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Sample records for 2-de protein spots

  1. Effects of thawing, refreezing and storage conditions of tissue samples and protein extracts on 2-DE spot intensity.

    PubMed

    Weist, Stephanie; Brunkau, Cindy; Wittke, Janosch; Eravci, Murat; Broedel, Oliver; Krause, Eberhard; Stephanowitz, Heike; Eravci, Selda; Baumgartner, Andreas

    2010-04-01

    We report that reliable quantitative proteome analyses can be performed with tissue samples stored at -80 degrees C for up to 10 years. However, storing protein extracts at 4 degrees C for 24 h and freezing protein extracts at -80 degrees C and thawing them significantly altered 41.6 and 17.5% of all spot intensities on 2-DE gels, respectively. Fortunately, these storing effects did not impair the reliability of quantifying 2-DE experiments. Nonetheless, the results show that freezing and storage conditions should be carefully controlled in proteomic experiments. PMID:20127687

  2. Spot Matching of 2-DE Images Using Distance, Intensity, and Pattern Information.

    PubMed

    Xin, Hua-Mei; Zhu, Yuemin

    2016-01-01

    The analysis of a large number of two-dimensional gel electrophoresis (2-DE) images requires developing automatic methods. In such analyses, spot matching plays a fundamental role, in particular for the identification of proteins. We describe a simple and accurate method which allows to automatically and accurately match spots in 2-DE images. The method consists of simultaneously exploiting the distance between the spots, their intensity, and the pattern formed by their spatial configuration. PMID:26611412

  3. Cold Spots in Protein Binding.

    PubMed

    Shirian, Jason; Sharabi, Oz; Shifman, Julia M

    2016-09-01

    Understanding the energetics and architecture of protein-binding interfaces is important for basic research and could potentially facilitate the design of novel binding domains for biotechnological applications. It is well accepted that a few key residues at binding interfaces (binding hot spots) are responsible for contributing most to the free energy of binding. In this opinion article, we introduce a new concept of 'binding cold spots', or interface positions occupied by suboptimal amino acids. Such positions exhibit a potential for affinity enhancement through various mutations. We give several examples of cold spots from different protein-engineering studies and argue that identification of such positions is crucial for studies of protein evolution and protein design. PMID:27477052

  4. Evaluation of protein extraction protocols for 2DE in marine ecotoxicoproteomics.

    PubMed

    Wu, Huifeng; Ji, Chenglong; Wei, Lei; Zhao, Jianmin

    2013-11-01

    In ecotoxicoproteomics, an accurate and reproducible extraction of proteins is a critical step for 2DE analysis and further protein identification using MS. The criteria for the assessment of protein extraction quality include protein yield, protein spots resolved in a 2DE gel, matched protein spots in replicate gels, reproducibility, and compatibility with MS. In this work, we evaluated three protein extraction systems, straightforward lysis buffer, trichloroacetic acid-acetone, and TRIzol reagent with some modifications, for the protein extraction from three animal species including mussel Mytilus galloprovincialis, flounder Paralichthys olivaceus, and polychaete Nereis diversicolor used in marine ecotoxicology. Our results indicated that these methods could extract significantly different protein profiles. The method using TRIzol reagent resulted in the most matched protein spots resolved in four replicate 2DE gels and highest reproducibilities for the gill of M. galloprovincialis and liver of P. olivaceus. However, a modified trichloroacetic acid-acetone solvent system was best for the whole soft tissue of N. diversicolor. This work provides the fundamental information of the extraction quality of protein extraction protocols from different marine animals, which may facilitate the selection of a suitable protein extraction protocol for ecotoxicoproteomics. PMID:24106175

  5. Improved solubilization of surface proteins from Listeria monocytogenes for 2-DE.

    PubMed

    Mujahid, Sana; Pechan, Tibor; Wang, Chinling

    2007-11-01

    Solubilization of bacterial surface (cell wall and membrane-associated) proteins for 2-DE is challenging, particularly in the case of Gram-positive bacteria. This is primarily due to strong protein association with the cell wall peptidoglycan and protein hydrophobicity. We solubilized surface proteins for 2-DE from the Gram-positive pathogen Listeria monocytogenes using mutanolysin, which digests cell wall peptidoglycan, and one of three different mixtures of zwitterionic detergent and chaotropes: (i) CHAPS/urea, (ii) amidosulfobetaine-14 (ASB-14)/urea/thiourea (iii) N-decyl-N,N'-dimethyl-3-ammonio-1-propanesulfonate/urea/thiourea. Cell lysis with mutanolysin followed by solubilization with ASB-14/urea/thiourea gave the highest overall protein yield with the best 2-DE resolution. Protein spot identification by MALDI-TOF/TOF-MS analysis revealed 29 characterized surface proteins of L. monocytogenes, 17 of which have not previously been reported on the surface proteome map. This is the first report describing the successful solubilization and 2-DE of L. monocytogenes proteins bound to the cell surface via an LPXTG motif or by a hydrophobic tail. The increase in surface proteome coverage obtained by mutanolysin and ASB-14/urea/thiourea solubilization suggests the utility of this method for future analytical and comparative studies of surface proteins from Listeria, and possibly other Gram-positive bacteria, using 2-DE proteomic analysis. An updated 2-DE reference map of L. monocytogenes surface proteins is presented. PMID:17922522

  6. Differential effects of mineral nutrition on wheat flour proteins determined by quantitative 2-DE and MS/MS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Flour protein composition changed significantly when plants of the hard red spring wheat Triticum aestivum cv Butte 86 were grown with or without post-anthesis fertilization with NPK. To measure changes in individual proteins, 369 protein spots were resolved and quantified by 2-DE of total flour pro...

  7. Differential effects of mineral nutrition on wheat flour proteins determined by quantitative 2-DE and MS/MS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Flour protein composition changed significantly when plants of the hard red spring wheat Triticum aestivum Butte 86 were grown with or without post-anthesis fertilization with NPK. To measure changes in individual proteins, 369 protein spots were resolved and quantified by 2-DE of total flour protei...

  8. Evaluation of protein N-glycosylation in 2-DE: Erythropoietin as a study case.

    PubMed

    Llop, Esther; Gallego, Ricardo Gutiérrez; Belalcazar, Viviana; Gerwig, Gerrit J; Kamerling, Johannis P; Segura, Jordi; Pascual, José A

    2007-12-01

    The structure, function, and physico-chemical properties of many proteins are determined by PTM, being glycosylation the most complex. This study describes how a combination of typical proteomics methods (2-DE) combines with glycomics strategies (HPLC, MALDI-TOF-MS, exoglycosidases sequencing) to yield comprehensive data about single spot-microheterogeneity, providing meaningful information for the detection of disease markers, pharmaceutical industry, antidoping control, etc. Recombinant erythropoietin and its hyperglycosylated analogue darbepoetin-alpha were chosen as showcases because of their relevance in these fields and the analytical challenge they represent. The combined approach yielded good results in terms of sample complexity (mixture glycoforms), reproducibility, sensitivity ( approximately 25 pmoles of glycoprotein/spot), and identification of the underlying protein. Heterogeneity was present in all spots but with a clear tendency; spots proximal to the anode contained the highest amount of tetra-antennary tetra-sialylated glycans, whereas the opposite occurred for spots proximal to the cathode with the majority of the structures being undersialylated. Spot microheterogeneity proved a consequence of the multiple glycosylation sites as they contributed directly to the number of possibilities to account for a discrete charge in a single spot. The interest of this combined glycoproteomics method resides in the efficiency for detecting and quantifying subtle dissimilarities originated from altered ratios of identical glycans including N-acetyl-lactosamine repeats, acetylation, or antigenic epitopes, that do not significantly contribute to the electrophoretic mobility, but affect the glycan microheterogeneity and the potential underlying related functionality. PMID:17973294

  9. Optimal protein extraction methods from diverse sample types for protein profiling by using Two-Dimensional Electrophoresis (2DE).

    PubMed

    Tan, A A; Azman, S N; Abdul Rani, N R; Kua, B C; Sasidharan, S; Kiew, L V; Othman, N; Noordin, R; Chen, Y

    2011-12-01

    There is a great diversity of protein samples types and origins, therefore the optimal procedure for each sample type must be determined empirically. In order to obtain a reproducible and complete sample presentation which view as many proteins as possible on the desired 2DE gel, it is critical to perform additional sample preparation steps to improve the quality of the final results, yet without selectively losing the proteins. To address this, we developed a general method that is suitable for diverse sample types based on phenolchloroform extraction method (represented by TRI reagent). This method was found to yield good results when used to analyze human breast cancer cell line (MCF-7), Vibrio cholerae, Cryptocaryon irritans cyst and liver abscess fat tissue. These types represent cell line, bacteria, parasite cyst and pus respectively. For each type of samples, several attempts were made to methodically compare protein isolation methods using TRI-reagent Kit, EasyBlue Kit, PRO-PREP™ Protein Extraction Solution and lysis buffer. The most useful protocol allows the extraction and separation of a wide diversity of protein samples that is reproducible among repeated experiments. Our results demonstrated that the modified TRI-reagent Kit had the highest protein yield as well as the greatest number of total proteins spots count for all type of samples. Distinctive differences in spot patterns were also observed in the 2DE gel of different extraction methods used for each type of sample. PMID:22433892

  10. KFC Server: interactive forecasting of protein interaction hot spots.

    PubMed

    Darnell, Steven J; LeGault, Laura; Mitchell, Julie C

    2008-07-01

    The KFC Server is a web-based implementation of the KFC (Knowledge-based FADE and Contacts) model-a machine learning approach for the prediction of binding hot spots, or the subset of residues that account for most of a protein interface's; binding free energy. The server facilitates the automated analysis of a user submitted protein-protein or protein-DNA interface and the visualization of its hot spot predictions. For each residue in the interface, the KFC Server characterizes its local structural environment, compares that environment to the environments of experimentally determined hot spots and predicts if the interface residue is a hot spot. After the computational analysis, the user can visualize the results using an interactive job viewer able to quickly highlight predicted hot spots and surrounding structural features within the protein structure. The KFC Server is accessible at http://kfc.mitchell-lab.org. PMID:18539611

  11. Structural hot spots for the solubility of globular proteins.

    PubMed

    Ganesan, Ashok; Siekierska, Aleksandra; Beerten, Jacinte; Brams, Marijke; Van Durme, Joost; De Baets, Greet; Van der Kant, Rob; Gallardo, Rodrigo; Ramakers, Meine; Langenberg, Tobias; Wilkinson, Hannah; De Smet, Frederik; Ulens, Chris; Rousseau, Frederic; Schymkowitz, Joost

    2016-01-01

    Natural selection shapes protein solubility to physiological requirements and recombinant applications that require higher protein concentrations are often problematic. This raises the question whether the solubility of natural protein sequences can be improved. We here show an anti-correlation between the number of aggregation prone regions (APRs) in a protein sequence and its solubility, suggesting that mutational suppression of APRs provides a simple strategy to increase protein solubility. We show that mutations at specific positions within a protein structure can act as APR suppressors without affecting protein stability. These hot spots for protein solubility are both structure and sequence dependent but can be computationally predicted. We demonstrate this by reducing the aggregation of human α-galactosidase and protective antigen of Bacillus anthracis through mutation. Our results indicate that many proteins possess hot spots allowing to adapt protein solubility independently of structure and function. PMID:26905391

  12. Structural hot spots for the solubility of globular proteins

    PubMed Central

    Ganesan, Ashok; Siekierska, Aleksandra; Beerten, Jacinte; Brams, Marijke; Van Durme, Joost; De Baets, Greet; Van der Kant, Rob; Gallardo, Rodrigo; Ramakers, Meine; Langenberg, Tobias; Wilkinson, Hannah; De Smet, Frederik; Ulens, Chris; Rousseau, Frederic; Schymkowitz, Joost

    2016-01-01

    Natural selection shapes protein solubility to physiological requirements and recombinant applications that require higher protein concentrations are often problematic. This raises the question whether the solubility of natural protein sequences can be improved. We here show an anti-correlation between the number of aggregation prone regions (APRs) in a protein sequence and its solubility, suggesting that mutational suppression of APRs provides a simple strategy to increase protein solubility. We show that mutations at specific positions within a protein structure can act as APR suppressors without affecting protein stability. These hot spots for protein solubility are both structure and sequence dependent but can be computationally predicted. We demonstrate this by reducing the aggregation of human α-galactosidase and protective antigen of Bacillus anthracis through mutation. Our results indicate that many proteins possess hot spots allowing to adapt protein solubility independently of structure and function. PMID:26905391

  13. Protein patterning: a comparison of direct spotting versus microcontact printing

    NASA Astrophysics Data System (ADS)

    Clancy, Kathryn F. A.; Nicolau, Dan V.

    2015-03-01

    Protein microarrays are used various research areas including drug discovery, diagnosis, and analysis of protein-ligand interactions. Their efficacy depends on a well-defined pattern of immobilized proteins that also have retained their bioactivity. Protein microarrays are classically fabricated using the robotic spotting drop method ("pin printing"), which can lead to spots with uneven protein concentration within the spotted area, leading to difficult to quantify readings. Among the alternative techniques, microcontact printing (μCP) with a poly(dimethylsiloxane) (PDMS) stamp appears to deliver more defined protein patterns on surfaces, while maintaining bioactivity for a wide range of proteins. Here we have quantitatively compared the distribution of fluorescently labeled proteins deposited using direct pipetting, pin printing and μCP printing with flat stamps onto various functionalized glass surfaces of different contact angles through fluorescent microscopy. The uniformity of the deposited protein spots across deposition techniques was also qualitatively analyzed. It was found that with the use of either the direct pipetting or pin printing techniques that protein concentration on surfaces varied largely across surfaces with different contact angles, whereas adsorption did not vary significantly when using the μCP printing Furthermore, when μCP printing was performed with flat relief structures the spot inhomogeneity was lower than when classical methods were used, and even less so when a pyramid relief structure was used. This suggests that μCP printing with pyramid relief structures could produce protein patterns on various surfaces and with increased spot uniformity to enable more reliable protein microarrays.

  14. [Fast Implementation Method of Protein Spots Detection Based on CUDA].

    PubMed

    Xiong, Bangshu; Ye, Yijia; Ou, Qiaofeng; Zhang, Haodong

    2016-02-01

    In order to improve the efficiency of protein spots detection, a fast detection method based on CUDA was proposed. Firstly, the parallel algorithms of the three most time-consuming parts in the protein spots detection algorithm: image preprocessing, coarse protein point detection and overlapping point segmentation were studied. Then, according to single instruction multiple threads executive model of CUDA to adopted data space strategy of separating two-dimensional (2D) images into blocks, various optimizing measures such as shared memory and 2D texture memory are adopted in this study. The results show that the operative efficiency of this method is obviously improved compared to CPU calculation. As the image size increased, this method makes more improvement in efficiency, such as for the image with the size of 2,048 x 2,048, the method of CPU needs 52,641 ms, but the GPU needs only 4,384 ms. PMID:27382745

  15. Correlation of Urine Biomarkers: Microalbuminuria and Spot Urine Protein among Diabetic Patients. Application of Spot Urine Protein in Diabetic Kidney Disease, Nephropathy, Proteinuria Estimation, Diagnosing and Monitoring.

    PubMed

    Aziz, Kamran M A

    2015-01-01

    Current study has invented a new method for utilizing spot urine protein among diabetic patients. There have been various efforts and strategies in research internationally to detect, diagnose and monitor nephropathy/DKD. Although 24-hour urine studies are gold standard, however, there exist some controversies about microalbuminuria and spot urine protein. The current study was designed to utilize spot urine protein among diabetic patients and to find its association with routine dipstick urine test for albumin, and microalbuminuria. The study demonstrated significant association of spot urine protein with urine dipstick albumin, and has demonstrated increasing spot urine protein with increasing albumin in urine (p-value < 0.0001). This study also demonstrated significantly higher levels of spot urine protein between the groups with nephropathy/DKD as compared to those without nephropathy/DKD (p-value < 0.0001). Similarly, spot urine protein and spot urine protein/creatinine were also significantly associated with microalbumin and microalbumin/creatinine in urine. Significant regression models for spot urine protein and microalbuminuria were also developed and proposed to detect and estimate microalbumin in urine while utilizing spot urine protein (< 0.0001). Synthesized regression equations and models can be used confidently to detect, rule out and monitor proteinuria and DKD. ROC curves were utilized to detect spot urine protein cutoff points for nephropathy and DKD with high specificity and sensitivity. Some important patents were also discussed in the paper regarding albuminuria/proteinuria detection and management. Current study has demonstrated and concluded, for the first time, that there exists a significant association of spot urine protein with routine dipstick albumin in urine and microalbuminuria. It is also essential to detect early, monitor and manage proteinuria, hypertension and dyslipidemia with good glycemic control to prevent diabetes

  16. High Resolution Quantitative Proteomics of HeLa Cells Protein Species Using Stable Isotope Labeling with Amino Acids in Cell Culture(SILAC), Two-Dimensional Gel Electrophoresis(2DE) and Nano-Liquid Chromatograpohy Coupled to an LTQ-OrbitrapMass Spectrometer*

    PubMed Central

    Thiede, Bernd; Koehler, Christian J.; Strozynski, Margarita; Treumann, Achim; Stein, Robert; Zimny-Arndt, Ursula; Schmid, Monika; Jungblut, Peter R.

    2013-01-01

    The proteomics field has shifted over recent years from two-dimensional gel electrophoresis (2-DE)-based approaches to SDS-PAGE or gel-free workflows because of the tremendous developments in isotopic labeling techniques, nano-liquid chromatography, and high-resolution mass spectrometry. However, 2-DE still offers the highest resolution in protein separation. Therefore, we combined stable isotope labeling with amino acids in cell culture of controls and apoptotic HeLa cells with 2-DE and the subsequent analysis of tryptic peptides via nano-liquid chromatography coupled to an LTQ-Orbitrap mass spectrometer to obtain quantitative data using the methods with the highest resolving power on all levels of the proteomics workflow. More than 1,200 proteins with more than 2,700 protein species were identified and quantified from 816 Coomassie Brilliant Blue G-250 stained 2-DE spots. About half of the proteins were identified and quantified only in single 2-DE spots. The majority of spots revealed one to five proteins; however, in one 2-DE spot, up to 23 proteins were identified. Only half of the 2-DE spots represented a dominant protein with more than 90% of the whole protein amount. Consequently, quantification based on staining intensities in 2-DE gels would in approximately half of the spots be imprecise, and minor components could not be quantified. These problems are circumvented by quantification using stable isotope labeling with amino acids in cell culture. Despite challenges, as shown in detail for lamin A/C and vimentin, the quantitative changes of protein species can be detected. The combination of 2-DE with high-resolution nano-liquid chromatography-mass spectrometry allowed us to identify proteomic changes in apoptotic cells that would be unobservable using any of the other previously employed proteomic workflows. PMID:23033477

  17. A feature-based approach to modeling protein-protein interaction hot spots.

    PubMed

    Cho, Kyu-il; Kim, Dongsup; Lee, Doheon

    2009-05-01

    Identifying features that effectively represent the energetic contribution of an individual interface residue to the interactions between proteins remains problematic. Here, we present several new features and show that they are more effective than conventional features. By combining the proposed features with conventional features, we develop a predictive model for interaction hot spots. Initially, 54 multifaceted features, composed of different levels of information including structure, sequence and molecular interaction information, are quantified. Then, to identify the best subset of features for predicting hot spots, feature selection is performed using a decision tree. Based on the selected features, a predictive model for hot spots is created using support vector machine (SVM) and tested on an independent test set. Our model shows better overall predictive accuracy than previous methods such as the alanine scanning methods Robetta and FOLDEF, and the knowledge-based method KFC. Subsequent analysis yields several findings about hot spots. As expected, hot spots have a larger relative surface area burial and are more hydrophobic than other residues. Unexpectedly, however, residue conservation displays a rather complicated tendency depending on the types of protein complexes, indicating that this feature is not good for identifying hot spots. Of the selected features, the weighted atomic packing density, relative surface area burial and weighted hydrophobicity are the top 3, with the weighted atomic packing density proving to be the most effective feature for predicting hot spots. Notably, we find that hot spots are closely related to pi-related interactions, especially pi . . . pi interactions. PMID:19273533

  18. Comparison of Proteins in Whole Blood and Dried Blood Spot Samples by LC/MS/MS

    NASA Astrophysics Data System (ADS)

    Chambers, Andrew G.; Percy, Andrew J.; Hardie, Darryl B.; Borchers, Christoph H.

    2013-09-01

    Dried blood spot (DBS) sampling methods are desirable for population-wide biomarker screening programs because of their ease of collection, transportation, and storage. Immunoassays are traditionally used to quantify endogenous proteins in these samples but require a separate assay for each protein. Recently, targeted mass spectrometry (MS) has been proposed for generating highly-multiplexed assays for biomarker proteins in DBS samples. In this work, we report the first comparison of proteins in whole blood and DBS samples using an untargeted MS approach. The average number of proteins identified in undepleted whole blood and DBS samples by liquid chromatography (LC)/MS/MS was 223 and 253, respectively. Protein identification repeatability was between 77 %-92 % within replicates and the majority of these repeated proteins (70 %) were observed in both sample formats. Proteins exclusively identified in the liquid or dried fluid spot format were unbiased based on their molecular weight, isoelectric point, aliphatic index, and grand average hydrophobicity. In addition, we extended this comparison to include proteins in matching plasma and serum samples with their dried fluid spot equivalents, dried plasma spot (DPS), and dried serum spot (DSS). This work begins to define the accessibility of endogenous proteins in dried fluid spot samples for analysis by MS and is useful in evaluating the scope of this new approach.

  19. A new spot quality control for protein macroarray based on immunological detection.

    PubMed

    Qiu, Shi; Song, Chunmei; Zhao, Shengguo; Li, Jianwu; Zeng, Haijuan; Wu, Shuyan; Guo, Huiqing; Li, Haolin; Liu, Cheng; Liu, Qing

    2015-06-01

    Protein macroarray is a new, simple and multiple biochemistry detection system, in which the test spots are more than 1mm diameter and results directly visible and instrumentation is not necessary. This technology, however, possesses recognized problems with spot quality and uniformity, issues that can limit its application. Previous methods have been developed for spot quality control, but they are complicated or require specific instrumentation. Therefore, we have developed a spot quality control buffer supplement with Ponceau S (SQCB-PS) as a direct and visible means of monitoring spot quality on nitrocellulose membrane prior to hybridization. In this report, 1% (w/v) Ponceau S and 10% (v/v) glycerol in spotting buffer were found to be optimal for spot quality control and food-borne pathogens multiple detection. Furthermore, the sensitivity and specificity of the protein macroarray were not compromised by spotting buffer with Ponceau S. Under optimal conditions, this visible spot quality control method makes the detection more reliable, and should enhance the wider use of the technique. PMID:25863388

  20. Electrophoretic extraction of proteins from two-dimensional electrophoresis gel spots

    DOEpatents

    Zhang, Jian-Shi; Giometti, C.S.; Tollaksen, S.L.

    1987-09-04

    After two-dimensional electrophoresis of proteins or the like, resulting in a polyacrylamide gel slab having a pattern of protein gel spots thereon, an individual protein gel spot is cored out from the slab, to form a gel spot core which is placed in an extraction tube, with a dialysis membrane across the lower end of the tube. Replicate gel spots can be cored out from replicate gel slabs and placed in the extraction tube. Molten agarose gel is poured into the extraction tube where the agarose gel hardens to form an immobilizing gel, covering the gel spot cores. The upper end portion of the extraction tube is filled with a volume of buffer solution, and the upper end is closed by another dialysis membrane. Upper and lower bodies of a buffer solution are brought into contact with the upper and lower membranes and are provided with electrodes connected to the positive and negative terminals of a dc power supply, thereby producing an electrical current which flows through the upper membrane, the volume of buffer solution, the agarose, the gel spot cores and the lower membrane. The current causes the proteins to be extracted electrophoretically from the gel spot cores, so that the extracted proteins accumulate and are contained in the space between the agarose gel and the upper membrane. 8 figs.

  1. Maize MeJA-responsive proteins identified by high-resolution 2-DE PAGE.

    PubMed

    Zhang, Yuliang; Pennerman, Kayla K; Yang, Fengshan; Yin, Guohua

    2015-12-01

    Exogenous methyl jasmonate (MeJA) is well-known to induce plant defense mechanisms effective against a wide variety of insect and microbial pests. High-resolution 2-DE gel electrophoresis was used to discover changes in the leaf proteome of maize exposed to MeJA. We sequenced 62 MeJA-responsive proteins by tandem mass spectroscopy, and deposited the mass spectra and identities in the EMBL-EBI PRIDE repository under reference number PXD001793. An analysis and discussion of the identified proteins in relation to maize defense against Asian corn borer is published by Zhang et al. (2015) [1]. PMID:26509185

  2. Electrophoretic extraction of proteins from two-dimensional electrophoresis gel spots

    DOEpatents

    Zhang, Jian-Shi; Giometti, Carol S.; Tollaksen, Sandra L.

    1989-01-01

    After two-dimensional electrophoresis of proteins or the like, resulting in a polyacrylamide gel slab having a pattern of protein gel spots thereon, an individual protein gel spot is cored out from the slab, to form a gel spot core which is placed in an extraction tube, with a dialysis membrane across the lower end of the tube. Replicate gel spots can be cored out from replicate gel slabs and placed in the extraction tube. Molten agarose gel is poured into the extraction tube where the agarose gel hardens to form an immobilizing gel, covering the gel spot cores. The upper end portion of the extraction tube is filled with a volume of buffer solution, and the upper end is closed by another dialysis membrane. Upper and lower bodies of a buffer solution are brought into contact with the upper and lower membranes and are provided with electrodes connected to the positive and negative terminals of a DC power supply, thereby producing an electrical current which flows through the upper membrane, the volume of buffer solution, the agarose, the gel spot cores and the lower membrane. The current causes the proteins to be extracted electrophoretically from the gel spot cores, so that the extracted proteins accumulate and are contained in the space between the agarose gel and the upper membrane. A high percentage extraction of proteins is achieved. The extracted proteins can be removed and subjected to partial digestion by trypsin or the like, followed by two-dimensional electrophoresis, resulting in a gel slab having a pattern of peptide gel spots which can be cored out and subjected to electrophoretic extraction to extract individual peptides.

  3. Prediction of hot spots in protein interfaces using a random forest model with hybrid features.

    PubMed

    Wang, Lin; Liu, Zhi-Ping; Zhang, Xiang-Sun; Chen, Luonan

    2012-03-01

    Prediction of hot spots in protein interfaces provides crucial information for the research on protein-protein interaction and drug design. Existing machine learning methods generally judge whether a given residue is likely to be a hot spot by extracting features only from the target residue. However, hot spots usually form a small cluster of residues which are tightly packed together at the center of protein interface. With this in mind, we present a novel method to extract hybrid features which incorporate a wide range of information of the target residue and its spatially neighboring residues, i.e. the nearest contact residue in the other face (mirror-contact residue) and the nearest contact residue in the same face (intra-contact residue). We provide a novel random forest (RF) model to effectively integrate these hybrid features for predicting hot spots in protein interfaces. Our method can achieve accuracy (ACC) of 82.4% and Matthew's correlation coefficient (MCC) of 0.482 in Alanine Scanning Energetics Database, and ACC of 77.6% and MCC of 0.429 in Binding Interface Database. In a comparison study, performance of our RF model exceeds other existing methods, such as Robetta, FOLDEF, KFC, KFC2, MINERVA and HotPoint. Of our hybrid features, three physicochemical features of target residues (mass, polarizability and isoelectric point), the relative side-chain accessible surface area and the average depth index of mirror-contact residues are found to be the main discriminative features in hot spots prediction. We also confirm that hot spots tend to form large contact surface areas between two interacting proteins. Source data and code are available at: http://www.aporc.org/doc/wiki/HotSpot. PMID:22258275

  4. Quantitation of proteinuria in nephrotic syndrome by spot urine protein creatinine ratio estimation in children.

    PubMed

    Biswas, A; Kumar, R; Chaterjee, A; Ghosh, J K; Basu, K

    2009-01-01

    In Nephrotic Syndrome the amount of protein excretion is a reflection of activity of disease. Quantitative measurement of proteinuria by a 24-hour urine collection has been the accepted method of evaluation. Recent studies have shown that calculation of protein/creatinine ratio in a spot urine sample correlates well with the 24-hour urine protein (24-HUP) excretion. A study was conducted to compare the accuracy of a spot urinary protein/creatinine ratio (P/C ratio) and urinary dipstick with the 24-hour urine protein. Fifty two samples from 26 patients of nephrotic syndrome were collected. This included a 24-hour urine sample followed by the next voided random spot sample. The protein/creatinine ratio was calculated and dipstick was performed on the spot sample. This was compared with the 24-hour urine protein excretion. The correlation between the three samples was statistically highly significant (p<0.001) for all levels of proteinuria. The normal value of protein/creatinine ratio in Indian children was also estimated on 50 normal children admitted in the ward without any renal diseases calculated to be 0.053 (SE of mean+/-0.003). PMID:19182753

  5. An automated decision-tree approach to predicting protein interaction hot spots.

    PubMed

    Darnell, Steven J; Page, David; Mitchell, Julie C

    2007-09-01

    Protein-protein interactions can be altered by mutating one or more "hot spots," the subset of residues that account for most of the interface's binding free energy. The identification of hot spots requires a significant experimental effort, highlighting the practical value of hot spot predictions. We present two knowledge-based models that improve the ability to predict hot spots: K-FADE uses shape specificity features calculated by the Fast Atomic Density Evaluation (FADE) program, and K-CON uses biochemical contact features. The combined K-FADE/CON (KFC) model displays better overall predictive accuracy than computational alanine scanning (Robetta-Ala). In addition, because these methods predict different subsets of known hot spots, a large and significant increase in accuracy is achieved by combining KFC and Robetta-Ala. The KFC analysis is applied to the calmodulin (CaM)/smooth muscle myosin light chain kinase (smMLCK) interface, and to the bone morphogenetic protein-2 (BMP-2)/BMP receptor-type I (BMPR-IA) interface. The results indicate a strong correlation between KFC hot spot predictions and mutations that significantly reduce the binding affinity of the interface. PMID:17554779

  6. A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces.

    PubMed

    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; Moreira, Irina S

    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 is trained on a large number of complexes and on a significantly larger number of different structural- and evolutionary sequence-based features. In particular, we added interface size, type of interaction between residues at the interface of the complex, number of different types of residues at the interface and the Position-Specific Scoring Matrix (PSSM), for a total of 79 features. We used twenty-seven algorithms from a simple linear-based function to support-vector machine models with different cost functions. The best model was achieved by the use of the conditional inference random forest (c-forest) algorithm with a dataset pre-processed by the normalization of features and with up-sampling of the minor class. The method has an overall accuracy of 0.80, an F1-score of 0.73, a sensitivity of 0.76 and a specificity of 0.82 for the independent test set. PMID:27472327

  7. A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces

    PubMed Central

    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.; Moreira, Irina S.

    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 is trained on a large number of complexes and on a significantly larger number of different structural- and evolutionary sequence-based features. In particular, we added interface size, type of interaction between residues at the interface of the complex, number of different types of residues at the interface and the Position-Specific Scoring Matrix (PSSM), for a total of 79 features. We used twenty-seven algorithms from a simple linear-based function to support-vector machine models with different cost functions. The best model was achieved by the use of the conditional inference random forest (c-forest) algorithm with a dataset pre-processed by the normalization of features and with up-sampling of the minor class. The method has an overall accuracy of 0.80, an F1-score of 0.73, a sensitivity of 0.76 and a specificity of 0.82 for the independent test set. PMID:27472327

  8. A Novel Gaussian Extrapolation Approach for 2-D Gel Electrophoresis Saturated Protein Spots.

    PubMed

    Natale, Massimo; Caiazzo, Alfonso; Ficarra, Elisa

    2016-01-01

    Analysis of images obtained from two-dimensional gel electrophoresis (2-D GE) is a topic of utmost importance in bioinformatics research, since commercial and academic software currently available have proven to be neither completely effective nor fully automatic, often requiring manual revision and refinement of computer generated matches. In this chapter, we present an effective technique for the detection and the reconstruction of over-saturated protein spots. Firstly, the algorithm reveals overexposed areas, where spots may be truncated, and plateau regions caused by smeared and overlapping spots. Next, it reconstructs the correct distribution of pixel values in these overexposed areas and plateau regions, using a two-dimensional least-squares fitting based on a generalized Gaussian distribution. Pixel correction in saturated and smeared spots allows more accurate proteins quantification, providing more reliable image analysis results. The method is validated for processing highly exposed 2-D GE images, comparing reconstructed spots with the corresponding non-saturated image. The results demonstrate that the algorithm enables correct spot quantification. PMID:26611417

  9. A practical approach to using spot urine protein/creatinine ratios for assessing proteinuria in pregnancy

    PubMed Central

    Marnoch, Catherine A; Larson, Lucia; Weitzen, Sherry; Phipps, Maureen G; Sung, C James; Powrie, Raymond O

    2008-01-01

    Objective: The aim of this study is to assess the diagnostic accuracy of the spot urine protein/creatinine ratio compared with the 24-hour urine protein in pregnancy. Study Design: In this prospective cohort study of inpatient pregnant women, the protein/creatinine ratio and dipstick protein were assessed from a single urine sample collected at the start of the 24-hour urine. Both tests were compared with the 24-hour urine protein for correlation and test characteristics. Results: In the 196 specimens analysed, we found a strong correlation between the spot urine protein/creatinine ratio and 24-hour urine protein (r 2 = 0.78, P < 0.01). A protein/creatinine ratio <0.1 ruled out significant proteinuria (≥300 mg/day) with sensitivity and negative predictive value 100%. A protein/creatinine ratio ≥0.4 detected significant proteinuria (specificity and positive predictive value of 100%). A protein/creatinine ratio ≥4.6 had a specificity and positive predictive value of 100% for detecting severe proteinuria (≥5000 mg/day). Urine dipsticks correlated poorly with the 24-hour urine protein (r 2 = 0.40, P = 0.826). Nineteen percent of dipsticks reading nil or trace were false-negative results. Conclusion: The spot urine protein/creatinine ratio correlated well with the 24-hour urine protein and performed better than the urine dipsticks. Significant proteinuria in pregnancy was excluded if the protein/creatinine ratio was <0.1 and identified when it was ≥0.4.

  10. Tomato spotted wilt virus NSm protein domains involved in tubule formation,movement and symptoms

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Direct demonstration of Tomato spotted wilt virus (TSWV) gene function has been slowed by the absence of a reliable reverse genetics system. A Tobacco mosaic virus (TMV)-based expression system was previously used by us to demonstrate that the TSWV NSm protein is able to support cell-to-cell movemen...

  11. Characterization of Tomato spotted wilt virus NSm protein domains involved in tubule formation, movement and symptoms

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Absence of a reliable reverse genetics system for Tomato spotted wilt virus (TSWV) has impeded direct demonstration of gene function. We previously used a Tobacco mosaic virus (TMV)-based expression system to demonstrate that the TSWV NSm protein is able to support cell-to-cell movement in the absen...

  12. PredHS: a web server for predicting protein-protein interaction hot spots by using structural neighborhood properties.

    PubMed

    Deng, Lei; Zhang, Qiangfeng Cliff; Chen, Zhigang; Meng, Yang; Guan, Jihong; Zhou, Shuigeng

    2014-07-01

    Identifying specific hot spot residues that contribute significantly to the affinity and specificity of protein interactions is a problem of the utmost importance. We present an interactive web server, PredHS, which is based on an effective structure-based hot spot prediction method. The PredHS prediction method integrates many novel structural and energetic features with two types of structural neighborhoods (Euclidian and Voronoi), and combines random forest and sequential backward elimination algorithms to select an optimal subset of features. PredHS achieved the highest performance identifying hot spots compared with other state-of-the-art methods, as benchmarked by using an independent experimentally verified dataset. The input to PredHS is protein structures in the PDB format with at least two chains that form interfaces. Users can visualize their predictions in an interactive 3D viewer and download the results as text files. PredHS is available at http://www.predhs.org. PMID:24852252

  13. The FTMap family of web servers for determining and characterizing ligand binding hot spots of proteins

    PubMed Central

    Kozakov, Dima; Grove, Laurie E.; Hall, David R.; Bohnuud, Tanggis; Mottarella, Scott; Luo, Lingqi; Xia, Bing; Beglov, Dmitri; Vajda, Sandor

    2016-01-01

    FTMap is a computational mapping server that identifies binding hot spots of macromolecules, i.e., regions of the surface with major contributions to the ligand binding free energy. To use FTMap, users submit a protein, DNA, or RNA structure in PDB format. FTMap samples billions of positions of small organic molecules used as probes and scores the probe poses using a detailed energy expression. Regions that bind clusters of multiple probe types identify the binding hot spots, in good agreement with experimental data. FTMap serves as basis for other servers, namely FTSite to predict ligand binding sites, FTFlex to account for side chain flexibility, FTMap/param to parameterize additional probes, and FTDyn to map ensembles of protein structures. Applications include determining druggability of proteins, identifying ligand moieties that are most important for binding, finding the most bound-like conformation in ensembles of unliganded protein structures, and providing input for fragment based drug design. FTMap is more accurate than classical mapping methods such as GRID and MCSS, and is much faster than the more recent approaches to protein mapping based on mixed molecular dynamics. Using 16 probe molecules, the FTMap server finds the hot spots of an average size protein in less than an hour. Since FTFlex performs mapping for all low energy conformers of side chains in the binding site, its completion time is proportionately longer. PMID:25855957

  14. Co-Occurring Atomic Contacts for the Characterization of Protein Binding Hot Spots

    PubMed Central

    Liu, Qian; Ren, Jing; Song, Jiangning; Li, Jinyan

    2015-01-01

    A binding hot spot is a small area at a protein-protein interface that can make significant contribution to binding free energy. This work investigates the substantial contribution made by some special co-occurring atomic contacts at a binding hot spot. A co-occurring atomic contact is a pair of atomic contacts that are close to each other with no more than three covalent-bond steps. We found that two kinds of co-occurring atomic contacts can play an important part in the accurate prediction of binding hot spot residues. One is the co-occurrence of two nearby hydrogen bonds. For example, mutations of any residue in a hydrogen bond network consisting of multiple co-occurring hydrogen bonds could disrupt the interaction considerably. The other kind of co-occurring atomic contact is the co-occurrence of a hydrophobic carbon contact and a contact between a hydrophobic carbon atom and a π ring. In fact, this co-occurrence signifies the collective effect of hydrophobic contacts. We also found that the B-factor measurements of several specific groups of amino acids are useful for the prediction of hot spots. Taking the B-factor, individual atomic contacts and the co-occurring contacts as features, we developed a new prediction method and thoroughly assessed its performance via cross-validation and independent dataset test. The results show that our method achieves higher prediction performance than well-known methods such as Robetta, FoldX and Hotpoint. We conclude that these contact descriptors, in particular the novel co-occurring atomic contacts, can be used to facilitate accurate and interpretable characterization of protein binding hot spots. PMID:26675422

  15. Maintenance Crude Protein Requirement of Penned Female Korean Spotted Deer (Cervus nippon)

    PubMed Central

    Yang, S. Y.; Oh, Y. K.; Ahn, H. S.; Kwak, W. S.

    2014-01-01

    This study was conducted to evaluate the protein requirement for maintenance of 2-year-old female Korean spotted deer. In the course of the experiment, each of three hand-reared female spotted deer was fed three diets that were iso-calorically formulated to contain low (approximately 7%), medium (12%), and high (17%) levels of crude protein (CP). Each of six trials included a 5-day transition, a 10-day preliminary, and a 7-day collection period. Dietary protein levels affected the apparent digestibility of CP (p<0.05) but not the apparent digestibility of dry matter, organic matter, or acid detergent fiber. All of the deer showed a positive CP balance on all of the diets. The maintenance CP requirement estimated by regression analysis was 4.17 g/kg metabolic body weight (W0.75)·d. The maintenance digestible CP requirement was 1.42 g/kg W0.75·d. The metabolic fecal CP was 1.95 g/kg W0.75·d. The blood urea nitrogen of spotted deer increased (p<0.05) as the dietary protein levels increased. PMID:25049923

  16. Comparison of protein-extraction methods for gills of the shore crab, Carcinus maenas (L.), and application to 2DE.

    PubMed

    Panchout, François; Letendre, Julie; Bultelle, Florence; Denier, Xavier; Rocher, Béatrice; Chan, Philippe; Vaudry, David; Durand, Fabrice

    2013-12-01

    As it is well-established that protein extraction constitutes a crucial step for two-dimensional electrophoresis (2DE), this work was done as a prerequisite to further the study of alterations in the proteome in gills of the shore crab Carcinus maenas under contrasted environmental conditions. Because of the presence of a chitin layer, shore crab gills have an unusual structure. Consequently, they are considered as a hard tissue and represent a challenge for optimal protein extraction. In this study, we compared three published extraction procedures for subsequent applications to 2DE: the first one uses homogenization process, the second one included an additional TCA-acetone precipitation step, and finally, the third one associated grinding in liquid nitrogen (N2) and TCA-acetone precipitation. Extracted proteins were then resolved using 1DE and 2DE. Although interesting patterns were obtained using 1DE with the three methods, only the one involving grinding in liquid N2 and TCA-acetone precipitation led to proper resolution after 2DE, showing a good level of reproducibility at technical (85%) and biological (84%) levels. This last method is therefore proposed for analysis of gill proteomes in the shore crab. PMID:24294114

  17. Hot spots and transient pockets: predicting the determinants of small-molecule binding to a protein-protein interface.

    PubMed

    Metz, Alexander; Pfleger, Christopher; Kopitz, Hannes; Pfeiffer-Marek, Stefania; Baringhaus, Karl-Heinz; Gohlke, Holger

    2012-01-23

    Protein-protein interfaces are considered difficult targets for small-molecule protein-protein interaction modulators (PPIMs ). Here, we present for the first time a computational strategy that simultaneously considers aspects of energetics and plasticity in the context of PPIM binding to a protein interface. The strategy aims at identifying the determinants of small-molecule binding, hot spots, and transient pockets, in a protein-protein interface in order to make use of this knowledge for predicting binding modes of and ranking PPIMs with respect to their affinity. When applied to interleukin-2 (IL-2), the computationally inexpensive constrained geometric simulation method FRODA outperforms molecular dynamics simulations in sampling hydrophobic transient pockets. We introduce the PPIAnalyzer approach for identifying transient pockets on the basis of geometrical criteria only. A sequence of docking to identified transient pockets, starting structure selection based on hot spot information, RMSD clustering and intermolecular docking energies, and MM-PBSA calculations allows one to enrich IL-2 PPIMs from a set of decoys and to discriminate between subgroups of IL-2 PPIMs with low and high affinity. Our strategy will be applicable in a prospective manner where nothing else than a protein-protein complex structure is known; hence, it can well be the first step in a structure-based endeavor to identify PPIMs. PMID:22087639

  18. Thyroid hormone responsive protein Spot14 enhances catalysis of fatty acid synthase in lactating mammary epithelium[S

    PubMed Central

    Rudolph, Michael C.; Wellberg, Elizabeth A.; Lewis, Andrew S.; Terrell, Kristina L.; Merz, Andrea L.; Maluf, N. Karl; Serkova, Natalie J.; Anderson, Steven M.

    2014-01-01

    Thyroid hormone responsive protein Spot 14 has been consistently associated with de novo fatty acid synthesis activity in multiple tissues, including the lactating mammary gland, which synthesizes large quantities of medium chain fatty acids (MCFAs) exclusively via FASN. However, the molecular function of Spot14 remains undefined during lactation. Spot14-null mice produce milk deficient in total triglyceride and de novo MCFA that does not sustain optimal neonatal growth. The lactation defect was rescued by provision of a high fat diet to the lactating dam. Transgenic mice overexpressing Spot14 in mammary epithelium produced total milk fat equivalent to controls, but with significantly greater MCFA. Spot14-null dams have no diminution of metabolic gene expression, enzyme protein levels, or intermediate metabolites that accounts for impaired de novo MCFA. When [13C] fatty acid products were quantified in vitro using crude cytosolic lysates, native FASN activity was 1.6-fold greater in control relative to Spot14-null lysates, and add back of Spot14 partially restored activity. Recombinant FASN catalysis increased 1.4-fold and C = 14:0 yield was enhanced 4-fold in vitro following addition of Spot14. These findings implicate Spot14 as a direct protein enhancer of FASN catalysis in the mammary gland during lactation when maximal MCFA production is needed. PMID:24771867

  19. Expression, purification and crystallization of a novel nonstructural protein VP9 from white spot syndrome virus

    SciTech Connect

    Liu, Yang; Sivaraman, J.; Hew, Choy L.

    2006-08-01

    The nonstructural protein VP9 from white spot syndrome virus (WSSV) has been identified and expressed in Escherichia coli. Native protein was purified and crystallized by vapour diffusion. The nonstructural protein VP9 from white spot syndrome virus (WSSV) has been identified and expressed in Escherichia coli. To facilitate purification, a cleavable His{sub 6} tag was introduced at the N-terminus. The native protein was purified and crystallized by vapour diffusion against mother liquor containing 2 M sodium acetate, 100 mM MES pH 6.3, 25 mM cadmium sulfate and 3% glycerol. Crystals were obtained within 7 d and diffracted to 2.2 Å; they belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 74.13, b = 78.21, c = 78.98 Å and four molecules in the asymmetric unit. The selenomethionine-labelled protein produced isomorphous crystals that diffracted to approximately 3.3 Å.

  20. DNA condensates organized by the capsid protein VP15 in White Spot Syndrome Virus

    SciTech Connect

    Liu Yingjie; Wu Jinlu; Chen Hu; Hew, Choy Leong; Yan Jie

    2010-12-20

    The White Spot Syndrome Virus (WSSV) has a large circular double-stranded DNA genome of around 300 kb and it replicates in the nucleus of the host cells. The machinery of how the viral DNA is packaged has been remained unclear. VP15, a highly basic protein, is one of the major capsid proteins found in the virus. Previously, it was shown to be a DNA binding protein and was hypothesized to participate in the viral DNA packaging process. Using Atomic Force Microscopy imaging, we show that the viral DNA is associated with a (or more) capsid proteins. The organized viral DNA qualitatively resembles the conformations of VP15 induced DNA condensates in vitro. Furthermore, single-DNA manipulation experiments revealed that VP15 is able to condense single DNA against forces of a few pico Newtons. Our results suggest that VP15 may aid in the viral DNA packaging process by directly condensing DNA.

  1. Acute-phase proteins investigation based on lectins affinity capture prior to 2-DE separation: application to serum from multiple sclerosis patients.

    PubMed

    Robotti, Andrea; Natale, Massimo; Albo, Alessandra Giuliano; Lis, Katarzyna; Perga, Simona; Marnetto, Fabiana; Gilli, Francesca; Bertolotto, Antonio

    2010-09-01

    Plasma acute-phase proteins (APPs) glyco-isoforms are important biomarkers of inflammatory processes such as those occurring in multiple sclerosis (MS). Specific analysis of these proteins is often hampered by sample biochemical complexity. The aim of our study was to set up a method to accurately visualize, identify and quantify APPs glyco-isoforms in human serum. An enrichment strategy based on affinity chromatography using the carbohydrate-binding proteins concanavalin A (ConA) and erythrina cristagalli lectin (ECL) was applied to pooled serum samples from 15 patients and 9 healthy individuals. Image analysis of 2-DE detected 30 spots with a fold change higher than 1.5. A total of 14 were statistically significant (p value<0.05): 7 up-regulated and 7 down-regulated in MS samples. ESI LC-Nanospray IT mass spectrometry analysis confirmed that all of them were APPs isoforms supporting the idea that the accurate analysis of differential glycosylation profiles in these biomarkers is instrumental to distinguish between MS patients and healthy subjects. Additionally, overlaps in ConA/ECL maps protein patterns suggest how the used lectins are able to bind sugars harbored by the same oligosaccharide structure. Among identified proteins, the presence of complex and/or hybrid type N-linked sugar structures is well known. Performing galectin-3 binding and Western blotting, we were able to demonstrate a correlation between hybrid type glyco-isoforms of β-haptoglobin and MS. In conclusion, although the patho-physiological role of the identified species still remains unclear and further validations are needed, these findings may have a relevant impact on disease-specific marker identification approaches. PMID:20715125

  2. Proteomic analysis of shrimp white spot syndrome viral proteins and characterization of a novel envelope protein VP466.

    PubMed

    Huang, Canhua; Zhang, Xiaobo; Lin, Qingsong; Xu, Xun; Hu, Zhihong; Hew, Choy-L

    2002-03-01

    White spot syndrome virus (WSSV) is at present one of the major pathogens in shrimp culture worldwide. The complete genome of this virus has been sequenced recently. To identify the structural and functional proteins of WSSV, the purified virions were separated by SDS-PAGE. Twenty-four protein bands were excised, in-gel digested with trypsin, and subjected to matrix-assisted laser desorption ionization-time of flight mass spectrometry and electrospray ionization tandem mass spectrometry, respectively. Eighteen proteins matching the open reading frames of WSSV genome were identified. Except for three known structural proteins and collagen, the functions of the remaining 14 proteins were unknown. Temporal analysis revealed that all the genes were transcribed in the late stage of WSSV infection except for vp121. Of the newly identified proteins, VP466 (derived from band 16) was further characterized. The cDNA encoding VP466 was expressed in Escherichia coli as a glutathione S-transferase (GST) fusion protein. Specific antibody was generated with the purified GST-VP466 fusion protein. Western blot showed that the mouse anti-GST-VP466 antibody bound specifically to a 51-kDa protein of WSSV. Immunogold labeling revealed that VP466 protein is a component of the viral envelope. Results in this investigation thus proved the effectiveness of proteomic approaches for discovering new proteins of WSSV. PMID:12096122

  3. Solvent accessible surface area-based hot-spot detection methods for protein-protein and protein-nucleic acid interfaces.

    PubMed

    Munteanu, Cristian R; Pimenta, António C; Fernandez-Lozano, Carlos; Melo, André; Cordeiro, Maria N D S; Moreira, Irina S

    2015-05-26

    Due to the importance of hot-spots (HS) detection and the efficiency of computational methodologies, several HS detecting approaches have been developed. The current paper presents new models to predict HS for protein-protein and protein-nucleic acid interactions with better statistics compared with the ones currently reported in literature. These models are based on solvent accessible surface area (SASA) and genetic conservation features subjected to simple Bayes networks (protein-protein systems) and a more complex multi-objective genetic algorithm-support vector machine algorithms (protein-nucleic acid systems). The best models for these interactions have been implemented in two free Web tools. PMID:25845030

  4. A relational Fuzzy C-Means algorithm for detecting protein spots in two-dimensional gel images.

    PubMed

    Rashwan, Shaheera; Faheem, Talaat; Sarhan, Amany; Youssef, Bayumy A B

    2010-01-01

    Two-dimensional polyacrylamide gel electrophoresis of proteins is a robust and reproducible technique. It is the most widely used separation tool in proteomics. Current efforts in the field are directed at the development of tools for expanding the range of proteins accessible with two-dimensional gels. Proteomics was built around the two-dimensional gel. The idea that multiple proteins can be analyzed in parallel grew from two-dimensional gel maps. Proteomics researchers needed to identify interested protein spots by examining the gel. This is time consuming, labor extensive and error prone. It is desired that the computer can analyze the proteins automatically by first detecting, then quantifying the protein spots in the 2D gel images. This paper focuses on the protein spot detection and segmentation of 2D gel electrophoresis images. We present a new technique for segmentation of 2D gel images using the Fuzzy C-Means (FCM) algorithm and matching spots using the notion of fuzzy relations. Through the experimental results, the new algorithm was found out to detect protein spots more accurately, then the current known algorithms. PMID:20865504

  5. Dried Blood Spot Proteomics: Surface Extraction of Endogenous Proteins Coupled with Automated Sample Preparation and Mass Spectrometry Analysis

    NASA Astrophysics Data System (ADS)

    Martin, Nicholas J.; Bunch, Josephine; Cooper, Helen J.

    2013-08-01

    Dried blood spots offer many advantages as a sample format including ease and safety of transport and handling. To date, the majority of mass spectrometry analyses of dried blood spots have focused on small molecules or hemoglobin. However, dried blood spots are a potentially rich source of protein biomarkers, an area that has been overlooked. To address this issue, we have applied an untargeted bottom-up proteomics approach to the analysis of dried blood spots. We present an automated and integrated method for extraction of endogenous proteins from the surface of dried blood spots and sample preparation via trypsin digestion by use of the Advion Biosciences Triversa Nanomate robotic platform. Liquid chromatography tandem mass spectrometry of the resulting digests enabled identification of 120 proteins from a single dried blood spot. The proteins identified cross a concentration range of four orders of magnitude. The method is evaluated and the results discussed in terms of the proteins identified and their potential use as biomarkers in screening programs.

  6. Transcription and identification of an envelope protein gene (p22) from shrimp white spot syndrome virus.

    PubMed

    Zhang, Xiaobo; Huang, Canhua; Xu, Xun; Hew, Choy L

    2002-02-01

    White spot syndrome virus (WSSV) is one of the most virulent pathogens causing high mortality in shrimp. In the present study, an open reading frame (termed the p22 gene) was revealed from a WSSV cDNA library. The gene was expressed as a fusion protein with glutathione S-transferase (GST) in Escherichia coli and purified. Specific antibody was raised using the purified fusion protein (GST-P22). Temporal analysis showed that the p22 gene was a late gene. After binding between purified WSSV virions and anti-GST-P22 IgG followed by labelling with gold-labelled secondary antibody, the gold particles, under a transmission electron microscope, could be found along the outer envelope of WSSV virions. This experiment suggests that the p22 gene encodes an envelope protein of the virus. PMID:11807241

  7. The Role of Water Occlusion for the Definition of a Protein Binding Hot-Spot.

    PubMed

    Moreira, Irina S

    2015-01-01

    Biological systems rely on the establishment of interactions between biomolecules, which take place in the aqueous environment of the cell. It was already demonstrated that a small set of residues at the interface, Hot-Spots(HS), contributes significantly to the binding free energy. However, these energetic determinants of affinity and specificity are still not fully understood. Moreover, the contribution of water to their HS character is also poorly characterized. In this review, we have focused on the structural data available that support the occlusion of HS from solvent, and therefore the "O-ring theory"not only on protein-protein but also on protein-DNA complexes. We also emphasized the use of Solvent Accessible Surface Area (SASA) features in a variety of machine-learning approaches that aim to detect binding HS. PMID:25986686

  8. Expression, purification and crystallization of a novel nonstructural protein VP9 from white spot syndrome virus.

    SciTech Connect

    Liu,Y.; Sivaraman, J.; Hew, C.

    2006-01-01

    The nonstructural protein VP9 from white spot syndrome virus (WSSV) has been identified and expressed in Escherichia coli. To facilitate purification, a cleavable His{sub 6} tag was introduced at the N-terminus. The native protein was purified and crystallized by vapor diffusion against mother liquor containing 2 M sodium acetate, 100 mM MES pH 6.3, 25 mM cadmium sulfate and 3% glycerol. Crystals were obtained within 7 d and diffracted to 2.2 Angstroms; they belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 74.13, b = 78.21, c = 78.98 Angstroms and four molecules in the asymmetric unit. The selenomethionine-labeled protein produced isomorphous crystals that diffracted to approximately 3.3 Angstroms.

  9. HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering.

    PubMed

    Bendl, Jaroslav; Stourac, Jan; Sebestova, Eva; Vavra, Ondrej; Musil, Milos; Brezovsky, Jan; Damborsky, Jiri

    2016-07-01

    HotSpot Wizard 2.0 is a web server for automated identification of hot spots and design of smart libraries for engineering proteins' stability, catalytic activity, substrate specificity and enantioselectivity. The server integrates sequence, structural and evolutionary information obtained from 3 databases and 20 computational tools. Users are guided through the processes of selecting hot spots using four different protein engineering strategies and optimizing the resulting library's size by narrowing down a set of substitutions at individual randomized positions. The only required input is a query protein structure. The results of the calculations are mapped onto the protein's structure and visualized with a JSmol applet. HotSpot Wizard lists annotated residues suitable for mutagenesis and can automatically design appropriate codons for each implemented strategy. Overall, HotSpot Wizard provides comprehensive annotations of protein structures and assists protein engineers with the rational design of site-specific mutations and focused libraries. It is freely available at http://loschmidt.chemi.muni.cz/hotspotwizard. PMID:27174934

  10. Antiviral RNA silencing suppression activity of Tomato spotted wilt virus NSs protein.

    PubMed

    Ocampo Ocampo, T; Gabriel Peralta, S M; Bacheller, N; Uiterwaal, S; Knapp, A; Hennen, A; Ochoa-Martinez, D L; Garcia-Ruiz, H

    2016-01-01

    In addition to regulating gene expression, RNA silencing is an essential antiviral defense system in plants. Triggered by double-stranded RNA, silencing results in degradation or translational repression of target transcripts. Viruses are inducers and targets of RNA silencing. To condition susceptibility, most plant viruses encode silencing suppressors that interfere with this process, such as the Tomato spotted wilt virus (TSWV) NSs protein. The mechanism by which NSs suppresses RNA silencing and its role in viral infection and movement remain to be determined. We cloned NSs from the Hawaii isolate of TSWV and using two independent assays show for the first time that this protein restored pathogenicity and supported the formation of local infection foci by suppressor-deficient Turnip mosaic virus and Turnip crinkle virus. Demonstrating the suppression of RNA silencing directed against heterologous viruses establishes the foundation to determine the means used by NSs to block this antiviral process. PMID:27323202

  11. HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering

    PubMed Central

    Bendl, Jaroslav; Stourac, Jan; Sebestova, Eva; Vavra, Ondrej; Musil, Milos; Brezovsky, Jan; Damborsky, Jiri

    2016-01-01

    HotSpot Wizard 2.0 is a web server for automated identification of hot spots and design of smart libraries for engineering proteins’ stability, catalytic activity, substrate specificity and enantioselectivity. The server integrates sequence, structural and evolutionary information obtained from 3 databases and 20 computational tools. Users are guided through the processes of selecting hot spots using four different protein engineering strategies and optimizing the resulting library's size by narrowing down a set of substitutions at individual randomized positions. The only required input is a query protein structure. The results of the calculations are mapped onto the protein's structure and visualized with a JSmol applet. HotSpot Wizard lists annotated residues suitable for mutagenesis and can automatically design appropriate codons for each implemented strategy. Overall, HotSpot Wizard provides comprehensive annotations of protein structures and assists protein engineers with the rational design of site-specific mutations and focused libraries. It is freely available at http://loschmidt.chemi.muni.cz/hotspotwizard. PMID:27174934

  12. Crystal Structure of Major Envelope Protein VP24 from White Spot Syndrome Virus

    PubMed Central

    Sun, Lifang; Su, Yintao; Zhao, Yanhe; Fu, Zheng-qing; Wu, Yunkun

    2016-01-01

    White spot syndrome virus (WSSV) is one of the major and most serious pathogen in the shrimp industry. As one of the most abundant envelope protein, VP24 acts as a core protein interacting with other structure proteins and plays an important role in virus assembly and infection. Here, we have presented the crystal structure of VP24 from WSSV. In the structure, VP24 consists of a nine-stranded β–barrel fold with mostly antiparallel β-strands, and the loops extending out the β–barrel at both N-terminus and C-terminus, which is distinct to those of the other two major envelope proteins VP28 and VP26. Structural comparison of VP24 with VP26 and VP28 reveals opposite electrostatic surface potential properties of them. These structural differences could provide insight into their differential functional mechanisms and roles for virus assembly and infection. Moreover, the structure reveals a trimeric assembly, suggesting a likely natural conformation of VP24 in viral envelope. Therefore, in addition to confirming the evolutionary relationship among the three abundant envelope proteins of WSSV, our structural studies also facilitate a better understanding of the molecular mechanism underlying special roles of VP24 in WSSV assembly and infection. PMID:27572278

  13. Multiplexed Quantitation of Endogenous Proteins in Dried Blood Spots by Multiple Reaction Monitoring - Mass Spectrometry

    PubMed Central

    Chambers, Andrew G.; Percy, Andrew J.; Yang, Juncong; Camenzind, Alexander G.; Borchers, Christoph H.

    2013-01-01

    Dried blood spot (DBS) sampling, coupled with multiple reaction monitoring mass spectrometry (MRM-MS), is a well-established approach for quantifying a wide range of small molecule biomarkers and drugs. This sampling procedure is simpler and less-invasive than those required for traditional plasma or serum samples enabling collection by minimally trained personnel. Many analytes are stable in the DBS format without refrigeration, which reduces the cost and logistical challenges of sample collection in remote locations. These advantages make DBS sample collection desirable for advancing personalized medicine through population-wide biomarker screening. Here we expand this technology by demonstrating the first multiplexed method for the quantitation of endogenous proteins in DBS samples. A panel of 60 abundant proteins in human blood was targeted by monitoring proteotypic tryptic peptides and their stable isotope-labeled analogs by MRM. Linear calibration curves were obtained for 40 of the 65 peptide targets demonstrating multiple proteins can be quantitatively extracted from DBS collection cards. The method was also highly reproducible with a coefficient of variation of <15% for all 40 peptides. Overall, this assay quantified 37 proteins spanning a range of more than four orders of magnitude in concentration within a single 25 min LC/MRM-MS analysis. The protein abundances of the 33 proteins quantified in matching DBS and whole blood samples showed an excellent correlation, with a slope of 0.96 and an R2 value of 0.97. Furthermore, the measured concentrations for 80% of the proteins were stable for at least 10 days when stored at −20 °C, 4 °C and 37 °C. This work represents an important first step in evaluating the integration of DBS sampling with highly-multiplexed MRM for quantitation of endogenous proteins. PMID:23221968

  14. Expression, purification and crystallization of two major envelope proteins from white spot syndrome virus

    SciTech Connect

    Tang, Xuhua; Hew, Choy Leong

    2007-07-01

    The crystallization of the N-terminal transmembrane region-truncated VP26 and VP28 of white spot syndrome virus is described. White spot syndrome virus (WSSV) is a major virulent pathogen known to infect penaeid shrimp and other crustaceans. VP26 and VP28, two major envelope proteins from WSSV, have been identified and overexpressed in Escherichia coli. In order to facilitate purification and crystallization, predicted N-terminal transmembrane regions of approximately 35 amino acids have been truncated from both VP26 and VP28. Truncated VP26 and VP28 and their corresponding SeMet-labelled proteins were purified and the SeMet proteins were crystallized by the hanging-drop vapour-diffusion method. Crystals of SeMet-labelled VP26 were obtained using a reservoir consisting of 0.1 M citric acid pH 3.5, 3.0 M sodium chloride and 1%(w/v) polyethylene glycol 3350, whereas SeMet VP28 was crystallized using a reservoir solution consisting of 25% polyethylene glycol 8000, 0.2 M calcium acetate, 0.1 M Na HEPES pH 7.5 and 1.5%(w/v) 1,2,3-heptanetriol. Crystals of SeMet-labelled VP26 diffract to 2.2 Å resolution and belong to space group R32, with unit-cell parameters a = b = 73.92, c = 199.31 Å. SeMet-labelled VP28 crystallizes in space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 105.33, b = 106.71, c = 200.37 Å, and diffracts to 2.0 Å resolution.

  15. Quantitation of tyrosine hydroxylase, protein levels: Spot immunolabeling with an affinity-purified antibody

    SciTech Connect

    Haycock, J.W. )

    1989-09-01

    Tyrosine hydroxylase was purified from bovine adrenal chromaffin cells and rat pheochromocytoma using a rapid (less than 2 days) procedure performed at room temperature. Rabbits were immunized with purified enzyme that was denatured with sodium dodecylsulfate, and antibodies to tyrosine hydroxylase were affinity-purified from immune sera. A Western blot procedure using the affinity-purified antibodies and {sup 125}I-protein A demonstrated a selective labeling of a single Mr approximately 62,000 band in samples from a number of different tissues. The relative lack of background {sup 125}I-protein A binding permitted the development of a quantitative spot immunolabeling procedure for tyrosine hydroxylase protein. The sensitivity of the assay is 1-2 ng of enzyme. Essentially identical standard curves were obtained with tyrosine hydroxylase purified from rat pheochromocytoma, rat corpus striatum, and bovine adrenal medulla. An extract of PC 12 cells (clonal rat pheochromocytoma cells) was calibrated against purified rat pheochromocytoma tyrosine hydroxylase and used as an external standard against which levels of tyrosine hydroxylase in PC12 cells and other tissue were quantified. With this procedure, qualitative assessment of tyrosine hydroxylase protein levels can be obtained in a few hours and quantitative assessment can be obtained in less than a day.

  16. Protein expression profiling by antibody array analysis with use of dried blood spot samples on filter paper.

    PubMed

    Jiang, Weidong; Mao, Ying Qing; Huang, Ruochun; Duan, Chaohui; Xi, Yun; Yang, Kai; Huang, Ruo-Pan

    2014-01-31

    Dried blood spot samples (DBSS) on filter paper offer several advantages compared to conventional serum/plasma samples: they do not require any phlebotomy or separation of blood by centrifugation; they are less invasive; they allow sample stability and shipment at room temperature; and they pose a negligible risk of infection with blood-borne viruses, such as HIV, HBV and HCV, to those who handle them. Therefore dried blood spot samples (DBSS) on filter paper can be a quick, convenient and inexpensive means of obtaining blood samples for biomarker discovery, disease screening, diagnosis and treatment monitoring in non-hospitalized, public health settings. In this study, we investigated for the first time the potential application of dried blood spot samples (DBSS) in protein expression profiling using antibody array technology. First, optimal conditions for array assay performance using dried blood spot samples (DBSS) was established, including sample elution buffer, elution time, elution temperature and assay blocking buffer. Second, we analyzed dried blood spot samples (DBSS) using three distinct antibody array platforms, including sandwich-based antibody arrays, quantitative antibody arrays and biotin-label-based antibody arrays. In comparison with paired serum samples, detection of circulating proteins in dried blood spot samples (DBSS) correlated well for both low- and high-abundance proteins on all three antibody array platforms. In conclusion, our study strongly indicates the novel application of multiplex antibody array platforms to analyze dried blood spot samples (DBSS) on filter paper represents a viable, cost-effective method for protein profiling, biomarker discovery and disease screening in a large, population-based survey. PMID:24287424

  17. Predicting hot spots in protein interfaces based on protrusion index, pseudo hydrophobicity and electron-ion interaction pseudopotential features

    PubMed Central

    Xia, Junfeng; Yue, Zhenyu; Di, Yunqiang; Zhu, Xiaolei; Zheng, Chun-Hou

    2016-01-01

    The identification of hot spots, a small subset of protein interfaces that accounts for the majority of binding free energy, is becoming more important for the research of drug design and cancer development. Based on our previous methods (APIS and KFC2), here we proposed a novel hot spot prediction method. For each hot spot residue, we firstly constructed a wide variety of 108 sequence, structural, and neighborhood features to characterize potential hot spot residues, including conventional ones and new one (pseudo hydrophobicity) exploited in this study. We then selected 3 top-ranking features that contribute the most in the classification by a two-step feature selection process consisting of minimal-redundancy-maximal-relevance algorithm and an exhaustive search method. We used support vector machines to build our final prediction model. When testing our model on an independent test set, our method showed the highest F1-score of 0.70 and MCC of 0.46 comparing with the existing state-of-the-art hot spot prediction methods. Our results indicate that these features are more effective than the conventional features considered previously, and that the combination of our and traditional features may support the creation of a discriminative feature set for efficient prediction of hot spots in protein interfaces. PMID:26934646

  18. Envelope Proteins of White Spot Syndrome Virus (WSSV) Interact with Litopenaeus vannamei Peritrophin-Like Protein (LvPT)

    PubMed Central

    Xie, Shijun; Zhang, Xiaojun; Zhang, Jiquan; Li, Fuhua; Xiang, Jianhai

    2015-01-01

    White spot syndrome virus (WSSV) is a major pathogen in shrimp cultures. The interactions between viral proteins and their receptors on the surface of cells in a frontier target tissue are crucial for triggering an infection. In this study, a yeast two-hybrid (Y2H) library was constructed using cDNA obtained from the stomach and gut of Litopenaeus vannamei, to ascertain the role of envelope proteins in WSSV infection. For this purpose, VP37 was used as the bait in the Y2H library screening. Forty positive clones were detected after screening. The positive clones were analyzed and discriminated, and two clones belonging to the peritrophin family were subsequently confirmed as genuine positive clones. Sequence analysis revealed that both clones could be considered as the same gene, LV-peritrophin (LvPT). Co-immunoprecipitation confirmed the interaction between LvPT and VP37. Further studies in the Y2H system revealed that LvPT could also interact with other WSSV envelope proteins such as VP32, VP38A, VP39B, and VP41A. The distribution of LvPT in tissues revealed that LvPT was mainly expressed in the stomach than in other tissues. In addition, LvPT was found to be a secretory protein, and its chitin-binding ability was also confirmed. PMID:26692362

  19. Induction of necrosis via mitochondrial targeting of Melon necrotic spot virus replication protein p29 by its second transmembrane domain

    SciTech Connect

    Mochizuki, Tomofumi; Hirai, Katsuyuki; Kanda, Ayami; Ohnishi, Jun; Ohki, Takehiro; Tsuda, Shinya

    2009-08-01

    The virulence factor of Melon necrotic spot virus (MNSV), a virus that induces systemic necrotic spot disease on melon plants, was investigated. When the replication protein p29 was expressed in N. benthamiana using a Cucumber mosaic virus vector, necrotic spots appeared on the leaf tissue. Transmission electron microscopy revealed abnormal mitochondrial aggregation in these tissues. Fractionation of tissues expressing p29 and confocal imaging using GFP-tagged p29 revealed that p29 associated with the mitochondrial membrane as an integral membrane protein. Expression analysis of p29 deletion fragments and prediction of hydrophobic transmembrane domains (TMDs) in p29 showed that deletion of the second putative TMD from p29 led to deficiencies in both the mitochondrial localization and virulence of p29. Taken together, these results indicated that MNSV p29 interacts with the mitochondrial membrane and that p29 may be a virulence factor causing the observed necrosis.

  20. Determining Degradation and Synthesis Rates of Arabidopsis Proteins Using the Kinetics of Progressive 15N Labeling of Two-dimensional Gel-separated Protein Spots*

    PubMed Central

    Li, Lei; Nelson, Clark J.; Solheim, Cory; Whelan, James; Millar, A. Harvey

    2012-01-01

    The growth and development of plant tissues is associated with an ordered succession of cellular processes that are reflected in the appearance and disappearance of proteins. The control of the kinetics of protein turnover is central to how plants can rapidly and specifically alter protein abundance and thus molecular function in response to environmental or developmental cues. However, the processes of turnover are largely hidden during periods of apparent steady-state protein abundance, and even when proteins accumulate it is unclear whether enhanced synthesis or decreased degradation is responsible. We have used a 15N labeling strategy with inorganic nitrogen sources coupled to a two-dimensional fluorescence difference gel electrophoresis and mass spectrometry analysis of two-dimensional IEF/SDS-PAGE gel spots to define the rate of protein synthesis (KS) and degradation (KD) of Arabidopsis cell culture proteins. Through analysis of MALDI-TOF/TOF mass spectra from 120 protein spots, we were able to quantify KS and KD for 84 proteins across six functional groups and observe over 65-fold variation in protein degradation rates. KS and KD correlate with functional roles of the proteins in the cell and the time in the cell culture cycle. This approach is based on progressive 15N labeling that is innocuous for the plant cells and, because it can be used to target analysis of proteins through the use of specific gel spots, it has broad applicability. PMID:22215636

  1. Identification of domains of the Tomato spotted wilt virus NSm protein involved in tubule formation, movement and symptomatology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Deletion and alanine-substitution mutants of the Tomato spotted wilt virus NSm protein were generated to identify domains involved in tubule formation, movement and symptomatology, using a heterologous expression system derived from Tobacco mosaic virus. Two regions of NSm were required for both tub...

  2. VP24 Is a Chitin-Binding Protein Involved in White Spot Syndrome Virus Infection

    PubMed Central

    Li, Zaipeng; Han, Yali; Xu, Limei

    2015-01-01

    ABSTRACT Oral ingestion is the major route of infection for the white spot syndrome virus (WSSV). However, the mechanism by which virus particles in the digestive tract invade host cells is unknown. In the present study, we demonstrate that WSSV virions can bind to chitin through one of the major envelope proteins (VP24). Mutagenesis analysis indicated that amino acids (aa) 186 to 200 in the C terminus of VP24 were required for chitin binding. Moreover, the P-VP24186–200 peptide derived from the VP24 chitin binding region significantly inhibited the VP24-chitin interaction and the WSSV-chitin interaction, implying that VP24 participates in WSSV binding to chitin. Oral inoculation experiments showed that P-VP24186–200 treatment reduced the number of virus particles remaining in the digestive tract during the early stage of infection and greatly hindered WSSV proliferation in shrimp. These data indicate that binding of WSSV to chitin through the viral envelope protein VP24 is essential for WSSV per os infection and provide new ideas for preventing WSSV infection in shrimp farms. IMPORTANCE In this study, we show that WSSV can bind to chitin through the envelope protein VP24. The chitin-binding domain of VP24 maps to amino acids 186 to 200 in the C terminus. Binding of WSSV to chitin through the viral envelope protein VP24 is essential for WSSV per os infection. These findings not only extend our knowledge of WSSV infection but also provide new insights into strategies to prevent WSSV infection in shrimp farms. PMID:26512091

  3. The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins.

    PubMed

    Kozakov, Dima; Grove, Laurie E; Hall, David R; Bohnuud, Tanggis; Mottarella, Scott E; Luo, Lingqi; Xia, Bing; Beglov, Dmitri; Vajda, Sandor

    2015-05-01

    FTMap is a computational mapping server that identifies binding hot spots of macromolecules-i.e., regions of the surface with major contributions to the ligand-binding free energy. To use FTMap, users submit a protein, DNA or RNA structure in PDB (Protein Data Bank) format. FTMap samples billions of positions of small organic molecules used as probes, and it scores the probe poses using a detailed energy expression. Regions that bind clusters of multiple probe types identify the binding hot spots in good agreement with experimental data. FTMap serves as the basis for other servers, namely FTSite, which is used to predict ligand-binding sites, FTFlex, which is used to account for side chain flexibility, FTMap/param, used to parameterize additional probes and FTDyn, for mapping ensembles of protein structures. Applications include determining the druggability of proteins, identifying ligand moieties that are most important for binding, finding the most bound-like conformation in ensembles of unliganded protein structures and providing input for fragment-based drug design. FTMap is more accurate than classical mapping methods such as GRID and MCSS, and it is much faster than the more-recent approaches to protein mapping based on mixed molecular dynamics. By using 16 probe molecules, the FTMap server finds the hot spots of an average-size protein in <1 h. As FTFlex performs mapping for all low-energy conformers of side chains in the binding site, its completion time is proportionately longer. PMID:25855957

  4. ICP35 Is a TREX-Like Protein Identified in White Spot Syndrome Virus

    PubMed Central

    Phairoh, Panapat; Suthibatpong, Thana; Rattanarojpong, Triwit; Jongruja, Nujarin; Senapin, Saengchan; Choowongkomon, Kiattawee; Khunrae, Pongsak

    2016-01-01

    ICP35 is a non-structural protein from White spot syndrome virus believed to be important in viral replication. Since ICP35 was found to localize in the host nucleus, it has been speculated that the function of ICP35 might be involved in the interaction of DNA. In this study, we overexpressed, purified and characterized ICP35. The thioredoxin-fused ICP35 (thio-ICP35) was strongly expressed in E. coli and be able to form itself into dimers. Investigation of the interaction between ICP35 and DNA revealed that ICP35 can perform DNase activity. Structural model of ICP35 was successfully built on TREX1, suggesting that ICP35 might adopt the folding similar to that of TREX1 protein. Several residues important for dimerization in TREX1 are also conserved in ICP35. Residue Asn126 and Asp132, which are seen to be in close proximity to metal ions in the ICP35 model, were shown through site-directed mutagenesis to be critical for DNase activity. PMID:27348862

  5. Intersubunit signaling in RecBCD enzyme, a complex protein machine regulated by Chi hot spots

    PubMed Central

    Amundsen, Susan K.; Taylor, Andrew F.; Reddy, Manjula; Smith, Gerald R.

    2007-01-01

    The Escherichia coli RecBCD helicase–nuclease, a paradigm of complex protein machines, initiates homologous genetic recombination and the repair of broken DNA. Starting at a duplex end, RecBCD unwinds DNA with its fast RecD helicase and slower RecB helicase on complementary strands. Upon encountering a Chi hot spot (5′-GCTGGTGG-3′), the enzyme produces a new 3′ single-strand end and loads RecA protein onto it, but how Chi regulates RecBCD is unknown. We report a new class of mutant RecBCD enzymes that cut DNA at novel positions that depend on the DNA substrate length and that are strictly correlated with the RecB:RecD helicase rates. We conclude that in the mutant enzymes when RecD reaches the DNA end, it signals RecB’s nuclease domain to cut the DNA. As predicted by this interpretation, the mutant enzymes cut closer to the entry point on DNA when unwinding is blocked by another RecBCD molecule traveling in the opposite direction. Furthermore, when RecD is slowed by a mutation altering its ATPase site such that RecB reaches the DNA end before RecD does, the length-dependent cuts are abolished. These observations lead us to hypothesize that, in wild-type RecBCD enzyme, Chi is recognized by RecC, which then signals RecD to stop, which in turn signals RecB to cut the DNA and load RecA. We discuss support for this “signal cascade” hypothesis and tests of it. Intersubunit signaling may regulate other complex protein machines. PMID:18079176

  6. Expression, Purification, Crystallization of Two Major Envelope Proteins from White Spot Syndrome Virus

    SciTech Connect

    Tang,X.; Hew, C.

    2007-01-01

    White spot syndrome virus (WSSV) is a major virulent pathogen known to infect penaeid shrimp and other crustaceans. VP26 and VP28, two major envelope proteins from WSSV, have been identified and overexpressed in Escherichia coli. In order to facilitate purification and crystallization, predicted N-terminal transmembrane regions of approximately 35 amino acids have been truncated from both VP26 and VP28. Truncated VP26 and VP28 and their corresponding SeMet-labelled proteins were purified and the SeMet proteins were crystallized by the hanging-drop vapor-diffusion method. Crystals of SeMet-labelled VP26 were obtained using a reservoir consisting of 0.1 M citric acid pH 3.5, 3.0 M sodium chloride and 1%(w/v) polyethylene glycol 3350, whereas SeMet VP28 was crystallized using a reservoir solution consisting of 25% polyethylene glycol 8000, 0.2 M calcium acetate, 0.1 M Na HEPES pH 7.5 and 1.5%(w/v) 1,2,3-heptanetriol. Crystals of SeMet-labelled VP26 diffract to 2.2 {angstrom} resolution and belong to space group R32, with unit-cell parameters a = b = 73.92, c = 199.31 {angstrom}. SeMet-labelled VP28 crystallizes in space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 105.33, b = 106.71, c = 200.37 {angstrom}, and diffracts to 2.0 {angstrom} resolution.

  7. Minichromosome maintenance protein 7 regulates phagocytosis in kuruma shrimp Marsupenaeus japonicas against white spot syndrome virus.

    PubMed

    Wang, Zhi; Zhu, Fei

    2016-08-01

    Minichromosome maintenance protein (MCM7) belongs to the MCM protein family and participates in the MCM complex by playing a role in the cell replication cycle and chromosome initiation of eukaryotes. Previously, we found that several genes, including MCM7, were over-expressed in Drosophila melanogaster after white spot syndrome virus (WSSV) infection. In this study, we aimed to further research the MCM7 of kuruma shrimp, Marsupenaeus japonicus (mjMCM7) and determine its role in the innate immune system. To this end, we cloned the entire 2307-bp mjMCM7 sequence, including a 1974-bp open reading frame (ORF) encoding a 658-aa-long protein. Real-time PCR showed that the gene was primarily expressed in the hemolymph and hepatopancreas and over-expressed in shrimp challenged with WSSV. Gene function study was carried out by knocking down the expression of MCM7 using small interference RNA (siRNA). The results revealed that β-actin, hemocyanin, prophenoloxidase (proPO) and tumor necrosis factor-α (TNF-α) were up-regulated while the cytoskeleton proteins such as myosin and Rho were significantly down-regulated at 24 h after treatment. The results indicate a possible relationship between mjMCM7 and the innate immune system, and suggest that mjMCM7 may play a role in phagocytosis. After WSSV challenge, WSSV copies and mortality count were both higher in the MCM7-siRNA-treated groups at 60 h after treatment, and the mortality count approached that of the control groups over time. The phagocytosis rate was significantly lower in the MCM7-siRNA-treated group than in the WSSV group. The findings of this study confirm that mjMCM7 positively regulates phagocytosis and plays an important role against WSSV. These results could help researchers to further understand the function of the MCM7 protein and reveal its potential role in the innate immunity of invertebrates. PMID:27276115

  8. Prediction of hot spots in protein interfaces using extreme learning machines with the information of spatial neighbour residues.

    PubMed

    Wang, Lin; Zhang, Wenjuan; Gao, Qiang; Xiong, Congcong

    2014-08-01

    The identification of hot spots, a small subset of protein interfaces that accounts for the majority of binding free energy, is becoming increasingly important for the research on protein-protein interaction and drug design. For each interface residue or target residue to be predicted, the authors extract hybrid features which incorporate a wide range of information of the target residue and its spatial neighbor residues, that is, the nearest contact residue in the other face (mirror-contact residue) and the nearest contact residue in the same face (intra-contact residue). Here, feature selection is performed using random forests to avoid over-fitting. Thereafter, the extreme learning machine is employed to effectively integrate these hybrid features for predicting hot spots in protein interfaces. By the 5-fold cross validation in the training set, their method can achieve accuracy (ACC) of 82.1% and Matthew's correlation coefficient (MCC) of 0.459, and outperforms some alternative machine learning methods in the comparison study. Furthermore, their method achieves ACC of 76.8% and MCC of 0.401 in the independent test set, and is more effective than the major existing hot spot predictors. Their prediction method offers a powerful tool for uncovering candidate residues in the studies of alanine scanning mutagenesis for functional protein interaction sites. PMID:25075532

  9. Molecular docking analyses of Avicennia marinaderived phytochemicals against white spot syndrome virus (WSSV) envelope protein-VP28

    PubMed Central

    Sahu, Sunil Kumar; Kathiresan, Kandasamy; Singh, Reena; Senthilraja, Poomalai

    2012-01-01

    White spot syndrome (WSS) is one of the most common and most disastrous diseases of shrimp worldwide. It causes up to 100% mortality within 3 to 4 days in commercial shrimp farms, resulting in large economic losses to the shrimp farming industry. VP28 envelope protein of WSSV is reported to play a key role in the systemic infection in shrimps. Considering the most sombre issue of viral disease in cultivated shrimp, the present study was undertaken to substantiate the inhibition potential of Avicennia marinaderived phytochemicals against the WSSV envelope protein VP28. Seven A. marina-derived phytochemicals namely stigmasterol, triterpenoid, betulin, lupeol, avicenol-A, betulinic acid and quercetin were docked against the WSSV protein VP28 by using Argus lab molecular docking software. The chemical structures of the phytochemicals were retrieved from Pubchem database and generated from SMILES notation. Similarly the protein structure of the envelope protein was obtained from protein data bank (PDB-ID: 2ED6). Binding sites were predicted by using ligand explorer software. Among the phytochemicals screened, stigmasterol, lupeol and betulin showed the best binding exhibiting the potential to block VP28 envelope protein of WSSV, which could possibly inhibit the attachment of WSSV to the host species. Further experimental studies will provide a clear understanding on the mode of action of these phytochemicals individually or synergistically against WSSV envelope protein and can be used as an inhibitory drug to reduce white spot related severe complications in crustaceans. PMID:23144547

  10. Comprehensive Experimental and Computational Analysis of Binding Energy Hot Spots at the NF-κB Essential Modulator (NEMO)/IKKβ Protein-Protein Interface

    PubMed Central

    Golden, Mary S.; Cote, Shaun M.; Sayeg, Marianna; Zerbe, Brandon S.; Villar, Elizabeth A.; Beglov, Dmitri; Sazinsky, Stephen L.; Georgiadis, Rosina M.; Vajda, Sandor; Kozakov, Dima; Whitty, Adrian

    2013-01-01

    We report a comprehensive analysis of binding energy hot spots at the protein-protein interaction (PPI) interface between NF-κB Essential Modulator (NEMO) and IκB kinase subunit β (IKKβ), an interaction that is critical for NF-κB pathway signaling, using experimental alanine scanning mutagenesis and also the FTMap method for computational fragment screening. The experimental results confirm that the previously identified NBD region of IKKβ contains the highest concentration of hot spot residues, the strongest of which are W739, W741 and L742 (ΔΔG = 4.3, 3.5 and 3.2 kcal/mol, respectively). The region occupied by these residues defines a potentially druggable binding site on NEMO that extends for ~16 Å to additionally include the regions that bind IKKβ L737 and F734. NBD residues D738 and S740 are also important for binding but do not make direct contact with NEMO, instead likely acting to stabilize the active conformation of surrounding residues. We additionally found two previously unknown hot spot regions centered on IKKβ residues L708/V709 and L719/I723. The computational approach successfully identified all three hot spot regions on IKKβ. Moreover, the method was able to accurately quantify the energetic importance of all hot spots residues involving direct contact with NEMO. Our results provide new information to guide the discovery of small molecule inhibitors that target the NEMO/IKKβ interaction. They additionally clarify the structural and energetic complementarity between “pocket-forming” and “pocket occupying” hot spot residues, and further validate computational fragment mapping as a method for identifying hot spots at PPI interfaces. PMID:23506214

  11. Consensus brain-derived protein, extraction protocol for the study of human and murine brain proteome using both 2D-DIGE and mini 2DE immunoblotting.

    PubMed

    Fernandez-Gomez, Francisco-Jose; Jumeau, Fanny; Derisbourg, Maxime; Burnouf, Sylvie; Tran, Hélène; Eddarkaoui, Sabiha; Obriot, Hélène; Dutoit-Lefevre, Virginie; Deramecourt, Vincent; Mitchell, Valérie; Lefranc, Didier; Hamdane, Malika; Blum, David; Buée, Luc; Buée-Scherrer, Valérie; Sergeant, Nicolas

    2014-01-01

    Two-dimensional gel electrophoresis (2DE) is a powerful tool to uncover proteome modifications potentially related to different physiological or pathological conditions. Basically, this technique is based on the separation of proteins according to their isoelectric point in a first step, and secondly according to their molecular weights by SDS polyacrylamide gel electrophoresis (SDS-PAGE). In this report an optimized sample preparation protocol for little amount of human post-mortem and mouse brain tissue is described. This method enables to perform both two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) and mini 2DE immunoblotting. The combination of these approaches allows one to not only find new proteins and/or protein modifications in their expression thanks to its compatibility with mass spectrometry detection, but also a new insight into markers validation. Thus, mini-2DE coupled to western blotting permits to identify and validate post-translational modifications, proteins catabolism and provides a qualitative comparison among different conditions and/or treatments. Herein, we provide a method to study components of protein aggregates found in AD and Lewy body dementia such as the amyloid-beta peptide and the alpha-synuclein. Our method can thus be adapted for the analysis of the proteome and insoluble proteins extract from human brain tissue and mice models too. In parallel, it may provide useful information for the study of molecular and cellular pathways involved in neurodegenerative diseases as well as potential novel biomarkers and therapeutic targets. PMID:24747743

  12. Liver spots

    MedlinePlus

    Sun-induced skin changes - liver spots; Senile or solar lentigines; Skin spots - aging; Age spots ... Liver spots are changes in skin color that occur in older skin. The coloring may be due to aging, exposure to the sun ...

  13. Analysis of PEG-fractionated high-molecular-mass proteins in human plasma by non-denaturing micro 2-DE and MALDI-MS PMF.

    PubMed

    Jin, Ya; Manabe, Takashi

    2009-10-01

    The process of 0-4% PEG precipitation of high-molecular-mass proteins (around and above 1x10(3) kDa) in human plasma was analyzed by non-denaturing micro 2-DE employing agarose IEF gels in the first dimension, and by MALDI-MS PMF. The PEG 0-2% precipitate could be mostly re-dissolved (fraction PS2%), but some part remained as precipitate (fraction PP2%). Non-denaturing 2-DE followed by MALDI-MS PMF showed that PS2% contained fibrinogen (Fb), fibronectin (FN), and their oligomers as the major components, and von Willebrand factor and coagulation factor XIII as the minor components. PP2% was directly subjected to MALDI-MS PMF and FN and Fb were assigned, suggesting it was formed by co-precipitation of the two proteins. The PEG 2-4% precipitate could be totally dissolved, but after freezing and thawing the solution, a small amount of precipitate appeared. MALDI-MS PMF analysis of the precipitate (PP4%) suggested that its major constituent is complement C1. The soluble fraction of the PEG 2-4% precipitate (PS4%), analyzed by non-denaturing 2-DE and MALDI-MS PMF, contained C4b-binding protein and its complex with complement C4, low-density lipoproteins, IgM, and complement C1 subcomponent q, together with Fb, FN, and their oligomers. When the PS4% fraction was analyzed by a Type-II 2-DE technique (non-denaturing IEF followed by SDS-PAGE, no reducing agent being used), several proteins in molecular mass range from 7x10(1) to 2x10(2) kDa appeared, suggesting that these proteins interacted with the high-molecular-mass proteins, then dissociated in the presence of SDS. PMID:19798675

  14. Characterization of the Bacterioferritin/Bacterioferritin Associated Ferredoxin Protein-Protein Interaction in Solution and Determination of Binding Energy Hot Spots.

    PubMed

    Wang, Yan; Yao, Huili; Cheng, Yuan; Lovell, Scott; Battaile, Kevin P; Midaugh, C Russell; Rivera, Mario

    2015-10-13

    Mobilization of iron stored in the interior cavity of BfrB requires electron transfer from the [2Fe−2S] cluster in Bfd to the core iron in BfrB. A crystal structure of the Pseudomonas aeruginosa BfrB:Bfd complex revealed that BfrB can bind up to 12 Bfd molecules at 12 structurally identical binding sites, placing the [2Fe−2S] cluster of each Bfd immediately above a heme group in BfrB [Yao, H., et al. (2012) J. Am. Chem. Soc., 134, 13470−13481]. We report here study aimed at characterizing the strength of the P. aeruginosa BfrB:Bfd association using surface plasmon resonance and isothermal titration calorimetry as well as determining the binding energy hot spots at the protein−protein interaction interface. The results show that the 12 Bfd-binding sites on BfrB are equivalent and independent and that the protein−protein association at each of these sites is driven entropically and is characterized by a dissociation constant (Kd) of approximately 3 μM. Determination of the binding energy hot spots was carried out by replacing certain residues that comprise the protein−protein interface with alanine and by evaluating the effect of the mutation on Kd and on the efficiency of core iron mobilization from BfrB. The results identified hot spot residues in both proteins [LB 68, EA 81, and EA 85 in BfrB (superscript for residue number and subscript for chain) and Y2 and L5 in Bfd] that network at the interface to produce a highly complementary hot region for the interaction. The hot spot residues are conserved in the amino acid sequences of Bfr and Bfd proteins from a number of Gram-negative pathogens, indicating that the BfrB:Bfd interaction is of widespread significance in bacterial iron metabolism. PMID:26368531

  15. Wheat Drought-Responsive Grain Proteome Analysis by Linear and Nonlinear 2-DE and MALDI-TOF Mass Spectrometry

    PubMed Central

    Jiang, Shan-Shan; Liang, Xiao-Na; Li, Xin; Wang, Shun-Li; Lv, Dong-Wen; Ma, Chao-Ying; Li, Xiao-Hui; Ma, Wu-Jun; Yan, Yue-Ming

    2012-01-01

    A comparative proteomic analysis of drought-responsive proteins during grain development of two wheat varieties Kauz (strong resistance to drought stress) and Janz (sensitive to drought stress) was performed by using linear and nonlinear 2-DE and MALDI-TOF mass spectrometry technologies. Results revealed that the nonlinear 2-DE had much higher resolution than the linear 2-DE. A total of 153 differentially expressed protein spots were detected by both 2-DE maps, of which 122 protein spots were identified by MALDI-TOF and MALDI-TOF/TOF mass spectrometry. The identified differential proteins were mainly involved in carbohydrate metabolism (26%), detoxification and defense (23%), and storage proteins (17%). Some key proteins demonstrated significantly different expression patterns between the two varieties. In particular, catalase isozyme 1, WD40 repeat protein, LEA and alpha-amylase inhibitors displayed an upregulated expression pattern in Kauz, whereas they were downregulated or unchanged in Janz. Small and large subunit ADP glucose pyrophosphorylase, ascorbate peroxidase and G beta-like protein were all downregulated under drought stress in Janz, but had no expression changes in Kauz. Sucrose synthase and triticin precursor showed an upregulated expression pattern under water deficits in both varieties, but their upregulation levels were much higher in Kauz than in Janz. These differentially expressed proteins could be related to the biochemical pathways for stronger drought resistance of Kauz. PMID:23443111

  16. Phosphotransferase protein EIIANtr interacts with SpoT, a key enzyme of the stringent response, in Ralstonia eutropha H16.

    PubMed

    Karstens, Katja; Zschiedrich, Christopher P; Bowien, Botho; Stülke, Jörg; Görke, Boris

    2014-04-01

    EIIA(Ntr) is a member of a truncated phosphotransferase (PTS) system that serves regulatory functions and exists in many Proteobacteria in addition to the sugar transport PTS. In Escherichia coli, EIIA(Ntr) regulates K(+) homeostasis through interaction with the K(+) transporter TrkA and sensor kinase KdpD. In the β-Proteobacterium Ralstonia eutropha H16, EIIA(Ntr) influences formation of the industrially important bioplastic poly(3-hydroxybutyrate) (PHB). PHB accumulation is controlled by the stringent response and induced under conditions of nitrogen deprivation. Knockout of EIIA(Ntr) increases the PHB content. In contrast, absence of enzyme I or HPr, which deliver phosphoryl groups to EIIA(Ntr), has the opposite effect. To clarify the role of EIIA(Ntr) in PHB formation, we screened for interacting proteins that co-purify with Strep-tagged EIIA(Ntr) from R. eutropha cells. This approach identified the bifunctional ppGpp synthase/hydrolase SpoT1, a key enzyme of the stringent response. Two-hybrid and far-Western analyses confirmed the interaction and indicated that only non-phosphorylated EIIA(Ntr) interacts with SpoT1. Interestingly, this interaction does not occur between the corresponding proteins of E. coli. Vice versa, interaction of EIIA(Ntr) with KdpD appears to be absent in R. eutropha, although R. eutropha EIIA(Ntr) can perfectly substitute its homologue in E. coli in regulation of KdpD activity. Thus, interaction with KdpD might be an evolutionary 'ancient' task of EIIA(Ntr) that was subsequently replaced by interaction with SpoT1 in R. eutropha. In conclusion, EIIA(Ntr) might integrate information about nutritional status, as reflected by its phosphorylation state, into the stringent response, thereby controlling cellular PHB content in R. eutropha. PMID:24515609

  17. Structure and Function Analysis of Nucleocapsid Protein of Tomato Spotted Wilt Virus Interacting with RNA Using Homology Modeling*

    PubMed Central

    Li, Jia; Feng, Zhike; Wu, Jianyan; Huang, Ying; Lu, Gang; Zhu, Min; Wang, Bi; Mao, Xiang; Tao, Xiaorong

    2015-01-01

    The nucleocapsid (N) protein of tomato spotted wilt virus (TSWV) plays key roles in assembling genomic RNA into ribonucleoprotein (RNP), which serves as a template for both viral gene transcription and genome replication. However, little is known about the molecular mechanism of how TSWV N interacts with genomic RNA. In this study, we demonstrated that TSWV N protein forms a range of higher ordered oligomers. Analysis of the RNA binding behavior of N protein revealed that no specific oligomer binds to RNA preferentially, instead each type of N oligomer is able to bind RNA. To better characterize the structure and function of N protein interacting with RNA, we constructed homology models of TSWV N and N-RNA complexes. Based on these homology models, we demonstrated that the positively charged and polar amino acids in its predicted surface cleft of TSWV N are critical for RNA binding. Moreover, by N-RNA homology modeling, we found that the RNA component is deeply embedded in the predicted protein cleft; consistently, TSWV N-RNA complexes are relatively resistant to digestion by RNase. Collectively, using homology modeling, we determined the RNA binding sites on N and found a new protective feature for N protein. Our findings also provide novel insights into the molecular details of the interaction of TSWV N with RNA components. PMID:25540203

  18. Identification and characterization of a prawn white spot syndrome virus gene that encodes an envelope protein VP31

    SciTech Connect

    Li Li; Xie Xixian; Yang Feng . E-mail: mbiotech@public.xm.fj.cn

    2005-09-15

    Based on a combination of SDS-PAGE and mass spectrometry, a protein with an apparent molecular mass of 31 kDa (termed as VP31) was identified from purified shrimp white spot syndrome virus (WSSV) envelope fraction. The resulting amino acid (aa) sequence matched an open reading frame (WSV340) of the WSSV genome. This ORF contained 783 nucleotides (nt), encoding 261 aa. A fragment of WSV340 was expressed in Escherichia coli as a glutathione S-transferase (GST) fusion protein with a 6His-tag, and then specific antibody was raised. Western blot analysis and the immunoelectron microscope method (IEM) confirmed that VP31 was present exclusively in the viral envelope fraction. The neutralization experiment suggested that VP31 might play an important role in WSSV infectivity.

  19. External Quality Control for Dried Blood Spot Based C-reactive Protein Assay: Experience from the Indonesia Family Life Survey and the Longitudinal Aging Study in India

    PubMed Central

    Hu, Peifeng; Herningtyas, Elizabeth H.; Kale, Varsha; Crimmins, Eileen M.; Risbud, Arun R.; McCreath, Heather; Lee, Jinkook; Strauss, John; O’Brien, Jennifer C.; Bloom, David E.; Seeman, Teresa E.

    2015-01-01

    Measurement of C-reactive protein, a marker of inflammation, in dried blood spots has been increasingly incorporated in community-based social surveys internationally. Although the dried blood spot based CRP assay protocol has been validated in the United States, it remains unclear whether laboratories in other less developed countries can generate C-reactive protein results of similar quality. We therefore conducted external quality monitoring for dried blood spot based C-reactive protein measurement for the Indonesia Family Life Survey and the Longitudinal Aging Study in India. Our results show that dried blood spot based C-reactive protein results in these two countries have excellent and consistent correlations with serum-based values and dried blood spot based results from the reference laboratory in the United States. Even though the results from duplicate samples may have fluctuations in absolute values over time, the relative order of C-reactive protein levels remains similar and the estimates are reasonably precise for population-based studies that investigate the association between socioeconomic factors and health. PMID:25879265

  20. Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC-MS/MS. 2. Similarity search between protein maps for the analysis of protein complexes.

    PubMed

    Jin, Ya; Yuan, Qi; Zhang, Jun; Manabe, Takashi; Tan, Wen

    2015-09-01

    Human bronchial smooth muscle cell soluble proteins were analyzed by a combined method of nondenaturing micro 2DE, grid gel-cutting, and quantitative LC-MS/MS and a native protein map was prepared for each of the identified 4323 proteins [1]. A method to evaluate the degree of similarity between the protein maps was developed since we expected the proteins comprising a protein complex would be separated together under nondenaturing conditions. The following procedure was employed using Excel macros; (i) maps that have three or more squares with protein quantity data were selected (2328 maps), (ii) within each map, the quantity values of the squares were normalized setting the highest value to be 1.0, (iii) in comparing a map with another map, the smaller normalized quantity in two corresponding squares was taken and summed throughout the map to give an "overlap score," (iv) each map was compared against all the 2328 maps and the largest overlap score, obtained when a map was compared with itself, was set to be 1.0 thus providing 2328 "overlap factors," (v) step (iv) was repeated for all maps providing 2328 × 2328 matrix of overlap factors. From the matrix, protein pairs that showed overlap factors above 0.65 from both protein sides were selected (431 protein pairs). Each protein pair was searched in a database (UniProtKB) on complex formation and 301 protein pairs, which comprise 35 protein complexes, were found to be documented. These results demonstrated that native protein maps and their similarity search would enable simultaneous analysis of multiple protein complexes in cells. PMID:26031785

  1. Liver spots

    MedlinePlus

    Sun-induced skin changes - liver spots; Senile or solar lentigines; Skin spots - aging; Age spots ... Liver spots are changes in skin color that occur in older skin. The coloring may be due to aging, exposure to the sun or other sources of ...

  2. The silencing suppressor (NSs) protein of the plant virus Tomato spotted wilt virus enhances heterologous protein expression and baculovirus pathogenicity in cells and lepidopteran insects.

    PubMed

    de Oliveira, Virgínia Carla; da Silva Morgado, Fabricio; Ardisson-Araújo, Daniel Mendes Pereira; Resende, Renato Oliveira; Ribeiro, Bergmann Morais

    2015-11-01

    In this work, we showed that cell death induced by a recombinant (vAcNSs) Autographa californica multiple nucleopolyhedrovirus (AcMNPV) expressing the silencing suppressor (NSs) protein of Tomato spotted wilt virus (TSWV) was enhanced on permissive and semipermissive cell lines. The expression of a heterologous gene (firefly luciferase) during co-infection of insect cells with vAcNSs and a second recombinant baculovirus (vAgppolhfluc) was shown to increase when compared to single vAgppolhfluc infections. Furthermore, the vAcNSs mean time-to-death values were significantly lower than those for wild-type AcMNPV on larvae of Spodoptera frugiperda and Anticarsia gemmatalis. These results showed that the TSWV-NSs protein could efficiently increase heterologous protein expression in insect cells as well as baculovirus pathogenicity and virulence, probably by suppressing the gene-silencing machinery in insects. PMID:26323262

  3. The NSs Protein of Tomato spotted wilt virus Is Required for Persistent Infection and Transmission by Frankliniella occidentalis

    PubMed Central

    Margaria, P.; Bosco, L.; Vallino, M.; Ciuffo, M.; Mautino, G. C.; Tavella, L.

    2014-01-01

    ABSTRACT Tomato spotted wilt virus (TSWV) is the type member of tospoviruses (genus Tospovirus), plant-infecting viruses that cause severe damage to ornamental and vegetable crops. Tospoviruses are transmitted by thrips in the circulative propagative mode. We generated a collection of NSs-defective TSWV isolates and showed that TSWV coding for truncated NSs protein could not be transmitted by Frankliniella occidentalis. Quantitative reverse transcription (RT)-PCR and immunostaining of individual insects detected the mutant virus in second-instar larvae and adult insects, demonstrating that insects could acquire and accumulate the NSs-defective virus. Nevertheless, adults carried a significantly lower viral load, resulting in the absence of transmission. Genome sequencing and analyses of reassortant isolates showed genetic evidence of the association between the loss of competence in transmission and the mutation in the NSs coding sequence. Our findings offer new insight into the TSWV-thrips interaction and Tospovirus pathogenesis and highlight, for the first time in the Bunyaviridae family, a major role for the S segment, and specifically for the NSs protein, in virulence and efficient infection in insect vector individuals. IMPORTANCE Our work is the first to show a role for the NSs protein in virus accumulation in the insect vector in the Bunyaviridae family: demonstration was obtained for the system TSWV-F. occidentalis, arguably one of the most damaging combination for vegetable crops. Genetic evidence of the involvement of the NSs protein in vector transmission was provided with multiple approaches. PMID:24623427

  4. The bud tip is the cellular hot spot of protein secretion in yeasts.

    PubMed

    Puxbaum, Verena; Gasser, Brigitte; Mattanovich, Diethard

    2016-09-01

    Yeasts are valuable hosts for recombinant protein production. Among them, Pichia pastoris is frequently used for production of secreted proteins, and much effort was made to improve the secretion efficiency of this expression platform. However, the knowledge on the secretion machinery is mainly based on studies in Saccharomyces cerevisiae. Therefore, it is of great interest for targeted improvement of the system to learn more about the secretion process in P. pastoris. Using human serum albumin, a protein which is produced in high quantities in P. pastoris, we show here the secretion pathway of this protein. During passage of the secretory route, the recombinant protein is mainly localized in the endoplasmic reticulum (ER) and in COPII vesicles, and is inherited to the daughter cell via the perinuclear ER. The final release to the cell exterior occurs at the bud, initiating at the bud tip and later spreading over the entire bud surface. The same polarized secretion pattern was observed for a recombinant antibody light chain and the native secretory protein Epx1 of P. pastoris. Clarifying the point of release of secretory proteins will have major impact on engineering the secretory pathway of P. pastoris and other budding yeasts. PMID:27338576

  5. Protein crystallography: From X-ray diffraction spots to a three dimensional image

    SciTech Connect

    Terwilliger, T.C.; Berendzen, J.

    1998-02-25

    Proteins are remarkable molecular machines that are essential for life. They can do many things ranging from the precise control of blood clotting to synthesizing complex organic compounds. Pictures of protein molecules are in high demand in biotechnology because they are important for applications such as drug discovery and for engineering enzymes for commercial use. X-ray crystallography is the most common method for determining the three-dimensional structures of protein molecules. When a crystal of a protein is placed in an X-ray beam, scattering of X-rays off the ordered molecules produces a diffraction pattern that can be measured on a position-sensitive CCD or image-plate detector. Protein crystals typically contain thousands of atoms and the diffraction data are generally measured to relatively low resolution. Consequently the direct methods approaches generally cannot be applied. Instead, if the crystal is modified by adding metal atoms at specific sites or by tuning the wavelength of the X-rays to cross an absorption edge of a metal atom in the crystal, then the information from these additional measurements is sufficient to first identify the /locations of the metal atoms. This information is then used along with the diffraction data to make a three-dimensional picture of electron densities. This picture can be used to determine the position of most or all of the atoms in the protein.

  6. Interactions of xenobiotics with steroid hormone receptors and the sex-steroid binding protein in spotted seatrout

    SciTech Connect

    Thomas, P.; Ghosh, S.; Pinter, J.; Sperry, T.; Breckenridge-Miller, D.; Laidley, C.W.

    1995-12-31

    A variety of xenobiotics, such as DDT, methoxychlor and PCB mixtures and Kepone have estrogenic actions and disrupt reproduction in mammals by binding to nuclear estrogen receptors (ER). These xenobiotics were tested for their ability to bind to the hepatic ER of a marine fish, spotted seatrout (Cynoscion nebulosus). Several of the DDT derivatives, Kepone and PCB mixtures also bound to the seatrout ER over a range of 10{sup {minus}5}--10{sup {minus}3}M. Moreover, Kepone was shown to have both estrogenic and antiestrogenic actions in an in vitro liver slice vitellogenesis assay. These estrogenic compounds were also tested for their ability to bind to nuclear and plasma membrane progestogen (20{beta}-S) receptors in ovarian tissues and to the sex-steroid binding protein in seatrout plasma. Kepone, methoxychlor and o,p{prime}-DDT caused concentration dependent displacement of {sup 3}H2O{beta}-S from its plasma membrane receptor and inhibition of 20{beta}-S induced final maturation in an in vitro assay over the range of 10{sup {minus}7}--10{sup {minus}3}M, but did not alter steroid binding to the nuclear progestogen receptor. Significant binding of methoxychlor and the other organochlorines to the sex steroid binding protein was also observed. It is concluded from these studies that a variety of xenobiotics with estrogenic actions can also bind to other steroid receptors and binding proteins to influence other endocrine-mediated processes.

  7. Fatty acid-binding protein (fabp) genes of spotted green pufferfish (Tetraodon nigroviridis): comparative genomics and spatial transcriptional regulation.

    PubMed

    Thirumaran, Aruloli; Wright, Jonathan M

    2014-05-01

    The fatty acid-binding protein (fabp) genes belong to the multigene family of intracellular lipid-binding proteins. To date, 12 different FABPs have been identified in vertebrate genomes. Owing to the teleost-specific genome duplication event, many fishes have duplicated copies of the fabp genes. Here, we identified and characterized the fabp genes of spotted green pufferfish (Tetraodon nigroviridis). Seven fabp genes were identified, out of which, two were retained in the pufferfish genome as duplicated copies. Each putative pufferfish Fabp protein shares greatest sequence identity and similarity with their teleost and tetrapod orthologs, and clustered together as a distinct clade in phylogenetic analysis. Conserved gene synteny was evident between the pufferfish fabp genes and the orthologs of human, zebrafish, three-spined stickleback, and medaka FABP/fabp genes, providing evidence that the duplicated copies of pufferfish fabp genes most likely arose as a result of the teleost-specific genome duplication event. The differential tissue-specific distribution of pufferfish fabp transcripts suggests divergent spatial regulation of duplicated pairs of fabp genes. PMID:25153522

  8. 2-DE using hemi-fluorinated surfactants.

    PubMed

    Starita-Geribaldi, Mireille; Thebault, Pascal; Taffin de Givenchy, Elisabeth; Guittard, Frederic; Geribaldi, Serge

    2007-07-01

    The synthesis of hemi-fluorinated zwitterionic surfactants was realized and assessed for 2-DE, a powerful separation method for proteomic analysis. These new fluorinated amidosulfobetaine (FASB-p,m) were compared to their hydrocarbon counterparts amidosulfobetaine (ASB-n) characterized by a hydrophilic polar head, a hydrophobic and lipophilic tail, and an amido group as connector. The tail of these FASB surfactants was in part fluorinated resulting in the modulation of its lipophilicity (or oleophobicity). Their effect on the red blood cell (RBC) membrane showed a specific solubilization depending on the length of the hydrophobic part. A large number of polypeptide spots appeared in the 2-DE patterns by using FASB-p,m. The oleophobic character of these surfactants was confirmed by the fact that Band 3, a highly hydrophobic transmembrane protein, was not solubilized by these fluorinated structures. The corresponding pellet was very rich in Band 3 and could then be solubilized by using a strong detergent such as amidosulfobetaine with an alkyl tail containing 14 carbon atoms (ASB-14). Thus, these hemi-fluorinated surfactants appeared as powerful tools when used at the first step of a two-step solubilization strategy using a hydrocarbon homologous surfactant in the second step. PMID:17577887

  9. Native protein mapping and visualization of protein interactions in the area of human plasma high-density lipoprotein by combining nondenaturing micro 2DE and quantitative LC-MS/MS.

    PubMed

    Jin, Ya; Bu, Shujie; Zhang, Jun; Yuan, Qi; Manabe, Takashi; Tan, Wen

    2014-07-01

    A human plasma sample was subjected to nondenaturing micro 2DE and a gel area (5 mm × 18 mm) that includes high-density lipoprotein (HDL) was cut into 1 mm × 1 mm squares, then the proteins in the 90 gel pieces were analyzed by quantitative LC-MS/MS. Grid-cutting of the gel was employed to; (i) ensure the total analysis of the proteins in the area, (ii) standardize the conditions of analysis by LC-MS/MS, (iii) reconstruct the protein distribution patterns from the quantity data. Totally 154 proteins were assigned in the 90 gel pieces and the quantity distribution of each was reconstructed as a color density pattern (a native protein map). The map of apolipoprotein (Apo) A-I showed a wide apparent mass distribution characteristic to HDL and was compared with the maps of the other 153 proteins. Eleven proteins showed maps of wide distribution that overlapped with the map of Apo A-I, and all have been reported to be the components of HDL. Further, seven minor proteins associated with HDL were detected at the gel positions of high Apo A-I quantity. These results for the first time visualized the localization of HDL apolipoproteins on a nondenaturing 2DE gel and strongly suggested their interactions. PMID:24668886

  10. Differential expression analysis of nuclear oligomerization domain proteins NOD1 and NOD2 in orange-spotted grouper (Epinephelus coioides).

    PubMed

    Hou, Qing-Hua; Yi, Shi-Bai; Ding, Xu; Zhang, Hui-Xian; Sun, Yan; Zhang, Yong; Liu, Xiao-Chun; Lu, Dan-Qi; Lin, Hao-Ran

    2012-11-01

    Nucleotide-binding oligomerization domain-containing proteins-1 and -2 (NOD1 and NOD2) are members of the NOD-like receptors (NLRs) family. They are both cytoplasmic receptors, and sense microbial infections/danger molecules to induce host innate immune response. In this study, the full-length ORF sequences of NOD1 and NOD2 were cloned, and the putative amino acid sequences were identified in orange-spotted grouper (Epinephelus coioides). The complete open reading frame (ORF) of grouper NOD1 contained 2823 bp encoding a 940 amino acid protein. Grouper NOD2 cDNA contained a 2967 bp ORF, encoding a protein of 988 amino acid residues. Both grouper NOD1 and NOD2 had similar domains to human and fish counterparts. Phylogenetic tree analysis showed that grouper NOD1 clustered with grass carp, zebrafish and channel catfish, while NOD2 was most closely related to fugu. Expression patterns of grouper NOD1 and NOD2 were next studied. NOD1 had the highest level of expression in skin while NOD2 in trunk kidney. Post Vibrio alginolyticus (strain EcGS020401), lipopolysaccharide (LPS) or PolyI:C challenges, gene expression of grouper NOD1 and NOD2 was stimulated to different extents. NOD1 showed a significant enhancement after LPS stimulation, but NOD2 increased more significantly after PolyI:C invasion, indicating that NOD1 and NOD2 may exert different effects on the eradication of bacteria and virus. The adaptor protein RIP-like-interacting CLARP kinase (RICK) and downstream molecule interleukin-8 (IL-8) were also induced at different levels after stimulation, which indicated that NOD1 and NOD2 signal transduction was involved in grouper innate immune protection against bacterial and viral infections. PMID:22982325

  11. The spot 14 protein inhibits growth and induces differentiation and cell death of human MCF-7 breast cancer cells

    PubMed Central

    2005-01-01

    The S14 (spot 14) gene encodes a protein that is predominantly expressed in lipogenic tissues, such as the liver, white and brown adipose tissues and the lactating mammary glands. Accumulated evidence suggests that S14 could play an important role in the induction of lipogenic enzymes. In humans, the S14 locus resides in the chromosome region 11q13, which is frequently amplified in breast tumours, and as a result, it has been suggested that this protein could play a role in the metabolism and growth of these kinds of tumours. In the present study, we have examined the effects of S14 overexpression in MCF-7 human breast cancer cells. We found that S14 causes (i) an inhibition of cell proliferation and of anchorage-independent growth, (ii) a marked reduction in the number of viable cells and (iii) the induction of differentiation and cell death of these cells. The inhibition of cell growth was associated with a decrease in the expression of cyclin D1 and a reduction of cyclin D1 promoter activity. Increased expression of S14 also caused the accumulation of cytochrome c in the cytosol and loss of mitochondrial membrane potential. These findings suggest that S14 may function as an important modulator of tumorigenesis in human breast by decreasing cell growth and inducing cell death and differentiation. PMID:15819613

  12. A cancer-predisposing "hot spot" mutation of the fumarase gene creates a dominant negative protein.

    PubMed

    Lorenzato, Annalisa; Olivero, Martina; Perro, Mario; Brière, Jean Jacques; Rustin, Pierre; Di Renzo, Maria Flavia

    2008-02-15

    The Fumarase (Fumarate Hydratase, FH) is a tumor suppressor gene whose germline heterozygous mutations predispose to hereditary leiomyomatosis and renal cell cancer (HLRCC). The FH gene encodes an enzyme of the Krebs cycle, functioning as a homotetramer and catalyzing the hydration of fumarate to malate. Among the numerous FH mutations reported so far, the R190H missense mutation is the most frequent in HLRCC patients. Here we show the functional analyses of the R190H, in comparison to the better characterized E319Q mutation. We first expressed wild-type and mutated proteins in FH deficient human skin fibroblasts, using lentiviral vectors. The wild-type transgene was able to restore the FH enzymatic activity in cells, while the R190H- and E319Q-FH were not. More interestingly, when the same transgenes were expressed in normal, FH-proficient cells, only the R190H-FH reduced the endogenous FH enzymatic activity. By enforcing the expression of equal amount of wild-type and R190H-FH in the same cell, we showed that the mutated FH protein directly inhibited enzymatic activity by nearly abrogating the FH homotetramer formation. These data demonstrate the dominant negative effect of the R190H missense mutation in the FH gene and suggest that the FH tumor-suppressing activity might be impaired in cells carrying a heterozygous mutation. PMID:17960613

  13. Yeast Surface Display of Two Proteins Previously Shown to Be Protective Against White Spot Syndrome Virus (WSSV) in Shrimp

    PubMed Central

    Ananphongmanee, Vorawit; Srisala, Jiraporn; Sritunyalucksana, Kallaya; Boonchird, Chuenchit

    2015-01-01

    Cell surface display using the yeasts Saccharomyces cerevisiae and Pichia pastoris has been extensively developed for application in bioindustrial processes. Due to the rigid structure of their cell walls, a number of proteins have been successfully displayed on their cell surfaces. It was previously reported that the viral binding protein Rab7 from the giant tiger shrimp Penaeus monodon (PmRab7) and its binding partner envelope protein VP28 of white spot syndrome virus (WSSV) could independently protect shrimp against WSSV infection. Thus, we aimed to display these two proteins independently on the cell surfaces of 2 yeast clones with the ultimate goal of using a mixture of the two clones as an orally deliverable, antiviral agent to protect shrimp against WSSV infection. PmRab7 and VP28 were modified by N-terminal tagging to the C-terminal half of S. cerevisiae α-agglutinin. DNA fragments, harboring fused-gene expression cassettes under control of an alcohol oxidase I (AOX1) promoter were constructed and used to transform the yeast cells. Immunofluorescence microscopy with antibodies specific to both proteins demonstrated that mutated PmRab7 (mPmRab7) and partial VP28 (pVP28) were localized on the cell surfaces of the respective clones, and fluorescence intensity for each was significantly higher than that of control cells by flow cytometry. Enzyme-linked immunosorbant assay (ELISA) using cells displaying mPmRab7 or pVP28 revealed that the binding of specific antibodies for each was dose-dependent, and could be saturated. In addition, the binding of mPmRab7-expressing cells with free VP28, and vice versa was dose dependent. Binding between the two surface-expressed proteins was confirmed by an assay showing agglutination between cells expressing complementary mPmRab7 and pVP28. In summary, our genetically engineered P. pastoris can display biologically active mPmRab7 and pVP28 and is now ready for evaluation of efficacy in protecting shrimp against WSSV by oral

  14. Yeast Surface Display of Two Proteins Previously Shown to Be Protective Against White Spot Syndrome Virus (WSSV) in Shrimp.

    PubMed

    Ananphongmanee, Vorawit; Srisala, Jiraporn; Sritunyalucksana, Kallaya; Boonchird, Chuenchit

    2015-01-01

    Cell surface display using the yeasts Saccharomyces cerevisiae and Pichia pastoris has been extensively developed for application in bioindustrial processes. Due to the rigid structure of their cell walls, a number of proteins have been successfully displayed on their cell surfaces. It was previously reported that the viral binding protein Rab7 from the giant tiger shrimp Penaeus monodon (PmRab7) and its binding partner envelope protein VP28 of white spot syndrome virus (WSSV) could independently protect shrimp against WSSV infection. Thus, we aimed to display these two proteins independently on the cell surfaces of 2 yeast clones with the ultimate goal of using a mixture of the two clones as an orally deliverable, antiviral agent to protect shrimp against WSSV infection. PmRab7 and VP28 were modified by N-terminal tagging to the C-terminal half of S. cerevisiae α-agglutinin. DNA fragments, harboring fused-gene expression cassettes under control of an alcohol oxidase I (AOX1) promoter were constructed and used to transform the yeast cells. Immunofluorescence microscopy with antibodies specific to both proteins demonstrated that mutated PmRab7 (mPmRab7) and partial VP28 (pVP28) were localized on the cell surfaces of the respective clones, and fluorescence intensity for each was significantly higher than that of control cells by flow cytometry. Enzyme-linked immunosorbant assay (ELISA) using cells displaying mPmRab7 or pVP28 revealed that the binding of specific antibodies for each was dose-dependent, and could be saturated. In addition, the binding of mPmRab7-expressing cells with free VP28, and vice versa was dose dependent. Binding between the two surface-expressed proteins was confirmed by an assay showing agglutination between cells expressing complementary mPmRab7 and pVP28. In summary, our genetically engineered P. pastoris can display biologically active mPmRab7 and pVP28 and is now ready for evaluation of efficacy in protecting shrimp against WSSV by oral

  15. Identification of domains of the Tomato spotted wilt virus NSm protein involved in tubule formation, movement and symptomatology.

    PubMed

    Li, Weimin; Lewandowski, Dennis J; Hilf, Mark E; Adkins, Scott

    2009-07-20

    Deletion and alanine-substitution mutants of the Tomato spotted wilt virus NSm protein were generated to identify domains involved in tubule formation, movement and symptomatology using a heterologous Tobacco mosaic virus expression system. Two regions of NSm, G(19)-S(159) and G(209)-V(283), were required for both tubule formation in protoplasts and cell-to-cell movement in plants, indicating a correlation between these activities. Three amino acid groups, D(154), EYKK(205-208) and EEEEE(284-288) were linked with long-distance movement in Nicotiana benthamiana. EEEEE(284-288) was essential for NSm-mediated long-distance movement, whereas D(154) was essential for tubule formation and cell-to-cell movement; indicating separate genetic controls for cell-to-cell and long-distance movement. The region I(57)-N(100) was identified as the determinant of foliar necrosis in Nicotiana benthamiana, and mutagenesis of HH(93-94) greatly reduced necrosis. These findings are likely applicable to other tospovirus species, especially those within the 'New World' group as NSm sequences are highly conserved. PMID:19481775

  16. High-resolution spot-scan electron microscopy of microcrystals of an alpha-helical coiled-coil protein.

    PubMed

    Bullough, P A; Tulloch, P A

    1990-09-01

    We describe the electron microscopy of a crystalline assembly of an alpha-helical coiled-coil protein extracted from the ootheca of the praying mantis. Electron diffraction patterns of unstained crystals show crystal lattice sampling of the coiled-coil molecular transform to a resolution beyond 1.5 A. Using a "spot-scan" method of electron imaging, micrographs of unstained crystals have been obtained that visibly diffract laser light from crystal spacings as small as 4.3 A. A projection map was calculated to 4 A using electron diffraction amplitudes and phases from computer-processed images. The projection map clearly shows modulations in density arising from the 5.1 A alpha-helical repeat, the first time this type of modulation has been revealed by electron microscopy. The crystals have p2 plane group symmetry with a = 92.4 A, b = 150.7 A, y = 92.4 degrees. Examination of tilted specimens shows that c is approximately 18 A, indicating that the unit cell is only one molecule thick. A preliminary interpretation shows tightly packed molecules some 400 A long lying with their long axes in the plane of the projection. The molecules have a coiled-coil configuration for most of their length. The possible modes of packing of the molecules in three dimensions are discussed. PMID:2398496

  17. Immune modulations and protection by translationally controlled tumor protein (TCTP) in Fenneropenaeus indicus harboring white spot syndrome virus infection.

    PubMed

    Rajesh, S; Kamalakannan, V; Narayanan, R B

    2014-07-01

    Fenneropenaeus indicus translationally controlled tumor protein (Fi-TCTP) was cloned and expressed using pET 100a-D-TOPO in prokaryotic expression system and it exhibited putative antioxidant activity as assessed in vitro by enhanced growth of Escherichia coli (E. coli) in presence of hydrogen peroxide. The protective efficacy of recombinant Fi-TCTP (rFi-TCTP) was evaluated in F. indicus by intramuscular and oral administration. Intramuscular injection of rFi-TCTP to shrimps, on subsequent white spot syndrome virus (WSSV) infection exhibited 42% relative percent survival. To understand the mechanism of protection, immunological parameters such as reactive oxygen species (ROS), phenoloxidase and mitochondrial membrane potential (MMP) were assessed in early (24h) and late (60h) stages of infection. rFi-TCTP pretreatment significantly lowers the WSSV induced ROS generation and respiratory burst during early and late stages of infection. Further, WSSV induced apoptotic changes such as reduced haemocyte count, loss in MMP and DNA fragmentation were significantly reduced during early and late stage of infection upon rFi-TCTP administration. Hence, the immunomodulatory studies suggest that protective effect of rFi-TCTP in treated shrimps, might be due to the reduction in ROS and apoptosis, following decreased mitochondrial damage together with reduced phenoloxidase activity and respiratory burst. PMID:24837973

  18. Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC-MS/MS. 1. Preparation of more than 4000 native protein maps.

    PubMed

    Jin, Ya; Zhang, Jun; Yuan, Qi; Manabe, Takashi; Tan, Wen

    2015-08-01

    Soluble proteins of human bronchial smooth muscle cells (HBSMC) were separated by nondenaturing micro 2DE and a 30 mm × 40 mm area of the CBB-stained slab gel (1.0 mm thick) was cut into 1.1 mm × 1.1 mm squares, then the proteins in the 972 gel pieces (squares) were applied to quantitative LC-MS/MS. Grid-cutting of the gel was employed to; (i) ensure the total analysis of the proteins in the area, (ii) standardize the conditions of analysis by LC-MS/MS, (iii) reconstruct the protein distribution patterns from the quantity data [1]. Totally 4323 proteins were identified in successfully analyzed 967 squares and the quantity distribution of each was reconstructed as a color density pattern (a native protein map). The quantity of the proteins distributed from 3.6% to 1 × 10(-5) % of the total protein quantity in the grid area. Each protein map was characterized by several features, including the position of quantity peak square, number of detected squares, and degree of concentration (focused or dispersed). About 4% of the proteins were detected in 100 or more squares, suggesting that they might be ubiquitous and interacting with other proteins. In contrast, many proteins showed more concentrated quantity distribution and the quantity peak positions of 565 proteins with a defined degree of concentration were summarized into a quantity peak map. These results for the first time visualized the distribution patterns of cellular proteins on a nondenaturing 2D gel. PMID:25931155

  19. Identification of proteins from Mycobacterium tuberculosis missing in attenuated Mycobacterium bovis BCG strains.

    PubMed

    Mattow, J; Jungblut, P R; Schaible, U E; Mollenkopf, H J; Lamer, S; Zimny-Arndt, U; Hagens, K; Müller, E C; Kaufmann, S H

    2001-08-01

    A proteome approach, combining high-resolution two-dimensional electrophoresis (2-DE) with mass spectrometry, was used to compare the cellular protein composition of two virulent strains of Mycobacterium tuberculosis with two attenuated strains of Mycobacterium bovis Bacillus Calmette-Guerin (BCG), in order to identify unique proteins of these strains. Emphasis was given to the identification of M. tuberculosis specific proteins, because we consider these proteins to represent putative virulence factors and interesting candidates for vaccination and diagnosis of tuberculosis. The genome of M. tuberculosis strain H37Rv comprises nearly 4000 predicted open reading frames. In contrast, the separation of proteins from whole mycobacterial cells by 2-DE resulted in silver-stained patterns comprising about 1800 distinct protein spots. Amongst these, 96 spots were exclusively detected either in the virulent (56 spots) or in the attenuated (40 spots) mycobacterial strains. Fifty-three of these spots were analyzed by mass spectrometry, of which 41 were identified, including 32 M. tuberculosis specific spots. Twelve M. tuberculosis specific spots were identified as proteins, encoded by genes previously reported to be deleted in M. bovis BCG. The remaining 20 spots unique for M. tuberculosis were identified as proteins encoded by genes that are not known to be missing in M. bovis BCG. PMID:11565788

  20. A Comparison of Antiserum and Protein A as Secondary Reagents to Assess Toxoplasma gondii Antibody Titers in Cats and Spotted Hyenas.

    PubMed

    Wait, L F; Srour, A; Smith, I G; Cassey, P; Sims, S K; McAllister, M M

    2015-06-01

    Toxoplasma gondii is a protozoal parasite with worldwide distribution that is able to infect a wide variety of mammals and birds. Our main goal was to screen for T. gondii antibody titers in a previously untested species, the spotted hyena ( Crocuta crocuta); however, this goal first required us to investigate serological procedures that could be suitable for hyenas. Cats are the closest domestic relations of hyenas, so T. gondii antibody titers were first compared in 26 feral cats with specific or nonspecific fluorophore-labeled secondary reagents, i.e., anti-cat IgG or protein A. Substitution of anti-cat IgG with protein A caused a statistically significant drop in titer measurements in cats (P = 0.01) with a reduction of the geometric mean titer equivalent to 1 doubling-dilution. The same procedures were then applied to captive spotted hyenas. Titers measured in 9 of 10 hyenas were identical whether anti-cat IgG or protein A was used as the secondary reagent: 5 had titers <1:16, 2 had titers of 1:16, and 2 had titers of 1:32. One hyena had maximum titers of 1:64 or 1:32 when anti-cat IgG or protein A was used, respectively. The use of protein A as the secondary reagent in serologic assays can be applied to a range of mammalian species and seems unlikely to affect test specificity; however, the use of protein A may reduce test sensitivity, as suggested in the present study using cats. Despite a control program, some exposure to T. gondii had occurred in the Zoo's spotted hyenas. PMID:25710628

  1. Spotted inflation

    SciTech Connect

    Matsuda, Tomohiro

    2010-11-01

    We describe new scenarios for generating curvature perturbations when inflaton (curvaton) has significant interactions. We consider a ''spot'', which arises from interactions associated with an enhanced symmetric point (ESP) on the trajectory. Our first example uses the spot to induce a gap in the field equation. We observe that the gap in the field equation may cause generation of curvature perturbation if it does not appear simultaneous in space. The mechanism is similar to the scenario of inhomogeneous phase transition. Then we observe that the spot interactions may initiate warm inflation in the cold Universe. Creation of cosmological perturbation is discussed in relation to the inflaton dynamics and the modulation associated with the spot interactions.

  2. Spot Dynamics

    NASA Astrophysics Data System (ADS)

    Houben, Howard

    2012-10-01

    What is the Great Red Spot? What are “spots” in general? The presence of many spots and similar features on Jupiter, the other giant planets, and the sun argues for a simple explanation based on conditions common to these bodies (but generally absent in terrestrial atmospheres). Consider two nearly conserved quantities: potential temperature (θ) and potential vorticity (PV). θ is a measure of entropy, which can only be modified by diabatic processes, and therefore atmospheric motions are predominantly along θ-surfaces. PV is the component of the vorticity perpendicular to the θ-surface. It therefore describes most of the motion along these θ-surfaces. It can be rigorously demonstrated that PV cannot be transported across θ-surfaces. In the deep atmospheres of the giant planets and the sun, the tropopause is a level of minimum θ (with convectively unstable negative θ gradients below in the troposphere and stable gradients above in the stratosphere). These fluid bodies also have strong variations of θ with latitude (belts and zones). Baroclinic instability is a process which leads to longitude variations of θ. So it is possible for θ-surfaces to close on themselves around a minimum, with PV confined to these surfaces. The enclosed volume is a spot. The integrated PV over the spot is 0! (Low PV corresponds to anti-cyclonic motion.) The closed θ-surfaces extend above the tropopause and can have deep roots (since θ gradients in the troposphere are generally smaller in magnitude than those in the stratosphere). Details of the flow within the spot depend on boundary conditions (i.e., the surrounding flow and, for sunspots, magnetic fields) and the horizontal/vertical aspect ratio of the spot. Interactions with other spots depend on the θ values of their respective boundaries. In terrestrial atmospheres, the intersection of many low-θ surfaces with the ground inhibits spot formation.

  3. Proteomic Screening of Antigenic Proteins from the Hard Tick, Haemaphysalis longicornis (Acari: Ixodidae)

    PubMed Central

    Kim, Young-Ha; slam, Mohammad Saiful; You, Myung-Jo

    2015-01-01

    Proteomic tools allow large-scale, high-throughput analyses for the detection, identification, and functional investigation of proteome. For detection of antigens from Haemaphysalis longicornis, 1-dimensional electrophoresis (1-DE) quantitative immunoblotting technique combined with 2-dimensional electrophoresis (2-DE) immunoblotting was used for whole body proteins from unfed and partially fed female ticks. Reactivity bands and 2-DE immunoblotting were performed following 2-DE electrophoresis to identify protein spots. The proteome of the partially fed female had a larger number of lower molecular weight proteins than that of the unfed female tick. The total number of detected spots was 818 for unfed and 670 for partially fed female ticks. The 2-DE immunoblotting identified 10 antigenic spots from unfed females and 8 antigenic spots from partially fed females. Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF) of relevant spots identified calreticulin, putative secreted WC salivary protein, and a conserved hypothetical protein from the National Center for Biotechnology Information and Swiss Prot protein sequence databases. These findings indicate that most of the whole body components of these ticks are non-immunogenic. The data reported here will provide guidance in the identification of antigenic proteins to prevent infestation and diseases transmitted by H. longicornis. PMID:25748713

  4. PRODUCTION OF POLYCLONAL ANTIBODIES AGAINST PELARGONIUM ZONATE SPOT VIRUS COAT PROTEIN EXPRESSED IN ESCHERICHIA COLI AND APPLICATION FOR IMMUNODIAGNOSIS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pelargonium zonate spot virus (PZSV), a new emerging disease on tomato in the United States, has been classified as the first member of new proposed genus, Anulavirus, within the family Bromoviridae and characterized as having unstable virions with weakly immunogenic properties. To develop serologic...

  5. SPOT Program

    NASA Technical Reports Server (NTRS)

    Smith, Jason T.; Welsh, Sam J.; Farinetti, Antonio L.; Wegner, Tim; Blakeslee, James; Deboeck, Toni F.; Dyer, Daniel; Corley, Bryan M.; Ollivierre, Jarmaine; Kramer, Leonard; Zimmerman, Patrick L.; Khatri, Reshma

    2010-01-01

    A Spacecraft Position Optimal Tracking (SPOT) program was developed to process Global Positioning System (GPS) data, sent via telemetry from a spacecraft, to generate accurate navigation estimates of the vehicle position and velocity (state vector) using a Kalman filter. This program uses the GPS onboard receiver measurements to sequentially calculate the vehicle state vectors and provide this information to ground flight controllers. It is the first real-time ground-based shuttle navigation application using onboard sensors. The program is compact, portable, self-contained, and can run on a variety of UNIX or Linux computers. The program has a modular objec-toriented design that supports application-specific plugins such as data corruption remediation pre-processing and remote graphics display. The Kalman filter is extensible to additional sensor types or force models. The Kalman filter design is also strong against data dropouts because it uses physical models from state and covariance propagation in the absence of data. The design of this program separates the functionalities of SPOT into six different executable processes. This allows for the individual processes to be connected in an a la carte manner, making the feature set and executable complexity of SPOT adaptable to the needs of the user. Also, these processes need not be executed on the same workstation. This allows for communications between SPOT processes executing on the same Local Area Network (LAN). Thus, SPOT can be executed in a distributed sense with the capability for a team of flight controllers to efficiently share the same trajectory information currently being computed by the program. SPOT is used in the Mission Control Center (MCC) for Space Shuttle Program (SSP) and International Space Station Program (ISSP) operations, and can also be used as a post -flight analysis tool. It is primarily used for situational awareness, and for contingency situations.

  6. Development of an integrated approach for evaluation of 2-D gel image analysis: Impact of multiple proteins in single spots on comparative proteomics in conventional 2-D gel/MALDI workflow

    Technology Transfer Automated Retrieval System (TEKTRAN)

    With 2-D gel mapping, it is often observed that essentially identical proteins migrate to different positions in the gel, while some seemingly well-resolved protein spots consist of multiple proteins. These observations can undermine the validity of gel-based comparative proteomic studies. Through...

  7. Effective protein extraction protocol for proteomics studies of Jerusalem artichoke leaves.

    PubMed

    Zhang, Meide; Shen, Shihua

    2013-07-01

    Protein extraction is a crucial step for proteomics studies. To establish an effective protein extraction protocol suitable for two-dimensional electrophoresis (2DE) analysis in Jerusalem artichoke (Helianthus tuberosus L.), three different protein extraction methods-trichloroacetic acid/acetone, Mg/NP-40, and phenol/ammonium acetate-were evaluated using Jerusalem artichoke leaves as source materials. Of the three methods, trichloroacetic acid/acetone yielded the best protein separation pattern and highest number of protein spots in 2DE analysis. Proteins highly abundant in leaves, such as Rubisco, are typically problematic during leaf 2DE analysis, however, and this disadvantage was evident using trichloroacetic acid/acetone. To reduce the influence of abundant proteins on the detection of low-abundance proteins, we optimized the trichloroacetic acid/acetone method by incorporating a PEG fractionation approach. After optimization, 363 additional (36.2%) protein spots were detected on the 2DE gel. Our results suggest that trichloroacetic acid/acetone method is a better protein extraction technique than Mg/NP-40 and phenol/ammonium acetate in Jerusalem artichoke leaf 2DE analysis, and that trichloroacetic acid/acetone method combined with PEG fractionation procedure is the most effective approach for leaf 2DE analysis of Jerusalem artichoke. PMID:23630184

  8. Comparison of first dimension IPG and NEPHGE techniques in two-dimensional gel electrophoresis experiment with cytosolic unfolded protein response in Saccharomyces cerevisiae

    PubMed Central

    2013-01-01

    Background Two-dimensional gel electrophoresis (2DE) is one of the most popular methods in proteomics. Currently, most 2DE experiments are performed using immobilized pH gradient (IPG) in the first dimension; however, some laboratories still use carrier ampholytes-based isoelectric focusing technique. The aim of this study was to directly compare IPG-based and non-equilibrium pH gradient electrophoresis (NEPHGE)-based 2DE techniques by using the same samples and identical second dimension procedures. We have used commercially available Invitrogen ZOOM IPGRunner and WITAvision systems for IPG and NEPHGE, respectively. The effectiveness of IPG-based and NEPHGE-based 2DE methods was compared by analysing differential protein expression during cytosolic unfolded protein response (UPR-Cyto) in Saccharomyces cerevisiae. Results Protein loss during 2DE procedure was higher in IPG-based method, especially for basic (pI > 7) proteins. Overall reproducibility of spots was slightly better in NEPHGE-based method; however, there was a marked difference when evaluating basic and acidic protein spots. Using Coomassie staining, about half of detected basic protein spots were not reproducible by IPG-based 2DE, whereas NEPHGE-based method showed excellent reproducibility in the basic gel zone. The reproducibility of acidic proteins was similar in both methods. Absolute and relative volume variability of separate protein spots was comparable in both 2DE techniques. Regarding proteomic analysis of UPR-Cyto, the results exemplified parameters of general comparison of the methods. New highly basic protein Sis1p, overexpressed during UPR-Cyto stress, was identified by NEPHGE-based 2DE method, whereas IPG-based method showed unreliable results in the basic pI range and did not provide any new information on basic UPR-Cyto proteins. In the acidic range, the main UPR-Cyto proteins were detected and quantified by both methods. The drawback of NEPHGE-based 2DE method is its failure to

  9. Crystal Structures of Major Envelope Proteins VP26 and VP28 from White Spot Syndrome Virus Shed Light on Their Evolutionary Relationship

    SciTech Connect

    Tang,X.; Wu, J.; Sivaraman, J.; Hew, C.

    2007-01-01

    White spot syndrome virus (WSSV) is a virulent pathogen known to infect various crustaceans. It has bacilliform morphology with a tail-like appendage at one end. The envelope consists of four major proteins. Envelope structural proteins play a crucial role in viral infection and are believed to be the first molecules to interact with the host. Here, we report the localization and crystal structure of major envelope proteins VP26 and VP28 from WSSV at resolutions of 2.2 and 2.0 {angstrom}, respectively. These two proteins alone account for approximately 60% of the envelope, and their structures represent the first two structural envelope proteins of WSSV. Structural comparisons among VP26, VP28, and other viral proteins reveal an evolutionary relationship between WSSV envelope proteins and structural proteins from other viruses. Both proteins adopt {beta}-barrel architecture with a protruding N-terminal region. We have investigated the localization of VP26 and VP28 using immunoelectron microscopy. This study suggests that VP26 and VP28 are located on the outer surface of the virus and are observed as a surface protrusion in the WSSV envelope, and this is the first convincing observation for VP26. Based on our studies combined with the literature, we speculate that the predicted N-terminal transmembrane region of VP26 and VP28 may anchor on the viral envelope membrane, making the core {beta}-barrel protrude outside the envelope, possibly to interact with the host receptor or to fuse with the host cell membrane for effective transfer of the viral infection. Furthermore, it is tempting to extend this host interaction mode to other structural viral proteins of similar structures. Our finding has the potential to extend further toward drug and vaccine development against WSSV.

  10. Evidence that the nonstructural protein of Tomato spotted wilt virus is the avirulence determinant in the interaction with resistant pepper carrying the TSW gene.

    PubMed

    Margaria, P; Ciuffo, M; Pacifico, D; Turina, M

    2007-05-01

    All known pepper cultivars resistant to Tomato spotted wilt virus (TSWV) possess a single dominant resistance gene, Tsw. Recently, naturally occurring resistance-breaking (RB) TSWV strains have been identified, causing major concerns. We used a collection of such strains to identify the specific genetic determinant that allows the virus to overcome the Tsw gene in Capsicum spp. A reverse genetic approach is still not feasible for TSWV; therefore, we analyzed reassortants between wild-type (WT) and RB strains. Our results confirmed that the S RNA, which encodes both the nucleocapsid protein (N) and a nonstructural protein (NSs), carries the genetic determinant responsible for Tsw resistance breakdown. We then used full-length S RNA segments or the proteins they encode to compare the sequences of WT and related RB strains, and obtained indirect evidence that the NSs protein is the avirulence factor in question. Transient expression of NSs protein from WT and RB strains showed that they both can equally suppress post-transcriptional gene silencing (PTGS). Moreover, biological characterization of two RB strains carrying deletions in the NSs protein showed that NSs is important in maintaining TSWV infection in newly emerging leaves over time, preventing recovery. Analysis of another RB strain phenotype allowed us to conclude that local necrotic response is not sufficient for resistance in Capsicum spp. carrying the Tsw gene. PMID:17506332

  11. Expression profile of key immune-related genes in Penaeus monodon juveniles after oral administration of recombinant envelope protein VP28 of white spot syndrome virus.

    PubMed

    Thomas, Ancy; Sudheer, Naduvilamuriparampu Saidumuhammed; Kiron, Viswanath; Bright Singh, Issac S; Narayanan, Rangarajan Badri

    2016-07-01

    White spot syndrome virus (WSSV) is the most catastrophic pathogen the shrimp industry has ever encountered. VP28, the abundant envelope protein of WSSV was expressed in bacteria, the purified protein administered orally to Penaeus monodon juveniles and its immune modulatory effects examined. The results indicated significant up-regulation of caspase, penaeidin, crustin, astakine, syntenin, PmRACK, Rab7, STAT and C-type lectin in animals orally administered with this antigen. This revealed the immune modulations in shrimps followed by oral administration of rVP28P which resulted in the reduced transcription of viral gene vp28 and delay in mortality after WSSV challenge. The study suggests the potential of rVP28P to elicit a non-specific immune stimulation in shrimps. PMID:27154537

  12. The bioactivity of teleost IL-6: IL-6 protein in orange-spotted grouper (Epinephelus coioides) induces Th2 cell differentiation pathway and antibody production.

    PubMed

    Chen, Hsin-Hung; Lin, Han-Tso; Foung, Yi-Fan; Han-You Lin, John

    2012-10-01

    Interleukin 6 (IL-6) is a protein secreted by T cells and macrophages and plays an important role in immune response. IL-6 regulates the proliferation and differentiation of T cells, and elicits immunoglobulin production in B cells. In this study, the cDNA il-6 (gil-6) sequence of the orange spotted grouper (Epinephelus coioides) was obtained. The deduced IL-6 (gIL-6) protein comprised 223 amino acids, the sequence shared approximately 30% similarity with mammalian IL-6, and between 47% and 69% similarity with other available teleost IL-6. The protein comprises the signal peptide, the IL-6 family signature, and conserved amino acid residues found in IL-6 sequences of other teleost. In order to understand the bioactivity and influence of gIL-6 on humoral immune response, recombinant gIL-6 (rgIL-6) synthesized by prokaryotes was injected into orange spotted groupers, and the immune-related gene expression at various times in various organs was observed. Our results revealed that the Th1 specific transcription factor t-bet was down-regulated and Th2 specific transcription factors gata3, and c-maf were up-regulated in immune organs, following IL-6 stimulation. Additionally, higher levels of igm mRNA and translated protein were detected in rgIL-6 stimulated fish. These results indicate that IL-6 in groupers regulates the differentiation of naїve T helper cells into Th2 cells and elicits the production of antibodies. PMID:22858412

  13. Fatty acid binding protein 10 in the orange-spotted grouper (Epinephelus coioides): characterization and regulation under pH and temperature stress.

    PubMed

    Qi, Zeng-hua; Liu, Yu-feng; Wang, Wei-Na; Xin, Yu; Xie, Fu-xing; Wang, An-Li

    2012-04-01

    We have isolated and characterized a fatty acid binding protein from the liver of the orange-spotted grouper (Epinephelus coioides). Amino acid sequence similarity of the Ec-FABP (E. coioides-FABP) was highest to FABP10s isolated from the livers of catfish, chicken, salamander and iguana. The open-reading frame of the Ec-FABP codes for a protein of 14.0 kDa with a calculated isoelectric point of 8.5. We first expressed a FABP10 protein from orange-spotted grouper (E. coioides) in Pichia pastoris, and then characterized the antioxidative potential of our recombinant Ec-FABP by DCF fluorescence assay. RT-PCR assays showed that endogenous Ec-FABP mRNA is most strongly expressed in liver with the most abundance and intestine. Change in the groupers' blood cells respiratory burst activity was examined during and after exposure to the pH and temperature stress using flow cytometry. Further analysis of Ec-FABP gene expression in liver tissue by quantitative real-time PCR demonstrated that Ec-FABP transcript levels increased when the fish were exposed to both pH and temperature stress, but the time when its mRNA expression level peaked differed under these stresses. Western blot analyses confirmed that the Ec-FABP protein was strongly expressed in the liver after exposure to the pH and temperature stress. These results suggest that Ec-FABP expression is stimulated by pH and temperature stress and that it may play important roles in general adaptive and antioxidant responses. PMID:22182678

  14. Identification of a Novel Nonstructural Protein, VP9, from White Spot Syndrome Virus: Its Structure Reveals a Ferredoxin Fold with Specific Metal Binding Sites

    SciTech Connect

    Liu,Y.; Wu, J.; Song, J.; Sivaraman, J.; Hew, C.

    2006-01-01

    White spot syndrome virus (WSSV) is a major pathogen in shrimp aquaculture. VP9, a full-length protein of WSSV, encoded by open reading frame wsv230, was identified for the first time in the infected Penaeus monodon shrimp tissues, gill, and stomach as a novel, nonstructural protein by Western blotting, mass spectrometry, and immunoelectron microscopy. Real-time reverse transcription-PCR demonstrated that the transcription of VP9 started from the early to the late stage of WSSV infection as a major mRNA species. The structure of full-length VP9 was determined by both X-ray and nuclear magnetic resonance (NMR) techniques. It is the first structure to be reported for WSSV proteins. The crystal structure of VP9 revealed a ferredoxin fold with divalent metal ion binding sites. Cadmium sulfate was found to be essential for crystallization. The Cd2+ ions were bound between the monomer interfaces of the homodimer. Various divalent metal ions have been titrated against VP9, and their interactions were analyzed using NMR spectroscopy. The titration data indicated that VP9 binds with both Zn2+ and Cd2+. VP9 adopts a similar fold as the DNA binding domain of the papillomavirus E2 protein. Based on our present investigations, we hypothesize that VP9 might be involved in the transcriptional regulation of WSSV, a function similar to that of the E2 protein during papillomavirus infection of the host cells.

  15. The novel white spot syndrome virus-induced gene, PmERP15, encodes an ER stress-responsive protein in black tiger shrimp, Penaeus monodon.

    PubMed

    Leu, Jiann-Horng; Liu, Kuan-Fu; Chen, Kuan-Yu; Chen, Shu-Hwa; Wang, Yu-Bin; Lin, Chung-Yen; Lo, Chu-Fang

    2015-04-01

    By microarray screening, we identified a white spot syndrome virus (WSSV)-strongly induced novel gene in gills of Penaeus monodon. The gene, PmERP15, encodes a putative transmembrane protein of 15 kDa, which only showed some degree of similarity (54-59%) to several unknown insect proteins, but had no hits to shrimp proteins. RT-PCR showed that PmERP15 was highly expressed in the hemocytes, heart and lymphoid organs, and that WSSV-induced strong expression of PmERP15 was evident in all tissues examined. Western blot analysis likewise showed that WSSV strongly up-regulated PmERP15 protein levels. In WSSV-infected hemocytes, immunofluorescence staining showed that PmERP15 protein was colocalized with an ER enzyme, protein disulfide isomerase, and in Sf9 insect cells, PmERP15-EGFP fusion protein colocalized with ER -Tracker™ Red dye as well. GRP78, an ER stress marker, was found to be up-regulated in WSSV-infected P. monodon, and both PmERP15 and GRP78 were up-regulated in shrimp injected with ER stress inducers tunicamycin and dithiothreitol. Silencing experiments showed that although PmERP15 dsRNA-injected shrimp succumbed to WSSV infection more rapidly, the WSSV copy number had no significant changes. These results suggest that PmERP15 is an ER stress-induced, ER resident protein, and its induction in WSSV-infected shrimp is caused by the ER stress triggered by WSSV infection. Furthermore, although PmERP15 has no role in WSSV multiplication, its presence is essential for the survival of WSSV-infected shrimp. PMID:25499032

  16. Mongolian spots.

    PubMed

    Gupta, Divya; Thappa, Devinder Mohan

    2013-01-01

    Mongolian spots (MS) are birthmarks that are present at birth and their most common location is sacrococcygeal or lumbar area. Lesions may be single or multiple and usually involve < 5% total body surface area. They are macular and round, oval or irregular in shape. The color varies from blue to greenish, gray, black or a combination of any of the above. The size varies from few to more than 20 centimetres. Pigmentation is most intense at the age of one year and gradually fades thereafter. It is rarely seen after the age of 6 years. Aberrant MS over occiput, temple, mandibular area, shoulders and limbs may be confused with other dermal melanocytoses and bruises secondary to child abuse, thus necessitating documentation at birth. Although regarded as benign, recent data suggest that MS may be associated with inborn errors of metabolism and neurocristopathies. Mongolian spots usually resolve by early childhood and hence no treatment is generally needed if they are located in the sacral area. However, sometimes it may be required for extrasacral lesions for cosmesis. PMID:23760316

  17. The Cytosolic Nucleoprotein of the Plant-Infecting Bunyavirus Tomato Spotted Wilt Recruits Endoplasmic Reticulum–Resident Proteins to Endoplasmic Reticulum Export Sites[C][W

    PubMed Central

    Ribeiro, Daniela; Jung, Maartje; Moling, Sjef; Borst, Jan Willem; Goldbach, Rob; Kormelink, Richard

    2013-01-01

    In contrast with animal-infecting viruses, few known plant viruses contain a lipid envelope, and the processes leading to their membrane envelopment remain largely unknown. Plant viruses with lipid envelopes include viruses of the Bunyaviridae, which obtain their envelope from the Golgi complex. The envelopment process is predominantly dictated by two viral glycoproteins (Gn and Gc) and the viral nucleoprotein (N). During maturation of the plant-infecting bunyavirus Tomato spotted wilt, Gc localizes at endoplasmic reticulum (ER) membranes and becomes ER export competent only upon coexpression with Gn. In the presence of cytosolic N, Gc remains arrested in the ER but changes its distribution from reticular into punctate spots. Here, we show that these areas correspond to ER export sites (ERESs), distinct ER domains where glycoprotein cargo concentrates prior to coat protein II vesicle–mediated transport to the Golgi. Gc concentration at ERES is mediated by an interaction between its cytoplasmic tail (CT) and N. Interestingly, an ER-resident calnexin provided with Gc-CT was similarly recruited to ERES when coexpressed with N. Furthermore, disruption of actin filaments caused the appearance of a larger amount of smaller ERES loaded with N-Gc complexes, suggesting that glycoprotein cargo concentration acts as a trigger for de novo synthesis of ERES. PMID:24045023

  18. Tissue protein imaging at 1 μm laser spot diameter for high spatial resolution and high imaging speed using transmission geometry MALDI TOF MS

    PubMed Central

    Zavalin, Andre; Yang, Junhai; Hayden, Kevin; Vestal, Marvin; Caprioli, Richard M.

    2015-01-01

    We have achieved protein imaging mass spectrometry capabilities at sub-cellular spatial resolution and at high acquisition speed by integrating a transmission geometry ion source with time of flight mass spectrometry. The transmission geometry principle allowed us to achieve a 1 μm laser spot diameter on target. A minimal raster step size of the instrument was 2.5 μm. Use of 2,5-dihydroxyacetophenone robotically sprayed on top of a tissue sample as a matrix together with additional sample preparation steps resulted in single pixel mass spectra from mouse cerebellum tissue sections having more than 20 peaks in a range 3–22 kDa. Mass spectrometry images were acquired in a standard step raster microprobe mode at 5 pixels/s and in a continuous raster mode at 40 pixels/s. PMID:25673247

  19. Dystrophin Hot-Spot Mutants Leading to Becker Muscular Dystrophy Insert More Deeply into Membrane Models than the Native Protein.

    PubMed

    Ameziane-Le Hir, Sarah; Paboeuf, Gilles; Tascon, Christophe; Hubert, Jean-François; Le Rumeur, Elisabeth; Vié, Véronique; Raguénès-Nicol, Céline

    2016-07-26

    Dystrophin (DYS) is a membrane skeleton protein whose mutations lead to lethal Duchenne muscular dystrophy or to the milder Becker muscular dystrophy (BMD). One third of BMD "in-frame" exon deletions are located in the region that codes for spectrin-like repeats R16 to R21. We focused on four prevalent mutated proteins deleted in this area (called RΔ45-47, RΔ45-48, RΔ45-49, and RΔ45-51 according to the deleted exon numbers), analyzing protein/membrane interactions. Two of the mutants, RΔ45-48 and RΔ45-51, led to mild pathologies and displayed a similar triple coiled-coil structure as the full-length DYS R16-21, whereas the two others, RΔ45-47 and RΔ45-49, induced more severe pathologies and showed "fractional" structures unrelated to the normal one. To explore lipid packing, small unilamellar liposomes (SUVs) and planar monolayers were used at various initial surface pressures. The dissociation constants determined by microscale thermophoresis (MST) were much higher for the full-length DYS R161-21 than for the mutants; thus the wild type protein has weaker SUV binding. Comparing surface pressures after protein adsorption and analysis of atomic force microscopy images of mixed protein/lipid monolayers revealed that the mutants insert more into the lipid monolayer than the wild type does. In fact, in both models every deletion mutant showed more interactions with membranes than the full-length protein did. This means that mutations in the R16-21 part of dystrophin disturb the protein's molecular behavior as it relates to membranes, regardless of whether the accompanying pathology is mild or severe. PMID:27367833

  20. Combination of virtual and experimental 2DE together with ESI LC-MS/MS gives a clearer view about proteomes of human cells and plasma.

    PubMed

    Naryzhny, Stanislav N; Zgoda, Victor G; Maynskova, Maria A; Novikova, Svetlana E; Ronzhina, Natalia L; Vakhrushev, Igor V; Khryapova, Elena V; Lisitsa, Andrey V; Tikhonova, Olga V; Ponomarenko, Elena A; Archakov, Alexander I

    2016-01-01

    Virtual and experimental 2DE coupled with ESI LC-MS/MS was introduced to obtain better representation of the information about human proteome. The proteins from HEPG2 cells and human blood plasma were run by 2DE. After staining and protein spot identification by MALDI-TOF MS, the protein maps were generated. The experimental physicochemical parameters (pI/Mw) of the proteoforms further detected by ESI LC-MS/MS in these spots were obtained. Next, the theoretical pI and Mw of identified proteins were calculated using program Compute pI/Mw (http://web.expasy.org/compute_pi/pi_tool-doc.html). Accordingly, the relationship between theoretical and experimental parameters was analyzed, and the correlation plots were built. Additionally, virtual/experimental information about different protein species/proteoforms from the same genes was extracted. As it was revealed from the plots, the major proteoforms detected in HepG2 cell line have pI/Mw parameters similar to theoretical values. In opposite, the minor protein species have mainly very different from theoretical pI and Mw parameters. A similar situation was observed in plasma in much higher degree. It means that minor protein species are heavily modified in cell and even more in plasma proteome. PMID:26454001

  1. Activating Transcription Factor 4 and X Box Binding Protein 1 of Litopenaeus vannamei Transcriptional Regulated White Spot Syndrome Virus Genes Wsv023 and Wsv083

    PubMed Central

    Li, Xiao-Yun; Pang, Li-Ran; Chen, Yong-Gui; Weng, Shao-Ping; Yue, Hai-Tao; Zhang, Ze-Zhi; Chen, Yi-Hong; He, Jian-Guo

    2013-01-01

    In response to endoplasmic reticulum (ER) stress, the signaling pathway termed unfolded protein response (UPR) is activated. To investigate the role of UPR in Litopenaeus vannamei immunity, the activating transcription factor 4 (designated as LvATF4) which belonged to a branch of the UPR, the [protein kinase RNA (PKR)-like ER kinase, (PERK)]-[eukaryotic initiation factor 2 subunit alpha (eIF2α)] pathway, was identified and characterized. The full-length cDNA of LvATF4 was 1972 bp long, with an open reading frame of 1299 bp long that encoded a 432 amino acid protein. LvATF4 was highly expressed in gills, intestines and stomach. For the white spot syndrome virus (WSSV) challenge, LvATF4 was upregulated in the gills after 3 hpi and increased by 1.9-fold (96 hpi) compared to the mock-treated group. The LvATF4 knock-down by RNA interference resulted in a lower cumulative mortality of L. vannamei under WSSV infection. Reporter gene assays show that LvATF4 could upregulate the expression of the WSSV gene wsv023 based on the activating transcription factor/cyclic adenosine 3′, 5′-monophosphate response element (ATF/CRE). Another transcription factor of L. vannamei, X box binding protein 1 (designated as LvXBP1), has a significant function in [inositol-requiring enzyme-1(IRE1) – (XBP1)] pathway. This transcription factor upregulated the expression of the WSSV gene wsv083 based on the UPR element (UPRE). These results suggest that in L. vannamei UPR signaling pathway transcription factors are important for WSSV and might facilitate WSSV infection. PMID:23638122

  2. Effects of Fe deficiency on the protein profile of Brassica napus phloem sap

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The aim of this work was to study the effect of Fe deficiency on the protein profile of phloem sap exudates from Brassica napus using 2-DE (IEF-SDS PAGE). The experiment was repeated thrice and two technical replicates per treatment were done. Two hundred sixty-three spots were consistently detected...

  3. The movement protein (NSm) of Tomato spotted wilt virus is the avirulence determinant in the tomato Sw-5 gene-based resistance.

    PubMed

    Peiró, Ana; Cañizares, M Carmen; Rubio, Luis; López, Carmelo; Moriones, Enrique; Aramburu, José; Sánchez-Navarro, Jesús

    2014-10-01

    The avirulence determinant triggering the resistance conferred by the tomato gene Sw-5 against Tomato spotted wilt virus (TSWV) is still unresolved. Sequence comparison showed two substitutions (C118Y and T120N) in the movement protein NSm present only in TSWV resistance-breaking (RB) isolates. In this work, transient expression of NSm of three TSWV isolates [RB1 (T120N), RB2 (C118Y) and non-resistance-breaking (NRB)] in Nicotiana benthamiana expressing Sw-5 showed a hypersensitive response (HR) only with NRB. Exchange of the movement protein of Alfalfa mosaic virus (AMV) with NSm supported cell-to-cell and systemic transport of the chimeric AMV RNAs into N. tabacum with or without Sw-5, except for the constructs with NBR when Sw-5 was expressed, although RB2 showed reduced cell-to-cell transport. Mutational analysis revealed that N120 was sufficient to avoid the HR, but the substitution V130I was required for systemic transport. Finally, co-inoculation of RB and NRB AMV chimeric constructs showed different prevalence of RB or NBR depending on the presence or absence of Sw-5. These results indicate that NSm is the avirulence determinant for Sw-5 resistance, and mutations C118Y and T120N are responsible for resistance breakdown and have a fitness penalty in the context of the heterologous AMV system. PMID:24690181

  4. Generation of recombinant monoclonal antibodies to study structure-function of envelope protein VP28 of white spot syndrome virus from shrimp

    SciTech Connect

    Wang Yuzhen; Zhang Xiaohua; Yuan Li; Xu Tao; Rao Yu; Li Jia; Dai Heping

    2008-08-08

    White spot syndrome virus (WSSV) is a major pathogen in shrimp aquaculture. VP28 is one of the most important envelope proteins of WSSV. In this study, a recombinant antibody library, as single-chain fragment variable (scFv) format, displayed on phage was constructed using mRNA from spleen cells of mice immunized with full-length VP28 expressed in Escherichia coli. After several rounds of panning, six scFv antibodies specifically binding to the epitopes in the N-terminal, middle, and C-terminal regions of VP28, respectively, were isolated from the library. Using these scFv antibodies as tools, the epitopes in VP28 were located on the envelope of the virion by immuno-electron microscopy. Neutralization assay with these antibodies in vitro suggested that these epitopes may not be the attachment site of WSSV to host cell receptor. This study provides a new way to investigate the structure and function of the envelope proteins of WSSV.

  5. The DNA virus white spot syndrome virus uses an internal ribosome entry site for translation of the highly expressed nonstructural protein ICP35.

    PubMed

    Kang, Shih-Ting; Wang, Han-Ching; Yang, Yi-Ting; Kou, Guang-Hsiung; Lo, Chu-Fang

    2013-12-01

    Although shrimp white spot syndrome virus (WSSV) is a large double-stranded DNA virus (∼300 kbp), it expresses many polycistronic mRNAs that are likely to use internal ribosome entry site (IRES) elements for translation. A polycistronic mRNA encodes the gene of the highly expressed nonstructural protein ICP35, and here we use a dual-luciferase assay to demonstrate that this protein is translated cap independently by an IRES element located in the 5' untranslated region of icp35. A deletion analysis of this region showed that IRES activity was due to stem-loops VII and VIII. A promoterless assay, a reverse transcription-PCR together with quantitative real-time PCR analysis, and a stable stem-loop insertion upstream of the Renilla luciferase open reading frame were used, respectively, to rule out the possibility that cryptic promoter activity, abnormal splicing, or read-through was contributing to the IRES activity. In addition, a Northern blot analysis was used to confirm that only a single bicistronic mRNA was expressed. The importance of ICP35 to viral replication was demonstrated in a double-stranded RNA (dsRNA) interference knockdown experiment in which the mortality of the icp35 dsRNA group was significantly reduced. Tunicamycin was used to show that the α subunit of eukaryotic initiation factor 2 is required for icp35 IRES activity. We also found that the intercalating drug quinacrine significantly inhibited icp35 IRES activity in vitro and reduced the mortality rate and viral copy number in WSSV-challenged shrimp. Lastly, in Sf9 insect cells, we found that knockdown of the gene for the Spodoptera frugiperda 40S ribosomal protein RPS10 decreased icp35 IRES-regulated firefly luciferase activity but had no effect on cap-dependent translation. PMID:24089551

  6. Quantitation of proteinuria by spot urine sampling.

    PubMed

    Agarwal, Indira; Kirubakaran, Chellam; Markandeyulu; Selvakumar

    2004-07-01

    Few studies have shown that calculation of protein/creatinine ratio in a spot urine sample correlates well with the 24-hour urine collection. A study was conducted to compare the accuracy of a spot urinary protein/creatinine ratio (P/C ratio) and urinary dipstick (albustix) with the 24-hour urine protein (24-HUP). Fifty samples from 26 patients were collected. This included a 24-hour urine sample followed by the next voided spot sample. The protein/creatinine ratio was calculated and dipstick (albustix) was performed on the spot sample. This was compared with the 24-hour urine protein excretion. The correlation between the three samples was statistically highly significant (p=<0.001) for all levels of proteinuria. The normal value of protein/creatinine ratio in Indian children was also estimated on 100 normal children attending the OPD and was calculated to be 0.053 (S.E of mean±0.003). PMID:23105455

  7. Finding the sweet spots of inhibition: understanding the targets of a functional antibody against Plasmodium vivax Duffy binding protein

    PubMed Central

    Ntumngia, Francis B.; King, Christopher L.; Adams, John H.

    2014-01-01

    Plasmodium vivax Duffy binding protein region II (DBPII) is an essential ligand for reticulocyte invasion, thereby making this molecule an attractive vaccine candidate against asexual blood-stage P. vivax. Similar to other Plasmodium blood-stage vaccine candidates, strain-specific immunity due to DBPII allelic variation may complicate vaccine efficacy. Targeting immune responses to more conserved epitopes that are potential targets of strain-transcending neutralizing immunity is necessary to avoid induction of strain-specific responses to dominant variant epitopes. In this article, we focus on different approaches to optimize the design of DBP immunogenicity to target conserved epitopes, which is important for developing a broadly effective vaccine against P. vivax. PMID:23068913

  8. Using 7 cm immobilized pH gradient strips to determine levels of clinically relevant proteins in wheat grain extracts

    PubMed Central

    Fekecsová, Sona; Danchenko, Maksym; Uvackova, Lubica; Skultety, Ludovit; Hajduch, Martin

    2015-01-01

    The aim of the work was to test a relatively simple proteomics approach based on phenol extraction and two-dimensional gel electrophoresis (2-DE) with 7 cm immobilized pH gradient strips for the determination of clinically relevant proteins in wheat grain. Using this approach, 157 2-DE spots were quantified in biological triplicate, out of which 55 were identified by matrix-assisted laser desorption/ionization – time of flight tandem mass spectrometry. Clinically relevant proteins associated with celiac disease, wheat dependent exercise induced anaphylaxis, baker’s asthma, and food allergy, were detected in 24 2-DE spots. However, alcohol-soluble gliadins were not detected with this approach. The comparison with a recent quantitative study suggested that gel-based and gel-free proteomics approaches are complementary for the detection and quantification of clinically relevant proteins in wheat grain. PMID:26124766

  9. Phylogenetic analysis of Tomato spotted wilt virus (TSWV) NSs protein demonstrates the isolated emergence of resistance-breaking strains in pepper.

    PubMed

    Almási, Asztéria; Csilléry, Gábor; Csömör, Zsófia; Nemes, Katalin; Palkovics, László; Salánki, Katalin; Tóbiás, István

    2015-02-01

    Resurgence of Tomato spotted wilt virus (TSWV) worldwide as well as in Hungary causing heavy economic losses directed the attention to the factors contributing to the outbreak of this serious epidemics. The introgression of Tsw resistance gene into various pepper cultivars seemed to solve TSWV control, but widely used resistant pepper cultivars bearing the same, unique resistance locus evoked the rapid emergence of resistance-breaking (RB) TSWV strains. In Hungary, the sporadic appearance of RB strains in pepper-producing region was first observed in 2010-2011, but in 2012 it was detected frequently. Previously, the non-structural protein (NSs) encoded by small RNA (S RNA) of TSWV was verified as the avirulence factor for Tsw resistance, therefore we analyzed the S RNA of the Hungarian RB and wild type (WT) isolates and compared to previously analyzed TSWV strains with RB properties from different geographical origins. Phylogenetic analysis demonstrated that the different RB strains had the closest relationship with the local WT isolates and there is no conserved mutation present in all the NSs genes of RB isolates from different geographical origins. According to these results, we concluded that the RB isolates evolved separately in geographic point of view, and also according to the RB mechanism. PMID:25331341

  10. Effects of a Dissostichus mawsoni-CaM recombinant proteins feed additive on the juvenile orange-spotted grouper (Epinephelus coioides) under the acute low temperature challenge.

    PubMed

    Luo, Sheng-Wei; Wang, Wei-Na; Cai, Luo; Qi, Zeng-Hua; Wang, Cong; Liu, Yuan; Peng, Chang-Lian; Chen, Liang-Biao

    2015-10-01

    The effects of Dissostichus mawsoni-Calmodulin (Dm-CaM) on growth performance, enzyme activities, respiratory burst, MDA level and immune-related gene expressions of the orange-spotted grouper (Epinephelus coioides) exposed to the acute low temperature stress were evaluated. The commercial diet supplemented with Dm-CaM protein was fed to the groupers for 6 weeks. No significant difference was observed in the specific growth rates, weight gains and survivals. After the feeding trial, the groupers were exposed to acute low temperature challenge. The groupers fed with Dm-CaM additive diet showed a significant decrease in the respiratory burst activity, while the blood cell number increased significantly at 25 °C by comparing with the control and additive control group. The enzymatic activity of SOD, ACP and ALP increased significantly in Dm-CaM additive group, while MDA level maintained stable with the lowest value. qRT-PCR analysis indicated that the up-regulated transcript expressions of CaM, C3, SOD2, LysC and HSPA4 were observed in Dm-CaM additive group. These results indicated that Dm-CaM additive diet may regulate the grouper immune response to the acute low temperature challenge. PMID:26122279

  11. The ER-Membrane Transport System Is Critical for Intercellular Trafficking of the NSm Movement Protein and Tomato Spotted Wilt Tospovirus.

    PubMed

    Feng, Zhike; Xue, Fan; Xu, Min; Chen, Xiaojiao; Zhao, Wenyang; Garcia-Murria, Maria J; Mingarro, Ismael; Liu, Yong; Huang, Ying; Jiang, Lei; Zhu, Min; Tao, Xiaorong

    2016-02-01

    Plant viruses move through plasmodesmata to infect new cells. The plant endoplasmic reticulum (ER) is interconnected among cells via the ER desmotubule in the plasmodesma across the cell wall, forming a continuous ER network throughout the entire plant. This ER continuity is unique to plants and has been postulated to serve as a platform for the intercellular trafficking of macromolecules. In the present study, the contribution of the plant ER membrane transport system to the intercellular trafficking of the NSm movement protein and Tomato spotted wilt tospovirus (TSWV) is investigated. We showed that TSWV NSm is physically associated with the ER membrane in Nicotiana benthamiana plants. An NSm-GFP fusion protein transiently expressed in single leaf cells was trafficked into neighboring cells. Mutations in NSm that impaired its association with the ER or caused its mis-localization to other subcellular sites inhibited cell-to-cell trafficking. Pharmacological disruption of the ER network severely inhibited NSm-GFP trafficking but not GFP diffusion. In the Arabidopsis thaliana mutant rhd3 with an impaired ER network, NSm-GFP trafficking was significantly reduced, whereas GFP diffusion was not affected. We also showed that the ER-to-Golgi secretion pathway and the cytoskeleton transport systems were not involved in the intercellular trafficking of TSWV NSm. Importantly, TSWV cell-to-cell spread was delayed in the ER-defective rhd3 mutant, and this reduced viral infection was not due to reduced replication. On the basis of robust biochemical, cellular and genetic analysis, we established that the ER membrane transport system serves as an important direct route for intercellular trafficking of NSm and TSWV. PMID:26863622

  12. The ER-Membrane Transport System Is Critical for Intercellular Trafficking of the NSm Movement Protein and Tomato Spotted Wilt Tospovirus

    PubMed Central

    Feng, Zhike; Xue, Fan; Xu, Min; Chen, Xiaojiao; Zhao, Wenyang; Garcia-Murria, Maria J.; Mingarro, Ismael; Liu, Yong; Huang, Ying; Jiang, Lei; Zhu, Min; Tao, Xiaorong

    2016-01-01

    Plant viruses move through plasmodesmata to infect new cells. The plant endoplasmic reticulum (ER) is interconnected among cells via the ER desmotubule in the plasmodesma across the cell wall, forming a continuous ER network throughout the entire plant. This ER continuity is unique to plants and has been postulated to serve as a platform for the intercellular trafficking of macromolecules. In the present study, the contribution of the plant ER membrane transport system to the intercellular trafficking of the NSm movement protein and Tomato spotted wilt tospovirus (TSWV) is investigated. We showed that TSWV NSm is physically associated with the ER membrane in Nicotiana benthamiana plants. An NSm-GFP fusion protein transiently expressed in single leaf cells was trafficked into neighboring cells. Mutations in NSm that impaired its association with the ER or caused its mis-localization to other subcellular sites inhibited cell-to-cell trafficking. Pharmacological disruption of the ER network severely inhibited NSm-GFP trafficking but not GFP diffusion. In the Arabidopsis thaliana mutant rhd3 with an impaired ER network, NSm-GFP trafficking was significantly reduced, whereas GFP diffusion was not affected. We also showed that the ER-to-Golgi secretion pathway and the cytoskeleton transport systems were not involved in the intercellular trafficking of TSWV NSm. Importantly, TSWV cell-to-cell spread was delayed in the ER-defective rhd3 mutant, and this reduced viral infection was not due to reduced replication. On the basis of robust biochemical, cellular and genetic analysis, we established that the ER membrane transport system serves as an important direct route for intercellular trafficking of NSm and TSWV. PMID:26863622

  13. Proteomic analysis of papaya fruit ripening using 2DE-DIGE.

    PubMed

    Nogueira, Silvia Beserra; Labate, Carlos Alberto; Gozzo, Fabio Cesar; Pilau, Eduardo Jorge; Lajolo, Franco Maria; Oliveira do Nascimento, João Roberto

    2012-02-01

    Papayas have a very short green life as a result of their rapid pulp softening as well as their susceptibility to physical injury and mold growth. The ripening-related changes take place very quickly, and there is a continued interest in the reduction of postharvest losses. Proteins have a central role in biological processes, and differential proteomics enables the discrimination of proteins affected during papaya ripening. A comparative analysis of the proteomes of climacteric and pre-climacteric papayas was performed using 2DE-DIGE. Third seven proteins corresponding to spots with significant differences in abundance during ripening were submitted to MS analysis, and 27 proteins were identified and classified into six main categories related to the metabolic changes occurring during ripening. Proteins from the cell wall (alpha-galactosidase and invertase), ethylene biosynthesis (methionine synthase), climacteric respiratory burst, stress response, synthesis of carotenoid precursors (hydroxymethylbutenyl 4-diphosphate synthase, GcpE), and chromoplast differentiation (fibrillin) were identified. There was some correspondence between the identified proteins and the data from previous transcript profiling of papaya fruit, but new, accumulated proteins were identified, which reinforces the importance of differential proteomics as a tool to investigate ripening and provides potentially useful information for maintaining fruit quality and minimizing postharvest losses. PMID:22134357

  14. The Lipopolysaccharide and β-1,3-Glucan Binding Protein Gene Is Upregulated in White Spot Virus-Infected Shrimp (Penaeus stylirostris)

    PubMed Central

    Roux, Michelle M.; Pain, Arnab; Klimpel, Kurt R.; Dhar, Arun K.

    2002-01-01

    Pattern recognition proteins such as lipopolysaccharide and β-1,3-glucan binding protein (LGBP) play an important role in the innate immune response of crustaceans and insects. Random sequencing of cDNA clones from a hepatopancreas cDNA library of white spot virus (WSV)-infected shrimp provided a partial cDNA (PsEST-289) that showed similarity to the LGBP gene of crayfish and insects. Subsequently full-length cDNA was cloned by the 5′-RACE (rapid amplification of cDNA ends) technique and sequenced. The shrimp LGBP gene is 1,352 bases in length and is capable of encoding a polypeptide of 376 amino acids that showed significant similarity to homologous genes from crayfish, insects, earthworms, and sea urchins. Analysis of the shrimp LGBP deduced amino acid sequence identified conserved features of this gene family including a potential recognition motif for β-(1→3) linkage of polysaccharides and putative RGD cell adhesion sites. It is known that LGBP gene expression is upregulated in bacterial and fungal infection and that the binding of lipopolysaccharide and β-1,3-glucan to LGBP activates the prophenoloxidase (proPO) cascade. The temporal expression of LGBP and proPO genes in healthy and WSV-challenged Penaeus stylirostris shrimp was measured by real-time quantitative reverse transcription-PCR, and we showed that LGBP gene expression in shrimp was upregulated as the WSV infection progressed. Interestingly, the proPO expression was upregulated initially after infection followed by a downregulation as the viral infection progressed. The downward trend in the expression of proPO coincided with the detection of WSV in the infected shrimp. Our data suggest that shrimp LGBP is an inducible acute-phase protein that may play a critical role in shrimp-WSV interaction and that the WSV infection regulates the activation and/or activity of the proPO cascade in a novel way. PMID:12072514

  15. Comparative Proteomic Analysis of Two Barley Cultivars (Hordeum vulgare L.) with Contrasting Grain Protein Content

    PubMed Central

    Guo, Baojian; Luan, Haiye; Lin, Shen; Lv, Chao; Zhang, Xinzhong; Xu, Rugen

    2016-01-01

    Grain protein contents (GPCs) of barley seeds are significantly different between feed and malting barley cultivars. However, there is still no insight into the proteomic analysis of seed proteins between feed and malting barley cultivars. Also, the genetic control of barley GPC is still unclear. GPCs were measured between mature grains of Yangsimai 3 and Naso Nijo. A proteome profiling of differentially expressed protein was established by using a combination of 2-DE and tandem mass spectrometry. In total, 502 reproducible protein spots in barley seed proteome were detected with a pH range of 4–7 and 6–11, among these 41 protein spots (8.17%) were detected differentially expressed between Yangsimai 3 and Naso Nijo. Thirty-four protein spots corresponding to 23 different proteins were identified, which were grouped into eight categories, including stress, protein degradation and post-translational modification, development, cell, signaling, glycolysis, starch metabolism, and other functions. Among the identified proteins, enolase (spot 274) and small subunit of ADP-glucose pyrophosphorylase (spot 271) are exclusively expressed in barley Yangsimai 3, which may be involved in regulating seed protein expression. In addition, malting quality is characterized by an accumulation of serpin protein, Alpha-amylase/trypsin inhibitor CMb and Alpha-amylase inhibitor BDAI-1. Most noticeably, globulin, an important storage protein in barley seed, undergoes post-translational processing in both cultivars, and also displays different expression patterns. PMID:27200019

  16. The Effect of Hypoxia and Hyperoxia on Growth and Expression of Hypoxia-Related Genes and Proteins in Spotted Gar Lepisosteus oculatus Larvae and Juveniles.

    PubMed

    Rimoldi, Simona; Terova, Genciana; Zaccone, Giacomo; Parker, Tim; Kuciel, Michal; Dabrowski, Konrad

    2016-06-01

    We studied the molecular responses to different water oxygen levels in gills and swim bladder of spotted gar (Lepisosteus oculatus), a bimodal breather. Fish at swim-up stage were exposed for 71 days to normoxic, hypoxic, and hyperoxic water conditions. Then, all aquaria were switched to normoxic conditions for recovery until the end of the experiment (120 days). Fish were sampled at the beginning of the experiment, and then at 71 days of exposure and at 8 days of recovery. We first cloned three hypoxia-related genes, hypoxia-inducible factor 2α (HIF-2α), Na(+) /H(+) exchanger 1 (NHE-1), and NHE-3, and uploaded their cDNA sequences in the GeneBank database. We then used One Step Taqman® real-time PCR to quantify the mRNA copies of target genes in gills and swim bladder of fish exposed to different water O2 levels. We also determined the protein expression of HIF-2α and neuronal nitric oxide synthase (nNOS) in the swim bladder by using confocal immunofluorescence. Hypoxic stress for 71 days significantly increased the mRNA copies of HIF-2α and NHE-1 in gills and swim bladder, whereas normoxic recovery for 8 days decreased the HIF-2α mRNA copies to control values in both tissues. We did not found significant changes in mRNA copies of the NHE-3 gene in either gills or swim bladder in response to hypoxia and hyperoxia. Unlike in normoxic swim bladder, double immunohistochemical staining in hypoxic and hyperoxic swim bladder using nNOS/HIF-2α showed extensive bundles of HIF-2α-positive nerve fibers in the trabecular musculature associated with a few varicose nNOS immunoreactive nerve terminals. PMID:27245617

  17. Proteomic Profiling Of Two-Dimensional Gel Electrophoresis Protein Expression Data

    NASA Astrophysics Data System (ADS)

    Ahmad, Norhaiza; Zhang, J.; Brown, P. J.; James, D. C.; Birch, J. R.; Racher, A. J.; Smales, C. M.

    2008-01-01

    We have undertaken two-dimensional gel electrophoresis (2-DE) proteomic profiling on a series of cell lines with different recombinant antibody production rates. Due to the nature of 2-DE proteomic investigations there will always be `process variability' factors in any data set collected in this way. Some of this variation will arise during sample preparation, gel running and staining, while further variation will arise from the gel analysis procedure. Therefore, in order to identify all significant changes in protein expression between biological samples when analysed by 2-DE, the system precision or `error', and how this correlates to protein abundance, must be known. Only then can the system be considered robust and investigators accurately and confidently report all observable statistically significant changes in protein expression. We introduce an expression variability test to identify protein spots whose expression correlates with increased antibody production. The results have highlighted a small number of candidate proteins for further investigation.

  18. Rocky Mountain spotted fever

    MedlinePlus

    Rocky Mountain spotted fever is a disease caused by a type of bacteria carried by ticks. ... Rocky Mountain spotted fever is caused by the bacteria Rickettsia rickettsii (R. Rickettsii) , which is carried by ticks. The ...

  19. Rocky Mountain spotted fever

    MedlinePlus

    ... page: //medlineplus.gov/ency/article/000654.htm Rocky Mountain spotted fever To use the sharing features on this page, please enable JavaScript. Rocky Mountain spotted fever is a disease caused by a ...

  20. Triton X-114 cloud point extraction to subfractionate blood plasma proteins for two-dimensional gel electrophoresis.

    PubMed

    Jessen, Flemming; Wulff, Tune

    2015-09-15

    A simple and reproducible procedure for enrichment of a plasma protein subfraction suitable for two-dimensional polyacrylamide gel electrophoresis (2DE) was developed, using a Triton X-114-based cloud point extraction (CPE). Appropriate conditions for such a CPE procedure were found by SDS-PAGE to be a plasma protein concentration of about 10mg/ml in 3% (w/v) Triton X-114. 2DE of proteins obtained by CPE of 400 μl of human plasma revealed about 200 spots constituting a spot pattern very different from the pattern of total plasma. The CPE procedure only had a limited contribution to the technical variation. Identification of about 60 spots, representing only 22 proteins, revealed that several proteins in the obtained subfraction were present in more isoforms or modifications. Among these were apolipoproteins (A-1, D, E, L1, and M), haptoglobin-related protein, phosphatidylcholine-sterol acyltransferase, serum amyloid A, and serum paraoxonase/arylesterase 1, which are proteins of a hydrophobic nature, as in plasma they relate to lipoprotein particles. Thus, Triton X-114-based CPE is a simple plasma prefractionation tool, attractive for detailed 2DE studies of hydrophobic plasma proteins and their isoforms or modifications. PMID:26080275

  1. Thermal denaturation produced degenerative proteins and interfered with MS for proteins dissolved in lysis buffer in proteomic analysis.

    PubMed

    Wang, Xuchu; Wang, Haiyan; Wang, Dan; Wang, Dongyang; Han, Bing; Tian, Weimin; Guo, Anping

    2011-02-01

    In 1-DE, proteins were traditionally mixed with the standard Laemmli buffer and boiled for several minutes. Recently, proteins dissolved in lysis buffer were used to produce better-resolved 2-DE gels, but thermal denaturation procedure still remained in some proteomic analysis. To determine the detailed effects of thermal denaturation on SDS-PAGE and MS, both 1-DE and 2-DE were performed using proteins heated at 100°C for different periods of time, and 17 protein bands/spots were positively identified by MALDI TOF/TOF MS/MS. Protein profiles on both 1-DE and 2-DE gels changed obviously and more polydisperse bands/spots were observed with increased heating time for over-heated samples. Based on these observations, an alternative protein marker-producing method was designed by directly dissolving protein standards without BSA into lysis buffer. This new kind of protein marker could be stored at room temperature for a long time, thus was more convenient for using and shipping. The identification of 17 proteins via MS and comparison of their identities revealed MASCOT-searched scores, number of both matched peptides, total searched peptides and sequence coverage became progressively lower with increasing denaturation intensity, probably due to the interference of thermal denaturation on trypsin cleavage efficiency and produced redundant modified peptides. Therefore, it was concluded that thermal denaturation not only changed the protein profiles and produced more polydisperse protein bands/spots, but also heavily interfered with the subsequent MS analysis, hence not recommended in future proteomic analysis for proteins dissolved in lysis buffer. PMID:21298662

  2. Poisson's spot with molecules

    SciTech Connect

    Reisinger, Thomas; Holst, Bodil; Patel, Amil A.; Smith, Henry I.; Reingruber, Herbert; Fladischer, Katrin; Ernst, Wolfgang E.; Bracco, Gianangelo

    2009-05-15

    In the Poisson-spot experiment, waves emanating from a source are blocked by a circular obstacle. Due to their positive on-axis interference an image of the source (the Poisson spot) is observed within the geometrical shadow of the obstacle. In this paper we report the observation of Poisson's spot using a beam of neutral deuterium molecules. The wavelength independence and the weak constraints on angular alignment and position of the circular obstacle make Poisson's spot a promising candidate for applications ranging from the study of large molecule diffraction to patterning with molecules.

  3. Poisson's spot with molecules

    NASA Astrophysics Data System (ADS)

    Reisinger, Thomas; Patel, Amil A.; Reingruber, Herbert; Fladischer, Katrin; Ernst, Wolfgang E.; Bracco, Gianangelo; Smith, Henry I.; Holst, Bodil

    2009-05-01

    In the Poisson-spot experiment, waves emanating from a source are blocked by a circular obstacle. Due to their positive on-axis interference an image of the source (the Poisson spot) is observed within the geometrical shadow of the obstacle. In this paper we report the observation of Poisson’s spot using a beam of neutral deuterium molecules. The wavelength independence and the weak constraints on angular alignment and position of the circular obstacle make Poisson’s spot a promising candidate for applications ranging from the study of large molecule diffraction to patterning with molecules.

  4. Identification of phosphorylation sites in the nucleocapsid protein (N protein) of SARS-coronavirus

    NASA Astrophysics Data System (ADS)

    Lin, Liang; Shao, Jianmin; Sun, Maomao; Liu, Jinxiu; Xu, Gongjin; Zhang, Xumin; Xu, Ningzhi; Wang, Rong; Liu, Siqi

    2007-12-01

    After decoding the genome of SARS-coronavirus (SARS-CoV), next challenge is to understand how this virus causes the illness at molecular bases. Of the viral structural proteins, the N protein plays a pivot role in assembly process of viral particles as well as viral replication and transcription. The SARS-CoV N proteins expressed in the eukaryotes, such as yeast and HEK293 cells, appeared in the multiple spots on two-dimensional electrophoresis (2DE), whereas the proteins expressed in E. coli showed a single 2DE spotE These 2DE spots were further examined by Western blot and MALDI-TOF/TOF MS, and identified as the N proteins with differently apparent pI values and similar molecular mass of 50 kDa. In the light of the observations and other evidences, a hypothesis was postulated that the SARS-CoV N protein could be phosphorylated in eukaryotes. To locate the plausible regions of phosphorylation in the N protein, two truncated N proteins were generated in E. coli and treated with PKC[alpha]. The two truncated N proteins after incubation of PKC[alpha] exhibited the differently electrophoretic behaviors on 2DE, suggesting that the region of 1-256 aa in the N protein was the possible target for PKC[alpha] phosphorylation. Moreover, the SARS-CoV N protein expressed in yeast were partially digested with trypsin and carefully analyzed by MALDI-TOF/TOF MS. In contrast to the completely tryptic digestion, these partially digested fragments generated two new peptide mass signals with neutral loss, and MS/MS analysis revealed two phosphorylated peptides located at the "dense serine" island in the N protein with amino acid sequences, GFYAEGSRGGSQASSRSSSR and GNSGNSTPGSSRGNSPARMASGGGK. With the PKC[alpha] phosphorylation treatment and the partially tryptic digestion, the N protein expressed in E. coli released the same peptides as observed in yeast cells. Thus, this investigation provided the preliminary data to determine the phosphorylation sites in the SARS-CoV N protein, and

  5. Protein profiles of bovine placenta derived from somatic cell nuclear transfer.

    PubMed

    Kim, Hong Rye; Kang, Jae Ku; Yoon, Jong Taek; Seong, Hwan Hoo; Jung, Jin Kwan; Lee, Hong Mie; Sik Park, Chang; Jin, Dong Il

    2005-11-01

    Practical application of animal cloning by somatic cell nuclear transfer (SCNT) has been hampered by an extremely low success rate. To address whether placental dysfunction in SCNT causes fetal loss during pregnancy, we have used a global proteomics approach using 2-DE and MS to analyze the differential protein patterns of three placentae from the afterbirth of cases of postnatal death, derived from SCNT of Korean Native cattle, and three normal placentae obtained from the afterbirth of fetuses derived from artificial insemination. Proteins within a pI range of 4.0-7.0 and 6.0-9.0 were analyzed separately by 2-DE in triplicate. A total of approximately 2000 spots were detected in placental 2-DE gels stained with CBB. In the comparison of normal and SCNT samples, 60 spots were identified as differentially expressed proteins, of which 33 spots were up-regulated proteins in SCNT placentae, while 27 spots were down-regulated proteins. Most of the proteins identified in this analysis appeared to be related with protein repair or protection, cytoskeleton, signal transduction, immune system, metabolism, extracellular matrix and remodeling, transcription regulation, cell structure or differentiation and ion transport. One of up-regulated proteins in SCNT was TIMP-2 protein known to be related to extracellular matrix and remodeling during pregnancy. Western blot analysis showed an increased level of TIMP-2 in SCNT placenta compared to normal. Our results revealed composite profiles of key proteins involved in abnormal placenta derived from SCNT, and suggested expression abnormality of these genes in SCNT placenta, resulting in fetal losses following SCNT. PMID:16196098

  6. Proteome analysis differentiates between two highly homologues germin-like proteins in Arabidopsis thaliana ecotypes Col-0 and Ws-2.

    PubMed

    Schlesier, Bernhard; Berna, Anne; Bernier, François; Mock, Hans-Peter

    2004-06-01

    A proteome approach based on 2-D gel electrophoresis (2-DE) was used to compare the protein patterns of the Arabidopsis ecotypes Col-0 and Ws-2. In leaf extracts a pair of protein spots were found to be diagnostic for each of the lines. Both pairs of spots were identified as closely related germin-like proteins differing in only one amino acid by using peptide mass finger printing of tryptic digests and by gaining additional data from post-source decay spectra in the MALDI-TOF analysis. Western blot analysis after separation of protein extracts by 2-DE confirmed results from Coomassie blue-stained gels and revealed additional immunoreactive spots for both ecotypes most likely representing dimers of the spots first identified. Western blot analysis and mass spectrometrical identification of the corresponding weakly stained protein in Coomassie blue-stained gels of the ecotype Col-0 also demonstrated for the first time the occurrence of AtGER3 protein in root extracts. Our results demonstrate the capacity of proteome analysis to analyse and distinguish closely related members of large protein families. PMID:15276453

  7. Immunoproteomic Analysis of the Excretory-Secretory Proteins from Spirometra mansoni Sparganum

    PubMed Central

    HU, Dan Dan; CUI, Jing; WANG, Li; LIU, Li Na; WEI, Tong; WANG, Zhong Quan

    2013-01-01

    Background Sparganosis is caused by the invasion of Spirometra sparganum into various tissues/organs. Subcutaneous sparganosis can be diagnosed by biopsy, while visceral/cerebral sparganosis is not easy to be diagnosed. The diagnosis depends largely on the detection of specific anti-sparganum antibodies. The specificity of the ELISA could be increased by using S. mansoni sparganum excretory–secretory (ES) antigens, but it also had the cross-reactions with sera of patients with cysticercosis or paragonimiasis. The aim of this study was to identify early specific diagnostic antigens in S. mansoni sparganum ES proteins. Methods The sparganum ES proteins were analyzed by two-dimensional electrophoresis (2-DE) and Western blot probed with early sera from infected mice at 14 days post-infection. The immunoreactive protein spots were characterized by MALDI-TOF/ TOF-MS. Results A total of approximately 149 proteins spots were detected with isoelectric point (pI) varying from 3 to 7.5 and molecular weight from 20 to 115 kDa and seven protein spots with molecular weight of 23-31 kDa were recognized by the infection sera. Three of seven spots were successfully identified and characterized as the same S. mansoni protein (cysteine protease), and the proteins of other 4 spots were not included in the databases. Conclusion The cysteine protease from S. mansoni ES proteins recognized by early infection sera might be the early diagnostic antigens for sparganosis. PMID:24454434

  8. The Earth's Hot Spots.

    ERIC Educational Resources Information Center

    Vink, Gregory E.; And Others

    1985-01-01

    Hot spots are isolated areas of geologic activity where volcanic eruptions, earthquakes, and upwelling currents occur far from plate boundaries. These mantle plumes are relatively stable and crustal plates drift over them. The nature and location of hot spots (with particular attention to the Hawaiian Islands and Iceland) are discussed. (DH)

  9. Jupiter's Great Red spot

    NASA Technical Reports Server (NTRS)

    1979-01-01

    This color composite made from Voyager 2 narrow-angle camera frames shows the Great Red Spot during the late Jovian afternoon. North of the Red Spot lies a curious darker section of the South Equatorial Belt (SEB), the belt in which the Red Spot is located. A bright eruption of material passing from the SEB northward into the diffuse equatorial clouds has been observed on all occasions when this feature passes north of the Red Spot. The remnants of one such eruption are apparent in this photograph. To the lower left of the Red Spot lies one of the three long-lived White Ovals. This photograph was taken on June 29, 1979, when Voyager 2 was over 9 million kilometers (nearly 6 million miles) from Jupiter. The smallest features visible are over 170 kilometers (106 miles) across.

  10. Poisson's Spot with Molecules

    NASA Astrophysics Data System (ADS)

    Reisinger, Thomas; Patel, Amil; Reingruber, Herbert; Fladischer, Katrin; Ernst, Wolfgang E.; Bracco, Gianangelo; Smith, Henry I.; Holst, Bodil

    2009-03-01

    In the Poisson-Spot experiment, waves emanating from a source are blocked by a circular obstacle. Due to their positive on-axis interference an image of the source (the Poisson spot) is observed within the geometrical shadow of the obstacle. The Poisson spot is the last of the classical optics experiments to be realized with neutral matter waves. In this paper we report the observation of Poisson's Spot using a beam of neutral deuterium molecules. The wavelength-independence and the weak constraints on angular alignment and position of the circular obstacle make Poisson's spot a promising candidate for applications ranging from the study of large-molecule diffraction and coherence in atom-lasers to patterning with large molecules.

  11. Spinal cord injury markedly altered protein expression patterns in the affected rat urinary bladder during healing stages.

    PubMed

    Lee, Ji-Young; Kim, Bong Jo; Sim, Gyujin; Kim, Gyu-Tae; Kang, Dawon; Jung, Jae Hun; Hwa, Jeong Seok; Kwak, Yeon Ju; Choi, Yeon Jin; Park, Young Sook; Han, Jaehee; Lee, Cheol Soon; Kang, Kee Ryeon

    2011-06-01

    The influence of spinal cord injury (SCI) on protein expression in the rat urinary bladder was assessed by proteomic analysis at different time intervals post-injury. After contusion SCI between T9 and T10, bladder tissues were processed by 2-DE and MALDI-TOF/MS at 6 hr to 28 days after SCI to identify proteins involved in the healing process of SCI-induced neurogenic bladder. Approximately 1,000 spots from the bladder of SCI and sham groups were visualized and identified. At one day after SCI, the expression levels of three protein were increased, and seven spots were down-regulated, including heat shock protein 27 (Hsp27) and heat shock protein 20 (Hsp20). Fifteen spots such as S100-A11 were differentially expressed seven days post-injury, and seven proteins including transgelin had altered expression patterns 28 days after injury. Of the proteins with altered expression levels, transgelin, S100-A11, Hsp27 and Hsp20 were continuously and variably expressed throughout the entire post-SCI recovery of the bladder. The identified proteins at each time point belong to eight functional categories. The altered expression patterns identified by 2-DE of transgelin and S100-A11 were verified by Western blot. Transgelin and protein S100-A11 may be candidates for protein biomarkers in the bladder healing process after SCI. PMID:21655070

  12. Watermarking spot colors

    NASA Astrophysics Data System (ADS)

    Alattar, Osama M.; Reed, Alastair M.

    2003-06-01

    Watermarking of printed materials has usually focused on process inks of cyan, magenta, yellow and black (CMYK). In packaging, almost three out of four printed materials include spot colors. Spot colors are special premixed inks, which can be produced in a vibrant range of colors, often outside the CMYK color gamut. In embedding a watermark into printed material, a common approach is to modify the luminance value of each pixel in the image. In the case of process color work pieces, the luminance change can be scaled to the C, M, Y and K channels using a weighting function, to produce the desired change in luminance. In the case of spot color art designs, there is only one channel available and the luminance change is applied to this channel. In this paper we develop a weighting function to embed the watermark signal across the range of different spot colors. This weighting function normalizes visibility effect and signal robustness across a wide range of different spot colors. It normalizes the signal robustness level over the range of an individual spot color"s intensity levels. Further, it takes into account the sensitivity of the capturing device to the different spot colors.

  13. Radiometry spot measurement system

    NASA Technical Reports Server (NTRS)

    Chen, Harry H.; Lawn, Stephen J.

    1994-01-01

    The radiometry spot measurement system (RSMS) has been designed for use in the Diffusive And Radiative Transport in Fires (DARTFire) experiment, currently under development at the NASA Lewis Research Center. The RSMS can measure the radiation emitted from a spot of specific size located on the surface of a distant radiation source within a controlled wavelength range. If the spot is located on a blackbody source, its radiation and temperature can be measured directly or indirectly by the RSMS. This report presents computer simulation results used to verify RSMS performance.

  14. Immunoproteomic analysis of the second-generation merozoite proteins of Eimeria tenella.

    PubMed

    Liu, Liheng; Xu, Lixin; Yan, Fengbin; Yan, Ruofeng; Song, Xiaokai; Li, Xiangrui

    2009-10-14

    Whole proteins of the second-generation merozoite of Eimeria tenella were analyzed by two-dimensional gel electrophoresis (2-DE) and western blot using the chicken sera infected artificially with E. tenella. Approximately 640 spots were detected on proteome map of the second-generation merozoite stained by Coomassie brilliant blue G-250 and 85 spots were recognized on western blot map as antigens. Forty four spots of the antigens were identified by matrix-assisted laser desorption ionization time-of-flight MS (MALDI-TOF-MS) and MALDI-TOF-TOF-MS. Twenty six proteins of E. tenella and three homologous proteins to other apicomplexan parasites or protozoan were identified using 'Mascot' server. These proteins included lactate dehydrogenase, enolase, 14-3-3 protein, microneme proteins, tubulin beta chain, SERPIN1 protein precursor, large subunit ribosomal protein L23 and surface antigens of E. tenella, heat shock protein (HSP70) of Eimeria acervulina, protein phosphatase type 1 of Toxoplasma gondii and hypothetical protein GSPATT00020155001 of Paramecium tetraurelia. The rest proteins were searched against the E. tenella protein sequence database using 'Mascot in-house' (version 2.1) search engine in automated mode and 11 unknown proteins were identified. After the amino acid sequence of the unknown proteins were searched using BLAST against non-redundant sequence databases (NCBI), surface antigen 12 of E. tenella and six homologous proteins to other apicomplexa parasites were found. They were membrane skeleton protein IMC2A, mitochondrial F1-ATP synthase beta subunit precursor, 3-oxoacyl-acyl-carrier-protein synthase and catalase of T. gondii, Vps26 of Plasmodium falciparum 3D7, and hypothetical protein TRIADDRAFT_60424 of Trichoplax adhaerens. No homologues of 8 spots of the 44 analyzed proteins were found. These proteins enriched the data of immunogenic proteins of the second-generation merozoite of E. tenella. PMID:19581052

  15. Combinatorial peptide ligand libraries for the analysis of low-expression proteins: Validation for normal urine and definition of a first protein MAP.

    PubMed

    Santucci, Laura; Candiano, Giovanni; Bruschi, Maurizio; D'Ambrosio, Chiara; Petretto, Andrea; Scaloni, Andrea; Urbani, Andrea; Righetti, Pier G; Ghiggeri, Gian M

    2012-02-01

    In this review, we report the evolution on experimental conditions for the analysis of normal urine based on combinatorial peptide ligand library (CPLL) treatment and successive 2-DE and 2-DE/MS analysis. The main topics are (i) definition of the urine sample requirements, (ii) optimization of the urine/ligand ratio, (iii) essay conditions, (iv) en bloc elution. Overall, normal urine protein composition as studied by 2-DE includes over 2600 spots. Relevant data on inter and intraessay reproducibility obtained by the analysis of different normal urines repeated several times are also here presented. We found a 73% reproducibility upon analysis of the same sample and 68% correspondence of protein composition among different normal urine samples. Based on the above results, we are completing the characterization with LC-MS of 249 spots. The composition of normal urine proteins after CPLLs is finally shown with the indication of those spots which are currently under identification. This map will be completed in a near future; in the meantime this would represent the basic reference sample for newly developed studies on human diseases. PMID:22246922

  16. Reactor hot spot analysis

    SciTech Connect

    Vilim, R.B.

    1985-08-01

    The principle methods for performing reactor hot spot analysis are reviewed and examined for potential use in the Applied Physics Division. The semistatistical horizontal method is recommended for future work and is now available as an option in the SE2-ANL core thermal hydraulic code. The semistatistical horizontal method is applied to a small LMR to illustrate the calculation of cladding midwall and fuel centerline hot spot temperatures. The example includes a listing of uncertainties, estimates for their magnitudes, computation of hot spot subfactor values and calculation of two sigma temperatures. A review of the uncertainties that affect liquid metal fast reactors is also presented. It was found that hot spot subfactor magnitudes are strongly dependent on the reactor design and therefore reactor specific details must be carefully studied. 13 refs., 1 fig., 5 tabs.

  17. SPOT4 Management Centre

    NASA Technical Reports Server (NTRS)

    Labrune, Yves; Labbe, X.; Roussel, A.; Vielcanet, P.

    1994-01-01

    In the context of the CNES SPOT4 program CISI is particularly responsible for the development of the SPOT4 Management Centre, part of the SPOT4 ground control system located at CNES Toulouse (France) designed to provide simultaneous control over two satellites. The main operational activities are timed to synchronize with satellite visibilities (ten usable passes per day). The automatic capability of this system is achieved through agenda services (sequence of operations as defined and planned by operator). Therefore, the SPOT4 Management Centre offers limited, efficient and secure human interventions for supervision and decision making. This paper emphasizes the main system characteristics as degree of automation, level of dependability and system parameterization.

  18. Lincoln's Spot Resolutions.

    ERIC Educational Resources Information Center

    Mueller, Jean West; Schamel, Wynell Burroughs

    1988-01-01

    Examines the events leading to and immediately following the declaration of war on Mexico in 1846. Includes the second and third pages of Abraham Lincoln's "Spot Resolutions" and presents teaching suggestions for interpreting the document and assessing public opinion. (GEA)

  19. Jupiter's Great Red Spot

    NASA Technical Reports Server (NTRS)

    1996-01-01

    This view of Jupiter's Great Red Spot is a mosaic of two images taken by the Galileo spacecraft. The image was created using two filters, violet and near-infrared, at each of two camera positions. The Great Red Spot is a storm in Jupiter's atmosphere and is at least 300 years-old. Winds blow counterclockwise around the Great Red Spot at about 400 kilometers per hour (250 miles per hour). The size of the storm is more than one Earth diameter (13,000 kilometers or 8,000 miles) in the north-south direction and more than two Earth diameters in the east-west direction. In this oblique view, where the Great Red Spot is shown on the planet's limb, it appears longer in the north-south direction. The image was taken on June 26, 1996.

    The Galileo mission is managed by NASA's Jet Propulsion Laboratory.

  20. Mononucleosis spot test

    MedlinePlus

    Monospot test; Heterophile antibody test; Heterophile agglutination test; Paul-Bunnell test; Forssman antibody test ... The mononucleosis spot test is done when symptoms of mononucleosis are ... Fatigue Fever Large spleen (possibly) Sore throat Tender ...

  1. SPOT4 Management Centre

    NASA Astrophysics Data System (ADS)

    Labrune, Yves; Labbe, X.; Roussel, A.; Vielcanet, P.

    1994-11-01

    In the context of the CNES SPOT4 program CISI is particularly responsible for the development of the SPOT4 Management Centre, part of the SPOT4 ground control system located at CNES Toulouse (France) designed to provide simultaneous control over two satellites. The main operational activities are timed to synchronize with satellite visibilities (ten usable passes per day). The automatic capability of this system is achieved through agenda services (sequence of operations as defined and planned by operator). Therefore, the SPOT4 Management Centre offers limited, efficient and secure human interventions for supervision and decision making. This paper emphasizes the main system characteristics as degree of automation, level of dependability and system parameterization.

  2. Proteomic evaluation of sheep serum proteins

    PubMed Central

    2012-01-01

    Background The applications of proteomic strategies to ovine medicine remain limited. The definition of serum proteome may be a good tool to identify useful protein biomarkers for recognising sub-clinical conditions and overt disease in sheep. Findings from bovine species are often directly translated for use in ovine medicine. In order to characterize normal protein patterns and improve knowledge of molecular species-specific characteristics, we generated a two-dimensional reference map of sheep serum. The possible application of this approach was tested by analysing serum protein patterns in ewes with mild broncho-pulmonary disease, which is very common in sheep and in the peripartum period which is a stressful time, with a high incidence of infectious and parasitic diseases. Results This study generated the first reference 2-DE maps of sheep serum. Overall, 250 protein spots were analyzed, and 138 identified. Compared with healthy sheep, serum protein profiles of animals with rhino-tracheo-bronchitis showed a significant decrease in protein spots identified as transthyretin, apolipoprotein A1 and a significant increase in spots identified as haptoglobin, endopin 1b and alpha1B glycoprotein. In the peripartum period, haptoglobin, alpha-1-acid glycoprotein, apolipoprotein A1 levels rose, while transthyretin content dropped. Conclusions This study describes applications of proteomics in putative biomarker discovery for early diagnosis as well as for monitoring the physiological and metabolic situations critical for ovine welfare. PMID:22630135

  3. Identification of early diagnostic antigens from major excretory-secretory proteins of Trichinella spiralis muscle larvae using immunoproteomics

    PubMed Central

    2014-01-01

    Background The excretory-secretory (ES) proteins of Trichinella spiralis muscle larvae (ML) come mainly from the excretory granules of the stichosome and the cuticles (membrane proteins), are directly exposed to the host’s immune system, and are the main target antigens, which induce the immune responses. Although the ES proteins are the most commonly used diagnostic antigens for trichinellosis, their main disadvantage are the false negative results during the early stage of infection. The aim of this study was to identify early specific diagnostic antigens from the main components of T. spiralis muscle larval ES proteins. Methods Two-dimensional electrophoresis (2-DE) combined with Western blot were used to screen the early diagnostic antigens from the main components of T. spiralis muscle larval ES proteins. The protein spots recognized by the sera from BALB/c mice infected with T. spiralis at 18 days post-infection (dpi) were identified by MALDI-TOF/TOF-MS and putatively annotated using GO terms obtained from the InterPro databases. Results The ES proteins were analyzed by 2-DE, and more than 33 protein spots were detected with molecular weight varying from 40 to 60 kDa and isoelectric point (pI) from 4 to 7. When probed with the sera from infected mice at 18 dpi, 21 protein spots were recognized and then identified, and they were characterized to correlate with five different proteins of T. spiralis, including two serine proteases, one deoxyribonuclease (DNase) II, and two kinds of trypsin. The five proteins were functionally categorized into molecular function and biological process according to GO hierarchy. Conclusions 2-DE and Western blot combined with MALDI-TOF/TOF-MS were used to screen the diagnostic antigens from the main components of T. spiralis muscle larval ES proteins. The five proteins of T. spiralis identified (two serine proteases, DNase II and two kinds of trypsin) might be the early specific diagnostic antigens of trichinellosis. PMID

  4. The cassava (Manihot esculenta Crantz) root proteome: protein identification and differential expression.

    PubMed

    Sheffield, Jeanne; Taylor, Nigel; Fauquet, Claude; Chen, Sixue

    2006-03-01

    Using high-resolution 2-DE, we resolved proteins extracted from fibrous and tuberous root tissues of 3-month-old cassava plants. Gel image analysis revealed an average of 1467 electrophoretically resolved spots on the fibrous gels and 1595 spots on the tuberous gels in pH 3-10 range. Protein spots from both sets of gels were digested with trypsin. The digests were subjected to nanoelectrospray quadrupole TOF tandem mass analysis. Currently, we have obtained 299 protein identifications for 292 gel spots corresponding to 237 proteins. The proteins span various functional categories from energy, primary and secondary metabolism, disease and defense, destination and storage, transport, signal transduction, protein synthesis, cell structure, and transcription to cell growth and division. Gel image analysis has shown unique, as well as up- and down-regulated proteins, present in the tuberous and the fibrous tissues. Quantitative and qualitative analysis of the cassava root proteome is an important step towards further characterization of differentially expressed proteins and the elucidation of the mechanisms underlying the development and biological functions of the two types of roots. PMID:16421938

  5. The Cucumber leaf spot virus p25 auxiliary replicase protein binds and modifies the endoplasmic reticulum via N-terminal transmembrane domains

    SciTech Connect

    Ghoshal, Kankana; Theilmann, Jane; Reade, Ron; Sanfacon, Helene; Rochon, D’Ann

    2014-11-15

    Cucumber leaf spot virus (CLSV) is a member of the Aureusvirus genus, family Tombusviridae. The auxiliary replicase of Tombusvirids has been found to localize to endoplasmic reticulum (ER), peroxisomes or mitochondria; however, localization of the auxiliary replicase of aureusviruses has not been determined. We have found that the auxiliary replicase of CLSV (p25) fused to GFP colocalizes with ER and that three predicted transmembrane domains (TMDs) at the N-terminus of p25 are sufficient for targeting, although the second and third TMDs play the most prominent roles. Confocal analysis of CLSV infected 16C plants shows that the ER becomes modified including the formation of punctae at connections between ER tubules and in association with the nucleus. Ultrastructural analysis shows that the cytoplasm contains numerous vesicles which are also found between the perinuclear ER and nuclear membrane. It is proposed that these vesicles correspond to modified ER used as sites for CLSV replication. - Highlights: • The CLSV p25 auxiliary replicase targets the endoplasmic reticulum (ER). • Targeting of CLSV p25 is associated with ER restructuring. • Restructuring of the ER occurs during CLSV infection. • CLSV p25 contains 3 predicted transmembrane domains 2 of which are required for ER targeting. • Vesicles derived from the ER may be sites of CLSV replication.

  6. IR Spot Weld Inspect

    SciTech Connect

    Chen, Jian; Feng, Zhili

    2014-01-01

    In automotive industry, destructive inspection of spot welds is still the mandatory quality assurance method due to the lack of efficient non-destructive evaluation (NDE) tools. However, it is costly and time-consuming. Recently at ORNL, a new NDE prototype system for spot weld inspection using infrared (IR) thermography has been developed to address this problem. This software contains all the key functions that ensure the NDE system to work properly: system input/output control, image acquisition, data analysis, weld quality database generation and weld quality prediction, etc.

  7. IR Spot Weld Inspect

    2014-01-01

    In automotive industry, destructive inspection of spot welds is still the mandatory quality assurance method due to the lack of efficient non-destructive evaluation (NDE) tools. However, it is costly and time-consuming. Recently at ORNL, a new NDE prototype system for spot weld inspection using infrared (IR) thermography has been developed to address this problem. This software contains all the key functions that ensure the NDE system to work properly: system input/output control, image acquisition, datamore » analysis, weld quality database generation and weld quality prediction, etc.« less

  8. Investigation of proteomic profiles of lamina of Ecklonia kurome (Laminariales): homology-based cross-species protein identification and analysis of the post-translational processing of vanadium-dependent bromoperoxidases using MALDI-TOF/TOF.

    PubMed

    Nagai, Kouhei; Morimoto, Koichi; Ikegami, Haruka; Kimura, Hajime; Yotsukura, Norishige

    2013-08-01

    Proteomic profiles of the lamina of Ecklonia kurome Okamura, one of the Japanese dominant laminarialean kelps, were investigated by two-dimensional electrophoresis (2-DE) and MALDI-TOF/TOF. Due to the absence of E. kurome DNA or protein databases, homology-based cross-species protein identification was performed using a combination of three database-searching algorithms, Mascot peptide mass fingerprinting, Mascot MS/MS ion search, and mass spectrometry-based BLAST. Proteins were extracted from the lamina by an ethanol/phenol method and subjected to 2-DE (pI 4-7, 10 % polyacrylamide gel). More than 700 spots were detected in the 2-DE gel with CBB, and 93 spots (24 proteins) were successfully identified by MALDI-TOF/TOF and the cross-species database searching. The identified proteins mainly consisted of cytoplasmic carbohydrate metabolic enzymes, chloroplast proteins involved in photosynthesis, and haloperoxidases. Interestingly, vanadium-dependent bromoperoxidases (vBPO), which is thought to be involved in halogen uptake, synthesis of halogenated products, and detoxification of reactive oxygen species, were separated into at least 23 different spots. By comparing mass spectra, amino acid sequences predicted from tandem mass spectra and haloperoxidase activities of the vBPOs, we found that (1) at least two types of vBPOs were expressed in the lamina of E. kurome and (2) two pro-vBPOs might be activated by specific cleavage at N- and C-terminal regions. PMID:23547002

  9. Bacterial leaf spot

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bacterial leaf spot has been reported in Australia (Queensland), Egypt, El Salvador, India, Japan, Nicaragua, Sudan, and the United States (Florida, Iowa, Kansas, Maryland, and Wisconsin). It occasionally causes locally severe defoliation and post-emergence damping-off and stunting. The disease is...

  10. Delta spots and great flares

    NASA Technical Reports Server (NTRS)

    Zirin, Harold; Liggett, Margaret A.

    1987-01-01

    The development of delta spots and the great flares they produce are reviewed based on 18 years of observations. Delta groups are found to develop in three ways: (1) by the eruption of a single complex active region formed below the surface; (2) by the eruption of large satellite spots near a large older spot; and (3) by the collision of spots of opposite polarity from different dipoles. It is shown that the present sample of 21 delta spots never separate once they lock together, and that the driving force for the shear is spot motion. Indicators for the prediction of the occurrence of great flares are identified.

  11. Effect of separation dimensions on resolution and throughput using very narrow-range IEF for 2-DE after solution phase isoelectric fractionation of a complex proteome.

    PubMed

    Lee, KiBeom; Pi, KyungBae

    2009-04-01

    This paper describes how the lengths of the first and second dimensions in narrow pH-range 2-DE affect the number of detected protein spots, by analysis of human breast carcinoma cell line lysates prefractionated by solution phase IEF. The aim is to maximize throughput while minimizing experimental costs. In this study, systematic evaluation of narrow-range IPG strip lengths showed that separation distances were very important, with dramatic increases in resolution when longer gels were used. Compared with 7 cm minigels, maximal resolution was obtained using 18 and 24 cm IPG strips. Systematic evaluation of SDS-PAGE gel length showed a far weaker influence of separation length on resolution in the second dimension compared with that observed for the IEF dimension. There was little benefit in using separation distances greater than 12-15 cm, at least with currently available electrophoresis units. The work shows that regions of the IPG strip not containing any proteins can be excised to fit a smaller gel if prefractionation using IEF in solution has been performed. As expected, larger 2-DE gel volumes resulting from the use of longer IPG strips and second dimension gels decreased detection sensitivity when equal protein loads were used. However, this effect could be readily eliminated by increasing the loads applied to IPG strips. PMID:19301322

  12. Arc spot grouping: An entanglement of arc spot cells

    SciTech Connect

    Kajita, Shin; Hwangbo, Dogyun; Ohno, Noriyasu; Tsventoukh, Mikhail M.; Barengolts, Sergey A.

    2014-12-21

    In recent experiments, clear transitions in velocity and trail width of an arc spot initiated on nanostructured tungsten were observed on the boundary of the thick and thin nanostructured layer regions. The velocity of arc spot was significantly decreased on the thick nanostructured region. It was suggested that the grouping decreased the velocity of arc spot. In this study, we try to explain the phenomena using a simple random walk model that has properties of directionality and self-avoidance. And grouping feature was added by installing an attractive force between spot cells with dealing with multi-spots. It was revealed that an entanglement of arc spot cells decreased the spot velocity, and spot cells tend to stamp at the same location many times.

  13. Arc spot grouping: An entanglement of arc spot cells

    NASA Astrophysics Data System (ADS)

    Kajita, Shin; Hwangbo, Dogyun; Ohno, Noriyasu; Tsventoukh, Mikhail M.; Barengolts, Sergey A.

    2014-12-01

    In recent experiments, clear transitions in velocity and trail width of an arc spot initiated on nanostructured tungsten were observed on the boundary of the thick and thin nanostructured layer regions. The velocity of arc spot was significantly decreased on the thick nanostructured region. It was suggested that the grouping decreased the velocity of arc spot. In this study, we try to explain the phenomena using a simple random walk model that has properties of directionality and self-avoidance. And grouping feature was added by installing an attractive force between spot cells with dealing with multi-spots. It was revealed that an entanglement of arc spot cells decreased the spot velocity, and spot cells tend to stamp at the same location many times.

  14. Added value of use of a purified protein derivative-based enzyme-linked immunosorbent spot assay for patients with Mycobacterium bovis BCG infection after intravesical BCG instillations.

    PubMed

    Heemstra, Karen A; Bossink, Ailko W J; Spermon, Roan; Bouwman, John J M; van der Kieft, Robert; Thijsen, Steven F T

    2012-06-01

    In this case series, we describe four cases in which the use of gamma interferon release assays with purified protein derivative (PPD) as a stimulating antigen was able to demonstrate PPD-specific immune activation. This may help to improve the adequate diagnosis of (systemic) Mycobacterium bovis BCG infections after intravesical BCG instillations for bladder carcinoma. PMID:22461529

  15. Added Value of Use of a Purified Protein Derivative-Based Enzyme-Linked Immunosorbent Spot Assay for Patients with Mycobacterium bovis BCG Infection after Intravesical BCG Instillations

    PubMed Central

    Bossink, Ailko W. J.; Spermon, Roan; Bouwman, John J. M.; van der Kieft, Robert; Thijsen, Steven F. T.

    2012-01-01

    In this case series, we describe four cases in which the use of gamma interferon release assays with purified protein derivative (PPD) as a stimulating antigen was able to demonstrate PPD-specific immune activation. This may help to improve the adequate diagnosis of (systemic) Mycobacterium bovis BCG infections after intravesical BCG instillations for bladder carcinoma. PMID:22461529

  16. Integrating Sustainable Hunting in Biodiversity Protection in Central Africa: Hot Spots, Weak Spots, and Strong Spots

    PubMed Central

    Fa, John E.; Olivero, Jesús; Farfán, Miguel Ángel; Márquez, Ana Luz; Vargas, Juan Mario; Real, Raimundo; Nasi, Robert

    2014-01-01

    Wild animals are a primary source of protein (bushmeat) for people living in or near tropical forests. Ideally, the effect of bushmeat harvests should be monitored closely by making regular estimates of offtake rate and size of stock available for exploitation. However, in practice, this is possible in very few situations because it requires both of these aspects to be readily measurable, and even in the best case, entails very considerable time and effort. As alternative, in this study, we use high-resolution, environmental favorability models for terrestrial mammals (N = 165) in Central Africa to map areas of high species richness (hot spots) and hunting susceptibility. Favorability models distinguish localities with environmental conditions that favor the species' existence from those with detrimental characteristics for its presence. We develop an index for assessing Potential Hunting Sustainability (PHS) of each species based on their ecological characteristics (population density, habitat breadth, rarity and vulnerability), weighted according to restrictive and permissive assumptions of how species' characteristics are combined. Species are classified into five main hunting sustainability classes using fuzzy logic. Using the accumulated favorability values of all species, and their PHS values, we finally identify weak spots, defined as high diversity regions of especial hunting vulnerability for wildlife, as well as strong spots, defined as high diversity areas of high hunting sustainability potential. Our study uses relatively simple models that employ easily obtainable data of a species' ecological characteristics to assess the impacts of hunting in tropical regions. It provides information for management by charting the geography of where species are more or less likely to be at risk of extinction from hunting. PMID:25372705

  17. Integrating sustainable hunting in biodiversity protection in Central Africa: hot spots, weak spots, and strong spots.

    PubMed

    Fa, John E; Olivero, Jesús; Farfán, Miguel Ángel; Márquez, Ana Luz; Vargas, Juan Mario; Real, Raimundo; Nasi, Robert

    2014-01-01

    Wild animals are a primary source of protein (bushmeat) for people living in or near tropical forests. Ideally, the effect of bushmeat harvests should be monitored closely by making regular estimates of offtake rate and size of stock available for exploitation. However, in practice, this is possible in very few situations because it requires both of these aspects to be readily measurable, and even in the best case, entails very considerable time and effort. As alternative, in this study, we use high-resolution, environmental favorability models for terrestrial mammals (N = 165) in Central Africa to map areas of high species richness (hot spots) and hunting susceptibility. Favorability models distinguish localities with environmental conditions that favor the species' existence from those with detrimental characteristics for its presence. We develop an index for assessing Potential Hunting Sustainability (PHS) of each species based on their ecological characteristics (population density, habitat breadth, rarity and vulnerability), weighted according to restrictive and permissive assumptions of how species' characteristics are combined. Species are classified into five main hunting sustainability classes using fuzzy logic. Using the accumulated favorability values of all species, and their PHS values, we finally identify weak spots, defined as high diversity regions of especial hunting vulnerability for wildlife, as well as strong spots, defined as high diversity areas of high hunting sustainability potential. Our study uses relatively simple models that employ easily obtainable data of a species' ecological characteristics to assess the impacts of hunting in tropical regions. It provides information for management by charting the geography of where species are more or less likely to be at risk of extinction from hunting. PMID:25372705

  18. Characterization of vegetative storage protein (VSP) and low molecular proteins induced by water deficit in stolon of white clover.

    PubMed

    Lee, Bok-Rye; Lee, Dong-Gi; Avice, Jean-Christophe; Kim, Tae-Hwan

    2014-01-01

    In stolon of white clover (Trifolium repens L.), the 17.3 kDa protein has been newly identified as a vegetative storage protein (VSP) which has preponderant roles in N accumulation and mobilization to sustain growth when capacity of N uptake is strongly reduced. To characterize the water deficit effect on this protein, the kinetic pattern of soluble protein, SDS-PAGE, Western blotting, and proteomic analysis was studied in the stolon of white clover during 28 days of water-deficit. Water deficit led to decrease protein concentration. SDS-PAGE revealed that two major proteins of 17.3 and 16 kDa were accumulated to high level in response to water stress. These proteins cross-reacted positively with antibodies raised against the 17.3 kDa VSP, a protein which shared biochemical features with stress proteins implied in dehydration tolerance. Using two-dimensional electrophoresis (2-DE) gel and matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF-MS) analysis, it was demonstrated that 19.5 and 17.3 kDa protein spots were up-regulated by water stress, and both spots were identical to nucleoside diphosphate kinase (NDPK) and lipid transfer proteins (LTPs), respectively. These results suggest that low molecular proteins induced by water-deficit in the stolon of white clover act as an alternative N reserves or play significant roles in plant protection against water-deficit stress. PMID:24299955

  19. The interaction of two-spotted spider mites, Tetranychus urticae Koch, with Cry protein production and predation by Amblyseius andersoni (Chant) in Cry1Ac/Cry2Ab cotton and Cry1F maize.

    PubMed

    Guo, Yan-Yan; Tian, Jun-Ce; Shi, Wang-Peng; Dong, Xue-Hui; Romeis, Jörg; Naranjo, Steven E; Hellmich, Richard L; Shelton, Anthony M

    2016-02-01

    Crops producing insecticidal crystal (Cry) proteins from the bacterium, Bacillus thuringiensis (Bt), are an important tool for managing lepidopteran pests on cotton and maize. However, the effects of these Bt crops on non-target organisms, especially natural enemies that provide biological control services, are required to be addressed in an environmental risk assessment. Amblyseius andersoni (Acari: Phytoseiidae) is a cosmopolitan predator of the two-spotted spider mite, Tetranychus urticae (Acari: Tetranychidae), a significant pest of cotton and maize. Tri-trophic studies were conducted to assess the potential effects of Cry1Ac/Cry2Ab cotton and Cry1F maize on life history parameters (survival rate, development time, fecundity and egg hatching rate) of A. andersoni. We confirmed that these Bt crops have no effects on the biology of T. urticae and, in turn, that there were no differences in any of the life history parameters of A. andersoni when it fed on T. urticae feeding on Cry1Ac/Cry2Ab or non-Bt cotton and Cry1F or non-Bt maize. Use of a susceptible insect assay demonstrated that T. urticae contained biologically active Cry proteins. Cry proteins concentrations declined greatly as they moved from plants to herbivores to predators and protein concentration did not appear to be related to mite density. Free-choice experiments revealed that A. andersoni had no preference for Cry1Ac/Cry2Ab cotton or Cry1F maize-reared T. urticae compared with those reared on non-Bt cotton or maize. Collectively these results provide strong evidence that these crops can complement other integrated pest management tactics including biological control. PMID:26545599

  20. Novel prediction method of beer foam stability using protein Z, barley dimeric alpha-amylase inhibitor-1 (BDAI-1) and yeast thioredoxin.

    PubMed

    Iimure, Takashi; Takoi, Kiyoshi; Kaneko, Takafumi; Kihara, Makoto; Hayashi, Katsuhiro; Ito, Kazutoshi; Sato, Kazuhiro; Takeda, Kazuyoshi

    2008-09-24

    Foam stability is an important quality trait of beer. Our previous results of two-dimensional gel electrophoresis (2DE) analyses of beer proteins implied a relationship between barley dimeric alpha-amylase inhibitor-1 (BDAI-1) and beer foam stability as judged by the NIBEM-T analyzer. To develop a novel prediction method of beer foam stability under different conditions of barley cultivar and malt modification, multiple linear regression analysis was applied. The spot intensities of major beer proteins on 2DE gel were quantified and used as explanatory variables. The foam stabilities of 25 beer samples each brewed from malt with different malt modification in one of the three cultivars (cultivars A, B, and C) were explained by the spot intensities of BDAI-1 at the 5% significance level ( r = 0.421). Furthermore, two other major protein spots (b0 and b5) were observed on the 2DE gels of Japanese commercial beer samples with different foam stability. Then, multiple regression for foam stability was calculated using these three spot intensities as explanatory variables. As a result, 72.1% of the beer foam stability in 25 beer samples was explained by a novel multiple regression equation calculated using spot b0 and BDAI-1 as positive explanatory variables and spot b5 as a negative variable. To verify the validity of the multiple regression equation and the explanatory variables, the beer foam stability in practical beer samples was analyzed. As a result, 81.5% of the beer foam stability in 10 Japanese commercial beer samples was also explained by using spot b0 and BDAI-1 as positive explanatory variables and spot b5 as a negative variable. Mass spectrometry analyses followed by database searches revealed that protein spots b0 and b5 were identified as protein Z originated from barley and thioredoxin originated from yeast, respectively. These results confirm that BDAI-1 and protein Z are foam-positive factors and identify yeast thioredoxin as a possible novel foam

  1. Poisson Spot with Magnetic Levitation

    ERIC Educational Resources Information Center

    Hoover, Matthew; Everhart, Michael; D'Arruda, Jose

    2010-01-01

    In this paper we describe a unique method for obtaining the famous Poisson spot without adding obstacles to the light path, which could interfere with the effect. A Poisson spot is the interference effect from parallel rays of light diffracting around a solid spherical object, creating a bright spot in the center of the shadow.

  2. Poisson spot with magnetic levitation

    NASA Astrophysics Data System (ADS)

    Hoover, Matthew; Everhart, Michael; D'Arruda, Jose

    2010-02-01

    In this paper we describe a unique method for obtaining the famous Poisson spot without adding obstacles to the light path, which could interfere with the effect. A Poisson spot is the interference effect from parallel rays of light diffracting around a solid spherical object, creating a bright spot in the center of the shadow.

  3. Great Red Spot (GRS)

    NASA Astrophysics Data System (ADS)

    Murdin, P.

    2000-11-01

    A huge permanent anticyclone in Jupiter's southern hemisphere, visible as a reddish oval at just over 20 °S. The earliest unequivocal observation was by Heinrich Schwabe in 1831 (the often-quoted sighting by Robert Hooke in 1664 now seems to have been of a similar but different spot). The GRS became a striking feature around 1880, when it developed a deep red coloration. It was also prominent in ...

  4. Proteomic profile of edible bird's nest proteins.

    PubMed

    Liu, Xiaoqing; Lai, Xintian; Zhang, Shiwei; Huang, Xiuli; Lan, Quanxue; Li, Yun; Li, Bifang; Chen, Wei; Zhang, Qinlei; Hong, Dezhi; Yang, Guowu

    2012-12-26

    Edible bird's nest (EBN) is made of the swiftlets' saliva, which has attracted rather more attention owing to its nutritious and medical properties. Although protein constitutes the main composition and plays an important role in EBN, few studies have focused on the proteomic profile of EBN. The purpose of this study was to produce a proteomic map and clarify common EBN proteins. Liquid-phase isoelectric focusing (LIEF) was combined with two-dimensional electrophoresis (2-DE) for comprehensive analysis of EBN proteins. From 20 to 100 protein spots were detected on 2-DE maps of EBN samples from 15 different sources. The proteins were mainly distributed in four taxa (A, B, C, and D) according to their molecular mass. Taxa A and D both contained common proteins and proteins that may be considered another characteristic of EBN. Taxon A was identified using MALDI-TOF-TOF/MS and found to be homologous to acidic mammalian chitinase-like ( Meleagris gallopavo ), which is in glycosyl hydrolase family 18. PMID:23214475

  5. Evaluation of Three Protein-Extraction Methods for Proteome Analysis of Maize Leaf Midrib, a Compound Tissue Rich in Sclerenchyma Cells.

    PubMed

    Wang, Ning; Wu, Xiaolin; Ku, Lixia; Chen, Yanhui; Wang, Wei

    2016-01-01

    Leaf morphology is closely related to the growth and development of maize (Zea mays L.) plants and final kernel production. As an important part of the maize leaf, the midrib holds leaf blades in the aerial position for maximum sunlight capture. Leaf midribs of adult plants contain substantial sclerenchyma cells with heavily thickened and lignified secondary walls and have a high amount of phenolics, making protein extraction and proteome analysis difficult in leaf midrib tissue. In the present study, three protein-extraction methods that are commonly used in plant proteomics, i.e., phenol extraction, TCA/acetone extraction, and TCA/acetone/phenol extraction, were qualitatively and quantitatively evaluated based on 2DE maps and MS/MS analysis using the midribs of the 10th newly expanded leaves of maize plants. Microscopy revealed the existence of substantial amounts of sclerenchyma underneath maize midrib epidermises (particularly abaxial epidermises). The spot-number order obtained via 2DE mapping was as follows: phenol extraction (655) > TCA/acetone extraction (589) > TCA/acetone/phenol extraction (545). MS/MS analysis identified a total of 17 spots that exhibited 2-fold changes in abundance among the three methods (using phenol extraction as a control). Sixteen of the proteins identified were hydrophilic, with GRAVY values ranging from -0.026 to -0.487. For all three methods, we were able to obtain high-quality protein samples and good 2DE maps for the maize leaf midrib. However, phenol extraction produced a better 2DE map with greater resolution between spots, and TCA/acetone extraction produced higher protein yields. Thus, this paper includes a discussion regarding the possible reasons for differential protein extraction among the three methods. This study provides useful information that can be used to select suitable protein extraction methods for the proteome analysis of recalcitrant plant tissues that are rich in sclerenchyma cells. PMID:27379139

  6. Evaluation of Three Protein-Extraction Methods for Proteome Analysis of Maize Leaf Midrib, a Compound Tissue Rich in Sclerenchyma Cells

    PubMed Central

    Wang, Ning; Wu, Xiaolin; Ku, Lixia; Chen, Yanhui; Wang, Wei

    2016-01-01

    Leaf morphology is closely related to the growth and development of maize (Zea mays L.) plants and final kernel production. As an important part of the maize leaf, the midrib holds leaf blades in the aerial position for maximum sunlight capture. Leaf midribs of adult plants contain substantial sclerenchyma cells with heavily thickened and lignified secondary walls and have a high amount of phenolics, making protein extraction and proteome analysis difficult in leaf midrib tissue. In the present study, three protein-extraction methods that are commonly used in plant proteomics, i.e., phenol extraction, TCA/acetone extraction, and TCA/acetone/phenol extraction, were qualitatively and quantitatively evaluated based on 2DE maps and MS/MS analysis using the midribs of the 10th newly expanded leaves of maize plants. Microscopy revealed the existence of substantial amounts of sclerenchyma underneath maize midrib epidermises (particularly abaxial epidermises). The spot-number order obtained via 2DE mapping was as follows: phenol extraction (655) > TCA/acetone extraction (589) > TCA/acetone/phenol extraction (545). MS/MS analysis identified a total of 17 spots that exhibited 2-fold changes in abundance among the three methods (using phenol extraction as a control). Sixteen of the proteins identified were hydrophilic, with GRAVY values ranging from -0.026 to -0.487. For all three methods, we were able to obtain high-quality protein samples and good 2DE maps for the maize leaf midrib. However, phenol extraction produced a better 2DE map with greater resolution between spots, and TCA/acetone extraction produced higher protein yields. Thus, this paper includes a discussion regarding the possible reasons for differential protein extraction among the three methods. This study provides useful information that can be used to select suitable protein extraction methods for the proteome analysis of recalcitrant plant tissues that are rich in sclerenchyma cells. PMID:27379139

  7. Alterations of proteins in MDCK cells during acute potassium deficiency.

    PubMed

    Peerapen, Paleerath; Ausakunpipat, Nardtaya; Chanchaem, Prangwalai; Thongboonkerd, Visith

    2016-06-01

    Chronic K(+) deficiency can cause hypokalemic nephropathy associated with metabolic alkalosis, polyuria, tubular dilatation, and tubulointerstitial injury. However, effects of acute K(+) deficiency on the kidney remained unclear. This study aimed to explore such effects by evaluating changes in levels of proteins in renal tubular cells during acute K(+) deficiency. MDCK cells were cultivated in normal K(+) (NK) (K(+)=5.3 mM), low K(+) (LK) (K(+)=2.5 mM), or K(+) depleted (KD) (K(+)=0 mM) medium for 24 h and then harvested. Cellular proteins were resolved by two-dimensional gel electrophoresis (2-DE) and visualized by SYPRO Ruby staining (5 gels per group). Spot matching and quantitative intensity analysis revealed a total 48 protein spots that had significantly differential levels among the three groups. Among these, 46 and 30 protein spots had differential levels in KD group compared to NK and LK groups, respectively. Comparison between LK and NK groups revealed only 10 protein spots that were differentially expressed. All of these differentially expressed proteins were successfully identified by Q-TOF MS and/or MS/MS analyses. The altered levels of heat shock protein 90 (HSP90), ezrin, lamin A/C, tubulin, chaperonin-containing TCP1 (CCT1), and calpain 1 were confirmed by Western blot analysis. Global protein network analysis showed three main functional networks, including 1) cell growth and proliferation, 2) cell morphology, cellular assembly and organization, and 3) protein folding in which the altered proteins were involved. Further investigations on these networks may lead to better understanding of pathogenic mechanisms of low K(+)-induced renal injury. PMID:26976750

  8. The dark spots of Arago.

    PubMed

    Fischer, Pascal; Skelton, Susan E; Leburn, Christopher G; Streuber, Casey T; Wright, Ewan M; Dholakia, Kishan

    2007-09-17

    We explore the diffraction and propagation of Laguerre- Gaussian beams of varying azimuthal index past a circular obstacle both experimentally and numerically. When the beam and obstacle centers are aligned the famous spot of Arago, which arises for zero azimuthal index, is replaced for non-zero azimuthal indices by a dark spot of Arago, a simple consequence of the conserved phase singularity at the beam center. We explore how the dark spot of Arago behaves as the beam and obstacle centers are progressively misaligned, and find that the central dark spot may break into several dark spots of Arago for higher incident azimuthal index beams. PMID:19547549

  9. Conserved Allosteric Hot Spots in the Transmembrane Domains of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Channels and Multidrug Resistance Protein (MRP) Pumps*

    PubMed Central

    Wei, Shipeng; Roessler, Bryan C.; Chauvet, Sylvain; Guo, Jingyu; Hartman, John L.; Kirk, Kevin L.

    2014-01-01

    ATP-binding cassette (ABC) transporters are an ancient family of transmembrane proteins that utilize ATPase activity to move substrates across cell membranes. The ABCC subfamily of the ABC transporters includes active drug exporters (the multidrug resistance proteins (MRPs)) and a unique ATP-gated ion channel (cystic fibrosis transmembrane conductance regulator (CFTR)). The CFTR channel shares gating principles with conventional ligand-gated ion channels, but the allosteric network that couples ATP binding at its nucleotide binding domains (NBDs) with conformational changes in its transmembrane helices (TMs) is poorly defined. It is also unclear whether the mechanisms that govern CFTR gating are conserved with the thermodynamically distinct MRPs. Here we report a new class of gain of function (GOF) mutation of a conserved proline at the base of the pore-lining TM6. Multiple substitutions of this proline promoted ATP-free CFTR activity and activation by the weak agonist, 5′-adenylyl-β,γ-imidodiphosphate (AMP-PNP). TM6 proline mutations exhibited additive GOF effects when combined with a previously reported GOF mutation located in an outer collar of TMs that surrounds the pore-lining TMs. Each TM substitution allosterically rescued the ATP sensitivity of CFTR gating when introduced into an NBD mutant with defective ATP binding. Both classes of GOF mutations also rescued defective drug export by a yeast MRP (Yor1p) with ATP binding defects in its NBDs. We conclude that the conserved TM6 proline helps set the energy barrier to both CFTR channel opening and MRP-mediated drug efflux and that CFTR channels and MRP pumps utilize similar allosteric mechanisms for coupling conformational changes in their translocation pathways to ATP binding at their NBDs. PMID:24876383

  10. Abundant storage protein depletion from tuber proteins using ethanol precipitation method: Suitability to proteomics study.

    PubMed

    Lee, Hye Min; Gupta, Ravi; Kim, Sun Hyung; Wang, Yiming; Rakwal, Randeep; Agrawal, Ganesh Kumar; Kim, Sun Tae

    2015-05-01

    High-abundance proteins (HAPs) hamper in-depth proteome study necessitating development of a HAPs depletion method. Here, we report a novel ethanol precipitation method (EPM) for HAPs depletion from total tuber proteins. Ethanol showed a dose-dependent effect on depletion of sporamin from sweet potato and patatin from potato tubers, respectively. The 50% ethanol was an optimal concentration. 2DE analysis of EPM-prepared sweet potato proteins also revealed enrichment of storage proteins (SPs) in ethanol supernatant (ES) resulting in detection of new low-abundance proteins in ethanol pellet (EP), compared to total fraction. The ES fraction showed even higher trypsin inhibitor activity than total proteins, further showing the efficacy of EPM in enrichment of sporamin in ES fraction. Application of this method was demonstrated for comparative proteomics of two sweet potato cultivars (Hwang-geum and Ho-bac) and purification of SP (sporamin) in its native form, as examples. Comparative proteomics identified many cultivar specific protein spots and selected spots were confidently assigned for their protein identity using MALDI-TOF-TOF analysis. Overall, the EPM is simple, reproducible, and economical for depletion of SPs and is suitable for downstream proteomics study. This study opens a door for its potential application to other tuber crops or fruits rich in carbohydrates. PMID:25689267

  11. Vitamin D Binding Protein Isoforms and Apolipoprotein E in Cerebrospinal Fluid as Prognostic Biomarkers of Multiple Sclerosis

    PubMed Central

    Lis, Katarzyna; Minari, Nicoletta; Falvo, Sara; Marnetto, Fabiana; Caldano, Marzia; Reviglione, Raffaella; Berchialla, Paola; Capobianco, Marco A.; Malentacchi, Maria; Corpillo, Davide; Bertolotto, Antonio

    2015-01-01

    Background Multiple sclerosis (MS) is a multifactorial autoimmune disease of the central nervous system with a heterogeneous and unpredictable course. To date there are no prognostic biomarkers even if they would be extremely useful for early patient intervention with personalized therapies. In this context, the analysis of inter-individual differences in cerebrospinal fluid (CSF) proteome may lead to the discovery of biological markers that are able to distinguish the various clinical forms at diagnosis. Methods To this aim, a two dimensional electrophoresis (2-DE) study was carried out on individual CSF samples from 24 untreated women who underwent lumbar puncture (LP) for suspected MS. The patients were clinically monitored for 5 years and then classified according to the degree of disease aggressiveness and the disease-modifying therapies prescribed during follow up. Results The hierarchical cluster analysis of 2-DE dataset revealed three protein spots which were identified by means of mass spectrometry as Apolipoprotein E (ApoE) and two isoforms of vitamin D binding protein (DBP). These three protein spots enabled us to subdivide the patients into subgroups correlated with clinical classification (MS aggressive forms identification: 80%). In particular, we observed an opposite trend of values for the two protein spots corresponding to different DBP isoforms suggesting a role of a post-translational modification rather than the total protein content in patient categorization. Conclusions These findings proved to be very interesting and innovative and may be developed as new candidate prognostic biomarkers of MS aggressiveness, if confirmed. PMID:26046356

  12. Spotting the enemy within: Targeted silencing of foreign DNA in mammalian genomes by the Krüppel-associated box zinc finger protein family.

    PubMed

    Wolf, Gernot; Greenberg, David; Macfarlan, Todd S

    2015-01-01

    Tandem C2H2-type zinc finger proteins (ZFPs) constitute the largest transcription factor family in animals. Tandem-ZFPs bind DNA in a sequence-specific manner through arrays of multiple zinc finger domains that allow high flexibility and specificity in target recognition. In tetrapods, a large proportion of tandem-ZFPs contain Krüppel-associated-box (KRAB) repression domains, which are able to induce epigenetic silencing through the KAP1 corepressor. The KRAB-ZFP family continuously amplified in tetrapods through segmental gene duplications, often accompanied by deletions, duplications, and mutations of the zinc finger domains. As a result, tetrapod genomes contain unique sets of KRAB-ZFP genes, consisting of ancient and recently evolved family members. Although several hundred human and mouse KRAB-ZFPs have been identified or predicted, the biological functions of most KRAB-ZFP family members have gone unexplored. Furthermore, the evolutionary forces driving the extraordinary KRAB-ZFP expansion and diversification have remained mysterious for decades. In this review, we highlight recent studies that associate KRAB-ZFPs with the repression of parasitic DNA elements in the mammalian germ line and discuss the hypothesis that the KRAB-ZFP family primarily evolved as an adaptive genomic surveillance system against foreign DNA. Finally, we comment on the computational, genetic, and biochemical challenges of studying KRAB-ZFPs and attempt to predict how these challenges may be soon overcome. PMID:26435754

  13. Red Spot Movie

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This brief movie shows counterclockwise atmospheric motion around Jupiter's Great Red Spot. The clip was made from blue-filter images taken with the narrow-angle camera on NASA's Cassini spacecraft during seven separate rotations of Jupiter between Oct. 1 and Oct. 5, 2000.

    The clip also shows the eastward and westward motion of the zonal jets, seen as the horizontal stripes flowing in opposite directions. The zonal jets circle the planet. As far as can be determined from both Earth-based and spacecraft measurements, the positions and speeds of the jets have not changed for 100 years. Since Jupiter is a fluid planet without a solid boundary, the jet speeds are measured relative to Jupiter's magnetic field, which rotates, wobbling like a top because of its tilt, every 9 hours 55.5 minutes. The movie shows motions in the magnetic reference frame, so winds to the west correspond to features that are rotating a little slower than the magnetic field, and eastward winds correspond to features rotating a little faster.

    Because the Red Spot is in the southern hemisphere, the direction of motion indicates it is a high-pressure center. Small bright clouds appear suddenly to the west of the Great Red Spot. Scientists suspect these small white features are lightning storms. The storms eventually merge with the Red Spot and surrounding jets, and may be the main energy source for the large-scale features.

    The smallest features in the movie are about 500 kilometers (about 300 miles) across. The spacing of the movie frames in time is not uniform; some consecutive images are separated by two Jupiter rotations, and some by one. The images have been re-projected using a simple cylindrical map projection. They show an area from 50 degrees north of Jupiter's equator to 50 degrees south, extending 100 degrees east-west, about one quarter of Jupiter's circumference.

    Cassini is a cooperative project of NASA, the European Space Agency and the Italian Space Agency. The Jet

  14. 2D-PAGE protein analysis of dinoflagellate Alexandrium minutum based on three different temperatures

    NASA Astrophysics Data System (ADS)

    Latib, Norhidayu Abdul; Norshaha, Safida Anira; Usup, Gires; Yusof, Nurul Yuziana Mohd

    2015-09-01

    Harmful algae bloom or red tide seems to be considered as threat to ecosystem, especially to human consumption because of the production of neurotoxin by dinoflagellates species such as Alexandrium minutum which can lead to paralytic shellfish poisoning. The aim of this study is to determine the most suitable method for protein extraction of A. minutum followed by determination of differential protein expression of A. minutum on three different temperatures (15°C, 26°C and 31.5°C). After the optimization, the protein extract was subjected to two-dimensional polyacrylamide gel electrophoresis (2-DE) to compare the intensity and distribution of the protein spots. Based on quantitative and qualitative protein assessment, use of Trizol reagent is the most suitable method to extract protein from A. minutum. 2-DE analysis of the samples results in different distribution and intensity of the protein spots were compared between 15°C, 26°C and 31.5°C.

  15. Identification and comparative proteomic study of quail and duck egg white protein using 2-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry analysis

    PubMed Central

    Hu, Shan; Qiu, Ning; Liu, Yaping; Zhao, Hongyan; Gao, Dan; Song, Rui; Ma, Meihu

    2016-01-01

    A proteomic study of egg white proteins from 2 major poultry species, namely quail (Coturnix coturnix) and duck (Anas platyrhynchos), was performed with comparison to those of chicken (Gallus gallus) through 2-dimensional polyacrylamide gel electrophoresis (2-DE) analysis. By using matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF MS/MS), 29 protein spots representing 10 different kinds of proteins as well as 17 protein spots designating 9 proteins were successfully identified in quail and duck egg white, respectively. This report suggested a closer relationship between quail and chicken egg white proteome patterns, whereas the duck egg white protein distribution on the 2-DE map was more distinct. In duck egg white, some well-known major proteins, such as ovomucoid, clusterin, extracellular fatty acid-binding protein precursor (ex-FABP), and prostaglandin D2 synthase (PG D2 synthase), were not detected, while two major protein spots identified as “deleted in malignant brain tumors 1” protein (DMBT1) and vitellogenin-2 were found specific to duck in the corresponding range on the 2-DE gel map. These interspecies diversities may be associated with the egg white protein functions in cell defense or regulating/supporting the embryonic development to adapt to the inhabiting environment or reproduction demand during long-term evolution. The findings of this work will give insight into the advantages involved in the application on egg white proteins from various egg sources, which may present novel beneficial properties in the food industry or related to human health. PMID:26957635

  16. Identification and comparative proteomic study of quail and duck egg white protein using 2-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry analysis.

    PubMed

    Hu, S; Qiu, N; Liu, Y; Zhao, H; Gao, D; Song, R; Ma, M

    2016-05-01

    A proteomic study of egg white proteins from 2 major poultry species, namely quail (Coturnix coturnix) and duck (Anas platyrhynchos), was performed with comparison to those of chicken (Gallus gallus) through 2-dimensional polyacrylamide gel electrophoresis (2-DE) analysis. By using matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF MS/MS), 29 protein spots representing 10 different kinds of proteins as well as 17 protein spots designating 9 proteins were successfully identified in quail and duck egg white, respectively. This report suggested a closer relationship between quail and chicken egg white proteome patterns, whereas the duck egg white protein distribution on the 2-DE map was more distinct. In duck egg white, some well-known major proteins, such as ovomucoid, clusterin, extracellular fatty acid-binding protein precursor (ex-FABP), and prostaglandin D2 synthase (PG D2 synthase), were not detected, while two major protein spots identified as "deleted in malignant brain tumors 1" protein (DMBT1) and vitellogenin-2 were found specific to duck in the corresponding range on the 2-DE gel map. These interspecies diversities may be associated with the egg white protein functions in cell defense or regulating/supporting the embryonic development to adapt to the inhabiting environment or reproduction demand during long-term evolution. The findings of this work will give insight into the advantages involved in the application on egg white proteins from various egg sources, which may present novel beneficial properties in the food industry or related to human health. PMID:26957635

  17. Haloferax mediterranei GlnK proteins are post-translationally modified by uridylylation.

    PubMed

    Pedro-Roig, Laia; Camacho, Mónica; Bonete, María José

    2013-04-01

    In this work we report for the first time a post-translational modification of PII homologues from the Archaea Domain. Haloferax mediterranei is the first haloarchaea whose PII proteins have been studied, it possesses two of them (GlnK1 and GlnK2 ), both encoded adjacent to a gene for the ammonia transporter Amt. An approach based on 2DE, anti-GlnK immunoblot and peptide mass fingerprint (MALDI-TOF-MS) of the reactive spots showed that GlnK proteins in H. mediterranei are post-translationally uridylylated. A third spot with lower pI suggests the existence of a non-descript post-translational modification in this protein family. PMID:23420616

  18. Albumin-Like Protein is the Major Protein Constituent of Luminal Fluid in the Human Endolymphatic Sac

    PubMed Central

    Kim, Sung Huhn; Kim, Un-Kyoung; Lee, Won-Sang; Bok, Jinwoong; Song, Jung-Whan; Seong, Je Kyung; Choi, Jae Young

    2011-01-01

    The endolymphatic sac (ES) is an inner ear organ that is connected to the cochleo-vestibular system through the endolymphatic duct. The luminal fluid of the ES contains a much higher concentration of proteins than any other compartment of the inner ear. This high protein concentration likely contributes to inner ear fluid volume regulation by creating an osmotic gradient between the ES lumen and the interstitial fluid. We characterized the protein profile of the ES luminal fluid of patients (n = 11) with enlarged vestibular aqueducts (EVA) by proteomics. In addition, we investigated differences in the protein profiles between patients with recent hearing deterioration and patients without hearing deterioration. The mean total protein concentration of the luminal fluid was 554.7±94.6 mg/dl. A total of 58 out of 517 spots detected by 2-DE were analyzed by MALDI-TOF MS. The protein profile of the luminal fluid was different from the profile of plasma. Proteins identified from 29 of the spots were also present in the MARC-filtered human plasma; however, the proteins identified from the other 25 spots were not detected in the MARC-filtered human plasma. The most abundant protein in the luminal fluid was albumin-like proteins, but most of them were not detected in MARC-filtered human plasma. The concentration of albumin-like proteins was higher in samples from patients without recent hearing deterioration than in patients with recent hearing deterioration. Consequently, the protein of ES luminal fluid is likely to be originated from both the plasma and the inner ear and considering that inner ear fluid volumes increase abnormally in patients with EVA following recent hearing deterioration, it is tempting to speculate that albumin-like proteins may be involved in the regulation of inner ear fluid volume through creation of an osmotic gradient during pathological conditions such as endolymphatic hydrops. PMID:21738753

  19. Detection of immunogenic parasite and host-specific proteins in the sera of active and chronic individuals infected with Toxoplasma gondii.

    PubMed

    Yeng, Chen; Osman, Emelia; Mohamed, Zeehaida; Noordin, Rahmah

    2010-12-01

    Toxoplasma gondii infection in pregnant women may result in abortion and foetal abnormalities, and may be life-threatening in immunocompromised hosts. To identify the potential infection markers of this disease, 2-DE and Western blot methods were employed to study the parasite circulating antigens and host-specific proteins in the sera of T. gondii-infected individuals. The comparisons were made between serum protein profiles of infected (n=31) and normal (n=10) subjects. Antigenic proteins were identified by immunoblotting using pooled sera and monoclonal anti-human IgM-HRP. Selected protein spots were characterised using mass spectrometry. Prominent differences were observed when serum samples of T. gondii-infected individuals and normal controls were compared. A significant up-regulation of host-specific proteins, α(2)-HS glycoprotein and α(1)-B glycoprotein, was also observed in the silver-stained gels of both active and chronic infections. However, only α(2)-HS glycoprotein and α(1)-B glycoprotein in the active infection showed immunoreactivity in Western blots. In addition, three spots of T. gondii proteins were detected, namely (i) hypothetical protein chrXII: 3984434-3 TGME 49, (ii) dual specificity protein phosphatase, catalytic domain TGME 49 and (iii) NADPH-cytochrome p450 reductase TGME 49. Thus, 2-DE approach followed by Western blotting has enabled the identification of five potential infection markers for the diagnosis of toxoplasmosis: three are parasite-specific proteins and two are host-specific proteins. PMID:21080484

  20. Isolation and characterizations of oxalate-binding proteins in the kidney.

    PubMed

    Roop-ngam, Piyachat; Chaiyarit, Sakdithep; Pongsakul, Nutkridta; Thongboonkerd, Visith

    2012-08-01

    Oxalate-binding proteins are thought to serve as potential modulators of kidney stone formation. However, only few oxalate-binding proteins have been identified from previous studies. Our present study, therefore, aimed for large-scale identification of oxalate-binding proteins in porcine kidney using an oxalate-affinity column containing oxalate-conjugated EAH Sepharose 4B beads for purification followed by two-dimensional gel electrophoresis (2-DE) to resolve the recovered proteins. Comparing with those obtained from the controlled column containing uncoupled EAH-Sepharose 4B (to subtract the background of non-specific bindings), a total of 38 protein spots were defined as oxalate-binding proteins. These protein spots were successfully identified by quadrupole time-of-flight mass spectrometry (MS) and/or tandem MS (MS/MS) as 26 unique proteins, including several nuclear proteins, mitochondrial proteins, oxidative stress regulatory proteins, metabolic enzymes and others. Identification of oxalate-binding domain using the PRATT tool revealed "L-x(3,5)-R-x(2)-[AGILPV]" as a functional domain responsible for oxalate-binding in 25 of 26 (96%) unique identified proteins. We report herein, for the first time, large-scale identification and characterizations of oxalate-binding proteins in the kidney. The presence of positively charged arginine residue in the middle of this functional domain suggested its significance for binding to the negatively charged oxalate. These data will enhance future stone research, particularly on stone modulators. PMID:22796524

  1. Proteomic Analysis of Trichinella spiralis Muscle Larval Excretory-Secretory Proteins Recognized by Early Infection Sera

    PubMed Central

    Wang, Li; Wang, Zhong Quan; Hu, Dan Dan; Cui, Jing

    2013-01-01

    Although the excretory-secretory (ES) proteins of Trichinella spiralis muscle larvae are the most commonly used diagnostic antigens for trichinellosis, their main disadvantage is the false negative results during the early stage of infection and cross-reaction of their main components (43, 45, 49, and 53 kDa) with sera of patients with other helminthiasis. The aim of this study was to identify early specific diagnostic antigens in T. spiralis ES proteins with 30–40 kDa. The ES proteins were analyzed by two-dimensional electrophoresis (2-DE), and a total of approximately 150 proteins spots were detected with isoelectric point (pI) varying from 4 to 7 and molecular weight from 14 to 66 kDa. When probed with sera from infected mice at 18 days postinfection, ten protein spots with molecular weight of 30–40 kDa were recognized and identified by MALDI-TOF/TOF-MS. All of ten spots were successfully identified and characterized to correlate with five different proteins, including two potential serine proteases, one antigen targeted by protective antibodies, one deoxyribonuclease (DNase) II, and one conserved hypothetical protein. These proteins might be the early specific diagnostic antigens for trichinellosis. PMID:23844355

  2. Differential expression proteins associated with bud dormancy release during chilling treatment of tree peony (Paeonia suffruticosa).

    PubMed

    Zhang, Y X; Yu, D; Tian, X L; Liu, C Y; Gai, S P; Zheng, G S

    2015-01-01

    Endo-dormant flower buds of tree peony must have sufficient chilling duration to reinitiate growth, which is a major obstacle to the forcing culture of tree peony in winter. We used a combination of two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionisation time of flight/time of flight mass spectrometry (MALDI-TOF/TOF MS) to identify the differentially expressed proteins of tree peony after three different chilling treatments: endo-dormancy, endo-dormancy release and eco-dormancy stages. More than 200 highly reproducible protein spots were detected, and 31 differentially expressed spots (P < 0.05) were selected for further analysis. Finally, 20 protein spots were confidently identified from databases, which were annotated and classified into seven functional categories: response to abiotic or biotic stimulus (four), metabolic processes (four), other binding (three), transcription or transcription regulation (two), biological processes (one), cell biogenesis (one) and unclassified (five). The results of qPCR of five genes were mainly consistent with that of the protein accumulation analysis as determined by 2-DE. This indicated that most of these genes were mainly regulated at transcriptional level. The activity of nitrate reductase and pyruvate dehydrogenase E1 was consistent with the 2-DE results. The proteomic profiles indicated activation of citrate cycle, amino acid metabolism, lipid metabolism, energy production, calcium signalling and cell growth processes by chilling fulfilment to facilitate dormancy release in tree peony. Analysis of functions of identified proteins will increase our knowledge of endo-dormancy release in tree peony. PMID:25091021

  3. Alteration of sperm protein profile induced by cigarette smoking.

    PubMed

    Chen, Xiaohui; Xu, Wangjie; Miao, Maohua; Zhu, Zijue; Dai, Jingbo; Chen, Zhong; Fang, Peng; Wu, Junqing; Nie, Dongsheng; Wang, Lianyun; Wang, Zhaoxia; Qiao, Zhongdong; Shi, Huijuan

    2015-07-01

    Cigarette smoking is associated with lower semen quality, but how cigarette smoking changes the semen quality remains unclear. The aim of this study was to screen the differentially expressed proteins in the sperm of mice with daily exposure to cigarette smoke. The 2D gel electrophoresis (2DE) and mass spectrometry (MS) analyses results showed that the mouse sperm protein profile was altered by cigarette smoking. And 22 of the most abundant proteins that correspond to differentially expressed spots in 2DE gels of the sperm samples were identified. These proteins were classified into different groups based on their functions, such as energy metabolism, reproduction, and structural molecules. Furthermore, the 2DE and MS results of five proteins (Aldoa, ATP5a1, Gpx4, Cs, and Spatc1) were validated by western blot analysis and reverse transcriptase-polymerase chain reaction. Results showed that except Spatc1 the other four proteins showed statistically significant different protein levels between the smoking group and the control group (P < 0.05). The expressions of three genes (Aldoa, Gpx4, and Spatc1) were significantly different (P < 0.05) at transcription level between the smoking group and the control group. In addition, five proteins (Aldoa, ATP5a1, Spatc1, Cs, and Gpx4) in human sperm samples from 30 male smokers and 30 non-smokers were detected by western blot analysis. Two proteins (Aldoa and Cs) that are associated with energy production were found to be significantly altered, suggesting that these proteins may be potential diagnostic markers for evaluation of smoking risk in sperm. Further study of these proteins may provide insight into the pathogenic mechanisms underlying infertility in smoking persons. PMID:26063603

  4. Exserohilum Leaf Spot on Tigergrass

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tigergrass (Thysanolaena maxima (Roxb.) Kuntze ) is a popular ornamental grass grown throughout landscapes in South Florida. In the summer of 2006, a leaf spot was observed on tigergrass in the landscape and a commercial nursery in Homestead, FL. The causal agent of the leaf spot was isolated, cha...

  5. Do Cupins Have a Function Beyond Being Seed Storage Proteins?

    PubMed

    Gábrišová, Daša; Klubicová, Katarína; Danchenko, Maksym; Gömöry, Dušan; Berezhna, Valentyna V; Skultety, Ludovit; Miernyk, Ján A; Rashydov, Namik; Hajduch, Martin

    2015-01-01

    Plants continue to flourish around the site of the Chernobyl Nuclear Power Plant disaster. The ability of plants to transcend the radio-contaminated environment was not anticipated and is not well understood. The aim of this study was to evaluate the proteome of flax (Linum usitatissimum L.) during seed filling by plants grown for a third generation near Chernobyl. For this purpose, seeds were harvested at 2, 4, and 6 weeks after flowering and at maturity, from plants grown in either non-radioactive or radio-contaminated experimental fields. Total proteins were extracted and the two-dimensional gel electrophoresis (2-DE) patterns analyzed. This approach established paired abundance profiles for 130 2-DE spots, e.g., profiles for the same spot across seed filling in non-radioactive and radio-contaminated experimental fields. Based on Analysis of Variance (ANOVA) followed by sequential Bonferroni correction, eight of the paired abundance profiles were discordant. Results from tandem mass spectrometry show that four 2-DE spots are discordant because they contain fragments of the cupin superfamily-proteins. Most of the fragments were derived from the N-terminal half of native cupins. Revisiting previously published data, it was found that cupin-fragments were also involved with discordance in paired abundance profiles of second generation flax seeds. Based on these observations we present an updated working model for the growth and reproductive success of flax in a radio-contaminated Chernobyl environment. This model suggests that the increased abundance of cupin fragments or isoforms and monomers contributes to the successful growth and reproduction of flax in a radio-contaminated environment. PMID:26793203

  6. Do Cupins Have a Function Beyond Being Seed Storage Proteins?

    PubMed Central

    Gábrišová, Daša; Klubicová, Katarína; Danchenko, Maksym; Gömöry, Dušan; Berezhna, Valentyna V.; Skultety, Ludovit; Miernyk, Ján A.; Rashydov, Namik; Hajduch, Martin

    2016-01-01

    Plants continue to flourish around the site of the Chernobyl Nuclear Power Plant disaster. The ability of plants to transcend the radio-contaminated environment was not anticipated and is not well understood. The aim of this study was to evaluate the proteome of flax (Linum usitatissimum L.) during seed filling by plants grown for a third generation near Chernobyl. For this purpose, seeds were harvested at 2, 4, and 6 weeks after flowering and at maturity, from plants grown in either non-radioactive or radio-contaminated experimental fields. Total proteins were extracted and the two-dimensional gel electrophoresis (2-DE) patterns analyzed. This approach established paired abundance profiles for 130 2-DE spots, e.g., profiles for the same spot across seed filling in non-radioactive and radio-contaminated experimental fields. Based on Analysis of Variance (ANOVA) followed by sequential Bonferroni correction, eight of the paired abundance profiles were discordant. Results from tandem mass spectrometry show that four 2-DE spots are discordant because they contain fragments of the cupin superfamily-proteins. Most of the fragments were derived from the N-terminal half of native cupins. Revisiting previously published data, it was found that cupin-fragments were also involved with discordance in paired abundance profiles of second generation flax seeds. Based on these observations we present an updated working model for the growth and reproductive success of flax in a radio-contaminated Chernobyl environment. This model suggests that the increased abundance of cupin fragments or isoforms and monomers contributes to the successful growth and reproduction of flax in a radio-contaminated environment. PMID:26793203

  7. Hot Spot Cosmic Accelerators

    NASA Astrophysics Data System (ADS)

    2002-11-01

    length of more than 3 million light-years, or no less than one-and-a-half times the distance from the Milky Way to the Andromeda galaxy, this structure is indeed gigantic. The region where the jets collide with the intergalactic medium are known as " hot spots ". Superposing the intensity contours of the radio emission from the southern "hot spot" on a near-infrared J-band (wavelength 1.25 µm) VLT ISAAC image ("b") shows three distinct emitting areas; they are even better visible on the I-band (0.9 µm) FORS1 image ("c"). This emission is obviously associated with the shock front visible on the radio image. This is one of the first times it has been possible to obtain an optical/near-IR image of synchrotron emission from such an intergalactic shock and, thanks to the sensitivity and image sharpness of the VLT, the most detailed view of its kind so far . The central area (with the strongest emission) is where the plasma jet from the galaxy centre hits the intergalactic medium. The light from the two other "knots", some 10 - 15,000 light-years away from the central "hot spot", is also interpreted as synchrotron emission. However, in view of the large distance, the astronomers are convinced that it must be caused by electrons accelerated in secondary processes at those sites . The new images thus confirm that electrons are being continuously accelerated in these "knots" - hence called "cosmic accelerators" - far from the galaxy and the main jets, and in nearly empty space. The exact physical circumstances of this effect are not well known and will be the subject of further investigations. The present VLT-images of the "hot spots" near 3C 445 may not have the same public appeal as some of those beautiful images that have been produced by the same instruments during the past years. But they are not less valuable - their unusual importance is of a different kind, as they now herald the advent of fundamentally new insights into the mysteries of this class of remote and active

  8. A Proteomic Approach for the Identification of Up-Regulated Proteins Involved in the Metabolic Process of the Leiomyoma

    PubMed Central

    Ura, Blendi; Scrimin, Federica; Arrigoni, Giorgio; Franchin, Cinzia; Monasta, Lorenzo; Ricci, Giuseppe

    2016-01-01

    Uterine leiomyoma is the most common benign smooth muscle cell tumor of the uterus. Proteomics is a powerful tool for the analysis of complex mixtures of proteins. In our study, we focused on proteins that were upregulated in the leiomyoma compared to the myometrium. Paired samples of eight leiomyomas and adjacent myometrium were obtained and submitted to two-dimensional gel electrophoresis (2-DE) and mass spectrometry for protein identification and to Western blotting for 2-DE data validation. The comparison between the patterns revealed 24 significantly upregulated (p < 0.05) protein spots, 12 of which were found to be associated with the metabolic processes of the leiomyoma and not with the normal myometrium. The overexpression of seven proteins involved in the metabolic processes of the leiomyoma was further validated by Western blotting and 2D Western blotting. Four of these proteins have never been associated with the leiomyoma before. The 2-DE approach coupled with mass spectrometry, which is among the methods of choice for comparative proteomic studies, identified a number of proteins overexpressed in the leiomyoma and involved in several biological processes, including metabolic processes. A better understanding of the mechanism underlying the overexpression of these proteins may be important for therapeutic purposes. PMID:27070597

  9. Protein abundance changes of Zygosaccharomyces rouxii in different sugar concentrations.

    PubMed

    Guo, Hong; Niu, Chen; Liu, Bin; Wei, JianPing; Wang, HuXuan; Yuan, YaHong; Yue, TianLi

    2016-09-16

    Zygosaccharomyces rouxii is a yeast which can cause spoilage in the concentrated juice industries. It exhibits resistance to high sugar concentrations but genome- and proteome-wide studies on Z. rouxii in response to high sugar concentrations have been poorly investigated. Herein, by using a 2-D electrophoresis based workflow, the proteome of a wild strain of Z. rouxii under different sugar concentrations has been analyzed. Proteins were extracted, quantified, and subjected to 2-DE analysis in the pH range 4-7. Differences in growth (lag phase), protein content (13.97-19.23mg/g cell dry weight) and number of resolved spots (196-296) were found between sugar concentrations. ANOVA test showed that 168 spots were different, and 47 spots, corresponding to 40 unique gene products have been identified. These protein species are involved in carbohydrate and energy metabolism, amino acid metabolism, response to stimulus, protein transport and vesicle organization, cell morphogenesis regulation, transcription and translation, nucleotide metabolism, amino-sugar nucleotide-sugar pathways, oxidoreductases balancing, and ribosome biogenesis. The present study provides important information about how Z. rouxii acts to cope with high sugar concentration at molecular levels, which might enhance our global understanding of Z. rouxii's high sugar-tolerance trait. PMID:27322723

  10. Mapping the leaf proteome of Miscanthus sinensis and its application to the identification of heat-responsive proteins.

    PubMed

    Sharmin, Shamima Akhtar; Alam, Iftekhar; Rahman, Md Atikur; Kim, Kyung-Hee; Kim, Yong-Goo; Lee, Byung-Hyun

    2013-09-01

    Miscanthus sinensis is a promising bioenergy crop; however, its genome is poorly represented in sequence databases. As an initial step in the comprehensive analysis of the M. sinensis proteome, we report a reference 2-DE protein map of the leaf. A total of 316 protein spots were excised from the gels, digested with trypsin and subjected to matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) or MALDI-TOF/TOF MS. Two hundred and thirty-two protein spots were identified, which are involved in a variety of cellular functions through distinct metabolic pathways. Functional annotation of the proteins revealed a nearly complete C3 and C4 cycle, starch and sugar synthesis pathway, glycolysis pathway, a significant portion of the pentose phosphate pathway, and many enzymes involved in secondary metabolism such as flavonoid/isoflavonoid, kaurene, chalcone, sesquiterpene and lignin biosynthesis. Other proteins belong to primary metabolism, transcription, protein synthesis, protein destination/storage, disease/defense, cell growth/division, transportation and signal transduction. To test the applicability of the constructed map, we studied the effect of heat stress on M. sinensis leaf proteome. Twenty-five protein spots were upregulated, five were newly induced and twenty-five spots were downregulated by heat treatment. The differentially accumulated proteins were involved in photosynthesis, energy metabolism, gene transcription, protein kinases and phosphatases, signal transduction, protein synthesis and heat shock responses. C4-specific pyruvate orthophosphate dikinase, Rubisco large subunit, Rubisco activase and some associated proteins were upregulated during heat stress and tend to restore upon recovery. Identification of these proteins provides some important clues regarding the way M. sinensis copes with hot climate. This work represents the first extensive proteomic description of M. sinensis and provides a reference map and heat

  11. Characterization of wheat gliadin proteins by combined two-dimensional gel electrophoresis and tandem mass spectrometry.

    PubMed

    Mamone, Gianfranco; Addeo, Francesco; Chianese, Lina; Di Luccia, Aldo; De Martino, Alessandra; Nappo, Annunziata; Formisano, Annarita; De Vivo, Pasqualina; Ferranti, Pasquale

    2005-07-01

    A proteomics-based approach was used for characterizing wheat gliadins from an Italian common wheat (Triticum aestivum) cultivar. A two-dimensional gel electrophoresis (2-DE) map of roughly 40 spots was obtained by submitting the 70% alcohol-soluble crude protein extract to isoelectric focusing on immobilized pH gradient strips across two pH gradient ranges, i.e., 3-10 or pH 6-11, and to sodium dodecyl sulfate-polyacrylamide electrophoresis in the second dimension. The chymotryptic digest of each spot was characterized by matrix-assisted laser desorption/ionization-time of flight mass spectrometry and nano electrospray ionization-tandem mass spectrometry (MS/MS) analysis, providing a "peptide map" for each digest. The measured masses were subsequently sought in databases for sequences. For accurate identification of the parent protein, it was necessary to determine de novo sequences by MS/MS experiments on the peptides. By partial mass fingerprinting, we identified protein molecules such as alpha/beta-, gamma-, omega-gliadin, and high molecular weight-glutenin. The single spots along the 2-DE map were discriminated on the basis of their amino acid sequence traits. alpha-Gliadin, the most represented wheat protein in databases, was highly conserved as the relative N-terminal sequence of the components from the 2-DE map contained only a few silent amino acid substitutions. The other closely related gliadins were identified by sequencing internal peptide chains. The results gave insight into the complex nature of gliadin heterogeneity. This approach has provided us with sound reference data for differentiating gliadins amongst wheat varieties. PMID:15952231

  12. Saturn's Hot Spot

    NASA Technical Reports Server (NTRS)

    2005-01-01

    This is the sharpest image of Saturn's temperature emissions taken from the ground; it is a mosaic of 35 individual exposures made at the W.M. Keck I Observatory, Mauna Kea, Hawaii on Feb. 4, 2004.

    The images to create this mosaic were taken with infrared radiation. The mosaic was taken at a wavelength near 17.65 microns and is sensitive to temperatures in Saturn's upper troposphere. The prominent hot spot at the bottom of the image is right at Saturn's south pole. The warming of the southern hemisphere was expected, as Saturn was just past southern summer solstice, but the abrupt changes in temperature with latitude were not expected. The tropospheric temperature increases toward the pole abruptly near 70 degrees latitude from 88 to 89 Kelvin (-301 to -299 degrees Fahrenheit) and then to 91 Kelvin (-296 degrees Fahrenheit) right at the pole.

    Ring particles are not at a uniform temperature everywhere in their orbit around Saturn. The ring particles are orbiting clockwise in this image. Particles are coldest just after having cooled down in Saturn's shadow (lower left). As they orbit Saturn, the particles increase in temperature up to a maximum (lower right) just before passing behind Saturn again in shadow.

    A small section of the ring image is missing because of incomplete mosaic coverage during the observing sequence.

  13. Rocky Mountain spotted fever.

    PubMed

    Comer, K M

    1991-01-01

    Rocky Mountain spotted fever is an endemic tickborne disease found throughout the United States and other regions of the world. Exposure may result in a spectrum of disease from subclinical infection to severe or fatal multiorgan collapse. The disease is maintained in nature in Ixodid tick vectors and their hosts. The most important ticks in the United States are Dermacentor variabilis and Dermacentor andersoni. Small mammals are the natural reservoirs in the wild. Dogs become infected when a tick harboring Rickettsia rickettsii feeds on the dog. Dogs do not develop sufficient rickettsemia to act as a reservoir in the transmission of Rickettsia rickettsii. Thus, although dogs act as sentinels to the presence of the disease, they cannot directly transmit infection. Signs in early stages of disease often are nonspecific. The most characteristic laboratory abnormality is thrombocytopenia, but serologic testing is necessary for confirmation of infection. Tetracycline and chloramphenicol are effective antibiotics to treat infection. Treatment should continue for 14 to 21 days to allow host immune defenses to develop and eradicate the organism. Prevention requires avoidance of tick-infested areas and rapid removal of ticks should exposure occur. PMID:2014623

  14. Empathy's blind spot.

    PubMed

    Slaby, Jan

    2014-05-01

    The aim of this paper is to mount a philosophical challenge to the currently highly visible research and discourse on empathy. The notion of empathetic perspective-shifting-a conceptually demanding, high-level construal of empathy in humans that arguably captures the core meaning of the term-is criticized from the standpoint of a philosophy of normatively accountable agency. Empathy in this demanding sense fails to achieve a true understanding of the other and instead risks to impose the empathizer's self-constitutive agency upon the person empathized with. Attempts to 'simulate' human agency, or attempts to emulate its cognitive or emotional basis, will likely distort their target phenomena in profound ways. Thus, agency turns out to be empathy's blind spot. Elements of an alternative understanding of interpersonal relatedness are also discussed, focusing on aspects of 'interaction theory'. These might do some of the work that high-level constructs of empathy had been supposed to do without running into similar conceptual difficulties. PMID:24420745

  15. Identification of developmentally-regulated proteins in Leishmania panamensis by proteome profiling of promastigotes and axenic amastigotes.

    PubMed

    Walker, John; Vasquez, Juan-José; Gomez, Maria Adelaida; Drummelsmith, Jolyne; Burchmore, Richard; Girard, Isabelle; Ouellette, Marc

    2006-05-01

    We have employed proteomics to identify proteins upregulated in the amastigote life-stage of Leishmaniapanamensis, using axenically-differentiated forms as models of authentic intracellular parasites. Resolution of the soluble proteomes of axenic amastigotes and promastigotes by two-dimensional electrophoresis (2DE) in the neutral pI range (5-7) revealed equivalent numbers of protein spots in both life-stages (644-682 using Coomassie Blue and 851-863 by silver staining). Although representing a relatively low proportion (8.1-10.8%) of the predicted 8000 gene products of Leishmania, these proteome maps enabled the reproducible detection of 75 differentially-regulated protein spots in amastigotes, comprising 24 spots "uniquely" expressed in this life-stage and 51 over-expressed by 1.2-5.7-fold compared to promastigotes. Of the 11 amastigote-specific spots analysed by mass spectrometry (MS), 5 yielded peptide sequences with no orthologues in Leishmania major, and the remaining 6 were identified as 7 distinct proteins (some of which were truncated isoforms) representing several functional classes: carbohydrate/energy metabolism (fructose 1,6-bisphosphate aldolase, glucose 6-phosphate dehydrogenase, pyruvate dehydrogenase), stress response (heat shock protein [HSP] 83), cell membrane/cytoskeleton (beta-tubulin), amino acid metabolism (cysteine synthase) and cell-cycle (ran-binding protein). Four additional over-expressed spots were tentatively identified as HSPs 60 and 70 and HSP 70-related proteins -1 and -4 by positional analogy with these landmark proteins in the Leishmania guyanensis proteome. Our data demonstrate the feasibility of proteomics as an approach to identify novel developmentally-regulated proteins linked to Leishmania differentiation and intracellular survival, while simultaneously pinpointing therapeutic targets. In particular, the amastigote-specific expression of cysteine synthase underlines the importance of de novo cysteine synthesis both as a

  16. Spot identification on 2D electrophoresis gel images

    NASA Astrophysics Data System (ADS)

    Wang, Weixing

    2006-09-01

    2-D electrophoresis gel images can be used for identifying and characterizing many forms of a particular protein encoded by a single gene. Conventional approaches to gel analysis require the three steps: (1) Spot detection on each gel; (2) Spot matching between gels; and (3) Spot quantification and comparison. Many researchers and developers attempt to automate all steps as much as possible, but errors in the detection and matching stages are common. In order to carry out gel image analysis, one first needs to accurately detect and measure the protein spots in a gel image. This paper presents the algorithms for automatically delineating gel spots. The fusion of two types of segmentation algorithms was implemented. One is edge (discontinuity) based type, and the other is region based type. The primary integration of the two types of image segmentation algorithms have been tested too, the test results clearly show that the integrated algorithm can automatically delineate gel spots not only on a simple image and also on a complex image, and it is much better that either only edge based algorithm or only region based algorithm. Based on the testing and analysis results, the fusion of edge information and region information for gel image segmentation is good for this kind of images.

  17. Protein expression in human trabecular meshwork: downregulation of RhoGDI by dexamethasone in vitro

    PubMed Central

    Yu, Minbin; Sun, Jing; Peng, Wei; Chen, Ziyan; Lin, Xianchai; Liu, Xuyang; Li, Mingtao

    2010-01-01

    Purpose The characterization of the human trabecular meshwork (TM) proteome is a valuable step toward understanding its role under normal and glaucomatous conditions. This study uses proteomic techniques to investigate the set of proteins expressed in normal human TM and to identify those differentially expressed in response to dexamethasone (DEX) treatment of TM cells (TMCs) in vitro. Methods TM tissue (TMT) was isolated from human donor eyes and pooled. Immortalized human TMCs were cultured with or without DEX. Protein extracts from each were separated by two-dimensional electrophoresis (2-DE). Protein spots in TMT gel were excised, destained, and subjected to in-gel tryptic digestion and identification with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). To determine those proteins whose expression patterns were affected by glucocorticoids, TMCs were treated with DEX and assayed by 3-(4,5-dimethylthiazol-2-yl)-2,5- diphenyltetrazolium bromide (MTT) dye and 2-DE. A differentially expressed protein, RhoGDI, was validated by both western blotting and immunocytological staining. Results The comprehensive protein set included more than 850 protein spots from both the TMT and TMCs, as visualized on 2-DE gel. Two-hundred-and-thirty-five spots were successfully identified in the TMT gel. The functional categories of the identified proteins were mainly comprised of metabolic process, cell adhesion, anti-apoptosis, cell motility, carbohydrate metabolic process, signal transduction, and regulation of transcription. During three days of DEX treatment, TMCs’ proliferation was inhibited in a time- and dose-dependent manner, as evidenced by MTT assay. In the 48 h cultured cell group, RhoGDI expression was reduced, as detected by 2-DE, western blotting, and immunocytological staining. In contrast, the expression of RhoA, a target of RhoGDI, increased in response to DEX treatment. Conclusions Using the classic proteomic workflow

  18. Combining subproteome enrichment and Rubisco depletion enables identification of low abundance proteins differentially regulated during plant defense.

    PubMed

    Widjaja, Ivy; Naumann, Kai; Roth, Udo; Wolf, Noreen; Mackey, David; Dangl, Jeffery L; Scheel, Dierk; Lee, Justin

    2009-01-01

    Transgenic Arabidopsis conditionally expressing the bacterial avrRpm1 type III effector under the control of a dexamethasone-responsive promoter were used for proteomics studies. This model system permits study of an individual effector without interference from additional bacterial components. Coupling of different prefractionation approaches to high resolution 2-DE facilitated the discovery of low abundance proteins - enabling the identification of proteins that have escaped detection in similar experiments. A total of 34 differentially regulated protein spots were identified. Four of these (a remorin, a protein phosphatase 2C (PP2C), an RNA-binding protein, and a C2-domain-containing protein) are potentially early signaling components in the interaction between AvrRpm1 and the cognate disease resistance gene product, resistance to Pseudomonas syringae pv. maculicola 1 (RPM1). For the remorin and RNA-binding protein, involvement of PTM and post-transcriptional regulation are implicated, respectively. PMID:19053141

  19. Proteome analysis of metabolic proteins (pI 4-7) in barley (Hordeum vulgare) malts and initial application in malt quality discrimination.

    PubMed

    Jin, Zhao; Mu, Yu-Wen; Sun, Jun-Yong; Li, Xiao-Min; Gao, Xian-Li; Lu, Jian

    2013-01-16

    Barley malt is essential for beer production. In the present study, the nonprolamin fractions including proteins with structural functions or metabolic activities were extracted from barley malts of the widely used cultivars Gangpi and Baudin in China. The metabolic proteomes (pI 4-7) were constructed and compared using two-dimensional electrophoresis (2DE) followed by matrix-assisted laser desorption/ionization-tandem time-of-flight mass spectrometry (MALDI-TOF/TOF) identification. There were 333 and 354 spots detected in the 2DE gels of Gangpi and Baudin malts, respectively, and about 90% of these spots were shared by the two malts. For all, 377 were successfully identified to 192 proteins, most of which were enzymes and enzyme inhibitors, suggesting important roles in barley malting and the mashing stage of brewing. The Baudin malt was found to contain more spots representing amylases, pathogen-related proteins, and chaperones than the Gangpi malt. In addition, enzymes involved in glycolysis and redox pathways showed significantly different profiles between the two malts, permitting a more in-depth elucidation of the relationship between differential proteins and malt qualities. PMID:23198685

  20. Comparative proteomics analysis of oral cancer cell lines: identification of cancer associated proteins

    PubMed Central

    2014-01-01

    Background A limiting factor in performing proteomics analysis on cancerous cells is the difficulty in obtaining sufficient amounts of starting material. Cell lines can be used as a simplified model system for studying changes that accompany tumorigenesis. This study used two-dimensional gel electrophoresis (2DE) to compare the whole cell proteome of oral cancer cell lines vs normal cells in an attempt to identify cancer associated proteins. Results Three primary cell cultures of normal cells with a limited lifespan without hTERT immortalization have been successfully established. 2DE was used to compare the whole cell proteome of these cells with that of three oral cancer cell lines. Twenty four protein spots were found to have changed in abundance. MALDI TOF/TOF was then used to determine the identity of these proteins. Identified proteins were classified into seven functional categories – structural proteins, enzymes, regulatory proteins, chaperones and others. IPA core analysis predicted that 18 proteins were related to cancer with involvements in hyperplasia, metastasis, invasion, growth and tumorigenesis. The mRNA expressions of two proteins – 14-3-3 protein sigma and Stress-induced-phosphoprotein 1 – were found to correlate with the corresponding proteins’ abundance. Conclusions The outcome of this analysis demonstrated that a comparative study of whole cell proteome of cancer versus normal cell lines can be used to identify cancer associated proteins. PMID:24422745

  1. Differential proteomics analysis of proteins from human diabetic and age-related cataractous lenses

    PubMed Central

    Zhu, Jing; Shao, Jun; Yao, Yong; Chu, Zhao Dong; Yu, Qian Qian; Zhao, Wei; Lin, Qing; Zhang, Zi Yin

    2013-01-01

    Backgound: To investigate the differential lens proteomics between diabetic cataract, age-related cataract, and natural subjects. Materials and Methods: Two-dimensional electrophoresis (2-DE), mass spectrometry (MS), and enzyme-linked immunosorbent assay (ELISA) were employed. Total soluble proteins in lenses of type I diabetic cataract, age-related cataract (nondiabetic) patients, and normal control were extracted and subjected to 2-DE. The differential protein spots were recovered, digested with trypsin, and further applied to MALDI-TOF-MS. ELISA analysis was used to determine the levels of differential proteins in lenses of three groups. Results: 2-DE analysis reflected that lens proteins of normal control, diabetic, and age-related cataract subjects were in the section of pH 5-9 and the relative molecular weights were 14-97 kDa, while relative molecular weight of more abundant crystallines was localized at 20-31 kDa. five differential protein spots were detected and identified using MALDI-TOF-MS, including beta-crystallin A3, alpha-crystallin B chain, chain A of crystal structure of truncated human beta-B1-crystallin, beta-crystallin B1, and an interesting unnamed protein product highly similar to alpha-crystallin B chain, respectively. ELISA analysis revealed that lenses of diabetic cataract patients should contain significantly more concentrations of beta-crystallin A3, alpha-crystallin B chain, and beta-crystallin B1 than those of age-related cataract patients and normal control. Conclusion: This study clearly reflected the differential proteins of diabetic cataract, age-related cataract lenses compared with natural subjects, and it is helpful for the further research on the principles and mechanisms of different types of cataract. PMID:24520233

  2. Multiplex staining of 2-DE gels for an initial phosphoproteome analysis of germinating seeds and early grown seedlings from a non-orthodox specie: Quercus ilex L. subsp. ballota [Desf.] Samp.

    PubMed Central

    Romero-Rodríguez, M. Cristina; Abril, Nieves; Sánchez-Lucas, Rosa; Jorrín-Novo, Jesús V.

    2015-01-01

    As a preliminary step in the phosphoproteome analysis of germinating seeds (0 and 24 h after seed imbibition) and early grown seedlings (216 h after seed imbibition) from a non-orthodox sp. Quercus ilex, a multiplex (SYPRO-Ruby and Pro-Q DPS) staining of high-resolution 2-DE gels was used. By using this protocol it was possible to detect changes in protein-abundance and/or phosphorylation status. This simple approach could be a good complementary alternative to the enrichment protocols used in the search for phosphoprotein candidates. While 482 spots were visualized with SYPRO-Ruby, 222 were with Pro-Q DPS. Statistically significant differences in spot intensity were observed among samples, these corresponding to 85 SYPRO-Ruby-, 20 Pro-Q-DPS-, and 35 SYPRO-Ruby and Pro-Q-DPS-stained spots. Fifty-five phosphoprotein candidates showing qualitative or quantitative differences between samples were subjected to MALDI-TOF-TOF MS analysis, with 20 of them being identified. Identified proteins belonged to five different functional categories, namely: carbohydrate and amino acid metabolism, defense, protein folding, and oxidation-reduction processes. With the exception of a putative cyclase, the other 19 proteins had at least one orthologous phosphoprotein in Arabidopsis thaliana, Medicago truncatula, N. tabacum, and Glycine max. Out of the 20 identified, seven showed differences in intensity in Pro-Q-DPS but not in SYPRO-Ruby-stained gels, including enzymes of the glycolysis and amino acid metabolism. This bears out that theory the regulation of these enzymes occurs at the post-translational level by phosphorylation with no changes at the transcriptional or translational level. This is different from the mechanism reported in orthodox seeds, in which concomitant changes in abundance and phosphorylation status have been observed for these enzymes. PMID:26322061

  3. Jupiter Great Red Spot Mosaic

    NASA Technical Reports Server (NTRS)

    1979-01-01

    This photo of Jupiter's Great Red Spot was taken by Voyager 1 in early March 1979. Distance from top to bottom of the picture is 15,000 miles (24,000 kilometers). Smallest features visible are about 20 miles (30 kilometers) across. The white feature below the Great Red Spot is one of several white ovals that were observed to form about 40 years ago; they move around Jupiter at a different velocity from the Red Spot. During the Voyager 1 encounter period, material was observed to revolve around the center of the spot with a period of six days. The Voyager project is managed for NASA's Office of Space Science by the Jet Propulsion Laboratory.

  4. Jupiter's Great Red Spot Region

    NASA Technical Reports Server (NTRS)

    1979-01-01

    This mosaic of the Great Red Spot shows that the region has changed significantly since the Voyager 1 encounter three months ago. Around the northern boundary a white cloud is seen, which extends to east of the region. The presence of this cloud prevents small cloud vertices from circling the spot in the manner seen in the Voyager 1 encounter. Another white oval cloud (different from the one present in this position three months ago) is seen south of the Great Red Spot. The internal structure of these spots is identical. Since they both rotate in an anticyclonic manner these observations indicate that they are meteorologically similar. This image was taken on July 6 from a range of 2,633,003 kilometers.

  5. Weird Warm Spot on Exoplanet

    NASA Video Gallery

    This animation illustrates an unexpected warm spot on the surface of a gaseous exoplanet. NASA's Spitzer Space Telescope discovered that the hottest part of the planet, shown here as bright, orange...

  6. Retinal spot size with wavelength

    NASA Astrophysics Data System (ADS)

    Rockwell, Benjamin A.; Hammer, Daniel X.; Kennedy, Paul K.; Amnotte, Rodney E.; Eilert, Brent; Druessel, Jeffrey J.; Payne, Dale J.; Phillips, Shana L.; Stolarski, David J.; Noojin, Gary D.; Thomas, Robert J.; Cain, Clarence P.

    1997-06-01

    We have made an indirect in-vivo determination of spot size focusing in the rhesus monkey model. Measurement of the laser induced breakdown threshold both in-vitro and in-vivo allow correlation and assignment of a spot size after focusing through the living eye. We discuss and analyze the results and show how trends in minimum visible lesion data should be assessed in light of chromatic aberration. National laser safety standards are based on minimal visual lesion (MVL) threshold studies in different animal models. The energy required for a retinal lesion depends upon may parameters including wavelength and retinal spot size. We attempt to explain trends in reported MVL threshold studies using a model of the eye which allows calculation of changes in retinal spot size due to chromatic aberration.

  7. Spot14/Spot14R expression may be involved in MSC adipogenic differentiation in patients with adolescent idiopathic scoliosis

    PubMed Central

    WANG, QIFEI; YANG, JUNLIN; LIN, XIANG; HUANG, ZIFANG; XIE, CHAOFAN; FAN, HENGWEI

    2016-01-01

    The aim of the present study was to evaluate the different expression levels of thyroid hormone responsive (THRSP; Spot14)/S14 related, Mig12 (S14R) during bone marrow mesenchymal stem cell (BM-MSC) adipogenesis in adolescent idiopathic scoliosis (AIS) patients. MSCs were retrospectively isolated from AIS patients and controls, and adipogenic differentiation was induced. Total RNA was extracted for Affymetrix 3′-IVT expression profiling microarrays and compared with the results from healthy controls. The results were confirmed by semiquantitative reverse transcription-polymerase chain reaction (RT-PCR) validation and the protein expression levels of Spot14 and its paralogous gene S14R by western blotting and immunohistochemistry. A total of 300 significantly altered mRNAs were detected (111 upregulated and 189 downregulated) and confirmed by RT-qPCR. The mRNA expression levels of seven genes, including Spot14, were altered by >2-fold in AIS patients. Spot14/S14R was selected for further investigation. The results of the western blotting demonstrated that mRNA and protein expression levels of Spot14/S14R were significantly higher in AIS patients than the controls (P<0.05). Immunohistochemistry demonstrated Spot14 was expressed in 85% (17/20 cases) in adipose tissue samples from AIS patients and 23.1% (3/13 cases) of adipose tissue samples from controls. The positive ratio of Spot14 in adipose tissue samples from AIS was significantly higher than the controls (P<0.001). The results of the present study indicated that Spot14/S14R were differently expressed in MSC adipogenesis in AIS patients, and they may be important in the abnormal adipogenic differentiation in AIS. PMID:27082501

  8. Spot14/Spot14R expression may be involved in MSC adipogenic differentiation in patients with adolescent idiopathic scoliosis.

    PubMed

    Wang, Qifei; Yang, Junlin; Lin, Xiang; Huang, Zifang; Xie, Chaofan; Fan, Hengwei

    2016-06-01

    The aim of the present study was to evaluate the different expression levels of thyroid hormone responsive (THRSP; Spot14)/S14 related, Mig12 (S14R) during bone marrow mesenchymal stem cell (BM-MSC) adipogenesis in adolescent idiopathic scoliosis (AIS) patients. MSCs were retrospectively isolated from AIS patients and controls, and adipogenic differentiation was induced. Total RNA was extracted for Affymetrix 3'‑IVT expression profiling microarrays and compared with the results from healthy controls. The results were confirmed by semiquantitative reverse transcription-polymerase chain reaction (RT-PCR) validation and the protein expression levels of Spot14 and its paralogous gene S14R by western blotting and immunohistochemistry. A total of 300 significantly altered mRNAs were detected (111 upregulated and 189 downregulated) and confirmed by RT‑qPCR. The mRNA expression levels of seven genes, including Spot14, were altered by >2‑fold in AIS patients. Spot14/S14R was selected for further investigation. The results of the western blotting demonstrated that mRNA and protein expression levels of Spot14/S14R were significantly higher in AIS patients than the controls (P<0.05). Immunohistochemistry demonstrated Spot14 was expressed in 85% (17/20 cases) in adipose tissue samples from AIS patients and 23.1% (3/13 cases) of adipose tissue samples from controls. The positive ratio of Spot14 in adipose tissue samples from AIS was significantly higher than the controls (P<0.001). The results of the present study indicated that Spot14/S14R were differently expressed in MSC adipogenesis in AIS patients, and they may be important in the abnormal adipogenic differentiation in AIS. PMID:27082501

  9. Variable protein profiles in extracellular products of the protistan parasite Perkinsus olseni among regions of the Spanish coast.

    PubMed

    Fernández-Boo, Sergio; Villalba, Antonio; Cao, Asunción

    2015-11-01

    The variability of the protein expression profiling in the extracellular products (ECPs) of in vitro cultured Perkinsus olseni deriving from 4 regions of the Spanish coast was evaluated. The regions involved were the rías of Arousa and Pontevedra (Galicia, NW Spain), Carreras River (Andalusia, SW Spain) and Delta de l'Ebre (Catalonia, NE Spain). P. olseni in vitro clonal cultures were produced from parasite isolates from four clams from each region. Proteins released by the in vitro cultured parasites were isolated and separated by two dimensional electrophoresis (2DE). Qualitative comparison of protein expression profiles in the P. olseni ECPs among clones from all the regions was performed with PD Quest software. Around 130 spots were counted in the gels from ECPs of P. olseni clones from each region, of which 23 spots were shared by clones from all the regions and various spots were representative from clones of one region (appear in every clonal culture from that region but did not in every one of the other regions). A total of 34 spots were excised from the gels and analysed for sequencing. The protein cathepsin B, involved in proteolysis, the signal recognition particle receptor subunit β, involved in protein transport through membranes, and a protein belonging to N-acetyl transferase superfamily, involved in biosynthesis, were identified in spots shared by P. olseni ECPs from all regions. Pepsin A precursor, involved in proteolysis; heat shock protein (HSP) 60; and phosphoserine aminotransferase, involved in biosynthesis, were representative of P. olseni ECPs from Ría de Arousa, while peroxiredoxin V, involved in oxidation-reduction, was representative of P. olseni ECPs from Ría de Pontevedra. Differences in released proteins suggest different virulence or resistance to host attack between parasites from different locations. PMID:26555510

  10. Proteomics of rice and Cochliobolus miyabeanus fungal interaction: insight into proteins at intracellular and extracellular spaces.

    PubMed

    Kim, Jin Yeong; Wu, Jingni; Kwon, Soon Jae; Oh, Haram; Lee, So Eui; Kim, Sang Gon; Wang, Yiming; Agrawal, Ganesh Kumar; Rakwal, Randeep; Kang, Kyu Young; Ahn, Il-Pyung; Kim, Beom-Gi; Kim, Sun Tae

    2014-10-01

    Necrotrophic fungal pathogen Cochliobolus miyabeanus causes brown spot disease in rice leaves upon infection, resulting in critical rice yield loss. To better understand the rice-C. miyabeanus interaction, we employed proteomic approaches to establish differential proteomes of total and secreted proteins from the inoculated leaves. The 2DE approach after PEG-fractionation of total proteins coupled with MS (MALDI-TOF/TOF and nESI-LC-MS/MS) analyses led to identification of 49 unique proteins out of 63 differential spots. SDS-PAGE in combination with nESI-LC-MS/MS shotgun approach was applied to identify secreted proteins in the leaf apoplast upon infection and resulted in cataloging of 501 unique proteins, of which 470 and 31 proteins were secreted from rice and C. miyabeanus, respectively. Proteins mapped onto metabolic pathways implied their reprogramming upon infection. The enzymes involved in Calvin cycle and glycolysis decreased in their protein abundance, whereas enzymes in the TCA cycle, amino acids, and ethylene biosynthesis increased. Differential proteomes also generated distribution of identified proteins in the intracellular and extracellular spaces, providing a better insight into defense responses of proteins in rice against C. miyabeanus. Established proteome of the rice-C. miyabeanus interaction serves not only as a good resource for the scientific community but also highlights its significance from biological aspects. PMID:25047395

  11. Evaluation of SPOT imagery data

    SciTech Connect

    Berger, Z.; Brovey, R.L.; Merembeck, B.F.; Hopkins, H.R.

    1988-01-01

    SPOT, the French satellite imaging system that became operational in April 1986, provides two major advances in satellite imagery technology: (1) a significant increase in spatial resolution of the data to 20 m multispectral and 10 m panchromatic, and (2) stereoscopic capabilities. The structural and stratigraphic mapping capabilities of SPOT data and compare favorably with those of other available space and airborne remote sensing data. In the Rhine graben and Jura Mountains, strike and dip of folded strata can be determined using SPOT stereoscopic imagery, greatly improving the ability to analyze structures in complex areas. The increased spatial resolution also allows many features to be mapped that are not visible on thematic mapper (TM) imagery. In the San Rafael swell, Utah, TM spectral data were combined with SPOT spatial data to map lithostratigraphic units of the exposed Jurassic and Cretaceous rocks. SPOT imagery provides information on attitude, geometry, and geomorphic expressions of key marker beds that is not available on TM imagery. Over the Central Basin platform, west Texas, SPOT imagery, compared to TM imagery, provided more precise information on the configuration of outcropping beds and drainage patterns that reflect the subtle surface expression of buried structures.

  12. Changes in the expression of hippocampal proteins in rats with recrudescence of morphine addiction

    PubMed Central

    QIU, HAITANG; GAO, YUFENG; FU, YIXIAO; DU, LIAN; QIU, TIAN; FENG, KUN; LUO, QINGHUA; MENG, HUAQING

    2013-01-01

    The high recrudescence rate of drug addiction has received attention worldwide and its mechanisms remain to be elucidated. This study aimed to analyse the disparate protein expression in the hippocampal tissue of rats with recrudescence of morphine addiction, as well as to provide clues for the exploration of the recrudescence mechanism. Sixteen male adult Sprague-Dawley rats were divided equally into the morphine and physiological saline groups. Effective nose pokes were determined as the main index. The proteins were separated using the immobilised pH gradient two-dimensional polyacrylamide gel electrophoresis (2-DE). Disparate protein spots were analysed using the PDQuest 2-DE software. Peptide dactylograms were obtained using the matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. The effective nose poke counts of the morphine group significantly increased during addiction maturation compared with the saline group (P<0.001). The post-recrudescence nose poke counts of the morphine group significantly increased compared with those before recrudescence (P<0.001). Fifteen disparate proteins were identified according to the protein electrophoresis of the morphine and physiological saline groups, including three proteins associated with energy metabolism, two ionic channel regulatory proteins, one heat shock protein and one exogenous substance metabolic enzyme. The energy metabolism and expression of cell metabolism-related proteins decreased in the hippocampus of rats with morphine recrudescence. PMID:23408778

  13. Identification of Proteins in Promastigote and Amastigote-like Leishmania Using an Immunoproteomic Approach

    PubMed Central

    Coelho, Vinicio T. S.; Oliveira, Jamil S.; Valadares, Diogo G.; Chávez-Fumagalli, Miguel A.; Duarte, Mariana C.; Lage, Paula S.; Soto, Manuel; Santoro, Marcelo M.; Tavares, Carlos A. P.; Fernandes, Ana Paula; Coelho, Eduardo A. F.

    2012-01-01

    Background The present study aims to identify antigens in protein extracts of promastigote and amastigote-like Leishmania (Leishmania) chagasi syn. L. (L.) infantum recognized by antibodies present in the sera of dogs with asymptomatic and symptomatic visceral leishmaniasis (VL). Methodology/Principal Findings Proteins recognized by sera samples were separated by two-dimensional electrophoresis (2DE) and identified by mass spectrometry. A total of 550 spots were observed in the 2DE gels, and approximately 104 proteins were identified. Several stage-specific proteins could be identified by either or both classes of sera, including, as expected, previously known proteins identified as diagnosis, virulence factors, drug targets, or vaccine candidates. Three, seven, and five hypothetical proteins could be identified in promastigote antigenic extracts; while two, eleven, and three hypothetical proteins could be identified in amastigote-like antigenic extracts by asymptomatic and symptomatic sera, as well as a combination of both, respectively. Conclusions/Significance The present study represents a significant contribution not only in identifying stage-specific L. infantum molecules, but also in revealing the expression of a large number of hypothetical proteins. Moreover, when combined, the identified proteins constitute a significant source of information for the improvement of diagnostic tools and/or vaccine development to VL. PMID:22272364

  14. Autoimmunoreactive IgGs Against Cardiac Lipid Raft-Associated Proteins in Patients with POTS

    PubMed Central

    Wang, Xiao-Li; Ling, Tian-You; Charlesworth, M. Cristine; Figueroa, Juan J.; Low, Phillip; Shen, Win-Kuang; Lee, Hon-Chi

    2013-01-01

    Lipid rafts are specialized plasma membrane microdomains that serve as platforms for integrating cellular signal transductions. We have recently reported that autoantibodies against cardiac membrane proteins are present in patients with postural orthostatic tachycardia syndrome (POTS). In this study, we examined the presence of autoimmunoreactive IgGs against lipid raft proteins in these patients. IgGs were purified from the sera of 10 patients and 7 normal controls. Cardiac lipid raft preparations were isolated from normal human heart tissue. The lipid raft-associated proteins were resolved by 2DE and immunoblotted against IgGs from each subject. Protein spots that reacted specifically with patient IgGs were identified by nanoLC-MS/MS. Thirty-four such protein spots, and 72 unique proteins were identified. The targets of autoimmunoreactive IgGs include proteins associated with caveolae structure, adrenergic signaling, calcium signaling, cytostructures, chaperone and energy metabolism. Multiple pathways were involved including those that regulate caveolae-mediated signaling, oxidative phosphorylation, fatty acid metabolism, protein ubiquitination, and cardiac β-adrenergic signaling. Our results suggest that cardiac lipid raft-associated proteins are targets of autoimmunoreactive IgGs from patients with POTS. Autoimmunity may play a role in the pathogenesis of POTS. PMID:23562385

  15. Proteomic analysis of surface proteins of Trichinella spiralis muscle larvae by two-dimensional gel electrophoresis and mass spectrometry

    PubMed Central

    2013-01-01

    Background Trichinella spiralis is a zoonotic tissue-dwelling parasitic nematode that infects humans and other mammals. Its surface proteins are recognized as antigenic in many infected hosts, being directly exposed to the host’s immune system and are the main target antigens that induce the immune responses. The larval surface proteins may also interact with intestinal epithelial cells and may play an important role in the invasion and development process of T. spiralis. The purpose of this study was to analyze and characterize the surface proteins of T. spiralis muscle larvae by two-dimensional gel electrophoresis (2-DE) and mass spectrometry. Methods The surface proteins of T. spiralis muscle larvae were stripped from the cuticle of live larvae by the cetyltrimethylammonium bromide (CTAB) and sodium deoxycholate. The surface protein stripping was examined by an immunofluorescent test (IFT). The surface proteins were analyzed by SDS-PAGE and Western blotting, and then identified by 2-DE and MALDI-TOF/TOF mass spectrometry analysis. Results The IFT results showed that the surface proteins-stripped larvae were not recognized by sera of mice immunized with surface antigens. Western blotting showed 7 of 12 protein bands of the surface proteins were recognized by mouse infection sera at 18 dpi and at 42 dpi. The 2-DE results showed that a total of approximately 33 proteins spots were detected with molecular weights varying from 10 to 66 kDa and isoelectric point (pI) from 4 to 7. Twenty-seven of 33 protein spots were identified and characterized to correlate with 15 different proteins. Out of the 14 proteins identified as T. spiralis proteins, 5 proteins (partial P49 antigen, deoxyribonuclease II family protein, two serine proteases, and serine proteinase) had catalytic and hydrolase activity. All of these 5 proteins were also associated with metabolic processes and 2 of the five proteins were associated with cellular processes. Conclusions In this study, T

  16. Proteomic analysis of pregnancy-related proteins from pig uterus endometrium during pregnancy

    PubMed Central

    2011-01-01

    Many important molecular events associated with implantation and development occur within the female reproductive tract, especially within the uterus endometrium, during pregnancy periods. The endometrium includes the mucosal lining of the uterus, which provides a suitable site for implantation and development of a fertilized egg and fetus. To date, the molecular cascades in the uterus endometrium during pregnancy periods in pigs have not been elucidated fully. In this study, we compared the functional regulated proteins in the endometrium during pregnancy periods with those in non-pregnant conditions and investigated changes in expression patterns during pregnancy (days 40, 70, and 93) using two-dimensional gel electrophoresis (2-DE) and western blotting. The functional regulated proteins were identified and discovered from differentially expressed proteins in the uterus endometrium during pregnancy. We discovered 820 protein spots in a proteomic analysis of uterus endometrium tissues with 2-DE gels. We identified 63 of the 98 proteins regulated differentially among non-pregnant and pregnant tissues (matched and unmatched spots). Interestingly, 10 of these 63 proteins are development-, cytoskeleton- and chaperon-related proteins such as transferrin, protein DJ-1, transgelin, galectin-1, septin 2, stathmin 1, cofilin 1, fascin 1, heat shock protein (HSP) 90β and HSP 27. The specific expression patterns of these proteins in the endometrium during pregnancy were confirmed by western blotting. Our results suggest that the expressions of these genes involved in endometrium function and endometrium development from early to late gestation are associated with the regulation of endometrium development for maintaining pregnancy. PMID:21791079

  17. Impact Modeling of Spot Welds

    NASA Astrophysics Data System (ADS)

    Yancey, Robert N.

    2004-06-01

    Resistance spot welds in most current finite element crash models are characterized as a rigid link at the location of the weld which transfers the load but is not designed to fail. Newer weld elements in the popular finite element analysis codes include the option of incorporating a failure criteria for the weld element. As many automotive companies move towards the use of high-strength steels, the dynamic behavior of the spot welds will become increasingly important and the failure of any welds should be incorporated during the simulation. The failure criteria will be influenced by mesh size, weld element properties, weld element type, surrounding material properties, strain rate, and weld placement. The influence of some of these parameters using current spot weld modeling techniques will be discussed along with recommendations for future work in this area.

  18. Spots on T Tauri stars

    NASA Astrophysics Data System (ADS)

    Bouvier, J.; Bertout, C.

    1989-02-01

    Periodic light curves were recorded for the following 15 T Tauri stars (for nine of which this was the first detection of periodic variability): V 410 Tau, DF Tau, UX Tau A, FK 1, FK 2, WK 2, DN Tau, GW Ori, SY Cha, LH(alpha) 332-20, LH(alpha) 332-21, CoD-33-deg 10685, RY Lup, SR 12, and SR 9. The previously reported periodic variability of the SY Cha and RY Lup stars was confirmed. These periodic variations are thought to result from rotational modulation by a group of spots at the stellar surface. The properties of spots on 11 stars were deduced from extensive light-curve synthesis. In most cases, they were found to be comparable to the properties of spots found on RS CVn stars.

  19. Comparison of Different Protein Extraction Methods for Gel-Based Proteomic Analysis of Ganoderma spp.

    PubMed

    Al-Obaidi, Jameel R; Saidi, Noor Baity; Usuldin, Siti Rokhiyah Ahmad; Hussin, Siti Nahdatul Isnaini Said; Yusoff, Noornabeela Md; Idris, Abu Seman

    2016-04-01

    Ganoderma species are a group of fungi that have the ability to degrade lignin polymers and cause severe diseases such as stem and root rot and can infect economically important plants and perennial crops such as oil palm, especially in tropical countries such as Malaysia. Unfortunately, very little is known about the complex interplay between oil palm and Ganoderma in the pathogenesis of the diseases. Proteomic technologies are simple yet powerful tools in comparing protein profile and have been widely used to study plant-fungus interaction. A critical step to perform a good proteome research is to establish a method that gives the best quality and a wide coverage of total proteins. Despite the availability of various protein extraction protocols from pathogenic fungi in the literature, no single extraction method was found suitable for all types of pathogenic fungi. To develop an optimized protein extraction protocol for 2-DE gel analysis of Ganoderma spp., three previously reported protein extraction protocols were compared: trichloroacetic acid, sucrose and phenol/ammonium acetate in methanol. The third method was found to give the most reproducible gels and highest protein concentration. Using the later method, a total of 10 protein spots (5 from each species) were successfully identified. Hence, the results from this study propose phenol/ammonium acetate in methanol as the most effective protein extraction method for 2-DE proteomic studies of Ganoderma spp. PMID:27016942

  20. Laser based spot weld characterization

    NASA Astrophysics Data System (ADS)

    Jonietz, Florian; Myrach, Philipp; Rethmeier, Michael; Suwala, Hubert; Ziegler, Mathias

    2016-02-01

    Spot welding is one of the most important joining technologies, especially in the automotive industry. Hitherto, the quality of spot welded joints is tested mainly by random destructive tests. A nondestructive testing technique offers the benefit of cost reduction of the testing procedure and optimization of the fabrication process, because every joint could be examined. This would lead to a reduced number of spot welded joints, as redundancies could be avoided. In the procedure described here, the spot welded joint between two zinc-coated steel sheets (HX340LAD+Z100MB or HC340LA+ZE 50/50) is heated optically on one side. Laser radiation and flash light are used as heat sources. The melted zone, the so called "weld nugget" provides the mechanical stability of the connection, but also constitutes a thermal bridge between the sheets. Due to the better thermal contact, the spot welded joint reveals a thermal behavior different from the surrounding material, where the heat transfer between the two sheets is much lower. The difference in the transient thermal behavior is measured with time resolved thermography. Hence, the size of the thermal contact between the two sheets is determined, which is directly correlated to the size of the weld nugget, indicating the quality of the spot weld. The method performs well in transmission with laser radiation and flash light. With laser radiation, it works even in reflection geometry, thus offering the possibility of testing with just one-sided accessibility. By using heating with collimated laser radiation, not only contact-free, but also remote testing is feasible. A further convenience compared to similar thermographic approaches is the applicability on bare steel sheets without any optical coating for emissivity correction. For this purpose, a proper way of emissivity correction was established.

  1. Color tunable LED spot lighting

    NASA Astrophysics Data System (ADS)

    Hoelen, C.; Ansems, J.; Deurenberg, P.; van Duijneveldt, W.; Peeters, M.; Steenbruggen, G.; Treurniet, T.; Valster, A.; ter Weeme, J. W.

    2006-08-01

    A new trend in illumination is to use dynamic light to set or dynamically vary the ambience of a room or office. For this we need color tunable spots that can reliably vary over at least a wide range of color temperatures, and preferably also more saturated colors. LEDs are in principle ideally suited for this application thanks to their nature of emitting light in a relatively narrow band. For color tunable spot lighting based on the concept of mixing RGB LED colors, the key results have been presented before. Limitations of these 3-intrinsic-color mixing systems with high color rendering properties are found in a limited operating temperature range due to wavelength shifts, a limited color temperature range, and a low maximum operating temperature due to a strong flux decrease with increasing temperature. To overcome these limitations, a 3-color R pcGB system with phosphor-converted red (R pc) and a 4-color RAGB system have been investigated. With both systems, a CRI of at least 80 can be maintained over the relevant color temperature range of approximately 2700 K to 6500 K. In this paper we compare these concepts on overall system aspects and report on the performance of prototype spot lamps. The main features of the RAGB and R pcGB spot lamp concepts can be summarized as: 1) The RAGB spot overcomes CRI and gamut shortcomings of RGB light sources and gives much freedom in wavelength selection, but suffers from temperature sensitivity and complex controls; 2) The R pcGB spot overcomes shortcomings concerning CRI and thermal dependence of RGB sources and enables relatively simple controls, but needs an improved overall red efficacy. With both color concepts, prototype spot lamps have been built. The amber to red emitting nitridosilicate-based phosphors can be wavelength-tuned for optimal performance, which is found at a peak emission around 610 nm for high color quality systems. This results in a simple and very robust system with good color consistency. For the

  2. Stabilized dried blood spot collection.

    PubMed

    McMorran, Darren; Chung, Dwayne Chung Kim; Toth, Monika; Liew, Oi Wah; Muradoglu, Murat; Ng, Tuck Wah

    2016-08-01

    During the collection phase of the dried blood spot method, practitioners need to ensure that there is no smearing of the blood sample on the filter paper or else readings from it will be invalid. This can be difficult to accomplish in the field if there is relative motion between the site of blood discharge on the finger and the filter paper. In this article, a gyroscope stabilization method is introduced and demonstrated to provide consistent and improved dried blood spot collection within a circular guide region notwithstanding the presence of rocking. PMID:27156813

  3. Mandibular defect reconstruction using three-dimensional polycaprolactone scaffold in combination with platelet-rich plasma and recombinant human bone morphogenetic protein-2: de novo synthesis of bone in a single case.

    PubMed

    Schuckert, Karl-Heinz; Jopp, Stefan; Teoh, Swee-Hin

    2009-03-01

    This publication describes the clinical case of a 71-year-old female patient. Using polycaprolactone (PCL) scaffold, platelet-rich plasma (PRP) and recombinant human bone morphogenetic protein-2 (rhBMP-2), a critical-sized defect in the anterior mandible was regenerated using de novo-grown bone. A bacterial infection had caused a periimplantitis in two dental implants leading to a large destruction in the anterior mandible. Both implants were removed under antibiotic prophylaxis. A PCL scaffold was prepared especially for this clinical case. In a second procedure with antibiotic prophylaxis, the bony defect was reopened. The PCL scaffold was fitted and charged with PRP and rhBMP-2 (1.2 mg). After complication-free wound healing, the radiological control demonstrated de novo-grown bone in the anterior mandible 6 months postoperatively. Dental implants were inserted in a third operation. A bone biopsy of the newly grown bone, as well as of the bordering local bone, was taken and histologically examined. The bone samples were identical and presented vital laminar bone. PMID:18767969

  4. Proteomic and SAGE profiling of murine melanoma progression indicates the reduction of proteins responsible for ROS degradation.

    PubMed

    de Souza, Gustavo A; Godoy, Lyris M F; Teixeira, Veronica R; Otake, Andreia H; Sabino, Adão; Rosa, José C; Dinarte, Anemari R; Pinheiro, Daniel G; Silva, Wilson A; Eberlin, Marcos N; Chammas, Roger; Greene, Lewis J

    2006-03-01

    Using 2-DE of total cell protein extracts, we compared soluble proteins from murine melanoma lines Tm1 and Tm5 with proteins from the nontumoral cell melan-a from which they were derived. Seventy-one of the 452 spots (average) detected with CBB were differentially accumulated, i.e., increased or decreased twofold. Forty-four spots were identified by PMF/MALDI-TOF, 15 with increased and 29 with decreased protein levels. SAGE showed that 17/34 (50%) of the differentially accumulated proteins, pI range 4-7, presented similar differences at the mRNA level. Major reductions in protein were observed in tumor cells of proteins that degrade reactive oxygen species (ROS). Decreases of > or = twofold in GST, superoxide dismutase, aldehyde dehydrogenase, thioredoxin, peroxiredoxin 2, and peroxiredoxin 6 protein were observed. SAGE indicated the reduction of other proteins involved in ROS degradation. As expected, the accumulation of exogenous peroxides was significantly higher in the tumor cells while the levels of glutathionylation were two times lower in the tumor cells compared to melan-a. The differential accumulation of proteins involved in oncogene/tumor suppressor pathways was observed. Melanoma cells can favor survival pathways activated by ROS by inhibiting p53 pathways and activation of Ras and c-myc pathways. PMID:16429458

  5. Complete mitochondrial genome of the Spotted dove (Streptopelia chinensis).

    PubMed

    Yan, Shou-Qing; Guo, Peng-Cheng; Li, Yu-Mei; Qi, Shun-Min; Bai, Chun-Yan; Zhao, Zhi-Hui; Sun, Jin-Hai

    2016-09-01

    The Spotted dove (Streptopelia chinensis) is a member of the bird family Columbidae. In this study, we report the complete mitochondrial genome of this species. The mitochondrial genome of Spotted dove is a circular molecule of 16,966 bp in size and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region. The total base composition is 30.1% for A, 32.1% for C, 13.9% for G, and 23.9% for T. These data will be useful for the phylogenetic and population diversity analyses of birds, especially Columbidae species. PMID:25600734

  6. Proteomics reveals differences in protein abundance and highly similar antigenic profiles between Besnoitia besnoiti and Besnoitia tarandi.

    PubMed

    García-Lunar, P; Regidor-Cerrillo, J; Ortega-Mora, L M; Gutiérrez-Expósito, D; Alvarez-García, G

    2014-10-15

    Besnoitia besnoiti and Besnoitia tarandi are two cyst-forming apicomplexan parasites of the genus Besnoitia. B. besnoiti uses cattle as an intermediate host, in which it causes a disease that progresses in two sequential phases: the acute anasarca stage and the chronic scleroderma stage. Reindeer and caribou act as intermediate hosts for B. tarandi, which causes clinical signs similar to those caused by B. besnoiti. Previous studies demonstrated high molecular similarity, as determined by 18S and ITS-1 RNA sequences, between these Besnoitia spp., and strong serological cross-reactivity between these species has recently been demonstrated. Thus, a difference gel electrophoresis approach and mass spectrometry analysis were used to describe the proteomes and explore differences in protein abundance between B. besnoiti and B. tarandi in tachyzoite extracts. Immunoproteomes were also compared using 2-DE immunoblotting with polyclonal sera from experimentally infected rabbits. From approximately 1400 spots detected in DIGE-gels, 28 and 29 spots were differentially abundant in B. besnoiti and B. tarandi tachyzoites, respectively (± 1.5-fold, p<0.05). Four and 13 spots were exclusively detected in B. besnoiti and B. tarandi, respectively. Of the 32 differentially abundant spots analyzed by MALDI-TOF/MS, 6 up-regulated B. besnoiti proteins (LDH; HSP90; purine nucleoside phosphorylase and 3 hypothetical proteins) and 6 up-regulated B. tarandi proteins (G3PDH; LDH; PDI; mRNA decapping protein and 2 hypothetical proteins) were identified. Interestingly, no specific antigen spots were recognized by sera on any of the Besnoitia species studied and a similar antigen profile has been observed for B. tarandi and B. besnoiti sera when cross reactions were studied. This fact corroborates the difficulty in discerning Besnoitia infections using current serological assays. The present study underscores the importance of sequencing the B. besnoiti genome for species diversity studies of

  7. Exobasidium leaf and fruit spot

    Technology Transfer Automated Retrieval System (TEKTRAN)

    During the past five or so years blueberry growers in south Mississippi have discovered the disease Exobasidium leaf and fruit spot on some of their blueberry plants. In the past this disease was considered to be of minor importance occurring infrequently on isolated farms. But in recent years it ...

  8. Isolation and characterizations of oxalate-binding proteins in the kidney

    SciTech Connect

    Roop-ngam, Piyachat; Chaiyarit, Sakdithep; Pongsakul, Nutkridta; Thongboonkerd, Visith

    2012-08-03

    Highlights: Black-Right-Pointing-Pointer The first large-scale characterizations of oxalate-binding kidney proteins. Black-Right-Pointing-Pointer The recently developed oxalate-conjugated EAH Sepharose 4B beads were applied. Black-Right-Pointing-Pointer 38 forms of 26 unique oxalate-binding kidney proteins were identified. Black-Right-Pointing-Pointer 25/26 (96%) of identified proteins had 'L-x(3,5)-R-x(2)-[AGILPV]' domain. -- Abstract: Oxalate-binding proteins are thought to serve as potential modulators of kidney stone formation. However, only few oxalate-binding proteins have been identified from previous studies. Our present study, therefore, aimed for large-scale identification of oxalate-binding proteins in porcine kidney using an oxalate-affinity column containing oxalate-conjugated EAH Sepharose 4B beads for purification followed by two-dimensional gel electrophoresis (2-DE) to resolve the recovered proteins. Comparing with those obtained from the controlled column containing uncoupled EAH-Sepharose 4B (to subtract the background of non-specific bindings), a total of 38 protein spots were defined as oxalate-binding proteins. These protein spots were successfully identified by quadrupole time-of-flight mass spectrometry (MS) and/or tandem MS (MS/MS) as 26 unique proteins, including several nuclear proteins, mitochondrial proteins, oxidative stress regulatory proteins, metabolic enzymes and others. Identification of oxalate-binding domain using the PRATT tool revealed 'L-x(3,5)-R-x(2)-[AGILPV]' as a functional domain responsible for oxalate-binding in 25 of 26 (96%) unique identified proteins. We report herein, for the first time, large-scale identification and characterizations of oxalate-binding proteins in the kidney. The presence of positively charged arginine residue in the middle of this functional domain suggested its significance for binding to the negatively charged oxalate. These data will enhance future stone research, particularly on stone

  9. Spinning-Spot Shadowless TIRF Microscopy.

    PubMed

    Ellefsen, Kyle L; Dynes, Joseph L; Parker, Ian

    2015-01-01

    Total internal reflection fluorescence (TIRF) microscopy is a powerful tool for visualizing near-membrane cellular structures and processes, including imaging of local Ca2+ transients with single-channel resolution. TIRF is most commonly implemented in epi-fluorescence mode, whereby laser excitation light is introduced at a spot near the periphery of the back focal plane of a high numerical aperture objective lens. However, this approach results in an irregular illumination field, owing to interference fringes and scattering and shadowing by cellular structures. We describe a simple system to circumvent these limitations, utilizing a pair of galvanometer-driven mirrors to rapidly spin the laser spot in a circle at the back focal plane of the objective lens, so that irregularities average out during each camera exposure to produce an effectively uniform field. Computer control of the mirrors enables precise scanning at 200 Hz (5ms camera exposure times) or faster, and the scan radius can be altered on a frame-by-frame basis to achieve near-simultaneous imaging in TIRF, widefield and 'skimming plane' imaging modes. We demonstrate the utility of the system for dynamic recording of local inositol trisphosphate-mediated Ca2+ signals and for imaging the redistribution of STIM and Orai proteins during store-operated Ca2+ entry. We further anticipate that it will be readily applicable for numerous other near-membrane studies, especially those involving fast dynamic processes. PMID:26308212

  10. Spinning-Spot Shadowless TIRF Microscopy

    PubMed Central

    Ellefsen, Kyle L.; Dynes, Joseph L.; Parker, Ian

    2015-01-01

    Total internal reflection fluorescence (TIRF) microscopy is a powerful tool for visualizing near-membrane cellular structures and processes, including imaging of local Ca2+ transients with single-channel resolution. TIRF is most commonly implemented in epi-fluorescence mode, whereby laser excitation light is introduced at a spot near the periphery of the back focal plane of a high numerical aperture objective lens. However, this approach results in an irregular illumination field, owing to interference fringes and scattering and shadowing by cellular structures. We describe a simple system to circumvent these limitations, utilizing a pair of galvanometer-driven mirrors to rapidly spin the laser spot in a circle at the back focal plane of the objective lens, so that irregularities average out during each camera exposure to produce an effectively uniform field. Computer control of the mirrors enables precise scanning at 200 Hz (5ms camera exposure times) or faster, and the scan radius can be altered on a frame-by-frame basis to achieve near-simultaneous imaging in TIRF, widefield and ‘skimming plane’ imaging modes. We demonstrate the utility of the system for dynamic recording of local inositol trisphosphate-mediated Ca2+ signals and for imaging the redistribution of STIM and Orai proteins during store-operated Ca2+ entry. We further anticipate that it will be readily applicable for numerous other near-membrane studies, especially those involving fast dynamic processes. PMID:26308212

  11. Two-dimensional electrophoresis analysis of proteins extracted from Alexandrium sp. LC3

    NASA Astrophysics Data System (ADS)

    Li, Hao; Miao, Jinlai; Cui, Fengxia; Li, Guangyou

    2007-10-01

    Two-dimensional electrophoresis(2-DE) of protein extracted and purified from Alexandrium sp. LC3 was conducted. In the SDS-PAGE study, the relative molecular weights of the proteins were mainly in the range of 14kDa-31kDa and 43kDa-66kDa, and more proteins were detected between 14kDa and 31kDa. With the improved protein preparation, the two-dimensional electrophoresis patterns indicated that the relative molecular weights of the proteins were between 14kDa and 100kDa, and most of them ranged from 14kDa to 31kDa. This was consistent with the result of the SDS-PAGE analysis. The isoelectric points were found to lie between 3.0 and 8.0, and most of them were in the range of 3.0 6.0. Better separation effect was acquired with pre-prepared immobilized gradient (IPG) strip (pH3 5.6), and about 320 protein spots could be visualized on the 2-DE map by staining. Within pH3 10 and pH3 5.6 strips, the protein samples of Alexandrium sp. LC3 could be separated well.

  12. Comparative proteomic analysis of oil palm leaves infected with Ganoderma boninense revealed changes in proteins involved in photosynthesis, carbohydrate metabolism, and immunity and defense.

    PubMed

    Jeffery Daim, Leona Daniela; Ooi, Tony Eng Keong; Ithnin, Nalisha; Mohd Yusof, Hirzun; Kulaveerasingam, Harikrishna; Abdul Majid, Nazia; Karsani, Saiful Anuar

    2015-08-01

    The basidiomycete fungal pathogen Ganoderma boninense is the causative agent for the incurable basal stem rot (BSR) disease in oil palm. This disease causes significant annual crop losses in the oil palm industry. Currently, there is no effective method for disease control and elimination, nor is any molecular marker for early detection of the disease available. An understanding of how BSR affects protein expression in plants may help identify and/or assist in the development of an early detection protocol. Although the mode of infection of BSR disease is primarily via the root system, defense-related genes have been shown to be expressed in both the root and leafs. Thus, to provide an insight into the changes in the global protein expression profile in infected plants, comparative 2DE was performed on leaf tissues sampled from palms with and without artificial inoculation of the Ganoderma fungus. Comparative 2DE revealed that 54 protein spots changed in abundance. A total of 51 protein spots were successfully identified by LC-QTOF MS/MS. The majority of these proteins were those involved in photosynthesis, carbohydrate metabolism as well as immunity and defense. PMID:25930948

  13. Fusion-Related Host Proteins Are Actively Regulated by NA during Influenza Infection as Revealed by Quantitative Proteomics Analysis

    PubMed Central

    Sui, Zhiwei; Wen, Bo; Gao, Zhimin; Chen, Quanjiao

    2014-01-01

    Three recombinant influenza A viruses with different neuraminidases (NAs) in the background of A/PR/8/34 (PR8), named rPR8-H5N1NA, rPR8-H9N2NA, and rPR8-H1N1NA, derived from H5N1, H9N2, H1N1 (swine) viruses, respectively, were constructed. We performed a quantitative proteomics analysis to investigate differential protein expression in Madin-Darby canine kidney (MDCK) cells infected with recombinant and wild-type influenza viruses to determine whether NA replacement would alter host cell gene expression. Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-TOF MS) and two-dimensional gel electrophoresis (2-DE), we identified 12 up-regulated and 49 down-regulated protein spots, including cytoskeletal proteins, molecular biosynthesis proteins, ubiquitin-proteasome pathway proteins, and heat shock proteins. The most significant changes in infected cells were observed for molecular biosynthesis proteins. We found more differentially expressed protein spots in cells infected with rPR8-H5N1NA or rPR8-H9N2NA viruses than cells infected with wild-type virus. Many of those proteins are postulated to be involved in cell-cell fusion, but the full mechanism remains to be explored. Meanwhile, our data demonstrate that the wild-type virus has evolutionary advantages over recombinant viruses. PMID:25153908

  14. Proteomic analysis of a segregant population reveals candidate proteins linked to mealiness in peach.

    PubMed

    Almeida, Andréa Miyasaka; Urra, Claudio; Moraga, Carol; Jego, Marcela; Flores, Alejandra; Meisel, Lee; González, Mauricio; Infante, Rodrigo; Defilippi, Bruno G; Campos-Vargas, Reinaldo; Orellana, Ariel

    2016-01-10

    Peaches are stored at low temperatures to delay ripening and increase postharvest life. However some varieties are susceptible to chilling injury,which leads to fruit mealiness, browning and flesh bleeding. In order to identify potentialmarkers associated with chilling injury,we performed proteomic analyses on a segregating population with contrasting susceptibility to chilling-induced mealiness. Chilling-induced mealiness was assessed by measuring juiciness in fruits that have been stored in cold and then allowed to ripen. Fruitmesocarp and leaf proteome from contrasting segregants were analyzed using 2-DE gels. Comparison of protein abundance between segregants revealed 133 spots from fruit mesocarp and 36 from leaf. Thirty four fruit mesocarp proteins were identified from these spots. Most of these proteins were related to ethylene synthesis, ABA response and stress response. Leaf protein analyses identified 22 proteins, most of which related to energy metabolism. Some of the genes that code for these proteins have been previously correlated with chilling injury through transcript analyses and co-segregation with mealiness QTLs. The results from this study, further deciphers the molecular mechanisms associated with chilling response in peach fruit, and identifies candidate proteins linked to mealiness in peach which may be used as putative markers for this trait. PMID:26459401

  15. Laser Pyrometer For Spot Temperature Measurements

    NASA Technical Reports Server (NTRS)

    Elleman, D. D.; Allen, J. L.; Lee, M. C.

    1988-01-01

    Laser pyrometer makes temperature map by scanning measuring spot across target. Scanning laser pyrometer passively measures radiation emitted by scanned spot on target and calibrated by similar passive measurement on blackbody of known temperature. Laser beam turned on for active measurements of reflectances of target spot and reflectance standard. From measurements, temperature of target spot inferred. Pyrometer useful for non-contact measurement of temperature distributions in processing of materials.

  16. Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.

    PubMed

    Link, A J; Robison, K; Church, G M

    1997-08-01

    Mining the emerging abundance of microbial genome sequences for hypotheses is an exciting prospect of "functional genomics". At the forefront of this effort, we compared the predictions of the complete Escherichia coli genomic sequence with the observed gene products by assessing 381 proteins for their mature N-termini, in vivo abundances, isoelectric points, molecular masses, and cellular locations. Two-dimensional gel electrophoresis (2-DE) and Edman sequencing were combined to sequence Coomassie-stained 2-DE spots representing the abundant proteins of wild-type E. coli K-12 strains. Greater than 90% of the abundant proteins in the E. coli proteome lie in a small isoelectric point and molecular mass window of 4-7 and 10-100 kDa, respectively. We identified several highly abundant proteins, YjbJ, YjbP, YggX, HdeA, and AhpC, which would not have been predicted from the genomic sequence alone. Of the 223 uniquely identified loci, 60% of the encoded proteins are proteolytically processed. As previously reported, the initiator methionine was efficiently cleaved when the penultimate amino acid was serine or alanine. In contrast, when the penultimate amino acid was threonine, glycine, or proline, cleavage was variable, and valine did not signal cleavage. Although signal peptide cleavage sites tended to follow predicted rules, the length of the putative signal sequence was occassionally greater than the consensus. For proteins predicted to be in the cytoplasm or inner membrane, the N-terminal amino acids were highly constrained compared to proteins localized to the periplasm or outer membrane. Although cytoplasmic proteins follow the N-end rule for protein stability, proteins in the periplasm or outer membrane do not follow this rule; several have N-terminal amino acids predicted to destabilize the proteins. Surprisingly, 18% of the identified 2-DE spots represent isoforms in which protein products of the same gene have different observed pI and M(r), suggesting they are

  17. Numerical simulations of hot spots

    NASA Astrophysics Data System (ADS)

    Norman, Michael L.

    Numerical simulations of hot spots and their associated jets are examined with emphasis on their dynamical variability. Attention is given to two-dimensional simulations, which incorporate dynamically passive and important magnetic fields in the ideal MHD limit. Distributions of total and polarized radio brightness have been derived for comparison with observations. The move toward three-dimensional simulations is documented, and hydrodynamical models for multiple hot spots are discussed. It is suggested that useful insights can be obtained from two-dimensional slab jet simulation, which relax the axisymmetric constraints while allowing high numerical resolution. In particular the dentist-drill model of Scheuer (1982) for working-surface variability is substantiated, and it is shown to result from self-excited jet instabilities near the working surface.

  18. Sweet Spots and Door Stops

    ERIC Educational Resources Information Center

    Thompson, Michael; Tsui, Stella; Leung, Chi Fan

    2011-01-01

    A sweet spot is referred to in sport as the perfect place to strike a ball with a racquet or bat. It is the point of contact between bat and ball where maximum results can be produced with minimal effort from the hand of the player. Similar physics can be applied to the less inspiring examples of door stops; the perfect position of a door stop is…

  19. Measurement of laser spot quality

    NASA Technical Reports Server (NTRS)

    Milster, T. D.; Treptau, J. P.

    1991-01-01

    Several ways of measuring spot quality are compared. We examine in detail various figures of merit such as full width at half maximum (FWHM), full width at 1/(e exp 2) maximum, Strehl ratio, and encircled energy. Our application is optical data storage, but results can be applied to other areas like space communications and high energy lasers. We found that the optimum figure of merit in many cases is Strehl ratio.

  20. Proteomic analysis of differentially expressed proteins in Penaeus monodon hemocytes after Vibrio harveyi infection

    PubMed Central

    2010-01-01

    Background Viral and bacterial diseases can cause mass mortalities in commercial shrimp aquaculture. In contrast to studies on the antiviral response, the responses of shrimps to bacterial infections by high throughput techniques have been reported only at the transcriptional level and not at the translational level. In this study, a proteomic analysis of shrimp hemocytes to identify differentially expressed proteins in response to a luminous bacterium Vibrio harveyi was evaluated for its feasibility and is reported for the first time. Results The two-dimensional gel electrophoresis (2-DE) patterns of the hemocyte proteins from the unchallenged and V. harveyi challenged shrimp, Penaeus monodon, at 24 and 48 h post infection were compared. From this, 27 differentially expressed protein spots, and a further 12 weakly to non-differentially regulated control spots, were selected for further analyses by the LC-ESI-MS/MS. The 21 differentially expressed proteins that could be identified by homologous annotation were comprised of proteins that are directly involved in the host defense responses, such as hemocyanin, prophenoloxidase, serine proteinase-like protein, heat shock protein 90 and alpha-2-macroglobulin, and those involved in signal transduction, such as the14-3-3 protein epsilon and calmodulin. Western blot analysis confirmed the up-regulation of hemocyanin expression upon bacterial infection. The expression of the selected proteins which were the representatives of the down-regulated proteins (the 14-3-3 protein epsilon and alpha-2-macroglobulin) and of the up-regulated proteins (hemocyanin) was further assessed at the transcription level using real-time RT-PCR. Conclusions This work suggests the usefulness of a proteomic approach to the study of shrimp immunity and revealed hemocyte proteins whose expression were up regulated upon V. harveyi infection such as hemocyanin, arginine kinase and down regulated such as alpha-2-macroglobulin, calmodulin and 14

  1. Proteomic Profiling and Protein Identification by MALDI-TOF Mass Spectrometry in Unsequenced Parasitic Nematodes

    PubMed Central

    Millares, Paul; LaCourse, E. James; Perally, Samirah; Ward, Deborah A.; Prescott, Mark C.; Hodgkinson, Jane E.; Brophy, Peter M.; Rees, Huw H.

    2012-01-01

    Lack of genomic sequence data and the relatively high cost of tandem mass spectrometry have hampered proteomic investigations into helminths, such as resolving the mechanism underpinning globally reported anthelmintic resistance. Whilst detailed mechanisms of resistance remain unknown for the majority of drug-parasite interactions, gene mutations and changes in gene and protein expression are proposed key aspects of resistance. Comparative proteomic analysis of drug-resistant and -susceptible nematodes may reveal protein profiles reflecting drug-related phenotypes. Using the gastro-intestinal nematode, Haemonchus contortus as case study, we report the application of freely available expressed sequence tag (EST) datasets to support proteomic studies in unsequenced nematodes. EST datasets were translated to theoretical protein sequences to generate a searchable database. In conjunction with matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF-MS), Peptide Mass Fingerprint (PMF) searching of databases enabled a cost-effective protein identification strategy. The effectiveness of this approach was verified in comparison with MS/MS de novo sequencing with searching of the same EST protein database and subsequent searches of the NCBInr protein database using the Basic Local Alignment Search Tool (BLAST) to provide protein annotation. Of 100 proteins from 2-DE gel spots, 62 were identified by MALDI-TOF-MS and PMF searching of the EST database. Twenty randomly selected spots were analysed by electrospray MS/MS and MASCOT Ion Searches of the same database. The resulting sequences were subjected to BLAST searches of the NCBI protein database to provide annotation of the proteins and confirm concordance in protein identity from both approaches. Further confirmation of protein identifications from the MS/MS data were obtained by de novo sequencing of peptides, followed by FASTS algorithm searches of the EST putative protein database. This

  2. A novel multi-scale Hessian based spot enhancement filter for two dimensional gel electrophoresis images.

    PubMed

    Shamekhi, Sina; Miran Baygi, Mohammad Hossein; Azarian, Bahareh; Gooya, Ali

    2015-11-01

    Two dimensional gel electrophoresis (2DGE) is a useful method for studying proteins in a wide variety of applications including identifying post-translation modification (PTM), biomarker discovery, and protein purification. Computerized segmentation and detection of the proteins are the two main processes that are carried out on the scanned image of the gel. Due to the complexities of 2DGE images and the presence of artifacts, the segmentation and detection of protein spots in these images are non-trivial, and involve supervised and time consuming processes. This paper introduces a new spot filter for enhancing, and separating the closely overlapping spots of protein in 2DGE images based on the multi-scale eigenvalue analysis of the image Hessian. Using a Gaussian spot model, we have derived closed form equations to compute the eigen components of the image Hessian of two overlapping spots in a multi-scale fashion. Based on this analysis, we have proposed a novel filter that suppresses the overlapping area and results in a better spot separation. The performance of the proposed filter has been evaluated on the synthetic and real 2DGE images. The comparison with three conventional techniques and a commercial software package reveals the superiority and effectiveness of the proposed filter. PMID:26409228

  3. ESA uncovers Geminga's `hot spot'

    NASA Astrophysics Data System (ADS)

    2004-07-01

    16 July 2004 Astronomers using ESA’s X-ray observatory XMM-Newton have detected a small, bright ‘hot spot’ on the surface of the neutron star called Geminga, 500 light-years away. The hot spot is the size of a football field and is caused by the same mechanism producing Geminga’s X-ray tails. This discovery identifies the missing link between the X-ray and gamma-ray emission from Geminga. hi-res Size hi-res: 1284 kb Credits: ESA, P. Caraveo (IASF, Milan) Geminga's hot spot This figure shows the effects of charged particles accelerated in the magnetosphere of Geminga. Panel (a) shows an image taken with the EPIC instrument on board the XMM-Newton observatory. The bright tails, made of particles kicked out by Geminga’s strong magnetic field, trail the neutron star as it moves about in space. Panel (b) shows how electrically charged particles interact with Geminga’s magnetic field. For example, if electrons (blue) are kicked out by the star, positrons (in red) hit the star’s magnetic poles like in an ‘own goal’. Panel (c) illustrates the size of Geminga’s magnetic field (blue) compared to that of the star itself at the centre (purple). The magnetic field is tilted with respect to Geminga’s rotation axis (red). Panel (d) shows the magnetic poles of Geminga, where charged particles hit the surface of the star, creating a two-million degrees hot spot, a region much hotter than the surroundings. As the star spins on its rotation axis, the hot spot comes into view and then disappears, causing the periodic colour change seen by XMM-Newton. An animated version of the entire sequence can be found at: Click here for animated GIF [low resolution, animated GIF, 5536 KB] Click here for AVI [high resolution, AVI with DIVX compression, 19128 KB] hi-res Size hi-res: 371 kb Credits: ESA, P. Caraveo (IASF, Milan) Geminga's hot spot, panel (a) Panel (a) shows an image taken with the EPIC instrument on board the XMM-Newton observatory. The bright tails, made of

  4. Phenotyping breast cancer cell lines EM-G3, HCC1937, MCF7 and MDA-MB-231 using 2-D electrophoresis and affinity chromatography for glutathione-binding proteins

    PubMed Central

    2010-01-01

    Background Transformed phenotypes are common to cell lines derived from various cancers. Proteome profiling is a valuable tool that may reveal uncharacteristic cell phenotypes in transformed cells. Changes in expression of glutathione S-transferases (GSTs) and other proteins interacting with glutathione (GSH) in model cell lines could be of particular interest. Methods We compared the phenotypes of breast cell lines EM-G3, HCC1937, MCF7 and MDA-MB-231 using 2-D electrophoresis (2-DE). We further separated GSH-binding proteins from the cell lines using affinity chromatography with GSH-Sepharose 4B, performed 2-DE analysis and identified the main protein spots. Results Correlation coefficients among 2-DE gels from the cell lines were lower than 0.65, pointing to dissimilarity among the cell lines. Differences in primary constituents of the cytoskeleton were shown by the 2-D protein maps and western blots. The spot patterns in gels of GSH-binding fractions from primary carcinoma-derived cell lines HCC1937 and EM-G3 were similar to each other, and they differed from the spot patterns of cell lines MCF7 and MDA-MB-231 that were derived from pleural effusions of metastatic mammary carcinoma patients. Major differences in the expression of GST P1-1 and carbonyl reductase [NADPH] 1 were observed among the cell lines, indicating differential abilities of the cell lines to metabolize xenobiotics. Conclusions Our results confirmed the applicability of targeted affinity chromatography to proteome profiling and allowed us to characterize the phenotypes of four breast cancer cell lines. PMID:20731849

  5. Enhanced Stability of Blood Matrices Using a Dried Sample Spot Assay to Measure Human Butyrylcholinesterase Activity and Nerve Agent Adducts

    PubMed Central

    Perez, Jonas W.; Pantazides, Brooke G.; Watson, Caroline M.; Thomas, Jerry D.; Blake, Thomas A.; Johnson, Rudolph C.

    2015-01-01

    Dried matrix spots are safer to handle and easier to store than wet blood products, but factors such as intra-spot variability and unknown sample volumes have limited their appeal as a sampling format for quantitative analyses. In this work, we introduce a dried spot activity assay for quantifying butyrylcholinesterase (BChE) specific activity which is BChE activity normalized to the total protein content in a sample spot. The method was demonstrated with blood, serum, and plasma spotted on specimen collection devices (cards) which were extracted to measure total protein and BChE activity using a modified Ellman assay. Activity recovered from dried spots was ∼80% of the initial spotted activity for blood and >90% for plasma and serum. Measuring total protein in the sample and calculating specific activity substantially improved quantification and reduced intra-spot variability. Analyte stability of nerve agent adducts was also evaluated, and the results obtained via BChE-specific activity measurements were confirmed by quantification of BChE adducts using a previously established LC-MS/MS method. The spotted samples were up to 10-times more resistant to degradation compared to unspotted control samples when measuring BChE inhibition by the nerve agents sarin and VX. Using this method, both BChE activity and adducts can be accurately measured from a dried sample spot. This use of a dried sample spot with normalization to total protein is robust, demonstrates decreased intra-spot variability without the need to control for initial sample volume, and enhances analyte stability. PMID:25955132

  6. Watermarking spot colors in packaging

    NASA Astrophysics Data System (ADS)

    Reed, Alastair; Filler, TomáÅ.¡; Falkenstern, Kristyn; Bai, Yang

    2015-03-01

    In January 2014, Digimarc announced Digimarc® Barcode for the packaging industry to improve the check-out efficiency and customer experience for retailers. Digimarc Barcode is a machine readable code that carries the same information as a traditional Universal Product Code (UPC) and is introduced by adding a robust digital watermark to the package design. It is imperceptible to the human eye but can be read by a modern barcode scanner at the Point of Sale (POS) station. Compared to a traditional linear barcode, Digimarc Barcode covers the whole package with minimal impact on the graphic design. This significantly improves the Items per Minute (IPM) metric, which retailers use to track the checkout efficiency since it closely relates to their profitability. Increasing IPM by a few percent could lead to potential savings of millions of dollars for retailers, giving them a strong incentive to add the Digimarc Barcode to their packages. Testing performed by Digimarc showed increases in IPM of at least 33% using the Digimarc Barcode, compared to using a traditional barcode. A method of watermarking print ready image data used in the commercial packaging industry is described. A significant proportion of packages are printed using spot colors, therefore spot colors needs to be supported by an embedder for Digimarc Barcode. Digimarc Barcode supports the PANTONE spot color system, which is commonly used in the packaging industry. The Digimarc Barcode embedder allows a user to insert the UPC code in an image while minimizing perceptibility to the Human Visual System (HVS). The Digimarc Barcode is inserted in the printing ink domain, using an Adobe Photoshop plug-in as the last step before printing. Since Photoshop is an industry standard widely used by pre-press shops in the packaging industry, a Digimarc Barcode can be easily inserted and proofed.

  7. Visceral leishmaniasis with Roth spots

    PubMed Central

    Meena, Jagdish; Juneja, Monica; Mishra, Devendra; Vats, Pallavi; Pawaria, Arti

    2014-01-01

    Visceral leishmaniasis (VL) is caused by the protozoan parasite Leishmania donovani and transmitted by the bite of infected sandfly Phlebotomus argentipes. The protozoa is obliged intracellularly and causes a wide spectrum of clinical syndromes: VL (‘kala azar’), cutaneous leishmaniasis and mucocutaneous leishmaniasis (espundia). Kala azar is the most aggressive form and if untreated causes high mortality. Here, we describe a case of VL that presented to us with high-grade fever and found to have Roth spots that were resolved after 15 days of therapy. PMID:25988048

  8. Nonbright spot AVO: Two examples

    SciTech Connect

    Ross, C.P.; Kinman, D.L.

    1994-12-31

    Utilization of amplitude-versus-offset (AVO) attribute sections such as the product of the normal incidence trace and gradient trace have been used extensively in bright spot (Class 3) AVO analysis and interpretation. However, while these sections have often worked well with Class 3 responses they are not reliable indicators of non-bright spot (Class 2) seismic anomalies. Analyzing Class 2 seismic data with AVO products will: (1) not detect the gas-charged reservoir because of near-zero acoustic impedance contrast between the sands and encasing shales, or (2) yield an incorrect (negative) AVO product if the normal incidence and gradient values are opposite in sign. Class 2 offset responses are divided into two sub-categories: those with phase reversals (Class 2p) and those without phase reversals (Class 2). An AVO procedure for these types of Class 2 anomalies is presented through two examples. The technique better exploits the nature of the prestack response, yielding a more definitive AVO attribute section, and the technique is adaptive to both Class 2 and Class 2p responses. When compared to a conventionally processed relative amplitude seismic section with characteristically low amplitude responses for near-zero acoustic impedance sands, this procedure clearly denotes the presence of gas-charged pore fluids within the reservoir.

  9. Still from Red Spot Movie

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This image is one of seven from the narrow-angle camera on NASA's Cassini spacecraft assembled as a brief movie of cloud movements on Jupiter. It was taken with a blue filter. The smallest features visible are about 500 kilometers (about 300 miles) across.

    Small bright clouds appear suddenly to the west of the Great Red Spot. Based on data from NASA's Galileo spacecraft, scientists suspect that these small white features are lightning storms, where falling raindrops create an electrical charge. The lightning storms eventually merge with the Red Spot and surrounding jets, and may be the main energy source for these large-scale features. Imaging observations of the darkside of the planet in the weeks following Cassini's closest approach to Jupiter on Dec. 30, 2000 will search for lightning storms like these.

    This image was re-projected by cylindrical-map projection of an image taken in the first week of October 2000. It shows an area from 50 degrees north of Jupiter's equator to 50 degrees south, extending 100 degrees east west, about one quarter of Jupiter's circumference.

    Cassini is a cooperative project of NASA, the European Space Agency and the Italian Space Agency. The Jet Propulsion Laboratory, a division of the California Institute of Technology in Pasadena, manages the Cassini mission for NASA's Office of Space Science, Washington, D.C.

  10. Spot and Runway Departure Advisor

    NASA Technical Reports Server (NTRS)

    Jung, Yoon Chul

    2013-01-01

    The Spot and Runway Departure Advisor (SARDA) is a research prototype of a decision support tool for ATC tower controllers to assist in manging and controlling traffic on the surface of an airport. SARDA employs a scheduler to generate an optimal runway schedule and gate push-back - spot release sequence and schedule that improves efficiency of surface operations. The advisories for ATC tower controllers are displayed on an Electronic Flight Strip (EFS) system. The human-in-the-loop simulation of the SARDA tool was conducted for east operations of Dallas-Ft. Worth International Airport (DFW) to evaluate performance of the SARDA tool and human factors, such as situational awareness and workload. The results indicates noticeable taxi delay reduction and fuel savings by using the SARDA tool. Reduction in controller workload were also observed throughout the scenario runs. The future plan includes modeling and simulation of the ramp operations of the Charlotte International Airport, and develop a decision support tool for the ramp controllers.

  11. Instructor Debrief Training in SPOT

    NASA Technical Reports Server (NTRS)

    Martin, Lynne; Orasanu, Judith; Villeda, Eric; Conners, Mary M. (Technical Monitor)

    2002-01-01

    One way to enhance the effectiveness of Special Purpose Operational Training' (SPOT) debriefing sessions may be for instructors to make explicit connections between the Crew Resource Management (CRM) concepts a carrier advocates and the behaviors displayed by the crew in question. A tool listing key behaviors from the scenario was devised, accompanied by an instructors' training session in which links were made between the behaviors and the underlying CRM processes they reflect. The aim of the tool is to assist instructors to focus the debriefing on the key SPOT/ CRM issues, in this case on planning. A second tool suggested ways to facilitate the discussion. Fourteen instructors at a major U.S. carrier took part in the training session and used the toolkit in their subsequent debriefs. Pre- and post-training debriefing samples from each instructor were compared to assess whether there were any changes in instructors' approaches to discussions in terms of the topics they covered and how they raised the points.

  12. Space Object Tracking (SPOT) facility

    NASA Astrophysics Data System (ADS)

    Shivitz, Robert; Kendrick, Richard; Mason, James; Bold, Matthew; Kubo, Tracy; Bock, Kevin; Tyler, David

    2014-07-01

    Lockheed Martin has built a Space Object Tracking (SPOT) facility at our Santa Cruz test site in Northern California. SPOT consists of three 1 meter optical telescopes controlled by a common site management system to individually or cooperatively task each system to observe orbital debris and earth orbiting satellites. The telescopes are mounted in Az/El fork mounts capable of rapid repointing and arc-sec class open loop tracking. Each telescope is installed in a separate clam shell dome and has aft mounted benches to facilitate installing various instrument suites. The telescope domes are mounted on movable rail carts that can be positioned arbitrarily along tracks to provide variable baselines for sparse aperture imaging. The individual telescopes achieved first light in June 2012 and have been used since to observe satellites and orbital debris. Typical observations consist of direct photometric imaging at visible and near infrared wavelengths, and also include spectroscopic and hypertemporal measurements. Rayleigh beacon adaptive optical systems for atmospheric aberration correction and high rate J-Band trackers for each telescope will be added in 2015. Coherent combinations of the three telescopes as an interferometric imaging array using actively stabilized free space variable delay optical paths and fringe tracking sensors is also planned. The first narrow band (I band) interferometric fringes will be formed in the summer of 2014, with wide band (R, I, H) interferometric imaging occurring by early 2015.

  13. Extended morphological processing: a practical method for automatic spot detection of biological markers from microscopic images

    PubMed Central

    2010-01-01

    Background A reliable extraction technique for resolving multiple spots in light or electron microscopic images is essential in investigations of the spatial distribution and dynamics of specific proteins inside cells and tissues. Currently, automatic spot extraction and characterization in complex microscopic images poses many challenges to conventional image processing methods. Results A new method to extract closely located, small target spots from biological images is proposed. This method starts with a simple but practical operation based on the extended morphological top-hat transformation to subtract an uneven background. The core of our novel approach is the following: first, the original image is rotated in an arbitrary direction and each rotated image is opened with a single straight line-segment structuring element. Second, the opened images are unified and then subtracted from the original image. To evaluate these procedures, model images of simulated spots with closely located targets were created and the efficacy of our method was compared to that of conventional morphological filtering methods. The results showed the better performance of our method. The spots of real microscope images can be quantified to confirm that the method is applicable in a given practice. Conclusions Our method achieved effective spot extraction under various image conditions, including aggregated target spots, poor signal-to-noise ratio, and large variations in the background intensity. Furthermore, it has no restrictions with respect to the shape of the extracted spots. The features of our method allow its broad application in biological and biomedical image information analysis. PMID:20615231

  14. Identification of quorum-sensing regulated proteins in the opportunistic pathogen Pseudomonas aeruginosa by proteomics.

    PubMed

    Arevalo-Ferro, Catalina; Hentzer, Morten; Reil, Gerold; Görg, Angelika; Kjelleberg, Staffan; Givskov, Michael; Riedel, Kathrin; Eberl, Leo

    2003-12-01

    The Gram-negative bacterium Pseudomonas aeruginosa is an opportunistic human pathogen which is responsible for severe nosocomial infections in immunocompromised patients and is the major pathogen in cystic fibrosis. The bacterium utilizes two interrelated quorum-sensing (QS) systems, which rely on N-acyl-homoserine lactone (AHL) signal molecules, to control the expression of virulence factors and biofilm development. In this study, we compared the protein patterns of the intracellular, extracellular and surface protein fractions of the PAO1 parent strain with those of an isogenic lasI rhlI double mutant by means of two-dimensional gel electrophoresis (2-DE). This analysis showed that the intensities of 23.7% of all detected protein spots differed more than 2.5-fold between the two strains. We only considered those protein spots truly QS regulated that were changed in the mutant in the absence of signal molecules but were rescued to the wild-type situation when the medium was supplemented with AHLs. These protein spots were characterized by MALDI-TOF peptide mapping. Twenty-seven proteins were identified that were previously reported to be AHL controlled, among them several well-characterized virulence factors. For one of the identified proteins, the serine protease PrpL, a biochemical assay was established to verify that expression of this factor is indeed QS regulated. Furthermore, it is shown that the quorum-sensing blocker C-30 specifically interferes with the expression of 67% of the AHL-controlled protein spots of the surface fraction, confirming the high specificity of the compound. Importantly, 20 novel QS-regulated proteins were identified, many of which are involved in iron utilization, suggesting a link between quorum sensing and the iron regulatory system. Two of these proteins, PhuR and HasAp, are components of the two distinct haem-uptake systems present in P. aeruginosa. In agreement with the finding that both proteins are positively regulated by the

  15. Variable-spot ion beam figuring

    NASA Astrophysics Data System (ADS)

    Wu, Lixiang; Qiu, Keqiang; Fu, Shaojun

    2016-03-01

    This paper introduces a new scheme of ion beam figuring (IBF), or rather variable-spot IBF, which is conducted at a constant scanning velocity with variable-spot ion beam collimated by a variable diaphragm. It aims at improving the reachability and adaptation of the figuring process within the limits of machine dynamics by varying the ion beam spot size instead of the scanning velocity. In contrast to the dwell time algorithm in the conventional IBF, the variable-spot IBF adopts a new algorithm, which consists of the scan path programming and the trajectory optimization using pattern search. In this algorithm, instead of the dwell time, a new concept, integral etching time, is proposed to interpret the process of variable-spot IBF. We conducted simulations to verify its feasibility and practicality. The simulation results indicate the variable-spot IBF is a promising alternative to the conventional approach.

  16. Characterizing flash-radiography source spots.

    PubMed

    Ekdahl, Carl

    2011-12-01

    Flash radiography of large hydrodynamic experiments driven by high explosives is a venerable diagnostic technique in use at many laboratories. The size of the radiographic source spot is often quoted as an indication of the resolving power of a particular flash-radiography machine. A variety of techniques for measuring spot size have evolved at the different laboratories, as well as different definitions of spot size. Some definitions are highly dependent on the source spot intensity distributions, and not necessarily well correlated with resolution. The concept of limiting resolution based on bar target measurements is introduced, and shown to be equivalent to the spatial wavenumber at a modulation transfer function value of 5%. This resolution is shown to be better correlated with the full width at half-maximum of the spot intensity distribution than it is with other definitions of spot size. PMID:22193263

  17. Protein

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Proteins are the major structural and functional components of all cells in the body. They are macromolecules that comprise 1 or more chains of amino acids that vary in their sequence and length and are folded into specific 3-dimensional structures. The sizes and conformations of proteins, therefor...

  18. Proteins.

    ERIC Educational Resources Information Center

    Doolittle, Russell F.

    1985-01-01

    Examines proteins which give rise to structure and, by virtue of selective binding to other molecules, make genes. Binding sites, amino acids, protein evolution, and molecular paleontology are discussed. Work with encoding segments of deoxyribonucleic acid (exons) and noncoding stretches (introns) provides new information for hypotheses. (DH)

  19. Identification of differentially accumulating pistil proteins associated with self-incompatibility of non-heading Chinese cabbage.

    PubMed

    Wang, L; Peng, H; Ge, T; Liu, T; Hou, X; Li, Y

    2014-01-01

    Non-heading Chinese cabbage (Brassica campestris L. ssp. chinensis Makino), an important vegetable crop in China, exhibits a typical sporophytic self-incompatibility (SI) system. To better understand the mechanism of SI response and identify potential candidate proteins involved in the SI system of this vegetable crop, the proteomic approach was taken to identify differential accumulating pistil proteins. Pistils were collected at 0 h and 2 h after self-pollination at anthesis in self-incompatible and compatible lines of non-heading Chinese cabbage, and total proteins were extracted and separated by two-dimensional gel electrophoresis (2-DE). A total of 25 protein spots that displayed differential abundance were identified by matrix-assisted laser desorption/ionisation-time of flight mass spectrometry (MALDI-TOF/TOF MS) and peptide mass fingerprinting (PMF). Among them, 22 protein spots were confidently established. The mRNA levels of the corresponding genes were detected by quantitative RT-PCR. The 22 identified protein spots are involved in energy metabolism (four), protein biosynthesis (three), photosynthesis (six), stress response and defence (five), and protein degradation (four). Among these potential candidate proteins, UDP-sugar pyrophosphorylase could be involved in sucrose degradation to influence pollen germination and growth. Glutathione S-transferases could be involved in pollen maturation, and affect pollen fertility. Senescence-associated cysteine protease, which is related to programmed cell death, could be mainly related to self pollen recognition of non-heading Chinese cabbage. The study will contribute to further investigations of molecular mechanism of sporophytic SI in Brassicaceae. PMID:23581423

  20. Pathogenesis-related proteins in somatic hybrid rice induced by bacterial blight.

    PubMed

    Yu, Chu L; Yan, Shun P; Wang, Chang C; Hu, Hai T; Sun, Wei N; Yan, Cheng Q; Chen, Jian P; Yang, Ling

    2008-07-01

    Rice bacterial blight, caused by Xanthomonasoryzae pv. Oryzae (Xoo), is one of the most serious rice diseases worldwide. The bacterial blight resistance trait from Oryza meyeriana, a wild rice species, was introduced into an elite japonica rice cultivar using asymmetric somatic hybridization. This study was carried out with the intention of understanding the molecular mechanism of incompatible interaction between Xoo and the stable somatic hybrids by using proteomic analyses. Proteins were extracted from leaves at 24, 48, and 72 h after Xoo inoculation and separated by 2-DE. A total of 77 protein spots changed their intensities significantly (p<0.05) by more than 1.5-fold at least at one time point. Sixty-four protein spots were successfully identified by MS analysis. Among them, 51 were known to be involved in photosynthesis. Up-regulation of Rubisco large subunit (RcbL) small fragments and down-regulation of RcbL big fragments indicated that intact RcbL and RcbL big fragments degraded following Xoo attack, which was further confirmed by Western blot analysis. The differential expression of proteins related to signal transduction, antioxidant defense, photosynthesis, metabolism, and protein turnover during the Xoo infection, suggests the existence of a complex regulatory network in the somatic hybrid rice that increases resistance toward Xoo infection and damage. PMID:18534637

  1. Origin of Jupiter's Great Red Spot

    SciTech Connect

    Luchkov, B.

    1981-09-01

    The Great Red Spot, a giant vortex in the Jovian atmosphere, may owe its origin to the structure of Jupiter's magnetic field and radiation belt. Several Spot parameters resemble those of the Brazil anomaly, a negative anomaly in the terrestrial field. It is shown qualitatively that the Spot has developed at the site of a negative anomaly in the Jovian field and is continually supplied by precipitation of energetic radiation-belt particles into the planet's atmosphere.

  2. Malaysian cockle (Anadara granosa) allergy: Identification of IgE-binding proteins and effects of different cooking methods.

    PubMed

    Zailatul, H M Y; Rosmilah, M; Faizal, B; Noormalin, A; Shahnaz, M

    2015-06-01

    The purpose of this study was to evaluate the effect of different cooking methods on the allergenicity of cockle and to identify proteins most frequently bound by IgE antibodies using a proteomics approach. Raw, boiled, fried and roasted extracts of the cockle were prepared. The protein profiles of the extracts were obtained by separation using sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and 2-dimensional gel electrophoresis (2-DE). IgE-immunoblotting was then performed with the use of individual sera from patients with cockle allergy and the major IgE-binding proteins were analyzed by mass-spectrometry. SDS-PAGE of raw extract showed 13 protein bands. Smaller numbers of protein bands were detected in the boiled, fried and roasted extracts. The 2-DE gel profile of the raw extract further separated the protein bands to ~50 protein spots with molecular masses between 13 to 180 kDa and isoelectric point (pI) values ranging from 3 to 10. Immunoblotting of raw extract exhibited 11 IgE-binding proteins with two proteins of 36 and 40 kDa as the major IgE-binding proteins, while the boiled extract revealed 3 IgE-binding proteins. Fried and roasted extracts only showed a single IgE-binding protein at 36 kDa. 2-DE immunoblotting of raw extract demonstrated 5 to 20 IgE reactive spots. Mass spectrometry analysis led to identification of 2 important allergens, tropomyosin (36 kDa) and arginine kinase (40 kDa). Heated extracts showed a reduction in the number of IgE-reactive bands compared with raw extract, which suggest that thermal treatment can be used as a tool in attempting to reduce cockle allergenicity. The degree of allergenicity of cockle was demonstrated in the order raw > boiled > fried ≈ roasted. Two important allergens reacting with more than 50% of patients' sera identified using mass spectrometric approaches were tropomyosin and arginine kinase. Thus, allergens found in this study would help in component based diagnosis, management of

  3. Hot spot and trench volcano separations

    NASA Technical Reports Server (NTRS)

    Lingenfelter, R. E.; Schubert, G.

    1974-01-01

    It is suggested that the distribution of separations between trench volcanos located along subduction zones reflects the depth of partial melting, and that the separation distribution for hot spot volcanoes near spreading centers provides a measure of the depth of mantle convection cells. It is further proposed that the lateral dimensions of mantle convection cells are also represented by the hot-spot separations (rather than by ridge-trench distances) and that a break in the distribution of hot spot separations at 3000 km is evidence for both whole mantle convection and a deep thermal plume origin of hot spots.

  4. Proteomic Analysis of Salt-Responsive Proteins in the Leaves of Mangrove Kandelia candel during Short-Term Stress

    PubMed Central

    Liang, Meng; Tan, Fanglin; Liang, Wenyu; Chen, Yiyong; Lin, Yongxiang; Huang, Li; Xing, Jianhong; Chen, Wei

    2014-01-01

    Salt stress is a major abiotic stress that limits crop productivity in many regions of the world. A comparative proteomic approach to identify salt stress-responsive proteins and to understand the molecular mechanisms was carried out in the woody halophyte Kandelia candel. Four-leaf-old K. candel seedlings were exposed to 150 (control), 300, 450, and 600 mM NaCl for 3 days. Proteins extracted from the leaves of K. candel seedlings were separated by two-dimensional gel electrophoresis (2-DE). More than 900 protein spots were detected on each gel, and 53 differentially expressed protein spots were located with at least two-fold differences in abundance on 2-DE maps, of which 48 were identified by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF-TOF/MS). The results showed that K. candel could withstand up to 450 mM NaCl stress by up-regulating proteins that are mainly involved in photosynthesis, respiration and energy metabolism, Na+ compartmentalization, protein folding and assembly, and signal transduction. Physiological data, including superoxide dismutase (SOD) and dehydroascorbate reductase (DHAR) activities, hydrogen peroxide (H2O2) and superoxide anion radicals (O2−) contents, as well as Na+ content and K+/Na+ ratios all correlated well with our proteomic results. This study provides new global insights into woody halophyte salt stress responses. Identification of differentially expressed proteins promotes better understanding of the molecular basis for salt stress reduction in K. candel. PMID:24416157

  5. A comparison of the Great Red Spot with temporary spots on Jupiter

    NASA Technical Reports Server (NTRS)

    Browne, G. C.; Meadows, A. J.

    1976-01-01

    The International Planetary Patrol collection of Jupiter photographs is used to examine the development of a temporary spot that was visible in the northern equatorial zone for a total of 211 days. The motion and color of this spot are compared with those of the Great Red Spot. It is shown that the temporary spot was bluer than the Great Red Spot and has a longitudinal oscillation of approximately 4 deg with a period of about 45 days, implying that it may have possessed a significant dynamical property in common with other temporary spots and the Great Red Spot. It is concluded that the present spot is more likely to have been associated with a hole in the cloud deck rather than with an elevated surface feature.

  6. Voyager 1 Red Spot Movie

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This movie shows the portion of Jupiter around the Great Red Spot as it swirls through more than 60 Jupiter days. Notice the difference in speed and direction of the various zones of the atmosphere. The interaction of the atmospheric clouds and storm shows how dynamic the Jovian atmosphere is.

    As Voyager 1 approached Jupiter in 1979, it took images of the planet at regular intervals. This sequence is made from 66 images taken once every Jupiter rotation period (about 10 hours). This time-lapse movie uses images taken every time Jupiter longitude 68W passed under the spacecraft. These images were acquired in the Blue filter from Jan. 6 to Feb. 3 1979. The spacecraft flew from 58 million kilometers to 31 million kilometers from Jupiter during that time.

    This time-lapse movie was produced at JPL by the Image Processing Laboratory in 1979.

  7. Ambystoma maculatum (spotted salamander). Reproduction

    USGS Publications Warehouse

    Glorioso, Brad M.; Waddle, Hardin; Hefner, Jeromi

    2012-01-01

    The Spotted Salamander is a wide-ranging salamander of the eastern United States that typically breeds in winter or early spring in ephemeral pools in lowland forests. Ambystoma maculatum is known to deposit 2-4 egg masses per year, each containing 1-250 eggs. As part of ongoing research into the ecology and reproductive biology of Spotted Salamanders in the Kisatchie District of Kisatchie National Forest in Natchitoches Parish, Louisiana, USA, we have been counting the number of embryos per egg mass. We captured seven female A. maculatum in a small pool, six of which were still gravid. We took standard measurements, including SVL, and then implanted a Passive Integrated Transponder (PIT tag) into each adult female as was the protocol. About an hour after processing these animals we marked new A. maculatum egg masses found in the same small pool using PVC pin flags pushed carefully through the outer jelly. We did not have enough time to process them that evening, and it was not until a few days later that we photographed those masses. We discovered that one of the masses contained a PIT tag in the outer jelly that corresponded to one of the six gravid females that were marked that same evening. To our knowledge, this is the first report of PIT tags being the means, albeit coincidentally, by which a particular egg mass of Ambystoma maculatum has been assigned to a particular female. For our purposes, losing the PIT tag from the adult female is counter to the goals of our study of this population, and we will no longer be implanting PIT tags into gravid females.

  8. Comparative protein profiles: potential molecular markers from spermatozoa of Acipenseriformes (Chondrostei, Pisces).

    PubMed

    Li, Ping; Hulak, Martin; Rodina, Marek; Sulc, Miroslav; Li, Zhi-Hua; Linhart, Otomar

    2010-12-01

    Sturgeon and paddlefish (Acipenseriformes), the source of roe consumed as caviar, are a unique and commercially valuable group of ancient fishes. In this study, comparative proteomics was used to analyze protein profiles of spermatozoa from five sturgeon species and one paddlefish: Siberian sturgeon (Acipenser baerii), sterlet (A. ruthenus), Russian sturgeon (A. gueldenstaedtii), starry sturgeon (A. stellatus), beluga (Huso huso), and Mississippi paddlefish (Polyodon spathula). Protein profiles of spermatozoa were determined by isoelectric focusing and two-dimensional electrophoresis (2-DE) high-resolution gels. The peptides, previously selected by 2-DE analysis as potentially species-specific, were obtained by "in-gel" tryptic digestion, followed by matrix-associated laser desorption/ionization time-of-flight/mass spectrometry (MALDI-TOF/MS). Among the 23 protein spots selected, 14 were identified as isoforms of enolase B present in all species, but with different isoelectric points or molecular mass. Exceptions were A. ruthenus and H. huso, species with a close phylogenetic relationship. Glycerol-3-phosphate dehydrogenase was detected exclusively in P. spathula. Phosphoglycerate kinase was detected only in A. ruthenus and H. huso, and 3 additional proteins (fructose bisphosphate aldolase A-2, glycogen phosphorylase type IV and glyceraldehyde-3-phosphate dehydrogenase) were found exclusively in A. gueldenstaedtii and H. huso. This study points to the application of proteomics for differential characterization and comparative studies of acipenseriform species at the molecular level. PMID:20869341

  9. Rocky Mountain spotted fever in Argentina

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cases of epidemic typhus have been documented in Argentina since 1919; however, no confirmed reports of spotted fever rickettsiosis were described in this country until 1999. We describe the first molecular confirmation of Rickettsia rickettsii, the etiologic agent of Rocky Mountain spotted fever (R...

  10. Hot Spot Removal System: System description

    SciTech Connect

    1997-09-01

    Hazardous wastes contaminated with radionuclides, chemicals, and explosives exist across the Department of Energy complex and need to be remediated due to environmental concerns. Currently, an opportunity is being developed to dramatically reduce remediation costs and to assist in the acceleration of schedules associated with these wastes by deploying a Hot Spot Removal System. Removing the hot spot from the waste site will remove risk driver(s) and enable another, more cost effective process/option/remedial alternative (i.e., capping) to be applied to the remainder of the site. The Hot Spot Removal System consists of a suite of technologies that will be utilized to locate and remove source terms. Components of the system can also be used in a variety of other cleanup activities. This Hot Spot Removal System Description document presents technologies that were considered for possible inclusion in the Hot Spot Removal System, technologies made available to the Hot Spot Removal System, industrial interest in the Hot Spot Removal System`s subsystems, the schedule required for the Hot Spot Removal System, the evaluation of the relevant technologies, and the recommendations for equipment and technologies as stated in the Plan section.

  11. HotSpot Software Configuration Management Plan

    SciTech Connect

    Walker, H; Homann, S G

    2009-03-12

    This Software Configuration Management Plan (SCMP) describes the software configuration management procedures used to ensure that the HotSpot dispersion model meets the requirements of its user base, which includes: (1) Users of the PC version of HotSpot for consequence assessment, hazard assessment and safety analysis calculations; and (2) Users of the NARAC Web and iClient software tools, which allow users to run HotSpot for consequence assessment modeling These users and sponsors of the HotSpot software and the organizations they represent constitute the intended audience for this document. This plan is intended to meet Critical Recommendations 1 and 3 from the Software Evaluation of HotSpot and DOE Safety Software Toolbox Recommendation for inclusion of HotSpot in the Department of Energy (DOE) Safety Software Toolbox. HotSpot software is maintained for the Department of Energy Office of Emergency Operations by the National Atmospheric Release Advisory Center (NARAC) at Lawrence Livermore National Laboratory (LLNL). An overview of HotSpot and NARAC are provided.

  12. Spotted knapweed, Centaurea stoebe, control options

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Spotted knapweed is a non native perennial forb that is spreading rapidly in the Western United States. This plant species produces a compound that retards the growth of many native plants, giving it a competitive advantage. Spotted knapweed has been identified in several areas of Alaska. A descript...

  13. Rocky Mountain Spotted Fever in Argentina

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We describe the first molecular confirmation of Rickettsia rickettsii, the cause of Rocky Mountain spotted fever (RMSF), from a tick vector, Amblyomma cajennense, and from a cluster of fatal spotted fever cases in Argentina. Questing A. cajennense ticks were collected at or near sites of presumed or...

  14. 7 CFR 1421.11 - Spot checks.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 10 2012-01-01 2012-01-01 false Spot checks. 1421.11 Section 1421.11 Agriculture Regulations of the Department of Agriculture (Continued) COMMODITY CREDIT CORPORATION, DEPARTMENT OF... ASSISTANCE LOANS AND LOAN DEFICIENCY PAYMENTS FOR 2008 THROUGH 2012 General § 1421.11 Spot checks. (a)...

  15. Differential spot-size focus servo

    NASA Technical Reports Server (NTRS)

    Milster, T. D.; Wang, M. S.; Froehlich, F. F.; Kann, J. L.; Treptau, J. P.; Erwin, K. E.

    1991-01-01

    We describe performance of a differential spot-size (wax-wane) focus servo. Crosstalk from the tracks are analyzed in the single detector and differential focus circuits. Magnitude of the crosstalk is reduced by a factor of three in the differential circuit. A false focus-error signal (FES) is present when the spot crosses sector marks at an angle.

  16. HotSpot Software Test Plan

    SciTech Connect

    Walker, H; Homann, S G

    2009-03-12

    This Software Test Plan (STP) describes the procedures used to verify and validate that the HotSpot Health Physics Codes meet the requirements of its user base, which includes: (1) Users of the PC version of HotSpot conducting consequence assessment, hazard assessment and safety analysis calculations; and (2) Users of the NARAC Web and iClient software tools, which allow users to run HotSpot for consequence assessment modeling. This plan is intended to meet Critical Recommendation 2 from the Software Evaluation of HotSpot and DOE Safety Software Toolbox Recommendation for inclusion of HotSpot in the Department of Energy (DOE) Safety Software Toolbox. These users and sponsors of the HotSpot software and the organizations they represent constitute the intended audience for this document. HotSpot software is maintained for the Department of Energy Office of Emergency Operations by the National Atmospheric Release Advisory Center (NARAC) at Lawrence Livermore National Laboratory (LLNL). An overview of HotSpot and NARAC are provided.

  17. Decabrominated diphenyl ether (BDE-209) and/or BDE-47 exposure alters protein expression in purified neural stem/progenitor cells determined by proteomics analysis.

    PubMed

    Song, Jie; Li, Zhi-hua; He, Yu-Tian; Liu, Chuan-Xin; Sun, Bin; Zhang, Chun-Fang; Zeng, Jie; Du, Pei-Li; Zhang, Hui-Li; Yu, Yan-hong; Chen, Dun-Jin

    2014-04-01

    Polybrominateddiphenyl ethers (PBDEs) are widely utilized as the additive brominated flame retardants in electronic devices, furniture, plastics, rubber foam, and textiles, which exhibit many negative biological effects, especially potential toxic effects on neurodevelopment. In the present study, we applied a proteomics approach to study the effects of decabromodiphenyl ether (BDE-209) and/or tetrabromodiphenyl ether (BDE-47) on the expression of proteins extracted from neural stem/progenitor cells and further explored mechanisms on neurodevelopmental toxicity. We sub-cultured 3-4 generations of neural stem/progenitor cells which were exposed to BDE-209 and/or BDE-47. After a 72-h exposure, we applied two-dimensional gel (2-DE) to identify differentially expressed proteins and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) to determine the protein identity of 25 spots. Western blot analysis was applied to determine the expression of cofilin-1 and vimentin. A total of 39 differential expression protein spots were identified by 2-DE after BDE-209 and/or BDE-47 exposure in the neural stem/progenitor cells, and 19 differentially expressed proteins were identified by MALDI-TOF-MS. Western blot analysis revealed that cofilin-1 and vimentin were differentially expressed in all groups. Expression of both proteins was decreased when the neural stem/progenitor cells were exposed to BDE-209 and were absent when exposed to both BDE-47 and BDE-209. BDE-209 and/or BDE-47 might alter the expression of some proteins of neural stem/progenitor cells. Nineteen proteins were identified by MALDI-TOF-MS, which will provide a useful basis for further study of the mechanisms underlying PBDE-mediated neurotoxicity. PMID:24239914

  18. New insight on crystal and spot development in hard and extra-hard cheeses: Association of spots with incomplete aggregation of curd granules.

    PubMed

    D'Incecco, P; Limbo, S; Faoro, F; Hogenboom, J; Rosi, V; Morandi, S; Pellegrino, L

    2016-08-01

    Chemical composition and structure of different types of macroparticles (specks, spots) and microparticles (microcrystals) present in hard and extra-hard cheeses were investigated. Light microscopy revealed that the small hard specks had the structure of crystalline tyrosine, as confirmed by amino acid analysis. Spots showed a complex structure, including several curd granules, cavities, and microcrystals, and were delimited by a dense protein layer. Spots contained less moisture and ash than the adjacent cheese area, and more protein, including significantly higher contents of valine, methionine, isoleucine, leucine, tyrosine, and phenylalanine. Microcrystals were observed by light and electron microscopy and analyzed by confocal micro-Raman. Among others, calcium phosphate crystals appeared to consist of a central star-shaped structure immersed in a matrix of free fatty acids plus leucine and phenylalanine in free form or in small peptides. A hypothetical mechanism for the formation of these structures has been formulated. PMID:27236764

  19. Laser Spot Detection Based on Reaction Diffusion

    PubMed Central

    Vázquez-Otero, Alejandro; Khikhlukha, Danila; Solano-Altamirano, J. M.; Dormido, Raquel; Duro, Natividad

    2016-01-01

    Center-location of a laser spot is a problem of interest when the laser is used for processing and performing measurements. Measurement quality depends on correctly determining the location of the laser spot. Hence, improving and proposing algorithms for the correct location of the spots are fundamental issues in laser-based measurements. In this paper we introduce a Reaction Diffusion (RD) system as the main computational framework for robustly finding laser spot centers. The method presented is compared with a conventional approach for locating laser spots, and the experimental results indicate that RD-based computation generates reliable and precise solutions. These results confirm the flexibility of the new computational paradigm based on RD systems for addressing problems that can be reduced to a set of geometric operations. PMID:26938537

  20. Laser Spot Detection Based on Reaction Diffusion.

    PubMed

    Vázquez-Otero, Alejandro; Khikhlukha, Danila; Solano-Altamirano, J M; Dormido, Raquel; Duro, Natividad

    2016-01-01

    Center-location of a laser spot is a problem of interest when the laser is used for processing and performing measurements. Measurement quality depends on correctly determining the location of the laser spot. Hence, improving and proposing algorithms for the correct location of the spots are fundamental issues in laser-based measurements. In this paper we introduce a Reaction Diffusion (RD) system as the main computational framework for robustly finding laser spot centers. The method presented is compared with a conventional approach for locating laser spots, and the experimental results indicate that RD-based computation generates reliable and precise solutions. These results confirm the flexibility of the new computational paradigm based on RD systems for addressing problems that can be reduced to a set of geometric operations. PMID:26938537

  1. TEVA-SPOT Toolkit 1.2

    2007-07-26

    The TEVA-SPOT Toolkit (SPOT) supports the design of contaminant warning systems (CWSs) that use real-time sensors to detect contaminants in municipal water distribution networks. Specifically, SPOT provides the capability to select the locations for installing sensors in order to maximize the utility and effectiveness of the CWS. SPOT models the sensor placement process as an optimization problem, and the user can specify a wide range of performance objectives for contaminant warning system design, including populationmore » health effects, time to detection, extent of contamination, volume consumed and number of failed detections. For example, a SPOT user can integrate expert knowledge during the design process by specigying required sensor placements or designating network locations as forbidden. Further, cost considerations can be integrated by limiting the design with user-specified installation costs at each location.« less

  2. Improved MRF spot characterization with QIS metrology

    NASA Astrophysics Data System (ADS)

    Westover, Sandi; Hall, Christopher; DeMarco, Michael

    2013-09-01

    Careful characterization of the removal function of sub-aperture polishing tools is critical for optimum polishing results. Magnetorheological finishing (MRF®) creates a polishing tool, or "spot", that is unique both for its locally high removal rate and high slope content. For a variety of reasons, which will be discussed, longer duration spots are beneficial to improving MRF performance, but longer spots yield higher slopes rendering them difficult to measure with adequate fidelity. QED's Interferometer for Stitching (QIS™) was designed to measure the high slope content inherent to non-null sub-aperture stitching interferometry of aspheres. Based on this unique capability the QIS was recently used to measure various MRF spots in an attempt to see if there was a corresponding improvement in MRF performance as a result of improved knowledge of these longer duration spots. The results of these tests will be presented and compared with those of a standard general purpose interferometer.

  3. Element spots in HgMn stars

    NASA Astrophysics Data System (ADS)

    Korhonen, H.

    2014-11-01

    A fraction of late B-type stars, the so-called HgMn stars, exhibit enhanced absorption lines of certain chemical elements, notably Hg and Mn, combined with an underabundance of He. For about a decade it has been known that the elements with anomalously high abundances in HgMn stars are distributed inhomogeneously over the stellar surface. Observation of the temporal evolution of those spots has been reported in a few HgMn stars, first of a secular evolution of the mercury spots in α And, and more recently of a fast evolution of yttrium and strontium spots in HD 11753. The fast evolution of spots in HD 11753 is combined with a slower change in the overall abundance of the elements affected. In this paper I review what is known about these ``elemental spots'' in HgMn stars and their secular and fast temporal evolution.

  4. Neptune's small dark spot (D2)

    NASA Technical Reports Server (NTRS)

    1999-01-01

    This bulls-eye view of Neptune's small dark spot (D2) was obtained by Voyager 2's narrow-angle camera. Banding surrounding the feature indicates unseen strong winds, while structures within the bright spot suggest both active upwelling of clouds and rotation about the center. A rotation rate has not yet been measured, but the V-shaped structure near the right edge of the bright area indicates that the spot rotates clockwise. Unlike the Great Red Spot on Jupiter, which rotates counterclockwise, if the D2 spot on Neptune rotates clockwise, the material will be descending in the dark oval region. The fact that infrared data will yield temperature information about the region above the clouds makes this observation especially valuable. The Voyager Mission is conducted by JPL for NASA's Office of Space Science and Applications.

  5. Nitrogen-Efficient and Nitrogen-Inefficient Indian Mustard Showed Differential Expression Pattern of Proteins in Response to Elevated CO2 and Low Nitrogen.

    PubMed

    Yousuf, Peerzada Y; Ganie, Arshid H; Khan, Ishrat; Qureshi, Mohammad I; Ibrahim, Mohamed M; Sarwat, Maryam; Iqbal, Muhammad; Ahmad, Altaf

    2016-01-01

    Carbon (C) and nitrogen (N) are two essential elements that influence plant growth and development. The C and N metabolic pathways influence each other to affect gene expression, but little is known about which genes are regulated by interaction between C and N or the mechanisms by which the pathways interact. In the present investigation, proteome analysis of N-efficient and N-inefficient Indian mustard, grown under varied combinations of low-N, sufficient-N, ambient [CO2], and elevated [CO2] was carried out to identify proteins and the encoding genes of the interactions between C and N. Two-dimensional gel electrophoresis (2-DE) revealed 158 candidate protein spots. Among these, 72 spots were identified by matrix-assisted laser desorption ionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF). The identified proteins are related to various molecular processes including photosynthesis, energy metabolism, protein synthesis, transport and degradation, signal transduction, nitrogen metabolism and defense to oxidative, water and heat stresses. Identification of proteins like PII-like protein, cyclophilin, elongation factor-TU, oxygen-evolving enhancer protein and rubisco activase offers a peculiar overview of changes elicited by elevated [CO2], providing clues about how N-efficient cultivar of Indian mustard adapt to low N supply under elevated [CO2] conditions. This study provides new insights and novel information for a better understanding of adaptive responses to elevated [CO2] under N deficiency in Indian mustard. PMID:27524987

  6. Nitrogen-Efficient and Nitrogen-Inefficient Indian Mustard Showed Differential Expression Pattern of Proteins in Response to Elevated CO2 and Low Nitrogen

    PubMed Central

    Yousuf, Peerzada Y.; Ganie, Arshid H.; Khan, Ishrat; Qureshi, Mohammad I.; Ibrahim, Mohamed M.; Sarwat, Maryam; Iqbal, Muhammad; Ahmad, Altaf

    2016-01-01

    Carbon (C) and nitrogen (N) are two essential elements that influence plant growth and development. The C and N metabolic pathways influence each other to affect gene expression, but little is known about which genes are regulated by interaction between C and N or the mechanisms by which the pathways interact. In the present investigation, proteome analysis of N-efficient and N-inefficient Indian mustard, grown under varied combinations of low-N, sufficient-N, ambient [CO2], and elevated [CO2] was carried out to identify proteins and the encoding genes of the interactions between C and N. Two-dimensional gel electrophoresis (2-DE) revealed 158 candidate protein spots. Among these, 72 spots were identified by matrix-assisted laser desorption ionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF). The identified proteins are related to various molecular processes including photosynthesis, energy metabolism, protein synthesis, transport and degradation, signal transduction, nitrogen metabolism and defense to oxidative, water and heat stresses. Identification of proteins like PII-like protein, cyclophilin, elongation factor-TU, oxygen-evolving enhancer protein and rubisco activase offers a peculiar overview of changes elicited by elevated [CO2], providing clues about how N-efficient cultivar of Indian mustard adapt to low N supply under elevated [CO2] conditions. This study provides new insights and novel information for a better understanding of adaptive responses to elevated [CO2] under N deficiency in Indian mustard. PMID:27524987

  7. 7 CFR 28.413 - Middling Light Spotted Color.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Middling Light Spotted Color. 28.413 Section 28.413... REGULATIONS COTTON CLASSING, TESTING, AND STANDARDS Standards Light Spotted Cotton § 28.413 Middling Light Spotted Color. Middling Light Spotted Color is color which in spot or color, or both, is between...

  8. Proteomic analysis of plasma membrane proteins in wheat roots exposed to phenanthrene.

    PubMed

    Shen, Yu; Du, Jiangxue; Yue, Le; Zhan, Xinhua

    2016-06-01

    Polycyclic aromatic hydrocarbons (PAHs) are potentially carcinogenic and toxic to humans through ingestion of contaminated food crops. PAHs can enter crop roots through proton/PAH symporters; however, to date, the symporter remains unclear. Here we reveal, for the first time, the plasma membrane proteome of Triticum aestivum seedling roots in response to phenanthrene (a model PAH) exposure. Two-dimensional gel electrophoresis (2-DE) coupled with MALDI-TOF/TOF-MS and protein database search engines were employed to analyze and identify phenanthrene-responsive proteins. Over 192 protein spots are reproducibly detected in each gel, while 8 spots are differentially expressed under phenanthrene treatment. Phenanthrene induces five up-regulated proteins distinguished as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase 2, enolase, heat shock protein 80-2, probable mediator of RNA polymerase II transcription subunit 37e (heat shock 70-kDa protein 1), and lactoylglutathione lyase. Three proteins identified as adenosine kinase 2, 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1c, and glyceraldehyde-3-phosphate dehydrogenase 3 are down-regulated under exposure to phenanthrene. The up-regulated proteins are related to plant defense response, antioxidant system, and glycolysis. The down-regulated proteins involve the metabolism of high-energy compounds and plant growth. Magnesium, which is able to bind to enolase, can enhance the transport of phenanthrene into wheat roots. Therefore, it is concluded that phenanthrene can induce differential expression of proteins in relation to carbohydrate metabolism, self-defense, and plant growth on wheat root plasma membrane. This study not only provides novel insights into PAH uptake by plant roots and PAH stress responses, but is also a good starting point for further determination and analyses of their functions using genetic and other approaches. PMID:26897580

  9. Geo Spots and Vortex Theory

    NASA Astrophysics Data System (ADS)

    Straser, Valentino

    2014-05-01

    ), when limited to particular regions, may have created in the past and perhaps still do to this day torsions in localized spots of the Earth's crust (Geo Spots), which over time have conditioned the distribution of tectonic stresses on the surface of the Earth at a regional scale.

  10. Exploring Proteins in Anopheles gambiae Male and Female Antennae through MALDI Mass Spectrometry Profiling

    PubMed Central

    Dani, Francesca R.; Francese, Simona; Mastrobuoni, Guido; Felicioli, Antonio; Caputo, Beniamino; Simard, Frederic; Pieraccini, Giuseppe; Moneti, Gloriano; Coluzzi, Mario; della Torre, Alessandra; Turillazzi, Stefano

    2008-01-01

    MALDI profiling and imaging mass spectrometry (IMS) are novel techniques for direct analysis of peptides and small proteins in biological tissues. In this work we applied them to the study of Anopheles gambiae antennae, with the aim of analysing expression of soluble proteins involved in olfaction perireceptor events. MALDI spectra obtained by direct profiling on single antennae and by the analysis of extracts, showed similar profiles, although spectra obtained through profiling had a richer ion population and higher signal to noise ratio. Male and female antennae showed distinct protein profiles. MALDI imaging experiments were also performed and differences were observed in the localization of some proteins. Two proteins were identified through high resolution measurement and top-down MS/MS experiments. A 8 kDa protein only present in the male antennae matched with an unannotated sequence of the An. gambiae genome, while the presence of odorant binding protein 9 (OBP-9) was confirmed through experiments of 2-DE, followed by MS and MS/MS analysis of digested spots. This work shows that MALDI MS profiling is a technique suitable for the analysis of proteins of small and medium MW in insect appendices, and allows obtaining data for several specimens which can be investigated for differences between groups. Proteins of interest can be identified through other complementary MS approaches. PMID:18665262

  11. Depletion of abundant plant RuBisCO protein using the protamine sulfate precipitation method.

    PubMed

    Kim, Yu Ji; Lee, Hye Min; Wang, Yiming; Wu, Jingni; Kim, Sang Gon; Kang, Kyu Young; Park, Ki Hun; Kim, Yong Chul; Choi, In Soo; Agrawal, Ganesh Kumar; Rakwal, Randeep; Kim, Sun Tae

    2013-07-01

    Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the most abundant plant leaf protein, hampering deep analysis of the leaf proteome. Here, we describe a novel protamine sulfate precipitation (PSP) method for the depletion of RuBisCO. For this purpose, soybean leaf total proteins were extracted using Tris-Mg/NP-40 extraction buffer. Obtained clear supernatant was subjected to the PSP method, followed by 13% SDS-PAGE analysis of total, PS-supernatant and -precipitation derived protein samples. In a dose-dependent experiment, 0.1% w/v PS was found to be sufficient for precipitating RuBisCO large and small subunits (LSU and SSU). Western blot analysis confirmed no detection of RuBisCO LSU in the PS-supernatant proteins. Application of this method to Arabidopsis, rice, and maize leaf proteins revealed results similar to soybean. Furthermore, 2DE analyses of PS-treated soybean leaf displayed enriched protein profile for the protein sample derived from the PS-supernatant than total proteins. Some enriched 2D spots were subjected to MALDI-TOF-TOF analysis and were successfully assigned for their protein identity. Hence, the PSP method is: (i) simple, fast, economical, and reproducible for RuBisCO precipitation from the plant leaf sample; (ii) applicable to both dicot and monocot plants; and (iii) suitable for downstream proteomics analysis. PMID:23576416

  12. The evolutionary turnover of recombination hot spots contributes to speciation in mice.

    PubMed

    Smagulova, Fatima; Brick, Kevin; Pu, Yongmei; Camerini-Otero, R Daniel; Petukhova, Galina V

    2016-02-01

    Meiotic recombination is required for the segregation of homologous chromosomes and is essential for fertility. In most mammals, the DNA double-strand breaks (DSBs) that initiate meiotic recombination are directed to a subset of genomic loci (hot spots) by sequence-specific binding of the PRDM9 protein. Rapid evolution of the DNA-binding specificity of PRDM9 and gradual erosion of PRDM9-binding sites by gene conversion will alter the recombination landscape over time. To better understand the evolutionary turnover of recombination hot spots and its consequences, we mapped DSB hot spots in four major subspecies of Mus musculus with different Prdm9 alleles and in their F1 hybrids. We found that hot spot erosion governs the preferential usage of some Prdm9 alleles over others in hybrid mice and increases sequence diversity specifically at hot spots that become active in the hybrids. As crossovers are disfavored at such hot spots, we propose that sequence divergence generated by hot spot turnover may create an impediment for recombination in hybrids, potentially leading to reduced fertility and, eventually, speciation. PMID:26833728

  13. The evolutionary turnover of recombination hot spots contributes to speciation in mice

    PubMed Central

    Smagulova, Fatima; Brick, Kevin; Pu, Yongmei; Camerini-Otero, R. Daniel; Petukhova, Galina V.

    2016-01-01

    Meiotic recombination is required for the segregation of homologous chromosomes and is essential for fertility. In most mammals, the DNA double-strand breaks (DSBs) that initiate meiotic recombination are directed to a subset of genomic loci (hot spots) by sequence-specific binding of the PRDM9 protein. Rapid evolution of the DNA-binding specificity of PRDM9 and gradual erosion of PRDM9-binding sites by gene conversion will alter the recombination landscape over time. To better understand the evolutionary turnover of recombination hot spots and its consequences, we mapped DSB hot spots in four major subspecies of Mus musculus with different Prdm9 alleles and in their F1 hybrids. We found that hot spot erosion governs the preferential usage of some Prdm9 alleles over others in hybrid mice and increases sequence diversity specifically at hot spots that become active in the hybrids. As crossovers are disfavored at such hot spots, we propose that sequence divergence generated by hot spot turnover may create an impediment for recombination in hybrids, potentially leading to reduced fertility and, eventually, speciation. PMID:26833728

  14. Buffer optimization for high resolution of human lung cancer tissue proteins by two-dimensional gel electrophoresis.

    PubMed

    Lee, Kibeom; Pi, Kyungbae; Lee, Keeman

    2009-01-01

    A problem in proteomic analysis of lung cancer tissue is the presence of complex components of different histological backgrounds (squamous cell carcinoma, small cell lung carcinoma, and adenocarcinoma). The efficient solubilization of protein components before two-dimensional electrophoresis (2-DE) is a very critical. Poor solubilization has been associated with a failure to detect proteins and diffuse, streaked and/or trailing protein spots. Here, we have optimized the solubilization of human lung cancer tissue to increase protein resolution. Isoelectric focusing (IEF) rehydration buffer containing a thiourea-urea mixture provided superior resolution, whereas a buffer without thiourea yielded consistently poor results. In addition, IEF rehydration buffers containing CHAPS and DTT gave superior resolution, whereas buffers containing Nonidet P-40 (NP-40) and/or Triton X-100 did not. A tributylphosphine-containing buffer gave consistently poor results. Using optimized conditions, we used 2-D gel analysis of human lung cancer tissue to identify 11 differentially-expressed protein spots by MALDI-mass spectrometry. This study provides a methodological tool to study the complex mammalian proteomes. PMID:18800191

  15. Differential protein profiles of postharvest Gynura bicolor D.C leaf treated by 1-methylcyclopropene and ethephon.

    PubMed

    Jiang, Li; Kang, Ruoyi; Zhang, Li; Jiang, Juan; Yu, Zhifang

    2015-06-01

    Proteins were extracted from G. bicolor that had been treated with 1-methylcyclopropene and ethephon and then stored at room temperature for 1, 3 and 7days. More than 300 protein spots were detected by 2-DE and 38 differentially abundant spots (P<0.05) were excised and analysed by using MALDI-TOF/TOF. Thirty-three proteins were finally confidently identified. According to the Clusters of Orthologous Groups of proteins, the proteins identified were classified into those responsible for metabolism (75.8%), information storage and processing (9.1%) and cellular processes and signaling (12.1%). Compared with ethephon and control treatments, 1-methylcyclopropene specifically increased the abundances of superoxide dismutase, peroxidase, carbonic anhydrase, nucleoside diphosphate kinases, glyceraldehyde 3-phosphate dehydrogenase, RuBisCO and ribulose bisphosphate carboxylase/oxygenase activase. 1-Methylcyclopropene protected leaf chloroplast and cells by enhancing stress response and defense, and delayed senescence by inhibiting substance and energy metabolisms. Therefore, 1-methylcyclopropene allowed better self-defense and delayed senescence of G. bicolor leaf. PMID:25624203

  16. HUBBLE FINDS NEW DARK SPOT ON NEPTUNE

    NASA Technical Reports Server (NTRS)

    2002-01-01

    NASA's Hubble Space Telescope has discovered a new great dark spot, located in the northern hemisphere of the planet Neptune. Because the planet's northern hemisphere is now tilted away from Earth, the new feature appears near the limb of the planet. The spot is a near mirror-image to a similar southern hemisphere dark spot that was discovered in 1989 by the Voyager 2 probe. In 1994, Hubble showed that the southern dark spot had disappeared. Like its predecessor, the new spot has high altitude clouds along its edge, caused by gasses that have been pushed to higher altitudes where they cool to form methane ice crystal clouds. The dark spot may be a zone of clear gas that is a window to a cloud deck lower in the atmosphere. Planetary scientists don t know how long lived this new feature might be. Hubble's high resolution will allow astronomers to follow the spot's evolution and other unexpected changes in Neptune's dynamic atmosphere. The image was taken on November 2, 1994 with Hubble's Wide Field Planetary Camera 2, when Neptune was 2.8 billion miles (4.5 billion kilometers) from Earth. Hubble can resolve features as small as 625 miles (1,000 kilometers) across in Neptune's cloud tops. Credit: H. Hammel (Massachusetts Institute of Technology) and NASA

  17. Rocky mountain spotted fever on the arm (image)

    MedlinePlus

    Rocky Mountain Spotted Fever is a disease transmitted to humans by a tick bite. The spots begin as flat (macular) red (erythematous) patches that may bleed into the skin, causing purplish spots (purpura). The disease ...

  18. Gel-based and gel-free proteomic analysis of Nicotiana tabacum trichomes identifies proteins involved in secondary metabolism and in the (a)biotic stress response.

    PubMed

    Van Cutsem, Emmanuel; Simonart, Géraldine; Degand, Hervé; Faber, Anne-Marie; Morsomme, Pierre; Boutry, Marc

    2011-02-01

    Nicotiana tabacum leaves are covered by trichomes involved in the secretion of large amounts of secondary metabolites, some of which play a major role in plant defense. However, little is known about the metabolic pathways that operate in these structures. We undertook a proteomic analysis of N. tabacum trichomes in order to identify their protein complement. Efficient trichome isolation was obtained by abrading frozen leaves. After homogenization, soluble proteins and a microsomal fraction were prepared by centrifugation. Gel-based and gel-free proteomic analyses were then performed. 2-DE analysis of soluble proteins led to the identification of 1373 protein spots, which were digested and analyzed by MS/MS, leading to 680 unique identifications. Both soluble proteins and microsomal fraction were analyzed by LC MALDI-MS/MS after trypsin digestion, leading to 858 identifications, many of which had not been identified after 2-DE, indicating that the two methods complement each other. Many enzymes putatively involved in secondary metabolism were identified, including enzymes involved in the synthesis of terpenoid precursors and in acyl sugar production. Several transporters were also identified, some of which might be involved in secondary metabolite transport. Various (a)biotic stress response proteins were also detected, supporting the role of trichomes in plant defense. PMID:21268273

  19. CMB cold spot from inflationary feature scattering

    NASA Astrophysics Data System (ADS)

    Wang, Yi; Ma, Yin-Zhe

    2016-05-01

    We propose a "feature-scattering" mechanism to explain the cosmic microwave background cold spot seen from WMAP and Planck maps. If there are hidden features in the potential of multi-field inflation, the inflationary trajectory can be scattered by such features. The scattering is controlled by the amount of isocurvature fluctuations, and thus can be considered as a mechanism to convert isocurvature fluctuations into curvature fluctuations. This mechanism predicts localized cold spots (instead of hot ones) on the CMB. In addition, it may also bridge a connection between the cold spot and a dip on the CMB power spectrum at ℓ ∼ 20.

  20. Finding your innovation sweet spot.

    PubMed

    Goldenberg, Jacob; Horowitz, Roni; Levav, Amnon; Mazursky, David

    2003-03-01

    Most new product ideas are either uninspired or impractical. So how can developers hit the innovation sweet spot--far enough from existing products to attract real interest but close enough that they are feasible to make and market? They can apply five innovation patterns that manipulate existing components of a product and its immediate environment to come up with something both ingenious and viable, say the authors. The subtraction pattern works by removing product components, particularly those that seem desirable or indispensable. Think of the legless high chair that attaches to the kitchen table. The multiplication pattern makes one or more copies of an existing component, then alters those copies in some important way. For example, the Gillette double-bladed razor features a second blade that cuts whiskers at a slightly different angle. By dividing an existing product into its component parts--the division pattern--you can see something that was an integrated whole in an entirely different light. Think of the modern home stereo--it has modular speakers, tuners, and CD and tape players, which allow users to customize their sound systems. The task unification pattern involves assigning a new task to an existing product element or environmental attribute, thereby unifying two tasks in a single component. An example is the defrosting filament in an automobile windshield that also serves as a radio antenna. Finally, the attribute dependency pattern alters or creates the dependent relationships between a product and its environment. For example, by creating a dependent relationship between lens color and external lighting conditions, eyeglass developers came up with a lens that changes color when exposed to sunlight. PMID:12632810

  1. A Dark Spot on Europa

    NASA Technical Reports Server (NTRS)

    1998-01-01

    This view taken by NASA's Galileo spacecraft of Jupiter's icy moon Europa focuses on a dark, smooth region whose center is the lowest area in this image. To the west (left), it is bounded by a cliff and terraces, which might have been formed by normal faulting. The slopes toward the east (right) leading into the dark spot are gentle.

    Near the center of the dark area, it appears the dark materials have covered some of the bright terrain and ridges. This suggests that when the dark material was deposited, it may have been a fluid or an icy slush.

    Only a few impact craters are visible, with some of them covered or flooded by dark material. Some appear in groups, which may indicate that they are secondary craters formed by debris excavated during a larger impact event. A potential source for these is the nearby crater Mannann`an.

    North is to the top of the picture which is centered at 1 degree south latitude and 225 degrees west longitude. The images in this mosaic have been re-projected to 50 meters (55 yards) per picture element. They were obtained by the Solid State Imaging (SSI) system on March 29, 1998, during Galileo's fourteenth orbit of Jupiter, at ranges as close as 1940 kilometers (1,200 miles) from Europa.

    The Jet Propulsion Laboratory, Pasadena, CA manages the Galileo mission for NASA's Office of Space Science, Washington, DC. JPL is an operating division of California Institute of Technology (Caltech).

    This image and other images and data received from Galileo are posted on the World Wide Web, on the Galileo mission home page at URL http://galileo.jpl.nasa.gov. Background information and educational context for the images can be found at URL http://www.jpl.nasa.gov/galileo/sepo

  2. The sweet spot of a baseball bat

    NASA Astrophysics Data System (ADS)

    Cross, Rod

    1998-09-01

    The sweet spot of a baseball bat, like that of a tennis racket, can be defined either in terms of a vibration node or a centre of percussion. In order to determine how each of the sweet spots influences the "feel" of the bat, measurements were made of the impact forces transmitted to the hands. Measurements of the bat velocity, and results for a freely suspended bat, were also obtained in order to assist in the interpretation of the force waveforms. The results show that both sweet spots contribute to the formation of a sweet spot zone where the impact forces on the hands are minimised. The free bat results are also of interest since they provided particularly elegant examples of wave excitation and propagation, suitable for a student demonstration or experiment.

  3. Ultrasonic hammer produces hot spots in solids

    NASA Astrophysics Data System (ADS)

    You, Sizhu; Chen, Ming-Wei; Dlott, Dana D.; Suslick, Kenneth S.

    2015-04-01

    Mechanical action can produce dramatic physical and mechanochemical effects when the energy is spatially or temporally concentrated. An important example of such phenomena in solids is the mechanical initiation of explosions, which has long been speculated to result from ‘hot spot’ generation at localized microstructures in the energetic material. Direct experimental evidence of such hot spots, however, is exceptionally limited; mechanisms for their generation are poorly understood and methods to control their locations remain elusive. Here we report the generation of intense, localized microscale hot spots in solid composites during mild ultrasonic irradiation, directly visualized by a thermal imaging microscope. These ultrasonic hot spots, with heating rates reaching ~22,000 K s-1, nucleate exclusively at interfacial delamination sites in composite solids. Introducing specific delamination sites by surface modification of embedded components provides precise and reliable control of hot spot locations and permits microcontrol of the initiation of reactions in energetic materials including fuel/oxidizer explosives.

  4. How Many Spots Does a Cheetah Have?

    ERIC Educational Resources Information Center

    Reed, Kristine M.

    2000-01-01

    Describes first grade students' mathematical investigation of the number of spots on a cheetah. The exploration of counting and estimation strategies that grew from the investigation gives evidence that mathematicians come in all ages. (ASK)

  5. Measuring microfocus focal spots using digital radiography

    SciTech Connect

    Fry, David A

    2009-01-01

    Measurement of microfocus spot size can be important for several reasons: (1) Quality assurance during manufacture of microfocus tubes; (2) Tracking performance and stability of microfocus tubes; (3) Determining magnification (especially important for digital radiography where the native spatial resolution of the digital system is not adequate for the application); (4) Knowledge of unsharpness from the focal spot alone. The European Standard EN 12543-5 is based on a simple geometrical method of calculating focal spot size from unsharpness of high magnification film radiographs. When determining microfocus focal spot dimensions using unsharpness measurements both signal-to-noise (SNR) and magnification can be important. There is a maximum accuracy that is a function of SNR and therefore an optimal magnification. Greater than optimal magnification can be used but it will not increase accuracy.

  6. Investigations of initiation spot size effects

    SciTech Connect

    Clarke, Steven A; Akinci, Adrian A; Leichty, Gary; Schaffer, Timothy; Murphy, Michael J; Munger, Alan; Thomas, Keith A

    2010-01-01

    As explosive components become smaller, a greater understanding of the effect of initiation spot size on detonation becomes increasingly critical. A series of tests of the effect of initiation spot size will be described. A series of DOI (direct optical initiation) detonators with initiation spots sizes from {approx}50 um to 1000um have been tested to determine laser parameters for threshold firing of low density PETN pressings. Results will be compared with theoretical predictions. Outputs of the initiation source (DOI ablation) have been characterized by a suite of diagnostics including PDV and schlieren imaging. Outputs of complete detonators have been characterized using PDV, streak, and/or schlieren imaging. At present, we have not found the expected change in the threshold energy to spot size relationship for DOI type detonators found in similar earlier for projectiles, slappers and EBWs. New detonators designs (Type C) are currently being tested that will allow the determination of the threshold for spot sizes from 250 um to 105um, where we hope to see change in the threshold vs. spot size relationship. Also, one test of an extremely small diameter spot size (50um) has resulted in preliminary NoGo only results even at energy densities as much as 8 times the energy density of the threshold results presented here. This gives preliminary evidence that 50um spot may be beyond the critical initiation diameter. The constant threshold energy to spot size relationship in the data to date does however still give some insight into the initiation mechanism of DOI detonators. If the DOI initiation mechanism were a 1D mechanism similar to a slapper or a flyer impact, the expected inflection point in the graph would have been between 300um and 500um diameter spot size, within the range of the data presented here. The lack of that inflection point indicates that the DOI initiation mechanism is more likely a 2D mechanism similar to a sphere or rod projectile. We expect to

  7. The hot spot of vegetation canopies

    NASA Technical Reports Server (NTRS)

    Myneni, Ranga B.; Kanemasu, Edward T.

    1988-01-01

    A conventional radiometer is used to identify the hot spot (the peak in reflected radiation in the retrosolar direction) of vegetation. A multiwavelength-band radiometer collected radiances on fully grown dense wheat and maize canopies on several clear sunny days. It is noted that the hot spot is difficult to detect in the near IR wavelengths because the shadows are much darker. In general, the retrosolar brightness is found to be higher for smaller sun polar angles than for larger angles.

  8. White-spot disease of salmon fry

    USGS Publications Warehouse

    Mazuranich, J.J.; Nielson, W.E.

    1959-01-01

     White-spot disease, sometimes referred to as coagulated-yolk disease, has been associated with excessive mortalities occurring among the fry and early fingerling stages of the fall chinook salmon (Oncorhynchus tshawytacha) at the U.S. Fish-Cultural Stations at Carson, Cook, Underwood, and Willard, Washington. This disease of eggs and fry should not be confused with the "white-spot" infection that is caused in fingerlings by members of the protozoan genus Ichthyophthirius.

  9. HotSpot Health Physics Codes

    2013-04-18

    The HotSpot Health Physics Codes were created to provide emergency response personnel and emergency planners with a fast, field-portable set of software tools for evaluating insidents involving redioactive material. The software is also used for safety-analysis of facilities handling nuclear material. HotSpot provides a fast and usually conservative means for estimation the radiation effects associated with the short-term (less than 24 hours) atmospheric release of radioactive materials.

  10. HotSpot Health Physics Codes

    2010-03-02

    The HotSpot Health Physics Codes were created to provide emergency response personnel and emergency planners with a fast, field-portable set of software tools for evaluating incidents involving radioactive material. The software is also used for safety-analysis of facilities handling nuclear material. HotSpot provides a fast and usually conservative means for estimation the radiation effects associated with the short-term (less than 24 hours) atmospheric release of radioactive materials.

  11. ATS Spotted MSI Analysis with Matlab

    SciTech Connect

    Bowen, Benjamin

    2012-02-09

    Samples are placed on a surface using an acoustic transfer system (ATS). This results in one ore more small droplets on a surface. Typically there are hundreds to thousands of these droplets arrayed in a regular coordinate system. The surface is analyzed using mass spectrometry imaging (MSI) and at each position, one or more mass spectra are recorded. The purpose of the software is to help the user assign locations to the spots and build a report for each spot.

  12. Detection of host-specific immunogenic proteins in the saliva of patients with oral squamous cell carcinoma.

    PubMed

    Mu, Alan Kang-Wai; Chan, Yunn Shy; Kang, Szu Szu; Azman, Siti Nuraishah; Zain, Rosnah Binti; Chai, Wen Lin; Chen, Yeng

    2014-01-01

    The main purpose of this article is to develop a new and reliable saliva-based clinical diagnostic method for the early detection of oral squamous cell carcinoma (OSCC). This study used an immunoproteomic approach which allowed the detection of immunogenic host proteins in patients' samples using pooled human antibodies. In an attempt to investigate potential biomarkers of OSCC, two-dimensional electrophoresis (2-DE) followed by immunoblotting of saliva from patients and controls were compared. The protein spots of interest were analyzed using 2-DE image analyzer and subsequently subjected to MALDI-TOF/TOF and then matched against NCBI database. The result showed that four protein clusters, namely Human Pancreatic Alpha-amylase (HPA), Human Salivary Amylase (sAA), keratin-10 (K-10), and Ga Module Complexed with Human Serum Albumin (GA-HSA), had exhibited immunoreactivity in western blot. The results are suggestive of the potential use of the differentially expressed saliva protein as tumor biomarkers for the detection of OSCC. However, further studies are recommended to validate this finding. PMID:24295181

  13. Rocket engine hot-spot detector

    NASA Astrophysics Data System (ADS)

    Collamore, F. N.

    1985-04-01

    On high performance devices such as rocket engines it is desirable to know if local hot spots or areas of reduced cooling margin exist. The objective of this program is to design, fabricate and test an electronic hot spot detector capable of sensing local hot spot on the exterior circumference of a regeneratively cooled combustion chamber in order to avoid hardware damage. The electronic hot spot sensor consists of an array of 120 thermocouple elements which are bonded in a flexible belt of polyimide film. The design temperature range is from +30 F to +400 F continuously with an intermittent temperature of 500 F maximum. The thermocouple belt consists of 120 equally spaced copper-Constantan thermocouple junctions which is wrapped around the OMS liquid rocket engine combustion chamber, to monitor temperatures of individual cooling channels. Each thermocouple is located over a cooling channel near the injector end of the combustion chamber. The thermocouple array sensor is held in place by a spring loaded clamp band. Analyses show that in the event of a blocked cooling channel the surface temperature of the chamber over the blocked channel will rise from a normal operating temperature of approx. 300 F to approx. 600 F. The hot spot detector will respond quickly to this change with a response time constant less than 0.05 seconds. The hot spot sensor assembly is fabricated with a laminated construction of layers of Kapton film and an outer protective layer of fiberglass reinforced silicone rubber.

  14. Nonbright-spot AVO: Two examples

    SciTech Connect

    Ross, C.P.; Kinman, D.L.

    1995-09-01

    The use of amplitude variation with offset (AVO) attribute sections such as the product of the normal incidence trace (A) and the gradient trace (B) have been used extensively in bright spot AVO analysis and interpretation. However, while these sections have often worked well with low acoustic impedance bright spot responses, they are not reliable indicators of nonbright-spot seismic anomalies. Analyzing nonbright-spot seismic data with common AVO attribute sections will: (1) not detect the gas-charged reservoir because of near-zero acoustic impedance contrast between the sands and encasing shales, or (2) yield an incorrect (negative) AVO product if the normal incidence and gradient values are opposite in sign. The authors divide nonbright-spot AVO offset responses into two subcategories: those with phase reversals and those without. An AVO analysis procedure for these anomalies is presented through two examples. The procedure exploits the nature of the prestack response, yielding a more definitive AVO attribute section, and this technique is adaptive to both subcategories of nonbright-spot AVO responses. This technique identifies the presence of gas-charged pore fluids within the reservoir when compared to a conventionally processed, relative amplitude seismic section with characteristically low amplitude responses for near-zero acoustic impedance contrast sands.

  15. Concentrator hot-spot testing, phase 1

    NASA Technical Reports Server (NTRS)

    Gonzalez, C. C.

    1987-01-01

    Results of a study to determine the hot-spot susceptibility of concentrator cells, to provide a hot-spot qualification test for concentrator modules, and to provide guidelines for reducing hot-spot susceptibility are presented. Hot-spot heating occurs in a photovoltaic module when the short-circuit current of a cell is lower than the string operating current forcing the cell into reverse bias with a concurrent power dissipation. Although the basis for the concentrator module hot-spot qualification test is the test developed for flat-plate modules, issues, such as providing cell illumination, introduce additional complexities into the testing procedure. The same general guidelines apply for protecting concentrator modules from hot-spot stressing as apply to flat-plate modules. Therefore, recommendations are made on the number of bypass diodes required per given number of series cells per module or source circuit. In addition, a new method for determining the cell temperature in the laboratory or in the field is discussed.

  16. Interpretation of the Jupiter Red Spot, 1

    NASA Technical Reports Server (NTRS)

    Kuiper, G. P.

    1973-01-01

    With the aid of 8900 micron CH4 filter photographs it is shown that the Red Spot is normally the highest cloud feature in the Jovian atmosphere, located squarely on the South Tropical Zone at 22 deg. S. The Red Spot is a rising column, obviously having its own energy source; it spreads outward at the top level, in anticyclonic rotation. It is concluded that the large and persistent Jovian cloud masses, of which the Red Spot is the largest, are major organized storm arrays embedded in a near stagnant atmosphere, each probably possessing numerous short-lived rising hot columns driven by released latent heat; and covered by a horizontally-expanding gigantic cirrus cloud system, in anti-cyclonic rotation. The meteorological theory of Organized Cumulus Convection is applied to the Red Spot and the White Ovals. Evidence exists that the array of hot towers under the Red Spot is eccentric. The 90-day and the occassional 5-8 year fluctuations in the motion of the Red Spot may be due to processes analogous to those found in the Earth's Tropical Convergence. The 90-day oscillation has been observed for 8 years.

  17. On the origin of delta spots. [on sun

    NASA Technical Reports Server (NTRS)

    Tang, F.

    1983-01-01

    Mount Wilson sunspot drawings from 1966 through 1980 were used in conjunction with H-alpha filtergrams from Big Bear Solar Observatory to examine the origin of delta spots, spots with bipolar umbrae within one penumbra. Of the six cases studied, five were formed by the union of non-paired spots. They are either shoved into one another by two neighboring growing bipoles or by a new spot borne piggy-back style on an existing spot of opposite polarity. Proper motions of the growing spots take on curvilinear paths around one another to avoid a collision. This is the shear motion observed in delta spots (Tanaka, 1979). In the remaining case, the delta spot was formed by spots that emerged as a pair. The findings indicate no intrinsic differences in the formation or the behavior between delta spots and spots of normal magnetic configuration.

  18. Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery.

    PubMed

    Hall, David R; Kozakov, Dima; Whitty, Adrian; Vajda, Sandor

    2015-11-01

    Analysis of binding energy hot spots at protein surfaces can provide crucial insights into the prospects for successful application of fragment-based drug discovery (FBDD), and whether a fragment hit can be advanced into a high-affinity, drug-like ligand. The key factor is the strength of the top ranking hot spot, and how well a given fragment complements it. We show that published data are sufficient to provide a sophisticated and quantitative understanding of how hot spots derive from a protein 3D structure, and how their strength, number, and spatial arrangement govern the potential for a surface site to bind to fragment-sized and larger ligands. This improved understanding provides important guidance for the effective application of FBDD in drug discovery. PMID:26538314

  19. Proteins differentially expressed in elicited cell suspension culture of Podophyllum hexandrum with enhanced podophyllotoxin content

    PubMed Central

    2012-01-01

    Background Podophyllotoxin (PTOX), the precursor for semi-synthesis of cancer therapeutics like etoposide, teniposide and etophos, is primarily obtained from an endangered medicinal herb, Podophyllum hexandrum Royle. PTOX, a lignan is biosynthetically derived from the phenylpropanoid pathway. The aim of this study is to investigate changes in the P. hexandrum cell proteome potentially related to PTOX accumulation in response to methyl jasmonate (MeJA) elicitation. High-resolution two-dimensional gel electrophoresis (2-DE) followed by colloidal Coomassie staining and mass spectrometric analysis was used to detect statistically significant changes in cell’s proteome. Result The HPLC analysis showed approximately 7–8 fold change in accumulation of PTOX, in the 12day old cell suspension culture (i.e. after 9days of elicitation) elicited with 100 μM MeJA as compared to the control. Using 2-DE a total of 233 spots was detected, out of which 105 spots were identified by MALDI TOF-TOF MS/MS. Data were subjected to functional annotation from a biological point of view through KEGG. The phenylpropanoid and monolignol pathway enzymes were identified, amongst these, chalcone synthase, polyphenol oxidase, caffeoyl CoA 3-O-methyltransferase, S-adenosyl-L-methionine-dependent methyltransferases, caffeic acid-O-methyl transferase etc. are noted as important. The relation of other differentially accumulated proteins with varied effects caused by elicitors on P. hexandrum cells namely stress and defense related protein, transcription and DNA replication and signaling are also discussed. Conclusions Elicitor-induced PTOX accumulation in P. hexandrum cell cultures provides a responsive model system to profile modulations in proteins related to phenylpropanoid/monolignol biosynthesis and other defense responses. Present findings form a baseline for future investigation on a non-sequenced medicinal herb P. hexandrum at molecular level. PMID:22621772

  20. Proteomics data in support of the quantification of the changes of bovine milk proteins during mammary gland involution.

    PubMed

    Boggs, Irina; Hine, Brad; Smolenksi, Grant; Hettinga, Kasper; Zhang, Lina; Wheeler, Thomas T

    2016-09-01

    Here we provide data from three proteomics techniques; two-dimensional electrophoresis (2-DE) followed by identification of selected spots using PSD MALDI-TOF MS/MS, one-dimensional gel electrophoresis followed by LC-MS/MS analysis of gel slices (GeLC) and dimethyl isotopic labelling of tryptic peptides followed by Orbitrap MS/MS (DML), to quantify the changes in the repertoire of bovine milk proteins that occurs after drying off. We analysed skim milk and whey sampled at day 0 and either day 3 or day 8 after drying off. These analyses identified 45 spots by MALDI-TOF, 51 proteins by GeLC and 161 proteins by DML, for which the detailed data work-up is presented as three Excel files. The data supplied in this article supports the accompanying publication "Changes in the repertoire of bovine milk proteins during mammary involution" (Boggs et al., 2015) [1]. Data are available via ProteomeXchange with identifiers ProteomeXchange: PXD003110 and ProteomeXchange: PXD003011. PMID:27274532

  1. Serine/threonine-protein phosphatase 1 α levels are paralleling olfactory memory formation in the CD1 mouse.

    PubMed

    Winding, Christiana; Sun, Yanwei; Höger, Harald; Bubna-Littitz, Hermann; Pollak, Arnold; Schmidt, Peter; Lubec, Gert

    2011-06-01

    Although olfactory discrimination has already been studied in several mouse strains, data on protein levels linked to olfactory memory are limited. Wild mouse strains Mus musculus musculus, Mus musculus domesticus and CD1 laboratory outbred mice were tested in a conditioned odor preference task and trained to discriminate between two odors, Rose and Lemon, by pairing one odor with a sugar reward. Six hours following the final test, mice were sacrificed and olfactory bulbs (OB) were taken for gel-based proteomics analyses and immunoblotting. OB proteins were extracted, separated by 2-DE and quantified using specific software (Proteomweaver). Odor-trained mice showed a preference for the previously rewarded odor suggesting that conditioned odor preference occurred. In CD1 mice levels, one out of 482 protein spots was significantly increased in odor-trained mice as compared with the control group; it was in-gel digested by trypsin and chymotrypsin and analyzed by tandem mass spectrometry (nano-ESI-LC-MS/MS). The spot was unambiguously identified as serine/threonine-protein phosphatase PP1-α catalytic subunit (PP-1A) and differential levels observed in gel-based proteomic studies were verified by immunoblotting. PP-1A is a key signalling element in synaptic plasticity and memory processes and is herein shown to be paralleling olfactory discrimination representing olfactory memory. PMID:21647921

  2. Comparative analysis of extractable proteins from Clostridium perfringens type A and type C strains showing varying degree of virulence.

    PubMed

    Dwivedi, Pratistha; Alam, Syed Imteyaz; Kumar, Om; Kumar, Ravi Bhushan

    2015-10-01

    The prevailing scenario of bioterrorism warrants development of medical countermeasures with expanded coverage of select agents. Clostridium perfringens is a pathogen of medical, veterinary and military importance, and has been listed as Validated Biological Agent. We employed 2DE-MS approach to identify a total of 134 unique proteins (529 protein spot features) from the extractable proteome of four type A and type C strains. Proteins showing altered expression under host-simulated conditions from virulent type A strain (ATCC13124) were also elucidated. Significant among the differentially expressed proteins were elongation factor, molecular chaperones, ribosomal proteins, carbamoyl phosphate synthase, clpB protein, choloylglycine hydrolase, phosphopyruvate hydratase, and trigger factor. Predictive elucidation, of putative virulence associated proteins and sequence conservation pattern of selected candidates, was carried out using homologous proteins from other bacterial select agents to screen for the commonality of putative antigenic determinants. Pathogens (17 select agents) were observed to form three discrete clusters; composition of I and II being consistent in most of the phylogenetic reconstructions. This work provides a basis for further validation of putative candidate proteins as prophylactic agents and for their ability to provide protection against clusters of pathogenic select bacterial agents; aimed at mitigating the shadows of biothreat. PMID:26238688

  3. New knowledge about 'white spots' in superalloys

    SciTech Connect

    Jackman, L.A. ); Maurer, G.E. ); Widge, S. )

    1993-05-01

    In April 1991, the first in a series of workshops was held to discuss ways in which the gas turbine industry could better understand defects in nickel-base superalloys. The group's primary objective was to better define, and expand knowledge about, segregation in superalloys such as Alloy 718 and Waspaloy,with emphasis on light-etching areas referred to as solute-lean defects or 'white spots'. This 'White Spots Committee' formed four subcommittees to focus efforts on classification, inspection, mechanisms, and mechanical properties. Completion of the tasks that these subcommittees have undertaken should greatly improve the gas turbine industry's understanding of the physical and mechanical nature of white spots. The primary purpose of this article is to formalize the characterization and classification of white spots in high-strength superalloys so that the metallurgical community can begin to use a common vocabulary when referring to them. An overview of formation mechanisms is presented along with a brief description of detection methods. Also discussed are preliminary test results, which should help shed light on the effects of solute-lean microstructures on tensile and fatigue properties. Although white spots are not limited to any single superalloy or class of superalloy, Alloy 718 is emphasized because it is so widely used, and because its relatively large solidus-liquidus temperature interval ([approximately]75 C, 135 F) and high niobium content ([approximately]5.3% Nb) make it prone to segregation. Three distinct types of white spots have been identified and named by the committee: discrete, dendritic, and solidification white spots.

  4. Hubble Finds New Dark Spot on Neptune

    NASA Technical Reports Server (NTRS)

    1995-01-01

    NASA's Hubble Space Telescope has discovered a new great dark spot, located in the northern hemisphere of the planet Neptune. Because the planet's northern hemisphere is now tilted away from Earth, the new feature appears near the limb of the planet.

    The spot is a near mirror-image to a similar southern hemisphere dark spot that was discovered in 1989 by the Voyager 2 probe. In 1994, Hubble showed that the southern dark spot had disappeared.

    Like its predecessor, the new spot has high altitude clouds along its edge, caused by gasses that have been pushed to higher altitudes where they cool to form methane ice crystal clouds. The dark spot may be a zone of clear gas that is a window to a cloud deck lower in the atmosphere.

    Planetary scientists don t know how long lived this new feature might be. Hubble's high resolution will allow astronomers to follow the spot's evolution and other unexpected changes in Neptune's dynamic atmosphere.

    The image was taken on November 2, 1994 with Hubble's Wide Field Planetary Camera 2, when Neptune was 2.8 billion miles (4.5 billion kilometers) from Earth. Hubble can resolve features as small as 625 miles (1,000 kilometers) across in Neptune's cloud tops.

    The Wide Field/Planetary Camera 2 was developed by the Jet Propulsion Laboratory and managed by the Goddard Spaced Flight Center for NASA's Office of Space Science.

    This image and other images and data received from the Hubble Space Telescope are posted on the World Wide Web on the Space Telescope Science Institute home page at URL http://oposite.stsci.edu/pubinfo/

  5. Different techniques for urinary protein analysis of normal and lung cancer patients.

    PubMed

    Tantipaiboonwong, Payungsak; Sinchaikul, Supachok; Sriyam, Supawadee; Phutrakul, Suree; Chen, Shui-Tein

    2005-03-01

    Many components in urine are useful in clinical diagnosis and urinary proteins are known as important components to define many diseases such as proteinuria, kidney, bladder and urinary tract diseases. In this study, we focused on the comparison of different sample preparation methods for isolating urinary proteins prior to protein analysis of pooled healthy and lung cancer patient samples. Selective method was used for preliminary investigation of some putative urinary protein markers. Urine samples were passed first through a gel filtration column (PD-10 desalting column) to remove high salts and subsequently concentrated. Remaining interferences were removed by ultrafiltration or four precipitation methods. The analysis of urinary proteins by high-performance liquid chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed many similarities in profiles among preparation methods and a few profiles were different between normal and lung cancer patients. In contrast, the results of two-dimensional gel electrophoresis (2-DE) showed more distinctly different protein patterns. Our finding showed that the sequential preparation of urinary proteins by gel filtration and ultrafiltration could retain most urinary proteins which demonstrated the highest protein spots on 2-D gels and able to identify preliminary urinary protein markers related to cancer. Although sequential preparation of urine samples by gel filtration and protein precipitation resulted in low amounts of proteins on 2-D gels, high Mr proteins were easily detected. Therefore, there are alternative choices for urine sample preparation for studying the urinary proteome and identifying urinary protein markers important for further preclinical diagnostic and therapeutic applications. PMID:15693063

  6. Possible Case of Novel Spotted Fever Group Rickettsiosis in Traveler Returning to Japan from India

    PubMed Central

    Sekizuka, Tsuyoshi; Fujita, Hiromi; Kawano, Ayako; Kawaguchi, Takeshi; Matsuda, Motohiro; Kubo, Kazuyoshi; Miyauchi, Shunichi; Umekita, Kunihiko; Nagatomo, Yasuhiro; Kuroda, Makoto; Takasaki, Tomohiko; Okayama, Akihiko

    2016-01-01

    A 60-year-old woman experienced fever, headache, rash, and altered vision after returning to Japan from India. Testing detected elevated antibody titers to spotted fever group rickettsia; PCR on blood yielded positive results for the rickettsial outer membrane protein A gene. We isolated a unique rickettsial agent and performed a full-genome analysis. PMID:27192498

  7. Possible Case of Novel Spotted Fever Group Rickettsiosis in Traveler Returning to Japan from India.

    PubMed

    Takajo, Ichiro; Sekizuka, Tsuyoshi; Fujita, Hiromi; Kawano, Ayako; Kawaguchi, Takeshi; Matsuda, Motohiro; Kubo, Kazuyoshi; Miyauchi, Shunichi; Umekita, Kunihiko; Nagatomo, Yasuhiro; Kuroda, Makoto; Takasaki, Tomohiko; Okayama, Akihiko; Ando, Shuji

    2016-06-01

    A 60-year-old woman experienced fever, headache, rash, and altered vision after returning to Japan from India. Testing detected elevated antibody titers to spotted fever group rickettsia; PCR on blood yielded positive results for the rickettsial outer membrane protein A gene. We isolated a unique rickettsial agent and performed a full-genome analysis. PMID:27192498

  8. Reaction of sorghum lines to zonate leaf spot and rough leaf spot

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Abundant, frequent rains, along with humid and cloudy conditions during the early part of the 2015 growing season, provided conducive conditions for an unusually severe outbreak of zonate leaf spot and rough leaf spot in a block of sorghum lines at the Texas A&M AgriLife Research Farm, Burleson Coun...

  9. Jupiter's Polar UV Great Dark Spot

    NASA Astrophysics Data System (ADS)

    West, R. A.; Griswold, D.; Porco, C.

    2003-05-01

    Jupiter's polar UV Great Dark Spot is an ephemeral but recurring feature first seen in near-UV (240-270 nm) images obtained by the Wide Field camera on the Hubble Space Telescope in October, 1997. A movie made from UV images taken by the Cassini Imaging Subsystem (ISS) in late 2000 (Porco et al., 2003, Science 299, 1541-1547) fortuitously captured the formation of the spot and covered a significant evolutionary phase as the spot took on a size and shape similar to Jupiter's Great Red Spot and then stretched in longitude and developed an angular boundary. Here we analyze images at additional wavelengths from HST and from Cassini ISS. The spot rapidly becomes invisible between 300 and about 440 nm. It is not seen in the 890-nm methane band which is sensitive to stratospheric particles, suggesting that the UV absorption is produced by a gaseous constituent and not an aerosol. As it evolves and drifts in System III longitude it stays centered on the perimeter defining a polar vortex region poleward of about 60 degrees north latitude which is remarkably featureless in the 890-nm methane movie made from ISS images.

  10. Auroral bright spots on the dayside oval

    SciTech Connect

    Lui, A.T.Y. ); Venkatesan, D.; Murphree, J.S. )

    1989-05-01

    Global auroral images from the ultraviolet imager on the Viking spacecraft are used to investigate spatially periodic bright spots on the dayside auroral oval that resemble beads on a string. The newly achieved temporal resolution of 1 min. or less in monitoring worldwide auroral distributions by the Viking imager contributes significant to the capability of observing this phenomenon. It is found that these are frequently seen in the 1,400-1,600 MLT sector. The series of bright spots are not, however, limited to this unique local time sector, since they are seen to extend into the prenoon sector on some occasions. They occur often during substorm intervals but are also seen unaccompanied by substorm activities in the nightside. There is neither a consistent north-south nor east-west direction of motion for all the dayside bright spots observed so far. The observation of the time scales for the transient intensifications of bright spots and the lack of consistent directions of their motion are consistent with the characteristics expected from the suggestion that these bright spots are related to the Kelvin-Helmholtz instability occurring within the magnetosphere.

  11. Protein expression analysis of rat testes induced testicular toxicity with several reproductive toxicants.

    PubMed

    Yamamoto, Toshinori; Fukushima, Tamio; Kikkawa, Rie; Yamada, Hiroshi; Horii, Ikuo

    2005-05-01

    The utilization of safety biomarkers to predict the possibility of compound-related toxicity provides several advantages for drug discovery and development, especially at an early stage. The objectives of this study were to investigate the effects of male reproductive toxicants on protein expression profiles in the rat testes and to identify potential biomarker candidates. Four well-known reproductive toxicants, ethylene glycol monomethyl ether (EGME), cyclophosphamide (CP), sulfasalazine (SASP) and 2,5-hexanedione (2,5-HD), were administered to male rats in a single dose, and protein expression profiles were investigated after 24 hr by two-dimensional gel electrophoresis (2DE). Histopathological examination of the testes and serum concentration analysis were also performed. From the results of the comparison of 2D-gels among different doses of a compound and among compounds, 52, 20, 24 and 111 spots were nominated as differentially expressed spots with EGME, CP, SASP and 2,5-HD treatments, respectively. Several spermatogenesis-involved proteins were identified, including glutathione S-transferase (GST), testis-specific heat shock protein 70-2 (HSP70-2), glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and phosphatidylethanolamine-binding protein (PEBP). Some of them were altered by more than one compound. In summary, remarkable histopathological findings were observed only in the EGME high-dose group, and most of the protein changes were detected before histopathological changes occurred. Therefore, the proteins identified in this study could potentially serve as biomarkers to evaluate male reproductive toxicity at an early stage of drug discovery and development. PMID:15928459

  12. On turbulent spots in plane Poiseuille flow

    NASA Technical Reports Server (NTRS)

    Henningson, Dan S.; Kim, John

    1992-01-01

    Turbulence characteristics inside a turbulent spot in plume Poiseuille flow are investigated by analyzing a data base obtained from a direct numerical simulation. The spot is found to consist of two distinct regions - a turbulent area and a wave area. The flow inside the turbulent area has a strong resemblance to that found in the fully developed turbulent channel. Suitably defined mean and rms fluctuations as well as the internal shear layer structures are found to be similar to the turbulent counterpart. In the wave area, the inflexional mean spanwise profiles cause a rapid growth of oblique waves, which break down to turbulence. The breakdown process of the oblique waves is reminiscent of the secondary instability observed during transition to turbulence in channel and boundary layer flows. Other detailed characteristics associated with the Poiseuille spot are presented and are compared with experimental results.

  13. Cartographic potential of SPOT image data

    NASA Technical Reports Server (NTRS)

    Welch, R.

    1985-01-01

    In late 1985, the SPOT (Systeme Probatoire d'Observation de la Terre) satellite is to be launched by the Ariane rocket from French Guiana. This satellite will have two High Resolution Visible (HRV) line array sensor systems which are capable of providing monoscopic and stereoscopic coverage of the earth. Cartographic applications are related to the recording of stereo image data and the acquisition of 20-m data in a multispectral mode. One of the objectives of this study involves a comparison of the suitability of SPOT and TM image data for mapping urban land use/cover. Another objective is concerned with a preliminary assessment of the potential of SPOT image data for map revision when merged with conventional map sheets converted to raster formats.

  14. Ocular hazards of industrial spot welding.

    PubMed

    Chou, B R; Cullen, A P

    1996-06-01

    Any welding process is perceived to be a radiation hazard to the eye. Site visits were made to an automotive assembly plant to assess the levels of optical radiation and other hazards on the production line. Measurements were taken with a scanning spectro-radiometer and optical power and energy meters at operating working distances at spot welding stations where nonrobotic procedures were performed. Ultraviolet (UV) irradiance levels produced while spot welding with electrodes operating at 10 to 15 kA and 10 to 20 V were several orders of magnitude below recommended safety limits for industrial exposure. Flashes were rich in visible light and infrared (IR) radiation, but not at hazardous levels. The principal hazards in manual spot welding with high-current electrodes are high-speed droplets of molten metal produced by the process. These are easily defended against by wraparound polycarbonate eye shields. PMID:8807655

  15. ATS Spotted MSI Analysis with Matlab

    2012-02-09

    Samples are placed on a surface using an acoustic transfer system (ATS). This results in one ore more small droplets on a surface. Typically there are hundreds to thousands of these droplets arrayed in a regular coordinate system. The surface is analyzed using mass spectrometry imaging (MSI) and at each position, one or more mass spectra are recorded. The purpose of the software is to help the user assign locations to the spots and buildmore » a report for each spot.« less

  16. Lissencephaly and mongolian spots in Hurler syndrome.

    PubMed

    Panteliadis, Christos P; Karatza, Eliza D; Tzitiridou, Maria K; Koliouskas, Dimitrios E; Spiroglou, Kleomenis S

    2003-07-01

    Hurler disease or syndrome is a disorder of mucopolysaccharide metabolism, inherited as an autosomal recessive trait. We describe a case of a 15-month-old female exhibiting with clinical and laboratory characteristics of the syndrome, central nervous system lesions (lissencephaly, excessive ventricular enlargement and Dandy Walker malformation with vermis atrophy, cerebellar cyst) and mongolian spots in the trunk and extremities. The combination of mongolian spots and severe central nervous system lesions in Hurler syndrome is considered a rare clinical occurrence, while the association with lissencephaly has never been reported. PMID:13679124

  17. Statistical Hot Spot Model for Explosive Detonation

    SciTech Connect

    Nichols, III, A L

    2005-07-14

    The Non-local Thermodynamic Equilibrium Statistical Hot Spot Model (NLTE SHS), a new model for explosive detonation, is described. In this model, the formation, ignition, propagation, and extinction of hot spots is explicitly modeled. The equation of state of the explosive mixture is treated with a non-local equilibrium thermodynamic assumption. A methodology for developing the parameters for the model is discussed, and applied to the detonation velocity diameter effect. Examination of these results indicates where future improvements to the model can be made.

  18. Statistical Hot Spot Model for Explosive Detonation

    SciTech Connect

    Nichols III, A L

    2004-05-10

    The Non-local Thermodynamic Equilibrium Statistical Hot Spot Model (NLTE SHS), a new model for explosive detonation, is described. In this model, the formation, ignition, propagation, and extinction of hot spots is explicitly modeled. The equation of state of the explosive mixture is treated with a nonlocal equilibrium thermodynamic assumption. A methodology for developing the parameters for the model is discussed, and applied to the detonation velocity diameter effect. Examination of these results indicates where future improvements to the model can be made.

  19. Variation in T-SPOT.TB spot interpretation between independent observers from different laboratories.

    PubMed

    Franken, Willeke P J; Thijsen, Steven; Wolterbeek, Ron; Bouwman, John J M; el Bannoudi, Hanane; Kik, Sandra V; van Dissel, Jaap T; Arend, Sandra M

    2009-10-01

    T-SPOT.TB is a specific assay for the diagnosis of tuberculosis. The assay needs to be performed with freshly isolated cells, and interpretation requires training. T-SPOT.TB has been used in various clinical-epidemiological settings, but so far no studies have evaluated the effect of interobserver variation in test reading. Our aim was to evaluate variation between different observers in reading T-SPOT.TB results. The study was nested within an ongoing cohort study, in which part of the T-SPOT.TB had been performed with frozen material. Culture plates were read visually by four different observers from two laboratories and by two automated readers. Of 313 T-SPOT.TB assays, 235 were performed with fresh cells and 78 were performed with frozen cells. No significant difference was found between results obtained with fresh cells and those obtained with frozen cells. The percentage of positive results varied between readers by maximally 15%; five/six raters were within a 6% difference in positive results. Analysis of the observed interrater differences showed that some individuals systematically counted more spots than others did. Because test interpretation includes subtraction of background values, this systematic variance had little influence on interindividual differences. The test result as positive or negative varied between independent raters, mainly due to samples with values around the cutoff. This warrants further study regarding determinants affecting the reading of T-SPOT.TB. PMID:19710293

  20. Overexpression of KH-type splicing regulatory protein regulates proliferation, migration, and implantation ability of osteosarcoma

    PubMed Central

    Pruksakorn, Dumnoensun; Teeyakasem, Pimpisa; Klangjorhor, Jeerawan; Chaiyawat, Parunya; Settakorn, Jongkolnee; Diskul-Na-Ayudthaya, Penchatr; Chokchaichamnankit, Daranee; Pothacharoen, Peraphan; Srisomsap, Chantragan

    2016-01-01

    Osteosarcoma is a common malignant bone tumor in children and adolescents. The current 5-year survival rate is ~60% and that seems to be reaching a plateau. In order to improve treatment outcomes of osteosarcoma, a better understanding of tumorigenesis and underlying molecular mechanisms is required for searching out possible new treatment targets. This study aimed to identify the potential proteins involving the pathogenesis of osteosarcoma using a proteomics approach. Proteins extracted from primary cell culture of osteosarcoma (n=7) and osteoblasts of cancellous bone (n=7) were studied. Using 2-DE based proteomics and LC-MS/MS analysis, we successfully determined seven differentially expressed protein spots. Four upregulated proteins and three downregulated proteins were observed in this study in which KH-type splicing regulatory protein (KSRP) was selected for further exploration. KSRP was significantly upregulated in osteosarcoma cells compared to osteoblasts using western blot assay. In addition, immunohistochemistry demonstrated that KSRP was also highly expressed in osteosarcoma tissue of independent cases from the experimental group. More importantly, KSRP silencing of osteosarcoma cell lines significantly decreased cell proliferation, migration ability, as well as implantation and growth ability in chick chorioallantoic membrane assay. Taken together, these findings demonstrate, that KSRP plays important roles in regulatory controls of osteosarcoma pathogenesis and serves as a potentially therapeutic target of osteosarcoma. PMID:27573585

  1. Overexpression of KH-type splicing regulatory protein regulates proliferation, migration, and implantation ability of osteosarcoma.

    PubMed

    Pruksakorn, Dumnoensun; Teeyakasem, Pimpisa; Klangjorhor, Jeerawan; Chaiyawat, Parunya; Settakorn, Jongkolnee; Diskul-Na-Ayudthaya, Penchatr; Chokchaichamnankit, Daranee; Pothacharoen, Peraphan; Srisomsap, Chantragan

    2016-09-01

    Osteosarcoma is a common malignant bone tumor in children and adolescents. The current 5-year survival rate is ~60% and that seems to be reaching a plateau. In order to improve treatment outcomes of osteosarcoma, a better understanding of tumorigenesis and underlying molecular mechanisms is required for searching out possible new treatment targets. This study aimed to identify the potential proteins involving the pathogenesis of osteosarcoma using a proteomics approach. Proteins extracted from primary cell culture of osteosarcoma (n=7) and osteoblasts of cancellous bone (n=7) were studied. Using 2-DE based proteomics and LC-MS/MS analysis, we successfully determined seven differentially expressed protein spots. Four upregulated proteins and three downregulated proteins were observed in this study in which KH-type splicing regulatory protein (KSRP) was selected for further exploration. KSRP was significantly upregulated in osteosarcoma cells compared to osteoblasts using western blot assay. In addition, immunohistochemistry demonstrated that KSRP was also highly expressed in osteosarcoma tissue of independent cases from the experimental group. More importantly, KSRP silencing of osteosarcoma cell lines significantly decreased cell proliferation, migration ability, as well as implantation and growth ability in chick chorioallantoic membrane assay. Taken together, these findings demonstrate, that KSRP plays important roles in regulatory controls of osteosarcoma pathogenesis and serves as a potentially therapeutic target of osteosarcoma. PMID:27573585

  2. A novel virus transmitted through pollination causes ring-spot disease on gentian (Gentiana triflora) ovaries.

    PubMed

    Atsumi, Go; Tomita, Reiko; Yamashita, Tetsuro; Sekine, Ken-Taro

    2015-02-01

    In this study, we identified a novel virus from gentian (Gentiana triflora) that causes ring-spots on ovaries. Furthermore, the virus causes unusual symptoms, ring-spots that appear specifically on the outer surface of the ovarian wall after pollination. Pollen grains carrying the virus were used to infect host plants by hand-pollination. RNA extracted from purified virions indicated that the virus had two segments, RNA1 and RNA2. The full-length cDNA sequence indicated that RNA1 had two ORFs: ORF1 had methyltransferase and helicase motifs, and ORF2 had an RNA-dependent RNA polymerase motif. RNA2 had five ORFs encoding a coat protein, triple gene block proteins 1-3 and a cysteine-rich protein. The length of RNA1 was 5519 bases and that of RNA2 was 3810 bases not including a polyU/polyA region between the first and second ORFs. Viral RNA does not have a polyA tail at the 3' end. Sequence similarity and phylogenetic analysis suggested that the virus is closely related to members of the genera Pecluvirus and Hordeivirus but distinct from them. These combined results suggest that the causal agent inducing ring-spot symptoms on gentian ovaries is a new virus belonging to the family Virgaviridae but not to any presently known genus. We tentatively name the virus gentian ovary ring-spot virus. PMID:25351517

  3. The PROTICdb database for 2-DE proteomics.

    PubMed

    Langella, Olivier; Zivy, Michel; Joets, Johann

    2007-01-01

    PROTICdb is a web-based database mainly designed to store and analyze plant proteome data obtained by 2D polyacrylamide gel electrophoresis (2D PAGE) and mass spectrometry (MS). The goals of PROTICdb are (1) to store, track, and query information related to proteomic experiments, i.e., from tissue sampling to protein identification and quantitative measurements; and (2) to integrate information from the user's own expertise and other sources into a knowledge base, used to support data interpretation (e.g., for the determination of allelic variants or products of posttranslational modifications). Data insertion into the relational database of PROTICdb is achieved either by uploading outputs from Mélanie, PDQuest, IM2d, ImageMaster(tm) 2D Platinum v5.0, Progenesis, Sequest, MS-Fit, and Mascot software, or by filling in web forms (experimental design and methods). 2D PAGE-annotated maps can be displayed, queried, and compared through the GelBrowser. Quantitative data can be easily exported in a tabulated format for statistical analyses with any third-party software. PROTICdb is based on the Oracle or the PostgreSQLDataBase Management System (DBMS) and is freely available upon request at http://cms.moulon.inra.fr/content/view/14/44/. PMID:17093318

  4. Lupus a Tough Disease to Spot, Treat

    MedlinePlus

    ... Español You Are Here: Home → Latest Health News → Article URL of this page: https://medlineplus.gov/news/fullstory_159098.html Lupus a Tough Disease to Spot, Treat But experts say scientists are working to unearth genetic causes of autoimmune ...

  5. 9 CFR 149.4 - Spot audit.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 9 Animals and Animal Products 1 2014-01-01 2014-01-01 false Spot audit. 149.4 Section 149.4 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE... results as a result of testing of certified swine from that site at the slaughter facility. (b) All...

  6. 9 CFR 149.4 - Spot audit.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 9 Animals and Animal Products 1 2012-01-01 2012-01-01 false Spot audit. 149.4 Section 149.4 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE... results as a result of testing of certified swine from that site at the slaughter facility. (b) All...

  7. 9 CFR 149.4 - Spot audit.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 9 Animals and Animal Products 1 2013-01-01 2013-01-01 false Spot audit. 149.4 Section 149.4 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE... results as a result of testing of certified swine from that site at the slaughter facility. (b) All...

  8. Hot-spot tectonics on Io

    NASA Technical Reports Server (NTRS)

    Mcewen, A. S.

    1985-01-01

    The thesis is that extensional tectonics and low-angle detachment faults probably occur on Io in association with the hot spots. These processes may occur on a much shorter timescale on Ion than on Earth, so that Io could be a natural laboratory for the study of thermotectonics. Furthermore, studies of heat and detachment in crustal extension on Earth and the other terresrial planets (especially Venus and Mars) may provide analogs to processes on Io. The geology of Io is dominated by volcanism and hot spots, most likely the result of tidal heating. Hot spots cover 1 to 2% of Io's surface, radiating at temperatures typically from 200 to 400 K, and occasionally up to 700K. Heat loss from the largest hot spots on Io, such as Loki Patera, is about 300 times the heat loss from Yellowstone, so a tremendous quantity of energy is available for volcanic and tectonic work. Active volcanism on Io results in a resurfacing rate as high as 10 cm per year, yet many structural features are apparent on the surface. Therefore, the tectonics must be highly active.

  9. Jupiter's Convection and Its Red Spot.

    PubMed

    Smoluchowski, R

    1970-06-12

    Physical properties of the liquid hydrogen-helium layer of Jupiter are calculated and used in evaluating convection and in interpreting the approximately constant rate of longitudinal motion of the Red Spot on the basis of the Hide-Streett model. PMID:17731041

  10. Dramatic Change in Jupiter's Great Red Spot

    NASA Technical Reports Server (NTRS)

    Simon, A. A.; Wong, M. H.; Rogers, J. H.; Orton, G. S.; de Pater, I.; Asay-Davis, X.; Carlson, R. W.; Marcus, P. S.

    2015-01-01

    Jupiter's Great Red Spot (GRS) is one of its most distinct and enduring features, having been continuously observed since the 1800's. It currently spans the smallest latitude and longitude size ever recorded. Here we show analyses of 2014 Hubble spectral imaging data to study the color, structure and internal dynamics of this long-live storm.

  11. Severe spotted fever group rickettsiosis, Australia.

    PubMed

    McBride, William J H; Hanson, Joshua P; Miller, Robert; Wenck, Drew

    2007-11-01

    We report 3 cases of spotted fever group rickettsial infection (presumed Queensland tick typhus) in residents of northern Queensland, Australia, who had unusually severe clinical manifestations. Complications included renal failure, purpura fulminans, and severe pneumonia. Clinical illness caused by Rickettsia australis may not be as benign as previously described. PMID:18217560

  12. 9 CFR 149.4 - Spot audit.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Spot audit. 149.4 Section 149.4 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE... the site is found not to be adhering to one or more of the required good production practices,...

  13. 9 CFR 149.4 - Spot audit.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 9 Animals and Animal Products 1 2011-01-01 2011-01-01 false Spot audit. 149.4 Section 149.4 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE... the site is found not to be adhering to one or more of the required good production practices,...

  14. Genetics of tan spot resistance in wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tan spot is a devastating foliar disease of wheat caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis. Much has been learned during the past two decades regarding the genetics of wheat-P. tritici-repentis interactions. Research has shown that the fungus produces at least three ho...

  15. Easy Demonstration of the Poisson Spot

    ERIC Educational Resources Information Center

    Gluck, Paul

    2010-01-01

    Many physics teachers have a set of slides of single, double and multiple slits to show their students the phenomena of interference and diffraction. Thomas Young's historic experiments with double slits were indeed a milestone in proving the wave nature of light. But another experiment, namely the Poisson spot, was also important historically and…

  16. The Content of Political Spot Ads.

    ERIC Educational Resources Information Center

    Joslyn, Richard A.

    1980-01-01

    An analysis of 156 television political spot advertisements revealed that the most prevalent type of content was issue-related (although very few advertisements revealed a specific candidate issue position), followed by content focusing on candidate qualities, then by references to certain demographic groups, and finally by the transmission of…

  17. 21 CFR 886.1435 - Maxwell spot.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Maxwell spot. 886.1435 Section 886.1435 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES...-powered device that is a light source with a red and blue filter intended to test macular function....

  18. Two New Hot Spots on Io

    NASA Technical Reports Server (NTRS)

    1997-01-01

    The Near-Infrared Mapping Spectrometer (NIMS) on Galileo obtained this image of half of Io's disk in darkness on September 19, 1997. This image, at 5 microns, shows several hot spots on Io, which are volcanic regions of enhanced thermal emission. The area shown is part of the leading hemisphere of Io.

    Two new hot spots are shown and indicated in the image (New, and Shamshu). Neither of these hot spots were seen by NIMS or the Solid State Imaging Experiment, (SSI) prior to this observation, becoming only recently active. Several other previously known hot spots are labelled in the image. Galileo was at a distance of 342,000 km from Io when this observation was made.

    The Jet Propulsion Laboratory, Pasadena, CA manages the mission for NASA's Office of Space Science, Washington, DC.

    The Jet Propulsion Laboratory, Pasadena, CA manages the mission for NASA's Office of Space Science, Washington, DC.

    This image and other images and data received from Galileo are posted on the World Wide Web, on the Galileo mission home page at URL http://galileo.jpl.nasa.gov.

  19. Digital Sun Sensor Multi-Spot Operation

    PubMed Central

    Rufino, Giancarlo; Grassi, Michele

    2012-01-01

    The operation and test of a multi-spot digital sun sensor for precise sun-line determination is described. The image forming system consists of an opaque mask with multiple pinhole apertures producing multiple, simultaneous, spot-like images of the sun on the focal plane. The sun-line precision can be improved by averaging multiple simultaneous measures. Nevertheless, the sensor operation on a wide field of view requires acquiring and processing images in which the number of sun spots and the related intensity level are largely variable. To this end, a reliable and robust image acquisition procedure based on a variable shutter time has been considered as well as a calibration function exploiting also the knowledge of the sun-spot array size. Main focus of the present paper is the experimental validation of the wide field of view operation of the sensor by using a sensor prototype and a laboratory test facility. Results demonstrate that it is possible to keep high measurement precision also for large off-boresight angles. PMID:23443388

  20. PPR Great Red Spot Temperature Map

    NASA Technical Reports Server (NTRS)

    1996-01-01

    This map shows temperature for the region around Jupiter's Great Red Spot and an area to the northwest. It corresponds to a level in Jupiter's atmosphere where the pressure is 1/2 of the of the Earth's at sea level (500 millibars), the same as it is near 6000 meters (20,000 feet) above sea level on Earth. The center of Great Red Spot appears colder than the surrounding areas, where air from below is being brought up. The 'panhandle' to the northwest is warmer and drier, and the gases there are descending, so it is much clearer of clouds. Compare this map to one released earlier at a higher place in the atmosphere (250 millibars or 12000 meters). The center of the Great Red Spot is warmer lower in the atmosphere, and a white 'hot spot' appears in this image that is not present at the higher place. This map was made from data taken by the Photopolarimeter/Radiometer (PPR) instrument on June 26, 1996.

    Launched in October 1989, Galileo entered orbit around Jupiter on December 7, 1995. The spacecraft's mission is to conduct detailed studies of the giant planet, its largest moons and the Jovian magnetic environment.

    JPL manages the Galileo mission for NASA's Office of Space Science, Washington, D.C.

    This image and other images and data received from Galileo are posted on the World Wide Web, on the Galileo mission home page at URL http://galileo.jpl.nasa.gov.

  1. The sweet spots in human communication.

    PubMed

    Salem, Philip

    2011-07-01

    In baseball, the sweet spot is a special place on a bat where the batter can hit the ball with the most power. It is the place where the performances of the batter and pitcher collide with maximum effect. It is the place where the dynamic tension between opponents leads to transformation. The dynamic tension in all living systems is between similarity and difference. Chaos and complexity scholars recognized this tension as amounts of information. When the amounts of information were high, but not too high, the system moved to the edge of chaos, to the complexity regime, to strange attractors, or to chaos, depending on the model. The sweet spot is that range of relative variety, just the proper mix of similarity and difference, leading to transformation. This essay contains a model of human communication as an emergent social process with its own sweet spots. The essay also includes a description of current literature highlighting tensions between similarity and difference, and there is an exploration of the potential to move from one basin of attraction to another. The primary constraints on finding communication sweet spots are paradigmatic - adopting a process orientation, discovering the proper parameters, bracketing sequences to define initial conditions, and understanding the strengths and weaknesses of various modeling techniques. PMID:21645437

  2. THE SPACE PUBLIC OUTREACH TEAM (SPOT)

    NASA Astrophysics Data System (ADS)

    Williamson, Kathryn; National Radio Astronomy Observatory; Montana Space Grant Consortium; West Virginia Space Grant Consortium; NASA Independent Verification and Validation Center

    2014-01-01

    The Space Public Outreach Team (SPOT) has shown over 17 years of success in bringing astronomy and space science-themed presentations to approximately 10,000 students per year in Montana, and the program is now being piloted in West Virginia through a joint partnership between the National Radio Astronomy Observatory (NRAO), the West Virginia Space Grant Consortium, and NASA Independent Verification and Validation Center. SPOT recruits and trains undergraduate presenters from all over the state to learn interactive slide shows that highlight the state’s on-going and world-class space science research. Presenters then travel to K-12 schools to deliver these presentations and provide teachers additional supplemental information for when the SPOT team leaves. As a large-scale, low-cost, and sustainable program being implemented in both Montana and West Virginia, SPOT has the potential to become a nation-wide effort that institutions in other states can model to increase their education and public outreach presence.

  3. The Little Red Spot: Closest View Yet

    NASA Technical Reports Server (NTRS)

    2007-01-01

    This is a mosaic of three New Horizons images of Jupiter's Little Red Spot, taken with the spacecraft's Long Range Reconnaissance Imager (LORRI) camera at 17:41 Universal Time on February 26 from a range of 3.5 million kilometers (2.1 million miles). The image scale is 17 kilometers (11 miles) per pixel, and the area covered measures 33,000 kilometers (20,000 miles) from top to bottom, two and one-half times the diameter of Earth.

    The Little Red Spot, a smaller cousin of the famous Great Red Spot, formed in the past decade from the merger of three smaller Jovian storms, and is now the second-largest storm on Jupiter. About a year ago its color, formerly white, changed to a reddish shade similar to the Great Red Spot, perhaps because it is now powerful enough to dredge up reddish material from deeper inside Jupiter. These are the most detailed images ever taken of the Little Red Spot since its formation, and will be combined with even sharper images taken by New Horizons 10 hours later to map circulation patterns around and within the storm.

    LORRI took the images as the Sun was about to set on the Little Red Spot. The LORRI camera was designed to look at Pluto, where sunlight is much fainter than it is at Jupiter, so the images would have been overexposed if LORRI had looked at the storm when it was illuminated by the noonday Sun. The dim evening illumination helped the LORRI camera obtain well-exposed images. The New Horizons team used predictions made by amateur astronomers in 2006, based on their observations of the motion of the Little Red Spot with backyard telescopes, to help them accurately point LORRI at the storm.

    These are among a handful of Jupiter system images already returned by New Horizons during its close approach to Jupiter. Most of the data being gathered by the spacecraft are stored onboard and will be downlinked to Earth during March and April 2007.

  4. Measuring microfocal spots using digital radiography

    SciTech Connect

    Fry, David A; Ewert, Uwe

    2009-01-01

    Measurement of microfocus spot size can be important for several reasons: (1) Quality assurance during manufacture of microfocus tubes; (2) Tracking performance and stability of microfocus tubes; (3) Determining magnification is especially important for digital radiography where the native spatial resolution of the digital system is not adequate for the application; and (4) Knowledge of unsharpness from the focal spot alone. The European Standard EN 12543-5 is based on a simple geometrical method of calculating focal spot size from unsharpness of high magnification film radiographs. The following equations are used for the focal spot size measurement: By similar triangles the following equations are presupposed: f/a = U/b and M = (a+b)/a. These equations can be combined to yield the well known expression: U = f(M - 1). Solving for f, f = U/(M-1). Therefore, the focal spot size, f, can be calculated by measuring the radiographic unsharpness and magnification of a known object. This is the basis for these tests. The European standard actually uses one-half of the unsharpness (which are then added together) from both sides of the object to avoid additional unsharpness contributions due to edge transmission unsharpness of the round test object (the outside of the object is measured). So the equation becomes f = (1/2 U{sub 1} + 1/2 U{sub 2})/(M-1). In practice 1/2 U is measured from the 50% to the 90% signal points on the transition profile from ''black'' to ''white,'' (positive image) or attenuated to unattenuated portion of the image. The 50% to 90% points are chosen as a best fit to an assumed Gaussian radiation distribution from the focal spot and to avoid edge transmission effects. 1/2 U{sub 1} + 1/2 U{sub 2} corresponds about to the full width at half height of a Gaussian focal spot. A highly absorbing material (Tungsten, Tungsten Alloy, or Platinum) is used for the object. Either wires or a sphere are used as the object to eliminate alignment issues. One

  5. Comparative metalloproteomic approaches for the investigation proteins involved in the toxicity of inorganic and organic forms of mercury in rice (Oryza sativa L.) roots.

    PubMed

    Li, Yunyun; Zhao, Jiating; Li, Yu-Feng; Xu, Xiaohan; Zhang, Bowen; Liu, Yongjie; Cui, Liwei; Li, Bai; Gao, Yuxi; Chai, Zhifang

    2016-07-13

    The toxicity mechanisms of rice roots under inorganic mercury (IHg) or methylmercury (MeHg) stress were investigated using metalloproteomic approaches. Rice seedlings were cultivated in nutrient solutions with IHg or MeHg for three weeks. Proteins were extracted from the roots and separated by two-dimensional electrophoresis (2-DE). Differentially expressed proteins were analyzed using ESI-MS/MS and identified by PMF. 26 and 29 protein spots were differentially expressed in the IHg- and MeHg-exposed roots, respectively. The proteins responsive to Hg exposure are involved in antioxidative defense, sulfur and glutathione metabolism, carbohydrate and energy metabolism, programmed cell death, and pathogen defense. Chitinase and salt stress-induced proteins exhibited a greater differentially expression in response to MeHg stress compared to IHg stress. Hg-binding proteins were detected by the combined use of 1-DE, SRXRF, and ESI-MS/MS. The results showed that Hg was bound to proteins of 15-25 kDa in rice roots under Hg stress. The Hg contents in the band under IHg stress were remarkably higher than those under MeHg. Hg binds to proteins, which leads to irreversible damage of root growth. Rice roots changed the related protein expression levels in response to Hg stress. These results may provide new insights into the mechanism of toxicity of IHg and MeHg in rice. PMID:26731542

  6. Spot Variation Fluorescence Correlation Spectroscopy Allows for Superresolution Chronoscopy of Confinement Times in Membranes

    PubMed Central

    Ruprecht, Verena; Wieser, Stefan; Marguet, Didier; Schütz, Gerhard J.

    2011-01-01

    Resolving the dynamical interplay of proteins and lipids in the live-cell plasma membrane represents a central goal in current cell biology. Superresolution concepts have introduced a means of capturing spatial heterogeneity at a nanoscopic length scale. Similar concepts for detecting dynamical transitions (superresolution chronoscopy) are still lacking. Here, we show that recently introduced spot-variation fluorescence correlation spectroscopy allows for sensing transient confinement times of membrane constituents at dramatically improved resolution. Using standard diffraction-limited optics, spot-variation fluorescence correlation spectroscopy captures signatures of single retardation events far below the transit time of the tracer through the focal spot. We provide an analytical description of special cases of transient binding of a tracer to pointlike traps, or association of a tracer with nanodomains. The influence of trap mobility and the underlying binding kinetics are quantified. Experimental approaches are suggested that allow for gaining quantitative mechanistic insights into the interaction processes of membrane constituents. PMID:21641330

  7. Miniaturizing sample spots for matrix-assisted laser desorption/ionization mass spectrometry

    PubMed Central

    Tu, Tingting; Gross, Michael L.

    2009-01-01

    The trend of miniaturization in bioanalytical chemistry is shifting from technical development to practical application. In matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), progress in miniaturizing sample spots has been driven by the needs to increase sensitivity and speed, to interface with other analytical microtechnologies, and to develop miniaturized instrumentation. We review recent developments in miniaturizing sample spots for MALDI-MS. We cover both target modification and microdispensing technologies, and we emphasize the benefits with respect to sensitivity, throughput and automation. We hope that this review will encourage further method development and application of miniaturized sample spots for MALDI-MS, so as to expand applications in analytical chemistry, protein science and molecular biology. PMID:20161086

  8. Hyperspectral analysis of columbia spotted frog habitat

    USGS Publications Warehouse

    Shive, J.P.; Pilliod, D.S.; Peterson, C.R.

    2010-01-01

    Wildlife managers increasingly are using remotely sensed imagery to improve habitat delineations and sampling strategies. Advances in remote sensing technology, such as hyperspectral imagery, provide more information than previously was available with multispectral sensors. We evaluated accuracy of high-resolution hyperspectral image classifications to identify wetlands and wetland habitat features important for Columbia spotted frogs (Rana luteiventris) and compared the results to multispectral image classification and United States Geological Survey topographic maps. The study area spanned 3 lake basins in the Salmon River Mountains, Idaho, USA. Hyperspectral data were collected with an airborne sensor on 30 June 2002 and on 8 July 2006. A 12-year comprehensive ground survey of the study area for Columbia spotted frog reproduction served as validation for image classifications. Hyperspectral image classification accuracy of wetlands was high, with a producer's accuracy of 96 (44 wetlands) correctly classified with the 2002 data and 89 (41 wetlands) correctly classified with the 2006 data. We applied habitat-based rules to delineate breeding habitat from other wetlands, and successfully predicted 74 (14 wetlands) of known breeding wetlands for the Columbia spotted frog. Emergent sedge microhabitat classification showed promise for directly predicting Columbia spotted frog egg mass locations within a wetland by correctly identifying 72 (23 of 32) of known locations. Our study indicates hyperspectral imagery can be an effective tool for mapping spotted frog breeding habitat in the selected mountain basins. We conclude that this technique has potential for improving site selection for inventory and monitoring programs conducted across similar wetland habitat and can be a useful tool for delineating wildlife habitats. ?? 2010 The Wildlife Society.

  9. Revised Thorium Abundances for Lunar Red Spots

    NASA Technical Reports Server (NTRS)

    Hagerty, J. J.; Lawrence, D. J.; Elphic, R. C.; Feldman, W. C.; Vaniman, D. T.; Hawke, B. R.

    2005-01-01

    Lunar red spots are features on the nearside of the Moon that are characterized by high albedo and by a strong absorption in the ultraviolet. These red spots include the Gruithuisen domes, the Mairan domes, Hansteen Alpha, the southern portion of Montes Riphaeus, Darney Chi and Tau, Helmet, and an area near the Lassell crater. It has been suggested that many of the red spots are extrusive, nonmare, volcanic features that could be composed of an evolved lithlogy enriched in thorium. In fact, Hawke et al. used morphological characteristics to show that Hansteen Alpha is a nonmare volcanic construct. However, because the apparent Th abundances (6 - 7 ppm) were lower than that expected for evolved rock types, Hawke et al. concluded that Hansteen Alpha was composed of an unknown rock type. Subsequent studies by Lawrence et al. used improved knowledge of the Th spatial distribution for small area features on the lunar surface to revisit the interpretation of Th abundances at the Hansteen Alpha red spot. As part of their study, Lawrence et al. used a forward modeling technique to show that the Th abundance at Hansteen Alpha is not 6 ppm, but is more likely closer to 25 ppm, a value consistent with evolved lithologies. This positive correlation between the morphology and composition of Hansteen Alpha provides support for the presence of evolved lithologies on the lunar surface. It is possible, however, that Hansteen Alpha represents an isolated occurrence of non-mare volcanism. That is why we have chosen to use the forward modeling technique of Lawrence et al. to investigate the Th abundances at other lunar red spots, starting with the Gruithuisen domes. Additional information is included in the original extended abstract.

  10. Bilateral Macular Roth Spots as a Manifestation of Subacute Endocarditis.

    PubMed

    Ceglowska, Karolina; Nowomiejska, Katarzyna; Kiszka, Agnieszka; Koss, Michael J; Maciejewski, Ryszard; Rejdak, Robert

    2015-01-01

    A 42-year-old man presented with a 2-day history of impaired vision in the right eye (OD). The best corrected visual acuity (BCVA) (LogMAR) was 1.1 for the right eye and 0.0 for the left eye (OS). Fundus examination revealed white-centered hemorrhages resembling Roth spots in both macular regions. The spectral-domain optical coherence tomography (SD-OCT) showed intraretinal pseudocysts and hyperreflective deposits in the areas corresponding to the Roth spots. Conducted blood tests revealed elevated D-dimer concentration, increased total number of neutrophils, high C-reactive protein concentration, and elevated erythrocyte sedimentation rate. Procalcitonin concentration, platelet count, and body temperature were within normal ranges. A blood culture was ordered and yielded Streptococcus mitis and intravenous antibiotics were started immediately. The patient started complaining of chest and left calf pain. The systemic examination revealed infective endocarditis accompanied by bicuspid aortic valve and paravalvular abscess formation. The patient underwent cardiac surgery with mechanical aortic valve implantation. After recovery, the patient's visual acuities improved fully. Control ophthalmic examination, including SD-OCT, showed no abnormalities. PMID:26839725

  11. Bilateral Macular Roth Spots as a Manifestation of Subacute Endocarditis

    PubMed Central

    Ceglowska, Karolina; Nowomiejska, Katarzyna; Kiszka, Agnieszka; Koss, Michael J.; Maciejewski, Ryszard; Rejdak, Robert

    2015-01-01

    A 42-year-old man presented with a 2-day history of impaired vision in the right eye (OD). The best corrected visual acuity (BCVA) (LogMAR) was 1.1 for the right eye and 0.0 for the left eye (OS). Fundus examination revealed white-centered hemorrhages resembling Roth spots in both macular regions. The spectral-domain optical coherence tomography (SD-OCT) showed intraretinal pseudocysts and hyperreflective deposits in the areas corresponding to the Roth spots. Conducted blood tests revealed elevated D-dimer concentration, increased total number of neutrophils, high C-reactive protein concentration, and elevated erythrocyte sedimentation rate. Procalcitonin concentration, platelet count, and body temperature were within normal ranges. A blood culture was ordered and yielded Streptococcus mitis and intravenous antibiotics were started immediately. The patient started complaining of chest and left calf pain. The systemic examination revealed infective endocarditis accompanied by bicuspid aortic valve and paravalvular abscess formation. The patient underwent cardiac surgery with mechanical aortic valve implantation. After recovery, the patient's visual acuities improved fully. Control ophthalmic examination, including SD-OCT, showed no abnormalities. PMID:26839725

  12. Comparative analysis of proteome changes induced by the two spotted spider mite Tetranychus urticae and methyl jasmonate in citrus leaves.

    PubMed

    Maserti, B E; Del Carratore, R; Croce, C M Della; Podda, A; Migheli, Q; Froelicher, Y; Luro, F; Morillon, R; Ollitrault, P; Talon, M; Rossignol, M

    2011-03-01

    Citrus plants are currently facing biotic and abiotic stresses. Therefore, the characterization of molecular traits involved in the response mechanisms to stress could facilitate selection of resistant varieties. Although large cDNA microarray profiling has been generated in citrus tissues, the available protein expression data are scarce. In this study, to identify differentially expressed proteins in Citrus clementina leaves after infestation by the two-spotted spider mite Tetranychus urticae, a proteome comparison was undertaken using two-dimensional gel electrophoresis. The citrus leaf proteome profile was also compared with that of leaves treated over 0-72h with methyl jasmonate, a compound playing a key role in the defense mechanisms of plants to insect/arthropod attack. Significant variations were observed for 110 protein spots after spider mite infestation and 67 protein spots after MeJA treatments. Of these, 50 proteins were successfully identified by liquid chromatography-mass spectrometry-tandem mass spectrometry. The majority constituted photosynthesis- and metabolism-related proteins. Five were oxidative stress associated enzymes, including phospholipid glutathione peroxidase, a salt stressed associated protein, ascorbate peroxidase and Mn-superoxide dismutase. Seven were defense-related proteins, such as the pathogenesis-related acidic chitinase, the protease inhibitor miraculin-like protein, and a lectin-like protein. This is the first report of differentially regulated proteins after T. urticae attack and exogenous MeJA application in citrus leaves. PMID:20926159

  13. Identification of Proteins from Interstitium of Trapezius Muscle in Women with Chronic Myalgia Using Microdialysis in Combination with Proteomics

    PubMed Central

    Olausson, Patrik; Gerdle, Björn; Ghafouri, Nazdar; Larsson, Britt; Ghafouri, Bijar

    2012-01-01

    Background Microdialysis (MD) of the trapezius muscle has been an attractive technique to investigating small molecules and metabolites in chronic musculoskeletal pain in human. Large biomolecules such as proteins also cross the dialysis membrane of the catheters. In this study we have applied in vivo MD in combination with two dimensional gel electrophoresis (2-DE) and mass spectrometry to identify proteins in the extracellular fluid of the trapezius muscle. Materials and Methods Dialysate from women with chronic trapezius myalgia (TM; n = 37), women with chronic wide spread pain (CWP; n = 18) and healthy controls (CON; n = 22) was collected from the trapezius muscle using a catheter with a cut-off point of 100 kDa. Proteins were separated by two-dimensional gel electrophoresis and visualized by silver staining. Detected proteins were identified by nano liquid chromatography in combination with tandem mass spectrometry. Results Ninety-seven protein spots were identified from the interstitial fluid of the trapezius muscle; 48 proteins in TM and 30 proteins in CWP had concentrations at least two-fold higher or lower than in CON. The identified proteins pertain to several functional classes, e.g., proteins involved in inflammatory responses. Several of the identified proteins are known to be involved in processes of pain such as: creatine kinase, nerve growth factor, carbonic anhydrase, myoglobin, fatty acid binding protein and actin aortic smooth muscle. Conclusions In this study, by using in vivo microdialysis in combination with proteomics a large number of proteins in muscle interstitium have been identified. Several of the identified proteins were at least two-fold higher or lower in chronic pain patients. The applied techniques open up for the possibility of investigating protein changes associated with nociceptive processes of chronic myalgia. PMID:23300707

  14. Proteomic identification of secreted proteins of Propionibacterium acnes

    PubMed Central

    2010-01-01

    Background The anaerobic Gram-positive bacterium Propionibacterium acnes is a human skin commensal that resides preferentially within sebaceous follicles; however, it also exhibits many traits of an opportunistic pathogen, playing roles in a variety of inflammatory diseases such as acne vulgaris. To date, the underlying disease-causing mechanisms remain ill-defined and knowledge of P. acnes virulence factors remains scarce. Here, we identified proteins secreted during anaerobic cultivation of a range of skin and clinical P. acnes isolates, spanning the four known phylogenetic groups. Results Culture supernatant proteins of P. acnes were separated by two-dimensional electrophoresis (2-DE) and all Coomassie-stained spots were subsequently identified by MALDI mass spectrometry (MALDI-MS). A set of 20 proteins was secreted in the mid-exponential growth phase by the majority of strains tested. Functional annotation revealed that many of these common proteins possess degrading activities, including glycoside hydrolases with similarities to endoglycoceramidase, β-N-acetylglucosaminidase and muramidase; esterases such as lysophospholipase and triacylglycerol lipase; and several proteases. Other secreted factors included Christie-Atkins-Munch-Petersen (CAMP) factors, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and several hypothetical proteins, a few of which are unique to P. acnes. Strain-specific differences were apparent, mostly in the secretion of putative adhesins, whose genes exhibit variable phase variation-like sequence signatures. Conclusions Our proteomic investigations have revealed that the P. acnes secretome harbors several proteins likely to play a role in host-tissue degradation and inflammation. Despite a large overlap between the secretomes of all four P. acnes phylotypes, distinct differences between predicted host-tissue interacting proteins were identified, providing potential insight into the differential virulence properties of P. acnes isolates

  15. Wearable Monitor Helps Spot 'Masked' High Blood Pressure

    MedlinePlus

    ... fullstory_158860.html Wearable Monitor Helps Spot 'Masked' High Blood Pressure Black people with undetected problem twice as likely ... doctors spot black people with "masked," or undetected, high blood pressure, a new study suggests. "Masked" high blood pressure ...

  16. Wearable Monitor Helps Spot 'Masked' High Blood Pressure

    MedlinePlus

    ... html Wearable Monitor Helps Spot 'Masked' High Blood Pressure Black people with undetected problem twice as likely ... MONDAY, May 16, 2016 (HealthDay News) -- Constant blood pressure monitoring could help doctors spot black people with " ...

  17. Turbulent Region Near Jupiter's Great Red Spot

    NASA Technical Reports Server (NTRS)

    1997-01-01

    True and false color mosaics of the turbulent region west of Jupiter's Great Red Spot. The Great Red Spot is on the planetary limb on the right hand side of each mosaic. The region west (left) of the Great Red Spot is characterized by large, turbulent structures that rapidly change in appearance. The turbulence results from the collision of a westward jet that is deflected northward by the Great Red Spot into a higher latitude eastward jet. The large eddies nearest to the Great Red Spot are bright, suggesting that convection and cloud formation are active there.

    The top mosaic combines the violet (410 nanometers) and near infrared continuum (756 nanometers) filter images to create a mosaic similar to how Jupiter would appear to human eyes. Differences in coloration are due to the composition and abundance of trace chemicals in Jupiter's atmosphere. The lower mosaic uses the Galileo imaging camera's three near-infrared (invisible) wavelengths (756 nanometers, 727 nanometers, and 889 nanometers displayed in red, green, and blue) to show variations in cloud height and thickness. Light blue clouds are high and thin, reddish clouds are deep, and white clouds are high and thick. Purple most likely represents a high haze overlying a clear deep atmosphere. Galileo is the first spacecraft to distinguish cloud layers on Jupiter.

    The mosaic is centered at 16.5 degrees south planetocentric latitude and 85 degrees west longitude. The north-south dimension of the Great Red Spot is approximately 11,000 kilometers. The smallest resolved features are tens of kilometers in size. North is at the top of the picture. The images used were taken on June 26, 1997 at a range of 1.2 million kilometers (1.05 million miles) by the Solid State Imaging (SSI) system on NASA's Galileo spacecraft.

    The Jet Propulsion Laboratory, Pasadena, CA manages the Galileo mission for NASA's Office of Space Science, Washington, DC. JPL is an operating division of California Institute of Technology

  18. Identification of Differentially Expressed Proteins from Leishmania amazonensis Associated with the Loss of Virulence of the Parasites

    PubMed Central

    Magalhães, Rubens D. M.; Duarte, Mariana C.; Mattos, Eliciane C.; Martins, Vivian T.; Lage, Paula S.; Chávez-Fumagalli, Miguel A.; Lage, Daniela P.; Menezes-Souza, Daniel; Régis, Wiliam C. B.; Manso Alves, Maria J.; Soto, Manuel; Tavares, Carlos A. P.; Nagen, Ronaldo A. P.; Coelho, Eduardo A. F.

    2014-01-01

    Background The present study analyzed whether or not the in vitro cultivation for long periods of time of pre-isolated Leishmania amazonensis from lesions of chronically infected BALB/c mice was able to interfere in the parasites' infectivity using in vivo and in vitro experiments. In addition, the proteins that presented a significant decrease or increase in their protein expression content were identified applying a proteomic approach. Methodology/Principal Findings Parasites were cultured in vitro for 150 days. Aliquots were collected on the day 0 of culture (R0), as well as after ten (R10; 50 days of culture), twenty (R20; 100 days of culture), and thirty (R30; 150 days of culture) passages, and were used to analyze the parasites' in vitro and in vivo infectivity, as well as to perform the proteomic approach. Approximately 837, 967, 935, and 872 spots were found in 2-DE gels prepared from R0, R10, R20, and R30 samples, respectively. A total of 37 spots presented a significant decrease in their intensity of expression, whereas a significant increase in protein content during cultivation could be observed for 19 proteins (both cases >2.0 folds). Some of these identified proteins can be described, such as diagnosis and/or vaccine candidates, while others are involved in the infectivity of Leishmania. It is interesting to note that six proteins, considered hypothetical in Leishmania, showed a significant decrease in their expression and were also identified. Conclusions/Significance The present study contributes to the understanding that the cultivation of parasites over long periods of time may well be related to the possible loss of infectivity of L. amazonensis. The identified proteins that presented a significant decrease in their expression during cultivation, including the hypothetical, may also be related to this loss of parasites' infectivity, and applied in future studies, including vaccine candidates and/or immunotherapeutic targets against leishmaniasis

  19. Proteomic analysis for nuclear proteins related to tumour malignant progression: a comparative proteomic study between malignant progressive cells and regressive cells.

    PubMed

    Kuramitsu, Yasuhiro; Hayashi, Eiko; Okada, Futoshi; Tanaka, Toshiyuki; Zhang, Xiulian; Ueyama, Yoshiya; Nakamura, Kazuyuki

    2010-06-01

    Tumour development and progression consists a series of multiple changes in gene expression. Progressive tumour cells acquire more aggressive properties manifested by rapid growth, invasiveness and metastatic ability, as well as increased genetic instability leading to multiple genetic alterations. Therefore, it is crucial to identify the possible intracellular and extracellular molecular mechanisms that accelerate tumour progression, in particular to identify nuclear proteins which interact with DNA. Nuclear proteomics provides an opportunity to qualitatively and quantitatively examine protein effectors that contribute to cellular phenotype. This study performed a differential display analysis for the expression of nuclear proteome between regressive tumour cell clone QR-32 and malignant progressive tumour cell clone QRsP-11 using two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS). Eight nuclear proteins whose expressions were different between QR-32 and QRsP-11 cells were identified. Seven of those protein spots, zinc finger protein ZXDC, lamin-A/C, far upstream clement-binding protein 1, heterogeneous nuclear ribonucleoprotein K, heterogeneous nuclear ribonucleoprotein A/B and guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, were down-regulated in QRsP-11, while one protein, nucleolin, was up-regulated in QRsP-11. PMID:20651356

  20. Jupiter's Great Red Spot and White Ovals

    NASA Technical Reports Server (NTRS)

    1979-01-01

    This photo of Jupiter was taken by Voyager 1 on the evening of March 1, 1979, from a distance of 2.7 million miles (4.3 million kilometers). The photo shows Jupiter's Great Red Spot (top) and one of the white ovals than can be seen in Jupiter's atmosphere from Earth. The white ovals were seen to form in 1939, and 1940, and have remained more or less constant ever since. None of the structure and detail evident in these features have ever been seen from Earth. The Great Red Spot is three times as large as Earth. Also evident in the picture is a great deal of atmospheric detail that will require further study for interpretation. The smallest details that can be seen in this picture are about 45 miles (80 kilometers across. JPL manages and controls the Voyager project for NASA's Office of Space Science.

  1. Wetlands mapping with spot multispectral scanner data

    SciTech Connect

    Mackey, H.E. Jr. ); Jensen, J.R. . Dept. of Geography)

    1989-01-01

    Government facilities such as the US Department of Energy's Savannah River Plant (SRP) near Aiken, South Carolina, often use remote sensing data to assist in environmental management. Airborne multispectral scanner (MSS) data have been acquired at SRP since 1981. Various types of remote sensing data have been used to map and characterize wetlands. Regional Landsat MSS and TM satellite data have been used for wetlands mapping by various government agencies and private organizations. Furthermore, SPOT MSS data are becoming available and provide opportunities for increased spacial resolution and temporal coverage for wetlands mapping. This paper summarizes the initial results from using five dates of SPOT MSS data from April through October, 1987, as a means to monitor seasonal wetland changes in freshwater wetlands of the SRP. 11 refs., 4 figs.

  2. Spot foreign exchange market and time series

    NASA Astrophysics Data System (ADS)

    Petroni, F.; Serva, M.

    2003-08-01

    We investigate high frequency price dynamics in foreign exchange market using data from Reuters information system (the dataset has been provided to us by Olsen and Associates). In our analysis we show that a naïve approach to the definition of price (for example using the spot mid price) may lead to wrong conclusions on price behavior as for example the presence of short term correlations for returns. For this purpose we introduce an algorithm which only uses the non arbitrage principle to estimate real prices from the spot ones. The new definition leads to returns which are not affected by spurious correlations. Furthermore, any apparent information (defined by using Shannon entropy) contained in the data disappears.

  3. Dynamically variable spot size laser system

    NASA Technical Reports Server (NTRS)

    Gradl, Paul R. (Inventor); Hurst, John F. (Inventor); Middleton, James R. (Inventor)

    2012-01-01

    A Dynamically Variable Spot Size (DVSS) laser system for bonding metal components includes an elongated housing containing a light entry aperture coupled to a laser beam transmission cable and a light exit aperture. A plurality of lenses contained within the housing focus a laser beam from the light entry aperture through the light exit aperture. The lenses may be dynamically adjusted to vary the spot size of the laser. A plurality of interoperable safety devices, including a manually depressible interlock switch, an internal proximity sensor, a remotely operated potentiometer, a remotely activated toggle and a power supply interlock, prevent activation of the laser and DVSS laser system if each safety device does not provide a closed circuit. The remotely operated potentiometer also provides continuous variability in laser energy output.

  4. Jupiter's Great Red Spot - A free atmospheric vortex

    NASA Technical Reports Server (NTRS)

    Ingersoll, A. P.

    1973-01-01

    A simple hydrodynamic model yields steady-state solutions with many of the properties of the Great Red Spot and the neighboring belts and zones of Jupiter. No special forcing mechanism is necessary to maintain the circulation of the Spot. This is consistent with observations which indicate that the Great Red Spot and the zones have similar dynamic properties.

  5. Jupiters great red spot: a free atmospheric vortex?

    PubMed

    Ingersoll, A P

    1973-12-28

    A simple hydrodynamic model yields steady-state solutions with many of the properties of the Great Red Spot and the neighboring belts and zones of Jupiter. No special forcing mechanism is necessary to maintain the circulation of the Spot. This is consistent with observations which indicate that the Great Red Spot and the zones have similar dynamic properties. PMID:17733115

  6. 21 CFR 892.1670 - Spot-film device.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Spot-film device. 892.1670 Section 892.1670 Food... DEVICES RADIOLOGY DEVICES Diagnostic Devices § 892.1670 Spot-film device. (a) Identification. A spot-film... medical purposes to position a radiographic film cassette to obtain radiographs during fluoroscopy....

  7. 50 CFR 223.212 - Southern DPS of spotted seal.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 10 2014-10-01 2014-10-01 false Southern DPS of spotted seal. 223.212... Applicable to Threatened Marine and Anadromous Species § 223.212 Southern DPS of spotted seal. The... the Southern Distinct Population Segment of spotted seal listed in § 223.102....

  8. 50 CFR 223.211 - Southern DPS of spotted seal.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 50 Wildlife and Fisheries 10 2012-10-01 2012-10-01 false Southern DPS of spotted seal. 223.211... Applicable to Threatened Marine and Anadromous Species § 223.211 Southern DPS of spotted seal. The... species shall apply to the Southern Distinct Population Segment of the spotted seal listed in §...

  9. 50 CFR 223.211 - Southern DPS of spotted seal.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 9 2011-10-01 2011-10-01 false Southern DPS of spotted seal. 223.211... Applicable to Threatened Marine and Anadromous Species § 223.211 Southern DPS of spotted seal. The... species shall apply to the Southern Distinct Population Segment of the spotted seal listed in §...

  10. Spot-Welding Gun Is Easy To Use

    NASA Technical Reports Server (NTRS)

    Morgan, Gene E.; Nguyen, Francis H.

    1991-01-01

    Electrical-resistance spot-welding gun designed to produce more welds per unit time by decreasing technician's effort and fatigue. Vacuum cups on frame secure welding gun to workpiece while compressed air drives welding tip against workpiece to make spot resistance weld. When weld completed, vacuum in frame cups released so frame and gun moved to position of next spot weld.

  11. Spot-Welding Gun With Pivoting Twin-Collet Assembly

    NASA Technical Reports Server (NTRS)

    Nguyen, Francis; Simpson, Gareth; Hoult, William S.

    1996-01-01

    Modified spot-welding gun includes pivoting twin-collet assembly that holds two spot-welding electrodes. Designed to weld highly conductive (30 percent gold) brazing-alloy foils to thin nickel alloy workpieces; also suitable for other spot-welding applications compatible with two-electrode configuration.

  12. Determination of the Nature of Spotting in Blanched Peanuts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The peanut spotting is a big problem responsible for significant loss by the peanut industry. The cause of the spotting has been identified in the lab as being due to infection by fungi. Secondary fungal metabolites and peanut stilbene phytoalexins were not involved in the spot formation. The nature...

  13. Johann Schroeter's 'Extremely Dark Spots Of Jupiter'

    NASA Astrophysics Data System (ADS)

    Dobbins, T.; Sheehan, W.

    1997-06-01

    Physical observations of Jupiter from the 18th century are rare. The most diligent observer of the planet of that era was Johann Schroeter, who in 1785-86 recorded multiple short-term, transient dark spots. Schroeter's observations are discussed in detail. Though somewhat reminiscent of the recent Shoemaker-Levy 9 impact events, the authors conclude that Schroeter's observations furnish a unique record of SEBn activity in the 18th century.

  14. Pips and spots in the microwave sky

    NASA Astrophysics Data System (ADS)

    Martinez-Gonzalez, E.; Sanz, J. L.

    1989-04-01

    Some local statistical properties in the microwave sky are analyzed such as mean number of hotspots over the celestial sphere, mean size of a hotspot, mean number of pips at fixed declination, and the 95 percent confidence interval for the threshold of the hottest spot or pip. It is concluded that the best strategy to detect the maximum number of hotspots would be to perform a double beam-switching experiment with a beam resolution and angular beam separation of about 2 deg.

  15. Modified Spot Welder Solders Flat Cables

    NASA Technical Reports Server (NTRS)

    Haehner, Carl L.

    1992-01-01

    Soldering device, essentially modified spot welder, melts high-melting-temperature solders without damaging plastic insulation on flat electrical cables. Solder preform rests on exposed conductor of cable, under connector pin. Electrodes press pin/preform/conductor sandwich together and supply pulse of current to melt preform, bonding pin to conductor. Anvil acts as support and heat sink. Device used to solder flexible ribbon cables to subminiature pin connectors.

  16. Habitat Suitability Index Models: Spotted Owl

    USGS Publications Warehouse

    Laymon, Stephen A.; Salwasser, Hal; Barrett, Reginald H.

    1985-01-01

    A review and synthesis of existing information were used to develop a Habitat Suitability Index (HSI) model for the spotted owl (Strix occidentalis). The model consolidates habitat use information into a framework appropriate for field application, and is scaled to produce an index between 0.0 (unsuitable habitat) to 1.0 (optimum habitat). HSI models are designed to be used with Habitat Evaluation Procedures previously developed by the U.S. Fish and Wildlife Service.

  17. DNA-nanostructure-assembly by sequential spotting

    PubMed Central

    2011-01-01

    Background The ability to create nanostructures with biomolecules is one of the key elements in nanobiotechnology. One of the problems is the expensive and mostly custom made equipment which is needed for their development. We intended to reduce material costs and aimed at miniaturization of the necessary tools that are essential for nanofabrication. Thus we combined the capabilities of molecular ink lithography with DNA-self-assembling capabilities to arrange DNA in an independent array which allows addressing molecules in nanoscale dimensions. Results For the construction of DNA based nanostructures a method is presented that allows an arrangement of DNA strands in such a way that they can form a grid that only depends on the spotted pattern of the anchor molecules. An atomic force microscope (AFM) has been used for molecular ink lithography to generate small spots. The sequential spotting process allows the immobilization of several different functional biomolecules with a single AFM-tip. This grid which delivers specific addresses for the prepared DNA-strand serves as a two-dimensional anchor to arrange the sequence according to the pattern. Once the DNA-nanoarray has been formed, it can be functionalized by PNA (peptide nucleic acid) to incorporate advanced structures. Conclusions The production of DNA-nanoarrays is a promising task for nanobiotechnology. The described method allows convenient and low cost preparation of nanoarrays. PNA can be used for complex functionalization purposes as well as a structural element. PMID:22099392

  18. First- and second-order Poisson spots

    NASA Astrophysics Data System (ADS)

    Kelly, William R.; Shirley, Eric L.; Migdall, Alan L.; Polyakov, Sergey V.; Hendrix, Kurt

    2009-08-01

    Although Thomas Young is generally given credit for being the first to provide evidence against Newton's corpuscular theory of light, it was Augustin Fresnel who first stated the modern theory of diffraction. We review the history surrounding Fresnel's 1818 paper and the role of the Poisson spot in the associated controversy. We next discuss the boundary-diffraction-wave approach to calculating diffraction effects and show how it can reduce the complexity of calculating diffraction patterns. We briefly discuss a generalization of this approach that reduces the dimensionality of integrals needed to calculate the complete diffraction pattern of any order diffraction effect. We repeat earlier demonstrations of the conventional Poisson spot and discuss an experimental setup for demonstrating an analogous phenomenon that we call a "second-order Poisson spot." Several features of the diffraction pattern can be explained simply by considering the path lengths of singly and doubly bent paths and distinguishing between first- and second-order diffraction effects related to such paths, respectively.

  19. Word Spotting and Recognition with Embedded Attributes.

    PubMed

    Almazán, Jon; Gordo, Albert; Fornés, Alicia; Valveny, Ernest

    2014-12-01

    This paper addresses the problems of word spotting and word recognition on images. In word spotting, the goal is to find all instances of a query word in a dataset of images. In recognition, the goal is to recognize the content of the word image, usually aided by a dictionary or lexicon. We describe an approach in which both word images and text strings are embedded in a common vectorial subspace. This is achieved by a combination of label embedding and attributes learning, and a common subspace regression. In this subspace, images and strings that represent the same word are close together, allowing one to cast recognition and retrieval tasks as a nearest neighbor problem. Contrary to most other existing methods, our representation has a fixed length, is low dimensional, and is very fast to compute and, especially, to compare. We test our approach on four public datasets of both handwritten documents and natural images showing results comparable or better than the state-of-the-art on spotting and recognition tasks. PMID:26353157

  20. Meniscal mineralisation in little spotted cats

    PubMed Central

    2013-01-01

    Background The aim of this study was to evaluate the stifle joints of little spotted cats in captivity using radiographic and CT studies. The hypothesis was that these animals would have meniscal mineralisation that could be detectable by imaging studies. Twelve intact little spotted cats (Leopardus tigrinus), 2 females and 10 males, aged from 1.5 to 11.11 years old and weighing 1.9–3.05 kg were studied. These animals, which were living in the Quinzinho de Barros Municipal Zoo, had no symptoms or known disease processes at the time of the study. The plain radiographs and computed tomography (CT) scans of both stifle joints were performed under general anaesthesia. Sequential transverse images were acquired on a spiral scanner. Results No signs of articular disease were observed in any of the animals. Radiographically, the meniscal mineralisation was detected as an oval radiopacity in the cranial compartment on the mediolateral projection, located within the area of the medial meniscus. On craniocaudal projection, the mineralisation was more difficult to visualise. In one of the animals, it was not possible to identify the meniscal mineralisation in either of the stifle joints. Using CT, meniscal mineralisation was best identified in the transverse plane images. Conclusions Meniscal mineralisation appears to be a normal anatomic feature in little spotted cats. PMID:23506083

  1. Focused grid-based resampling for protein docking and mapping.

    PubMed

    Mamonov, Artem B; Moghadasi, Mohammad; Mirzaei, Hanieh; Zarbafian, Shahrooz; Grove, Laurie E; Bohnuud, Tanggis; Vakili, Pirooz; Ch Paschalidis, Ioannis; Vajda, Sandor; Kozakov, Dima

    2016-04-30

    The fast Fourier transform (FFT) sampling algorithm has been used with success in application to protein-protein docking and for protein mapping, the latter docking a variety of small organic molecules for the identification of binding hot spots on the target protein. Here we explore the local rather than global usage of the FFT sampling approach in docking applications. If the global FFT based search yields a near-native cluster of docked structures for a protein complex, then focused resampling of the cluster generally leads to a substantial increase in the number of conformations close to the native structure. In protein mapping, focused resampling of the selected hot spot regions generally reveals further hot spots that, while not as strong as the primary hot spots, also contribute to ligand binding. The detection of additional ligand binding regions is shown by the improved overlap between hot spots and bound ligands. © 2016 Wiley Periodicals, Inc. PMID:26837000

  2. Superluminal Spot Pair Events in Astronomical Settings: Sweeping Beams

    NASA Astrophysics Data System (ADS)

    Nemiroff, Robert J.

    2015-02-01

    Sweeping beams of light can cast spots moving with superluminal speeds across scattering surfaces. Such faster-than-light speeds are well-known phenomena that do not violate special relativity. It is shown here that under certain circumstances, superluminal spot pair creation and annihilation events can occur that provide unique information to observers. These spot pair events are not particle pair events-they are the sudden creation or annihilation of a pair of relatively illuminated spots on a scattering surface. Real spot pair illumination events occur unambiguously on the scattering surface when spot speeds diverge, while virtual spot pair events are observer dependent and perceived only when real spot radial speeds cross the speed of light. Specifically, a virtual spot pair creation event will be observed when a real spot's speed toward the observer drops below c, while a virtual spot pair annihilation event will be observed when a real spot's radial speed away from the observer rises above c. Superluminal spot pair events might be found angularly, photometrically, or polarimetrically, and might carry useful geometry or distance information. Two example scenarios are briefly considered. The first is a beam swept across a scattering spherical object, exemplified by spots of light moving across Earth's Moon and pulsar companions. The second is a beam swept across a scattering planar wall or linear filament, exemplified by spots of light moving across variable nebulae including Hubble's Variable Nebula. In local cases where the sweeping beam can be controlled and repeated, a three-dimensional map of a target object can be constructed. Used tomographically, this imaging technique is fundamentally different from lens photography, radar, and conventional lidar.

  3. Tomato spotted wilt and early leaf spot reactions in peanut genotypes from the U.S. and China

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tomato spotted wilt, caused by Tomato spotted wilt virus (TSWV), and early leaf spot caused by Cercospora arachidicola are important diseases of peanut (Arachis hypogaea). As part of a study examining genotypic and phenotypic variation, disease reactions to these two diseases were evaluated in twe...

  4. Tomato spotted wilt and early leaf spot reaction in peanut genotypes from the U.S. and China

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tomato spotted wilt, caused by Tomato spotted wilt virus (TSWV), and early leaf spot caused by Cercospora arachidicola are important diseases of peanut (Arachis hypogaea). As part of a study examining genotypic and phenotypic variation, disease reactions to these two diseases were evaluated in twe...

  5. A rapid method for depletion of Rubisco from soybean (Glycine max) leaf for proteomic analysis of lower abundance proteins.

    PubMed

    Krishnan, Hari B; Natarajan, Savithiry S

    2009-12-01

    2-DE analysis of complex plant proteomes has limited dynamic resolution because only abundant proteins can be detected. Proteomic assessment of the low abundance proteins within leaf tissue is difficult when it is comprised of 30-50% of the CO(2) fixation enzyme Rubisco. Resolution can be improved through depletion of Rubisco using fractionation techniques based upon different physiological or biochemical principles. We have developed a fast and simple fractionation technique using 10 mM Ca(2+) and 10 mM phytate to precipitate Rubisco from soybean leaf soluble protein extract. This method is not only rapid, but also inexpensive, and capable of removing 85% of the extremely abundant Rubisco enzyme from soybean leaf soluble protein extract. This method allowed for roughly 230 previously inconspicuous protein spots in soybean leaf to be more easily detectable (3-fold increase in vol%) using fluorescent detection and allowed 28 phosphorylated proteins previously undetected, to be isolated and identified by MALDI-TOF-MS. PMID:19766275

  6. Spot1 end of life disposition manoeuvres

    NASA Astrophysics Data System (ADS)

    Alby, F.

    The Earth observation satellites of the SPOT family are on a Sun synchronous orbit at 822 km altitude. The on-orbit lifetime of objects at this altitude is about 2 centuries, which represents an important risk to the other satellites. The space debris issue has conducted the main Agencies to adopt mitigation guidelines with the objective to reduce the population of objects orbiting the Earth In 1999 CNES published its own standard presenting the management, design and operation rules. This document is fully compliant with the IADC mitigation guidelines approved in 2002 by 11 space Agencies or countries and submitted to UNCOPUOS in February 2003 The space debris mitigation requirements expressed in the CNES standard and in the IADC mitigation guidelines require to limit the orbital lifetime in LEO to less than 25 years. Although not applicable to Spot 1, launched earlier in 1986, this rule was voluntarily applied and the decision to de-orbit Spot 1 was taken. The corresponding operations, performed in November 2003, were complex due to a large number of constraints such as the unusual flight domain, the on-board sensors, the short ground station visibilities or the incertitudes relative to the estimation of the remaining fuel in the tanks. In the preliminary phase, the orbit was lowered 15 km below the operational orbit to avoid any collision risk with the other Spot satellites. Then, in a second phase, a series of 8 apogee boosts lowered progressively the perigee altitude to 619 km. Finally, a large last manoeuvre was performed to empty the tanks and to reduce at maximum the perigee altitude. A succession of 4 ground stations visibilities allowed a real time monitoring of this manoeuvre. In particular the effect of gas bubbles in the propulsion system was observed through telemetry confirming the fuel exhausting. The batteries were then disconnected and the telemetry emitter was switched off. According to the obtained perigee altitude, the on-orbit lifetime of Spot

  7. Spot 1 end of life disposition manoeuvres

    NASA Astrophysics Data System (ADS)

    Alby, F.

    The Earth observation satellites of the SPOT family are on a Sun-synchronous orbit at 822 km altitude. The on-orbit lifetime of objects at this altitude is about two centuries, which represents an important risk to the other satellites. The space debris issue has caused the main Agencies to adopt mitigation guidelines with the objective to reduce the population of objects orbiting the Earth. In 1999, CNES published its own standard presenting the management, design and operation rules. This document is fully compliant with the Inter Agency Space Debris Coordination Committee (IADC) mitigation guidelines approved in 2002 by 11 Space Agencies and submitted to United Nations Committee on Peaceful Uses of Outer Space in February 2003. The space debris mitigation requirements expressed in the CNES standard and in the IADC mitigation guidelines limit the orbital lifetime in LEO to less than 25 years. Although not applicable to Spot 1, launched earlier in 1986, this rule was voluntarily applied and the decision to deorbit Spot 1 was taken. The corresponding operations, performed in November 2003, were complex due to a large number of constraints such as the unusual flight domain, the on-board sensors, the short ground station visibilities or the uncertainties in the estimation of the remaining fuel in the tanks. In the preliminary phase, the orbit was lowered 15 km below the operational orbit to avoid any collision risk with the other Spot satellites. Then, in a second phase, a series of eight apogee boosts lowered progressively the perigee altitude to 619 km. Finally, a large last manoeuvre was performed to empty the tanks and to reduce the perigee altitude the maximum amount. A succession of four ground stations visibilities allowed a real time monitoring of this manoeuvre. In particular the effect of gas bubbles in the propulsion system was observed through telemetry confirming the fuel depletion. The batteries were then disconnected and the telemetry emitter was

  8. Protein Drug Targets of Lavandula angustifolia on treatment of Rat Alzheimer's Disease.

    PubMed

    Zali, Hakimeh; Zamanian-Azodi, Mona; Rezaei Tavirani, Mostafa; Akbar-Zadeh Baghban, Alireza

    2015-01-01

    Different treatment strategies of Alzheimer's disease (AD) are being studied for treating or slowing the progression of AD. Many pharmaceutically important regulation systems operate through proteins as drug targets. Here, we investigate the drug target proteins in beta-amyloid (Aβ) injected rat hippocampus treated with Lavandula angustifolia (LA) by proteomics techniques. The reported study showed that lavender extract (LE) improves the spatial performance in AD animal model by diminishing Aβ production in histopathology of hippocampus, so in this study neuroprotective proteins expressed in Aβ injected rats treated with LE were scrutinized. Rats were divided into three groups including normal, Aβ injected, and Aβ injected that was treated with LE. Protein expression profiles of hippocampus tissue were determined by two-dimensional electrophoresis (2DE) method and dysregulated proteins such as Snca, NF-L, Hspa5, Prdx2, Apoa1, and Atp5a1were identified by MALDI-TOF/TOF. KEGG pathway and gene ontology (GO) categories were used by searching DAVID Bioinformatics Resources. All detected protein spots were used to determine predictedinteractions with other proteins in STRING online database. Different isoforms of important protein, Snca that exhibited neuroprotective effects by anti-apoptotic properties were expressed. NF-L involved in the maintenance of neuronal caliber. Hspa5 likewise Prdx2 displays as anti-apoptotic protein that Prdx2 also involved in the neurotrophic effects. Apoa1 has anti-inflammatory activity and Atp5a1, produces ATP from ADP. To sum up, these proteins as potential drug targets were expressed in hippocampus in response to effective components in LA may have therapeutic properties for the treatment of AD and other neurodegenerative diseases. PMID:25561935

  9. Friction Stir Spot Welding of Advanced High Strength Steels

    SciTech Connect

    Hovanski, Yuri; Grant, Glenn J.; Santella, M. L.

    2009-11-13

    Friction stir spot welding techniques were developed to successfully join several advanced high strength steels. Two distinct tool materials were evaluated to determine the effect of tool materials on the process parameters and joint properties. Welds were characterized primarily via lap shear, microhardness, and optical microscopy. Friction stir spot welds were compared to the resistance spot welds in similar strength alloys by using the AWS standard for resistance spot welding high strength steels. As further comparison, a primitive cost comparison between the two joining processes was developed, which included an evaluation of the future cost prospects of friction stir spot welding in advanced high strength steels.

  10. Superluminal Sweeping Spot Pair Events in Astronomical Settings

    NASA Astrophysics Data System (ADS)

    Nemiroff, Robert J.

    2015-01-01

    Sweeping beams of light can cast spots that move superluminally across scattering surfaces. Such faster-than-light speeds are well-known phenomena that do not violate special relativity. It is shown that under certain circumstances, superluminal spot pair creation and annihilation events can occur that provide unique information to observers. These spot pair events are not particle pair events -- they are the sudden creation or annihilation of a pair of relatively illuminated spots on a scattering surface. Astronomical settings where superluminal spot pairs might be found include Earth's Moon, passing asteroids, pulsars, and variable nebula. Potentially recoverable information includes three dimensional imaging, relative geometric size factors, and distances.

  11. SPOT HRVIR: A significant improvement of high resolution visible SPOT camera to i.r. wavelengths

    NASA Astrophysics Data System (ADS)

    Jouan, J.; Reulet, J. F.; Costes, G.

    Since March 1986, the SPOT-HRV cameras are imaging the Earth in a 10 m resolution panchromatic mode and three 20 m resolution spectral modes all in the visible and near infra-red wavelengths. The interest of medium i.r. imaging for observing vegetation has raised in the past and the implementation of a 1.6 μm band was decided by CNES for SPOT 4. New 3000 elements detector matrix had to be developed. This work is nearly completed now through a contract placed at Thomson by CNES. In parallel, the focal plane of the previous HRV cameras has been completely redesigned and the video electronics has also been significantly improved taking into account both some problems identified on SPOT 1 in orbit and the implementation of the MIR band. A significant change in integration and test is introduced by the operating temperature of the MIR detectors to be accurately controlled at 5°C and a calibration of the whole instrument in vacuum is foreseen. Following a presentation of HRV-SPOT 1 main flight results, technical and programmatical points of the SPOT 4 HRVIR situation is presented in the paper.

  12. Amorphous-silicon module hot-spot testing

    NASA Technical Reports Server (NTRS)

    Gonzalez, C. C.

    1985-01-01

    Hot spot heating occurs when cell short-circuit current is lower than string operating current. Amorphous cell hot spot are tested to develop the techniques required for performing reverse bias testing of amorphous cells. Also, to quantify the response of amorphous cells to reverse biasing. Guidelines are developed from testing for reducing hot spot susceptibility of amorphous modules and to develop a qualification test for hot spot testing of amorphous modules. It is concluded that amorphous cells undergo hot spot heating similarly to crystalline cells. Comparison of results obtained with submodules versus actual modules indicate heating levels lower in actual modules. Module design must address hot spot testing and hot spot qualification test conducted on modules showed no instabilities and minor cell erosion.

  13. Dynamic focal spots registration algorithm for freeform surface measurement

    NASA Astrophysics Data System (ADS)

    Guo, Wenjiang; Zhao, Liping; Chen, I.-Ming

    2013-06-01

    In a wavefront sensing system, the raw data for surface reconstruction, either the slope matrix or curvature matrix, is obtained through centroiding on the focal spot images. Centroiding is to calculate the first moment within a certain area of interest, which encloses the focal spot. As the distribution of focal spots is correlated to the surface sampling condition, while a uniform rectangular grid is good enough to register all the focal spots of a uniformly sampled near flat surface, the focal spots of aspherical or freeform surfaces have varying shapes and sizes depending on the surface geometry. In this case, the normal registration method is not applicable. This paper proposed a dynamic focal spots registration algorithm to automatically analyze the image, identify and register every focal spot for centroiding at one go. Through experiment on a freeform surface with polynomial coefficients up to 10th order, the feasibility and effectiveness of the proposed algorithm is proved.

  14. Star spot location estimation using Kalman filter for star tracker.

    PubMed

    Liu, Hai-bo; Yang, Jian-kun; Wang, Jiong-qi; Tan, Ji-chun; Li, Xiu-jian

    2011-04-20

    Star pattern recognition and attitude determination accuracy is highly dependent on star spot location accuracy for the star tracker. A star spot location estimation approach with the Kalman filter for a star tracker has been proposed, which consists of three steps. In the proposed approach, the approximate locations of the star spots in successive frames are predicted first; then the measurement star spot locations are achieved by defining a series of small windows around each predictive star spot location. Finally, the star spot locations are updated by the designed Kalman filter. To confirm the proposed star spot location estimation approach, the simulations based on the orbit data of the CHAMP satellite and the real guide star catalog are performed. The simulation results indicate that the proposed approach can filter out noises from the measurements remarkably if the sampling frequency is sufficient. PMID:21509065

  15. A proteomic-based approach for the characterization of some major structural proteins involved in host-parasite relationships from the silkworm parasite Nosema bombycis (Microsporidia).

    PubMed

    Wang, Jian-Yang; Chambon, Christophe; Lu, Chang-De; Huang, Ke-Wei; Vivarès, Christian P; Texier, Catherine

    2007-05-01

    Nosema bombycis is the causative agent of the silkworm Bombyx mori pebrine disease which inflicts severe worldwide economical losses in sericulture. Little is known about host-parasite interactions at the molecular level for this spore-forming obligate intracellular parasite which belongs to the fungi-related Microsporidia phylum. Major microsporidian structural proteins from the spore wall (SW) and the polar tube (PT) are known to be involved in host invasion. We developed a proteomic-based approach to identify few N. bombycis proteins belonging to these cell structures. Protein extraction protocols were optimized and four N. bombycis spore protein extracts were compared by SDS-PAGE and 2-DE to establish complementary proteomic profiles. Three proteins were shown to be located at the parasite SW. Moreover, 17 polyclonal antibodies were raised against major N. bombycis proteins from all extracts, and three spots were shown to correspond to polar tube proteins (PTPs) by immunofluorescent assay and transmission electron microscopy immunocytochemistry on cryosections. Specific patterns for each PTP were obtained by MALDI-TOF-MS and MS/MS. Peptide sequence tags were deduced by de novo sequencing using Peaks Online and DeNovoX, then evaluated by MASCOT and SEQUEST searches. Identification parameters were higher than false-positive hits, strengthening our strategy that could be enlarged to a nongenomic context. PMID:17407187

  16. Prevalence of antibodies to spotted fever group rickettsiae along the eastern coast of the Adriatic sea.

    PubMed Central

    Radulovic, S; Walker, D H; Weiss, K; Dzelalija, B; Morovic, M

    1993-01-01

    A seroepidemiological survey in coastal Croatia detected antibodies reactive with Rickettsia conorii in 4.2% of sera by immunofluorescence assay and in 5.0% of sera by enzyme immunoassay. Western immunoblotting demonstrated antibodies to the 120-kDa surface protein in all 20 positive serum samples examined and to rickettsial lipopolysaccharide in 3 of these serum samples. Humans in this area are clearly being exposed to spotted fever rickettsiae. PMID:8370756

  17. Humoral immune response of the small-spotted catshark, Scyliorhinus canicula.

    PubMed

    Crouch, Kathryn; Smith, Lauren E; Williams, Rebecca; Cao, Wei; Lee, Mike; Jensen, Allan; Dooley, Helen

    2013-05-01

    Cartilaginous fishes are the oldest group in which an adaptive immune system based on immunoglobulin-superfamily members is found. This manuscript compares humoral immune function in small-spotted catshark (Scyliorhinus canicula) with that described for spiny dogfish (Squalus acanthias), another member of the Squalomorphi superorder, and nurse shark, the model for humoral immunity in elasmobranchs and a member of the Galeomorphi superorder. Although small-spotted catshark and nurse shark are separated by over 200 million years we found that immunoglobulin isoforms are well conserved between the two species. However, the plasma protein profile of small-spotted catshark was most similar to that of spiny dogfish, with low levels of pentameric IgM, and IgNAR present as a multimer in plasma rather than a monomer. We show that an antigen-specific monomeric IgM response, with a profile similar to that described previously for nurse sharks, can be raised in small-spotted catshark. Lacking polyclonal or monoclonal antibody reagents for detecting catshark IgNAR we investigated phage-display and recombinant Fc-fusion protein expression as alternative methods to look for an antigen-specific response for this isotype. However, we could find no evidence of an antigen-specific IgNAR in the animals tested using either of these techniques. Thus, unlike nurse sharks where antigen-specific monomeric IgM and IgNAR appear together, it seems there may be a temporal or complete 'uncoupling' of these isotypes during a humoral response in the small-spotted catshark. PMID:23439398

  18. Jupiter's Great Red Spot in Cassini image

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This true color image of Jupiter, taken by NASA's Cassini spacecraft, is composed of three images taken in the blue, green and red regions of the spectrum. All images were taken from a distance of 77.6 million kilometers (48.2 million miles) on Oct. 8, 2000.

    Different chemical compositions of the cloud particles lead to different colors. The cloud patterns reflect different physical conditions -- updrafts and downdrafts -- in which the clouds form. The bluish areas are believed to be regions devoid of clouds and covered by high haze.

    The Great Red Spot (below and to the right of center) is a giant atmospheric storm as wide as two Earths and over 300 years old, with peripheral winds of 483 kilometers per hour (300 miles per hour). This image shows that it is trailed to the north by a turbulent region, caused by atmospheric flow around the spot.

    The bright white spots in this region are lightning storms, which were seen by NASA's Galileo spacecraft when it photographed the night side of Jupiter. Cassini will track these lightning storms and measure their lifetimes and motions when it passes Jupiter in late December and looks back on the darkside of the planet. Cassini is currently en route to its ultimate destination, Saturn.

    The resolution is 466 kilometers (290 miles) per picture element.

    Cassini is a cooperative project of NASA, the European Space Agency and the Italian Space Agency. The Jet Propulsion Laboratory, a division of the California Institute of Technology in Pasadena, Calif., manages the Cassini mission for NASA's Office of Space Science, Washington, D.C.

  19. Genetics of tan spot resistance in wheat.

    PubMed

    Faris, Justin D; Liu, Zhaohui; Xu, Steven S

    2013-09-01

    Tan spot is a devastating foliar disease of wheat caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis. Much has been learned during the past two decades about the genetics of wheat-P. tritici-repentis interactions. Research has shown that the fungus produces at least three host-selective toxins (HSTs), known as Ptr ToxA, Ptr ToxB, and Ptr ToxC, that interact directly or indirectly with the products of the dominant host genes Tsn1, Tsc2, and Tsc1, respectively. The recent cloning and characterization of Tsn1 provided strong evidence that the pathogen utilizes HSTs to subvert host resistance mechanisms to cause disease. However, in addition to host-HST interactions, broad-spectrum, race non-specific resistance QTLs and recessively inherited qualitative 'resistance' genes have been identified. Molecular markers suitable for marker-assisted selection against HST sensitivity genes and for race non-specific resistance QTLs have been developed and used to generate adapted germplasm with good levels of tan spot resistance. Future research is needed to identify novel HSTs and corresponding host sensitivity genes, determine if the recessively inherited resistance genes are HST insensitivities, extend the current race classification system to account for new HSTs, and determine the molecular basis of race non-specific resistance QTLs and their relationships with host-HST interactions at the molecular level. Necrotrophic pathogens such as P. tritici-repentis are likely to become increasingly significant under a changing global climate making it imperative to further characterize the wheat-P. tritici-repentis pathosystem and develop tan spot resistant wheat varieties. PMID:23884599

  20. Neptune - Changes in Great Dark Spot

    NASA Technical Reports Server (NTRS)

    1989-01-01

    These images show changes in the clouds around Neptune's Great Dark Spot (GDS) over a four and one-half-day period. From top to bottom the images show successive rotations of the planet an interval of about 18 hours. The GDS is at a mean latitude of 20 degrees south, and covers about 30 degrees of longitude. The violet filter of the Voyager narrow angle camera was used to produce these images at distances ranging from 17 million kilometers (10.5 million miles) at the top, to 10 million kilometers (6.2 million miles) at bottom. The images have been mapped on to a rectangular latitude longitude grid to remove the effects of changing viewing geometry and the changing distance to Neptune. The sequence shows a large change in the western end (left side) of the GDS, where a dark extension apparent in the earlier images converges into an extended string of small dark spots over the next five rotations. This 'string of beads' extends from the GDS at a surprisingly large angle relative to horizontal lines of constant latitude. The large bright cloud at the southern (bottom) border of the GDS is a more or less permanent companion of the GDS. The apparent motion of smaller clouds at the periphery of the GDS suggests a counterclockwise rotation of the GDS reminiscent of flow around the Great Red Spot in Jupiter's atmosphere. This activity of the GDS is surprising because the total energy flux from the sun and from Neptune's interior is only 5 percent as large as the total energy flux on Jupiter.

  1. Identification of proteins involved in desiccation tolerance in the red seaweed Pyropia orbicularis (Rhodophyta, Bangiales).

    PubMed

    López-Cristoffanini, Camilo; Zapata, Javier; Gaillard, Fanny; Potin, Philippe; Correa, Juan A; Contreras-Porcia, Loretto

    2015-12-01

    Extreme reduction in cellular water content leads to desiccation, which, if persistent, affects the physiology of organisms, mainly through oxidative stress. Some organisms are highly tolerant to desiccation, including resurrection plants and certain intertidal seaweeds. One such species is Pyropia orbicularis, a rhodophycean that colonizes upper intertidal zones along the Chilean coast. Despite long, daily periods of air exposure due to tides, this alga is highly tolerant to desiccation. The present study examined the proteome of P. orbicularis by 2DE and LC-MS/MS analyses to determine the proteins associated with desiccation tolerance (DT). The results showed that, under natural conditions, there were significant changes in the protein profile during low tide as compared to naturally hydrated plants at high tide. These changes were mainly in newly appeared proteins spots such as chaperones, monodehydroascorbate reductase, and manganese superoxide dismutase, among others. Previously undescribed proteins under desiccation conditions included phycobiliproteins, glyoxalase I, and phosphomannomutase. These changes evidenced that several physiological responses involved in DT are activated during low tide, including decreased photosynthetic activity, increased antioxidant capacity, and the preservation of cell physiology by regulating water content, cell wall structure, and cell volume. Similar responses have been observed in resurrection plants and bryophytes exposed to desiccation. Therefore, the coordinated activation of different desiccation tolerance pathways in P. orbicularis could explain the successful biological performance of this seaweed in the upper intertidal rocky zones. PMID:26154304

  2. False Color Mosaic Great Red Spot

    NASA Technical Reports Server (NTRS)

    1996-01-01

    False color representation of Jupiter's Great Red Spot (GRS) taken through three different near-infrared filters of the Galileo imaging system and processed to reveal cloud top height. Images taken through Galileo's near-infrared filters record sunlight beyond the visible range that penetrates to different depths in Jupiter's atmosphere before being reflected by clouds. The Great Red Spot appears pink and the surrounding region blue because of the particular color coding used in this representation. Light reflected by Jupiter at a wavelength (886 nm) where methane strongly absorbs is shown in red. Due to this absorption, only high clouds can reflect sunlight in this wavelength. Reflected light at a wavelength (732 nm) where methane absorbs less strongly is shown in green. Lower clouds can reflect sunlight in this wavelength. Reflected light at a wavelength (757 nm) where there are essentially no absorbers in the Jovian atmosphere is shown in blue: This light is reflected from the deepest clouds. Thus, the color of a cloud in this image indicates its height. Blue or black areas are deep clouds; pink areas are high, thin hazes; white areas are high, thick clouds. This image shows the Great Red Spot to be relatively high, as are some smaller clouds to the northeast and northwest that are surprisingly like towering thunderstorms found on Earth. The deepest clouds are in the collar surrounding the Great Red Spot, and also just to the northwest of the high (bright) cloud in the northwest corner of the image. Preliminary modeling shows these cloud heights vary over 30 km in altitude. This mosaic, of eighteen images (6 in each filter) taken over a 6 minute interval during the second GRS observing sequence on June 26, 1996, has been map-projected to a uniform grid of latitude and longitude. North is at the top.

    Launched in October 1989, Galileo entered orbit around Jupiter on December 7, 1995. The spacecraft's mission is to conduct detailed studies of the giant planet

  3. Protein Profile in Corpus Luteum during Pregnancy in Korean Native Cows

    PubMed Central

    Chung, H. J.; Kim, K. W.; Han, D. W.; Lee, H. C.; Yang, B. C.; Chung, H. K.; Shim, M. R.; Choi, M. S.; Jo, E. B.; Jo, Y. M.; Oh, M. Y.; Jo, S. J.; Hong, S. K.; Park, J. K.; Chang, W. K.

    2012-01-01

    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. PMID:25049514

  4. A 'turbulent spot' in an axisymmetric free shear layer. II

    NASA Astrophysics Data System (ADS)

    Hussain, A. K. M. F.; Kleis, S. J.; Sokolov, M.

    1980-05-01

    The paper considers a turbulent spot in an axisymmetric free shear layer induced by a spark triggered in the boundary layer. The spot was educed by the method of iterative alignment of individual realizations through maximization of cross-relation between individual realizations and ensemble average. The dynamics of the turbulent mixing-layer spot, whose signature is buried in the large-amplitude random fluctuations, is much more complicated than that of the boundary layer spot. The spacing between sparks was so chosen that at a measurement station the passage time of a spot was less than 4% of the interval between the spots; thus, there was no interaction between two induced spots, and on the front or the back of the spot, the phase-average properties approach the constant time-mean values. It is shown that the spot structure plays a dominant role in entrainment and vorticity transport, and that the coherent (spot) structure vorticity is not significantly larger than the mixing-layer mean vorticity.

  5. Spot addressing for microarray images structured in hexagonal grids.

    PubMed

    Giannakeas, Nikolaos; Kalatzis, Fanis; Tsipouras, Markos G; Fotiadis, Dimitrios I

    2012-04-01

    In this work, an efficient method for spot addressing in images, which are generated by the scanning of hexagonal structured microarrays, is proposed. Initially, the blocks of the image are separated using the projections of the image. Next, all the blocks of the image are processed separately for the detection of each spot. The spot addressing procedure begins with the detection of the high intensity objects, which are probably the spots of the image. Next, the Growing Concentric Hexagon algorithm, which uses the properties of the hexagonal grid, is introduced for the detection of the non-hybridized spots. Finally, the Voronoi diagram is applied to the centers of the detected spots for the gridding of the image. The method is evaluated using spots generated from the scanning of the Beadchip of Illumina, which is used for the detection of Single Nucleotide Polymorphisms in the human genome, and uses hexagonal structure for the location of the spots. For the evaluation, the detected centers for each of the spot in the image are compared to the centers of the annotation, obtaining up to 98% accuracy for the spot addressing procedure. PMID:21924515

  6. The fractal nature of vacuum arc cathode spots

    SciTech Connect

    Anders, Andre

    2005-05-27

    Cathode spot phenomena show many features of fractals, for example self-similar patterns in the emitted light and arc erosion traces. Although there have been hints on the fractal nature of cathode spots in the literature, the fractal approach to spot interpretation is underutilized. In this work, a brief review of spot properties is given, touching the differences between spot type 1 (on cathodes surfaces with dielectric layers) and spot type 2 (on metallic, clean surfaces) as well as the known spot fragment or cell structure. The basic properties of self-similarity, power laws, random colored noise, and fractals are introduced. Several points of evidence for the fractal nature of spots are provided. Specifically power laws are identified as signature of fractal properties, such as spectral power of noisy arc parameters (ion current, arc voltage, etc) obtained by fast Fourier transform. It is shown that fractal properties can be observed down to the cutoff by measurement resolution or occurrence of elementary steps in physical processes. Random walk models of cathode spot motion are well established: they go asymptotically to Brownian motion for infinitesimal step width. The power spectrum of the arc voltage noise falls as 1/f {sup 2}, where f is frequency, supporting a fractal spot model associated with Brownian motion.

  7. Effects of spot size and spot spacing on lateral penumbra reduction when using a dynamic collimation system for spot scanning proton therapy

    NASA Astrophysics Data System (ADS)

    Hyer, Daniel E.; Hill, Patrick M.; Wang, Dongxu; Smith, Blake R.; Flynn, Ryan T.

    2014-11-01

    The purpose of this work was to investigate the reduction in lateral dose penumbra that can be achieved when using a dynamic collimation system (DCS) for spot scanning proton therapy as a function of two beam parameters: spot size and spot spacing. This is an important investigation as both values impact the achievable dose distribution and a wide range of values currently exist depending on delivery hardware. Treatment plans were created both with and without the DCS for in-air spot sizes (σair) of 3, 5, 7, and 9 mm as well as spot spacing intervals of 2, 4, 6 and 8 mm. Compared to un-collimated treatment plans, the plans created with the DCS yielded a reduction in the mean dose to normal tissue surrounding the target of 26.2-40.6% for spot sizes of 3-9 mm, respectively. Increasing the spot spacing resulted in a decrease in the time penalty associated with using the DCS that was approximately proportional to the reduction in the number of rows in the raster delivery pattern. We conclude that dose distributions achievable when using the DCS are comparable to those only attainable with much smaller initial spot sizes, suggesting that the goal of improving high dose conformity may be achieved by either utilizing a DCS or by improving beam line optics.

  8. Effects of spot size and spot spacing on lateral penumbra reduction when using a dynamic collimation system for spot scanning proton therapy.

    PubMed

    Hyer, Daniel E; Hill, Patrick M; Wang, Dongxu; Smith, Blake R; Flynn, Ryan T

    2014-11-21

    The purpose of this work was to investigate the reduction in lateral dose penumbra that can be achieved when using a dynamic collimation system (DCS) for spot scanning proton therapy as a function of two beam parameters: spot size and spot spacing. This is an important investigation as both values impact the achievable dose distribution and a wide range of values currently exist depending on delivery hardware. Treatment plans were created both with and without the DCS for in-air spot sizes (σair) of 3, 5, 7, and 9 mm as well as spot spacing intervals of 2, 4, 6 and 8 mm. Compared to un-collimated treatment plans, the plans created with the DCS yielded a reduction in the mean dose to normal tissue surrounding the target of 26.2-40.6% for spot sizes of 3-9 mm, respectively. Increasing the spot spacing resulted in a decrease in the time penalty associated with using the DCS that was approximately proportional to the reduction in the number of rows in the raster delivery pattern. We conclude that dose distributions achievable when using the DCS are comparable to those only attainable with much smaller initial spot sizes, suggesting that the goal of improving high dose conformity may be achieved by either utilizing a DCS or by improving beam line optics. PMID:25330783

  9. Improving Trichoderma reesei Cel7B thermostability by targeting the weak spots.

    PubMed

    Zhang, Shujun; Wang, Yefei; Song, Xiangfei; Hong, Jingbo; Zhang, Yu; Yao, Lishan

    2014-10-27

    For proteins that denature irreversibly, the denaturation is typically triggered by a partial unfolding, followed by a permanent change (e.g., aggregation). The regions that initiate the partial unfolding are named "weak spots". In this work, a molecular dynamics (MD) simulation and data analysis protocol is developed to identify the weak spots of Trichoderma reesei Cel7B, an important endoglucanase in cellulose hydrolysis, through assigning the local melting temperature (Tmp) to individual residue pairs. To test the predicted weak spots, a total of eight disulfide bonds were designed in these regions and all enhanced the enzyme thermostability. The increased stability, quantified by ΔT50 (which is the T50 difference between the mutant and the wild type enzyme), is negatively correlated with the MD-predicted Tmp, demonstrating the effectiveness of the protocol and highlighting the importance of the weak spots. Strengthening interactions in these regions proves to be a useful strategy in improving the thermostability of Tr. Cel7B. PMID:25286389

  10. Comparative proteomic analysis of Salmonella enterica serovar Typhimurium ppGpp-deficient mutant to identify a novel virulence protein required for intracellular survival in macrophages

    PubMed Central

    2010-01-01

    Background The global ppGpp-mediated stringent response in pathogenic bacteria plays an important role in the pathogenesis of bacterial infections. In Salmonella enterica serovar Typhimurium (S. Typhimurium), several genes, including virulence genes, are regulated by ppGpp when bacteria are under the stringent response. To understand the control of virulence genes by ppGpp in S. Typhimurium, agarose 2-dimensional electrophoresis (2-DE) combined with mass spectrometry was used and a comprehensive 2-DE reference map of amino acid-starved S. Typhimurium strain SH100, a derivative of ATCC 14028, was established. Results Of the 366 examined spots, 269 proteins were successfully identified. The comparative analysis of the wild-type and ppGpp0 mutant strains revealed 55 proteins, the expression patterns of which were affected by ppGpp. Using a mouse infection model, we further identified a novel virulence-associated factor, STM3169, from the ppGpp-regulated and Salmonella-specific proteins. In addition, Salmonella strains carrying mutations in the gene encoding STM3169 showed growth defects and impaired growth within macrophage-like RAW264.7 cells. Furthermore, we found that expression of stm3169 was controlled by ppGpp and SsrB, a response regulator of the two-component system located on Salmonella pathogenicity island 2. Conclusions A proteomic approach using a 2-DE reference map can prove a powerful tool for analyzing virulence factors and the regulatory network involved in Salmonella pathogenesis. Our results also provide evidence of a global response mediated by ppGpp in S. enterica. PMID:21176126

  11. Steady state protein levels in Geobacter metallireducens grown with Iron (III) citrate or nitrate as terminal electron acceptor.

    SciTech Connect

    Ahrendt, A. J.; Tollaksen, S. L.; Lindberg, C.; Zhu, W.; Yates, J. R., III; Nevin, K. P.; Lovley, D.; Giometti, C. S.; Biosciences Division; The Scripps Research Inst.; Univ. of Massachusetts

    2007-01-01

    Geobacter species predominate in aquatic sediments and submerged soils where organic carbon sources are oxidized with the reduction of Fe(III). The natural occurrence of Geobacter in some waste sites suggests this microorganism could be useful for bioremediation if growth and metabolic activity can be regulated. 2-DE was used to monitor the steady state protein levels of Geobacter metallireducens grown with either Fe(III) citrate or nitrate to elucidate metabolic differences in response to different terminal electron acceptors present in natural environments populated by Geobacter. Forty-six protein spots varied significantly in abundance (p<0.05) between the two growth conditions; proteins were identified by tryptic peptide mass and peptide sequence determined by MS/MS. Enzymes involved in pyruvate metabolism and the tricarboxylic acid (TCA) cycle were more abundant in cells grown with Fe(III) citrate, while proteins associated with nitrate metabolism and sensing cellular redox status along with several proteins of unknown function were more abundant in cells grown with nitrate. These results indicate a higher level of flux through the TCA cycle in the presence of Fe(III) compared to nitrate. The oxidative stress response observed in previous studies of Geobacter sulfurreducens grown with Fe(III) citrate was not seen in G. metallireducens.

  12. SPOT4 Operational Control Center (CMP)

    NASA Technical Reports Server (NTRS)

    Zaouche, G.

    1993-01-01

    CNES(F) is responsible for the development of a new generation of Operational Control Center (CMP) which will operate the new heliosynchronous remote sensing satellite (SPOT4). This Operational Control Center takes large benefit from the experience of the first generation of control center and from the recent advances in computer technology and standards. The CMP is designed for operating two satellites all the same time with a reduced pool of controllers. The architecture of this CMP is simple, robust, and flexible, since it is based on powerful distributed workstations interconnected through an Ethernet LAN. The application software uses modern and formal software engineering methods, in order to improve quality and reliability, and facilitate maintenance. This software is table driven so it can be easily adapted to other operational needs. Operation tasks are automated to the maximum extent, so that it could be possible to operate the CMP automatically with very limited human interference for supervision and decision making. This paper provides an overview of the SPOTS mission and associated ground segment. It also details the CMP, its functions, and its software and hardware architecture.

  13. Ammonium Hydrosulfide and Jupiter's Great Red Spot

    NASA Astrophysics Data System (ADS)

    Loeffler, M. J.; Hudson, R.; Chanover, N.; Simon, A. A.

    2014-12-01

    The color and composition of Jupiter's Great Red Spot (GRS) has been debated for more than a century. While there are numerous hypotheses for the origin of Jupiter's GRS, recent work suggests that the GRS's color could originate from multiple components (Carlson et al., 2012; Simon et al., submitted). In light of this, we have recently begun conducting in situ laboratory experiments that test whether ammonium hydrosulfide, NH4SH, or its radiation decomposition products contribute to the GRS spectrum. In this presentation, we will discuss some of our most recent results, where we have studied the stability of NH4SH samples as a function of temperature using infrared and mass spectrometry. Funding for this work has been provided by NASA's Planetary Atmospheres and Outer Planets Research programs. ReferencesCarlson, R. W., K. H. Baines, M. S. Anderson, G. Filacchione. Chromophores from photolyzed ammonia reacting with acetylene: Application to Jupiter's Great Red Spot, DPS, 44, 2012. Simon, A. A., J. Legarreta, F. Sanz-Requena, S. Perez-Hoyos, E. Garcia-Melendo, R. W. Carlson. Spectral Comparison and Stability of Red Regions on Jupiter. J. Geophys. Res. - Planets, submitted.

  14. Spotting words in handwritten Arabic documents

    NASA Astrophysics Data System (ADS)

    Srihari, Sargur; Srinivasan, Harish; Babu, Pavithra; Bhole, Chetan

    2006-01-01

    The design and performance of a system for spotting handwritten Arabic words in scanned document images is presented. Three main components of the system are a word segmenter, a shape based matcher for words and a search interface. The user types in a query in English within a search window, the system finds the equivalent Arabic word, e.g., by dictionary look-up, locates word images in an indexed (segmented) set of documents. A two-step approach is employed in performing the search: (1) prototype selection: the query is used to obtain a set of handwritten samples of that word from a known set of writers (these are the prototypes), and (2) word matching: the prototypes are used to spot each occurrence of those words in the indexed document database. A ranking is performed on the entire set of test word images-- where the ranking criterion is a similarity score between each prototype word and the candidate words based on global word shape features. A database of 20,000 word images contained in 100 scanned handwritten Arabic documents written by 10 different writers was used to study retrieval performance. Using five writers for providing prototypes and the other five for testing, using manually segmented documents, 55% precision is obtained at 50% recall. Performance increases as more writers are used for training.

  15. Medical students’ attitudes and perspectives regarding novel computer-based practical spot tests compared to traditional practical spot tests

    PubMed Central

    Wijerathne, Buddhika; Rathnayake, Geetha

    2013-01-01

    Background Most universities currently practice traditional practical spot tests to evaluate students. However, traditional methods have several disadvantages. Computer-based examination techniques are becoming more popular among medical educators worldwide. Therefore incorporating the computer interface in practical spot testing is a novel concept that may minimize the shortcomings of traditional methods. Assessing students’ attitudes and perspectives is vital in understanding how students perceive the novel method. Methods One hundred and sixty medical students were randomly allocated to either a computer-based spot test (n=80) or a traditional spot test (n=80). The students rated their attitudes and perspectives regarding the spot test method soon after the test. The results were described comparatively. Results Students had higher positive attitudes towards the computer-based practical spot test compared to the traditional spot test. Their recommendations to introduce the novel practical spot test method for future exams and to other universities were statistically significantly higher. Conclusions The computer-based practical spot test is viewed as more acceptable to students than the traditional spot test. PMID:26451213

  16. Endothelin Receptor B2 (EDNRB2) Gene Is Associated with Spot Plumage Pattern in Domestic Ducks (Anas platyrhynchos).

    PubMed

    Li, Ling; Li, Dan; Liu, Li; Li, Shijun; Feng, Yanping; Peng, Xiuli; Gong, Yanzhang

    2015-01-01

    Endothelin receptor B subtype 2 (EDNRB2) is a seven-transmembrane G-protein coupled receptor. In this study, we investigated EDNRB2 gene as a candidate gene for duck spot plumage pattern according to studies of chicken and Japanese quail. The entire coding region was cloned by the reverse transcription polymerase chain reaction (RT-PCR). Sequence analysis showed that duck EDNRB2 cDNA contained a 1311 bp open reading frame and encoded a putative protein of 436 amino acids residues. The transcript shared 89%-90% identity with the counterparts in other avian species. A phylogenetic tree based on amino acid sequences showed that duck EDNRB2 was evolutionary conserved in avian clade. The entire coding region of EDNRB2 were sequenced in 20 spot and 20 non-spot ducks, and 13 SNPs were identified. Two of them (c.940G>A and c.995G>A) were non-synonymous substitutions, and were genotyped in 647 ducks representing non-spot and spot phenotypes. The c.995G>A mutation, which results in the amino acid substitution of Arg332His, was completely associated with the spot phenotype: all 152 spot ducks were carriers of the AA genotype and the other 495 individuals with non-spot phenotype were carriers of GA or GG genotype, respectively. Segregation in 17 GA×GG and 22 GA×GA testing combinations confirmed this association since the segregation ratios and genotypes of the offspring were in agreement with the hypothesis. In order to investigate the underlying mechanism of the spot phenotype, MITF gene was used as cell type marker of melanocyte progenitor cells while TYR and TYRP1 gene were used as cell type markers of mature melanocytes. Transcripts of MITF, TYR and TYRP1 gene with expected size were identified in all pigmented skin tissues while PCR products were not obtained from non-pigmented skin tissues. It was inferred that melanocytes are absent in non-pigmented skin tissues of spot ducks. PMID:25955279

  17. Endothelin Receptor B2 (EDNRB2) Gene Is Associated with Spot Plumage Pattern in Domestic Ducks (Anas platyrhynchos)

    PubMed Central

    Li, Ling; Li, Dan; Liu, Li; Li, Shijun; Feng, Yanping; Peng, Xiuli; Gong, Yanzhang

    2015-01-01

    Endothelin receptor B subtype 2 (EDNRB2) is a seven-transmembrane G-protein coupled receptor. In this study, we investigated EDNRB2 gene as a candidate gene for duck spot plumage pattern according to studies of chicken and Japanese quail. The entire coding region was cloned by the reverse transcription polymerase chain reaction (RT-PCR). Sequence analysis showed that duck EDNRB2 cDNA contained a 1311bp open reading frame and encoded a putative protein of 436 amino acids residues. The transcript shared 89%-90% identity with the counterparts in other avian species. A phylogenetic tree based on amino acid sequences showed that duck EDNRB2 was evolutionary conserved in avian clade. The entire coding region of EDNRB2 were sequenced in 20 spot and 20 non-spot ducks, and 13 SNPs were identified. Two of them (c.940G>A and c.995G>A) were non-synonymous substitutions, and were genotyped in 647 ducks representing non-spot and spot phenotypes. The c.995G>A mutation, which results in the amino acid substitution of Arg332His, was completely associated with the spot phenotype: all 152 spot ducks were carriers of the AA genotype and the other 495 individuals with non-spot phenotype were carriers of GA or GG genotype, respectively. Segregation in 17 GA×GG and 22 GA×GA testing combinations confirmed this association since the segregation ratios and genotypes of the offspring were in agreement with the hypothesis. In order to investigate the underlying mechanism of the spot phenotype, MITF gene was used as cell type marker of melanocyte progenitor cells while TYR and TYRP1 gene were used as cell type markers of mature melanocytes. Transcripts of MITF, TYR and TYRP1 gene with expected size were identified in all pigmented skin tissues while PCR products were not obtained from non-pigmented skin tissues. It was inferred that melanocytes are absent in non-pigmented skin tissues of spot ducks. PMID:25955279

  18. Spot: A Programming Language for Verified Flight Software

    NASA Technical Reports Server (NTRS)

    Bocchino, Robert L., Jr.; Gamble, Edward; Gostelow, Kim P.; Some, Raphael R.

    2014-01-01

    The C programming language is widely used for programming space flight software and other safety-critical real time systems. C, however, is far from ideal for this purpose: as is well known, it is both low-level and unsafe. This paper describes Spot, a language derived from C for programming space flight systems. Spot aims to maintain compatibility with existing C code while improving the language and supporting verification with the SPIN model checker. The major features of Spot include actor-based concurrency, distributed state with message passing and transactional updates, and annotations for testing and verification. Spot also supports domain-specific annotations for managing spacecraft state, e.g., communicating telemetry information to the ground. We describe the motivation and design rationale for Spot, give an overview of the design, provide examples of Spot's capabilities, and discuss the current status of the implementation.

  19. A Novel Detection Platform for Shrimp White Spot Syndrome Virus Using an ICP11-Dependent Immunomagnetic Reduction (IMR) Assay

    PubMed Central

    Liu, Bing-Hsien; Lin, Yu-Chen; Ho, Chia-Shin; Yang, Che-Chuan; Chang, Yun-Tsui; Chang, Jui-Feng; Li, Chun-Yuan; Cheng, Cheng-Shun; Huang, Jiun-Yan; Lee, Yen-Fu; Hsu, Ming-Hung; Lin, Feng-Chun; Wang, Hao-Ching; Lo, Chu-Fang; Yang, Shieh-Yueh; Wang, Han-Ching

    2015-01-01

    Shrimp white spot disease (WSD), which is caused by white spot syndrome virus (WSSV), is one of the world’s most serious shrimp diseases. Our objective in this study was to use an immunomagnetic reduction (IMR) assay to develop a highly sensitive, automatic WSSV detection platform targeted against ICP11 (the most highly expressed WSSV protein). After characterizing the magnetic reagents (Fe3O4 magnetic nanoparticles coated with anti ICP11), the detection limit for ICP11 protein using IMR was approximately 2 x 10−3 ng/ml, and the linear dynamic range of the assay was 0.1~1 x 106 ng/ml. In assays of ICP11 protein in pleopod protein lysates from healthy and WSSV-infected shrimp, IMR signals were successfully detected from shrimp with low WSSV genome copy numbers. We concluded that this IMR assay targeting ICP11 has potential for detecting the WSSV. PMID:26380977

  20. Oriented Protein Nanoarrays on Block Copolymer Template.

    PubMed

    Shen, Lei; Zhu, Jintao

    2016-03-01

    Here, a simple yet robust method is developed to fabricate oriented protein nanoarrays by employing a block copolymer (BCP) template, which presents nano-scaled spot areas at high-density arrays. Unlike the conventional BCP nanolithography, the BCP platform described here resists nonspecific protein adsorption and prevents the denaturation of immobilized proteins in aqueous solution. The orderly arranged array areas are functionalized by linking chemistry which allows for the precise control of protein orientation. This approach allows us to generate potentially oriented protein nanoarrays at high-density array spots, which is useful for miniaturized nanoarrays within high-throughput proteomic applications. PMID:26785818

  1. Nondestructive spot test method for magnesium and magnesium alloys

    NASA Technical Reports Server (NTRS)

    Wilson, M. L. (Inventor)

    1973-01-01

    A method for spot test identification of magnesium and various magnesium alloys commonly used in aerospace applications is described. The spot test identification involves color codes obtained when several drops of 3 M hydrochloric acid are placed on the surface to be tested. After approximately thirty seconds, two drops of this reacted acid is transferred to each of two depressions in a spot plate for additions of other chemicals with subsequent color changes indicating magnesium or its alloy.

  2. Eye-spots in Lepidoptera attract attention in humans

    PubMed Central

    Yorzinski, Jessica L.; Platt, Michael L.; Adams, Geoffrey K.

    2015-01-01

    Many prey species exhibit defensive traits to decrease their chances of predation. Conspicuous eye-spots, concentric rings of contrasting colours, are one type of defensive trait that some species exhibit to deter predators. We examined the function of eye-spots in Lepidoptera to determine whether they are effective at deterring predators because they resemble eyes (‘eye mimicry hypothesis’) or are highly salient (‘conspicuous signal hypothesis’). We recorded the gaze behaviour of men and women as they viewed natural images of butterflies and moths as well as images in which the eye-spots of these insects were modified. The eye-spots were modified by removing them, scrambling their colours, or replacing them with elliptical or triangular shapes that had either dark or light centres. Participants were generally more likely to look at, spend more time looking at and be faster to first fixate the eye-spots of butterflies and moths that were natural compared with ones that were modified, including the elliptical eye-spots with dark centres that most resembled eyes as well as the scrambled eye-spots that had the same contrast as the natural eye-spots. Participants were most likely to look at eye-spots that were numerous, had a large surface area and were located close to the insects' heads. Participants' pupils were larger when viewing eye-spots compared with the rest of the insects' body, suggesting a greater arousal when viewing eye-spots. Our results provide some support for the conspicuous signal hypothesis (and minimal support for the eye mimicry hypothesis) and suggest that eye-spots may be effective at deterring predators because they are highly conspicuous signals that draw attention. PMID:26543589

  3. Dominant inheritance of overo spotting in paint horses.

    PubMed

    Bowling, A T

    1994-01-01

    Analysis of selected studbook records of the American Paint Horse Association, consisting of 687 foals sired by 13 overo stallions from non-overo mares, supports the inheritance of overo spotting as an autosomal dominant gene. More than one gene may control patterns registered as overo. Additional studies are necessary to explain the sporadic occurrence of overo spotting from nonspotted quarter horse parents and to confirm the inheritance of overo spotting in other breeds. PMID:8014463

  4. Measurement of nugget size of spot weld by digital shearography

    NASA Astrophysics Data System (ADS)

    Yang, Lianxiang; Samala, Praveen R.; Liu, Sheng; Long, Kah Wah; Lee, Yung-Li

    2005-08-01

    Resistance spot welding is now widely used in the fabrication of sheet metals, mainly due to the cost and time considerations. Friction stir spot welding is getting more and more acceptance in the automotive industries. Such spot welds are found in nearly all products where sheet metal is joined. Obviously the quality of the spot weld has a direct impact on the quality of the product. The most important quality target of spot welds is the size of the weld nuggets. If the weld nuggets are improperly or incompletely formed, or the area surrounding the nugget is smaller than required, the structural integrity of the entire part may be uncertain. Furthermore these inconsistencies are usually internal and are seldom visible to optical inspection. This study is focused on the quality analysis of the spot welds by using "Digital Shearography". The paper mainly focuses on developing a novel, whole field technique for non-destructive inspecting the size of spot-welds, both for the resistance spot weld and the friction stir spot weld.

  5. Long-term market brisk, spot remains sluggish

    SciTech Connect

    1996-05-01

    Spot market activity totaled almost 54,000 lbs of U3O8 equivalent. The restricted uranium spot market price range had a slight increase from a high last month of $15.60/lb U3O8 to a hgih this month of $16.00/lb U3O8. The unrestricted uranium spot market price range remained at last month`s prices for the first time in recent weeks. Spot prices for conversion and SWU also held steady at their March levels.

  6. Photovoltaic module hot spot durability design and test methods

    NASA Technical Reports Server (NTRS)

    Arnett, J. C.; Gonzalez, C. C.

    1981-01-01

    As part of the Jet Propulsion Laboratory's Low-Cost Solar Array Project, the susceptibility of fat-plate modules to hot-spot problems is investigated. Hot-spot problems arise in modules when the cells become back-biased and operate in the negative-voltage quadrant, as a result of short-circuit current mismatch, cell cracking or shadowing. The details of a qualification test for determining the capability of modules of surviving field hot-spot problems and typical results of this test are presented. In addition, recommended circuit-design techniques for improving the module and array reliability with respect to hot-spot problems are presented.

  7. Insulating behavior of magnetic spots in proton-bombarded graphite

    NASA Astrophysics Data System (ADS)

    Schindler, K.; García, N.; Esquinazi, P.; Ohldag, H.

    2008-07-01

    Kelvin probe force microscopy measurements on micrometer small magnetic spots produced by proton bombardment on bulk graphite reveal a charge transfer from the center of the spot to an external ring with potential variation on the order of 50 mV. The total charge in the spot is neutral. The results can be well understood in terms of practically unscreened potentials, an insulating property, although the nonbombarded, surrounding graphite region exhibits good conductance. Scanning transmission x-ray microscopy measurements on magnetic spots prepared on graphitic films reveal similar charge distribution. The insulating behavior is fundamental to understand the magnetism in graphite.

  8. Radiometric terrain correction of SPOT5 image

    NASA Astrophysics Data System (ADS)

    Feng, Xiuli; Zhang, Feng; Wang, Ke

    2007-06-01

    Remote sensing SPOT5 images have been widely applied to the surveying of agriculture and forest resources and to the monitoring of ecology environment of mountain areas. However, the accuracy of land-cover classification of mountain areas is often influenced by the topographical shadow effect. Radiometric terrain correction is important for this kind of application. In this study, a radiometric terrain correction model which based on the rationale of moment matching was made in ERDAS IMAGINE by using the Spatial Modeler Language. Lanxi city in China as the study area, a SPOT5 multispectral image with the spatial resolution of 10 m of that mountain area was corrected by the model. Furthermore, in order to present the advantage of this new model in radiometric terrain correction of remote sensing SPOT5 image, the traditional C correction approach was also applied to the same area to see its difference with the result of the radiometric terrain correction model. The results show that the C correction approach keeps the overall statistical characteristics of spectral bands. The mean and the standard deviation value of the corrected image are the same as original ones. However, the standard deviation value became smaller by using the radiometric terrain correction model and the mean value changed accordingly. The reason of these changes is that before the correction, the histogram of the original image is represented as the 'plus-skewness distribution' due to the relief-caused shade effect, after the correction of the model, the histogram of the image is represented as the normal distribution and the shade effect of the relief has been removed. But as for the result of the traditional C approach, the skewness of the histogram remains the same after the correction. Besides, some portions of the mountain area have been over-corrected. So in my study area, the C correction approach can't remove the shade effect of the relief ideally. The results show that the radiometric

  9. Jupiter's Great Red Spot and other vortices

    NASA Technical Reports Server (NTRS)

    Marcus, Philip S.

    1993-01-01

    A theoretical explanation of Jupiter's Great Red Spot (GRS) as the self-organization of vorticity in turbulence is presented. A number of properties of the GRS and other Jovian vortices that are unambiguous from the data are listed. The simplest possible model that explains these properties one at a time rather than in a difficult all-encompassing planetary global circulation model is presented. It is shown that Jovian vortices reflect the behavior of quasi-geostrophic (QG) vortices embedded in an east-west wind with bands of uniform potential vorticity. It is argued that most of the properties of the Jovian vortices can be easily explained and understood with QG theory. Many of the signatures of QG vortices are apparent on Voyager images. In numerical and laboratory experiments, QG vortices relax to approximately steady states like the Jovian vortices, rather than oscillating or rotating Kida ellipses.

  10. Interpretation of the Jupiter red spot. I.

    NASA Technical Reports Server (NTRS)

    Kuiper, G. P.

    1973-01-01

    The LPL research programs on Jupiter include continuing photographic coverage of the planet in color and in several wavelength bands; IR image scans especially around 5 microns; medium and high-resolution spectral studies in the photographic and the lead-sulfide regions, with laboratory comparisons; photometric and polarimetric studies; far-IR measurements at high altitudes; chemical studies designed to match formation of Jovian cloud particles; and participation in the NASA Pioneer missions. Some preliminary interpretative remarks are given which are in part suggested by the remarkable IR spectra and IR images of the earth and Mars obtained at NASA-Goddard. This leads to a discussion of the Red Spot and the White Ovals.

  11. Laboratory simulation of Jupiter's Great Red SPOT

    NASA Astrophysics Data System (ADS)

    Sommeria, J.; Meyers, S. D.; Swinney, H. L.

    1988-02-01

    The existence of isolated large stable vortices like the Great Red Spot in the turbulent atmospheres of Jupiter and Saturn is a challenging problem in fluid mechanics. To test the numerical simulation finding of Marcus (1988) that a single stable vortex develops for a wide variety of conditions in a turbulent shear flow in a rotating annulus, an experiment was conducted using a rotating annulus filled with fluid pumped in the radial direction. The annulus rotates rigidly, but the action of the Coriolis force on the radially pumped fluid produces a counterrotating jet. Coherent vortices spontaneously form in this turbulent jet, and for a wide range of rotation and pumping rates the flow evolves until only one large vortex remains.

  12. Spot and Runway Departure Advisor (SARDA)

    NASA Technical Reports Server (NTRS)

    Jung, Yoon

    2016-01-01

    Spot and Runway Departure Advisor (SARDA) is a decision support tool to assist airline ramp controllers and ATC tower controllers to manage traffic on the airport surface to significantly improve efficiency and predictability in surface operations. The core function of the tool is the runway scheduler which generates an optimal solution for runway sequence and schedule of departure aircraft, which would minimize system delay and maximize runway throughput. The presentation also discusses the latest status of NASA's current surface research through a collaboration with an airline partner, where a tool is developed for airline ramp operators to assist departure pushback operations. The presentation describes the concept of the SARDA tool and results from human-in-the-loop simulations conducted in 2012 for Dallas-Ft. Worth International Airport and 2014 for Charlotte airport ramp tower.

  13. Where Are the Hottest Spots on Earth?

    NASA Astrophysics Data System (ADS)

    Mildrexler, David J.; Zhao, Maosheng; Running, Steven W.

    2006-10-01

    The location of the hottest spot on the Earth's surface has long been a source of interest and curiosity. With images of blazing desert landscapes, several places have proudly claimed the title of `hottest place on Earth.' Death Valley, California, the hottest place in North America, held the world record air temperature of 56.7°C from 1913 to 1922, until the current world record air temperature of 58.0°C was recorded in 1922 in El Azizia, Libya. Until recently, only point-based air temperature measurements in scattered locations were available to researchers trying to understand maximum temperatures. This incomplete picture, based largely on the locations of weather stations, clearly suggested that hotter air temperatures were occurring, but measurements on the scale needed to locate the hottest place simply were not practical.

  14. Spot Spraying Reduces Herbicide Concentrations in Runoff.

    PubMed

    Melland, Alice R; Silburn, D Mark; McHugh, Allen D; Fillols, Emilie; Rojas-Ponce, Samuel; Baillie, Craig; Lewis, Stephen

    2016-05-25

    Rainfall simulator trials were conducted on sugar cane paddocks across dry-tropical and subtropical Queensland, Australia, to examine the potential for spot spraying to reduce herbicide losses in runoff. Recommended rates of the herbicides glyphosate, 2,4-D, fluoroxypyr, atrazine, and diuron were sprayed onto 0, 20, 40, 50, 70, or 100% of the area of runoff plots. Simulated rainfall was applied 2 days after spraying to induce runoff at one plant cane and three ratoon crop sites. Over 50% of all herbicides were transported in the dissolved phase of runoff, regardless of the herbicide's sediment-water partition coefficient. For most sites and herbicides, runoff herbicide concentrations decreased with decreasing spray coverage and with decreasing herbicide load in the soil and cane residues. Importantly, sites with higher infiltration prior to runoff and lower total runoff had lower runoff herbicide concentrations. PMID:26479195

  15. Fundamentals of friction stir spot welding

    NASA Astrophysics Data System (ADS)

    Badarinarayan, Harsha

    The recent spike in energy costs has been a major contributor to propel the use of light weight alloys in the transportation industry. In particular, the automotive industry sees benefit in using light weight alloys to increase fuel efficiency and enhance performance. In this context, light weight design by replacing steel with Al and/or Mg alloys have been considered as promising initiatives. The joining of structures made of light weight alloys is therefore very important and calls for more attention. Friction Stir Spot Welding (FSSW) is an evolving technique that offers several advantages over conventional joining processes. The fundamentals aspects of FSSW are systematically studied in this dissertation. The effects and influence of process inputs (weld parameters and tool geometry) on the process output (weld geometry and static strength) is studied. A Design of Experiments (DoE) is carried out to identify the effect of each process parameter on weld strength. It is found that the tool geometry, and in particular the pin profile has a significant role in determining the weld geometry (hook, stir zone size etc.) which in turn influences the failure mode and weld strength. A novel triangular pin tool geometry is proposed that suppresses the hook formation and produces welds with twice the static strength as those produced with conventional cylindrical pin tools. An experimental and numerical approach is undertaken to understand the effect of pin geometry on the material flow and failure mechanism of spot welds. In addition, key practical issues have been addressed such as quantification of tool life and a methodology to control tool plunge depth during welding. Finally, by implementing the findings of this dissertation, FSSW is successfully performed on a closure panel assembly for an automotive application.

  16. CORTICAL REPRESENTATION OF SPACE AROUND THE BLIND SPOT

    PubMed Central

    Awater, Holger; Kerlin, Jess R.; Evans, Karla K.; Tong, Frank

    2006-01-01

    The neural mechanism that mediates perceptual filling-in of the blind spot is still under discussion. One hypothesis proposes that the cortical representation of the blind spot is activated only under conditions that elicit perceptual filling-in, and requires congruent stimulation on both sides of the blind spot. Alternatively, the passive remapping hypothesis proposes that inputs from regions surrounding the blind spot infiltrate the representation of the blind spot in cortex. This theory predicts that independent stimuli presented to the left and right of the blind spot should lead to neighboring/overlapping activations in visual cortex when the blind-spot eye is stimulated, but separated activations when the fellow eye is stimulated. Using functional MRI, we directly tested the remapping hypothesis by presenting flickering checkerboard wedges to the left or right of the spatial location of the blind spot, either to the blind-spot eye or to the fellow eye. Irrespective of which eye was stimulated, we found separate activations corresponding to the left and right wedges. We identified the centroid of the activations on a cortical flat map and measured the distance between activations. Distance measures of the cortical gap across the blind spot were accurate and reliable (mean distance 6-8 mm across subjects, SD ~1 mm within subjects). Contrary to the predictions of the remapping hypothesis, cortical distances between activations to the two wedges were equally large for the blind-spot eye and fellow eye in areas V1 and V2/V3. Remapping therefore appears unlikely to account for perceptual filling-in at an early cortical level. PMID:16033933

  17. Operator- and software-related post-experimental variability and source of error in 2-DE analysis.

    PubMed

    Millioni, Renato; Puricelli, Lucia; Sbrignadello, Stefano; Iori, Elisabetta; Murphy, Ellen; Tessari, Paolo

    2012-05-01

    In the field of proteomics, several approaches have been developed for separating proteins and analyzing their differential relative abundance. One of the oldest, yet still widely used, is 2-DE. Despite the continuous advance of new methods, which are less demanding from a technical standpoint, 2-DE is still compelling and has a lot of potential for improvement. The overall variability which affects 2-DE includes biological, experimental, and post-experimental (software-related) variance. It is important to highlight how much of the total variability of this technique is due to post-experimental variability, which, so far, has been largely neglected. In this short review, we have focused on this topic and explained that post-experimental variability and source of error can be further divided into those which are software-dependent and those which are operator-dependent. We discuss these issues in detail, offering suggestions for reducing errors that may affect the quality of results, summarizing the advantages and drawbacks of each approach. PMID:21394601

  18. Identification of Host-Immune Response Protein Candidates in the Sera of Human Oral Squamous Cell Carcinoma Patients

    PubMed Central

    Chen, Yeng; Azman, Siti Nuraishah; Kerishnan, Jesinda P.; Zain, Rosnah Binti; Chen, Yu Nieng; Wong, Yin-Ling; Gopinath, Subash C. B.

    2014-01-01

    One of the most common cancers worldwide is oral squamous cell carcinoma (OSCC), which is associated with a significant death rate and has been linked to several risk factors. Notably, failure to detect these neoplasms at an early stage represents a fundamental barrier to improving the survival and quality of life of OSCC patients. In the present study, serum samples from OSCC patients (n = 25) and healthy controls (n = 25) were subjected to two-dimensional gel electrophoresis (2-DE) and silver staining in order to identify biomarkers that might allow early diagnosis. In this regard, 2-DE spots corresponding to various up- and down-regulated proteins were sequenced via high-resolution MALDI-TOF mass spectrometry and analyzed using the MASCOT database. We identified the following differentially expressed host-specific proteins within sera from OSCC patients: leucine-rich α2-glycoprotein (LRG), alpha-1-B-glycoprotein (ABG), clusterin (CLU), PRO2044, haptoglobin (HAP), complement C3c (C3), proapolipoprotein A1 (proapo-A1), and retinol-binding protein 4 precursor (RBP4). Moreover, five non-host factors were detected, including bacterial antigens from Acinetobacter lwoffii, Burkholderia multivorans, Myxococcus xanthus, Laribacter hongkongensis, and Streptococcus salivarius. Subsequently, we analyzed the immunogenicity of these proteins using pooled sera from OSCC patients. In this regard, five of these candidate biomarkers were found to be immunoreactive: CLU, HAP, C3, proapo-A1 and RBP4. Taken together, our immunoproteomics approach has identified various serum biomarkers that could facilitate the development of early diagnostic tools for OSCC. PMID:25272005

  19. Microscopic and biochemical evidence of differentially virulent field isolates of Diplocarpon rosae causing black spot disease of roses.

    PubMed

    Gachomo, Emma W; Kotchoni, Simeon O

    2010-01-01

    Black spot disease caused by Diplocarpon rosae is one of the most widespread diseases of roses that are very difficult to control due to the generative reproduction and complex genetic constitution of roses and up to now the control of black spot still requires intensive use of systemic fungicides. Here we report for the first time evidence of differentially virulent field isolates of D. rosae. Using a combination of fungal structures, disease symptoms and host cells protein expression pattern analysis we here provide direct biochemical evidence that tropical field isolates of D. rosae are more virulent and caused disease symptoms earlier than their temperate counterparts. The tropical fungal field isolates strongly induced an excessive accumulation of ROS and repressed activity of pathogenesis-related proteins such as peroxidases, chitinase and phenylalanine ammonia lyase compared to their temperate counterparts. These findings bring insights into a hidden pathogenic characteristic of tropical D. rosae field isolates compared to their temperate counterparts and open a novel dimension of parameters to be considered when controlling black spot disease of roses by fungicides in tropical versus temperate regions. Interestingly, we found that treatment of rose leaves with ROS (H2O2) prior to fungal inoculation promoted plant defense response regardless of the isolate virulence based on protein expression pattern analysis, suggesting that ROS (H2O2) can be efficiently incorporated into black spot disease management. PMID:20137960

  20. Analysis of the use of dried blood spot measurements in disease screening.

    PubMed

    Lakshmy, Ramakrishnan

    2008-03-01

    The collection of dried blood spots on filter paper offers a powerful tool in screening programs and in large population-based surveys. The method has the advantage of being less invasive and relatively painless and is particularly suitable for collection in neonates and the elderly. Blood can be collected and transported economically without requiring a cold chain. The use of blood spots for the measurement of insulin, high sensitivity C-reactive protein, and triglycerides is reported. A good correlation between measurement of these analytes in dried blood and sera suggests that the method is valid and has the potential to be used for the screening of cardiometabolic risk factors. This method of blood collection is particularly suited for developing countries where cost cutting is important. PMID:19885349

  1. Structural basis for human PRDM9 action at recombination hot spots

    PubMed Central

    Patel, Anamika; Horton, John R.; Wilson, Geoffrey G.; Zhang, Xing; Cheng, Xiaodong

    2016-01-01

    The multidomain zinc finger (ZnF) protein PRDM9 (PRD1–BF1–RIZ1 homologous domain-containing 9) is thought to influence the locations of recombination hot spots during meiosis by sequence-specific DNA binding and trimethylation of histone H3 Lys4. The most common variant of human PRDM9, allele A (hPRDM9A), recognizes the consensus sequence 5′-NCCNCCNTNNCCNCN-3′. We cocrystallized ZnF8–12 of hPRDM9A with an oligonucleotide representing a known hot spot sequence and report the structure here. ZnF12 was not visible, but ZnF8–11, like other ZnF arrays, follows the right-handed twist of the DNA, with the α helices occupying the major groove. Each α helix makes hydrogen-bond (H-bond) contacts with up to four adjacent bases, most of which are purines of the complementary DNA strand. The consensus C:G base pairs H-bond with conserved His or Arg residues in ZnF8, ZnF9, and ZnF11, and the consensus T:A base pair H-bonds with an Asn that replaces His in ZnF10. Most of the variable base pairs (N) also engage in H bonds with the protein. These interactions appear to compensate to some extent for changes from the consensus sequence, implying an adaptability of PRDM9 to sequence variations. We investigated the binding of various alleles of hPRDM9 to different hot spot sequences. Allele C was found to bind a C-specific hot spot with higher affinity than allele A bound A-specific hot spots, perhaps explaining why the former is dominant in A/C heterozygotes. Allele L13 displayed higher affinity for several A-specific sequences, allele L9/L24 displayed lower affinity, and allele L20 displayed an altered sequence preference. These differences can be rationalized structurally and might contribute to the variation observed in the locations and activities of meiotic recombination hot spots. PMID:26833727

  2. Evaluating SPOT 5 Multispectral Imagery for Crop Yield Estimation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High resolution satellite imagery has the potential for mapping within-field variability in crop growth and yield. This study examined SPOT 5 multispectral imagery for estimating grain sorghum yield. A SPOT 5 image with 10-m spatial resolution and four spectral bands (green, red, near-infrared and m...

  3. Turbulence characteristics inside a turbulent spot in plane Poiseuille flow

    NASA Technical Reports Server (NTRS)

    Henningson, D. S.; Kim, John; Alfredsson, P. Henrik

    1988-01-01

    In wall-bounded shear flows the transition to turbulence through localized disturbances goes through a pattern starting with a development of shear layers. The localized normal velocity fluctuations induce normal vorticity through the lift-up effect. These shear layers become unstable to secondary disturbances, and if the amplitudes of the disturbances are large enough, a turbulent spot develops. Investigations of the spot in boundary layers has shown that the turbulent part of the spot is very similar to a fully developed boundary layer. Wygnanski et al. (1976) showed that the mean profile at the center-symmetry plane has a logarithmic region and Johansson et al. (1987) showed that both the higher-order statistics and flow structures in the spot were the same as in the corresponding fully developed flow. In what respects the turbulence inside the Poiseuille spot is similar to fully developed turbulent channel flow is studied. The numerically simulated spot is used, where the characteristics inside the spot are compared to those of the wave packet in the wingtip area. A recent experimental investigation of the velocity field associated with the Poiseuille spot by Klingmann et al. is used for comparison.

  4. Omental milky spots in screening gastric cancer stem cells.

    PubMed

    Cao, L; Hu, X; Zhang, Y; Sun, X T

    2011-01-01

    The existence of cancer stem and progenitor cells in solid tumors has been widely postulated. However, neither the cancer stem cells nor the cancer progenitor cells have been definitively identified and functionally characterized. Here we propose a new strategy to identify and isolate gastric cancer stem cells -using omental milky spots to screen gastric cancer stem cells in peritoneal metastasis mouse models of gastric cancer. In this study, we used the property that the macrophages in omental milky spots are cytotoxic against tumor cells and so able to screen and collect cancer stem cells. Our findings suggest that macrophages in omental milky spots have not only cytotoxic properties against tumor cells but also provide a microenvironment within milky spots in which cancer stem cells are capable to survive and grow into micrometastasis. Omental milky spot become a cancer stem cell niche in this situation. Further we studied the omental milky spots for screening gastric cancer cells (OMSS-GCCs) and found that omental milky spot enriched the volume of gastric cancer stem cells. Tumors were consistently generated after an injection of 1×103 OMSS-GCCs. OMSS-GCCs high express CD133 and low express CD324. Omental milky spots are a highly efficient "natural filter" for screening gastric cancer stem cells. PMID:21067262

  5. 21 CFR 892.1670 - Spot-film device.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Spot-film device. 892.1670 Section 892.1670 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES RADIOLOGY DEVICES Diagnostic Devices § 892.1670 Spot-film device. (a) Identification. A...

  6. 21 CFR 892.1670 - Spot-film device.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Spot-film device. 892.1670 Section 892.1670 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES RADIOLOGY DEVICES Diagnostic Devices § 892.1670 Spot-film device. (a) Identification. A...

  7. 21 CFR 892.1670 - Spot-film device.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Spot-film device. 892.1670 Section 892.1670 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES RADIOLOGY DEVICES Diagnostic Devices § 892.1670 Spot-film device. (a) Identification. A...

  8. 21 CFR 892.1670 - Spot-film device.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Spot-film device. 892.1670 Section 892.1670 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES RADIOLOGY DEVICES Diagnostic Devices § 892.1670 Spot-film device. (a) Identification. A...

  9. The Blind Spot: Re-Educating Ourselves about Visual Images

    ERIC Educational Resources Information Center

    Farkas, N.; Donnelly, K. M.; Henriksen, P. N.; Ramsier, R. D.

    2004-01-01

    A simple blind spot activity has been devised to help students discard misconceptions about image formation by lenses. Our hands-on experiment, in which students determine the location and size of their blind spots, is suitable for various age groups at different educational levels. The activity provides an opportunity to teach students how to…

  10. Intraday price dynamics in spot and derivatives markets

    NASA Astrophysics Data System (ADS)

    Kim, Jun Sik; Ryu, Doojin

    2014-01-01

    This study examines intraday relationships among the spot index, index futures, and the implied volatility index based on the VAR(1)-asymmetric BEKK-MGARCH model. Analysis of a high-frequency dataset from the Korean financial market confirms that there is a strong intraday market linkage between the spot index, KOSPI200 futures, and VKOSPI and that asymmetric volatility behaviour is clearly present in the Korean market. The empirical results indicate that the futures return shock affects the spot market more severely than the spot return shock affects the futures market, though there is a bi-directional causal relationship between the spot and futures markets. Our results, based on a high-quality intraday dataset, satisfy both the positive risk-return relationship and asymmetric volatility effect, which are not reconciled in the frameworks of previous studies.

  11. Ultrasonic assessment of tension shear strength in resistance spot welding

    NASA Astrophysics Data System (ADS)

    Moghanizadeh, Abbas

    2015-05-01

    Resistance spot welding is extensively used to join sheet steel in the automotive industry. Ultrasonic non-destructive techniques for evaluation of the mechanical properties of resistance spot welding are presented. The aim of this study is to develop the capability of the ultrasonic techniques as an efficient tool in the assessment of the welding characterization. Previous researches have indicated that the measurements of ultrasonic attenuation are sensitive to grain- size variations in an extensive range of metallic alloys. Other researchers have frequently described grain sizes which are able to have significant effects on the physical characteristics of the material. This research provides a novel method to estimate the tension-shear strengths of the resistance spot welding directly from the ultrasonic attenuation measurements. The effects of spot welding parameters on the ultrasonic waves are further investigated. The results confirm that it is possible to determine the spot welding parameters for individual quality by using ultrasonic test.

  12. Extensive Mongolian spots: a clinical sign merits special attention.

    PubMed

    Ashrafi, Mahmood Reza; Shabanian, Reza; Mohammadi, Mahmood; Kavusi, Susan

    2006-02-01

    Although typical and limited Mongolian spots are benign skin markings at birth which fade and disappear as the child grows, extensive Mongolian spots deserve special attention as possible indications of associated inborn error of metabolism. A few cases of extensive Mongolian spots in association with inheritable storage diseases have been reported. Some hypotheses have been put forward, but further investigation is necessary to elucidate the causative factors. This report describes three infants with generalized Mongolian spots, two infants with GM1 gangliosidosis type 1, and one in association with Hurler syndrome. Findings of generalized Mongolian spots in newborns may lead to an early detection and early treatment before irreversible organ damage occurs. PMID:16458829

  13. Friction Stir Spot Welding of DP780 Carbon Steel

    SciTech Connect

    Santella, M. L.; Hovanski, Yuri; Frederick, Alan; Grant, Glenn J.; Dahl, Michael E.

    2009-09-15

    Friction stir spot welds were made in uncoated and galvannneled DP780 sheets using polycrystalline boron nitride stir tools. The tools were plunged at either a single continuous rate or in two segments consisting of a relatively high rate followed by a slower rate of shorter depth. Welding times ranged from 1-10 s. Increasing tool rotation speed from 800 to 1600 rpm increased strength values. The 2-segment welding procedures also produced higher strength joints. Average lap-shear strengths exceeding 10.3 kN were consistently obtained in 4 s on both the uncoated and the galvannealed DP780. The likelihood of diffusion and mechanical interlocking contributing to bond formation was supported by metallographic examinations. A cost analysis based on spot welding in automobile assembly showed that for friction stir spot welding to be economically competitive with resistance spot welding the cost of stir tools must approach that of resistance spot welding electrode tips.

  14. Algorithm of semicircular laser spot detection based on circle fitting

    NASA Astrophysics Data System (ADS)

    Wang, Zhengzhou; Xu, Ruihua; Hu, Bingliang

    2013-07-01

    In order to obtain the exact center of an asymmetrical and semicircular aperture laser spot, a method for laser spot detection method based on circle fitting was proposed in this paper, threshold of laser spot image was segmented by the method of gray morphology algorithm, rough edge of laser spot was detected in both vertical and horizontal direction, short arcs and isolated edge points were deleted by contour growing, the best circle contour was obtained by iterative fitting and the final standard round was fitted in the end. The experimental results show that the precision of the method is obviously better than the gravity model method being used in the traditional large laser automatic alignment system. The accuracy of the method to achieve asymmetrical and semicircular laser spot center meets the requirements of the system.

  15. Multifocal array with controllable polarization in each focal spot.

    PubMed

    Zhu, Linwei; Sun, Meiyu; Zhang, Dawei; Yu, Junjie; Wen, Jing; Chen, Jiannong

    2015-09-21

    We propose a method for producing multifocal spot arrays (MSAs) capable of controlling the position and polarization orientation of each focal spot with radially polarized Bessel-Gaussian beam. Based on a simple analytical equation that can be used to manipulate the position of the focal spot, we design a type of multi-zone plate (MZP) composed of many fan-shaped subareas which accordingly generate lateral position-controllable multifocal spots. By adding a π-phase difference between a division line passing through the center of the back aperture with different orientations to corresponding subareas of the MZP, we realize MSAs in which orientations of the linear polarization in each focal spot can be arbitrarily manipulated. Such position and polarization controllable MSAs may potentially have applications in many fields. PMID:26406670

  16. A procedure to determine the planar integral spot dose values of proton pencil beam spots

    SciTech Connect

    Anand, Aman; Sahoo, Narayan; Zhu, X. Ronald; Sawakuchi, Gabriel O.; Poenisch, Falk; Amos, Richard A.; Ciangaru, George; Titt, Uwe; Suzuki, Kazumichi; Mohan, Radhe; Gillin, Michael T.

    2012-02-15

    Purpose: Planar integral spot dose (PISD) of proton pencil beam spots (PPBSs) is a required input parameter for beam modeling in some treatment planning systems used in proton therapy clinics. The measurement of PISD by using commercially available large area ionization chambers, like the PTW Bragg peak chamber (BPC), can have large uncertainties due to the size limitation of these chambers. This paper reports the results of our study of a novel method to determine PISD values from the measured lateral dose profiles and peak dose of the PPBS. Methods: The PISDs of 72.5, 89.6, 146.9, 181.1, and 221.8 MeV energy PPBSs were determined by area integration of their planar dose distributions at different depths in water. The lateral relative dose profiles of the PPBSs at selected depths were measured by using small volume ion chambers and were investigated for their angular anisotropies using Kodak XV films. The peak spot dose along the beam's central axis (D{sub 0}) was determined by placing a small volume ion chamber at the center of a broad field created by the superposition of spots at different locations. This method allows eliminating positioning uncertainties and the detector size effect that could occur when measuring it in single PPBS. The PISD was then calculated by integrating the measured lateral relative dose profiles for two different upper limits of integration and then multiplying it with corresponding D{sub 0}. The first limit of integration was set to radius of the BPC, namely 4.08 cm, giving PISD{sub RBPC}. The second limit was set to a value of the radial distance where the profile dose falls below 0.1% of the peak giving the PISD{sub full}. The calculated values of PISD{sub RBPC} obtained from area integration method were compared with the BPC measured values. Long tail dose correction factors (LTDCFs) were determined from the ratio of PISD{sub full}/PISD{sub RBPC} at different depths for PPBSs of different energies. Results: The spot profiles were

  17. An approach for addressing hard-to-detect hot spots.

    PubMed

    Abelquist, Eric W; King, David A; Miller, Laurence F; Viars, James A

    2013-05-01

    The Multi-Agency Radiation Survey and Site Investigation Manual (MARSSIM) survey approach is comprised of systematic random sampling coupled with radiation scanning to assess acceptability of potential hot spots. Hot spot identification for some radionuclides may not be possible due to the very weak gamma or x-ray radiation they emit-these hard-to-detect nuclides are unlikely to be identified by field scans. Similarly, scanning technology is not yet available for chemical contamination. For both hard-to-detect nuclides and chemical contamination, hot spots are only identified via volumetric sampling. The remedial investigation and cleanup of sites under the Comprehensive Environmental Response, Compensation, and Liability Act typically includes the collection of samples over relatively large exposure units, and concentration limits are applied assuming the contamination is more or less uniformly distributed. However, data collected from contaminated sites demonstrate contamination is often highly localized. These highly localized areas, or hot spots, will only be identified if sample densities are high or if the environmental characterization program happens to sample directly from the hot spot footprint. This paper describes a Bayesian approach for addressing hard-to-detect nuclides and chemical hot spots. The approach begins using available data (e.g., as collected using the standard approach) to predict the probability that an unacceptable hot spot is present somewhere in the exposure unit. This Bayesian approach may even be coupled with the graded sampling approach to optimize hot spot characterization. Once the investigator concludes that the presence of hot spots is likely, then the surveyor should use the data quality objectives process to generate an appropriate sample campaign that optimizes the identification of risk-relevant hot spots. PMID:23528274

  18. Meteorology of Jupiter's Equatorial Hot Spots and Plumes from Cassini

    NASA Technical Reports Server (NTRS)

    Choi, David Sanghun; Showman, Adam P.; Vasavada, Ashwin R.; Simon-Miller, Amy A.

    2013-01-01

    We present an updated analysis of Jupiter's equatorial meteorology from Cassini observations. For two months preceding the spacecraft's closest approach, the Imaging Science Subsystem (ISS) onboard regularly imaged the atmosphere. We created time-lapse movies from this period in order to analyze the dynamics of equatorial hot spots and their interactions with adjacent latitudes. Hot spots are relatively cloud-free regions that emit strongly at 5 lm; improved knowledge of these features is crucial for fully understanding Galileo probe measurements taken during its descent through one. Hot spots are quasistable, rectangular dark areas on visible-wavelength images, with defined eastern edges that sharply contrast with surrounding clouds, but diffuse western edges serving as nebulous boundaries with adjacent equatorial plumes. Hot spots exhibit significant variations in size and shape over timescales of days and weeks. Some of these changes correspond with passing vortex systems from adjacent latitudes interacting with hot spots. Strong anticyclonic gyres present to the south and southeast of the dark areas appear to circulate into hot spots. Impressive, bright white plumes occupy spaces in between hot spots. Compact cirrus-like 'scooter' clouds flow rapidly through the plumes before disappearing within the dark areas. These clouds travel at 150-200 m/s, much faster than the 100 m/s hot spot and plume drift speed. This raises the possibility that the scooter clouds may be more illustrative of the actual jet stream speed at these latitudes. Most previously published zonal wind profiles represent the drift speed of the hot spots at their latitude from pattern matching of the entire longitudinal image strip. If a downward branch of an equatorially-trapped Rossby wave controls the overall appearance of hot spots, however, the westward phase velocity of the wave leads to underestimates of the true jet stream speed.

  19. Dynamic array spot shaping for laser micro machining

    NASA Astrophysics Data System (ADS)

    Bich, A.; Weible, K. J.; Voelkel, R.; Zimmermann, M.; Harder, I.; Lindlein, N.; Masson, J.; Bitterli, R.; Noell, W.; Scharf, T.

    2009-08-01

    Laser manufacturing of microstructures using a single focus is a well known technology. Multi-spot optics are applied for process parallelizing if the demand on throughput in mass production rises or large areas of material have to be processed. Diffractive optical elements (DOEs) are used for parallel laser processing of a repetitive structure. These elements split the beam into a periodic spot pattern, where each spot shows the same shape and energy. This allows simultaneous manufacturing of several equal shaped structures at the same time. For patterning a surface this is state of the art and the appropriate technique to reduce processing time while maintaining a high lateral resolution as well as a good relative positioning of the structure due to the DOE. We investigate the usage of microlens arrays as multifunctional elements for forming an arbitrary shaped laser beam into a spot-, a ring-spot- or a line-array pattern. It can be shown that the intensity distribution of each spot is equal to the intensity distribution of all other spots in the whole pattern. The shape of the spots is defined by the angular distribution of the incident beam. We demonstrate that besides other optical properties the output beam profile strongly depends on the Fresnel-Number and is influenced by diffraction and interference effects. We present important design rules which consider geometrical and physical optics. The properties of the spot arrays, like spot diameter, Rayleigh length and beam divergence in dependency of beam and system properties are investigated. Finally we will show some laser micro structuring and micro drilling results in different materials.

  20. KFC2: a knowledge-based hot spot prediction method based on interface solvation, atomic density, and plasticity features.

    PubMed

    Zhu, Xiaolei; Mitchell, Julie C

    2011-09-01

    Hot spots constitute a small fraction of protein-protein interface residues, yet they account for a large fraction of the binding affinity. Based on our previous method (KFC), we present two new methods (KFC2a and KFC2b) that outperform other methods at hot spot prediction. A number of improvements were made in developing these new methods. First, we created a training data set that contained a similar number of hot spot and non-hot spot residues. In addition, we generated 47 different features, and different numbers of features were used to train the models to avoid over-fitting. Finally, two feature combinations were selected: One (used in KFC2a) is composed of eight features that are mainly related to solvent accessible surface area and local plasticity; the other (KFC2b) is composed of seven features, only two of which are identical to those used in KFC2a. The two models were built using support vector machines (SVM). The two KFC2 models were then tested on a mixed independent test set, and compared with other methods such as Robetta, FOLDEF, HotPoint, MINERVA, and KFC. KFC2a showed the highest predictive accuracy for hot spot residues (True Positive Rate: TPR = 0.85); however, the false positive rate was somewhat higher than for other models. KFC2b showed the best predictive accuracy for hot spot residues (True Positive Rate: TPR = 0.62) among all methods other than KFC2a, and the False Positive Rate (FPR = 0.15) was comparable with other highly predictive methods. PMID:21735484