in various diagnostic and therapeutic conditioning.

Combining blue native polyacrylamide gel electrophoresis with liquid chromatography tandem mass spectrometry as an effective strategy for analyzing potential membrane protein complexes of Mycobacterium bovis bacillus Calmette-Guérin

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Li Weijun

2011-01-01

Full Text Available Abstract Background Tuberculosis is an infectious bacterial disease in humans caused primarily by Mycobacterium tuberculosis, and infects one-third of the world's total population. Mycobacterium bovis bacillus Calmette-Guérin (BCG vaccine has been widely used to prevent tuberculosis worldwide since 1921. Membrane proteins play important roles in various cellular processes, and the protein-protein interactions involved in these processes may provide further information about molecular organization and cellular pathways. However, membrane proteins are notoriously under-represented by traditional two-dimensional polyacrylamide gel electrophoresis (2-D PAGE and little is known about mycobacterial membrane and membrane-associated protein complexes. Here we investigated M. bovis BCG by an alternative proteomic strategy coupling blue native PAGE to liquid chromatography tandem mass spectrometry (LC-MS/MS to characterize potential protein-protein interactions in membrane fractions. Results Using this approach, we analyzed native molecular composition of protein complexes in BCG membrane fractions. As a result, 40 proteins (including 12 integral membrane proteins, which were organized in 9 different gel bands, were unambiguous identified. The proteins identified have been experimentally confirmed using 2-D SDS PAGE. We identified MmpL8 and four neighboring proteins that were involved in lipid transport complexes, and all subunits of ATP synthase complex in their monomeric states. Two phenolpthiocerol synthases and three arabinosyltransferases belonging to individual operons were obtained in different gel bands. Furthermore, two giant multifunctional enzymes, Pks7 and Pks8, and four mycobacterial Hsp family members were determined. Additionally, seven ribosomal proteins involved in polyribosome complex and two subunits of the succinate dehydrogenase complex were also found. Notablely, some proteins with high hydrophobicity or multiple transmembrane

Combining blue native polyacrylamide gel electrophoresis with liquid chromatography tandem mass spectrometry as an effective strategy for analyzing potential membrane protein complexes of Mycobacterium bovis bacillus Calmette-Guérin.

Science.gov (United States)

Zheng, Jianhua; Wei, Candong; Zhao, Lina; Liu, Liguo; Leng, Wenchuan; Li, Weijun; Jin, Qi

2011-01-18

Tuberculosis is an infectious bacterial disease in humans caused primarily by Mycobacterium tuberculosis, and infects one-third of the world's total population. Mycobacterium bovis bacillus Calmette-Guérin (BCG) vaccine has been widely used to prevent tuberculosis worldwide since 1921. Membrane proteins play important roles in various cellular processes, and the protein-protein interactions involved in these processes may provide further information about molecular organization and cellular pathways. However, membrane proteins are notoriously under-represented by traditional two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and little is known about mycobacterial membrane and membrane-associated protein complexes. Here we investigated M. bovis BCG by an alternative proteomic strategy coupling blue native PAGE to liquid chromatography tandem mass spectrometry (LC-MS/MS) to characterize potential protein-protein interactions in membrane fractions. Using this approach, we analyzed native molecular composition of protein complexes in BCG membrane fractions. As a result, 40 proteins (including 12 integral membrane proteins), which were organized in 9 different gel bands, were unambiguous identified. The proteins identified have been experimentally confirmed using 2-D SDS PAGE. We identified MmpL8 and four neighboring proteins that were involved in lipid transport complexes, and all subunits of ATP synthase complex in their monomeric states. Two phenolpthiocerol synthases and three arabinosyltransferases belonging to individual operons were obtained in different gel bands. Furthermore, two giant multifunctional enzymes, Pks7 and Pks8, and four mycobacterial Hsp family members were determined. Additionally, seven ribosomal proteins involved in polyribosome complex and two subunits of the succinate dehydrogenase complex were also found. Notablely, some proteins with high hydrophobicity or multiple transmembrane helixes were identified well in our work. In this

Dynamics of snap-off and pore-filling events during two-phase fluid flow in permeable media.

Science.gov (United States)

Singh, Kamaljit; Menke, Hannah; Andrew, Matthew; Lin, Qingyang; Rau, Christoph; Blunt, Martin J; Bijeljic, Branko

2017-07-12

Understanding the pore-scale dynamics of two-phase fluid flow in permeable media is important in many processes such as water infiltration in soils, oil recovery, and geo-sequestration of CO 2 . The two most important processes that compete during the displacement of a non-wetting fluid by a wetting fluid are pore-filling or piston-like displacement and snap-off; this latter process can lead to trapping of the non-wetting phase. We present a three-dimensional dynamic visualization study using fast synchrotron X-ray micro-tomography to provide new insights into these processes by conducting a time-resolved pore-by-pore analysis of the local curvature and capillary pressure. We show that the time-scales of interface movement and brine layer swelling leading to snap-off are several minutes, orders of magnitude slower than observed for Haines jumps in drainage. The local capillary pressure increases rapidly after snap-off as the trapped phase finds a position that is a new local energy minimum. However, the pressure change is less dramatic than that observed during drainage. We also show that the brine-oil interface jumps from pore-to-pore during imbibition at an approximately constant local capillary pressure, with an event size of the order of an average pore size, again much smaller than the large bursts seen during drainage.

Oviductal morphology in relation to hormonal levels in the snapping turtle, Chelydra serpentina.

Science.gov (United States)

Alkindi, A Y A; Mahmoud, I Y; Woller, M J; Plude, J L

2006-02-01

Microscopic and in situ visual observations were used to relate circulating hormone levels to morphological changes in the oviduct of the snapping turtle Chelydra serpentina throughout the ovarian cycle. Increase in levels of progesterone (P), estradiol (E2) and testosterone (T) levels coincide with an increase in number and growth of endometrial glands, luminal epithelial cells and secretory droplets throughout the oviduct. Testosterone and estradiol levels rose significantly (P < 0.05) after the May-June period and remained high throughout the rest of the summer. Progesterone levels remained stable throughout the summer, with a brief decline in July due to luteolysis. Hormonal values declined significantly (P < 0.001) at the end of the ovarian cycle in the fall. In situ visual observation of fresh oviducts at different stages of gravidity in recently ovulated turtles revealed that proteinaceous like components from the endometrial glands were released into the lumen to form fibers. The morphological features of the oviduct remained active throughout the summer months even though the snapping turtle is a monoclutch species which deposits all the eggs in late-May to mid-June. The high steroid levels correlate with and may be responsible for the secretory activity present throughout the summer and their decline correlates with change to low secretory activity in the fall. Calcium deposition accompanied by morphological changes in luminal cells are suggestive of secretory activity. In the egg-bearing turtles, uterine Ca2+ concentrations measured by flame atomic absorption spectrophotometry revealed significantly higher Ca2+ concentrations (P < 0.001) in eggs with soft shell than eggs without shell. There was a significant increase in calcium granules and proteinaceous fibers in luminal surface of the uterus during the period of eggshelling. This supports the fact that in the snapping turtle like in other reptiles, eggshelling process occurs in the uterus.

IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking.

Science.gov (United States)

Su, Chinh; Nguyen, Thuy-Diem; Zheng, Jie; Kwoh, Chee-Keong

2014-01-01

Protein-protein docking is an in silico method to predict the formation of protein complexes. Due to limited computational resources, the protein-protein docking approach has been developed under the assumption of rigid docking, in which one of the two protein partners remains rigid during the protein associations and water contribution is ignored or implicitly presented. Despite obtaining a number of acceptable complex predictions, it seems to-date that most initial rigid docking algorithms still find it difficult or even fail to discriminate successfully the correct predictions from the other incorrect or false positive ones. To improve the rigid docking results, re-ranking is one of the effective methods that help re-locate the correct predictions in top high ranks, discriminating them from the other incorrect ones. Our results showed that the IFACEwat increased both the numbers of the near-native structures and improved their ranks as compared to the initial rigid docking ZDOCK3.0.2. In fact, the IFACEwat achieved a success rate of 83.8% for Antigen/Antibody complexes, which is 10% better than ZDOCK3.0.2. As compared to another re-ranking technique ZRANK, the IFACEwat obtains success rates of 92.3% (8% better) and 90% (5% better) respectively for medium and difficult cases. When comparing with the latest published re-ranking method F2Dock, the IFACEwat performed equivalently well or even better for several Antigen/Antibody complexes. With the inclusion of interfacial water, the IFACEwat improves mostly results of the initial rigid docking, especially for Antigen/Antibody complexes. The improvement is achieved by explicitly taking into account the contribution of water during the protein interactions, which was ignored or not fully presented by the initial rigid docking and other re-ranking techniques. In addition, the IFACEwat maintains sufficient computational efficiency of the initial docking algorithm, yet improves the ranks as well as the number of the near

Identifying mechanisms that structure ecological communities by snapping model parameters to empirically observed tradeoffs.

Science.gov (United States)

Thomas Clark, Adam; Lehman, Clarence; Tilman, David

2018-04-01

Theory predicts that interspecific tradeoffs are primary determinants of coexistence and community composition. Using information from empirically observed tradeoffs to augment the parametrisation of mechanism-based models should therefore improve model predictions, provided that tradeoffs and mechanisms are chosen correctly. We developed and tested such a model for 35 grassland plant species using monoculture measurements of three species characteristics related to nitrogen uptake and retention, which previous experiments indicate as important at our site. Matching classical theoretical expectations, these characteristics defined a distinct tradeoff surface, and models parameterised with these characteristics closely matched observations from experimental multi-species mixtures. Importantly, predictions improved significantly when we incorporated information from tradeoffs by 'snapping' characteristics to the nearest location on the tradeoff surface, suggesting that the tradeoffs and mechanisms we identify are important determinants of local community structure. This 'snapping' method could therefore constitute a broadly applicable test for identifying influential tradeoffs and mechanisms. © 2018 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Effects of Thiamethoxam-Treated Seed on Mexican Bean Beetle (Coleoptera: Coccinellidae), Nontarget Arthropods, and Crop Performance in Southwestern Virginia Snap Beans.

Science.gov (United States)

Nottingham, L; Kuhar, T P; Kring, T; Herbert, D A; Arancibia, R; Schultz, P

2017-12-08

Thiamethoxam is a neonicotinoid insecticide commonly applied directly to the seeds (seed-treatment) of commercial snap beans, Phaseolus vulgaris L. While previous studies have examined target and nontarget effects of thiamethoxam seed-treatments in snap beans and other crops, to our knowledge, none have been conducted in agroecosystems predominated by the pest Mexican bean beetle, Epilachna varivestis Mulsant (Coleoptera: Coccinellidae). This study examined the effects of thiamethoxam-treated snap beans on E. varivestis, other arthropods, and crop performance in southwestern Virginia. Greenhouse experiments were conducted to evaluate residual toxicity of treated snap beans to E. varivestis and a key predator, Podisus maculiventris (Say) (Hemiptera: Pentatomidae). Treated plants were highly toxic to E. varivestis at 13 d, moderately toxic from 16 to 20 d, and minimally toxic at 24 d. P. maculiventris was unaffected by exposure to treated plants or by feeding on E. varivestis that consumed treated plants. Small plot field experiments in 2014 and 2015 showed no significant effects of thiamethoxam seed-treatments on E. varivestis densities, other arthropods, crop injury, or yield. In 2016, planting was delayed by persistent rain, resulting in early E. varivestis colonization. In this year, thiamethoxam-treated plants had significantly lower densities and feeding injury from E. varivestis, followed by significantly higher yields. Natural enemies were unaffected by seed-treatments in all field experiments. These experiments demonstrated that thiamethoxam seed-treatments provide control of E. varivestis when beetles infest fields within 2 to 3 wk after planting; but otherwise provide negligible advantages. Negative effects from thiamethoxam seed-treatments on nontarget arthropods appear minimal for snap beans in this region. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please

Ion channel activity of membrane vesicles released from sea urchin sperm during the acrosome reaction

International Nuclear Information System (INIS)

Schulz, Joseph R.; Vega-Beltran, Jose L. de la; Beltran, Carmen; Vacquier, Victor D.; Darszon, Alberto

2004-01-01

The sperm acrosome reaction (AR) involves ion channel activation. In sea urchin sperm, the AR requires Ca 2+ and Na + influx and K + and H + efflux. During the AR, the plasma membrane fuses with the acrosomal vesicle membrane forming hybrid membrane vesicles that are released from sperm into the medium. This paper reports the isolation and preliminary characterization of these acrosome reaction vesicles (ARVs), using synaptosome-associated protein of 25 kDa (SNAP-25) as a marker. Isolated ARVs have a unique protein composition. The exocytosis regulatory proteins vesicle-associated membrane protein and SNAP-25 are inside ARVs, as judged by protease protection experiments, and membrane associated based on Triton X-114 partitioning. ARVs fused with planar bilayers display three main types of single channel activity. The most frequently recorded channel is cationic, weakly voltage dependent and has a low open probability that increases with negative potentials. This channel is activated by cAMP, blocked by Ba 2+ , and has a PK + /PNa + selectivity of 4.5. ARVs represent a novel membrane preparation suitable to deepen our understanding of ion channel activity in the AR and during fertilization

Free 25-Hydroxyvitamin D: Impact of Vitamin D Binding Protein Assays on Racial-Genotypic Associations

Energy Technology Data Exchange (ETDEWEB)

Nielson, Carrie M.; Jones, Kerry S.; Chun, Rene F.; Jacobs, Jon M.; Wang, Ying; Hewison, Martin; Adams, John S.; Swanson, Christine M.; Lee, Christine G.; Vanderschueren, Dirk; Pauwels, Steven; Prentice, Ann; Smith, Richard D.; Shi, Tujin; Gao, Yuqian; Schepmoes, Athena A.; Zmuda, Joseph M.; Lapidus, Jodi; Cauley, Jane A.; Bouillon, Roger; Schoenmakers, Inez; Orwoll, Eric S.

2016-05-01

Total 25-hydroxyvitamin D (25OHD) is a marker of vitamin D status and is lower in African Americans than in whites. Whether this difference holds for free 25OHOD (f25OHD) is unclear, considering reported genetic-racial differences in vitaminDbinding protein (DBP) used to calculate f25OHD.

The use of blood protein polymorphism to estimate genetic distance among populations of Indonesian native sheep, St. Croix and Merino

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Agus Suparyanto

2002-03-01

Full Text Available The genetic distance among populations of Indonesia native sheep (Ciamis, Garut, Sumatera and Garahan, St. Croix and Merino were estimated to investigate the genetic relationship among those breeds. Blood protein polymorphism of transferin (Tf, post-transferin (PTf, albumin (Alb, post-albumin (PAlb were detected from blood plasma, while haemoglobine (Hb was detected from erythrocyte using Polyacrylamide Gel Electrophoresis (PAGE. Results of PAGE showed that Tf was controlled by 6 alleles, while Alb by 4 alleles, PTf by 3 Alleles and PAlb and Hb by 2 alleles. Value of breeding coefficient within individual subpopulations (FIS for Tf (-0,0014, Alb (-0,0046 and Hb (0,0256 were not significantly different by noel. These results show that data of gene frequency are still following Hardy-Weinberg Equilibrium and inbreeding inside the sub population did not occur. The closest distance among the native breeds is the subpopulations of Ciamis and Garut due to neighboring area and similar traits of Thin Tail Sheep. The genetic distance of both population to Sumatera Thin Tail Sheep and Garahan Fat Tail are quite far. In addition to that results all Indonesian native breed were distinctly different from St. Croix and Merino.

An efficacy trial of brief lifestyle intervention delivered by generalist community nurses (CN SNAP trial

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Fanaian Mahnaz

2010-02-01

Full Text Available Abstract Background Lifestyle risk factors, in particular smoking, nutrition, alcohol consumption and physical inactivity (SNAP are the main behavioural risk factors for chronic disease. Primary health care (PHC has been shown to be an effective setting to address lifestyle risk factors at the individual level. However much of the focus of research to date has been in general practice. Relatively little attention has been paid to the role of nurses working in the PHC setting. Community health nurses are well placed to provide lifestyle intervention as they often see clients in their own homes over an extended period of time, providing the opportunity to offer intervention and enhance motivation through repeated contacts. The overall aim of this study is to evaluate the impact of a brief lifestyle intervention delivered by community nurses in routine practice on changes in clients' SNAP risk factors. Methods/Design The trial uses a quasi-experimental design involving four generalist community nursing services in NSW Australia. Services have been randomly allocated to an 'early intervention' group or 'late intervention' (comparison group. 'Early intervention' sites are provided with training and support for nurses in identifying and offering brief lifestyle intervention for clients during routine consultations. 'Late intervention site' provide usual care and will be offered the study intervention following the final data collection point. A total of 720 generalist community nursing clients will be recruited at the time of referral from participating sites. Data collection consists of 1 telephone surveys with clients at baseline, three months and six months to examine change in SNAP risk factors and readiness to change 2 nurse survey at baseline, six and 12 months to examine changes in nurse confidence, attitudes and practices in the assessment and management of SNAP risk factors 3 semi-structured interviews/focus with nurses, managers and clients

Thermodynamic properties of an extremely rapid protein folding reaction.

Science.gov (United States)

Schindler, T; Schmid, F X

1996-12-24

The cold-shock protein CspB from Bacillus subtilis is a very small beta-barrel protein, which folds with a time constant of 1 ms (at 25 degrees C) in a U reversible N two-state reaction. To elucidate the energetics of this extremely fast reaction we investigated the folding kinetics of CspB as a function of both temperature and denaturant concentration between 2 and 45 degrees C and between 1 and 8 M urea. Under all these conditions unfolding and refolding were reversible monoexponential reactions. By using transition state theory, data from 327 kinetic curves were jointly analyzed to determine the thermodynamic activation parameters delta H H2O++, delta S H2O++, delta G H2O++, and delta C p H2O++ for unfolding and refolding and their dependences on the urea concentration. 90% of the total change in heat capacity and 96% of the change in the m value (m = d delta G/d[urea]) occur between the unfolded state and the activated state. This suggests that for CspB the activated state of folding is unusually well structured and almost equivalent to the native protein in its interactions with the solvent. As a consequence of this native-like activated state a strong temperature-dependent enthalpy/entropy compensation is observed for the refolding kinetics, and the barrier to refolding shifts from being largely enthalpic at low temperature to largely entropic at high temperature. This shift originates not from the changes in the folding protein chains itself, but from the changes in the protein-solvent interactions. We speculate that the absence of intermediates and the native-like activated state in the folding of CspB are correlated with the small size and the structural type of this protein. The stabilization of a small beta-sheet as in CspB requires extensive non-local interactions, and therefore incomplete sheets are unstable. As a consequence, the critical activated state is reached only very late in folding. The instability of partially folded structure is a means to

The Multifaceted Role of SNARE Proteins in Membrane Fusion.

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Han, Jing; Pluhackova, Kristyna; Böckmann, Rainer A

2017-01-01

Membrane fusion is a key process in all living organisms that contributes to a variety of biological processes including viral infection, cell fertilization, as well as intracellular transport, and neurotransmitter release. In particular, the various membrane-enclosed compartments in eukaryotic cells need to exchange their contents and communicate across membranes. Efficient and controllable fusion of biological membranes is known to be driven by cooperative action of SNARE proteins, which constitute the central components of the eukaryotic fusion machinery responsible for fusion of synaptic vesicles with the plasma membrane. During exocytosis, vesicle-associated v-SNARE (synaptobrevin) and target cell-associated t-SNAREs (syntaxin and SNAP-25) assemble into a core trans-SNARE complex. This complex plays a versatile role at various stages of exocytosis ranging from the priming to fusion pore formation and expansion, finally resulting in the release or exchange of the vesicle content. This review summarizes current knowledge on the intricate molecular mechanisms underlying exocytosis triggered and catalyzed by SNARE proteins. Particular attention is given to the function of the peptidic SNARE membrane anchors and the role of SNARE-lipid interactions in fusion. Moreover, the regulatory mechanisms by synaptic auxiliary proteins in SNARE-driven membrane fusion are briefly outlined.

Snaps to Connect Coaxial and Microstrip Lines in Wearable Systems

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Tiiti Kellomäki

2012-01-01

Full Text Available Commercial snaps (clothing fasteners can be used to connect a coaxial cable to a microstrip line. This is useful in the context of wearable antennas, especially in consumer applications and disposable connections. The measured S-parameters of the transition are presented, and an equivalent circuit and approximate equations are derived for system design purposes. The proposed connection is usable up to 1.5 GHz (10 dB return loss condition, and the frequency range can be extended to 2 GHz if a thinner, more flexible coaxial cable is used.

76 FR 35787 - Updated Trafficking Definition and Supplemental Nutrition Assistance Program (SNAP)-FDPIR Dual...

Science.gov (United States)

2011-06-20

...-Rulemaking Portal: Go to http://www.regulations.gov . Preferred method; follow the online instructions for... included in the record and will be made available to the public. Please be advised that the substance of... definition of trafficking in SNAP benefits is as follows: ``Trafficking means the buying or selling of...

Exploring the association of urban or rural county status and environmental, nutrition- and lifestyle-related resources with the efficacy of SNAP-Ed (Supplemental Nutrition Assistance Program-Education) to improve food security.

Science.gov (United States)

Rivera, Rebecca L; Dunne, Jennifer; Maulding, Melissa K; Wang, Qi; Savaiano, Dennis A; Nickols-Richardson, Sharon M; Eicher-Miller, Heather A

2018-04-01

To investigate the association of policy, systems and environmental factors with improvement in household food security among low-income Indiana households with children after a Supplemental Nutrition Assistance Program-Education (SNAP-Ed) direct nutrition education intervention. Household food security scores measured by the eighteen-item US Household Food Security Survey Module in a longitudinal randomized and controlled SNAP-Ed intervention study conducted from August 2013 to April 2015 were the response variable. Metrics to quantify environmental factors including classification of urban or rural county status; the number of SNAP-authorized stores, food pantries and recreational facilities; average fair market housing rental price; and natural amenity rank were collected from government websites and data sets covering the years 2012-2016 and used as covariates in mixed multiple linear regression modelling. Thirty-seven Indiana counties, USA, 2012-2016. SNAP-Ed eligible adults from households with children (n 328). None of the environmental factors investigated were significantly associated with changes in household food security in this exploratory study. SNAP-Ed improves food security regardless of urban or rural location or the environmental factors investigated. Expansion of SNAP-Ed in rural areas may support food access among the low-income population and reduce the prevalence of food insecurity in rural compared with urban areas. Further investigation into policy, systems and environmental factors of the Social Ecological Model are warranted to better understand their relationship with direct SNAP-Ed and their impact on diet-related behaviours and food security.

Compressibility of the protein-water interface

Science.gov (United States)

Persson, Filip; Halle, Bertil

2018-06-01

The compressibility of a protein relates to its stability, flexibility, and hydrophobic interactions, but the measurement, interpretation, and computation of this important thermodynamic parameter present technical and conceptual challenges. Here, we present a theoretical analysis of protein compressibility and apply it to molecular dynamics simulations of four globular proteins. Using additively weighted Voronoi tessellation, we decompose the solution compressibility into contributions from the protein and its hydration shells. We find that positively cross-correlated protein-water volume fluctuations account for more than half of the protein compressibility that governs the protein's pressure response, while the self correlations correspond to small (˜0.7%) fluctuations of the protein volume. The self compressibility is nearly the same as for ice, whereas the total protein compressibility, including cross correlations, is ˜45% of the bulk-water value. Taking the inhomogeneous solvent density into account, we decompose the experimentally accessible protein partial compressibility into intrinsic, hydration, and molecular exchange contributions and show how they can be computed with good statistical accuracy despite the dominant bulk-water contribution. The exchange contribution describes how the protein solution responds to an applied pressure by redistributing water molecules from lower to higher density; it is negligibly small for native proteins, but potentially important for non-native states. Because the hydration shell is an open system, the conventional closed-system compressibility definitions yield a pseudo-compressibility. We define an intrinsic shell compressibility, unaffected by occupation number fluctuations, and show that it approaches the bulk-water value exponentially with a decay "length" of one shell, less than the bulk-water compressibility correlation length. In the first hydration shell, the intrinsic compressibility is 25%-30% lower than in

Compressibility of the protein-water interface.

Science.gov (United States)

Persson, Filip; Halle, Bertil

2018-06-07

The compressibility of a protein relates to its stability, flexibility, and hydrophobic interactions, but the measurement, interpretation, and computation of this important thermodynamic parameter present technical and conceptual challenges. Here, we present a theoretical analysis of protein compressibility and apply it to molecular dynamics simulations of four globular proteins. Using additively weighted Voronoi tessellation, we decompose the solution compressibility into contributions from the protein and its hydration shells. We find that positively cross-correlated protein-water volume fluctuations account for more than half of the protein compressibility that governs the protein's pressure response, while the self correlations correspond to small (∼0.7%) fluctuations of the protein volume. The self compressibility is nearly the same as for ice, whereas the total protein compressibility, including cross correlations, is ∼45% of the bulk-water value. Taking the inhomogeneous solvent density into account, we decompose the experimentally accessible protein partial compressibility into intrinsic, hydration, and molecular exchange contributions and show how they can be computed with good statistical accuracy despite the dominant bulk-water contribution. The exchange contribution describes how the protein solution responds to an applied pressure by redistributing water molecules from lower to higher density; it is negligibly small for native proteins, but potentially important for non-native states. Because the hydration shell is an open system, the conventional closed-system compressibility definitions yield a pseudo-compressibility. We define an intrinsic shell compressibility, unaffected by occupation number fluctuations, and show that it approaches the bulk-water value exponentially with a decay "length" of one shell, less than the bulk-water compressibility correlation length. In the first hydration shell, the intrinsic compressibility is 25%-30% lower than

Parsimonious Charge Deconvolution for Native Mass Spectrometry

Science.gov (United States)

2018-01-01

Charge deconvolution infers the mass from mass over charge (m/z) measurements in electrospray ionization mass spectra. When applied over a wide input m/z or broad target mass range, charge-deconvolution algorithms can produce artifacts, such as false masses at one-half or one-third of the correct mass. Indeed, a maximum entropy term in the objective function of MaxEnt, the most commonly used charge deconvolution algorithm, favors a deconvolved spectrum with many peaks over one with fewer peaks. Here we describe a new “parsimonious” charge deconvolution algorithm that produces fewer artifacts. The algorithm is especially well-suited to high-resolution native mass spectrometry of intact glycoproteins and protein complexes. Deconvolution of native mass spectra poses special challenges due to salt and small molecule adducts, multimers, wide mass ranges, and fewer and lower charge states. We demonstrate the performance of the new deconvolution algorithm on a range of samples. On the heavily glycosylated plasma properdin glycoprotein, the new algorithm could deconvolve monomer and dimer simultaneously and, when focused on the m/z range of the monomer, gave accurate and interpretable masses for glycoforms that had previously been analyzed manually using m/z peaks rather than deconvolved masses. On therapeutic antibodies, the new algorithm facilitated the analysis of extensions, truncations, and Fab glycosylation. The algorithm facilitates the use of native mass spectrometry for the qualitative and quantitative analysis of protein and protein assemblies. PMID:29376659

Surgical Treatment of Snapping Scapula Syndrome Due to Malunion of Rib Fractures.

Science.gov (United States)

Ten Duis, Kaj; IJpma, Frank F A

2017-02-01

This report describes a case of snapping scapula syndrome (SSS) caused by malunited rib fractures. Abrasion of the deformed ribs was performed with good results. SSS as a cause of shoulder pain after thoracic trauma has to be considered and can be treated by a surgical abrasion technique. Copyright © 2017 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

Super-Resolution Microscopy Reveals the Native Ultrastructure of the Erythrocyte Cytoskeleton

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Leiting Pan

2018-01-01

Full Text Available The erythrocyte cytoskeleton is a textbook prototype for the submembrane cytoskeleton of metazoan cells. While early experiments suggest a triangular network of actin-based junctional complexes connected by ∼200-nm-long spectrin tetramers, later studies indicate much smaller junction-to-junction distances in the range of 25-60 nm. Through super-resolution microscopy, we resolve the native ultrastructure of the cytoskeleton of membrane-preserved erythrocytes for the N and C termini of β-spectrin, F-actin, protein 4.1, tropomodulin, and adducin. This allows us to determine an ∼80-nm junction-to-junction distance, a length consistent with relaxed spectrin tetramers and theories based on spectrin abundance. Through two-color data, we further show that the cytoskeleton meshwork often contains nanoscale voids where the cell membrane remains intact and that actin filaments and capping proteins localize to a subset of, but not all, junctional complexes. Together, our results call for a reassessment of the structure and function of the submembrane cytoskeleton.

Subacute casemix classification for stroke rehabilitation in Australia. How well does AN-SNAP v2 explain variance in outcomes?

Science.gov (United States)

Kohler, Friedbert; Renton, Roger; Dickson, Hugh G; Estell, John; Connolly, Carol E

2011-02-01

We sought the best predictors for length of stay, discharge destination and functional improvement for inpatients undergoing rehabilitation following a stroke and compared these predictors against AN-SNAP v2. The Oxfordshire classification subgroup, sociodemographic data and functional data were collected for patients admitted between 1997 and 2007, with a diagnosis of recent stroke. The data were factor analysed using Principal Components Analysis for categorical data (CATPCA). Categorical regression analyses was performed to determine the best predictors of length of stay, discharge destination, and functional improvement. A total of 1154 patients were included in the study. Principal components analysis indicated that the data were effectively unidimensional, with length of stay being the most important component. Regression analysis demonstrated that the best predictor was the admission motor FIM score, explaining 38.9% of variance for length of stay, 37.4%.of variance for functional improvement and 16% of variance for discharge destination. The best explanatory variable in our inpatient rehabilitation service is the admission motor FIM. AN- SNAP v2 classification is a less effective explanatory variable. This needs to be taken into account when using AN-SNAP v2 classification for clinical or funding purposes.

Neighbourhood and consumer food environment is associated with dietary intake among Supplemental Nutrition Assistance Program (SNAP) participants in Fayette County, Kentucky.

Science.gov (United States)

Gustafson, Alison; Lewis, Sarah; Perkins, Sarah; Wilson, Corey; Buckner, Elizabeth; Vail, Ann

2013-07-01

The aim of the study was to determine the association between dietary outcomes and the neighbourhood food environment (street network distance from home to stores) and consumer food environment (Nutrition Environment Measurement Survey-Stores (NEMS-S) audit). The neighbourhood food environment was captured by creating 0?5-mile and 1-mile network distance (street distance) around each participant’s home and the nearest food venue (convenience store, grocery store, supermarket, farmers’ market and produce stand). The consumer food environment was captured by conducting NEMS-S in all grocery stores/supermarkets within 0?5 and 1 mile of participants’ homes. Fayette County, KY, USA. Supplemental Nutrition Assessment Program (SNAP) participants, n 147. SNAP participants who lived within 0?5 mile of at least one farmers’ market/produce stand had higher odds of consuming one serving or more of vegetables (OR56?92; 95% CI 4?09, 11?69), five servings or more of grains (OR51?76; 95% CI 1?01, 3?05) and one serving or more of milk (OR53?79; 95% CI 2?14, 6?71) on a daily basis. SNAP participants who lived within 0?5 mile of stores receiving a high score on the NEMS-S audit reported higher odds of consuming at least one serving of vegetables daily (OR53?07; 95% CI 1?78, 5?31). Taken together, both the neighbourhood food environment and the consumer food environment are associated with a healthy dietary intake among SNAP participants.

Comparison of the catalytic properties of the botulinum neurotoxin subtypes A1 and A5.

Science.gov (United States)

Wang, Dongxia; Krilich, Joan; Pellett, Sabine; Baudys, Jakub; Tepp, William H; Barr, John R; Johnson, Eric A; Kalb, Suzanne R

2013-12-01

Clostridium botulinum neurotoxins (BoNTs) cause the life-threatening disease botulism through the inhibition of neurotransmitter release by cleaving essential SNARE proteins. There are seven serologically distinctive types of BoNTs and many subtypes within a serotype have been identified. BoNT/A5 is a recently discovered subtype of type A botulinum neurotoxin which possesses a very high degree of sequence similarity and identity to the well-studied A1 subtype. In the present study, we examined the endopeptidase activity of these two BoNT/A subtypes and our results revealed significant differences in substrate binding and cleavage efficiency between subtype A5 and A1. Distinctive hydrolysis efficiency was observed between the two toxins during cleavage of the native substrate SNAP-25 versus a shortened peptide mimic. N-terminal truncation studies demonstrated that a key region of the SNAP-25, including the amino acid residues at 151 through 154 located in the remote binding region of the substrate, contributed to the differential catalytic properties between A1 and A5. Elevated binding affinity of the peptide substrate resulted from including these important residues and enhanced BoNT/A5's hydrolysis efficiency. In addition, mutations of these amino acid residues affect the proteolytic performance of the two toxins in different ways. This study provides a better understanding of the biological activity of these toxins, their performance characteristics in the Endopep-MS assay to detect BoNT in clinical samples and foods, and is useful for the development of peptide substrates. © 2013. Published by Elsevier B.V. All rights reserved.

Production components and yield of bushing snap bean in conventional and organic production systems

Directory of Open Access Journals (Sweden)

Guilherme Renato Gomes

2017-10-01

Full Text Available Production systems influence crops differently, mainly in terms of yield. However, there are few studies that have evaluated different bushing snap bean genotypes in different systems. Thus, this study aimed to evaluate the production components and yield of bushing snap beans in conventional and organic production systems. The experimental design was a randomized complete block, in a factorial 6 × 2 arrangement, corresponding to six genotypes and two production systems, with three replications. The genotypes Isla Manteiga Baixo®, Isla Macarrão Baixo®, Feltrin Vicenza Amarelo Baixo®, and Feltrin Macarrão Napoli®, UEL 1, and UEL 2 were submitted to the following determinations: days to flowering; plant height; medium number of pods per plant; average pod mass, length, and diameter; and yield of commercial pods. A joint analysis of variance was conducted by applying the F test, with mean comparison performed using the Tukey’s test (p < 0.05. Anthesis of the genotypes Feltrin Vicenza Amarelo Baixo, UEL 2, Isla Macarrão Baixo, and Feltrin Macarrão Napoli is anticipated in the conventional production system. The genotype UEL 2 shows higher precocity in anthesis within the conventional system. The genotypes Isla Manteiga Baixo and UEL 1 produce more pods per plant in the conventional system. In the organic system, the genotype Feltrin Macarrão Napoli produces double the number of pods per plant compared with Isla Manteiga Baixo. The organic system leads to greater plant height and average mass, length, and diameter of pods in relation to the conventional system. The commercial pod yield of bushing snap bean is not altered by differences in the production system or genotype.

Binding free energy analysis of protein-protein docking model structures by evERdock.

Science.gov (United States)

Takemura, Kazuhiro; Matubayasi, Nobuyuki; Kitao, Akio

2018-03-14

To aid the evaluation of protein-protein complex model structures generated by protein docking prediction (decoys), we previously developed a method to calculate the binding free energies for complexes. The method combines a short (2 ns) all-atom molecular dynamics simulation with explicit solvent and solution theory in the energy representation (ER). We showed that this method successfully selected structures similar to the native complex structure (near-native decoys) as the lowest binding free energy structures. In our current work, we applied this method (evERdock) to 100 or 300 model structures of four protein-protein complexes. The crystal structures and the near-native decoys showed the lowest binding free energy of all the examined structures, indicating that evERdock can successfully evaluate decoys. Several decoys that show low interface root-mean-square distance but relatively high binding free energy were also identified. Analysis of the fraction of native contacts, hydrogen bonds, and salt bridges at the protein-protein interface indicated that these decoys were insufficiently optimized at the interface. After optimizing the interactions around the interface by including interfacial water molecules, the binding free energies of these decoys were improved. We also investigated the effect of solute entropy on binding free energy and found that consideration of the entropy term does not necessarily improve the evaluations of decoys using the normal model analysis for entropy calculation.

Temperature effects on snapping performance in the common snapper Chelydra serpentina (Reptilia, Testudines).

Science.gov (United States)

Vervust, Bart; Brecko, Jonathan; Herrel, Anthony

2011-01-01

Studies on the effect of temperature on whole-animal performance traits other than locomotion are rare. Here we investigate the effects of temperature on the performance of the turtle feeding apparatus in a defensive context. We measured bite force and the kinematics of snapping in the Common Snapping Turtle (Chelydra serpentina) over a wide range of body temperatures. Bite force performance was thermally insensitive over the broad range of temperatures typically experienced by these turtles in nature. In contrast, neck extension (velocity, acceleration, and deceleration) and jaw movements (velocity, acceleration, and deceleration) showed clear temperature dependence with peak acceleration and deceleration capacity increasing with increasing temperatures. Our results regarding the temperature dependence of defensive behavior are reflected by the ecology and overall behavior of this species. These data illustrate the necessity for carefully controlling T(b) when carrying out behavioral and functional studies on turtles as temperature affects the velocity, acceleration, and deceleration of jaw and neck extension movements. More generally, these data add to the limited but increasing number of studies showing that temperature may have important effects on feeding and defensive performance in ectotherms. © 2010 Wiley-Liss, Inc.

Revealing Ligand Binding Sites and Quantifying Subunit Variants of Noncovalent Protein Complexes in a Single Native Top-Down FTICR MS Experiment

Science.gov (United States)

Li, Huilin; Wongkongkathep, Piriya; Van Orden, Steve L.; Ogorzalek Loo, Rachel R.; Loo, Joseph A.

2014-12-01

"Native" mass spectrometry (MS) has been proven to be increasingly useful for structural biology studies of macromolecular assemblies. Using horse liver alcohol dehydrogenase (hADH) and yeast alcohol dehydrogenase (yADH) as examples, we demonstrate that rich information can be obtained in a single native top-down MS experiment using Fourier transform ion cyclotron mass spectrometry (FTICR MS). Beyond measuring the molecular weights of the protein complexes, isotopic mass resolution was achieved for yeast ADH tetramer (147 kDa) with an average resolving power of 412,700 at m/z 5466 in absorption mode, and the mass reflects that each subunit binds to two zinc atoms. The N-terminal 89 amino acid residues were sequenced in a top-down electron capture dissociation (ECD) experiment, along with the identifications of the zinc binding site at Cys46 and a point mutation (V58T). With the combination of various activation/dissociation techniques, including ECD, in-source dissociation (ISD), collisionally activated dissociation (CAD), and infrared multiphoton dissociation (IRMPD), 40% of the yADH sequence was derived directly from the native tetramer complex. For hADH, native top-down ECD-MS shows that both E and S subunits are present in the hADH sample, with a relative ratio of 4:1. Native top-down ISD of the hADH dimer shows that each subunit (E and S chains) binds not only to two zinc atoms, but also the NAD/NADH ligand, with a higher NAD/NADH binding preference for the S chain relative to the E chain. In total, 32% sequence coverage was achieved for both E and S chains.

2'-5'-Oligoadenylate Synthetase-Like Protein Inhibits Respiratory Syncytial Virus Replication and Is Targeted by the Viral Nonstructural Protein 1.

Science.gov (United States)

Dhar, Jayeeta; Cuevas, Rolando A; Goswami, Ramansu; Zhu, Jianzhong; Sarkar, Saumendra N; Barik, Sailen

2015-10-01

2'-5'-Oligoadenylate synthetase-like protein (OASL) is an interferon-inducible antiviral protein. Here we describe differential inhibitory activities of human OASL and the two mouse OASL homologs against respiratory syncytial virus (RSV) replication. Interestingly, nonstructural protein 1 (NS1) of RSV promoted proteasome-dependent degradation of specific OASL isoforms. We conclude that OASL acts as a cellular antiviral protein and that RSV NS1 suppresses this function to evade cellular innate immunity and allow virus growth. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Separation and Enrichment of Lectin from Zihua Snap-Bean (Phaseolus vulgaris Seeds by PEG 600–Ammonium Sulfate Aqueous Two-Phase System

Directory of Open Access Journals (Sweden)

Bin Jiang

2017-09-01

Full Text Available A fast and efficient method based on a polyethylene glycol (PEG 600/(NH42SO4 aqueous two-phase system for extracting lectin from Zihua snap-bean (Phaseolus vulgaris seeds was established. According to a Box–Behnken design (BBD, involving four factors at three levels each subjected to analysis of variance (ANOVA and response surface analysis, the protein recovery and the purification factor of lectin in the top phase were used as the response values of the variance analysis to acquire the multivariate quadratic regression model. SDS–PAGE electrophoresis and the hemagglutination test were used to detect the distribution of lectin in the aqueous two-phase system (ATPS. The obtained data indicated that lectin was preferentially partitioned into the PEG-rich phase, and the ATPS, composed of 15% (NH42SO4 (w/w, 18% PEG 600 (w/w, 0.4 g/5 g NaCl and 1 mL crude extract, showed good selectivity for lectin when the pH value was 7.5. Under the optimal conditions, most of the lectin was assigned to the top phase in the ATPS, and the hemagglutination activity of the purified lectin in the top phase was 3.08 times that of the crude extract. Consequently, the PEG 600/(NH42SO4 aqueous two-phase system was an effective method for separating and enriching lectin directly from the crude extract of Zihua snap-bean seeds.

Diffusion of Integral Membrane Proteins in Protein-Rich Membranes

DEFF Research Database (Denmark)

Javanainen, Matti; Martinez-Seara, Hector; Metzler, Ralf

2017-01-01

of being protein-poor, native cell membranes are extremely crowded with proteins. On the basis of extensive molecular simulations, we here demonstrate that protein crowding of the membrane at physiological levels leads to deviations from the SD relation and to the emergence of a stronger Stokes......-like dependence D ∝ 1/R. We propose that this 1/R law mainly arises due to geometrical factors: smaller proteins are able to avoid confinement effects much better than their larger counterparts. The results highlight that the lateral dynamics in the crowded setting found in native membranes is radically different......The lateral diffusion of embedded proteins along lipid membranes in protein-poor conditions has been successfully described in terms of the Saffman-Delbrück (SD) model, which predicts that the protein diffusion coefficient D is weakly dependent on its radius R as D ∝ ln(1/R). However, instead...

Highly active promoters and native secretion signals for protein production during extremely low growth rates in Aspergillus niger.

Science.gov (United States)

Wanka, Franziska; Arentshorst, Mark; Cairns, Timothy C; Jørgensen, Thomas; Ram, Arthur F J; Meyer, Vera

2016-08-20

The filamentous ascomycete Aspergillus niger is used in many industrial processes for the production of enzymes and organic acids by batch and fed-batch cultivation. An alternative technique is continuous cultivation, which promises improved yield and optimized pipeline efficiency. In this work, we have used perfusion (retentostat) cultivation to validate two promoters that are suitable for A. niger continuous cultivation of industrially relevant products. Firstly, promoters of genes encoding either an antifungal protein (Panafp) or putative hydrophobin (PhfbD) were confirmed as active throughout retentostat culture by assessing mRNA and protein levels using a luciferase (mluc) reporter system. This demonstrated the anafp promoter mediates a high but temporally variable expression profile, whereas the hfbD promoter mediates a semi-constant, moderate-to-high protein expression during retentostat culture. In order to assess whether these promoters were suitable to produce heterologous proteins during retentostat cultivation, the secreted antifungal protein (AFP) from Aspergillus giganteus, which has many potential biotechnological applications, was expressed in A. niger during retentostat cultivation. Additionally, this assay was used to concomitantly validate that native secretion signals encoded in anafp and hfbD genes can be harnessed for secretion of heterologous proteins. Afp mRNA and protein abundance were comparable to luciferase measurements throughout retentostat cultivation, validating the use of Panafp and PhfbD for perfusion cultivation. Finally, a gene encoding the highly commercially relevant thermal hysteresis protein (THP) was expressed in this system, which did not yield detectable protein. Both hfbD and anafp promoters are suitable for production of useful products in A. niger during perfusion cultivation. These findings provide a platform for further optimisations for high production of heterologous proteins with industrial relevance.

Improved hemocompatibility of silicone rubber extracorporeal tubing via solvent swelling-impregnation of S-nitroso-N-acetylpenicillamine (SNAP) and evaluation in rabbit thrombogenicity model.

Science.gov (United States)

Brisbois, Elizabeth J; Major, Terry C; Goudie, Marcus J; Bartlett, Robert H; Meyerhoff, Mark E; Handa, Hitesh

2016-06-01

Blood-contacting devices, including extracorporeal circulation (ECC) circuits, can suffer from complications due to platelet activation and thrombus formation. Development of nitric oxide (NO) releasing polymers is one method to improve hemocompatibility, taking advantage of the ability of low levels of NO to prevent platelet activation/adhesion. In this study a novel solvent swelling method is used to load the walls of silicone rubber tubing with the NO donor S-nitroso-N-acetylpenicillamine (SNAP). This SNAP-silicone rubber tubing exhibits an NO flux of ca. 1×10(-10)molcm(-2)min(-1), which mimics the range of NO release from the normal endothelium, which is stable for at least 4h. Images of the tubing before and after swelling, obtained via scanning electron microscopy, demonstrate that this swelling method has little effect on the surface properties of the tubing. The SNAP-loaded silicone rubber and silicone rubber control tubing are used to fabricate ECC circuits that are evaluated in a rabbit model of thrombogenicity. After 4h of blood flow, the SNAP-loaded silicone rubber circuits were able to preserve the blood platelet count at 64% of baseline (vs. 12% for silicone rubber control). A 67% reduction in the degree of thrombus formation within the thrombogenicity chamber was also observed. This study demonstrates the ability to improve the hemocompatibility of existing/commercial silicone rubber tubing via a simple solvent swelling-impregnation technique, which may also be applicable to other silicone-based blood-contacting devices. Localized nitric oxide (NO) release can be achieved from biomedical grade polymers doped with S-nitroso-N-acetylpenicillamine (SNAP). Despite the promising in vitro and in vivo biocompatibility results reported for these NO releasing polymers, many of these materials may face challenges in being translated to clinical applications, especially in the areas of polymer processing and manufacturing. In this study, we report a solvent

Nanobodies: site-specific labeling for super-resolution imaging, rapid epitope-mapping and native protein complex isolation

Science.gov (United States)

Pleiner, Tino; Bates, Mark; Trakhanov, Sergei; Lee, Chung-Tien; Schliep, Jan Erik; Chug, Hema; Böhning, Marc; Stark, Holger; Urlaub, Henning; Görlich, Dirk

2015-01-01

Nanobodies are single-domain antibodies of camelid origin. We generated nanobodies against the vertebrate nuclear pore complex (NPC) and used them in STORM imaging to locate individual NPC proteins with nanobody sequence and labeled the resulting proteins with fluorophore-maleimides. As nanobodies are normally stabilized by disulfide-bonded cysteines, this appears counterintuitive. Yet, our analysis showed that this caused no folding problems. Compared to traditional NHS ester-labeling of lysines, the cysteine-maleimide strategy resulted in far less background in fluorescence imaging, it better preserved epitope recognition and it is site-specific. We also devised a rapid epitope-mapping strategy, which relies on crosslinking mass spectrometry and the introduced ectopic cysteines. Finally, we used different anti-nucleoporin nanobodies to purify the major NPC building blocks – each in a single step, with native elution and, as demonstrated, in excellent quality for structural analysis by electron microscopy. The presented strategies are applicable to any nanobody and nanobody-target. DOI: http://dx.doi.org/10.7554/eLife.11349.001 PMID:26633879

Complete amino acid sequences of the ribosomal proteins L25, L29 and L31 from the archaebacterium Halobacterium marismortui.

Science.gov (United States)

Hatakeyama, T; Kimura, M

1988-03-15

Ribosomal proteins were extracted from 50S ribosomal subunits of the archaebacterium Halobacterium marismortui by decreasing the concentration of Mg2+ and K+, and the proteins were separated and purified by ion-exchange column chromatography on DEAE-cellulose. Ten proteins were purified to homogeneity and three of these proteins were subjected to sequence analysis. The complete amino acid sequences of the ribosomal proteins L25, L29 and L31 were established by analyses of the peptides obtained by enzymatic digestion with trypsin, Staphylococcus aureus protease, chymotrypsin and lysylendopeptidase. Proteins L25, L29 and L31 consist of 84, 115 and 95 amino acid residues with the molecular masses of 9472 Da, 12293 Da and 10418 Da respectively. A comparison of their sequences with those of other large-ribosomal-subunit proteins from other organisms revealed that protein L25 from H. marismortui is homologous to protein L23 from Escherichia coli (34.6%), Bacillus stearothermophilus (41.8%), and tobacco chloroplasts (16.3%) as well as to protein L25 from yeast (38.0%). Proteins L29 and L31 do not appear to be homologous to any other ribosomal proteins whose structures are so far known.

Micro-Sugar-Snap and -Wire-Cut Cookie Baking with Trans- and Zero-Trans-Fat Shortenings

Science.gov (United States)

The effect of trans- and zero-trans-fat shortenings on cookie-baking performance was evaluated, using the two AACC micro-cookie-baking methods. Regardless of fat type, sugar-snap cookies made with a given flour were larger in diameter, smaller in height, and greater in weight loss during baking tha...

Native flagellin does not protect mice against an experimental Proteus mirabilis ascending urinary tract infection and neutralizes the protective effect of MrpA fimbrial protein.

Science.gov (United States)

Scavone, Paola; Umpiérrez, Ana; Rial, Analía; Chabalgoity, José A; Zunino, Pablo

2014-06-01

Proteus mirabilis expresses several virulence factors including MR/P fimbriae and flagella. Bacterial flagellin has frequently shown interesting adjuvant and protective properties in vaccine formulations. However, native P. mirabilis flagellin has not been analyzed so far. Native P. mirabilis flagellin was evaluated as a protective antigen and as an adjuvant in co-immunizations with MrpA (structural subunit of MR/P fimbriae) using an ascending UTI model in the mouse. Four groups of mice were intranasally treated with either MrpA, native flagellin, both proteins and PBS. Urine and blood samples were collected before and after immunization for specific antibodies determination. Cytokine production was assessed in immunized mice splenocytes cultures. Mice were challenged with P. mirabilis, and bacteria quantified in kidneys and bladders. MrpA immunization induced serum and urine specific anti-MrpA antibodies while MrpA coadministered with native flagellin did not. None of the animals developed significant anti-flagellin antibodies. Only MrpA-immunized mice showed a significant decrease of P. mirabilis in bladders and kidneys. Instead, infection levels in MrpA-flagellin or flagellin-treated mice showed no significant differences with the control group. IL-10 was significantly induced in splenocytes of mice that received native flagellin or MrpA-flagellin. Native P. mirabilis flagellin did not protect mice against an ascending UTI. Moreover, it showed an immunomodulatory effect, neutralizing the protective role of MrpA. P. mirabilis flagellin exhibits particular immunological properties compared to other bacterial flagellins.

SNAP Participants? Eating Patterns over the Benefit Month: A Time Use Perspective

OpenAIRE

Hamrick, Karen S.; Andrews, Margaret

2016-01-01

Individuals receiving monthly benefits through the U.S. Supplemental Nutrition Assistance Program (SNAP) often fall short of food at the end of the month and some report feelings of hunger. To investigate this situation, we used time diaries from the 2006-08 American Time Use Survey and Eating & Health Module to identify the timing of days where respondents reported no eating occurrences. Analysis includes descriptive statistics, a logit model, and a simulated benefit month. We found that SNA...

Information encoded in non-native states drives substrate-chaperone pairing.

Science.gov (United States)

Mapa, Koyeli; Tiwari, Satyam; Kumar, Vignesh; Jayaraj, Gopal Gunanathan; Maiti, Souvik

2012-09-05

Many proteins refold in vitro through kinetic folding intermediates that are believed to be by-products of native-state centric evolution. These intermediates are postulated to play only minor roles, if any, in vivo because they lack any information related to translation-associated vectorial folding. We demonstrate that refolding intermediate of a test protein, generated in vitro, is able to find its cognate chaperone, from the whole complement of Escherichia coli soluble chaperones. Cognate chaperone-binding uniquely alters the conformation of non-native substrate. Importantly, precise chaperone targeting of substrates are maintained as long as physiological molar ratios of chaperones remain unaltered. Using a library of different chaperone substrates, we demonstrate that kinetically trapped refolding intermediates contain sufficient structural features for precise targeting to cognate chaperones. We posit that evolution favors sequences that, in addition to coding for a functional native state, encode folding intermediates with higher affinity for cognate chaperones than noncognate ones. Copyright © 2012 Elsevier Ltd. All rights reserved.

Wheat CBL-interacting protein kinase 25 negatively regulates salt tolerance in transgenic wheat

OpenAIRE

Jin, Xia; Sun, Tao; Wang, Xiatian; Su, Peipei; Ma, Jingfei; He, Guangyuan; Yang, Guangxiao

2016-01-01

CBL-interacting protein kinases are involved in plant responses to abiotic stresses, including salt stress. However, the negative regulating mechanism of this gene family in response to salinity is less reported. In this study, we evaluated the role of TaCIPK25 in regulating salt response in wheat. Under conditions of high salinity, TaCIPK25 expression was markedly down-regulated in roots. Overexpression of TaCIPK25 resulted in hypersensitivity to Na+ and superfluous accumulation of Na+ in tr...

Structural Characterization of a Thrombin-Aptamer Complex by High Resolution Native Top-Down Mass Spectrometry

Science.gov (United States)

Zhang, Jiang; Loo, Rachel R. Ogorzalek; Loo, Joseph A.

2017-09-01

Native mass spectrometry (MS) with electrospray ionization (ESI) has evolved as an invaluable tool for the characterization of intact native proteins and non-covalently bound protein complexes. Here we report the structural characterization by high resolution native top-down MS of human thrombin and its complex with the Bock thrombin binding aptamer (TBA), a 15-nucleotide DNA with high specificity and affinity for thrombin. Accurate mass measurements revealed that the predominant form of native human α-thrombin contains a glycosylation mass of 2205 Da, corresponding to a sialylated symmetric biantennary oligosaccharide structure without fucosylation. Native MS showed that thrombin and TBA predominantly form a 1:1 complex under near physiological conditions (pH 6.8, 200 mM NH4OAc), but the binding stoichiometry is influenced by the solution ionic strength. In 20 mM ammonium acetate solution, up to two TBAs were bound to thrombin, whereas increasing the solution ionic strength destabilized the thrombin-TBA complex and 1 M NH4OAc nearly completely dissociated the complex. This observation is consistent with the mediation of thrombin-aptamer binding through electrostatic interactions and it is further consistent with the human thrombin structure that contains two anion binding sites on the surface. Electron capture dissociation (ECD) top-down MS of the thrombin-TBA complex performed with a high resolution 15 Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer showed the primary binding site to be at exosite I located near the N-terminal sequence of the heavy chain, consistent with crystallographic data. High resolution native top-down MS is complementary to traditional structural biology methods for structurally characterizing native proteins and protein-DNA complexes. [Figure not available: see fulltext.

Optimizing FRET-FLIM Labeling Conditions to Detect Nuclear Protein Interactions at Native Expression Levels in Living Arabidopsis Roots

KAUST Repository

Long, Yuchen

2018-05-15

Protein complex formation has been extensively studied using Förster resonance energy transfer (FRET) measured by Fluorescence Lifetime Imaging Microscopy (FLIM). However, implementing this technology to detect protein interactions in living multicellular organism at single-cell resolution and under native condition is still difficult to achieve. Here we describe the optimization of the labeling conditions to detect FRET-FLIM in living plants. This study exemplifies optimization procedure involving the identification of the optimal position for the labels either at the N or C terminal region and the selection of the bright and suitable, fluorescent proteins as donor and acceptor labels for the FRET study. With an effective optimization strategy, we were able to detect the interaction between the stem cell regulators SHORT-ROOT and SCARECROW at endogenous expression levels in the root pole of living Arabidopsis embryos and developing lateral roots by FRET-FLIM. Using this approach we show that the spatial profile of interaction between two transcription factors can be highly modulated in reoccurring and structurally resembling organs, thus providing new information on the dynamic redistribution of nuclear protein complex configurations in different developmental stages. In principle, our optimization procedure for transcription factor complexes is applicable to any biological system.

Is the isolated ligand binding domain a good model of the domain in the native receptor?

Science.gov (United States)

Deming, Dustin; Cheng, Qing; Jayaraman, Vasanthi

2003-05-16

Numerous studies have used the atomic level structure of the isolated ligand binding domain of the glutamate receptor to elucidate the agonist-induced activation and desensitization processes in this group of proteins. However, no study has demonstrated the structural equivalence of the isolated ligand binding fragments and the protein in the native receptor. In this report, using visible absorption spectroscopy we show that the electronic environment of the antagonist 6-cyano-7-nitro-2,3-dihydroxyquinoxaline is identical for the isolated protein and the native glutamate receptors expressed in cells. Our results hence establish that the local structure of the ligand binding site is the same in the two proteins and validate the detailed structure-function relationships that have been developed based on a comparison of the structure of the isolated ligand binding domain and electrophysiological consequences in the native receptor.

Effects of thermally induced denaturation on technological-functional properties of whey protein isolate-based films.

Science.gov (United States)

Schmid, M; Krimmel, B; Grupa, U; Noller, K

2014-09-01

This study examined how and to what extent the degree of denaturation affected the technological-functional properties of whey protein isolate (WPI)-based coatings. It was observed that denaturation affected the material properties of WPI-coated films significantly. Surface energy decreased by approximately 20% compared with native coatings. Because the surface energy of a coating should be lower than that of the substrate, this might result in enhanced wettability characteristics between WPI-based solution and substrate surface. Water vapor barrier properties increased by about 35% and oxygen barrier properties increased by approximately 33%. However, significant differences were mainly observed between coatings made of fully native WPI and ones with a degree of denaturation of 25%. Higher degrees of denaturation did not lead to further improvement of material properties. This observation offers cost-saving potential: a major share of denatured whey proteins may be replaced by fully native ones that are not exposed to energy-intensive heat treatment. Furthermore, native WPI solutions can be produced with higher dry matter content without gelatinizing. Hence, less moisture has to be removed through drying, resulting in reduced energy consumption. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

EBT Payment for Online Grocery Orders: a Mixed-Methods Study to Understand Its Uptake among SNAP Recipients and the Barriers to and Motivators for Its Use.

Science.gov (United States)

Martinez, Olivia; Tagliaferro, Barbara; Rodriguez, Noemi; Athens, Jessica; Abrams, Courtney; Elbel, Brian

2018-04-01

To examine Supplemental Nutrition Assistance Program (SNAP) recipients' use of the first online supermarket accepting Electronic Benefit Transfer (EBT) payment. In this mixed-methods study, the authors collected EBT purchase data from an online grocer and attempted a randomized controlled trial in the South Bronx, New York City, followed by focus groups with SNAP beneficiaries aged ≥18 years. Participants were randomized to shop at their usual grocery store or an online supermarket for 3 months. Focus groups explored barriers and motivators to online EBT redemption. Few participants made online purchases, even when incentivized in the randomized controlled trial. Qualitative findings highlighted a lack of perceived control over the online food selection process as a key barrier to purchasing food online. Motivators included fast, free shipping and discounts. Electronic Benefit Transfer for online grocery purchases has the potential to increase food access among SNAP beneficiaries, but challenges exist to this new food buying option. Understanding online food shopping barriers and motivators is critical to the success of policies targeting the online expansion of SNAP benefits. Copyright © 2017 Society for Nutrition Education and Behavior. Published by Elsevier Inc. All rights reserved.

Optimization of protein fractionation by skim milk microfiltration: Choice of ceramic membrane pore size and filtration temperature.

Science.gov (United States)

Jørgensen, Camilla Elise; Abrahamsen, Roger K; Rukke, Elling-Olav; Johansen, Anne-Grethe; Schüller, Reidar B; Skeie, Siv B

2016-08-01

The objective of this study was to investigate how ceramic membrane pore size and filtration temperature influence the protein fractionation of skim milk by cross flow microfiltration (MF). Microfiltration was performed at a uniform transmembrane pressure with constant permeate flux to a volume concentration factor of 2.5. Three different membrane pore sizes, 0.05, 0.10, and 0.20µm, were used at a filtration temperature of 50°C. Furthermore, at pore size 0.10µm, 2 different filtration temperatures were investigated: 50 and 60°C. The transmission of proteins increased with increasing pore size, giving the permeate from MF with the 0.20-µm membrane a significantly higher concentration of native whey proteins compared with the permeates from the 0.05- and 0.10-µm membranes (0.50, 0.24, and 0.39%, respectively). Significant amounts of caseins permeated the 0.20-µm membrane (1.4%), giving a permeate with a whitish appearance and a casein distribution (αS2-CN: αS1-CN: κ-CN: β-CN) similar to that of skim milk. The 0.05- and 0.10-µm membranes were able to retain all caseins (only negligible amounts were detected). A permeate free from casein is beneficial in the production of native whey protein concentrates and in applications where transparency is an important functional characteristic. Microfiltration of skim milk at 50°C with the 0.10-µm membrane resulted in a permeate containing significantly more native whey proteins than the permeate from MF at 60°C. The more rapid increase in transmembrane pressure and the significantly lower concentration of caseins in the retentate at 60°C indicated that a higher concentration of caseins deposited on the membrane, and consequently reduced the native whey protein transmission. Optimal protein fractionation of skim milk into a casein-rich retentate and a permeate with native whey proteins were obtained by 0.10-µm MF at 50°C. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All

Sequence-specific assignment of methyl groups from the neuronal SNARE complex using lanthanide-induced pseudocontact shifts

International Nuclear Information System (INIS)

Pan, Yun-Zu; Quade, Bradley; Brewer, Kyle D.; Szabo, Monika; Swarbrick, James D.; Graham, Bim; Rizo, Josep

2016-01-01

Neurotransmitter release depends critically on the neuronal SNARE complex formed by syntaxin-1, SNAP-25 and synaptobrevin, as well as on other proteins such as Munc18-1, Munc13-1 and synaptotagmin-1. Although three-dimensional structures are available for these components, it is still unclear how they are assembled between the synaptic vesicle and plasma membranes to trigger fast, Ca 2+ -dependent membrane fusion. Methyl TROSY NMR experiments provide a powerful tool to study complexes between these proteins, but assignment of the methyl groups of the SNARE complex is hindered by its limited solubility. Here we report the assignment of the isoleucine, leucine, methionine and valine methyl groups of the four SNARE motifs of syntaxin-1, SNAP-25 and synaptobrevin within the SNARE complex based solely on measurements of lanthanide-induced pseudocontact shifts. Our results illustrate the power of this approach to assign protein resonances without the need of triple resonance experiments and provide an invaluable tool for future structural studies of how the SNARE complex binds to other components of the release machinery.

Sequence-specific assignment of methyl groups from the neuronal SNARE complex using lanthanide-induced pseudocontact shifts

Energy Technology Data Exchange (ETDEWEB)

Pan, Yun-Zu; Quade, Bradley; Brewer, Kyle D. [University of Texas Southwestern Medical Center, Department of Biophysics (United States); Szabo, Monika; Swarbrick, James D.; Graham, Bim [Monash Institute of Pharmaceutical Sciences, Monash University (Australia); Rizo, Josep, E-mail: Jose.Rizo-Rey@UTSouthwestern.edu [University of Texas Southwestern Medical Center, Department of Biophysics (United States)

2016-12-15

Neurotransmitter release depends critically on the neuronal SNARE complex formed by syntaxin-1, SNAP-25 and synaptobrevin, as well as on other proteins such as Munc18-1, Munc13-1 and synaptotagmin-1. Although three-dimensional structures are available for these components, it is still unclear how they are assembled between the synaptic vesicle and plasma membranes to trigger fast, Ca{sup 2+}-dependent membrane fusion. Methyl TROSY NMR experiments provide a powerful tool to study complexes between these proteins, but assignment of the methyl groups of the SNARE complex is hindered by its limited solubility. Here we report the assignment of the isoleucine, leucine, methionine and valine methyl groups of the four SNARE motifs of syntaxin-1, SNAP-25 and synaptobrevin within the SNARE complex based solely on measurements of lanthanide-induced pseudocontact shifts. Our results illustrate the power of this approach to assign protein resonances without the need of triple resonance experiments and provide an invaluable tool for future structural studies of how the SNARE complex binds to other components of the release machinery.

Energetic frustrations in protein folding at residue resolution: a homologous simulation study of Im9 proteins.

Directory of Open Access Journals (Sweden)

Yunxiang Sun

Full Text Available Energetic frustration is becoming an important topic for understanding the mechanisms of protein folding, which is a long-standing big biological problem usually investigated by the free energy landscape theory. Despite the significant advances in probing the effects of folding frustrations on the overall features of protein folding pathways and folding intermediates, detailed characterizations of folding frustrations at an atomic or residue level are still lacking. In addition, how and to what extent folding frustrations interact with protein topology in determining folding mechanisms remains unclear. In this paper, we tried to understand energetic frustrations in the context of protein topology structures or native-contact networks by comparing the energetic frustrations of five homologous Im9 alpha-helix proteins that share very similar topology structures but have a single hydrophilic-to-hydrophobic mutual mutation. The folding simulations were performed using a coarse-grained Gō-like model, while non-native hydrophobic interactions were introduced as energetic frustrations using a Lennard-Jones potential function. Energetic frustrations were then examined at residue level based on φ-value analyses of the transition state ensemble structures and mapped back to native-contact networks. Our calculations show that energetic frustrations have highly heterogeneous influences on the folding of the four helices of the examined structures depending on the local environment of the frustration centers. Also, the closer the introduced frustration is to the center of the native-contact network, the larger the changes in the protein folding. Our findings add a new dimension to the understanding of protein folding the topology determination in that energetic frustrations works closely with native-contact networks to affect the protein folding.

Attitudes and Experiences of Close Interethnic Friendships Among Native Emerging Adults: A Mixed-Methods Investigation

OpenAIRE

Jones, Merrill L.

2017-01-01

This study included 114 Native adults and 6 Native/non-Native pairs of friends (age 18-25). Experiences and attitudes for close interethnic friendships were investigated. Friendship patterns and predictors were quantitatively assessed for the 114 Natives, with qualitative examination of the development and qualities of the six friend pairs. Results of quantitative analysis revealed that 80% of this sample reported friendship investment with Whites, and 55% reported friendship investment wi...

Critical Windows of Cardiovascular Susceptibility to Developmental Hypoxia in Common Snapping Turtle (Chelydra serpentina) Embryos.

Science.gov (United States)

Tate, Kevin B; Kohl, Zachary F; Eme, John; Rhen, Turk; Crossley, Dane A

2015-01-01

Environmental conditions fluctuate dramatically in some reptilian nests. However, critical windows of environmental sensitivity for cardiovascular development have not been identified. Continuous developmental hypoxia has been shown to alter cardiovascular form and function in embryonic snapping turtles (Chelydra serpentina), and we used this species to identify critical periods during which hypoxia modifies the cardiovascular phenotype. We hypothesized that incubation in 10% O2 during specific developmental periods would have differential effects on the cardiovascular system versus overall somatic growth. Two critical windows were identified with 10% O2 from 50% to 70% of incubation, resulting in relative heart enlargement, either via preservation of or preferential growth of this tissue, while exposure to 10% O2 from 20% to 70% of incubation resulted in a reduction in arterial pressure. The deleterious or advantageous aspects of these embryonic phenotypes in posthatching snapping turtles have yet to be explored. However, identification of these critical windows has provided insight into how the developmental environment alters the phenotype of reptiles and will also be pivotal in understanding its impact on the fitness of egg-laying reptiles.

Riboflavin protects mice against liposaccharide-induced shock through expression of heat shock protein 25

Science.gov (United States)

Riboflavin (vitamin B2) is a water-soluble vitamin essential for normal cellular functions, growth and development. The study was aimed at investigating the effects of vitamin B2 on the survival rate, and expressions of tissue heat shock protein 25 (HSP25) and heat shock factor 1 (HSF1) in mice und...

Carbon dioxide (CO2) laser treatment of cutaneous papillomas in a common snapping turtle, Chelydra serpentina.

Science.gov (United States)

Raiti, Paul

2008-06-01

Carbon dioxide (CO2) laser was used to treat multiple cutaneous papillomas on an adult female common snapping turtle, Chelydra serpentina serpentina. A combination of excisional and ablative techniques provided excellent intraoperative visibility and postoperative results due to the laser's unique ability to incise and vaporize soft tissue.

MetaUniDec: High-Throughput Deconvolution of Native Mass Spectra

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Reid, Deseree J.; Diesing, Jessica M.; Miller, Matthew A.; Perry, Scott M.; Wales, Jessica A.; Montfort, William R.; Marty, Michael T.

2018-04-01

The expansion of native mass spectrometry (MS) methods for both academic and industrial applications has created a substantial need for analysis of large native MS datasets. Existing software tools are poorly suited for high-throughput deconvolution of native electrospray mass spectra from intact proteins and protein complexes. The UniDec Bayesian deconvolution algorithm is uniquely well suited for high-throughput analysis due to its speed and robustness but was previously tailored towards individual spectra. Here, we optimized UniDec for deconvolution, analysis, and visualization of large data sets. This new module, MetaUniDec, centers around a hierarchical data format 5 (HDF5) format for storing datasets that significantly improves speed, portability, and file size. It also includes code optimizations to improve speed and a new graphical user interface for visualization, interaction, and analysis of data. To demonstrate the utility of MetaUniDec, we applied the software to analyze automated collision voltage ramps with a small bacterial heme protein and large lipoprotein nanodiscs. Upon increasing collisional activation, bacterial heme-nitric oxide/oxygen binding (H-NOX) protein shows a discrete loss of bound heme, and nanodiscs show a continuous loss of lipids and charge. By using MetaUniDec to track changes in peak area or mass as a function of collision voltage, we explore the energetic profile of collisional activation in an ultra-high mass range Orbitrap mass spectrometer. [Figure not available: see fulltext.

Harvesting and wood transport planning with SNAP III program (Scheduling and Network Analysis Program in a pine plantation in Southeast Brazil

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Lopes Eduardo da Silva

2003-01-01

Full Text Available The objective of this study was to verify the potential of SNAP III (Scheduling and Network Analysis Program as a support tool for harvesting and wood transport planning in Brazil harvesting subsystem definition and establishment of a compatible route were assessed. Initially, machine operational and production costs were determined in seven subsystems for the study area, and quality indexes, construction and maintenance costs of forest roads were obtained and used as SNAP III program input data. The results showed, that three categories of forest road occurrence were observed in the study area: main, secondary and tertiary which, based on quality index, allowed a medium vehicle speed of about 41, 30 and 24 km/hours and a construction cost of about US$ 5,084.30, US$ 2,275.28 and US$ 1,650.00/km, respectively. The SNAP III program used as a support tool for the planning, was found to have a high potential tool in the harvesting and wood transport planning. The program was capable of defining efficiently, the harvesting subsystem on technical and economical basis, the best wood transport route and the forest road to be used in each period of the horizon planning.

Immobilization of azurin with retention of its native electrochemical properties at alkylsilane self-assembled monolayer modified indium tin oxide

International Nuclear Information System (INIS)

Ashur, Idan; Jones, Anne K.

2012-01-01

Highlights: ► Immobilization of azurin at indium tin oxide causes modification of the native redox properties. ► Azurin was immobilized at alkylsilane self-assembled monolayer on indium tin oxide. ► Native, solution redox properties are retained for the immobilized protein on the SAM. ► Technique should be widely applicable to other redox proteins. - Abstract: Indium tin oxide (ITO) is a promising material for developing spectroelectrochemical methods due to its combination of excellent transparency in the visible region and high conductivity over a broad range of potential. However, relatively few examples of immobilization of redox proteins at ITO with retention of the ability to transfer electrons with the underlying material with native characteristics have been reported. In this work, we utilize an alkylsilane functionalized ITO surface as a biocompatible interface for immobilization of the blue copper protein azurin. Adsorption of azurin at ITO as well as ITO coated with self-assembled monolayers of (3-mercaptopropyl)trimethoxysilane (MPTMS) and n-decyltrimethoxysilane (DTMS) was achieved, and immobilized protein probed using protein film electrochemistry. The native redox properties of the protein were perturbed by adsorption directly to ITO or to the MPTMS layer on an ITO surface. However, azurin adsorbed at a DTMS covered ITO surface retained native electrochemical properties (E 1/2 = 122 ± 5 mV vs. Ag/AgCl) and could exchange electrons directly with the underlying ITO layer without need for an intervening chemical mediator. These results open new opportunities for immobilizing functional redox proteins at ITO and developing spectroelectrochemical methods for investigating them.

Endoscopically assisted resection of a scapular osteochondroma causing snapping scapula syndrome

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Futani Hiroyuki

2007-03-01

Full Text Available Abstract Background Osteochondroma is the most common benign bone tumor in the scapula. This condition might lead to snapping scapula syndrome, which is characterized by painful, audible, and/or palpable abnormal scapulothoracic motion. In the present case, this syndrome was successfully treated by use of endoscopically assisted resection of the osteochondroma. Case presentation A 41-year-old man had a tolerable pain in his scapular region over a 10 years' period. The pain developed gradually with shoulder motion, in particular with golf swing since he was aiming a professional golf player career. On physical examination, "clunking" was noted once from 90 degrees of abduction to 180 degrees of shoulder motion. A trans-scapular roentgenogram and computed tomography images revealed an osteochondroma located at the anterior and inferior aspect of the scapula. Removal of the tumor was performed by the use of endoscopically assisted resection. One portal was made at the lateral border of the scapula to introduce a 2.7-mm-diameter, 30 degrees Hopkins telescope. The tumor was resected in a piece-by-piece manner by the use of graspers through the same portal. Immediately after the operation pain relief was obtained, and the "clunking" disappeared. CT images showed complete tumor resection. The patient could start playing golf one week after the surgery. Conclusion Endoscopically assisted resection of osteochondroma of the scapula provides a feasible technique to treat snapping scapula syndrome and obtain early functional recovery with a short hospital stay and cosmetic advantage.

Comparative assessment of recombinant and native immunogenic forms of Fasciola hepatica proteins for serodiagnosis of sheep fasciolosis.

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Mokhtarian, Kobra; Meamar, Ahmad Reza; Khoshmirsafa, Majid; Razmjou, Elham; Masoori, Leila; Khanmohammadi, Majid; Akhlaghi, Lame; Falak, Reza

2018-01-01

Laboratory diagnosis of sheep fasciolosis is commonly performed by coprological examinations; however, this method may lead to false negative results during the acute phase of the infection. Furthermore, the poor sensitivity of coprological methods is considered to be a paradox in the chronic phase of the infection. In this study, we compared the immunoreactivity of native and recombinant forms of Fasciola hepatica excretory/secretory antigens and determined their capabilities for the development of F. hepatica-specific immunoassays. Immunoreactivity and specificity of recombinant and native forms of F. hepatica antigens, including fatty acid binding protein (FABP), glutathione-S-transferase (GST), and cathepsin L-1 (CL1), in parallel with native forms of FABP and GST, were studied for serodiagnosis of the chronic form of sheep fasciolosis, individually or in combination with each other by enzyme-linked immunosorbent assays (ELISA). The correlation of the findings was assessed by receiver-operator characteristic (ROC); furthermore, the specificity and sensitivity were assessed by Youden's J. Serologic cross-reactivity was evaluated using samples from healthy sheep (n = 40), Fasciola-infected sheep (n = 30), and sheep with other parasitic infections (n = 43). The FABPs were determined to be greater than 95% sensitive for F. hepatica serodiagnosis. The most desirable diagnostic recombinant antigen was rCL1, which showed 100% sensitivity and 97% specificity in ELISA and was capable of discriminating the positive and negative samples by maximum Youden's J results. We conclude that rCL1 can be used for routine serodiagnosis of chronic fasciolosis. Thus, it could be advantageous in development of immunoassays for screening of ovine herds in fasciolosis-endemic areas and as a reliable agent for detection of fasciolosis in non-endemic regions.

Site-Selective Conjugation of Native Proteins with DNA

DEFF Research Database (Denmark)

Trads, Julie Brender; Tørring, Thomas; Gothelf, Kurt Vesterager

2017-01-01

Conjugation of DNA to proteins is increasingly used in academia and industry to provide proteins with tags for identification or handles for hybridization to other DNA strands. Assay technologies such as immuno-PCR and proximity ligation and the imaging technology DNA-PAINT require DNA-protein....... The introduction of a bioorthogonal handle at a specific position of a protein by recombinant techniques provides an excellent approach to site-specific conjugation, but for many laboratories and for applications where several proteins are to be labeled, the expression of recombinant proteins may be cumbersome...... conjugates. In DNA nanotechnology, the DNA handle is exploited to precisely position proteins by self-assembly. For these applications, site-selective conjugation is almost always desired because fully functional proteins are required to maintain the specificity of antibodies and the activity of enzymes...

A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces

NARCIS (Netherlands)

Melo, Rita; Fieldhouse, Robert; Melo, André; Correia, João D G; Cordeiro, Maria Natália D S; Gümüş, Zeynep H; Costa, Joaquim; Bonvin, Alexandre M J J; de Sousa Moreira, Irina

2016-01-01

Understanding protein-protein interactions is a key challenge in biochemistry. In this work, we describe a more accurate methodology to predict Hot-Spots (HS) in protein-protein interfaces from their native complex structure compared to previous published Machine Learning (ML) techniques. Our model

Examining the Heterogeneous Genome Content of Multipartite Viruses BMV and CCMV by Native Mass Spectrometry

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van de Waterbeemd, Michiel; Snijder, Joost; Tsvetkova, Irina B.; Dragnea, Bogdan G.; Cornelissen, Jeroen J.; Heck, Albert J. R.

2016-06-01

Since the concept was first introduced by Brian Chait and co-workers in 1991, mass spectrometry of proteins and protein complexes under non-denaturing conditions (native MS) has strongly developed, through parallel advances in instrumentation, sample preparation, and data analysis tools. However, the success rate of native MS analysis, particularly in heterogeneous mega-Dalton (MDa) protein complexes, still strongly depends on careful instrument modification. Here, we further explore these boundaries in native mass spectrometry, analyzing two related endogenous multipartite viruses: the Brome Mosaic Virus (BMV) and the Cowpea Chlorotic Mottle Virus (CCMV). Both CCMV and BMV are approximately 4.6 megadalton (MDa) in mass, of which approximately 1 MDA originates from the genomic content of the virion. Both viruses are produced as mixtures of three particles carrying different segments of the genome, varying by approximately 0.1 MDA in mass (~2%). This mixture of particles poses a challenging analytical problem for high-resolution native MS analysis, given the large mass scales involved. We attempt to unravel the particle heterogeneity using both Q-TOF and Orbitrap mass spectrometers extensively modified for analysis of very large assemblies. We show that manipulation of the charging behavior can provide assistance in assigning the correct charge states. Despite their challenging size and heterogeneity, we obtained native mass spectra with resolved series of charge states for both BMV and CCMV, demonstrating that native MS of endogenous multipartite virions is feasible.

Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes

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Uchikoga Nobuyuki

2010-05-01

Full Text Available Abstract Background Protein-protein docking for proteins with large conformational changes was analyzed by using interaction fingerprints, one of the scales for measuring similarities among complex structures, utilized especially for searching near-native protein-ligand or protein-protein complex structures. Here, we have proposed a combined method for analyzing protein-protein docking by taking large conformational changes into consideration. This combined method consists of ensemble soft docking with multiple protein structures, refinement of complexes, and cluster analysis using interaction fingerprints and energy profiles. Results To test for the applicability of this combined method, various CaM-ligand complexes were reconstructed from the NMR structures of unbound CaM. For the purpose of reconstruction, we used three known CaM-ligands, namely, the CaM-binding peptides of cyclic nucleotide gateway (CNG, CaM kinase kinase (CaMKK and the plasma membrane Ca2+ ATPase pump (PMCA, and thirty-one structurally diverse CaM conformations. For each ligand, 62000 CaM-ligand complexes were generated in the docking step and the relationship between their energy profiles and structural similarities to the native complex were analyzed using interaction fingerprint and RMSD. Near-native clusters were obtained in the case of CNG and CaMKK. Conclusions The interaction fingerprint method discriminated near-native structures better than the RMSD method in cluster analysis. We showed that a combined method that includes the interaction fingerprint is very useful for protein-protein docking analysis of certain cases.

Diabetes alters KIF1A and KIF5B motor proteins in the hippocampus.

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Filipa I Baptista

Full Text Available Diabetes mellitus is the most common metabolic disorder in humans. Diabetic encephalopathy is characterized by cognitive and memory impairments, which have been associated with changes in the hippocampus, but the mechanisms underlying those impairments triggered by diabetes, are far from being elucidated. The disruption of axonal transport is associated with several neurodegenerative diseases and might also play a role in diabetes-associated disorders affecting nervous system. We investigated the effect of diabetes (2 and 8 weeks duration on KIF1A, KIF5B and dynein motor proteins, which are important for axonal transport, in the hippocampus. The mRNA expression of motor proteins was assessed by qRT-PCR, and also their protein levels by immunohistochemistry in hippocampal slices and immunoblotting in total extracts of hippocampus from streptozotocin-induced diabetic and age-matched control animals. Diabetes increased the expression and immunoreactivity of KIF1A and KIF5B in the hippocampus, but no alterations in dynein were detected. Since hyperglycemia is considered a major player in diabetic complications, the effect of a prolonged exposure to high glucose on motor proteins, mitochondria and synaptic proteins in hippocampal neurons was also studied, giving particular attention to changes in axons. Hippocampal cell cultures were exposed to high glucose (50 mM or mannitol (osmotic control; 25 mM plus 25 mM glucose for 7 days. In hippocampal cultures incubated with high glucose no changes were detected in the fluorescence intensity or number of accumulations related with mitochondria in the axons of hippocampal neurons. Nevertheless, high glucose increased the number of fluorescent accumulations of KIF1A and synaptotagmin-1 and decreased KIF5B, SNAP-25 and synaptophysin immunoreactivity specifically in axons of hippocampal neurons. These changes suggest that anterograde axonal transport mediated by these kinesins may be impaired in hippocampal

Flexibility damps macromolecular crowding effects on protein folding dynamics: Application to the murine prion protein (121-231)

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Bergasa-Caceres, Fernando; Rabitz, Herschel A.

2014-01-01

A model of protein folding kinetics is applied to study the combined effects of protein flexibility and macromolecular crowding on protein folding rate and stability. It is found that the increase in stability and folding rate promoted by macromolecular crowding is damped for proteins with highly flexible native structures. The model is applied to the folding dynamics of the murine prion protein (121-231). It is found that the high flexibility of the native isoform of the murine prion protein (121-231) reduces the effects of macromolecular crowding on its folding dynamics. The relevance of these findings for the pathogenic mechanism are discussed.

Native aggregation as a cause of origin of temporary cellular structures needed for all forms of cellular activity, signaling and transformations.

Science.gov (United States)

Matveev, Vladimir V