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Sample records for high abundant proteins

  1. Protein Biophysics Explains Why Highly Abundant Proteins Evolve Slowly

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    Adrian W.R. Serohijos

    2012-08-01

    Full Text Available The consistent observation across all kingdoms of life that highly abundant proteins evolve slowly demonstrates that cellular abundance is a key determinant of protein evolutionary rate. However, other empirical findings, such as the broad distribution of evolutionary rates, suggest that additional variables determine the rate of protein evolution. Here, we report that under the global selection against the cytotoxic effects of misfolded proteins, folding stability (ΔG, simultaneous with abundance, is a causal variable of evolutionary rate. Using both theoretical analysis and multiscale simulations, we demonstrate that the anticorrelation between the premutation ΔG and the arising mutational effect (ΔΔG, purely biophysical in origin, is a necessary requirement for abundance–evolutionary rate covariation. Additionally, we predict and demonstrate in bacteria that the strength of abundance–evolutionary rate correlation depends on the divergence time separating reference genomes. Altogether, these results highlight the intrinsic role of protein biophysics in the emerging universal patterns of molecular evolution.

  2. Total protein or high-abundance protein: Which offers the best loading control for Western blotting?

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    Thacker, Jonathan S; Yeung, Derrick H; Staines, W Richard; Mielke, John G

    2016-03-01

    Western blotting routinely involves a control for variability in the amount of protein across immunoblot lanes. Normalizing a target signal to one found for an abundantly expressed protein is widely regarded as a reliable loading control; however, this approach is being increasingly questioned. As a result, we compared blotting for two high-abundance proteins (actin and glyceraldehyde 3-phosphate dehydrogenase [GAPDH]) and two total protein membrane staining methods (Ponceau and Coomassie Brilliant Blue) to determine the best control for loading variability. We found that Ponceau staining optimally balanced accuracy and precision, and we suggest that this approach be considered as an alternative to normalizing with a high-abundance protein.

  3. Evaluation of three high abundance protein depletion kits for umbilical cord serum proteomics

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    Nie Jing

    2011-05-01

    Full Text Available Abstract Background High abundance protein depletion is a major challenge in the study of serum/plasma proteomics. Prior to this study, most commercially available kits for depletion of highly abundant proteins had only been tested and evaluated in adult serum/plasma, while the depletion efficiency on umbilical cord serum/plasma had not been clarified. Structural differences between some adult and fetal proteins (such as albumin make it likely that depletion approaches for adult and umbilical cord serum/plasma will be variable. Therefore, the primary purposes of the present study are to investigate the efficiencies of several commonly-used commercial kits during high abundance protein depletion from umbilical cord serum and to determine which kit yields the most effective and reproducible results for further proteomics research on umbilical cord serum. Results The immunoaffinity based kits (PROTIA-Sigma and 5185-Agilent displayed higher depletion efficiency than the immobilized dye based kit (PROTBA-Sigma in umbilical cord serum samples. Both the PROTIA-Sigma and 5185-Agilent kit maintained high depletion efficiency when used three consecutive times. Depletion by the PROTIA-Sigma Kit improved 2DE gel quality by reducing smeared bands produced by the presence of high abundance proteins and increasing the intensity of other protein spots. During image analysis using the identical detection parameters, 411 ± 18 spots were detected in crude serum gels, while 757 ± 43 spots were detected in depleted serum gels. Eight spots unique to depleted serum gels were identified by MALDI- TOF/TOF MS, seven of which were low abundance proteins. Conclusions The immunoaffinity based kits exceeded the immobilized dye based kit in high abundance protein depletion of umbilical cord serum samples and dramatically improved 2DE gel quality for detection of trace biomarkers.

  4. Influence of Acute High Glucose on Protein Abundance Changes in Murine Glomerular Mesangial Cells

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    Michelle T. Barati

    2016-01-01

    Full Text Available The effects of acute exposure to high glucose levels as experienced by glomerular mesangial cells in postprandial conditions and states such as in prediabetes were investigated using proteomic methods. Two-dimensional gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry methods were used to identify protein expression patterns in immortalized rat mesangial cells altered by 2 h high glucose (HG growth conditions as compared to isoosmotic/normal glucose control (NG⁎ conditions. Unique protein expression changes at 2 h HG treatment were measured for 51 protein spots. These proteins could be broadly grouped into two categories: (1 proteins involved in cell survival/cell signaling and (2 proteins involved in stress response. Immunoblot experiments for a protein belonging to both categories, prohibitin (PHB, supported a trend for increased total expression as well as significant increases in an acidic PHB isoform. Additional studies confirmed the regulation of proteasomal subunit alpha-type 2 and the endoplasmic reticulum chaperone and oxidoreductase PDI (protein disulfide isomerase, suggesting altered ER protein folding capacity and proteasomal function in response to acute HG. We conclude that short term high glucose induces subtle changes in protein abundances suggesting posttranslational modifications and regulation of pathways involved in proteostasis.

  5. Immunodepletion of high-abundant proteins from acute and chronic wound fluids to elucidate low-abundant regulators in wound healing

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    Chojnacki Caroline

    2010-12-01

    Full Text Available Abstract Background The process of wound healing consists of several well distinguishable and finely tuned phases. For most of these phases specific proteins have been characterized, although the underlying mechanisms of regulation are not yet fully understood. It is an open question as to whether deficits in wound healing can be traced back to chronic illnesses such as diabetes mellitus. Previous research efforts in this field focus largely on a restricted set of marker proteins due to the limitations detection by antibodies imposes. For mechanistic purposes the elucidation of differences in acute and chronic wounds can be addressed by a less restricted proteome study. Mass spectrometric (MS methods, e.g. multi dimensional protein identification technology (MudPIT, are well suitable for this complex theme of interest. The human wound fluid proteome is extremely complex, as is human plasma. Therefore, high-abundant proteins often mask the mass spectrometric detection of lower-abundant ones, which makes a depletion step of such predominant proteins inevitable. Findings In this study a commercially available immunodepletion kit was evaluated for the detection of low-abundant proteins from wound fluids. The dynamic range of the entire workflow was significantly increased to 5-6 orders of magnitude, which makes low-abundant regulatory proteins involved in wound healing accessible for MS detection. Conclusion The depletion of abundant proteins is absolutely necessary in order to analyze highly complex protein mixtures such as wound fluids using mass spectrometry. For this the used immunodepletion kit is a first but important step in order to represent the entire dynamic range of highly complex protein mixtures in the future.

  6. Identification of Candidate Biomarkers in Ovarian Cancer Serum by Depletion of Highly Abundant Proteins and Differential In Gel Electrophoresis

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    Andersen, John D.; Boylan, Kristin L.M.; Xue, Feifei S.; Anderson, Lorraine B.; Witthuhn, Bruce A.; Markowski, Todd W.; Higgins, LeeAnn; Skubitz, Amy P.N.

    2012-01-01

    Ovarian cancer is the fifth leading cause of cancer death for women in the U.S., yet survival rates are over 90% when it is diagnosed at an early stage, highlighting the need for biomarkers for early detection. To enhance the discovery of tumor-specific proteins which could represent novel serum biomarkers for ovarian cancer, we depleted serum of highly abundant proteins which can mask the detection of proteins present in serum at low concentrations. Three commercial immunoaffinity columns were used in parallel to deplete the highly abundant proteins in serum from 60 patients with serous ovarian carcinoma and 60 non-cancer controls. Medium and low abundance serum proteins from each serum pool were then evaluated by the quantitative proteomic technique of Differential-In-Gel-Electrophoresis (DIGE). The number of protein spots that were elevated in ovarian cancer sera by at least 2-fold ranged from 36 to 248, depending upon the depletion and separation methods. From the 33 spots picked for MS analysis, nine different proteins were identified, including the novel candidate ovarian cancer biomarkers leucine-rich alpha-2 glycoprotein-1 and ficolin 3. Western blotting validated the relative increases in serum protein levels for three of the proteins identified, demonstrating the utility of this approach for the identification of novel serum biomarkers for ovarian cancer. PMID:20162585

  7. Comparative study of human and mouse postsynaptic proteomes finds high compositional conservation and abundance differences for key synaptic proteins.

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    Alex Bayés

    Full Text Available Direct comparison of protein components from human and mouse excitatory synapses is important for determining the suitability of mice as models of human brain disease and to understand the evolution of the mammalian brain. The postsynaptic density is a highly complex set of proteins organized into molecular networks that play a central role in behavior and disease. We report the first direct comparison of the proteome of triplicate isolates of mouse and human cortical postsynaptic densities. The mouse postsynaptic density comprised 1556 proteins and the human one 1461. A large compositional overlap was observed; more than 70% of human postsynaptic density proteins were also observed in the mouse postsynaptic density. Quantitative analysis of postsynaptic density components in both species indicates a broadly similar profile of abundance but also shows that there is higher abundance variation between species than within species. Well known components of this synaptic structure are generally more abundant in the mouse postsynaptic density. Significant inter-species abundance differences exist in some families of key postsynaptic density proteins including glutamatergic neurotransmitter receptors and adaptor proteins. Furthermore, we have identified a closely interacting set of molecules enriched in the human postsynaptic density that could be involved in dendrite and spine structural plasticity. Understanding synapse proteome diversity within and between species will be important to further our understanding of brain complexity and disease.

  8. Lactate dehydrogenase A as a highly abundant eye lens protein in platypus (Ornithorhynchus anatinus): upsilon (upsilon)-crystallin.

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    van Rheede, Teun; Amons, Reinout; Stewart, Niall; de Jong, Wilfried W

    2003-06-01

    Vertebrate eye lenses mostly contain two abundant types of proteins, the alpha-crystallins and the beta/gamma-crystallins. In addition, certain housekeeping enzymes are highly expressed as crystallins in various taxa. We now observed an unusual approximately 41-kd protein that makes up 16% to 18% of the total protein in the platypus eye lens. Its cDNA sequence was determined, which identified the protein as muscle-type lactate dehydrogenase A (LDH-A). It is the first observation of LDH-A as a crystallin, and we designate it upsilon (upsilon)-crystallin. Interestingly, the related heart-type LDH-B occurs as an abundant lens protein, known as epsilon-crystallin, in many birds and crocodiles. Thus, two members of the ldh gene family have independently been recruited as crystallins in different higher vertebrate lineages, suggesting that they are particularly suited for this purpose in terms of gene regulatory or protein structural properties. To establish whether platypus LDH-A/upsilon-crystallin has been under different selective constraints as compared with other vertebrate LDH-A sequences, we reconstructed the vertebrate ldh-a gene phylogeny. No conspicuous rate deviations or amino acid replacements were observed.

  9. Exploiting the multiplexing capabilities of tandem mass tags for high-throughput estimation of cellular protein abundances by mass spectrometry.

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    Ahrné, Erik; Martinez-Segura, Amalia; Syed, Afzal Pasha; Vina-Vilaseca, Arnau; Gruber, Andreas J; Marguerat, Samuel; Schmidt, Alexander

    2015-09-01

    The generation of dynamic models of biological processes critically depends on the determination of precise cellular concentrations of biomolecules. Measurements of system-wide absolute protein levels are particularly valuable information in systems biology. Recently, mass spectrometry based proteomics approaches have been developed to estimate protein concentrations on a proteome-wide scale. However, for very complex proteomes, fractionation steps are required, increasing samples number and instrument analysis time. As a result, the number of full proteomes that can be routinely analyzed is limited. Here we combined absolute quantification strategies with the multiplexing capabilities of isobaric tandem mass tags to determine cellular protein abundances in a high throughput and proteome-wide scale even for highly complex biological systems, such as a whole human cell line. We generated two independent data sets to demonstrate the power of the approach regarding sample throughput, dynamic range, quantitative precision and accuracy as well as proteome coverage in comparison to existing mass spectrometry based strategies.

  10. Amyloid proteins are highly abundant in water-repellent but not wettable soils: microbial differentiation matters to soils

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    van Keulen, Geertje; Quinn, Gerry; Sinclair, Kat; Dudley, Ed; Swain, Martin; Doerr, Stefan; Matthews, Peter; Francis, Lewis; Gazze, Andrea; Hallin, Ingrid

    2017-04-01

    Soil water repellency is a common phenomenon affecting the hydrological responses of many soil and land use types in different climates. This in turn leads to decreased water infiltration, reduced vegetation cover, fertiliser run off and soil erosion. The fundamental (biological) causes of (bulk) soil repellency and its dynamic behaviour remain poorly understood. We have applied soil metaproteomics, the systemic extraction and identification of proteins from a soil, to understand the biological (adaptive) processes and potential for bio-modification of mineral surfaces, which occur at the molecular level in soils switching between wettable and repellent states. Extreme, moderate and sub-critical water-repellent UK silt-loam soils under permanent grass vegetation, including Park Grass at Rothamsted Research, were sampled below the root zone depth under wettable and repellent conditions. Soils were subjected to our new extraction methods for determining the specific ultrahydrophobic and total metaproteomes. Using our ultrahydrophobic extraction protocol, we have identified more than 200, mostly novel amyloid, proteins, which could be extracted from water-repellent soils, but were absent in the comparable wettable soils. One of the novel amyloid proteins was highly abundant in all soils, which has the potential as a soil biomarker for precision land management, especially in irrigation. Comparative profiling of the total metaproteomes of wettable and repellent soils has revealed similarities and dissimilarities in microbial diversity and their activities, which have created a deeper understanding of soil system processes common and adaptive to soil moisture and to the severity of repellence.

  11. The highly abundant protein Ag-Ibp55 from Ascaridia galli represents a novel type of lipid-binding proteins

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    Jordanova, R; Radoslavov, G; Fischer, P; Torda, A; Lottspeich, F; Boteva, R; Walter, RD; Bankov, [No Value; Liebau, E

    2005-01-01

    Lipid-binding proteins exhibit important functions in lipid transport, cellular signaling, gene transcription, and cytoprotection. Their functional analogues in nematodes are nematode polyprotein allergens/antigens and fatty acid and retinoid-binding proteins. This work describes a novel 55-kDa prot

  12. Late Embryogenesis Abundant (LEA proteins in legumes

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    Marina eBattaglia

    2013-06-01

    Full Text Available Plants are exposed to different external conditions that affect growth, development, and productivity. Water deficit is one of these adverse conditions caused by drought, salinity, and extreme temperatures. Plants have developed different responses to prevent, ameliorate or repair the damage inflicted by these stressful environments. One of these responses is the activation of a set of genes encoding a group of hydrophilic proteins that typically accumulate to high levels during seed dehydration, at the last stage of embryogenesis, hence named Late Embryogenesis Abundant (LEA proteins. LEA proteins also accumulate in response to water limitation in vegetative tissues, and have been classified in seven groups based on their amino acid sequence similarity and on the presence of distinctive conserved motifs. These proteins are widely distributed in the plant kingdom, from ferns to angiosperms, suggesting a relevant role in the plant response to this unfavorable environmental condition. In this review, we analyzed the LEA proteins from those legumes whose complete genomes have been sequenced such as Phaseolus vulgaris, Glycine max, Medicago truncatula, Lotus japonicus, Cajanus cajan and Cicer arietinum. Considering their distinctive motifs, LEA proteins from the different groups were identified, and their sequence analysis allowed the recognition of novel legume specific motifs. Moreover, we compile their transcript accumulation patterns based on publicly available data. In spite of the limited information on these proteins in legumes, the analysis and data compiled here confirms the high correlation between their accumulation and water deficit, reinforcing their functional relevance under this detrimental conditions.

  13. Oolemmal proteomics – identification of highly abundant heat shock proteins and molecular chaperones in the mature mouse egg and their localization on the plasma membrane

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    Calvert, Meredith E; Digilio, Laura C; Herr, John C; Coonrod, Scott A

    2003-01-01

    Background The mature mouse egg contains the full complement of maternal proteins required for fertilization, the transition to zygotic transcription, and the beginning stages of embryogenesis. Many of these proteins remain to be characterized, therefore in this study we have identified highly abundant egg proteins using a proteomic approach and found that several of these proteins also appear to localize to the egg surface. Characterization of such molecules will provide important insight into the cellular events of fertilization and early development. Methods In order to identify some of the more abundant egg proteins, whole egg extracts were resolved on coomassie-stained two-dimensional (2D) PAGE gels. Several highly abundant protein spots were cored and microsequenced by tandem mass spectrometry (TMS), and determined to be molecular chaperone proteins. Concurrent experiments were performed to identify oolemmal proteins using 2D avidin blotting. Proteins spots that appeared to be surface labeled by biotinylation were correlated with the initial coomassie-stained reference gel. Surprisingly, some of the surface labelled proteins corresponded to those abundant chaperone proteins previously identified. To confirm whether these molecules are accumulating at the oolemmal surface in eggs, we performed immunofluoresence on live, zona-free eggs using antibodies to HSP70, HSP90, GRP94, GRP78, calreticulin and calnexin. Results The putative surface-labeled proteins identified by biotinylation included the molecular chaperones HSP70 (MW 70 KDa, pI 5.5), HSP90a (MW 85 KDa, pI 4.9), GRP94 (MW 92 KDa, pI 4.7), GRP78 (MW 72 KDa, pI 5.0), Oxygen regulated protein 150 (ORP150; MW 111 KDa, pI 5.1), Calreticulin (MW 48 KDa, pI 4.3), Calnexin (MW 65 KDa, pI 4.5), and Protein disulfide isomerase (PDI; MW 57 KDa, pI 4.8). Immunofluoresence results showed that antibodies to HSP90, GRP94, GRP78 and calreticulin were reactive with oolemmal proteins. We were unable to confirm surface

  14. Oolemmal proteomics – identification of highly abundant heat shock proteins and molecular chaperones in the mature mouse egg and their localization on the plasma membrane

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    Herr John C

    2003-02-01

    Full Text Available Abstract Background The mature mouse egg contains the full complement of maternal proteins required for fertilization, the transition to zygotic transcription, and the beginning stages of embryogenesis. Many of these proteins remain to be characterized, therefore in this study we have identified highly abundant egg proteins using a proteomic approach and found that several of these proteins also appear to localize to the egg surface. Characterization of such molecules will provide important insight into the cellular events of fertilization and early development. Methods In order to identify some of the more abundant egg proteins, whole egg extracts were resolved on coomassie-stained two-dimensional (2D PAGE gels. Several highly abundant protein spots were cored and microsequenced by tandem mass spectrometry (TMS, and determined to be molecular chaperone proteins. Concurrent experiments were performed to identify oolemmal proteins using 2D avidin blotting. Proteins spots that appeared to be surface labeled by biotinylation were correlated with the initial coomassie-stained reference gel. Surprisingly, some of the surface labelled proteins corresponded to those abundant chaperone proteins previously identified. To confirm whether these molecules are accumulating at the oolemmal surface in eggs, we performed immunofluoresence on live, zona-free eggs using antibodies to HSP70, HSP90, GRP94, GRP78, calreticulin and calnexin. Results The putative surface-labeled proteins identified by biotinylation included the molecular chaperones HSP70 (MW 70 KDa, pI 5.5, HSP90a (MW 85 KDa, pI 4.9, GRP94 (MW 92 KDa, pI 4.7, GRP78 (MW 72 KDa, pI 5.0, Oxygen regulated protein 150 (ORP150; MW 111 KDa, pI 5.1, Calreticulin (MW 48 KDa, pI 4.3, Calnexin (MW 65 KDa, pI 4.5, and Protein disulfide isomerase (PDI; MW 57 KDa, pI 4.8. Immunofluoresence results showed that antibodies to HSP90, GRP94, GRP78 and calreticulin were reactive with oolemmal proteins. We were unable to

  15. Oolemmal proteomics--identification of highly abundant heat shock proteins and molecular chaperones in the mature mouse egg and their localization on the plasma membrane.

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    Calvert, Meredith E; Digilio, Laura C; Herr, John C; Coonrod, Scott A

    2003-02-14

    The mature mouse egg contains the full complement of maternal proteins required for fertilization, the transition to zygotic transcription, and the beginning stages of embryogenesis. Many of these proteins remain to be characterized, therefore in this study we have identified highly abundant egg proteins using a proteomic approach and found that several of these proteins also appear to localize to the egg surface. Characterization of such molecules will provide important insight into the cellular events of fertilization and early development. In order to identify some of the more abundant egg proteins, whole egg extracts were resolved on coomassie-stained two-dimensional (2D) PAGE gels. Several highly abundant protein spots were cored and microsequenced by tandem mass spectrometry (TMS), and determined to be molecular chaperone proteins. Concurrent experiments were performed to identify oolemmal proteins using 2D avidin blotting. Proteins spots that appeared to be surface labeled by biotinylation were correlated with the initial coomassie-stained reference gel. Surprisingly, some of the surface labelled proteins corresponded to those abundant chaperone proteins previously identified. To confirm whether these molecules are accumulating at the oolemmal surface in eggs, we performed immunofluoresence on live, zona-free eggs using antibodies to HSP70, HSP90, GRP94, GRP78, calreticulin and calnexin. The putative surface-labeled proteins identified by biotinylation included the molecular chaperones HSP70 (MW 70 KDa, pI 5.5), HSP90a (MW 85 KDa, pI 4.9), GRP94 (MW 92 KDa, pI 4.7), GRP78 (MW 72 KDa, pI 5.0), Oxygen regulated protein 150 (ORP150; MW 111 KDa, pI 5.1), Calreticulin (MW 48 KDa, pI 4.3), Calnexin (MW 65 KDa, pI 4.5), and Protein disulfide isomerase (PDI; MW 57 KDa, pI 4.8). Immunofluoresence results showed that antibodies to HSP90, GRP94, GRP78 and calreticulin were reactive with oolemmal proteins. We were unable to confirm surface localization of HSP70 or

  16. Fabrication of diverse pH-sensitive functional mesoporous silica for selective removal or depletion of highly abundant proteins from biological samples.

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    Wang, Jiaojiao; Lan, Jingfeng; Li, Huihui; Liu, Xiaoyan; Zhang, Haixia

    2017-01-01

    In proteomic studies, poor detection of low abundant proteins is a major problem due to the presence of highly abundant proteins. Therefore, the specific removal or depletion of highly abundant proteins prior to analysis is necessary. In response to this problem, a series of pH-sensitive functional mesoporous silica materials composed of 2-(diethylamino)ethyl methacrylate and methacrylic acid units were designed and synthesized via atom transfer radical polymerization. These functional mesoporous silica materials were characterized and their ability for adsorption and separation of proteins was evaluated. Possessing a pH-sensitive feature, the synthesized functional materials showed selective adsorption of some proteins in aqueous or buffer solutions at certain pH values. The specific removal of a particular protein from a mixed protein solution was subsequently studied. The analytical results confirmed that all the target proteins (bovine serum albumin, ovalbumin, and lysozyme) can be removed by the proposed materials from a five-protein mixture in a single operation. Finally, the practical application of this approach was also evaluated by the selective removal of certain proteins from real biological samples. The results revealed that the maximum removal efficiencies of ovalbumin and lysozyme from egg white sample were obtained as 99% and 92%, respectively, while the maximum removal efficiency of human serum albumin from human serum sample was about 80% by the proposed method. It suggested that this treatment process reduced the complexity of real biological samples and facilitated the identification of hidden proteins in chromatograms. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Element abundances at high redshift

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    Meyer, D.M.; Welty, D.E.; York, D.G. (Northwestern Univ., Evanston, IL (USA); Chicago Univ., IL (USA))

    1989-08-01

    Abundances of Si(+), S(+), Cr(+), Mn(+), Fe( ), and Zn(+) are considered for two absorption-line systems in the spectrum of the QSO PKS 0528 - 250. Zinc and sulfur are underabundant, relative to H, by a factor of 10 compared to their solar and Galactic interstellar abundances. The silicon-, chromium-, iron-, and nickel-to-hydrogen ratios are less than the solar values and comparable to the local interstellar ratios. A straightforward interpretation is that nucleosynthesis in these high-redshift systems has led to only about one-tenth as much heavy production as in the gas clouds around the sun, and that the amount of the observed underabundances attributable to grain depletion is small. The dust-to-gas ratio in these clouds is less than 8 percent of the Galactic value. 25 refs.

  18. Element abundances at high redshift

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    Meyer, David M.; Welty, D. E.; York, D. G.

    1989-01-01

    Abundances of Si(+), S(+), Cr(+), Mn(+), Fe(_), and Zn(+) are considered for two absorption-line systems in the spectrum of the QSO PKS 0528 - 250. Zinc and sulfur are underabundant, relative to H, by a factor of 10 compared to their solar and Galactic interstellar abundances. The silicon-, chromium-, iron-, and nickel-to-hydrogen ratios are less than the solar values and comparable to the local interstellar ratios. A straightforward interpretation is that nucleosynthesis in these high-redshift systems has led to only about one-tenth as much heavy production as in the gas clouds around the sun, and that the amount of the observed underabundances attributable to grain depletion is small. The dust-to-gas ratio in these clouds is less than 8 percent of the Galactic value.

  19. Protein abundance profiling of the Escherichia coli cytosol

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    Mann Matthias

    2008-02-01

    Full Text Available Abstract Background Knowledge about the abundance of molecular components is an important prerequisite for building quantitative predictive models of cellular behavior. Proteins are central components of these models, since they carry out most of the fundamental processes in the cell. Thus far, protein concentrations have been difficult to measure on a large scale, but proteomic technologies have now advanced to a stage where this information becomes readily accessible. Results Here, we describe an experimental scheme to maximize the coverage of proteins identified by mass spectrometry of a complex biological sample. Using a combination of LC-MS/MS approaches with protein and peptide fractionation steps we identified 1103 proteins from the cytosolic fraction of the Escherichia coli strain MC4100. A measure of abundance is presented for each of the identified proteins, based on the recently developed emPAI approach which takes into account the number of sequenced peptides per protein. The values of abundance are within a broad range and accurately reflect independently measured copy numbers per cell. As expected, the most abundant proteins were those involved in protein synthesis, most notably ribosomal proteins. Proteins involved in energy metabolism as well as those with binding function were also found in high copy number while proteins annotated with the terms metabolism, transcription, transport, and cellular organization were rare. The barrel-sandwich fold was found to be the structural fold with the highest abundance. Highly abundant proteins are predicted to be less prone to aggregation based on their length, pI values, and occurrence patterns of hydrophobic stretches. We also find that abundant proteins tend to be predominantly essential. Additionally we observe a significant correlation between protein and mRNA abundance in E. coli cells. Conclusion Abundance measurements for more than 1000 E. coli proteins presented in this work

  20. Detection and quantitation of twenty-seven cytokines, chemokines and growth factors pre- and post-high abundance protein depletion in human plasma

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    Seong-Beom Ahn

    2014-06-01

    Full Text Available Cytokines, chemokines and growth factors (CCGFs in human plasma are analyzed for identification of biomarkers. However concentrations of CCGFs are very low; it is difficult to identify and quantify low abundance proteins in the presence of the high abundance proteins (HAPs unless HAPs are removed prior to analysis. However, there is a concern that the low abundance proteins such as CCGFs may also be removed during the HAP depletion process. In this study, we have examined whether or not depletion of the HAPs enhances detection of the CCGFs by immuno-assays. Top 14 HAPs were depleted from 10 healthy volunteers’ plasma using MARS-14 immuno-depletion column and a total of 27 CCGFs were analyzed by bead-based multiplexed immuno-assay. All 27 CCGFs were detected in neat plasma (NP, 25 were detected in flow through fraction (FT and 21 were detected in bound protein (BP fraction. Concentrations of 22 CCGFs were significantly higher in NP compared to FT and BP. Only one CCGF had higher concentration in FT compared to NP. The remaining 2 CCGFs were not different between NP and FT. It was counter-productive for the detection of 24 CCGFs after HAP removal, primarily due to post-depletion protein precipitation and/or re-suspension of pellets.

  1. Fundamental constraints on the abundances of chemotaxis proteins

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    Bitbol, Anne-Florence

    2015-01-01

    Flagellated bacteria, such as Escherichia coli, perform directed motion in gradients of concentration of attractants and repellents in a process called chemotaxis. The E. coli chemotaxis signaling pathway is a model for signal transduction, but it has unique features. We demonstrate that the need for fast signaling necessitates high abundances of the proteins involved in this pathway. We show that further constraints on the abundances of chemotaxis proteins arise from the requirements of self-assembly, both of flagellar motors and of chemoreceptor arrays. All these constraints are specific to chemotaxis, and published data confirm that chemotaxis proteins tend to be more highly expressed than their homologs in other pathways. Employing a chemotaxis pathway model, we show that the gain of the pathway at the level of the response regulator CheY increases with overall chemotaxis protein abundances. This may explain why, at least in one E. coli strain, the abundance of all chemotaxis proteins is higher in media w...

  2. On ribosome load, codon bias and protein abundance.

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    Stefan Klumpp

    Full Text Available Different codons encoding the same amino acid are not used equally in protein-coding sequences. In bacteria, there is a bias towards codons with high translation rates. This bias is most pronounced in highly expressed proteins, but a recent study of synthetic GFP-coding sequences did not find a correlation between codon usage and GFP expression, suggesting that such correlation in natural sequences is not a simple property of translational mechanisms. Here, we investigate the effect of evolutionary forces on codon usage. The relation between codon bias and protein abundance is quantitatively analyzed based on the hypothesis that codon bias evolved to ensure the efficient usage of ribosomes, a precious commodity for fast growing cells. An explicit fitness landscape is formulated based on bacterial growth laws to relate protein abundance and ribosomal load. The model leads to a quantitative relation between codon bias and protein abundance, which accounts for a substantial part of the observed bias for E. coli. Moreover, by providing an evolutionary link, the ribosome load model resolves the apparent conflict between the observed relation of protein abundance and codon bias in natural sequences and the lack of such dependence in a synthetic gfp library. Finally, we show that the relation between codon usage and protein abundance can be used to predict protein abundance from genomic sequence data alone without adjustable parameters.

  3. Sequential extraction results in improved proteome profiling of medicinal plant Pinellia ternata tubers, which contain large amounts of high-abundance proteins.

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    Xiaolin Wu

    Full Text Available Pinellia ternata tuber is one of the well-known Chinese traditional medicines. In order to understand the pharmacological properties of tuber proteins, it is necessary to perform proteome analysis of P. ternata tubers. However, a few high-abundance proteins (HAPs, mainly mannose-binding lectin (agglutinin, exist in aggregates of various sizes in the tubers and seriously interfere with proteome profiling by two-dimensional electrophoresis (2-DE. Therefore, selective depletion of these HAPs is a prerequisite for enhanced proteome analysis of P. ternata tubers. Based on differential protein solubility, we developed a novel protocol involving two sequential extractions for depletion of some HAPs and prefractionation of tuber proteins prior to 2-DE. The first extraction using 10% acetic acid selectively extracted acid-soluble HAPs and the second extraction using the SDS-containing buffer extracted remaining acid-insoluble proteins. After application of the protocol, 2-DE profiles of P. ternata tuber proteins were greatly improved and more protein spots were detected, especially low-abundance proteins. Moreover, the subunit composition of P. ternata lectin was analyzed by electrophoresis. Native lectin consists of two hydrogen-bonded subunits (11 kDa and 25 kDa and the 11 kDa subunit was a glycoprotein. Subsequently, major HAPs in the tubers were analyzed by mass spectrometry, with nine protein spots being identified as lectin isoforms. The methodology was easy to perform and required no specialized apparatus. It would be useful for proteome analysis of other tuber plants of Araceae.

  4. A gestational high protein diet affects the abundance of muscle transcripts related to cell cycle regulation throughout development in porcine progeny.

    Directory of Open Access Journals (Sweden)

    Michael Oster

    Full Text Available BACKGROUND: In various animal models pregnancy diets have been shown to affect offspring phenotype. Indeed, the underlying programming of development is associated with modulations in birth weight, body composition, and continual diet-dependent modifications of offspring metabolism until adulthood, producing the hypothesis that the offspring's transcriptome is permanently altered depending on maternal diet. METHODOLOGY/PRINCIPAL FINDINGS: To assess alterations of the offspring's transcriptome due to gestational protein supply, German Landrace sows were fed isoenergetic diets containing protein levels of either 30% (high protein--HP or 12% (adequate protein--AP throughout their pregnancy. Offspring muscle tissue (M. longissimus dorsi was collected at 94 days post conception (dpc, and 1, 28, and 188 days post natum (dpn for use with Affymetrix GeneChip Porcine Genome Arrays and subsequent statistical and Ingenuity pathway analyses. Numerous transcripts were found to have altered abundance at 94 dpc and 1 dpn; at 28 dpn no transcripts were altered, and at 188 dpn only a few transcripts showed a different abundance between diet groups. However, when assessing transcriptional changes across developmental time points, marked differences were obvious among the dietary groups. Depending on the gestational dietary exposure, short- and long-term effects were observed for mRNA expression of genes related to cell cycle regulation, energy metabolism, growth factor signaling pathways, and nucleic acid metabolism. In particular, the abundance of transcripts related to cell cycle remained divergent among the groups during development. CONCLUSION: Expression analysis indicates that maternal protein supply induced programming of the offspring's genome; early postnatal compensation of the slight growth retardation obvious at birth in HP piglets resulted, as did a permanently different developmental alteration and responsiveness to the common environment of the

  5. Proteomics characterization of abundant Golgi membrane proteins.

    Science.gov (United States)

    Bell, A W; Ward, M A; Blackstock, W P; Freeman, H N; Choudhary, J S; Lewis, A P; Chotai, D; Fazel, A; Gushue, J N; Paiement, J; Palcy, S; Chevet, E; Lafrenière-Roula, M; Solari, R; Thomas, D Y; Rowley, A; Bergeron, J J

    2001-02-16

    A mass spectrometric analysis of proteins partitioning into Triton X-114 from purified hepatic Golgi apparatus (84% purity by morphometry, 122-fold enrichment over the homogenate for the Golgi marker galactosyl transferase) led to the unambiguous identification of 81 proteins including a novel Golgi-associated protein of 34 kDa (GPP34). The membrane protein complement was resolved by SDS-polyacrylamide gel electrophoresis and subjected to a hierarchical approach using delayed extraction matrix-assisted laser desorption ionization mass spectrometry characterization by peptide mass fingerprinting, tandem mass spectrometry to generate sequence tags, and Edman sequencing of proteins. Major membrane proteins corresponded to known Golgi residents, a Golgi lectin, anterograde cargo, and an abundance of trafficking proteins including KDEL receptors, p24 family members, SNAREs, Rabs, a single ARF-guanine nucleotide exchange factor, and two SCAMPs. Analytical fractionation and gold immunolabeling of proteins in the purified Golgi fraction were used to assess the intra-Golgi and total cellular distribution of GPP34, two SNAREs, SCAMPs, and the trafficking proteins GBF1, BAP31, and alpha(2)P24 identified by the proteomics approach as well as the endoplasmic reticulum contaminant calnexin. Although GPP34 has never previously been identified as a protein, the localization of GPP34 to the Golgi complex, the conservation of GPP34 from yeast to humans, and the cytosolically exposed location of GPP34 predict a role for a novel coat protein in Golgi trafficking.

  6. Detecting significant changes in protein abundance

    Directory of Open Access Journals (Sweden)

    Kai Kammers

    2015-06-01

    Full Text Available We review and demonstrate how an empirical Bayes method, shrinking a protein's sample variance towards a pooled estimate, leads to far more powerful and stable inference to detect significant changes in protein abundance compared to ordinary t-tests. Using examples from isobaric mass labelled proteomic experiments we show how to analyze data from multiple experiments simultaneously, and discuss the effects of missing data on the inference. We also present easy to use open source software for normalization of mass spectrometry data and inference based on moderated test statistics.

  7. Depletion of abundant plasma proteins by poly(N-isopropylacrylamide-acrylic acid) hydrogel particles

    DEFF Research Database (Denmark)

    Such-Sanmartín, Gerard; Ventura-Espejo, Estela; Jensen, Ole N

    2014-01-01

    at higher efficiency than low abundance proteins, which are enriched in the supernatants, whereas (2) hydrogel particles incubated with high concentrations of plasma capture and irreversibly trap abundant proteins. During the elution step, irreversibly trapped proteins remain captured while low abundance...... (SRM) liquid chromatography (LC)-MS/MS. This novel use of hydrogel particles opens new perspectives for biomarker analysis based on mass spectrometry....

  8. Protein abundance profiling of the Escherichia coli cytosol

    DEFF Research Database (Denmark)

    Ishihama, Y.; Schmidt, T.; Rappsilber, J.

    2008-01-01

    PAI approach which takes into account the number of sequenced peptides per protein. The values of abundance are within a broad range and accurately reflect independently measured copy numbers per cell. As expected, the most abundant proteins were those involved in protein synthesis, most notably ribosomal...... sample. Using a combination of LC-MS/MS approaches with protein and peptide fractionation steps we identified 1103 proteins from the cytosolic fraction of the Escherichia coli strain MC4100. A measure of abundance is presented for each of the identified proteins, based on the recently developed em...... protein and mRNA abundance in E. coli cells. Conclusion: Abundance measurements for more than 1000 E. coli proteins presented in this work represent the most complete study of protein abundance in a bacterial cell so far. We show significant associations between the abundance of a protein and its...

  9. SOLiD-SAGE of endophyte-infected red fescue reveals numerous effects on host transcriptome and an abundance of highly expressed fungal secreted proteins.

    Directory of Open Access Journals (Sweden)

    Karen V Ambrose

    Full Text Available One of the most important plant-fungal symbiotic relationships is that of cool season grasses with endophytic fungi of the genera Epichloë and Neotyphodium. These associations often confer benefits, such as resistance to herbivores and improved drought tolerance, to the hosts. One benefit that appears to be unique to fine fescue grasses is disease resistance. As a first step towards understanding the basis of the endophyte-mediated disease resistance in Festuca rubra we carried out a SOLiD-SAGE quantitative transcriptome comparison of endophyte-free and Epichloë festucae-infected F. rubra. Over 200 plant genes involved in a wide variety of physiological processes were statistically significantly differentially expressed between the two samples. Many of the endophyte expressed genes were surprisingly abundant, with the most abundant fungal tag representing over 10% of the fungal mapped tags. Many of the abundant fungal tags were for secreted proteins. The second most abundantly expressed fungal gene was for a secreted antifungal protein and is of particular interest regarding the endophyte-mediated disease resistance. Similar genes in Penicillium and Aspergillus spp. have been demonstrated to have antifungal activity. Of the 10 epichloae whole genome sequences available, only one isolate of E. festucae and Neotyphodium gansuense var inebrians have an antifungal protein gene. The uniqueness of this gene in E. festucae from F. rubra, its transcript abundance, and the secreted nature of the protein, all suggest it may be involved in the disease resistance conferred to the host, which is a unique feature of the fine fescue-endophyte symbiosis.

  10. SOLiD-SAGE of endophyte-infected red fescue reveals numerous effects on host transcriptome and an abundance of highly expressed fungal secreted proteins.

    Science.gov (United States)

    Ambrose, Karen V; Belanger, Faith C

    2012-01-01

    One of the most important plant-fungal symbiotic relationships is that of cool season grasses with endophytic fungi of the genera Epichloë and Neotyphodium. These associations often confer benefits, such as resistance to herbivores and improved drought tolerance, to the hosts. One benefit that appears to be unique to fine fescue grasses is disease resistance. As a first step towards understanding the basis of the endophyte-mediated disease resistance in Festuca rubra we carried out a SOLiD-SAGE quantitative transcriptome comparison of endophyte-free and Epichloë festucae-infected F. rubra. Over 200 plant genes involved in a wide variety of physiological processes were statistically significantly differentially expressed between the two samples. Many of the endophyte expressed genes were surprisingly abundant, with the most abundant fungal tag representing over 10% of the fungal mapped tags. Many of the abundant fungal tags were for secreted proteins. The second most abundantly expressed fungal gene was for a secreted antifungal protein and is of particular interest regarding the endophyte-mediated disease resistance. Similar genes in Penicillium and Aspergillus spp. have been demonstrated to have antifungal activity. Of the 10 epichloae whole genome sequences available, only one isolate of E. festucae and Neotyphodium gansuense var inebrians have an antifungal protein gene. The uniqueness of this gene in E. festucae from F. rubra, its transcript abundance, and the secreted nature of the protein, all suggest it may be involved in the disease resistance conferred to the host, which is a unique feature of the fine fescue-endophyte symbiosis.

  11. Protein abundance profiling of the Escherichia coli cytosol

    DEFF Research Database (Denmark)

    Ishihama, Y.; Schmidt, T.; Rappsilber, J.

    2008-01-01

    Background: Knowledge about the abundance of molecular components is an important prerequisite for building quantitative predictive models of cellular behavior. Proteins are central components of these models, since they carry out most of the fundamental processes in the cell. Thus far, protein...... sample. Using a combination of LC-MS/MS approaches with protein and peptide fractionation steps we identified 1103 proteins from the cytosolic fraction of the Escherichia coli strain MC4100. A measure of abundance is presented for each of the identified proteins, based on the recently developed em......PAI approach which takes into account the number of sequenced peptides per protein. The values of abundance are within a broad range and accurately reflect independently measured copy numbers per cell. As expected, the most abundant proteins were those involved in protein synthesis, most notably ribosomal...

  12. The highly abundant chlorophyll-protein complex of iron-deficient Synechococcus sp. PCC7942 (CP43') is encoded by the isiA gene.

    Science.gov (United States)

    Burnap, R L; Troyan, T; Sherman, L A

    1993-11-01

    A chlorophyll (Chl)-protein complex designated CPVI-4 becomes the major pigment-protein complex in Synechococcus sp. PCC7942 cells grown under conditions of iron limitation. Work by Laudenbach et al. (J Bacteriol [1988] 170: 5018-5026) has identified an iron-repressible operon, designated isiAB, containing the flavodoxin gene and a gene predicted to encode a Chl-binding protein resembling CP43 of photosystem II. To test the hypothesis that the CP43-like protein is a component of the CPVI-4 complex, we have inactivated the isiAB operon in Synechococcus sp. PCC7942 using directed insertional mutagenesis. Mutant cells grown under conditions of iron limitation exhibit pronounced changes in their spectroscopic and photosynthetic properties relative to similarly grown wild-type cells. Notably, the strong 77 K fluorescence emission at 685 nm, which dominates the spectrum of iron-deficient wild-type cells, is dramatically reduced in the mutant. The loss of this emission appears to unmask the otherwise obscured photosystem II emissions at 685 and 695 nm. Most importantly, mildly denaturing gel electrophoresis shows that mutant cells no longer express the CPVI-4 complex, indicating that the isiA gene encodes a component of this abundant Chl-protein complex.

  13. High abundance of Serine/Threonine-rich regions predicted to be hyper-O-glycosylated in the secretory proteins coded by eight fungal genomes

    Directory of Open Access Journals (Sweden)

    González Mario

    2012-09-01

    Full Text Available Abstract Background O-glycosylation of secretory proteins has been found to be an important factor in fungal biology and virulence. It consists in the addition of short glycosidic chains to Ser or Thr residues in the protein backbone via O-glycosidic bonds. Secretory proteins in fungi frequently display Ser/Thr rich regions that could be sites of extensive O-glycosylation. We have analyzed in silico the complete sets of putatively secretory proteins coded by eight fungal genomes (Botrytis cinerea, Magnaporthe grisea, Sclerotinia sclerotiorum, Ustilago maydis, Aspergillus nidulans, Neurospora crassa, Trichoderma reesei, and Saccharomyces cerevisiae in search of Ser/Thr-rich regions as well as regions predicted to be highly O-glycosylated by NetOGlyc (http://www.cbs.dtu.dk. Results By comparison with experimental data, NetOGlyc was found to overestimate the number of O-glycosylation sites in fungi by a factor of 1.5, but to be quite reliable in the prediction of highly O-glycosylated regions. About half of secretory proteins have at least one Ser/Thr-rich region, with a Ser/Thr content of at least 40% over an average length of 40 amino acids. Most secretory proteins in filamentous fungi were predicted to be O-glycosylated, sometimes in dozens or even hundreds of sites. Residues predicted to be O-glycosylated have a tendency to be grouped together forming hyper-O-glycosylated regions of varying length. Conclusions About one fourth of secretory fungal proteins were predicted to have at least one hyper-O-glycosylated region, which consists of 45 amino acids on average and displays at least one O-glycosylated Ser or Thr every four residues. These putative highly O-glycosylated regions can be found anywhere along the proteins but have a slight tendency to be at either one of the two ends.

  14. Automatic abundance analysis of high resolution spectra

    CERN Document Server

    Bonifacio, P; Bonifacio, Piercarlo; Caffau, Elisabetta

    2003-01-01

    We describe an automatic procedure for determining abundances from high resolution spectra. Such procedures are becoming increasingly important as large amounts of data are delivered from 8m telescopes and their high-multiplexing fiber facilities, such as FLAMES on ESO-VLT. The present procedure is specifically targeted for the analysis of spectra of giants in the Sgr dSph; however, the procedure may be, in principle, tailored to analyse stars of any type. Emphasis is placed on the algorithms and on the stability of the method; the external accuracy rests, ultimately, on the reliability of the theoretical models (model-atmospheres, synthetic spectra) used to interpret the data. Comparison of the results of the procedure with the results of a traditional analysis for 12 Sgr giants shows that abundances accurate at the level of 0.2 dex, comparable with that of traditional analysis of the same spectra, may be derived in a fast and efficient way. Such automatic procedures are not meant to replace the traditional ...

  15. Nitrogen Abundances in High-z DLAs

    CERN Document Server

    Molaro, P; D'Odorico, V; Péroux, C

    2003-01-01

    Determination of chemical abundances for elements produced mainly by Type I SNae and intermediate mass stars in high redshift DLAs probes the early chemical build-up on time-scales comparable with their production. Nitrogen shows a peculiar behaviour never detected before in any other class of objects. For [N/H] < -3 there is a plateau with [N/Si]= -1.45(\\pm 0.05). We interpret this as empirical evidence for primary N production by massive stars in young systems where AGB stars have not yet had time to make their contribution. The plateau provides the observational integrated yields for N production by massive stars which are theoretically rather uncertain. High N/Si and solar [alpha/iron-peak] ratios are observed at high redshift and place at an earlier epoch the onset of star formation. On the other hand, low N/Si, i.e. young objects, are observed also at relatively low redshifts. These evidences suggest that DLAs started to be formed at a very early epoch but their formation has been extended up to late...

  16. Quasar Elemental Abundances at High Redshifts

    DEFF Research Database (Denmark)

    Dietrich, M.; Hamann, F.; Shields, J. C.

    2003-01-01

    We examine rest-frame ultraviolet spectra of 70 high redshift quasars (z>3.5) to study the chemical enrichment history of the gas closely related to the quasars, and thereby estimate the epoch of first star formation. The fluxes of several ultraviolet emission lines were investigated within...... the framework of the most recent photoionization models to estimate the metallicity of the gas associated with the high-z quasars. Standard photoionization parameters and the assumption of secondary nitrogen enrichment indicate an average abundance of Z/Z_sol = 4 to 5 in the line emitting gas. Assuming a time...... scale of t_evol = 0.5 - 0.8 Gyrs for the chemical enrichment of the gas, the first major star formation for quasars with z>=4 should have started at a redshift of z_f = 6 - 8, corresponding to an age of the universe of several 10^8 yrs (H_o = 65 km/s/Mpc, Omega_M = 0.3, Omega_Lambda = 0.7). We note...

  17. Quasar Elemental Abundances at High Redshifts

    CERN Document Server

    Dietrich, M; Shields, J C; Constantin, A; Heidt, J; Jäger, K; Vestergaard, M; Wagner, S J

    2003-01-01

    We examine rest-frame ultraviolet spectra of 70 high redshift quasars (z>3.5) to study the chemical enrichment history of the gas closely related to the quasars, and thereby estimate the epoch of first star formation. The fluxes of several ultraviolet emission lines were investigated within the framework of the most recent photoionization models to estimate the metallicity of the gas associated with the high-z quasars. Standard photoionization parameters and the assumption of secondary nitrogen enrichment indicate an average abundance of Z/Z_sol = 4 to 5 in the line emitting gas. Assuming a time scale of t_evol = 0.5 - 0.8 Gyrs for the chemical enrichment of the gas, the first major star formation for quasars with z>=4 should have started at a redshift of z_f = 6 - 8, corresponding to an age of the universe of several 10^8 yrs (H_o = 65 km/s/Mpc, Omega_M = 0.3, Omega_Lambda = 0.7). We note that this also appears to be the era of re-ionization of the universe. Finally, there is some evidence for a positive lum...

  18. 甲醇沉淀法去除人血清高丰度蛋白质的实验研究%Establishment of methyl alcohol precipitation method for removing high abundant proteins in human serum

    Institute of Scientific and Technical Information of China (English)

    曹璐颖; 李克; 郑文杰

    2012-01-01

    Objective The common method of depleting the high abundant proteins in human serum is too complicated and ex -pensive to be applied to clinical practice . In this study, an effective and simple method of methyl alcohol precipitation was established for the removal of serum high abundant proteins. Methods The serum albumin of healthy controls was precipitated by different volume methyl alcohol. The removal effect was analyzed with one -dimensional sodium dodecyl sulfate -polyacrylamide gel electrophoresis ( SDS-PAGE) and quantitative method of albumin. Results Compared with the gel images of the original serum , the band of protein with molecular weight between 50000-80000 was removed. The results showed that the average concentration of albumin in the serum was de -creased from (47.65-.35) g/L to (1.16-.08) g/L. The removal ratio of protein was over 97% and the percentage of albumin in the total protein of serum was decreased from 65.4% to49.3%. The significantly statistical differences were observed (P<0.001). And the low abundance proteins could be seen and reserved . Conclusion The methyl alcohol depletion strategy may offer an effective and simple method to remove albumin from human serum , which provided a technical support for further study of serum proteomics .%目的 常用人血清高丰度蛋白质(high abundant proteins,HAP)去除方法操作较繁且成本高,文中探索建立简便有效的甲醇沉淀法去除人血清HAP.方法 用不同体积的甲醇处理血清样品,然后与原血清样品上样进行十二烷基磺酸钠聚丙烯酰胺凝胶电泳(sodium dodecyl sulfate-polyacrylamide gel electrophoresis,SDS-PAGE)分析,并对去除HAP后的样品进行蛋白定量检测.结果 SDS-PAGE显示,经甲醇处理过的血清样品与原血清电泳结果 相比,相对分子质量在50000~80000 间的清蛋白等HAP被明显去除,血清清蛋白平均浓度显著降低,由(47.65±0.35)g /L下降至(1.16±0.08)g /L,去除率达97%以上,

  19. Chromatofocusing fractionation and two-dimensional difference gel electrophoresis for low abundance serum proteins.

    Science.gov (United States)

    Qin, Shuzhen; Ferdinand, Angeline S; Richie, Jerome P; O'Leary, Michael P; Mok, Samuel C; Liu, Brian C-S

    2005-08-01

    The technical challenge to analysis of the serum proteome is that the serum proteins are present at unequal concentrations. A few are so dominant, such as serum albumin and immunoglobulins, that they mask detection of other proteins. Because of these high abundance proteins, current technologies, while theoretically capable of analyzing protein amounts spanning four orders of magnitude, are only able to analyze proteins ranging over two orders of magnitude and cannot analyze the lower abundance proteins that may be the next biomarkers and drug targets. To facilitate the identification of low abundance proteins, we fractionated serum samples from patients with prostate cancer and patients with benign prostate hyperplasia using anion displacement liquid chromatofocusing chromatography, which separates proteins by a pH gradient and a positively charged column. Differential expression of proteins from fractions was then determined and identified by IEF gels and 2-D DIGE. Results demonstrate improved resolution of proteins within the chosen pH gradient when compared to the unfractionated samples. Several proteins that were differentially expressed in serum from patients with prostate cancer were identified in the fractionated serum. Three of these proteins, squamous cell carcinoma antigen 1 (SCCA1), calgranulin B, and haptoglobin-related protein, are present in the serum at levels below the classical protein level of mg/mL. SCCA1 is normally expressed in serum at ng/mL levels, and calgranulin B is an intracellular protein. Our results demonstrate that the use of anion displacement liquid chromatofocusing chromatography may reduce the complexity of the serum proteome by separating proteins into distinct pH ranges, and facilitate the identification of low abundance proteins.

  20. Sensing Small Changes in Protein Abundance: Stimulation of Caco-2 Cells by Human Whey Proteins.

    Science.gov (United States)

    Cundiff, Judy K; McConnell, Elizabeth J; Lohe, Kimberly J; Maria, Sarah D; McMahon, Robert J; Zhang, Qiang

    2016-01-04

    Mass spectrometry (MS)-based proteomic approaches have largely facilitated our systemic understanding of cellular processes and biological functions. Cutoffs in protein expression fold changes (FCs) are often arbitrarily determined in MS-based quantification with no demonstrable determination of small magnitude changes in protein expression. Therefore, many biological insights may remain veiled due to high FC cutoffs. Herein, we employ the intestinal epithelial cell (IEC) line Caco-2 as a model system to demonstrate the dynamicity of tandem-mass-tag (TMT) labeling over a range of 5-40% changes in protein abundance, with the variance controls of ± 5% FC for around 95% of TMT ratios when sampling 9-12 biological replicates. We further applied this procedure to examine the temporal proteome of Caco-2 cells upon exposure to human whey proteins (WP). Pathway assessments predict subtle effects due to WP in moderating xenobiotic metabolism, promoting proliferation and various other cellular functions in differentiating enterocyte-like Caco-2 cells. This demonstration of a sensitive MS approach may open up new perspectives in the system-wide exploration of elusive or transient biological effects by facilitating scrutiny of narrow windows of proteome abundance changes. Furthermore, we anticipate this study will encourage more investigations of WP on infant gastrointestinal tract development.

  1. Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway.

    Science.gov (United States)

    Shi, Tujin; Niepel, Mario; McDermott, Jason E; Gao, Yuqian; Nicora, Carrie D; Chrisler, William B; Markillie, Lye M; Petyuk, Vladislav A; Smith, Richard D; Rodland, Karin D; Sorger, Peter K; Qian, Wei-Jun; Wiley, H Steven

    2016-07-12

    Various genetic mutations associated with cancer are known to alter cell signaling, but it is not clear whether they dysregulate signaling pathways by altering the abundance of pathway proteins. Using a combination of RNA sequencing and ultrasensitive targeted proteomics, we defined the primary components-16 core proteins and 10 feedback regulators-of the epidermal growth factor receptor (EGFR)-mitogen-activated protein kinase (MAPK) pathway in normal human mammary epithelial cells and then quantified their absolute abundance across a panel of normal and breast cancer cell lines as well as fibroblasts. We found that core pathway proteins were present at very similar concentrations across all cell types, with a variance similar to that of proteins previously shown to display conserved abundances across species. In contrast, EGFR and transcriptionally controlled feedback regulators were present at highly variable concentrations. The absolute abundance of most core proteins was between 50,000 and 70,000 copies per cell, but the adaptors SOS1, SOS2, and GAB1 were found at far lower amounts (2000 to 5000 copies per cell). MAPK signaling showed saturation in all cells between 3000 and 10,000 occupied EGFRs, consistent with the idea that adaptors limit signaling. Our results suggest that the relative stoichiometry of core MAPK pathway proteins is very similar across different cell types, with cell-specific differences mostly restricted to variable amounts of feedback regulators and receptors. The low abundance of adaptors relative to EGFR could be responsible for previous observations that only a fraction of total cell surface EGFR is capable of rapid endocytosis, high-affinity binding, and mitogenic signaling.

  2. [Functions of late embryogenesis abundant proteins in desiccation-tolerance of organisms: a review].

    Science.gov (United States)

    Liu, Yun; Liu, Guobao; Li, Ranhui; Zou, Yongdong; Zheng, Yizhi

    2010-05-01

    Late embryogenesis abundant (LEA) proteins are well associated with the desiccation tolerance in organisms. LEA proteins are categorized into at least seven groups by virtue of similarities in their deduced amino acid sequences. Most of the LEA proteins have the characteristics of high hydrophilicity and thermo-stability. The LEA proteins are in unstructured conformation in aqueous solution. However, they adopted amphiphilic alpha-helix structure during desiccation condition. LEA proteins are localized to the different organelles in the cells, i.e. cytoplasm, endoplasmic reticulum, mitochondria and nucleus. The multi-functional capacity of LEA proteins are suggested, as protein stabilization, protection of enzyme activity, membrane association and stabilization, antioxidant function, metal-ion binding or DNA protection, etc. Here, we review the structural and functional characteristics of LEA proteins to provide a reference platform to understand their protective mechanisms during the adaptive response to desiccation in organisms.

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

    Science.gov (United States)

    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.

  4. Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway

    Energy Technology Data Exchange (ETDEWEB)

    Shi, T.; Niepel, M.; McDermott, J. E.; Gao, Y.; Nicora, C. D.; Chrisler, W. B.; Markillie, L. M.; Petyuk, V. A.; Smith, R. D.; Rodland, K. D.; Sorger, P. K.; Qian, W. -J.; Wiley, H. S.

    2016-07-12

    It is not known whether cancer cells generally show quantitative differences in the expression of signaling pathway proteins that could dysregulate signal transduction. To explore this issue, we first defined the primary components of the EGF-MAPK pathway in normal human mammary epithelial cells, identifying 16 core proteins and 10 feedback regulators. We then quantified their absolute abundance across a panel of normal and cancer cell lines. We found that core pathway proteins were expressed at very similar levels across all cell types. In contrast, the EGFR and transcriptionally controlled feedback regulators were expressed at highly variable levels. The absolute abundance of most core pathway proteins was between 50,000- 70,000 copies per cell, but the adaptors SOS1, SOS2, and GAB1 were found at far lower levels (2,000-5,000 per cell). MAPK signaling showed saturation in all cells between 3,000-10,000 occupied EGFR, consistent with the idea that low adaptor levels limit signaling. Our results suggest that the core MAPK pathway is essentially invariant across different cell types, with cell- specific differences in signaling likely due to variable levels of feedback regulators. The low abundance of adaptors relative to the EGFR could be responsible for previous observation of saturable signaling, endocytosis, and high affinity EGFR.

  5. Assessment of Label-Free Quantification in Discovery Proteomics and Impact of Technological Factors and Natural Variability of Protein Abundance.

    Science.gov (United States)

    Al Shweiki, Mhd Rami; Mönchgesang, Susann; Majovsky, Petra; Thieme, Domenika; Trutschel, Diana; Hoehenwarter, Wolfgang

    2017-04-07

    We evaluated the state of label-free discovery proteomics focusing especially on technological contributions and contributions of naturally occurring differences in protein abundance to the intersample variability in protein abundance estimates in this highly peptide-centric technology. First, the performance of popular quantitative proteomics software, Proteome Discoverer, Scaffold, MaxQuant, and Progenesis QIP, was benchmarked using their default parameters and some modified settings. Beyond this, the intersample variability in protein abundance estimates was decomposed into variability introduced by the entire technology itself and variable protein amounts inherent to individual plants of the Arabidopsis thaliana Col-0 accession. The technical component was considerably higher than the biological intersample variability, suggesting an effect on the degree and validity of reported biological changes in protein abundance. Surprisingly, the biological variability, protein abundance estimates, and protein fold changes were recorded differently by the software used to quantify the proteins, warranting caution in the comparison of discovery proteomics results. As expected, ∼99% of the proteome was invariant in the isogenic plants in the absence of environmental factors; however, few proteins showed substantial quantitative variability. This naturally occurring variation between individual organisms can have an impact on the causality of reported protein fold changes.

  6. Unfoldomics of prostate cancer: on the abundance and roles of intrinsically disordered proteins in prostate cancer.

    Science.gov (United States)

    Landau, Kevin S; Na, Insung; Schenck, Ryan O; Uversky, Vladimir N

    2016-01-01

    Prostatic diseases such as prostate cancer and benign prostatic hyperplasia are highly prevalent among men. The number of studies focused on the abundance and roles of intrinsically disordered proteins in prostate cancer is rather limited. The goal of this study is to analyze the prevalence and degree of disorder in proteins that were previously associated with the prostate cancer pathogenesis and to compare these proteins to the entire human proteome. The analysis of these datasets provides means for drawing conclusions on the roles of disordered proteins in this common male disease. We also hope that the results of our analysis can potentially lead to future experimental studies of these proteins to find novel pathways associated with this disease.

  7. Regular patterns for proteome-wide distribution of protein abundance across species.

    Directory of Open Access Journals (Sweden)

    Fan Zhong

    Full Text Available A proteome of the bio-entity, including cell, tissue, organ, and organism, consists of proteins of diverse abundance. The principle that determines the abundance of different proteins in a proteome is of fundamental significance for an understanding of the building blocks of the bio-entity. Here, we report three regular patterns in the proteome-wide distribution of protein abundance across species such as human, mouse, fly, worm, yeast, and bacteria: in most cases, protein abundance is positively correlated with the protein's origination time or sequence conservation during evolution; it is negatively correlated with the protein's domain number and positively correlated with domain coverage in protein structure, and the correlations became stronger during the course of evolution; protein abundance can be further stratified by the function of the protein, whereby proteins that act on material conversion and transportation (mass category are more abundant than those that act on information modulation (information category. Thus, protein abundance is intrinsically related to the protein's inherent characters of evolution, structure, and function.

  8. High-resolution abundance analysis of HD 140283

    CERN Document Server

    Siqueira-Mello, C; Barbuy, B; Spite, M; Spite, F; Korotin, S A

    2015-01-01

    HD 140283 is a reference subgiant that is metal poor and confirmed to be a very old star. The abundances of this type of old star can constrain the nature and nucleosynthesis processes that occurred in its (even older) progenitors. The present study may shed light on nucleosynthesis processes yielding heavy elements early in the Galaxy. A detailed abundance analysis of a high-quality spectrum is carried out, with the intent of providing a reference on stellar lines and abundances of a very old, metal-poor subgiant. We aim to derive abundances from most available and measurable spectral lines. The analysis is carried out using high-resolution (R = 81 000) and high signal-to-noise ratio (800 < S/N/pixel < 3400) spectrum, in the wavelength range 3700 - 10475, obtained with a seven-hour exposure time, using the ESPaDOnS at the CFHT. The calculations in LTE were performed with the OSMARCS 1D atmospheric model and the spectrum synthesis code Turbospectrum, while the analysis in NLTE is based on the MULTI code...

  9. Intake of Meat Proteins Substantially Increased the Relative Abundance of Genus Lactobacillus in Rat Feces.

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    Yingying Zhu

    Full Text Available Diet has been shown to have a critical influence on gut bacteria and host health, and high levels of red meat in diet have been shown to increase colonic DNA damage and thus be harmful to gut health. However, previous studies focused more on the effects of meat than of meat proteins. In order to investigate whether intake of meat proteins affects the composition and metabolic activities of gut microbiota, feces were collected from growing rats that were fed with either meat proteins (from beef, pork or fish or non-meat proteins (casein or soy for 14 days. The resulting composition of gut microbiota was profiled by sequencing the V4-V5 region of the 16S ribosomal RNA genes and the short chain fatty acids (SCFAs were analyzed using gas chromatography. The composition of gut microbiota and SCFA levels were significantly different between the five diet groups. At a recommended dose of 20% protein in the diet, meat protein-fed rats had a higher relative abundance of the beneficial genus Lactobacillus, but lower levels of SCFAs and SCFA-producing bacteria including Fusobacterium, Bacteroides and Prevotella, compared with the soy protein-fed group. Further work is needed on the regulatory pathways linking dietary protein intake to gut microbiota.

  10. A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast.

    Science.gov (United States)

    Blein-Nicolas, Mélisande; Albertin, Warren; da Silva, Telma; Valot, Benoît; Balliau, Thierry; Masneuf-Pomarède, Isabelle; Bely, Marina; Marullo, Philippe; Sicard, Delphine; Dillmann, Christine; de Vienne, Dominique; Zivy, Michel

    2015-08-01

    Heterosis is a universal phenomenon that has major implications in evolution and is of tremendous agro-economic value. To study the molecular manifestations of heterosis and to find factors that maximize its strength, we implemented a large-scale proteomic experiment in yeast. We analyzed the inheritance of 1,396 proteins in 55 inter- and intraspecific hybrids obtained from Saccharomyces cerevisiae and S. uvarum that were grown in grape juice at two temperatures. We showed that the proportion of heterotic proteins was highly variable depending on the parental strain and on the temperature considered. For intraspecific hybrids, this proportion was higher at nonoptimal temperature. Unexpectedly, heterosis for protein abundance was strongly biased toward positive values in interspecific hybrids but not in intraspecific hybrids. Computer modeling showed that this observation could be accounted for by assuming concave relationships between protein abundances and their controlling factors, in line with the metabolic model of heterosis. These results point to nonlinear processes that could play a central role in heterosis.

  11. A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast*

    Science.gov (United States)

    Blein-Nicolas, Mélisande; Albertin, Warren; da Silva, Telma; Valot, Benoît; Balliau, Thierry; Masneuf-Pomarède, Isabelle; Bely, Marina; Marullo, Philippe; Sicard, Delphine; Dillmann, Christine; de Vienne, Dominique; Zivy, Michel

    2015-01-01

    Heterosis is a universal phenomenon that has major implications in evolution and is of tremendous agro-economic value. To study the molecular manifestations of heterosis and to find factors that maximize its strength, we implemented a large-scale proteomic experiment in yeast. We analyzed the inheritance of 1,396 proteins in 55 inter- and intraspecific hybrids obtained from Saccharomyces cerevisiae and S. uvarum that were grown in grape juice at two temperatures. We showed that the proportion of heterotic proteins was highly variable depending on the parental strain and on the temperature considered. For intraspecific hybrids, this proportion was higher at nonoptimal temperature. Unexpectedly, heterosis for protein abundance was strongly biased toward positive values in interspecific hybrids but not in intraspecific hybrids. Computer modeling showed that this observation could be accounted for by assuming concave relationships between protein abundances and their controlling factors, in line with the metabolic model of heterosis. These results point to nonlinear processes that could play a central role in heterosis. PMID:25971257

  12. Highly siderophile element abundances in Eoarchean komatiite and basalt protoliths

    Science.gov (United States)

    Frank, Elizabeth A.; Maier, Wolfgang D.; Mojzsis, Stephen J.

    2016-03-01

    Plume-derived, Mg-rich, volcanic rocks (komatiites, high-Mg basalts, and their metamorphic equivalents) can record secular changes in the highly siderophile element (HSE) abundances of mantle sources. An apparent secular time-dependent enrichment trend in HSE abundances from Paleoarchean to Paleoproterozoic mantle-derived rocks could represent the protracted homogenization of a Late Veneer chondritic contaminant into the pre-Late Veneer komatiite source. To search for a possible time dependence of a late accretion signature in the Eoarchean mantle, we report new data from rare >3700 Myr-old mafic and ultramafic schists locked in supracrustal belts from the Inukjuak domain (Québec, Canada) and the Akilia association (West Greenland). Our analysis shows that some of these experienced HSE mobility and/or include a cumulate component (Touboul et al. in Chem Geol 383:63-75, 2014), whereas several of the oldest samples show some of the most depleted HSE abundances measured for rocks of this composition. We consider these new data for the oldest documented rocks of komatiite protolith in light of the Late Veneer hypothesis.

  13. Hexapeptide libraries for enhanced protein PTM identification and relative abundance profiling in whole human saliva

    OpenAIRE

    Bandhakavi, Sricharan; van Riper, Susan K.; Tawfik, Pierre N; Matthew D Stone; Haddad, Tufia; Rhodus, Nelson L.; Carlis, John V.; Griffin, Timothy J.

    2011-01-01

    Dynamic range compression (DRC) by hexapeptide libraries increases MS/MS-based identification of lower-abundance proteins in complex mixtures. However, two unanswered questions impede fully realizing DRC’s potential in shotgun proteomics. First, does DRC enhance identification of post-translationally modified proteins? Second, can DRC be incorporated into a workflow enabling relative protein abundance profiling? We sought to answer both questions analyzing human whole saliva. Addressing quest...

  14. Identification of Differentially Abundant Proteins of Edwardsiella ictaluri during Iron Restriction.

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    Pradeep R Dumpala

    Full Text Available Edwardsiella ictaluri is a Gram-negative facultative anaerobe intracellular bacterium that causes enteric septicemia in channel catfish. Iron is an essential inorganic nutrient of bacteria and is crucial for bacterial invasion. Reduced availability of iron by the host may cause significant stress for bacterial pathogens and is considered a signal that leads to significant alteration in virulence gene expression. However, the precise effect of iron-restriction on E. ictaluri protein abundance is unknown. The purpose of this study was to identify differentially abundant proteins of E. ictaluri during in vitro iron-restricted conditions. We applied two-dimensional difference in gel electrophoresis (2D-DIGE for determining differentially abundant proteins and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF/TOF MS for protein identification. Gene ontology and pathway-based functional modeling of differentially abundant proteins was also conducted. A total of 50 unique differentially abundant proteins at a minimum of 2-fold (p ≤ 0.05 difference in abundance due to iron-restriction were detected. The numbers of up- and down-regulated proteins were 37 and 13, respectively. We noted several proteins, including EsrB, LamB, MalM, MalE, FdaA, and TonB-dependent heme/hemoglobin receptor family proteins responded to iron restriction in E. ictaluri.

  15. Nanomagnetic competition assay for low-abundance protein biomarker quantification in unprocessed human sera.

    Science.gov (United States)

    Li, Yuanpeng; Srinivasan, Balasubramanian; Jing, Ying; Yao, Xiaofeng; Hugger, Marie A; Wang, Jian-Ping; Xing, Chengguo

    2010-03-31

    A novel giant magnetoresistive sensor and uniform high-magnetic-moment FeCo nanoparticles (12.8 nm)-based detecting platform with minimized detecting distance was developed for rapid biomolecule quantification from body fluids. Such a system demonstrates specific, accurate, and quick detection and quantification of interleukin-6, a low-abundance protein and a potential cancer biomarker, directly in 4 muL of unprocessed human sera. This platform is expected to facilitate the identification and validation of disease biomarkers. It may eventually lead to a low-cost personal medical device for chronic disease early detection, diagnosis, and prognosis.

  16. Hexapeptide libraries for enhanced protein PTM identification and relative abundance profiling in whole human saliva

    Science.gov (United States)

    Bandhakavi, Sricharan; Van Riper, Susan K; Tawfik, Pierre N; Stone, Matthew D; Haddad, Tufia; Rhodus, Nelson L.; Carlis, John V.; Griffin, Timothy J

    2011-01-01

    SUMMARY Dynamic range compression (DRC) by hexapeptide libraries increases MS/MS-based identification of lower-abundance proteins in complex mixtures. However, two unanswered questions impede fully realizing DRC’s potential in shotgun proteomics. First, does DRC enhance identification of post-translationally modified proteins? Second, can DRC be incorporated into a workflow enabling relative protein abundance profiling? We sought to answer both questions analyzing human whole saliva. Addressing question one, we coupled DRC with covalent glycopeptide enrichment and MS/MS. With DRC we identified ~2 times more N-linked glycoproteins and their glycosylation sites than without DRC, dramatically increasing the known salivary glycoprotein catalog. Addressing question two, we compared differentially stable isotope-labeled saliva samples pooled from healthy and metastatic breast cancer women using a multidimensional peptide fractionation-based workflow, analyzing in parallel one sample portion with DRC and one portion without. Our workflow categorizes proteins with higher absolute abundance, whose relative abundance ratios are altered by DRC, from proteins of lower absolute abundance detected only after DRC. Within each of these salivary protein categories we identified novel abundance changes putatively associated with breast cancer, demonstrating feasibility and benefits of DRC for relative abundance profiling. Collectively, our results bring us closer to realizing the full potential of DRC for proteomic studies. PMID:21142092

  17. An abundant evolutionarily conserved CSB-PiggyBac fusion protein expressed in Cockayne syndrome.

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    John C Newman

    2008-03-01

    Full Text Available Cockayne syndrome (CS is a devastating progeria most often caused by mutations in the CSB gene encoding a SWI/SNF family chromatin remodeling protein. Although all CSB mutations that cause CS are recessive, the complete absence of CSB protein does not cause CS. In addition, most CSB mutations are located beyond exon 5 and are thought to generate only C-terminally truncated protein fragments. We now show that a domesticated PiggyBac-like transposon PGBD3, residing within intron 5 of the CSB gene, functions as an alternative 3' terminal exon. The alternatively spliced mRNA encodes a novel chimeric protein in which CSB exons 1-5 are joined in frame to the PiggyBac transposase. The resulting CSB-transposase fusion protein is as abundant as CSB protein itself in a variety of human cell lines, and continues to be expressed by primary CS cells in which functional CSB is lost due to mutations beyond exon 5. The CSB-transposase fusion protein has been highly conserved for at least 43 Myr since the divergence of humans and marmoset, and appears to be subject to selective pressure. The human genome contains over 600 nonautonomous PGBD3-related MER85 elements that were dispersed when the PGBD3 transposase was last active at least 37 Mya. Many of these MER85 elements are associated with genes which are involved in neuronal development, and are known to be regulated by CSB. We speculate that the CSB-transposase fusion protein has been conserved for host antitransposon defense, or to modulate gene regulation by MER85 elements, but may cause CS in the absence of functional CSB protein.

  18. Association between ferritin, high sensitivity c-reactive protein (hsCRP and relative abundance of Hepcidin mRNA with the risk of type 2 diabetes in obese subjects

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    Mónica Andrews Guzmán

    Full Text Available Obesity and Type 2 diabetes mellitus share a strong pro-inflammatory profile. It has been observed that iron is a risk factor in the development of type 2 diabetes. The aim of this study was to evaluate the relationship between iron nutritional status and inflammation with the risk of type 2 diabetes development in obese subjects. We studied 30 obese men with type 2 diabetes (OBDM; 30 obese subjects without diabetes (OB and 30 healthy subjects (Cn. We isolated peripheral mononuclear cells (PMCs and challenged them with high Fe concentrations. Total mRNA was isolated and relative abundance of TNF-αIL-6 and hepcidin were determined by qPCR. Iron status, biochemical, inflammatory and oxidative stress parameters were also characterized. OBDM and OB patients showed increased hsCRP levels compared to the Cn group. OBDM subjects showed higher levels of ferritin than the Cn group. TNF-α and IL-6 mRNA relative abundances were increased in OBDM PMCs treated with high/Fe. Hepcidin mRNA was increased with basal and high iron concentration. We found that the highest quartile of ferritin was associated with an increased risk of type 2 diabetes when it was adjusted to BMI and HOMA-IR; this association was independent of the inflammatory status. The highest level of hepcidin gene expression also showed a trend of increased risk of diabetes, however it was not significant. Levels of hsCRP over 2 mg/L showed a significant trend of increasing the risk of diabetes. In conclusion, iron may stimulate the expression of pro-inflammatory genes (TNF-α and IL-6, and both hepcidin and ferritin gene expression levels could be a risk factor for the development of type 2 diabetes. Subjects that have an increased cardiovascular risk also have a major risk to develop type 2 diabetes, which is independent of the BMI and insulin resistance state.

  19. Association between ferritin, high sensitivity C-reactive protein (hsCRP) and relative abundance of Hepcidin mRNA with the risk of type 2 diabetes in obese subjects.

    Science.gov (United States)

    Andrews Guzmán, Mónica; Arredondo Olguín, Miguel

    2014-09-01

    Obesity and Type 2 diabetes mellitus share a strong pro-inflammatory profile. It has been observed that iron is a risk factor in the development of type 2 diabetes. The aim of this study was to evaluate the relationship between iron nutritional status and inflammation with the risk of type 2 diabetes development in obese subjects. We studied 30 obese men with type 2 diabetes (OBDM); 30 obese subjects without diabetes (OB) and 30 healthy subjects (Cn). We isolated peripheral mononuclear cells (PMCs) and challenged them with high Fe concentrations. Total mRNA was isolated and relative abundance of TNF-, IL-6 and hepcidin were determined by qPCR. Iron status, biochemical, inflammatory and oxidative stress parameters were also characterized. OBDM and OB patients showed increased hsCRP levels compared to the Cn group. OBDM subjects showed higher levels of ferritin than the Cn group. TNF-α and IL-6 mRNA relative abundances were increased in OBDM PMCs treated with high/Fe. Hepcidin mRNA was increased with basal and high iron concentration. We found that the highest quartile of ferritin was associated with an increased risk of type 2 diabetes when it was adjusted to BMI and HOMA-IR; this association was independent of the inflammatory status. The highest level of hepcidin gene expression also showed a trend of increased risk of diabetes, however it was not significant. Levels of hsCRP over 2 mg/L showed a significant trend of increasing the risk of diabetes. In conclusion, iron may stimulate the expression of pro-inflammatory genes (TNF-α and IL- 6), and both hepcidin and ferritin gene expression levels could be a risk factor for the development of type 2 diabetes. Subjects that have an increased cardiovascular risk also have a major risk to develop type 2 diabetes, which is independent of the BMI and insulin resistance state.

  20. Abundantly and rarely expressed Lhc protein genes exhibit distinct regulation patterns in plants.

    Science.gov (United States)

    Klimmek, Frank; Sjödin, Andreas; Noutsos, Christos; Leister, Dario; Jansson, Stefan

    2006-03-01

    We have analyzed gene regulation of the Lhc supergene family in poplar (Populus spp.) and Arabidopsis (Arabidopsis thaliana) using digital expression profiling. Multivariate analysis of the tissue-specific, environmental, and developmental Lhc expression patterns in Arabidopsis and poplar was employed to characterize four rarely expressed Lhc genes, Lhca5, Lhca6, Lhcb7, and Lhcb4.3. Those genes have high expression levels under different conditions and in different tissues than the abundantly expressed Lhca1 to 4 and Lhcb1 to 6 genes that code for the 10 major types of higher plant light-harvesting proteins. However, in some of the datasets analyzed, the Lhcb4 and Lhcb6 genes as well as an Arabidopsis gene not present in poplar (Lhcb2.3) exhibited minor differences to the main cooperative Lhc gene expression pattern. The pattern of the rarely expressed Lhc genes was always found to be more similar to that of PsbS and the various light-harvesting-like genes, which might indicate distinct physiological functions for the rarely and abundantly expressed Lhc proteins. The previously undetected Lhcb7 gene encodes a novel plant Lhcb-type protein that possibly contains an additional, fourth, transmembrane N-terminal helix with a highly conserved motif. As the Lhcb4.3 gene seems to be present only in Eurosid species and as its regulation pattern varies significantly from that of Lhcb4.1 and Lhcb4.2, we conclude it to encode a distinct Lhc protein type, Lhcb8.

  1. Overexpression Analysis of emv2 gene coding for Late Embryogenesis Abundant Protein from Vigna radiata (Wilczek

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    Rajesh S.

    2008-10-01

    Full Text Available Late embryogenesis abundant (LEA proteins are speculated to protect against water stress deficit in plants. An over expression system for mungbean late embryogenesis abundant protein, emv2 was constructed in a pET29a vector, designated pET-emv2 which is responsible for higher expression under the transcriptional/translational control of T7/lac promoter incorporated in the Escherichia coli BL21 (DE3.Induction protocol was optimized for pET recombinants harboring the target gene. Overexpressed EMV2 protein was purified to homogeneity and the protein profile monitored by SDS-PAGE.

  2. Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications.

    Science.gov (United States)

    Gu, W; Crawford, E D; O'Donovan, B D; Wilson, M R; Chow, E D; Retallack, H; DeRisi, J L

    2016-03-04

    Next-generation sequencing has generated a need for a broadly applicable method to remove unwanted high-abundance species prior to sequencing. We introduce DASH (Depletion of Abundant Sequences by Hybridization). Sequencing libraries are 'DASHed' with recombinant Cas9 protein complexed with a library of guide RNAs targeting unwanted species for cleavage, thus preventing them from consuming sequencing space. We demonstrate a more than 99 % reduction of mitochondrial rRNA in HeLa cells, and enrichment of pathogen sequences in patient samples. We also demonstrate an application of DASH in cancer. This simple method can be adapted for any sample type and increases sequencing yield without additional cost.

  3. Two novel heat-soluble protein families abundantly expressed in an anhydrobiotic tardigrade.

    Science.gov (United States)

    Yamaguchi, Ayami; Tanaka, Sae; Yamaguchi, Shiho; Kuwahara, Hirokazu; Takamura, Chizuko; Imajoh-Ohmi, Shinobu; Horikawa, Daiki D; Toyoda, Atsushi; Katayama, Toshiaki; Arakawa, Kazuharu; Fujiyama, Asao; Kubo, Takeo; Kunieda, Takekazu

    2012-01-01

    Tardigrades are able to tolerate almost complete dehydration by reversibly switching to an ametabolic state. This ability is called anhydrobiosis. In the anhydrobiotic state, tardigrades can withstand various extreme environments including space, but their molecular basis remains largely unknown. Late embryogenesis abundant (LEA) proteins are heat-soluble proteins and can prevent protein-aggregation in dehydrated conditions in other anhydrobiotic organisms, but their relevance to tardigrade anhydrobiosis is not clarified. In this study, we focused on the heat-soluble property characteristic of LEA proteins and conducted heat-soluble proteomics using an anhydrobiotic tardigrade. Our heat-soluble proteomics identified five abundant heat-soluble proteins. All of them showed no sequence similarity with LEA proteins and formed two novel protein families with distinct subcellular localizations. We named them Cytoplasmic Abundant Heat Soluble (CAHS) and Secretory Abundant Heat Soluble (SAHS) protein families, according to their localization. Both protein families were conserved among tardigrades, but not found in other phyla. Although CAHS protein was intrinsically unstructured and SAHS protein was rich in β-structure in the hydrated condition, proteins in both families changed their conformation to an α-helical structure in water-deficient conditions as LEA proteins do. Two conserved repeats of 19-mer motifs in CAHS proteins were capable to form amphiphilic stripes in α-helices, suggesting their roles as molecular shield in water-deficient condition, though charge distribution pattern in α-helices were different between CAHS and LEA proteins. Tardigrades might have evolved novel protein families with a heat-soluble property and this study revealed a novel repertoire of major heat-soluble proteins in these anhydrobiotic animals.

  4. Two novel heat-soluble protein families abundantly expressed in an anhydrobiotic tardigrade.

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    Ayami Yamaguchi

    Full Text Available Tardigrades are able to tolerate almost complete dehydration by reversibly switching to an ametabolic state. This ability is called anhydrobiosis. In the anhydrobiotic state, tardigrades can withstand various extreme environments including space, but their molecular basis remains largely unknown. Late embryogenesis abundant (LEA proteins are heat-soluble proteins and can prevent protein-aggregation in dehydrated conditions in other anhydrobiotic organisms, but their relevance to tardigrade anhydrobiosis is not clarified. In this study, we focused on the heat-soluble property characteristic of LEA proteins and conducted heat-soluble proteomics using an anhydrobiotic tardigrade. Our heat-soluble proteomics identified five abundant heat-soluble proteins. All of them showed no sequence similarity with LEA proteins and formed two novel protein families with distinct subcellular localizations. We named them Cytoplasmic Abundant Heat Soluble (CAHS and Secretory Abundant Heat Soluble (SAHS protein families, according to their localization. Both protein families were conserved among tardigrades, but not found in other phyla. Although CAHS protein was intrinsically unstructured and SAHS protein was rich in β-structure in the hydrated condition, proteins in both families changed their conformation to an α-helical structure in water-deficient conditions as LEA proteins do. Two conserved repeats of 19-mer motifs in CAHS proteins were capable to form amphiphilic stripes in α-helices, suggesting their roles as molecular shield in water-deficient condition, though charge distribution pattern in α-helices were different between CAHS and LEA proteins. Tardigrades might have evolved novel protein families with a heat-soluble property and this study revealed a novel repertoire of major heat-soluble proteins in these anhydrobiotic animals.

  5. Two Novel Heat-Soluble Protein Families Abundantly Expressed in an Anhydrobiotic Tardigrade

    Science.gov (United States)

    Yamaguchi, Ayami; Tanaka, Sae; Yamaguchi, Shiho; Kuwahara, Hirokazu; Takamura, Chizuko; Imajoh-Ohmi, Shinobu; Horikawa, Daiki D.; Toyoda, Atsushi; Katayama, Toshiaki; Arakawa, Kazuharu; Fujiyama, Asao; Kubo, Takeo; Kunieda, Takekazu

    2012-01-01

    Tardigrades are able to tolerate almost complete dehydration by reversibly switching to an ametabolic state. This ability is called anhydrobiosis. In the anhydrobiotic state, tardigrades can withstand various extreme environments including space, but their molecular basis remains largely unknown. Late embryogenesis abundant (LEA) proteins are heat-soluble proteins and can prevent protein-aggregation in dehydrated conditions in other anhydrobiotic organisms, but their relevance to tardigrade anhydrobiosis is not clarified. In this study, we focused on the heat-soluble property characteristic of LEA proteins and conducted heat-soluble proteomics using an anhydrobiotic tardigrade. Our heat-soluble proteomics identified five abundant heat-soluble proteins. All of them showed no sequence similarity with LEA proteins and formed two novel protein families with distinct subcellular localizations. We named them Cytoplasmic Abundant Heat Soluble (CAHS) and Secretory Abundant Heat Soluble (SAHS) protein families, according to their localization. Both protein families were conserved among tardigrades, but not found in other phyla. Although CAHS protein was intrinsically unstructured and SAHS protein was rich in β-structure in the hydrated condition, proteins in both families changed their conformation to an α-helical structure in water-deficient conditions as LEA proteins do. Two conserved repeats of 19-mer motifs in CAHS proteins were capable to form amphiphilic stripes in α-helices, suggesting their roles as molecular shield in water-deficient condition, though charge distribution pattern in α-helices were different between CAHS and LEA proteins. Tardigrades might have evolved novel protein families with a heat-soluble property and this study revealed a novel repertoire of major heat-soluble proteins in these anhydrobiotic animals. PMID:22937162

  6. LEA (Late Embryogenesis Abundant proteins and their encoding genes in Arabidopsis thaliana

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    Hincha Dirk K

    2008-03-01

    Full Text Available Abstract Background LEA (late embryogenesis abundant proteins have first been described about 25 years ago as accumulating late in plant seed development. They were later found in vegetative plant tissues following environmental stress and also in desiccation tolerant bacteria and invertebrates. Although they are widely assumed to play crucial roles in cellular dehydration tolerance, their physiological and biochemical functions are largely unknown. Results We present a genome-wide analysis of LEA proteins and their encoding genes in Arabidopsis thaliana. We identified 51 LEA protein encoding genes in the Arabidopsis genome that could be classified into nine distinct groups. Expression studies were performed on all genes at different developmental stages, in different plant organs and under different stress and hormone treatments using quantitative RT-PCR. We found evidence of expression for all 51 genes. There was only little overlap between genes expressed in vegetative tissues and in seeds and expression levels were generally higher in seeds. Most genes encoding LEA proteins had abscisic acid response (ABRE and/or low temperature response (LTRE elements in their promoters and many genes containing the respective promoter elements were induced by abscisic acid, cold or drought. We also found that 33% of all Arabidopsis LEA protein encoding genes are arranged in tandem repeats and that 43% are part of homeologous pairs. The majority of LEA proteins were predicted to be highly hydrophilic and natively unstructured, but some were predicted to be folded. Conclusion The analyses indicate a wide range of sequence diversity, intracellular localizations, and expression patterns. The high fraction of retained duplicate genes and the inferred functional diversification indicate that they confer an evolutionary advantage for an organism under varying stressful environmental conditions. This comprehensive analysis will be an important starting point for

  7. Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis

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    McDermott Jason E

    2012-04-01

    Full Text Available Abstract Background High-throughput methods for obtaining global measurements of transcript and protein levels in biological samples has provided a large amount of data for identification of 'target' genes and proteins of interest. These targets may be mediators of functional processes involved in disease and therefore represent key points of control for viruses and bacterial pathogens. Genes and proteins that are the most highly differentially regulated are generally considered to be the most important. We present topological analysis of co-abundance networks as an alternative to differential regulation for confident identification of target proteins from two related global proteomics studies of hepatitis C virus (HCV infection. Results We analyzed global proteomics data sets from a cell culture study of HCV infection and from a clinical study of liver biopsies from HCV-positive patients. Using lists of proteins known to be interaction partners with pathogen proteins we show that the most differentially regulated proteins in both data sets are indeed enriched in pathogen interactors. We then use these data sets to generate co-abundance networks that link proteins based on similar abundance patterns in time or across patients. Analysis of these co-abundance networks using a variety of network topology measures revealed that both degree and betweenness could be used to identify pathogen interactors with better accuracy than differential regulation alone, though betweenness provides the best discrimination. We found that though overall differential regulation was not correlated between the cell culture and liver biopsy data, network topology was conserved to an extent. Finally, we identified a set of proteins that has high betweenness topology in both networks including a protein that we have recently shown to be essential for HCV replication in cell culture. Conclusions The results presented show that the network topology of protein co-abundance

  8. Late embryogenesis abundant proteins protect human hepatoma cells during acute desiccation.

    Science.gov (United States)

    Li, Shumin; Chakraborty, Nilay; Borcar, Apurva; Menze, Michael A; Toner, Mehmet; Hand, Steven C

    2012-12-18

    Expression of late embryogenesis abundant (LEA) proteins is highly correlated with desiccation tolerance in anhydrobiotic animals, selected land plants, and bacteria. Genes encoding two LEA proteins, one localized to the cytoplasm/nucleus (AfrLEA2) and one targeted to mitochondria (AfrLEA3m), were stably transfected into human HepG2 cells. A trehalose transporter was used for intracellular loading of this disaccharide. Cells were rapidly and uniformly desiccated to low water content (spin-drying technique. Immediately on rehydration, control cells without LEA proteins or trehalose exhibited 0% membrane integrity, compared with 98% in cells loaded with trehalose and expressing AfrLEA2 or AfrLEA3m; surprisingly, AfrLEA3m without trehalose conferred 94% protection. Cell proliferation across 7 d showed an 18-fold increase for cells dried with AfrLEA3m and trehalose, compared with 27-fold for nondried controls. LEA proteins dramatically enhance desiccation tolerance in mammalian cells and offer the opportunity for engineering biostability in the dried state.

  9. System wide analyses have underestimated protein abundances and the importance of transcription in mammals.

    Science.gov (United States)

    Li, Jingyi Jessica; Bickel, Peter J; Biggin, Mark D

    2014-01-01

    Large scale surveys in mammalian tissue culture cells suggest that the protein expressed at the median abundance is present at 8,000-16,000 molecules per cell and that differences in mRNA expression between genes explain only 10-40% of the differences in protein levels. We find, however, that these surveys have significantly underestimated protein abundances and the relative importance of transcription. Using individual measurements for 61 housekeeping proteins to rescale whole proteome data from Schwanhausser et al. (2011), we find that the median protein detected is expressed at 170,000 molecules per cell and that our corrected protein abundance estimates show a higher correlation with mRNA abundances than do the uncorrected protein data. In addition, we estimated the impact of further errors in mRNA and protein abundances using direct experimental measurements of these errors. The resulting analysis suggests that mRNA levels explain at least 56% of the differences in protein abundance for the 4,212 genes detected by Schwanhausser et al. (2011), though because one major source of error could not be estimated the true percent contribution should be higher. We also employed a second, independent strategy to determine the contribution of mRNA levels to protein expression. We show that the variance in translation rates directly measured by ribosome profiling is only 12% of that inferred by Schwanhausser et al. (2011), and that the measured and inferred translation rates correlate poorly (R(2) = 0.13). Based on this, our second strategy suggests that mRNA levels explain ∼81% of the variance in protein levels. We also determined the percent contributions of transcription, RNA degradation, translation and protein degradation to the variance in protein abundances using both of our strategies. While the magnitudes of the two estimates vary, they both suggest that transcription plays a more important role than the earlier studies implied and translation a much smaller

  10. System wide analyses have underestimated protein abundances and the importance of transcription in mammals

    Directory of Open Access Journals (Sweden)

    Jingyi Jessica Li

    2014-02-01

    Full Text Available Large scale surveys in mammalian tissue culture cells suggest that the protein expressed at the median abundance is present at 8,000–16,000 molecules per cell and that differences in mRNA expression between genes explain only 10–40% of the differences in protein levels. We find, however, that these surveys have significantly underestimated protein abundances and the relative importance of transcription. Using individual measurements for 61 housekeeping proteins to rescale whole proteome data from Schwanhausser et al. (2011, we find that the median protein detected is expressed at 170,000 molecules per cell and that our corrected protein abundance estimates show a higher correlation with mRNA abundances than do the uncorrected protein data. In addition, we estimated the impact of further errors in mRNA and protein abundances using direct experimental measurements of these errors. The resulting analysis suggests that mRNA levels explain at least 56% of the differences in protein abundance for the 4,212 genes detected by Schwanhausser et al. (2011, though because one major source of error could not be estimated the true percent contribution should be higher. We also employed a second, independent strategy to determine the contribution of mRNA levels to protein expression. We show that the variance in translation rates directly measured by ribosome profiling is only 9% of that inferred by Schwanhausser et al. (2011, and that the measured and inferred translation rates correlate poorly (R2 = 0.14. Based on this, our second strategy suggests that mRNA levels explain ∼84% of the variance in protein levels. We also determined the percent contributions of transcription, RNA degradation, translation and protein degradation to the variance in protein abundances using both of our strategies. While the magnitudes of the two estimates vary, they both suggest that transcription plays a more important role than the earlier studies implied and translation

  11. Highly Multiplexed Profiling of Low Abundance Tumor Mutations in Plasma

    Science.gov (United States)

    Wiggin, Matthew; Pel, Joel; Vysotskaia, Valentina; Broemeling, David; Marziali, Andre; Hanson, Dan

    2013-01-01

    We have demonstrated a novel somatic mutation enrichment methodology demonstrating multiplexed detection of tumor mutations in plasma with sensitivity as low as 0.01% compared to normal DNA. This highly sensitive detection of low abundance mutations is achieved using electrophoretic separation and enrichment of DNA fragments containing point mutations over their wild-type counterparts. Commercialized as the OnTarget platform by Boreal Genomics, the system enriches nucleic acid samples for specific targets prior to amplification and detection, enabling the use of next-generation sequencing (NGS) or other detection assays for plasma or FFPE-based mutation detection and profiling. We present data demonstrating highly sensitive and multiplexed detection of panels of up to 100 mutations in plasma samples, improving the sensitivity of NGS assays to below 0.01% mutant content. We also report on concordance studies comparing low tumor content FFPE tissue and matched plasma in human samples demonstrating that OnTarget represents a robust, highly sensitive and multiplexed platform for non-invasive tumor monitoring.

  12. Two Novel Heat-Soluble Protein Families Abundantly Expressed in an Anhydrobiotic Tardigrade

    OpenAIRE

    Ayami Yamaguchi; Sae Tanaka; Shiho Yamaguchi; Hirokazu Kuwahara; Chizuko Takamura; Shinobu Imajoh-Ohmi; Horikawa, Daiki D.; Atsushi Toyoda; Toshiaki Katayama; Kazuharu Arakawa; Asao Fujiyama; Takeo Kubo; Takekazu Kunieda

    2012-01-01

    Tardigrades are able to tolerate almost complete dehydration by reversibly switching to an ametabolic state. This ability is called anhydrobiosis. In the anhydrobiotic state, tardigrades can withstand various extreme environments including space, but their molecular basis remains largely unknown. Late embryogenesis abundant (LEA) proteins are heat-soluble proteins and can prevent protein-aggregation in dehydrated conditions in other anhydrobiotic organisms, but their relevance to tardigrade a...

  13. Nitrogen 15 abundance in protein fractions of beans fertilized with (15NH42SO4

    Directory of Open Access Journals (Sweden)

    Chaud Saula Goulart

    2002-01-01

    Full Text Available Studies evaluating the protein nutritive value of beans labelled with 15N, ussing nitrogen balance and the quantitation of faecal and urinary endogenous nitrogen, determined by isotopic dilution, have been extensively used. The objective of this research was to verify if the isotopic labelling of raw, freeze dried beans (Phaseolus vulgaris L., cultivar Piratã 1 with 1.394 atoms%15N, resulted in the same abundance of the whole flour and of the protein fractions extracted from the beans with 0.5 mol L-1 NaCl. The isotopic abundance found in the whole bean flour, in the protein extract, in the globulin and albumin fractions were respectively: 1.394 ± 0.011; 1.403 ± 0.012; 1.399 ± 0.007 and 1.399 ± 0.028 atoms % of 15N, presenting no difference (P > 0.05. However, a difference was found (P < 0.05 between the above mentioned abundances and the isotopic abundance found in the nitrogen of the proteins in the extraction residue, which was 0.969 ± 0.084. Since the abundances did not differ, the protein nutritive indexes, such as digestibility and biological value, determined from the nitrogen balance and corrected for isotopic dilution, would not be affected by extracting the proteins from the beans with 0.5 mol L¹ NaCl. If working with the nitrogen balance of the residual proteins after extraction and even with the whole flours, these indexes could present incorrect values, since the isotopic labelling of the residual proteins was less than that of the protein fractions.

  14. Visualization and Dissemination of Multidimensional Proteomics Data Comparing Protein Abundance During Caenorhabditis elegans Development

    Science.gov (United States)

    Riffle, Michael; Merrihew, Gennifer E.; Jaschob, Daniel; Sharma, Vagisha; Davis, Trisha N.; Noble, William S.; MacCoss, Michael J.

    2015-11-01

    Regulation of protein abundance is a critical aspect of cellular function, organism development, and aging. Alternative splicing may give rise to multiple possible proteoforms of gene products where the abundance of each proteoform is independently regulated. Understanding how the abundances of these distinct gene products change is essential to understanding the underlying mechanisms of many biological processes. Bottom-up proteomics mass spectrometry techniques may be used to estimate protein abundance indirectly by sequencing and quantifying peptides that are later mapped to proteins based on sequence. However, quantifying the abundance of distinct gene products is routinely confounded by peptides that map to multiple possible proteoforms. In this work, we describe a technique that may be used to help mitigate the effects of confounding ambiguous peptides and multiple proteoforms when quantifying proteins. We have applied this technique to visualize the distribution of distinct gene products for the whole proteome across 11 developmental stages of the model organism Caenorhabditis elegans. The result is a large multidimensional dataset for which web-based tools were developed for visualizing how translated gene products change during development and identifying possible proteoforms. The underlying instrument raw files and tandem mass spectra may also be downloaded. The data resource is freely available on the web at http://www.yeastrc.org/wormpes/.

  15. Snake venoms are integrated systems, but abundant venom proteins evolve more rapidly.

    Science.gov (United States)

    Aird, Steven D; Aggarwal, Shikha; Villar-Briones, Alejandro; Tin, Mandy Man-Ying; Terada, Kouki; Mikheyev, Alexander S

    2015-08-28

    While many studies have shown that extracellular proteins evolve rapidly, how selection acts on them remains poorly understood. We used snake venoms to understand the interaction between ecology, expression level, and evolutionary rate in secreted protein systems. Venomous snakes employ well-integrated systems of proteins and organic constituents to immobilize prey. Venoms are generally optimized to subdue preferred prey more effectively than non-prey, and many venom protein families manifest positive selection and rapid gene family diversification. Although previous studies have illuminated how individual venom protein families evolve, how selection acts on venoms as integrated systems, is unknown. Using next-generation transcriptome sequencing and mass spectrometry, we examined microevolution in two pitvipers, allopatrically separated for at least 1.6 million years, and their hybrids. Transcriptomes of parental species had generally similar compositions in regard to protein families, but for a given protein family, the homologs present and concentrations thereof sometimes differed dramatically. For instance, a phospholipase A2 transcript comprising 73.4 % of the Protobothrops elegans transcriptome, was barely present in the P. flavoviridis transcriptome (venoms. Protein evolutionary rates were positively correlated with transcriptomic and proteomic abundances, and the most abundant proteins showed positive selection. This pattern holds with the addition of four other published crotaline transcriptomes, from two more genera, and also for the recently published king cobra genome, suggesting that rapid evolution of abundant proteins may be generally true for snake venoms. Looking more broadly at Protobothrops, we show that rapid evolution of the most abundant components is due to positive selection, suggesting an interplay between abundance and adaptation. Given log-scale differences in toxin abundance, which are likely correlated with biosynthetic costs, we

  16. Construction of a two-dimensional liquid chromatography separation system for high abundance proteins depletion in human plasma%去除血浆中高丰度蛋白质的二维液相色谱体系的建立

    Institute of Scientific and Technical Information of China (English)

    朱绍春; 张学洋; 高明霞; 晏国全; 张祥民

    2011-01-01

    High abundance proteins existing in human plasma severely impede the detection of low abundance proteins. This is one of the most difficult problems encountered in plasma pro-teomics research. We developed a two-dimensional liquid chromatography system with strong anion exchange chromatography-reversed-phase liquid chromatography ( SAX-RPLC) for the extensive separation of plasma proteins and selective depletion of high abundance proteins. TSKgel SuperQ-5PW was selected as the first dimensional separation column for crude human plasma fractionation and Jupiter C4 column was selected as the second dimensional separation column. Separation gradients of the two-dimensional liquid chromatography system were optimized to ensure an extensive separation of plasma proteins. Ten peaks with high signal intensities ( >20 mAU) at 215 nm during the second dimensional separation were collected and identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). As a result, 32 proteins, all of which were reported to be high abundance proteins in plasma, including human serum albumin (HAS), immunoglobulin G (IgG) and so on were successfully identified. This system provides an effective method for future depletion of more high abundance proteins and in-depth research in human plasma proteomics.%血浆中高丰度蛋白质的存在严重干扰低丰度蛋白质的检测,是困扰血浆蛋白质组学研究的技术瓶颈之一.针对这一热点问题,建立了一种二维液相色谱(强阴离子交换色谱-反相高效液相色谱)分离系统,对血浆中的高丰度蛋白质进行了色谱定位并进行去除.选择TSKgel SuperQ-5PW为第一维色谱分离柱,第二维色谱分离采用Jupiter C4柱,对第一维的馏分进行进一步的分离.通过梯度优化,血浆样品经过二维系统得到充分分离.第二维分离过程中从紫外信号强度高(215 nm,大于20 mAU)的峰中选择10个峰,利用液相色谱-串联质谱鉴定出32种高丰度蛋白质,

  17. Iron Abundance Diagnostics in High-Redshift QSOs

    CERN Document Server

    Corbin, M R; Freduling, N K W; Corbin, Michael R.; Korista, Kirk T.; Freduling, Nalaka Kodituwakku & Wolfram

    2004-01-01

    The abundance of alpha-process elements such as magnesium and carbon relative to iron measured from the broad emission lines of QSOs can serve as a diagnostic of the star formation and chemical enrichment histories of their host galaxies. We investigate the relationship between Fe/Mg and Fe/C abundance ratios and the resulting Fe II / Mg II 2800A and Fe II / 1900A-blend flux ratios, both of which have been measured in QSOs out to redshifts of approximately six. Using a galactic chemical evolution model based on a starburst in a giant elliptical galaxy, we find that these flux ratios are good tracers of the chemical enrichment of the nuclei. However, the values of these ratios measured in objects at redshifts of approximately six suggest that iron enrichment has occurred more rapidly in these objects than predicted by the assumed elliptical starburst model, under currently favored cosmologies.

  18. Lithium abundances in high- and low-alpha halo stars

    DEFF Research Database (Denmark)

    Nissen, P. E.; Schuster, W. J.

    2012-01-01

    is well fitted by a relation A(Li) = a0 + a1 M + a2 Z + a3 M Z, where a0, a1, a2, and a3 are constants. Extrapolating this relation to Z = 0 leads to A(Li)= 2.58 ± 0.08 close to the primordial Li abundance predicted from standard Big Bang nucleosynthesis calculations and the WMAP baryon density. A...

  19. Synergistic effects of high fat feeding and apolipoprotein E deletion on enterocytic amyloid-beta abundance

    Directory of Open Access Journals (Sweden)

    Dhaliwal Satvinder S

    2008-04-01

    Full Text Available Abstract Background Amyloid-β (Aβ, a key protein found in amyloid plaques of subjects with Alzheimer's disease is expressed in the absorptive epithelial cells of the small intestine. Ingestion of saturated fat significantly enhances enterocytic Aβ abundance whereas fasting abolishes expression. Apolipoprotein (apo E has been shown to directly modulate Aβ biogenesis in liver and neuronal cells but it's effect in enterocytes is not known. In addition, apo E modulates villi length, which may indirectly modulate Aβ as a consequence of differences in lipid absorption. This study compared Aβ abundance and villi length in wild-type (WT and apo E knockout (KO mice maintained on either a low-fat or high-fat diet. Wild-type C57BL/6J and apo E KO mice were randomised for six-months to a diet containing either 4% (w/w unsaturated fats, or chow comprising 16% saturated fats and 1% cholesterol. Quantitative immunohistochemistry was used to assess Aβ abundance in small intestinal enterocytes. Apo E KO mice given the low-fat diet had similar enterocytic Aβ abundance compared to WT controls. Results The saturated fat diet substantially increased enterocytic Aβ in WT and in apo E KO mice, however the effect was greater in the latter. Villi height was significantly greater in apo E KO mice than for WT controls when given the low-fat diet. However, WT mice had comparable villi length to apo E KO when fed the saturated fat and cholesterol enriched diet. There was no effect of the high-fat diet on villi length in apo E KO mice. Conclusion The findings of this study are consistent with the notion that lipid substrate availability modulates enterocytic Aβ. Apo E may influence enterocytic lipid availability by modulating absorptive capacity.

  20. Pharmacological zinc and phytase supplementation enhance metallothionein mRNA abundance and protein concentration in newly weaned pigs.

    Science.gov (United States)

    Martínez, Michelle M; Hill, Gretchen M; Link, Jane E; Raney, Nancy E; Tempelman, Robert J; Ernst, Catherine W

    2004-03-01

    The swine industry feeds pharmacological zinc (Zn) to newly weaned pigs to improve health. Because most swine diets are plant-based with a high phytic acid content, we hypothesized that adding phytase to diets could reduce the amount of Zn required to obtain beneficial responses. The role of metallothionein (MT) in Zn homeostasis could be important in this positive response. Thus, the goal of this study was to investigate the effect of dietary Zn and phytase on relative MT mRNA abundance and protein concentration in newly weaned pigs. Diets containing adequate (150 mg Zn/kg) or pharmacological concentrations of Zn (1000 or 2000 mg Zn/kg), as zinc oxide, with or without phytase [0, 500 phytase units (FTU)/kg, Natuphos, BASF] were fed in a 3 x 2 factorial design. Plasma and tissue minerals were measured in pigs killed after 14 d of dietary intervention. Hepatic and renal relative MT mRNA abundance and protein were greater (P pigs fed 1000 mg Zn/kg with phytase, or 2000 mg Zn/kg with or without phytase vs. the remaining treatments. Intestinal mucosa MT mRNA abundance and protein were greater (P pigs fed 2000 mg Zn/kg with phytase than in pigs fed 2000 mg Zn/kg alone or 1000 mg Zn/kg with phytase. Pigs fed 1000 mg Zn/kg plus phytase or 2000 mg Zn/kg with or without phytase had higher plasma, hepatic, and renal Zn than those fed the adequate Zn diets or 1000 mg Zn/kg. We conclude that feeding 1000 mg Zn/kg with phytase enhances MT mRNA abundance and protein and Zn absorption to the same degree as 2000 mg Zn/kg with and without phytase.

  1. Changes In Protein Abundance Are Observed In Bacterial Isolates from a Natural Host

    Directory of Open Access Journals (Sweden)

    Megan Anne Rees

    2015-10-01

    Full Text Available Bacterial proteomic studies frequently use strains cultured in synthetic liquid media over many generations. It is uncertain whether bacterial proteins expressed under these conditions will be the same as the repertoire found in natural environments, or when bacteria are infecting a host organism. Thus, genomic and proteomic characterisation of bacteria derived from the host environment in comparison to reference strains grown in the lab, should aid understanding of pathogenesis. Isolates of Corynebacterium pseudotuberculosis were obtained from the nodes of three naturally infected sheep and compared to a laboratory reference strain using bottom-up proteomics, after whole genome sequencing of each of the field isolates. These comparisons were performed following growth in liquid media that allowed us to reach the required protein amount for proteomic analysis. Over 1350 proteins identified in the isolated strains, from which unique proteome features were revealed. Several of the identified proteins demonstrated a significant abundance difference in the field isolates compared to the reference strain even though there were no obvious differences in the DNA sequence of the corresponding gene or in nearby non-coding DNA. Higher abundance in the field isolates was observed for proteins related to hypoxia and nutrient deficiency responses as well as to thiopeptide biosynthesis.

  2. Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in GeneSpecific Translation Efficiency in Yeast

    DEFF Research Database (Denmark)

    Lahtvee, Petri-Jaan; Sanchez, Benjamin J.; Smialowska, Agata

    2017-01-01

    to model translation efficiencies and found that they vary more than 400-fold between genes. Non-linear regression analysis detected that mRNA abundance and translation elongation were the dominant factors controlling protein synthesis, explaining 61% and 15% of its variance. Metabolic flux balance......Protein synthesis is the most energy-consuming process in a proliferating cell, and understanding what controls protein abundances represents a key question in biology and biotechnology. We quantified absolute abundances of 5,354 mRNAs and 2,198 proteins in Saccharomyces cerevisiae under ten...

  3. Lithium abundances in high- and low-alpha halo stars

    DEFF Research Database (Denmark)

    Nissen, P. E.; Schuster, W. J.

    2012-01-01

    A previous study of F and G main-sequence stars in the solar neighborhood has revealed the existence of two distinct halo populations with a clear separation in [alpha /Fe] for the metallicity range -1.4 < [Fe/H] < -0.7. The kinematics of the stars and models of galaxy formation suggest that the ......A previous study of F and G main-sequence stars in the solar neighborhood has revealed the existence of two distinct halo populations with a clear separation in [alpha /Fe] for the metallicity range -1.4 ... is well fitted by a relation A(Li) = a0 + a1 M + a2 Z + a3 M Z, where a0, a1, a2, and a3 are constants. Extrapolating this relation to Z = 0 leads to A(Li)= 2.58 ± 0.08 close to the primordial Li abundance predicted from standard Big Bang nucleosynthesis calculations and the WMAP baryon density. A...

  4. High Mobility Group Proteins and Their Post-Translational Modifications

    OpenAIRE

    Zhang, Qingchun; Wang, Yinsheng

    2008-01-01

    The high mobility group (HMG) proteins, including HMGA, HMGB and HMGN, are abundant and ubiquitous nuclear proteins that bind to DNA, nucleosome and other multi-protein complexes in a dynamic and reversible fashion to regulate DNA processing in the context of chromatin. All HMG proteins, like histone proteins, are subjected to extensive post-translational modifications (PTMs), such as lysine acetylation, arginine/lysine methylation and serine/threonine phosphorylation, to modulate their inter...

  5. Protein abundance of clinically relevant multidrug transporters along the entire length of the human intestine.

    Science.gov (United States)

    Drozdzik, Marek; Gröer, Christian; Penski, Jette; Lapczuk, Joanna; Ostrowski, Marek; Lai, Yurong; Prasad, Bhagwat; Unadkat, Jashvant D; Siegmund, Werner; Oswald, Stefan

    2014-10-01

    Intestinal transporters are crucial determinants in the oral absorption of many drugs. We therefore studied the mRNA expression (N = 33) and absolute protein content (N = 10) of clinically relevant transporters in healthy epithelium of the duodenum, the proximal and distal jejunum and ileum, and the ascending, transversal, descending, and sigmoidal colon of six organ donors (24-54 years). In the small intestine, the abundance of nearly all studied proteins ranged between 0.2 and 1.6 pmol/mg with the exception of those of OCT3 (intestinal segment. ABCB1, ABCG2, PEPT1, and ASBT were significantly more abundant in jejunum and ileum than in colon. In contrast to this, the level of expression of ABCC2, ABCC3, and OCT3 was found to be highest in colon. Site-dependent differences in the levels of gene and protein expression were observed for ABCB1 and ASBT. Significant correlations between mRNA and protein levels have been found for ABCG2, ASBT, OCT3, and PEPT1 in the small intestine. Our data provide further physiological pieces of the puzzle required to predict intestinal drug absorption in humans.

  6. Exoproteome analysis reveals higher abundance of proteins linked to alkaline stress in persistent Listeria monocytogenes strains.

    Science.gov (United States)

    Rychli, Kathrin; Grunert, Tom; Ciolacu, Luminita; Zaiser, Andreas; Razzazi-Fazeli, Ebrahim; Schmitz-Esser, Stephan; Ehling-Schulz, Monika; Wagner, Martin

    2016-02-02

    The foodborne pathogen Listeria monocytogenes, responsible for listeriosis a rare but severe infection disease, can survive in the food processing environment for month or even years. So-called persistent L. monocytogenes strains greatly increase the risk of (re)contamination of food products, and are therefore a great challenge for food safety. However, our understanding of the mechanism underlying persistence is still fragmented. In this study we compared the exoproteome of three persistent strains with the reference strain EGDe under mild stress conditions using 2D differential gel electrophoresis. Principal component analysis including all differentially abundant protein spots showed that the exoproteome of strain EGDe (sequence type (ST) 35) is distinct from that of the persistent strain R479a (ST8) and the two closely related ST121 strains 4423 and 6179. Phylogenetic analyses based on multilocus ST genes showed similar grouping of the strains. Comparing the exoproteome of strain EGDe and the three persistent strains resulted in identification of 22 differentially expressed protein spots corresponding to 16 proteins. Six proteins were significantly increased in the persistent L. monocytogenes exoproteomes, among them proteins involved in alkaline stress response (e.g. the membrane anchored lipoprotein Lmo2637 and the NADPH dehydrogenase NamA). In parallel the persistent strains showed increased survival under alkaline stress, which is often provided during cleaning and disinfection in the food processing environments. In addition, gene expression of the proteins linked to stress response (Lmo2637, NamA, Fhs and QoxA) was higher in the persistent strain not only at 37 °C but also at 10 °C. Invasion efficiency of EGDe was higher in intestinal epithelial Caco2 and macrophage-like THP1 cells compared to the persistent strains. Concurrently we found higher expression of proteins involved in virulence in EGDe e.g. the actin-assembly-inducing protein ActA and the

  7. Highly thermostable fluorescent proteins

    Science.gov (United States)

    Bradbury, Andrew M [Santa Fe, NM; Waldo, Geoffrey S [Santa Fe, NM; Kiss, Csaba [Los Alamos, NM

    2012-05-01

    Thermostable fluorescent proteins (TSFPs), methods for generating these and other stability-enhanced proteins, polynucleotides encoding such proteins, and assays and method for using the TSFPs and TSFP-encoding nucleic acid molecules are provided. The TSFPs of the invention show extremely enhanced levels of stability and thermotolerance. In one case, for example, a TSFP of the invention is so stable it can be heated to 99.degree. C. for short periods of time without denaturing, and retains 85% of its fluorescence when heated to 80.degree. C. for several minutes. The invention also provides a method for generating stability-enhanced variants of a protein, including but not limited to fluorescent proteins.

  8. Highly thermostable fluorescent proteins

    Science.gov (United States)

    Bradbury, Andrew M.; Waldo, Geoffrey S.; Kiss, Csaba

    2011-03-22

    Thermostable fluorescent proteins (TSFPs), methods for generating these and other stability-enhanced proteins, polynucleotides encoding such proteins, and assays and method for using the TSFPs and TSFP-encoding nucleic acid molecules are provided. The TSFPs of the invention show extremely enhanced levels of stability and thermotolerance. In one case, for example, a TSFP of the invention is so stable it can be heated to 99.degree. C. for short periods of time without denaturing, and retains 85% of its fluorescence when heated to 80.degree. C. for several minutes. The invention also provides a method for generating stability-enhanced variants of a protein, including but not limited to fluorescent proteins.

  9. How much can we trust high-resolution spectroscopic stellar chemical abundances?

    Science.gov (United States)

    Blanco-Cuaresma, S.; Nordlander, T.; Heiter, U.; Jofré, P.; Masseron, T.; Casamiquela, L.; Tabernero, H. M.; Bhat, S. S.; Casey, A. R.; Meléndez, J.; Ramírez, I.

    2017-03-01

    To study stellar populations, it is common to combine chemical abundances from different spectroscopic surveys/studies where different setups were used. These inhomogeneities can lead us to inaccurate scientific conclusions. In this work, we studied one aspect of the problem: When deriving chemical abundances from high-resolution stellar spectra, what differences originate from the use of different radiative transfer codes?

  10. How much can we trust high-resolution spectroscopic stellar chemical abundances?

    CERN Document Server

    Blanco-Cuaresma, S; Heiter, U; Jofré, P; Masseron, T; Casamiquela, L; Tabernero, H M; Bhat, S S; Casey, A R; Meléndez, J; Ramírez, I

    2016-01-01

    To study stellar populations, it is common to combine chemical abundances from different spectroscopic surveys/studies where different setups were used. These inhomogeneities can lead us to inaccurate scientific conclusions. In this work, we studied one aspect of the problem: When deriving chemical abundances from high-resolution stellar spectra, what differences originate from the use of different radiative transfer codes?

  11. Metal-rich absorbers at high redshifts: abundance patterns

    CERN Document Server

    Levshakov, S A; Molaro, P; Reimers, D; Hou, J L

    2009-01-01

    (Abbreviated) From six spectra of high-z QSOs, we select eleven metal-rich, Z>=Z_solar, and optically-thin to the ionizing radiation, N(HI)0, which supposes that the nitrogen enrichment occurs irregularly. In some cases, the lines of MgII 2796, 2803 appear to be shifted, probably as a result of an enhanced content of heavy isotopes 25Mg and 26Mg in the absorbing gas relative to the solar isotopic composition. Seven absorbers are characterized by low mean ionization parameter U, log U2 whereas all others are found at z ~= 1.8. Comparing the space number density of metal-rich absorbers with the comoving density of star-forming galaxies at z ~= 2, we estimate that the circumgalactic volume of each galaxy is populated by 10^7 - 10^8 such absorbers with total mass <=1/100th of the stellar galactic mass. Possible effects of high metal content on the peak values of star-forming and AGN activities at z~2 are discussed.

  12. Protamine sulfate precipitation method depletes abundant plant seed-storage proteins: A case study on legume plants.

    Science.gov (United States)

    Kim, Yu Ji; Wang, Yiming; Gupta, Ravi; Kim, So Wun; Min, Chul Woo; Kim, Yong Chul; Park, Ki Hun; Agrawal, Ganesh Kumar; Rakwal, Randeep; Choung, Myoung-Gun; Kang, Kyu Young; Kim, Sun Tae

    2015-05-01

    Depletion of abundant proteins is one of the effective ways to improve detection and identification of low-abundance proteins. Our previous study showed that protamine sulfate precipitation (PSP) method can deplete abundant ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) from leaf proteins and is suitable for their in-depth proteome investigation. In this study, we provide evidence that the PSP method can also be effectively used for depletion of abundant seed-storage proteins (SSPs) from the total seed proteins of diverse legume plants including soybean, broad bean, pea, wild soybean, and peanut. The 0.05% protamine sulfate (PS) was sufficient to deplete major SSPs from all legumes tested except for peanut where 0.1% PS was required. SDS-PAGE, Western blotting and 2DE analyses of PS-treated soybean and peanut seed proteins showed enriched spots in PS-supernatant than total proteins. Coefficient of variation percentage (%CV) and principal component analysis of 2DE spots support the reproducibility, suitability, and efficacy of the PSP method for quantitative and comparative seed proteome analysis. MALDI-TOF-TOF successfully identified some protein spots from soybean and peanut. Hence, this simple, reproducible, economical PSP method has a broader application in depleting plant abundant proteins including SSPs in addition to RuBisCO, allowing discussion for comprehensive proteome establishment and parallel comparative studies in plants.

  13. One-step non-chromatography purification of a low abundant fucosylated protein from complex plant crude extract

    Directory of Open Access Journals (Sweden)

    Lindsay Arnold

    2015-08-01

    Full Text Available Effective methods for isolation and purification of glycoproteins and other glycoconjugates are important to biopharmaceutical industry and diagnostic industry. They are also critical to an emerging field of glycoproteomics. In this work, we applied the newly-developed affinity ligand, a fusion protein of elastic like polymer (ELP and a bacterial lectin, in an affinity precipitation process to purify soybean peroxidase (SBP based on the presence of fucoseon the protein surface. We addressed, in particular, the challenge of purifying a low abundant protein from a complex dilute crude plant extract. The novel affinity precipitation developed in this work was very promising. One step binding and precipitation resulted in >95% recovery yield directly from crude extract and a 22.7 fold purification, giving a specific activity of 420 U/mg. The SBP isolated using this affinity precipitation meets or exceeds the quality specifications of reagent grade products by Sigma. We showed that the recovery yield had a strong dependence on the molar ratio of ligand to target fucosylated protein, with a ratio of three giving nearly full recovery, which could be predicted based on the total fucose content per protein molecule and the number of binding site per ligand molecule. We additionally developed a method of ligand regeneration and investigated its reuse. A simple wash with pH buffer was shown to be effective to regenerate the binding capacity for the ligand, and the ligand could be used for 10 times, giving an averaged 80% isolation yield based on initial input of soybean peroxidase. Taken together, an effective method of affinity precipitation was developed, which could be used to enrich a low abundant target glycoprotein from a complex mixture with a high recovery yield. The high selectivity for fucosylated protein and its ease of operation make this method particularly useful for purification of low abundant glycoprotein from natural sources. This work

  14. Discrepancy between mRNA and protein abundance: Insight from information retrieval process in computers

    Science.gov (United States)

    Wang, Degeng

    2008-01-01

    Discrepancy between the abundance of cognate protein and RNA molecules is frequently observed. A theoretical understanding of this discrepancy remains elusive, and it is frequently described as surprises and/or technical difficulties in the literature. Protein and RNA represent different steps of the multi-stepped cellular genetic information flow process, in which they are dynamically produced and degraded. This paper explores a comparison with a similar process in computers - multi-step information flow from storage level to the execution level. Functional similarities can be found in almost every facet of the retrieval process. Firstly, common architecture is shared, as the ribonome (RNA space) and the proteome (protein space) are functionally similar to the computer primary memory and the computer cache memory respectively. Secondly, the retrieval process functions, in both systems, to support the operation of dynamic networks – biochemical regulatory networks in cells and, in computers, the virtual networks (of CPU instructions) that the CPU travels through while executing computer programs. Moreover, many regulatory techniques are implemented in computers at each step of the information retrieval process, with a goal of optimizing system performance. Cellular counterparts can be easily identified for these regulatory techniques. In other words, this comparative study attempted to utilize theoretical insight from computer system design principles as catalysis to sketch an integrative view of the gene expression process, that is, how it functions to ensure efficient operation of the overall cellular regulatory network. In context of this bird’s-eye view, discrepancy between protein and RNA abundance became a logical observation one would expect. It was suggested that this discrepancy, when interpreted in the context of system operation, serves as a potential source of information to decipher regulatory logics underneath biochemical network operation. PMID

  15. Conformation of a group 2 late embryogenesis abundant protein from soybean. Evidence of poly (L-proline)-type II structure.

    Science.gov (United States)

    Soulages, Jose L; Kim, Kangmin; Arrese, Estela L; Walters, Christina; Cushman, John C

    2003-03-01

    Late embryogenesis abundant (LEA) proteins are members of a large group of hydrophilic, glycine-rich proteins found in plants, algae, fungi, and bacteria known collectively as hydrophilins that are preferentially expressed in response to dehydration or hyperosmotic stress. Group 2 LEA (dehydrins or responsive to abscisic acid) proteins are postulated to stabilize macromolecules against damage by freezing, dehydration, ionic, or osmotic stress. However, the structural and physicochemical properties of group 2 LEA proteins that account for such functions remain unknown. We have analyzed the structural properties of a recombinant form of a soybean (Glycine max) group 2 LEA (rGmDHN1). Differential scanning calorimetry of purified rGmDHN1 demonstrated that the protein does not display a cooperative unfolding transition upon heating. Ultraviolet absorption and circular dichroism spectroscopy revealed that the protein is in a largely hydrated and unstructured conformation in solution. However, ultraviolet absorption and circular dichroism measurements collected at different temperatures showed that the protein exists in equilibrium between two extended conformational states: unordered and left-handed extended helical or poly (L-proline)-type II structures. It is estimated that 27% of the residues of rGmDHN1 adopt or poly (L-proline)-type II-like helical conformation at 12 degrees C. The content of extended helix gradually decreases to 15% as the temperature is increased to 80 degrees C. Studies of the conformation of the protein in solution in the presence of liposomes, trifluoroethanol, and sodium dodecyl sulfate indicated that rGmDHN1 has a very low intrinsic ability to adopt alpha-helical structure and to interact with phospholipid bilayers through amphipathic alpha-helices. The ability of the protein to remain in a highly extended conformation at low temperatures could constitute the basis of the functional role of GmDHN1 in the prevention of freezing, desiccation

  16. Characterization of threonine side chain dynamics in an antifreeze protein using natural abundance {sup 13}C NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Daley, Margaret E.; Sykes, Brian D. [University of Alberta, Department of Biochemistry, CIHR Group in Protein Structure and Function and Protein Engineering Network of Centres of Excellence (Canada)

    2004-06-15

    The dynamics of threonine side chains of the Tenebrio molitor antifreeze protein (TmAFP) were investigated using natural abundance {sup 13}C NMR. In TmAFP, the array of threonine residues on one face of the protein is responsible for conferring its ability to bind crystalline ice and inhibit its growth. Heteronuclear longitudinal and transverse relaxation rates and the {sup 1}H-{sup 13}C NOE were determined in this study. The C{alpha}H relaxation measurements were compared to the previously measured {sup 15}N backbone parameters and these are found to be in agreement. For the analysis of the threonine side chain motions, the model of restricted rotational diffusion about the {chi}{sub 1} dihedral angle was employed [London and Avitabile (1978) J. Am. Chem. Soc., 100, 7159-7165]. We demonstrate that the motion experienced by the ice binding threonine side chains is highly restricted, with an approximate upper limit of less than {+-}25 deg.

  17. Study of model systems to test the potential function of Artemia group 1 late embryogenesis abundant (LEA) proteins.

    Science.gov (United States)

    Warner, Alden H; Guo, Zhi-hao; Moshi, Sandra; Hudson, John W; Kozarova, Anna

    2016-01-01

    Embryos of the brine shrimp, Artemia franciscana, are genetically programmed to develop either ovoviparously or oviparously depending on environmental conditions. Shortly upon their release from the female, oviparous embryos enter diapause during which time they undergo major metabolic rate depression while simultaneously synthesize proteins that permit them to tolerate a wide range of stressful environmental events including prolonged periods of desiccation, freezing, and anoxia. Among the known stress-related proteins that accumulate in embryos entering diapause are the late embryogenesis abundant (LEA) proteins. This large group of intrinsically disordered proteins has been proposed to act as molecular shields or chaperones of macromolecules which are otherwise intolerant to harsh conditions associated with diapause. In this research, we used two model systems to study the potential function of the group 1 LEA proteins from Artemia. Expression of the Artemia group 1 gene (AfrLEA-1) in Escherichia coli inhibited growth in proportion to the number of 20-mer amino acid motifs expressed. As well, clones of E. coli, transformed with the AfrLEA-1 gene, expressed multiple bands of LEA proteins, either intrinsically or upon induction with isopropyl-β-thiogalactoside (IPTG), in a vector-specific manner. Expression of AfrLEA-1 in E. coli did not overcome the inhibitory effects of high concentrations of NaCl and KCl but modulated growth inhibition resulting from high concentrations of sorbitol in the growth medium. In contrast, expression of the AfrLEA-1 gene in Saccharomyces cerevisiae did not alter the growth kinetics or permit yeast to tolerate high concentrations of NaCl, KCl, or sorbitol. However, expression of AfrLEA-1 in yeast improved its tolerance to drying (desiccation) and freezing. Under our experimental conditions, both E. coli and S. cerevisiae appear to be potentially suitable hosts to study the function of Artemia group 1 LEA proteins under environmentally

  18. Investigation of SnSPR1, a novel and abundant surface protein of Sarcocystis neurona merozoites.

    Science.gov (United States)

    Zhang, Deqing; Howe, Daniel K

    2008-04-15

    An expressed sequence tag (EST) sequencing project has produced over 15,000 partial cDNA sequences from the equine pathogen Sarcocystis neurona. While many of the sequences are clear homologues of previously characterized genes, a significant number of the S. neurona ESTs do not exhibit similarity to anything in the extensive sequence databases that have been generated. In an effort to characterize parasite proteins that are novel to S. neurona, a seemingly unique gene was selected for further investigation based on its abundant representation in the collection of ESTs and the predicted presence of a signal peptide and glycolipid anchor addition on the encoded protein. The gene was expressed in E. coli, and monospecific polyclonal antiserum against the recombinant protein was produced by immunization of a rabbit. Characterization of the native protein in S. neurona merozoites and schizonts revealed that it is a low molecular weight surface protein that is expressed throughout intracellular development of the parasite. The protein was designated Surface Protein 1 (SPR1) to reflect its display on the outer surface of merozoites and to distinguish it from the ubiquitous SAG/SRS surface antigens of the heteroxenous Coccidia. Interestingly, infection assays in the presence of the polyclonal antiserum suggested that SnSPR1 plays some role in attachment and/or invasion of host cells by S. neurona merozoites. The work described herein represents a general template for selecting and characterizing the various unidentified gene sequences that are plentiful in the EST databases for S. neurona and other apicomplexans. Furthermore, this study illustrates the value of investigating these novel sequences since it can offer new candidates for diagnostic or vaccine development while also providing greater insight into the biology of these parasites.

  19. Structuring high-protein foods

    NARCIS (Netherlands)

    Purwanti, N.

    2012-01-01

    Increased protein consumption gives rise to various health benefits. High-protein intake can lead to muscle development, body weight control and suppression of sarcopenia progression. However, increasing the protein content in food products leads to textural changes over time. These changes result i

  20. Maternal bisphenol A exposure alters rat offspring hepatic and skeletal muscle insulin signaling protein abundance.

    Science.gov (United States)

    Galyon, Kristina D; Farshidi, Farnoosh; Han, Guang; Ross, Michael G; Desai, Mina; Jellyman, Juanita K

    2017-03-01

    The obesogenic and diabetogenic effects of the environmental toxin bisphenol A during critical windows of development are well recognized. Liver and skeletal muscle play a central role in the control of glucose production, utilization, and storage. We hypothesized that maternal bisphenol A exposure disrupts insulin signaling in rat offspring liver and skeletal muscle. We determined the protein expression of hepatic and skeletal muscle insulin signaling molecules including insulin receptor beta, its downstream target insulin receptor substrate 1 and glucose transporters (glucose transporter 2, glucose transporter 4), and hepatic glucose-regulating enzymes phosphoenolpyruvate carboxykinase and glucokinase. Rat dams had ad libitum access to filtered drinking water (control) or drinking water with bisphenol A from 2 weeks prior to mating and through pregnancy and lactation. Offspring litters were standardized to 4 males and 4 females and nursed by the same dam. At weaning, bisphenol A exposure was removed from all offspring. Glucose tolerance was tested at 6 weeks and 6 months. Liver and skeletal muscle was collected from 3 week old and 10 month old offspring for protein expression (Western blot) of insulin receptor beta, insulin receptor substrate 1, glucose transporter 2, glucose transporter 4, phosphoenolpyruvate carboxykinase, and glucokinase. Male, but not female, bisphenol A offspring had impaired glucose tolerance at 6 weeks and 6 months. Both male and female adult offspring had higher glucose-stimulated insulin secretion as well as the ratio of stimulated insulin to glucose. Male bisphenol A offspring had higher liver protein abundance of the 200 kDa insulin receptor beta precursor (2-fold), and insulin receptor substrate 1 (1.5-fold), whereas glucose transporter 2 was 0.5-fold of the control at 3 weeks of age. In adult male bisphenol A offspring, the abundance of insulin receptor beta was higher (2-fold) and glucose transporter 4 was 0.8-fold of the control in

  1. In-depth analysis of low abundant proteins in bovine colostrum using different fractionation techniques

    DEFF Research Database (Denmark)

    Nissen, Asger; Bendixen, Emøke; Ingvartsen, Klaus Lønne

    2012-01-01

    in the nonfractionated colostrum (NF) and seven fractions (F1-F7) using six different fractionation techniques. Fractionation contributed with 69 additional proteins in the fluid phase compared with NF. Different fractionation techniques each resulted in detection of unique subsets of proteins. Whey production by high...

  2. Functional insights into the late embryogenesis abundant (LEA) protein family from Dendrobium officinale (Orchidaceae) using an Escherichia coli system.

    Science.gov (United States)

    Ling, Hong; Zeng, Xu; Guo, Shunxing

    2016-12-22

    Late embryogenesis abundant (LEA) proteins, a diverse family, accumulate during seed desiccation in the later stages of embryogenesis. LEA proteins are associated with tolerance to abiotic stresses, such as drought, salinity and high or cold temperature. Here, we report the first comprehensive survey of the LEA gene family in Dendrobium officinale, an important and widely grown medicinal orchid in China. Based on phylogenetic relationships with the complete set of Arabidopsis and Oryza LEA proteins, 17 genes encoding D. officinale LEAs (DofLEAs) were identified and their deduced proteins were classified into seven groups. The motif composition of these deduced proteins was correlated with the gene structure found in each LEA group. Our results reveal the DofLEA genes are widely distributed and expressed in tissues. Additionally, 11 genes from different groups were introduced into Escherichia coli to assess the functions of DofLEAs. Expression of 6 and 7 DofLEAs in E. coli improved growth performance compared with the control under salt and heat stress, respectively. Based on qPCR data, all of these genes were up-regulated in various tissues following exposure to salt and heat stresses. Our results suggest that DofLEAs play an important role in responses to abiotic stress.

  3. Sc and neutron-capture abundances in Galactic low- and high-α field halo stars

    Science.gov (United States)

    Fishlock, C. K.; Yong, D.; Karakas, A. I.; Alves-Brito, A.; Meléndez, J.; Nissen, P. E.; Kobayashi, C.; Casey, A. R.

    2017-01-01

    We determine relative abundance ratios for the neutron-capture elements Zr, La, Ce, Nd, and Eu for a sample of 27 Galactic dwarf stars with -1.5 < [Fe/H] <-0.8. We also measure the iron-peak element Sc. These stars separate into three populations (low- and high-α halo and thick-disc stars) based on the [α/Fe] abundance ratio and their kinematics as discovered by Nissen & Schuster. We find differences between the low- and high-α groups in the abundance ratios of [Sc/Fe], [Zr/Fe], [La/Zr], [Y/Eu], and [Ba/Eu] when including Y and Ba from Nissen & Schuster. For all ratios except [La/Zr], the low-α stars have a lower abundance compared to the high-α stars. The low-α stars display the same abundance patterns of high [Ba/Y] and low [Y/Eu] as observed in present-day dwarf spheroidal galaxies, although with smaller abundance differences, when compared to the high-α stars. These distinct chemical patterns have been attributed to differences in the star formation rate between the two populations and the contribution of low-metallicity, low-mass asymptotic giant branch (AGB) stars to the low-α population. By comparing the low-α population with AGB stellar models, we place constraints on the mass range of the AGB stars.

  4. Isolation of Low Abundance Proteins and Cells Using Buoyant Glass Microbubble Chromatography

    Directory of Open Access Journals (Sweden)

    Steingrimur Stefansson

    2013-01-01

    Full Text Available Conventional protein affinity chromatography relies on highly porous resins that have large surface areas. These properties are ideal for fast flow separation of proteins from biological samples with maximum yields, but these properties can also lead to increased nonspecific protein binding. In certain applications where the purity of an isolated protein is more important than the yield, using a glass solid phase could be advantageous as glass is nonporous and hydrophilic and has a low surface area and low nonspecific protein binding. As a proof of principle, we used protein A-conjugated hollow glass microbubbles to isolate fluorescently labeled neurofilament heavy chain spiked into serum and compared them to protein A Sepharose and protein A magnetic beads (Dynabeads using an anti-neurofilament protein antibody. As expected, a greater volume of glass bubbles was required to match the binding capacity of the magnetic beads and Sepharose resins. On the other hand, nonspecific protein binding to glass bubbles was greatly reduced compared to the other resins. Additionally, since the glass bubbles are buoyant and transparent, they are well suited for isolating cells from biological samples and staining them in situ.

  5. Protein degradation rate is the dominant mechanism accounting for the differences in protein abundance of basal p53 in a human breast and colorectal cancer cell line.

    Science.gov (United States)

    Lakatos, Eszter; Salehi-Reyhani, Ali; Barclay, Michael; Stumpf, Michael P H; Klug, David R

    2017-01-01

    We determine p53 protein abundances and cell to cell variation in two human cancer cell lines with single cell resolution, and show that the fractional width of the distributions is the same in both cases despite a large difference in average protein copy number. We developed a computational framework to identify dominant mechanisms controlling the variation of protein abundance in a simple model of gene expression from the summary statistics of single cell steady state protein expression distributions. Our results, based on single cell data analysed in a Bayesian framework, lends strong support to a model in which variation in the basal p53 protein abundance may be best explained by variations in the rate of p53 protein degradation. This is supported by measurements of the relative average levels of mRNA which are very similar despite large variation in the level of protein.

  6. VizieR Online Data Catalog: High-precision abundances for stars with planets (Ramirez+, 2014)

    Science.gov (United States)

    Ramirez, I.; Melendez, J.; Asplund, M.

    2013-11-01

    High-precision stellar parameters and chemical abundances are presented for 111 stars; 52 of them are late-F type dwarfs and 59 are metal-rich solar analogs. The atomic linelist employed in the derivation of chemical abundances is also given. This linelist includes hyperfine structure parameters for some species. The stars' isochrone masses and ages are also reported, along with estimates of chromospheric activity. (5 data files).

  7. Abundance and diversity of dockerin-containing proteins in the fiber-degrading rumen bacterium, Ruminococcus flavefaciens FD-1.

    Directory of Open Access Journals (Sweden)

    Marco T Rincon

    Full Text Available BACKGROUND: The cellulosome is a multi-enzyme machine, which plays a key role in the breakdown of plant cell walls in many anaerobic cellulose-degrading microorganisms. Ruminococcus flavefaciens FD-1, a major fiber-degrading bacterium present in the gut of herbivores, has the most intricate cellulosomal organization thus far described. Cellulosome complexes are assembled through high-affinity cohesin-dockerin interactions. More than two-hundred dockerin-containing proteins have been identified in the R. flavefaciens genome, yet the reason for the expansion of these crucial cellulosomal components is yet unknown. METHODOLOGY/PRINCIPAL FINDINGS: We have explored the full spectrum of 222 dockerin-containing proteins potentially involved in the assembly of cellulosome-like complexes of R. flavefaciens. Bioinformatic analysis of the various dockerin modules showed distinctive conservation patterns within their two Ca(2+-binding repeats and their flanking regions. Thus, we established the conceptual framework for six major groups of dockerin types, according to their unique sequence features. Within this framework, the modular architecture of the parent proteins, some of which are multi-functional proteins, was evaluated together with their gene expression levels. Specific dockerin types were found to be associated with selected groups of functional components, such as carbohydrate-binding modules, numerous peptidases, and/or carbohydrate-active enzymes. In addition, members of other dockerin groups were linked to structural proteins, e.g., cohesin-containing proteins, belonging to the scaffoldins. CONCLUSIONS/SIGNIFICANCE: This report profiles the abundance and sequence diversity of the R. flavefaciens FD-1 dockerins, and provides the molecular basis for future understanding of the potential for a wide array of cohesin-dockerin specificities. Conserved differences between dockerins may be reflected in their stability, function or expression within

  8. LEA polypeptide profiling of recalcitrant and orthodox legume seeds reveals ABI3-regulated LEA protein abundance linked to desiccation tolerance.

    Science.gov (United States)

    Delahaie, Julien; Hundertmark, Michaela; Bove, Jérôme; Leprince, Olivier; Rogniaux, Hélène; Buitink, Julia

    2013-11-01

    In contrast to orthodox seeds that acquire desiccation tolerance during maturation, recalcitrant seeds are unable to survive drying. These desiccation-sensitive seeds constitute an interesting model for comparative analysis with phylogenetically close species that are desiccation tolerant. Considering the importance of LEA (late embryogenesis abundant) proteins as protective molecules both in drought and in desiccation tolerance, the heat-stable proteome was characterized in cotyledons of the legume Castanospermum australe and it was compared with that of the orthodox model legume Medicago truncatula. RNA sequencing identified transcripts of 16 homologues out of 17 LEA genes for which polypeptides are detected in M. truncatula seeds. It is shown that for 12 LEA genes, polypeptides were either absent or strongly reduced in C. australe cotyledons compared with M. truncatula seeds. Instead, osmotically responsive, non-seed-specific dehydrins accumulated to high levels in the recalcitrant cotyledons compared with orthodox seeds. Next, M. truncatula mutants of the abscisic acid insensitive3 (ABI3) gene were characterized. Mature Mtabi3 seeds were found to be desiccation sensitive when dried below a critical water content of 0.4 g H2O g DW(-1). Characterization of the LEA proteome of the Mtabi3 seeds revealed a subset of LEA proteins with severely reduced abundance that were also found to be reduced or absent in C. australe cotyledons. Transcripts of these genes were indeed shown to be ABI3 responsive. The results highlight those LEA proteins that are critical to desiccation tolerance and suggest that comparable regulatory pathways responsible for their accumulation are missing in both desiccation-sensitive genotypes, revealing new insights into the mechanistic basis of the recalcitrant trait in seeds.

  9. Characterization of a group 1 late embryogenesis abundant protein in encysted embryos of the brine shrimp Artemia franciscana.

    Science.gov (United States)

    Sharon, Michelle A; Kozarova, Anna; Clegg, James S; Vacratsis, Panayiotis O; Warner, Alden H

    2009-04-01

    Late embryogenesis abundant (LEA) proteins are hydrophilic molecules that are believed to function in desiccation and low-temperature tolerance in some plants and plant propagules, certain prokaryotes, and several animal species. The brine shrimp Artemia franciscana can produce encysted embryos (cysts) that enter diapause and are resistant to severe desiccation. This ability is based on biochemical adaptations, one of which appears to be the accumulation of the LEA protein that is the focus of this study. The studies described herein characterize a 21 kDa protein in encysted Artemia embryos as a group 1 LEA protein. The amino acid sequence of this protein and its gene have been determined and entered into the NCBI database (no. EF656614). The LEA protein consists of 182 amino acids and it is extremely hydrophilic, with glycine (23%), glutamine (17%), and glutamic acid (12.6%) being the most abundant amino acids. This protein also consists of 8 tandem repeats of a 20 amino acid sequence, which is characteristic of group 1 LEA proteins from non-animal species. The LEA protein and its gene are expressed only in encysted embryos and not in larvae or adults. Evidence is presented to show that the LEA protein functions in the prevention of drying-induced protein aggregation, which supports its functional role in desiccation tolerance. This report describes, for the first time, the purification and characterization of a group 1 LEA protein from an animal species.

  10. Universal stress protein Rv2624c alters abundance of arginine and enhances intracellular survival by ATP binding in mycobacteria

    Science.gov (United States)

    Jia, Qiong; Hu, Xinling; Shi, Dawei; Zhang, Yan; Sun, Meihao; Wang, Jianwei; Mi, Kaixia; Zhu, Guofeng

    2016-01-01

    The universal stress protein family is a family of stress-induced proteins. Universal stress proteins affect latency and antibiotic resistance in mycobacteria. Here, we showed that Mycobacterium smegmatis overexpressing M. tuberculosis universal stress protein Rv2624c exhibits increased survival in human monocyte THP-1 cells. Transcriptome analysis suggested that Rv2624c affects histidine metabolism, and arginine and proline metabolism. LC-MS/MS analysis showed that Rv2624c affects the abundance of arginine, a modulator of both mycobacteria and infected THP-1 cells. Biochemical analysis showed that Rv2624c is a nucleotide-binding universal stress protein, and an Rv2624c mutant incapable of binding ATP abrogated the growth advantage in THP-1 cells. Rv2624c may therefore modulate metabolic pathways in an ATP-dependent manner, changing the abundance of arginine and thus increasing survival in THP-1 cells. PMID:27762279

  11. Group 3 late embryogenesis abundant proteins from embryos of Artemia franciscana: structural properties and protective abilities during desiccation.

    Science.gov (United States)

    Boswell, Leaf C; Menze, Michael A; Hand, Steven C

    2014-01-01

    Group 3 late embryogenesis abundant (LEA) proteins are highly hydrophilic, and their expression is associated with desiccation tolerance in both plants and animals. Here we show that two LEA proteins from embryos of Artemia franciscana, AfrLEA2 and AfrLEA3m, are intrinsically disordered in solution but upon desiccation gain secondary structure, as measured by circular dichroism. Trifluoroethanol and sodium dodecyl sulfate are both shown to induce α-helical structure in AfrLEA2 and AfrLEA3m. Bioinformatic predictions of secondary-structure content for both proteins correspond most closely to conformations measured in the dry state. Because some LEA proteins afford protection to desiccation-sensitive proteins during drying and subsequent rehydration, we tested for this capacity in AfrLEA2 and AfrLEA3m. The protective capacities vary, depending on the target enzyme. For the cytoplasmic enzyme lactate dehydrogenase, neither AfrLEA2 nor AfrLEA3m, with or without trehalose present, was able to afford protection better than that provided by bovine serum albumin (BSA) under the same conditions. However, for another cytoplasmic enzyme, phosphofructokinase, both AfrLEA2 and AfrLEA3m in the presence of trehalose were able to afford protection far greater than that provided by BSA with trehalose. Finally, for the mitochondrial enzyme citrate synthase, 400-μg/mL AfrLEA3m without trehalose provided significantly more protection than the same concentration of either AfrLEA2 or BSA.

  12. Extended longevity lines of Drosophila melanogaster: abundance of yolk protein gene mRNA in fat body and ovary.

    Science.gov (United States)

    Carlson, K A; Harshman, L G

    1999-04-01

    Lines of Drosophila melanogaster selected for late-life female reproduction typically exhibit correlated responses of reduced early fecundity and increased longevity. This relationship suggests a tradeoff between reproductive effort and somatic maintenance, which in turn, underlies some evolutionary theories of senescence. The mechanistic basis of the apparent tradeoff between increased longevity and reduced early-age fecundity has remained obscure. The present manuscript addresses the issues of whether the reduced early-age fecundity in selected lines corresponds to reduced yolk-protein mRNA production, and whether long-lived flies exhibit somatic maintenance in terms of relatively reduced yolk-protein mRNA production in the fat body. Yolk protein is one of the most abundant proteins used for female reproduction. By comparing a set of lines selected for late life reproduction with the corresponding control lines, we show that that yolk-protein gene mRNA relative abundance during the first four days posteclosion did not correspond to reduced early-life fecundity in the selected lines. In D. melanogaster, yolk protein is produced in the fat body and ovarian follicle cells. On the fourth day posteclosion, relatively more yolk-protein gene mRNA was present in the fat body. On day 1 posteclosion, supplemental yeast did not alter relative yolk-protein gene mRNA abundance. However, on day 4 posteclosion, supplemental yeast stimulated yolk-protein gene mRNA production in the fat body, which suggests an underlying mechanism for the nutrition-based phenotypic plasticity of fecundity previously documented in these lines. On medium without supplemental yeast, the relatively low abundance of fat body yolk-protein gene mRNA in the selected lines on day 4 posteclosion corresponds to a prediction derived from the disposable soma theory.

  13. Identification of low abundance polyA-binding proteins in Arabidopsis chloroplast using polyA-affinity column.

    Science.gov (United States)

    Ni, Rui-Juan; Shen, Zhuo; Yang, Chuan-Ping; Wu, Ya-Dan; Bi, Ying-Dong; Wang, Bai-Chen

    2010-02-01

    Proteins could be well separated and further identified by the use of 2-DE and related techniques. Yet, there are many proteins could not be detected even by more effective dyes because of their inherent low abundance or their low resolution. As a result, polyA-affinity column was used as a method to enrich polyA-binding proteins and then identified by MALDI-TOF-MS. In this study, 23 Arabidopsis chloroplast protein spots coded by 18 genes were identified, and majority of these proteins were classified into three related categories according to their annotations in the Swiss-Prot database, including NAD-, RNA-, and ATP-binding motifs, respectively. The major goal of the present Arabidopsis chloroplast proteomics project was to identify novel polyA-binding proteins or protein isoforms located in Arabidopsis chloroplasts and the specific research of cellular proteins with extremely low transcription levels could be fulfilled.

  14. Sc and neutron-capture abundances in Galactic low- and high-alpha field halo stars

    DEFF Research Database (Denmark)

    Fishlock, Cherie K.; Yong, D.; Karakas, Amanda I.

    2017-01-01

    We determine relative abundance ratios for the neutron-capture elements Zr, La, Ce, Nd and Eu for a sample of 27 Galactic dwarf stars with -1.5 <[Fe/H] <-0.8. We also measure the iron-peak element Sc. These stars separate into three populations (low-and high-a halo and thick-disc stars) based on ...

  15. High Dispersion Spectroscopy of Solar-type Superflare Stars. III. Lithium Abundances

    CERN Document Server

    Honda, Satoshi; Maehara, Hiroyuki; Notsu, Shota; Shibayama, Takuya; Nogami, Daisaku; Shibata, Kazunari

    2015-01-01

    We report on the abundance analysis of Li in solar-type (G-type main sequence) superflare stars which were found by the analysis of Kepler photometric data. Li is a key element to understand the evolution of the stellar convection zone which reflects the age of solar-type stars. We performed the high dispersion spectroscopy of solar-type superflare stars with Subaru/HDS, and confirmed that 34 stars show no evidence of binarity in our previous study. In this study, we derived the Li abundances of these 34 objects. We investigate correlations of Li abundance with stellar atmospheric parameters, rotational velocity, and superflare activities to understand the nature of superflare stars and the possibility of the nucleosynthesis of Li by superflares. We confirm the large dispersion in the Li abundance, and the correlation with stellar parameters is not seen. As compared with the Li abundance in Hyades cluster which is younger than the Sun, it is suggested that half of the observed stars are younger than Hyades cl...

  16. A New View of the Surface of Mars: High-Resolution Rock Abundance from MGS TES

    Science.gov (United States)

    Nowicki, S.; Christensen, P.

    2001-12-01

    Mars Global Surveyor Thermal Emission Spectrometer data from the most dust-free seasons on Mars were used to calculate the areal percentage of rocks and finer materials such as dust and sand. Rock is defined as a surface material that has a thermal inertia of 1250 J/m2-s1/2-K (30 cal/cm2-s1/2-K) or greater. A surface with a high rock abundance value could be exposed bedrock, blocky debris, well-cemented materials or a combination. Globally, the TES and IRTM data agree well, with no rocks exposed in the large dusty regions such as Tharsis and Arabia, and exposure of rocks in small (a few km) areas where likely eolian or mass-wasting processes actively remove dust from the ancient rocky surface. Analysis of high-resolution TES rock abundance suggests that there are extremely varied surfaces within relatively small regions, and places an upper limit of ~45 % rocks in the rockiest regions. Thermal inertia and rock abundance are correlate to some degree over much of the planet, but the highest thermal inertia surfaces often do not have the highest rock abundances. A global perspective will be presented here, with detailed look at a few high-resolution ares including Ares Vallis/Pathfinder, Valles Marineris, and the proposed landing sites for the 2003 MER landers.

  17. Dynamin-related proteins Vps1p and Dnm1p control peroxisome abundance in Saccharomyces cerevisiae

    NARCIS (Netherlands)

    Kuravi, Kasinath; Nagotu, Shirisha; Krikken, Arjen M; Sjollema, Klaas; Deckers, Markus; Erdmann, Ralf; Veenhuis, Marten; van der Klei, Ida J

    2006-01-01

    Saccharomyces cerevisiae contains three dynamin-related-proteins, Vps1p, Dnm1p and Mgm1p. Previous data from glucose-grown VPS1 and DNM1 null mutants suggested that Vps1p, but not Dnm1p, plays a role in regulating peroxisome abundance. Here we show that deletion of DNM1 also results in reduction of

  18. Chemical abundances in a high velocity RR Lyrae star near the bulge

    CERN Document Server

    Hansen, Camilla Juul; Koch, Andreas; Xu, Siyi; Kunder, Andrea; Ludwig, Hans-Guenter

    2016-01-01

    Low-mass, variable, high-velocity stars are interesting study cases for many aspects of Galactic structure and evolution. Until recently, the only known high- or hyper-velocity stars were young stars thought to originate from the Galactic centre. Wide-area surveys like APOGEE and BRAVA have found several low-mass stars in the bulge with Galactic rest-frame velocities larger than 350 km/s. In this study we present the first abundance analysis of a low-mass, RR Lyrae star, located close to the Galactic bulge, with a space motion of ~ -400 km/s. Using medium-resolution spectra, we derive abundances (including upper limits) of 11 elements. These allow us to chemically tag the star and discuss its origin, although our derived abundances and metallicity, at [Fe/H] =-0.9 dex, do not point toward one unambiguous answer. Based on the chemical tagging, we cannot exclude that it originated in the bulge. However, combining its retrograde orbit and the derived abundances suggests that the star was accelerated from the out...

  19. Stable isotope labelled mass spectrometry for quantification of the relative abundances for expressed proteins induced by PeaT1

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The protein elicitor from the mycelium of Alternaria tenuissima has been isolated.The elicitor triggered resistance to the tobacco mosaic virus in tobacco by inducing relative oxygen species,but without causing hypersensitive necrosis.The elicitor is reported to impart resistance against Verticillium dahliae and to increase yield in cotton,but its mechanism is not yet clear.In this study,the stable isotope labelled mass spectrometry method was used to quantify the relative abundances of protein expression induced by PeaT1 in Arabidopsis.A significant difference in the relative abundances for the expression of different proteins related to metabolism,modification,regulatory,defense,stress and antioxidation was found in Arabidopsis.

  20. Structural insights into a secretory abundant heat-soluble protein from an anhydrobiotic tardigrade, Ramazzottius varieornatus.

    Science.gov (United States)

    Fukuda, Yohta; Miura, Yoshimasa; Mizohata, Eiichi; Inoue, Tsuyoshi

    2017-08-01

    Upon stopping metabolic processes, some tardigrades can undergo anhydrobiosis. Secretory abundant heat-soluble (SAHS) proteins have been reported as candidates for anhydrobiosis-related proteins in tardigrades, which seem to protect extracellular components and/or secretory organelles. We determined structures of a SAHS protein from Ramazzottius varieornatus (RvSAHS1), which is one of the toughest tardigrades. RvSAHS1 shows a β-barrel structure similar to fatty acid-binding proteins (FABPs), in which hydrophilic residues form peculiar hydrogen bond networks, which would provide RvSAHS1 with better tolerance against dehydration. We identified two putative ligand-binding sites: one that superimposes on those of some FABPs and the other, unique to and conserved in SAHS proteins. These results indicate that SAHS proteins constitute a new FABP family. © 2017 Federation of European Biochemical Societies.

  1. Increased reactive oxygen species production and lower abundance of complex I subunits and carnitine palmitoyltransferase 1B protein despite normal mitochondrial respiration in insulin-resistant human skeletal muscle

    DEFF Research Database (Denmark)

    Lefort, Natalie; Glancy, Brian; Bowen, Benjamin

    2010-01-01

    the higher ROS production. Tandem mass spectrometry identified protein abundance differences per mitochondrial mass in insulin resistance, including lower abundance of complex I subunits and enzymes involved in the oxidation of branched-chain amino acids (BCAA) and fatty acids (e.g., carnitine...... palmitoyltransferase 1B). CONCLUSIONS: We provide data suggesting normal oxidative capacity of mitochondria in insulin-resistant skeletal muscle in parallel with high rates of ROS production. Furthermore, we show specific abundance differences in proteins involved in fat and BCAA oxidation that might contribute...... to the accumulation of lipid and BCAA frequently associated with the pathogenesis of insulin resistance....

  2. High-resolution abundance analysis of very metal-poor r-I stars

    CERN Document Server

    Siqueira-Mello, C; Barbuy, B; Spite, M; Spite, F; Beers, T C; Caffau, E; Bonifacio, P; Cayrel, R; François, P; Schatz, H; Wanajo, S

    2014-01-01

    Moderately r-process-enriched stars (r-I) are at least four times as common as those that are greatly enriched in r-process elements (r-II), and the abundances in their atmospheres are important tools for obtaining a better understanding of the nucleosynthesis processes responsible for the origin of the elements beyond the iron peak. The main aim of this work is to derive abundances for a sample of seven metal-poor stars with classified as r-I stars, to understand the role of these stars for constraining the astrophysical nucleosynthesis event(s) that is(are) responsible for the production of the r-process, and to investigate whether they differ, in any significant way, from the r-II stars. We carried out a detailed abundance analysis based on high-resolution spectra obtained with the VLT/UVES spectrograph. The OSMARCS LTE 1D model atmosphere grid was employed, along with the spectrum synthesis code Turbospectrum. We have derived abundances of light elements Li, C, and N, alpha-elements, odd-Z elements, iron-...

  3. FIRST SPECTROSCOPIC EVIDENCE FOR HIGH IONIZATION STATE AND LOW OXYGEN ABUNDANCE IN Ly{alpha} EMITTERS ,

    Energy Technology Data Exchange (ETDEWEB)

    Nakajima, Kimihiko; Shimasaku, Kazuhiro; Hashimoto, Takuya; Ono, Yoshiaki [Department of Astronomy, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Ouchi, Masami [Kavli Institute for the Physics and Mathematics of the Universe (WPI), University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8583 (Japan); Lee, Janice C., E-mail: nakajima@astron.s.u-tokyo.ac.jp [Space Telescope Science Institute, Baltimore, MD 21218 (United States)

    2013-05-20

    We present results from Keck/NIRSPEC and Magellan/MMIRS follow-up spectroscopy of Ly{alpha} emitters (LAEs) at z = 2.2 identified in our Subaru narrowband survey. We successfully detect H{alpha} emission from seven LAEs, and perform a detailed analysis of six LAEs free from active galactic nucleus activity, two out of which, CDFS-3865 and COSMOS-30679, have [O II] and [O III] line detections. They are the first [O II]-detected LAEs at high-z, and their [O III]/[O II] ratios and R23-indices provide the first simultaneous determinations of ionization parameter and oxygen abundance for LAEs. CDFS-3865 has a very high ionization parameter (q{sub ion}=2.5{sup +1.7}{sub -0.8} Multiplication-Sign 10{sup 8} cm s{sup -1}) and a low oxygen abundance (12+ log (O/H)=7.84{sup +0.24}{sub -0.25}) in contrast with moderate values of other high-z galaxies such as Lyman break galaxies (LBGs). COSMOS-30679 also possesses a relatively high ionization parameter (q{sub ion}=8{sup +10}{sub -4} Multiplication-Sign 10{sup 7} cm s{sup -1}) and a low oxygen abundance (12+ log (O/H)=8.18{sup +0.28}{sub -0.28}). Both LAEs appear to fall below the mass-metallicity relation of z {approx} 2 LBGs. Similarly, a low metallicity of 12 + log (O/H) < 8.4 is independently indicated for typical LAEs from a composite spectrum and the [N II]/H{alpha} index. Such high ionization parameters and low oxygen abundances can be found in local star-forming galaxies, but this extreme local population occupies only {approx}0.06% of the Sloan Digital Sky Survey spectroscopic galaxy sample with a number density {approx}100 times smaller than that of LAEs. With their high ionization parameters and low oxygen abundances, LAEs would represent an early stage of galaxy formation dominated by massive stars in compact star-forming regions. High-q{sub ion} galaxies like LAEs would produce ionizing photons efficiently with a high escape fraction achieved by density-bounded H II regions, which would significantly contribute to

  4. Analysis of the plasma proteome in COPD: Novel low abundance proteins reflect the severity of lung remodeling.

    Science.gov (United States)

    Merali, Salim; Barrero, Carlos A; Bowler, Russell P; Chen, Diane Er; Criner, Gerard; Braverman, Alan; Litwin, Samuel; Yeung, Anthony; Kelsen, Steven G

    2014-04-01

    The search for COPD biomarkers has largely employed a targeted approach that focuses on plasma proteins involved in the systemic inflammatory response and in lung injury and repair. This proof of concept study was designed to test the idea that an open, unbiased, in-depth proteomics approach could identify novel, low abundance plasma proteins i.e., ng/mL concentration, which could serve as potential biomarkers. Differentially expressed proteins were identified in a discovery group with severe COPD (FEV1 <45% predicted; n = 10). Subjects with normal lung function matched for age, sex, ethnicity and smoking history served as controls (n = 10). Pooled plasma from each group was exhaustively immunodepleted of abundant proteins, d separated by 1-D gel electrophoresis and extensively fractionated prior to LC-tandem mass spectroscopy (GeLC-MS). Thirty one differentially expressed proteins were identified in the discovery group including markers of lung defense against oxidant stress, alveolar macrophage activation, and lung tissue injury and repair. Four of the 31 proteins (i.e., GRP78, soluble CD163, IL1AP and MSPT9) were measured in a separate verification group of 80 subjects with varying COPD severity by immunoassay. All 4 were significantly altered in COPD and 2 (GRP78 and soluble CD163) correlated with both FEV1 and the extent of emphysema. In-depth, plasma proteomic analysis identified a group of novel, differentially expressed, low abundance proteins that reflect known pathogenic mechanisms and the severity of lung remodeling in COPD. These proteins may also prove useful as COPD biomarkers.

  5. Heterologous Expression of MeLEA3: A 10 kDa Late Embryogenesis Abundant Protein of Cassava, Confers Tolerance to Abiotic Stress in Escherichia coli with Recombinant Protein Showing In Vitro Chaperone Activity.

    Science.gov (United States)

    Barros, Nicolle L F; da Silva, Diehgo T; Marques, Deyvid N; de Brito, Fabiano M; dos Reis, Savio P; de Souza, Claudia R B

    2015-01-01

    Late embryogenesis abundant (LEA) proteins are small molecular weight proteins involved in acquisition of tolerance to drought, salinity, high temperature, cold, and freezing stress in many plants. Previous studies revealed a cDNA sequence coding for a 10 kDa atypical LEA protein, named MeLEA3, predicted to be located into mitochondria with potential role in salt stress response of cassava (Manihot esculenta Crantz). Here we aimed to produce the recombinant MeLEA3 protein by heterologous expression in Escherichia coli and evaluate the tolerance of bacteria expressing this protein under abiotic stress. Our result revealed that the recombinant MeLEA3 protein conferred a protective function against heat and salt stress in bacterial cells. Also, the recombinant MeLEA3 protein showed in vitro chaperone activity by protection of NdeI restriction enzyme activity under heat stress.

  6. Estimating sufficient reductions of the predictors in abundant high-dimensional regressions

    CERN Document Server

    Cook, R Dennis; Rothman, Adam J; 10.1214/11-AOS962

    2012-01-01

    We study the asymptotic behavior of a class of methods for sufficient dimension reduction in high-dimension regressions, as the sample size and number of predictors grow in various alignments. It is demonstrated that these methods are consistent in a variety of settings, particularly in abundant regressions where most predictors contribute some information on the response, and oracle rates are possible. Simulation results are presented to support the theoretical conclusion.

  7. Chemical Abundances of the Highly Obscured Galactic Globular Clusters 2MASS GC02 and Mercer 5

    CERN Document Server

    Penaloza, Francisco; Vasquez, Sergio; Borissova, Jura; Kurtev, Radostin; Zoccali, Manuela

    2015-01-01

    We present the first high spectral resolution abundance analysis of two newly discovered Galactic globular clusters, namely Mercer 5 and 2MASS GC02 residing in regions of high interstellar reddening in the direction of the Galactic center. The data were acquired with the Phoenix high-resolution near-infrared echelle spectrograph at Gemini South (R~50000) in the 15500.0 A - 15575.0 A spectral region. Iron, Oxygen, Silicon, Titanium and Nickel abundances were derived for two red giant stars, in each cluster, by comparing the entire observed spectrum with a grid of synthetic spectra generated with MOOG. We found [Fe/H] values of -0.86 +/- 0.12 and -1.08 +/- 0.13 for Mercer 5 and 2MASS GC02 respectively. The [O/Fe], [Si/Fe] and [Ti/Fe] ratios of the measured stars of Mercer 5 follow the general trend of both bulge field and cluster stars at this metallicity, and are enhanced by > +0.3. The 2MASS GC02 stars have relatively lower ratios, but still compatible with other bulge clusters. Based on metallicity and abund...

  8. Norvaline and Norleucine May Have Been More Abundant Protein Components during Early Stages of Cell Evolution

    Science.gov (United States)

    Alvarez-Carreño, Claudia; Becerra, Arturo; Lazcano, Antonio

    2013-10-01

    The absence of the hydrophobic norvaline and norleucine in the inventory of protein amino acids is readdressed. The well-documented intracellular accumulation of these two amino acids results from the low-substrate specificity of the branched-chain amino acid biosynthetic enzymes that act over a number of related α-ketoacids. The lack of absolute substrate specificity of leucyl-tRNA synthase leads to a mischarged norvalyl-tRNALeu that evades the translational proofreading activites and produces norvaline-containing proteins, (cf. Apostol et al. J Biol Chem 272:28980-28988, 1997). A similar situation explains the presence of minute but detectable amounts of norleucine in place of methionine. Since with few exceptions both leucine and methionine are rarely found in the catalytic sites of most enzymes, their substitution by norvaline and norleucine, respectively, would have not been strongly hindered in small structurally simple catalytic polypeptides during the early stages of biological evolution. The report that down-shifts of free oxygen lead to high levels of intracellular accumulation of pyruvate and the subsequent biosynthesis of norvaline (Soini et al. Microb Cell Factories 7:30, 2008) demonstrates the biochemical and metabolic consequences of the development of a highly oxidizing environment. The results discussed here also suggest that a broader definition of biomarkers in the search for extraterrestrial life may be required.

  9. Region-Specific Protein Abundance Changes in the Brain of MPTP-induced Parkinson’s Disease Mouse Model

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Xu; Zhou, Jianying; Chin, Mark H; Schepmoes, Athena A; Petyuk, Vladislav A; Weitz, Karl K; Petritis, Brianne O; Monroe, Matthew E; Camp, David G; Wood, Stephen A; Melega, William P; Bigelow, Diana J; Smith, Desmond J; Qian, Weijun; Smith, Richard D

    2010-02-15

    Parkinson’s disease (PD) is characterized by dopaminergic neurodegeneration in the nigrostriatal region of the brain; however, the neurodegeneration extends well beyond dopaminergic neurons. To gain a better understanding of the molecular changes relevant to PD, we applied two-dimensional LC-MS/MS to comparatively analyze the proteome changes in four brain regions (striatum, cerebellum, cortex, and the rest of brain) using a MPTP-induced PD mouse model with the objective to identify nigrostriatal-specific and other region-specific protein abundance changes. The combined analyses resulted in the identification of 4,895 non-redundant proteins with at least two unique peptides per protein. The relative abundance changes in each analyzed brain region were estimated based on the spectral count information. A total of 518 proteins were observed with significant MPTP-induced changes across different brain regions. 270 of these proteins were observed with specific changes occurring either only in the striatum and/or in the rest of the brain region that contains substantia nigra, suggesting that these proteins are associated with the underlying nigrostriatal pathways. Many of the proteins that exhibit significant abundance changes were associated with dopamine signaling, mitochondrial dysfunction, the ubiquitin system, calcium signaling, the oxidative stress response, and apoptosis. A set of proteins with either consistent change across all brain regions or with changes specific to the cortex and cerebellum regions were also detected. One of the interesting proteins is ubiquitin specific protease (USP9X), a deubiquination enzyme involved in the protection of proteins from degradation and promotion of the TGF-β pathway, which exhibited altered abundances in all brain regions. Western blot validation showed similar spatial changes, suggesting that USP9X is potentially associated with neurodegeneration. Together, this study for the first time presents an overall picture of

  10. Water abundances in high-mass protostellar envelopes: Herschel observations with HIFI

    CERN Document Server

    Marseille, M; Herpin, F; Wyrowski, F; Chavarria, L; Pietropaoli, B

    2015-01-01

    We derive the dense core structure and the water abundance in four massive star-forming regions which may help understand the earliest stages of massive star formation. We present Herschel-HIFI observations of the para-H2O 1_11-0_00 and 2_02-1_11 and the para-H2-18O 1_11-0_00 transitions. The envelope contribution to the line profiles is separated from contributions by outflows and foreground clouds. The envelope contribution is modelled using Monte-Carlo radiative transfer codes for dust and molecular lines (MC3D and RATRAN), with the water abundance and the turbulent velocity width as free parameters. While the outflows are mostly seen in emission in high-J lines, envelopes are seen in absorption in ground-state lines, which are almost saturated. The derived water abundances range from 5E-10 to 4E-8 in the outer envelopes. We detect cold clouds surrounding the protostar envelope, thanks to the very high quality of the Herschel-HIFI data and the unique ability of water to probe them. Several foreground cloud...

  11. Abundant class III acidic chitinase homologue in tamarind (Tamarindus indica) seed serves as the major storage protein.

    Science.gov (United States)

    Rao, Devavratha H; Gowda, Lalitha R

    2008-03-26

    The phyla Leguminosae contains protease inhibitors, lectins, chitinases, and glycohydrolases as major defense proteins in their seeds. Electrophoretic analysis of the seed proteins of tamarind ( Tamarindus indica L.), an agri-waste material, indicated the unusual presence of two major proteins comparable to overexpression of recombinant proteins. These proteins were identified by amino-terminal analysis to be (1) Kunitz-type trypsin inhibitor and (2) class III endochitinase (34000 Da). These two proteins were purified to apparent homogeneity by a single-step chitin bead affinity chromatography and characterized. The Kunitz inhibitor was specific toward inhibiting trypsin with a stoichiometry of 1:1. The 33000 +/- 1000 Da protein, accounting for >50% of the total seed protein, is an acidic glycoprotein exhibiting a very low endotype hydrolytic activity toward chitin derivatives. SDS-PAGE followed by densitometry of tamarind seed germination indicates the disappearance of the chitinase with the concomitant appearance of a cysteine endopeptidase. On the basis of its abundance, accumulation without any pathogenesis-related stimulus, temporal regulation, amino acid composition, and very low enzyme activity, this 34000 Da protein designated "tamarinin" physiologically serves as the major storage protein.

  12. Expression Profiles of 12 Late Embryogenesis Abundant Protein Genes from Tamarix hispida in Response to Abiotic Stress

    Directory of Open Access Journals (Sweden)

    Caiqiu Gao

    2014-01-01

    Full Text Available Twelve embryogenesis abundant protein (LEA genes (named ThLEA-1 to -12 were cloned from Tamarix hispida. The expression profiles of these genes in response to NaCl, PEG, and abscisic acid (ABA in roots, stems, and leaves of T. hispida were assessed using real-time reverse transcriptase-polymerase chain reaction (RT-PCR. These ThLEAs all showed tissue-specific expression patterns in roots, stems, and leaves under normal growth conditions. However, they shared a high similar expression patterns in the roots, stems, and leaves when exposed to NaCl and PEG stress. Furthermore, ThLEA-1, -2, -3, -4, and -11 were induced by NaCl and PEG, but ThLEA-5, -6, -8, -10, and -12 were downregulated by salt and drought stresses. Under ABA treatment, some ThLEA genes, such as ThLEA-1, -2, and -3, were only slightly differentially expressed in roots, stems, and leaves, indicating that they may be involved in the ABA-independent signaling pathway. These findings provide a basis for the elucidation of the function of LEA genes in future work.

  13. SPAK and OSR1 Sensitive Cell Membrane Protein Abundance and Activity of KCNQ1/E1 K+ Channels

    Directory of Open Access Journals (Sweden)

    Bernat Elvira

    2015-11-01

    Full Text Available Background/Aims: KCNQ1/E1 channels are expressed in diverse tissues and serve a variety of functions including endolymph secretion in the inner ear, cardiac repolarization, epithelial transport and cell volume regulation. Kinases involved in regulation of epithelial transport and cell volume include SPAK (SPS1-related proline/alanine-rich kinase and OSR1 (oxidative stress-responsive kinase 1, which are under control of WNK (with-no-K[Lys] kinases. The present study explored whether KCNQ1/E1 channels are regulated by SPAK and/or OSR1. Methods: cRNA encoding KCNQ1/E1 was injected into Xenopus oocytes with or without additional injection of cRNA encoding wild-type SPAK, constitutively active T233ESPAK, WNK insensitive T233ASPAK, catalytically inactive D212ASPAK, wild-type OSR1, constitutively active T185EOSR1, WNK insensitive T185AOSR1 and catalytically inactive D164AOSR1. Voltage gated K+ channel activity was quantified utilizing dual electrode voltage clamp and KCNQ1/E1 channel protein abundance in the cell membrane utilizing chemiluminescence of KCNQ1/E1 containing an extracellular Flag tag epitope (KCNQ1-Flag/E1. Results: KCNQ1/E1 activity and KCNQ1-Flag/E1 protein abundance were significantly enhanced by wild-type SPAK and T233ESPAK, but not by T233ASPAK and D212ASPAK. Similarly, KCNQ1/E1 activity and KCNQ1-Flag/E1 protein abundance were significantly increased by wild-type OSR1 and T185EOSR1, but not by T185AOSR1 and D164AOSR1. Conclusions: SPAK and OSR1 participate in the regulation of KCNQ1/E1 protein abundance and activity.

  14. Proteomic analysis of the excretory-secretory products from larval stages of Ascaris suum reveals high abundance of glycosyl hydrolases.

    Directory of Open Access Journals (Sweden)

    Tao Wang

    Full Text Available BACKGROUND: Ascaris lumbricoides and Ascaris suum are socioeconomically important and widespread parasites of humans and pigs, respectively. The excretory-secretory (ES molecules produced and presented at the parasite-host interface during the different phases of tissue invasion and migration are likely to play critical roles in the induction and development of protective immune and other host responses. METHODOLOGY/PRINCIPAL FINDINGS: The aim of this study was to identify the ES proteins of the different larval stages (L3-egg, L3-lung and L4 by LC-MS/MS. In total, 106 different proteins were identified, 20 in L3-egg, 45 in L3-lung stage and 58 in L4. Although most of the proteins identified were stage-specific, 15 were identified in the ES products of at least two stages. Two proteins, i.e. a 14-3-3-like protein and a serpin-like protein, were present in the ES products from the three different larval stages investigated. Interestingly, a comparison of ES products from L4 with those of L3-egg and L3-lung showed an abundance of metabolic enzymes, particularly glycosyl hydrolases. Further study indicated that most of these glycolytic enzymes were transcriptionally upregulated from L4 onwards, with a peak in the adult stage, particularly in intestinal tissue. This was also confirmed by enzymatic assays, showing the highest glycosidase activity in protein extracts from adult worms gut. CONCLUSIONS/SIGNIFICANCE: The present proteomic analysis provides important information on the host-parasite interaction and the biology of the migratory stages of A. suum. In particular, the high transcriptional upregulation of glycosyl hydrolases from the L4 stage onwards reveals that the degradation of complex carbohydrates forms an essential part of the energy metabolism of this parasite once it establishes in the small intestine.

  15. Metagenomics and single-cell genomics reveal high abundance of comammox Nitrospira in a rapid gravity sand filter treating groundwater

    DEFF Research Database (Denmark)

    Palomo, Alejandro; Fowler, Jane; Gülay, Arda;

    , the ecological relevance of comammox remains unknown. In this study, we analyzed the microbial communities from various locations within a groundwater-fed rapid sand filter (RSF), where Nitrospira were at very high relative abundances. Through metagenomics, a highly abundant composite multi-genome of Nitrospira...

  16. Effects of dietary nitrogen concentration on messenger RNA expression and protein abundance of urea transporter-B and aquaporins in ruminal papillae from lactating Holstein cows

    DEFF Research Database (Denmark)

    Røjen, Betina Amdisen; Poulsen, Søren Brandt; Theil, Peter Kappel

    2011-01-01

    To test the hypothesis that dietary N concentrations affect gut epithelial urea transport by modifying the expression of urea transporter B (UT-B) and aquaporins (AQP), the mRNA expression and protein abundance of UT-B and AQP3, AQP7, AQP8, and AQP10 were investigated in ruminal papillae from 9...... lactating dairy cows. Ruminal papillae were harvested from cows fed low N (12.9% crude protein) and high N (17.1% crude protein) diets in a crossover design with 21-d periods. The mRNA expression was determined by real-time reverse transcription-PCR and protein abundance by immunoblotting. The mRNA...... expression of UT-B was not affected by dietary treatment, whereas mRNA expression of AQP3, 7, and 10 were greater in the high N compared with the low N fed cows. Using peptide-derived rabbit antibodies to cow AQP3, 7, and 8, immunoblotting revealed bands of approximately 27, 27, and 24 kDa in ruminal...

  17. GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater

    KAUST Repository

    Bayer, Kristina

    2015-01-08

    The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20 273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater.

  18. 14-3-3-β and -{varepsilon} contribute to activation of the osmoprotective transcription factor NFAT5 by increasing its protein abundance and its transactivating activity.

    Science.gov (United States)

    Izumi, Yuichiro; Burg, Maurice B; Ferraris, Joan D

    2014-01-01

    Abstract Having previously found that high NaCl causes rapid exit of 14-3-3 isoforms from the nucleus, we used siRNA-mediated knockdown to test whether 14-3-3s contribute to the high NaCl-induced increase in the activity of the osmoprotective transcription factor NFAT5. We find that, when NaCl is elevated, knockdown of 14-3-3-β and/or 14-3-3-ε decreases NFAT5 transcriptional activity, as assayed both by luciferase reporter and by the mRNA abundance of the NFAT5 target genes aldose reductase and the sodium- and chloride-dependent betaine transporter, BGT1. Knockdown of other 14-3-3 isoforms does not significantly affect NFAT5 activity. 14-3-3-β and/or 14-3-3-ε do not act by affecting the nuclear localization of NFAT5, but by at least two other mechanisms: (1) 14-3-3-β and 14-3-3-ε increase protein abundance of NFAT5 and (2) they increase NFAT5 transactivating activity. When NaCl is elevated, knockdown of 14-3-3-β and/or 14-3-3-ε reduces the protein abundance of NFAT5, as measured by Western blot, without affecting the level of NFAT5 mRNA, and the knockdown also decreases NFAT5 transactivating activity, as measured by luciferase reporter. The 14-3-3s increase NFAT5 protein, not by increasing its translation, but by decreasing the rate at which it is degraded, as measured by cycloheximide chase. It is not clear at this point whether the 14-3-3s affect NFAT5 directly or indirectly through their effects on other proteins that signal activation of NFAT5.

  19. Isotopic Abundances and Ratios in Arsenic Irradiated by High-Energy Neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Parker, W. E. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Hall, J. M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2010-06-07

    This document provides derivations of the 73As, 74As and 75As isotopic abundances and ratios in an arsenic sample irradiated by high-energy (14 MeV) neutrons for 0 ≤ t ≤ T, where T is short compared to the natural decay times of the reaction products (t1/2 (73As) ~ 80.3 d, t1/2 (74As) ~ 17.8 d). The document also outlines the historic approach used to analyze arsenic data from experiments.

  20. High Resolution HDS/SUBARU chemical abundances of the young stellar cluster Palomar 1

    CERN Document Server

    Monaco, L; Correnti, M; Bonifacio, P; Geisler, D

    2010-01-01

    Context. Palomar\\,1 is a peculiar globular cluster (GC). It is the youngest Galactic GC and it has been tentatively associated to several of the substructures recently discovered in the Milky Way (MW), including the Canis Major (CMa) overdensity and the Galactic Anticenter Stellar Structure (GASS). Aims. In order to provide further insights into its origin, we present the first high resolution chemical abundance analysis for one red giant in Pal\\,1. Methods. We obtained high resolution (R=30000) spectra for one red giant star in Pal\\,1 using the High Dispersion Spectrograph (HDS) mounted at the SUBARU telescope. We used ATLAS-9 model atmospheres coupled with the SYNTHE and WIDTH calculation codes to derive chemical abundances from the measured line equivalent widths of 18 among $\\alpha$, Iron-peak, light and heavy elements. Results. The Palomar~1 chemical pattern is broadly compatible to that of the MW open clusters population and similar to disk stars. It is, instead, remarkably different from that of the Sa...

  1. High food abundance permits the evolution of placentotrophy: evidence from a placental lizard, Pseudemoia entrecasteauxii.

    Science.gov (United States)

    Van Dyke, James U; Griffith, Oliver W; Thompson, Michael B

    2014-08-01

    Mechanisms of reproductive allocation are major determinants of fitness because embryos cannot complete development without receiving sufficient nutrition from their parents. The nourishment of offspring via placentas (placentotrophy) has evolved repeatedly in vertebrates, including multiple times in squamate reptiles (lizards and snakes). Placentotrophy has been suggested to evolve only if food is sufficiently abundant throughout gestation to allow successful embryogenesis. If scarcity of food prevents successful embryogenesis, females should recoup nutrients allocated to embryos via abortion, reabsorption, and/or cannibalism. We tested these hypotheses in the placentotrophic southern grass skink Pseudemoia entrecasteauxii. We fed females one of four diets (high constant, high variable, low constant, and low variable) during gestation and tested the effects of both food amount and schedule of feeding on developmental success, cannibalism rate, placental nutrient transport, offspring size, and maternal growth and body condition. Low food availability reduced developmental success, placental nutrient transport, offspring size, and maternal growth and body condition. Cannibalism of offspring also increased when food was scarce. Schedule of feeding did not affect offspring or mothers. We suggest that high food abundance and ability to abort and cannibalize poor-quality offspring are permissive factors necessary for placentotrophy to be a viable strategy of reproductive allocation.

  2. Analysis of the c-src gene product structure, abundance, and protein kinase activity in human neuroblastoma and glioblastoma cells.

    Science.gov (United States)

    O'Shaughnessy, J; Deseau, V; Amini, S; Rosen, N; Bolen, J B

    1987-01-01

    We have compared in different human neuroblastoma cell lines and human glioblastoma cells the expression level, structure, and tyrosine-specific protein kinase activity of pp60c-src. Our results show that not all human neuroblastoma cell lines express pp60c-src molecules with amino-terminal structural alterations. In neuroblastoma cells which possess pp60c-src with altered gel migration, the diminished polyacrylamide gel mobility of pp60c-src was found not to be dependent upon amino-terminal phosphorylations since extensive treatment of these molecules with phosphatase did not significantly change their gel migration properties. Similar differences in gel migration were observed when RNA from the various neuroblastoma and glioblastoma cells was translated in vitro using either rabbit reticulocyte or wheat germ lysates. White the level of c-src mRNA in the different cells analyzed was found to be similar, the abundance of pp60c-src in these same cells was found to vary by as much as 12-fold. This suggests that the abundance of pp60c-src in human neuroendocrine tumors is regulated through post-transcriptional and/or post-translational events which may be related to the stage of neuronal differentiation of the cells. Based upon determination of pp60c-src abundance by immunoblot analysis, we demonstrate that pp60c-src molecules derived from human neuroblastoma and glioblastoma cells have very similar in vitro protein kinase activities.

  3. Engineering protein processing of the mammary gland to produce abundant hemophilia B therapy in milk.

    Science.gov (United States)

    Zhao, Jianguo; Xu, Weijie; Ross, Jason W; Walters, Eric M; Butler, Stephen P; Whyte, Jeff J; Kelso, Lindsey; Fatemi, Mostafa; Vanderslice, Nicholas C; Giroux, Keith; Spate, Lee D; Samuel, Melissa S; Murphy, Cliff N; Wells, Kevin D; Masiello, Nick C; Prather, Randall S; Velander, William H

    2015-09-21

    Both the low animal cell density of bioreactors and their ability to post-translationally process recombinant factor IX (rFIX) limit hemophilia B therapy to transgenic pigs to make rFIX in milk at about 3,000-fold higher output than provided by industrial bioreactors. However, this resulted in incomplete γ-carboxylation and propeptide cleavage where both processes are transmembrane mediated. We then bioengineered the co-expression of truncated, soluble human furin (rFurin) with pro-rFIX at a favorable enzyme to substrate ratio. This resulted in the complete conversion of pro-rFIX to rFIX while yielding a normal lactation. Importantly, these high levels of propeptide processing by soluble rFurin did not preempt γ-carboxylation in the ER and therefore was compartmentalized to the Trans-Golgi Network (TGN) and also to milk. The Golgi specific engineering demonstrated here segues the ER targeted enhancement of γ-carboxylation needed to biomanufacture coagulation proteins like rFIX using transgenic livestock.

  4. Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR)

    Science.gov (United States)

    Gomez, Sandra; Adalid-Peralta, Laura; Palafox-Fonseca, Hector; Cantu-Robles, Vito Adrian; Soberón, Xavier; Sciutto, Edda; Fragoso, Gladis; Bobes, Raúl J.; Laclette, Juan P.; Yauner, Luis del Pozo; Ochoa-Leyva, Adrián

    2015-01-01

    Excretory/Secretory (ES) proteins play an important role in the host-parasite interactions. Experimental identification of ES proteins is time-consuming and expensive. Alternative bioinformatics approaches are cost-effective and can be used to prioritize the experimental analysis of therapeutic targets for parasitic diseases. Here we predicted and functionally annotated the ES proteins in T. solium genome using an integration of bioinformatics tools. Additionally, we developed a novel measurement to evaluate the potential antigenicity of T. solium secretome using sequence length and number of antigenic regions of ES proteins. This measurement was formalized as the Abundance of Antigenic Regions (AAR) value. AAR value for secretome showed a similar value to that obtained for a set of experimentally determined antigenic proteins and was different to the calculated value for the non-ES proteins of T. solium genome. Furthermore, we calculated the AAR values for known helminth secretomes and they were similar to that obtained for T. solium. The results reveal the utility of AAR value as a novel genomic measurement to evaluate the potential antigenicity of secretomes. This comprehensive analysis of T. solium secretome provides functional information for future experimental studies, including the identification of novel ES proteins of therapeutic, diagnosis and immunological interest. PMID:25989346

  5. Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR).

    Science.gov (United States)

    Gomez, Sandra; Adalid-Peralta, Laura; Palafox-Fonseca, Hector; Cantu-Robles, Vito Adrian; Soberón, Xavier; Sciutto, Edda; Fragoso, Gladis; Bobes, Raúl J; Laclette, Juan P; Yauner, Luis del Pozo; Ochoa-Leyva, Adrián

    2015-05-19

    Excretory/Secretory (ES) proteins play an important role in the host-parasite interactions. Experimental identification of ES proteins is time-consuming and expensive. Alternative bioinformatics approaches are cost-effective and can be used to prioritize the experimental analysis of therapeutic targets for parasitic diseases. Here we predicted and functionally annotated the ES proteins in T. solium genome using an integration of bioinformatics tools. Additionally, we developed a novel measurement to evaluate the potential antigenicity of T. solium secretome using sequence length and number of antigenic regions of ES proteins. This measurement was formalized as the Abundance of Antigenic Regions (AAR) value. AAR value for secretome showed a similar value to that obtained for a set of experimentally determined antigenic proteins and was different to the calculated value for the non-ES proteins of T. solium genome. Furthermore, we calculated the AAR values for known helminth secretomes and they were similar to that obtained for T. solium. The results reveal the utility of AAR value as a novel genomic measurement to evaluate the potential antigenicity of secretomes. This comprehensive analysis of T. solium secretome provides functional information for future experimental studies, including the identification of novel ES proteins of therapeutic, diagnosis and immunological interest.

  6. Effects of EPA and DHA on lipid droplet accumulation and mRNA abundance of PAT proteins in caprine monocytes.

    Science.gov (United States)

    Lecchi, Cristina; Invernizzi, Guido; Agazzi, Alessandro; Modina, Silvia; Sartorelli, Paola; Savoini, Giovanni; Ceciliani, Fabrizio

    2013-04-01

    The present study investigated the in vitro effects on caprine monocytes of two ω-3 PUFAs, namely eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) on lipid droplet formation, an emerging process of fundamental importance in innate immunity regulation. The mRNA abundance of PAT protein family (PLIN1, PLIN2 and PLIN3), involved in the formation and trafficking of the droplets, was also assessed. The effects of EPA and DHA on monocyte apoptosis were studied as well. The number of lipid droplets per cell was found to be dependent on both type and concentration of fatty acid. ω-3 PUFAs upregulated PLIN3 and PLIN2 gene expression, as well as apoptosis rate. The present findings suggest that PUFA might modify innate immune functions of goat monocytes by interfering with the formation of lipid droplets and by upregulating proteins belonging to PAT protein family.

  7. Isolation and characterization of multiple abundant lipid transfer protein isoforms in developing sesame (Sesamum indicum L.) seeds.

    Science.gov (United States)

    Choi, Ah Mi; Lee, Saet Buyl; Cho, Sung Ho; Hwang, Inhwan; Hur, Cheol-Goo; Suh, Mi Chung

    2008-02-01

    Sesame (Sesamum indicum) is an important oilseed crop; approximately 50% of the seed dry weight is storage oil. In a previous report, developing sesame seed expressed sequence tags (ESTs) revealed that ESTs encoding lipid transfer protein (LTPs) were one of the most abundant groups of sesame ESTs. LTP functions in the transfer of wax or cutin monomers and in the defense response against pathogen attack. To study the biological role of the abundant LTP isoforms in developing seeds, 122 ESTs out of 3328 sesame ESTs were analyzed against Arabidopsis and rice proteome databases. LTP fraction, which was partially purified from developing sesame seeds, actively transferred fluorescent phospholipids and bound to fatty acids. Full-length cDNAs of five out of 21 LTP isoforms were isolated and named SiLTP1-SiLTP5. The predicted amino acid sequences of the five SiLTPs harbor typical characteristics of LTPs, including conserved arrangement of cysteine residues. Northern blot analysis revealed that the five SiLTP isoforms were most abundantly expressed in developing seeds, but were also detected in flower tissues. Also, SiLTP3 and SiLTP4 transcripts were expressed in leaves and seed-pot walls, respectively. In addition, SiLTP2 and SiLTP4 transcripts were significantly induced in 6-day-old sesame seedlings by application of NaCl, mannitol, and abscisic acid (ABA). Transient expression of green fluorescent protein (GFP)-fusion constructs in Arabidopsis protoplasts revealed that SiLTP1 and SiLTP2 were secreted by different pathways. Taken together, the abundant LTPs in developing sesame seeds are involved in lipid transfer into the extracellular matrix. Possible biological roles of SiLTPs related to organ-specific expression and abiotic stresses are discussed.

  8. Pro-inflammatory flagellin proteins of prevalent motile commensal bacteria are variably abundant in the intestinal microbiome of elderly humans.

    Directory of Open Access Journals (Sweden)

    B Anne Neville

    Full Text Available Some Eubacterium and Roseburia species are among the most prevalent motile bacteria present in the intestinal microbiota of healthy adults. These flagellate species contribute "cell motility" category genes to the intestinal microbiome and flagellin proteins to the intestinal proteome. We reviewed and revised the annotation of motility genes in the genomes of six Eubacterium and Roseburia species that occur in the human intestinal microbiota and examined their respective locus organization by comparative genomics. Motility gene order was generally conserved across these loci. Five of these species harbored multiple genes for predicted flagellins. Flagellin proteins were isolated from R. inulinivorans strain A2-194 and from E. rectale strains A1-86 and M104/1. The amino-termini sequences of the R. inulinivorans and E. rectale A1-86 proteins were almost identical. These protein preparations stimulated secretion of interleukin-8 (IL-8 from human intestinal epithelial cell lines, suggesting that these flagellins were pro-inflammatory. Flagellins from the other four species were predicted to be pro-inflammatory on the basis of alignment to the consensus sequence of pro-inflammatory flagellins from the β- and γ- proteobacteria. Many fliC genes were deduced to be under the control of σ(28. The relative abundance of the target Eubacterium and Roseburia species varied across shotgun metagenomes from 27 elderly individuals. Genes involved in the flagellum biogenesis pathways of these species were variably abundant in these metagenomes, suggesting that the current depth of coverage used for metagenomic sequencing (3.13-4.79 Gb total sequence in our study insufficiently captures the functional diversity of genomes present at low (≤1% relative abundance. E. rectale and R. inulinivorans thus appear to synthesize complex flagella composed of flagellin proteins that stimulate IL-8 production. A greater depth of sequencing, improved evenness of sequencing

  9. Polychaete richness and abundance enhanced in anthropogenically modified estuaries despite high concentrations of toxic contaminants.

    Directory of Open Access Journals (Sweden)

    Katherine A Dafforn

    Full Text Available Ecological communities are increasingly exposed to multiple chemical and physical stressors, but distinguishing anthropogenic impacts from other environmental drivers remains challenging. Rarely are multiple stressors investigated in replicated studies over large spatial scales (>1000 kms or supported with manipulations that are necessary to interpret ecological patterns. We measured the composition of sediment infaunal communities in relation to anthropogenic and natural stressors at multiple sites within seven estuaries. We observed increases in the richness and abundance of polychaete worms in heavily modified estuaries with severe metal contamination, but no changes in the diversity or abundance of other taxa. Estuaries in which toxic contaminants were elevated also showed evidence of organic enrichment. We hypothesised that the observed response of polychaetes was not a 'positive' response to toxic contamination or a reduction in biotic competition, but due to high levels of nutrients in heavily modified estuaries driving productivity in the water column and enriching the sediment over large spatial scales. We deployed defaunated field-collected sediments from the surveyed estuaries in a small scale experiment, but observed no effects of sediment characteristics (toxic or enriching. Furthermore, invertebrate recruitment instead reflected the low diversity and abundance observed during field surveys of this relatively 'pristine' estuary. This suggests that differences observed in the survey are not a direct consequence of sediment characteristics (even severe metal contamination but are related to parameters that covary with estuary modification such as enhanced productivity from nutrient inputs and the diversity of the local species pool. This has implications for the interpretation of diversity measures in large-scale monitoring studies in which the observed patterns may be strongly influenced by many factors that covary with anthropogenic

  10. Re-examining High Abundance SDSS Mass-Metallicity Outliers: High N/O, Evolved Wolf-Rayet Galaxies?

    CERN Document Server

    Berg, Danielle A; Marble, Andrew R

    2011-01-01

    We present new MMT spectroscopic observations of four dwarf galaxies representative of a larger sample observed by the Sloan Digital Sky Survey (SDSS) and identified by Peeples et al. (2008) as low-mass, high oxygen abundance outliers from the mass-metallicity relation. Peeples et al. (2008) showed that these four objects (with metallicity estimates of 8.5 =~ 0.10), each of which tend to bias estimates based on strong emission lines toward high oxygen abundances. These spectra all fall in a regime where the "standard" strong line methods for metallicity determinations are not well calibrated either empirically or by photoionization modeling. By comparing our spectra directly to photoionization models, we estimate oxygen abundances in the range of 7.9 =< 12 + log(O/H) =< 8.4, consistent with the scatter of the mass-metallicity relation. We discuss the physical nature of these galaxies that leads to their unusual spectra (and previous classification as outliers), finding their low excitation, elevated N/O...

  11. High-Protein Diets: Are They Safe?

    Science.gov (United States)

    Healthy Lifestyle Nutrition and healthy eating Are high-protein diets safe for weight loss? Answers from Katherine ... L.D. For most healthy people, a high-protein diet generally isn't harmful, particularly when followed ...

  12. Ferritin acts as the most abundant binding protein for snowdrop lectin in the midgut of rice brown planthoppers (Nilaparvata lugens).

    Science.gov (United States)

    Du, J; Foissac, X; Carss, A; Gatehouse, A M; Gatehouse, J A

    2000-04-01

    The mannose-specific snowdrop lectin [Galanthus nivalis agglutinin (GNA)] displays toxicity to the rice brown planthopper Nilaparvata lugens. A 26kDa GNA-binding polypeptide from N. lugens midgut was identified by lectin blotting and affinity chromatography, and characterized by N-terminal sequencing. This polypeptide is the most abundant binding protein for GNA in the N. lugens midgut. A cDNA (fersub2) encoding this protein was isolated from an N. lugens cDNA library. The deduced amino acid sequence shows significant homology to ferritin subunits from Manduca sexta and other arthropods, plants and vertebrates, and contains a putative N-glycosylation site. Native ferritin was purified from whole insects as a protein of more than 400kDa in size and characterized biochemically. Three subunits of 20, 26 and 27kDa were released from the native complex. The 26kDa subunit binds GNA, and its N-terminal sequence was identical to that of fersub2. A second cDNA (fersub1), exhibiting strong homology with dipteran ferritin, was identified as an abundant cDNA in an N. lugens midgut-specific cDNA library, and could encode the larger ferritin subunit. The fersub1 cDNA carries a stem-loop structure (iron-responsive element) upstream from the start codon, similar to structures that have been shown to play a role in the control of ferritin synthesis in other insects.

  13. Diversity, abundance, and sex-specific expression of chemosensory proteins in the reproductive organs of the locust Locusta migratoria manilensis.

    Science.gov (United States)

    Zhou, Xian-Hong; Ban, Li-Ping; Iovinella, Immacolata; Zhao, Li-Jing; Gao, Qian; Felicioli, Antonio; Sagona, Simona; Pieraccini, Giuseppe; Pelosi, Paolo; Zhang, Long; Dani, Francesca Romana

    2013-01-01

    Chemosensory proteins (CSPs) are small soluble proteins often associated with chemosensory organs in insects but include members involved in other functions, such as pheromone delivery and development. Although the CSPs of the sensory organs have been extensively studied, little is known on their functions in other parts of the body. A first screening of the available databases has identified 70 sequences encoding CSPs in the oriental locust Locusta migratoria manilensis. Applying proteomic analysis, we have identified 17 of them abundantly expressed in the female reproductive organs, but only one (CSP91) in male organs. Bacterially expressed CSP91 binds fatty acids with a specificity for oleic and linoleic acid, as well as medium-length alcohols and esters. The same acids have been detected as the main gas chromatographic peaks in the dichloromethane extracts of reproductive organs of both sexes. The abundance and the number of CSPs in female reproductive organs indicates important roles for these proteins. We cannot exclude that different functions can be associated with each of the 17 CSPs, including delivery of semiochemicals, solubilization of hormones, direct control of development, or other unknown tasks.

  14. Petrogenesis of high-CaO lavas from Mauna Kea, Hawaii: Constraints from trace element abundances

    Science.gov (United States)

    Huang, Shichun; Humayun, Munir

    2016-07-01

    The role of a mafic component in the petrogenesis of Oceanic Island Basalts (OIBs) is highly debated. As the best studied OIB, Hawaiian lavas provide critical insights into OIB genesis. At a given MgO content, the CaO content in the melt has been used to distinguish between partial melts of peridotite and garnet pyroxenite/eclogite. However, calculations using the BATCH program show that CaO contents in volatile-free melts saturated with all four phases, garnet, clinopyroxene, orthopyroxene and olivine, are controlled by both degrees of partial melting and source compositions, and low melt CaO content is not diagnostic of partial melts from garnet pyroxenite/eclogite. This is an important consideration in understanding the origin of high-CaO lavas recovered from the Hawaii Scientific Drilling Project (HSDP). Detailed geochemical and isotopic studies have been focused on the HSDP high- and low-SiO2 group lavas, and high-CaO lavas were not well studied because they were not included in the original reference suite samples. Here, we report trace element abundances obtained on a suite of high-CaO glasses and compared the trace element abundances of high-CaO lavas to those in high- and low-SiO2 lavas. When normalized to the average composition of low-SiO2 lavas, high-CaO lavas form a U-shaped trace element pattern, enriched in both the most incompatible (Nb, Th) and the least incompatible (Sc, V) elements. This compositional distinction is best explained if high-CaO parental magma represents a mixture of a low degree partial melt of the low-SiO2 mantle source with a high degree (>80%) partial melt derived from a mafic cumulate component. This mafic cumulate must be clinopyroxene-rich, and it could be delaminated mafic cumulate formed under arcs during continent formation, lower continental crust, recycled lower oceanic crust, or high pressure cumulates from a magma chamber.

  15. Elemental Abundances in Two High Column Density Damped Lyman Alpha Systems at z < 1.5

    CERN Document Server

    Rao, S M; Howk, J C; Wolfe, A M; Rao, Sandhya M.; Prochaska, Jason X.; Wolfe, Arthur M.

    2004-01-01

    We present Keck/HIRES abundance measurements and metal-line kinematic profiles of the damped Lyman alpha systems (DLAs) towards the quasars Q0933+733 (z_abs=1.479) and Q0948+433 (z_abs=1.233). These two DLAs have among the five highest HI column densities at any redshift: N(HI)=4.2E21 cm^{-2}. The metal-line data, presented here for the first time, reveal that these DLAs are noteworthy for several other reasons as well. 1) The Q0933+733 DLA exhibits simple kinematic structure with unusually narrow velocity widths as measured from its unsaturated metal lines (delta v=16 km/s). At 2.6% solar, it has the second lowest metallicity at z -1) and a significant alpha-enhancement. The strong metal lines of this DLA have made possible the detection of TiII1910, CoII2012, and MgI2026. 3) We find that the relative gas-phase abundances of both DLAs follow the general trend seen at high redshift, e.g., enhanced Zn/Fe and Si/Fe, and sub-solar Mn/Fe, indicating that there is little evolution in the nucleosynthetic patterns o...

  16. Discovery of earth-abundant nitride semiconductors by computational screening and high-pressure synthesis.

    Science.gov (United States)

    Hinuma, Yoyo; Hatakeyama, Taisuke; Kumagai, Yu; Burton, Lee A; Sato, Hikaru; Muraba, Yoshinori; Iimura, Soshi; Hiramatsu, Hidenori; Tanaka, Isao; Hosono, Hideo; Oba, Fumiyasu

    2016-06-21

    Nitride semiconductors are attractive because they can be environmentally benign, comprised of abundant elements and possess favourable electronic properties. However, those currently commercialized are mostly limited to gallium nitride and its alloys, despite the rich composition space of nitrides. Here we report the screening of ternary zinc nitride semiconductors using first-principles calculations of electronic structure, stability and dopability. This approach identifies as-yet-unreported CaZn2N2 that has earth-abundant components, smaller carrier effective masses than gallium nitride and a tunable direct bandgap suited for light emission and harvesting. High-pressure synthesis realizes this phase, verifying the predicted crystal structure and band-edge red photoluminescence. In total, we propose 21 promising systems, including Ca2ZnN2, Ba2ZnN2 and Zn2PN3, which have not been reported as semiconductors previously. Given the variety in bandgaps of the identified compounds, the present study expands the potential suitability of nitride semiconductors for a broader range of electronic, optoelectronic and photovoltaic applications.

  17. Highly abundant and stage-specific mRNAs in the obligate pathogen Bremia lactucae.

    Science.gov (United States)

    Judelson, H S; Michelmore, R W

    1990-01-01

    Germinating spores of the obligate pathogen Bremia lactucae (lettuce downy mildew) contain several unusually abundant species of mRNA. Thirty-nine cDNA clones corresponding to prevalent transcripts were isolated from a library synthesized using poly(A)+ RNA from germinating spores; these clones represented only five distinct classes. Each corresponding mRNA accounted for from 0.4 to 9 percent by mass of poly(A)+ RNA from germinating spores and together represented greater than 20 percent of the mRNA. The expression of the corresponding genes, and a gene encoding Hsp70, was analyzed in spores during germination and during growth in planta. The Hsp70 mRNA and mRNA from one abundant cDNA clone (ham34) were expressed constitutively. Two clones (ham9 and ham12) hybridized only to mRNA from spores and germinating spores. Two clones (ham37 and ham27) showed hybridization specific to germinating spores. Quantification of the number of genes homologous to each cDNA clone indicated that four clones corresponded to one or two copies per haploid genome, and one hybridized to an approximately 11-member family of genes. A sequence of the gene corresponding to ham34 was obtained to investigate its function and to identify sequences conferring high levels of gene expression for use in constructing vectors for the transformation of B. lactucae.

  18. Discovery of earth-abundant nitride semiconductors by computational screening and high-pressure synthesis

    Science.gov (United States)

    Hinuma, Yoyo; Hatakeyama, Taisuke; Kumagai, Yu; Burton, Lee A.; Sato, Hikaru; Muraba, Yoshinori; Iimura, Soshi; Hiramatsu, Hidenori; Tanaka, Isao; Hosono, Hideo; Oba, Fumiyasu

    2016-01-01

    Nitride semiconductors are attractive because they can be environmentally benign, comprised of abundant elements and possess favourable electronic properties. However, those currently commercialized are mostly limited to gallium nitride and its alloys, despite the rich composition space of nitrides. Here we report the screening of ternary zinc nitride semiconductors using first-principles calculations of electronic structure, stability and dopability. This approach identifies as-yet-unreported CaZn2N2 that has earth-abundant components, smaller carrier effective masses than gallium nitride and a tunable direct bandgap suited for light emission and harvesting. High-pressure synthesis realizes this phase, verifying the predicted crystal structure and band-edge red photoluminescence. In total, we propose 21 promising systems, including Ca2ZnN2, Ba2ZnN2 and Zn2PN3, which have not been reported as semiconductors previously. Given the variety in bandgaps of the identified compounds, the present study expands the potential suitability of nitride semiconductors for a broader range of electronic, optoelectronic and photovoltaic applications. PMID:27325228

  19. Highly efficient luminescent solar concentrators based on earth-abundant indirect-bandgap silicon quantum dots

    Science.gov (United States)

    Meinardi, Francesco; Ehrenberg, Samantha; Dhamo, Lorena; Carulli, Francesco; Mauri, Michele; Bruni, Francesco; Simonutti, Roberto; Kortshagen, Uwe; Brovelli, Sergio

    2017-02-01

    Building-integrated photovoltaics is gaining consensus as a renewable energy technology for producing electricity at the point of use. Luminescent solar concentrators (LSCs) could extend architectural integration to the urban environment by realizing electrode-less photovoltaic windows. Crucial for large-area LSCs is the suppression of reabsorption losses, which requires emitters with negligible overlap between their absorption and emission spectra. Here, we demonstrate the use of indirect-bandgap semiconductor nanostructures such as highly emissive silicon quantum dots. Silicon is non-toxic, low-cost and ultra-earth-abundant, which avoids the limitations to the industrial scaling of quantum dots composed of low-abundance elements. Suppressed reabsorption and scattering losses lead to nearly ideal LSCs with an optical efficiency of η = 2.85%, matching state-of-the-art semi-transparent LSCs. Monte Carlo simulations indicate that optimized silicon quantum dot LSCs have a clear path to η > 5% for 1 m2 devices. We are finally able to realize flexible LSCs with performances comparable to those of flat concentrators, which opens the way to a new design freedom for building-integrated photovoltaics elements.

  20. Protein Abundances can Distinguish Between Naturally-occurring and Laboratory Strains of Yersinia pestis, the Causative Agent of Plague

    Energy Technology Data Exchange (ETDEWEB)

    Merkley, Eric D.; Sego, Landon H.; Lin, Andy; Leiser, Owen P.; Kaiser, Brooke LD; Adkins, Joshua N.; Keim, Paul S.; Wagner, David M.; Kreuzer, Helen W.

    2017-08-30

    Adaptive processes in bacterial species can occur rapidly in laboratory culture, leading to genetic divergence between naturally occurring and laboratory-adapted strains. Differentiating wild and closely-related laboratory strains is clearly important for biodefense and bioforensics; however, DNA sequence data alone has thus far not provided a clear signature, perhaps due to lack of understanding of how diverse genome changes lead to adapted phenotypes. Protein abundance profiles from mass spectrometry-based proteomics analyses are a molecular measure of phenotype. Proteomics data contains sufficient information that powerful statistical methods can uncover signatures that distinguish wild strains of Yersinia pestis from laboratory-adapted strains.

  1. Sodium-pump gene-expression, protein abundance and enzyme activity in isolated nephron segments of the aging rat kidney

    Science.gov (United States)

    Scherzer, Pnina; Gal-Moscovici, Anca; Sheikh-Hamad, David; Popovtzer, Mordecai M

    2015-01-01

    Aging is associated with alteration in renal tubular functions, including sodium handling and concentrating ability. Na-K-ATPase plays a key role in driving tubular transport, and we hypothesized that decreased concentrating ability of the aging kidney is due in part to downregulation of Na-K-ATPase. In this study, we evaluated Na and K balance, aldosterone levels, and Na-K-ATPase gene expression, protein abundance, and activity in aging rat kidney. Na-K-ATPase activity (assayed microfluorometrically), mRNA (RT-PCR), and protein abundance (immunoblotting) were quantitated in the following isolated nephron segments: PCT, PST, MTAL, DCT, and CCD from 2, 8, 15, and 24 month-old-rats. In the course of aging, creatinine clearance decreased from 0.48 ± 0.02 mL/min/100 g BW to 0.28 ± 0.06 (P < 0.001) and aldosterone decreased from 23.6 ± 0.8 ng/dL to 13.2 ± 0.6 (P < 0.001). Serum Na+ and K+ increased by 4.0% and 22.5%, respectively. Na-K-ATPase activity, mRNA, and protein abundance of the α1 subunit displayed similar trends in all assayed segments; increasing in PCT and PST; decreasing in MTAL and DCT; increasing in CCD: in PCT they increased by 40%, 75%, and 250%, respectively; while in PST they increased by 80%, 50%, and 100%, respectively (P < 0.001). In MTAL they declined by 36%, 24%, and 34%, respectively, and in DCT by 38%, 59%, and 60%, respectively (P < 0.001). They were higher in CCD by 110%, 115%, and 246%, respectively (P < 0.001). Rats maintained Na/K balance; however with a steady state elevated serum K+. These results reveal quantitative changes in axial distribution of Na-K-ATPase at the level of gene expression, protein abundance, and activity in the nephrons of aging animals and may explain, in part, the pathophysiology of the senescent kidney. PMID:26056060

  2. Identification of an abundant 56 kDa protein implicated in food allergy as granule-bound starch synthase.

    Science.gov (United States)

    Krishnan, Hari B; Chen, Ming-Hsuan

    2013-06-01

    Rice, the staple food of south and east Asian counties, is considered to be hypoallergenic. However, several clinical studies have documented rice-induced allergy in sensitive patients. Rice proteins with molecular weights of 14-16, 26, 33, and 56 kDa have been identified as allergens. Recently, it was documented that the 56 kDa rice allergen was responsible for rice-induced anaphylaxis. The 14-16 kDa allergens have been identified as α-amylase inhibitors; the 26 kDa protein has been identified as α-globulin; and the 33 kDa protein has been identified as glyoxalase I. However, the identity of the 56 kDa rice allergen has not yet been determined. In this study, we demonstrate that serum from patients allergic to maize shows IgE binding to a 56 kDa protein that was present in both maize and rice but not in the oil seeds soybean and peanut. The 56 kDa IgE-binding protein was abundant in the rice endosperm. We have purified this protein from rice endosperm and demonstrated its reactivity to IgE antibodies from the serum of maize-allergic patients. The purified protein was subjected to matrix-assisted laser desorption ionization-time of flight-tandem mass spectrometry analysis, resulting in identification of this rice allergen as granule-bound starch synthase, a product of the Waxy gene. Immunoblot analysis using protein extracts from a waxy mutant of rice revealed the absence of the 56 kDa IgE-binding protein. Our results demonstrate that the 56 kDa rice allergen is granule-bound starch synthase and raise the possibility of using waxy mutants of rice as a potential source of the hypoallergenic diet for patients sensitized to the 56 kDa rice allergen.

  3. Effects of Tamarindus indica fruit pulp extract on abundance of HepG2 cell lysate proteins and their possible consequential impact on metabolism and inflammation.

    Science.gov (United States)

    Chong, Ursula R W; Abdul-Rahman, Puteri S; Abdul-Aziz, Azlina; Hashim, Onn H; Mat-Junit, Sarni

    2013-01-01

    The fruit pulp extract of Tamarindus indica has been reported for its antioxidant and hypolipidemic properties. In this study, the methanol extract of T. indica fruit pulp was investigated for its effects on the abundance of HepG2 cell lysate proteins. Cell lysate was extracted from HepG2 cells grown in the absence and presence of the methanol extract of T. indica fruit pulp. Approximately 2500 spots were resolved using two-dimensional gel electrophoresis and the abundance of 20 cellular proteins was found to be significantly reduced. Among the proteins of reduced abundance, fourteen, including six proteins involved in metabolism (including ethanolamine phosphate cytidylyltransferase), four mitochondrial proteins (including prohibitin and respiratory chain proteins), and four proteins involved in translation and splicing, were positively identified by mass spectrometry and database search. The identified HepG2 altered abundance proteins, when taken together and analyzed by Ingenuity Pathways Analysis (IPA) software, are suggestive of the effects of T. indica fruit pulp extract on metabolism and inflammation, which are modulated by LXR/RXR. In conclusion, the methanol fruit pulp extract of T. indica was shown to cause reduced abundance of HepG2 mitochondrial, metabolic, and regulatory proteins involved in oxidative phosphorylation, protein synthesis, and cellular metabolism.

  4. Effects of Tamarindus indica Fruit Pulp Extract on Abundance of HepG2 Cell Lysate Proteins and Their Possible Consequential Impact on Metabolism and Inflammation

    Directory of Open Access Journals (Sweden)

    Ursula R. W. Chong

    2013-01-01

    Full Text Available The fruit pulp extract of Tamarindus indica has been reported for its antioxidant and hypolipidemic properties. In this study, the methanol extract of T. indica fruit pulp was investigated for its effects on the abundance of HepG2 cell lysate proteins. Cell lysate was extracted from HepG2 cells grown in the absence and presence of the methanol extract of T. indica fruit pulp. Approximately 2500 spots were resolved using two-dimensional gel electrophoresis and the abundance of 20 cellular proteins was found to be significantly reduced. Among the proteins of reduced abundance, fourteen, including six proteins involved in metabolism (including ethanolamine phosphate cytidylyltransferase, four mitochondrial proteins (including prohibitin and respiratory chain proteins, and four proteins involved in translation and splicing, were positively identified by mass spectrometry and database search. The identified HepG2 altered abundance proteins, when taken together and analyzed by Ingenuity Pathways Analysis (IPA software, are suggestive of the effects of T. indica fruit pulp extract on metabolism and inflammation, which are modulated by LXR/RXR. In conclusion, the methanol fruit pulp extract of T. indica was shown to cause reduced abundance of HepG2 mitochondrial, metabolic, and regulatory proteins involved in oxidative phosphorylation, protein synthesis, and cellular metabolism.

  5. Chernobyl seed project. Advances in the identification of differentially abundant proteins in a radio-contaminated environment

    Directory of Open Access Journals (Sweden)

    Namik Mammad Oglu Rashydov

    2015-07-01

    Full Text Available Plants have the ability to grow and successfully reproduce in radio-contaminated environments, which has been highlighted by nuclear accidents at Chernobyl (1986 and Fukushima (2011. The main aim of this article is to summarize the advances of the Chernobyl seed project which has the purpose to provide proteomic characterization of plants grown in the Chernobyl area. We present a summary of comparative proteomic studies on soybean and flax seeds harvested from radio-contaminated Chernobyl areas during two successive generations. Using experimental design developed for radio-contaminated areas, altered abundances of glycine betaine, seed storage proteins, and proteins associated with carbon assimilation into fatty acids were detected. Similar studies in Fukushima radio-contaminated areas might complement these data. The results from these Chernobyl experiments can be viewed in a user-friendly format at a dedicated web-based database freely available at www.chernobylproteomics.sav.sk.

  6. Chernobyl seed project. Advances in the identification of differentially abundant proteins in a radio-contaminated environment.

    Science.gov (United States)

    Rashydov, Namik M; Hajduch, Martin

    2015-01-01

    Plants have the ability to grow and successfully reproduce in radio-contaminated environments, which has been highlighted by nuclear accidents at Chernobyl (1986) and Fukushima (2011). The main aim of this article is to summarize the advances of the Chernobyl seed project which has the purpose to provide proteomic characterization of plants grown in the Chernobyl area. We present a summary of comparative proteomic studies on soybean and flax seeds harvested from radio-contaminated Chernobyl areas during two successive generations. Using experimental design developed for radio-contaminated areas, altered abundances of glycine betaine, seed storage proteins, and proteins associated with carbon assimilation into fatty acids were detected. Similar studies in Fukushima radio-contaminated areas might complement these data. The results from these Chernobyl experiments can be viewed in a user-friendly format at a dedicated web-based database freely available at http://www.chernobylproteomics.sav.sk.

  7. High quality protein microarray using in situ protein purification

    Directory of Open Access Journals (Sweden)

    Fleischmann Robert D

    2009-08-01

    Full Text Available Abstract Background In the postgenomic era, high throughput protein expression and protein microarray technologies have progressed markedly permitting screening of therapeutic reagents and discovery of novel protein functions. Hexa-histidine is one of the most commonly used fusion tags for protein expression due to its small size and convenient purification via immobilized metal ion affinity chromatography (IMAC. This purification process has been adapted to the protein microarray format, but the quality of in situ His-tagged protein purification on slides has not been systematically evaluated. We established methods to determine the level of purification of such proteins on metal chelate-modified slide surfaces. Optimized in situ purification of His-tagged recombinant proteins has the potential to become the new gold standard for cost-effective generation of high-quality and high-density protein microarrays. Results Two slide surfaces were examined, chelated Cu2+ slides suspended on a polyethylene glycol (PEG coating and chelated Ni2+ slides immobilized on a support without PEG coating. Using PEG-coated chelated Cu2+ slides, consistently higher purities of recombinant proteins were measured. An optimized wash buffer (PBST composed of 10 mM phosphate buffer, 2.7 mM KCl, 140 mM NaCl and 0.05% Tween 20, pH 7.4, further improved protein purity levels. Using Escherichia coli cell lysates expressing 90 recombinant Streptococcus pneumoniae proteins, 73 proteins were successfully immobilized, and 66 proteins were in situ purified with greater than 90% purity. We identified several antigens among the in situ-purified proteins via assays with anti-S. pneumoniae rabbit antibodies and a human patient antiserum, as a demonstration project of large scale microarray-based immunoproteomics profiling. The methodology is compatible with higher throughput formats of in vivo protein expression, eliminates the need for resin-based purification and circumvents

  8. A simple microfluidic platform to study age-dependent protein abundance and localization changes in Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Margarita Cabrera

    2017-04-01

    Full Text Available The budding yeast Saccharomyces cerevisiae divides asymmetrically, with a smaller daughter cell emerging from its larger mother cell. While the daughter lineage is immortal, mother cells age with each cell division and have a finite lifespan. The replicative ageing of the yeast mother cell has been used as a model to study the ageing of mitotically active human cells. Several microfluidic platforms, which use fluid flow to selectively remove daughter cells, have recently been developed that can monitor cell physiology as mother cells age. However, these platforms are not trivial to set up and users often require many hours of training. In this study, we have developed a simple system, which combines a commercially available microfluidic platform (the CellASIC ONIX Microfluidic Platform and a genetic tool to prevent the proliferation of daughter cells (the Mother Enrichment Program, to monitor protein abundance and localization changes during approximately the first half of the yeast replicative lifespan. We validated our system by observing known age-dependent changes, such as decreased Sir2 abundance, and have identified a protein with a previously unknown age-dependent change in localization.

  9. Zooplankton abundance, species composition and ecology of tropical high-mountain crater lake Wonchi, Ethiopia

    Directory of Open Access Journals (Sweden)

    Fasil Degefu

    2014-11-01

    Full Text Available The highlands of Ethiopia represent some of the remnants of undisturbed aquatic ecosystems; they are however highly threatened by significant socio–economic developments and associated anthropogenic impacts. Lake Wonchi is one of the few remaining fairly pristine high–mountain crater lakes in the central highlands and has never been investigated in detail. We present a first study on zooplankton taxa composition, abundance and biomass conducted over more than one year including the underlying environmental drivers. The lake is basic (pH 7.9-8.9, dilute (specific conductivity 185-245 µS cm-1 and oligotrophic with mean trophic status index of 36. The zooplankton community composition showed low species richness comprising a total of fourteen taxa with six cladocerans, one copepod and seven rotifers. Simpson´s index of diversity with values between 0.6 and 0.8 pointed towards a homogenous taxa occurrence within the single sample units. The overall mean (±SD standing biomass of zooplankton was 62.02±25.76 mg dry mass m-3,which is low compared to other highland and rift valley lakes in Ethiopia. Cyclopoid copepods, in particular Thermocyclops ethiopiensis were the most abundant group and contributed 50% to the total zooplankton abundance followed by cladocerans (38% and rotifers (12%. Non-metric multi-dimensional scaling resulted in a 3-dimensional model, which revealed similar community composition on successive sampling dates except in December/January and May. Temperature, alkalinity, conductivity and nitrate-N had significant influence on this seasonal pattern. A weak, but significant positive correlation (r=0.482, N=20, P=0.037 between Chlorophyll a and zooplankton biomass mirrors a bottom-up effect of phytoplankton biomass on zooplankton dynamics. The zooplankton of Lake Wonchi displayed some degree of segregation along the epi– and metalimnion during this study, but diel vertical migration was not observed. The results show that fish

  10. A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast*

    OpenAIRE

    Blein-Nicolas, Mélisande; Albertin, Warren; Da Silva, Telma; Valot, Benoît; Balliau, Thierry; Masneuf-Pomarède, Isabelle; Bely, Marina; Marullo, Philippe; Sicard, Delphine; Dillmann, Christine; de Vienne, Dominique; Zivy, Michel

    2015-01-01

    Heterosis is a universal phenomenon that has major implications in evolution and is of tremendous agro-economic value. To study the molecular manifestations of heterosis and to find factors that maximize its strength, we implemented a large-scale proteomic experiment in yeast. We analyzed the inheritance of 1,396 proteins in 55 inter- and intraspecific hybrids obtained from Saccharomyces cerevisiae and S. uvarum that were grown in grape juice at two temperatures. We showed that the proportion...

  11. Dietary flavonoid fisetin increases abundance of high-molecular-mass hyaluronan conferring resistance to prostate oncogenesis.

    Science.gov (United States)

    Lall, Rahul K; Syed, Deeba N; Khan, Mohammad Imran; Adhami, Vaqar M; Gong, Yuansheng; Lucey, John A; Mukhtar, Hasan

    2016-09-01

    We and others have shown previously that fisetin, a plant flavonoid, has therapeutic potential against many cancer types. Here, we examined the probable mechanism of its action in prostate cancer (PCa) using a global metabolomics approach. HPLC-ESI-MS analysis of tumor xenografts from fisetin-treated animals identified several metabolic targets with hyaluronan (HA) as the most affected. Efficacy of fisetin on HA was then evaluated in vitro and also in vivo in the transgenic TRAMP mouse model of PCa. Size exclusion chromatography-multiangle laser light scattering (SEC-MALS) was performed to analyze the molar mass (Mw) distribution of HA. Fisetin treatment downregulated intracellular and secreted HA levels both in vitro and in vivo Fisetin inhibited HA synthesis and degradation enzymes, which led to cessation of HA synthesis and also repressed the degradation of the available high-molecular-mass (HMM)-HA. SEC-MALS analysis of intact HA fragment size revealed that cells and animals have more abundance of HMM-HA and less of low-molecular-mass (LMM)-HA upon fisetin treatment. Elevated HA levels have been shown to be associated with disease progression in certain cancer types. Biological responses triggered by HA mainly depend on the HA polymer length where HMM-HA represses mitogenic signaling and has anti-inflammatory properties whereas LMM-HA promotes proliferation and inflammation. Similarly, Mw analysis of secreted HA fragment size revealed less HMM-HA is secreted that allowed more HMM-HA to be retained within the cells and tissues. Our findings establish that fisetin is an effective, non-toxic, potent HA synthesis inhibitor, which increases abundance of antiangiogenic HMM-HA and could be used for the management of PCa. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  12. THE ABUNDANCE, DIVERSITY AND METABOLIC FOOTPRINT OF SOIL NEMATODES IS HIGHEST IN HIGH ELEVATION ALPINE GRASSLANDS

    Directory of Open Access Journals (Sweden)

    Alan Kergunteuil

    2016-07-01

    Full Text Available Nematodes are key components of soil biodiversity and represent valuable bio-indicators of soil food webs. Numerous community indices have been developed in order to track variations in soil ecosystem processes, but their use is mainly restricted to anthropogenic stresses. In this study, we propose to expand the use of nematodes’ derived ecological indices in order to shed light on variations of soil food webs in natural systems distributed along elevation gradients. For this purpose, we aimed at determining how elevation affects the community structure and the trophic diversity by studying the abundance, the composition and the functional diversity of nematode communities. Nematode communities were sampled every 200 m across five transects that span about 2000 m in elevation in the Alps. To understand the underlying ecological parameters driving these patterns we studied both abiotic factors (soil properties and biotic factors (trophic links, relationships with plant diversity. We found that (1 nematode abundance increases with elevation of lowland forests and alpine meadows; (2 differences in nematodes communities rely on habitat-specific functional diversity (e.g. tolerance to harsh environments, colonizer/persister status while most trophic groups are ubiquitous; and (3 the metabolic footprint of the complete nematode community increases with elevation. We thus conclude that the contribution of soil dwelling nematodes to belowground ecosystem processes, including carbon and energy flow, is stronger at high elevation. The resulting cascading effects on the soil food web structure are discussed from an ecosystem functioning perspective. Overall, this study highlights the importance of nematodes in soil ecosystems and brings insights in their enhanced role along ecological gradients.

  13. BacS: an abundant bacteroid protein in Rhizobium etli whose expression ex planta requires nifA.

    Science.gov (United States)

    Jahn, Olivia J; Davila, Guillermo; Romero, David; Noel, K Dale

    2003-01-01

    Rhizobium etli CFN42 bacteroids from bean nodules possessed an abundant 16-kDa protein (BacS) that was found in the membrane pellet after cell disruption. This protein was not detected in bacteria cultured in tryptone-yeast extract. In minimal media, it was produced at low oxygen concentration but not in a mutant whose nifA was disrupted. N-terminal sequencing of the protein led to isolation of a bacS DNA fragment. DNA hybridization and nucleotide sequencing revealed three copies of the bacS gene, all residing on the main symbiotic plasmid of strain CFN42. A stretch of 304 nucleotides, exactly conserved upstream of all three bacS open reading frames, had very close matches with the NifA and sigma 54 consensus binding sequences. The only bacS homology in the genetic sequence databases was to three hypothetical proteins of unknown function, all from rhizobial species. Mutation and genetic complementation indicated that each of the bacS genes gives rise to a BacS polypeptide. Mutants disrupted or deleted in all three genes did not produce the BacS polypeptide but were Nod+ and Fix+ on Phaseolus vulgaris.

  14. Molecular evolution of myelin basic protein, an abundant structural myelin component.

    Science.gov (United States)

    Nawaz, Schanila; Schweitzer, Jörn; Jahn, Olaf; Werner, Hauke B

    2013-08-01

    Rapid nerve conduction in jawed vertebrates is facilitated by the myelination of axons, which evolved in ancient cartilaginous fish. We aim to understand the coevolution of myelin and the major myelin proteins. We found that myelin basic protein (MBP) derived from living cartilaginous fish (sharks and rays) associated with the plasma membrane of glial cells similar to the phosphatidylinositol (4,5)-bisphosphate (PIP₂)-binding marker PH-PLCδ1, and that ionomycin-induced PIP₂-hydrolysis led to its cellular redistribution. We identified two paralogous mbp genes in multiple teleost species, consistent with a genome duplication at the root of the teleost clade. Zebrafish mbpb is organized in a complex transcription unit together with the unrelated gene-of-the-oligodendrocyte-lineage (golli) while mbpa does not encode GOLLI. Moreover, the embryonic expression of mbpa and mbpb differed, indicating functional specialization after duplication. However, both mbpa and mbpb-mRNAs were detected in mature oligodendrocytes and Schwann cells, MBPa and MBPb were mass spectrometrically identified in zebrafish myelin, both associated with the plasma membrane via PIP₂, and the ratio of nonsynonymous to synonymous nucleotide-substitution rates (Ka/Ks) was low. Together, this indicates selective pressure to conserve many aspects of the cellular expression and function of MBP across vertebrate species. We propose that the PIP₂-binding function of MBP is evolutionarily old and that its emergence in ancient gnathostomata provided glial cells with the competence to myelinate.

  15. Assessment of current mass spectrometric workflows for the quantification of low abundant proteins and phosphorylation sites

    Directory of Open Access Journals (Sweden)

    Manuel Bauer

    2015-12-01

    Full Text Available The data described here provide a systematic performance evaluation of popular data-dependent (DDA and independent (DIA mass spectrometric (MS workflows currently used in quantitative proteomics. We assessed the limits of identification, quantification and detection for each method by analyzing a dilution series of 20 unmodified and 10 phosphorylated synthetic heavy labeled reference peptides, respectively, covering six orders of magnitude in peptide concentration with and without a complex human cell digest background. We found that all methods performed very similarly in the absence of background proteins, however, when analyzing whole cell lysates, targeted methods were at least 5–10 times more sensitive than directed or DDA methods. In particular, higher stage fragmentation (MS3 of the neutral loss peak using a linear ion trap increased dynamic quantification range of some phosphopeptides up to 100-fold. We illustrate the power of this targeted MS3 approach for phosphopeptide monitoring by successfully quantifying 9 phosphorylation sites of the kinetochore and spindle assembly checkpoint component Mad1 over different cell cycle states from non-enriched pull-down samples. The data are associated to the research article ‘Evaluation of data-dependent and data-independent mass spectrometric workflows for sensitive quantification of proteins and phosphorylation sites׳ (Bauer et al., 2014 [1]. The mass spectrometry and the analysis dataset have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org via the PRIDE partner repository with the dataset identifier PXD000964.

  16. Differential protein abundance and function of UT-B urea transporters in human colon.

    Science.gov (United States)

    Collins, D; Winter, D C; Hogan, A M; Schirmer, L; Baird, A W; Stewart, G S

    2010-03-01

    Facilitative UT-B urea transporters enable the passage of urea across cell membranes. Gastrointestinal urea transporters are thought to play a significant role in the urea nitrogen salvaging process that occurs between mammalian hosts and their gut bacteria. This study investigated the expression of UT-B urea transporters in different segments of human colon. Immunoblot analysis showed that human colon expressed a 35-kDa glycosylated UT-B protein in the colonic mucosa. The 35-kDa UT-B transporter was predominantly located in plasma membrane-enriched samples (P UT-B transporters were located throughout colonocytes situated in the upper portion of the colonic crypts. Bidirectional trans-epithelial urea transport was significantly greater in the ascending colon than the descending colon (P UT-B protein in different sections of the human colon, strongly correlating to regions that contain the largest populations of intestinal bacteria. This study suggests an important role for UT-B urea transporters in maintaining the symbiotic relationship between humans and their gut bacteria.

  17. High throughput recombinant protein production of fungal secreted proteins

    DEFF Research Database (Denmark)

    Vala, Andrea Lages Lino; Roth, Doris; Grell, Morten Nedergaard

    2011-01-01

    a high-throughput protein production system with a special focus on fungal secreted proteins. We use a ligation independent cloning to clone target genes into expression vectors for E. coli and P. pastoris and a small scale test expression to identify constructs producing soluble protein. Expressed...... interaction), between fungi of the order Entomophthorales and aphids (pathogenic interaction), and in the mycoparasitic interaction between the oomycetes Pythium oligandrum and P. ultimum. In general, the high-throughput protein production system can lead to a better understanding of fungal/host interactions...

  18. Velocity and abundance precisions for future high-resolution spectroscopic surveys: a study for 4MOST

    CERN Document Server

    Caffau, E; Sbordone, L; Sartoretti, P; Hansen, C J; Royer, F; Leclerc, N; Bonifacio, P; Christlieb, N; Ludwig, H G; Grebel, E K; de Jong, R S; Chiappini, C; Walcher, J; Mignot, S; Feltzing, S; Cohen, M; Minchev, I; Helmi, A; Piffl, T; Depagne, E; Schnurr, O

    2012-01-01

    In preparation for future, large-scale, multi-object, high-resolution spectroscopic surveys of the Galaxy, we present a series of tests of the precision in radial velocity and chemical abundances that any such project can achieve at a 4m class telescope. We briefly discuss a number of science cases that aim at studying the chemo-dynamical history of the major Galactic components (bulge, thin and thick disks, and halo) - either as a follow-up to the Gaia mission or on their own merits. Based on a large grid of synthetic spectra that cover the full range in stellar parameters of typical survey targets, we devise an optimal wavelength range and argue for a moderately high-resolution spectrograph. As a result, the kinematic precision is not limited by any of these factors, but will practically only suffer from systematic effects, easily reaching uncertainties <1 km/s. Under realistic survey conditions (namely, considering stars brighter than r=16 mag with reasonable exposure times) we prefer an ideal resolving...

  19. Growing three-dimensional biomorphic graphene powders using naturally abundant diatomite templates towards high solution processability

    Science.gov (United States)

    Chen, Ke; Li, Cong; Shi, Liurong; Gao, Teng; Song, Xiuju; Bachmatiuk, Alicja; Zou, Zhiyu; Deng, Bing; Ji, Qingqing; Ma, Donglin; Peng, Hailin; Du, Zuliang; Rümmeli, Mark Hermann; Zhang, Yanfeng; Liu, Zhongfan

    2016-11-01

    Mass production of high-quality graphene with low cost is the footstone for its widespread practical applications. We present herein a self-limited growth approach for producing graphene powders by a small-methane-flow chemical vapour deposition process on naturally abundant and industrially widely used diatomite (biosilica) substrates. Distinct from the chemically exfoliated graphene, thus-produced biomorphic graphene is highly crystallized with atomic layer-thickness controllability, structural designability and less noncarbon impurities. In particular, the individual graphene microarchitectures preserve a three-dimensional naturally curved surface morphology of original diatom frustules, effectively overcoming the interlayer stacking and hence giving excellent dispersion performance in fabricating solution-processible electrodes. The graphene films derived from as-made graphene powders, compatible with either rod-coating, or inkjet and roll-to-roll printing techniques, exhibit much higher electrical conductivity (~110,700 S m-1 at 80% transmittance) than previously reported solution-based counterparts. This work thus puts forward a practical route for low-cost mass production of various powdery two-dimensional materials.

  20. High frequency (hourly) variation in vertical distribution and abundance of meroplanktonic larvae in nearshore waters during strong internal tidal forcing

    Science.gov (United States)

    Liévana MacTavish, A.; Ladah, L. B.; Lavín, M. F.; Filonov, A.; Tapia, Fabian J.; Leichter, J.

    2016-04-01

    We related the vertical distribution and abundance of nearshore meroplankton at hourly time scales with internal tidal wave events. We proposed that significant changes in plankter abundance would occur across internal tidal fronts, and that surface and bottom strata would respond in opposite fashions. First-mode internal tidal bores propagating in the alongshore direction were detected in water-column currents and baroclinic temperature changes. Surface and bottom currents always flowed in opposite directions, and abrupt flow reversals coincided with large temperature changes during arrival of bores. Crab zoeae and barnacle cyprids were more abundant in the bottom strata, whereas barnacle nauplii showed the opposite pattern. Significant changes in vertical distribution and abundance of target meroplankters occurred across internal tidal fronts, especially for crabs at depth, with surface and bottom organisms responding in opposite fashions. Changes in plankter abundance were significantly correlated with current flows in the strata where they were most abundant. The manner in which plankters were affected (increasing or decreasing abundance) appeared to be modulated by their vertical position within the water column. The significant differences found at the high frequencies of this study, maintained across sampling days, suggest that nearshore meroplankton populations may have greater and more consistent temporal and vertical variability than previously considered.

  1. The effect of cryopreservation on DNA damage, gene expression and protein abundance in vertebrate

    Directory of Open Access Journals (Sweden)

    Sujune Tsai

    2012-01-01

    Full Text Available Cryopreservation techniques allow the long-term storage of a wide variety of biological material without significant deterioration in quality. Immediate post-thaw survival is most often used to assess the effect of the freeze-thaw process on cells. However, this parameter provides no information on possible subtle effects of cryopreservation, including DNA damage, alteration of mRNA levels and protein function that may not be evident immediately post thaw. These potential adverse effects don’t necessarily result in cell death. While there are many comprehensive reviews of gamete and embryo cryopreservation in vertebrate species, we review here the publications relating to cryopreservation impact on the genome of sperm, embryos and oocytes.

  2. HIGH PRECISION ABUNDANCES OF THE OLD SOLAR TWIN HIP 102152: INSIGHTS ON Li DEPLETION FROM THE OLDEST SUN

    Energy Technology Data Exchange (ETDEWEB)

    Monroe, TalaWanda R.; Melendez, Jorge; Tucci Maia, Marcelo; Freitas, Fabricio C. [Departamento de Astronomia do IAG/USP, Universidade de Sao Paulo, Rua do Matao 1226, Cidade Universitaria, 05508-900 Sao Paulo, SP (Brazil); Ramirez, Ivan [McDonald Observatory, The University of Texas at Austin, Austin, TX 78712 (United States); Yong, David; Asplund, Martin; Alves-Brito, Alan; Casagrande, Luca [Research School of Astronomy and Astrophysics, The Australian National University, Cotter Road, Weston, ACT 2611 (Australia); Bergemann, Maria [Max Planck Institute for Astrophysics, Postfach 1317, D-85741 Garching (Germany); Bedell, Megan; Bean, Jacob [Department of Astronomy and Astrophysics, University of Chicago, 5640 S. Ellis Ave., Chicago, IL 60637 (United States); Lind, Karin [Institute of Astronomy, University of Cambridge, Madingley Road, Cambridge CB3 0HA (United Kingdom); Castro, Matthieu; Do Nascimento, Jose-Dias [Departamento de Fisica Teorica e Experimental, Universidade Federal do Rio Grande do Norte, 59072-970 Natal, RN (Brazil); Bazot, Michael, E-mail: tmonroe@usp.br [Centro de Astrofisica da Universidade do Porto, Rua das Estrelas, 4150-762 Porto (Portugal)

    2013-09-10

    We present the first detailed chemical abundance analysis of the old 8.2 Gyr solar twin, HIP 102152. We derive differential abundances of 21 elements relative to the Sun with precisions as high as 0.004 dex ({approx}<1%), using ultra high-resolution (R = 110,000), high S/N UVES spectra obtained on the 8.2 m Very Large Telescope. Our determined metallicity of HIP 102152 is [Fe/H] = -0.013 {+-} 0.004. The atmospheric parameters of the star were determined to be 54 K cooler than the Sun, 0.09 dex lower in surface gravity, and a microturbulence identical to our derived solar value. Elemental abundance ratios examined versus dust condensation temperature reveal a solar abundance pattern for this star, in contrast to most solar twins. The abundance pattern of HIP 102152 appears to be the most similar to solar of any known solar twin. Abundances of the younger, 2.9 Gyr solar twin, 18 Sco, were also determined from UVES spectra to serve as a comparison for HIP 102152. The solar chemical pattern of HIP 102152 makes it a potential candidate to host terrestrial planets, which is reinforced by the lack of giant planets in its terrestrial planet region. The following non-local thermodynamic equilibrium Li abundances were obtained for HIP 102152, 18 Sco, and the Sun: log {epsilon} (Li) = 0.48 {+-} 0.07, 1.62 {+-} 0.02, and 1.07 {+-} 0.02, respectively. The Li abundance of HIP 102152 is the lowest reported to date for a solar twin, and allows us to consider an emerging, tightly constrained Li-age trend for solar twin stars.

  3. Increased Abundance of Proteins Involved in Phytosiderophore Production in Boron-Tolerant Barley1[C][W

    Science.gov (United States)

    Patterson, John; Ford, Kris; Cassin, Andrew; Natera, Siria; Bacic, Antony

    2007-01-01

    Boron (B) phytotoxicity affects cereal-growing regions worldwide. Although B-tolerant barley (Hordeum vulgare) germplasm is available, molecules responsible for this tolerance mechanism have not been defined. We describe and use a new comparative proteomic technique, iTRAQ peptide tagging (iTRAQ), to compare the abundances of proteins from B-tolerant and -intolerant barley plants from a ‘Clipper’ × ‘Sahara’ doubled-haploid population selected on the basis of a presence or absence of two B-tolerance quantitative trait loci. iTRAQ was used to identify three enzymes involved in siderophore production (Iron Deficiency Sensitive2 [IDS2], IDS3, and a methylthio-ribose kinase) as being elevated in abundance in the B-tolerant plants. Following from this result, we report a potential link between iron, B, and the siderophore hydroxymugineic acid. We believe that this study highlights the potency of the iTRAQ approach to better understand mechanisms of abiotic stress tolerance in cereals, particularly when applied in conjunction with bulked segregant analysis. PMID:17478636

  4. The case for high precision in elemental abundances of stars in the era of large spectroscopic surveys

    CERN Document Server

    Lindegren, Lennart

    2013-01-01

    A number of large spectroscopic surveys of stars in the Milky Way are under way or are being planned. In this context it is important to discuss the extent to which elemental abundances can be used as discriminators between different (known and unknown) stellar populations in the Milky Way. We aim to establish the requirements in terms of precision in elemental abundances, as derived from spectroscopic surveys of the Milky Way's stellar populations, in order to detect interesting substructures in elemental abundance space. We present a simple relation between the minimum number of stars needed to detect a given substructure and the precision of the measurements. The results are in agreement with recent small- and large-scale studies, with high and low precision, respectively. Large-number statistics cannot fully compensate for low precision in the abundance measurements and each survey should carefully evaluate what the main science drivers are for the survey and ensure that the chosen observational strategy ...

  5. A combined HNCA/HNCO experiment for {sup 15}N labeled proteins with {sup 13}C at natural abundance

    Energy Technology Data Exchange (ETDEWEB)

    Kupce, Eriks [Varian Inc. (United Kingdom); Muhandiram, D.R.; Kay, Lewis E. [University of Toronto, Protein Engineering Network Centers of Excellence and Departments of Medical Genetics, Biochemistry and Chemistry (Canada)], E-mail: kay@pound.med.utoronto.ca

    2003-10-15

    A triple resonance NMR experiment is presented for the simultaneous recording of HNCA and HNCO data sets on {sup 15}N, natural abundance {sup 13}C samples. The experiment exploits the fact that transfers of magnetization from {sup 15}N to {sup 13}CO and from {sup 15}N to {sup 13}C{sup {alpha}} (and back) proceed independently for samples that are not enriched in {sup 13}C. A factor of 2 in measuring time is gained by recording the two data sets simultaneously with no compromise in spectral quality. An application to a 0.5 mM {sup 15}N labeled sample of protein-L is presented with all expected correlations observed in spectra recorded with a cryogenic probe at 500 MHz.

  6. Purification and in vitro chaperone activity of a class I small heat-shock protein abundant in recalcitrant chestnut seeds.

    Science.gov (United States)

    Collada, C; Gomez, L; Casado, R; Aragoncillo, C

    1997-09-01

    A 20-kD protein has been purified from cotyledons of recalcitrant (desiccation-sensitive) chestnut (Castanea sativa) seeds, where it accumulates at levels comparable to those of major seed storage proteins. This protein, termed Cs smHSP 1, forms homododecameric complexes under nondenaturing conditions and appears to be homologous to cytosolic class I small heat-shock proteins (smHSPs) from plant sources. In vitro evidence has been obtained that the isolated protein can function as a molecular chaperone; it increases, at stoichiometric levels, the renaturation yields of chemically denatured citrate synthase and also prevents the irreversible thermal inactivation of this enzyme. Although a role in desiccation tolerance has been hypothesized for seed smHSPs, this does not seem to be the case for Cs smHSP 1. We have investigated the presence of immunologically related proteins in orthodox and recalcitrant seeds of 13 woody species. Our results indicate that the presence of Cs smHSP 1-like proteins, even at high levels, is not enough to confer desiccation tolerance, and that the amount of these proteins does not furnish a reliable criterion to identify desiccation-sensitive seeds. Additional proteins or mechanisms appear necessary to keep the viability of orthodox seeds upon shedding.

  7. High Resolution Spectroscopy of Vega-like Stars: Abundances and Circumstellar Gas

    Science.gov (United States)

    Dunkin, S. K.; Barlow, M. J.; Ryan, Sean G.

    1996-01-01

    Vega-like stars are main-sequence stars exhibiting excess infrared emission. In an effort to improve the information available on this class of star, 13 stars have been analyzed which have been classed as Vega-like, or have an infra-red excess attributable to dust in their circumstellar environment. In a separate paper stellar properties such as effective temperature and log g have been derived and in this poster we highlight the results of the photospheric abundance analysis also carried out during this work. King recently drew attention to the possible link between Vega-like stars and the photospheric metal-depleted class of A-stars, the Lambda Bootis stars. Since Vega-like stars are thought to have disks of dust, it might be expected that accretion of depleted gas onto the surface of these stars may cause this same phenomenon. In the 6 stars studied for depletions, none showed the extreme underabundance patterns observed in Lambda Bootis stars. However, depletions of silicon and magnesium were found in two of the sample, suggesting that these elements are in silicate dust grains in the circumstellar environment of these stars. Absorption lines attributed to circumstellar gas have been positively identified in three stars in our sample. Individual cases show evidence either of high-velocity outflowing gas, variability in the circumstellar lines observed, or evidence of circumstellar gas in excited lines of Fe II. No previous identification of circumstellar material has been made for two of the stars in question.

  8. Interplay between human high mobility group protein 1 and replication protein A on psoralen-cross-linked DNA

    DEFF Research Database (Denmark)

    Reddy, Madhava C; Christensen, Jesper; Vasquez, Karen M

    2005-01-01

    Human high mobility group box (HMGB) 1 and -2 proteins are highly conserved and abundant chromosomal proteins that regulate chromatin structure and DNA metabolism. HMGB proteins bind preferentially to DNA that is bent or underwound and to DNA damaged by agents such as cisplatin, UVC radiation......, and benzo[a]pyrenediol epoxide (BPDE). Binding of HMGB1 to DNA adducts is thought to inhibit nucleotide excision repair (NER), leading to cell death, but the biological roles of these proteins remain obscure. We have used psoralen-modified triplex-forming oligonucleotides (TFOs) to direct a psoralen-DNA...... interstrand cross-link (ICL) to a specific site to determine the effect of HMGB proteins on recognition of these lesions. Our results reveal that human HMGB1 (but not HMGB2) binds with high affinity and specificity to psoralen ICLs, and interacts with the essential NER protein, replication protein A (RPA...

  9. Scalable Synthesis of Defect Abundant Si Nanorods for High-Performance Li-Ion Battery Anodes.

    Science.gov (United States)

    Wang, Jing; Meng, Xiangcai; Fan, Xiulin; Zhang, Wenbo; Zhang, Hongyong; Wang, Chunsheng

    2015-06-23

    Microsized nanostructured silicon-carbon composite is a promising anode material for high energy Li-ion batteries. However, large-scale synthesis of high-performance nano-Si materials at a low cost still remains a significant challenge. We report a scalable low cost method to synthesize Al/Na-doped and defect-abundant Si nanorods that have excellent electrochemical performance with high first-cycle Coulombic efficiency (90%). The unique Si nanorods are synthesized by acid etching the refined and rapidly solidified eutectic Al-Si ingot. To maintain the high electronic conductivity, a thin layer of carbon is then coated on the Si nanorods by carbonization of self-polymerized polydopamine (PDA) at 800 °C. The carbon coated Si nanorods (Si@C) electrode at 0.9 mg cm(-2) loading (corresponding to area-specific-capacity of ∼2.0 mAh cm(-2)) exhibits a reversible capacity of ∼2200 mAh g(-1) at 100 mA g(-1) current, and maintains ∼700 mAh g(-1) over 1000 cycles at 1000 mA g(-1) with a capacity decay rate of 0.02% per cycle. High Coulombic efficiencies of 87% in the first cycle and ∼99.7% after 5 cycles are achieved due to the formation of an artificial Al2O3 solid electrolyte interphase (SEI) on the Si surface, and the low surface area (31 m(2) g(-1)), which has never been reported before for nano-Si anodes. The excellent electrochemical performance results from the massive defects (twins, stacking faults, dislocations) and Al/Na doping in Si nanorods induced by rapid solidification and Na salt modifications; this greatly enhances the robustness of Si from the volume changes and alleviates the mechanical stress/strain of the Si nanorods during the lithium insertion/extraction process. Introducing massive defects and Al/Na doping in eutectic Si nanorods for Li-ion battery anodes is unexplored territory. We venture this uncharted territory to commercialize this nanostructured Si anode for the next generation of Li-ion batteries.

  10. KvLEA, a New Isolated Late Embryogenesis Abundant Protein Gene from Kosteletzkya virginica Responding to Multiabiotic Stresses.

    Science.gov (United States)

    Tang, Xiaoli; Wang, Hongyan; Chu, Liye; Shao, Hongbo

    2016-01-01

    The LEA proteins are a kind of hydrophilic proteins, playing main functions in desiccation tolerance. However, their importance as a kind of stress proteins in abiotic stress is being clarified little by little. In this study we isolated, cloned, and identified the first KvLEA gene in Kosteletzkya virginica. Bioinformatic analysis showed that the protein encoded by this gene had common properties of LEA proteins and the multiple sequences alignment and phylogenetic analysis further showed that this protein had high homology with two Arabidopsis LEA proteins. Gene expression analysis revealed that this gene had a higher expression in root and it was induced obviously by salt stress. Moreover, the transcripts of KvLEA were also induced by other abiotic stresses including drought, high temperature, chilling, and ABA treatment. Among these abiotic stresses, ABA treatment brought about the biggest changes to this gene. Collectively, our research discovered a novel LEA gene and uncovered its involvement in multiabiotic stresses in K. virginica. This research not only enriched studies on LEA gene in plant but also would accelerate more studies on K. virginica in the future.

  11. KvLEA, a New Isolated Late Embryogenesis Abundant Protein Gene from Kosteletzkya virginica Responding to Multiabiotic Stresses

    Directory of Open Access Journals (Sweden)

    Xiaoli Tang

    2016-01-01

    Full Text Available The LEA proteins are a kind of hydrophilic proteins, playing main functions in desiccation tolerance. However, their importance as a kind of stress proteins in abiotic stress is being clarified little by little. In this study we isolated, cloned, and identified the first KvLEA gene in Kosteletzkya virginica. Bioinformatic analysis showed that the protein encoded by this gene had common properties of LEA proteins and the multiple sequences alignment and phylogenetic analysis further showed that this protein had high homology with two Arabidopsis LEA proteins. Gene expression analysis revealed that this gene had a higher expression in root and it was induced obviously by salt stress. Moreover, the transcripts of KvLEA were also induced by other abiotic stresses including drought, high temperature, chilling, and ABA treatment. Among these abiotic stresses, ABA treatment brought about the biggest changes to this gene. Collectively, our research discovered a novel LEA gene and uncovered its involvement in multiabiotic stresses in K. virginica. This research not only enriched studies on LEA gene in plant but also would accelerate more studies on K. virginica in the future.

  12. Bee bread increases honeybee haemolymph protein and promote better survival despite of causing higher Nosema ceranae abundance in honeybees.

    Science.gov (United States)

    Basualdo, Marina; Barragán, Sergio; Antúnez, Karina

    2014-08-01

    Adequate protein nutrition supports healthy honeybees and reduces the susceptibility to disease. However little is known concerning the effect of the diet on Nosema ceranae development, an obligate intracellular parasite that disturbs the protein metabolism of honeybees (Apis mellifera). Here we tested the effect of natural (bee bread) and non-natural protein diets (substitute) on haemolymph proteins titers of honeybee and N. ceranae spore production. The natural diet induced higher levels of protein and parasite development, but the survival of bees was also higher than with non-natural diets. The data showed that the administration of an artificially high nutritious diet in terms of crude protein content is not sufficient to promote healthy bees; rather the protein ingested should be efficiently assimilated. The overall results support the idea that the physiological condition of the bees is linked to protein levels in the haemolymph, which affects the tolerance to parasite; consequently the negative impact of the parasite on host fitness is not associated only with the level of infection.

  13. Nitrogen 15 abundance in protein fractions of beans fertilized with ({sup 15}NH{sub 4}){sub 2}SO{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Chaud, Saula Goulart; Oliveira, Admar Costa de [Universidade Estadual de Campinas, SP (Brazil). Faculdade de Estudos Agricolas. Dept. de Planejamento Alimentar e Nutricao; Trivelin, Paulo Cesar Ocheuze [Centro de Energia Nuclear na Agricultura (CENA), Piracicaba, SP (Brazil). Lab. de Isotopos Estaveis]. E-mail: admarco@fea.unicamp.br

    2002-12-01

    Studies evaluating the protein nutritive value of beans labelled with 15 N, using nitrogen balance and the quantitation of faecal and urinary endogenous nitrogen, determined by isotopic dilution, have been extensively used. The objective of this research was to verify if the isotopic labelling of raw, freeze dried beans (Phaseolus vulgaris L., cultivar Pirata 1) with 1.394 atoms % 15 N, resulted in the same abundance of the whole flour and of the protein fractions extracted from the beans with 0.5 mol L{sup -1} NaCl. The isotopic abundance found in the whole bean flour, in the protein extract, in the globulin and albumin fractions were respectively: 1.394 +- 0.011; 1.403 +- 0.012; 1.399 +- 0.007 and 1.399 +- 0.028 atoms % of 15 N, presenting no difference (P > 0.05). However, a difference was found (P < 0.05) between the above mentioned abundances and the isotopic abundance found in the nitrogen of the proteins in the extraction residue, which was 0.969 +- 0.084. Since the abundances did not differ, the protein nutritive indexes, such as digestibility and biological value, determined from the nitrogen balance and corrected for isotopic dilution, would not be affected by extracting the proteins from the beans with 0.5 mol L 1 NaCl. If working with the nitrogen balance of the residual proteins after extraction and even with the whole flours, these indexes could present incorrect values, since the isotopic labelling of the residual proteins was less than that of the protein fractions. (author)

  14. Chemical Abundances in Field Red Giants from High-Resolution H-Band Spectra using the APOGEE Spectral Linelist

    CERN Document Server

    Smith, Verne V; Shetrone, Matthew D; Meszaros, Szabolcs; Prieto, Carlos Allende; Bizyaev, Dmitry; Perez, Ana Garcia; Majewski, Steven R; Schiavon, Ricardo; Holtzman, Jon; Johnson, Jennifer A

    2012-01-01

    High-resolution H-band spectra of five bright field K, M, and MS giants, obtained from the archives of the Kitt Peak National Observatory (KPNO) Fourier Transform Spectrometer (FTS), are analyzed to determine chemical abundances of 16 elements. The abundances were derived via spectrum synthesis using the detailed linelist prepared for the SDSS III Apache Point Galactic Evolution Experiment (APOGEE), which is a high-resolution near-infrared spectroscopic survey to derive detailed chemical abundance distributions and precise radial velocities for 100,000 red giants sampling all Galactic stellar populations. Measured chemical abundances include the cosmochemically important isotopes 12C, 13C, 14N, and 16O, along with Mg, Al, Si, K, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, and Cu. A comparison of the abundances derived here with published values for these stars reveals consistent results to ~0.1 dex. The APOGEE spectral region and linelist is, thus, well-suited for probing both Galactic chemical evolution, as well as inter...

  15. Abundances in Damped Lyman-$\\alpha$ Systems and Chemical Evolution of High Redshift Galaxies

    CERN Document Server

    Lü, L; Barlow, T A; Lu, Limin; Sargent, Wallace L.W.; Barlow, Thomas A.

    1997-01-01

    Recent abundance measurements in damped Lyman-alpha galaxies, supplemented with unpublished Keck observations, are discussed. The metallicity distribution with cosmic time is examined for clues about the degree of enrichment, the onset of initial star formation, and the nature of the galxies. The relative abundances of the elements are compared with the abundnce pattern in Galactic halo stars and in the Sun, taking into account of the effects of dust depletion, in order to gain insight into the stellar processes and the time scales by which the enrichment occurred.

  16. Late Embryogenesis Abundant Proteins

    NARCIS (Netherlands)

    Shih, M.D.; Hoekstra, F.A.; Hsing, Y.I.C.

    2008-01-01

    During the late maturation stage of seed development, water content decreases greatly. One of the most striking characteristics of mature orthodox seeds is their ability to withstand severe desiccation. Mechanisms of plant drought/desiccation tolerance have been studied by numerous groups, and a bro

  17. Protein profile of exhaled breath condensate determined by high resolution mass spectrometry.

    Science.gov (United States)

    Muccilli, Vera; Saletti, Rosaria; Cunsolo, Vincenzo; Ho, Jenny; Gili, Elisa; Conte, Enrico; Sichili, Stefania; Vancheri, Carlo; Foti, Salvatore

    2015-02-01

    A method based on liquid chromatography/high resolution tandem mass spectrometry coupled with electrophoretic separation, for determination and relative quantification of the protein composition of exhaled breath condensate (EBC), was developed. Application of the procedure to a sample of EBC, pooled from nine healthy subjects, resulted in the identification of 167 unique gene products, 113 of which not previously reported in EBC samples. The abundance of the protein identified was estimated by means of the exponentially modified protein abundance index protocol (emPAI). Cytokeratins were by far the most abundant proteins in EBC samples. Many of the identified proteins were associated with multiple cellular location with cytoplasm constituting the largest group. Cytosol, nucleus, membrane, cytoskeleton and extracellular were other abundantly represented locations. No amylase was detected, suggesting the absence of saliva protein contamination. The profile obtained represents the most comprehensive protein characterization of EBC so far reported and demonstrates that this approach provides a powerful tool for investigating the protein profile of EBC samples. Compared with analogous investigations, this study also shows that the protein profile of EBC is strongly affected by the sampling method adopted.

  18. CHEMICAL ABUNDANCES IN FIELD RED GIANTS FROM HIGH-RESOLUTION H-BAND SPECTRA USING THE APOGEE SPECTRAL LINELIST

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Verne V.; Cunha, Katia [National Optical Astronomy Observatories, Tucson, AZ 85719 (United States); Shetrone, Matthew D. [Department of Astronomy and McDonald Observatory, University of Texas, Austin, TX 78712 (United States); Meszaros, Szabolcs; Allende Prieto, Carlos [Instituto d' Astrofisica de Canarias, E-38205, La Laguna, Tenerife (Spain); Bizyaev, Dmitry [Apache Point Observatory, Sunspot, NM 88349 (United States); Garcia Perez, Ana; Majewski, Steven R. [Department of Astronomy, University of Virginia, Charlottesville, VA 22904 (United States); Schiavon, Ricardo [Astrophysics Research Institute, Liverpool John Moores University, Liverpool L3 5UX (United Kingdom); Holtzman, Jon [Department of Astronomy, New Mexico State University, Las Cruces, NM 88003 (United States); Johnson, Jennifer A., E-mail: vsmith@noao.edu [Department of Astronomy, Ohio State University, Columbus, OH 43210 (United States)

    2013-03-01

    High-resolution H-band spectra of five bright field K, M, and MS giants, obtained from the archives of the Kitt Peak National Observatory Fourier transform spectrometer, are analyzed to determine chemical abundances of 16 elements. The abundances were derived via spectrum synthesis using the detailed linelist prepared for the Sloan Digital Sky Survey III Apache Point Galactic Evolution Experiment (APOGEE), which is a high-resolution near-infrared spectroscopic survey to derive detailed chemical abundance distributions and precise radial velocities for 100,000 red giants sampling all Galactic stellar populations. The red giant sample studied here was chosen to probe which chemical elements can be derived reliably from the H-band APOGEE spectral region. These red giants consist of two K-giants ({alpha} Boo and {mu} Leo), two M-giants ({beta} And and {delta} Oph), and one thermally pulsing asymptotic giant branch (TP-AGB) star of spectral type MS (HD 199799). Measured chemical abundances include the cosmochemically important isotopes {sup 12}C, {sup 13}C, {sup 14}N, and {sup 16}O, along with Mg, Al, Si, K, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, and Cu. The K and M giants exhibit the abundance signature of the first dredge-up of CN-cycle material, while the TP-AGB star shows clear evidence of the addition of {sup 12}C synthesized during {sup 4}He-burning thermal pulses and subsequent third dredge-up. A comparison of the abundances derived here with published values for these stars reveals consistent results to {approx}0.1 dex. The APOGEE spectral region and linelist is thus well suited for probing both Galactic chemical evolution, as well as internal nucleosynthesis and mixing in populations of red giants via high-resolution spectroscopy.

  19. Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages

    KAUST Repository

    Lescot, Magali

    2015-11-27

    Genes encoding reverse transcriptases (RTs) are found in most eukaryotes, often as a component of retrotransposons, as well as in retroviruses and in prokaryotic retroelements. We investigated the abundance, classification and transcriptional status of RTs based on Tara Oceans marine metagenomes and metatranscriptomes encompassing a wide organism size range. Our analyses revealed that RTs predominate large-size fraction metagenomes (>5 μm), where they reached a maximum of 13.5% of the total gene abundance. Metagenomic RTs were widely distributed across the phylogeny of known RTs, but many belonged to previously uncharacterized clades. Metatranscriptomic RTs showed distinct abundance patterns across samples compared with metagenomic RTs. The relative abundances of viral and bacterial RTs among identified RT sequences were higher in metatranscriptomes than in metagenomes and these sequences were detected in all metatranscriptome size fractions. Overall, these observations suggest an active proliferation of various RT-assisted elements, which could be involved in genome evolution or adaptive processes of plankton assemblage.

  20. Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages.

    Science.gov (United States)

    Lescot, Magali; Hingamp, Pascal; Kojima, Kenji K; Villar, Emilie; Romac, Sarah; Veluchamy, Alaguraj; Boccara, Martine; Jaillon, Olivier; Iudicone, Daniele; Bowler, Chris; Wincker, Patrick; Claverie, Jean-Michel; Ogata, Hiroyuki

    2016-05-01

    Genes encoding reverse transcriptases (RTs) are found in most eukaryotes, often as a component of retrotransposons, as well as in retroviruses and in prokaryotic retroelements. We investigated the abundance, classification and transcriptional status of RTs based on Tara Oceans marine metagenomes and metatranscriptomes encompassing a wide organism size range. Our analyses revealed that RTs predominate large-size fraction metagenomes (>5 μm), where they reached a maximum of 13.5% of the total gene abundance. Metagenomic RTs were widely distributed across the phylogeny of known RTs, but many belonged to previously uncharacterized clades. Metatranscriptomic RTs showed distinct abundance patterns across samples compared with metagenomic RTs. The relative abundances of viral and bacterial RTs among identified RT sequences were higher in metatranscriptomes than in metagenomes and these sequences were detected in all metatranscriptome size fractions. Overall, these observations suggest an active proliferation of various RT-assisted elements, which could be involved in genome evolution or adaptive processes of plankton assemblage.

  1. TRACING THE EVOLUTION OF HIGH-REDSHIFT GALAXIES USING STELLAR ABUNDANCES

    Energy Technology Data Exchange (ETDEWEB)

    Crosby, Brian D.; O’Shea, Brian W. [Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824 (United States); Beers, Timothy C. [Department of Physics and JINA—Center for the Evolution of the Elements, University of Notre Dame, 225 Nieuwland Science Hall, Notre Dame, IN 46556 (United States); Tumlinson, Jason, E-mail: crosby.bd@gmail.com [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States)

    2016-03-20

    This paper presents the first results from a model for chemical evolution that can be applied to N-body cosmological simulations and quantitatively compared to measured stellar abundances from large astronomical surveys. This model convolves the chemical yield sets from a range of stellar nucleosynthesis calculations (including asymptotic giant branch stars, Type Ia and II supernovae, and stellar wind models) with a user-specified stellar initial mass function (IMF) and metallicity to calculate the time-dependent chemical evolution model for a “simple stellar population” (SSP) of uniform metallicity and formation time. These SSP models are combined with a semianalytic model for galaxy formation and evolution that uses merger trees from N-body cosmological simulations to track several α- and iron-peak elements for the stellar and multiphase interstellar medium components of several thousand galaxies in the early (z ≥ 6) universe. The simulated galaxy population is then quantitatively compared to two complementary data sets of abundances in the Milky Way stellar halo and is capable of reproducing many of the observed abundance trends. The observed abundance ratio distributions are best reproduced with a Chabrier IMF, a chemically enriched star formation efficiency of 0.2, and a redshift of reionization of 7. Many abundances are qualitatively well matched by our model, but our model consistently overpredicts the carbon-enhanced fraction of stars at low metallicities, likely owing to incomplete coverage of Population III stellar yields and supernova models and the lack of dust as a component of our model.

  2. Estimating the abundance of airborne pollen and fungal spores at variable elevations using an aircraft: how high can they fly?

    Science.gov (United States)

    Damialis, Athanasios; Kaimakamis, Evangelos; Konoglou, Maria; Akritidis, Ioannis; Traidl-Hoffmann, Claudia; Gioulekas, Dimitrios

    2017-03-01

    Airborne pollen and fungal spores are monitored mainly in highly populated, urban environments, for allergy prevention purposes. However, their sources can frequently be located outside cities’ fringes with more vegetation. So as to shed light to this paradox, we investigated the diversity and abundance of airborne pollen and fungal spores at various environmental regimes. We monitored pollen and spores using an aircraft and a car, at elevations from sea level to 2,000 m above ground, in the region of Thesssaloniki, Greece. We found a total of 24 pollen types and more than 15 spore types. Pollen and spores were detected throughout the elevational transect. Lower elevations exhibited higher pollen concentrations in only half of plant taxa and higher fungal spore concentrations in only Ustilago. Pinaceae and Quercus pollen were the most abundant recorded by airplane (>54% of the total). Poaceae pollen were the most abundant via car measurements (>77% of the total). Cladosporium and Alternaria spores were the most abundant in all cases (aircraft: >69% and >17%, car: >45% and >27%, respectively). We conclude that pollen and fungal spores can be diverse and abundant even outside the main source area, evidently because of long-distance transport incidents.

  3. Steroidogenic acute regulatory protein in white sturgeon (Acipenser transmontanus): cDNA cloning, sites of expression and transcript abundance in corticosteroidogenic tissue after an acute stressor.

    Science.gov (United States)

    Kusakabe, Makoto; Zuccarelli, Micah D; Nakamura, Ikumi; Young, Graham

    2009-06-01

    The white sturgeon, Acipenser transmontanus, is a primitive bony fish that is recognized as an important emerging species for aquaculture. However, many aspects of its stress and reproductive physiology remain unclear. These processes are controlled by various steroid hormones. In order to investigate the regulation of steroidogenesis associated with acute stress in sturgeon, a cDNA-encoding steroidogenic acute regulatory protein (StAR) was isolated from white sturgeon. The putative amino acid sequence of sturgeon StAR shares high homology (over 60%) with other vertebrates. Phylogenetic analysis grouped sturgeon StAR within Actinopterygii, but it was clearly segregated from teleost StARs. RT-PCR analysis revealed that transcripts were most abundant in yellow corpuscles found throughout the kidney and weaker signals were detected in gonad and kidney. Very weak signals were also detected in brain and spleen by quantitative real-time PCR. In situ hybridization revealed that StAR is expressed in the cells of yellow corpuscles. No significant changes in StAR gene expression were detected in response to an acute handling stress. These results suggest that StAR is highly conserved throughout vertebrates, but the expression of the functional protein during the stress response may be partially regulated post-transcriptionally.

  4. A late embryogenesis abundant protein HVA1 regulated by an inducible promoter enhances root growth and abiotic stress tolerance in rice without yield penalty.

    Science.gov (United States)

    Chen, Yi-Shih; Lo, Shuen-Fang; Sun, Peng-Kai; Lu, Chung-An; Ho, Tuan-Hua D; Yu, Su-May

    2015-01-01

    Regulation of root architecture is essential for maintaining plant growth under adverse environment. A synthetic abscisic acid (ABA)/stress-inducible promoter was designed to control the expression of a late embryogenesis abundant protein (HVA1) in transgenic rice. The background of HVA1 is low but highly inducible by ABA, salt, dehydration and cold. HVA1 was highly accumulated in root apical meristem (RAM) and lateral root primordia (LRP) after ABA/stress treatments, leading to enhanced root system expansion. Water-use efficiency (WUE) and biomass also increased in transgenic rice, likely due to the maintenance of normal cell functions and metabolic activities conferred by HVA1 which is capable of stabilizing proteins, under osmotic stress. HVA1 promotes lateral root (LR) initiation, elongation and emergence and primary root (PR) elongation via an auxin-dependent process, particularly by intensifying asymmetrical accumulation of auxin in LRP founder cells and RAM, even under ABA/stress-suppressive conditions. We demonstrate a successful application of an inducible promoter in regulating the spatial and temporal expression of HVA1 for improving root architecture and multiple stress tolerance without yield penalty.

  5. Inferring high-confidence human protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Yu Xueping

    2012-05-01

    Full Text Available Abstract Background As numerous experimental factors drive the acquisition, identification, and interpretation of protein-protein interactions (PPIs, aggregated assemblies of human PPI data invariably contain experiment-dependent noise. Ascertaining the reliability of PPIs collected from these diverse studies and scoring them to infer high-confidence networks is a non-trivial task. Moreover, a large number of PPIs share the same number of reported occurrences, making it impossible to distinguish the reliability of these PPIs and rank-order them. For example, for the data analyzed here, we found that the majority (>83% of currently available human PPIs have been reported only once. Results In this work, we proposed an unsupervised statistical approach to score a set of diverse, experimentally identified PPIs from nine primary databases to create subsets of high-confidence human PPI networks. We evaluated this ranking method by comparing it with other methods and assessing their ability to retrieve protein associations from a number of diverse and independent reference sets. These reference sets contain known biological data that are either directly or indirectly linked to interactions between proteins. We quantified the average effect of using ranked protein interaction data to retrieve this information and showed that, when compared to randomly ranked interaction data sets, the proposed method created a larger enrichment (~134% than either ranking based on the hypergeometric test (~109% or occurrence ranking (~46%. Conclusions From our evaluations, it was clear that ranked interactions were always of value because higher-ranked PPIs had a higher likelihood of retrieving high-confidence experimental data. Reducing the noise inherent in aggregated experimental PPIs via our ranking scheme further increased the accuracy and enrichment of PPIs derived from a number of biologically relevant data sets. These results suggest that using our high

  6. Young stars and ionized nebulae in M83: comparing chemical abundances at high metallicity

    CERN Document Server

    Bresolin, Fabio; Urbaneja, Miguel A; Gieren, Wolfgang; Ho, I-Ting; Pietrzynski, Grzegorz

    2016-01-01

    We present spectra of 14 A-type supergiants in the metal-rich spiral galaxy M83. We derive stellar parameters and metallicities, and measure a spectroscopic distance modulus m-M = 28.47 +\\- 0.10 (4.9 +\\- 0.2 Mpc), in agreement with other methods. We use the stellar characteristic metallicity of M83 and other systems to discuss a version of the galaxy mass-metallicity relation that is independent of the analysis of nebular emission lines and the associated systematic uncertainties. We reproduce the radial metallicity gradient of M83, which flattens at large radii, with a chemical evolution model, constraining gas inflow and outflow processes. We carry out a comparative analysis of the metallicities we derive from the stellar spectra and published HII region line fluxes, utilizing both the direct, Te-based method and different strong-line abundance diagnostics. The direct abundances are in relatively good agreement with the stellar metallicities, once we apply a modest correction to the nebular oxygen abundance...

  7. High pressure effects on allergen food proteins.

    Science.gov (United States)

    Somkuti, Judit; Smeller, László

    2013-12-15

    There are several proteins, which can cause allergic reaction if they are inhaled or ingested. Our everyday food can also contain such proteins. Food allergy is an IgE-mediated immune disorder, a growing health problem of great public concern. High pressure is known to affect the structure of proteins; typically few hundred MPa pressure can lead to denaturation. That is why several trials have been performed to alter the structure of the allergen proteins by high pressure, in order to reduce its allergenicity. Studies have been performed both on simple protein solutions and on complex food systems. Here we review those allergens which have been investigated under or after high pressure treatment by methods capable of detecting changes in the secondary and tertiary structure of the proteins. We focus on those allergenic proteins, whose structural changes were investigated by spectroscopic methods under pressure in correlation with the observed allergenicity (IgE binding) changes. According to this criterion we selected the following allergen proteins: Mal d 1 and Mal d 3 (apple), Bos d 5 (milk), Dau c 1 (carrot), Gal d 2 (egg), Ara h 2 and Ara h 6 (peanut), and Gad m 1 (cod).

  8. Combining Phytate/Ca2+Fractionation with Trichloroacetic Acid/Acetone Precipitation Improved Separation of Low-Abundant Proteins of Wheat (Triticum aestivum L.) Leaf for Proteomic Analysis

    Institute of Scientific and Technical Information of China (English)

    Muhammad A R F Sultan; LIU Hui; CHENG Yu-Feng; ZHANG Pei-pei; ZHAO Hui-xian

    2013-01-01

    Proteomic assessment of low-abundance leaf proteins is hindered by the large quantity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) present within plant leaf tissues. In the present study, total proteins were extracted from wheat (Triticum aestivum L.) leaves by a conventional trichloroacetic acid (TCA)/acetone method and a protocol first developed in this work. Phytate/Ca2+fractionation and TCA/acetone precipitation were combined to design an improved TCA/acetone method. The extracted proteins were analysed by two-dimensional gel electrophoresis (2-DE). The resulting 2-DE images were compared to reveal major differences. The results showed that large quantities of Rubisco were deleted from wheat leaf proteins prepared by the improved method. As many as (758±4) protein spots were detected from 2-DE images of protein extracts obtained by the improved method, 130 more than those detected by the TCA/acetone method. Further analysis indicated that more protein spots could be detected at regions of pI 4.00-4.99 and 6.50-7.00 in the improved method-based 2-DE images. Our findings indicated that the improved method is an efficient protein preparation protocol for separating low-abundance proteins in wheat leaf tissues by 2-DE analysis. The proposed protocol is simple, fast, inexpensive and also applicable to protein preparations of other plants.

  9. Trace element abundances of high-MgO glasses from Kilauea, Mauna Loa and Haleakala volcanoes, Hawaii

    Science.gov (United States)

    Wagner, T.P.; Clague, D.A.; Hauri, E.H.; Grove, T.L.

    1998-01-01

    We performed an ion-microprobe study of eleven high-MgO (6.7-14.8 wt%) tholeiite glasses from the Hawaiian volcanoes Kilauea, Mauna Loa and Haleakala. We determined the rare earth (RE), high field strength, and other selected trace element abundances of these glasses, and used the data to establish their relationship to typical Hawaiian shield tholeiite and to infer characteristics of their source. The glasses have trace element abundance characteristics generally similar to those of typical shield tholeiites, e.g. L(light)REE/H(heavy)REE(C1) > 1. The Kilauea and Mauna Loa glasses, however, display trace and major element characteristics that cross geochemical discriminants observed between Kilauea and Mauna Loa shield lavas. The glasses contain a blend of these discriminating chemical characteristics, and are not exactly like the typical shield lavas from either volcano. The production of these hybrid magmas likely requires a complexly zoned source, rather than two unique sources. When corrected for olivine fractionation, the glass data show correlations between CaO concentration and incompatible trace element abundances, indicating that CaO may behave incompatibly during melting of the tholeiite source. Furthermore, the tholeiite source must contain residual garnet and clinopyroxene to account for the variation in trace element abundances of the Kilauea glasses. Inversion modeling indicates that the Kilauea source is flat relative to C1 chondrites, and has a higher bulk distribution coefficient for the HREE than the LREE.

  10. Oat (Avena sativa) seed extract as an antifungal food preservative through the catalytic activity of a highly abundant class I chitinase.

    Science.gov (United States)

    Sørensen, Hans Peter; Madsen, Lone Søvad; Petersen, Jørgen; Andersen, Jesper Tapdrup; Hansen, Anne Maria; Beck, Hans Christian

    2010-03-01

    Extracts from different higher plants were screened for the ability to inhibit the growth of Penicillium roqueforti, a major contaminating species in industrial food processing. Oat (Avena sativa) seed extracts exhibited a high degree of antifungal activity and could be used directly on rye bread to prevent the formation of P. roqueforti colonies. Proteins in the oat seed extracts were fractionated by column chromatography and proteins in fractions containing antifungal activity were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and database searches. Identified antifungal candidates included thaumatin-like proteins, 1,3-beta-glucanase, permatin precursor, pathogenesis-related protein type 1, and chitinases of class I and II. Class I chitinase could be specifically removed from the extracts and was found to be indispensable for 50% of the P. roqueforti inhibiting activity. The purified class I chitinase has a molecular weight of approximately 34 kDa, optimal chitinase activity at pH 7, and exists as at least two basic isoforms (pI values of 7.6 and 8.0). Partial sequencing of the class I chitinase isoforms by LC-MS/MS revealed a primary structure with high similarity to class I chitinases of wheat (Triticum aestivum), barley (Hordeum vulgare), and rye (Secale cereale). Oat, wheat, barley, and rye seed extracts were compared with respect to the abundance of the class I chitinase and decrease in antifungal activity when class I chitinase is removed. We found that the oat seed class I chitinase is at least ten times more abundant than the wheat, barley, and rye homologs and that oat seed extracts are highly active toward P. roqueforti as opposed to extracts of other cereal seeds.

  11. Interleukin (IL)-1 in rat parturition: IL-1 receptors 1 and 2 and accessory proteins abundance in pregnant rat uterus at term - regulation by progesterone.

    Science.gov (United States)

    Ishiguro, Tomohito; Takeda, Jun; Fang, Xin; Bronson, Heather; Olson, David M

    2016-07-01

    The role of interleukin-1 (IL-1), a pro-inflammatory cytokine, in parturition is typically noted by changes in its concentrations. Studying the expression of its receptor family, IL-1 receptor (IL-1R) 1, IL-1R2, IL-1R accessory protein (IL-1RAcP), and its predominantly brain isoform, IL-1RAcPb, during late gestation in the uterus in the Long-Evans rat is another. We assessed changes in their mRNA and protein relative abundance in the uterus and compared IL-1RAcP and IL-1RAcPb mRNA abundance in uterus, cervix, ovaries, placenta, and whole blood of Long-Evans rats during late gestation or in RU486 and progesterone-treated dams using quantitative real-time PCR and western immunoblotting. IL-1R1, IL-1RAcP, and IL-1RAcPb mRNA abundance significantly increased in the uterus at delivery whereas IL-1R2 mRNA abundance significantly decreased. IL-1R1 protein increased at term and IL-1R2 protein decreased at term compared to nonpregnant uteri. IL1-RAcPb mRNA abundance was less than IL-1RAcP, but in the lower uterine segment it was the highest of all tissues examined. RU486 stimulated preterm delivery and an increase in IL-1R1 mRNA abundance whereas progesterone administration extended pregnancy and suppressed the increase in IL-1R1. These data suggest that changes in uterine sensitivity to IL-1 occur during late gestation and suggest another level of regulation for the control of delivery. The roles for IL-1RAcP and IL-1RAcPb need to be determined, but may relate to different intracellular signaling pathways.

  12. CpLEA5, the Late Embryogenesis Abundant Protein Gene from Chimonanthus praecox, Possesses Low Temperature and Osmotic Resistances in Prokaryote and Eukaryotes

    Directory of Open Access Journals (Sweden)

    Yiling Liu

    2015-11-01

    Full Text Available Plants synthesize and accumulate a series of stress-resistance proteins to protect normal physiological activities under adverse conditions. Chimonanthus praecox which blooms in freezing weather accumulates late embryogenesis abundant proteins (LEAs in flowers, but C. praecox LEAs are little reported. Here, we report a group of five LEA genes of C. praecox (CpLEA5, KT727031. Prokaryotic-expressed CpLEA5 was employed in Escherichia coli to investigate bioactivities and membrane permeability at low-temperature. In comparison with the vacant strains, CpLEA5-containing strains survived in a 20% higher rate; and the degree of cell membrane damage in CpLEA5-containing strains was 55% of that of the vacant strains according to a conductivity test, revealing the low-temperature resistance of CpLEA5 in bacteria. CpLEA5 was also expressed in Pichia pastoris. Interestingly, besides low-temperature resistance, CpLEA5 conferred high resistance to salt and alkali in CpLEA5 overexpressing yeast. The CpLEA5 gene was transferred into Arabidopsis thaliana to also demonstrate CpLEA5 actions in plants. As expected, the transgenic lines were more resistant against low-temperature and drought while compared with the wild type. Taken together, CpLEA5-conferred resistances to several conditions in prokaryote and eukaryotes could have great value as a genetic technology to enhance osmotic stress and low-temperature tolerance.

  13. Quantification of bacterial and archaeal symbionts in high and low microbial abundance sponges using real-time PCR

    KAUST Repository

    Bayer, Kristina

    2014-07-09

    In spite of considerable insights into the microbial diversity of marine sponges, quantitative information on microbial abundances and community composition remains scarce. Here, we established qPCR assays for the specific quantification of four bacterial phyla of representative sponge symbionts as well as the kingdoms Eubacteria and Archaea. We could show that the 16S rRNA gene numbers of Archaea, Chloroflexi, and the candidate phylum Poribacteria were 4-6 orders of magnitude higher in high microbial abundance (HMA) than in low microbial abundance (LMA) sponges and that actinobacterial 16S rRNA gene numbers were 1-2 orders higher in HMA over LMA sponges, while those for Cyanobacteria were stable between HMA and LMA sponges. Fluorescence in situ hybridization of Aplysina aerophoba tissue sections confirmed the numerical dominance of Chloroflexi, which was followed by Poribacteria. Archaeal and actinobacterial cells were detected in much lower numbers. By use of fluorescence-activated cell sorting as a primer- and probe-independent approach, the dominance of Chloroflexi, Proteobacteria, and Poribacteria in A. aerophoba was confirmed. Our study provides new quantitative insights into the microbiology of sponges and contributes to a better understanding of the HMA/LMA dichotomy. The authors quantified sponge symbionts in eight sponge species from three different locations by real time PCR targetting 16S rRNA genes. Additionally, FISH was performed and diversity and abundance of singularized microbial symbionts from Aplysina aerophoba was determined for a comprehensive quantification work. © 2014 Federation of European Microbiological Societies.

  14. High abundance of BDNF within glutamatergic presynapses of cultured hippocampal neurons

    Directory of Open Access Journals (Sweden)

    Thomas eAndreska

    2014-04-01

    Full Text Available In the mammalian brain, the neurotrophin brain-derived neurotrophic factor (BDNF has emerged as a key factor for synaptic refinement, plasticity and learning. Although BDNF-induced signaling cascades are well known, the spatial aspects of the synaptic BDNF localization remained unclear. Recent data provide strong evidence for an exclusive presynaptic location and anterograde secretion of endogenous BDNF at synapses of the hippocampal circuit. In contrast, various studies using BDNF overexpression in cultured hippocampal neurons support the idea that postsynaptic synapses and other dendritic structures are the preferential sites of BDNF localization and release. In this study we used rigorously tested anti-BDNF antibodies and achieved a dense labeling of endogenous BDNF close to synapses. Confocal microscopy showed natural BDNF close to many, but not all glutamatergic synapses, while neither GABAergic synapses nor postsynaptic structures carried a typical synaptic BDNF label. To visualize the BDNF distribution within the fine structure of synapses, we implemented super resolution fluorescence imaging by direct stochastic optical reconstruction microscopy (dSTORM. Two-color dSTORM images of neurites were acquired with a spatial resolution of ~20 nm. At this resolution, the synaptic scaffold proteins Bassoon and Homer exhibit hallmarks of mature synapses and form juxtaposed bars, separated by a synaptic cleft. BDNF imaging signals form granule-like clusters with a mean size of ~60 nm and are preferentially found within the fine structure of the glutamatergic presynapse. Individual glutamatergic presynapses carried up to 90% of the synaptic BDNF immunoreactivity, and only a minor fraction of BDNF molecules was found close to the postsynaptic bars. Our data proof that hippocampal neurons are able to enrich and store high amounts of BDNF in small granules within the mature glutamatergic presynapse, at a principle site of synaptic plasticity.

  15. Ultra-diffuse galaxies: the high-spin tail of the abundant dwarf galaxy population

    CERN Document Server

    Amorisco, N C

    2016-01-01

    Recent observations have revealed the existence of an abundant population of faint, low surface brightness (SB) galaxies, which appear to be numerous and ubiquitous in nearby galaxy clusters, including the Virgo, Coma and Fornax clusters. With median stellar masses of dwarf galaxies, these ultra-diffuse galaxies (UDGs) have unexpectedly large sizes, corresponding to a mean SB of $24\\lesssim\\langle\\mu_e\\rangle_r\\ {\\rm mag}^{-1} {\\rm arcsec}^2\\lesssim27$ within the effective radius. We show that the UDG population represents the tail of galaxies formed in dwarf-sized haloes with higher-than-average angular momentum at collapse. By adopting the standard model of disk formation -- in which the size of galaxies is set by the spin of the halo -- we recover both the abundance of UDGs as a function of the host cluster mass and the distribution of sizes within the UDG population. According to this model, UDGs are not failed $L_*$ galaxies, but genuine dwarfs, and their low SB is not uniquely connected to the harsh clu...

  16. Earth-Abundant and Non-Toxic SiX (X = S, Se) Monolayers as Highly Efficient Thermoelectric Materials

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Ji-Hui; Yuan, Qinghong; Deng, Huixiong; Wei, Su-Huai; Yakobson, Boris I.

    2017-01-12

    Current thermoelectric (TE) materials often have low performance or contain less abundant and/or toxic elements, thus limiting their large-scale applications. Therefore, new TE materials with high efficiency and low cost are strongly desirable. Here we demonstrate that SiS and SiSe monolayers made from nontoxic and earth-abundant elements intrinsically have low thermal conductivities arising from their low-frequency optical phonon branches with large overlaps with acoustic phonon modes, which is similar to the state-of-the-art experimentally demonstrated material SnSe with a layered structure. Together with high thermal power factors due to their two-dimensional nature, they show promising TE performances with large figure of merit (ZT) values exceeding 1 or 2 over a wide range of temperatures. We establish some basic understanding of identifying layered materials with low thermal conductivities, which can guide and stimulate the search and study of other layered materials for TE applications.

  17. High-resolution spectroscopy of RGB stars in the Sagittarius Streams. I. Radial velocities and chemical abundances

    OpenAIRE

    Monaco, L.; Bellazzini, M; Bonifacio, P.; A. Buzzoni; Ferraro, F. R.; Marconi, G; Sbordone, L.; S. Zaggia

    2006-01-01

    Context. The Sagittarius (Sgr) dwarf spheroidal galaxy is currently being disrupted under the strain of the Milky Way. A reliable reconstruction of Sgr star formation history can only be obtained by combining core and stream information. Aims. We present radial velocities for 67 stars belonging to the Sgr Stream. For 12 stars in the sample we also present iron (Fe) and $\\alpha$-element (Mg, Ca) abundances. Methods. Spectra were secured using different high resolution facilities: UVES@VLT, HAR...

  18. High Protein Diet and Huntington's Disease.

    Directory of Open Access Journals (Sweden)

    Chiung-Mei Chen

    Full Text Available Huntington's disease (HD is a neurodegenerative disorder caused by the huntingtin (HTT gene with expanded CAG repeats. In addition to the apparent brain abnormalities, impairments also occur in peripheral tissues. We previously reported that mutant Huntingtin (mHTT exists in the liver and causes urea cycle deficiency. A low protein diet (17% restores urea cycle activity and ameliorates symptoms in HD model mice. It remains unknown whether the dietary protein content should be monitored closely in HD patients because the normal protein consumption is lower in humans (~15% of total calories than in mice (~22%. We assessed whether dietary protein content affects the urea cycle in HD patients. Thirty HD patients were hospitalized and received a standard protein diet (13.7% protein for 5 days, followed by a high protein diet (HPD, 26.3% protein for another 5 days. Urea cycle deficiency was monitored by the blood levels of citrulline and ammonia. HD progression was determined by the Unified Huntington's Disease Rating Scale (UHDRS. The HPD increased blood citrulline concentration from 15.19 μmol/l to 16.30 μmol/l (p = 0.0378 in HD patients but did not change blood ammonia concentration. A 2-year pilot study of 14 HD patients found no significant correlation between blood citrulline concentration and HD progression. Our results indicated a short period of the HPD did not markedly compromise urea cycle function. Blood citrulline concentration is not a reliable biomarker of HD progression.

  19. High throughput protein-protein interaction data: clues for the architecture of protein complexes

    Directory of Open Access Journals (Sweden)

    Pang Chi

    2008-11-01

    Full Text Available Abstract Background High-throughput techniques are becoming widely used to study protein-protein interactions and protein complexes on a proteome-wide scale. Here we have explored the potential of these techniques to accurately determine the constituent proteins of complexes and their architecture within the complex. Results Two-dimensional representations of the 19S and 20S proteasome, mediator, and SAGA complexes were generated and overlaid with high quality pairwise interaction data, core-module-attachment classifications from affinity purifications of complexes and predicted domain-domain interactions. Pairwise interaction data could accurately determine the members of each complex, but was unexpectedly poor at deciphering the topology of proteins in complexes. Core and module data from affinity purification studies were less useful for accurately defining the member proteins of these complexes. However, these data gave strong information on the spatial proximity of many proteins. Predicted domain-domain interactions provided some insight into the topology of proteins within complexes, but was affected by a lack of available structural data for the co-activator complexes and the presence of shared domains in paralogous proteins. Conclusion The constituent proteins of complexes are likely to be determined with accuracy by combining data from high-throughput techniques. The topology of some proteins in the complexes will be able to be clearly inferred. We finally suggest strategies that can be employed to use high throughput interaction data to define the membership and understand the architecture of proteins in novel complexes.

  20. Golden alga presence and abundance are inversely related to salinity in a high-salinity river ecosystem, Pecos River, USA

    Science.gov (United States)

    Israël, Natascha M.D.; VanLandeghem, Matthew M.; Denny, Shawn; Ingle, John; Patino, Reynaldo

    2014-01-01

    Prymnesium parvum (golden alga, GA) is a toxigenic harmful alga native to marine ecosystems that has also affected brackish inland waters. The first toxic bloom of GA in the western hemisphere occurred in the Pecos River, one of the saltiest rivers in North America. Environmental factors (water quality) associated with GA occurrence in this basin, however, have not been examined. Water quality and GA presence and abundance were determined at eight sites in the Pecos River basin with or without prior history of toxic blooms. Sampling was conducted monthly from January 2012 to July 2013. Specific conductance (salinity) varied spatiotemporally between 4408 and 73,786 mS/cm. Results of graphical, principal component (PCA), and zero-inflated Poisson (ZIP) regression analyses indicated that the incidence and abundance of GA are reduced as salinity increases spatiotemporally. LOWESS regression and correlation analyses of archived data for specific conductance and GA abundance at one of the study sites retrospectively confirmed the negative association between these variables. Results of PCA also suggested that at nutrient (nitrogen and phosphorus) concentrations whereas at higher salinity, GA was observed only at mid-to-high nutrient levels. Generally consistent with earlier studies, results of ZIP regression indicated that GA presence is positively associated with organic phosphorus and in samples where GA is present, GA abundance is positively associated with organic nitrogen and negatively associated with inorganic nitrogen. This is the first report of an inverse relation between salinity and GA presence and abundance in riverine waters and of interaction effects of salinity and nutrients in the field. These observations contribute to a more complete understanding of environmental conditions that influence GA distribution in inland waters.

  1. Nontoxic and abundant copper zinc tin sulfide nanocrystals for potential high-temperature thermoelectric energy harvesting.

    Science.gov (United States)

    Yang, Haoran; Jauregui, Luis A; Zhang, Genqiang; Chen, Yong P; Wu, Yue

    2012-02-01

    Improving energy/fuel efficiency by converting waste heat into electricity using thermoelectric materials is of great interest due to its simplicity and reliability. However, many thermoelectric materials are composed of either toxic or scarce elements. Here, we report the experimental realization of using nontoxic and abundant copper zinc tin sulfide (CZTS) nanocrystals for potential thermoelectric applications. The CZTS nanocrystals can be synthesized in large quantities from solution phase reaction and compressed into robust bulk pellets through spark plasma sintering and hot press while still maintaining nanoscale grain size inside. Electrical and thermal measurements have been performed from 300 to 700 K to understand the electron and phonon transports. Extra copper doping during the nanocrystal synthesis introduces a significant improvement in the performance.

  2. Abundant carbon substrates drive extremely high sulfate reduction rates and methane fluxes in Prairie Pothole Wetlands.

    Science.gov (United States)

    Dalcin Martins, Paula; Hoyt, David W; Bansal, Sheel; Mills, Christopher T; Tfaily, Malak; Tangen, Brian A; Finocchiaro, Raymond G; Johnston, Michael D; McAdams, Brandon C; Solensky, Matthew J; Smith, Garrett J; Chin, Yu-Ping; Wilkins, Michael J

    2017-08-01

    Inland waters are increasingly recognized as critical sites of methane emissions to the atmosphere, but the biogeochemical reactions driving such fluxes are less well understood. The Prairie Pothole Region (PPR) of North America is one of the largest wetland complexes in the world, containing millions of small, shallow wetlands. The sediment pore waters of PPR wetlands contain some of the highest concentrations of dissolved organic carbon (DOC) and sulfur species ever recorded in terrestrial aquatic environments. Using a suite of geochemical and microbiological analyses, we measured the impact of sedimentary carbon and sulfur transformations in these wetlands on methane fluxes to the atmosphere. This research represents the first study of coupled geochemistry and microbiology within the PPR and demonstrates how the conversion of abundant labile DOC pools into methane results in some of the highest fluxes of this greenhouse gas to the atmosphere ever reported. Abundant DOC and sulfate additionally supported some of the highest sulfate reduction rates ever measured in terrestrial aquatic environments, which we infer to account for a large fraction of carbon mineralization in this system. Methane accumulations in zones of active sulfate reduction may be due to either the transport of free methane gas from deeper locations or the co-occurrence of methanogenesis and sulfate reduction. If both respiratory processes are concurrent, any competitive inhibition of methanogenesis by sulfate-reducing bacteria may be lessened by the presence of large labile DOC pools that yield noncompetitive substrates such as methanol. Our results reveal some of the underlying mechanisms that make PPR wetlands biogeochemical hotspots, which ultimately leads to their critical, but poorly recognized role in regional greenhouse gas emissions. © 2017 John Wiley & Sons Ltd.

  3. Abundant carbon substrates drive extremely high sulfate reduction rates and methane fluxes in Prairie Pothole Wetlands

    Science.gov (United States)

    Martins, Paula; Hoyt, David W.; Bansal, Sheel; Mills, Christopher; Tfaily, Malak; Tangen, Brian; Finocchiaro, Raymond; Johnston, Michael D.; McAdams, Brandon C.; Solensky, Matthew J.; Smith, Garrett J.; Chin, Yu-Ping; Wilkins, Michael J.

    2017-01-01

    Inland waters are increasingly recognized as critical sites of methane emissions to the atmosphere, but the biogeochemical reactions driving such fluxes are less well understood. The Prairie Pothole Region (PPR) of North America is one of the largest wetland complexes in the world, containing millions of small, shallow wetlands. The sediment pore waters of PPR wetlands contain some of the highest concentrations of dissolved organic carbon (DOC) and sulfur species ever recorded in terrestrial aquatic environments. Using a suite of geochemical and microbiological analyses, we measured the impact of sedimentary carbon and sulfur transformations in these wetlands on methane fluxes to the atmosphere. This research represents the first study of coupled geochemistry and microbiology within the PPR and demonstrates how the conversion of abundant labile DOC pools into methane results in some of the highest fluxes of this greenhouse gas to the atmosphere ever reported. Abundant DOC and sulfate additionally supported some of the highest sulfate reduction rates ever measured in terrestrial aquatic environments, which we infer to account for a large fraction of carbon mineralization in this system. Methane accumulations in zones of active sulfate reduction may be due to either the transport of free methane gas from deeper locations or the co-occurrence of methanogenesis and sulfate reduction. If both respiratory processes are concurrent, any competitive inhibition of methanogenesis by sulfate-reducing bacteria may be lessened by the presence of large labile DOC pools that yield noncompetitive substrates such as methanol. Our results reveal some of the underlying mechanisms that make PPR wetlands biogeochemical hotspots, which ultimately leads to their critical, but poorly recognized role in regional greenhouse gas emissions.

  4. Integrated process for high conversion and high yield protein PEGylation.

    Science.gov (United States)

    Pfister, David; Morbidelli, Massimo

    2016-08-01

    Over the past decades, PEGylation has become a powerful technique to increase the in vivo circulation half-life of therapeutic proteins while maintaining their activity. The development of new therapeutic proteins is likely to require further improvement of the PEGylation methods to reach even better selectivity and yield for reduced costs. The intensification of the PEGylation process was investigated through the integration of a chromatographic step in order to increase yield and conversion for the production of mono-PEGylated protein. Lysozyme was used as a model protein to demonstrate the feasibility of such approach. In the integrated reaction/separation process, chromatography was used as fractionation technique in order to isolate and recycle the unreacted protein from the PEGylated products. This allows operating the reactor with short reaction times so as to minimize the production of multi-PEGylated proteins (i.e., conjugated to more than one polymer). That is, the reaction is stopped before the desired product (i.e., the mono-PEGylated protein) can further react, thus leading to limited conversion but high yield. The recycling of the unreacted protein was then considered to drive the protein overall conversion to completion. This approach has great potential to improve processes whose yield is limited by the further reaction of the product leading to undesirable by-products. Biotechnol. Bioeng. 2016;113: 1711-1718. © 2016 Wiley Periodicals, Inc.

  5. Chemical Abundances in Twelve Red Giants of the Large Magellanic Cloud from High-Resolution Infrared Spectroscopy

    CERN Document Server

    Smith, V V; Cunha, K; Plez, B; Lambert, D L; Pilachowski, C A; Barbuy, B; Melendez, J; Balachandran, S C; Bessell, M S; Geisler, D; Hesser, J E; Winge, C

    2002-01-01

    High-resolution infrared spectra (R=50,000) have been obtained for twelve red-giant members of the LMC with the Gemini South 8.3-meter telescope plus Phoenix spectrometer. Quantitative chemical abundances of carbon-12, carbon-13, nitrogen-14, and oxygen-16 were derived from molecular lines of CO, CN, and OH, while sodium, scandium, titanium, and iron abundances were derived from neutral atomic lines. The LMC giants have masses from about 1 to 4 solar masses and span a metallicity range from [Fe/H]= -1.1 to -0.3. The program red giants all show evidence of first dredge-up mixing, with low 12C/13C ratios, and low 12C correlated with high 14N abundances. Comparisons of the oxygen-to-iron ratios in the LMC and the Galaxy indicate that the trend of [O/Fe] versus [Fe/H] in the LMC falls about 0.2 dex below the Galactic trend. Such an offset can be modeled as due to an overall lower rate of supernovae per unit mass in the LMC relative to the Galaxy, as well as a slightly lower ratio of supernovae of type II to super...

  6. Predator diversity and abundance provide little support for the enemies hypothesis in forests of high tree diversity.

    Science.gov (United States)

    Schuldt, Andreas; Both, Sabine; Bruelheide, Helge; Härdtle, Werner; Schmid, Bernhard; Zhou, Hongzhang; Assmann, Thorsten

    2011-01-01

    Predatory arthropods can exert strong top-down control on ecosystem functions. However, despite extensive theory and experimental manipulations of predator diversity, our knowledge about relationships between plant and predator diversity--and thus information on the relevance of experimental findings--for species-rich, natural ecosystems is limited. We studied activity abundance and species richness of epigeic spiders in a highly diverse forest ecosystem in subtropical China across 27 forest stands which formed a gradient in tree diversity of 25-69 species per plot. The enemies hypothesis predicts higher predator abundance and diversity, and concomitantly more effective top-down control of food webs, with increasing plant diversity. However, in our study, activity abundance and observed species richness of spiders decreased with increasing tree species richness. There was only a weak, non-significant relationship with tree richness when spider richness was rarefied, i.e. corrected for different total abundances of spiders. Only foraging guild richness (i.e. the diversity of hunting modes) of spiders was positively related to tree species richness. Plant species richness in the herb layer had no significant effects on spiders. Our results thus provide little support for the enemies hypothesis--derived from studies in less diverse ecosystems--of a positive relationship between predator and plant diversity. Our findings for an important group of generalist predators question whether stronger top-down control of food webs can be expected in the more plant diverse stands of our forest ecosystem. Biotic interactions could play important roles in mediating the observed relationships between spider and plant diversity, but further testing is required for a more detailed mechanistic understanding. Our findings have implications for evaluating the way in which theoretical predictions and experimental findings of functional predator effects apply to species-rich forest

  7. Specificity and transcriptional activity of microbiota associated with low and high microbial abundance sponges from the Red Sea

    KAUST Repository

    Moitinho-Silva, Lucas

    2013-08-20

    Marine sponges are generally classified as high microbial abundance (HMA) and low microbial abundance (LMA) species. Here, 16S rRNA amplicon sequencing was applied to investigate the diversity, specificity and transcriptional activity of microbes associated with an LMA sponge (Stylissa carteri), an HMA sponge (Xestospongia testudinaria) and sea water collected from the central Saudi Arabia coast of the Red Sea. Altogether, 887 068 denoised sequences were obtained, of which 806 661 sequences remained after quality control. This resulted in 1477 operational taxonomic units (OTUs) that were assigned to 27 microbial phyla. The microbial composition of S. carteri was more similar to that of sea water than to that of X. testudinaria, which is consistent with the observation that the sequence data set of S. carteri contained many more possibly sea water sequences (~24%) than the X. testudinaria data set (~6%). The most abundant OTUs were shared between all three sources (S. carteri, X. testudinaria, sea water), while rare OTUs were unique to any given source. Despite this high degree of overlap, each sponge species contained its own specific microbiota. The X. testudinaria-specific bacterial taxa were similar to those already described for this species. A set of S. carteri-specific bacterial taxa related to Proteobacteria and Nitrospira was identified, which are likely permanently associated with S. carteri. The transcriptional activity of sponge-associated microorganisms correlated well with their abundance. Quantitative PCR revealed the presence of Poribacteria, representing typical sponge symbionts, in both sponge species and in sea water; however, low transcriptional activity in sea water suggested that Poribacteria are not active outside the host context. © 2013 John Wiley & Sons Ltd.

  8. A barley SKP1-like protein controls abundance of the susceptibility factor RACB and influences the interaction of barley with the barley powdery mildew fungus.

    Science.gov (United States)

    Reiner, Tina; Hoefle, Caroline; Hückelhoven, Ralph

    2016-02-01

    In an increasing number of plant-microbe interactions, it has become evident that the abundance of immunity-related proteins is controlled by the ubiquitin-26S proteasome system. In the interaction of barley with the biotrophic barley powdery mildew fungus Blumeria graminis f.sp. hordei (Bgh), the RAC/ROP [RAT SARCOMA-related C3 botulinum toxin substrate/RAT SARCOMA HOMOLOGUE (RHO) of plants] guanosine triphosphatase (GTPase) HvRACB supports the fungus in a compatible interaction. By contrast, barley HvRBK1, a ROP-binding receptor-like cytoplasmic kinase that interacts with and can be activated by constitutively activated HvRACB, limits fungal infection success. We have identified a barley type II S-phase kinase 1-associated (SKP1)-like protein (HvSKP1-like) as a molecular interactor of HvRBK1. SKP1 proteins are subunits of the SKP1-cullin 1-F-box (SCF)-E3 ubiquitin ligase complex that acts in the specific recognition and ubiquitination of protein substrates for subsequent proteasomal degradation. Transient induced gene silencing of either HvSKP1-like or HvRBK1 increased protein abundance of constitutively activated HvRACB in barley epidermal cells, whereas abundance of dominant negative RACB only weakly increased. In addition, silencing of HvSKP1-like enhanced the susceptibility of barley to haustorium establishment by Bgh. In summary, our results suggest that HvSKP1-like, together with HvRBK1, controls the abundance of HvRACB and, at the same time, modulates the outcome of the barley-Bgh interaction. A possible feedback mechanism from RAC/ROP-activated HvRBK1 on the susceptibility factor HvRACB is discussed.

  9. Precision Chemical Abundance Measurements

    DEFF Research Database (Denmark)

    Yong, David; Grundahl, Frank; Meléndez, Jorge;

    2012-01-01

    This talk covers preliminary work in which we apply a strictly differential line-by-line chemical abundance analysis to high quality UVES spectra of the globular cluster NGC 6752. We achieve extremely high precision in the measurement of relative abundance ratios. Our results indicate that the ob......This talk covers preliminary work in which we apply a strictly differential line-by-line chemical abundance analysis to high quality UVES spectra of the globular cluster NGC 6752. We achieve extremely high precision in the measurement of relative abundance ratios. Our results indicate...... that the observed abundance dispersion exceeds the measurement uncertainties and that many pairs of elements show significant correlations when plotting [X1/H] vs. [X2/H]. Our tentative conclusions are that either NGC 6752 is not chemically homogeneous at the ~=0.03 dex level or the abundance variations...

  10. A new copper containing MALDI matrix that yields high abundances of [peptide + Cu]+ ions.

    Science.gov (United States)

    Wu, Zhaoxiang; Fernandez-Lima, Francisco A; Perez, Lisa M; Russell, David H

    2009-07-01

    The dinuclear copper complex (alpha-cyano-4-hydroxycinnamic acid (CHCA) copper salt (CHCA)(4)Cu(2)), synthesized by reacting CHCA with copper oxide (CuO), yields increased abundances of [M + xCu - (x-1)H](+) (x = 1-6) ions when used as a matrix for matrix-assisted laser desorption ionization (355 nm Nd:YAG laser). The yield of [M + xCu - (x-1)H](+) (x = 1 to approximately 6) ion is much greater than that obtained by mixing peptides with copper salts or directly depositing peptides onto oxidized copper surfaces. The increased ion yields for [M + xCu - (x-1)H](+) facilitate studies of biologically important copper binding peptides. For example, using this matrix we have investigated site-specific copper binding of several peptides using fragmentation chemistry of [M + Cu](+) and [M + 2Cu - H](+) ions. The fragmentation studies reveal interesting insight on Cu binding preferences for basic amino acids. Most notable is the fact that the binding of a single Cu(+) ion and two Cu(+) ions are quite different, and these differences are explained in terms of intramolecular interactions of the peptide-Cu ionic complex.

  11. Systematic assessment of survey scan and MS2-based abundance strategies for label-free quantitative proteomics using high-resolution MS data.

    Science.gov (United States)

    Tu, Chengjian; Li, Jun; Sheng, Quanhu; Zhang, Ming; Qu, Jun

    2014-04-04

    Survey-scan-based label-free method have shown no compelling benefit over fragment ion (MS2)-based approaches when low-resolution mass spectrometry (MS) was used, the growing prevalence of high-resolution analyzers may have changed the game. This necessitates an updated, comparative investigation of these approaches for data acquired by high-resolution MS. Here, we compared survey scan-based (ion current, IC) and MS2-based abundance features including spectral-count (SpC) and MS2 total-ion-current (MS2-TIC), for quantitative analysis using various high-resolution LC/MS data sets. Key discoveries include: (i) study with seven different biological data sets revealed only IC achieved high reproducibility for lower-abundance proteins; (ii) evaluation with 5-replicate analyses of a yeast sample showed IC provided much higher quantitative precision and lower missing data; (iii) IC, SpC, and MS2-TIC all showed good quantitative linearity (R(2) > 0.99) over a >1000-fold concentration range; (iv) both MS2-TIC and IC showed good linear response to various protein loading amounts but not SpC; (v) quantification using a well-characterized CPTAC data set showed that IC exhibited markedly higher quantitative accuracy, higher sensitivity, and lower false-positives/false-negatives than both SpC and MS2-TIC. Therefore, IC achieved an overall superior performance than the MS2-based strategies in terms of reproducibility, missing data, quantitative dynamic range, quantitative accuracy, and biomarker discovery.

  12. Chemical Abundances for the Outer Halo Cluster Pal 4 from Co-added High-Resolution Spectroscopy

    CERN Document Server

    Koch, Andreas

    2010-01-01

    Context: Chemical element abundances for distant Galactic globular clusters (GCs) hold important clues to the origin of the Milky Way halo and its substructures. Aims: We study the chemical composition of red giant stars in Pal 4 - one of the most remote GCs in the Milky Way - and compare our abundance measurements to those for both low surface brightness dwarf galaxies, and GCs in the inner and the outer halo. Methods: By co-adding high-resolution, low-S/N Keck/HIRES spectra of 19 stars along the red giant branch, we estimate chemical abundance ratios of 20 alpha-, iron peak-, and neutron-capture elements. Our method gives total uncertainties on most element-to-iron ratios of typically 0.2 dex. Results: We measure [Fe/H] = -1.41 +- 0.04 (statistical) +- 0.17 (systematic) and an alpha-enhancement of [alpha/Fe] = +0.38 +- 0.11 dex, which is consistent with the canonical value of +0.4 dex found for Galactic halo field stars and most halo GCs at this metallicity. Although Pal 4 has higher enhancements in the hea...

  13. High-precision abundances of Sc, Mn, Cu, and Ba in solar twins. Trends of element ratios with stellar age

    CERN Document Server

    Nissen, P E

    2016-01-01

    A previous study of correlations between element abundance ratios, [X/Fe], and ages of solar twin stars is extended to include Sc, Mn, Cu, and Ba. HARPS spectra with S/N > 600 are used to derive very precise (+/- 0.01 dex) differential abundances, and stellar ages with internal errors less than 1 Gyr are obtained by interpolation in the logg - Teff diagram between isochrones calculated with the Aarhus Stellar Evolution Code. For stars younger than 6 Gyr, [X/Fe] is tightly correlated with stellar age for all elements. For ages between 6 and 9 Gyr, the [X/Fe] - age correlations break down and the stars split up into two groups having respectively high and low [X/Fe] for the odd-Z elements. It is concluded that while stars in the solar neighborhood younger than about 6 Gyr were formed from interstellar gas with a smooth chemical evolution, older stars have originated from regions enriched by supernovae with different neutron excesses. Furthermore, the correlations between abundance ratios and stellar age suggest...

  14. Quantification of bacterial and archaeal symbionts in high and low microbial abundance sponges using real-time PCR.

    Science.gov (United States)

    Bayer, Kristina; Kamke, Janine; Hentschel, Ute

    2014-09-01

    In spite of considerable insights into the microbial diversity of marine sponges, quantitative information on microbial abundances and community composition remains scarce. Here, we established qPCR assays for the specific quantification of four bacterial phyla of representative sponge symbionts as well as the kingdoms Eubacteria and Archaea. We could show that the 16S rRNA gene numbers of Archaea, Chloroflexi, and the candidate phylum Poribacteria were 4-6 orders of magnitude higher in high microbial abundance (HMA) than in low microbial abundance (LMA) sponges and that actinobacterial 16S rRNA gene numbers were 1-2 orders higher in HMA over LMA sponges, while those for Cyanobacteria were stable between HMA and LMA sponges. Fluorescence in situ hybridization of Aplysina aerophoba tissue sections confirmed the numerical dominance of Chloroflexi, which was followed by Poribacteria. Archaeal and actinobacterial cells were detected in much lower numbers. By use of fluorescence-activated cell sorting as a primer- and probe-independent approach, the dominance of Chloroflexi, Proteobacteria, and Poribacteria in A. aerophoba was confirmed. Our study provides new quantitative insights into the microbiology of sponges and contributes to a better understanding of the HMA/LMA dichotomy.

  15. [Investigation of the abundance of proteins secreted by Fasciola hepatica, which is exposed to environmental change in experimental studies, with an advanced proteomic approach].

    Science.gov (United States)

    Haçarız, Orçun; Baykal, Ahmet Tarık

    2014-06-01

    Investigation of the abundance of proteins secreted by Fasciola hepatica, which is exposed to environmental change after it is removed from the main host, with an advanced proteomic approach. Adult Fasciola hepatica parasites, obtained from the main host, were directly placed in phosphate-buffered saline (PBS, at room temperature) and incubated at 37°C for 2 hours (after arrival at the Institute within 1 hour). After this, without applying extra procedures, such as washing the parasites, secreted parasite proteins in PBS were investigated using an advanced proteomic method [a mass spectrometry system with electrospray ionization and quadrupole time-of-flight source coupled to ultra performance liquid chromatography, nano UPLC-ESI-QTOF-MS] with a reviewed F. hepatica protein database (Universal Protein Resource; UniProt) and data-independent acquisition method. With the proteomic analysis of the PBS, after incubation with the parasites, cathepsin L protease 1, fatty acid-binding protein 1 and 2, thioredoxin peroxidase (TPx), and kunitz-type proteinase inhibitor were identified. The abundance of Fasciola hepatica TPx was approximately 2-6 times higher than that of the other proteins identified in this study (p<0.01). The stress on the parasite stem from environmental change could be associated with the stimulation of the secretion of TPx. The application of advanced proteomic approaches could provide useful data in the development of effective protective methods against the parasite.

  16. Predicting abundance and variability of ice nucleating particles in precipitation at the high-altitude observatory Jungfraujoch

    Science.gov (United States)

    Stopelli, Emiliano; Conen, Franz; Morris, Cindy E.; Herrmann, Erik; Henne, Stephan; Steinbacher, Martin; Alewell, Christine

    2016-07-01

    Nucleation of ice affects the properties of clouds and the formation of precipitation. Quantitative data on how ice nucleating particles (INPs) determine the distribution, occurrence and intensity of precipitation are still scarce. INPs active at -8 °C (INPs-8) were observed for 2 years in precipitation samples at the High-Altitude Research Station Jungfraujoch (Switzerland) at 3580 m a.s.l. Several environmental parameters were scanned for their capability to predict the observed abundance and variability of INPs-8. Those singularly presenting the best correlations with observed number of INPs-8 (residual fraction of water vapour, wind speed, air temperature, number of particles with diameter larger than 0.5 µm, season, and source region of particles) were implemented as potential predictor variables in statistical multiple linear regression models. These models were calibrated with 84 precipitation samples collected during the first year of observations; their predictive power was successively validated on the set of 15 precipitation samples collected during the second year. The model performing best in calibration and validation explains more than 75 % of the whole variability of INPs-8 in precipitation and indicates that a high abundance of INPs-8 is to be expected whenever high wind speed coincides with air masses having experienced little or no precipitation prior to sampling. Such conditions occur during frontal passages, often accompanied by precipitation. Therefore, the circumstances when INPs-8 could be sufficiently abundant to initiate the ice phase in clouds may frequently coincide with meteorological conditions favourable to the onset of precipitation events.

  17. High abundances of potentially active ammonia-oxidizing bacteria and archaea in oligotrophic, high-altitude lakes of the Sierra Nevada, California, USA.

    Directory of Open Access Journals (Sweden)

    Curtis J Hayden

    Full Text Available Nitrification plays a central role in the nitrogen cycle by determining the oxidation state of nitrogen and its subsequent bioavailability and cycling. However, relatively little is known about the underlying ecology of the microbial communities that carry out nitrification in freshwater ecosystems--and particularly within high-altitude oligotrophic lakes, where nitrogen is frequently a limiting nutrient. We quantified ammonia-oxidizing archaea (AOA and bacteria (AOB in 9 high-altitude lakes (2289-3160 m in the Sierra Nevada, California, USA, in relation to spatial and biogeochemical data. Based on their ammonia monooxygenase (amoA genes, AOB and AOA were frequently detected. AOB were present in 88% of samples and were more abundant than AOA in all samples. Both groups showed >100 fold variation in abundance between different lakes, and were also variable through time within individual lakes. Nutrient concentrations (ammonium, nitrite, nitrate, and phosphate were generally low but also varied across and within lakes, suggestive of active internal nutrient cycling; AOB abundance was significantly correlated with phosphate (r(2 = 0.32, p<0.1, whereas AOA abundance was inversely correlated with lake elevation (r(2 = 0.43, p<0.05. We also measured low rates of ammonia oxidation--indicating that AOB, AOA, or both, may be biogeochemically active in these oligotrophic ecosystems. Our data indicate that dynamic populations of AOB and AOA are found in oligotrophic, high-altitude, freshwater lakes.

  18. Dynamics of a Highly Flexible Protein

    DEFF Research Database (Denmark)

    Andersen, Lisbeth

    Protein dynamics are important for protein function. Especially, dynamics plays an important role in ligand-binding where the induced fit and conformational selection binding mechanisms represent the extremes in a continuum of dynamic mechanisms. The difference between the mechanisms lies...... in the sequence of events; either the protein changes it conformation after initial binding of the ligand (induced fit) or before binding of the ligand (conformational selection). The nuclear co-activator binding domain (NCBD) interacts with many different binding partners to control gene transcription. High...... malleability are the subject of this defense. Using nuclear magnetic resonance (NMR) spectroscopy, the dynamics of NCBD have been investigated on timescales ranging from picoseconds to milliseconds using relaxation dispersion experiments, residual dipolar couplings and methyl group deuterium relaxation. From...

  19. Dynamic proteome profiling of individual proteins in human skeletal muscle after a high-fat diet and resistance exercise.

    Science.gov (United States)

    Camera, Donny M; Burniston, Jatin G; Pogson, Mark A; Smiles, William J; Hawley, John A

    2017-08-30

    It is generally accepted that muscle adaptation to resistance exercise (REX) training is underpinned by contraction-induced, increased rates of protein synthesis and dietary protein availability. By using dynamic proteome profiling (DPP), we investigated the contribution of both synthesis and breakdown to changes in abundance on a protein-by-protein basis in human skeletal muscle. Age-matched, overweight males consumed 9 d of a high-fat, low-carbohydrate diet during which time they either undertook 3 sessions of REX or performed no exercise. Precursor enrichment and the rate of incorporation of deuterium oxide into newly synthesized muscle proteins were determined by mass spectrometry. Ninety proteins were included in the DPP, with 28 proteins exhibiting significant responses to REX. The most common pattern of response was an increase in turnover, followed by an increase in abundance with no detectable increase in protein synthesis. Here, we provide novel evidence that demonstrates that the contribution of synthesis and breakdown to changes in protein abundance induced by REX differ on a protein-by-protein basis. We also highlight the importance of the degradation of individual muscle proteins after exercise in human skeletal muscle.-Camera, D. M., Burniston, J. G., Pogson, M. A., Smiles, W. J., Hawley, J. A. Dynamic proteome profiling of individual proteins in human skeletal muscle after a high-fat diet and resistance exercise. © FASEB.

  20. A high precision chemical abundance analysis of the HAT-P-1 stellar binary: constraints on planet formation

    CERN Document Server

    Liu, F; Ramirez, I; Yong, D; Melendez, J

    2014-01-01

    We present a high-precision, differential elemental abundance analysis of the HAT-P-1 stellar binary based on high-resolution, high signal-to-noise ratio Keck/HIRES spectra. The secondary star in this double system is known to host a transiting giant planet while no planets have yet been detected around the primary star. The derived metallicities ([Fe/H]) of the primary and secondary stars are identical within the errors: $0.146 \\pm 0.014$ dex ($\\sigma$ = 0.033 dex) and $0.155 \\pm 0.007$ dex ($\\sigma$ = 0.023 dex), respectively. Extremely precise differential abundance ratios of 23 elements have been measured (mean error of $\\sigma$([X/Fe]) = 0.013 dex) and are found to be indistinguishable between the two stars: $\\Delta$[X/Fe] (secondary - primary) = $+0.001 \\pm 0.006$ dex ($\\sigma$ = 0.008 dex). The striking similarity in the chemical composition of the two stellar components in HAT-P-1 is contrary to the possible 0.04 dex level difference seen in 16 Cyg A+B, which also hosts a giant planet, at least 3 time...

  1. A High Resolution Fourier-Transform Spectrometer for the Measurement of Atmospheric Column Abundances

    Science.gov (United States)

    Cageao, R.; Sander, S.; Blavier, J.; Jiang, Y.; Nemtchinov, V.

    2000-01-01

    A compact, high resolution Fourier-transform spectrometer for atmospheric near ultraviolet spectroscopy has been installed at the Jet Propulsion Laboratory's Table Mountain Facility (34.4N, 117.7 W, elevation 2290m).

  2. Proteomic analysis reveals differential accumulation of small heat shock proteins and late embryogenesis abundant proteins between ABA-deficient mutant vp5 seeds and wild-type Vp5 seeds in maize

    Directory of Open Access Journals (Sweden)

    Xiaolin eWu

    2015-01-01

    Full Text Available ABA is a major plant hormone that plays important roles during many phases of plant life cycle, including seed development, maturity and dormancy, and especially the acquisition of desiccation tolerance. Understanding of the molecular basis of ABA-mediated plant response to stress is of interest not only in basic research on plant adaptation but also in applied research on plant productivity. Maize mutant viviparous-5 (vp5, deficient in ABA biosynthesis in seeds, is a useful material for studying ABA-mediated response in maize. Due to carotenoid deficiency, vp5 endosperm is white, compared to yellow Vp5 endosperm. However, the background difference at proteome level between vp5 and Vp5 seeds is unclear. This study aimed to characterize proteome alterations of maize vp5 seeds and to identify ABA-dependent proteins during seed maturation. We compared the embryo and endosperm proteomes of vp5 and Vp5 seeds by gel-based proteomics. Up to 46 protein spots, most in embryos, were found to be differentially accumulated between vp5 and Vp5. The identified proteins included small heat shock proteins (sHSPs, late embryogenesis abundant (LEA proteins, stress proteins, storage proteins and enzymes among others. However, EMB564, the most abundant LEA protein in maize embryo, accumulated in comparable levels between vp5 and Vp5 embryos, which contrasted to previously characterized, greatly lowered expression of emb564 mRNA in vp5 embryos. Moreover, LEA proteins and sHSPs displayed differential accumulations in vp5 embryos: six out of eight identified LEA proteins decreased while nine sHSPs increased in abundance. Finally, we discussed the possible causes of global proteome alterations, especially the observed differential accumulation of identified LEA proteins and sHSPs in vp5 embryos. The data derived from this study provides new insight into ABA-dependent proteins and ABA-mediated response during maize seed maturation.

  3. Implications of high-temperature events and water deficits on protein profiles in wheat (Triticum aestivum L. cv. Vinjett) grain

    DEFF Research Database (Denmark)

    Yang, Fen; Jørgensen, Anders Dysted; Li, Huawei

    2011-01-01

    Increased climatic variability is resulting in an increase of both the frequency and the magnitude of extreme climate events. Therefore, cereals may be exposed to more than one stress event in the growing season, which may ultimately affect crop yield and quality. Here, effects are reported...... and glutenins) in grains and stress-induced changes on the albumin and gliadin proteomes were investigated by 2-DE and MS. The synthesis of individual protein fractions was shown to be affected by both the type and time of the applied stresses. Identified drought or high-temperature-responsive proteins included...... proteins involved in primary metabolism, storage and stress response such as late embryogenesis abundant proteins, peroxiredoxins and alpha-amylase/trypsin inhibitors. Several proteins, e.g. heat shock protein and 14-3-3 protein changed in abundance only under multiple high temperatures....

  4. Abundance and diversity of methanogens: potential role in high arsenic groundwater in Hetao Plain of Inner Mongolia, China.

    Science.gov (United States)

    Wang, Y H; Li, P; Dai, X Y; Zhang, R; Jiang, Z; Jiang, D W; Wang, Y X

    2015-05-15

    To investigate the community diversity and abundance of methanogens and their potential role in high arsenic groundwater, 17 groundwater samples from Hetao Plain of Inner Mongolia were investigated with an integrated method including 16S rRNA gene clone library, quantitative polymerase chain reaction and geochemistry analyses. Total arsenic (AsTot) concentrations were 82.7-1088.7 μg/L and arsenite (AsIII) mostly dominated in these samples with percentages of 0.04-0.79. CH₄ concentrations ranged from 0.01 to 292 μg/L and distinctly elevated only when AsTot were relatively high and SO₄(2-) were distinctly low. Principal component analysis indicated that these samples were divided into three groups according to the variations of AsTot, CH₄ and SO₄(2-). AsTot concentrations were distinctly high in the group with high CH₄ and low SO₄(2-) comparing to the other two groups (one with high CH₄ and high SO₄(2-), the other with low CH₄ and SO₄(2-)). The mcrA gene (methyl coenzyme-M reductase gene) based phylogenetic analysis of methanogens population showed that methanogenic archaea was diverse but mainly composed of Methanomicrobiales, Methanosarcinales, Methanobacteria and unidentified groups, with Methanomicrobiales being distinctly dominant (50.6%). The mcrA gene abundance in high arsenic groundwater ranged from 3.01 × 10(3) to 3.80 × 10(6)copies/L and accounted for 0-30.2% of total archaeal 16S rRNA genes. The abundance of mcrA genes was positively correlated with the concentrations of AsTot (R=0.59), AsIII (R=0.57) and FeII (R=0.79), while it was negatively correlated with oxidation-reduction potential (R=-0.66) and SO₄(2-) concentration (R=-0.64). These results implied that methanogenic archaea might accelerate As release in groundwater aquifers in Hetao Plain.

  5. Large-scale spatial variation in palm fruit abundance across a tropical moist forest estimated from high-resolution aerial photographs

    NARCIS (Netherlands)

    Jansen, Patrick A.; Bohlman, Stephanie A.; Garzon-Lopez, Carol X.; Olff, Han; Muller-Landau, Helene C.; Wright, S. Joseph; Svenning, Jens-Christian

    2008-01-01

    Fruit abundance is a critical factor in ecological studies of tropical forest animals and plants, but difficult to measure at large spatial scales. We tried to estimate spatial variation in fruit abundance on a relatively large spatial scale using low altitude, high-resolution aerial photography. We

  6. High-resolution abundance analysis of red giants in the metal-poor bulge globular cluster HP~1

    CERN Document Server

    Barbuy, B; Vemado, A; Ernandes, H; Ortolani, S; Saviane, I; Bica, E; Minniti, D; Dias, B; Momany, Y; Hill, V; Zoccali, M; Siqueira-Mello, C

    2016-01-01

    The globular cluster HP~1 is projected at only 3.33 degrees from the Galactic center. Together with its distance, this makes it one of the most central globular clusters in the Milky Way. It has a blue horizontal branch (BHB) and a metallicity of [Fe/H]~-1.0. This means that it probably is one of the oldest objects in the Galaxy. Abundance ratios can reveal the nucleosynthesis pattern of the first stars as well as the early chemical enrichment and early formation of stellar populations. High-resolution spectra obtained for six stars were analyzed to derive the abundances of the light elements C, N, O, Na, and Al, the alpha-elements Mg, Si, Ca, and Ti, and the heavy elements Sr, Y , Zr, Ba, La, and Eu.} High-resolution spectra of six red giants that are confirmed members of the bulge globular cluster HP~1 were obtained with the 8m VLT UT2-Kueyen telescope with the UVES spectrograph in FLAMES-UVES configuration. The spectroscopic parameter derivation was based on the excitation and ionization equilibrium of FeI...

  7. Highly hydrophilic proteins in prokaryotes and eukaryotes are common during conditions of water deficit.

    Science.gov (United States)

    Garay-Arroyo, A; Colmenero-Flores, J M; Garciarrubio, A; Covarrubias, A A

    2000-02-25

    The late embryogenesis abundant (LEA) proteins are plant proteins that are synthesized at the onset of desiccation in maturing seeds and in vegetative organs exposed to water deficit. Here, we show that most LEA proteins are comprised in a more widespread group, which we call "hydrophilins." The defining characteristics of hydrophilins are high glycine content (>6%) and a high hydrophilicity index (>1.0). By data base searching, we show that this criterion selectively differentiates most known LEA proteins as well as additional proteins from different taxons. We found that within the genomes of Escherichia coli and Saccharomyces cerevisiae, only 5 and 12 proteins, respectively, meet our criterion. Despite their deceivingly loose definition, hydrophilins usually represent stress. Evidence for the participation of one of the E. coli hydrophilins in the adaptive response to hyperosmotic conditions is presented. Apparently, hydrophilins represent analogous adaptations to a common problem in such diverse taxons as prokaryotes and eukaryotes.

  8. High energy density rechargeable magnesium battery using earth-abundant and non-toxic elements

    Science.gov (United States)

    Orikasa, Yuki; Masese, Titus; Koyama, Yukinori; Mori, Takuya; Hattori, Masashi; Yamamoto, Kentaro; Okado, Tetsuya; Huang, Zhen-Dong; Minato, Taketoshi; Tassel, Cédric; Kim, Jungeun; Kobayashi, Yoji; Abe, Takeshi; Kageyama, Hiroshi; Uchimoto, Yoshiharu

    2014-07-01

    Rechargeable magnesium batteries are poised to be viable candidates for large-scale energy storage devices in smart grid communities and electric vehicles. However, the energy density of previously proposed rechargeable magnesium batteries is low, limited mainly by the cathode materials. Here, we present new design approaches for the cathode in order to realize a high-energy-density rechargeable magnesium battery system. Ion-exchanged MgFeSiO4 demonstrates a high reversible capacity exceeding 300 mAh.g-1 at a voltage of approximately 2.4 V vs. Mg. Further, the electronic and crystal structure of ion-exchanged MgFeSiO4 changes during the charging and discharging processes, which demonstrates the (de)insertion of magnesium in the host structure. The combination of ion-exchanged MgFeSiO4 with a magnesium bis(trifluoromethylsulfonyl)imide-triglyme electrolyte system proposed in this work provides a low-cost and practical rechargeable magnesium battery with high energy density, free from corrosion and safety problems.

  9. High abundance and expression of transposases in bacteria from the Baltic Sea.

    Science.gov (United States)

    Vigil-Stenman, Theoden; Ininbergs, Karolina; Bergman, Birgitta; Ekman, Martin

    2017-07-21

    Transposases are mobile genetic elements suggested to have an important role in bacterial genome plasticity and host adaptation but their transcriptional activity in natural bacterial communities is largely unexplored. Here we analyzed metagenomes and -transcriptomes of size fractionated (0.1-0.8, 0.8-3.0 and 3.0-200 μm) bacterial communities from the brackish Baltic Sea, and adjacent marine waters. The Baltic Sea transposase levels, up to 1.7% of bacterial genes and 2% of bacterial transcripts, were considerably higher than in marine waters and similar to levels reported for extreme environments. Large variations in expression were found between transposase families and groups of bacteria, with a two-fold higher transcription in Cyanobacteria than in any other phylum. The community-level results were corroborated at the genus level by Synechococcus transposases reaching up to 5.2% of genes and 6.9% of transcripts, which is in contrast to marine Synechococcus that largely lack these genes. Levels peaked in Synechococcus from the largest size fraction, suggesting high frequencies of lateral gene transfer and high genome plasticity in colony-forming picocyanobacteria. Together, the results support an elevated rate of transposition-based genome change and adaptation in bacterial populations of the Baltic Sea, and possibly also of other highly dynamic estuarine waters.The ISME Journal advance online publication, 21 July 2017; doi:10.1038/ismej.2017.114.

  10. Dietary Yeast Cell Wall Extract Alters the Proteome of the Skin Mucous Barrier in Atlantic Salmon (Salmo salar): Increased Abundance and Expression of a Calreticulin-Like Protein.

    Science.gov (United States)

    Micallef, Giulia; Cash, Phillip; Fernandes, Jorge M O; Rajan, Binoy; Tinsley, John W; Bickerdike, Ralph; Martin, Samuel A M; Bowman, Alan S

    2017-01-01

    In order to improve fish health and reduce use of chemotherapeutants in aquaculture production, the immunomodulatory effect of various nutritional ingredients has been explored. In salmon, there is evidence that functional feeds can reduce the abundance of sea lice. This study aimed to determine if there were consistent changes in the skin mucus proteome that could serve as a biomarker for dietary yeast cell wall extract. The effect of dietary yeast cell wall extract on the skin mucus proteome of Atlantic salmon was examined using two-dimensional gel electrophoresis. Forty-nine spots showed a statistically significant change in their normalised volumes between the control and yeast cell wall diets. Thirteen spots were successfully identified by peptide fragment fingerprinting and LC-MS/MS and these belonged to a variety of functions and pathways. To assess the validity of the results from the proteome approach, the gene expression of a selection of these proteins was studied in skin mRNA from two different independent feeding trials using yeast cell wall extracts. A calreticulin-like protein increased in abundance at both the protein and transcript level in response to dietary yeast cell wall extract. The calreticulin-like protein was identified as a possible biomarker for yeast-derived functional feeds since it showed the most consistent change in expression in both the mucus proteome and skin transcriptome. The discovery of such a biomarker is expected to quicken the pace of research in the application of yeast cell wall extracts.

  11. Dietary Yeast Cell Wall Extract Alters the Proteome of the Skin Mucous Barrier in Atlantic Salmon (Salmo salar): Increased Abundance and Expression of a Calreticulin-Like Protein

    Science.gov (United States)

    Micallef, Giulia; Cash, Phillip; Fernandes, Jorge M. O.; Rajan, Binoy; Tinsley, John W.; Bickerdike, Ralph

    2017-01-01

    In order to improve fish health and reduce use of chemotherapeutants in aquaculture production, the immunomodulatory effect of various nutritional ingredients has been explored. In salmon, there is evidence that functional feeds can reduce the abundance of sea lice. This study aimed to determine if there were consistent changes in the skin mucus proteome that could serve as a biomarker for dietary yeast cell wall extract. The effect of dietary yeast cell wall extract on the skin mucus proteome of Atlantic salmon was examined using two-dimensional gel electrophoresis. Forty-nine spots showed a statistically significant change in their normalised volumes between the control and yeast cell wall diets. Thirteen spots were successfully identified by peptide fragment fingerprinting and LC-MS/MS and these belonged to a variety of functions and pathways. To assess the validity of the results from the proteome approach, the gene expression of a selection of these proteins was studied in skin mRNA from two different independent feeding trials using yeast cell wall extracts. A calreticulin-like protein increased in abundance at both the protein and transcript level in response to dietary yeast cell wall extract. The calreticulin-like protein was identified as a possible biomarker for yeast-derived functional feeds since it showed the most consistent change in expression in both the mucus proteome and skin transcriptome. The discovery of such a biomarker is expected to quicken the pace of research in the application of yeast cell wall extracts. PMID:28046109

  12. Distribution and abundance of Canadian High Arctic belugas, 1974-1979

    Directory of Open Access Journals (Sweden)

    William R Koski

    2002-07-01

    Full Text Available We conducted >236,000 km of aerial surveys and some supplementary studies of belugas (Delphinapterus leucas in the central and eastern Canadian High Arctic in 974-79. Belugas that wintered in the “North Water” in Baffin Bay moved southwest into Lancaster Sound in April and early May. The main westward migration into Lancaster Sound occurred over a 2 to 3 week period during late June to late July. Estuaries along Somerset Island were occupied for <3 weeks from mid-July to mid-August. Little feeding occurred in estuaries. From mid-August until fall migration began in mid-September belugas occupied estuaries and offshore waters in Peel Sound. Fall migration eastward through Lancaster Sound was exclusively along the south coast of Devon Island, highly co-ordinated, and rapid; most of the population passed through the sound in <1 week. The whales then moved north along the east coast of Devon Island; some entered Jones Sound while others crossed directly to SE Ellesmere Island. Most calving occurred in July and early August; calving was not seen in estuaries and probably occurred offshore. Excluding calves, adults and yearlings formed 77% and 8.4%, respectively, of the population. The proportion of calves during mid-August was consistent with a triennial calving cycle. During late summer, belugas fed on coastal concentrations of polar cod (Boreogadus saida, under pan ice offshore (probably on cod, and in deep offshore waters. The size of the Canadian High Arctic population in the late 1970s was estimated to be at least 10,250 to 12,000 animals without allowing for animals that may have passed between surveys or that were below the surface at the time of the counts.

  13. Hydrothermal carbonization of abundant renewable natural organic chemicals for high-performance supercapacitor electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Wei, Lu [School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0245 (United States); School of Materials Science and Engineering, Northwestern Polytechnical University, Xi' an, Shaanxi 710072 (China); Sevilla, Marta [Instituto Nacional del Carbon (CSIC), P.O. Box 73, Oviedo 33080 (Spain); School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD (United Kingdom); Fuertes, Antonio B. [Instituto Nacional del Carbon (CSIC), P.O. Box 73, Oviedo 33080 (Spain); Mokaya, Robert [School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD (United Kingdom); Yushin, Gleb [School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0245 (United States)

    2011-05-15

    Cellulose, potato starch, and eucalyptus wood saw dust were transformed into porous carbons with micropore surface areas of up to 2387 m{sup 2}/g. The specific capacitance of the produced carbons approaches 236 F/g (100 F/cc) when measured in a symmetric configuration in an organic electrolyte. Charge-discharge tests showed excellent capacitance retention with capacitance of up to 175 F/g at an ultra-high current density of 20 A/g. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  14. Cell-Dock: high-performance protein-protein docking.

    Science.gov (United States)

    Pons, Carles; Jiménez-González, Daniel; González-Álvarez, Cecilia; Servat, Harald; Cabrera-Benítez, Daniel; Aguilar, Xavier; Fernández-Recio, Juan

    2012-09-15

    The application of docking to large-scale experiments or the explicit treatment of protein flexibility are part of the new challenges in structural bioinformatics that will require large computer resources and more efficient algorithms. Highly optimized fast Fourier transform (FFT) approaches are broadly used in docking programs but their optimal code implementation leaves hardware acceleration as the only option to significantly reduce the computational cost of these tools. In this work we present Cell-Dock, an FFT-based docking algorithm adapted to the Cell BE processor. We show that Cell-Dock runs faster than FTDock with maximum speedups of above 200×, while achieving results of similar quality. The source code is released under GNU General Public License version 2 and can be downloaded from http://mmb.pcb.ub.es/~cpons/Cell-Dock. djimenez@ac.upc.edu or juanf@bsc.es Supplementary data are available at Bioinformatics online.

  15. Late Embryogenesis Abundant (LEA Constitutes a Large and Diverse Family of Proteins Involved in Development and Abiotic Stress Responses in Sweet Orange (Citrus sinensis L. Osb..

    Directory of Open Access Journals (Sweden)

    Andresa Muniz Pedrosa

    Full Text Available Late Embryogenesis Abundant (LEA proteins are an ubiquitous group of polypeptides that were first described to accumulate during plant seed dehydration, at the later stages of embryogenesis. Since then they have also been recorded in vegetative plant tissues experiencing water limitation and in anhydrobiotic bacteria and invertebrates and, thereby, correlated with the acquisition of desiccation tolerance. This study provides the first comprehensive study about the LEA gene family in sweet orange (Citrus sinensis L. Osb., the most important and widely grown fruit crop around the world. A surprisingly high number (72 of genes encoding C. sinensis LEAs (CsLEAs were identified and classified into seven groups (LEA_1, LEA_2, LEA_3 and LEA_4, LEA_5, DEHYDRIN and SMP based on their predicted amino acid sequences and also on their phylogenetic relationships with the complete set of Arabidopsis thaliana LEA proteins (AtLEAs. Approximately 60% of the CsLEAs identified in this study belongs to the unusual LEA_2 group of more hydrophobic LEA proteins, while the other LEA groups contained a relatively small number of members typically hydrophilic. A correlation between gene structure and motif composition was observed within each LEA group. Investigation of their chromosomal localizations revealed that the CsLEAs were non-randomly distributed across all nine chromosomes and that 33% of all CsLEAs are segmentally or tandemly duplicated genes. Analysis of the upstream sequences required for transcription revealed the presence of various stress-responsive cis-acting regulatory elements in the promoter regions of CsLEAs, including ABRE, DRE/CRT, MYBS and LTRE. Expression analysis using both RNA-seq data and quantitative real-time RT-PCR (qPCR revealed that the CsLEA genes are widely expressed in various tissues, and that many genes containing the ABRE promoter sequence are induced by drought, salt and PEG. These results provide a useful reference for further

  16. Snow cover and extreme winter warming events control flower abundance of some, but not all species in high arctic Svalbard.

    Science.gov (United States)

    Semenchuk, Philipp R; Elberling, Bo; Cooper, Elisabeth J

    2013-08-01

    The High Arctic winter is expected to be altered through ongoing and future climate change. Winter precipitation and snow depth are projected to increase and melt out dates change accordingly. Also, snow cover and depth will play an important role in protecting plant canopy from increasingly more frequent extreme winter warming events. Flower production of many Arctic plants is dependent on melt out timing, since season length determines resource availability for flower preformation. We erected snow fences to increase snow depth and shorten growing season, and counted flowers of six species over 5 years, during which we experienced two extreme winter warming events. Most species were resistant to snow cover increase, but two species reduced flower abundance due to shortened growing seasons. Cassiope tetragona responded strongly with fewer flowers in deep snow regimes during years without extreme events, while Stellaria crassipes responded partly. Snow pack thickness determined whether winter warming events had an effect on flower abundance of some species. Warming events clearly reduced flower abundance in shallow but not in deep snow regimes of Cassiope tetragona, but only marginally for Dryas octopetala. However, the affected species were resilient and individuals did not experience any long term effects. In the case of short or cold summers, a subset of species suffered reduced reproductive success, which may affect future plant composition through possible cascading competition effects. Extreme winter warming events were shown to expose the canopy to cold winter air. The following summer most of the overwintering flower buds could not produce flowers. Thus reproductive success is reduced if this occurs in subsequent years. We conclude that snow depth influences flower abundance by altering season length and by protecting or exposing flower buds to cold winter air, but most species studied are resistant to changes. Winter warming events, often occurring

  17. 187Re-187Os systematics, highly siderophile element, S-Se-Te abundances in the components of unequilibrated L chondrites

    Science.gov (United States)

    Kadlag, Yogita; Becker, Harry

    2016-01-01

    The 187Re-187Os systematics, abundances of highly siderophile elements (HSE: Re, platinum group elements and Au), Te, Se and S as well as major and minor elements were determined in separated components of two unequilibrated L chondrites QUE 97008 (L3.05) and Ceniceros (L3.7). The 187Re-187Os systematics are disturbed in the components of both meteorites, most likely due to open system behavior of Re during terrestrial weathering of QUE 97008 and alteration on the L chondrite parent body as indicated by an internal errorchron generated for components of Ceniceros. The HSE abundance patterns suggest that the bulk rock abundances were mainly controlled by two different end members. Non-magnetic fractions display lower Re/Os and HSE/Ir than CI chondrites. Chondrules, metal-troilite spherules and fine magnetic fractions, are depleted in refractory HSE and show higher Rh/Ir, Pd/Ir and Au/Ir than in CI chondrites. The different HSE compositions indicate the presence of unequilibrated alloys and loss of refractory HSE-rich carrier phases from the precursors of some L chondrite components. Gold is decoupled from other HSE in magnetic fractions and shows chalcophile affinities with a grain size dependent variation similar to S and Se, presumably inherited from preaccretionary processes. Tellurium is depleted in all components compared to other analysed siderophile elements, and its abundance was most likely controlled by fractional condensation and different geochemical affinities. The volatility dependent depletion of Te requires different physical and chemical conditions than typical for the canonical condensation sequence as represented by carbonaceous chondrites. Tellurium also shows variable geochemical behavior, siderophile in Ceniceros, predominantly chalcophile in QUE 97008. These differences may have been inherited from element partitioning during chondrule formation. Selenium and S on the other hand are almost unfractionated from each other and only show

  18. High-resolution spectroscopy of RGB stars in the Sagittarius Streams. I. Radial velocities and chemical abundances

    CERN Document Server

    Monaco, L; Bonifacio, P; Buzzoni, A; Ferraro, F R; Marconi, G; Sbordone, L; Zaggia, S

    2006-01-01

    Aims. The Sagittarius (Sgr) dwarf spheroidal galaxy is currently disrupting under the strain of the Milky Way. A reliable reconstructions of Sgr star formation history can only be obtained joining core and stream informations. We present radial velocities for 67 stars belonging to the Sgr Stream. For 12 stars in the sample we also present iron (Fe) and $\\alpha$-element (Mg, Ca) abundances. Methods. Spectra were secured using different high resolution facilities: UVES@VLT, HARPS@3.6m and SARG@TNG. Radial velocities are obtained through cross correlation with a template spectra. Concerning chemical analysis, for the various elements, selected line equivalent widths (EWs) were measured and abundances computed using the WIDTH code and ATLAS model atmospheres. Results. The velocity dispersion of the trailing tail is found to be $\\sigma$=8.3$\\pm$0.9 km s$^{-1}, i.e. significantly lower than in the core of the Sgr galaxy and marginally lower than previous estimates in the same portion of the stream. Stream stars fol...

  19. A high abundance of massive galaxies 3-6 billion years after the Big Bang.

    Science.gov (United States)

    Glazebrook, Karl; Abraham, Roberto G; McCarthy, Patrick J; Savaglio, Sandra; Chen, Hsiao-Wen; Crampton, David; Murowinski, Rick; Jørgensen, Inger; Roth, Kathy; Hook, Isobel; Marzke, Ronald O; Carlberg, R G

    2004-07-08

    Hierarchical galaxy formation is the model whereby massive galaxies form from an assembly of smaller units. The most massive objects therefore form last. The model succeeds in describing the clustering of galaxies, but the evolutionary history of massive galaxies, as revealed by their visible stars and gas, is not accurately predicted. Near-infrared observations (which allow us to measure the stellar masses of high-redshift galaxies) and deep multi-colour images indicate that a large fraction of the stars in massive galaxies form in the first 5 Gyr (refs 4-7), but uncertainties remain owing to the lack of spectra to confirm the redshifts (which are estimated from the colours) and the role of obscuration by dust. Here we report the results of a spectroscopic redshift survey that probes the most massive and quiescent galaxies back to an era only 3 Gyr after the Big Bang. We find that at least two-thirds of massive galaxies have appeared since this era, but also that a significant fraction of them are already in place in the early Universe.

  20. Identification and monitoring of host cell proteins by mass spectrometry combined with high performance immunochemistry testing.

    Directory of Open Access Journals (Sweden)

    Katrin Bomans

    Full Text Available Biotherapeutics are often produced in non-human host cells like Escherichia coli, yeast, and various mammalian cell lines. A major focus of any therapeutic protein purification process is to reduce host cell proteins to an acceptable low level. In this study, various E. coli host cell proteins were identified at different purifications steps by HPLC fractionation, SDS-PAGE analysis, and tryptic peptide mapping combined with online liquid chromatography mass spectrometry (LC-MS. However, no host cell proteins could be verified by direct LC-MS analysis of final drug substance material. In contrast, the application of affinity enrichment chromatography prior to comprehensive LC-MS was adequate to identify several low abundant host cell proteins at the final drug substance level. Bacterial alkaline phosphatase (BAP was identified as being the most abundant host cell protein at several purification steps. Thus, we firstly established two different assays for enzymatic and immunological BAP monitoring using the cobas® technology. By using this strategy we were able to demonstrate an almost complete removal of BAP enzymatic activity by the established therapeutic protein purification process. In summary, the impact of fermentation, purification, and formulation conditions on host cell protein removal and biological activity can be conducted by monitoring process-specific host cell proteins in a GMP-compatible and high-throughput (> 1000 samples/day manner.

  1. High throughput recombinant protein production of fungal secreted proteins

    DEFF Research Database (Denmark)

    Vala, Andrea Lages Lino; Roth, Doris; Grell, Morten Nedergaard

    2011-01-01

    Secreted proteins are important for both symbiotic and pathogenic interactions between fungi and their hosts. Our research group uses screens and genomic mining to discover novel proteins involved in these processes. To efficiently study the large number of candidate proteins, we are establishing...

  2. Exceptional heat stability of high protein content dispersions containing whey protein particles

    NARCIS (Netherlands)

    Saglam, D.; Venema, P.; Vries, de R.J.; Linden, van der E.

    2014-01-01

    Due to aggregation and/or gelation during thermal treatment, the amount of whey proteins that can be used in the formulation of high protein foods e.g. protein drinks, is limited. The aim of this study was to replace whey proteins with whey protein particles to increase the total protein content and

  3. Extensive determination of glycan heterogeneity reveals an unusual abundance of high mannose glycans in enriched plasma membranes of human embryonic stem cells.

    Science.gov (United States)

    An, Hyun Joo; Gip, Phung; Kim, Jaehan; Wu, Shuai; Park, Kun Wook; McVaugh, Cheryl T; Schaffer, David V; Bertozzi, Carolyn R; Lebrilla, Carlito B

    2012-04-01

    Most cell membrane proteins are known or predicted to be glycosylated in eukaryotic organisms, where surface glycans are essential in many biological processes including cell development and differentiation. Nonetheless, the glycosylation on cell membranes remains not well characterized because of the lack of sensitive analytical methods. This study introduces a technique for the rapid profiling and quantitation of N- and O-glycans on cell membranes using membrane enrichment and nanoflow liquid chromatography/mass spectrometry of native structures. Using this new method, the glycome analysis of cell membranes isolated from human embryonic stem cells and somatic cell lines was performed. Human embryonic stem cells were found to have high levels of high mannose glycans, which contrasts with IMR-90 fibroblasts and a human normal breast cell line, where complex glycans are by far the most abundant and high mannose glycans are minor components. O-Glycosylation affects relatively minor components of cell surfaces. To verify the quantitation and localization of glycans on the human embryonic stem cell membranes, flow cytometry and immunocytochemistry were performed. Proteomics analyses were also performed and confirmed enrichment of plasma membrane proteins with some contamination from endoplasmic reticulum and other membranes. These findings suggest that high mannose glycans are the major component of cell surface glycosylation with even terminal glucoses. High mannose glycans are not commonly presented on the surfaces of mammalian cells or in serum yet may play important roles in stem cell biology. The results also mean that distinguishing stem cells from other mammalian cells may be facilitated by the major difference in the glycosylation of the cell membrane. The deep structural analysis enabled by this new method will enable future mechanistic studies on the biological significance of high mannose glycans on stem cell membranes and provide a general tool to examine

  4. Aestivation Induces Changes in the mRNA Expression Levels and Protein Abundance of Two Isoforms of Urea Transporters in the Gills of the African Lungfish, Protopterus annectens

    Science.gov (United States)

    Chng, You R.; Ong, Jasmine L. Y.; Ching, Biyun; Chen, Xiu L.; Hiong, Kum C.; Wong, Wai P.; Chew, Shit F.; Lam, Siew H.; Ip, Yuen K.

    2017-01-01

    The African lungfish, Protopterus annectens, is ammonotelic in water despite being ureogenic. When it aestivates in mucus cocoon on land, ammonia is detoxified to urea. During the maintenance phase of aestivation, urea accumulates in the body, which is subsequently excreted upon arousal. Urea excretion involves urea transporters (UT/Ut). This study aimed to clone and sequence the ut isoforms from the gills of P. annectens, and to test the hypothesis that the mRNA and/or protein expression levels of ut/Ut isoforms could vary in the gills of P. annectens during the induction, maintenance, and arousal phases of aestivation. Two isoforms of ut, ut-a2a and ut-a2b, were obtained from the gills of P. annectens. ut-a2a consisted of 1227 bp and coded for 408 amino acids with an estimated molecular mass of 44.7 kDa, while ut-a2b consisted of 1392 bp and coded for 464 amino acids with an estimated molecular mass of 51.2 kDa. Ut-a2a and Ut-a2b of P. annectens had a closer phylogenetic relationship with Ut/UT of tetrapods than Ut of fishes. While the mRNA expression pattern of ut-a2a and ut-a2b across various tissues of P. annectens differed, the transcript levels of ut-a2a and ut-a2b in the gills were comparable, indicating that they might be equally important for branchial urea excretion during the initial arousal phase of aestivation. During the maintenance phase of aestivation, the transcript level of ut-a2a increased significantly, but the protein abundance of Ut-a2a remained unchanged in the gills of P. annectens. This could be an adaptive feature to prepare for an increase in the production of Ut-a2a upon arousal. Indeed, arousal led to a significant increase in the branchial Ut-a2a protein abundance. Although the transcript level of ut-a2b remained unchanged, there were significant increases in the protein abundance of Ut-a2b in the gills of P. annectens throughout the three phases of aestivation. The increase in the protein abundance of Ut-a2b during the maintenance

  5. Early Earth differentiation investigated through 142Nd, 182W, and highly siderophile element abundances in samples from Isua, Greenland

    Science.gov (United States)

    Rizo, H.; Walker, R. J.; Carlson, R. W.; Touboul, M.; Horan, M. F.; Puchtel, I. S.; Boyet, M.; Rosing, M. T.

    2016-02-01

    We report new data for W concentrations, stable W isotopic compositions, high-precision 182W/184W ratios, highly siderophile element (HSE) abundances and 187Re-187Os systematics in a suite of 3.8-3.3 Ga mafic and ultramafic rocks from the Isua supracrustal belt, and the Paleoarchean terrane in the northwestern part of the belt. These data are compared with published data for 146Sm-142Nd systematics in the same samples. The samples from the Isua supracrustal belt show well resolved excesses of 182W/184W of up to ∼21 ppm, consistent with previous W isotopic data reported by Willbold et al. (2011). While there is abundant evidence that W was mobilized in the crust accessed by the Isua supracrustal suite, the isotopic anomalies are interpreted to primarily reflect processes that affected the mantle precursors to these rocks. The origin of the 182W excesses in these rocks remains uncertain. The Isua mantle source could represent a portion of the post-core-formation mantle that was isolated from late accretionary additions (e.g., Willbold et al., 2011). However, the combined 182W, Re-Os isotopic systematics and HSE abundances estimated for the source of the Isua basalts are difficult to reconcile with this interpretation. The W isotope variations were more likely produced as a result of fractionation of the Hf/W ratio in the mantle during the lifetime of 182Hf, i.e., during the first 50 Ma of Solar System history. This could have occurred as a result of differentiation in an early magma ocean. The Isua suite examined is also characterized by variable 142Nd/144Nd, but the variations do not correlate with the variations in 182W/184W. Further, samples with ages between 3.8 and 3.3 Ga show gradual diminution of 142Nd anomalies until these are no longer resolved from the modern mantle isotopic composition. By contrast, there is no diminishment of 182W variability with time, suggesting different mechanisms of origin and retention of isotopic variations for these two extinct

  6. Distribution and abundance of breeding birds and small mammals in the high salt marsh and the adjacent upland critical edge in southern Maine

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The primary objective of the study was to document breeding bird and small mammal distribution and abundance in the high salt marsh and the adjacent riparian zone...

  7. Computational and statistical analyses of amino acid usage and physico-chemical properties of the twelve late embryogenesis abundant protein classes.

    Directory of Open Access Journals (Sweden)

    Emmanuel Jaspard

    Full Text Available Late Embryogenesis Abundant Proteins (LEAPs are ubiquitous proteins expected to play major roles in desiccation tolerance. Little is known about their structure - function relationships because of the scarcity of 3-D structures for LEAPs. The previous building of LEAPdb, a database dedicated to LEAPs from plants and other organisms, led to the classification of 710 LEAPs into 12 non-overlapping classes with distinct properties. Using this resource, numerous physico-chemical properties of LEAPs and amino acid usage by LEAPs have been computed and statistically analyzed, revealing distinctive features for each class. This unprecedented analysis allowed a rigorous characterization of the 12 LEAP classes, which differed also in multiple structural and physico-chemical features. Although most LEAPs can be predicted as intrinsically disordered proteins, the analysis indicates that LEAP class 7 (PF03168 and probably LEAP class 11 (PF04927 are natively folded proteins. This study thus provides a detailed description of the structural properties of this protein family opening the path toward further LEAP structure - function analysis. Finally, since each LEAP class can be clearly characterized by a unique set of physico-chemical properties, this will allow development of software to predict proteins as LEAPs.

  8. Foetal life protein restriction in male mink (Neovison vison) kits lowers post-weaning protein oxidation and the relative abundance of hepatic fructose-1,6-bisphosphatase mRNA.

    Science.gov (United States)

    Matthiesen, C F; Blache, D; Thomsen, P D; Tauson, A-H

    2012-01-01

    Foetal life malnutrition has been studied intensively in a number of animal models. Results show that especially foetal life protein malnutrition can lead to metabolic changes later in life. This might be of particular importance for strict carnivores, for example, cat and mink (Neovison vison) because of their higher protein requirement than in other domestic mammals. This study aimed to investigate the effects of low protein provision during foetal life to male mink kits on their protein metabolism during the early post-weaning period of rapid growth and to investigate whether foetal life protein deficiency affects the response to adequate or deficient protein provision post weaning. Further, we intended to study whether the changes in the gene expression of key enzymes in foetal hepatic tissue caused by maternal protein deficiency were manifested post-weaning. A total of 32 male mink kits born to mothers fed either a low-protein diet (LP), that is, 14% of metabolizable energy (ME) from protein (foetal low - FL), n = 16, or an adequate-protein (AP) diet, that is, 29% of ME from protein (foetal adequate - FA), n = 16) in the last 16.3 ± 1.8 days of pregnancy were used. The FL offspring had lower birth weight and lower relative abundance of fructose-1,6-bisphosphatase (Fru-1,6-P2ase) and pyruvate kinase mRNA in foetal hepatic tissue than FA kits. The mothers were fed a diet containing adequate protein until weaning. At weaning (7 weeks of age), half of the kits from each foetal treatment group were fed an AP diet (32% of ME from protein; n = 8 FA and 8 FL) and the other half were fed a LP diet (18% of ME from protein; n = 8 FA and 8 FL) until 9.5 weeks of age, yielding four treatment groups (i.e. FA-AP, FA-LP, FL-AP and FL-LP). Low protein provision in foetal life lowered the protein oxidation post-weaning compared with the controls (P = 0.006), indicating metabolic flexibility and a better ability to conserve protein. This could not, however, be supported by

  9. High Abundance of the Epibenthic Trachymedusa Ptychogastria polaris Allman, 1878 (Hydrozoa, Trachylina) in Subpolar Fjords along the West Antarctic Peninsula

    Science.gov (United States)

    Smith, Craig R.; Lindsay, Dhugal J.; Bentlage, Bastian; Youngbluth, Marsh J.

    2017-01-01

    Medusae can be conspicuous and abundant members of seafloor communities in deep-sea benthic boundary layers. The epibenthic trachymedusa, Ptychogastria polaris Allman, 1878 (Hydrozoa: Trachylina: Ptychogastriidae) occurs in the cold, high latitude systems of both the northern and southern hemispheres, with a circumpolar distribution in Arctic and sub-Arctic areas, and disjunct reports of a few individuals from Antarctica. In January-February 2010, during benthic megafaunal photosurveys in three subpolar fjords along the West Antarctic Peninsula (Andvord, Flandres and Barilari Bays), P. polaris was recorded in Antarctic Peninsula waters. The trachymedusa, identified from megacore-collected specimens, was a common component of the epifauna in the sediment floored basins at 436–725 m depths in Andvord and Flandres Bays, reaching densities up to 13 m-2, with mean densities in individual basins ranging from 0.06 to 4.19 m-2. These densities are 2 to 400-fold higher than previously reported for P. polaris in either the Arctic or Antarctic. This trachymedusa had an aggregated distribution, occurring frequently in Andvord Bay, but was often solitary in Flandres Bay, with a distribution not significantly different from random. Epibenthic individuals were similar in size, typically measuring 15–25 mm in bell diameter. A morphologically similar trachymedusa, presumably the same species, was also observed in the water column near the bottom in all three fjords. This benthopelagic form attained abundances of up to 7 m-2 of seafloor; however, most P. polaris (~ 80%), were observed on soft sediments. Our findings indicate that fjords provide a prime habitat for the development of dense populations of P. polaris, potentially resulting from high and varied food inputs to the fjord floors. Because P. polaris resides in the water column and at the seafloor, large P. polaris populations may contribute significantly to pelagic-benthic coupling in the WAP fjord ecosystems. PMID

  10. High Abundance of the Epibenthic Trachymedusa Ptychogastria polaris Allman, 1878 (Hydrozoa, Trachylina) in Subpolar Fjords along the West Antarctic Peninsula.

    Science.gov (United States)

    Grange, Laura J; Smith, Craig R; Lindsay, Dhugal J; Bentlage, Bastian; Youngbluth, Marsh J

    2017-01-01

    Medusae can be conspicuous and abundant members of seafloor communities in deep-sea benthic boundary layers. The epibenthic trachymedusa, Ptychogastria polaris Allman, 1878 (Hydrozoa: Trachylina: Ptychogastriidae) occurs in the cold, high latitude systems of both the northern and southern hemispheres, with a circumpolar distribution in Arctic and sub-Arctic areas, and disjunct reports of a few individuals from Antarctica. In January-February 2010, during benthic megafaunal photosurveys in three subpolar fjords along the West Antarctic Peninsula (Andvord, Flandres and Barilari Bays), P. polaris was recorded in Antarctic Peninsula waters. The trachymedusa, identified from megacore-collected specimens, was a common component of the epifauna in the sediment floored basins at 436-725 m depths in Andvord and Flandres Bays, reaching densities up to 13 m-2, with mean densities in individual basins ranging from 0.06 to 4.19 m-2. These densities are 2 to 400-fold higher than previously reported for P. polaris in either the Arctic or Antarctic. This trachymedusa had an aggregated distribution, occurring frequently in Andvord Bay, but was often solitary in Flandres Bay, with a distribution not significantly different from random. Epibenthic individuals were similar in size, typically measuring 15-25 mm in bell diameter. A morphologically similar trachymedusa, presumably the same species, was also observed in the water column near the bottom in all three fjords. This benthopelagic form attained abundances of up to 7 m-2 of seafloor; however, most P. polaris (~ 80%), were observed on soft sediments. Our findings indicate that fjords provide a prime habitat for the development of dense populations of P. polaris, potentially resulting from high and varied food inputs to the fjord floors. Because P. polaris resides in the water column and at the seafloor, large P. polaris populations may contribute significantly to pelagic-benthic coupling in the WAP fjord ecosystems.

  11. High abundances of oxalic, azelaic, and glyoxylic acids and methylglyoxal in the open ocean with high biological activity: Implication for secondary OA formation from isoprene

    Science.gov (United States)

    Bikkina, Srinivas; Kawamura, Kimitaka; Miyazaki, Yuzo; Fu, Pingqing

    2014-05-01

    Atmospheric dicarboxylic acids (DCA) are a ubiquitous water-soluble component of secondary organic aerosols (SOA), which can act as cloud condensation nuclei (CCN), affecting the Earth's climate. Despite the high abundances of oxalic acid and related compounds in the marine aerosols, there is no consensus on what controls their distributions over the open ocean. Marine biological productivity could play a role in the production of DCA, but there is no substantial evidence to support this hypothesis. Here we present latitudinal distributions of DCA, oxoacids and α-dicarbonyls in the marine aerosols from the remote Pacific. Their concentrations were found several times higher in more biologically influenced aerosols (MBA) than less biologically influenced aerosols. We propose isoprene and unsaturated fatty acids as sources of DCA as inferred from significantly higher abundances of isoprene-SOA tracers and azelaic acid in MBA. These results have implications toward the reassessment of climate forcing feedbacks of marine-derived SOA.

  12. Proteomic Characterization of Differential Abundant Proteins Accumulated between Lower and Upper Epidermises of Fleshy Scales in Onion (Allium cepa L.) Bulbs

    Science.gov (United States)

    Wu, Xiaolin

    2016-01-01

    The onion (Allium cepa L.) is widely planted worldwide as a valuable vegetable crop. The scales of an onion bulb are a modified type of leaf. The one-layer-cell epidermis of onion scales is commonly used as a model experimental material in botany and molecular biology. The lower epidermis (LE) and upper epidermis (UE) of onion scales display obvious differences in microscopic structure, cell differentiation and pigment synthesis; however, associated proteomic differences are unclear. LE and UE can be easily sampled as single-layer-cell tissues for comparative proteomic analysis. In this study, a proteomic approach based on 2-DE and mass spectrometry (MS) was applied to compare LE and UE of fleshy scales from yellow and red onions. We identified 47 differential abundant protein spots (representing 31 unique proteins) between LE and UE in red and yellow onions. These proteins are mainly involved in pigment synthesis, stress response, and cell division. Particularly, the differentially accumulated chalcone-flavanone isomerase and flavone O-methyltransferase 1-like in LE may result in the differences in the onion scale color between red and yellow onions. Moreover, stress-related proteins abundantly accumulated in both LE and UE. In addition, the differential accumulation of UDP-arabinopyranose mutase 1-like protein and β-1,3-glucanase in the LE may be related to the different cell sizes between LE and UE of the two types of onion. The data derived from this study provides new insight into the differences in differentiation and developmental processes between onion epidermises. This study may also make a contribution to onion breeding, such as improving resistances and changing colors. PMID:28036352

  13. Quantification of intermediate-abundance proteins in serum by multiple reaction monitoring mass spectrometry in a single-quadrupole ion trap.

    Science.gov (United States)

    Lin, Shanhua; Shaler, Thomas A; Becker, Christopher H

    2006-08-15

    A method is presented to quantify intermediate-abundance proteins in human serum using a single-quadrupole linear ion trap mass spectrometer-in contrast, for example, to a triple-quadrupole mass spectrometer. Stable-isotope-labeled (tryptic) peptides are spiked into digested protein samples as internal standards, aligned with the traditional isotope dilution approach. As a proof-of-concept experiment, four proteins of intermediate abundance were selected, coagulation factor V, adiponectin, C-reactive protein (CRP), and thyroxine binding globulin. Stable-isotope-labeled peptides were synthesized with one tryptic sequence from each of these proteins. The normal human serum concentration ranges of these proteins are from 1 to 30 microg/mL (or 20 to 650 pmol/mL). These labeled peptides and their endogenous counterparts were analyzed by LC-MS/MS using multiple reaction monitoring, a multiplexed form of the selected reaction monitoring technique. For these experiments, only one chromatographic dimension (on-line reversed-phase capillary column) was used. Improved limits of detection will result with multidimensional chromatographic methods utilizing more material per sample. Standard curves of the spiked calibrants were generated with concentrations ranging from 3 to 700 pmol/mL using both neat solutions and peptides spiked into the complex matrix of digested serum protein solution where ion suppression effects and interferences are common. Endogenous protein concentrations were determined by comparing MS/MS peak areas of the endogenous peptides to the isotopically labeled internal calibrants. The derived concentrations from a normal human serum pool (neglecting loss of material during sample processing) were 9.2, 110, 120, and 246 pmol/mL for coagulation factor V, adiponectin, CRP, and thyroxine binding globulin, respectively. These concentrations generally agree with the reported normal ranges for these proteins. As a measure of analytical reproducibility of this

  14. High-precision abundances of Sc, Mn, Cu, and Ba in solar twins. Trends of element ratios with stellar age

    Science.gov (United States)

    Nissen, P. E.

    2016-09-01

    Aims: A previous study of correlations between element abundances and ages of solar twin stars in the solar neighborhood is extended to include Sc, Mn, Cu, and Ba to obtain new information on the nucleosynthetic history of these elements. Methods: HARPS spectra with S/N ≳ 600 are used to derive very precise (σ ~ 0.01 dex) differential abundances of Sc, Mn, Cu, and Ba for 21 solar twins and the Sun. The analysis is based on MARCS model atmospheres with parameters determined from the excitation and ionization balance of Fe lines. Stellar ages with internal errors less than 1 Gyr are obtained by interpolation in the log g - Teff diagram between isochrones based on the Aarhus Stellar Evolution Code. Results: For stars younger than 6 Gyr, [Sc/Fe], [Mn/Fe], [Cu/Fe], and [Ba/Fe] are tightly correlated with stellar age, which is also the case for the other elements previously studied; linear relations between [X/Fe] and age have χ^2red ˜ 1, and for most stars the residuals do not depend on elemental condensation temperature. For ages between 6 and 9 Gyr, the [X/Fe] - age correlations break down and the stars split up into two groups having respectively high and low [X/Fe] for the odd-Z elements Na, Al, Sc, and Cu. Conclusions: While stars in the solar neighborhood younger than ~ 6 Gyr were formed from interstellar gas with a smooth chemical evolution, older stars seem to have originated from regions enriched by supernovae with different neutron excesses. Correlations between abundance ratios and stellar age suggest that: (i) Sc is made in Type II supernovae along with the α-capture elements; (ii) the Type II to Ia yield ratio is about the same for Mn and Fe; (iii) Cu is mainly made by the weak s-process in massive stars; (iv) the Ba/Y yield ratio for asymptotic giant branch stars increases with decreasing stellar mass; (v) [Y/Mg] and [Y/Al] can be used as chemical clocks when determining ages of solar metallicity stars. Based on data products from observations made

  15. Chemical abundances in the protoplanetary disc LV 2 (Orion) - II. High-dispersion VLT observations and microjet properties

    Science.gov (United States)

    Tsamis, Y. G.; Walsh, J. R.

    2011-11-01

    Integral field spectroscopy of the LV 2 proplyd is presented taken with the Very Large Telescope (VLT)/FLAMES Argus array at an angular resolution of 0.31 × 0.31 arcsec2 and velocity resolutions down to 2 km s-1 pixel-1. Following subtraction of the local M42 emission, the spectrum of LV 2 is isolated from the surrounding nebula. We measured the heliocentric velocities and widths of a number of lines detected in the intrinsic spectrum of the proplyd, as well as in the adjacent Orion nebula falling within a 6.6 × 4.2 arcsec2 field of view. It is found that far-ultraviolet to optical collisional lines with critical densities, Ncr, ranging from 103 to 109 cm-3 suffer collisional de-excitation near the rest velocity of the proplyd correlating tightly with their critical densities. Lines of low Ncr are suppressed the most. The bipolar jet arising from LV 2 is spectrally and spatially well detected in several emission lines. We compute the [O III] electron temperature profile across LV 2 in velocity space and measure steep temperature variations associated with the red-shifted lobe of the jet, possibly being due to a shock discontinuity. From the velocity-resolved analysis the ionized gas near the rest frame of LV 2 has Te= 9200 ± 800 K and Ne˜ 106 cm-3, while the red-shifted jet lobe has Te≈ 9000-104 K and Ne˜ 106-107 cm-3. The jet flow is highly ionized but contains dense semineutral clumps emitting neutral oxygen lines. The abundances of N+, O2 +, Ne2 +, Fe2 +, S+and S2 +are measured for the strong red-shifted jet lobe. Iron in the core of LV 2 is depleted by 2.54 dex with respect to solar as a result of sedimentation on dust, whereas the efficient destruction of dust grains in the fast microjet raises its Fe abundance to at least 30 per cent solar. Sulphur does not show evidence of significant depletion on dust, but its abundance both in the core and the jet is only about half solar. Based on observations made with ESO telescopes at the Paranal Observatory

  16. Water emission from the high-mass star-forming region IRAS 17233-3606. High water abundances at high velocities

    CERN Document Server

    Leurini, S; Wyrowski, F; Codella, C; Csengeri, T; van der Tak, F; Beuther, H; Flower, D R; Comito, C; Schilke, P

    2014-01-01

    We investigate the physical and chemical processes at work during the formation of a massive protostar based on the observation of water in an outflow from a very young object previously detected in H2 and SiO in the IRAS 17233-3606 region. We estimated the abundance of water to understand its chemistry, and to constrain the mass of the emitting outflow. We present new observations of shocked water obtained with the HIFI receiver onboard Herschel. We detected water at high velocities in a range similar to SiO. We self-consistently fitted these observations along with previous SiO data through a state-of-the-art, one-dimensional, stationary C-shock model. We found that a single model can explain the SiO and H2O emission in the red and blue wings of the spectra. Remarkably, one common area, similar to that found for H2 emission, fits both the SiO and H2O emission regions. This shock model subsequently allowed us to assess the shocked water column density, N(H2O)=1.2x10^{18} cm^{-2}, mass, M(H2O)=12.5 M_earth, a...

  17. Protein profiling reveals inter-individual protein homogeneity of arachnoid cyst fluid and high qualitative similarity to cerebrospinal fluid

    Directory of Open Access Journals (Sweden)

    Berle Magnus

    2011-05-01

    the majority of abundant proteins in AC fluid also can be found in CSF. Compared to plasma, as many as 104 proteins in AC were not found in the list of 3017 plasma proteins. Conclusions Based on the protein content of AC fluid, our data indicate that temporal AC is a homogenous condition, pointing towards a similar AC filling mechanism for the 14 patients examined. Most of the proteins identified in AC fluid have been identified in CSF, indicating high similarity in the qualitative protein content of AC to CSF, whereas this was not the case between AC and plasma. This indicates that AC is filled with a liquid similar to CSF. As far as we know, this is the first proteomics study that explores the AC fluid proteome.

  18. High-resolution spectroscopy of RGB stars in the Sagittarius streams. I. Radial velocities and chemical abundances

    Science.gov (United States)

    Monaco, L.; Bellazzini, M.; Bonifacio, P.; Buzzoni, A.; Ferraro, F. R.; Marconi, G.; Sbordone, L.; Zaggia, S.

    2007-03-01

    Context: The Sagittarius (Sgr) dwarf spheroidal galaxy is currently being disrupted under the strain of the Milky Way. A reliable reconstruction of Sgr star formation history can only be obtained by combining core and stream information. Aims: We present radial velocities for 67 stars belonging to the Sgr Stream. For 12 stars in the sample we also present iron (Fe) and α-element (Mg, Ca) abundances. Methods: Spectra were secured using different high resolution facilities: UVES@VLT, HARPS@3.6 m, and SARG@TNG. Radial velocities are obtained through cross correlation with a template spectra. Concerning chemical analysis, for the various elements, selected line equivalent widths were measured and abundances computed using the WIDTH code and ATLAS model atmospheres. Results: The velocity dispersion of the trailing tail is found to be σ = 8.3 ± 0.9 km s-1, i.e., significantly lower than in the core of the Sgr galaxy and marginally lower than previous estimates in the same portion of the stream. Stream stars follow the same trend as Sgr main body stars in the [ α/Fe] vs. [Fe/H] plane. However, stars are, on average, more metal poor in the stream than in the main body. This effect is slightly stronger in stars belonging to more ancient wraps of the stream, according to currently accepted models of Sgr disruption. Based on observations taken at ESO VLT Kueyen telescope (Cerro Paranal, Chile, program: 075.B-0127(A)) and 3.6 m telescope (La Silla, Chile). Also based on spectroscopic observations taken at the Telescopio Nazionale Galileo, operated by the Fundación G. Galilei of INAF at the Spanish Observatorio del Roque de los Muchachos of the IAC (La Palma, Spain). Appendix A and Table [see full text] are only available in electronic form at http://www.aanda.org

  19. Food Abundance Is the Main Determinant of High-Altitude Range Use in Snub-Nosed Monkeys

    Directory of Open Access Journals (Sweden)

    Cyril C. Grueter

    2012-01-01

    Full Text Available High-altitude dwelling primates have to optimize navigating a space that contains both a vertical and horizontal component. Black-and-white or Yunnan snub-nosed monkeys (Rhinopithecus bieti are extreme by primate standards in inhabiting relatively cold subalpine temperate forests at very high altitudes where large seasonal variation in climate and food availability is expected to profoundly modulate their ranging strategies so as to ensure a positive energy balance. A “semi-nomadic” group of R. bieti was followed for 20 months in the montane Samage Forest, Baimaxueshan Nature Reserve, Yunnan, PRC, which consisted of evergreen conifers, oaks, and deciduous broadleaf trees. The aim of this study was to disentangle the effects of climate and phenology on patterns of altitudinal range use. Altitude used by the group ranged from a maximum of 3550 m in July 2007 to a minimum of 3060 m in April 2006. The proportional use of lichen, the monkeys’ staple fallback food, in the diet explained more variation in monthly use of altitudes than climatic factors and availability of flush and fruit. The abundance of lichens at high altitudes, the lack of alternative foods in winter, and the need to satisfy the monkey's basal energetic requirements explain the effect of lichenivory on use of altitudes.

  20. The role of cholesteryl ester transfer protein and phospholipid transfer protein in the remodeling of plasma high-density lipoproteins.

    Science.gov (United States)

    Lagrost, L

    1997-08-01

    Recent studies demonstrated that alterations in the size distribution of high-density lipoproteins (HDLs) constitute reliable markers for the risk of coronary artery disease. These observations suggested that the determination of the size distribution of HDL subpopulations by using polyacrylamide gradient gel electrophoresis might constitute an effective tool in clinical practice for the detection of patients with elevated risk. During the last decade, concordant observations revealed that all the HDL subpopulations are metabolically interrelated, and their relative abundances are dependent on the activity of several plasma factors, among them the cholesteryl ester transfer protein (CETP) and the phospholipid transfer protein (PLTP). As reviewed in the present article, although both CETP and PLTP can promote the size redistribution or conversion of HDL, the two plasma lipid transfer proteins can alter differently the plasma HDL distribution profile through distinct mechanisms. (Trends Cardiovasc Med 1997;7:218-224). © 1997, Elsevier Science Inc.

  1. Whey protein particles modulate mechanical properties of gels at high protein concentrations

    NARCIS (Netherlands)

    Saglam, D.; Venema, P.; Vries, de R.J.; Berg, van den L.; Linden, van der E.

    2014-01-01

    We have studied the influence of dense whey protein particles on the mechanical properties of whey protein isolate (WPI) gels at high protein concentrations (16–22% (w/w)). Incorporation of dense whey protein particles in the gel, while keeping the total protein concentration constant, leads to a co

  2. Depth-specific fluctuations of gene expression and protein abundance modulate the photophysiology in the seagrass Posidonia oceanica

    Science.gov (United States)

    Procaccini, Gabriele; Ruocco, Miriam; Marín-Guirao, Lázaro; Dattolo, Emanuela; Brunet, Christophe; D’Esposito, Daniela; Lauritano, Chiara; Mazzuca, Silvia; Serra, Ilia Anna; Bernardo, Letizia; Piro, Amalia; Beer, Sven; Björk, Mats; Gullström, Martin; Buapet, Pimchanok; Rasmusson, Lina M.; Felisberto, Paulo; Gobert, Sylvie; Runcie, John W.; Silva, João; Olivé, Irene; Costa, Monya M.; Barrote, Isabel; Santos, Rui

    2017-01-01

    Here we present the results of a multiple organizational level analysis conceived to identify acclimative/adaptive strategies exhibited by the seagrass Posidonia oceanica to the daily fluctuations in the light environment, at contrasting depths. We assessed changes in photophysiological parameters, leaf respiration, pigments, and protein and mRNA expression levels. The results show that the diel oscillations of P. oceanica photophysiological and respiratory responses were related to transcripts and proteins expression of the genes involved in those processes and that there was a response asynchrony between shallow and deep plants probably caused by the strong differences in the light environment. The photochemical pathway of energy use was more effective in shallow plants due to higher light availability, but these plants needed more investment in photoprotection and photorepair, requiring higher translation and protein synthesis than deep plants. The genetic differentiation between deep and shallow stands suggests the existence of locally adapted genotypes to contrasting light environments. The depth-specific diel rhythms of photosynthetic and respiratory processes, from molecular to physiological levels, must be considered in the management and conservation of these key coastal ecosystems. PMID:28211527

  3. Depth-specific fluctuations of gene expression and protein abundance modulate the photophysiology in the seagrass Posidonia oceanica

    Science.gov (United States)

    Procaccini, Gabriele; Ruocco, Miriam; Marín-Guirao, Lázaro; Dattolo, Emanuela; Brunet, Christophe; D’Esposito, Daniela; Lauritano, Chiara; Mazzuca, Silvia; Serra, Ilia Anna; Bernardo, Letizia; Piro, Amalia; Beer, Sven; Björk, Mats; Gullström, Martin; Buapet, Pimchanok; Rasmusson, Lina M.; Felisberto, Paulo; Gobert, Sylvie; Runcie, John W.; Silva, João; Olivé, Irene; Costa, Monya M.; Barrote, Isabel; Santos, Rui

    2017-02-01

    Here we present the results of a multiple organizational level analysis conceived to identify acclimative/adaptive strategies exhibited by the seagrass Posidonia oceanica to the daily fluctuations in the light environment, at contrasting depths. We assessed changes in photophysiological parameters, leaf respiration, pigments, and protein and mRNA expression levels. The results show that the diel oscillations of P. oceanica photophysiological and respiratory responses were related to transcripts and proteins expression of the genes involved in those processes and that there was a response asynchrony between shallow and deep plants probably caused by the strong differences in the light environment. The photochemical pathway of energy use was more effective in shallow plants due to higher light availability, but these plants needed more investment in photoprotection and photorepair, requiring higher translation and protein synthesis than deep plants. The genetic differentiation between deep and shallow stands suggests the existence of locally adapted genotypes to contrasting light environments. The depth-specific diel rhythms of photosynthetic and respiratory processes, from molecular to physiological levels, must be considered in the management and conservation of these key coastal ecosystems.

  4. Highly siderophile element (HSE) abundances in the mantle of Mars are due to core formation at high pressure and temperature

    Science.gov (United States)

    Righter, K.; Danielson, L. R.; Pando, K. M.; Williams, J.; Humayun, M.; Hervig, R. L.; Sharp, T. G.

    2015-04-01

    Highly siderophile elements (HSEs) can be used to understand accretion and core formation in differentiated bodies, due to their strong affinity for FeNi metal and sulfides. Coupling experimental studies of metal-silicate partitioning with analyses of HSE contents of Martian meteorites can thus offer important constraints on the early history of Mars. Here, we report new metal-silicate partitioning data for the PGEs and Au and Re across a wide range of pressure and temperature space, with three series designed to complement existing experimental data sets for HSE. The first series examines temperature effects for D(HSE) in two metallic liquid compositions—C-bearing and C-free. The second series examines temperature effects for D(Re) in FeO-bearing silicate melts and FeNi-rich alloys. The third series presents the first systematic study of high pressure and temperature effects for D(Au). We then combine our data with previously published partitioning data to derive predictive expressions for metal-silicate partitioning of the HSE, which are subsequently used to calculate HSE concentrations of the Martian mantle during continuous accretion of Mars. Our results show that at midmantle depths in an early magma ocean (equivalent to approximately 14 GPa, 2100 °C), the HSE contents of the silicate fraction are similar to those observed in the Martian meteorite suite. This is in concert with previous studies on moderately siderophile elements. We then consider model calculations that examine the role of melting, fractional crystallization, and sulfide saturation/undersaturation in establishing the range of HSE contents in Martian meteorites derived from melting of the postcore formation mantle. The core formation modeling indicates that the HSE contents can be established by metal-silicate equilibrium early in the history of Mars, thus obviating the need for a late veneer for HSE, and by extension volatile siderophile elements, or volatiles in general.

  5. High-throughput characterization of intrinsic disorder in proteins from the Protein Structure Initiative.

    Science.gov (United States)

    Johnson, Derrick E; Xue, Bin; Sickmeier, Megan D; Meng, Jingwei; Cortese, Marc S; Oldfield, Christopher J; Le Gall, Tanguy; Dunker, A Keith; Uversky, Vladimir N

    2012-10-01

    The identification of intrinsically disordered proteins (IDPs) among the targets that fail to form satisfactory crystal structures in the Protein Structure Initiative represents a key to reducing the costs and time for determining three-dimensional structures of proteins. To help in this endeavor, several Protein Structure Initiative Centers were asked to send samples of both crystallizable proteins and proteins that failed to crystallize. The abundance of intrinsic disorder in these proteins was evaluated via computational analysis using predictors of natural disordered regions (PONDR®) and the potential cleavage sites and corresponding fragments were determined. Then, the target proteins were analyzed for intrinsic disorder by their resistance to limited proteolysis. The rates of tryptic digestion of sample target proteins were compared to those of lysozyme/myoglobin, apomyoglobin, and α-casein as standards of ordered, partially disordered and completely disordered proteins, respectively. At the next stage, the protein samples were subjected to both far-UV and near-UV circular dichroism (CD) analysis. For most of the samples, a good agreement between CD data, predictions of disorder and the rates of limited tryptic digestion was established. Further experimentation is being performed on a smaller subset of these samples in order to obtain more detailed information on the ordered/disordered nature of the proteins.

  6. Proteome Scale-Protein Turnover Analysis Using High Resolution Mass Spectrometric Data from Stable-Isotope Labeled Plants.

    Science.gov (United States)

    Fan, Kai-Ting; Rendahl, Aaron K; Chen, Wen-Ping; Freund, Dana M; Gray, William M; Cohen, Jerry D; Hegeman, Adrian D

    2016-03-04

    Protein turnover is an important aspect of the regulation of cellular processes for organisms when responding to developmental or environmental cues. The measurement of protein turnover in plants, in contrast to that of rapidly growing unicellular organismal cultures, is made more complicated by the high degree of amino acid recycling, resulting in significant transient isotope incorporation distributions that must be dealt with computationally for high throughput analysis to be practical. An algorithm in R, ProteinTurnover, was developed to calculate protein turnover with transient stable isotope incorporation distributions in a high throughput automated manner using high resolution MS and MS/MS proteomic analysis of stable isotopically labeled plant material. ProteinTurnover extracts isotopic distribution information from raw MS data for peptides identified by MS/MS from data sets of either isotopic label dilution or incorporation experiments. Variable isotopic incorporation distributions were modeled using binomial and beta-binomial distributions to deconvolute the natural abundance, newly synthesized/partial-labeled, and fully labeled peptide distributions. Maximum likelihood estimation was performed to calculate the distribution abundance proportion of old and newly synthesized peptides. The half-life or turnover rate of each peptide was calculated from changes in the distribution abundance proportions using nonlinear regression. We applied ProteinTurnover to obtain half-lives of proteins from enriched soluble and membrane fractions from Arabidopsis roots.

  7. Targeting protein-protein interactions with trimeric ligands: high affinity inhibitors of the MAGUK protein family.

    Directory of Open Access Journals (Sweden)

    Klaus B Nissen

    Full Text Available PDZ domains in general, and those of PSD-95 in particular, are emerging as promising drug targets for diseases such as ischemic stroke. We have previously shown that dimeric ligands that simultaneously target PDZ1 and PDZ2 of PSD-95 are highly potent inhibitors of PSD-95. However, PSD-95 and the related MAGUK proteins contain three consecutive PDZ domains, hence we envisioned that targeting all three PDZ domains simultaneously would lead to more potent and potentially more specific interactions with the MAGUK proteins. Here we describe the design, synthesis and characterization of a series of trimeric ligands targeting all three PDZ domains of PSD-95 and the related MAGUK proteins, PSD-93, SAP-97 and SAP-102. Using our dimeric ligands targeting the PDZ1-2 tandem as starting point, we designed novel trimeric ligands by introducing a PDZ3-binding peptide moiety via a cysteine-derivatized NPEG linker. The trimeric ligands generally displayed increased affinities compared to the dimeric ligands in fluorescence polarization binding experiments and optimized trimeric ligands showed low nanomolar inhibition towards the four MAGUK proteins, thus being the most potent inhibitors described. Kinetic experiments using stopped-flow spectrometry showed that the increase in affinity is caused by a decrease in the dissociation rate of the trimeric ligand as compared to the dimeric ligands, likely reflecting the lower probability of simultaneous dissociation of all three PDZ ligands. Thus, we have provided novel inhibitors of the MAGUK proteins with exceptionally high affinity, which can be used to further elucidate the therapeutic potential of these proteins.

  8. High Redshift Intergalactic C IV Abundance Measurements from the Near-Infrared Spectra of Two z~6 QSOs

    CERN Document Server

    Simcoe, R A

    2006-01-01

    New measurements of the z~6 intergalactic CIV abundance are presented, using moderate resolution IR spectra of two QSOs taken with GNIRS on Gemini South. These data were systematically searched for high redshift CIV absorption lines, using objective selection criteria. Comprehensive tests were performed to quantify sample incompleteness, as well as the rate of false positive CIV identifications. The trend of constant $\\Omega_{CIV}(z)$ observed at z~2-5 appears to continue to z~6, the highest observed redshift. The CIV sample is also consistent with the redshift-invariant form of the CIV column density distribution reported by Songaila (2001) at lower redshift, although with fairly large uncertainties due to a smaller sample size and noisier infrared data. The constant value of $\\Omega_{CIV}$ does not necessarily imply that the IGM was infused with an early metallicity ``floor,'' but the presence of early CIV does indicate that heavy-element enrichment began < 1 Gyr after the Big Bang. The lack of a decline...

  9. Ultra-High Sensitivity Techniques for the Determination of 3 He /4 He Abundances in Helium by Accelerator Mass Spectrometry

    Science.gov (United States)

    Mumm, H. P.; Huber, M.; Bauder, W.; Abrams, N.; Deibel, C.; Huffer, C.; Huffman, P.; Schelhammer, K.; Janssens, R.; Jiang, C.; Scott, R.; Pardo, R.; Rehm, K.; Vondrasek, R.; Swank, C.; O'Shaughnessy, C.; Paul, M.; Yang, L.

    2017-01-01

    We report the development of an Accelerator Mass Spectrometry technique to measure the 3He/4He isotopic ratio using a radio frequency (RF) discharge source and the ATLAS facility at Argonne National Laboratory. Control over 3He/4He ratio in helium several orders of magnitude lower than natural abundance is critical for neutron lifetime and source experiments using liquid helium. Due to low ultimate beam currents, the ATLAS accelerator and beam line were tuned using a succession of species of the same M/q. A unique RF source was developed for the experiment due to large natural 3He backgrounds. Analog H_3 + and DH + molecular ions are eliminated by dissociation via a gold stripper foil near the detector. The stripped ions were dispersed in a magnetic spectrograph and 3He2 + ions counted in the focal plane detector. This technique is sensitive to 3 He /4 He ratios in the regime of 10-12 with backgrounds that appear to be below 10-14. The techniques used to reduce the backgrounds and remaining outstanding problems will be presented along with results from measurements on high purity 4He samples.

  10. Endophytic fungi from the genus Colletotrichum are abundant in the Phaseolus vulgaris and have high genetic diversity.

    Science.gov (United States)

    Gonzaga, L L; Costa, L E O; Santos, T T; Araújo, E F; Queiroz, M V

    2015-02-01

    To evaluate the diversity of endophytic fungi from the leaves of the common bean and the genetic diversity of endophytic fungi from the genus Colletotrichum using IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism) analyses. The fungi were isolated by tissue fragmentation and identified by analysing the morphological features and sequencing the internal transcribed spacer (ITS) regions and the rDNA large subunit (LSU). Twenty-seven different taxa were identified. Colletotrichum was the most commonly isolated genera from the common bean (32.69% and 24.29% of the total isolates from the Ouro Negro and Talismã varieties, respectively). The IRAP and REMAP analyses revealed a high genetic diversity in the Colletotrichum endophytic isolates and were able to discriminate these isolates from the phytopathogen Colletotrichum lindemuthianum. Fungi from the genus Colletotrichum are abundant in the Phaseolus vulgaris endophytic community, and the IRAP and REMAP markers can be used to rapidly distinguish between C. lindemuthianum and other Colletotrichum members that are frequently found as endophytes. This is the first report of the diversity of endophytic fungi present in the common bean and the use of IRAP and REMAP markers to assess the genetic diversity of endophytic fungi from the genus Colletotrichum. © 2014 The Society for Applied Microbiology.

  11. High efficiency enrichment of low-abundance peptides by novel dual-platform graphene@SiO2@PMMA.

    Science.gov (United States)

    Yin, Peng; Zhao, Man; Deng, Chunhui

    2012-11-21

    For the first time, dual-platform graphene@SiO(2)@poly(methyl methacrylate) (PMMA) material was synthesized, and successfully applied to efficiently enrich low-abundance peptides for mass spectrometry analysis.

  12. Microstructural Changes in High-Protein Nutrition Bars Formulated with Extruded or Toasted Milk Protein Concentrate.

    Science.gov (United States)

    Banach, J C; Clark, S; Lamsal, B P

    2016-02-01

    Milk protein concentrates with more than 80% protein (that is, MPC80) are underutilized as the primary protein source in high-protein nutrition bars as they impart crumbliness and cause hardening during storage. High-protein nutrition bar texture changes are often associated with internal protein aggregations and macronutrient phase separation. These changes were investigated in model high-protein nutrition bars formulated with MPC80 and physically modified MPC80s. High-protein nutrition bars formulated with extruded MPC80s hardened slower than those formulated with toasted or unmodified MPC80. Extruded MPC80 had reduced free sulfhydryl group exposure, whereas measurable increases were seen in the toasted MPC80. High-protein nutrition bar textural performance may be related to the number of exposed free sulfhydryl groups in MPC80. Protein aggregations resulting from ingredient modification and high-protein nutrition bar storage were studied with sodium dodecyl sulfate polyacrylamide gel electrophoresis. Disulfide-based protein aggregations and changes in free sulfhydryl concentration were not consistently relatable to high-protein nutrition bar texture change. However, the high-protein nutrition bars formulated with extruded MPC80 were less prone to phase separations, as depicted by confocal laser scanning microscopy, and underwent less texture change during storage than those formulated with toasted or unmodified MPC80.

  13. Plasma marker proteins associated with the progression of lung cancer in obese mice fed a high-fat diet.

    Science.gov (United States)

    Choi, Jung-Won; Liu, Hao; Song, Hyerim; Park, Jung Han Yoon; Yun, Jong Won

    2012-06-01

    Recent studies have indicated that obesity increases the risk of developing several types of cancers including lung cancer, which is the leading cause of cancer death worldwide. In the present study, we attempted to discover marker proteins associated with lung cancer progression mediated by treatment of a high-fat diet (HFD) using 2DE combined with MALDI-TOF-MS. Image analysis and further statistical analysis allowed for the detection and identification of 14 proteins, which consequently were classified into two groups based on their regulation patterns in response to diet and tumor. Interestingly, the protein abundances of ten proteins exhibited a synergistic effect when treated with HFD in tumor-bearing mice (Group I). Proteins that had a higher abundance in the plasma of tumor-bearing mice included FGB, Tf, Hpx, Cp, and Hp and the proteins that had a lower abundance included A1AT precursor, PON1, TTRt, and α2-M. These proteins can be used as molecular markers that contribute simultaneously to both obesity and cancer. Four other proteins showed an increase (complement C3 and FGA) or decrease (Apo H and AT III precursor) in the only tumor-bearing mice independently of diet (Group II). The marker proteins identified here may lead to the development of new therapeutics for obesity-causative treatment of lung cancer. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Conversion of high and low pollen protein diets into protein in worker honey bees (Hymenoptera: Apidae).

    Science.gov (United States)

    Basualdo, M; Barragán, S; Vanagas, L; García, C; Solana, H; Rodríguez, E; Bedascarrasbure, E

    2013-08-01

    Adequate protein levels are necessary to maintain strong honey bee [Apis mellifera (L.)] colonies. The aim of this study was to quantify how pollens with different crude protein contents influence protein stores within individual honey bees. Caged bees were fed one of three diets, consisting of high-protein-content pollen, low-protein-content pollen, or protein-free diet as control; measurements were made based on protein content in hemolymph and fat body, fat body weight, and body weight. Vitellogenin in hemolymph was also measured. Bees fed with high crude protein diet had significantly higher levels of protein in hemolymph and fat bodies. Caged bees did not increase pollen consumption to compensate for the lower protein in the diet, and ingesting approximately 4 mg of protein per bee could achieve levels of 20 microg/microl protein in hemolymph. Worker bees fed with low crude protein diet took more time in reaching similar protein content of the bees that were fed with high crude protein diet. The data showed that fat bodies and body weight were not efficient methods of measuring the protein status of bees. The determination of total protein or vitellogenin concentration in the hemolymph from 13-d-old bees and protein concentration of fat bodies from 9-d-old bees could be good indicators of nutritional status of honey bees.

  15. Indexing the relative abundance of age-0 white sturgeons in an impoundment of the lower Columbia River from highly skewed trawling data

    Science.gov (United States)

    Counihan, T.D.; Miller, A.I.; Parsley, M.J.

    1999-01-01

    The development of recruitment monitoring programs for age-0 white sturgeons Acipenser transmontanus is complicated by the statistical properties of catch-per-unit-effort (CPUE) data. We found that age-0 CPUE distributions from bottom trawl surveys violated assumptions of statistical procedures based on normal probability theory. Further, no single data transformation uniformly satisfied these assumptions because CPUE distribution properties varied with the sample mean (??(CPUE)). Given these analytic problems, we propose that an additional index of age-0 white sturgeon relative abundance, the proportion of positive tows (Ep), be used to estimate sample sizes before conducting age-0 recruitment surveys and to evaluate statistical hypothesis tests comparing the relative abundance of age-0 white sturgeons among years. Monte Carlo simulations indicated that Ep was consistently more precise than ??(CPUE), and because Ep is binomially rather than normally distributed, surveys can be planned and analyzed without violating the assumptions of procedures based on normal probability theory. However, we show that Ep may underestimate changes in relative abundance at high levels and confound our ability to quantify responses to management actions if relative abundance is consistently high. If data suggest that most samples will contain age-0 white sturgeons, estimators of relative abundance other than Ep should be considered. Because Ep may also obscure correlations to climatic and hydrologic variables if high abundance levels are present in time series data, we recommend ??(CPUE) be used to describe relations to environmental variables. The use of both Ep and ??(CPUE) will facilitate the evaluation of hypothesis tests comparing relative abundance levels and correlations to variables affecting age-0 recruitment. Estimated sample sizes for surveys should therefore be based on detecting predetermined differences in Ep, but data necessary to calculate ??(CPUE) should also be

  16. Globular Cluster Abundances from High-Resolution, Integrated-Light Spectroscopy. IV. The Large Magellanic Cloud: $\\alpha$, Fe-peak, Light, and Heavy Elements

    CERN Document Server

    Colucci, J E; Cameron, S A; McWilliam, A

    2011-01-01

    We present detailed chemical abundances in 8 clusters in the Large Magellanic Cloud (LMC). We measure abundances of 22 elements for clusters spanning a range in age of 0.05 to 12 Gyr, providing a comprehensive picture of the chemical enrichment and star formation history of the LMC. The abundances were obtained from individual absorption lines using a new method for analysis of high resolution ($R\\sim$25,000) integrated light spectra of star clusters. This method was developed and presented in Papers I, II, and III of this series. In this paper, we develop an additional integrated light $\\chi^2$-minimization spectral synthesis technique to facilitate measurement of weak ($\\sim$15 m\\AA) spectral lines and abundances in low signal-to-noise ratio data (S/N$\\sim$30). Additionally, we supplement the integrated light abundance measurements with detailed abundances that we measure for individual stars in the youngest clusters (Age$+0.5$) and increases with decreasing age, indicating a strong contribution of low-meta...

  17. 14‐3‐3‐β and ‐ε contribute to activation of the osmoprotective transcription factor NFAT5 by increasing its protein abundance and its transactivating activity

    Science.gov (United States)

    Izumi, Yuichiro; Burg, Maurice B.; Ferraris, Joan D.

    2014-01-01

    Abstract Having previously found that high NaCl causes rapid exit of 14‐3‐3 isoforms from the nucleus, we used siRNA‐mediated knockdown to test whether 14‐3‐3s contribute to the high NaCl‐induced increase in the activity of the osmoprotective transcription factor NFAT5. We find that, when NaCl is elevated, knockdown of 14‐3‐3‐β and/or 14‐3‐3‐ε decreases NFAT5 transcriptional activity, as assayed both by luciferase reporter and by the mRNA abundance of the NFAT5 target genes aldose reductase and the sodium‐ and chloride‐dependent betaine transporter, BGT1. Knockdown of other 14‐3‐3 isoforms does not significantly affect NFAT5 activity. 14‐3‐3‐β and/or 14‐3‐3‐ε do not act by affecting the nuclear localization of NFAT5, but by at least two other mechanisms: (1) 14‐3‐3‐β and 14‐3‐3‐ε increase protein abundance of NFAT5 and (2) they increase NFAT5 transactivating activity. When NaCl is elevated, knockdown of 14‐3‐3‐β and/or 14‐3‐3‐ε reduces the protein abundance of NFAT5, as measured by Western blot, without affecting the level of NFAT5 mRNA, and the knockdown also decreases NFAT5 transactivating activity, as measured by luciferase reporter. The 14‐3‐3s increase NFAT5 protein, not by increasing its translation, but by decreasing the rate at which it is degraded, as measured by cycloheximide chase. It is not clear at this point whether the 14‐3‐3s affect NFAT5 directly or indirectly through their effects on other proteins that signal activation of NFAT5. PMID:24771694

  18. Pex35 is a regulator of peroxisome abundance

    DEFF Research Database (Denmark)

    Yofe, Ido; Soliman, Kareem; Chuartzman, Silvia G

    2017-01-01

    Peroxisomes are cellular organelles with vital functions in lipid, amino acid, and redox metabolism. The cellular formation and dynamics of peroxisomes are governed by PEX genes, however, the regulation of peroxisome abundance is yet poorly understood. Here we use a high-content microscopy screen...... to identify novel regulators of peroxisome size and abundance. Our screen led to the identification of a previously uncharacterized gene, which we term PEX35, which affects peroxisome abundance. PEX35 encodes a peroxisomal membrane protein, a remote homolog to several curvature generating human proteins. We...

  19. Is a malleable protein necessarily highly dynamic?

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Poulsen, Flemming Martin; Teilum, Kaare

    2012-01-01

    core of NCBD in the ligand-free state and in a well-folded complex with the ligand activator for thyroid hormone and retinoid receptors using multiple NMR methods including methyl chemical shifts, coupling constants, and methyl order parameters. From all NMR measures, the aliphatic side chains...... in the hydrophobic core are slightly more dynamic in the free protein than in the complex, but have mobility comparable to the hydrophobic cores of average folded proteins. Urea titration monitored by NMR reveals that all parts of the protein, including the side-chain packing in the hydrophobic core, denatures...... in a single cooperative process. The molten globule characteristics of NCBD are thus restricted to a slowly fluctuating tertiary structure. Consequently, the conformational plasticity of the protein is most likely related to its low overall stability rather than an intrinsically flexible protein structure...

  20. Rapid and individual-specific glycoprofiling of the low abundance N-glycosylated protein tissue inhibitor of metalloproteinases-1

    DEFF Research Database (Denmark)

    Thaysen-Andersen, Morten; Thøgersen, Ida B.; Nielsen, Hans Jørgen

    2007-01-01

    and immunoaffinity chromatography. The corresponding TIMP-1 glycoprofiles were determined to be highly similar, comprising mainly bi- and triantennary complex oligosaccharides. Additionally it was shown that platelet-derived TIMP-1 displayed a similar glycoprofile. This is the first study to investigate...

  1. Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation

    DEFF Research Database (Denmark)

    Bassani-Sternberg, Michal; Pletscher-Frankild, Sune; Jensen, Lars Juhl

    2015-01-01

    HLA class I molecules reflect the health state of cells to cytotoxic T cells by presenting a repertoire of endogenously derived peptides. However, the extent to which the proteome shapes the peptidome is still largely unknown. Here we present a high-throughput mass-spectrometry-based workflow tha...

  2. Na+/K+-ATPase α1 identified as an abundant protein in the blood-labyrinth barrier that plays an essential role in the barrier integrity.

    Directory of Open Access Journals (Sweden)

    Yue Yang

    Full Text Available The endothelial-blood/tissue barrier is critical for maintaining tissue homeostasis. The ear harbors a unique endothelial-blood/tissue barrier which we term "blood-labyrinth-barrier". This barrier is critical for maintaining inner ear homeostasis. Disruption of the blood-labyrinth-barrier is closely associated with a number of hearing disorders. Many proteins of the blood-brain-barrier and blood-retinal-barrier have been identified, leading to significant advances in understanding their tissue specific functions. In contrast, capillaries in the ear are small in volume and anatomically complex. This presents a challenge for protein analysis studies, which has resulted in limited knowledge of the molecular and functional components of the blood-labyrinth-barrier. In this study, we developed a novel method for isolation of the stria vascularis capillary from CBA/CaJ mouse cochlea and provided the first database of protein components in the blood-labyrinth barrier as well as evidence that the interaction of Na(+/K(+-ATPase α1 (ATP1A1 with protein kinase C eta (PKCη and occludin is one of the mechanisms of loud sound-induced vascular permeability increase.Using a mass-spectrometry, shotgun-proteomics approach combined with a novel "sandwich-dissociation" method, more than 600 proteins from isolated stria vascularis capillaries were identified from adult CBA/CaJ mouse cochlea. The ion transporter ATP1A1 was the most abundant protein in the blood-labyrinth barrier. Pharmacological inhibition of ATP1A1 activity resulted in hyperphosphorylation of tight junction proteins such as occludin which increased the blood-labyrinth-barrier permeability. PKCη directly interacted with ATP1A1 and was an essential mediator of ATP1A1-initiated occludin phosphorylation. Moreover, this identified signaling pathway was involved in the breakdown of the blood-labyrinth-barrier resulting from loud sound trauma.The results presented here provide a novel method for

  3. Highly viscous dough-forming properties of marama protein.

    Science.gov (United States)

    Amonsou, Eric O; Taylor, John R N; Naushad Emmambux, M; Gyebi Duodu, K; Minnaar, Amanda

    2012-10-01

    Marama bean is an indigenous southern African oilseed legume with an unusual protein composition. Hence, its rheological properties were studied. Marama protein formed a highly viscous and extensible dough when compared to soya and gluten. With a dough of 38% moisture, marama protein extensibility was very high (304% of its original length), twice that of gluten and soya, and this increased considerably (>3-fold) when the moisture content was increased to 45%. With added peroxidase, the storage modulus (G') of marama protein dough increased with time, suggesting the formation of new and strong protein networks. Dityrosine crosslinks were detected in the doughs. Marama protein showed a single transition with a denaturation temperature higher than soya glycinin. Marama protein was more hydrophobic and contained more β-sheet structure than did soya. Thus, the highly viscous and extensible rheological behaviour of marama protein is probably related to its high β-sheet conformation, hydrophobic interactions and tyrosine crosslinks.

  4. The physical conditions, metallicity and metal abundance ratios in a highly magnified galaxy at z = 3.6252

    Energy Technology Data Exchange (ETDEWEB)

    Bayliss, Matthew B. [Department of Physics, Harvard University, 17 Oxford Street, Cambridge, MA 02138 (United States); Rigby, Jane R. [Observational Cosmology Lab, NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States); Sharon, Keren; Johnson, Traci [Department of Astronomy, The University of Michigan, 500 Church Street Ann Arbor, MI 48109 (United States); Wuyts, Eva [Max Plank Institute for Extraterrestrial Physics, Gießenbachstrae, D-85741 Garching bei München (Germany); Florian, Michael; Gladders, Michael D. [Department of Astronomy and Astrophysics, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637 (United States); Oguri, Masamune, E-mail: mbayliss@cfa.harvard.edu [Department of Physics, University of Tokyo, Tokyo 113-0033 (Japan)

    2014-08-01

    We present optical and near-IR imaging and spectroscopy of SGAS J105039.6+001730, a strongly lensed galaxy at z = 3.6252 magnified by >30×, and derive its physical properties. We measure a stellar mass of log(M{sub *}/M{sub ☉}) = 9.5 ± 0.35, star formation rates from [O II] λλ3727 and Hβ of 55 ± 25 and 84 ± 24 M{sub ☉} yr{sup –1}, respectively, an electron density of n{sub e} ≤ 10{sup 3} cm{sup –2}, an electron temperature of T{sub e} ≤ 14,000 K, and a metallicity of 12 + log(O/H) = 8.3 ± 0.1. The strong C III] λλ1907,1909 emission and abundance ratios of C, N, O, and Si are consistent with well-studied starbursts at z ∼ 0 with similar metallicities. Strong P Cygni lines and He II λ1640 emission indicate a significant population of Wolf-Rayet stars, but synthetic spectra of individual populations of young, hot stars do not reproduce the observed integrated P Cygni absorption features. The rest-frame UV spectral features are indicative of a young starburst with high ionization, implying either (1) an ionization parameter significantly higher than suggested by rest-frame optical nebular lines, or (2) differences in one or both of the initial mass function and the properties of ionizing spectra of massive stars. We argue that the observed features are likely the result of a superposition of star forming regions with different physical properties. These results demonstrate the complexity of star formation on scales smaller than individual galaxies, and highlight the importance of systematic effects that result from smearing together the signatures of individual star forming regions within galaxies.

  5. High abundances of viruses in a deep-sea hydrothermal vent system indicates viral mediated microbial mortality

    Science.gov (United States)

    Ortmann, Alice C.; Suttle, Curtis A.

    2005-08-01

    Little is known about the distribution and abundance of viruses at deep-sea hydrothermal vents. Based on estimates made using epifluorescence microscopy and the dye YoPro-1, much higher viral abundances were observed at active hydrothermal vents than in the surrounding deep sea. This indicates that viral production was occurring and that viruses were a source of microbial mortality. Samples collected from three actively venting sites (Clam Bed, S&M and Salut) within the Endeavour Ridge system off the west coast of North America had viral abundances ranging from 1.45×10 5 to 9.90×10 7 ml -1, while the abundances of prokaryotes ranged from 1.30×10 5 to 4.46×10 6 ml -1. The abundances of viruses and prokaryotes in samples collected along the neutrally buoyant plume associated with the Main Endeavour Field were lower than at actively venting sites, with a mean of 5.3×10 5 prokaryotes ml -1 (s.d. 2.9×10 5, n=64) and 3.50×10 6 viruses ml -1 (s.d. 1.89×10 6, n=64), but were higher than non-plume samples (2.7×10 5 prokaryotes ml -1, s.d. 5.0×10 4, n=15 and 2.94×10 6 viruses ml -1, s.d. 1.08×10 6, n=15). Prokaryotic and viral abundances in non-hydrothermal regions were as much as 10-fold higher than found in previous studies, in which sample fixation likely resulted in underestimates. This suggests that viral infection may be a greater source of prokaryotic mortality throughout the deep sea than previously recognized. Overall, our results indicate that virus-mediated mortality of prokaryotes at these hydrothermal-vent environments is significant and may reduce energy flow to higher trophic levels.

  6. Fe₃O₄/PVIM-Ni²⁺ magnetic composite microspheres for highly specific separation of histidine-rich proteins.

    Science.gov (United States)

    Zhang, Yuting; Li, Dian; Yu, Meng; Ma, Wanfu; Guo, Jia; Wang, Changchun

    2014-06-11

    Integration of the advantages of immobilized metal-ion affinity chromatography (IMAC) and magnetic microspheres is considered as an ideal pathway for quick and convenient separation of his-tagged proteins, but rare reports concern the natural histidine-rich proteins. In this article, a novel route was presented to fabricate magnetic microspheres composed of a high-magnetic-response magnetic supraparticle (Fe3O4) core and a Ni(2+)-immobilized cross-linked polyvinyl imidazole (PVIM) shell via reflux-precipitation polymerization. The unique as-prepared Fe3O4/PVIM-Ni(2+) microspheres possessed uniform flower-like structure, high magnetic responsiveness, abundant binding sites, and very easy synthesis process. Taking advantage of the pure PVIM-Ni(2+) interface and high Ni(2+) loading amount, the microspheres exhibited remarkable selectivity, excellent sensitivity, large enrichment capacity, and high recyclability in immobilization and separation of his-tagged recombinant proteins. More interestingly, it was found that the Fe3O4/PVIM-Ni(2+) microspheres also showed excellent performance for removal of the natural histidine-rich bovine serum albumin (BSA) from the complex real sample of fetal bovine serum due to the exposed histidine residues. Considering their multiple merits, this new type of Fe3O4/PVIM-Ni(2+) nanomaterial displays great potential in enriching low-abundant his-tagged proteins or removing high-abundant histidine-rich natural proteins for proteomic analysis.

  7. High rabbit abundance proves detrimental to the population growth rate in European rabbit (Oryctolagus cuniculus L. extensive breeding enclosures

    Directory of Open Access Journals (Sweden)

    L. Ruiz-Aizpurua

    2014-09-01

    Full Text Available The European rabbit (Oryctolagus cuniculus L. is a key prey species in Mediterranean ecosystems that has declined in its natural ranges as a result of diseases and loss of habitat. This situation has led to the production of wild rabbits in enclosures in which they can acclimate and breed. The efficiency of these enclosures as extensive breeding systems is defined by their population growth rate (PGR. The aim of this study is to analyse the effect of rabbit abundance on the PGR. This has been done by creating general linear models to explain autumn and spring PGR with the use of rabbit abundance estimates, enclosure size, aerial predation and previous PGR as possible explanatory variables. Rabbit abundance and enclosure size negatively affected the autumn PGR, while only rabbit abundance affected the spring PGR in the best-fit models. It is suggested that maintaining rabbit densities at fewer than 30 rabbits per hectare might help to optimise the efficiency inside enclosures.

  8. High Caloric Diet for ALS Patients: High Fat, High Carbohydrate or High Protein

    Directory of Open Access Journals (Sweden)

    Sarvin Sanaie

    2015-01-01

    Full Text Available ALS is a fatal motor neurodegenerative disease characterized by muscle atrophy and weakness, dysarthria, and dysphagia. The mean survival of ALS patients is three to five years, with 50% of those diagnosed dying within three years of onset (1. A multidisciplinary approach is crucial to set an appropriate plan for metabolic and nutritional support in ALS. Nutritional management incorporates a continuous assessment and implementation of dietary modifications throughout the duration of the disease. The nutritional and metabolic approaches to ALS should start when the diagnosis of ALS is made and should become an integral part of the continuous care to the patient, including nutritional surveillance, dietary counseling, management of dysphagia, and enteral nutrition when needed. Malnutrition and lean body mass loss are frequent findings in ALS patients necessitating comprehensive energy requirement assessment for these patients. Malnutrition is an independent prognostic factor for survival in ALS with a 7.7 fold increase in risk of death. Malnutrition is estimated to develop in one quarter to half of people with ALS (2. Adequate calorie and protein provision would diminish muscle loss in this vulnerable group of patients. Although appropriate amount of energy to be administered is yet to be established, high calorie diet is expected to be effective for potential improvement of survival; ALS patients do not normally receive adequate  intake of energy. A growing number of clinicians suspect that a high calorie diet implemented early in their disease may help people with ALS meet their increased energy needs and extend their survival. Certain high calorie supplements appear to be safe and well tolerated by people with ALS according to studies led by Universitäts klinikum Ulm's and, appear to stabilize body weight within 3 months. In a recent study by Wills et al., intake of high-carbohydrate low-fat supplements has been recommended in ALS patients (3

  9. Targeting Protein-Protein Interactions with Trimeric Ligands: High Affinity Inhibitors of the MAGUK Protein Family

    DEFF Research Database (Denmark)

    Nissen, Klaus B; Kedström, Linda Maria Haugaard; Wilbek, Theis S

    2015-01-01

    PDZ domains in general, and those of PSD-95 in particular, are emerging as promising drug targets for diseases such as ischemic stroke. We have previously shown that dimeric ligands that simultaneously target PDZ1 and PDZ2 of PSD-95 are highly potent inhibitors of PSD-95. However, PSD-95...... of trimeric ligands targeting all three PDZ domains of PSD-95 and the related MAGUK proteins, PSD-93, SAP-97 and SAP-102. Using our dimeric ligands targeting the PDZ1-2 tandem as starting point, we designed novel trimeric ligands by introducing a PDZ3-binding peptide moiety via a cysteine-derivatized NPEG...

  10. Dynamics of a Highly Flexible Protein

    DEFF Research Database (Denmark)

    Andersen, Lisbeth

    Protein dynamics are important for protein function. Especially, dynamics plays an important role in ligand-binding where the induced fit and conformational selection binding mechanisms represent the extremes in a continuum of dynamic mechanisms. The difference between the mechanisms lies......-resolution structures of NCBD in complex with four binding partners are currently known and while three of them are practically identical and resemble the major conformation in the unbound ensemble, one shows NCBD adopting an alternative and markedly different conformation. The mechanisms underlying this conformational...

  11. Two semi-automated computational approaches for spectroscopic analysis of stellar photospheres: detailed characterization at high resolution and abundance determination at medium resolution

    CERN Document Server

    Milone, Andre; Sansom, Anne; Sanchez-Blazquez, Patricia

    2013-01-01

    We report on two distinct computational approaches to self-consistently measure photospheric properties of large samples of stars. Both procedures consist of a set of several semi-integrated tasks based on shell and Python scripts, which efficiently run either our own codes or open source software commonly adopted by the astronomical community. One approach aims to derive the main stellar photospheric parameters and abundances of a few elements by analysing high-resolution spectra from a given public library homogeneously constructed. The other one is applied to recover the abundance of a single element in stars with known photospheric parameters by using mid-resolution spectra from another open homogeneous database and calibrating derived abundances. Both semi-automated computational approaches provide homogeneity and objectivity to every step of the process and represent a fast way to reach partial and final results as well as to estimate measurement errors, making possible to systematically evaluate and im...

  12. Abundances of the elements in sharp-lined early-type stars from IUE high-dispersion spectrograms; 2, the nitrogen deficiency in mercury- manganese stars

    CERN Document Server

    Roby, S W; Adelman, S J

    1999-01-01

    For pt.I see ibid., vol.419, no.1, p.276-85 (1993). The authors determine nitrogen abundances from co-added IUE high-dispersion SWP spectrograms of four HgMn stars and five normal or superficially normal main-sequence B and A stars. They find N deficiencies in the HgMn stars greater than previously reported (depletion factors of 135-400 relative to the Sun). N abundance discrepancies from UV and IR studies of normal stars are discussed in light of possible non-LTE effects. Their data set for their sample of HgMn stars (observed with a consistent strategy to maximize the benefits of co-additions) is an improvement over the single or few images previously used to derive N abundances for most of these stars. (37 refs).

  13. Integrated proteomic and N-glycoproteomic analyses of doxorubicin sensitive and resistant ovarian cancer cells reveal glycoprotein alteration in protein abundance and glycosylation.

    Science.gov (United States)

    Ji, Yanlong; Wei, Shasha; Hou, Junjie; Zhang, Chengqian; Xue, Peng; Wang, Jifeng; Chen, Xiulan; Guo, Xiaojing; Yang, Fuquan

    2017-01-06

    Ovarian cancer is one of the most common cancer among women in the world, and chemotherapy remains the principal treatment for patients. However, drug resistance is a major obstacle to the effective treatment of ovarian cancers and the underlying mechanism is not clear. An increased understanding of the mechanisms that underline the pathogenesis of drug resistance is therefore needed to develop novel therapeutics and diagnostic. Herein, we report the comparative analysis of the doxorubicin sensitive OVCAR8 cells and its doxorubicin-resistant variant NCI/ADR-RES cells using integrated global proteomics and N-glycoproteomics. A total of 1525 unique N-glycosite-containing peptides from 740 N-glycoproteins were identified and quantified, of which 253 N-glycosite-containing peptides showed significant change in the NCI/ADR-RES cells. Meanwhile, stable isotope labeling by amino acids in cell culture (SILAC) based comparative proteomic analysis of the two ovarian cancer cells led to the quantification of 5509 proteins. As about 50% of the identified N-glycoproteins are low-abundance membrane proteins, only 44% of quantified unique N-glycosite-containing peptides had corresponding protein expression ratios. The comparison and calibration of the N-glycoproteome versus the proteome classified 14 change patterns of N-glycosite-containing peptides, including 8 up-regulated N-glycosite-containing peptides with the increased glycosylation sites occupancy, 35 up-regulated N-glycosite-containing peptides with the unchanged glycosylation sites occupancy, 2 down-regulated N-glycosite-containing peptides with the decreased glycosylation sites occupancy, 46 down-regulated N-glycosite-containing peptides with the unchanged glycosylation sites occupancy. Integrated proteomic and N-glycoproteomic analyses provide new insights, which can help to unravel the relationship of N-glycosylation and multidrug resistance (MDR), understand the mechanism of MDR, and discover the new diagnostic and

  14. Development of low-cost technology for the next generation of high efficiency solar cells composed of earth abundant elements

    Energy Technology Data Exchange (ETDEWEB)

    Agrawal, Rakesh [Purdue Univ., West Lafayette, IN (United States)

    2014-09-28

    The development of renewable, affordable, and environmentally conscious means of generating energy on a global scale represents a grand challenge of our time. Due to the “permanence” of radiation from the sun, solar energy promises to remain a viable and sustainable power source far into the future. Established single-junction photovoltaic technologies achieve high power conversion efficiencies (pce) near 20% but require complicated manufacturing processes that prohibit the marriage of large-scale throughput (e.g. on the GW scale), profitability, and quality control. Our approach to this problem begins with the synthesis of nanocrystals of semiconductor materials comprising earth abundant elements and characterized by material and optoelectronic properties ideal for photovoltaic applications, namely Cu2ZnSn(S,Se)4 (CZTSSe). Once synthesized, such nanocrystals are formulated into an ink, coated onto substrates, and processed into completed solar cells in such a way that enables scale-up to high throughput, roll-to-roll manufacturing processes. This project aimed to address the major limitation to CZTSSe solar cell pce’s – the low open-circuit voltage (Voc) reported throughout literature for devices comprised of this material. Throughout the project significant advancements have been made in fundamental understanding of the CZTSSe material and device limitations associated with this material system. Additionally, notable improvements have been made to our nanocrystal based processing technique to alleviate performance limitations due to the identified device limitations. Notably, (1) significant improvements have been made in reducing intra- and inter-nanoparticle heterogeneity, (2) improvements in device performance have been realized with novel cation substitution in Ge-alloyed CZTGeSSe absorbers, (3) systematic analysis of absorber sintering has been conducted to optimize the selenization process for large grain CZTSSe absorbers, (4) novel electrical

  15. Development of low-cost technology for the next generation of high efficiency solar cells composed of earth abundant elements

    Energy Technology Data Exchange (ETDEWEB)

    Agrawal, Rakesh [Purdue Univ., West Lafayette, IN (United States)

    2014-09-28

    The development of renewable, affordable, and environmentally conscious means of generating energy on a global scale represents a grand challenge of our time. Due to the “permanence” of radiation from the sun, solar energy promises to remain a viable and sustainable power source far into the future. Established single-junction photovoltaic technologies achieve high power conversion efficiencies (pce) near 20% but require complicated manufacturing processes that prohibit the marriage of large-scale throughput (e.g. on the GW scale), profitability, and quality control. Our approach to this problem begins with the synthesis of nanocrystals of semiconductor materials comprising earth abundant elements and characterized by material and optoelectronic properties ideal for photovoltaic applications, namely Cu2ZnSn(S,Se)4 (CZTSSe). Once synthesized, such nanocrystals are formulated into an ink, coated onto substrates, and processed into completed solar cells in such a way that enables scale-up to high throughput, roll-to-roll manufacturing processes. This project aimed to address the major limitation to CZTSSe solar cell pce’s – the low open-circuit voltage (Voc) reported throughout literature for devices comprised of this material. Throughout the project significant advancements have been made in fundamental understanding of the CZTSSe material and device limitations associated with this material system. Additionally, notable improvements have been made to our nanocrystal based processing technique to alleviate performance limitations due to the identified device limitations. Notably, (1) significant improvements have been made in reducing intra- and inter-nanoparticle heterogeneity, (2) improvements in device performance have been realized with novel cation substitution in Ge-alloyed CZTGeSSe absorbers, (3) systematic analysis of absorber sintering has been conducted to optimize the selenization process for large grain CZTSSe absorbers, (4) novel electrical

  16. Perturbations of amino acid metabolism associated with glyphosate-dependent inhibition of shikimic acid metabolism affect cellular redox homeostasis and alter the abundance of proteins involved in photosynthesis and photorespiration.

    Science.gov (United States)

    Vivancos, Pedro Diaz; Driscoll, Simon P; Bulman, Christopher A; Ying, Liu; Emami, Kaveh; Treumann, Achim; Mauve, Caroline; Noctor, Graham; Foyer, Christine H

    2011-09-01

    The herbicide glyphosate inhibits the shikimate pathway of the synthesis of amino acids such as phenylalanine, tyrosine, and tryptophan. However, much uncertainty remains concerning precisely how glyphosate kills plants or affects cellular redox homeostasis and related processes in glyphosate-sensitive and glyphosate-resistant crop plants. To address this issue, we performed an integrated study of photosynthesis, leaf proteomes, amino acid profiles, and redox profiles in the glyphosate-sensitive soybean (Glycine max) genotype PAN809 and glyphosate-resistant Roundup Ready Soybean (RRS). RRS leaves accumulated much more glyphosate than the sensitive line but showed relatively few changes in amino acid metabolism. Photosynthesis was unaffected by glyphosate in RRS leaves, but decreased abundance of photosynthesis/photorespiratory pathway proteins was observed together with oxidation of major redox pools. While treatment of a sensitive genotype with glyphosate rapidly inhibited photosynthesis and triggered the appearance of a nitrogen-rich amino acid profile, there was no evidence of oxidation of the redox pools. There was, however, an increase in starvation-associated and defense proteins. We conclude that glyphosate-dependent inhibition of soybean leaf metabolism leads to the induction of defense proteins without sustained oxidation. Conversely, the accumulation of high levels of glyphosate in RRS enhances cellular oxidation, possibly through mechanisms involving stimulation of the photorespiratory pathway.

  17. Implications of high-temperature events and water deficits on protein profiles in wheat (Triticum aestivum L. cv. Vinjett) grain.

    Science.gov (United States)

    Yang, Fen; Jørgensen, Anders D; Li, Huawei; Søndergaard, Ib; Finnie, Christine; Svensson, Birte; Jiang, Dong; Wollenweber, Bernd; Jacobsen, Susanne

    2011-05-01

    Increased climatic variability is resulting in an increase of both the frequency and the magnitude of extreme climate events. Therefore, cereals may be exposed to more than one stress event in the growing season, which may ultimately affect crop yield and quality. Here, effects are reported of interaction of water deficits and/or a high-temperature event (32°C) during vegetative growth (terminal spikelet) with either of these stress events applied during generative growth (anthesis) in wheat. Influence of combinations of stress on protein fractions (albumins, globulins, gliadins and glutenins) in grains and stress-induced changes on the albumin and gliadin proteomes were investigated by 2-DE and MS. The synthesis of individual protein fractions was shown to be affected by both the type and time of the applied stresses. Identified drought or high-temperature-responsive proteins included proteins involved in primary metabolism, storage and stress response such as late embryogenesis abundant proteins, peroxiredoxins and α-amylase/trypsin inhibitors. Several proteins, e.g. heat shock protein and 14-3-3 protein changed in abundance only under multiple high temperatures.

  18. Highly Sensitive Detection of Low-Abundance White Spot Syndrome Virus by a Pre-Amplification PCR Method.

    Science.gov (United States)

    Pan, Xiaoming; Zhang, Yanfang; Sha, Xuejiao; Wang, Jing; Li, Jing; Dong, Ping; Liang, Xingguo

    2017-03-28

    White spot syndrome virus (WSSV) is a major threat to the shrimp farming industry and so far there is no effective therapy for it, and thus early diagnostic of WSSV is of great importance. However, at the early stage of infection, the extremely low-abundance of WSSV DNA challenges the detection sensitivity and accuracy of PCR. To effectively detect low-abundance WSSV, here we developed a pre-amplification PCR (pre-amp PCR) method to amplify trace amounts of WSSV DNA from massive background genomic DNA. Combining with normal specific PCR, 10 copies of target WSSV genes were detected from ~10(10) magnitude of backgrounds. In particular, multiple target genes were able to be balanced amplified with similar efficiency due to the usage of the universal primer. The efficiency of the pre-amp PCR was validated by nested-PCR and quantitative PCR, and pre-amp PCR showed higher efficiency than nested-PCR when multiple targets were detected. The developed method is particularly suitable for the super early diagnosis of WSSV, and has potential to be applied in other low-abundance sample detection cases.

  19. Deuterium abundance and cosmology

    CERN Document Server

    Vidal-Madjar, A; Lemoine, M

    1996-01-01

    We review the status of the measurements of the deuterium abundance from the local interstellar medium to the solar system and high redshifts absorbers toward quasars. We present preliminary results toward a white dwarf and a QSO. We conclude that the deuterium evolution from the Big-Bang to now is still not properly understood.

  20. Carbon Abundances of Three Carbon-Enhanced Metal-Poor Stars from High-Resolution Gemini-S/bHROS Spectra of the 8727A [C I] Line

    CERN Document Server

    Schuler, S C; Sivarani, T; Asplund, M; Smith, V V; Cunha, K; Beers, T C

    2008-01-01

    We present the results from an analysis of the 8727ang forbidden [C I] line in high-resolution Gemini-S/bHROS spectra of three CEMP stars. We find the [C/Fe] ratios based on the [C I] abundances of the two most Fe-rich stars in our sample (HIP 0507-1653: [Fe/H] = -1.42 and HIP 0054-2542: [Fe/H] = -2.66) to be in good agreement with previously determined CH and C_2 line-based values. For the most Fe-deficient star in our sample (HIP 1005-1439: [Fe/H] = -3.08), however, the [C/Fe] ratio is found to be 0.34 dex lower than the published molecular-based value. We have carried out 3D local thermodynamic equilibrium (LTE) calculations for [C I], and the resulting corrections are found to be modest for all three stars, suggesting that the discrepancy between the [C I] and molecular-based C abundances of HIP 1005-1439 is due to more severe 3D effects on the molecular lines. Carbon abundances are also derived from C I high-excitation lines and are found to be 0.45-0.64 dex higher than the [C I]-based abundances. Previo...

  1. Metalloproteomics: High-Throughput Structural and Functional Annotation of Proteins in Structural Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Shi,W.; Zhan, C.; Lgnatov, A.; Manjasetty, B.; Marinkovic, N.; Sullivan, M.; Huang, R.; Chance, M.; Li, H.; et al.

    2005-01-01

    A high-throughput method for measuring transition metal content based on quantitation of X-ray fluorescence signals was used to analyze 654 proteins selected as targets by the New York Structural GenomiX Research Consortium. Over 10% showed the presence of transition metal atoms in stoichiometric amounts; these totals as well as the abundance distribution are similar to those of the Protein Data Bank. Bioinformatics analysis of the identified metalloproteins in most cases supported the metalloprotein annotation; identification of the conserved metal binding motif was also shown to be useful in verifying structural models of the proteins. Metalloproteomics provides a rapid structural and functional annotation for these sequences and is shown to be {approx}95% accurate in predicting the presence or absence of stoichiometric metal content. The project's goal is to assay at least 1 member from each Pfam family; approximately 500 Pfam families have been characterized with respect to transition metal content so far.

  2. High-Resolution Mapping of Protein Concentration Reveals Principles of Proteome Architecture and Adaptation

    Directory of Open Access Journals (Sweden)

    Emmanuel D. Levy

    2014-05-01

    Full Text Available A single yeast cell contains a hundred million protein molecules. How these proteins are organized to orchestrate living processes is a central question in biology. To probe this organization in vivo, we measured the local concentration of proteins based on the strength of their nonspecific interactions with a neutral reporter protein. We first used a cytosolic reporter and measured local concentrations for ∼2,000 proteins in S. cerevisiae, with accuracy comparable to that of mass spectrometry. Localizing the reporter to membranes specifically increased the local concentration measured for membrane proteins. Comparing the concentrations measured by both reporters revealed that encounter frequencies between proteins are primarily dictated by their abundances. However, to change these encounter frequencies and restructure the proteome, as in adaptation, we find that changes in localization have more impact than changes in abundance. These results highlight how protein abundance and localization contribute to proteome organization and reorganization.

  3. Analysis of genetic diversity of the heat shock protein 70 gene on the basis of abundant sequence polymorphisms in chicken breeds.

    Science.gov (United States)

    Gan, J K; Jiang, L Y; Kong, L N; Zhang, X Q; Luo, Q B

    2015-03-06

    This study was designed to detect the sequence variation of the chicken heat shock protein 70 (HSP70) gene. A total of 102 individuals from 8 native Chinese breeds together with Dwarf White Chicken and Red Junglefowl were used to detect sequence variations. The coding regions of the chicken HSP70 gene from 102 individuals were cloned and sequenced. Thirty-six variations were identified, which included 34 single nucleotide polymorphisms and 2 indel mutations. Fifty-seven haplotypes were observed, of which, 43 were breed-specific and 14 were shared. There were 7 Red Junglefowl-specific haplotypes, while Haidong and Silkie only had 2 specific haplotypes. Eleven and 3 haplotypes were shared between and within species, respectively. The variation in nucleotide diversity (Pi) and average number of nucleotide differences (K) among species were consistent. The total Pi of HSP70 was 0.0016, and the total K was 4.1998. The Pi value of Red Junglefowl was the highest (0.0018) and K was 4.8000, while the Pi of Silkie was the lowest (0.0010) and K was 2.5000. These results demonstrated that variation in chicken HSP70 was abundant between and within species.

  4. Manufacture and application of high milk protein powder

    OpenAIRE

    Mistry, Vikram

    2002-01-01

    International audience; A procedure was developed for the production of a high milk protein powder that was rich in both milk proteins, casein and whey proteins, and free of lactose. The method utilized ultrafiltration and diafiltration with no pH adjustment and a relatively low temperature. Spray drying was conducted at low temperatures (120 to 125 °C inlet air temperature, 75 to 80 °C outlet air temperature). The resulting powder contained at least 84% total protein (casein and whey protein...

  5. High prevalence of cestodes in Artemia spp. throughout the annual cycle: relationship with abundance of avian final hosts

    Science.gov (United States)

    Sánchez, Marta I.; Nikolov, Pavel N.; GEorgieva, Darina D.; Georgiev, Boyko B.; Vasileva, Gergana P.; Pankov, Plamen; Paracuellos, Mariano; Lafferty, Kevin D.; Green, Andy J.

    2013-01-01

    Brine shrimp, Artemia spp., act as intermediate hosts for a range of cestode species that use waterbirds as their final hosts. These parasites can have marked influences on shrimp behavior and fecundity, generating the potential for cascading effects in hypersaline food webs. We present the first comprehensive study of the temporal dynamics of cestode parasites in natural populations of brine shrimp throughout the annual cycle. Over a 12-month period, clonal Artemia parthenogenetica were sampled in the Odiel marshes in Huelva, and the sexual Artemia salina was sampled in the Salinas de Cerrillos in Almería. Throughout the year, 4–45 % of A. parthenogenetica were infected with cestodes (mean species richness = 0.26), compared to 27–72 % of A. salina (mean species richness = 0.64). Ten cestode species were recorded. Male and female A. salina showed similar levels of parasitism. The most prevalent and abundant cestodes were those infecting the most abundant final hosts, especially the Greater Flamingo Phoenicopterus ruber. In particular, the flamingo parasite Flamingolepis liguloides had a prevalence of up to 43 % in A. parthenogenetica and 63.5 % in A. salina in a given month. Although there was strong seasonal variation in prevalence, abundance, and intensity of cestode infections, seasonal changes in bird counts were weak predictors of the dynamics of cestode infections. However, infection levels of Confluaria podicipina in A. parthenogenetica were positively correlated with the number of their black-necked grebe Podiceps nigricollis hosts. Similarly, infection levels of Anomotaenia tringae and Anomotaenia microphallos in A. salina were correlated with the number of shorebird hosts present the month before. Correlated seasonal transmission structured the cestode community, leading to more multiple infections than expected by chance.

  6. High prevalence of cestodes in Artemia spp. throughout the annual cycle: relationship with abundance of avian final hosts.

    Science.gov (United States)

    Sánchez, Marta I; Nikolov, Pavel N; Georgieva, Darina D; Georgiev, Boyko B; Vasileva, Gergana P; Pankov, Plamen; Paracuellos, Mariano; Lafferty, Kevin D; Green, Andy J

    2013-05-01

    Brine shrimp, Artemia spp., act as intermediate hosts for a range of cestode species that use waterbirds as their final hosts. These parasites can have marked influences on shrimp behavior and fecundity, generating the potential for cascading effects in hypersaline food webs. We present the first comprehensive study of the temporal dynamics of cestode parasites in natural populations of brine shrimp throughout the annual cycle. Over a 12-month period, clonal Artemia parthenogenetica were sampled in the Odiel marshes in Huelva, and the sexual Artemia salina was sampled in the Salinas de Cerrillos in Almería. Throughout the year, 4-45 % of A. parthenogenetica were infected with cestodes (mean species richness = 0.26), compared to 27-72 % of A. salina (mean species richness = 0.64). Ten cestode species were recorded. Male and female A. salina showed similar levels of parasitism. The most prevalent and abundant cestodes were those infecting the most abundant final hosts, especially the Greater Flamingo Phoenicopterus ruber. In particular, the flamingo parasite Flamingolepis liguloides had a prevalence of up to 43 % in A. parthenogenetica and 63.5 % in A. salina in a given month. Although there was strong seasonal variation in prevalence, abundance, and intensity of cestode infections, seasonal changes in bird counts were weak predictors of the dynamics of cestode infections. However, infection levels of Confluaria podicipina in A. parthenogenetica were positively correlated with the number of their black-necked grebe Podiceps nigricollis hosts. Similarly, infection levels of Anomotaenia tringae and Anomotaenia microphallos in A. salina were correlated with the number of shorebird hosts present the month before. Correlated seasonal transmission structured the cestode community, leading to more multiple infections than expected by chance.

  7. High Ozone (O3) Affects the Fitness Associated with the Microbial Composition and Abundance of Q Biotype Bemisia tabaci

    Science.gov (United States)

    Hong, Yanyun; Yi, Tuyong; Tan, Xiaoling; Zhao, Zihua; Ge, Feng

    2016-01-01

    Ozone (O3) affects the fitness of an insect, such as its development, reproduction and protection against fungal pathogens, but the mechanism by which it does so remains unclear. Here, we compared the fitness (i.e., the growth and development time, reproduction and protection against Beauveria bassiana (B. bassiana) of Q biotype whiteflies fumigated under hO3 (280 ± 20 ppb) and control O3 (50 ± 10 ppb) concentrations. Moreover, we determined that gene expression was related to development, reproduction and immunity to B. bassiana and examined the abundance and composition of bacteria and fungi inside of the body and on the surface of the Q biotype whitefly. We observed a significantly enhanced number of eggs that were laid by a female, shortened developmental time, prolonged adult lifespan, decreased weight of one eclosion, and reduced immunity to B. bassiana in whiteflies under hO3, but hO3 did not significantly affect the expression of genes related to development, reproduction and immunity. However, hO3 obviously changed the composition of the bacterial communities inside of the body and on the surface of the whiteflies, significantly reducing Rickettsia and enhancing Candidatus_Cardinium. Similarly, hO3 significantly enhanced Thysanophora penicillioides from the Trichocomaceae family and reduced Dothideomycetes (at the class level) inside of the body. Furthermore, positive correlations were found between the abundance of Candidatus_Cardinium and the female whitefly ratio and the fecundity of a single female, and positive correlations were found between the abundance of Rickettsia and the weight of adult whiteflies just after eclosion and immunity to B. bassiana. We conclude that hO3 enhances whitefly development and reproduction but impairs immunity to B. bassiana, and our results also suggest that the changes to the microbial environments inside of the body and on the surface could be crucial factors that alter whitefly fitness under hO3. PMID:27799921

  8. HIPPI: highly accurate protein family classification with ensembles of HMMs

    Directory of Open Access Journals (Sweden)

    Nam-phuong Nguyen

    2016-11-01

    Full Text Available Abstract Background Given a new biological sequence, detecting membership in a known family is a basic step in many bioinformatics analyses, with applications to protein structure and function prediction and metagenomic taxon identification and abundance profiling, among others. Yet family identification of sequences that are distantly related to sequences in public databases or that are fragmentary remains one of the more difficult analytical problems in bioinformatics. Results We present a new technique for family identification called HIPPI (Hierarchical Profile Hidden Markov Models for Protein family Identification. HIPPI uses a novel technique to represent a multiple sequence alignment for a given protein family or superfamily by an ensemble of profile hidden Markov models computed using HMMER. An evaluation of HIPPI on the Pfam database shows that HIPPI has better overall precision and recall than blastp, HMMER, and pipelines based on HHsearch, and maintains good accuracy even for fragmentary query sequences and for protein families with low average pairwise sequence identity, both conditions where other methods degrade in accuracy. Conclusion HIPPI provides accurate protein family identification and is robust to difficult model conditions. Our results, combined with observations from previous studies, show that ensembles of profile Hidden Markov models can better represent multiple sequence alignments than a single profile Hidden Markov model, and thus can improve downstream analyses for various bioinformatic tasks. Further research is needed to determine the best practices for building the ensemble of profile Hidden Markov models. HIPPI is available on GitHub at https://github.com/smirarab/sepp .

  9. Microbial community diversities and taxa abundances in soils along a seven-year gradient of potato monoculture using high throughput pyrosequencing approach.

    Directory of Open Access Journals (Sweden)

    Xing Liu

    Full Text Available BACKGROUND: Previous studies have focused on linking soil community structure, diversity, or specific taxa to disturbances. Relatively little attention has been directed to crop monoculture soils, particularly potato monoculture. Information about microbial community changes over time between monoculture and non-monoculture treatments is lacking. Furthermore, few studies have examined microbial communities in potato monoculture soils using a high throughput pyrosequencing approach. METHODOLOGY/PRINCIPAL FINDINGS: Soils along a seven-year gradient of potato monoculture were collected and microbial communities were characterized using high throughput pyrosequencing approach. Principal findings are as follows. First, diversity (H(Shannon and richness (S(Chao1 indices of bacterial community, but not of fungal community, were linearly decreased over time and corresponded to a decline of soil sustainability represented by yield decline and disease incidence increase. Second, Fusarium, the only soilborne pathogen-associated fungal genus substantially detected, was linearly increased over time in abundance and was closely associated with yield decline. Third, Fusarium abundance was negatively correlated with soil organic matter (OM and total nitrogen (TN but positively with electrical conductivity (EC. Fourth, Fusarium was correlated in abundances with 6 bacterial taxa over time. CONCLUSIONS: Soil bacterial and fungal communities exhibited differential responses to the potato monoculture. The overall soil bacterial communities were shaped by potato monoculture. Fusarium was the only soilborne pathogen-associated genus associated with disease incidence increase and yield decline. The changes of soil OM, TN and EC were responsible for Fusarium enrichment, in addition to selections by the monoculture crop. Acidobacteria and Nitrospirae were linearly decreased over time in abundance, corresponding to the decrease of OM, suggesting their similar

  10. Abundances of disk and bulge giants from high-resolution optical spectra. I. O, Mg, Ca, and Ti in the solar neighborhood and Kepler field samples

    Science.gov (United States)

    Jönsson, H.; Ryde, N.; Nordlander, T.; Pehlivan Rhodin, A.; Hartman, H.; Jönsson, P.; Eriksson, K.

    2017-02-01

    Context. The Galactic bulge is an intriguing and significant part of our Galaxy, but it is hard to observe because it is both distant and covered by dust in the disk. Therefore, there are not many high-resolution optical spectra of bulge stars with large wavelength coverage, whose determined abundances can be compared with nearby, similarly analyzed stellar samples. Aims: We aim to determine the diagnostically important alpha elements of a sample of bulge giants using high-resolution optical spectra with large wavelength coverage. The abundances found are compared to similarly derived abundances from similar spectra of similar stars in the local thin and thick disks. In this first paper we focus on the solar neighborhood reference sample. Methods: We used spectral synthesis to derive the stellar parameters as well as the elemental abundances of both the local and bulge samples of giants. We took special care to benchmark our method of determining stellar parameters against independent measurements of effective temperatures from angular diameter measurements and surface gravities from asteroseismology. Results: In this first paper we present the method used to determine the stellar parameters and elemental abundances, evaluate them, and present the results for our local disk sample of 291 giants. Conclusions: When comparing our determined spectroscopic temperatures to those derived from angular diameter measurements, we reproduce these with a systematic difference of +10 K and a standard deviation of 53 K. The spectroscopic gravities reproduce those determined from asteroseismology with a systematic offset of +0.10 dex and a standard deviation of 0.12 dex. When it comes to the abundance trends, our sample of local disk giants closely follows trends found in other works analyzing solar neighborhood dwarfs, showing that the much brighter giant stars are as good abundance probes as the often used dwarfs. Based on observations made with the Nordic Optical Telescope

  11. Globular Cluster Abundances from High-Resolution, Integrated-Light Spectroscopy. II. Expanding the Metallicity Range for Old Clusters and Updated Analysis Techniques

    CERN Document Server

    Colucci, J E; McWilliam, A

    2016-01-01

    We present abundances of globular clusters in the Milky Way and Fornax from integrated light spectra. Our goal is to evaluate the consistency of the integrated light analysis relative to standard abundance analysis for individual stars in those same clusters. This sample includes an updated analysis of 7 clusters from our previous publications and results for 5 new clusters that expand the metallicity range over which our technique has been tested. We find that the [Fe/H] measured from integrated light spectra agrees to $\\sim$0.1 dex for globular clusters with metallicities as high as [Fe/H]=$-0.3$, but the abundances measured for more metal rich clusters may be underestimated. In addition we systematically evaluate the accuracy of abundance ratios, [X/Fe], for Na I, Mg I, Al I, Si I, Ca I, Ti I, Ti II, Sc II, V I, Cr I, Mn I, Co I, Ni I, Cu I, Y II, Zr I, Ba II, La II, Nd II, and Eu II. The elements for which the integrated light analysis gives results that are most similar to analysis of individual stellar ...

  12. reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra

    Science.gov (United States)

    Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R.; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W.; Moritz, Robert L.

    2015-11-01

    Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post-search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the iterations that follow. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website.

  13. reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra.

    Science.gov (United States)

    Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W; Moritz, Robert L

    2015-11-01

    Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post-search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the iterations that follow. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website. Graphical Abstract ᅟ.

  14. A Recalibration of Strong Line Oxygen Abundance Diagnostics via the Direct Method and Implications for the High Redshift Universe

    CERN Document Server

    Brown, Jonathan S; Andrews, Brett H

    2016-01-01

    We use direct method oxygen abundances in combination with strong optical emission lines, stellar masses ($M_{\\star}$), and star formation rates (SFRs) to recalibrate the N2, O3N2, and N2O2 oxygen abundance diagnostics. We stack spectra of $\\sim$200,000 star-forming galaxies from the Sloan Digital Sky Survey in bins of $M_{\\star}$ and SFR offset from the star forming main sequence to measure the weak emission lines needed to apply the direct method. All three new calibrations are reliable to within $\\pm 0.10$ dex from $\\log(M_{\\star}/M_{\\odot}) \\sim 7.5 - 10.5$ and up to at least $200~M_{\\odot}$ yr$^{-1}$ in SFR. The N2O2 diagnostic is the least subject to systematic biases. We apply the diagnostics to galaxies in the local universe and investigate the $M_{\\star}$-$Z$-${\\rm SFR}$ relation. The N2 and O3N2 diagnostics suggest the SFR dependence of the $M_{\\star}$-$Z$-${\\rm SFR}$ relation varies with both $M_{\\star}$ and $\\Delta \\log(SSFR)$, whereas the N2O2 diagnostic suggests a nearly constant dependence on S...

  15. Ultrathin Vein-Like Iridium-Tin Nanowires with Abundant Oxidized Tin as High-Performance Ethanol Oxidation Electrocatalysts.

    Science.gov (United States)

    Zhu, Meiwu; Shao, Qi; Pi, Yecan; Guo, Jun; Huang, Bin; Qian, Yong; Huang, Xiaoqing

    2017-09-01

    Iridium (Ir) holds great promise for ethanol oxidation reaction (EOR), while its practical applications suffer from the limited shape-controlled synthesis due to its low-energy barrier for nucleation. To overcome this limitation, the preparation of a new class of ultrathin vein-like Ir-tin nanowires (IrSn NWs) with abundant oxidized Sn is reported. By tuning the ratio of Ir to Sn, the optimized Ir67 Sn33 /C exhibits the highest mass density of 95.6 mA mg(-1) Ir for EOR at low potential (0.04 V), which is 4.1-fold and 20-fold higher than that of Ir/C and the commercial Pt/C, respectively. It also exhibits the smallest Tafel slope of 153 mV dec(-1) and superior stability after 2 h chronoamperometric measurement. Electrochemical measurements and X-ray photoelectron spectra results confirm that the abundant oxidized Sn promotes a complete oxidization of ethanol into CO2 at low potential. This work highlights the importance of non-noble metal on enhancing the EOR performance. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Abundant immunohistochemical expression of dopamine D2 receptor and p53 protein in meningiomas: follow-up, relation to gender, age, tumor grade, and recurrence

    Directory of Open Access Journals (Sweden)

    G. Trott

    2015-05-01

    Full Text Available Meningiomas are common, usually benign tumors, with a high postoperative recurrence rate. However, the genesis and development of these tumors remain controversial. We aimed to investigate the presence and implications of a mutated p53 protein and dopamine D2 receptor in a representative series of meningiomas and to correlate these findings with age, gender, tumor grade, and recurrence. Tumor tissue samples of 157 patients diagnosed with meningioma (37 males and 120 females, mean age 53.6±14.3 years who underwent surgical resection between 2003 and 2012 at our institution were immunohistochemically evaluated for the presence of p53 protein and dopamine D2 receptor and were followed-up to analyze tumor recurrence or regrowth. Tumors were classified as grades I (n=141, 89.8%, II (n=13, 8.3%, or grade III (n=3, 1.9%. Dopamine D2 receptor and p53 protein expression were positive in 93.6% and 49.7% of the cases, respectively. Neither of the markers showed significant expression differences among different tumor grades or recurrence or regrowth statuses. Our findings highlight the potential role of p53 protein in meningioma development and/or progression. The high positivity of dopamine D2 receptor observed in this study warrants further investigation of the therapeutic potential of dopamine agonists in the evolution of meningiomas.

  17. Abundant immunohistochemical expression of dopamine D{sub 2} receptor and p53 protein in meningiomas: follow-up, relation to gender, age, tumor grade, and recurrence

    Energy Technology Data Exchange (ETDEWEB)

    Trott, G.; Pereira-Lima, J.F.S.; Leães, C.G.S. [Programa de Graduação em Patologia, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS (Brazil); Centro de Neuroendocrinologia, Complexo Hospitalar Santa Casa de Porto Alegre, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS (Brazil); Ferreira, N.P. [Centro de Neuroendocrinologia, Complexo Hospitalar Santa Casa de Porto Alegre, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS (Brazil); Barbosa-Coutinho, L.M. [Programa de Graduação em Patologia, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS (Brazil); Oliveira, M.C. [Programa de Graduação em Patologia, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS (Brazil); Centro de Neuroendocrinologia, Complexo Hospitalar Santa Casa de Porto Alegre, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS (Brazil)

    2015-03-03

    Meningiomas are common, usually benign tumors, with a high postoperative recurrence rate. However, the genesis and development of these tumors remain controversial. We aimed to investigate the presence and implications of a mutated p53 protein and dopamine D{sub 2} receptor in a representative series of meningiomas and to correlate these findings with age, gender, tumor grade, and recurrence. Tumor tissue samples of 157 patients diagnosed with meningioma (37 males and 120 females, mean age 53.6±14.3 years) who underwent surgical resection between 2003 and 2012 at our institution were immunohistochemically evaluated for the presence of p53 protein and dopamine D{sub 2} receptor and were followed-up to analyze tumor recurrence or regrowth. Tumors were classified as grades I (n=141, 89.8%), II (n=13, 8.3%), or grade III (n=3, 1.9%). Dopamine D{sub 2} receptor and p53 protein expression were positive in 93.6% and 49.7% of the cases, respectively. Neither of the markers showed significant expression differences among different tumor grades or recurrence or regrowth statuses. Our findings highlight the potential role of p53 protein in meningioma development and/or progression. The high positivity of dopamine D{sub 2} receptor observed in this study warrants further investigation of the therapeutic potential of dopamine agonists in the evolution of meningiomas.

  18. Categorizing Biases in High-Confidence High-Throughput Protein-Protein Interaction Data Sets

    Science.gov (United States)

    2011-01-01

    Interactions Functional Diversity in Protein Interaction Data Sets—Al- though genomic-scale protein-protein interaction detection campaigns are by design...mapped out in Fig. 2 show that the different data sets covered distinct parts of the interaction space, with some FIG. 1. Functional diversity among

  19. Identification of highly active flocculant proteins in bovine blood.

    Science.gov (United States)

    Piazza, George J; Nuñez, Alberto; Garcia, Rafael A

    2012-03-01

    Synthetic polymeric flocculants are used extensively for wastewater remediation, soil stabilization, and reduction in water leakage from unlined canals. Sources of highly active, inexpensive, renewable flocculants are needed to replace synthetic flocculants. High kaolin flocculant activity was documented for bovine blood (BB) and blood plasma with several anticoagulant treatments. BB serum also had high flocculant activity. To address the hypothesis that some blood proteins have strong flocculating activity, the BB proteins were separated by SEC. Then, the major proteins of the flocculant-active fractions were separated by SDS-PAGE. Identity of the major protein components was determined by tryptic digestion and peptide analysis by MALDI TOF MS. The sequence of selected peptides was confirmed using TOF/TOF-MS/MS fragmentation. Hemoglobin dimer (subunits α and β) was identified as the major protein component of the active fraction in BB; its high flocculation activity was confirmed by testing a commercial sample of hemoglobin. In the same manner, three proteins from blood plasma (fibrinogen, γ-globulin, α-2-macroglobulin) were found to be highly active flocculants, but bovine serum albumin, α-globulin, and β-globulin were not flocculants. On a mass basis, hemoglobin, γ-globulin, α-2-macroglobulin were as effective as anionic polyacrylamide (PAM), a widely used synthetic flocculant. The blood proteins acted faster than PAM, and unlike PAM, the blood proteins flocculants did not require calcium salts for their activity.

  20. Silting up and development of anoxic conditions enhanced by high abundance of the geoengineer species Ophiothrix fragilis

    Science.gov (United States)

    Murat, A.; Méar, Y.; Poizot, E.; Dauvin, J. C.; Beryouni, K.

    2016-04-01

    In the English Channel, the brittle-star Ophiothrix fragilis is a common epifaunal species typically found on pebbles in habitats with strong tidal currents. This species forms dense aggregations on the seafloor, supporting populations that can reach up to 7500 ind m-2 in the eastern part of the Baie de Seine, offshore from Antifer harbour. Here, O. fragilis occurs in an area with unexpected amounts of fine-grained sediment. Some of these mud deposits are made up of unusually compact black muds, an indication of the development of anoxic conditions in surficial sediments. To highlight a potential link between silting up and dense O. fragilis populations, and identify the interactions between environmental conditions and the population dynamics of this species, we analyse the data from three surveys corresponding to exceptional situations: (1) just after a Seine flood; (2) just after a storm and (3) after a period of ten months without any flood or storm. Four parameters are taken into account: number of brittle stars per 0.25 m2, Fine Fraction percentage, Total Organic Carbon and Total Sulphur. The main environmental forcings appear to be Seine river inflow, regional circulation dependent on tidal currents and the occurrence of storms. O. fragilis is able to geoengineer its environment in various ways and at different rates. Silting up is enhanced by increasing abundance of O. fragilis and takes place at a very fast rate. As a result, floods and storms reflecting instantaneous events give rise to a steady-state situation established between the abundance of this species and the fine fraction percentage. Anoxic conditions are dependent on the degradation of organic matter and require more time to be established. After many months in the absence of any disturbing events, anoxic conditions are developed in non-compacted muddy sediments (stability situation) and represent the normal surficial situation when the sediment becomes compacted (compact black muds). The

  1. Globular Cluster Abundances from High-resolution, Integrated-light Spectroscopy. II. Expanding the Metallicity Range for Old Clusters and Updated Analysis Techniques

    Science.gov (United States)

    Colucci, Janet E.; Bernstein, Rebecca A.; McWilliam, Andrew

    2017-01-01

    We present abundances of globular clusters (GCs) in the Milky Way and Fornax from integrated-light (IL) spectra. Our goal is to evaluate the consistency of the IL analysis relative to standard abundance analysis for individual stars in those same clusters. This sample includes an updated analysis of seven clusters from our previous publications and results for five new clusters that expand the metallicity range over which our technique has been tested. We find that the [Fe/H] measured from IL spectra agrees to ∼0.1 dex for GCs with metallicities as high as [Fe/H] = ‑0.3, but the abundances measured for more metal-rich clusters may be underestimated. In addition we systematically evaluate the accuracy of abundance ratios, [X/Fe], for Na i, Mg i, Al i, Si i, Ca i, Ti i, Ti ii, Sc ii, V i, Cr i, Mn i, Co i, Ni i, Cu i, Y ii, Zr i, Ba ii, La ii, Nd ii, and Eu ii. The elements for which the IL analysis gives results that are most similar to analysis of individual stellar spectra are Fe i, Ca i, Si i, Ni i, and Ba ii. The elements that show the greatest differences include Mg i and Zr i. Some elements show good agreement only over a limited range in metallicity. More stellar abundance data in these clusters would enable more complete evaluation of the IL results for other important elements. This paper includes data gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile.

  2. Optimizing high performance computing workflow for protein functional annotation.

    Science.gov (United States)

    Stanberry, Larissa; Rekepalli, Bhanu; Liu, Yuan; Giblock, Paul; Higdon, Roger; Montague, Elizabeth; Broomall, William; Kolker, Natali; Kolker, Eugene

    2014-09-10

    Functional annotation of newly sequenced genomes is one of the major challenges in modern biology. With modern sequencing technologies, the protein sequence universe is rapidly expanding. Newly sequenced bacterial genomes alone contain over 7.5 million proteins. The rate of data generation has far surpassed that of protein annotation. The volume of protein data makes manual curation infeasible, whereas a high compute cost limits the utility of existing automated approaches. In this work, we present an improved and optmized automated workflow to enable large-scale protein annotation. The workflow uses high performance computing architectures and a low complexity classification algorithm to assign proteins into existing clusters of orthologous groups of proteins. On the basis of the Position-Specific Iterative Basic Local Alignment Search Tool the algorithm ensures at least 80% specificity and sensitivity of the resulting classifications. The workflow utilizes highly scalable parallel applications for classification and sequence alignment. Using Extreme Science and Engineering Discovery Environment supercomputers, the workflow processed 1,200,000 newly sequenced bacterial proteins. With the rapid expansion of the protein sequence universe, the proposed workflow will enable scientists to annotate big genome data.

  3. In-situ annotation of carbohydrate diversity, abundance, and degradability in highly complex mixtures using NMR spectroscopy

    DEFF Research Database (Denmark)

    Meier, Sebastian

    2014-01-01

    Many functions of carbohydrates depend on the detection of short structural motifs, approximately up to hexasaccharide length, by receptors or catalysts. This study investigates the usefulness of state-of-the-art 1H–13C nuclear-magnetic-resonance (NMR) spectroscopy for characterizing the diversity......, abundance, and degradability of such short structural motifs in plant-derived carbohydrates. Assignments of carbohydrate signals for 1H–13C NMR spectra of beer, wine, and fruit juice yield up to >130 assignments in situ, i.e. in individual samples without separation or derivatization. More than 500...... structural motifs can be resolved over a concentration range of ~103 in experiments of a few hours duration. The diversity of carbohydrate units increases according to power laws at lower concentrations for both cereal and fruit-derived samples. Simple graphs resolve the smaller overall contribution of more...

  4. Abundance, activity, and diversity of archaeal and bacterial communities in both uncontaminated and highly copper-contaminated marine sediments.

    Science.gov (United States)

    Besaury, Ludovic; Ghiglione, Jean-François; Quillet, Laurent

    2014-04-01

    We analyzed the impact of copper mine tailing discharges on benthic Archaea and Bacteria around the city of Chanaral in northern Chile. Quantitative PCR (Q-PCR) showed that the bacteria dominated the prokaryotic community at both sites, but only the bacteria showed a decrease in abundance in the copper-contaminated site. Q-PCR on reverse transcripts indicated a higher activity of both bacterial and archaeal communities in the contaminated site, suggesting an adaptation of the two communities to copper. This hypothesis was reinforced by the concomitant augmentation of the copper-resistant copA gene coding for a P-type ATP-ase pump in the contaminated site. The metabolically active bacterial community of the contaminated site was dominated by Gammaproteobacteria related to Ectothiorhodospiraceae and Chromatiaceae and by Alphaproteobacteria phylum related to Rhodobacteraceae. The metabolically active archaeal community was dominated by one lineage belonging to unclassified Euryarchaeota and to methanogenic Archaea.

  5. High dietary protein intake, reducing or eliciting insulin resistance?

    NARCIS (Netherlands)

    Rietman, A.; Schwarz, J.; Tome, D.; Kok, F.J.; Mensink, M.R.

    2014-01-01

    Dietary proteins have an insulinotropic effect and thus promote insulin secretion, which indeed leads to enhanced glucose clearance from the blood. In the long term, however, a high dietary protein intake is associated with an increased risk of type 2 diabetes. Moreover, branched-chain amino acids (

  6. High dietary protein intake, reducing or eliciting insulin resistance?

    NARCIS (Netherlands)

    Rietman, A.; Schwarz, J.; Tome, D.; Kok, F.J.; Mensink, M.R.

    2014-01-01

    Dietary proteins have an insulinotropic effect and thus promote insulin secretion, which indeed leads to enhanced glucose clearance from the blood. In the long term, however, a high dietary protein intake is associated with an increased risk of type 2 diabetes. Moreover, branched-chain amino acids

  7. A highly efficient pipeline for protein expression in Leishmania tarentolae using infrared fluorescence protein as marker

    Directory of Open Access Journals (Sweden)

    Mueller-Roeber Bernd

    2010-05-01

    . The facile in-cell and in-gel detection tools built on IFP make Leishmania amenable for high-throughput expression of proteins from plant and animal sources.

  8. Automated High Throughput Protein Crystallization Screening at Nanoliter Scale and Protein Structural Study on Lactate Dehydrogenase

    Energy Technology Data Exchange (ETDEWEB)

    Li, Fenglei [Iowa State Univ., Ames, IA (United States)

    2006-08-09

    The purposes of our research were: (1) To develop an economical, easy to use, automated, high throughput system for large scale protein crystallization screening. (2) To develop a new protein crystallization method with high screening efficiency, low protein consumption and complete compatibility with high throughput screening system. (3) To determine the structure of lactate dehydrogenase complexed with NADH by x-ray protein crystallography to study its inherent structural properties. Firstly, we demonstrated large scale protein crystallization screening can be performed in a high throughput manner with low cost, easy operation. The overall system integrates liquid dispensing, crystallization and detection and serves as a whole solution to protein crystallization screening. The system can dispense protein and multiple different precipitants in nanoliter scale and in parallel. A new detection scheme, native fluorescence, has been developed in this system to form a two-detector system with a visible light detector for detecting protein crystallization screening results. This detection scheme has capability of eliminating common false positives by distinguishing protein crystals from inorganic crystals in a high throughput and non-destructive manner. The entire system from liquid dispensing, crystallization to crystal detection is essentially parallel, high throughput and compatible with automation. The system was successfully demonstrated by lysozyme crystallization screening. Secondly, we developed a new crystallization method with high screening efficiency, low protein consumption and compatibility with automation and high throughput. In this crystallization method, a gas permeable membrane is employed to achieve the gentle evaporation required by protein crystallization. Protein consumption is significantly reduced to nanoliter scale for each condition and thus permits exploring more conditions in a phase diagram for given amount of protein. In addition

  9. Filtering high-throughput protein-protein interaction data using a combination of genomic features

    Directory of Open Access Journals (Sweden)

    Patil Ashwini

    2005-04-01

    Full Text Available Abstract Background Protein-protein interaction data used in the creation or prediction of molecular networks is usually obtained from large scale or high-throughput experiments. This experimental data is liable to contain a large number of spurious interactions. Hence, there is a need to validate the interactions and filter out the incorrect data before using them in prediction studies. Results In this study, we use a combination of 3 genomic features – structurally known interacting Pfam domains, Gene Ontology annotations and sequence homology – as a means to assign reliability to the protein-protein interactions in Saccharomyces cerevisiae determined by high-throughput experiments. Using Bayesian network approaches, we show that protein-protein interactions from high-throughput data supported by one or more genomic features have a higher likelihood ratio and hence are more likely to be real interactions. Our method has a high sensitivity (90% and good specificity (63%. We show that 56% of the interactions from high-throughput experiments in Saccharomyces cerevisiae have high reliability. We use the method to estimate the number of true interactions in the high-throughput protein-protein interaction data sets in Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens to be 27%, 18% and 68% respectively. Our results are available for searching and downloading at http://helix.protein.osaka-u.ac.jp/htp/. Conclusion A combination of genomic features that include sequence, structure and annotation information is a good predictor of true interactions in large and noisy high-throughput data sets. The method has a very high sensitivity and good specificity and can be used to assign a likelihood ratio, corresponding to the reliability, to each interaction.

  10. Abundances of iron-binding photosynthetic and nitrogen-fixing proteins of Trichodesmium both in culture and in situ from the North Atlantic.

    Directory of Open Access Journals (Sweden)

    Sophie Richier

    Full Text Available Marine cyanobacteria of the genus Trichodesmium occur throughout the oligotrophic tropical and subtropical oceans, where they can dominate the diazotrophic community in regions with high inputs of the trace metal iron (Fe. Iron is necessary for the functionality of enzymes involved in the processes of both photosynthesis and nitrogen fixation. We combined laboratory and field-based quantifications of the absolute concentrations of key enzymes involved in both photosynthesis and nitrogen fixation to determine how Trichodesmium allocates resources to these processes. We determined that protein level responses of Trichodesmium to iron-starvation involve down-regulation of the nitrogen fixation apparatus. In contrast, the photosynthetic apparatus is largely maintained, although re-arrangements do occur, including accumulation of the iron-stress-induced chlorophyll-binding protein IsiA. Data from natural populations of Trichodesmium spp. collected in the North Atlantic demonstrated a protein profile similar to iron-starved Trichodesmium in culture, suggestive of acclimation towards a minimal iron requirement even within an oceanic region receiving a high iron-flux. Estimates of cellular metabolic iron requirements are consistent with the availability of this trace metal playing a major role in restricting the biomass and activity of Trichodesmium throughout much of the subtropical ocean.

  11. Development of gel-filter method for high enrichment of low-molecular weight proteins from serum.

    Directory of Open Access Journals (Sweden)

    Lingsheng Chen

    Full Text Available The human serum proteome has been extensively screened for biomarkers. However, the large dynamic range of protein concentrations in serum and the presence of highly abundant and large molecular weight proteins, make identification and detection changes in the amount of low-molecular weight proteins (LMW, molecular weight ≤ 30kDa difficult. Here, we developed a gel-filter method including four layers of different concentration of tricine SDS-PAGE-based gels to block high-molecular weight proteins and enrich LMW proteins. By utilizing this method, we identified 1,576 proteins (n = 2 from 10 μL serum. Among them, 559 (n = 2 proteins belonged to LMW proteins. Furthermore, this gel-filter method could identify 67.4% and 39.8% more LMW proteins than that in representative methods of glycine SDS-PAGE and optimized-DS, respectively. By utilizing SILAC-AQUA approach with labeled recombinant protein as internal standard, the recovery rate for GST spiked in serum during the treatment of gel-filter, optimized-DS, and ProteoMiner was 33.1 ± 0.01%, 18.7 ± 0.01% and 9.6 ± 0.03%, respectively. These results demonstrate that the gel-filter method offers a rapid, highly reproducible and efficient approach for screening biomarkers from serum through proteomic analyses.

  12. Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species.

    Directory of Open Access Journals (Sweden)

    Albert Lee

    2008-12-01

    Full Text Available A complete description of the transcriptome of an organism is crucial for a comprehensive understanding of how it functions and how its transcriptional networks are controlled, and may provide insights into the organism's evolution. Despite the status of Saccharomyces cerevisiae as arguably the most well-studied model eukaryote, we still do not have a full catalog or understanding of all its genes. In order to interrogate the transcriptome of S. cerevisiae for low abundance or rapidly turned over transcripts, we deleted elements of the RNA degradation machinery with the goal of preferentially increasing the relative abundance of such transcripts. We then used high-resolution tiling microarrays and ultra high-throughput sequencing (UHTS to identify, map, and validate unannotated transcripts that are more abundant in the RNA degradation mutants relative to wild-type cells. We identified 365 currently unannotated transcripts, the majority presumably representing low abundance or short-lived RNAs, of which 185 are previously unknown and unique to this study. It is likely that many of these are cryptic unstable transcripts (CUTs, which are rapidly degraded and whose function(s within the cell are still unclear, while others may be novel functional transcripts. Of the 185 transcripts we identified as novel to our study, greater than 80 percent come from regions of the genome that have lower conservation scores amongst closely related yeast species than 85 percent of the verified ORFs in S. cerevisiae. Such regions of the genome have typically been less well-studied, and by definition transcripts from these regions will distinguish S. cerevisiae from these closely related species.

  13. High dietary protein decreases fat deposition induced by high-fat and high-sucrose diet in rats

    NARCIS (Netherlands)

    Chaumontet, C.; Schwarz, J.; Even, P.C.; Simonin-Foucault, A.; Piedcoq, J.; Fromentin, G.; Azzout-Marniche, D.; Tome, D.

    2015-01-01

    High-protein diets are known to reduce adiposity in the context of high carbohydrate and Western diets. However, few studies have investigated the specific high-protein effect on lipogenesis induced by a high-sucrose (HS) diet or fat deposition induced by high-fat feeding. We aimed to determine the

  14. Reverse Phase Protein Arrays for High-Throughput Protein Measurements in Mammospheres

    DEFF Research Database (Denmark)

    Pedersen, Marlene Lemvig; Block, Ines; List, Markus

    Protein Array (RPPA)-based readout format integrated into robotic siRNA screening. This technique would allow post-screening high-throughput quantification of protein changes. Recently, breast cancer stem cells (BCSCs) have attracted much attention, as a tumor- and metastasis-driving subpopulation...

  15. Haptoglobin-related protein is a high-affinity hemoglobin-binding plasma protein

    DEFF Research Database (Denmark)

    Nielsen, Marianne Jensby; Petersen, Steen Vang; Jacobsen, Christian

    2006-01-01

    Haptoglobin-related protein (Hpr) is a primate-specific plasma protein associated with apolipoprotein L-I (apoL-I)-containing high-density lipoprotein (HDL) particles shown to be a part of the innate immune defense. Despite the assumption hitherto that Hpr does not bind to hemoglobin, the present...

  16. High resolution study of the abundance pattern of the heavy elements in very metal-poor field stars

    CERN Document Server

    Spite, Monique

    2013-01-01

    The abundances of heavy elements in EMP stars are not well explained by the simple view of an initial basic "rapid" process. In a careful and homogeneous analysis of the "First stars" sample (eighty per cent of the stars have a metallicity [Fe/H]=-3.1$\\pm$0.4), it has been shown that at this metallicity [Eu/Ba] is constant, and therefore the Eu-rich stars (generally called "r-rich") are also Ba-rich. The very large variation of [Ba/Fe] (existence of "r-poor" and "r-rich" stars) induces that the early matter was not perfectly mixed. On the other hand, the distribution of the values of [Sr/Ba] vs. [Ba/Fe] appears with well defined upper and lower envelopes. No star was found with [Sr/Ba]<-0.5 and the scatter of [Sr/Ba] increases regularly when [Ba/Fe] decreases. To explain this behavior, we suggest that an early "additional" process forming mainly first peak elements would affect the initial composition of the matter. For a same quantity of accreted matter, this additional Sr production would barely affect t...

  17. The Physical Conditions, Metallicity and Metal Abundance Ratios In a Highly Magnified Galaxy at z = 3.6252

    CERN Document Server

    Bayliss, Matthew B; Sharon, Keren; Wuyts, Eva; Florian, Michael; Gladders, Michael D; Johnson, Traci; Oguri, Masamune

    2013-01-01

    We present optical and near-IR imaging and spectroscopy of SGAS J105039.6$+$001730, a strongly lensed galaxy at z $=$ 3.6252 magnified by $>$30$\\times$, and derive its physical properties. We measure a stellar mass of log(M$_{*}$/M$_{\\odot}$) $=$ 9.5 $\\pm$ 0.35, star formation rates from [O II]$\\lambda$$\\lambda$3727 and H-$\\beta$ of 55 $\\pm$ 20 and 84 $\\pm$ 17 M$_{\\odot}$ yr$^{-1}$, respectively, an electron density of n$_{e} \\leq$ 10$^{3}$ cm$^{-2}$, an electron temperature of T$_{e} \\leq$ 14000 K, and a metallicity of 12+log(O/H) $=$ 8.3 $\\pm$ 0.1. The strong C III]$\\lambda$$\\lambda$1907,1909 emission and abundance ratios of C, N, O and Si are consistent with well-studied starbursts at z $\\sim$ 0 with similar metallicities. Strong P Cygni lines and He II$\\lambda$1640 emission indicate a significant population of Wolf-Rayet stars, but synthetic spectra of individual populations of young, hot stars do not reproduce the observed integrated P Cygni absorption features. The rest-frame UV spectral features are in...

  18. Neutron-capture element abundances in the planetary nebula NGC 5315 from deep high-resolution optical and near-IR spectrophotometry

    CERN Document Server

    Madonna, S; Sterling, N C; Luridiana, V

    2016-01-01

    We have done a spectroscopical analysis of the type I planetary nebula (PN) NGC 5315, through high-resolution (R$\\sim$40000) optical spectroscopy with UVES at the 8.2m Very Large Telescope, and medium-resolution (R$\\sim$4800) near-IR spectroscopy with FIRE at the 6.5m Magellan Baade telescope, covering a wide spectral range from 0.31 $\\mu$m to 2.50 $\\mu$m. The main aim of this work is to investigate the slow neutron(n)-capture process (the s-process) in the Asymptotic Giant Branch (AGB) star progenitor of a type I PNe. We detected and identified about 700 features, including lines from the n-capture elements Kr, Se, and possibly Br and Xe. We compute physical conditions using line ratios of common ions. Ionic abundances are computed for the species with available atomic data. We calculate total abundances using recent ionization correction factors (ICFs) or by summing ionic abundances. Our results for common elements are in good agreement with previous works on the same object. We do not find a substantial s-...

  19. Neutron-capture element abundances in the planetary nebula NGC 5315 from deep high-resolution optical and near-IR spectrophotometry

    Science.gov (United States)

    Madonna, S.; García-Rojas, J.; Sterling, N. C.; Luridiana, V.

    2017-03-01

    We have done a spectroscopical analysis of the type I planetary nebula (PN) NGC 5315, through high-resolution (R ˜ 40000) optical spectroscopy with UVES at the 8.2m Very Large Telescope, and medium-resolution (R ˜ 4800) near-IR spectroscopy with FIRE at the 6.5m Magellan Baade telescope, covering a wide spectral range from 0.31 μm to 2.50μm. The main aim of this work is to investigate the slow neutron(n)-capture process (the s-process) in the Asymptotic Giant Branch (AGB) star progenitor of a type I PNe. We detected and identified about 700 features, including lines from the n-capture elements Kr, Se, and possibly Br and Xe. We compute physical conditions using line ratios of common ions. Ionic abundances are computed for the species with available atomic data. We calculate total abundances using recent ionization correction factors (ICFs) or by summing ionic abundances. Our results for common elements are in good agreement with previous works on the same object. We do not find a substantial s-process enrichment in NGC 5315, which is typical for type I PNe.

  20. Abiotic stress induces change in Cinnamoyl CoA Reductase (CCR) protein abundance and lignin deposition in developing seedlings of Leucaena leucocephala.

    Science.gov (United States)

    Srivastava, Sameer; Vishwakarma, Rishi K; Arafat, Yasir Ali; Gupta, Sushim K; Khan, Bashir M

    2015-04-01

    Aboitic stress such as drought and salinity are class of major threats, which plants undergo through their lifetime. Lignin deposition is one of the responses to such abiotic stresses. The gene encoding Cinnamoyl CoA Reductase (CCR) is a key gene for lignin biosynthesis, which has been shown to be over-expressed under stress conditions. In the present study, developing seedlings of Leucaena leucocephala (Vernacular name: Subabul, White popinac) were treated with 1 % mannitol and 200 mM NaCl to mimic drought and salinity stress conditions, respectively. Enzyme linked immunosorbant assay (ELISA) based expression pattern of CCR protein was monitored coupled with Phlorogucinol/HCl activity staining of lignin in transverse sections of developing L. leucocephala seedlings under stress. Our result suggests a differential lignification pattern in developing root and stem under stress conditions. Increase in lignification was observed in mannitol treated stems and corresponding CCR protein accumulation was also higher than control and salt stress treated samples. On the contrary CCR protein was lower in NaCl treated stems and corresponding lignin deposition was also low. Developing root tissue showed a high level of CCR content and lignin deposition than stem samples under all conditions tested. Overall result suggested that lignin accumulation was not affected much in case of developing root however developing stems were significantly affected under drought and salinity stress condition.

  1. Integrated and comparative proteomics of high-oil and high-protein soybean seeds.

    Science.gov (United States)

    Xu, Xiu Ping; Liu, Hui; Tian, Lihong; Dong, Xiang Bai; Shen, Shi Hua; Qu, Le Qing

    2015-04-01

    We analysed the global protein expression in seeds of a high-oil soybean cultivar (Jiyu 73, JY73) by proteomics. More than 700 protein spots were detected and 363 protein spots were successfully identified. Comparison of the protein profile of JY73 with that of a high-protein cultivar (Zhonghuang 13, ZH13) revealed 40 differentially expressed proteins, including oil synthesis, redox/stress, hydrolysis and storage-related proteins. All redox/stress proteins were less or not expressed in JY73, whereas the expression of the major storage proteins, nitrogen and carbon metabolism-related proteins was higher in ZH13. Biochemical analysis of JY73 revealed that it was in a low oxidation state, with a high content of polyunsaturated fatty acids and vitamin E. Vitamin E was more active than antioxidant enzymes and protected the soybean seed in a lower oxidation state. The characteristics of high oil and high protein in soybean, we revealed, might provide a reference for soybean nutrition and soybean breeding.

  2. Structural evidence for solvent-stabilisation by aspartic acid as a mechanism for halophilic protein stability in high salt concentrations.

    Science.gov (United States)

    Lenton, Samuel; Walsh, Danielle L; Rhys, Natasha H; Soper, Alan K; Dougan, Lorna

    2016-07-21

    Halophilic organisms have adapted to survive in high salt environments, where mesophilic organisms would perish. One of the biggest challenges faced by halophilic proteins is the ability to maintain both the structure and function at molar concentrations of salt. A distinct adaptation of halophilic proteins, compared to mesophilic homologues, is the abundance of aspartic acid on the protein surface. Mutagenesis and crystallographic studies of halophilic proteins suggest an important role for solvent interactions with the surface aspartic acid residues. This interaction, between the regions of the acidic protein surface and the solvent, is thought to maintain a hydration layer around the protein at molar salt concentrations thereby allowing halophilic proteins to retain their functional state. Here we present neutron diffraction data of the monomeric zwitterionic form of aspartic acid solutions at physiological pH in 0.25 M and 2.5 M concentration of potassium chloride, to mimic mesophilic and halophilic-like environmental conditions. We have used isotopic substitution in combination with empirical potential structure refinement to extract atomic-scale information from the data. Our study provides structural insights that support the hypothesis that carboxyl groups on acidic residues bind water more tightly under high salt conditions, in support of the residue-ion interaction model of halophilic protein stabilisation. Furthermore our data show that in the presence of high salt the self-association between the zwitterionic form of aspartic acid molecules is reduced, suggesting a possible mechanism through which protein aggregation is prevented.

  3. Potential interaction between warfarin and high dietary protein intake.

    Science.gov (United States)

    Hornsby, Lori B; Hester, E Kelly; Donaldson, Amy R

    2008-04-01

    A 55-year-old Caucasian man was receiving warfarin therapy after undergoing aortic valve replacement. His international normalized ratio (INR) was stabilized with warfarin 95 mg/week for 5 weeks. Commencement of a low-carbohydrate, high-protein diet resulted in a series of subtherapeutic INRs that led to a 16% increase in the dosage requirement to maintain therapeutic INRs. After the patient discontinued the diet, his INR increased, and several dosage reductions were required until his INR stabilized with his original dosage of 95 mg/week. Two additional case reports have described a possible interaction between warfarin and a high-protein diet. The potential for increased dietary protein intake to raise serum albumin levels and/or cytochrome P450 activity has been postulated as mechanisms for the resulting decrease in INRs. Given the available animal and human data that demonstrate alterations in drug metabolism in the presence of altered dietary protein intake, an increase in warfarin metabolism due to cytochrome P450 activation appears to be the most likely cause. In addition to the previously reported cases, this case indicates a potential interaction between warfarin and a high-protein diet. Because of the popularity of high-protein diets and because of the risks associated with inadequate or excessive warfarin anticoagulation, patients and health care providers should be aware of this interaction to ensure appropriate monitoring when warranted.

  4. High-resolution mapping of protein sequence-function relationships.

    Science.gov (United States)

    Fowler, Douglas M; Araya, Carlos L; Fleishman, Sarel J; Kellogg, Elizabeth H; Stephany, Jason J; Baker, David; Fields, Stanley

    2010-09-01

    We present a large-scale approach to investigate the functional consequences of sequence variation in a protein. The approach entails the display of hundreds of thousands of protein variants, moderate selection for activity and high-throughput DNA sequencing to quantify the performance of each variant. Using this strategy, we tracked the performance of >600,000 variants of a human WW domain after three and six rounds of selection by phage display for binding to its peptide ligand. Binding properties of these variants defined a high-resolution map of mutational preference across the WW domain; each position had unique features that could not be captured by a few representative mutations. Our approach could be applied to many in vitro or in vivo protein assays, providing a general means for understanding how protein function relates to sequence.

  5. Global Geometric Affinity for Revealing High Fidelity Protein Interaction Network

    Science.gov (United States)

    Fang, Yi; Benjamin, William; Sun, Mengtian; Ramani, Karthik

    2011-01-01

    Protein-protein interaction (PPI) network analysis presents an essential role in understanding the functional relationship among proteins in a living biological system. Despite the success of current approaches for understanding the PPI network, the large fraction of missing and spurious PPIs and a low coverage of complete PPI network are the sources of major concern. In this paper, based on the diffusion process, we propose a new concept of global geometric affinity and an accompanying computational scheme to filter the uncertain PPIs, namely, reduce the spurious PPIs and recover the missing PPIs in the network. The main concept defines a diffusion process in which all proteins simultaneously participate to define a similarity metric (global geometric affinity (GGA)) to robustly reflect the internal connectivity among proteins. The robustness of the GGA is attributed to propagating the local connectivity to a global representation of similarity among proteins in a diffusion process. The propagation process is extremely fast as only simple matrix products are required in this computation process and thus our method is geared toward applications in high-throughput PPI networks. Furthermore, we proposed two new approaches that determine the optimal geometric scale of the PPI network and the optimal threshold for assigning the PPI from the GGA matrix. Our approach is tested with three protein-protein interaction networks and performs well with significant random noises of deletions and insertions in true PPIs. Our approach has the potential to benefit biological experiments, to better characterize network data sets, and to drive new discoveries. PMID:21559288

  6. Abundance and diversity of bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants revealed by high-throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Zhu Wang

    Full Text Available Biological nitrification/denitrification is frequently used to remove nitrogen from tannery wastewater containing high concentrations of ammonia. However, information is limited about the bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants (WWTPs due to the low-throughput of the previously used methods. In this study, 454 pyrosequencing and Illumina high-throughput sequencing, combined with molecular methods, were used to comprehensively characterize structures and functions of nitrification and denitrification bacterial communities in aerobic and anaerobic sludge of two full-scale tannery WWTPs. Pyrosequencing of 16S rRNA genes showed that Proteobacteria and Synergistetes dominated in the aerobic and anaerobic sludge, respectively. Ammonia-oxidizing bacteria (AOB amoA gene cloning revealed that Nitrosomonas europaea dominated the ammonia-oxidizing community in the WWTPs. Metagenomic analysis showed that the denitrifiers mainly included the genera of Thauera, Paracoccus, Hyphomicrobium, Comamonas and Azoarcus, which may greatly contribute to the nitrogen removal in the two WWTPs. It is interesting that AOB and ammonia-oxidizing archaea had low abundance although both WWTPs demonstrated high ammonium removal efficiency. Good correlation between the qPCR and metagenomic analysis is observed for the quantification of functional genes amoA, nirK, nirS and nosZ, indicating that the metagenomic approach may be a promising method used to comprehensively investigate the abundance of functional genes of nitrifiers and denitrifiers in the environment.

  7. Molecular Characterization of Aquaporin 1 and Aquaporin 3 from the Gills of the African Lungfish, Protopterus annectens, and Changes in Their Branchial mRNA Expression Levels and Protein Abundance during Three Phases of Aestivation.

    Science.gov (United States)

    Chng, You R; Ong, Jasmine L Y; Ching, Biyun; Chen, Xiu L; Hiong, Kum C; Wong, Wai P; Chew, Shit F; Lam, Siew H; Ip, Yuen K

    2016-01-01

    African lungfishes can undergo long periods of aestivation on land during drought. During aestivation, lungfishes are confronted with desiccation and dehydration, and their gills become non-functional and covered with a thick layer of dried mucus. Aquaporins (Aqps) are a superfamily of integral membrane proteins which generally facilitate the permeation of water through plasma membranes. This study aimed to obtain the complete cDNA coding sequences of aqp1 and aqp3 from the gills of Protopterus annectens, and to determine their branchial mRNA and protein expression levels during the induction, maintenance and arousal phases of aestivation. Dendrogramic analyses of the deduced Aqp1 and Aqp3 amino acid sequences of P. annectens revealed their close relationships with those of Latimeria chalumnae and tetrapods. During the induction phase, there were significant decreases in the transcript levels of aqp1 and aqp3 in the gills of P. annectens, but the branchial Aqp1 and Aqp3 protein abundance remained unchanged. As changes in transcription might precede changes in translation, this could be regarded as an adaptive response to decrease the protein abundance of Aqp1 and Aqp3 in the subsequent maintenance phase of aestivation. As expected, the branchial transcript levels and protein abundance of aqp1/Aqp1 and aqp3/Aqp3 were significantly down-regulated during the maintenance phase, probably attributable to the shutdown of branchial functions and the cessation of volume regulation of branchial epithelial cells. Additionally, these changes could reduce the loss of water through branchial epithelial surfaces, supplementing the anti-desiccating property of the dried mucus. Upon arousal, it was essential for the lungfish to restore branchial functions. Indeed, the protein abundance of Aqp1 recovered partially, with complete recovery of mRNA expression level and protein abundance of Aqp3, in the gills of P. annectens after 3 days of arousal. These results provide insights into

  8. Molecular characterization of aquaporin 1 and aquaporin 3 from the gills of the African lungfish, Protopterus annectens, and changes in their branchial mRNA expression levels and protein abundance during three phases of aestivation

    Directory of Open Access Journals (Sweden)

    You R. Chng

    2016-11-01

    Full Text Available African lungfishes can undergo long periods of aestivation on land during drought. During aestivation, lungfishes are confronted with desiccation and dehydration, and their gills become non-functional and covered with a thick layer of dried mucus. Aquaporins (Aqps are a superfamily of integral membrane proteins which generally facilitate the permeation of water through plasma membranes. This study aimed to obtain the complete cDNA coding sequences of aqp1 and aqp3 from the gills of Protopterus annectens, and to determine their branchial mRNA and protein expression levels during the induction, maintenance and arousal phases of aestivation. Dendrogramic analyses of the deduced Aqp1 and Aqp3 amino acid sequences of P. annectens revealed their close relationships with those of Latimeria chalumnae and tetrapods. During the induction phase, there were significant decreases in the transcript levels of aqp1 and aqp3 in the gills of P. annectens, but the branchial Aqp1 and Aqp3 protein abundance remained unchanged. As changes in transcription may precede changes in translation, this could be regarded as an adaptive response to decrease the protein abundance of Aqp1 and Aqp3 in the subsequent maintenance phase of aestivation. As expected, the branchial transcript levels and protein abundance of aqp1/Aqp1 and aqp3/Aqp3 were significantly down-regulated during the maintenance phase, probably attributable to the shutdown of branchial functions and the cessation of volume regulation of branchial epithelial cells. Additionally, these changes could reduce the loss of water through branchial epithelial surfaces, supplementing the anti-desiccating property of the dried mucus. Upon arousal, it was essential for the lungfish to restore branchial functions. Indeed, the protein abundance of Aqp1 recovered partially, with complete recovery of mRNA expression level and protein abundance of Aqp3, in the gills of P. annectens. These results provide insights into how P

  9. High abundance of salps in the coastal Gulf of Alaska during 2011: A first record of bloom occurrence for the northern Gulf

    Science.gov (United States)

    Li, Kaizhi; Doubleday, Ayla J.; Galbraith, Moira D.; Hopcroft, Russell R.

    2016-10-01

    Atypical high abundances of two salp species occurred in the coastal Gulf of Alaska during 2011. Salpa aspera dominated numerically in aggregate form during spring, and became uncommon during summer, while Cyclosalpa bakeri increased from low during spring to high abundance during summer. Both species were absent, or nearly so, by fall. C. bakeri abundance was positively correlated to surface temperature in spring and summer, and both species abundances were negatively correlated to chlorophyll a. The proportion of aggregate forms of both species was higher than that of solitary forms during spring and summer. The length-frequency of S. aspera aggregate individuals ranged primarily from 10 to 50 mm, and solitary forms reached 130 mm, while C. bakeri aggregates were 10-25 mm, with solitary forms up to 75 mm. Estimated biomass of S. aspera was 0.35±0.64 mg C m-3 in southeastern Alaska during spring then decreased to 0.03±0.12 mg C m-3 during summer. Estimated biomass of C. bakeri was 0.03±0.06 mg C m-3 over the entire sampling domain during spring, then rose to 0.15±0.25 mg C m-3 during summer. The volume of water filtered daily by S. aspera was estimated to be up to 17% of the 200 m water column at some stations during spring, but only up to ~3.5% during summer. Substantially higher grazing impact was possible if animals were largely confined to the surface mixed layer (typically 20-30 m thick). The average volume filtrated was higher during spring for S. aspera, but for C. bakeri it was higher during summer. We propose that the combined effect of the northward transport of seed populations, their rapid biomass increase through asexual reproduction, and the high clearance rate of salps contributed to atypically low chlorophyll a in the Gulf of Alaska during spring and summer of 2011. This unusual event impacted ecosystem function during 2011, and might be expected to increase in frequency as the Gulf continues to respond to climate variations.

  10. Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site.

    Science.gov (United States)

    Stingl, Ulrich; Tripp, Harry James; Giovannoni, Stephen J

    2007-08-01

    The introduction of high-throughput dilution-to-extinction culturing (HTC) of marine bacterioplankton using sterilized natural sea water as media yielded isolates of many abundant but previously uncultured marine bacterial clades. In early experiments, bacteria from the SAR11 cluster (class Alphaproteobacteria), which are presumed to be the most abundant prokaryotes on earth, were cultured. Although many additional attempts were made, no further strains of the SAR11 clade were obtained. Here, we describe improvements to the HTC technique, which led to the isolation of 17 new SAR11 strains from the Oregon coast and the Sargasso Sea, accounting for 28% and 31% of all isolates in these experiments. Phylogenetic analysis of the internal transcribed spacer (ITS) region showed that the isolates from the Oregon coast represent three different subclusters of SAR11, while isolates from the Sargasso Sea were more uniform and represented a single ITS cluster. A PCR assay proved the presence of proteorhodopsin (PR) in nearly all SAR11 isolates. Analysis of PR amino-acid sequences indicated that isolates from the Oregon coast were tuned to either green or blue light, while PRs from strains obtained from the Sargasso Sea were exclusively tuned to maximum absorbance in the blue. Interestingly, phylogenies based on PR and ITS did not correlate, suggesting lateral gene transfer. In addition to the new SAR11 strains, many novel strains belonging to clusters of previously uncultured or undescribed species of different bacterial phyla, including the first strain of the highly abundant alphaproteobacterial SAR116 clade, were isolated using the modified methods.

  11. High abundance of genetic Bacteroidetes markers for total fecal pollution in pristine alpine soils suggests lack in specificity for feces

    Science.gov (United States)

    Vierheilig, Julia; Farnleitner, Andreas H.; Kollanur, Denny; Blöschl, Günter; Reischer, Georg H.

    2012-01-01

    Two frequently applied genetic Bacteroidetes markers for total fecal pollution (AllBac and BacUni) were found in high numbers in pristine soil samples of two alpine catchment areas casting doubt on their value as fecal indicators. This finding underlines the necessity to evaluate assays locally and against non-intestinal samples before application. PMID:22285854

  12. Quantitative analysis of low-abundance serological proteins with peptide affinity-based enrichment and pseudo-multiple reaction monitoring by hybrid quadrupole time-of-flight mass spectrometry.

    Science.gov (United States)

    Kim, Kwang Hoe; Ahn, Yeong Hee; Ji, Eun Sun; Lee, Ju Yeon; Kim, Jin Young; An, Hyun Joo; Yoo, Jong Shin

    2015-07-02

    Multiple reaction monitoring (MRM) is commonly used for the quantitative analysis of proteins during mass pectrometry (MS), and has excellent specificity and sensitivity for an analyte in a complex sample. In this study, a pseudo-MRM method for the quantitative analysis of low-abundance serological proteins was developed using hybrid quadrupole time-of-flight (hybrid Q-TOF) MS and peptide affinity-based enrichment. First, a pseudo-MRM-based analysis using hybrid Q-TOF MS was performed for synthetic peptides selected as targets and spiked into tryptic digests of human serum. By integrating multiple transition signals corresponding to fragment ions in the full scan MS/MS spectrum of a precursor ion of the target peptide, a pseudo-MRM MS analysis of the target peptide showed an increased signal-to-noise (S/N) ratio and sensitivity, as well as an improved reproducibility. The pseudo-MRM method was then used for the quantitative analysis of the tryptic peptides of two low-abundance serological proteins, tissue inhibitor of metalloproteinase 1 (TIMP1) and tissue-type protein tyrosine phosphatase kappa (PTPκ), which were prepared with peptide affinity-based enrichment from human serum. Finally, this method was used to detect femtomolar amounts of target peptides derived from TIMP1 and PTPκ, with good coefficients of variation (CV 2.7% and 9.8%, respectively), using a few microliters of human serum from colorectal cancer patients. The results suggest that pseudo-MRM using hybrid Q-TOF MS, combined with peptide affinity-based enrichment, could become a promising alternative for the quantitative analysis of low-abundance target proteins of interest in complex serum samples that avoids protein depletion.

  13. High-resolution protein structure determination by serial femtosecond crystallography.

    Science.gov (United States)

    Boutet, Sébastien; Lomb, Lukas; Williams, Garth J; Barends, Thomas R M; Aquila, Andrew; Doak, R Bruce; Weierstall, Uwe; DePonte, Daniel P; Steinbrener, Jan; Shoeman, Robert L; Messerschmidt, Marc; Barty, Anton; White, Thomas A; Kassemeyer, Stephan; Kirian, Richard A; Seibert, M Marvin; Montanez, Paul A; Kenney, Chris; Herbst, Ryan; Hart, Philip; Pines, Jack; Haller, Gunther; Gruner, Sol M; Philipp, Hugh T; Tate, Mark W; Hromalik, Marianne; Koerner, Lucas J; van Bakel, Niels; Morse, John; Ghonsalves, Wilfred; Arnlund, David; Bogan, Michael J; Caleman, Carl; Fromme, Raimund; Hampton, Christina Y; Hunter, Mark S; Johansson, Linda C; Katona, Gergely; Kupitz, Christopher; Liang, Mengning; Martin, Andrew V; Nass, Karol; Redecke, Lars; Stellato, Francesco; Timneanu, Nicusor; Wang, Dingjie; Zatsepin, Nadia A; Schafer, Donald; Defever, James; Neutze, Richard; Fromme, Petra; Spence, John C H; Chapman, Henry N; Schlichting, Ilme

    2012-07-20

    Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.

  14. Characterization of seed storage proteins in high protein genotypes of cowpea [Vigna unguiculata (L.) Walp].

    Science.gov (United States)

    Gupta, Prachi; Singh, Rohtas; Malhotra, S; Boora, K S; Singal, H R

    2010-01-01

    Twenty one genotypes and two check varieties viz. CS-88 and V-240 of cowpea [Vigna unguiculata (L.) Walp. ] were screened for total proteins. The total protein content ranged from 22.4 (HC-3) to 27.9 % (HC-98-64) in 21 genotypes whereas in check varieties it was 25.6 (V-240) and 26.0 % (CS-88). Seven genotypes viz. HC-6, HC-5, CP-21, LST-II-C-12, CP-16, COVU-702 and HC-98-64 having high protein content (26.7 to 27.9 %) were selected for further characterization of their seed storage proteins. Globulins were the major protein fraction ranging from 55.6 (LST-II-C-12) to 58.8 % (CP-16 and HC-6) of total protein. Glutelins was the second major fraction ranging from 14.4 to 15.6 % followed by albumins (8.2 to 11.9 %) and prolamins (2.3 to 5.0 %). Content of free amino acids also showed variations amongst genotypes with COVU-702 having maximum and LST-II-C-12 having minimum content. Essential amino acid analysis revealed that S-amino acids (cysteine and methionine) were the first limiting amino acids followed by tryptophan. From the results presented here it could be suggested that two genotypes viz. LST-II-C-12 and HC-5 be used in breeding programmes aimed at developing high protein moth bean varieties with good quality.

  15. Exploring novel food proteins and processing technologies : a case study on quinoa protein and high pressure –high temperature processing

    NARCIS (Netherlands)

    Avila Ruiz, Geraldine

    2016-01-01

    Foods rich in protein are nowadays high in demand worldwide. To ensure a sustainable supply and a high quality of protein foods, novel food proteins and processing technologies need to be explored to understand whether they can be used for the development of high-quality protein foods. Therefore, th

  16. Snow cover and extreme winter warming events control flower abundance of some, but not all species in high arctic Svalbard

    DEFF Research Database (Denmark)

    Semenchuk, Philipp R.; Elberling, Bo; Cooper, Elisabeth J.

    2013-01-01

    The High Arctic winter is expected to be altered through ongoing and future climate change. Winter precipitation and snow depth are projected to increase and melt out dates change accordingly. Also, snow cover and depth will play an important role in protecting plant canopy from increasingly more...... season length and by protecting or exposing flower buds to cold winter air, but most species studied are resistant to changes....

  17. Five willow varieties cultivated across diverse field environments reveal stem density variation associated with high tension wood abundance.

    Science.gov (United States)

    Berthod, Nicolas; Brereton, Nicholas J B; Pitre, Frédéric E; Labrecque, Michel

    2015-01-01

    Sustainable and inexpensive production of biomass is necessary to make biofuel production feasible, but represents a challenge. Five short rotation coppice willow cultivars, selected for high biomass yield, were cultivated on sites at four diverse regions of Quebec in contrasting environments. Wood composition and anatomical traits were characterized. Tree height and stem diameter were measured to evaluate growth performance of the cultivars according to the diverse pedoclimatic conditions. Each cultivar showed very specific responses to its environment. While no significant variation in lignin content was observed between sites, there was variation between cultivars. Surprisingly, the pattern of substantial genotype variability in stem density was maintained across all sites. However, wood anatomy did differ between sites in a cultivar (producing high and low density wood), suggesting a probable response to an abiotic stress. Furthermore, twice as many cellulose-rich G-fibers, comprising over 50% of secondary xylem, were also found in the high density wood, a finding with potential to bring higher value to the lignocellulosic bioethanol industry.

  18. Castration alters protein balance after high-frequency muscle contraction.

    Science.gov (United States)

    Steiner, Jennifer L; Fukuda, David H; Rossetti, Michael L; Hoffman, Jay R; Gordon, Bradley S

    2017-02-01

    Resistance exercise increases muscle mass by shifting protein balance in favor of protein accretion. Androgens independently alter protein balance, but it is unknown whether androgens alter this measure after resistance exercise. To answer this, male mice were subjected to sham or castration surgery 7-8 wk before undergoing a bout of unilateral, high-frequency, electrically induced muscle contractions in the fasted or refed state. Puromycin was injected 30 min before euthanasia to measure protein synthesis. The tibialis anterior was analyzed 4 h postcontraction. In fasted mice, neither basal nor stimulated rates of protein synthesis were affected by castration despite lower phosphorylation of mechanistic target of rapamycin in complex 1 (mTORC1) substrates [p70S6K1 (Thr389) and 4E-BP1 (Ser65)]. Markers of autophagy (LC3 II/I ratio and p62 protein content) were elevated by castration, and these measures remained elevated above sham values after contractions. Furthermore, in fasted mice, the protein content of Regulated in Development and DNA Damage 1 (REDD1) was correlated with LC3 II/I in noncontracted muscle, whereas phosphorylation of uncoordinated like kinase 1 (ULK1) (Ser757) was correlated with LC3 II/I in the contracted muscle. When mice were refed before contractions, protein synthesis and mTORC1 signaling were not affected by castration in either the noncontracted or contracted muscle. Conversely, markers of autophagy remained elevated in the muscles of refed, castrated mice even after contractions. These data suggest the castration-mediated elevation in baseline autophagy reduces the absolute positive shift in protein balance after muscle contractions in the refed or fasted states.

  19. Improved method for identification of low abundance proteins using 2D-gel electrophoresis, MALDI-TOF and TOF/TOF

    Science.gov (United States)

    Introduction: Differential protein expression studies have been routinely performed in our laboratory to determine the health effects of environmentally-important chemicals. In this abstract, improvements in the in-gel protein digestion, MALDI plate spotting and data acquisition...

  20. Improved method for identification of low abundance proteins using 2D-gel electrophoresis, MALDI-TOF and TOF/TOF

    Science.gov (United States)

    Introduction: Differential protein expression studies have been routinely performed in our laboratory to determine the health effects of environmentally-important chemicals. In this abstract, improvements in the in-gel protein digestion, MALDI plate spotting and data acquisition...

  1. The MRC-5 human embryonal lung fibroblast two-dimensional gel cellular protein database: quantitative identification of polypeptides whose relative abundance differs between quiescent, proliferating and SV40 transformed cells

    DEFF Research Database (Denmark)

    Celis, J E; Dejgaard, K; Madsen, Peder;

    1990-01-01

    (1323 with isoelectric focusing and 572 with nonequilibrium pH gradient electrophoresis) are recorded in this database, containing quantitative and qualitative data on the relative abundance of cellular proteins synthesized by quiescent, proliferating and SV40 transformed MRC-5 fibroblasts. Of the 592...... proteins quantitated so far, the levels of 138 were up- or down-regulated (51 and 87, respectively) by two times or more in the transformed cells as compared to their normal proliferating counterparts, while only 14 behaved similarly in quiescent cells. Seven MRC-5 SV40 proteins, including plastin and two...... cells (AMA) database (Celis et al., Electrophoresis 1990, 11, 989-1071) for those polypeptides of known and unknown identity that have been matched to AMA polypeptides. As more information is gathered in this and other laboratories, including data on oncogene proteins and transcription factors...

  2. Oat (Avena sativa) seed extract as an antifungal food preservative through the catalytic activity of a highly abundant class I chitinase

    DEFF Research Database (Denmark)

    Sørensen, Hans Peter; Madsen, Lone Søvad; Petersen, Jørgen;

    2010-01-01

    to prevent the formation of P. roqueforti colonies. Proteins in the oat seed extracts were fractionated by column chromatography and proteins in fractions containing antifungal activity were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and database searches. Identified antifungal......Extracts from different higher plants were screened for the ability to inhibit the growth of Penicillium roqueforti, a major contaminating species in industrial food processing. Oat (Avena sativa) seed extracts exhibited a high degree of antifungal activity and could be used directly on rye bread...... candidates included thaumatin-like proteins, 1,3-beta-glucanase, permatin precursor, pathogenesis-related protein type 1, and chitinases of class I and II. Class I chitinase could be specifically removed from the extracts and was found to be indispensable for 50% of the P. roqueforti inhibiting activity...

  3. Understanding the structural ensembles of a highly extended disordered protein.

    Science.gov (United States)

    Daughdrill, Gary W; Kashtanov, Stepan; Stancik, Amber; Hill, Shannon E; Helms, Gregory; Muschol, Martin; Receveur-Bréchot, Véronique; Ytreberg, F Marty

    2012-01-01

    Developing a comprehensive description of the equilibrium structural ensembles for intrinsically disordered proteins (IDPs) is essential to understanding their function. The p53 transactivation domain (p53TAD) is an IDP that interacts with multiple protein partners and contains numerous phosphorylation sites. Multiple techniques were used to investigate the equilibrium structural ensemble of p53TAD in its native and chemically unfolded states. The results from these experiments show that the native state of p53TAD has dimensions similar to a classical random coil while the chemically unfolded state is more extended. To investigate the molecular properties responsible for this behavior, a novel algorithm that generates diverse and unbiased structural ensembles of IDPs was developed. This algorithm was used to generate a large pool of plausible p53TAD structures that were reweighted to identify a subset of structures with the best fit to small angle X-ray scattering data. High weight structures in the native state ensemble show features that are localized to protein binding sites and regions with high proline content. The features localized to the protein binding sites are mostly eliminated in the chemically unfolded ensemble; while, the regions with high proline content remain relatively unaffected. Data from NMR experiments support these results, showing that residues from the protein binding sites experience larger environmental changes upon unfolding by urea than regions with high proline content. This behavior is consistent with the urea-induced exposure of nonpolar and aromatic side-chains in the protein binding sites that are partially excluded from solvent in the native state ensemble.

  4. Simultaneous preparation of naturally abundant and rare catechins by tannase-mediated biotransformation combining high speed counter current chromatography.

    Science.gov (United States)

    Xia, Guobin; Hong, Shan; Liu, Songbai

    2014-05-15

    Simultaneous preparation of naturally rare catechins, EGC and EC, has been realized by tannase-mediated biotransformation combining high speed counter current chromatography. In addition, simultaneous preparation of the four catechins, EGCG, ECG, EGC, and EC in green tea extract has also been achieved by HSCCC under the normal phase and the reversed phase modes. The identity of the catechins was determined by HPLC-DAD-ESI-MS and quantification of the catechins was performed by HPLC-DAD. In a typical HSCCC separation, 27.2 mg 98.8% EGCG, 14.1 mg 94.7% EGC, and 9.3 mg 97.5% EC were obtained. This new method is efficient, time-saving and valuable for biological studies.

  5. Effects of high external electric fields on protein conformation

    Science.gov (United States)

    Pompa, Pier Paolo; Bramanti, Alessandro; Maruccio, Giuseppe; del Mercato, Loretta Laureana; Chiuri, Rocco; Cingolani, Roberto; Rinaldi, Ross

    2005-06-01

    Resistance of biomolecules to high electric fields is a main concern for nanobioelectronics/nanobiosensing applications, and it is also a relevant issue from a fundamental perspective, to understand the dielectric properties and structural dynamics of proteins. In nanoscale devices, biomolecules may experience electric fields as high as 107 V/m in order to elicit charge transport/transfer. Understanding the effects of such fields on their structural integrity is thus crucial to assess the reliability of biomolecular devices. In this study, we show experimental evidence for the retention of native-like fold pattern by proteins embedded in high electric fields. We have tested the metalloprotein azurin, deposited onto SiO2 substrates in air with proper electrode configuration, by applying high static electric fields (up to 106-107 V/m). The effects on the conformational properties of protein molecules have been determined by means of intrinsic fluorescence measurements. Experimental results indicate that no significant field-induced conformational alteration occurs. This behavior is also discussed and supported by theoretical predictions of the intrinsic intra-protein electric fields. As the general features of such inner fields are not peculiar of azurin, the conclusions presented here should have general validity.

  6. High-Resolution X-ray Spectroscopy of Hercules X-1 with the XMM-Newton RGS CNO Element Abundance Measurements and Density Diagnostics of a Photoionized Plasma

    CERN Document Server

    Jiménez-Garate, M A; Den Herder, J W A; Zane, S; Ramsay, G

    2002-01-01

    We analyze the high-resolution X-ray spectrum of Hercules X-1, an intermediate-mass X-ray binary, which was observed with the XMM-Newton Reflection Grating Spectrometer. We measure the elemental abundance ratios by use of spectral models, and we detect material processed through the CNO-cycle. The CNO abundances, and in particular the ratio N/O > 4.0 times solar, provide stringent constraints on the evolution of the binary system. The low and short-on flux states of Her X-1 exhibit narrow line emission from C VI, N VI, N VII, O VII, O VIII, Ne IX, and Ne X ions. The spectra show signatures of photoionization. We measure the electron temperature, quantify photoexcitation in the He alpha lines, and set limits on the location and density of the gas. The recombination lines may originate in the accretion disk atmosphere and corona, or on the X-ray illuminated face of the mass donor (HZ Her). The spectral variation over the course of the 35 d period provides additional evidence for the precession of the disk. Duri...

  7. The Abundance, Ortho/Para Ratio, and Deuteration of Water in the High-Mass Star Forming Region NGC 6334 I

    CERN Document Server

    Emprechtinger, M; Rolffs, R; Schilke, P; Monje, R R; Comito, C; Ceccarelli, C; Neufeld, D A; van der Tak, F F S

    2012-01-01

    We present Herschel/HIFI observations of 30 transitions of water isotopologues toward the high-mass star forming region NGC 6334 I. The line profiles of H_2^{16}O, H_2^{17}O, H_2^{18}O, and HDO show a complex pattern of emission and absorption components associated with the embedded hot cores, a lower-density envelope, two outflow components, and several foreground clouds, some associated with the NGC 6334 complex, others seen in projection against the strong continuum background of the source. Our analysis reveals an H2O ortho/para ratio of 3 +/- 0.5 in the foreground clouds, as well as the outflow. The water abundance varies from ~10^{-8} in the foreground clouds and the outer envelope to ~10^{-6} in the hot core. The hot core abundance is two orders of magnitude below the chemical model predictions for dense, warm gas, but within the range of values found in other Herschel/HIFI studies of hot cores and hot corinos. This may be related to the relatively low gas and dust temperature (~100 K), or time depende...

  8. High pressure-low temperature processing of food proteins.

    Science.gov (United States)

    Dumay, Eliane; Picart, Laetitia; Regnault, Stéphanie; Thiebaud, Maryse

    2006-03-01

    High pressure-low temperature (HP-LT) processing is of interest in the food field in view of: (i) obtaining a "cold" pasteurisation effect, the level of microbial inactivation being higher after pressurisation at low or sub-zero than at ambient temperature; (ii) limiting the negative impact of atmospheric pressure freezing on food structures. The specific effects of freezing by fast pressure release on the formation of ice I crystals have been investigated on oil in water emulsions stabilized by proteins, and protein gels, showing the formation of a high number of small ice nuclei compared to the long needle-shaped crystals obtained by conventional freezing at 0.1 MPa. It was therefore of interest to study the effects of HP-LT processing on unfolding or dissociation/aggregation phenomena in food proteins, in view of minimizing or controlling structural changes and aggregation reactions, and/or of improving protein functional properties. In the present studies, the effects of HP-LT have been investigated on protein models such as (i) beta-lactoglobulin, i.e., a whey protein with a well known 3-D structure, and (ii) casein micelles, i.e., the main milk protein components, the supramolecular structure of which is not fully elucidated. The effects of HP-LT processing was studied up to 300 MPa at low or sub-zero temperatures and after pressure release, or up to 200 MPa by UV spectroscopy under pressure, allowing to follow reversible structural changes. Pressurisation of approximately 2% beta-lactoglobulin solutions up to 300 MPa at low/subzero temperatures minimizes aggregation reactions, as measured after pressure release. In parallel, such low temperature treatments enhanced the size reduction of casein micelles.

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

    DEFF Research Database (Denmark)

    Rinalducci, Sara; Campostrini, Natascia; Antonioli, Paolo

    2005-01-01

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

  10. Predicting protein-protein interactions from sequence using correlation coefficient and high-quality interaction dataset.

    Science.gov (United States)

    Shi, Ming-Guang; Xia, Jun-Feng; Li, Xue-Ling; Huang, De-Shuang

    2010-03-01

    Identifying protein-protein interactions (PPIs) is critical for understanding the cellular function of the proteins and the machinery of a proteome. Data of PPIs derived from high-throughput technologies are often incomplete and noisy. Therefore, it is important to develop computational methods and high-quality interaction dataset for predicting PPIs. A sequence-based method is proposed by combining correlation coefficient (CC) transformation and support vector machine (SVM). CC transformation not only adequately considers the neighboring effect of protein sequence but describes the level of CC between two protein sequences. A gold standard positives (interacting) dataset MIPS Core and a gold standard negatives (non-interacting) dataset GO-NEG of yeast Saccharomyces cerevisiae were mined to objectively evaluate the above method and attenuate the bias. The SVM model combined with CC transformation yielded the best performance with a high accuracy of 87.94% using gold standard positives and gold standard negatives datasets. The source code of MATLAB and the datasets are available on request under smgsmg@mail.ustc.edu.cn.

  11. Raccoon abundance inventory report

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the results of a raccoon abundance inventory on Clarence Cannon National Wildlife Refuge in 2012. Determining raccoon abundance allows for...

  12. High Pressure Cryocooling of Protein Crystals: The Enigma of Water

    Science.gov (United States)

    Gruner, Sol M.

    2010-03-01

    A novel high-pressure cryocooling technique for preparation biological samples for x-ray analysis is described. The method, high-pressure cryocooling, involves cooling samples to cryogenic temperatures (e.g., 100 K) in high-pressure Helium gas (up to 200 MPa). It bears both similarities and differences to high-pressure cooling methods that have been used to prepare samples for electron microscopy, and has been especially useful for cryocooling of macromolecular crystals for x-ray diffraction. Examples will be given where the method has been effective in providing high quality crystallographic data for difficult samples, such as cases where ligands needed to be stabilized in binding sites to be visualized, or where very high resolution data were required. The talk concludes with a discussion of data obtained by high-pressure cryocooling that pertains to two of the most important problems in modern science: the enigma of water and how water affects the activity of proteins.

  13. Voltage-Gated Na+ Channel Isoforms and Their mRNA Expression Levels and Protein Abundance in Three Electric Organs and the Skeletal Muscle of the Electric Eel Electrophorus electricus.

    Science.gov (United States)

    Ching, Biyun; Woo, Jia M; Hiong, Kum C; Boo, Mel V; Wong, Wai P; Chew, Shit F; Ip, Yuen K

    2016-01-01

    This study aimed to obtain the coding cDNA sequences of voltage-gated Na+ channel (scn) α-subunit (scna) and β-subunit (scnb) isoforms from, and to quantify their transcript levels in, the main electric organ (EO), Hunter's EO, Sach's EO and the skeletal muscle (SM) of the electric eel, Electrophorus electricus, which can generate both high and low voltage electric organ discharges (EODs). The full coding sequences of two scna (scn4aa and scn4ab) and three scnb (scn1b, scn2b and scn4b) were identified for the first time (except scn4aa) in E. electricus. In adult fish, the scn4aa transcript level was the highest in the main EO and the lowest in the Sach's EO, indicating that it might play an important role in generating high voltage EODs. For scn4ab/Scn4ab, the transcript and protein levels were unexpectedly high in the EOs, with expression levels in the main EO and the Hunter's EO comparable to those of scn4aa. As the key domains affecting the properties of the channel were mostly conserved between Scn4aa and Scn4ab, Scn4ab might play a role in electrogenesis. Concerning scnb, the transcript level of scn4b was much higher than those of scn1b and scn2b in the EOs and the SM. While the transcript level of scn4b was the highest in the main EO, protein abundance of Scn4b was the highest in the SM. Taken together, it is unlikely that Scna could function independently to generate EODs in the EOs as previously suggested. It is probable that different combinations of Scn4aa/Scn4ab and various Scnb isoforms in the three EOs account for the differences in EODs produced in E. electricus. In general, the transcript levels of various scn isoforms in the EOs and the SM were much higher in adult than in juvenile, and the three EOs of the juvenile fish could be functionally indistinct.

  14. Chronic high fat feeding increases anxiety-like behaviour and reduces transcript abundance of glucocorticoid signalling genes in the hippocampus of female rats.

    Science.gov (United States)

    Sivanathan, Shathveekan; Thavartnam, Kabriya; Arif, Shahneen; Elegino, Trisha; McGowan, Patrick O

    2015-06-01

    The consumption of diets high in saturated fats and obesity have been associated with impaired physical and mental health. Previous studies indicate that chronic high fat diet consumption leads to systemic inflammation in humans and non-human animal models. Studies in non-human animals suggest that altered physiological responses to stress are also a consequence of high fat diet consumption. Glucocorticoid signalling mechanisms may link immune and stress-related pathways in the brain, and were shown to be significantly altered in the brains of female rat offspring of mothers exposed to chronic high fat diet during pregnancy and lactation. For adult females, the consequence of chronic high fat diet consumption on these signalling pathways and their relationship to stress-related behaviour is not known. In this study, we examined the effects of chronic consumption of a high fat diet compared to a low fat control diet among adult female Long Evans rats. We found significant differences in weight gain, caloric intake, anxiety-related behaviours, and glucocorticoid-related gene expression over a 10-week exposure period. As expected, rats in the high fat diet group gained the most weight and consumed the greatest number of calories. Rats in the high fat diet group showed significantly greater levels of anxiety-related behaviour in the Light Dark and Open Field tasks compared to rats in the low fat diet group. Rats consuming high fat diet also exhibited reduced transcript abundance in the hippocampus of stress-related mineralocorticoid receptor and glucocorticoid receptor genes, as well as nuclear factor kappa beta gene expression, implicated in inflammatory processes. Together, these data indicate that chronic high fat diet consumption may increase anxiety-like behaviour at least in part via alterations in glucocorticoid signalling mechanisms in limbic brain regions.

  15. Development of a Chip/Chip/SRM platform using digital chip isoelectric focusing and LC-Chip mass spectrometry for enrichment and quantitation of low abundance protein biomarkers in human plasma.

    Science.gov (United States)

    Rafalko, Agnes; Dai, Shujia; Hancock, William S; Karger, Barry L; Hincapie, Marina

    2012-02-03

    Protein biomarkers are critical for diagnosis, prognosis, and treatment of disease. The transition from protein biomarker discovery to verification can be a rate limiting step in clinical development of new diagnostics. Liquid chromatography-selected reaction monitoring mass spectrometry (LC-SRM MS) is becoming an important tool for biomarker verification studies in highly complex biological samples. Analyte enrichment or sample fractionation is often necessary to reduce sample complexity and improve sensitivity of SRM for quantitation of clinically relevant biomarker candidates present at the low ng/mL range in blood. In this paper, we describe an alternative method for sample preparation for LC-SRM MS, which does not rely on availability of antibodies. This new platform is based on selective enrichment of proteotypic peptides from complex biological peptide mixtures via isoelectric focusing (IEF) on a digital ProteomeChip (dPC) for SRM quantitation using a triple quadrupole (QQQ) instrument with an LC-Chip (Chip/Chip/SRM). To demonstrate the value of this approach, the optimization of the Chip/Chip/SRM platform was performed using prostate specific antigen (PSA) added to female plasma as a model system. The combination of immunodepletion of albumin and IgG with peptide fractionation on the dPC, followed by SRM analysis, resulted in a limit of quantitation of PSA added to female plasma at the level of ∼1-2.5 ng/mL with a CV of ∼13%. The optimized platform was applied to measure levels of PSA in plasma of a small cohort of male patients with prostate cancer (PCa) and healthy matched controls with concentrations ranging from 1.5 to 25 ng/mL. A good correlation (r(2) = 0.9459) was observed between standard clinical ELISA tests and the SRM-based assay. Our data demonstrate that the combination of IEF on the dPC and SRM (Chip/Chip/SRM) can be successfully applied for verification of low abundance protein biomarkers in complex samples.

  16. Highly Branched Pentasaccharide-Bearing Amphiphiles for Membrane Protein Studies

    DEFF Research Database (Denmark)

    Ehsan, Muhammad; Du, Yang; Scull, Nicola J

    2016-01-01

    structural and functional analysis feasible. Although a number of novel agents have been developed to overcome the limitations of conventional detergents, most have traditional head groups such as glucoside or maltoside. In this study, we introduce a class of amphiphiles, the PSA/Es with a novel highly...... branched pentasaccharide hydrophilic group. The PSA/Es conferred markedly increased stability to a diverse range of membrane proteins compared to conventional detergents, indicating a positive role for the new hydrophilic group in maintaining the native protein integrity. In addition, PDCs formed by PSA....../Es were smaller and more suitable for electron microscopic analysis than those formed by DDM, indicating that the new agents have significant potential for the structure-function studies of membrane proteins....

  17. Rheological properties of highly concentrated protein-stabilized emulsions.

    Science.gov (United States)

    Dimitrova, Tatiana D; Leal-Calderon, Fernando

    2004-05-20

    We prepared concentrated quasi monodisperse hexadecane-in-water emulsions stabilized by various proteins and investigated their rheological properties. Some protein-stabilized emulsions possess remarkably high elasticity and at the same time they are considerably fragile--they exhibit coalescence at yield strain and practically do not flow. The elastic storage modulus G' and the loss modulus G" of the emulsions were determined for different oil volume fractions above the random close packing. Surprisingly, the dimensionless elastic moduli G'/(sigma/a), sigma being the interfacial tension, and a being the mean drop radius, obtained for emulsions stabilized by different proteins do not collapse on a single master curve. They are almost always substantially higher than the corresponding values obtained for equivalent Sodium Dodecyl Sulfate (SDS)-stabilized emulsions. The unusually high elasticity cannot be attributed to a specificity of the continuous phase, because the osmotic equation of state of our emulsions is found identical to the one obtained for samples stabilized by classical surfactants. In parallel, we mimicked the thin films that separate the droplets in the concentrated emulsion and found that the protein adsorption layers contain a substantial number of sticky surface aggregates. These severely obstruct local rearrangements of individual drops in respect to their neighbors which leads to coalescence at yield strain. Furthermore, we found that G'/(sigma/a) is correlated (for a given oil volume fraction) to the dilatational elastic modulus, of the protein layer adsorbed on the droplets. The intrinsic elasticity of the protein layers, together with the blocked local rearrangements are considered as the main factors determining the unusual bulk elasticity of the studied emulsions.

  18. Can microbes compete with cows for sustainable protein production - A feasibility study on high quality protein

    Science.gov (United States)

    Vestergaard, Mike; Chan, Siu Hung Joshua; Jensen, Peter Ruhdal

    2016-11-01

    An increasing population and their increased demand for high-protein diets will require dramatic changes in the food industry, as limited resources and environmental issues will make animal derived foods and proteins, gradually more unsustainable to produce. To explore alternatives to animal derived proteins, an economic model was built around the genome-scale metabolic network of E. coli to study the feasibility of recombinant protein production as a food source. Using a novel model, we predicted which microbial production strategies are optimal for economic return, by capturing the tradeoff between the market prices of substrates, product output and the efficiency of microbial production. A case study with the food protein, Bovine Alpha Lactalbumin was made to evaluate the upstream economic feasibilities. Simulations with different substrate profiles at maximum productivity were used to explore the feasibility of recombinant Bovine Alpha Lactalbumin production coupled with market prices of utilized materials. We found that recombinant protein production could be a feasible food source and an alternative to traditional sources.

  19. THE ABUNDANCE, ORTHO/PARA RATIO, AND DEUTERATION OF WATER IN THE HIGH-MASS STAR-FORMING REGION NGC 6334 I

    Energy Technology Data Exchange (ETDEWEB)

    Emprechtinger, M.; Lis, D. C.; Monje, R. R. [California Institute of Technology, Cahill Center for Astronomy and Astrophysics 301-17, Pasadena, CA 91125 (United States); Rolffs, R.; Schilke, P. [Physikalisches Institut, Universitaet zu Koeln, Zuelpicher Str. 77, D-50937 Koeln (Germany); Comito, C. [Max-Planck-Institut fuer Radioastronomie, Auf dem Huegel 69, D-53121 Bonn (Germany); Ceccarelli, C. [UJF-Grenoble 1/CNRS-INSU, Institut de Planetologie et d' Astrophysique de Grenoble (IPAG) UMR 5274, Grenoble F-38041 (France); Neufeld, D. A. [Department of Physics and Astronomy Johns Hopkins University, Baltimore, MD 21218 (United States); Van der Tak, F. F. S., E-mail: dcl@caltech.edu [SRON Netherlands Institute for Space Research and Kapteyn Astronomical Institute, University of Groningen, Groningen (Netherlands)

    2013-03-01

    We present Herschel/HIFI observations of 30 transitions of water isotopologues toward the high-mass star-forming region NGC 6334 I. The line profiles of H{sup 16} {sub 2}O, H{sup 17} {sub 2}O, H{sup 18} {sub 2}O, and HDO show a complex pattern of emission and absorption components associated with the embedded hot cores, a lower-density envelope, two outflow components, and several foreground clouds, some associated with the NGC 6334 complex, others seen in projection against the strong continuum background of the source. Our analysis reveals an H{sub 2}O ortho/para ratio of 3 {+-} 0.5 in the foreground clouds, as well as the outflow. The water abundance varies from {approx}10{sup -8} in the foreground clouds and the outer envelope to {approx}10{sup -6} in the hot core. The hot core abundance is two orders of magnitude below the chemical model predictions for dense, warm gas, but within the range of values found in other Herschel/HIFI studies of hot cores and hot corinos. This may be related to the relatively low gas and dust temperature ({approx}100 K), or time-dependent effects, resulting in a significant fraction of water molecules still locked up in dust grain mantles. The HDO/H{sub 2}O ratio in NGC 6334 I, {approx}2 Multiplication-Sign 10{sup -4}, is also relatively low, but within the range found in other high-mass star-forming regions.

  20. Formation of Apollo 16 impactites and the composition of late accreted material: Constraints from Os isotopes, highly siderophile elements and sulfur abundances

    Science.gov (United States)

    Gleißner, Philipp; Becker, Harry

    2017-03-01

    Fe-Ni metal-schreibersite-troilite intergrowths in Apollo 16 impact melt rocks and new highly siderophile element (HSE) and S abundance data indicate that millimeter-scale closed-system fractional crystallization processes during cooling of impactor-derived metal melt droplets in impact-melts are the main reason for compositional variations and strong differences in abundances and ratios of HSE in multiple aliquots from Apollo 16 impact melt rocks. Element ratios obtained from linear regression of such data are therefore prone to error, but weighted averages take into account full element budgets in the samples and thus represent a more accurate estimate of their impactor contributions. Modeling of solid metal-liquid metal partitioning in the Fe-Ni-S-P system and HSE patterns in impactites from different landing sites suggest that bulk compositions of ancient lunar impactites should be representative of impact melt compositions and that large-scale fractionation of the HSE by in situ segregation of solid metal or sulfide liquid in impact melt sheets most likely did not occur. The compositional record of lunar impactites indicates accretion of variable amounts of chondritic and non-chondritic impactor material and the mixing of these components during remelting of earlier ejecta deposits. The non-chondritic composition appears most prominently in some Apollo 16 impactites and is characterized by suprachondritic HSE/Ir ratios which increase from refractory to moderately volatile HSE and exhibit a characteristic enrichment of Ru relative to Pt. Large-scale fractional crystallization of solid metal from sulfur and phosphorous rich metallic melt with high P/S in planetesimal or embryo cores is currently the most likely process that may have produced these compositions. Similar materials or processes may have contributed to the HSE signature of the bulk silicate Earth (BSE).

  1. High dietary protein decreases fat deposition induced by high-fat and high-sucrose diet in rats.

    Science.gov (United States)

    Chaumontet, Catherine; Even, Patrick C; Schwarz, Jessica; Simonin-Foucault, Angélique; Piedcoq, Julien; Fromentin, Gilles; Azzout-Marniche, Dalila; Tomé, Daniel

    2015-10-28

    High-protein diets are known to reduce adiposity in the context of high carbohydrate and Western diets. However, few studies have investigated the specific high-protein effect on lipogenesis induced by a high-sucrose (HS) diet or fat deposition induced by high-fat feeding. We aimed to determine the effects of high protein intake on the development of fat deposition and partitioning in response to high-fat and/or HS feeding. A total of thirty adult male Wistar rats were assigned to one of the six dietary regimens with low and high protein, sucrose and fat contents for 5 weeks. Body weight (BW) and food intake were measured weekly. Oral glucose tolerance tests and meal tolerance tests were performed after 4th and 5th weeks of the regimen, respectively. At the end of the study, the rats were killed 2 h after ingestion of a calibrated meal. Blood, tissues and organs were collected for analysis of circulating metabolites and hormones, body composition and mRNA expression in the liver and adipose tissues. No changes were observed in cumulative energy intake and BW gain after 5 weeks of dietary treatment. However, high-protein diets reduced by 20 % the adiposity gain induced by HS and high-sucrose high-fat (HS-HF) diets. Gene expression and transcriptomic analysis suggested that high protein intake reduced liver capacity for lipogenesis by reducing mRNA expressions of fatty acid synthase (fasn), acetyl-CoA carboxylase a and b (Acaca and Acacb) and sterol regulatory element binding transcription factor 1c (Srebf-1c). Moreover, ketogenesis, as indicated by plasma β-hydroxybutyrate levels, was higher in HS-HF-fed mice that were also fed high protein levels. Taken together, these results suggest that high-protein diets may reduce adiposity by inhibiting lipogenesis and stimulating ketogenesis in the liver.

  2. High-fat diet induced isoform changes of the Parkinson's disease protein DJ-1.

    Science.gov (United States)

    Poschmann, Gereon; Seyfarth, Katrin; Besong Agbo, Daniela; Klafki, Hans-Wolfgang; Rozman, Jan; Wurst, Wolfgang; Wiltfang, Jens; Meyer, Helmut E; Klingenspor, Martin; Stühler, Kai

    2014-05-02

    Genetic and environmental factors mediate via different physiological and molecular processes a shifted energy balance leading to overweight and obesity. To get insights into the underlying processes involved in energy intake and weight gain, we compared hypothalamic tissue of mice kept on a high-fat or control diet for 10 days by a proteomic approach. Using two-dimensional difference gel electrophoresis in combination with LC-MS/MS, we observed significant abundance changes in 15 protein spots. One isoform of the protein DJ-1 was elevated in the high-fat diet group in three different mouse strains SWR/J, C57BL/6N, and AKR/J analyzed. Large-scale validation of DJ-1 isoforms in individual samples and tissues confirmed a shift in the pattern of DJ-1 isoforms toward more acidic isoforms in several brain and peripheral tissues after feeding a high-fat diet for 10 days. The identification of oxidation of cysteine 106 as well as 2-succinyl modification of the same residue by mass spectrometry not only explains the isoelectric shift of DJ-1 but also links our results to similar shifts of DJ-1 observed in neurodegenerative disease states under oxidative stress. We hypothesize that DJ-1 is a common physiological sensor involved in both nutrition-induced effects and neurodegenerative disease states.

  3. Abundance analysis of DAZ white dwarfs

    CERN Document Server

    Kawka, Adela; Dinnbier, Frantisek; Cibulkova, Helena; Nemeth, Peter

    2010-01-01

    We present an abundance analysis of a sample of 33 hydrogen-rich (DA) white dwarfs. We have used archival high-resolution spectra to measure abundances of calcium, magnesium and iron in a set of 30 objects. In addition, we present preliminary calcium abundances in three new white dwarfs based on low-dispersion spectra. We investigate some abundance ratios (Mg/Ca, Fe/Ca) that may help uncover the composition of the accretion source.

  4. Chlorine Abundances in Cool Stars

    CERN Document Server

    Maas, Z G; Hinkle, K

    2016-01-01

    Chlorine abundances are reported in 15 evolved giants and one M dwarf in the solar neighborhood. The Cl abundance was measured using the vibration-rotation 1-0 P8 line of H$^{35}$Cl at 3.69851 $\\mu$m. The high resolution L-band spectra were observed using the Phoenix infrared spectrometer on the Kitt Peak Mayall 4m telescope. The average [$^{35}$Cl/Fe] abundance in stars with --0.72$<$[Fe/H]$<$0.20 is [$^{35}$Cl/Fe]=(--0.10$\\pm$0.15) dex. The mean difference between the [$^{35}$Cl/Fe] ratios measured in our stars and chemical evolution model values is (0.16$\\pm$0.15) dex. The [$^{35}$Cl/Ca] ratio has an offset of $\\sim$0.35 dex above model predictions suggesting chemical evolution models are under producing Cl at the high metallicity range. Abundances of C, N, O, Si, and Ca were also measured in our spectral region and are consistent with F and G dwarfs. The Cl versus O abundances from our sample match Cl abundances measured in planetary nebula and \\ion{H}{2} regions. In one star where both H$^{35}$Cl a...

  5. Flare Plasma Iron Abundance

    Science.gov (United States)

    Dennis, Brian R.; Dan, Chau; Jain, Rajmal; Schwartz, Richard A.; Tolbert, Anne K.

    2008-01-01

    The equivalent width of the iron-line complex at 6.7 keV seen in flare X-ray spectra suggests that the iron abundance of the hottest plasma at temperatures >approx.10 MK may sometimes be significantly lower than the nominal coronal abundance of four times the photospheric value that is commonly assumed. This conclusion is based on X-ray spectral observations of several flares seen in common with the Ramaty High Energy Solar Spectroscopic Imager (RHESSI) and the Solar X-ray Spectrometer (SOXS) on the second Indian geostationary satellite, GSAT-2. The implications of this will be discussed as it relates to the origin of the hot flare plasma - either plasma already in the corona that is directly heated during the flare energy release process or chromospheric plasma that is heated by flare-accelerated particles and driven up into the corona. Other possible explanations of lower-than-expected equivalent widths of the iron-line complex will also be discussed.

  6. Habituation to low or high protein intake does not modulate basal or postprandial muscle protein synthesis rates: a randomized trial

    NARCIS (Netherlands)

    Gorissen, S.H.; Horstman, Astrid; Franssen, Rinske; Kouw, I.W.; Wall, B.T.; Burd, N.A.; Groot, de C.P.G.M.; Loon, van L.J.C.

    2017-01-01

    Background: Muscle mass maintenance is largely regulated by basal muscle protein synthesis rates and the ability to increase muscle protein synthesis after protein ingestion. To our knowledge, no previous studies have evaluated the impact of habituation to either low protein intake (LOW PRO) or high

  7. High Hydrostatic Pressure Pretreatment of Whey Protein Isolates Improves Their Digestibility and Antioxidant Capacity

    Directory of Open Access Journals (Sweden)

    Michèle M. Iskandar

    2015-05-01

    Full Text Available Whey proteins have well-established antioxidant and anti-inflammatory bioactivities. High hydrostatic pressure processing of whey protein isolates increases their in vitro digestibility resulting in enhanced antioxidant and anti-inflammatory effects. This study compared the effects of different digestion protocols on the digestibility of pressurized (pWPI and native (nWPI whey protein isolates and the antioxidant and anti-inflammatory properties of the hydrolysates. The pepsin-pancreatin digestion protocol was modified to better simulate human digestion by adjusting temperature and pH conditions, incubation times, enzymes utilized, enzyme-to-substrate ratio and ultrafiltration membrane molecular weight cut-off. pWPI showed a significantly greater proteolysis rate and rate of peptide appearance regardless of digestion protocol. Both digestion methods generated a greater relative abundance of eluting peptides and the appearance of new peptide peaks in association with pWPI digestion in comparison to nWPI hydrolysates. Hydrolysates of pWPI from both digestion conditions showed enhanced ferric-reducing antioxidant power relative to nWPI hydrolysates. Likewise, pWPI hydrolysates from both digestion protocols showed similar enhanced antioxidant and anti-inflammatory effects in a respiratory epithelial cell line as compared to nWPI hydrolysates. These findings indicate that regardless of considerable variations of in vitro digestion protocols, pressurization of WPI leads to more efficient digestion that improves its antioxidant and anti-inflammatory properties.

  8. Sterile Filtration of Highly Concentrated Protein Formulations: Impact of Protein Concentration, Formulation Composition, and Filter Material.

    Science.gov (United States)

    Allmendinger, Andrea; Mueller, Robert; Huwyler, Joerg; Mahler, Hanns-Christian; Fischer, Stefan

    2015-10-01

    Differences in filtration behavior of concentrated protein formulations were observed during aseptic drug product manufacturing of biologics dependent on formulation composition. The present study investigates filtration forces of monoclonal antibody formulations in a small-scale set-up using polyvinylidene difluoride (PVDF) or polyethersulfone (PES) filters. Different factors like formulation composition and protein concentration related to differences in viscosity, as well as different filtration rates were evaluated. The present study showed that filtration behavior was influenced by the presence or absence of a surfactant in the formulation, which defines the interaction between filter membrane and surface active formulation components. This can lead to a change in filter resistance (PES filter) independent on the buffer system used. Filtration behavior was additionally defined by rheological non-Newtonian flow behavior. The data showed that high shear rates resulting from small pore sizes and filtration pressure up to 1.0 bar led to shear-thinning behavior for highly concentrated protein formulations. Differences in non-Newtonian behavior were attributed to ionic strength related to differences in repulsive and attractive interactions. The present study showed that the interplay of formulation composition, filter material, and filtration rate can explain differences in filtration behavior/filtration flux observed for highly concentrated protein formulations thus guiding filter selection.

  9. High Mobility Group Box Protein-1 in Wound Repair

    Directory of Open Access Journals (Sweden)

    Mauro Patrone

    2012-09-01

    Full Text Available High-mobility group box 1 protein (HMGB1, a member of highly conserved non-histone DNA binding protein family, has been studied as transcription factor and growth factor. Secreted extracellularly by activated monocytes and macrophages or passively released by necrotic or damaged cells, extracellular HMGB1 is a potent mediator of inflammation. Extracellular HMGB1 has apparently contrasting biological actions: it sustains inflammation (with the possible establishment of autoimmunity or of self-maintaining tissue damage, but it also activates and recruits stem cells, boosting tissue repair. Here, we focus on the role of HMGB1 in physiological and pathological responses, the mechanisms by which it contributes to tissue repair and therapeutic strategies base on targeting HMGB1.

  10. Reverse Phase Protein Arrays for High-throughput Toxicity Screening

    DEFF Research Database (Denmark)

    Pedersen, Marlene Lemvig; Block, Ines; List, Markus

    High-throughput screening is extensively applied for identification of drug targets and drug discovery and recently it found entry into toxicity testing. Reverse phase protein arrays (RPPAs) are used widespread for quantification of protein markers. We reasoned that RPPAs also can be utilized...... beneficially in automated high-throughput toxicity testing. An advantage of using RPPAs is that, in addition to the baseline toxicity readout, they allow testing of multiple markers of toxicity, such as inflammatory responses, which do not necessarily cumulate in cell death. We used transfection of si...... a robotic screening platform. Furthermore, we automated sample tracking and data analysis by developing a bundled bioinformatics tool named “MIRACLE”. Automation and RPPA-based viability/toxicity readouts enable rapid testing of large sample numbers, while granting the possibility for flexible consecutive...

  11. High-throughput protein analysis integrating bioinformatics and experimental assays.

    Science.gov (United States)

    del Val, Coral; Mehrle, Alexander; Falkenhahn, Mechthild; Seiler, Markus; Glatting, Karl-Heinz; Poustka, Annemarie; Suhai, Sandor; Wiemann, Stefan

    2004-01-01

    The wealth of transcript information that has been made publicly available in recent years requires the development of high-throughput functional genomics and proteomics approaches for its analysis. Such approaches need suitable data integration procedures and a high level of automation in order to gain maximum benefit from the results generated. We have designed an automatic pipeline to analyse annotated open reading frames (ORFs) stemming from full-length cDNAs produced mainly by the German cDNA Consortium. The ORFs are cloned into expression vectors for use in large-scale assays such as the determination of subcellular protein localization or kinase reaction specificity. Additionally, all identified ORFs undergo exhaustive bioinformatic analysis such as similarity searches, protein domain architecture determination and prediction of physicochemical characteristics and secondary structure, using a wide variety of bioinformatic methods in combination with the most up-to-date public databases (e.g. PRINTS, BLOCKS, INTERPRO, PROSITE SWISSPROT). Data from experimental results and from the bioinformatic analysis are integrated and stored in a relational database (MS SQL-Server), which makes it possible for researchers to find answers to biological questions easily, thereby speeding up the selection of targets for further analysis. The designed pipeline constitutes a new automatic approach to obtaining and administrating relevant biological data from high-throughput investigations of cDNAs in order to systematically identify and characterize novel genes, as well as to comprehensively describe the function of the encoded proteins.

  12. Streptococcus mutans protein synthesis during mixed-species biofilm development by high-throughput quantitative proteomics.

    Science.gov (United States)

    Klein, Marlise I; Xiao, Jin; Lu, Bingwen; Delahunty, Claire M; Yates, John R; Koo, Hyun

    2012-01-01

    Biofilms formed on tooth surfaces are comprised of mixed microbiota enmeshed in an extracellular matrix. Oral biofilms are constantly exposed to environmental changes, which influence the microbial composition, matrix formation and expression of virulence. Streptococcus mutans and sucrose are key modulators associated with the evolution of virulent-cariogenic biofilms. In this study, we used a high-throughput quantitative proteomics approach to examine how S. mutans produces relevant proteins that facilitate its establishment and optimal survival during mixed-species biofilms development induced by sucrose. Biofilms of S. mutans, alone or mixed with Actinomyces naeslundii and Streptococcus oralis, were initially formed onto saliva-coated hydroxyapatite surface under carbohydrate-limiting condition. Sucrose (1%, w/v) was then introduced to cause environmental changes, and to induce biofilm accumulation. Multidimensional protein identification technology (MudPIT) approach detected up to 60% of proteins encoded by S. mutans within biofilms. Specific proteins associated with exopolysaccharide matrix assembly, metabolic and stress adaptation processes were highly abundant as the biofilm transit from earlier to later developmental stages following sucrose introduction. Our results indicate that S. mutans within a mixed-species biofilm community increases the expression of specific genes associated with glucan synthesis and remodeling (gtfBC, dexA) and glucan-binding (gbpB) during this transition (Pspecies biofilms (vs. single-species biofilms) demonstrating fundamental differences in the matrix assembly, survival and biofilm maintenance in the presence of other organisms. Our data provide insights about how S. mutans optimizes its metabolism and adapts/survives within the mixed-species community in response to a dynamically changing environment. This reflects the intricate physiological processes linked to expression of virulence by this bacterium within complex biofilms.

  13. Proteomic Analysis of Pathogenic Fungi Reveals Highly Expressed Conserved Cell Wall Proteins

    Directory of Open Access Journals (Sweden)

    Jackson Champer

    2016-01-01

    Full Text Available We are presenting a quantitative proteomics tally of the most commonly expressed conserved fungal proteins of the cytosol, the cell wall, and the secretome. It was our goal to identify fungi-typical proteins that do not share significant homology with human proteins. Such fungal proteins are of interest to the development of vaccines or drug targets. Protein samples were derived from 13 fungal species, cultured in rich or in minimal media; these included clinical isolates of Aspergillus, Candida, Mucor, Cryptococcus, and Coccidioides species. Proteomes were analyzed by quantitative MSE (Mass Spectrometry—Elevated Collision Energy. Several thousand proteins were identified and quantified in total across all fractions and culture conditions. The 42 most abundant proteins identified in fungal cell walls or supernatants shared no to very little homology with human proteins. In contrast, all but five of the 50 most abundant cytosolic proteins had human homologs with sequence identity averaging 59%. Proteomic comparisons of the secreted or surface localized fungal proteins highlighted conserved homologs of the Aspergillus fumigatus proteins 1,3-β-glucanosyltransferases (Bgt1, Gel1-4, Crf1, Ecm33, EglC, and others. The fact that Crf1 and Gel1 were previously shown to be promising vaccine candidates, underlines the value of the proteomics data presented here.

  14. Scalable photonic crystal chips for high sensitivity protein detection.

    Science.gov (United States)

    Liang, Feng; Clarke, Nigel; Patel, Parth; Loncar, Marko; Quan, Qimin

    2013-12-30

    Scalable microfabrication technology has enabled semiconductor and microelectronics industries, among other fields. Meanwhile, rapid and sensitive bio-molecule detection is increasingly important for drug discovery and biomedical diagnostics. In this work, we designed and demonstrated that photonic crystal sensor chips have high sensitivity for protein detection and can be mass-produced with scalable deep-UV lithography. We demonstrated label-free detection of carcinoembryonic antigen from pg/mL to μg/mL, with high quality factor photonic crystal nanobeam cavities.

  15. Metaproteomics reveals abundant transposase expression in mutualistic endosymbionts

    Energy Technology Data Exchange (ETDEWEB)

    Kleiner, Manuel [Max Planck Institute for Marine Microbiology; Young, Jacque C [ORNL; Shah, Manesh B [ORNL; Verberkmoes, Nathan C [ORNL; Dubilier, Nicole [Max Planck Institute for Marine Microbiology

    2013-01-01

    Transposases, enzymes that catalyze the movement of mobile genetic elements, are the most abundant genes in nature. While many bacteria encode an abundance of transposases in their genomes, the current paradigm is that transposase gene expression is tightly regulated and generally low due to its severe mutagenic effects. In the current study, we detected the highest number of transposase proteins ever reported in bacteria, in symbionts of the gutless marine worm Olavius algarvensis using metaproteomics. At least 26 different transposases from 12 different families were detected and genomic and proteomic analyses suggest many of these are active. This high expression of transposases indicates that the mechanisms for their tight regulation have been disabled or destroyed. Based on recent studies on other symbionts and pathogens that showed high transposase transcription, we speculate that abundant transposase expression might be common in symbionts and pathogens.

  16. Anti-Viral Antibody Profiling by High Density Protein Arrays

    Science.gov (United States)

    Bian, Xiaofang; Wiktor, Peter; Kahn, Peter; Brunner, Al; Khela, Amritpal; Karthikeyan, Kailash; Barker, Kristi; Yu, Xiaobo; Magee, Mitch; Wasserfall, Clive H.; Gibson, David; Rooney, Madeleine E; Qiu, Ji; LaBaer, Joshua

    2015-01-01

    Viral infections elicit anti-viral antibodies and have been associated with various chronic diseases. Detection of these antibodies can facilitate diagnosis, treatment of infection and understanding of the mechanisms of virus associated diseases. In this work, we assayed anti-viral antibodies using a novel high density-nucleic acid programmable protein array (HD-NAPPA) platform. Individual viral proteins were expressed in situ directly from plasmids encoding proteins in an array of microscopic reaction chambers. Quality of protein display and serum response was assured by comparing intra- and inter- array correlation within or between printing batches with average correlation coefficients of 0.91 and 0.96, respectively. HD-NAPPA showed higher signal to background (S/B) ratio compared with standard NAPPA on planar glass slides and ELISA. Antibody responses to 761 antigens from 25 different viruses were profiled among patients with juvenile idiopathic arthritis (JIA) and type 1 diabetes (T1D). Common as well as unique antibody reactivity patterns were detected between patients and healthy controls. We believe HD-viral-NAPPA will enable the study of host-pathogen interactions at unprecedented dimensions and elucidate the role of pathogen infections in disease development. PMID:25758251

  17. Highly Flexible Protein-Peptide Docking Using CABS-Dock.

    Science.gov (United States)

    Ciemny, Maciej Paweł; Kurcinski, Mateusz; Kozak, Konrad Jakub; Kolinski, Andrzej; Kmiecik, Sebastian

    2017-01-01

    Protein-peptide molecular docking is a difficult modeling problem. It is even more challenging when significant conformational changes that may occur during the binding process need to be predicted. In this chapter, we demonstrate the capabilities and features of the CABS-dock server for flexible protein-peptide docking. CABS-dock allows highly efficient modeling of full peptide flexibility and significant flexibility of a protein receptor. During CABS-dock docking, the peptide folding and binding process is explicitly simulated and no information about the peptide binding site or its structure is used. This chapter presents a successful CABS-dock use for docking a potentially therapeutic peptide to a protein target. Moreover, simulation contact maps, a new CABS-dock feature, are described and applied to the docking test case. Finally, a tutorial for running CABS-dock from the command line or command line scripts is provided. The CABS-dock web server is available from http://biocomp.chem.uw.edu.pl/CABSdock/ .

  18. Cloning and Characterization of a Novel cDNA Encoding Late Embryogenesis-Abundant Protein 5 Like (LEA-5) Gene from Cara Cara Navel Orange Fruit(Citrus sinensis Osbeck)

    Institute of Scientific and Technical Information of China (English)

    TAO Neng-guo; YE Jun-li; XU Juan; DENG Xiu-xin

    2006-01-01

    LEA5 gene was postulated related with both stress and hormone responses. In an attempt to find genes exclusively expressed during fruit ripening of Cara Cara navel orange, a novel cDNA clone encoding late embryogenesis-abundant protein 5 like gene (CitLEA5-1) was obtained. It was 582 bp in length, containing 97 deduced amino acids. Compared with the stress-induced LEA5 from leaves of Citrus sinensis, CitLEA5-1 had a shorter 3' untranslated region (UTR). Semiquantitative RT-PCR analysis revealed that CitLEA5-1 was transcriptional regulated during fruit ripening of Cara Cara navel orange.

  19. Metabolic responses to high protein diet in Korean elite bodybuilders with high-intensity resistance exercise

    Directory of Open Access Journals (Sweden)

    Choue Ryowon

    2011-07-01

    Full Text Available Abstract Background High protein diet has been known to cause metabolic acidosis, which is manifested by increased urinary excretion of nitrogen and calcium. Bodybuilders habitually consumed excessive dietary protein over the amounts recommended for them to promote muscle mass accretion. This study investigated the metabolic response to high protein consumption in the elite bodybuilders. Methods Eight elite Korean bodybuilders within the age from 18 to 25, mean age 21.5 ± 2.6. For data collection, anthropometry, blood and urinary analysis, and dietary assessment were conducted. Results They consumed large amounts of protein (4.3 ± 1.2 g/kg BW/day and calories (5,621.7 ± 1,354.7 kcal/day, as well as more than the recommended amounts of vitamins and minerals, including potassium and calcium. Serum creatinine (1.3 ± 0.1 mg/dl and potassium (5.9 ± 0.8 mmol/L, and urinary urea nitrogen (24.7 ± 9.5 mg/dl and creatinine (2.3 ± 0.7 mg/dl were observed to be higher than the normal reference ranges. Urinary calcium (0.3 ± 0.1 mg/dl, and phosphorus (1.3 ± 0.4 mg/dl were on the border of upper limit of the reference range and the urine pH was in normal range. Conclusions Increased urinary excretion of urea nitrogen and creatinine might be due to the high rates of protein metabolism that follow high protein intake and muscle turnover. The obvious evidence of metabolic acidosis in response to high protein diet in the subjects with high potassium intake and intensive resistance exercise were not shown in this study results. However, this study implied that resistance exercise with adequate mineral supplementation, such as potassium and calcium, could reduce or offset the negative effects of protein-generated metabolic changes. This study provides preliminary information of metabolic response to high protein intake in bodybuilders who engaged in high-intensity resistance exercise. Further studies will be needed to determine the effects of the intensity

  20. TEMPORAL VARIATION IN THE ABUNDANCE AND DISTRIBUTION OF POECILIOPSIS FASCIATA IN NEAR-SHORE HABITAT OF THE HIGH ELEVATION LAKE, LAGO DE ACHICHILCA, PUEBLA, MEXICO

    Directory of Open Access Journals (Sweden)

    Montoya-Ayala Raymundo

    2012-04-01

    Full Text Available The distribution of organisms within a pond or lake can reflect the result of a variety of factors. We examined the distribution and abundance of the fish, Poecilioposis fasciata, in Lago de Achichilca, Puebla, Mexico, as well as how the distribution and abundance varied among months. Dissolved oxygen, temperature, and salinity varied among months. The abundance of P. fasciata peaked in December and February. For the months when fish were observed, their abundances were positively related to dissolved oxygen concentration and were generally not related to temperature. Our results make it clear that there is substantial seasonal variation in the abundances of P. fasciata and that within months, their distributions are likely driven more by dissolved oxygen than either temperature or salinity.

  1. A computational framework for boosting confidence in high-throughput protein-protein interaction datasets.

    Science.gov (United States)

    Hosur, Raghavendra; Peng, Jian; Vinayagam, Arunachalam; Stelzl, Ulrich; Xu, Jinbo; Perrimon, Norbert; Bienkowska, Jadwiga; Berger, Bonnie

    2012-08-31

    Improving the quality and coverage of the protein interactome is of tantamount importance for biomedical research, particularly given the various sources of uncertainty in high-throughput techniques. We introduce a structure-based framework, Coev2Net, for computing a single confidence score that addresses both false-positive and false-negative rates. Coev2Net is easily applied to thousands of binary protein interactions and has superior predictive performance over existing methods. We experimentally validate selected high-confidence predictions in the human MAPK network and show that predicted interfaces are enriched for cancer -related or damaging SNPs. Coev2Net can be downloaded at http://struct2net.csail.mit.edu.

  2. Highly Charged Protein Ions: The Strongest Organic Acids to Date.

    Science.gov (United States)

    Zenaidee, Muhammad A; Leeming, Michael G; Zhang, Fangtong; Funston, Toby T; Donald, William A

    2017-07-10

    The basicity of highly protonated cytochrome c (cyt c) and myoglobin (myo) ions were investigated using tandem mass spectrometry, ion-molecule reactions (IMRs), and theoretical calculations as a function of charge state. Surprisingly, highly charged protein ions (HCPI) can readily protonate non-polar molecules and inert gases, including Ar, O2 , and N2 in thermal IMRs. The most HCPIs that can be observed are over 130 kJ mol(-1) less basic than the least basic neutral organic molecules known (tetrafluoromethane and methane). Based on theoretical calculations, it is predicted that protonated cyt c and myo ions should spontaneously lose a proton to vacuum for charge states in which every third residue is protonated. In this study, HCPIs are formed where every fourth residue on average is protonated. These results indicate that protein ions in higher charge states can be formed using a low-pressure ion source to reduce proton-transfer reactions between protein ions and gases from the atmosphere. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Effect of high contents of dietary animal-derived protein or carbohydrates on canine faecal microbiota

    Directory of Open Access Journals (Sweden)

    Hang Ingrid

    2012-06-01

    Full Text Available Abstract Background Considerable evidence suggests that food impacts both the gastro-intestinal (GI function and the microbial ecology of the canine GI tract. The aim of this study was to evaluate the influence of high-carbohydrate (HC, high-protein (HP and dry commercial (DC diets on the canine colonic microbiota in Beagle dogs. Diets were allocated according to the Graeco-Latin square design. For this purpose, microbial DNA was isolated from faecal samples and separated by density gradient centrifugation, resulting in specific profiling based on the guanine-cytosine content (%G + C. In addition, 16 S rRNA gene amplicons were obtained from the most abundant %G + C peaks and analysed by sequence analysis, producing a total of 720 non-redundant sequences (240 sequences per diet. Results The DC diet sample showed high abundance of representatives of the orders Clostridiales, Lactobacillales, Coriobacteriales and Bacteroidales. Sequence diversity was highest for DC diet samples and included representatives of the orders Lactobacillales and Bacteroidales, which were not detected in samples from the HP and HC diets. These latter two diets also had reduced levels of representatives of the family Lachnospiraceae, specifically Clostridial cluster XIVa. The HC diet favoured representatives of the order Erysipelotrichales, more specifically the Clostridial cluster XVIII, while the HP diet favoured representatives of the order Fusobacteriales. Conclusions This study detected Coriobacteriales in dog faeces, possibly due to the non-selective nature of the %G + C profiling method used in combination with sequencing. Moreover, our work demonstrates that the effect of diet on faecal microbiota can be explained based on the metabolic properties of the detected microbial taxa.

  4. The absence of protein Y4yS affects negatively the abundance of T3SS Mesorhizobium loti secretin, RhcC2, in bacterial membranes.

    Science.gov (United States)

    Mercante, Virginia; Duarte, Cecilia M; Sánchez, Cintia M; Zalguizuri, Andrés; Caetano-Anollés, Gustavo; Lepek, Viviana C

    2015-01-01

    Mesorhizobium loti MAFF303099 has a functional type III secretion system (T3SS) that is involved in the determination of nodulation competitiveness on Lotus. The M. loti T3SS cluster contains gene y4yS (mlr8765) that codes for a protein of unknown function (Y4yS). A mutation in the y4yS gene favors the M. loti symbiotic competitive ability on Lotus tenuis cv. Esmeralda and affects negatively the secretion of proteins through T3SS. Here we localize Y4yS in the bacterial membrane using a translational reporter peptide fusion. In silico analysis indicated that this protein presents a tetratricopeptide repeat (TPR) domain, a signal peptide and a canonical lipobox LGCC in the N-terminal sequence. These features that are shared with proteins required for the formation of the secretin complex in type IV secretion systems and in the Tad system, together with its localization, suggest that the y4yS-encoded protein is required for the formation of the M. loti T3SS secretin (RhcC2) complex. Remarkably, analysis of RhcC2 in the wild-type and M. loti y4yS mutant strains indicated that the absence of Y4yS affects negatively the accumulation of normal levels of RhcC2 in the membrane.

  5. The absence of protein Y4yS affects negatively the abundance of T3SS Mesorhizobium loti secretin, RhcC2, in bacterial membranes

    Directory of Open Access Journals (Sweden)

    Virginia eMercante

    2015-01-01

    Full Text Available Mesorhizobium loti MAFF303099 has a functional type III secretion system (T3SS that is involved in the determination of nodulation competitiveness on Lotus. The M. loti T3SS cluster contains gene y4yS (mlr8765 that codes for a protein of unknown function (Y4yS. A mutation in the y4yS gene favors the M. loti symbiotic competitive ability on Lotus tenuis cv. Esmeralda and affects negatively the secretion of proteins through T3SS. Here we localize Y4yS in the bacterial membrane using a translational reporter peptide fusion. In silico analysis indicated that this protein presents a tetratricopeptide repeat (TPR domain, a signal peptide and a canonical lipobox LGCC in the N-terminal sequence. These features that are shared with proteins required for the formation of the secretin complex in type IV secretion systems and in the Tad system, together with its localization, suggest that the y4yS-encoded protein is required for the formation of the M. loti T3SS secretin (RhcC2 complex. Remarkably, analysis of RhcC2 in the wild-type and M. loti y4yS mutant strains indicated that the absence of Y4yS affects negatively the accumulation of normal levels of RhcC2 in the membrane.

  6. The Rise of the AGB in the Galactic Halo: Mg Isotopic Ratios and High Precision Elemental Abundances in M71 Giants

    CERN Document Server

    Melendez, Jorge

    2009-01-01

    High-resolution (R ~ 100 000), high signal-to-noise spectra of M71 giants have been obtained with HIRES at the KeckI Telescope in order to measure their Mg isotopic ratios, as well as elemental abundances of C, N, O, Na, Mg, Al, Si, Ca, Ti, Ni, Zr and La. We demonstrate that M71 has two populations, the first having weak CN, normal O, Na, Mg, and Al, and a low ratio of 26Mg/Mg (~4%) consistent with models of galactic chemical evolution with no contribution from AGB stars. The Galactic halo could have been formed from the dissolution of globular clusters prior to their intermediate mass stars reaching the AGB. The second population has enhanced Na and Al accompanied by lower O and by higher 26Mg/Mg (~8%), consistent with models which do incorporate ejecta from AGB stars via normal stellar winds. All the M71 giants have identical [Fe/H], [Si/Fe], [Ca/Fe], [Ti/Fe] and [Ni/Fe] to within sigma = 0.04 dex (10%). We therefore infer that the timescale for formation of the first generation of stars we see today in thi...

  7. High Throughput Screening for Drugs that Modulate Intermediate Filament Proteins

    Science.gov (United States)

    Sun, Jingyuan; Groppi, Vincent E.; Gui, Honglian; Chen, Lu; Xie, Qing; Liu, Li

    2016-01-01

    Intermediate filament (IF) proteins have unique and complex cell and tissue distribution. Importantly, IF gene mutations cause or predispose to more than 80 human tissue-specific diseases (IF-pathies), with the most severe disease phenotypes being due to mutations at conserved residues that result in a disrupted IF network. A critical need for the entire IF-pathy field is the identification of drugs that can ameliorate or cure these diseases, particularly since all current therapies target the IF-pathy complication, such as diabetes or cardiovascular disease, rather than the mutant IF protein or gene. We describe a high throughput approach to identify drugs that can normalize disrupted IF proteins. This approach utilizes transduction of lentivirus that expresses green-fluorescent-protein-tagged keratin 18 (K18) R90C in A549 cells. The readout is drug ‘hits’ that convert the dot-like keratin filament distribution, due to the R90C mutation, to a wildtype-like filamentous array. A similar strategy can be used to screen thousands of compounds and can be utilized for practically any IF protein with a filament-disrupting mutation, and could therefore potentially target many IF-pathies. ‘Hits’ of interest require validation in cell culture then using in vivo experimental models. Approaches to study the mechanism of mutant-IF normalization by potential drugs of interest are also described. The ultimate goal of this drug screening approach is to identify effective and safe compounds that can potentially be tested for clinical efficacy in patients. PMID:26795471

  8. Fluorescent biosensors for high throughput screening of protein kinase inhibitors.

    Science.gov (United States)

    Prével, Camille; Pellerano, Morgan; Van, Thi Nhu Ngoc; Morris, May C

    2014-02-01

    High throughput screening assays aim to identify small molecules that interfere with protein function, activity, or conformation, which can serve as effective tools for chemical biology studies of targets involved in physiological processes or pathways of interest or disease models, as well as templates for development of therapeutics in medicinal chemistry. Fluorescent biosensors constitute attractive and powerful tools for drug discovery programs, from high throughput screening assays, to postscreen characterization of hits, optimization of lead compounds, and preclinical evaluation of candidate drugs. They provide a means of screening for inhibitors that selectively target enzymatic activity, conformation, and/or function in vitro. Moreover, fluorescent biosensors constitute useful tools for cell- and image-based, multiplex and multiparametric, high-content screening. Application of fluorescence-based sensors to screen large and complex libraries of compounds in vitro, in cell-based formats or whole organisms requires several levels of optimization to establish robust and reproducible assays. In this review, we describe the different fluorescent biosensor technologies which have been applied to high throughput screens, and discuss the prerequisite criteria underlying their successful application. Special emphasis is placed on protein kinase biosensors, since these enzymes constitute one of the most important classes of therapeutic targets in drug discovery.

  9. Role of Dietary Soy Protein in Obesity

    OpenAIRE

    Manuel T. Velasquez, Sam J. Bhathena

    2007-01-01

    Soy protein is an important component of soybeans and provides an abundant source of dietary protein. Among the dietary proteins, soy protein is considered a complete protein in that it contains ample amounts of all the essential amino acids plus several other macronutrients with a nutritional value roughly equivalent to that of animal protein of high biological value. Soy protein is unique among the plant-based proteins because it is associated with isoflavones, a group of compounds with a v...

  10. Two trypanosome-specific proteins are essential factors for 5S rRNA abundance and ribosomal assembly in Trypanosoma brucei.

    Science.gov (United States)

    Hellman, Kristina M; Ciganda, Martin; Brown, Silvia V; Li, Jinlei; Ruyechan, William; Williams, Noreen

    2007-10-01

    We have previously identified and characterized two novel nuclear RNA binding proteins, p34 and p37, which have been shown to bind 5S rRNA in Trypanosoma brucei. These two proteins are nearly identical, with one major difference, an 18-amino-acid insert in the N-terminal region of p37, as well as three minor single-amino-acid differences. Homologues to p34 and p37 have been found only in other trypanosomatids, suggesting that these proteins are unique to this ancient family. We have employed RNA interference (RNAi) studies in order to gain further insight into the interaction between p34 and p37 with 5S rRNA in T. brucei. In our p34/p37 RNAi cells, decreased expression of the p34 and p37 proteins led to morphological alterations, including loss of cell shape and vacuolation, as well as to growth arrest and ultimately to cell death. Disruption of a higher-molecular-weight complex containing 5S rRNA occurs as well as a dramatic decrease in 5S rRNA levels, suggesting that p34 and p37 serve to stabilize 5S rRNA. In addition, an accumulation of 60S ribosomal subunits was observed, accompanied by a significant decrease in overall protein synthesis within p34/p37 RNAi cells. Thus, the loss of the trypanosomatid-specific proteins p34 and p37 correlates with a diminution in 5S rRNA levels as well as a decrease in ribosome activity and an alteration in ribosome biogenesis.

  11. Small-Molecule Transport by CarO, an Abundant Eight-Stranded β-Barrel Outer Membrane Protein from Acinetobacter baumannii.

    Science.gov (United States)

    Zahn, Michael; D'Agostino, Tommaso; Eren, Elif; Baslé, Arnaud; Ceccarelli, Matteo; van den Berg, Bert

    2015-07-17

    Outer membrane (OM) β-barrel proteins composed of 12-18 β-strands mediate cellular entry of small molecules in Gram-negative bacteria. Small OM proteins with barrels of 10 strands or less are not known to transport small molecules. CarO (carbapenem-associated outer membrane protein) from Acinetobacter baumannii is a small OM protein that has been implicated in the uptake of ornithine and carbapenem antibiotics. Here we report crystal structures of three isoforms of CarO. The structures are very similar and show a monomeric eight-stranded barrel lacking an open channel. CarO has a substantial extracellular domain resembling a glove that contains all the divergent residues between the different isoforms. Liposome swelling experiments demonstrate that full-length CarO and a "loop-less" truncation mutant mediate small-molecule uptake at low levels but that they are unlikely to mediate passage of carbapenem antibiotics. These results are confirmed by biased molecular dynamics simulations that allowed us to quantitatively model the transport of selected small molecules.

  12. Differential Effects of High-Protein Diets Derived from Soy and Casein on Blood-Brain Barrier Integrity in Wild-type Mice.

    Science.gov (United States)

    Snelson, Matthew; Mamo, John C L; Lam, Virginie; Giles, Corey; Takechi, Ryusuke

    2017-01-01

    A number of studies report that a diet high in protein influences cognitive performance, but the results are inconsistent. Studies demonstrated that protein from different food sources has differential effects on cognition. It is increasingly recognized that the integrity of cerebrovascular blood-brain barrier (BBB) is pivotal for central nervous system function. However, to date, no studies have reported the effects of high-protein diets on BBB integrity. Therefore, in this study, the effects of diets enriched in casein or soy protein on BBB permeability were investigated. Immunomicroscopy analyses of cerebral parenchymal immunoglobulin G extravasation indicated significant BBB disruption in the cortex of young adult mice maintained on high-casein diet for 12 weeks, while no signs of BBB dysfunction were observed in mice fed with control or high-soy protein diet. Moreover, cortical expression of glial fibrillary acidic protein (GFAP) was significantly greater in mice fed the high-casein diet compared to control mice, indicating heightened astrocyte activation, whereas mice maintained on a soy-enriched diet showed no increase of GFAP abundance. Plasma concentrations of homocysteine were markedly greater in mice maintained on a high-casein diet in comparison to control mice. Collectively, these findings suggest that a diet enriched in casein but not soy protein may induce astrocyte activation through exaggerated BBB permeability by increased plasma homocysteine. The outcomes indicate the differential effects of protein sources on BBB and neuroinflammation, which may provide an important implication for dietary guidelines for protein supplementation.

  13. The apogee red-clump catalog: Precise distances, velocities, and high-resolution elemental abundances over a large area of the Milky Way's disk

    Energy Technology Data Exchange (ETDEWEB)

    Bovy, Jo [Institute for Advanced Study, Einstein Drive, Princeton, NJ 08540 (United States); Nidever, David L. [Department of Astronomy, University of Michigan, Ann Arbor, MI 48109 (United States); Rix, Hans-Walter [Max-Planck-Institut für Astronomie, Königstuhl 17, D-69117 Heidelberg (Germany); Girardi, Léo; Rodrigues, Thaíse S. [Osservatorio Astronomico di Padova-INAF, Vicolo dell' Osservatorio 5, I-35122 Padova (Italy); Zasowski, Gail [Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218 (United States); Chojnowski, S. Drew; Majewski, Steven R. [Department of Astronomy, University of Virginia, Charlottesville, VA, 22904 (United States); Holtzman, Jon; Hayden, Michael R. [New Mexico State University, Las Cruces, NM 88003 (United States); Epstein, Courtney; Johnson, Jennifer A.; Pinsonneault, Marc H.; Andrews, Brett [Department of Astronomy, The Ohio State University, Columbus, OH 43210 (United States); Frinchaboy, Peter M. [Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX 76129 (United States); Stello, Dennis [Sydney Institute for Astronomy (SIfA), School of Physics, University of Sydney, NSW 2006 (Australia); Allende Prieto, Carlos [Instituto de Astrofísica de Canarias (IAC), E-38200 La Laguna, Tenerife (Spain); Basu, Sarbani [Department of Astronomy, Yale University, P.O. Box 208101, New Haven, CT 06520-8101 (United States); Beers, Timothy C. [National Optical Astronomy Observatory, Tucson, AZ 85719 (United States); Bizyaev, Dmitry, E-mail: bovy@ias.edu [Apache Point Observatory and New Mexico State University, P.O. Box 59, Sunspot, NM, 88349-0059 (United States); and others

    2014-08-01

    The Sloan Digital Sky Survey III's Apache Point Observatory Galactic Evolution Experiment (APOGEE) is a high-resolution near-infrared spectroscopic survey covering all of the major components of the Galaxy, including the dust-obscured regions of the inner Milky Way disk and bulge. Here we present a sample of 10,341 likely red-clump stars (RC) from the first two years of APOGEE operations, selected based on their position in color-metallicity-surface-gravity-effective-temperature space using a new method calibrated using stellar evolution models and high-quality asteroseismology data. The narrowness of the RC locus in color-metallicity-luminosity space allows us to assign distances to the stars with an accuracy of 5%-10%. The sample extends to typical distances of about 3 kpc from the Sun, with some stars out to 8 kpc, and spans a volume of approximately 100 kpc{sup 3} over 5 kpc ≲ R ≲ 14 kpc, |Z| ≲ 2 kpc, and –15° ≲ Galactocentric azimuth ≲ 30°. The APOGEE red-clump (APOGEE-RC) catalog contains photometry from the Two Micron All Sky Survey, reddening estimates, distances, line-of-sight velocities, stellar parameters and elemental abundances determined from the high-resolution APOGEE spectra, and matches to major proper motion catalogs. We determine the survey selection function for this data set and discuss how the RC selection samples the underlying stellar populations. We use this sample to limit any azimuthal variations in the median metallicity within the ≈45° azimuthal region covered by the current sample to be ≤0.02 dex, which is more than an order of magnitude smaller than the radial metallicity gradient. This result constrains coherent non-axisymmetric flows within a few kiloparsecs from the Sun.

  14. Foetal life protein restriction in male mink (Neovison vison) kits lowers post-weaning protein oxidation and the relative abundance of hepatic fructose-1,6-bisphosphatase mRNA

    DEFF Research Database (Denmark)

    Matthiesen, Connie Marianne Frank; Blache, D.; Thomsen, Preben Dybdahl;

    2012-01-01

    protein deficiency affects the response to adequate or deficient protein provision post weaning. Further, we intended to study whether the changes in the gene expression of key enzymes in foetal hepatic tissue caused by maternal protein deficiency were manifested post-weaning. A total of 32 male mink kits...... (P restriction leads to changes in post-weaning protein metabolism through lower protein oxidation of male mink kits....

  15. An update on medium- and low-abundant blood plasma proteome of horse.

    Science.gov (United States)

    Lepczyński, A; Ożgo, M; Dratwa-Chałupnik, A; Robak, P; Pyć, A; Zaborski, D; Herosimczyk, A

    2017-07-10

    The main objectives of the study were to: (1) deeply analyse the serum protein composition of Equus caballus, (2) assess the effectiveness of the high-abundant protein depletion and improve the concentration of medium- and low-abundant proteins. The analysis were performed on the blood plasma of three healthy part-Arabian mares. The implementation of two-dimensional electrophoresis and matrix-assisted laser desorption/ionisation - time of flight mass spectrometry allowed us to establish a horse plasma proteome map. Serum proteins were resolved at pH 4 to 7, followed by 12% SDS-PAGE. As a result 136 spots were successfully identified, representing the products of 46 unique genes. Of these, 22 gene products have not been previously identified in horse serum/plasma samples using proteomic tools. Gene ontology analysis showed that almost 30% of all identified gene products belong to the coagulation and complement cascades. These results can undoubtedly serve as a useful and prospective prerequisite for the future analysis of horse plasma proteome changes in different physiological and pathophysiological conditions. The use of the medium- and low-abundant protein enrichment tool increased their abundance and allowed us to identify a higher number of protein gene products. The highest depletion efficiency was observed for the most abundant plasma proteins, that is albumin, IgG heavy chains and serotransferrin.

  16. High CJD infectivity remains after prion protein is destroyed.

    Science.gov (United States)

    Miyazawa, Kohtaro; Emmerling, Kaitlin; Manuelidis, Laura

    2011-12-01

    The hypothesis that host prion protein (PrP) converts into an infectious prion form rests on the observation that infectivity progressively decreases in direct proportion to the decrease of PrP with proteinase K (PK) treatment. PrP that resists limited PK digestion (PrP-res, PrP(sc)) has been assumed to be the infectious form, with speculative types of misfolding encoding the many unique transmissible spongiform encephalopathy (TSE) agent strains. Recently, a PK sensitive form of PrP has been proposed as the prion. Thus we re-evaluated total PrP (sensitive and resistant) and used a cell-based assay for titration of infectious particles. A keratinase (NAP) known to effectively digest PrP was compared to PK. Total PrP in FU-CJD infected brain was reduced to ≤0.3% in a 2 h PK digest, yet there was no reduction in titer. Remaining non-PrP proteins were easily visualized with colloidal gold in this highly infectious homogenate. In contrast to PK, NAP digestion left 0.8% residual PrP after 2 h, yet decreased titer by >2.5 log; few residual protein bands remained. FU-CJD infected cells with 10× the infectivity of brain by both animal and cell culture assays were also evaluated. NAP again significantly reduced cell infectivity (>3.5 log). Extreme PK digestions were needed to reduce cell PrP to report on maximal PrP destruction and titer. It is likely that one or more residual non-PrP proteins may protect agent nucleic acids in infectious particles.

  17. High content screening for G protein-coupled receptors using cell-based protein translocation assays

    DEFF Research Database (Denmark)

    Grånäs, Charlotta; Lundholt, Betina Kerstin; Heydorn, Arne

    2005-01-01

    G protein-coupled receptors (GPCRs) have been one of the most productive classes of drug targets for several decades, and new technologies for GPCR-based discovery promise to keep this field active for years to come. While molecular screens for GPCR receptor agonist- and antagonist-based drugs...... as valuable discovery tools for several years. The application of high content cell-based screening to GPCR discovery has opened up additional possibilities, such as direct tracking of GPCRs, G proteins and other signaling pathway components using intracellular translocation assays. These assays provide...... the capability to probe GPCR function at the cellular level with better resolution than has previously been possible, and offer practical strategies for more definitive selectivity evaluation and counter-screening in the early stages of drug discovery. The potential of cell-based translocation assays for GPCR...

  18. Homologous high-throughput expression and purification of highly conserved E coli proteins

    Directory of Open Access Journals (Sweden)

    Duchmann Rainer

    2007-06-01

    Full Text Available Abstract Background Genetic factors and a dysregulated immune response towards commensal bacteria contribute to the pathogenesis of Inflammatory Bowel Disease (IBD. Animal models demonstrated that the normal intestinal flora is crucial for the development of intestinal inflammation. However, due to the complexity of the intestinal flora, it has been difficult to design experiments for detection of proinflammatory bacterial antigen(s involved in the pathogenesis of the disease. Several studies indicated a potential association of E. coli with IBD. In addition, T cell clones of IBD patients were shown to cross react towards antigens from different enteric bacterial species and thus likely responded to conserved bacterial antigens. We therefore chose highly conserved E. coli proteins as candidate antigens for abnormal T cell responses in IBD and used high-throughput techniques for cloning, expression and purification under native conditions of a set of 271 conserved E. coli proteins for downstream immunologic studies. Results As a standardized procedure, genes were PCR amplified and cloned into the expression vector pQTEV2 in order to express proteins N-terminally fused to a seven-histidine-tag. Initial small-scale expression and purification under native conditions by metal chelate affinity chromatography indicated that the vast majority of target proteins were purified in high yields. Targets that revealed low yields after purification probably due to weak solubility were shuttled into Gateway (Invitrogen destination vectors in order to enhance solubility by N-terminal fusion of maltose binding protein (MBP, N-utilizing substance A (NusA, or glutathione S-transferase (GST to the target protein. In addition, recombinant proteins were treated with polymyxin B coated magnetic beads in order to remove lipopolysaccharide (LPS. Thus, 73% of the targeted proteins could be expressed and purified in large-scale to give soluble proteins in the range of 500

  19. Primordial Deuterium Abundance Measurements

    CERN Document Server

    Levshakov, S A; Takahara, F; Levshakov, Sergei A.; Kegel, Wilhelm H.; Takahara, Fumio

    1997-01-01

    Deuterium abundances measured recently from QSO absorption-line systems lie in the range from 3 10^{-5} to 3 10^{-4}, which shed some questions on standard big bang theory. We show that this discordance may simply be an artifact caused by inadequate analysis ignoring spatial correlations in the velocity field in turbulent media. The generalized procedure (accounting for such correlations) is suggested to reconcile the D/H measurements. An example is presented based on two high-resolution observations of Q1009+2956 (low D/H) [1,2] and Q1718+4807 (high D/H) [8,9]. We show that both observations are compatible with D/H = 4.1 - 4.6 10^{-5}, and thus support SBBN. The estimated mean value = 4.4 10^{-5} corresponds to the baryon-to-photon ratio during SBBN eta = 4.4 10^{-10} which yields the present-day baryon density Omega_b h^2 = 0.015.

  20. Distribution of Prokaryotic Abundance and Microbial Nutrient Cycling Across a High-Alpine Altitudinal Gradient in the Austrian Central Alps is Affected by Vegetation, Temperature, and Soil Nutrients.

    Science.gov (United States)

    Hofmann, Katrin; Lamprecht, Andrea; Pauli, Harald; Illmer, Paul

    2016-10-01

    Studies of the altitudinal distributions of soil microorganisms are rare or have led to contradictory results. Therefore, we studied archaeal and bacterial abundance and microbial-mediated activities across an altitudinal gradient (2700 to 3500 m) on the southwestern slope of Mt. Schrankogel (Central Alps, Austria). Sampling sites distributed over the alpine (2700 to 2900 m), the alpine-nival (3000 to 3100 m), and the nival altitudinal belts (3200 to 3500 m), which are populated by characteristic plant assemblages. Bacterial and archaeal abundances were measured via quantitative real-time PCR (qPCR). Moreover, microbial biomass C, microbial activity (dehydrogenase), and enzymes involved in carbon (CM-cellulase), nitrogen (protease), phosphorus (alkaline phosphatase), and sulfur (arylsulfatase) cycling were determined. Abundances, microbial biomass C, and activities almost linearly decreased along the gradient. Archaeal abundance experienced a sharper decrease, thus pointing to pronounced sensitivity toward environmental harshness. Additionally, abundance and activities were significantly higher in soils of the alpine belt compared with those of the nival belt, whereas the alpine-nival ecotone represented a transitional area with intermediate values, thus highlighting the importance of vegetation. Archaeal abundance along the gradient was significantly related to soil temperature only, whereas bacterial abundance was significantly related to temperature and dissolved organic carbon (DOC). Soil carbon and nitrogen concentrations explained most of the variance in enzyme activities involved in the cycling of C, N, P, and S. Increasing temperature could therefore increase the abundances and activities of microorganisms either directly or indirectly via expansion of alpine vegetation to higher altitudes and increased plant cover.

  1. (E)-Propyl α-Cyano-4-Hydroxyl Cinnamylate: A High Sensitive and Salt Tolerant Matrix for Intact Protein Profiling by MALDI Mass Spectrometry

    Science.gov (United States)

    Wang, Sheng; Xiao, Zhaohui; Xiao, Chunsheng; Wang, Huixin; Wang, Bing; Li, Ying; Chen, Xuesi; Guo, Xinhua

    2016-04-01

    Low-abundance samples and salt interference are always of great challenges for the practical protein profiling by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Herein, a series of carboxyl-esterified derivatives of α-cyano-4-hydroxycinnamic acid (CHCA) were synthesized and evaluated as matrices for MALDI-MS analysis of protein. Among them, (E)-propyl α-cyano-4-hydroxyl cinnamylate (CHCA-C3) was found to exhibit excellent assay performance for intact proteins by improving the detection sensitivity 10 folds compared with the traditional matrices [i.e., super2,5-dihydroxybenzoic acid (superDHB), sinapic acid (SA), and CHCA]. In addition, CHCA-C3 was shown to have high tolerance to salts, the ion signal of myoglobin was readily detected even in the presence of urea (8 M), NH4HCO3 (2 M), and KH2PO4 (500 mM), meanwhile sample washability was robust. These achievements were mainly attributed to improved ablation ability and increased hydrophobicity or affinity of CHCA-C3 to proteins in comparison with hydrophilic matrixes, leading to more efficient ionization of analyte. Furthermore, direct analysis of proteins from crude egg white demonstrated that CHCA-C3 was a highly efficient matrix for the analysis of low-abundance proteins in complex biological samples. These outstanding performances indicate the tremendous potential use of CHCA-C3 in protein profiling by MALDI-MS.

  2. The shift from low to high non-structural protein 1 expression in rotavirus-infected MA-104 cells

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    Laura Martinez-Alvarez

    2013-06-01

    Full Text Available A hallmark of group/species A rotavirus (RVA replication in MA-104 cells is the logarithmic increase in viral mRNAs that occurs four-12 h post-infection. Viral protein synthesis typically lags closely behind mRNA synthesis but continues after mRNA levels plateau. However, RVA non-structural protein 1 (NSP1 is present at very low levels throughout viral replication despite showing robust protein synthesis. NSP1 has the contrasting properties of being susceptible to proteasomal degradation, but being stabilised against proteasomal degradation by viral proteins and/or viral mRNAs. We aimed to determine the kinetics of the accumulation and intracellular distribution of NSP1 in MA-104 cells infected with rhesus rotavirus (RRV. NSP1 preferentially localises to the perinuclear region of the cytoplasm of infected cells, forming abundant granules that are heterogeneous in size. Late in infection, large NSP1 granules predominate, coincident with a shift from low to high NSP1 expression levels. Our results indicate that rotavirus NSP1 is a late viral protein in MA-104 cells infected with RRV, presumably as a result of altered protein turnover.

  3. Dietary whey protein lowers serum C-peptide concentration and duodenal SREBP-1c mRNA abundance, and reduces occurrence of duodenal tumors and colon aberrant crypt foci in azoxymethane-treated male rats.

    Science.gov (United States)

    Xiao, Rijin; Carter, Julie A; Linz, Amanda L; Ferguson, Matthew; Badger, Thomas M; Simmen, Frank A

    2006-09-01

    We evaluated partially hydrolyzed whey protein (WPH) for inhibitory effects on the development of colon aberrant crypt foci (ACF) and intestinal tumors in azoxymethane (AOM)-treated rats. Pregnant Sprague-Dawley rats and their progeny were fed AIN-93G diets containing casein (CAS, control diet) or WPH as the sole protein source. Colons and small intestines from the male progeny were obtained at 6, 12, 20 and 23 weeks after AOM treatment. At 6 and 23 weeks, post-AOM, WPH-fed rats had fewer ACF than did CAS-fed rats. Intestinal tumors were most frequent at 23 weeks, post-AOM. At this time point, differences in colon tumor incidence with diet were not observed; however, WPH-fed rats had fewer tumors in the small intestine (7.6% vs. 26% incidence, P=.004). Partially hydrolized whey protein suppressed circulating C-peptide concentration (a stable indicator of steady-state insulin secretion) at all four time points relative to the corresponding CAS-fed animals. The relative mRNA abundance for the insulin-responsive, transcription factor gene, SREBP-1c, was reduced by WPH in the duodenum but not colon. Results indicate potential physiological linkages of dietary protein type with circulating C-peptide (and by inference insulin), local expression of SREBP-1c gene and propensity for small intestine tumorigenesis.

  4. Sunspots, Starspots, and Elemental Abundances

    Science.gov (United States)

    Doschek, George A.; Warren, Harry P.

    2017-08-01

    The composition of plasma in solar and stellar atmospheres is not fixed, but varies from feature to feature. These variations are organized by the First Ionization Potential (FIP) of the element. Solar measurements often indicate that low FIP elements (10 eV, such as C, N, O, Ar, He) compared to abundances in the photosphere. Stellar observations have also shown similar enrichments. An inverse FIP effect, where the low FIP elements are depleted, has been observed in stellar coronae of stars believed to have large starspots in their photospheres. The abundances are important for determining radiative loss rates in models, tracing the origin of the slow solar wind, and for understanding wave propagation in the chromosphere and corona. Recently, inverse FIP effects have been discovered in the Sun (Doschek, Warren, & Feldman 2015, ApJ, 808, L7) from spectra obtained by the Extreme-ultraviolet Imaging Spectrometer (EIS) on the Hinode spacecraft. The inverse FIP regions seem always to be near sunspots and cover only a very small area (characteristic length = a few arcseconds). However, in pursuing the search for inverse FIP regions, we have found that in some sunspot groups the coronal abundance at a temperature of 3-4 MK can be near photospheric over much larger areas of the sun near the sunspots (e.g., 6,000 arcsec2). Also, sometimes the abundances at 3-4 MK are in between coronal and photospheric values. This can occur in small areas of an active region. It is predicted (Laming 2015, Sol. Phys., 12, 2) that the FIP effect should be highly variable in the corona. Several examples of coronal abundance variations are presented. Our work indicates that a comprehensive re-investigation of solar abundances is highly desirable. This work is supported by a NASA Hinode grant.

  5. Autopilot: an online data acquisition control system for the enhanced high-throughput characterization of intact proteins.

    Science.gov (United States)

    Durbin, Kenneth R; Fellers, Ryan T; Ntai, Ioanna; Kelleher, Neil L; Compton, Philip D

    2014-02-04

    The ability to study organisms by direct analysis of their proteomes without digestion via mass spectrometry has benefited greatly from recent advances in separation techniques, instrumentation, and bioinformatics. However, improvements to data acquisition logic have lagged in comparison. Past workflows for Top Down Proteomics (TDPs) have focused on high throughput at the expense of maximal protein coverage and characterization. This mode of data acquisition has led to enormous overlap in the identification of highly abundant proteins in subsequent LC-MS injections. Furthermore, a wealth of data is left underutilized by analyzing each newly targeted species as unique, rather than as part of a collection of fragmentation events on a distinct proteoform. Here, we present a major advance in software for acquisition of TDP data that incorporates a fully automated workflow able to detect intact masses, guide fragmentation to achieve maximal identification and characterization of intact protein species, and perform database search online to yield real-time protein identifications. On Pseudomonas aeruginosa, the software combines fragmentation events of the same precursor with previously obtained fragments to achieve improved characterization of the target form by an average of 42 orders of magnitude in confidence. When HCD fragmentation optimization was applied to intact proteins ions, there was an 18.5 order of magnitude gain in confidence. These improved metrics set the stage for increased proteome coverage and characterization of higher order organisms in the future for sharply improved control over MS instruments in a project- and lab-wide context.

  6. Comparison of the Folding Mechanism of Highly Homologous Proteins in the Lipid-binding Protein Family

    Science.gov (United States)

    The folding mechanism of two closely related proteins in the intracellular lipid binding protein family, human bile acid binding protein (hBABP) and rat bile acid binding protein (rBABP) were examined. These proteins are 77% identical (93% similar) in sequence Both of these singl...

  7. Comparison of the Folding Mechanism of Highly Homologous Proteins in the Lipid-binding Protein Family

    Science.gov (United States)

    The folding mechanism of two closely related proteins in the intracellular lipid binding protein family, human bile acid binding protein (hBABP) and rat bile acid binding protein (rBABP) were examined. These proteins are 77% identical (93% similar) in sequence Both of these singl...

  8. Protein denaturation of whey protein isolates (WPIs) induced by high intensity ultrasound during heat gelation.

    Science.gov (United States)

    Frydenberg, Rikke P; Hammershøj, Marianne; Andersen, Ulf; Greve, Marie T; Wiking, Lars

    2016-02-01

    In this study, the impact of high intensity ultrasound (HIU) on proteins in whey protein isolates was examined. Effects on thermal behavior, secondary structure and nature of intra- and intermolecular bonds during heat-induced gelling were investigated. Ultrasonication (24 kHz, 300 W/cm(2), 2078 J/mL) significantly reduced denaturation enthalpies, whereas no change in secondary structure was detected by circular dichroism. The thiol-blocking agent N-ethylmaleimide was applied in order to inhibit formation of disulfide bonds during gel formation. Results showed that increased contents of α-lactalbumin (α-La) were associated with increased sensitivity to ultrasonication. The α-La:β-lactoglobulin (β-Lg) ratio greatly affected the nature of the interactions formed during gelation, where higher amounts of α-La lead to a gel more dependent on disulfide bonds. These results contribute to clarifying the mechanisms mediating the effects of HIU on whey proteins on the molecular level, thus moving further toward implementing HIU in the processing chain in the food industry. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. MAPA distinguishes genotype-specific variability of highly similar regulatory protein isoforms in potato tuber.

    Science.gov (United States)

    Hoehenwarter, Wolfgang; Larhlimi, Abdelhalim; Hummel, Jan; Egelhofer, Volker; Selbig, Joachim; van Dongen, Joost T; Wienkoop, Stefanie; Weckwerth, Wolfram

    2011-07-01

    Mass Accuracy Precursor Alignment is a fast and flexible method for comparative proteome analysis that allows the comparison of unprecedented numbers of shotgun proteomics analyses on a personal computer in a matter of hours. We compared 183 LC-MS analyses and more than 2 million MS/MS spectra and could define and separate the proteomic phenotypes of field grown tubers of 12 tetraploid cultivars of the crop plant Solanum tuberosum. Protein isoforms of patatin as well as other major gene families such as lipoxygenase and cysteine protease inhibitor that regulate tuber development were found to be the primary source of variability between the cultivars. This suggests that differentially expressed protein isoforms modulate genotype specific tuber development and the plant phenotype. We properly assigned the measured abundance of tryptic peptides to different protein isoforms that share extensive stretches of primary structure and thus inferred their abundance. Peptides unique to different protein isoforms were used to classify the remaining peptides assigned to the entire subset of isoforms based on a common abundance profile using multivariate statistical procedures. We identified nearly 4000 proteins which we used for quantitative functional annotation making this the most extensive study of the tuber proteome to date.

  10. Drying and hydration of proteins at high concentration

    NARCIS (Netherlands)

    Bouman, J.

    2015-01-01

    Proteins are the building blocks of life and serve a wide range of essential functions in organisms. Many metabolic reactions in organisms are catalysed by enzymes, DNA is replicated by proteins and in cells proteins often facilitate active transport of e.g. glucose or ions. Proteins also serve an e

  11. Streptococcus mutans protein synthesis during mixed-species biofilm development by high-throughput quantitative proteomics.

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    Marlise I Klein

    Full Text Available Biofilms formed on tooth surfaces are comprised of mixed microbiota enmeshed in an extracellular matrix. Oral biofilms are constantly exposed to environmental changes, which influence the microbial composition, matrix formation and expression of virulence. Streptococcus mutans and sucrose are key modulators associated with the evolution of virulent-cariogenic biofilms. In this study, we used a high-throughput quantitative proteomics approach to examine how S. mutans produces relevant proteins that facilitate its establishment and optimal survival during mixed-species biofilms development induced by sucrose. Biofilms of S. mutans, alone or mixed with Actinomyces naeslundii and Streptococcus oralis, were initially formed onto saliva-coated hydroxyapatite surface under carbohydrate-limiting condition. Sucrose (1%, w/v was then introduced to cause environmental changes, and to induce biofilm accumulation. Multidimensional protein identification technology (MudPIT approach detected up to 60% of proteins encoded by S. mutans within biofilms. Specific proteins associated with exopolysaccharide matrix assembly, metabolic and stress adaptation processes were highly abundant as the biofilm transit from earlier to later developmental stages following sucrose introduction. Our results indicate that S. mutans within a mixed-species biofilm community increases the expression of specific genes associated with glucan synthesis and remodeling (gtfBC, dexA and glucan-binding (gbpB during this transition (P<0.05. Furthermore, S. mutans up-regulates specific adaptation mechanisms to cope with acidic environments (F1F0-ATPase system, fatty acid biosynthesis, branched chain amino acids metabolism, and molecular chaperones (GroEL. Interestingly, the protein levels and gene expression are in general augmented when S. mutans form mixed-species biofilms (vs. single-species biofilms demonstrating fundamental differences in the matrix assembly, survival and biofilm

  12. High-performance cation-exchange chromatofocusing of proteins.

    Science.gov (United States)

    Kang, Xuezhen; Frey, Douglas D

    2003-03-28

    Chromatofocusing using high-performance cation-exchange column packings, as opposed to the more commonly used anion-exchange column packings, is investigated with regard to the performance achieved and the range of applications possible. Linear or convex gradients in the range from pH 2.6 to 9 were formed using a variety of commercially available column packings that provide a buffering capacity in different pH ranges, and either polyampholytes or simple mixtures having a small number (three or fewer) of buffering species as the elution buffer. The resolutions achieved using cation-exchange or anion-exchange chromatofocusing were in general comparable, although for certain pairs of proteins better resolution could be achieved using one type of packing as compared to the other, evidently due to the way electrostatic charges are distributed on the protein surface. Several chromatofocusing methods were investigated that take advantage of the acid-base properties of commercially available cation-exchange column packings. These include the use of gradients with a composite shape, the use of very low pH ranges, and the use of elution buffers containing a single buffering species. The advantages of chromatofocusing over ion-exchange chromatography using a salt gradient at constant pH were illustrated by employing the former method and a cation-exchange column packing to separate beta-lactoglobulins A and B, which is a separation reported to be impossible using the latter method and a cation-exchange column packing. Trends in the apparent isoelectric points determined using cation- and anion-exchange chromatofocusing were interpreted using applicable theories. Results of this study indicate that cation-exchange chromatofocusing is a useful technique which is complementary to anion-exchange chromatofocusing and isoelectric focusing for separating proteins at both the analytical and preparative scales.

  13. A microfluidic, high throughput protein crystal growth method for microgravity.

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    Carl W Carruthers

    Full Text Available The attenuation of sedimentation and convection in microgravity can sometimes decrease irregularities formed during macromolecular crystal growth. Current terrestrial protein crystal growth (PCG capabilities are very different than those used during the Shuttle era and that are currently on the International Space Station (ISS. The focus of this experiment was to demonstrate the use of a commercial off-the-shelf, high throughput, PCG method in microgravity. Using Protein BioSolutions' microfluidic Plug Maker™/CrystalCard™ system, we tested the ability to grow crystals of the regulator of glucose metabolism and adipogenesis: peroxisome proliferator-activated receptor gamma (apo-hPPAR-γ LBD, as well as several PCG standards. Overall, we sent 25 CrystalCards™ to the ISS, containing ~10,000 individual microgravity PCG experiments in a 3U NanoRacks NanoLab (1U = 10(3 cm.. After 70 days on the ISS, our samples were returned with 16 of 25 (64% microgravity cards having crystals, compared to 12 of 25 (48% of the ground controls. Encouragingly, th